gebhart/patrepeval huggingface dataset:
Analysis of Estrogen Response Element Binding by Genetically Selected Steroid Receptor DNA Binding Domain Mutants Exhibiting Altered Specificity and Enhanced Affinity (1999)

To analyze the role of amino acids in the steroid receptor DNA binding domain (DBD) recognition helix in binding of the receptor to the estrogen response element (ERE), we adapted the powerful P22 challenge phage selection system for use with a vertebrate protein. We used the progesterone receptor DNA binding domain and selected for mutants that gained the ability to bind to the ERE. We used a mutagenesis protocol based on degenerate oligonucleotides to create a large and diverse pool of mutants in which 10 nonconsensus amino acids in the DNA recognition helix of the progesterone receptor DNA binding domain were randomly mutated. After a single cycle of modified P22 challenge phage selection, 37 mutant proteins were identified, all of which lost the ability to bind to the progesterone response element. In gel mobility shift assays, approximately 70% of the genetically selected mutants bound to the consensus ERE with a >4-fold higher affinity than the naturally occurring estrogen receptor DBD. In the P-box region of the DNA recognition helix, the selected mutants contained the amino acids found in the wild-type estrogen receptor DBD, as well as other amino acid combinations seen in naturally occurring steroid/nuclear receptors that bind the aGGTCA half-site. We also obtained high affinity DBDs with Trp(585) as the first amino acid of the P-box, although this is not found in the known steroid/nuclear receptors. In the linker region between the two zinc fingers, G597R was by far the most common mutation. In transient transfections in mammalian cells using promoter interference assays, the mutants displayed enhanced affinity for the ERE. When linked to an activation domain, the transfected mutants activated transcription from ERE-containing reporter genes. We conclude that the P-box amino acids can display considerable variation and that the little studied linker amino acids play an important role in determining affinity for the ERE. This work also demonstrates that the P22 challenge phage genetic selection system, modified for use with a mammalian protein, provides a novel, single cycle selection for steroid/nuclear receptor DBDs with altered specificity and greatly enhanced affinity for their response elements.
Tridimensional Personality Questionnaire Factors in Major Depressive Disorder: Relationship to Anxiety Disorder Comorbidity and Age of Onset (2005)

Features of temperament are related to patterns of anxiety disorder comorbidity and age of onset among patients with MDD. Higher levels of HA and lower levels of RD and NS were associated with an increased risk of anxiety disorder comorbidity in our sample. HA may also be related to early onset of depression.
Invited Review: Redox modulation of skeletal muscle contraction: what we know and what we don't (2001)

Over the past decade, reactive oxygen species (ROS) and nitric oxide (NO) derivatives have been established as physiological modulators of skeletal muscle function. This mini-review addresses the roles of these molecules as endogenous regulators of muscle contraction. The article is organized in two parts. First, established concepts are briefly outlined. This section provides an overview of ROS production by muscle, antioxidant buffers that oppose ROS effects, enzymatic synthesis of NO in muscle, the effects of endogenous ROS on contractile function, and NO as a contractile modulator. Second, a selected group of unresolved topics are highlighted. These more controversial issues include putative source(s) of regulatory ROS, the relative importance of the two NO synthase isoforms constitutively coexpressed by muscle fibers, molecular mechanisms of ROS and NO action, and the physiological relevance of redox regulation. By discussing current questions, as well as the established paradigm, this article is intended to further debate and stimulate research in this area.
Blepharospasm: demographic and clinical survey of 250 patients. (1984)

The pathophysiologic mechanisms of blepharospasm are poorly understood and the condition is often misdiagnosed. In an attempt to improve our understanding of blepharospasm, 250 patients with blepharospasm were surveyed. This heretofore largest reported series of blepharospasm patients reveals findings of clinical and demographic interest. For example, there is a 3 to 1 female preponderance, the age of onset is in the fifth or sixth decade of life in two-thirds of patients, the onset is usually gradual with progressive deterioration and involuntary spasms of other portions of face and body. Although specific ocular abnormalities may predispose a patient to blepharospasm, in most cases the blepharospasm is a form of focal dystonia often associated with other involuntary movements and neurologic abnormalities. Increased awareness of blepharospasm among primary care physicians as well as ophthalmologists, neurologists, psychiatrists, and other specialists should lead to early recognition and management of this disabling condition.
Lyme arthritis. Spirochetes found in synovial microangiopathic lesions. (1985)

In 17 patients with Lyme disease, synovial specimens, obtained by synovectomy or needle biopsy, showed nonspecific villous hypertrophy, synovial cell hyperplasia, prominent microvasculature, lymphoplasmacellular infiltration, and sometimes lymphoid follicles. The larger surgically obtained specimens also showed striking deposition of fibrin in synovial stroma and a form of endarteritis obliterans. In 2 patients, spirochetes were seen in and around blood vessels by the Dieterle silver stain. Compared with 55 cases of other synovial disease, obliterative microvascular lesions were seen only in Lyme synovia, but marked stromal deposition of fibrin seemed nonspecific. These findings imply that the Lyme spirochete may survive for years in affected synovium and may be directly responsible for the microvascular injury.
<i>The Principles of Quantum Mechanics</i> (1958)

We are now going to put some order in our ideas and do theoretical physics. During the years 1925 to 1927, quantum mechanics took shape and accumulated successes. But three persons, and not the least, addressed the question of its structure. In Zürich there was Erwin Schrödinger, in Göttingen David Hilbert, and in Cambridge Paul Adrien Maurice Dirac.KeywordsHilbert SpaceQuantum MechanicScalar ProductState VectorComplex Vector SpaceThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Conserved vertebrate <i>mir-451</i> provides a platform for Dicer-independent, Ago2-mediated microRNA biogenesis (2010)

Canonical animal microRNAs (miRNAs) are generated by sequential cleavage of precursor substrates by the Drosha and Dicer RNase III enzymes. Several variant pathways exploit other RNA metabolic activities to generate functional miRNAs. However, all of these pathways culminate in Dicer cleavage, suggesting that this is a unifying feature of miRNA biogenesis. Here, we show that maturation of miR-451, a functional miRNA that is perfectly conserved among vertebrates, is independent of Dicer. Instead, structure-function and knockdown studies indicate that Drosha generates a short pre-mir-451 hairpin that is directly cleaved by Ago2 and followed by resection of its 3' terminus. We provide stringent evidence for this model by showing that Dicer knockout cells can generate mature miR-451 but not other miRNAs, whereas Ago2 knockout cells reconstituted with wild-type Ago2, but not Slicer-deficient Ago2, can process miR-451. Finally, we show that the mir-451 backbone is amenable to reprogramming, permitting vector-driven expression of diverse functional miRNAs in the absence of Dicer. Beyond the demonstration of an alternative strategy to direct gene silencing, these observations open the way for transgenic rescue of Dicer conditional knockouts.
Rift Valley fever vaccine--antibody and immune response in cattle to a live and an inactivated vaccine. (1979)

In a study of the response in cattle to a live and an inactivated Rift Valley fever (RVF) vaccine prepared from cell cultures infected with RVF virus, the effects of varying doses and combinations of these vaccines were compared. The antibody response to a primary injection of either vaccines was poor when measured by the serum virus neutralization test (SVN) and the haemagglutination-inhibition test (HI) but a booster dose of inactivated vaccine evoked a good anamnestic response in cattle previously injected with either of these vaccines. Cattle vaccinated with the live vaccine but negative to the SVN or the HI for RVF were immune when challenged with a virulent RVF virus isolated from a cow during 1974.
Improvement of Vision in Macular Degeneration Associated with Intravenous Zinc and Selenium Therapy: Two Cases (1990)

(1990). Improvement of Vision in Macular Degeneration Associated with Intravenous Zinc and Selenium Therapy: Two Cases. Journal of Nutritional Medicine: Vol. 1, No. 2, pp. 133-138.
Discovery of topological Weyl fermion lines and drumhead surface states in a room temperature magnet (2019)

Topological matter is known to exhibit unconventional surface states and anomalous transport owing to unusual bulk electronic topology. In this study, we use photoemission spectroscopy and quantum transport to elucidate the topology of the room temperature magnet Co<sub>2</sub>MnGa. We observe sharp bulk Weyl fermion line dispersions indicative of nontrivial topological invariants present in the magnetic phase. On the surface of the magnet, we observe electronic wave functions that take the form of drumheads, enabling us to directly visualize the crucial components of the bulk-boundary topological correspondence. By considering the Berry curvature field associated with the observed topological Weyl fermion lines, we quantitatively account for the giant anomalous Hall response observed in this magnet. Our experimental results suggest a rich interplay of strongly interacting electrons and topology in quantum matter.
A Vector Approach to Regression Analysis and Its Implications to Heavy-Duty Diesel Emissions (2001)

An alternative approach is presented for the regression of response data on predictor variables that are not logically or physically separable. The methodology is demonstrated by its application to a data set of heavy-duty diesel emissions. Because of the covariance of fuel properties, it is found advantageous to redefine the predictor variables as vectors, in which the original fuel properties are components, rather than as scalars each involving only a single fuel property. The fuel property vectors are defined in such a way that they are mathematically independent and statistically uncorrelated. Because the available data set does not allow definitive separation of vehicle and fuel effects, and because test fuels used in several of the studies may be unrealistically contrived to break the association of fuel variables, the data set is not considered adequate for development of a full-fledged emission model. Nevertheless, the data clearly show that only a few basic patterns of fuel-property variation affect emissions and that the number of these patterns is considerably less than the number of variables initially thought to be involved. These basic patterns, referred to as ''eigenfuels,'' may reflect blending practice in accordance with their relative weighting in specific circumstances. The methodology is believed to be widely applicable in a variety of contexts. It promises an end to the threat of collinearity and the frustration of attempting, often unrealistically, to separate variables that are inseparable.
The microRNA-200 family: small molecules with novel roles in cancer development, progression and therapy (2015)

MicroRNAs (miRNAs) are a large family of small non-coding RNAs that negatively regulate protein-coding gene expression post-transcriptionally via base pairing between the 5' seed region of a miRNA and the 3' untranslated region (3'UTR) of a messenger RNA (mRNA). Recent evidence has supported the critical role that miRNAs play in many diseases including cancer. The miR-200 family consisting of 5 members (miR-200a, -200b, -200c, -141, -429) is an emerging miRNA family that has been shown to play crucial roles in cancer initiation and metastasis, and potentially be important for the diagnosis and treatment of cancer. While miR-200s were found to be critically involved in the metastatic colonization to the lungs in mouse mammary xenograft tumor models, a large number of studies demonstrated their strong suppressive effects on cell transformation, cancer cell proliferation, migration, invasion, tumor growth and metastasis. This review aims to discuss research findings about the role of the miR-200 family in cancer initiation, each step of cancer metastatic cascade, cancer diagnosis and treatment. A comprehensive summary of currently validated miR-200 targets is also presented. It is concluded that miR-200 family may serve as novel targets for the therapy of multiple types of cancer.
HLA-DQ8 (DQB1*0302)-Restricted Th17 Cells Exacerbate Experimental Autoimmune Encephalomyelitis in HLA-DR3-Transgenic Mice (2009)

Among all of the genetic factors associated with multiple sclerosis (MS) susceptibility, MHC class II molecules have the strongest association. Although a direct role of DR alleles in MS have been confirmed, it has been difficult to understand the role of DQ alleles in disease pathogenesis due to strong linkage disequilibrium with certain DR alleles. Population studies have indicated that DQ alleles may play a modulatory role in progression of MS. Using HLA class II transgenic (Tg) mice, we investigated gene complementation between DR and DQ genes in the disease process. Previously, using single Tg mice (expressing HLA-DR or DQ gene), we showed that PLP(91-110) peptide induced experimental autoimmune encephalomyelitis (EAE) only in DR3.Abeta degrees mice, suggesting that DR3 (DRB1*0301) is a disease susceptibility gene in the context of PLP. We also showed that DQ6 protects development of EAE in DQ6/DR3 double Tg mice by production of anti-inflammatory IFN-gamma. In this study, we investigated the ability of DQ8 to modulate disease in DR3/DQ8 double Tg mice. Introduction of DQ8 onto DR3 Tg mice led to higher disease incidence and increased disease severity on immunization with PLP(91-110), indicating that DQ8 had an exacerbating effect on the development of EAE. Increased susceptibility in DR3/DQ8 Tg mice was due to increased production of proinflammatory cytokine IL-17 by DQ8-restricted T cells. HLA-DR3/DQ8 mice with EAE also demonstrated increased inflammation and demyelination in CNS as compared with single DR3 Tg mice. Thus double Tg mouse provides a novel model to study epistatic interactions between HLA class II molecules in inflammatory and demyelinating disease.
A Survey on Financial Fraud Detection Methodologies (2012)

to levitate and rapid escalation of E-Commerce, cases of financial fraud allied with it are also intensifying and which results in trouncing of billions of dollars worldwide each year. Fraud detection involves scrutinizing the behavior of populations of users in order to ballpark figure, detect, or steer clear of objectionable behavior: Undesirable behavior is a extensive term including delinquency: swindle, infringement, and account evasion. Factually, swindle transactions are speckled with genuine transactions and simple pattern matching techniques are not often sufficient to detect those frauds accurately. In this survey we, will focuses on classifying fraudulent behaviors, identifying the major sources and characteristics of the data based on which fraud detection has been conducted. This paper provide a comprehensive survey and review of different techniques to detect the financial fraud detection used in various fraud like credit card fraud detection, online auction fraud, telecommunication fraud detection, and computer intrusion detection.
Pediatric Short Bowel Syndrome (2005)

Cholestasis and age-adjusted small bowel length are the major predictors of mortality in pediatric SBS. Age-adjusted small bowel length and ICV are the major predictors of weaning from PN. These data permit better prediction of outcomes of pediatric SBS, which may help to direct future management of these challenging patients.
Combined Ruthenium(II) and Lipase Catalysis for Efficient Dynamic Kinetic Resolution of Secondary Alcohols. Insight into the Racemization Mechanism (2005)

Pentaphenylcyclopentadienyl ruthenium complexes (3) are excellent catalysts for the racemization of secondary alcohols at ambient temperature. The combination of this process with enzymatic resolution of the alcohols results in a highly efficient synthesis of enantiomerically pure acetates at room temperature with short reaction times for most substrates. This new reaction was applied to a wide range of functionalized alcohols including heteroaromatic alcohols, and for many of the latter, enantiopure acetates were efficiently prepared for the first time via dynamic kinetic resolution (DKR). Different substituted cyclopentadienyl ruthenium complexes were prepared and studied as catalysts for racemization of alcohols. Pentaaryl-substituted cyclopentadienyl complexes were found to be highly efficient catalysts for the racemization. Substitution of one of the aryl groups by an alkyl group considerably slows down the racemization process. A study of the racemization of (S)-1-phenylethanol catalyzed by ruthenium hydride eta(5)-Ph(5)CpRu(CO)(2)H (8) indicates that the racemization takes place within the coordination sphere of the ruthenium catalyst. This conclusion was supported by the lack of ketone exchange in the racemization of (S)-1-phenylethanol performed in the presence of p-tolyl methyl ketone (1 equiv), which gave <1% of 1-(p-tolyl)ethanol. The structures of ruthenium chloride and iodide complexes 3a and 3c and of ruthenium hydride complex 8 were confirmed by X-ray analysis.
Hiding data accesses in steganographic file system (2004)

To support ubiquitous computing, the underlying data have to be persistent and available anywhere-anytime. The data thus have to migrate from devices local to individual computers, to shared storage volumes that are accessible over open network. This potentially exposes the data to heightened security risks. We propose two mechanisms, in the context of a steganographic file system, to mitigate the risk of attacks initiated through analyzing data accesses from user applications. The first mechanism is intended to counter attempts to locate data through updates in between snapshots - in short, update analysis. The second mechanism prevents traffic analysis - identifying data from I/O traffic patterns. We have implemented the first mechanism on Linux and conducted experiments to demonstrate its effectiveness and practicality. Simulation results on the second mechanism also show its potential for real world applications.
Nitroxides in Mechanistic Studies: Ageing of Gold Nanoparticles and Nitroxide Transformation in Acids (2010)

The work described in this thesis includes the applications of nitroxide in the mechanistic studies of two very different research topics. \n\nChapter 2 describes the investigation of ageing of gold nanoparticles (AuNPs) and its mechanistic implications. By utilizing a customized bisnitroxide disulfide, ligand place-exchange reactions of AuNPs were studied by Electron Paramagnetic Resonance (EPR) Spectroscopy and a nitroxide spin label was introduced onto the gold surface in the process. Ageing of thiolate protected AuNPs results in reduced reactivity in the disulfide exchange. By studying the ligand and temperature dependence of this process and the effect of ageing on the maximum extent of exchange, the presence of different binding sites on the surface of AuNPs was proposed. \n\nChapter 3 describes the mechanistic studies of nitroxide-based polymerization inhibitors in various organic monomers. The presence of nitroxide radicals was utilized to report dissolved oxygen concentration which is essential in the inhibition of polymerization. Oxygen-related broadening was deconvoluted from the EPR spectra of nitroxide radicals using an oximetry fitting method. By adopting this method, the inhibition mechanism and associated chemistry of nitroxides in self-initiated polymerization of acrylic acid was investigated. The synergism of nitroxides with other types of inhibitors was proposed. An unusual decay of nitroxide radicals in acid at high temperature was observed.\n\nFollowing Chapter 3, Chapter 4 describes the detailed mechanistic investigation of nitroxide decay in acid at high temperature. N-oxoammonium salt, a product of acid-catalyzed disproportionation of nitroxides, was found to decompose at high temperature. Mechanistic investigation of this reaction leads to identification of the important role of hydroxylamine in the mechanism of nitroxide inhibited polymerization of acidic monomers. \n
The Obesity-Associated <i>FTO</i> Gene Encodes a 2-Oxoglutarate-Dependent Nucleic Acid Demethylase (2007)

Variants in the FTO (fat mass and obesity associated) gene are associated with increased body mass index in humans. Here, we show by bioinformatics analysis that FTO shares sequence motifs with Fe(II)- and 2-oxoglutarate-dependent oxygenases. We find that recombinant murine Fto catalyzes the Fe(II)- and 2OG-dependent demethylation of 3-methylthymine in single-stranded DNA, with concomitant production of succinate, formaldehyde, and carbon dioxide. Consistent with a potential role in nucleic acid demethylation, Fto localizes to the nucleus in transfected cells. Studies of wild-type mice indicate that Fto messenger RNA (mRNA) is most abundant in the brain, particularly in hypothalamic nuclei governing energy balance, and that Fto mRNA levels in the arcuate nucleus are regulated by feeding and fasting. Studies can now be directed toward determining the physiologically relevant FTO substrate and how nucleic acid methylation status is linked to increased fat mass.
Radiation from High-Pressure Plasmas (1968)

If the temperature dependence of the total radiation source strength and the continuum radiation source strength of a gas are known, the contribution of the line radiation can be determined. The investigation of the line factor L shows that it is independent of pressure over a wide temperature and pressure range. Therefore, to determine the total radiation source strength of a gas at high pressure, one need calculate only the continuum radiation at high pressure and use the measured or calculated line factor of the gas at atmospheric pressure. This method was applied to argon and the total radiation source strength u=F (temperature, pressure), in the range 9000≤T≤15 000°K and 1≤p≤100 atm was determined using the existing values measured at 1 atm.
Kojic acid: Applications and development of fermentation process for production (2010)

Kojic acid, 5-hydroxy-2-hydroxymethyl-g-pyrone, has many potential industrial applications. In this review, the properties and diverse applications of kojic acid in industries are described. The review also discusses the advance in kojic acid fermentation, focusing on the process development in micro-organisms and strain selection, medium and culture optimization, as well as fermentation modes for commercially viable industrial scale production. The performances of various fermentation techniques that have been applied for the production of kojic acid are compared, while the advantages and disadvantages of each technique are discussed in this paper.

	 

	Key words: Kojic acid, mild antibiotic, anti-browning agent, tyrosinase inhibitor, submerged fermentation, resuspended cell system, surface culture.