gebhart/patrepeval huggingface dataset:
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla (2009)

The adult human distal gut microbial community is typically dominated by 2 bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here, we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from Eubacterium rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the Firmicutes possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole-genome transcriptional profiling, high-resolution proteomic analysis, and biochemical assays of microbial-microbial and microbial-host interactions. B. thetaiotaomicron adapts to E. rectale by up-regulating expression of a variety of polysaccharide utilization loci encoding numerous glycoside hydrolases, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is used by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of its major bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability.
Peg and Dowel Fusion of the Proximal Interphalangeal Joint (1980)

The clawtoe or hammertoe deformity if frequently encountered in office practice. The etiology of this condition remains obscure, although intrinsic atrophy or imbalance was suspected as early as 1863 by Duchenne. Arthrodesing the proximal interphalangeal joint converts the more powerful flexor tendon to a flexor of the metatarsophalangeal joint, thereby alleviating pressure on the metatarsal head and distributing the weight more evenly on the forefoot. Arthrodesing is accomplished by the peg and dowel method, with the fourth toe presenting the most technical difficulties. An extensor tenotomy or dorsal capsulotomy of the metatarsophalangeal joint is frequently necessary to realign the toe with the corresponding metatarsal ray. A collodion dressing is used to immobilize the toe for a period of 4 to 6 weeks, with a fusion rate of 97% in 73 toes. All patients were contacted, with 87% responding favorably and stating that they had relief of their pain and were able to resume wearing normal footwear.
Microsomal triglyceride transfer protein and its role in apoB-lipoprotein assembly (2003)

Apolipoprotein B (apoB) and microsomal triglyceride transfer protein (MTP) are necessary for lipoprotein assembly. ApoB consists of five structural domains, betaalpha(1)-beta(1)-alpha(2)-beta(2)-alpha(3). We propose that MTP contains three structural motifs (N-terminal beta-barrel, central alpha-helix, and C-terminal lipid cavity) and three functional domains (lipid transfer, membrane associating, and apoB binding). MTP's lipid transfer activity is required for the assembly of lipoproteins. This activity renders nascent apoB secretion-competent and may be involved in the import of triglycerides into the lumen of endoplasmic reticulum. In addition, MTP binds to apoB with high affinity involving ionic interactions. MTP interacts at multiple sites in the N-terminal betaalpha(1) structural domain of apoB. A novel antagonist that inhibits apoB-MTP binding decreases apoB secretion. Furthermore, site-directed mutagenesis and deletion analyses that inhibit apoB-MTP binding decrease apoB secretion. Lipids modulate protein-protein interactions between apoB and MTP. Lipids associated with MTP increase apoB-MTP binding whereas lipids associated with apoB decrease this binding. Thus, specific antagonist, site-directed mutagenesis, deletion analyses, and modulation studies support the notion that apoB-MTP binding plays a role in lipoprotein biogenesis. However, specific steps in lipoprotein assembly that require apoB-MTP binding have not been identified. ApoB-MTP binding may be important for the prevention of degradation and lipidation of nascent apoB.
PALM (2011)

Concurrency control on B + trees is primarily achieved with latches, but serialization and contention can hinder scalability. As core counts on current processors increase, it is imperative to develop scalable latch-free techniques for concurrency control. We present PALM, a novel technique for performing multiple concurrent queries on in-memory B + trees. PALM is based on the Bulk Synchronous Parallel model, which guarantees freedom from deadlocks and race conditions. Input queries are grouped and processed in atomic batches , and work proceeds in stages that preclude contention. Transitions between stages are accomplished with scalable point-to-point communication. PALM exploits data-and thread-level parallelism on modern many-core architectures, and performs 40M 1 updates/second on trees with 128M keys, and 128M updates/second on trees with 512K keys on the latest CPU architectures. Our throughput is 2.3X--19X that of state-of-the-art concurrent update algorithms on in-memory B + trees. PALM obtains close to peak throughput at very low response times of less than 350μs, even for large trees. We also evaluate PALM on the Intel ® Many Integrated Core (Intel ® MIC) architecture, and demonstrate a speedup of 1.5--2.1X for out-of-cache tree sizes on an Intel ® Knights Ferry over a pair of Intel ® Xeon ® processors DP X5680 (Westmere-EP) in a dual-socket configuration.
YOUQMON (2013)

YouTube is changing the way operators manage network performance monitoring. In this paper we introduce YOUQMON, a novel on-line monitoring system for assessing the Quality of Experience (QoE) undergone by HSPA/3G customers watching YouTube videos, using network-layer measurements only. YOUQMON combines passive traffic analysis techniques to detect stalling events in YouTube video streams, with a QoE model to map stallings into a Mean Opinion Score reflecting the end-user experience. We evaluate the stalling detection performance of YOUQMON with hundreds of YouTube video streams, and present results showing the feasibility of performing real-time YouTube QoE monitoring in an operational mobile broadband network.
Modeling Glanzmann thrombasthenia using patient specific iPSCs and restoring platelet aggregation function by CD41 overexpression (2017)

Glanzmann thrombasthenia (GT) is a rare monogenic hemorrhagic disorder involving aggregation defect of non-nuclear platelets. In this study we generated induced pluripotent stem cells (iPSCs) from skin fibroblasts of a GT patient with complex heterogeneous mutations of ITGA2B gene. GT-iPSCs could be successfully differentiated into platelets (GT-iPS-platelets). GT-iPS-platelets were CD41-/CD42b+/CD61- and were platelet activation marker (PAC-1) negative after adenosine diphosphate (ADP) activation. Furthermore, GT-iPS-platelets were defective in platelet aggregation tests in vitro. Moreover, exogenous expression of the wild-type ITGA2B gene in GT-iPS platelets restored CD41 expression and normal platelet aggregation. Our study suggested that patient-specific iPSCs could be a potential target of stem cell based gene therapy for platelet diseases.
Recombinant CLIC1 (NCC27) Assembles in Lipid Bilayers via a pH-dependent Two-state Process to Form Chloride Ion Channels with Identical Characteristics to Those Observed in Chinese Hamster Ovary Cells Expressing CLIC1 (2002)

CLIC1 (NCC27) is an unusual, largely intracellular, ion channel that exists in both soluble and membrane-associated forms. The soluble recombinant protein can be expressed in Escherichia coli, a property that has made possible both detailed electrophysiological studies in lipid bilayers and an examination of the mechanism of membrane integration. Soluble E. coli-derived CLIC1 moves from solution into artificial bilayers and forms chloride-selective ion channels with essentially identical conductance, pharmacology, and opening and closing kinetics to those observed in CLIC1-transfected Chinese hamster ovary cells. The process of membrane integration of CLIC1 is pH-dependent. Following addition of protein to the trans solution, small conductance channels with slow kinetics (SCSK) appear in the bilayer. These SCSK modules then appear to undergo a transition to form a high conductance channel with fast kinetics. This has four times the conductance of the SCSK and fast kinetics that characterize the native channel. This suggests that the CLIC1 ion channel is likely to consist of a tetrameric assembly of subunits and indicates that despite its size and unusual properties, it is able to form a completely functional ion channel in the absence of any other ancillary proteins.
Ginkgolide and bilobalide biosynthesis in Ginkgo biloba. I : Sites of synthesis, translocation and accumulation of ginkgolides and bilobalide (1997)

Ginkgo biloba trees contain specific terpene compounds, ginkgolides (diterpene) and bilobalide (pentanorditerpene). Ginkgolide A (GA) and ginkgolide B (GB) are the main molecular forms of ginkgolides. These compounds are present in young seedlings and accumulate within roots and leaves, but not in stems. In vitro experiments showed a correlation between accumulation of terpenes and rhizogenesis. Ginkgolides and bilobalide could easily be formed from 14 CO 2 when the photosynthesis conditions were optimized. Ginkgolide A was first labelled. as early as 8 h after application of 14 CO 2 . The ginkgolide labelling reached a maximum at day 3 followed by a steady state around day 10. Bilobalide labelling, occurred later and showed a maximum at day 6. The chronology of ginkgolide labelling indicated a possible in situ bioconversion of ginkgolides from GA to GC, by successive additions of hydroxyl group. With both 14 CO 2 and (U- 14 C) glucose, the labelled terpenes were first detected in roots. and subsequently in stems and leaves. These complementary experiments indicate that all the enzymic steps leading to the Ginkgo diterpene end products take place in the roots but not in the leaves. Ginkgo roots are, at the same time. a site of biosynthesis and accumulation of ginkgolides and bilobalide. whereas leaves seem to act only as a sink. The balance of 14 C-labelled terpenes in the whole plant during the chase period (27 days) indicates that terpenes seem to be translocated from the roots to the leaves in a source-sink manner. However, the possible involvement of modified terpene molecules in the transport process as well as the localization of the translocation pathway are not known.
Complete nucleotide sequence of the gene encoding the rat apolipoprotein E (1986)

Journal Article Complete nucleotide sequence of the gene encoding the rat apolipoprotein E Get access Chikafusa Fukazawa, Chikafusa Fukazawa Search for other works by this author on: Oxford Academic PubMed Google Scholar Akiyo Matsumoto, Akiyo Matsumoto Search for other works by this author on: Oxford Academic PubMed Google Scholar John M. Taylor John M. Taylor 1Gladstone Foundation Laboratories, Cardiovascular Research Institute, University of CaliforniaSan Francisco, CA 94140, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 14, Issue 23, 9 December 1986, Pages 9527–9528, https://doi.org/10.1093/nar/14.23.9527 Published: 09 December 1986
Influence of Endogenous Neuropeptide Y (NPY) on the Sympathetic-Parasympathetic Interaction in the Canine Heart (2005)

The purpose of this study was to examine the sympathetic-parasympathetic interactions on heart rate through release of neuropeptide Y (NPY) and its action on prejunctional NPY Y2 receptors on vagal and sympathetic nerve fibers. In other studies on various preparations and in various organs, attenuation of transmitter release has in fact been demonstrated through activation of the NPY Y2 receptor. In the present study on anesthetized dogs we examine, however, for the first time if vagal bradycardia is attenuated by endogenous NPY released during intense cardiac sympathetic stimulation. In addition, we explore if sympathetic transmitter release and heart rate, during moderate sympathetic stimulation, are affected through this receptor system. The significance of the NPY Y2 receptor was revealed by performing experiments before and after administration of its specific receptor antagonist BIIE0246. We found that attenuation of the bradycardia during vagal nerve stimulation was dose-dependently counteracted by BIIE0246 and that the tachycardia elicited by sympathetic stimulation remained unaffected after NPY Y2 receptor blockade. Thus, endogenous NPY appears to attenuate vagal bradycardia by stimulating prejunctional NPY Y2 receptors on cardiac vagal nerve terminals and, less efficiently, to attenuate transmitter release and tachycardia through a feedback loop on the cardiac sympathetic nerve fibers.
Interleukin‐1β+3953 allele 2: association with disease status in adult periodontitis (1998)

Adult periodontitis is a complex multifactorial disease whose etiology is not well defined. The pro-inflammatory and bone resorptive properties of interleukin-1 beta (IL-1beta) strongly suggest a role for this cytokine in the pathogenesis of periodontal disease. In the study reported here, the frequency of IL-1beta genotypes including allele 2 of the IL-1beta+3953 restriction fragment length bi-allelic polymorphism was significantly increased in patients with advanced adult periodontitis compared to those with early and moderate disease. Furthermore, allele 2 was associated with increased production of IL-1beta by activated peripheral blood polymorphonuclear cells of patients with advanced disease, although this increase failed to reach statistical significance. Finally, the data obtained revealed significant linkage disequilibrium between allele 2 of the IL-1beta+3953 polymorphism and allele 2 of the bi-allelic IL-1alpha-889 polymorphism in both patients and orally healthy controls. These findings provide new insight into the possible role of IL-1alpha and beta gene polymorphisms in the susceptibility to adult periodontitis.
Senescence of Cultured Porcine Coronary Arterial Endothelial Cells Is Associated with Accelerated Oxidative Stress and Activation of NFĸB (2009)

After multiple passaging in vitro, porcine coronary endothelial cells exhibited dysfunction and senescence associated with reduced proliferative capacity, increased oxidative stress, and activation of the NFkappaB and p53 signaling pathways.
Direct write dispenser printing of a zinc microbattery with an ionic liquid gel electrolyte (2010)

The need for energy dense microbatteries with miniature dimensions has prompted the development of unconventional materials, cell geometries, and processing methods. This work will highlight our materials investigations, deposition methods and the device performance of a printed zinc–manganese dioxide rechargeable microbattery utilizing an ionic liquid gel electrolyte. We have developed a direct write dispenser printing method with the ability to fabricate multilayer structures and precisely deposit and pattern these components onto any substrates. The use of a unique room-temperature ionic liquid swelled into a polymer to form a gel electrolyte with solid-like mechanical strength and liquid-like ion transport properties has enabled the simple fabrication of stacked microbattery structures with the potential to be easily integrated directly onto a microdevice substrate. Initial microbattery tests and cycle behavior are discussed, and after an initial activation of the cathode material, an experimental cell discharge capacity and energy density of 0.98 mA h cm−2 and 1.2 mW h cm−2 were measured, respectively.
Determination of the primary amino acid sequence specifying the alpha-bungarotoxin binding site on the alpha subunit of the acetylcholine receptor from Torpedo californica. (1985)

A region of the alpha subunit of the nicotinic acetylcholine receptor containing the alpha-bungarotoxin-binding domain was mapped on the primary amino acid sequence in relation to asparagine-141, the presumed site of N-linked glycosylation. Proteolytic fragments of the alpha subunit, immobilized onto positively charged membrane filters, that bind 125I-labeled bungarotoxin were further analyzed on the basis of the size of the fragments and the presence of asparagine-141 as determined by susceptibility to digestion with endoglycosidase H. The bungarotoxin-binding site was found not to reside between amino acid residues 1 and 140 since bungarotoxin-binding fragments that are considerably larger than 140 amino acids and lack N-linked oligosaccharide chains were detected. The size of the smallest bungarotoxin-binding fragment containing asparagine-141 and the size of fragments produced by digestion with V8 protease further indicated that the bungarotoxin-binding site is contained within amino acid residues 153-241. A 32-amino acid synthetic peptide comprising a portion of this region (residues 173-204) was tested for its ability to bind 125I-labeled bungarotoxin. 125I-labeled bungarotoxin bound to the peptide and was competed by unlabeled bungarotoxin and d-tubocurarine with IC50 values of 0.5 microM and 2 mM, respectively. We conclude that a major determinant of the bungarotoxin-binding site on the alpha subunit resides between residues 173 and 204.
Overexpression of Catalase Targeted to Mitochondria Attenuates Murine Cardiac Aging (2009)

This study shows that cardiac aging in the mouse closely recapitulates human aging and demonstrates the critical role of mitochondrial reactive oxygen species in cardiac aging and the impact of cardiac aging on survival. These findings also support the potential application of mitochondrial antioxidants in reactive oxygen species-related cardiovascular diseases.
A Wide Field-of-view Head Mounted Projective Display using Hyperbolic Half-silvered Mirrors (2007)

The development of a wide field-of-view (FOV) head mounted display (HMD) has been a technological challenge for decades. Previous HMDs tackled this problem using multiple display units (tiling) or multiple curved mirrors. The former approach tends to be expensive and heavy, whereas the latter approach tends to suffer from image distortion and a small exit pupil. In order to provide a wide FOV image with a large exit pupil, the present paper proposes a novel head mounted projective display (HMPD) using a hyperbolic half-silvered mirror, rather than a conventional planar mirror. The first bench-top prototype has successfully shown wide field-of-view projection capability.
Noninfectious virus-like particles produced by Moloney murine leukemia virus-based retrovirus packaging cells deficient in viral envelope become infectious in the presence of lipofection reagents (1997)

Retrovirus packaging cell lines expressing the Moloney murine leukemia virus gag and pol genes but lacking virus envelope genes produce virus-like particles constitutively, whether or not they express a transcript from an integrated retroviral provirus. In the absence of a proviral transcript, the assembled particles contain processed gag and reverse transcriptase, and particles made by cells expressing an integrated lacZ provirus also contain viral RNA. The virus-like particles from both cell types are enveloped and are secreted/budded into the extracellular space but are noninfectious. Their physicochemical properties are similar to those of mature retroviral particles. The noninfectious gag pol RNA particles can readily be made infectious by the addition of lipofection reagents to produce preparations with titers of up to 10(5) colony-forming units per ml.
Twenty-five years in the making: flecainide is safe and effective for the management of atrial fibrillation (2010)

Atrial fibrillation (AF) is the most common arrhythmia in clinical practise and its prevalence is increasing. Over the last 25 years, flecainide has been used extensively worldwide, and its capacity to reduce AF symptoms and provide long-term restoration of sinus rhythm (SR) has been well documented. The increased mortality seen in patients treated with flecainide in the Cardiac Arrhythmia Suppression Trial (CAST) study, published in 1991, still deters many clinicians from using flecainide, denying many new AF patients a valuable treatment option. There is now a body of evidence that clearly demonstrates that flecainide has a favourable safety profile in AF patients without significant left ventricular disease or coronary heart disease. As a result of this evidence, flecainide is now recommended as one of the first-line treatment options for restoring and maintaining SR in patients with AF under current treatment guidelines. The objective of this article is to review the literature pertaining to the pharmacological characteristics, safety and efficacy of flecainide, and to place this drug in the context of current therapeutic management strategies for AF.
Ablation of Transient Receptor Potential Vanilloid 1 Abolishes Endothelin-Induced Increases in Afferent Renal Nerve Activity (2009)

Endothelin 1 (ET-1) and its receptors, ETA and ETB, play important roles in regulating renal function and blood pressure, and these components are expressed in sensory nerves. Activation of transient receptor potential vanilloid (TRPV) 1 channels expressed in sensory nerves innervating the renal pelvis enhances afferent renal nerve activity (ARNA), diuresis, and natriuresis. We tested the hypothesis that ET-1 increases ARNA via activation of ETB, whereas ETA counterbalances ETB in wild-type (WT) but not TRPV1-null mutant mice. ET-1 alone or with BQ123, an ETA antagonist, perfused into the left renal pelvis increased ipsilateral ARNA in WT but not in TRPV1-null mutant mice, and ARNA increases were greater in the latter. [Ala1, 3,11,15]-endothelin 1, an ETB agonist, increased ARNA that was greater than that induced by ET-1 in WT mice only. [Ala1, 3,11,15]-endothelin 1-induced increases in ARNA were abolished by chelerythrine, a protein kinase C inhibitor, but not by H89, a protein kinase A inhibitor. Chelerythrine, H89, and BQ788, an ETB antagonist, did not affect ARNA triggered by capsaicin in WT mice. Substance P release from the renal pelvis was increased by [Ala1, 3,11,15]-endothelin 1 in WT mice only, and the increase was abolished by chelerythrine but not by H89. Chelerythrine, H89, and BQ788 did not affect capsaicin-induced substance P release. Our data show that ET1 increases ARNA via activation of ETB, whereas ETA counterbalances ETB in WT but not in TRPV1-null mutant mice, suggesting that TRPV1 mediates ETB-dependent increases in ARNA, diuresis, and natriuresis possibly via the protein kinase C pathway.