Miracle-dz/UniFAR-FTUs huggingface dataset:
Serological and genomic detection of bovine leukemia virus in human and cattle samples

Bovine leukemia virus (BLV) is a retrovirus responsible for lymphoproliferative disorders in cattle. Although infections of BLV in animals are well known, little is known about its capacity to infect humans. This study investigated the presence of anti-BLV antibodies and BLV proviruses in human and cattle samples. An indirect enzyme-linked immunosorbent assay (ELISA) was used to detect anti-BLV antibodies while nested PCR was employed to identify BLV provirus sequences. The overall prevalence of anti-BLV antibodies in human and cattle samples were 12.50% and 16.73%, respectively. When using ELISA as a reference test, sensitivity and specificity for nested PCR were 0.625 and 0.970, respectively. The predictive value of a positive test was 0.862 and the predictive value of a negative test was 0.897. The percentage of cattle correctly classified by nested PCR assay was 89.1%. Nested PCR and Southern blot analysis, using primers specific for BLV gag sequences, revealed that BLV proviruses were detectable in cattle and human samples. Our results highlight the risk of human exposure to BLV and the need for further investigations to determine whether BLV infection poses a health hazard for humans.
Development of autoantibodies before the clinical onset of systemic lupus erythematosus.

BACKGROUND Although much is known about the natural history of systemic lupus erythematosus (SLE), the development of SLE autoantibodies before the diagnosis of the disease has not been extensively explored. We investigated the onset and progression of autoantibody development before the clinical diagnosis. METHODS The Department of Defense Serum Repository contains approximately 30 million specimens prospectively collected from more than 5 million U.S. Armed Forces personnel. We evaluated serum samples obtained from 130 persons before they received a diagnosis of SLE, along with samples from matched controls. RESULTS In 115 of the 130 patients with SLE (88 percent), at least one SLE autoantibody tested was present before the diagnosis (up to 9.4 years earlier; mean, 3.3 years). Antinuclear antibodies were present in 78 percent (at a dilution of 1:120 or more), anti-double-stranded DNA antibodies in 55 percent, anti-Ro antibodies in 47 percent, anti-La antibodies in 34 percent, anti-Sm antibodies in 32 percent, anti-nuclear ribonucleoprotein antibodies in 26 percent, and antiphospholipid antibodies in 18 percent. Antinuclear, antiphospholipid antibodies, anti-Ro, and anti-La antibodies were present earlier than anti-Sm and anti-nuclear ribonucleoprotein antibodies (a mean of 3.4 years before the diagnosis vs. 1.2 years, P=0.005). Anti-double-stranded DNA antibodies, with a mean onset 2.2 years before the diagnosis, were found later than antinuclear antibodies (P=0.06) and earlier than anti-nuclear ribonucleoprotein antibodies (P=0.005). For many patients, the earliest available serum sample was positive; therefore, these measures of the average time from the first positive antibody test to the diagnosis are underestimates of the time from the development of antibodies to the diagnosis. Of the 130 initial matched controls, 3.8 percent were positive for one or more autoantibodies. CONCLUSIONS Autoantibodies are typically present many years before the diagnosis of SLE. Furthermore, the appearance of autoantibodies in patients with SLE tends to follow a predictable course, with a progressive accumulation of specific autoantibodies before the onset of SLE, while patients are still asymptomatic.
Velvet worm development links myriapods with chelicerates

Despite the advent of modern molecular and computational methods, the phylogeny of the four major arthropod groups (Chelicerata, Myriapoda, Crustacea and Hexapoda, including the insects) remains enigmatic. One particular challenge is the position of myriapods as either the closest relatives to chelicerates (Paradoxopoda/Myriochelata hypothesis), or to crustaceans and hexapods (Mandibulata hypothesis). While neither hypothesis receives conclusive support from molecular analyses, most morphological studies favour the Mandibulata concept, with the mandible being the most prominent feature of this group. Although no morphological evidence was initially available to support the Paradoxopoda hypothesis, a putative synapomorphy of chelicerates and myriapods has recently been put forward based on studies of neurogenesis. However, this and other morphological characters remain of limited use for phylogenetic systematics owing to the lack of data from an appropriate outgroup. Here, we show that several embryonic characters are synapomorphies uniting the chelicerates and myriapods, as revealed by an outgroup comparison with the Onychophora or velvet worms. Our findings, thus provide, to our knowledge, first morphological/embryological support for the monophyly of the Paradoxopoda and suggest that the mandible might have evolved twice within the arthropods.
Lack of association between the matrix metalloproteinase-2 -1306C>T polymorphism and breast cancer susceptibility: a meta-analysis.

BACKGROUND Since inconsistent results have been reported regarding the relation between the matrix metalloproteinase-2 (MMP-2) -1306C>T polymorphism and susceptibility for breast cancer, we performed a meta-analysis to investigate the issue. MATERIALS AND METHODS An internet search of PubMed and EMBASE was performed to identify eligible studies. Pooled odds ratios (ORs) with their corresponding confidence intervals (CIs) were calculated to evaluate any association between MMP-2 -1306C>T polymorphism and breast cancer susceptibility. RESULTS Nine case-control studies were included in the meta-analysis, involving 9,858 cases and 10,871 controls. Overall, there was no evidence of any association between the MMP-2 -1306C>T polymorphism and breast cancer susceptibility in different genetic models (T-allele vs C-allele: OR=0.95, 95%CI, 0.82-1.10, p=0.49; TT vs CC: OR=1.03, 95%CI, 0.90-1.19, p=0.66; TT+TC vs CC: OR=0.93, 95%CI, 0.78-1.10, p=0.38; TT vs TC+CC: OR=1.02, 95%CI, 0.89-1.17, p=0.77). In the subgroup analysis by ethnicity, CC was associated with a significant increase in breast susceptibility among Latin-Americans in the dominant model (OR=0.61, 95%CI, 0.40-0.93, p=0.02), but the association disappeared in other models. No significant association was observed among Europeans, East Asians and others in different genetic models. In the subgroup analysis by their source of controls, no significant association between MMP-2 -1306C>T polymorphism and breast cancer susceptibility was noted among population-based studies and hospital-based studies in different genetic models. CONCLUSIONS The results of this meta-analysis suggest that MMP-2 -1306C>T polymorphism is not associated with breast cancer susceptibility, although the association among Latin-Americans in the dominant model was significant.
Host Galaxies Catalog Used in LIGO Searches for Compact Binary Coalescence Events

An up-to-date catalog of nearby galaxies considered to be hosts of binary compact objects is provided, with complete information about sky position, distance, extinction-corrected blue luminosity, and error estimates. With our current understanding of binary evolution, rates of formation and coalescence for binary compact objects scale with massive-star formation, and hence the (extinction-corrected) blue luminosity of host galaxies. Coalescence events in binary compact objects are among the most promising gravitational-wave sources for ground-based gravitational-wave detectors such as LIGO. Our catalog and associated error estimates are important for the interpretation of analyses carried out for LIGO, in constraining the rates of compact binary coalescence, given an astrophysical population model for the sources considered. We discuss how the notion of effective distance, created to account for the antenna pattern of a gravitational-wave detector, must be used in conjunction with our catalog. We also note that the catalog provided can be used in other astronomical analysis of populations that scale with galaxy blue luminosity.
Current status of laparoscopic liver resection for hepatocellular carcinoma

Laparoscopic liver resection (LLR) is becoming widely accepted for the treatment of hepatocellular carcinoma (HCC). Laparoscopic left lateral sectionectomy and minor laparoscopic liver resection are now considered standard approaches, especially for tumors located in the anterolateral segments of the liver. Laparoscopic left lateral sectionectomy in adult donors is also gaining acceptance for child liver transplantation in many centers. Major LLRs, including left hepatectomy and right hepatectomy, have been recently attempted. Laparoscopic donor hepatectomy is becoming more popular owing to increasing demand from young living donors who appreciate its minimal invasiveness and excellent cosmetic outcomes. Several centers have performed total laparoscopic donor right hepatectomy in adult-to-adult living donor liver transplantation. Many meta-analyses have shown that LLR is better than open liver resection in terms of short-term outcomes, principally cosmetic outcomes. Although no randomized control trials have compared LLR with open liver resection, the long-term oncologic outcomes were similar for both procedures in recent case-matched studies.
Drainage basin object-based method for regional-scale landform classification: a case study of loess area in China

Abstract Landform classification is one of the most important procedures in recognizing and dividing earth surface landforms. However, topographical homogeneity and differences in regional-scale landforms are often ignored by traditional pixel- and object-based landform classification methods based on digital elevation models (DEMs). In this work, a drainage basin object-based method for classifying regional-scale landforms is proposed. Drainage basins with least critical areas are first delineated from DEMs. Then, terrain derivatives of mean elevation, mean slope, drainage density, drainage depth, and terrain texture are employed to characterize the morphology of the drainage basins. Finally, a decision tree based on the topographical characteristics of the drainage basins is constructed and employed to determine the landform classification law. The experiment is validated in the landform classification of regional-scale loess areas in China. Results show that clear boundaries exist in different landforms at the regional scale. Landform type in a specific region shows significant topographical homogeneity under its specific regional geomorphological process. Classification accuracies are 87.3 and 86.3% for the field investigation and model validation, respectively. Spatial patterns of classified landforms and their proximity to sediment sources and other factors can be regarded as indicators of the evolutionary process of loess landform formation.
Fluoropyrimidines plus cisplatin versus gemcitabine/gemcitabine plus cisplatin in locally advanced and metastatic biliary tract carcinoma - a retrospective study.

AIM This is a retrospective study of patients with advanced biliary tract carcinoma (BTC), who were treated with different regimens of chemotherapy. METHODS We studied patients with advanced BTC registered at the Department of Oncology at the Fundeni Clinical Institute between 2004 and 2008. The following data were analyzed: rate of response, progression free survival (PFS) to first and second line of chemotherapy, overall survival (OS) and drug toxicity. Ninety-six patients were eligible having either advanced intra or extrahepatic cholangiocarcinoma, or gallbladder cancer with no prior chemotherapy. RESULTS Out of 96 patients, 57 (59.4%) received fluoropyrimidines (FP)+cisplatin and 39 (40.6%) gemcitabine (Gem)+/-cisplatin. The median PFS for FP+cisplatin was 5.9 months (95%CI 5-6.9) and for Gem+/-cisplatin 6.3 months (95%CI 5.4-7.1), p=0.661. Median OS for FP+cisplatin was 10.3 months (95%CI 7.5-13.1) and for Gem+/-cisplatin 9.1 months (95%CI 7.0-11.2), p=0.098. On disease progression, 46 patients received second line CT (Gem or FP+/-platinum compounds). Median OS for patients with FP based first line and Gem+/-cisplatin in second line was 19 months (95%CI 8.9-29) higher than for the reverse sequence: 13.2 months (95%CI 12-14.4), but not statistically significant (p=0.830). All patients were evaluated for toxicities. Most patients (75.5%) reported at least one adverse event. CONCLUSION Our results through direct comparison of FP+cisplatin with Gem+/-cisplatin as first line treatment did not show any statistical differences in terms of rate of response, PFS and OS. However, our study showed that FP+cisplatin as first line and Gem based second line therapy gave a better OS rate.
Contribution of molecular flexibility to the elastic–plastic properties of molecular crystal α-RDX

We show in this work that the mechanical properties of molecular crystals are strongly affected by the flexibility of the constituent molecules. To this end, we explore several kinematically restrained models of the molecular crystal cyclotrimethylene trinitramine in the α phase. We evaluate the effect of gradually removing the flexibility of the molecule on various crystal-scale parameters such as the elastic constants, the lattice parameters, the thermal expansion coefficients, the stacking fault energy and the critical stress for the motion of a dislocation (the Peierls–Nabarro stress). The values of these parameters evaluated with the fully refined, fully flexible atomistic model of the crystal are taken as reference. It is observed that the elastic constants, the lattice parameters and their dependence on pressure, and the thermal expansion coefficient can be accurately predicted with models that consider the NO2 and CH2 groups rigid, and the N–N bonds and the bonds of the triazine ring inextensible. Eliminating the dihedral flexibility of the ring leads to larger errors. The model in which the entire molecule is considered rigid or is mapped to a blob leads to even larger errors. Only the fully flexible, reference model provides accurate values for the stacking fault energy and the Peierls–Nabarro critical stress. Removing any component of the molecular flexibility leads to large errors in these parameters. These results also provide guidance for the development of coarse grained models of molecular crystals.
Squib: Expressive Power of Abstract Meaning Representations

The syntax of abstract meaning representations (AMRs) can be defined recursively, and a systematic translation to first-order logic (FOL) can be specified, including a proper treatment of negation. AMRs without recurrent variables are in the decidable two-variable fragment of FOL. The current definition of AMRs has limited expressive power for universal quantification (up to one universal quantifier per sentence). A simple extension of the AMR syntax and translation to FOL provides the means to represent projection and scope phenomena.
The role of water channel aquaporin 3 in the mechanism of TNF‐α‐mediated proinflammatory events: Implication in periodontal inflammation

Aquaporin 3 (AQP3) is the predominant water channel protein in human keratinocytes and acts as an inflammatory mediator in some lesions. A chronic, inflammatory process of periodontitis is related with a dramatic change of surrounding fluid homeostasis to plasma extravasation. The exact pattern of aquaporin (AQP) water channel expression and its mechanism in periodontal disease is still unknown. We describe herein an up‐regulated AQP3 expression in the epithelial lesion with chronic periodontitis and its functional role. The levels of AQP3 expression in inflamed gingival epithelial tissues were significantly higher than those of healthy subjects. Consistent with these results, AQP3 expression (i.e., levels of mRNA and protein) in cultured rat primary gingival epithelial cells and the human gingival epithelial cell line Ca9‐22 were strongly increased in response to TNF‐α treatment through the 55 kDa TNF‐α receptor (TNFR I). In this context, small interfering RNA‐ (siRNA)‐mediated “aqp‐3 gene silencing,” which could reduce AQP3 expression by more than 65%, significantly attenuated selected proinflammatory events of ICAM‐1 expression induced by TNF‐α in Ca9‐22. A sixfold increase in leukocyte adherence to TNF‐α‐stimulated epithelial cells was demonstrated by an adherence assay (P < 0.001) and pretreatment with AQP3 siRNA and anti‐ICAM‐1 antibody reduced leukocyte retention by 85% (P < 0.001). Our study indicates for the first time a novel important mode in the regulation of the inflammatory response through TNF‐α/TNFR I ligation at the site of epithelial lesions by specialized membrane channel AQP3 and ICAM‐1 protein, which is closely implicated in the development of periodontitis mechanisms. J. Cell. Physiol. 217: 338–349, 2008. © 2008 Wiley‐Liss, Inc.
Circadian nature of a rhythm expressed by an invertaseless strain of Neurospora crassa.

A new strain of Neurospora crassa which exhibits a rhythm of conidiation when growing along an agar surface in a growth tube is described. The rhythm has been shown to be circadian for it meets the following criteria: A) the period under constant environmental conditions in the dark is about 24 hours (22.7 hours at 25 degrees ); B) the period is relatively temperature-independent (Q(10) is between 0.95 and 1.21 for temperature range of 18 to 35 degrees ); C) the rhythm persists in continuous darkness at constant temperature for a minimum of 14 days without damping out; and D) the phase of the rhythm can be shifted by a single brief exposure to light. The sensitivity of this strain to light has been demonstrated further by the entrainment of the rhythm to a period of 24.0 hours using a suitable light-dark regime, and by the inhibition by light of the appearance of a rhythm; i.e., continuous conidiation occurs when the strain is subjected to continuous light. The new strain is compared to 2 other strains of Neurospora which also express a rhythm, patch and clock.
Similarities and differences between policy gradient methods and evolution strategies

Natural policy gradient methods and the covariance matrix adaptation evolution strategy, two variable metric methods proposed for solving reinforcement learning tasks, are contrasted to point out their con- ceptual similarities and differences. Experiments on the cart pole bench- mark are conducted as a first attempt to compare their performance. Reinforcement learning (RL) algorithms search for a policy mapping states of the environment to (a probability distribution over) the actions an agent can take in those states. The goal is to find a behavior such that some notion of future reward is maximized. Direct policy search methods address this task by directly learning parameters of a function explicitly representing the policy. Here we consider two general approaches to conduct direct policy search, namely policy gradient methods (PGMs) and evolution strategies (ESs). We will argue that these approaches are quite similar. This makes it all the more surprising that so far there has been no systematic comparison of PGMs and ESs applied to the same test problems and operating on the same class of policies with the same parameterization. This paper is our attempt to draw such a comparison, on a conceptual level and by conducting first empirical studies. We restrict our consideration to the natural actor critic algorithm (NAC, (1, 2)) and the covari- ance matrix adaptation ES (CMA-ES, (3)), which are compared in the context of optimization in (4). We picked these two because they can be considered state- of-the-art, they are our favorite direct policy search method and evolutionary RL algorithm, respectively, and they are both variable metric methods. In section 2 we briefly review the NAC algorithm and the CMA-ES. Section 3 describes the conceptual relations of these two approaches and in section 4 we use a simple toy problem to compare the methods empirically.
Mortality rates in patients with ST-elevation vs. non-ST-elevation acute myocardial infarction: observations from an unselected cohort.

AIMS Acute myocardial infarction (AMI) is categorized, according to the presenting electrocardiogram, into non-ST-elevation myocardial infarction (non-STEMI), ST-elevation myocardial infarction (STEMI), or bundle branch block myocardial infarction (BBBMI). Data on the prognostic significance of these categories mainly originate from voluntary based registries or large-scale clinical trials and may be hampered by selection and information bias. The aim of this historical cohort study was to evaluate the prognostic significance of different categories of AMI in an unselected cohort. METHODS AND RESULTS From 1 November 1999 to 31 October 2001, patient records were reviewed from all admissions to hospitals serving a study region with 139,000 inhabitants. An Endpoint Committee determined whether patients fulfilled the European Society of Cardiology criteria of AMI. A total of 654 patients with AMI were identified. The proportion having non-STEMI, STEMI, and BBBMI was 54, 39 and 6%, and the associated 1 year mortality was 31, 21, and 55%, respectively (log rank 54, P<0.001). The more favourable outcome observed in patients with STEMI remained significant according to multivariable analysis (P=0.044). CONCLUSION In an unselected cohort of patients admitted with AMI, the mortality was considerably higher than expected from voluntary-based registries and large-scale clinical trials. The most favourable outcome is observed in patients with STEMI.
Vegetation Structure and Diversity of Wadi Wasaa, Jazan, Saudi Arabia

This study is the first report conducted on Wadi Wasaa of Jazan area in Saudi Arabia. Total of 95 species belonging to 75 genera and 31 families were recorded from the study area, Poaceae and Euphorbiaceae both are the dominant families constituted 23% of the total species of the study area followed by Apocynaceae , Malvaceae. , Chamaephytes and therophytes were the prevailed life forms, indicating a typical desert life-form spectrum (chameo-therophytic) type, followed by phanerophytes. The chorological analysis revealed a total of 26 species representing 27% fell under monoregional, 56 species (59.0%) as biregional area and four species were detected under pluriregional region. Cover abundance values were visually estimated and used to form ten clusters of plant community types by statistical methods with Euclidian Distance and Ward method using SPSS program (ver.20). The Shannon-Wiener diversity index was used to estimate diversity, richness and evenness of the recorded species where it revealed the highest diversity index (H) was Original Research Article