gebhart/patrepeval huggingface dataset:
DNA Vaccination by Electroporation and Boosting with Recombinant Proteins Enhances the Efficacy of DNA Vaccines for Schistosomiasis Japonica (2009)

Schistosomiasis japonica is an endemic, zoonotic disease of major public health importance in China. Control programs combining chemotherapy and snail killing have not been able to block transmission of infection in lakes and marsh regions. Vaccination is needed as a complementary approach to the ongoing control programs. In the present study, we wanted to determine if the efficacies of DNA vaccines encoding the 23-kDa tetraspanin membrane protein (SjC23), triose phosphate isomerase (SjCTPI), and sixfold-repeated genes of the complementarity determining region 3 (CDR3) in the H chain of NP30 could be enhanced by boosting via electroporation in vivo and/or with cocktail protein vaccines. Mice vaccinated with cocktail DNA vaccines showed a significant worm reduction of 32.88% (P < 0.01) and egg reduction of 36.20% (P < 0.01). Vaccine efficacy was enhanced when animals were boosted with cocktail protein vaccines; adult worm and liver egg burdens were reduced 45.35% and 48.54%, respectively. Nearly identical results were obtained in mice boosted by electroporation in vivo, with adult worm and egg burdens reduced by 45.00% and 50.88%, respectively. The addition of a protein vaccine boost to this regimen further elevated efficacy to approximately 60% for adult worm burden and greater than 60% for liver egg reduction. The levels of interleukin-2, gamma interferon, and the ratios of immunoglobulin G2a (IgG2a)/IgG1 clearly showed that cocktail DNA vaccines induced CD4(+) Th1-type responses. Boosting via either electroporation or with recombinant proteins significantly increased associated immune responses over those seen in mice vaccinated solely with DNA vaccines. Thus, schistosome DNA vaccine efficacy was significantly enhanced via boosting by electroporation in vivo and/or cocktail protein vaccines.
Electrochemical oxidation of PFOA and PFOS in concentrated waste streams (2018)

Abstract The electrochemical oxidation (EO) of environmentally persistent perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) with a Magnéli phase Ti 4 O 7 electrode was investigated in this study. After 3 hours (hr) of electrolysis, 96.0 percent of PFOA (10 milligrams per liter [mg/L] in 100 milliliters [mL] 100 millimolar [mM] Na 2 SO 4 solution) was removed following pseudo first‐order kinetics ( k = 0.0226 per minute [min]) with the degradation half‐life of 30.7 min. Under the same treatment conditions, PFOS (10 mg/L in 100 mL 100 mM Na 2 SO 4 solution) removal reached 98.9 percent with a pseudo first‐order degradation rate constant of 0.0491/min and the half‐life of 14.1 min. Although, the degradation of PFOA was slower than PFOS, when subjected to EO treatment in separate solutions, PFOA appeared to degrade faster than PFOS when both are present in the same solution, indicating possible competition between PFOA and PFOS during Ti 4 O 7 anode‐based EO treatment with PFOA having the competitive advantage. Moreover, the EO treatment was applied to degrade highly concentrated PFOA (100.5 mg/L) and PFOS (68.6 mg/L) in ion‐exchange resin regenerant (still bottom) with high organic carbon content (15,800 mg/L). After 17‐hr electrolysis, the total removal of PFOA and PFOS was 77.2 and 96.5 percent, respectively, and the fluoride concentration increased from 0.84 mg/L to 836 mg/L. Also, the dark brown color of the original solution gradually faded during EO treatment. In another test using still bottom samples with lower total organic carbon (9,880 mg/L), the PFOA (15.5 mg/L) and PFOS (25.5 mg/L) concentrations were reduced to levels below the limits of quantification after 16‐hr treatment. In addition, the performance of EO treatment using different batch reactor setups was compared in this study, including one‐sided (one anode:one cathode) and two‐sided (one anode:two cathodes) setups. The two‐sided reactor configuration significantly enhanced the degradation efficiency, likely due to the larger anode area available for reactions.
The Effect of Nitrous Oxide on Cortical Cerebral Blood Flow during Anesthesia with Halothane and Isoflurane, with and without Morphine, in the Rabbit (1987)

The effect of nitrous oxide on cortical cerebral blood flow (CBF) was examined during a varying background anesthetic state in the New Zealand White rabbit. Seventy percent nitrous oxide resulted in significant and similar increases in CBF during anesthesia with both 0.5 MAC of halothane (44 +/- 14 to 63 +/- 17 ml.100 g-1.min-1) (mean +/- SD) and anesthesia with isoflurane (34 +/- 9 to 41 +/- 11 ml.100 g-1.min-1). During anesthesia with 1.0 MAC halothane or isoflurane, N2O also increased CBF, but the increments (halothane, 73 +/- 34 to 111 +/- 54 ml.100 g-1 min-1; isoflurane 34 +/- 13 to 69 +/- 34 ml.100 g-1.min-1) were significantly greater than those observed at 0.5 MAC. When 0.5 MAC halothane or isoflurane was supplemented with morphine (10 mg/kg followed by an infusion of 2 mg.kg-1.min-1), the CBF effect of N2O was not significantly different from that observed with 0.5 MAC alone. It was concluded that, in the rabbit, the effects of N2O on cortical CBF vary with the background anesthetic state and that the increase in CBF caused by N2O becomes greater as the end-tidal concentration of halothane or isoflurane increases from 0.5 to 1.0 MAC. Morphine, when added to 0.5 MAC of halothane or isoflurane, does not alter the effect of 70% N2O on cortical CBF.
VHDL generator for a high performance convolutional neural network FPGA-based accelerator (2017)

Convolutional Neural Network (CNN) has been proven as a highly accurate and effective algorithm that has been used in a variety of applications such as handwriting digit recognition, visual recognition, and image classification. As a matter of fact, state-of-the-art CNNs are computationally intensive; however, their parallel and modular nature make platforms like FPGAs well suited for the acceleration process. A typical CNN takes a very long development round on FPGAs, hence in this paper, we propose a tool which allows developers, through a configurable user-interface, to automatically generate VHDL code for their desired CNN model. The generated code or architecture is modular, massively parallel, reconfigurable, scalable, fully pipelined, and adaptive to different CNN models. We demonstrate the automatic VHDL generator and its adaptability by implementing a small-scale CNN model “LeNet” and a large-scale one “AlexNet”. The parameters of small scale models are automatically hard-coded as constants (part of the programmable logic) to overcome the memory bottleneck issue. On a Xilinx Virtex-7 running at 200 MHz, the system is capable of processing up to 125k images/s of size 28×28 for LeNet and achieved a peak performance of 611.52 GOP/s and 414 FPS for AlexNet.
Alpha7 nicotinic acetylcholine receptor is required for amyloid pathology in brain endothelial cells induced by Glycoprotein 120, methamphetamine and nicotine (2017)

One of the most challenging issues in HIV-associated neurocognitive disorders (HAND) caused by HIV-1 virotoxins and drug abuse is the lack of understanding the underlying mechanisms that are commonly associated with disorders of the blood-brain barrier (BBB), which mainly consists of brain microvascular endothelial cells (BMEC). Here, we hypothesized that Glycoprotein 120 (gp120), methamphetamine (METH) and nicotine (NT) can enhance amyloid-beta (Aβ) accumulation in BMEC through Alpha7 nicotinic acetylcholine receptor (α7 nAChR). Both in vitro (human BMEC) (HBMEC) and in vivo (mice) models of BBB were used to dissect the role of α7 nAChR in up-regulation of Aβ induced by gp120, METH and NT. Aβ release from and transport across HBMEC were significantly increased by these factors. Methyllycaconitine (MLA), an antagonist of α7 nAChR, could efficiently block these pathogenic effects. Furthermore, our animal data showed that these factors could significantly increase the levels of Aβ, Tau and Ubiquitin C-Terminal Hydrolase L1 (UCHL1) in mouse cerebrospinal fluid (CSF) and Aβ in the mouse brains. These pathogenicities were significantly reduced by MLA, suggesting that α7 nAChR may play an important role in neuropathology caused by gp120, METH and NT, which are the major pathogenic factors contributing to the pathogenesis of HAND.
A Controlled Prospective Outcome Study of Implantable Electrical Stimulation With Spinal Instrumentation in a High-Risk Spinal Fusion Population (1999)

The results from using both instrumentation and electrical stimulation in a high-risk pool of patients show a statistically significant difference, with higher rates of fusion and clinical success than in a similar pool that did not receive stimulation.
WIFI FINGERPRINTING INDOOR POSITIONING WITH MULTIPLE ACCESS-POINTS IN A SINGLE BASE STATION USING PROBABILISTIC METHOD (2017)

WiFi fingerprinting for indoor positioning is well known as one of the most efficient techniques to estimate indoor target location instead of other existing methods which are triangulation and proximity. This method requires a training phase to collect Receiving Signal Strength (RSS) samples that will be utilized in location estimation phase using matching algorithms. Recently, most commercially indoor positioning solutions used on smartphone utilizes the current building infrastructure to estimate personnel location where wireless router is used as an Access Point (AP) in each base station to extract the RSS values. However, for buildings with inadequate infrastructure setup, implementing multiple base stations using a single AP in each base station would require an exhaustive resources of manpower and time especially for a small scale positioning setup. There are also not enough distinct RSS values at each location covered by a single base station. Thus, WiFi fingerprinting using multiple APs with omnidirectional and directional antennas in a single base station employing a probabilistic approach has been proposed to minimize the infrastructure setup. Based on experimental results, the proposed multiple APs in a single base station was found to reduce the number of base stations required to achieve the same or better accuracy as existing approach using the same number of APs. The feasibility of multiple APs in a single base station was demonstrated using kernel estimation with the results indicating the ability of the proposed work with an accuracy of 1.82 m to outperform the existing work by minimizing 22% of Root Mean Square Error (RMSE).
Applications of Self-Degradable Particulate Diverters in Wellbore Stimulations: Hydraulic Fracturing and Matrix Acidizing Case Studies (2018)

Abstract Particulate diversions are widely used for stimulation treatments. Usual field practice is to increase the volume of solid particles to create a considerable pressure response. However, an excessive dose of particles challenges particle removal and results in unexpectedly longer clean-up time. Self-degradable particulate diverter systems can overcome this shortcoming. The current study investigates the mechanisms of self-degradable particle transport and progressive clogging involved in fluid diversion. Engineering solutions and case studies for applying this new diversion technology in fracturing unconventional formations and acidizing carbonate reservoirs are discussed separately. An integrated workflow and numerical models have been established and verified with experimental data and field experience. In the hydraulic fracture stimulation analysis, a wellbore-scale computational fluid dynamics and discrete element method (CFD-DEM) is employed to understand the physics of particle slurry transport and particle jamming at an opening. A three-dimensional reservoir-scale simulator is used and coupled with particulate diversion mechanisms for fracturing. To simulate the carbonate-acidizing procedure, an in-house numerical engine was developed and used to design the diversion of acidic fluid. The stimulated reservoir extent and associated production are predicted to compare the fluid diversion efficiency between various designs and to show the robustness and effectiveness of engineered particle designs. Two field data sets are utilized to demonstrate the applications of new particulate diverters in hydraulic fracturing and matrix acidizing respectively. Analysis suggests that the success of the new diverter system application is governed by the particle characteristics (size, shape, ratio and concentration) and diverter slurry displacement (rate, viscosity and volume of displacing fluid). The models and workflows are capable of designing fit-for-purpose diverters and their application in different stimulations, including both hydraulic fracturing and matrix acidizing. As demonstrated in our studies, non-engineered designs could result in low fluid-diversion efficiency or even failure of reservoir stimulations. Engineered self-degradable particulate diverters can plug the openings (including perforations and induced wormholes) and withstand differential pressure to divert stimulation fluid (either fracturing slurry or acidic fluid) into under-stimulated regions for effective fracturing and acidizing. According to our case studies, particulate diverters can be designed to enhance fluid diversion efficiency and optimize the use of particles. The case studies demonstrate the practical applicability and advantages of using self-degradable particulate diverters in both hydraulic fracturing and matrix acidizing operations. The integrated workflow and analysis proved useful to guide the field executions for successful fluid diversions.
Interleaved water and fat imaging and applications to lipid quantitation using the gradient reversal technique (2007)

The proposed MRI technique permits interleaved water and fat imaging, with which spectrally well-separated water and fat images at the identical slice locations could be obtained in a single acquisition without increasing scan time. The technique could be used for in vivo quantitative mapping of lipid content and applied to investigations using small animal experiment models.
A theoretical investigation of the pyrazole phototransposition (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA theoretical investigation of the pyrazole phototranspositionRobert E. Connors, James W. Pavlik, Douglas S. Burns, and Edyth M. KurzweilCite this: J. Org. Chem. 1991, 56, 22, 6321–6326Publication Date (Print):October 1, 1991Publication History Published online1 May 2002Published inissue 1 October 1991https://pubs.acs.org/doi/10.1021/jo00022a020https://doi.org/10.1021/jo00022a020research-articleACS PublicationsRequest reuse permissionsArticle Views124Altmetric-Citations10LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
CRISPR/Cas9-mediated gene manipulation to create single-amino-acid-substituted and floxed mice with a cloning-free method (2017)

Clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) technology is a powerful tool to manipulate the genome with extraordinary simplicity and speed. To generate genetically modified animals, CRISPR/Cas9-mediated genome editing is typically accomplished by microinjection of a mixture of Cas9 DNA/mRNA and single-guide RNA (sgRNA) into zygotes. However, sgRNAs used for this approach require manipulation via molecular cloning as well as in vitro transcription. Beyond these complexities, most mutants obtained with this traditional approach are genetically mosaic, yielding several types of cells with different genetic mutations. Recently, a growing body of studies has utilized commercially available Cas9 protein together with sgRNA and a targeting construct to introduce desired mutations. Here, we report a cloning-free method to target the mouse genome by pronuclear injection of a commercial Cas9 protein:crRNA:tracrRNA:single-strand oligodeoxynucleotide (ssODN) complex into mouse zygotes. As illustration of this method, we report the successful generation of global gene-knockout, single-amino-acid-substituted, as well as floxed mice that can be used for conditional gene-targeting. These models were produced with high efficiency to generate non-mosaic mutant mice with a high germline transmission rate.
JNK antagonizes Akt-mediated survival signals by phosphorylating 14-3-3 (2005)

Life and death decisions are made by integrating a variety of apoptotic and survival signals in mammalian cells. Therefore, there is likely to be a common mechanism that integrates multiple signals adjudicating between the alternatives. In this study, we propose that 14-3-3 represents such an integration point. Several proapoptotic proteins commonly become associated with 14-3-3 upon phosphorylation by survival-mediating kinases such as Akt. We reported previously that cellular stresses induce c-Jun NH2-terminal kinase (JNK)-mediated 14-3-3zeta phosphorylation at Ser184 (Tsuruta, F., J. Sunayama, Y. Mori, S. Hattori, S. Shimizu, Y. Tsujimoto, K. Yoshioka, N. Masuyama, and Y. Gotoh. 2004. EMBO J. 23:1889-1899). Here, we show that phosphorylation of 14-3-3 by JNK releases the proapoptotic proteins Bad and FOXO3a from 14-3-3 and antagonizes the effects of Akt signaling. As a result of dissociation, Bad is dephosphorylated and translocates to the mitochondria, where it associates with Bcl-2/Bcl-x(L). Because Bad and FOXO3a share the 14-3-3-binding motif with other proapoptotic proteins, we propose that this JNK-mediated phosphorylation of 14-3-3 regulates these proapoptotic proteins in concert and makes cells more susceptible to apoptotic signals.
Brightness measurements of a gallium liquid metal ion source (2008)

The virtual source size of a liquid metal ion source is an order of magnitude larger than the size of the region from which the ions are emitted at the source. This source size has a direct effect on the reduced brightness and, hence, on the performance of these sources. The variation of the virtual source size of a gallium liquid metal ion source as a function of the angular current density at the source has been measured. This was done by measuring the source image size from images of a pencil lead sample taken with an FEI focused ion beam system. The measurements indicate that the virtual source size grows from about 50–80nm when the emission current increases from 1to10μA. The experimental data on the virtual source size are compared with the theory on stochastic Coulomb interactions in the source region. On the basis of these measurements the authors show that the reduced brightness deteriorates with an increasing angular current density. The maximum reduced brightness measured was 1×106A∕(m2srV).
A new method of Wiener filtering and its application to interference mitigation for communications (2002)

A new multistage Wiener filter is introduced which utilizes a decomposition based on orthogonal projections. A reduced-rank Wiener filter is developed based on this new structure which is not basis oriented, but evolves a basis which is a function of the multistage decomposition. The performance of this new Wiener filtering structure is evaluated using a comparative computer analysis model. It is demonstrated that the low-complexity multistage reduced-rank Wiener filter is capable of outperforming the more complex eigendecomposition-based methods.
Mining long-term search history to improve search accuracy (2006)

Long-term search history contains rich information about a user's search preferences, which can be used as search context to improve retrieval performance. In this paper, we study statistical language modeling based methods to mine contextual information from long-term search history and exploit it for a more accurate estimate of the query language model. Experiments on real web search data show that the algorithms are effective in improving search accuracy for both fresh and recurring queries. The best performance is achieved when using clickthrough data of past searches that are related to the current query.
CopyCatchers are versatile active genetic elements that detect and quantify inter-homolog somatic gene conversion (2021)

CRISPR-based active genetic elements, or gene-drives, copied via homology-directed repair (HDR) in the germline, are transmitted to progeny at super-Mendelian frequencies. Active genetic elements also can generate widespread somatic mutations, but the genetic basis for such phenotypes remains uncertain. It is generally assumed that such somatic mutations are generated by non-homologous end-joining (NHEJ), the predominant double stranded break repair pathway active in somatic cells. Here, we develop CopyCatcher systems in Drosophila to detect and quantify somatic gene conversion (SGC) events. CopyCatchers inserted into two independent genetic loci reveal unexpectedly high rates of SGC in the Drosophila eye and thoracic epidermis. Focused RNAi-based genetic screens identify several unanticipated loci altering SGC efficiency, one of which (c-MYC), when downregulated, promotes SGC mediated by both plasmid and homologous chromosome-templates in human HEK293T cells. Collectively, these studies suggest that CopyCatchers can serve as effective discovery platforms to inform potential gene therapy strategies.
Exploiting the Influence of Oxidization on Ultra-Fine Copper and Nickel Sulfide Containing Pt-Pd in Yunnan Mine (2013)

It is known that oxidation is one of the most common ways for penlandite to be introducted into tailing during traditional coarse-particle sulfide flotation. However, it could become much more complicated and challenging problems for the low-grade, fine-disseminated Cu-Ni sulfides containing Pt and Pd in Yunnan Mine, accompanied with more than 75% of the content of MgO in the ore sample is. Direct flotation tests had been conducted to extract the metallic values as much as possible by adding traditional depressants and collectors, such as carboxylmethyl cellulose, starch, sodium silicate, butyl xanthate, (BX), butyl ammonium dithophosphate (BA) and etc., the relatively satisfied recoveries of Cu, Ni, Pt and Pd in the concentrate from bench flotation tests were obtained, however, more than 30% of metallic values still lost in the slime. In this study, bench flotation tests for the ore sample fromYunnan Mine, micro-flotation tests of serpentines and pentlandite from Jinchuan Mine and their settling rate tests were conducted to figure out how the oxidation influence the recovery of the ultra-fine nickel sulfide. All the tests results pointed to the presence of over-oxidation on the ultra-fine nickel sulfide surface and lead to the loss of Ni containing Pt and Pd in the slime tailing. Some methods which tried to slow the speed of oxidation on mineral surface during grinding and flotation were introduced in order to recover the values before over-oxidation of sulfides; however, the slime coating of serpentines also may play an important role in disturbing the floatability of ultra-fine sulfide.