gebhart/patrepeval huggingface dataset:
The Human Obesity Gene Map: The 2005 Update (2006)

This paper presents the 12th update of the human obesity gene map, which incorporates published results up to the end of October 2005. Evidence from single-gene mutation obesity cases, Mendelian disorders exhibiting obesity as a clinical feature, transgenic and knockout murine models relevant to obesity, quantitative trait loci (QTL) from animal cross-breeding experiments, association studies with candidate genes, and linkages from genome scans is reviewed. As of October 2005, 176 human obesity cases due to single-gene mutations in 11 different genes have been reported, 50 loci related to Mendelian syndromes relevant to human obesity have been mapped to a genomic region, and causal genes or strong candidates have been identified for most of these syndromes. There are 244 genes that, when mutated or expressed as transgenes in the mouse, result in phenotypes that affect body weight and adiposity. The number of QTLs reported from animal models currently reaches 408. The number of human obesity QTLs derived from genome scans continues to grow, and we now have 253 QTLs for obesity-related phenotypes from 61 genome-wide scans. A total of 52 genomic regions harbor QTLs supported by two or more studies. The number of studies reporting associations between DNA sequence variation in specific genes and obesity phenotypes has also increased considerably, with 426 findings of positive associations with 127 candidate genes. A promising observation is that 22 genes are each supported by at least five positive studies. The obesity gene map shows putative loci on all chromosomes except Y. The electronic version of the map with links to useful publications and relevant sites can be found at http://obesitygene.pbrc.edu.
Mapping parallelism to multi-cores (2009)

The efficient mapping of program parallelism to multi-core processors is highly dependent on the underlying architecture. This paper proposes a portable and automatic compiler-based approach to mapping such parallelism using machine learning. It develops two predictors: a data sensitive and a data insensitive predictor to select the best mapping for parallel programs. They predict the number of threads and the scheduling policy for any given program using a model learnt off-line. By using low-cost profiling runs, they predict the mapping for a new unseen program across multiple input data sets. We evaluate our approach by selecting parallelism mapping configurations for OpenMP programs on two representative but different multi-core platforms (the Intel Xeon and the Cell processors). Performance of our technique is stable across programs and architectures. On average, it delivers above 96% performance of the maximum available on both platforms. It achieve, on average, a 37% (up to 17.5 times) performance improvement over the OpenMP runtime default scheme on the Cell platform. Compared to two recent prediction models, our predictors achieve better performance with a significant lower profiling cost.
THE SUSCEPTIBILITY OF SWINE TO THE VIRUS OF HUMAN INFLUENZA (1936)

Swine inoculated intranasally with human influenza virus alone develop an ill defined, mild, and usually afebrile illness of short duration. At postmortem the anterior lobes of the lungs of such animals contain scant, scattered areas of lobular atelectasis. Transmission of the virus for 5 serial passages through two groups of swine failed noticeably to enhance its pathogenicity for this species. The disease produced in swine by infection with human influenza virus alone is indistinguishable clinically and pathologically from that caused by infection with swine influenza virus alone. Transmission of human influenza virus from swine to swine by contact succeeded in only one of four attempts. Swine inoculated intranasally with a mixture of human influenza virus and H. influenzae suis usually develop a febrile, depressing illness similar to mild swine influenza. The pneumonia encountered in such animals at autopsy is similar to but less extensive than that seen in swine influenza. In some animals H. influenzae suis fails to become established and the disease then seen is identical with that caused by human influenza virus alone. The human influenza virus recovered after 5 serial transfers in swine was immunologically the same as that with which the experiments were begun.
A visual bag of words method for interactive qualitative localization and mapping (2007)

Localization for low cost humanoid or animal-like personal robots has to rely on cheap sensors and has to be robust to user manipulations of the robot. We present a visual localization and map-learning system that relies on vision only and that is able to incrementally learn to recognize the different rooms of an apartment from any robot position. This system is inspired by visual categorization algorithms called bag of words methods that we modified to make fully incremental and to allow a user-interactive training. Our system is able to reliably recognize the room in which the robot is after a short training time and is stable for long term use. Empirical validation on a real robot and on an image database acquired in real environments are presented.
Induction of Cytosolic Calcium Flux by CD20 Is Dependent upon B Cell Antigen Receptor Signaling (2008)

The anti-CD20 monoclonal antibody (mAb) rituximab is now routinely used for the treatment of non-Hodgkins lymphoma and is being examined in a wide range of other B-cell disorders, such as rheumatoid arthritis. Despite intensive study, the mechanism of action still remains uncertain. In the current study, anti-CD20 mAb-induced calcium signaling was investigated. Previously, we grouped anti-CD20 mAbs into Type I (rituximab-like) and Type II (B1-like) based upon various characteristics such as their ability to induce complement activation and redistribute CD20 into detergent-insoluble membrane domains. Here we show that only Type I mAbs are capable of inducing a calcium flux in B cells and that this is tightly correlated with the expression of the B-cell antigen receptor (BCR). Inhibitor analysis revealed that the signaling cascade employed by CD20 was strikingly similar to that utilized by the BCR, with inhibitors of Syk, Src, and PI3K, but not EGTA, p38, or ERK1/2, completely ablating calcium flux. Furthermore, binding of Type I but not Type II mAbs caused direct association of CD20 with the BCR as measured by FRET and resulted in the phosphorylation of BCR-specific adaptor proteins BLNK and SLP-76. Crucially, variant Ramos cells lacking BCR expression but with unchanged CD20 expression were completely unable to induce calcium flux following ligation of CD20. Collectively, these data indicate that CD20 induces cytosolic calcium flux through its ability to associate with and "hijack" the signaling potential of the BCR.
Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid (1996)

Colanic acid (CA) is an extracellular polysaccharide produced by most Escherichia coli strains as well as by other species of the family Enterobacteriaceae. We have determined the sequence of a 23-kb segment of the E. coli K-12 chromosome which includes the cluster of genes necessary for production of CA. The CA cluster comprises 19 genes. Two other sequenced genes (orf1.3 and galF), which are situated between the CA cluster and the O-antigen cluster, were shown to be unnecessary for CA production. The CA cluster includes genes for synthesis of GDP-L-fucose, one of the precursors of CA, and the gene for one of the enzymes in this pathway (GDP-D-mannose 4,6-dehydratase) was identified by biochemical assay. Six of the inferred proteins show sequence similarity to glycosyl transferases, and two others have sequence similarity to acetyl transferases. Another gene (wzx) is predicted to encode a protein with multiple transmembrane segments and may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The first three genes of the cluster are predicted to encode an outer membrane lipoprotein, a phosphatase, and an inner membrane protein with an ATP-binding domain. Since homologs of these genes are found in other extracellular polysaccharide gene clusters, they may have a common function, such as export of polysaccharide from the cell.
An Empirical Evaluation on Online Chinese Handwriting Databases (2012)

Several online Chinese handwriting databases have been proposed recently. Though they have been introduced in detail, to date, no one has ever evaluated these databases with experimental comparison. To help the researchers use the corresponding database properly for algorithm evaluation and real application, we compare the property of the handwriting characters in these databases, and evaluate them with the same experimental setup and handwriting recognizer. Moreover, we analyze the connection between the property and the corresponding recognition accuracy for the handwriting characters in different databases. These empirical evaluation results can help the researchers choose the right database for different algorithms and applications.
Therapeutic Applications of DNA and RNA Aptamers (2009)

Structured single-stranded nucleic acids, or aptamers, bind target molecules with high affinity and specificity, which translates into unique therapeutic possibilities. Currently, aptamers can be identified to most proteins, including blood-clotting factors, cell-surface receptors, and transcription factors. Chemical modifications to the oligonucleotides enhance their pharmacokinetics and pharmacodynamics, thus extending their therapeutic potential. Several aptamers have entered the clinical pipeline for applications and diseases such as macular degeneration, coronary artery bypass graft surgery, and various types of cancer. Furthermore, the functional repertoire of aptamers has expanded with the descriptions of multivalent agonistic aptamers and aptamers-siRNA chimeras. This review highlights those aptamers and aptamer-based approaches with particular likelihood of achieving therapeutic application.
Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallography (2009)

Due to the close resemblance of the 66.3 kDa protein to members of the Ntn hydrolase superfamily a hydrolytic activity on substrates containing a non-peptide amide bond seems reasonable. The structural homology which comprises both the overall fold and essential active site residues also implies an autocatalytic maturation process of the lysosomal 66.3 kDa protein. Upon the proteolytic cleavage between S248 and C249, a deep pocket becomes solvent accessible, which harbors the putative active site of the 66.3 kDa protein.
Optimal Magnetic Sensor Vests for Cardiac Source Imaging (2016)

Magnetocardiography (MCG) non-invasively provides functional information about the heart. New room-temperature magnetic field sensors, specifically magnetoresistive and optically pumped magnetometers, have reached sensitivities in the ultra-low range of cardiac fields while allowing for free placement around the human torso. Our aim is to optimize positions and orientations of such magnetic sensors in a vest-like arrangement for robust reconstruction of the electric current distributions in the heart. We optimized a set of 32 sensors on the surface of a torso model with respect to a 13-dipole cardiac source model under noise-free conditions. The reconstruction robustness was estimated by the condition of the lead field matrix. Optimization improved the condition of the lead field matrix by approximately two orders of magnitude compared to a regular array at the front of the torso. Optimized setups exhibited distributions of sensors over the whole torso with denser sampling above the heart at the front and back of the torso. Sensors close to the heart were arranged predominantly tangential to the body surface. The optimized sensor setup could facilitate the definition of a standard for sensor placement in MCG and the development of a wearable MCG vest for clinical diagnostics.
The Compression Cache: Using On-line Compression to Extend Physical Memory. (1993)

This paper describes a method for trading off computation for disk or network I/O by using less expensive on-line compression. By using some memory to store data in compressed format, it may be possible to fit the working set of one or more large applications in relatively small memory. For working sets that are too large to fit in memory even when compressed, compression still provides a benefit by reducing bandwidth and space requirements. Overall, the effectiveness of this compression cache depends on application behavior and the relative costs of compression and I/O. Measurements using Sprite on a DECstation 1 5000/200 workstation with a local disk indicate that some memory-intensive applications running with a compression cache can run two to three times faster than on an unmodified system. Better speedups would be expected in a system with a greater disparity between the speed of its processor and the bandwidth to its backing store. 1 Introduction Over the past decade, the pr...
The Culture of Surveillance: G-Men Redux and Total Information Awareness (2003)

Part of the U.S. Defense Advanced Research Projects Agency’s Information Awareness Office, the Total Information Awareness (TIA) project, enacted in the wake of September 11th, aims to capture the information signature of citizens suspected of terrorism or criminal acts. Technical means (including computer algorithms and human analysis) afford the government the ability to track those involved in low-intensity/low-density forms of warfare and crime, its ultimate goal to track individuals through collecting as much information about them as possible.Various public interest groups have criticized this initiative, particularly on the basis of privacy and security risks, identity theft, misuse of information, and overt citizen surveillance. This article will provide an overview of TIA and situate it within an ongoing political economy of the military-industrial complex, now revamped for an emerging security industry.
Monoclonal Antibodies at Age 20: Promise at Last? (1995)

When they were first produced 2 decades ago, monoclonal antibodies were enthusiastically touted as “magic bullets” that would find wide application in medical therapeutics and diagnostics. But a variety of problems including severe immune reactions prevented them from living up to the early hype. A recent conference on monoclonals and cancer therapy suggests, however, that some of the difficulties are slowly being overcome.
Image‐Based Crack Detection for Real Concrete Surfaces (2007)

Abstract In this paper, we introduce a novel image‐based approach to detect cracks in concrete surfaces. Crack detection is important for the inspection, diagnosis, and maintenance of concrete structures. However, conventional image‐based approaches cannot achieve precise detection since the image of the concrete surface contains various types of noise due to different causes such as concrete blebs, stain, insufficient contrast, and shading. In order to detect the cracks with high fidelity, we assume that they are composed of thin interconnected textures and propose an image‐based percolation model that extracts a continuous texture by referring to the connectivity of brightness and the shape of the percolated region, depending on the length criterion of the scalable local image processing techniques. Additionally, noise reduction based on the percolation model is proposed. We evaluated the validity of the proposed technique by using precision recall and receiver operating characteristic (ROC) analysis by means of some experiments with actual concrete surface images. Copyright © 2007 Institute of Electrical Engineers of Japan. Published by John Wiley &amp; Sons, Inc.
Evaluation of cyclooxygenase-2 inhibitor for potential chemopreventive properties in colon carcinogenesis. (1996)

Epidemiological and laboratory studies indicate an inverse relationship between the risk of colon cancer development and intake of nonsteroidal antiinflammatory agents, including aspirin. One of the mechanisms by which nonsteroidal antiinflammatory agents inhibit colon carcinogenesis is through the inhibition of prostaglandin production by cyclooxygenase isozymes (COX-1 and COX-2). Overexpression of COX-2 has been observed in colon tumors. Thus, selective inhibitors of COX-2 could potentially serve as chemopreventive agents. We have assessed the chemopreventive properties of SC-58635, a COX-2 inhibitor, and of sulindac, as a positive control, in a double-blind study, using azoxymethane-induced colonic aberrant crypt foci (ACF) as a measure of efficacy. Five-week-old male F344 rats were fed the control diet (modified AIN-76A) or experimental diets containing 150 or 1500 ppm SC-58635, 320 ppm sulindac, or 1500 ppm placebo. Two weeks later, all animals except those in vehicle (normal saline)-treated groups were s.c. injected with azoxymethane (15 mg/kg of body weight, once weekly for 2 weeks). At 16 weeks of age, all rats were sacrificed and colons were evaluated for ACF. As expected, dietary administration of sulindac suppressed ACF development as such and reduced crypt multiplicity in terms of number of aberrant crypts/ focus. Administration of 1500 ppm SC-58635 inhibited total ACF induction and crypt multiplicity by about 40-49%. Our finding that SC-58635 significantly suppressed colonic ACF formation and crypt multiplicity strengthens the hypothesis that a selective COX-2 inhibitor possesses chemopreventive activity against colon carcinogenesis.
Joint Source–Channel Communication for Distributed Estimation in Sensor Networks (2007)

Power and bandwidth are scarce resources in dense wireless sensor networks and it is widely recognized that joint optimization of the operations of sensing, processing and communication can result in significant savings in the use of network resources. In this paper, a distributed joint source-channel communication architecture is proposed for energy-efficient estimation of sensor field data at a distant destination and the corresponding relationships between power, distortion, and latency are analyzed as a function of number of sensor nodes. The approach is applicable to a broad class of sensed signal fields and is based on distributed computation of appropriately chosen projections of sensor data at the destination - phase-coherent transmissions from the sensor nodes enable exploitation of the distributed beamforming gain for energy efficiency. Random projections are used when little or no prior knowledge is available about the signal field. Distinct features of the proposed scheme include: (1) processing and communication are combined into one distributed projection operation; (2) it virtually eliminates the need for in-network processing and communication; (3) given sufficient prior knowledge about the sensed data, consistent estimation is possible with increasing sensor density even with vanishing total network power; and (4) consistent signal estimation is possible with power and latency requirements growing at most sublinearly with the number of sensor nodes even when little or no prior knowledge about the sensed data is assumed at the sensor nodes.
Evidence that the tightly bound magnesium in tubulin is associated with the N‐site GTP (1990)

In an attempt to determine whether the tightly bound Mg2+ found in purified tubulin in associated with the N-site GTP or the E-site GDP or GTP, we removed the E-site nucleotide by several means: (i) alkaline phosphatase treatment; (ii) displacement using excess GMPPCP; and (iii) polymerizing tubulin in the presence of alkaline phosphatase and non-hydrolyzable analogues. The Mg2+ content remained equal to about 1 mol/mol tubulin under conditions where denaturation did not occur. Moreover, the Mg/GTP ratio always remained equal to 1. These results indicate that the Mg2+ is associated with the N-site GTP.
Role of Dynactin in Endocytic Traffic: Effects of Dynamitin Overexpression and Colocalization with CLIP-170 (1999)

The flow of material from peripheral, early endosomes to late endosomes requires microtubules and is thought to be facilitated by the minus end-directed motor cytoplasmic dynein and its activator dynactin. The microtubule-binding protein CLIP-170 may also play a role by providing an early link to endosomes. Here, we show that perturbation of dynactin function in vivo affects endosome dynamics and trafficking. Endosome movement, which is normally bidirectional, is completely inhibited. Receptor-mediated uptake and recycling occur normally, but cells are less susceptible to infection by enveloped viruses that require delivery to late endosomes, and they show reduced accumulation of lysosomally targeted probes. Dynactin colocalizes at microtubule plus ends with CLIP-170 in a way that depends on CLIP-170's putative cargo-binding domain. Overexpression studies using p150(Glued), the microtubule-binding subunit of dynactin, and mutant and wild-type forms of CLIP-170 indicate that CLIP-170 recruits dynactin to microtubule ends. These data suggest a new model for the formation of motile complexes of endosomes and microtubules early in the endocytic pathway.
Increased expression of STAT3 in SLE T cells contributes to enhanced chemokine-mediated cell migration (2007)

Exposure of T cells to inflammatory cytokines leads to phosphorylation-dependent activation of signal transducer and activator of transcription (STAT) 3. T cells from patients with systemic lupus erythematosus (SLE) display increased levels of total and phosphorylated STAT3 which resides primarily in the nucleus. Increased STAT3 is associated with increased expression of target genes. Silencing of STAT3 expression using a small interfering RNA approach resulted in decreased chemokine-provoked SLE T cell migration. Our data suggest that inhibition of STAT3 expression may reverse the signaling aberrations involved in SLE T cell migration.
Pim Family Kinases Enhance Tumor Growth of Prostate Cancer Cells (2005)

Recent analyses indicate that the expression of the Pim-1 protein kinase is elevated in biopsies of prostate tumors. To identify the mechanism by which the Pim kinases may affect the growth of prostate tumors, we expressed Pim-1, Pim-2, or a kinase-dead Pim-2 protein in human PC3 prostate cancer cells. On implantation of the transfectants in nude mice, the growth of the cells expressing Pim-1 or Pim-2 was significantly faster than the growth of the control cells transfected with the neomycin-resistant gene or the kinase-dead Pim-2 protein. When grown in medium, the doubling time of the Pim-1 and Pim-2 transfectants was faster (0.75 days) than that of the control cells (1.28 days). We, therefore, examined the ability of Pim to control the phosphorylation of proteins that regulate protein synthesis. On growth factor starvation or rapamycin treatment, the Pim-1 and Pim-2 transfectants maintained their ability to phosphorylate 4E-BP1 and S6 kinase, although this phosphorylation did not occur in the control-transfected PC3 cells. We have found that the cellular levels of c-Myc were elevated in the Pim-1 and Pim-2 transfectants under these conditions. The Pim-1 and Pim-2 transfectants have lower levels of serine/threonine protein phosphatase 2A (PP2A) activity and the alpha- and beta-subunit B56gamma of the PP2A phosphatase do not coimmunoprecipitate in these cells. Thus, the effects of Pim on PP2A activity may mediate the levels of c-Myc and the phosphorylation of proteins needed for increased protein synthesis. Both of these changes could have a significant impact on tumor growth.