gebhart/patrepeval huggingface dataset:
Hematopoietic growth factors for graft failure after bone marrow transplantation: a randomized trial of granulocyte-macrophage colony- stimulating factor (GM-CSF) versus sequential GM-CSF plus granulocyte- CSF (1995)

Delay in hematologic recovery after bone marrow transplantation (BMT) can extend and amplify the risks of infection and hemorrhage, compromise patients' survival, and increase the duration and cost of hospitalization. Because current studies suggest that granulocyte-macrophage (GM) colony-stimulating factor (CSF) may potentiate the sensitivity of hematopoietic progenitor cells to G-CSF, we performed a prospective, randomized trial comparing GM-CSF (250 micrograms/m2/d x 14 days) versus sequential GM-CSF x 7 days followed by G-CSF (5 micrograms/kg/d x 7 days) as treatment for primary or secondary graft failure after BMT. Eligibility criteria included failure to achieve a white blood cell (WBC) count > or = 100/microL by day +21 or > or = 300/microL by day +28, no absolute neutrophil count (ANC) > or = 200/microL by day +28, or secondary sustained neutropenia after initial engraftment. Forty-seven patients were enrolled: 23 received GM-CSF (10 unrelated, 8 related allogeneic, and 5 autologous), and 24 received GM-CSF followed by G-CSF (12 unrelated, 7 related allogeneic, and 5 autologous). For patients receiving GM-CSF alone, neutrophil recovery (ANC > or = 500/microL) occurred between 2 and 61 days (median, 8 days) after therapy, while those receiving GM-CSF+G-CSF recovered at a similar rate of 1 to 36 days (median, 6 days; P = .39). Recovery to red blood cell (RBC) transfusion independence was slow, occurring 6 to 250 days (median, 35 days) after enrollment with no significant difference between the two treatment groups (GM-CSF: median, 30 days; GM-CSF+G-CSF; median, 42 days; P = .24). Similarly, platelet transfusion independence was delayed until 4 to 249 days (median, 32 days) after enrollment, with no difference between the two treatment groups (GM-CSF: median, 28 days; GM-CSF+G-CSF: median, 42 days; P = .38). Recovery times were not different between patients with unrelated donors and those with related donors or autologous transplant recipients. Survival at 100 days after enrollment was superior after treatment with GM-CSF alone. Only 1 of 23 patients treated with GM-CSF died versus 7 of 24 treated with GM-CSF+G-CSF who died 16 to 84 days (median, 38 days) after enrollment, yielding Kaplan-Meier 100-day survival estimates of 96% +/- 8% for GM-CSF versus 71% +/- 18% for GM-CSF+G-CSF (P = .026). These data suggest that sequential growth factor therapy with GM-CSF followed by G-CSF offers no advantage over GM-CSF alone in accelerating trilineage hematopoiesis or preventing lethal complications in patients with poor graft function after BMT.(ABSTRACT TRUNCATED AT 400 WORDS)
Towards a unified understanding of the copper sites in particulate methane monooxygenase: an X-ray absorption spectroscopic investigation (2021)

The enzymatic conversion of the greenhouse gas, methane, to a liquid fuel, methanol, is performed by methane monooxygenases (MMOs) under mild conditions. The copper stoichiometry of particulate MMO (pMMO) has been long debated, with a dicopper site previously proposed on the basis of a 2.51 Å Cu-Cu feature in extended X-ray absorption fine structure (EXAFS) data. However, recent crystallographic data and advanced electron paramagnetic resonance (EPR) characterization support the presence of only mononuclear copper sites. To reconcile these data, we have collected high-energy resolution fluorescence detected (HERFD) and partial fluorescence yield (PFY) EXAFS spectra of <i>Methylococcus</i> (<i>M</i>.) <i>capsulatus</i> (Bath) pMMO. Both methods reveal only monocopper sites. These data were compared to previously published pMMO PFY-EXAFS data from <i>M. capsulatus</i> (Bath) and <i>Methylomicrobium alcaliphilum</i> 20Z, supporting dicopper and monocopper sites, respectively. The FT-EXAFS feature previously attributed to a dicopper site can be reproduced by the inclusion of a metallic copper background signal. The exact position of this feature is dependent on the nature of the sample and the percentage of background contamination, indicating that visual inspection is not sufficient for identifying background metallic contributions. Additionally, an undamaged X-ray absorption spectrum was obtained, consistent with the copper oxidation-state speciation determined by EPR quantification. X-ray photodamage studies suggest that the previously observed Cu(i) XAS features are in part attributable to photodamage. This study illustrates the complex array of factors involved in EXAFS measurement and modeling of pMMO and more generally, dilute metalloproteins with multiple metal centers.
Fast Image Reconstruction Based on a Radon Inversion Formula Appropriate for Rapidly Collected Data (1977)

An arrangement of a single x-ray source and a circular array (centered at the source) of detectors allows rapid collection of a number of x-ray projections of a cross section of an object. A class of appropriately fast algorithms for reconstructing the internal structure of the cross section from such data is rigorously derived starting from the classical Radon inversion formula. A new Radon inversion formula for divergent beams is given as a singlular integral. It is shown that this singular integral can be regularized a number of ways, each one of which leads to an efficient numerical evaluation. The structure, and hence the speed, of the resulting algorithms is similar to the so-called “convolution reconstruction techniques” which have been previously derived for data slowly collected along parallel rays and have been found both fast and accurate. It is demonstrated that, provided the same number of x-ray photons is used, the method of this paper gives as accurate reconstructions for diverging x-rays as previously used algorithms gave for parallel x-rays. Medical applicability of the method is demonstrated by the reconstruction of the total content of the thorax of an intact dog from diverging x-ray projections, as well as realistic mathematically described phantoms representing the human head and thorax from computer generated projections along diverging beams.
Lower-extremity venous thrombosis: comparison of venography, impedance plethysmography, and intravenous manometry. (1988)

This study was undertaken to compare impedance plethysmography with lower-extremity venography and venous manometry in the diagnosis of acute deep venous thrombosis (DVT) of the lower extremity. Ninety-six extremities were studied. In this population, in which the prevalence of acute DVT was 43.8%, plethysmography had a sensitivity of 86.8% and a specificity of 72.0%. The predictive value of abnormal findings at plethysmography was 70.2%, and the predictive value of normal findings at plethysmography was 87.8%. Venous manometry was performed successfully in 89 extremities. A statistically significant difference was shown in the mean intravenous pressure between patients with and without acute DVT. However, there was considerable overlap between the two populations, limiting the predictive value of impedance plethysmography in any given patient.
DropletMicroarray: facile formation of arrays of microdroplets and hydrogel micropads for cell screening applications (2012)

We describe a one-step method for creating thousands of isolated pico- to microliter-sized droplets with defined geometry and volume. Arrays of droplets are instantly formed as liquid moves along a superhydrophilic-superhydrophobic patterned surface. Bioactive molecules, nonadherent cells, or microorganisms can be trapped in the fully isolated microdroplets for high-throughput screening, or in hydrogel micropads for screening in 3D microenvironments.
Kinetics and functional implications of Th1 and Th2 cytokine production following activation of peripheral blood mononuclear cells in primary culture (1996)

The importance of cytokine production in some disease processes is now widely recognized. To investigate temporal relationships between cytokines, we stimulated peripheral blood mononuclear cells (PBMC) in vitro using the T cell mitogen phytohemagglutinin (PHA) and various antigens chosen to induce predominantly Th1 (streptokinase: streptodornase or purified protein derivative) or Th2 (Dermatophagoides pteronyssinus, bee or wasp venom: allergens in sensitive subjects) responses. Cytokine production was measured by sensitive bioassays or enzyme-linked immunosorbent assays. Of the 30 subjects studied, 10 were normal and 20 individuals were allergic to either D. pteronyssinus (n = 10) or bee venom (n = 10) (examined before specific allergen immunotherapy). We examined the temporal profiles of a panel of cytokines produced in primary culture. In PHA-driven cultures, cytokines were found to be sequentially produced in the order interleukin (IL)-2, IL-4, IL-5, IL-3, interferon (IFN)-gamma, IL-10, IL-6, IL-12 and tumor necrosis factor (TNF)-alpha. The response to allergen in allergic patients was predominantly Th2 in nature, with the production of IL-4, IL-5, IL-6 and IL-10, but little or no IFN-gamma. IL-2, IL-3, TNF-alpha and IL-12 were also produced in low amounts. The response of both atopic and normal subjects to recall bacterial antigens was predominantly Th1, with high levels of IFN-gamma, IL-2 and TNF-alpha. The relevance of the order, amount and speed of production, characteristic kinetics (production, consumption, homeostatic regulation) and the cell source of the cytokines are discussed.
Lattice dynamics in elemental modulated Sb2Te3 films (2015)

Abstract The crystallinity and the lattice dynamics in elemental modulated Sb Te films are investigated microscopically using high energy synchrotron radiation diffraction combined with Sb nuclear inelastic scattering. The correlation length is found to be finite but less than 100 Å. The element specific density of phonon states is extracted. A comparison with the element specific density of phonon states in bulk Sb Te confirms that the main features in the density of phonon states arise from the layered structure. The average speed of sound at , is almost the same compared to bulk Sb Te at , . Similarly, the change in the acoustic cut‐off energy is within the experimental detection limit. Thus, we suggest that the lattice thermal conductivity in elemental modulated Sb Te films should not be significantly changed from its bulk value.
Ultrabroadband infrared pump-probe spectroscopy using chirped-pulse upconversion (2014)

We have demonstrated infrared pump-probe spectroscopy using chirped-pulse upconversion with a nonlinear mixing in a gas. Ultrafast dynamics of free carrier in Ge was clearly observed in the range 200–5000 cm−1.
Estimating Hydraulic Fracture Geometry by Analyzing the Pressure Interference Between Fractured Horizontal Wells (2018)

Abstract Pressure interference measurements in fractured horizontal wells have been used to characterize hydraulic fractures (Kampfer and Dawson, 2016; Roussel and Agrawal, 2017). Past work has modeled this interference using static reservoir gridblocks as a proxy for hydraulic fractures. In this paper, we show that to accurately interpret the pressure response observed in a fractured monitor well, one needs to explicitly model the fractures and their propagation as a compliant discontinuity in the reservoir. A fully-coupled 3-D geomechanical reservoir model which models fractures explicitly as open and compliant channels has been developed to simulate pressure interference between hydraulic fractures in a multi-well pad. Using this model, we simulate dynamic fracture propagation at the treatment well while monitoring pressure at the monitor well. The pressure response inside the monitor well fracture is calculated accurately by explicitly modeling the monitor well fracture as a compliant discontinuity in the reservoir rock. We study the impact of mechanical stress interference between the fractures. The model is then used to simulate and analyze the treatment pressure response observed in a pair of wells in the Permian Basin. Simulation results indicate that hydraulic fracture propagation towards the monitor well results in changes in stress on the monitor fracture. Closure and opening of the monitor fracture is manifested directly as an increase/decrease in pressure in the monitor well fracture. We show that this pressure change in the monitor well is observed primarily because of the elastic effect of mechanically squeezing the monitor fracture by the dynamically propagating hydraulic fracture (not by direct hydraulic communication). As such it is essential to model the compliance of the fractures as has been done in this study. This monitor well pressure response is systematically analyzed to estimate fracture geometry for field data obtained from a Permian Basin well pad. Our representation of the propagating hydraulic fracture and the monitoring well fracture as compliant discontinuities in the reservoir is for the first time shown to be essential to capture the pressure response observed in the field. Previous models have simplified the problem by representing the fracture as static reservoir grid-blocks, and such models are clearly inadequate. Our model captures the impact of a propagating hydraulic fracture on the pressure response observed in a fractured monitor well much more accurately. Such pressure interference analysis can provide operators with a semi-quantitative estimate of hydraulic fracture geometry, relatively inexpensively.
Abstract P184: Exploring Sex Differences in Immune Cell Profiles of Male, Premenopausal Female, and Postmenopausal Female Mice to Understand Susceptibility to Immune Mediated Hypertension (2019)

T cells are required for the development of hypertension in male and postmenopausal female mice while premenopausal females are protected from T cell mediated hypertension. To better understand sex differences in immune-cell mediated hypertensive responses, we sought to determine if there were any significant differences in the immune cell profiles of premenopausal female (F), VCD-treated postmenopausal female (PMF), and male (M) mice. Spleens were collected from all mice and processed for flow cytometric analysis of T cell populations (n=8/group). Analysis of splenic T cell populations revealed no significant difference in the frequency of CD3+ or CD4+ T cells between groups (CD3+: F 33.4%, PMF 30.3%, M 30.2% of total lymphocytes, CD4+: F 64.8%, PMF 70.7%, M 67.5% of CD3+ cells). However, postmenopausal females had a significantly lower frequency of splenic CD8+ T cells compared to both males and premenopausal females (CD8+: F 27.9%, PMF 19.5%*, M 25.3% of CD3+ cells *p&lt;0.05 vs M and F). Additionally, premenopausal females displayed significantly increased expression of the memory marker CD44 and the anti-inflammatory marker CTLA-4 on CD4+ cells compared to both males and postmenopausal females (MFI CD44: F 334.8*, PMF 269.4, M 280.4, MFI CTLA-4: F 100.7*, PMF 80.9, M 86.8 *p&lt;0.01 vs M and PMF). Additional flow cytometric staining was performed to evaluate sex differences in splenic Antigen Presenting Cell (APC) populations (n=8/group). The frequency of CD11b+ APCs, thought to primarily represent macrophage populations, were significantly reduced in postmenopausal females compared to premenopausal females but there was no significant difference from males (CD11b +: F 14.6%, PMF 11.8%*, M 12.9% of monocytes *p&lt;0.05 vs F). Additionally, CD11c+ dendritic cell populations were found to be significantly reduced in postmenopausal females compared to both males and premenopausal females (CD11c+: F 4.1%, PMF 2.8%*, M 3.9% of all monocytes *p&lt;0.01 vs M and F). Taken together, these results indicate a significant difference in the baseline immune environment between male, premenopausal female and postmenopausal females which likely contribute to sex-differences in susceptibility to immune-mediated hypertension.
[Joint effect of birth weight and obesity measures on abnormal glucose metabolism at adulthood]. (2016)

There was strong interaction effect between birth weight and overweight (especially central obesity) at adulthood on abnormal glucose metabolism at adulthood. Effective measures should be adopted to prevent and control adult obesity in order to offset the adverse effect of birth weight on long-term health risk.
Analysis for low-molecular-weight carbohydrates is needed to account for all energy-contributing nutrients in some feed ingredients, but physical characteristics do not predict in vitro digestibility of dry matter (2018)

An experiment was conducted to quantify nutrient and fiber fractions of feed ingredients and to determine in vitro apparent ileal digestibility (IVAID) and in vitro apparent total tract digestibility (IVATTD) of DM and OM in each ingredient. Ten ingredients that vary in fiber concentration and composition were used: corn, wheat, soybean meal (SBM), canola meal, distillers dried grains with solubles (DDGS), corn germ meal, copra expellers, sugar beet pulp (SBP), synthetic cellulose (SF), and pectin. Correlations between chemical and physical characteristics of ingredients and IVAID and IVATTD of DM and OM were determined. The physical characteristics measured included bulk density, water-binding capacity (WBC), swelling, and viscosity. The analyzed GE was compared with values for GE calculated from all energy-contributing components. Results indicated that the analyzed chemical composition of most ingredients added to 100% or greater, except for DDGS, SBP, and SF, where nutrients added to only 94.29%, 88.90%, and 96.09%, respectively. The difference between the sum of the calculated GE of the analyzed components and the analyzed GE of the ingredients ranged from -2.25 MJ/kg in DDGS to 1.74 MJ/kg in pectin. No correlation was observed between swelling, WBC, or viscosity and IVAID or IVATTD of DM or OM. The concentration of insoluble dietary fiber (IDF) and total dietary fiber (TDF) was negatively correlated (P < 0.05) with IVAID and IVATTD of DM and OM. There was a tendency for NDF (r = -0.60) and ADF (r = -0.61) to be negatively correlated (P < 0.10) with IVAID of DM. However, no correlation was observed between the concentration of CP, GE, acid-hydrolyzed ether extract, lignin, or soluble dietary fiber and IVAID and IVATTD of DM and OM. The stronger correlations between IDF, TDF, and insoluble non-starch polysaccharides and IVAID and IVATTD of DM and OM than between ADF and NDF and IVAID and IVATTD of DM and OM indicate that the concentration of TDF in feed ingredients is a better predictor of the digestibility of DM and OM than values for NDF and ADF. In conclusion, the calculated GE of some feed ingredients was in agreement with the analyzed GE, which gives confidence that energy-contributing components were accounted for, but for DDGS and SBP, it was not possible to account for all analyzed GE. Concentrations of IDF and TDF, but not the physical characteristics of feed ingredients, may be used to estimate IVAID and IVATTD of DM and OM in feed ingredients.
Microfibril‐microvessel connections in the rabbit eye: Correlative confocal and electron microscopy (1991)

The connections between elastic tissue and microvessels (arterioles, capillaries, and venules) in the rabbit eye were examined by light and electron microscopy. In particular, confocal scanning laser microscopy of tissue stained with orcein and examined by fluorescence using a rhodamine filter was correlated with electron microscopic observations. The goal was an analysis of the way in which elastic tissue of the uvea (i.e., choroid, ciliary body, and iris) and the optic nerve of the eye connect to the microvessels in these structures. Confocal microscopy revealed these connections advantageously and showed how they link the elastic tissue meshwork in the perivascular tissue spaces with the wall of the blood vessels. Electron microscopy showed that the connections consist of bundles of 10-12 nm diameter microfilaments that insert into vascular basement membranes. These connections may contribute to the vascular response to changes in blood pressure or intraocular pressure in the eye.
Abstract 4846: Automated RNA and DNA purification from FFPE samples (2015)

Abstract Formalin-fixed, paraffin-embedded (FFPE) samples are commonly used for archiving pathology samples for use by many researchers including clinical research labs. These samples provide a valuable tool for retrospective studies of diseases such as cancer. Traditional methods for the purification of DNA or RNA from FFPE tissue samples are often labor intensive, include the use of hazardous organic reagents, and involve difficult pre-processing steps. Here, we describe development of automated methods for the purification of RNA or DNA from FFPE tissue sections using the Maxwell® RSC Instrument, which can process between 1 and 16 samples. DNA was purified from FFPE mouse brain, liver, lung, skin and spleen as well as FFPE human colon. RNA was purified from FFPE mouse brain, liver, lung, skin and spleen as well as FFPE human breast tissue. Eluates were tested for inhibition in qPCR or RT-qPCR. A comparison with another automated method was performed with FFPE mouse spleen and skin and a human tissue. The Maxwell RSC methods produced high quality amplifiable DNA or RNA from a variety of sample types with little or no inhibition. In addition, these methods simplified pre-processing, minimized hands-on time, and did not use hazardous organics. Citation Format: Michelle Mandrekar, Douglas Horejsh, Samantha Lewis, Chris Moreland, Marjeta Urh. Automated RNA and DNA purification from FFPE samples. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4846. doi:10.1158/1538-7445.AM2015-4846
Estimation and Control of Tidal Current in Curved Tracking (2013)

This paper proposes three methods to reduce a tracking error attributable to tidal current in a curved tracking of track control system for a ship. In the curved tracking because the heading is changed even if the current is constant, the current component acting to the ship is changed. Present linear estimator that derives from reference coordinate system contains yaw elements and cannot be operated because of becoming non-linear in the curved tracking. The first proposal method derives the linear estimator from earth-fixed coordinate system not to contain the yaw elements. To realize a constant radius route using trajectory tracking control, the present method updates the turning rate by the updated speed obtained from the updating condition that compares the forward ground speed to a threshold value. It also corrects the sideways velocity component of the current by a side-slip angle through a feed-forward control. To reduce the present radius error attributable to the discontinuous update operation, the second proposal method modifies the updating condition, the updated speed, and the threshold value. The present feed-forward rudder angle for the side-slip angle correction has a case that exceeds the preset value. The third proposal method analyzes the maximum feed-forward rudder angle and defines a conditional expression not to become the maximum greater than the preset value. The proposed methods verifies the validity by simulations.