gebhart/patrepeval huggingface dataset:
Sequence and immunogenicity of the 70-kDa heat shock protein of Mycobacterium leprae (1991)

The gene encoding the Mycobacterium leprae 70-kDa heat shock protein has been isolated from a cosmid library using a fragment of the clone JKL2. Southern blot analysis of a positive clone identified a 4.4-kb fragment containing the entire coding region of the gene plus 2.4 kb upstream. Sequencing revealed the gene to encode a 621-amino acid protein, bearing 56% identity with the Escherichia coli dnaK gene product and 47% and 46% identity with the human and Caenorhabditis elegans hsp70, respectively. Comparison with the C-terminal 203 amino acids of the Mycobacterium tuberculosis 71-kDa Ag yielded 70% identity. Recombinant M. leprae p70 was produced in E. coli as a fusion protein (rp70f) with a portion of the schistosomal glutathione-S-transferase, using the expression vector, pGEX-2T. Cleavage with thrombin resulted in the release of a 70.0-kDa protein (rp70c) from the glutathione-S-transferase. Examination of the proteins by immunoblotting demonstrated that anti-M. leprae mAb, L7, and sera from lepromatous leprosy patients bound to both the cleaved and fusion proteins. We compared the T cell reactivity of the M. leprae recombinant proteins with that of mAb affinity-purified bacille Calmette-Guerin (BCG) 70-kDa Ag using proliferation assays. PBMC of BCG vaccinees responded to both M. leprae cleaved and fusion p70, though more subjects responded to the rp70c (18 of 20) than to rp70f (13 of 20). Responses were generally higher to rp70c than to rp70f, however all responses to the M. leprae recombinant proteins were lower than to mAb affinity-purified BCG p70. Thus, the M. leprae 70-kDa heat shock protein elicits T and B cell responses in subjects exposed to mycobacteria, despite its homology with the human hsp70.
The preparation of 3,6‐bis(3‐hexylthien‐2‐yl)‐s‐tetrazine and its conjugated polymers (2011)

Abstract We demonstrated, for the first time, that 3,6‐bis(3‐hexylthien‐2‐yl)‐ s ‐tetrazine (TTz) with hexyl group at the 3‐position of thiophene rings can be prepared using a modified sulfur‐assisted Pinner synthesis. Although the hexyl group creates large steric hindrance to the tetrazine ring formation reaction, and the reaction under a traditional condition only produces trace amount of the target product, the yield of this reaction under a modified reaction condition using anhydrous hydrazine at 68 °C can reach 65%. Two new copolymers of the resulting TTz and hexyl‐ or 2‐ethylhexyl‐substituted cyclepentadithiophene have been prepared. The polymers show a broader light absorption in film than in solution attributing to the large distribution of effective conjugation length of polymer chain due to the existence of both cis‐ and trans‐orientations of the 3‐hexylthiophene units in the planar polymer chain in solid state. Although the polymers show a narrow band gap and a deep HOMO level, which are desirable for generating an efficient light absorption and a larger open circuit voltage ( V oc ) of the resulting solar cell devices, the device performance is not as good as expected. It is attributed to the random distribution of the cis‐ and trans‐conformations along the polymer chain. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011.
Interleukin-6 Gene Polymorphism Confers Susceptibility to Pulmonary Hypertension in Chronic Obstructive Pulmonary Disease (2006)

International audience
Internalization of Escherichia coli into Human Kidney Epithelial Cells: Comparison of Fecal and Pyelonephritis-Associated Strains (1994)

A gentamicin survival assay, using primary human renal epithelial cells and Escherichia coli strains isolated from the feces of asymptomatic individuals and from the urine or blood of patients with acute pyelonephritis, was used to investigate bacterial internalization as a model for renal parenchymal invasion in pyelonephritis. E. coli strains, regardless of their origin, efficiently entered into human renal epithelial cells, a process inhibited by cytochalasin D. While the percentage of survival of nonhemolytic pyelonephritis isolates did not differ from that of fecal isolates, survival of hemolytic pyelonephritis strains was lower than that of nonhemolytic strains, perhaps as a consequence of the greater cytotoxicity of hemolytic strains. There was no evidence of intracellular multiplication of E. coli. These results demonstrate that human renal epithelial cells are capable of efficient uptake of E. coli regardless of the source of the bacteria.
Interleukin‐18 gene polymorphisms and haplotypes in patients with oral lichen planus: a study in an ethnic Chinese cohort (2007)

Interleukin (IL)-18, a proinflammatory cytokine, induces T-helper 1 differentiation and cytotoxic T-lymphocyte functions, both of which have been proposed in the pathogenesis of oral lichen planus (OLP) - an oral disease resembles oral mucosal graft-versus-host disease (GVHD) both clinically and histologically. The aim of this study was to evaluate the association of single nucleotide polymorphisms (SNPs) in the IL18 gene on the chromosome 11q22 in patients with OLP. Four SNPs of the IL18 gene at positions -137G/C (rs187238), -607C/A (rs1946518), -656G/T (rs1946519), and 1248A/G (rs189667) were analyzed in 151 patients with OLP and 143 normal controls using polymerase chain reaction-sequence-specific primers method, and the serum level of IL-18 protein was determined by enzyme-linked immunosorbent assay (ELISA). The data revealed that there is a significant difference in IL18-607 genotype distributions between the patient group and the control group (P < 0.001), and the polymorphism -137G/C also appears to be statistically associated with the more severe erosive subtype (eOLP) (P = 0.023). The identified polymorphisms at the IL-18 promoter region (i.e. -137GG) are likely to exert positive effect on the production of IL-18 protein in OLP, as detected by ELISA. Using phase software, four haplotypes were deduced from the two polymorphisms -607C/A and -137G/C, named haplotypes I to IV, and the haplotypes I, II, and IV are significantly associated with OLP (P < 0.001). Our data suggest that the identified IL18 polymorphisms may be associated with the pathogenesis of OLP in this Chinese cohort by upregulation of IL-18 production in vivo.
Email archive overviews using subject indexes (2002)

Archived discussion lists are becoming significant reference sources. This paper describes a new type of overview for such lists, using a back-of-the-book style index containing headwords selected from subject lines and subentries derived from their subject-line-contexts.
Biochemical Aspects of Fumaric Acid Accumulation by Rhizopus arrhizus (1986)

The accumulation and excretion of fumaric acid, and to a lesser extent malic and succinic acids, by Rhizopus arrhizus occurs under aerobic conditions in a high-glucose medium containing a limiting amount of nitrogen and a neutralizing agent (CaCO(3)). An overall four-carbon dicarboxylic acid molar yield of up to 145% (moles of acid produced per mole of glucose utilized) is obtained after incubation for 4 to 5 days. Evidence is presented that fumarate is synthesized from pyruvate via a carboxylation reaction yielding oxaloacetate, which is then converted to malate and further on to fumarate via the reductive reactions of the tricarboxylic acid cycle. The possible formation of fumarate from the normal (oxidative) operation of the tricarboxylic acid cycle was not excluded by the data. Yield, C nuclear magnetic resonance, and enzymatic activity studies were carried out in a strain of R. arrhizus which produces high levels of fumarate from glucose and carbonate. The observed high fumarate molar yield (greater than 100%) can therefore be explained in terms of the carboxylation of pyruvate and the operation of the reductive reactions of the tricarboxylic acid cycle under aerobic conditions.
Broad‐Spectrum Antimicrobial Star Polycarbonates Functionalized with Mannose for Targeting Bacteria Residing inside Immune Cells (2016)

In this study, a series of star-shaped polycarbonates are synthesized by metal-free organocatalytic ring-opening polymerization of benzyl chloride (BnCl) and mannose-functionalized cyclic carbonate monomers (MTC-BnCl and MTC-ipman) with heptakis-(2,3-di-O-acetyl)-β-cyclodextrin (DA-β-CD) as macroinitiator. The distributions and compositions of pendent benzyl chloride and protected mannose group (ipman) units are facilely modulated by varying the polymerization sequence and feed ratio of the monomers, allowing precise control over the molecular composition, and the resulting polymers have narrow molecular weight distribution. After deprotection of ipman groups and quaternization with various N,N-dimethylalkylamines, these star polymers with optimized compositions of cationic and mannose groups in block and random forms exhibit strong bactericidal activity and low hemolysis. Furthermore, the optimal mannose-functionalized polymer demonstrates mannose receptor-mediated intracellular bactericidal activity against BCG mycobacteria without inducing cytotoxicity on mammalian cells at the effective dose. Taken together, the materials designed in this study have potential use as antimicrobial agents against diseases such as tuberculosis, which is caused by intracellular bacteria.
DNA methylation of Sleeping Beauty with transposition into the mouse genome (2005)

The Sleeping Beauty transposon is a recently developed non-viral vector that can mediate insertion of transgenes into the mammalian genome. Foreign DNA elements that are introduced tend to invoke a host-defense mechanism resulting in epigenetic changes, such as DNA methylation, which may induce transcriptional inactivation of mammalian genes. To assess potential epigenetic modifications associated with Sleeping Beauty transposition, we investigated the DNA methylation pattern of transgenes inserted into the mouse genome as well as genomic regions flanking the insertion sites with bisulfite-mediated genomic sequencing. Transgenic mouse lines were created with two different Sleeping Beauty transposons carrying either the Agouti or eGFP transgene. Our results showed that DNA methylation in the keratin-14 promoter and Agouti transgene were negligible. In addition, two different genomic loci flanking the Agouti insertion site exhibited patterns of DNA methylation similar to wild-type mice. In contrast, high levels of DNA methylation were observed in the eGFP transgene and its ROSA26 promoter. These results indicate that transposition via Sleeping Beauty into the mouse genome may result in a significant level of de novo DNA methylation. This may depend on a number of different factors including the cargo DNA sequence, chromosomal context of the insertion site, and/or host genetic background.
Expression and Function of a Biological Pacemaker in Canine Heart (2003)

HCN2 overexpression provides an I(f)-based pacemaker sufficient to drive the heart when injected into a localized region of atrium, offering a promising gene therapy for pacemaker disease.
Detection algorithms for hyperspectral imaging applications (2002)

We introduce key concepts and issues including the effects of atmospheric propagation upon the data, spectral variability, mixed pixels, and the distinction between classification and detection algorithms. Detection algorithms for full pixel targets are developed using the likelihood ratio approach. Subpixel target detection, which is more challenging due to background interference, is pursued using both statistical and subspace models for the description of spectral variability. Finally, we provide some results which illustrate the performance of some detection algorithms using real hyperspectral imaging (HSI) data. Furthermore, we illustrate the potential deviation of HSI data from normality and point to some distributions that may serve in the development of algorithms with better or more robust performance. We therefore focus on detection algorithms that assume multivariate normal distribution models for HSI data.
Characterization of oxygen ordering in (La, Sr)FeO3 – δby atomic resolution Z‐contrast imaging and electron energy‐loss spectroscopy (2002)

Journal Article Characterization of oxygen ordering in (La, Sr)FeO3 – δ by atomic resolution Z‐contrast imaging and electron energy‐loss spectroscopy Get access Robert F. Klie, Robert F. Klie University of Illinois at Chicago, 845 West Taylor Street #2236, Chicago, IL 60607, USA To whom correspondence should be addressed. E‐mail: rfklie@uic.edu Search for other works by this author on: Oxford Academic PubMed Google Scholar Nigel D. Browning Nigel D. Browning University of Illinois at Chicago, 845 West Taylor Street #2236, Chicago, IL 60607, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Electron Microscopy, Volume 51, Issue suppl_1, 27 March 2002, Pages S59–S66, https://doi.org/10.1093/jmicro/51.Supplement.S59 Published: 27 March 2002 Article history Received: 13 November 2000 Accepted: 20 August 2001 Published: 27 March 2002
The role of neurotrophins in the pathophysiology of allergic rhinitis (2010)

Neurotrophins represent prime candidates in upper airway pathophysiology in allergic rhinitis. Research on neurotrophins in allergic rhinitis is thus becoming a progressively more exciting field and may reveal new and promising therapeutic options for the future.
Endothelium and NOTCH specify and amplify aorta-gonad-mesonephros–derived hematopoietic stem cells (2015)

Hematopoietic stem cells (HSCs) first emerge during embryonic development within vessels such as the dorsal aorta of the aorta-gonad-mesonephros (AGM) region, suggesting that signals from the vascular microenvironment are critical for HSC development. Here, we demonstrated that AGM-derived endothelial cells (ECs) engineered to constitutively express AKT (AGM AKT-ECs) can provide an in vitro niche that recapitulates embryonic HSC specification and amplification. Specifically, nonengrafting embryonic precursors, including the VE-cadherin-expressing population that lacks hematopoietic surface markers, cocultured with AGM AKT-ECs specified into long-term, adult-engrafting HSCs, establishing that a vascular niche is sufficient to induce the endothelial-to-HSC transition in vitro. Subsequent to hematopoietic induction, coculture with AGM AKT-ECs also substantially increased the numbers of HSCs derived from VE-cadherin⁺CD45⁺ AGM hematopoietic cells, consistent with a role in supporting further HSC maturation and self-renewal. We also identified conditions that included NOTCH activation with an immobilized NOTCH ligand that were sufficient to amplify AGM-derived HSCs following their specification in the absence of AGM AKT-ECs. Together, these studies begin to define the critical niche components and resident signals required for HSC induction and self-renewal ex vivo, and thus provide insight for development of defined in vitro systems targeted toward HSC generation for therapeutic applications.
GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation (2008)

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.
The MicroRNA Spectrum in 12 Body Fluids (2010)

MicroRNAs are ubiquitous in all the body fluid types tested. Fluid type-specific miRNAs may have functional roles associated with the surrounding tissues. In addition, the changes in miRNA spectra observed in the urine samples from patients with different urothelial conditions demonstrates the potential for using concentrations of specific miRNAs in body fluids as biomarkers for detecting and monitoring various physiopathological conditions.
Zinc and depression. An update. (2006)

Unsatisfactory clinical efficacy and a variety of adverse effects of current antidepressant drugs have incited search for better therapy. Zinc, an antagonist of the glutamate/N-methyl-D-aspartate (NMDA) receptor, exhibits antidepressant-like activity in rodent tests/models of depression. Similarly to antidepressants, zinc induces brain derived neurotrophic factor (BDNF) gene expression and increases level of synaptic pool of zinc in the hippocampus. Clinical observations demonstrated serum hypozincemia in depression, which was normalized by effective antidepressant treatment. Moreover, our preliminary clinical study demonstrated the benefit of zinc supplementation in antidepressant therapy. All the data indicate the important role of zinc homeostasis in psychopathology and therapy of depression and potential clinical antidepressant activity of this ion.
Alpha‐Gal on bioprostheses: xenograft immune response in cardiac surgery (2005)

Our data suggest that implantation of bioprostheses in cardiac surgery induces a xenograft-specific immune response. Procedures diminishing the presence of alpha-Gal on bioprostheses, such as utilization of genetically manipulated alpha-Gal-deficient xenograft or pretreatment with alpha-Galactosidase, might diminuate the immune response against bioprostheses and extend durability.
Internal medicine : diagnosis & therapy (1993)

A comprehensive guide to the management of the most important diseases, covering diagnosis and therapy in an easy-to-use format. This edition of the pocket-sized manual has been revised and updated to reflect the rapid growth and recent developments occurring in this ever-changing field.
Marine magnetotellurics for petroleum exploration, Part II: Numerical analysis of subsalt resolution (1998)

Abstract In areas where seismic imaging of the base of salt structures is difficult, seaborne electromagnetic techniques offer complementary as well as independent structural information. Numerical models of 2-D and 3-D salt structures demonstrate the capability of the marine magnetotelluric (MT) technique to map the base of the salt structures with an average depth accuracy of better than 10%. The mapping of the base of the salt with marine MT is virtually unaffected by internal variation within the salt. Three-dimensional anticlinal structures with a horizontal aspect ratio greater than two can be interpreted adequately via two-dimensional inversions. Marine MT can distinguish between salt structures which possess deep vertical roots and those which do not. One measure of the relative accuracy of MT and seismic methods can be made by considering the vertical and lateral position errors in the locations of interfaces caused by neglecting velocity anisotropy in migration. For the shallow part of the section where two-way travel times are on the order of 1 s, the vertical and lateral position errors in the locations of salt-sediment interfaces from 2-D MT inversion is more than twice the expected migration error in reflectors in transversely isotropic sediments, such as those in the Gulf of Mexico. Deeper in the section where two-way times are on the order of 4 s, lateral position errors in migration become comparable to those of the MT inverse, whereas seismic vertical position errors remain more than a factor of two smaller than MT errors. This analysis shows that structural mapping accuracy would be improved using MT and seismic together.
Use of fluorescent dye BCECF to measure intracellular pH in cortical collecting tubule (1989)

The compound 2'-7'-bis(carboxyethyl)-5(6)-carboxyfluorescein (BCECF) is being extensively used to measure intracellular pH (pHi) in a variety of tissue preparations. Use of this dye in the isolated perfused rabbit cortical collecting tubule (CCT) revealed two previously unreported findings. Apical incubation via luminal perfusion with the acetoxymethyl ester of BCECF (BCECF-AM) resulted in intense uptake into a minority cell population. Basolateral incubation via the peritubular bathing solution resulted in apparent homogenous uptake into all cells. The minority cells were identified as intercalated cells by the use of fluorescent probes specific for intercalated cells. Minority cell pHi was 7.34 +/- 0.06 (n = 9); majority cell pHi was 7.41 +/- 0.05 (n = 6). In addition, prolonged excitation of BCECF resulted in adverse effects. Intense continuous excitation for 1-3 min resulted in a fall in apparent pHi of 0.53 +/- 0.05 pH units (n = 6, P less than 0.001). After reloading with fresh BCECF-AM, the calculated pHi was 0.05 +/- 0.07 pH units higher than before prolonged excitation (P = NS), suggesting that the apparent decrease was due to changes in the pH sensitivity of BCECF as a result of the prolonged excitation. Prolonged excitation of cells with pHi clamped at 7.50 resulted in a decline in apparent pHi at the rate of 0.15 +/- 0.02 pH units/min (n = 4).(ABSTRACT TRUNCATED AT 250 WORDS)
A direct method for fast three‐dimensional serial reconstruction (1990)

A method for accurate three-dimensional reconstruction of openly connected porous structures is described. The method is based on embedding of a specimen in a contrast coloured epoxy resin and serial sectioning in a standard hard tissue microtome. A PC-based image processing system is used for direct digitization of the cut surface, and by thresholding two-phase images are obtained. The process is fully automated, and about 170 sections can be produced, digitized, dichotomized, and stored per hour. As an example of its applications, the method is used on trabecular bone, which is an anisotropic porous structure.
Diaminobenzobisthiazoles and related compounds (1967)

In the preparation of benzobisthiazoles from m- and p-phenylenediamines by thiocyanation or by ring closure of derived thioureas the linear tricyclic compound is usually the major or the only product. 3,6-Diamino-1,2-phenylene di(hydrogen thiosulphate)(the so-called p-phenylenediamino-2,5-bisthiosulphuric acid) is the 2,3-isomer and correction is required to structures assigned to its derivatives, e.g., the diaminophenylenedithiol, the bisdiazosulphide, and certain benzobisthiazoles. Formation of fused thiazole rings in derivatives of 2-naphthylamine and 6-aminoquinoline occurs in the 1- and 5-positions respectively.