gebhart/patrepeval huggingface dataset:
High-Pressure Liquid Chromatographic Determination of Indomethacin in Plasma, After Ointment Application and Oral Administration (1981)

A sensitive, simple and rapid method for the quantitation of indomethacin in plasma using 1-(p-fluorobenzoyl)-5-methoxy-2-methylindole acetic acid as the internal standard was developed. The method is based on reversed phase high-pressure liquid chromatography using a mobile phase continuing acetonitrile - 0.1M acetic acid (55/45 v/v). Indomethacin quantities as low as 0.1 mcg/ml can be assayed with a relative standard deviation of ± 0.07. Sensitivity can be increased by using lower sensitivity settings.
THROMBOPOIETIN: UNDERSTANDING AND MANIPULATING PLATELET PRODUCTION (1997)

Until recently, platelet production was the least understood aspect of blood cell development. This gap in our understanding resulted from the scarcity of megakaryocytes, the marrow precursor of blood platelets, and from confusion surrounding the cytokines and hormones that support their development. The recent cloning and characterization of thrombopoietin (TPO) has profoundly changed our understanding of platelet production. Using in vitro assay systems, several groups have shown that TPO supports the proliferation of megakaryocytic progenitor cells and their differentiation into mature platelet-producing cells. Moreover, and somewhat surprisingly, TPO also acts in synergy with other pluripotent cytokines on the hematopoietic stem cell to augment development of erythroid and myeloid progenitors. These in vitro effects correlate well with the in vivo biology of the hormone. When administered to normal animals, TPO expands the numbers of hematopoietic progenitors of all lineages and greatly accelerates platelet production. Moreover, when TPO or its receptor is genetically eliminated, progenitor cell levels of all lineages are reduced, and platelet production is profoundly impaired. In animals administered cytoreductive therapy, the use of TPO is associated with accelerated hematopoietic recovery, not only of megakaryocytes and platelets, but also of erythrocytes and leukocytes. It, thus, is hoped that TPO may play an important role in reducing the myelosuppressive complications of naturally occurring and iatrogenic states of marrow failure.
Dysregulation of WNT5A/ROR2 Signaling Characterizes the Progression of Barrett-Associated Esophageal Adenocarcinoma (2016)

The dysregulation of WNT5A/ROR2 noncanonical WNT signaling in Barrett-associated esophageal adenocarcinoma introduces possible prognostic markers and novel targets for tailored therapy of this malignancy. Mol Cancer Res; 14(7); 647-59. ©2016 AACR.
Functional White-Laser Imaging to Study Brain Oxygen Uncoupling/Recoupling in Songbirds (2010)

Contrary to the intense debate about brain oxygen dynamics and its uncoupling in mammals, very little is known in birds. In zebra finches, picosecond optical tomography with a white laser and a streak camera can measure in vivo oxyhemoglobin (HbO 2 ) and deoxyhemoglobin (Hb) concentration changes following physiologic stimulation (familiar calls and songs). Picosecond optical tomography showed sufficient submicromolar sensitivity to resolve the fast changes in the hippocampus and auditory forebrain areas with 250 μm resolution. The time course is composed of (1) an early 2-second-long event with a significant decrease in Hb and HbO 2 levels of −0.7 and −0.9 μmol/L, respectively, (2) a subsequent increase in blood oxygen availability with a plateau of HbO 2 (+ 0.3 μmol/L), and (3) pronounced vasodilatation events immediately after the end of the stimulus. One of the findings of our study is the direct link between blood oxygen level-dependent signals previously published in birds and our results. Furthermore, the early vasoconstriction event and poststimulus ringing seem to be more pronounced in birds than in mammals. These results in birds, tachymetabolic vertebrates with a long lifespan, can potentially yield new insights, e.g., into brain aging.
Understanding the behavior of database operations under program control (2012)

Applications that combine general program logic with persistent databases (e.g., three-tier applications) often suffer large performance penalties from poor use of the database. We introduce a program analysis technique that combines information flow in the program with commutativity analysis of its database operations to produce a unified dependency graph for database statements, which provides programmers with a high-level view of how costly database operations are and how they are connected in the program. As an example application of our analysis we describe three optimizations that can be discovered by examining the structure of the dependency graph; each helps remove communication latency from the critical path of a multi-tier system. We implement our technique in a tool for Java applications using JDBC and experimentally validate it using the multi-tier component of the Dacapo benchmark.
Analysis of colony-stimulating factors and macrophage progenitor cells in mice immunized against Listeria monocytogenes by adoptive transfer (1987)

Experiments were performed to elucidate the role of colony-stimulating factors in host defenses to the intracellular pathogen Listeria monocytogenes. Mice were protected against Listeria sp. by adoptive transfer of immune spleen cells and were then challenged with listeriae intravenously. Control mice were injected with spleen cells from uninfected mice. Adoptively immunized (immune) mice had significantly fewer listeriae in spleens and livers 2 and 4 days after Listeria challenge than did control mice. During acute infection, colony-stimulating activity in serum was increased earlier (10 h) in immune mice than in controls. Concentrations of colony-stimulating activity were equal at 24 h. By 48 h, values were decreased in immune mice, but were elevated in control mice. Similar changes were noted when a specific colony-stimulating factor, macrophage colony-stimulating factor, was measured in serum by using a radioimmunoassay. The changes in serum colony-stimulating activity in mice adoptively immunized with immune spleen cells were eliminated if spleen cells were first treated with anti-Thy-1.2 monoclonal antibodies. The number of macrophage progenitor cells in bone marrow and spleen were also determined as measures of the hemopoietic potential in these organs. The number of macrophage progenitor cells in bone marrow was higher in immune animals than control animals at 1, 2, and 4 days of infection. Similarly, the number of these cells in spleens was higher during the early stages of infection in immune mice. These results indicate that both the regulation of leukocyte production and the transfer of specific cellular immunity by spleen cells are associated, and they therefore suggest that hemopoietic regulatory factors play a role in immune host defenses.
Cyclopropene Rearrangement in the Polymerization of Sterculic Acid (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCyclopropene Rearrangement in the Polymerization of Sterculic AcidKenneth L. Rinehart Jr., Stanley I. Goldberg, Cuthbert L. Tarimu, and Townley P. CulbertsonCite this: J. Am. Chem. Soc. 1961, 83, 1, 225–231Publication Date (Print):January 1, 1961Publication History Published online1 May 2002Published inissue 1 January 1961https://pubs.acs.org/doi/10.1021/ja01462a044https://doi.org/10.1021/ja01462a044research-articleACS PublicationsRequest reuse permissionsArticle Views151Altmetric-Citations20LEARN 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
Characterization of border traps in III-V MOSFETs using an RF transconductance method (2013)

The significant defect-induced increase in transconductance at high frequencies in some III-V MOSFETs is utilized to reveal the spatial distribution and energy profile of traps in the gate dielectric. The frequency response of the border traps is modeled as a distributed RC network inserted in the small signal model. Surface-channel InGaAs MOSFETs with Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> /HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> high-k gate dielectric are evaluated; especially the effects of inserting an InP cap layer in the gate stack.
Detection of Hepatitis A Virus in the Feces of Patients with Naturally Acquired Infections (1980)

A prospective study was carried out on 200 patients admitted to Fairfield Hospital, Melbourne, Australia, with acute hepatitis A to determine the frequency with which virus could be detected in their feces. Evidence of infection with hepatitis A virus (HAV) was obtained by detecting IgM specific for HAV in a single serum sample or by demonstrating a rising titer of antibody in paired sera by solid-phase radioimmunoassay. HAV was detected in the feces of 59 of the 200 patients by solid-phase radioimmunoassay and immune electron microscopy. When patients were admitted within one week of the onset of dark urine, 45% were found to be shedding HAV, whereas only 11% of specimens obtained from patients admitted during the second week contained virus. HAV was not detected in fecal specimens collected more than 14 days after the onset of dark urine. These findings suggest that patients admitted to hospital with hepatitis A may still be infectious and that appropriate precautions against fecal contamination should be maintained.
Optimized electrode configuration for various plasma focus gas mixtures (1995)

Summary form only given, as follows. The Mather-type 25-kj dense plasma focus (DPF) at the University of Illinois is currently being used to study electrode designs intended to optimize performance with various fusion fuels of interest for space propulsion applications. The DPF device consists of 20x2-/spl mu/f capacitors in parallel arranged in four perpendicular arms (12.5 kJ at 25 keV). The current during the discharge can reach 700 kA (/spl sim/500 kA pinch current). For space propulsion, the DPF operates similarly to other MPD devices, but with the added advantage that, when suitable fuels are used, fusion reactions occur in the plasma that pinches at the tip of the inner electrode, adding energy to the flowing jet gas. This enhances the thrust-to-weight ratio of the thruster. Theory predicts that advanced fuels such as /sup 3/He-D yield high temperature (100 keV) and dense (/spl sim/10/sup 22/ cm/sup -3/) plasmoids when the dimensions of the anode and cathode are optimized. It has already been shown on the University of Illinois' facility that using D/sub 2/ with the suitable electrode dimensions, neutron yields about six times higher than for conventional electrode configuration operating with the same current and total energy were achieved. We report them on the results obtained with a /sup 4/He-D mixture, using electrode dimensions optimized for that mixture. Optimizing the electrode configuration requires matching dimensions with the rundown time of the plasma along the electrode.
Localization of transforming growth factor-beta 1 in mitochondria of murine heart and liver. (1991)

Using both electron microscopic immunohistochemistry and cell fractionation techniques, we show that transforming growth factor-beta 1 (TGF-beta 1) is found in mitochondria of rat and mouse cardiac myocytes and rat hepatocytes. Four different polyclonal antibodies, raised against various epitopes encompassing the mature portion of the TGF-beta 1 molecule as well as the pro-region of its precursor, were used for the electron microscopy studies. The localization of TGF-beta 1 in mitochondria was confirmed by detection of the native peptide in mitochondria isolated from rat heart and liver; the majority of native TGF-beta 1 found in liver homogenates was recovered in highly pure mitochondrial fractions. The functional role of TGF-beta in the mitochondrion is unknown at present.
Leak K+ channel mRNAs in dorsal root ganglia: Relation to inflammation and spontaneous pain behaviour (2012)

Two pore domain potassium (K2P) channels (KCNKx.x) cause K⁺ leak currents and are major contributors to resting membrane potential. Their roles in dorsal root ganglion (DRG) neurons normally, and in pathological pain models, are poorly understood. Therefore, we examined mRNA levels for 10 K2P channels in L4 and L5 rat DRGs normally, and 1 day and 4 days after unilateral cutaneous inflammation, induced by intradermal complete Freund's adjuvant (CFA) injections. Spontaneous foot lifting (SFL) duration (spontaneous pain behaviour) was measured in 1 day and 4 day rats <1h before DRG harvest. mRNA levels for KCNK channels and Kv1.4 relative to GAPDH (n=4-6 rats/group) were determined with real-time RT-PCR. This study is the first to demonstrate expression of THIK1, THIK2 and TWIK2 mRNA in DRGs. Abundance in normal DRGs was, in descending order: Kv1.4>TRESK(KCNK18)>TRAAK(KCNK4)>TREK2(KCNK10)=TWIK2(KCNK6)>TREK1 (KCNK2)=THIK2(KCNK12)>TASK1(KCNK3)>TASK2(KCNK5)>THIK1(KCNK13)=TASK3(KCNK9). During inflammation, the main differences from normal in DRG mRNA levels were bilateral, suggesting systemic regulation, although some channels showed evidence of ipsilateral modulation. By 1 day, bilateral K2P mRNA levels had decreased (THIK1) or increased (TASK1, THIK2) but by 4 days they were consistently decreased (TASK2, TASK3) or tended to decrease (excluding TRAAK). The decreased TASK2 mRNA was mirrored by decreased protein (TASK2-immunoreactivity) at 4 days. Ipsilateral mRNA levels at 4days compared with 1 day were lower (TRESK, TASK1, TASK3, TASK2 and THIK2) or higher (THIK1). Ipsilateral SFL duration during inflammation was positively correlated with ipsilateral TASK1 and TASK3 mRNAs, and contralateral TASK1, TRESK and TASK2 mRNAs. Thus changes in K2P mRNA levels occurred during inflammation and for 4 K2P channels were associated with spontaneous pain behaviour (SFL). K2P channels and their altered expression are therefore associated with inflammation-induced pain.
Angular-momentum coupled optical waves in chirally-coupled-core fibers (2011)

A new type of interaction between optical waves occurs in chirally-coupled-core (CCC) fibers. Instead of linear-translational symmetry of conventional cylindrical fibers, CCC fibers are helical-translation symmetric, and, consequently, interaction between CCC fiber modes involves both spin and orbital angular momentum of the waves. Experimentally this has been verified by observing a multitude of new phase-matching resonances in the transmitted super-continuum spectrum, and theoretically explained through modal theory developed in helical reference frame. This enables new degrees of freedom in controlling fiber modal properties.
A Specific Breath Metabolome Signature Identifies Patients With Inflammatory Bowel Diseases (2015)

Introduction: Inflammatory bowel diseases (IBD), which include Crohn's disease (CD) and ulcerative colitis (UC), have a heterogenous presentation. Accurate non-invasive biomarkers for diagnosis, stratification and prediction of IBD courses are limited. We analyzed volatile organic compounds (VOCs) in the breath of IBD, other gastroenterological inflammatory controls (IC) and healthy controls (HC) for diagnosis and differentiation of IBD as well as their link with disease location, activity and phenotype. Methods: A prospective study of diagnostic testing was conducted at a tertiary referral center, recruiting CD, UC, IC and HC. Exclusion criteria were the use of antibiotics two weeks prior to breath analysis, history of diverting ileostomy, colostomy or total abdominal colectomy. Detailed clinical data was obtained, including diagnosis, disease duration and location, complications, medication intake, clinical disease activity scores (Lichtiger/Harvey Bradshaw Index) and CT/MRE disease activity score. The VOC profile was analyzed using selective ion flow tube-mass spectrometry in 1) the breath of subjects following a mouth rinse with water and 2) the headspace of 19 serum samples warmed to 37°C. Appropriate statistical tests were used (Table 1). Twenty two distinct VOCs were analyzed. Results: Ninety four subjects with CD (n=24), UC (n=11), IC (n=6) and HC (n=53); (mean age +/-SD (in years) at 45.9±12.9, 43.9±15.9, 59.8±16.4, 42.6±14.6 respectively) were recruited. We observed differences in 8/22 VOCs (IBD vs. HC), 8/22 (CD vs. HC), 3/22 (UC vs. HC), 3/22 (IC vs. HC) or 2/22 (IBD vs. IC) respectively (p < 0.05; Table 1, Figure 1).Breath ethanol levels were higher in CD patients with strictures and fistulae compared to no complications (123.2 parts per billion (ppb) (103.0-153.4) median [P25, P75]) vs. 89.1ppb (84.1-91.3), p= 0.025).There was no link between the level of VOCs with disease location, clinical or radiologic disease activity as well as lab parameters or type of medication used. The serum headspace VOCs ethanol and triethyl amine were higher in IBD vs. HC. Acetone and pentane showed strong correlations (rho =0.91 and 0.71, respectively) between serum headspace and breath.Figure 1Conclusion: A specific breath metabolome pattern is associated with IBD, but not IBD subtypes or disease activity. Analysis of a broader spectrum of VOCs can potentially aid in the development of breath prints to diagnose or differentiate inflammatory bowel disorders.Figure 2
The Future of Rice Genomics: Sequencing the Collective Oryza Genome (2010)

Abstract The main objectives of the “ Oryza Map Alignment Project” (OMAP) are to characterize the rice genome from a comparative standpoint by establishing a genus-wide and genome-scale comparative framework from representative species. Here, we report our progress in the analyses of these datasets and emerging “comparative phylogenomics” insights into Oryza evolution at two different resolutions—chromosomal and sequence levels. We demonstrate the abundance and impact of structural variations (SV) on genome diversity using African Oryza as a model. The molecular basis of SV was inferred using three genus-wide vertical sequence datasets. Combined, these data demonstrate that a single reference genome sequence for the genus Oryza is insufficient to comprehensively capture the genomic and allelic diversity present within the genus. Towards this end, we present a strategy to generate high-quality and cost-effective de novo reference sequences of collective Oryza . The application and broader scientific impact of the OMAP resources under an international cooperative effort (I-OMAP) are discussed.
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications (2006)

Proliferating cell nuclear antigen (PCNA) acts as a biologically essential processivity factor that encircles DNA and provides binding sites for polymerase, flap endonuclease-1 (FEN-1) and ligase during DNA replication and repair. We have computationally characterized the interactions of human and Archaeoglobus fulgidus PCNA trimer with double-stranded DNA (ds DNA) using multi-nanosecond classical molecular dynamics simulations. The results reveal the interactions of DNA passing through the PCNA trimeric ring including the contacts formed, overall orientation and motion with respect to the sliding clamp. Notably, we observe pronounced tilting of the axis of dsDNA with respect to the PCNA ring plane reflecting interactions between the DNA phosphodiester backbone and positively charged arginine and lysine residues lining the PCNA inner surface. Covariance matrix analysis revealed a pattern of correlated motions within and between the three equivalent subunits involving the PCNA C-terminal region and linker strand associated with partner protein binding sites. Additionally, principal component analysis identified low frequency global PCNA subunit motions suitable for translocation along duplex DNA. The PCNA motions and interactions with the DNA minor groove, identified here computationally, provide an unexpected basis for PCNA to act in the coordinated handoff of intermediates from polymerase to FEN-1 to ligase during DNA replication and repair.
Infrared scanning near‐field optical microscopy investigates order and clusters in model membranes (2008)

Due to its surface sensitivity and high spatial resolution, scanning near-field optical microscopy (SNOM) has a significant potential to study the lateral organization of membrane domains and clusters. Compared to other techniques, infrared near-field microscopy in the spectroscopic mode has the advantage to be sensitive to specific chemical bonds. In fact, spectroscopic SNOM in the infrared spectral range (IR-SNOM) reveals the chemical content of the sample with a lateral resolution around 100 nm (Cricenti et al., 1998a, 1998b, 2003). Model lipid membranes were studied by IR-SNOM at several wavelengths. Topographical micrographs reveal the presence of islands at the surface and the optical images indicate the formation of locally ordered multiple bilayers - both critically important features for biotechnology and medical applications.
Linking and Navigating Data in a P2P File-Sharing Network (2009)

We demonstrate a tool for publishing and navigating linked data over the highly dynamic infrastructure of a P2P filesharing network. Our links are based on a URI scheme which allows unambiguous designation of replicated data items, regardless of their location in the network. In a true decentralized P2P spirit, users publish and distribute the links just like other data items.
The Immunomodulatory Actions of Prostaglandin E2 on Allergic Airway Responses in the Rat (2002)

PGE(2) has been reported to inhibit allergen-induced airway responses in sensitized human subjects. The aim of this study was to investigate the mechanism of anti-inflammatory actions of PGE(2) in an animal model of allergic asthma. BN rats were sensitized to OVA using Bordetella pertussis as an adjuvant. One week later, an aerosol of OVA was administered. After a further week, animals were anesthetized with urethan, intubated, and subjected to measurements of pulmonary resistance (R(L)) for a period of 8 h after OVA challenge. PGE(2) (1 and 3 micro g in 100 micro l of saline) was administered by insufflation intratracheally 30 min before OVA challenge. The early response was inhibited by PGE(2) (3 micro g). The late response was inhibited by both PGE(2) (1 and 3 micro g). Bronchoalveolar lavage fluid from OVA-challenged rats showed eosinophilia and an increase in the number of cells expressing IL-4 and IL-5 mRNA. These responses were inhibited by PGE(2). Bronchoalveolar lavage fluid levels of cysteinyl-leukotrienes were elevated after OVA challenge and were reduced after PGE(2) to levels comparable with those of sham challenged animals. We conclude that PGE(2) is a potent anti-inflammatory agent that may act by reducing allergen-induced Th2 cell activation and cysteinyl-leukotriene synthesis in the rat.