gebhart/patrepeval huggingface dataset:
Loopy Belief Propagation for Approximate Inference: An Empirical Study (2013)

Recently, researchers have demonstrated that loopy belief propagation - the use of Pearls polytree algorithm IN a Bayesian network WITH loops OF error- correcting codes.The most dramatic instance OF this IS the near Shannon - limit performance OF Turbo Codes codes whose decoding algorithm IS equivalent TO loopy belief propagation IN a chain - structured Bayesian network. IN this paper we ask : IS there something special about the error - correcting code context, OR does loopy propagation WORK AS an approximate inference schemeIN a more general setting? We compare the marginals computed using loopy propagation TO the exact ones IN four Bayesian network architectures, including two real - world networks : ALARM AND QMR.We find that the loopy beliefs often converge AND WHEN they do, they give a good approximation TO the correct marginals.However,ON the QMR network, the loopy beliefs oscillated AND had no obvious relationship TO the correct posteriors. We present SOME initial investigations INTO the cause OF these oscillations, AND show that SOME simple methods OF preventing them lead TO the wrong results.
Sensitivity, specificity, and predictive power of the “Brief Risk‐resilience Index forSCreening,” a brief pan‐diagnostic web screen for emotional health (2012)

Few standardized tools are available for time-efficient screening of emotional health status across diagnostic categories, especially in primary care. We evaluated the 45-question Brief Risk-resilience Index for SCreening (BRISC) and the 15-question mini-BRISC in identifying poor emotional health and coping capacity across a range of diagnostic groups - compared with a detailed clinical assessment - in a large sample of adult outpatients. Participants 18-60 years of age (n = 1079) recruited from 12 medical research and clinical sites completed the computerized assessments. Three index scores were derived from the full BRISC and the mini-BRISC: one for risk (negativity-positivity bias) and two for coping (resilience and social capacity). Summed answers were converted to standardized z-scores. BRISC scores were compared with detailed health assessment and diagnostic interview (for current psychiatric, psychological, and neurological conditions) by clinicians at each site according to diagnostic criteria. Clinicians were blinded to BRISC scores. Clinical assessment stratified participants as having "clinical" (n = 435) or "healthy" (n = 644) diagnostic status. Receiver operating characteristic analyses showed that a z-score threshold of -1.57 on the full BRISC index of emotional health provided an optimal classification of "clinical" versus "healthy" status (sensitivity: 81.2%, specificity: 92.7%, positive predictive power: 80.2%, and negative predictive power: 93.1%). Comparable findings were revealed for the mini-BRISC. Negativity-positivity bias index scores contributed the most to prediction. The negativity-positivity index of emotional health was most sensitive to classifying major depressive disorder (100%), posttraumatic stress disorder (95.8%), and panic disorder (88.7%). The BRISC and mini-BRISC both offer a brief, clinically useful screen to identify individuals at risk of disorders characterized by poor emotion regulation, from those with good emotional health and coping.
The Tandem BRCT Domains of Ect2 Are Required for Both Negative and Positive Regulation of Ect2 in Cytokinesis (2004)

Epithelial cell transforming protein 2 (Ect2) is a guanine nucleotide exchange factor (GEF) for Rho GTPases, molecular switches essential for the control of cytokinesis in mammalian cells. Aside from the canonical Dbl homology/pleckstrin homology cassette found in virtually all Dbl family members, Ect2 contains N-terminal tandem BRCT domains. In this study, we address the role of the Ect2 BRCT domains in the regulation of Ect2 activity and cytokinesis. First, we show that the depletion of endogenous Ect2 by small interfering RNA induces multinucleation, suggesting that Ect2 is required for cytokinesis. In addition, we provide evidence that Ect2 normally exists in an inactive conformation, which is at least partially due to an intramolecular interaction between the BRCT domains and the C-terminal domain of Ect2. This intramolecular interaction masks the catalytic domain responsible for guanine nucleotide exchange toward RhoA. Consistent with a role in regulating Ect2 GEF activity, overexpression of an N-terminal Ect2 containing the tandem BRCT domains, but not single BRCT domain or BRCT domain mutant, leads to a failure in cytokinesis. Surprisingly, although ectopically expressed wild-type Ect2 rescues the multinucleation resulting from the depletion of endogenous Ect2, expression of a BRCT mutant of Ect2 failed to restore proper cytokinesis in these cells. Taken together, the results of our study indicate that the tandem BRCT domains of Ect2 play dual roles in the regulation of Ect2. Whereas these domains negatively regulate Ect2 GEF activity in interphase cells, they are also required for the proper function of Ect2 during cytokinesis.
Molecular recognition directed self-assembly of ordered supramolecular strands by cocrystallization of complementary molecular components (1990)

The interaction of two suitably designed complementary ditopic molecular components (1,2) and (3,4) generates spontaneously an organized supramolecular architecture displaying molecular sorting and orientation.
Clinical Efficacy of Plasmapheresis in Patients with Neuromyelitis Optica Spectrum Disorder and Effects on Circulating Anti-Aquaporin-4 Antibody Levels (2013)

Background and PurposezzAlthough plasmapheresis is becoming standard practice as a rescue therapy for neuromyelitis optica (NMO), evidence for the therapeutic efficacy of plasmapheresis is limited, and the effect of plasmapheresis on anti-aquaporin-4 (AQP4) levels in patients with NMO has not been reported. Here, our objective was to evaluate the clinical efficacy of therapeutic plasmapheresis and its effect on anti-AQP4 antibody levels in patients with NMO spectrum disorder (NMOSD).
Immunization against the colonization factor antigen I of enterotoxigenic Escherichia coli by administration of a bivalent Salmonella typhimurium aroA strain (1998)

An expression plasmid (pCFA-1) carrying the cfaB gene that codes for the enterotoxigenic Escherichia coli (ETEC) fimbrial adhesin colonization factor antigen I (CFA/I) subunit was constructed and used to transform a derivative of the attenuated Salmonella typhimurium aroA vaccine strain SL3261 carrying an F'lacIq. Treatment of the transformed strain with isopropyl-beta-D-thiogalactopyranoside (IPTG) resulted in elevated in vitro expression of the CFA/I subunit. Although flagellar function and lipopolysaccharide (LPS) synthesis were similar in both the parental and the recombinant strains, spleen colonization was reduced in the recombinant strain. All BALB/c mice parenterally inoculated with the recombinant strain developed significant anti-CFA/I and anti-LPS serum antibody titers (P < 0.05). Moreover, 2 of 5 mice orally inoculated with the engineered Salmonella strain developed anti-CFA/I intestinal IgA (P > 0.05) while 4/5 of the same mice developed anti-LPS IgA (P < 0.05). The results indicate that the vaccine strain elicited an antibody response against the bacterial host both after oral and intravenous immunization while the response against the CFA/I antigen was significant only after inoculation by the intravenous route.
Abstract 1385: The ATP-binding Cassette A1 (ABCA1)-mediated Apolipoprotein A-I Lipidation Occurs at the Plasma Membrane and not in the Endocytic Compartments (2007)

The ATP-binding Cassette Transporter A1 (ABCA1) is required for the biogenesis of HDL through the lipidation of lipid-poor apolipoprotein A-I (apoA-I). ApoA-I has been suggested to internalize with ABCA1, presumably to acquire lipids from the endosomal compartments, an important hub for cholesterol trafficking. The aim of our work is to determine how apoA-I get endocytosed and whether this internalization contributes to the biogenesis of HDL. When examined by confocal microscopy, we found that Cy3.5-apoA-I endocytosed rather slowly (t 1/2 = 15 min, in baby hamster kidney cells expressing ABCA1) and poorly co-localized with transferrin, consistent with a pathway independent of clathrin-coated pits. ApoA-I was instead found perfectly co-localized with FITC-dextran, a bulk phase uptake marker and, at later time points, with LysoTracker. This strongly indicates that majority of internalized apoA-I was delivered to the lysosomes. ABCA1 was not found to co-localize with endocytosed apoA-I. Similar observations were obtained in mouse macrophages and normal human fibroblasts. Next, in order to determine the functional significance of endocytosis to cholesterol efflux, we used sucrose or latrunculin A to inhibit apoA-I endocytosis. We show that apoA-I, transferrin and dextran uptake were abolished, but cholesterol efflux was not decreased. To specifically determine whether internalized apoA-I contributes to the biogenesis of HDL, we developed a method to strip off apoA-I from the cell surface. Our results show that internalized apoA-I do not significantly contribute to the biogenesis of HDL (&lt; 20%). Together, our results suggest that the plasma membrane is the main platform where ABCA1-mediated lipidation of apoA-I occurs. Internalized apoA-I is mostly targeted for lysosomal degradation and therefore does not significantly contribute to the biogenesis of HDL.
Interactive Feature Tracking using K-D Trees and Dynamic Programming (2006)

A new approach to template tracking is presented, incorporating three distinct contributions. Firstly, an explicit definition for a feature track is given. Secondly, the advantages of an image preprocessing stage are demonstrated and, in particular, the effectiveness of highly compressed image patch data stored in k-d trees for fast and discriminatory image patch searches. Thirdly, the k-d trees are used to generate multiple track hypotheses which are efficiently merged to give the optimal solution using dynamic programming. The explicit separation of feature detection and trajectory determination creates the basis for the novel use of k-d trees and dynamic programming. Multiple appearances and occlusion handling are seamlessly integrated into this framework. Appearance variation through the sequence is robustly handled in an iterative process. The work presented is a significant foundation for a powerful off-line feature tracking system, particularly in the context of interactive applications.
Design students' experience of engagement and creativity (2007)

The terms creativity and engagement are used broadly throughout the literature and are in common usage in our education and design language. Students, however, understand these terms in unexpected ways and this can sometimes cause a disjunction between the teacher's intention for the learning activity and the ways in which the student may go about it. In this article we tease out the relationships between engagement and creativity for student learning in design. Our data suggest that engagement relies on certain conditions and attributes that have to be met before a student makes a personally meaningful commitment to study. Engagement here means some form of interlocking between the student and the task, or some form of attentiveness facilitated by the teacher or the environment. By creativity we mean the meshing between person, process and product which is then appreciated by the broader design community. We suggest that understanding creativity as a complex attribute contributes to the nature and quality of student engagement with their learning and the profession.
Pharmacokinetics and Pharmacodynamics of Lisdexamfetamine Compared with D-Amphetamine in Healthy Subjects (2017)

<b>Rationale:</b> Lisdexamfetamine is a prodrug of D-amphetamine used for the treatment of attention-deficit/hyperactivity disorder (ADHD). Lisdexamfetamine is thought to have a prolonged pharmacokinetic profile compared with oral D-amphetamine, possibly associated with lower drug liking and a lower risk of oral misuse. However, differences in the pharmacokinetics and pharmacodynamics of lisdexamfetamine and D-amphetamine have not been directly compared. <b>Methods:</b> Equimolar doses of D-amphetamine (40 mg) and lisdexamfetamine (100 mg), and placebo were administered in 24 healthy subjects in a randomized, double-blind, placebo-controlled, cross-over study. Plasma concentrations of amphetamine, subjective effects, and vital signs were repeatedly assessed. The pharmacokinetic parameters were determined using compartmental modeling. <b>Results:</b> The increase in plasma concentrations of amphetamine had a 0.6 ± 0.6 h (mean ± SD) longer lag time and reached peak levels 1.1 ± 1.5 h later after lisdexamfetamine administration compared with D-amphetamine administration, but no differences in maximal concentrations or total exposure (AUC) were found between the two treatments. Consistent with the pharmacokinetics, the subjective and cardiovascular stimulant effects of lisdexamfetamine also occurred later compared with D-amphetamine. However, no differences in peak ratings of potentially abuse-related subjective drug effects (e.g., drug liking, drug high, stimulation, happy, well-being, and self-confidence) were observed after lisdexamfetamine administration compared with D-amphetamine administration. Lisdexamfetamine and D-amphetamine also produced similar peak increases in mean arterial blood pressure, heart rate, body temperature, pupil size, and adverse effects. <b>Conclusion:</b> The pharmacokinetics and pharmacodynamics of lisdexamfetamine are similar to D-amphetamine administered 1h later. Lisdexamfetamine is likely associated with a similar risk of oral abuse as D-amphetamine. The study was registered at ClinicalTrials.gov (NCT02668926).
Oral treatment with Eubacterium hallii improves insulin sensitivity in db/db mice (2016)

An altered intestinal microbiota composition is associated with insulin resistance and type 2 diabetes mellitus. We previously identified increased intestinal levels of <i>Eubacterium hallii</i>, an anaerobic bacterium belonging to the butyrate-producing <i>Lachnospiraceae</i> family, in metabolic syndrome subjects who received a faecal transplant from a lean donor. To further assess the effects of <i>E. hallii</i> on insulin sensitivity, we orally treated obese and diabetic <i>db/db</i> mice with alive <i>E. hallii</i> and glycerol or heat-inactive <i>E. hallii</i> as control. Insulin tolerance tests and hyperinsulinemic-euglycemic clamp experiments revealed that alive <i>E. hallii</i> treatment improved insulin sensitivity compared control treatment. In addition, <i>E. hallii</i> treatment increased energy expenditure in <i>db/db</i> mice. Active <i>E. hallii</i> treatment was found to increase faecal butyrate concentrations and to modify bile acid metabolism compared with heat-inactivated controls. Our data suggest that <i>E. hallii</i> administration potentially alters the function of the intestinal microbiome and that microbial metabolites may contribute to the improved metabolic phenotype.
Reduction of Mortality with Antithrombin III in Septicemic Rats: A Study of Klebsiella pneumoniae Induced Sepsis (1993)

Experimental gram-negative sepsis was induced in the rat by Klebsiella pneumoniae. Although bacteria are susceptible to the treatment with the antibiotic Tobramycin, DIC could not be prevented. DIC was manifested by a leuko- and thrombocytopenia, decreases in fibrinogen and AT III and an increase of the aPTT. In this model the therapeutic treatment with human AT III was evaluated. To determine the optimal concentration of AT III a prestudy in a LPS induced DIC in the rat was performed. It was shown that a bolus i.v. injection of 500 U/kg improved survival and DIC, and was thus chosen for the Klebsiella sepsis model. The infectious load was adjusted to yield a mortality rate of 90-100% in the untreated Klebsiella group and a reduction to about 40-50% of the mortality rate by Tobramycin. It was found that AT III reduced mortality in the Klebsiella induced sepsis not only when given prophylactically but was effective even when administrated in a late stage of the DIC, i.e. 3 or 5 h post infection.
Library of libraries: approach to synthetic combinatorial library design and screening of "pharmacophore" motifs. (1995)

Construction of synthetic combinatorial libraries is described that allows for the generation of a library of motifs rather than a library of compounds. Peptide libraries based on this strategy were synthesized and screened with model targets streptavidin and anti-beta-endorphin antibody. The screens resulted in observation of expected motifs providing evidence of the effectiveness of the suggested approach.
Identification and organization of genes for diutan polysaccharide synthesis from Sphingomonas sp. ATCC 53159 (2008)

A cluster of genes for diutan polysaccharide synthesis was isolated from a library of Sphingomonas sp. ATCC 53159 genomic DNA by complementation of glucosyl-isoprenylphosphate transferase-deficient mutants of Sphingomonas elodea ATCC 31461 (producing gellan) and Xanthomonas campestris (producing xanthan). The synthesis of polysaccharide in these strains shares a common first step, transfer of glucose-1-phosphate from UDP-glucose to the isoprenylphosphate lipid. The cluster of 24 genes was compared to genes for biosynthesis of gellan, and S-88 sphingan from Sphingomonas sp. ATCC 31554. Diutan, gellan and S-88 sphingan have a common four-sugar backbone but different side chains, one rhamnose for S-88 sphingan, a two-rhamnose side chain for diutan and no side chain for gellan. The genes for biosynthesis of diutan, gellan and S-88 sphingan were similar in general organization but differed in location of some genes, in particular, dpsG (putative polymerase), dpsR (putative lyase) and dpsS (putative repeat unit transporter). An unidentified reading frame urf31, present in the gene clusters for diutan and S-88 sphingan but not gellan, had similarity to glycosyl transferase group 2 proteins, and was detrimental when cloned in Sphingomonas elodea producing gellan that lacks a side chain, but not in Sphingomonas ATCC 31554 producing S-88 sphingan with a rhamnose side chain. Gene urf31 could possibly encode a side-chain rhamnosyl transferase. Another gene urf31.4 was unique to the diutan gene cluster. A plasmid containing 20 of the 24 genes resulted in a slight increase in the amount of diutan produced, but a significant increase in the rheological properties of diutan.
Cyanobacterial Non-mevalonate Pathway (2005)

(E)-4-Hydroxy-3-methylbut-2-enyl diphosphate synthase (GcpE), which catalyzes the conversion of 2-C-methyl-D-erythritol cyclodiphosphate (MEcPP) into (E)-4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP), is an essential enzyme of the non-mevalonate (2-C-methyl-D-erythritol-4-phosphate (MEP)) pathway for isoprenoid biosynthesis. The terminal steps of the MEP pathway are still not fully understood, although this pathway is necessary for survival in various organisms such as cyanobacteria, plastids of algae and higher plants, and the apicoplast of human malaria parasites. To determine the efficient redox partner for thermophilic cyanobacterial GcpE, We have expressed the gcpE and petF genes in Escherichia coli and studied the protein-protein interaction of GcpE protein with ferredoxin I (PetF) from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. Recombinant GcpE protein was purified by an N-terminal His(6) tag and reconstituted as a [4Fe-4S](2+) metalloprotein. GcpE was shown to interact strongly with PetF via the bacterial two-hybrid system designed to detect protein-protein interactions. Moreover, a direct protein-protein interaction between PetF and GcpE was confirmed in an in vitro glutathione S-transferase (GST) pull-down assay. To investigate electron transfer activity from PetF to GcpE, we also constructed a NADPH-dependent reducing shuttle system with purified recombinant ferredoxin-NADP(+) oxidoreductase (PetH) and PetF. The result demonstrated that PetF has the ability to transfer electrons to GcpE. Thus, the combined data provide the first evidence that GcpE is a ferredoxin-dependent enzyme in T. elongatus BP-1.
Proteolipid protein gene duplications causing Pelizaeus‐Merzbacher disease: Molecular mechanism and phenotypic manifestations (1999)

Pelizaeus-Merzbacher disease (PMD) is an X-linked disorder characterized by dysmyelination of the central nervous system (CNS) caused by mutations involving the proteolipid protein gene (PLP). In addition to point and frameshift mutations in the coding region, duplications involving the entire PLP have been recognized recently as a major genetic abnormality causing PMD. We devised an interphase fluorescence in situ hybridization (FISH) assay to establish an efficient screening test for PLP duplication. Thirteen patients from 11 Japanese PMD families were determined to have PLP duplications. This molecular diagnostic FISH test also readily detected female carriers. Molecular analysis revealed that the size of the duplication and location of the breakpoints showed striking variation. Fiber FISH demonstrated that the duplication is tandem in nature. Haplotype analysis indicated an intrachromosomal origin for the duplication. These results suggest that an unequal sister chromatid exchange in male meiosis is likely to be the major mechanism leading to the formation of the duplication. Patients with the duplication commonly present with a mild PMD phenotype. Two patients with an exceptionally severe clinical phenotype carried large duplications, suggesting that either the larger duplicated segment incorporates additional dosage-sensitive genes or that the location of the duplication junction may affect the phenotype. Ann Neurol 1999;45:624–632
Rigid-rod polymers. 2. Synthesis and thermal properties of para-aromatic polymers with 2,6-benzobisthiazole units in the main chain (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRigid-rod polymers. 2. Synthesis and thermal properties of para-aromatic polymers with 2,6-benzobisthiazole units in the main chainJames F. Wolfe, Bock H. Loo, and F. E. ArnoldCite this: Macromolecules 1981, 14, 4, 915–920Publication Date (Print):July 1, 1981Publication History Published online1 May 2002Published inissue 1 July 1981https://pubs.acs.org/doi/10.1021/ma50005a005https://doi.org/10.1021/ma50005a005research-articleACS PublicationsRequest reuse permissionsArticle Views2378Altmetric-Citations284LEARN 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
A Two Step Synthesis of the Nucleoside Q Precursor 2-Amino-5-cyanopyrrolo[2,3-d]pyrimidin 4-one (PreQo) (1996)

Abstract PreQo (1) is prepared in a 70 % yield by the condensation of chloro(formyl)acetonitrile (2) with 2,6-diaminopyrimidin-4-one (3), and subsequently converted to its amide derivative 5. Isolation of the intermediate 4 in the condensation reaction was also observed giving further insight into the proposed mechanism.