Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome‐wide patterns of divergence during allopatric evolution

Recent studies have revealed repeated patterns of genomic divergence associated with species formation. Such patterns suggest that natural selection tends to target a set of available genes, but is also indicative that closely related taxa share evolutionary constraints that limit genetic variability. Studying patterns of genomic divergence among populations within the same species may shed light on the underlying evolutionary processes. Here, we examine transcriptome‐wide divergence and polymorphism in the marine copepod Tigriopus californicus, a species where allopatric evolution has led to replicate sets of populations with varying degrees of divergence and hybrid incompatibility. Our analyses suggest that relatively small effective population sizes have resulted in an exponential decline of shared polymorphisms during population divergence and also facilitated the fixation of slightly deleterious mutations within allopatric populations. Five interpopulation comparisons at three different stages of divergence show that nonsynonymous mutations tend to accumulate in a specific set of proteins. These include proteins with central roles in cellular metabolism, such as those encoded in mtDNA, but also include an additional set of proteins that repeatedly show signatures of positive selection during allopatric divergence. Although our results are consistent with a contribution of nonadaptive processes, such as genetic drift and gene expression levels, generating repeatable patterns of genomic divergence in closely related taxa, they also indicate that adaptive evolution targeting a specific set of genes contributes to this pattern. Our results yield insights into the predictability of evolution at the gene level.
A Nonlinear Dynamics Perspective of Wolfram's New Kind of Science Part III: Predicting the Unpredictable

We prove rigorously the four cellular automata local rules 110, 124, 137 and 193 have identical dynamic behaviors capable of universal computations. We exploit Felix Klein's remarkable Vierergruppe to partition the 256 local rules studied empirically by Wolfram into 89 global equivalence classes of which only 50 may exhibit complex dynamics. We define a 24-element rotation group which induces 30 local equivalence classes of nonlinear difference equations whose parameters can be mapped into each other among members of the same class.
Synovial immunopathological changes associated with successful abatacept therapy in a case of severe refractory psoriatic arthritis

The overlapping characteristics of rheumatoid arthritis and psoriatic arthritis (PsA) in terms of T-cell and macrophage infiltration and cytokine patterns suggest that targeted therapies could have a similar effect in both diseases.1 Tumour necrosis factor alpha (TNFα) blockers have shown efficacy in PsA, but a significant proportion of patients do not respond or are intolerant to these drugs.2 In these patients, agents blocking T-cell activation are a potential therapeutic option. Preliminary data have shown efficacy of abatacept in psoriasis vulgaris3 and spondyloarthropathy.4 However, data on the effects of abatacept in PsA are lacking. We describe the clinical and immunopathological effects of abatacept in a patient with PsA refractory to TNFα therapy. A …
Prevalence of Venous Thromboembolic Events After Elective Major Thoracolumbar Degenerative Spine Surgery

Study Design: A case-control study. Objective: The purposes of this study were to establish the prevalence of venous thromboembolic disease in patients undergoing elective major thoracolumbar degenerative spine surgery and identify risk factors. Summary of Background Data: Venous thromboembolic events (VTE) are a serious complication of orthopedic surgery, but the prevalence of VTE after elective thoracolumbar degenerative spine surgery is not well known. Methods: This was a case-control study of 5766 consecutive elective thoracolumbar degenerative spine surgeries. Symptomatic pulmonary emboli (PE) were diagnosed by spiral chest CT scans, nuclear scintigraphic ventilation-perfusion, and angiography. Deep vein thromboses (DVT) were diagnosed by venous duplex scans. The prevalence of VTE was analyzed according to patient demographic variables and type of surgery performed. Results: The prevalence of developing a VTE was 1.5% (89/5766), with a prevalence of symptomatic PE of 0.88% (51/5766) and DVT of 0.66% (38/5766). There were 47% males and 53% females with a mean age of 60.3 years. In patients undergoing 5-segment fusions the prevalence of PE was 3.1% (P=0.022). Patients who had ≥4 segments fused had a prevalence of PE of 1.7% (P=0.014). The odds of having a PE in those above 65 years at the time of surgery were 2.196 times as large as for those below 65 years. Noncontributory factors included sex, instrumentation, and revision surgery. Conclusions: This case-control study of 5766 patients who underwent elective thoracolumbar degenerative spine surgery revealed a prevalence of VTE of 1.5%, with a prevalence of PE of 0.88% and DVT of 0.66%. Patients with increasingly extensive surgery had a higher risk of PE, specifically those undergoing fusion of ≥5 segments.
Sexual Harassment in the Health Care Industry: A Follow-Up Inquiry

A nationwide survey of hospital human resources managers reveals that allegations of sexual harassment in hospitals are increasing. Reported statistics for a 4.5-year period show that nurses continue to bring the largest number of charges. Most are “hostile environment” allegations, and most formal charges are levied against coworkers. When compared to data gathered in an earlier survey, these statistics show an alarming trend. A significant increase in allegations occurred in 1999 and 2000, corresponding to two US Supreme Court rulings that clarify an employer's responsibility to eliminate this form of sexual discrimination from the workplace.
Burden of rotavirus gastroenteritis in children <5 years of age in Greece: hospital-based prospective surveillance (2008–2010)

Objectives This study describes the epidemiology of rotavirus (RV) gastroenteritis (GE) disease following the introduction of RV vaccination in Greece in 2006. Design A prospective hospital-based surveillance. Setting A multicentre study was conducted at six hospitals in Greece between July 2008 and March 2010. The hospitals selected served 70% of the paediatric population in Greece. Participants Children aged <5 years who visited the emergency rooms (ERs) or hospitalised with acute GE or acquired acute GE 48 h after hospitalisation and with a confirmed RV-positive stool test were enrolled. Primary and secondary outcome measures The occurrence of RVGE among all acute GE ER visits and hospitalisations and the occurrence of nosocomial RVGE are reported with 95% exact CI. Age-specific proportions of RVGE, seasonality and prevalence of RV genotypes were estimated. Incidence rates of nosocomial acute GE and RVGE are expressed in terms of 1000 children-years with 95% exact Poisson CI. Median duration of hospitalisation and prolongation of hospitalisation due to nosocomial RVGE were reported. Results RVGE proportions were 10.7% (95% CI 5.5% to 18.3%) and 23.8% (95% CI 20.0% to 28.0%) of acute GE ER visits and hospitalisations, respectively; and 21.6% (95% CI 9.8% to 38.2%) of nosocomial acute GE cases. The majority of RVGE cases occurred in children aged <24 months (53%). RV infection peaked between December and May (31.4%). The most common RV genotypes were G4 (59.6%) and P[8] (75.2%). The median duration of RVGE hospitalisation was 4 days (range 1–10 days). Incidence of nosocomial RVGE was 0.3 (95% CI 0.2 to 0.7)/1000 children-years. The median prolongation of hospitalisation due to nosocomial RVGE was 5 days (range 4–7 days). Conclusions Our analysis report low proportions of RVGE among acute GE cases in Greece which may be attributable to available RV vaccination in Greece. Future impact/effectiveness studies are necessary to confirm this finding. Clinical Trial Registration NCT00751686.
Selection and phenotypic characterization of nonhemagglutinating mutants of Porphyromonas gingivalis

To further investigate the relationship between fimbriae and the hemagglutinating adhesin HA-Ag2 of Porphyromonas gingivalis, three spontaneous mutants of the type strain ATCC 33277 were selected by a hemadsorption procedure. They were characterized for hemagglutination, trypsin-like and lectin-binding activities, and hydrophobicity and for the presence of fimbriae. The presence of the 42-kDa (the fimbrilin subunit) and the 43- and 49-kDa (the HA-Ag2 components) polypeptides was investigated by immunoblotting using polyclonal and monoclonal antibodies directed to fimbriae and to the hemagglutinating adhesin HA-Ag2. Cells from two of the three mutants (M1 and M2) exhibited no or little hemagglutination activity and very low trypsin-like activity and did not show the 43- and 49-kDa polypeptides. Abnormal fimbriation in M1 was deduced from the following observations of cells grown for 18 h: absence of the 42-kDa polypeptide and of a 14-kDa polypeptide and no fimbriae visible on electron micrographs. While the cells of mutant M2, irrespective of the age of the culture, were found to lack the 43- and 49-kDa polypeptides and hemagglutination activity, the supernatants of cultures grown for 72 h had high hemagglutination and trypsin-like activities and revealed the presence of the 42-, 43-, and 49-kDa polypeptides. This suggests that M2 may be missing some molecules which anchor the components to the cell surface. Mutant M3 showed levels of activities similar to those of the parental strain but lacked the 43-kDa polypeptide. Other pleiotropic effects observed for the mutants included loss of dark pigmentation and lower hydrophobicity. The data from this study fuel an emerging consensus whereby fimbriation, hemagglutination, and proteolytic activities, as well as other functions in P. gingivalis, are intricate.
Cigarette smoking among college students with disabilities : National College Health Assessment II , Fall 2008 e Spring 2009

Background: People with disabilities are 1.5 times more likely to smoke than their peers without disabilities, intensifying risk of health related disparities and further loss of function. When compared with the general population, college students also have a higher smoking prevalence. This study explores smoking rates among college students with disabilities. Objective/hypothesis: College students with disabilities have an increased likelihood of smoking, as compared with students without disabilities. Type of disability also influences smoking rates. Methods: This study explores the association between smoking and disability using multiple regression analyses and data from the National College Health Assessment II (NCHA II), Fall 2008eSpring 2009 (N 5 79,915). People with disabilities comprised 15.6% of the total sample: 3.4% reported a physical disability, 8.3% reported a mental disability, 2.5% reported a sensory disability, and 3.7% reported a learning disability. Results: Smoking prevalence among those reporting disabilities was 23.1% versus 15% in those without disabilities. Those reporting mental disabilities had the highest rates (29.9%), followed by those with learning disabilities (23.7%), sensory disabilities (19.8%), and physical disabilities (16.4%). Students with disabilities were 1.23 times more likely to report current smoking than those without any disabilities, controlling for other factors (OR 1.23, 95% CI 1.16e1.30). Discussion: Results are consistent with previous research regarding the general adult population. Epidemiologic data demonstrating differences in risk behaviors for young adults with disabilities are important in allocation of resources. Findings of this study highlight the need for tailored smoking cessation programs for college students with disabilities. 2013 Elsevier Inc. All rights reserved.
Automated Fluorescence Analysis of CAG Repeats at the Human Androgen Receptor Gene (HUMARA): Evaluation of Polymorphism in an Italian Sample and Report of a New Allele

The HUMARA CAG repeats polymorphism was studied in an Italian population sample. Polymerase chain reaction amplification and automated fluorescent analysis were used. A total of 19 and 15 repeats was observed in female and male subjects, respectively, and one new allele was found. The authors conclude that this X-linked short tandem repeat, typed without ambiguity and with a heterozygosity of 0.902, is useful in parentage testing of female subjects.
Variable-Region-Identical Antibodies Differing in Isotype Demonstrate Differences in Fine Specificity and Idiotype1

A central tenet of the current understanding of the relationship between Ab structure and function is that the variable region domain is solely responsible for Ag specificity. However, this view was recently challenged by the observation that families of mouse-human chimeric Abs with identical V regions demonstrate differences in fine specificity and by reports of changes in Ab Id structure with isotype switching. Here we revisited this question by evaluating the reactivity of two families of murine IgG switch variants that differed in V region usage for Cryptococcus neoformans glucuronoxylomannan, glucuronoxylomannan peptide mimetics, and anti-Id mAbs. The results reveal isotype-related differences in fine specificities and Id for two mAb isotype switched families, thus establishing the validity of this observation with sets of homologous Abs. The results suggest that the C region affects V region protein conformation, leading to differences in fine specificity and Id. The finding that isotype can affect fine specificity has major implications for current concepts of the generation of secondary responses, idiotypic network regulation, and isotype function. Given that isotype class switching and Ig gene somatic hypermutation share molecular mechanisms, these observations unify these processes in the sense that both can alter specificity and affinity.
Cigarette smoking by New Zealand doctors and nurses: results from the 1996 population census.

AIM To determine the prevalence of cigarette smoking among New Zealand doctors and nurses and to examine intercensal trends in smoking behaviour. METHODS The 1996 New Zealand population census included two questions on cigarette smoking. The data for doctors and nurses have been analysed and compared with results from the 1976 and 1981 censuses. RESULTS There were 7335 doctor respondents and 30,507 nurses. Five percent of male and female doctors smoke cigarettes regularly compared with 15% in 1981, 20% in 1976 and 35% in 1963. Almost 90% of doctors aged less than 30 years have never smoked and reductions in smoking have occurred in all specialties. Eighteen percent of nurses (18% females, 27% males) are smokers compared with 31% of females and 39% of males in 1981. The highest prevalence is among psychiatric nurses (31%) while only 10% of midwives and Plunket nurses are smokers. CONCLUSIONS Doctors continue to lead the New Zealand community in non-smoking and the goal of a smokefree medical profession by the year 2000 may be achievable. In contrast to 1981, the prevalence of smoking by female nurses (18%) is now less than women in the general New Zealand population (23%). Substantial reductions in smoking have occurred in all categories of the nursing profession.
Feedback and Feeding in the Context of Galaxy Evolution with SPICA: Direct Characterisation of Molecular Outflows and Inflows

Abstract A far-infrared observatory such as the SPace Infrared telescope for Cosmology and Astrophysics, with its unprecedented spectroscopic sensitivity, would unveil the role of feedback in galaxy evolution during the last ~10 Gyr of the Universe (z = 1.5–2), through the use of far- and mid-infrared molecular and ionic fine structure lines that trace outflowing and infalling gas. Outflowing gas is identified in the far-infrared through P-Cygni line shapes and absorption blueshifted wings in molecular lines with high dipolar moments, and through emission line wings of fine-structure lines of ionised gas. We quantify the detectability of galaxy-scale massive molecular and ionised outflows as a function of redshift in AGN-dominated, starburst-dominated, and main-sequence galaxies, explore the detectability of metal-rich inflows in the local Universe, and describe the most significant synergies with other current and future observatories that will measure feedback in galaxies via complementary tracers at other wavelengths.
Circulation in the reptilian heart (Caiman sclerops)

Current views on the circulatory mechanics of the crocodilian heart present a picture of a relatively inefficient organ which allows mixing of aerated and non-areated blood. Indeed, this concept has a logical anatomical basis. Although there is a complete interventricular septum, the left aortic arch takes its origin along with the pulmonary artery from the right ventricular chamber. The left arch, then, should clearly receive venous blood. Connecting the bases of the two aortic arches is a foramen, the Foramen Panizzae, through which it has been reasoned some aerated blood from the right aortic arch enters the left arch resulting in a “mixed” condition of left aortic blood. Estimates of the degree of mixing range from “considerable” to “slight. ” Considerable work has been directed toward the descriptive anatomy of the reptilian heart (for resume see Mathur, ’46) ; however, functional interpretations are based chiefly upon the concept of “mixing. ” The viewpoint that the left aortic arch has been lost in the avian ancestors due to a selective pressure against the mixed condition of the left aortic blood is based upon the “mixing” concept. Panizza in 1833 (Greil, ’03) published an account of the heart of Crocodilus lucius (Alligator mississippiensis) in ’ From a thesis for the Doctor of Philosophy, University of Illinois.
AccGenSVM: Selectively Transferring from Previous Hypotheses

In our research, we consider transfer learning scenarios where a target learner does not have access to the source data, but instead to hypotheses or models induced from it. This is called the Hypothesis Transfer Learning (HTL) problem. Previous approaches concentrated on transferring source hypotheses as a whole. We introduce a novel method for selectively transferring elements from previous hypotheses learned with Support Vector Machines. The representation of an SVM hypothesis as a set of support vectors allows us to treat this information as privileged to aid learning during a new task. Given a possibly large number of source hypotheses, our approach selects the source support vectors that more closely resemble the target data, and transfers their learned coefficients as constraints on the coefficients to be learned. This strategy increases the importance of relevant target data points based on their similarity to source support vectors, while learning from the target data. Our method shows important improvements on the convergence rate on three classification datasets of varying sizes, decreasing the number of iterations by up to 56% on average compared to learning with no transfer and up to 92% compared to regular HTL, while maintaining similar accuracy levels.
TheRole ofRoboticsTeams’CollaborationQualityon TeamPerformance in aRoboticsTournament

Background Working effectively in teams is an important 21st century skill as well as a fundamental component of the ABET professional competencies. However, successful teamwork is challenging, and empirical studies with adolescents concerning how the collaboration quality of team members is related to team performance are limited. Purpose/Hypothesis This study investigated the relationship between team collaboration quality and team performance in a robotics competition using multiple measures of team performance, including both objective task performance and expert judge evaluations, on a diverse set of supporting performance dimensions. Design/Method Data included Table Score, Robot Design, Research Project, Core Values, and Collaboration Quality scores for 366 youths on 61 K-8 robotics teams that participated in a FIRST LEGO League Championship. Regression and mediation analyses were conducted to explore the relation between effective team collaboration and team performance. Furthermore, analysis of variance was conducted to explore the relationship between Collaboration Quality and team experience. Results Collaboration Quality was a good predictor of robotics team performance across all measures (with R 5 .50 and p< .001). Mediation analysis revealed that the Robot Design acted as a full mediator for the predictive effect of Collaboration Quality on the Table Score. In addition, the cumulative amount of team experience was significantly related to Collaboration Quality. Conclusions Overall, this study using collaboration performance assessments and actual competition data with a large number of teams confirms the importance of high-quality teamwork in producing superior products with students engaged in authentic engineering tasks.
Sleep habits, excessive daytime sleepiness and school performance in high school students

Abstract A questionnaire survey was carried out to examine the sleep habits and excessive daytime sleepiness (EDS) of 3871 high school students with a mean age of 16.8 years in Korea. The results showed that mean total sleep time was 6.3 h/day for male students and 6.5 h/day for female students, which may be insufficient for adolescence during puberty. The overall prevalence of EDS (defined as an Epworth sleepiness scale score of >10) was 15.9% (14.9% for boys and 18.2% for girls). The prevalence of EDS increased significantly (P < 0.001) with a decline in school performance.
G 6 PC 2 A Negative Regulator of Basal Glucose-Stimulated Insulin Secretion

Elevated fasting blood glucose (FBG) is associated with increased risk for the development of type 2 diabetes and cardiovascular-associated mortality. Genome-wide association studies (GWAS) have linked polymorphisms in G6PC2 with variations in FBG and body fat, although not insulin sensitivity or glucose tolerance. G6PC2 encodes an islet-specific, endoplasmic reticulum–resident glucose-6-phosphatase catalytic subunit. A combination of in situ perfused pancreas, in vitro isolated islet, and in vivo analyses were used to explore the function of G6pc2 in mice. G6pc2 deletion had little effect on insulin sensitivity and glucose tolerance, whereas body fat was reduced in female G6pc2 knockout (KO) mice on both a chow and high-fat diet, observations that are all consistent with human GWAS data. G6pc2 deletion resulted in a leftward shift in the dose-response curve for glucose-stimulated insulin secretion (GSIS). As a consequence, under fasting conditions in which plasma insulin levels were identical, blood glucose levels were reduced in G6pc2 KO mice, again consistent with human GWAS data. Glucose6-phosphatase activity was reduced, whereas basal cytoplasmic calcium levels were elevated in islets isolated from G6pc2 KO mice. These data suggest that G6pc2 represents a novel, negative regulator of basal GSIS that acts by hydrolyzing glucose6-phosphate, thereby reducing glycolytic flux.
THE SIMULTANEOUS CONJUGACY PROBLEM IN GROUPS OF PIECEWISE LINEAR FUNCTIONS

Guba and Sapir asked, in their joint paper [8], if the simultaneous conjugacy problem was solvable in Diagram Groups or, at least, for Thompson's group F. We give an elementary proof for the solution of the latter question. This relies purely on the description of F as the group of piecewise linear orientation-preserving homeomorphisms of the unit. The techniques we develop allow us also to solve the ordinary conjugacy problem as well, and we can compute roots and centralizers. Moreover, these techniques can be generalized to solve the same questions in larger groups of piecewise-linear homeomorphisms.