gebhart/patrepeval huggingface dataset:
Pten deletion leads to the expansion of a prostatic stem/progenitor cell subpopulation and tumor initiation (2006)

PTEN (phosphatase and tensin homolog deleted on chromosome 10) is a potent tumor suppressor gene frequently mutated in human prostate cancers. Deletion of Pten in a murine model of prostate cancer recapitulates the disease progression seen in humans. Using defined cell lineage markers, we demonstrate that PTEN negatively regulates p63-positive prostatic basal cell proliferation without blocking differentiation. Concomitant with basal cell proliferation is the expansion of a prostate stem/progenitor-like subpopulation as evidenced by the progressive increase of stem cell antigen-1 (Sca-1)- and BCL-2-positive cells. This observation provides strong evidence that basal cell proliferation can be an initiating event for precancerous lesions. Sca-1(+) and BCL-2(+) progenitors may serve as cancer-initiating cells in this model.
Selective processing of submandibular rat 1 protein at dibasic cleavage sites (1994)

The amino acid sequence of submandibular rat 1 (SMR1) protein, deduced from its cDNA sequence, led to the prediction that the SMR1 gene encodes a hormone-like precursor [Rosinski-Chupin, I., Tronik, D. & Rougeon, F. (1988) Proc. Natl Acad. Sci. USA 85, 8553-8557]. SMR1 contains an N-terminal putative secretory signal sequence and a tetrapeptide (QHNP), located between dibasic amino acids which constitute the most common signal for prohormone processing. We have isolated and characterized from the male rat submandibular gland and its secretions three structurally related peptides, namely an undecapeptide (VRGPRRQHNPR), a hexapeptide (RQHNPR) and a pentapeptide (QHNPR) generated from SMR1 by selective proteolytic cleavages at pairs of arginine residues. The biosynthesis of these peptides is subjected to distinct regulatory pathways depending on the organ, sex and age of the rat. Furthermore, the peptides are differentially distributed in the submandibular gland and in resting or epinephrine-elicited submandibular salivary secretions, suggesting distinct proteolytic pathways for their maturation. The undecapeptide is generated in the gland of both male and female rats, but under basal conditions it is only released into the saliva in male animals. The hexapeptide is produced in large amounts in the gland of adult male rats and released into the saliva in both resting and stimulated conditions. The pentapeptide appears only in the male saliva and is present mostly under stimulated conditions. In addition, administration of epinephrine induces the release of the hexapeptide from the submandibular gland into the bloodstream. The evidence indicates that the rat submandibular gland can function as a dual exocrine and endocrine organ for the SMR1-derived hexapeptide, as has been reported for nerve growth factor, epidermal growth factor, renin and kallikrein. Although the biological activities of the SMR1-derived peptides are not yet known, their high production and adrenergic-induced release only into the saliva and bloodstream of adult male rats, suggest a physiological involvement in some male-specific processes.
A comparative study on the genes for three porins of the Escherichia coli outer membrane. DNA sequence of the osmoregulated ompC gene. (1983)

The DNA sequence of the ompC gene which encodes one of the outer membrane porins has been determined. The gene appears to encode a secretory precursor of OmpC protein consisting of a total of 367 amino acid residues with a signal peptide of 21 amino acid residues at its NH2-terminal end. The 5' end noncoding region including the promoter of the ompC gene is extremely [A-T]-rich, and the codon usage in the ompC gene is unusual as are those in genes for other abundant outer membrane proteins. The promoter sequence of the ompC gene was compared with that of the ompF gene, both of which are controlled by the osmoregulatory operon, ompB. The deduced amino acid sequence of the OmpC protein showed extensive homology with that of the other porins (OmpF and PhoE proteins). The homology in the primary amino acid sequences, as well as the coding DNA sequences among the porins, indicates that the structural genes for the three porins evolved from a common ancestral gene. Comparison of the amino acid sequences among the OmpC, OmpF, and PhoE porins will be discussed with regard to structure and function.
Follicular lymphoma immunoglobulin κ light chains are affected by the antigen selection process, but to a lesser degree than their partner heavy chains (1997)

Follicular lymphoma cells carry surface immunoglobulin whose heavy chain variable (VH) regions exhibit considerable divergence from the aminoacid sequence predicted by the germline nucleotide sequence as a result of the somatic hypermutation process. The present study examined the extent of somatic hypermutation in follicular lymphoma kappa light chain variable region (V kappa) genes about which the available data is limited. DNA extracted from fresh frozen lymph node tissue of 14 patients with follicular lymphoma at diagnosis was subjected to polymerase chain reaction (PCR) amplification aimed at detecting clonal VH and VL (L: light chain) gene rearrangements. Clonal V kappa gene rearrangements were detected in 10/14 cases. Amplified VH and V kappa genes of these 10 cases were directly sequenced by the dideoxy-chain termination method. In all cases, rearranged VH genes demonstrated numerous mutations clustering in the complementarity determining regions (CDRs), in keeping with previous reports. The degree of divergence of the rearranged V kappa genes from the closest homologous germline V kappa genes varied significantly. Furthermore, two patterns of mutations were observed: (i) in six cases (60%), mutations were most often of the replacement (R) type (changing the aminoacid sequence of the encoded polypeptide) in the CDRs and of the silent (S) type (leaving the aminoacid sequence of the encoded polypeptide unchanged) in the framework regions (FWRs) resulting in R:S ratios significantly greater than would have occurred by chance: (ii) in four cases (40%), very few or no mutations were observed and the distribution of mutations as well as the R:S mutation ratios did not differ significantly from what would have occurred by chance alone. These findings imply that, compared to their partner heavy chains, the kappa light chains of follicular lymphoma neoplastic B-cells' surface immunoglobulin (sIg): (i) are less affected by somatic hypermutation: (ii) play a less significant role in the antigen selection process.
cDNA cloning and functional expression of the Schistosoma mansoni protective antigen triose-phosphate isomerase. (1992)

M.1 monoclonal antibody has previously been shown to passively transfer partial resistance to schistosome infection within mice and to recognize a 28-kDa antigen that has peptide sequence homology with triose-phosphate isomerase (TPI; D-glyceraldehyde-3-phosphate ketol-isomerase, EC 5.3.1.1). We have now isolated the complete coding DNA for Schistosoma mansoni TPI and confirmed that this cDNA encodes the 28-kDa antigen recognized by M.1. The predicted translation product has strong homology with other TPIs, particularly from higher eukaryotes, and the sequence homology is greatest in regions known to form the active site. The complete coding DNA has been expressed within an Escherichia coli host to produce high levels of soluble, recombinant S. mansoni TPI protein. The product is recognized and purified by the M.1 antibody and is a functional TPI with an intrinsic specific activity comparable to that of rabbit and yeast TPI.
Estradiol Inhibits Leukocyte Adhesion and Transendothelial Migration in Rabbits In Vivo (1999)

The mechanism by which estrogens protect against atherosclerosis is not known. We evaluated in vivo whether there is a gender difference in monocyte adhesion and subendothelial migration in hypercholesterolemic rabbits and whether any gender differences observed are due to estradiol. Monocyte adhesion and subendothelial migration were assessed in a blinded fashion by analyzing a standardized segment of aorta using a scanning electron microscope. We also assessed whether estradiol modulates induction of vascular cell adhesion molecule-1 (VCAM-1) protein using Western blot and flow cytometric analyses. We observed that male rabbits develop more monocyte adhesion and subendothelial migration than do female rabbits during hypercholesterolemia. We also observed that oophorectomized rabbits given physiological estradiol supplementation demonstrate fewer adherent and subendothelial monocytes than do oophorectomized rabbits given placebo. VCAM-1 protein expression was increased in aortae obtained from hypercholesterolemic, oophorectomized animals supplemented with placebo, and this increase was attenuated by estradiol. Finally, in cultured rabbit aortic endothelial cells stimulated with lysophosphatidylcholine, we observed an increase in VCAM-1 protein that was inhibited in a concentration-dependent fashion by estradiol. We have demonstrated in vivo that there is a gender difference in monocyte adhesion to endothelial cells and transendothelial migration after hypercholesterolemia and that this gender difference is due in part to estradiol. Our results also suggest that estradiol inhibits monocyte adhesion by inhibiting expression of VCAM-1.
The Focal Adhesion Kinase Suppresses Transformation-associated, Anchorage-independent Apoptosis in Human Breast Cancer Cells (2000)

The focal adhesion kinase (FAK) is a mediator of cell-extracellular matrix signaling events and is overexpressed in tumor cells. In order to rapidly down-regulate FAK function in normal and transformed mammary cells, we have used adenoviral gene transduction of the carboxyl-terminal domain of FAK (FAK-CD). Transduction of adenovirus containing FAK-CD in breast cancer cells caused loss of adhesion, degradation of p125(FAK), and induced apoptosis. Furthermore, breast tumor cells that were viable without matrix attachment also underwent apoptosis upon interruption of FAK function, demonstrating that FAK is a survival signal in breast tumor cells even in the absence of matrix signaling. In addition, both anchorage-dependent and anchorage-independent apoptotic signaling required Fas-associated death domain and caspase-8, suggesting that a death receptor-mediated apoptotic pathway is involved. Finally, FAK-CD had no effect on adhesion or viability in normal mammary cells, despite the loss of tyrosine phosphorylation of p125(FAK). These results indicate that FAK-mediated signaling is required for both cell adhesion and anchorage-independent survival and the disruption of FAK function involves the Fas-associated death domain and caspase-8 apoptotic pathway.
Aspects of the Pelagic Ecology and Behavior of the Black-Capped Petrel (Pterodroma hasitata) (1987)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Developmental hyperbilirubinemia and CNS toxicity in mice humanized with theUDP glucuronosyltransferase 1(UGT1) locus (2010)

High levels of unconjugated bilirubin (UCB) in newborn children is associated with a reduction in hepatic UDP glucuronosyltransferase (UGT) 1A1 activity that can lead to CNS toxicity, brain damage, and even death. Little is known regarding those events that lead to UCB accumulation in brain tissue, and therefore, we sought to duplicate this condition in mice. The human UGT1 locus, encoding all 9-UGT1A genes including UGT1A1, was expressed in Ugt1(-/-) mice. Because the most common clinical condition associated with jaundice in adults is Gilbert's syndrome, which is characterized by an allelic polymorphism in the UGT1A1 promoter, hyperbilirubinemia was monitored in humanized UGT1 mice that expressed either the Gilbert's UGT1A1*28 allele [Tg(UGT1(A1*28))Ugt1(-/-) mice] or the normal UGT1A1*1 allele [Tg(UGT1(A1*1))Ugt1(-/-) mice]. Adult Tg(UGT1(A1*28))Ugt1(-/-) mice expressed elevated levels of total bilirubin (TB) compared with Tg(UGT1(A1*1))Ugt1(-/-) mice, confirming that the promoter polymorphism associated with the UGT1A1*28 allele contributes to hyperbilirubinemia in mice. However, TB accumulated to near toxic levels during neonatal development, a finding that is independent of the Gilbert's UGT1A1*28 promoter polymorphism. Whereas serum TB levels eventually returned to adult levels, TB clearance in neonatal mice was not associated with hepatic UGT1A1 expression. In approximately 10% of the humanized UGT1 mice, peak TB levels culminated in seizures followed by death. UCB deposition in brain tissue and the ensuing seizures were associated with developmental milestones and can be prevented by enhancing regulation of the UGT1A1 gene in neonatal mice.
First demonstration of multi-junction receivers in a grid-connected concentrator module (2005)

This paper discusses the approach taken by Concentrating Technologies (CT), Spectrolab, and Arizona Public Service (APS) to demonstrate a High Concentration Photovoltaic (HCPV) module using Spectrolab's GaInP/GaInAs/Ge triple-junction solar cells. This module is currently connected to an inverter, feeding electricity into the grid at the Solar Test & Research (STAR) facility of APS in Tempe, AZ. Although the module output is small, under 1 kW AC, it is the world's first demonstration of a grid-connected utility module using the same triple-junction solar cell technology that have been used to power satellites and other spacecrafts. This paper also discusses the next steps required to increase module efficiency and enhance its reliability. The economics of the MJ receivers in the context of this module are also discussed.
The immunological challenge to developing a vaccine to the blood stages of malaria parasites (2004)

Twenty-one years after malaria antigens were first cloned, a vaccine still appears to be a long way off. There have been periods of great excitement, and in model systems, subunit vaccine homologs can induce robust protection. However, significant challenges exist concerning antigenic variation and polymorphism, immunological non-responsiveness to individual vaccine antigens, parasite-induced apoptosis of immune effector and memory cells, and immune deviation as a result of maternal immunity and alterations of dendritic cell function. Novel approaches will be required. This review addresses some of the approaches that might present malaria antigens in a way designed to induce superior immune responses or that target novel conserved epitopes. Cell-mediated immunity, acting independently of antibody, may exert potent anti-parasite effects, and identification of multiple target antigens/epitopes could lead to the development of vaccines with profound efficacy.
Solvated Interaction Energy (SIE) for Scoring Protein−Ligand Binding Affinities. 1. Exploring the Parameter Space (2007)

We present a binding free energy function that consists of force field terms supplemented by solvation terms. We used this function to calibrate the solvation model along with the binding interaction terms in a self-consistent manner. The motivation for this approach was that the solute dielectric-constant dependence of calculated hydration gas-to-water transfer free energies is markedly different from that of binding free energies (J. Comput. Chem. 2003, 24, 954). Hence, we sought to calibrate directly the solvation terms in the context of a binding calculation. The five parameters of the model were systematically scanned to best reproduce the absolute binding free energies for a set of 99 protein-ligand complexes. We obtained a mean unsigned error of 1.29 kcal/mol for the predicted absolute binding affinity in a parameter space that was fairly shallow near the optimum. The lowest errors were obtained with solute dielectric values of Din = 20 or higher and scaling of the intermolecular van der Waals interaction energy by factors ranging from 0.03 to 0.15. The high apparent Din and strong van der Waals scaling may reflect the anticorrelation of the change in solvated potential energy and configurational entropy, that is, enthalpy-entropy compensation in ligand binding (Biophys. J. 2004, 87, 3035-3049). Five variations of preparing the protein-ligand data set were explored in order to examine the effect of energy refinement and the presence of bound water on the calculated results. We find that retaining water in the final protein structure used for calculating the binding free energy is not necessary to obtain good results; that is the continuum solvation model is sufficient. Virtual screening enrichment studies on estrogen receptor and thymidine kinase showed a good ability of the binding free energy function to recover true hits in a collection of decoys.
Identification of DNA sequences flanking the breakpoint of human t(14q21q) Robertsonian translocations. (1992)

We have employed molecular probes and in situ hybridization to investigate the DNA sequences flanking the breakpoint of a group of t(14q21q) Robertsonian translocations. In all the families studied, the probands were patients with Down syndrome who carried a de novo t(14q21q) translocation. The DNA probes used were two alphoid sequences, alphaRI and alphaXT, which are specific for the centromeres of chromosomes 13 and 21 and of chromosomes 14 and 22, respectively; a satellite III sequence, pTRS-47, which is specific for the proximal p11 region of chromosomes 14 and 22; and a newly defined satellite III DNA, pTRS-63, which is specific for the distal p11 region of chromosome 14. The two alphoid probes detected approximately the same amount of autoradiographic signal on the translocated chromosomes as was expected for chromosomes 14 and 21 of the originating parent, suggesting that there has been no loss of these centromeric sequences during the translocation events. Results with the two satellite III probes indicated that the domain corresponding to pTRS-47 was retained in the translocated chromosomes, whereas the domain for pTRS-63 was lost. These results have allowed us to place the translocation breakpoint between the pTRS-47 and pTRS-63 domains within the p11 region of chromosome 14.
Inhibition of alanine racemase by alanine phosphonate: detection of an imine linkage to pyridoxal 5'-phosphate in the enzyme-inhibitor complex by solid-state nitrogen-15 nuclear magnetic resonance (1988)

Inhibition of alanine racemase from the Gram-positive bacterium Bacillus stearothermophilus by (1-aminoethyl) phosphonic acid (Ala-P) proceeds via a two-step reaction pathway in which reactivation occurs very slowly. In order to determine the mechanism of inhibition, we have recorded low-temperature, solid-state 15N NMR spectra from microcrystals of the [15N]Ala-P-enzyme complex, together with spectra of a series of model compounds that provide the requisite database for the interpretation of the 15N chemical shifts. Proton-decoupled spectra of the microcrystals exhibit a line at approximately 150 ppm, which conclusively demonstrates the presence of a protonated Ala-P-PLP aldimine and thus clarifies the structure of the enzyme-inhibitor complex. We also report the pH dependence of Ala-P binding to alanine racemase.
The entity-relationship model (1975)

A data model, called the entity-relationship model, is proposed. This model incorporates some of the important semantic information in the real world. A special diagramatic technique is introduced as a tool for data base design. An example of data base design and description using the model and the diagramatic technique is given. Some implications on data integrity, information retrieval, and data manipulation are discussed.The entity-relationship model can be used as a basis for unification of different views of data: the network model, the relational model, and the entity set model. Semantic ambiguities in these models are analyzed. Possible ways to derive their views of data from the entity-relationship model are presented.
Identification of the major late human cytomegalovirus matrix protein pp65 as a target antigen for CD8+ virus‐specific cytotoxic T lymphocytes (1994)

Primary cytomegalovirus (CMV) infection and reactivation of persistent CMV are associated with significant morbidity and mortality in immunocompromised individuals. Although recovery from CMV disease is correlated with the development of CMV-specific cytotoxic T lymphocytes (CTL), the major viral target antigens to which the response is directed are ill-defined, though they may comprise viral structural elements. We now identify the CMV matrix protein pp65 as a significant target antigen for CD8+ class I major histocompatibility complex (MHC)-restricted CMV-specific CTL derived from the peripheral blood of four of five latently infected individuals. CMV-specific CTL recognition of pp65 on target cells occurs prior to the onset of viral gene expression and persists throughout the duration of the replicative cycle. Recognition in the absence of viral gene expression suggests that abundant viral protein enters the normal trafficking pathway upon viral penetration and is readily made available to MHC molecules for presentation at the cell surface. Thus pp65 specific CTL may represent an important effector population for early control and limitation of CMV infection and disease. The observation that CMV-specific CTL can be induced in vitro using peptide fragments derived from pp65 supports the future use and manipulation of this and similar effector populations in a clinical setting.
Genetic and metabolic diversity of pink-pigmented facultative methylotrophs in phyllosphere of tropical plants (2008)

Diversity of Pink-Pigmented Facultative Methylotrophs (PPFMs) in phyllosphere of cotton, maize and sunflower was determined based on differential carbon-substrate utilization profile and Random Amplified Polymorphic DNA data. Results indicate that six diversified groups of PPFMs are found in these crops. Sunflower and maize phyllosphere harbor four different groups of methylobacteria while cotton has only two groups.
The Acute-Phase Response in Relation to Radiographic Progression in Early Rheumatoid Arthritis: A Prospective Study During the First Three Years of the Disease (1993)

Studies on the relationship between acute-phase protein (APP) production, clinical disease activity and progression of radiological damage in RA have been hampered by three factors: patients are studied at different stages of the disease; APP levels are taken incidentally rather than serially; and inter-individual differences in the relationship between the extent of the acute-phase reaction and the progression of radiological damage are not accounted for. A group of 110 newly diagnosed (complaints < 1 year) patients with RA were analysed for a follow-up period of at least three years. Damage was assessed radiologically according to the modified method of Sharp. As radiological progression is a cumulative event, APP production was also calculated by plotting serial CRP levels over time. Overall, a highly significant correlation was found between CRP production and radiological progression; however, a wide variation was observed due to inter-individual differences. The greatest variation was found in the lower range of CRP values, where inter-individual variation could not be accounted for by HLA-DR4, positive RF, sex or age. In conclusion, the prognostic use of serial measurement of APPs for the assessment of radiological progression is limited due to inter-individual variation. Knowledge of the factors underlying these inter-individual differences will increase the applicability of CRP in the prediction of joint damage for individual patients.