gebhart/patrepeval huggingface dataset:
Affinity chromatography of mammalian and yeast nucleosomes. Two modes of binding of transcriptionally active mammalian nucleosomes to organomercurial-agarose columns, and contrasting behavior of the active nucleosomes of yeast. (1990)

The reasons for the selective binding of nucleosomes from transcriptionally active genes to the organomercurial-agarose columns have been investigated. At least two modes of binding are identified by a new two-stage elution procedure that discriminates between nucleosomes which are retained by the Hg-column because of their salt-labile associations with SH-reactive non-histone proteins, and nucleosomes in which a conformational change has made the thiol groups of histone H3 accessible to SH-reagents. The first class is released from the column in 0.5 M NaCl; the second class is eluted in 10 mM dithiothreitol which displaces the bound H3-thiols. In mammalian cells, both classes of Hg-bound nucleosomes are enriched in the DNA sequences being transcribed at the time, and their histones H3 and H4 are hyperacetylated. In yeast cells, in which histone H3 lacks cysteinyl residues, only a small fraction of nucleosomes binds to the mercury column, and it has no enrichment of DNA sequences derived from the actively transcribed GAL, HIS4, and ACT1 genes. Since few nucleosomes remain on the column after elution in 0.5 M NaCl, the bound nucleosomes of yeast are retained primarily because of salt-labile associations with thiol-reactive nonhistone proteins. Thus, the presence of histone H3-thiol groups appears to be essential for the mercury binding of the second class of nucleosomes which, in mammalian cells, is derived from the transcriptionally active genes. The results support models of reversible nucleosome unfolding during transcription in mammalian cells to reveal previously inaccessible H3-SH groups, and they also indicate that other thiol-containing proteins, including high mobility group 1 and 2, become closely but transiently associated with the chromatin subunits during their transcription.
Designed heterodimerizing leucine zippers with a ranger of pIs and stabilities up to 10−15 M (2001)

Abstract We have designed a heterodimerizing leucine zipper system to target a radionuclide to prelocalized noninternalizing tumor‐specific antibodies. The modular nature of the leucine zipper allows us to iteratively use design rules to achieve specific homodimer and heterodimer affinities. We present circular‐dichroism thermal denaturation measurements on four pairs of heterodimerizing leucine zippers. These peptides are 47 amino acids long and contain four or five pairs of electrostatically attractive g ↔ e′ (i, i′ +5) interhelical heterodimeric interactions. The most stable heterodimer consists of an acidic leucine zipper and a basic leucine zipper that melt as homodimers in the micro (T m = 28°C) or nanomolar (T m = 40°C) range, respectively, but heterodimerize with a T m &gt;90°C, calculated to represent femtamolar affinities. Modifications to this pair of acidic and basic zippers, designed to destabilize homodimerization, resulted in peptides that are unstructured monomers at 4 μM and 6°C but that heterodimerize with a T m = 74°C or K d(37) = 1.1 × 10 −11 M. A third heterodimerizing pair was designed to have a more neutral isoelectric focusing point (pI) and formed a heterodimer with T m = 73°C. We can tailor this heterodimerizing system to achieve pharmacokinetics aimed at optimizing targeted killing of cancer cells.
ChemInform Abstract: Metal‐Assisted Aldol Condensation of Chiral α‐Halogenated Imide Enolates: A Stereocontrolled Chiral Epoxide Synthesis. (1986)

Abstract Amethodology for preparing chiral α,β‐epoxy esters by a modified Darzens procedure is described.
Role of syndecan-1 in leukocyte-endothelial interactions in the ocular vasculature. (2002)

The results indicate a role for syndecan-1 as a negative regulator of leukocyte-mediated inflammatory responses. Thus, syndecan-1 could have use as a target for prevention of pathologic leukocyte-endothelial interactions in angiogenesis and inflammation.
The First Negishi Cross-Coupling Reaction of Two Alkyl Centers Utilizing a Pd−N-Heterocyclic Carbene (NHC) Catalyst (2005)

The development of an NHC-based system capable of cross-coupling sp(3)-sp(3) centers in high yield has been a long-standing challenge. This communication describes the use of a Pd-NHC catalytic system that achieves room-temperature Negishi cross-couplings of unactivated, primary bromides and alkyl organozinc reagents with a variety of functionality. [reaction: see text]
High-Transparency, Self-Standable Gel-SLIPS Fabricated by a Facile Nanoscale Phase Separation (2013)

Slippery liquid-infused porous surfaces (SLIPSs) that were both highly transparent and free-standing (self-standability) were fabricated by an extremely simple process using non-solvent-induced phase separation (NIPS) of a poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP)/di-n-butyl phthalate solution. We call these "Gel-SLIPS" because the porous PVDF-HFP film fabricated using the NIPS process has been used as a gel electrolyte in a lithium-ion battery. In previous reports, SLIPS fabrication required complex processes, high annealing temperatures, and drying. Gel-SLIPS can be fabricated from the adjusted solution and the lubricant at room temperature and pressure in 5 min by squeegee, cast, or dip methods. NIPS is based on a quick phase separation process in situ, and reduction of the surface energy is not required because of the considerable fluorine in PVDF-HFP. Moreover, because of the flexible nanonetwork structure of PVDF-HFP, Gel-SLIPS exhibited self-standability and high transmittance (>87% at 600 nm). Gel-SLIPS is thus highly versatile in terms of the fabrication process and film characteristics.
National Study of Emergency Department Visits for Burn Injuries, 1993 to 2004 (2007)

No studies have examined U.S. burn epidemiology from the perspective of the Emergency Department. We sought to describe patient characteristics, injury types, and Emergency Department practice patterns. Data were collected from the National Hospital Ambulatory Medical Care Survey between 1993 and 2004. Emergency Department visit rates for burn injury decreased from 1993 to 2004 with a peak of 2.8 (95% confidence interval [CI] 2.1-3.4) per 1000 U.S. population in 1995 and a nadir of 1.6 (95% CI 1.2-2.0) per 1000 in 2004. The Emergency Department visit rate for burn injuries was greater for men than women (2.7 [95% CI 2.4-3.0] vs 1.8 [95% CI 1.6-2.0] per 1000) and for black than white subjects (3.4 [95% CI 2.8-3.9] vs 2.1 [95%CI 1.9-2.3] per 1000), though all these groups showed decreases. Emergency Department visit rates for burns were greatest in the first and third decades (3.3 [95% CI 2.8-3.7] and 3.5 [95% CI 3.0-4.0] per 1000, respectively) and decreased thereafter. The upper extremity was the most commonly burned part of the body (37% of total) and most burns of specified depth were partial thickness (48% of total). Less than half of patients received analgesics (47%) or topical antibiotics (38%). Emergency Department visits for burns are declining, but rates remain high in men, black individuals, and children. Burn-prevention efforts should target these groups. Upper-extremity and partial-thickness injuries are common, and less than half of patients receive analgesics or topical antibiotics. Collaboration between burn specialists and Emergency Department personnel should focus on the care of these types of injuries.
Coping with complexity - the role of distributed information in environmental and resource management. (2000)

If humankind is to succeed in managing the world's resources, and in conserving the biodiversity of nature, then we need really comprehensive and reliable information -a global information warehouse -from which to plan.Building and maintaining such a system is a huge task.Contributing information needs to be a routine part of the activity of every organisation.Nor can a global warehouse be centralised; it needs to be distributed across every contributing agency.Achieving this goal will require work in three areas.First, data collation requires data standards directed towards crucial problems, the systematic use of metadata, and the coordination of data sources via information networks.Secondly, interpretation will require flexible query systems.These can exploit new object technologies that makes possible distributed processing.Finally, and perhaps the greatest challenge of all, is to interpret vast amounts of information effectively.The new field of complexity theory is beginning to provide relevant principles and methods. GreenCoping with complexity the role of distributed...
Interrogating a High-Density SNP Map for Signatures of Natural Selection (2002)

Identifying genomic regions that have been targets of natural selection remains one of the most important and challenging areas of research in genetics. To this end, we report an analysis of 26,530 single nucleotide polymorphisms (SNPs) with allele frequencies that were determined in three populations. Specifically, we calculated a measure of genetic differentiation, F(ST), for each locus and examined its distribution at the level of the genome, the chromosome, and individual genes. Through a variety of analyses, we have found statistically significant evidence supporting the hypothesis that selection has influenced extant patterns of human genetic variation. Importantly, by contrasting the F(ST) of individual SNPs to the empirical genome-wide distribution of F(ST), our results are not confounded by tenuous assumptions of population demographic history. Furthermore, we have identified 174 candidate genes with distribution of genetic variation that indicates that they have been targets of selection. Our work provides a first generation natural selection map of the human genome and provides compelling evidence that selection has shaped extant patterns of human genomic variation.
Association of Hashimoto's thyroiditis with thyroid cancer (2014)

This prospective study investigates the relationship between Hashimoto's thyroiditis (HT) and thyroid cancer (TC) in patients with thyroid nodules (TNs). We prospectively examined 2100 patients with 2753 TNs between January 5, 2010 and August 15, 2013. A total of 2023 patients with 2669 TNs met the inclusion criteria of TN ≥5 mm and age ≥18 years. Each patient had blood drawn before fine-needle aspiration biopsy (FNAB) for the following measurements: TSH, free thyroxine, free tri-iodothyronine, thyroid peroxidase antibody (TPOAb), and antithyroglobulin antibody (TgAb). Diagnosis of TC was based on pathology analysis of thyroidectomy tissue. The associations of TC with the independent variables were determined by univariate and multivariate logistic regression analysis and reported as adjusted odds ratio (OR) with 95% CI. A total of 248 malignant nodules were found in 233 patients. There was an association of TC with both increased serum TgAb concentration and age<45 years. An elevated serum TgAb concentration was found in 10.2% of patients (182 of 1790) with benign nodules as compared with 20.6% of patients (48 of 233) with malignant nodules (P≤0.0001). TgAb (OR=2.24: CI=1.57, 3.19) and TSH ≥1 μIU/ml (OR (95% CI)) OR: 1.49 (1.09, 2.03) were significant predictors of TC in multivariate analysis controlling for age and gender. TC was not associated with serum concentrations of TPOAb. In patients with TN, elevated serum concentration of TgAb and TSH ≥1 μIU/ml are independent predictors for TC. The association between HT and TC is antibody specific.
Engineering Cytochrome P450 BM-3 for Oxidation of Polycyclic Aromatic Hydrocarbons (2001)

Cytochrome P450 BM-3, a self-sufficient P450 enzyme from Bacillus megaterium that catalyzes the subterminal hydroxylation of long-chain fatty acids, has been engineered into a catalyst for the oxidation of polycyclic aromatic hydrocarbons. The activities of a triplet mutant (A74G/F87V/L188Q) towards naphthalene, fluorene, acenaphthene, acenaphthylene, and 9-methylanthracene were 160, 53, 109, 287, and 22/min, respectively. Compared with the activities of the wild type towards these polycyclic aromatic hydrocarbons, those of the mutant were improved by up to 4 orders of magnitude. The coupling efficiencies of the mutant towards naphthalene, fluorene, acenaphthene, acenaphthylene, and 9-methylanthracene were 11, 26, 5.4, 15, and 3.2%, respectively, which were also improved several to hundreds fold. The high activities of the mutant towards polycyclic aromatic hydrocarbons indicate the potential of engineering P450 BM-3 for the biodegradation of these compounds in the environment.
Kinetics of hydrolysis of dimeric and trimeric methionine hydroxy analog free acid under physiological conditions of pH and temperature (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetics of hydrolysis of dimeric and trimeric methionine hydroxy analog free acid under physiological conditions of pH and temperatureHans G. Koban and Edgar KobersteinCite this: J. Agric. Food Chem. 1984, 32, 2, 393–396Publication Date (Print):March 1, 1984Publication History Published online1 May 2002Published inissue 1 March 1984https://doi.org/10.1021/jf00122a052Request reuse permissionsArticle Views79Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (461 KB) Get e-Alertsclose Get e-Alerts
Tracking Femtosecond Laser Pulses in Space and Time (2001)

We show that the propagation of a femtosecond laser pulse inside a photonic structure can be directly visualized and tracked as it propagates using a time-resolved photon scanning tunneling microscope. From the time-dependent and phase-sensitive measurements, both the group velocity and the phase velocity are unambiguously and simultaneously determined. It is expected that this technique will find applications in the investigation of the local dynamic behavior of photonic crystals and integrated optical circuits.
Effect of an Intravenous Gammaglobulin Preparation on the Opsonophagocytic Activity of Preterm Serum against Coagulase‐Negative Staphylococci (1990)

ABSTRACT. Recent reports have described cases of septicaemia caused by coagulase‐negative staphylococci in preterm neonates, mainly due to the use of artificial intravenous devices. It was of interest to examine if intravenous immunoglobulin therapy, known to be effective in group B streptococcal infections of neonates, had a similar beneficial effect in coagulase‐negative staphylococcal infections. Opsonophagocytosis of coagulase‐negative staphylococci by normal polymorphonuclear leukocytes in the presence of cord blood serum supplemented with the commercial IgG preparation ‘Sandoglobulin’ was investigated, using luminol‐dependent chemiluminescence. It was found that with two different coagulase‐negative staphylococcal strains, Sandoglobulin had a concentration‐dependent enhancing effect on the chemiluminescent response. This effect was demonstrated in the presence of native as well as inactivated cord blood serum and in the presence of sera from preterm infants (28‐33 weeks). It is concluded that intravenous Sandoglobulin therapy may be effective in the treatment of preterm infants with severe coagulase‐negative staphylococcal infections.
Preparation, Stabilization and Some Properties of Purified Human Plasmin* (1964)

Summary 1. Lysine increased the solubility, decreased the SK requirement and increased the stability of plasmin prepared from purified plasminogen by SK activation. 2. A procedure is presented for the rapid and quantitative conversion of plasminogen to plasmin and storage of the plasmin in stable form at neutral pH as a lyophilized powder. 3. Approximately 10% for the plasminogen molecule was split off during its activation. No carbohydrate was lost. 4. The plasmin isolated was homogeneous in the ultracentrifuge at pH 2.5 and was quantitatively convertible to plasminogen activator by the addition of SK.
Synthesis and biological evaluation of some cyclic phosphoramidate nucleoside derivatives (1990)

(E)-5-(2-Bromovinyl)-2'-deoxy-5'-O-(3-methyl-2-oxo-5-formyl-1,3,2- oxazaphosphacyclopentan-2-yl)uridine has been synthesized and, under physiological conditions and without the necessity for enzyme activity, has been shown to yield the 5'-nucleotide in vitro. Unfortunately this compound is not sufficiently stable in solution for it to be tested in vivo. The biological properties of this and some related derivatives of (E)-5-(2-bromovinyl)-2'-deoxyuridine and acyclovir have been evaluated in in vitro and in vivo systems designed to show the effects of any intracellular liberation of the nucleotide. Although some of the derivatives are probably acting as prodrugs of the active nucleosides, there is no evidence for the liberation of meaningful concentrations of the 5'-nucleotide by any of the compounds.
An Experimental System for Imaging the Reversible Adsorption of Amphiphiles at Aqueous−Liquid Crystal Interfaces (2002)

We report an experimental system that permits optical imaging of the reversible adsorption of amphiphiles at stable, planar interfaces formed between aqueous phases and immiscible thermotropic liquid crystals. Copper grids (hole sizes of 19−292 μm and thicknesses of 18−20 μm) supported on glass surfaces treated using octadecyltrichlorosilane were impregnated with nematic 4-cyano-4‘-pentylbiphenyl (5CB). Films of 5CB confined within the grids were stable (did not dewet the grid) to immersion into either water, aqueous solutions of sodium dodecyl sulfate (SDS), or aqueous solutions of SDS containing NaCl. Whereas the anchoring of 5CB on the copper grid dominated the appearance of the 5CB when using grids with hole sizes of 19 μm, reversible changes in the orientation of the liquid crystal (observed using polarized light) caused by adsorption of SDS at the liquid crystal−aqueous interface were readily observed when using grids with hole sizes larger than 19 μm. With increasing concentrations of SDS in the aqueous phase, a series of reproducible and distinct surface-driven distortions were observed within the 5CB confined to the grid. We also observed the effects of added NaCl on the distortions induced within the liquid crystal to be consistent with increased adsorption of SDS caused by screening of the electrostatic interactions between the SDS adsorbed at the interface. This result suggests that the orientation of the 5CB is influenced by the areal density of SDS molecules at the liquid crystal−aqueous interface (probably through steric interactions). Because the aqueous phase contacting the liquid crystal can be exchanged (thus permitting the addition and removal of reactants), this experimental system is a simple and broadly useful one for investigations in which liquid crystals are used to amplify interfacial phenomena at fluid interfaces into optical images.
Cholesterol-Lowering Probiotics as Potential Biotherapeutics for Metabolic Diseases (2012)

Cardiovascular diseases are one of the major causes of deaths in adults in the western world. Elevated levels of certain blood lipids have been reported to be the principal cause of cardiovascular disease and other disabilities in developed countries. Several animal and clinical trials have shown a positive association between cholesterol levels and the risks of coronary heart disease. Current dietary strategies for the prevention of cardiovascular disease advocate adherence to low-fat/low-saturated-fat diets. Although there is no doubt that, in experimental conditions, low-fat diets offer an effective means of reducing blood cholesterol concentrations on a population basis, these appear to be less effective, largely due to poor compliance, attributed to low palatability and acceptability of these diets to the consumers. Due to the low consumer compliance, attempts have been made to identify other dietary components that can reduce blood cholesterol levels. Supplementation of diet with fermented dairy products or lactic acid bacteria containing dairy products has shown the potential to reduce serum cholesterol levels. Various approaches have been used to alleviate this issue, including the use of probiotics, especially Bifidobacterium spp. and Lactobacillus spp.. Probiotics, the living microorganisms that confer health benefits on the host when administered in adequate amounts, have received much attention on their proclaimed health benefits which include improvement in lactose intolerance, increase in natural resistance to infectious disease in gastrointestinal tract, suppression of cancer, antidiabetic, reduction in serum cholesterol level, and improved digestion. In addition, there are numerous reports on cholesterol removal ability of probiotics and their hypocholesterolemic effects. Several possible mechanisms for cholesterol removal by probiotics are assimilation of cholesterol by growing cells, binding of cholesterol to cellular surface, incorporation of cholesterol into the cellular membrane, deconjugation of bile via bile salt hydrolase, coprecipitation of cholesterol with deconjugated bile, binding action of bile by fibre, and production of short-chain fatty acids by oligosaccharides. The present paper reviews the mechanisms of action of anti-cholesterolemic potential of probiotic microorganisms and probiotic food products, with the aim of lowering the risks of cardiovascular and coronary heart diseases.
Oxidative Stress in Neurodegenerative Diseases: From Molecular Mechanisms to Clinical Applications (2017)

Increasing numbers of individuals, particularly the elderly, suffer from neurodegenerative disorders. These diseases are normally characterized by progressive loss of neuron cells and compromised motor or cognitive function. Previous studies have proposed that the overproduction of reactive oxygen species (ROS) may have complex roles in promoting the disease development. Research has shown that neuron cells are particularly vulnerable to oxidative damage due to their high polyunsaturated fatty acid content in membranes, high oxygen consumption, and weak antioxidant defense. However, the exact molecular pathogenesis of neurodegeneration related to the disturbance of redox balance remains unclear. Novel antioxidants have shown great potential in mediating disease phenotypes and could be an area of interest for further research. In this review, we provide an updated discussion on the roles of ROS in the pathological mechanisms of Alzheimer's disease, Huntington's disease, Parkinson's disease, amyotrophic lateral sclerosis, and spinocerebellar ataxia, as well as a highlight on the antioxidant-based therapies for alleviating disease severity.