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academia | What are the 25th-75th percentile ranges for the annual income for graduate students in the United States? | And are there differences in average income between different types of fields, or different types of schools?
The diagram below says that the average income for grad students is $17k/year. But I'm more commonly seeing incomes in the range of $25k-$30k/year on PhysicsGRE.com...
| VQAonline_00000001.png | Note that those statistics are often averaged over all possible disciplines, and therefore, since there is such a wide disparity of stipend levels between different schools, and between different disciplines at the same school.
At the institution I attended for graduate school, engineers had stipends approximately 30% higher than the science majors (chemistry, physics, math, etc.). Similarly, at the undergraduate institution I attended, a similar disparity existed between science and humanities graduate students.
It is also important to ask if master's students, who often don't receive a salary at all, are included in that average. (And, since humanities students tend to stay longer, they may skew the statistics even more than one might expect.)
(One final note to directly address the question: competitive national fellowships in the US currently pay between $30,000 and $35,000 per year as a stipend. I would estimate, then, that most stipends are significantly below that amount. I'd say something in the range of $20,000-$30,000 would be appropriate in STEM fields, and probably $15,000-$20,000 for full-time humanities PhD's.)
| https://academia.stackexchange.com/questions/684 |
academia | How to improve quality of figures after reviewers have mentioned it? | The paper we are working on was accepted and we got a comment saying "Quality of Figures could be improved".
All the figures that are given have been exported from matplotlib and have all the standard labels with different color schemes and have attached the sample as well.
So what do I do? make it more pretty? or use a different package?
Note - This is just a sample, and the real one has a set of 6 plots big enough to fit in almost half a page
| VQAonline_00000111.png | The illustration you provide seems like a standard plot that can be seen in most journals. That said, it can certainly be improved; many journals do not seem to care what they publish. What is acceptable also varies from person to person. There are however some standards that should be followed and your figure fall short on a few points. Many of the comments made to your post outline some of the improvements and I will also reiterate them here.
A figure should be understandable when shown without its figure caption. Your figure falls short of this. By understandable I do not mean the deep scientific significance of what is shown but to understand what is shown. This is a point made by Tufte (2001) and is a good guideline for finishing any figure.
Axis labels should include units. You have latitude and longitude which would be in degrees. The color scale is more problematic because I do not understand what it should be showing, units would obviously help.
Axis labels should start with capital letters so Lat/Lon or Latitude/Longitude.
The heading of the subplots containg a time stamp should be consistent. The ISO standard for date/time is yyyy-mm-dd HH:MM:SS. So I would suggest using this consistently or (which might be better for a more general audience) use an unambiguous date and time format such as "dd month, yyyy, HHMM hrs" (e.g. 29 April, 2022, 1200 hrs). The problem with date and time is that almost every country has their own standard.
The third diagram in the top row has no x-axis label and tick labels
The number of tick labels could be reduced so that the axes are not overloaded with information. Every second label can be removed while keeping the tick marks
The resolution of the coloured fields should reflect the resolution of the data shown in the fields. If the data is as coarse as it looks in the figure, then that is how it should be shown.
Figures must be made to work in their final size in the publication. Submitting vector based formats avoids many problems. When exporting to a bitmap one should consider the necessary resolution (in dpi) to make the illustration sharp in its final size. A figure such as yours that include bitmap fields should follow the same guidelines but obviously the fields in your subfigures will not change in apparent resolution as was stated in the previous point.
The data is latitude/longitude based running from c. 10 degrees N(?) to c. 80 degrees N(?). The width of the space between longitude lines will obviously decrease from S to N so that a square representation is not strictly correct. The plots are better representing reality if they are shown in some cartographic projection. This is clearly something many will ignore and maybe not even consider but it is one aspect to consider.
Any graphing package or software is not perfect. It is always useful to learn to use for example the open source Inkscape to edit standard output from plotting packages or software to optimse your graphics before publication.
Considering the colour scale I cannot see anything wrong. Aspects to consider regarding choice of colour scale include what is standard (if any), what may make sense depending on what is shown and what can be read by someone with colour blindness.
So there are several aspects that can be improved or at least considered. At the same time providing a comment such as the one you appear to have received without any exemplification of what to do is quite useless on behalf of the reviewer/editor.
Reference
Tufte, E.R. 2001. The visual display of quantitative information. Second Edition. Cheshire, CT: Graphics Press.
| https://academia.stackexchange.com/questions/184099 |
academia | What does the envelope sign after the author name mean? | I'm in the process of writing a paper for an upcoming conference. The conference provides a LaTeX template which can be found here: Information for Authors of Springer Computer Science Proceedings.
Looking at the proceedings of the previous years I noticed a little envelope after the name of the first authors.
However, I was not able to figure out what it means. So my question is what is the meaning of the little envelope after the name of the first author?
| VQAonline_00000078.png | With Springer journals, the envelope simply indicates that they are the nominated corresponding author for the paper.
Sources: this forum topic and a Springer 'Instructions to Authors' PDF.
| https://academia.stackexchange.com/questions/115668 |
academia | Can you abbreviate the title of the Proceeedings of the IEEE? | I found this on Page 34 of IEEE EDITORIAL STYLE MANUAL, it's about how to edit the reference. I don't understand the following sentence:
NOTE: The only exception to this rule is PROCEEDINGS OF THE IEEE, which never carried an acronym on the masthead
Does it mean when cite a paper from PROCEEDINGS OF THE IEEE, do not cite it in an abbreviation form. If it is, why the following example ( Page 35 of IEEE EDITORIAL STYLE MANUAL) gave an abbreviation form:
| VQAonline_00000032.png | The part you quote does not refer to the name of the Journal but to the vol. ##, no. ## section of the citation and is applicable to those earlier than 1988.
So the 1981 citation would be
IEEE Trans. Automat. Contr., vol. AC-26, no.1, pp. 1–34, Jan. 1981.
while a citation from the same journal past 1988 would be
IEEE Trans. Automat. Contr., vol. 40, no.1, pp. 1–34, Jan. 1995.
The exception to the Proc. of IEEE applies here, as it never had an abbreviation in the volume and it has always been:
Proc. IEEE, vol. 11, no. 3, pp. 1-11, Jan. 1978.
The example they provide is correct.
| https://academia.stackexchange.com/questions/38514 |
academia | Should grading take all students' performance into account? | This question is partially related to this question.
By trying to understand which one is the correct way to grade an exam I came out with this doubt. Should each exam be considered as independent or should a mark be assigned based on the other students' performance.
As an example
if all the students final exams are from 80% to 100% correct should be considered the fact that the exam was too easy while grading it?
if all the students final exams are from 30% to 60% correct should be considered the fact that maybe the exam was too hard while grading it?
To resume, while preparing/grading the exams should the results respect somehow the normal distribution or should each one be graded independently?
EDIT:
Based on my career as a student for every exam we had statistical results from all the students (min, max, avg) with the grades distribution. Most of them respected the normal distribution. So what it is not clear to me is if it depends on how the teacher create the exam, on how it is graded or just on how usually students perform.
| VQAonline_00000062.png | If the goal is to help students learn, then you should grade against an absolute standard (often called a rubric), and you should not grade by comparing students to each other. Experimentally, it has been found that if students believe their grades are under their own control, they will learn more. If students believe they cannot control their grades (because it depends on classmates' performance) then they will learn less. The difference in attitudes is known as a locus of control in psychology. According to the locus of control research, grading against an absolute standard will help students.
If you goal is to limit the number of students who pass, you might chose differently from what I suggest. But I don't agree with that goal.
| https://academia.stackexchange.com/questions/86301 |
academia | Contribution of gifts and hospital services to university revenue | This question is based on the pie-charts shown in this link, such as this one for the University of Michigan.
In most of these charts, around 5% of the revenue comes from gifts. What are these exactly?
How do hospitals and clinical services play such a critical role for the revenue?
| VQAonline_00000002.png | Gifts are donations, typically from former students but they could come from anyone. That's just how higher education works in the US, and the tradition of making these donations is a big factor in how some US universities have become very wealthy (some of the donations are spent each year, but many are added to the endowment). The donations qualify for a tax deduction, so there's an element of government subsidy as well.
Hospitals and clinical services can loom large because university teaching hospitals are huge and medical services are very expensive. (You can have thousands of employees, some of them very well paid, and elaborate equipment.) However, this is really not relevant. The medical revenue is typically paying for the hospital activities and medical education, but not used to subsidize the rest of the university. Many universities do not have hospitals or medical schools.
| https://academia.stackexchange.com/questions/1660 |
academia | A small part of my transcript is hard to read; can I get into trouble? | My university does not provide official transcripts in English, so I sent mine to a certified translator for translation. There is a footer on each page in Persian, and unfortunately, on one page, this footer covers the cumulative GPA and total passed credits of a summer semester; it is not unreadable but hard to read.
Since December 15 is the deadline of some of the universities I want to apply for, there is no time for me to ask for another certified translated transcript. Do you think applying with this transcript might be a problem?
| VQAonline_00000109.png | Apply with this transcript and to be on the safe side make sure you mention your grades (especially the parts that are hard to read) somewhere else where they are easy to read. In this case, someone who wants to 'confirm' your declaration can 'easily' (or with a little effort) check with the image you showed.
Perhaps also provide the originals? I am assuming the grades will be in the same numerals so at least the numbers can be read.
| https://academia.stackexchange.com/questions/178719 |
ai | How exactly is $Pr(s \rightarrow x, k, \pi)$ deduced by "unrolling", in the proof of the policy gradient theorem? | In the proof of the policy gradient theorem in the RL book of Sutton and Barto (that I shamelessly paste here):
there is the "unrolling" step that is supposed to be immediately clear
With just elementary calculus and re-arranging of terms
Well, it's not. :) Can someone explain this step in more detail?
How exactly is $Pr(s \rightarrow x, k, \pi)$ deduced by "unrolling"?
| VQAonline_00000240.png | The unrolling step is due to the fact you end up with an equation that you can keep expanding indefinitely.
Note that we start with calculating $\nabla v_\pi(s)$ and arrive at
$$\nabla v_\pi(s) = \sum_a\left[ \nabla \pi(a|s) q_\pi(s,a) + \pi(a|s) \sum_{s'}p(s'|s,a) \nabla v_\pi (s') \right]\;,$$
which contains a term for $\nabla v_\pi(s')$. This is a recursive relationship, similar to the bellman equation, so we can substitute in a term for $\nabla v_\pi(s')$ which will be a term similar just with $\nabla v_\pi(s'')$. As I mentioned, we can do this indefinitely which leads us to
$$\nabla v_\pi(s) = \sum_{x \in \mathcal{S}} \sum_{k=0}^\infty \mathbb{P}(s\rightarrow x, k, \pi) \sum_a \nabla \pi(a|x) q_\pi(x,a)\;.$$
We need the term $\sum_{x \in \mathcal{S}} \sum_{k=0}^\infty \mathbb{P}(s\rightarrow x, k, \pi)$ because we want to take an average over the state space, however due to unrolling there are many different $s_t$'s that we need to average over (this comes from the $s',s'',s''',...$ in the unrolling) so we also need to add the probability state of transitioning from state $s$ to $x$ in $k$ time steps, where we sum over an infinite horizon due to the repeated unrolling.
If you are wondering what happens to the terms $\pi(a|s)$ and $p(s'|s,a)$ terms and why they are not explicitly shown in this final form, it is because this is exactly what the $\mathbb{P}(s\rightarrow x, k, \pi)$ represents. The average over all possible states accounts for the $p(s'|s,a)$ and the fact that we follow policy $\pi$ in the probability statement accounts for the $\pi(a|s)$.
| https://ai.stackexchange.com/questions/22094 |
ai | How can reinforcement learning be unsupervised learning if it uses deep learning? | I was watching a video in my online course where I'm learning about A.I. I am a very beginner in it.
At one point in the course, the instructor says that reinforcement learning (RL) needs a deep learning model (NN) to perform an action. But for that, we need expected results in our model for the NN to learn how to predict the Q-values.
Nevertheless, at the beginning of the course, they said to me that RL is an unsupervised learning approach because the agent performs the action, receives the response from the environment, and finally takes the more likely action, that is, with the highest Q value.
But if I'm using deep learning in RL, for me, RL looks like a supervised learning approach. I'm a little confused about these things, could someone give me clarifications about them?
| VQAonline_00000228.png | Supervised learning
The supervised learning (SL) problem is formulated as follows.
You are given a dataset $\mathcal{D} = \{(x_i, y_i)_{i=1}^N$, which is assumed to be drawn i.i.d. from an unknown joint probability distribution $p(x, y)$, where $x_i$ represents the $i$th input and $y_i$ is the corresponding label. You choose a loss function $\mathcal{L}: V \times U \rightarrow \mathbb{R}$. Then your goal is to minimize the so-called empirical risk
$$R_{\mathcal{D}}[f]=\frac{1}{N} \sum_{i=1}^N \mathcal{L}(x_i, f(x_i)) \tag{0}\label{0}$$
with respect to $f$. In other words, you want to find the $f$ that minimizes the average above, which can also be formally written as
$$
f^* = \operatorname{argmin}_f R[f] \tag{1}\label{1}
$$
The problem \ref{1} is called the empirical risk minimization because it is a proxy problem for the expected risk minimization (but you can ignore this for now).
Reinforcement learning
In reinforcement learning, you typically imagine that there's an agent that interacts, in time steps, with an environment by taking actions. At each time step $t$, the agent takes $a_t$ in the state $s_t$, receives a reward $r_t$ from the environment and the agent and the environment move to another state $s_{t+1}$.
The goal of the agent is to maximize the expected return
$$\mathbb{E}\left[ G_t \right] = \mathbb{E}\left[ \sum_{i=t+1}^\infty R_i \right]$$
where $t$ is the current time step (so we don't care about the past), $R_i$ is a random variable that represents the probable reward at time step $i$, and $G_t = \sum_{i=t+1}^\infty R_i $ is the so-called return (i.e. a sum of future rewards, in this case, starting from time step $t$), which is also a random variable.
In this context, the most important job of the programmer is to define a function $\mathcal{R}(s, a)$, the reward function, which provides the reinforcement (or reward) signal to the RL agent. $\mathcal{R}(s, a)$ will deterministically or stochastically determine the reward that the agent receives every time it takes action $a$ in the state $s$. (Note that $\mathcal{R}$ is different from $R_i$, which is a random variable that represents the reward at time step $i$).
What is the difference between SL and RL?
In RL, you (the programmer) need to define the reward function $\mathcal{R}$ and you want to maximize the expected return. On the other hand, in SL you are given (or you collect) a dataset $\mathcal{D}$, you choose $\mathcal{L}$ in \ref{0}, and the goal is to find the function $f^*$ that minimizes the empirical risk. So, these have different settings and goals, so they are different!
However, every SL problem can be cast as an RL problem. See this answer. Similarly, in certain cases, you can formulate an RL as an SL problem. So, although the approaches are different, they are related.
Is RL an unsupervised learning approach?
In RL, you do not tell the agent what action it needs to take. You only say that the action that was taken was "bad", "good" or "so so". The agent needs to figure out which actions to take based on your feedback. In SL, you explicitly say that, for this input $x_i$, the output should be $y_i$.
Some people may consider RL is an unsupervised learning approach, but I think this is wrong, because, in RL, the programmer still needs to define the reward function, so RL isn't totally unsupervised and it's also not totally supervised. For this reason, many people consider RL an approach that sits between UL and SL.
What is deep learning?
The term/expression deep learning (DL) refers to the use of deep neural networks (i.e. neural networks with many layers, where "many" can refer to more than 1 or 1000, i.e. it depends on the context) in machine learning, either supervised, unsupervised, or reinforcement learning. So, you can apply deep learning to SL, RL and UL. So, DL is not only restricted to SL.
| https://ai.stackexchange.com/questions/20891 |
ai | On-policy state distribution for episodic tasks on Sutton & Barto, page 199 | In Sutton & Barto's "Reinforcement Learning: An Introduction", 2nd edition, page 199, they describe the on-policy distribution for episodic tasks in the following box:
I don't understand how this can be done without taking the length of the episode into account. Suppose a task has 10 states, has probability 1 of starting at the first state, then moves to any state uniformly until the episode terminates. If the episode has 100 time steps, then probability of the first state is proportional to $1 + 100\times 1/10$; if it has $1000$ time steps, it will be proportional to $1 + 1000\times 1/10$. However, the formula given would make it proportional to $1 + 1/10$ in both cases. What am I missing?
| VQAonline_00000199.png | Let's first assume that there is only one action so that $\pi(a|s) = 1$ for every state - action pair which simplifies the discussion.
Now let's consider a case with 100 time steps, 10 states and uniform distribution for starting state $s_0$ with $h(s_0) = 1$. The result would be
\begin{align}
\eta(s_0) &= 1 + \sum_{i = 0}^9 \eta(s_i) \cdot p(s_0|s_i) =\\
&= 1 + \sum_{i = 0}^9 10 \cdot \frac{1}{10} = 11
\end{align}
Now let's consider a case with 1000 time steps where other settings are the same as in the first case.
\begin{align}
\eta(s_0) &= 1 + \sum_{i = 0}^{9} \eta(s_i) \cdot p(s_0|s_i) =\\
&= 1 + \sum_{i = 0}^{9} 100 \cdot \frac{1}{10} = 101
\end{align}
In the first case
\begin{equation}
\mu(s_0) = \frac{11}{9\cdot 10 + 11} = 0.1089
\end{equation}
and in the second case you have
\begin{equation}
\mu(s_0) = \frac{101}{9\cdot 100 + 101} = 0.1009
\end{equation}
so it looks like you are correct that $\mu(s)$ depends on the length of the episode, but they didn't really say that it doesn't. Obviously as the length of the episode increases so will the number of times a certain state was visited so you could say that formula implicitly depends on the number of time steps. If $h(s_i)$ is equal for every state then results would be the same in both cases regardless of number of time steps. Also, as the number of possible states grows very large, as it usually is in real problems, the results would be approaching each other as the number of states grows.
| https://ai.stackexchange.com/questions/16616 |
ai | What is the variant of the minimax tree with 3 types of nodes called? | I have a task on my class to find all the nodes, calculate their values and choose the best way for the player on the given game graph:
Everything is fine, but I have no idea what these dots are. Is this a third player, or just a 'split' for player1 move? Some kind of heuristics?
| VQAonline_00000121.png | The triangles pointing up are Max' nodes. We assume it starts. Then follows a random choice of moves at the circles, for instance, with a die. The triangles pointing down are from Min. This variant is called Expectiminimax, see https://en.wikipedia.org/wiki/Expectiminimax_tree.
At that circles you have to multiply the possibilities on the edges below that nodes to your current value and sum all products up. The circles in your picture mean that Min dices.
| https://ai.stackexchange.com/questions/2760 |
ai | Understanding the perceptron algorithm in the book "A Course in Machine Learning" | The following text is from Hal Daumé III's "A Course in Machine Learning" online text book (Page-41).
I understand that $D$ is the size of the input vector $x$.
What is $y$? Why is it introduced in the algorithm? How/where/when is the initial value of $y$ given?
What is the rationale of testing $ya \leq 0$ for updating weights?
| VQAonline_00000119.png | Y is the desired output of the perceptron (often referred to as target) , for the given set of input vectors.
Rationale behind Y.a<=0 :
Prerequisite knowledge :
A=A-B : Moves vector A away from direction of vector B
A=A+B : Moves A in the direction of B
A (.) B >0 ; A vector is directed acutely (<90 deg.) towards B vector
A (.) B <0 ; A vector is directed away from (>90 deg.) from B vector [(.) denotes dot (scalar) product and bold letters indicate vectors]
W is augmented vector (includes threshold as another weight along with normal input weights)
X is augmented input (includes -1 as extra input (corresponding to threshold) along with other normal inputs
a(activation) = W (.) X
a >=0 ; Perceptron output 1
a<0 ; Perceptron output -1 (Not zero as implicit in the given algorithm I think)
Now Rationale :
(Y.a<0)
This means
Either of the following :
Y=-1 and a>0 ; in this case the target output is -1 but as a>0 so the Perceptron outputs 1. So we must move the weight vector away from this set of input vector, so that angle between them increases and the dot product (a) becomes < 0 so that we can get the target output.
Hence : W=W-X
Or ,W=W + (-1)*X
Or, W=W+YX
Y=1 and a<0
This means the target output is 1 but as the activation is <0 so Perceptron is outputting -1. So we must move the weight vector close to this set of input vector so that the activation can become >0 (angle decreases) and the Perceptron can output the desired output.
So :
W = W+X
Or W=W + YX
Again , Y.a=0 is a boundary case.
By now I think you can understand the rationale behind Y.a=0. If any doubt , comment to this answer , I will explain it.
Sorry for so much long answer though. :) :)
| https://ai.stackexchange.com/questions/2545 |
ai | What does the notation $[m]=\{1, \ldots, m\}$ mean in the equation of the empirical error? | The empirical error equation given in the book Understanding Machine Learning: From Theory to Algorithms is
My intuition for this equation is: total wrong predictions divided by the total number of samples $m$ in the given sample set $S$ (Correct me if I'm wrong). But, in this equation, the $m$ takes $\{ 1, \dots, m \}$. How is this actually calculated, as I thought it should be one number (the size of the sample)?
| VQAonline_00000195.png | This is a commonly used notation in theoretical computer science.
$[m]$ is not the variable $m$, but is instead the set of integers from $1$ to $m$ inclusive. The empirical error equation thus reads in English:
The cardinality of a set consisting of the elements $i$ of the set of integers $[m]$ such that the hypothesis given input $x_i$ disagrees with label $y_i$, normalized by $m$.
| https://ai.stackexchange.com/questions/15852 |
ai | Why does GLIE+MC Control Algorithm use a single episode of Monte Carlo evaluation? | GLIE+MC control Algorithm:
My question is why does this algorithm use only a single Monte Carlo episode (during PE step) to compute the $Q(s,a)$? In my understanding this has the following drawbacks:
If we have multiple terminal states then we will only reach one (per Policy Iteration step PE+PI).
It is highly unlikely that we will visit all the states (during training), and a popular scheduling algorithm for exploration constant $\epsilon = 1/k$ where $k$ is apparently the episode number, ensures that exploration decays very very rapidly. This ensures that we may never visit a state during our entire training.
So why this algorithm uses single MC episode and why not multiple episodes in a single Policy Iteration step so that the agent gets a better feel of the environment?
| VQAonline_00000187.png | I feel the general answer is that we want to be as efficient as possible in learning from experience.
Policy improvement here always produces an equivalent or better policy, so delaying the improvement step to gather more episodes will only slow down learning.
I would note too that often a different kind of Monte Carlo learning is used. Instead the speed of the update is typically controlled with a new hyper parameter $\alpha$, instead of keeping track of the visit counts. The Q estimate is then updated something like:
$$
Q \leftarrow Q + \alpha \left (G - Q \right)
$$
The value of $\alpha$ then lets you tune how much evaluation vs improvement happens. This is called constant alpha Monte Carlo. Often this is used as a stepping stone to introduce TD methods, e.g., in 6.1 of the Sutton and Barto book.
| https://ai.stackexchange.com/questions/13307 |
anime | What's the coordinate ability? | I'm on chapter 57 on Attack on Titan, and a "coordinate ability" keeps getting mentioned -- here by Hanji, but also earlier by either Bertholdt or Reiner (who apparently didn't want it to fall into the wrong hands). But what exactly is this coordinate ability?
I skipped a lot of the chapters up to 34 because they were just rehashings of the stuff in the anime, and I skimmed over a lot of the Survey Corps action in the woods, since it was getting too repetitious for me, so it's possible I might just have missed something.
Edit (taken from my comment in the answers): As an explanation to other readers, I was confused about this since at least in English, "coordinate" is pretty ambiguous without any further qualification. (It could be something geographical.) From the way Reiner and Bertholdt were talking about it, it sounded a bit like it could simply be a piece of crucial information that Eren might have in his lost memory.
Moreover, because of how Hanji was describing it merely as a "coordinate ability", it still wasn't clear to me.
| VQAonline_00000639.png | Titans can have different types of abilities, like shifting back to human form (aka Titan Shifters), or putting armor on themselves (eg: Armored Titan, Annie hiding the back of her neck, ...). The third ability that was shown, was that of the Coordinate.
The Coordinate ability is basically the ability to control Titans. If the ability is controlled properly it can command all Titans to do whatever you want them to do.
This is how humans were able to built the walls as sturdy and as big as they are right now.
As far as the story goes, it does not seem to work on Titan Shifters and there is supposed to be only one Titan with the Coordinate ability.
Although the Beast Titan was shown to have a similar ability.
| https://anime.stackexchange.com/questions/21157 |
anime | What does the word "jiken" on young Luffy's shirt mean in Japanese? | In One Piece manga, young Luffy wears a shirt containing the word "jiken".
What does "jiken" mean in Japanese?
| VQAonline_00000887.png | In this context, jiken (事件) means "incident" or "case".
The full picture indicates tamago jiken which literally means "the egg incident" where a chick is killed due to the egg getting cracked.
There might not be any deeper meaning considering Oda's nature of humor.
| https://anime.stackexchange.com/questions/57122 |
anime | Exactly what is Aizawa-sensei's quirk? | In My Hero Academia, chapter 6:
Midoriya throws the ball, and Aizawa erases his Quirk, making him fail a first time.
During this time, he grabs the student with his scarf, while not touching it. The drawn version is ambiguous, but the anime version is clear about that statement.
How so ? His quirk is only quirk erasing, not something about gravity or scarf controlling. Is there even a valid reason about that ?
Links to evidence:
Video extract (sorry for the commercial channel)
| VQAonline_00000818.png | Aizawa-sensei's quirk is Erasure:
Shota's Quirk gives him the ability to nullify anyone's Quirk by looking at them.
The cloth like material is not a quirk nor is it quirk controlled. It is called the Capturing Weapon:
The Capturing Weapon is a cloth-like equipment made from carbon fibers and a special metal alloy. Shota Aizawa wears it around his neck at all times.
He is able to manipulate the weapon to ensnare his targets and immobilize them. He uses the weapon as a powerful combo with his Erasure Quirk and as a precaution for Mutant-type Quirk users who are immune to his nullification power.
| https://anime.stackexchange.com/questions/43598 |
anime | What's the song when Mikasa talks to her squad leader while on the mission helping Eren to seal the wall with a rock in episode 12? | On season 1 episode 12, there's a song when Mikasa talks to her squad leader while on a mission helping Eren to seal the wall with a rock, as shown on the following picture.
What's that song?
| VQAonline_00000826.png | It’s Vogel im Kafig. It’s on the OST or you can find it on YouTube here: https://youtu.be/M2LdF1RlSL0.
| https://anime.stackexchange.com/questions/44909 |
anime | Why is Ulquiorra the only Espada with a second release? | In Bleach Ulquiorra is the only Espada with a second release, and he admits he has not shown Aizen. So I have come to a few questions:
Why would he not show Aizen how powerful he is?
Why is he the only Espada with a second release?
If Aizen knew about his second release, where would he be in the Espada rankings?
| VQAonline_00000533.png | Answer to first question:
A. Just in case.
Ulquiorra’s a pretty careful guy. He likes to make plans. And stick to them. So it’s possible that he hides his second release just because he knows that it’s good to have an ace in the hole, just in case he ever needs it. Not that he’s planning to use it for any nefarious purposes - he just figures, why tell if he didn’t have to?
Ulquiorra: Also, I’m not really a talker.
B. As a tiny act of rebellion.
Or you could read Ulquiorra as more of a Grimmjow-figure. You know, someone may recognize that Aizen is too powerful to actively rebel against, but who needs to do SOMETHING a little rebellious just to stay sane. Grimmjow leaves meetings early and sneaks off to the world of the living; Ulquiorra hides his second release. And this allows them to put up with working for a freakin’ shinigami.
Grimmjow: Um…I’m pretty sure that rebellion doesn’t count if nobody knows about it.
Ulquiorra: And that’s why you get spiritual pressure slammed to the floor, and I don’t.
C. Because he was actively disloyal to Aizen.
It’s possible, though, that this wasn’t a tiny act of rebellion, but rather a big one - that Ulquiorra had some sort of secret plan to rebel against Aizen someday, and he was saving his second release for that time. In which case letting Aizen go off to the WOL with the top three espada was a damn good plan. Ulquiorra would have had the castle to himself if he hadn’t been killed by Ichigo. So close, Ulquiorra.
Ulquiorra: And I was really looking forward to sitting on that throne, too.
Aizen: Yeah, white marble is comfier than you’d think.
Source: "Why does Ulquiorra keep his second release secret?" on bleachlists.tumblr.com
Answer to second question:
I came across an answer while scavenging the net (and I think it's pretty good):
Well..the arrancars sword and the soul reapers swords are the same except for how they are released or how to manifest themselves after they are released. Arrancars have the power of soul reapers and soul reapers swords have 2 different forms shikai (1st form) and then bankai (2nd Form or release state). Now most Arrancars only have 1 sword release thats their resurreccion, resurreccion means resurrection and if u notice all arrancar release states are in spanish for some weird reason, but they only have one b/c arrancars have only been around for only about 1 year or a couple of months b/c they didn't come into existence till azien stole hogyoku out of Rukia's chest. Seeing how they're a new form of hollow but with soul reaper powers they probably have not explored all of their powers unlike soul reapers who have been around for over a 1000 years which means they would know more about their swords and how they operate. So basically the 2nd form Resurreccion segunda, which means 2nd resurrection, is the 2nd form of the sword similar to a soul reapers bankai. So in other words Arrancars haven't been around for a while which is why a lot of them don't know the other form unlike soul reapers who know both forms b/c they've been around forever. Now every arrancar has one but Ulquiorra was just the first to learn it.
Source: "Why does Ulquiorra have two forms?" on Yahoo Answers
Answer for Third one:
Ofcourse Aizen knew.
...[m]aybe Ulquiorra just wanted to know how much Aizen really watched, or how much he could just deduce by being insanely smart. So he kept his release hidden to see if Aizen could figure it out for himself. And like any guy who tests a god, this just didn’t end well for poor Ulquiorra.
Aizen: Is there really any doubt that I knew?
and about the ranking:
Maybe he wanted to stay out of the top 3.
Maybe Ulquiorra just didn’t want to be in the top 3, and knew that with his second release taken into account, he would be. Ulquiorra’s smart - he might have guessed that the people who went with Aizen to Fake Karakura Town wouldn’t be coming back. Or maybe he just really likes the number 4.
Ulquiorra: Actually, I just know how important the number 3 is to Halibel.
Halibel: …
Ulquiorra: Don’t worry, we’re not having a moment.
Halibel: Oh, good!
Source: "Why does Ulquiorra keep his second release secret?" on bleachlists.tumblr.com
| https://anime.stackexchange.com/questions/8836 |
anime | Is this girl really from Bleach? | On some sites which have ads I've been seeing the following image
possibly NSFW if you look hard enough
Now I've only seen up to episode 130 and I've never seen her before. However she kind of looks like Lighting (AKA Clare Farron) from Final Fantasy XIII.
I am wondering: is this girl really from Bleach? If so when would I see her in the series (which episode or chapter), and if not where is she from?
| VQAonline_00000579.png | This isn't a Bleach character. This is, as you guessed, Lightning from Final Fantasy XIII, at least according to this page on TheAnimeGallery.
| https://anime.stackexchange.com/questions/13821 |
anime | Why do Aya and Youko consider going to a ramen shop alone so amazing? | Consider the following page from Kiniro Mosaic.
Some context, in case you don't know the series: The three girls are in high school. Karen is the blonde, Aya is the girl with black twin-tails, and Youko is the girl with short light hair. Karen is half-British, has never lived in Japan before, and still has some trouble with the language and culture. That's why she says "It might be something normal for you two Japanese people, but for someone like me, it was a big adventure."
It was shown earlier that Karen is pretty outgoing, but the joke here seems to be that Karen thinks going to a ramen shop is something that's only a big deal to her because she's foreign, and it turns out that it's also a big deal to natives Aya and Youko. But why do Aya and Youko consider this "amazing" and "grown-up"? Youko's line about fast food restaurants suggests there's some cultural reference concerning ramen shops that I'm missing.
| VQAonline_00000580.png | Shall I assume that these characters are in high school or younger? In that case, yes, it not so common for high schoolers to hang out at a ramen restaurant compared to a fast food place like McDonald's or a family restaurant like Jonythan's where they can stay for a long time using the drink bar (all-you-can-drink soft drinks/juice/coffee/tea), study there, chat with friends, etc. Ramen restaurants are generally not upscale and, as you can see in the illustration, strangers may sit next to each other at bar-like seating, so this makes it convenient for middle-aged salarymen to eat lunch there alone (again, this is shown in the illustration). Ramen shops are not very conducive for having conversations, hanging out, and staying past when you empty your bowl. Thus, it's not a place that usually has a family or young people vibe.
If these characters are university students, it is less likely that the Japanese girls would consider Karen fearless, because university students tend to want to eat cheap and quick food, so ramen joints work for that, but it is still that case that many female college students wouldn't go to a ramen shop alone, and possibly wouldn't even go there in a group unless that group includes a male friend, because they will assume that the place will be full of college guys and older men. It's more common for Japanese university girls to eat at regular restaurants and cute cafés.
| https://anime.stackexchange.com/questions/13828 |
astronomy | How is interstellar gas density mapped from GAIA data? | I found the image below in Space.com's article This 3D Color Map of 1.7 Billion Stars in the Milky Way Is the Best Ever Made.
The caption for this image reads:
The Gaia spacecraft gathered observations for this all-sky view of the Milky Way and neighboring galaxies between July 2014 and May 2016, releasing the data on April 25, 2018. This image shows all the stars' colors and brightness (top), the total density of stars (middle) and the distribution of interstellar gas and dust across the galaxy (bottom). Credit: ESA/Gaia/DPAC
The first two maps reflect data obtained from analysis of GAIA's measurement of starlight as explained in this answer, but the third map is described as "the distribution of interstellar gas and dust across the galaxy."
As far as I understand, GAIA does not transmit all complete image data to Earth, but instead does a significant amount of image processing, object detection, classification and analysis, and other data reduction in order to extract positions and radial velocity measurements for point-like objects such as stars, though of course small solar system bodies such as comets and asteroids end up in the raw data as well.
Question: How is interstellar gas density obtained from GAIA data?
| VQAonline_00001103.png | Two techniques immediately spring to mind.
For the stars you detect, you can compare their colours and luminosities (Gaia provides photometric colours and distances) with what you expect for a star of that type at that distance. The difference between what you expect and what you observe tells you the reddening and extinction caused by interstellar dust, integrated in a column towards that star. By going through this process for lots of stars in different directions you build up a 3D picture of the distribution of dust.
The measurements are mostly insensitive to gas - simple extrapolation between dust and gas is often assumed.
A second technique would be just to compare how many stars you can see and with what brightness distribution, with a model for the Galactic stellar population and dust distribution. This is an old-fashioned way of estimating dust extinction, works well locally, but I suspect not what is used in that map, for the simple reasons that Gaia also provides the distances to stars, and one of the purposes of the mission is to improve the Galactic model, not assume it.
| https://astronomy.stackexchange.com/questions/26057 |
astronomy | What is the thickness of the Solar System disk? | What is the thickness in AU of the all planets' orbital plane height combined in the Solar System?
Excluding Pluto.
Looking for h
| VQAonline_00001302.png | The thickness of the planetary disc is dominated by Neptune, due to its large orbital radius.
We can calculate a planet's maximum distance from the ecliptic $h$ from the inclination angle of its orbit $\theta$ and its aphelion distance $r$. We get a right triangle, with $r$ as the hypotenuse, so
$$h = r\sin\theta$$
The table below was calculated using data from the NASA Planetary Fact Sheet. Angles are in degrees, distances are in millions of kilometres.
Planet distance from the ecliptic plane.
Name
Inclination
Aphelion
Distance
Mercury
7.0
69.8
8.506
Venus
3.4
108.9
6.458
Earth
0.0
152.1
0.000
Mars
1.9
249.2
8.262
Jupiter
1.3
816.6
18.526
Saturn
2.5
1514.5
66.062
Uranus
0.8
3003.6
41.937
Neptune
1.8
4545.7
142.784
So the total thickness of the disc is $2×142.784 = 285.568$ million kilometres, which is almost $1.91$ au.
Here's the Python code I used to create that table:
from math import sin, radians
names = (
'Mercury', 'Venus', 'Earth',
'Mars', 'Jupiter', 'Saturn',
'Uranus', 'Neptune',
)
# Orbit data from https://nssdc.gsfc.nasa.gov/planetary/factsheet/
# Inclination to ecliptic plane
inc = [7.0, 3.4, 0.0, 1.9, 1.3, 2.5, 0.8, 1.8]
# Aphelion in millions of kilometres
aph = [69.8, 108.9, 152.1, 249.2, 816.6, 1514.5, 3003.6, 4545.7]
print("|Name | Inclination | Aphelion | Distance|")
print("|-|-|-|-|")
for n, th, r in zip(names, inc, aph):
# Perpendicular distance to eciptic
h = r * sin(radians(th))
print(f"|{n} | {th} | {r} | {h:.3f}|")
Here's a live version of the script running on the SageMathCell server.
As John Holtz mentions in the comments, the true $h$ value for a planet may be smaller than the value shown in my table. The table's $h$ value only occurs if the planet's argument of periapsis is ±90°. Fortunately, Neptune's argument of periapsis is currently ~272°, so my $h$ value should be fairly close to the true value.
James K has supplied a list of orbit inclinations to the Solar System's invariable plane. Here's the table using those values.
Planet distance from the Solar System invariable plane.
Name
Inclination
Aphelion
Distance
Mercury
6.34
69.8
7.708
Venus
2.19
108.9
4.161
Earth
1.57
152.1
4.167
Mars
1.67
249.2
7.262
Jupiter
0.32
816.6
4.561
Saturn
0.93
1514.5
24.582
Uranus
1.02
3003.6
53.468
Neptune
0.72
4545.7
57.121
That reduces Neptune's $h$ considerably! Uranus may even be the current "winner", depending on their arguments of periapsis with respect to the invariable plane.
| https://astronomy.stackexchange.com/questions/41927 |
astronomy | What are these objects near Mirach | Night sky objects always interested me, nowadays Im trying to observe and photograph some of these objects. My phone is iPhone 6S, i used SkyGuide app to find positions, NightCap to photograph. Im sure brightest star is Mirach according to SkyGuide app.
It's photographed at 00:30 at my local time (Istanbul, London + 3), SkyGuide says Mirach's azimuth was 77° 11’ 28” .
| VQAonline_00001126.png | If this is really Mirach, then I would say the point-like object above and a little to the left of it is the star mu And (another designation: 37 And) in the same constellation of Andromeda. Then the next point-like object slightly further above and to the left from mu And would be the star nu And (35 And). And a barely visible fuzzy object above nu And would be the Andromeda galaxy (M31). Then in the left lower corner we see another star Nembus (51 And), and above it the star phi And (42 And). And at the same height with nu And farther to the right from it at the edge of the building there is the star pi And (29 And).
I would strongly suggest you to use Stellarium (www.stellarium.org) for identification of nearly any night sky object visible at your or any other location on Earth at any time.
| https://astronomy.stackexchange.com/questions/27399 |
astronomy | Camera settings for Astrophotography | I own an Orion 10015 StarBlast 4.5 Astro Reflector Telescope and I recently bought a Lumix G7 camera then I bought the adapter needed to attach the camera to the telescope.
I tested it today at morning while it was still dark and for some reason I cannot focus the things I am seeing through the camera attached to the telescope.
I was trying to focus Venus and other objectives but I got this, do the camera need to have some specific settings for it? The telescope by itself works as usual, I use it almost every day.
Thanks in advance.
These are the adapters.
https://www.amazon.com.mx/gp/product/B07DB8B7VN/ref=ppx_yo_dt_b_asin_title_o03_s00?ie=UTF8&psc=1
https://www.amazon.com.mx/gp/product/B0000665V6/ref=ppx_yo_dt_b_asin_title_o04_s00?ie=UTF8&psc=1
| VQAonline_00001366.png | The Celestron adapter you are using is designed for telescopes having focal length greater than 650mm or "slow" telescopes, or to be more specific, you will have greater travel of the knob to achieve focus which suits this kind of barlow but your telescope is of 450mm or "fast", which is the opposite of the latter. So this will actually impact the focus and it has nothing to do with camera settings, what you can do is try to lengthen the adapter and if the problem is still not solved, buy an adapter that is designed to do the job for your telescope. Get a Universal T-adapter, which is an adapter and also a barlow lens that will suit almost every telescope. See if the telescope is collimated, although it has nothing to do with the focus adjustment it might improve viewing experience a lot, If you are not familiar with the term collimation, see a bright star you can see in your night sky and zoom it with eyepiece on until you see the secondary mirror obstruction and the spider vanes, if the dark circle is at the center it is collimated and you don't need to worry, if not adjust the screws in the secondary mirror until you see the circle at the center. And for some astrophotography tips see my answer here
| https://astronomy.stackexchange.com/questions/49006 |
astronomy | What are these dark spots on Mars' north pole? | I was exploring Mars in Google maps and I found these dark spots, like tree shadows on the north pole. I don't have any idea what they might be.
View this in Google maps.
| VQAonline_00001062.png | They look similar to the "dark dune spots" of the southern hemisphere, associated with accumulation of melting liquid at the bottom of dunes during warming seasons: https://en.wikipedia.org/wiki/Geyser_(Mars)
| https://astronomy.stackexchange.com/questions/21324 |
astronomy | Why does Jupiter have so many moons? | Jupiter has a great many moons - in the hundreds, and they're still being discovered.
What is the current theory for where all these moons came from? Are they rocks flying through space captured by Jupiter's gravity?
| VQAonline_00000927.png | Mass.
The more massive a body, the larger the gap between its lowest and highest orbit; the range of speeds at which a random body entering its gravity is likely to remain as its satellite. Sun has millions of satellites if you count all the asteroids; smaller planets tend to have one or two moons at most (Pluto with five being a notable and not fully explained exception)
To a lesser degree there's a matter of shape too. A regularly round body will have more regular and stable orbit than a potato-shaped one. Jupiter, being a gas giant is perfectly round. This doesn't play that much of a role though, especially with higher orbits.
And last but not least, no destabilizing influence of other bodies. It's very hard to maintain a lunar orbit - artificial satellites around our Moon last only a couple years each, because relatively close neighborhood of Earth tends to destabilize orbit of anything orbiting the Moon. Jupiter being a single massive planet with relatively tiny (relatively to its mass) moons doesn't have them influence each other all that much.
| https://astronomy.stackexchange.com/questions/321 |
astronomy | Are Tharsis Montes and Hellas Basin a result of the same event? | Looking at Mars map:
the highest, biggest mountains and their associated highlands are essentially antipodes of the deepest, huge basin. Roughly 180 degrees away, similar latitude except opposite sides of equator... this immediately brings to mind the idea that an asteroid impacted the area of Hellas Basin, and the shockwave traveled clear across the planet causing a bulge of Tharsis Rise, and causing multiple volcanoes to sprout there.
Is there anything to this impression, or am I entirely wrong?
| VQAonline_00001214.png |
Are Tharsis Montes and Hellas Basin a result of the same event?
You were not the first to have seen that the Hellas Basin and parts of the Tharsis Rise are roughly antipodal (Peterson 1978, Williams and Greeley 1994). The Tharsis Montes themselves are far too close to the equator to be considered antipodal to the Hellas Basin. The shield volcano Alba Mons however is almost exactly antipodal to the Hellas Basin.
This shield volcano is a bit to the north of the Tharsis Rise proper, and well to the north of the Tharsis Montes. Both Peterson and Williams suggested that the Hellas Basin impact might well have triggered the vulcanism that resulted in Alba Mons.
There's an issue with this hypothesis, which is that the apparent ages do not align. Improved remote observations of Mars has provided a tool for estimating ages of Mars features: crater density. Based on crater density, the Hellas Basin appears to be very old, at least 3.8 billion years old (Carr 2010). Alba Mons, while also quite old, isn't that old. It formed at least 200 million years after the Hellas Basin impact and perhaps as much as a billion years after (Ivanov 2006).
Bottom line: If the huge impact that formed the Hellas Basin did have any antipodal effects, those effects are buried under the magma that formed Alba Mons several hundred million years later.
References:
Carr, Michael H., and James W. Head III. "Geologic history of Mars." Earth and Planetary Science Letters 294.3-4 (2010): 185-203.
Ivanov, Mikhail A., and James W. Head. "Alba Patera, Mars: Topography, structure, and evolution of a unique late Hesperian–early Amazonian shield volcano." Journal of Geophysical Research: Planets 111.E9 (2006).
Peterson, J. E. "Antipodal effects of major basin-forming impacts on Mars." Lunar and Planetary Science Conference. Vol. 9. 1978.
Williams, David A., and Ronald Greeley. "Assessment of antipodal-impact terrains on Mars." Icarus 110.2 (1994): 196-202.
| https://astronomy.stackexchange.com/questions/34749 |
aviation | Why are the engines of the Airbus A400M slightly tilted down? |
Picture: Youtube.
Firstly, are the engines really tilted down? I have tried to check another picture over the net, seems they are really tilted down slightly. But need confirmation from you experts, however.
Second, if it is true, what is the reason?
| VQAonline_00002230.png | Just about all propeller driven airplanes big and small have the engine thrust line canted down a couple degrees from the wing chord line (not necessarily the longitudinal axis - that depends on the wing incidence), roughly equal to the cruising AOA, so that the thrust line is aligned a little closer to the free stream at cruise. On the A400 it looks like the nacelles are creating a bit of an optical illusion that exaggerates the effect, although the propellers do appear to be canted a bit relative to the fuselage. Thrust lines may also be offset to mitigate undesired pitching moments caused by thrust.
Single engine airplanes with the engine on the nose also often cant the engine to the side several degrees as well, to compensate for P factor and torque effects, reducing the amount of fin offset required at the tail. Look straight down on a typical single like a 172, with the prop stopped horizontally, and you can see the prop isn't quite parallel to the wings. Once you gain awareness of this you start to notice that most single engine planes you see have engines that are cockeyed, as if they were bent.
| https://aviation.stackexchange.com/questions/69935 |
aviation | How do you know the maximum load a control surface can withstand? |
source
This is a separate strength testing (load testing) of the elevator of an airplane, how was the load determined? How did the engineers determine the maximum elevator load?
| VQAonline_00002076.png | Elevator loads are the function of the design and flight envelope. Looks like a small plane, so look up for example CS-VA 391 (or the correct national code for your category) how to calculate the loads. Base air force distribution on the horizontal tail can usually be assumed to be triangular, and increment from control surface deflection need to be added, also usually approximated as a triangular distribution acting from the hinge line.
| https://aviation.stackexchange.com/questions/55663 |
aviation | What are these "pimples" on the jet engine for? | When looking into the General Electric CJ 805-23B jet engine, I have discovered that all forward section of the compressor is covered by a number of near identically looking "pimples". What are these tiny devices for, what are they doing? And why only front section of the compressor has them?
| VQAonline_00002111.png | They are the roots of the variable stator vanes that control the direction of the airstream as it enters each compressor stage to manage and optimize the angle of attack of the compressor blades in each stage. The vanes are connected to the ring shaped gang bar and somewhere around the circumference there is an hydraulic actuator, or a series of them, that drives the gang bar rings to move all the vanes connected to it at the same time. The hydraulic actuator is usually powered with pressurized fuel and is operated by the fuel control system to keep the vanes at the optimal rotational position.
This video (thanks, @Mackk) shows how the vanes operate:
| https://aviation.stackexchange.com/questions/57923 |
aviation | Why is FAA Aircraft Certification Service department named as AIR? | The acronym AIR doesn't match with the functional name "Aircraft Certification Service"
"AIR (the Aircraft Certification Service) is the department within the FAA that develops and administers safety standards for aircraft and related products that are manufactured in the United States or are used by operators of aircraft registered in the United States"
Ref1
Ref2
| VQAonline_00002492.png | Because it's not an acronym. It's an administrative designation code for the office. While many are acronyms, others are not. The key is to make sure they are unique across the agency. They are in effect tied to mail distribution in large government buildings. It's a lot easier to write AIR-130 than Aircraft Certification Service, Engineering Directorate.
Once you get out of headquarters, the regional/local offices tend more to the standard acronym for the office: Aircraft Certification Office (ACO), Flight Standards District Office (FSDO), Manufacturing and Inspection District Office (MIDO).
If you dig through the FAA organization you'll see that the major office codes have two common properties: they all start with an "A" and are three characters long.
While Air Traffic Organization (ATO), Human Resource Management (AHR), Commercial Space Transportation (AST), are at least an approximate acronym; Airports (ARP), Finance and Management (AFN), and Aviation Safety (AVS) are more of an abbreviation.
Flight Standards (AFS) and Aircraft Certification Office (AIR) are under AVS.
As to why AIR was chosen, I can only speculate as it was done a very long time ago and from experience in other government agencies, when these are set it's typically some staffer to the front office that proposes the structure and the boss signs off on it. So at most you'll find a directive that says what it is but is unlikely to specify the rational for each.
Personal speculation would be that AIR comes from 'Airworthiness' or looking way back, it was originally the Aeronautics Branch. AIR could be drawn from that or an early mission statement that tied them to 'Inspection and Regulation'. Take your pick.
| https://aviation.stackexchange.com/questions/92714 |
aviation | Can I log time in a Cri-Cri twin-engine aircraft? | I was looking at potential experimental projects when I read this fascinating website about a tiny aerobatic-capable twin-engine airplane. It's light enough to be an ultralight, but much too fast:
Aside from the obvious fun of flying this little plane, I wondered whether:
I'd be able to log time in the Cri-Cri as multi-time? My guess is yes.
Assuming I'm MEL-IFR, could I log multi-IFR with a two-way radio, altimeter, Dynon-type AI, HI and at least one cert. VOR & glide slope? An approach cert. GPS setup would be too heavy I assume. My guess is this is wishful thinking...
| VQAonline_00001433.png | What a positively delightful looking aircraft!
I see no reason you couldn't log time in this as multi-engine time - it clearly has two engines, with two separate sets of controls (at least throttles, from what I can see).
Similarly I see no reason you couldn't fly it IFR as an experimental aircraft, provided it's "properly equipped" (consult the FARs for all the details on what you need), passes an IFR pitot/static test, and has appropriate radios (Transponder which you'd likely need anyway, Com, and Nav).
Whether you'd want to take it up in real weather is another matter though :-)
For that matter if you want GPS you could certainly have it without much weight penalty: throw in a Garmin GNS 430W and cover the Nav/Com and GPS in one ~7-8lb box. Whether or not that kind of investment in what's basically a single-seat super-ultralight is "worth it" is a judgment call only you could make, but it definitely seems possible.
| https://aviation.stackexchange.com/questions/2791 |
aviation | Is it legal to smoke in your own plane? | I was just curious, in the past, smoking on planes was permitted.
What is the law surrounding smoking in your own private plane?
| VQAonline_00001399.png | The short answer to "Can I smoke in my own private aircraft?" is "Yes, usually".
As Promised, I looked up the relevant FAR (23.853 - Passenger & Crew Compartment Interiors).
The actual rule is long and verbose, but pretty common sense. The important regulatory bits for most personal aircraft are just two points though. You must:
Have "an adequate number" of self-contained ash trays
You don't want flicked ash or a snubbed cigarette to start an in-flight fire.
Have "No Smoking" signs you can illuminate, if the passenger/crew compartments are separated
This doesn't apply to most of us since our "personal" airplanes are light singles, but if you've got a fancy twin with a curtain or door between you and the passengers you'll need those signs.
For "commuter category" aircraft there are even more requirements. Those requirements don't apply to most "personal" planes, so even though it's probably a good idea to meet some of those requirements if you're going to allow smoking in your personal aircraft they're not legally required.
All that said, while it's likely legal (unless you've removed your ashtrays or your plane didn't come with them) common sense generally dictates you don't want to smoke in your plane - It's bad for the vacuum-driven instruments' filters, will require even more attention to cleaning the inside of your windows, and a loose cigarette in turbulence or a bunch of ashes blown about by an open air vent can be a pretty substantial distraction.
| https://aviation.stackexchange.com/questions/613 |
aviation | Does a skinless fuselage add to the likeliness of an unrecoverable spin? | While at Air Venture this week, I happened to hear a pilot of a small experimental airplane say that he liked the skinless (Naked) look his airframe had at one point during the build, but that he believed flying it that way made it more susceptible to an unrecoverable (I assume flat) spin.
Thinking about it later, I realized that I wasn't sure I understood how this could be. My understanding of airplane behaviour is that a flat spin is mostly a result of CG being to far aft. Anyway, I was wondering if anyone knew this?
| VQAonline_00002203.png | Well, I would solve with transparent Monokote if it was a model. No accounting for people's taste.
Although some very early aircraft featured that look, designers soon realized that covered "slab" sides not only reduced drag, but also improved directional stability. Note that covered area aft of CG acts as an extension of the empennage, allowing for a smaller Vertical stabilizer. Many 100 years ago were comparitively tiny.
As far as behavior in a spin, what he has on the tail may be sufficient for safety, as well as good CG management. But I would certainly not recommend denuding your fuselage for a certain "look" without some expert advice and testing.
Designers do compare side area ahead of CG to aft of CG to estimate yawing tendency in a slip. So he may be OK.
| https://aviation.stackexchange.com/questions/66903 |
avp | Blocky video artifact problem on Canon 600D | When shooting video with my Canon 600D I get artefacts like the following in the pictures: (not throughout the whole video but only for a second and then its gone again, but comes back after a few seconds)
They are always in the bottom part of the image. (Although not visible on the LiveView Screen when viewed in camera)
I tried to view the video on several devices and its always the same.
I use a Class 10 SD Card, so this should not be an issue.
Searching on google for the problem had no success.
| VQAonline_00002575.png | This is dropped data. It may be a problem with either your memory card or your camera itself. h.264 data, which is the format your video is recorded in, works off of a concept known as Group of Pictures. Basically, many of the frames of video don't store information about what they look like, but rather what they look like related to previous or future frames. The entire group of pictures is then decoded together. A group of pictures typically covers somewhere around half a second to 3/4 of a second of video.
Additionally, image data is encoded in blocks within each frame. When the data is encoded properly with sufficient bandwidth, these blocks blend seamlessly and you can't tell they are there. If the data rate is too low or something gets corrupted, then they become obvious though.
This is what has occurred in your video. During the recording, some data was dropped, resulting in the remaining data being shifted over and thus when the video is decoded, the image blocks are given information that doesn't line up correctly, resulting in the blocky look you are seeing.
Since full frames are only stored every 15 frames or so, the video can't recover from the error until the next full frame (I frame) is reached. This is because the decoder only knows what changed from the neighboring frame for B (based on former and next frame) and P (based on previous frame) frames. Thus, it works from the corrupt frame and produces further corrupt frames.
It is possible that the camera is trying to record proper data, but the SD card is not bothering to write it down correctly. It is also possible that the encoder within the camera is corrupting the data and that the SD card is writing the data it is given faithfully. The best bet to troubleshoot is to try a different SD card and see if the problem continues in the same manner.
If the SD card does not fix the problem, I would suggest contacting Canon's customer support for further assistance with getting your camera fixed.
| https://avp.stackexchange.com/questions/11989 |
avp | How to get a crisp, exact color match for lossless screen-cast? | Background
Recording a screen-cast (no audio) in Xubuntu Linux. The following image shows a side-by-side comparison of the video (left) versus the desktop (right):
The screen-cast is recorded using:
ffmpeg -r 30 -f x11grab -s $WIN_GEO -i :0.0+$WIN_XY -vcodec huffyuv -preset ultrafast -qp 0 output.mkv
Here, $WIN_GEO stores the browser dimensions (1030x794) and $WIN_XY has the browser location (1020x221).
$ cat /etc/issue
Ubuntu Trusty Tahr (development branch) \n \l
Problem
The colours in the video differ from the colours shown on the desktop, resulting in a slightly blurry playback. I have read that this could be due to conversion between RGB and YUV colours.
Question
How do you record a desktop video (screen-cast) that when played back (e.g., using mplayer, VLC, or ffplay) results in an exact match to the original desktop colours and crispness?
Related
Relevant pages:
http://www.unixuser.org/~euske/vnc2swf/
http://technically.us/pictures/test.html
http://ubuntuforums.org/showthread.php?t=1392026
https://askubuntu.com/questions/347574/how-to-do-screencasting-desktop-recording-with-high-quality-audio-and-video
http://step4wd.com/2012/08/03/recording-screencast-in-ubuntu-linux/
https://unix.stackexchange.com/questions/73622/how-to-get-near-perfect-screen-recording-quality
https://unix.stackexchange.com/questions/65970/washed-out-colours-with-screencast-software-but-not-screenshot-on-ubuntu-all-ve
https://trac.ffmpeg.org/wiki/How%20to%20grab%20the%20desktop%20%28screen%29%20with%20FFmpeg
http://rayslinux.blogspot.ca/2012/04/capturing-linux-desktop-via-command.html
| VQAonline_00002567.png | Capturing the video frames in XWD format then converting to PNG yields results that are almost pixel perfect when encoded with ffmpeg.
Install xvidcap:
mkdir -p $HOME/dev
cd $HOME/dev
svn checkout svn://svn.code.sf.net/p/xvidcap/code/trunk xvidcap-code
cd xvidcap*
./autogen.sh
LIBS="-ldl -lX11 -lXext" ./configure --prefix=/usr/local
make && sudo make install
Capture stills at 25 frames per second:
mkdir -p $HOME/video
cd $HOME/video
xvidcap --fps 25 --quality 100 --cap_geometry 1024x768+768+288 --file out%05d.xwd
This creates a series of X Windows capture files inside $HOME/video. Convert the files to PNG format using ImageMagick then combine into a video:
for i in out*.xwd; do convert -define png:color-type=2 $i $(basename $i .xwd).png; done
ffmpeg -i out%05d.png -c:v huffyuv -preset veryslow -qp 0 -qscale:v 0 output.avi
An example script:
echo "Click window to capture..."
INFO=$(xwininfo -frame)
WIN_GEO=$(echo $INFO | grep -oEe 'geometry [0-9]+x[0-9]+' | grep -oEe '[0-9]+x[0-9]+')
WIN_XY=$(echo $INFO | grep -oEe 'Corners:\s+\+[0-9]+\+[0-9]+' | grep -oEe '[0-9]+\+[0-9]+' | sed -e 's/\+/,/' )
OUTPUT_DIR=$HOME/video
echo Capturing to $OUTPUT_DIR...
rm -rf $OUTPUT_DIR
mkdir -p $OUTPUT_DIR
cd $OUTPUT_DIR
WIN_XY=$(echo $WIN_XY | tr , +)
xvidcap --fps 25 --quality 100 --cap_geometry $WIN_GEO+$WIN_XY --file out%05d.xwd
# Convert captured images to PNG format
echo "Converting XWD to PNG..."
for i in out*.xwd; do convert -define png:color-type=2 $i $(basename $i .xwd).png; done
ffmpeg -i out%05d.png -c:v huffyuv -preset veryslow -qp 0 -qscale:v 0 output.avi
This creates a high-quality video that looks sharp with VLC, can be edited in OpenShot, and uploaded to various video hosts. Playback with MPlayer yields slightly fuzzy and off-coloured results.
| https://avp.stackexchange.com/questions/10428 |
avp | placing text in video filmed environments | I really love mixing reallife environment with floating text over buildings or virtual paintings on the walls.
When the camera moves, the text also moves and looks like it is really attached to the surface. I hope you have the idea of what I'm trying to tell. Here are some questions:
What (1 entry level, 1 professional) Software can be used or is typically used?
Does the Software detect the movement or is it neccessary to move the decal every frame?
| VQAonline_00002558.png | The general technique you're asking about is called motion tracking, of which there exist different types: Feature ("point") tracking, planar tracking, and 3D match moving. After Effects (and the bundled Mocha) is probably the best entry level software to each of these methods, but it definitely leaves room for professional growth. Apple's Motion includes a more basic toolset, is only suited to feature tracking, but is more beginner-friendly.
When text is flatly attached to a simple, clearly visible surface such as a picture frame, you can use Feature tracking to track the corners of the object, and "corner pin" an image or text into the frame. The software will do its best to automate the process of tracking each corner, but if, for instance, an object passes in front of one of the points, you may have to manually keyframe its movement.
Planar tracking goes a step further and tracks the movement of full flat surfaces. Mocha, bundled with After Effects, is a planar tracker. It's fast and flexible, and you can achieve better results more reliably, but it's a little more complicated. To mask out an obstruction, for instance, you must rotoscope out the offending object.
You would only use 3D matchmoving if you wanted your text to be three dimensional, cast realistic shadows, receive image-based lighting, reflections, transparencies, in other words, be a realistic object in your scene. This is the most complicated method because it requires a back and forth workflow through tracking, 3d modeling, and compositing software. Different combinations of software packages will lump one or more of these steps within the same application.
An example of a dedicated professional motion tracking application is Boujou, although there are others (PFtrack comes to mind).
Hope this gives you a place to start.
| https://avp.stackexchange.com/questions/7340 |
avp | How do I resize the canvas of a image layer in After Effects? | I'm using After Effects CC 2017. I've imported a PNG image with transparency, then I added a simple CC Light Wipe effect:
The problem is that the range of the lights produced by this effect are limited to the image size, so it produces an annonying thingy. Is there a way to resize the canvas of the layer of the image or another way to solve this (avoiding the need to resize the image canvas using external programs like Photoshop)?.
I really tried to find out the answer researching in Google before asking here but I only found questions about resizing the entire compossition in the compossition settings...
| VQAonline_00002652.png | Add an adjustment layer on top (right-click in empty area of the layer names. Go to New menu) Apply the effect to that.
| https://avp.stackexchange.com/questions/20225 |
avp | Why is my video alternating between blurry and sharp? | I notice this on a regular basis while watching videos I've downloaded. The image will alternate pretty quickly between blurry and sharp and sometimes the effect is quite drastic. Below is an example image of a tree and the difference between two frames.
What is this effect called and why does it happen? I'm fairly certain it has to do with compression but what is going on?
If you receive a video like this and there's nothing you can do with how it was rendered or processed, is there anything you can do after the fact to minimize the effect? Settings in your video player maybe?
This particular screen shot was taken in Windows Media Player on Windows 7 playing an AVI file. The effect is still visible in VLC and I first noticed this while playing video through my PS3 off a harddrive. I can't say for sure, but I'm fairly certain that it's happened on multiple file types as well.
| VQAonline_00002546.png | The effect that you've seen is a side effect of the compression algorithm that was used to encode the video.
The most common compression algorithms (MPEG-4 and MPEG-2 among them) compress different frames with different methods, and that is why two very close and relatively similar frames may look so different.
The frame that looks pretty good is likely a keyframe. This is a frame that has all its pixels represented in the encoded stream. The compression introduces some loss of quality, but since the whole image is encoded the result typically looks good.
The image that looks bad is a frame that is not fully represented in the encoded stream. To make videos smaller, for certain parts of the picture the encoder references parts of previous frames that the player/decoder keeps stored in memory, so only the parts that are different are stored for the frame. Because of this these frames end up being a sort of collage. If the bitrate is too low, then you end up with really washed up images like the one you show. But increasing the bitrate enough helps dissimulate this effect, to the point that it is barely or not noticeable. Consider that all the TV that you watch (digital over the air, satellite, FIOS, cable, etc.) is encoded in this way.
For MPEG-2 it is common practice to insert a keyframe in the stream every half a second (15 frames for 29.97fps video, 12 frames for 25fps). For H.264 sometimes they go even longer than half a second.
In general, the image quality of a compressed video is at its highest at the keyframe points, and then slowly starts to degrade, going up again with the next keyframe.
For a more detailed explanation of frame types used in compression algorithms see the Wikipedia article Video compression picture types.
Unfortunately a player cannot improve the quality of the video, since the problem is that the information to reproduce the frame with better quality isn't there. The only ways to address this is by increasing the bitrate when encoding and/or increase the number of keyframes.
On the player side I think the only thing you can do is play the video in a smaller window, so then these artifacts will be less visible.
| https://avp.stackexchange.com/questions/4054 |
avp | How to get 'outer' composition's current time? | Suppose I've got 2 sequences, one named OUTER and one named INNER. Composition INNER is inside composition OUTER. INNER is shorter than OUTER and is placed in the middle of it's timeline. Inside INNER there is a text object which I want to display OUTER's current time - but I found out this is not so straightforward as I thought. My first idea was to create a solid namer TIMER inside OUTER and link the INNER's text object 'Source Text' to comp("OUTER").layer("TIMER").time and despite that this layer lasts from the beginning to the end of OUTER, the text shown from OUTER's perspective is always starting with 0.0 when INNER starts.
For the sake of clarity, here is the pic:
Is there a proper way to get linked composition's current time?
| VQAonline_00002632.png | If you change the inner text layer's source text to this it will work:
thisCompLayer = comp("outer").layer(thisComp.name);
thisCompLayer.time + thisCompLayer.startTime
You just offset the time to cope with the later start time.
Looks like when AE calculates values from another composition it just calculates them for the current comp's time. It makes sense, because there could be multiple copies, or no copies at all of the inner comp in the outer comp.
| https://avp.stackexchange.com/questions/17550 |
avp | My colors look awful, I can't tell why | I'm an amateur that recently made a video clip using the DJI Mavic Pro drone.
The footage itself turned out great, but the coloring is off.
The problem is, I can't tell what exactly is off, it just looks awful.
I tried to do some color correction in my video software, but I couldn't get it right.
Here is a single frame of the video, with no color correction:
I came here to ask what parameters I have to consider to make it look more natural, or if that isn't enough, what I should change when recording the video. (exposure, filters?)
| VQAonline_00002674.png | 'Awful' is pretty extreme - I don't actually think it looks that bad.
Perhaps it's a little bit over exposed (the car is almost glowing, it's that white) so you might want to consider an ND filter if you're filming outdoors (and you can get one of those for your drone).
Colour-wise, it does look like it's tipping towards the blue-end of the spectrum. Maybe try throwing a little more yellow/orange into the mix. However, that could just be my monitor. Do, please, check your monitor settings, too, they may be throwing off your perception.
This guy seems to know his stuff in regards to Mavic colour grading:
Maybe give that a watch and see if it helps :)
| https://avp.stackexchange.com/questions/23924 |
beer | What dishes pair well the Maltese Harruba liqueur? | What food stuffs pair well with the Maltese liqueur Harruba?
A friend of mine has several bottles of this sweet liqueur and we are hoping to make it into a meal of something more than just the ordinary.
The carob tree, in Maltese called Harruba (Ceratonia siliqua) has been a prominent component of the Maltese vegetation for several centuries. The fruit beans of this tree, also known as ‘St. John’s bread’ formed a substantial part of the diet of the local population during the hard times of World War II.
Carob beans, harvested by Maltese farmers, are crushed, roasted and boiled to produce a syrupy liquid with aromas and colour reminiscent of cocoa to which orange extracts are then added. Zeppi’s Harruba liqueur can be served chilled, on the rocks or can also be taken neat to close off an exquisite meal. Harmless sediment may form at the bottom of the bottle due to the nature of the product. -
Mediterranean Maltese Liqueur
| VQAonline_00002755.png | I'd say it is probably too sweet to be enjoyed as part of a meal except as an aperitif as @Eric suggested.
Since Carob tastes like chocolate and this is a sweet strong liqueur. Maybe consider using it in a Tiramisu recipe as a substitute for Marsala? I have used Amaretto in this way before and it was delicious!
Carob is often used as a substitute for chocolate so any liqueur based recipes where you want a hint of chocolate flavour would benefit from this. Maybe in a beef based dish (as we know a hint of dark chocolate in a beef casserole or chilli is a great trick!)
I found this article online which could give you some inspiration.
| https://beer.stackexchange.com/questions/7833 |
beer | Other than the USA, do any other countries have dry counties? | Other than the USA, do any other countries have dry counties?
I understand that the term county may not exist in some counties, so one can adopt a different term that may be better suited for a particular countries.
What is a dry county?
A dry county is a county in the United States whose government forbids the sale of any kind of alcoholic beverages. Some prohibit off-premises sale, some prohibit on-premises sale, and some prohibit both. Hundreds of dry counties exist across the United States, a majority of them in the South. A number of smaller jurisdictions also exist, such as cities, towns, and townships, which prohibit the sale of alcoholic beverages. These are known as dry cities, dry towns, or dry townships.
Map showing dry (red), wet (blue), and mixed (yellow) counties in the United States as of March 2012.
| VQAonline_00002747.png | Yes. Currently the list of Countries that have prohibition (and their counties) are:
Afghanistan
Bangladesh
Brunei
Iran
Indonesia (prohibition in small business shops)
India (prohibition in the states of Kerala, Gujarat, Bihar, Nagaland, Manipur and the union territory of Lakshwadeep)
Libya
Kuwait
Maldives (excluding non-Muslims)
Mauritania
Pakistan (excluding non-Muslims)
Saudi Arabia
Sudan
Somalia
United Arab Emirates (prohibition in the emirate of Sharjah)
Yemen
Most of these are in Muslim-majority countries while India only prohibits alcohol in some states and their residing counties.
I am interchanging county and country because not all countries that have counties or states that have been divided into counties.
| https://beer.stackexchange.com/questions/6759 |
beer | Vaping Alcohol - fad or here to stay? | Just recently I discovered that not only can I vape in stead of smoking, but I can also vape instead of drinking. What's vaping alcohol all about? Well, you put a shot of spirits into an orb, which sits over a small candle (tea-light), and then through a glass or metal straw inhale the results.(check it out here with buzzfeed)
This is what the Vaportini looks like - credit Vaportini
I understand that the alcohol bypasses the liver stage and just goes straight to your head and lungs. So, none of that 'oops, I've drunk too much - excuse me whilst I visit the bathroom' nonsense, with this method you apparently don't get to expell what your body can't handle.
With all this in mind, is there a limit (average) that can be vaped without doing myself some serious brain damage? What also is the effect on the lungs? Is this just another fad or is this the future?
| VQAonline_00002743.png | Limit: So, I would speculate that if you're "vaping" the same quantity of alcohol as you might instead drink, then you're facing the same risk. It's the same as drinking alcohol - the risk is cumulative and hard to define - it really depends on how much you drink and how often.
Effect on lungs: Frankly this is hard to say, as I am quite confident there have been no large scale (AKA reputable) studies (nor can I find any) performed on the effect of vaping alcohol on lung tissues. I would expect the effects to be minimal, but then again, personally, I'd probably still just stick to drinking my alcohol.
I can't provide any scientific basis to this, but I am thoroughly confident that vaping is simply a fad or novelty to enjoy - think of the increased costs and lack of accessibility compared to just drinking alcohol - you simply need a bottle of beer and a fridge, or a bottle of spirits and a glass versus a specialised glass, tea candle, vapour catching vessel and a glass or metal straw (seriously, who keeps one of them around?).
| https://beer.stackexchange.com/questions/6641 |
beer | What to do with 50 (?) years old sake? | I found a bottle of sake in my grandfathers basement.
As there are no Latin characters indicating the age of the bottle (and I don't speak Japanese), I used google Translator and found the following on a card which I assume can be sent back to the manufacturer to give feedback.
差出有効期間昭和45年12月14日迄（切手はいりません）
which is translated to:
Sent validity period Until December 14, 1970 (stamps are not required)
So I guess it must be produced somewhere around 1970
Does sake age well?
Can I sell the bottle, as in: is it worth anything due to its age?
How do I know if I can still drink it safely?
| VQAonline_00002750.png | Due its high alcohol content, you will still be able to drink the sake without worrying about your health.
However, the recommended consumption period is usually one year after bottling. After that, the maker cannot guarantee the flavor of the sake. Whatever the flavor of your sake is right now, whether it aged well or went plain ugly, is not the flavor of the sake as advertised by the sake maker. Oh, and if the bottle is open, like wine, sake will oxidize rapidly.
Sake may or may not age well, depending on the sake. I don't have enough knowledge to say what those differences are, though from my experience, old sake can become either a tad acidic or more rich in its original flavor.
You may be able to sell the bottle so someone interested, but I don't think there is a giant market for it outside of Japan (though I may be wrong about that). In Japan, there would be plenty demand for old sake there.
By law, there should be a date on the bottle (not sure if they print that on the box) which indicates the "month of bottling". Although, that law may not have existed 50 years back...
Note there is a chance it will go bad in the case it is nama (fresh) sake, which you can tell if you see 生 somewhere on the label. Nama sake is sake that does not undergo the two pasteurization processes after being made, so the yeast is still alive. Taste guarantee is only about a half a year, and something 50 years old will probably taste yogurty or cheesy.
| https://beer.stackexchange.com/questions/7146 |
beer | Beers that are popular but hyper-localized | I grew up near Baltimore, Maryland (USA), and spent a few years living in the city. One very popular beer in Baltimore is National Bohemian ("Natty Boh" in local parlance). You can see the beer's one-eyed mascot, Mr. Boh, all over the city. Apparently more than half a million cases of Natty Boh are sold in the city of Baltimore each year, which seems pretty high for a city with population 620,000.
One thing that I've found very odd is that outside of the small state of Maryland, you really can't find the beer at all, and 90% of the beer's sales are within the city of Baltimore. Thus, while the beer is reasonably popular, the interest is hyper-localized to a single city.
Are there other examples of beers that have high sales volume but are hyper-localized, or are Baltimore and Natty Boh unique in this respect? Is there some sort of economic or marketing phenomenon behind hyper-localized popularity of a high-volume beer?
| VQAonline_00002735.png | Most of the long running local brands have been acquired by the conglomerates and continue to operate and distribute in a limited range, as there is little to no financial motive to further the distribution of these brands.
| https://beer.stackexchange.com/questions/4578 |
beer | Cause of seasonal difference in beer production | I was recently crunching some numbers about beer production in the United States (data from the Alcohol and Tobacco Tax and Trade Bureau), and I noticed pretty significant seasonality in the production of beer:
Average production peaks in June (on average 18.1 million barrels) and is lowest in November and December (on average 14.1 million barrels). Are these ~25% seasonal swings in production based on some technical aspect of the brewing process, or are they based on something else (e.g. demand)?
| VQAonline_00002736.png | One thing you should take into consideration is that this chart certainly represents macro breweries production, once they still have the vast majority of the market-share, as opposite to craft breweries. So, we are talking here mainly about light lagers, known to be consumed as a refreshing beverage.
So, to me, it's pretty clear that the production increases as the weather warms up, peaking at the summer, and then falls down again towards chiller seasons. Considering distribution and other delaying factors, the peak at June would match the peak consumption at mid-July through mid-August.
PS: I don't live in USA, and this is merely a theory I came up with, but which seems feasible to me.
| https://beer.stackexchange.com/questions/4580 |
beer | Things people put in bottles of liquor or liqueur and are sold commercially? | People put the strangest things in bottles of liquor to be sold commercially. We have all probably heard of liquor stores, pubs or other drinking establishments occasionally selling tequila with a worm in the bottle. Be what the history of the mescal worm is: true or false is not my question.
The other day, I was in a local liquor store and noticed bottle of liquor called Eau de Vie de Poire in the Bottle with a real full sized pear inside the bottle containing 40% (ABV) of pear brandy. One can see how they get the pear in a bottle here and here.
Eau de Vie de Poire Pear In The Bottle
My question is quite simple: What other things are sold in bottles of liquor or liqueur commercially other than fruit or possibly worms (tequila)?
| VQAonline_00002749.png | You can see pretty much anything in the bottle. This article provides a good first look (trigger warning!).
Besides the stuff described there I witnessed bottles with exotic fish, giant prawns, and kelp. I even tasted some of them; we were not amused.
| https://beer.stackexchange.com/questions/7030 |
bicycles | Identify year of specialized s-works tarmac? | Can anyone identify this specialized s-works tarmac? The seller says it's a 2013, but I haven't found it.
| VQAonline_00003321.png | Looking on bikepedia.com, I can only find listings from 2012 and 2013 for Specialized Tarmac SL4 Pro, or S-Works Tarmac SL4. The frame in the photo seems to have decals for both 'S Works' AND 'Pro' (on the seat tube). This seems inconsistent with any photographs I can see on google images. SWorks frames tend to have 'SL4' on the seat tube instead but I have only seen photos taken from the drive side.
Also, the colour of the red decals on the bike seem a suspiciously similar shade to those on the wheels, which makes me skeptical even further. I haven't seen any google images results in this paint scheme, and expect that you haven't either, hence the question here.
I would ask the seller for more information, for warranty documentation, proof of purchase, a frame number that you can check with Specialized etc. Maybe it's all legit and original, or maybe it's been resprayed. If so, the owner shouldn't have any issue with answering your questions. But if it seems too good to be true, be prepared to walk away.
| https://bicycles.stackexchange.com/questions/55806 |
bicycles | Can't remove crank arm on older Mercier | I'm rebuilding an older Mercier and have decided to tackle the bottom bracket. I've read a few articles and watched a few videos on how to remove the crank but none of them look anything like what I've got on this bike.
Basically, there are bolt threads on one side and a 'nub' on the other side that would indicate that this is what I would remove the crank arm with, but I'm not having any luck removing the bolt.
I've attached a picture as I'm sure I'm probably not using the correct terms for some of these parts.
| VQAonline_00002861.png | What you are looking at is called a "Cottered Crank". The shaped cotter pin holds the crank in place and they can be next to impossible to remove without significant effort or a cotter pin press.
Sheldon Brown has an excellent article on removing cottered cranks using a hammer and pipe, which is a method I have used before, albeit multiple decades ago.
When you get it off you may want to consider replacing the bottom bracket and cranks with a more modern design that is easier to maintain, unless this is a restoration job and you want to stay true to the original.
| https://bicycles.stackexchange.com/questions/10856 |
bicycles | How to mount TT shifters and TT brake levers together? | I am starting a new project to build a custom bike with bullhorn handlebar. It'd most likely be made either with road or hybrid type of frame. I am planning on having both front and real derailleurs, and brakes (writing all this because, you know, fixies :) There are many unknowns/choices (obviously!), but I am really struggling with one detail in particular: shifters and brake lever mount to the bullhorn handlebar. I was searching a lot and came across this bike:
This is way aero for my taste, but check out that brake lever/shifter combo on the right side of the handlebar. Does anyone know what these components are? I searched Vision's site, but couldn't find TT brake level with opened top to which TT shifter could be mounted. And the lever doesn't look to be crosstop one; so I am really confused.
Does anyone know how can this be done? Thanks!
| VQAonline_00003142.png | I can't tell for sure what's going on in that picture, but I think it's a modified older Vision lever that clamps on the OD rather than inside the bars, and then the shifter is just stuck out the end. Ways of doing it with off the shelf parts that I know of are the Jtek Aerobrake, Ultegra ST-6871 and DA ST-9071, the Record and Athena tri/tt EPS levers, and SRAM eTap blips (their equivalent, kind of).
| https://bicycles.stackexchange.com/questions/41998 |
bicycles | Steel rims responsible for slicing tubes? | I have an old Giant dutch bike and it has steel rims. Since I'm a big boy I felt that the 60PSI on the tyres is not enough and pumped my tyres to the maximum of 85PSI which is what my Schwalbe Marathon Plus tyres were supposed to be able to take in. It was great, riding was so much easier all of a sudden! Not the slowest guy on the road anymore, really fast if I wanted to in fact! I loved it.
Unfortunately a few days after I came to find one of the tubes neatly sliced. The tyre untouched. I wasn't sure what had happened but walked to work that day and planned to bring it to the workshop asap. When the day came I exited my house and found the other tube sliced in the exact same way.
I have meanwhile talked to lots of people. Some say it has to do with the steel rims even though I can't make any sense of that. I have also encountered people that said I just need the right tubes and tyres and it shouldn't happen anymore.
I'm now thinking of either buying a new bike, exchanging the wheels(which would be more expensive than the initial price tag of the bike) or give new tubes/new rimband and maybe different tyres a shot?
Does anyone have experience with this sort of thing or any sort of input?
this didn't help: Tire popping out of rim when inflating tube
| VQAonline_00003006.png | OK if the tire was blown off the rim then I highly suspect that is the whole story.
When the tube leaks out the because tire bead has come out the tube will burst and you will see a slit.
A tube outside a tire cannot take much pressure.
Most likely when you went from 60 to 85 psi it was enough pressure to push the tire off the rim (bead).
I have seen this with some older bikes. The rim is a little small.
Look for tires that run small and run at lower pressures.
You might also have a mismatch like a 27 on a 700c.
A Schwalbe Marathon Plus is a pretty hefty tire and tend to fit a little tight so this is kind of strange. But it did happen after you went to 85 PSI.
Maybe give it a try again at 60 PSI. Even if you get a new bike you would have this as a backup.
| https://bicycles.stackexchange.com/questions/29255 |
bicycles | Is this a crack on the carbon frame? | I have just noticed this on the top of my saddle bar and where the seat post clamp is. Is it a crack probably caused by the saddle pressure?
| VQAonline_00003388.png | Doesn’t look like a crack, looks more like a surface void that formed during the resin injection molding. These types of imperfections are not uncommon, especially on the inside of the frame where you can’t see them. Less common to see them on the outside as they are usually caught in quality control inspections. While they are not ideal, as areas with voids will be somewhat weaker than areas without voids (depending on the size and depth of the void), they are not critical like a crack.
| https://bicycles.stackexchange.com/questions/60186 |
bicycles | Cannot steer my bike with with new adult training wheels | I just had adult training wheels put on my bike and I cannot steer it properly. The roads in my neighborhood are all cambered (raised in the middle) and the bike keeps pulling strongly to the right. I have to lean my body way out to the left to conteract the pull to the right. The training wheels are set almost right on the ground. Should I move them higher so there is space between the wheels and the ground? Or am I doing something wrong? Thanks.
Zaffer
Addemdum: I made a diagram (see attached). I think I need to raise both training wheels at least an inch and get used to the idea of having zero or only one training wheel on the ground at a time.
| VQAonline_00003710.png | Bicycles (and other two-wheeled vehicles like motorcycles) constantly need righting while riding. That is done mostly by the rider. If the bicycle starts to tip to the side, you automatically steer to the same side so you induce an opposite effect. This is helped by the head angle, the wheel trail and the gyroscopic effect, but active steering plays the biggest role. If a bicycle leans to one side for a longer time, it starts to turn or it falls over. (In fact, this is how you steer a bike in a corner: you steer in the opposite direction to make it lean into the corner and then you just keep it leaning until you've taken the turn.)
If you're cycling on the right side of a cambered road, the part of the road you're riding on slopes to the right. On a normal bike this isn't a problem since you can ride upright regardless of the slope.
Compared to this, a bicycle with training wheels is a completely different vehicle. It doesn't need righting and it doesn't need to lean into corners. In fact, if you try to ride it like a normal bike it leads to the experience you described. Your training wheels make the bike lean to the right, perpendicular to the road surface. Your natural reaction to the bike leaning to the right is to steer to the right to counteract the leaning. You then trick your brain into thinking the bike is already upright by leaning left relative to the bicycle.
If you would lift the training wheels a little, you would create a vehicle that behaves like a bicycle when it is upright but makes it impossible to lean into corners and actually throws you off if you try to go into a corner at any speed.
The solution is to remove the training wheels completely. Training wheels suck and they don't teach you how to ride but they also hinder your progress.
| https://bicycles.stackexchange.com/questions/85604 |
bicycles | (Light?) rust removal from chain | Situation:
I'm new to the world of trike maintenance. My son and I purchased recumbent trikes at the end of last summer. The weather for the past couple of months has been cold, snowy, cold, and...cold (Northern Pennsylvania climate.) So I cleaned them, tried my hand at lubricating the chains for the third time since owning them, and put them up in the shed to keep them out of the sun and precipitation.
This weekend looks like the first time in awhile that we might be able to go for a ride without freezing the fingers off. I took a look at the trikes, anticipating having to add air to tires and maybe clean the disc brakes, and saw the chains:
The top is one trike, the bottom two are the other...
On soliciting some info, I was told that is "definitely rust." Apparently I didn't do something right when I put them in the shed for a month of storage, or rust is not easy to fend off. As I said, I'm new to this, and trying to improve maintenance skills. I'm hoping this isn't so bad that the chains require removal or replacement at this point.
Questions:
How bad in shape are these chains, relatively speaking?
I have yet to find a definitive answer to this; how do I clear off the rust? WD-40, followed by degreaser and relubricate them?
These are chains that came stock with the trikes. I wonder if the future fix is to get a particular type of rust-resistant chain?
Being winter in PA, the roads will no doubt be salty from road melt material. I'm trying to keep the trikes cleaned, touch up paint where chips are found, wipe them down, etc...but there's a lot of contradictory advice on how to do certain things. Any advice/fixes for the questions above would be appreciated...
| VQAonline_00003376.png | As long, as you can easily move the links of your chain, there's no problem. Just lube them and ride them, and they'll be fine. The movement will rub any rust from the critical places. You may need to work the chain for a while before the links become free, a creeping oil should help get the links moving again.
That said, there are two ways to ensure that a chain won't rust (as quickly as yours):
Make sure they are always well-lubed. A surface that's covered by oil is not covered by humid air, and cannot rust. May work well during storage, not so well when you actually use the bike.
Use chains with an anti-rust coating. I have quite good experiences with this, though the chains are a bit more expensive. I'm not sure how robust the anti-rust coating is against sliding through a front deraileur, though (I only ride IGH). In any case, I've never had a rust-proof chain go stiff.
Of course, anti-rust coated chains still like being kept well-lubed...
| https://bicycles.stackexchange.com/questions/59467 |
bioinformatics | How to increase the size of the shapes that denotes effect sizes of different datasets and metaanalysis? | I am doing metaanalysis with forestplot from ggforestplot package. I have 7 different datasets from 7 different countries. After metaanalysis, I have 7 Effect sizes and a Meta-analysis effect size, i.e., total of 8 effect sizes. Now, I have generated a forest plot using this code:
# Forestplot
my_plot <- forestplot(
df = final,
estimate = estimate,
logodds = FALSE,
colour = country=="metaanalysis",
shape = country,
title = "Associations to disease accross populations",
xlab = "Effect Size",
#xlim = c(-1.5, 1.5),
xtickbreaks = c(-1.0, -0.5, -0.45, -0.4, 0, 0.4, 0.45,0.5, 1.0)
)+
# You may also want to add a manual shape scale to mark meta-analysis with a
# diamond shape
ggplot2::scale_shape_manual(
values = c(5L, 0L, 1L, 2L, 8L, 19L, 4L, 3L),
)
But, the shapes denoting the countries and the metanalysis seem very small. How can I make them larger for better visualization? Can anyone please help me?
Representative data for replication:
final <- data.frame(
stringsAsFactors = FALSE,
name = c("RIBOSYN2-PWY__flavin_biosynthesis_I_(bacteria_and_plants)",
"PWY-6385__peptidoglycan_biosynthesis_III_(mycobacteria)",
"PWY-6151__S-adenosyl-L-methionine_cycle_I",
"PWY-6387__UDP-N-acetylmuramoyl-pentapeptide_biosynthesis_I_(meso-diaminopimelate_containing)",
"PWY-6700__queuosine_biosynthesis",
"PEPTIDOGLYCANSYN-PWY__peptidoglycan_biosynthesis_I_(meso-diaminopimelate_containing)",
"PWY-6386__UDP-N-acetylmuramoyl-pentapeptide_biosynthesis_II_(lysine-containing)",
"PWY-5667__CDP-diacylglycerol_biosynthesis_I",
"PWY0-1319__CDP-diacylglycerol_biosynthesis_II",
"PWY-6122__5-aminoimidazole_ribonucleotide_biosynthesis_II",
"PWY-6277__superpathway_of_5-aminoimidazole_ribonucleotide_biosynthesis",
"PWY-6163__chorismate_biosynthesis_from_3-dehydroquinate",
"TRPSYN-PWY__L-tryptophan_biosynthesis",
"PANTOSYN-PWY__pantothenate_and_coenzyme_A_biosynthesis_I",
"GLYCOCAT-PWY__glycogen_degradation_I_(bacterial)",
"P161-PWY__acetylene_degradation",
"FUC-RHAMCAT-PWY__superpathway_of_fucose_and_rhamnose_degradation",
"P108-PWY__pyruvate_fermentation_to_propanoate_I",
"PWY-7328__superpathway_of_UDP-glucose-derived_O-antigen_building_blocks_biosynthesis",
"TCA__TCA_cycle_I_(prokaryotic)",
"PWY-6901__superpathway_of_glucose_and_xylose_degradation","PWY66-400__glycolysis_VI_(metazoan)",
"FUCCAT-PWY__fucose_degradation",
"PRPP-PWY__superpathway_of_histidine,_purine,_and_pyrimidine_biosynthesis",
"PWY-7234__inosine-5'-phosphate_biosynthesis_III",
"TRPSYN-PWY__L-tryptophan_biosynthesis",
"PWY-6122__5-aminoimidazole_ribonucleotide_biosynthesis_II",
"PWY-6277__superpathway_of_5-aminoimidazole_ribonucleotide_biosynthesis",
"RIBOSYN2-PWY__flavin_biosynthesis_I_(bacteria_and_plants)",
"PWY-6163__chorismate_biosynthesis_from_3-dehydroquinate",
"PWY-5667__CDP-diacylglycerol_biosynthesis_I",
"PWY0-1319__CDP-diacylglycerol_biosynthesis_II",
"PANTOSYN-PWY__pantothenate_and_coenzyme_A_biosynthesis_I",
"RIBOSYN2-PWY__flavin_biosynthesis_I_(bacteria_and_plants)",
"PWY-6386__UDP-N-acetylmuramoyl-pentapeptide_biosynthesis_II_(lysine-containing)",
"RIBOSYN2-PWY__flavin_biosynthesis_I_(bacteria_and_plants)",
"PANTOSYN-PWY__pantothenate_and_coenzyme_A_biosynthesis_I",
"PWY-6385__peptidoglycan_biosynthesis_III_(mycobacteria)",
"PWY-6387__UDP-N-acetylmuramoyl-pentapeptide_biosynthesis_I_(meso-diaminopimelate_containing)","PWY-6700__queuosine_biosynthesis",
"PWY-6151__S-adenosyl-L-methionine_cycle_I",
"PWY0-1319__CDP-diacylglycerol_biosynthesis_II",
"PWY-5667__CDP-diacylglycerol_biosynthesis_I",
"PEPTIDOGLYCANSYN-PWY__peptidoglycan_biosynthesis_I_(meso-diaminopimelate_containing)",
"PWY-6387__UDP-N-acetylmuramoyl-pentapeptide_biosynthesis_I_(meso-diaminopimelate_containing)",
"PWY-6385__peptidoglycan_biosynthesis_III_(mycobacteria)",
"PANTOSYN-PWY__pantothenate_and_coenzyme_A_biosynthesis_I",
"PEPTIDOGLYCANSYN-PWY__peptidoglycan_biosynthesis_I_(meso-diaminopimelate_containing)","PWY-5667__CDP-diacylglycerol_biosynthesis_I",
"PWY0-1319__CDP-diacylglycerol_biosynthesis_II"),
estimate = c(0.492903365186722,
0.490116714405755,0.470681520902659,0.465726944992238,
0.461786439528495,0.455469435286562,0.449174326308655,
0.433755737833203,0.433670791448977,0.412009484469875,
0.412009484469875,0.409849212159568,0.407818381473059,
0.406187518931948,-0.405573831841341,-0.407806403622317,
-0.418351108232386,-0.419107645158175,-0.420781760133428,
-0.441930843508614,-0.444723954813865,-0.451224756237618,
-0.504642907784859,-0.515843696383127,-0.523823484265933,
1.01203740887784,0.860911808112254,0.860911808112254,
0.782824395343453,0.779871038531055,0.763412247455786,
0.763412247455786,0.744965434413444,0.735086809796288,
0.733132943355509,0.731855318166865,0.730523378560539,
0.728356885227315,0.694487466356475,0.694335496605963,
0.68469489116557,0.680753784497535,0.680732580641012,
0.668909750729078,0.665107737526883,0.662352062210176,
0.643767077562848,0.640204416487105,0.639460661647805,
0.637911093993277),
se = c(0.10858902830706,
0.101375498952004,0.101193730594653,0.101213265518358,
0.101165178275411,0.101149604926044,0.101114528367103,
0.101177617463096,0.101176196339295,0.10102421433221,
0.10102421433221,0.100910703206783,0.101046445558438,
0.12265509469116,0.10486856029419,0.103267024648877,0.100867566762125,
0.11467836793049,0.10790947678297,0.100997454994136,
0.101684644439116,0.103275688295495,0.101358559584742,
0.101485340026678,0.131050876787633,0.12672527384678,
0.0911987727585976,0.0911987727585976,0.0473284627336248,
0.120947206065826,0.120594420271743,0.120594420271743,
0.120207965256539,0.12000489747134,0.119965054342127,
0.0890575546896603,0.0468935746714197,
0.0890043416222531,0.119198789457309,0.0466102635462743,
0.119011209638725,0.0883056120686039,0.0883053113523379,
0.0881390968551948,0.0880862640207957,0.118593197976584,
0.0877953030586674,0.118192523540133,0.0462081105569776,
0.0461972348759043),
country = c("metaanalysis","metaanalysis",
"metaanalysis","metaanalysis","metaanalysis",
"metaanalysis","metaanalysis","metaanalysis","metaanalysis",
"metaanalysis","metaanalysis","metaanalysis",
"metaanalysis","metaanalysis","metaanalysis","metaanalysis",
"metaanalysis","metaanalysis","metaanalysis",
"metaanalysis","metaanalysis","metaanalysis","metaanalysis",
"metaanalysis","metaanalysis","Swedish","Kazakh","Kazakh",
"Japanese","Swedish","Swedish","Swedish","Swedish",
"Swedish","Swedish","Kazakh","Japanese","Kazakh",
"Swedish","Japanese","Swedish","Kazakh","Kazakh",
"Kazakh","Kazakh","Swedish","Kazakh","Swedish","Japanese",
"Japanese")
)
Output:
Thanks
| VQAonline_00003840.png | A quick look at the code for forestplot shows that geom_effect is what needs to be modified. If you add a value for fatten changes the size of the shapes in the the figure (but not in the legend), or a value for size will change the shape, line and legend sizes (add to not geom_effect not to the aes layer)
This may be easier said than done as forestplot also seems to call an unexposed function (function quo_is_null). A couple of simple hacks are possible; copy and make your own forestplot in the default environment and remove the call to the function (it seems to just check if pvalue is set), or change the environment of the "new" forestplot to ggforestplot
envorionment(forestplot) <- envornment(ggforestplot::forestplot)
There may be other less awkward methods, but this will work. Fatten changed to size 6 which is massive.
forestplot <-
function (df, name = name, estimate = estimate, se = se, pvalue = NULL,
colour = NULL, shape = NULL, logodds = FALSE, psignif = 0.05,
ci = 0.95, ...)
{
stopifnot(is.data.frame(df))
stopifnot(is.logical(logodds))
name <- enquo(name)
estimate <- enquo(estimate)
se <- enquo(se)
pvalue <- enquo(pvalue)
colour <- enquo(colour)
shape <- enquo(shape)
args <- list(...)
const <- stats::qnorm(1 - (1 - ci)/2)
df <- df %>% dplyr::mutate(`:=`(!!name, factor(!!name, levels = !!name %>%
unique() %>% rev(), ordered = TRUE)), .xmin = !!estimate -
const * !!se, .xmax = !!estimate + const * !!se, .filled = TRUE,
.label = sprintf("%.2f", !!estimate))
if (logodds) {
df <- df %>% mutate(.xmin = exp(.data$.xmin), .xmax = exp(.data$.xmax),
`:=`(!!estimate, exp(!!estimate)))
}
if (!quo_is_null(pvalue)) {
df <- df %>% dplyr::mutate(.filled = !!pvalue < !!psignif)
}
g <- ggplot2::ggplot(df, aes(x = !!estimate, y = !!name))
if (logodds) {
if ("xtickbreaks" %in% names(args)) {
g <- g + scale_x_continuous(trans = "log10", breaks = args$xtickbreaks)
}
else {
g <- g + scale_x_continuous(trans = "log10", breaks = scales::log_breaks(n = 7))
}
}
g <- g + theme_forest() + scale_colour_ng_d() + scale_fill_ng_d() +
geom_stripes() + geom_vline(xintercept = ifelse(test = logodds,
yes = 1, no = 0), linetype = "solid", size = 0.4, colour = "black")
g <- g + geom_effect(ggplot2::aes(xmin = .data$.xmin, xmax = .data$.xmax,
colour = !!colour, shape = !!shape, filled = .data$.filled),
position = ggstance::position_dodgev(height = 0.5),
fatten=6) +
ggplot2::scale_shape_manual(values = c(21L, 22L, 23L,
24L, 25L)) + guides(colour = guide_legend(reverse = TRUE),
shape = guide_legend(reverse = TRUE))
if ("title" %in% names(args)) {
g <- g + labs(title = args$title)
}
if ("subtitle" %in% names(args)) {
g <- g + labs(subtitle = args$subtitle)
}
if ("caption" %in% names(args)) {
g <- g + labs(caption = args$caption)
}
if ("xlab" %in% names(args)) {
g <- g + labs(x = args$xlab)
}
if (!"ylab" %in% names(args)) {
args$ylab <- ""
}
g <- g + labs(y = args$ylab)
if ("xlim" %in% names(args)) {
g <- g + coord_cartesian(xlim = args$xlim)
}
if ("ylim" %in% names(args)) {
g <- g + ylim(args$ylim)
}
if ("xtickbreaks" %in% names(args) & !logodds) {
g <- g + scale_x_continuous(breaks = args$xtickbreaks)
}
g
}
environment(forestplot) <- environment(ggforestplot::forestplot)
| https://bioinformatics.stackexchange.com/questions/15804 |
bioinformatics | Identify side chain atoms in BioPandas dataframe | I am currently implementing some metrics I could use for comparing two conformations of the same protein in Python.
For example, I know I could use the RMSD of all protein ATOMS in BioPandas using this:
biopandas.pdb.PandasPdb.rmsd(conformation1.df['ATOM'], conformation2.df['ATOM'])
Are there some out-of-the-box tools in Python for measuring the RMSD between the side chains of the two conformations? When trying to do this manually, the main issue is how to identify side chain atoms, which is not clear for me. I know how to get all atoms from a residue using BioPandas:
aminoacids = list(PandasPdb().read_pdb(my_pdb_filename).df['ATOM'].groupby(['chain_id', 'residue_number', 'residue_name']))
Now aminoacids[i] is a dataframe containing all the atoms of the i-th aminoacid, like this:
From here, it's not clear how to separate back bone atoms from side chain atoms. It's clear that the one with atom_number 'CA' will be the alpha-Carbon, but I am not sure how to identify the others. But once the separation is done, the side chain RMSD could be measure for example using Bio.SVDSuperimposer.SVDSuperimposer which works directly on the array of 3D coordinates of the atoms.
Thanks!
| VQAonline_00003856.png | As you suggest one way of solving your problem would be by selecting all atoms that don't have backbone atoms names. In a pdb file I believe backbone atoms would be named 'CA', 'HA', 'N', 'HN' or 'H', 'C' and 'O'. Beware of the N-terminal (where the hydrogens would be named either 'H1', 'H2' & 'H3'; or 'HN1', 'HN2' and 'HN3') and the C-terminal (the other oxygen would be named 'OXT').
One way of doing it is by using the handy selections from pandas dataframes. It's probably a more elegant way than making a list of dataframes.
from biopandas.pdb import PandasPdb
bpdf_1 = PandasPdb().fetch_pdb('1t48').df['ATOM']
bpdf_2 = PandasPdb().fetch_pdb('1t49').df['ATOM']
# Function returns a list of boolean. True when it's not a backbone atom.
sel = lambda df: df['atom_name'].str.contains('[^(CA|HA|N|C|O|HN|H)]$')
# The number of atom is not the same, so I only align the first 200
sidechain_rmsd = PandasPdb.rmsd(bpdf_1[sel][:200], bpdf_2[sel][:200])
The regex says something like "(not (CA or HA or …)) end of line". The end of line is important, otherwise any atom containing N, C, O or H in their name would be excluded (so most of them).
Note that with this method it's still possible to use the PandasPdb selectors. For example, to only consider heavy atoms (no hydrogen):
sidechain_rmsd = PandasPdb.rmsd(bpdf_1[sel][:200],
bpdf_2[sel][:200],
s='heavy')
EDIT:
Another way to do it would be:
sidechain_rmsd = PandasPdb.rmsd(bpdf_1[:200],
bpdf_2[:200],
s='main chain',
invert=True)
You don't need any selection in this case, BUT this is a bad idea if you have hydrogens, as it will also align them (including the backbone ones).
| https://bioinformatics.stackexchange.com/questions/18690 |
bioinformatics | GROMACS RMSF Result Analysis Problem | This is RMSF for protein from GROMACS after 100ns simulation-
I have few questions-
Residue numbers are starting from 1650 to 1850, has it ignore LIG
and HOH as residues?
There are three lines, so are there three chains and their residue number is same?
Are the straight lines connecting these chains or this is kind of loop something?
Since I am seeing 2nm or 20A fluctuation, is the protein quite disturbed?
| VQAonline_00003846.png |
The residue numbering in a PDB file mainly depend on the person who deposited it. There are usually reasons for how things are numbered, but ultimately you should look at PDB file, and check the details on how the structure was obtained. To give you an example, during my PhD I worked on a protein that had some missing residues at the N-terminus. That was because the N-term was very unstable and they didn't manage to crystallise it properly.
You need to check the PDB, but it is possible that the 3 chains have the same residue numbering (A1-200, B1-200). This is common in structures where you have multiple identical sub-units (e.g. dimers).
The lines are merely an artefact. Those lines are the attempt of the engine to draw a single line for all the chains. You go from residue 1850 of chain 1 to residue 1650 of chain 2, and so on. Some tools handle this behaviour, others don't. I would suggest you to parse the PDB yourself and plot (e.g. ggplot) each chain as a layer of the same figures .
It is indeed, but only you can tell if this is good or bad. It really depends on how you calculate the RMSF. Was it on the backbone or on the side-chains? How is your dynamics? High temperature? Does you protein partially unfold? are the chains separating?
| https://bioinformatics.stackexchange.com/questions/17602 |
bioinformatics | Highly heterozygous reads mapping | I have short (67bp) Hi-C reads from a highly heterozygous organism (~15% between-haplotype SNP divergence) and I have both reference haplotypes.
I wanted to try and compare different haplotyping softwares for Hi-C reads using these reads as benchmarking dataset. When mapping the reads separately to each haplotype, I get good mapping statistics. When I map the reads to a single haplotype with all the heterozygous SNPs masked (into N's), I get very poor mapping rates.
I would like to be able to map the reads when the real haplotypes are unknown (reference is a mix of haplotypes).
I use minimap2 to map the reads with the sr preset. I tried decreasing the mismatch penalty (-B) to 1 and increasing the --score-N value, but this had no effect.
As shown in the attached IGV screenshot, coverage drops to 0 when the SNP density increases.
Is it feasible to map reads with such a high heterozygosity on a single (masked) reference ? Should I use another tool ?
| VQAonline_00003788.png | I believe you may be able to map your reads, but I don't know how to do that with minimap2.
I recommend running gsnap, which is more SNP tolerant and provides a number of parameters which are likely to help.
For instance, I believe that most aligners will treat 'N' characters as mismatches when you align. GSNAP has parameters to account for this.
--query-unk-mismatch=INT Whether to count unknown (N) characters in the query as a mismatch
(0=no (default), 1=yes)
--genome-unk-mismatch=INT Whether to count unknown (N) characters in the genome as a mismatch
(0=no, 1=yes (default))
It also has a mismatch parameter similar to the one you described for minimap2.
-m, --max-mismatches=FLOAT Maximum number of mismatches allowed
Try running with the 'genome-unk-mismatch' parameter above (with the masked reference). That may be your best bet. There are also other parameters that may help, but this should be a good start.
| https://bioinformatics.stackexchange.com/questions/6791 |
bioinformatics | reverse translation from amino acid string to DNA strings | what is the opposite of .translate() function calls ?
I mean let's say I am given an amino acid string CYCLIC, how do I obtain all the possible combinations of DNA strings before the translation process ?
Note: I was told that degeneracy has an important role in this particular aspect, but I am not entirely sure about the degeneracy calculation in the following screenshot highlighted in yellow color.
The degenerate code is as follows:
table = {
'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',
'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L',
'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P',
'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q',
'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R',
'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V',
'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A',
'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G',
'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S',
'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_',
'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W',
}
| VQAonline_00003867.png | Given the table above the solution for CYCLE is:
from itertools import product
prot = 'CYCLE'
degenDict = dict()
for v,k in table.items():
if k in degenDict:
degenDict[k].append(v)
else:
degenDict[k]=[]
degenDict[k].append(v)
nucs = [degenDict[resid] for resid in prot]
for degenNuc in product(*nucs):
print(''.join(degenNuc))
TGCTACTGCCTAGAA
TGCTACTGCCTAGAG
TGCTACTGCCTCGAA
TGCTACTGCCTCGAG
TGCTACTGCCTGGAA
TGCTACTGCCTGGAG
TGCTACTGCCTTGAA
TGCTACTGCCTTGAG
TGCTACTGCTTAGAA
TGCTACTGCTTAGAG
TGCTACTGCTTGGAA
TGCTACTGCTTGGAG
TGCTACTGTCTAGAA
TGCTACTGTCTAGAG
TGCTACTGTCTCGAA
TGCTACTGTCTCGAG
TGCTACTGTCTGGAA
TGCTACTGTCTGGAG
TGCTACTGTCTTGAA
TGCTACTGTCTTGAG
TGCTACTGTTTAGAA
TGCTACTGTTTAGAG
TGCTACTGTTTGGAA
TGCTACTGTTTGGAG
TGCTATTGCCTAGAA
TGCTATTGCCTAGAG
TGCTATTGCCTCGAA
TGCTATTGCCTCGAG
TGCTATTGCCTGGAA
TGCTATTGCCTGGAG
TGCTATTGCCTTGAA
TGCTATTGCCTTGAG
TGCTATTGCTTAGAA
TGCTATTGCTTAGAG
TGCTATTGCTTGGAA
TGCTATTGCTTGGAG
TGCTATTGTCTAGAA
TGCTATTGTCTAGAG
TGCTATTGTCTCGAA
TGCTATTGTCTCGAG
TGCTATTGTCTGGAA
TGCTATTGTCTGGAG
TGCTATTGTCTTGAA
TGCTATTGTCTTGAG
TGCTATTGTTTAGAA
TGCTATTGTTTAGAG
TGCTATTGTTTGGAA
TGCTATTGTTTGGAG
TGTTACTGCCTAGAA
TGTTACTGCCTAGAG
TGTTACTGCCTCGAA
TGTTACTGCCTCGAG
TGTTACTGCCTGGAA
TGTTACTGCCTGGAG
TGTTACTGCCTTGAA
TGTTACTGCCTTGAG
TGTTACTGCTTAGAA
TGTTACTGCTTAGAG
TGTTACTGCTTGGAA
TGTTACTGCTTGGAG
TGTTACTGTCTAGAA
TGTTACTGTCTAGAG
TGTTACTGTCTCGAA
TGTTACTGTCTCGAG
TGTTACTGTCTGGAA
TGTTACTGTCTGGAG
TGTTACTGTCTTGAA
TGTTACTGTCTTGAG
TGTTACTGTTTAGAA
TGTTACTGTTTAGAG
TGTTACTGTTTGGAA
TGTTACTGTTTGGAG
TGTTATTGCCTAGAA
TGTTATTGCCTAGAG
TGTTATTGCCTCGAA
TGTTATTGCCTCGAG
TGTTATTGCCTGGAA
TGTTATTGCCTGGAG
TGTTATTGCCTTGAA
TGTTATTGCCTTGAG
TGTTATTGCTTAGAA
TGTTATTGCTTAGAG
TGTTATTGCTTGGAA
TGTTATTGCTTGGAG
TGTTATTGTCTAGAA
TGTTATTGTCTAGAG
TGTTATTGTCTCGAA
TGTTATTGTCTCGAG
TGTTATTGTCTGGAA
TGTTATTGTCTGGAG
TGTTATTGTCTTGAA
TGTTATTGTCTTGAG
TGTTATTGTTTAGAA
TGTTATTGTTTAGAG
TGTTATTGTTTGGAA
TGTTATTGTTTGGAG
| https://bioinformatics.stackexchange.com/questions/19498 |
bioinformatics | TCGA: gene IDs not appearing and other concerns | I want to download RNA-seq datasets of 4 or 5 different types of cancer from the TCGA to investigate what is happening with my gene of interest. The problem is that I'm a physician and I don't know people used to deal with Big Data to help me.
I'm using a Bioconductor program called TCGAbiolinks and I'm able to download some datasets using the following script:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TCGAbiolinks")
browseVignettes("TCGAbiolinks")
library(TCGAbiolinks)
library(dplyr)
library(DT)
query <- GDCquery(project = "TCGA-BRCA",
data.category = "Gene expression",
file.type = "normalized_results",
data.type = "Gene expression quantification",
experimental.strategy = "RNA-Seq",
barcode = c("TCGA-AN-A046", "TCGA-AC-A23H"),
legacy = TRUE)
GDCdownload(query, method = "api", files.per.chunk = 10)
# GDCprepare transforms data in R format
# The default GDCprepare output is a SummarizedExperiment (SE) object,
# but you can also set to output the data frame.
data <- GDCprepare(query, summarizedExperiment = FALSE)
The problems is that: 1) the gene list is not appearing in the first column; 2) I don't know how many datasets I'll be able to download and analyse without a server.. I'm working with my Macbook..
Can someone familiar with the TCGA website or with the TCGAbiolinks help me with this project? I've been trying to progress in the last months, but the TCGA is a complex website and I'm feeling lost. I use R, I don't know SQL or other programming languages..
| VQAonline_00003831.png | I had to play around a little to understand the object, but here's what I got:
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(TCGAbiolinks)
> query <- GDCquery(project = "TCGA-BRCA",
+ data.category = "Gene expression",
+ file.type = "normalized_results",
+ data.type = "Gene expression quantification",
+ experimental.strategy = "RNA-Seq",
+ barcode = c("TCGA-AN-A046", "TCGA-AC-A23H"),
+ legacy = TRUE)
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg19
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-BRCA
--------------------
oo Filtering results
--------------------
ooo By experimental.strategy
ooo By data.type
ooo By file.type
ooo By barcode
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------
> GDCdownload(query, method = "api", files.per.chunk = 10)
Downloading data for project TCGA-BRCA
GDCdownload will download 3 files. A total of 1.306357 MB
Downloading chunk 1 of 1 (3 files, size = 1.306357 MB) as Wed_Aug_19_12_20_11_2020_0.tar.gz
Downloading: 580 kB
> data <- GDCprepare(query, summarizedExperiment = TRUE)
------------------
oo Reading 3 files
------------------
|====================================================|100% Completed after 0 s
------------------
oo Merging 3 files
------------------
Accessing grch37.ensembl.org to get gene information
Downloading genome information (try:0) Using: Human genes (GRCh37.p13)
Starting to add information to samples
=> Add clinical information to samples
=> Adding TCGA molecular information from marker papers
=> Information will have prefix 'paper_'
brca subtype information from:doi.org/10.1016/j.ccell.2018.03.014
> head(data)
class: RangedSummarizedExperiment
dim: 6 3
metadata(1): data_release
assays(1): normalized_count
rownames(6): A1BG A2M ... RP11-986E7.7 AADAC
rowData names(3): gene_id entrezgene ensembl_gene_id
colnames(3): TCGA-AN-A046-01A-21R-A034-07 TCGA-AC-A23H-11A-12R-A157-07
TCGA-AC-A23H-01A-11R-A157-07
colData names(83): barcode patient ... paper_PARADIGM Clusters
paper_Pan-Gyn Clusters
I see from this representation that I can use metadata(data), assays(data), etc to get more information.
> head(SummarizedExperiment::assays(data))
List of length 1
names(1): normalized_count
Alright, so this is a named list. I know how to deal with lists: I can use either the index ([[1]]) or the name ($normalized_count)
> head(SummarizedExperiment::assays(data)$normalized_count)
TCGA-AN-A046-01A-21R-A034-07 TCGA-AC-A23H-11A-12R-A157-07 TCGA-AC-A23H-01A-11R-A157-07
A1BG 121.9879 38.5795 13.6874
A2M 9703.8622 37640.8373 4767.0490
NAT1 8488.0727 114.8582 270.4753
NAT2 6.0583 4.2938 2.3804
RP11-986E7.7 33016.6641 11308.3460 3894.9639
AADAC 1.1359 219.6976 1.1902
I can now get more information on the samples using colData(). I'm truncating the output below because there are 83 columns.
> SummarizedExperiment::colData(data)
DataFrame with 3 rows and 83 columns
barcode patient sample shortLetterCode definition sample_submitter_id sample_type state
<character> <character> <character> <character> <character> <character> <character> <character>
TCGA-AN-A046-01A-21R-A034-07 TCGA-AN-A046-01A-21R-A034-07 TCGA-AN-A046 TCGA-AN-A046-01A TP Primary solid Tumor TCGA-AN-A046-01A Primary Tumor released
TCGA-AC-A23H-11A-12R-A157-07 TCGA-AC-A23H-11A-12R-A157-07 TCGA-AC-A23H TCGA-AC-A23H-11A NT Solid Tissue Normal TCGA-AC-A23H-11A Solid Tissue Normal released
TCGA-AC-A23H-01A-11R-A157-07 TCGA-AC-A23H-01A-11R-A157-07 TCGA-AC-A23H TCGA-AC-A23H-01A TP Primary solid Tumor TCGA-AC-A23H-01A Primary Tumor released
sample_id is_ffpe sample_type_id tissue_type submitter_id days_to_collection oct_embedded pathology_report_uuid
<character> <logical> <character> <character> <character> <integer> <character> <character>
TCGA-AN-A046-01A-21R-A034-07 57aff09f-0e97-4e65-a227-3dc7a8516367 FALSE 01 Not Reported TCGA-AN-A046 27 true 1304FB17-A20A-4EBC-9CC8-1554808AC1F6
TCGA-AC-A23H-11A-12R-A157-07 7df59ca8-7e51-4581-9d7f-8bba0395ce17 FALSE 11 Not Reported TCGA-AC-A23H 478 false NA
TCGA-AC-A23H-01A-11R-A157-07 d7e3b628-d5fd-4e79-9c4a-6409330fb8a7 FALSE 01 Not Reported TCGA-AC-A23H 478 false A7C7D409-D086-4A9B-8C8F-E7E231D5891D
I can get more information on the genes using rowData():
> SummarizedExperiment::rowData(data)
DataFrame with 19947 rows and 3 columns
gene_id entrezgene ensembl_gene_id
<character> <integer> <character>
A1BG A1BG 1 ENSG00000121410
A2M A2M 2 ENSG00000175899
NAT1 NAT1 9 ENSG00000171428
NAT2 NAT2 10 ENSG00000156006
RP11-986E7.7 RP11-986E7.7 12 ENSG00000273259
... ... ... ...
RASAL2-AS1 RASAL2-AS1 100302401 ENSG00000224687
LINC00882 LINC00882 100302640 ENSG00000242759
FTX FTX 100302692 ENSG00000230590
TICAM2 TICAM2 100302736 ENSG00000243414
SLC25A5-AS1 SLC25A5-AS1 100303728 ENSG00000224281
You want the assay data as a data.matrix, I guess. That'd be:
> data_as_matrix <- data.matrix(SummarizedExperiment::assays(data)$normalized_count)
My session Info:
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] TCGAbiolinks_2.16.1
loaded via a namespace (and not attached):
[1] bitops_1.0-6 matrixStats_0.56.0 bit64_0.9-7.1 doParallel_1.0.15 RColorBrewer_1.1-2 progress_1.2.2
[7] httr_1.4.2 GenomeInfoDb_1.24.2 backports_1.1.8 tools_4.0.2 R6_2.4.1 DBI_1.1.0
[13] BiocGenerics_0.34.0 colorspace_1.4-1 tidyselect_1.1.0 gridExtra_2.3 prettyunits_1.1.1 bit_1.1-15.2
[19] curl_4.3 compiler_4.0.2 rvest_0.3.6 Biobase_2.48.0 xml2_1.3.2 DelayedArray_0.14.0
[25] rtracklayer_1.48.0 scales_1.1.1 survMisc_0.5.5 readr_1.3.1 genefilter_1.70.0 askpass_1.1
[31] rappdirs_0.3.1 stringr_1.4.0 digest_0.6.25 Rsamtools_2.4.0 foreign_0.8-80 R.utils_2.9.2
[37] rio_0.5.16 XVector_0.28.0 pkgconfig_2.0.3 dbplyr_1.4.4 readxl_1.3.1 rlang_0.4.7
[43] ggthemes_4.2.0 RSQLite_2.2.0 generics_0.0.2 zoo_1.8-8 jsonlite_1.7.0 BiocParallel_1.22.0
[49] zip_2.0.4 car_3.0-8 dplyr_1.0.0 R.oo_1.23.0 RCurl_1.98-1.2 magrittr_1.5
[55] GenomeInfoDbData_1.2.3 Matrix_1.2-18 Rcpp_1.0.5 munsell_0.5.0 S4Vectors_0.26.1 abind_1.4-5
[61] lifecycle_0.2.0 R.methodsS3_1.8.0 stringi_1.4.6 carData_3.0-4 SummarizedExperiment_1.18.1 zlibbioc_1.34.0
[67] plyr_1.8.6 BiocFileCache_1.12.0 grid_4.0.2 blob_1.2.1 parallel_4.0.2 ggrepel_0.8.2
[73] forcats_0.5.0 crayon_1.3.4 survminer_0.4.8 lattice_0.20-41 haven_2.3.1 Biostrings_2.56.0
[79] splines_4.0.2 GenomicFeatures_1.40.0 annotate_1.66.0 hms_0.5.3 knitr_1.29 pillar_1.4.6
[85] ggpubr_0.4.0 GenomicRanges_1.40.0 ggsignif_0.6.0 codetools_0.2-16 biomaRt_2.44.1 stats4_4.0.2
[91] XML_3.99-0.5 glue_1.4.1 downloader_0.4 data.table_1.13.0 vctrs_0.3.2 selectr_0.4-2
[97] foreach_1.5.0 cellranger_1.1.0 gtable_0.3.0 openssl_1.4.2 purrr_0.3.4 tidyr_1.1.0
[103] km.ci_0.5-2 assertthat_0.2.1 ggplot2_3.3.2 openxlsx_4.1.5 xfun_0.16 xtable_1.8-4
[109] broom_0.7.0 rstatix_0.6.0 survival_3.1-12 tibble_3.0.3 iterators_1.0.12 KMsurv_0.1-5
[115] GenomicAlignments_1.24.0 AnnotationDbi_1.50.1 memoise_1.1.0 IRanges_2.22.2 ellipsis_0.3.1
| https://bioinformatics.stackexchange.com/questions/14166 |
bioinformatics | wget for links inside html pages | I am trying to download a file from the following repository: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR7276474
As you can see, there are several layers to the webpage. For example, clicking on the download tab doesn't change the URL and, the link is not a 'download link' per ce - where simply clicking the link automates a download. I have tried some of the answers on the forum, where they have advised using quotes and the operation:
wget "url/?target=link". This however does not work in the following instance.
Basically, I want to download the file labeled 'P1TLH.bam', in the download tab of the link provided:
| VQAonline_00003791.png | If you want to download a file, you need to use the link to that file. Your original attempt, wget https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR7276474 wouldn't work since that's a link to the trace page of the relevant run. If you want to download something else, just right click on the link (the one in the screenshot in your question), copy the URL and use that:
wget https://sra-download.ncbi.nlm.nih.gov/traces/sra64/SRZ/007276/SRR7276474/P1TLH.bam
| https://bioinformatics.stackexchange.com/questions/6949 |
biology | What causes "ear rumbling"? | The video Ear rumbling happens below the range of human hearing demonstrates that the "ear rumbling" sound is actual sound and can be recorded by a sensitive microphone near the ear.
What is it exactly that produces this vibration and how is it radiated as sound waves into the air?
If it is subsonic, then why does it sounds like noise rather than being inaudible?
| VQAonline_00004314.png | I'm able to create rumbling in my ears at will. Unlike the poster of the video, I don't need to yawn to do so; I can do it without my face appearing to move. I actually discovered this alongside another ability of mine when I was little: the ability to create warmth flowing from the base of my neck outwards into the rest of my body. After some research I figured out that the warmth I'm able to create is actually part of voluntary piloerection (its use for warmth is mentioned here), while the ability to create a rumbling sound is simply the contraction of the tensor tympani, a muscle in the ear. Voluntary control over either one of these things is supposed to be rare, but I've found claims of several other people online who can do both (example1, example2).
Anyways, Wikipedia gives a brief explanation of how the ear rumbling works, which also specifically mentions "yawning deeply" as a trigger:
Contracting muscles produce vibration and sound. Slow twitch fibers produce 10 to 30 contractions per second (equivalent to 10 to 30 Hz sound frequency). Fast twitch fibers produce 30 to 70 contractions per second (equivalent to 30 to 70 Hz sound frequency). The vibration can be witnessed and felt by highly tensing one's muscles, as when making a firm fist. The sound can be heard by pressing a highly tensed muscle against the ear, again a firm fist is a good example. The sound is usually described as a rumbling sound.
Some individuals can voluntarily produce this rumbling sound by contracting the tensor tympani muscle of the middle ear. The rumbling sound can also be heard when the neck or jaw muscles are highly tensed as when yawning deeply. This phenomenon has been known since (at least) 1884.
It also seems like this type of noise can happen with conditions such as Tonic Tensor Tympani Syndrome.
The tensor tympani connects directly to the handle of the malleus, so I'd assume that's why it can be heard by the person doing it. Apparently this also causes the eardrum to move. This means it's classified as objective tinnitus.
Here are some relevant studies I found:
Voluntary contraction of the tensor tympani muscle
and its audiometric effects
Voluntary Eardrum Movement : A Marker for Tensor Tympani Contraction? (paywall)
Tonic contractions of the tensor tympani muscle: a key to some
non-specific middle ear symptoms? Hypothesis and data from
temporal bone experiments (paywall)
| https://biology.stackexchange.com/questions/80419 |
biology | A strange insect | I saw this ant-like insect in Brazil, close to Rio de Janeiro. It was around 2 cm long. I tried to use google's search by image, but no luck. Does any one know the name of the species?
| VQAonline_00004255.png | Insects like this are commonly called "velvet ants", but they are wasps, not ants. This insect is in the family Mutillidae, and it's called Hopolocrates cephalotes.
(https://www.inaturalist.org/taxa/629302-Hoplocrates-cephalotes/browse_photos)
| https://biology.stackexchange.com/questions/71526 |
biology | How close genetically is the most human-like chimpanzee to the most chimp-like human? | I understand that:
Chimpanzees are the closest species to humans genetically. Only 1%-6% of their genes are different.
Within any species there is genetic diversity, i.e. no two individuals have the same exact DNA sequence.
This variability applies to humans and chimps.
Thus, there exists a pair consisting of a human and a chimp that will have the smallest number of different (edit: genes) DNA base-pairs within the two populations. One can say that the pair forms an "inter-species genetic gap".
Question: What is the smallest estimated inter-species genetic gap between humans and chimpanzees?
Edit: I changed the last point to base-pairs instead of genes. Most of the comments seem to suggest the population genetic variabilities are much, much smaller than the genetic distance between the populations. Visually, that looks something like this:
Is this a fairly accurate picture of the human-chimp genetic distance?
| VQAonline_00004155.png | You may be interested in this 2005 Nature paper from the Chimpanzee Sequencing and Analysis Consortium: Initial sequence of the chimpanzee genome and comparison with the human genome. It breaks down the most common categories of genetic variation:
Single-nucleotide substitutions occur at a mean rate of 1.23% between copies of the human and chimpanzee genome, with 1.06% or less corresponding to fixed divergence between the species.
So if we accept their analysis, ~1% (it says "or less", but elsewhere in the paper they estimate a lower bound of ~0.96%) of the genome difference consists of fixed single-nucleotide differences between species.
Small insertions and deletions: On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 40–45 Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total ~90 Mb. This difference corresponds to ~3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions; this confirms and extends several recent studies.
So another ~3% comes from small insertions and deletions, which gives around a ~4% fixed divergence between populations. This rough estimate of the fixed genetic distance between humans and chimpanzees is probably a reasonable estimate of the distance between the nearest human-chimpanzee pair.
If you also want to know how far apart the two furthest humans are, as @Remi.b mentioned, the populations we've sequenced don't span the whole diversity of our species, but it is likely much smaller. You could look at some of the HapMap or Human Genome Diversity Project papers. For reference, when Watson's genome was sequenced, they reported around 0.1% of the sequence to be different from the reference genome, but that isn't a particularly diverse comparison.
You may also be interested in this paper comparing the human, chimpanzee, and bonobo genomes: http://www.nature.com/nature/journal/v486/n7404/full/nature11128.html.
| https://biology.stackexchange.com/questions/52088 |
biology | Coefficient of Inbreeding - implementation issue | The formula for the coefficient of inbreeding is as follows...
I have a family tree going back 9 generations. Say I find a common ancestor X in the 4th generation on the mothers side and in the 5th generation on the fathers side. I can work out that constituent of F... but what do I do about all the ancestors of X (they will all also be common ancestors). Do I also work out their values and add them to F?... or do I ignore them? The descriptions of the COI I have seen do not make this clear.
| VQAonline_00004096.png | The $F_i$ term is the term that accounts for inbreeding of your common ancestor X. If that common ancestor is not inbred then the term is 0 and the calculation is a little easier. Using the example you have given:
X ─┬─ Y
│
┌──┴──┐
GGGF GGM
│ │
GGF │
│ GM
GF │
│ │
F ─┬─ M
│
Mick
In this case, the common ancestors are not inbred so the $F_i$ terms go away ($1+F_i = 1$). There are two paths of common ancestry (via X and Y), therefore the calculation of the two paths from the father (F) and mother (M) to X and Y is:
$F_{Mick} = \frac12^{n_{F,X}+n_{M,X}+1}(1+F_X)+\frac12^{n_{F,Y}+n_{M,Y}+1}(1+F_Y) $
$F_{Mick} = \frac12^{4+3+1}(1+0)+\frac12^{4+3+1}(1+0) $
$F_{Mick} = \frac{1}{256} + \frac{1}{256} = 0.0078 = 0.78\% $
In a more complex case, such as where ancestor X was inbred, $F_i$ cannot be ignored. In the following example, X's parents were first cousins:
U ─┬─ V
│
┌──┴──┐
XGF XGM
│ |
XF─┬─XM
│
X ─┬─ Y
│
┌──┴──┐
GGGF GGM
│ │
GGF │
│ GM
GF │
│ │
F ─┬─ M
│
Mick
For this, we must first calculate $F_X$ (i.e. how inbred X is):
$F_X = \frac12^{n_{XF,U}+n_{XM,U}+1}(1+F_U)+\frac12^{n_{XF,V}+n_{XM,V}+1}(1+F_V) $
$F_X = \frac12^{2+2+1}(1+0)+\frac12^{2+2+1}(1+0)$
$F_X = \frac{1}{32} + \frac{1}{32} = 0.0625 = 6.25\% $
Then we can input this $F_X$ into the same calculation as done before for the simple case:
$F_{Mick} = \frac12^{n_{F,X}+n_{M,X}+1}(1+F_X)+\frac12^{n_{F,Y}+n_{M,Y}+1}(1+F_Y) $
$F_{Mick} = \frac12^{4+3+1}(1+0.0625)+\frac12^{4+3+1}(1+0)$
$F_{Mick} = 0.00415 + \frac{1}{256} = 0.0081 = 0.81\% $
A good explanation of these calculations with further examples can be found here: The Coefficient of Inbreeding (F) and its applications. The calculations can get quite complicated even with relatively simple inbreeding.
| https://biology.stackexchange.com/questions/41024 |
biology | By just looking at an unlabeled picture, how do you know it is a protein? | I'm learning about proteins and need to understand this concept. What makes this colourful ball of squiggles identifiable? Why is it a protein, and not any other biomolecule (like DNA for example)? What are the colours showing? What are the variations in the shape of the image?
Basically, the question is: What is this image trying to tell me about this protein?
| VQAonline_00004160.png | Shapes
This is a common way of illustrating a protein and is often called a "protein cartoon". There are other common ways of illustrating proteins.
This cartoon shows you where α helices are (spirals) and where β sheets are (arrows) which are important structural elements. The strings connecting those structural elements are flexible "loop" regions.
If you want to query this against other structures and see which protein it is, check out PhyreStorm. You'll need the PDB file, not just an image.
Colour
The colouring is also common. The N-terminus (the first amino acid) is coloured blue, and the colours go through the rainbow to red, the C-terminus (the last amino acid in the polypeptide chain).
| https://biology.stackexchange.com/questions/52426 |
biology | How can SNP arrays be used to detect deletions within a gene? | I am reading a journal paper where the researchers are studying the effect of disease-causing mutations in the IL1RAPL1 gene. In the first figure of this paper, they show pedigrees of families where they have family members with the disease-causing mutations.
For the BMC family, they found using a SNP array that a deletion of ~200 kb between intron 5 and 6 of the IL1RAPL1 gene results in an in-frame deletion of exon 6.
I am having trouble interpreting the graph in Figure D, which is the results of the SNP array analysis. Aren't SNP arrays used for detecting single nucleotide polymorphisms? I am confused because in this paper they are using a SNP array to detect a gene deletion.
Any insights are appreciated.
| VQAonline_00004422.png | In the materials and methods of the paper, you will observe the following statement regarding the CNV (deletion) analysis:
CNV analysis was performed using CNV-WebStore (38).
That citation points to this paper, a software package designed to infer CNVs such as deletions from array data.
Recall that SNP arrays are essentially asking "how much DNA from the sample is sticking to each of N probes against specific sequences". The SNP is inferred by comparing how much DNA sticks to one allele vs the other allele on the array. If a specific sequence assayed by the array is simply missing, then you will observe a corresponding decrease in signal.
This is signified by panel D of the figure that you include, where signal in the pink region is dramatically lower.
| https://biology.stackexchange.com/questions/107947 |
biology | Is there some genetic variance underlying music appreciation? | Is there any research done on the genetic variance for Music appreciation?
If not, why is there no genetic variance for this trait?
| VQAonline_00003977.png | In 2013,
Dr. Liisa Ukkola-Vuoti, University of Helsinki, Finland, done a detailed GWCNV(Genome-Wide Copy Number Variation) Analysis of certain group of people for musical creativity and aptitude.
Genome-Wide Copy Number Variation Analysis in Extended Families and Unrelated Individuals Characterized for Musical Aptitude and Creativity in Music
They did a Genome Wide Copy Number Variations (CNVs) in five extended
pedigrees and in 172 unrelated subjects characterized for musical
aptitude and creative functions in music
Muscial Aptitude is taken as Sum of Scores of Auditory structuring ability, Seashores test for pitch and for time. Along with data on creativity in music was surveyed using a web-based questionnaire.
Several CNVRs containing genes that affect neurodevelopment, learning
and memory were detected.
A deletion at 5q31.1 covering the protocadherin-α gene cluster (Pcdha 1-9) was found co-segregating with low music test scores (COMB) in both sample sets. Pcdha is involved in neural migration, differentiation and synaptogenesis.
Creativity in music was found to co-segregate with a duplication covering glucose mutarotase gene (GALM) at 2p22. GALM has influence on serotonin
release and membrane trafficking of the human serotonin transporter.
Genes related to serotonergic systems have been shown to associate not only with psychiatric disorders but also with creativity and music perception.
Both, Pcdha and GALM, are related to the serotonergic systems influencing cognitive and motor functions, important for music perception and practice.
A 1.3 Mb duplication was identified in a subject with low COMB scores in the region previously linked with absolute pitch (AP) at 8q24.
No differences in the CNV burden was detected among the high/low music test scores or creative/non-creative groups.
In summary, CNVs and genes found in this study are related to
cognitive functions. Our result suggests new candidate genes for music
perception related traits and supports the previous results from AP
study.
Source:
[1] Genome-Wide Copy Number Variation Analysis in Extended Families and Unrelated Individuals Characterized for Musical Aptitude and Creativity in Music
[2] Musical Aptitude Is Associated with AVPR1A-Haplotypes
| https://biology.stackexchange.com/questions/19924 |
boardgames | City card and predicting when Supply piles will run low | This card kind of has me stumped. In my experience, the vast majority of games deplete the Province or Colony pile before any other, ending the game. Which means in most circumstances, this card is basically an overpriced Village, which isn't a very strong card to begin with.
It seems to me the key is knowing when Supply piles are likely to run low. Are there any things to look for in the setup of 10 Kingdom cards to help predict when this might happen? Or are you better off waiting until it actually does happen before investing in this card?
| VQAonline_00004440.png | More supply piles tend to go in 5 or 6 player games.
Cards that synergize with themselves tend to get bought out quickly - like Caravan, Treasure Map, and Laboratory. Extra buys also seem to increase the rate at which Kingdom cards get bought out.
Terminal actions (ones that do not give you +1 Action) tend to get bought less frequently, as each player would only consider 1-2 copies anyway. It seems lower cost cards (2 and 3) aren't bought out very much. 4-5 costs appear to go fastest.
I have noticed City itself is frequently the first one to get bought out if any will, and that immediately boosts all of them. Generally I tend to wait on City until I notice people are grabbing Kingdom cards, but I also generally lose to the guy who bought 5 of them.
| https://boardgames.stackexchange.com/questions/1262 |
boardgames | What is this descent figure? | I was wandering around on boardgamegeek and I saw this picture of a guy painting Descent figures, but the post doesn't exists anymore - thank you google - and the figures are just amazing
I'm not sure this is descent figure, but photos are taken on Descent v2 tiles so I guess it may be an extension I don't know.
| VQAonline_00004566.png | It is the Ice Wyrm, from Descent second edition.
| https://boardgames.stackexchange.com/questions/28481 |
boardgames | Carcassone - placing barn figure in field | Game : Carcassone with expansion "Abbey & Mayor".
Question - theoretically barn can be placed:
A) only if my farmer has already been placed in field?
B) regarding if any farmers already exist in fields?
| VQAonline_00004654.png | According to the rules, the barn can be placed in a field as long as that field doesn't already have a barn. Farmers are no concern when placing the barn:
You may place your barn on a field already occupied by farmers. You may not,
however, place your barn on a field already occupied by another barn. Once
placed, a barn remains in play until the end of the game.
| https://boardgames.stackexchange.com/questions/44369 |
boardgames | Canceling King Arthurs boosted attack on cards with no effects | In Unmatched: Battle of Legends Vol 1 King Arthur has a special ability:
When King Arthur attacks, you may BOOST that attack. Play the BOOST
card, face down, along with your attack card.
If your opponent cancels the effects on your attack card, the BOOST is
discarded without effect.
One of King Arthurs cards is Excalibur. There is no effect on the card just a title. If my opponent plays a card that happens to cancel any card effects would a Boosted Excalibur lose the boosted bonus?
| VQAonline_00004720.png | From Jenn S. at Restoration Games
Essentially, Arthur's special ability is an effect that can get
canceled, so the Boost would be discarded.
There is some further discussion on it in this BoardGameGeek thread:
Feint vs boosted Excalibur.
TL;DR even with Excalibur, the boost would be discarded if an opponent's card discards effects.
| https://boardgames.stackexchange.com/questions/54384 |
boardgames | What's the use of blinking a creature out (such as with Essence Flux)? | Essence Flux says:
Exile target creature you control, then return that card to the battlefield under its owner's control. If it's a Spirit, put a +1/+1 counter on it.
So, say I have a 1/1 Sanctuary Cat cast onto the battlefield. According to above, I would exile it, then return it right back? Is that right? I don't see what purpose this serves unless it was a spirit. Could you clarify if I have this right and what the benefit is?
| VQAonline_00004584.png | There are many uses for so-called "flicker" effects like from Essence Flux.
The namesake Flicker was the first card to exile and immediately return the target. This is where the mechanic got its unofficial name.
The creature that returns is a whole new object without any relation to its previous existence. That means that, for example:
The creature will trigger all applicable "enters the battlefield" and "leaves the battlefield" abilities.
If the creature you blink is being targeted by a spell or ability, then it will lose track of the creature and not affect it, or will fizzle if that creature was the only target.
Auras and equipments attached to the creature will fall off of it, and counters get removed.
It will return untapped.
All temporary effects, such as from Giant Growth or Death Wind, will be removed.
The new creature has no damage marked on it, so it's like an improved regeneration effect.
If you blink the creature during combat, it will be removed from combat and will neither deal nor take any damage, but (if it was already assigned as a blocker), the creature blocked by it will still be blocked.
Other blink cards such as Flicker can also target enemy creatures (though not at instant speed), which can be a very valuable play at the right time.
In short, blink effects are a powerful trick that can throw a wrench in your opponent's plans at a crucial moment. The +1/+1 counter for spirits is more of a bonus in most cases, but of course it allows you to get even more utility out of this spell.
| https://boardgames.stackexchange.com/questions/32379 |
boardgames | Bonus traps from Essen Spielmesse 2019, what are the rules for them? | I was at the Essen Spielmesse 2019 and enjoyed the game Obscurio. I bought the game and at the booth they gave us some bonus traps to use in the game. However no rules were given with the traps and we have no idea how to use them. We could hazard a guess, but would love some official guidelines on how they should be played if they are pulled out of the bag.
| VQAonline_00004681.png | Someone asked the same question on boardgamegeek, and someone found the rules on the publisher's website, they are:
Music hall (Music note):
Affects step 2 and 4
The wizards can only communicate by singing, the Grimoire is not affected by this token
Raving mad (Cards with the arrows around the outside and question mark on them):
Affects step 2
Take the loyalty card from each wizard and mix them facedown. Deal them to each Wizard. This token is then removed from the game and cannot be pulled again
Aphonia (Speech bubble with the X in it):
Affects step 2 and 4
The wizards can only communicate through gestures and mimes, they may not talk, sing, nor make any verbal noise of any kind. The Grimoire is not affected by this token.
| https://boardgames.stackexchange.com/questions/49173 |
boardgames | Do I have to sacrifice non-token dragons to Day of the Dragons? | The Card Day of the Dragons says the following:
When Day of the Dragons leaves the battlefield, sacrifice all Dragons you control. Then return the exiled cards to the battlefield under your control.
Note the part I've highlighted. What exactly does that mean?
For example, if I invoke a dragon card after using the enchantment (Dromar, the Banisher for example), when the enchantment leaves play do I have to sacrifice both my 5/5 Dragon tokens and Dromar?
| VQAonline_00004505.png | Yes, you would have to sacrifice all dragons creatures and creature tokens under your control, regardless of where they came from or when they were cast. All Dragons means all permanents (creatures, tokens) that have have Dragon in their supertype or subtype. "Under your control" should be clear.
| https://boardgames.stackexchange.com/questions/13093 |
bricks | Is there a Technique or Algorithm for Building Spheres? | There are times when I would like to build a sphere or a dome like this one:
From Small Lego Sphere Project
While this example is great, I find it difficult to scale it to another size, whether smaller or larger, without it...not looking roundish anymore.
Is there a tool available that can design a sphere or dome based on a size?
| VQAonline_00004747.png | This website generates a sphere in LDraw format: http://lego.bldesign.org/sphere/
Here's a link if you want to learn how it can be done: http://groups.csail.mit.edu/graphics/classes/6.837/F04/assignments/assignment5/
(there are other ways too)
| https://bricks.stackexchange.com/questions/549 |
bricks | How do I build this robot car? | I want to start using more LEGO Technic, but I'm not sure what the best way is to buy the parts without breaking the bank.
I'd really like to make a robot like the ones shown in this video.
Making Lego Car CLIMB Obstacles
They identify these parts:
SBrick https://www.sbrick.com/sbrick.html
BrickController 2 app (Android)
PlayStation 4 wireless controller
But where do I get the rest? Their channel recommends BrickLink, but that mostly seems to be individual pieces and vintage bits of Lego (unless I'm using it all wrong?)
Is there a low-cost way to buy most of the things shown here? Should I buy a kilogram of used Technic elements on eBay and hope for the best?
Which motors, gearing systems, and batteries are they using here? How are they connected to the SBrick? Is there a single kit that gets me 90% of the way there?
| VQAonline_00004941.png | There are several ways you can start with LEGO Technic.
If you have no elements whatsoever the best (cost-efficient) approach is to buy a set that contains most of the parts. Or a couple of sets. Bulk lots could also be useful, however, they may not contain the most expensive elements (like motors). Specific elements could be acquired from Bricklink or BrickOwl.
It is also cost-efficient to buy sets that contain electronic elements already since these are usually more expensive when bought individually.
Which motors, gearing systems, and batteries are they using here?
Motor - Power Functions M-Motor (as a "set") or Electric, Motor 9V Power Functions M with Dark Bluish Gray Bottom (as an "element")
Gears - multiple have been used in a video. You can find all of them in the Technic, Gear section. These are used in the pictured model:
Technic, Gear 24 Tooth (2nd Version - 1 Axle Hole)
Technic, Gear Worm Screw, Long, Axle Opening Type II
Technic, Gearbox 2 x 4 x 3 1/3
Technic, Gear 40 Tooth
Battery - battery box used in the video is Electric 9V Battery Box Power Functions (Rechargeable) with Dark Bluish Gray Bottom. It is rather expensive and I suggest much cheaper and commonly found Electric 9V Battery Box Power Functions (Non-Rechargeable) with Dark Bluish Gray Bottom instead.
Please be advised both motors and battery boxes belong to the Power Functions system which has been recently discontinued by LEGO.
How are they connected to the SBrick?
SBrick is a controller and has connections compatible with the ones used by the Power Functions system. Each motor has a cable with a connector, so no extra cables are needed here.
Is there a single kit that gets me 90% of the way there?
The Pictured model doesn't use a huge bunch of elements, so it is rather hard to define what 90% is. Personally, I would probably look for some used sets with motors and battery box. And acquire the rest from Bricklink.
| https://bricks.stackexchange.com/questions/16742 |
bricks | What is the meaning of the available color lists in Bricklink searches? | Recent AFOL; figuring out Bricklink.
I'm trying to understand the color lists that are retrieved by searches in Bricklink.
Using Bricklink, I searched for part 3068a (2x2 tile without Groove), and looking at availability, and so forth.
Four categories of color lists are given in Bricklink:
Lots for Sale
On Wanted list
Price Guide info
Known Colors
The colors displayed in these categories puzzle me. For example, how is it possible for a color to be in the "Lots for Sale" list, and not be in the "Known Colors" list? Other possible discrepancies exist in these lists.
What do these lists of colors represent?
Here's a link to the available color lists for part 3068a:
https://www.bricklink.com/v2/catalog/catalogitem.page?id=17085#T=C
For part 3068a, I scraped the data, looking for differences.
Here's a screenshot of part of the results, highlighting a couple of colors that are in lots for sale and are priced, but are not in the known color list:
| VQAonline_00004905.png | Lots for Sale - this contains colors in which current part is being listed for sale.
On Wanted list - this shows which colors Bricklink members have added to their "wanted list". It doesn't mean parts in this color have existed. Most likely this being used to add non-existing color to list of wanted items and mark for notification. In such case if wanted item ever to appear for sale (and seller pushed this notification) person with desired item would be notified.
Price Guide info - here you can see sale/price history for each color for the past 6 months as well as items currently listed for sale.
Known Colors - here you can find colors which appear in released sets. Bricks in this list are tied to set inventories produced by community of Bricklink. If there ever be an error with inventory or it has alternative selection of bricks, this is being addressed by fixing or adding an alternative inventory for the same set. Every Bricklink member is welcome to make these fixes.
There could be several reasons why there are more colors for sale than on a list of known colors:
An error is an obvious thing. It is quite easy to make a mistake while listing individual part for sale if it has been produced in similar colors, or has variety in shape (with/without groove). Some shades of Blue and Pink are hard to distinguish. Shape differences aren't always so easy to notice too.
Some parts you see for sale may have been prototypes, test bricks or
produced for specific project (like life-size LEGO Bugatti has a ton of non-existing parts) which may have made their way somehow from the factory. This is not something you could request for as LEGO is trying to not let these items into the market.
One more thing to note. If you find a part in odd color and it isn't listed as HTF (Hard To Find) or Special Color, this is most likely a mistake while listing. Odd parts have quite a high value (depends on availability). Although it doesn't hurt to contact the seller to confirm the case before ordering.
| https://bricks.stackexchange.com/questions/13458 |
bricks | Why did Technic bricks have holes in the studs? | Lego Technic (/ Expert Builder) bricks have always had a very different design than the normal Lego brick, with peg holes lining the sides serving fairly obvious purposes, but they also have had (as long as I can remember) hollow studs on the top:
Now that these pieces are appearing in non-Technic sets I've seen them used often to hold things - they're about the same size as a minifigure's grip, so wrenches, guns, gems, and other decorative elements that need to stand are often stuck into them.
But Technic has no minifigures and features only sparse decoration. I don't recall ever seeing a Technic set that uses the holes. It seems like they would be much more difficult to mold especially as far back as Technic's introduction in the late 1970s.
So why were they introduced in Technic? (Or am I wrong, and they were not introduced in Technic / Expert Builder?) Did they serve a functional purpose, or were they just another visual marker to separate it from "regular" Lego during its introduction?
| VQAonline_00004742.png | From principles of molding, you want a uniform part thickness throughout if possible. This facilitates plastic flow as well as dimensional stability (you want uniform shrinkage on cooling.) Removing a divot from the underside of a stud serves this purpose in a regular brick. The Technic brick with through holes would have had a large amount of solid plastic under the stud compared to regular bricks, which could create undesirable shrinkage and warping from stress in cooling. So removing the top divot helps there.
However, if you examine a 1x16 beam from Expert Builder, you can observe a plastic channel running along the underside between studs 4 to 13 (which are injection gates; also stud 8, or 9.) The 1x8 doesn't have this. This channel would let the plastic flow away from the injection gate without turning too many corners. It's also possible LEGO used a reciprocal molding action where plastic is pressed in one gate, then another, in a rocking action, to facilitate welding of the multiple injection streams. Solid studs might lessen the effectiveness of this process, but the channel helps it. If the channel was necessary to produce a 1x16 beam back in the day, and the channel forced hollow studs, then the hollow stud style was the only way to make a 1x16 beam. The technical difficulty of making a new, longer brick (beam) may have influenced the look of the whole Expert Builder system.
That's only my theory, but you can still see the channel for yourself.
My tests also indicate the hollow stud separates from another beam more easily than a common solid stud would.
It remains possible though that they were just maximizing the usefulness of the part by making the stud hollow. Though the fun part of being an engineer is maximizing more than one property at once.
So my thought is the hollow stud came from various molding principles. Cost of plastic comes after that (and yes, if you can save a bit, you do.)
Another interesting trivia: the Technic studs were each freehand drafted in the early Expert Builder instruction booklets. I joked about reproducing this while showing some Lego employees (in 2001) what could be done with non-representational rendering, for instance a pen-and-ink renderer with random jitter.
| https://bricks.stackexchange.com/questions/196 |
bricks | How do I run the LEGO Technic V6 engine using a Lego electric motor? | I am not into LEGO, don't know anything about it, so I will try to be as specific as possible.
My goal is to spin the LEGO Technic V6 engine (preferably at some realistic RPM's like thousands).
Since I can't combust air and gasoline inside, my simple idea was to run it with LEGO electric motor from LEGO Technic Power Functions Motor Set 8293.
Obviously, I need to connect them somehow and make them run. I don't have any other LEGO pieces available. What do I need to buy (the minimum) to get this running?
Here's the type of V6 that I'm referring to:
Hope that explains what I want and I hope someone can help me, I will be very thankful!
| VQAonline_00004892.png | Assuming that your motor already has a Technic axle available, you'll need:
Any Technic motor. You probably want an M motor (8883).
An appropriate battery box or other power source. If you selected the above motor, you probably want the PF battery box that uses AA batteries (8881).
Any Technic elements that you want to actually mount the motor onto the V6. In the case of the above, you could get away with a shorter axle and a few Technic pins. If I were you, I'd either purchase a small Technic set (e.g. https://brickset.com/sets/42088-1/Cherry-Picker), or an assortment of Technic elements on Bricklink.
Most Technic motors aren't especially fast (~400 RPM). If you want an RPM up in the thousands, you'll need at least a couple of gears as well.
| https://bricks.stackexchange.com/questions/11367 |
bricks | How can I find brick part number from a picture? | I found some books I like, but the book only give pictures of the parts. For example, this one
How can I know the part number (for example in bricklink) from the picture?
| VQAonline_00004854.png | You'll need to start learning the nomenclature for those pieces.
For example the long straight pieces you have there with holes on top are "Technic, Brick 1 x 12 with Holes"
The pieces with rounded ends are lift arms. You can browse through the list of them here or take a stab at their descriptions using the width and number of pin holes. For example the purple on you have there is
1 hole wide
9 holes long
as think as a normal LEGO brick (some are half that thickness)
Bent with 6 on one line and 4 on the other
so "Technic, Liftarm 1 x 9 Bent (6 - 4) Thick"
| https://bricks.stackexchange.com/questions/9073 |
bricks | Can you identify these column decorators? | I want to decorate some columns with these little round ionic scroll-looking things. Does anyone know the part number?
| VQAonline_00004901.png | Brick, Modified 1 x 1 with Scroll with Hollow Stud
https://www.bricklink.com/v2/catalog/catalogitem.page?P=20310&idColor=2
| https://bricks.stackexchange.com/questions/13262 |
buddhism | What raised mudra is depicted on the Buddha rupa at the London Peace Pagoda and what does it mean? |
What raised mudra is depicted on this particular Buddha rupa at the London Peace Pagoda and what does it mean? Also, which Buddha is this?
| VQAonline_00004983.png | This guide -- The Battersea Park Peace Pagoda -- says,
In this statue the Vitarka Mudra, associated with explaining the Buddha’s teachings, with the right hand right raised and the tips of the forefinger and thumb touching, is combined with the Tarjani Mudra for warding off evil, with forefinger and little finger outstretched.
| https://buddhism.stackexchange.com/questions/44988 |
buddhism | Does 'karma' mean that everything that happens to us is under our control, or only that we are responsible for it? | Does 'karma' mean that everything that happens to us is under our control, or only that we are responsible for it? I thought that only substantial beings could be completely in control of everything that happens to them, and not just because things are impermanent.
Also, conditioned things are a result of past karma, which is often said to be an unconscious process of seeds becoming ripe. So surely it would only be under out control over the course of very many lives, at least?
The Points of Controversy -- theravada -- refute the claim that everything is from karma, including karma, of the rajagirikas and siddhatthikas. But it does not show that for anything but new karma. The sautrantikas taught that there is no life faculty sustaining events between life and death, because karma alone is "sufficient" to account for all destinies.
this is accepted by all Buddhists... theravada or mahayana
The Lioness in Bloom, p33
Further, Bodhidharma exhorted
the practice of following conditions, sentient beings lack a self and
are all whirled around by conditions and karma; suffering and joy are
to be equally accepted, for both arise from conditions. If I
encounter excellent karmic recompense, such as honor and so forth, it
is in response to causes in my past lives. Even if I should encounter
such recompense in the present, the necessary conditions for it will
exhaust themselves, and it will again cease to exist. What is there
to be joyful about in its existence? Gain and loss follow conditions.
Mind has neither increase nor decrease. Unmoved by the winds of joy,
one is mysteriously in accordance with the path. Therefore, it is
called the practice of following conditions.
Bodhidharnma, Two Entrances
| VQAonline_00004981.png | Not everything is caused by karma. Some things are caused by other reasons, like the weather. The Sivaka Sutta talks about this. There's a summary at the bottom:
Bile, phlegm, and also wind,
Imbalance and climate too,
Carelessness and assault,
With kamma result as the eighth.
To quote the sutta in detail:
“Some feelings, Sīvaka, arise here originating from phlegm disorders …
originating from wind disorders … originating from an imbalance of the
three … produced by change of climate … produced by careless behaviour
… caused by assault … produced as the result of kamma: that some
feelings arise here produced as the result of kamma one can know for
oneself, and that is considered to be true in the world. Now when
those ascetics and brahmins hold such a doctrine and view as this,
‘Whatever a person experiences, whether it be pleasant or painful or
neither-painful-nor-pleasant, all that is caused by what was done in
the past,’ they overshoot what one knows by oneself and they
overshoot what is considered to be true in the world. Therefore I say
that this is wrong on the part of those ascetics and brahmins.”
The Acintita Sutta states that you can't work out karma and its results precisely:
"The [precise working out of the] results of kamma is an
unconjecturable that is not to be conjectured about, that would bring
madness & vexation to anyone who conjectured about it.
What's more skillful is to develop one's virtue (sila), concentration (samadhi) and wisdom (pañña) as stated in the Lonaphala Sutta. That will mitigate the ill effects of past karma (actions).
As for future karma (actions), to avoid accumulating karma debts, it is skillful to adopt the following skillful thinking from the Themes Sutta:
“And for the sake of what benefit should a woman or a man, a
householder or one gone forth, often reflect thus: ‘I am the owner of
my kamma, the heir of my kamma; I have kamma as my origin, kamma as my
relative, kamma as my resort; I will be the heir of whatever kamma,
good or bad, that I do’? People engage in misconduct by body, speech,
and mind. But when one often reflects upon this theme, such misconduct
is either completely abandoned or diminished. It is for the sake of
this benefit that a woman or a man, a householder or one gone forth,
should often reflect thus: ‘I am the owner of my kamma, the heir of my
kamma; I have kamma as my origin, kamma as my relative, kamma as my
resort; I will be the heir of whatever kamma, good or bad, that I do.’
| https://buddhism.stackexchange.com/questions/39874 |
buddhism | Why is Kwan Yin riding a sea turtle? | And maybe to save two related questions, why does Samantabhadra ride an elephant and Majursri ride a lion?
I was meditating with Kwan Yin statute and that was the main distraction, I had no idea why Kwan Yin is on a sea turtle.
| VQAonline_00004953.png | Okay, I did my own research and here is what I've come up with so far. Interestingly, the artist is making a reference to this Pali suttra:
"Monks, suppose that this great earth were totally covered with water,
and a man were to toss a yoke with a single hole there. A wind from
the east would push it west, a wind from the west would push it east.
A wind from the north would push it south, a wind from the south would
push it north. And suppose a blind sea-turtle were there. It would
come to the surface once every one hundred years. Now what do you
think: would that blind sea-turtle, coming to the surface once every
one hundred years, stick his neck into the yoke with a single hole?"
"It would be a sheer coincidence, lord, that the blind sea-turtle,
coming to the surface once every one hundred years, would stick his
neck into the yoke with a single hole."
"It's likewise a sheer coincidence that one obtains the human state.
It's likewise a sheer coincidence that a Tathagata, worthy & rightly
self-awakened, arises in the world. It's likewise a sheer coincidence
that a doctrine & discipline expounded by a Tathagata appears in the
world. Now, this human state has been obtained. A Tathagata, worthy &
rightly self-awakened, has arisen in the world. A doctrine &
discipline expounded by a Tathagata appears in the world.
"Therefore your duty is the contemplation: 'This is stress...This is
the origination of stress...This is the cessation of stress...This is
the path of practice leading to the cessation of stress.'"
http://uwf.edu/wmikulas/webpage/leaves/website/canon/samyutta/sn56-48.html
Other Bodhisattvas and Buddhas are often described as riding a particular animal.
Samantabhadra is explicitly described as riding an elephant in his sutra. Samantabhadra's elephant appears to be another awe inspiring flourish. (At least from my reading of the excerpt of Samantabhadra Meditation Sūtra in Wikipedia.
Wikipedia says of Manjusri and his lion: "Mañjuśrī is often depicted as riding on a blue lion, or sitting on the skin of a lion. This represents the use of wisdom to tame the mind, which is compared to riding or subduing a ferocious lion." Wikipedia doesn't explain why the lions, but elsewhere it's suggested that lions were sort a family symbol of the Sakyas, or it's just a reference to the pali sutra about "The lions Roar", ref: http://www.accesstoinsight.org/lib/authors/nanamoli/wheel390.html
http://en.wikipedia.org/wiki/Shakyasimha
| https://buddhism.stackexchange.com/questions/1541 |
buddhism | How is it wrong to believe that a self exists, or that it doesn't? |
the one place where the Buddha was asked point-blank whether or not
there was a self, he refused to answer. When later asked why, he said
that to hold either that there is a self or that there is no self is
to fall into extreme forms of wrong view that make the path of
Buddhist practice impossible.
It seems to me, and I may be wrong, that the skandhas can be identified as a self, as long as they aren't then taken to be in any way unchanged from moment to moment
Encyclopedia of Buddhism, By Damien Keown, Charles S. Prebish
So I was wondering if that above silence means that any dharma can fulfill the role of that empirical self.
An example would be: Adam tastes the apple
Supposing this "taste" can be considered a kind of self, then if Adam sees smells touches feels nothing, just tastes the apple, there is "continuity" and he's still Adam. But as long as he does have other senses, and from moment to moment, the taste of apple doesn't make him who is he.
I've never read any commentary which claims this is what the empirical self is in Buddhism, so would be really surprised that this counts as a categorical denial of substantial self.
| VQAonline_00004966.png | Buddha kept silent in response to Vacchagotta’s question because answering it in either way, it would have been misunderstood. This nature of the self is beyond the level of understanding of Vacchagotta. He is not yet at that stage in his spiritual development. Buddha never denies the existence of the self. He rejects annihilationism. Read the Alagaddupama Sutta (MN 22), Yamaka Sutta (SN 22.85), Kalama Sutta (AN 3.65), Ananda Sutta SN 44.10. In fact Buddha explained this when asked by the Venerable Ananda about his silence regarding Vacchagotta’s question. He said that this would have lead Vacchagotta to misinterpret the answer in a way that would bring him further attachment.
With regard to self, the Buddha said to Ananda in the Mahaparinibbana Sutta, to stay as those who have the self as island, as those who have the self as refuge, as those who have no other refuge. (DN 16). As per the scriptures existence is real, but it is transitory.
| https://buddhism.stackexchange.com/questions/15898 |
buddhism | In the movie Spring Summer Fall Winter and Spring, why does the master cry? | Here is the movie: Spring Summer Fall Winter and Spring 2003
The plot is that the student having attachment to a woman, leave the temple and marries her. Years fly by, and the student returns because he kills her, after her affair. The master helps him to let the anger out before being caught by the police, and then he immolates himself. After that, he leaves some śarīra.
My question is: why would the master cries before the immolation?
My answer is that he disappoints with the student. But isn't that disappointment an attachment?
| VQAonline_00004977.png |
My question is: why would the master cries before the immolation?
The "Winter" segment of the movie kind of gave the hint. Notice in this segment, after being paroled from prison for the crime of killing his wife, the now middle-age apprentice returns to the floating monastery and begins to take on the role of his previous master. And as with the movie's title's central theme, which reflects the cyclical nature of Samsara, the same exact history repeats itself with the scene of a woman abandoning her baby son, then the baby becomes the boy apprentice who is shown tormenting a turtle in the Spring-Again segment,... etc. Putting together all the pieces of the puzzle, it points to the original old master's own dark past with its own dark kamma before he renounced it to become a good monk. So although after years of training and gaining certain level of attainment, he's still not free of his kammic debt. And so he cries not only out of sadness for his student but also for himself, that his self immolation doesn't mean total and final complete liberation, there's still "more work to be done" and life will go on and on until all kammic debts' been completedly exhausted, hence the image of the water snake swimming away after the self immolation.
| https://buddhism.stackexchange.com/questions/35686 |
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VQAonline
🌐 Homepage | 🤗 Dataset | 📖 arXiv
Dataset Description
We introduce VQAonline, the first VQA dataset in which all contents originate from an authentic use case.
VQAonline includes 64K visual questions sourced from an online question answering community (i.e., StackExchange).
It differs from prior datasets; examples include that it contains:
- (1) authentic context that clarifies the question
- (2) an answer the individual asking the question validated as acceptable from all community provided answers,
- (3) answers that are considerably longer (e.g., a mean of 173 words versus typically 11 words or fewer in prior work)
- (4) user-chosen topics for each visual question from 105 diverse topics revealing the dataset’s inherent diversity.
Download
To download, you can use the following code:
git clone https://huggingface.co/datasets/ChongyanChen/VQAonline
Dataset Structure
In total, the VQAonline dataset contains 64,696 visual questions.
We designed VQAonline to support few-shot settings given the recent exciting developments around in-context few-shot learning with foundation models. Thus, we split the dataset as follows:
- Training set: 665 visual questions
- Validation set: 285 visual questions
- Test set: 63,746 visual questions
The questions, contexts, and answers are provided in the json files.
Due to the constraint of huggingface, we separate the image files into 7 folders (named from images1 to images7), each of which contains 10,000 image files, except for folder "images 7".
Contact
- Chongyan Chen: chongyanchen_hci@utexas.edu
Citation
BibTeX:
@article{chen2023vqaonline,
title={Fully Authentic Visual Question Answering Dataset from Online Communities},
author={Chen, Chongyan and Liu, Mengchen and Codella, Noel and Li, Yunsheng and Yuan, Lu and Gurari, Danna},
journal={arXiv preprint arXiv:2311.15562},
year={2023}
}
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