gebhart/patrepeval huggingface dataset:
Organization of Ovine Corticotropin-Releasing Factor Immunoreactive Cells and Fibers in the Rat Brain: An Immunohistochemical Study (1983)

The distribution of corticotropin-releasing factor (CRF)-immunoreactive cells and fibers has been examined in the brains of normal adult rats, and in the brains of animals that had been pretreated with intraventricular injections of colchicine, or had been adrenalectomized 3-60 days before perfusion. The results suggest that CRF immunoreactivity is localized in at least three functionally distinct systems. First, most of the CRF-stained fibers in the neurohemal zone of the median eminence, which presumably modulate the release of ACTH and beta-endorphin from the pituitary, appear to arise in the paraventricular nucleus of the hypothalamus (PVH). About 2,000 CRF-stained cells are distributed throughout all eight parts of the PVH, although a majority (80%) of the cells are concentrated in the parvocellular division, and a smaller number (about 15%) are found in parts of the magnocellular division in which oxytocinergic cells predominate. This appears to be the only CRF-stained pathway in the brain that is affected (increased staining intensity) by adrenalectomy. Second, a series of cell groups in the basal telencephalon, hypothalamus, and brain stem that are known to play a role in the mediation of autonomic responses contain CRF-stained neurons. These areas, which are interconnected by stained fibers in the medial forebrain bundle and the periventricular system, include the central nucleus of the amygdala, substantia innominata, bed nucleus of the stria terminalis, medial and lateral preoptic areas, lateral hypothalamic area, central gray, laterodorsal tegmental nucleus, locus ceruleus, parabrachial nucleus, dorsal vagal complex, and regions containing the A1 and A5 catecholamine cell groups. And third, scattered CRF-stained cells are found throughout most areas of the cerebral cortex. Most such cells are confined to layers II and III in the neocortex, and their bipolar shape suggests that they are interneurons. These cells are most common in limbic regions including prefrontal areas, the cingulate gyrus, and areas bordering the rhinal fissure. Scattered immunoreactive cells are also found in dorsal parts of the dentate gyrus and Ammon's horn. These results suggest that the PVH plays a critical role in the modulation of ACTH and beta-endorphin release from the pituitary, and that CRF-containing pathways in the brain are involved in the mediation of autonomic responses.
Risk Factors for Surgical Site Infection in Emergency Colorectal Surgery: A Retrospective Analysis (2014)

The risk factors for incisional SSI in emergency colorectal surgery were incision contamination and obesity. Moreover, the incidence of incisional SSI among the incision class IV operations increased significantly with increasing extents of contamination. As a tactic for management of dirty abdominal wounds, we suggest that primary skin closure is suitable in cases of perforation of a prepared colon or colon perforation with localized contamination. On the other hand, in cases of colon perforation with generalized contamination, delayed primary skin closure or leaving an incision open to heal by secondary intention should be considered.
Plants used traditionally to treat malaria in Brazil: the archives of Flora Medicinal (2007)

The archives of Flora Medicinal, an ancient pharmaceutical laboratory that supported ethnomedical research in Brazil for more than 30 years, were searched for plants with antimalarial use. Forty plant species indicated to treat malaria were described by Dr. J. Monteiro da Silva (Flora Medicinal leader) and his co-workers. Eight species, Bathysa cuspidata, Cosmos sulphureus, Cecropia hololeuca, Erisma calcaratum, Gomphrena arborescens, Musa paradisiaca, Ocotea odorifera, and Pradosia lactescens, are related as antimalarial for the first time in ethnobotanical studies. Some species, including Mikania glomerata, Melampodium divaricatum, Galipea multiflora, Aspidosperma polyneuron, and Coutarea hexandra, were reported to have activity in malaria patients under clinical observation. In the information obtained, also, there were many details about the appropriate indication of each plant. For example, some plants are indicated to increase others' potency. There are also plants that are traditionally employed for specific symptoms or conditions that often accompany malaria, such as weakness, renal failure or cerebral malaria. Many plants that have been considered to lack activity against malaria due to absence of in vitro activity against Plasmodium can have other mechanisms of action. Thus researchers should observe ethnomedical information before deciding which kind of screening should be used in the search of antimalarial drugs.
Field effect transistors with SrTiO3 gate dielectric on Si (2000)

SrTiO 3 has been grown epitaxially by molecular beam epitaxy on Si. The capacitance of this 110 Å dielectric film is electrically equivalent to less than 10 Å of SiO2. This structure has been used to make capacitors and metal oxide semiconductor field effect transistors. The interface trap density between the SrTiO3 and the Si is 6.4×1010 states/cm2 eV and the inversion layer mobility is 221 and 62 cm2/V s for n- and p-channel devices, respectively. The gate leakage in these devices is two orders of magnitude smaller than a similar SiO2 gate dielectric field effect transistor.
Simplifying the rounding for Newton-Raphson algorithm with parallel remainder (2009)

This work presents a variable latency rounding method based on the calculation in parallel of a remainder estimation for Newton-Raphson algorithm. The value obtained is the remainder of the algorithm result without any transformation. Because of this a new rounding method based on this value has to be proposed. This method avoid the traditional remainder calculation in 91% of the cases for division and 88% of the cases for square root.
HOWHOST-MICROBIALINTERACTIONSSHAPE THENUTRIENTENVIRONMENT OF THEMAMMALIANINTESTINE (2002)

Humans and other mammals are colonized by a vast, complex, and dynamic consortium of microorganisms. One evolutionary driving force for maintaining this metabolically active microbial society is to salvage energy from nutrients, particularly carbohydrates, that are otherwise nondigestible by the host. Much of our understanding of the molecular mechanisms by which members of the intestinal microbiota degrade complex polysaccharides comes from studies of Bacteroides thetaiotaomicron, a prominent and genetically manipulatable component of the normal human and mouse gut. Colonization of germ-free mice with B. thetaiotaomicron has shown how this anaerobe modifies many aspects of intestinal cellular differentiation/gene expression to benefit both host and microbe. These and other studies underscore the importance of understanding precisely how nutrient metabolism serves to establish and sustain symbiotic relationships between mammals and their bacterial partners.
Root colonization of a rice growth promoting strain of Enterobacter cloacae (2011)

Enterobacter cloacae GS1 was isolated by in-planta enrichment of a rice rhizoplane bacterial community. It displayed strong seed adherence ability (2.5 × 10(5) cfu/seed) and colonized rice roots reaching up to 1.65 × 10(9) cfu/g of fresh root weight in a gnotobiotic root colonization system. E. cloacae GS1 was motile, able to solubilize tricalcium phosphate, and produced indole acetic acid like substances (15 μg/ml). As an introduced bioinoculant in non-sterile soil, E. cloacae GS1 colonized rice roots and significantly improved the fresh weight, root length, shoot length, and nitrogen content in inoculated rice seedlings as compared to uninoculated controls. This isolate was tagged with green fluorescent protein and various stages of root colonization in gnotobiotic hydroponic environment and non-sterile soil environment were followed by fluorescence microscopy. Owing to its effective root colonizing ability and growth promoting potential, Enterobacter cloacae GS1 is a promising symbiotic bioinoculant for rice.
Alphavirus RNA Genome Repair and Evolution: Molecular Characterization of Infectious Sindbis Virus Isolates Lacking a Known Conserved Motif at the 3′ End of the Genome (2000)

The 3' nontranslated region of the genomes of Sindbis virus (SIN) and other alphaviruses carries several repeat sequence elements (RSEs) as well as a 19-nucleotide (nt) conserved sequence element (3'CSE). The 3'CSE and the adjoining poly(A) tail of the SIN genome are thought to act as viral promoters for negative-sense RNA synthesis and genome replication. Eight different SIN isolates that carry altered 3'CSEs were studied in detail to evaluate the role of the 3'CSE in genome replication. The salient findings of this study as it applies to SIN infection of BHK cells are as follows: i) the classical 19-nt 3'CSE of the SIN genome is not essential for genome replication, long-term stability, or packaging; ii) compensatory amino acid or nucleotide changes within the SIN genomes are not required to counteract base changes in the 3' terminal motifs of the SIN genome; iii) the 5' 1-kb regions of all SIN genomes, regardless of the differences in 3' terminal motifs, do not undergo any base changes even after 18 passages; iv) although extensive addition of AU-rich motifs occurs in the SIN genomes carrying defective 3'CSE, these are not essential for genome viability or function; and v) the newly added AU-rich motifs are composed predominantly of RSEs. These findings are consistent with the idea that the 3' terminal AU-rich motifs of the SIN genomes do not bind directly to the viral polymerase and that cellular proteins with broad AU-rich binding specificity may mediate this interaction. In addition to the classical 3'CSE, other RNA motifs located elsewhere in the SIN genome must play a major role in template selection by the SIN RNA polymerase.
853. Persistent Expression of Single Chain Antibodies Mediated by AAV5 and AAVrh.10 Vectors (2005)

Top of pageAbstract
Passive transfer of immunity with monoclonal antibodies is an effective strategy to augment host defenses, but it is a challenge to maintain effective antibody levels due to the short half-life of the antibodies and the consequent requirement for repetitive administration once every 1 to 4 wk. We have recently demonstrated (Kasuya et al. Molecular Therapy 2005; 11:237-244) the efficiency of an adenovirus (Ad)-based gene transfer vector in delivering single chain antibodies, but while effective, the protective immunity lasted only 2 wk secondary to the immune responses against the Ad vector. To refine the technology to provide a longer duration of antibody expression, we tested the hypothesis that a gene encoding a single chain antibody delivered by adeno-associated virus (AAV) vectors would exhibit sustained antibody expression in the serum of experimental animals. To test this hypothesis, the gene encoding a cobratoxin-specific single chain antibody was cloned into two vectors, one based on an AAV serotype 5 vector (AAV5|[alpha]|CTX) and one based on the non-human primate AAV serotype rh.10 (AAVrh.10|[alpha]|CTX). The expression cassette in these vectors consists of (5' to 3'): the chicken |[beta]|-actin promoter; an Ig|[kappa]| secretion signal to direct expression into the extracellular space; the cDNA sequence corresponding to the anti-cobratoxin single chain antibody, including a human constant |[kappa]| (C|[kappa]|) domain; and the SV40 poly A signal. The expression of the antibody from both vectors was confirmed by Western analysis of infected cell supernatants. Groups of 5 BALB/c mice received a dose of 1011 particle units (pu) by the intrapleural route. Mice that received AAV5|[alpha]|CTX had serum Ig|[kappa]| titers that reached a peak of 102 at 4 wk. These levels remained stable through an 8 wk observation period. For mice that received 1011 pu of the AAVrh.10|[alpha]|CTX, the anti-human Ig|[kappa]| titer rose from undetectable levels at wk 0 to 9|[times]|102 at 4 wk, a level 9-fold higher levels than that for the AAV5-based vector. These levels also remained stable through the 8 wk observation period. These data demonstrate that it is possible to achieve sustained expression of antibodies using AAV-based vectors, and that AAVrh.10-based vectors provide a higher efficiency of antibody gene expression compared to AAV5-based vectors when administered by the intrapleural route. This strategy should prove useful in applications requiring persistent augmentation of host defenses with monoclonal antibodies.
Bacterial metapopulations in nanofabricated landscapes (2006)

We have constructed a linear array of coupled, microscale patches of habitat. When bacteria are inoculated into this habitat landscape, a metapopulation emerges. Local bacterial populations in each patch coexist and weakly couple with neighbor populations in nearby patches. These spatially distributed bacterial populations interact through local extinction and colonization processes. We have further built heterogeneous habitat landscapes to study the adaptive dynamics of the bacterial metapopulations. By patterning habitat differences across the landscape, our device physically implements an adaptive landscape. In landscapes with higher niche diversity, we observe rapid adaptation to large-scale, low-quality (high-stress) areas. Our results illustrate the potential lying at the interface between nanoscale biophysics and landscape evolutionary ecology.
Sacral nerve stimulation for faecal incontinence: patient selection, service provision and operative technique (2011)

The short-term outcome of sacral nerve stimulation is dependent on patient factors and operative technique. Despite this, specific preoperative predictive factors of treatment success have yet to be identified.
C3b receptor activity on transfected cells expressing glycoprotein C of herpes simplex virus types 1 and 2 (1988)

Glycoprotein C from herpes simplex virus type 1 (gC-1 from HSV-1) acts as a receptor for the C3b fragment of the third component of complement on HSV-1-infected cell surfaces. Direct binding assays with purified gC-1 and C3b demonstrate that other viral and cellular proteins are not required for this interaction. Although C3b receptor activity is not expressed on HSV-2-infected cell surfaces, purified gC-2 specifically binds C3b in direct binding assays, suggesting that gC-1 and gC-2 are functionally similar. Here, we used a transient transfection system to further characterize the role of gC-1 and gC-2 as C3b receptors and to localize the site(s) on gC involved in C3b binding. The genes for gC-1 and gC-2 were each cloned into a eucaryotic expression vector containing the Rous sarcoma virus long terminal repeat as the promoter and transfected into NIH 3T3 cells. The expressed proteins were similar in molecular size, extent of carbohydrate processing, and antigenic properties to gC-1 and gC-2 purified from infected cells. Using a double-label immunofluorescence assay, we found that both gC-1 and gC-2 were expressed on the surfaces of transfected cells and bound C3b. These results suggest that other proteins expressed during HSV-2 infection prevent receptor activity. We constructed three in-frame deletion mutants of gC-2 to identify domains on the protein important for C3b receptor activity. These mutants lacked amino acids 26 to 73, 219 to 244, or 318 to 346. The mutant protein lacking residues 26 to 73 was reactive with two monoclonal antibodies recognizing distinct epitopes, showed a wild-type pattern of carbohydrate processing, and bound C3b on the transfected cell surface. These results suggest that residues 26 to 73 are not involved in C3b binding. The other two mutant proteins were present on the cell surface, but did not bind C3b. In addition, these mutant proteins showed altered patterns of carbohydrate processing, formed aggregates, and were no longer recognized by the monoclonal antibodies. These properties indicate that removal of residues 219 to 244 or 318 to 346 disrupted the native conformation of gC-2, possibly owing to an alteration in the spacing between critical cysteine residues.
Gliadin T Cell Epitope Selection by Tissue Transglutaminase in Celiac Disease (2002)

Tissue transglutaminase (TG2) can modify proteins by transamidation or deamidation of specific glutamine residues. TG2 has a major role in the pathogenesis of celiac disease as it is both the target of disease-specific autoantibodies and generates deamidated gliadin peptides that are recognized by CD4(+), DQ2-restricted T cells from the celiac lesions. Capillary electrophoresis with fluorescence-labeled gliadin peptides was used to separate and quantify deamidated and transamidated products. In a competition assay, the affinity of TG2 to a set of overlapping gamma-gliadin peptides was measured and compared with their recognition by celiac lesion T cells. Peptides differed considerably in their competition efficiency. Those peptides recognized by intestinal T cell lines showed marked competition indicating them as excellent substrates for TG2. The enzyme fine specificity of TG2 was characterized by synthetic peptide libraries and mass spectrometry. Residues in positions -1, +1, +2, and +3 relative to the targeted glutamine residue influenced the enzyme activity, and proline in position +2 had a particularly positive effect. The characterized sequence specificity of TG2 explained the variation between peptides as TG2 substrates indicating that the enzyme is involved in the selection of gluten T cell epitopes. The enzyme is mainly localized extracellularly in the small intestine where primary amines as substrates for the competing transamidation reaction are present. The deamidation could possibly take place in this compartment as an excess of primary amines did not completely inhibit deamidation of gluten peptides at pH 7.3. However, lowering of the pH decreased the reaction rate of the TG2-catalyzed transamidation, whereas the rate of the deamidation reaction was considerably increased. This suggests that the deamidation of gluten peptides by TG2 more likely takes place in slightly acidic environments.
Antioxidants and Atherosclerotic Heart Disease (1997)

Epidemiologic studies have provided evidence of an inverse relation between coronary artery disease and antioxidant intake, and vitamin E supplementation in particular. The oxidative-modification hypothesis implies that reduced atherosclerosis is a result of the production of LDL that is resistant to oxidation, but linking the reduced oxidation of LDL to a reduction in atherosclerosis has been problematic. Several important additional mechanisms may underlie the role of antioxidants in preventing the clinical manifestations of coronary artery disease (Fig. 2). Specifically, there is evidence that plaque stability, vasomotor function, and the tendency to thrombosis are subject to modification by specific antioxidants. For example, cellular antioxidants inhibit monocyte adhesion, protect against the cytotoxic effects of oxidized LDL, and inhibit platelet activation. Furthermore, cellular antioxidants protect against the endothelial dysfunction associated with atherosclerosis by preserving endothelium-derived nitric oxide activity. We speculate that these mechanisms have an important role in the benefits of antioxidants.
Multiplexed Protein Quantification with Barcoded Hydrogel Microparticles (2010)

We demonstrate the use of graphically encoded hydrogel microparticles for the sensitive and high-throughput multiplexed detection of clinically relevant protein panels in complex media. Combining established antibody capture techniques with advances in both microfluidic synthesis and analysis, we detected 1-8 pg/mL amounts of three cytokines (interleuken-2, interleuken-4, and tumor necrosis factor alpha) in single and multiplexed assays without the need for filtration or blocking agents. A range of hydrogel porosities was investigated to ensure rapid diffusion of targets and reagents into the particle as well as to maintain the structural integrity of particles during rinsing procedures and high-velocity microfluidic scanning. Covalent incorporation of capture antibodies using a heterobifunctional poly(ethylene glycol) linker enabled one-step synthesis and functionalization of particles using only small amounts of valuable reagents. In addition to the use of three separate types of single-probe particles, the flexibility of the stop-flow lithography (SFL) method was leveraged to spatially segregate the three probes for the aforementioned target set on an individual encoded particle, thereby demonstrating the feasibility of single-particle diagnostic panels. This study establishes the gel-particle platform as a versatile tool for the efficient quantification of protein targets and significantly advances efforts to extend the advantages of both hydrogel substrates and particle-based arrays to the field of clinical proteomics.
Circular dichroism and molecular modeling yield a structure for the complex of human immunodeficiency virus type 1 trans-activation response RNA and the binding region of Tat, the trans-acting transcriptional activator. (1992)

Transcription in the human immunodeficiency virus type 1 (HIV-1) retrovirus is regulated by binding the viral Tat protein (trans-acting transcriptional activator) to the trans-activation response (TAR) RNA sequence. Here, vacuum UV circular dichroism (VUV-CD) is used to study the structure of TAR and its complex with two peptide fragments that are important for Tat binding to TAR. The VUV-CD spectrum of TAR is typical of A-form RNA and is minimally perturbed when bound to either the short or the long Tat peptide. The CD spectra of the complexes indicate an extended structure in the arginine-rich region of Tat from amino acid residue 47 through residue 58 and a short alpha-helix within the adjacent 59-72 region. Models of TAR and its peptide complexes are constructed to integrate these spectroscopic results with current biochemical data. The model suggests that (i) the arginine-rich 49-58 region is primarily responsible for electrostatic interactions with the phosphates of the RNA, (ii) the arginine side chains can additionally interact with substituent groups of the nucleotide bases to confer base recognition in the complex, (iii) the recognition of uracil-23 in TAR is facilitated by the peptide backbone, and (iv) the glutamine-rich face of an alpha-helix within the 59-72 region pairs to bases UGG at nucleotide positions 31-33 in the TAR loop and thus provides an additional motif in the Tat trans-activating protein to recognize TAR RNA.