gebhart/patrepeval huggingface dataset:
Open metadata formats: efficient XML-based communication for high performance computing (2002)

High-performance computing faces considerable change as the Internet and the Grid mature. Applications that once were tightly-coupled and monolithic are now decentralized, with collaborating components spread across diverse computational elements. Such distributed systems most commonly communicate through the exchange of structured data. Definition and translation of metadata is incorporated in all systems that exchange structured data. We observe that the manipulation of this metadata can be decomposed into three separate steps: discovery, binding of program objects to the metadata, and marshaling of data to and from wire formats. We have designed a method of representing message formats in XML, using datatypes available in the XML Schema specification. We have implemented a tool, XMIT that uses such metadata and exploits this decomposition in order to provide flexible run-time metadata definition facilities for an efficient binary communication mechanism. We also demonstrate that the use of XMIT makes possible such flexibility at little performance cost.
Potent and selective inactivation of cysteine proteinases with N-peptidyl-O-acyl hydroxylamines (1989)

A series of N-peptidyl-O-acyl hydroxylamines was synthesized and tested as inactivators of cysteine proteinases. Depending on the structure of the peptidyl residue of the inhibitors, rapid and complete irreversible inactivation of the lysosomal cathepsins, B, L and S, may be achieved. The most effective inhibitors display second-order rate constants of the inactivation in the range 10(5)-10(6) M-1.s-1. By contrast, the activity of the aminoendopeptidase cathepsin H is only negligibly affected by the N-terminal-protected peptidyl inhibitors.
In vitro and in vivo studies with flutrimazole, a new imidazole derivative with antifungal activity. (1992)

1-[(2-Fluorophenyl)(4-fluorophenyl)phenylmethyl]-1H-imidazole (flutrimazole, UR-4056, CAS 119006-77-8) is a new topical imidazole antifungal agent which displays potent broad-spectrum in vitro activity against dermatophytes, filamentous fungi and yeasts, saprophytic and pathogenic to animals and humans (MIC = 0.025-5.0 micrograms/ml). In most of these studies the activity of flutrimazole was comparable to that of clotrimazole and markedly higher than that of bifonazole (MIC differences of greater than or equal to 1 order of magnitude). Tested against Scopulariopsis brevicaulis (8 strains), both flutrimazole and clotrimazole exhibited fungistatic and fungicidal activity, and clotrimazole appeared something less active (MIC = 0.3-2.5 micrograms/ml) than flutrimazole (MIC = 0.15-0.6 micrograms/ml). In animal experiments, topical application of 1% and 2% flutrimazole, as a cream or solution, was highly effective in models of rat vaginal candidiasis and guinea-pig trichophytosis, giving a rate of cured or cured plus markedly improved animals higher than 80%. Flutrimazole shares the mode of action of other imidazole or triazole-containing antifungals, i.e. inhibition of fungal lanosterol 14 alpha-demethylase, as it strongly inhibits ergosterol biosynthesis in a cell-free homogenate of Candida albicans, with an IC50 value of 0.071 mumol/l.
The Effect of Pulse Rate Changes on the Clinical Outcome of Sacral Neuromodulation (2011)

On the group level none of the 4 pulse rates appeared to have a significantly different effect on clinical outcome or sacral neuromodulation related pain. However, an individualized approach to optimize treatment efficacy by changing the pulse rate appears to be useful.
Differential Pattern of Expression and Sugar Regulation of Arabidopsis thaliana ADP-glucose Pyrophosphorylase-encoding Genes (2004)

ADP-glucose pyrophoshorylase (ADP-Glc PPase) catalyzes the first and limiting step in starch biosynthesis. In plants, the enzyme is composed of two types of subunits (small and large) and is allosterically regulated by 3-phosphoglycerate and phosphate. The pattern of expression and sugar regulation of the six Arabidopsis thaliana ADP-Glc PPase-encoding genes (two small subunits, ApS1 and ApS2; and four large subunits, ApL1-ApL4) has been studied. Based on mRNA expression, ApS1 is the main small subunit or catalytic isoform responsible for ADP-Glc PPase activity in all tissues of the plant. Large subunits play a regulatory role, and the data presented define a clear functional distinction among them. ApL1 is the main large subunit in source tissues, whereas ApL3 and, to a lesser extent, ApL4 are the main isoforms present in sink tissues. Thus, in source tissues, ADP-Glc PPase would be finely regulated by the 3-phosphoglycerate/phosphate ratio, whereas in sink tissues, the enzyme would be dependent on the availability of substrates for starch synthesis. Sugar regulation of ADP-Glc PPase genes is restricted to ApL3 and ApL4 in leaves. Sugar induction of ApL3 and ApL4 transcription in leaves allows the establishment of heterotetramers less sensitive to the allosteric effectors, resembling the situation in sink tissues. The results presented on the expression pattern and sugar regulation allow us to propose a gene evolution model for the Arabidopsis ADP-Glc PPase gene family.
Alfred D. Low (1993)

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Two years of lamivudine therapy in anti‐HBe‐positive patients with chronic hepatitis B (2001)

There is no standard therapy for patients with anti-HBe-positive chronic hepatitis B. The aims of this study were to analyse the efficacy of lamivudine therapy for two years in these patients and to study the sequence variations in the precore and polymerase hepatitis B virus (HBV) regions in relation to therapy. Sixteen patients with chronic anti-HBe-positive hepatitis were treated with lamivudine (100 mg) once daily for 2 years. Levels of alanine aminotransferase (ALT), HBV-DNA and HBsAg were monitored during therapy. The polymerase and precore genes were amplified by polymerase chain reaction and their products were sequenced directly. Thirteen of 16 patients (81%) had a virological and biochemical response after 1 year of therapy and 11 (69%) maintained the complete response after 2 years of lamivudine therapy. Among the three patients without initial virological or biochemical response at year 1, prolonging therapy to 2 years was not associated with an increase in the response. YMDD variants were detected in 19% of cases in the first year and in 44% in the second year: YVDD being the most frequent mutations detected during year 1 and YIDD during year 2 of therapy. YMDD variants were found in 7-27% of cases with complete response depending on the duration of therapy. Our results show that prolonging lamivudine therapy is safe, well tolerated and maintains viral inhibition in anti-HBe-positive patients. However, its efficacy tends to decrease overtime and it is associated with an increase in YMDD variants, even in some cases, of complete response.
Plasma PCSK9 levels are significantly modified by statins and fibrates in humans (2008)

These results suggest that in vivo (1) statins directly increase PCSK9 expression while (2) fibrates affect PCSK9 expression indirectly through its modulation of cholesterol levels and (3) that these therapies could be improved by combination with a PCSK9 inhibitor, constituting a novel hypercholesterolemic therapy, since PCSK9 was significantly upregulated by both treatments.
Entrapment of Migrating Hippocampal Neural Cells in Three-Dimensional Peptide Nanofiber Scaffold (2004)

Isolation and expansion of self-renewing neural cells ex vivo are required for neural tissue repair in regenerative medicine. Neurogenesis occurs in restricted areas of postnatal mammalian brain including dentate gyrus and subventricular zone. We developed a simple method to entrap migrating neural cells (potential neuroprogenitors) from postnatal hippocampal organotypic cultures in three-dimensional (3-D) peptide nanofiber scaffolds. A few hours after placing the hippocampal slices in culture, cell proliferation activity at the "interface zone" between the tissue slice and the membrane culture surface was observed. Pulse-chase experiments using 5-bromodeoxyuridine (BrdU), which measures mitotic activity, showed that a number of cells incorporated BrdU at the interface zone. The number of BrdU(+) cells increased exponentially during the first 3 days of exposure to the label. The BrdU(+) cells also stained positive for glial fibrillary acidic protein (2.2 +/- 0.5%), a marker for astroglia; and for betaIII tubulin (7.3 +/- 2.8%) and nestin (2.7 +/- 0.9%), markers for neural progenitors. When hippocampal slices were cultured on a peptide nanofiber scaffold layer (~500 microm thick), a more extended interface zone between each tissue slice and the scaffold was formed. Moreover, the migrating BrdU(+) cell population entrapped in the 3-D peptide scaffold was readily isolated by mechanically disrupting the scaffold and then used for conventional 2-D culture systems for further studies. This simple method may be useful not only in developing technology for neural progenitor cell isolation and enrichment in vitro, but also for expanding cells for cell-based therapies of regenerative medicine.
Tumor suppressors p53, p63, and p73 inhibit migrating cancer stem cells by increasing the expression of stem cell suppressing miRNAs (2010)

Abstract ZEB1/2 has been shown to suppress the expression of the tumor suppressors E-cadherin, TA-p73, INK4b, CDKN1a, and thereby promotes epithelial to mesenchymal transition, invasion, and metastasis. I have recently shown that p53-dependent miRs, such as miR-192, 215, 145, 203, 200b/c, 183, suppress the expression of ZEB1/2. Another recent study showed that ZEB1/2 suppresses the expression of miR-200b/c, miR-203, &amp; miR-183, which in turn, inhibit the expression of stem cell factors, such as Sox-2, Klf-4, and BMI. ZEB1/2, by inhibiting the expression of stem cell factors suppressing miRs, it up regulates the expression of stem cell factors. By up regulating the stem cell factors and down regulating metastasis suppressors, ZEB1/2 promotes both metastasis and migration of cancer stem cells. p53/p63/p73, by down regulating the expression of ZEB1/2 through its target miRNAs, it could activate the expression of stem cell suppressing miRNAs, such as miR-200b/c, miR-203 &amp; miR-183. Thereby, it could inhibit the expression of stem cell factors, such as Sox-2, Klf-4 and BMI-1(an inhibitor of INK4a/ARF). In addition, p53/p63/p73 appears to inhibit the expression of other EMT inducers, such as Snail1/2 and Twist, expression through its target miRs. Remarkably, bioinformatics analysis of stem cell factors suppressing miRNAs, miR-200, miR-183, miR-141, and miR-203, promoters revealed a number of p53/p63/p73 responsive elements, indicating that they could be direct transcriptional targets of p53/TA-p63/p73. Together, these data suggest that p53/TA-p63/p73, by suppressing the expression of ZEB1/2, Snail1/2, and Twist through its target miRs, it could inhibit migration, metastasis, and proliferation of cancer stem cells. In conclusion, the data presented here provide mechanistic insights into how TA-p63/p73 and p53 function as metastasis suppressors.
Structure of a λ-type Bence-Jones protein at 3.5-Å resolution (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure of a λ-type Bence-Jones protein at 3.5-Å resolutionMarianne Schiffer, Rowland L. Girling, Kathryn R. Ely, and Allen B. EdmundsonCite this: Biochemistry 1973, 12, 23, 4620–4631Publication Date (Print):November 1, 1973Publication History Published online1 May 2002Published inissue 1 November 1973https://pubs.acs.org/doi/10.1021/bi00747a013https://doi.org/10.1021/bi00747a013research-articleACS PublicationsRequest reuse permissionsArticle Views181Altmetric-Citations255LEARN 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
Effect of nerve growth factor on AP-1, NF-?B, and Oct DNA binding activity in apoptotic PC12 cells: Extrinsic and intrinsic elements (1996)

Both intrinsic signals, such as serum and neurotrophic factor deprivation, and extrinsic events or agents, such as oxidative stress and glucose deprivation, can induce cell death in pheochromocytoma (PC12) cells. Also, treatment with nerve growth factor (NGF) reduces cell death due to the treatments mentioned. Serumless-induced cell death, as a model of apoptosis, has been intensively investigated in PC12 cells. In the present study, we investigated the molecular components of H2O2-induced cell death and compared it with serumless-induced cell death. Exposure of PC12 cells to intermediate concentrations of H2O2 (100 microM) induced nuclear condensation and DNA fragmentation, indicating that there is an apoptotic component in H2O2-induced cell death. Since transcription factors have been shown to play an essential role in the control of cellular proliferation, differentiation, and survival, we measured changes in the DNA binding activities of the transcription factors activator protein-1 (AP-1), nuclear factor kappa B (NF-kappa B), and octamer-binding protein (Oct) by electrophoretic mobility shift assay (EMSA) after H2O2 treatment and serum deprivation, both in the absence and presence of exogenous NGF in PC12 cells. AP-1 DNA binding activity transiently increased during apoptosis due to serum deprivation, and NGF treatment further stimulated AP-1 DNA binding activity in a more persistent fashion. NF-kappa B DNA binding activity only increased slightly after serum deprivation, and NGF treatment of PC12 cells decreased NF-kappa B binding activity in the late stages of serum deprivation. Oct DNA binding activity decreased after serum deprivation, while NGF had an opposite effect. AP-1 DNA binding activity also transiently increased after H2O2 treatment, as did NF-kappa B DNA binding activity. Our results suggest that AP-1 is likely to be a common component of signaling pathways associated with both the induction or suppression of apoptosis induced by intrinsic or extrinsic stimuli.
Immune Responses to Allogeneic and Xenogeneic Implants of Collagen and Collagen Derivatives (1990)

Whereas xenogeneic collagen has provided a safe and effective biomaterial for numerous medical applications, there are few instances in which data permit the correlation of the immunologic profile of well-defined devices with their clinical sequelae. A major exception is the use of injectable bovine dermal collagen for soft-tissue contour correction. The low incidence of hypersensitivity has been studied in the context of clinical efficacy and safety with several devices. The findings indicate that such immunity usually results in the manifestation of local symptoms of dermal inflammation at sites of treatment that resolve as the implant is resorbed by the host. In contrast, more immunogenic hemostatic agents may elicit a more frequent or vigorous immune response that is not clinically visible or relevant in that application. Recent experiences with collagen-based devices for the repair and regeneration of bone have also demonstrated that the presence of immunity to their collagenous or non-collagenous components does not necessarily predict adverse clinical sequelae. Indeed, numerous specific data indicate that this immunity can exist as an epiphenomenon with no effect on osteogenesis. To get a true composite picture of biocompatibility, significant steps must be taken to characterize biomaterials properly and to ensure that immunologic, clinical, histologic, and other pertinent laboratory data are viewed in relation to one another and not in isolation.
Procyanidin Content of Grape Seed and Pomace, and Total Anthocyanin Content of Grape Pomace as Affected by Extrusion Processing (2009)

Extrusion processing can be used to increase procyanidin monomer and dimer contents in grape seed and pomace. Procyanidins in grape by-products have many health benefits, but most are present as large molecular weight compounds, which are poorly absorbed. Extrusion processing appears to be a promising technology to increase levels of the bioactive low molecular weight procyanidins.
Reliable network connections (2002)

We present two systems, reliable sockets (rocks) and reliable packets (racks), that provide transparent network connection mobility using only user- level mechanisms. Each system can detect a connection failure within seconds of its occurrence, preserve the endpoint of a failed connection in a suspended state for an arbitrary period of time, and automatically reconnect, even when one end of the connection changes IP address, with correct recovery of in-flight data. To allow rocks and racks to interoperate with ordinary clients and servers, we introduce a general user-level Enhancement Detection Protocol that enables the remote detection of rocks and racks, or any other socket enhancement system, but does not affect applications that use ordinary sockets. Rocks and racks provide the same functionality but have different implementation models: rocks intercept and modify the behavior of the sockets API by using an interposed library, while racks uses a packet filter to intercept and modify the packets exchanged over a connection. Racks and rocks introduce small throughput and latency overheads that we deem acceptable for the level of mobility and reliability they provide.
Escape and synchronization of a Brownian particle (1992)

The escape and synchronization of a 1-\ensuremath{\mu}m Brownian particle from an optical trap is presented. The probability distribution of residence times within a given well is exponential with a cutoff at short time. Temporal modulation of the well leads to synchronization.
A dialogue system for telephone-based services integrating spoken and written language (2002)

We describe a dialogue system for telephone-based services that integrates, spoken (dialogue component) and written language (optical character recognition-OCR). This system has been developed for a car insurance company in the framework of the LE-1 1802 project ACCeSS, but can be easily adapted to a different task. Handwritten application forms from prospective clients, concerning new contracts, are processed by the OCR component and the extracted information is stored on a local customers' database. The dialogue component reads the customers' database and collects the missing information of the application forms by calling the corresponding customer and asking about the blank or ambiguous fields. The system is currently tested at the company's site.
Remote hydraulic syringe actuator: its use to avoid radiation exposure during intraoperative arteriography. (1980)

A simple, inexpensive device consisting of a double hydraulic syringe system and a holding fixture was devised for intraoperative arteriography to avoid exposure of personnel to radiation. The procedure of intraoperative angiography has thus become safer, less time consuming, and more reliable in obtaining high-quality angiographic studies.
Expression of matrix metalloproteinase (gelatinase) in T1 adenocarcinoma of the lung (1997)

The expression of matrix metalloproteinase-2 (MMP-2; 72 kDa type IV collagenase/gelatinase A) and MMP-9 (92 kDa type IV collagenase/gelatinase B) was immunohistochemically investigated in 79 T1 adenocarcinomas of the lung using non-commercial polyclonal anti-MMP-2 and -9 antibodies. Thirty-two (41%) and 22 (28%) among the 79 cases were positive in the tumor cells for MMP-2 and -9, respectively. The incidences of MMP-2 and -9 immunoreactivities were higher (64 and 45%, respectively) in poorly differentiated tumors than in well differentiated tumors (36 and 25%, respectively), and lower in bronchioloalveolar carcinoma (22 and 10%, respectively) compared with other subtypes of adenocarcinoma. The prognosis for patients with MMP-2 and/or -9 positive immunoreactivities was significantly poorer than for those with a MMP-negative tumor (P < 0.05). The degree of collagenization was divided into four grades, and tumors with a small to abundant amount of collagen (grade 2 and grade 3 fibrosis) had a higher incidence of immunoreactivity to both types of MMP. It is estimated that these expressions might be responsible for tumor invasion, metastasis, and for grade 2 and grade 3 fibrosis in T1 adenocarcinoma of the lung.
Patient perception of tics and other movement disorders (1991)

To determine the subjective perception patients have of abnormal movements, 170 patients with various hyperkinesias were interviewed with questions directed at the "voluntary" or intentional versus "involuntary" aspects of their symptoms. One hundred and two of 110 patients with non-tic disorders thought that the abnormal movements were entirely involuntary. Forty-one of 60 tic disorder patients stated that all their motor and phonic tics were intentionally produced. Fifteen others had both voluntary and involuntary components, usually with the former predominating. A "voluntary" response could be used to predict the correct diagnostic category (tic versus non-tic) in 8 of 9 patients for whom the referral category was incorrect. These results suggest that a large proportion of the motor and phonic symptoms experienced by tic patients are irresistibly but purposefully executed, more akin to compulsions than to the other "involuntary" hyperkinesias with which they are commonly discussed.
Deciphering the Impact of Common Genetic Variation on Lung Cancer Risk: A Genome-Wide Association Study (2009)

To explore the impact of common variation on the risk of developing lung cancer, we conducted a two-phase genome-wide association (GWA) study. In phase 1, we compared the genotypes of 511,919 tagging single nucleotide polymorphisms (SNP) in 1,952 cases and 1,438 controls; in phase 2, 30,568 SNPs were genotyped in 2,465 cases and 3,005 controls. SNP selection was based on best supported P values from phase 1 and two other GWA studies of lung cancer. In the combined analysis of phases 1 and 2, the strongest associations identified were defined by SNPs mapping to 15q25.1 (rs12914385; P = 3.19 x 10(-16)), 5p15.33 (rs4975616; P = 6.66 x 10(-7)), and 6p21.33 (rs3117582; P = 9.13 x 10(-7)). Variation at 15q25.1, but not 5p15.33 or 6p21.33, was strongly associated with smoking behavior with risk alleles correlated to higher consumption. Variation at 5p15.33 was shown to significantly influence induction of lung cancer histology. Pooling data from the four series provided 21,620 genotypes for 7,560 cases and 8,205 controls. A meta-analysis provided increased support that variation at 15q25.1 (rs8034191; P = 3.24 x 10(-26)), 5p15.33 (rs4975616; P = 2.99 x 10(-9)), and 6p21.33 (rs3117582; P = 4.46 x 10(-10)) influences lung cancer risk. The next best-supported associations were attained at 15q15.2 (rs748404: P = 1.08 x 10(-6)) and 10q23.31 (rs1926203; P = 1.28 x 10(-6)). These data indicate few common variants account for 1% of the excess familial risk underscoring the necessity of having additional large sample series for gene discovery.