Miracle-dz/UniFAR-FTUs huggingface dataset:
Vitamin D Levels in Patients With Type 2 Diabetes Mellitus

Background Vitamin D may influence many diseases, including type 2 diabetes mellitus. Patients and Methods We studied serum levels of 25-hydroxyvitamin D (25(OH)D) and associated characteristics in type 2 diabetic outpatients with pharmacologic treatment attended in internal medicine offices in a first-level hospital from Extremadura (Southern Spain). Results We included a total of 103 patients. Seventy-two patients (69.9%) had serum levels of 25(OH)D lower than 20 ng/mL. There was inverse correlation between serum levels of 25(OH)D and glycosylated hemoglobin (r = −0.74, P = 0.01). In 78 patients without insulin therapy, we found inverse correlation between serum levels of 25(OH)D and fasting serum insulin (r = −0.82, P = 0.001) and Homeostasis Model Assessment–Insulin Resistance (r = −0.51, P < 0.001). Conclusions Vitamin D deficiency is common in type 2 diabetic patients. There are inverse correlations between vitamin D and metabolic control and insulin resistance.
Distilling an Ensemble of Greedy Dependency Parsers into One MST Parser

We introduce two first-order graph-based dependency parsers achieving a new state of the art. The first is a consensus parser built from an ensemble of independently trained greedy LSTM transition-based parsers with different random initializations. We cast this approach as minimum Bayes risk decoding (under the Hamming cost) and argue that weaker consensus within the ensemble is a useful signal of difficulty or ambiguity. The second parser is a "distillation" of the ensemble into a single model. We train the distillation parser using a structured hinge loss objective with a novel cost that incorporates ensemble uncertainty estimates for each possible attachment, thereby avoiding the intractable cross-entropy computations required by applying standard distillation objectives to problems with structured outputs. The first-order distillation parser matches or surpasses the state of the art on English, Chinese, and German.
Deformation and fluid flow of a major out‐of‐sequence thrust located at seismogenic depth in an accretionary complex: Nobeoka Thrust in the Shimanto Belt, Kyushu, Japan

Nobeoka Thrust in Kyushu, southwest Japan, was investigated to understand the relationship between the seismogenic out‐of‐sequence thrust (OST) and fluid flow in accretionary prisms. The Nobeoka Thrust is a fossilized OST, being active at seismogenic depth. The hanging wall exhibits a penetrative plastic deformation, while a brittle, cataclastic mélange‐like occurrence characterizes the footwall, although both of them have same shale and sandstone‐dominant protolith. Vitrinite reflectance analyses indicate that the maximum temperatures of the hanging wall and footwall are approximately 320 and 250°C, respectively. This thermal gap across the thrust corresponds to 8.6–14.4 km of displacement assuming a 28–47°C/km geothermal gradient. The brittle damage zone of the thrust is asymmetric: only 2 m for hanging wall side and 100 m for footwall. Three types of mineral veins, quartz, and carbonate are well developed, especially in the damaged footwall: the tension crack‐filling vein, the fault‐filling vein, and postmélange one. The first is harmonious with fabric, perpendicular to the P surface. Fluid inclusion geothermobarometry indicates the P‐T of fluid in the intensively damaged zone of the footwall is ∼300°C, 230–250 MPa, higher than that from vitrinite reflectance, which suggests that hydrothermal fluid flow is associated with deformation. The same type vein in the lowest portion of the footwall‐damaged zone includes a much lower P‐T fluid. This difference suggests that continuous underplating caused the damaged zone to propagate downward with cooling and shallowing, which differs from faults characterized by shear localization and might be unique to aquiferous OST in accretionary complexes.
Prediction of Cardiovascular Events and All-Cause Mortality With Erectile Dysfunction: A Systematic Review and Meta-Analysis of Cohort Studies

Background— Erectile dysfunction (ED) carries an independent risk for cardiovascular (CV) events. We conducted a meta-analysis of all longitudinal studies for determining the ability of ED to predict risk of clinical events and to dissect factors influencing this ability. Methods and Results— We conducted a comprehensive search of electronic databases through July 2012. Longitudinal studies that reported relative risk (RR) estimates with 95% confidence intervals (CIs) were included. Of the 14 studies included (92 757 participants; mean follow-up, 6.1 years; 16 articles), 13 (14 articles) reported results on total CV events (91 831 individuals), 4 on CV mortality (34 761 individuals), 4 on myocardial infarction (35 523 individuals), 6 on cerebrovascular events (27 689 individuals), and 5 on all-cause mortality (17 869 individuals). The pooled RRs for the above-mentioned end points were 1.44 (95% CI, 1.27–1.63), 1.19 (95% CI, 0.97–1.46), 1.62 (95% CI, 1.34–1.96), 1.39 (95% CI, 1.23–1.57), and 1.25 (95% CI, 1.12–1.39), respectively, for men with versus without ED. The RR was higher in intermediate- compared with high- or low-CV-risk populations and with younger age. The RR for studies that diagnosed ED with the use of a questionnaire compared with a single question was higher (RR, 1.61; 95% CI, 1.38–1.86 versus RR, 1.27; 95% CI, 1.18–1.37, respectively; P=0.006). Conclusions— ED is associated with increased risk of CV events and all-cause mortality. RR is higher at younger ages, in intermediate-risk groups, and when a questionnaire is used instead of a single question.
The derivation of continuum limits of neuronal networks with gap-junction couplings

We consider an idealized network, formed by N neurons individually described by the FitzHugh-Nagumo equations and connected by electrical synapses. The limit for N to infinity of the resulting discrete model is thoroughly investigated, with the aim of identifying a model for a continuum of neurons having an equivalent behaviour. Two strategies for passing to the limit are analysed: i) a more conventional approach, based on a fixed nearest-neighbour connection topology accompanied by a suitable scaling of the diffusion coefficients; ii) a new approach, in which the number of connections to any given neuron varies with N according to a precise law, which simultaneously guarantees the non-triviality of the limit and the locality of neuronal interactions. Both approaches yield in the limit a pde-based model, in which the distribution of action potential obeys a nonlinear reaction-convection-diffusion equation; convection accounts for the possible lack of symmetry in the connection topology. Several convergence issues are discussed, both theoretically and numerically.
The "universal" leucine codon CTG in the secreted aspartyl proteinase 1 (SAP1) gene of Candida albicans encodes a serine in vivo

A number of Candida species possess a tRNA(Ser)-like species that recognizes CTG codons that normally specify leucine (Leu) in the universal code of codon usage. Mass spectrometry and Edman sequencing of peptides from the secreted aspartyl proteinase isoenzyme (Sap1) demonstrate that positions specified by the CTG codon contain a nonmodified serine (Ser) in Candida albicans.
Differential Insulitic Profiles Determine the Extent of β-Cell Destruction and the Age at Onset of Type 1 Diabetes

Type 1 diabetes (T1D) results from a T cell–mediated destruction of pancreatic β-cells following the infiltration of leukocytes (including CD8+, CD4+, and CD20+ cells) into and around pancreatic islets (insulitis). Recently, we reported that two distinct patterns of insulitis occur in patients with recent-onset T1D from the U.K. and that these differ principally in the proportion of infiltrating CD20+ B cells (designated CD20Hi and CD20Lo, respectively). We have now extended this analysis to include patients from the Network for Pancreatic Organ Donors with Diabetes (U.S.) and Diabetes Virus Detection (DiViD) study (Norway) cohorts and confirm that the two profiles of insulitis occur more widely. Moreover, we show that patients can be directly stratified according to their insulitic profile and that those receiving a diagnosis before the age of 7 years always display the CD20Hi profile. By contrast, individuals who received a diagnosis beyond the age of 13 years are uniformly defined as CD20Lo. This implies that the two forms of insulitis are differentially aggressive and that patients with a CD20Hi profile lose their β-cells at a more rapid rate. In support of this, we also find that the proportion of residual insulin-containing islets (ICIs) increases in parallel with age at the onset of T1D. Importantly, those receiving a diagnosis in, or beyond, their teenage years retain ∼40% ICIs at diagnosis, implying that a functional deficit rather than an absolute β-cell loss may be causal for disease onset in these patients. We conclude that appropriate patient stratification will be critical for correct interpretation of the outcomes of intervention therapies targeted to islet-infiltrating immune cells in T1D.
MicroRNA in Cardiovascular Calcification: Focus on Targets and Extracellular Vesicle Delivery Mechanisms

Cardiovascular calcification is a prominent feature of chronic inflammatory disorders—such as chronic kidney disease, type 2 diabetes mellitus, and atherosclerosis—that associate with significant morbidity and mortality. The concept that similar pathways control both bone remodeling and vascular calcification is widely accepted, but the precise mechanisms of calcification remain largely unknown. The central role of microRNAs (miRNA) as fine-tune regulators in the cardiovascular system and bone biology has gained acceptance and has raised the possibility for novel therapeutic targets. Additionally, circulating miRNAs have been proposed as biomarkers for a wide range of cardiovascular diseases, but knowledge of miRNA biology in cardiovascular calcification is very limited. This review focuses on the role of miRNAs in cardiovascular disease, with emphasis on osteogenic processes. Herein, we discuss the current understanding of miRNAs in cardiovascular calcification. Furthermore, we identify a set of miRNAs common to diseases associated with cardiovascular calcification (chronic kidney disease, type 2 diabetes mellitus, and atherosclerosis), and we hypothesize that these miRNAs may provide a molecular signature for calcification. Finally, we discuss this novel hypothesis with emphasis on known biological and pathological osteogenic processes (eg, osteogenic differentiation, release of calcifying matrix vesicles). The aim of this review is to provide an organized discussion of the known links between miRNA and calcification that provide emerging concepts for future studies on miRNA biology in cardiovascular calcification, which will be critical for developing new therapeutic strategies.
From Diagnosis to Death: A Case Study of Coping With Breast Cancer as Seen Through Online Discussion Group Messages

To understand the underlying psychosocial reactions against the unfolding of medical events that announce the disease progression, the objective of this analysis was to identify the patterns of online discussion group message themes in relation to the medical timeline of one woman's breast cancer trajectory. 202 messages posted by Darlene (our studied case) were analyzed by 2 independent coders using a grounded theory approach. The findings suggest that the pattern of messages was clearly correlated with distress-inducing events. The most frequent interaction theme was about building friendship with peers through communication of encouragement, validation, appreciation, and life sharing. Narratives of medical progression were constantly updated to identify similarities with peers. Family issues were increasingly raised at the end of life.
Single-Dose Mucosal Immunization with a Candidate Universal Influenza Vaccine Provides Rapid Protection from Virulent H5N1, H3N2 and H1N1 Viruses

Background The sudden emergence of novel influenza viruses is a global public health concern. Conventional influenza vaccines targeting the highly variable surface glycoproteins hemagglutinin and neuraminidase must antigenically match the emerging strain to be effective. In contrast, “universal” vaccines targeting conserved viral components could be used regardless of viral strain or subtype. Previous approaches to universal vaccination have required protracted multi-dose immunizations. Here we evaluate a single dose universal vaccine strategy using recombinant adenoviruses (rAd) expressing the conserved influenza virus antigens matrix 2 and nucleoprotein. Methodology/Principal Findings In BALB/c mice, administration of rAd via the intranasal route was superior to intramuscular immunization for induction of mucosal responses and for protection against highly virulent H1N1, H3N2, or H5N1 influenza virus challenge. Mucosally vaccinated mice not only survived, but had little morbidity and reduced lung virus titers. Protection was observed as early as 2 weeks post-immunization, and lasted at least 10 months, as did antibodies and lung T cells with activated phenotypes. Virus-specific IgA correlated with but was not essential for protection, as demonstrated in studies with IgA-deficient animals. Conclusion/Significance Mucosal administration of NP and M2-expressing rAd vectors provided rapid and lasting protection from influenza viruses in a subtype-independent manner. Such vaccines could be used in the interval between emergence of a new virus strain and availability of strain-matched vaccines against it. This strikingly effective single-dose vaccination thus represents a candidate off-the-shelf vaccine for emergency use during an influenza pandemic.
Optimal ensemble averaging of neural networks

Based on an observation about the different effect of ensemble averaging on the bias and variance portions of the prediction error, we discuss training methodologies for ensembles of networks. We demonstrate the effect of variance reduction and present a method of extrapolation to the limit of an infinite ensemble. A significant reduction of variance is obtained by averaging just over initial conditions of the neural networks, without varying architectures or training sets. The minimum of the ensemble prediction error is reached later than that of a single network. In the vicinity of the minimum, the ensemble prediction error appears to be flatter than that of the single network, thus simplifying optimal stopping decision. The results are demonstrated on sunspots data, where the predictions are among the best obtained, and on the 1993 energy prediction competition data set B. †School of Physics and Astronomy. ury@tarazan.tau. ac.il. ‡School of Mathematical Sciences. nin@math.tau. ac.il. §School of Physics and .
A Study of the Abnormalities of the Skull, Teeth and Lenses in Mongolism.

MONGOLISM, which represents about 5%/G to 10%S of all cases of mental deficiency, is a disease entity in which the defect in mental development is associated in a unique way with a large number of physical defects.26 These are found in many parts of the body, although some are more strongly associated with mongolism than others. It is appropriate, therefore, to distinguish those lesions which are found in other aments, and even in normal people, from those which are characteristic of mongolism because of their distinct nature and because of their frequent occurrence. These stigmata form the basis of the diagnosis of mongolism and they include the peculiar shape of the cranium, the dysplastic features with slanting palpebral fissures and epicanthic folds, the depressed nasal bridge, the dwarfed stature, the characteristic appearance of the brain and cerebellum9' 10, 18, 19 and the condition of the skin27 with particular regard to the fine dermal ridges. ",' 35 Numerous observations have been made since Langdon Down gave his classical description of the mongolian imbecile in 1866 and, although a large amount of information has accumulated since that time, the etiology of the basic disease and the pathogenesis of the associated physical defects are matters. of controversy.3 15, 31, 36 Many etiological factors have been suggested: a hereditary influence, an inferiority of the germ plasm and various prenatal environmental agents, but so far no conclusive evidence has been obtained of the true nature of the factors responsible for the condition. In previous papers data have been presented on the occurrence of congenital changes in the skull and teeth44 45 and eyes43 in three series of mongo-
EmailValet: Learning User Preferences for Wireless Email

This paper presents EmailValet, a system that learns users’ emailreading preferences on email-capable wireless platforms – specifically, on two-way pagers with small ”qwerty” keyboards and an 8-line 30-character display. In use by the authors for about three months, it has gathered data on email-reading preferences over more than 8900 email messages received by the authors during this period. The paper presents results comparing the ability of different learning methods to form models that can predict whether a given message should be forwarded to the user’s wireless device. Our results show that the best performance of one method, over a range of established learning methods developed on the information retrieval and machine learning communities, was able to achieve a break-even point of over 53% for one user that had received over 5000 messages. We also find that, in general, all methods are able to achieve better performance than what would be achieved by a baseline of simply forwarding all messages to the wireless device, and that many methods are able to find procedures that, although they forward only a small fraction of the messages that a user would want, achieve 100% precision on those messages that it does actually choose to forward.
Transcriptome Analysis of Silver Carp (Hypophthalmichthys molitrix) by Paired-End RNA Sequencing

The silver carp (Hypophthalmichthys molitrix) is among the most intensively pond-cultured fish species and is used in the wild to counteract water bloom in China. However, little genomic information is available for this species, especially regarding its ability to grow rapidly in water, even water contaminated with high concentrations of poisonous microcystin. In this study, we performed de novo transcriptome assembly and analysis of the 17.10 million short-read sequences produced by the Illumina paired-end sequencing technology. Using an improved multiple k-mer contig assembly method coupled with further scaffolding, 85 759 sequences were obtained. There were 23 044 sequences annotated with 3423 gene ontology terms for 104 196 term occurrences and the three corresponding organizing principles. A total of 38 200 assembled sequences were involved in 218 predicted Kyoto Encyclopedia of Genes and Genomes metabolic pathways. We also recovered 41 of 44 genes involved in the biosynthesis of glutathione. Of these, five genes were identified as experienced positive selection between silver carp and zebrafish, as determined by the likelihood ratio test. This report is the first annotated review of the silver carp transcriptome. These data will be of interest to researchers investigating the evolution and biological processes of the silver carp. This work also provides an archive for future studies of recent speciation and evolution of Cyprinidae fishes and can be used in comparative studies of other fishes.
Managing Mismatches in Voltage Stacking with CoreUnfolding

Five percent to 25% of power could be wasted before it is delivered to the computational resources on a die, due to inefficiencies of voltage regulators and resistive loss. The power delivery could benefit if, at the same power, the delivered voltage increases and the current decreases. This article presents CoreUnfolding, a technique that leverages voltage Stacking to improve power delivery efficiency. Our experiments show that about 10% system-wide power can be saved, the voltage regulator area can be reduced by 30%, di/dt improves 49%, and the power pin count is reduced by 40% (≈ 20% reduction in packaging costs), with negligible performance degradation.
Multiplexed Antibody Detection With an Array of Silicon-on-Insulator Microring Resonators

Optical cavities are considered promising devices for biosensing to satisfy the high demands of the growing proteomics market. We present a prototype sensor for multiplexed label-free monitoring of biomolecular interactions based on an array of three-by-four silicon-on-insulator microring resonators fabricated by standard complementary metal-oxide semiconductor (CMOS) technology. Parallel readout was performed with an infrared camera. We have demonstrated the simultaneous detection of several model antibodies in a highly specific way. For that, we integrated the optical chip with low-temperature polydimethylsiloxane (PDMS) packaging, enabling excellent compatibility with the receptor molecules. We obtain a very selective biomolecular interaction by grafting a 2.5-nm poly(ethylene glycol) layer to the silicon. Using silicon on insulator as the material platform offers high sensitivity through miniaturization and low-cost mass fabrication through standard CMOS technology steps. The sensors in this interrogation method are able to detect 3.4 pg/mm2 of a protein overlayer or a theoretical total mass of about 74 ag. For this novel lab on a chip, the fabrication, chemistry, readout, and packaging are developed to be scalable to detect hundreds of affinity interactions within several minutes.
Hyperactivity in a mouse model of the antiphospholipid syndrome

In the antiphospholipid syndrome (APS), antibodies to a complex of phospholipids and beta2-glycoprotein I (β2-GPI) are associated with recurrent thromboembolic events, spontaneous abortions, thrombocytopenia and central nervous system (CNS) disturbances. Animals immunized with b2-GPI develop the systemic manifestations of APS but the involvement of the (CNS) in these animals has not been studied. The objective of the present study was to examine mice with induced experimental APS for behavioral changes. Female Balb/C mice were immunized once with β2-GPI in complete Freund's adjuvant (CFA) or with CFA alone. Four months after immunization the mice were tested in the staircase apparatus and the following two variables were measured: (1) number of rears; and (2) number of stairs climbed by the mice. Immunization with β2-GPI resulted in elevated levels of circulating anti-negatively charged phospholipids and anti-β2-GPI antibodies. The APS mice exhibited hyperactive behavior as reflected by more frequent rears (P < 0.023) and higher number of stairs climbed (P < 0.019) by the mice in 3 min. This simple test demonstrated that experimental APS animals are significantly hyperactive and may serve as a marker for CNS involvement in this model.