gebhart/patrepeval huggingface dataset:
Aerodynamic/Aeroacoustic testing in Anechoic Closed Test Sections of Low-Speed Wind Tunnels (2010)

This paper describes new anechoic closed test sections in Japan Aerospace Exploration Agency (JAXA) and Virginia Tech (VT) not only for an aeroacoustic but also for an aerodynamic testing ability in Low-speed wind tunnels. The anechoic closed test section with Kevlar wall is an innovative concept and had been originally developed at VT. It was later applied to JAXA’s 2m x 2m wind tunnel. By using a high-lift device model, the JAXA's new test section was evaluated and validated acoustically by comparing to VT anechoic test results. Moreover, the aerodynamic characteristics in the new test section were also evaluated by comparing to results of the same model in JAXA's closed hard-wall test section. New wall interference correction procedure is proposed for the Kevlar wall test section, and it showed very good agreement with well-known corrected hard-wall results. This anechoic test section is useful and a promising tool for both aerodynamic and aeroacoustic testing.
<i>In Vivo</i> Near-Infrared Fluorescence Imaging of Integrin α<sub>2</sub>β<sub>1</sub> in Prostate Cancer with Cell-Penetrating-Peptide–Conjugated DGEA Probe (2011)

This study demonstrated that the introduction of a CPP sequence can facilitate the internalization of an integrin-targeted peptide probe in vitro. Moreover, a cleavable peptide linker successfully reduced kidney uptake while preserving good tumor uptake in vivo.
Removal of dry etch damage in <i>p</i>-type GaN by wet etching of sacrificial oxide layer (2004)

We describe etch-induced damage in p-type GaN caused by an inductively coupled Cl2/Ar/O2 plasma and a method for its removal by means of wet etching. When p-GaN was etched by a Cl2/Ar/O2 plasma, an oxide layer was formed on the p-GaN surface by the oxygen in the plasma. The electrical properties of the etched p-GaN films deteriorated, as a result of the oxide on the surface, as well as etch-induced damage. However, a HF postwet etching of the dry-etched samples effectively removed the sacrificial oxide layer on the surface that contained the etch-induced defects and damage, resulting in improved characteristics in surface morphology and photoluminescence in the etched p-type GaN.
Efficient Neural Architecture Search via Parameter Sharing (2018)

We propose Efficient Neural Architecture Search (ENAS), a fast and inexpensive approach for automatic model design. In ENAS, a controller learns to discover neural network architectures by searching for an optimal subgraph within a large computational graph. The controller is trained with policy gradient to select a subgraph that maximizes the expected reward on the validation set. Meanwhile the model corresponding to the selected subgraph is trained to minimize a canonical cross entropy loss. Thanks to parameter sharing between child models, ENAS is fast: it delivers strong empirical performances using much fewer GPU-hours than all existing automatic model design approaches, and notably, 1000x less expensive than standard Neural Architecture Search. On the Penn Treebank dataset, ENAS discovers a novel architecture that achieves a test perplexity of 55.8, establishing a new state-of-the-art among all methods without post-training processing. On the CIFAR-10 dataset, ENAS designs novel architectures that achieve a test error of 2.89%, which is on par with NASNet (Zoph et al., 2018), whose test error is 2.65%.
Cell-mediated immune response in vitro. I. The development of suppressor cells and cytotoxic lymphocytes in mixed lymphocyte cultures. (1976)

During the in vitro development of cytotoxic lymphocytes (CL), suppressor cells also develop. Spleen cells or lymph node cells harvested from mixed lymphocyte cultures (MLC) on day 2 (day-2 MLC) and added to a fresh MLC suppressed the development of CL. This suppressive effect was sensitive to treatment with anti-theta and C. The suppressive effect of day-2 MLC was not due to cytotoxic effects nor to altered kinetics of the development of both suppressor cells and CL. Although CL develop from hydrocortisone-treated spleen cells, day-2 MLC of hydrocortisone-treated spleen cells did not suppress the development of CL. These studies suggest that suppressor cells and CL are derived from different T cell subpopulations.
Analysis of the enhancer element that controls expression of sevenless in the developing Drosophila eye. (1991)

The sevenless gene encodes a protein-tyrosine kinase receptor expressed in a complex pattern during the development of the Drosophila melanogaster eye. We have previously shown that this pattern is regulated transcriptionally by an enhancer located in the body of the sevenless gene. Here we extend our analysis of the sevenless enhancer, defining a 475-base-pair fragment that contains elements necessary for the correct qualitative and quantitative expression of the sevenless gene. Within this fragment are sequence elements conserved in the sevenless gene of a distantly related Drosophila species and protected from DNase I digestion by nuclear extracts isolated from adult heads and imaginal discs. Partial deletions of the 475-base-pair fragment result in preferential loss of expression in different subsets of cells. These results suggest that the normal pattern of expression is generated by the combined action of separate cell-specific regulatory elements.
Direct optimization method to study constrained systems within density-functional theory (2005)

Consider a system with an arbitrary constraint on its electron density (e.g., that there are $N$ charges on a certain group of atoms). We show that in Kohn-Sham density functional theory, the minimum energy state consistent with the constraint is actually a maximum with respect to the constraint potential, and that this solution is unique. This leads us to an efficient algorithm for calculations on constrained systems. Illustrative studies are shown for charge transfer in the zincbacteriochlorin-bacteriochlorin complex, polyene and alkane chains.
Characterization of the CO-induced, CO-tolerant hydrogenase from Rhodospirillum rubrum and the gene encoding the large subunit of the enzyme (1996)

In the presence of carbon monoxide, the photosynthetic bacterium Rhodospirillum rubrum induces expression of proteins which allow the organism to metabolize carbon monoxide in the net reaction CO + H2O --> CO2 + H2. These proteins include the enzymes carbon monoxide dehydrogenase (CODH) and a CO-tolerant hydrogenase. In this paper, we present the complete amino acid sequence for the large subunit of this hydrogenase and describe the properties of the crude enzyme in relation to other known hydrogenases. The amino acid sequence deduced from the CO-induced hydrogenase large-subunit gene (cooH) shows significant similarity to large subunits of other Ni-Fe hydrogenases. The closest similarity is with HycE (58% similarity and 37% identity) from Escherichia coli, which is the large subunit of an Ni-Fe hydrogenase (isoenzyme 3). The properties of the CO-induced hydrogenase are unique. It is exceptionally resistant to inhibition by carbon monoxide. It also exhibits a very high ratio of H2 evolution to H2 uptake activity compared with other known hydrogenases. The CO-induced hydrogenase is tightly membrane bound, and its inhibition by nonionic detergents is described. Finally, the presence of nickel in the hydrogenase is addressed. Analysis of wild-type R. rubrum grown on nickel-depleted medium indicates a requirement for nickel for hydrogenase activity. However, analysis of strain UR294 (cooC insertion mutant defective in nickel insertion into CODH) shows that independent nickel insertion mechanisms are utilized by hydrogenase and CODH. CooH lacks the C-terminal peptide that is found in other Ni-Fe hydrogenases; in other systems, this peptide is cleaved during Ni processing.
Identification of a nonsense mutation in the carboxyl-terminal region of DNA-dependent protein kinase catalytic subunit in the scid mouse. (1996)

DNA-dependent protein kinase (DNA-PK) consists of a heterodimeric protein (Ku) and a large catalytic subunit (DNA-PKcs). The Ku protein has double-stranded DNA end-binding activity that serves to recruit the complex to DNA ends. Despite having serine/threonine protein kinase activity, DNA-PKcs falls into the phosphatidylinositol 3-kinase superfamily. DNA-PK functions in DNA double-strand break repair and V(D)J recombination, and recent evidence has shown that mouse scid cells are defective in DNA-PKcs. In this study we have cloned the cDNA for the carboxyl-terminal region of DNA-PKcs in rodent cells and identified the existence of two differently spliced products in human cells. We show that DNA-PKcs maps to the same chromosomal region as the mouse scid gene. scid cells contain approximately wild-type levels of DNA-PKcs transcripts, whereas the V-3 cell line, which is also defective in DNA-PKcs, contains very reduced transcript levels. Sequence comparison of the carboxyl-terminal region of scid and wild-type mouse cells enabled us to identify a nonsense mutation within a highly conserved region of the gene in mouse scid cells. This represents a strong candidate for the inactivating mutation in DNA-PKcs in the scid mouse.
Valuing young families: child protection and family support strategies with adolescent mothers (1996)

This article is based on a study about young mothers' experiences of parenting and their suggestions for child protection and family support strategies. This paper disputes the notion that young mothers are deficient parents, and instead highlights the social stressors faced by many young families. It is argued that, rather than focussing on the individual family or young mother, family work could be better oriented toward resourcing and supporting adolescent families to care for their members.
Selective alteration of substrate specificity by replacement of aspartic acid-189 with lysine in the binding pocket of trypsin (1987)

To test the role of Asp-189 which is located at the base of the substrate binding pocket in determining the specificity of trypsin toward basic substrates, this residue was replaced with a lysine residue by site-directed mutagenesis. Both rat trypsinogen and Lys-189 trypsinogen were expressed and secreted into the periplasmic space of Escherichia coli. The proteins were purified to homogeneity and activated by porcine enterokinase, and their catalytic activities were determined on natural and synthetic substrates. Lys-189 trypsin displayed no catalytic activity toward arginyl and lysyl substrates. Further, there was no compensatory change in specificity toward acidic substrates; no cleavage of aspartyl or glutamyl bonds was detected. Additional studies of substrate specificity involving gas-phase sequence analyses of digested natural substrates revealed an inherent but low chymotrypsin-like activity of trypsin. This activity was retained but modified by the Asp to Lys change at position 189. In addition to hydrolyzing phenylalanyl and tyrosyl peptide bonds, the mutant enzyme has the unique property of cleaving leucyl bonds. On the basis of computer graphic modeling studies of the Lys-189 side chain, it appears that the positively charged NH2 group is directed outside the substrate binding pocket. The resulting hydrophobic cavity may explain the altered substrate specificity of the mutant enzyme. The relatively low chymotrypsin-like activity of both recombinant enzymes may be due to distorted positioning of the scissile bond with respect to the catalytic triad rather than to the lack of sufficient interaction between the hydrophobic side chains and the substrate binding pocket of the enzyme.
Cryogenic refractive indices and temperature coefficients of cadmium telluride from 6 μm to 22 μm (1979)

The index of refraction and its variation with wavelength and temperature were measured for cadmium telluride made by chemical vapor deposition (CVD). The measurement at 20 K using liquid helium as coolant is reported for the first time. The refractive index at 10 microm and 20 K is 2.6466, and the average temperature coefficient at 10 microm and in the range 20-80 K is 4.9 x 10(-5)/K.
Localization of a Factor X Interactive Site in the A1 Subunit of Factor VIIIa (1997)

The protein cofactor, factor (F) VIIIa, is required for the efficient conversion of the substrate FX to FXa by the serine protease FIXa. The interaction between human FVIII (and its constituent subunits) and FX was characterized using a solid phase binding assay performed in the absence of phospholipid and FIXa. Saturable binding of FX to heterodimeric FVIII, the FVIII heavy chain (contiguous A1-A2 domains), the FVIIIa-derived A1/A3-C1-C2 dimer, and the isolated A1 subunit was observed with estimated Kd values ranging from approximately 1 to 3 microM. The interaction of FX with FVIII was inhibited by moderate ionic strength and was Ca2+-dependent, consistent with the salt sensitivity observed in a phospholipid-independent FXa generation assay. Negligible binding to FX was observed for the isolated A2 and A3-C1-C2 subunits of FVIIIa, suggesting that the A1 subunit of FVIII contains a primary binding site for FX. A synthetic peptide to the COOH-terminal acidic region of the A1 subunit, designated FVIII337-372, bound FX and effectively competed with A1 for FX binding (Ki = approximately 16 microM). Cross-linking between the FVIII337-372 peptide and the FX heavy chain was observed following reaction with 1-ethyl-3-[(diethylamino)propyl]carbodiimide. The presence of FX reduced the rate of activated protein C-catalyzed cleavage at Arg336 by approximately 5-fold. These results identify a primary FX interactive site on the cofactor of the intrinsic FXase.
Glucose‐induced production of hydrogen sulfide may protect the pancreatic beta‐cells from apoptotic cell death by high glucose (2008)

We examined the expression of the major H(2)S-producing enzymes, cystathionine-beta-synthase (CBS) and cystathionine-gamma-lyase (CSE). CBS was ubiquitously distributed in the mouse pancreas, but CSE was found only in the exocrine. Freshly isolated islets expressed CBS, while CSE was faint. However, high glucose increased the CSE expression in the beta-cells. L-Cysteine or NaHS suppressed islet cell apoptosis with high glucose, and increased glutathione content in MIN6 beta-cells. Pretreatment with L-cysteine improved the secretory responsiveness following stimulation with glucose. The CSE inhibitor DL-propargylglycine antagonized these L-cysteine effects. We suggest H(2)S may function as an 'intrinsic brake' which protects beta-cells from glucotoxicity.
Non-invasive prenatal testing for aneuploidy and beyond: challenges of responsible innovation in prenatal screening (2015)

This paper contains a joint ESHG/ASHG position document with recommendations regarding responsible innovation in prenatal screening with non-invasive prenatal testing (NIPT). By virtue of its greater accuracy and safety with respect to prenatal screening for common autosomal aneuploidies, NIPT has the potential of helping the practice better achieve its aim of facilitating autonomous reproductive choices, provided that balanced pretest information and non-directive counseling are available as part of the screening offer. Depending on the health-care setting, different scenarios for NIPT-based screening for common autosomal aneuploidies are possible. The trade-offs involved in these scenarios should be assessed in light of the aim of screening, the balance of benefits and burdens for pregnant women and their partners and considerations of cost-effectiveness and justice. With improving screening technologies and decreasing costs of sequencing and analysis, it will become possible in the near future to significantly expand the scope of prenatal screening beyond common autosomal aneuploidies. Commercial providers have already begun expanding their tests to include sex-chromosomal abnormalities and microdeletions. However, multiple false positives may undermine the main achievement of NIPT in the context of prenatal screening: the significant reduction of the invasive testing rate. This document argues for a cautious expansion of the scope of prenatal screening to serious congenital and childhood disorders, only following sound validation studies and a comprehensive evaluation of all relevant aspects. A further core message of this document is that in countries where prenatal screening is offered as a public health programme, governments and public health authorities should adopt an active role to ensure the responsible innovation of prenatal screening on the basis of ethical principles. Crucial elements are the quality of the screening process as a whole (including non-laboratory aspects such as information and counseling), education of professionals, systematic evaluation of all aspects of prenatal screening, development of better evaluation tools in the light of the aim of the practice, accountability to all stakeholders including children born from screened pregnancies and persons living with the conditions targeted in prenatal screening and promotion of equity of access.
Insulin Resistance Is Associated With Increased Serum Concentration of IGF-Binding Protein–Related Protein 1 (IGFBP-rP1/MAC25) (2006)

IGF-binding protein (IGFBP)-related protein 1 (IGFBP-rP1) has been shown to bind both IGFs and insulin, albeit with low affinity, and to inhibit insulin signaling. We hypothesized that IGFBP-rP1 is associated with insulin resistance and components of the IGF system in humans. To this aim, a cross-sectional study was conducted in 113 nondiabetic and 43 type 2 diabetic men. Insulin sensitivity (insulin sensitivity index [S(i)] from intravenous glucose tolerance tests in nondiabetic subjects, or the rate constant for disappearance of glucose [K(ITT)] from insulin tolerance tests in type 2 diabetic subjects), circulating IGFBP-rP1 (from enzyme-linked immunosorbent assay), adiponectin (from radioimmunoassay), C-reactive protein (CRP; from immunoturbidimetry), soluble tumor necrosis factor receptor 2 (sTNFR2; from enzyme-amplified sensitivity immunoassay), and IGF system parameters (IGF-I, free IGF-I, and IGFBP-1 from immunoradiometric assay) were assessed in all subjects. Among nondiabetic men, those in the highest quartile for circulating IGFBP-rP1 exhibited decreased S(i) and adiponectin (both P < 0.01) as well as increased CRP and sTNFR2 (both P < 0.05). Circulating IGFBP-rP1 was also found to be increased in previously undiagnosed type 2 diabetic patients (P = 0.01) but not in known type 2 diabetic patients receiving pharmacological therapy. Although no changes in IGF system components were evident by IGFBP-rP1 quartiles in nondiabetic subjects, independent positive associations of IGFBP-rP1 with circulating fasting IGFBP-1 were evident after adjustment for insulin resistance parameters in both nondiabetic and type 2 diabetic subjects, with IGFBP-rP1 explaining 2 and 11% of IGFBP-1 variance, respectively. In additional multivariate analyses, S(i), sTNFR2, and age stood as independent predictive variables of IGFBP-rP1 (together explaining 18% of its variance) in nondiabetic subjects, and BMI became the only independent predictive variable of IGFBP-rP1 (explaining 26% of its variance) in type 2 diabetic men. These findings show for the first time that circulating IGFBP-rP1 is increased with insulin resistance, and they also suggest novel interactions between IGFBP-rP1 and the IGF system in humans.
Use of an Immunoaffinity-Mass Spectrometry-based Approach for the Quantification of Protein Biomarkers from Serum Samples of Lung Cancer Patients (2008)

It is a challenging task to verify and quantify potential biomarkers expressed at elevated levels in sera from cancer patients. An immunoaffinity-mass spectrometry-based approach has been developed using antibodies to enrich proteins of interest from sera followed by mass spectrometry-based quantification. Antibodies specific to the protein of interest were immobilized to hydrazide resin via the carbohydrate moiety on the Fc region of the antibody. Captured proteins were eluted, reduced, alkylated, and digested with trypsin. Peptides were analyzed by LC coupled with multiple reaction monitoring approach, and quantification was achieved by the addition of stable isotope-labeled (heavy) standard peptides. Using this methodology, we were able to achieve a linear response from 15 to 250 ng/ml for carcinoembryonic antigen (CEA), a known tumor biomarker. Moreover we observed elevated levels of CEA in sera samples from lung cancer patients that to our knowledge is the first time that circulating CEA has been detected by mass spectrometry-based analysis. This approach was further applied to potential protein biomarkers discovered from tumor cell lines and tumor tissues. A linear response was obtained from a multiplex spiking experiment in normal human sera for secretory leukocyte peptidase inhibitor (4-500 ng/ml), tissue factor pathway inhibitor (TFPI) (42-1000 ng/ml), tissue factor pathway inhibitor 2 (TFPI2) (2-250 ng/ml), and metalloproteinase inhibitor 1 (TIMP1) (430-1000 ng/ml). A replicate experiment for a single concentration value yielded a relative coefficient of variation better than 11% for TFPI, secretory leukocyte peptidase inhibitor, and TFPI2. The expression level of the proteins in lung cancer patient sera was assayed by an immunoaffinity-multiple reaction monitoring method, and the results were comparable with those obtained from ELISA. This immunoaffinity-mass spectrometry-based quantification approach thus provides a specific and accurate assay for verifying the expression of potential biomarkers in patient serum samples especially for those proteins for which the necessary reagents for ELISA development are unavailable.
Bovine Rhinitis Viruses Are Common in U.S. Cattle with Bovine Respiratory Disease (2015)

Bovine rhinitis viruses (BRV) are established etiological agents of bovine respiratory disease complex however little research into their epidemiology and ecology has been published for several decades. In the U.S., only bovine rhinitis A virus 1 (BRAV1) has been identified while bovine rhinitis A virus 2 (BRAV2) and bovine rhinitis B virus (BRBV) were previously only identified in England and Japan, respectively. Metagenomic sequencing of a nasal swab from a bovine respiratory disease (BRD) diagnostic submission from Kansas identified contigs with approximately 90% nucleotide similarity to BRAV2 and BRBV. A combination of de novo and templated assemblies using reference genomes yielded near complete BRAV2 and BRBV genomes. The near complete genome of bovine rhinitis A virus 1 (BRAV1) was also determined from a historical isolate to enable further molecular epidemiological studies. A 5'-nuclease reverse transcription PCR assay targeting the 3D polymerase gene was designed and used to screen 204 archived BRD clinical specimens. Thirteen (6.4%) were positive. Metagenomic sequencing of six positive samples identified mixed BRAV1/BRAV2, BRAV1/BRBV and BRAV2/BRBV infections for five samples. One sample showed infection only with BRAV1. Seroprevalence studies using a cell culture adapted BRBV found immunofluorescence assay-reactive antibodies were common in the herds analyzed. Altogether, these results demonstrate that BRV infections are common in cattle with respiratory disease and that BRAV1, BRAV2 and BRBV co-circulate in U.S. cattle and have high similarity to viruses isolated more than 30 years ago from diverse locations.