gebhart/patrepeval huggingface dataset:
A hierarchical approach to parallel multiquery scheduling (1995)

There has been a good deal of progress made recently toward the efficient parallelization of individual phases of single queries in multiprocessor database systems. In this paper we devise and experimentally evaluate a number of scheduling algorithms designed to handle multiple parallel queries. (Scheduling in this context implies the determination of both processor allotments and temporal processor assignments to individual queries and query phases.) One of these algorithms performs the best in our experiments. This algorithm is hierarchical in nature: In the first phase, a good quality precedence based schedule is created for each individual query and each possible number of processors. This component employs dynamic programming. In the second phase, the results of the first phase are used to create an overall schedule of the full set of queries. This component is based on previously published work on nonprecedence-based malleable scheduling. Even though the problem we are considering is NP-hard in the strong sense, the multiple query schedules generated by our hierarchical algorithm are seen experimentally to achieve high quality results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The 34-kilodalton membrane immunogen of Treponema pallidum is a lipoprotein (1990)

Treponema pallidum subsp. pallidum and Escherichia coli incorporated exogenous [3H]palmitate into the 34-kilodalton (kDa) pathogen-specific antigen of T. pallidum. Radiolabeled fatty acid remained associated with the protein upon immunoprecipitation and after boiling in sodium dodecyl sulfate, acetone precipitation, and extensive extractions in organic solvents, suggesting that the fatty acid was covalently bound to the protein. Detection of [3H]palmitate after alkaline and acid hydrolyses confirmed the identity of the incorporated label. Globomycin inhibited maturation of the recombinant 34-kDa antigen, suggesting that E. coli uses the lipoprotein-specific signal peptidase II to process the treponemal antigen. Globomycin also inhibited processing of the 34-kDa antigen, as well as the 44.5- and 15-kDa antigens, in T. pallidum, implying that T. pallidum also possesses the lipoprotein export pathway common to both gram-negative and gram-positive bacteria. Ethanol inhibited processing of the 34-kDa antigen in minicells, suggesting that the 34-kDa antigen normally is translocated through the cytoplasmic membrane. Comparison of the Triton X-114 phase partitioning behavior of the 34-kDa antigen produced either by minicells or by a cell-free translation system indicated that the covalent attachment of fatty acid conferred hydrophobic biochemical properties to the 34-kDa antigen, consistent with the hypothesis that the attached lipid anchors the 34-kDa antigen into the membrane.
Novel light-emitting diodes involving heterocyclic aromatic conjugated polymers (1995)

We report the fabrication and properties of three-, four-, and five-layer electroluminescent devices fabricated from light emissive N-based heterocyclic novel polymeric derivatives of PPP and PPV with which they are isoelectronic. They include poly(pyridine vinylene), (PPyV), and poly(2,5-dihexadecanoxy phenylene vinylene pyridyl vinylene), (PPV.PPyV). Some of the devices operate in both forward and reverse bias modes thus enabling operation in an ac mode. One type of device has the general construction: M/I/polymer/I/ITO where M equals Cu or Al, I equals polyaniline (emeraldine base, EB) or poly(3-hexylthiophene), (P3HT), and polymer equals PPV.PPyV. Under low frequency ac (sinusoidal) driving, light pulses with twice the driving frequency were observed in a device where M equals Al or Cu, I equals EB and polymer equals PPV.PPyV; and in a device where M equals Al, I equals P3HT and polymer equals PPV.PPyV. In the latter device the electroluminescence spectrum in the reverse bias mode differed from that in the forward bias mode. It was also shown that blends of PPyV in Nylon 6,6 exhibit a lower operating voltage than the pure polymer.
A new vascular polyester prosthesis impregnated with cross-linked dextran (2002)

It is essential that a synthetic vascular graft is preclotting prior to implantation in order to prevent blood leaking through the graft wall. We have impregnated a knitted polyester prosthesis with cross-linked dextran. The aim of this study was to develop a process for obtaining an impervious prosthesis and to compare the characteristics of this dextran-impregnated graft with those of a commercially available collagen-impregnated graft. This new vascular prosthesis was coated with dextran; sodium trimetaphosphate was utilized as the cross-linking agent. In an attempt to determine the optimal conditions for impregnation, the dynamic viscosity of the dextran solution was measured during the cross-linking reaction. The results suggest that the dynamic viscosity is correlated with the concentrations of dextran, sodium hydroxide, and sodium trimetaphosphate. The effect of temperature on the dynamic viscosity was also investigated. The water permeability, the coating weight, and the structure of the dextran-impregnated graft were compared with those of a collagen-impregnated prosthesis. The water permeability of the vascular grafts was reduced by dextran impregnation, from 1010 ml/min per cm2 for the control to 0.04 ml/min per cm2 under standard testing conditions. The dextran coating is capable of rendering the graft impervious to water. The coating weight of the graft treated with dextran was approximately the same as the weight of the collagen-impregnated graft. Finally, the morphology of the prosthetic wall was analyzed using scanning electron microscopy. The promotion of endothelial cell recovery was only observed for the polyester grafts treated with dextran or collagen.
Peptides Designed To Spatially Depict the Epstein-Barr Virus Major Virion Glycoprotein gp350 Neutralization Epitope Elicit Antibodies That Block Virus-Neutralizing Antibody 72A1 Interaction with the Native gp350 Molecule (2015)

The production of virus-neutralizing antibodies targeting the Epstein-Barr virus (EBV) major surface glycoprotein gp350 is important for the prevention of infectious mononucleosis and EBV-related cancers. The data presented here provide the first in silico map of the gp350 interaction with a virus-blocking monoclonal antibody. Immunization with gp350 peptides identified by in silico mapping generated antibodies that cross-react with the EBV gp350 molecule and block recognition of the gp350 molecule by a virus-neutralizing antibody. Through its ability to focus the immune system exclusively on the gp350 sequence important for viral entry, these peptides may form the basis of an EBV vaccine candidate. This strategy would sidestep the production of other irrelevant gp350 antibodies that divert the immune system from generating a protective antiviral response or that impede access to the virus-blocking epitope by protective antibodies.
Transfer RNA-derived fragments in aging Caenorhabditis elegans originate from abundant homologous gene copies (2021)

Small RNAs that originate from transfer RNA (tRNA) species, tRNA-derived fragments (tRFs), play diverse biological functions but little is known for their association with aging. Moreover, biochemical aspects of tRNAs limit discovery of functional tRFs by high throughput sequencing. In particular, genes encoding tRNAs exist as multiple copies throughout genome, and mature tRNAs have various modified bases, contributing to ambiguities for RNA sequencing-based analysis of tRFs. Here, we report age-dependent changes of tRFs in Caenorhabditis elegans. We first analyzed published RNA sequencing data by using a new strategy for tRNA-associated sequencing reads. Our current method used unique mature tRNAs as a reference for the sequence alignment, and properly filtered out false positive enrichment for tRFs. Our analysis successfully distinguished de novo mutation sites from differences among homologous copies, and identified potential RNA modification sites. Overall, the majority of tRFs were upregulated during aging and originated from 5'-ends, which we validated by using Northern blot analysis. Importantly, we revealed that the major source of tRFs upregulated during aging was the tRNAs with abundant gene copy numbers. Our analysis suggests that tRFs are useful biomarkers of aging particularly when they originate from abundant homologous gene copies.
Phase II trial of extended dose anti-CTLA-4 antibody ipilimumab (formerly MDX-010) with a multipeptide vaccine for resected stages IIIC and IV melanoma (2009)

9023 Background: Ipilimumab is a human anti-CTLA-4 antibody shown to have clinical activity in melanoma that is associated with immune-related adverse events (IrAEs). Methods: 50 HLA A*0201 positive patients with resected stages IIIC/IV melanoma received MART-1/gp100/tyrosinase peptides with adjuvant Montanide ISA 51 12 times subcutaneously with Ipilimumab at 3 or 10 mg/kg intravenously every 8 weeks for 12 months, and 25 HLA A *0201 negative patients received Ipilimumab alone at 10 mg/kg. Primary endpoints were toxicity and the achievement of a 40% rate of tolerable IrAEs. Immune responses measured by ELISPOT and tetramer assays, and time to relapse were also assessed. 3 melanoma peptides were administered at 1000 mcg/dose each. Results: Median age was 58, with 44 men and 31 women. 46 patients had stage IV, and 29 had stage IIIC resected disease. 19/75 (25%) patients had grades 3–4 IrAEs that were dose-limiting. No patient with dose limiting toxicity required hospitalization and all returned to baseline status with the use of systemic steroids. Assays of induction of IL-17 secreting T cells showed a positive association with freedom from relapse (p=0.049). Change in slope of the increase in total lymphocyte count at four weeks was also associated with a trend toward freedom from relapse and development of an IrAE. 27 of 75 patients have relapsed with a median of 23 months of follow-up. 10 were again rendered NED surgically and are alive without disease. 68 patients are alive, 10 with disease. Only 1/19 patients with grade 3/4 IrAE has died of disease, compared to 6/56 without a dose limiting IBE. 23 of 27 relapses occurred without a grade 3/4 IrAE, compared with 15 IrAEs in 48 patients without a relapse. ELISPOT assays showed that patients at 10 mg/kg actually had decreased responsiveness in fresh PBMC to PHA and the CEF (CMV, EBV, FLU) pool of peptides. Conclusions: IrAEs are associated with clinical benefit in patients with resected high-risk melanoma receiving Ipilimumab with or without a peptide vaccine. Increases in IL-17 secreting CD4 T cells and the slope of increase in total lymphocytes over 4 weeks are associated with freedom from relapse. These data support testing the current regimen at 10 mg/kg in a larger randomized trial. [Table: see text]
Ribonuclease Inhibitors (2003)

RNA analysis and quantification require completely intact, nondegraded RNA samples to produce optimal results. Although nonenzymatic hydrolysis of phosphodiester bonds is favored by high temperature or pH and the presence of divalent cations (Mg2+, Mn2+), an RNA sample is most likely to be rapidly degraded by a contaminating ribonuclease (RNase). RNases are difficult to completely remove or inactivate during RNA isolation procedures, and they may be introduced into the sample inadvertently during its handling. There are several possible sources for RNases in the laboratory. RNases are ubiquitous in the environment, and are found on pollen, dust, and fingerpaint grease. Routine lab procedures, such as ribonuclease protection assays or degrading RNA in plasmid preparations, introduce highly purified, concentrated RNases. RNase may be in the powdered reagents used to make the stock solutions or in the tips and tubes used for handling the RNA.
An Abscisic Acid-AtNAP Transcription Factor-SAG113 Protein Phosphatase 2C Regulatory Chain for Controlling Dehydration in Senescing Arabidopsis Leaves    (2011)

AtNAP is a NAC family transcription factor gene that plays a key role in leaf senescence but its underlying mechanisms are not known. SENESCENCE-ASSOCIATED GENE113 (SAG113), a gene encoding a Golgi-localized protein phosphatase 2C family protein phosphatase, mediates abscisic acid (ABA)-regulated stomatal movement and water loss specifically during leaf senescence. Here we report that SAG113 is a direct target gene of the AtNAP transcription factor. We found that both AtNAP and SAG113 were induced by leaf senescence and ABA. When AtNAP was chemically induced, SAG113 was also induced whereas when AtNAP was knocked out, the ABA- and senescence-induced expression of SAG113 was reduced. These data suggest that the expression of SAG113 is predominantly dependent on AtNAP. Functionally, overexpression of SAG113 restored the markedly delayed leaf senescence phenotype in atnap knockouts to wild type. Yeast (Saccharomyces cerevisiae) one-hybrid experiments and electrophoresis mobility shift assays showed that AtNAP could physically bind to the SAG113 promoter in vivo and in vitro, respectively. Site-directed mutagenesis revealed that AtNAP binds to a 9-bp core sequence of the SAG113 promoter, 5'CACGTAAGT3'. These results indicate that there is a unique regulatory chain, ABA-AtNAP-SAG113 protein phosphastase 2C, which controls stomatal movement and water loss during leaf senescence.
Biochemical technology for the detoxification of geothermal brines and the recovery of trace metals (1995)

Studies conducted at BNL, have shown that a cost-efficient and environmentally acceptable biochemical technology for detoxification of geothermal sludges is most satisfactory, as well as technically achievable. This technology is based on biochemical reactions by which certain extremophilic microorganisms interact with inorganic matrices of geothermal origin. The biochemical treatment of wastes generated by power plants using geothermal energy is a versatile technology adaptable to several applications beyond that of rendering hazardous and/or mixed wastes to non-hazardous by products, which meet regulatory requirements. This technology may be used for solubilization or recovery of a few metals to the isolation of many metals including radionuclides. In the metal recovery mode, an aqueous phase is generated which meets regulatory standards. The resulting concentrate contains valuable trace metals and salts which can be further converted into income generating products which can off-set the initial investment costs associated with the new biotechnology. In this paper, recent developments in this emerging technology will be discussed.
A Novel Sulfatase from<i>Pseudomonas testosteroni</i>Hydrolyzing Lithocholic Acid Sulfate (1992)

Pseudomonas testosteroni ATCC 11996 was found to produce a novel bile acid sulfate sulfatase that hydrolyzes the sulfate ester bond in lithocholic acid sulfate (LCA-S). The enzyme synthesis was induced by several kinds of bile acids including LCA-S. Mn2+ functioned as an essential component for the enzyme synthesis and suppressed it. This sulfatase hydrolyzes LCA-S to isolithocholic acid and sulfuric acid with inversion of α- to β-configuration of the hydroxyl group at the third position of lithocholic acid.
Integer Variable .CHI.-Based Cross Twisted Ate Pairing and Its Optimization for Barreto-Naehrig Curve (2009)

It is said that the lower bound of the number of iterations of Miller's algorithm for pairing calculation is log2 r/φ(k), where φ(·) is the Euler's function, r is the group order, and k is the embedding degree. Ate pairing reduced the number of the loops of Miller's algorithm of Tate pairing from ⌊log2 r⌋ to ⌊ log2(t-1)⌋, where t is the Frobenius trace. Recently, it is known to systematically prepare a pairing-friendly elliptic curve whose parameters are given by a polynomial of integer variable “χ.” For such a curve, this paper gives integer variable χ-based Ate (Xate) pairing that achieves the lower bound. In the case of the well-known Barreto-Naehrig pairing-friendly curve, it reduces the number of loops to ⌊log2χ⌋. Then, this paper optimizes Xate pairing for Barreto-Naehrig curve and shows its efficiency based on some simulation results.
A unified approach to semi-autonomous control of passenger vehicles in hazard avoidance scenarios (2009)

This paper describes the design of unified active safety framework that combines trajectory planning, threat assessment, and semi-autonomous control of passenger vehicles into a single constrained-optimal-control-based system. This framework allows for multiple actuation modes, diverse trajectory-planning objectives, and varying levels of autonomy. The vehicle navigation problem is formulated as a constrained optimal control problem with constraints bounding a navigable region of the road surface. A model predictive controller iteratively plans the best-case vehicle trajectory through this constrained corridor. The framework then uses this trajectory to assess the threat posed to the vehicle and intervenes in proportion to this threat. This approach minimizes controller intervention while ensuring that the vehicle does not depart from a navigable corridor of travel. Simulated results are presented here to demonstrate the framework's ability to incorporate multiple threat thresholds and configurable intervention laws while sharing control with a human driver.
Ferroportin1-Deficient Zebrafish Treated with Iron Dextran Develop Anemia Despite Increased Macrophage Iron Stores. (2004)

Abstract Patients with type 4 hemochromatosis exhibit iron accumulation in the reticuloendothelial system and a tendency to develop anemia following venesection. These patients are heterozygous for mutations in the intestinal and macrophage iron exporter, ferroportin1 (fpn1), however it is not known whether these mutations cause a gain or loss of function. Of current animal models, only the Tp85c allele of the zebrafish anemia mutant weissherbst (weh) encodes a missense mutation (L167F) in the conserved region of fpn1, between transmembrane helix 3 and 4, where several missense mutations have been identified in individuals with type 4 hemochromatosis. Tp85c homozygote zebrafish die within 10–14 days post-fertilization, however administering iron dextran injections allows them to survive. To explore the effects of fpn1 deficiency on blood development and iron homeostasis in adult zebrafish, we raised Tp85c homozygotes along with control cohorts of injected and uninjected heterozygotes and wild types. Iron dextran injections were discontinued at 4 months of age in all cohorts. Although iron accumulation was observed in all iron-injected fish, only homozygotes exhibited iron accumulation in the intestinal epithelium on Perl’s staining, consistent with a block in enterocyte export. At 6 months of age, none of the cohorts were anemic, however at 12 months of age, only the homozygotes developed hypochromic anemia, characterized by reduced levels of hemoglobin per erythrocyte and impaired late erythroid maturation. Histologic evaluation of the anemic homozygotes revealed increased numbers of iron-loaded macrophages in the liver and in the kidney, the zebrafish bone marrow equivalent. Quantitative realtime rt-PCR, performed on liver and intestinal tissues at 1 year of age, revealed that homozygotes had increased intestinal expression of fpn1 compared to the other cohorts. Hepatic transcript levels of the secreted iron-regulator hepcidin were profoundly decreased in homozygotes, consistent with response to anemia. In contrast, hepatic transcript levels for transferrin, fpn1, and DMT1 were not significantly different among the cohorts. In summary, we provide evidence that Tp85c is a loss of function mutation affecting enterocytes and macrophages. After iron dextran injections were discontinued, Tp85c homozygotes developed anemia, despite increased macrophage iron stores. These studies support the hypothesis that fpn1-deficiency impairs iron cycling and suggest this as a possible mechanism in type 4 hemochromatosis.
Functional-morphological studies on in vitro cardionatrin release. (1986)

Atrial natriuretic peptides (ANP) are hormones produced by the heart atrial cardiocytes in mammals. The main function of these peptides appears to be that of modulating the actions of the renin-angiotensin-aldosterone system. In the rat ANP are stored within specific atrial granules, mainly as a 126-amino acid peptide (cardionatrin IV) which is processed to a 28-amino acid peptide (cardionatrin I) just prior to or during release from cardiocytes. Development of an isolated perifused rat atria preparation has allowed quantitative and qualitative studies on ANP release. Increasing mechanical load in this preparation gives an increased rate of release of immunoreactive cardionatrin. This finding suggests that there is an intrinsic 'stretch-secretion coupling' in the atria.
Grafting starch xanthate with vinyl monomers and hydrogen peroxide in foam rubber production (1979)

Abstract Starch xanthate with degrees of substitution (D.S.) ranging from 0.12 to 0.56 reacted with vinyl monomers (acrolein, acrylamide, acrylic acid, acrylonitrile, methyl acrylate, or styrene) and hydrogen peroxide to form aqueous gels of starch–polyvinyl monomer graft copolymer. The same reactions conducted in a rubber latex medium resulted in a self‐acidifying, self‐heating, and self‐foaming coagulation to give a foam rubber. Such products were formed from several synthetic latices (NBR, SBR, polyisoprene, and polychloroprene types) and natural rubber latex; noted for each were the effects of the D.S., of monomer and peroxide concentrations, and of starch:elastomer ratios. The dried foams were evaluated by standard strength tests. Foam rubber of acceptable extensibility and enhanced tensile strength (up to 110 psi) was obtained with 0.12–0.15 D.S. xanthate and with proper balance of vinyl monomer, peroxide, and starch:elastomer ratio. Resilience was fair to good, but compression set was rather poor compared to most foam rubbers of general use.
Prostate Cancer Markers (2004)

In 1936 prostatic acid phosphatase (PAP) became the key serum marker for monitoring prostate cancer (PCa) treatment (1–3). Approximately 50 yr later, prostate-specific antigen (PSA) emerged as the most useful serum marker for PCa management followed a few years later by the watershed application for early detection. In spite of the many tumor marker candidates proposed and studied for over 50 yr, these two prostate proteins remained the most clinically requested PCa serum tests (Table 1). With the accumulation of human genome sequence knowledge and extraordinary methodological advances in gene arrays and proteomics, new PCa molecular tests appear to be on the horizon. Although the biological rationale for a marker’s function may not be known when research is initiated, marker candidates with biological basis for their function, will likely be the most useful. Therefore, the biological function of a marker is an important factor to consider when assessing the potential of new markers. Table 2 and Fig. 1 illustrate PCa markers catagorized by biological activity. What are the clinical utilities and deficiencies for PSA today and what are the features of PAP and PSA, which contribute to the long standing utility of these markers? These properties will be important when assessing the potential of new markers for PCa.
Generation and Characterization of Monkey Embryonic Stem Cells (2006)

Nonhuman primate embryonic stem (ES) cells are very important for preclinical research of the medical application of human ES cells. Because primate ES cells show significant differences from mouse ES cells, we have been optimizing protocols for the establishment and maintenance of monkey ES cells. The latest methods for derivation and culture of cynomolgus monkey ES cells are described in detail.