Miracle-dz/UniFAR-FTUs huggingface dataset:
Design of a minimal protein oligomerization domain by a structural approach

Because of the simplicity and regularity of the α‐helical coiled coil relative to other structural motifs, it can be conveniently used to clarify the molecular interactions responsible for protein folding and stability. Here we describe the de novo design and characterization of a two heptad‐repeat peptide stabilized by a complex network of inter‐ and intrahelical salt bridges. Circular dichroism spectroscopy and analytical ultracentrifugation show that this peptide is highly α‐helical and 100% dimeric under physiological buffer conditions. Interestingly, the peptide was shown to switch its oligomerization state from a dimer to a trimer upon increasing ionic strength. The correctness of the rational design principles used here is supported by details of the atomic structure of the peptide deduced from X‐ray crystallography. The structure of the peptide shows that it is not a molten globule but assumes a unique, native‐like conformation. This de novo peptide thus represents an attractive model system for the design of a molecular recognition system.
"Out of the Parlors and into the Streets": The Changing Tactical Repertoire of the U.S. Women's Suffrage Movements

Little empirical research exists on major changes in the strategies and tactics of social movements, but some researchers argue that organizational readiness and political opportunities produce such changes. This article examines the circumstances that led some state woman suffrage movements to use a bold new tactic, the suffrage parade, beginning in the early twentieth century. An event-history analysis reveals that organizational readiness and political opportunities had little to do with change in the suffragists' strategic approach. Rather, the change occurred when movements consisted of a diverse assortment of organizations, when movement organizations were less centrally structured, when conflict existed among movement members, when movements engaged in fundraising, and when the suffragists had recently experienced significant political defeat. The model of tactical change presented here better explains the impetuses for such a shift than do earlier explanations.
MUAP Classification Based on Wavelet Packet and Fuzzy Clustering Technique

The present study compares several methods with regard to feature extraction and classification of motor unit action potentials (MUAPs) for electromyography (EMG) signal decomposition. The technique was applied to single-channel, short-period real myoelectric signals from normal subjects and artificially generated EMG recordings. All the real EMG recordings were made from the biceps brachii of healthy subjects during voluntary contraction at different force. A model, based on the phenomenon of EMG signal, is used to test the proposed technique on synthetic signals with known features. In contrast to previously developed methods based on EMG signal decomposition performance, our technique has two important distinctive characteristics. Firstly, we applied the local discriminant optimal wavelet packet for the feature extraction of MUAPs. Secondly, we optimized the MUAP classification result using the fuzzy C-means clustering technique to improve the EMG decomposition accuracy. Therefore, the method is substantially automatic and has been evaluated with synthetic and experimentally recorded myoelectric signals.
Prevalence of Delayed-Onset Posttraumatic Stress Disorder in Military Personnel: Is There Evidence for This Disorder? Results of a Prospective UK Cohort Study

Abstract Delayed-onset posttraumatic stress disorder (PTSD) is defined as onset at least 6 months after a traumatic event. This study investigates the prevalence of delayed-onset PTSD in 1397 participants from a two-phase prospective cohort study of UK military personnel. Delayed-onset PTSD was categorized as participants who did not meet the criteria for probable PTSD (assessed using the PTSD Checklist Civilian version) at phase 1 but met the criteria by phase 2. Of the participants, 3.5% met the criteria for delayed-onset PTSD. Subthreshold PTSD, common mental disorder (CMD), poor/fair self-reported health, and multiple physical symptoms at phase 1 and the onset of alcohol misuse or CMD between phases 1 and 2 were associated with delayed-onset PTSD. Delayed-onset PTSD exists in this UK military sample. Military personnel who developed delayed-onset PTSD were more likely to have psychological ill-health at an earlier assessment, and clinicians should be aware of the potential comorbidity in these individuals, including alcohol misuse. Leaving the military or experiencing relationship breakdown was not associated.
Intrinsic galaxy alignments from the 2SLAQ and SDSS surveys: luminosity and redshift scalings and implications for weak lensing surveys

Correlations between intrinsic shear and the density field on large scales, a potentially important contaminant for cosmic shear surveys, have been robustly detected at low redshifts with bright galaxies in Sloan Digital Sky Survey (SDSS) data. Here we present a more detailed characterization of this effect, which can cause anticorrelations between gravitational lensing shear and intrinsic ellipticity (GI correlations). This measurement uses 36 278 luminous red galaxies (LRGs) from the SDSS spectroscopic sample with 0.15 3σ detections of the effect on large scales (up to 60 h−1 Mpc) for all galaxy subsamples within the SDSS LRG sample; for the 2SLAQ sample, we find a 2σ detection for a bright subsample, and no detection for a fainter subsample. Fitting formulae are provided for the scaling of the GI correlations with luminosity, transverse separation and redshift (for which the 2SLAQ sample, while small, provides crucial constraints due to its longer baseline in redshift). We estimate contamination in the measurement of σ8 for future cosmic shear surveys on the basis of the fitted dependence of GI correlations on galaxy properties. We find contamination to the power spectrum ranging from −1.5 per cent (optimistic) to −33 per cent (pessimistic) for a toy cosmic shear survey using all galaxies to a depth of R = 24 using scales l ≈ 500, though the central value of predicted contamination is −6.5 per cent. This corresponds to a bias in σ8 of Δσ8 = −0.004 (optimistic), −0.02 (central) or −0.10 (pessimistic). We provide a prescription for inclusion of this error in cosmological parameter estimation codes. The principal uncertainty is in the treatment of the L ≤ L blue galaxies, for which we have no detection of the GI signal, but which could dominate the GI contamination if their GI amplitude is near our upper limits. Characterization of the tidal alignments of these galaxies, especially at redshifts relevant for cosmic shear, should be a high priority for the cosmic shear community.
pathVar: a new method for pathway-based interpretation of gene expression variability

Identifying the pathways that control a cellular phenotype is the first step to building a mechanistic model. Recent examples in developmental biology, cancer genomics, and neurological disease have demonstrated how changes in the variability of gene expression can highlight important genes that are under different degrees of regulatory control. Simple statistical tests exist to identify differentially-variable genes; however, methods for investigating how changes in gene expression variability in the context of pathways and gene sets are under-explored. Here we present pathVar, a new method that provides functional interpretation of gene expression variability changes at the level of pathways and gene sets. pathVar is based on a multinomial exact test, or an asymptotic Chi-squared test as a more computationally-efficient alternative. The method can be used for gene expression studies from any technology platform in all biological settings either with a single phenotypic group, or two-group comparisons. To demonstrate its utility, we applied the method to a diverse set of diseases, species and samples. Results from pathVar are benchmarked against analyses based on average expression and two methods of GSEA, and demonstrate that analyses using both statistics are useful for understanding transcriptional regulation. We also provide recommendations for the choice of variability statistic that have been informed through analyses on simulations and real data. Based on the datasets selected, we show how pathVar can be used to gain insight into expression variability of single cell versus bulk samples, different stem cell populations, and cancer versus normal tissue comparisons.
Progressive Public Relations, Sweatshops, and the Net

The anti-Nike sweatshop movement represents an emerging form of conscious, civic consumerism. In the short term, activists, many of them U.S. university students, have been successful at politicizing the decisions of marketing and sports establishments at major universities by focusing media attention on the production-consumption chain of university merchandise through sit-ins and demonstrations. The public reaction of Nike’s CEO, Phil Knight, to these events vaulted the students’ concerns into the mainstream media. Building on lessons from the South African divestment effort, students recognize that institutions to which they pay tuition can be used to make institutional and political change. In addition, activists have also framed the sweatshop issue to their contemporaries in terms of individual consumer choice—a mark of personal identity politics—and put their creativity to work by staging unorthodox “sweatshop fashion shows” at Niketowns, GAP stores, and Abercrombie and Fitch. This article has two objectives. First, it tracks the role of these public relations professionals in shaping and defining the sweatshop awareness movement, and second, it examines the campaign against Nike as a window into an emerging form of political activism suited to computer-savvy youth, lifestyle politics, global interdependency, and consumer choice. Linked by e-mail, the Internet, and common symbols, these political actors, mostly under the age of 30, are becoming increasingly visible players in the media debate about transnational corporate responsibility in the global economy.
Habilitation Psychologique: Validation dune Mesure en Langue Franaise

This article aims at validating a French measure of psychological empowerment at work, following Spreitzer’s (1995) fourdimensional conceptualization. To do so, this instrument was administered to three samples of Canadian workers. Study 1 (N = 120) explored the factorial structure of the French instrument and verified its psychometric properties. Then, Study 2 was conducted with two independent samples (N = 222, N = 248) to confirm the factorial structure of the instrument and to verify its nomological validity. Results indicate that the French instrument has a factorial structure consistent with Spreitzer’s (1995) conceptualization and that this measure is correlated with antecedents and outcomes included in its nomological network.
EFFECTS OF HOST SOCIALITY ON ECTOPARASITE POPULATION BIOLOGY

Theory predicts a positive relationship between parasite infection intensity and host density. However, this generalization is complicated in natural systems by differences in life history among parasite taxa, e.g., transmissibility. Accordingly, predictions relating host density to parasite load should be specific to each parasite taxon. To illustrate this, we studied parasites that differed greatly in life history in the context of the Galapagos hawk's (Buteo galapagoensis) variably cooperative mating system. Two louse (Phthiraptera) species were collected: Colpocephalum turbinatum (Amblycera), with 53 host species, and Degeeriella regalis (Ischnocera), with 10 host species, although B. galapagoensis was the only known Galapagos host. Sixty territorial adult male hawks from 26 groups of 1–6 males were quantitatively sampled for lice. Average abundance and intensity of C. turbinatum but not D. regalis were significantly larger in large groups of hawks than small groups. Males from the same polyandrous group harbored significantly correlated abundances of C. turbinatum but not D. regalis. Prevalence, average abundance, and intensity of C. turbinatum were significantly higher than D. regalis. These are the first results to demonstrate significant differences in a suite of population responses between these louse suborders in the context of host sociality.
Common Factors in Christian Women's Preferences for Support When Dealing with a Spouse's Sexually Addictive or Compulsive Behaviors: The C.A.V.E.D. Theory

While research exists on many issues relating to wives of sex addicts, there is a void in the literature regarding the kinds of support women find most beneficial when dealing with a spouse's sexually addictive or compulsive behavior. Using a qualitative, grounded theory methodology, 22 Christian women from Canada and the United States were interviewed to identify the types of support they found most beneficial when dealing with this multifaceted problem in a marriage. Additionally, the common factors of support which are summarized by the acronym C.A. V.E. D. (Connection, Advocacy, Validation, Education and Direction) emerged from the analysis of the interviews.
Oxalate-curcumin–based probe for micro- and macroimaging of reactive oxygen species in Alzheimer’s disease

Significance It has long been speculated that Alzheimer’s disease (AD) is tightly associated with oxidative stress and high concentrations of reactive oxygen species (ROS) in the brain. However, comprehensive evidence from living beings is rare. In this report, inspired by the “chemistry of glow stick,” we designed oxalate-curcumin–based imaging probes to provide evidence of high ROS concentrations in AD brains in animal studies at micro- and macrolevels. At the microlevel, our imaging method identified “active” amyloid beta plaques and cerebral amyloid angiopathy via dual-color two-photon imaging. At the macrolevel, our probe could detect relatively high ROS concentrations in AD brains using near-IR fluorescence imaging. We believe that our method will be an indispensable tool for investigating ROS in living beings. Alzheimer’s disease (AD) is an irreversible neurodegenerative disorder that has a progression that is closely associated with oxidative stress. It has long been speculated that the reactive oxygen species (ROS) level in AD brains is much higher than that in healthy brains. However, evidence from living beings is scarce. Inspired by the “chemistry of glow stick,” we designed a near-IR fluorescence (NIRF) imaging probe, termed CRANAD-61, for sensing ROS to provide evidence at micro- and macrolevels. In CRANAD-61, an oxalate moiety was utilized to react with ROS and to consequentially produce wavelength shifting. Our in vitro data showed that CRANAD-61 was highly sensitive and rapidly responsive to various ROS. On reacting with ROS, its excitation and emission wavelengths significantly shifted to short wavelengths, and this shifting could be harnessed for dual-color two-photon imaging and transformative NIRF imaging. In this report, we showed that CRANAD-61 could be used to identify “active” amyloid beta (Aβ) plaques and cerebral amyloid angiopathy (CAA) surrounded by high ROS levels with two-photon imaging (microlevel) and to provide relative total ROS concentrations in AD brains via whole-brain NIRF imaging (macrolevel). Lastly, we showed that age-related increases in ROS levels in AD brains could be monitored with our NIRF imaging method. We believe that our imaging with CRANAD-61 could provide evidence of ROS at micro- and macrolevels and could be used for monitoring ROS changes under various AD pathological conditions and during drug treatment.
Measuring and Advancing Experimental Design Ability in an Introductory Course without Altering Existing Lab Curriculum

Introductory biology courses provide an important opportunity to prepare students for future courses, yet existing cookbook labs, although important in their own way, fail to provide many of the advantages of semester-long research experiences. Engaging, authentic research experiences aid biology students in meeting many learning goals. Therefore, overlaying a research experience onto the existing lab structure allows faculty to overcome barriers involving curricular change. Here we propose a working model for this overlay design in an introductory biology course and detail a means to conduct this lab with minimal increases in student and faculty workloads. Furthermore, we conducted exploratory factor analysis of the Experimental Design Ability Test (EDAT) and uncovered two latent factors which provide valid means to assess this overlay model’s ability to increase advanced experimental design abilities. In a pre-test/post-test design, we demonstrate significant increases in both basic and advanced experimental design abilities in an experimental and comparison group. We measured significantly higher gains in advanced experimental design understanding in students in the experimental group. We believe this overlay model and EDAT factor analysis contribute a novel means to conduct and assess the effectiveness of authentic research experiences in an introductory course without major changes to the course curriculum and with minimal increases in faculty and student workloads.
Blended Game-Based Learning Environments: Extending a Serious Game into a Learning Content Management System

Serious games have recognized potential as a means to tackle many challenges in education, ranging from stimulating increased learner motivation, to transferring challenging concepts in a novel and engaging form. They are commonly shown to work most effectively in blended approaches to learning, whereby the game plays a core role in a wider pedagogic approach, often based around an experiential or exploratory model. In this paper, we explore how the integration of a serious game, and more generally gaming paradigms, can be extended to a learning content management system (LCMS) to support a blended and holistic approach to their use in education. Through a case study within the EU-Funded Adaptive Learning via Intuitive/Interactive, Collaborative and Emotional Systems (ALICE) project, we demonstrate a technical integration of a gaming engine with a proprietary LCMS, and discuss the broader pedagogic benefits of such an approach. In particular, we note how this method can support an 'intuitive guided' or scaffolded approach to learning, where the learner is given the potential to explore a non-linear learning environment, whilst scaffolding and blending provides the guidance towards ensuring targeted learning objectives are met.
HMDB 3.0—The Human Metabolome Database in 2013

The Human Metabolome Database (HMDB) (www.hmdb.ca) is a resource dedicated to providing scientists with the most current and comprehensive coverage of the human metabolome. Since its first release in 2007, the HMDB has been used to facilitate research for nearly 1000 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 3.0) has been significantly expanded and enhanced over the 2009 release (version 2.0). In particular, the number of annotated metabolite entries has grown from 6500 to more than 40 000 (a 600% increase). This enormous expansion is a result of the inclusion of both ‘detected’ metabolites (those with measured concentrations or experimental confirmation of their existence) and ‘expected’ metabolites (those for which biochemical pathways are known or human intake/exposure is frequent but the compound has yet to be detected in the body). The latest release also has greatly increased the number of metabolites with biofluid or tissue concentration data, the number of compounds with reference spectra and the number of data fields per entry. In addition to this expansion in data quantity, new database visualization tools and new data content have been added or enhanced. These include better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy and better, more interactive pathway maps. This article describes these enhancements to the HMDB, which was previously featured in the 2009 NAR Database Issue. (Note to referees, HMDB 3.0 will go live on 18 September 2012.).
Chronic alcohol self-administration in monkeys shows long-term quantity/frequency categorical stability.

BACKGROUND The current criteria for alcohol use disorders (AUDs) do not include consumption (quantity/frequency) measures of alcohol intake, in part due to the difficulty of these measures in humans. Animal models of ethanol (EtOH) self-administration have been fundamental in advancing our understanding of the neurobiological basis of AUD and can address quantity/frequency measures with accurate measurements over prolonged periods of time. The nonhuman primate model of voluntary oral alcohol self-administration has documented both binge drinking and drinking to dependence and can be used to test the stability of consumption measures over time. METHODS Here, an extensive set of alcohol intakes (g/kg/d) was analyzed from a large multi-cohort population of Rhesus (Macaca mulatta) monkeys (n = 31). Daily EtOH intake was uniformly distributed over chronic (12 months) access for all animals. RESULTS Underlying this distribution of intakes were subpopulations of monkeys that exhibited distinctive clustering of drinking patterns, allowing us to categorically define very heavy drinking (VHD), heavy drinking (HD), binge drinking (BD), and low drinking (LD). These categories were stable across the 12 months assessed by the protocol, but exhibited fluctuations when examined at shorter intervals. CONCLUSIONS The establishment of persistent drinking categories based on quantity/frequency suggests that consumption variables can be used to track long-term changes in behavioral, molecular, or physiochemical mechanisms related to our understanding of diagnosis, prevention, intervention, and treatment efficacies.
Optimization Models and Algorithms for Joint Uplink/Downlink UMTS Radio Network Planning With SIR-Based Power Control

Universal mobile telecommunication system (UMTS) networks should be deployed according to cost-effective strategies that optimize a cost objective and satisfy target quality-of-service (QoS) requirements. In this paper, we propose novel algorithms for joint uplink/downlink UMTS radio planning with the objective of minimizing total power consumption in the network. Specifically, we define two components of the radio planning problem: 1) continuous-based site placement and 2) integer-based site selection. In the site-placement problem, our goal is to find the optimal locations of UMTS base stations (BSs) in a certain geographic area with a given user distribution to minimize the total power expenditure such that a satisfactory level of downlink and uplink signal-to-interference ratio (SIR) is maintained with bounded outage constraints. We model the problem as a constrained optimization problem with SIR-based uplink and downlink power control scheme. An algorithm is proposed and implemented using pattern search techniques for derivative-free optimization with augmented Lagrange multiplier estimates to support general constraints. In the site-selection problem, we aim to select the minimum set of BSs from a fixed set of candidate sites that satisfies quality and outage constraints. We develop an efficient elimination algorithm by proposing a method for classifying BSs that are critical for network coverage and QoS. Finally, the problem is reformulated to take care of location constraints whereby the placement of BSs in a subset of the deployment area is not permitted due to, e.g., private property limitations or electromagnetic radiation constraints. Experimental results and optimal tradeoff curves are presented and analyzed for various scenarios.