gebhart/patrepeval huggingface dataset:
Petrophysical Evaluation for Enhancing Hydraulic Stimulation in Horizontal Shale Gas Wells (2010)

Abstract The economic recovery of gas from shale reservoirs requires optimal multistage hydraulic stimulation in horizontal wells. Important parameters to consider in shale-gas evaluation include gas-filled porosity and total organic content. Mechanical rock properties, including a calculated brittleness index, along with mineralogy, are also required to target and design individual horizontal fracture stages in the best zones. This type of formation evaluation in horizontal wells requires careful correlation and calibration to petrophysical measurements obtained in either vertical pilot holes or direct offset wells. This paper presents a comprehensive approach to the evaluation of an unconventional resource play drilled in the Haynesville Shale in east Texas. Using openhole and logging-while-drilling (LWD) logs, conventional core analysis, and a chemostratigraphy analysis of drill cuttings, a shale analysis linking mineralogy, free gas, effective porosity, a shale brittleness index, and a clay linked transverse anisotropy is verified on separate vertical and horizontal control wells. Beyond that, pulsed neutron spectroscopy logs were run to develop a cased-hole evaluation solution from N-N (neural network) modeling that could replicate openhole wireline or LWD logs, and chemostratigraphy mineralogy results. Subsequently, two horizontal wells were logged with LWD tools and afterward, through casing, using the pulsed neutron log and neural network calibration. Fracture stages for the logged horizontal wells were then evaluated vs. the log data. Generally, lower normalized treating pressures per fracture stage are noted where lower clay volumes exhibit less transverse anisotropy and a higher calculated shale brittleness index. Radioactive tracer and production log data also confirm lower amounts of gas production from zones that are apparently fractured, but are more ductile and clay-rich.
Simultaneous high-resolution analysis of vaccinia virus and host cell transcriptomes by deep RNA sequencing (2010)

Deep RNA sequencing was used to simultaneously analyze vaccinia virus (VACV) and HeLa cell transcriptomes at progressive times following infection. VACV, the prototypic member of the poxvirus family, replicates in the cytoplasm and contains a double-stranded DNA genome with approximately 200 closely spaced open reading frames (ORFs). The acquisition of a total of nearly 500 million short cDNA sequences allowed construction of temporal strand-specific maps of the entire VACV transcriptome at single-base resolution and analysis of over 14,000 host mRNAs. Before viral DNA replication, transcripts from 118 VACV ORFs were detected; after replication, transcripts from 93 additional ORFs were characterized. The high resolution permitted determination of the precise boundaries of many mRNAs including read-through transcripts and location of mRNA start sites and adjacent promoters. Temporal analysis revealed two clusters of early mRNAs that were synthesized in the presence of inhibitors of protein as well as DNA synthesis, indicating that they do not correspond to separate immediate- and delayed-early classes as defined for other DNA viruses. The proportion of viral RNAs reached 25-55% of the total at 4 h. This rapid change, resulting in a relative decrease of the vast majority of host mRNAs, can contribute to the profound shutdown of host protein synthesis and blunting of antiviral responses. At 2 h, however, a minority of cellular mRNAs was increased. The overrepresented functional categories of the up-regulated RNAs were NF-kappaB cascade, apoptosis, signal transduction, and ligand-mediated signaling, which likely represent the host response to invasion.
Evaluation of the An-Ident system and an indole spot test for the rapid differentiation of porcine treponemes (1991)

The An-Ident strip system (Analytab Products Inc., St-Laurent, Quebec, Canada) was evaluated for its ability to differentiate Treponema hyodysenteriae from Treponema innocens. Of the 20 tests included on this strip, 15 yielded identical results for the two species. Among the other five assays, none could be considered as a positive discriminator for the two species. However, when an indole spot test with 1% p-dimethylaminocinnamaldehyde was used in parallel, all reference strains and 97% of the isolates of T. hyodysenteriae were positive, whereas all isolates of T. innocens were negative. Our results indicate that An-Indent is of little value for the differentiation of the two species. Our results also suggest that a rapid and simple differentiation between T. hyodysenteriae and T. innocens can be achieved by using the hemolysis and ring phenomenon tests in conjunction with an indole spot test.
Immune Privilege in the Anterior Chamber of the Eye (2002)

Since the 19th century, it has been recognized that the anterior chamber of the eye permits the prolonged, and sometimes permanent, survival of foreign tissue and tumor grafts. It was initially believed that the absence of patent lymphatics draining the interior of the eye prevented antigens from reaching regional lymphoid tissues. However, sequestration of intraocular antigens alone cannot account for ocular immune privilege, and a clear picture is now emerging that a constellation of anatomical, physiological, and dynamic immunoregulatory factors contribute to ocular immune privilege. Ocular fluids contain a potpourri of immunosuppressive and immunoregulatory factors that suppress T-cell proliferation and secretion of proinflammatory cytokines. The interior of the eye is decorated with Fas ligand (CD95L), which induces apoptosis of infiltrating inflammatory cells. Antigens introduced into the eye induce a unique immune deviation in which TH1 responses, namely delayed-type hypersensitivity (DTH), are actively suppressed. Thus, ocular immune privilege is sustained by factors that suppress immune cell proliferation and purge immune cells that enter the eye and by a dynamic immunoregulatory process that suppresses antigen-specific DTH. Suppression of certain inflammatory responses is an important adaptation for preventing immune-mediated injury to ocular tissues that have little or no capacity to regenerate. Thus, immune privilege is a crucial adaptation for preserving vision.
Protein Design and Phage Display (2001)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProtein Design and Phage DisplayRonald H. HoessView Author Information Dupont Pharmaceuticals Company, Experimental Station E336/205, Wilmington, Delaware 19880 Cite this: Chem. Rev. 2001, 101, 10, 3205–3218Publication Date (Web):August 18, 2001Publication History Received2 February 2001Published online18 August 2001Published inissue 1 October 2001https://pubs.acs.org/doi/10.1021/cr000056bhttps://doi.org/10.1021/cr000056bresearch-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views2317Altmetric-Citations131LEARN 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-Alertsclose SUBJECTS:Biopolymers,Genetics,Immunology,Peptides and proteins,Viruses Get e-Alerts
Bispecific Antibodies and Antibody–Drug Conjugates (ADCs) Bridging HER2 and Prolactin Receptor Improve Efficacy of HER2 ADCs (2017)

The properties of cell surface proteins targeted by antibody-drug conjugates (ADCs) have not been fully exploited; of particular importance are the rate of internalization and the route of intracellular trafficking. In this study, we compared the trafficking of HER2, which is the target of the clinically approved ADC ado-trastuzumab emtansine (T-DM1), with that of prolactin receptor (PRLR), another potential target in breast cancer. In contrast to HER2, we found that PRLR is rapidly and constitutively internalized, and traffics efficiently to lysosomes, where it is degraded. The PRLR cytoplasmic domain is necessary to promote rapid internalization and degradation, and when transferred to HER2, enhances HER2 degradation. In accordance with these findings, low levels of cell surface PRLR (∼30,000 surface receptors per cell) are sufficient to mediate effective killing by PRLR ADC, whereas cell killing by HER2 ADC requires higher levels of cell surface HER2 (∼10<sup>6</sup> surface receptors per cell). Noncovalently cross-linking HER2 to PRLR at the cell surface, using a bispecific antibody that binds to both receptors, dramatically enhances the degradation of HER2 as well as the cell killing activity of a noncompeting HER2 ADC. Furthermore, in breast cancer cells that coexpress HER2 and PRLR, a HER2xPRLR bispecific ADC kills more effectively than HER2 ADC. These results emphasize that intracellular trafficking of ADC targets is a key property for their activity and, further, that coupling an ADC target to a rapidly internalizing protein may be a useful approach to enhance internalization and cell killing activity of ADCs. <i>Mol Cancer Ther; 16(4); 681-93. ©2017 AACR</i>.
Mannan derivatives induce phenotypic and functional maturation of mouse dendritic cells (2006)

Mannan, a polysaccharide isolated from yeast binds to C-type lectins of the mannose receptor family, expressed by antigen-presenting cells (APCs) including dendritic cells (DCs) and macrophages. As these receptors mediate endocytosis, they have been targeted with ligands to deliver antigens into APCs to initiate immune responses. Immunization with tumour antigen MUC1 conjugated to oxidized mannan (OM) or reduced mannan (RM) induced differential immune responses in mice, and only mice immunized with OM-MUC1 elicited strong MUC1-specific cytotoxic T lymphocyte responses and protected mice from a MUC1 tumour challenge. In this study, the adjuvant effect of mannan and its derivatives including OM and RM, in comparison to lipopolysaccharide, on DCs were investigated. Mannan, OM and RM were capable of stimulating mouse bone marrow-derived DC in vitro, eliciting enhanced allogeneic T-cell proliferation and enhancing OTI/OTII peptide-specific T-cell responses. Injection of mice with mannan, OM and RM induced a mature phenotype of lymph node and splenic DCs. Analysis by reverse transcription-polymerase chain reaction indicated that Manna, OM and RM also stimulated up-regulation of inflammatory cytokines including interleukin-1beta and tumour necrosis factor-alpha, and differential T helper 1 (Th1)/Th2 cytokines. Subsequent experiments demonstrated that activation of DCs was Toll-like receptor-4-dependent. The data presented here, together with evidence reported previously on OM and RM in induction of immune responses in vivo, suggest that OM and RM exert a dual capacity to target antigen to APCs as well as mature DCs.
Azapurine nucleosides. 3. Synthesis of 7-(.beta.-D-ribofuranosyl)imidazo[4,5-d]-.gamma.-triazin-4-one (2-azainosine) and related derivatives (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAzapurine nucleosides. 3. Synthesis of 7-(.beta.-D-ribofuranosyl)imidazo[4,5-d]-.gamma.-triazin-4-one (2-azainosine) and related derivativesMasajiro Kawana, George A. Ivanovics, Robert J. Rousseau, and Roland K. RobinsCite this: J. Med. Chem. 1972, 15, 8, 841–843Publication Date (Print):August 1, 1972Publication History Published online1 May 2002Published inissue 1 August 1972https://pubs.acs.org/doi/10.1021/jm00278a012https://doi.org/10.1021/jm00278a012research-articleACS PublicationsRequest reuse permissionsArticle Views87Altmetric-Citations24LEARN 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-Alertsclose Get e-Alerts
The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis (2006)

Floral development at the Arabidopsis shoot apical meristem occurs in response to environmental cues that are perceived in different tissues. Photoperiod is detected in the vascular tissue of the leaf (phloem) and promotes production of a systemic signal that induces flowering at the meristem. Vernalization, the response to winter temperatures, overcomes a block on photoperiodic floral induction. In Arabidopsis, this block is caused by inhibitors of flowering that comprise several related MADS-box transcription factors, the most prominent of which is FLC. We show that FLC delays flowering by repressing production in the leaf of at least two systemic signals, one of which is controlled by the RAF kinase inhibitor-like protein FT. Reducing expression of these signals indirectly represses expression of genes involved in floral induction at the meristem. In addition, FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. Repression of genes acting at multiple levels in this hierarchy is required for the extreme delay in flowering caused by FLC. An FLC:HA fusion protein binds directly in vivo to the promoter regions of FD and SOC1 and to the first intron of FT. Thus vernalization relieves transcriptional repression of key regulatory genes in both the leaf and meristem, allowing production of systemic signals in the leaves and conferring competence on the meristem to respond to these signals.
A genetic study of Hirschsprung disease. (1990)

Hirschsprung disease, or congenital aganglionic megacolon, is commonly assumed to be a sex-modified multifactorial trait. To test this hypothesis, complex segregation analysis was performed on data on 487 probands and their families. Demographic information on probands and the recurrence risk to relatives of probands are presented. An increased sex ratio (3.9 male:female) and an elevated risk to sibs (4%), as compared with the population incidence (0.02%), are observed, with the sex ratio decreasing and the recurrence risk to sibs increasing as the aganglionosis becomes more extensive. Down syndrome was found at an increased frequency among affected individuals but not among their unaffected sibs, and the increase was not associated with maternal age. Complex segregation analysis was performed on these family data. The families were classified into separate categories by extent of aganglionosis. For cases with aganglionosis beyond the sigmoid colon, the mode of inheritance is compatible with a dominant gene with incomplete penetrance, while for cases with aganglionosis extending no farther than the sigmoid colon, the inheritance pattern is equally likely to be either multifactorial or due to a recessive gene with very low penetrance. A model of gene action with random effects during morphogenesis is compatible with our observations.
Early Enteral Feeding in Postsurgical Cancer Patients (1996)

Early enteral feeding with FOSL-HN was safe and well tolerated. Results suggest that the use of such a formula during the postoperative period may reduce the number of infections and gastrointestinal complications per patient, as well as improve renal and liver function through modulation of urinary prostaglandin levels. Additional clinical trials to fully quantify clinical benefits and optimize nutritional support with FOSL-HN should be undertaken.
Performance assessment measures for univariate feedforward/feedback control (1993)

Abstract An analysis of variance for univariate feedforward/feedback systems has been derived which allows the variance contributions due to both disturbances and controllers to be established. A performance index which assesses the performance of the overall control scheme has been developed. Estimates of the analysis of variance and performance index can be obtained using ordinary closed loop data and least squares regression. These quantities can be used on‐line or off‐line for either the design of new controllers or as a means of assessing the performance of existing feedforward/feedback control schemes. The practicality of the results in the paper are demonstrated using simulated and industrial data.
Physiologic Oxygen Concentration Enhances the Stem-Like Properties of CD133+ Human Glioblastoma Cells In vitro (2009)

In vitro investigations of tumor stem-like cells (TSC) isolated from human glioblastoma (GB) surgical specimens have been done primarily at an atmospheric oxygen level of 20%. To determine whether an oxygen level more consistent with in situ conditions affects their stem cell-like characteristics, we compared GB TSCs grown under conditions of 20% and 7% oxygen. Growing CD133(+) cells sorted from three GB neurosphere cultures at 7% O(2) reduced their doubling time and increased the self-renewal potential as reflected by clonogenicity. Furthermore, at 7% oxygen, the cultures exhibited an enhanced capacity to differentiate along both the glial and neuronal pathways. As compared with 20%, growth at 7% oxygen resulted in an increase in the expression levels of the neural stem cell markers CD133 and nestin as well as the stem cell markers Oct4 and Sox2. In addition, whereas hypoxia inducible factor 1alpha was not affected in CD133(+) TSCs grown at 7% O(2), hypoxia-inducible factor 2alpha was expressed at higher levels as compared with 20% oxygen. Gene expression profiles generated by microarray analysis revealed that reducing oxygen level to 7% resulted in the up-regulation and down-regulation of a significant number of genes, with more than 140 being commonly affected among the three CD133(+) cultures. Furthermore, Gene Ontology categories up-regulated at 7% oxygen included those associated with stem cells or GB TSCs. Thus, the data presented indicate that growth at the more physiologically relevant oxygen level of 7% enhances the stem cell-like phenotype of CD133(+) GB cells.
Switching response modeling of the CMOS inverter for sub-micron devices (1998)

In this paper an accurate, analytical model for the evaluation of the CMOS inverter delay in the sub- micron regime, is presented. A detailed analysis of the inverter operation is provided which results to accurate expressions describing the output waveform. These analytical expressions are valid for all the inverter operation regions and input waveform slopes. They take into account the influences of the short- circuit current during switching, and the gate-to- drain coupling capacitance. The presented model shows clearly the influence of the inverter design characteristics, the load capacitance, and the slope of the input waveform driving the inverter on the propagation delay. The results are in excellent agreement with SPICE simulations.
The Kinetics of the Cerium(IV)—Chloride Reaction. The Cerium(IV)—Thallous Reaction in the Presence of Chloride (1953)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Kinetics of the Cerium(IV)—Chloride Reaction. The Cerium(IV)—Thallous Reaction in the Presence of ChlorideFrederick R. Duke and Curtis E. BorchersCite this: J. Am. Chem. Soc. 1953, 75, 21, 5186–5188Publication Date (Print):November 1, 1953Publication History Published online1 May 2002Published inissue 1 November 1953https://pubs.acs.org/doi/10.1021/ja01117a010https://doi.org/10.1021/ja01117a010research-articleACS PublicationsRequest reuse permissionsArticle Views128Altmetric-Citations12LEARN 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-Alertsclose Get e-Alerts
St. John's wort induces hepatic drug metabolism through activation of the pregnane X receptor (2000)

St. John's wort (Hypericum perforatum) is an herbal remedy used widely for the treatment of depression. Recent clinical studies demonstrate that hypericum extracts increase the metabolism of various drugs, including combined oral contraceptives, cyclosporin, and indinavir. In this report, we show that hyperforin, a constituent of St. John's wort with antidepressant activity, is a potent ligand (K(i) = 27 nM) for the pregnane X receptor, an orphan nuclear receptor that regulates expression of the cytochrome P450 (CYP) 3A4 monooxygenase. Treatment of primary human hepatocytes with hypericum extracts or hyperforin results in a marked induction of CYP3A4 expression. Because CYP3A4 is involved in the oxidative metabolism of >50% of all drugs, our findings provide a molecular mechanism for the interaction of St. John's wort with drugs and suggest that hypericum extracts are likely to interact with many more drugs than previously had been realized.