gebhart/patrepeval huggingface dataset:
Aggregation of the intracellular domain of the type 1 tumor necrosis factor receptor defined by the two-hybrid system. (1994)

The yeast-based two hybrid system has been used to determine whether oligomerization of the intracellular domain of the 55-kDa type 1 tumor necrosis factor (TNF) receptor may occur during TNF action. This assay depends upon reconstitution of the function of the GAL4 transcriptional activator through interaction of a protein fused to the GAL4 DNA binding domain with a protein fused to the transcriptional activation domain of GAL4. Fusion of the type 1 TNF receptor intracellular domain with the DNA binding domain and the transactivation domain of GAL4 led to activation of the lacZ indicator gene, demonstrating interaction of the receptor intracellular domain with itself. A HeLa cell cDNA library was searched for proteins that interact with the intracellular domain of the type 1 TNF receptor. A protein corresponding to amino acids 329-426 in the type 1 TNF receptor intracellular domain was identified by this screen. The aggregation domain was further defined by testing the ability of deletion mutants of the type 1 TNF receptor intracellular region to interact with the complete intracellular domain. These experiments map the aggregation domain to a sequence of amino acids previously shown to be responsible for mediating TNF-induced cytotoxicity. These results suggest that aggregation of type 1 TNF receptor intracellular domains may be important in TNF signal transduction.
β-Catenin Regulates Acetylcholine Receptor Clustering in Muscle Cells through Interaction with Rapsyn (2007)

Agrin is believed to be a factor used by motoneurons to direct acetylcholine receptor (AChR) clustering at the neuromuscular junction. However, exactly how agrin mediates this effect remains unclear. Here we demonstrate that the beta-catenin interacts with rapsyn, a molecule key for AChR clustering. Agrin stimulation increases the association of beta-catenin with surface AChRs. Suppression of beta-catenin expression inhibited agrin-induced AChR clustering, suggesting a necessary role of beta-catenin in this event. The beta-catenin action did not appear to require the function of T-cell factors (TCFs), suggesting a mechanism independent of TCF-mediated transcription. In contrast, prevention of beta-catenin from interacting with alpha-catenin attenuated agrin-induced AChR clustering. These results suggest that beta-catenin may serve as a link between AChRs and alpha-catenin-associated cytoskeleton, revealing a novel function of beta-catenin in synaptogenesis.
Nanoparticle-Templated Assembly of Viral Protein Cages (2006)

Self-assembly of regular protein surfaces around nanoparticle templates provides a new class of hybrid biomaterials with potential applications in medical imaging and in bioanalytical sensing. We report here the first example of efficiently self-assembled virus-like particles (VLPs) having a brome mosaic virus protein coat and a functionalized gold core. The present study indicates that functionalized gold particles can initiate VLP assembly by mimicking the electrostatic behavior of the nucleic acid component of the native virus. These VLP constructs are symmetric, with the protein stoichiometry and packaging properties indicating similarity to the icosahedral packing of the capsid. Moreover, a pH-induced swelling transition of the VLPs is observed, in direct analogy to the native virus.
I-TRAF is a novel TRAF-interacting protein that regulates TRAF-mediated signal transduction. (1996)

Tumor necrosis factor (TNF) receptor-associated factor (TRAF) proteins associate with and transduce signals from TNF receptor 2, CD40, and presumably other members of the TNF receptor superfamily. TRAF2 is required for CD40- and TNF-mediated activation of the transcription factor NF-kappa B. Here we describe the isolation and characterization of a novel TRAF-interacting protein, I-TRAF, that binds to the conserved TRAF-C domain of the three known TRAFs. Overexpression of I-TRAF inhibits TRAF2-mediated NF-kappa B activation signaled by CD40 and both TNF receptors. Thus, I-TRAF appears as a natural regulator of TRAF function that may act by maintaining TRAFs in a latent state.
Surviving the end of frequency scaling with reconfigurable dataflow computing (2011)

Over the past decade x86 processors have come to dominate the world's largest supercomputers. However in the future conventional multicore processors are unlikely to be able to deliver the necessary performance per $ and per W to achieve exascale performance. Heterogeneous computing is emerging as a powerful alternative to conventional multi-core to help address these challenges. In this paper we describe our approach to Maximum Performance Computing - building applicationspecific computers which complement conventional x86 processors with high performance dataflow engines implemented on FPGA to provide 10-100x improvements in performance and performance/W. We describe the MaxCompiler programming system which allows software engineers to create dataflow engines optimized for their particular applications, and discuss an example application that has been accelerated using this methodology.
Roles of Soft Segment Length in Structure and Property of Soy Protein Isolate/Waterborne Polyurethane Blend Films (2016)

Waterborne polyurethanes (WPUs) with varying lengths of soft segment were synthesized and used to physically modify soy protein isolate (SPI), a protein with good film-forming ability and oxygen barrier characteristic but poor toughness and water resistance, via a simple blending technique without any compatibilizer. The effects of soft segment structure of WPU on the structure and property of resultant blend films were investigated. The tensile strength, elongation at break, and water resistance of the SPI-based films were improved and modulated by adding WPUs with different lengths of soft segment. Compared with neat SPI film, the equilibrium water uptake was decreased by 138% at most for a blend film, and the tensile strength and elongation at break were improved by 96% and 82%, respectively. All the blend films possessed uniform cross-section structures due to the strong interactions between SPI and WPU. Moreover, the blend films exhibited a satisfied water vapor barrier property. It was proved that the modification of SPI with WPU might be an effective way to fabricate SPI-based films for practical applications.
WSX-1 and Glycoprotein 130 Constitute a Signal-Transducing Receptor for IL-27 (2004)

The recently discovered cytokine IL-27 belongs to the IL-6/IL-12 family of cytokines and induced proliferation of naive CD4(+) T cells and the generation of a Th1-type adaptive immune response. Although binding of IL-27 to the cytokine receptor WSX-1 was demonstrated, this interaction proved insufficient to mediate cellular effects. Hence, IL-27 was believed to form a heteromeric signaling receptor complex with WSX-1 and another, yet to be identified, cytokine receptor subunit. In this study, we describe that WSX-1 together with gp130 constitutes a functional signal-transducing receptor for IL-27. We show that neither of the two subunits itself is sufficient to mediate IL-27-induced signal transduction, but that the combination of both is required for this event. Expression analysis of WSX-1 and gp130 by quantitative PCR suggests that IL-27 might have a variety of cellular targets besides naive CD4(+) T cells: we demonstrate gene induction of a subset of inflammatory cytokines in primary human mast cells and monocytes in response to IL-27 stimulation. Thus, IL-27 not only contributes to the development of an adaptive immune response through its action on CD4(+) T cells, it also directly acts on cells of the innate immune system.
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011 (2010)

The concept of homology drives speculation on a gene’s function in any given species when its biological roles in other species are characterized. With reference to a specific species radiation homologous relations define orthologs, i.e. descendants from a single gene of the ancestor. The large-scale delineation of gene genealogies is a challenging task, and the numerous approaches to the problem reflect the importance of the concept of orthology as a cornerstone for comparative studies. Here, we present the updated OrthoDB catalog of eukaryotic orthologs delineated at each radiation of the species phylogeny in an explicitly hierarchical manner of over 100 species of vertebrates, arthropods and fungi (including the metazoa level). New database features include functional annotations, and quantification of evolutionary divergence and relations among orthologous groups. The interface features extended phyletic profile querying and enhanced text-based searches. The ever-increasing sampling of sequenced eukaryotic genomes brings a clearer account of the majority of gene genealogies that will facilitate informed hypotheses of gene function in newly sequenced genomes. Furthermore, uniform analysis across lineages as different as vertebrates, arthropods and fungi with divergence levels varying from several to hundreds of millions of years will provide essential data for uncovering and quantifying long-term trends of gene evolution. OrthoDB is freely accessible from http://cegg.unige.ch/orthodb.
Reduction of Adhesions with Composite AlloDerm/Polypropylene Mesh Implants for Abdominal Wall Reconstruction (2004)

Ventral hernia repair often includes the use of structural prosthetic materials, such as polypropylene mesh, that can induce dense abdominal adhesions to peritoneal structures. AlloDerm (LifeCell Corp., Branchburg, N.J.), a commercially available decellularized human dermal analogue with its native basement membrane components intact, is gradually revascularized and replaced with autologous tissue after implantation. The authors hypothesized that AlloDerm integrated with polypropylene mesh would reduce adhesions and provide a biodegradable scaffold to generate an autologous vascularized tissue layer separating the abdominal viscera from the mesh. Ventral hernia defects (3 x 1 cm) in 19 guinea pigs were repaired using an inlay technique with polypropylene mesh alone (n = 6) or with composite implants constructed by integrating polypropylene mesh and AlloDerm with its basement membrane surface oriented toward (polypropylene/AlloIn, n = 7) or away from (polypropylene/ AlloOut, n = 6) the peritoneal cavity. At 4 weeks, the authors determined the amount of mesh implant surface area covered by adhesions, the strength of the adhesions [graded from 0 (none) to 3], and the incidence of bowel adhesions. Histologic analyses were performed on full-thickness tissue sections from the repair sites. The mean surface areas affected by adhesions and mean adhesion strength were significantly lower in the polypropylene/AlloIn (area, 12.4 percent; mean grade, 1.0) and polypropylene/AlloOut (area, 9.5 percent; mean grade, 0.5) groups than in the polypropylene group (area, 79.5 percent; mean grade, 2.9); there were no such differences between the polypropylene/AlloIn and polypropylene/AlloOut groups. The bowel was adherent to 67 percent of polypropylene repairs and 0 percent of the composite mesh repairs. The AlloDerm was remodeled to form a vascularized tissue layer beneath the mesh in composite repairs, unlike the significantly thinner, dense scar layer that formed in the polypropylene repairs. Immunohistochemical labeling for factor VIII showed neovascularization throughout the AlloDerm. The AlloDerm thus functioned as a biodegradable tissue scaffold, guiding the formation of a thick, well-vascularized tissue layer separating the polypropylene mesh from intraperitoneal structures. This significantly reduced both the amount of surface area covered by adhesions and adhesion strength. Basement membrane orientation had no effect. Composite mesh implants composed of structural prosthetic materials integrated with AlloDerm may have useful clinical applications for abdominal wall reconstruction by reducing adhesions and providing a vascularized tissue layer to separate and protect the peritoneal structures from polypropylene mesh fibers.
Atrial Septostomy: A Contemporary Review (2015)

Pulmonary arterial hypertension (PAH) is a rare disease, but it boasts significant morbidity and mortality. Although remarkable achievements have been made in the medical treatment of PAH, there is a role for invasive or surgical procedures in patients with progressive disease despite optimal medical therapy or with no access to such therapy. Atrial septostomy creates a right-to-left intracardiac shunt to decompress the overloaded right ventricle. Despite significant advances to validate and improve this palliative procedure, as well as recent reports of improved outcomes, it is only slowly being adopted. This article aims to detail the history, indications, contraindications, procedural techniques, and outcomes of atrial septostomy. We will also shed light on some of the newer interventions, inspired by the same physiological concept, that are being evaluated as potential palliative modalities in patients with PAH.
17β-ESTRADIOL HAS A BIPHASIC EFFECT ON GH CELL GROWTH1 (1983)

Estrogen causes mammotroph and pituitary tumor growth in vivo; we therefore studied its effect on growth of GH cells, a clonal line of rat pituitary tumor cells. Medium supplemented with gelding serum enabled us to detect effects of estradiol which are masked by the higher estrogen concentrations of commercially available horse serum. GH cells were treated with estradiol for 7 days. Cell number was affected in a biphasic fashion: estradiol at 10(-11) M and 3 X 10(-11) M increased cell number 6- to 13-fold. Concentrations between 3 X 10(-11) M and 10(-9) M caused a dose-dependent decrease from the maximal cell number. The half maximal concentration for this inhibitory effect was about 10(-10) M. Prolactin production was stimulated 3-to 11-fold by estradiol, also with a half-maximal concentration of 10(-10) M. We conclude that estradiol has at least 3 distinguishable effects on GH cells: stimulation of growth at concentrations below 3 X 10(-11) M, and inhibition of growth at higher concentrations, as well as the well known stimulation of prolactin production.
Comparative membrane locations and activities of human monoamine oxidases expressed in yeast (1991)

Human monoamine oxidases A and B were expressed under the control of a galactose inducible promoter in Saccharomyces cerevisiae. The two MAO isoenzymes were found located in the yeast mitochondrial outer membrane, probably in different orientations as suggested by controlled proteolysis experiments. A high level of both human MAO-A or -B activities is measured in intact mitochondria without the need for any detergent solubilisation step. The substrate and inhibitor selectivities of the membrane-bound MAOs are highly similar to those of purified human enzymes. The level of MAO-B activity, however, is selectively lowered when bound to the membrane.
Intra- and Intermolecular Interactions between Intracellular Domains of Receptor Protein-tyrosine Phosphatases (2002)

The presence of two protein-tyrosine phosphatase (PTP) domains is a striking feature in most transmembrane receptor PTPs (RPTPs). The generally inactive membrane-distal PTP domains (RPTP-D2s) bind and are proposed to regulate the membrane-proximal PTP domains (RPTP-D1s). We set out to characterize the interactions between RPTP-D1s and RPTP-D2s in vivo by co-immunoprecipitation of hemagglutinin-tagged fusion proteins encoding the transmembrane domain and RPTP-D1 and myc-tagged RPTP-D2. Seven RPTPs from four different subfamilies were used: RPTPalpha, RPTPepsilon, LAR, RPTPvarsigma, RPTPdelta, CD45, and RPTP(mu). We found that RPTP-D2s bound to RPTPs with different affinities. The presence of intrinsic RPTP-D2 altered the binding specificity toward other RPTP-D2s positively or negatively, depending on the identity of the RPTPs. Furthermore, the C terminus of RPTP-D2s and the "wedge" in RPTP-D1s played a central role in binding specificity. Finally, full-length RPTPalpha and LAR heterodimerized in an oxidative stress-dependent manner. Like RPTPalpha-D2, the LAR-D2 conformation was affected by oxidative stress, suggesting a common regulatory mechanism for RPTP complex formation. Taken together, interactions between RPTP-D1s and RPTP-D2s are a common but specific mechanism that is likely to be regulated. The RPTP-D2s and the wedge structures are crucial determinants of binding specificity, thus regulating cross-talk between RPTPs.
Intraocular Sustained-Release Delivery Systems for Triamcinolone Acetonide (2009)

Recently, the use of triamcinolone acetonide (TA) injection has increased dramatically in treatment for several ocular diseases. Among them, macular diseases such as macular edema due to diabetic retinopathy, venous occlusive diseases, ocular inflammation and age-related macular degeneration (AMD) are very common vision threatening disorders and are great challenges to treat. In these types of chronic retinal diseases, repeated intraocular injections of TA are often required which increases the likelihood of complications. In order to achieve sustained-release, maintain therapeutic levels of TA over longer times and reduce frequency of intravitreal injections, researchers are investigating different implantable devices or injectable systems. However, as of yet, there is no sustained-release product for TA available on the commercial market. This review discusses and compares different sustained-release devices or injectable systems that are currently being developed.
D19S51 is closely linked with and maps distal to the myotonic dystrophy locus on 19q. (1991)

Recent genetic linkage studies have mapped the myotonic dystrophy (DM) locus to 19q13.3. All closely linked DM markers identified to date have been located on the centromeric side of the disease locus, with a relatively large genetic interval (9 cM) observed between the nearest distal marker and DM. We show here that the recently described marker p134C is tightly linked to DM (peak lod score 35.8 at peak recombination fraction .006) and confirm the previous suggestion that the p134C locus, D19S51 maps distal to the disease locus. D19S51 and the closest proximal flanking loci, ERCC1 and D19S115 (pE0.8), define a small genetic interval of less than 2 cM that contains the DM locus.
Probing microRNAs with microarrays: Tissue specificity and functional inference (2004)

MicroRNAs (miRNAs) are short, stable, noncoding RNAs involved in post-transcriptional gene silencing via hybridization to mRNA. Few have been thoroughly characterized in any species. Here, we describe a method to detect miRNAs using micro-arrays, in which the miRNAs are directly hybridized to the array. We used this method to analyze miRNA expression across 17 mouse organs and tissues. More than half of the 78 miRNAs detected were expressed in specific adult tissues, suggesting that miRNAs have widespread regulatory roles in adults. By comparing miRNA levels to mRNA levels determined in a parallel microarray analysis of the same tissues, we found that the expression of target mRNAs predicted on the basis of sequence complementarity is unrelated to the tissues in which the corresponding miRNA is expressed.
Intrastrain Variants of Herpes Simplex Virus Type 1 Isolated from a Neonate with Fatal Disseminated Infection Differ in the ICP34.5 Gene, Glycoprotein Processing, and Neuroinvasiveness (1999)

Two intrastrain variants of herpes simplex virus type 1 (HSV-1) were isolated from a newborn with fatal disseminated infection. A small-plaque-producing variant (SP7) was the predominant virus (>99%) in the brain, and a large-plaque-producing variant (LP5) was the predominant virus (>99%) in the lung and gastrointestinal tract. EcoRI and BamHI restriction fragment patterns indicated that SP7 and LP5 are related strains. The large-plaque variants produced plaques similar in size to those produced by HSV-1 KOS. Unlike LP5 or KOS, SP7 was highly cell associated and processing of glycoprotein C and glycoprotein D was limited to precursor forms in infected Vero cells. The large-plaque phenotype from KOS could be transferred into SP7 by cotransfection of plasmids containing the EK or JK EcoRI fragment or a 3-kb plasmid with the UL34.5 gene of HSV-1 KOS together with SP7 DNA. PCR analysis using primers from within the ICP34.5 gene indicated differences for SP7, LP5, and KOS. Sequencing data indicated two sets of deletions in the UL34.5 gene that distinguish SP7 from LP5. Both SP7 and LP5 variants were neurovirulent (lethal following intracranial inoculation of young BALB/c mice); however, the LP5 variant was much less able to cause lethal neuroinvasive disease (footpad inoculation) whereas KOS caused no disease. Passage of SP7 selected for viruses (SLP-5 and SLP-10) which were attenuated for lethal neuroinvasive disease, were not cell-associated, and differed in the UL34.5 gene. UL34.5 from SLP-5 or SLP-10 resembled that of KOS. These findings support a role for UL34.5 in promoting virus egress and for neuroinvasive disease.
The role of microRNA in metastatic colorectal cancer and its significance in cancer prognosis and treatment. (2012)

microRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression by targeting specific mRNAs. microRNAs play a role in several physiological processes in the cell, including migration, proliferation, differentiation and apoptosis. Apart from their role in regular metabolism, abnormal profiles of miRNA expression accompany cancer transformation, including colorectal cancer (CRC) metastasis. microRNAs may play a role in each phase of CRC metastasis including angiogenesis, invasion, intravasation, circulation, extravasation and metastatic colonization. microRNA levels may serve as a predictive CRC marker, which was confirmed by the serum level of miR-29a targeting KLF4, a marker of cell stemness, and the plasma level of miR-221 down-regulating c-Kit, Stat5A and ETS1, which are signal transducers and transcription factor, respectively. In turn, the level of miR-143 in CRC cells decreasing the amount of MACC1 (metastasis-associated in colon cancer-1) and oncogenic KRAS protein, may be utilized as a prognostic marker. Also, single nucleotide polymorphisms of genes encoding miRNAs, including miR-423 and miR-608, which correlate with tumor recurrence, may be useful as diagnostic, prognostic and predictive indicators in CRC metastasis. Pre-miR-34a and pre-miR-199a decreased the level of Axl, a tyrosine-protein kinase receptor, so they can be considered as drugs in antimetastatic therapy. On the other hand, miR-222 targeting ADAM-17, a disintegrin and metalloproteinase, and miR-328 interacting with ABCG2, an ABC transporter, may overcome drug resistance of cancer cells. microRNAs may be considered in wide-range application to facilitate CRC metastasis diagnosis, prognosis, prediction and therapy, however, further clinical, epidemiological and in vitro studies should be conducted to verify their utility.
Neuroanatomical Pattern of Mitochondrial Complex I Pathology Varies between Schizophrenia, Bipolar Disorder and Major Depression (2008)

These results suggest that the neuroanatomical pattern of complex I pathology parallels the diversity and similarities in clinical symptoms of these mental disorders.
Role of Mutant CFTR in Hypersusceptibility of Cystic Fibrosis Patients to Lung Infections (1996)

Cystic fibrosis (CF) patients are hypersusceptible to chronic Pseudomonas aeruginosa lung infections. Cultured human airway epithelial cells expressing the delta F508 allele of the cystic fibrosis transmembrane conductance regulator (CFTR) were defective in uptake of P. aeruginosa compared with cells expressing the wild-type allele. Pseudomonas aeruginosa lipopolysaccharide (LPS)-core oligosaccharide was identified as the bacterial ligand for epithelial cell ingestion; exogenous oligosaccharide inhibited bacterial ingestion in a neonatal mouse model, resulting in increased amounts of bacteria in the lungs. CFTR may contribute to a host-defense mechanism that is important for clearance of P. aeruginosa from the respiratory tract.