Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptional Differences between Diapausing and Non-Diapausing D. montana Females Reared under the Same Photoperiod and Temperature

Background A wide range of insects living at higher latitudes enter diapause at the end of the warm season, which increases their chances of survival through harsh winter conditions. In this study we used RNA sequencing to identify genes involved in adult reproductive diapause in a northern fly species, Drosophila montana. Both diapausing and non-diapausing flies were reared under a critical day length and temperature, where about half of the emerging females enter diapause enabling us to eliminate the effects of varying environmental conditions on gene expression patterns of the two types of female flies. Results RNA sequencing revealed large differences between gene expression patterns of diapausing and non-diapausing females, especially in genes involved with metabolism, fatty acid biosynthesis, and metal and nucleotide binding. Differently expressed genes included several gene groups, including myosin, actin and cytochromeP450 genes, which have been previously associated with diapause. This study also identified new candidate genes, including some involved in cuticular hydrocarbon synthesis or regulation (desat1 and desat2), and acyl-CoA Δ11-desaturase activity (CG9747), and few odorant-binding protein genes (e.g. Obp44A). Also, several transposable elements (TEs) showed differential expression between the two female groups motivating future research on their roles in diapause. Conclusions Our results demonstrate that the adult reproductive diapause in D. montana involves changes in the expression level of a variety of genes involved in key processes (e.g. metabolism and fatty acid biosynthesis) which help diapausing females to cope with overwintering. This is consistent with the view that diapause is a complex adaptive phenotype where not only sexual maturation is arrested, but also changes in adult physiology are required in order to survive over the winter.
The Use of Question Types to Match Questions in FAQFinder

One useful way to find the answer to a question is to search a library of previously-answered questions. This is the idea behind FAQFinder, a Web-based natural language questionanswering system which uses Frequently Asked Questions (FAQ) files to answer users’ questions. FAQFinder tries to answer a user’s question by retrieving a similar FAQ question, if one exists, and its answer. FAQFinder uses several metrics to judge the similarity of user and FAQ questions. In this paper, we discuss a metric based on question type, which we recently added to the system. We discuss the taxonomy of question types used, and present experimental results which indicate that the incorporation of question type information has substantially improved FAQFinder’s performance.
Changes in cyclooxygenase metabolites in experimental periodontitis in Macaca mulatta.

The four principal metabolites of cyclooxygenase (CO) were examined during the progression of experimental periodontitis in the rhesus monkey Macaca mulatta. Thirty-two monkeys were divided in four disease-matched groups. Three groups were treated with flurbiprofen, a potent CO inhibitor, at either 0.027, 0.27 or 7.1 mg/kg/day delivered systemically by a subcutaneously-implanted osmotic mini-pump. We have previously described the findings indicating that flurbiprofen treatment significantly retarded clinical attachment loss (ALOSS), redness and radiographic bone loss (BLOSS). This investigation focuses on the changes in CO metabolites which occur during disease progression of ligature-induced periodontitis and on the dose-response relationship of flurbiprofen, as it relates to disease inhibition and the suppression of ARA metabolites within the crevicular fluid (CF). In untreated animals there was a statistically significant 3-fold increase in CF levels of prostaglandin E2 (PGE2) and thromboxane B2 (TxB2) at 3 months, as compared to baseline, which positively correlated with increases in redness, bleeding, ALOSS and BLOSS. CF-PGE2 and TxB2 levels reached a 6-fold peak at 6 months and returned to baseline by 12 months. Flurbiprofen (Fb) prevented the 3-month rise in TxB2, but did not affect the increase in PGE2. At 6 months, Fb administration caused a dose-dependent inhibition of both PGE2 and TxB2. Probit analysis of the dose-response data revealed that the concentration of Fb which caused a 50% inhibition of CF-TxB2 level (the IC50 value for TxB2 synthesis) was approximately two logs lower than the IC50 value for PGE2 synthesis, i.e. TxA2-IC50 = 0.013 vs. PGE2-IC50 = 1.35 mg flurbiprofen/kg/d. The slopes of the PGE2 and TxB2 inhibition curves were identical, consistent with a similar mechanism or singular enzyme for the site of action of Fb inhibition of CO activity. However, the kinetics and sensitivity of Fb inhibition were significantly different for the CO activity responsible for TxB2 and PGE2 synthesis, perhaps due to different compartmentalization of CO within different cell types.
Neuroprotective effects of the mGlu5R antagonist MPEP towards quinolinic acid‐induced striatal toxicity: involvement of pre‐ and post‐synaptic mechanisms and lack of direct NMDA blocking activity

The aim of this work was to investigate the potential neuroprotective effects of the metabotropic glutamate receptor 5 (mGlu5R) antagonist 2‐Methyl‐6‐(phenylethynyl)‐pyridine (MPEP) towards quinolinic acid (QA)–induced striatal excitoxicity. Intrastriatal MPEP (5 nmol/0.5 µL) significantly attenuated the body weight loss, the electroencephalographic alterations, the impairment in spatial memory and the striatal damage induced by bilateral striatal injection of QA (210 nmol/0.7 µL). In a second set of experiments, we aimed to elucidate the mechanisms underlying the neuroprotective effects of MPEP. In microdialysis studies in naive rats MPEP (80–250 µm through the dialysis probe) significantly reduced the increase in glutamate levels induced by 5 mm QA. In primary cultures of striatal neurons MPEP (50 µm) reduced the toxicity induced by direct application of glutamate [measured as release of lactate dehydrogenase [LDH]). Finally, we found that 50 µm MPEP was unable to directly block NMDA‐induced effects (namely field potential reduction in corticostriatal slices, as well as LDH release and intracellular calcium increase in striatal neurons). We conclude that: (i) MPEP has neuroprotective effects towards QA‐induced striatal excitotoxicity; (ii) both pre‐ and post‐synaptic mechanisms are involved; (iii) the neuroprotective effects of MPEP do not appear to involve a direct blockade of NMDA receptors.
Quantum theory of an antiferromagnet on a triangular lattice in a magnetic field

The reorientation process in a magnetic field in two-dimensional isotropic and XY quantum Heisenberg antiferromagnets is shown to occur through the intermediate phase with unbroken continuous symmetry and constant magnetization equal to one third of the saturation value. The same reorientation process is also found in the more complicated classical models.
The simultaneous detection of both enteroviruses and adenoviruses in environmental water samples including tap water with an integrated cell culture–multiplex‐nested PCR procedure

Aims: To evaluate an integrated cell culture (ICC)–multiplex‐nested PCR using the buffalo green monkey kidney (BGMK) cells for the simultaneous detection of both enteroviruses and adenoviruses in surface water and tap water samples and optimize the procedure for more sensitive detection of virus showing no apparent cytopathic effect (CPE).
Characterization of natural fiber and composites – A review

The natural fiber-reinforced polymer composite materials offered extensive range of properties which are suitable for large number of engineering application. The natural fibers have been abundantly available in the world. It has unique properties compared to synthetic fiber and reduces the plastic usage. This article reports the extraction process of natural fibers, characterization of natural fibers, and preparation of natural fiber-reinforced composites. The mechanical properties such as tensile, flexural, impact, and dynamic properties as well as thermal and machinability properties of the composites with and without chemically treated fibers were reported. The water absorption capability of the composites and its effect on mechanical properties were also reported.
DRAF: A Low-Power DRAM-Based Reconfigurable Acceleration Fabric

FPGAs are a popular target for application-specific accelerators because they lead to a good balance between flexibility and energy efficiency. However, FPGA lookup tables introduce significant area and power overheads, making it difficult to use FPGA devices in environments with tight cost and power constraints. This is the case for datacenter servers, where a modestly-sized FPGA cannot accommodate the large number of diverse accelerators that datacenter applications need. This paper introduces DRAF, an architecture for bit-level reconfigurable logic that uses DRAM subarrays to implement dense lookup tables. DRAF overlaps DRAM operations like bitline precharge and charge restoration with routing within the reconfigurable routing fabric to minimize the impact of DRAM latency. It also supports multiple configuration contexts that can be used to quickly switch between different accelerators with minimal latency. Overall, DRAF trades off some of the performance of FPGAs for significant gains in area and power. DRAF improves area density by 10x over FPGAs and power consumption by more than 3x, enabling DRAF to satisfy demanding applications within strict power and cost constraints. While accelerators mapped to DRAF are 2-3x slower than those in FPGAs, they still deliver a 13x speedup and an 11x reduction in power consumption over a Xeon core for a wide range of datacenter tasks, including analytics and interactive services like speech recognition.
Long-Range HIV Genotyping Using Viral RNA and Proviral DNA for Analysis of HIV Drug Resistance and HIV Clustering

ABSTRACT The goal of the study was to improve the methodology of HIV genotyping for analysis of HIV drug resistance and HIV clustering. Using the protocol of Gall et al. (A. Gall, B. Ferns, C. Morris, S. Watson, M. Cotten, M. Robinson, N. Berry, D. Pillay, and P. Kellam, J Clin Microbiol 50:3838–3844, 2012, doi:10.1128/JCM.01516-12), we developed a robust methodology for amplification of two large fragments of viral genome covering about 80% of the unique HIV-1 genome sequence. Importantly, this method can be applied to both viral RNA and proviral DNA amplification templates, allowing genotyping in HIV-infected subjects with suppressed viral loads (e.g., subjects on antiretroviral therapy [ART]). The two amplicons cover critical regions across the HIV-1 genome (including pol and env), allowing analysis of mutations associated with resistance to protease inhibitors, reverse transcriptase inhibitors (nucleoside reverse transcriptase inhibitors [NRTIs] and nonnucleoside reverse transcriptase inhibitors [NNRTIs]), integrase strand transfer inhibitors, and virus entry inhibitors. The two amplicons generated span 7,124 bp, providing substantial sequence length and numbers of informative sites for comprehensive phylogenic analysis and greater refinement of viral linkage analyses in HIV prevention studies. The long-range HIV genotyping from proviral DNA was successful in about 90% of 212 targeted blood specimens collected in a cohort where the majority of patients had suppressed viral loads, including 65% of patients with undetectable levels of HIV-1 RNA loads. The generated amplicons could be sequenced by different methods, such as population Sanger sequencing, single-genome sequencing, or next-generation ultradeep sequencing. The developed method is cost-effective—the cost of the long-range HIV genotyping is under $140 per subject (by Sanger sequencing)—and has the potential to enable the scale up of public health HIV prevention interventions.
Host–guest energetic nanocomposites based on self-assembly of multi-nitro organic molecules in nanochannels of mesoporous materials

Host–guest energetic nanocomposites have been synthesized by self-assembly of the high energy density compound HNIW in nanometer-scale channels of an ordered mesoporous material SBA-15. The complete impregnation of HNIW can be achieved in acetone solvent at ambient temperature, and the maximum amount was around 70 wt%. Structural characterizations were systematically provided by XRD, TEM, N2 adsorption, TG, 13C solid-state NMR and FT-IR. The tendency of multi-nitro organic molecules to self-assemble when the solvent evaporated has been described. Hydrogen bond interactions were considered as the main driving force, so the choices of matched host matrix and guest organic compounds were pivotal for implementing this process. The thermal properties of nanocomposites were measured by DSC analysis. Compared with pure HNIW and a physical mixture, the decomposition peak temperature of the confined crystals decreased about 11 °C, while the total amount of heat released slightly increased. This strategy can also be expanded to other similar host–guest systems.
Normal levels of acetyl coenzyme A and of acetylcholine in the brains of thiamin‐deficient rats 1

IN A RECENT publication, HEINRICH et al. (1973) reported reduced levels of acetylcholine (ACh) and of acetyl-CoA in the brains of thiamin-deficient rats. They pointed out that several groups have studied the levels of ACh in the brains of thiamin-deficient animals, and that about half of these workers have found a decrease and the other half normal levels (CHENEY et al., 1969; MCCANDLESS & SCHENKER, 1970). HEINRICH et al. (1973) also indicated that their's was the first published report of the levels of acetyl-CoA in the brains of thiamin-deficient animals. Because we had also studied this problem and had found normal levels of acetylCoA, ACh, and choline in such animals, we now briefly report the details of our studies.
Multidetector Computed Tomography Pulmonary Angiography: Does Arm Position Affect Pulmonary Artery Enhancement?

Objective: To evaluate whether arm position affects pulmonary artery enhancement in computed tomographic pulmonary angiography (CTPA). Methods: Study protocol had local ethics committee approval. Eighty-six patients who received 16 detector row CTPA for suspected pulmonary embolism were scanned with their contrast-injected arm resting at their side and compared with 94 patients who were scanned with both arms resting above their head. Two radiologists assessed pulmonary artery enhancement with a region-of-interest measurement of the main pulmonary artery density, scored the degree of beam-hardening artifact arising from the superior vena cava (SVC) and from the dependent arm that crossed the pulmonary arteries (1 = no artifact, 5 = artery obscured), and measured the degree of central venous compression of the injected veins at the thoracic inlet. A 2-tailed t test was performed to compare pulmonary artery density and central venous compression. Results: There was no difference in pulmonary artery enhancement between the 2 arm positions. Mean density of contrast in the main pulmonary artery was 329 Hounsfield units (HU) (95% confidence interval (CI), 310-350) in the arm-down group, compared with 325 HU (95% CI, 306-346) in the arm-up group (P = 0.65). Greater compression of the central veins occurred in the arm-up group (48.5%; 95% CI, 42.3%-54.8%) than in the arm-down group (22.3%; 95% CI, 16.8%-27.8%) (P < 0.05). There was also more beam hardening arising from contrast in the SVC in the arm-up group (P < 0.0001). Conclusions: Arm position does not affect pulmonary arterial enhancement during CTPA. There was greater central venous compression and more beam-hardening artifact arising from the SVC when the arm was held above the head.
Nanotechnologies to Enable High‐Performance Superconductors for Energy Applications

High Temperature Superconductors (HTS) wires or coated conductors (CC) hold promise to revolutionize the transmission of electricity enabling the present electric grid to meet the world’s growing energy needs. Although superconducting wires can carry 150 times more power than copper wires of the same cross section, further performance improvements are necessary for the superconducting technology to become costcompetitive. This objective can be achieved by introducing and controlling nano-sized defects and non-superconducting phases within the superconducting film’s matrix. Such nanostructures, when carefully engineered, significantly increase the loss-free current sustained by the superconductor through a mechanism known as flux pinning. This chapter is a review of the various types of nanostructures that are artificially introduced in superconducting films to enhance the superconductor’s performance. Different approaches, materials, and techniques are discussed and the most recent results in this field compared. The last section of this chapter discusses an additional example of
Premarket Evaluation of a Commercial Glycoprotein G-Based Enzyme Immunoassay for Herpes Simplex Virus Type-Specific Antibodies

ABSTRACT A new commercial glycoprotein G-based enzyme immunoassay (gG-EIA) was compared with Western blotting (WB) for detection of herpes simplex virus type 1 (HSV-1) or HSV-2 type-specific antibodies in 193 serum samples. Sensitivity for HSV-1 was 95%; specificity was 96%. Sensitivity for HSV-2 was 98%; specificity was 97%. Twelve of 13 serum samples with equivocal gG-EIA results were serotyped by WB.
Contrast properties of entropic criteria for blind source separation : a unifying framework based on information-theoretic inequalities/

In the recent years, Independent Component Analysis (ICA) has become a fundamental tool in adaptive signal and data processing, especially in the field of Blind Source Separation (BSS). Even though there exist some methods for which an algebraic solution to the ICA problem may be found, other iterative methods are very popular. Among them is the class of information-theoretic approaches, laying on entropies. The associated objective functions are maximized based on optimization schemes, and on gradient-ascent techniques in particular. Two major issues in this field are the following: 1) Does the global maximum point of these entropic objectives correspond to a satisfactory solution of BSS ? and 2) as gradient techniques are used, optimization algorithms look in fact for local maximum points, so what about the meaning of these local optima from the BSS problem point of view? Even though there are some partial answers to these questions in the literature, most of them are based on simulation and conjectures; formal developments are often lacking. This thesis aims at filling this lack and providing intuitive justifications, too. We focus the analysis on Renyi's entropy-based contrast functions. Our results show that, generally speaking, Renyi's entropy is not a suitable contrast function for BSS, even though we recover the well-known results saying that Shannon's entropy-based objectives are contrast functions. We also show that the range-based contrast functions can be built under some conditions on the sources. The BSS problem is stated in the first chapter, and viewed under the information (theory) angle. The two next chapters address specifically the above questions. Finally, the last chapter deals with range-based ICA, the only ``entropy-based contrast' which, based on the enclosed results, is also a discriminant contrast function, in the sense that it is theoretically free of spurious local optima. Geometrical interpretations and surprising examples are given. The interest of this approach is confirmed by testing the algorithm on the MLSP 2006 data analysis competition benchmark; the proposed method outperforms the previously obtained results on large-scale and noisy mixture samples obtained through ill-conditioned mixing matrices.
AUTOMATIC GENRE CLASSIFICATION OF HOME PAGES ON THE WEB

Abstract The World Wide Web contains many web pages, consisting of a wide variety of genres.Finding a method to automatically determine the genre of these web pages couldgreatly improve the search results of search engines on the web. Knowledge aboutthe genres of web pages could be used to allow a user to search for web pages withinparticular genres. A web page’s genre could also be used for ranking the web page incases where one genre is know to be more valuable to a particular query than anothergenre. One of the largest genres of web pages is the home page genre. The homepage genre can be thought of as a hierarchy that includes the sub-genres, personalhome page, corporate home page and organization home page. A web page’s genrecan be identiﬁed by extracting features from the page and then using those featuresto determine the web page’s genre. In this research, feature sets are used to train andtest a neural network for genre classiﬁcation. The neural network will classify webpages as personal, corporate and organization home pages.viii
FAS-1377 G/A (rs2234767) Polymorphism and Cancer Susceptibility: A Meta-Analysis of 17,858 Cases and 24,311 Controls

Background and Objectives Disruption of apoptosis has been implicated in carcinogenesis. Specifically, various single-nucleotide polymorphisms (SNPs) in apoptotic genes, such as FAS-1377 G/A SNP, have been associated with cancer risk. FAS-1377 G/A SNP has been shown to alter FAS gene promoter transcriptional activity. Down-regulation of FAS and cell death resistance is key to many cancers, but an association between FAS-1377 G/A SNP and cancer risk is uncertain. Therefore, we conducted a meta-analysis of the current literature to clarify this relationship. Methodology/Principal Findings From PubMed and Chinese language (CNKI and WanFang) databases, we located articles published up to March 5, 2013, obtaining 44 case-control studies from 41 different articles containing 17,858 cases and 24,311 controls based on search criteria for cancer susceptibility related to the FAS gene -1377 G/A SNP. Odds ratios (ORs) and 95% confidence intervals (CI) revealed association strengths. Data show that the -1377 G allele was protective against cancer risk. Similar associations were detected in “source of control,” ethnicity and cancer type subgroups. Lower cancer risk was found in both smokers with a GG+GA genotype and in non-smokers with the GG+GA genotype, when compared to smokers and nonsmokers with the AA genotype. Males carrying the -1377G allele (GG+GA) had lower cancer incidence than those with the AA genotype. Individuals who carried both FAS-1377(GG+GA)/FASL-844(TT+TC) genotypes appeared to have lower risk of cancer than those who carried both FAS-1377 AA/FASL-844 CC genotypes. Conclusions/Significance The FAS-1377 G/A SNP may decrease cancer risk. Studies with larger samples to study gene-environment interactions are warranted to understand the role of FAS gene polymorphisms, especially -1377 G/A SNP, in cancer risk.