Miracle-dz/UniFAR-FTUs huggingface dataset:
Testing membrane protein native state discrimination by FACTSMEM

The recently developed implicit membrane model FACTSMEM is tested for its ability of native state discrimination of transmembrane (TM) proteins. Five TM proteins are included in the test, and 450 decoys generated by the structure prediction program ROSETTA are considered. The performance of FACTSMEM is evaluated via relative potential energies and Z-scores. The results are compared to the ones obtained with the membrane models IMM1, GBSAIM, GBSW and HDGB according to the benchmark of Yuzlenko and Lazaridis published in their paper “Membrane Protein Native State Discrimination by Implicit Membrane Models”. However, it was not possible to reproduce the results of Yuzlenko and Lazaridis when using the same membrane models and simulation specifications as in their work. Therefore, it is not possible to make any conclusions with regard to the ability of FACTSMEM (and the other implicit membrane models) to discriminate the native state of membrane proteins. The reason for this are structural problems inherent to the decoys. Therefore, to assess the performance of FACTSMEM, this work should be repeated using another set of decoys.
ProtoMap: automatic classification of protein sequences and hierarchy of protein families

The ProtoMap site offers an exhaustive classification of all proteins in the SWISS-PROT database, into groups of related proteins. The classification is based on analysis of all pairwise similarities among protein sequences. The analysis makes essential use of transitivity to identify homologies among proteins. Within each group of the classification, every two members are either directly or transitively related. However, transitivity is applied restrictively in order to prevent unrelated proteins from clustering together. The classification is done at different levels of confidence, and yields a hierarchical organization of all proteins. The resulting classification splits the protein space into well-defined groups of proteins, which are closely correlated with natural biological families and superfamilies. Many clusters contain protein sequences that are not classified by other databases. The hierarchical organization suggested by our analysis may help in detecting finer subfamilies in families of known proteins. In addition it brings forth interesting relationships between protein families, upon which local maps for the neighborhood of protein families can be sketched. The ProtoMap web server can be accessed at http://www.protomap. cs.huji. ac.il
Building protest online: engagement with the digitally networked #not1more protest campaign on Twitter

Abstract This article examines engagement with digitally networked, politically contentious actions. Maintaining engagement over time is a key challenge for social movements attempting to network digitally. This article argues that proximity serves as a condition to address this challenge, because it configures the personal networks upon which transmission depends. This is a paradox of digital activism: it has the capacity to transcend barriers; however, proximity is essential for sustaining relations over time. Examining Twitter data from the #not1more protest campaign against immigrant deportations in the United States, quantitative and social network analyses show a differentiated development of engagement, which results in a particular geographical configuration with the following attributes. First, there is a robust and connected backbone of core organizers and activists located in particular major cities. Second, local groups engage with the campaign with direct actions in other cities. Third, a large and transitory contingent of geographically dispersed users direct attention to the campaign. We conclude by elaborating how this geographically differentiated configuration helps to sustain engagement with digitally networked action.
Antiarrhythmic Effects of Ranolazine in a Guinea Pig in Vitro Model of Long-QT Syndrome

Prolongation of the QT interval of the ECG is associated with increased risk of torsades de pointes ventricular tachycardia. Ranolazine, a novel antianginal agent, is reported to decrease the delayed rectifier potassium current, IKr, and to increase action potential duration (APD) and the QT interval. However, ranolazine is also reported to reduce late sodium current (late INa), a depolarizing current that contributes to prolongation of the plateau of the ventricular action potential. We hypothesized that ranolazine would decrease APD and the occurrence of arrhythmias when late INa is increased. Therefore, we measured the effects of ranolazine alone and in the presence of anemone toxin (ATX)-II, whose action mimics the sodium channelopathy associated with long-QT3 syndrome, on epicardial monophasic action potentials and ECGs recorded from guinea pig isolated hearts. Ranolazine (0.1–50 μM) prolonged monophasic APD at 90% repolarization (MAPD90) by up to 22% but did not cause either early afterdepolarizations (EADs) or ventricular tachycardia (VT). ATX-II (1–20 nM) markedly increased APD and caused EADs and VT. Ranolazine (5–30 μM) significantly attenuated increases in MAPD90 and reduced episodes of EADs and VT produced by ATX-II. Ranolazine also attenuated the synergistic effect of MAPD90 increase caused by combinations of ATX-II and blockers of IK [E-4031; 1-[2-(6-methyl-2-pyridyl)ethyl]-4-methylsulfonylaminobenzoyl)piperidine]. Thus, although ranolazine alone prolonged APD, it reduced APD and ventricular arrhythmias caused by agents that increased late INa and decreased IK.
Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences†

REPs are highly repeated intergenic palindromic sequences often clustered into structures called BIMEs including two individual REPs separated by short linker of variable length. They play a variety of key roles in the cell. REPs also resemble the sub-terminal hairpins of the atypical IS200/605 family of insertion sequences which encode Y1 transposases (TnpAIS200/IS605). These belong to the HUH endonuclease family, carry a single catalytic tyrosine (Y) and promote single strand transposition. Recently, a new clade of Y1 transposases (TnpAREP) was found associated with REP/BIME in structures called REPtrons. It has been suggested that TnpAREP is responsible for REP/BIME proliferation over genomes. We analysed and compared REP distribution and REPtron structure in numerous available E. coli and Shigella strains. Phylogenetic analysis clearly indicated that tnpAREP was acquired early in the species radiation and was lost later in some strains. To understand REP/BIME behaviour within the host genome, we also studied E. coli K12 TnpAREP activity in vitro and demonstrated that it catalyses cleavage and recombination of BIMEs. While TnpAREP shared the same general organization and similar catalytic characteristics with TnpAIS200/IS605 transposases, it exhibited distinct properties potentially important in the creation of BIME variability and in their amplification. TnpAREP may therefore be one of the first examples of transposase domestication in prokaryotes.
Trainees’ experience of cognitive behavioural therapy training: a mixed methods systematic review

Abstract Research in the field of cognitive behavioural therapy (CBT) has primarily focused on the acquisition and development of skills and competence. Little is known regarding the experience of training from trainees’ perspectives. This systematic review aimed to review and critique the research conducted on the experience of CBT training. Four electronic databases were searched for published studies reporting on the experience of CBT training. Thirteen articles were selected based on pre-determined inclusion and exclusion criteria and were assessed for quality using the Quality Assessment Tool for Studies with Diverse Designs (QATSDD; Sirriyeh et al., 2012). Due to the lack of consistency in the study designs and outcome measures used, a narrative synthesis of the findings was conducted. Findings were categorized within three themes for synthesis: ‘experience of benefit’, ‘internal processes of engagement’ and ‘external influences on engagement’. Overall, this review was able to draw conclusions regarding the experiences of aspects of CBT training from relatively good quality research. However, the review also highlights the lack of studies exploring specific hypotheses regarding the experience of training.
Exploratory analysis of brain connectivity with ICA

Covariance-based methods of exploration of functional connectivity of the brain from functional magnetic resonance imaging (fMRI) experiments, such as principal component analysis (PCA) and structural equation modeling (SEM), require a priori knowledge such as an anatomical model to infer functional connectivity. In this research, a hybrid method, combining independent component analysis (ICA) and SEM, which is capable of deriving functional connectivity in an exploratory manner without the need of a prior model is introduced. The spatial ICA (SICA) derives independent neural systems or sources involved in task-related brain activation, while an automated method based on the SEM finds the structure of the connectivity among the elements in independent neural systems. Unlike second-order approaches used in earlier studies, the task-related neural systems derived from the ICA provide brain connectivity in the complete statistical sense. The use and efficacy of this approach is illustrated on two fMRI datasets obtained from a visual task and a language reading task.
Start-up dynamics of TCP's congestion control and avoidance schemes

Over the years, Transmission Control Protocol (TCP) in the Internet protocol (IP) suite has become the most widely used form of networking between computers. With the recent developments in high-speed networking and applications that use TCP, performance issues in TCP are of increasing interest and importance. The performance (e.g. throughput, number of dropped packets, etc.) during the start-up epoch is of particular concern, because an increasing number of applications use TCP for short data transfers, which complete before TCP even settles into its steady-state behavior. During this initial epoch, as TCP hunts for reasonable operating parameters, its congestion control and avoidance schemes display interesting transient dynamics that affect the performance. One reasonable approach to examining such performance issues is to study and understand the dynamics of current TCP implementations. Thus, this thesis makes observations on the subtle congestion control and avoidance dynamics of one particular implementation of TCP, U.C. Berkeley's BSD Net/2 release, with specific attention to the start-up epoch. Based on these observations, this thesis proposes some simple changes to this implementation to improve its performance during the start-up epoch. Thesis Supervisor: Dr. David D. Clark Title: Senior Research Scientist, Laboratory for Computer Science ·I___I_*IPCI___·_U___I
Analysis of scheduling algorithms that provide 100% throughput in input-queued switches

Internet routers frequently use a crossbar switch to interconnect linecards. The crossbar switch is scheduled using an algorithm that picks a new crossbar configuration every cycle. Several scheduling algorithms have been shown to guarantee 100% throughput under a variety of traffic patterns. The first such algorithm was the maximum weight matching (MWM) algorithm in which the weight is the sum of the occupan-cies of the queues. We explore whether alternative weight functions, such as using the sum of the square of the occupancies, leads to stronger or weaker stability. The first result of this paper is that a broad class of weight functions give rise to strong stability, including the sum of the squares, the sum of the cubes and so on. A counter-intuitive result, indicating a limitation of the Lyapunov method, is that the sum of the square root of the occupancies is not included in this class, even though simulation suggests that the resulting average delay is lower than for the other functions. We also consider the simpler , , randomized scheduling algorithm (TASS) proposed by Tassiulas. We show similar results for different weight functions as for MWM. We finally show that TASS gives 100% throughput when the weights are noisy, or out-of-date.
How Corrupt Are Universities? Audit Culture, Fraud Prevention, and the Big Four Accountancy Firms

Corruption narratives, like witchcraft accusations, offer a lens for analyzing social relations, economic interests, and hidden structures of power. Developing this theme, I examine discourses of corruption in the context of growing concerns about fraud prevention and anti-corruption in universities. Moving beyond critiques of university administrations as bureaucratic, self-serving entities whose interests are increasingly antithetical to the academic mission of the university, I ask, What is corruption in academia and how does this assumed problem relate to academic capitalism and the rise of audit culture? The empirical context for my study is the extraordinary increase in institutionalized fraud-prevention programs, particularly those offered by the “Big Four” accountancy firms. Taking as my case study the introduction of a whistle-blower hotline at one Australasian university, I examine the politics and interests behind such schemes. The increasing involvement of accountancy firms in nonauditing work, including anti-corruption services, illustrates how corruption narratives operate as market-making strategies. I examine how commercialization, risk management, and auditing proliferate anti-corruption initiatives and how audit firms collude in the risk and corruption that they claim to ameliorate. I conclude by assessing the implications for the anthropology of corruption of the growing penetration of universities by an increasingly commercially focused tax industry that, some argue, cannot even be trusted to regulate itself.
SEASONAL CHANGES AND MORNING BLOOD PRESSURE SURGE. WHICH ROLE FOR OUTDOOR AND INDOOR AIR TEMPERATURE?: PP.29.147

Objective: Important climate related variations of clinic and ambulatory blood pressure (BP) have been repeatedly reported. However, notwithstanding the wide use of indoor climate control systems, specially in winter, no information is available regarding the role of air temperature values measured proximally to the patient, in particular when focussing on specific components of the 24 h BP profile, such as the morning BP surge (MBPS). Design and Methods: To investigate whether MBPS is affected by outdoor air temperature or by the air temperature measured proximally to the patient, 2120 hypertensives underwent 24 h ambulatory blood pressure (ABP) monitoring with a battery-powered “HOBO” temperature data logger fitted to the carrying pouch of the ABP monitor. Predictors of MBPS were investigated with a multivariate stepwise regression model including age, gender, body mass index, office systolic BP, 24 h average ABP, mean 24 h outdoor atmospheric pressure and mean 24 h air temperature measured both outdoor and by HOBO as independent variables. Results: Stepwise multiple regression analysis carried out in the 1728 subjects included in the final analysis selected outdoor air temperature(beta = -0.09;p < 0.0001), 24 h ABP(beta = -0.72;p < 0.0001), and age(beta = -0.06;p < 0.002) as negative independent predictors of MBPS, with systolic office BP selected as a positive independent predictor (beta = 1,04;p < 0.0001)(r = 0.610); no significant effect of HOBO air temperature was observed. When subjects were stratified according to age, the effect on MBPS of outdoor air temperature was detectable in subjects >65 yrs (beta = -0.086; p < 0.002), whereas the only determinants of MBPS in subjects < 50 yrs were office SBP (positive) and 24 h average SBP(negative). Conclusions: These results confirm and extend previous observation on the occurrence of seasonal changes in 24 h BP profiles, by providing new evidence that only air temperature measured outdoor affects BP morning surge in addition to office BP, 24 h ABP and age, whereas no role appears to be played by air temperature measured proximally to the patient. The clinical implications of these findings for BP control would need to be further tested by ad hoc studies.
Correlation between Cognitive Deficits and Tensor Magnetic Resonance Parameters in Patients with Chronic Diffuse Axonal Injury

Background: The apparent diffusion coefficient (ADC) values and the fractional anisotropy (FA) values calculated from diffusion tensor imaging (DTI) in the acute stage of diffuse axonal injury (DAI) are mainly used for prediction of prognosis. However, neuropsychological outcome correlates more closely with magnetic resonance imaging (MRI) findings from the chronic stage than with those obtained during the acute phase. The purpose of the study was to design a protocol that will assess the spread of neural deficit and provide an accurate prognosis for patients with DAI. Methods: We compared ADC values and FA values calculated from DTI of the anterior and posterior corpus callosum in four patients (mean ± SD: 24.0 ± 4.5 years) with DAI and cognitive disorders with those of 10 normal control subjects (23.3 ± 1.3 years). All patients had chronic-stage DAI with no significant MRI abnormality. Although they maintained self-care task, they were unable to adapt to social life because of cognitive disorders.
Fast and sensitive mapping of bisulfite-treated sequencing data

MOTIVATION Cytosine DNA methylation is one of the major epigenetic modifications and influences gene expression, developmental processes, X-chromosome inactivation, and genomic imprinting. Aberrant methylation is furthermore known to be associated with several diseases including cancer. The gold standard to determine DNA methylation on genome-wide scales is 'bisulfite sequencing': DNA fragments are treated with sodium bisulfite resulting in the conversion of unmethylated cytosines into uracils, whereas methylated cytosines remain unchanged. The resulting sequencing reads thus exhibit asymmetric bisulfite-related mismatches and suffer from an effective reduction of the alphabet size in the unmethylated regions, rendering the mapping of bisulfite sequencing reads computationally much more demanding. As a consequence, currently available read mapping software often fails to achieve high sensitivity and in many cases requires unrealistic computational resources to cope with large real-life datasets. RESULTS In this study, we present a seed-based approach based on enhanced suffix arrays in conjunction with Myers bit-vector algorithm to efficiently extend seeds to optimal semi-global alignments while allowing for bisulfite-related substitutions. It outperforms most current approaches in terms of sensitivity and performs time-competitive in mapping hundreds of millions of sequencing reads to vertebrate genomes. AVAILABILITY The software segemehl is freely available at http://www.bioinf. uni-leipzig.de/Software/segemehl.
Factors Influencing Seatbelt Utilization in Louisiana and Strategies to Improve Usage Rate

Seat belts are credited with saving thousands of lives each year, yet a significant portion of the US population (13%) does not use a seat belt every time they are in a moving vehicle. A majority of states, including Louisiana, have belt-use rates below the national average (87%). National as well as state data show that, as belt use nears 90%, it is harder to increase belt use among the low-use populations, who are most at-risk for fatal or serious injury crashes. Individuals in low-use populations are traditionally described as groups sharing certain demographic characteristics (e.g., males aged 18-34) and lifestyle factors (e.g., unmarried, lower socioeconomic position, pickup truck drivers, etc.). Previous efforts to increase seat belt use among low-use populations have had limited success. For the most part, states have relied on legislative (e.g., primary seat belt laws) and enforcement strategies (e.g., Click-it-or-Ticket [CIOT], high-visibility enforcement, etc.) to increase belt use; however, in order to see a meaningful increase in seat belt use among low-use groups, individuals making up these groups must change their behavior. At the individual level, TECHSUMMARYApril 2017 State Project No. 30001662 / LTRC Project No. 14-2SA
Correlating automated and human assessments of machine translation quality

We describe a large-scale investigation of the correlation between human judgments of machine translation quality and the automated metrics that are increasingly used to drive progress in the field. We compare the results of 124 human evaluations of machine translated sentences to the scores generated by two automatic evaluation metrics (BLEU and NIST). When datasets are held constant or file size is sufficiently large, BLEU and NIST scores closely parallel human judgments. Surprisingly, this was true even though these scores were calculated using just one human reference. We suggest that when human evaluators are forced to make decisions without sufficient context or domain expertise, they fall back on strategies that are not unlike determining n-gram precision.
Not All Perceptual Gaps Were Created Equal: Explicating the Third-Person Perception (TPP) as a Cognitive Fallacy

Explicating the third-person perception (TPP) as a cognitive fallacy in the process of comparative social judgment of media effects, we propose that not all self–other perceptual gaps in media effects should be considered as TPP. When there is reasonably valid and accurate information regarding self vis-à-vis others on media consumption and vulnerability to media influence, the associated self–other gaps in media effects are not exaggerations, hence, not TPP. TPP results from cognitive biases in information retrieval and application in the process of comparative social judgments. Such biases are in the forms of self-other information differential, assimilation, contrast, and anchoring effects. Caveats in interpretation of extant evidence and implications for future TPP research are discussed.
Systematic Phonics Instruction Helps Students Learn to Read: Evidence from the National Reading Panel’s Meta-Analysis

A quantitative meta-analysis evaluating the effects of systematic phonics instruction compared to unsystematic or no-phonics instruction on learning to read was conducted using 66 treatment-control comparisons derived from 38 experiments. The overall effect of phonics instruction on reading was moderate, d = 0.41. Effects persisted after instruction ended. Effects were larger when phonics instruction began early (d = 0.55) than after first grade (d = 0.27). Phonics benefited decoding, word reading, text comprehension, and spelling in many readers. Phonics helped low and middle SES readers, younger students at risk for reading disability (RD), and older students with RD, but it did not help low achieving readers that included students with cognitive limitations. Synthetic phonics and larger-unit systematic phonics programs produced a similar advantage in reading. Delivering instruction to small groups and classes was not less effective than tutoring. Systematic phonics instruction helped children learn to read better than all forms of control group instruction, including whole language. In sum, systematic phonics instruction proved effective and should be implemented as part of literacy programs to teach beginning reading as well as to prevent and remediate reading difficulties.