gebhart/patrepeval huggingface dataset:
Construction of the gyrB Database for the Identification and Classification of Bacteria (1998)

Nucleotide sequences of small-subunit rRNA (16S rRNA) are most commonly used for the identification and characterization of bacteria and their complex communities. However, 16S rRNA evolves slowly and is often not very convenient to resolve bacterial strains at the species level. Wehave therefore attempted to develop a rapid and more convenient system for bacterial identification using the gyrB gene sequences. Wechose the gyrB gene, because (i) it is rarely transmitted horizontally, (ii) its molecular evolution rate is higher than that of 16S rRNA, and (iii) the gene is distributed ubiquitously among bacterial species. We PCR-amplified the 1.2 kb-long gyrB segments from about 1,000 bacterial species by using degenerate primers and determined their nucleotide sequences. The resultant data have been assembled into the gyrB database accessible via WWW.
[Effect of thiamine and its antimetabolite oxythiamine on the proliferative activity of carcinosarcoma Walker 256 cells]. (1987)

The microscopic studies of tumours from rats injected with thiamine at a dose of 20 mg/kg for 5 days have shown that sites of hemorrhages and necrosis are considerably more extensive than in tumours of control animals. Injections of the same doses of oxythiamine increase the rate of pathologic mitoses in tumour cells and decrease the tumour weight by 45%, limit the synthesis of thiamine diphosphate and inhibit the transketolase activity in tissues.
Use of the Triplex Scanner in Diagnosis of Deep Venous Thrombosis (1989)

We report our experience with 264 patients who underwent triplex scans for venous occlusive disease over a 10-month period. Venography was obtained in 30 of these patients. Correlation between the two procedures was 100%. The anatomic location of thrombosis and the extent of disease were identical in both studies. The presence of intraluminal clot by angiodynography is detected by looking for changes in the venous color-flow patterns and in the B-mode image. Newer clots have low echogenicity and are seen as large black areas in the gray-scale image. Older clots are more echogenic. The presence of enlarged venous collateral veins as well as absence of color flow and inability to compress the veins confirm the diagnosis of acute deep venous thrombosis. The results of angiodynography alone can be used safely in diagnosing acute deep venous thrombosis in patients. Equally important, treatment can be withheld safety in a patient with normal results.
Detrimental Contribution of the Toll-Like Receptor (TLR)3 to Influenza A Virus–Induced Acute Pneumonia (2006)

Influenza A virus (IAV) is the etiological agent of a highly contagious acute respiratory disease that causes epidemics and considerable mortality annually. Recently, we demonstrated, using an in vitro approach, that the pattern recognition Toll-like receptor (TLR)3 plays a key role in the immune response of lung epithelial cells to IAV. In view of these data and the fact that the functional role of TLR3 in vivo is still debated, we designed an investigation to better understand the role of TLR3 in the mechanisms of IAV pathogenesis and host immune response using an experimental murine model. The time-course of several dynamic parameters, including animal survival, respiratory suffering, viral clearance, leukocyte recruitment into the airspaces and secretion of critical inflammatory mediators, was compared in infected wild-type and TLR3(-/-) mice. First, we found that the pulmonary expression of TLR3 is constitutive and markedly upregulated following influenza infection in control mice. Notably, when compared to wild-type mice, infected TLR3-/- animals displayed significantly reduced inflammatory mediators, including RANTES (regulated upon activation, normal T cell expressed and secreted), interleukin-6, and interleukin-12p40/p70 as well as a lower number of CD8+ T lymphocytes in the bronchoalveolar airspace. More important, despite a higher viral production in the lungs, mice deficient in TLR3 had an unexpected survival advantage. Hence, to our knowledge, our findings show for the first time that TLR3-IAV interaction critically contributes to the debilitating effects of a detrimental host inflammatory response.
Neurohumoral modulators and sodium balance in experimental heart failure (1993)

The acute and chronic interactions of the renal nerves, atrial natriuretic factor (ANF), and mineralocorticoids for the regulation of sodium balance were examined in dogs with an arteriovenous (AV) fistula and the syndrome of high-output heart failure (HOHF) (n = 6). After the AV fistula and bilateral renal denervation, the animals avidly retained sodium for 5-7 days and then regained sodium balance for the subsequent 3 wk. This compensation was associated with the sustained elevations of plasma ANF and the normalization of plasma renin. Subsequent administration of deoxycorticosterone acetate (DOCA) for 10 days produced consistent sodium retention despite additional elevations in plasma ANF. All of these responses were similar to previous studies in AV fistula dogs with intact renal nerves. In a separate part of the study, the renal actions of acute synthetic ANF infusions were examined in these renal-denervated AV fistula dogs before and after DOCA. In the pre-DOCA experiments, ANF infusions at 15, 30, and 100 ng.kg-1.min-1 produced dose-related increases in urinary sodium excretion and significant elevations in creatinine clearance. In the presence of DOCA, urinary sodium excretion was markedly attenuated during identical ANF infusions. The composite results suggest that mineralocorticoids have an important modulatory role for the regulation of sodium balance in experimental HOHF. However, compared with earlier studies in compensated AV fistula dogs with intact renal nerves, the present studies demonstrate that blockade of efferent renal sympathetic nerve activity can restore the natriuretic expression of acute elevations in circulating ANF.
Face segmentation using skin-color map in videophone applications (1999)

This paper addresses our proposed method to automatically segment out a person's face from a given image that consists of a head-and-shoulders view of the person and a complex background scene. The method involves a fast, reliable, and effective algorithm that exploits the spatial distribution characteristics of human skin color. A universal skin-color map is derived and used on the chrominance component of the input image to detect pixels with skin-color appearance. Then, based on the spatial distribution of the detected skin-color pixels and their corresponding luminance values, the algorithm employs a set of novel regularization processes to reinforce regions of skin-color pixels that are more likely to belong to the facial regions and eliminate those that are not. The performance of the face-segmentation algorithm is illustrated by some simulation results carried out on various head-and-shoulders test images. The use of face segmentation for video coding in applications such as videotelephony is then presented. We explain how the face-segmentation results can be used to improve the perceptual quality of a videophone sequence encoded by the H.261-compliant coder.
Kink-free AlInAs/GaInAs/InP HEMTs grown by molecular beam epitaxy (1990)

Kink-free AlInAs/GaInAs/InP HEMTs have been fabricated from an MBE structure grown under normal growth condition. Devices with 1 μm gate-length exhibit an extrinsic transconductance of 450mS/mm and a maximum drain current of 600mA/mm which represent the best results for 1 μm gate devices. The DC output conductance shows no kink over the entire gate bias range. The elimination of the kink is attributed to the high quality AlInAs buffer layer and a low mismatch between the AlInAs buffer layer and InP substrate.
Is There a “Most Perfect Fluid” Consistent with Quantum Field Theory? (2007)

It was recently conjectured that the ratio of the shear viscosity to entropy density eta/s for any fluid always exceeds [formula: see text]. A theoretical counterexample to this bound can be constructed from a nonrelativistic gas by increasing the number of species in the fluid while keeping the dynamics essentially independent of the species type. The question of whether the underlying structure of relativistic quantum field theory generically inhibits the realization of such a system and thereby preserves the possibility of a universal bound is considered here. Using rather conservative assumptions, it is shown here that a metastable gas of heavy mesons in a particular controlled regime of QCD provides a realization of the counterexample and is consistent with a well-defined underlying relativistic quantum field theory. Thus, quantum field theory appears to impose no lower bound on eta/s, at least for metastable fluids.
Defined monoclonal antibodies to Escherichia coli β‐galactosidase as a tool for characterisation of recombinant expression products (1989)

Mouse monoclonal antibodies were prepared against beta-galactosidase (EC 3.2.1.23) of Escherichia coli. The binding sites of these monoclonal antibodies within the beta-galactosidase molecule were estimated by immunoblot analyses to various defined peptide regions of beta-galactosidase, encoded by expression plasmids. Monoclonal antibodies were characterised, which either bind to the amino-terminal or to the carboxy-terminal region or to an internal section of beta-galactosidase. These defined monoclonal antibodies were shown to be a useful tool for characterisation of beta-galactosidase fusion proteins expressed in Escherichia coli.
Vascular endothelial growth factor promotes the activation of hepatic stellate cells in chronic schistosomiasis (2016)

The activation of hepatic stellate cells (HSCs) is a key event in fibrotic pathogenesis. However, the mechanism involving activation of HSCs in chronic schistosomiasis is not entirely clear. Human HSC LX-2 and human umbilical vein endothelial cells (ECs) were cultured with Schistosoma japonicum antigens (SA) in vitro. Fibrosis-associated genes and cell proliferation were analyzed. HSCs were isolated from mice of chronic schistosomiasis with or without praziquantel (PZQ) treatment, followed by the microarray analysis for the liver fibrosis-associated pathways. Although SA inhibited the activation and proliferation of HSCs, it induced the EC proliferation and vascular endothelial growth factor-a (VEGF) production. VEGF significantly increased the proliferation of HSCs and upregulated the expression of collagen and α-smooth muscle actin. For in vivo study, we found that several fibrosis-associated pathways were involved in the HSCs during the reversal of liver fibrosis caused by schistosomiasis, including VEGF, platelet-derived growth factor, tumor necrosis factor and endothelin-1 pathways. The Ingenuity Pathway Analysis showed that VEGF directly regulated several pro-fibrotic and immune cytokine genes in HSCs, including integrin, fibronectin, interferon-γ, interleukin (IL)-6 and IL-10. Our data indicated the critical role of VEGF signaling in HSC activation in chronic schistosomiasis and highlighted several promising genes and pathways in HSCs as potential targets for therapeutic treatment of liver fibrosis.
Effect of three suppressors on the expression of powdery mildew resistance genes in barley (1996)

Three recessive mutagen-induced alleles that partially suppress the phenotypic expression of the semidominant powdery mildew resistance gene Mla12 have been studied. When each suppressor is present in homozygous condition, the infection type 0, conferred by gene Mla12 when homozygous, is changed to intermediate infection types. The three suppressor lines were crossed with seven near-isogenic lines with different powdery mildew resistance genes and one, M100, was crossed with nine additional lines. Seedlings of parents and from the F1and F2 generations were tested with powdery mildew isolates that possessed the appropriate avirulence and virulence genes. The segregation of phenotypes in the F2 generation disclosed that the three suppressors affected the phenotypic expression of three resistance genes, whereas that of four resistance genes remained unaffected. The suppressor in mutant M100 affected the phenotypic expression of 9 of the 10 additional resistance genes present. It is suggested that the three suppressors are mutationally modified genes involved in host defence processes. This implies that different resistance genes employ different, but overlapping, spectra of defence processes, or signal transduction pathways. Key words : barley, Hordeum vulgare, powdery mildew, Erysiphe graminis hordei, mutation, resistance, suppressor.
Investigation of carbon fluxes in central metabolic pathways of Corynebacterium glutamicum (1996)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1996.
Bacterial Origin and Community Composition in the Barley Phytosphere as a Function of Habitat and Presowing Conditions (2000)

An understanding of the factors influencing colonization of the rhizosphere is essential for improved establishment of biocontrol agents. The aim of this study was to determine the origin and composition of bacterial communities in the developing barley (Hordeum vulgare) phytosphere, using denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified from extracted DNA. Discrete community compositions were identified in the endorhizosphere, rhizoplane, and rhizosphere soil of plants grown in an agricultural soil for up to 36 days. Cluster analysis revealed that DGGE profiles of the rhizoplane more closely resembled those in the soil than the profiles found in the root tissue or on the seed, suggesting that rhizoplane bacteria primarily originated from the surrounding soil. No change in bacterial community composition was observed in relation to plant age. Pregermination of the seeds for up to 6 days improved the survival of seed-associated bacteria on roots grown in soil, but only in the upper, nongrowing part of the rhizoplane. The potential occurrence of skewed PCR amplification was examined, and only minor cases of PCR bias for mixtures of two different DNA samples were observed, even when one of the samples contained plant DNA. The results demonstrate the application of culture-independent, molecular techniques in assessment of rhizosphere bacterial populations and the importance of the indigenous soil population in colonization of the rhizosphere.
Current state on development of neuroprotective agents for cerebral ischemia (2002)

The improvement of decreased cerebral blood flow using thrombolytic agents, anti-thrombin drugs, and antiplatelet drugs has been essential for acute ischemic stroke. Edaravone, a free radical scavenger, has been commercially available as a novel neuroprotective agent for ischemic stroke in Japan from 2001. The appearance of a neuroprotective agent implies that therapeutic strategy can be expanded through a combination with thrombolysis. In the previous development, several cases have reported that neuroprotective compounds failed in clinical trials. However, recent studies have clarified that the cerebral ischemia induced the neuronal cell death by mediating multiple mechanisms with necrosis and/or apoptosis. The cytotoxicity derived from the NO/peroxynitrite/free radical generating system, one of intracellular Ca2+ signaling, is a typical event in ischemic injury, which is protected by edaravone. Furthermore, it is suggested that suppression of excessively activated voltage-dependent Na+ and Ca2+ channels is effective as a strategy for neuroprotection, since abnormal excitatory stimuli in the neuronal network result in the cerebral infarction. The development of several compounds having different mechanisms of action for acute stroke is in progress. It is therefore prospected that the various novel neuroprotective agents will be provided for assuring the option of therapeutic strategy, since the reinforcement of medical stroke care including diagnosis contributes to the prolongation of the therapeutic time window.
p55CDC25 is a nuclear protein required for the initiation of mitosis in human cells. (1991)

The cdc25+ gene of fission yeast encodes a phosphotyrosine phosphatase that dephosphorylates tyrosine-15 of p34cdc2 and thereby activates p34cdc2/cyclin to bring about entry into M phase. We have recently cloned a human homolog, CDC25, which rescues the M-phase initiation defect of yeast cdc25 temperature-sensitive mutants. Antibodies raised against the CDC25 gene product specifically recognize human proteins of approximately 55 and approximately 52 kDa. Microinjection of affinity-purified anti-CDC25 antibodies into HeLa cells inhibits entry into mitosis. These observations suggest that the CDC25 gene products are essential for the initiation of mitosis in human cells, similar to their homologs in fission yeast and Drosophila. CDC25 gene products, like p34CDC2, are localized primarily in the nucleus during interphase, suggesting that activation of p34CDC2/cyclin by p52/p55CDC25 occurs within the nucleus.
Ruthenium-Catalyzed Asymmetric Electrophilic Fluorination of 1,3-Dicarbonyl Compounds (2007)

Upon activation with (Et3O)PF6 (2 equiv), the ruthenium(II) complex [RuCl2(PNNP)] (1; PNNP is (1S,2S)-N,N‘-bis(o-(diphenylphosphino)benzylidene)cyclohexane-1,2-diamine) catalyzes the electrophilic fluorination of 1,3-dicarbonyl compounds by N-fluorobenzenesulfonimide (NFSI). Oxygen donors, in particular Et2O as cosolvent, increase the activity of the catalyst and, in some cases, the enantioselectivity. The absolute configuration of 2-tert-butoxycarbonyl-2-fluorocyclopentanone (5a), which is obtained with up to 93% ee in catalysis, was determined to be R by derivatization to (1S)-(−)-camphanic acid (1R,2R)-2-tert-butoxycarbonyl-2-fluoro-cyclopentyl ester (7) and X-ray analysis. A model for enantioselection is proposed on the basis of the known structures of the dicationic complex [Ru(4a)(PNNP)]2+ (2a; 4a is 2-tert-butoxycarbonylcyclopentanone), which is formed under catalysis conditions, and of its monocationic enolato analogue (3a). The stoichiometric reactions of 2a and 3a with NFSI in pure CH2Cl2 and in the presence of substrate, product, or Et2O show that proton-transfer processes promoted by oxygen donors are pivotal in catalysis.
Review of the Ocular Angiogenesis Animal Models (2009)

Increasing interest in developing reliable and reproducible models to study angiogenesis has emerged due to recent advances in the treatment of eye disease with pathologic angiogenesis. This review provides a summary of the principal ocular animal models for angiogenesis. Models of anterior segment neovascularization include the corneal micropocket assay, used to study the influence of specific molecules/proteins in angiogenesis, and corneal chemical and suture induced injury, which mimic more closely the complex nature of the human disease. Angiogenesis models of the posterior segment include the well-known laser-induced injury of the choroid/Bruch's membrane, as well as the oxygen induced retinopathy and models of injections of pro-angiogenic/inflammatory molecules. In addition, knockout or knock-in transgenic mice provide powerful tools in studying the role of specific proteins in angiogenesis.
Luminescence Tuning of Upconversion Nanocrystals (2010)

Upconversion luminescence tuning of beta-NaYF(4) nanorods under 980 nm excitation has successfully been achieved by tridoping with Ln(3+) ions with different electronic structures. The effects of Ce(3+) ions on NaYF(4):Yb(3+)/Ho(3+) as well as Gd(3+) ions on NaYF(4):Yb(3+)/Tm(3+)(Er(3+)) have been studied in detail. By tridoping with Ce(3+) ions, not only were unusual (5)G(5)-->(5)I(7) and (5)F(2)/(3)K(8)-->(5)I(8) transitions from Ho(3+) ions and 5d-->4f transitions from Ce(3+) ions observed in NaYF(4):Yb(3+)/Ho(3+) nanorods, but also an increase in the intensity of (5)F(5)-->(5)I(8) relative to (5)S(2)/(5)F(4)-->(5)I(8) with increasing Ce(3+) concentration, which can be attributed to efficient energy transfers of (5)I(6) (Ho)+(2)F(5/2) (Ce)-->(5)I(7) (Ho)+(2)F(7/2) (Ce) and (5)S(2)/(5)F(4) (Ho)+(2)F(5/2) (Ce)-->(5)F(5) (Ho)+(2)F(7/2) (Ce). Interestingly, with increasing pump power density, the luminescence of NaYF(4):Yb(3+)/Ho(3+) nanorods is always dominated by the (5)S(2)/(5)F(4)-->(5)I(8) transition, whereas the luminescence of Ce(3+)-tridoped NaYF(4):Yb(3+)/Ho(3+) nanorods is dominated by the (5)S(2)/(5)F(4)-->(5)I(8) and (5)G(5)-->(5)I(7) transitions in turn. These observations are discussed on the basis of a rate equation model. Furthermore, Gd(3+)-tridoped NaYF(4):Yb(3+)/Tm(3+)(Er(3+)) nanorods can emit multicolor upconversion emissions spanning from the UV to the near-infrared under 980 nm excitation. (6)P(5/2)-->(8)S(7/2) ( approximately 306 nm) and (6)P(7/2)-->(8)S(7/2) ( approximately 311 nm) transitions from Gd(3+) ions were observed. In addition to the aforementioned luminescence properties, these Gd(3+)-tridoped nanorods also exhibit paramagnetic behavior at room temperature and superparamagnetic behavior at 2 or 5 K.
Diffraction properties of substrate guided-wave holograms (1995)

Substrate guided-wave (SGW) holograms, recorded and reconstructed using light waves guided through optical substrates, are currently being incorporated into visual displays, optical integrated circuits, and nondestructive testing systems. In this paper, a coupled wave approach is used to analyze the diffraction properties of SGW holograms. The expressions obtained allow SGW holograms to be compared with conventional transmission and reflection holograms. The analysis is restricted to cases in which holograms are recorded and reconstructed using plane waves. The object beam is also assumed to be at normal incidence to the hologram. Results are presented for holograms recorded on a silver halide emulsion and illuminated using a krypton laser. The study shows that SGW holograms have higher diffraction efficiencies under the Bragg condition, higher angular selectivities, and more moderate wavelength selectivities than holograms recorded using conventional means.
Relationship Between Internal Risk Factors for Development of Decubitus Ulcers and the Blood Flow Response Following Pressure Load (2001)

The objective of this study was to investigate the extent to which internal risk factors for the development of decubitus ulcers are related to the blood flow response following the relief of a pressure load. There were 122 nursing home patients (43 men, 69 women, mean age: 81 +/- 8 years; range: 60-97). The following potential, internal risk factors for the development of decubitus ulcers were assessed: chronic disorders (diabetes mellitus, cardiovascular disease [congestive heart failure, history of myocardial infarct or angina pectoris] and cerebrovascular accident), fever, blood pressure, nutritional status, serum hemoglobin concentration, and serum urea and serum creatinine concentrations. Skin temperature response (latency time and total response time) was measured following relief of a 100 kPa test pressure. The presence of cardiovascular disease, cerebrovascular accident, poor nutritional condition, high serum urea and male gender showed a significant relationship with an impaired blood flow response. The delayed latency found showed a similarity to the so-called "no-reflow phenomenon." The association of cardiovascular disease and a cerebrovascular accident with a delay in the blood flow response may result from endothelial damage. A poor nutritional condition may be associated with a deficit of scavengers of oxygen-derived free radicals. The presence of free radicals may damage endothelium during reperfusion, thus influencing the blood flow response. The association of high serum urea with delayed vasodilatation may theoretically be explained by the association of serum urea and impaired kidney functioning, since the kidney is an important organ in the production of vasoactive substances. Serum urea can also be considered a measure for nutritional condition. Gender may function as a substitute for other, unmeasured factors that are related to blood flow response.