gebhart/patrepeval huggingface dataset:
Measuring General Aviation Pilot Judgment Using a Situational Judgment Technique (2003)

Abstract This paper reports on 2 studies that were conducted to develop and to evaluate a situational judgment test (SJT) for general aviation (GA) pilots. An initial 51-item test was constructed in which each item described an in-flight situation that required a decision on the part of the pilot and 4 alternative solutions to the situation. Subject matter experts were used to generate a scoring key from the alternatives that the experts recommended for a typical GA pilot. In Study 1, the test was administered in paper-and-pencil format to 246 participants. Results from that first study showed that the test had acceptable psychometric properties in terms of internal consistency and distribution. In Study 2, the test was administered to 467 participants over the Internet. Analyses resulted in the reduction of the test to 39 items, with an internal consistency reliability (coefficient alpha) of .747. Construct validation was accomplished through correlation with a measure of the number of times the participant had been involved in an accident or other hazardous aviation event. Pilots who had higher (better) scores on the SJT were found to have experienced fewer hazardous events, which was taken as supporting the construct validity of the test. Evaluation of mode of administration (paper-and-pencil vs. Internet) showed that the 2 forms were equivalent. These results suggest that the SJT has potential for use in the assessment of judgment or aeronautical decision making by GA pilots, and might be useful in the evaluation of training. The implications of the findings, regarding equivalence of the 2 administration formats, are discussed.
Adjuvants That Improve the Ratio of Antigen-Specific Effector to Regulatory T Cells Enhance Tumor Immunity (2013)

Antitumor immunity is strongly influenced by the balance of tumor antigen-specific effector T cells (Teff) and regulatory T cells (Treg). However, the impact that vaccine adjuvants have in regulating the balance of antigen-specific T-cell populations is not well understood. We found that antigen-specific Tregs were induced following subcutaneous vaccination with either OVA or melanoma-derived peptides, with a restricted expansion of Teffs. Addition of the adjuvants CpG-ODN or Poly(I:C) preferentially amplified Teffs over Tregs, dramatically increasing the antigen-specific Teff:Treg ratios and inducing polyfunctional effector cells. In contrast, two other adjuvants, imiquimod and Quil A saponin, favored an expansion of antigen-specific Tregs and failed to increase Teff:Treg ratios. Following therapeutic vaccination of tumor-bearing mice, high ratios of tumor-specific Teffs:Tregs in draining lymph nodes were associated with enhanced CD8(+) T-cell infiltration at the tumor site and a durable rejection of tumors. Vaccine formulations of peptide+CpG-ODN or Poly(I:C) induced selective production of proinflammatory type I cytokines early after vaccination. This environment promoted CD8(+) and CD4(+) Teff expansion over that of antigen-specific Tregs, tipping the Teff to Treg balance to favor effector cells. Our findings advance understanding of the influence of different adjuvants on T-cell populations, facilitating the rational design of more effective cancer vaccines.
Cumulative Association of Five Genetic Variants with Prostate Cancer (2008)

SNPs in five chromosomal regions plus a family history of prostate cancer have a cumulative and significant association with prostate cancer.
Gsα enhances commitment of mesenchymal progenitors to the osteoblast lineage but restrains osteoblast differentiation in mice (2011)

The heterotrimeric G protein subunit Gsα stimulates cAMP-dependent signaling downstream of G protein-coupled receptors. In this study, we set out to determine the role of Gsα signaling in cells of the early osteoblast lineage in vivo by conditionally deleting Gsα from osterix-expressing cells. This led to severe osteoporosis with fractures at birth, a phenotype that was found to be the consequence of impaired bone formation rather than increased resorption. Osteoblast number was markedly decreased and osteogenic differentiation was accelerated, resulting in the formation of woven bone. Rapid differentiation of mature osteoblasts into matrix-embedded osteocytes likely contributed to depletion of the osteoblast pool. In addition, the number of committed osteoblast progenitors was diminished in both bone marrow stromal cells (BMSCs) and calvarial cells of mutant mice. In the absence of Gsα, expression of sclerostin and dickkopf1 (Dkk1), inhibitors of canonical Wnt signaling, was markedly increased; this was accompanied by reduced Wnt signaling in the osteoblast lineage. In summary, we have shown that Gsα regulates bone formation by at least two distinct mechanisms: facilitating the commitment of mesenchymal progenitors to the osteoblast lineage in association with enhanced Wnt signaling; and restraining the differentiation of committed osteoblasts to enable production of bone of optimal mass, quality, and strength.
Development of a Combined Biological and Chemical Process for Production of Industrial Aromatics from Renewable Resources (2007)

Production of industrial aromatic chemicals from renewable resources could provide a competitive alternative to traditional chemical synthesis routes. This review describes the engineering of microorganisms for the production of p-hydroxycinnamic acid (pHCA) and p-hydroxystyrene (pHS) from glucose. The initial process concept was demonstrated using a tyrosine-producing Escherichia coli strain that overexpressed both fungal phenylalanine/tyrosine ammonia lyase (PAL) and bacterial pHCA decarboxylase (pdc) genes. Further development of this bioprocess resulted in uncoupling the pHCA and pHS production steps to mitigate their toxicity to the production host. The final process consists of a fermentation step to convert glucose to tyrosine using a tyrosine-overproducing E. coli strain. This step is followed by a single biotransformation reaction to deaminate tyrosine to pHCA through immobilized E. coli cells that overexpress the Rhodotorula glutinis PAL gene. Finally, chemical decarboxylation of pHCA produces pHS. This multifaceted approach, which integrates biology, chemistry, and engineering, has allowed development of an economical process at scales suitable for industrial applications.
Epitope mapping and reactivity of autoantibodies to the E2 component of 2-oxoglutarate dehydrogenase complex in primary biliary cirrhosis using recombinant 2-oxoglutarate dehydrogenase complex (1996)

Five different target mitochondrial autoantigens recognized by sera from patients with primary biliary cirrhosis (PBC) have been identified as subunits of the following 2-oxo acid dehydrogenase complexes: the pyruvate dehydrogenase complex (PDC), the branched chain 2-oxo acid dehydrogenase complex (BCOADC), and the 2-oxoglutarate dehydrogenase complex (OGDC). Unlike the E2 subunits of PDC (PDC-E2) and BCOADC (BCOADC-E2), the E2 subunits of OGDC (OGDC-E2) reactivity of PBC sera and the reactive epitope of OGDC-D2 have not hitherto been studied in detail. In this report, we took advantage of a recombinant fusion protein for OGDC-E2 to address these issues. Eighty of 268 (29.9%) PBC patient sera but none of the 45 controls reacted with recombinant OGDC-E2. The recombinant OGDC-E2 was judged to express the immunodominant epitope, because when sera from patients with PBC were preabsorbed with the recombinant fusion protein, such sera were depleted of reactivity against 48 kD OGDC-E2 when probed on beef heart mitochondria (BHM) but retained reactivity toward PDC-E2 and/or BCOADC-E2. Furthermore, affinity-purified PBC sera against recombinant OGDC-E2 reacted only with native OGDC-E2 and not with any other enzyme components of the 2-oxo acid dehydrogenase complex. Antimitochondrial autoantibodies (AMA) against OGDC-E2 included immunoglobulin (Ig)G2, IgG3 and IgM and the relative titers were as follows: IgG2 > IgG3 > IgM. Finally, using overlapping recombinant polypeptides, it was determined that a minimum of 81 amino acids (residues 67-147) corresponding to the lipoyl domain of OGDC-E2 are necessary for reactivity, suggesting that a conformational autoepitope is recognized by AMA. These data suggest that each of the 2-oxo acid dehydrogenase enzymes has distinct antigenicity despite their similarities in structure and function. The availability of recombinant OGDC-E2 autoantigen will allow the design of additional studies to further our understanding of the role of mitochondrial autoantigens in the pathogenesis of PBC.
Selective preconcentration for capillary zone electrophoresis using protein G immunoaffinity capillary chromatography (1995)

Capillaries with 150 microns inner diameter were packed with a perfused protein G chromatographic support and used as immunoaffinity preconcentrators for capillary zone electrophoresis. Antibody was loaded onto the protein G support to form an immunoaffinity stationary phase. Injection of samples onto the column caused selective retention and preconcentration of antigen. Injection of appropriate buffers onto the column caused desorption of the antibody and antigen which were then separated by capillary zone electrophoresis. The combination was used on-line and off-line. For on-line combination, a flow-gated interface coupled the two columns and allowed injection of desorbed zones onto the electrophoresis system. Off-line coupling required collection of desorbed fractions and then injection onto the electrophoresis system. Flow rates as high as 100 microL/min were used to load sample onto the affinity column. Desorbing flow rates had to be 1 microL/min or less to prevent excessive dilution during desorption. Using the system, 1 mL insulin samples could be loaded onto the affinity column and desorbed in volumes as small as 1 microL for 1000-fold preconcentration. The use of the preconcentrator with serum samples spiked with insulin was demonstrated.
Developmental Regulation of the Sulfation Profile of Chondroitin Sulfate Chains in the Chicken Embryo Brain (1997)

Developmentally regulated and cell type-specific expression of distinct sulfated glycosaminoglycan structures on cell surface proteoglycans is increasingly recognized as providing information relevant to cell-cell interactions and differentiation in developing organisms. In this report, developmental regulation of both the sulfation profile of chondroitin sulfate chains and activities of chondroitin 4-sulfotransferase (C4ST) and chondroitin 6-sulfotransferase (C6ST) were evaluated in embryonic chicken brain. The results revealed that the sulfation profile and the sulfotransferase activities changed markedly with development, and these alterations were precisely coordinated. Specifically, the proportions of both chondroitin 6-sulfate to 4-sulfate and C6ST to C4ST activities progressively decreased with development. In addition, the total amounts of both chondroitin sulfate chains and the sulfotransferase activities were highest during early embryonic stages and decreased sharply as the development reached completion. The developmental expression of the C6ST gene was also found to parallel the developmental down-regulation of both the C6ST activity and the chondroitin 6-sulfate structure. These findings suggest that the developmentally regulated expression of the sulfotransferases is a predominant factor for stage-specific regulation of chondroitin sulfate structures.
Toxicity of chlorhexidine on odontoblast-like cells (2010)

Regardless of the exposure time, all CHX concentrations had a high direct cytotoxic effect to cultured MDPC-23 cells.
Effects of collagen type on the behavior of annulus fibrosus cells from the canine intervertebral disc in collagen-glycosaminoglycan matrices (2002)

The intervertebral disc (IVD) is the natural cartilaginous cushion found between the osseous vertebrae of the spinal column.It is an essential element for the flexibility of the spinal column but as it generally degenerates with age, with the resulting loss of structural and functional integrity of the disc.Any damage to the IVD, be it natural or accidental, is unlikely to heal and may even worsen with time.Tissue engineering has the potential to provide solutions to the problems of IVD degeneration by facilitating its regeneration.The purpose of this research was to investigate a collagen-based scaffold material for IVD tissue engineering.Specifically, this thesis evaluated in vitro the effects of the collagen type from which the scaffold was fabricated on the behavior of canine annulus fibrosus (AF) cells .AF cells from 6 different canine animals were grown in monolayer culture through two passages.Porous type I and type II collagen-glycosaminoglycan (GAG) scaffolds (also referred to in this thesis as "matrices") were manufactured by a freeze-drying method and then cross-linked by dehydrothermaland carbodiimide treatments.Specimens of the scaffolds, 9mm in diameter, were punched out of sheets of the matrices and seeded with 2 million cells from each of the 6 animals by a pipetting method.Scaffolds were cultured for 1 day, and 2, 4, 6 and 8 weeks.Scaffold dimensions were measured every 2 or 3 days when medium was changed.Prior to terminating the culture, samples were radiolabeled with 3 5 S-sulfate and 3 Hproline to quantify biosynthetic activity.Scaffolds were then dried and weighed, and selected variables were measured: dry weight, biosynthetic activity (protein and GAG synthesis), DNA content (reflecting cell number), GAG content, protein content, and collagen content.Histology, histochemistry, and immunohistochemistry were also performed to assess the cell distribution and the presence of total collagen, type II collagen specifically, and proteoglycans.This thesis presents all the results of these experiments and the findings that are associated with them.It also provides a comparison with prior work and provides suggestions for a possible next step in intervertebral disc regeneration using cell-seeded collagen-GAG scaffolds.
13αH-Olean-18-ene Derivatives. Forced Wolff-Kishner Reduction Products of 19-Oxoolean-12-ene Derivatives (1978)

Abstract Methyl 2α,3β,23-triacetoxy-13αH-olean-18-en-28-oate (4) and methyl 2α,3β-diacetoxy-13αH-olean-18-en-28-oate (7) were obtained from methyl 2α,3β,23-triacetoxy-19-oxoolean-12-en-28-oate (2) and from methyl 2α,3β-diacetoxy-19-oxoolean-12-en-28-oate (5), respectively, by the forced Wolff-Kishner reduction and subsequent acetylation and methylation. Methyl 2α,3β-diacetoxy-13βH-olean-18-en-28-oate (10), prepared from methyl 2,3-di-O-acetylarjunate (13) via methyl 2α,3β-diacetoxy-19α-hydroxy-12-oxooleanan-28-oate (18) and methyl 2α,3β-diacetoxy-19α-hydroxyoleanan-28-oate (19), was shown to be not identical with 7. This led to a 13αH-olean-18-ene structure for 7.
Unique Characteristics of the Pyrrolysine System in the 7th Order of Methanogens: Implications for the Evolution of a Genetic Code Expansion Cassette (2014)

Pyrrolysine (Pyl), the 22nd proteogenic amino acid, was restricted until recently to few organisms. Its translational use necessitates the presence of enzymes for synthesizing it from lysine, a dedicated amber stop codon suppressor tRNA, and a specific amino-acyl tRNA synthetase. The three genomes of the recently proposed Thermoplasmata-related 7th order of methanogens contain the complete genetic set for Pyl synthesis and its translational use. Here, we have analyzed the genomic features of the Pyl-coding system in these three genomes with those previously known from Bacteria and Archaea and analyzed the phylogeny of each component. This shows unique peculiarities, notably an amber tRNA(Pyl) with an imperfect anticodon stem and a shortened tRNA(Pyl) synthetase. Phylogenetic analysis indicates that a Pyl-coding system was present in the ancestor of the seventh order of methanogens and appears more closely related to Bacteria than to Methanosarcinaceae, suggesting the involvement of lateral gene transfer in the spreading of pyrrolysine between the two prokaryotic domains. We propose that the Pyl-coding system likely emerged once in Archaea, in a hydrogenotrophic and methanol-H2-dependent methylotrophic methanogen. The close relationship between methanogenesis and the Pyl system provides a possible example of expansion of a still evolving genetic code, shaped by metabolic requirements.
Enantiomerically Pure Acetals as Ligands for Asymmetric Catalysis (1994)

Enantiomerically pure acetals derived from C2-symmetric diols have been examined as ligands for asymmetric catalysis. Ligands in which the acetal is tethered to an auxiliary donor atom have afforded good levels of enantioselectivity in palladium catalysed allylic substitution (up to 88% ee).
The biochemical characterization of E2, a T cell surface molecule involved in rosettes (1989)

We have previously identified a molecule on the T cell surface, which, in addition to CD2 is involved in the rosette phenomenon. This is a 32-kDa single polypeptide chain which we have termed E2. The studies reported here show striking patterns on the glycosylation status of E2. It is a heavily sialylated and glycosylated molecule, the sugar moieties accounting for almost half of its relative molecular mass (Mr). It carries no N-linked sugar residues, only O-linked oligosaccharides. Despite heavy glycosylation, the molecule appears to behave homogeneously on gel electrophoresis, both in terms of Mr and pI. Neuraminidase treatment of E2 lowered its Mr to 28 kDa; this was further decreased to 18 kDa after removal of O-linked sugar residues by treatment with O-glycanase. An identical reduction in size was observed after treatment with trifluoromethane sulfonic acid, showing that the molecule carries no detectable N-linked sugar residues. Moreover, endoglycosidase F and endoglycosidase H treatment of either the immunoprecipitates from 125I surface-labeled thymocytes, or of a purified preparation of E2, did not reduce the Mr of E2, nor did tunicamycin treatment of T cells. Two-dimensional gel electrophoresis revealed two discrete spots of acidic pI (4.4 and 4.6) that were still seen after neuraminidase treatment, though they had moderately shifted. Pulse-chase experiments revealed a single 28-kDa precursor form that could have been the unsialylated molecule. Finally, sequencing 14 amino acid residues of the N-terminal side revealed no homology with known proteins. Since the sugar moieties of adhesion protein could play an important role, the results obtained in this study will prove valuable to our understanding of the role exerted by the E2 molecule.
Gated Self-Matching Networks for Reading Comprehension and Question Answering (2017)

In this paper, we present the gated selfmatching networks for reading comprehension style question answering, which aims to answer questions from a given passage. We first match the question and passage with gated attention-based recurrent networks to obtain the question-aware passage representation. Then we propose a self-matching attention mechanism to refine the representation by matching the passage against itself, which effectively encodes information from the whole passage. We finally employ the pointer networks to locate the positions of answers from the passages. We conduct extensive experiments on the SQuAD dataset. The single model achieves 71.3% on the evaluation metrics of exact match on the hidden test set, while the ensemble model further boosts the results to 75.9%. At the time of submission of the paper, our model holds the first place on the SQuAD leaderboard for both single and ensemble model.
Application of Fourier-space image-restoration techniques to turbulence compensation and sparse-aperture imaging (1994)

Image reconstruction is important in any application in which the sensing apparatus or the intervening medium significantly corrupts the recorded data. Deconvolution processes are the oldest and best understood, and for many practical problems Fourier domain deconvolution is the method of choice because acceptable results can usually be obtained with a minimum of computational effort. This report describes two practical applications of the Fourier deconvolution process in which detailed knowledge of the system's instantaneous optical transfer function is effectively utilized. In the first example, speckle imagery is combined with wavefront-sensor data to produce diffraction-limited images of celestial objects; the results are shown to compare favorably with the output of a fully operational adaptive optics system, the second application involves a sparse-aperture collection system that could be incorporated into a lightweight space telescope; this discussion includes an assessment of the practical utility of sparse-aperture receivers in a realistic signal-to-noise environment
Prevention of Intra-abdominal Adhesions Using the Antiangiogenic COX-2 Inhibitor Celecoxib (2005)

Selective COX-2 inhibitors, in particular celecoxib, provide durable inhibition of intra-abdominal adhesions through an antiangiogenic mechanism.
Bipolar Membranes Inhibit Product Crossover in CO2 Electrolysis Cells (2018)

Abstract As electrocatalysts and electrolyzer designs for CO 2 reduction continue to improve in terms of current density and product selectivity, product crossover from the cathode to the anode is a loss mechanism that is relatively unexplored. The crossover rates of formate, methanol, and ethanol, which are desirable CO 2 reduction products, are compared in electrolyzers containing anion‐exchange membranes and bipolar membranes. The crossover of formate, an anionic CO 2 reduction product, occurs by electromigration through anion‐exchange membranes, and its rate increases linearly with current density. Crossover of electroneutral methanol or ethanol through anion‐exchange membranes occurs to a lesser extent through both diffusion and electroosmotic drag, the latter increasing with current density in anion‐exchange membranes. In contrast, the outward fluxes of protons and hydroxide ions generated in bipolar membranes inhibit the crossover of both anionic and neutral products, even with membranes that contain high surface area junctions. Calculated electroosmotic drag coefficients for each of the neutral products confirm the better performance of bipolar membranes in terms of product losses.
Novel low temperature setting nanocrystalline calcium phosphate cements for bone repair: Osteoblast cellular response and gene expression studies (2007)

Low temperature setting calcium phosphate cements (CPC) formed from reactive calcium phosphate precursors are receiving great attention in the fields of orthopaedics and tissue engineering. The purpose of this study was to evaluate the mechanical properties and osteocompatibility of a novel calcium deficient hydroxyapatite (CDSHA) with a Ca/P ratio of 1.6 developed in our laboratories and compare it to a previously developed calcium deficient hydroxyapatite (CDHA) with a Ca/P ratio of 1.5. The results demonstrated that the calcium-deficient hydroxyapatites (HA) formed from the CPCs were similar to biological HA at physiological temperature and the elastic moduli of CDHA and CDSHA were found to be 174.42 +/- 20.41 MPa (p < 0.05) and 115.86 +/- 24.8 MPa (p < 0.05), respectively. The surface morphologies of the two calcium deficient HA's formed were identical with a micro/nano porous structure as evidenced from SEM. The cellular proliferation on CDHA, and CDSHA, was comparable to the control, tissue culture polystyrene (TCPS) (p < 0.05). Alkaline phosphatase activity was significantly elevated on CDHA and CDSHA matrices at early time points when compared with the control (TCPS) (p < 0.05). Osteoblast cells gene expression on CDHA, and CDSHA showed type I collagen, alkaline phosphatase, osteocalcin, and osteopontin activity at both 7 and 14 days of culture. Thus, novel calcium-deficient HAs, CDHA, and CDSHA formed at low temperature are promising candidates for orthopaedic applications based on their ability to promote osteoblast cell adhesion and gene expression in vitro.