gebhart/patrepeval huggingface dataset:
Complete genomes of two Human hepatitis A virus isolates from China: analysis and comparison with other isolates. (2002)

Complete sequences of the genomes of two wild type (wt) Human hepatitis A virus (HHAV) isolates, LU38 and LY6 from China were determined and compared with those of wt HHAV isolates AH1, AH2, AH3, FH1, FH2, FH3, GBM, HM175, LA and MBB. The genomes of both LU38 and LY6 consisting of 7477 nucleotides (nts) contained a 5'-non-translated region (5'-NTR, 733 nts), an open reading frame (ORF, 6681 nts), and a 3'-NTR (63 nts) followed by a poly(A)-tail. It encoded a polyprotein of 2227 amino acids (aa) Sequence comparison showed that LU38 shared the highest identities of 98.1% for nt (140 differences) and 99.2% for as (17 differences) with AH1, and the lowest identities of 91.4% for nt (741 differences) with HM175 and 98.1% for aa (43 differences) with GBM. LY6 shared the highest identities of 97.4% for nt (196 differences) and 98.7% for aa (28 differences) with H1 and the lowest identities of 91.2% for nt (642 differences) with HM175 and 97.7% for as (51 differences) with GBM. The subgenotyping revealed that the LU38 and LY6 isolates are of IA subgenotype. The phylogenetic analysis showed that LU38 is closest to AH1 and the LY6 to FH3, suggesting that the epidemiological link of hepatitis A (HA) had developed in China and Japan.
Phospholipase C-δ1 Is a Critical Target for Tumor Necrosis Factor Receptor–Mediated Protection against Adriamycin-Induced Cardiac Injury (2006)

The clinical application of adriamycin, an exceptionally good chemotherapeutic agent, is limited by its dose-related cardiomyopathy. Our recent study showed that tumor necrosis factor-alpha (TNF-alpha) receptors mediated cytoprotective signaling against adriamycin-induced mitochondrial injury and cardiomyocyte apoptosis. In the present study, we investigated the potential targets of TNF receptor-mediated cytoprotective signaling by global genome microarray analysis using wild-type and TNF receptor-deficient mice. Microarray analysis revealed that adriamycin treatment induced the down-regulation of several mitochondrial functions and energy production-related genes in double TNF receptor-deficient mice, notably, phospholipase C-delta1, a protein involved in fatty acid metabolism and calcium regulation. The role of phospholipase C-delta1 in TNF receptor-mediated cardioprotection against adriamycin-induced injury was evaluated by measuring changes in cardiac function using high-frequency ultrasound biomicroscopy. Selective inhibition of phospholipase C activity in wild-type mice by its inhibitor, U73122, exacerbated adriamycin-induced cardiac dysfunction. Inhibition of phospholipase C-delta1 resulted in the significant decrease of left ventricular ejection fraction and fractional shortening, and the decreased levels were similar to those observed in adriamycin-treated double TNF receptor-deficient mice. The data derived from the global genome analysis identified phospholipase C-delta1 as an important target for TNF receptors and revealed the critical role of TNF receptor signaling in the protection against adriamycin-induced cardiotoxicity.
Severe Community-acquired Pneumonia: Risk Factors and Follow-up Epidemiology (1999)

The aim of the study was to determine risk factors for severe community-acquired pneumonia (CAP) as well as to compare microbial patterns of severe CAP to a previous study from our respiratory intensive care unit (ICU) originating from 1984 to 1987. Patients admitted to the ICU according to clinical judgment were defined as having severe CAP. For the study of risk factors, a hospital-based case-control design was used, matching each patient with severe CAP to a patient hospitalized with CAP but not requiring ICU admission. Microbial investigation included noninvasive and invasive techniques. Overall, 89 patients with severe CAP were successfully matched to a control patient. The presence of an alcohol ingestion of >/= 80 g/d (odds ratio [OR] 3.9, 95% confidence interval [CI] 1.4 to 10.6, p = 0.008) was found to be an independent risk factor for severe CAP and prior ambulatory antimicrobial treatment (OR 0.37, 95% CI 0.17 to 0.79, p = 0.009) to be protective. Streptococcus pneumoniae (24%) continued to be the most frequent pathogen; however, 48% of strains were drug-resistant. "Atypical" bacterial pathogens were significantly more common (17% versus 6%, p = 0.006) and Legionella spp. less common (2% versus 14%, p = 0.004) than in our previous study, whereas gram-negative enteric bacilli (GNEB) and Pseudomonas aeruginosa continued to represent important pathogens (6% and 5%, respectively). Our findings provide additional evidence for the importance of the initiation of early empiric antimicrobial treatment for a favorable outcome of CAP. Variations of microbial patterns are only in part due to different epidemiological settings. Therefore, initial empiric antimicrobial treatment will also have to take into account local trends of changing microbial patterns.
Underlying Causes and Survival in Patients with Heart Failure (2000)

Heart failure is a major health problem in the United States. It is estimated that 4.6 million Americans are currently treated for heart failure and that approximately 550,000 new cases are diagnosed each year.1 Despite advances in therapy, including the widespread use of angiotensin-converting–enzyme inhibitors and the introduction of beta-adrenergic antagonists, mortality associated with heart failure remains high.2 In a recent community-based survey, one-year and five-year survival rates after the onset of heart failure were 76 percent and 35 percent, respectively.3 In 1998, heart failure contributed to 260,000 deaths in the United States.1 The accurate assessment of prognosis in heart . . .
Development of PCR for screening of enteroaggregative Escherichia coli (1995)

In this study, we determined the sequence of the EcoRI-PstI fragment of the plasmid pCVD432, also termed the enteroaggregative Escherichia coli (EAggEC) probe. A primer pair complementary to this probe was designed for PCR amplification of a 630-bp region. Comparison of the analysis of the EAggEC probe sequence with those in database libraries revealed no significant similarity to any known bacterial gene. Pure cultures of E. coli cells, as well as mixed cultures from stool specimens, were investigated with the PCR assay, the EAggEC probe test, and the adherence test. Of 50 E. coli strains which demonstrated aggregative adherence to HEp-2 cells, 43 (86%) were positive with the EAggEC PCR. All 43 of these strains reacted with the EAggEC probe. Six EAggEC strains gave negative results by both molecular techniques. In contrast, only 4 of 418 (0.96%) strains representing other categories of diarrheagenic E. coli demonstrated a positive PCR result. The PCR was also successful in screening for the presence of EAggEC in enriched cultures grown from stool specimens. Compared with cell culture assays and colony hybridization, our findings revealed that the PCR assay was more rapid, simple, and highly sensitive and can therefore be recommended as a screening method for EAggEC in the clinical laboratory.
Differential Scanning Calorimetry (2003)

Differential scanning calorimetry (DSC) is now generally accepted as the technique of choice to determine the energetics of protein folding/ unfolding transitions and the thermodynamic mechanisms underlying those reactions. Despite this fact, the theoretical framework necessary for the analysis of calorimetric data is not available to the general scientist in a comprehensive way. The purpose of this chapter is to present in a succinct form the fundamental theory of differential scanning calorimetry, to summarize the information that can be obtained with this technique, and to alert the reader of some potential problems in data interpretation.
Automated MALDI Matrix Deposition Method with Inkjet Printing for Imaging Mass Spectrometry (2007)

Careful matrix deposition on tissue samples for matrix-assisted laser desorption/ionization (MALDI) is critical for producing reproducible analyte ion signals. Traditional methods for matrix deposition are often considered an art rather than a science, with significant sample-to-sample variability. Here we report an automated method for matrix deposition, employing a desktop inkjet printer (<$200) with 5760 x 1440 dpi resolution and a six-channel piezoelectric head that delivers 3 pL/drop. The inkjet printer tray, designed to hold CDs and DVDs, was modified to hold microscope slides. Empty ink cartridges were filled with MALDI matrix solutions, including DHB in methanol/water (70:30) at concentrations up to 40 mg/mL. Various samples (including rat brain tissue sections and standards of small drug molecules) were prepared using three deposition methods (electrospray, airbrush, inkjet). A linear ion trap equipped with an intermediate-pressure MALDI source was used for analyses. Optical microscopic examination showed that matrix crystals were formed evenly across the sample. There was minimal background signal after storing the matrix in the cartridges over a 6-month period. Overall, the mass spectral images gathered from inkjet-printed tissue specimens were of better quality and more reproducible than from specimens prepared by the electrospray and airbrush methods.
Argumentation through a distributed self-stabilizing approach (2002)

Abstract Argumentation is receiving an increasing attention as a technique for practical and uncertain reasoning underlying the realization of intelligent autonomous agents. Since a decentralized organization has been proposed by several authors as an appropriate paradigm for the design of agent architectures, we propose in this article, a distributed approach to argumentation, in which several independent asynchronous processes carry out argumentation activity, by exploiting local information only. The final result of this process is the computation of the defeat status of the arguments: we devise a general distributed algorithm, which does not rely on any specific notion of defeat between arguments. The issue of coordination has been explicitly tackled by ensuring the property of self-stabilization for the algorithm. A proof of its correctness, as well as an analysis of its complexity, is provided. Keywords: ArgumentationDistributed ComputingAgents
Organizational Research: Determining Organizational Research: Determining Appropriate Sample Size in Survey Research Appropriate Sample Size in Survey Research (2001)

The determination of sample size is a common task for many organizational researchers. Inappropriate, inadequate, or excessive sample sizes continue to influence the quality and accuracy of research. This manuscript describes the procedures for determining sample size for continuous and categorical variables using Cochran’s (1977) formulas. A discussion and illustration of sample size formulas, including the formula for adjusting the sample size for smaller populations, is included. A table is provided that can be used to select the sample size for a research problem based on three alpha levels and a set error rate. Procedures for determining the appropriate sample size for multiple regression and factor analysis, and common issues in sample size determination are examined. Non-respondent sampling issues are addressed.
Identification of Multiple Osteoclast Precursor Populations in Murine Bone Marrow (2006)

We provided a refined analysis of the precise subpopulations of murine BM that are capable of differentiating into OCLs in vitro when treated with M-CSF and RANKL.
Electrical Stimulation Modulates Fate Determination of Differentiating Embryonic Stem Cells (2006)

A clear understanding of cell fate regulation during differentiation is key in successfully using stem cells for therapeutic applications. Here, we report that mild electrical stimulation strongly influences embryonic stem cells to assume a neuronal fate. Although the resulting neuronal cells showed no sign of specific terminal differentiation in culture, they showed potential to differentiate into various types of neurons in vivo, and, in adult mice, contributed to the injured spinal cord as neuronal cells. Induction of calcium ion influx is significant in this differentiation system. This phenomenon opens up possibilities for understanding novel mechanisms underlying cellular differentiation and early development, and, perhaps more importantly, suggests possibilities for treatments in medical contexts.
A technic for the detection of rupture of the membranes. A review and preliminary report. (1976)

Correct diagnosis of rupture of the fetal membranes is sometimes difficult. A new technic is proposed to confirm the diagnosis of rupture of the membranes based on the introduction of sodium fluorescein into the amniotic cavity via transabdominal amniocentesis.
Docking Studies on αvβ3 Integrin Ligands:  Pharmacophore Refinement and Implications for Drug Design (2003)

Starting from the first crystal structure of the extracellular segment of the alpha(v)beta(3) integrin receptor with a cyclic RGD ligand bound to the active site, structural models for the interactions of known ligands with the alpha(v)beta(3) integrin receptor were generated by automated computational docking. The obtained complexes were evaluated for their consistency with structure-activity relationships and site-directed mutagenesis data. A comparison between the calculated interaction free energies and the experimental biological activities was also made. All the possible interactions of the investigated compounds at the active site and the probable ligand binding conformations provide an improved basis for structure-based rational ligand design. Additionally, our docking results allow a further validation and refinement of the pharmacophore model previously postulated by us.
TET2 gene mutation is a frequent and adverse event in chronic myelomonocytic leukemia (2009)

TET2 gene alterations are more frequent in chronic myelomonocytic leukemia than in other subgroups of hematopoietic diseases studied so far and could negatively affect the patients' outcome. The striking association between TET2 gene alterations and monocytosis, already observed in patients with systemic mastocytosis, could indicate a negative role of TET2 in the control of monocytic lineage determination.
Extended application of suffix trees to data compression (2002)

A practical scheme for maintaining an index for a sliding window in optimal time and space, by use of a suffix tree, is presented. The index supports location of the longest matching substring in time proportional to the length of the match. The total time for build and update operations is proportional to the size of the input. The algorithm, which is simple and straightforward, is presented in detail. The most prominent lossless data compression scheme, when considering compression performance, is prediction by partial matching with unbounded context lengths (PPM). However, previously presented algorithms are hardly practical, considering their extensive use of computational resources. We show that our scheme can be applied to PPM-style compression, obtaining an algorithm that runs in linear time, and in space bounded by an arbitrarily chosen window size. Application to Ziv-Lempel (1977) compression methods is straightforward and the resulting algorithm runs in linear time.
Treatment of Refractory Immune Thrombocytopenic Purpura with an Anti-Fcγ-Receptor Antibody (1986)

THE production of antiplatelet antibodies and removal of IgG-coated platelets by the mononuclear phagocyte system play an important part in the pathogenesis of immune thrombocytopenic purpura. The coating of platelets with immunoglobulin results in their removal in the spleen and liver, presumably by receptors for the Fc fragment of IgG (Fcγ).1 , 2 Prolongation of Fcγ-receptor-mediated clearance of opsonized red cells after splenectomy1 , 3 and infusions of high doses of intravenous gamma globulin,4 , 5 in conjunction with favorable clinical responses to these therapies, support this hypothesis. Some patients, however, respond to neither of these treatments nor to other, less specific forms of immunosuppression, such . . .
Integrin Function in T-Cell Homing to Lymphoid and Nonlymphoid Sites: Getting There and Staying There (2009)

The continuous recirculation of naive T cells and their subsequent migration to tissue following activation is crucial for maintaining protective immunity against invading pathogens. The preferential targeting of effector and memory T cells to tissue is instructed during priming and mediated by cell surface expressed adhesion receptors such as integrins. Integrins arc involved in nearly all aspects of T-cell life, including naive T-cell circulation, activation, and finally effector T-cell trafficking and localization. Recent research has revealed that microenvironmental factors present during T-cell priming result in the specific regulation of adhesion/integrin and chemokine receptor expression. Once antigen-experienced T cells enter tissue, further changes in integrin expression may occur that arc critical for T-cell localization, retention, effector function, and survival. This review discusses the function of integrin expression on T cells and the multiple roles integrins play on naive T cells and in directing effector T-cell trafficking to nonlymphoid sites in order to maintain protective adaptive immunity at body barriers.
Colonic mucosal microbiome differs from stool microbiome in cirrhosis and hepatic encephalopathy and is linked to cognition and inflammation (2012)

Although hepatic encephalopathy (HE) is linked to the gut microbiota, stool microbiome analysis has not found differences between HE and no-HE patients. This study aimed to compare sigmoid mucosal microbiome of cirrhotic patients to controls, between HE vs. no-HE patients, and to study their linkage with cognition and inflammation. Sixty cirrhotic patients (36 HE and 24 no-HE) underwent cognitive testing, stool collection, cytokine (Th1, Th2, Th17, and innate immunity), and endotoxin analysis. Thirty-six patients (19 HE and 17 no-HE) and 17 age-matched controls underwent sigmoid biopsies. Multitag pyrosequencing (including autochthonous genera, i.e., Blautia, Roseburia, Fecalibacterium, Dorea) was performed on stool and mucosa. Stool and mucosal microbiome differences within/between groups and correlation network analyses were performed. Controls had significantly higher autochthonous and lower pathogenic genera compared with cirrhotic patients, especially HE patients. HE patients had worse MELD (model for end-stage liver disease) score and cognition and higher IL-6 and endotoxin than no-HE. Mucosal microbiota was different from stool within both HE/no-HE groups. Between HE/no-HE patients, there was no difference in stool microbiota but mucosal microbiome was different with lower Roseburia and higher Enterococcus, Veillonella, Megasphaera, and Burkholderia abundance in HE. On network analysis, autochthonous genera (Blautia, Fecalibacterium, Roseburia, and Dorea) were associated with good cognition and decreased inflammation in both HE/no-HE, whereas genera overrepresented in HE (Enterococcus, Megasphaera, and Burkholderia) were linked to poor cognition and inflammation. Sigmoid mucosal microbiome differs significantly from stool microbiome in cirrhosis. Cirrhotic, especially HE, patients' mucosal microbiota is significantly different from controls with a lack of potentially beneficial autochthonous and overgrowth of potentially pathogenic genera, which are associated with poor cognition and inflammation.
Viewing characteristics based personalized ad streaming in an interactive TV environment (2004)

The growth in digital TV penetration has resulted in an enormous research initiative in community-specific and home/user-specific target advertising. We propose a channel surfing analysis (CSA) algorithm for predicting the "user(s) in front" of TV by a dynamic analysis of channel viewing characteristics. Such a user identification can be used along with a home information system to decide categorically about the nature of advertisements that are likely to have an impact. The proposed CSA algorithm uses a time-based FSM representation of channel viewing (remote usage) patterns that can be analyzed and processed in multiple ways leading to sophisticated algorithms. Taking into account the fact that not all channel switches provide equal cues about user characteristics, we suggest a multiscale approach to analyze the FSM at various levels of abstraction. We are in the process of integrating the CSA algorithm with an MHP (multimedia home platform) based interactive TV platform that is currently under development.
Aspartate‐assisted immune stimulation: Its importance in antitumor and antiviral protection (1986)

Immune stimulators such as Corynebacterium parvum (CP) are useful for antitumoral and antiviral therapy. However, the immune trigger cannot be reactivated without adversely affecting the disease. We have tried to amplify the results yielded by a single injection of CP by using either interleukin-2 (IL2) or aspartate salts (ASP). In the present report, we show that IL2 has no detectable clinical effect. In contrast, the addition of an ASP salt increases the antiviral and antitumoral protection afforded by the CP-induced trigger. Moreover, treatment using only ASP slightly protects against tumor development and significantly increases antiviral resistance during experimental encephalomyocarditis (EMC) infection. This ASP-assisted CP immune stimulation improves antitumoral resistance even when ascitic tumors have already developed. In the latter case, tumor regression can even be detected. Since ASP increases T-cell cytotoxicity in vitro and aggravates spontaneous T-cell lymphomas in AKR mice, the involvement of T-cell-mediated immunity may explain antitumoral and antiviral effects. We propose the use of this therapeutic model for human cancer therapy, and possibly for treating AIDS.
Block of proliferation 1 (BOP1) plays an oncogenic role in hepatocellular carcinoma by promoting epithelial-to-mesenchymal transition (2011)

Our findings underline an important role for BOP1 in HCC invasiveness and metastasis potentials through inducing EMT and promoting actin cytoskeleton remodeling.
The Inositol 1,4,5-Trisphosphate Receptor Is Required to Signal Autophagic Cell Death (2007)

The signaling pathways governing pathophysiologically important autophagic (ACD) and necrotic (NCD) cell death are not entirely known. In the Dictyostelium eukaryote model, which benefits from both unique analytical and genetic advantages and absence of potentially interfering apoptotic machinery, the differentiation factor DIF leads from starvation-induced autophagy to ACD, or, if atg1 is inactivated, to NCD. Here, through random insertional mutagenesis, we found that inactivation of the iplA gene, the only gene encoding an inositol 1,4,5-trisphosphate receptor (IP3R) in this organism, prevented ACD. The IP3R is a ligand-gated channel governing Ca(2+) efflux from endoplasmic reticulum stores to the cytosol. Accordingly, Ca(2+)-related drugs also affected DIF signaling leading to ACD. Thus, in this system, a main pathway signaling ACD requires IP3R and further Ca(2+)-dependent steps. This is one of the first insights in the molecular understanding of a signaling pathway leading to autophagic cell death.