gebhart/patrepeval huggingface dataset:
Corticotropin-releasing hormone physiology (2006)

Corticotropin-releasing hormone (CRH), also known as corticotropin-releasing factor, is a highly conserved peptide hormone comprising 41 amino acid residues. Its name derives from its role in the anterior pituitary, where it mediates the release of corticotropin (ACTH) leading to the release of adrenocortical steroids. CRH is the major hypothalamic activator of the hypothalamic–pituitary–adrenal (HPA) axis. Major functions of the HPA include: (i) influencing fetal development of major organ systems including lung, liver, and gut, (ii) metabolic functions, including the maintenance of normal blood glucose levels during the fasting state via glycogenolysis and gluconeogenesis, (iii) modulation of immune function, and (iv) maintenance of cardiovascular tone. In addition, CRH, acting both directly and via the HPA, has a role in regulating several neuroendocrine functions including behavior, food intake, reproduction, growth, immune function, and autonomic function. CRH has been localized to the paraventricular nucleus (PVN) of the hypothalamus, which projects to the median eminence and other hypothalamic and midbrain targets. The CRH gene is composed of two exons. The CRH promoter contains a cAMP-response element, and the intron contains a restrictive element-1/neuron restrictive silencing element (RE-1/NRSE) sequence. Recently, a family of CRH-related peptides, termed the urocortins, has been identified. These peptides probably play a role in integrating multiple aspects of the stress-response, although their functions are largely unknown. Both CRH and the urocortins interact with two transmembrane G-protein-coupled cell surface receptors, CRH-R1, and CRH-R2, which differ in their patterns of tissue distribution. In addition, the binding affinities for CRH and the urocortins to the two receptors differ considerably, and may contribute to the different actions of these peptides.
An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis H37Rv, and comparison with Mycobacterium leprae. (1996)

An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis, was constructed by using a twin-pronged approach. Pulsed-field gel electrophoretic analysis enabled cleavage sites for Asn I and Dra I to be positioned on the 4.4-Mb circular chromosome, while, in parallel, clones from two cosmid libraries were ordered into contigs by means of fingerprinting and hybridization mapping. The resultant contig map was readily correlated with the physical map of the genome via the landmarked restriction sites. Over 165 genes and markers were localized on the integrated map, thus enabling comparisons with the leprosy bacillus, Mycobacterium leprae, to be undertaken. Mycobacterial genomes appear to have evolved as mosaic structures since extended segments with conserved gene order and organization are interspersed with different flanking regions. Repetitive sequences and insertion elements are highly abundant in M. tuberculosis, but the distribution of IS6110 is apparently nonrandom.
Role of arginine in the binding of thiamin pyrophosphate to Escherichia coli pyruvate oxidase (1982)

The mode of interaction between Escherichia coli pyruvate oxidase and its cofactor, thiamin pyrophosphate (TPP), was studied with the aid of arginine-directed reagents. The enzyme is rapidly inactivated by either phenylglyoxal or 2,3-butanedione, with the cofactor, TPP, offering partial protection against these reagents. The inactivation by phenylglyoxal was found to be reversible. Experiments with [7-14C]phenylglyoxal showed that while several arginine residues react with this reagent, TPP can prevent the labeling of one such residue. Furthermore, inactivation by 2,3-butanedione is attended by at least a 100-fold decrease in affinity of the enzyme for TPP. These results suggest a direct role for arginine in the binding of the cofactor.
Mammographic density, breast cancer risk and risk prediction (2007)

In this review, we examine the evidence for mammographic density as an independent risk factor for breast cancer, describe the risk prediction models that have incorporated density, and discuss the current and future implications of using mammographic density in clinical practice. Mammographic density is a consistent and strong risk factor for breast cancer in several populations and across age at mammogram. Recently, this risk factor has been added to existing breast cancer risk prediction models, increasing the discriminatory accuracy with its inclusion, albeit slightly. With validation, these models may replace the existing Gail model for clinical risk assessment. However, absolute risk estimates resulting from these improved models are still limited in their ability to characterize an individual's probability of developing cancer. Promising new measures of mammographic density, including volumetric density, which can be standardized using full-field digital mammography, will likely result in a stronger risk factor and improve accuracy of risk prediction models.
Ostene, a New Water-Soluble Bone Hemostasis Agent (2006)

Traditional formulations of bone wax are composed largely of beeswax and are well known to interfere with bone healing and cause inflammatory reactions. Ostene, a newly available bone hemostasis agent made of water-soluble alkylene oxide copolymers, was evaluated. The soft tissue response to Ostene was compared with bone wax and a polyethylene control after implantation into the paravertebral muscles of three rabbits. After 2 weeks, Ostene elicited no fibrous response, the polyethylene elicited a thin (less than 0.5 mm) fibrous response, and the bone wax was encased in a fibrous capsule 0.6 to 1.0 mm thick infiltrated with inflammatory cells. The effects of Ostene were compared with bone wax in a femur defect model in eight rabbits. Ostene showed no evidence of an adverse response in the cortical defect site, medullary cavity, or the surrounding tissue at 4 and 8 weeks. In contrast, bone wax at both time intervals elicited a foreign body response consisting of fibrous tissue infiltrated by macrophages, giant cells, and lymphocytes at the sites of the bone defects. Bone wax also displaced the bone marrow and interfered with bone ingrowth into the defects. Ostene provides the clinician a water-soluble bone hemostasis material that does not demonstrate the adverse tissue response or the interference with bone healing seen with the use of bone wax.
Cdc42 and Rac Family GTPases Regulate Mode and Speed but Not Direction of Primary Fibroblast Migration during Platelet-Derived Growth Factor-Dependent Chemotaxis (2009)

Cdc42 and Rac family GTPases are important regulators of morphology, motility, and polarity in a variety of mammalian cell types. However, comprehensive analysis of their roles in the morphological and behavioral aspects of chemotaxis within a single experimental system is still lacking. Here we demonstrate using a direct viewing chemotaxis assay that of all of the Cdc42/Rac1-related GTPases expressed in primary fibroblasts, Cdc42, Rac1, and RhoG are required for efficient migration towards platelet-derived growth factor (PDGF). During migration, Cdc42-, Rac1-, and RhoG-deficient cells show aberrant morphology characterized as cell elongation and cell body rounding, loss of lamellipodia, and formation of thick membrane extensions, respectively. Analysis of individual cell trajectories reveals that cell speed is significantly reduced, as well as persistence, but to a smaller degree, while the directional response to the gradient of PDGF is not affected. Combined knockdown of Cdc42, Rac1, and RhoG results in greater inhibition of cell speed than when each protein is knocked down alone, but the cells are still capable of migrating toward PDGF. We conclude that, Cdc42, Rac1, and RhoG function cooperatively during cell migration and that, while each GTPase is implicated in the control of morphology and cell speed, these and other Cdc42/Rac-related GTPases are not essential for the directional response toward PDGF.
MOLECULAR ASSOCIATION IN DEXTRAN AND IN BRANCHED AMYLACEOUS CARBOHYDRATES (1948)

A property of polysaccharides which is of major importance both practically and fundamentally is orderly association between portions of the same or of adjacent molecules.This property depends upon both the physical and chemical constitution of the polysaccharide and data on it provide a means for correlating physical properties with chemical structure.Little specific information is available on molecular association in branched polysaccharides.The industrial importance of starch and the biological significance of glycogen and certain bacterial polysaccharides make such information desirable.This paper presents information on molecular association in the bacterial polysaccharide, dextran from Leuconostoc mesenteroides, and in branched amylaceous substances.Orderly molecular association has been detected by x-ray analysis, and the tendency towards orderly association has been related to the physical and chemical constitution of these polysaccharides.Data are given on typical x-ray diffraction powder patterns of dextran, and on the relation of molecular association to the hydration and ease of dissolution of branched polysaccharides.
Inhibition of mammalian nitric oxide synthases by agmatine, an endogenous polyamine formed by decarboxylation of arginine (1996)

Agmatine, decarboxylated arginine, is a metabolic product of mammalian cells. Considering the close structural similarity between L-arginine and agmatine, we investigated the interaction of agmatine and nitric oxide synthases (NOSs), which use L-arginine to generate nitric oxide (NO) and citrulline. Brain, macrophages and endothelial cells were respectively used as sources for NOS isoforms I, II and III. Enzyme activity was measured by the production of nitrites or L-citrulline. Agmatine was a competitive NOS inhibitor but not an NO precursor. Ki values were approx. 660 microM (NOS I), 220 microM (NOS II) and 7.5 mM (NOS III). Structurally related polyamines did not inhibit NOS activity. Agmatine, therefore, may be an endogenous regulator of NO production in mammals.
Gata4andHnf1αare partially required for the expression of specific intestinal genes during development (2007)

The terminal differentiation phases of intestinal development in mice occur during cytodifferentiation and the weaning transition. Lactase-phlorizin hydrolase (LPH), liver fatty acid binding protein (Fabp1), and sucrase-isomaltase (SI) are well-characterized markers of these transitions. With the use of gene inactivation models in mature mouse jejunum, we have previously shown that a member of the zinc finger transcription factor family (Gata4) and hepatocyte nuclear factor-1alpha (Hnf1alpha) are each indispensable for LPH and Fabp1 gene expression but are both dispensable for SI gene expression. In the present study, we used these models to test the hypothesis that Gata4 and Hnf1alpha regulate LPH, Fabp1, and SI gene expression during development, specifically focusing on cytodifferentiation and the weaning transition. Inactivation of Gata4 had no effect on LPH gene expression during either cytodifferentiation or suckling, whereas inactivation of Hnf1alpha resulted in a 50% reduction in LPH gene expression during these same time intervals. Inactivation of Gata4 or Hnf1alpha had a partial effect ( approximately 50% reduction) on Fabp1 gene expression during cytodifferentiation and suckling but no effect on SI gene expression at any time during development. Throughout the suckling period, we found a surprising and dramatic reduction in Gata4 and Hnf1alpha protein in the nuclei of absorptive enterocytes of the jejunum despite high levels of their mRNAs. Finally, we show that neither Gata4 nor Hnf1alpha mediates the glucocorticoid-induced precocious maturation of the intestine but rather are downstream targets of this process. Together, these data demonstrate that specific intestinal genes have differential requirements for Gata4 and Hnf1alpha that are dependent on the developmental time frame in which they are expressed.
A survey of information retrieval and filtering methods (1995)

We survey the major techniques for information retrieval. In the first part, we provide an overview of the traditional ones (full text scanning, inversion, signature files and clustering). In the second part we discuss attempts to include semantic information (natural language processing, latent semantic indexing and neural networks). 1 Introduction This survey is divided in two parts. In the first part, we survey the traditional methods for text retrieval. There are two reasons for that: (a) knowledge of these methods is useful as the background information for the newer developments and (b) variations or extensions of these methods are in the heart of newer methods. Specifically, we examine full text scanning with recent developments on approximate searching; inversion-based methods, which are the fastest available and which will probably be used as the search engine in any information-retrieval system; methods using signature files; and methods using clustering, which is the tradit...
Expression pattern and, surprisingly, gene length shape codon usage inCaenorhabditis,Drosophila, andArabidopsis (1999)

We measured the expression pattern and analyzed codon usage in 8,133, 1,550, and 2,917 genes, respectively, from Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana. In those three species, we observed a clear correlation between codon usage and gene expression levels and showed that this correlation is not due to a mutational bias. This provides direct evidence for selection on silent sites in those three distantly related multicellular eukaryotes. Surprisingly, there is a strong negative correlation between codon usage and protein length. This effect is not due to a smaller size of highly expressed proteins. Thus, for a same-expression pattern, the selective pressure on codon usage appears to be lower in genes encoding long rather than short proteins. This puzzling observation is not predicted by any of the current models of selection on codon usage and thus raises the question of how translation efficiency affects fitness in multicellular organisms.
Prevalence of Epstein-Barr Virus Reactivation in Pregnancy (2010)

Recent evidence suggests a link between Epstein-Barr virus (EBV) reactivation and chronic stress in nonpregnant adults, possibly due to decreased cellular immune response. Our objective was to determine the prevalence of EBV seropositivity in a diverse cohort of pregnant women and whether maternal demographic characteristics were associated with EBV reactivation. In this cross-sectional study, we evaluated midpregnancy serum specimens from 64 healthy pregnant women for presence of EBV viral capsid antigen, EBV nuclear antigen, and EBV early antigen. The subjects were reported as EBV seronegative, EBV seropositive with reactivation, and EBV seropositive without reactivation. The maternal demographics of the seropositive women with EBV reactivation were compared with their nonreactivated counterparts. Chi-square and Student T test were used for statistical analysis. In our pregnant cohort, 63 (98%) of the 64 women were EBV seropositive. Among these seropositive women, 22 (35%) women demonstrated EBV reactivation in pregnancy. EBV reactivation was not associated with maternal age, race, parity, or insurance type. In our diverse pregnant cohort, 98% of women analyzed were EBV seropositive with 35% demonstrating EBV reactivation in the pregnancy by the second trimester. The pathophysiology and clinical implications of EBV reactivation during pregnancy need further study.
Subcellular localization of the Vif protein of human immunodeficiency virus type 1 (1994)

The Vif (viral infectivity factor) protein of human immunodeficiency virus type 1 (HIV-1) has been shown to dramatically enhance the infectivity of HIV-1 virus particles during virus production. The subcellular localization of Vif was examined to elucidate cellular pathways which may be important for Vif function. Indirect immunofluorescence staining of Vif demonstrated a diffuse cytoplasmic distribution and showed that most Vif was not associated with the Golgi complex, a proposed site of localization (B. Guy, M. Geist, K. Dott, D. Spehner, M.-P. Kieny, and J.-P. Lecocq, J. Virol. 65:1325-1331, 1991). Subcellular fractionation of transfected COS cells and HIV-1-infected Jurkat and CEM cells demonstrated that Vif is a cytoplasmic protein which exists in both a soluble cytosolic form and membrane-associated form. The membrane-associated form of Vif is a peripheral membrane protein which is tightly associated with the cytoplasmic side of cellular membranes. The C terminus of Vif was required for the stable association of Vif with membranes. The C terminus was also essential for Vif function, suggesting that the association of Vif with membranes is likely to be important for its biological activity. The highly conserved regions at residues 103 to 115 and 142 to 150 were important for Vif function but did not affect membrane association, indicating that these regions are likely to be important for other, as-yet-unknown functions.
A data-driven organization of the dynamic programming beam search for continuous speech recognition (2005)

This paper describes a data-driven organization of the dynamic programming beam search for large vocabulary, continuous speech recognition. This organization can be viewed as an extension of the one-pass dynamic programming algorithm for connected word recognition. In continuous speech recognition we are faced with a huge search space, and search hypotheses have to be formed at the 10-ms level. The organization of the search presented has the following characteristics. Its computational cost is proportional only to the number of hypotheses actually generated and is independent of the overall size of the potential search space. There is no limit on the number of word hypotheses, there is only a limit to the overall number of hypotheses due to memory constraints. The implementation of the search has been studied and tested on a continuous speech data base comprising 20672 words.
Differential extraction of hydrophobic proteins from chloroplast envelope membranes: a subcellular‐specific proteomic approach to identify rare intrinsic membrane proteins (1999)

Identification of rare hydrophobic membrane proteins is a major biological problem that is limited by the specific biochemical approaches required to extract these proteins from membranes and purify them. This is especially true for membranes, such as plastid envelope membranes, that have a high lipid content, present a wide variety of specific functions and therefore contain a large number of unique, but minor, proteins. We have optimized a procedure, based on the differential solubilization of membrane proteins in chloroform/methanol mixtures, to extract and concentrate the most hydrophobic proteins from chloroplast envelope membrane preparations, while more hydrophilic proteins were excluded. In addition to previously characterized chloroplast envelope proteins, such as the phosphate/triose phosphate translocator, we have identified new proteins that were shown to contain putative transmembrane alpha-helices. Moreover, using different chloroform/methanol mixtures, we have obtained differential solubilization of envelope proteins as a function of their hydrophobicity. All the proteins identified were genuine chloroplast envelope proteins, most of them being localized within the inner membrane. Our procedure enables direct mapping (by classical SDS-PAGE) and identification of hydrophobic membrane proteins, whatever their isoelectric point was, that are minor components of specific subcellular compartments. Thus, it complements other techniques that give access to peripheral membrane proteins. If applied to various cell membranes, it is anticipated that it can expedite the identification of hydrophobic proteins involved in transport systems for ions or organic solutes, or it may act as signal receptors or to control metabolic processes and vesicle trafficking.
Size, Shape, and Low Energy Electronic Structure of Carbon Nanotubes (1997)

A theory of the long-wavelength low-energy electronic structure of graphite-derived nanotubules is presented. The propagating $\ensuremath{\pi}$ electrons are described by wrapping a massless two dimensional Dirac Hamiltonian onto a curved surface. The effects of the tubule size, shape, and symmetry are included through an effective vector potential which we derive for this model. The rich gap structure for all straight single wall cylindrical tubes is obtained analytically in this theory, and the effects of inhomogeneous shape deformations on nominally metallic armchair tubes are analyzed.
Effects of intravenous administration of human bone marrow stromal cells after intracerebral hemorrhage in rats (2006)

Intravenous administration of hBMSCs significantly improves neurological function in rats subjected to ICH. This improvement in the treated animals is associated with reduced tissue loss and increased local presence of the hBMSCs, mitotic activity, immature neurons, synaptogenesis, and neuronal migration.
Evolution of Functional Six-Nucleotide DNA (2015)

Axiomatically, the density of information stored in DNA, with just four nucleotides (GACT), is higher than in a binary code, but less than it might be if synthetic biologists succeed in adding independently replicating nucleotides to genetic systems. Such addition could also add functional groups not found in natural DNA, but useful for molecular performance. Here, we consider two new nucleotides (Z and P, 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribo-furanosyl)-2(1H)-pyridone and 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one). These are designed to pair via complete Watson-Crick geometry. These were added to a library of oligonucleotides used in a laboratory in vitro evolution (LIVE) experiment; the GACTZP library was challenged to deliver molecules that bind selectively to liver cancer cells, but not to untransformed liver cells. Unlike in classical in vitro selection, low levels of mutation allow this system to evolve to create binding molecules not necessarily present in the original library. Over a dozen binding species were recovered. The best had Z and/or P in their sequences. Several had multiple, nearby, and adjacent Zs and Ps. Only the weaker binders contained no Z or P at all. This suggests that this system explored much of the sequence space available to this genetic system and that GACTZP libraries are richer reservoirs of functionality than standard libraries.
Repression of the retinoic acid receptor-alpha gene by the Wilms' tumor suppressor gene product, wt1. (1995)

The Wilms' tumor (WT) suppressor gene, WT1, encodes a zinc finger DNA binding protein (wt1) which functions as a transcriptional regulator. Germline WT1 mutations predispose to WTs and in many cases are associated with urogenital anomalies. Identification of wt1 downstream targets is essential to understanding regulatory processes involved in development of this system. In this study, we demonstrate that wt1 can repress transcription of the retinoic acid receptor-alpha 1 (RAR-alpha 1) promoter. Transient transfection, deletion mutagenesis, and mobility shift assays suggest that wt1 mediates repression of the human RAR-alpha 1 promoter through a GC-rich DNA binding motif (5'-GCGGGGGCG-3'), at positions -111 to -120 bp (relative to the transcription initiation site). In contrast, the murine RAR-alpha 1 promoter contains a cryptic binding motif and is not responsive to wt1. These results indicate that some wt1-regulatory pathways are not conserved across species, suggesting a molecular basis for differences in phenotypes between humans and mice harboring WT1 lesions.