Miracle-dz/UniFAR-FTUs huggingface dataset:
Using phylogeny and functional traits for assessing community assembly along environmental gradients: A deterministic process driven by elevation

Abstract Community assembly processes is the primary focus of community ecology. Using phylogenetic‐based and functional trait‐based methods jointly to explore these processes along environmental gradients are useful ways to explain the change of assembly mechanisms under changing world. Our study combined these methods to test assembly processes in wide range gradients of elevation and other habitat environmental factors. We collected our data at 40 plots in Taibai Mountain, China, with more than 2,300 m altitude difference in study area and then measured traits and environmental factors. Variance partitioning was used to distinguish the main environment factors leading to phylogeny and traits change among 40 plots. Principal component analysis (PCA) was applied to colligate other environment factors. Community assembly patterns along environmental gradients based on phylogenetic and functional methods were studied for exploring assembly mechanisms. Phylogenetic signal was calculated for each community along environmental gradients in order to detect the variation of trait performance on phylogeny. Elevation showed a better explanatory power than other environment factors for phylogenetic and most traits’ variance. Phylogenetic and several functional structure clustered at high elevation while some conserved traits overdispersed. Convergent tendency which might be caused by filtering or competition along elevation was detected based on functional traits. Leaf dry matter content (LDMC) and leaf nitrogen content along PCA 1 axis showed conflicting patterns comparing to patterns showed on elevation. LDMC exhibited the strongest phylogenetic signal. Only the phylogenetic signal of maximum plant height showed explicable change along environmental gradients. Synthesis. Elevation is the best environment factors for predicting phylogeny and traits change. Plant's phylogenetic and some functional structures show environmental filtering in alpine region while it shows different assembly processes in middle‐ and low‐altitude region by different trait/phylogeny. The results highlight deterministic processes dominate community assembly in large‐scale environmental gradients. Performance of phylogeny and traits along gradients may be independent with each other. The novel method for calculating functional structure which we used in this study and the focus of phylogenetic signal change along gradients may provide more useful ways to detect community assembly mechanisms.
Combining cryptography with biometrics effectively

We propose the first practical and secure way to integrate the iris biometric into cryptographic applications. A repeatable binary string, which we call a biometric key, is generated reliably from genuine iris codes. A well-known difficulty has been how to cope with the 10 to 20% of error bits within an iris code and derive an errorfree key. To solve this problem, we carefully studied the error patterns within iris codes, and devised a two-layer error correction technique that combines Hadamard and Reed-Solomon codes. The key is generated from a subject’s iris image with the aid of auxiliary error-correction data, which do not reveal the key, and can be saved in a tamper-resistant token such as a smart card. The reproduction of the key depends on two factors: the iris biometric and the token. The attacker has to procure both of them to compromise the key. We evaluated our technique using iris samples from 70 different eyes, with 10 samples from each eye. We found that an error-free key can be reproduced reliably from genuine iris codes with a 99.5% success rate. We can generate up to 140 bits of biometric key, more than enough for 128-bit AES. The extraction of a repeatable binary string from biometrics opens new possible applications, where a strong binding is required between a person and cryptographic operations. For example, it is possible to identify individuals without maintaining a central database of biometric templates, to which privacy objections might be raised.
Who is your ideal mentor? An exploratory study of mentor prototypes

Purpose – One of the main aspects of a mentoring relationship involves the expectations that mentees have of an ideal mentor. However, the traits that mentees envision in an ideal mentor are unclear. The purpose of this paper is to present series of studies examined mentees’ ideas about their ideal mentor’s physical characteristics and mentoring functions. The authors also examined gender and racial (white/nonwhite) differences in ideal mentor preferences. Design/methodology/approach – The two studies examined what mentees envision when they picture their ideal mentor, and whether the ideal mentor prototypes varied by participants’ ethnicity and gender. Study 2 further examined mentees’ ideal mentor characteristics in a forced choice ranking scale and the ideal mentor scale (Rose, 2003). Findings – When asked to describe their ideal mentor’s appearance, participants provided detailed descriptions of the ideal mentor’s features. They also emphasized mentoring characteristics and behaviors, such as guidance.
Triptolide induces protective autophagy through activation of the CaMKKβ-AMPK signaling pathway in prostate cancer cells

Triptolide, an active compound extracted from the Chinese herb thunder god vine (Tripterygium wilfordii Hook F.), has potent anti-tumor activity. Recently, triptolide was found to induce autophagy in cancer cells. However, the effects of triptolide on autophagy in human prostate cancer (PCa) cells have not yet been clearly elucidated. In this study, we demonstrated that triptolide induces autophagy in three PCa cell lines, PC-3, LNCaP and C4–2. Furthermore, we found that triptolide mediates intracellular accumulation of free calcium by stimulating the endoplasmic reticulum (ER) stress response. This activates the CaMKKβ-AMPK signaling pathway, which in turn inhibits mTOR and activates both ULK1 and Beclin 1, finally resulting in autophagy. Moreover, we found that treatment with autophagy inhibitors 3-methyladenine (3-MA) and chloroquine (CQ) enhances triptolide-induced PCa cell death and growth inhibition. Using a PC-3-xenografted mouse model, we showed that blocking autophagy with CQ significantly promoted triptolide-induced tumor growth inhibition in vivo. Overall, our results show that triptolide induces protective autophagy through the CaMKKβ-AMPK pathway in PCa cells, implying that a combination of triptolide with autophagy inhibitors may potentially be an effective therapeutic strategy for PCa.
Age-related macular degeneration and quality of life: how to interpret a research paper in health-related quality of life

Purpose of review To review how to critically appraise a research article pertaining to changes in health-related quality of life (HRQoL) related to interventions for age-related macular degeneration (AMD). Recent findings We searched PubMed using a strategy that combined the text-words, “macular degeneration” and “quality of life” (n = 73; January 17, 2004), while limiting the search to “clinical trials” (n = 6; of which 3 were published within the past year). A randomized clinical trial evaluating the efficacy of self-management as an intervention for AMD has been selected to introduce the reader to the concept of how to critically review a research paper pertaining to HRQoL in AMD. Other pertinent articles used in this review include recent results published from the Age-Related Eye Disease Study and the Submacular Surgery Trial. Summary The NEI-VFQ is a reliable, valid, and responsive tool when applied to patients with AMD. Self-management of patients with AMD has been demonstrated to improve their HRQoL by way of an internally valid randomized clinical trial. In this issue of Current Opinion in Ophthalmology, we confront the issue of how to assess the validity and importance of a research paper pertaining to the issue of quality of life. To introduce this topic, we will present a real world clinical example to better understand how quality of life may aid in medical decision making.
A negative-overhead, self-timed pipeline

This paper presents a novel variation of wave pipelining that we call "surfing. " In previous wave pipelined designs, timing uncertainty grows monotonically as events propagate through gates or other logic elements. We bound this dispersion by propagating a timing pulse along with the data values. Our logic elements have delays that are smaller in the presence of the pulse than in its absence. This produces a "surfing" effect: events are bound in close proximity to the timing pulse. We demonstrate this approach with the design of a 4 /spl times/ 12 multiplier. Spice simulations from the extracted layout indicate that this design is robust in the presence of fabrication parameter variation and power supply noise. Because timing is maintained by accelerating the logic, our designs achieve lower latency than their purely combinational equivalents. Thus, the control overhead for these designs is indeed negative.
The Algorithmic Details of Tractable MFC

where the P (u, v) is the probability of an edge between u and v and δ((u, v)∈Bl) is an indicator whether the edge (u, v) is in the Bl or not. Hence, from eq.(1.2) and eq.(1.4), Algorithm 1: Infer the most probable T ∗ i from Bi Input: (1) Candidate set Bi (Bl = 〈kl, Cl, wl〉 where Cl is a subtree of Gi and wl is the value to its foreground). Output: (1) Candidate tree T ∗ i and (2) Pruned B∗ i (⊂ Bi). 1: Set A be an N×N zero matrix where N=|Si|. Set B∗ i←∅. foreach Bl = 〈kl, Cl, wl〉 ∈ Bi do foreach s ∈ Cl do foreach t ∈ Cl, t 6= s do A(s, t)← A(s, t) + wl end 2: Let T ∗ i be the maximum spanning tree of A. foreach Bl = 〈kl, Cl, wl〉 ∈ Bi do if all edges (u, v) ∈ Cl is in T ∗ i then B∗ i ← Bl. end
Sequence Typing Confirms that a Predominant Listeria monocytogenes Clone Caused Human Listeriosis Cases and Outbreaks in Canada from 1988 to 2010

ABSTRACT Human listeriosis outbreaks in Canada have been predominantly caused by serotype 1/2a isolates with highly similar pulsed-field gel electrophoresis (PFGE) patterns. Multilocus sequence typing (MLST) and multi-virulence-locus sequence typing (MVLST) each identified a diverse population of Listeria monocytogenes isolates, and within that, both methods had congruent subtypes that substantiated a predominant clone (clonal complex 8; virulence type 59; proposed epidemic clone 5 [ECV]) that has been causing human illness across Canada for more than 2 decades.
A new reweight scheme for bilateral and non-local means approach for image denoising

Additive noise removal from a given image is an important task in digital image processing for which denoising algorithms are used. The goal of any denoising algorithm is to attenuate the noise properly and to preserve the useful content of an image. Although various denoising algorithms have been proposed to remove noise but there is still scope of improvement. The main focus of this paper is, first, analyze the basic denoising approaches and to compare them, second, to study post-stage filtering technique using method noise and reweight schemes. In this case study, we observe through our experiments that the post-filtering techniques have more potential to attenuate the noise properly, which is left by the initially applied denoising approach. The denoising performance of all considered methods is compared using two parameters: PSNR and MSSIM.
A Bayesian Student Model without Hidden Nodes and its Comparison with Item Response Theory

The Bayesian framework offers a number of techniques for inferring an individual's knowledge state from evidence of mastery of concepts or skills. A typical application where such a technique can be useful is Computer Adaptive Testing (CAT). A Bayesian modeling scheme, POKS, is proposed and compared to the traditional Item Response Theory (IRT), which has been the prevalent CAT approach for the last three decades. POKS is based on the theory of knowledge spaces and constructs item-to-item graph structures without hidden nodes. It aims to offer an effective knowledge assessment method with an efficient algorithm for learning the graph structure from data. We review the different Bayesian approaches to modeling student ability assessment and discuss how POKS relates to them. The performance of POKS is compared to the IRT two parameter logistic model. Experimental results over a 34 item Unix test and a 160 item French language test show that both approaches can classify examinees as master or non-master effectively and efficiently, with relatively comparable performance. However, more significant differences are found in favor of POKS for a second task that consists in predicting individual question item outcome. Implications of these results for adaptive testing and student modeling are discussed, as well as the limitations and advantages of POKS, namely the issue of integrating concepts into its structure.
Image Characterization via Multilayer Neural Networks

The achievement of image retrieval systems severally depends on the way the data is represented. This paper proposes a new image representation through an intelligent mechanism via neural networks for semantic-gap and dimensionality reduction. The goal of the multilayer neural network is to represent high-level semantic concepts and knowledge through a pre-defined set of images. As a consequence of this low-level into high-level feature transformation there is a semantic gap reduction between human perception and automatic feature extraction. The experimental results show the effective performance of the proposed technique.
Dexmedetomidine Injection into the Locus Ceruleus Produces Antinociception

Background alpha2 -Adrenergic agonists such as clonidine and dexmedetomidine are known to produce sedation and analgesia in humans. The sedative effect of these agents is thought to occur through supraspinal pathways, involving the locus ceruleus (LC) and its projections in rats. While the antinociceptive response to alpha2 agonists, given intrathecally, is mediated predominantly in the spinal cord, other sites of action have not been systematically studied. The authors examined whether alpha2 -adrenergic receptors in the LC mediate an antinociceptive effect. Methods For administration of different drugs into the LC, guide cannulas were placed with their tips in the LC in male Sprague-Dawley rats. Dexmedetomidine (3.5 micro gram/0.2 micro liter) was microinjected into the LC through the cannula, or given systemically by intraperitoneal injection (50 micro gram/kg). The antinociceptive effect of dexmedetomidine was measured using the tail-flick latency response. To determine the sites through which dexmedetomidine injection into the LC produces antinociception, the authors examined whether this response could be perturbed by the specific alpha2 -adrenergic antagonists atipamezole and L659,066 and pertussis toxin administered either into the LC or intrathecally before injection of dexmedetomidine systemically or directly into the LC. To eliminate the possibility that drug administered in one site (LC or intrathecal) could reach the other site, the dispositional characteristics of radiolabeled dexmedetomidine (LC) or atipamezole (intrathecal) were studied. Results Dexmedetomidine placed into the LC produces a dose-dependent increase in the tail-flick latency. This antinociceptive effect was blocked by pertussis toxin and by the alpha2 antagonists atipamezole and L659,066 placed in the LC. Intrathecal administration of atipamezole and pertussis toxin also blocked the antinociceptive effect of dexmedetomidine placed in the LC.3 Hydrogen-dexmedetomidine introduced into the LC did not reach the spinal cord in pharmacologically active concentrations; also, intrathecally administered3 Hydrogen-atipamezole did not reach the LC in appreciable amounts. The systemic administration of dexmedetomidine produced an increase in tail-flick latency, and this effect was attenuated by the injection of atipamezole and L695,066 into the LC. Conclusions Part of the mechanism by which dexmedetomidine produces an antinociceptive effect is by an action directly on the LC, demonstrated by these studies in which antinociception produced by injection of this drug into the LC can be blocked by specific alpha2 antagonists injected into the LC. Furthermore, the action of dexmedetomidine in the LC in turn may result in an increase in activation of alpha2 adrenoceptors in the spinal cord, because the antinociceptive effect of LC dexmedetomidine injection also can be blocked by intrathecal injection of atipamezole and pertussis toxin.
Effects of size of mix and trituration time on physical properties of amalgam.

It is well known that the mercury-alloy ratio and trituration time greatly influence the physical properties of the amalgam, and there are a great number of studies about this. Nowadays, the standard approach to this problem is that the optimum trituration time varies according to the size of the mix, and trituration time should be extended as the size of mix increases. Reference books [1-2] and manufacturer's instructions on the use of alloys also advise the same approach. However, few stydies have been made to check the validity of this approach. Recently, attention has been called to the fact that the trituration sound suddenly changes during mechanical trituration of an amalgam. The following report has appeared opposing the previously described established theory [3] : The time to sound change between the start of trituration and the point of sound change is shortened with the increase in the size of mix, indicating that the trituration time should be shortened as the volume increases. This report was also confirmed by a visual observation in the amalgam mix just after the point of soundchange and was in contradiction with the generally accepted theory. In order to explicate which theory is true, the generally accepted theory or the new opposing theory, concerning correlation between size of mix and trituration time, the authors investigated this problem from the aspect of the physical properties of the amalgam. That is, for the purpose of reaching a correct conclusion, the experimental order was arranged at random statistically so that the relation between the size of mix and tirituration time could be analyzed in detail.
Bacteria isolated from the airways of paediatric patients with bronchiectasis according to HIV status.

BACKGROUND Knowledge of which bacteria are found in the airways of paediatric patients with bronchiectasis unrelated to cystic fibrosis (CF) is important in defining empirical antibiotic guidelines for the treatment of acute infective exacerbations. OBJECTIVE To describe the bacteria isolated from the airways of children with non-CF bronchiectasis according to their HIV status. METHODS Records of children with non-CF bronchiectasis who attended the paediatric pulmonology clinic at Chris Hani Baragwanath Academic Hospital, Johannesburg, South Africa, from April 2011 to March 2013, or were admitted to the hospital during that period, were reviewed. Data collected included patient demographics, HIV status, and characteristics of the airway samples and types of bacteria isolated. RESULTS There were 66 patients with non-CF bronchiectasis over the 2-year study period. The median age was 9.1 years (interquartile range 7.2 - 12.1). The majority of patients (78.8%) were HIV-infected. A total of 134 samples was collected (median 1.5 per patient, range 1 - 7), of which 81.3% were expectorated or induced sputum samples. Most bacteria were Gram negatives (72.1%). Haemophilus influenzae was the most common bacterium identified (36.0%), followed by Streptococcus pneumoniae (12.6%), Moraxella catarrhalis (11.1%) and Staphylococcus aureus (10.6%). There were no differences between HIV-infected and uninfected patients in prevalence or type of pathogens isolated. CONCLUSION Bacterial isolates from the airways of children with non-CF bronchiectasis were similar to those in other paediatric populations and were not affected by HIV status.
Simplicity in Solving the Frame Problem

This paper presents an approach for reasoning about action and change which appeals to the principle of Occam's razor— roughly stating that the simplest explanations are the best ones—as the underlying theme of commonsense reasoning. We conduct a preliminary investigation of how appealing to simplicity allows us to address some of the challenges faced when reasoning about the effects of actions. In particular, we apply Occam's razor to the transformations between worlds specified by an action. To formalise these notions we use Kolmogorov complexity to identify the intended (simplest) transformation given an action description. We give some preliminary support for our claims by showing that the formalism captures our intuitions on some simple examples.
Structural mechanisms underlying the function of epithelial sodium channel/acid-sensing ion channel

Purpose of reviewThe epithelial sodium channel/degenerin family encompasses a group of cation-selective ion channels that are activated or modulated by a variety of extracellular stimuli. This review describes findings that provide new insights into the molecular mechanisms that control the function of these channels. Recent findingsEpithelial sodium channels facilitate Na+ reabsorption in the distal nephron and hence have a role in fluid volume homeostasis and arterial blood pressure regulation. Acid-sensing ion channels are broadly distributed in the nervous system where they contribute to the sensory processes. The atomic structure of acid-sensing ion channel 1 illustrates the complex trimeric architecture of these proteins. Each subunit has two transmembrane spanning helices, a highly organized ectodomain and intracellular N-terminus and C-terminus. Recent findings have begun to elucidate the structural elements that allow these channels to sense and respond to extracellular factors. This review emphasizes the roles of the extracellular domain in sensing changes in the extracellular milieu and of the residues in the extracellular–transmembrane domains interface in coupling extracellular changes to the pore of the channel. SummaryEpithelial sodium channels and acid-sensing ion channels have evolved to sense extracellular cues. Future research should be directed toward elucidating how changes triggered by extracellular factors translate into pore opening and closing events.
Steady-State Visual Evoked Potentials Can Be Explained by Temporal Superposition of Transient Event-Related Responses

Background One common criterion for classifying electrophysiological brain responses is based on the distinction between transient (i.e. event-related potentials, ERPs) and steady-state responses (SSRs). The generation of SSRs is usually attributed to the entrainment of a neural rhythm driven by the stimulus train. However, a more parsimonious account suggests that SSRs might result from the linear addition of the transient responses elicited by each stimulus. This study aimed to investigate this possibility. Methodology/Principal Findings We recorded brain potentials elicited by a checkerboard stimulus reversing at different rates. We modeled SSRs by sequentially shifting and linearly adding rate-specific ERPs. Our results show a strong resemblance between recorded and synthetic SSRs, supporting the superposition hypothesis. Furthermore, we did not find evidence of entrainment of a neural oscillation at the stimulation frequency. Conclusions/Significance This study provides evidence that visual SSRs can be explained as a superposition of transient ERPs. These findings have critical implications in our current understanding of brain oscillations. Contrary to the idea that neural networks can be tuned to a wide range of frequencies, our findings rather suggest that the oscillatory response of a given neural network is constrained within its natural frequency range.