gebhart/patrepeval huggingface dataset:
Does Pay for Performance Improve Cardiovascular Care in a “Real-World” Setting? (2011)

The objective was to investigate the impact of a pay-for-performance program (P4P) on quality care and outcomes among cardiovascular disease (CVD) patients. Claims data were used to identify CVD patients in a commercial plan in 1999-2006. Multivariate analyses were employed to examine the impact of P4P on quality care (lipid monitoring and treatment) and quality care on outcomes (new coronary events, hospitalizations, and lipid control). Patients who were treated by physicians participating in P4P were more likely to receive quality care than patients who were not. Patients who received quality care were less likely to have new coronary events (odds ratio [OR] = 0.80; 95% confidence interval [CI] = 0.69-0.92), be hospitalized (OR = 0.76; 95% CI = 0.69-0.83), or have uncontrolled lipids (OR = 0.67; 95% CI = 0.61-0.73) than patients who did not. A P4P program was associated with increased lipid monitoring and treatment. Receipt of this quality care was associated with improved lipid control and reduced likelihood of new coronary events and hospitalizations.
Reformulation of existing antiretroviral drugs (2013)

In this review, we describe the objectives of new formulations, recent advances including combinations, copackaged drugs, nanomedicine, pediatric products and new routes of delivery and the challenges that lie ahead.
Comparative studies of 193-nm photodissociation and TOF-TOFMS analysis of bradykinin analogues: The effects of charge site(s) and fragmentation timescales (2006)

The dissociation reactions of [M + H]+, [M + Na]+, and [M + Cu]+ ions of bradykinin (amino acid sequence RPPGFSPFR) and three bradykinin analogues (RPPGF, RPPGFSPF, PPGFSPFR) are examined by using 193-nm photodissociation and post-source decay (PSD) TOF-TOF-MS techniques. The photodissociation apparatus is equipped with a biased activation cell, which allows us to detect fragment ions that are formed by dissociation of short-lived (<1 mus) photo-excited ions. In our previously reported photodissociation studies, the fragment ions were formed from ions dissociating with lifetimes that exceeded 10 mus; thus these earlier photofragment ion spectra and post-source decay (PSD) spectra [composite of both metastable ion (MI) and collision-induced dissociation (CID)] were quite similar. On the other hand, short-lived photo-excited ions dissociate by simple bond cleavage reactions and other high-energy dissociation channels. We also show that product ion types and abundances vary with the location of the charge on the peptide ion. For example, H+ and Na+ cations can bind to multiple polar functional groups (basic amino acid side chains) of the peptide, whereas Cu+ ions preferentially bind to the guanidino group of the arginine side-chain and the N-terminal amine group. Furthermore, when Cu+ is the charge carrier, the abundances of non-sequence informative ions, especially loss of small neutral molecules (H2O and NH3) is decreased for both photofragment ion and PSD spectra relative to that observed for [M + H]+ and [M + Na]+ peptide ions.
Shear Response under Reversed Cyclic Loading (2016)

A series of three shear panels with transverse reinforcing ratios ranging from 0.23 to 0.68% were tested to failure under reversed cyclic loading. All of the tests showed a reduction in strength of at least 20% with respect to predictions from reliable monotonic analyses. Extensive experimental results including strain distributions and cracking patterns were analyzed to explain this discrepancy, and it was determined that shear behavior under reversed cyclic conditions is not well captured by a single rotating crack model; rather, explicit consideration of both diagonal crack systems is required. This analysis has shown that the behavior can be rationally explained by considering the evolution of crack slip and crack closing hysteresis.
Simple Amine/Pd(OAc)2-Catalyzed Suzuki Coupling Reactions of Aryl Bromides under Mild Aerobic Conditions (2004)

A new palladium catalyst (DAPCy) made from Pd(OAc)(2) and commercially available, inexpensive dicyclohexylamine has been developed for the Suzuki coupling reaction of aryl bromides with boronic acids to give the coupling products in good to high yields. The air-stable catalyst was characterized and well-defined by X-ray crystallography. A catalytic system involving DAPCy in dioxane demonstrates a temperature-dependent reactivity toward aryl bromides with different electronic substituents, and selectively couples electron-deficient aryl bromides with boronic acids over electron-rich ones at room temperature. Another catalytic system employing DAPCy in EtOH provides a general and convenient method to prepare biaryls from aryl bromides and boronic acids with a broad range of functional groups at room temperature and under aerobic conditions.
Dual-Stream Recurrent Neural Network for Video Captioning (2018)

Recent progress in using recurrent neural networks (RNNs) for video description has attracted an increasing interest, due to its capability to encode a sequence of frames for caption generation. While existing methods have studied various features (e.g., CNN, 3D CNN, and semantic attributes) for visual encoding, the representation and fusion of heterogeneous information from multi-modal spaces have not fully explored. Consider that different modalities are often asynchronous, frame-level multi-modal fusion (e.g., concatenation and linear fusion) will negatively influence each modality. In this paper, we propose a dual-stream RNN (DS-RNN) framework to jointly discover and integrate the hidden states of both visual and semantic streams for video caption generation. First, an encoding RNN is used for each stream to flexibly exploit the hidden states of respective modality. Specifically, we proposed an attentive multi-grained encoder module to enhance the local feature learning with global semantics feature. Then, a dual-stream decoder is deployed to integrate the asynchronous yet complementary sequential hidden states from both streams for caption generation. Extensive experiments on three benchmark datasets, namely, MSVD, MSR-VTT, and MPII-MD, show that DS-RNN achieves competitive performance against the state-of-the-art. Additional ablation studies were conducted on various variants of the proposed DS-RNN.
CMUT with mechanically coupled plate actuators -Linearized electrostatic modeling (2019)

This paper derives an analytical model of the electrostatic transduction of a capacitive micromachined ultrasonic transducer (CMUT) with mechanically coupled plate actuators. The mass of the coupling geometry significantly affects the dynamic deflection shape of the plate actuators. As the electrostatic transduction of a CMUT depends on the distance between both electrodes of these capacitive systems, the static and dynamic deflection shapes are taken into account for the small signal electrostatic behavior. The analysis of the electrostatic lumped elements, varying with the bias voltage, reveals a dependence on the deflection shape. A comparison with finite element simulations shows good agreement with the analytical model.
Fabrication of Magnesium Foam by Precursor Method Using Machined Chips (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Novel Cross-Reactive Monoclonal Antibodies against Ebolavirus Glycoproteins Show Protection in a Murine Challenge Model (2017)

Out of an estimated 31,100 cases since their discovery in 1976, ebolaviruses have caused approximately 13,000 deaths. The vast majority (∼11,000) of these occurred during the 2013-2016 West African epidemic. Three out of five species in the genus are known to cause Ebola Virus Disease in humans. Several monoclonal antibodies against the ebolavirus glycoprotein are currently in development as therapeutics. However, there is still a paucity of monoclonal antibodies that can cross-react between the glycoproteins of different ebolavirus species, and the mechanism of these monoclonal antibody therapeutics is still not understood in detail. Here, we generated a panel of eight murine monoclonal antibodies (MAbs) utilizing a prime-boost vaccination regimen with a <i>Zaire ebolavirus</i> glycoprotein expression plasmid followed by infection with a vesicular stomatitis virus expressing the <i>Zaire ebolavirus</i> glycoprotein. We tested the binding breadth of the resulting monoclonal antibodies using a set of recombinant surface glycoproteins from Reston, Taï Forest, Bundibugyo, Zaire, Sudan, and Marburg viruses and found two antibodies that showed pan-ebolavirus binding. An <i>in vivo Stat2</i><sup>-/-</sup> mouse model was utilized to test the ability of these MAbs to protect from infection with a vesicular stomatitis virus expressing the <i>Zaire ebolavirus</i> glycoprotein. Several of our antibodies, including the broadly binding ones, protected mice from mortality despite lacking neutralization capability <i>in vitro</i>, suggesting their protection may be mediated by Fc-FcR interactions. Indeed, three antibodies displayed cellular phagocytosis and/or antibody-dependent cell-mediated cytotoxicity <i>in vitro</i> Our antibodies, specifically the two identified cross-reactive monoclonal antibodies (KL-2E5 and KL-2H7), might add to the understanding of anti-ebolavirus humoral immunity.<b>IMPORTANCE</b> This study describes the generation of a panel of novel anti-ebolavirus glycoprotein monoclonal antibodies, including two antibodies with broad cross-reactivity to all known ebolavirus species. The antibodies were raised using a heterologous DNA-viral vector prime-boost regimen, resulting in a high proportion of cross-reactive antibodies (25%). Similar vaccination regimens have been used successfully to induce broad protection against influenza viruses in humans, and our limited data indicate that this might be a useful strategy for filovirus vaccines as well. Several of our antibodies showed protective efficacy when tested in a novel murine challenge model and may be developed into future therapeutics.
Residual Bulk Image Characterization using Photon Transfer Techniques (2017)

Trapped charge can lead to a source of error when making low level Photon Transfer ("PTC") measurements. Residual signal can corrupt low level dark and light-on measurements leading to incorrect signal measurements when performing frame differencing required for the data reduction in the PTC procedure. To quantify the effect of trapping, the trap characteristics of capacity and decay rate versus temperature were studied for a commercially produced full frame CCD. Photon Transfer noise analysis was used to measure trap capacity, trap leakage rate, dark shot noise and thermal generation of dark signal as a function of cooling.
2105 Stress analysis of mandible model with some tilted-implants by 3D-FEM with elevator muscle (2010)

Stress analysis of mandible model with some tilted -implants by 3D -FEM with elevator muscle
Benchmark Dose Analysis of DNA Damage Biomarker Responses Provides Compound Potency and Adverse Outcome Pathway Information for the Topoisomerase II Inhibitor Class of Compounds (2020)

Genetic toxicology data have traditionally been utilized for hazard identification to provide a binary call for a compound's risk. Recent advances in the scientific field, especially with the development of high-throughput methods to quantify DNA damage, have influenced a change of approach in genotoxicity assessment. The in vitro MultiFlow® DNA Damage Assay is one such method which multiplexes γH2AX, p53, phospho-histone H3 biomarkers into a single-flow cytometric analysis (Bryce et al., [2016]: Environ Mol Mutagen 57:546-558). This assay was used to study human TK6 cells exposed to each of eight topoisomerase II poisons for 4 and 24 hr. Using PROAST v65.5, the Benchmark Dose approach was applied to the resulting flow cytometric datasets. With "compound" serving as covariate, all eight compounds were combined into a single analysis, per time point and endpoint. The resulting 90% confidence intervals, plotted in Log scale, were considered as the potency rank for the eight compounds. The in vitro MultiFlow data showed a maximum confidence interval span of 1Log, which indicates data of good quality. Patterns observed in the compound potency rank were scrutinized by using the expert rule-based software program Derek Nexus, developed by Lhasa Limited. Compound sub-classification and structural alerts were considered contributory to the potencies observed for the topoisomerase II poisons studied herein. The Topo II poison Adverse Outcome Pathway was evaluated with MultiFlow endpoints serving as Key Events. The step-wise approach described herein can be considered as a foundation for risk assessment of compounds within a specific mode of action of interest. Environ. Mol. Mutagen. 2020. © 2020 Wiley Periodicals, Inc.
The piglet acute diarrhea model for evaluating efficacy of treatment and control of cryptosporidiosis (2018)

<i>Cryptosporidium</i> spp. are ranked as the second leading pathogens causing life-threatening diarrhea in children under 2 years of age. Although <i>Cryptosporidium hominis</i> causes three quarters of the cases of cryptosporidiosis, studies on <i>C. hominis</i> are limited since natural disease due to <i>C. hominis</i> is host-restricted to humans only. In this mini-review, we demonstrate the successfully adoption, propagation, and utility of the <i>C. hominis</i> strain TU502, isolated originally from an infant with diarrhea in Uganda, in gnotobiotic piglets. The TU502 <i>C. hominis</i> strain and the gnotobiotic piglet model currently are the only available preclinical tools to evaluate therapeutics that specifically target <i>C. hominis</i>. Infection in this gnotobiotic piglet model displays similar clinical symptoms of diarrhea observed in humans. Here we further describe how this unique model of acute diarrhea, can be used for drug discovery and testing of vaccine candidates against cryptosporidiosis. The shared anatomical, physiological and immunological characteristics between piglets and human infants makes the model ideal for evaluating the efficacy of therapeutics and vaccines against cryptosporidiosis as they become available.
Development of an Efficient Manufacturing Process to GSK2248761A API (2018)

Amidation of indole 2-carboxylate 1 with ammonia gas via the imidazolide 2 gave GSK2248761A API 3, which was in development for the treatment of HIV. Three significant impurities, namely the phosphinic acid 4, the N-acyl urea 8, and the indoloyl carboxamide 6, were formed during the reaction, and the original process was unable to produce API within clinical specification when run at scale. Investigation into the origin, fate, and control of these impurities led to a new process which was able to produce API within clinical specification.
Promotion of Human Early Embryonic Development and Blastocyst Outgrowth In Vitro Using Autocrine/Paracrine Growth Factors (2012)

Studies using animal models demonstrated the importance of autocrine/paracrine factors secreted by preimplantation embryos and reproductive tracts for embryonic development and implantation. Although in vitro fertilization-embryo transfer (IVF-ET) is an established procedure, there is no evidence that present culture conditions are optimal for human early embryonic development. In this study, key polypeptide ligands known to be important for early embryonic development in animal models were tested for their ability to improve human early embryo development and blastocyst outgrowth in vitro. We confirmed the expression of key ligand/receptor pairs in cleavage embryos derived from discarded human tri-pronuclear zygotes and in human endometrium. Combined treatment with key embryonic growth factors (brain-derived neurotrophic factor, colony-stimulating factor, epidermal growth factor, granulocyte macrophage colony-stimulating factor, insulin-like growth factor-1, glial cell-line derived neurotrophic factor, and artemin) in serum-free media promoted >2.5-fold the development of tri-pronuclear zygotes to blastocysts. For normally fertilized embryos, day 3 surplus embryos cultured individually with the key growth factors showed >3-fold increases in the development of 6-8 cell stage embryos to blastocysts and >7-fold increase in the proportion of high quality blastocysts based on Gardner's criteria. Growth factor treatment also led to a 2-fold promotion of blastocyst outgrowth in vitro when day 7 surplus hatching blastocysts were used. When failed-to-be-fertilized oocytes were used to perform somatic cell nuclear transfer (SCNT) using fibroblasts as donor karyoplasts, inclusion of growth factors increased the progression of reconstructed SCNT embryos to >4-cell stage embryos. Growth factor supplementation of serum-free cultures could promote optimal early embryonic development and implantation in IVF-ET and SCNT procedures. This approach is valuable for infertility treatment and future derivation of patient-specific embryonic stem cells.
Observation of a Critical Time Scale for Supercavitation Development and the Effect of Gas Leakage (2008)

A critical time scale that describes the spontaneous growth of small stable cavities into developed supercavitation over blunt free flying cylindrical slug projectiles was observed experimentally. The projectiles were ejected using a modified gas-gun mechanism consisting of a barrel and explosive charge. Upon ignition, high pressure gases translated the projectiles down the launch barrel and into quiescent water where they were digitally imaged for analysis. Results indicate that the initially small cavities appeared downstream of the projectile forebody and grew up the projectile, partially or completely enveloping the projectile. This study introduces a mechanism to explain supercavity development over impulsively translated projectiles. As a projectile is accelerated from rest in the barrel a vortex ring is produced. Small nuclei present in the ambient flow field expand as they encounter the separated flow around the blunt forebody and become entrained in the vortex ring. The subsequent increase in vortex circulation as the projectile continues to accelerate causes the pressure in the vortex ring to drop below the Blake critical pressure, at which point the initially stable cavity rapidly grows. The small cavities grow from aft to fore as the supercavity develops, traveling at speeds up to 4 times the initial projectile velocity.
Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space (2012)

Increased information on the encoded mammalian genome is expected to facilitate an integrated understanding of complex anatomical structure and function based on the knowledge of gene products. Determination of gene expression-anatomy associations is crucial for this understanding. To elicit the association in the three-dimensional (3D) space, we introduce a novel technique for comprehensive mapping of endogenous gene expression into a web-accessible standard space: Transcriptome Tomography. The technique is based on conjugation of sequential tissue-block sectioning, all fractions of which are used for molecular measurements of gene expression densities, and the block- face imaging, which are used for 3D reconstruction of the fractions. To generate a 3D map, tissues are serially sectioned in each of three orthogonal planes and the expression density data are mapped using a tomographic technique. This rapid and unbiased mapping technique using a relatively small number of original data points allows researchers to create their own expression maps in the broad anatomical context of the space. In the first instance we generated a dataset of 36,000 maps, reconstructed from data of 61 fractions measured with microarray, covering the whole mouse brain (ViBrism: http://vibrism.riken.jp/3dviewer/ex/index.html) in one month. After computational estimation of the mapping accuracy we validated the dataset against existing data with respect to the expression location and density. To demonstrate the relevance of the framework, we showed disease related expression of Huntington's disease gene and Bdnf. Our tomographic approach is applicable to analysis of any biological molecules derived from frozen tissues, organs and whole embryos, and the maps are spatially isotropic and well suited to the analysis in the standard space (e.g. Waxholm Space for brain-atlas databases). This will facilitate research creating and using open-standards for a molecular-based understanding of complex structures; and will contribute to new insights into a broad range of biological and medical questions.
Growth and Optical Properties of InGaAs via Ge-Based Virtual Substrates: A New Chemistry Based Strategy (2010)

In this study, we report the epitaxial integration of InGaAs films on Ge/Si(100) virtual substrates for photonic applications. Ge buffer layers with thicknesses of 400-700 nm were grown directly on vicinal (5 degrees miscut) and on-axis Si (100) wafers using a new low-temperature, chemistry-based approach that allows unprecedented control of film microstructure, morphology and purity at CMOS-compatible conditions. In0.01Ga0.49As0.50 films lattice matched to Ge and with thicknesses in the range of 800-2500 nm were then deposited on both Ge/Si substrates and bulk Ge wafers using industrial MOCVD. All materials were characterized by high-resolution X-ray diffraction, atomic force microscopy, transmission electron microscopy, time-resolved and steady-state photoluminescence, as well as cathodoluminescence. It is found that the properties of the InGaAs/Ge/Si(100) samples are comparable with those grown directly on bulk Ge platforms. Most importantly the films grown on miscut Ge templates are devoid of deleterious antiphase boundaries, making them promising candidates for large scale production of III-V photovoltaics.
Broadband frequency-domain near-infrared spectral tomography using a mode-locked Ti:sapphire laser (2009)

Frequency-domain near-infrared (NIR) diffuse spectral tomography with a mode-locked Ti:sapphire laser is presented, providing tunable multiwavelength quantitative spectroscopy with maximal power for thick tissue imaging. The system was developed to show that intrinsically high stability can be achieved with many wavelengths in the NIR range, using a mode-locked signal of 80 MHz with heterodyned lock-in detection. The effect of cumulative noise from multiple wavelengths of data on the reconstruction process was studied, and it was shown that inclusion of more wavelengths can reduce skew in the noise distribution. This normalization of the data variance then minimizes errors in estimation of chromophore concentrations. Simulations and tissue phantom experiments were used to quantify this improvement in image accuracy for recovery of tissue hemoglobin and oxygen saturation.
Refinement of an Established Procedure and Its Application for Identification of Hypoxia in Prostate Cancer Xenografts (2021)

We have developed a combined autoradiographic/laser-guided microdissection method with broad applicability. Using this approach on fresh frozen tumor material, thereby minimizing the degree of RNA degradation, we showed that the 15-gene hypoxia gene classifier developed in HNSCC may be applicable for adenocarcinomas such as prostate cancer.
Slow Light Waveguide and Enhanced Area Microcavity Engineering for High Sensitivity Photonic Crystal Sensors (2013)

We experimentally demonstrate that in photonic crystal sensors with side-coupled cavity-waveguide, group velocity of propagating mode in the coupled waveguide at the resonant mode frequency enhances sensitivity in addition to microcavity mode engineering.