Miracle-dz/UniFAR-FTUs huggingface dataset:
Exit of newly synthesized membrane proteins from the trans cisterna of the Golgi complex to the plasma membrane

The intracellular location at which the G protein of vesicular stomatitis virus accumulated when transport was blocked at 20 degrees C has been studied by biochemical, cytochemical, and immunocytochemical methods. Our results indicated that the viral G protein was blocked in that cisterna of the Golgi stack which stained for acid phosphatase. At 20 degrees C this trans cisterna became structurally altered by the accumulation of G protein. This alteration was characterized by extensive areas of membrane buds which were covered by a cytoplasmic coat. These coated structures were of two kinds--those that labeled with anti-clathrin antibodies and those that did not. The clathrin- coated pits consistently did not label with anti-G antibodies. Upon warming infected cells to 32 degrees C, G protein appeared on the surface within minutes. Concomitantly, the trans cisterna lost its characteristic structural organization. Double-labeling experiments were performed in which G protein localization was combined with staining for horseradish peroxidase, which had been taken up from the extracellular medium by endocytosis. The results suggest that the trans cisterna was distinct from the endosome compartment and that the latter was not an obligatory station in the route taken by G protein to the cell surface.
Limitations of functional magnetic resonance imaging in mapping function near a vascular lesion: A case study

Abstract We present a case of functional reorganization of the somatosensory system in a 15 year-old female with a history of perinatal stroke of the middle cerebral artery. The patient presented with hemiparesis and epilepsy and underwent comprehensive pre-surgical evaluation for epilepsy surgery, including mapping of somatosensory function with functional magnetic resonance imaging (fMRI). The fMRI results indicated inter-hemispheric reorganization of somatosensory function from the left to the right hemisphere, and showed no residual somatosensory function in the peri-lesional area of the affected left hemisphere. However, following implantation of subdural electroencephalography (EEG) electrodes, recordings from left hemisphere lesional and peri-lesional areas showed evoked electrophysiological responses to tactile stimulation. Bedside and intra-operative stimulation mapping confirmed multiple somatosensory responsive sites in the left hemisphere in or near the lesion, in contradiction of the fMRI results. Since the BOLD signal is a measure of the local ratio of oxygenated to deoxygenated blood, fMRI represents only an indirect measure of neuronal activity. Modeling of fMRI activation depends on intact neurovascular coupling and adequate signal to noise ratios, which may be altered in the presence of a vascular lesion. Our results suggest that pre-surgical mapping of cortical function with fMRI can be unreliable in the presence of a vascular lesion and can lead to false-negative results. In such cases, direct measures of electrophysiological activity, such as electrocorticography, scalp EEG and MEG should be preferred.
Design of bandgap grid structures

This paper discusses issues related to designing band-gaps in periodic plane grid structures. Finite element analysis is used to solve the dynamic behavior of a representative unit cell and Bloch–Floquet theory is used to extend the results to the infinite structure. Particular attention is given to the addition of non-structural masses that are introduced as design variables. These are used to create desirable features in the dispersion diagram. Physical insight is presented into the optimal choice of locations where masses should be added and the results of several numerical examples are provided to highlight this and other features of how band-gaps can be created and located at desired frequency ranges. The effect of the skew angle of the underlying grid structure is also explored, as are mathematical refinements of the modelling of the beam elements and the rotational inertia of the added masses. A scaling feature between the size of the reducible and the irreducible reference cell is exploited and the manner in which this can simplify optimization approaches is discussed.
Using a semantic network for information extraction

This paper describes the approach to knowledge representation taken in the LaSIE Information Extraction (IE) system. Unlike many IE systems that skim texts and use large collections of shallow, domain-specific patterns and heuristics to fill in templates, LaSIE attempts a fuller text analysis, first translating individual sentences to a quasi-logical form, and then constructing a weak discourse model of the entire text from which template fills are finally derived. Underpinning the system is a general ‘world model’, represented as a semantic net, which is extended during the processing of a text by adding the classes and instances described in that text. In the paper we describe the system's knowledge representation formalisms, their use in the IE task, and how the knowledge represented in them is acquired, including experiments to extend the system's coverage using the WordNet general purpose semantic network. Preliminary evaluations of our approach, through the Sixth DARPA Message Understanding Conference, indicate comparable performance to shallower approaches. However, we believe its generality and extensibility offer a route towards the higher precision that is required of IE systems if they are to become genuinely usable technologies.
Searching in the Plane

In this paper we initiate a new area of study dealing with the best way to search a possibly unbounded region for an object. The model for our search algorithms is that we must pay costs proportional to the distance of the next probe position relative to our current position. This model is meant to give a realistic cost measure for a robot moving in the plane. We also examine the effect of decreasing the amount of a priori information given to search problems. Problems of this type are very simple analogues of non-trivial problems on searching an unbounded region, processing digitized images, and robot navigation. We show that for some simple search problems, knowing the general direction of the goal is much more informative than knowing the distance to the goal.
Are Data Sets Like Documents?: Evaluating Similarity-Based Ranked Search over Scientific Data

The past decade has seen a dramatic increase in the amount of data captured and made available to scientists for research. This increase amplifies the difficulty scientists face in finding the data most relevant to their information needs. In prior work, we hypothesized that Information Retrieval-style ranked search can be applied to data sets to help a scientist discover the most relevant data amongst the thousands of data sets in many formats, much like text-based ranked search helps users make sense of the vast number of Internet documents. To test this hypothesis, we explored the use of ranked search for scientific data using an existing multi-terabyte observational archive as our test-bed. In this paper, we investigate whether the concept of varying relevance, and therefore ranked search, applies to numeric data-that is, are data sets are enough like documents for Information Retrieval techniques and evaluation measures to apply? We present a user study that demonstrates that data set similarity resonates with users as a basis for relevance and, therefore, for ranked search. We evaluate a prototype implementation of ranked search over data sets with a second user study and demonstrate that ranked search improves a scientist's ability to find needed data.
Two-Way Relaying over OFDM: Optimized Tone Permutation and Power Allocation

We consider an amplify-and-forward scheme for two-way relaying over OFDM, in which two nodes wish to exchange information via a relay. Assuming full channel knowledge, we perform power allocation for the relay and both information-exchanging nodes, as well as tone permutation at the relay, so as to maximize the sum capacity. A dual decomposition technique is employed for power allocation, while a greedy approach is proposed for tone permutation. In particular, we explore an interesting water-filling behavior displayed by this power allocation solution. Numerical results demonstrate that substantial capacity gains are achieved by implementing the two proposed solutions, either individually or successively.
O-bearing Molecules in Carbon-rich Proto-Planetary Objects

We present Infrared Space Observatory long-wavelength spectrometer observations of the proto-planetary nebula CRL 618, a star evolving very fast toward the planetary nebula stage. In addition to the lines of 12CO, 13CO, HCN, and HNC, we report on the detection of H2O and OH emission together with the fine-structure lines of [O I] at 63 and 145 μm. The abundance of the latter three species relative to 12CO are 4 × 10-2, 8 × 10-4, and 4.5 (approximate value) in the regions where they are produced. We suggest that O-bearing species other than CO are produced in the innermost region of the circumstellar envelope. The UV photons from the central star photodissociate most of the molecular species produced in the asymptotic giant branch (AGB) phase and allow a chemistry dominated by standard ion-neutral reactions. They not only allow these reactions for the formation of O-bearing species but also modify the abundances of C-rich molecules like HCN and HNC for which we found an abundance ratio of ≃1, which is much lower than in AGB stars. The molecular abundances in the different regions of the circumstellar envelope have been derived from radiative transfer models and from our knowledge of its physical structure.
HMTT: A Hybrid Hardware/Software Tracing System for Bridging Memory Trace's Semantic Gap

Memory trace analysis is an important technology for architecture research, system software (i.e., OS, compiler) optimization, and application performance improvements. Hardware-snooping is an effective and efficient approach to monitor and collect memory traces. Compared with software-based approaches, memory traces collected by hardware-based approaches are usually lack of semantic information, such as process/function/loop identifiers, virtual address and I/O access. In this paper we propose a hybrid hardware/software mechanism which is able to collect memory reference trace as well as semantic information. Based on this mechanism, we designed and implemented a prototype system called HMTT (Hybrid Memory Trace Tool) which adopts a DIMMsnooping mechanism to snoop on memory bus and a software-controlled tracing mechanism to inject semantic information into normal memory trace. To the best of our knowledge, the HMTT system is the first hardware tracing system capable of correlating memory trace with high-level events. Comprehensive validations and evaluations show that the HMTT system has both hardware's (e.g., no distortion or pollution) and software's advantages (e.g., flexibility and more information).
Enhanced baroreflex sensitivity in free-moving calponin knockout mice.

Calponin is an actin binding protein in vascular smooth muscle that modifies contractile responses. However, its role in mean arterial pressure (MAP) regulation has not been clarified. To assess this, MAP and heart rate (HR) were measured in calponin knockout (KO) mice, and the results were compared with those in wild-type (WT) mice. The measurements were performed every 100 ms during a 60-min free-moving state each day for 3 days. Mice in both groups rested during approximately 70% of the total measuring period. The mean HR during rest was significantly lower in KO mice than in WT mice but with no significant difference in MAP between the groups. The change in HR response (deltaHR) to spontaneous change in MAP (deltaMAP) varied in a wider range in KO mice with an 80% increase in the coefficient of variation for HR (P < 0.05), whereas MAP in KO mice was controlled in a narrow range similar to that in WT mice. The baroreflex sensitivity (deltaHR/deltaMAP), determined from the change in HR to the spontaneous change in MAP, was twofold higher in KO mice than that in WT mice (P < 0.01), whereas there were no significant differences in the baroreflex sensitivity determined by intravascular administration of phenylephrine and sodium nitroprusside between the two groups (P > 0.1). The MAP response to the administrated doses of phenylephrine in KO mice was reduced to one-half of that in WT mice (P < 0.01) but with no significant difference in the response to sodium nitroprusside between the groups. The differences in HR variability and the spontaneous baroreflex sensitivity between the two groups completely disappeared after carotid sinus denervation. These results suggest that the higher variability in HR for KO mice was caused by the increased spontaneous arterial baroreflex sensitivity, though not detected by the intra-arterial administration of the drug, and that the higher variability of HR may be a compensatory adaptation to the blunted alpha-adrenergic response of peripheral vessels to sympathetic nervous activity.
Evaluating Students ’ Evaluations ∗

This paper contrasts measures of teacher effectiveness with the students’ evaluations for the same teachers using administrative data from Bocconi University (Italy). The effectiveness measures are estimated by comparing the subsequent performance both in follow-on coursework and in the labor market of students who are randomly assigned to teachers in each of their compulsory courses. We find that, even in a setting where the syllabuses are fixed and all teachers in the same course present exactly the same material, teachers still matter substantially. The average difference in subsequent performance between students who were assigned to the best and worst teacher (on the effectiveness scale) is approximately 23% of a standard deviation in the distribution of exam grades, corresponding to over 3% of the average grade. Moreover, teacher effectiveness appears to be negatively correlated with the students’ evaluations; in other words, teachers who are associated with better subsequent performance receive worst evaluations from their students. On the other hand, teachers who are associated with high grades in their own exam are associated with good evaluations. We rationalize these results with a simple model where teachers can either engage in real teaching or teach to the test, the former requiring higher students’ effort than the latter. Teaching to the test guarantees high grades in the current course but does not improve future outcomes. Hence, if students provide higher evaluations to courses in which they get higher grades, the model is capable of predicting our empirical finding that good teachers get bad evaluations, especially when teaching to the test is very effective (for example, with multiple choice tests). Consistently with the predictions of the model, we also find that classes in which high-skill students are over-represented produce evaluations that are more in line with estimated teacher effectiveness. JEL Codes: I20
New method for studying neutrino mixing and mass differences

Neutrino masses and mixing can be investigated by studying the behavior of a radioactive bare nucleus which decays by emitting an electron into the open atomic K shell BEFORE and DURING its weak decay by neutrino emission. The initial nuclear state has a momentum spread required by Heisenberg. The wave packet contains pairs of components with different momenta which can produce neutrinos in two mass eigenstates with exactly the same energy and different momenta. These neutrino amplitudes mix to produce a single electron-neutrino state with the same energy. Since there is no information on which mass eigenstates produced the neutrino this is a typical quantum mechanics "two-slit" or "which path" experiment. A transition between the same initial and a final states can go via two paths with a phase difference producing interference and oscillations. Here the two paths are in momentum space A new oscillation phenomenon providing information about neutrino mixing is obtained by following the nucleus before and during the decay. The analysis starts with Stodolsky's proof that interference between states having different energies cannot be observed in realistic experiments. Results then follow from simple rigorous quantum mechanics without the hand waving and loopholes which have confused many previous neutrino oscillation investigations.
An efficient approach for Intrusion Detection using data mining methods

Intrusion Detection System (IDS) is becoming a vital component of any network in today's world of Internet. IDS are an effective way to detect different kinds of attacks in an interconnected network thereby securing the network. An effective Intrusion Detection System requires high accuracy and detection rate as well as low false alarm rate. This paper focuses on a hybrid approach for intrusion detection system (IDS) based on data mining techniques. The main research method is clustering analysis with the aim to improve the detection rate and decrease the false alarm rate. Most of the previously proposed methods suffer from the drawback of k-means method with low detection rate and high false alarm rate. This paper presents a hybrid data mining approach encompassing feature selection, filtering, clustering, divide and merge and clustering ensemble. A method for calculating the number of the cluster centroid and choosing the appropriate initial cluster centroid is proposed in this paper. The IDS with clustering ensemble is introduced for the effective identification of attacks to achieve high accuracy and detection rate as well as low false alarm rate.
The Effect of Cryotherapy on the Normal Ankle Joint Position Sense

Purpose To determine whether a fifteen-minute water immersion treatment affects the normal ankle joint position sense (JPS) at the middle range of dorsiflexion and plantar flexion actively and passively. Methods Thirty healthy female volunteers aged between 18 and 30 years were treated by a 15-minute cryotherapy (6 ± 1°C). The subject's skin temperature over antromedial aspect of dominant ankle was measured by the Mayomed device before, immediate and 15 minutes after water immersion. Ankle JPS was tested trough the pedal goniometer at 3 stages similar to the skin temperature. ANOVA (α = 0.05) was performed on each of variables using SPSS 19.0 software. Results Skin temperature was seen to decrease after water immersion but subjects did not return to pre-test skin temperature after 15 minutes (P<0.001). The research found no significant difference in JPS at middle range of dorsiflexion and plantar flexion actively and passively before and after cryotherapy. Conclusion These findings suggest that 15-minute water immersion at 6°C dose not significantly alter the middle range of plantar flexion/ dorsiflexion JPS at the ankle and is not deleterious to JPS.
Design using Finite Element Analysis of Switched Reluctance Motor for Electric Vehicle

In this paper, switched reluctance motor (SRM) to be employed electric vehicle (EV) is designed using finite element method (FEM). The static torque of SRM is estimated with the magnetic field analysis. The temperature rise with time of SRM is estimated with the heat transfer analysis. First, the static torque and temperature rise with time of 600W SRM included in an experiment set, and are compared with the calculated results using FEM under the same conditions. The validity of magnetic field analysis and heat transfer analysis is verified by the comparisons. Also, the 60 [kW] SRM employed in EV, whose output characteristics are equal to 1500 [cc] gasoline engine, is designed with the magnetic field analysis and heat transfer analysis
Ribosome-translocon complex mediates calcium leakage from endoplasmic reticulum stores

Under resting conditions, the endoplasmic reticulum (ER) intraluminal free calcium concentration ([Ca2+]ER) reflects a balance between active uptake by Ca2+-ATPases and passive efflux via `leak channels'. Despite their physiological importance and ubiquitous leak pathway mechanism, very little is known about the molecular nature of these channels. As it has been suggested that the open translocon pore complex of the ER is permeable to ions and neutral molecules, we hypothesized that the ribosome-bound translocon would be permeable to calcium after treatment with puromycin, a translation inhibitor that specifically releases polypeptide chains. At this time, the translocon channel is left open. We measured the fluctuations in cytoplasmic and luminal calcium concentrations using fluorescent dyes (fura-2 and magfura-2, respectively). The calcium release induced by thapsigargin (a Ca2+-ATPase inhibitor) was lower after puromycin treatment. Puromycin also reduced the [Ca2+]ER level when perfused into the medium, but was ineffective after anisomycin pre-treatment (an inhibitor of the peptidyl transferase). Puromycin had a similar effect in the presence of heparin and ryanodine. This puromycin-evoked [Ca2+]ER decrease was specific to the translocon. We conclude that the translocon complex is a major calcium leak channel. This work reveals a new role for the translocon which is involved in the control of the [Ca2+]ER and could therefore supervise many physiological processes, including gene expression and apoptosis.
Resuspension of phytodetritus from the sea floor: A laboratory flume study

Mass settling of phytoplankton can result in the accumulation of a layer of phytodetritus on the sea floor. In order to determine the fate of this organic matter, we must know whether the phytodetritus may be returned to the water column by resuspension. This study was designed to measure the critical bed shear stress ( τ0crit) for resuspension of phytodetritus and to test whether τ0crit differs (1) among types of phytodetritus with different phytoplankton species composition and (2) within type among ages. Phytodetritus was created from cultured Skeletonema costatum and from natural assemblages dominated by Chaetoceros spp. , collected near the end of diatom blooms in Cape Cod Bay and Woods Hole, Massachusetts. Resuspension of phytodetritus decomposed 1‐ to 11‐d was measured in a laboratory flume. Overall, τ0crit for the diatom‐derived detritus ranged by a factor of four (0.018–0.068 N m−2), with significant differences in τ0crit among types and ages of phytodetritus. Reasons for these differences are suggested, such as species‐specific differences in size, shape, porosity, and stickiness of the detrital matrix, as well as changes in these parameters that occurred during decomposition. Values for critical shear velocity, which ranged from 0.4 to 0.6 cm s−1 for Chaetoceros‐derived detritus and from 0.5 to 0.8 cm s−1 for Skeletonema‐derived detritus, validated indirect estimates from field studies. An interesting finding with special relevance in lake and coastal systems was the importance of wave‐forced resuspension, suggesting that coupling of settled phytodetritus and other sticky organic flocs to the water column is enhanced by waves.