gebhart/patrepeval huggingface dataset:
p53- and Drug-Induced Apoptotic Responses Mediated by BH3-Only Proteins Puma and Noxa (2003)

Apoptosis provoked by DNA damage requires the p53 tumor suppressor, but which of the many p53-regulated genes are required has remained unknown. Two genes induced by this transcription factor, noxa and puma (bbc3), stand out, because they encode BH3-only proteins, proapoptotic members of the Bcl-2 family required to initiate apoptosis. In mice with either noxa or puma disrupted, we observed decreased DNA damage-induced apoptosis in fibroblasts, although only loss of Puma protected lymphocytes from cell death. Puma deficiency also protected cells against diverse p53-independent cytotoxic insults, including cytokine deprivation and exposure to glucocorticoids, the kinase inhibitor staurosporine, or phorbol ester. Hence, Puma and Noxa are critical mediators of the apoptotic responses induced by p53 and other agents.
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis (2002)

During a systematic analysis of conserved gene context in prokaryotic genomes, a previously undetected, complex, partially conserved neighborhood consisting of more than 20 genes was discovered in most Archaea (with the exception of Thermoplasma acidophilum and Halobacterium NRC-1) and some bacteria, including the hyperthermophiles Thermotoga maritima and Aquifex aeolicus. The gene composition and gene order in this neighborhood vary greatly between species, but all versions have a stable, conserved core that consists of five genes. One of the core genes encodes a predicted DNA helicase, often fused to a predicted HD-superfamily hydrolase, and another encodes a RecB family exonuclease; three core genes remain uncharacterized, but one of these might encode a nuclease of a new family. Two more genes that belong to this neighborhood and are present in most of the genomes in which the neighborhood was detected encode, respectively, a predicted HD-superfamily hydrolase (possibly a nuclease) of a distinct family and a predicted, novel DNA polymerase. Another characteristic feature of this neighborhood is the expansion of a superfamily of paralogous, uncharacterized proteins, which are encoded by at least 20-30% of the genes in the neighborhood. The functional features of the proteins encoded in this neighborhood suggest that they comprise a previously undetected DNA repair system, which, to our knowledge, is the first repair system largely specific for thermophiles to be identified. This hypothetical repair system might be functionally analogous to the bacterial-eukaryotic system of translesion, mutagenic repair whose central components are DNA polymerases of the UmuC-DinB-Rad30-Rev1 superfamily, which typically are missing in thermophiles.
Sacral Nerve Neuromodulation Is Effective Treatment for Fecal Incontinence in the Presence of a Sphincter Defect, Pudendal Neuropathy, or Previous Sphincter Repair (2010)

Sacral nerve neuromodulation results in a significant improvement in fecal incontinence and Fecal Incontinence Quality of Life scores after medium-term follow-up, even when there is a sphincter defect or pudendal neuropathy.
Protein Kinase C δ (PKCδ) Splice Variants Modulate Apoptosis Pathway in 3T3L1 Cells during Adipogenesis (2013)

Increased food intake and lack of physical activity results in excess energy stored in adipocytes, and this imbalance contributes to obesity. New adipocytes are required for storage of energy in the white adipose tissue. This process of adipogenesis is widely studied in differentiating 3T3L1 preadipocytes in vitro. We have identified a key signaling kinase, protein kinase C delta (PKCδ), whose alternative splice variant expression is modulated during adipogenesis. We demonstrate that PKCδII splice variant promotes survival in differentiating 3T3L1 cells through the Bcl2 pathway. Here we demonstrate that resveratrol, a naturally occurring polyphenol, increases apoptosis and inhibits adipogenesis along with disruption of PKCδ alternative splicing during 3T3L1 differentiation. Importantly, we have identified a PKCδII splice variant inhibitor. This inhibitor may be a valuable tool with therapeutic implications in obesity.
Integration between point-of-care cardiac markers in an emergency/cardiology department and the central laboratory: methodological and preliminary clinical evaluation (2005)

To achieve rapid assessment of chest pain in emergency/cardiology departments, a short turnaround time for cardiac marker testing is necessary. Nevertheless, Total Quality Management principles must be incorporated into the management of point-of-care testing (POCT); in this setting we implemented the Stratus CS assay as POCT for cardiac markers in our emergency/cardiology department. The analytical performance of the troponin I method was evaluated; information connectivity between the Stratus CS data management system and the laboratory information system was implemented and practical training of testing personnel was carried out at the POCT site. A total of 41 non-ST-segment elevation patients admitted to the hospital were followed to evaluate the appropriateness of hospital admission, formulated on the basis of the cardiac troponin-I level measured at the POCT site by clinical staff. Our preliminary clinical data suggest that the high sensitivity of the Stratus CS troponin method could play an important role in the early identification of patients with acute myocardial infarction in a low to intermediate-risk population for acute coronary syndrome. Our POCT model suggests that the central laboratory could ensure that the POCT program remains in compliance with quality requirements. Nevertheless, our comparison studies suggest that the implementation of POCT requires a high level of integration between cardiologists and pathologists to guarantee appropriate interpretation of the monitoring results for suspected ACS patients.
Myofascial pain syndrome. (1987)

Myofascial pain, a general descriptive term, is applied to painful sensations that extend along one or more skeletal muscles and their fascia. Trigger points, discrete hyperesthetic areas within the muscle and its fascia, are characteristically found in myofascial pain. On the other hand, myofascial pain syndrome is a painful condition characterized by the presence of trigger points, local and referred pain, tenderness, referred autonomic phenomena as well as anxiety and depression. Patients affected by myofascial pain, trigger points, or myofascial pain syndrome, represent a significant population group requesting services in the offices of general practitioners, orthopaedic surgeons, and physicians treating musculoskeletal disorders.
Defining lupus cases for clinical studies: the Boston weighted criteria for the classification of systemic lupus erythematosus. (2002)

The Boston Criteria identify a larger number of patients compared with the current ACR criteria, while retaining face validity. This reflects the inclusion of patients with objective findings of SLE but less than 4 ACR criteria. Our Boston Criteria system could minimize selection bias and increase the generalizability of clinical SLE studies.
Development and characterization of a long-acting recombinant hFSH agonist (2003)

rhFSH-N2 has prolonged half-life and increased bioactivity compared with native rhFSH. This rhFSH agonist, and other analogues containing additional N-oligosaccharides may have important clinical applications.
Application of flow cytometry for biomarker‐based cervical cancer cells detection (2008)

The Pap test used for cervical cancer screening is subjective, labor-intensive, and has relatively low sensitivity and specificity for the detection of underlying clinically significant lesions. The objective of this study is to develop a biomarker/flow cytometry-based approach for cervical cancer screening. Immunofluorescence technology to quantify cervical cell expression of two biomarkers p16(INK4A) and Mcm5 was developed and evaluated by both microscopy and flow cytometry. The capability of using biomarker/flow cytometry approach to detect rare-event dysplastic cells in a large background of benign epithelial and inflammatory cells was evaluated. The results indicate that flow cytometry could detect 0.01% dysplastic cells in a background of normal cervical epithelial cells with the combination of the two biomarkers. Thirty-two clinical specimens were used to test the biomarker/flow cytometry-based approach and the results were compared with the liquid-based cervical cytology. The experiment yielded 100% sensitivity and 93% specificity with reference to the liquid-based cervical cytology. This study indicates the promise of using multi-color fluorescence flow cytometry for biomarker-based cervical cancer screening. This molecular-based, potentially high-throughput and automated method is expected to provide an alternative/auxiliary means of cervical cancer screening.
Secondary structural features in the 70S RNAs of Moloney murine leukemia and Rous sarcoma viruses as observed by electron microscopy (1981)

The secondary structural features in the 70S RNAs of the Prague strain of avian Rous sarcoma virus, subgroup A (PR-RSV-A), and Moloney murine leukemia virus (M-MuLV) were compared by electron microscopy. The PR-RSV-A genome contained two subunits joined by a linkage structure as in the genomes of M-MuLV and other mammalian retroviruses. In both viral genomes, a highly reproducible hairpin occurred at about 70 nucleotides from the 5' end of each subunit and contained 320 +/- 8 nucleotides. The stable point of linkage between the subunits in both viral genomes involved fewer than 50 nucleotides and occurred at 466 +/- 9 nucleotides from the 5' end. This places the linkage about 350 nucleotides further toward the 3' end of the subunit than the binding site of primer tRNA. Another structural feature common to both genomes was a loop in each subunit. In M-MuLV, the loop contained 3.9 +/- 0.10 kilobases (kb) and occurred at a distance of 2.2 +/- 0.05 kb from the 5' end. In PR-RSV-A, the loop was smaller (2.3 +/- 0.10 kb) and further (3.3 +/- 0.10 kb) from the 5' end. When M-MuLV RNA was heated to 70, 85, or 90 degrees C and cooled, the hairpin consistently reformed at the 5' end. No other structures typical of the native molecules reappeared. In RNA samples heated to 70 degrees C, a new loop reproducibly occurred near the 5' end of each subunit, but this loop was not found in samples heated to higher temperatures. Based on all of these findings, we conclude that the genome of PR-RSV-A shares several features with M-MuLV and other mammalian retroviruses and that the primer tRNA molecules are not involved in the linkage of the two subunits in either genome. We also conclude that the dimer linkage and the loops in subunits are typical of the native molecules and that their formation requires a special environment.
CagA Tyrosine Phosphorylation in Gastric Epithelial Cells Caused by Helicobacter pylori in Patients with Gastric Adenocarcinoma (2003)

CagA tyrosine phosphorylation, which is significantly greater in strains from gastric adenocarcinoma patients, may play a role in gastric carcinogenesis, and could be a better marker of more virulent strains than the cag pathogenicity island in Asia, where the cag pathogenicity island is present in nearly all H. pylori strains. Sequence diversity of tyrosine phosphorylation motifs on CagA was not related to the presence of tyrosine phosphorylation. The absence of tyrosine phosphorylation motif might result in negative tyrosine phosphorylation phenotypes, but such motifs are not the sole factors associated with CagA tyrosine phosphorylation.
In Vivo Bioluminescent Imaging of Influenza A Virus Infection and Characterization of Novel Cross-Protective Monoclonal Antibodies (2013)

Influenza A virus is a major human pathogen responsible for seasonal epidemics as well as pandemic outbreaks. Due to the continuing burden on human health, the need for new tools to study influenza virus pathogenesis as well as to evaluate new therapeutics is paramount. We report the development of a stable, replication-competent luciferase reporter influenza A virus that can be used for in vivo imaging of viral replication. This imaging is noninvasive and allows for the longitudinal monitoring of infection in living animals. We used this tool to characterize novel monoclonal antibodies that bind the conserved stalk domain of the viral hemagglutinin of H1 and H5 subtypes and protect mice from lethal disease. The use of luciferase reporter influenza viruses allows for new mechanistic studies to expand our knowledge of virus-induced disease and provides a new quantitative method to evaluate future antiviral therapies.
CD27/CD70 Interaction Augments IgE Secretion by Promoting the Differentiation of Memory B Cells into Plasma Cells (1998)

The induction of IgE switching in B cells requires several signals given by cytokines and cell contact-delivered signals. Here, we investigated the role of CD27/CD70 interaction in B cell IgE synthesis. The addition of CD27 ligand (CD70) transfectants to B cell cultures increased the IgE synthesis synergistically in the presence of IL-4 plus anti-CD40 mAb (anti-CD40). The effect of CD70 transfectants was dose dependent and was completely blocked by anti-CD70 mAb. CD27+ B cells had the ability to produce IgE, which was increased by contact with CD70 transfectants, whereas CD27- B cells did not produce IgE. CD27/CD70 interaction enhanced B cell proliferation in the presence of IL-4 or IL-4 plus anti-CD40. The augmentation of B cell proliferation by CD70 transfectants was apparent in CD27+ B cells, but was mild in CD27- B cells. The helper activity for IgE synthesis by the CD27/CD70 interaction did not contribute to the enhancement of germline epsilon transcripts. Flow cytometric and morphological analyses demonstrated that the addition of CD70 transfectants to B cell cultures remarkably promoted differentiation into plasma cells in the presence of IL-4 and CD40 signaling. Finally, CD27 cross-linking resulted in the up-regulation of positive regulatory domain I-binding factor-1. Taken together, our findings indicate that signaling via CD27 on B cells induces IgE synthesis, in cooperation with IL-4 and CD40 signaling, by promoting the generation of plasma cells through up-regulation of positive regulatory domain I-binding factor-1.
Dynamic spike threshold reveals a mechanism for synaptic coincidence detection in cortical neurons in vivo (2000)

Cortical neurons are sensitive to the timing of their synaptic inputs. They can synchronize their firing on a millisecond time scale and follow rapid stimulus fluctuations with high temporal precision. These findings suggest that cortical neurons have an enhanced sensitivity to synchronous synaptic inputs that lead to rapid rates of depolarization. The voltage-gated currents underlying action potential generation may provide one mechanism to amplify rapid depolarizations. We have tested this hypothesis by analyzing the relations between membrane potential fluctuations and spike threshold in cat visual cortical neurons recorded intracellularly in vivo. We find that visual stimuli evoke broad variations in spike threshold that are caused in large part by an inverse relation between spike threshold and the rate of membrane depolarization preceding a spike. We also find that spike threshold is inversely related to the rate of rise of the action potential upstroke, suggesting that increases in spike threshold result from a decrease in the availability of Na(+) channels. By using a simple neuronal model, we show that voltage-gated Na(+) and K(+) conductances endow cortical neurons with an enhanced sensitivity to rapid depolarizations that arise from synchronous excitatory synaptic inputs. Thus, the basic mechanism responsible for action potential generation also enhances the sensitivity of cortical neurons to coincident synaptic inputs.
[Construction of eukaryote expression vector carrying human soluble interleukin-1 receptor gene]. (2003)

The sIL-1R gene was successfully inserted into the eukaryote expression vector plasmid pcDNA 3.1(+) by the recombination technique in vitro.
Mechanical Stimuli to Airway Remodeling (2001)

The airway is exposed to a variety of mechanical stimuli, the most prominent of which is the acute compressive stress caused by bronchoconstriction. The folding of the airway wall into a rosette pattern during bronchoconstriction creates a complex stress field, with the highest stresses compressing the epithelial layer at the inner surface of the airway wall. The epithelial cells lining the airway possess the capacity to modulate the inflammatory environment of the airway wall, and produce factors that influence the recruitment, proliferation, and activity of fibroblasts and smooth muscle cells. A variety of in vitro studies have demonstrated that airway epithelial cells, along with lung fibroblasts and smooth muscle cells, are responsive to mechanical stimuli. Airway epithelial cells exposed to compressive stresses matched to those occurring in the constricted airway increase expression of genes relevant to airway remodeling, and increase the collagen synthesis of cocultured fibroblasts. These findings demonstrate that mechanical stress may contribute to the remodeling of the asthmatic airway.
Model Driven Design of Distribution Patterns forWeb Service Compositions (2006)

Increasingly, distributed systems are being constructed by composing a number of discrete components. This practice, termed composition, is particularly prevalent within the Web service domain. Here, enterprise systems are built from many existing discrete applications, often legacy applications exposed using Web service interfaces. There are a number of architectural configurations or distribution patterns, which express how a composed system is to be deployed. However, the amount of code required to realise these distribution patterns is considerable. In this paper, we propose a novel Model Driven Architecture using UML 2.0, which takes existing Web service interfaces as its input and generates an executable Web service composition, based on a distribution pattern chosen by the software architect.
Regulation of Osteoblast Differentiation Mediated by Bone Morphogenetic Proteins, Hedgehogs, and Cbfa1 (2000)

Osteoblasts arise from common progenitors with chondrocytes, muscle and adipocytes, and various hormones and local factors regulate their differentiation. We review here regulation of osteoblast differentiation mediated by the local factors such as bone morphogenetic proteins (BMPs) and hedgehogs and the transcription factor, core-binding factor alpha-1 (Cbfa1). BMPs are the most potent regulators of osteoblast differentiation among the local factors. Sonic and Indian hedgehogs are involved in osteoblast differentiation by interacting with BMPs. Cbfa1, a member of the runt domain gene family, plays a major role in the processes of a determination of osteoblast cell lineage and maturation of osteoblasts. Cbfa1 is an essential transcription factor for osteoblast differentiation and bone formation, because Cbfa1-deficient mice completely lacked bone formation due to maturation arrest ofosteoblasts. Although the regulatory mechanism of Cbfa1 expression has not been fully clarified, BMPs are an important local factor that up-regulates Cbfa1 expression. Thus, the intimate interaction between local factors such as BMPs and hedgehogs and the transcription factor, Cbfa1, is important to osteoblast differentiation and bone formation.
Urolithins, Intestinal Microbial Metabolites of Pomegranate Ellagitannins, Exhibit Potent Antioxidant Activity in a Cell-Based Assay (2009)

Many health benefits of pomegranate products have been attributed to the potent antioxidant action of their tannin components, mainly punicalagins and ellagic acid. While moving through the intestines, ellagitannins are metabolized by gut bacteria into urolithins that readily enter systemic circulation. In this study, the antioxidant properties of seven urolithin derivatives were evaluated in a cell-based assay. This method is biologically more relevant because it reflects bioavailability of the test compound to the cells, and the antioxidant action is determined in the cellular environment. Our results showed that the antioxidant activity of urolithins was correlated with the number of hydroxy groups as well as the lipophilicity of the molecule. The most potent antioxidants are urolithins C and D with IC(50) values of 0.16 and 0.33 microM, respectively, when compared to IC(50) values of 1.1 and 1.4 microM of the parent ellagic acid and punicalagins, respectively. The dihydroxylated urolithin A showed weaker antioxidant activity, with an IC(50) value 13.6 microM, however, the potency was within the range of urolithin A plasma concentrations. Therefore, products of the intestinal microbial transformation of pomegranate ellagitannins may account for systemic antioxidant effects.
COMPARATIVE STUDY OF JUSTICE IN ORGANIZATION AND ITS IMPACT ON EMPLOYEE COMMITMENT (2014)

The intention of this study was to observe the position/occurrence and effect of justice on employees' commitment in three different areas namely multinational, local private and government organizations. The study found the impacts of distributive, procedural, informational and interpersonal type of justice on commitment. Further the paper compared the results and tried to explain the reasons for variations. Pretested questionnaire, based on five likert scale, was distributed by stratified random sampling technique. Interviews were arranged especially for qualitative and exploratory part of the paper. Mean value, correlation, Alpha, Beta, R, R-Squire, ANOVA and T-test results which found through SPSS. In multinational organizations reasonable justice and commitment was observed while the results were inverse in local private organizations. In government sector justice was not perceived but a questionable commitment was detected. In multinational and local private organizations the study found the impact of justice on commitment but in government sector the study explored the reasons for no relation between justice and commitment. Organizational commitment was found more sensitive to procedural justice. Multinational organizations are valued more than local private organization in Pakistan. Some of the government organizations are going downward even with good resources. This study showed the backside of the picture by providing reasons. Sample size was small. In government sector some factors were exposed which were disturbing the relation of justice and commitment. More exploratory work is required in this area. The study suggests that the owners and managers of organizations should provide exemplary justice which will enhance commitment and will clear the road to the peak.
A rotational micro biopsy device for the capsule endoscope (2005)

Recently the technology of capsule endoscopy has developed dramatically and many researchers are making efforts to combine surgical function into the capsule type endoscope. In this paper, the micro biopsy module which is a part of the capsule endoscope is proposed. The proposed module is less than 2 mm in thickness and has a diameter of 10 mm. It consists of a trigger with paraffin block, rotational tissue-cutting razor with a torsion spring and controller. This module makes it possible for the capsule endoscope to obtain a sample tissue inside the small intestine which can not be reached by a conventional biopsy device. Through dedicated experiments, tissue samples were successfully extracted using the proposed biopsy module and the cells in samples were extracted and tested by a microscope.