gebhart/patrepeval huggingface dataset:
Operational Strategies to Selectively Produce Purple Bacteria for Microbial Protein in Raceway Reactors (2021)

Purple non-sulfur bacteria (PNSB) show potential for microbial protein production on wastewater as animal feed. They offer good selectivity (i.e., low microbial diversity and high abundance of one species) when grown anaerobically in the light. However, the cost of closed anaerobic photobioreactors is prohibitive for protein production. Although open raceway reactors are cheaper, their feasibility to selectively grow PNSB is thus far unexplored. This study developed operational strategies to boost PNSB abundance in the biomass of a raceway reactor fed with volatile fatty acids. For a flask reactor run at a 2 day sludge retention time (SRT), matching the chemical oxygen demand (COD) loading rate to the removal rate in the light period prevented substrate availability during the dark period and increased the PNSB abundance from 50-67 to 88-94%. A raceway reactor run at a 2 day SRT showed an increased PNSB abundance from 14 to 56% when oxygen supply was reduced (no stirring at night). The best performance was achieved at the highest surface-to-volume ratio (10 m<sup>2</sup> m<sup>-3</sup> increased light availability) showing productivities up to 0.2 g protein L<sup>-1</sup> day<sup>-1</sup> and a PNSB abundance of 78%. This study pioneered in PNSB-based microbial protein production in raceway reactors, yielding high selectivity while avoiding the combined availability of oxygen, COD, and darkness.
Comparative physiology of phenanthrene degradation by two dissimilar pseudomonads isolated from a creosote-contaminated soil (1994)

Two species of bacteria, identified as Pseudomonas stutzeri (P-16) and Pseudomonas saccharophila (P-15) by fatty acid methyl ester analysis, were found in a phenanthrene enrichment culture of a creosote-contaminated soil. The organisms are shown to be physiologically dissimilar, and their genetic relatedness is discussed. Phenanthrene degradation by both organisms followed Michaelis-Menten kinetics, allowing for the determination of half-saturation (Ks) and maximum activity coefficients, using nonlinear regression. Both organisms utilized kinetically similar enzymes for phenanthrene uptake and oxidation, as evidenced by similar Ks coefficients of approximately 0.2 mg/L and temperature optima of 40 degrees C, but levels of expression differed with different media. Each organism degraded phenanthrene via salicylic acid, but patterns of intermediate metabolism were shown to differ. P-15 excreted 1-hydroxy-2-naphthoic acid during growth on phenanthrene and demonstrated Michaelis-Menten kinetics for the oxidation of 1-hydroxy-2-naphthoic acid by resting cells. P-16 excreted only trace amounts of 1-hydroxy-2-naphthoic acid and demonstrated linear kinetics in response to 1-hydroxy-2-naphthoic acid concentration. P-15 was found to form thick biofilms on phenanthrene crystals and was characterized by a hydrophobic cell surface, whereas P-16 grew mostly in suspension and was hydrophilic. Neither organism produced significant amounts of biosurfactants when grown on phenanthrene. The implications of these findings for the design of systems to remediate contaminated soil are discussed.
Inelastic Electron Tunneling Spectra of Lubricant Oil Additives on Native Aluminum Oxide Surfaces (1993)

Zinc dithiophosphates (ZnDTPs) have been used extensively as antiwear agents for over 30 years. The mechanism of action of these remarkable materials is not well understood. In particular, the molecular composition of the antiwear film produced by the ZnDTPs remains an area requiring investigation. In this paper, the molecular composition of adsorbed ZnDTPs on aluminum oxide (Al2O3) surfaces has been studied by inelastic electron tunneling spectroscopy (IETS), a highly sensitive molecular spectroscopy specifically applicable to surface species at low coverages. As such, it complements other surface science techniques for determining surface compositions. A vibrational spectroscopy, IETS utilizes the literature on group characteristic frequencies available from the very extensive correlations developed for infrared and Raman spectra. Thus, functional groups may be identified that are formed by the reaction of a lubricating oil additive with a metal surface covered by a native oxide. By IETS, we show that ZnDTP aryl esters are dissociatively chemisorbed, and do not appear to form P = S groups bonded to the surface. By contrast, primary and secondary ZnDTPs retain the phosphate ester groups and bond to the surface by the P = S group to different degrees. These spectral differences are qualitatively correlated with the observed antiwear performance of these materials.
Programmable matter with self-reconfiguring robots (2010)

Programmable matter aims to bring machines and materials closer together. We wish to create smart materials whose properties can be programmed, or, alternatively, machines that look and feel more like materials. Programmable matter will be achieved when we will have the ability to create objects whose physical properties, for example shape, stiffness, optical characteristics, acoustic characteristics, and viscosity can be programmed. We are working toward creating materials with embedded sensing, actuation, communication, computation, and connection, which we call SAC3 materials. We are developing two concepts: smart SAC3 sheets that self-fold into origami shapes, and smart SAC3 pebbles that self-sculpt into desired objects. This work is at the intersection of theory, algorithms, device design, and control.
Slow Auger Relaxation in HgTe Colloidal Quantum Dots (2018)

The biexciton lifetimes in HgTe colloidal quantum dots are measured as a function of particle size. Samples produced by two synthetic methods, leading to partially aggregated or well-dispersed particles, exhibit markedly different dynamics. The relaxation characteristics of partially aggregated HgTe inhibit reliable determinations of the Auger lifetime. In well-dispersed HgTe quantum dots, the biexciton lifetime increases approximately linearly with particle volume, confirming trends observed in other systems. The extracted Auger coefficient is three orders of magnitude smaller than that for bulk HgCdTe materials with similar energy gaps. We discuss these findings in the context of understanding Auger relaxation in quantum-confined systems and their relevance to mid-infrared optoelectronic devices based on HgTe colloidal quantum dots.
Promoter hypermethylation of estrogen receptor alpha gene is correlated to estrogen receptor negativity in Iranian patients with sporadic breast cancer. (2012)

ERα methylation occurs with high frequency in the breast tumors of Iranian breast cancer patients and may play a considerable role in pathogenesis of ERα negative tumors as a poor prognosis and more aggressive category. The reversible nature of DNA methylation may provide new therapeutic possibilities in ER negative breast tumors.
A semiconductor quantum dot-based ratiometric electrochemical aptasensor for the selective and reliable determination of aflatoxin B1 (2019)

In recent years, a ratiometric electrochemical method has been investigated due to its ability to effectively reduce the background electrical signals via the introduction of an internal calibration mechanism, which has great practical significance in the detection of mycotoxins in foods. Herein, we report a ratiometric electrochemical aptasensor based on two semiconductor quantum dots (i.e. CdTe and PbS QDs) for the detection of aflatoxin B1 (AFB1). The aptasensor was fabricated by immobilizing PbS QD-coated silica hybrid spheres (SiO2@PbS) onto CdTe QD-modified Fe3O4@SiO2 (Fe3O4@SiO2/CdTe) surface through biorecognition between the aptamer and complementary DNAs, where PbS QDs acted as external signal labels and CdTe QDs acted as internal reference labels. In the presence of AFB1, the aptamer connected to SiO2@PbS preferred to form an aptamer/AFB1 complex, which brought about the separation of SiO2@PbS linked with the CdTe QDs; with the addition of more AFB1 to the solution, the amount of SiO2@PbS present on the Fe3O4@SiO2/CdTe surface reduced. After several steps of endonuclease cleavage, magnetic separation, and dissolution with acid, the square wave voltammetry signals of Pb2+ and Cd2+ maintained an inverse relationship with the target content based on the SWV stripping measurements; the proposed method had the wide linear range of 5 pg mL-1-50 ng mL-1 and the determination limit of 4.5 pg mL-1 (S/N = 3) and was applied for the detection of AFB1 in peanuts. The proposed aptasensor has an important practical significance for the development of food safety.
Erratum: “Investigations on the local entrainment velocity in a turbulent jet” [Phys. Fluids 24, 105110 (2012)] (2013)

First Page
Identification of Uncertainties in the Geometry of Geophysical Objects (2010)

•We propose a numerical method for the reconstruction of the geometry of geophysical layers from temperature measurements. We use the “speed method” for shape optimization with Lagrangian formulation of the problem. • The level-set function is describing the geometry of the unknown interface. A steepest descent direction is used to evolve the level-set in the normal direction with different numerical schemes. • Performance of the algorithm for different cases and good reconstruction with noisy simulated data. • Joined reconstruction of the layers and identification of the physical properties in case of uncertainties in the parameters.
A round trip time and time-out aware traffic conditioner for differentiated services networks (2003)

TCP connection throughput is inversely proportional to the connection round trip time (RTT). To mitigate TCP bias to short RTT connections, a differentiated services traffic conditioner can ensure connections with long RTTs do not starve when connections with short RTTs get all extra resources after achieving the target rates. Current proposals for RTT-aware conditioners work well for a small number of connections when most TCP connections are in the congestion avoidance phase. If there is a large number of TCP connections, however, connections time-out and go to slow start. We show that current RTT-aware conditioners over-protect long RTT flows and starve short RTT flows in this case. We design and evaluate a conditioner based on RTT as well as the retransmission time-out (RTO). The proposed RTT-RTO aware traffic conditioner works well for realistic situations with a large number of connections. Simulation results in a variety of situations confirm that the conditioner mitigates RTT bias.
Signal-dependent noise characterization in Haar filterbank representation (2007)

Owing to the properties of joint time-frequency analysis that compress energy and approximately decorrelate temporal redundancies in sequential data, filterbank and wavelets are popular and convenient platforms for statistical signal modeling. Motivated by the prior knowledge and empirical studies, much of the emphasis in signal processing has been placed on the choice of the prior distribution for these transform coefficients. In this paradigm however, the issues pertaining to the loss of information due to measurement noise are difficult to reconcile because the effects of point-wise signal-dependent noise permeate across scale and through multiple coefficients. In this work, we show how a general class of signal-dependent noise can be characterized to an arbitrary precision in a Haar filterbank representation, and the corresponding maximum a posteriori estimate for the underlying signal is developed. Moreover, the structure of noise in the transform domain admits a variant of Stein's unbiased estimate of risk conducive to processing the corrupted signal in the transform domain. We discuss estimators involving Poisson process, a situation that arises often in real-world applications such as communication, signal processing, and imaging.
Spectroscopic Properties of Amine‐substituted Analogues of Firefly Luciferin and Oxyluciferin (2016)

Spectroscopic and photophysical properties of firefly luciferin and oxyluciferin analogues with an amine substituent (NH<sub>2</sub> , NHMe and NMe<sub>2</sub> ) at the C6' position were studied based on absorption and fluorescence measurements. Their π-electronic properties were investigated by DFT and TD-DFT calculations. These compounds showed fluorescence solvatochromism with good quantum yields. An increase in the electron-donating strength of the substituent led to the bathochromic shift of the fluorescence maximum. The fluorescence maxima of the luciferin analogues and the corresponding oxyluciferin analogues in a solvent were well correlated with each other. Based on the obtained data, the polarity of a luciferase active site was explained. As a result, the maximum wavelength of bioluminescence for a luciferin analogue was readily predicted by measuring the photoluminescence of the luciferin analogue in place of that of the corresponding oxyluciferin analogue.
Chapter 5: Machine Translation Evaluation and Optimization (2011)

The evaluation of machine translation (MT) systems is a vital field of research, both for determining the effectiveness of existing MT systems and for optimizing the performance of MT systems. This part describes a range of different evaluation approaches used in the GALE community and introduces evaluation protocols and methodologies used in the program. We discuss the development and use of automatic, human, task-based and semi-automatic (human-in-the-loop) methods of evaluating machine translation, focusing on the use of a human-mediated translation error rate HTER as the evaluation standard used in GALE. We discuss the workflow associated with the use of this measure, including post editing, quality control, and scoring. We document the evaluation tasks, data, protocols, and results of recent GALE MT Evaluations. In addition, we present a range of different approaches for optimizing MT systems on the basis of different measures. We outline the requirements and specific problems when using different optimization approaches and describe how the characteristics of different MT metrics affect the optimization. Finally, we describe novel recent and ongoing work on the development of fully automatic MT evaluation metrics that have the potential to substantially improve the effectiveness of evaluation and optimization of MT systems. Progress in the field of machine translation relies on assessing the quality of a new system through systematic evaluation, such that the new system can be shown to perform better than pre-existing systems. The difficulty arises in the definition of a better system. When assessing the quality of a translation, there is no single correct answer; rather, there may be any number of possible correct translations. In addition, when two translations are only partially correct – but in different ways – it is difficult to distinguish quality. Moreover, quality assessments may be dependent on the intended use for the translation, e.g., the tone of a translation may be crucial in some applications, but irrelevant in other applications.
Salt-Sensitive Blood Pressure in Mice With Increased Expression of Aldosterone Synthase (2007)

To study the effects of modestly increased expression of aldosterone synthase (AS), we generated mice (AS(hi/hi)) by replacing the 3' untranslated region of AS mRNA with that from a stable mRNA. AS(hi/hi) mice on a normal-salt diet had 1.5 times the wild-type AS mRNA in adrenals, although their blood pressure and plasma aldosterone did not differ from wild-type mice. Changes in dietary salt did not affect the blood pressure of wild-type mice, but AS(hi/hi) mice had approximately 10-mm Hg higher blood pressure on a high-salt diet than on a low-salt diet and than wild-type mice on either diet. The AS(hi/hi) mice on a high-salt diet also had higher plasma aldosterone, lower plasma potassium, and greater renal expression of the alpha subunit of epithelial sodium channel compared with wild-type mice. The AS(hi/hi) mice on a high-salt diet also had more water intake and urine volume and less urine osmolality than wild-type mice. On a low-salt diet, AS(hi/hi) mice maintained normal blood pressure with less activation of the renin-angiotensin-aldosterone system than wild-type mice. The AS(hi/hi) mice also had less water intake and urine volume and higher urine osmolality than wild-type mice. On a medium high-salt diet, AS(hi/hi) mice were more susceptible than wild-type mice to infusion of angiotensin II, having a higher blood pressure, greater cardiac hypertrophy, and increased oxidative stress. Thus, a modest increase in AS expression makes blood pressure more sensitive to salt, suggesting that genetically increased AS expression in humans may contribute to hypertension and cardiovascular complications in societies with high-salt diets.
The variation of the strain-hardening exponent due to grain size distributions in engineering metallic sheet materials. (1987)

Grain-size distributions of commercially pure aluminum, copper and 6-4 brass are well approximated by a log-normal distribution function, and it is shown that the strain-hardening exponents of copper and 6-4 brass under tension increase with their median and standard deviation. Based on the nth-power flow curve and the distribution function whose upper grain-size is limited to 3.5 times the mean-grain diameter, the composite flow curve for a metal comprising various grain sizes is expressed by either an equal-strain or an equal-stress model. The equal-strain model gives the lower flow stress limit snd the equal-stress model yields the upper one, and the experimental data appears in between or closely around these two neighboring limits. The relation between the strain hardening exponent and statistical variables can be calculated from these. The former model predicts the upper boundary of the strain-hardening exponent and the latter predicts the lower boundary, with respect to the median and the standard deviation, and the experimental data on 6-4 brass are given in between them.
Heart-lung transplantation: an overview. (1990)

Heart-lung transplantation is in a state of evolution, but for selected patients with end-stage cardiopulmonary and pulmonary disease, it can offer long-term rehabilitation. In the 8 years since heart-lung transplantation was begun at Stanford, much experience has accrued and significant improvements have been made. Advances that have made heart-lung transplantation feasible include better immunosuppression, particularly the triple-drug protocol of cyclosporine, azathioprine, and corticosteroids which decreases the incidence of obliterative bronchiolitis. Techniques of improved lung preservation have made distal donor procurement a reality, and increasing numbers of lung and heart-lung transplantations are now being performed. More importantly, better recipient and donor selection has occurred such that the perioperative mortality has been reduced from 35 to 16 per cent. Currently, the major threat facing survivors of heart-lung transplantation is the insidious development of restrictive airway disease. Our impression is that the development of obliterative bronchiolitis results from repeated rejection episodes or possibly an injury mechanism following severe viral pneumonia. The common pathway seems to be repeated injury and repair mechanism, with the end-stage being obliterative bronchiolitis by scar formation. As suggested, the injury mechanism is probably that of repeated or chronic rejection. To further support the hypothesis of an immunerelated etiology, obliterative bronchiolitis has occurred in recipients of bone marrow transplants if they develop graft-versus-host disease. In an attempt to ameliorate the effects of rejection on airway function, we have increased our maintenance immunosuppression by adding azathioprine. Consequently, patients with early obliterative bronchiolitis on enhanced immunosuppression have had stabilization of the airway disease, and we have noted a significant reduction in the occurrence of obliterative bronchiolitis from 62 per cent in Group 1 patients to 20 per cent in Group 2 patients. Since obliterative bronchiolitis may be reversed by early recognition and treatment of rejection, we have aggressively used bronchoscopy with transbronchial lung biopsy and bronchoalveolar lavage for surveillance of both rejection and infection in our recent patients. Open lung biopsy has not been used since 1986 to diagnose rejection, and we are encouraged that bronchoscopic surveillance is sensitive and effective. The primary goal of the bronchoscopic evaluation protocol was to monitor the patients closely and to treat both rejection and infection early and effectively. Concurrently, we are also measuring pulmonary function parameters, which includes FEV1, FEF 25-75, PaO2, total lung capacities, and profusion gradients. The desired outcome was the maintenance of normal airway dynamics by reversing airway disease at a reversible stage.(ABSTRACT TRUNCATED AT 400 WORDS)
Au34−: A Chiral Gold Cluster? (2007)

Gold prospecting: Trapped-ion electron diffraction, photoelectron spectroscopy, and density functional theory are used to establish the structure of the free gold cluster ion Au34−. The results suggest a chiral cluster with an internal trigonal pyramid and C3 point symmetry.
Impact of successive interference cancellation on the capacity of wireless networks: Joint optimal link scheduling and power control (2013)

In this paper, we study the performance of multi-hop wireless networks when both proper interference control and effective spatial reuse are jointly considered. For the former, we assume nodes endowed with Successive Interference Cancellation (SIC) capabilities at the physical layer and for the latter, we advocate joint link scheduling and power allocation. We study the achievable performance of such networks through a cross-layer design framework. We formulate the joint problem of routing, link scheduling and power allocation as a mixed integer non-linear program (MINLP) and we use column generation (CG) to decompose and linearize it, and hence, solve it. Our numerical results show that when SIC and power control are combined, around 75% performance improvement in dense networks may be achieved in comparison with a network that does not incorporate any advanced interference management techniques.
Ultrafiltration sur membrane minérale de laits acidifiés à divers pH par voie biologique ou chimique et de coagulum lactique (1988)

(with varying pH) and of lactic coagulum.
OPTIMIZATION OF AN ANIMAL TEST PROTOCOL FOR TOXICOGENOMICS STUDIES (I); REQUIREMENT STUDY OF A PROTOCOL (2007)

Toxicogenomics is a promising new tool for prediction of chemical toxicities including carcinogenicity in a relatively short period. However, it is important to develop a reliable animal test protocol for toxicogenomics studies. The preparation of RNA and tissues is also crucial, since it greatly influences outcomes of gene expression analysis. In the present study, we examined an animal test protocol by comparing gene expression data from different conditions and proposed a reliable animal test protocol for toxicogenomic studies. With regard to the preparation of tissues and RNA, here we present evidence that quality of RNA and tissues is well-preserved even after freezer storage for up to 2.5 years. Gene expression levels were compared using a GeneChip System (RGU34A, Affymetrix, Santa Clara, CA, USA) between RNA samples that were freshly prepared, stored at -80 degrees C or re-prepared from tissue kept at -20 degrees C. None showed degradation and no significant differences in expression were evident among the three sets of samples. The data demonstrate that gene expression analysis by DNA microarray is suitable for RNA or tissues that have been stored at an appropriate temperature.