gebhart/patrepeval huggingface dataset:
Proposal for a peptidoglycan‐associating alpha‐helical motif in the C‐terminal regions of some bacterial cell‐surface proteins (1995)

International audience
Biological Action of Leptin as an Angiogenic Factor (1998)

Leptin is a hormone that regulates food intake, and its receptor (OB-Rb) is expressed primarily in the hypothalamus. Here, it is shown that OB-Rb is also expressed in human vasculature and in primary cultures of human endothelial cells. In vitro and in vivo assays revealed that leptin has angiogenic activity. In vivo, leptin induced neovascularization in corneas from normal rats but not in corneas from fa/fa Zucker rats, which lack functional leptin receptors. These observations indicate that the vascular endothelium is a target for leptin and suggest a physiological mechanism whereby leptin-induced angiogenesis may facilitate increased energy expenditure.
Influence Of Electronic Delocalization In Metal-to-Ligand Charge Transfer Excited States (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfluence Of Electronic Delocalization In Metal-to-Ligand Charge Transfer Excited StatesGeoffrey F. Strouse, Jon R. Schoonover, Richard Duesing, Stephen Boyde, Wayne E. Jr. Jones, and Thomas J. MeyerCite this: Inorg. Chem. 1995, 34, 2, 473–487Publication Date (Print):January 1, 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://pubs.acs.org/doi/10.1021/ic00106a009https://doi.org/10.1021/ic00106a009research-articleACS PublicationsRequest reuse permissionsArticle Views1731Altmetric-Citations194LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection (2006)

Retroviruses differ in their preferences for sites for viral DNA integration in the chromosomes of infected cells. Human immunodeficiency virus (HIV) integrates preferentially within active transcription units, whereas murine leukemia virus (MLV) integrates preferentially near transcription start sites and CpG islands. We investigated the viral determinants of integration-site selection using HIV chimeras with MLV genes substituted for their HIV counterparts. We found that transferring the MLV integrase (IN) coding region into HIV (to make HIVmIN) caused the hybrid to integrate with a specificity close to that of MLV. Addition of MLV gag (to make HIVmGagmIN) further increased the similarity of target-site selection to that of MLV. A chimeric virus with MLV Gag only (HIVmGag) displayed targeting preferences different from that of both HIV and MLV, further implicating Gag proteins in targeting as well as IN. We also report a genome-wide analysis indicating that MLV, but not HIV, favors integration near DNase I-hypersensitive sites (i.e., +/- 1 kb), and that HIVmIN and HIVmGagmIN also favored integration near these features. These findings reveal that IN is the principal viral determinant of integration specificity; they also reveal a new role for Gag-derived proteins, and strengthen models for integration targeting based on tethering of viral IN proteins to host proteins.
Drug metabolism in drug discovery and development (2018)

Drug metabolism as a discipline plays an important role in drug discovery and development and the effects of drug metabolism on pharmacokinetics (PK), pharmacodynamics (PD), and safety should be carefully considered. This communication provides an overview of common strategies in the area of drug metabolism for improving PK/PD and safety profiles of drug candidates; these include, but are not limited to, collaboration with medicinal chemists on structure-activity relationships (SAR) to overcome high clearance, using deuterium replacement to further optimize a lead, prodrug approaches to circumvent formulation and delivery difficulties, and addressing issues such as species differences in metabolism, drug-drug interactions (DDI) and formation of reactive metabolites.
Towards the Photonic Nose: A Novel Platform for Molecule and Bacteria Identification (2009)

“Smelling” chemicals and bacteria by using structural color: the photonic nose is a novel platform for the identification of volatile chemicals based on color changes of porous Bragg stack arrays with potential for applications in chemical sensing and bacteria identification. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Combinatorial Methods for the Synthesis of Aluminophosphate Molecular Sieves (1999)

Automatic dispensing of reagents into autoclave blocks followed by synthesis, isolation, and automated structure analysis with X-ray diffractometry represents an efficient methodology for the combinatorial synthesis of microporous materials. The figure shows a typical diffractogram of as-synthesized AFI-type molecular sieves taken with a CCD camera.
Other transgenic mutation assays: Development of a novel mousetk+/− embryonic stem cell line for use in mutagenicity studies (1996)

A tk+/- mouse embryonic stem (ES) cell line, designated 1G2, has been created in which one allele of the thymidine kinase (tk) gene was inactivated by targeted homologous recombination. This line is an analog of the mouse lymphoma tk+/- L5178Y cell line, which is used widely to assess the mutagenicity of chemical agents. Treatment of 1G2 cells with the alkylating agent N-ethyl-N-nitrosourea (ENU) resulted in a dose-related increase in trifluorothymidine-resistant colonies. Mutant frequencies of 152 and 296 per 10(6) cells were determined for 0.1 and 0.3 mg/ml doses of ENU, compared with a spontaneous mutant frequency of 15 per 10(6) cells. The data indicate that tk+/- 1G2 ES cells may be useful for the creation of a transgenic mouse model for assessing in vivo mutation using an endogenous autosomal gene.
Wnt/β-Catenin/Tcf Signaling Induces the Transcription of Axin2, a Negative Regulator of the Signaling Pathway (2002)

Axin2/Conductin/Axil and its ortholog Axin are negative regulators of the Wnt signaling pathway, which promote the phosphorylation and degradation of beta-catenin. While Axin is expressed ubiquitously, Axin2 mRNA was seen in a restricted pattern during mouse embryogenesis and organogenesis. Because many sites of Axin2 expression overlapped with those of several Wnt genes, we tested whether Axin2 was induced by Wnt signaling. Endogenous Axin2 mRNA and protein expression could be rapidly induced by activation of the Wnt pathway, and Axin2 reporter constructs, containing a 5.6-kb DNA fragment including the promoter and first intron, were also induced. This genomic region contains eight Tcf/LEF consensus binding sites, five of which are located within longer, highly conserved noncoding sequences. The mutation or deletion of these Tcf/LEF sites greatly diminished induction by beta-catenin, and mutation of the Tcf/LEF site T2 abolished protein binding in an electrophoretic mobility shift assay. These results strongly suggest that Axin2 is a direct target of the Wnt pathway, mediated through Tcf/LEF factors. The 5.6-kb genomic sequence was sufficient to direct the tissue-specific expression of d2EGFP in transgenic embryos, consistent with a role for the Tcf/LEF sites and surrounding conserved sequences in the in vivo expression pattern of Axin2. Our results suggest that Axin2 participates in a negative feedback loop, which could serve to limit the duration or intensity of a Wnt-initiated signal.
Alteration of zif268 zinc-finger motifs gives rise to non-native zinc-co-ordination sites but preserves wild-type DNA recognition (1998)

Zinc fingers are among the major structural motifs found in proteins that are involved in eukaryotic gene regulation. Many of these zinc-finger domains are involved in DNA binding. This study investigated whether the zinc-co-ordinating (Cys)2(His)2 motif found in the three zinc fingers of zif268 could be replaced by a (Cys)4 motif while still preserving DNA recognition. (Cys)2(His)2-to-(Cys)4 mutations were generated in each of the three zinc fingers of zif268 individually, as well as in fingers 1 and 3, and fingers 2 and 3 together. Whereas finger 1 and finger 3 tolerate the switch, such an alteration in finger 2 renders the polypeptide incapable of DNA recognition. The protein-DNA interaction was examined in greater detail by using a methylation-interference assay. The mutant polypeptides containing the (Cys)4 motif in fingers 1 or 3 recognize DNA in a manner identical to the wild-type protein, suggesting that the (Cys)4 motif appears to give rise to a properly folded finger. Additional results indicate that a zif268 variant containing a (Cys)2(His)(Ala) arrangement in finger 1 is also capable of DNA recognition in a manner identical to the wild-type polypeptide. This appears to be the first time that such alterations, in the context of an intact DNA-binding domain, have still allowed for specific DNA recognition. Taken together, the work presented here enhances our understanding of the relationship between metal ligation and DNA-binding by zinc fingers.
Pegloticase in gout treatment - safety issues, latest evidence and clinical considerations (2017)

Gout is a common rheumatic condition, with increasing prevalence in recent decades. The mainstay of treatment for gout is oral urate-lowering therapy (ULT), typically with xanthine oxidase inhibitors (XOIs). Unfortunately, a proportion of patients have persistent gout that is refractory to ULT. Pegloticase, a recombinant pegylated uricase, has been approved by the US Food and Drug Administration for the treatment of refractory gout. However, concern has been raised regarding the risk of infusion reactions, which are now understood to be largely due to the development of antipegloticase antibodies. Discontinuation of pegloticase upon failure to lower serum urate has been shown to markedly reduce infusion reaction risk, but deprives patients of what, in many cases, is a last-resort treatment. In this manuscript, we review the rationale, mechanism of action, efficacy and safety of pegloticase. Additionally, we focus on potential strategies to reduce pegloticase immunogenicity and potentially make this important agent available to a wider group of patients requiring treatment.
Recent advances in deep learning for speech research at Microsoft (2013)

Deep learning is becoming a mainstream technology for speech recognition at industrial scale. In this paper, we provide an overview of the work by Microsoft speech researchers since 2009 in this area, focusing on more recent advances which shed light to the basic capabilities and limitations of the current deep learning technology. We organize this overview along the feature-domain and model-domain dimensions according to the conventional approach to analyzing speech systems. Selected experimental results, including speech recognition and related applications such as spoken dialogue and language modeling, are presented to demonstrate and analyze the strengths and weaknesses of the techniques described in the paper. Potential improvement of these techniques and future research directions are discussed.
Universal Tre (uTre) recombinase specifically targets the majority of HIV‐1 isolates (2014)

Current drugs against HIV can suppress the progression to AIDS but cannot clear the patient from the virus. Because of potential side effects of these drugs and the possible development of drug resistance, finding a cure for HIV infection remains a high priority of HIV/AIDS research. We recently generated a recombinase (termed Tre) tailored to efficiently eradicate the provirus from the host genome of HIV-1 infected cells by specifically targeting a sequence that is present in the long terminal repeats (LTRs) of the viral DNA [1]. In vivo analyses in HIV-infected humanized mice demonstrated highly significant antiviral effects of Tre recombinase [2]. However, the fact that Tre recognizes a particular HIV-1 subtype A strain may limit its broad therapeutic application. To advance our Tre-based strategy towards a universally efficient cure, we have engineered a new, universal recombinase (uTre) applicable to the majority of HIV-1 infections by the various virus strains and subtypes. We employed the search tool SeLOX [3] in order to find a well-conserved HIV-1 proviral sequence that could serve as target site for a universal Tre from sequences compiled in the Los Alamos HIV Sequence Database. We selected a candidate (termed loxLTRu) with a mean conservation rate of 94% throughout the major HIV-1 subtype groups A, B and C. We applied loxLTRu as substrate in our established substrate-linked protein evolution (SLiPE) process [4] and evolved the uTre recombinase in 142 evolution cycles. Highly specific enzymatic activity on loxLTRu is demonstrated for uTre in both Escherichia coli and human cells. Naturally occurring viral variants with single mutations within the loxLTRu sequence are also shown to be efficiently targeted by uTre, further increasing the range of applicability of the recombinase. Potential off-target sites in the human genome are not recombined by uTre. Furthermore, uTre expression in primary human T cells shows no obvious Tre-related cytopathic or genotoxic effects. Finally, uTre expressing mice show no undesired phenotypes during their normal lifespan. We have developed a broad-range HIV-1 LTR specific recombinase that has the potential to be effective against the vast majority of HIV-1 strains and to cure HIV-1 infected cells from the infection. These results strongly encouraged us in our confidence that a Tre recombinase-mediated HIV eradication strategy may become a valuable component of a future therapy for HIV-infected patients.
FPGA hardware synthesis from MATLAB (2002)

Field Programmable Gate Arrays (FPGAs) have been recently used as an effective platform for implementing many image/signal processing applications. MATLAB is one of the most popular languages to model image/signal processing applications. We present the MATCH compiler that takes MATLAB as input and produces a hardware in RTL VHDL, which can be mapped to an FPGA using commercial CAD tools. This dramatically reduces the time to implement an application on an FPGA. We present results on some image and signal processing algorithms for which hardware was synthesized using our compiler for the Xilinx XC4028 FPGA with an external memory. We also present comparisons with manually designed hardware for the applications. Our results indicate that FPGA hardware can be generated automatically reducing the design time from days to minutes, with the tradeoff that the automatically generated hardware is 5 times slower than the manually designed hardware.
Programación de oleoductos: presentación del problema y revisión de enfoques. (2005)

El transporte de hidrocarburos por oleoducto es el medio que ofrece los costes variables mas bajos asi como un regimen de operacion altamente fiable. Por estas razones, el volumen de productos transportados mediante oleoducto representa una proporcion muy alta con respecto al total. Sin embargo, y pesar de la frecuencia de uso de este medio de transporte y de la importancia de la buena programacion de los oleoductos, la literatura dedicada a este aspecto es relativamente escasa. Una de las posibles razones que justifica este hecho es la elevada complejidad del problema. En la presente comunicacion se examinan los principales trabajos realizados. Dada la complejidad del problema, estos trabajos se caracterizan, y diferencian unos de otros, por el tipo de simplificaciones asumidas (ya sean de caracter topologico, relativas al tamano del programa, al horizonte temporal considerado, a la operacion del oleoducto o la manera en la que se estiman los indices relevantes que permiten evaluarla bondad de un programa). En la comunicacion se examinan y comentan los articulos mas relevantes sobre este tema y se valoran tanto sus ventajas como sus inconvenientes.
The discrete representation of spatially continuous images (1980)

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1980.
Comparison of Weekly Treatment of Postmenopausal Osteoporosis with AlendronateVersusRisedronate Over Two Years (2006)

Patients receiving 70 mg OW alendronate had greater gains in BMD, were more likely to maintain or gain BMD, and had greater reductions in bone turnover markers than patients receiving 35 mg OW risedronate after 24 months, with no differences in upper gastrointestinal tolerability.
On the use of artificial neural networks for the analysis of survival data (1997)

Artificial neural networks are a powerful tool for analyzing data sets where there are complicated nonlinear interactions between the measured inputs and the quantity to be predicted. We show that the results obtained when neural networks are applied to survival data depend critically on the treatment of censoring in the data. When the censoring is modeled correctly, neural networks are a robust model independent technique for the analysis of very large sets of survival data.
The T-box transcription factor Tbx18 maintains the separation of anterior and posterior somite compartments (2004)

The compartmentalization of somites along their anterior-posterior (AP) axis is pivotal to the segmental organization of the vertebrate axial skeleton and the peripheral nervous system. Anterior and posterior somite halves contribute to different vertebral elements. They are also characterized by different proliferation rates and properties with respect to neural crest cell migration and spinal nerve passage. AP-somite polarity is generated in the anterior presomitic mesoderm by Mesp2 and Delta/Notch signaling. Here, we demonstrate that maintenance of AP-somite polarity is mediated by the T-box transcription factor Tbx18. Mice deficient for Tbx18 show expansion of pedicles with transverse processes and proximal ribs, elements derived from the posterior lateral sclerotome. AP-somite polarity is established in Tbx18 mutant embryos but is not maintained. During somite maturation, posterior somite compartments expand most likely because of posterior cells invading the anterior somite half. In the anterior lateral sclerotome, Tbx18 acts as an antiapoptotic factor. Ectopic expression experiments suggest that Tbx18 can promote anterior at the expense of posterior somite compartments. In summary, Tbx18 appears to act downstream of Mesp2 and Delta/Notch signaling to maintain the separation of anterior and posterior somite compartments.
A bHLH transcription factor mediates organ, region and flower type specific signals on dihydroflavonol‐4‐reductase (dfr) gene expression in the inflorescence ofGerbera hybrida(Asteraceae) (1998)

The angiosperm family Asteraceae is characterized by composite inflorescences, which are highly organized structures consisting of different types of flowers. In order to approach the control of floral organ differentiation in Asteraceae at molecular level, we are studying regulation of flavonoid biosynthesis in Gerbera hybrida. Dihydroflavonol-4-reductase (dfr) expression is regulated according to anthocyanin pigmentation patterns in all tested gerbera varieties at several anatomical levels. We have isolated a promoter for one of the dfr genes, Pgdfr2. Gerbera plants transgenic for a Pgdfr2-uidA construct reveal that the activity of the Pgdfr2 promoter from one variety follows the pigmentation in other varieties which have different color patterns. It is thus evident that the observed complex regulation of dfr expression occurs in trans. In order to identify the trans-acting regulators, we isolated a cDNA (gmyc1) homologous to the previously characterized genes encoding bHLH-type regulators of the anthocyanin pathway in plants. The expression of gmyc1 in different varieties suggests that it has a major role in regulating dfr activity in corolla and carpel, but not in pappus and stamen. Specifically in gerbera, the identical patterns of gmyc1 and dfr expression in corolla tissue suggest that GMYC1 also regulates dfr expression in a region and flower type specific manner. Our studies show that in gerbera GMYC1-dfr interaction is part of several developmental processes characteristic for Asteraceae (such as specification of flower types across the composite inflorescence), whereas in other processes (such as differentiation of sepal as pappus) other regulators control dfr expression to determine the spatial specificity.
Resonant cavity LED's optimized for coupling to polymer optical fibers (1999)

Planar resonant-cavity light-emitting diodes have been optimized to meet optical interconnect requirements. The microcavity effect is exploited to increase the extraction efficiency into a given numerical aperture and to reduce the crosstalk in parallel optical interconnect applications. Devices are fabricated with an overall quantum efficiency of 3.7% into a polymer optical fiber with a numerical aperture of 0.5 and a FWHM beam divergence angle of 105/spl deg/ at a drive current of 1 mA.
Multi-Label Classification Using Dependent and Independent Dual Space Reduction (2013)

Journal Article Multi-Label Classification Using Dependent and Independent Dual Space Reduction Get access Eakasit Pacharawongsakda, Eakasit Pacharawongsakda School of Information, Computer, and Communication Technology, Sirindhorn International Institute of Technology, Thammasat University, Pathum Thani, Thailand Search for other works by this author on: Oxford Academic Google Scholar Thanaruk Theeramunkong Thanaruk Theeramunkong * School of Information, Computer, and Communication Technology, Sirindhorn International Institute of Technology, Thammasat University, Pathum Thani, Thailand *Corresponding author: thanaruk@siit.tu.ac.th Search for other works by this author on: Oxford Academic Google Scholar The Computer Journal, Volume 56, Issue 9, September 2013, Pages 1113–1135, https://doi.org/10.1093/comjnl/bxs169 Published: 18 February 2013 Article history Received: 28 March 2012 Revision received: 19 November 2012 Published: 18 February 2013