gebhart/patrepeval huggingface dataset:
Antimicrobial Resistance in Escherichia coli Isolates from Swine and Wild Small Mammals in the Proximity of Swine Farms and in Natural Environments in Ontario, Canada (2008)

Wild animals not normally exposed to antimicrobial agents can acquire antimicrobial agent-resistant bacteria through contact with humans and domestic animals and through the environment. In this study we assessed the frequency of antimicrobial resistance in generic Escherichia coli isolates from wild small mammals (mice, voles, and shrews) and the effect of their habitat (farm or natural area) on antimicrobial resistance. Additionally, we compared the types and frequency of antimicrobial resistance in E. coli isolates from swine on the same farms from which wild small mammals were collected. Animals residing in the vicinity of farms were five times more likely to carry E. coli isolates with tetracycline resistance determinants than animals living in natural areas; resistance to tetracycline was also the most frequently observed resistance in isolates recovered from swine (83%). Our results suggest that E. coli isolates from wild small mammals living on farms have higher rates of resistance and are more frequently multiresistant than E. coli isolates from environments, such as natural areas, that are less impacted by human and agricultural activities. No Salmonella isolates were recovered from any of the wild small mammal feces. This study suggests that close proximity to food animal agriculture increases the likelihood that E. coli isolates from wild animals are resistant to some antimicrobials, possibly due to exposure to resistant E. coli isolates from livestock, to the resistance genes of these isolates, or to antimicrobials through contact with animal feed.
Heme Oxygenase and Angiogenic Activity of Endothelial Cells: Stimulation by Carbon Monoxide and Inhibition by Tin Protoporphyrin-IX (2003)

The activity of heme oxygenase enzymes (HOs) is responsible for the endogenous source of carbon monoxide (CO). Their activities can be inhibited by tin protoporphyrin-IX (SnPPIX). Recent data indicate the involvement of HOs in the regulation of angiogenesis. Here, we investigated the role of the HO pathway in the production and angiogenic activity of vascular endothelial growth factor (VEGF) in endothelial cells treated with SnPPIX, or cultured in the presence of a CO-releasing molecule (CO-RM). Addition of CO-RM or induction of HO-1 by hemin resulted in a threefold elevation in CO production in culture medium (up to 20.3 microg/L) and was associated with a 30% increase in VEGF synthesis. Much higher levels of CO (up to 60 microg/L) and a further increase in VEGF production (by 277%) were measured in cells treated with prostaglandin-J(2), a potent activator of HO-1. SnPPIX prevented the induction of CO generation and inhibited VEGF synthesis. Moreover, SnPPIX reduced the VEGF-elicited angiogenic activities of endothelial cells by decreasing their proliferation (by 26%), migration (by 46%), formation of tubes on Matrigel (by 48%), and outgrowth of capillaries from endothelial spheroids (by 30%). In contrast, overexpression of HO-1 or incubation of cells with CO-RM led to an increase in capillary sprouting. Thus, HO activity up-regulates VEGF production and augments the capability of endothelial cells to respond to exogenous stimulation.
Addicted to Death (2004)

The development of an invasive cancer involves a progressive switch from predominantly apoptotic (scheduled) to necrotic (unscheduled) tumor cell death. This switch is associated with chronic and increasing release of intracellular factors that in turn promote reactive angiogenesis and stromal proliferation and mediates the disordered tumor microenvironment associated with local immune suppression. The authors review the relevant immunobiology of these factors, including the nuclear protein HMGB1; the products of purine metabolism (uric acid, ATP, and adenosine); the S100 family members; and the heat shock proteins, which we believe drive futile cycles of cell death followed by reparative cell growth. The authors also present a novel and provocative hypothesis that suggests that most of the derangements that we associate with progression of cancer and the associated immunologic consequences can indeed be ascribed to the consequences of disordered tumor cell death rather than cell growth. Thus the fundamental defect in invasive human cancers, in the authors' view, is not one of cell growth but rather one of disordered cell death, resulting in turn in a tumor microenvironment that encourages tumor growth, progression, and local immunosuppression, a condition the authors have termed "addicted to death." This new understanding could inform and drive the development of more effective biologic therapies for patients with cancer.
Studies on Nitrogen-containing Heterocyclic Compounds. XXXV. Syntheses and Reduction of 4-Amino-2-cyano-1, 3-dimethoxy-1, 2, 3, 4-tetrahydroisoquinolines (1979)

Reaction of 4-bromo-2-cyano-1, 3-dimethoxy-1, 2, 3, 4-tetrahydroisoquinoline with aniline (or diethylamine), in the presence of a phase-transition catalyst, results in fascile formation of 4-anilino (or diethylamino)-2-cyano-1, 3-dimethoxy-1, 2, 3, 4-tetrahydroisoquinoline. Application of sodium borohydride to this compound in ethanol afforded 4-anilino (or diethylamino)-2-methyl-1, 2, 3, 4-tetrahydroisoquinoline in a high yield. Use of methylmagnesium iodide in place of sodium borohydride produced 4-anilino-2-cyano-1-methyl-1, 2-dihydroisoquinoline and 4-anilino-1-methylisoquinoline. It was clarified from these products that the reduction of N-C≡N group passed through a diaminomethane derivative.
Molecular regulation of GLUT-4 targeting in 3T3-L1 adipocytes. (1995)

Insulin stimulates glucose transport in muscle and adipose tissue by triggering the movement of the glucose transporter GLUT-4 from an intracellular compartment to the cell surface. Fundamental to this process is the intracellular sequestration of GLUT-4 in nonstimulated cells. Two distinct targeting motifs in the amino and carboxy termini of GLUT-4 have been previously identified by expressing chimeras comprised of portions of GLUT-4 and GLUT-1, a transporter isoform that is constitutively targeted to the cell surface, in heterologous cells. These motifs-FQQI in the NH2 terminus and LL in the COOH terminus-resemble endocytic signals that have been described in other proteins. In the present study we have investigated the roles of these motifs in GLUT-4 targeting in insulin-sensitive cells. Epitope-tagged GLUT-4 constructs engineered to differentiate between endogenous and transfected GLUT-4 were stably expressed in 3T3-L1 adipocytes. Targeting was assessed in cells incubated in the presence or absence of insulin by subcellular fractionation. The targeting of epitope-tagged GLUT-4 was indistinguishable from endogenous GLUT-4. Mutation of the FQQI motif (F5 to A5) caused GLUT-4 to constitutively accumulate at the cell surface regardless of expression level. Mutation of the dileucine motif (L489L490 to A489A490) caused an increase in cell surface distribution only at higher levels of expression, but the overall cells surface distribution of this mutant was less than that of the amino-terminal mutants. Both NH2- and COOH-terminal mutants retained insulin-dependent movement from an intracellular to a cell surface locale, suggesting that neither of these motifs is involved in the insulin-dependent redistribution of GLUT-4. We conclude that the phenylalanine-based NH2-terminal and the dileucine-based COOH-terminal motifs play important and distinct roles in GLUT-4 targeting in 3T3-L1 adipocytes.
PF0610, a Novel Winged Helix−Turn−Helix Variant Possessing a Rubredoxin-like Zn Ribbon Motif from the Hyperthermophilic Archaeon, Pyrococcus furiosus, (2006)

PF0610, a protein from the hyperthermophile Pyrococcus furiosus, has homologues only in other archaeal species and in three species of Fe(III)-reducing bacteria. It is thought to have a helix-turn-helix (HTH) domain at the N-terminus and possesses two CXXC motifs characteristic of metal binding proteins. We have determined the solution structure of the Zn-bound protein using NMR. PF0610 is a novel winged helix-turn-helix (wHTH) protein with a rubredoxin-like Zn ribbon as its W1 segment. In addition, it possesses a large number of basic residues on its surface. Clusters of basic residues can be found on both helix H3 and the metal-binding loops of W1, suggesting that it might be a DNA-binding protein. Accordingly, gel shift assays using both linear and circular DNA showed that PF0610 does bind DNA, at least in a sequence-independent fashion. Modeling the PF0610-DNA interaction based on other wHTH protein-DNA structures revealed that besides helix H3, basic residues around the second CXXC motif in the metal-binding loop could make extensive contacts with DNA. However, the bulkiness of the W1 region implies that the DNA conformation may be distorted upon PF0610 binding. PF0610 is the first protein known to have a Zn ribbon-embedded wHTH fold and, as such, has potential roles both as a metal-dependent transcription regulator and as a component of the chromosome packing system in P. furiosus. The discovery of this novel structure represents the addition of another branch to the winged HTH protein family and could contribute to our understanding of transcription regulatory processes in P. furiosus.
Formation of Supported Bilayers on Silica Substrates (2009)

We have investigated the formation of phospholipid bilayers of the neutral (zwitterionic) lipid dimyristoyl-phosphatidylcholine (DMPC) on various glass surfaces from vesicles in various aqueous solutions and temperatures using a number of complementary techniques: the surface forces apparatus (SFA), quartz crystal microbalance (QCM), fluorescence recovery after photobleaching (FRAP), fluorescence microscopy, and streaming potential (SP) measurements. The process involves five stages: vesicle adhesion to the substrate surfaces via electrostatic and van der Waals forces, steric interactions with neighboring vesicles, rupture, spreading via hydrophobic fusion of bilayer edges, and ejection of excess lipid, trapped water, and ions into the solution. The forces between DMPC bilayers and silica were measured in the SFA in phosphate buffered saline (PBS), and the adhesion energy was found to be 0.5-1 mJ/m(2) depending on the method of bilayer preparation. This value is stronger than the expected adhesion predicted by van der Waals interactions. Theoretical analysis of the bilayer-silica interaction shows that the strong attraction is likely due to an attractive electrostatic interaction between the uncharged bilayer and negatively charged silica owing to the surfaces interacting at "constant potential." However, the bilayer-silica interaction in distilled water was found to be repulsive at all distances, which is attributed to the surfaces interacting at "constant charge." These results are consistent with QCM measurements that show vesicles readily forming bilayers on silica in high salt but only weakly adhering in low salt conditions. We conclude that the electrostatic interaction is the most important interaction in determining the adhesion between neutral bilayers and charged hydrophilic surfaces. SP and FRAP experiments gave insights into the bilayer formation process as well as information on the surface coverage, lateral diffusion of the lipid molecules, and surface potential of the bilayers during the spreading process.
Economics of New Oncology Drug Development (2007)

The market success of oncology drugs has induced a substantial amount of investment in oncology drug development in the last decade or so. However, given the great need for further progress, the extent to which efforts to develop new oncology drugs will grow depends on future public-sector investment in basic research, developments in translational medicine, and regulatory reforms that advance drug-development science.
Arginine metabolism: nitric oxide and beyond (1998)

Arginine is one of the most versatile amino acids in animal cells, serving as a precursor for the synthesis not only of proteins but also of nitric oxide, urea, polyamines, proline, glutamate, creatine and agmatine. Of the enzymes that catalyse rate-controlling steps in arginine synthesis and catabolism, argininosuccinate synthase, the two arginase isoenzymes, the three nitric oxide synthase isoenzymes and arginine decarboxylase have been recognized in recent years as key factors in regulating newly identified aspects of arginine metabolism. In particular, changes in the activities of argininosuccinate synthase, the arginases, the inducible isoenzyme of nitric oxide synthase and also cationic amino acid transporters play major roles in determining the metabolic fates of arginine in health and disease, and recent studies have identified complex patterns of interaction among these enzymes. There is growing interest in the potential roles of the arginase isoenzymes as regulators of the synthesis of nitric oxide, polyamines, proline and glutamate. Physiological roles and relationships between the pathways of arginine synthesis and catabolism in vivo are complex and difficult to analyse, owing to compartmentalized expression of various enzymes at both organ (e.g. liver, small intestine and kidney) and subcellular (cytosol and mitochondria) levels, as well as to changes in expression during development and in response to diet, hormones and cytokines. The ongoing development of new cell lines and animal models using cDNA clones and genes for key arginine metabolic enzymes will provide new approaches more clearly elucidating the physiological roles of these enzymes.
Ranking with Uncertain Labels (2007)

Most techniques for image analysis consider the image labels fixed and without uncertainty. In this paper, we address the problem of ordinal/rank label prediction based on training samples with uncertain labels. First, the core ranking model is designed as the bilinear fusing of multiple candidate kernels. Then, the parameters for feature selection and kernel selection are learned by maximum a posteriori for given samples and uncertain labels. The convergency provable Expectation-Maximization (EM) method is used for inferring these parameters. The effectiveness of the proposed algorithm is finally validated by the extensive experiments on age ranking task. The FG-NET and Yamaha aging database are used for the experiments, and our algorithm significantly outperforms those state-of-the-art algorithms ever reported in literature.
Costimulatory blockade with mTor inhibition abrogates effector T-cell responses allowing regulatory T-cell survival in renal transplantation (2011)

The advent of novel immunosuppressive strategies in renal transplantation, with immunomodulatory properties, might facilitate long-term allograft survival. T-cell depletion, costimulation-blockade and mTor inhibition have been shown to favour anti-donor hyporesponsiveness. Recently, the combination of rATG, belatacept (Bela) and sirolimus (SRL) has been used in kidney transplantation, showing very low incidence of acute rejection and excellent 12-month graft and patient survival. Herein, we have analysed the 1-year evolution of memory/effector and regulatory T cells and assessed the donor-specific T-cell alloimmune response in a group of these patients and compared with others treated with a calcineurin-inhibitor(CNI)-based (rATG/tacrolimus/MMF), and two other Bela-based regimens (rATG/Bela/MMF and basiliximab/Bela/MMF/steroids). During the first year after transplantation, patients receiving rATG/Bela/SRL had significantly higher percentage of Tregs upon the memory T-cell compartment and showed a potent anti-donor suppressive activity. In an in vitro naive and memory/effector T-cell co-culture, the combination of costimulation-blockade and SRL could abrogate both antigen-specific T-cell responses as efficiently as using a CNI drug. The combination of T-cell depletion, costimulation-blockade and mTor inhibition seems to be able to allow Treg survival and inhibit donor-specific alloreactive effector immune responses after kidney transplantation in humans.
Cloning of Human Mineralocorticoid Receptor Complementary DNA: Structural and Functional Kinship with the Glucocorticoid Receptor (1987)

Low-stringency hybridization with human glucocorticoid receptor (hGR) complementary DNA was used to isolate a new gene encoding a predicted 107-kilodalton polypeptide. Expression studies demonstrate its ability to bind aldosterone with high affinity and to activate gene transcription in response to aldosterone, thus establishing its identity as the human mineralocorticoid receptor (hMR). This molecule also shows high affinity for glucocorticoids and stimulates a glucocorticoid-responsive promoter. Together the hMR and hGR provide unexpected functional diversity in which hormone-binding properties, target gene interactions, and patterns of tissue-specific expression may be used in a combinatorial fashion to achieve complex physiologic control.
Synthesis and Characterization of Tunable Poly(Ethylene Glycol): Gelatin Methacrylate Composite Hydrogels (2011)

Poly(ethylene glycol) (PEG) hydrogels are popular for cell culture and tissue-engineering applications because they are nontoxic and exhibit favorable hydration and nutrient transport properties. However, cells cannot adhere to, remodel, proliferate within, or degrade PEG hydrogels. Methacrylated gelatin (GelMA), derived from denatured collagen, yields an enzymatically degradable, photocrosslinkable hydrogel that cells can degrade, adhere to and spread within. To combine the desirable features of each of these materials we synthesized PEG-GelMA composite hydrogels, hypothesizing that copolymerization would enable adjustable cell binding, mechanical, and degradation properties. The addition of GelMA to PEG resulted in a composite hydrogel that exhibited tunable mechanical and biological profiles. Adding GelMA (5%-15% w/v) to PEG (5% and 10% w/v) proportionally increased fibroblast surface binding and spreading as compared to PEG hydrogels (p<0.05). Encapsulated fibroblasts were also able to form 3D cellular networks 7 days after photoencapsulation only within composite hydrogels as compared to PEG alone. Additionally, PEG-GelMA hydrogels displayed tunable enzymatic degradation and stiffness profiles. PEG-GelMA composite hydrogels show great promise as tunable, cell-responsive hydrogels for 3D cell culture and regenerative medicine applications.
Molecular Sieve Catalysts for the Regioselective and Shape- Selective Oxyfunctionalization of Alkanes in Air (2001)

Framework-substituted, molecular-sieve, aluminophosphate, microporous solids are the centerpieces of a new approach to the aerobic oxyfunctionalization of saturated hydrocarbons. The sieves, and the few percent of the Al(III) sites within them that are replaced by catalytically active, transition-metal ions in high oxidation states (Co(III), Mn(III), Fe(III)), are designed so as to allow free access of oxygen in to and out of the interior of these high-area solids. Certain metal-substituted, molecular sieves permit only end-on approach of linear alkanes to the active centers, thereby favoring enhanced reactivity of the terminal methyl groups. By optimizing cage dimension, with respect to that of the hydrocarbon reactant, as well as adjusting the average separation of active centers within a cage, and by choosing the sieve with the appropriate pore aperture, highly selective conversions such as n-hexane to hexanoic acid or adipic acid, and cyclohexane to cyclohexanol, cyclohexanone, or adipic acid, may be effected at low temperature, heterogeneously in air.
Angiotensin-converting Enzyme Is a Modifier of Hypertensive End Organ Damage (2009)

Severe forms of hypertension are characterized by high blood pressure combined with end organ damage. Through the development and refinement of a transgenic rat model of malignant hypertension incorporating the mouse renin gene, we previously identified a quantitative trait locus on chromosome 10, which affects malignant hypertension severity and morbidity. We next generated an inducible malignant hypertensive model where the timing, severity, and duration of hypertension was placed under the control of the researcher, allowing development of and recovery from end organ damage to be investigated. We have now generated novel consomic Lewis and Fischer rat strains with inducible hypertension and additional strains that are reciprocally congenic for the refined chromosome 10 quantitative trait locus. We have captured a modifier of end organ damage within the congenic region and, using a range of bioinformatic, biochemical and molecular biological techniques, have identified angiotensin-converting enzyme as the modifier of hypertension-induced tissue microvascular injury. Reciprocal differences between angiotensin-converting enzyme and the anti-inflammatory tetrapeptide, N-acetyl-Ser-Asp-Lys-Pro in the kidney, a tissue susceptible to end organ damage, suggest a mechanism for the amelioration of hypertension-dependent damage.
Nitrite and Nitrate Are Formed by Endogenous Synthesis in the Human Intestine (1978)

Studies of nitrate balance in humans and analyses of fecal and ileostomy samples indicate that nitrite and nitrate are formed de novo in the intestine, possibly by heterotrophic nitrification. These findings significantly alter our previous conceptions of human exposure to nitrite and suggest an even wider role for nitrite in the etiology of human cancer.
The extracellular hyaluronidase gene (hylA) ofStreptococcus pyogenes (2000)

Group A streptococci produce an extracellular hyaluronidase (hyaluronate lyase) which may be associated with the spread of the organism during infection. The gene for this hyaluronidase (hylA) encodes an 868 amino acid protein with a molecular size of 99636 Da. Cleavage of the proposed signal peptide results in an extracellular protein of 95941 Da. Comparison with other bacterial hyaluronidases indicates strong similarities to the genes from Streptococcus pneumoniae, Streptococcus agalactiae and Staphylococcus aureus. A region internal to the hylA gene was amplified from all 175 strains of Streptococcus pyogenes tested suggesting a widespread distribution of the gene.
The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans (2002)

The complete genomic sequence of an intracellular bacterial pathogen, Mycoplasma penetrans HF-2 strain, was determined. The HF-2 genome consists of a 1 358 633 bp single circular chromosome containing 1038 predicted coding sequences (CDSs), one set of rRNA genes and 30 tRNA genes. Among the 1038 CDSs, 264 predicted proteins are common to the Mycoplasmataceae sequenced thus far and 463 are M.penetrans specific. The genome contains the two-component system but lacks the essential cellular gene, uridine kinase. The relatively large genome of M.penetrans HF-2 among mycoplasma species may be accounted for by both its rich core proteome and the presence of a number of paralog families corresponding to 25.4% of all CDSs. The largest paralog family is the p35 family, which encodes surface lipoproteins including the major antigen, P35. A total of 44 genes for p35 and p35 homologs were identified and 30 of them form one large cluster in the chromosome. The genetic tree of p35 paralogs suggests the occurrence of dynamic chromosomal rearrangement in paralog formation during evolution. Thus, M.penetrans HF-2 may have acquired diverse repertoires of antigenic variation-related genes to allow its persistent infection in humans.