Miracle-dz/UniFAR-FTUs huggingface dataset:
Professional and Home-Made Face Masks Reduce Exposure to Respiratory Infections among the General Population

Background Governments are preparing for a potential influenza pandemic. Therefore they need data to assess the possible impact of interventions. Face-masks worn by the general population could be an accessible and affordable intervention, if effective when worn under routine circumstances. Methodology We assessed transmission reduction potential provided by personal respirators, surgical masks and home-made masks when worn during a variety of activities by healthy volunteers and a simulated patient. Principal Findings All types of masks reduced aerosol exposure, relatively stable over time, unaffected by duration of wear or type of activity, but with a high degree of individual variation. Personal respirators were more efficient than surgical masks, which were more efficient than home-made masks. Regardless of mask type, children were less well protected. Outward protection (mask wearing by a mechanical head) was less effective than inward protection (mask wearing by healthy volunteers). Conclusions/Significance Any type of general mask use is likely to decrease viral exposure and infection risk on a population level, in spite of imperfect fit and imperfect adherence, personal respirators providing most protection. Masks worn by patients may not offer as great a degree of protection against aerosol transmission.
Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution

Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses. Furthermore, effector genes are often found in rapidly evolving chromosome compartments which are difficult to assemble. We review how population and comparative genomics toolsets can be combined to address these challenges. We highlight studies that associated genome-scale polymorphisms with pathogen lifestyles and adaptation to different environments. We show how genome-wide association studies can be used to identify effectors and other pathogenicity-related genes underlying rapid adaptation. We also discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes. We argue that an understanding of genome evolution provides important insight into the trajectory of host-pathogen co-evolution.
Online cancer education and immigrants: effecting culturally appropriate websites.

UNLABELLED The online population is becoming increasingly diverse. Cancer information websites are a popular destination. However, culturally-appropriate cancer information websites are lacking. METHODS An Internet behavior and preference study was conducted in Caribbean immigrant women. 60 English-speaking Caribbean immigrant women in New York City participated in website review sessions. RESULTS Three-quarters of the participants used computers regularly. Over 80% accessed the Internet from home. Over 50% felt confident using the Internet. However, only 6% used the Internet to search for health information. CONCLUSION A "cultural digital divide" exists. The Internet should be tailored to immigrants to facilitate web-based cancer education.
Tissue injury and hypoxia promote malignant progression of prostate cancer by inducing CXCL13 expression in tumor myofibroblasts

Significance Prostate cancer often responds to hormone ablation therapy or chemotherapy by becoming more aggressive and metastatic. B cells recruited into hormone-deprived tumors by C-X-C motif chemokine 13 (CXCL13) play an important role in this process. We investigated how androgen ablation induces CXCL13 expression and found that CXCL13 is expressed by myofibroblasts within the tumor microenvironment that become activated as a result of low oxygen tension and hypoxia in androgen-deprived tumors. Hypoxia activates hypoxia-inducible factor 1 (HIF-1) and induces TGF-β expression, which converts fibroblasts to myofibroblasts and stimulates CXCL13 production. We show that several treatments that block CXCL13 expression, including immunodepletion of myofibroblasts, blockade of TGF-β signaling, and phosphodiesterase-5 (PDE5) inhibitors, inhibit B-cell recruitment into androgen-deprived prostate tumors and prevent the emergence of a more aggressive type of cancer. Prostate cancer (PC) is a slowly progressing malignancy that often responds to androgen ablation or chemotherapy by becoming more aggressive, acquiring a neuroendocrine phenotype, and undergoing metastatic spread. We found that B lymphocytes recruited into regressing androgen-deprived tumors by C-X-C motif chemokine 13 (CXCL13), a chemokine whose expression correlates with clinical severity, play an important role in malignant progression and metastatic dissemination of PC. We now describe how androgen ablation induces CXCL13 expression. In both allografted and spontaneous mouse PC, CXCL13 is expressed by tumor-associated myofibroblasts that are activated on androgen ablation through a hypoxia-dependent mechanism. The same cells produce CXCL13 after chemotherapy. Myofibroblast activation and CXCL13 expression also occur in the normal prostate after androgen deprivation, and CXCL13 is expressed by myofibroblasts in human PC. Hypoxia activates hypoxia-inducible factor 1 (HIF-1) and induces autocrine TGF-β signaling that promotes myofibroblast activation and CXCL13 induction. In addition to TGF-β receptor kinase inhibitors, myofibroblast activation and CXCL13 induction are blocked by phosphodiesterase 5 (PDE5) inhibitors. Both inhibitor types and myofibroblast immunodepletion block the emergence of castration-resistant PC in the transgenic adenocarcinoma of the mouse prostate (TRAMP) model of spontaneous metastatic PC with neuroendocrine differentiation.
Addressing Ethical and Methodological Challenges in Research with Refugee-background Young People: Reflections from the Field

Ethical complexities associated with research involving vulnerable and marginalized population groups are well recognized, while practical solutions to these challenges are somewhat less well described. In this article we focus on strategies for addressing interrelated practical, methodological and ethical issues which may arise during research with refugee-background participants considered vulnerable. The article draws on a study exploring the impact of social networks and support on the resettlement experiences of newly-arrived migrant youth of refugee background in Australia. Three key sets of issues are discussed: developing research processes that maximize the benefits of involvement for participants while reducing potential harms; enhancing capacities for participants to give informed consent; and adapting research methods to heighten their relevance to the circumstances of participants’ lives and enhance their engagement in the research. We argue that promoting ethical practice and methodological validity are mutually reinforcing objectives and illustrate how processes of ethical reflexivity were applied to resolve methodological challenges, promote autonomy and capacity of research participants and enhance the potential for outcomes to be rigorous and useful.
The pay-offs of preprocessing for German-English statistical machine translation

In this paper, we present the result of our work on improving the preprocessing for German-English statistical machine translation. We implemented and tested various improvements aimed at i) converting German texts to the new orthographic conventions; ii) performing a new tokenization for German; iii) normalizing lexical redundancy with the help of POS tagging and morphological analysis; iv) splitting German compound words with frequency based algorithm and; v) reducing singletons and out-of-vocabulary words. All these steps are performed during preprocessing on the German side. Combining all these processes, we reduced 10% of the singletons, 2% OOV words, and obtained 1.5 absolute (7% relative) BLEU improvement on the WMT 2010 German to English News translation task.
Strong reciprocity, social structure, and the evolution of cooperative behavior

ion results have broad applicability, ranging from colonies of social amoebae or ants to corporations or nations interacting in markets and policy arenas. In all of these cases, actors in a system with no central controller face a trade-off between individual goals and the needs of the collective. Results from evolutionary simulations of simple economic games show that when individual incentives, in the form of punishment, are coupled with social structure, especially complex social networks, cooperation evolves quite readily despite traditional economic predictions to the contrary. These simulation results are then synthesized with experimental work of others to present a challenge to standard, narrow definitions of rationality. This challenge asserts that, by defining rational actors as absolute utility maximizers, standard rational choice theory lacks an evolutionary context and typically ignores regard that agents may have for others in the local environment. Such relative considerations become important when potential interactions of a society’s individuals are not broad and random, but are governed by iv emergent social networks as they are in real societies. Finally, analysis of the implications of these findings to efficacy of international environmental agreements suggest that conventional strategies for overcoming global social dilemmas may be inadequate when other-regarding preferences influence national strategies.
Code Park: A New 3D Code Visualization Tool

We introduce Code Park, a novel tool for visualizing codebases in a 3D game-like environment. Code Park aims to improve a programmer's understanding of an existing codebase in a manner that is both engaging and intuitive, appealing to novice users such as students. It achieves these goals by laying out the codebase in a 3D park-like environment. Each class in the codebase is represented as a 3D room-like structure. Constituent parts of the class (variable, member functions, etc.) are laid out on the walls, resembling a syntax-aware "wallpaper". The users can interact with the codebase using an overview, and a first-person viewer mode. We conducted two user studies to evaluate Code Park's usability and suitability for organizing an existing project. Our results indicate that Code Park is easy to get familiar with and significantly helps in code understanding compared to a traditional IDE. Further, the users unanimously believed that Code Park was a fun tool to work with.
Structural and Functional Evidence for Bacillus subtilis PaiA as a Novel N1-Spermidine/Spermine Acetyltransferase*

Bacillus subtilis PaiA has been implicated in the negative control of sporulation as well as production of degradative enzymes. PaiA shares recognizable sequence homology with N-acetyltransferases, including those that can acetylate spermidine/spermine substrates. We have determined the crystal structure of PaiA in complex with CoA at 1.9 Å resolution and found that PaiA is a member of the N-acetyltransferase superfamily of enzymes. Unexpectedly, we observed the binding of an oxidized CoA dimer in the active site of PaiA, and the structural information suggests the substrates of the enzyme could be linear, positively charged compounds. Our biochemical characterization is also consistent with this possibility, since purified PaiA possesses N1-acetyltransferase activity toward polyamine substrates including spermidine and spermine. Further, conditional overexpression of PaiA in bacteria results in increased acetylation of endogenous spermidine pools. Thus, our structural and biochemical analyses indicate that PaiA is a novel N-acetyltransferase capable of acetylating both spermidine and spermine. In this way, the pai operon may function in regulating intracellular polyamine concentrations and/or binding capabilities. In addition to preventing toxicity due to polyamine excess, this function may also serve to regulate expression of certain bacterial gene products such as those involved in sporulation.
A Gain-of-Function Mutation in the M-domain of Cardiac Myosin-binding Protein-C Increases Binding to Actin*

Background: Cardiac myosin-binding protein C (cMyBP-C) regulates heart muscle contraction by influencing actomyosin interactions. Results: Amino acids within the tri-helix bundle of the M-domain contribute to the functional effects of cMyBP-C. Conclusion: Amino acids outside of phosphorylation sites influence function of the M-domain. Significance: The tri-helix bundle is important to the regulatory role of cMyBP-C, likely through actin-binding interactions. The M-domain is the major regulatory subunit of cardiac myosin-binding protein-C (cMyBP-C) that modulates actin and myosin interactions to influence muscle contraction. However, the precise mechanism(s) and the specific residues involved in mediating the functional effects of the M-domain are not fully understood. Positively charged residues adjacent to phosphorylation sites in the M-domain are thought to be critical for effects of cMyBP-C on cross-bridge interactions by mediating electrostatic binding with myosin S2 and/or actin. However, recent structural studies revealed that highly conserved sequences downstream of the phosphorylation sites form a compact tri-helix bundle. Here we used site-directed mutagenesis to probe the functional significance of charged residues adjacent to the phosphorylation sites and conserved residues within the tri-helix bundle. Results confirm that charged residues adjacent to phosphorylation sites and residues within the tri-helix bundle are important for mediating effects of the M-domain on contraction. In addition, four missense variants within the tri-helix bundle that are associated with human hypertrophic cardiomyopathy caused either loss-of-function or gain-of-function effects on force. Importantly, the effects of the gain-of-function variant, L348P, increased the affinity of the M-domain for actin. Together, results demonstrate that functional effects of the M-domain are not due solely to interactions with charged residues near phosphorylatable serines and provide the first demonstration that the tri-helix bundle contributes to the functional effects of the M-domain, most likely by binding to actin.
Energy-Efficient Vector OFDM PLC Systems With Dynamic Peak-Based Threshold Estimation

Power line communication (PLC) has made remarkable strides to become a key enabler of smart grid and its applications. Existing PLC systems are based on orthogonal frequency division multiplexing (OFDM), which has a high peak-to-average power ratio (PAPR). This paper presents vector OFDM (VOFDM) with advanced signal processing at the receiver to improve the energy efficiency of the PLC system. Results show that, due to its low PAPR properties, VOFDM is less sensitive to impulsive noise and provides a reduction of 5.8 dB in transmit power requirement relative to conventional OFDM. Furthermore, unlike the existing impulsive noise cancellation methods, the adopted signal processing technique also improves the SNR at the receiver by 2.1 dB, which further reduces the power requirement of the PLC transceiver. Together, these can simplify design, reduce cost, and improve energy efficiency of future PLC transceivers.
A Global Trade Model for the Euro Area

We propose a model for analyzing euro area trade based on the interaction between macroeconomic and trade variables. First, we show that macroeconomic variables are necessary to generate accurate short-term trade forecasts; this result can be explained by the high correlation between trade and macroeconomic variables, with the latter being released in a more timely manner. Second, the model tracks well the dynamics of trade variables conditional on the path of macroeconomic variables during the great recession; this result makes our model a reliable tool for scenario analysis. Third, we quantify the contribution of the most important euro area trading partners (regions) to the aggregate extra euro area developments: we evaluate the impact of an increase of the external demand from a specific region on the extra euro area trade.
Cynophobic Fear Adaptively Extends Peri-Personal Space

Peri-personal space (PPS) is defined as the space immediately surrounding our bodies, which is critical in the adaptation of our social behavior. As a space of interaction with the external world, PPS is involved in the control of motor action as well as in the protection of the body. The boundaries of this PPS are known to be flexible but so far, little is known about how PPS boundaries are influenced by unreasonable fear. We hypothesized that unreasonable fear extends the neural representation of the multisensory space immediately surrounding the body in the presence of a feared object, with the aim of expanding the space of protection around the body. To test this hypothesis, we explored the impact of unreasonable fear on the size of PPS in two groups of non-clinical participants: dog-fearful and non-fearful participants. The sensitivity to cynophobia was assessed with a questionnaire. We measured participants’ PPS extent in the presence of threatening (dog growling) and non-threatening (sheep bleating) auditory stimuli. The sound stimuli were processed through binaural rendering so that the virtual sound sources were looming toward participants from their rear hemi-field. We found that, when in the presence of the auditory dog stimulus, the PPS of dog-fearful participants is larger than that of non-fearful participants. Our results demonstrate that PPS size is adaptively modulated by cynophobia and suggest that anxiety tailors PPS boundaries when exposed to fear-relevant features. Anxiety, with the exception of social phobia, has rarely been studied as a disorder of social interaction. These findings could help develop new treatment strategies for anxious disorders by involving the link between space and interpersonal interaction in the approach of the disorder.
Fructose Levels Are Markedly Elevated in Cerebrospinal Fluid Compared to Plasma in Pregnant Women

Background Fructose, unlike glucose, promotes feeding behavior in rodents and its ingestion exerts differential effects in the human brain. However, plasma fructose is typically 1/1000th of glucose levels and it is unclear to what extent fructose crosses the blood-brain barrier. We investigated whether local endogenous central nervous system (CNS) fructose production from glucose via the polyol pathway (glucose→sorbitol→fructose) contributes to brain exposure to fructose. Methods In this observational study, fasting glucose, sorbitol and fructose concentrations were measured using gas-chromatography-liquid mass spectroscopy in cerebrospinal fluid (CSF), maternal plasma, and venous cord blood collected from 25 pregnant women (6 lean, 10 overweight/obese, and 9 T2DM/gestational DM) undergoing spinal anesthesia and elective cesarean section. Results As expected, CSF glucose was ~60% of plasma glucose levels. In contrast, fructose was nearly 20-fold higher in CSF than in plasma (p < 0.001), and CSF sorbitol was ~9-times higher than plasma levels (p < 0.001). Moreover, CSF fructose correlated positively with CSF glucose (ρ 0.45, p = 0.02) and sorbitol levels (ρ 0.75, p < 0.001). Cord blood sorbitol was also ~7-fold higher than maternal plasma sorbitol levels (p = 0.001). There were no differences in plasma, CSF, and cord blood glucose, fructose, or sorbitol levels between groups. Conclusions These data raise the possibility that fructose may be produced endogenously in the human brain and that the effects of fructose in the human brain and placenta may extend beyond its dietary consumption.
Population Genetics of Nosema apis and Nosema ceranae: One Host (Apis mellifera) and Two Different Histories

Two microsporidians are known to infect honey bees: Nosema apis and Nosema ceranae. Whereas population genetics data for the latter have been released in the last few years, such information is still missing for N. apis. Here we analyze the patterns of nucleotide polymorphism at three single-copy loci (PTP2, PTP3 and RPB1) in a collection of Apis mellifera isolates from all over the world, naturally infected either with N. apis (N = 22) or N. ceranae (N = 23), to provide new insights into the genetic diversity, demography and evolution of N. apis, as well as to compare them with evidence from N. ceranae. Neutral variation in N. apis and N. ceranae is of the order of 1%. This amount of diversity suggests that there is no substantial differentiation between the genetic content of the two nuclei present in these parasites, and evidence for genetic recombination provides a putative mechanism for the flow of genetic information between chromosomes. The analysis of the frequency spectrum of neutral variants reveals a significant surplus of low frequency variants, particularly in N. ceranae, and suggests that the populations of the two pathogens are not in mutation-drift equilibrium and that they have experienced a population expansion. Most of the variation in both species occurs within honey bee colonies (between 62%-90% of the total genetic variance), although in N. apis there is evidence for differentiation between parasites isolated from distinct A. mellifera lineages (20%-34% of the total variance), specifically between those collected from lineages A and C (or M). This scenario is consistent with a long-term host-parasite relationship and contrasts with the lack of differentiation observed among host-lineages in N. ceranae (< 4% of the variance), which suggests that the spread of this emergent pathogen throughout the A. mellifera worldwide population is a recent event.
Cognitive factors related to regular physical activity in college students

Background & Aim : Despite the well evidenced health benefits of regular physical activity, many Iranian college students do not engage in physical activity sufficiently. The aim of this study was to assess cognitive factors related to regular physical activity in college students in Hormozgan University of Medical Sciences, Bandar Abbass, Iran. Methods & Materials : A total of 314 students from three schools of the Hormozgan University of Medical Sciences were selected randomly. Of the total number of students, 249 students filled out the questionnaires completely (response rate = 79.3%). Exercise Benefits/Barriers scale, Selfefficacy scale, Exercise norms scale, and Planning for exercise scale were used to assess cognitive factors regarding physical activity; the Cronbach's alpha of these scales were 0.87, 0.83, 0.73, and 0.82, respectively. Results : The mean age of participants was 21.7 ± 2.7. Of all the participants, 46.2% were male. Only 26.5% (n = 66) were engaged in regular physical activity. Perceived barriers to exercise, selfefficacy to exercise, planning for exercise, and exercise norms had a significant relationship with physical activity (P < 0.05). However, there was no significant relationship between perceived benefits to exercise and physical activity. Conclusion : For increasing physical activity in college students, self-efficacy and social support improvement is suggested.