gebhart/patrepeval huggingface dataset:
An Integrated Linkage, Chromosome, and Genome Map for the Yellow Fever Mosquito Aedes aegypti (2013)

This study developed an integrated linkage, chromosome, and genome map-iMap-for the yellow fever mosquito. Our discovery of the localization of multiple QTLs in a few major chromosome clusters suggests a possibility that the transmission of various pathogens is controlled by the same genomic loci. Thus, the iMap will facilitate the identification of genomic determinants of traits responsible for susceptibility or refractoriness of the mosquito to diverse pathogens.
Total and High-Molecular-Weight Adiponectin and Risk of Coronary Heart Disease and Ischemic Stroke in Older Adults (2012)

In community-living elders, total and HMW adiponectin showed similar U-shaped relationships with CVD. The inverse relation in the lower range, but not the direct association at the higher end, disappeared after inclusion of putative intermediates, suggesting that high levels may reflect adverse processes separate from adiponectin's beneficial glycometabolic properties.
2,4-Bis(arylamino)-5-methylpyrimidines as Antimicrobial Agents (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT2,4-Bis(arylamino)-5-methylpyrimidines as Antimicrobial AgentsDolly. Ghosh and Mina. MukherjeeCite this: J. Med. Chem. 1967, 10, 5, 974–975Publication Date (Print):September 1, 1967Publication History Published online1 May 2002Published inissue 1 September 1967https://pubs.acs.org/doi/10.1021/jm00317a062https://doi.org/10.1021/jm00317a062research-articleACS PublicationsRequest reuse permissionsArticle Views117Altmetric-Citations6LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome (2009)

Transcriptome studies are revealing that the eukaryotic genome actively transcribes a diverse repertoire of large noncoding RNAs (ncRNAs), many of which are unannotated and distinct from the small RNAs that have garnered much attention in recent years. Why are they so pervasive, and do they have a function? X-chromosome inactivation (XCI) is a classic epigenetic phenomenon associated with many large ncRNAs. Here, I provide a perspective on how XCI is achieved in mice and suggest how this knowledge can be applied to the rest of the genome. Emerging data indicate that long ncRNAs can function as guides and tethers, and may be the molecules of choice for epigenetic regulation: First, unlike proteins and small RNAs, large ncRNAs remain tethered to the site of transcription, and can therefore uniquely direct allelic regulation. Second, ncRNAs command a much larger sequence space than proteins, and can therefore achieve very precise spatiotemporal control of development. These properties imply that long noncoding transcripts may ultimately rival small RNAs and proteins in their versatility as epigenetic regulators, particularly for locus- and allele-specific control.
Transient Receptor Potential Cation Channels in Disease (2007)

The transient receptor potential (TRP) superfamily consists of a large number of cation channels that are mostly permeable to both monovalent and divalent cations. The 28 mammalian TRP channels can be subdivided into six main subfamilies: the TRPC (canonical), TRPV (vanilloid), TRPM (melastatin), TRPP (polycystin), TRPML (mucolipin), and the TRPA (ankyrin) groups. TRP channels are expressed in almost every tissue and cell type and play an important role in the regulation of various cell functions. Currently, significant scientific effort is being devoted to understanding the physiology of TRP channels and their relationship to human diseases. At this point, only a few channelopathies in which defects in TRP genes are the direct cause of cellular dysfunction have been identified. In addition, mapping of TRP genes to susceptible chromosome regions (e.g., translocations, breakpoint intervals, increased frequency of polymorphisms) has been considered suggestive of the involvement of these channels in hereditary diseases. Moreover, strong indications of the involvement of TRP channels in several diseases come from correlations between levels of channel expression and disease symptoms. Finally, TRP channels are involved in some systemic diseases due to their role as targets for irritants, inflammation products, and xenobiotic toxins. The analysis of transgenic models allows further extrapolations of TRP channel deficiency to human physiology and disease. In this review, we provide an overview of the impact of TRP channels on the pathogenesis of several diseases and identify several TRPs for which a causal pathogenic role might be anticipated.
Branched rolling circle amplification method for measuring serum circulating microRNA levels for early breast cancer detection (2018)

Serum circulating microRNAs (c-miRNAs) are serving as useful biomarkers for cancer diagnosis. Here, we describe the development of a one-step branched rolling circle amplification (BRCA) method to measure serum c-miRNAs levels for early diagnosis of breast cancer. Four c-miRNAs, c-miRNA16 (c-miR-16), c-miRNA21 (c-miR-21), c-miRNA155 (c-miR-155), and c-miRNA195 (c-miR-195) were isolated from the serum of 49 breast cancer patients and 19 healthy controls. Among them, 45 breast cancer patients and 15 healthy controls were analyzed using one-step BRCA, 4 breast cancer patients and 4 healthy controls were analyzed by quantitative real-time PCR assay [corrected]. The serum levels of c-miR16, c-miR21, c-miR155, and c-miR195 were higher (P < 0.0001) in stage I breast cancer patients than healthy controls. These levels were also higher in several breast cancer molecular subtypes (HER-2 over-expression, Luminal A, Luminal B, and triple negative breast cancer) than in healthy control subjects. The diagnostic accuracy of c-miR16, c-miR21, c-miR155, and c-miR195 for early diagnosis of breast cancer was confirmed by receiver operating characteristic (ROC) curve assay. These results show that the BRCA method can be used to measure serum c-miRNAs levels, and that this method has high accuracy, sensitivity, and specificity. Moreover, both BRCA approach and quantitative real-time PCR (qRT-PCR) method show that the serum levels of c-miR16, c-miR21, c-miR155, and c-miR195 could be used as biomarkers to improve the early diagnosis of breast cancer, and distinguish different breast cancer molecular subtypes.
CLONED POTASSIUM CHANNELS FROM EUKARYOTES AND PROKARYOTES (1997)

Potassium channels contribute to the excitability of neurons and signaling in the nervous system. They arise from multiple gene families including one for voltage-gated potassium channels and one for inwardly rectifying potassium channels. Features of potassium permeation, channel gating and regulation, and subunit interaction have been analyzed. Potassium channels of similar design have been found in animals ranging from jellyfish to humans, as well as in plants, yeast, and bacteria. Structural similarities are evident for the pore-forming alpha subunits and for the beta subunits, which could potentially regulate channel activity according to the level of energy and/or reducing power of the cell.
Nonprogression of coronary artery atherosclerosis in homozygous familial hypercholesterolemia after 31 months of repetitive plasma exchange (1986)

The effects of plasma exchange performed every two weeks for 31 months in combination with diet and drug therapy were studied in a patient with receptor-defective homozygous familial hypercholesterolemia. Coronary angiography performed three years prior to commencing plasma exchange was compared to angiography 31 months after starting the program. Comparison of the angiograms taken six years apart showed no progression of coronary atheroma in the main left coronary artery in which a 30% narrowing was originally seen. An internal mammary artery-coronary artery bypass remained widely patent and showed no development of atherosclerosis. Plasma cholesterol levels were reduced 46% by plasma exchange, diet and drug compared to diet and drug alone. Achilles tendon xanthoma diminished significantly. It appears that plasma exchange combined with diet and drug therapy, while not producing regression of existing atheromatous lesions, does retard or prevent further progression.
Learning higher-order structures in natural images (2003)

The theoretical principles that underlie the representation and computation of higher-order structure in natural images are poorly understood. Recently, there has been considerable interest in using information theoretic techniques, such as independent component analysis, to derive representations for natural images that are optimal in the sense of coding efficiency. Although these approaches have been successful in explaining properties of neural representations in the early visual pathway and visual cortex, because they are based on a linear model, the types of image structure that can be represented are very limited. Here, we present a hierarchical probabilistic model for learning higher-order statistical regularities in natural images. This non-linear model learns an efficient code that describes variations in the underlying probabilistic density. When applied to natural images the algorithm yields coarse-coded, sparse-distributed representations of abstract image properties such as object location, scale and texture. This model offers a novel description of higher-order image structure and could provide theoretical insight into the response properties and computational functions of lower level cortical visual areas.
Immunopathogenesis of brain abscess. (2004)

Brain abscess represents a significant medical problem despite recent advances made in detection and therapy. Due to the emergence of multi-drug resistant strains and the ubiquitous nature of bacteria, the occurrence of brain abscess is likely to persist. Our laboratory has developed a mouse experimental brain abscess model allowing for the identification of key mediators in the CNS anti-bacterial immune response through the use of cytokine and chemokine knockout mice. Studies of primary microglia and astrocytes from neonatal mice have revealed that S. aureus, one of the main etiologic agents of brain abscess in humans, is a potent stimulus for proinflammatory mediator production. Recent evidence from our laboratory indicates that Toll-like receptor 2 plays a pivotal role in the recognition of S. aureus and its cell wall product peptidoglycan by glia, although other receptors also participate in the recognition event. This review will summarize the consequences of S. aureus on CNS glial activation and the resultant neuroinflammatory response in the experimental brain abscess model.
High‐sensitivity detection using isotachophoresis with variable cross‐section geometry (2011)

We present a theoretical and experimental study on increasing the sensitivity of ITP assays by varying channel cross-section. We present a simple, unsteady, diffusion-free model for plateau mode ITP in channels with axially varying cross-section. Our model takes into account detailed chemical equilibrium calculations and handles arbitrary variations in channel cross-section. We have validated our model with numerical simulations of a more comprehensive model of ITP. We show that using strongly convergent channels can lead to a large increase in sensitivity and simultaneous reduction in assay time, compared to uniform cross-section channels. We have validated our theoretical predictions with detailed experiments by varying channel geometry and analyte concentrations. We show the effectiveness of using strongly convergent channels by demonstrating indirect fluorescence detection with a sensitivity of 100 nM. We also present simple analytical relations for dependence of zone length and assay time on geometric parameters of strongly convergent channels. Our theoretical analysis and experimental validations provide useful guidelines on optimizing chip geometry for maximum sensitivity under constraints of required assay time, chip area and power supply.
Typing of human papillomaviruses in cervical intraepithelial neoplasia grade 3 biopsies from cape town (1989)

DNA from 98 cervical intraepithelial neoplasia grade 3 (CIN 3) biopsies was screened, using the Southern blotting hybridization technique, for human papillomavirus (HPV) types 6, 11, 16, 18, 31, 33, and 35. HPV 16 was detected in 16 biopsies (16%), HPV 33 in eight biopsies (8%), HPV 31 in two biopsies (2%), and HPV 18 in one biopsy (1%). One of the biopsies contained both HPV 31 and 18. Six biopsies (6%) contained an HPV type very similar but not identical to HPV 16, and 35 biopsies were positive for HPV, but the Pst 1 restriction fragments were distinct from any of the HPV types used as probes. HPV was not detected in 32% (32/98) of the biopsies screened.
Discovery and Structure−Activity Relationship of 3-Methoxy-N-(3-(1-methyl-1H-pyrazol-5-yl)-4-(2-morpholinoethoxy)phenyl)benzamide (APD791): A Highly Selective 5-Hydroxytryptamine2A Receptor Inverse Agonist for the Treatment of Arterial Thrombosis (2010)

Serotonin, which is stored in platelets and is released during thrombosis, activates platelets via the 5-HT(2A) receptor. 5-HT(2A) receptor inverse agonists thus represent a potential new class of antithrombotic agents. Our medicinal program began with known compounds that displayed binding affinity for the recombinant 5-HT(2A) receptor, but which had poor activity when tested in human plasma platelet inhibition assays. We herein describe a series of phenyl pyrazole inverse agonists optimized for selectivity, aqueous solubility, antiplatelet activity, low hERG activity, and good pharmacokinetic properties, resulting in the discovery of 10k (APD791). 10k inhibited serotonin-amplified human platelet aggregation with an IC(50) = 8.7 nM and had negligible binding affinity for the closely related 5-HT(2B) and 5-HT(2C) receptors. 10k was orally bioavailable in rats, dogs, and monkeys and had an acceptable safety profile. As a result, 10k was selected further evaluation and advanced into clinical development as a potential treatment for arterial thrombosis.
Tetrahydrobiopterin as a Treatment for Autism Spectrum Disorders: A Double-Blind, Placebo-Controlled Trial (2013)

These results indicate that BH4 offers promise in reducing symptoms of ASD. Clinical Trials.gov Identifier: NCT00850070.
Cell density and cell generation in the periodontal ligament of mice (1983)

The number of cell nuclei per mm2 and the volume density of cell nuclei and blood vessels in the periodontal ligament at different levels of the mesial root of the first mandibular molar of the adult mouse and in different areas of the ligament at each level have been examined in the light microscope. Significantly higher numbers of cell nuclei per mm2 were observed adjacent to bone, cementum, and blood vessels than in the avascular body of the ligament at all levels and on all aspects of the root. This distribution of number of cell nuclei per mm2 was constant over 4 1/2 months of aging and a doubling of body weight. The volume density of cell nuclei was significantly higher in cells adjacent to bone and cementum and in gingival connective tissue than in both the vicinity of blood vessels and the body of the ligament. The blood vessels, which were present predominantly in the bone-related half of the ligament, were absent from the zone immediately adjacent to cementum. The labeling indexes of periodontal ligament cells were determined from autoradiographs of the mesial root of the first mandibular molar of the mouse after pulse-labeling with 3H-Tdr. Labeling indexes were highest in zones adjacent to blood vessels, and the labeling index was significantly higher in the middle of the ligament than in zones adjacent to bone and cementum, and consequently was inversely related to cell density.
Communication Web Services Composition and Integration (2006)

Nowadays, the development of services that span over both the Internet and telephony networks is driving significant efforts towards the integration of services offered by IT providers with telecom operators ones. Web services have often been recommended for providing, composing and realizing telecom services but introducing them means facing up with several challenges. This work sharpens benefits and drawbacks of Web service applications within a telecom environment focusing in particular on JAIN SLEE architecture, which defines a standard environment targeted at communication-based applications
Shared buffer memory switch for an ATM exchange (1993)

An asynchronous transfer mode (ATM) switch architecture called a shared buffer memory switch whose output cell buffers are shared among all the output ports of the switch is proposed. Experimental measurements and a discussion about the traffic characteristics of the switch architecture are carried out to determine how much buffer memory will be reduced through buffer sharing under various traffic conditions and to roughly estimate how many buffers are needed for the switch to meet certain requirements. The resultant estimate shows that buffer sharing reduces the necessary buffer memory to less than 1/5 of what would otherwise be required, and the required buffer size is about 128 cells/output for a 32*32 switch when considering bursty traffic conditions. LSI implementation is also discussed to show that a 32*32 switch can be composed of about 12 chips mounted on one printed board.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Variability of osp genes and gene products among species of Lyme disease spirochetes (1993)

A comparison of the osp operon in 24 Lyme disease isolates, including representatives from each of the three established species, Borrelia burgdorferi, Borrelia garinii, and group VS461, was conducted. Several properties were assessed to determine whether the variability observed in this operon was reflective of the species of the isolate. At the transcriptional level, start site and Northern (RNA) blot analyses were conducted. B. garinii and VS461 group isolates were found to possess an untranslated leader sequence 6 nucleotides longer than that observed in B. burgdorferi isolates. By Northern blot analyses all Lyme disease isolates, except the B. garinii isolate VS102, were found to produce a polycistronic full-length ospAB message. Isolate VS102 produced a truncated message lacking the ospB portion of the transcript. Southern blot analyses suggest that the deletion occurred at the DNA level and was not due to a posttranscriptional event. Analysis of the outer surface proteins by two-dimensional gel electrophoresis demonstrated that the OspB isoelectric points were variable, with the OspB of B. garinii isolates exhibiting a pronounced acidic shift. The reactivity of different isolates to OspA and -B monoclonal antibodies and to a hyperimmune anti-ospAB serum was also variable. The results presented here demonstrate genotypic and phenotypic heterogeneity in the osp operon at both the inter- and intraspecies levels. The results have implications concerning the use of the osp genes or their gene products in the development of a Lyme disease vaccine, as diagnostic markers of Lyme disease, and in subtyping of Lyme disease isolates.
Adaptive lesion formation using dual mode ultrasound array system (2017)

We present the results from an ultrasound-guided focused ultrasound platform designed to perform real-time monitoring and control of lesion formation. Real-time signal processing of echogenicity changes during lesion formation allows for identification of signature events indicative of tissue damage. The detection of these events triggers the cessation or the reduction of the exposure (intensity and/or time) to prevent overexposure. A dual mode ultrasound array (DMUA) is used for forming single- and multiple-focus patterns in a variety of tissues. The DMUA approach allows for inherent registration between the therapeutic and imaging coordinate systems providing instantaneous, spatially-accurate feedback on lesion formation dynamics. The beamformed RF data has been shown to have high sensitivity and specificity to tissue changes during lesion formation, including in vivo. In particular, the beamformed echo data from the DMUA is very sensitive to cavitation activity in response to HIFU in a variety of modes, e.g. boiling cavitation. This form of feedback is characterized by sudden increase in echogenicity that could occur within milliseconds of the application of HIFU (see http://youtu.be/No2wh-ceTLs for an example). The real-time beamforming and signal processing allowing the adaptive control of lesion formation is enabled by a high performance GPU platform (response time within 10 msec). We present results from a series of experiments in bovine cardiac tissue demonstrating the robustness and increased speed of volumetric lesion formation for a range of clinically-relevant exposures. Gross histology demonstrate clearly that adaptive lesion formation results in tissue damage consistent with the size of the focal spot and the raster scan in 3 dimensions. In contrast, uncontrolled volumetric lesions exhibit significant pre-focal buildup due to excessive exposure from multiple full-exposure HIFU shots. Stopping or reducing the HIFU exposure upon the detection of such an events has been shown to produce precisely controlled lesions with no evidence of overexposure even when fast raster scan of volumetric HIFU lesion is attempted. We also show that the DMUA beamformed echo data is capable of detecting underexposure condition at the target location, e.g. due to the obstruction of the HIFU beam resulting from cavitation activity in the path of the beam. The results clearly demonstrate the advantage of adaptive lesion formation in reducing the treatment time while confining the tissue damage to the target volume.
New Pathway for Long-Chain n -Alkane Synthesis via 1-Alcohol in Vibrio furnissii M1 (2005)

Alkane biosynthesis in the bacterium Vibrio furnissii M1 involves the synthesis of long-chain alkanes via 1-alcohol. Evidence for this novel pathway are the following. (i) Both even- and odd-carbon-number n-alkanes were produced from glucose, while only even-carbon-number fatty acids were produced in V. furnissii M1. This result cannot be explained by the decarbonylation pathway. (ii) Pentadecane and hexadecane were produced from 1-hexadecanoic acid by membrane fractions of V. furnissii M1, and radioisotope precursor-tracer experiments, in which 1-[1-(14)C]hexadecanoic acid was fed, identified the corresponding alcohol, aldehyde, and alkane derivatives. Since all metabolites maintained the radioisotope label at 1-C, they were produced by a pathway in which the carbon structure was retained, i.e., a reduction pathway. (iii) n-Hexadecane was produced when 1-hexadecanol was fed to membrane preparations.