gebhart/patrepeval huggingface dataset:
Treatment of suture line bleeding with a novel synthetic surgical sealant in a canine iliac PTFE graft model (2001)

CoSeal™ surgical sealant (CoSeal) was evaluated for inhibiting suture line bleeding using a canine iliac PTFE graft model. Both iliac arteries of 12 heparinized canines were grafted with PTFE. CoSeal was applied to the suture lines of one graft in each animal. The contra-lateral graft served as a control and bleeding was controlled with gauze and pressure (tamponade). The cross-clamps were removed 30 s following application of CoSeal. Times to hemostasis and volume of blood loss at each graft site were determined. Compared to tamponade control, CoSeal significantly reduced the time to hemostasis (average of 5 min vs. greater than 15 min, p < 0.05) and blood loss (19 g vs. 284 g, p < 0.05). Small amounts of CoSeal were visible grossly or histologically at day 7. Histology showed moderate to marked inflammation in CoSeal sites and moderate inflammation in control sites at day 7. At 30 and 60 days, no CoSeal was visible grossly or histologically. Histology showed moderate inflammation in both CoSeal treated sites and in control sites at day 30 and mild to moderate inflammation in both CoSeal and control sites at day 60. CoSeal significantly reduced the time to hemostasis and blood loss in comparison to tamponade. © 2001 John Wiley & Sons, Inc. J Biomed Mater Res (Appl Biomater) 58: 308–312, 2001
Dense arrays of ordered GaAs nanostructures by selective area growth on substrates patterned by block copolymer lithography (2000)

GaAs has been selectively grown in a hexagonally ordered array of nanometer-scale holes with a density as high as ∼1011/cm2 by metalorganic chemical vapor deposition. This array of holes was created using block copolymer lithography, in which a thin layer of diblock copolymer was used as an etching mask to make dense holes in a 15-nm-thick SiNx film. These selectively grown nanoscale features are estimated to be 23 nm in diameter with narrow lateral size and height distributions as characterized by field-emission scanning electron microscopy and tapping mode atomic force microscopy. The narrow size distribution and uniform spatial position of the nanoscale dots we report offer potential advantages over self-assembled dots grown by the Stranski–Krastanow mode.
Human Immunodeficiency Virus Type 1-Specific Immune Responses in Primates upon Sequential Immunization with Adenoviral Vaccine Carriers of Human and Simian Serotypes (2004)

Two triple immunization vaccine regimens with adenoviral vectors with E1 deleted expressing Gag of human immunodeficiency virus type 1 were tested for induction of T- and B-cell-mediated-immune responses in mice and in nonhuman primates. The vaccine carriers were derived from distinct serotypes of human and simian adenoviruses that fail to elicit cross-neutralizing antibodies expected to dampen the effect of booster immunizations. Both triple immunization regimens induced unprecedented frequencies of gamma interferon-producing CD8(+) T cells to Gag in mice and monkeys that remained remarkably stable over time. In addition, monkeys developed Gag-specific interleukin-2-secreting T cells, presumably belonging to the CD4(+) T-cell subset, and antibodies to both Gag and the adenoviral vaccine carriers.
IL-8 Regulates Mucin Gene Expression at the Posttranscriptional Level in Lung Epithelial Cells (2009)

Airway inflammation and mucus hypersecretion/overproduction/obstruction are pathophysiological characteristics of cystic fibrosis, asthma, and chronic obstructive pulmonary disease. Up-regulation of airway mucin genes by inflammatory/immune response mediators is one of the major contributors to mucin overproduction. IL-8, a potent proinflammatory mediator and neutrophil chemoattractant, is present at high levels in the airway secretions of such patients. In this study, the effects of IL-8 on expression of two major airway mucin genes, MUC5AC and MUC5B, were evaluated. IL-8 increased the mRNA abundance of both mucin genes in two human respiratory tract-derived cell lines (A549 and NCI-H292) in a time- and concentration-dependent manner. IL-8 also increased MUC5AC and MUC5B mRNA levels in primary normal differentiated human bronchial epithelial cells, with a high concentration of IL-8 required to increase MUC5B mRNA levels. IL-8 did not transcriptionally up-regulate MUC5AC gene expression, but rather increased the stability of the MUC5AC transcript, suggesting regulation at the posttranscriptional level. In addition, IL-8 altered the levels of RNA-binding proteins to specific domains in the 3'-untranslated region of the MUC5AC transcript. Taken together, these data indicate that the IL-8-induced binding of RNA-binding proteins to the 3'-untranslated region of MUC5AC is a potential mechanism for regulating MUC5AC gene expression at the posttranscriptional level, thus suggesting a new role whereby IL-8 sustains mucin gene expression in inflamed airways.
Specific Targeting of Tau Oligomers in Htau Mice Prevents Cognitive Impairment and Tau Toxicity Following Injection with Brain-Derived Tau Oligomeric Seeds (2014)

Neurodegenerative disease is one of the greatest health crises in the world and as life expectancy rises, the number of people affected will continue to increase. The most common neurodegenerative disease, Alzheimer's disease, is a tauopathy, characterized by the presence of aggregated tau, namely in the form of neurofibrillary tangles. Historically, neurofibrillary tangles have been considered the main tau species of interest in Alzheimer's disease; however, we and others have shown that tau oligomers may be the most toxic form and the species responsible for the spread of pathology. We developed a novel anti-tau oligomer-specific mouse monoclonal antibody (TOMA) and investigated the potential of anti-tau oligomer passive immunization in preventing the toxicity of tau pathology in Htau mice. We injected pure brain-derived tau oligomers intracerebrally in 3-month-old wild-type and Htau mice and investigated the protective effects of a single 60 μg TOMA injection when compared to the same dose of non-specific IgG and found that TOMA conferred protection against the accumulation of tau oligomers and cognitive deficits for up to 1 month after treatment. Additionally, we injected pure brain-derived tau oligomers intracerebrally in 3-month-old wild-type and Htau mice and treated animals with biweekly injections of 60 μg TOMA or non-specific IgG. We found that long-term administration of TOMA was effective as a preventative therapy, inhibiting oligomeric tau and preserving memory function. These results support the critical role of oligomeric tau in disease progression and validate tau oligomers as a potential drug target.
Liposome mediated gene transfer into the rat oesophagus (1997)

In vivo gene transfer into the esophagus is feasible and safe, and the route of administration largely determines cell type specificity. This novel approach will enable in vivo studies of growth, differentiation, and malignant transformation in the oesophagus, and may open new avenues to the confinement of oesophageal malignancies.
A review of the effects of forage condensed tannins on ruminal fermentation and bloat in grazing cattle (2000)

Condensed tannins (CT) are polyphenolic secondary plant products that are widespread in the plant kingdom. By definition, CT bind to protein and are regarded as "antinutritional" compounds which reduce protein digestibility. Variations in CT chemistry alter protein binding capacities among polymers from different plant species and developmental stages. Condensed tannins interact with proteins in feed, saliva and microbial cells, with microbial exoenzymes, and with endogenous proteins or other feed components, which alters digestive processes as compared with diets free of CT. Tannin levels exceeding 40 to 50 g kg −1 DM in forages may reduce protein and DM digestibility of the forages by ruminants. At low to moderate levels, CT increase the quantity of dietary protein, especially essential amino acids, flowing to the small intestine. Unlike alfalfa, legumes that contain CT do not cause bloat. Dietary CT may provide a means to beneficially manipulate protein digestion and/or prevent pasture bloat in ruminants. Research efforts are also currently being directed to genetically modify alfalfa to de-repress its CT biosynthetic pathway, or to move genes encoding steps of this pathway into alfalfa from other legumes. The effects of CT in forage legumes on digestion in ruminants and the potential use of tannin-rich forages for preventing bloat in grazing systems are discussed. Key words: Tannins, bloat, by-pass protein, cattle, grazing, alfalfa
Elevated interleukin-12 in progressive multiple sclerosis correlates with disease activity and is normalized by pulse cyclophosphamide therapy. (1998)

Multiple sclerosis is postulated to be a Th1-type cell-mediated autoimmune disease. We investigated cytokine profiles in patients with progressive multiple sclerosis by using intracytoplasmic staining. We found increased IL-12 production by monocytes and increased IFN-gamma production by T cells in untreated patients as compared with controls. In patients treated with methotrexate, methylprednisolone, or cyclophosphamide/methylprednisolone (CY/MP), only CY/MP treatment normalized the elevated IL-12 production. Furthermore, CY/MP-treated patients had decreased IFN-gamma and increased IL-4, IL-5, and TGF-beta expression. Patients followed prospectively before and after starting CY/MP treatment showed a gradual decrease in IL-12 and IFN-gamma production and an increase in IL-4 and IL-5. In vitro, addition of 4-hydroperoxycyclophosphamide, a metabolite of cyclophosphamide decreased IL-12 production in mononuclear cell cultures. When patients were classified as having active or stable disease, IL-12 production correlated with disease activity. In summary, our results demonstrate a Th1-type cytokine bias in peripheral blood mononuclear cells of untreated progressive MS patients that is reversed by CY/MP treatment and is associated with Th2 and TGF-beta (Th3) type responses. These findings provide a basis for immune monitoring of patients with MS and suggest that treatments that downregulate IL-12 may prove to be beneficial in progressive MS.
Supersaturating infusional humanized anti-CD33 monoclonal antibody HuM195 in myelogenous leukemia. (1998)

Humanized anti-CD33 monoclonal antibody HuM195 specifically targets myeloid leukemias in vivo and has been shown to produce molecular remissions in patients with acute promyelocytic leukemia who are in clinical remission. Previous human trials have used low intermittent dosing of HuM195 at 3 mg/m2/day, which is adequate to saturate all available CD33 sites in vivo. In the current trial, we investigated supersaturating doses of HuM195. Ten patients with relapsed or refractory myelogenous leukemia (nine acute myelogenous leukemias and one chronic myelogenous leukemia) were treated on days 1-4 and 15-18 with a 4-h daily infusion of HuM195 at three different dose levels: 12, 24, and 36 mg/m2/day. The total maximum dose of HuM195 was 576 mg. The most common toxicities were grade II fever and rigors, seen more frequently at the highest dose. Interestingly, a transient and reversible drop in hemoglobin of 1-3 g/dl was seen during the infusion in several patients. Flow cytometric analysis showed that antigen sites in the peripheral blood and bone marrow (BM) remained saturated with HuM195 during the entire 4-week trial period. At these high doses, the average plasma half-life of HuM195 was approximately 1 week, compared to 38 h, seen in previous studies. Human anti-HuM195 immune responses were not observed. One patient with acute myelogenous leukemia, whose disease was refractory to two rounds of chemotherapy, with < 10% blasts in his BM, achieved a complete remission, lasting > 32 months, at the first dose level. Another three patients showed a reduction in leukemic BM cells. These studies suggest that high doses of HuM195 achieve a long serum half-life, with tolerable toxicity and without immunogenicity. In addition, antileukemic activity was seen.
Functional integration of DNA purification and concentration into a real time micro-PCR chip (2010)

Microfluidic devices for on-chip amplification of DNA from various biological and environmental samples have gained extensive attention over the past decades with many applications including molecular diagnostics of disease, food safety and biological warfare testing. But the integration of sample preparation functions into the chip remains a major hurdle for practical application of the chip-based diagnostic system. We present a PCR-based molecular diagnostic device comprised of a microfabricated chip and a centrifugal force assisted liquid handling tube (CLHT) that is designed to carry out concentration and purification of DNA and subsequent amplification of the target gene in a single chip. The reaction chamber of the chip contains an array of pillar structures to increase the surface area for capturing DNA from a raw sample of macro volume in the presence of kosmotropic agents. The CLHT was designed to provide an effective interface between sample preparation and the microfluidic PCR chip. We have characterized the effect of various fluidic parameters including DNA capture, amplification efficiency and centrifugal pressure generated upon varying sample volume. We also evaluated the performance of this system for quantitative detection of E. coli O157:H7. From the samples containing 10(1) to 10(4) cells per mL, the C(T) value linearly increased from 25.1 to 34.8 with an R(2) value greater than 0.98. With the effectiveness and simplicity of operation, this system will provide an effective interface between macro and micro systems and bridge chip-based molecular diagnosis with practical applications.
Bilateral removal of carotid bodies for asthma. (1965)

The removal of carotid bodies (glomectomy) for relief of asthma has been widely practised since Nakayama (1961) reported an improvement in 2,535 of 3,914 Japanese patients. Very variable results have been found. Improvement, for ex- ample, has been reported by Overholt (1963b) in 82/. of cases with asthma treated by unilateral removal, by Sedwitz (1963) in 822%, by Fletcher, Gaikwad, and In contrast, in the only controlled studies, O'Rourke and O'Rourke (1964) and Marschke, Beall, Stern, and Murray (1965) found that unilateral glomectomy was no better than a sham operation. Segal and Dulfano (1965) emphasized the difficulty of assessing results by describing the clinical details of 15 patients treated elsewhere. None was considered to have benefited, although seven had been reported to be improved in accounts published elsewhere.
Role of the H helix in heparin binding to protein C inhibitor. (1994)

Protein C inhibitor (PCI) is a plasma serine proteinase inhibitor (serpin) that is a major physiological regulator of activated protein C. Inhibition of its target proteinase is accelerated by heparin in a reaction that involves the binding of both inhibitor and proteinase to heparin to form a ternary complex. This study was undertaken to understand the role of the H helix region (residues 264-278) of PCI in heparin binding and used (i) a recombinant truncated PCI fusion protein of the first 294 residues, (ii) H helix synthetic peptides containing single Arg/Lys-->Glu substitutions, and (iii) site-directed Ala mutagenesis of 4 basic residues (Arg-269, Lys-270, Lys-276, and Lys-277) in the H helix region of full-length recombinant PCI (rPCI) expressed in Baculovirus. The PCI fusion protein interfered in heparin-accelerated PCI-proteinase inhibition reactions, and it bound to heparin-Sepharose. Compared to the wild-type PCI fusion protein, deletion of the H helix from the fusion protein resulted in a reduction of both heparin-Sepharose binding and the ability to compete for heparin during PCI-proteinase inhibition reactions. Competition assays with H helix synthetic peptides revealed that the R269E altered peptide was the least effective at blocking heparin-catalyzed PCI-proteinase inhibition reactions. Compared with full-length active wild-type rPCI, R269A: K270A and K276A:K277A rPCI both had reduced heparin-Sepharose binding, but only R269A:K270A rPCI showed a loss of heparin-accelerated proteinase inhibition for both activated protein C and thrombin. We conclude that a major heparin-binding site of PCI is the H helix, unlike its heparin-binding serpin homologues antithrombin and heparin cofactor II, which bind heparin primarily through the D helix.
Maintaining Integrity Constraints among Distributed Ontologies (2011)

The data of Semantic Web exist in machine readable format called RDF, in order to promote data exchange on the web based on their semantics. As an expressive knowledge representation language for the Semantic Web, Web Ontology Language (OWL) plays an important role in modeling information in a semantic way. However, due to the nature of knowledge bases, ontologies tend to be very large, distributed, and interconnected. Thus, maintaining constraints and enforcing data consistency for a group of ontologies become very challenging. In addition, frequent updates on ontologies necessitate an automatic approach to checking for potential constraint violations before any change takes place. In this study, we conducted a pioneer study and presented a framework for checking global constraints and ensuring integrity on data that span multiple ontologies. As an update is issued to a single site, global constraints that can be potentially violated are broken down into sub constraints that only involve a very small subset of ontologies. The checking of sub-constraints runs effectively in parallel and returns results about each subset. The collection of these results determines the violation of global constraints.
Activation of β-Catenin-Tcf Signaling in Colon Cancer by Mutations in β-Catenin or APC (1997)

Inactivation of the adenomatous polyposis coli (APC) tumor suppressor gene initiates colorectal neoplasia. One of the biochemical activities associated with the APC protein is down-regulation of transcriptional activation mediated by beta-catenin and T cell transcription factor 4 (Tcf-4). The protein products of mutant APC genes present in colorectal tumors were found to be defective in this activity. Furthermore, colorectal tumors with intact APC genes were found to contain activating mutations of beta-catenin that altered functionally significant phosphorylation sites. These results indicate that regulation of beta-catenin is critical to APC's tumor suppressive effect and that this regulation can be circumvented by mutations in either APC or beta-catenin.
The Operator and Early Promoter Region of the Shiga Toxin Type 2-Encoding Bacteriophage 933W and Control of Toxin Expression (2004)

The genes encoding Shiga toxin (Stx), the major virulence factor of Shiga toxin-producing Escherichia coli, are carried in the genomes of bacteriophages that belong to the lambdoid family of phages. Previous studies demonstrated that induction of prophages encoding stx significantly enhances the production and/or release of Stx from the bacterium. Therefore, factors that regulate the switch between lysogeny and lytic growth, e.g., repressor, operator sites, and associated phage promoters, play important roles in regulating the production and/or release of Stx. We report the results of genetic and biochemical studies characterizing these elements of the Stx-encoding bacteriophage 933W. Like lambda, 933W has three operator repeats in the right operator region (OR), but unlike lambda and all other studied lambdoid phages, which have three operator repeats in the left operator region (OL), 933W only has two operator repeats in OL. As was observed with lambda, the 933W OR and OL regions regulate transcription from the early PR and PL promoters, respectively. A lysogen carrying a 933W derivative encoding a noncleavable repressor fails to produce Stx, unlike a lysogen carrying a 933W derivative encoding a cleavable repressor. This finding provides direct evidence that measurable expression of the stx genes encoded by a 933W prophage requires induction of that prophage with the concomitant initiation of phage gene expression.
TRAF-4 expression in epithelial progenitor cells. Analysis in normal adult, fetal, and tumor tissues. (1998)

TRAF-4 was discovered because of its expression in breast cancers and is a member of the tumor necrosis factor (TNF) receptor-associated factor (TRAF) family of putative signal-transducing proteins. In vitro binding assays demonstrated that TRAF-4 interacts with the cytosolic domain of the lymphotoxin-beta receptor (LT beta R) and weakly with the p75 nerve growth factor receptor (NGFR) but not with TNFR1, TNFR2, Fas, or CD40. Immunofluorescence analysis of TRAF-4 in transfected cells demonstrated localization to cytosol but not nucleus. Immunohistochemical assays of normal human adult tissues revealed prominent cytosolic immunostaining in thymic epithelial cells and lymph node dendritic cells but not in lymphocytes or thymocytes, paralleling the reported patterns of LT beta R expression. The basal cell layer of most epithelia in the body was very strongly TRAF-4 immunopositive, including epidermis, nasopharynx, respiratory tract, salivary gland, and esophagus. Similar findings were obtained in 12- to 18-week human fetal tissue, indicating a highly restricted pattern of expression even during development in the mammary gland, epithelial cells of the terminal ducts were strongly TRAF-4 immunopositive whereas myoepithelial cells and most of the mammary epithelial cells lining the extralobular ducts were TRAF-4 immunonegative. Of 84 primary breast cancers evaluated, only 7 expressed TRAF-4. Ductal carcinoma in situ (DCIS) lesions were uniformly TRAF-4 immunonegative (n = 21). In the prostate, the basal cells were strongly immunostained for TRAF-4, whereas the secretory epithelial cells were TRAF-4 negative. Basal cells in prostate hypertrophy (n = 6) and prostatic intraepithelial neoplasia (PIN; n = 6) were strongly TRAF-4 positive, but none of the 32 primary and 16 metastatic prostate cancer specimens examined contained TRAF-4-positive malignant cells. Although also expressed in some types of mesenchymal cells, these findings suggest that TRAF-4 is a marker of normal epithelial stem cells, the expression of which often ceases on differentiation and malignant transformation.
Molecular cloning of a Neurospora crassa carotenoid biosynthetic gene (albino-3) regulated by blue light and the products of the white collar genes. (1989)

The albino-3 (al-3) gene of Neurospora crassa, which probably encodes the carotenoid biosynthetic enzyme geranylgeranyl pyrophosphate synthetase, was cloned. The N. crassa triple mutant al-3 qa-2 aro-9 was transformed to qa-2+ with mixtures of plasmids bearing N. crassa DNA inserts, and the transformants were screened for the al-3+ phenotype. One al-3+ qa-2+ transformant (AL3-1) was examined in detail and shown to contain intact vector sequences integrated into the N. crassa genome. The vector and some flanking sequences were recovered from AL3-1 after restriction, ligation, and selection of chloramphenicol-resistant transformants of Escherichia coli. The flanking sequences were subsequently used to detect the al-3-containing plasmid in the mixture of about 1,800 plasmids. Restriction fragment length polymorphism mapping was carried out to confirm the identity of the cloned fragment. The level of the al-3 mRNA was shown to be increased 15-fold in light-induced (compared with that in dark-grown) wild-type mycelia. The light-dependent increase in al-3 mRNA levels was not observed in presumed regulatory mutant (white collar) strains.