gebhart/patrepeval huggingface dataset:
A Conserved Binding Motif Defines Numerous Candidate Target Proteins for Both Cdc42 and Rac GTPases (1995)

Rho, Rac, and Cdc42 are small GTPases that regulate the formation of a variety of actin structures and the assembly of associated integrin complexes, but little is known about the target proteins that mediate their effects. Here we have used a motif-based search method to identify putative effector proteins for Rac and Cdc42. A search of the GenBankTM data base for similarity with the minimum Cdc42/Rac interactive binding (CRIB) region of a potential effector protein p65PAK has identified over 25 proteins containing a similar motif from a range of different species. These candidate Cdc42/Rac-binding proteins include family members of the mixed lineage kinases (MLK), a novel tyrosine kinase from Drosophila melanogaster (DPR2), a human protein MSE55, and several novel yeast and Caenorhabditis elegans proteins. Two murine p65PAK isoforms and a candidate protein from C. elegans, F09F7.5, interact strongly with the GTP form of both Cdc42 and Rac, but not Rho in a filter binding assay. Three additional candidate proteins, DPR2, MSE55, and MLK3 showed binding to the GTP form of Cdc42 and weaker binding with Rac, and again no interaction with Rho. These results indicate that proteins containing the CRIB motif bind to Cdc42 and/or Rac in a GTP-dependent manner, and they may, therefore, participate in downstream signaling.
HIF–prolyl hydroxylase inhibition results in endogenous erythropoietin induction, erythrocytosis, and modest fetal hemoglobin expression in rhesus macaques (2007)

The hypoxia-inducible factor (HIF) pathway is crucial in mitigating the deleterious effects of oxygen deprivation. HIF-alpha is an essential component of the oxygen-sensing mechanisms and under normoxic conditions is targeted for degradation via hydroxylation by HIF-prolyl hydroxylases. Several HIF-prolyl hydroxylase inhibitors (PHIs) induced erythropoietin (epo) expression in vitro and in mice, with peak epo expression ranging from 5.6- to 207-fold above control animals. Furthermore, several PHIs induced fetal hemoglobin (HbF) expression in primary human erythroid cells in vitro, as determined by flow cytometry. One PHI, FG-2216, was further tested in a nonhuman primate model without and with chronic phlebotomy. FG-2216 was orally bioavailable and induced significant and reversible Epo induction in vivo (82- to 309-fold at 60 mg/kg). Chronic oral dosing in male rhesus macaques was well tolerated, significantly increased erythropoiesis, and prevented anemia induced by weekly phlebotomy. Furthermore, modest increases in HbF-containing red cells and reticulocytes were demonstrated by flow cytometry, though significant increases in HbF were not demonstrated by high-pressure liquid chromatography (HPLC). HIF PHIs represent a novel class of molecules with broad potential clinical application for congenital and acquired anemias.
Approaches to Limiting Emergence of Antimicrobial Resistance in Bacteria in Human Populations (1997)

Infectious diseases continue to be major threats to human health around the world. Within the past few years, several divergent groups of organisms have emerged as significant causes of morbidity and mortality. Included among these are bacteria that are refractory to therapy because of the development of resistance to multiple antimicrobial agents. Multidrug resistance in strains of Mycobacterium tuberculosis, Streptococcus pneumoniae, Shigella dysenteriae, Salmonella typhi, and Enterococcus faecium has been reported. Surveillance of resistant microorganisms in the United States and abroad is fragmentary and targets relatively few organisms. Surveillance is further hampered by the fact that detection of some novel resistance mechanisms is difficult by means of current laboratory methods. Both clinicians and public health officials are likely to continue to face a variety of challenges regarding surveillance, treatment, prevention, and control of drug-resistant infections.
Toward Physiological Understanding of Glucose Tolerance: Minimal-Model Approach (1989)

Glucose tolerance depends on a complex interaction among insulin secretion from the beta-cells, clearance of the hormone, and the actions of insulin to accelerate glucose disappearance and inhibit endogenous glucose production. An additional factor, less well recognized, is the ability of glucose per se, independent of changes in insulin, to increase glucose uptake and suppress endogenous output (glucose effectiveness). These factors can be measured in the intact organism with physiologically based minimal models of glucose utilization and insulin kinetics. With the glucose minimal model, insulin sensitivity (SI) and glucose effectiveness (SG) are measured by computer analysis of the frequently sampled intravenous glucose tolerance test. The test involves intravenous injection of glucose followed by tolbutamide or insulin and frequent blood sampling. SI varied from a high of 7.6 x 10(-4) min-1.microU-1.ml-1 in young Whites to 2.3 x 10(-4) min-1.microU-1.ml-1 in obese nondiabetic subjects; in all of the nondiabetic subjects, SG was normal. In subjects with non-insulin-dependent diabetes mellitus (NIDDM), not only was SI reduced 90% below normal (0.61 +/- 0.16 x 10(-4) min-1.microU-1.ml-1), but in this group alone, SG was reduced (from 0.026 +/- 0.008 to 0.014 +/- 0.002 min-1); thus, defects in SI and SG are synergistic in causing glucose intolerance in NIDDM. One assumption of the minimal model is that the time delay in insulin action on glucose utilization in vivo is due to sluggish insulin transport across the capillary endothelium. This was tested by comparing insulin concentrations in plasma with those in lymph (representing interstitial fluid) during euglycemic-hyperinsulinemic glucose clamps. Lymph insulin was lower than plasma insulin at basal (12 vs. 18 microU/ml) and at steady state, indicating significant loss of insulin from the interstitial space, presumably due to cellular uptake of the insulin-receptor complex. Additionally, during clamps, lymph insulin changed more slowly than plasma insulin, but the rate of glucose utilization followed a time course identical with that of lymph (r = .96) rather than plasma (r = .71). Thus, lymph insulin, which may be reflective of interstitial fluid, is the signal to which insulin-sensitive tissues are responding. These studies support the concept that, at physiological insulin levels, the time for insulin to cross the capillary endothelium is the process that determines the rate of insulin action in vivo.(ABSTRACT TRUNCATED AT 400 WORDS)
The impacts of electronic commerce on auditing practices: an auditing process model for evidence collection and validation (2000)

The main purposes of this paper are twofold. First, the paper identifies and discusses the potential impacts of electronic commerce on auditing practices in the emerging paperless on-line transaction environment. Second, it provides two auditing process models that incorporate modern network security techniques and show how an audit can be conducted in an EC environment. A periodical auditing process model (PAPM) is proposed to demonstrate how secure electronic technologies can be used to facilitate the auditor's evidence collection and validation process for annual and semi-annual audits. We also present a continuous auditing process model (CAPM) which extends the functions of PAPM for continuous auditing. In CAPM, a real-time transaction monitoring system is used to link to firms' accounting information systems for assisting the auditor to detect abnormal activities and generate exception reports on a continuous basis. The CAPM approach intends not only to ensure integrity and effectiveness of the entire accounting system, but also to guarantee the correctness and usefulness of the constantly generated financial statements for public dissemination. The main contribution of this paper is that it illustrates a conceptual framework which shows the feasibility of continuously auditing electronic transactions in the EC environment. Copyright © 2000 John Wiley & Sons, Ltd.
Intelligent assistance in operation of active catheter for minimum invasive surgery (2002)

It is important to assist doctors in operating the (active) catheter in complex and narrow brain blood vessels aiming at the minimum invasive surgery. We propose the concept of the intelligent medical assistance system for the operation of the active catheter. To realize the system we built a prototype of a basic system consisting of a joy-stick and a 3D computer graphics display. The joystick is used for the command input and the force display. We evaluated the effectiveness of the prototype and the proposed assistance methods through the experiments.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Zero-Collision RFID Tags Identification Based on CDMA (2009)

One of the killer applications for radio frequency identification (RFID) system is the automatic identification of physical objects. To do that, each object must be labeled with a RFID tag containing identifying data. However, collisions occur when several tags send their data simultaneously. This paper proposes a secure scheme for zero-collision RFID tags identification based on code division multiple access (CDMA) and hash-chain mechanics. The scheme not only allows several tags send their identifying data simultaneously without collision, but also provides the following secure properties for RFID reader and tags: mutual authentication, tag anonymity, robustness and forward secrecy.
In vitro transdifferentiation of embryonic rat retinal pigment epithelium to neural retina (1995)

Divergence of neural retinal and retinal pigment epithelial (RPE) lineages from the optic vesicle neuroepithelium starts at a very early stage of eye development. Partially or even fully differentiated RPEs of some vertebrate species are capable of transforming into neural retina. In the present study, we have shown that mammalian RPE possesses the ability to transdifferentiate into neural retina at early embryonic stages. If cultured in serum-free medium, presumptive rat RPE became pigmented and expressed a molecular marker of mature RPE. In the presence of basic fibroblast growth factor (bFGF), cultured early embryonic rat RPE did not acquire pigment and grew to form retina-like multilayer structure containing neuronal cells and cells that express markers of retinal ganglion, amacrine and rod photoreceptor cells. The effects of bFGF occurred independently of effects on cell division and became irreversible after periods that varied with tissue age. This study has demonstrated that already differentiated embryonic rat RPE still retain the ability to become neural retina up to certain stage.
Mass production of uniform-sized nanoporous silicon nanowire anodes via block copolymer lithography (2011)

We present a simple, mass production of nonporous and nanoporous silicon nanowire anodes by combining block copolymer masks and metal catalytic etching. Carbon coated nanoporous silicon nanowire anodes exhibit a highly stable cycling performance with a reversible charge capacity of 1500 mA h g−1.
Preparation and base-catalyzed reactions of some β-halohydroperoxides (1968)

The reaction between olefins, N-chloroacetamide or 1,3-dibromo-5,5-dimethylhydantoin, and hydrogen peroxide affords β-halohydroperoxides in good yields. These compounds react extremely rapidly in basic solution to give products which depend upon their structure. The 3-halo-2,3-dimethyl-2-butyl hydroperoxides form 2,3-dimethyl-3-hydroperoxy-1-butene and from the 2-halo-1,2-dimethylcyclohexyl hydroperoxides 1-methyl-2-methylene-cyclohexyl hydroperoxide is obtained. No allylic hydroperoxide can be detected from the reaction between base and 3-bromo-2-methyl-2-butyl hydroperoxide. Mainly cleavage products, acetone and acetaldehyde, are formed together with some 2,3-epoxy-2-methylbutane. The reaction between base and 2-bromo-1-phenylethyl hydroperoxide gives styrene oxide, benzoic acid, and some benzaldehyde. From trans-2-bromocyclohexyl hydroperoxide, trans-2-bromocyclohexanol, cyclohexene oxide, and some trans-1,2-cyclohexanediol are obtained upon reaction with base. No evidence for the formation of the allylic hydroperoxide was obtained.
Negative electrospray ionization mass spectrometry of synthetic and chemically modified oligonucleotides (1994)

We report here on the analysis of synthetic oligonucleotides by electrospray ionization mass spectrometry (ESI-MS). After intensive removal of salt ions (especially sodium cations), negative ion mass spectra, allowing mass measurement with an accuracy of 0.01%, were obtained on several oligonucleotides up to 80 nucleotides. In most cases, the resolution was sufficient to observe n-1 and n-2 forms due to internal deletions during automated synthesis, and to identify the missing nucleotides. A 132-mer, whose size is close to the limit of automated chemical synthesis, was also successfully mass measured. A quantitative study showed that ESI-MS can provide quantitative data on oligonucleotides of similar size and structure. The described methodology is used to characterize oligonucleotide analogues such as phosphorothioate oligonucleotides designed for antisense applications. Finally, analyses in the positive ion mode on a trimer TpTpT in the presence of different amine bases were performed and allowed a better understanding of the influence of these bases on the ions formation.
[Analysis of the expression of Slit/Robo genes and the methylation status of their promoters in the hepatocellular carcinoma cell lines]. (2009)

The hypermethylation status of Slit/Robo signaling pathway related genes is a universal event in the HCC. The hypermethylation status of Slit1, Slit2, Slit3 genes associated with the loss of expression or reduced expression. Those data suggest that Slit/Robo pathway may play a significant role in the progress or metastasis of HCC.
Strategies for the identification of novel inhibitors of deubiquitinating enzymes (2008)

Dysregulation of the UPS (ubiquitin-proteasome system) has been implicated in a wide range of pathologies including cancer, neurodegeneration and viral infection. Inhibiting the proteasome has been shown to be an effective therapeutic strategy in humans; yet toxicity with this target remains high. DUBs (deubiquitinating enzymes) represent an alternative target in the UPS with low predicted toxicity. Currently, there are no DUB inhibitors that have been used clinically. To address this situation, Progenra has developed a novel assay to measure the proteolytic cleavage of Ub (ubiquitin) or UBL (Ub-like protein) conjugates such as SUMO (small Ub-related modifier), NEDD8 (neural-precursor-cell-expressed, developmentally down-regulated 8) or ISG15 (interferon-stimulated gene 15) by isopeptidases. In this review, current platforms for detecting DUB inhibitors are discussed and the advantages and disadvantages of the approaches are underlined.
Bioequivalence evaluation of new megestrol acetate formulations in humans. (1985)

The bioequivalence of two new investigational 160 mg tablets, one containing the regular form and the other a micronized form of megestrol acetate, was determined relative to a commercially available 40 mg tablet. The tablets were administered to 24 male subjects in a three-way crossover study, balanced for sequence, with 1 week between administrations. The 40 mg tablets were administered qid at 8 AM, 12 PM, 6 PM, and 10 PM, while the 160 mg tablets were administered once at 8 AM. Plasma samples were collected at appropriate times up to 96 hours after administration and were analyzed for megestrol acetate with a validated high-performance liquid chromatographic procedure. Based on the times to maximum plasma concentrations (2.5 to 2.8 h) the rate of absorption was the same for each of the tablets. Relative to the 40 mg qid dose, the 160 mg regular and the 160 mg micronized tablets had mean relative bioavailabilities of 97% and 118%, respectively.
Qualitative and quantitative analysis of orthotopic bone regeneration by marrow (1996)

A rat model of a femoral segmental defect was used to specifically test the hypothesis that autogenous marrow has the osteogenic capability to heal a bone defect. The variables analyzed included the ratio of the marrow volume to the defect, implantation of live or dead marrow, and remodeling of established nonunions by implantation of live marrow. The uniqueness of this model allows biomechanical evaluation of the new bone formed by the implant. When live marrow was implanted, woven bone formed at 3 weeks, progressing to early lamellar bone at 6 weeks, with subsequent remodeling for as long as 12 weeks in a volumetric fashion (p < 0.05). Bone marrow, when placed in a fresh femoral defect and given in sufficient amounts, produced a rate of union comparable with that of autologous bone grafts. Mature lamellar bone formed by marrow was evaluated biomechanically; the results were statistically comparable with those of cancellous bone grafts at 12 weeks. Significant bone formation occurred when marrow was percutaneously injected in femoral nonunions, although union and remodeling did not take place in this rat model. Implantation of dead marrow resulted in rare cellular infiltration and minimal bone formation in a manner comparable with that of autogenous cancellous bone grafts. These results indicate that bone marrow can lead to structurally functional bone regeneration in an orthotopic location.
Exploring Difficulties in Parsing Imperatives and Questions (2011)

This paper analyzes the effect of the structural variation of sentences on parsing performance. We examine the performance of both shallow and deep parsers for two sentence constructions: imperatives and questions. We first prepare an annotated corpus for each of these sentence constructions by extracting sentences from a fiction domain that cover various types of imperatives and questions. The target parsers are then adapted to each of the obtained corpora as well as the existing query-focused corpus. Analysis of the experimental results reveals that the current mainstream parsing technologies and adaptation techniques cannot cope with different sentence constructions even with much in-domain data. 1
Electric Field–directed Cell Motility Involves Up-regulated Expression and Asymmetric Redistribution of the Epidermal Growth Factor Receptors and Is Enhanced by Fibronectin and Laminin (1999)

Wounding corneal epithelium establishes a laterally oriented, DC electric field (EF). Corneal epithelial cells (CECs) cultured in similar physiological EFs migrate cathodally, but this requires serum growth factors. Migration depends also on the substrate. On fibronectin (FN) or laminin (LAM) substrates in EF, cells migrated faster and more directly cathodally. This also was serum dependent. Epidermal growth factor (EGF) restored cathodal-directed migration in serum-free medium. Therefore, the hypothesis that EGF is a serum constituent underlying both field-directed migration and enhanced migration on ECM molecules was tested. We used immunofluorescence, flow cytometry, and confocal microscopy and report that 1) EF exposure up-regulated the EGF receptor (EGFR); so also did growing cells on substrates of FN or LAM; and 2) EGFRs and actin accumulated in the cathodal-directed half of CECs, within 10 min in EF. The cathodal asymmetry of EGFR and actin staining was correlated, being most marked at the cell-substrate interface and showing similar patterns of asymmetry at various levels through a cell. At the cell-substrate interface, EGFRs and actin frequently colocalized as interdigitated, punctate spots resembling tank tracks. Cathodal accumulation of EGFR and actin did not occur in the absence of serum but were restored by adding ligand to serum-free medium. Inhibition of MAPK, one second messenger engaged by EGF, significantly reduced EF-directed cell migration. Transforming growth factor beta and fibroblast growth factor also restored cathodal-directed cell migration in serum-free medium. However, longer EF exposure was needed to show clear asymmetric distribution of the receptors for transforming growth factor beta and fibroblast growth factor. We propose that up-regulated expression and redistribution of EGFRs underlie cathodal-directed migration of CECs and directed migration induced by EF on FN and LAM.
Software agents (1994)

article Free Access Share on Software agents Authors: Michael R. Genesereth Stanford Univ., Stanford, CA Stanford Univ., Stanford, CAView Profile , Steven P. Ketchpel Stanford Univ., Stanford, CA Stanford Univ., Stanford, CAView Profile Authors Info & Claims Communications of the ACMVolume 37Issue 7July 1994 pp 48–ff.https://doi.org/10.1145/176789.176794Published:01 July 1994Publication History 810citation1,659DownloadsMetricsTotal Citations810Total Downloads1,659Last 12 Months41Last 6 weeks7 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
<title>Implementation experiences of bandwidth guarantee on a wireless LAN</title> (2001)

Rether was originally developed to support guaranteed Quality of Service (QoS) for shared Ethernet LANs. With the growing popularity of wireless LANs, we modified the Rether protocol to provide QoS guarantee on wireless networks. In this paper, we present the design and implementation of the Wireless Rether protocol for 802.11 networks. We also describe our experiences with wireless LAN hardware. Wireless Rether supports QoS for TCP and UDP traffic in both upstream and downstream directions. The protocol can seamlessly inter-operate with any priority-based QoS mechanisms (such as Diffserv on the wired networks that connect the wireless access network to the rest of the Internet. QoS requirements of real-time applications are specified as a simple configurable policy table. Legacy networking applications can benefit from QoS guarantees provided by Wireless Rether without requiring any modifications.
A New RNA Synthetic Method with a 2‘- O -(2-Cyanoethoxymethyl) Protecting Group (2005)

A novel method for the synthesis of RNA oligomers with 2-cyanoethoxymethyl (CEM) as the 2'-hydroxyl protecting group has been developed. The new method allows the synthesis of oligoribonucleotides with an efficiency and final purity comparable to that obtained in DNA synthesis. [structure: see text]
1-GHz and 2.8-GHz CMOS injection-locked ring oscillator prescalers (2002)

We implemented prescalers that can operate up to 2.8-GHz by exploiting the injection locking phenomena in differential CMOS ring oscillators. We tested a 5-stage, 1-GHz injection-locked modulo-8 prescaler fabricated in a 0.24-/spl mu/m CMOS technology that consumes 350 /spl mu/W of power and occupies 0.012 mm/sup 2/ of die area. The locking range is 20 MHz and the locked phase noise is -110 dBc/Hz @ 100 kHz. A 2.8-GHz, 3-stage, modulo-4 divider is also presented.