gebhart/patrepeval huggingface dataset:
In Vivo Adeno-Associated Viral Vector–Mediated Genetic Engineering of White and Brown Adipose Tissue in Adult Mice (2013)

Adipose tissue is pivotal in the regulation of energy homeostasis through the balance of energy storage and expenditure and as an endocrine organ. An inadequate mass and/or alterations in the metabolic and endocrine functions of adipose tissue underlie the development of obesity, insulin resistance, and type 2 diabetes. To fully understand the metabolic and molecular mechanism(s) involved in adipose dysfunction, in vivo genetic modification of adipocytes holds great potential. Here, we demonstrate that adeno-associated viral (AAV) vectors, especially serotypes 8 and 9, mediated efficient transduction of white (WAT) and brown adipose tissue (BAT) in adult lean and obese diabetic mice. The use of short versions of the adipocyte protein 2 or uncoupling protein-1 promoters or micro-RNA target sequences enabled highly specific, long-term AAV-mediated transgene expression in white or brown adipocytes. As proof of concept, delivery of AAV vectors encoding for hexokinase or vascular endothelial growth factor to WAT or BAT resulted in increased glucose uptake or increased vessel density in targeted depots. This method of gene transfer also enabled the secretion of stable high levels of the alkaline phosphatase marker protein into the bloodstream by transduced WAT. Therefore, AAV-mediated genetic engineering of adipose tissue represents a useful tool for the study of adipose pathophysiology and, likely, for the future development of new therapeutic strategies for obesity and diabetes.
Effective Use of Variational Embedding Capacity in Expressive End-to-End Speech Synthesis (2019)

Recent work has explored sequence-to-sequence latent variable models for expressive speech synthesis (supporting control and transfer of prosody and style), but has not presented a coherent framework for understanding the trade-offs between the competing methods. In this paper, we propose embedding capacity (the amount of information the embedding contains about the data) as a unified method of analyzing the behavior of latent variable models of speech, comparing existing heuristic (non-variational) methods to variational methods that are able to explicitly constrain capacity using an upper bound on representational mutual information. In our proposed model (Capacitron), we show that by adding conditional dependencies to the variational posterior such that it matches the form of the true posterior, the same model can be used for high-precision prosody transfer, text-agnostic style transfer, and generation of natural-sounding prior samples. For multi-speaker models, Capacitron is able to preserve target speaker identity during inter-speaker prosody transfer and when drawing samples from the latent prior. Lastly, we introduce a method for decomposing embedding capacity hierarchically across two sets of latents, allowing a portion of the latent variability to be specified and the remaining variability sampled from a learned prior. Audio examples are available on the web.
Poly(3-hexylthiophene) Nanotube Array Surfaces with Tunable Wetting and Contact Thermal Energy Transport (2015)

Solution casting using a sacrificial template is a simple technique to fabricate vertical arrays of polymer nanotubes. However, because of their close proximity and high aspect ratios, large capillary forces cause nanotubes to cluster as the array dries; researchers often use special drying techniques to avoid this clustering. Here, we exploit the clustering of regioregular poly(3-hexylthiophene) (rr-P3HT) nanotubes in a unique template etching process to create surfaces that exhibit tunable wetting and contact thermal energy transport. Vertical arrays of rr-P3HT nanotubes are cast from solution in nanoscale alumina templates, and a solution etching process is used to partially release the nanotubes from the template. The clustering of rr-P3HT nanotube tips upon template etching produces hierarchical surface structuring with a distinct pattern of interconnected ridges, and the spacing between the ridges increases with increased template etch times. These changes in morphology cause the water contact angle to increase from 141° to 168° as the etch time is increased from 4 to 12 min. When assembled into an interface, the morphological changes cause the thermal contact resistance of the vertical rr-P3HT nanotube arrays to increase linearly at a rate of approximately 6 mm(2)·K/W per 2 min etch interval (after 6 min of etching is surpassed). The effective thermal conductivity of the rr-P3HT nanotube arrays is 1 ± 0.2 W/mK independent of the etch time, which is approximately 5 times higher than the bulk rr-P3HT film value.
Transmit diversity based on space-time block codes in frequency selective Rayleigh fading DS-CDMA systems (2002)

Exploring the temporal and spatial domains both at the receiver and transmitter offers important means for considerably improving the system performance in cellular networks. In this paper, the impact of using open-loop transmit diversity based on space-time block codes in a multi-user DS-CDMA system operating in a frequency selective fading environment is explored. A non-joint linear multi-user detection and space-time decoding approach is proposed. It is shown that by introducing a simple constraint with respect to the spatio-temporal cross-correlation properties of the space-time code-corresponding to introducing interleaving-any space-time block code can be used as the base for the transmit diversity scheme. Simulation results using the complex (2,2,2) space-time block code known as Alamouti's (see IEEE Trans. on Select Areas in Communications, vol.16, p.1451-58, 1998) code, indicates that large diversity gains are achievable and that the amount of overhead originating from training data can be reduced considerably using the proposed approach.
Thrombin inhibitors. 3. Carboxyl-containing amide derivatives of N.alpha.-substituted L-arginine (1980)

A series of N alpha-(arylsulfonyl)-L-arginine amide derivatives having carboxamide N-substituents with a carboxyl group was prepared and tested as inhibitors of the clotting activity of thrombin. The most inhibitory compounds were obtained when a carboxyl group was introduced into the carbon next to the amide nitrogen of N alpha-(arylsulfonyl)-L-arginine amide derivatives, e.g., N alpha-(arylsulfonyl)-L-arginyl-N-butyl-, N-(methoxyethyl)- or N-(tetrahydrofurfuryl)glycine and 4-alkyl-1-[N alpha-(arylsulfonyl)-L-arginyl]-2-piperidinecarboxylic acid, with an I50 of 1-3 X 10(-7) M.
Frequency-domain multichannel optical detector for noninvasive tissue spectroscopy and oximetry (1995)

We have designed a multisource frequency-domain spectrometer for the optical study of biological tissues. Eight multiplexed, intensity-modulated LEDs are employed as the light sources. Four of them emit light at a peak wavelength of 715 nm (λ<sub>1</sub>); the other four, 850 nm (λ<sub>2</sub>). The frequency of intensity modulation is 120 MHz. This instrument measures the frequency-domain parameters phase, dc intensity, and ac amplitude at the two wavelengths λ<sub>1</sub> and λ<sub>2</sub> and for different distances between light source and detector. From these frequency-domain raw data, the absolute values of the absorption and reduced scattering coefficients of tissue at λ<sub>1</sub> and λ<sub>2</sub> are obtained. The oxy- and deoxyhemoglobin concentrations, and hence the hemoglobin saturation, are then analytically derived from the molar extinction coefficients. Acquisition times as short as hundreds of milliseconds provide real-time monitoring of the measured parameters. We performed a systematic test <i>in vitro</i> to quantify the precision and accuracy of the instrument reading. We also report <i>in vivo</i> measurements. This spectrometer can be packaged as a compact portable unit.
Web application security engineering (2006)

Integrating security throughout the life cycle can improve overall Web application security. With a detailed review of the steps involved in applying security-specific activities throughout the software development life cycle, the author walks practitioners through effective, efficient application design, development, and testing. With this article, the author shares a way to improve Web application security by integrating security throughout the life cycle. The ideas he present here are based on empirical evidence from consulting with hundreds of customers - real-world scenarios with real project constraints and security concerns - across a variety of scenarios and putting into practice the security techniques that the experts know. The result is an approach that has evolved and refined itself over time
Ultraviolet antireflection coatings for use in silicon detector design (2011)

We report on the development of coatings for a charged-coupled device (CCD) detector optimized for use in a fixed dispersion UV spectrograph. Because of the rapidly changing index of refraction of Si, single layer broadband antireflection (AR) coatings are not suitable to increase quantum efficiency at all wavelengths of interest. Instead, we describe a creative solution that provides excellent performance over UV wavelengths. We describe progress in the development of a coated CCD detector with theoretical quantum efficiencies (QEs) of greater than 60% at wavelengths from 120 to 300 nm. This high efficiency may be reached by coating a backside-illuminated, thinned, delta-doped CCD with a series of thin film AR coatings. The materials tested include MgF(2) (optimized for highest performance from 120-150 nm), SiO(2) (150-180 nm), Al(2)O(3) (180-240 nm), MgO (200-250 nm), and HfO(2) (240-300 nm). A variety of deposition techniques were tested and a selection of coatings that minimized reflectance on a Si test wafer were applied to functional devices. We also discuss future uses and improvements, including graded and multilayer coatings.
Cholecystokinin antagonists. Synthesis and biological evaluation of 3-substituted 1,4-benzodiazepin-2-amines (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCholecystokinin antagonists. Synthesis and biological evaluation of 3-substituted 1,4-benzodiazepin-2-aminesMark G. Bock, Robert M. DiPardo, Ben E. Evans, Kenneth E. Rittle, Roger M. Freidinger, Raymond S. L. Chang, and Victor J. LottiCite this: J. Med. Chem. 1988, 31, 1, 264–268Publication Date (Print):January 1, 1988Publication History Published online1 May 2002Published inissue 1 January 1988https://pubs.acs.org/doi/10.1021/jm00396a042https://doi.org/10.1021/jm00396a042research-articleACS PublicationsRequest reuse permissionsArticle Views160Altmetric-Citations18LEARN 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
Rapid Construction of Adenoviral Vectors by Lambda Phage Genetics (2002)

Continued improvements of adenoviral vectors require the investigation of novel genome configurations. Since adenovirus can be generated directly by transfecting packaging cell lines with viral genomes isolated from plasmid DNA, it is possible to separate genome construction from virus production. In this way failure to generate a virus is not associated with an inability to generate the desired genome. We have developed a novel lambda-based system that allows rapid modification of the viral genome by double homologous recombination in Escherichia coli. The recombination reaction and newly generated genome may reside in a recombination-deficient bacterial host for enhanced plasmid stability. Furthermore, the process is independent of any restriction endonucleases. The strategy relies on four main steps: (i) homologous recombination between an adenovirus cosmid and a donor plasmid (the donor plasmid carries the desired modification[s] and flanking regions of homology to direct its recombination into the viral genome); (ii) in vivo packaging of the recombinant adenoviral cosmids during a productive lambda infection; (iii) transducing a recombination-deficient E. coli lambda lysogen with the generated lysate (the lysogen inhibits the helper phage used to package the recombinant andenoviral cosmid from productively infecting and destroying the host bacteria); (iv) effectively selecting for the desired double-recombinant cosmid. Approximately 10,000 double-recombinant cosmids are recovered per reaction with essentially all of them being the correct double-recombinant molecule. This system was used to generate quickly and efficiently adenoviral genomes deficient in the E1/E3 and E1/E3/E4 regions. The basis of this technology allows any region of the viral genome to be readily modified for investigation of novel configurations.
Production of diesel fuel from light olefins (1986)

Mobile Research and Development Corporation has developed a catalytic process for converting light olefinic compounds to high quality gasoline and distillate. The process has been named Mobil Olefin to Gasoline and Distillate (MOGD) Process. Based on the Mobile zeolite catalyst ZSM-5, light olefins can be shape selectively oligomerized to higher molecular weight iso-olefins. In the gasoline boiling range, these olefins have a high octane number and for the diesel fuel range product a high cetane number and low pour point following hydrogenation. Through normally designed to process propylene or butylene, MOGD is applicable to a wide range of feed streams ranging from ethylene to 400/sup 0/F endpoint olefinic naphtha. The process has been tested using commercially-produced catalyst in refinery scale equipment.
On the origin of photoluminescence in spark-eroded (porous) silicon (1993)

Photoluminescence measurements and high-resolution transmission electron microscopy studies on spark-treated (porous) silicon have been performed. Contrary to suggestions put forward by others, it has been found that spark erosion does not yield structures comparable to those obtained for irradiated, that is, damaged silica. Instead, evidence is given that spark treatment of single crystalline silicon wafers produces randomly oriented nanometer-sized silicon crystallites surrounded by a SiO2 matrix. This configuration is believed to be responsible for the observed room temperature visible photoluminescence.
Applications with a Rydberg Atom-based Radio Frequency Antenna/Receiver (2019)

We discuss several recent extensions of quantum radio frequency (RF) electric field sensors to antenna/receiver applications. These Rydberg atom-based sensors have been previously studied for SI-traceable RF field measurements. We demonstrate the reception of modulated signals, including analog audio and pseudorandom bit sequences, RF phase detection, weak field detection, and the recording of musical instruments.
Recombinant Organisms (Patent US 2015/0275243 A1) (2015)

The invention relates to genetically modified organisms with enhanced production of omega-3 long chain polyunsaturated fatty acids.
From stack inspection to access control: a security analysis for libraries (2004)

We present a new static analysis for reviewing the security of libraries for systems, such as JVMs or the CLR, that rely on stack inspection for access control. We describe its implementation for the CLR. Our tool inputs a set of libraries plus a description of the permissions granted to unknown, potentially hostile code. It constructs a permission-sensitive call graph, which can be queried to identify potential security defects. It has been applied to large pre-existing libraries. We also develop a new formal model of the essentials of access control in the CLR (types, classes and inheritance, access modifiers, permissions, and stack inspection). In this model, we state and prove the correctness of the analysis.
<sup/> Synthesis and Characterization of Electroactive Gellan Gum Spongy-Like Hydrogels for Skeletal Muscle Tissue Engineering Applications (2017)

Advances on materials' research for tissue engineering (TE) applications have shown that animal cells respond directly to the material physical, chemical, mechanical, and electrical stimuli altering a variety of cell signaling cascades, which consequently result in phenotypic and genotypic alterations. Gellan gum (GG) spongy-like hydrogels (SLH) with open microstructure, mechanical properties, and cell performance have shown promising results for soft TE applications. Taking advantage of intrinsic properties of GG-SLH and polypyrrole (PPy) electroactivity, we developed electroactive PPy-GG-SLH envisaging their potential use for skeletal muscle TE. Three different methods of in situ chemical oxidative polymerization were developed based on the availability of pyrrole: freely dissolved in solution (method I and III) or immobilized into GG hydrogels (method II). PPy was homogeneously distributed within (method I and III) and on the surface (method II) of GG-SLH, as also confirmed by Fourier Transform infrared spectra. PPy-GG-SLH showed higher conductivity than GG-SLH (p < 0.05) whereas PPy-GG-SLH (method I and II) showed the best conductivity among the 3 methods (∼1 to 2 × 10<sup>-4</sup> S/cm). The microarchitecture of PPy-GG-SLH (method I) was similar to GG-SLH but PPy-GG-SLH (method II and III) presented smaller pore sizes and lower porosity. PPy-GG-SLH (method I and II) compressive modulus (∼450-500 KPa) and recovering capacity (∼75-90%) was higher than GG-SLH, nevertheless the mechanical properties of PPy-GG-SLH (method III) were lower. The water uptake of PPy-GG-SLH was rapidly up to 2500% and were stable along 60 days of degradation being the maximum weight loss 20%. Mechanically stable and electroactive PPy-GG-SLH (method I and II) were analyzed regarding cellular performance. PPy-GG-SLH were not cytotoxic for L929 cells. In addition, L929 and C2C12 myoblast cells were able to adhere and spread within PPy-GG-SLH, showing improved spreading in comparison to GG-SLH performance. Overall, PPy-GG-SLH show promising features as an alternative electroactive platform to analyze the influence of electrical stimulation on skeletal muscle cells.
Dielectric Nanofluids for Electrostatic Machines & Actuators (2019)

Dielectric suspensions consisting of sterically coated, nano-scale barium titanium particles in the organic ester, isoamyl isovalerate, were developed to enhance the field forces in electrostatic machinery. The relative permittivity and conductivity of the suspensions were measured experimentally, as was the electrostatic force developed upon application of significant electric fields. At a particle concentration of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">%</sup> by volume, the relative permittivity of the suspension was approximately 50% greater than that of the base solvent. However, this improvement came at the expense of detriments to the conductivity and rheology of the suspension. These challenges must be addressed before dielectric suspensions can be used in such challenging applications.
The multiply-detected macrodiversity scheme for wireless systems (2002)

We introduce a novel macrodiversity scheme for wireless cellular systems, multiply-detected macrodiversity (MDM), in which all the received versions of a mobile's signal are used to maximize the probability of a correct decision. The MDM performance in fading conditions shows significant improvement; e.g., for a channel occupancy above 0.2, the BER is decreased by two to five orders of magnitude throughout 50% to 90% of cell coverage area. We consider the co-channel interference resulting from the six closest interferers (referred to as interfering cells).
Triblock peptide–oligonucleotide chimeras (POCs): programmable biomolecules for the assembly of morphologically tunable and responsive hybrid materials (2017)

Peptide–oligonucleotide chimeras (POCs) assemble into morphologically tunable materials. Design rules for POC assembly are used to predict and alter assembly morphology.
Measuring the effects of topical moisturizers on changes in stratum corneum thickness, water gradients and hydration<i>in vivo</i> (2008)

(i) In vivo CRS was validated as a technique to measure SC thickness on both palmoplantar and, particularly, on nonpalmoplantar skin sites. (ii) Moisturizers improve skin moisturization but in this study only formulation A improved SC thickness, water gradients and hydration as measured by CRS. We hypothesize that this was due to compositional differences between the products. We believe that niacinamide (nicotinamide, vitamin B(3)) is probably contributing significantly to this effect, as it has been proven to increase epidermal lipogenesis and SC barrier function in other studies. These results show that by using CRS, we were able for the first time to determine the effect of moisturizer on multiple SC barrier endpoints including SC thickness, and water content as a function of depth and total SC water content.
Next Generation Extractants for Cesium Separation from High-Level Waste: From Fundamental Concepts to Site Implementation (2002)

This project seeks a fundamental understanding and major improvement in cesium separation from high-level waste by cesium-selective calixcrown extractants. Systems of particular interest involve novel solvent-extraction systems containing specific members of the calix[4]arene-crown-6 family, alcohol solvating agents, and alkylamines. Questions being addressed bear upon cesium binding strength, extraction selectivity, cesium stripping, and extractant solubility. Enhanced properties in this regard will specifically benefit applied projects funded by the USDOE Office of Environmental Management to clean up sites such as the Savannah River Site (SRS), Hanford, and the Idaho National Environmental and Engineering Laboratory. The most direct beneficiary will be the SRS Salt Processing Project, which has recently identified the Caustic-Side Solvent Extraction (CSSX) process employing a calixcrown as its preferred technology for cesium removal from SRS high-level tank waste.
AugmentedCode: Examining the Effects of Natural Language Resources in Code Retrieval Models (2021)

Code retrieval is allowing software engineers to search codes through a natural language query, which relies on both natural language processing and software engineering techniques. There have been several attempts on code retrieval from searching snippet codes to function codes. In this paper, we introduce Augmented Code (AugmentedCode) retrieval which takes advantage of existing information within the code and constructs augmented programming language to improve the code retrieval models' performance. We curated a large corpus of Python and showcased the the framework and the results of augmented programming language which outperforms on CodeSearchNet and CodeBERT with a Mean Reciprocal Rank (MRR) of 0.73 and 0.96, respectively. The outperformed fine-tuned augmented code retrieval model is published in HuggingFace at https://huggingface.co/Fujitsu/AugCode and a demonstration video is available at: https://youtu.be/mnZrUTANjGs .