gebhart/patrepeval huggingface dataset:
Mechanism for nitrogen isotope fractionation during ammonium assimilation by <i>Escherichia coli</i> K12 (2013)

Organisms that use ammonium as the sole nitrogen source discriminate between [(15)N] and [(14)N] ammonium. This selectivity leaves an isotopic signature in their biomass that depends on the external concentration of ammonium. To dissect how differences in discrimination arise molecularly, we examined a wild-type (WT) strain of Escherichia coli K12 and mutant strains with lesions affecting ammonium-assimilatory proteins. We used isotope ratio mass spectrometry (MS) to assess the nitrogen isotopic composition of cell material when the strains were grown in batch culture at either high or low external concentrations of NH3 (achieved by controlling total NH4Cl and pH of the medium). At high NH3 (≥ 0.89 µM), discrimination against the heavy isotope by the WT strain (-19.2‰) can be accounted for by the equilibrium isotope effect for dissociation of NH4(+) to NH3 + H(+). NH3 equilibrates across the cytoplasmic membrane, and glutamine synthetase does not manifest an isotope effect in vivo. At low NH3 (≤ 0.18 µM), discrimination reflects an isotope effect for the NH4(+) channel AmtB (-14.1‰). By making E. coli dependent on the low-affinity ammonium-assimilatory pathway, we determined that biosynthetic glutamate dehydrogenase has an inverse isotope effect in vivo (+8.8‰). Likewise, by making unmediated diffusion of NH3 across the cytoplasmic membrane rate-limiting for cell growth in a mutant strain lacking AmtB, we could deduce an in vivo isotope effect for transport of NH3 across the membrane (-10.9‰). The paper presents the raw data from which our conclusions were drawn and discusses the assumptions underlying them.
Beltway Buffers: Avoiding the OS Traffic Jam (2008)

Beltway buffers are operating system I/O paths optimised for high-throughput network applications. The key architectural feature of Beltway buffers is that all I/O takes place in long-lived, allocation-free, shared ringbuffers. Advantages of this design are (1) improved throughput through system-wide copy, context-switch and allocation avoidance and judicious use of the data cache, (2) transparent integration of peripheral hardware and (3) simplicity and familiarity due to comprehensive use of the POSIX file interface for accessing streams.
Slider-disk interaction and its effect on the flying performance of slider (1999)

This paper reports a novel optical head-disk interaction tester setup and experimental investigations into the effects of slider-disk interaction in nanometer spaced head-disk interface. The setup revealed quantitatively the lubricant induced change of slider-disk spacing before the slider enters its fully flying status. The setup was also applied to investigate the slider sinking process which is caused by the meniscus force when the slider starts to rest on disk surface. Results shows that such a setup has the advantage of quantitative characterization of slider-disk interface compared with acoustic emission method. Furthermore, the results also demonstrate its advantages in reflecting the actual interaction between slider, lube, and disk surface, compared with the current optical flying height testers.
Novel Thermoelectric Cooling of Magnetic Sensors (2009)

In situ thermoelectric cooling of GMR nanowires is a novel method to obtain reliable and more sensitive GMR devices. Bismuth telluride (BixTey) caps were used to provide localized thermoelectric cooling of GMR nanowires. BixTey nanowires were electrodeposited from aqueous acidic solutions containing different Bi3+ and HTeO2+ concentrations. GMR layered structures were electrodeposited from a Co-rich electrolyte using a pulsed potential technique. The highest Seebeck coefficients of -318.7 µV/K and 117 µV/K were measured for n-type and p-type nanowires, respectively. P-type nanowires were obtained for low Te concentrations (<30%). Initial experiments were conducted to study the effect of thermoelectric cooling on sensitivity of GMR nanowires. Results showed that using BixTey caps can improve magnetic sensitivity of GMR nanowires.
Significance of non-starter lactic acid bacteria in cheddar cheese (1998)

Factors that affect the growth of adventitious lactobacilli in cheddar cheese, their growth substrates and their contribution to cheese quality are discussed. Research on the use of Lactobacillus spp. as adjunct starters to accelerate cheese ripening and intensify and/or modify cheese flavour is reviewed.
Precisely Shaped, Uniformly Formed Gold Nanocubes with Ultrahigh Reproducibility in Single-Particle Scattering and Surface-Enhanced Raman Scattering (2018)

Synthesizing plasmonic nanostructures in an ultraprecise manner is of paramount importance because the nanometer-scale structural details can significantly affect their plasmonic properties. Au nanocubes (AuNCs) have been a highly promising, heavily studied nanostructure with high potential in various fields, but an ultraprecise synthesis from 10 to 100 nm in size over a large number of AuNCs has not been well established. Precisely structured AuNC-based studies for a highly reproducible, quantitative plasmonic signal generation [e.g., quantitative surface-enhanced Raman scattering (SERS)] are needed for reliable use and exploration in the beneficial properties of AuNCs. Here, we developed a strategy for AuNC synthesis with the desired size and shape, ranging from 17 to 78 nm particularly with highly controlled corner sharpness, by precisely controlling the growth rate of different facets and AuNC-specific flocculation which enabled ultrahigh yields (∼98-99%). Importantly, the precisely shaped AuNCs can scatter light in a spectrally reproducible manner, and the SERS enhancement factors (EFs) for the AuNC dimers are very narrowly distributed (the EFs of 72 nm sharp-cornered cube dimers have a distribution within 1 order of magnitude). Our results pave the paths to ultrahigh yield synthesis of metal nanocubes with a precise size and shape and offer single-particle-level spectral controllability and reproducibility over a large number of particles.
Clinical significance of integrin alpha 6 mRNA expression in gastric carcinoma (1997)

Integrin alpha 6 is believed to be involved in malignant biological development. High tumor/normal (T/N) ratio of integrin alpha 6 was observed in intestinal type tumors in gastric carcinoma. In an immunohistochemical study, an intense and continuous staining was seen at the basement layer in the intestinal type tumors. Concerning the variant, there was a significant correlation between the expression ratio of variant B/variant A and the depth of tumor invasion. In conclusion, i) integrin alpha 6 expression was intimately correlated with histologic differentiation, and ii) the overexpression of variant B may be correlated with tumor invasion of gastric carcinoma.
Chronic Obstructive Pulmonary Disease (1981)

While the prospects of "curing" a patient of emphysema, chronic bronchitis, or asthma are poor, prompt institution of appropriate drug therapy and adjunctive measures can keep the patient from becoming a respiratory cripple.
Bacterial Ice Nucleation in Monodisperse D<sub>2</sub>O and H<sub>2</sub>O-in-Oil Emulsions (2016)

Ice nucleation is of fundamental significance in many areas, including atmospheric science, food technology, and cryobiology. In this study, we investigated the ice-nucleation characteristics of picoliter-sized drops consisting of different D2O and H2O mixtures with and without the ice-nucleating bacteria Pseudomonas syringae. We also studied the effects of commonly used cryoprotectants such as ethylene glycol, propylene glycol, and trehalose on the nucleation characteristics of D2O and H2O mixtures. The results show that the median freezing temperature of the suspension containing 1 mg/mL of a lyophilized preparation of P. syringae is as high as -4.6 °C for 100% D2O, compared to -8.9 °C for 100% H2O. As the D2O concentration increases every 25% (v/v), the profile of the ice-nucleation kinetics of D2O + H2O mixtures containing 1 mg/mL Snomax shifts by about 1 °C, suggesting an ideal mixing behavior of D2O and H2O. Furthermore, all of the cryoprotectants investigated in this study are found to depress the freezing phenomenon. Both the homogeneous and heterogeneous freezing temperatures of these aqueous solutions depend on the water activity and are independent of the nature of the solute. These findings enrich our fundamental knowledge of D2O-related ice nucleation and suggest that the combination of D2O and ice-nucleating agents could be a potential self-ice-nucleating formulation. The implications of self-nucleation include a higher, precisely controlled ice seeding temperature for slow freezing that would significantly improve the viability of many ice-assisted cryopreservation protocols.
A plasmid vector for an extreme thermophile, Thermus thermophilus (1990)

The host-vector system for an extreme thermophile, Thermus thermophilus HB27, was developed. The host strain has a mutation in tryptophan synthetase gene (trpB), and the mutation was determined to be a missense mutation by DNA sequence analysis. A Thermus-E. coli shuttle vector pYK109 was constructed. pYK109 consists of Thermus cryptic plasmid pTT8, tryptophan synthetase gene (trpB) of Thermus T2 and E. coli plasmid vector pUC13. pYK109 transformed T. thermophilus HB27 trpB5 to Trp+ at a frequency of 10(6) transformants per microgram DNA.
Optimal network design: the base station placement problem (2002)

In this paper, we consider the problem of selecting both the base station locations and transmission powers of a cellular communication system based on the information of communication traffic distribution. The objective is to maximize the minimum throughput among the mobiles. The mobility model for each mobile is assumed to be a random walk and independent of other mobiles. The maximum throughput region and the scheduling policy which can have such a throughput region are characterized. Then the optimal locations and powers of the base stations are solved numerically.
Near Ambient Pressure XPS at ALBA (2013)

The ALBA light source has started to operate this year. One of the seven beamlines built in the first phase is the CIRCE beamline (BL24), with two endstations in different branches, dedicated to Photoemission Electron Microscopy (PEEM) and Near Ambient Pressure Photoelectron spectroscopy (NAPP). In this communication we present the NAPP endstation. A differentially pumped electron energy analyzer allows extending the standard X-ray Photoelectron Spectroscopy (XPS) technique, which traditionally required ultra-high vacuum (UHV) conditions, to sample pressures up to 20 mbar. The surface reactivity and structure in more realistic environments can reveal dramatic differences with respect to the solid-vacuum studies. A novel differentially pumped system for the photon beam entrance and other state-of-the-art instrumentation built by SPECS GmbH (Berlin, Germany) are briefly described.
Phased set associative cache design for reduced power consumption (2009)

In this paper, improvised versions of the set associative cache accessing technique have been proposed to reduce the power consumption. In phased cache the cache-access process is divided into two phases. In the first phase all the tag in the set are examined in parallel. In the next phase, if there is a hit, then a data access is performed for the hit way. The average energy consumption is reduced as we are not accessing the data together with tag in each phase. Behavioral implementation of these mechanisms was carried out using Verilog HDL. Synthesis of the design was done in Xilinx 10.1. The Xilinx Xpower analyzer is used to find the power consumption. The results show an average of 41% reduction in power consumption as compared to the conventional sequential set associative cache and an average of 21% power reduction as compared to conventional parallel set associative cache architecture.
Modern pharmacological models of Alzheimer’s disease (2017)

In vivo experimental models of Alzheimers disease are powerfultools for studying the mechanisms of pathogenesis and thesearch for new therapeutic agents. Pharmacological models,based on the injection of neurotoxins (beta-amyloid fragments,cholinotoxins, ibotenic acid) into the brain allow simulation thecognitive impairment typical for Alzheimers disease, and yieldevaluation the impact of drugs on various indicators (biochemical,genetic, electrophysiological). The most validity was showedfor the in vivo model of neurotoxic beta-amyloid fragmentsinjection into basal forebrain nuclei.
A Dynamic Film Model of the Pulsating Heat Pipe (2011)

This article deals with the numerical modeling of the pulsating heat pipe (PHP) and is based on the film evaporation/condensation model recently applied to the single-bubble PHP (Das et al., 2010, “Thermally Induced Two-Phase Oscillating Flow Inside a Capillary Tube,” Int. J. Heat Mass Transfer, 53(19–20), pp. 3905–3913). The described numerical code can treat the PHP of an arbitrary number of bubbles and branches. Several phenomena that occur inside the PHP are taken into account: coalescence of liquid plugs, film junction or rupture, etc. The model reproduces some of the experimentally observed regimes of functioning of the PHP such as chaotic or intermittent oscillations of large amplitudes. Some results on the PHP heat transfer are discussed.
Fundamentals Of Topographic Substrate Leveling (1988)

The leveling of 100 - 500 μm wide, 1 pm deep isolated holes and trenches by 1 - 3 μm thick silicone oil films was observed by measuring film thickness changes at the centers of the features using a non-contact, interferometric technique. The dependence of the leveling time t on feature width w, film viscosity n and the initial film thickness h0 was investigated and compared to theoretical predictions. Experimental data were obtained for various values of w, n and ho. Except when the film thickness was about 1 μm the data for each different type of geometry fell on a single curve when the degree of leveling or planarization was plotted against T E tyh03/nw4 where y is the surface tension of the film. At the same value of T, the degree of planarization of isolated holes was about twice that of isolated trenches. The planarization vs. T curves should apply to all Newtonian liquids and may be used to predict the degree of planarization that will be achieved at specified leveling times by materials having specified values of n, h0 and Y. Thus, the curves may be useful in selecting planarizing materials for semiconductor fabrication steps that require substrate topography leveling. Simulations of the leveling process based on capillarity-driven flow were performed and agreed well with the experimental data. The simulations predicted some interesting and unexpected behavior that was observed experimentally. At short times the planarization worsened before improving at longer times, and humps appeared in the film profiles that apparently are a first step in minimizing surface energy. Such simulations may prove to be useful in predicting the difficulty of planarizing various types of topographic geometries.
A Borescope Based Optical Surface Scanner (2007)

The surface characterization is one of the areas where the optical methods play a significant role. There are many different methodologies and techniques available for such optical characterization studies. Illumination of the target surface area and transmitting the optical signal back to the detector is one of the crucial steps in optical characterization techniques and access to the target area restricts the implementation of optical techniques. In the previous years, we reported on using a borescope based approach for scanning surfaces that are not easily accessible. The method has used triangulation principle for characterizing the surface topology. In those reports, we have shown the principle of proof, introduced the equipment and test setup and demonstrated some of the approaches used for eliminating image distortions that are significant when borescopes are used for transmitting optical signals. In this study, we will report on the final form of the borescope based optical scanner and provide some results obtained through this scanner. The results from the scanner will be compared to the results obtained through a standard confocal laser profilemeter and we will discuss scan resolution, accuracy and speed issues by using those comparative benchmarking.
Changes in serum cartilage marker levels indicate altered cartilage metabolism in families with the osteoarthritis-related type II collagen gene COL2A1 mutation (1999)

Study of the macromolecular constituents of cartilage released into serum in subjects with familial OA revealed altered metabolism in OA, as demonstrated by elevated COMP and KS levels. Other constituents, the 846 epitope and CPII, were not altered, indicating dissociation of cartilage anabolism and breakdown. Future sequential studies will provide an opportunity to define biochemical changes as familial OA develops and to monitor therapeutic responses.
The global burden of disease attributable to contaminated injections given in health care settings (2003)

As part of the 2000 Global Burden of Disease study, we quantified the death and disability from injection-associated infections with hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV). We modelled the fraction of incident infections attributable to health care injections in the year 2000 on the basis of the annual number of injections, the proportion of injections administered with reused equipment, the probability of transmission following percutaneous exposure, the prevalence of active infection, the prevalence of immunity and the total incidence. Infections in 2000 were converted into disability-adjusted life years (DALYs) in 2000-2030 using natural history parameters, background mortality, duration of disease, disability weights, age weights and a 3% discount rate. Four Global Burden of Disease regions where reuse of injection equipment in the absence of sterilization was negligible were excluded from the analysis. In the remaining 10 regions, in 2000, persons received an average of 3.4 injections per year, 39.3% of which were given with reused equipment. In 2000, contaminated injections caused an estimated 21 million HBV infections, two million HCV infections and 260,000 HIV infections, accounting for 32%, 40% and 5%, respectively, of new infections for a burden of 9,177,679 DALYs between 2000 and 2030. Injection overuse and unsafe practices account for a substantial burden of death and disability worldwide. There is a need for policies and plans for the safe and appropriate use of injections in countries where practices are poor.
Multifrequency tympanometry and evoked otoacoustic emissions in neonates during the first 24 hours of life. (1997)

Multifrequency, complex-component tympanograms and transient evoked otoacoustic emissions (EOAEs) were recorded in 55 neonates less than 24 hours of age. The purpose of the investigation was to determine the normal middle ear immittance characteristics of neonates less than 24 hours old (the approximate discharge age of well-babies) and to assess whether an association exists between transient EOAE response and middle ear status in neonatal ears. The tympanometric patterns recorded in the 55 neonates were, in general, not typical of those observed in older children and adults. Complex patterns were recorded at low probe frequencies indicating differences in the contribution of mass, stiffness, and resistance elements to admittance in the neonatal middle ear. Results from EOAE screening indicated a pass rate or partial pass rate of 82 percent. Although no clear association emerged between admittance characteristics and EOAE results, some interesting tendencies were noted.
Scalable byzantine fault tolerance via partial decentralization (2022)

Byzantine consensus is a critical component in many permissioned Blockchains and distributed ledgers. We propose a new paradigm for designing BFT protocols called DQBFT that addresses three major performance and scalability challenges that plague past protocols: (i) high communication costs to reach geo-distributed agreement, (ii) uneven resource utilization hampering performance, and (iii) performance degradation under varying node and network conditions and high-contention workloads. Specifically, DQBFT divides consensus into two parts: 1) durable command replication without a global order, and 2) consistent global ordering of commands across all replicas. DQBFT achieves this by decentralizing the heavy task of replicating commands while centralizing the ordering process. Under the new paradigm, we develop a new protocol, Destiny that uses a combination of three techniques to achieve high performance and scalability: using a trusted subsystem to decrease consensus's quorum size, using threshold signatures to attain linear communication costs, reducing client communication. Our evaluations on 300-replica geo-distributed deployment reveal that DQBFT protocols achieve significant performance gains over prior art: ≈3x better throughput and ≈50% better latency.
Electrical Properties of Trilayer Organic Light-Emitting Diodes With a Mixed Emitting Layer (2009)

We investigate the electrical properties of three different trilayer organic light-emitting diodes (OLEDs), one of which is based on a conventional layered structure and the others on a blended structure where an emitting layer (EML) is uniformly or stepwise mixed with an electron transport layer (ETL), Tris-(8-hydroxyquinoline) aluminum ( Alq <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ). By way of simulations, we visualize the electrical behaviors that provide a clear understanding on why the uniformly mixed structure enhances further the longevity of OLEDs, compared to the other configurations. Namely, the uniformly mixed structure has the lowest concentration of positive charges in the ETL (thereby reducing oxidative degradation of Alq <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ) and weakest electric field (decreasing the probability of Joule heating), followed by the stepwise mixed one and then the layered one. However, such blended structures show lower recombination efficiency due to the delocalization of carriers (recombination), which has been demonstrated by simulations of the current balance.
Uterotropic effects of dietary equol administration in ovariectomized Sprague–Dawley rats (2007)

Long-term high-dose dietary equol administration to ovariectomized rats exerts uterotropic effects at the cellular and molecular level which question the safety of uncontrolled and unlimited consumption of soy or red clover supplements by postmenopausal women with intact uteri.