gebhart/patrepeval huggingface dataset:
Molecular cloning and expression of an additional epidermal growth factor receptor-related gene. (1990)

Epidermal growth factor (EGF), transforming growth factor alpha (TGF-alpha), and amphiregulin are structurally and functionally related growth regulatory proteins. These secreted polypeptides all bind to the 170-kDa cell-surface EGF receptor, activating its intrinsic kinase activity. However, amphiregulin exhibits different activities than EGF and TGF-alpha in a number of biological assays. Amphiregulin only partially competes with EGF for binding EGF receptor, and amphiregulin does not induce anchorage-independent growth of normal rat kidney cells (NRK) in the presence of TGF-beta. Amphiregulin also appears to abrogate the stimulatory effect of TGF-alpha on the growth of several aggressive epithelial carcinomas that overexpress EGF receptor. These findings suggest that amphiregulin may interact with a separate receptor in certain cell types. Here we report the cloning of another member of the human EGF receptor (HER) family of receptor tyrosine kinases, which we have named "HER3/ERRB3." The cDNA was isolated from a human carcinoma cell line, and its 6-kilobase transcript was identified in various human tissues. We have generated peptide-specific antisera that recognizes the 160-kDa HER3 protein when transiently expressed in COS cells. These reagents will allow us to determine whether HER3 binds amphiregulin or other growth regulatory proteins and what role HER3 protein plays in the regulation of cell growth.
Green Tea Epigallocatechin Gallate Exhibits Anticancer Effect in Human Pancreatic Carcinoma Cells via the Inhibition of Both Focal Adhesion Kinase and Insulin-Like Growth Factor-I Receptor (2010)

The exact molecular mechanism by which epigallocatechin gallate (EGCG) suppresses human pancreatic cancer cell proliferation is unclear. We show here that EGCG-treated pancreatic cancer cells AsPC-1 and BxPC-3 decrease cell adhesion ability on micro-pattern dots, accompanied by dephosphorylations of both focal adhesion kinase (FAK) and insulin-like growth factor-1 receptor (IGF-1R) whereas retained the activations of mitogen-activated protein kinase and mammalian target of rapamycin. The growth of AsPC-1 and BxPC-3 cells can be significantly suppressed by EGCG treatment alone in a dose-dependent manner. At a dose of 100 μM which completely abolishes activations of FAK and IGF-1R, EGCG suppresses more than 50% of cell proliferation without evidence of apoptosis analyzed by PARP cleavage. Finally, the MEK1/2 inhibitor U0126 enhances growth-suppressive effect of EGCG. Our data suggests that blocking FAK and IGF-1R by EGCG could prove valuable for targeted therapy, which can be used in combination with other therapies, for pancreatic cancer.
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries (2011)

Genome targeting methods enable cost-effective capture of specific subsets of the genome for sequencing. We present here an automated, highly scalable method for carrying out the Solution Hybrid Selection capture approach that provides a dramatic increase in scale and throughput of sequence-ready libraries produced. Significant process improvements and a series of in-process quality control checkpoints are also added. These process improvements can also be used in a manual version of the protocol.
Association of 75/80-kDa Phosphoproteins and the Tyrosine Kinases Lyn, Fyn, and Lck with the B Cell Molecule CD20 (1995)

CD20, a non-glycosylated cell-surface protein expressed exclusively on B lymphocytes, is one of a family of 4-pass transmembrane molecules that also includes the beta chain of the high affinity receptor for IgE. The precise function of CD20 is unknown, although in vitro effects of CD20-specific antibodies on resting B cells indicate that it is able to transduce an extracellular signal affecting the G0/G1 cell cycle transition. Previous studies have demonstrated that CD20-initiated intracellular signals involve tyrosine kinase activation and that CD20 is tightly associated with both serine and tyrosine kinases. Here, analysis of CD20-associated molecules has revealed that CD20 is associated with the Src family tyrosine kinases p56/53lyn, p56lck, and p59fyn and with 75/80-kDa proteins phosphorylated in vivo on tyrosine residues. Mutagenesis of CD20 was performed to define regions of CD20 involved in intermolecular interactions. Mutants were analyzed in the human T lymphoblastoid cell line Molt-4, in which ectopically expressed wild-type CD20 associated with p59fyn, p56lck, and 75/80-kDa phosphoproteins. Deletion of major portions of the cytoplasmic regions of CD20 did not abolish its association with either p75/80 or tyrosine kinases. The interaction between CD20 and the Src-related kinases is therefore likely to be independent of CD20 cytoplasmic domains and may occur indirectly. The interaction may be mediated by the p75/80 phosphoproteins, which were found to be tightly associated with the Src family kinases isolated from the CD20 complex.
Chemokine Up-Regulation and Activated T Cell Attraction by Maturing Dendritic Cells (1999)

Langerhans' cells migrating from contact-sensitized skin were found to up-regulate expression of macrophage-derived chemokine (MDC) during maturation into lymph node dendritic cells (DCs). Naïve T cells did not migrate toward MDC, but antigen-specific T cells rapidly acquired MDC responsiveness in vivo after a subcutaneous injection of antigen. In chemotaxis assays, maturing DCs attracted activated T cells more strongly than naïve T cells. These studies identified chemokine up-regulation as part of the Langerhans' cell maturation program to immunogenic T cell-zone DC. Preferential recruitment of activated T cells may be a mechanism used by maturing DCs to promote encounters with antigen-specific T cells.
The Effect of Difluoromethylornithine on Decreasing Prostate Size and Polyamines in Men: Results of a Year-Long Phase IIb Randomized Placebo-Controlled Chemoprevention Trial (2008)

In this randomized placebo-controlled trial, DFMO induced a decrease of prostate putrescine levels and rate of prostate growth. The potential of this compound for prostate cancer or hyperplasia should be further studied.
Treating Human Autoimmunity: Current Practice and Future Prospects (2012)

Autoimmune diseases are caused by immune cells attacking the host tissues they are supposed to protect. Recent advances suggest that maintaining a balance of effector and regulatory immune function is critical for avoiding autoimmunity. New therapies, including costimulation blockade, regulatory T cell therapy, antigen-specific immunotherapy, and manipulating the interleukin-2 pathway, attempt to restore this balance. This review discusses these advances as well as the challenges that must be overcome to target these therapies to patients suffering from autoimmune disease while avoiding the pitfalls of general immunosuppression.
Cellular Immune Responses against Hepatitis C Virus (2005)

Cellular immune responses are typically important in recovery from acute infections, and studies of acute hepatitis C confirm that broadly directed CD4+ and CD8+ T cell responses are associated with spontaneous clearance of infection. However, a major unanswered question is what role the cellular immune response plays in progression of liver disease during chronic infection. Classic models of hepatitis C suggest that cellular immune responses promote liver injury, either by causing direct cytolysis of infected cells or by promoting inflammation. However, clinical evidence suggests that persons with cellular immune dysfunction, such as that due to with human immunodeficiency virus (HIV) infection, have more-rapid disease progression. Recent data suggest that cellular immune responses do serve to limit the progression of liver disease, even if they are ineffective at clearance of virus. There is limited information on the effect of HIV coinfection on the cellular immune response to hepatitis C virus, but further study of this issue might shed light on the pathogenesis of liver disease in both immunocompromised and nonimmunocompromised hosts.
A universal lattice code decoder for fading channels (1999)

We present a maximum-likelihood decoding algorithm for an arbitrary lattice code when used over an independent fading channel with perfect channel state information at the receiver. The decoder is based on a bounded distance search among the lattice points falling inside a sphere centered at the received point. By judicious choice of the decoding radius we show that this decoder can be practically used to decode lattice codes of dimension up to 32 in a fading environment.
Hepatitis C Virus 감염 환자에서 Hepatitis B Virus 중복 감염이 간세포암 발생에 미치는 영향 (2000)

Background/Aims: Korea is an endemic area of hepatitis B virus (HBV) infection. The routes of HBV and hepatitis C virus (HCV) infection are similar. The purposes of this study were to evaluate the effect of HBV infection on the development of anti-HCV-positive hepatocellular carcinoma (HCC) and to study the pattern of viral interaction in the patients with dual infection of HBV and HCV. Methods: One hundred thirty-seven consecutive anti-HCV-positive patients were divided into two groups: HCC group (N=58) and Non-HCC group (N=79). Various clinical, serological parameters and viral replicative status reflecting serum HBV DNA and HCV RNA positivity were compared between two groups. Results: According to multiple logistic regression analysis, male and positivity of HCV RNA, HBsAg, and HBV DNA were statistically significant variables associated with the development of HCC. The mean age at the diagnosis of HCC in the patients with dual infection was significantly younger than that of patients with HCV alone. Among 13 patients with dual infection, one third showed co-replication of HBV and HCV, but two thirds revealed only one viral replication. Conclusions: HBV infection seems to increase the risk of HCC in the anti-HCV-positive patients. To elucidate the complex profiles of viral interaction between HBV and HCV, further study may be needed. (Kor J Gastroenterol 2000;35:82 - 92)
Effects of increased adrenomedullary activity and taurine in young patients with borderline hypertension. (1987)

Recent studies showed that taurine, a sulphonic amino acid, could decrease blood pressure and increase sympathoadrenal tone in DoCA-salt-treated hypertensive rats. To determine whether taurine exerts its antihypertensive action in man in a similar fashion, we studied the effect of oral administration of taurine (6 g for 7 days) on blood pressure and plasma catecholamines in 19 young patients with borderline hypertension in a double-blind, placebo-controlled fashion. Systolic blood pressure in the 10 patients who were treated with taurine decreased by 9.0 +/- 2.9 mm Hg (mean +/- SE; p less than .05 by paired t test), compared with a 2.7 +/- 2.3 mm Hg decrease (NS) in the nine patients treated with placebo and diastolic blood pressure in the taurine-treated patients decreased by 4.1 +/- 1.7 mm Hg (p less than .05) compared with 1.2 +/- 3.0 mm Hg (NS) in the placebo-treated subjects. In the patients receiving taurine plasma epinephrine (E) decreased significantly, with a negligible decrease in plasma norepinephrine (NE). The effect of taurine on plasma catecholamines and the response of plasma E after the stimulation with glucagon was also studied in 12 borderline hypertensive and nine age-matched normotensive subjects. Basal plasma E was significantly higher in borderline hypertensive than in normal subjects, but basal plasma NE did not differ in the two groups.(ABSTRACT TRUNCATED AT 250 WORDS)
The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA) (2002)

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of hospital-acquired infections that are becoming increasingly difficult to combat because of emerging resistance to all current antibiotic classes. The evolutionary origins of MRSA are poorly understood, no rational nomenclature exists, and there is no consensus on the number of major MRSA clones or the relatedness of clones described from different countries. We resolve all of these issues and provide a more thorough and precise analysis of the evolution of MRSA clones than has previously been possible. Using multilocus sequence typing and an algorithm, BURST, we analyzed an international collection of 912 MRSA and methicillin-susceptible S. aureus (MSSA) isolates. We identified 11 major MRSA clones within five groups of related genotypes. The putative ancestral genotype of each group and the most parsimonious patterns of descent of isolates from each ancestor were inferred by using BURST, which, together with analysis of the methicillin resistance genes, established the likely evolutionary origins of each major MRSA clone, the genotype of the original MRSA clone and its MSSA progenitor, and the extent of acquisition and horizontal movement of the methicillin resistance genes. Major MRSA clones have arisen repeatedly from successful epidemic MSSA strains, and isolates with decreased susceptibility to vancomycin, the antibiotic of last resort, are arising from some of these major MRSA clones, highlighting a depressing progression of increasing drug resistance within a small number of ecologically successful S. aureus genotypes.
The Impact of Nanoparticle Protein Corona on Cytotoxicity, Immunotoxicity and Target Drug Delivery (2015)

In a perfect sequence of events, nanoparticles (NPs) are injected into the bloodstream where they circulate until they reach the target tissue. The ligand on the NP surface recognizes its specific receptor expressed on the target tissue and the drug is released in a controlled manner. However, once injected in a physiological environment, NPs interact with biological components and are surrounded by a protein corona (PC). This can trigger an immune response and affect NP toxicity and targeting capabilities. In this review, we provide a survey of recent findings on the NP-PC interactions and discuss how the PC can be used to modulate both cytotoxicity and the immune response as well as to improve the efficacy of targeted delivery of nanocarriers.
Neutrophils are indispensable for hematopoietic stem cell mobilization induced by interleukin-8 in mice (2002)

The CXC chemokine interleukin-8 (IL-8/CXCL8) induces rapid mobilization of hematopoietic progenitor cells (HPCs). Previously we showed that mobilization could be prevented completely in mice by pretreatment with neutralizing antibodies against the beta2-integrin LFA-1 (CD11a). In addition, murine HPCs do not express LFA-1, indicating that mobilization requires a population of accessory cells. Here we show that polymorphonuclear cells (PMNs) serve as key regulators in IL-8-induced HPC mobilization. The role of PMNs was studied in mice rendered neutropenic by administration of a single injection of antineutrophil antibodies. Absolute neutropenia was observed up to 3-5 days with a rebound neutrophilia at day 7. The IL-8-induced mobilizing capacity was reduced significantly during the neutropenic phase, reappeared with recurrence of the PMNs, and was increased proportionally during the neutrophilic phase. In neutropenic mice, the IL-8-induced mobilizing capacity was restored by the infusion of purified PMNs but not by infusion of mononuclear cells. Circulating metalloproteinase gelatinase B (MMP-9) levels were detectable only in neutropenic animals treated with PMNs in combination with IL-8, showing that in vivo activated PMNs are required for the restoration of mobilization. However, IL-8-induced mobilization was not affected in MMP-9-deficient mice, indicating that MMP-9 is not indispensable for mobilization. These data demonstrate that IL-8-induced mobilization of HPCs requires the in vivo activation of circulating PMNs.
Distribution of ataxin-7 in normal human brain and retina (2000)

Spinocerebellar ataxia 7 (SCA7) is a neurodegenerative disease caused by the expansion of a CAG repeat encoding a polyglutamine tract in the protein ataxin-7. We developed antibodies directed against two different parts of the ataxin-7 protein and studied its distribution in brain and peripheral tissue from healthy subjects. Normal ataxin-7 was widely expressed in brain, retina and peripheral tissues, including striated muscle, testis and thyroid gland. In the brain, expression of ataxin-7 was not limited to areas in which neurones degenerate, and the level of expression was not related to the severity of neuronal loss. Immunoreactivity was low in some vulnerable populations of neurones, such as Purkinje cells. In neurones, ataxin-7 was found in the cell bodies and in processes. Nuclear labelling was also observed in some neurones, but was not related to the distribution of intranuclear inclusions observed in an SCA7 patient. In this patient, the proportion of neurones with nuclear labelling was higher, on average, in regions with neuronal loss. Double immunolabelling coupled with confocal microscopy showed that ataxin-7 colocalized with BiP, a marker of the endoplasmic reticulum, but not with markers of mitochondria or the trans-Golgi network.
Clonal deletion of thymocytes as a tumor escape mechanism (1998)

Clonal deletion of thymocytes is a major event in T-cell tolerance and might represent a tumor escape mechanism. Previously, we have shown that class II-restricted, Id-specific, CD4+ T cells in T-cell receptor (TCR)-transgenic mice confer resistance against the MOPC315 plasmacytoma. In this report, we have investigated whether monoclonal immunoglobulin (Ig) produced by a plasmacytoma can induce deletion of thymocytes specific for the variable parts of Ig, i.e., the idiotype (Id). Large numbers of MOPC315 tumor cells were injected s.c. in the TCR-transgenic mice to overwhelm the CD4+ T-cell-mediated protection. When the MOPC315 plasmacytomas reached a weight of approximately 0.5 g (serum myeloma protein M315 about 50 microg/ml), immature CD4+ 8+ and mature CD4+ transgenic thymocytes became progressively deleted. Apoptotic thymocytes were already detectable when tumors were 2 mm in diameter (serum M315: 5 microg/ml, or 0.03 microM). The negative selection was Id-specific, because an Id-negative plasmacytoma failed to induce deletion. Injection of purified MOPC315-myeloma protein (M315) i.p. caused a profound reduction of Id-specific thymocytes. Enriched thymic dendritic cells (DC) from tumor-bearing animals were found to be primed with lambda2(315) and induced apoptosis of thymocytes in vitro. Our results indicate that circulating myeloma protein is processed and presented by thymic antigen-presenting cells (APC), and induces deletion of Id-specific thymocytes. Deletion of tumor-specific thymocytes may represent a tumor escape mechanism in patients with cancers that secrete or shed tumor antigens. The possibility that vaccination with tumor Ig or genes encoding for it may induce tolerance instead of protection should be taken into consideration.
Emerging treatments for noise-induced hearing loss (2011)

NIHL, in principle, can be prevented. With the current pace of development, oral drugs to protect against NIHL should be available within the next 5-10 years. Positive results from ongoing trials combined with additional laboratory tests might accelerate the time from the bench to clinical treatment.
Wear and Deformation of Patellar Components in Total Knee Arthroplasty (1989)

Clinical experience has shown that deformation of patella components can lead to loosening or excessive particulate debris, requiring revision. Factors affecting patella performance are the degree of congruity, the shear forces occurring due to tracking variations, and the excessive patellofemoral forces, particularly at higher flexion angles. A method was devised to load the patella with a constant force against the femoral component. The load was applied through a range of flexion. The deformation and wear patterns resembled those of retrieved clinical specimens. All-plastic components suffered from local deformation and underlying bone failure, whereas metal backing led to eventual penetration of the metal onto the femoral flange. Increased conformity of the patella component onto the femoral flange improved the situation for all-plastic and metal-backed designs by increasing the contact area and the available thickness of plastic.
Folding of a large protein at high structural resolution (2013)

Kinetic folding of the large two-domain maltose binding protein (MBP; 370 residues) was studied at high structural resolution by an advanced hydrogen-exchange pulse-labeling mass-spectrometry method (HX MS). Dilution into folding conditions initiates a fast molecular collapse into a polyglobular conformation (<20 ms), determined by various methods including small angle X-ray scattering. The compaction produces a structurally heterogeneous state with widespread low-level HX protection and spectroscopic signals that match the equilibrium melting posttransition-state baseline. In a much slower step (7-s time constant), all of the MBP molecules, although initially heterogeneously structured, form the same distinct helix plus sheet folding intermediate with the same time constant. The intermediate is composed of segments that are distant in the MBP sequence but adjacent in the native protein where they close the longest residue-to-residue contact. Segments that are most HX protected in the early molecular collapse do not contribute to the initial intermediate, whereas the segments that do participate are among the less protected. The 7-s intermediate persists through the rest of the folding process. It contains the sites of three previously reported destabilizing mutations that greatly slow folding. These results indicate that the intermediate is an obligatory step on the MBP folding pathway. MBP then folds to the native state on a longer time scale (~100 s), suggestively in more than one step, the first of which forms structure adjacent to the 7-s intermediate. These results add a large protein to the list of proteins known to fold through distinct native-like intermediates in distinct pathways.
Identification and Characterization of Escherichia coli Thioesterase III That Functions in Fatty Acid β-Oxidation (2008)

When Escherichia coli is grown on oleic acid as the sole carbon source, most of this fatty acid is completely degraded by beta-oxidation. However, approximately 10% of the oleic acid is only partially degraded to 3,5- cis-tetradecadienoyl-CoA, which is hydrolyzed to 3,5- cis-tetradecadienoic acid and released into the growth medium. An investigation of thioesterases involved in this novel pathway of beta-oxidation led to the identification of a new thioesterase (thioesterase III) that is induced by growth of E. coli on oleic acid. This enzyme was partially purified and identified as the ybaW gene product by mass spectrometric analysis of tryptic peptides. The ybaW gene, which has a putative consensus sequence for binding the fatty acid degradation repressor, was cloned and expressed in E. coli. Thioesterase III was shown to be a long-chain acyl-CoA thioesterase that is most active with 3,5-tetradecadienoyl-CoA, a minor metabolite of oleate beta-oxidation. Its substrate specificity and induction by fatty acids agree with its proposed function in the thioesterase-dependent pathway of beta-oxidation. Thioesterase III is proposed to hydrolyze metabolites of beta-oxidation that are resistant to further degradation and that would inhibit the flux through the pathway if they were allowed to accumulate.