gebhart/patrepeval huggingface dataset:
Detectable Changes in The Blood Transcriptome Are Present after Two Weeks of Antituberculosis Therapy (2012)

Significant changes in the transcriptional signatures measured by blood tests were readily detectable just 2 weeks after treatment initiation. These findings suggest that blood transcriptional signatures could be used as early surrogate biomarkers of successful treatment response.
Stellate cells are mesenchymal stem cells (2014)

Background Vitamin A-storing hepatic stellate cells (HSC) are mainly known for their contribution to fibrogenesis in chronic liver disease, but their identity and function in normal liver remained unclear. Since HSC possess stem/ progenitor cell characteristics [1] their contribution to stem cell-associated functions in the liver was investigated. Stem cell functions in the liver were reported during fetal hematopoiesis and tissue repair after severe injury when the proliferation of hepatocytes is impaired. By using several in vitro and in vivo approaches evidence was provided that stellate cells represent mesenchymal stem cells (MSC), which can support hematopoietic stem/progenitor cells in the fetal liver and contribute to the regeneration of injured liver as multipotent adult stem cells.
Cellular compartmentalization of secondary metabolism (2015)

Fungal secondary metabolism is often considered apart from the essential housekeeping functions of the cell. However, there are clear links between fundamental cellular metabolism and the biochemical pathways leading to secondary metabolite synthesis. Besides utilizing key biochemical precursors shared with the most essential processes of the cell (e.g., amino acids, acetyl CoA, NADPH), enzymes for secondary metabolite synthesis are compartmentalized at conserved subcellular sites that position pathway enzymes to use these common biochemical precursors. Co-compartmentalization of secondary metabolism pathway enzymes also may function to channel precursors, promote pathway efficiency and sequester pathway intermediates and products from the rest of the cell. In this review we discuss the compartmentalization of three well-studied fungal secondary metabolite biosynthetic pathways for penicillin G, aflatoxin and deoxynivalenol, and summarize evidence used to infer subcellular localization. We also discuss how these metabolites potentially are trafficked within the cell and may be exported.
Photoisomerization of Azobenzenecarboxylic Acids and Their Potassium Salts:  Evidence of Structural Volume Changes Associated with Hydrogen Bond Formation (1999)

The contractions determined by laser-induced optoacoustic spectroscopy (LIOAS) for the E → Z photoisomerization of the three isomers (para, meta, and ortho) of azobenzenecarboxylates in 0.01 M potassium phosphate buffer (pH 8) are rationalized in terms of the difference in the chromophore−water hydrogen bonds strength between the photoisomer and the parent compound. The relatively high concentration of K+ is needed to solubilize the compounds by means of interrupting the intermolecular interactions. At this salt concentration a large portion of the anions is paired with potassium ions. Due to the reduced conjugation, a stronger interaction of the nitrogens' lone pairs and water is expected in the Z isomers, leading to the contraction upon isomerization. A higher K+ concentration reduces the structural volume change as a consequence of its perturbing the hydrogen bond network. No structural volume change was observed for the E → Z photoisomerization of meta-azobenzenecarboxylic acid in a series of cyclic alkanes, consistent with the assignment of the changes to variations in the hydrogen bonds strengths, in view of the lack of those bonds in the cycloalkanes. Despite the relatively large error of the Z−E energy differences derived from LIOAS, they are near those reported for nonsubstituted azobenzene and larger than those calculated for both free acid and lithium salts. With the LIOAS-derived structural volume changes ΔVR and the quantitative relationship ΔSR = (cpρ/β)ik ΔVR/T [(cpρ/β)ik = 14 kJ cm-3, the ratio of thermoelastic parameters at the isokinetic temperature in water, ca. 300 K], a large entropic term, in turn determined by the specific solute−water interactions, is calculated for the Z → E thermal isomerization.
[The need for the use of chromogens for quantifying Leishmania promastigotes on plates from 96 wells]. (2001)

The existing difficulties in the treatment of leishmaniasis justify the testing of the effect of new products on parasite forms in the search of a therapeutic alternative for the parasitosis. Given the need of establishing a method to evaluate the activity of natural synthetic products in vitro under the Cuban conditions, this paper was aimed at defining the usefulness of p-nitrophenilphosphate as a chromogenic substance for quantification of parasites in plaques from 96 wells. To standardize this colorimetric method the stages of the parasite growth curve were set. The study of linearity and selection of the sample size, which was optional for these assays, showed that it was possible to obtain maximum linear determination coefficient with 20 mm. Likewise, the variation coefficient was compared with and without the chromogen and the effect of changes in culture medium on the reading of absorbances was analyzed. The set limit of quantification proved the need of using chromogen for the purposes of this paper and the general results allow to recommend this less subjective, simpler and quicker methodology to test products of interest in this field.
Predicting mab product yields from cultivation media components, using near‐infrared and 2D‐fluorescence spectroscopies (2011)

The yield of monoclonal antibody (Mab) production processes depends on media formulation, inocula quality, and process conditions. As in industrial processes tight cultivation conditions are used, and inocula quality and viable cell densities are controlled to reasonable levels, media formulation and raw materials lot-to-lot variability in quality will have, in those circumstances, the highest impact on process performance. In the particular Mab process studied, two different raw materials were used: a complex carbon and nitrogen source made of specific peptones and defined chemical media containing multiple components. Using different spectroscopy techniques for each of the raw material types, it was concluded that for the complex peptone-based ingredient, near-infrared (NIR) spectroscopy was more capable of capturing lot-to-lot variability. For the chemically defined media containing fluorophores, two-dimensional (2D)-fluorescence spectroscopy was more capable of capturing lot-to-lot variability. Because in Mab cultivation processes both types of raw materials are used, combining the NIR and 2D-fluorescence spectra for each of the media components enabled predictive models for yield to be developed that out-performed any other model involving either one raw material alone, or only one type of spectroscopic tool for both raw materials. For each particular raw material, the capability of each spectroscopy to detect lot-to-lot differences was demonstrated after spectra preprocessing and specific wavelength regions selection. The work described and the findings reported here open up several possibilities that could be used to feed-forward control the process. These include, for example, enabling specific actions to be taken regarding media formulation with particular lots, and all types of predictive control actions aimed at increasing batch-to-batch yield and product quality consistency at harvest.
Cation radical salts of phenazine (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCation radical salts of phenazineZ. G. Soos, H. J. Keller, W. Moroni, and D. NoetheCite this: J. Am. Chem. Soc. 1977, 99, 15, 5040–5044Publication Date (Print):June 1, 1977Publication History Published online1 May 2002Published inissue 1 June 1977https://pubs.acs.org/doi/10.1021/ja00457a024https://doi.org/10.1021/ja00457a024research-articleACS PublicationsRequest reuse permissionsArticle Views531Altmetric-Citations37LEARN 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
Micro-aperture surface emitting laser for near field optical data storage (2003)

An ultra-high density optical memory using near field optics has been attracting much interest for future data storage. Betzig and coworkers (1992) demonstrated optical recording by an optical scanning microscope (NSOM) and suggested the possibility of tera byte data storage. One of the authors (K. Goto) proposed (1998) a tera byte optical memory system using a VCSEL array. One of the key issues in the proposed optical disk system is to realize an optical head consisting of a 2-dimensional VCSEL array. In near-field optics memory, there still remains the difficulty in getting a high output power efficiently from a sub-wavelength sized aperture. It is especially important to realize a high efficiency VCSEL for optical heads by reducing the total power consumption in arrays. We proposed a metal aperture VCSEL for producing near field light with high efficiency. In the study, we carried out a near field analysis of a micro-aperture VCSEL and present some basic process technologies for realizing the proposed device.
Airway Epithelial Cells: Current Concepts and Challenges (2008)

The adult human bronchial tree is covered with a continuous layer of epithelial cells that play a critical role in maintaining the conduit for air, and which are central to the defenses of the lung against inhaled environmental concomitants. The epithelial sheet functions as an interdependent unit with the other lung components. Importantly, the structure and/or function of airway epithelium is deranged in major lung disorders, including chronic obstructive pulmonary disease, asthma, and bronchogenic carcinoma. Investigations regarding the airway epithelium have led to many advances over the past few decades, but new developments in genetics and stem cell/progenitor cell biology have opened the door to understanding how the airway epithelium is developed and maintained, and how it responds to environmental stress. This article provides an overview of the current state of knowledge regarding airway epithelial stem/progenitor cells, gene expression, cell-cell interactions, and less frequent cell types, and discusses the challenges for future areas of investigation regarding the airway epithelium in health and disease.
Application of a Direct Flow Cytometric Erythrocyte Immunofluorescence Assay in Dogs with Immune-Mediated Hemolytic Anemia and Comparison to the Direct Antiglobulin Test (2001)

A direct flow cytometric erythrocyte immunofluorescence assay (FC) was developed and compared with the direct antiglobulin test (DAT) for detection of erythrocyte-bound immunoglobulin (IgG and IgM) and complement (C3) in dogs with immune-mediated hemolytic anemia (IMHA). Tests were performed on erythrocytes from 13 healthy nonanemic dogs and from 13 anemic dogs with IMHA. The FC and DAT were negative for erythrocyte-bound immunoglobulin in all healthy dogs. The FC was negative for erythrocyte-bound C3 in 12 healthy dogs and positive in 1 healthy dog, and the DAT was negative for C3 in all healthy dogs. Of the 13 IMHA dogs tested for erythrocyte-bound IgG, 12 were positive using the FC and 7 were positive using the DAT. Sensitivity for the detection of erythrocyte-bound IgG in the 26 dogs was 92% for FC and 53% for DAT. Specificity for detection of erythrocyte bound IgG for FC and DAT was 100%. The addition of IgM and/ or C3 did not increase the sensitivity for FC or DAT. In this group of dogs, the FC provided a more rapid, cost-effective, sensitive, objective method to quantitate erythrocyte-bound immunoglobulin and/or complement compared with the currently used DAT.
Image-Based Atmospheric Corrections - Revisited and Improved (1996)

A major benefit of multitemporal, remotely sensed images is their applicability to change detection over time. Because of concerns about global and environmental change, these data are becoming increasingly more important. However, to maximize the usefulness of the data from a multitemporal point of view, an easy-to-use, cost-effective, and accurate radiometric calibration and correction procedure is needed. The atmosphere effects the radiance received at the satellite by scattering, absorbing, and refracting light; corrections for these effects, as well as for sensor gains and offsets, solar irradiance, and solar zenith angles, must be included in radiometric correction procedures that are used to convert satellite-recorded digital counts to ground reflectances. To generate acceptable radiometric correction results, a model is required that typically uses in-situ atmospheric measurements and radiative transfer code (RTC) to correct for atmospheric effects. The main disadvantage of this type of correction procedure is that it requires in-situ field measurements during each satellite overflight. This is unacceptable for many applications and is often impossible, as when using historical data or when working in very remote locations. The optimum radiometric correction procedure is one based solely on the digital image and requiring no in-situ field measurements during the satellite overflight. The darkobject subtraction (DOS) method, a strictly image-based technique, is an attempt to achieve this ideal procedure. However, the accuracy is not acceptable for many applications, mostly because it corrects only for the additive scattering effect and not for the multiplicative transmittance effect. This paper presents an entirely image-based procedure that expands on the ~10s model by including a simple multiplicative correction for the effect of atmospheric transmittance. Two straightforward methods to derive the multiplicative transmittance-correction coefficient are presented. The COSITZ) or COST method uses the cosine of the solar zenith angle, which, to a first order, is a good approximation of the atmospheric transmittance for the dates und sites used in this study. The default TAUS method uses the average of the transmittance values computed by using in-situ atmospheric field measurements made during seven different satellite overflights. Published and unpublished data made available for this study by Moran et al. (1992) are used, and my model results are compared with their results. The corrections generated by the entirely image-based COST model are as accurate as those generated by the models that used in-situ atmospheric field measurements and RTC software.
Role of<i>β</i>-Casein in Milk Curdling (1982)

Journal Article Role of β-Casein in Milk Curdling Get access Se-Eok Yun, Se-Eok Yun Department of Food Science and Technology, Faculty of Agriculture, Nagoya University, Chikusa-ku, Nagoya 464, Japan Search for other works by this author on: Oxford Academic Google Scholar Kunio Ohmiya, Kunio Ohmiya Department of Food Science and Technology, Faculty of Agriculture, Nagoya University, Chikusa-ku, Nagoya 464, Japan Search for other works by this author on: Oxford Academic Google Scholar Shoichi Shimizu Shoichi Shimizu Department of Food Science and Technology, Faculty of Agriculture, Nagoya University, Chikusa-ku, Nagoya 464, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 46, Issue 2, 1 February 1982, Pages 443–449, https://doi.org/10.1080/00021369.1982.10865077 Published: 01 February 1982 Article history Received: 02 July 1981 Published: 01 February 1982
Photochemical reactions in organized monolayer assemblies. I. Cis-trans isomerization of thioindigo dyes (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemical reactions in organized monolayer assemblies. I. Cis-trans isomerization of thioindigo dyesDavid G. WhittenCite this: J. Am. Chem. Soc. 1974, 96, 2, 594–596Publication Date (Print):January 1, 1974Publication History Published online1 May 2002Published inissue 1 January 1974https://pubs.acs.org/doi/10.1021/ja00809a052https://doi.org/10.1021/ja00809a052research-articleACS PublicationsRequest reuse permissionsArticle Views155Altmetric-Citations57LEARN 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
Enzyme Immunoassay for Autoantibodies to Human Liver-Type Arginase and Its Clinical Application (2000)

The ELISA for anti-liver-type arginase autoantibody improved the detectability of autoimmune hepatitis when compared with established assays for liver-specific autoantibodies.
Thickness determination of thin oxide layers on metal surfaces using X-ray photoelectron spectroscopy. (1991)

薄い金属酸化膜試料の膜厚をX線光電子分光法により測定した.試料としてAl2O3/Al,PbO/Pb,MgO/Mg,SiO2/Siを用いた.光電子スペクトルは酸化物と金属成分に対応したダブルピーク構造を示す.各々のピーク強度を光電子取り出し角度を変えて測定し角度ごとに膜厚を求めた.又光電子平均自由行程の違いによる影響を見るためX線源としてマグネシウムKα線及びアルミニウムKα線を用いた.各X線源に対して得られた膜厚は6%の誤差範囲で一致した.表面粗さが無視できる平滑な試料に対してはあるひとつの光電子取り出し角度(θ)の測定で十分であることが確かめられた.しかし鉛試料の場合膜厚はθとともに系統的に変化しており表面粗さの影響を受けていることが分かった.この様な試料に対しては複数のθについて測定を行い膜厚を決める必要があることが確認された.大気中に長期間放置したAl2O3/Al及びSiO2/Si試料の膜厚は各々約33Å,11Åと導出された.
Aspen stand conditions on elk winter ranges in the northern Yellowstone, USA (2005)

Aspen (Populus tremuloides) stands inside and outside Yellowstone National Park (YNP), Wyoming, USA, were compared to test whether the lack of overstory aspen recruitment observed in YNP extended to winter ranges of elk (Cervus elaphus) in adjacent national forests. Remote sensing and field-collected data were obtained from aspen stands in YNP (n = 93), the Gallatin National Forest (n = 63), and the Sunlight/Crandall elk wintering area (n = 54) of the Shoshone National Forest. Remote sensing results indicated aspen canopy coverage decline in all three sites from the 1950s to the 1990s, but the proportional rate of decline was greater in YNP than in the national forest sites. Field data indicated that the density of live aspen overstory stems were significantly lower in YNP compared to the two national forest sites. Live aspen stems < 10 cm diameter at breast height were observed in YNP only in stands located in scree habitats, but were commonly observed in the national forest sites. Among the three study areas, no significant differences were observed in density of aspen ramets, the percentage of browsed ramets, or the density of conifers within aspen stands. However, the two national forest sites had a higher percentage of aspen stands containing ramets > 100 cm tall and a lower incidence of bark scarring on overstory aspen stems compared to YNP. Within YNP, aspen stands on scree habitat had a lower percentage of browsed ramets and more stems in small size classes compared to aspen stands in other habitat types. Collectively, these results indicate that while aspen cover has declined across all sites, the national forest sites have had successful recruitment of replacement overstory aspen stems. In contrast, overstory aspen in YNP are recruiting only in areas protected from browsing, such as on scree habitat. We suggest that differences in ungulate densities and foraging behaviors may explain the differences in aspen regeneration observed among the three sites.
Dyeability of Nomex® Aramid Yarn (1986)

Treatments in highly polar solvents, such as dimethyl formamide, dimethyl acet amide, and dimethyl sulfoxide, under suitable conditions have been found to improve the dyeability of Nomex® yam so that it can be dyed under atmospheric conditions in a reasonable length of time without the aid of a carrier. Essentially, these solvents provide chemical energy to the yam, permitting rearrangements of the polymer chains through breakage and reformation of interchain hydrogen bonding. The changes in dyeability may be attributed to orientation changes or to microvoid formation occurring in the fiber structure during treatment.
Cytokine gene regulation by PGE2, LTB4 and PAF (1992)

The initial response of the host to noxious stimuli produces a nonspecific inflammatory response. A more specific immune response is believed to be modulated by two classes of molecules: lipid mediators (PG, LT and PAF) and cytokines, synthesized by phagocytes and parenchyreal cells. In this review we discuss the increasing evidence of the interrelationship between eicosanoids, PAF and cytokines: IL-1 and TNF induce PG synthesis in various cells and PG, in turn, modulate cytokine production. We focused on the regulatory effects of LTB(4), PGE(2) and PAF on cytokine gene expression.
Comparison of CSS and SAGD Performance in the Clearwater Formation at Cold Lake (2002)

Abstract Data are available for four SAGD projects and two CSS projects operating in the Clearwater formation at Cold Lake. This paper uses these data to compare the energy efficiency and recovery performance of SAGD and CSS. For the conditions outlined in this paper, field data demonstrate that: Bitumen recovery using SAGD is generally uneconomic in the Clearwater formation.Bitumen recovery using CSS in the Clearwater formation:Produces as much as 50% or more bitumen/m3 external gas consumed than SAGD; andWill result in significantly higher overall bitumen recoveries (as a percentage of OBIP) than SAGD. These observations are consistent with industry experience in non-Clearwater SAGD and CSS operations. In addition, operating and design data for commercial SAGD and CSS projects is used to demonstrate that: Due to differences in steam quality, SOR is not an appropriate indicator of energy efficiency. Energy efficiency comparisons are more appropriately based on the quantity of external gas required to produce 1-m3 of bitumen.To convert SOR data to an external gas requirement, the following conversion factors are proposed: 1-m3 wet (80% quality) steam requires approximately 60-m3 gas.1-m3 dry (100% quality) steam requires approximately 75-m3 gas.The use of project specific EBIP, versus OBIP, in calculating recovery makes meaningful comparisons difficult.