Miracle-dz/UniFAR-FTUs huggingface dataset:
Highly Discordant Nuclear and Mitochondrial DNA Diversities in Atka Mackerel

Abstract Levels of neutral genetic diversity largely reflect effective population size (Ne), which is influenced by physical and biological environmental variables. While large populations of marine fishes generally harbor higher diversities than freshwater species, historical demography or the effects of natural selection may significantly reduce Ne and differentially affect genomic diversities. Here, we surveyed levels of genetic diversity and examined genetic structure among populations of the Atka mackerel Pleurogrammus monopterygius across most of its geographic range by screening variation at nine nuclear microsatellite DNA markers (n = 745) and in a 468-base-pair segment of the mitochondrial DNA (mtDNA) control region (n = 119). Samples from Japan to the western Gulf of Alaska were collected between 2004 and 2006 at six locations, including temporal replicates at two sites. Microsatellite allele frequency homogeneity across the North Pacific indicated an apparent lack of genetic population substructure. While levels of polymorphism at microsatellite loci were typical for marine fishes (haplotype diversity h = 0.34–0.96), mtDNA control region diversity was extremely low (nucleotide diversity = 0.00007; h = 0.033). Only three mtDNA haplotypes, two occurring as singletons, were detected among 119 individuals. The strong contrast between microsatellite and mtDNA diversities appears to be due to the smaller Ne for mtDNA, perhaps resulting from population bottlenecks during postglacial colonizations of the central North Pacific or the effects of natural selection on mtDNA.
Measuring Extreme Market Risk: The Sri Lankan Context

Abstract Many empirical studies have been carried out in developed and emerging markets using methods to account for extreme market risk. A front-runner in the methods used is Extreme Value Theory (EVT). In this study, these methods are applied to the All Share Price Index (ASPI) of the Colombo Stock Exchange (CSE) to obtain risk forecasts for VaR (Value at Risk) and ES (Expected Shortfall) at 99% confidence level. Recognizing the merits of both conditional and unconditional models for risk measures the most suitable unconditional model and conditional model are found for the ASPI. Contrary to other studies the Historical Simulation method was found to be more appropriate for obtaining static estimates than the static EVT model. The Two-Step Approach of McNeil and Frey which combines EVT and Generalized Auto-Regressive Conditional Heteroskedasticity (GARCH) methodologies was found to be the most appropriate conditional model. Backtesting of models is done using a binomial test, Christoferssen’s conditional coverage test and McNeil and Frey’s ES test.
Antagonistic modulation of gliomagenesis by Pax6 and Olig2 in PDGF‐induced oligodendroglioma

Gliomas are aggressive tumors of the central nervous system originating from proliferating neural cells. Regulators of neural stem or progenitor cells biology may thus influence aspects of brain tumorigenesis, such as the maintenance of tumor‐propagating potential. We investigated the role of Pax6, a neurogenic transcription factor already suggested as a positive prognostic marker for human gliomas, in a well‐characterized in vivo model of PDGF‐B‐driven oligodendroglioma. In this system, the expression of Pax6 severely impairs tumor propagation by inducing a reduction of cell proliferation and the acquisition of differentiation traits in tumor‐initiating cells. The overexpression of Pax6 correlates with a downregulation of Olig2, a bHLH transcription factor that normally antagonizes Pax6 in adult neurogenic niches and that plays a key role in the maintenance of neural stem and progenitor cells. Furthermore, we found that Olig2 is strictly required to maintain the malignancy of oligodendroglioma cells, since its silencing by interfering RNA abrogates tumor propagation. We finally show evidence that this function depends, at least in part, on the silencing of ID4, a dominant negative bHLH protein, whose upregulation follows Olig2 loss. In our model, the upregulation of ID4 mimics the loss of Olig2 in impairing the tumor‐propagating potential of glioma cells. Our data, therefore, establish the relevance of physiological regulators of neural stem cell biology in regulating glial tumor malignancy and provide support for their functional interactions in this context.
Good Jobs and Recidivism

I estimate the impact of employment opportunities on recidivism among 1.7 million offenders released from a California state prison between 1993 and 2009. The institutional structure of the California criminal justice system as well as location-, skill-, and industry-specific job accession data provide a unique framework to identify a causal effect of labor demand on criminal behavior. I find that increases in construction and manufacturing employment opportunities at the time of release are associated with significantly lower recidivism rates. Other types of employment opportunities, including those typically accessible to individuals with criminal records but characterized by much lower wages, do not influence recidivism rates. My results illustrate the importance of considering job quality when estimating the impact of employment opportunities on crime and when designing programs to help former inmates successfully reenter noninstitutionalized society.
Differential Sensitivity to ACTH, but Not Stress, in Two Sources of Outbred Sprague-Dawley Rats

Adrenocorticotropic hormone (ACTH) is the major regulator of adrenocortical steroidogenesis in mammals. By comparing the sensitivity to ACTH of isolated adrenocortical cells from two sources of the same strain (Sprague-Dawley, SD) of outbred rats, we have identified a source of rat with low sensitivity to ACTH in vitro. Cells isolated from Holtzman SD rats had a high sensitivity to ACTH (minimal effective concentration 50 pg/ml), whereas Taconic SD rats had a low sensitivity (minimal effective concentration 250 pg/ml; maximal steroidogenesis <50% of Holtzman cells). The responsiveness to analogues of cyclic adenosine monophosphate and cholesterol was also significantly lower in Taconic SD rats. Taconic adrenals were smaller, had significantly more mitochondria per cell, but approximately 20% less total lipid droplet volume per cell. There was no difference in latency to ACTH in vitro; however, steroidogenesis plateaued in Taconic cells after 25 min, while Holtzman cells secreted corticosterone almost linearly for at least 120 min. By contrast, the cyclic adenosine monophosphate secretion increased at the same rate for at least 120 min in cells from both sources. There were no differences between cells from the two sources in immunoreactive steroidogenic enzyme content. In vivo, the magnitude of the ACTH and corticosterone responses to two types of stress were similar in both sources. The thymus glands of Holtzman rats were significantly larger than those of Taconic rats. It is concluded that: (1) reduced sensitivity to ACTH in vitro in Taconic SD rats results from differences in the later stages of the steroidogenic pathway; (2) factors in addition to ACTH are required for maximal steroidogenesis in Taconic SD rats; (3) a comparison of the steroidogenic pathways in adrenal cells from these two sources of outbred rats should be useful in further delineating the relative importance of putative intracellular signalling mechanisms involved in initiation and maintenance of steroidogenesis, and (4) these data suggest that different sources of the same strain of rats sufficiently diverge over time to become separate strains (‘substrains’). Overreliance on a single source of laboratory rodent may obscure natural variability in endocrine responses to stress and provide a misleading indication of homogeneity of responses.
All-Optical Modulation and Ultrafast Switching in MWIR with Sub-Wavelength Structured Silicon

We investigated and optimised the performance of the all-optical reflective modulation of the Mid-Wave Infrared (MWIR) signal by means of the optically-pumped sub-wavelength-structured optical membranes made of silicon. The membranes were optically pumped by a 60-femtosecond, 800-nm laser, while another laser operating in the MWIR ranging between 4 and 6 μ m was used to probe the optical response and modulation. We were able to achieve the conditions providing the modulation depth of 80% using the pump fluence of 3.8 mJ/cm 2 . To get a better insight into the performance and the modulation mechanism, we developed an optical model based on a combination of the Wentzel–Kramers–Brillouin approximation, Drude and Maxwell–Garnett theories. The model allowed us to estimate the values of the dielectric function, carrier concentration and scattering rate of the optically-excited membrane in the MWIR range. Using the model, we optimised the performance and found the conditions at which the reflective modulation can be operated with the ultrafast response of 0.55 ps and modulation contrast of 30%.
How Did Financial Development Affect the Performance of European Firms Before and After the 2008 Credit Crisis?

The recent credit crisis led to a serious downturn in the United States and the rest of the world. This article analyzes the relationship between the crisis and financial development based upon European firm-level data. It studies how the level of financial development interacts with a firm’s dependence on external financing, as well as its size and age, in determining a firm’s earnings. It also tries to identify which factors explain the spread of shocks and their impacts on different firms during the crisis period. The results show that financial development is positively related to a firm’s earnings. Surprisingly, however, it can also exacerbate the impact of a crisis.
Cardiac-respiratory-somatic relationships and feedback effects in a multiple session heart rate control experiment.

An experiment addressing several unresolved issues in operant in human subjects was performed. Cardiac-respiratory relationships. cardiac-somatic re! :atl~}nshipls. effects of biofeedback, and individual differences were examined in terms of their across multiple training sessions. Thirty subjects participated in 3 training sessions. Each session began with" trials HR change without feedback followed by 8 trials with "proportional" feedback of HR. 01'1 half the trials HR decrease was attempted while HR increase was attempted on the other half. Sulbjeds instructed to keep their respiration rate (RR) constant and not to engage in undue movement or muscle activity. Results indicated that subjects were able to produce significant HR increases and decreases from baseline levels, but these changes were accompanied by parallel changes in respiratory and somatic variables which persisted across sessions. Analysis of data from individual was . ·f"' . ",. to explore the nature of Individual differences in cardlac-respiratory-somatic The el'ects of biofeedback were unimpressive, suggesting at best a minor improvement in cardiac control with increased respiratory concomitance. Cardiac control, feedback and cardiac-somatic patterns were stable over sessions. There was evidence of some reduction In If'lu'riiIU·. ifl! '<! nill'·llItl'I! "V parallelism across sessions. DESCRIPTORS: Operant conditioning, Heart rate, Respiration, Cardiac-somatic rel.aUon! ihil~. Biofeedback, Individual differences. In spite of difficulties which have surfaced with research on operant conditioning of cardiac re­ sponses in animals (Miller & Dworkin. 1974). re­ search of this nature with human subjects has con­ tinued. Human research, although unlikely to an­ swer definitively the question of whether a . 'pure " cardiac response can be operantly conditioned, has potential for answering a number of questions con­ cerning the relationship between autonomic and central processes. Although a large body of human research exists, many basic questions remain unan­ swered. In a recent review of operant conditioning of cardiac functions, McCanne and Sandman (1976) identified several areas in need of further research induding: the precise nature of the relationship of
Effect of combining platelet-rich plasma with anorganic bovine bone on vertical bone regeneration: early healing assessment in rabbit calvariae.

PURPOSE The purpose of this study was to evaluate the combination of anorganic bovine bone allograft (ABB) with platelet-rich plasma (PRP) when used in vertical bone augmentation. MATERIALS AND METHODS Sixteen healthy 6-month-old female New Zealand rabbits were used in this study. Rabbits were randomly divided into two groups of eight animals each. Created calvarial defects were grafted with ABB or PRP in the first group whereas, in the second group, one cylinder was filled with PRP+ABB and the contralateral cylinder was left ungrafted to be filled by autologous blood (control cylinder). Six weeks after intervention, animals were sacrificed and biopsies were taken. Densitometric, histologic, and histomorphometric analyses were performed to evaluate bone mineral density, vertical bone augmentation, and remaining graft volume, respectively. Statistical analyses were performed with the Mann-Whitney test, using a significance level of P < . 05. RESULTS Six weeks after rabbit calvariae were augmented, data analysis revealed that the mixture of PRP and ABB produced twice the vertical bone volume of ABB alone (P < .0001). CONCLUSION Based upon this study of 16 rabbits, it appears that the combination of ABB with PRP resulted in increased vertical bone augmentation when compared with autologous blood in similarly sized created defects.
A preoperative metabolic marker of parkinsonian apathy following subthalamic nucleus stimulation

Subthalamic nucleus deep brain stimulation (STN‐DBS) in Parkinson's disease (PD) has been associated with the development of postoperative apathy. Debate on the causes of postoperative apathy continues, and the dominant hypothesis is that stimulation or dopaminergic drug reductions are causal in its development. We hypothesized that a preoperative predisposition to apathy also could exist. To this end, we sought to identify a preoperative metabolic pattern using [18]Fluorodeoxyglucose Positron Emission Tomography (PET), which could be associated with the occurrence of postoperative apathy after STN‐DBS for PD.
Development and validation of a mortality risk model for pediatric sepsis

Abstract Pediatric sepsis is a burdensome public health problem. Assessing the mortality risk of pediatric sepsis patients, offering effective treatment guidance, and improving prognosis to reduce mortality rates, are crucial. We extracted data derived from electronic medical records of pediatric sepsis patients that were collected during the first 24 hours after admission to the pediatric intensive care unit (PICU) of the Hunan Children's hospital from January 2012 to June 2014. A total of 788 children were randomly divided into a training (592, 75%) and validation group (196, 25%). The risk factors for mortality among these patients were identified by conducting multivariate logistic regression in the training group. Based on the established logistic regression equation, the logit probabilities for all patients (in both groups) were calculated to verify the model's internal and external validities. According to the training group, 6 variables (brain natriuretic peptide, albumin, total bilirubin, D-dimer, lactate levels, and mechanical ventilation in 24 hours) were included in the final logistic regression model. The areas under the curves of the model were 0.854 (0.826, 0.881) and 0.844 (0.816, 0.873) in the training and validation groups, respectively. The Mortality Risk Model for Pediatric Sepsis we established in this study showed acceptable accuracy to predict the mortality risk in pediatric sepsis patients.
The non-healing diabetic foot wound: fact or fiction?

Wounds on the feet of diabetic patients are often labeled as "non-healing. " This article discusses the basis for and the dangers of such a classification. The evidence suggests that if the foot has an adequate vascular supply and no significant infection, a plantar wound that does not heal is the result of poor treatment and/or poor compliance. Wounds that do not heal despite optimal treatment and compliance are extremely rare and need to be referred to the appropriate specialist for care.
Incontinence Severity and Major Depression in Incontinent Women

Objective: Research has shown an association between urinary incontinence and depression. Studies that use community-based samples and major depressive disorder diagnostic criteria are needed. The objective of this study was to estimate the prevalence of and factors associated with major depression in women with urinary incontinence. Methods: We conducted an age-stratified postal survey of 6,000 women aged 30–90 years. Subjects were randomly selected from enrollees in a large health maintenance organization in Washington state. Main outcome measures were prevalence of current major depression and adjusted odds ratios for factors associated with major depression in women with urinary incontinence. Results: The response rate was 64% (n = 3,536) after applying exclusion criteria. The prevalence of urinary incontinence was 42% (n = 1,458). The prevalence of major depression was 3.7% (n = 129), with 2.2% in those without incontinence versus 6.1% in those with incontinence. Among women with incontinence, major depression prevalence rates differed by incontinence severity (2.1% in mild, 5.7% in moderate, and 8.3% in severe) and incontinence type (4.7% in stress, 6.6% in urge/mixed). Obesity (odds ratio [OR] 2.3, 95% confidence interval [CI] 1.3–4.0), current smoking (OR 2.7, 95% CI 1.5–4.9), lower educational attainment (OR 2.0, 95% CI 1.2–3.3), moderate incontinence (OR 2.7, 95% CI 1.1–6.6), and severe incontinence (OR 3.8, 95% CI 1.6–9.1) were each associated with increased odds of major depression in women with urinary incontinence, controlling for age and medical comorbidity. Compared with women with incontinence alone, women with comorbid incontinence and major depression had significantly greater decrements in quality of life and functional status and increased incontinence symptom burden. Conclusion: Women with moderate-to-severe urinary incontinence should be screened for comorbid major depression and offered treatment if depression is present. Level of Evidence: II-2
Global Proteomics Analysis of Protein Lysine Methylation

Lysine methylation is a common protein post‐translational modification dynamically mediated by protein lysine methyltransferases (PKMTs) and protein lysine demethylases (PKDMs). Beyond histone proteins, lysine methylation on non‐histone proteins plays a substantial role in a variety of functions in cells and is closely associated with diseases such as cancer. A large body of evidence indicates that the dysregulation of some PKMTs leads to tumorigenesis via their non‐histone substrates. However, most studies on other PKMTs have made slow progress owing to the lack of approaches for extensive screening of lysine methylation sites. However, recently, there has been a series of publications to perform large‐scale analysis of protein lysine methylation. In this unit, we introduce a protocol for the global analysis of protein lysine methylation in cells by means of immunoaffinity enrichment and mass spectrometry. © 2016 by John Wiley & Sons, Inc.
Bisphenol A exposure and associations with obesity among adults: a critical review

Abstract Objective To review the literature on bisphenol A (BPA) exposure and obesity in human populations. Design Systematic review of the literature via searches of PubMed, EMBASE, Web of Science and reference lists for articles published to 1 August 2014. Setting China, Italy, Japan, Republic of Korea, Sweden, UK, USA. Subjects Adults (≥18 years). Results Eighteen articles were identified and included in the review. Twelve studies included secondary evaluations of BPA exposure and BMI, and six studies evaluated body composition as the primary outcome. All analyses were cross-sectional and no study included in the review received a positive quality rating (twelve negative, six neutral). Eight studies observed a statistically significant positive association between urinary or serum BPA levels and BMI, and ten studies observed no association. Studies where BMI was a primary outcome and studies of neutral quality were more likely to observe an association. Conclusions Study results are conflicting and significant methodological issues limit the ability to draw conclusions from these studies. Prospective studies that measure BPA exposure and changes in body weight and composition are needed to establish temporality, causality and the direction of any observed associations.
The inhibition effect of low-intensity pulsed ultrasound on osteoclasts progenitor cells

The healing of bone fracture with low-intensity pulsed uItrasound (LIPUS) associated with bone formation by osteoblasts has been validated in previous studies. Yet, littIe has been known about the effect of LIPUS on the osteoclasts during the bone remodeling process. To extensively explore this issue, osteoblast precursor cells were insonified by LIPUS in which that the insonification effect was verified by differentiation and other activities of cells. Experiments were performed on the osteoclast precursor cells formed by the differentiation of RAW 264.7 cell line via cuItured the cells in the growth medium containing receptor-activated nuclear factor K B ligand (RANKL) for 3 days. The 1 MHz LIPUS, with calibrated 125 mW/cm2 SATA intensity, 20% duty cycle of a 1 kHz pulse repetition frequency, was arranged to daily insonify the osteoclast precursor cells in the period between the 3rd and 6th day during cuIturing. The morphology and number of tartrate resistant acid phosphatase (TRAP) positive multi-nucleated osteoclasts were observed and measured. Gene expression of receptor activator of nuclear factor K B (RANK), cathepsine K, matrix metalloproteinase 9 (MMP9), and TRAP were determined by reverse transcription polymerase chain reaction (RT-PCR). Following the LIPUS insonification, the bone resorptive activity of osteoclast precursor cells tended to be inhibited. The number of TRAP positive multi-nucleated osteoclasts for the experimental group was lower than that of the control group. The resorption pits on the calcium phosphate film also found to be inhibited by LIPUS insonification, where the pit formation of the experimental group was smaller than that of the control group. RT-PCR resuIts reveled that LIPUS decreased the mRNA levels of RANK, TRAP, cathepsin K, and MMP9 mRNA. The LIPUS insonification suppress osteoclast differentiation by the inhibition of multi-nucleated osteoclast formation be demonstrated in this study. These resuIts suggest that the inhibition effect of LIPUS on osteoclasts is through the reduction of RANKL induced expression of cathepsin K and MMP9 for modulating bone remodeling process.