gebhart/patrepeval huggingface dataset:
Adenovirus-Mediated Gene Transfer of the Human TIMP-1 Gene Inhibits Smooth Muscle Cell Migration and Neointimal Formation in Human Saphenous Vein (1998)

Neointimal formation involving smooth muscle cell (SMC) migration and proliferation is a common feature of atherosclerosis, restenosis after angioplasty, and vein graft intimal thickening. Extracellular matrix remodeling by metalloproteinase (MMP) enzymes is an essential component of neointimal formation and therefore MMPs are a potential target for localized gene therapy. To evaluate this concept using human tissue, we used the highly reproducible organ culture model of neointimal formation in human saphenous vein to investigate the effect of adenovirus-mediated gene transfer of tissue inhibitor of metalloproteinase 1 (TIMP-1) and the bacterial LacZ gene (RAd35) as a control. Incubating veins with 100 microl of RAd35 (1.2 x 10(10) pfu/ml) led to expression of LacZ in 39 +/- 7% of surface cells but had no effect on SMC proliferation, migration, or neointimal formation. Similar infection with RAdTIMP-1 increased explanation of TIMP-1 in surface cells and significantly inhibited neointimal formation and SMC migration after 14 days by 54% and 78%, respectively (n = 6, p < 0.05 Student's paired t test). No effect on SMC proliferation or deleterious effect on cell viability was observed. A specific MMP inhibitory effect was detected using in situ zymography. These data confirm the importance of MMPs in neointimal formation and highlight the potential for application of TIMP gene therapy.
Molecular Cloning and Characterization of a Novel CXC Chemokine Macrophage Inflammatory Protein-2γ Chemoattractant for Human Neutrophils and Dendritic Cells (2000)

Chemokines play important roles in leukocyte trafficking as well as function regulation. In this study, we described the identification and characterization of a novel CXC chemokine from a human dendritic cell (DC) cDNA library, the full-length cDNA of which contains an open reading frame encoding 111 aa with a putative signal peptide of 34 aa. This CXC chemokine shares greatest homology with macrophage inflammatory protein (MIP)-2alphabeta, hence is designated as MIP-2gamma. Mouse MIP-2gamma was identified by electrocloning and is highly homologous to human MIP-2gamma. Northern blotting revealed that MIP-2gamma was constitutively and widely expressed in most normal tissues with the greatest expression in kidney, but undetectable in most tumor cell lines except THP-1 cells. In situ hybridization analysis demonstrated that MIP-2gamma was mainly expressed by the epithelium of tubules in the kidney and hepatocytes in the liver. Although no detectable expression was observed in freshly isolated or PMA-treated monocytes, RT-PCR analysis revealed MIP-2gamma expression by monocyte-derived DC. Recombinant MIP-2gamma from 293 cells is about 9.5 kDa in size and specifically detectable by its polyclonal Ab developed by the immunization with its 6His-tagged fusion protein. The eukaryotically expressed MIP-2gamma is a potent chemoattractant for neutrophils, and weaker for DC, but inactive to monocytes, NK cells, and T and B lymphocytes. Receptor binding assays showed that MIP-2gamma does not bind to CXCR2. This implies that DC might contribute to the innate immunity through the production of neutrophil-attracting chemokines and extends the knowledge about the regulation of DC migration.
Biofilm Formation on Dental Restorative and Implant Materials (2010)

Biomaterials for the restoration of oral function are prone to biofilm formation, affecting oral health. Oral bacteria adhere to hydrophobic and hydrophilic surfaces, but due to fluctuating shear, little biofilm accumulates on hydrophobic surfaces in vivo. More biofilm accumulates on rough than on smooth surfaces. Oral biofilms mostly consist of multiple bacterial strains, but Candida species are found on acrylic dentures. Biofilms on gold and amalgam in vivo are thick and fully covering, but barely viable. Biofilms on ceramics are thin and highly viable. Biofilms on composites and glass-ionomer cements cause surface deterioration, which enhances biofilm formation again. Residual monomer release from composites influences biofilm growth in vitro, but effects in vivo are less pronounced, probably due to the large volume of saliva into which compounds are released and its continuous refreshment. Similarly, conflicting results have been reported on effects of fluoride release from glass-ionomer cements. Finally, biomaterial-associated infection of implants and devices elsewhere in the body is compared with oral biofilm formation. Biomaterial modifications to discourage biofilm formation on implants and devices are critically discussed for possible applications in dentistry. It is concluded that, for dental applications, antimicrobial coatings killing bacteria upon contact are more promising than antimicrobial-releasing coatings.
ABA triblock copolymers with a ring‐opening metathesis polymerization/macromolecular chain‐transfer agent approach (2006)

Abstract Block copolymers containing polystyrene and polycyclooctene were synthesized with a ring‐opening metathesis polymerization/chain‐transfer approach. Polystyrene, containing appropriately placed olefins, was prepared by anionic polymerization and served as a macromolecular chain‐transfer agent for the ring‐opening metathesis polymerization of cyclooctene. These unsaturated polymers were subsequently converted to the corresponding saturated triblock copolymers with a simple heterogeneous catalytic hydrogenation step. The molecular and morphological characterization of the block copolymers was consistent with the absence of significant branching in the central polycyclooctene and polyethylene blocks [high melting temperatures (114–127 °C) and levels of crystallinity (17–42%)]. A dramatic improvement in both the long‐range order and the mechanical properties of a microphase‐separated, symmetric polystyrene–polycyclooctene–polystyrene block copolymer sample was observed after fractionation. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 361–373, 2007
<title>Automation of systems enabling search on stored video data</title> (1997)

In the European project SMASH mass-market storage systems for domestic use are under study. Besides the storage technology that is developed in this project, the related objective of user-friendly browsing/query of video data is studied as well. Key issues in developing a user-friendly system are (1) minimizing the user-intervention in preparatory steps (extraction and storage of representative information needed for browsing/query), (2) providing an acceptable representation of the stored video content in view of a higher automation level, (3) the possibility for performing these steps directly on the incoming stream at storage time, and (4) parameter-robustness of algorithms used for these steps. This paper proposes and validate novel approaches for automation of mentioned preparatory phases. A detection method for abrupt shot changes is proposed, using locally computed threshold based on a statistical model for frame-to-frame differences. For the extraction of representative frames (key frames) an approach is presented which distributes a given number of key frames over the sequence depending on content changes in a temporal segment of the sequence. A multimedia database is introduced, able to automatically store all bibliographic information about a recorded video as well as a visual representation of the content without any manual intervention from the user.
Purification of the receptor for platelet-derived growth factor from porcine uterus. (1987)

The receptor for platelet-derived growth factor has been purified to homogeneity on a large scale from porcine uterus. The purification procedure utilizes solubilization of uterus membranes by Triton X-100, followed by sequential chromatographies on wheat germ agglutinin-Sepharose, fast protein liquid chromatography Mono-Q, and anti-phosphotyrosine-Sepharose. About 160 micrograms of homogeneous and functionally active 170-kDa receptor could be purified from 5 kg of uterus tissue. The pure receptor responded to platelet-derived growth factor stimulation by autophosphorylation, indicating that the receptor has a kinase domain as an integral part of the molecule. A rabbit antiserum was produced against the pure receptor, which specifically recognizes the intact 170-kDa receptor.
Prospects for Pharmacological Intervention in Alzheimer Disease (2000)

Alzheimer disease (AD) involves neuronal degeneration with impaired cholinergic transmission in the cerebral cortex and hippocampus in areas of the brain particularly associated with memory and higher intellectual functioning. Other neurotransmitter deficits also occur, but the mechanisms underlying the widespread impairment of synaptic functions remain uncertain. Research on the molecular basis of AD has elucidated a pathogenic pathway from which a range of rational pharmacological interventions has emerged. Although at least 3 cholinesterase inhibitors (tacrine hydrochloride, donepezil, and rivastigmine tartrate) are now available and provide patients with modest relief, the most promising strategy involves approaches to retarding, halting, or preventing the formation or accumulation of beta-amyloid (Abeta) plaques. Estrogen is believed to have antioxidant or other anti-Abeta effects, as hormonal replacement therapy in women with menopause is associated with a reduced risk or delayed onset of AD. The association between nonsteroidal anti-inflammatory drugs and a reduced risk of AD has not yet been confirmed, but these agents may protect the brain from the reactive glial and microglial responses associated with Abeta deposition. Also, recent studies suggested that antioxidants, such as vitamin E taken alone or in combination with selegiline hydrochloride, can delay the progression of AD. Despite these encouraging results, no current therapy has been shown to halt or reverse the underlying disease process. The proof of the principle that anti-Abeta drugs will work in the transgenic models of AD is eagerly awaited with the expectation that they will eventually prove successful in humans.
Clearance and beyond: the complementary roles of GFR measurement and injury biomarkers in acute kidney injury (AKI) (2011)

Acute kidney injury (AKI) is a common and frequently fatal illness in critically ill patients. The reliance on daily measurements of serum creatinine as a surrogate of glomerular filtration rate (GFR) not only delays diagnosis and development of successful therapies but also hinders insight into the pathophysiology of human AKI. Measurement of GFR under non-steady-state conditions remains an elusive gold standard against which biomarkers of renal injury need to be judged. Approaches to the rapid (near real-time) measurement of GFR are explored. Even if real-time GFR was available, absent baseline information will always limit diagnosis of AKI based on GFR or serum creatinine to a detection of change. Biomarkers of renal cellular injury have provided new strategies to facilitate detection and early intervention in AKI. However, the diagnostic and predictive performance of urinary biomarkers of injury vary, depending on both the time after renal injury and on the preinjury GFR. Progress in understanding the role of each novel biomarker in the causal pathways of AKI promises to enhance their diagnostic potential. We predict that combining rapid measures of GFR with biomarkers of renal injury will yield substantive progress in the treatment of AKI.
A simple microwave technique for plasma density measurement using frequency modulation (1984)

Describes a simple method of determining the phase variation unambiguously during microwave interferometric measurement. The frequency of the Klystron source is modulated with the help of staircase voltage pulse. The height of each stair is adjusted such that the corresponding phase shift in the test branch with an additional path length is 90 degrees . Signals, proportional to cosine and sine of the phase shift due to plasma, can be generated in the same channel and plasma density information can be inferred. The microwave hardware remains the same as in conventional interferometry and the cost of such a scheme is low.
The biological half-lives of four rat immunoglobulin isotypes. (1980)

Purified preparations of monoclonal rat IgG2a, IgG1, IgM and monomeric IgA, and of polyclonal IgG, were lightly radiolabelled with 125I and injected intravenously into rats. Blood samples were taken so that the half-life of each immunoglobulin isotype could be calculated. Half-life was defined as the time taken for the specific radioactivity present in the blood 24 h after injection to fall by half. The half-life values thus obtained were 106 h for IgG2a, 53 h for IgG1, 63 h for polyclonal IgG, 25 h for IgM and 27 h for monomeric IgA.
Methan Emission by Gut Symbionts of Termites (2009)

2 Abstract: Methanogenesis is a microbial process in which organic matter is assimilated and metabolized with the ultimate production of biogas that contains methane and carbon dioxide in the approximate ratio of 2:1. It represents a major electron sink in the metabolism of termites. An understanding of the dominant methanogens inside termite gut and their efficiency in the production of methane can find applications in the technology of methanogenesis. In this study, two methanogenic bacteria viz., Methanobacteria and Methanosarcina were identified and isolated. The effect of six methanogenic substrates, acetate, formate, tri methylamine, mono methylamine, methanol and H + CO , in situ emission by 22 Methanosarcina isolated from termite gut was studied under different temperatures. Maximum methane release was found to be 1596.32 µmol/g/h at 30 ± 2°C when acetate was used as a substrate while hydrogen and formate were found to be very poor substrates for the production of methane at both the temperatures. Among different castes of termites methane and carbon dioxide emission were maximum for higher termites (Macrotermitidae). In situ, queens of higher termites produced 0.69 and 0.30 µmol/g/h of methane and carbon dioxide respectively.
Rosiglitazone suppresses human lung carcinoma cell growth through PPARγ-dependent and PPARγ-independent signal pathways (2006)

Abstract Peroxisome proliferator-activated receptors γ (PPARγ) exert diverse effects on cancer cells. Recent studies showed that rosiglitazone, a synthetic ligand for PPARγ, inhibits cell growth. However, the exact mechanisms underlying this effect are still being explored, and the relevance of these findings to lung cancer remains unclear. Here, we report that rosiglitazone reduced the phosphorylation of Akt and increased phosphatase and tensin homologue (PTEN) protein expression in non–small cell lung carcinoma (NSCLC) cells (H1792 and H1838), and this was associated with inhibition of NSCLC cell proliferation. These effects were blocked or diminished by GW9662, a specific PPARγ antagonist. However, transfection with a CMX-PPARγ2 overexpression vector restored the effects of rosiglitazone on Akt, PTEN, and cell growth in the presence of GW9662. In addition, rosiglitazone increased the phosphorylation of AMP-activated protein kinase α (AMPKα), a downstream kinase target for LKB1, whereas it decreased phosphorylation of p70 ribosomal protein S6 kinase (p70S6K), a downstream target of mammalian target of rapamycin (mTOR). Of note, GW9662 did not affect the phosphorylation of AMPKα and p70S6K protein. The inhibitory effect of rosiglitazone on NSCLC cell growth was enhanced by the mTOR inhibitor rapamycin; however, it was blocked, in part, by the AMPKα small interfering RNA. Taken together, these findings show that rosiglitazone, via up-regulation of the PTEN/AMPK and down-regulation of the Akt/mTOR/p70S6K signal cascades, inhibits NSCLC cell proliferation through PPARγ-dependent and PPARγ-independent signals. [Mol Cancer Ther 2006;5(2):430–7]
Animal models of renal dysfunction: acute kidney injury (2009)

Various animal models of ARF are used for the development of therapeutic/preventive interventions, including toxic, hypoxic and septic models. Incomplete understanding of the outstanding complexity of human ARF often leads to too simplistic interventional concepts or to misconceptions, based on models with limited clinical relevance. Thus, for the appropriateness of animal models, the use of models inflicting severe injury, though highly reproducible and consistent, should be weighted against more clinically relevant models. Such models often consist of milder insults, supplemented with the induction of predisposing factors or supportive measures, encountered in the clinical practice. In the perspective of the compound pathogenesis of ARF, assessment of the degree of renal dysfunction is not enough as a single end point, and should be complemented by the evaluation of parameters such as renal microcirculation, oxygenation, cellular adaptive response and morphology. New imaging technologies and biomarkers bring about new insight in this evolving field.
Single-Molecule Fluorescence Analysis in Solution (1996)

Over the past five years, several groups have developed the capability to detect and identify single fluorescent molecules in solution as the molecules flow through a focused laser beam. The history of the approach to single-molecule detection in fluid solution is shown in Fig. 1. Approximately one dozen molecular species have been detected at this level of sensitivity. Fluorescence-based, single-molecule detection techniques are expected to have a significant impact in fields where fluorescence detection and quantification are broadly applied, e.g., analytical chemistry, biology, and medicine. Single-molecule detection is a new way of doing analytical chemistry, and new applications will arise. In this article, we describe our approach to single-molecule detection and explore assays that can be done at the single-species level that would be difficult or impossible with bulk measurements.
Drug Absorption, Distribution, and Elimination (2003)

Abstract The chapter provides basic quantitative explanations of practical pharmacokinetic concepts that are key to understanding how drugs enter and depart from the body. The parameters that are discussed include hepatic and renal clearance, bioavailability, extraction ratio, half‐life, and volume of distribution. Relationships between these parameters are defined, and their utility for the design of dosing regimens to provide effective and nontoxic therapy is shown with some examples. The application of pharmacokinetics plays an essential role in the various preclinical and clinical phases of drug development, as well as in other areas such as environmental toxicology.
Entry of Amphotropic and 10A1 Pseudotyped Murine Retroviruses Is Restricted in Hematopoietic Stem Cell Lines (1998)

Although transduction with amphotropic murine leukemia virus (MLV) vectors has been optimized successfully for hematopoietic differentiated progenitors, gene transfer to early hematopoietic cells (stem cells) is still highly restricted. A similar restriction to gene transfer was observed in the mouse stem cell line FDC-Pmix compared with transfer in the more mature myeloid precursor cell line FDC-P1 and the human erythroleukemia cell line K562. Gene transfer was not improved when the vector was pseudotyped with gp70SU of the 10A1 strain of MLV, which uses the receptor of the gibbon ape leukemia virus (Pit1), in addition to the amphotropic receptor (Pit2). Although 10A1 and amphotropic gp70SU bound to FDC-P1, K562, and fibroblasts, no binding to FDC-Pmix cells was detected. This indicates that FDC-Pmix cells lack functional Pit2 and Pit1 receptors. Pseudotyping with the vesicular stomatitis virus G protein improved transduction efficiency in FDC-Pmix stem cells by 2 orders of magnitude, to fibroblast levels, confirming a block to retroviral infection at the receptor level.
Adrenocortical Function in Cows with the Downer Cow Syndrome A Preliminary Report (1990)

To find out if cows with the downer cow syndrome have enhanced or exhausted adrenocortical function, fifteen downer cows were examined for adrenocortical response to 25 IU of adrenocorticotropic hormone (ACTH) between 1 and 9 days postpartum. Of the 15 cows, only two cows recovered following treatment, 10 cows were slaughtered due to poor prognosis and 3 cows were found dead. Four cows with milk fever also were investigated for adrenocortical function. Both the downer cows and cows with milk fever had significantly higher basal and ACTH-stimulated plasma glucocorticoid concentrations than cows without any postpartum complications on day 1 to 2 postpartum (P less than 0.05). There was a tendency that the downer cows which recovered later did not show enhanced adrenocortical function on day 4 to 5 and day 7 to 9 postpartum, while the downer cows with poor prognosis had significantly enhanced adrenocortical activity on the same days postpartum. The enhanced adrenocortical function shown in the milk fever cows on day 1 to 2 postpartum returned to a nearly normal state after their recovery. The results indicate the downer cows with poor prognosis had greatly enhanced adrenocortical function.
Isolation and characterization of bone marrow multipotential mesenchymal progenitor cells (2002)

This study shows the distinct phenotype, morphology, and method of isolation of BM MPCs. The findings may have implications for defining the physiologic roles of MPCs in arthritis, bone diseases, and joint regeneration.
PROUD: a sea-of-gates placement algorithm (1988)

An efficient method is proposed for placing modules in large and highly complex sea-of-gates chips that include preplaced I/O pads and macrocells. PROUD repeatedly solves sparse linear equations. A resistive network analogy of the placement problem and convexity of the objective function are key concepts in this algorithm. The algorithm was tested on nine real circuits. For a triple-metal-layer, 100000-gate sea-of-gate design with 26000 instances, the constructive phase took 50 minutes on a VAX 8650 and yielded excellent results for total wire length. Extensions of the method are considered.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure (2012)

Antibodies are capable of specifically recognizing and binding antigens. Identification of the antigen-binding site, commonly dubbed paratope, is of high importance both for medical and biological applications. To date, the identification of antigen-binding regions (ABRs) relies on tools for the identification of complementarity-determining regions (CDRs). However, we have shown that up to 22% of the residues that actually bind the antigen fall outside the traditionally defined CDRs. The Paratome web server predicts the ABRs of an antibody, given its amino acid sequence or 3D structure. It is based on a set of consensus regions derived from a structural alignment of a non-redundant set of all known antibody-antigen complexes. Given a query sequence or structure, the server identifies the regions in the query antibody that correspond to the consensus ABRs. An independent set of antibody-antigen complexes was used to test the server and it was shown to correctly identify at least 94% of the antigen-binding residues. The Paratome web server is freely available at http://www.ofranlab.org/paratome/.