gebhart/patrepeval huggingface dataset:
Identification of human minor histocompatibility antigens based on genetic association with highly parallel genotyping of pooled DNA (2008)

Minor histocompatibility (H) antigens are the molecular targets of allo-immunity responsible both for the development of antitumor effects and for graft-versus-host disease (GVHD) in allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, despite their potential clinical use, our knowledge of human minor H antigens is largely limited by the lack of efficient methods of their characterization. Here we report a robust and efficient method of minor H gene discovery that combines whole genome association scans (WGASs) with cytotoxic T-lymphocyte (CTL) assays, in which the genetic loci of minor H genes recognized by the CTL clones are precisely identified using pooled-DNA analysis of immortalized lymphoblastoid cell lines with/without susceptibility to those CTLs. Using this method, we have successfully mapped 2 loci: one previously characterized (HMSD encoding ACC-6), and one novel. The novel minor H antigen encoded by BCL2A1 was identified within a 26 kb linkage disequilibrium block on chromosome 15q25, which had been directly mapped by WGAS. The pool size required to identify these regions was no more than 100 individuals. Thus, once CTL clones are generated, this method should substantially facilitate discovery of minor H antigens applicable to targeted allo-immune therapies and also contribute to our understanding of human allo-immunity.
Low PAPR Spatial Modulation for SC-FDMA (2016)

Although spatial modulation (SM) presents an attractive multiple-input-multiple-output (MIMO) technique, it increases peak-to-average power ratio (PAPR) on all transmit antennas when applied directly to single-carrier frequency-division multiple access (SC-FDMA). Therefore, we propose an SM modification, which is called low-PAPR SM (LPSM), to preserve the low PAPR level of SC-FDMA and to achieve the benefits of SM. In addition, as the optimal maximum-likelihood detection (MLD) receiver has a very high computational complexity when applied to SC-FDMA system, we observed suboptimal receivers for SC-FDMA with LPSM. In addition to low-complexity linear receivers, we proposed and analyzed two receivers: near-MLD and improved minimum mean square error (iMMSE) receivers. The near-MLD receiver achieves performance very near to MLD with significantly lower complexity, whereas the iMMSE receiver presents a tradeoff between MLD and linear receivers in terms of performance and complexity.
A general method for removal of a 4-methyl group from triterpenoids. Synthesis of 4β-demethylglycyrrhetinic acid (1973)

Using 4,4-dimethyl-5α-cholestan-3-one (1) as a model compound, a short high-yielding sequence has been developed for removing a 4-methyl group from triterpenoids. The method makes use of the ‘abnormal’ Beckmann reaction which 3-hydroxyimino-4,4-dimethylsteroids undergo to yield 3,4-seco-nitriles. Epoxidation of the 4-methylene group, followed by treatment of the 3,4-seco-epoxy-nitrile with boron trifluoride in refluxing toluene affords the 4β-demethyl-3-ketone in an overall yield of 40–50%. The general nature of the method has been demonstrated in the conversion of dihydrolanosterol into 4α,14α-dimethyl-5α-cholest-8-en-3-one (17) and 4α,14α-dimethyl-5α-cholestane-3,11-dione (3), and in the synthesis of 3β-hydroxy-11-oxo-24-nor-18β-olean-12-en-30-oic acid (4β-demethylglycyrrhetinic acid)(27) and 3,11-dioxo-24-nor-18β-olean-12-en-30,22β-olactone (31).
Peroxynitrite‐Induced Alterations in Synaptosomal Membrane Proteins (1999)

Peroxynitrite (ONOO ) is a highly reactive, oxidizing anion with a half-life of <1 s that is formed by reaction of superoxide radical anion with nitric oxide. Several reports of ONOO--induced oxidation of lipids, proteins, DNA, sulfhydryls, and inactivation of key enzymes have appeared. ONOO- has also been implicated as playing a role in the pathology of several neurodegenerative disorders, such as Alzheimer's disease (AD) and amyotrophic lateral sclerosis, among others. Continuing our laboratory's interest in free radical oxidative stress in brain cells in AD, the present study was designed to investigate the damage to brain neocortical synaptosomal membrane proteins and the oxidation-sensitive enzyme glutamine synthetase (GS) caused by exposure to ONOO-. These synaptosomal proteins and GS have previously been shown by us and others to have been oxidatively damaged in AD brain and also following treatment of synaptosomes with amyloid beta-peptide. The results of the current study showed that exposure to physiological levels of ONOO- induced significant protein conformational changes, demonstrated using electron paramagnetic resonance in conjunction with a protein-specific spin label, and caused oxidation of proteins, measured by the increase in protein carbonyls. ONOO- also caused inactivation of GS and led to neuronal cell death examined in a hippocampal cell culture system. All these detrimental effects of ONOO- were successfully attenuated by the thiol-containing antioxidant tripeptide glutathione. This research shows that ONOO- can oxidatively modify both membranous and cytosolic proteins, affecting both their physical and chemical nature. These findings are discussed with reference to the potential involvement of ONOO- in AD neurodegeneration.
Calcium Metal in Liquid Ammonia for Selective Reduction of Organic Compounds (1996)

Selective reduction of functional groups by use of dissolving calcium metal was performed, and the results are in comparison with those by lithium and sodium metals. Reduction with 2.0−2.2 equiv of calcium led chromone (1) to 4-chromanone (2, 75% yield), coumarin (4) to dihydrocoumarin (5, 76% yield) and 3-(2-hydroxyphenyl)-1-propanol (6, 6% yield), α-tetralone (7) to 1,2,3,4-tetrahydro-1-naphthol (8, 81% yield), and β-methoxystyrene (12) to methyl phenethyl ether (13, 85% yield). Performance of reductions on the same substrates by use of 4.0 equiv of lithium or sodium metal gave over-reduced products. Reduction of indole-3-carboxaldehyde (15) to 3-indolemethanol (16), 1-acetylnaphthalene (17) to 1-acetyl-3,4-dihydronaphthalene (18), and trans-4-phenyl-3-buten-2-one (19) to 4-phenyl-2-butanone (20) were accomplished by use of calcium, lithium, and sodium metals, among which calcium gave the highest yields (80−90%). Being a milder reducing agent than lithium and sodium, calcium metal in liquid ammonia offered a better selectivity.
Disodium cromoglycate can inhibit virus-induced cytopathic effects in vitro. (1977)

Investigations showed: haemoglobin 12 8 g/dl; white cell count 11 3 x 109!l (11 300/mm3), with 15 % eosinophils; blood urea 10-3 mmol/I (62 mg/ 100 ml); blood glucose 5-4 mmol/l (98 mg/100 ml); and serum sodium 129 mmol(mEq)/l, potassium 5-2 mmol(mEq)/l, and chloride 97 mmol (mEq)/l.Chest and abdominal x-ray pictures were normal.Antinuclear factor and thyroid and parietal cell antibodies were absent.The basal plasma cortisol concentration was low and there was no response to prolonged stimulation with tetracosactrin, which confirmed primary adrenocortical failure.Sweat was collected from his back and tested for electrolytes.Two months after treatment with cortisone acetate and fludrocortisone the patient felt well and had gained weight.The skin over his legs was normal.No local treatment was given for the ichthyosis.Much of the hyperpigmentation was reversible.The sweat test was repeated (see table ).Sweat electrolyte concentrations (mmol/l) before and after corticosteroids Before treatmentAfter treatment Sodium (normal 51l9 2SD 42 2) 87-0 18 0 Chloride (normal 29 7-2SD 17 7) 71-0 3-2 Potassium (normal 7-5 ± 2SD 3-2) 3-7 16-0Conversion: SI to traditional units-Sweat electrolytes: 1 mmol/l = 1 mEq, .
Attribute Reduction of Set-valued Information System Based on Dominance Relation (2013)

A new dominance relation isdefined in set-valued information system based on similarity grade of attributevalue sets the problem of attribute reduction and the judgment in set-valuedinformation system are studied, from which a new approach to attributereductions is provided in set-valued information system, and the influence ofsimilarity level on attribute reduction are discussed.
Homologous nucleotide sequences at the 5' termini of messenger RNAs synthesized from the yeast enolase and glyceraldehyde-3-phosphate dehydrogenase gene families. The primary structure of a third yeast glyceraldehyde-3-phosphate dehydrogenase gene. (1983)

Genomic DNA containing a third yeast glyceraldehyde-3-phosphate dehydrogenase structural gene has been isolated on a bacterial plasmid designated pgap11. The complete nucleotide sequence of this structural gene was determined. The gene contains no intervening sequences, codon usage is highly biased, and the nucleotide sequence of the coding portion of this gene is 90% homologous to the other two glyceraldehyde-3-phosphate dehydrogenase genes (Holland, J. P., and Holland, M. J. (1980) J. Biol. Chem. 255, 2596-2605). Based on the extent of nucleotide sequence divergence among the three glyceraldehyde-3-phosphate dehydrogenase genes, it is likely that they arose as a consequence of two duplication events and the gene contained on the hybrid plasmid designated pgap11 is a product of the first duplication event. All three structural genes share extensive nucleotide sequence homology in the 5'-noncoding regions adjacent to the three respective translational initiation codons. The gene contained on pgap11 is not homologous to the others downstream from the respective translational termination codon, however. The 5' termini of messenger RNAs synthesized from the three glyceraldehyde-3-phosphate dehydrogenase and two yeast enolase genes have been mapped to sites ranging from 36 to 82 nucleotides upstream from the respective translational initiation codons. In each case the 5' terminus of the mRNA maps to a region of strong nucleotide sequence homology which is shared by all five structural genes. These latter data confirm that all five structural genes are expressed during vegetative cell growth and further support the hypothesis that a portion of the 5'-noncoding flanking region of the yeast glyceraldehyde-3-phosphate dehydrogenase and enolase genes evolved from a common precursor sequence.
Liquid marbles: principles and applications (2011)

The ability of particles to adhere to a fluid–fluid interface can stabilize the formation of an emulsion. When the encapsulated fluid is a liquid and the fluid in which it is immersed is air, the object formed is called a “Liquid Marble”. Here we discuss how liquid marbles can be created, their fundamental properties and their transport and potential uses. We show how they arise naturally as an insect waste disposal system, from impact of droplets on powders and on hydrophobic soil, and in the mixing of particulate containing liquids. Our principal aim is to review research on macroscopic single marbles and their potential uses in sensors and droplet microfluidics. However, we also illustrate the similarity between liquid marbles, Pickering emulsions and “Dry Water”, and the potential application of assemblies of liquid marbles within cosmetics and pharmaceutical formulations. Finally, we discuss how modifying the surface structure of particles and providing heterogeneous surface chemistry on particles (e.g. Janus particles) might provide new types of liquid marbles and applications.
Estrogen—the Good, the Bad, and the Unexpected (2005)

I. IntroductionII. The Concept of Local Estrogen BiosynthesisIII. Aromatase and Its GeneIV. The ArKO MouseV. The ArKO Mouse and the Metabolic SyndromeVI. The Metabolic Syndrome in Humans with Natural Mu-tations in AromataseVII. Summary of the Metabolic Effects of EstrogensVIII. Local Aromatase Expression in the Breast and BreastCancerIX. Role of LRH-1 in Aromatase Expression in the Breast
Parabacteroides johnsonii sp. nov., isolated from human faeces (2007)

A bacterial strain isolated from human faeces, M-165T, was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile, menaquinone profile and phylogenetic position (based on 16S rRNA gene sequence analysis). A 16S rRNA gene sequence analysis showed that the isolate was a member of the genus Parabacteroides. Strain M-165T was closely related to Parabacteroides merdae strains, showing 98 % sequence similarity. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative, rod-shaped and was able to grow on media containing 20 % bile. Although the phenotypic characteristics of the strain M-165T were similar to those of P. merdae, the isolate could be differentiated from P. merdae by means of API 20A tests for L-arabinose and L-rhamnose fermentation. DNA-DNA hybridization experiments revealed the genomic distinctiveness of the novel strain with respect to P. merdae JCM 9497T (<or=60 % DNA-DNA relatedness). The DNA G+C content of the strain is 47.6 mol%. On the basis of these data, strain M-165T represents a novel species of the genus Parabacteroides, for which the name Parabacteroides johnsonii sp. nov. is proposed. The type strain is M-165T (=JCM 13406T=DSM 18315T).
The Age-Related Eye Disease Study Severity Scale for Age-Related Macular Degeneration (2005)

The scale provides convenient risk categories and has acceptable reproducibility. Progression along it may prove to be useful as a surrogate for progression to advanced AMD.
Seasonal Variation in Migraine (2005)

Our group has previously shown that migraineurs, as opposed to individuals with other headaches, are more likely to have headache during the bright arctic summer than during the polar night season. We set out to investigate the impact of seasonal light exposure in migraine with and without aura. We performed a questionnaire-based study of 169 female volunteer migraineurs in an arctic area where light conditions during summer and winter seasons are extreme. We included 98 patients with migraine with aura (MA) and 71 with migraine without aura (MoA). One hundred and seven patients (63%) reported seasonal variation in migraine attack frequency. Close to half (47%) of patients with aura, but only 17% of patients without aura, reported more frequent attacks during the light season (P < 0.001). Patients with MA reported interictal light hypersensitivity and light exposure as an attack precipitating factor significantly more often than individuals with MoA. They also reported significantly more frequent use of sunglasses to prevent attacks. We found no significant differences between MA and MoA as regards sleep disturbances, use of oral contraceptives, impact of headache or circadian variations. Seasonal periodicity of migraine in an arctic population with more frequent attacks during the light season is a convincing phenomenon in MA but not in MoA. The amount of light exposure seems to be pivotal to this variation.
Interactions of Sequence Variants inInterleukin-1 Receptor–Associated Kinase4and theToll-Like Receptor 6-1-10Gene Cluster Increase Prostate Cancer Risk (2006)

Chronic or recurrent inflammation has been suggested as a causal factor in several human malignancies, including prostate cancer. Genetic predisposition is also a strong risk factor in the development of prostate cancer. In particular, Toll-like receptors (TLR), especially the TLR6-1-10 gene cluster, are involved in prostate cancer development. Interleukin-1 receptor-associated kinases (IRAK) 1 and 4 are critical components in the TLR signaling pathway. In this large case-control study, we tested two hypotheses: (a) sequence variants in IRAK1 and IRAK4 are associated with prostate cancer risk and (b) sequence variants in IRAK1/4 and TLR1-6-10 interacts and confers a stronger risk to prostate cancer. We analyzed 11 single nucleotide polymorphisms (four in IRAK1 and seven in IRAK4) among 1,383 newly diagnosed prostate cancer patients and 780 population controls in Sweden. Although the single-nucleotide polymorphisms in IRAK1 and IRAK4 alone were not significantly associated with prostate cancer risk, one single-nucleotide polymorphism in IRAK4, when combined with the high-risk genotype at TLR6-1-10, conferred a significant excess risk of prostate cancer. In particular, men with the risk genotype at TLR6-1-10 and IRAK4-7987 CG/CC had an odds ratio of 9.68 (P = 0.03) when compared with men who had wild-type genotypes. Our findings suggest synergistic effects between sequence variants in IRAK4 and the TLR 6-1-10 gene cluster. Although this study was based on a priori hypothesis and was designed to address many common issues facing this type of study, our results need confirmation in even larger studies.
Fourth-generation sequencing in the cell and the clinic (2014)

Nearly 40 years ago, DNA was sequenced for the first time. Since then, DNA sequencing has undergone continuous development, passing through three generations of sequencing technology. We are now entering the beginning of a new phase of genomic analysis in which massively parallel sequencing is performed directly in the cell. Two methods have recently been described for in situ RNA sequencing, one targeted and one untargeted, that rely on ligation chemistry. This fourth generation of sequencing technology opens up prospects for transcriptomic analysis, biomarker validation, diagnosis and patient stratification for cancer treatment.
Production of recombinant protein G through high-density fermentation of engineered bacteria as well as purification (2015)

Recombinant Streptococcus Protein G (PG) is a cell wall protein, which, when combined with mammal immunoglobulin, is used in separating antibody technology. High-density fermentation technologies using an engineered recombinant PG-producing bacteria as well as PG separation and purification technologies have a direct impact on the availability and application of PG. Through primary and secondary seed cultivation, a recombinant E. coli strain was subjected to high-density fermentation with controlled feed supplement concentration under stimulation with isopropyl β-D-1-thiogalactopyranoside. The present study investigated the effect of factors including inoculum size, oxygen levels, pH and the cultivating method on the fermentation process, as well as the effect of the separation and purification technologies, including ultrasonication, nickel column affinity chromatography, Sephadex G-25 gel filtration chromatography and diethylaminoethanol-sepharose fast flow ion exchange chromatography on the yield and purity of PG. The efficiency of extraction was detected using SDS-PAGE. High-density fermentation yielded 80-150 g/l of bacteria and 1 g PG was obtained from one liter broth. The present study delivered a highly efficient novel method via which PG can be obtained at a high concentration and a purity >95%.
Spirochetes Isolated from the Blood of Two Patients with Lyme Disease (1983)

We isolated spirochetes from the blood of 2 of 36 patients in Long Island and Westchester County, New York, who had signs and symptoms suggestive of Lyme disease. The spirochetes were morphologically similar and serologically identical to organisms recently found to infect lxodes dammini ticks, which are endemic to the area and have been epidemiologically implicated as vectors of Lyme disease. In both patients, there was a rise in specific antispirochetal antibodies in paired specimens of serum. We conclude that the l. dammini spirochete has an etiologic role in Lyme disease.
Electronic Communication through π‐Conjugated Wires in Covalently Linked Porphyrin/C60 Ensembles (2005)

Novel photo- and electroactive triads, in which pi-conjugated p-phenylenevinylene oligomers (oPPVs) of different length are connected to a photoexcited-state electron donor (i.e., zinc tetraphenylporphyrin) and an electron acceptor (i.e., C(60)), were designed, synthesized, and tested as electron-transfer model systems. A detailed physicochemical investigation, concentrating mainly on long-range charge separation and charge recombination and kinetics, revealed small attenuation factors beta of 0.03+/-0.005 A(-1). Energy matching between the HOMO levels of C(60) and oPPVs emerged as a key parameter for supporting molecular-wire-like behavior: It favors rapid and efficient electron or hole injection into the oPPV wires. Large electronic coupling values were determined as a result of paraconjugation in the oPPV moieties.
Insulin and its receptor: structure, function and evolution (2004)

I present here a personal perspective on more than three decades of research into the structural biology of the insulin-receptor interaction. The solution of the three-dimensional structure of insulin in 1969 provided a detailed understanding of the insulin surfaces involved in self-assembly. In subsequent years, hundreds of insulin analogues were prepared by insulin chemists and molecular biologists, with the goal of relating the structure to the biological function of the molecule. The design of methods for direct receptor-binding studies in the 1970s, and the cloning of the receptor in the mid 1980s, provided the required tools for detailed structure-function studies. In the absence of a full three-dimensional structure of the insulin-receptor complex, I attempt to assemble the existing pieces of the puzzle generated by our and other laboratories, in order to generate a plausible mechanistic model of the insulin-receptor interaction that explains its kinetics and negative cooperativity.
Growing Unculturable Bacteria (2012)

The bacteria that can be grown in the laboratory are only a small fraction of the total diversity that exists in nature. At all levels of bacterial phylogeny, uncultured clades that do not grow on standard media are playing critical roles in cycling carbon, nitrogen, and other elements, synthesizing novel natural products, and impacting the surrounding organisms and environment. While molecular techniques, such as metagenomic sequencing, can provide some information independent of our ability to culture these organisms, it is essentially impossible to learn new gene and pathway functions from pure sequence data. A true understanding of the physiology of these bacteria and their roles in ecology, host health, and natural product production requires their cultivation in the laboratory. Recent advances in growing these species include coculture with other bacteria, recreating the environment in the laboratory, and combining these approaches with microcultivation technology to increase throughput and access rare species. These studies are unraveling the molecular mechanisms of unculturability and are identifying growth factors that promote the growth of previously unculturable organisms. This minireview summarizes the recent discoveries in this area and discusses the potential future of the field.
Recombinant Human Tumor Necrosis Factor Produces Hemodynamic Changes Characteristic of Sepsis and Endotoxemia (1989)

Tumor necrosis factor (TNF) is a macrophage-derived peptide mediator released during endotoxemia and sepsis. We examined the systemic and visceral hemodynamic response to low doses of human recombinant TNF in rats. Each animal received a 30-minute intravenous infusion of either saline solution (n = 8) or TNF (n = 8) in a dose of 0.25 mg/kg or 1.0 mg/kg. Thermodilution cardiac output, blood pressure, pulse, vascular resistance, effective hepatic blood flow (galactose clearance), and effective renal plasma flow (p-aminohippurate clearance) were determined at time = 2 hours. The 0.25-mg/kg dose had no apparent effect on systemic hemodynamics. The 1.0-mg/kg dose produced a hyperdynamic systemic circulatory response with an elevated cardiac output, tachycardia, and a diminished systemic vascular resistance. Effective hepatic blood flow was exquisitely sensitive to even the lowest dose of TNF, with a 29% reduction despite the normal cardiac output. Renal flow was unaffected by either dose. Tumor necrosis factor-induced systemic and visceral hemodynamic changes are remarkably similar to those seen in gram-negative sepsis, suggesting that TNF may occupy a proximal position in the pathogenesis of overwhelming infection.