gebhart/patrepeval huggingface dataset:
Transmission Efficiency (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
A Novel Oncogenic Role of Inositol Phosphatase SHIP2 in ER-Negative Breast Cancer Stem Cells: Involvement of JNK/Vimentin Activation (2014)

Overexpression of SH2-containing-5'-inositol phosphatase-2 (SHIP2) correlates with poor survival in breast cancer. However, its role in breast cancer stem cells (BCSCs) remains unclear. Here, we showed that the percentage of SHIP2(+) cells was positively correlated with that of CD24(-) CD44(+) cells in 60 breast cancer specimens. Among 20 estrogen receptor (ER)-negative samples, 17 had greater SHIP2 expression in CD24(-) CD44(+) subpopulation than the remaining subpopulation. Data mining of microarray analysis of 295 breast tumors showed a significant correlation of higher SHIP2 expression with distant metastasis. Examination of patient-derived mouse xenografts revealed that SHIP2 protein and its tyrosine 1135 phosphorylation were significantly higher in BCSCs, identified as CD24(-) CD44(+) or aldehyde dehydrogenase (ALDH(+)), than non-BCSCs. SHIP2 silencing or inhibitor of SHIP2 phosphatase significantly decreased mammosphere-forming efficiency, ALDH(+) subpopulation in vitro and tumorigenicity of BCSCs in vivo. Overexpression of SHIP2 enhanced the expression of epithelial-mesenchymal transition markers including vimentin (VIM), which was mainly expressed in ER-negative breast cancer cells with higher level in mammospheres than monolayer culture. Ablation of c-Jun N-terminal kinase 1 (JNK1), JNK2, or VIM diminished the increased ALDH(+) population and tumorigenicity, induced by SHIP2 overexpression. BCSCs displayed greater expression of phospho-JNK than non-BCSCs and silencing of JNK suppressed SHIP2-mediated upregulation of VIM. Furthermore, SHIP2 overexpression enhanced Akt activation, but Akt inhibition failed to influence SHIP2-induced phospho-JNK/VIM upregulation. In conclusion, SHIP2 plays a key role in BCSCs of ER-negative breast cancers through activation of Akt and JNK with upregulation of VIM and may serve as a target for therapy directed at BCSCs.
Body Mass Index, Cigarette Smoking, and Other Characteristics as Predictors of Self-Reported, Physician-Diagnosed Gallbladder Disease in Male College Alumni (1998)

Despite the high prevalence of gallbladder disease in industrialized countries, little is known about the predictors of the disease, especially in men. The authors prospectively studied 16,785 alumni of Harvard University, aged 15-24 years, who were followed for up to 61 years. The health characteristics of these men were ascertained from their college entrance physical examination done in 1916-1950, and updated via mailed questionnaires in 1962 or 1966 (1962/1966). Alumni subsequently self-reported physician-diagnosed gallbladder disease on further mailed questionnaires in 1972 or 1977. Between college time and 1962/1966, 371 gallbladder disease cases occurred. An additional 314 cases occurred after 1962/1966. With respect to college characteristics, after adjustment for potential confounders, the authors found that body mass index (BMI), smoking, physical activity, blood pressure, and consumption of alcohol, coffee, or tea were unrelated to risk. However, BMI in 1962/1966 was directly related to risk of subsequent gallbladder disease, as was BMI gain since college (p, trend = 0.002 and 0.013, respectively). Compared with men with BMI < 22.0, men with BMI > or = 27.0 had a rate ratio of 2.71 (95% confidence interval (CI) 1.57-4.66) for risk of contracting the disease. Men who gained > or = 6.0 BMI units since college had a rate ratio of 1.46 (95% CI 0.86-2.46) compared with men who gained -0.9 to +0.9 BMI units. Compared with never smokers, men who smoked pipes or cigars or < 1 pack of cigarettes daily in 1962/1966 had a rate ratio of 1.43 (95% CI 1.00-2.06), while heavier cigarette smokers had a rate ratio of 1.52 (95% CI 1.03-2.24). Neither physical activity nor physician-diagnosed hypertension or diabetes mellitus in 1962/1966 predicted risk.
Studies on a septic rabbit model which develops MOF associated with DIC; Effects of anticoagulant therapy. (1988)

The present study was conducted to analyse the predisposed conditions developing multiple organ failure (MOF) in sepsis. Primarily a sepsis model was established to confirm the hypothesis that DIC predisposes MOP.Fecal suspension was injected fined into ligated biliary tree in Japan male rabbits. After the insult, serial blood sampling disclosed the onset of DIC with decrease of pletelet counts, leukocyte counts, and fibrinogen concentrations and with prolongation of PT and APTT values. Simultaneously serum bilirubin and creatinine levels elevated. Plasma endotoxin concentrations also gradually elevated. In the histological examinations of the liver, multiple focal necrosis and neutrophil infiltration into sinusoid were observed.Heparin (50u/kg/h) and MD 805 (a specific trombin inhibitor; 300μg/kg/h) treatments significantly prevented decrease of platelet counts and elevation of bilirubin and creatinine levels in sepsis. The histological changes of the liver were minimized by both heparin and MD 805. Thus, these results indicate that hypercoagulable state undoubtedly contributes to the progression of MOF, which can be controlled by anticoagulant therapy.
Beam-deflection optical tomography of a flame (1987)

We report three-dimensional index-of-refraction measurements in a methane-air slot diffusion flame and a methane-air slot subsonic jet using beam-deflection optical tomography. The horizontal and vertical spatial resolutions are 0.26 and 0.635 mm, respectively. The peak temperature is calculated from the index-of-refraction map for the flame and compared with thermocouple temperature measurements.
Delineation of Three Classes of CEA Antigenic Determinants: Identification of Membrane-Associated CEA as an Independent Species of CEA (1977)

Abstract The immunochemical relationship between membrane-associated CEA (CEA-M) and isolated conventional whole CEA and the species CEA-S was investigated. These glycoproteins gave precipitin reactions of apparent identity by using antisera to CEA-M and CEA-S; however, the binding of each of these glycoproteins relative to one another by anti-tumor glycoprotein, anti-CEA-S, and anti-CEA-M anti-sera differed to a significant degree, indicative of some degree of nonidentity. Competitive inhibition radioimmunoassay with a 125I CEA-S ligand and a broadly reactive anti-CEA-S antiserum demonstrated that all three glycoproteins possessed in common antigenic determinants of the CEA group of glycoproteins but at apparent different concentration. These appeared to reflect the presence of CEA group-specific determinants. On the other hand, when 125I CEA-M and an anti-CEA-M antiserum were used in competitive inhibition assays, both CEA and CEA-S were antigenically deficient relative to CEA-M. After absorption of the anti-CEA-M with CEA, CEA-M produced complete inhibition, SDS-unfolded CEA produced 60% inhibition and CEA was unreactive. This antiserum was further absorbed with SDS-unfolded CEA and used in assay with 125I CEA-M. Although CEA-M remained reactive, CEA or CEA subjected to denaturants such as SDS, 2-mercaptoethanol, and SDS with 2-mercaptoethanol did not inhibit this assay system, indicating the absence of the remaining determinants present on CEA-M. Based on these observations we have proposed the existence not only of CEA group-specific determinants but also the existence of CEA cryptic determinants that may be generated from soluble forms of CEA and CEA-S by unfolding and exposure of cryptic sites. In addition, the existence of CEA species-specific determinants, which appear to be unique to a particular species of CEA, have been demonstrated. In a CEA-M-specific radioimmunoassay system with CEA-M absorbed antiserum the CEA-M species-specific determinants can be directly demonstrated in micro-some-rich homogenates of colonic adenocarcinomas. Thus, molecules bearing CEA-M species-specific determinants are produced by cells and are not an artifact of isolation of CEA-M. Demonstration of this third class of determinants on CEA-M in this study establishes that it is an independent species of CEA.
Protocol for the 3HP Options Trial: a hybrid type 3 implementation-effectiveness randomized trial of delivery strategies for short-course tuberculosis preventive therapy among people living with HIV in Uganda (2020)

ClinicalTrials.gov: NCT03934931 ; Registered 2 May 2019.
High‐Temperature Superconducting ( HTS ) Leads (2016)

The article contains sections titled: Introduction High‐Field Magnets Low‐Field Magnets Outlook
Altered adrenal and gonadal steroids biosynthesis in patients with burn injury (2016)

Burn injury alters endogenous steroid biosynthesis, with decreased testosterone concentrations and elevated estrone concentrations, during the first 21 days after the injury. Concentrations of glucocorticoids, progestagens and androgen precursors correlated positively with the area of burn injury. The finding of increased estrone following burn injury needs to be confirmed in a larger hypothesis-driven study.
Mechanism of Regioselective Ring-Opening Reactions of 1,2-Epoxyoctane Catalyzed by Tris(pentafluorophenyl)borane: A Combined Experimental, Density Functional Theory, and Microkinetic Study (2018)

A nonconventional, water-mediated catalytic mechanism was proposed to explain the effects of residual water on the reactivity and regioselectivity of tris(pentafluorophenyl)borane catalyst in the ring-opening reaction of 1,2-epoxyoctane by 2-propanol. This nonconventional mechanism was proposed to operate in parallel with conventional Lewis acid-catalyzed ring-opening. Microkinetic modeling was conducted to validate the proposed reaction mechanism, with all kinetic and thermodynamic parameters derived from density functional theory (DFT) calculations. Experimental data at a variety of temperatures and water contents were captured by the model after adjustments within reasonable limits set by experimental benchmarking and accuracy of theory of a small subset of parameters. In addition, the microkinetic model was able to generate accurate predictions at reaction conditions that were not used for parameter estimation. Detailed analysis of the net reaction rates showed that >95% of the reaction flux passed through conventional Lewis-acid pathways at water levels <500 ppm, even though the borane-epoxide adduct never accounted for more than 30% of the catalyst speciation under reaction conditions. With increasing water, as much as 80% of the reaction flux utilized water-mediated reaction intermediates. Within the water-mediated mechanisms, different hydrogen bond acceptors (HBAs) influenced the reaction regioselectivity. Overall, this validated mechanism and microkinetic model provided better understanding of industrially important ring-opening catalysis with this catalyst in the presence of water and could facilitate future improvement of catalyst regioselectivity and reactivity.
Inducible Nitric Oxide Synthase Deficiency in Myeloid Cells Does Not Prevent Diet-Induced Insulin Resistance (2010)

Recent findings denote an important contribution of macrophage inflammatory pathways in causing obesity-related insulin resistance. Inducible nitric oxide synthase (iNOS) is activated in proinflammatory macrophages and modestly elevated in insulin-responsive tissues. Although the benefits of systemic iNOS inhibition in insulin-resistant models have been demonstrated, the role of macrophage iNOS in metabolic disorders is not clear. In the current work, we used bone marrow transplantation (BMT) to generate mice with myeloid iNOS deficiency [iNOS BMT knockout (KO)]. Interestingly, disruption of iNOS in myeloid cells did not protect mice from high-fat diet-induced obesity and insulin resistance. When mice were treated with the iNOS inhibitor, N6-(1-Iminoethyl)-L-lysine hydrochloride (L-NIL), we observed a significant and comparable improvement of glucose homeostasis and insulin sensitivity in both wild-type and iNOS BMT KO mice. We further demonstrated that absence of iNOS in primary macrophages did not affect acute TLR4 signaling pathways and had only a modest and mixed effect on inflammatory gene expression. With respect to TNFalpha treatment, iNOS KO macrophages showed, if anything, a greater inflammatory response. In summary, we conclude that iNOS inhibition in tissues other than myeloid cells is responsible for the beneficial effects in obesity/insulin resistance.
Differential Expression and Sequence-specific Interaction of Karyopherin α with Nuclear Localization Sequences (1997)

The process of nuclear protein transport requires the interaction of several different proteins, either directly or indirectly with nuclear localization or targeting sequences (NLS). Recently, a number of karyopherins alpha, or NLS-binding proteins, have been identified. We have found that the karyopherins hSRP1 and hSRP1alpha are differentially expressed in various leukocyte cell lines and could be induced in normal human peripheral blood lymphocytes. We show that the two karyopherins bind with varied specificities in a sequence specific manner to different NLSs and that the sequence specificity is modulated by other cytosolic proteins. There was a correlation between binding of karyopherins alpha to different NLSs and their ability to be imported into the nucleus. Taken together, these data provide evidence for multiple levels of control of the nuclear import process.
Phenomenology of Zn diffusion and incorporation in InP grown by organometallic vapor-phase epitaxy (OMVPE) (1995)

The diffusion characteristics and incorporation characteristics of Zn dopants in OMVPE-grown InP are studied. The Zn diffusion constant depends strongly on concentration and increases by four orders of magnitude in the Zn concentration range 2×1018–8×1018 cm−3. This drastic concentration dependence of the Zn diffusion constant is shown to determine the Zn incorporation characteristics during OMVPE growth. A spread of Zn dopants into intentionally undoped regions may result at high Zn doping concentrations in InP.
Editorial: Targeting the Tumor Microenvironment for a More Effective and Efficient Cancer Immunotherapy (2020)

EDITORIAL article Front. Immunol., 15 May 2020Sec. Cancer Immunity and Immunotherapy Volume 11 - 2020 | https://doi.org/10.3389/fimmu.2020.00933
Supplementary Tables from Genomic Landscape Established by Allelic Imbalance in the Cancerization Field of a Normal Appearing Airway (2023)

&lt;p&gt;Supplementary Tables 1-3 Supplementary Table 1. Location and number of NSCLC, normal and field of cancerization specimens analyzed for genome-wide allelic imbalance Supplementary Table 2. Summary of identified allelic imbalance events in the normal-appearing airway field of cancerization in early-stage NSCLC Supplementary Table 3. Airway events with negative B-allele frequency correlations&lt;/p&gt;
Structural and Electrical Investigation of C60–Graphene Vertical Heterostructures (2015)

Graphene, with its unique electronic and structural qualities, has become an important playground for studying adsorption and assembly of various materials including organic molecules. Moreover, organic/graphene vertical structures assembled by van der Waals interaction have potential for multifunctional device applications. Here, we investigate structural and electrical properties of vertical heterostructures composed of C60 thin film on graphene. The assembled film structure of C60 on graphene is investigated using transmission electron microscopy, which reveals a uniform morphology of C60 film on graphene with a grain size as large as 500 nm. The strong epitaxial relations between C60 crystal and graphene lattice directions are found, and van der Waals ab initio calculations support the observed phenomena. Moreover, using C60-graphene heterostructures, we fabricate vertical graphene transistors incorporating n-type organic semiconducting materials with an on/off ratio above 3 × 10(3). Our work demonstrates that graphene can serve as an excellent substrate for assembly of molecules, and attained organic/graphene heterostructures have great potential for electronics applications.
ChemInform Abstract: Multiring Macrocycles Bearing Diaza‐18‐crown‐6 Units: Preparation and Characterization by Electrospray Mass Spectrometry. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Analysis of acute lymphoblastic leukemia drug sensitivity by changes in impedance via stromal cell adherence (2021)

The bone marrow is a frequent location of primary relapse after conventional cytotoxic drug treatment of human B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Because stromal cells have a major role in promoting chemotherapy resistance, they should be included to more realistically model in vitro drug treatment. Here we validated a novel application of the xCELLigence system as a continuous co-culture to assess long-term effects of drug treatment on BCP-ALL cells. We found that bone marrow OP9 stromal cells adhere to the electrodes but are progressively displaced by dividing patient-derived BCP-ALL cells, resulting in reduction of impedance over time. Death of BCP-ALL cells due to drug treatment results in re-adherence of the stromal cells to the electrodes, increasing impedance. Importantly, vincristine inhibited proliferation of sensitive BCP-ALL cells in a dose-dependent manner, correlating with increased impedance. This system was able to discriminate sensitivity of two relapsed Philadelphia chromosome (Ph) positive ALLs to four different targeted kinase inhibitors. Moreover, differences in sensitivity of two CRLF2-drivenBCP-ALL cell lines to ruxolitinib were also seen. These results show that impedance can be used as a novel approach to monitor drug treatment and sensitivity of primary BCP-ALL cells in the presence of protective microenvironmental cells.
Rapid Intraoperative Molecular Characterization of Glioma (2015)

The genotyping method described herein can establish the diagnosis of low-cellularity tumors like glioma and could be adapted to the point-of-care diagnosis of other lesions that are similarly defined by highly recurrent somatic mutations.
The Transformable Factory: Adapting Automotive Production Capacities (2016)

In the complex field of fast changing market conditions and decreasing predictability of market development, a factory has to adapt its production capacities quickly and with minimal effort. This paper introduces a novel methodology, recommending the best method of capacity planning to change production volumes and to ensure optimal operation in a car factory with respect to several Key Performance Indicators (KPIs), e.g. OEE or energy efficiency. The plant's volume transformability will be increased by not only one, but rather many different possible responses to be analyzed by simulation: the so-called production variants. An algorithm determines the most dominant, pre-analyzed production variants from a data base and visualizes the responding strategies based on the predicted KPIs. After a user- and scenario-based weighting by a so-called Balanced Performance Indicator (BPI), an optimal production variant will be selected. Above all, this assistance system provides more variety and transparency for adapting capacities and supports the factory planning both for greenfields by improved testing und comparability of production variants and for brownfields by giving recommendations for action during run-time. Additionally, real measured data can be retrieved in a closed-loop into the data base to design a continuous learning system. The concept has been methodically implemented and validated in a virtual material flow simulation of an automotive body shop cell and is linked to a real demonstration facility at the Brandenburg University of Cottbus-Senftenberg. Test runs confirm significant saving potential in energy consumption and OEE losses for the given target capacity.
Information Criteria for Dynamic Contrast-Enhanced Magnetic Resonance Imaging (2013)

Inflammatory lesions form in the brain and spinal cord of patients with multiple sclerosis (MS). In many active MS lesions, blood flows abnormally into the white matter of the brain due to breakdown of the blood-brain barrier (BBB), which is know to be associated with morbidity and disability. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) allows quantitative study of blood flow and permeability dynamics throughout the brain. In our study, we observe 15 patients who undergo DCE-MRI periodically throughout a year. In this paper, we design and study spatiotemporal parameters of interest that cannot be obtained by visual inspection. Examples of such parameters are the rate and maximum intensity observed in regions of interest. We develop semi parametric methods for this quantification of BBB disruption at each visit.
Efficient Adaptive Blind MAI Suppression in DS/CDMA by Embedded Constraint Parallel Projection Techniques (2006)

The paper presents two novel blind set-theoretic adaptive filtering algorithms for multiple access interference (MAI) suppression in DS/CDMA systems. We naturally formulate the problem of MAI suppression as minimizing asymptotically a sequence of cost functions under some linear constraint defined by the desired user's signature. The proposed algorithms embed the constraint in the direction of adaptation, and thus the adaptive filter moves toward the optimal filter without stepping away from the constraint set. In addition, using parallel processors, the proposed algorithms attain good performance behavior with low computational complexity. Geometric interpretation clarifies an advantage of the proposed methods over some conventional methods. Simulation results demonstrate that the proposed algorithms achieve much faster convergence than conventional methods with a moderate number of concurrent processors.