Miracle-dz/UniFAR-FTUs huggingface dataset:
The Intracellular DNA Sensor IFI16 Gene Acts as Restriction Factor for Human Cytomegalovirus Replication

Human interferon (IFN)-inducible IFI16 protein, an innate immune sensor of intracellular DNA, modulates various cell functions, however, its role in regulating virus growth remains unresolved. Here, we adopt two approaches to investigate whether IFI16 exerts pro- and/or anti-viral actions. First, the IFI16 gene was silenced using specific small interfering RNAs (siRNA) in human embryo lung fibroblasts (HELF) and replication of DNA and RNA viruses evaluated. IFI16-knockdown resulted in enhanced replication of Herpesviruses, in particular, Human Cytomegalovirus (HCMV). Consistent with this, HELF transduction with a dominant negative form of IFI16 lacking the PYRIN domain (PYD) enhanced the replication of HCMV. Second, HCMV replication was compared between HELFs overexpressing either the IFI16 gene or the LacZ gene. IFI16 overexpression decreased both virus yield and viral DNA copy number. Early and late, but not immediate-early, mRNAs and proteins were strongly down-regulated, thus IFI16 may exert its antiviral effect by impairing viral DNA synthesis. Constructs with the luciferase reporter gene driven by deleted or site-specific mutated forms of the HCMV DNA polymerase (UL54) promoter demonstrated that the inverted repeat element 1 (IR-1), located between −54 and −43 relative to the transcription start site, is the target of IFI16 suppression. Indeed, electrophoretic mobility shift assays and chromatin immunoprecipitation demonstrated that suppression of the UL54 promoter is mediated by IFI16-induced blocking of Sp1-like factors. Consistent with these results, deletion of the putative Sp1 responsive element from the HCMV UL44 promoter also relieved IFI16 suppression. Together, these data implicate IFI16 as a novel restriction factor against HCMV replication and provide new insight into the physiological functions of the IFN-inducible gene IFI16 as a viral restriction factor.
Assaying Locomotor Activity to Study Circadian Rhythms and Sleep Parameters in Drosophila

Most life forms exhibit daily rhythms in cellular, physiological and behavioral phenomena that are driven by endogenous circadian (≡24 hr) pacemakers or clocks. Malfunctions in the human circadian system are associated with numerous diseases or disorders. Much progress towards our understanding of the mechanisms underlying circadian rhythms has emerged from genetic screens whereby an easily measured behavioral rhythm is used as a read-out of clock function. Studies using Drosophila have made seminal contributions to our understanding of the cellular and biochemical bases underlying circadian rhythms. The standard circadian behavioral read-out measured in Drosophila is locomotor activity. In general, the monitoring system involves specially designed devices that can measure the locomotor movement of Drosophila. These devices are housed in environmentally controlled incubators located in a darkroom and are based on using the interruption of a beam of infrared light to record the locomotor activity of individual flies contained inside small tubes. When measured over many days, Drosophila exhibit daily cycles of activity and inactivity, a behavioral rhythm that is governed by the animal's endogenous circadian system. The overall procedure has been simplified with the advent of commercially available locomotor activity monitoring devices and the development of software programs for data analysis. We use the system from Trikinetics Inc., which is the procedure described here and is currently the most popular system used worldwide. More recently, the same monitoring devices have been used to study sleep behavior in Drosophila. Because the daily wake-sleep cycles of many flies can be measured simultaneously and only 1 to 2 weeks worth of continuous locomotor activity data is usually sufficient, this system is ideal for large-scale screens to identify Drosophila manifesting altered circadian or sleep properties.
MODELING OF THE HERMES SUBMILLIMETER SOURCE LENSED BY A DARK MATTER DOMINATED FOREGROUND GROUP OF GALAXIES

We present the results of a gravitational lensing analysis of the bright zs = 2.957 submillimeter galaxy (SMG) HERMES found in the Herschel/SPIRE science demonstration phase data from the Herschel Multi-tiered Extragalactic Survey (HerMES) project. The high-resolution imaging available in optical and near-IR channels, along with CO emission obtained with the Plateau de Bure Interferometer, allows us to precisely estimate the intrinsic source extension and hence estimate the total lensing magnification to be μ = 10.9 ± 0.7. We measure the half-light radius Reff of the source in the rest-frame near-UV and V bands that characterize the unobscured light coming from stars and find Reff, * = [2.0 ± 0.1] kpc, in good agreement with recent studies on the SMG population. This lens model is also used to estimate the size of the gas distribution (Reff, gas = [1.1 ± 0.5] kpc) by mapping back in the source plane the CO (J = 5 → 4) transition line emission. The lens modeling yields a relatively large Einstein radius REin = 4. ″10 ± 0. ″02, corresponding to a deflector velocity dispersion of [483 ± 16] km s−1. This shows that HERMES is lensed by a galaxy group-size dark matter halo at redshift zl ∼ 0.6. The projected dark matter contribution largely dominates the mass budget within the Einstein radius with fdm(< REin) ∼ 80%. This fraction reduces to fdm(< Reff, G1 ≃ 4.5 kpc) ∼ 47% within the effective radius of the main deflecting galaxy of stellar mass M*, G1 = [8.5 ± 1.6] × 1011 M☉. At this smaller scale the dark matter fraction is consistent with results already found for massive lensing ellipticals at z ∼ 0.2 from the Sloan Lens ACS Survey.
Sociology and Social Work Undergraduates’ Experiences Participating in a Research Project on Campus Sexual Assault and Misconduct

In this article, we discuss the application of a collaborative, team-based, semester-long research project in undergraduate sociology and social work research methods courses at a midsize southeastern university. The goal of the endeavor was to engage undergraduates in research on students’ perceptions and knowledge about sexual assault and misconduct on their college campus. Surveys focusing on sexual assault and misconduct modeled after the Association of American Universities’ Campus Climate Survey and the Illinois Rape Myth Acceptance Scale were distributed to students in introductory classes on campus. The data from the surveys were then used in various assignments in the social work and sociology research methods courses to demonstrate to students the multitude of steps involved in the research process. The assignments culminated in a research paper and presentation at the end of the semester. We use data collected from end of the semester student evaluations to better understand students’ learning experiences by participating in this hands-on research project in the sociology and social work methods courses.
Understanding Multicore Cache Behavior of Loop-based Parallel Programs via Reuse Distance Analysis

Understanding multicore memory behavior is crucial, but can be challenging due to the cache hierarchies employed in modern CPUs. In today’s hierarchies, performance is determined by complex thread interactions, such as interference in shared caches and replication and communication in private caches. Researchers normally perform simulation to sort out these interactions, but this can be costly and not very insightful. An alternative is reuse distance (RD) analysis. RD analysis for multicore processors is becoming feasible because recent research has developed new notions of reuse distance that can analyze thread interactions. In particular, concurrent reuse distance (CRD) models shared cache interference, while private-stack reuse distance (PRD) models private cache replication and communication. Previous multicore RD research has centered around developing techniques and verifying accuracy. In this paper, we apply multicore RD analysis to better understand memory behavior. We focus on loop-based parallel programs, an important class of programs for which RD analysis provides high accuracy. First, we develop techniques to isolate thread interactions, permitting analysis of their relative contributions. Then, we use our techniques to extract several new insights that can help architects optimize multicore cache hierarchies. One of our findings is that data sharing
Female political representation in the aftermath of ethnic violence: A comparative analysis of Burundi and Rwanda

We study the impact of electoral gender quotas in post-war Burundi and Rwanda on women’s political representation. First, we look at descriptive representation by studying the number of female representatives and the prestige of their positions in the legislative and executive branches of government. Second, we focus on political representation as perceived by ordinary women, before, during, and after the introduction of gender quotas. We find that, both in Rwanda and Burundi, descriptive female political representation significantly increased with the introduction of gender quotas, with the share of women in parliament and ministries consistently exceeding 30 per cent. While women still disproportionally end up in ministries of relatively lower prestige, the gap with men is closing as more women have joined the executive branches of power. We do not find any tangible effect on women’s perceived political representation. Among the possible explanations, we discuss the authoritarian nature of the regime and the crowding out of gender identity by ethnic identity. We argue that these explanations are not entirely consistent with our data and put forward a third explanation, i.e. that the perception of political representation depends on the implementation of policies—thus substantive representation, not descriptive representation—and that men and women are to a very large extent appreciative of the same policies.
The New Personal Influence: How Our Facebook Friends Influence the News We Read

Has the introduction of social media into the information landscape changed the heuristics individuals use when selecting news? Social media allow users to easily share and endorse political content. These features facilitate personal influence, possibly increasing the salience of partisan information, making users more likely to read endorsed content. To test this possibility, I utilize snowball sampling to conduct a survey experiment featuring mock Facebook News Feeds. These feeds contain different levels of social media activity attributed to different sources, varying from fictional individuals to subjects’ own friends and family members. I find that online endorsements and discussions serve as heuristics when deciding which content to consume, outweighing partisan selectivity. This effect is only significant when the activity comes from friends or family members, as social influence attributed to fictional individuals has no effect on information selectivity.
Bargainer Characteristics in Distributive and Integrative Negotiation

Negotiation researchers theorize that individual differences are determinants of bargaining processes and outcomes but have yet to establish empirically the role of individual differences. In 2 studies the authors used bargaining simulations to examine the roles of personality and cognitive ability in distributive (Study 1) and integrative (Study 2) negotiation. The authors hypothesized and found evidence that Extraversion and Agreeableness are liabilities in distributive bargaining encounters. For both Extraversion and Agreeableness there were interactions between personality and negotiator aspirations such that personality effects were more pronounced in the absence of high aspirations. Contrary to predictions, Conscientiousness was generally unrelated to bargaining success. Cognitive ability played no role in distributive bargaining but was markedly related to the attainment of joint outcomes in a situation with integrative potential.
Comparative Genome of GK and Wistar Rats Reveals Genetic Basis of Type 2 Diabetes

The Goto-Kakizaki (GK) rat, which has been developed by repeated inbreeding of glucose-intolerant Wistar rats, is the most widely studied rat model for Type 2 diabetes (T2D). However, the detailed genetic background of T2D phenotype in GK rats is still largely unknown. We report a survey of T2D susceptible variations based on high-quality whole genome sequencing of GK and Wistar rats, which have generated a list of GK-specific variations (228 structural variations, 2660 CNV amplification and 2834 CNV deletion, 1796 protein affecting SNVs or indels) by comparative genome analysis and identified 192 potential T2D-associated genes. The genes with variants are further refined with prior knowledge and public resource including variant polymorphism of rat strains, protein-protein interactions and differential gene expression. Finally we have identified 15 genetic mutant genes which include seven known T2D related genes (Tnfrsf1b, Scg5, Fgb, Sell, Dpp4, Icam1, and Pkd2l1) and eight high-confidence new candidate genes (Ldlr, Ccl2, Erbb3, Akr1b1, Pik3c2a, Cd5, Eef2k, and Cpd). Our result reveals that the T2D phenotype may be caused by the accumulation of multiple variations in GK rat, and that the mutated genes may affect biological functions including adipocytokine signaling, glycerolipid metabolism, PPAR signaling, T cell receptor signaling and insulin signaling pathways. We present the genomic difference between two closely related rat strains (GK and Wistar) and narrow down the scope of susceptible loci. It also requires further experimental study to understand and validate the relationship between our candidate variants and T2D phenotype. Our findings highlight the importance of sequenced-based comparative genomics for investigating disease susceptibility loci in inbreeding animal models.
Biogenesis of the pore architecture of a voltage-gated potassium channel

The pore domain of voltage-gated potassium (Kv) channels consists of transmembrane helices S5 and S6, the turret, the pore helix, the selectivity filter, and the loop preceding S6, with a tertiary reentrant structure between S5 and S6. Using biogenic intermediates, mass tagging (pegylation), and a molecular tape measure, we explored the possibility that the first stages of pore formation occur prior to oligomerization of the transmembrane core. Pegylation of introduced cysteines shows that the pore helix, but not the turret, forms a compact secondary structure in the terminal 20 Å of the ribosomal tunnel. We assessed the tertiary fold of the pore loop in monomeric constructs by determining the relative accessibilities of select cysteines using the kinetics of pegylation. Turret residues are accessible at the extracellular surface. In contrast, pore helix residues are less accessible. All-atom molecular dynamics simulations of a single Kv monomer in a solvated lipid membrane indicate that secondary and tertiary folds are stable over 650 ns. These results are consistent with acquisition of a tertiary reentrant pore architecture at the monomer stage of Kv biogenesis and begin to define a plausible sequence of folding events in the formation of Kv channels.
Study of internet addiction: Prevalence, pattern, and psychopathology among health professional undergraduates

Background: Internet has become an essential part of our daily life, especially among adolescents and youth. It is mainly used for education, entertainment, social networking, and information sharing. Its excessive use among health care providers is becoming a major concern. Aims: The aim of our study was to estimate the prevalence, understand the pattern, and to determine the association between psychopathology and internet addiction among health profession undergraduates. Materials and Methods: A cross-sectional study was conducted among 846 students of various faculties from Deemed University. Students were assessed with semi-structured data, Internet Addiction Test and Mental Health Inventory, after giving them brief instructions. Students were classified into normal students and addicted students for comparison. Results: The total prevalence of internet addiction was 19.85%, with moderate and severe addiction being 19.5% and 0.4%, respectively. Internet addiction was associated with gender, computer ownership, preferred time of internet use, login status, and mode of internet access (P < 0.05). It was also associated with anxiety, depression, loss of emotional/behavioral control, emotional ties, life satisfaction, psychological distress, and lower psychological well-being (P < 0.05). Conclusion: Significant association was found between psychopathology and internet addiction. Male gender, login status, emotional ties, and psychological distress were found to be important predictors of internet addiction among students. Hence, these parameters should be taken into consideration while promoting awareness of problematic internet use and educating students regarding healthy internet use.
A comparative study of monotone nonparametric kernel estimates

In this paper we present a detailed numerical comparison of three monotone nonparametric kernel regression estimates, which isotonize a nonparametric curve estimator. The first estimate is the classical smoothed isotone estimate of Brunk [Brunk, H.D. , 1955, Maximum likelihood estimates of monotone parameters. The Annals of Mathematical Statistics, 26, 607–616. ]. The second method has recently been proposed by Hall and Huang [Hall, P. and Huang, L. -S. , 2001, Nonparametric kernel regression subject to monotonicity constraints. The Annals of Statistics, 29, 624–647. ] and modifies the weights of a commonly used kernel estimate such that the resulting estimate is monotone. The third estimate was recently proposed by Dette et al. [Dette, H. , Neumeyer, N. and Pilz, K.F. , 2003, A simple non-parametric estimator of a monotone regression function. Technical report, Department of Mathematics. Available online at: http://www.ruhr-uni-bochum.de/mathematik3/preprint.htm] and combines density and regression estimation techniques to obtain a monotone curve estimate of the inverse of the isotone regression function. The three concepts are briefly reviewed and their finite sample properties are studied by means of a simulation study. Although all estimates are first-order asymptotically equivalent (provided that the unknown regression function is isotone) some differences for moderate sample sizes are observed.
Backward binding as a psych effect: A binding illusion?

Abstract Bound anaphors inside subjects challenge the c-command requirement for binding. At least in some languages, experiencer-object verbs such as worry or please are reported to license this type of backward dependence. In many cases, the underlying facts are based on unstable intuitions potentially influenced by intervening factors, such as accidental coreference and binding illusions. This article reports the results of an experiment on backward binding with accusative and dative experiencer-object verbs in German; in this experiment, crucial sources of variation are controlled. The results show that verb class (experiencer-object vs. agentive) has a significant effect on variable binding, both for dative and for accusative verbs. This result cannot be accounted for through accidental coreference and is not reducible to effects of sentence aspect, the latter being correlated with the distinction between experiencer-object and agentive verbs. These findings are evidence for backward binding as a genuine psych effect in German.
Q A ] 3 0 N ov 1 99 8 q-alg / 9811175 Vertex Models with Alternating Spins

The diagonalisation of the transfer matrices of solvable vertex models with alternating spins is given. The crystal structure of (semi-)infinite tensor products of finite dimensional Uq(ŝl2) crystals with alternating dimensions is determined. Upon this basis the vertex models are formulated and then solved by means of Uq(ŝl2) intertwiners.
Tissue Factor: molecular recognition and cofactor function

One aspect of the inflammatory response is the activation of the coagulation protease cascade resulting from the expression of tissue factor (TF) on vascular cells. TF is the cell‐surface receptor for the coagulation serine protease factor VIIa, providing cofactor function by “switching on” the catalytic site of the bound enzyme and by contributing to the assembly with macromolecular substrate. The recently determined crystal structure of the TF extracellular domain shows two β‐strand modules of C2 immunoglobulin‐like topology that align at a 125° angle with an extensive intermodule interface. Mutagenesis studies have identified residues in both modules that are important for the binding of ligand. The deduced ligand interface extends from the convex side of the molecule into the concave side of the elbow angle. Specific binding residues control the catalytic activity of the bound protease. At the lower end of the carboxyl‐terminal module, basic residues form part of a region that is important for both recognition and activation of macromolecular substrate and, potentially, for modulation of proteolytic function. After combining the biochemical data with the crystal structure, a model of TF function can be proposed in which the catalytic activity of the active site of the protease and the extended recognition of macromolecular substrates are separately controlled by distinct structural sites of the cofactor. —Martin, D. M. A. , Boys, C. W. G. , Ruf, W. Tissue factor: molecular recognition and cofactor function. FASEB J. 9, 852‐859 (1995)
Alkaline anion-exchange radiation-grafted membranes for possible electrochemical application in fuel cells

Vinylbenzyl chloride was grafted onto PVDF and FEP polymer films using radiation-grafting methodology. Subsequent reaction with trimethylamine and ion-exchange with potassium hydroxide yields alkaline anion-exchange membranes that are capable of conducting hydroxide ions; such membranes may be suitable for use in low temperature direct methanol fuel cells for portable devices. The PVDF based materials underwent an undesirable degradation and were found to be less suitable for this class of membrane. FEP-based materials exhibited superior structural stability, conductivities up to 0.02 S cm−1 at room temperature, and good retention of ion-exchange capacities when treated in water at 60 °C.
Genomic expression profiling and bioinformatics analysis of pancreatic cancer

Pancreatic cancer is a polygenic disease and the fourth leading cause of cancer-associated mortality worldwide; however, the tumorigenesis of pancreatic cancer remains poorly understood. Research at a molecular level, which includes the exploration of biomarkers for early diagnosis and specific targets for therapy, may effectively aid in the diagnosis of pancreatic cancer in its early stages and in the development of targeted molecular-biological approaches for treatment, thus improving prognosis. By conducting expression profiling in para-carcinoma, carcinoma and relapse of human pancreatic tissues, 319 genes or transcripts with differential expression levels >3-fold between these tissue types were identified. Further analysis with Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes demonstrated that the translation, nucleus assembly processes and molecular functions associated with vitamin B6 and pyridoxal phosphate binding in pancreatic carcinoma were abnormal. Pancreatic cancer was additionally identified to be closely associated with certain autoimmune diseases, including type I diabetes mellitus and systemic lupus erythematosus.