gebhart/patrepeval huggingface dataset:
Modeling of Zinc Bromide Energy Storage for Vehicular Applications (2009)

Energy storage devices such as lithium-ion and nickel-metal hydrate batteries and ultracapacitors have been considered for utilization in plug-in hybrid electric vehicles (HEVs) and HEVs to improve efficiency and performance and reduce gas mileage. In this paper, we analyze and model an advanced energy storage device, namely, zinc bromide, for vehicular applications. This system has high energy and power density, high efficiency, and long life. A series of tests has been conducted on the storage to create an electrical model of the system. The modeling results show that the open-circuit voltage of the battery is a direct function of the battery's state of charge (SOC). In addition, the battery internal resistance is also a function of SOC at constant temperature. A Kalman filtering technique is also designed to adjust the estimated SOC according to battery current.
Cellular gene expression for calbidin‐D<sub>28k</sub> in mouse kidney (1990)

Gene expression for calbindin-D28k, the 28,000 relative molecular mass vitamin D-dependent calcium-binding protein, was measured in cells of the murine nephron by in situ hybridization on tissue sections (hybridization cytochemistry). Radiolabeled (35S-UTP), single-stranded RNA complementary to calbindin-D28k-mRNA (probe RNA) was prepared from linearized cDNA template and used for the hybridizations. Autoradiography was carried out and cellular levels of hybridization signal (silver grains) were quantified. After correction for background the concentration of silver grains was more than 350% greater in the distal tubule than in either the proximal tubule or the glomerulus. The relative cellular level of mRNA in the cytoplasm, as reflected in silver grains/cell, of the distal tubules with probe RNA was 3.4 times greater than that with control RNA. Cells of the distal tubule were the only apparent sites of specific hybridization with probe RNA. The presence of calbindin-D28k-mRNA in the distal tubule corresponded to the localization of calbindin-D28k by immunocytochemistry.
Differential Regulation of Noxa in Normal Melanocytes and Melanoma Cells by Proteasome Inhibition: Therapeutic Implications (2005)

Melanoma is the most aggressive form of skin cancer and advanced stages are invariably resistant to conventional therapeutic agents. Using bortezomib as a prototypic proteasome inhibitor, we have identified a novel and critical role of the proteasome in the maintenance of the malignant phenotype of melanoma cells that could have direct translational implications. Thus, melanoma cells from early, intermediate, and late stages of the disease could not sustain proteasome inhibition and underwent an effective activation of caspase-dependent and -independent death programs. This effect was tumor cell selective, because under similar conditions, normal melanocytes remained viable. Intriguingly, and despite of interfering with a cellular machinery in charge of controlling the half-life of the vast majority of cellular proteins, bortezomib did not promote a generalized disruption of melanoma-associated survival factors (including NF-kappaB, Bcl-2, Bcl-x(L), XIAP, TRAF-2, or FLIP). Instead, we identified a dramatic induction in vitro and in vivo of the BH3-only protein Noxa in melanoma cells (but not in normal melanocytes) in response to proteasome inhibition. RNA interference validated a critical role of Noxa for the cytotoxic effect of bortezomib. Notably, the proteasome-dependent regulation of Noxa was found to extend to other tumor types, and it could not be recapitulated by standard chemotherapeutic drugs. In summary, our results revealed Noxa as a new biomarker to gauge the efficacy of bortezomib specifically in tumor cells, and provide a new strategy to overcome tumor chemoresistance.
HPLC and Phospholipids Part I: General Considerations (1984)

Abstract The objective of part I of this series is to highlight the major problems and considerations related to possible applications of HPLC to phospholipid analysis. Problems related to phospholipid HPLC are identified and discussed and the relevant literature is reviewed. Different HPLC separation systems and detection systems are described, incl. their relative merits and possible pitfalls.
Adaptive evolution of G-protein coupled receptor genes. (1989)

The phylogeny and patterns of nucleotide substitutions in the visual pigment genes, adrenergic receptor genes, muscarinic receptor genes, and in the human mas oncogene were studied by comparing their DNA sequences. The evolutionary tree obtained shows that the visual pigment genes and mas oncogene form one cluster and that the receptor genes form another. In the evolution of rhodopsin genes, synonymous substitutions outnumber nonsynonymous substitutions. This is consistent with the neutral theory of molecular evolution. However, the early evolutionary stages of alpha- and beta-adrenergic and muscarinic receptors are notable for significantly more nonsynonymous substitutions than synonymous substitutions, suggesting the acquisition of novel functional adaptations. Variable rates of nonsynonymous changes in different domains of these proteins reveal DNA segments that might have been important in their functional adaptations.
The binding site for [<sup>3</sup>H]glibenclamide in the rat cerebral cortex does not recognize K‐channel agonists or antagonists other than sulphonylureas (1991)

The binding of the potent oral antidiabetic sulphonylurea [3H]glibenclamide was studied in rat cerebral cortex membranes. A single population of high affinity and saturable binding sites with equilibrium constants, Kd = 0.2 +/- 0.06 nM and Bmax = 58.6 +/- 6.2 fmol/mg protein was found. Specific [3H]glibenclamide binding to rat cerebral cortex membranes was inhibited by glibenclamide and other sulphonylureas, glibenclamide being the most potent drug and the sulphonylurea of the second generation chlorpropamide the least potent. This observation suggests that this site may be related to the hypoglycaemic properties of sulphonylureas and possibly to their interaction with ATP-sensitive K(+)-channel. Nevertheless, other non-selective K(+)-channel antagonists such as TEA, 4-aminopyridine, quinine, quinidine or apamin failed to interact with this site (IC50 greater than 100 microM). Similarly, both non-selective K(+)-channel agonists such as cromakalim, pinacidil or minoxidil as well as the pancreatic ATP-sensitive K(+)-channel agonist diazoxide failed to interact with this site. It may thus be concluded that this site, under the present experimental conditions, represents a drug specific recognition site which may be coupled to the hypoglycaemic activity of sulphonylureas, possibly on a particulate ATP-dependent K(+)-channel.
Optical Diagnostics of Electrical Discharge Water-Spray Reactors for Chemical Synthesis (2012)

Low-power (250–500 mW) pulsed gliding-arc discharge reactors that utilize water sprayed as a fine aerosol into an argon carrier gas have been previously shown to produce molecular hydrogen <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$(\hbox{H}_{2})$</tex></formula> and hydrogen peroxide <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$(\hbox{H}_{2}\hbox{O}_{2})$</tex></formula> with high energy yields. In this paper, optical emission spectroscopy in the range of 230–1000 nm is used to assess the formation of radicals in the plasma region of the reactor as functions of spatial position and liquid flow rate. Radical intensities of OH (309 nm) were the highest at 10 mm downstream from the point of discharge initiation, and the gradient of the OH radical intensities between 10 and 15 mm was higher for the higher liquid flow rates that correspond to the highest production rates and efficiencies of hydrogen peroxide. These results support the hypothesis that hydrogen peroxide production efficiency increases with rapid OH radical quenching.
Highly Active, Regioselective, and Enantioselective Hydroformylation with Rh Catalysts Ligated by Bis-3,4-diazaphospholanes (2005)

Azines made by the reaction of hydrazine with ortho-formylbenzoic acid react with 1,2-diphosphinobenzene and either succinyl chloride or phthaloyl chloride in ca. 30% yield to give rac-bis-3,4-diazaphospholanes bearing benzoic acid groups in the 2 and 5 positions. Condensation of the benzoic acid functionalities with enantiomerically pure amines affords diastereomeric benzoamides which can be separated by flash chromatography. Application of the resolved bis-3,4-diazaphosholanes to Rh-catalyzed enantioselective hydroformylation of styrene, allyl cyanide, and vinyl acetate under mild pressures (20-500 psig of CO/H2) and temperatures (40-120 degrees C) reveals high activities and selectivities for all three substrates. At 60 degrees C and 500 psig syn gas, the best ligand provides outstanding regio- and enantioselectivities (styrene, 89% ee, b:l = 30:1; allyl cyanide, 87% ee, b:l = 4.8:1; vinyl acetate, 95% ee, b:l = 40:1) while achieving turnover frequencies of ca. 3000 h-1.
Recent advances in the detection of repeat expansions with short-read next-generation sequencing (2018)

Short tandem repeats (STRs), also known as microsatellites, are commonly defined as consisting of tandemly repeated nucleotide motifs of 2-6 base pairs in length. STRs appear throughout the human genome, and about 239,000 are documented in the Simple Repeats Track available from the UCSC (University of California, Santa Cruz) genome browser. STRs vary in size, producing highly polymorphic markers commonly used as genetic markers. A small fraction of STRs (about 30 loci) have been associated with human disease whereby one or both alleles exceed an STR-specific threshold in size, leading to disease. Detection of repeat expansions is currently performed with polymerase chain reaction-based assays or with Southern blots for large expansions. The tests are expensive and time-consuming and are not always conclusive, leading to lengthy diagnostic journeys for patients, potentially including missed diagnoses. The advent of whole exome and whole genome sequencing has identified the genetic cause of many genetic disorders; however, analysis pipelines are focused primarily on the detection of short nucleotide variations and short insertions and deletions (indels). Until recently, repeat expansions, with the exception of the smallest expansion (SCA6), were not detectable in next-generation short-read sequencing datasets and would have been ignored in most analyses. In the last two years, four analysis methods with accompanying software (ExpansionHunter, exSTRa, STRetch, and TREDPARSE) have been released. Although a comprehensive comparative analysis of the performance of these methods across all known repeat expansions is still lacking, it is clear that these methods are a valuable addition to any existing analysis pipeline. Here, we detail how to assess short-read data for evidence of expansions, reviewing all four methods and outlining their strengths and weaknesses. Implementation of these methods should lead to increased diagnostic yield of repeat expansion disorders for known STR loci and has the potential to detect novel repeat expansions.
Advancing Human Genetics Research and Drug Discovery through Exome Sequencing of the UK Biobank (2020)

Abstract The UK Biobank Exome Sequencing Consortium (UKB-ESC) is a unique private/public partnership between the UK Biobank and eight biopharma companies that will sequence the exomes of all ∼500,000 UK Biobank participants. Here we describe early results from the exome sequence data generated by this consortium for the first ∼200,000 UKB subjects and the key features of this project that enabled the UKB-ESC to come together and generate this data. Exome sequencing data from the first 200,643 UKB enrollees are now accessible to the research community. Approximately 10M variants were observed within the targeted regions, including: 8,086,176 SNPs, 370,958 indels and 1,596,984 multi-allelic variants. Of the ∼8M variants observed, 84.5% are coding variants and include 2,139,318 (25.3%) synonymous, 4,549,694 (53.8%) missense, 453,733 (5.4%) predicted loss-of-function (LOF) variants (initiation codon loss, premature stop codons, stop codon loss, splicing and frameshift variants) affecting at least one coding transcript. This open access data provides a rich resource of coding variants for rare variant genetic studies, and is particularly valuable for drug discovery efforts that utilize rare, functionally consequential variants. Over the past decade, the biopharma industry has increasingly leveraged human genetics as part of their drug discovery and development strategies. This shift was motivated by technical advances that enabled cost-effective human genetics research at scale, the emergence of electronic health records and biobanks, and a maturing understanding of how human genetics can increase the probability of successful drug development. Recognizing the need for large-scale human genetics data to drive drug discovery, and the unique value of the open data access policies and contribution terms of the UK Biobank, the UKB-ESC was formed. This precompetitive collaboration has further strengthened the ties between academia and industry and provided teams an unprecedented opportunity to interact with and learn from the wider research community.
Design of a high-speed packet switch with fine-grained quality-of-service guarantees (2002)

We present a new input-queued switch architecture designed to support deadline-ordered scheduling at extremely high-speeds. In particular, deadline-ordered scheduling is enabled through a combination of hardware-based sorted priority queues called P-heaps and a round-robin crossbar scheduler. The priority queues are implemented using a novel scalable pipelined heap-based architecture. Using a 0.35 micron CMOS standard-cell technology, we demonstrate a 32-port switch capable of sustaining 10 Gb/s line rates.
ESTROGEN: PHYSIOLOGY, PHARMACOLOGY, AND FORMULATIONS FOR REPLACEMENT THERAPY (2002)

Estrogen is the central component in 6 of the 100 most widely prescribed medications in the United States today. This steroid has several therapeutic uses including contraceptive applications, treatment of menopausal symptoms, and the prevention of osteoporosis. A wide variety of estrogen replacement therapy (ERT) and estrogen plus progestational hormonal replacement therapy (HRT) preparations are available. In addition, there are an increasing number of products with estrogenic properties that are being promoted as alternatives to drugs containing estrogen, such as phytoestrogens and selective estrogen receptor modifiers (SERMs). This article reviews the physiology of estrogenic effects, estrogen metabolism, and the pharmacokinetics of marketed preparations.
SCRIPTAID AND SUBEROYLANILIDE HYDROXAMIC ACID ARE HISTONE DEACETYLASE INHIBITORS WITH POTENT ANTI–TOXOPLASMA GONDII ACTIVITY IN VITRO (2007)

Toxoplasma gondii is a well-recognized cause of disease in congenitally infected and immunocompromised individuals. Histone deacetylases (HDAC) comprise a family of enzymes that participate in the regulation of chromatin structure, gene expression, and cell signaling in eukaryotes. Toxoplasma gondii expresses a HDAC Class I enzyme homologous to human hdac3. Previous work showed that the histone deacetylase inhibitors (HDI) apicidin and valproic acid inhibit T. gondii infections in vitro. The present study compares the activity of hydroxamic-acid histone deacetylase inhibitors against the RH strain of T. gondii growing in HS68 human foreskin fibroblast cells. Nanomolar concentrations of suberoylanilide hydroxamic acid (SAHA), suberic bishydroxamic acid (SBHA), scriptaid, and trichostatin A (TSA) inhibited T. gondii tachyzoite proliferation. Scriptaid was the most potent hydroxamic acid inhibitor (IC50 = 39 nM). In comparison, the carboxylate histone deacetylase inhibitors sodium valproate, sodium butyrate, and 4-phenylbutyrate were less potent (IC50 range 1-5 mM). All of the inhibitors tested, except SBHA, completely protected the HS68 monolayers from T. gondii at concentrations 3-6 times greater than their respective IC50. In contrast, nicotinamide, an inhibitor of NADI-dependent Class III HDAC, had minimal activity against T. gondii in our in vitro assays. We conclude that the hydroxamic acid class of histone deacetylase inhibitors exhibit potent anti-T. gondii activity in vitro.
Analytical Issues with Natriuretic Peptides - has this been Overly Simplified? (2016)

Natriuretic peptides (NPs) were first described as cardiac biomarkers more than two decades ago. Since that time, numerous studies have confirmed NPs' diagnostic and prognostic utilities as biomarkers of myocardial function. However, we must now admit that despite the NPs' relatively long period of use in clinical practice, our understanding of the biochemistry and the variety of circulating forms of NPs, as well as of their potential as biomarkers, remains far from being complete and comprehensive. The highly complex nature and wide diversity of circulating forms of NPs make their accurate measurements in plasma far more complex than initially believed. A highly simplistic view of the NPs' use is that elevated values of NPs indicate the severity of heart failure and thus reflect the prognosis. However, as shown by a variety of studies, deep understanding of how the NP system works will be required for correct interpretation of test results in routine practice of cardiovascular disease. In this review, we summarize the recent advances in understanding of the complexity of the NP system and discuss related analytical issues, which open new horizons, as well as challenges for clinical diagnostics.
Ge/SiGe quantum wells on Si(111): Growth, structural, and optical properties (2014)

The epitaxial growth of Ge/Si0.15Ge0.85 multiple quantum wells (MQWs) on Si(111) substrates is demonstrated. A 3 μm thick reverse, double-step virtual substrate with a final composition of Si0.10Ge0.90 has been employed. High resolution XRD, TEM, AFM and defect etching analysis has been used for the study of the structural properties of the buffer and of the QWs. The QW stack is characterized by a threading dislocation density of about 3 × 107 cm−2 and an interdiffusion layer at the well/barrier interface of 2.1 nm. The quantum confined energy levels of this system have been calculated using the k·p and effective mass approximation methods. The Ge/Si0.15Ge0.85 MQWs have been characterized through absorption and photoluminescence measurements. The optical spectra have been compared with those of Ge/Si0.15Ge0.85 QWs grown on Si(001) through a thick graded virtual substrate.
Viewpoint quality and scene understanding (2005)

Virtual worlds exploration techniques become nowadays more and more important. The methods are used in wide variety of domains  from graph drawing to robot motion. This paper is dedicated to virtual world exploration techniques which have to help a human being to understand a 3d scene. Improved methods of viewpoint quality estimation are presented in the paper. Using these methods, a real-time technique allowing to choose a good viewpoint for a virtual scene is also proposed.
Machine vision method for small feature measurements (2004)

Small features such as bevels and edge profiles are a common and often critical feature on many manufactured parts. In the past, the only ways to measure such features was to make a wax mold of the feature and slice it for measurement on an optical comparator, or to do a slow mechanical tracing with a stylus or CMM type measurement system. This paper describes the application of machine vision tools, using controlled lighting to highlight shape information such as curvature, combined with 2D vision processing to extract the 3D shape based upon surface modeling.
Strontium and SrO epitaxy on hydrogen-terminated Si(111) (1994)

Epitaxy of Sr and SrO films onto hydrogen-terminated Si (111) has been demonstrated. The use of hydrogen-terminated Si (111) has enabled the epitaxy of metallic Sr films, whereas direct epitaxy on a clean 7×7 Si (111) surface has not been successful. The alternate supply of Sr and O during growth has made it possible to grow good epitaxial SrO films. It has been revealed by electron energy loss spectroscopy that stoichiometric SrO films are obtained by this method.
A low-noise low-power IF amplifier with input and output impedance matching (2002)

An IF amplifier has been designed which uses signal feedback to match the source and load impedances. This eliminates external matching components, reduces the noise figure, and increases the efficiency of the output stage. The IF amplifier concept is realized in the form of a BiCMOS integrated circuit.
The cytotoxic T lymphocyte antigen-4 is a major Graves' disease locus (1999)

Graves' disease (GD) is an autoimmune thyroid disorder that is inherited as a complex trait. We have genotyped 77 affected sib-pairs with autoimmune thyroid disease for eight polymorphic markers spanning the cytotoxic T lymphocyte antigen-4 ( CTLA-4 ) region of chromosome 2q31-q33, and for five markers spanning the major histocompatibility complex ( MHC ) region of chromosome 6p21. Non-parametric analysis showed linkage of GD to the CTLA-4 region with a peak non-parametric linkage (NPL) score of 3.43 ( P = 0.0004) at the marker D2S117. The proportion of affected full-sibs sharing zero alleles (z0) reached a minimum of 0.113 close to D2S117, giving a locus-specific lambdas for this region of 2.2. Families with brother-sister sib-pairs showed a peak NPL of 3.46 ( P = 0.0003, lambdas > 10) at D2S117, compared with 2.00 ( P = 0.02, lambdas = 1.9) in the families with only affected females, suggesting a stronger influence in families with affected males. Association between GD and the G allele of the Thr17Ala polymorphism within the CTLA-4 gene ( CTLA4A/G ) was observed using unaffected sib controls ( P = 0.005). Lesser evidence for linkage was found at the MHC locus, with a peak NPL score of 1.95 ( P = 0.026), between the markers D6S273 and TNFalpha. We demonstrate that the CTLA-4 locus (lambdas = 2.2) and the MHC locus (lambdas = 1.6) together confer approximately 50% of the inherited susceptibility to GD disease in our population.
The writer independent online handwriting recognition system frog on hand and cluster generative statistical dynamic time warping (2004)

In this paper, we give a comprehensive description of our writer-independent online handwriting recognition system frog on hand. The focus of this work concerns the presentation of the classification/training approach, which we call cluster generative statistical dynamic time warping (CSDTW). CSDTW is a general, scalable, HMM-based method for variable-sized, sequential data that holistically combines cluster analysis and statistical sequence modeling. It can handle general classification problems that rely on this sequential type of data, e.g., speech recognition, genome processing, robotics, etc. Contrary to previous attempts, clustering and statistical sequence modeling are embedded in a single feature space and use a closely related distance measure. We show character recognition experiments of frog on hand using CSDTW on the UNIPEN online handwriting database. The recognition accuracy is significantly higher than reported results of other handwriting recognition systems. Finally, we describe the real-time implementation of frog on hand on a Linux Compaq iPAQ embedded device.
Image Detection and Registration (2006)

This chapter contains sections titled: Template Matching Matched Filtering of Continuous Images Matched Filtering of Discrete Images Image Registration