gebhart/patrepeval huggingface dataset:
Exome Sequencing and Prediction of Long-Term Kidney Allograft Function (2016)

Current strategies to improve graft outcome following kidney transplantation consider information at the human leukocyte antigen (HLA) loci. Cell surface antigens, in addition to HLA, may serve as the stimuli as well as the targets for the anti-allograft immune response and influence long-term graft outcomes. We therefore performed exome sequencing of DNA from kidney graft recipients and their living donors and estimated all possible cell surface antigens mismatches for a given donor/recipient pair by computing the number of amino acid mismatches in trans-membrane proteins. We designated this tally as the allogenomics mismatch score (AMS). We examined the association between the AMS and post-transplant estimated glomerular filtration rate (eGFR) using mixed models, considering transplants from three independent cohorts (a total of 53 donor-recipient pairs, 106 exomes, and 239 eGFR measurements). We found that the AMS has a significant effect on eGFR (mixed model, effect size across the entire range of the score: -19.4 [-37.7, -1.1], P = 0.0042, χ2 = 8.1919, d.f. = 1) that is independent of the HLA-A, B, DR matching, donor age, and time post-transplantation. The AMS effect is consistent across the three independent cohorts studied and similar to the strong effect size of donor age. Taken together, these results show that the AMS, a novel tool to quantify amino acid mismatches in trans-membrane proteins in individual donor/recipient pair, is a strong, robust predictor of long-term graft function in kidney transplant recipients.
Characterization of a Novel Heat Shock Protein (Hsp22.5) Involved in the Pathogenesis of Mycobacterium tuberculosis (2011)

Tuberculosis is a worldwide health problem, given that one-third of the world's population is currently infected with Mycobacterium tuberculosis. Understanding the regulation of virulence on the molecular level will provide a better understanding of how M. tuberculosis can establish chronic infection. Using in vivo microarray analysis (IVMA), we previously identified a group of genes that are activated in BALB/c mouse lungs compared to in vitro cultures, including the rv0990c gene. Our analysis indicated that this gene is a member of the heat shock regulon and was activated under other stress conditions, including survival in macrophages or during the late phase of chronic tuberculosis in the murine lungs. Deletion of rv0990c from the genome of M. tuberculosis strain H37Rv affected the transcriptional profiles of many genes (n = 382) and operons involved in mycobacterial survival, including the dormancy regulon, ATP synthesis, respiration, protein synthesis, and lipid metabolism. Comparison of the proteomes of the mutant to those of the wild-type strain further confirmed the differential expression of 15 proteins, especially those involved in the heat shock response (e.g., DnaK and GrpE). Finally, the rv0990c mutant strain showed survival equivalent to that of the isogenic wild-type strain during active tuberculosis in guinea pigs, despite showing significant attenuation in BALB/c mice during the chronic phase of the disease. Overall, we suggest that rv0990c encodes a heat shock protein that plays an important role in mycobacterial virulence. Hence, we renamed rv0990c heat shock protein 22.5 (hsp22.5), reflecting its molecular mass.
Abstract 3248: New inhibitors of the Shp2 phosphatase (2011)

Abstract The Shp2 protein tyrosine phosphatase (PTP) mediates signal transduction of growth factor receptors and regulates cellular activities critical to tumor growth and metastasis. In the basal state, the interactions between the N-SH2 and PTP domains keep the phosphatase in an auto inhibited closed conformation. Upon growth factor or cytokine stimulation, the SH2 domains of Shp2 binds to tyrosine phosphorylated docking proteins such as Gab1 and Gab2, which activates Src, Ras, and the Erk1/2 (Erk) mitogen-activated protein (MAP) kinase pathway. Shp2 gain-of-function mutations are found in leukemias and solid tumors and are linked to Noonan syndrome. Although Shp2 is involved in pathogenesis of human cancers, it is not clear how Shp2 mediates tumorigenesis. Shp2 is therefore believed to be an important enzyme for targeted cancer therapy. Since no potent and selective Shp2 PTP inhibitor is currently available for chemical biology studies and experimental therapy, we and others have been actively engaged in the search for such agents. In our continuing efforts to develop potent and selective Shp2 inhibitors to serve as both chemical probes to further our understanding of the role and signaling mechanisms of Shp2 in human diseases and as potential drugs for cancer therapy. We will report the screening of a focused library of a set of commercially available salicylic acid derivatives using the in vitro DIFMUP phosphatase assay for their ability to inhibit the Shp2 phosphatase domain. Activity of hits was confirmed using the Biomol Green assay to determine inhibition of dephosphorylation of a Shp2 peptide substrate derived from EphR. One such hit was a thiazole containing salicylic acid that inhibits Shp2 with an IC50 (DIFMUP) of 100 µM. We will report the design and synthesis of salicylic acid libraries along with their benzoic acid counterparts. The most potent compound to date is HM2-08-4 which has an IC50 (DIFMUP) 1.1 µM. Emerging structure-activity relationships as well as modeling and X-ray studies will be discussed. The preliminary use of selected compounds as tools to probe the pharmacological inhibition of Shp2 and elucidate its role in cancer will be described. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3248. doi:10.1158/1538-7445.AM2011-3248
<title>High-speed high-precision optically controlled sample and hold circuit for analog to digital conversion</title> (1994)

A novel bridge type opto-electronic (OE) sample and hold circuit based upon current steering is presented and experimentally tested. Comparison between this circuit and a more conventional or direct OE sample and hold circuit which draws charge directly from the signal source shows that the bridge type is clearly superior in performance to the direct OE circuit. When a high speed signal is to be sampled with considerable precision, the bridge type OE sample and hold circuit offers high charging capability, much needed signal isolation, and reduced time jitter, distinct advantages over electronic sample and hold circuits.
Endolysin-Based Autolytic <i>E. coli</i> System for Facile Recovery of Recombinant Proteins (2021)

Recovery of recombinant proteins from the <i>Escherichia coli</i> cytoplasm depends on cell disruption by mechanical, chemical, and/or enzymatic methods, which usually cause incomplete cell breakage or protein denaturation. Controllable autolytic <i>E. coli</i> strains have been designed to facilitate the purification of recombinant proteins; however, these strains suffer from low recovery yield, slow cell lysis, or extensive strain engineering. Herein, we report an improved, highly efficient programmable autolytic <i>E. coli</i> platform, in which cell lysis is initiated upon the induced expression of T4 lysozyme with N-terminal fusion of a cell-penetrating peptide. Through the engineering of the peptide sequence and copy number, and by incorporating the fusion lytic gene into the <i>E. coli</i> genome, more than 99.97% of cells could be lysed within 30 min of induction regardless of cell age. We further tested the expression and release of a recombinant enzyme lysostaphin (Lst) and demonstrated that 4 h induction of the lytic gene after 3 h of Lst expression resulted in 98.97% cell lysis. Lst obtained from this system had the same yield, yet 1.63-fold higher activity, compared with that obtained from cells lysed by freeze-thawing and sonication. This autolytic platform shows potential for use in large-scale microbial production of proteins and other biopolymers.
Recombinant bacillus Calmette–Guérin (BCG) vaccines expressing the<i>Mycobacterium tuberculosis</i>30-kDa major secretory protein induce greater protective immunity against tuberculosis than conventional BCG vaccines in a highly susceptible animal model (2000)

Tuberculosis (TB) continues to ravage humanity, causing 2 million deaths per year. A vaccine against TB more potent than the current live vaccine, bacillus Calmette-Guérin (BCG), is desperately needed. Using two commercially available strains of BCG as host strains, BCG Connaught and Tice, we have constructed two recombinant BCG vaccines stably expressing and secreting the 30-kDa major secretory protein of Mycobacterium tuberculosis (M. tb.), the primary causative agent of TB. We have tested the efficacy of the two strains in the highly susceptible guinea pig model of pulmonary TB, a model noteworthy for its close resemblance to human TB. Animals immunized with the recombinant BCG vaccines and challenged by aerosol with a highly virulent strain of M. tb. had 0.5 logs fewer M. tb. bacilli in their lungs and 1 log fewer bacilli in their spleens on average than animals immunized with their parental conventional BCG vaccine counterparts. Statistically, these differences were highly significant. Paralleling these results, at necropsy, animals immunized with the recombinant BCG vaccines had fewer and smaller lesions in the lung, spleen, and liver and significantly less lung pathology than animals immunized with the parental BCG vaccines. The recombinant vaccines are the first vaccines against TB more potent than the current commercially available BCG vaccines, which were developed nearly a century ago.
Performance comparison of titanium-oxide resistive switching memories using GeO<i><sub>x</sub></i> and AlO<i><sub>x</sub></i> capping layers for flexible application (2014)

To meet the requirements of flexible memory applications, we have compared two capping layers of GeOx and AlOx on a TiOy resistive random access memory (RRAM) at room temperature. A Ni/GeOx/TiOy/TaN RRAM shows a large resistance window of >102, 85 °C retention, a high-resistance-state (HRS) activation energy (Ea) of 0.52 eV, and a good DC cycling of 103 cycles, which are significantly better than those of a Ni/AlOx/TiOy/TaN RRAM, which has a high-defect-density dielectric of AlOx.
Method of setting a pile without noise or vibration and apparatus therefor (1979)

First Page
Ag<sub>4</sub>V<sub>2</sub>O<sub>6</sub>F<sub>2</sub>: An Electrochemically Active and High Silver Density Phase. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Synthesis and Biological Activities of New 2-Substituted 1,4-Benzoxazine Derivatives. (1991)

A series of new 1,4-benzoxazine derivatives (XI, XII) possessing (4-phenyl-1-piperazinyl)alkyl moieties at the 2-position and related compounds (XIII) were synthesized and tested for calcium antagonistic, calmodulin antagonistic and antihypertensive activities. Various compounds had in vitro calmodulin antagonistic activity superior or comparable to that of trifluoperazine. Among these compounds, tetrahydronaphtho[2,3-b] [1,4]oxazine derivatives such as 51, 53, 54, 58, 59, 60, 73 and 75 showed potent antihypertensive effects in spontaneously hypertensive rats. Optical isomers of 51 were also synthesized and evaluated biologically. No differences in biological activities were seen between the enantiomers.
Antineoplastic Agents. 400. Synthesis of the Indian Ocean Marine Sponge Cyclic Heptapeptide Phakellistatin 2<sup>,1a</sup> (1999)

Solution-phase synthesis of the marine sponge constituent phakellistatin 2 (1), cyclo(Tyr-Pro-Phe-Pro-Ile-Ile-Pro), was completed using a combination of stepwise coupling and (4 + 3) segment condensation. Use of diethyl phosphorocyanidate for the peptide bond formations gave the linear heptapeptide in 54% yield. Cyclization was achieved in high yields utilizing TBTU (2), BOP-C1 (3), PyBroP (4), and HOAt (5), resulting in 50-65% yields of phakellistatin 2 (1) depending on the method employed. The synthetic cyclic peptide was chemically but not biologically identical with the natural product.
ChemInform Abstract: Acid‐Stable 2′‐Fluoro Purine Dideoxynucleosides as Active Agents Against HIV. (1990)

Abstract The preparation of the title compounds (I) as acid‐stable analogues of the anti‐HIV 2 drugs (II) is described in the original paper.
Ensemble-Level Upscaling for Efficient Estimation of Fine-Scale Production Statistics (2008)

Summary Upscaling is often needed in reservoir simulation to coarsen highly detailed geological descriptions. Most existing upscaling procedures aim to reproduce fine-scale results for a particular geological model (realization). In this work, we develop and test a new approach, ensemble-level upscaling, for efficiently generating up-scaled two-phase flow parameters (e.g., upscaled relative permeabilities) for multiple geological realizations. The ensemble-level upscaling approach aims to achieve agreement between the fine-and coarse-scale flow models at the ensemble level, rather than realization-by-realization agreement, as is the intent of existing upscaling techniques. For this purpose, flow-based upscaling calculations are combined with a statistical procedure based on a cluster analysis. This approach allows us to compute numerically the upscaled two-phase flow functions for only a small fraction of the coarse blocks. For the majority of blocks, these functions are estimated statistically on the basis of single-phase velocity information (attributes), determined when the upscaled single-phase parameters are calculated. The procedure is designed to maintain close correspondence between the cumulative distribution functions (CDFs) for the numerically computed and statistically estimated two-phase flow functions. We apply the method to 2D synthetic models of multiple realizations for uncertainty quantification. Models with different geological heterogeneity and fluid-mobility ratios are considered. It is shown that the method consistently corrects the biases evident in primitive coarse-scale predictions and can capture the ensemble statistics (e.g., P50, P10, P90) of the fine-scale results almost as accurately as the full flow-based upscaling procedures but with much less computational effort. The overall approach is flexible and can be used with any combination of upscaling procedures.
Method for sequestering CO.sub.2 and SO.sub.2 utilizing a plurality of waste streams (2023)

A neutralization/sequestration process is provided for concomitantly addressing capture and sequestration of both CO.sub.2 and SO.sub.2 from industrial gas byproduct streams. The invented process concomitantly treats and minimizes bauxite residues from aluminum production processes and brine wastewater from oil/gas production processes. The benefits of this integrated approach to coincidental treatment of multiple industrial waste byproduct streams include neutralization of caustic byproduct such as bauxite residue, thereby decreasing the risk associated with the long-term storage and potential environmental of storing caustic materials, decreasing or obviating the need for costly treatment of byproduct brines, thereby eliminating the need to purchase CaO or similar scrubber reagents typically required for SO.sub.2 treatment of such gasses, and directly using CO.sub.2 from flue gas to neutralize bauxite residue/brine mixtures, without the need for costly separation of CO.sub.2 from the industrial byproduct gas stream by processes such as liquid amine-based scrubbers.
Building authentic midbrain dopaminergic neurons from stem cells - lessons from development (2012)

Abstract The challenge with controlling the differentiation of human pluripotent cells to generate functional dopaminergic neurons for the treatment of Parkinson’s disease has undergone significant progress in recent years. Here, we summarize the differences between newer and older protocols for generating midbrain dopaminergic neurons from human pluripotent stem cells, and we highlight the importance of following developmental pathways during differentiation. The field has now developed to a point where it is timely to take human pluripotent stem cells one step closer to clinical use, and cell criteria to be fulfilled for such developments are outlined in this review.
MR Safe Robotic Manipulator for MRI-Guided Intracardiac Catheterization (2018)

This paper introduces a robotic manipulator to realize robot-assisted intracardiac catheterization in magnetic resonance imaging (MRI) environment. MRI can offer high-resolution images to visualize soft tissue features such as scars or edema. We hypothesize that robotic catheterization, combined with the enhanced monitoring of lesions creation using MRI intraoperatively, will significantly improve the procedural safety, accuracy, and effectiveness. This is designed particularly for cardiac electrophysiological (EP) intervention, which is an effective treatment of arrhythmia. We present the first MR Safe robot for intracardiac EP intervention. The robot actuation features small hysteresis, effective force transmission, and quick response, which has been experimentally verified for its capability to precisely telemanipulate a standard clinically used EP catheter. We also present timely techniques for real-time positional tracking in MRI and intraoperative image registration, which can be integrated with the presented manipulator to improve the performance of teleoperated robotic catheterization.
Automatic localization of a language-independent sub-network on deep neural networks trained by multi-lingual speech (2013)

Deep neural networks (DNNs) have been successfully applied to automatic speech recognition (ASR). However, no study has investigated the possibility of building a language-independent sub-network DNN as the basis for further training of any new language using a simple plug-in of the sub-network. In this paper, we propose a novel technique to split a DNN into language-independent and -dependent sub-networks using multi-lingual speech training data. Our basic assumption is that, in a DNN for speech processing, language-independent feature processing is done in stages that are near to the input layer, while language-dependent processing is performed in stages that are near to the output layer. Based on this assumption, we propose a technique to simultaneously optimize multiple sub-networks in a DNN trained with multi-lingual speech data. The language-dependent and -independent processing boundaries in individual sub-networks are segmented automatically. We test our technique in phoneme classification experiments. The results demonstrate that a language-independent sub-network DNN extracted by our technique can be used as a universal network for speech processing of additional new languages.
Development of a portable therapeutic ultrasound system for military, medical and research use (2009)

In the past two decades therapeutic ultrasound has obtained attention by the medical community as a tool to relieve arthritis, improve rehabilitation, and enhance wound healing processes. In the research realm, therapeutic ultrasound and its effects on tissue properties are currently being studied to great lengths. For example, researchers are assessing the ability of ultrasound for large molecule transdermal drug delivery, in targeted chemotherapy delivery to brain cancer, and cellular gene-transfer applications. Even though many applications of therapeutic ultrasound exist, the basic instrumentation has not changed much in the past 50 years. Here, we present a novel therapeutic ultrasound system we developed in our laboratory that is capable of producing acoustic power outputs well over the therapeutic range greater than 50 W, lightweight (under 6 lb), portable (a foot print of 4x6x2 in.3), and rechargeable battery powered. The portable therapeutic ultrasound unit has the potential to replace plug-in medical systems and rf amplifiers used in research, both of which are bulky and burdensome. The portable system is capable of between-office and field service on its long lasting internal battery, making it especially useful for military, ambulatory, and house-call medical applications.
Distinct Physiological Roles of Fructokinase Isozymes Revealed by Gene-Specific Suppression of <i>Frk1</i> and <i>Frk2</i>Expression in Tomato (2002)

There are two divergent fructokinase isozymes, Frk1 and Frk2 in tomato (Lycopersicon esculentum Mill.) plants. To investigate the physiological functions of each isozyme, the expression of each fructokinase mRNA was independently suppressed in transgenic tomato plants, and the respective phenotypes were evaluated. Suppression of Frk1 expression resulted in delayed flowering at the first inflorescence. Suppression of Frk2 did not effect flowering time but resulted in growth inhibition of stems and roots, reduction of flower and fruit number, and reduction of seed number per fruit. Localization of Frk1 and Frk2 mRNA accumulation by in situ hybridization in wild-type tomato fruit tissue indicated that Frk2 is expressed specifically in early tomato seed development. Fruit hexose and starch content were not effected by the suppression of either Frk gene alone. The results collectively indicate that flowering time is specifically promoted by Frk1 and that Frk2 plays specific roles in contributing to stem and root growth and to seed development. Because Frk1 and Frk2 gene expression was suppressed individually in transgenic plants, other significant metabolic roles of fructokinases may not have been observed if Frk1 and Frk2 play, at least partially, redundant metabolic roles.
An active optical remote sensing system for vegetation index determination (2005)

An airborne hyperspectral remote sensing system, initially for use to verify theories for rapid, accurate determination of vegetation indices, is described. The system, called AVIS (Airborne Vegetation Index Sensor), is mounted on a helicopter and employees a Xenon flash lamp to illuminate the Earth's surface. The backscattered radiation is measured with better than 10 nm resolution in the visible and near-IR over a shiftable 400 nm bandpass. Background subtraction is used for daytime flights. By its nature, AVIS measures the hot spot, resulting in no shadowing. It is a versatile system, minimizing atmospheric effects and eliminating view angle variables and other ambiguities and assumptions associated with general algorithm development and verification which arise when using the sun as a test source.
Relation between Signal Quality and Groove Shape in Magneto-Optical Disk(1) (1987)

The effect of groove shape on recording media was measured with a static measurement system developed by the authors to investigate media magneto-optic characteristics in the microscopic range. Reflectivity decreased as the depth of the groove increased due to the groove diffraction effect. Decrease in reflectivity also seemed to be the cause of reduction in the rotation angle. The coercive force only reached a critical variation point when the groove was shallow, which seemed to be because grooves deeper than the 20nm film thickness of the experimental samples divided the media in two.
Effect on Fracture Pressure by Adding Iron-Based and Calcium-Based Nanoparticles to a Nonaqueous Drilling Fluid for Permeable Formations (2016)

This paper presents a comprehensive experimental evaluation to investigate the effects of adding iron-based and calcium-based nanoparticles (NPs) to nonaqueous drilling fluids (NAFs) as a fluid loss additive and for wellbore strengthening applications in permeable formations. API standard high-pressure-high-temperature (HPHT) filter press in conjunction with ceramic disks is used to quantify fluid loss reduction. Hydraulic fracturing experiments are carried out to measure fracturing and re-opening pressures. A significant enhancement in both filtration and strengthening was achieved by means of in situ prepared NPs. Our results demonstrate that filtration reduction is essential for successful wellbore strengthening; however, excessive reduction could affect the strengthening negatively.