Miracle-dz/UniFAR-FTUs huggingface dataset:
The Fourth Transmembrane Domain of the Helicobacter pylori Na+/H+ Antiporter NhaA Faces a Water-filled Channel Required for Ion Transport*

Cysteine-scanning mutagenesis was performed from Ser-130 to Leu-160 in the fourth transmembrane domain (TM4) of the Na+/H+ antiporter NhaA from Helicobacter pylori to determine the topology of each residue and to identify functionally important residues. All of the mutants were based on cysteine-less NhaA (Cys-less NhaA), which functions very similarly to the wild-type protein, and were expressed at a level similar to Cys-less NhaA. Discontinuity of [14C]N-ethylmaleimide (NEM)-reactive residues suggested that TM4 comprises residues Gly-135 to Val-156. Even within TM4, NEM reactivity was high for I136C, D141C to A143C, L146C, M150C, and G153C to R155C. These residues are thought to be located on one side of the α-helical structure of TM4 and to face a putative water-filled channel. Pretreatment of intact cells with membrane-impermeable maleimide did not inhibit [14C]NEM binding to the NEM-reactive residues within TM4, suggesting that the putative channel opens toward the cytoplasm. NEM reactivity of the A143C mutant was significantly inhibited by Li+. The T140C and D141C mutants showed lower affinity for Na+ and Li+ as transport substrates, but their maximal antiporter velocities (Vmax) were relatively unaffected. Whereas the I142C and F144C mutants completely lost their Li+/H+ antiporter activity, I142C had a lower Vmax for the Na+/H+ antiporter. F144C exhibited a markedly lower Vmax and a partially reduced affinity for Na+. These results suggest that Thr-140, Asp-141, and Phe-144 are located in the end portion of a putative water-filled channel and may provide the binding site for Na+, Li+, and/or H+. Furthermore, residues Ile-142 to Phe-144 may be important for the conformational change that accompanies ion transport in NhaA.
Dynamic Learning of Keyword-Based Preferences for News Recommendation

The accurate recommendation of daily news requires a detailed knowledge of the topics of interest to the user. The dynamic and continuous analysis of the content of the news that are read (or ignored) by the user every day may lead to the automatic, unsupervised and non-intrusive learning of the positive (and negative) preferences of the user with respect to a set of keywords. These preferences may then be used to rank the daily news, so that the user is recommended those items that match better with his/her interests. The cyclic preference learning methodology described in this paper is illustrated with a case example based on real news from the British newspaper The Guardian, in which promising results have been obtained.
Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

Motivation: Interpretation and communication of genomic data require flexible and quantitative tools to analyze and visualize diverse data types, and yet, a comprehensive tool to display all common genomic data types in publication quality figures does not exist to date. To address this shortcoming, we present Sushi.R, an R/Bioconductor package that allows flexible integration of genomic visualizations into highly customizable, publication-ready, multi-panel figures from common genomic data formats including Browser Extensible Data (BED), bedGraph and Browser Extensible Data Paired-End (BEDPE). Sushi.R is open source and made publicly available through GitHub (https://github.com/dphansti/Sushi) and Bioconductor (http://bioconductor.org/packages/release/bioc/html/Sushi.html). Contact: mpsnyder@stanford.edu or dphansti@stanford.edu
The effect of a pre-university mathematics bridging course on adult learners’ self-efficacy and retention rates in STEM subjects

In August 2008, the Mathematics Learning Centre at the University of Limerick initiated a mathematics bridging course, entitled ‘Head Start Maths’, to provide mathematics revision for adult learners about to embark on science or technology degree programmes. The aim of Head Start Maths was to revise mathematics fundamentals before the commencement of third-level education so as to lessen the anxiety levels of adult learners towards mathematics. Negative preconceptions have been noted as being of major concern with adult learners, both preconceptions of mathematics in general and also of their own abilities. In addition to this, it was hoped that Head Start Maths might lead to increased retention rates among adult learners and lead to less dropouts within the first semester. Results found that there were statistically significant increases in self-efficacy scores across some, but not all, of the mathematical topic areas and that there was an increase in the retention rates of adult learners who participated in Head Start Maths compared to those who did not.
Conformal structures with $G_{2(2)}$-ambient metrics

We present conformal structures in signature (3,2) for which the holonomy of the Fefferman-Graham ambient metric is equal to the non-compact exceptional Lie group G_{2(2)}. We write down the resulting 8-parameter family of G_{2(2)}-metrics in dimension seven explicitly in an appropriately chosen coordinate system on the ambient space.
How basic-level objects facilitate question-asking in a categorization task

The ability to categorize information is essential to everyday tasks such as identifying the cause of an event given a set of likely explanations or pinpointing the correct from a set of possible diagnoses by sequentially probing questions. In three studies, we investigated how the level of inclusiveness at which objects are presented (basic-level vs. subordinate-level) influences children's (7- and 10-year-olds) and adults' performance in a sequential binary categorization task. Study 1 found a robust facilitating effect of basic-level objects on the ability to ask effective questions in a computerized version of the Twenty Questions game. Study 2 suggested that this facilitating effect might be due to the kinds of object-differentiating features participants generate when provided with basic-level as compared to subordinate-level objects. Study 3 ruled out the alternative hypothesis that basic-level objects facilitate the selection of the most efficient among a given set of features.
Phenotypic and genotypic characterization of Streptococcus agalactiae in pregnant women. First study in a province of Argentina

Group B Streptococcus (GBS) is the leading cause of neonatal infections. Our purpose was to characterize GBS colonization in pregnant women, current serotypes, resistance phenotypes and genes associated with virulence. In Misiones, Argentina, there are no previous data on this topic. Vaginal-rectal swabs from 3125 pregnant women were studied between 2004 and 2010. GBS strains were identified by conventional and serological methods (Phadebact Strep B Test, ETC International, Bactus AB, Sweden). Serotypes were detected using Strep-B Latex (Statens Serum Institut, Denmark). Resistance phenotypes were determined by the double-disk test. Genes were studied by PCR. Maternal colonization was 9.38%. Resistance to erythromycin was 11.6%, and the constitutive phenotype was the predominant one. Serotype Ia was the most frequent, whereas serotypes IV, VI, VII and VIII were not detected. The lmb, bca and hylB genes were detected in more than 79% of the strains. In this study, the colonization rate with GBS and the serotype distribution were compared with studies reported in other areas of the country. The high resistance to erythromycin in Misiones justifies performing antibiotic susceptibility testing. The serotype distribution, the genes encoding putative virulence factors, and the patterns of resistance phenotypes of GBS may vary in different areas. They thus need to be evaluated in each place to devise strategies for prevention.
Towards low-cost, high-sensitivity, integrated biosensors

The early detection of pathogens in a solution sample using a biosensor and associated electronics manufactured in a mainstream semiconductor process is currently attracting much research and development interests around the globe. This is primarily because such a system will be low-cost, easily manufactured, and can offer very high sensitivities, thus potentially stopping the rapid spread of diseases due to water or food contamination. In this paper, we describe our current research on the design and development of an electrolyte-insulator-semiconductor field-effect transistor to detect hybridization of target DNA oligonucleotides using functionalized probes tethered to the insulator's surface of the transistor. This biological sensor, when integrated with associated signal conditioning and processing circuits, promises high sensitivity and cheaper manufacturing costs than current labeled DNA microarray optical sensing systems.
An Aplysia Type 4 Phosphodiesterase Homolog Localizes at the Presynaptic Terminals of Aplysia Neuron and Regulates Synaptic Facilitation

The cAMP-dependent signaling pathway is critically involved in memory-related synaptic plasticity. cAMP-specific type 4 phosphodiesterases (PDE4) play a role in this process by regulating the cAMP concentration. However, it is unclear how PDE4 is involved in regulating synaptic plasticity. To address this issue in Aplysia sensory-to-motor synapses, we identified a long isoform of the PDE4 homolog in Aplysia kurodai (apPDE), with genetic and biochemical properties similar to those of mammalian PDE4s. Furthermore, apPDE is localized to the membrane and presynaptic region. Both apPDE overexpression and knock-down impaired short- and long-term facilitation, indicating that an appropriate expression level of apPDE in synaptic regions is required for normal synaptic facilitation. By using fluorescence resonance energy transfer-based measurement of in vivo protein kinase A (PKA) activation, we found that the PKA activation by 5-hydroxytryptamine (5-HT) was impaired in both apPDE-overexpressed and knock-down synapses. Analogous to the inhibition of apPDE by RNA interference, chronic rolipram treatment before 5-HT stimulation also impaired the PKA activation by 5-HT, suggesting that regulation of the synaptic cAMP level by PDE4 is critical for normal synaptic facilitation. Together, we suggest that PDE4s localized in the synapses play a critical role in regulating the optimum cAMP level required for normal synaptic plasticity.
Characterization of structural variants with single molecule and hybrid sequencing approaches

MOTIVATION Structural variation is common in human and cancer genomes. High-throughput DNA sequencing has enabled genome-scale surveys of structural variation. However, the short reads produced by these technologies limit the study of complex variants, particularly those involving repetitive regions. Recent 'third-generation' sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates. RESULTS We present MultiBreak-SV, an algorithm to detect structural variants (SVs) from single molecule sequencing data, paired read sequencing data, or a combination of sequencing data from different platforms. We demonstrate that combining low-coverage third-generation data from Pacific Biosciences (PacBio) with high-coverage paired read data is advantageous on simulated chromosomes. We apply MultiBreak-SV to PacBio data from four human fosmids and show that it detects known SVs with high sensitivity and specificity. Finally, we perform a whole-genome analysis on PacBio data from a complete hydatidiform mole cell line and predict 1002 high-probability SVs, over half of which are confirmed by an Illumina-based assembly.
Replaying past changes in multi-developer projects

What was I working on before the weekend? and What were the members of my team working on during the last week? are common questions that are frequently asked by a developer. They can be answered if one keeps track of who changes what in the source code. In this work, we present Replay, a tool that allows one to replay past changes as they happened at a fine-grained level, where a developer can watch what she has done or understand what her colleagues have done in past development sessions. With this tool, developers are able to not only understand what sequence of changes brought the system to a certain state (e.g., the introduction of a defect), but also deduce reasons for why her colleagues performed those changes. One of the applications of such a tool is also discovering the changes that broke the code of a developer.
Hybrid CPU Management for Adapting to the Diversity of Virtual Machines

As an important cornerstone for clouds, virtualization plays a vital role in building this emerging infrastructure. Virtual machines (VMs) with a variety of workloads may run simultaneously on a physical machine in the cloud platform. The scheduling algorithm used in Xen schedules virtual CPUs (VCPUs) of a VM asynchronously and guarantees the proportion of the CPU time allocated to the VM. This proportional sharing (PS) method is beneficial as it simplifies the implementation of CPU scheduling in the virtual machine monitor (VMM), and can deliver near-native performance for some workloads. However, when workloads in VMs are concurrent applications such as multithreaded programs with the synchronization operation, it has been demonstrated that this method in the VMM can reduce the performance, due to the negative impact of virtualization on synchronization. To address this issue, we present a hybrid scheduling framework for CPU management in the VMM to adapt to the diversity of VMs running simultaneously on a physical machine. We implement a hybrid scheduler based on Xen, and experimental results indicate that the hybrid CPU management method is feasible to mitigate the negative influence of virtualization on synchronization, and improve the performance of concurrent applications in the virtualized system, while maintaining the performance of high-throughput applications.
The Social Psychology of Perceiving Others Accurately

We are constantly forming impressions about those around us. Social interaction depends on understanding others’ behavior – assessing one another’s personality, emotions, thoughts and feelings, attitudes, deceptiveness, group memberships, and other personal characteristics through facial expressions, appearance, body language, voice, and spoken language. But how accurate are impressions and when does such accuracy matter? How is accuracy achieved, and are some people more successful at achieving it than others? This comprehensive overview summarizes classic and cutting-edge research on this fast-expanding field andwill be essential reading for anyone interested in the psychology of interpersonal perception. A wide range of experts in the field explore topics including age and gender effects, psychopathology, culture and ethnicity, workplaces and leadership, clinicians’ skills, empathy, metaperception, and training people to be more accurate in their perceptions of others.
Optimal Horizons for Inflation Targeting

In this paper we investigate the problem of selecting an optimal horizon for inflation targeting in the United Kingdom. Since there are two key ways of thinking about an optimal horizon, we look at optimal horizons for both of these interpretations. In addition, to see whether our results are robust in the face of model uncertainty, we compute optimal horizons for two different models with divergent structural and dynamic characteristics.
The geographies of urban density

As the world increasingly urbanizes, the imaginaries, conceptions and politics of urban density will become increasingly urgent for research, policy, practice and activism. Density is a keyword in the history of how the city has been conceived and understood, and is firmly back on the global urban agenda. However, we lack sustained studies of how the geographies of density have been defined, lived, and contested. This paper develops a topological approach to urban density, considers key ways in which density has been politicized, and examines an emerging research area that understands the life and politics of density as ‘intensive heterogeneities’.
Fast Approximation of Algebraic Reconstruction Methods for Tomography

Most reconstruction algorithms for transmission tomography can be subdivided in two classes: variants of filtered backprojection (FBP) and iterative algebraic methods. FBP is very fast and yields accurate results when a large number of projections are available, with high signal-to-noise ratio and a full angular range. Algebraic methods require much more computation time, yet they are more flexible in dealing with limited data problems and noise. In this paper, we propose an algorithm that combines the best of these two approaches: for a given linear algebraic method, a filter is computed that can be used within the FBP algorithm. The FBP reconstructions that result from using this filter strongly resemble the algebraic reconstructions and have many of their favorable properties, while the required reconstruction time is similar to standard-FBP. Based on a series of experiments, for both simulation data and experimental data, we demonstrate the merits of the proposed algorithm.
Attitude stabilization of a four-rotor aerial robot

In this paper, we propose a quaternion-based feedback control scheme for exponential attitude stabilization of a four-rotor vertical take-off and landing (VTOL) aerial robot known as the quadrotor aircraft. The proposed controller is based upon the compensation of the Coriolis and gyroscopic torques and the use of a PD/sup 2/ feedback structure, where the proportional action is in terms of the quaternion vector and the two derivative actions are in terms of the airframe angular velocity and the quaternion velocity. We also show that the model-independent PD controller, where the proportional action is in terms of the quaternion vector and the derivative action is in terms of the airframe angular velocity, without compensation of the Coriolis and gyroscopic torques, provides asymptotic stability for our problem. Simulation results are also provided to show the effectiveness of the proposed controller.
Multi core implementation of a trellis based syndrome decoder with adaptive complexity

This paper investigates the implementation of a trellis based syndrome decoder on symmetric multiprocessor (SMP) platforms. Two advantages of the proposed approach will be exposed: First, compared to conventional parallel Viterbi decoder implementations, the syndrome decoder achieves a higher parallel efficiency in terms of speedup on the SMP platform. This is realized by reducing the computational overhead of the parallel Viterbi algorithm implementation. Second, it offers an adaptive complexity, i.e. the number of decoding operations decreases with improving transmission conditions. This property can be exploited to reduce the average energy consumption of a radio receiver. Measurement results are shown for two SMP platforms: ARM's MPCore and Intel's Core i7.
The Moving Tablet Of The Eye

1. Informing contemporary research 1.1 Introduction 1.2 Scanning the way the eyes move 1.3 Modern eye movement measuring techniques 1.4 The moving tablet of the eye 2. Origins of eye movement research 2.1 Introduction 2.2 Binocular eye movements 2.3 Oculomotor anatomy and physiology 2.4 Internal motions of the eye 2.5 External motions of the eye 2.6 Afterimages 2.7 William Charles Wells 2.8 Erasmus Darwin's 'Zoonomia' 3. Nystagmus 3.1 Introduction 3.2 Visual vertigo 3.3 Wells on vertigo 3.4 Darwin on vertigo 3.5 Wells and Darwin 3.6 Purkinje and Flourens 3.7 Mach, Breuer and Crum Brown 3.8 James and Barany 3.9 Griffith and Dodge 4. Saccades and fixations 4.1 Introduction 4.2 Fixations 4.3 Saccades 4.4 Did Javal discover saccades? 4.5 Developments from Dodge 5. Visual motion illusions and eye movements 5.1 Introduction 5.2 Induced motion 5.3 Motion aftereffect 5.4 Visual vertigo 5.5 Autokinetic motion 5.6 Stroboscopic motion 5.7 Vection 5.8 Eye movements and visual motion 6. Perceptual stability and eye movements 6.1 Introduction 6.2 Stability during eye movements 6.3 Stability and saccades 6.4 Stability and fixation 7. Summary and conclusions 7.1 Introduction 7.2 Emergence of methods for measuring eye movements 7.3 Eye movement and eye position 7.4 Normal and abnormal eye movements 7.5 Sleep and wakefulness 7.6 Developmental trends 7.7 Perceptual and cognitive processes 7.8 Moving tablets - literature on eye movements
Drinfel'd twists and algebraic Bethe ansatz

We study representation theory of Drinfel'd twists, in terms of what we call F matrices, associated to finite dimensional irreducible modules of quantum affine algebras, and which factorize the corresponding (unitary) R matrices. We construct explicitly such factorizing F matrices for irreducible tensor products of the fundamental representations of the quantum affine algebra sl2 and its associated Yangian. We then apply these constructions to the XXX and XXZ quantum spins chains of finite length in the framework of the Algebraic Bethe Ansatz.
Effect of Oscillator Jitters on Distributed Energy Beamforming for Wireless Energy Transfer

In wireless energy transfer (WET), distributed energy beamforming is promising to solve energy scarcity problem while to alleviate potential health and safety problems. In this letter, we investigate the effect of oscillator jitters on distributed energy beamforming in a multiple-input-multiple-output (MIMO) WET system where both carrier frequency offset (CFO) and phase noise (PHN) are considered. We theoretically derive the ratio of energy loss because of oscillator jitters and its upper bound. It is found that the upper bound on the ratio of energy loss is not related with distributed MIMO channel and distributed energy beamforming. Simulation results demonstrate that the ratio of energy loss because of PHN and CFO increases almost linearly and quadratically with the increase of block duration, respectively.
Short-term Effects of a Physical Activity Intervention on Obesity and Aerobic Fitness of Adolescent Girls

Background: In the past two decades, physical activity has decreased during both childhood and adolescence, and particularly adolescence. It seems that schools are attractive settings in which to implement interventions designed in order to promote physical activity in children; but in Iranian students, few studies have evaluated the effects of such interventions on overweight and obese children. The aim of this study was to evaluate the effects of a short-term school-based physical activity on obesity and aerobic fitness in 12–14 years aged girls. Methods: This is a study with single group pretest and posttest design, in which 129 middle school girls in city of Isfahan were assessed based on preventive plan of inactivity in children at the Provincial Health Office. Variables, including weight, height, body mass index (BMI), waist-hip ratio (WHR), body fat percentage and aerobic power of subjects were measured using valid tests. Results: This study showed that subjects’ body fat percentage changed about 3.6% (37.74% pretest vs. 36.39% posttest), VO2 max changed 7.43% (29.72 pretest vs. 31.93 posttest), WHR changed 1.12% (0.89 pretest vs. 0.88 posttest), whereas BMI was changed 1.65% (27.80 pretest vs. 27.34 posttest). Findings also revealed that there were significant differences between fat percent, (P = 0.001) and VO2 max (P = 0.001) of subjects, but there was no difference between BMI of them in pre- and post-tests (P = 0.361). Conclusions: These results suggest that even a short-term exercise intervention may lead to positive changes in body fat percentage, WHR and aerobic fitness of overweight children. Therefore, school-based physical activity interventions can be an effective preventive strategy to control obesity and overweight in students.