gebhart/patrepeval huggingface dataset:
<i>bic</i> , a Novel Gene Activated by Proviral Insertions in Avian Leukosis Virus-Induced Lymphomas, Is Likely To Function through Its Noncoding RNA (1997)

The bic locus is a common retroviral integration site in avian leukosis virus (ALV)-induced B-cell lymphomas originally identified by infection of chickens with ALVs of two different subgroups (Clurman and Hayward, Mol. Cell. Biol. 9:2657-2664, 1989). Based on its frequent association with c-myc activation and its preferential activation in metastatic tumors, the bic locus is thought to harbor a gene that can collaborate with c-myc in lymphomagenesis and presumably plays a role in late stages of tumor progression. In the present study, we have cloned and characterized two novel genes, bdw and bic, at the bic locus. bdw encoded a putative novel protein of 345 amino acids. However, its expression did not appear to be altered in tumor tissues, suggesting that it is not involved in oncogenesis. The bic gene consisted of two exons and was expressed as two spliced and alternatively polyadenylated transcripts at low levels in lymphoid/hematopoietic tissues. In tumors harboring bic integrations, proviruses drove bic gene expression by promoter insertion, resulting in high levels of expression of a chimeric RNA containing bic exon 2. Interestingly, bic lacked an extensive open reading frame, implying that it may function through its RNA. Computer analysis of RNA from small exon 2 of bic predicted extensive double-stranded structures, including a highly ordered RNA duplex between nucleotides 316 and 461. The possible role of bic in cell growth and differentiation is discussed in view of the emerging evidence that untranslated RNAs play a role in growth control.
Spot size converters for low cost PICs (1999)

The coupling loss and the packaging cost of photonic integrated circuits (PICs) can be much reduced by monolithic integrated mode size converters (tapers). During the past years, many taper designs have been reported. This paper presents a classification from an optical point of view.
Interleukin-6 regulates the zinc transporter Zip14 in liver and contributes to the hypozincemia of the acute-phase response (2005)

Infection and inflammation produce systemic responses that include hypozincemia and hypoferremia. The latter involves regulation of the iron transporter ferroportin 1 by hepcidin. The mechanism of reduced plasma zinc is not known. Transcripts of the two zinc transporter gene families (ZnT and Zip) were screened for regulation in mouse liver after turpentine-induced inflammation and LPS administration. Zip14 mRNA was the transporter transcript most up-regulated by inflammation and LPS. IL-6 knockout (IL-6(-/-)) mice did not exhibit either hypozincemia or the induction of Zip14 with turpentine inflammation. However, in IL-6(-/-) mice, LPS produced a milder hypozincemic response but no Zip14 induction. Northern analysis showed Zip14 up-regulation was specific for the liver, with one major transcript. Immunohistochemistry, using an antibody to an extracellular Zip14 epitope, showed both LPS and turpentine increased abundance of Zip14 at the plasma membrane of hepatocytes. IL-6 produced increased expression of Zip14 in primary hepatocytes cultures and localization of the protein to the plasma membrane. Transfection of mZip14 cDNA into human embryonic kidney cells increased zinc uptake as measured by both a fluorescent probe for free Zn(2+) and (65)Zn accumulation, as well as by metallothionein mRNA induction, all indicating that Zip14 functions as a zinc importer. Zip14 was localized in plasma membrane of the transfected cells. These in vivo and in vitro experiments demonstrate that Zip14 expression is up-regulated through IL-6, and that this zinc transporter most likely plays a major role in the mechanism responsible for hypozincemia that accompanies the acute-phase response to inflammation and infection.
An Economics Approach to Hard Computational Problems (1997)

A general method for combining existing algorithms into new programs that are unequivocally preferable to any of the component algorithms is presented. This method, based on notions of risk in economics, offers a computational portfolio design procedure that can be used for a wide range of problems. Tested by solving a canonical NP-complete problem, the method can be used for problems ranging from the combinatorics of DNA sequencing to the completion of tasks in environments with resource contention, such as the World Wide Web.
Recombination of pseudorabies virus vaccine strains in swine (1991)

We report here genetic recombination between 2 USDA-licensed vaccine strains of pseudorabies virus co-inoculated into swine. The vaccine strains, one of which was a conventionally attenuated strain and the other, a genetically engineered deleted strain containing a negative immunologic marker, had complementary genomes. Co-inoculation resulted in the creation of novel strains of pseudorabies virus containing negative immunologic markers with restored virulence genes. Plaque-purified recombinant progeny viruses were found in 2 litters of pigs in which both strains were co-inoculated IM, a litter in which both strains were co-inoculated oronasally, and a litter in which the conventionally attenuated strain was inoculated oronasally and the genetically engineered strain was inoculated IM. Recombinant phenotypes and recombinant restriction fragment patterns were observed. The creation, spread, and potential misdiagnosis of these types of recombinant strains could disrupt control and eradication programs that are based on the serologic identification of swine infected with potentially virulent strains of pseudorabies virus.
Experimental determination of the emission cross-section spectrum of the pump transition of praseodymium (1995)

A novel technique is presented which allows the experimental determination of the emission cross-section spectrum of the pump transition of praseodymium in ZBLAN glass. The technique is based on measuring the population density of the upper level as a function of pump power as well as wavelength. The emission and absorption cross-section spectra of the pump transition are calculated from the measured population density data. The emission cross-section spectrum gained by this technique is an important step towards more accurate modelling of Pr/sup 3+/-doped fiber amplifiers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Production & Characterization of a Unique Dextran from an Indigenous <i>Leuconostoc mesenteroides </i>CMG713 (2008)

On the basis of high enzyme activity a newly isolated strain of L. mesenteroides CMG713 was selected for dextran production. For maximum yield of dextran, effects of various parameters such as pH, temperature, sucrose concentration and incubation period were studied. L. mesenteroides CMG713 produced maximum dextran after 20 hours of incubation at 30 masculineC with 15% sucrose at pH 7.0. The molecular mass distribution of dextran produced by this strain showed that its molecular mass was about 2.0 million Da. Dextran analysis by (13)C-NMR spectrometry showed no signals corresponding to any other linkages except alpha-(1-->6) glycosidic linkage in the main chain, which has not been reported before. Physico-chemical properties of this unique dextran were also studied. These optimised conditions could be used for the commercial production of this unique high molecular weight dextran, which have significant industrial perspectives.
Efficient evaluation of generalized path pattern queries on XML data (2008)

Finding the occurrences of structural patterns in XML data is a key operation in XML query processing. Existing algorithms for this operation focus almost exclusively on path-patterns or tree-patterns. Requirements in flexible querying of XML data have motivated recently the introduction of query languages that allow a partial specification of path-patterns in a query. In this paper, we focus on the efficient evaluation of partial path queries, a generalization of path pattern queries. Our approach explicitly deals with repeated labels (that is, multiple occurrences of the same label in a query).
A Convenient Synthesis of 2,4(3<u>H</u>,5<u>H</u>)-Furandione (β-Tetronic Acid) (1981)

Abstract The chemical versatility of 2,4(3H,5H)-furandione (β-tetronic acid, 1) and its synthetic applicability are of considerable current interest1b,2a-k. The multifunctional character of this small molecule confers an intriguing synthetic potential which has prompted us to develop synthetic schemes utilizing it as a synthon for certain heterocyclic systems.
Structural Studies of Rutile-Type Metal Dioxides (1997)

The structures of the four metal dioxides GeO 2 , SnO 2 , RuO 2 and IrO 2 (germanium, tin, ruthenium and iridium dioxides, respectively) have been redetermined by Rietveld refinement from neutron diffraction powder data. The four dioxides all adopt the rutile-type structure, space group P 42/ mnm (no. 136), with a = 4.4066 (1), 4.7374 (1), 4.4968 (2) and 4.5051 (3), c = 2.8619 (1), 3.1864 (1), 3.1049 (1) and 3.1586 (2) Å, and x = 0.3060 (1), 0.3056 (1), 0.3053 (1) and 0.3077 (3), respectively. These results are compared with those for other metal dioxides that adopt the rutile structure and trends in structural and thermal vibrations for a series of 11 metal dioxides which adopt the rutile-type structure are described.
On automated message processing in electronic commerce and work support systems (1997)

Electronic messaging, whether in an office environment or for electronic commerce, is normally carried out in natural language, even when supported by information systems. For a variety of reasons, it would be useful if electronic messaging systems could have semantic access to, that is, access to the meanings and contents of, the messages they process. Given that natural language understanding is not a practicable alternative, there remain three approaches to delivering systems with semantic access: electronic data interchange (EDI), tagged messages, and the development of a formal language for business communication (FLBC). We favor the latter approach. In this article we compare and contrast these three approaches, present a theoretical basis for an FLBC (using speech act theory), and describe a prototype implementation.
TOTAL SERUM CHOLESTEROL AND CANCER MORTALITY IN A MIDDLE-AGED MALE POPULATION (1980)

The assessment of total cholesterol level as a risk factor for cancer mortality was studied from data of the Paris Prospective Study of Coronary Heart Disease. A total of 7603 French male government employees aged 43-52 years were followed for an average of 6.6 years. One hunderd and thirty-four cancer deaths were registered with a mean survival time of 4.9 +/- 2.9 years. At entry in the study, future cancer cases were older than survivors and had a lower corpulence index and lower cholesterol value (212 vs 223 mg/100 ml, SD = 43 mg/100 ml) than those of survivors. The intitial cholesterol level did not differ significantly among cancer sites. The mean cholesterol value increased steadily with survival time (p < 0.02) and reached the mean survivors level in men with survival time longer than seven years. Longitudinal cholesterol measurements obtained among 81% of future cancer cases showed a mean decrease, after an average of 3.0 years, comparable to the one estimated from croos-sectional data. The association between low cholesterol and cancer mortality during a period up to seven years before death is not likely to represent an etiologic link but in all probability reflects the advance of the clinical course of cancer.
The biological inorganic chemistry of zinc ions (2016)

The solution and complexation chemistry of zinc ions is the basis for zinc biology. In living organisms, zinc is redox-inert and has only one valence state: Zn(II). Its coordination environment in proteins is limited by oxygen, nitrogen, and sulfur donors from the side chains of a few amino acids. In an estimated 10% of all human proteins, zinc has a catalytic or structural function and remains bound during the lifetime of the protein. However, in other proteins zinc ions bind reversibly with dissociation and association rates commensurate with the requirements in regulation, transport, transfer, sensing, signalling, and storage. In contrast to the extensive knowledge about zinc proteins, the coordination chemistry of the "mobile" zinc ions in these processes, i.e. when not bound to proteins, is virtually unexplored and the mechanisms of ligand exchange are poorly understood. Knowledge of the biological inorganic chemistry of zinc ions is essential for understanding its cellular biology and for designing complexes that deliver zinc to proteins and chelating agents that remove zinc from proteins, for detecting zinc ion species by qualitative and quantitative analysis, and for proper planning and execution of experiments involving zinc ions and nanoparticles such as zinc oxide (ZnO). In most investigations, reference is made to zinc or Zn<sup>2+</sup> without full appreciation of how biological zinc ions are buffered and how the d-block cation Zn<sup>2+</sup> differs from s-block cations such as Ca<sup>2+</sup> with regard to significantly higher affinity for ligands, preference for the donor atoms of ligands, and coordination dynamics. Zinc needs to be tightly controlled. The interaction with low molecular weight ligands such as water and inorganic and organic anions is highly relevant to its biology but in contrast to its coordination in proteins has not been discussed in the biochemical literature. From the discussion in this article, it is becoming evident that zinc ion speciation is important in zinc biochemistry and for biological recognition as a variety of low molecular weight zinc complexes have already been implicated in biological processes, e.g. with ATP, glutathione, citrate, ethylenediaminedisuccinic acid, nicotianamine, or bacillithiol.
Herpesviruses encode an unusual protein-serine/threonine kinase which is nonessential for growth in cultured cells (1992)

We have performed large-scale random oligonucleotide insertion mutagenesis on a 41-kbp genomic segment derived from the unique long (UL) region of the alphaherpesvirus pseudorabies virus (PRV). This procedure has resulted in the generation of a series of PRV strains, each carrying a single gene whose termination of translation is induced by the inserted oligonucleotide. To relate the genes that were involved in the mutagenization to genes previously identified in herpes simplex virus type 1, the prototype alphaherpesvirus, we have performed cross-hybridization studies. In this way, we have mapped the location of the homolog of a gene which was described to have sequence characteristics of a eukaryotic phosphotransferase. We characterized the phenotype of a mutant PRV strain lacking this putative phosphotransferase also the phenotype of a PRV strain lacking, in addition to the UL-encoded putative phosphotransferase, the protein kinase encoded within the unique short region of the virus. To assess the enzymatic activity of the UL region-encoded phosphotransferase, we expressed the gene transiently in a eukaryotic expression system. Immunoprecipitation of the protein followed by kinase assays and phosphoamino acid analyses revealed protein-serine/threonine kinase activity. Implications of sequence divergence of this protein from classical protein-serine/threonine kinases for kinase structure and function are discussed in view of the recent resolution of the structure of the catalytic domain of cyclic AMP-dependent protein kinase.
Isolation and Characterization of Mouse Innate Lymphoid Cells (2014)

Innate lymphoid cells (ILCs) are rare populations of cytokine-producing lymphocytes and are divided into three groups, namely ILC1, ILC2, and ILC3, based on the cytokines that they produce. They comprise less than 1% of lymphocytes in mucosal tissues and express no unique cell surface markers. Therefore, they can only be identified by combinations of multiple cell surface markers and further characterized by cytokine production in vitro. Thus, multicolor flow cytometry is the only reliable method to purify and characterize ILCs. Here we describe the methods for cell preparation, flow cytometric analysis, and purification of murine ILC2 and ILC3.
<i>In situ</i>HREM irradiation study of point-defect clustering in MBE-grown strained<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Si</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn><mml:mi>−</mml:mi><mml:mi>x</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Ge</mml:mi></mml:mrow><mml:mrow><mml:mi>x</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mo>/</mml:mo><mml:mo>(</mml:mo><mml:mn>001</mml:mn><mml:mo>)</mml:mo><mml:mn/><mml:mi mathvariant="normal">Si</mml:mi></mml:math>structures (2000)

We present a detailed analysis of the point-defect clustering in strained ${\mathrm{S}\mathrm{i}/\mathrm{S}\mathrm{i}}_{1\ensuremath{-}x}{\mathrm{Ge}}_{x}/(001)\mathrm{Si}$ structures, including the interaction of the point defects with the strained interfaces and the sample surface during 400 kV electron irradiation at room temperature. Point-defect cluster formation is very sensitive to the type and magnitude of the strain in the Si and ${\mathrm{Si}}_{1\ensuremath{-}x}{\mathrm{Ge}}_{x}$ layers. A small compressive strain $(\ensuremath{-}0.3%)$ in the SiGe alloy causes an aggregation of vacancies in the form of metastable [110]-oriented chains. They are located on {113} planes and further recombine with interstitials. Tensile strain in the Si layer causes an aggregation of interstitial atoms in the forms of additional [110] rows which are inserted on {113} planes with [001]-split configurations. The chainlike configurations are characterized by a large outward lattice relaxation for interstitial rows $(0.13\ifmmode\pm\else\textpm\fi{}0.01\mathrm{nm})$ and a very small inward relaxation for vacancy chains $(0.02\ifmmode\pm\else\textpm\fi{}0.01\mathrm{nm}).$ A compressive strain higher than $\ensuremath{-}0.5%$ strongly decreases point-defect generation inside the strained SiGe alloy due to the large positive value of the formation volume of a Frenkel pair. This leads to the suppression of point-defect clustering in a strained SiGe alloy so that SiGe relaxes via a diffusion of vacancies from the Si layer, giving rise to an intermixing at the Si/SiGe interface. In material with a 0.9% misfit a strongly increased flow of vacancies from the Si layer to the SiGe layer and an increased biaxial strain in SiGe both promote the preferential aggregation of vacancies in the (001) plane, which relaxes to form intrinsic $60\ifmmode^\circ\else\textdegree\fi{}$ dislocation loops.
MicroRNA-378 limits activation of hepatic stellate cells and liver fibrosis by suppressing Gli3 expression (2016)

Hedgehog (Hh) signalling regulates hepatic fibrogenesis. MicroRNAs (miRNAs) mediate various cellular processes; however, their role in liver fibrosis is unclear. Here we investigate regulation of miRNAs in chronically damaged fibrotic liver. MiRNA profiling shows that expression of miR-378 family members (miR-378a-3p, miR-378b and miR-378d) declines in carbon tetrachloride (CCl4)-treated compared with corn-oil-treated mice. Overexpression of miR-378a-3p, directly targeting Gli3 in activated hepatic stellate cells (HSCs), reduces expression of Gli3 and profibrotic genes but induces gfap, the inactivation marker of HSCs, in CCl4-treated liver. Smo blocks transcriptional expression of miR-378a-3p by activating the p65 subunit of nuclear factor-κB (NF-κB). The hepatic level of miR-378a-3p is inversely correlated with the expression of Gli3 in tumour and non-tumour tissues in human hepatocellular carcinoma. Our results demonstrate that miR-378a-3p suppresses activation of HSCs by targeting Gli3 and its expression is regulated by Smo-dependent NF-κB signalling, suggesting miR-378a-3p has therapeutic potential for liver fibrosis.
A New Strategy for Recycling and Preparation of Poly(<scp>l</scp>-lactic acid):  Hydrolysis in the Melt (2003)

Poly(L-lactide) [i.e., poly(L-lactic acid) (PLLA)] was hydrolyzed in the melt in high-temperature and high-pressure water at the temperature range of 180-350 degrees C for a period of 30 min, and formation, racemization, and decomposition of lactic acids and molecular weight change of PLLA were investigated. The highest maximum yield of l-lactic acid, ca. 90%, was attained at 250 degrees C in the hydrolysis periods of 10-20 min. Too-high hydrolysis temperatures such as 350 degrees C induce the dramatic racemization and decomposition of formed lactic acids, resulting in decreased maximum yield of L-lactic acid. The hydrolysis of PLLA proceeds homogeneously and randomly via a bulk erosion mechanism. The molecular weight of PLLA decreased exponentially without formation of low-molecular-weight specific peaks originating from crystalline residues. The activation energy for the hydrolysis (deltaE(h)) of PLLA in the melt (180-250 degrees C) was 12.2 kcal x mol(-1), which is lower than 20.0 kcal x mol(-1) for PLLA and 19.9 kcal x mol(-1) for poly(dl-lactide) [i.e., poly(DL-lactic acid)] as a solid in the temperature range below the glass-transition temperature (21-45 degrees C). This study reveals that hydrolysis of PLLA in the melt is an effective and simple method to obtain l-lactic acid and to prepare PLLA having different molecular weights without containing the specific low-molecular-weight chains, because of the removal of the effect caused by crystalline residues.
Proactive drive failure prediction for large scale storage systems (2013)

Most of the modern hard disk drives support Self-Monitoring, Analysis and Reporting Technology (SMART), which can monitor internal attributes of individual drives and predict impending drive failures by a thresholding method. As the prediction performance of the thresholding algorithm is disappointing, some researchers explored various statistical and machine learning methods for predicting drive failures based on SMART attributes. However, the failure detection rates of these methods are only up to 50% ~ 60% with low false alarm rates (FARs). We explore the ability of Backpropagation (BP) neural network model to predict drive failures based on SMART attributes. We also develop an improved Support Vector Machine (SVM) model. A real-world dataset concerning 23,395 drives is used to verify these models. Experimental results show that the prediction accuracy of both models is far higher than previous works. Although the SVM model achieves the lowest FAR (0.03%), the BP neural network model is considerably better in failure detection rate which is up to 95% while keeping a reasonable low FAR.