gebhart/patrepeval huggingface dataset:
Cloning, analysis, and expression of murine perforin 1 cDNA, a component of cytolytic T-cell granules with homology to complement component C9. (1989)

The nucleotide sequence coding for the cytotoxic T-lymphocyte (CTL) protein perforin 1 (P1) has been determined and the corresponding protein sequence has been derived. Murine CTL cDNA libraries contained in the vector lambda gt11 were screened by using a monospecific antiserum to purified P1. Three recombinant phages were isolated and their cDNA inserts were sequenced. The derived protein sequence contains 554 amino acids and displays, as expected, considerable homology with certain functional domains in the complement components C9, C8 alpha, C8 beta, and C7. The identity of P1 cDNA clones was verified by prokaryotic expression and the reactivities of antisera produced to the expressed proteins. In addition, antisera were produced to two synthetic peptides located in the center and C-terminal portions of P1. All antisera reacted with purified P1. In Northern blot analyses, P1 cDNA probes recognized a 2.9-kilobase mRNA only in CTL. Perforin mRNA was found in all cloned CTL and in all mixed lymphocyte reactions that gave rise to cytotoxic cells. Perforin mRNA was also detected in virus-specific CTL that had been generated in vivo and isolated from liver tissue of mice infected with lymphocytic choriomeningitis virus. The cell-specific expression of perforin is consistent with its postulated role in cytolysis.
Efficient and Progressive Algorithms for Distributed Skyline Queries over Uncertain Data (2011)

The skyline operator has received considerable attention from the database community, due to its importance in many applications including multicriteria decision making, preference answering, and so forth. In many applications where uncertain data are inherently exist, i.e., data collected from different sources in distributed locations are usually with imprecise measurements, and thus exhibit kind of uncertainty. Taking into account the network delay and economic cost associated with sharing and communicating large amounts of distributed data over an internet, an important problem in this scenario is to retrieve the global skyline tuples from all the distributed local sites with minimum communication cost. Based on the well-known notation of the probabilistic skyline query over centralized uncertain data, in this paper, we propose the notation of distributed skyline queries over uncertain data. Furthermore, two communication- and computation-efficient algorithms are proposed to retrieve the qualified skylines from distributed local sites. Extensive experiments have been conducted to verify the efficiency, the effectiveness and the progressiveness of our algorithms with both the synthetic and real data sets.
Effects of Changes in Central Venous Pressure on Upper Airway Size in Patients With Obstructive Sleep Apnea (1996)

Intraluminal airway pressure and pharyngeal muscle activity are widely recognized as major determinants of the size and collapsibility of the upper airway. In addition, changes in the volume or pressure of tissue surrounding the pharyngeal airway may significantly influence its size. The present study used fast computed tomography (CT) to determine the effects of changes in central venous pressure (CVP) on upper airway size. Ten awake male patients with obstructive sleep apnea (OSA) were studied. Scans were performed at functional residual capacity (FRC) and at the end of a tidal inspiration (VTei) under three conditions of CVP: (1) at baseline (CVP nl) with patients lying supine; (2) at decreased CVP (CVP-) by inflating blood pressure cuffs to 40 mm Hg on both legs; and (3) at increased CVP (CVP+) by elevating both legs to 33 degrees. At FRC, changes in CVP had no significant effect on either mean or minimum cross-sectional area (CSA) of the upper airway. In contrast, an analysis of variance (ANOVA) indicated that alterations in CVP were associated with changes in mean CSA (p = 0.03) and to a lesser extent in minimum CSA (p = 0.07) at VTei. With the legs elevated (CVP+), neither mean nor minimum CSA showed any significant change with tidal breathing. However, after leg-cuff inflation (CVP-), highly significant increases in both mean (163 +/- 22 to 218 +/- 19 mm2, p = 0.001) and minimum (48 +/- 8 to 85 +/- 12 mm2, p = 0.02) CSA were detected. Changes in mean and minimum CSA with tidal breathing at baseline (CVP nl) were intermediate. These results indicate that changes in CVP significantly alter the response of the upper airway to tidal breathing. They further suggest that increases in upper airway size with tidal breathing may be related to reduction in venous blood volume in pharyngeal and neck tissues as the generation of negative intrathoracic pressure during inspiration increases venous return to the chest.
Attention-deficit hyperactivity disorder (ADHD) stimulant medications as cognitive enhancers (2013)

Recent increases in attention deficit hyperactivity disorder (ADHD) diagnoses, and the escalation of stimulant prescriptions, has raised concern about diversion and abuse of stimulants, as well as the ethics of using these drugs as "cognitive enhancers."Such concern appears misplaced in the face of substantial evidence that stimulant drugs do not improve the academic performance of ADHD-diagnosed students. Moreover, numerous studies have found little or no benefit of stimulants on neuropsychological tests of ADHD-diagnosed as well as normal, individuals. This paper examines the apparent paradox: why don't drugs that improve "attention," produce better academic outcomes in ADHD-diagnosed students? We found that stimulant drugs significantly improved impairment of episodic memory in ADHD-diagnosed undergraduate students. Nevertheless, we also found consistent academic deficits between ADHD students and their non-ADHD counterparts, regardless of whether or not they used stimulant medications. We reviewed the current literature on the behavioral effects of stimulants, to try to find an explanation for these conflicting phenomena. Across a variety of behavioral tasks, stimulants have been shown to reduce emotional reactions to frustration, improve the ability to detect errors, and increase effortful behavior. However, all of these effects would presumably enhance academic performance. On the other hand, the drugs were also found to promote "risky behavior" and to increase susceptibility to environmental distraction. Such negative effects, including the use of drugs to promote wakefulness for last minute study, might explain the lack of academic benefit in the "real world," despite their cognitive potential. Like many drugs, stimulants influence behavior in multiple ways, depending on the environmental contingencies. Depending on the circumstances, stimulants may, or may not, enhance cognition.
Correlates Between Host and Viral Transcriptional Program Associated with Different Oncolytic Vaccinia Virus Isolates (2012)

Vaccinia virus (VACV) has emerged as an attractive tool in oncolytic virotherapy. VACV replication efficiency plays a crucial role in the therapeutic outcome. However, little is known about the influence of host factors on viral replication efficiency and permissiveness of a host cell line to infection and oncolysis. In this study, replication of the attenuated VACV GLV-1h68 strain and three wild-type VACV isolates was determined in two autologous human melanoma cell lines (888-MEL and 1936-MEL). Host gene expression and viral gene expression in infected cells were evaluated via respective expression array platforms. Microarray analyses followed by sequential statistical approaches characterized human genes that change specifically due to virus infection. Viral gene transcription correlated with viral replication in a time-dependent manner. A set of human genes revealed strong correlations with the respective viral gene expression. Finally we identified a set of human genes with possible predictive value for viral replication in an independent dataset. The results demonstrate a probable correlation between viral replication, early gene expression, and the respective host response, and thus a possible involvement of human host factors in viral early replication. The characterization of human target genes that influence viral replication could help answer the question of host cell permissiveness to oncolytic virotherapy and provide important information for the development of novel recombinant vaccinia viruses with improved features to enhance replication rate and hence trigger therapeutic outcome. Reinboth and colleagues use a whole genome human array and a custom-made vaccinia virus (VACV) array to simultaneously analyze viral and host gene expression. Using this approach they identify a set of human genes that may influence viral replication and help to answer questions pertaining to host cell permissiveness during oncolytic virotherapy.
Visceral manifestations in hereditary haemorrhagic telangiectasia type 2 (2003)

Hereditary haemorrhagic telangiectasia (HHT) is a genetic vascular disorder characterised by epistaxis, telangiectases, and visceral manifestations. The two known disease types, HHT1 and HHT2, are caused by mutations in the endoglin (ENG) and ALK-1 genes, respectively. A higher frequency of pulmonary arteriovenous malformations (AVMs) has been reported for HHT1 while HHT2 is thought to be associated with a lower penetrance and milder disease manifestations. In this study, we present 10 families with an ALK-1 genotype. Visceral manifestations were detected in 24 (26%) of the 93 HHT2 patients from nine of the families and included gastrointestinal bleeding (14%), intrahepatic shunts (6%), and AVMs in the lung (4%) and brain (3%). Gastrointestinal bleeding, the most frequent visceral manifestation, was reported in six of the 10 families, mostly in patients over the age of 50. These patients also had frequent epistaxis and suffered from anaemia, often requiring blood transfusions. The identification of ALK-1 mutations in subjects with a suspected diagnosis and without clinical signs of HHT argue in favour of a molecular diagnosis. We also analysed the data published on 44 families with HHT2 and conclude that visceral manifestations occur in 26 of these families and affect 30% of HHT2 patients. This is considered an underestimate given incomplete and variable screening for lung, brain, and/or liver involvement in different clinical centres. These findings, however, stress the need for an early diagnosis of HHT that can be useful for the early control of associated visceral involvement.
Genetic influence on neurogenesis in the dentate gyrus of adult mice (1997)

To address genetic influences on hippocampal neurogenesis in adult mice, we compared C57BL/6, BALB/c, CD1(ICR), and 129Sv/J mice to examine proliferation, survival, and differentiation of newborn cells in the dentate gyrus. Proliferation was highest in C57BL/6; the survival rate of newborn cells was highest in CD1. In all strains approximately 60% of surviving newborn cells had a neuronal phenotype, but 129/SvJ produced more astrocytes. Over 6 days C57BL/6 produced 0.36% of their total granule cell number of 239,000 as new neurons, BALB/c 0.30% of 242,000, CD1 (ICR) 0.32% of 351,000, and 129/SvJ 0.16% of 280,000. These results show that different aspects of adult hippocampal neurogenesis are differentially influenced by the genetic background.
PATHWAYS OF PROTEIN FOLDING (1993)

Advances in spectroscopy, protein engineering, and peptide synthesis have had a dramatic impact on the understanding of the structures and stabilities of transient folding intermediates. The data available from a variety of proteins point to the existence of three common stages of folding. 1. Initially, the unfolded protein collapses to a presumably more compact form containing substantial nonpolar surfaces and secondary structure. This species has little thermodynamic stability and encompasses an ensemble of conformations that are in dynamic equilibrium and may contain non-native elements of structure. This reaction occurs in less than 5 ms and, from a thermodynamic perspective, may be a noncooperative transition. The relatively high content of secondary structure implies that this manifold of states must be far smaller than the manifold for the unfolded protein. 2. The next phase involves the further development of secondary and the beginnings of specific tertiary structure throughout the protein as well as of measurable stability. Nativelike elements of structure appear, possibly in the form of subdomains that are yet to be properly docked. In many instances, the packing is not as tight as is ultimately found in the native conformation, suggesting that the side chains are in general more mobile. Some elements of surface structure, such as loops and the peripheries of sheets and helices, are not yet well defined. This stage, which may consist of more than a single kinetic step, occurs in the 5-1000 ms time range. The ensemble of conformations is much reduced from the first stage; however, it is far from a single, highly populated form. 3. The final stage in folding corresponds to the concerted formation of many noncovalent interactions throughout the protein. The solidlike interior packing is achieved; the final secondary structure forms and the surface structures settle into place. The breadth of these conformational changes reflects the global cooperativity characteristic of protein folding reactions. A pictorial representation of the kinetic and thermodynamic aspects of this process is shown in Figure 1. This folding scheme emphasizes the progressive development of structure and stability through an ever-slowing set of reactions. Because the product of each stage of folding, with the exception of the final step, is an ensemble of related but not identical species, it is an oversimplification to describe the process as a pathway. Perhaps it is better described as a series of transitions between manifolds of structures that are in dynamic equilibrium within any given set.(ABSTRACT TRUNCATED AT 400 WORDS)
Ontology-based Device Descriptions and triple store based device repository for automation devices (2010)

Device descriptions play an important role in the design and commissioning of modern automation systems and help reducing the design time and costs. However, all established device descriptions are specialized for certain purposes and suffer from several weaknesses. This hinders a further design automation, which is strongly needed for the more and more complex automation systems. To overcome these problems, this paper presents novel Ontology-based Device Descriptions (ODDs) along with a layered ontology architecture and triple store based database backend. It enables a formal, unified and extensible specification of devices, ensures their comparability and facilitates a computer enabled retrieval, selection and interoperability evaluation. The scalability of the approach to several ten thousand devices is demonstrated.
Hypomorphic sialidase expression decreases serum cholesterol by downregulation of VLDL production in mice (2012)

Lipoprotein metabolism is an important contributing factor in the development and progression of atherosclerosis. Plasma lipoproteins and their receptors are heavily glycosylated and sialylated, and levels of sialic acids modulate their biological functions. Sialylation is controlled by the activities of sialyltranferases and sialidases. To address the impact of sialidase (neu1) activity on lipoprotein metabolism, we have generated a mouse model with a hypomorphic neu1 allele (B6.SM) that displays reduced sialidase expression and sialidase activity. The objectives of this study are to determine the impact of sialidase on the rate of hepatic lipoprotein secretion and lipoprotein uptake. Our results indicate that hepatic levels of cholesterol and triglycerides are significantly higher in B6.SM mice compared with C57Bl/6 mice; however, VLDL-triglyceride production rate is lower. In addition, B6.SM mice show significantly lower levels of hepatic microsomal triglyceride transfer protein (MTP) and active sterol-regulatory element binding protein (SREBP)-2 but higher levels of diglyceride acyltransferase (DGAT)2; these are all indicative of increased hepatic lipid storage. Rescue of sialidase activity in hypomorphic sialidase mice using helper-dependent adenovirus resulted in increased VLDL production and an increase in MTP levels. Furthermore, hypomorphic sialidase expression results in stabilization of hepatic LDL receptor (LDLR) protein expression, which enhances LDL uptake. These findings provide novel evidence for a central role of sialidase in the cross talk between the uptake and production of lipoproteins.
Phase I immunotherapy with a modified vaccinia virus (MVA) expressing human MUC1 as antigen‐specific immunotherapy in patients with MUC1‐positive advanced cancer (2003)

The administration of TG4010 was generally well tolerated in patients with metastatic tumors, and transient disease stabilization was observed in several patients, warranting further clinical studies with the product.
Syndecan-1 Transmembrane and Extracellular Domains Have Unique and Distinct Roles in Cell Spreading (2003)

Raji cells expressing syndecan-1 (Raji-S1) adhere and spread when plated on heparan sulfate-binding extracellular matrix ligands or monoclonal antibody 281.2, an antibody directed against the syndecan-1 extracellular domain. Cells plated on monoclonal antibody 281.2 initially extend a broad lamellipodium, a response accompanied by membrane ruffling at the cell margin. Membrane ruffling then becomes polarized, leading to an elongated cell morphology. Previous work demonstrated that the syndecan-1 cytoplasmic domain is not required for these activities, suggesting important roles for the syndecan-1 transmembrane and/or extracellular domains in the assembly of a signaling complex necessary for spreading. Work described here demonstrates that truncation of the syndecan-1 extracellular domain does not affect the initial lamellipodial extension in the Raji-S1 cells but does inhibit the active membrane ruffling that is necessary for cell polarization. Replacement of the entire syndecan-1 transmembrane domain with leucine residues completely blocks the cell spreading. These data demonstrate that the syndecan-1 transmembrane and extracellular domains have important but distinct roles in Raji-S1 cell spreading; the extracellular domain mediates an interaction that is necessary for dynamic cytoskeletal rearrangements whereas an interaction of the transmembrane domain is required for the initial spreading response.
Development of Formulations ofPseudomonas fluorescensfor Control of Chickpea Wilt (1995)

Pseudomonas fluorescens strains were obtained from the rhizosphere of different crops and strains that showed inhibitory action against the chickpea (Cicer arietinum) wilt pathogen Fusarium oxysporum f. sp. ciceris were selected for further studies. The efficacy of various carriers in sustaining the population of these strains in storage was assessed. In talc-based and peat-based formulations the bacteria survived even up to 240 days of storage although the population declined from 30 days. When chickpea seeds were treated with talc-based formulations, P. fluorescens survived on the seeds for at least 180 days. When the treated seeds were sown in soil, the antagonist moved to the rhizosphere and survived well in it. Biopriming of seeds increased rhizosphere population. Seed treatment with the antagonist formulation effectively controlled chickpea wilt disease in the two field trials and increased the yield. When seed treatment was followed by root zone application the efficacy of P. fluorescens formulations increased. Pseudomonas fluorescens did not inhibit the beneficial N-fixing bacteria Rhizobium and Azospirillum in vitro and seed treatment fungicides (thiram and carbendazim) were not inhibitory to P. fluorescens in vitro.
Postcolumn Derivatization Liquid Chromatographic Method for Paralytic Shellfish Toxins (1995)

Abstract More than 20 analogues of saxitoxin occur naturally. An accurate analytical method applicable to all saxitoxins is required because of the recent findings that decarbamoyl toxins and C (N-sulfocarbamoyl- 11-hydroxysulfate) toxins are metabolites of marine animals or major products of some dinoflagellate species. Almost all the toxins could be determined by ion-interaction chromatography on a silica-based reversed-phase (C8) column with postcolumn periodate oxidation and fluorescence detection. Toxin groups of different net charges were separately determined by isocratic elution using different mobile phases. For determination of the saxitoxin group (net charge, 2+) and the gonyautoxin group (net charge, 1+), use of 1-heptanesulfonate as counterion, with or without acetonitrile in the mobile phase, resulted in resolution of decarbamoyl toxins from their carbamate analogues. C toxins having both M-sulfocarbamoyl and 11-hydroxysulfate moieties on the same molecule were completely resolved using the tetrabutylammonium ion. High sensitivity with detection limits ranging from 20 to 110 fmol were achieved as a result of reduced band broadening and optimized reaction conditions. For applications to biological matrixes, a cleanup procedure using a C18 solid-phase extraction cartridge was effective in preventing false peaks. When applied to low-toxicity shellfish, the liquid chromatographic method gave higher values than the standard mouse bioassay, because of underestimation by the bioassay.
Peritubular cells are the site of erythropoietin synthesis in the murine hypoxic kidney. (1988)

Erythropoietin (Epo)-producing cells were identified in the murine hypoxic kidney by in situ hybridization. Profound anemia was induced in order to greatly increase Epo production. This resulted in high levels of Epo mRNA in the kidney. 35S-labeled DNA fragments of the murine Epo gene were used as probes for in situ hybridization. Control experiments conducted in parallel included kidneys of nonanemic mice, RNase-treated hypoxic kidney sections, and 35S-labeled non-Epo-related DNA. The Epo probe gave a specific hybridization signal in the hypoxic kidney in the cortex and to a lesser extent in the outer medulla. Glomerular and tubular cells were not labeled. All positive cells were identified as peritubular cells. Using immunofluorescence, we showed that cells with the same topography contained Factor VIII-related antigen. These data demonstrated that peritubular cells, most likely endothelial cells, constitute the major site of Epo production in the murine hypoxic kidney.
Electrostatic stabilization of fluid microstructures (2002)

A liquid surface of arbitrary shape is, in general, dynamically unstable due to gradients in Laplace pressure. This greatly limits the class of morphologies eligible for artificial fluid microstructures. In this work, we demonstrate that a wide class of these otherwise unstable surface morphologies can be stabilized using electrostatic fields. Complex stable fluid microstructures were generated in a conventional electrowetting setup operated at high voltage. We present an electrostatic model that explains the stability and the scale of the stable structures as a function of external control parameters. The stability as well as the universality of these structures naturally leads to novel concepts in microfluidic technology.