gebhart/patrepeval huggingface dataset:
Activation of the contact system of plasma proteolysis in the adult respiratory distress syndrome. (1988)

Adult respiratory distress syndrome (ARDS) is a complex pulmonary clinicopathologic condition associated with pulmonary endothelial injury and blood coagulation activation. In patients with ARDS from all causes, factor VII levels were significantly reduced. Patients with ARDS caused by sepsis had more evidence of intravascular coagulation and fibrinolysis than did patients with trauma-related ARDS by having significantly (p less than or equal to 0.05) increased prothrombin times, activated partial thromboplastin times, and fibrin degradation products, and decreased antithrombin III concentration. We sought to determine whether the proteins of the contact system of plasma proteolysis (factor XII, prekallikrein, high molecular weight kininogen, and C1 inhibitor) were also activated after acute lung injury. Patients with ARDS caused by either trauma or sepsis had significantly (p less than or equal to 0.01) reduced factor XII levels, high molecular weight kininogen functional activity, prekallikrein activity, and prekallikrein antigen levels compared with controls. In both the sepsis-related and trauma-related ARDS groups, C1 inhibitor activity was significantly reduced but C1 inhibitor antigen levels were significantly elevated from control. These findings showed that the proteins of the contact system were more extensively activated in ARDS than were the proteins that contribute to later reactions in intravascular coagulation and fibrinolysis. Activation of the contact system proteins could be the result of endothelial injury occurring as part of ARDS. Intravascular coagulation and fibrinolysis in patients with ARDS also arise from components independent from contact system activation.
Hepatic Gene Expression Profiles Differentiate Presymptomatic Patients With Mild Versus Severe Nonalcoholic Fatty Liver Disease (2013)

By demonstrating specific metabolic and repair pathways that are differentially activated in livers with severe NAFLD, gene profiling identified novel targets that can be exploited to improve diagnosis and treatment of patients who are at greatest risk for NAFLD-related morbidity and mortality.
Multilevel Graph Partitioning Schemes. (1995)

Abstract – In this paper we present experiments with a class of graph partitioning algorithms that reduce the size of the graph by collapsing vertices and edges, partition the smaller graph, and then uncoarsen it to construct a partition for the original graph. We investigate the effectiveness of many different choices for all three phases: coarsening, partition of the coarsest graph, and refinement. In particular, we present a new coarsening heuristic (called heavy-edge heuristic) for which the size of the partition of the coarse graph is within a small factor of the size of the final partition obtained after multilevel refinement. We also present a new scheme for refining during uncoarsening that is much faster than the Kernighan-Lin refinement. We test our scheme on a large number of graphs arising in various domains including finite element methods, linear programming, VLSI, and transportation. Our experiments show that our scheme consistently produces partitions that are better than those produced by spectral partitioning schemes in substantially smaller timer (10 to 35 times faster than multilevel spectral bisection). Also, when our scheme is used to compute fill reducing orderings for sparse matrices, it substantially outperforms the widely used multiple minimum degree algorithm. 1
Calcium-dependent phospholipid- (and membrane-) binding proteins (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCalcium-dependent phospholipid- (and membrane-) binding proteinsClaude B. KleeCite this: Biochemistry 1988, 27, 18, 6645–6653Publication Date (Print):September 6, 1988Publication History Published online1 May 2002Published inissue 6 September 1988https://doi.org/10.1021/bi00418a001RIGHTS & PERMISSIONSArticle Views244Altmetric-Citations285LEARN 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 InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
In vitro assay for neutralizing antibody to hepatitis C virus: Evidence for broadly conserved neutralization epitopes (2003)

Our understanding of the humoral immune response to hepatitis C virus (HCV) is limited because the virus can be studied only in humans and chimpanzees and because previously described neutralization assays have not been robust or simple to perform. Nevertheless, epidemiologic and laboratory studies suggested that neutralizing Ab to HCV might be important in preventing infection. We have recently described a neutralization assay based on the neutralization of pseudotyped murine retrovirus constructs bearing HCV envelope glycoproteins on their surface. We have applied the assay to well characterized clinical samples from HCV-infected patients and chimpanzees, confirmed the existence of neutralizing Ab to HCV, and validated most previously reported neutralizations of the virus. We did not find neutralizing anti-HCV in resolving infections but did find relatively high titers (>1:320) of such Ab in chronic infections. Neutralizing Ab was directed not only to epitope(s) in the hypervariable region of the E2 envelope protein but also to one or more epitopes elsewhere in the envelope of the virus. Neutralizing Ab was broadly reactive and could neutralize pseudotype particles bearing the envelope glycoproteins of two different subgenotypes (1a and 1b). The ability to assay neutralizing anti-HCV should permit an assessment of the prospects for successful Ab-mediated passive and active immunoprophylaxis against hepatitis C.
STUDIES IN THE POLYOXYPHENOL SERIES: VIII. THE OXIDATION OF SUBSTANCES RELATED TO VANILLIN WITH SODIUM CHLORITE AND CHLORINE DIOXIDE (1955)

The research confirmed the fact that chlorine dioxide and sodium chlorite were not equivalent in their oxidizing properties. At 22 °C. or less, the oxidation of pyrogallol by aqueous sodium chlorite at pH 6 was very slow, but became very rapid on the acid side of pH 3.5. The amorphous, colored products probably did not include purpurogallin. Under similar circumstances p-hydroxybenzaldehyde was unaffected at pH 6; 22% was oxidized to p-benzoquinone (Dakin's reaction) at pH 5, and this amount increased to 39% at pH 1. The yield of benzoquinone was about 24% regardless of pH within the above range when aqueous chlorine dioxide was the oxidant. Sodium chlorite at pH 0.9 produced a 91% yield of methoxy-p-quinone from methoxy-p-hydroquinone; at pH 4 this product was mixed with 56% of 4,4′-dimethoxydiquinone, but near pH 6 a slower oxidation did not proceed beyond 4,4′-dimethoxyquinhydrone. Aqueous chlorine dioxide yielded at least 92% of monomeric methoxyquinone at all pH values between 1 and 6, probably in accord with the equation,[Formula: see text] The simultaneous formation of hydrogen peroxide was suspected, but not proved. In sharp distinction to the behavior of free phenols, veratraldehyde was not oxidized by aqueous chlorine dioxide between pH 6 and pH 3, but at pH 1 a slow reaction yielded up to 15% of veratric acid. Sodium chlorite produced about 92% of the same acid at pH 1 and pH 4, but its action was negligible at pH 5. Since by-product chlorine dioxide was ineffective at pH 4, it was possible to confirm the validity of the Jeanes–Isbell equation for the reduction of chlorous acid:[Formula: see text]The oxidation of acetylated vanillin was complicated by the occurrence of deacetylation. Red, chlorinated oils with quinoidal properties were also formed in most of the above oxidations.
Defective Interleukin (IL)-18–mediated Natural Killer and T Helper Cell Type 1 Responses in IL-1 Receptor–associated Kinase (IRAK)-deficient Mice (1999)

Interleukin (IL)-18 is functionally similar to IL-12 in mediating T helper cell type 1 (Th1) response and natural killer (NK) cell activity but is related to IL-1 in protein structure and signaling, including recruitment of IL-1 receptor-associated kinase (IRAK) to the receptor and activation of c-Jun NH2-terminal kinase (JNK) and nuclear factor (NF)-kappaB. The role of IRAK in IL-18-induced responses was studied in IRAK-deficient mice. Significant defects in JNK induction and partial impairment in NF-kappaB activation were found in IRAK-deficient Th1 cells, resulting in a dramatic decrease in interferon (IFN)-gamma mRNA expression. In vivo Th1 response to Propionibacterium acnes and lipopolysaccharide in IFN-gamma production and induction of NK cytotoxicity by IL-18 were severely impaired in IRAK-deficient mice. IFN-gamma production by activated NK cells in an acute murine cytomegalovirus infection was significantly reduced despite normal induction of NK cytotoxicity. These results demonstrate that IRAK plays an important role in IL-18-induced signaling and function.
Reversal by Vasopressin of Intractable Hypotension in the Late Phase of Hemorrhagic Shock (1999)

Vasopressin is a uniquely effective pressor in the irreversible phase of hemorrhagic shock unresponsive to volume replacement and catecholamine vasopressors. Vasopressin deficiency may contribute to the pathogenesis of this condition.
Inhibitors of Histone Deacetylase as New Anticancer Agents (2001)

Inhibitors of histone deacetylase (HDAC) are an emerging class of anticancer agents. They induce hyperacetylation in chromatin usually resulting in activation of certain genes. They induce terminal cell differentiation and/or apoptosis in cancer cells. Histone deacetylase activity is recruited by co-repressor proteins to certain regions of the chromatin and aberrant histone acetylation caused by that recruitment is responsible for the pathogenesis of certain cancers on a molecular level. Inhibitors of HDAC have been identified in natural sources and also synthetic inhibitors are available. The best studied inhibitor is trichostatin A, a hydroxamic acid that exerts its activity by complexation of a zinc ion that is supposed to mediate the acetamide cleavage at the catalytic site. There are several synthetic hydroxamic acids that bear resemblance to trichostatin. Another class of potent inhibitors are naturally occurring and synthetic cyclotetrapeptides that all contain an unusual amino acid with an epoxyketone, ketone or hydroxamic acid function in the side chain. Phenylacetate, phenylbutyrate, butyrate and similar short chain fatty acids are also weak inhibitors. Further inhibitors from natural sources are the epoxide depudecin and depsipeptide FR 901228. The benzamide MS-275 belongs to a new class of synthetic HDAC inhibitors and displays oral activity in animal models. First clinical studies have shown that histone hyperacetylation can be achieved safely in humans and that treatment of cancer is possible. Thus, inhibitors of HDAC are one of the most promising class of new anticancer agents. New screening assays are useful tools that will facilitate identification of further inhibitors.
Symmetry Breakdown in the ON and OFF Pathways of the Retina at Night: Functional Implications (2010)

Several recent studies have shown that the ON and OFF channels of the visual system are not simple mirror images of each other, that their response characteristics are asymmetric (Chichilnisky and Kalmar, 2002; Sagdullaev and McCall, 2005). How the asymmetries bear on visual processing is not well understood. Here, we show that ON and OFF ganglion cells show a strong asymmetry in their temporal adaptation to photopic (day) and scotopic (night) conditions and that the asymmetry confers a functional advantage. Under photopic conditions, the ON and OFF ganglion cells show similar temporal characteristics. Under scotopic conditions, the two cell classes diverge-ON cells shift their tuning to low temporal frequencies, whereas OFF cells continue to respond to high. This difference in processing corresponds to an asymmetry in the natural world, one produced by the Poisson nature of photon capture and persists over a broad range of light levels. This work characterizes a previously unknown divergence in the ON and OFF pathways and its utility to visual processing. Furthermore, the results have implications for downstream circuitry and thus offer new constraints for models of downstream processing, since ganglion cells serve as building blocks for circuits in higher brain areas. For example, if simple cells in visual cortex rely on complementary interactions between the two pathways, such as push-pull interactions (Alonso et al., 2001; Hirsch, 2003), their receptive fields may be radically different under scotopic conditions, when the ON and OFF pathways are out of sync.
BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods (2017)

The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world. In this work, we introduce a framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). The portability of these applications (BIDS Apps) is achieved by using container technologies that encapsulate all binary and other dependencies in one convenient package. BIDS Apps run on all three major operating systems with no need for complex setup and configuration and thanks to the comprehensiveness of the BIDS standard they require little manual user input. Previous containerized data processing solutions were limited to single user environments and not compatible with most multi-tenant High Performance Computing systems. BIDS Apps overcome this limitation by taking advantage of the Singularity container technology. As a proof of concept, this work is accompanied by 22 ready to use BIDS Apps, packaging a diverse set of commonly used neuroimaging algorithms.
Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain (2016)

The human brain has enormously complex cellular diversity and connectivities fundamental to our neural functions, yet difficulties in interrogating individual neurons has impeded understanding of the underlying transcriptional landscape. We developed a scalable approach to sequence and quantify RNA molecules in isolated neuronal nuclei from a postmortem brain, generating 3227 sets of single-neuron data from six distinct regions of the cerebral cortex. Using an iterative clustering and classification approach, we identified 16 neuronal subtypes that were further annotated on the basis of known markers and cortical cytoarchitecture. These data demonstrate a robust and scalable method for identifying and categorizing single nuclear transcriptomes, revealing shared genes sufficient to distinguish previously unknown and orthologous neuronal subtypes as well as regional identity and transcriptomic heterogeneity within the human brain.
Integrin α2β1-independent activation of platelets by simple collagen-like peptides: collagen tertiary (triple-helical) and quaternary (polymeric) structures are sufficient alone for α2β1-independent platelet reactivity (1995)

The platelet reactivities of two simple collagen-like synthetic peptides, Gly-Lys-Hyp-(Gly-Pro-Hyp)10-Gly-Lys-Hyp-Gly and Gly-Cys-Hyp-(Gly-Pro-Hyp)10-Gly-Cys-Hyp-Gly, were investigated. Both peptides adopted a stable triple-helical conformation in solution. Following cross-linking, both peptides proved to be highly platelet-aggregatory, more active than collagen fibres, inducing aggregation at concentrations as low as 20 ng/ml. These peptides formed microaggregates in solution, and cross-linking was thought to stabilize these structures, allowing expression of their platelet reactivity at 37 degrees C. Like collagen fibres, the peptides caused platelet secretion and release of arachidonate from platelet membrane lipids as well as activation of integrin alpha IIb beta 3 culminating in aggregation. Monoclonal antibodies directed against the integrin alpha 2 beta 1 failed to prevent aggregation release of arachidonate or platelet adhesion to the peptides. Our results indicate that collagen can activate platelets by a mechanism that is independent of integrin alpha 2 beta 1 and for which collagen tertiary and quaternary structures are sufficient alone for activity without the involvement of highly specific cell-recognition sequences.
Cellular internalization and targeting of semiconductor quantum dots (2005)

Peptide-mediated internalization and organelle targeting of quantum dots.
Signal space detectors for MTR-coded magnetic recording channels (1998)

In this paper, we present signal space detectors for use with maximum transition run (MTR) codes. A three-dimensional signal space detector Is first derived for an MTR=2 coded channel. The bit error rate performance of this detector is close to MTR-coded FDTS/DF(2) throughout the user density range of interest. The detector is then modified to be used with a time-variant MTR code. Simulation as well as experimental results are presented.
Syntheses of 2'-deoxypseudouridine, 2'-deoxyformycin B, and 2',3'-dideoxyformycin B by palladium-mediated glycal-aglycon coupling (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSyntheses of 2'-deoxypseudouridine, 2'-deoxyformycin B, and 2',3'-dideoxyformycin B by palladium-mediated glycal-aglycon couplingHan Cheng Zhang and G. Doyle Daves Jr.Cite this: J. Org. Chem. 1992, 57, 17, 4690–4696Publication Date (Print):August 1, 1992Publication History Published online1 May 2002Published inissue 1 August 1992https://pubs.acs.org/doi/10.1021/jo00043a029https://doi.org/10.1021/jo00043a029research-articleACS PublicationsRequest reuse permissionsArticle Views933Altmetric-Citations71LEARN 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
Package Boosting for Readaption of Cascaded Classifiers (2010)

This contribution presents an efficient and useful way to readapt a cascaded classifier. We introduce Package Boosting which combines the advantages of Real Adaboost and Online Boosting for the realization of the strong learners in each cascade layer. We also examine the conditions which need to be fulfilled by a cascade in order to meet the requirements of an online algorithm and present the evaluation results of the system.
Kinetics of the catalytic esterification of castor oil with lauric acid using n‐butyl benzene as a water entrainer (2003)

Abstract The esterification of castor oil with lauric acid was investigated using tetra n ‐butyl titanate (TBT), SnCl 2 ·2H 2 O (stannous chloride), CoCl 2 ·6H 2 O (cobalt chloride), and (CH 3 COO) 2 Zn·2H 2 O (zinc acetate dihydrate) as catalysts. Effects of catalyst concentration and reaction temperature on the progress of the reaction were investigated. TBT was the best catalyst for the esterification of castor oil with lauric acid at temperatures lower than 200°C. The reaction was first order with respect to each reactant. The activation energy for the esterification reaction of castor oil with lauric acid using TBT was 26.69 kcal/mol. The rate constants obtained for the esterification of castor oil with decanoic, lauric, palmitic, and stearic acids were nearly the same (15.80, 15.44, 15.06, and 14.67 mL mol −1 min −1 ), as were the rate constants obtained for the reaction of castor oil and hydrogenated castor oil.
Highly Enantioselective Access to Primary Propargylamines:  4-Piperidinone as a Convenient Protecting Group (2006)

[reaction: see text] We report a highly enantioselective, catalytic three-component coupling of aldehydes, alkynes, and 4-piperidone hydrochloride hydrate to afford the corresponding tertiary propargylamines in useful yields. The selective cleavage of the piperidone protecting group using either ammonia/EtOH or a polymer-supported scavenger amine furnishes primary propargylamines.
(2'-5')Oligoadenylate in rat liver: modulation after partial hepatectomy. (1983)

(2'-5')Oligoadenylate synthetase [(2'-5')A synthetase], which synthesizes a series of oligoadenylates ppp-(A2'p)n5'A [collectively referred to as (2'-5')A], has been described previously in rat liver cells, where its concentration varied with the growth status of this organ--i.e., it decreased during the early phase of rat liver regeneration after partial hepatectomy. Because double-stranded RNA, the only known activator of this enzyme, has been detected in rat liver nuclei, (2'-5')A synthesis could occur in this tissue in vivo. Analysis of rat liver cell extract after HPLC by the endonuclease-based radiobinding assay revealed several components with retention times similar to (2'-5')A trimer- and tetramer-like material. A further characterization of these compounds by their susceptibility to alkaline phosphatase and snake venom phosphodiesterase, their resistance to micrococcal nuclease, and their ability to activate an endonuclease indicated the natural occurrence of oligonucleotides indistinguishable from authentic (2'-5')A in rat liver cells. Using the combination of the radiobinding assay and a simplified (2'-5')A extraction procedure that does not involve HPLC, we further show that the early drop of (2'-5')A synthetase activity during rat liver regeneration was accompanied by a similar decrease in intracellular (2'-5')A concentration. The three characteristic phases of the (2'-5')A synthetase kinetics during the first 40 hr of liver regeneration were mimicked by the kinetics of the synthesis of the (2'-5')A oligonucleotides themselves: between 6 and 20 hr after hepatectomy, there was a sharp decrease in (2'-5')A concentration; between 20 and 24 hr, the concentration of (2'-5')A reached a minimum; at 36 hr or after the first wave of DNA synthesis (the major event of liver regeneration), the (2'-5')A concentration returned to normal. In this characterization of the (2'-5')A oligonucleotide family in a functional tissue of an animal that had not been previously treated with interferon or infected with virus, the data are compatible with a physiological role of the (2'-5')A system acting as an intracellular component of the regulatory mechanisms leading to cell proliferation or differentiation.