gebhart/patrepeval huggingface dataset:
Inhibitory Effects of Dexamethasone on Hepatocyte Growth Factor–Induced DNA Synthesis and Proliferation in Primary Cultures of Adult Rat Hepatocytes (2011)

We investigated the effects of dexamethasone on hepatocyte growth factor (HGF)-induced DNA synthesis and proliferation in serum-free primary cultures of adult rat hepatocytes. Isolated hepatocytes were cultured at a density of 3.3 × 10(4) cells/cm(2) in Williams' medium E containing 5% newborn bovine serum and various concentrations of dexamethasone for 1, 2, and 3 h. After a 3-h attachment period, the medium was then changed, and cells were cultured in serum-free dexamethasone (10(-10) M)-containing Williams' medium E with or without glucocorticoid receptor antagonists. After addition of dexamethasone to the culture medium, the growth-stimulating effects of HGF (5 ng/mL) on the primary cultured hepatocytes were time- and dose-dependently inhibited. The mineralcorticoid aldosterone (10(-7) M) did not produce the same growth-inhibitory effects as dexamethasone (10(-8) M). The inhibitory effects of dexamethasone were reversed by treatment with the glucocorticoid-receptor antagonist mifepristone (RU486, 10(-6) M) or a monoclonal antibody against glucocorticoid receptor (100 ng/mL). In addition, the growth-inhibitory dose of dexamethasone did not affect HGF-induced receptor tyrosine kinase and extracellular signal-regulated kinase 2 phosphorylation. These results indicate that dexamethasone dose-dependently delays and inhibits HGF-induced DNA synthesis and proliferation through its own intracellular receptor in primary cultures of adult rat hepatocytes.
Consideration of Skewed Slots in the Performance Calculations of a Four-Quadrant Transducer (2004)

Consideration of Skewed Slots in the Performance Calculations of a Four-Quadrant Transducer
Designing 3D test wrappers for pre-bond and post-bond test of 3D embedded cores (2011)

3D integration is a promising new technology for tightly integrating multiple active silicon layers into a single chip stack. Both the integration of heterogeneous tiers and the partitioning of functional units across tiers leads to significant improvements in functionality, area, performance, and power consumption. Managing the complexity of 3D design is a significant challenge that will require a system-on-chip approach, but the application of SOC design to 3D necessitates extensions to current test methodology. In this paper, we propose extending test wrappers, a popular SOC DFT technique, into the third dimension. We develop an algorithm employing the Best Fit Decreasing and Kernighan-Lin Partitioning heuristics to produce 3D wrappers that minimize test time, maximize reuse of routing resources across test modes, and allow for different TAM bus widths in different test modes. On average the two variants of our algorithm reuse 93% and 92% of the test wrapper wires while delivering test times of just 0.06% and 0.32% above the minimum.
Comparison of sequential and 7-, 10-, 14-d triple therapy forHelicobacter pyloriinfection (2012)

There are no significant differences between 10-d sequential eradication therapy for H. pylori and any duration of standard triple treatment in Korean patients.
Fracture mechanics of idealised bituminous mixes (2014)

The durability of asphalt pavements is strongly impaired by cracks, caused primarily by traffic loads and environmental effects. In this work, fracture behaviour of idealised asphalt mixes is investigated. Experiments on idealised asphalt mixes under pure-tension mode (mode I cracking) were performed and fracture parameters were evaluated. In these three-point bend fracture tests, the test variables were temperature and load rate. The test data were stored in an asphalt materials database and special-purpose tools were implemented to analyse and handle the laboratory data automatically. Fracture mechanism maps were constructed, showing the conditions associated with ductile, brittle and ductile–brittle transition regimes of behaviour. The mechanism maps show the failure response of the material in terms of the stress intensity factor, strain energy release rate and J-integral as a function of the temperature-compensated crack mouth opening strain rate. Fracture behaviour of asphalt mix specimens was simulated by cohesive zone model in conjunction with a novel material constitutive model for asphalt mixes. The finite element model agrees well with the experimental results and provides insights into fracture response of the notched asphalt mix beam specimens.
Large cell change (liver cell dysplasia) and hepatocellular carcinoma in cirrhosis: Matched case-control study, pathological analysis, and pathogenetic hypothesis (1997)

Large cell change (LCC), characterized by cellular enlargement, nuclear pleomorphism and hyperchromasia, and multinucleation of hepatocytes, is a common lesion in cirrhotic livers, but its nature, significance, and pathogenesis remain uncertain. Therefore, we assessed the prognostic value of LCC as a marker of subsequent hepatocellular carcinoma (HCC) through a case-control study that compared pretransplant liver biopsy specimens from 37 cirrhotic liver transplant recipients with HCC to specimens from a control group of recipients without HCC, matched for sex, age (+/-5 years), and cause of cirrhosis. LCC was identified in 16 (43%) of the study and 7 (19%) of the control group biopsy specimens. By matched-pair analysis, LCC conveyed a moderately increased risk of later HCC with an estimated odds ratio of 3.3 (95% CI, 1.2-15; P = .038). However, a pathology review of 45 HCCs showed adjoining LCC in only 12 (27%) and did not suggest a morphological transition or a histogenetic association between the two lesions. LCC hepatocytes displayed a low proliferative rate by Ki-67 or proliferating cell nuclear antigen immunostaining (labeling indices of 0.27 and 0.73) but showed a greater degree of apoptosis than normal hepatocytes (labeling indices of 1.9 and 0.23; P = .03) To reconcile these findings, we propose that LCC derives from derangements in the hepatocyte's normal process of polyploidization. Such derangements, possibly caused by chronic inflammation-induced DNA damage, could yield a population of enlarged liver cells with nuclear atypia and pleomorphism, frequent binuclearity, and minimal proliferation. According to this hypothesis, LCC would be a habitual feature of cirrhosis and a regular accompaniment of HCC but would not represent a direct malignant precursor.
Geophysical Characterization of the Red Lake Peatland Complex, Northern Minnesota (2008)

The Red Lake Peatland Complex in Northern Minnesota is one of the largest and most studied peatlands in North America (140 km2), but the logistical impediments of working in such large remote wetlands limit direct subsurface data collection to a few widely spaced samples. This mid‐continent forested bog complex is comprised of three major peat landforms, each of which was surveyed using ground penetrating radar (GPR), electrical resistivity, and induced polarization (IP): (1) a raised, ombrotrophic, wooded crest; (2) a sphagnum lawn down slope of the bog crest; (3) a spring fen water track where water flows across the peat surface around ovoid wooded islands. GPR was used to obtain peat thickness and to distinguish the peat stratigraphy as a function of variable water content between organic soil horizons. Resistivity data was collected to characterize the peat thickness and structure and to image the hydrogeologic framework beneath the organic soil. The results form a novel data set of a well studied bog complex, offering new insights into the peat structure and hydrogeologic framework. These observations have implications for general models of peatland development and carbon cycling.
[Initial experience with the NOVACOR left heart assist system in transition for heart transplantation at the Grosshadern Clinic]. (1993)

We recently used an electrically powered left ventricular assist device (NOVACOR Corp., Oakland, Calif.) to support the circulation of a 17-year-old man with profound circulatory impairment. He had been regularly listed for cardiac transplantation previously because of dilated cardiomyopathy, and decompensated acutely with severe biventricular failure before a suitable donor heart became available. Isolated left ventricular support with the NOVACOR system provided adequate haemodynamics and recovery of right ventricular, hepatic and renal function. After 2 days of support, orthotopic heart transplantation could be performed successfully. Five days after transplantation he developed a massive cerebral haemorrhage during a hypertensive crisis of which he recovered completely after neurosurgery without any residuals. He ist currently doing extremely well some 14 months after transplantation.
cDNA cloning of mouse NKR-P1 and genetic linkage with LY-49. Identification of a natural killer cell gene complex on mouse chromosome 6 (1991)

NK cells lyse tumor cells and virally infected cells, but the molecular basis for this phenomenon has not been defined. A mAb specific for the rat cell surface molecule, NKR-P1, stimulates rat NK cell lytic activity and is reactive with all rat NK cells, suggesting that this molecule may play a significant role in NK cell function. We have previously described another NK cell-specific Ag, Ly-49, that belongs to a family of cross-hybridizing genes on distal mouse chromosome 6. The rat NKR-P1 Ag shares several features with the mouse Ly-49 Ag, including selective cell surface expression on NK cells, homology to the C-type lectins, expression as a type II integral membrane protein, and disulfide-linked homodimeric structure. To further examine the relationship of NKR-P1 to Ly-49, we have cloned the cDNA encoding a mouse homologue of NKR-P1 (mNKR-P1). The mouse and rat NKR-P1-deduced polypeptide sequences are highly conserved, suggesting a similar tertiary structure. By examination of DNA from informative recombinant inbred mice with Southern blot analysis, we have determined that mNKR-P1 is encoded by a distinct gene that is genetically linked to the Ly-49 locus, lying within 0.5 centi-Morgan (cM) of Ly-49. Although the deduced amino acid sequences of mNKR-P1 and Ly-49 reveal that these proteins are structurally similar, they are only 24% identical at the amino acid level and the cDNA sequences do not demonstrate significant nucleotide homology. Our studies suggest that we have identified a region on mouse chromosome 6 that includes distinct NK-specific genes that encode structurally related proteins (type II integral membrane proteins, C-type lectin super-gene family) but which demonstrate considerable heterogeneity. We have termed this genetic region the NK complex.
A conceptual framework for evaluating variable speed generator options for wind energy applications (1995)

Interest in variable speed generating technology has accelerated as greater emphasis on overall efficiency and superior dynamic and control properties in wind-electric generating systems are sought. This paper reviews variable speed technology options providing advantages and disadvantages of each. Furthermore, the dynamic properties of variable speed systems are contrasted with synchronous operation. Finally, control properties of variable speed systems are examined.
New Synthetic Process for Bosutinib (2015)

A new and improved synthetic route to bosutinib is described on a hectogram scale. The key step is the intramolecular cyclization of a 3-(2-aminophenyl)-3-oxopropanenitrile with <i>N</i>,<i>N</i>-dimethylformamide dimethyl acetal to form the 3-cyano-4-hydroxyquinoline ring of 7-(3-chloropropoxy)-6-methoxy-4-oxo-1,4-dihydroquinoline-3-carbonitrile. A practical synthetic method to 2,4-dichloro-5-methoxyaniline is also established. Bosutinib is obtained in 18.0% yield over nine steps from acetovanillone with 98.9% purity (HPLC).
Growth Conditions Control the Elastic and Electrical Properties of ZnO Nanowires (2015)

Great efforts have been made to synthesize ZnO nanowires (NWs) as building blocks for a broad range of applications because of their unique mechanical and mechanoelectrical properties. However, little attention has been paid to the correlation between the NWs synthesis condition and these properties. Here we demonstrate that by slightly adjusting the NW growth conditions, the cross-sectional shape of the NWs can be tuned from hexagonal to circular. Room temperature photoluminescence spectra suggested that NWs with cylindrical geometry have a higher density of point defects. In situ transmission electron microscopy (TEM) uniaxial tensile-electrical coupling tests revealed that for similar diameter, the Young's modulus and electrical resistivity of hexagonal NWs is always larger than that of cylindrical NWs, whereas the piezoresistive coefficient of cylindrical NWs is generally higher. With decreasing diameter, the Young's modulus and the resistivity of NWs increase, whereas their piezoresistive coefficient decreases, regardless of the sample geometry. Our findings shed new light on understanding and advancing the performance of ZnO-NW-based devices through optimizing the synthesis conditions of the NWs.
ChemInform Abstract: SULFONES IN HORNER‐WITTIG SYNTHESIS OF ALKENES (1980)

Abstract Die Phosphonate (I) werden mit den Alkylhalogeniden (II) zu den C‐Alkylderivaten (III) umgesetzt.
Sequence-specific inhibition of a designed metallopeptide catalyst (2012)

Rhodium metallopeptides catalyze proximity-driven modification of peptide and protein substrates with enzyme-like selectivity. In this communication, we demonstrate that designed metallopeptide catalysts can be inhibited in a sequence-specific manner, mimicking the inhibition and regulation of natural enzymes. We demonstrate sub-micromolar inhibition by a histidine-containing inhibitor peptide, taking advantage of cooperative supramolecular assembly and inorganic coordination.
The Diagnosis of Absence of the Corpus Callosum by Ultrasound (1982)

A case of absence of the corpus callosum is described in which the correct diagnosis was made by ultrasonography. The diagnosis led to appropriate investigations and the subsequent discovery of associated hypothalamic hypopituitarism.
Th2 response polarization during infection with the helminth parasite Schistosoma mansoni (2004)

T-helper 2 (Th2) cell responses play a critical role in protection against helminth infections. In the case of Schistosoma mansoni, an important helminth parasite of man, data from a mouse model of human disease have shown that Th2 responses are essential to allow host survival. In this infection, parasite eggs are the primary stimulus for Th2 response development. Recent work has shown that egg molecules exert multiple levels of control over the development of host interferon-gamma-associated inflammatory responses. Soluble egg antigen inhibits the ability of dendritic cells to make interleukin-12 and induces Th2-polarized adaptive immune responses that in combination with regulatory T-cell responses effectively limit Th1 response development. In this article, we discuss the factors influencing Th2 response polarization during infection with S. mansoni.
Penning micro-trap for quantum computing (2023)

Trapped ions in radio-frequency traps are among the leading approaches for realizing quantum computers, due to high-fidelity quantum gates and long coherence times. However, the use of radio-frequencies presents a number of challenges to scaling, including requiring compatibility of chips with high voltages, managing power dissipation and restricting transport and placement of ions. By replacing the radio-frequency field with a 3 T magnetic field, we here realize a micro-fabricated Penning ion trap which removes these restrictions. We demonstrate full quantum control of an ion in this setting, as well as the ability to transport the ion arbitrarily in the trapping plane above the chip. This unique feature of the Penning micro-trap approach opens up a modification of the Quantum CCD architecture with improved connectivity and flexibility, facilitating the realization of large-scale trapped-ion quantum computing, quantum simulation and quantum sensing.
Immune characterization in platinum resistant ovarian cancer patients treated with pembrolizumab and guadecitabine (2022)

Abstract Immune checkpoint inhibitors (ICI) have limited activity in ovarian cancer (OC). Accumulating preclinical and early clinical results support that interventions targeting the epigenome could elicit an inflamed tumor milieu to augment ICI. Here we explore the clinical and biological activity of guadecitabine, a second generation Hypomethylating agents (HMA), given in low dose as a priming strategy before pembrolizumab, a humanized anti-PD1 antibody in a clinical trial for patients with recurrent, platinum-resistant OC. Among 35 evaluable patients, there were 3 partial responses (8.6%) and 8 (22.9%) patients with stable disease, resulting in clinical benefit rate (CBR) of 31.4%. Median duration of clinical benefit was 6.8 months. High dimensional immune profiling of PBMCs showed higher frequency of naive and/or central memory CD4+ T cells and of classical monocytes in patients with durable CBR. Higher baseline density of CD8+ T and CD20+ B cells and presence of tertiary lymphoid structures in tumors were associated with durable CBR. The molecular features such as expression levels of PD-L1 or A2AR linked to therapeutic benefit for resistant OC. Our study provides an in-depth view of the immune milieu of platinum resistant OC and of the effects of the combination of HMAs and pembrolizumab on the interactions between immune cell populations and tumor cells. Supported by USAMRMC/CDMRP (W81XWH170141)
Robust economic model predictive control based on a periodicity constraint (2019)

Summary This paper proposes robust economic model predictive control based on a periodicity constraint for linear systems subject to unknown‐but‐bounded additive disturbances. In this economic MPC design, a periodic steady‐state trajectory is not required and thus assumed unknown, which precludes the use of enforcing terminal state constraints as in other standard economic formulations. Instead, based on the desired periodicity of system operation, we optimize the economic performance over a set of periodic trajectories that include the current state. To achieve robust constraint satisfaction, we use a tube‐based technique in the economic MPC formulation. The mismatches between the nominal model and the closed‐loop system with perturbations are limited using a local control law. With the proposed robust tube‐based strategy, recursive feasibility is guaranteed. Moreover, under a convexity assumption, the closed‐loop convergence of the closed‐loop system is analyzed, and an optimality certificate is provided to check if the closed‐loop trajectory reaches a neighborhood of the optimal nominal periodic steady trajectory using Karush‐Kuhn‐Tucker optimality conditions. Finally, through numerical examples, we show the effectiveness of the proposed approach.
Effects of bee density and sublethal imidacloprid exposure on cluster temperatures of caged honey bees (2018)

Survivorship, syrup consumption, and cluster temperatures of honey bees were kept in hoarding cages with different numbers of bees. Cages with either 50, 100, 150, or 200 bees each were monitored over 4–6 weeks in incubators with 12h/12h 30° C/15° C temperature cycles to induce clustering. Survivorship and syrup consumption rates per bee were not different among the bee density groups, but cluster temperatures were. Cluster temperatures ranged from 0.45°C above incubator temperature in the 50 bee cages to 4.05° C in the 200 bee cages over the 1st 7 days, with each additional bee adding on average 0.02° C to cluster temperature. In another set of experiments, cages were established with about 200 bees each, and imidacloprid added to the syrup at 0, 5, 20, and 100 ppb. Imidacloprid in the syrup did not affect bee survivorship but it did reduce syrup consumption per bee, with bees fed 100 ppb imidacloprid syrup consuming on average 631 mg per bee over 28 days while average consumption among the other groups ranged from 853 to 914 mg. Cluster temperature was affected by imidacloprid treatment: bees fed 5 ppb imidacloprid syrup had higher cluster temperatures over the 1st 10 days, 4.17° C above incubator temperature, than either bees fed 100 ppb syrup or control (2.35 and 3.19° C, respectively).
A Hardware Runtime for Task-Based Programming Models (2019)

Task-based programming models such as OpenMP 5.0 and OmpSs are simple to use and powerful enough to exploit task parallelism of applications over multicore, manycore and heterogeneous systems. However, their software-only runtimes introduce relevant overhead when targeting fine-grained tasks, resulting in performance losses. To overcome this drawback, we present a hardware runtime Picos++ that accelerates critical runtime functions such as task dependence analysis, nested task support, and heterogeneous task scheduling. As a proof-of-concept, the Picos++ hardware runtime has been integrated with a compiler infrastructure that supports parallel task-based programming models. A FPGA SoC running Linux OS has been used to implement the hardware accelerated part of Picos++, integrated with a heterogeneous system composed of 4 symmetric multiprocessor (SMP) cores and several hardware functional accelerators (HwAccs) for task execution. Results show significant improvements on energy and performance compared to state-of-the-art parallel software-only runtimes. With Picos++, applications can achieve up to 7.6x speedup and save up to 90 percent of energy, when using 4 threads and up to 4 HwAccs, and even reach a speedup of 16x over the software alternative when using 12 HwAccs and small tasks.
Isolation of Total RNA from Yeast Cell Cultures: Figure 1. (2012)

This article describes two procedures for isolating total RNA from yeast cell cultures. The first allows the convenient isolation of total RNA from early log-phase cultures (vegetative cells). RNA isolated in this way is intact and sufficiently pure for use in microarray experiments, primer extension, and RNase protection mapping. With additional treatment to remove contaminating genomic DNA, the preparation is suitable for reverse transcription-polymerase chain reaction (RT-PCR), quantitative PCR (qPCR), cDNA library construction, high-throughput sequencing of RNA, or other manipulations. However, compared to vegetative cells, the isolation of RNA from cells late in meiosis (asci and ascospores) requires additional effort. This is because a tough cell wall composed of heavily cross-linked polysaccharides and proteins is built around the four spores during meiosis and ascospore development. Therefore, an alternative protocol is presented for extracting RNA from cells late in meiosis. This alternative may also be preferable for cells from stationary cultures or from yeast strains and other fungal species isolated from the environment.
Tolerance and Determinant Hierarchy (2007)

The overall T cell response to a multideterminant antigen consists of the sum of responses to a limited number of different determinants on the protein. Antigen-presenting cells (APCs) are crucial in delimiting the determinants on the protein to which a response will be mounted. This influence is apparent at two levels. First, the determinants that are generated and displayed by APCs in the thymus are pivotal in shaping the T cell repertoire that will be available for responding to antigen determinants in the periphery. Second, antigen processing affects the selection of determinants that become displayed by the various peripheral APC populations that are involved in inducing and promoting a T cell response. We have studied the effect of the display hierarchy on tolerance induction to individual determinants in transgenic mice expressing different serum levels of hen egg lysozyme. We have also analysed aspects of the processing machinery that contribute to shaping the hierarchy of determinant display on MHC class II molecules: proteolysis and reduction of disulfide bonds.