Miracle-dz/UniFAR-FTUs huggingface dataset:
How to Make a Dolphin: Molecular Signature of Positive Selection in Cetacean Genome

Cetaceans are unique in being the only mammals completely adapted to an aquatic environment. This adaptation has required complex changes and sometimes a complete restructuring of physiology, behavior and morphology. Identifying genes that have been subjected to selection pressure during cetacean evolution would greatly enhance our knowledge of the ways in which genetic variation in this mammalian order has been shaped by natural selection. Here, we performed a genome-wide scan for positive selection in the dolphin lineage. We employed models of codon substitution that account for variation of selective pressure over branches on the tree and across sites in a sequence. We analyzed 7,859 nuclear-coding ortholog genes and using a series of likelihood ratio tests (LRTs), we identified 376 genes (4.8%) with molecular signatures of positive selection in the dolphin lineage. We used the cow as the sister group and compared estimates of selection in the cetacean genome to this using the same methods. This allowed us to define which genes have been exclusively under positive selection in the dolphin lineage. The enrichment analysis found that the identified positively selected genes are significantly over-represented for three exclusive functional categories only in the dolphin lineage: segment specification, mesoderm development and system development. Of particular interest for cetacean adaptation to an aquatic life are the following GeneOntology targets under positive selection: genes related to kidney, heart, lung, eye, ear and nervous system development.
Urban and rural disparity in tobacco use and knowledge about oral cancer among adolescents: An epidemiological survey on 12 and 15-year school going students

Aims and Objectives: To assess and compare the tobacco use prevalence; to understand and compare attitudes and knowledge related to tobacco use and its health impact among urban and rural students; and to assess urban and rural disparity in the use of tobacco among 12 and 15-year-old adolescents in the urban and rural schools in Chhattisgarh, India. Materials and Methods: A cross-sectional study was conducted among 12 and 15-year-old and urban and rural school going children in Durg District. Scientifically, based on the data obtained from the pilot study, sample size was calculated. A total of 1000 children were selected to be a part of the study and were interviewed face-to-face using a detailed pretested, close-ended questionnaire. The Statistical Package for the Social Sciences version 16.0 (SPSS Pvt. Ltd, Chicago, IL, USA) was used for the statistical analyses. Results: Prevalence of tobacco consumption was 48.8%. Males were involved predominantly in consuming tobacco. The knowledge and attitude was better in the school children of urban areas than the school children of rural areas; more of the urban school children were involved in smoking cigarette. Rural children outnumbered urban children in the smokeless tobacco consumption. Conclusion: Prevalence of tobacco consumption among school children remains high with a wide disparity among urban and rural children. There is an urgent need to have a rural orientation in the National Tobacco Control Program that is currently being developed by the Government of India and giving relevance to the youth.
Practical consensus recommendations regarding role of mastectomy in metastatic breast cancer

Abstract Whether to recommend mastectomy in metastatic disease or not has been a matter of debate. Is local therapy, such as mastectomy, of any benefit in advanced breast cancer is the main question. This expert group used data from published literature, practical experience and opinion of a large group of academic oncologists to arrive at these practical consensus recommendations for the benefit of community oncologists.
Reflection impulsivity in binge drinking: behavioural and volumetric correlates

The degree to which an individual accumulates evidence prior to making a decision, also known as reflection impulsivity, can be affected in psychiatric disorders. Here, we study decisional impulsivity in binge drinkers, a group at elevated risk for developing alcohol use disorders, comparing two tasks assessing reflection impulsivity and a delay discounting task, hypothesizing impairments in both subtypes of impulsivity. We also assess volumetric correlates of reflection impulsivity focusing on regions previously implicated in functional magnetic resonance imaging studies. Sixty binge drinkers and healthy volunteers were tested using two different information‐gathering paradigms: the beads task and the Information Sampling Task (IST). The beads task was analysed using a behavioural approach and a Bayesian model of decision making. Delay discounting was assessed using the Monetary Choice Questionnaire. Regression analyses of primary outcomes were conducted with voxel‐based morphometry analyses. Binge drinkers sought less evidence prior to decision in the beads task compared with healthy volunteers in both the behavioural and computational modelling analysis. There were no group differences in the IST or delay discounting task. Greater impulsivity as indexed by lower evidence accumulation in the beads task was associated with smaller dorsolateral prefrontal cortex and inferior parietal volumes. In contrast, greater impulsivity as indexed by lower evidence accumulation in the IST was associated with greater dorsal cingulate and precuneus volumes. Binge drinking is characterized by impaired reflection impulsivity suggesting a deficit in deciding on the basis of future outcomes that are more difficult to represent. These findings emphasize the role of possible therapeutic interventions targeting decision‐making deficits.
The Relative Impact of Psychosocial Well-being and Mental Health on the Relationship between Economic Circumstance and Religiosity

Common sentiment argues that when financial situations get worse, individuals turn to religion for support and solace. This study challenges that sentiment and identifies circumstances when the opposite is true. Employing existential security and stress coping literature as a theoretical lens and utilizing three distinct moments from the Americans’ Changing Lives Study (1986, 1994 and 2011); this work shows that individuals turn away from religion in times of decreased economic security; further, there are circumstances such that when depression increases, religious behavior actually decreases.
Elevated fasting plasma cortisol is associated with ischemic heart disease and its risk factors in people with type 2 diabetes: the Edinburgh type 2 diabetes study.

CONTEXT Increased activity of the hypothalamic-pituitary-adrenal (HPA) axis may underlie the metabolic syndrome, but whether circulating cortisol levels predict cardiovascular end points is less clear. People with type 2 diabetes are at increased cardiovascular disease risk and thus are suitable to study associations of plasma cortisol with cardiovascular risk. OBJECTIVE We aimed to assess whether altered HPA axis activity was associated with features of the metabolic syndrome and ischemic heart disease in people with type 2 diabetes. DESIGN AND SETTING We conducted a cross-sectional cohort study in the general community, including 919 men and women aged 67.9 (4.2) yr with type 2 diabetes (the Edinburgh Type 2 Diabetes Study). INTERVENTION We measured fasting morning plasma cortisol. MAIN OUTCOME MEASUREMENT Associations between cortisol levels, features of the metabolic syndrome, obesity, and ischemic heart disease were determined. RESULTS Elevated plasma cortisol levels were associated with raised fasting glucose and total cholesterol levels (P < 0.001). These findings remained significant after adjustment for potential confounding factors (P < 0.001). Elevated cortisol levels were associated with prevalent ischemic heart disease (>800 vs. <600 nmol/liter; odds ratio, 1.58; P = 0.02). This association remained significant after adjustment for duration and control of diabetes and other cardiovascular risk factors (P = 0.03). CONCLUSIONS The previously described associations between HPA axis activation and features of the metabolic syndrome are present among people with type 2 diabetes. Elevated plasma cortisol is also associated with a greater prevalence of ischemic heart disease, independent of conventional risk factors. Understanding the role of cortisol in the pathogenesis of ischemic heart disease merits further exploration.
Prevalence and social drivers of HIV among married and cohabitating heterosexual adults in south-eastern Tanzania: analysis of adult health community cohort data

Background In sub-Saharan Africa, the prevalence of HIV among married and cohabiting couples is substantial. Information about the underlying social drivers of HIV transmission in couples is critical for the development of structural approaches to HIV prevention, but not readily available. We explored the association between social drivers, practices, and HIV status among stable couples in Ifakara, Tanzania. Design Using a cross-sectional design, we analyzed data from a sample of 3,988 married or cohabiting individuals, aged 15 years and older from the MZIMA adult health community cohort study of 2013. Sociodemographic factors (sex, income, age, and education), gender norms (perceived acceptability for a wife to ask her partner to use a condom when she knows he is HIV positive), marriage characteristics (being in a monogamous or a polygamous marriage, being remarried), sexual behavior practices (lifetime number of sexual partners and concurrent sexual partners), health system factors (ever used voluntary HIV counseling and testing), and lifestyle patterns (alcohol use) were used to explore the odds of being HIV positive, with 95% confidence intervals. Results Prevalence of HIV/AIDS was 6.7% (5.9% males and 7.1% females). Gender norms, that is, perception that a woman is not justified to ask her husband to use a condom even when she knows he has a disease (adjusted odds ratio AOR=1.51, 95% CI 1.06–2.17), marital characteristics, that is, being remarried (AOR=1.49, 95% CI 1.08–2.04), and sexual behavior characteristics, that is, lifetime number of sexual partners (2–4: AOR=1.47, 95% CI 1.02–2.11; 5+: AOR=1.61, 95% CI 1.05–2.47) were the main independent predictors of HIV prevalence. Conclusions Among married or cohabiting individuals, the key social drivers/practices that appeared to make people more vulnerable for HIV are gender norms, marriage characteristics (being remarried), and sexual behavior practices (lifetime number of sexual partners). Married and cohabiting couples are an important target group for HIV prevention efforts in Tanzania. In addition to individual interventions, structural interventions are needed to address the gender norms, remarriage, and sexual practices that shape differential vulnerability to HIV in stable couples.
Genome-wide Determinants of Proviral Targeting, Clonal Abundance and Expression in Natural HTLV-1 Infection

The regulation of proviral latency is a central problem in retrovirology. We postulate that the genomic integration site of human T lymphotropic virus type 1 (HTLV-1) determines the pattern of expression of the provirus, which in turn determines the abundance and pathogenic potential of infected T cell clones in vivo. We recently developed a high-throughput method for the genome-wide amplification, identification and quantification of proviral integration sites. Here, we used this protocol to test two hypotheses. First, that binding sites for transcription factors and chromatin remodelling factors in the genome flanking the proviral integration site of HTLV-1 are associated with integration targeting, spontaneous proviral expression, and in vivo clonal abundance. Second, that the transcriptional orientation of the HTLV-1 provirus relative to that of the nearest host gene determines spontaneous proviral expression and in vivo clonal abundance. Integration targeting was strongly associated with the presence of a binding site for specific host transcription factors, especially STAT1 and p53. The presence of the chromatin remodelling factors BRG1 and INI1 and certain host transcription factors either upstream or downstream of the provirus was associated respectively with silencing or spontaneous expression of the provirus. Cells expressing HTLV-1 Tax protein were significantly more frequent in clones of low abundance in vivo. We conclude that transcriptional interference and chromatin remodelling are critical determinants of proviral latency in natural HTLV-1 infection.
The transcription factors Egr 1 and Egr 2 have opposing influences on adipocyte differentiation

The zinc finger-containing transcription factors Egr1 (Krox24) and Egr2 (Krox20) have been implicated in the proliferation and differentiation of many cell types. Egr2 has earlier been shown to play a positive role in adipocyte differentiation, but the function of Egr1 in this context is unknown. We compared the roles of Egr1 and Egr2 in the differentiation of murine 3T3-L1 adipocytes. Egr1 protein was rapidly induced after addition of differentiation cocktail, whereas Egr2 protein initially remained low before increasing on days 1 and 2, concomitant with the disappearance of Egr1. In marked contrast to the effects of Egr2, differentiation was inhibited by ectopic expression of Egr1 and potentiated by knockdown of Egr1. The pro-adipogenic effects of Egr1 knockdown were particularly notable when isobutylmethylxanthine (IBMX) was omitted from the differentiation medium. However, knockdown of Egr1 did not affect CCAAT/enhancer binding protein (C/EBP)b protein expression or phosphorylation of CREB Ser133. Further, Egr1 did not directly affect the activity of promoters for the master adipogenic transcription factors, C/EBPa or peroxisome proliferator-activated receptor-c2, as assessed in luciferase reporter assays. These data indicate that Egr1 and Egr2 exert opposing influences on adipocyte differentiation and that the careful regulation of both is required for maintaining appropriate levels of adipogenesis. Further, the pro-differentiation effects of IBMX involve suppression of the inhibitory influence of Egr1. Cell Death and Differentiation (2009) 16, 782–789; doi:10.1038/cdd.2009. 11; published online 20 February 2009
Approaches to Speaker Detection and Tracking in Conversational Speech

Dunn, Robert B. , Reynolds, Douglas A. , and Quatieri, Thomas F. , Approaches to Speaker Detection and Tracking in Conversational Speech, Digital Signal Processing10(2000), 93? 112.Two approaches to detecting and tracking speakers in multispeaker audio are described. Both approaches use an adapted Gaussian mixture model, universal background model (GMM-UBM) speaker detection system as the core speaker recognition engine. In one approach, the individual log-likelihood ratio scores, which are produced on a frame-by-frame basis by the GMM-UBM system, are used to first partition the speech file into speaker homogenous regions and then to create scores for these regions. We refer to this approach as internal segmentation. Another approach uses an external segmentationalgorithm, based on blind clustering, to partition the speech file into speaker homogenous regions. The adapted GMM-UBM system then scores each of these regions as in the single-speaker recognition case. We show that the external segmentation system outperforms the internal segmentation system for both detection and tracking. In addition, we show how different components of the detection and tracking algorithms contribute to the overall system performance.
Preferences for Vaccination

Purpose. The purpose of this study is to examine to what extent health literacy is associated with parental preferences concerning childhood vaccination. Methods. A cross-sectional study was conducted among 467 Dutch parents of newborns aged 6 weeks (response rate of 37%). A self-reported questionnaire was used to measure health literacy by means of Chew’s Set of Brief Screening Questions, as well as parental preferences for rotavirus vaccination by means of a discrete choice experiment. Five rotavirus-related characteristics were included (i.e., vaccine effectiveness, frequency of severe side effects, location of vaccination, protection duration, and out-of-pocket costs). Panel latent class models were conducted, and health literacy and educational level were added to the class probability model to determine the association between health literacy and study outcomes. Results. Lower educated and lower health literate respondents considered protection duration to be more important and vaccine effectiveness and frequency of severe side effects to be less important compared with higher educated and higher health literate respondents. While all respondents were willing to vaccinate against rotavirus when the vaccine was offered as part of the National Immunization Program, only lower educated and lower health literate parents were willing to vaccinate when the vaccine was offered on the free market. Conclusion: Health literacy is associated with parents’ preferences for rotavirus vaccination. Whether differences in vaccination decisions are actually due to varying preferences or might be better explained by varying levels of understanding should be further investigated. To contribute to more accurate interpretation of study results, it may be advisable that researchers measure and report health literacy when they study vaccination decision behavior.
Aspiration-Based Partner Switching Boosts Cooperation in Social Dilemmas

Most previous studies concerning linking dynamics often assumed that links pairing individuals should be identified and treated differently during topology adjusting procedure, in order to promote cooperation. A common assumption was that cooperators were expected to avoid being exploited by quickly breaking up relationships with defectors. Then the so-called prosocial links linking two cooperators (abbreviated as CC links hereafter) would be much favored by evolution, whereby cooperation was promoted. However, we suggest that this is not always necessary. Here, we developed a minimal model in which an aspiration-based partner switching mechanism was embedded to regulate the evolution of cooperation in social dilemmas. Individuals adjusted social ties in a self-questioning manner in line with the learning theory. Less game information was involved during dynamic linking and all links were tackled anonymously irrespective of their types (i.e., CD links, DD links, or CC links). The main results indicate that cooperation flourishes for a broad range of parameters. The denser the underlying network, the more difficult the evolution of cooperation. More importantly, moderate aspirations do much better in promoting the evolution of altruistic behavior and for most cases there exists the optimal aspiration level that most benefits cooperation. Too strong or too weak selection intensity turns out to be pretty conducive to the evolution of cooperation in such a dynamical system.
Learner Perspectives of Online Problem-Based Learning and Applications from Cognitive Load Theory

Problem-based learning (PBL) courses have historically been situated in physical classrooms involving in-person interactions. As online learning is embraced in higher education, programs that use PBL can integrate online platforms to support curriculum delivery and facilitate student engagement. This report describes student perspectives of the online PBL experience, interpreted through the lens of Cognitive Load Theory. Fifty-two undergraduate health professional students participated in this descriptive survey. The responses revealed that, overall, learners perceived the platform to be suitable for conducting online PBL, that distractions in the online environment were no greater than those experienced in physical classroom, and that online PBL was as effective as in-class PBL for learning. In online PBL, the technological capabilities and limitations of the online platform were identified by students as the key sources of hindrances and facilitators to learning. Suggestions for implementing online PBL using instructional principles from Cognitive Load Theory and multimedia learning are offered.
Internet-in-a-Box: Emulating datacenter network architectures using FPGAs

In this paper we describe the Internet-in-a-box datacenter network emulator, an FPGA-based tool for researchers to rapidly experiment with O(10,000) node datacenter network architectures. Our basic approach to emulation involves constructing a model of the target architecture by composing simplified hardware models of key datacenter building blocks, including switches, routers, links, and servers. Since models in our system are implemented in programmable hardware, designers have full control over emulated buffer sizes, line rates, topologies, and many other network properties. Full system control also gives researchers a significant degree of system visibility. Additionally, because our node model emulates servers using a full SPARC v8 ISA compatible processor, each node in the network is capable of running real applications. This allows researchers to study a network under complex real-world workloads at a scale that matches that of a large datacenter today. Moreover, because the system is a private testbed, experiments can be deterministic and therefore reproduced by other researchers. Lastly, the system is cost effective for designers, and we show that using FPGA technology on the market today we can actually emulate a network of 256-nodes for about $2,000.
Accelerated Electrons in Cassiopeia A: An Explanation for the Hard X-Ray Tail

We propose a model for the hard X-ray (>10 keV) emission observed from the supernova remnant Cas A. Lower hybrid waves are generated in strong (mG) magnetic fields, generally believed to reside in this remnant, by shocks reflected from density inhomogeneities. These then accelerate electrons to energies of several tens of keV. Around 4% of the X-ray-emitting plasma electrons need to be in this accelerated distribution, which extends up to electron velocities of order the electron Alfvén speed and is directed along magnetic field lines. Bremsstrahlung from these electrons produces the observed hard X-ray emission. Such waves and accelerated electrons have been observed in situ at comet Halley, and we discuss the viability of the extrapolation from this case to the parameters relevant to Cas A.
‘Just’ punishment? Offenders’ views on the meaning and severity of punishment

In England and Wales, ‘punishment’ is a central element of criminal justice. What punishment entails exactly, however, and how it relates to the other aims of sentencing (crime reduction, rehabilitation, public protection and reparation), remains contested. This article outlines different conceptualizations of punishment and explores to what extent offenders subscribe to these perspectives. The analysis is supported by findings from two empirical studies on the subjective experiences of imprisonment and probation, respectively. Semi-structured interviews were conducted with 15 male and 15 female prisoners and seven male and two female probationers. Two primary conceptualizations of punishment were identified: ‘punishment as deprivation of liberty’ and ‘punishment as hard treatment’. The comparative subjective severity of different sentences and the collateral (unintended) consequences of punishment are also discussed. It is shown that there are large individual differences in the interpretation and subjective experience of punishment, which has implications for the concept of retributive proportionality, as well as the function of punishment more generally.