gebhart/patrepeval huggingface dataset:
Bipartite graph partitioning and data clustering (2001)

Many data types arising from data mining applications can be modeled as bipartite graphs, examples include terms and documents in a text corpus, customers and purchasing items in market basket analysis and reviewers and movies in a movie recommender system. In this paper, we propose a new data clustering method based on partitioning the underlying bipartite graph. The partition is constructed by minimizing a normalized sum of edge weights between unmatched pairs of vertices of the bipartite graph. We show that an approximate solution to the minimization problem can be obtained by computing a partial singular value decomposition (SVD) of the associated edge weight matrix of the bipartite graph. We point out the connection of our clustering algorithm to correspondence analysis used in multivariate analysis. We also briefly discuss the issue of assigning data objects to multiple clusters. In the experimental results, we apply our clustering algorithm to the problem of document clustering to illustrate its effectiveness and efficiency.
[Reduced expression of Diceri is associated with poor prognosis in patients with nasopharyngeal carcinoma]. (2015)

Dicerl was downregulated in NPC tissues at both the mRNA and the protein levels, and low expression of Dicerl could be served as novel prognostic biomarker for NPC patients.
Development of a Microcantilever-Based Pathogen Detector (2002)

The ability to detect small amounts of materials, especially whole organisms, is important for medical diagnostics and national security issues. Engineered micro-mechanical systems can serve as multifunctional, highly sensitive, real time, immunospecific biological detectors under certain circumstances. We present qualitative detection of specific Salmonella strains using a functionalized silicon nitride microcantilever. Detection is achieved due to differential surface stress on the cantilever surface in-situ. Scanning electron micrographs indicate that less than 25 adsorbed bacteria are required for detection.
Measurement of tidal volume by using transthoracic impedance variations in rats (1999)

The application of impedance pneumography for monitoring respiration in small animals has been limited by problems with calibration. With improved instrumentation, we describe the calibration of tidal volume in anesthetized rats. The detection of changes in voltage, reflecting the electrical impedance variations associated with respiration, was optimized by using disposable adhesive silver-silver chloride electrodes, advanced circuitry, and analog-to-digital recording instrumentation. We found a linear relationship between change in impedance and tidal volume in individual rats (R2 >/= 98%), which was strongly influenced by rat weight. Consequently, a calibration equation incorporating change in impedance and rat weight was derived to predict tidal volume. Comparison of the predicted and true tidal volumes revealed a mean R2 >/= 98%, slopes of approximately 1, intercepts of approximately 0, and bias of approximately 0.07 ml. The predicted volumes were not significantly affected by either frequency of respiration or pulmonary edema. We conclude that impedance pneumography provides a valuable tool for the noninvasive measurement of tidal volume in anesthetized rats.
miR-19b targets pulmonary endothelial syndecan-1 following hemorrhagic shock (2020)

Hemorrhagic shock results in systemic injury to the endothelium contributing to post-shock morbidity and mortality. The mechanism involves syndecan-1, the backbone of the endothelial glycocalyx. We have shown in a rodent model that lung syndecan-1 mRNA is reduced following hemorrhage, whereas the molecular mechanism underlying the mRNA reduction is not clear. In this study, we present evidence that miR-19b targets syndecan-1 mRNA to downregulate its expression. Our results demonstrate that miR-19b was increased in hemorrhagic shock patients and in-vitro specifically bound to syndecan-1 mRNA and caused its degradation. Further, hypoxia/reoxygenation (H/R), our in vitro hemorrhage model, increased miR-19b expression in human lung microvascular endothelial cells, leading to a decrease in syndecan-1 mRNA and protein. H/R insult and miR-19b mimic overexpression comparably exaggerated permeability and enhanced endothelial barrier breakdown. The detrimental role of miR-19b in inducing endothelial dysfunction was confirmed in vivo. Lungs from mice undergoing hemorrhagic shock exhibited a significant increase in miR-19b and a concomitant decrease in syndecan-1 mRNA. Pretreatment with miR-19b oligo inhibitor significantly decreased lung injury, inflammation, and permeability and improved hemodynamics. These findings suggest that inhibition of miR-19b may be a putative therapeutic avenue for mitigating post shock pulmonary endothelial dysfunction in hemorrhage shock.
Antifungal properties of lactoferricin B, a peptide derived from the N-terminal region of bovine lactoferrin (1994)

Journal Article Antifungal properties of lactoferricin B, a peptide derived from the N‐terminal region of bovine lactoferrin Get access W. Bellamy, W. Bellamy Nutritional Science Laboratory, Morinaga Milk Industry Co. Ltd, Zama City, Kanagawa, Japan Search for other works by this author on: Oxford Academic Google Scholar K. Yamauchi, K. Yamauchi Nutritional Science Laboratory, Morinaga Milk Industry Co. Ltd, Zama City, Kanagawa, Japan Search for other works by this author on: Oxford Academic Google Scholar H. Wakabayashi, H. Wakabayashi Nutritional Science Laboratory, Morinaga Milk Industry Co. Ltd, Zama City, Kanagawa, Japan Search for other works by this author on: Oxford Academic Google Scholar M. Takase, M. Takase Nutritional Science Laboratory, Morinaga Milk Industry Co. Ltd, Zama City, Kanagawa, Japan Search for other works by this author on: Oxford Academic Google Scholar N. Takakura, N. Takakura Nutritional Science Laboratory, Morinaga Milk Industry Co. Ltd, Zama City, Kanagawa, Japan Search for other works by this author on: Oxford Academic Google Scholar S. Shimamura, S. Shimamura Nutritional Science Laboratory, Morinaga Milk Industry Co. Ltd, Zama City, Kanagawa, Japan Search for other works by this author on: Oxford Academic Google Scholar M. Tomita M. Tomita Nutritional Science Laboratory, Morinaga Milk Industry Co. Ltd, Zama City, Kanagawa, Japan Search for other works by this author on: Oxford Academic Google Scholar Letters in Applied Microbiology, Volume 18, Issue 4, 1 April 1994, Pages 230–233, https://doi.org/10.1111/j.1472-765X.1994.tb00854.x Published: 01 April 1994 Article history Accepted: 13 November 1993 Published: 01 April 1994
An algorithm to use in adaptive wideband duplexer for software radio (2003)

This paper proposes a new algorithm to control an adaptive duplexer for multiband software radio. It uses a wideband low isolation device combined with a two-tap/two-loop adjustable canceller to eliminate the need for multiple switched high isolation duplexers. The taps are adjusted to provide isolation peaks in the transmit and receive bands. The algorithm is based on the superposition of squared errors and achieved 66 dB isolation of the transmit signal and a 37 dB cancellation of the transmitter noise in the receiver band.
Molecular identification and structural requirement of vasoactive intestinal peptide (VIP) receptors in the human colon adenocarcinoma cell line, HT-29 (1985)

The human colon adenocarcinoma cell line HT-29 in culture exhibits a cyclic AMP production system highly sensitive to vasoactive intestinal peptide (VIP), making HT-29 cells a unique cultured cell system for studying the mechanism of VIP action [Laburthe, Rousset, Boissard, Chevalier, Zweibaum & Rosselin (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 2772-2775]. The quantitative characteristics of VIP receptors in HT-29 cells and their structural requirement and molecular size were studied. 125I-labeled VIP bound in a time-dependent manner to HT-29 cell homogenates. At equilibrium (60 min incubation at 30 degrees C), unlabelled VIP in the 0.01-10 nM concentration range competed with 125I-VIP for binding to cell homogenates. Scatchard analysis of binding data gave a straight line, indicating that VIP bound to a single population of sites with a KD of 0.12 +/- 0.02 nM and a capacity of 120 +/- 9 fmol/mg of protein. The structural requirement of these receptors was studied with peptides structurally related to VIP, either natural or synthetic. Several peptides inhibited 125I-VIP binding to HT-29 cell homogenates with the following order of potency, which is typical of the human VIP receptor: VIP (IC50 = 0.1 nM) greater than VIP-(2-28)-peptide (IC50 = 13 nM) greater than human growth hormone releasing factor (IC50 = 56 nM) greater than peptide histidine isoleucine amide (IC50 = 80 nM) greater than secretin (IC50 greater than 10 000 nM). To characterize the molecular component(s) of the VIP receptor in HT-29 cells, 125I-VIP was covalently bound to cell homogenates by using the cross-linker dithiobis(succinimidyl propionate). Sodium dodecyl sulphate/polyacrylamide-gel autoradiographic studies of affinity-labelled cell homogenates revealed two major bands, corresponding to 125I-VIP-protein complexes of Mr 66 000 and 16 000. The labelling of the Mr-66 000 component was specific, since it was abolished by native VIP, whereas that of the Mr-16 000 component was not. Densitometric scanning of autoradiographs indicated that the labelling of the Mr-66 000 complex was inhibited by low VIP concentrations in the 0.1-10 nM range (IC50 = 0.6 nM), but was unaffected by 1 microM-glucagon or octapeptide of cholecystokinin. It was also decreased by VIP-(2-28)-peptide with a potency 1% that of VIP. Assuming that one molecule of 125I-VIP bound per molecule of protein, one protein of Mr 63 000 was identified as a component of the VIP receptor in HT-29 cells.
CD24 Expression Causes the Acquisition of Multiple Cellular Properties Associated with Tumor Growth and Metastasis (2005)

The glycosylphosphatidylinositol-anchored membrane protein CD24 functions as an adhesion molecule for P-selectin and L1 and plays a role in B-cell development and neurogenesis. Over the last few years, a large body of literature has also implicated CD24 expression in tumorigenesis and progression. Here, we show that ectopic CD24 expression can be sufficient to promote tumor metastasis in experimental animals. By developing a doxycycline-inducible system for the expression of CD24 in breast cancer cells, we have also analyzed the cellular properties that CD24 expression influences. We found that CD24 expression increased tumor cell proliferation. Furthermore, in addition to promoting binding to P-selectin, CD24 expression also indirectly stimulated cell adhesion to fibronectin, collagens I and IV, and laminin through the activation of alpha3beta1 and alpha4beta1 integrin activity. Moreover, CD24 expression supported rapid cell spreading and strongly induced cell motility and invasion. CD24-induced proliferation and motility were integrin independent. Together, these observations implicate CD24 in the regulation of multiple cell properties of direct relevance to tumor growth and metastasis.
Disruption of Malate:Quinone Oxidoreductase IncreasesL-Lysine Production byCorynebacterium glutamicum (2006)

Genomic analysis of a classically derived L-lysine-producing mutant, Corynebacterium glutamicum B-6, identified a nonsense mutation in the mqo gene, which encodes malate:quinone oxidoreductase (MQO). The effect of mqo disruption on L-lysine production was investigated in a defined L-lysine producer, C. glutamicum AHP-3, showing approximately 18% increased production. To explore the underlying mechanisms of the increase, the mqo-disrupted strain was analyzed from the viewpoints of redox balance, activities of membrane-bound dehydrogenases, and transcriptome. The intracellular [NADH]/[NAD] ratio in the strain remained unchanged. Also, there were no significant differences in the activities of the membrane-bound dehydrogenases examined. However, transcriptome analysis showed that some TCA cycle genes, such as acn, sucC, and sucD, were down-regulated in the strain. These results suggest that the loss of MQO activity down-regulates the flux of the TCA cycle to maintain the redox balance and results in redirection of oxaloacetate into L-lysine biosynthesis.
Apoptosis and necrosis: two distinct events induced, respectively, by mild and intense insults with N-methyl-D-aspartate or nitric oxide/superoxide in cortical cell cultures. (1995)

N-Methyl-D-aspartate (NMDA) receptor-mediated neurotoxicity may depend, in part, on the generation of nitric oxide (NO.) and superoxide anion (O2.-), which react to form peroxynitrite (OONO-). This form of neurotoxicity is thought to contribute to a final common pathway of injury in a wide variety of acute and chronic neurologic disorders, including focal ischemia, trauma, epilepsy, Huntington disease, Alzheimer disease, amyotrophic lateral scelerosis, AIDS dementia, and other neurodegenerative diseases. Here, we report that exposure of cortical neurons to relatively short durations or low concentrations of NMDA, S-nitrosocysteine, or 3-morpholinosydnonimine, which generate low levels of peroxynitrite, induces a delayed form of neurotoxicity predominated by apoptotic features. Pretreatment with superoxide dismutase and catalase to scavenge O2.- partially prevents the apoptotic process triggered by S-nitrosocysteine or 3-morpholinosydnonimine. In contrast, intense exposure to high concentrations of NMDA or peroxynitrite induces necrotic cell damage characterized by acute swelling and lysis, which cannot be ameliorated by superoxide dismutase and catalase. Thus, depending on the intensity of the initial insult, NMDA or nitric oxide/superoxide can result in either apoptotic or necrotic neuronal cell damage.
Fourier depth of field (2009)

Optical systems used in photography and cinema produce depth-of-field effects, that is, variations of focus with depth. These effects are simulated in image synthesis by integrating incoming radiance at each pixel over the lense aperture. Unfortunately, aperture integration is extremely costly for defocused areas where the incoming radiance has high variance, since many samples are then required for a noise-free Monte Carlo integration. On the other hand, using many aperture samples is wasteful in focused areas where the integrand varies little. Similarly, image sampling in defocused areas should be adapted to the very smooth appearance variations due to blurring. This article introduces an analysis of focusing and depth-of-field in the frequency domain, allowing a practical characterization of a light field's frequency content both for image and aperture sampling. Based on this analysis we propose an adaptive depth-of-field rendering algorithm which optimizes sampling in two important ways. First, image sampling is based on conservative bandwidth prediction and a splatting reconstruction technique ensures correct image reconstruction. Second, at each pixel the variance in the radiance over the aperture is estimated and used to govern sampling. This technique is easily integrated in any sampling-based renderer, and vastly improves performance.
Flt3 Ligand Regulates Dendritic Cell Development from Flt3+ Lymphoid and Myeloid-committed Progenitors to Flt3+ Dendritic Cells In Vivo (2003)

Stimulation of Flt3 receptor tyrosine kinase through its cognate ligand expands early hematopoietic progenitor and dendritic cells (DCs) in humans and mice. The exact developmental stages at which hematopoietic progenitors express Flt3, are responsive to its ligand, and subsequently develop to DCs, are not known. Here we show that common lymphoid and common myeloid progenitors, as well as steady state DCs in thymus, spleen, and epidermis, express Flt3. The receptor is down-regulated once definitive B cell, T cell, and megakaryocyte/erythrocyte commitment occurs, and Flt3 is not detectable on other steady state hematopoietic cell populations. Upon in vivo Flt3 ligand (Flt3L) administration, Flt3+ progenitor cells and their progeny DCs are expanded, whereas Flt3- downstream progenitors are not, or are only slightly increased. Transplantation of common lymphoid and common myeloid progenitors and subsequent Flt3L injection increases progeny DCs of both precursor populations. These findings provide a definitive map of Flt3 expression in the hematopoietic hierarchy and directly demonstrate that Flt3L can drive DC development along both the lymphoid and myeloid developmental pathways from Flt3+ progenitors to Flt3+ DCs.
Purely functional lazy nondeterministic programming (2011)

Abstract Functional logic programming and probabilistic programming have demonstrated the broad benefits of combining laziness (nonstrict evaluation with sharing of the results) with nondeterminism. Yet these benefits are seldom enjoyed in functional programming because the existing features for nonstrictness, sharing, and nondeterminism in functional languages are tricky to combine. We present a practical way to write purely functional lazy nondeterministic programs that are efficient and perspicuous. We achieve this goal by embedding the programs into existing languages (such as Haskell, SML, and OCaml) with high-quality implementations, by making choices lazily and representing data with nondeterministic components, by working with custom monadic data types and search strategies, and by providing equational laws for the programmer to reason about their code.
Intestinal permeability is increased in burn patients shortly after injury. (1990)

There is increasing direct experimental and indirect clinical evidence to indicate that under certain conditions intestinal barrier function may be lost in trauma victims. No direct measurements, however, have been performed in patients to determine whether intestinal permeability is increased shortly after a major thermal injury in the absence of infection. Fifteen hemodynamically stable burn patients with burns on more than 20% of their body surface (39% +/- 12%) had their intestinal permeability measured within 24 hours of injury with use of the two nonmetabolizable sugars lactulose and mannitol as permeability markers. Lactulose absorption was fourfold higher in the patients (223 +/- 54 mumol) than in the controls (58 +/- 11 mumole; p less than 0.02), whereas the lactulose/mannitol ratio was threefold higher (5.2 vs 1.7; p less than 0.05). Thus intestinal permeability was increased in patients with moderate to major burn injuries shortly after injury.
Gastrointestinal Toxicity With Celecoxib vs Nonsteroidal Anti-inflammatory Drugs for Osteoarthritis and Rheumatoid Arthritis (2000)

In this study, celecoxib, at dosages greater than those indicated clinically, was associated with a lower incidence of symptomatic ulcers and ulcer complications combined, as well as other clinically important toxic effects, compared with NSAIDs at standard dosages. The decrease in upper GI toxicity was strongest among patients not taking aspirin concomitantly. JAMA. 2000;284:1247-1255
Quest for Fire (2000)

There is an accumulating body evidence that atherosclerosis is either caused by or accompanied by oxidative events in the vessel wall. These oxidative events have been implicated in proatherogenic modification of proteins, alteration of gene expression, promotion of inflammation, remodeling of vessels, and perturbations of vascular tone. This body of literature has led to a dogma that oxidation is a prerequisite for the atherosclerotic process. In particular, oxidation of lipoproteins by activated macrophages in the subintimal space has been postulated to be an important early step in the atherosclerotic process.
Making and using DNA microarrays: a short course at Cold Spring Harbor Laboratory. (2000)

The conundrum is familiar. You are sent back in time to the Middle Ages with no artifact from the present, brought before the local ruler, and given 24 hours to prove you are indeed from the future, to impress the ruler and his advisors in some way, before you are executed in some suitably hideous fashion. What do you do? Toying with this conundrum reveals how little we know in a practical sense about the everyday items that surround us. Can you fix your carand your computer? My guess is that few, if any, readers can do so. And so it was with some trepidation that Cold Spring Harbor Laboratory agreed to host a short course in the Fall of 1999, funded in part by the National Cancer Institute, in which students, primarily biologists, would not only print, use, and analyze DNA microarrays but would start the course by building the machines used to print the arrays. For some time, Patrick Brown and colleagues (Chu et al. 1998;DeRisi et al. 1997; Lashkari et al. 1997) at Stanford had been advocating the idea that smaller laboratories could enter the fray and hype surrounding these emerging microarray technologies by building machines rather than by buying them, a self-help philosophy that was strengthened by the Brown laboratory's web-based publication in June 1998 of the MGuide, a step-by-step guide to construct the arrayer, complete with parts list. Indeed, a number of laboratories have gone ahead and built their own machines.
Meeting of Research Leaders Spotlights African Development, Disaster Planning (2008)

MAPUTO, MOZAMBIQUE—Battered by cyclones, prone to major floods, and still recovering from a lengthy civil war, this southeastern African country might seem like an unlikely meeting spot for the world's learned societies. But the International Council for Science (ICSU), bypassing the usual tourist magnets, chose to hold its general assembly session on 20 to 24 October in Mozambique's scarred but rebuilding capital, Maputo. ICSU did so in part to advance its strategy of expanding activities and boosting science in Africa, says its executive director, Swedish microbiologist Thomas Rosswall. “We are reaching out to the scientific communities in the developing world,” he says, noting that ICSU has opened regional offices in Africa, Latin America, and Asia, and is planning a fourth in the Arab world.
Analysis of period mRNA cycling in Drosophila head and body tissues indicates that body oscillators behave differently from head oscillators. (1994)

The period (per) gene is thought to be part of the Drosophila circadian pacemaker. The circadian fluctuations in per RNA and protein that constitute the per feedback loop appear to be required for pacemaker function, and have been measured in head neuronal tissues that are necessary for locomotor activity and eclosion rhythms. The per gene is also expressed in a number of neuronal and nonneuronal body tissues for which no known circadian phenomena have been described. To determine whether per might affect some circadian function in these body tissues, per RNA cycling was examined. These studies show that per RNA cycles in the same phase and amplitude in head and body tissues during light-dark cycles. One exception to this is the lack of per RNA cycling in the ovary, which also appears to be the only tissue in which PER protein is primarily cytoplasmic. In constant darkness, however, the amplitude of per RNA cycling dampens much more quickly in bodies than in heads. Taken together, these results indicate that circadian oscillators are present in head and body tissues in which PER protein is nuclear and that these oscillators behave differently.