Miracle-dz/UniFAR-FTUs huggingface dataset:
A MULTILOCUS PERSPECTIVE ON COLONIZATION ACCOMPANIED BY SELECTION AND GENE FLOW

Abstract The colonization of novel habitats involves complex interactions between founder events, selection, and ongoing migration, and can lead to diverse evolutionary outcomes from local extinction to adaptation to speciation. Although there have been several studies of the demography of colonization of remote habitats, less is known about the demographic consequences of colonization of novel habitats within a continuous species range. Populations of the Eastern Fence Lizard, Sceloporus undulatus, are continuously distributed across two dramatic transitions in substrate color in southern New Mexico and have undergone rapid adaptation following colonization of these novel environments. Blanched forms inhabit the gypsum sand dunes of White Sands and melanic forms are found on the black basalt rocks of the Carrizozo lava flow. Each of these habitats formed within the last 10,000 years, allowing comparison of genetic signatures of population history for two independent colonizations from the same source population. We present evidence on phenotypic variation in lizard color, environmental variation in substrate color, and sequence variation for mitochondrial DNA and 19 independent nuclear loci. To confirm the influence of natural selection and gene flow in this system, we show that phenotypic variation is best explained by environmental variation and that neutral genetic variation is related to distance between populations, not partitioned by habitat. The historical demography of colonization was inferred using an Approximate Bayesian Computation (ABC) framework that incorporates known geological information and allows for ongoing migration with the source population. The inferences differed somewhat between mtDNA and nuclear markers, but overall provided strong evidence of historical size reductions in both white sand and black lava populations at the time of colonization. Populations in both novel habitats appear to have undergone partial but incomplete recovery from the initial bottleneck. Both ABC analyses and measures of mtDNA sequence diversity also suggested that population reductions were more severe in the black lava compared to the white sands habitat. Differences observed between habitats may be explained by differences in colonization time, habitat geometry, and strength or response to natural selection for substrate matching. Finally, effective population size reductions in this system appear to be more dramatic when colonization is accompanied by a change in selection regime. Our analyses are consistent with a demographic cost of adaptation to novel environments and show that it is possible to infer aspects of the historical demography of local adaptation even in the presence of ongoing gene flow.
Dynamics of FtsZ Assembly during Sporulation in Streptomyces coelicolor A3(2)

ABSTRACT FtsZ, the bacterial tubulin homologue, is the main player in at least two distinct processes of cell division during the development of Streptomyces coelicolor A3(2). It forms cytokinetic rings and is required for the formation of both the widely spaced hyphal cross walls in the substrate mycelium and the specialized septation that converts sporogenic aerial hyphae into spores. The latter developmentally controlled septation involves the coordinated assembly of large numbers of FtsZ rings in each sporulating hyphal cell. We used an FtsZ-enhanced green fluorescent protein (EGFP) translational fusion to visualize the progression of FtsZ ring assembly in vivo during sporulation of aerial hyphae. This revealed that the regular placement of multiple FtsZ rings and initiation of cytokinesis was preceded by a protracted phase during which spiral-shaped FtsZ intermediates were detected along the length of the aerial hyphal cell. Time course experiments indicated that they were remodeled and gradually replaced by regularly spaced FtsZ rings. Such spiral-shaped filaments could also be detected with immunofluorescence microscopy using an antiserum against FtsZ. Based on our observations, we propose a model for the progression of Z-ring assembly during sporulation of S. coelicolor. Furthermore, mutants lacking the developmental regulatory genes whiA, whiB, whiG, whiH, and whiI were investigated. They failed in up-regulation of the expression of FtsZ-EGFP in aerial hyphae, which is consistent with the known effects of these genes on ftsZ transcription.
Fas antigen stimulation induces marked apoptosis of T lymphocytes in human immunodeficiency virus-infected individuals

Apoptosis (programmed cell death) of T lymphocytes has been proposed as a mechanism which plays an important role in the pathogenesis of human immunodeficiency virus (HIV) disease. Activation of Fas (CD95) can either result in costimulation of proliferation and cytokine production or in the induction of apoptosis of T lymphocytes. This raises the possibility that Fas is involved in the observed T cell apoptosis during HIV disease. In this report we show that peripheral blood CD4+ and CD8+ T lymphocytes from HIV-infected individuals undergo apoptosis in vitro in response to antibody stimulation (cross-linking) of Fas at a much higher frequency than from uninfected controls. This anti-Fas- induced T cell apoptosis is markedly higher than spontaneous T cell apoptosis in HIV-infected individuals. Antibodies against other members of the tumor necrosis factor (TNF)/nerve growth factor receptor family such as CD27, CD30, CD40, 4-1BB, p55 TNF receptor, p75 TNF receptor, and TNF receptor-related protein did not result in any increase of T cell apoptosis above that spontaneously observed in HIV+ individuals. Anti-Fas-induced apoptosis was much higher in symptomatic HIV-infected individuals; and the magnitude of anti-Fas-induced CD4+ T cell apoptosis correlated inversely with peripheral blood CD4+ T cell absolute counts. Surface expression of Fas on T cells was also found to be higher in HIV-infected individuals. Resting and activated CD4+ and CD8+ T cells both underwent apoptosis in response to anti-Fas antibody. L-Selectin positive memory CD4+ T cells were especially susceptible to anti-Fas-induced apoptosis. These findings show that CD4+ and CD8+ T lymphocytes in HIV-infected individuals are primed in vivo to undergo apoptosis in response to Fas stimulation, suggesting that Fas signaling may be responsible for the T lymphocyte functional defects and depletion observed in HIV disease.
Risks of Preterm Delivery and Small for Gestational Age Infants: Effects of Nondaily and Low‐Intensity Daily Smoking During Pregnancy

BACKGROUND Few studies have examined the effects of nondaily smoking or low-intensity daily smoking and infant outcomes. We examined the associations between preterm delivery and small for gestational age (SGA) infants in relation to both nondaily and daily smoking. METHODS We used population-based data on women who delivered live singleton infants using the 2009-11 Pregnancy Risk Assessment Monitoring System. Women's smoking status in the last 3 months of pregnancy was categorised as nonsmokers, quitters, nondaily smokers (<1 cigarette/day), and daily smokers. Controlling for maternal age, maternal race/ethnicity, education, marital status, prepregnancy body mass index (BMI), trimester of prenatal care entry, parity, and alcohol use, we estimated adjusted prevalence ratios (PR) for the outcomes of preterm delivery (<37 weeks' gestation) and SGA. RESULTS Of the 88 933 women, 13.1%, 1.7%, and 9.6% of the sample were quitters, nondaily smokers, and daily smokers, respectively, in the last 3 months of pregnancy. While nondaily smoking was not associated with preterm delivery, daily smoking was. However, we found no dose-response relationship with the number of cigarettes smoked per day. Risk of delivering a SGA infant was increased for both nondaily and daily smokers (PR 1.4, 95% CI 1.1, 1.8 and PR 2.0, 95% CI 1.9, 2.2 respectively). CONCLUSIONS Nondaily smoking in the last 3 months of pregnancy was associated with an increased risk of delivering a SGA infant. Pregnant women should be counselled that smoking, including nondaily and daily smoking, can adversely affect birth outcomes.
Errorless learning and spaced retrieval techniques to relearn instrumental activities of daily living in mild Alzheimer’s disease: A case report study

Previous studies on cognitive training in Alzheimer’s disease (AD) were principally aimed at making patients learn items not related to functional needs. However, AD patients also experience difficulties with instrumental activities of daily living (IADL). The goal of the present multiple baseline case report study was to assess the preliminary efficacy and tolerability of an individualized cognitive training program using the errorless learning (EL) and spaced-retrieval (SR) techniques to relearn forgotten IADLs in mild AD. Following an exhaustive neuropsychological assessment, two participants received two training sessions per week during four weeks. Participant A was trained to use his voice mail and Participant B, to manage the messages from his answering machine. The results showed that the program was well tolerated and improved performance on the trained tasks. These ameliorations were maintained over a 5-week period. The effects of the training did not have any impact on global cognitive functions since the results on these measures remained relatively stable. This case report demonstrated preliminary efficacy of a new cognitive training program using EL and SR techniques tailored to the needs of AD patients. This is an important finding since the loss of these capacities alters autonomy in AD patients.
Behavioural disorders in children with epilepsy: early improvement after surgery

OBJECTIVES Epilepsy surgery has proved to be a successful intervention method to achieve freedom from seizures or seizure relief in children with pharmacoresistant epilepsy. Long term studies on operated children suggest that behavioural disorders, which are often seen before surgery, improve after surgery. However, the early postoperative development of behavioural problems has not been systematically evaluated. METHODS Parents of 28 children with pharmacoresistant focal epilepsies completed the child behaviour checklist (CBCL) preoperatively and 3 months after surgery. Surgeries comprised 24 focal resections (13 temporal, 11 extratemporal), two hemispherectomies, and two callosotomies. Twenty eight conservatively treated children with comparable CBCL scores served as a control group. A repeated measurement multivariate analysis of variance (MANOVA) and a regression analysis were computed to compare the development of behaviour between both groups and to identify predictors of postoperative changes in behaviour. RESULTS Preoperatively 39% of the children exhibited significant behavioural problems, a further 11% were within the borderline range. The MANOVA disclosed a significant interaction between time of examination and group (F=2.23, p<0.05). The surgery group showed significant improvements on the scales “internalising problems”, “externalising problems”, “attention problems”, and “thought problems”. Behavioural problems in the control group, however, remained unchanged. No changes were seen in social problems in both groups. The significant predictor of total behavioural improvement was a good seizure outcome (R 2=0.11, p<0.05). Age, sex, onset, and duration of epilepsy, the site of the focus, and changes in antiepileptic drug regimen did not influence changes in behaviour. CONCLUSIONS The data demonstrate an early improvement of behavioural problems after epilepsy surgery in children. The behavioural improvements can be assumed to result directly from the removal of the epileptic focus. They are not predictable on the basis of information available preoperatively, but depend on the seizure outcome.
Discriminant analysis

In many ways, discriminant analysis parallels multiple regression analysis. The main difference between these two techniques is that regression analysis deals with a continuous dependent variable, while discriminant analysis must have a discrete dependent variable. The methodology used to complete a discriminant analysis is similar to regression analysis. You plot each independent variable versus the group variable. You often go through a variable selection phase to determine which independent variables are beneficial. You conduct a residual analysis to determine the accuracy of the discriminant equations.
Psychological Treatment for Adolescent Depression: Perspectives on the Past, Present, and Future

Abstract The objective of this review is to summarise the evidence for mindfulness and acceptance approaches in the treatment of adolescent depression. The article begins by summarising the outcomes of three broad approaches to the treatment of adolescent depression — primary prevention, pharmacotherapy, and psychotherapy — in order to advocate for advances in treatment. With regard to psychotherapy, we restrict this to comparisons of meta-analytic studies, in order to cover the breadth of the outcome literature. In the second half of this article, we introduce the reader to mindfulness and acceptance-based psychotherapy, with a particular focus on Acceptance and Commitment Therapy (ACT) and the applicability with adolescents. We provide an overview of the philosophical arguments that underlie this approach to psychotherapy and consider how each of these might contribute to treatment approaches for adolescents with depression.
Asymptomatic bacteriuria and urinary tract infections among renal allograft recipients

Purpose of review Bacteriuria is common among renal allograft recipients. It can be categorized into asymptomatic bacteriuria (ASB) and urinary tract infection (UTI). However, in medical literature, the classifications of bacteriuria are often not clear or ASB is also classified as a UTI. This contributes to difficulties in interpretation of the incidence and risk factors of these two entities. In this review, we describe the epidemiology, risk factors, management and the impact on renal allograft function of these two entities separately according to the recent literature. Recent findings Risk factors for ASB are not completely comparable to the risk factors of UTIs. Persistent ASB has been associated with development of acute rejection and allograft pyelonephritis. The available data suggest that treatment of ASB is not very effective. Prophylaxis with trimethoprim–sulfamethoxazole does not prevent UTIs such as allograft pyelonephritis. Blood stream infections and emphysematous allograft pyelonephritis are associated with renal allograft loss. Summary ASB is the most common manifestation of bacteriuria after renal transplantation. More effective interventions are needed to prevent bacteriuria. Renal allograft recipients with persistent ASB should be closely monitored since they could be at risk for developing not only UTIs, such as allograft pyelonephritis, but also acute rejection.
Characterization and application of HfO2 - SiO2 mixtures produced by ion-beam sputtering technology

In the past years the usage of mixed oxides coatings lead to an important improvement of laser damage threshold and quality of optical elements. In this study influence of post treatment procedure - ex-situ annealing - is examined in terms of quality, optical constants and laser induced damage threshold (LIDT) of mixed HfO2 and SiO2 coatings. Monolayer thin films containing different fractions of HfO2 are deposited with ion beam sputtering technology (IBS.) All samples are post annealed at different temperatures and optimal regimes are defined. Refractive index and absorption coefficient dispersion is evaluated from transmission spectra measurements. Surface roughness of all samples is characterized before and after deposition and annealing, using atomic force microscopy (AFM). Microstructural changes are identified from changes in surface topography. Further, optical resistance was characterized by 5.7 ns duration pulses for 355 nm wavelength laser radiation, performing 1-on-1 sample exposure tests with high resolution micro-focusing approach for monolayer samples and S-on-1 tests for multilayer reflectors. Morphology of damaged sites was analyzed through optical microscopy. Finally, conclusions about annealing effect for mixed HfO2 and SiO2 monolayer and multilayer coatings are made.
The use of cholesterol-lowering medications after coronary revascularization.

BACKGROUND In clinical trials, cholesterol-lowering medications have been proven to decrease mortality and morbidity and are strongly recommended as secondary prevention for patients with established coronary artery disease. Whether physicians and patients follow this recommendation is unknown. Our objective was to determine the rate at which patients fill at least one prescription for cholesterol-lowering medications after coronary revascularization. METHODS Using the computerized administrative databases of the Régie de l'assurance maladie du Québec, we identified all elderly patients (older than 65 years) who had a coronary revascularization procedure (percutaneous coronary intervention or coronary artery bypass graft) between Apr. 1, 1995, and Dec. 31, 1997, and who survived until hospital discharge. We also determined the percentage of these patients who filled one or more prescriptions for cholesterol-lowering drug therapy before Dec. 31, 1999, or death, whichever date came first. We used multivariate logistic regression models to examine the independent associations between filling a prescription for a cholesterol-lowering drug, patient characteristics and the type and year of coronary revascularization. RESULTS We identified 11 958 elderly patients who had a coronary revascularization between Apr. 1, 1995, and Dec. 31, 1997. During a follow-up period that averaged 3 years, 4443 (37.2%) patients did not fill a prescription for a cholesterol-lowering medication. Patients who were male, of advanced age, who had diabetes or congestive heart failure were less likely to fill a prescription for a cholesterol-lowering medication. Patients whose initial revascularization procedure was coronary artery bypass grafting were also less likely than those who had angioplasty to start cholesterol-lowering medication (relative risk [RR] 0.77, 95% confidence interval [CI] 0.73 - 0.81). Use of cholesterol lowering medications before the revascularization procedure was very strongly associated with future drug use (RR 7.20, 95% CI 6.83-7.58). INTERPRETATION In this population-based study of revascularized patients, we observed a substantial underutilization of cholesterol-lowering medications after revascularization. Our observations suggest an important role for continuity of care in the treatment of cardiovascular patients undergoing revascularization procedures.
Development of diversity array technology (DArT) markers for assessment of population structure and diversity in Aegilops tauschii

Aegilops tauschii Coss. is the D-genome donor to hexaploid bread wheat (Triticum aestivum) and is the most promising wild species as a genetic resource for wheat breeding. To study the population structure and diversity of 81 Ae. tauschii accessions collected from various regions of its geographical distribution, the genomic representation of these lines were used to develop a diversity array technology (DArT) marker array. This Ae. tauschii array and a previously developed DArT wheat array were used to scan the genomes of the 81 accessions. Out of 7500 markers (5500 wheat and 2000 Ae. tauschii), 4449 were polymorphic (3776 wheat and 673 Ae. tauschii). Phylogenetic and population structure studies revealed that the accessions could be divided into three groups. The two Ae. tauschii subspecies could also be separately clustered, suggesting that the current taxonomy might be valid. DArT markers are effective to detect very small polymorphisms. The information obtained about Ae. tauschii in the current study could be useful for wheat breeding. In addition, the new DArT array from this Ae. tauschii population is expected to be an effective tool for hexaploid wheat studies.
Suicide Risk Assessment and Prevention: A Systematic Review Focusing on Veterans.

OBJECTIVE Suicide rates in veteran and military populations in the United States are high. This article reviews studies of the accuracy of methods to identify individuals at increased risk of suicide and the effectiveness and adverse effects of health care interventions relevant to U.S. veteran and military populations in reducing suicide and suicide attempts. METHODS Trials, observational studies, and systematic reviews relevant to U.S. veterans and military personnel were identified in searches of MEDLINE, PsycINFO, SocINDEX, and Cochrane databases (January 1, 2008, to September 11, 2015), on Web sites, and in reference lists. Investigators extracted and confirmed data and dual-rated risk of bias for included studies. RESULTS Nineteen studies evaluated accuracy of risk assessment methods, including models using retrospective electronic records data and clinician- or patient-rated instruments. Most methods demonstrated sensitivity ≥80% or area-under-the-curve values ≥. 70 in single studies, including two studies based on electronic records of veterans and military personnel, but specificity varied. Suicide rates were reduced in six of eight observational studies of population-level interventions. Only two of ten trials of individual-level psychotherapy reported statistically significant differences between treatment and usual care. CONCLUSIONS Risk assessment methods have been shown to be sensitive predictors of suicide and suicide attempts, but the frequency of false positives limits their clinical utility. Research to refine these methods and examine clinical applications is needed. Studies of suicide prevention interventions are inconclusive; trials of population-level interventions and promising therapies are required to support their clinical use.
Time Resolved Observation of BOLD Effect in Muscle During Isometric Exercise

Introduction The BOLD-contrast mechanism arises from the change of blood oxygenation during cortical activation as a consequence of the increased arterial blood supply, which is most likely due to the increased oxygen demand. It has been originally suggested for the observation of neuronal activation (1). Recently it could be demonstrated, that changes in blood oxygen level can also be used for the observation of myocardial perfusion. In skeletal muscles an increase in perfusion as been observed by Frank using arterial spin label (ASL) techniques (2). The purpose of this study was to demonstrate, whether a BOLD-effect arises during muscle exercise and to assess its temporal signature.