gebhart/patrepeval huggingface dataset:
Cutting Edge: The HLA-A*0101-Restricted HY Minor Histocompatibility Antigen Originates from DFFRY and Contains a Cysteinylated Cysteine Residue as Identified by a Novel Mass Spectrometric Technique (1999)

In this report, we describe the use of novel mass spectrometry instrumentation to identify a male-specific minor histocompatibility Ag restricted by HLA-A*0101 (A1-HY). This Ag has the sequence IVDC*LTEMY, where C* represents a cysteine disulfide bonded to a second cysteine residue. The core peptide sequence is found in the protein product of DFFRY, a Y chromosome gene not previously identified as the source of an HY Ag. The male-specific form of the peptide differs from its X chromosomal counterpart by the substitution of serine for the C* residue. Both peptides are expressed on the cell surface at 30 or fewer copies per cell. However, A1-HY-specific CTL recognize the DFFRY-derived peptide at a 1500-fold lower dose than the female homologue. Thus, these studies have identified a new source of HY epitopes and provide additional information about the influence of posttranslational modifications of class I-associated peptides on T cell recognition.
Regulation of colony-stimulating factor 1-dependent macrophage precursor proliferation by type beta transforming growth factor. (1988)

Transforming growth factor (TGF) type beta, a potent growth modulator, has recently been shown to inhibit the proliferation and function of several types of immune cells. This report investigates the effect of human platelet purified TGF-beta on CSF-1-induced proliferation in liquid cultures. We used two cell types to study TGF-beta effects, bone marrow precursors and a c-myc partially transformed CSF-1-dependent macrophage cell line designated BMM-8. We found that CSF-1-dependent proliferation of both cell types was strongly inhibited by TGF-beta in a dose-dependent manner. Approximately 1.6 and 8 pM TGF-beta inhibited 50% of CSF-1 proliferation of the bone marrow precursors and BMM-8, respectively. Inhibition appeared to be reversible, as bone marrow and BMM-8 cells proliferated in response to CSF-1 after preincubation of the cells in TGF-beta. Interestingly, inhibition of hematopoietic cells was observed only after a lag period of 24 to 48 h after onset of cultures. TGF-beta inhibition was partially diminished when increasing amounts of CSF-1 were added to the cultures. TGF-beta inhibition did not involve secondary inhibitory factors such as IFN or PG, both of which have been previously shown to suppress CSF responsiveness. Finally, flow cytometric analysis of the cell cycle indicated that within 48 h, TGF-beta-treated BMM-8 cells were prevented from entering S phase. These results suggest that TGF-beta may play an important role in the negative regulation of macrophage production.
Dynamic Regulation of the Translation Initiation Helicase Complex by Mitogenic Signal Transduction to Eukaryotic Translation Initiation Factor 4G (2012)

Eukaryotic translation initiation factor 4F (eIF4F), comprising the cap-binding protein eIF4E, the helicase eIF4A, and the central scaffold eIF4G, is a convergence node for a complex signaling network that controls protein synthesis. Together with eIF3 and eIF4A/4B, eIF4G recruits ribosomal subunits to mRNAs and facilitates 5' untranslated region unwinding. Mammalian eIF4G contains three HEAT domains and unstructured regions involved in protein-protein interactions. Despite detailed eIF4G structure data, the mechanisms controlling initiation scaffold formation remain obscure. We found a new, highly regulated eIF4B/-3 binding site within the HEAT-1/-2 interdomain linker, harboring two phosphorylation sites that we identified as substrates for Erk1/2 and casein kinase 2. Phorbol ester-induced sequential phosphorylation of both sites detached HEAT-2 from the complex with eIF4A/-4B/-3 and stimulated the association of HEAT-3 with the mitogen-activated protein kinase signal integrating kinase Mnk1. Our results provide a mechanistic link between intracellular signal transduction and dynamic initiation complex formation coordinated by flexible eIF4G structure.
BET bromodomain protein inhibition is a therapeutic option for medulloblastoma (2013)

Medulloblastoma is the most common malignant brain tumor of childhood, and represents a significant clinical challenge in pediatric oncology, since overall survival currently remains under 70%. Patients with tumors overexpressing MYC or harboring a MYC oncogene amplification have an extremely poor prognosis. Pharmacologically inhibiting MYC expression may, thus, have clinical utility given its pathogenetic role in medulloblastoma. Recent studies using the selective small molecule BET inhibitor, JQ1, have identified BET bromodomain proteins, especially BRD4, as epigenetic regulatory factors for MYC and its targets. Targeting MYC expression by BET inhibition resulted in antitumoral effects in various cancers. Our aim here was to evaluate the efficacy of JQ1 against preclinical models for high-risk MYC-driven medulloblastoma. Treatment of medulloblastoma cell lines with JQ1 significantly reduced cell proliferation and preferentially induced apoptosis in cells expressing high levels of MYC. JQ1 treatment of medulloblastoma cell lines downregulated MYC expression and resulted in a transcriptional deregulation of MYC targets, and also significantly altered expression of genes involved in cell cycle progression and p53 signalling. JQ1 treatment prolonged the survival of mice harboring medulloblastoma xenografts and reduced the tumor burden in these mice. Our preclinical data provide evidence to pursue testing BET inhibitors, such as JQ1, as molecular targeted therapeutic options for patients with high-risk medulloblastomas overexpressing MYC or harboring MYC amplifications.
Effect of dietary curcumin and dibenzoylmethane on formation of 7,12- dimethylbenz[a]anthracene-induced mammary tumors and lymphomas/leukemias in Sencar mice (1998)

Female Sencar mice (6 weeks old) were administered 1 mg of 7,12-dimethylbenz[a]anthracene (DMBA) by oral gavage once a week for 5 weeks. At 20 weeks after the first dose of DMBA, 68% of mice developed mammary tumors (the average 1.08 tumors per mouse) and 45% had lymphomas/leukemias. Feeding 1% dibenzoylmethane (DBM) in AIN 76A diet, starting at 2 weeks before the first dose of DMBA and continuing until the end of the experiment, inhibited both the multiplicity and incidence of DMBA-induced mammary tumor by 97%. The incidence of lymphomas/leukemias was completely inhibited by 1% DBM diet. In contrast, feeding 2% curcumin diet had little or no effect on the incidence of mammary tumors, and the incidence of lymphomas/leukemias was reduced by 53%.
Microfluidic system integration in sample preparation chip-sets - a summary (2005)

An increasing complexity of microfluidic chips and systems used for biochemical assay applications calls for the development of new strategies towards their functionality integration in order to achieve optimum assay performance. Approaches to an integration of microfluidic chips into diagnostic fluidic systems are reviewed with the emphasis on the selection of assay application, integration scheme, interfacing, and fabrication platform. In particular, we discuss a system containing polymer microfluidic chip-sets capable of cell pre-concentration from a complex sample matrix using immunomagnetic separations.
Multiple Regulatory Domains Control IRF-7 Activity in Response to Virus Infection (2000)

Recent studies implicate the interferon regulatory factors (IRF), IRF-3 and IRF-7, as key activators of Type 1 interferon genes, as well as the RANTES (regulated on activation normal T cell expressed) chemokine gene. Both IRF-3 and IRF-7 are regulated in part by virus-induced C-terminal phosphorylation, leading to nuclear translocation, stimulation of DNA binding, and transcriptional activities. Structure-function studies with IRF-7 suggested a complex organization of the C-terminal region, with a constitutive activation domain located between amino acids 150-246, an accessory inducibility region at the very end of IRF-7 between amino acids 467 and 503, and an inhibitory region (amino acids 341-467) adjacent to the C-terminal end that interferes with transactivation. Furthermore, an element that increases basal and virus-inducible activity is located between amino acids 278 and 305. A transcriptionally active form of IRF-7 was also generated by substitution of Ser-477 and Ser-479 residues with the phosphomimetic Asp. IRF-7, particularly IRF-7(S477D/S479D), was a strong transactivator of type I interferon and RANTES chemokine gene expression. Unlike wild type IRF-3, IRF-7 overexpression was able to stimulate inteferon gene expression in the absence of virus infection. Using tagged versions of IRF-7 and IRF-3, the formation of homo- and heterodimers was detected by co-immunoprecipitation. These results demonstrate that IRF-3 and IRF-7 transcription factors possess distinct structural characteristics that impart complementary rather than redundant functional roles in cytokine gene activation.
Auxin Signaling in Arabidopsis Leaf Vascular Development (2003)

A number of observations have implicated auxin in the formation of vascular tissues in plant organs. These include vascular strand formation in response to local auxin application, the effects of impaired auxin transport on vascular patterns and suggestive phenotypes of Arabidopsis auxin response mutants. In this study, we have used molecular markers to visualize auxin response patterns in developing Arabidopsis leaves as well as Arabidopsis mutants and transgenic plants to trace pathways of auxin signal transduction controlling the expression of early procambial genes. We show that in young Arabidopsis leaf primordia, molecular auxin response patterns presage sites of procambial differentiation. This is the case not only in normal development but also upon experimental manipulation of auxin transport suggesting that local auxin signals are instrumental in patterning Arabidopsis leaf vasculature. We further found that the activity of the Arabidopsis gene MONOPTEROS, which is required for proper vascular differentiation, is also essential in a spectrum of auxin responses, which include the regulation of rapidly auxin-inducible AUX/IAA genes, and discovered the tissue-specific vascular expression profile of the class I homeodomain-leucine zipper gene, AtHB20. Interestingly, MONOPTEROS activity is a limiting factor in the expression of AtHB8 and AtHB20, two genes encoding transcriptional regulators expressed early in procambial development. Our observations connect general auxin signaling with early controls of vascular differentiation and suggest molecular mechanisms for auxin signaling in patterned cell differentiation.
[Should thalidomide be rehabilitated?]. (1983)

Thalidomide (alpha-N-phtalimido-glutarimide) was withdrawn from sale in 1961 since it was held responsible for the birth of hundreds of phocomelus children. Despite this teratogenic potential, thalidomide remains a useful tool in the treatment of erythema nodosum leprosum, as well as in discoid lupus erythematosus when antimalarial drugs are ineffective or contraindicated. In addition, good results have been reported in several diseases such as actinic prurigo, polymorphous light eruption, Behçet syndrome, Weber-Christian disease, prurigo nodularis, pyoderma gangrenosum and ulcerative colitis. The mechanism of action is under debate but it is likely that thalidomide has immunomodulating properties by controlling T-suppressor lymphocytes, and anti-inflammatory effects, particularly an inhibition of neutrophil chemotaxis. Several attempts at synthesis of effective thalidomide derivatives devoid of teratogenic effects are ongoing.
Combining serial analysis of gene expression and array technologies to identify genes differentially expressed in breast cancer. (1999)

Several methods have been used recently to determine gene expression profiles of cell populations. Here we demonstrate the strength of combining two approaches, serial analysis of gene expression (SAGE) and DNA arrays, to help elucidate pathways in breast cancer progression by finding genes consistently expressed at different levels in primary breast cancers, metastatic breast cancers, and normal mammary epithelial cells. SAGE profiles of 21PT and 21MT, two well-characterized breast tumor cell lines, were compared with SAGE profiles of normal breast epithelial cells to identify differentially expressed genes. A subset of these candidates was then placed on an array and screened with clinical breast tumor samples to find genes and expressed sequence tags that are consistently expressed at different levels in diseased and normal tissues. In addition to finding the predicted overexpression of known breast cancer markers HER-2/neu and MUC-1, the powerful coupling of SAGE and DNA arrays resulted in the identification of genes and potential pathways not implicated previously in breast cancer. Moreover, these techniques also generated information about the differences and similarities of expression profiles in primary and metastatic breast tumors. Thus, combining SAGE and custom array technology allowed for the rapid identification and validation of the clinical relevance of many genes potentially involved in breast cancer progression. These differentially expressed genes may be useful as tumor markers and prognostic indicators and may be suitable targets for various forms of therapeutic intervention.
The tomato Blind gene encodes a MYB transcription factor that controls the formation of lateral meristems (2002)

The multitude of forms observed in flowering plants is largely because of their ability to establish new axes of growth during postembryonic development. This process is initiated by the formation of secondary meristems that develop into vegetative or reproductive branches. In the blind and torosa mutants of tomato, initiation of lateral meristems is blocked during shoot and inflorescence development, leading to a strong reduction in the number of lateral axes. In this study, it is shown that blind and torosa are allelic. The Blind gene has been isolated by positional cloning, and it was found that the mutant phenotype is caused by a loss of function of an R2R3 class Myb gene. RNA interference-induced blind phenocopies confirmed the identity of the isolated gene. Double mutant analysis shows that Blind acts in a novel pathway different from the one to which the previously identified Lateral suppressor gene belongs. The findings reported add a new class of transcription factors to the group of genes controlling lateral meristem initiation and reveal a previously uncharacterized function of R2R3 Myb genes.
Effects of Transdermal Nicotine on Learning, Memory, Verbal Fluency, Concentration, and General Health in a Healthy Sample at Risk for Dementia (2001)

Nicotinic receptor loss has been implicated in the pathogenesis of Alzheimer's disease. The present study investigated the effects of chronic low-dose transdermal nicotine in a cohort of nondemented, healthy volunteers (mean age 63 years). The majority of subjects (85%) had a first-degree relation with dementia. Subjects were tested using a before, during, and after design on a battery of tests known to be sensitive to early cognitive decline. A mixed pattern of results was seen, with significant changes occurring with verbal learning, object learning, delayed recall, and word retrieval. Nicotine had no effect on measures of concentration or psychomotor speed. The effects were most noticeable in subjects at the lower end of baseline test performance on the tasks used. The results are discussed with reference to the relationship between strategic nicotinic receptor loss and measurable psychometric change. The potential therapeutic role of nicotinic agonists in preclinical "at risk" individuals is supported by the results of this study.
Sublingual absorption of selected opioid analgesics (1988)

Ongoing interest in the improvement of pain management with opioid analgesics had led to the investigation of sublingual opioid absorption. The present report determined the percent absorption of selected opioid analgesics from the oral cavity of normal subjects under conditions of controlled pH and swallowing when a 1.0 ml aliquot of the test drug was placed under the tongue for a 10-minute period. Compared with morphine sulfate at pH 6.5 (18% absorption), buprenorphine (55%), fentanyl (51%), and methadone (34%) were absorbed to a significantly greater extent (p less than 0.05), whereas levorphanol, hydromorphone, oxycodone, heroin, and the opioid antagonist naloxone were not. Overall, lipophilic drugs were better absorbed than were hydrophilic drugs. Plasma morphine concentration-time profiles indicate that the apparent sublingual bioavailability of morphine is only 9.0% +/- 11.9% (SD) of that after intramuscular administration. In the same subjects the estimated sublingual absorption was 22.4% +/- 9.2% (SD), indicating that the sublingual absorption method may overestimate apparent bioavailability. When the oral cavity was buffered to pH 8.5, methadone absorption was increased to 75%. Thus, an alkaline pH microenvironment that favors the unionized fraction of opioids increased sublingual drug absorption. Although absorption was found to be independent of drug concentration, it was contact time dependent for methadone and fentanyl but not for buprenorphine. These results indicate that although the sublingual absorption and apparent sublingual bioavailability of morphine are poor, the sublingual absorption of methadone, fentanyl, and buprenorphine under controlled conditions is relatively high.
The three zinc-containing alcohol dehydrogenases from baker's yeast,Saccharomyces cerevisiae (2002)

This review is a summary of our current knowledge of the structure, function and mechanism of action of the three zinc-containing alcohol dehydrogenases, YADH-1, YADH-2 and YADH-3, in baker's yeast, Saccharomyces cerevisiae. The opening section deals with the substrate specificity of the enzymes, covering the steady-state kinetic data for its most known substrates. In the following sections, the kinetic mechanism for this enzyme is reported, along with the values of all rate constants in the mechanism. The complete primary structures of the three isoenzymes of YADH are given, and the model of the 3D structure of the active site is presented. All known artificial mutations in the primary structure of the YADH are covered in full and described in detail. Further, the chemical mechanism of action for YADH is presented along with the complement of steady-state and ligand-binding data supporting this mechanism. Finally, the bio-organic chemistry of the hydride-transfer reactions catalyzed by the enzyme is covered: this chemistry explains the narrow substrate specificity and the enantioselectivity of the yeast enzyme.
The Association of Early Adolescent Problem Behavior With Adult Psychopathology (2005)

Early adolescent problem behavior identifies a subset of youth who are at an especially high and generalized risk for developing adult psychopathology.
Development of New Organ Preservation Solutions in Kyoto University (2004)

Although lung transplantation (LTx) has been established as a therapeutic approach for end-stage respiratory failure, several problems remain to be solved. In addition to the serious problem of donor shortage, primary graft failure, which is mostly caused by ischemia-reperfusion injury, a serious problem, and represents one of the most frequent causes of early mortality. The development of a highly reliable organ preservation solution that reduces ischemia-reperfusion injury will improve the functioning of transplanted organs and alleviate the donor shortage. We first evaluated the importance of saccharides and electrolytes in the lung preservation solution. We proved the superiority of trehalose, a non-reducing disaccharide, and the efficiency of the extracellular-type (low potassium) ion composition, and we also developed an extracellular-type trehalose containing Kyoto (ET-Kyoto) solution. Furthermore, several agents for vascular endothelial protection were evaluated, and finally, a more effective solution named "new ET-Kyoto solution" was developed, by adding N-acetylcysteine, dibutyryl adenosine 3', 5'-cyclic monophosphate, and nitroglycerin to the "conventional" ET-Kyoto solution. The new ET-Kyoto solution enabled canine LTx to last up to 30 hours. ET-Kyoto solution has so far been used and produced good results in five clinical LTx throughout Japan and South Korea. Although it was initially developed for lung preservation, its effectiveness in the preservation of various organs/ tissues, such as the trachea, kidney, skin/muscle flap, amputated digits, liver, and pancreas, has also been experimentally and clinically shown. In this paper, clinical and experimental findings with ET-Kyoto solution have been accumulated to further analyze its effect, safety, and chemical stability. We hope to provide ET-Kyoto solution as the standard organ/tissue preserving solution throughout the world.
Attachment of enterotoxigenic Escherichia coli to human intestinal cells (1983)

An adherence test was developed with human ileal cells isolated from patients with a long-standing ileostomy by saline lavage through the stoma. Enterotoxigenic Escherichia coli isolated from humans bound to the human ileal cells to a greater extent (1.2 x 10(6) bacteria bound) than did control E. coli strains, including K99 pili antigen-producing strains (whether originally isolated from pigs or calves), the rabbit pathogen RDEC-1, the laboratory-derived nontoxigenic strain 334LL, or human normal fecal strains. However, K88 strains, either K88ab or K88ac, bound to the human ileal cells as well as did enterotoxigenic E. coli. Ileal cells isolated from two donors with different blood types behaved similarly. These cells remained viable and retained their binding ability for at least 3 days when stored in tissue culture medium at 4 degrees C.
Dextromethorphan: Cellular Effects Reducing Neuronal Hyperactivity (1994)

Dextromethorphan is a dextrorotary morphinan without affinity for opioid receptors, commonly used as an antitussive medication. During the past 5 years, interest in the compound and its demethylated derivative, dextrorphan, has been revived because additional neuroprotective and antiepileptic properties were found in in vitro studies, animal experiments, and a few clinical cases. Both morphinans are able to inhibit N-methyl-D-aspartate (NMDA) receptor channels and voltage-operated calcium and sodium channels with different potencies. The inhibition of the NMDA receptor is believed to be the predominant mechanism of action responsible for the anticonvulsant and neuroprotective properties of the compounds.
[Cesarean section in pregnancy complicated by severe hepatitis and heart disease]. (1990)

In this article, we reported the analysis of two severe diseases complicating pregnancy: 1,918 cases of heart disease in last 36 years and 22 cases of severe hepatitis in last 16 years. The conclusion was that on active therapy and close cooperation with cardiologist, pregnancy complicated with heart disease of grade III-IV cardiac function can be taken as an indication of Cesarean section. This operation performed at a proper time is good for the mother and also the baby. The traditional idea that Cesarean section could only be done for an obstetrical reason is not quite adequate. For primiparas with severe hepatitis, a supportive therapy with fresh blood transfusion, albumin and Cesarean section under local anesthesia might be the method of choice, its mortality rate being much lower than a vaginal delivery.