gebhart/patrepeval huggingface dataset:
The Tetraspan Protein EMP2 Modulates the Surface Expression of Caveolins and Glycosylphosphatidyl Inositol-linked Proteins (2004)

Caveolae are a subset of lipid rafts enriched in glycosphingolipids and cholesterol-rich domains, but selectively lacking glycosylphosphatidyl inositol-anchored proteins (GPI-APs). Caveolin proteins are the organizing component of caveolae, but the corresponding proteins for other classes of lipid rafts are poorly defined. Epithelial membrane protein-2 (EMP2), a member of the four-transmembrane superfamily, facilitates plasma membrane delivery of certain integrins. In this study, we found by laser confocal microscopy that EMP2 was associated with GPI-APs (detected by the GPI-AP binding bacterial toxin proaerolysin). Biochemical membrane fractionation and methyl-beta-cyclodextrin treatment demonstrated that this association occurred within lipid rafts. EMP2 did not associate with caveolin-bearing membrane structures, and recombinant overexpression of EMP2 in NIH3T3 cells decreased caveolin-1 and caveolin-2 protein levels while increasing the surface expression of GPI-APs. Conversely, a ribozyme construct that specifically cleaves the EMP2 transcript reduced surface GPI-APs and increased caveolin protein expression. These findings suggest that EMP2 facilitates the formation and surface trafficking of lipid rafts bearing GPI-APs, and reduces caveolin expression, resulting in impaired formation of caveolae.
Erythrocyte Fatty Acid Composition and the Metabolic Syndrome: A National Heart, Lung, and Blood Institute GOLDN Study (2007)

Polyunsaturated fats are inversely associated with the MetS, whereas saturated fatty acids are positively associated with the MetS, probably through their effect on lipids, adiposity, insulin, and blood pressure.
mRNA sequence of three respiratory syncytial virus genes encoding two nonstructural proteins and a 22K structural protein (1985)

An mRNA sequence of two human respiratory syncytial viral nonstructural protein genes and of a gene for a 22,000-molecular-weight (22K) protein was obtained by cDNA cloning and DNA sequencing. Sequences corresponding to the 5' ends of the respective transcripts were deduced directly by primer extension and dideoxy nucleotide sequencing of the mRNAs. The availability of a bicistronic clone (pRSC6) confirmed the gene order for this portion of the genome. Contrary to other unsegmented negative-stranded RNA viruses, a 19-nucleotide intercistronic sequence was present between the NS1 and NS2 genes. The translation of cloned viral sequences in the bicistronic and monocistronic clones (pRSNS1 and pRSNS2) revealed two moderately hydrophobic proteins of 15,568 and 14,703 daltons. Their similarity in molecular size explained our earlier inability to resolve these proteins. A DNA sequence of an additional recombinant plasmid (pRSA2) revealed a long open reading frame encoding a 22,156-dalton protein containing 194 amino acids. It was relatively basic and moderately hydrophobic. A protein of this size was readily translated in vitro from a viral mRNA hybrid selected by this plasmid and corresponded to an unglycosylated 22K protein seen in purified extracellular virus but not associated with detergent- and salt-resistant cores. A second open reading frame of 90 amino acids partially overlapping with the C terminus of the 22K protein was also present within this sequence. This was reminiscent of the viral matrix protein gene which was previously shown by us to contain two overlapping reading frames. The finding of three additional viral transcripts encoding at least three identifiable proteins in human respiratory syncytial virus was a novel departure from the usual genetic organization of paramyxoviruses. The 5' ends of all three transcripts had a 5'NGGGCAAAU sequence that is common to all viral transcripts analyzed so far. Although there was no obvious homology immediately upstream of the polyadenylate tail, an AGUUA (AGUAA in the case of NS2) was present between 1 and 4 nucleotides upstream of the polyadenylate end of NS1 and 22K protein mRNAs.
Pulmonary Aspergillosis in Patients With AIDS (1994)

Unlike other risk groups that tend to contract only one form of pulmonary aspergillosis, AIDS patients can develop the whole spectrum of aspergillosis-related pulmonary disorders, including chronic cavitary, invasive, and bronchial forms of aspergillosis. Clinical symptoms are nonspecific and major risk factors include neutropenia, which is often a side effect of various therapies for AIDS, and steroid administration. Patients with the chronic cavitary form of disease have an unusually high mortality due to fatal hemoptysis. Patients with bilateral pulmonary infiltrates and aspergillosis have a high mortality due to disseminated infection.
Structure of positive streamers inside gaseous bubbles immersed in liquids (2009)

Electric discharges and streamers in liquids typically proceed through vapour phase channels produced by the streamer or in gaseous bubbles. The bubbles can originate by enthalpy changes produced by the discharge or can be artificially injected into the liquid. Experiments on streamers in bubbles immersed in liquids have shown that the discharge propagates either along the surface of the bubble or through the volume of the bubble as in conventional streamer propagation in air. In this paper we report on results of a computational investigation of streamer propagation through bubbles immersed in liquids. We found that the dielectric constant of the liquid in large part determines the path the streamer takes. Streamers in bubbles immersed in a liquid with a high permittivity preferentially propagate along the surface of the bubble. Liquids with low permittivity can result in the streamer propagating along the axis of the bubble. The permittivity at which this transition occurs is a function of the applied voltage, size of the bubble and the conductivity of the liquid.
Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit (1999)

We demonstrate here that the previously described bacterial promoter upstream element (UP element) consists of two distinct subsites, each of which, by itself, can bind the RNA polymerase holoenzyme alpha subunit carboxy-terminal domain (RNAP alphaCTD) and stimulate transcription. Using binding-site-selection experiments, we identify the consensus sequence for each subsite. The selected proximal subsites (positions -46 to -38; consensus 5'-AAAAAARNR-3') stimulate transcription up to 170-fold, and the selected distal subsites (positions -57 to -47; consensus 5'-AWWWWWTTTTT-3') stimulate transcription up to 16-fold. RNAP has subunit composition alpha(2)betabeta'sigma and thus contains two copies of alphaCTD. Experiments with RNAP derivatives containing only one copy of alphaCTD indicate, in contrast to a previous report, that the two alphaCTDs function interchangeably with respect to UP element recognition. Furthermore, function of the consensus proximal subsite requires only one copy of alphaCTD, whereas function of the consensus distal subsite requires both copies of alphaCTD. We propose that each subsite constitutes a binding site for a copy of alphaCTD, and that binding of an alphaCTD to the proximal subsite region (through specific interactions with a consensus proximal subsite or through nonspecific interactions with a nonconsensus proximal subsite) is a prerequisite for binding of the other alphaCTD to the distal subsite.
Evidence for mitochondrial localization of a novel human sialidase (NEU4) (2005)

Based on the human cDNA sequence predicted to represent the NEU4 sialidase gene in public databases, a cDNA covering the entire coding sequence was isolated from human brain and expressed in mammalian cells. The cDNA encodes two isoforms: one possessing an N-terminal 12-amino-acid sequence that is predicted to be a mitochondrial targeting sequence, and the other lacking these amino acids. Expression of the isoforms is tissue specific, as assessed by reverse transcription-PCR. Brain, muscle and kidney contained both isoforms; liver showed the highest expression, and the short form was predominant in this organ. In transiently transfected COS-1 cells, enzyme activity was markedly increased with gangliosides as well as with glycoproteins and oligosaccharides as substrates compared with the control levels. This differs from findings with other human sialidases. Although the isoforms were not distinguishable with regard to substrate specificity, they exhibited differential subcellular localizations. Immunofluorescence microscopy and biochemical fractionation demonstrated that an exogenously expressed haemagglutinin-tagged long form of NEU4 was concentrated in mitochondria in several human culture cell types, whereas the short form was present in intracellular membranes, indicating that the sequence comprising the N-terminal 12 amino acid residues acts as a targeting signal for mitochondria. Co-localization of the long form to mitochondria was further supported by efficient targeting of the N-terminal region fused to enhanced green fluorescent protein, and by the targeting failure of a mutant with an amino acid substitution in this region. NEU4 is possibly involved in regulation of apoptosis by modulation of ganglioside G(D3), which accumulates in mitochondria during apoptosis and is the best substrate for the sialidase.
A message-passing algorithm with damping (2005)

We propose a modified belief propagation algorithm, with over-relaxed dynamics. Such an algorithm turns out to be generally more stable and faster than ordinary belief propagation. We characterize the performance of the algorithm, employed as a tool for combinatorial optimization, on the random satisfiability problem. Moreover, we trace a connection with a recently proposed double-loop algorithm for minimizing Bethe and Kikuchi free energies.
Mechanical behaviour of articular cartilage under tensile cyclic load (2001)

The most impressive of the outcomes of this study is the scatter of the data. Considering all the specimens used, the range of number of load cycles to failure was between 2 and 1.5 million. The zonal variation in fatigue behaviour was similar to that in tensile modulus reported previously; the surface and deep layers seemed to have better fatigue properties whether tested in the direction parallel or perpendicular to that of the collagen in the superficial layer. The middle layer was far weaker, suggesting that highly packed and ordered fibres in the surface and deep zones have better mechanical properties than the more random and loose fibres in the middle zone. The variation in fibre organization through the cartilage thickness was also reflected in the differences observed in the elongation of the specimen during the test. The surface and deep zones had a higher stiffness than the middle zone. Cartilage had better fatigue resistance when the specimen was loaded in a direction parallel rather than perpendicular to the collagen within the surface layer. This was true whether specimens were harvested from the superficial, intermediate or deep layer. There were many factors that confounded attempts to estimate the likely fatigue life from the data obtained in such a study.
Induction of Alloantigen-specific Anergy in Human Peripheral Blood Mononuclear Cells by Alloantigen Stimulation with Co-stimulatory Signal Blockade (2011)

Allogeneic hematopoietic stem cell transplantation (AHSCT) offers the best chance of cure for many patients with congenital and acquired hematologic diseases. Unfortunately, transplantation of alloreactive donor T cells which recognize and damage healthy patient tissues can result in Graft-versus-Host Disease (GvHD). One challenge to successful AHSCT is the prevention of GvHD without associated impairment of the beneficial effects of donor T cells, particularly immune reconstitution and prevention of relapse. GvHD can be prevented by non-specific depletion of donor T cells from stem cell grafts or by administration of pharmacological immunosuppression. Unfortunately these approaches increase infection and disease relapse. An alternative strategy is to selectively deplete alloreactive donor T cells after allostimulation by recipient antigen presenting cells (APC) before transplant. Early clinical trials of these allodepletion strategies improved immune reconstitution after HLA-mismatched HSCT without excess GvHD. However, some allodepletion techniques require specialized recipient APC production and some approaches may have off-target effects including depletion of donor pathogen-specific T cells and CD4 T regulatory cells .One alternative approach is the inactivation of alloreactive donor T cells via induction of alloantigen-specific hyporesponsiveness. This is achieved by stimulating donor cells with recipient APC while providing blockade of CD28-mediated co-stimulation signals.This "alloanergization" approach reduces alloreactivity by 1-2 logs while preserving pathogen- and tumor-associated antigen T cell responses in vitro. The strategy has been successfully employed in 2 completed and 1 ongoing clinical pilot studies in which alloanergized donor T cells were infused during or after HLA-mismatched HSCT resulting in rapid immune reconstitution, few infections and less severe acute and chronic GvHD than historical control recipients of unmanipulated HLA-mismatched transplantation. Here we describe our current protocol for the generation of peripheral blood mononuclear cells (PBMC) which have been alloanergized to HLA-mismatched unrelated stimulator PBMC. Alloanergization is achieved by allostimulation in the presence of monoclonal antibodies to the ligands B7.1 and B7.1 to block CD28-mediated costimulation. This technique does not require the production of specialized stimulator APC and is simple to perform, requiring only a single and relatively brief ex vivo incubation step. As such, the approach can be easily standardized for clinical use to generate donor T cells with reduced alloreactivity but retaining pathogen-specific immunity for adoptive transfer in the setting of AHSCT to improve immune reconstitution without excessive GvHD.
PPARs in Alzheimer′s Disease (2008)

Peroxisome proliferator-activated receptors (PPARs) are well studied for their peripheral physiological and pathological impact, but they also play an important role for the pathogenesis of various disorders of the central nervous system (CNS) like multiple sclerosis, amyotrophic lateral sclerosis, Alzheimer's, and Parkinson's disease. The observation that PPARs are able to suppress the inflammatory response in peripheral macrophages and in several models of human autoimmune diseases lead to the idea that PPARs might be beneficial for CNS disorders possessing an inflammatory component. The neuroinflammatory response during the course of Alzheimer's disease (AD) is triggered by the neurodegeneration and the deposition of the beta-amyloid peptide in extracellular plaques. Nonsteroidal anti-inflammatory drugs (NSAIDs) have been considered to delay the onset and reduce the risk to develop Alzheimer's disease, while they also directly activate PPARgamma. This led to the hypothesis that NSAID protection in AD may be partly mediated by PPARgamma. Several lines of evidence have supported this hypothesis, using AD-related transgenic cellular and animal models. Stimulation of PPARgamma receptors by synthetic agonist (thiazolidinediones) inducing anti-inflammatory, anti-amyloidogenic, and insulin sensitising effects may account for the observed effects. Several clinical trials already revealed promising results using PPAR agonists, therefore PPARs represent an attractive therapeutic target for the treatment of AD.
Role of Mitogen-Activated Protein Kinases in CpG DNA-Mediated IL-10 and IL-12 Production: Central Role of Extracellular Signal-Regulated Kinase in the Negative Feedback Loop of the CpG DNA-Mediated Th1 Response (2002)

The mitogen-activated protein kinases, extracellular signal-regulated kinase (ERK), and p38, are activated in response to infectious agents and innate immune stimulators such as CpG DNA, and regulate the subsequent initiation and termination of immune responses. CpG DNA activates p38 and ERK with slightly different kinetics in monocytic cells. The present studies investigated the roles of these two key mitogen-activated protein kinases in regulating the CpG DNA-induced production of pro- and anti-inflammatory cytokines in the macrophage-like cell line RAW264.7. p38 activity was essential for the induction of both IL-10 and IL-12 expression by CpG DNA. In contrast, CpG DNA-mediated ERK activation was shown to suppress IL-12 production, but to be essential for the CpG DNA-induced IL-10 production. Studies using rIL-10 and IL-10 gene-deficient mice demonstrated that the inhibitory effect of ERK on CpG DNA-mediated IL-12 production is indirect, due to the role of ERK in mediating IL-10 production. These results demonstrate that ERK and p38 differentially regulate the production of pro- and anti-inflammatory cytokines in APCs that have been activated by CpG DNA. CpG DNA-induced p38 activity is required for the resulting innate immune activation. In contrast, ERK plays a central negative regulatory role in the CpG DNA-mediated Th1 type response by promoting production of the Th2 type cytokine, IL-10.
Susceptibility to rheumatoid arthritis maps to a T-cell epitope shared by the HLA-Dw4 DR beta-1 chain and the Epstein-Barr virus glycoprotein gp110. (1989)

Rheumatoid arthritis is associated with the HLA antigen HLA-DR4. Disease susceptibility maps to the amino acid sequence QKRAA located in the third hypervariable region of the DR beta-1 chain. This region is thought to be a site of recognition for the T-cell antigen receptor. We searched for an antigen in the human environment that could induce T-cell recognition of this sequence. An analysis of protein and DNA databases revealed that the Epstein-Barr virus glycoprotein gp110, which is encoded by the BALF4 open reading frame, contains the sequence QKRAAQRAA, which is highly homologous to the rheumatoid arthritis susceptibility determinant. Experiments using antibodies to synthetic peptides showed that the QKRAA determinant is expressed on the gp110 protein. Humans with serologic evidence of Epstein-Barr virus infection had serum antibodies to gp110 and peripheral blood T cells that recognized peptides from gp110 and HLA-Dw4 encompassing the QKRAA determinant.
Selective beat signal averaging and spectral analysis of beat intervals to determine the mechanisms of premature ventricular contractions (2002)

Selective beat signal averaging and spectral analysis were implemented to identify whether reentry, triggered activity or parasystole is the mechanism of the isolated premature ventricular contraction (PVC). 2-hour, high resolution ECG recordings were digitally obtained from 9 patients with frequent PVCs (>250/hr). For reentry, in 7/9 patients with a positive average for late potentials (LP) there were no changes of LP in sinus beats before and after PVCs. However, changes in the T/U waves in the difference waveform between the pre-PVC beat and its precedent beat (in 2/9 patients), and their T/U wave amplitudes (in 9/9 patients, mean amplitude difference of 0.0269 mV) implied a triggered activity, mechanism. Also, significant periodicities in PVC interval series and low correlation between sinus and PVC intervals (in 9/9 patients), suggested a parasystolic mechanism. Based on the limited data set, triggered activity and parasystole may be significant PVC mechanisms while reentry may not.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children (2005)

Children with autistic spectrum disorders (ASDs) tend to suffer from severe gastrointestinal problems. Such symptoms may be due to a disruption of the indigenous gut flora promoting the overgrowth of potentially pathogenic micro-organisms. The faecal flora of patients with ASDs was studied and compared with those of two control groups (healthy siblings and unrelated healthy children). Faecal bacterial populations were assessed through the use of a culture-independent technique, fluorescence in situ hybridization, using oligonucleotide probes targeting predominant components of the gut flora. The faecal flora of ASD patients contained a higher incidence of the Clostridium histolyticum group (Clostridium clusters I and II) of bacteria than that of healthy children. However, the non-autistic sibling group had an intermediate level of the C. histolyticum group, which was not significantly different from either of the other subject groups. Members of the C. histolyticum group are recognized toxin-producers and may contribute towards gut dysfunction, with their metabolic products also exerting systemic effects. Strategies to reduce clostridial population levels harboured by ASD patients or to improve their gut microflora profile through dietary modulation may help to alleviate gut disorders common in such patients.
Market power and efficiency in a computational electricity market with discriminatory double-auction pricing (2001)

This study reports experimental market power and efficiency outcomes for a computational wholesale electricity market operating in the short run under systematically varied concentration and capacity conditions. The pricing of electricity is determined by means of a clearinghouse double auction with discriminatory midpoint pricing. Buyers and sellers use a modified Roth-Erev individual reinforcement learning algorithm (1995) to determine their price and quantity offers in each auction round. It is shown that high market efficiency is generally attained and that market microstructure is strongly predictive for the relative market power of buyers and sellers, independently of the values set for the reinforcement learning parameters. Results are briefly compared against results from an earlier study in which buyers and sellers instead engage in social mimicry learning via genetic algorithms.
Comparametric equations with practical applications in quantigraphic image processing (2000)

It is argued that, hidden within the flow of signals from typical cameras, through image processing, to display media, is a homomorphic filter. While homomorphic filtering is often desirable, there are some occasions where it is not. Thus, cancellation of this implicit homomorphic filter is proposed, through the introduction of an antihomomorphic filter. This concept gives rise to the principle of quantigraphic image processing, wherein it is argued that most cameras can be modeled as an array of idealized light meters each linearly responsive to a semi-monotonic function of the quantity of light received, integrated over a fixed spectral response profile. This quantity depends only on the spectral response of the sensor elements in the camera. A particular class of functional equations, called comparametric equations, is introduced as a basis for quantigraphic image processing. These are fundamental to the analysis and processing of multiple images differing only in exposure. The "gamma correction" of an image is presented as a simple example of a comparametric equation, for which it is shown that the underlying quantigraphic function does not pass through the origin. Thus, it is argued that exposure adjustment by gamma correction is inherently flawed, and alternatives are provided. These alternatives, when applied to a plurality of images that differ only in exposure, give rise to a new kind of processing in the "amplitude domain". The theoretical framework presented in this paper is applicable to the processing of images from nearly all types of modern cameras. This paper is a much revised draft of a 1992 peer-reviewed but unpublished report by the author, entitled "Lightspace and the Wyckoff principle."