gebhart/patrepeval huggingface dataset:
Biomarkers in acute myocardial infarction (2010)

Myocardial infarction causes significant mortality and morbidity. Timely diagnosis allows clinicians to risk stratify their patients and select appropriate treatment. Biomarkers have been used to assist with timely diagnosis, while an increasing number of novel markers have been identified to predict outcome following an acute myocardial infarction or acute coronary syndrome. This may facilitate tailoring of appropriate therapy to high-risk patients. This review focuses on a variety of promising biomarkers which provide diagnostic and prognostic information. Heart-type Fatty Acid Binding Protein and copeptin in combination with cardiac troponin help diagnose myocardial infarction or acute coronary syndrome in the early hours following symptoms. An elevated N-Terminal Pro-B-type Natriuretic Peptide has been well validated to predict death and heart failure following a myocardial infarction. Similarly other biomarkers such as Mid-regional pro-Atrial Natriuretic Peptide, ST2, C-Terminal pro-endothelin 1, Mid-regional pro-Adrenomedullin and copeptin all provide incremental information in predicting death and heart failure. Growth differentiation factor-15 and high-sensitivity C-reactive protein predict death following an acute coronary syndrome. Pregnancy associated plasma protein A levels following chest pain predicts risk of myocardial infarction and revascularisation. Some biomarkers such as myeloperoxidase and high-sensitivity C-reactive protein in an apparently healthy population predicts risk of coronary disease and allows clinicians to initiate early preventative treatment. In addition to biomarkers, various well-validated scoring systems based on clinical characteristics are available to help clinicians predict mortality risk, such as the Thrombolysis In Myocardial Infarction score and Global Registry of Acute Coronary Events score. A multimarker approach incorporating biomarkers and clinical scores will increase the prognostic accuracy. However, it is important to note that only troponin has been used to direct therapeutic intervention and none of the new prognostic biomarkers have been tested and proven to alter outcome of therapeutic intervention. Novel biomarkers have improved prediction of outcome in acute myocardial infarction, but none have been demonstrated to alter the outcome of a particular therapy or management strategy. Randomised trials are urgently needed to address this translational gap before the use of novel biomarkers becomes common practice to facilitate tailored treatment following an acute coronary event.
Microarray Genotyping Resource to Determine Population Stratification in Genetic Association Studies of Complex Disease (2004)

We have developed a robust microarray genotyping chip that will help advance studies in genetic epidemiology. In population-based genetic association studies of complex disease, there could be hidden genetic substructure in the study populations, resulting in false-positive associations. Such population stratification may confound efforts to identify true associations between genotype/haplotype and phenotype. Methods relying on genotyping additional null single nucleotide polymorphism (SNP) markers have been proposed, such as genomic control (GC) and structured association (SA), to correct association tests for population stratification. If there is an association of a disease with null SNPs, this suggests that there is a population subset with different genetic background plus different disease susceptibility. Genotyping over 100 null SNPs in the large numbers of patient and control DNA samples that are required in genetic association studies can be prohibitively expensive. We have therefore developed and tested a resequencing chip based on arrayed primer extension (APEX) from over 2000 DNA probe features that facilitate multiple interrogations of each SNP, providing a powerful, accurate, and economical means to simultaneously determine the genotypes at 110 null SNP loci in any individual. Based on 1141 known genotypes from other research groups, our GC SNP chip has an accuracy of 98.5%, including non-calls.
Carcinogenesis study in mice by 3-methylbutanal methylformylhydrazone of Gyromitra esculenta. (1990)

3-Methylbutanal methylformylhydrazone (3-MBMFH) was given to Swiss mice by intragastric instillations at weekly intervals 53 or 2 times at 50 micrograms/g body weight. The treatments induced tumors of the lungs, liver, gallbladder, preputial glands and thyroid. The tumor incidences in the group treated 53 times were 84, 32, 10, 0 and 0% in females, and 76, 38, 6, 48 and 0% in the males, respectively. In the group treated twice the incidences were 38, 0, 4, 0 and 10% in females, and 30, 0, 2, 0 and 6% in males, respectively. The corresponding tumor incidences in the untreated controls were 26, 0, 0, 0 and 0% in females, and 26, 0, 0, 0 and 0% in males, respectively. The light microscopic examination of these neoplasms showed adenomas and adenocarcinomas of lungs, hepatomas and liver cell carcinomas, adenomas and adenocarcinomas of gallbladder, squamous cell papillomas and carcinomas of preputial glands; and, adenomas and adenocarcinomas of thyroid. Gyromitra esculenta mushroom contains 3-MBMFH along with the other hydrazine derivatives. Because at least five ingredients of this fungus exhibit carcinogenic properties, the health hazard implications should be considered.
Pertussis toxin has eukaryotic-like carbohydrate recognition domains. (1992)

Bordetella pertussis is bound to glycoconjugates on human cilia and macrophages by multiple adhesins, including pertussis toxin. The cellular recognition properties of the B oligomer of pertussis toxin were characterized and the location and structural requirements of the recognition domains were identified by site-directed mutagenesis of recombinant pertussis toxin subunits. Differential recognition of cilia and macrophages, respectively, was localized to subunits S2 and S3 of the B oligomer. Despite greater than 80% sequence homology between these subunits, ciliary lactosylceramide exclusively recognized S2 and leukocytic gangliosides bound only S3. Substitution at residue 44, 45, 50, or 51 in S2 resulted in a shift of carbohydrate recognition from lactosylceramide to gangliosides. Mutational exchange of amino acid residues 37-52 between S2 and S3 interchanged their carbohydrate and target cell specificity. Comparison of these carbohydrate recognition sequences to those of plant and animal lectins revealed that regions essential for function of the prokaryotic lectins were strongly related to a subset of eukaryotic carbohydrate recognition domains of the C type.
P2P content sharing in spontaneous multi-hop wireless networks (2010)

Spontaneous multi-hop wireless networks provide a new environment for sharing content among communities of end users. Nodes interested in some content can share it on a multi-hop basis by relying on the collaboration of intermediate nodes. Organizing the communication overlay in such an environment is then a challenging task especially given the mobility of the nodes, the interference, and the scarcity of resources. In this work, we propose and implement a general, stand-alone and efficient P2P content sharing protocol for wireless ad hoc networks. We consider general and realistic scenarios ranging from a single overlay to multiple overlays coexisting in the same network, and for every single overlay, we consider different peer densities in the network. The main challenges are overlay disconnections, routing overhead, low sharing opportunities and instability of distant paths. Our protocol proposes efficient solutions for these problems leading to the best download times while guaranteeing the maximum sharing opportunities among the peers. We validate our protocol through extensive simulations and experimentations on the ORBIT platform.
The mRNA quantitative analysis, prokaryotic expression and structure prediction of hepatocarcinogenesis related gene idh3α under AFB1 stress (2011)

By differential proteomics analysis, it was found that the expression level of IDH3α (Isocitrate dehydrogenase 3α) in mouse liver was significantly increased under the stress of Aflatoxin B1. To validate the result of differential proteomics analysis, fluorescence quantitative PCR was used to detect the changing trend of idh3α mRNA volume induced by Aflatoxin B1 in mouse liver. The result showed that the expression volume of idh3αmRNA showed an increasing trend with the increase of Aflatoxin B1 concentration, which corresponded with the result of differential proteomics analysis. The protokaryon expression vector for idh3α was constructed in the study with pET28a as a recipient plasmid. The expression vector (pET28a-idh3α) was used to transform BL21, after which the positive expression strain (Escherichia coli BL21/pET28a-idh3α) was induced to express with 100 mmol/L IPTG under 28°C for 4 h, and the prokaryotic expression product of IDH3α was successfully detected by SDS-PAGE electrophoresis. The molecule structure of IDH3α was predicted by bioinformatics analysis, and the results showed that the total number of negatively and positively charged residues were 42 and 39, respectively. Five hydrohpobic domains were predicted in the protein, and its average hydrophobicity was -0.069. There was 43% α-helix and 20% β-pleated sheet in the molecule, and the tertiary structure of IDH3α was constituted by 12 α-helices and 12 β-pleated sheets. Based on the results of bioinformatics analysis, the fragments of 1-17 and 112-123 residues of IDH3α were selected as candidates for further effective polyclonal antibody preparation. The results of this study paved way for further exploration of the role of idh3α in the process of liver carceration induced by Aflatoxin B1.

	 

	Key words: IDH3α, aflatoxinB1, liver, canceration, bioinformatics analysis.
Markedly Elevated Levels of Interferon (IFN)‐σ, IFN‐α, Interleukin (IL)‐2, IL‐10, and Tumor Necrosis Factor‐α Associated with Fatal Ebola Virus Infection (1999)

The role of immune mechanisms in the pathogenesis of Ebola hemorrhagic fever (EHF) remains to be elucidated. In this report, the serum cytokine levels of patients who died of EHF were compared with those of patients who recovered and those of control patients. A marked elevation of interferon (IFN)-gamma levels (>100 pg/mL) was observed in sequential serum samples from all fatal EHF cases compared with patients who recovered or controls. Markedly elevated serum levels of interleukin (IL)-2, IL-10, tumor necrosis factor (TNF)-alpha, and IFN-alpha were also noted in fatal EHF cases; however, they had a greater degree of variability. No differences were noted in serum levels of IL-4 and IL-6. mRNA quantitation from blood clots of the same patients showed relatively elevated levels of TNF-alpha and IFN-alpha in samples from EHF patients. Taken together, these results suggest that a high degree of immune activation accompanies and potentially contributes to a fatal outcome in EHF patients.
Specific and sensitive plate assay for bacterial lipases (1987)

A plate assay to detect bacterial lipase (EC 3.1.1.3) in a medium containing trioleoylglycerol and the fluorescent dye rhodamine B is presented. Substrate hydrolysis causes the formation of orange fluorescent halos around bacterial colonies visible upon UV irradiation. The logarithm of lipase activity from cell-free culture supernatants is linearly correlated with the diameter of halos, thereby allowing quantitation of lipase activities ranging from 1 to 30 nkat.
Conversion of M serotype 24 of Streptococcus pyogenes to M serotypes 5 and 18: effect on resistance to phagocytosis and adhesion to host cells (1997)

In this study, we utilized recombinant strains expressing the M5 and M18 proteins and M- mutants of group A streptococci to compare the abilities of these M proteins to confer resistance to phagocytosis and to mediate adhesion to host cells. The data indicate that the M5 and M18 proteins can confer resistance to phagocytosis, that fibrinogen is required for this resistance, and that these M proteins can mediate adhesion to HEp-2 cells.
T cell major histocompatibility complex class II molecules down‐regulate CD4+ T cell clone responses following LAG‐3 binding (1996)

T cell response to its antigen requires recognition by the T cell receptor together with a co-receptor molecule, either CD4 or CD8. Additional molecules have been identified that are capable of delivering the co-stimulatory signals provided by APC. Following T cell priming, a number of T cell activation antigens are expressed that may play a role in the inactivation phase of the T cell response. The lymphocyte activation gene (LAG)-3 protein and its counter-receptors, the major histocompatibility complex (MHC) class II molecules, are such activation antigens whose interaction may result in the down-regulation of the ongoing immune response. To investigate the role of LAG-3/class II molecule interaction, we produced a soluble form of LAG-3 by fusing the extracellular Ig domains of this membrane protein to the constant region of human IgG1 (LAG-3Ig). Here, we show a direct and specific binding of LAG-3Ig to class II molecules on the cell surface. In addition, we show that LAG-3/class II molecule interaction leads to the down-regulation of CD4+ Ag-specific T cell clone proliferation and cytokine secretion. This inhibitory effect is observed at the level of the effector cells and not the APC and is also found with anti-CD3 mAb, PHA + PMA or low-dose IL-2 driven stimulation in the absence of APC. These functional studies indicate that T cell MHC class II molecules down-regulate T cell proliferation following LAG-3 binding and suggest a role for LAG-3 in the control of the CD4+ T cell response.
CaGrid Workflow Toolkit: A taverna based workflow tool for cancer grid (2010)

By extending the Taverna Workbench, caGrid Workflow Toolkit provided a comprehensive solution to compose and coordinate services in caGrid, which would otherwise remain isolated and disconnected from each other. Using it users can access more than 140 services and are offered with a rich set of features including discovery of data and analytical services, query and transfer of data, security protections for service invocations, state management in service interactions, and sharing of workflows, experiences and best practices. The proposed solution is general enough to be applicable and reusable within other service-computing infrastructures that leverage similar technology stack.
Serum 25-Hydroxyvitamin D in Patients with Chronic Renal Failure on Long-Term Treatment with High Doses of Vitamin D<sub>2</sub> (1980)

The present study was aimed at answering the following two questions: (1) What is the effect of high dose vitamin D treatment on the serum level of 25-hydroxyvitamin D (25-OH-D) in patients with chronic renal failure (CRF)? (2) Is there any effect of urinary protein loss on the serum 25-OH-D levels during treatment with pharmacological doses of vitamin D? 42 patients with CRF were studied. They were treated conservatively by a low protein diet and received 15 mg of vitamin D2 once a week. Long-term administration of vitamin D caused a significant (5- to 7-fold) increase of plasma 25-OH-D level irrespective of the degree of proteinuria. This increase was noted only during the first 5 months of vitamin D2 treatment. Surprisingly only in some patients moderate hypercalcemia (> 2.75 mmol/l) was found. From the results obtained it is concluded that (1) patients with CRF differ from normal subjects in handling of high doses of vitamin D and (2) high dosage treatment with vitamin D may prevent hypocalcemia in patients with CRF in spite of high proteinuria.
Query Indices and a 2008 Downturn: Israeli Data (2009)

"Predicting the Present with Google Trends" (Choi, Varian, 2008) offers a nowcasting model, suggesting that the popularity of web searches tracked by Google over time may be applied as an indicator of contemporaneous economic activity, before the official data become available and/or are revised. Such evidence was found in different countries with respect to automobile sales, home sales, retail trade and travel. Using Google's Insights for Search application, which aggregates search terms by large socioeconomic categories, I test the predictive ability of Israeli query indices. At a monthly frequency, six predictive categories were found: Human Resources (Recruitment and Staffing), Home Appliances, Travel, Real Estate, Food and Drink and Beauty and Personal Care. According to the pair-wise Granger causality tests, the strongest predictor is in the Human Resources category (Recruitment and Staffing). The latter, taken at a quarterly frequency, is a leading indicator with regard to the job openings ratio, currently surveyed by the Ministry of Industry, Trade and Labor, and consequently may help in drawing monthly inferences about the unemployment rate. The large fraction of innovation variance explained by other selected categories is related to the employment rate. It suggests an attitudinal interpretation of the queries effect, which may be conveyed through the employment channel. In-sample Bayesian probabilities of a downturn computed between 2004:2 and 2009:2, peak in the first half of 2007 and since March 2008, conforming official assessments of a slowdown in economic growth and an economic decline, respectively. Real-time simulations made since December 2007 signal a downturn likely to occur from April 2008. For monitoring purposes, an index of Home Appliances queries has been incorporated as an instrumental variable in the State-of-the-Economy composite index, while current assessments of private consumption (trade and services revenue) have been improved, in terms of RMSE. The operative use of query data, however, may encounter problems that deserve attention. First, query indices may appear not to be stationary, due to alternative social search which is not tracked by the Google engine. Second, the predictive ability of query indices may vary over time.
Interaction of a Peptidomimetic Aminimide Inhibitor with Elastase (1995)

The crystal structure of an aminimide analog of a dipeptide inhibitor of porcine pancreatic elastase bound to its target serine protease has been solved. The peptidomimetic molecule binds in the same fashion as the class of dipeptides from which it was derived, making similar interactions with the subsites on the elastase surface. Because aminimides are readily synthesized from a wide variety of starting materials, they form the basis for a combinatorial chemistry approach to rational drug design.
Add-on blockade of pro renin receptor in imidapril-treated diabetic SHRsp (2010)

To examine the involvement of (pro)renin receptor in the accelerated organ damage in streptozotocin-induced diabetic male SHRsp, the rats fed a high-salt diet were divided into 5 groups: a group treated with the vehicle, a group treated with 15 mg/kg/day of imidapril (ACEi), a group treated with 60 mg/kg/day of imidapril (High ACEi), a group treated with handle region peptide (HRP), and a group treated with both ACEi and HRP (ACEi+HRP). After 8 weeks, the arterial pressure was similar in the vehicle and HRP groups and decreased in the ACEi-treated groups. The renal angiotensin II content decreased similarly in the groups treated with ACEi and/or HRP. Urinary protein excretion also decreased in the ACEi, High ACEi, and HRP groups and significantly further decreased in the ACEi+HRP group. The heart weight of the ACEi+HRP group was significantly lower than that of any other groups, although the cardiac angiotensin II levels decreased similarly in the groups treated with ACEi and/or HRP. Thus, (pro)renin receptor contributes to the accelerated pathogenesis in the heart and kidneys of diabetic SHRsp.
The turbo decoding algorithm and its phase trajectories (2001)

This paper analyzes phase trajectories and fixed points of the turbo decoding algorithm as a function of the signal-to-noise ratio (SNR). By exploiting the large length of turbo codes, the turbo decoding algorithm is treated as a single-parameter dynamical system, parameterized (approximately) by the SNR. This parameterization, along "with" extensive simulations at practical SNRs and asymptotic analysis as SNR goes to zero and infinity, is used to subdivide the entire SNR range into three regions with the "waterfall region" in the middle. The turbo decoding algorithm has distinctive phase trajectories and convergence properties in these three SNR regions. This paper also investigates existence and properties of fixed points in these SNR regions. The main fixed points of the turbo decoding algorithm are classified into two categories. In a wide range of SNRs (corresponding to bit-error rates less than 10/sup -1/), the decoding algorithm has "unequivocal" fixed points which correspond to mostly correct decisions on the information bits. Within this range, toward the lower values of SNR, there is another fixed point which corresponds to many erroneous decision on the information bits. Fixed points of this type are referred to as "indecisive" fixed points. It turns out that the indecisive fixed points bifurcate and disappear for SNRs in the waterfall region. This paper associates the qualitative transition of phase trajectories in the waterfall region to the bifurcation of indecisive fixed points. These bifurcations also explain empirically observed quasi-periodic and periodic phase trajectories of the turbo decoding algorithm.
Powdery mildew (Podosphaera xanthii) resistance in melon is categorized into two types based on inhibition of the infection processes (2006)

Physiological races of powdery mildew (Podosphaera xanthii) cause different symptoms in eight melon lines. Infection by races 1, 2, and 5 was examined in different melon lines. After a compatible reaction, conidia germination, haustorium initiation from the germ tube, germ tube branching, and sporulation occurred within 12, 24, 48, and 120 h, respectively, and the conidia matured within 240 h. In contrast, type i and ii inhibition were identified through incompatible reactions. The germ tube and haustorium were initiated from conidia, but no germ tube branching occurred in the lines with type i resistance within 48-240 h. In type ii resistance, germ tube branching was observed within 120 h, but no sporulation was observed within 240 h. The number of fluorescing epidermal cells was higher within 24 h in type i, and within 48-120 h in type ii resistance lines than in susceptible lines. Callose accumulation around the haustorium was detected in type ii resistance lines within 48-120 h. This suggests that the rapid hypersensitive response (HR) within 24 h has an important role in the type i response, while HR and callose accumulation in the type ii response occur slowly between 48 and 120 h. Of the resistant lines, PMR 45 and WMR 29 showed a type i incompatible response; the PI 414723 response was entirely type ii; and PMR 5, PI 124112, and MR-1 showed different responses depending on the race. Therefore, the two types of incompatible responses were intermixed in the same germplasm.