gebhart/patrepeval huggingface dataset:
Non‐Toxic Glycosylated Gold Nanoparticle‐Amphotericin B Conjugates Reduce Biofilms and Intracellular Burden of Fungi and Parasites (2021)

Abstract Infections by intracellular pathogens cause significant morbidity and mortality due to lack of efficient drug delivery. Amphotericin B, currently used to treat leishmaniasis and cryptococcosis, is very toxic and cannot eradicate intracellular Cryptococcus neoformans ( C. neoformans ). Glycosylated gold nanoparticles are water dispersible and biocompatible with very little toxicity. While amphotericin B is insoluble in water at neutral pH, conjugates of amphotericin B and ultra‐small gold nanoparticles (AuNP) are better dispersible in water. Amphotericin B conjugated glycosylated gold nanoparticles (AmpoB@AuNP) are more efficacious in treating both extracellular and intracellular forms of Leishmania mexicana ( L. mexicana ) than amphotericin B alone. In addition, AmpoB@AuNP are effective in reducing C. neoformans biofilms by 80% and intracellular C. neoformans burden by &gt;90%. Furthermore, AmpoB@AuNP are not haemolytic at 50 µg mL −1 and are significantly less toxic to murine macrophages than amphotericin B. Ultra‐small AuNPs are attractive delivery agents to treat intracellular infections and AmpoB@AuNP may be useful for treating C. neoformans infections in immunocompromised patients.
Speaker adaptation using regularization and network adaptation for hybrid MMI-NN/HMM speech recognition (1999)

This paper describes, how to perform speaker adaptation for a hybrid large vocabulary speech recognition system. The hybrid system is based on a Maximum Mutual Information Neural Network (MMINN), which is used as a Vector Quantizer (VQ) for a discrete HMM speech recognizer. The combination of MMINNs and HMMs has shown good performance on several large vocabulary speech recognition tasks like RM and WSJ. This paper now presents two approaches to perform speaker adaptation with this hybrid system. The first approach is a transformation of the feature space, which is performed by a neural network with maximum likelihood (ML) as objective function for the complete system, which means, that the parameters of the NN are estimated in order to match the HMM-parameters of the pre-trained speaker independent system. The second approach is to adapt the HMM parameters depending on the amount of training data available per HMM, using a regularization approach. Both approaches can be applied jointly, which further improves the recognition accuracy.
Victream (2017)

In data-parallel computing that uses a graphic processing unit (GPU), processing of large data requires that multiple GPUs be used in the computer to increase its execution performance. Increasing processing performance by using multiple computing resources has been enabled by the development of computing frameworks based on a directed acyclic graph (DAG). However, their performance degrades in out-of-core processing, which often occurs in processing of large data on GPUs with limited memory capacity. The GPU data input/output (I/O) for data swapping between host memory and GPU memory during the execution of a user DAG is usually a performance bottleneck. A computing framework called "Victream" is proposed to overcome this drawback. It uses a novel scheduler that involves two methods to minimize the total amount of GPU data I/O of data swapping. First, it performs locality-aware scheduling. When it schedules a task, it selects one that requires the minimum amount of data swapping and reuses as much of the data residing in GPU memory as possible. Second, it extends the locality-aware scheduling so that GPUs can execute data prefetching. Prefetching data that are swapped out from a GPU enables efficient use of bottleneck GPU I/O resources. To prefetch the input data of future tasks, it is required to determine the schedule of future tasks. Victream's scheduler (hereafter, the Victream scheduler) extends the locality-aware scheduling so that it can schedule future tasks to enable data prefetching that is executed in the way that minimizes the amount of data I/O of data swapping. Evaluation of a Victream prototype showed that the performance of Victream is better than that of conventional frameworks by up to 117%.
Deep Quantization for MIMO Channel Estimation (2019)

Quantizers play a critical role in digital signal processing systems. In practice, quantizers are typically implemented using scalar analog-to-digital converters (ADCs), commonly utilizing a fixed uniform quantization rule which is ignorant of the task of the system. Recent works have shown that the performance of quantization systems utilizing scalar ADCs can be significantly improved by properly processing the analog signal prior to quantization. However, the implementation of such systems requires complete knowledge of the underlying model, which may not be available in practice. In this work we design task-oriented quantization systems with scalar ADCs using deep learning, focusing on the task of multiple-input multiple-output (MIMO) channel estimation. By utilizing deep learning, we construct a task-based quantization system, overcoming the need to explicitly recover the system model and to find the proper quantization rule for it. Our results indicate that the proposed method results in practical MIMO systems with scalar ADCs which are capable of approaching the optimal performance limits dictated by indirect rate-distortion theory, achievable using vector quantizers and requiring complete knowledge of the underlying statistical model.
Easily deconstructed, high aspect ratio cellulose nanofibres from Triodia pungens; an abundant grass of Australia's arid zone (2015)

The production of high aspect ratio cellulose nanofibres without resorting to very harsh mechanical and/or chemical processing steps remains a challenge that hinders progress in the fast-moving nanocellulose field.
PICOSECOND RELAXATION DYNAMICS OF A TEMPERATURE DEPENDENT AMIDE I BAND IN MYOGLOBIN (2003)

Author Institution: Department of Physics, Princeton University; Dept. of Physics, Oklahoma State University; Dept. of Physics, FOM Institute for Plasma Physics
Microfluidic cell fragmentation for mechanical phenotyping of cancer cells (2016)

Circulating tumor cells (CTCs) shed from the primary tumor undergo significant fragmentation in the microvasculature, and very few escape to instigate metastases. Inspired by this in vivo behavior of CTCs, we report a microfluidic method to phenotype cancer cells based on their ability to arrest and fragment at a micropillar-based bifurcation. We find that in addition to cancer cell size, mechanical properties determine fragmentability. We observe that highly metastatic prostate cancer cells are more resistant to fragmentation than weakly metastatic cells, providing the first indication that metastatic CTCs can escape rupture and potentially initiate secondary tumors. Our method may thus be useful in identifying phenotypes that succumb to or escape mechanical trauma in microcirculation.
Optimal Allocation of Filters against DDoS Attacks (2007)

Distributed denial-of-service (DDoS) attacks are a major problem in the Internet today. During a DDoS attack, a large number of compromised hosts send unwanted traffic to the victim, thus exhausting the resources of the victim and preventing it from serving its legitimate clients. One of the main mechanisms against DDoS is filtering, which allows routers to selectively block unwanted traffic. Given the magnitude of DDoS attacks and the high cost of filters in the routers today, the successful mitigation of a DDoS attack using filtering crucially depends on the efficient allocation of filtering resources. In this paper, we consider a single router with a limited number of available filters. We study how to optimally allocate filters to attack sources, or entire domains of attack sources, so as to maximize the amount of good traffic preserved, under a constraint on the number of filters. First, we look at the single-tier problem, where the collateral damage on legitimate traffic is high due to the filtering at the granularity of attack domains. Second, we look at the two-tier problem, where we have an additional constraint on the number of filters and filtering is performed at the granularity of attackers and/or domains. We formulate both problems as optimization problems, and we evaluate the optimal solution over a range of realistic attack-scenarios. Our results demonstrate that efficient filter allocation significantly improves the tradeoff between the number of filters used and the amount of legitimate traffic preserved.
Generating Better Medicines for Cancer (2013)

The complexity of tumor biology warrants tailored drug delivery for overcoming the major challenges faced by cancer therapies. The versatility of the PRINT<sup>®</sup> (Particle Replication In Non-wetting Templates) process has enabled the preparation of shape- and size-specific particles with a wide range of chemical compositions and therapeutic cargos. Different particle matrices and drugs may be combined in a plug-and-play approach, such that physico-chemical characteristics of delivery vectors may be optimized for biocompatibility, cargo stability and release, circulation half-life, and efficacy. Thus, the engineering of particles for cancer therapy with specific biophysical behaviors and cellular responses has been demonstrated via the PRINT process.
Unlocking P(V): Reagents for chiral phosphorothioate synthesis (2018)

Phosphorothioate nucleotides have emerged as powerful pharmacological substitutes of their native phosphodiester analogs with important translational applications in antisense oligonucleotide (ASO) therapeutics and cyclic dinucleotide (CDN) synthesis. Stereocontrolled installation of this chiral motif has long been hampered by the systemic use of phosphorus(III) [P(III)]-based reagent systems as the sole practical means of oligonucleotide assembly. A fundamentally different approach is described herein: the invention of a P(V)-based reagent platform for programmable, traceless, diastereoselective phosphorus-sulfur incorporation. The power of this reagent system is demonstrated through the robust and stereocontrolled synthesis of various nucleotidic architectures, including ASOs and CDNs, via an efficient, inexpensive, and operationally simple protocol.
Real-time GPU implementation of transverse oscillation vector velocity flow imaging (2014)

Rapid estimation of blood velocity and visualization of complex flow patterns are important for clinical use of diagnostic ultrasound. This paper presents real-time processing for two-dimensional (2-D) vector flow imaging which utilizes an off-the-shelf graphics processing unit (GPU). In this work, Open Computing Language (OpenCL) is used to estimate 2-D vector velocity flow <i>in vivo</i> in the carotid artery. Data are streamed live from a BK Medical 2202 Pro Focus UltraView Scanner to a workstation running a research interface software platform. Processing data from a 50 millisecond frame of a duplex vector flow acquisition takes 2.3 milliseconds seconds on an Advanced Micro Devices Radeon HD 7850 GPU card. The detected velocities are accurate to within the precision limit of the output format of the display routine. Because this tool was developed as a module external to the scanner's built-in processing, it enables new opportunities for prototyping novel algorithms, optimizing processing parameters, and accelerating the path from development lab to clinic.
Syntheses of organometallic monomers containing cobalt and manganese (1992)

Abstract Direct electrophilic substitution of the cyclopentadienyl ring of cymantrene has been used to prepare five cymantrenyl‐monomers with unsaturated sidechains. Direct substitution of cymantrene with acryloyl‐ and methacryloyl chloride under Friedel‐Crafts conditions has led to acryloyl‐ and methacryloylcymantrene. The complexes have been characterized using 1 H and 13 C NMR, IR and elemental analysis. Both complexes polymerize under treatment with AIBN at 60–70°C. The chelated complex [n 5 ‐C 5 H 4 (CH 2 CH=CH 2 )]‐Co[(NH) 2 C 6 H 4 ], was prepared from the treatment of [n 5 ‐C 5 H 4 (CH 2 CH=CH 2 )]Co(CO) 2 with I 2 followed by (NH) 2 C 6 H 4 and base. The complex was characterized with 1 H NMR and IR but failed to undergo free‐radical polymerization. The strategies used to prepare organometallic polymers are discussed.
ULTRA-MINIATURIZED POWER CONVERTER MODULES USING MICROMACHINED COPPER SCAFFOLDS (2012)

This paper presents ultra-miniature (<2 mm 3 ) power converter modules with high power density (77 W/cm 3 ) enabled by micromachined 3D copper scaffolds containing high-inductancedensity (130 nH/mm 2 ) air-core power inductors. The scaffolds are formed by electroplating multiple, 30-!m-thick layers of copper within patterned photoresist molds, yielding freestanding copper traces with >10:1 aspect ratios. After backfilling with a chemically-resistant polymer, the scaffolds are then fully detached from the silicon fabrication wafer by wet-etching an underlying oxide layer. Surface-mount switch/controller chips and capacitors are attached by solder reflow to the copper scaffolds, forming selfcontained converter modules.
Anti-pterins as Tools to Characterize the Function of Tetrahydrobiopterin in NO Synthase (1998)

Nitric oxide synthases (NOS) are homodimeric enzymes that NADPH-dependently convertl-arginine to nitric oxide andl-citrulline. Interestingly, all NOS also require (6<i>R</i>)-5,6,7,8-tetrahydro-l-biopterin (H<sub>4</sub>Bip) for maximal activity although the mechanism is not fully understood. Basal NOS activity, <i>i.e.</i> that in the absence of exogenous H<sub>4</sub>Bip, has been attributed to enzyme-associated H<sub>4</sub>Bip. To elucidate further H<sub>4</sub>Bip function in purified NOS, we developed two types of pterin-based NOS inhibitors, termed anti-pterins. In contrast to type II anti-pterins, type I anti-pterins specifically displaced enzyme-associated H<sub>4</sub>Bip and inhibited H<sub>4</sub>Bip-stimulated NOS activity in a fully competitive manner but, surprisingly, had no effect on basal NOS activity. Moreover, for a number of different NOS preparations basal activity (percent of<i>V</i> <sub>max</sub>) was frequently higher than the percentage of pterin saturation and was not affected by preincubation of enzyme with H<sub>4</sub>Bip. Thus, basal NOS activity appeared to be independent of enzyme-associated H<sub>4</sub>Bip. The lack of intrinsic 4<i>a</i>-pterincarbinolamine dehydratase activity argued against classical H<sub>4</sub>Bip redox cycling in NOS. Rather, H<sub>4</sub>Bip was required for both maximal activity and stability of NOS by binding to the oxygenase/dimerization domain and preventing monomerization and inactivation duringl-arginine turnover. Since anti-pterins were also effective in intact cells, they may become useful in modulating states of pathologically high nitric oxide formation.
A temperature-to-digital converter for a MEMS-based programmable oscillator with better than &#x00B1;0.5ppm frequency stability (2012)

MEMS-based programmable oscillators have emerged as a promising alternative to crystal-based frequency references, with previously reported work demonstrating sub-ps integrated jitter [1]. Here we show frequency stability better than ±0.5ppm from -40 to 85°C, along with Allan Deviation (i.e., long term jitter) better than 0.005 ppm for 0.1, 1, and 10 second strides. Since the MEMS resonator has a well-defined temperature dependence, the key to this performance is a stable and low-noise temperature-to-digital converter (TDC) that utilizes a thermistor on the same die as the MEMS resonator.
Quaternary Ammonium Salts Interact with Enolates and Sulfonates via Formation of Multiple +N-C-H Hydrogen Bonding Interactions (2022)

We report herein sharp physical evidence, i.e., single-crystal X-ray diffraction and 1H-NMR spectral data, confirming that quaternary ammonium species interact with anions via a set of directional ion–dipole cooperative +N-C-H unusual H-bonding interactions and not via pure non-directional ionic electrostatic interactions. This finding, which has been often invoked by calculations, is herein substantiated by the preparation of two model compounds and an analysis of their X-ray crystal structures in the solid state and 1H-NMR spectra in solution. These observations are particularly pertinent for the rational design of novel catalyses and catalysts and providing guidance to an understanding of these species in solution and during asymmetric enantioselective catalysis.
ChemInform Abstract: Water‐Mediated Catalyst Preactivation: An Efficient Protocol for C—N Cross‐Coupling Reactions. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The KumbhThon technical hackathon for Nashik: A model for STEM education and social entrepreneurship (2014)

Local needs in urban settings create opportunities for STEM students and professionals to work together with city stakeholders to develop original innovative solutions. In preparation for the upcoming Kumbh Mela festival to be held in Nashik, India in 2015, a technical hackathon was convened with students and faculty, technology professionals and entrepreneurs as mentors and instructors. Over the 72-hour event, teams ideated concepts, created rapid prototypes, and tested hardware, software, and social entrepreneurship business models. Stakeholder inputs gathered prior to the event guided the project goals. Top projects were advanced through rapid prototyping and demonstrations. Through this experience students applied principles of design to solving real-world local needs and provided innovative solutions for improved resilience and responsiveness.
Altered Hyperlipidemia, Hepatic Steatosis, and Hepatic Peroxisome Proliferator-Activated Receptors in Rats with Intake of Tart Cherry (2008)

Elevated plasma lipids, glucose, insulin, and fatty liver are among components of metabolic syndrome, a phenotypic pattern that typically precedes the development of Type 2 diabetes. Animal studies show that intake of anthocyanins reduces hyperlipidemia, obesity, and atherosclerosis and that anthocyanin-rich extracts may exert these effects in association with altered activity of tissue peroxisome proliferator-activated receptors (PPARs). However, studies are lacking to test this correlation using physiologically relevant, whole food sources of anthocyanins. Tart cherries are a rich source of anthocyanins, and whole cherry fruit intake may also affect hyperlipidemia and/or affect tissue PPARs. This hypothesis was tested in the Dahl Salt-Sensitive rat having insulin resistance and hyperlipidemia. For 90 days, Dahl rats were pair-fed AIN-76a-based diets supplemented with either 1% (wt:wt) freeze-dried whole tart cherry or with 0.85% additional carbohydrate to match macronutrient and calorie provision. After 90 days, the cherry-enriched diet was associated with reduced fasting blood glucose, hyperlipidemia, hyperinsulinemia, and reduced fatty liver. The cherry diet was also associated with significantly enhanced hepatic PPAR-alpha mRNA, enhanced hepatic PPAR-alpha target acyl-coenzyme A oxidase mRNA and activity, and increased plasma antioxidant capacity. In conclusion, physiologically relevant tart cherry consumption reduced several phenotypic risk factors that are associated with risk for metabolic syndrome and Type 2 diabetes. Tart cherries may represent a whole food research model of the health effects of anthocyanin-rich foods and may possess nutraceutical value against risk factors for metabolic syndrome and its clinical sequelae.
Inhibition of HIV-1 RNase H Activity by Nucleotide Dimers and Monomers (1996)

Nucleotide dimers and monomers were shown to inhibit human immunodeficiency virus type 1 (HIV) RNase H activity. Several effective inhibitors were identified and placed into three general groups based on biochemical characterization of their inhibition, The first group (group A) inhibited HIV RNase H and the closely related feline immunodeficiency virus (FIV) RNase H, but did not inhibit less related retroviral or cellular RNases H or HIV reverse transcriptase (RT). The second group (group B) inhibited the RNase H activity of several retroviruses as well as the reverse transcriptase function of HIV RT. The third group (group C) inhibited RNases H from retroviral and cellular sources but did not inhibit HIV RT. Kinetic analyses of HIV RNase H inhibition were conducted and all three types of inhibitors exhibited a competitive mode of inhibition with regard to substrate. The small nucleotides described here represent the most potent (Ki values from 0.57 to 16 μM) and selective inhibitors of HIV RNase H reported to date. Further structure - function analyses of these molecules may lead to the discovery of unique, potent antiretroviral therapeutics.
Construction of a Point-Focusing Small-Angle X-Ray Scattering Diffractometer for the Study of Fluctuations in Solutions (1991)

A point-focusing diffractometer for the measurement of the small-angle X-ray scattering (SAXS) from molecular solutions has been constructed. This diffractometer consists of a double bent LiF monochromator whose focal length is 700 mm for Cu K α radiation, a sample cell with 0.1 mm-thick mica windows, a bath circulator coupled with a cell holder, and a PSPC system. With this diffractometer, small-angle resolution of better than 0.42° is achieved. To evaluate the performance of the diffractometer, the SAXS on several pure liquids and aqueous solutions was measured. The results show that this diffractometer produces incident beams intense enough to measure SAXS on the solutions, making the collimation effect negligible simultaneously.
Penile urethra replacement with autologous cell-seeded tubularized collagen matrices (2012)

Acellular collagen matrices have been used as an onlay material for urethral reconstruction. However, cell-seeded matrices have been recommended for tubularized urethral repairs. In this study we investigated whether long segmental penile urethral replacement using autologous cell-seeded tubularized collagen-based matrix is feasible. Autologous bladder epithelial and smooth muscle cells from nine male rabbits were grown and seeded onto preconfigured tubular matrices constructed from decellularized bladder matrices obtained from lamina propria. The entire anterior penile urethra was resected in 15 rabbits. Urethroplasties were performed with tubularized matrices seeded with cells in nine animals, and with matrices without cells in six. Serial urethrograms were performed at 1, 3 and 6 months. Retrieved urethral tissues were analysed using histo- and immunohistochemistry, western blot analyses and organ bath studies. The urethrograms showed that animals implanted with cell-seeded matrices maintained a wide urethral calibre without strictures. In contrast, the urethras with unseeded scaffolds collapsed and developed strictures. Histologically, a transitional cell layer surrounded by muscle was observed in the cell-seeded constructs. The epithelial and smooth muscle phenotypes were confirmed with AE1/AE3 and α-actin antibodies. Organ bath studies of the neourethras confirmed both physiological contractility and the presence of neurotransmitters. Tubularized collagen matrices seeded with autologous cells can be used successfully for long segmental penile urethra replacement, while implantation of tubularized collagen matrices without cells leads to poor tissue development and stricture formation. The cell-seeded collagen matrices are able to form new tissue, which is histologically similar to native urethra.