Miracle-dz/UniFAR-FTUs huggingface dataset:
Determinants of Human Adipose Tissue Gene Expression: Impact of Diet, Sex, Metabolic Status, and Cis Genetic Regulation

Weight control diets favorably affect parameters of the metabolic syndrome and delay the onset of diabetic complications. The adaptations occurring in adipose tissue (AT) are likely to have a profound impact on the whole body response as AT is a key target of dietary intervention. Identification of environmental and individual factors controlling AT adaptation is therefore essential. Here, expression of 271 transcripts, selected for regulation according to obesity and weight changes, was determined in 515 individuals before, after 8-week low-calorie diet-induced weight loss, and after 26-week ad libitum weight maintenance diets. For 175 genes, opposite regulation was observed during calorie restriction and weight maintenance phases, independently of variations in body weight. Metabolism and immunity genes showed inverse profiles. During the dietary intervention, network-based analyses revealed strong interconnection between expression of genes involved in de novo lipogenesis and components of the metabolic syndrome. Sex had a marked influence on AT expression of 88 transcripts, which persisted during the entire dietary intervention and after control for fat mass. In women, the influence of body mass index on expression of a subset of genes persisted during the dietary intervention. Twenty-two genes revealed a metabolic syndrome signature common to men and women. Genetic control of AT gene expression by cis signals was observed for 46 genes. Dietary intervention, sex, and cis genetic variants independently controlled AT gene expression. These analyses help understanding the relative importance of environmental and individual factors that control the expression of human AT genes and therefore may foster strategies aimed at improving AT function in metabolic diseases.
Interplay between Basic Residues of Hepatitis C Virus Glycoprotein E2 with Viral Receptors, Neutralizing Antibodies and Lipoproteins

Positively-charged amino acids are located at specific positions in the envelope glycoprotein E2 of the hepatitis C virus (HCV): two histidines (H) and four arginines (R) in two conserved WHY and one RGERCDLEDRDR motifs, respectively. Additionally, the E2 hypervariable region 1 (HVR1) is rich in basic amino acids. To investigate the role(s) of these residues in HCV entry, we subjected to comparative infection and sedimentation analysis cell culture-produced (HCVcc, genotype 2a) wild type virus, a panel of alanine single-site mutants and a HVR1-deletion variant. Initially, we analyzed the effects of these mutations on E2-heparan sulfate (HS) interactions. The positive milieu of the HVR1, formulated by its basic amino acids (key residues the conserved H386 and R408), and the two highly conserved basic residues H488 and R648 contributed to E2-HS interactions. Mutations in these residues did not alter the HCVcc-CD81 entry, but they modified the HCVcc-scavenger receptor class B type I (SR-BI) dependent entry and the neutralization by anti-E2 or patients IgG. Finally, separation by density gradients revealed that mutant viruses abolished partially or completely the infectivity of low density particles, which are believed to be associated with lipoproteins. This study shows that there exists a complex interplay between the basic amino acids located in HVR1 and other conserved E2 motifs with the HS, the SR-BI, and neutralizing antibodies and suggests that HCV-associated lipoproteins are implicated in these interactions.
Pancreatic carcinoma in carriers of a specific 19 base pair deletion of CDKN2A/p16 (p16-leiden).

PURPOSE The purpose is to document the clinical, pathological, and genetic features of pancreatic carcinoma (PC) in carriers of a specific p16-Leiden mutation (a 19-bp deletion in exon 2 of the CDKN2A gene). EXPERIMENTAL DESIGN Clinical data and paraffin embedded tissue were obtained from 12 patients of p16-Leiden-positive families with PC. Because of the known 19-bp germ-line deletion, we could specifically analyze the genotype of the wild-type allele for loss of heterozygosity. K-ras codon 12 mutations were determined and immunohistochemical testing for p16, Tp53, Smad4, and cyclooxygenase 2 was performed. RESULTS The average age of subjects that developed PC (8 males) was 58 years (range, 43-74 years). Histology was considered as conventional ductal adenocarcinoma in 11 of 12 and neuroendocrine carcinoma (1 of 12). The carcinomas were located in the head (10 of 12), corpus (1 of 12), and tail (1 of 12) of the pancreas. The specific p16-Leiden mutation was confirmed in the tissue of all subjects. Loss of heterozygosity of the wild-type allele was present in 2 of 7 tumors analyzed. Immunostaining for p16 was negative in 10 of 10. Tp53 mutations were detected in 5 of 12. Smad4 was negative in 5 of 12 and cyclooxygenase 2 was overexpressed in 11 of 12. K-ras codon 12 mutations were present in 9 of 10 and in three precursor lesions even before abrogation of p16 protein expression was seen (one of three). CONCLUSIONS The p16-Leiden deletion was associated with progression toward conventional ductal adenocarcinomas in all cases but one. Our observations might support the feasibility of early diagnosis of PC in p16-Leiden mutation carriers and might also indicate that chemoprevention needs consideration.
Infection with a Helminth Parasite Prevents Experimental Colitis via a Macrophage-Mediated Mechanism1

The propensity of a range of parasitic helminths to stimulate a Th2 or regulatory cell-biased response has been proposed to reduce the severity of experimental inflammatory bowel disease. We examined whether infection with Schistosoma mansoni, a trematode parasite, altered the susceptibility of mice to colitis induced by dextran sodium sulfate (DSS). Mice infected with schistosome worms were refractory to DSS-induced colitis. Egg-laying schistosome infections or injection of eggs did not render mice resistant to colitis induced by DSS. Schistosome worm infections prevent colitis by a novel mechanism dependent on macrophages, and not by simple modulation of Th2 responses, or via induction of regulatory CD4+ or CD25+ cells, IL-10, or TGF-β. Infected mice had marked infiltration of macrophages (F4/80+CD11b+CD11c−) into the colon lamina propria and protection from DSS-induced colitis was shown to be macrophage dependent. Resistance from colitis was not due to alternatively activated macrophages. Transfer of colon lamina propria F4/80+ macrophages isolated from worm-infected mice induced significant protection from colitis in recipient mice treated with DSS. Therefore, we propose a new mechanism whereby a parasitic worm suppresses DSS-induced colitis via a novel colon-infiltrating macrophage population.
Expressing the Behavior of Three Very Different Concurrent Systems by Using Natural Extensions of Separation Logic

Separation Logic is a non-classical logic used to verify pointer-intensive code. In this paper, however, we show that Separation Logic, along with its natural extensions, can also be used as a specification language for concurrent-system design. To do so, we express the behavior of three very different concurrent systems: a Subway, a Stopwatch, and a 2x2 Switch. The Subway is originally implemented in LUSTRE, the Stopwatch in Esterel, and the 2x2 Switch in Bluespec.
Estimating node degree in bait-prey graphs

MOTIVATION Proteins work together to drive biological processes in cellular machines. Summarizing global and local properties of the set of protein interactions, the interactome, is necessary for describing cellular systems. We consider a relatively simple per-protein feature of the interactome: the number of interaction partners for a protein, which in graph terminology is the degree of the protein. RESULTS Using data subject to both stochastic and systematic sources of false positive and false negative observations, we develop an explicit probability model and resultant likelihood method to estimate node degree on portions of the interactome assayed by bait-prey technologies. This approach yields substantial improvement in degree estimation over the current practice that naively sums observed edges. Accurate modeling of observed data in relation to true but unknown parameters of interest gives a formal point of reference from which to draw conclusions about the system under study. AVAILABILITY All analyses discussed in this text can be performed using the ppiStats and ppiData packages available through the Bioconductor project (http://www.bioconductor.org).
The Role and Identification

In recent years, online chat has become a dominant mode of communication. This text-based medium has the potential of improving information awareness within an organization, but only if the critical information within messages can be identified and directed to where it is most needed. Such a goal has many challenges that traditional Information Extraction (IE) approaches have rarely addressed: the text is “dirty” (containing typos, misspellings, sparse punctuation, etc.), messages are fragmented and refer implicitly to previous messages and shared knowledge, messages from multiple topics are interleaved, etc. Past work in conversation analysis has included in-depth discussions of dialog acts, i.e., the individual utterances that comprise conversations. This paper describes how dialog acts within online chat differ from those within two-person voice conversations. It then presents methods for identifying dialog acts and the role that dialog acts play in identifying individual conversations within a chat stream. Identifying conversations is a necessary step for extracting actionable information, such as identifying individuals with specific expertise, recognizing reports of offline activities, and alerting decision makers to critical developments. Finally, we describe Chat-IE, a prototype software system that performs live dialog identification on chat streams.
Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods.

The normal microbial flora of the vagina plays an important role in preventing genital and urinary tract infections in women. Thus an accurate understanding of the composition and ecology of the ecosystem is important to understanding the aetiology of these diseases. Common wisdom is that lactobacilli dominate the normal vaginal microflora of post-pubertal women. However, this conclusion is based on methods that require cultivation of microbial populations; an approach that is known to yield a biased and incomplete assessment of microbial community structure. In this study cultivation-independent methods were used to analyse samples collected from the mid-vagina of five normal healthy Caucasian women between the ages of 28 and 44. Total microbial community DNA was isolated following resuspension of microbial cells from vaginal swabs. To identify the constituent numerically dominant populations in each community 16S rRNA gene libraries were prepared following PCR amplification using the 8f and 926r primers. From each library, the DNA sequences of approximately 200 16S rRNA clones were determined and subjected to phylogenetic analyses. The diversity and kinds of organisms that comprise the vaginal microbial community varied among women. Species of Lactobacillus appeared to dominate the communities in four of the five women. However, the community of one woman was dominated by Atopobium sp. , whereas a second woman had appreciable numbers of Megasphaera sp. , Atopobium sp. and Leptotrichia sp. , none of which have previously been shown to be common members of the vaginal ecosystem. Of the women whose communities were dominated by lactobacilli, there were two distinct clusters, each of which consisted of a single species. One class consisted of two women with genetically divergent clones that were related to Lactobacillus crispatus, whereas the second group of two women had clones of Lactobacillus iners that were highly related to a single phylotype. These surprising results suggest that culture-independent methods can provide new insights into the diversity of bacterial species found in the human vagina, and this information could prove to be pivotal in understanding risk factors for various infectious diseases.
Explicitly considering relevance within the language modeling framework

Whilst the event of relevance is central to the Binary Independence Retrieval model, Language Modeling focuses on the estimation of the document model. In this paper, we review the different past formulations of the Language Modeling (query likelihood) approach. We find that these previous formulations largely ignore relevance by making implicit or explicit assumptions. The main contribution of this work is an alternative formulation that specifically relates relevance and language modeling in a sound probabilistic framework. This leads to valuable insights into the application of Language Modeling to Information Retrieval, including how the approach handles relevance information and how the approach can be further developed.
The cytoskeleton of the neuron—an essay in celebration of Paul Letourneau's career

The neuronal cytoskeleton consists of microtubules, actin filaments, neurofilaments, and an array of accessory proteins that regulate and modify these three main filament systems. This essay celebrates the career of Paul Letourneau, a pioneer of the neuronal cytoskeleton, to whom the community owes a debt of gratitude. © 2011 Wiley Periodicals, Inc. Develop Neurobiol, 2011
FPGA architecture for object extraction in Wireless Multimedia Sensor Network

This paper presents the architecture of a FPGA-based efficient image processing system suited to Wireless Multimedia Sensor Networks. The system consists of two major processing elements: a customized processor for the networking functions and an image processing block. The latter enables the system to detect and extract any updated objects in captured images in real-time. The proposed architecture is optimized to achieve high speed processing with minimum hardware requirement and power consumption. Experimental results show that for a detected object of average size, the proposed architecture helps to reduce the total energy consumption by approximately twenty times compared to the energy consumed for raw image transmission. The system was successfully designed and implemented on FPGA. Implementation results of a network utilizing the proposed architecture reveal that this novel approach is suitable for Wireless Multimedia Sensor Network due to low hardware and low energy requirement for image communication.
Studies on the Interaction Mechanism of Pyrene Derivatives with Human Tumor-Related DNA

Pyrene derivatives can be carcinogenic, teratogenic and mutagenic, thus having the potential to cause malignant diseases. In this work, the interactions of two selected pyrene derivatives (1-OHP and 1-PBO) and human tumor-related DNA (p53 DNA and C-myc DNA) are investigated by spectroscopic and non-native polyacrylamide gel electrophoresis (PAGE) methods. Using fluorescence spectrometry and circular dichroism (CD), DNA interactions of pyrene derivatives are confirmed to occur mainly via the groove binding mode supported by the intercalation into the base pairs of DNA. There is an obvious binding order of pyrene derivatives to the targeted DNA, 1-OHP > 1-PBO. The binding constants of 1-OHP are 1.16 × 106 L·mol−1 and 4.04 × 105 L·mol−1 for p53 DNA and C-myc DNA, respectively, while that of 1-PBO are only 2.04 × 103 L·mol−1 and 1.39 × 103 L·mol−1 for p53 DNA and C-myc DNA, respectively. Besides, the binding of pyrene derivatives to p53 DNA is stronger than that for C-myc DNA. CD and PAGE results indicate that the binding of pyrene derivatives can affect the helical structures of DNA and further induce the formation of double-chain antiparallel G-quadruplex DNA of hybrid G-rich sequences.
Mining Social Response to Crisis via Electronic Media

In this paper, we are interested in using text mining to analyze textual data obtained from electronic social media in order to find out social concerns on crisis. In particular, we explore the temporal theme patterns in the natural catastrophe, i.e. the Yushu Earthquake, and compare the foci of the Chinese public, Chinese government and the overseas. By incorporating sources of information with a variety of aspects, we can distill not only snapshots of social concerns at given times but also the evolution of these concerns over time. Our intension is to assist the government in publicizing appropriate information and making intelligent decisions.
Hepatocellular carcinoma: from gene to public health.

Liver diseases associated with chronic hepatitis B virus (HBV) infection, including hepatocellular carcinoma, account for more than 1 million deaths annually worldwide. In addition to HBV infection, other risk factors are involved in the etiology of hepatocellular carcinoma and, among these, dietary exposure to the carcinogenic aflatoxins is of particular importance in certain regions of southeast Asia and sub-Saharan Africa. The relative contributions of these two risk factors and the mechanism of the interaction between them in the pathogenesis of hepatocellular carcinoma are still poorly understood. The recently developed individual biochemical and molecular markers of aflatoxin exposure, i.e., aflatoxin-albumin adducts in blood and a specific GC to TA transversion mutation in codon 249 of the p53 gene (249ser p53 mutation) in hepatocellular carcinomas, permit a better quantitative estimation of aflatoxin exposure in different populations of the world. A comprehensive summary of the data from our laboratory and the literature, based on a large number (>1000) of individual cases of hepatocellular carcinoma, is presented here and shows the following: 1) A high level and high prevalence of exposure to aflatoxins occur in West Africa, Mozambique, and some regions of China; 2) a high prevalence of the 249ser p53 mutation is detected in these countries; and 3) hepatocellular carcinomas from countries with low or no exposure to aflatoxins show a very low prevalence of the 249ser p53 mutation and distinctly different p53 mutation spectra, probably indicating different etiologies. Experimental and epidemiologic studies demonstrate an interaction between HBV infection and aflatoxins in hepatocarcinogenesis. The relevance of the biochemical/molecular markers of aflatoxin exposure, HBV vaccination, and the reduction of aflatoxin exposure, in addition to the interaction between HBV infection and other risk factors in liver carcinogenesis, are discussed with regard to the implementation of measures for primary prevention.
Discriminating between Second Language Learning Text-Types

Text classification remains one of the major fields of research in natural language processing. This paper evaluates the use of the computational tool Coh-Metrix as a means to distinguish between seemingly similar text-types. Using a discriminant analysis on a corpus of second language reading texts, this paper demonstrates that CohMetrix is able to significantly distinguish authentic texttypes from ones that have been specifically simplified for second language readers. This paper offers important findings for text classification research and for second language reading materials developers and second language teachers by demonstrating that moderate, shallow, textual changes can affect discourse structures.
Rape Victim Advocates Experiences With Law Enforcement in the Emergency Room

One of the first people a sexual assault survivor will encounter in the emergency room is a specially trained rape victim advocate. Along with rape victim advocates, many survivors will come across law enforcement in the emergency room. This study explores rape victim advocates perception of how survivors are treated in the emergency room by law enforcement. Data from interviews with 23 female advocates indicate a complex relationship that includes positive interactions with police as well as victim blaming and a lack of knowledge about how sexual assault affects survivors. Suggestions for future research are provided.
Supplementary Material for Online Adaptor Grammars with Hybrid Inference

In this document, we outline the definition of an adaptor grammar and the generative process of our model (Section 1). This allows us to define a joint distribution over adapted grammars and observations (Section 2). Uncovering the latent variables of the model (grammars and productions) requires posterior inference. We use online hybrid variational inference, which requires three components: positing a variational distribution (Section 3), deriving the mean-field updates (Section 4), and then adapting those updates into the online setting (Section 5). Section 6 serves as a reference to review all of the notation used in this document.
XCBC and XNIT - Tools for Cluster Implementation and Management in Research and Training

The Extreme Science and Engineering Discovery Environment has created a suite of software designed to facilitate the local management of computer clusters for scientific research and integration of such clusters with the US open research national cyberinfrastructure. This suite of software is distributed in two ways. One distribution is called the XSEDE-compatible basic cluster (XCBC), a Rocks Roll that does an “all at once, from scratch” installation of core components. The other distribution is called the XSEDE National Integration Toolkit (XNIT), so that specific tools can be downloaded and installed in portions as appropriate on existing clusters. In this paper, we describe the software included in XCBC and XNIT, and examine the use of XCBC installed on the LittleFe cluster design created by the Earlham College Cluster Computing Group as a teaching tool to show the deployment of XCBC from Rocks. In addition, the demonstration of the commercial Limulus HPC200 Deskside Cluster solution is shown as a viable, off-the-shelf cluster that can be adapted to become an XSEDE-like cluster through the use of the XNIT repository. We demonstrate that both approaches to cluster management - use of SCBC to build clusters from scratch and use of XNIT to expand capabilities of existing clusters - aid cluster administrators in administering clusters that are valuable locally and facilitate integration and interoperability of campus clusters with national cyberinfrastructure. We also demonstrate that very economical clusters can be useful tools in education and research. Categories and Subject Descriptors Theory of computation - Parallel computing models; Computer systems organization - Grid computing; Computer systems organization - Special purpose systems.
A 2-GHz 6.1-mA Fully-Differential CMOS Phase-Locked Loop

A fully-differential 2-GHz phase-locked loop (PLL) was designed and fabricated in 0.18-mum CMOS process. The PLL rejects the common noise due to fully-differential VCO and differential charge pump. The VCO has a 16.15% tuning range (from 1.8998GHz to 2.2335GHz) due to a combination of analog and digital tuning technique (4-bit binary switch-capacitor array). With the pn-junction varactors, the phase noise of the VCO varies only about 2dB in the tuning range. The current consumption of the PLL is only about 6.1mA from a 1.8 V power supply. It is comparable to the results reported in recent literatures. The phase noise of the PLL at 2.033 GHz can achieve -117.17dBc/Hz at 1 MHz frequency offset from the carrier.