gebhart/patrepeval huggingface dataset:
Optimal Selection of SNP Markers for Disease Association Studies (2004)

Genetic association studies with population samples hold the promise of uncovering the susceptibility genes underlying the heritability of complex or common disease. Most association studies rely on the use of surrogate markers, single-nucleotide polymorphism (SNP) being the most suitable due to their abundance and ease of scoring. SNP marker selection is aimed to increase the chances that at least one typed SNP would be in linkage disequilibrium (LD) with the disease causative variant, while at the same time controlling the cost of the study in terms of the number of markers genotyped and samples. Empirical studies reporting block-like segments in the genome with high LD and low haplotype diversity have motivated a marker selection strategy whereby subsets of SNPs that 'tag' the common haplotypes of a region are picked for genotyping, avoiding typing redundant SNPs. Based on these initial observations, a plethora of 'tagging' algorithms for selecting minimum informative subsets of SNPs has recently appeared in the literature. These differ mostly in two major aspects: the quality or correlation measure used to define tagging and the algorithm used for the minimization of the final number of tagging SNPs. In this review we describe the available tagging algorithms utilizing a 3-step unifying framework, point out their methodological and conceptual differences, and make an assessment of their assumptions, performance, and scalability.
Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture (2014)

Integrated 'omics have been used on pure cultures and co-cultures, yet they have not been applied to complex microbial communities to examine questions of perturbation response. In this study, we used integrated 'omics to measure the perturbation response of a cellulose-degrading bioreactor community fed with microcrystalline cellulose (Avicel). We predicted that a pH decrease by addition of a pulse of acid would reduce microbial community diversity and temporarily reduce reactor function in terms of cellulose degradation. However, 16S rDNA gene pyrosequencing results revealed increased alpha diversity in the microbial community after the perturbation, and a persistence of the dominant community members over the duration of the experiment. Proteomics results showed a decrease in activity of proteins associated with Fibrobacter succinogenes 2 days after the perturbation followed by increased protein abundances 6 days after the perturbation. The decrease in cellulolytic activity suggested by the proteomics was confirmed by the accumulation of Avicel in the reactor. Metabolomics showed a pattern similar to that of the proteome, with amino acid production decreasing 2 days after the perturbation and increasing after 6 days. This study demonstrated that community 'omics data provide valuable information about the interactions and function of anaerobic cellulolytic community members after a perturbation.
2′,3′-Anhydrouridine. A useful synthetic intermediate (1998)

2,2′-Anhydro-1-(β-D-arabinofuranosyl)uracil 1 reacts with sodium hydride in dry DMSO to give 2′,3′-anhydrouridine 2. When the latter compound 2 is heated below its melting point or treated with triethylamine in methanol, it isomerises back to the 2,2′-anhydronucleoside 1. Treatment of compound 1 with sodium ethanethiolate or the sodium salt of benzyl mercaptan in the presence of an excess of the corresponding thiol in DMA gives 2′-S-ethyl- or 2′-S-benzyl-2′-thiouridine (4 or 11) in high yield; however, treatment of the 2,2′-anhydronucleoside 1 first with sodium hydride in DMA and then with a deficiency (with respect to sodium hydride) of ethanethiol or benzyl mercaptan gives the corresponding 3′-S-ethyl or 3′-S-benzyl derivative (3 or 12) in high yield. When the 2,2′-anhydronucleoside 1 is allowed to react with an excess of potassium tert-butoxide in DMSO, the 3′,5′-anhydronucleoside 13 is obtained in good yield. The latter compound 13 undergoes hydrolysis in aqueous trifluoroacetic acid to give 1-(β-D-xylofuranosyl)uracil 14 in high yield. The 3′-S-benzyl derivative 12 is converted by Raney nickel desulfurisation into 3′-deoxyuridine 15 which, in turn, is converted into 3′-deoxycytidine 17 in good yield. X-Ray crystallographic data relating to compounds 11 and 12 are also reported.
Digital Diffractive Optics: Analytic Type (2009)

This chapter contains sections titled: Analytic and Numeric Digital Diffractives The Notion of Diffraction Orders Diffraction Gratings Diffractive Optical Elements Diffractive Interferogram Lenses
Personality and the Problems of Everyday Life: The Role of Neuroticism In Exposure and Reactivity to Daily Stressors (1991)

This article investigates mechanisms through which neuroticism leads to distress in daily life. Neuroticism may lead to distress through exposing people to a greater number of stressful events, through increasing their reactivity to those events, or through a mechanism unrelated to environmental events. This article evaluates the relative importance of these three explanations. Subjects were 339 persons who provided daily reports of minor stressful events and mood for 6 weeks. Exposure and reactivity to these minor stressors explained over 40% of the distress difference between high- and low-neuroticism subjects. Reactivity to stressors accounted for twice as much of the distress difference as exposure to stressors. These results suggest that reactions within stressful situations are more important than situation selection in explaining how neuroticism leads to distress in daily life.
Mesoporous Alumina Molecular Sieves (1996)

The hydrolysis of tri-sec-butoxyaluminum in the presence of nonionic surfactants leads to mesoporous alumina molecular sieves with wormlike arrays of channels with uniform diameters in the range 2.4 – 4.7 nm, depending on the nature of the surfactant. Molecular sieves of this type are of interest as possible catalysts and catalyst supports. The transmission electron micrograph of an alumina of this type is shown on the right.
INTACT PROTEIN SEPARATIONS WITH INHERENTLY BIOCOMPATIBLE ORMOCOMP SEPARATION CHIP WITH INTEGRATED ELECTROSPRAY IONIZATION EMITTER (2011)

In this study, inherently biocompatible hybrid polymer, Ormocomp, is introduced to fabrication of monolithicall y integrated capillary electrophoresis electrospray ionization (CE-ESI) microchips. The fabrication process results in very thin (~100 µm), freestanding microchips which facilitates efficient ionization from the microchannel outlet. Thanks to their inherent resistance to biofouling, Ormocomp microchips enable efficient separation of intact proteins without need for any chemical or physical surface modification prior to use. Since no surface active ingredients are required, very simple background electrolytes can be used, which ensures good ionization efficiency, and thus, reliable and high-quality mass spectrometric (MS) detection of the separated proteins.
The Session Initiation Protocol (SIP) Referred-By Mechanism (2004)

The Session Initiation Protocol (SIP) REFER method provides a
mechanism where one party (the referrer) gives a second party (the
referee) an arbitrary URI to reference. If that URI is a SIP URI, the
referee will send a SIP request, often an INVITE, to that URI (the
refer target). This document extends the REFER method, allowing the
referrer to provide information about the REFER request to the refer
target using the referee as an intermediary. This information includes
the identity of the referrer and the URI to which the referrer
referred. The mechanism utilizes S/MIME to help protect this
information from a malicious intermediary. This protection is
optional, but a recipient may refuse to accept a request unless it is
present. [STANDARDS-TRACK]
Antibody‐independent targeted quantification of TMPRSS2‐ERG fusion protein products in prostate cancer (2014)

Fusions between the transmembrane protease serine 2 (TMPRSS2) and ETS related gene (ERG) represent one of the most specific biomarkers that define a distinct molecular subtype of prostate cancer. Studies of TMPRSS2‐ERG gene fusions have seldom been performed at the protein level, primarily due to the lack of high‐quality antibodies suitable for quantitative studies. Herein, we applied a recently developed PRISM (high‐pressure high‐resolution separations with intelligent selection and multiplexing)‐SRM (selected reaction monitoring) strategy for quantifying ERG protein in prostate cancer cell lines and tumors. The highly sensitive PRISM‐SRM assays provided confident detection of 6 unique ERG peptides in both TMPRSS2‐ERG positive cell lines and tissues, but not in cell lines or tissues lacking the TMPRSS2‐ERG rearrangement, clearly indicating that ERG protein expression is significantly increased in the presence of the TMPRSS2‐ERG gene fusion. Significantly, our results provide evidence that two distinct ERG protein isoforms are simultaneously expressed in TMPRSS2‐ERG positive samples as evidenced by the concomitant detection of two mutually exclusive peptides in two patient tumors and in the VCaP prostate cancer cell line. Three peptides, shared across almost all fusion protein products, were determined to be the most abundant peptides, providing “signature” peptides for detection of ERG over‐expression resulting from TMPRSS2‐ERG gene fusion. The PRISM‐SRM assays provide valuable tools for studying TMPRSS2‐ERG gene fusion protein products in prostate cancer.
Comparison of antigen presentation of influenza A nucleoprotein expressed in attenuated AroA- Salmonella typhimurium with that of live virus (1993)

Rationally attenuated strains of Salmonella expressing foreign proteins represent a potentially important vaccine delivery system. The characteristics of Ag presentation of influenza nucleoprotein expressed in an AroA- strain of Salmonella typhimurium (SL3262-pNP-2) have therefore been compared with those of soluble purified nucleoprotein (NP) and infectious influenza virus. This represents three distinct modes of internalization of the same protein into APC. Human monocytes and the monocytic leukemia cell line THP-1 infected with SL3261-pNP-2 were found to present several different epitopes from NP to human CD4+ class II-restricted T lymphocytes. Ag presentation to these T cell clones was enhanced by pretreatment of THP-1 cells with IFN-gamma but not TNF-alpha. Bacterial phagocytosis and Ag presentation of NP were increased after opsonization of Salmonella with immune serum. Macrophages infected with SL3261-pNP-2 were unable to present NP to class I-restricted T cells. In contrast, cells infected with live influenza virus, although recognized by NP-specific class I-restricted CTL, were inefficiently recognized by NP-specific class II-restricted T cells. Ag presentation to CD4+ T cell clones by monocytes of SL3261-pNP-2, purified recombinant NP, and live influenza virus, but not the synthetic peptide 206-229, was inhibited by chloroquine and the protease inhibitors pepstatin A and leupeptin, suggesting that the major route of processing in each case was via the exogenous pathway. T cell recognition of NP via all of these Ag delivery systems was also abrogated by cycloheximide and brefeldin A treatment, indicating a requirement for recently synthesized MHC class II molecules in presentation of whole NP after processing but not for the corresponding synthetic peptide.
Nitric Oxide, Tetrahydrobiopterin, Oxidative Stress, and Endothelial Dysfunction in Hypertension (2008)

Endothelial dysfunction in the setting of cardiovascular risk factors such as hypercholesterolemia, diabetes mellitus, chronic smoking, as well hypertension, is, at least in part, dependent of the production of reactive oxygen species (ROS) and the subsequent decrease in vascular bioavailability of nitric oxide (NO). ROS-producing enzymes involved in increased oxidative stress within vascular tissue include NADPH oxidase, xanthine oxidase, and mitochondrial superoxide producing enzymes. Superoxide produced by the NADPH oxidase may react with NO, thereby stimulating the production of the NO/superoxide reaction product peroxynitrite. Peroxynitrite in turn has been shown to uncouple eNOS, therefore switching an antiatherosclerotic NO producing enzyme to an enzyme that may accelerate the atherosclerotic process by producing superoxide. Increased oxidative stress in the vasculature, however, is not restricted to the endothelium and also occurs within the smooth muscle cell layer. Increased superoxide production has important consequences with respect to signaling by the soluble guanylate cyclase and the cGMP-dependent kinase I, which activity and expression is regulated in a redox-sensitive fashion. The present review will summarize current concepts concerning eNOS uncoupling, with special focus on the role of tetrahydrobiopterin in mediating eNOS uncoupling.
Induction of PC12 cell differentiation by flavonoids is dependent upon extracellular signal‐regulated kinase activation (2004)

Many of the physiological benefits attributed to flavonoids are thought to stem from their potent antioxidant and free radical scavenging properties. Recently, it was shown that flavonoids protect nerve cells from oxidative stress by multiple mechanisms, only one of which is directly related to their antioxidant activity, suggesting that specific flavonoids may have other properties that could make them useful in the treatment of conditions that lead to nerve cell death. In particular, it was asked if any flavonoid could mimic neurotrophic proteins. To examine this possibility, we looked at the ability of flavonoids to induce nerve cell differentiation using PC12 cells. PC12 cells were treated with a variety of flavonoids to determine if there was a correlation between their neuroprotective activity and their neurite outgrowth-promoting activity. In addition, the signaling pathways required for flavonoid-induced differentiation were examined. We found that only a small subset of the flavonoids that were neuroprotective could induce neurite outgrowth by an extracellular signal-regulated kinase-dependent process. There was a strong correlation between the concentrations of the flavonoids that were neuroprotective and the concentrations that induced differentiation. These results suggest that the consumption of specific flavonoids could have further beneficial effects on nerve cells following injury, in pathological conditions or in normal aging.
Synthesis of hydroxystilbenes and their derivatives via Heck reaction (2007)

A group of differently substituted acetoxy- and methoxystilbenes were synthesised via Heck reaction. A comparison between the use--as coupling reagents--of iodobenzene derivatives and diazonium salts was performed. A successful microwave-assisted demethylation by pyridine hydrochloride of some methoxystilbenes was carried out.
Recombinant Parainfluenza Virus 5 Expressing Hemagglutinin of Influenza A Virus H5N1 Protected Mice against Lethal Highly Pathogenic Avian Influenza Virus H5N1 Challenge (2012)

ABSTRACT A safe and effective vaccine is the best way to prevent large-scale highly pathogenic avian influenza virus (HPAI) H5N1 outbreaks in the human population. The current FDA-approved H5N1 vaccine has serious limitations. A more efficacious H5N1 vaccine is urgently needed. Parainfluenza virus 5 (PIV5), a paramyxovirus, is not known to cause any illness in humans. PIV5 is an attractive vaccine vector. In our studies, a single dose of a live recombinant PIV5 expressing a hemagglutinin (HA) gene of H5N1 (rPIV5-H5) from the H5N1 subtype provided sterilizing immunity against lethal doses of HPAI H5N1 infection in mice. Furthermore, we have examined the effect of insertion of H5N1 HA at different locations within the PIV5 genome on the efficacy of a PIV5-based vaccine. Interestingly, insertion of H5N1 HA between the leader sequence, the de facto promoter of PIV5, and the first viral gene, nucleoprotein (NP), did not lead to a viable virus. Insertion of H5N1 HA between NP and the next gene, V/phosphorprotein (V/P), led to a virus that was defective in growth. We have found that insertion of H5N1 HA at the junction between the small hydrophobic (SH) gene and the hemagglutinin-neuraminidase (HN) gene gave the best immunity against HPAI H5N1 challenge: a dose as low as 1,000 PFU was sufficient to protect against lethal HPAI H5N1 challenge in mice. The work suggests that recombinant PIV5 expressing H5N1 HA has great potential as an HPAI H5N1 vaccine.
Theranostics Using Antibodies and Antibody-Related Therapeutics (2017)

In theranostics, radiolabeled compounds are used to determine a treatment strategy by combining therapeutics and diagnostics in the same agent. Monoclonal antibodies (mAbs) and antibody-related therapeutics represent a rapidly expanding group of cancer medicines. Theranostic approaches using these drugs in oncology are particularly interesting because antibodies are designed against specific targets on the tumor cell membrane and immune cells as well as targets in the tumor microenvironment. In addition, these drugs are relatively easy to radiolabel. Noninvasive molecular imaging techniques, such as SPECT and PET, provide information on the whole-body distribution of radiolabeled mAbs and antibody-related therapeutics. Molecular antibody imaging can potentially elucidate drug target expression, tracer uptake in the tumor, tumor saturation, and heterogeneity for these parameters within the tumor. These data can support drug development and may aid in patient stratification and monitoring of the treatment response. Selecting a radionuclide for theranostic purposes generally starts by matching the serum half-life of the mAb or antibody-related therapeutic and the physical half-life of the radionuclide. Furthermore, PET imaging allows better quantification than the SPECT technique. This information has increased interest in theranostics using PET radionuclides with a relatively long physical half-life, such as <sup>89</sup>Zr. In this review, we provide an overview of ongoing research on mAbs and antibody-related theranostics in preclinical and clinical oncologic settings. We identified 24 antibodies or antibody-related therapeutics labeled with PET radionuclides for theranostic purposes in patients. For this approach to become integrated in standard care, further standardization with respect to the procedures involved is required.
Dehydroepiandrosterone Retards Atherosclerosis Formation Through Its Conversion to Estrogen (2000)

Dehydroepiandrosterone (DHEA) is speculated to have an antiatherosclerotic effect, although the mechanism of action remains unclear. The objective of the current study was to determine whether the antiatherosclerotic effect of DHEA is related to its conversion to estrogen and to define the role of nitric oxide (NO) in the antiatherosclerotic effect of DHEA. Forty-eight oophorectomized rabbits were divided into 5 groups and fed the following diets for 10 weeks: group 1, a regular rabbit diet plus 1% cholesterol (a high-cholesterol diet [HCD]); group 2, an HCD plus 0.3% DHEA; group 3, an HCD plus 0.3% DHEA and fadrozole (2.0 mg x kg(-1) x d(-1)), a specific aromatase inhibitor; group 4, an HCD plus 17beta-estradiol (20 microg x kg(-1) x d(-1)); and group 5, a regular diet. Atherosclerotic lesions, lipid deposition in aortic vessels, and basal and stimulated NO release were measured in the aforementioned groups of rabbits. NO release was measured by using an NO-selective electrode as well as by measuring vascular responses and the plasma NO metabolites nitrite and nitrate. The plasma total cholesterol level was increased, but there were no significant differences in lipid profile in the 4 groups of rabbits that were fed the HCD. The area occupied by atherosclerosis in the thoracic aorta was diminished by approximately 60% in the DHEA-treated rabbits (group 2) compared with the HCD group of rabbits (group 1); there was a corresponding 80% decrease in the estradiol group (group 4) but only a 30% decrease in the DHEA plus fadrozole group (group 3). In the aortas of rabbits from groups 1 and 3, the acetylcholine-induced and tone-related basal NO-mediated relaxations were diminished compared with those of the controls (group 5). However, these relaxations were restored in the aortas of group 2 and 4 rabbits, and an increase in NO release was observed in groups 2 and 4 compared with groups 1 and 3, as measured by an NO-selective electrode. Injection of neither solvent (20% ethanol/distilled water) nor fadrozole significantly affected the atherosclerotic area or the NO-related responses described above. We conclude that approximately 50% of the total antiatherosclerotic effect of DHEA was achieved through the conversion of DHEA to estrogen. NO may also play a role in the antiatherosclerotic effect of DHEA and 17beta-estradiol.
N.m.r. and molecular-modelling studies of the solution conformation of heparin (1993)

The solution conformations of heparin and de-N-sulphated, re-N-acetylated heparin have been determined by a combination of n.m.r. spectroscopic and molecular-modelling techniques. The 1H- and 13C-n.m.r. spectra of these polysaccharides have been assigned. Observed 1H-1H nuclear Overhauser enhancements (n.O.e.s) have been simulated using the program NOEMOL [Forster, Jones and Mulloy (1989) J. Mol. Graph. 7, 196-201] for molecular models derived from conformational-energy calculations; correlation times for the simulations were chosen to fit experimentally determined 13C spin-lattice relaxation times. In order to achieve good agreement between calculated and observed 1H-1H n.O.e.s it was necessary to assume that the reorientational motion of the polysaccharide molecules was not isotropic, but was that of a symmetric top. The resulting model of heparin in solution is similar to that determined in the fibrous state by X-ray-diffraction techniques [Nieduszynski, Gardner and Atkins (1977) Am. Chem. Soc. Symp. Ser. 48, 73-80].
Fibrosis and diseases of the eye (2007)

Most diseases that cause catastrophic loss of vision do so as a result of abnormal angiogenesis and wound healing, often in response to tissue ischemia or inflammation. Disruption of the highly ordered tissue architecture in the eye caused by vascular leakage, hemorrhage, and concomitant fibrosis can lead to mechanical disruption of the visual axis and/or biological malfunctioning. An increased understanding of inflammation, wound healing, and angiogenesis has led to the development of drugs effective in modulating these biological processes and, in certain circumstances, the preservation of vision. Unfortunately, such pharmacological interventions often are too little, too late, and progression of vision loss frequently occurs. The recent development of progenitor and/or stem cell technologies holds promise for the treatment of currently incurable ocular diseases.