Miracle-dz/UniFAR-FTUs huggingface dataset:
Larsen Ice Shelf Has Progressively Thinned

The retreat and collapse of Antarctic Peninsula ice shelves in tandem with a regional atmospheric warming has fueled speculation as to how these events may be related. Satellite radar altimeter measurements show that between 1992 and 2001 the Larsen Ice Shelf lowered by up to 0.27 ± 0.11 meters per year. The lowering is explained by increased summer melt-water and the loss of basal ice through melting. Enhanced ocean-driven melting may provide a simple link between regional climate warming and the successive disintegration of sections of the Larsen Ice Shelf.
A Guaranteed Similarity Metric Learning Framework for Biological Sequence Comparison

Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. The distance and similarity between two sequence are very important and widely studied. During the last decades, Similarity(distance) metric learning is one of the hottest topics of machine learning/data mining as well as their applications in the bioinformatics field. It is feasible to introduce machine learning technology to learn similarity metric from biological data. In this paper, we propose a novel framework of guaranteed similarity metric learning (GMSL) to perform alignment of biology sequences in any feature vector space. It introduces the <inline-formula> <tex-math notation="LaTeX">$(\epsilon, \gamma, \tau)$</tex-math><alternatives> <inline-graphic xlink:type="simple" xlink:href="zhang-ieq1-2495186.gif"/></alternatives></inline-formula>-goodness similarity theory to Mahalanobis metric learning. As a theoretical guaranteed similarity metric learning approach, GMSL guarantees that the learned similarity function performs well in classification and clustering. Our experiments on the most used datasets demonstrate that our approach outperforms the state-of-the-art biological sequences alignment methods and other similarity metric learning algorithms in both accuracy and stability.
The solution space geometry of random linear equations

We consider random systems of linear equations over GF(2) in which every equation binds k variables. We obtain a precise description of the clustering of solutions in such systems. In particular, we prove that with probability that tends to 1 as the number of variables, n, grows: for every pair of solutions σ,τ, either there exists a sequence of solutions starting at σ and ending at τ such that successive solutions have Hamming distance O(log n), or every sequence of solutions starting at σ and ending at τ contains a pair of successive solutions with distance Ω(n). Furthermore, we determine precisely which pairs of solutions are in each category. Key to our results is establishing the following high probability property of cores of random hypergraphs which is of independent interest. Every vertex not in the r‐core of a random k‐uniform hypergraph can be removed by a sequence of O(log n) steps, where each step amounts to removing one vertex of degree strictly less than r at the time of removal. © 2013 Wiley Periodicals, Inc. Random Struct. Alg. , 46, 197–231, 2015
Topology, divergence dates, and macroevolutionary inferences vary between different tip-dating approaches applied to fossil theropods (Dinosauria)

Dated phylogenies of fossil taxa allow palaeobiologists to estimate the timing of major divergences and placement of extinct lineages, and to test macroevolutionary hypotheses. Recently developed Bayesian ‘tip-dating’ methods simultaneously infer and date the branching relationships among fossil taxa, and infer putative ancestral relationships. Using a previously published dataset for extinct theropod dinosaurs, we contrast the dated relationships inferred by several tip-dating approaches and evaluate potential downstream effects on phylogenetic comparative methods. We also compare tip-dating analyses to maximum-parsimony trees time-scaled via alternative a posteriori approaches including via the probabilistic cal3 method. Among tip-dating analyses, we find opposing but strongly supported relationships, despite similarity in inferred ancestors. Overall, tip-dating methods infer divergence dates often millions (or tens of millions) of years older than the earliest stratigraphic appearance of that clade. Model-comparison analyses of the pattern of body-size evolution found that the support for evolutionary mode can vary across and between tree samples from cal3 and tip-dating approaches. These differences suggest that model and software choice in dating analyses can have a substantial impact on the dated phylogenies obtained and broader evolutionary inferences.
Thermostability and molecular encapsulation within an engineered caged protein scaffold

Self‐assembling biological complexes such as viral capsids have been manipulated to function in innovative nanotechnology applications. The E2 component of pyruvate dehydrogenase from Bacillus stearothermophilus forms a dodecahedral complex and potentially provides another platform for these purposes. In this investigation, we show that this protein assembly exhibits unusual stability and can be modified to encapsulate model drug molecules. To distill the E2 protein down to its structural scaffold core, we synthesized a truncated gene optimized for expression in Escherichia coli. The correct assembly and dodecahedral structure of the resulting scaffold was confirmed with dynamic light scattering and transmission electron microscopy. Using circular dichroism and differential scanning calorimetry, we found the thermostability of the complex to be unusually high, with an onset temperature of unfolding at 81.1 ± 0.9°C and an apparent midpoint unfolding temperature of 91.4 ± 1.4°C. To evaluate the potential of this scaffold for encapsulation of guest molecules, we made variants at residues 381 and 239 which altered the physicochemical properties of the hollow internal cavity. These mutants, yielding 60 and 120 mutations within this cavity, assembled into the correct architecture and exhibited high thermostability that was comparable to the wild‐type scaffold. To show the applicability of this scaffold, two different fluorescent dye molecules were covalently coupled to the cysteine mutant at site 381. We demonstrate that these mutations can introduce non‐native functionality and enable molecular encapsulation within the cavity while still retaining the dodecahedral structure. The unusually robust nature of this scaffold and its amenability to internal changes reveal its potential for nanoscale applications. Biotechnol. Bioeng. 2008;101: 654–664. © 2008 Wiley Periodicals, Inc.
Precise Client-side Protection against DOM-based Cross-Site Scripting

The current generation of client-side Cross-Site Scripting filters rely on string comparison to detect request values that are reflected in the corresponding response's HTML. This coarse approximation of occurring data flows is incapable of reliably stopping attacks which leverage nontrivial injection contexts. To demonstrate this, we conduct a thorough analysis of the current state-of-the-art in browser-based XSS filtering and uncover a set of conceptual shortcomings, that allow efficient creation of filter evasions, especially in the case of DOM-based XSS. To validate our findings, we report on practical experiments using a set of 1,602 real-world vulnerabilities, achieving a rate of 73% successful filter bypasses. Motivated by our findings, we propose an alternative filter design for DOM-based XSS, that utilizes runtime taint tracking and taint-aware parsers to stop the parsing of attacker-controlled syntactic content. To examine the efficiency and feasibility of our approach, we present a practical implementation based on the open source browser Chromium. Our proposed approach has a low false positive rate and robustly protects against DOM-based XSS exploits.
Learning a Plan in the Limit

Induction is one of the major forms of reasoning; it is therefore essential to include it in a commonsense reasoning framework. This paper examines a class of induction-based planning problems. These problems can be solved, but not in the classical sense, where one and only one output—a correct solution—is to be provided. Here a sequence of outputs, or hypothetical solutions, is output, with finitely of them being possibly incorrect, up to a point where the sequence becomes constant, having converged to a correct solution. Still it is usually not possible to ever discover when convergence has taken place, hence it is usually not possible to definitely know that the problem has been solved, a behavior known in the literature on inductive inference, or formal learning theory, as identification in the limit. We present a semantics for iterative (looping) planning based on identification in the limit, with the planner learning from positive examples (as opposed for instance to negative examples, or answers to queries). Potential plans are repeatedly hypothesized, and a correct plan will be converged upon iff such a plan exists. We show that this convergence happens precisely when a particular logical entailment relation is satisfied. The existing system KPLANNER, which generates iterative plans by generalizing over two examples, is analogous to a fragment of this procedure. We describe an optimizing version, which attempts to satisfy a goal in the best possible way by defining preferences on plans, in the form of an order relation. We also discuss potential extensions to planning which cannot be solved by induction (and a fortiori, cannot be solved in the classical sense).
The Few, the Changing, the Different: Pubertal Onset, Perceived School Climate and Body Image in Ethnically Diverse Sixth Grade Girls

The present study examined the impact of pubertal onset, race/ethnicity, and school racial/ethnic composition on girls' body image and perceived school climate (school safety, school liking, and loneliness in school) during the middle school transition. The sample (N = 1,626) included 6th grade Black, Mexican American, White, and Asian girls from 20 diverse middle schools. Hierarchical analyses supported both the early-timing and stressful change hypothesis. That is, experiencing pubertal onset before or during the transition to middle school was associated with more loneliness, less liking of school, and more negative body image. Alternatively, for girls who were non-starters (i.e., who had not begun their first menstruation by the end of the 6th grade), liking of school and feelings of loneliness were buffered. However, findings varied according to students' self-reported race/ethnicity and the ethnic composition of their school. Perceiving oneself as a minority was particularly threatening for girls, especially girls who were White. Findings suggest that both school racial/ethnic contextual factors and pubertal onset status should be considered when examining ways to facilitate the 6th grade transition for girls.
Human amygdala reactivity is diminished by the β-noradrenergic antagonist propranolol

Background Animal models of anxiety disorders emphasize the crucial role of locus ceruleus–noradrenergic (norepinephrine, NE) signaling, the basolateral amygdala (BLA) and their interactions in the expression of anxiety-like behavioral responses to stress. Despite clinical evidence for the efficacy of a β-noradrenergic receptor blockade with propranolol in the alleviation of anxiety symptoms and the secondary prevention of post traumatic stress disorder, preclinical evidence for a β-noradrenergic modulation of BLA activity in humans is missing. Method We combined functional magnetic resonance imaging in healthy volunteers with probabilistic mapping of intra-amygdalar responses to fearful, neutral and happy facial expressions to test the hypothesis that a β-noradrenergic receptor blockade with propranolol would inactivate the BLA. Results Consistent with our a priori hypothesis, propranolol diminished BLA responses to facial expressions, independent of their emotional valence. The absence of activity changes in probabilistically defined visual control regions underscores the specific action of propranolol in the BLA. Conclusions Our findings provide the missing link between the anxiolytic potential of propranolol and the biological basis of β-noradrenergic activation in the human BLA as a key target for the pharmacological inhibition of anxiety neurocircuitry. Moreover, our findings add to emerging evidence that NE modulates both the reactivity (sensitivity) and the operating characteristics (specificity) of the BLA via β-noradrenergic receptors.
Neural regulation of muscle acetylcholine receptor epsilon- and alpha- subunit gene promoters in transgenic mice

The effects of denervation were investigated in mice with transgenes containing promoter elements from the muscle acetylcholine receptor epsilon- and alpha-subunit genes. The promoter sequences were coupled to a nuclear localization signal-beta-galactosidase fusion gene (nlacZ) as a reporter. While many postsynaptic specializations form in the embryo, expression of the epsilon subunit is induced during the first two postnatal weeks. When muscles were denervated at birth, before the onset of epsilon expression, epsilon nlacZ still appeared at the former synaptic sites on schedule. This result suggests that the nerve leaves a localized "trace" in the muscle that can continue to regulate transcription. An additional finding was that epsilon nlacZ expression was much stronger in denervated than in intact muscles. This suggests that the epsilon promoter is similar to the other subunits in containing elements that are activated on cessation of neural activity. However, even after denervation, epsilon nlacZ expression was always confined to the synaptic region whereas alpha nlacZ expression increased in nuclei along the entire length of the fiber. This suggests that while the epsilon gene is similar in its activity dependence to other subunit genes, it is unique in that local nerve-derived signals are essential for its expression. Consequently, inactivity enhances epsilon expression only in synaptic nuclei where such signals are present, but enhances expression throughout the muscle fiber. Truncations and an internal deletion of the epsilon promoter indicate that cis-elements essential for the response to synaptic signals are contained within 280 bp of the transcription start site. In contrast to these results in young animals, denervation in older animals leads to an unexpected reduction in nlacZ activity. However, mRNA measurements indicated that transgene expression was increased in these animals. This discordance between nlacZ mRNA and enzyme activity, demonstrates a previously unknown limitation of nlacZ as a reporter gene in transgenic animals.
L'étudiant européen voyageur, un nouvel "étranger" : aspects de l'adaptation interculturelle des étudiants européens

Quels sont les caracteres de l'experience de l'etudiant europeen voyageur en sejour d'un an dans une culture autre que la sienne ? Notre reponse met en scene deux ensembles de donnees. Le premier ensemble s'articule autour du concept de "l'etranger", definit par Simmel (1908) et integre un corpus de textes appartenant a la sociologie de l'etranger qui analysent les caracteres de ce nouveau "type social" et mettent en evidence diverses figures d'etrangers. Nous supposons que l'etudiant voyageur constitue une variante de ce kaleidoscope dans des conditions sociales autres. Le second ensemble comprend les donnees recueillies en situation d'entretien aupres de cinquante etudiants europeens representant trois cas d'insertion distincts, au terme de leur annee a l'etranger. Au travers de leur temoignage, l'experience de mobilite temporaire de l'etudiant se definit, dans ses aspects tendanciels et singuliers dans les champs spatial, temporel, social, relationnel et symbolique. L'experience etudiante dans le contexte europeen implique un apprentissage de l'espace, variable en fonction des contextes d'insertion qui invite a repenser l'espace vital comme portable et global. Sa position temporelle met en evidence l'equilibre delicat entre permanence et precarite, entre le fil continu qui inscrit le voyage dans une trajectoire personnelle et les risques de l'aventure recherchee. La position sociale de l'etudiant voyageur, entre distance et proximite, appartenance et rupture, constitue un rite de passage qui met a l'epreuve son initiative pour s'amenager un territoire familier et se construire un tissu social. Les strategies mises en oeuvre font apparaitre ses competences d'adaptation et en particulier le role crucial joue par le capital linguistique et les competences communicatives dans ce processus de re-socialisation.
Biosonar performance of foraging beaked whales (Mesoplodon densirostris)

SUMMARY Toothed whales (Cetacea, odontoceti) emit sound pulses to probe their surroundings by active echolocation. Non-invasive, acoustic Dtags were placed on deep-diving Blainville's beaked whales (Mesoplodon densirostris) to record their ultrasonic clicks and the returning echoes from prey items, providing a unique view on how a whale operates its biosonar during foraging in the wild. The process of echolocation during prey capture in this species can be divided into search, approach and terminal phases, as in echolocating bats. The approach phase, defined by the onset of detectable echoes recorded on the tag for click sequences terminated by a buzz, has interclick intervals (ICI) of 300-400 ms. These ICIs are more than a magnitude longer than the decreasing two-way travel time to the targets, showing that ICIs are not given by the two-way-travel times plus a fixed, short lag time. During the approach phase, the received echo energy increases by 10.4(±2) dB when the target range is halved, demonstrating that the whales do not employ range-compensating gain control of the transmitter, as has been implicated for some bats and dolphins. The terminal/buzz phase with ICIs of around 10 ms is initiated when one or more targets are within approximately a body length of the whale (2-5 m), so that strong echo returns in the approach phase are traded for rapid updates in the terminal phase. It is suggested that stable ICIs in the search and approach phases facilitate auditory scene analysis in a complex multi-target environment, and that a concomitant low click rate allows the whales to maintain high sound pressure outputs for prey detection and discrimination with a pneumatically driven, bi-modal sound generator.
Joint association of genome-wide association study-identified susceptibility loci and dietary patterns in risk of renal cell carcinoma among non-Hispanic whites.

Dietary factors may affect risk of renal cell carcinoma (RCC). In an ongoing case-control study of RCC initiated in Houston, Texas, in 2002, we identified 3 empirically derived dietary patterns: "fruits and vegetables," "American/Western," and "Tex-Mex. " Among 659 RCC cases and 699 controls, we evaluated associations of these dietary patterns with RCC risk and whether the associations varied by obesity status, smoking status, physical activity level, history of hypertension, and genetic variants previously identified via genome-wide association studies. Among persons in the highest categories of adherence versus the lowest, the "fruits and vegetables" dietary pattern was associated with an approximately 50% lower RCC risk (Ptrend < 0.001), while "American/Western" dietary pattern scores were positively associated with a 2-fold higher risk (Ptrend < 0.001). We observed synergistic interaction between the American/Western pattern and hypertension status: The odds ratio (highest tertile vs. lowest) among persons with hypertension was 2.23 (95% confidence interval: 1.43, 3.45), as compared with 1.76 (95% confidence interval: 1.16, 2.70) among persons without hypertension (additive Pinteraction = 0.01). A variant (rs718314) in the inositol 1,4,5-trisphosphate receptor, type 2 gene (ITPR2) was found to interact with the American/Western dietary pattern in relation to RCC risk (additive Pinteraction = 0.03). ITPR2 has been shown to affect nutrient metabolism and central obesity. Dietary patterns, genetic variants, and host characteristics may individually and jointly influence susceptibility to RCC.
Testing for linearity

The problem of testing for linearity and the number of regimes in the context of self-exciting threshold autoregressive (SETAR) models is reviewed. We describe least-squares methods of estimation and inference. The primary complication is that the testing problem is non-standard, due to the presence of parameters which are only defined under the alternative, so the asymptotic distribution of the test statistics is non-standard. Simulation methods to calculate asymptotic and bootstrap distributions are presented. As the sampling distributions are quite sensitive to conditional heteroskedasticity in the error, careful modeling of the conditional variance is necessary for accurate inference on the conditional mean. We illustrate these methods with two applications--annual sunspot means and monthly U.S. industrial production. We find that annual sunspots and monthly industrial production are SETAR(2) processes. Copyright 1999 by Blackwell Publishers Ltd
Evolving a Neural Network Location Evaluator to Play Ms. Pac-Man

Ms. Pac-Man is a challenging, classic arcade game with a certain cult status. This paper reports attempts to evolve a Pac-Man player, where the control algorithm uses a neural network to evaluate the possible next moves. The evolved neural network takes a handcrafted feature vector based on a candidate maze location as input, and produces a score for that location as output. Results are reported on two simulated versions of the game: deterministic and nondeterministic. The results show that useful behaviours can be evolved that are frequently capable of clearing the first level, but are still susceptible to making poor decisions. Currently, the best evolved players play at the level of a reasonable human novice.
Scalable PEEC-SPICE modelling for EMI analysis of power electronic packages and subsystems

In this paper we present a method for scaling component and subsystem models for electromagnetic interference (EMI) analysis of power electronic systems using a SPICE simulator. The modelling is done using the partial element equivalent circuit (PEEC) method for extracting the component's parasitic impedance matrices and to create SPICE compatible component sub-circuits. The scaling method consists of separating system components with negligible cross-coupling, combining component pins for reducing the impedance matrix sizes, and scaling the semiconductor device models to combine paralleled chips into one model. The method allows selective scaling and therefore, finding the right balance between required level of detail and computing effort. Comparisons to measurements have shown that the models are very accurate, especially at turn-off and on-state