gebhart/patrepeval huggingface dataset:
Conserved and Exposed Epitopes on Intact, Native, Primary Human Immunodeficiency Virus Type 1 Virions of Group M (2000)

We have examined the exposure and conservation of antigenic epitopes on the surface envelope glycoproteins (gp120 and gp41) of 26 intact, native, primary human immunodeficiency virus type 1 (HIV-1) group M virions of clades A to H. For this, 47 monoclonal antibodies (MAbs) derived from HIV-1-infected patients were used which were directed at epitopes of gp120 (specifically V2, C2, V3, the CD4-binding domain [CD4bd], and C5) and epitopes of gp41 (clusters I and II). Of the five regions within gp120 examined, MAbs bound best to epitopes in the V3 and C5 regions. Only moderate to weak binding was observed by most MAbs to epitopes in the V2, C2, and CD4bd regions. Two anti-gp41 cluster I MAbs targeted to a region near the tip of the hydrophilic immunodominant domain bound strongly to >90% of isolates tested. On the other hand, binding of anti-gp41 cluster II MAbs was poor to moderate at best. Binding was dependent on conformational as well as linear structures on the envelope proteins of the virions. Further studies of neutralization demonstrated that MAbs that bound to virions did not always neutralize but all MAbs that neutralized bound to the homologous virus. This study demonstrates that epitopes in the V3 and C5 regions of gp120 and in the cluster I region of gp41 are well exposed on the surface of intact, native, primary HIV-1 isolates and that cross-reactive epitopes in these regions are shared by many viruses from clades A to H. However, only a limited number of MAbs to these epitopes on the surface of HIV-1 isolates can neutralize primary isolates.
Leukemia Inhibitory Factor Induces Endothelial Differentiation in Cardiac Stem Cells (2005)

The importance of interleukin 6 (IL-6)-related cytokines in cardiac homeostasis has been studied extensively; however, little is known about their biological significance in cardiac stem cells. Here we describe that leukemia inhibitory factor (LIF), a member of IL-6-related cytokines, activated STAT3 and ERK1/2 in cardiac Sca-1+ stem cells. LIF stimulation resulted in the induction of endothelial cell-specific genes, including VE-cadherin, Flk-1, and CD31, whereas neither smooth muscle nor cardiac muscle marker genes such as GATA4, GATA6, Nkx-2.5, and calponin were up-regulated. Immunocytochemical examination showed that about 25% of total cells were positively stained with anti-CD31 antibody 14 days after LIF stimulation. Immunofluorescent microscopic analyses identified the Sca-1+ cells that were also positively stained with anti-von Willebrand factor antibody, indicating the differentiating process of Sca-1+ cells into the endothelial cells. IL-6, which did not activate STAT3 and ERK1/2, failed to induce the differentiation of cardiac stem cells into the endothelial cells. In cardiac stem cells, the transduction with dominant negative STAT3 abrogated the LIF-induced endothelial differentiation. And the inhibition of ERK1/2 with the MEK1/2 inhibitor U0126 also prevented the differentiation of Sca-1+ cells into endothelial cells. Thus, both STAT3 and ERK1/2 are required for LIF-mediated endothelial differentiation in cardiac stem cells. Collectively, it is proposed that LIF regulates the commitment of cardiac stem cells into the endothelial cell lineage, contributing to neovascularization in the process of tissue remodeling and/or regeneration.
KnowLife: a versatile approach for constructing a large knowledge graph for biomedical sciences (2015)

KnowLife is a large knowledge base for health and life sciences, automatically constructed from different Web sources. As a unique feature, KnowLife is harvested from different text genres such as scientific publications, health portals, and online communities. Thus, it has the potential to serve as one-stop portal for a wide range of relations and use cases. To showcase the breadth and usefulness, we make the KnowLife KB accessible through the health portal (http://knowlife.mpi-inf.mpg.de).
Tensile Loading of Ropes of Single Wall Carbon Nanotubes and their Mechanical Properties (2000)

The mechanical response of 15 single wall carbon nanotube (SWCNT) ropes under tensile load was measured. For 8 of these ropes strain data were obtained and they broke at strain values of 5.3% or lower. The force-strain data are well fit by a model that assumes the load is carried by the SWCNTs on the perimeter of each rope. This model provides an average breaking strength of SWCNTs on the perimeter of each rope; the 15 values range from 13 to 52 GPa (mean 30 GPa). Based on the same model the 8 average Young's modulus values determined range from 320 to 1470 GPa (mean 1002 GPa).
Differential oncogene expression and susceptibility to apoptosis in the human leukemia HL60 cell lines: implications for etoposide resistance. (1995)

Mechanisms of etoposide (VP-16) resistance have been evaluated in a human promyelocytic leukemia HL60 cell line. HL60 resistant (HL60/AR) cells were selected for resistance with adriamycin and were 250-fold resistant to VP-16. We have found that while a significantly higher (10 to 15-fold more) dose of VP-16 was required to induce similar amounts of SDS-KCI-precipitable DNA-protein complex formation in the resistant cell line, there was no difference in the repair of VP-16-induced DNA damage, indicating that differential DNA repair was not involved in VP-16 resistance in HL60 cells. VP-16 treatment significantly inhibited c-myc expression and induced c-jun and c-fos expressions in sensitive cells. In contrast, VP-16 had no effect on c-myc, c-jun or c-fos expressions in resistant cells. The level of bcl2 oncogene was similar in both cell lines; however, treatment with VP-16 resulted in a time- and dose-dependent degradation of the genomic DNA into oligo-sized DNA only in the sensitive cells, indicating that differential expressions of oncogenes (c-myc, c-jun, and c-fos) and susceptibility to apoptosis may play important roles in the sensitivity and resistance to VP-16 in HL60 cells.
Coordinate Control of Muscle Cell Survival by Distinct Insulin-like Growth Factor Activated Signaling Pathways (2000)

Peptide growth factors control diverse cellular functions by regulating distinct signal transduction pathways. In cultured myoblasts, insulin-like growth factors (IGFs) stimulate differentiation and promote hypertrophy. IGFs also maintain muscle cell viability. We previously described C2 skeletal muscle lines lacking expression of IGF-II. These cells did not differentiate, but underwent progressive apoptotic death when incubated in differentiation medium. Viability could be sustained and differentiation enabled by IGF analogues that activated the IGF-I receptor; survival was dependent on stimulation of phosphatidylinositol 3-kinase (PI3-kinase). We now find that IGF action promotes myoblast survival through two distinguishable PI3-kinase-regulated pathways that culminate in expression of the cyclin-dependent kinase inhibitor, p21. Incubation with IGF-I or transfection with active PI3-kinase led to rapid induction of MyoD and p21, and forced expression of either protein maintained viability in the absence of growth factors. Ectopic expression of MyoD induced p21, and inhibition of p21 blocked MyoD-mediated survival, thus defining one PI3-kinase-dependent pathway as leading first to MyoD, and then to p21 and survival. Unexpectedly, loss of MyoD expression did not impede IGF-mediated survival, revealing a second pathway involving activation by PI3-kinase of Akt, and subsequent induction of p21. Since inhibition of p21 caused death even in the presence of IGF-I, these results establish a central role for p21 as a survival factor for muscle cells. Our observations also define a MyoD-independent pathway for regulating p21 in muscle, and demonstrate that distinct mechanisms help ensure appropriate expression of this key protein during differentiation.
Effects of Amplification Facilitators on Diagnostic PCR in the Presence of Blood, Feces, and Meat (2000)

The full potential of diagnostic PCR is limited, in part, by the presence of inhibitors in complex biological samples that reduce the amplification efficiency. Therefore, different pre-PCR treatments are being used to reduce the effects of PCR inhibitors. The aim of the present study was to investigate the effects of 16 amplification facilitators to enhance DNA amplification in the presence of blood, feces, or meat. Different concentrations of amplification facilitators and inhibitory samples were added to PCR mixtures containing rTth or Taq DNA polymerase. The addition of 0.6% (wt/vol) bovine serum albumin to reaction mixtures containing Taq DNA polymerase reduced the inhibitory effect of blood and allowed DNA amplification in the presence of 2% instead of 0.2% (vol/vol) blood. Furthermore, the addition of bovine serum albumin (BSA) to reaction mixtures containing feces or meat enhanced the amplification capacities of both polymerases. Taq DNA polymerase was able to amplify DNA in the presence of 4% instead of 0.4% (vol/vol) feces and 4% instead of 0.2% (vol/vol) meat, and rTth was able to amplify DNA in the presence of 4% instead of 0.4% (vol/vol) feces and 20% instead of 2% (vol/vol) meat. The single-stranded DNA binding T4 gene 32 protein (gp32) had a relieving effect similar to that of BSA, except when it was added to PCR mixtures of rTth containing meat and of Taq DNA polymerase containing feces. The relieving effects of betaine and a cocktail of proteinase inhibitors were more sample specific. The addition of 11.7% (wt/vol) betaine allowed Taq DNA polymerase to amplify DNA in the presence of 2% (vol/vol) blood, while the addition of proteinase inhibitors allowed DNA amplification by both polymerases in the presence of 4% (vol/vol) feces. When various combinations of betaine, BSA, gp32, and proteinase inhibitors were tested, no synergistic or additive effects were observed. The effects of facilitators on real-time DNA synthesis instead of conventional PCR were also studied.
Antifreeze Proteins of the Beetle Dendroides canadensis Enhance One Another's Activities (2005)

Larvae of the beetle Dendroides canadensis produce a family of 13 antifreeze proteins (DAFPs), four of which are in the hemolymph. Antifreeze proteins lower the noncolligative freezing point of water (in the presence of ice) below the melting point, producing a difference between the freezing and melting points termed thermal hysteresis. This activity (THA) is dependent upon DAFP specific activity, concentration, and the presence of enhancers. Enhancers may be low molecular mass enhancers, such as glycerol, or other proteins. The protein enhancers complex with the DAFPs, thereby blocking a larger surface area of the potential seed ice crystal and consequently lowering the freezing point. A yeast two-hybrid screen was performed using certain hemolymph DAFPs as "bait" in an effort to identify endogenous protein enhancers. Among the positive proteins identified as interacting with the bait DAFPs, and confirmed by co-immunoprecipitation, were other DAFPs. When pure DAFPs were added to one another, those identified by the yeast two-hybrid screen as interacting with one another exhibited a synergistic enhancement of thermal hysteresis activity. In contrast, those DAFPs which the screen indicated did not interact failed to enhance one anothers' activities. DAFPs-1 and -2 interact and enhance one another. Point mutations of one of the interacting DAFPs (DAFP-2) indicated that both of the two amino acid residues that differ between DAFPs-1 and -2 were required for interaction. Glycerol enhanced the THA of the DAFPs only when DAFPs known to interact were present in the test solution. Addition of glycerol to a test solution containing only one DAFP did not produce enhancement. Therefore, glycerol enhances activity by stimulating interactions between DAFPs.
Rapid, Sensitive and Real-Time Multiplexing Platform for the Analysis of Protein and Nucleic-Acid Biomarkers (2015)

We describe a multiplexing technology, named Evalution, based on novel digitally encoded microparticles in microfluidic channels. Quantitative multiplexing is becoming increasingly important for research and routine clinical diagnostics, but fast, easy-to-use, flexible and highly reproducible technologies are needed to leverage the advantages of multiplexing. The presented technology has been tailored to ensure (i) short assay times and high reproducibility thanks to reaction-limited binding regime, (ii) dynamic control of assay conditions and real-time binding monitoring allowing optimization of multiple parameters within a single assay run, (iii) compatibility with various immunoassay formats such as coflowing the samples and detection antibodies simultaneously and hence simplifying workflows, (iv) analyte quantification based on initial binding rates leading to increased system dynamic range and (v) high sensitivity via enhanced fluorescence collection. These key features are demonstrated with assays for proteins and nucleic acids showing the versatility of this technology.
<title>Scene description, composition, and playback systems for MPEG-4</title> (1998)

We discuss a few selected aspects of MPEG-4 Systems which includes a representation of description of multimedia scenes, delivery of coded multimedia objects and the scene description, composition, and synchronized playback. We first present an overview of BIFS, the MPEG-4 scene description language, as well as a brief background of VRML, on which BIFS is based. We then discuss the basics of a (nonadaptive) MPEG-4 playback system, including issues in BIFS and media decoding. The state of the software implementation in MPEG-4 of the 2D scene player and the 3D scene player is then discussed. Thus, the novel aspects of MPEG-4 Systems version 1 work which is near completion, is reviewed. We also discuss related aspects of the ongoing work on version 2 of MPEG-4 Systems. This includes additional work on scene description, referred to as advanced BIFS, and work on Java<SUP>TM</SUP> based extension of MPEG- 4 System to an adaptive system referred to as MPEG-J. The work on advanced BIFS, extends the version 1 scene description by a number of additional capabilities. The work on MPEG-J involves design of architecture to control version 1 system, and set of API. Thus, the status of some of the ongoing work on MPEG-4 Systems version 2 is also reviewed.
Crystallization and preliminary X-ray diffraction of human interleukin-7 bound to unglycosylated and glycosylated forms of its α-receptor (2007)

The interleukin-7 (IL-7) signaling pathway plays an essential role in the development, proliferation and homeostasis of T and B cells in cell-mediated immunity. Understimulation and overstimulation of the IL-7 signaling pathway leads to severe combined immunodeficiency, autoimmune reactions, heart disease and cancers. Stimulation of the IL-7 pathway begins with IL-7 binding to its alpha-receptor, IL-7R alpha. Protein crystals of unglycosylated and glycosylated complexes of human IL-7-IL-7R alpha extracellular domain (ECD) obtained using a surface entropy-reduction approach diffract to 2.7 and 3.0 A, respectively. Anomalous dispersion methods will be used to solve the unglycosylated IL-7-IL-7R alpha ECD complex structure and this unglycosylated structure will then serve as a model in molecular-replacement attempts to solve the structure of the glycosylated IL-7-alpha-receptor complex.
Evaluating antibodies for their capacity to induce cell-mediated lysis of malignant B cells. (1998)

Promising results from clinical trials have led to renewed interest in effector mechanisms operating in antibody-based therapy of leukemia and lymphoma. We tested a panel of B-cell antibodies from the Sixth Human Leukocyte Differentiation Antigen workshop for their capacity to mediate antibody-dependent cellular cytotoxicity, often considered to be one of the most potent effector mechanisms in vivo. As effector cells, mononuclear cells and polymorphonuclear (PMN) cells from healthy donors were compared with Fc gammaRI (CD64)-expressing PMN cells from patients receiving granulocyte colony-stimulating factor (G-CSF) treatment. Of the 29 IgG workshop antibodies binding most strongly to the tested malignant human B-cell lines, only 3 consistently induced target cell lysis. These three antibodies were determined to be HLA DR reactive. Experiments with a panel of HLA class II antibodies showed the involvement of individual Fc gamma receptors on effector cells to be strongly dependent on the antibody isotype. We then compared killing mediated by chimeric IgG1 antibodies with that from Fc gammaRI-directed bispecific antibodies, targeting classical HLA class II, or the Lym-1 and Lym-2 antigens. The latter two are variant forms of HLA class II, which are highly expressed on the surface of malignant B cells but which are found only at low levels in normal cells. With blood from G-CSF-treated donors, bispecific antibodies showed enhanced killing compared to their chimeric IgG1 derivatives, because they were more effective in recruiting Fc gammaRI-expressing PMN cells. G-CSF- and Fc gammaRI-directed bispecific antibodies to HLA class II, therefore, seem to be an attractive combination for lymphoma therapy.
The Relation Between De Novo Atherosclerosis Remodeling and Angioplasty-Induced Remodeling in an Atherosclerotic Yucatan Micropig Model (1998)

Geometric remodeling in de novo atherosclerosis and in restenosis after balloon angioplasty constitutes a change in total arterial circumference that, together with plaque growth or neointima formation, determines the lumen of the artery. The heterogeneous nature of arterial obstructions raises the question of whether early and late outcomes (restenosis) of angioplasty are affected by the degree and direction of de novo atherosclerotic remodeling. This study was designed to assess the relationship between atherosclerotic remodeling and the degree and mechanism of restenosis after balloon angioplasty. Atherosclerosis was induced in 27 peripheral arteries of 18 Yucatan micropigs by a combination of denudation and atherogenic diet. Balloon angioplasty was performed, with serial intravascular ultrasound and quantitative angiography before and after intervention and at 42 days' follow-up. We used the relative media-bounded area (MBA), defined as the MBA of the treated site divided by the MBA of the reference, before angioplasty as a measure of remodeling in de novo atherosclerosis and late MBA loss as a measure of remodeling after balloon angioplasty. Relative MBA before angioplasty was not correlated with angiographic and echographic acute gain after balloon angioplasty (r=.22, P=.28 and r=.14, P=.48) or with late lumen loss (r=-.05, P=.81 and r=.19, P=.33). No correlation was found between relative MBA and late MBA loss (r=.14 and P=.48). In the atherosclerotic Yucatan micropig, remodeling during de novo atherosclerosis has no relevance for acute gain and late lumen loss after balloon angioplasty. Both the direction and the extent of remodeling after balloon angioplasty are not related to the direction and extent of remodeling during de novo atherosclerosis.
Immunity to Respiratory Viruses (2008)

The respiratory tract is characterized by an extensive surface area that is in direct contact with the environment, posing a significant problem for effective immune surveillance. Yet most respiratory pathogens are quickly recognized and controlled by a coordinated response involving the innate and adaptive arms of the immune system. The investigation of pulmonary immunity to respiratory viruses during a primary infection has demonstrated that multiple innate and adaptive immune mechanisms are necessary for efficient antiviral responses, and the inhibition of any single mechanism can have disastrous consequences for the host. Furthermore, the investigation of recall responses in the lung has shown that protection from a secondary challenge infection is a complex and elegant process that occurs in distinct stages. In this review, we discuss recent advances that describe the roles of individual components during primary and secondary responses to respiratory virus infections and how these discoveries have added to our understanding of antiviral immunity in the lung.
Effect of β-hydroxy-β-methylbutyrate Supplementation During Energy Restriction in Female Judo Athletes (2010)

Supplementation of β-hydroxy-β-methylbutyrate (HMB) has been suggested to help increase muscle mass or reduce body fat in resistance-trained subjects and patients in catabolic states. The aim of this preliminary study was to investigate the effect of oral supplementation of 3 g·day−1 HMB for 3 days on body composition and exercise performance in well-trained female judo athletes during energy restriction. Eight female judo athletes were matched for body weight and divided into HMB and control groups. All subjects consumed food containing 20kcal·kg−1 with carbohydrate 3.6g·kg−1, protein 1.33g·kg−1, and fat 0.03g·kg−1 each day. Body weight and body fat percentage were significantly decreased in the HMB group, but remained unchanged in the control group after the study period. Muscle mass and the anaerobic performance of the lower and upper body were unchanged in both groups. The HMB group showed significant increases in total cholesterol, blood urea nitrogen, and uric acid after the study period. The control group did not show any significant changes in all blood parameters. This study suggested that short-term supplementation of HMB during energy restriction may help to reduce body fat but has no effect on lean body mass or exercise performance in female athletes.
ELAV tumor antigen, Hel-N1, increases translation of neurofilament M mRNA and induces formation of neurites in human teratocarcinoma cells (1999)

Human ELAV proteins are implicated in cell growth and differentiation via regulation of mRNA expression in the cytoplasm. In human embryonic teratocarcinoma (hNT2) cells transfected with the human neuronal ELAV-like protein, Hel-N1, neurites formed, yet cells were not terminally differentiated. Cells in which neurite formation was associated with Hel-N1 overexpression, also expressed increased levels of endogenous neurofilament M (NF-M) protein, which distributed along the neurites. However, steady-state levels of NF-M mRNA remained similar whether or not hNT2 cells were transfected with Hel-N1. These findings suggest that turnover of NF-M mRNA was not affected by Hel-N1 expression, despite the fact that Hel-N1 can bind to the 3' UTR of NF-M mRNA and was found directly associated with NF-M mRNA in transfected cells. Analysis of the association of NF-M mRNA with the translational apparatus in Hel-N1 transfectants showed nearly complete recruitment to heavy polysomes, indicating that Hel-N1 caused an increase in translational initiation. Our results suggest that the stability and/or translation of ARE-containing mRNAs can be regulated independently by the ELAV protein, Hel-N1, depending upon sequence elements in the 3' UTRs and upon the inherent turnover rates of the mRNAs that are bound to Hel-N1 in vivo.