gebhart/patrepeval huggingface dataset:
Improved development of in vitro-derived bovine embryos by use of a nitric oxide scavenger in a cumulus-granulosa cell coculture system (1998)

This study was conducted to examine the hypothesis that nitric oxide (NO) affects prehatching development of bovine oocytes fertilized in vitro. In experiment 1, inseminated oocytes were cultured in a cumulus-granulosa cell (CG) coculture system to which 0.008 or 0.04 mM of sodium nitroprusside (SNP), a spontaneous NO releaser, was added at 18 or 60 hr postinsemination. Embryo development was greatly (P < 0.001) inhibited by the addition of SNP, regardless of time of addition or SNP concentration. In experiment 2, eight-cell embryos were cultured singly in a defined medium, to which 0.0016, 0.008, or 0.04 mM of SNP was added. Development to the blastocyst stage was greatly (P < 0.001) decreased after addition of SNP compared with no addition. Higher (P < 0.02) concentration of NO metabolites was found in developmentally arrested embryos than in developing embryos at 144 hr postinsemination (experiment 3). In experiment 4, blastocyst formation of oocytes cocultured with CGs was significantly (P < 0.02) increased after addition of hemoglobin (Hb, 1 microgram/ml), an NO scavenger. Prehatching development of oocytes was significantly (P < 0.05) increased after addition of Hb at different time intervals (18, 60, or 144 hr postinsemination) in experiment 5. Embryo development was not enhanced by Hb addition to the culture medium in the absence of CGs (experiment 6). Prehatching development of eight-cell embryos derived from a Hb-containing culture system was not promoted by the further addition of Hb after transfer of the embryos to a defined and CG-free single-embryo culture system (experiment 7). In conclusion, NO, which may be secreted from CGs, has an inhibitory role in prehatching development of bovine oocytes fertilized in vitro, and use of an NO scavenger, Hb, in a coculture system enhances blastocyst formation.
Implementation of smart elevator system based on wireless multi-hop AdHoc sensor networks (2011)

In modern day world, time has become a precious resource. Therefore, different strategies and techniques are constantly being employed in all fields of life to save every bit of time. Increasingly many of such applications involve wireless sensor networks. A highly potential system that can be made significantly more efficient using WSNs is an elevator system. There have been numerous attempts to improve the serving efficiency of the elevator system over the course of time. This paper proposes to utilize the elevator system in a more productive manner so that more number of people can be served in a lesser time. Hence, people will be able to spend this valuable time on other important and crucial matters rather than waiting for the elevator and wasting their time in vain. To achieve this goal, we implement the elevator system based on a wireless adhoc network of intelligent floors (equipped with sensors) which can communicate with each other in a multi-hop fashion. In this way, every floor is aware of the traffic conditions, i.e., the number of upward/downward requesting-passengers, waiting at every other floor and the elevator positions in real-time and hence can make efficient decisions of where to direct/stop the elevator.
PacketUsher: A DPDK-based packet I/O engine for commodity PC (2016)

Deploying network applications on commodity PC is increasingly important because of its flexibility and cheapness. Due to high packet I/O overheads, the performance of these applications are low. In this paper, we present PacketUsher, an efficient packet I/O engine based on the libraries of DPDK. By replacing standard I/O routine with PacketUsher, we can remarkably accelerate both I/O-intensive and compute-intensive applications on commodity PC. As a case study of I/O-intensive application, our RFC 2544 benchmark over PacketUsher achieves same testing results as dedicated commercial device. For compute-intensive application, the performance of our application-layer traffic generator over PacketUsher is more than 4 times of the original value and outperforms existing frameworks by about 3 times.
Acoustogenic Probes: A New Frontier in Photoacoustic Imaging (2018)

Photoacoustic imaging (PAI) is a powerful imaging modality capable of mapping the absorption of light in biological tissue via the PA effect. When chromophores are optically excited, subsequent energy loss in the form of heat generates local thermoelastic expansion. Repeated excitation from a pulsed laser induces pressure fluctuations that propagate through tissue and can be detected as ultrasound waves. By combining ultrasonic detection with optical excitation, PAI enables high-resolution image acquisition at centimeter depths. PAI is also relatively inexpensive and relies on safe, nonionizing excitation light in the near-infrared window, making it an attractive alternative to other common biomedical imaging modalities. Research in our group is aimed at developing small-molecule activatable probes that can be used for analyte detection in deep tissue via PAI. These probes contain reactive triggers that undergo a selective chemical reaction in the presence of specific stimuli to produce a spectral change that can be observed via PAI. Chemically tuning the absorbance profile of the probe and the reacted product such that they are both within the PA imaging window enables ratiometric imaging when each species is irradiated at a specific wavelength. Ratiometric imaging is an important design feature of these probes as it minimizes error associated with tissue-dependent signal fluctuations and instrumental variation. In this Account, we discuss key properties for designing small-molecule PA probes that can be applied for in vivo studies and the challenges associated with this area of probe development. We also highlight examples from our group including probes capable of detecting metal ions (Cu(II)), reactive nitrogen species (NO), and oxygen tension (hypoxia). Each of these targets can be sensed using a modular design strategy based on influencing the electronic and spectral properties of a NIR-absorbing dye platform. We demonstrate that ideal small-molecule PA probes have high molar absorptivity, low fluorescence quantum yields, and selective triggers that can reliably report on a single analyte in a complex biological setting. Probes must also be highly chemo- and photostable to enable long-term imaging studies. We show that these PA probes react rapidly and selectively and can be utilized for deep-tissue imaging in mouse models of various diseases. Overall, these examples represent a new class of biomedical imaging tools that seek to enable high-resolution molecular imaging capable of improving diagnostic methods and elucidating new biological discoveries. We anticipate that the combination of small-molecule PA probes with new PAI technology will enable noninvasive detection of analytes relevant to disease progression and mapping of tissue microenvironments.
High-efficiency homologous recombination in the oil-producing alga <i>Nannochloropsis</i> sp. (2011)

Algae have reemerged as potential next-generation feedstocks for biofuels, but strain improvement and progress in algal biology research have been limited by the lack of advanced molecular tools for most eukaryotic microalgae. Here we describe the development of an efficient transformation method for Nannochloropsis sp., a fast-growing, unicellular alga capable of accumulating large amounts of oil. Moreover, we provide additional evidence that Nannochloropsis is haploid, and we demonstrate that insertion of transformation constructs into the nuclear genome can occur by high-efficiency homologous recombination. As examples, we generated knockouts of the genes encoding nitrate reductase and nitrite reductase, resulting in strains that were unable to grow on nitrate and nitrate/nitrite, respectively. The application of homologous recombination in this industrially relevant alga has the potential to rapidly advance algal functional genomics and biotechnology.
Magnetic Resonance Multiphase Flow Meter: Gas Flow Measurement Principle and Wide Range Testing Results (2014)

This paper starts with a brief summary of the liquid measuring principle and continues with a description of the Magnetic Resonance Imaging (MRI) methodology which is used to quantify gas phase fraction and velocity. This explanation is supported with illustrative measurement data. As such, this paper can be understood as an extension of the paper on the Magnetic Resonance (MR) based multiphase flowmeter presented last year[1]. Meanwhile, extensive tests have been carried out with the industrialized version of the MR meter in various test laboratories, covering a wide range of flow rates, GVF’s, WLR’s, salinities, viscosities and pressures. The results of these tests will be presented in this paper, illustrating the performance of the latest version of the MR-based multiphase flow meter.
Effects of Botox® and Neuronox® on muscle force generation in mice (2007)

The current study determined the dose-response relationship for inhibition of muscle force of two commercially available botulinum neurotoxin type-A (BoNTA) preparations (Botox and Neuronox) in a murine model and characterized the time course of recovery from the toxin-induced muscle paralysis. The effect of freezing reconstituted toxin on toxin potency was also determined. The gastrocnemius muscles in male CD-1 mice were injected with either saline or BoNTA (0.3-3.0 U/kg), and muscle force generation was examined following stimulation of the tibial nerve (single twitch and 15-200 Hz tetany). Botox and Neuronox produced nearly equivalent decrements in muscle force (30%-90%) at 4 days after toxin injection. At 28 days after injection (1 U/kg), muscle force had recovered from the effects of both toxin preparations. Maintaining reconstituted toxin at -80 degrees C for up to 5 months did not result in significant loss of toxin activity. The results of this study suggest that Botox and Neuronox produce equivalent responses in a murine model, and, in contrast to other models, muscle recovery is rapid with doses of toxin that produce less than maximal decrements in muscle force.
Continuous flow synthesis of ZSM-5 zeolite on the order of seconds (2016)

The hydrothermal synthesis of zeolites carried out in batch reactors takes a time so long (typically, on the order of days) that the crystallization of zeolites has long been believed to be very slow in nature. We herein present a synthetic process for ZSM-5, an industrially important zeolite, on the order of seconds in a continuous flow reactor using pressurized hot water as a heating medium. Direct mixing of a well-tuned precursor (90 °C) with the pressurized water preheated to extremely high temperature (370 °C) in the millimeter-sized continuous flow reactor resulted in immediate heating to high temperatures (240-300 °C); consequently, the crystallization of ZSM-5 in a seed-free system proceeded to completion within tens of or even several seconds. These results indicate that the crystallization of zeolites can complete in a period on the order of seconds. The subtle design combining a continuous flow reactor with pressurized hot water can greatly facilitate the mass production of zeolites in the future.
Osmotic Ultrafiltration with Dextran Sodium Sulfate Potential for use in Peritoneal Dialysis (1979)

Dextran sodium sulfate was evaluated in vitro as a potential non-absorbable osmotic agent for peritoneal dialysis. It was compared to poly(sodium acrylate) which has been shown previously to be effective in rats, but probably toxic. Dextran sodium sulfate induced osmotic ultrafiltration rates as high as 20 ml/min in water but only 2 ml/min in solution containing non-polymer electrolytes presumably because of Gibbs-Donnan effects. Compared to acrylate the dextran polymer has less sodium per gram, lower osmotic activity of polymer sodium, and yields less ultrafiltration at given transmembrane osmolalities. A nontoxic polymer more like acrylate would seem more promising as an osmotic agent for peritoneal dialysis.
Synthesis of perfluoropoly(ethylene glycol) ethers: CF<sub>3</sub>–[O–CF<sub>2</sub>–CF<sub>2</sub>]<sub>n</sub>–O–R<sub>f</sub>(R<sub>f</sub>= CF<sub>3</sub>or C<sub>2</sub>F<sub>5</sub>; n= 1–5) (1977)

A new synthetic method for the preparation of high molecular weight fluorocarbon ethers has been developed; polyethylene oxide was caused to react with elemental fluorine under conditions carefully regulated to fragment and perfluorinate the polyether system and yield a number of new fluorocarbon ethers.
Characterization of an ADP-Ribosyltransferase Toxin (AexT) from <i>Aeromonas salmonicida</i> subsp. <i>salmonicida</i> (2002)

An ADP-ribosylating toxin named Aeromonas salmonicida exoenzyme T (AexT) in A. salmonicida subsp. salmonicida, the etiological agent of furunculosis in fish, was characterized. Gene aexT, encoding toxin AexT, was cloned and characterized by sequence analysis. AexT shows significant sequence similarity to the ExoS and ExoT exotoxins of Pseudomonas aeruginosa and to the YopE cytotoxin of different Yersinia species. The aexT gene was detected in all of the 12 A. salmonicida subsp. salmonicida strains tested but was absent from all other Aeromonas species. Recombinant AexT produced in Escherichia coli possesses enzymatic ADP-ribosyltransferase activity. Monospecific polyclonal antibodies directed against purified recombinant AexT detected the toxin produced by A. salmonicida subsp. salmonicida and cross-reacted with ExoS and ExoT of P. aeruginosa. AexT toxin could be detected in a wild type (wt) strain of A. salmonicida subsp. salmonicida freshly isolated from a fish with furunculosis; however, its expression required contact with RTG-2 rainbow trout gonad cells. Under these conditions, the AexT protein was found to be intracellular or tightly cell associated. No AexT was found when A. salmonicida subsp. salmonicida was incubated in cell culture medium in the absence of RTG-2 cells. Upon infection with wt A. salmonicida subsp. salmonicida, the fish gonad RTG-2 cells rapidly underwent significant morphological changes. These changes were demonstrated to constitute cell rounding, which accompanied induction of production of AexT and which led to cell lysis after extended incubation. An aexT mutant which was constructed from the wt strain with an insertionally inactivated aexT gene by allelic exchange had no toxic effect on RTG-2 cells and was devoid of AexT production. Hence AexT is directly involved in the toxicity of A. salmonicida subsp. salmonicida for RTG-2 fish cells.
Anaerobic Fermentation of Glycerol in <i>Paenibacillus macerans</i> : Metabolic Pathways and Environmental Determinants (2009)

Paenibacillus macerans is one of the species with the broadest metabolic capabilities in the genus Paenibacillus, able to ferment hexoses, deoxyhexoses, pentoses, cellulose, and hemicellulose. However, little is known about glycerol metabolism in this organism, and some studies have reported that glycerol is not fermented. Despite these reports, we found that several P. macerans strains are capable of anaerobic fermentation of glycerol. One of these strains, P. macerans N234A, grew fermentatively on glycerol at a maximum specific growth rate of 0.40 h(-1) and was chosen for further characterization. The use of [U-13C]glycerol and further analysis of extracellular metabolites and proteinogenic amino acids via nuclear magnetic resonance (NMR) spectroscopy allowed identification of ethanol, formate, acetate, succinate, and 1,2-propanediol (1,2-PDO) as fermentation products and demonstrated that glycerol is incorporated into cellular components. A medium formulation with low concentrations of potassium and phosphate, cultivation at acidic pH, and the use of a CO2-enriched atmosphere stimulated glycerol fermentation and are proposed to be environmental determinants of this process. The pathways involved in glycerol utilization and synthesis of fermentation products were identified using NMR spectroscopy in combination with enzyme assays. Based on these studies, the synthesis of ethanol and 1,2-PDO is proposed to be a metabolic determinant of glycerol fermentation in P. macerans N234A. Conversion of glycerol to ethanol fulfills energy requirements by generating one molecule of ATP per molecule of ethanol synthesized. Conversion of glycerol to 1,2-PDO results in the consumption of reducing equivalents, thus facilitating redox balance. Given the availability, low price, and high degree of reduction of glycerol, the high metabolic rates exhibited by P. macerans N234A are of paramount importance for the production of fuels and chemicals.
Molecular Epidemiological and Phylogenetic Associations of Two Novel Putative Virulence Genes, <i>iha</i> and <i> iroN <sub>E. coli</sub> </i> , among <i>Escherichia coli</i> Isolates from Patients with Urosepsis (2000)

Two novel putative Escherichia coli virulence genes, iha and iroN from E. coli (iroN(E. coli)), were detected in 55 and 39%, respectively, of 67 E. coli isolates from patients with urosepsis. iha and iroN(E. coli) exhibited divergent associations with other putative virulence genes, phylogenetic markers, host characteristics, and antimicrobial resistance.
Practical Liposomal Formulation for Taxanes with Polyethoxylated Castor Oil and Ethanol with Complete Encapsulation Efficiency and High Loading Efficiency (2017)

Taxanes including paclitaxel and docetaxel are effective anticancer agents preferably sufficient for liposomal drug delivery. However, the encapsulation of these drugs with effective amounts into conventional liposomes is difficult due to their high hydrophobicity. Therefore, an effective encapsulation strategy for liposomal taxanes has been eagerly anticipated. In this study, the mixture of polyethoxylated castor oil (Cremophor EL) and ethanol containing phosphate buffered saline termed as CEP was employed as a solvent of the inner hydrophilic core of liposomes where taxanes should be incorporated. Docetaxel-, paclitaxel-, or 7-oxacetylglycosylated paclitaxel-encapsulating liposomes were successfully prepared with almost 100% of encapsulation efficiency and 29.9, 15.4, or 29.1 mol% of loading efficiency, respectively. We then applied the docetaxel-encapsulating liposomes for targeted drug delivery. Docetaxel-encapsulating liposomes were successfully developed HER2-targeted drug delivery by coupling HER2-specific binding peptide on liposome surface. The HER2-targeting liposomes exhibited HER2-specific internalization and enhanced anticancer activity in vitro. Therefore, we propose the sophisticated preparation of liposomal taxanes using CEP as a promising formulation for effective cancer therapies.
Minimizing Delay in Shared Pipelines (2013)

Pipelines are widely used to increase throughput in multi-core chips by parallelizing packet processing. Typically, each packet type is serviced by a dedicated pipeline. However, with the increase in the number of packet types and their number of required services, there are not enough cores for pipelines. In this paper, we study pipeline sharing, such that a single pipeline can be used to serve several packet types. Pipeline sharing decreases the needed total number of cores, but typically increases pipeline lengths and therefore packet delays. We consider the optimization problem of allocating cores between different packet types such that the average delay is minimized. We suggest a polynomial-time algorithm that finds the optimal solution when the packet types preserve a specific property. We also present a greedy algorithm for the general case. Last, we examine our solutions on synthetic examples, on packet-processing applications, and on real-life H.264 standard requirements.
Probabilistic Distance-Based Arbitration: Providing Equality of Service for Many-Core CMPs (2010)

Emerging many-core chip multiprocessors will integrate dozens of small processing cores with an on-chip interconnect consisting of point-to-point links. The interconnect enables the processing cores to not only communicate, but to share common resources such as main memory resources and I/O controllers. In this work, we propose an arbitration scheme to enable equality of service (EoS) in access to a chip's shared resources. That is, we seek to remove any bias in a core's access to a shared resource based on its location in the CMP. We propose using probabilistic arbitration combined with distance-based weights to achieve EoS and overcome the limitation of conventional round-robin arbiter. We describe how nonlinear weights need to be used with probabilistic arbiters and propose three different arbitration weight metrics - fixed weight, constantly increasing weight, and variably increasing weight. By only modifying the arbitration of an on-chip router, we do not require any additional buffers or virtual channels and create a simple, low-cost mechanism for achieving EoS. We evaluate our arbitration scheme across a wide range of traffic patterns. In addition to providing EoS, the proposed arbitration has additional benefits which include providing quality-of-service features (such as differentiated service) and providing fairness in terms of both throughput and latency that approaches the global fairness achieved with age-base arbitration - thus, providing a more stable network by achieving high sustained throughput beyond saturation.
Digital Slot: A Tool for Optimization and Development of New Hydraulic Fracturing Technologies (2021)

Abstract We present the digital slot — a tool for the development of new hydraulic fracturing technologies via digitization of slurry flow in narrow channels. We consider slurry containing fluid, proppant, and fiber components. The flow is described by a continuum mathematical model based on the lubrication theory. The numerical algorithm utilizes Lagrangian approach with finite volume pressure solver. We present the results of laboratory validation and simulation examples showing the key effects affecting solids transport in hydraulic fracturing: settling, bridging, gravity slumping, materials degradation, viscosity contrast, and bank formation.
Crystallization of community-acquired respiratory distress syndrome toxin from<i>Mycoplasma pneumoniae</i> (2010)

Community-acquired respiratory distress syndrome toxin (CARDS TX) is a 591-amino-acid protein with ADP-ribosyltransferase and vacuolating activities that damages the cells lining the respiratory tracts of patients infected with the bacterial pathogen Mycoplasma pneumoniae. Crystals of CARDS TX were grown in space group C2, with unit-cell parameters a = 191.4, b = 107.4, c = 222.1 A, beta = 90.6 degrees. A complete 2.2 A data set was obtained from a single CARDS TX crystal.