gebhart/patrepeval huggingface dataset:
Deletion at 13q21 is associated with aggressive prostate cancers. (2000)

Previous cytogenetic and molecular genetic analyses suggest that the q21 band of chromosome 13 harbors a tumor suppressor gene(s) involved in prostatic carcinogenesis. The precise genetic location, however, has not been defined. In this study, we examined prostate cancer specimens and cell lines/xenograft for genetic deletions at 13q21, using the methods of tissue microdissection and duplex PCR. Deletions at 13q21 were detected in 13 of 147 (9%) prostate cancer samples. Deletion of the same region was also detected in the LNCaP cell line and the PC-82 xenograft of prostate cancer. The overlapping region of deletion in LNCaP and PC-82 spans 3.1 cM or 2.9 cR, which is equivalent to 1-3 Mb. The endothelin receptor B gene, a possible tumor suppressor gene at 13q21, was not located in the region of deletion. Among the 13 prostate neoplasms with deletion at 13q21, 5 were metastases, and 7 were poorly differentiated primary tumors. The only primary tumor that was not poorly differentiated but had deletion occurred in one of the youngest patients (49 years) at diagnosis. These results provide evidence that 13q21 may harbor an unidentified gene(s) whose inactivation occurs in some aggressive carcinomas of the prostate. In addition, this study provides a framework for the cloning and identification of the 13q21 gene(s).
Impact of a mass immunization campaign against serogroup C meningococcus in the Province of Quebec, Canada. (1996)

A mass immunization campaign was conducted in the Province of Quebec, Canada, during the winter of 1993, following an increase in the incidence of meningococcal disease, which was mainly caused by a virulent clone of Neisseria meningitidis, serogroup C, serotype 2a. About 1.6 million doses of the polysaccharide vaccine were administered, covering 84% of the target population aged between 6 months and 20 years; the overall cost was about 25.5 million Canadian dollars. Cases notified to the regional health authorities by clinicians, hospital laboratories, and the provincial reference laboratory from January 1990 up to March 1994 have been included in the analysis. In the first year following the campaign, the incidence of the disease dropped markedly among vaccinees as well as the unvaccinated fraction of the target population, while it remained unchanged among persons aged more than 20 years. This suggests the existence of herd immunity. The overall field efficacy of the vaccine was 79%, more in teenagers and less in under-5-year-olds. A minimum of 37 cases were prevented during the first year.
The extended XQL for querying and updating large XML databases (2001)

XQL has been argued as just a model for asking for specific sets of elements with very limited query capability. This paper proposes several extensions of XQL to address the issues. The extensions include full-text indexed search, path variables, joins, session-based navigations, and updates. Effort has been spent to preserve the conciseness of the language syntax. Its corresponding query processor with optimization mechanism has been prototyped and available online. Finally, implementation issues are discussed.
H-2-unrestricted adjuvant effect of cholera toxin B subunit on murine antibody responses to influenza virus haemagglutinin. (1991)

Cholera toxin B subunit (CTB) has been shown to augment the antibody responses to influenza virus haemagglutinin (HA) in BALB/c mice immunized with HA vaccine together with CTB. In this study, mouse strain differences in the adjuvant effect of CTB on anti-HA antibody responses were investigated along with those in the antibody responses to CTB or HA, using various inbred and H-2 congenic strains. The antibody responsiveness to CTB depended on the H-2 haplotype of the strain: strains with the H-2b haplotype were high responders, those with H-2a, H-2k and H-2s were low responders, and those with H-2d were intermediate. The responsiveness to HA was also related to the H-2 haplotype: H-2a and H-2k strains were high responders, H-2b and H-2s strains were low responders, and H-2d strains were intermediate. However, the degree of the adjuvant effect of CTB on anti-HA antibody responses was almost constant, regardless of the H-2 haplotype or other genetic backgrounds of the strain. The lack of genetic restriction of the adjuvant effect would be favourable for application of CTB-combined HA vaccine to humans, who are genetically diverse. Moreover, these results suggest that the immunogenicity and adjuvanticity of CTB differ essentially in their mechanisms.
PSA Concentrations in Seminal Plasma (1998)

Prostate specific antigen (PSA) is an important tumor marker for the detection and monitoring of prostate cancer. PSA is secreted by the prostatic epithelial cells into the lumen of the prostate duct during the formation of seminal plasma. PSA is a 30 kDa serine protease that cleaves biological substrates in seminal fluid, including seminogelin I, seminogelin II, and fibronectin, into small peptides, resulting in increased sperm motility (1)(2)(3)(4). PSA has also been shown to cleave other biological substrates, including insulin-like growth factor-binding protein-3 and laminin, indicating …
Genetic Approaches to Cardiovascular Disease (1995)

Molecular genetic analyses of long-QT syndrome, supravalvular aortic stenosis, and Williams syndrome have begun to unravel the mechanisms underlying these inherited disorders. Rapid genetic testing for Williams syndrome is now available using a simple cytogenetic test, fluorescence in situ hybridization, but additional work will be required for long-QT syndrome and autosomal-dominant supravalvular aortic stenosis. Improved diagnosis and mechanistic understanding of these disorders should lead to rational treatment and prevention.
A Molecular Switch Based on Potential-Induced Changes of Oxidation State (2005)

We have measured the conductance of a hepta-aniline oligomer attached to gold electrodes held under potential control in electrolyte. It increases fifteen-fold (to 5.3+/-0.4 nS) on oxidation from the leucoemeraldine form to the emeraldine salt. The single-molecule current-voltage characteristic, linear in toluene, displays negative differential resistance in an acidic electrolyte. The negative differential resistance is accounted for by modification of the local surface potential by the applied bias. These results connect electrochemical data directly to molecular electronic behavior in a two-terminal device.
Diversity of Lipopolysaccharide Structures inCampylobacter jejuni (1997)

Immune blots of electrophoresed lipopolysaccharides extracted from 38 Campylobacter jejuni serostrains suggested the presence of O chains in 16 strains and their absence in 22. Structural analysis confirmed the presence of O chains in serostrains O:19, O:23, and O:36 and the absence of O chains in serostrains O:1, O:2, and O:3. The O:19 strain has O repeat units of beta-D-glucuronic acid amidated with 2-amino-2-deoxyglycerol and N-acetylglucosamine. The 0:36 O chain has four different but closely related repeat units that each consist of N-acetylglucosamine, galactose, and a heptose that is varied in structure from one repeat unit to the next. The O:23 O chain has three different repeat units identical to three of O:36. Except for O:3, core oligosaccharides of strains with or without O chains contain sialic acid (Neu5Ac) in the terminal regions that in many cases mimic the structures of human gangliosides. Three neuropathic isolates were found to have a core terminal trisaccharide (Neu5Ac alpha2-->8Neu5Ac alpha2-->3Galbeta1) that was not found in nonneuropathic strains.
SYNTHESIS OF PROCAINAMIDE METABOLITES. N-ACETYL DESETHYLPROCAINAMIDE AND DESETHYLPROCAINAMIDE (1996)

(1996). SYNTHESIS OF PROCAINAMIDE METABOLITES. N-ACETYL DESETHYLPROCAINAMIDE AND DESETHYLPROCAINAMIDE. Organic Preparations and Procedures International: Vol. 28, No. 4, pp. 470-474.
Programmed cell death during regression of the MCF-7 human breast cancer following estrogen ablation. (1991)

To study the mechanism of regression of human mammary cancer following estrogen ablation, estrogen-responsive MCF-7 human mammary adenocarcinoma cells were inoculated into ovariectomized female nude mice supplemented with exogenous 17 beta-estradiol (E2) via an E2 implant. Implants were then removed when MCF-7 tumors were 400 mm3 in size. Removal of the E2 implants resulted in a 50% tumor regression by 2 weeks following E2 ablation. Associated with this regression is a rapid (i.e., within 1 day following E2 ablation) enhanced expression of the transforming growth factor beta 1 and TRPM-2-genes, two genes the expression of which has been previously demonstrated to be enhanced in a variety of cell types induced to undergo programmed cell death (i.e., apoptosis). The enhanced expression of transforming growth factor beta 1 and TRPM-2 is not a nonspecific response since the expression of other genes, like c-fos, c-H-ras, and pS2, decrease following E2 ablation. Fragmentation of tumor DNA into nucleosomal oligomers and histological appearance of apoptotic bodies are characteristic early events that precede the dramatic reduction in tumor volume following E2 ablation. These results demonstrate that the regression of MCF-7 human mammary cancers in nude mice following estrogen ablation is due to a sequence of biochemical and morphological changes that result in both the cessation of cell proliferation and activation of programmed death or apoptosis of these MCF-7 cancer cells. Clarification of the biochemical pathway involved in the activation of this programmed cell death should identify new targets of therapy for even estrogen-independent human mammary cancer cells.
Inhibitory Effect of Herbal Medicines on Rotavirus Infectivity. (2000)

The inhibitory effect of some traditional herbal medicines on the infectivity of rotavirus, which predominantly occurs in sporadic diarrhea in infants and young children, was investigated. Among the 34 kinds of herbal medicines tested, the fruit of Citrus aurantium had the most potent inhibitory activity on rotavirus infection. The active components of the fruit of Citrus aurantium were neohesperidin and hesperidin. Their 50% inhibitory concentrations were 25 and 10 microM, respectively.
STRUCTURE AND FUNCTION OF THE PRE-T CELL RECEPTOR (1997)

The pre-T cell receptor (pre-TCR) that minimally consists of the TCR beta chain and the disulfide-linked pre-T cell receptor alpha (pT alpha) chain in association with signal-transducing CD3 molecules rescues from programmed cell death cells with productive TCR beta rearrangements. The pre-TCR induces expansion and differentiation of these cells such that they become TCR alpha beta bearing CD4+8+ thymocytes, which express only a single TCR beta chain and then either die of neglect or--upon TCR-ligand interaction--undergo either positive or negative selection. The newly discovered pT alpha gene encodes a transmembrane protein that belongs to the Ig superfamily and contains a cytoplasmic tail that, however, has no essential function in signal transduction, which is mediated by CD3 molecules and most likely p56lck. Experiments in pT alpha gene-deficient mice show that the pre-TCR has a crucial role in maturation as well as allelic exclusion of alpha beta T cells but is not required for the development of gamma delta-expressing cells. The function of the pre-TCR cannot be fully assumed by an alpha beta TCR that is expressed abnormally early in T cell development.
EcoCyc: a comprehensive database resource for Escherichia coli (2004)

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein-ligand interactions.
Acute Lung Injury Induced by Lipopolysaccharide Is Independent of Complement Activation (2008)

Although acute lung injury (ALI) is an important problem in humans, its pathogenesis is poorly understood. Airway instillation of bacterial LPS, a known complement activator, represents a frequently used model of ALI. In the present study, pathways in the immunopathogenesis of ALI were evaluated. ALI was induced in wild-type, C3(-/-), and C5(-/-) mice by airway deposition of LPS. To assess the relevant inflammatory mediators, bronchoalveolar lavage fluids were evaluated by ELISA analyses and various neutralizing Abs and receptor antagonists were administered in vivo. LPS-induced ALI was neutrophil-dependent, but it was not associated with generation of C5a in the lung and was independent of C3, C5, or C5a. Instead, LPS injury was associated with robust generation of macrophage migration inhibitory factor (MIF), leukotriene B(4) (LTB4), and high mobility group box 1 protein (HMGB1) and required engagement of receptors for both MIF and LTB4. Neutralization of MIF or blockade of the MIF receptor and/or LTB4 receptor resulted in protection from LPS-induced ALI. These findings indicate that the MIF and LTB4 mediator pathways are involved in the immunopathogenesis of LPS-induced experimental ALI. Most strikingly, complement activation does not contribute to the development of ALI in the LPS model.
Mechanisms of immunity to respiratory syncytial virus in cotton rats (1983)

Active immunity and maternally transmitted passive immunity to respiratory syncytial virus (RSV) were studied in cotton rats. Animals infected with respiratory syncytial virus developed complete resistance to pulmonary reinfection, which lasted at least 18 months. Nasal resistance was of shorter duration and began to diminish in 8 months. Pulmonary resistance was transferred by parabiosis, but nasal resistance was not. Adoptive transfer studies with fractionated convalescent blood showed that serum antibody, but not circulating lymphocytes, conferred pulmonary resistance. Immune females conferred antibody to their young prenatally and postnatally, with most of the antibody being transferred via colostrum and milk. Maternally transmitted immunity was more effective in the lungs than in the nose and was transient in both organs. Foster nursing experiments showed colostrum and milk to be the most important routes of immune transfer. Although resistance in infants generally correlated with serum neutralizing antibody levels, several exceptions to this correlation suggested that immune factors other than neutralizing antibody may also play an important role in maternal passive immunity.
ChemInform Abstract: Design, Synthesis, and Evaluation of CC‐1065 and Duocarmycin Analogues Incorporating the 2,3,10,10a‐Tetrahydro‐1H‐cyclopropa(d)benzo(f)quinol‐ 5‐one (CBQ) Alkylation Subunit: Identification and Structural Origin of Subtle Stereoelectronic Features that Govern Reactivity and Regioselectivity. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Structural resolution of carbohydrate positional and structural isomers based on gas-phase ion mobility-mass spectrometry (2010)

This report describes the rapid characterization of positional and structural carbohydrate isomers based on structural separations provided by ion mobility-mass spectrometry (IM-MS). Many of the diseases associated with glycoprotein variation can be more effectively treated with earlier detection substantiating the need for high-throughput methodologies for glycan characterization. This remains particularly difficult due to heterogeneity, branching, and large size of carbohydrate moieties which creates the potential for numerous isobaric positional and structural isomers that are difficult to characterize using conventional MS methods. IM-MS provides rapid (μs to ms) structural separations by IM and subsequent identification by MS which presents a means for characterization of positional and structural carbohydrate isomers. To chart the structural variation observed in IM-MS, the ion-neutral collision cross sections for over 300 carbohydrates are reported. This diversity can also be varied through the utility of using different alkali metals to tune separation selectivity via alkali metal-carbohydrate coordination. Furthermore, the advantages of combining either pre- and/or post-IM fragmentation prior to MS analysis is demonstrated for enhanced confidence in carbohydrate identification.
Interrelationship between mitosis and endomitosis in cultures of human megakaryocyte progenitor cells [published erratum appears in Blood 1987 May;69(5):1547] (1987)

Sera from dogs rendered aplastic by total-body irradiation stimulate human bone marrow megakaryocyte progenitors to form megakaryocyte colonies in plasma clot cultures. In this investigation, we evaluated the effects of varying concentrations of such sera on both the mitotic and endomitotic phases of human megakaryocyte development in vitro. When low concentrations of aplastic canine sera (2.5% to 5.0% [vol/vol]) were added to cultures of human peripheral blood mononuclear cells in place of normal AB serum, megakaryocyte colony formation was augmented fivefold, cell numbers per colony increased approximately 2.5- fold, and the geometric mean megakaryocyte ploidy almost doubled. Further increasing the aplastic canine serum concentration from 10% to 30% (vol/vol) stimulated no additional colony formation. However, there was a further augmentation of cell numbers per colony associated with a progressive decrease in the mean megakaryocyte ploidy. Megakaryocyte cultures were harvested after 7, 12, 15, and 19 days of incubation, and these demonstrated that the lower mean ploidy values found at the higher concentrations of aplastic canine serum did not result from delayed endoreduplication. At all aplastic serum concentrations evaluated, there existed a strong correlation between nuclear ploidy and cell diameter. We conclude that both the mitotic and endomitotic events in human megakaryocytopoiesis may be influenced by a factor or factors present in aplastic canine serum. At lower in vitro concentrations, such sera stimulate both mitosis and endomitosis, which promotes the development of megakaryocyte colonies composed of larger cells with a higher mean ploidy. With increasing aplastic serum concentrations, colony formation plateaus and mitosis is favored over endomitosis. This results in colonies composed of more numerous but smaller megakaryocytes with a lower mean ploidy. Our data suggest that the size and extent of polyploidization that can be achieved by a developing megakaryocyte may be influenced by the mitotic prior history of its immediate precursor cell.
Effects of subinhibitory concentrations of vancomycin or cefamandole on biofilm production by coagulase-negative staphylococci (1990)

The density of the biofilm layer produced on a plastic surface by 23 clinical isolates and 1 reference strain of slime-positive, coagulase-negative staphylococci was measured following growth in subinhibitory concentrations (sub-MICs) of cefamandole or vancomycin ranging from 2 to 0.008 micrograms/ml. All strains were susceptible to less than or equal to 2 micrograms of each agent per ml. The mean biofilm density produced by each strain was calculated from a total of eight determinations at each sub-MIC and was compared with the mean biofilm density of a drug-free control after correcting for differences in growth. The results showed that the density of the biofilm layer produced by 10 (42%) of 24 strains and 13 (54%) of 24 strains was significantly increased (P less than 0.006) at one or more sub-MICs of cefamandole or vancomycin, respectively. In contrast, the density of the biofilm produced by 9 (38%) of 24 and 2 (8%) of 24 strains was significantly reduced at one or more sub-MICs of cefamandole and vancomycin, respectively, and the biofilm density of 7 of these strains was decreased only when the sub-MIC was one-half the MIC. The biofilm density of six strains (five versus cefamandole and one versus vancomycin) was both enhanced and reduced by different sub-MICs of the same agent. None of the strains produced a detectable biofilm at or above the MIC for the strain. These data indicate that antimicrobial agents such as cefamandole or vancomycin could potentially enhance the biofilm matrix produced by certain slime-positive, coagulase-negative staphylococci on the surface of a biomedical implant if concentrations of these agents fall below the MIC for the infecting strain.
Bioactive Silk Protein Biomaterial Systems for Optical Devices (2008)

Silk-based biomaterial systems have been previously explored for a variety of medical and nonmedical materials needs. The unique biophysical features of silks provide options to generate highly tailored structures and morphologies with this unique family of fibrous proteins. To exploit these features, we have optimized the all aqueous processing of silk fibroin into novel surface nanopatterned protein materials. We have exploited control of this nanomorphology to optimize the optical features of these silk protein systems. We demonstrate control of surface morphology down to 125 nm, with fidelity over large length scales. This surface nanopatterning allows the silk protein to be formed into diffractive optics such as diffraction gratings, pattern generators, and lenses due to novel aqueous processing into optically clear materials via control of beta sheet crystallinity. Further, we incorporate biological components, such as hemoglobin and the enzyme peroxidase, during the process of forming the silk diffraction gratings. The ambient processing of the silk protein in water, in combination with these bioactive components, allows these entrained molecules to retain activity and provide added functions and selectivity to the optically active silk films. Thus, combinations of biochemical and optical readout is feasible and provides in a single, disposable/all degradable element with both spectral discrimination and biological function. These new surface nanopatterned, bioactive silk protein-based material systems offer a unique combination of features potentially useful for a range of biosensor needs, particularly when considered in concert with the remarkable mechanical properties of these proteins, their biocompatibility, and controllable biodegradation.