Miracle-dz/UniFAR-FTUs huggingface dataset:
IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex

The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group.
Renal Function in Chinese HIV-Positive Individuals following Initiation of Antiretroviral Therapy

Aim To identify the prevalence and predictors of abnormal renal function among HIV-positive Chinese patients prior to antiretroviral therapy (ART) initiation and to evaluate subsequent changes in renal function after ART exposure. Methods We conducted a nationwide cohort study of subjects who enrolled in the national Chinese ART program from January 1, 2012 to December 31, 2012. We estimated the glomerular filtration rate (eGFR) of subjects prior to and after initiating ART. Risk factors for abnormal renal function, as defined by eGFR <60 ml/min/1.73m2, at baseline and follow-up were assessed by logistic regression and Cox proportional hazards regression models, respectively. Results Among 41,862 subjects, at ART baseline, 3.3% had a baseline eGFR <60 ml/min/1.73m2 and 24.2% had eGFR = 60–90 ml/min/1.73m2. Adjusted baseline risk factors for baseline eGFR <60 ml/min/1.73m2 were older age (Adjusted odds ratio [AOR] = 5.19, 95% confidence interval [CI]: 4.52–5.67), female (AOR = 1.68, 95% CI: 1.47–1.93), hemoglobin <120g/L (AOR = 1.68, 95% CI: 1.47–1.93), blood glucose >6.1 mmol/L (AOR = 1.46, 95% CI: 1.25–1.72), and hepatitis C co-infection (AOR = 1.36, 95% CI: 1.06–1.73). Among subjects with baseline eGFR >90 ml/min/1.73m2, the incidence of the eGFR falling to <60 ml/min/1.73m2 was 0.92/100 person-years after a median of 15.0 months of ART. Being on a tenofovir with lopinavir/ritonavir regimen (Adjusted hazard ratio [AHR] = 3.02, 95% CI: 1.96–4.66) and having an unsuppressed viral load (AHR = 2.70, 95% CI: 1.80–4.03) were independent predictors for eGFR <60 ml/min/1.73m2 after ART initiation as well as older age, female, and hemoglobin <120 g/L. Conclusion A high proportion of HIV-positive subjects in China presented with abnormal renal function prior to ART initiation. But the incidence of the eGFR decrease after ART was low. Patient renal function should be regularly monitored by eGFR before initiating and during ART.
Asian Influenza in Pregnancy and Congenital Defects

Influenza caused by the Asian strain of virus A first became epidemic in Great Britain in the latter half of the year 1957. Available statistics show that it spread rapidly and widely, affecting the southern parts of the country rather later than the northern. Most of the strains isolated from patients through out the country were shown to be of the Asian variety (McDonald, 1958; Ministry of Health, 1960). In a detailed inquiry into its incidence in a general practice situated on the south-eastern outskirts of London (Woodall, Rowson, and McDonald, 1958), it was shown that the epidemic in that area lasted about 8 weeks, that the main incidence lay between mid-September and late October, and that the peak was reached in the week ending October 13. About one-third of persons of all ages, children as well as adults were recorded as attacked, and it was con cluded, from a comparison with national insurance statistics, that this prevalence was not unlike that for the country as a whole. In particular we may note from this local investigation that of 253 women in the childbearing age group of 15-39 years, influenza was diagnosed in as many as 28 per cent. Under such conditions as these the opportunity was taken to investigate the possible effects of this new (or renewed) influenza virus upon the foetus when the illness concerned a woman in pregnancy.
A Systematic Assessment of Accuracy in Detecting Somatic Mosaic Variants by Deep Amplicon Sequencing: Application to NF2 Gene

The accurate detection of low-allelic variants is still challenging, particularly for the identification of somatic mosaicism, where matched control sample is not available. High throughput sequencing, by the simultaneous and independent analysis of thousands of different DNA fragments, might overcome many of the limits of traditional methods, greatly increasing the sensitivity. However, it is necessary to take into account the high number of false positives that may arise due to the lack of matched control samples. Here, we applied deep amplicon sequencing to the analysis of samples with known genotype and variant allele fraction (VAF) followed by a tailored statistical analysis. This method allowed to define a minimum value of VAF for detecting mosaic variants with high accuracy. Then, we exploited the estimated VAF to select candidate alterations in NF2 gene in 34 samples with unknown genotype (30 blood and 4 tumor DNAs), demonstrating the suitability of our method. The strategy we propose optimizes the use of deep amplicon sequencing for the identification of low abundance variants. Moreover, our method can be applied to different high throughput sequencing approaches to estimate the background noise and define the accuracy of the experimental design.
Coding Early Naturalists' Accounts into Long-Term Fish Community Changes in the Adriatic Sea (1800–2000)

The understanding of fish communities' changes over the past centuries has important implications for conservation policy and marine resource management. However, reconstructing these changes is difficult because information on marine communities before the second half of the 20th century is, in most cases, anecdotal and merely qualitative. Therefore, historical qualitative records and modern quantitative data are not directly comparable, and their integration for long-term analyses is not straightforward. We developed a methodology that allows the coding of qualitative information provided by early naturalists into semi-quantitative information through an intercalibration with landing proportions. This approach allowed us to reconstruct and quantitatively analyze a 200-year-long time series of fish community structure indicators in the Northern Adriatic Sea (Mediterranean Sea). Our analysis provides evidence of long-term changes in fish community structure, including the decline of Chondrichthyes, large-sized and late-maturing species. This work highlights the importance of broadening the time-frame through which we look at marine ecosystem changes and provides a methodology to exploit, in a quantitative framework, historical qualitative sources. To the purpose, naturalists' eyewitness accounts proved to be useful for extending the analysis on fish community back in the past, well before the onset of field-based monitoring programs.
Using the text to evaluate short answers for reading comprehension exercises

Short answer questions for reading comprehension are a common task in foreign language learning. Automatic short answer scoring is the task of automatically assessing the semantic content of a student’s answer, marking it e.g. as correct or incorrect. While previous approaches mainly focused on comparing a learner answer to some reference answer provided by the teacher, we explore the use of the underlying reading texts as additional evidence for the classification. First, we conduct a corpus study targeting the links between sentences in reading texts for learners of German and answers to reading comprehension questions based on those texts. Second, we use the reading text directly for classification, considering three different models: an answer-based classifier extended with textual features, a simple text-based classifier, and a model that combines the two according to confidence of the text-based classification. The most promising approach is the first one, results for which show that textual features improve classification accuracy. While the other two models do not improve classification accuracy, they do investigate the role of the text and suggest possibilities for developing automatic answer scoring systems with less supervision needed from instructors.
Hippocampal blood flow in normal aging measured with arterial spin labeling at 3T

Due to methodological difficulties related to the small size, variable distribution of hippocampal arteries, and the location of the hippocampus in the proximity of middle cranial fossa, little is known about hippocampal blood flow (HBF). We have tested the utility of a pulsed arterial spin labeling sequence based on multi‐shot true fast imaging in steady precession to measure HBF in 34 normal volunteers (17 women, 17 men, 26–92 years old). Flow sensitivity to a mild hypercapnic challenge was also examined. Coregistered 3D MPRAGE sequence was used to eliminate from hippocampal and cortical regions of interest all voxel with <75% of gray matter. Large blood vessels were also excluded. HBF in normal volunteers averaged 61.2 ± 9.0 mL/(100 g min). There was no statistically significant age or gender effect. Under a mild hypercapnia challenge (end tidal CO2 pressure increase of 6.8 ± 1.9 mmHg over the baseline), HBF response was 14.1 ± 10.8 mL/(100 g min), whereas cortical gray matter flow increased by 18.0 ± 12.2 mL/(100 g min). Flow response among women was significantly larger than in the men. The average absolute difference between two successive HBF measures was 3.6 mL/(100 g min) or 5.4%. The 3T true fast imaging in steady precession arterial spin labeling method offers a HBF measurement strategy that combines good spatial resolution, sensitivity, and minimal image distortions. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
WHY DO PEOPLE ( NOT ) ANNUITIZE ?

Why do people (not) annuitize? While several theoretical studies have tried to address this question, empirical evidence on annuitization is scant. To fill this void, I use a novel dataset with more than 140,000 actual payout decisions made by employees choosing between monthly income for life (i.e., an annuity) and a lump sum payment. Four sets of results emerge from my analysis. First, there is no evidence in this sample of an annuity puzzle: more than two-thirds of employees select an annuity. Second, standard explanations of annuitization, such as asymmetric information on life expectancy and risk aversion, are confirmed in the data: women, higher earners and older employees are more likely to take an annuity. Third, I document that recent stock market performance affect this payout decision: after positive (negative) stock market returns employees are less (more) likely to choose an annuity. Finally, consistent with quasi-hyperbolic discounting and preferences for immediacy, I find that procrastinators are more likely to take the lump sum. Robustness checks for these results and their policy implications conclude the paper.
The Effects of Hyperhydrating Supplements Containing Creatine and Glucose on Plasma Lipids and Insulin Sensitivity in Endurance-Trained Athletes

The addition of carbohydrate (CHO) in the form of simple sugars to creatine (Cr) supplements is central. The study aimed to determine whether ingestion of glucose (Glu) simultaneously with Cr and glycerol (Cr/Gly) supplement is detrimental to plasma lipids of endurance-trained individuals and find out whether modification arising can be attenuated by replacing part of the Glu with alpha lipoic acid (Ala). Twenty-two endurance-trained cyclists were randomized to receive Cr/Gly/Glu (11.4 g Cr-H2O, 1 g Gly/kg BM, and 150 g Glu) or Cr/Gly/Glu/Ala (11.4 g Cr-H2O, 1 g Gly/kg BM, 100 g Glu, and 1 g Ala) for 7 days. Fasting concentration of TAG increased significantly (P < 0.01) after supplementation with Cr/Gly/Glu (before: 0.9 ± 0.2 mmol/L; after: 1.3 ± 0.4 mmol/L) and Cr/Gly/Glu/Ala (before: 0.8 ± 0.2 mmol/L; after: 1.2 ± 0.5 mmol/L) but changes were not different between the groups. Supplementation significantly (P < 0.05) increased the TAG to HDL-cholesterol ratio but had no effect on fasting concentration of total, HDL-, and LDL-cholesterol and insulin resistance. Thus, addition of Glu to Cr containing supplements enhances plasma TAG concentration and the TAG to HDL-cholesterol ratio and this enhancement cannot be attenuated by partial replacement of Glu with Ala.
Morphological Variation of Primary Reproductive Structures in Males of Five Families of Neotropical Bats

Bats present unique features among mammals with respect to reproduction, and although neotropical bats do not have a hibernation period, many of their reproductive characteristics vary seasonally and interspecifically. Thus, this work aimed to examine the reproductive structures of 18 species belonging to five families of Brazilian bats. The gross anatomy of the testes varied little; however, the epididymis of Emballonuridae and Vespertilionidae showed exceptional structures with a large elongation of the caudal region. We observed a wide variation in the positioning of the testes: Phyllostomidae and Noctilionidae presented external testes; Emballonuridae and Molossidae presented migratory testes that may be in intra‐abdominal or external positions; and Vespertilionidae displayed scrotal testes. In the histological evaluation, we observed a different pattern in vespertilionid species, with testicular regression and sperm retention/storage in the cauda epididymis in the five species analyzed. Similar testicular regression was observed in Molossops temminckii; however, sperm retention/storage was not observed in this species. These data suggest that although the species analyzed are tropical species that do not present a prolonged period of torpor (hibernation), they still maintain a period of seminiferous tubule regression and sperm storage very similar to that observed in hibernating bats. Anat Rec, 2013. © 2012 Wiley Periodicals, Inc.
The Effects of Size and Shape of Iron Particles on the Microwave Absorbing Properties of Composite Absorbers

High values of magnetic permeability and dielectric permittivity of polymer composite containing flake-shaped iron particles were prepared by the mechanical milling of two batches of iron powders [Fe(A) and Fe(B)] under controlled conditions. The frequency-dependent complex permittivity (ε'-jε") and permeability (μ'-jμ") of resin composites with 40 wt. % of flake-shaped iron particles are investigated in 2-18 GHz. The results show that all ε', μ', μ" substantially increase due to the increase of milling time and the size of the flake-shaped particles. The enhancement of space-charge polarization increases the permittivity of the composite absorbers. The frequency dispersion μ" of of flake-shaped Fe/epoxy composites show a higher resonance frequency (around 3 GHz) which exceeds the Snoek's limit in the gigahertz range due to their low eddy current loss coming from the particle shape effects. For 40 wt. % composite with 2 mm thickness, the predicted reflection loss reaches -19.4 dB at 14.9 GHz for Fe(A)/2 hr, -28.0 dB at 8.96 GHz for Fe(A)/4 hr, -31.6 dB at 11.6 GHz and -42.9 dB for Fe(B)/2 hr at 7.84 GHz for Fe(B)/4 hr as magnetic fillers.
Spontaneous muscle action potentials fail to develop without fetal‐type acetylcholine receptors

In mammals, two combinations of muscle nicotinic acetylcholine receptors (AChRs) are used: α2βγδ (γ‐AChR) or α2βϵδ (ϵ‐AChR). After birth, γ‐AChRs are replaced by ϵ‐AChRs (γ/ϵ‐switch). The two receptors have different conductances and open times. During perinatal period, the long open time γ‐AChRs generate random myofiber action potentials from uniquantal miniature end‐plate potentials (mEPPs). ϵ‐AChRs are suitable for strong adult muscle activities. Since the effect of the γ/ϵ‐switch on neuromuscular development was unclear, despite the many differences in channel characteristics, we carried out this study to generate γ‐subunit‐deficient mice. Homozygotes born alive survived for 2 days in a stable condition, and were able to move their forelimbs. Endplate AChRs included ϵ‐subunits, and muscle fibers had multiple neuromuscular junctions. Both pre‐ and postsynapses were abnormal and spontaneous action potentials generated from mEPPs were totally absent. Results suggest a requirement for γ‐AChRs in mediating synaptically‐induced action potential activity critical for neuromuscular development.
Optimal Algorithms for Smooth and Strongly Convex Distributed Optimization in Networks

In this paper, we determine the optimal convergence rates for strongly convex and smooth distributed optimization in two settings: centralized and decentralized communications over a network. For centralized (i.e. master/slave) algorithms, we show that distributing Nesterov's accelerated gradient descent is optimal and achieves a precision e > 0 in time O(√kg(1 + Δτ) ln(l/e)), where kg is the condition number of the (global) function to optimize, Δ is the diameter of the network, and τ (resp. l) is the time needed to communicate values between two neighbors (resp. perform local computations). For decentralized algorithms based on gossip, we provide the first optimal algorithm, called the multi-step dual accelerated (MSDA) method, that achieves a precision e e 0 in time O(√kl(1 + τ/√γ)ln(1/e)), where kl is the condition number of the local functions and γ is the (normalized) eigengap of the gossip matrix used for communication between nodes. We then verify the efficiency of MSDA against state-of-the-art methods for two problems: least-squares regression and classification by logistic regression.
BROADENED AND ELEVATED HUMORAL IMMUNE RESPONSE TO EBNA1 IN PEDIATRIC MULTIPLE SCLEROSIS

Epidemiologic studies suggest that childhood viral exposures are important determinants of multiple sclerosis (MS) risk in both adults and children1 and, so far, Epstein-Barr virus (EBV) stands out as the infectious agent for which there is the most compelling evidence for an association with the disease.1–3 ### Patients, healthy donors, and methods. Twenty-three children with a diagnosis of definite MS and 17 demographically matched healthy peers were enrolled at the Department of Pediatrics and Pediatric Neurology, University of Gottingen, Germany (table e-1 on the Neurology ® Web site at www.neurology.org). Virus-specific antibody responses were assessed using standardized ELISA kits (Bio-Quant, San Diego, CA) for IgG antibodies directed against the EBV- encoded viral capsid antigen (EBV-VCA), the HCMV-derived early antigens (HCMV-EA), the immunogenic C-terminus of the latent EBV nuclear antigen-1 (EBNA1, aa 458-641), and toward EBV-infected B cell lysates.4 In order to assess the specificity of EBNA1-targeting IgG, 211 dodecamer peptides, overlapping by nine amino acids and covering the entire sequence of EBNA1 (aa 1-641), were covalently linked to cellulose membranes as described previously.5 Positive spots were identified as blue or purple. Individual membranes were processed and evaluated blinded to the clinical diagnosis. ### Results. A total of 91% and 87% of MS cases compared to 64% and 58% of controls showed IgG responses toward EBV-VCA and EBNA1, respectively. The frequency of HCMV-EA seropositivity did not differ between both …
Antiepileptic drugs–ECT combination: Need for systematic studies

Dear Editors, We read with interest the article by Rubner et al. (2009). The authors have commented, and rightly so, that a combination of anticonvulsant medications and electroconvulsive therapy (ECT) is an “ observed reality ” – a substantial portion (45%) of patients received this combination in their survey. The article highlights an important lacuna in the evidence-based practice of ECT. The offi cial guidelines have been contradictory with regard to combining anticonvulsants and ECT. The American Psychiatric Association ' s Taskforce on ECT recommends withdrawal of antiepileptic drugs (when used as mood stabilisers) during ECT (American Psychiatric Association 2001); the UK guidelines recommend continuation of these drugs during an ECT course (Scott 2005). This contradiction is not surprising, given that there is very little systematic research on this clinically important topic. Consistent with the fi ndings of Rubner et al. (2009), we observed that of the 201 bipolar disorder patients who received ECT in 2 calendar years of 2006 and 2007, 79 (39.3%) patients received a combination of ECT and antiepileptic drugs at the National Institute of Mental Health & Neurosciences (NIMHANS), Bangalore, India (Virupaksha et al. 2010). Patients on antiepileptic drugs had a higher seizure threshold, greater increase in the threshold over the course of ECT, and had received more number of ECTs to achieve a level of clinical improvement that was comparable to those who were not on antiepileptic drugs. This difference was signifi cant even after controlling for possible confounders. In 29 (36.7%) patients the treating team had skipped the dose of the antiepileptic drugs on the night before; in the rest no such dose adjustment was effected. The lack of clarity in approaching this issue was highlighted in a questionnaire survey of ECT practice among psychiatrists (Rakesh et al. 2010). We asked about their practice when confronted with a clinical situation of starting ECT in a patient on an anticonvulsant mood stabilizer. Seventeen senior registrars and 26 consultants at NIMHANS answered the survey. Their mean (SD) experience after MD was 11.95 (10.83) years. Not surprisingly, the preferences varied widely. About a third of the clinicians (33%) preferred to continue the antiepileptic drug at full dose; about half of them (51%) stated that they would reduce the dose to half and about 16% preferred to stop them completely during ECT. These observations show that while a combination of ECT and antiepileptic drugs is fairly common, there is a striking lack of consensus regarding the best method of combining them. Relative merits and demerits of the different approaches can only be found out by prospective randomized controlled trials of comparing these approaches. We suggest that such studies are urgently required to provide evidence-based care for scores of psychiatric patients who need combination treatment with antiepileptic drugs and ECT.