gebhart/patrepeval huggingface dataset:
Methylation of <i>p16</i> CpG Island Associated with Malignant Progression of Oral Epithelial Dysplasia: A Prospective Cohort Study (2009)

p16 Methylation was correlated with malignant transformation of oral epithelial dysplasia and is a potential biomarker for prediction of prognosis of mild or moderate oral epithelial dysplasia.
Method for Isolation of PCR-Ready Genomic DNA from Zebrafish Tissues (2007)

Here we describe a method for the isolation of PCR-ready genomic DNA from various zebrafish tissues that is based on a previously published murine protocol. The DNA solutions are of sufficient quality to allow PCR detection of transgenes from all commonly used zebrafish tissues. In sperm, transgene amplification was successful even when diluted 1000-fold, allowing easy identification of transgenic founders. Given its speed and low cost, we anticipate that the adoption of this method will streamline DNA isolation for zebrafish research.
(-)epicatechin induces and modulates endothelium-dependent relaxation in isolated rat mesenteric artery rings. (2002)

The results indicate that the endothelium-dependent vasodilation by (-)epicatechin is mainly mediated through nitric oxide and low concentration of (-)epicatechin augments endothelium-dependent vasorelaxation in the rat mesenteric arteries.
Trust region Newton methods for large-scale logistic regression (2007)

Large-scale logistic regression arises in many applications such as document classification and natural language processing. In this paper, we apply a trust region Newton method to maximize the log-likelihood of the logistic regression model. The proposed method uses only approximate Newton steps in the beginning, but achieves fast convergence in the end. Experiments show that it is faster than the commonly used quasi Newton approach for logistic regression. We also compare it with linear SVM implementations.
A Fast Neutron Detector (1952)

A fast neutron detector with an efficiency of a few percent and the capability of detecting neutrons in the presence of intense gamma-ray backgrounds has been developed. The detector consists of a ZnS and Lucite molded cylinder used in conjunction with a 5819 photomultiplier tube. This detector is well suited to experiments requiring ``good geometry'' and pulse speeds of the order of 0.1 μsec.
Sampling and Analysis Techniques for Trace Volatile Organic Emissions from Consumer Products (1988)

Comparisons are made of two techniques for the trace analysis of volatile organic compound (VOC) emissions from consumer products: direct on-line sampling and analysis and on-line solid sorbent collection followed by off-line analysis. Two types of direct analyses are examined. The first consists of direct injection of emissions from a sample loaded environmental chamber into a gas chromatograph equipped with a flame ionization detector (FID) for compound identification. Direct injection of headspace collected emissions into a gas chromatograph equipped with a mass selective detector is the second direct method scrutinized. The more traditional technique of solid sorbent collection of the volatile organic emissions followed by thermal desorption (TD)/gas chromatographic (GC)/mass spectrometric (MS) analysis is compared to both direct on-line methods.
Possibility to Detect Upgoing Sleptons (2005)

chn-zhang-Chao-abs1-he23
An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition (2015)

This article provides an overview of the first BioASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BioASQ assesses the ability of systems to semantically index very large numbers of biomedical scientific articles, and to return concise and user-understandable answers to given natural language questions by combining information from biomedical articles and ontologies. The 2013 BioASQ competition comprised two tasks, Task 1a and Task 1b. In Task 1a participants were asked to automatically annotate new PubMed documents with MeSH headings. Twelve teams participated in Task 1a, with a total of 46 system runs submitted, and one of the teams performing consistently better than the MTI indexer used by NLM to suggest MeSH headings to curators. Task 1b used benchmark datasets containing 29 development and 282 test English questions, along with gold standard (reference) answers, prepared by a team of biomedical experts from around Europe and participants had to automatically produce answers. Three teams participated in Task 1b, with 11 system runs. The BioASQ infrastructure, including benchmark datasets, evaluation mechanisms, and the results of the participants and baseline methods, is publicly available. A publicly available evaluation infrastructure for biomedical semantic indexing and QA has been developed, which includes benchmark datasets, and can be used to evaluate systems that: assign MeSH headings to published articles or to English questions; retrieve relevant RDF triples from ontologies, relevant articles and snippets from PubMed Central; produce “exact” and paragraph-sized “ideal” answers (summaries). The results of the systems that participated in the 2013 BioASQ competition are promising. In Task 1a one of the systems performed consistently better from the NLM’s MTI indexer. In Task 1b the systems received high scores in the manual evaluation of the “ideal” answers; hence, they produced high quality summaries as answers. Overall, BioASQ helped obtain a unified view of how techniques from text classification, semantic indexing, document and passage retrieval, question answering, and text summarization can be combined to allow biomedical experts to obtain concise, user-understandable answers to questions reflecting their real information needs.
Cell cycle-related phosphatases CDC25A and B expression correlates with survival in ovarian cancer patients. (2001)

Alterations in cell cycle regulating proteins are common in many cancer types. Recent data suggest a possible link between CDC25 phosphatases overexpression and malignancy. Our objective was to evaluate the expression of the three cell cycle-related phosphatases CDC25A, CDC25B and CDC25C in patients with ovarian cancer. All the patients had a minimal follow up of three years. CDC25A, CDC25B and CDC25C expression were investigated by immunohistochemistry in 106 patients with ovarian cancer. CDC25A and CDC25B were found expressed in almost all the samples analyzed, while CDC25C was undetectable in more than 80% of the patients. The low evaluable data on CDC25C expression, did not allow any association between the expression of this phosphatase and prognosis. The expression of CDC25A and CDC25B showed some evidences of association with a poor prognosis (p = 0.034 and p = 0.058 respectively). This relationship was independent of other factors such as tumor grade, histotype, stage and residual tumor after surgery. In the same patients the examined parameters (residual tumor, grade, stage and histotype) did show the expected relation with survival. The results indicate that high CDC25A and CDC25B expression is related to a worse prognosis in ovarian cancer patients. CDC25 phosphatases expression can be regarded as a possible prognostic factor for ovarian cancer and these proteins should be evaluated as potential molecular targets of novel drugs against this human neoplasm.
Plastic Degradability and Agricultural Product Utilization (1990)

Factors important in the commercialization of a process and in product acceptance in the areas of waste product disposal and increased use of agricultural materials are discussed. The relationships of market volumes to cost, achievement of cost performance through blending and the paradox of good compatibility and film properties with domain accessibility in the scenario of achieving degradability in commodity packaging are discussed. Greater use of agricultural products in which the thrust is not based on low cost secondary products is suggested, and an example of the role of noneconomic factors in the success of a new process and product is given in the concluding section.
Methods to Assay <em>Drosophila</em> Behavior (2012)

Drosophila melanogaster, the fruit fly, has been used to study molecular mechanisms of a wide range of human diseases such as cancer, cardiovascular disease and various neurological diseases(1). We have optimized simple and robust behavioral assays for determining larval locomotion, adult climbing ability (RING assay), and courtship behaviors of Drosophila. These behavioral assays are widely applicable for studying the role of genetic and environmental factors on fly behavior. Larval crawling ability can be reliably used for determining early stage changes in the crawling abilities of Drosophila larvae and also for examining effect of drugs or human disease genes (in transgenic flies) on their locomotion. The larval crawling assay becomes more applicable if expression or abolition of a gene causes lethality in pupal or adult stages, as these flies do not survive to adulthood where they otherwise could be assessed. This basic assay can also be used in conjunction with bright light or stress to examine additional behavioral responses in Drosophila larvae. Courtship behavior has been widely used to investigate genetic basis of sexual behavior, and can also be used to examine activity and coordination, as well as learning and memory. Drosophila courtship behavior involves the exchange of various sensory stimuli including visual, auditory, and chemosensory signals between males and females that lead to a complex series of well characterized motor behaviors culminating in successful copulation. Traditional adult climbing assays (negative geotaxis) are tedious, labor intensive, and time consuming, with significant variation between different trials(2-4). The rapid iterative negative geotaxis (RING) assay(5) has many advantages over more widely employed protocols, providing a reproducible, sensitive, and high throughput approach to quantify adult locomotor and negative geotaxis behaviors. In the RING assay, several genotypes or drug treatments can be tested simultaneously using large number of animals, with the high-throughput approach making it more amenable for screening experiments.
Optimisation of a multipartite human immunodeficiency virus based vector system; control of virus infectivity and large-scale production (2005)

By taking a systematic approach to optimising all aspects of our five-plasmid lentiviral vector system we improved titre, safety, large-scale production, and demonstrated that infectivity could be specifically controlled.
<scp>P</scp>yk2 is essential for astrocytes mobility following brain lesion (2015)

Proline-rich tyrosine kinase 2 (Pyk2) is a calcium-dependent, non-receptor protein-tyrosine kinase of the focal adhesion kinase (FAK) family. Pyk2 is enriched in the brain, especially the forebrain. Pyk2 is highly expressed in neurons but is also present in astrocytes, where its role is not known. We used Pyk2 knockout mice (Pyk2(-/-) ) developed in our laboratory to investigate the function of Pyk2 in astrocytes. Morphology and basic properties of astrocytes in vivo and in culture were not altered in the absence of Pyk2. However, following stab lesions in the motor cortex, astrocytes-mediated wound filling was slower in Pyk2(-/-) than in wild-type littermates. In an in vitro wound healing model, Pyk2(-/-) astrocytes migrated slower than Pyk2(+/+) astrocytes. The role of Pyk2 in actin dynamics was investigated by treating astrocytic cultures with the actin-depolymerizing drug latrunculin B. Actin filaments re-polymerization after latrunculin B treatment was delayed in Pyk2(-/-) astrocytes as compared with wild-type astrocytes. We mimicked wound-induced activation by treating astrocytes in culture with tumor-necrosis factor alpha (TNFα), which increased Pyk2 phosphorylation at Tyr402. TNFα increased PKC activity, and Rac1 phosphorylation at Ser71 similarly in wild-type and Pyk2-deficient astrocytes. Conversely, we found that gelsolin, an actin-capping protein known to interact with Pyk2 in other cell types, was less enriched at the leading edge of migrating Pyk2(-/-) astrocytes, suggesting that its lack of recruitment mediated in part the effects of the mutation. This work shows the critical role of Pyk2 in astrocytes migration during wound healing.
T-Cell lymphoma cell lines (HUT102 and HUT78) established at the National Cancer Institute: History and importance to understanding the biology, clinical features, and therapy of cutaneous T-cell lymphomas (CTCL) and adult T-cell leukemia-lymphomas (ATLL) (1996)

Efforts at the National Cancer Institute to generate continuous in vitro cultures from patients with mycosis fungoides and the Sezary syndrome, neoplasms with a mature T-helper phenotype, led to the establishment of two cell lines, HUT78 and HUT102. Further characterization of these cell lines led to the identification of the first human retrovirus, HTLV-1, in the HUT102 cells, and the clinical description of the syndrome of HTLV-1 associated acute T-cell leukemia/lymphoma; the serum antibody test to screen for this virus was developed from the serum of the patient from whom the cell line was derived. The HUT78 cell line was pivotal in the identification and characterization of the HIV retrovirus in that a subclone, H9, proved to be permissive for replication of HIV in vitro. Propagation of HIV in vitro in H9 cells allowed for the development of immunological reagents to screen blood supplies for the presence of the virus. Further biologic and molecular studies of these lines have led not only to a better understanding of the underlying diseases but also to the development of rational therapeutic approaches.
A product-line requirements approach to safe reuse in multi-agent systems (2005)

The dynamic nature of highly autonomous agents within distributed systems is difficult to specify with existing requirements techniques. However, capturing the possibly shifting configurations of agents in the requirements specification is essential for safe reuse of agents. The contribution of this work is an extensible agent-oriented requirements specification template for distributed systems that supports safe reuse. We make two basic claims for this idea. First, by adopting a product-line-like approach, it exploits component reuse during system evolution. Second, the template allows ready integration with an existing tool-supported, safety analysis technique sensitive to dynamic variations within the components (i.e., agents) of a system. To illustrate these claims, we apply the requirements specification template and safety analysis to a real-world context-aware, distributed satellite system.
Graphene Oxides as Substrate for Enhanced Mammalian Cell Growth (2012)

Graphene Oxides as Substrate for Enhanced Mammalian Cell Growth Graphene oxides (GOs), widely used as precursors in the reduction for single-layer graphene materials (rGOs), have found application potentials independent of those for graphene. In particular, the excellent aqueous compatibility of GOs has attracted growing interest in their biological applications. Studies on cellular interactions of GOs have been centered on the cytotoxicity evaluations. Beyond cytotoxicity, however, the cellular interactions of GOs apparently have other consequences. In this work, GOs as coating on solid-state substrate were found to be significantly enhancing mammalian cell growth, despite the fact that GOs in a more concentrated aqueous suspension were somewhat toxic to the same cell lines. Results for a comparison of cell growth on other surfaces based on carbon nanomaterials, including rGOs, carbon nanotubes, and composites of GOs with carbon nanotubes, are presented and discussed.
Carotenoids and Carotenogenesis in Anoxygenic Photosynthetic Bacteria (2006)

More than 50 genera including about 130 species of anoxygenic photosynthetic bacteria have been described. These bacteria produce around 100 different carotenoids. In this chapter, the carotenoid compositions of all the photosynthetic bacteria so far described are summarized. All of the carotenogenesis genes from Rhodobacter, and some of them from other bacteria have been cloned, and the characteristics of their products have been investigated. Schmidt (1978) proposed four main pathways for carotenogenesis. In this chapter, five main pathways within anaerobic photosynthetic bacteria are now suggested based on these new findings: the spirilloxanthin pathway (normal spirilloxanthin, unusual spirilloxanthin, spheroidene, and carotenal pathways). the okenone pathway (okenone, and R.g.-keto carotenoid pathways), the isorenieratene pathway (isorenieratene, and chlorobactene pathways), the γ- and β-carotene pathway, and the diapocarotene pathway. In addition, carotenoid glucosides and carotenoid glucoside fatty acid esters have also been found in some species. The Rhodospirillaceae and Chromatiaceae have the spirilloxanthin or the okenone pathway depending on the genus or species. All of the Ectothiorhodospiraceae have the spirilloxanthin pathway. The isorenieratene, the and γ- and β-carotene, and the diapocarotene pathways are found specifically in the Chlorobiaceae, Chloroflexaceae, and Heliobacteriaceae, respectively. Aerobic photosynthetic bacteria mostly have the spirilloxanthin pathway, further most of these species have unusual carotenoids including ‘non-photosynthetic’ carotenoids, such as carotenoid sulfates and carotenoic acids, which have no photosynthetic functions.
Rechargeable lithium-aluminum/iron sulfide batteries for high energy density (2003)

A rechargeable lithium aluminum/iron sulfide battery has been built and tested. Prismatic LiAl/FeS cells provide a delivered energy to 80% depth of discharge (DOD) of 217 Wh/1 and a peak power of 375 W/l. Cycle life of over 365 cycles was achieved at the C/3 rate. Pulse self-discharge and driving cycle tests were also performed for an electric vehicle application. The molten salt electrolyte requires an operational temperature of about 450 degrees C. A thermal control system composed of heating elements, thermal enclosure, and heat exchanger was engineered and tested. The components for a 8 kWh battery were developed and evaluated. This high temperature rechargeable battery is suitable for applications requiring high specific energy and minimal volume.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Volatile Flavor Components of Kogyoku Apples (1984)

Journal Article Volatile Flavor Components of Kogyoku Apples Get access Izumi Yajima, Izumi Yajima Kawasaki Research Laboratories, T. Hasegawa Co., 335 Kariyado, Nakahara-ku, Kawasaki 210, Japan Search for other works by this author on: Oxford Academic Google Scholar Tetsuya Yanai, Tetsuya Yanai Kawasaki Research Laboratories, T. Hasegawa Co., 335 Kariyado, Nakahara-ku, Kawasaki 210, Japan Search for other works by this author on: Oxford Academic Google Scholar Mikio Nakamura, Mikio Nakamura Kawasaki Research Laboratories, T. Hasegawa Co., 335 Kariyado, Nakahara-ku, Kawasaki 210, Japan Search for other works by this author on: Oxford Academic Google Scholar Hidemasa Sakakibara, Hidemasa Sakakibara Kawasaki Research Laboratories, T. Hasegawa Co., 335 Kariyado, Nakahara-ku, Kawasaki 210, Japan Search for other works by this author on: Oxford Academic Google Scholar Kazuo Hayashi Kazuo Hayashi Kawasaki Research Laboratories, T. Hasegawa Co., 335 Kariyado, Nakahara-ku, Kawasaki 210, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 48, Issue 4, 1 April 1984, Pages 849–855, https://doi.org/10.1080/00021369.1984.10866249 Published: 01 April 1984 Article history Received: 25 May 1983 Published: 01 April 1984
Novel ring‐opening polymerization of lactide by lipase (1998)

Abstract Six‐membered D,L‐, L,L‐ and D,D‐lactides were polymerized by lipase over a temperature range of 80 to 130 °C to yield the polylactide with a molecular weight ( M w ) of greater than 270000. Among the lipases tested, lipase PS gave the greatest molecular weight of polylactide. The polymerization of D,L‐lactide by lipase was better than that of L,L‐ and D,D‐lactides. The polymerization of lactide by lipase showed the characteristic features, such as induction period for the initiation of polymerization, formation of oligomer and subsequent formation of high molecular weight polylactide, which may imply the characteristic polymerization by lipase. Immobilization of lipase on celite significantly enhanced the polymerization of lactide particularly with respect to the low concentration of the enzyme and the M w of the resultant polymer. It was found that there is no clear relationship between enzymatic polymerizability and enzymatic degradability with respect to the enzyme origin and the stereochemistry of lactide.
Preparation of Therapeutic Dose of <sup>177</sup>Lu-DOTA-TATE Using a Novel Single Vial Freeze-dried Kit: A Comparison with ‘In-situ’ Preparation at Hospital Radiopharmacy (2014)

The kit was useful for the convenient preparation of therapeutic dose of (177)Lu-DOTA-TATE, suitable for human administration. The use of kit is expected to reduce the batch failure and radiation exposure to the working personnel.
Engineering an Alcohol Dehydrogenase for Balancing Kinetics in NADPH Regeneration with 1,4-Butanediol as a Cosubstrate (2019)

Cofactor regeneration using diols as “smart cosubstrates” is one of the most promising approaches, due to the thermodynamic preference and 0.5-equiv requirement. In order to establish an efficient NADPH regeneration system with 1,4-butanediol (1,4-BD), a NADP+-dependent alcohol dehydrogenase from Kluyveromyces polysporus (KpADH) was engineered to solve the kinetic imbalance. Several hotspots were identified through molecular dynamic simulation and subjected to saturation and combinatorial mutagenesis. Variant KpADHV84I/Y127M exhibited a lower KM of 15.1 mM and a higher kcat of 30.1 min–1 than WTKpADH. The oxidation of 1,4-BD to 4-hydroxybutanal was found to be the rate-limiting step, for which the kcat/KM value of double mutant KpADHV84I/Y127M was 2.00 min–1·mM–1, 11.6-fold higher than that of WTKpADH. KpADHV84I/Y127M preferred diols with a longer chain length (C5–C6). The ratio of kcat/KM toward 2-hydroxytetrahydrofuran (2-HTHF), in comparison to 1,4-BD, in KpADHV84I/Y127M was dramatically reduced by almost 100-fold compared to WTKpADH, which was advantageous for NADPH regeneration. As much as 100 mM phenylpyruvic acid could be reduced into d-phenylalanine with 99.2% conversion in 6 h using merely 0.5 equiv of 1,4-BD. Both the improved catalytic efficiency toward 1,4-BD and the balanced kcat/KM between 1,4-BD and 2-HTHF contributed to the higher NADPH regeneration efficiency. This study provides guidance for engineering alcohol dehydrogenases for cosubstrate specificity toward diols and its application in NADPH regeneration for the preparation of chiral compounds of pharmaceutical relevance.
Transverse dento-skeletal relationships and third molar impaction. (1981)

Abstract This study shows a significant relationship between lower third molar impaction and the ratio between bilateral molar and ramus widths.