gebhart/patrepeval huggingface dataset:
Comparative effectiveness of somatotropin and anabolic steroids in feedlot steers2 (1995)

Crossbred steers (n = 252, BW = 379 +/- 28 kg) were allotted to 42 pens in a 2 x 3 factorial arrangement of treatments: control or steroid implant (STR; estradiol benzoate+progesterone [three lighter blocks reimplanted on d 84] and trenbolone acetate [reimplanted on d 63]), and either 0, 80, or 160 mg/wk of recombinant bovine somatotropin (bST). Steers were adapted to the finishing diet (12% roughage equivalent, 13% CP) before the start of the experiment and fed for 84 or 119 d. Blood samples were taken on d 0, 14, 28, 56, and 84 for plasma urea N (PUN), serum somatotropin (ST), plasma insulin-like growth factor I (IGF-I), and plasma amino acid assay. Few interactions were noted (P > .1). Gain was increased by both treatments: 1.30 vs 1.66 kg/d for control vs. STR (P < .001) and 1.44, 1.49, and 1.51 kg/d (linear, P = .07) for 0, 80, and 160 mg of bST/wk, respectively. Gain efficiency was also improved: 169 vs 205 g/kg (P < .001) and 177, 189, and 195 g/kg (linear, P < .001), respectively. Average PUN was decreased (P < .001) 29% by STR and decreased 17 and 29% by 80 and 160 mg of bST/wk, respectively (linear, P < .001). Somatotropin decreased mean serum ST compared with controls; STR increased ST 36% compared with controls. Average plasma IGF-I was increased (P < .001) 12% by STR and 13 and 19% (linear, P < .001) by 80 and 160 mg of bST/wk, respectively. Both STR and bST influenced (P < .05) plasma amino acid profiles. Indicators of carcass fatness were decreased linearly (P < .05) by bST; STR implant tended to decrease carcass fatness and increase longissimus muscle area, which was related to carcass weight. The anabolic effects of STR and bST were found to be additive and possibly independent in feedlot steers.
Two-Dimensional Simulation of Direct Methanol Fuel Cell. A New (Embedded) Type of Current Collector (2000)

A two‐dimensional numerical model of the direct methanol fuel cell with gas fuel is developed. Simulation of the cell with current collectors of conventional geometry reveal the formation of fuel‐depleted, "shaded" regions in the cathode and anode catalyst layers. These regions are positioned in front of current collectors, farther from the gas channel windows. Another disadvantage of the conventional geometry is the concentration of electron current at the edges of current collectors. Based on the simulation results, a new design of current collectors is suggested. It is beneficial to position current collectors inside the backing and catalyst layers, parallel to the flow of the fuel. These embedded collectors do not produce shaded regions in the catalyst layers. Two plausible geometries of such collectors are considered: of rectangular and circular shape. Simulations show that depending on the transport properties of the backing and catalyst layers the embedded current collectors may significantly improve the performance of the fuel cell. This conclusion is valid also for hydrogen‐oxygen fuel cells. © 2000 The Electrochemical Society. All rights reserved.
ARTD10 substrate identification on protein microarrays: regulation of GSK3β by mono-ADP-ribosylation (2013)

Our findings indicate that substrates of ADP-ribosyltransferases can be identified using protein microarrays. The discovered substrates of ARTD10 and ARTD8 provide the first sets of proteins that are modified by mono-ADP-ribosyltransferases in vitro. By studying one of the ARTD10 substrates more closely, the kinase GSK3β, we identified mono-ADP-ribosylation as a negative regulator of kinase activity.
Functional expression of Ca<sup>2+</sup> ‐mobilizing α‐thrombin receptors in mRNA‐injected <i>Xenopus</i> oocytes (1990)

alpha-Thrombin (TH) initiates a program of intracellular events that lead to DNA replication in quiescent CCL39 Chinese hamster lung fibroblasts via membrane receptors that have yet to be characterized at a molecular level. Functional TH receptors were expressed in Xenopus laevis oocytes following injection of poly(A)+ RNA from TH-responsive CCL39 cells; their presence was demonstrated by TH-stimulated 45Ca2+ efflux or Ca2(+)-dependent Cl- channel activation. In voltage clamp experiments on microinjected oocytes a Ca2(+)-activated Cl- current was detected in response to TH (0.2-10 U/ml). The TH response was blocked by a specific TH inhibitor, and potentiated by addition of FGF or intracellular injection of GTP-gamma-S.
Decreased contractile efficiency and increased nonmechanical energy cost in hyperthyroid rabbit heart. Relation between O2 consumption and systolic pressure-volume area or force-time integral. (1990)

Both systolic pressure-volume area (PVA) and force-time integral (FTI) have been used as measures of oxygen consumption per beat (VO2) in the isolated left ventricle. The reciprocal of the slope of the VO2-PVA relation has been considered to reflect the chemomechanical energy transduction efficiency of the contractile machinery (contractile efficiency), whereas its VO2 intercept consists of energy cost of excitation-contraction coupling and basal metabolism. To examine whether the increase in myosin isoform V1/V3 ratio in hyperthyroid rabbits decreases contractile efficiency and to determine overall mechanisms of higher oxygen consumption in hyperthyroid hearts, the VO2-PVA and VO2-FTI relations as well as the end-systolic pressure-volume relation were assessed in cross-circulated, isovolumically beating hearts isolated from normal, hyperthyroid, and hypothyroid rabbits. Normalized initial slopes of the rising limb of the curvilinearly fitted end-systolic pressure-volume relation (E'max, ventricular contractility index) were similar for normal and hyperthyroid groups. However, the slopes and VO2 intercepts of the VO2-PVA and VO2-FTI relations were greater in hyperthyroid hearts than in normal hearts. Accordingly, in the hyperthyroid hearts, the contractile efficiency (27 +/- 6%) was lower and left ventricular VO2 for excitation-contraction coupling (0.028 +/- 0.004 ml O2/beat/100 g) was higher than in normal hearts (40 +/- 4% and 0.021 +/- 0.005 ml O2/beat/100 g, respectively). This decreased contractile efficiency in the hyperthyroid hearts was attributable to myosin isoform alteration rather than to increased beta-adrenoceptors because isoproterenol did not affect the slope of the VO2-PVA relation in all groups. In contrast, the slope of the VO2-FTI relation was significantly increased by isoproterenol in all groups. Neither the VO2-PVA nor the VO2-FTI relations in hypothyroid hearts were different from those in normal hearts except for significantly lower VO2 for basal metabolism. We conclude that in hyperthyroid rabbits, the left ventricle has decreased contractile efficiency and increased energy cost of excitation-contraction coupling and that the decreased contractile efficiency in hyperthyroid hearts is probably due to the increased V1/V3 ratio of the myosin isoform component. In addition, this study demonstrates that the VO2-PVA and VO2-FTI relations dissociate depending on the intervention, even in the same isovolumic contraction mode.
Sinogram synthesis using convolutional-neural-network for sparsely view-sampled CT (2018)

Reducing the number of projections in computed tomography (CT) has been exploited as a low-dose option in conjunction with advanced iterative image reconstruction algorithms. While such iterative image reconstruction methods do provide useful images and valuable insights of the inverse imaging problems, it is an intriguing issue whether missing view projection data in the sinogram can be successfully recovered. There have been reported several approaches to interpolating the missing sinogram data. Deep-learning based super-resolution techniques in the field of natural image enhancement have been recently introduced and showed promising results. Inspired by the super-resolution techniques, we have earlier proposed a sinogram inpainting method that uses a convolutional-neural-network for sparsely viewsampled CT. Despite of the encouraging initial results, our previously proposed method had two drawbacks. The measured sinogram was contaminated in the process of filling the missing sinogram by the deep learning network. Additionally, the sum of the interpolated sinogram in the direction of detector row at each view angle was not preserved. In this study, we improve our previously developed deep-learning based sinogram synthesis method by adding new layers and modifying the size of receptive field in the deep learning network to overcome the above limitations. From the quantitative evaluations on the image accuracy and quality using real patients’ CT images, we show that the new approach synthesizes more accurate sinogram and thus leads to higher quality of CT image than the previous one.
Glucose-Dependent Insulin Secretion in Pancreatic β-Cell Islets from Male Rats Requires Ca2+ Release via ROS-Stimulated Ryanodine Receptors (2015)

Glucose-stimulated insulin secretion (GSIS) from pancreatic β-cells requires an increase in intracellular free Ca2+ concentration ([Ca2+]). Glucose uptake into β-cells promotes Ca2+ influx and reactive oxygen species (ROS) generation. In other cell types, Ca2+ and ROS jointly induce Ca2+ release mediated by ryanodine receptor (RyR) channels. Therefore, we explored here if RyR-mediated Ca2+ release contributes to GSIS in β-cell islets isolated from male rats. Stimulatory glucose increased islet insulin secretion, and promoted ROS generation in islets and dissociated β-cells. Conventional PCR assays and immunostaining confirmed that β-cells express RyR2, the cardiac RyR isoform. Extended incubation of β-cell islets with inhibitory ryanodine suppressed GSIS; so did the antioxidant N-acetyl cysteine (NAC), which also decreased insulin secretion induced by glucose plus caffeine. Inhibitory ryanodine or NAC did not affect insulin secretion induced by glucose plus carbachol, which engages inositol 1,4,5-trisphosphate receptors. Incubation of islets with H2O2 in basal glucose increased insulin secretion 2-fold. Inhibitory ryanodine significantly decreased H2O2-stimulated insulin secretion and prevented the 4.5-fold increase of cytoplasmic [Ca2+] produced by incubation of dissociated β-cells with H2O2. Addition of stimulatory glucose or H2O2 (in basal glucose) to β-cells disaggregated from islets increased RyR2 S-glutathionylation to similar levels, measured by a proximity ligation assay; in contrast, NAC significantly reduced the RyR2 S-glutathionylation increase produced by stimulatory glucose. We propose that RyR2-mediated Ca2+ release, induced by the concomitant increases in [Ca2+] and ROS produced by stimulatory glucose, is an essential step in GSIS.
Surgical Site Signing and “Time Out” (2009)

Orthopaedic surgeons should recognize the value of preoperative skin signing for all procedures and the additional value of the "time out" protocol. We recommend that surgeons strive for 100% compliance with both strategies.
Basic science priorities for therapeutics research. (2003)

For more than 10 years, drug discovery efforts have concentrated on relatively few viral targets: reverse transcriptase (RT) and protease (PR). While viral load can be reduced by combining RT and PR inhibitors in regimens referred to as highly active antiretroviral therapy (HAART), recent studies suggest that many treatment failures occur because of the development of drug resistance and lack of adherence to complicated and often toxic regimens. Recently, new classes of agents directed at the virus binding and entry process have entered the development pipeline, with one such agent now approved for use in patients with HIV. Early data suggests, however, that the development of resistance will continue to be a problem as new agents are introduced into HAART regimens. With regard to the immune system, it has become clear that the damage caused by HIV infection is only partially reversed by HAART. Vaccination represents a major new immunologic approach to complement drug treatment. Thus, while advances continue to be made, there remains an urgent need for the identification of new host and viral targets, novel drugs and delivery systems, and immunologic approaches to address the dual problems of drug resistance and toxicity. To address this need, the Division of AIDS has established basic science priorities in the following areas of therapeutics research: host and viral targets, inhibitors, vaccines, innate immunity, viral reservoirs, and gene therapy.
Mutagenesis: Investigating the process and processing the outcome for crop improvement (2005)

The discoveries during the late 1920s that the genetic material is amenable to changes excited geneticists who saw new opportunities for both basic and practical applications. During the 1950s, induced mutagenesis was widely pursued in the US, Europe, Japan and China. In India, Swaminathan and his team at the Indian Agricultural Research Institute, New Delhi initiated a major programme on mutagenesis in crop plants. These studies were broadly aimed at understanding the process of mutation, testing the efficacy of various mutagens, identifying optimum dose and the best method of treatment for different crop species; isolation of mutants of basic and applied value; elucidating the biological effects of radiation-treated media, seeds and vegetative propagules on the organisms consuming them.
Fluid Flow Increases Type II Collagen Deposition and Tensile Mechanical Properties in Bioreactor-Grown Tissue-Engineered Cartilage (2006)

A novel parallel-plate bioreactor has been designed to apply a consistent level of fluid flow-induced shear stress to tissue-engineered articular cartilage in order to improve the matrix composition and mechanical properties and more nearly approximate to that of native tissue. Primary bovine articular chondrocytes were seeded into the bioreactor at high densities (1.7 x 10(6) cell/cm2) without a scaffold and cultured for two weeks under static, no-flow conditions. A mean fluid flow-induced shear stress of 1 dyne/cm2 was then applied continuously for 3 days. The application of flow produced constructs with significantly (p < 0.05) higher amounts of total collagen (via hydroxyproline) and specifically type II collagen (via ELISA) (25.3 +/- 2.5% and 22.1 +/- 4.7% of native tissue, respectively) compared to static controls (22.4 +/- 1.7% and 9.5 +/- 2.3%, respectively). Concurrently, the tensile Young's modulus and ultimate strength were significantly increased in flow samples (2.28 +/- 0.19 MPa and 0.81 +/- 0.07 MPa, respectively) compared to static controls (1.55 +/- 0.10 MPa and 0.62 +/- 0.05 MPa, respectively). This study suggests that flow-induced shear stresses and/or enhanced mass transport associated with the hydrodynamic environment of our novel bioreactor may be an effective functional tissue-engineering strategy for improving matrix composition and mechanical properties in vitro.
Fast Sliding Window Classification with Convolutional Neural Networks (2014)

Convolutional Neural Networks (CNNs) have repeatedly been shown to be the state of the art method for natural signal classification -- image classification in particular. Unfortunately, due to the high model complexity CNNs often cannot be used for object detection tasks with real-time constraints, where many predictions have to be made on sub-windows of a large input image. We demonstrate how two recent advances in CNN efficiency can be combined, with modifications, to provide a substantial speedup for sliding window classification. An in depth analysis of the various factors that can impact performance is presented.
SEMANTIC SEGMENTATION OF AERIAL IMAGES IN URBAN AREAS WITH CLASS-SPECIFIC HIGHER-ORDER CLIQUES (2015)

Abstract. In this paper we propose an approach to multi-class semantic segmentation of urban areas in high-resolution aerial images with classspecific object priors for buildings and roads. What makes model design challenging are highly heterogeneous object appearances and shapes that call for priors beyond standard smoothness or co-occurrence assumptions. The data term of our energy function consists of a pixel-wise classifier that learns local co-occurrence patterns in urban environments. To specifically model the structure of roads and buildings, we add high-level shape representations for both classes by sampling large sets of putative object candidates. Buildings are represented by sets of compact polygons, while roads are modeled as a collection of long, narrow segments. To obtain the final pixel-wise labeling, we use a CRF with higher-order potentials that balances the data term with the object candidates. We achieve overall labeling accuracies of > 80%.
Macrophage‐dependent induction of the <i>Salmonella</i> pathogenicity island 2 type III secretion system and its role in intracellular survival (1998)

Salmonella pathogenicity island 2 (SPI-2) encodes a putative type III secretion system necessary for systemic infection in animals. We have investigated the transcriptional organization and regulation of SPI-2 by creating gfp fusions throughout the entire gene cluster. These gfp fusions demonstrated that SPI-2 genes encoding structural, regulatory and previously uncharacterized putative secreted proteins are preferentially expressed in the intracellular environment of the host macrophage. Furthermore, the transcription of these genes within host cells was dependent on the two-component regulatory system SsrA/SsrB and an acidic phagosomal environment. Most SPI-2 mutants failed to replicate to the same level as wild-type strains in murine macrophages and human epithelial cells. In orally infected mice, SPI-2 mutants colonized the Peyer's patches but did not progress to the mesenteric lymph nodes. We conclude that SPI-2 genes are specifically expressed upon entry into mammalian cells and are required for intracellular growth in host cells in vivo and in vitro.
Fabrication of Polymeric 3-D Micro-Structures Using Ferrofluid Molds (2006)

In this paper, we report a new and simple fabrication method for 3-D polymeric microstructures using low viscosity mineral oil-based ferrofluids in combination with polydimethylsiloxane (PDMS) and UV curable epoxy. The diameter and height of ferrofluid spikes/domes which usually form upon the application of a magnetic field was controlled by a micromachined membrane having holes of various dimensions. Holes or various dimensions (60, 100, and 200 µ m) were fabricated in a thin silicon membrane covering a ferrofluid reservoir. The heights of fabricated polymeric microstructures corresponding to the above mentioned hole sizes were equal to the hole diameters, while their base diameters were reduced by 10-30%. This approach provides a new technique to easily fabricate various size 3-D micro-structures on the same plane by controlling the magnetic field strength, ferrofluid viscosity, and hole dimensions.
Involvement of the consensus sequence motif at coil 2b in the assembly and stability of vimentin filaments (1992)

Nearly all intermediate filament (IF) proteins share two sequence motifs located at the N- and the C-terminal ends of their helical rod domain ('coil 1a' and 'coil 2b', respectively). To examine the structural role of the coil 2b motif, we have performed in vitro assembly studies and in vivo microinjection experiments employing two site-specific reagents: (a) a 20-residue synthetic peptide (C-2) representing the conserved motif itself and (b) a monoclonal antibody (anti-IFA) that recognises an epitope within the conserved coil 2b sequence. We demonstrate here that vimentin protofilaments, when induced to assemble in the presence of C-2 or anti-IFA, show a lower propensity to polymerise and yield various abberant structures. The few filaments that are formed under these conditions appear much shorter than normal IFs and are unravelled or aggregated. Furthermore, when preformed vimentin filaments are exposed to C-2 or anti-IFA, most of the normal IFs are converted into shorter filamentous forms that possess an abberant morphology. None of these effects is seen when vimentin subunits are coincubated with control peptides. Microinjection of anti-IFA into the cytoplasm of interphasic 3T3 cells provokes collapse of vimentin IFs into a juxtanuclear mass and formation of numerous amorphous aggregates distributed throughout the cytoplasm. These two effects are not seen when the anti-IFA is microinjected into the cell nucleus. Our results provide experimental evidence supporting previous suggestions for a role for the conserved coil 2b sequence in filament assembly. We propose that this region is interacting with other sites along the vimentin molecule and that these interactions are essential for proper protofilament-protofilament alignment and filament stability.
An Expression of the Sweet Potato GBSSI Gene in Escherichia coli (2000)

A starch synthase cDNA clone (spss67) was isolated from tuberous roots of sweet potato. This clone contained an open reading frame corresponding to a protein of 608 amino acid residues, which also included three consensus regions of starch synthases. Amino acid sequence analyses showed that the protein product of spss67 shared a high degree of homology with other plant granule-bound starch synthase I (GBSSI). Comparisons of N-terminal amino acid sequence of spss67 cDNA protein product with that of the native protein isolated from sweet potato indicated that the protein contained a signal peptide of 77 amino acids, and the transit peptide had hydrophobic regions in the initiation and end of peptide that was also present in GBSSI of other plant species. In addition, the protein product of spss67 expressed in E. coli could be recognized by anti-GBSSI antibody of potato. Moreover, this protein exhibited a high activity of starch synthase when amylose was used as a primer, but the activity was not significant when the primer was replaced by amylopectin or glycogen. Studies based on the sequence analyses, western blotting and priming activity indicated that the product of spss67 clone was a GBSSI.
A One-Step Strategy for End-Functionalized Donor–Acceptor Conjugated Polymers (2013)

A modular and robust method for preparing end-functionalized donor–acceptor (D–A) narrow bandgap conjugated polymers is reported that avoids multistep reactions and postpolymerization modification. The strategy is well-controlled and affords functional materials with predictable molecular weight and high end-group fidelity. To exemplify this synthetic strategy, narrow bandgap conjugated polymers based on PDPP2FT were prepared that contain perylene diimide (PDI) units at the chain-ends. Monte Carlo simulations confirm the high degree of chain-end functionalization while photoluminescence studies reveal the unique photophysical properties of the end-functional polymers with efficient charge transfer occurring between the main polymer chain and PDI end-groups that results exclusively from their covalent linkage.
Integrated Family Centres: Directions for Future Developments (2001)

Two major types of family centre can be identified. The first type aims to support families in the community by offering a range of practical services to alleviate stress. The second type of centre focuses on assessment and therapeutic intervention in families where children are at risk of abuse. In practice, many centres fulfil both functions and can be termed 'integrated centres'. This paper reports on an evaluation of an integrated centre. The evaluation was conducted on three levels: the managerial level, the level of professionals who work in the centre, and on the level of the families who use the centre. Findings show a contradiction between the two different kinds of services provided by the centre. The contradiction results in the professionals experiencing tension in their role and the families expressing ambivalent feelings about the approach taken to them. The authors outline ways to resolve the tension by suggesting an alternative role for integrated centres.