gebhart/patrepeval huggingface dataset:
Identification of additional genes belonging to the LexA regulon in <i>Escherichia coli</i> (2000)

Exposure of Escherichia coli to a variety of DNA-damaging agents results in the induction of the global 'SOS response'. Expression of many of the genes in the SOS regulon are controlled by the LexA protein. LexA acts as a transcriptional repressor of these unlinked genes by binding to specific sequences (LexA boxes) located within the promoter region of each LexA-regulated gene. Alignment of 20 LexA binding sites found in the E. coli chromosome reveals a consensus of 5'-TACTG(TA)5CAGTA-3'. DNA sequences that exhibit a close match to the consensus are said to have a low heterology index and bind LexA tightly, whereas those that are more diverged have a high heterology index and are not expected to bind LexA. By using this heterology index, together with other search criteria, such as the location of the putative LexA box relative to a gene or to promoter elements, we have performed computational searches of the entire E. coli genome to identify novel LexA-regulated genes. These searches identified a total of 69 potential LexA-regulated genes/operons with a heterology index of <15 and included all previously characterized LexA-regulated genes. Probes were made to the remaining genes, and these were screened by Northern analysis for damage-inducible gene expression in a wild-type lexA+ cell, constitutive expression in a lexA(Def) cell and basal expression in a non-inducible lexA(Ind-) cell. These experiments have allowed us to identify seven new LexA-regulated genes, thus bringing the present number of genes in the E. coli LexA regulon to 31. The potential function of each newly identified LexA-regulated gene is discussed.
Glass-clad single-crystal germanium optical fiber (2009)

Long lengths (250 meters) of a flexible 150 microm diameter glass-clad optical fiber containing a 15 microm diameter crystalline and phase-pure germanium core was fabricated using conventional optical fiber draw techniques. X-ray diffraction and spontaneous Raman scattering measurements showed the core to be very highly crystalline germanium with no observed secondary phases. Elemental analysis confirmed a very well-defined core-clad interface with a step-profile in composition and nominally 4 weight-percent oxygen having diffused into the germanium core from the glass cladding. For this proof-of-concept fiber, polycrystalline n-type germanium of unknown dopant concentration was used. The measured infrared transparency of the starting material was poor and, as a likely outcome, the attenuation of the resultant fiber was too high to be measured. However, the larger Raman cross-section, infrared and terahertz transparency of germanium over silicon should make these fibers of significant value for fiber-based mid- to long-wave infrared and terahertz waveguides and Raman-shifted infrared light sources once high-purity, high-resistivity germanium is employed.
Biomimetic optical directional microphone with structurally coupled diaphragms (2008)

A biomimetic directional microphone based on structurally coupled diaphragms and a fiber-optic detection system is presented. The microphone design aims to mimic the fly Ormia Ochracea’s ear structure and capture its performance. Experiments show that the designed microphone amplifies the interaural time difference (ITD) by 4.4 times and has a directional sensitivity of 6.5 μs/deg. An important finding is that one needs to utilize both the rocking and translational vibration modes to obtain the appropriate ITD amplification without sacrifice of directional sensitivity. This work can serve as a foundation for realizing fly-ear inspired miniature directional microphones.
PlGF: A Multitasking Cytokine with Disease-Restricted Activity (2012)

Placental growth factor (PlGF) is a member of the vascular endothelial growth factor (VEGF) family that also comprises VEGF-A (VEGF), VEGF-B, VEGF-C, and VEGF-D. Unlike VEGF, PlGF is dispensable for development and health but has diverse nonredundant roles in tissue ischemia, malignancy, inflammation, and multiple other diseases. Genetic and pharmacological gain-of-function and loss-of-function studies have identified molecular mechanisms of this multitasking cytokine and characterized the therapeutic potential of delivering or blocking PlGF for various disorders.
Optimization of Flow Channel Design and Operating Parameters on Proton Exchange Membrane Fuel Cell Using MATLAB (2016)

Operating parameters like pressure, temperature, the stoichiometric ratio of reactants, relative humidity and design parameters like rib width to channel width (L:C), the shape of the flow channel and the number of passes on the flow channel are influencing the performance of the Proton Exchange Membrane Fuel Cell (PEMFC). In this paper, optimization of operating and design parameters such as pressure, temperature, inlet reactant mass flow rate and various rib width to channel width (L:C) 1:1, 1:2, 2:1 and 2:2 on serpentine and interdigitated flow channel of 25cm2 active area of the PEMFC was considered. Creo Parametric 1.0 and CFD Fluent 14.0 software packages were used to create the 3 Dimensional (3- D) model and simulation of PEMFC. The optimization was carried out on the various parameters with MINITAB 17 software and MATLAB software. From the first stage, the Landing to channel width (L: C) - 1:1 of serpentine and the interdigitated flow channel has the maximum influence on fuel cell performance and square of response factor (R2) was achieved from the Taguchi method by MINITAB 17 software as 99.48 and 99.71 % respectively. In the second stage, the regression equation or mathematical model obtained from MINITAB 17 software were fed into the MATLAB software to get optimized parameters. Further the power densities were obtained corresponding to the optimized parameters using the CFD Fluent 14.0 software.
Light‐chain removal by plasmapheresis in myeloma‐associated renal failure (2007)

In both patients, plasmapheresis failed to effectively lower sFLC levels. The results provide initial biologic data supporting the conclusions of a recent randomized multicenter clinical trial in which plasmapheresis was an ineffective adjunct to chemotherapy for myeloma-associated acute renal failure.
Determination of sulfonamides and trimethoprim using high temperature HPLC with simultaneous temperature and solvent gradient (2008)

A fast HPLC method for the analysis of eight selected sulfonamides (SA) and trimethoprim has been developed with the use of high temperature HPLC. The separation could be achieved in less than 1.5 min on a 50 mm sub 2 microm column with simultaneous solvent and temperature gradient programming. Due to the lower viscosity of the mobile phase and the increased mass transfer at higher temperatures, the separation could be performed on a conventional HPLC system obtaining peak widths at half height between 0.6 and 1.3 s.
Robust PCA via Outlier Pursuit (2012)

Singular-value decomposition (SVD) [and principal component analysis (PCA)] is one of the most widely used techniques for dimensionality reduction: successful and efficiently computable, it is nevertheless plagued by a well-known, well-documented sensitivity to outliers. Recent work has considered the setting where each point has a few arbitrarily corrupted components. Yet, in applications of SVD or PCA, such as robust collaborative filtering or bioinformatics, malicious agents, defective genes, or simply corrupted or contaminated experiments may effectively yield entire points that are completely corrupted. We present an efficient convex optimization-based algorithm that we call outlier pursuit, which under some mild assumptions on the uncorrupted points (satisfied, e.g., by the standard generative assumption in PCA problems) recovers the exact optimal low-dimensional subspace and identifies the corrupted points. Such identification of corrupted points that do not conform to the low-dimensional approximation is of paramount interest in bioinformatics, financial applications, and beyond. Our techniques involve matrix decomposition using nuclear norm minimization; however, our results, setup, and approach necessarily differ considerably from the existing line of work in matrix completion and matrix decomposition, since we develop an approach to recover the correct column space of the uncorrupted matrix, rather than the exact matrix itself. In any problem where one seeks to recover a structure rather than the exact initial matrices, techniques developed thus far relying on certificates of optimality will fail. We present an important extension of these methods, which allows the treatment of such problems.
CO/sub 2/ recovery from flue gas (1984)

There is a growing demand for CO/sub 2/ for enhanced oil recovery. One of the historic sources of CO/sub 2/ has been from ammonia plants, but in recent years the availability of CO/sub 2/ from ammonia plant syngas has dropped significantly due to rising natural gas prices and low-priced imported ammonia. Natural deposits of CO/sub 2/ are relatively pure and may require little or no processing but are not accessible to some major markets. In addition, the combined total of natural CO/sub 2/ and CO/sub 2/ from process vents cannot fill the estimated demand. Several factors dictate the economic feasibility of CO/sub 2/ injection for enhanced oil recovery: the price per barrel of oil, profit, production costs, taxes, CO/sub 2/ required per incremental barrel of oil, and the cost of the CO/sub 2/. The site requirements and CO/sub 2/ costs are major factors in assessing economic feasibility for a given price per barrel of oil with a fixed production, tax, and profit schedule. Flue gas provides a readily available supply of low-cost CO/sub 2/, if recovery costs can be brought to within the field guidelines for profitability for a given CO/sub 2/ to incremental barrel ratio.
A rigid approach of generalized power flow analysis for distribution systems (2002)

The novel approach developed in this paper is for the accurate determination of power flow in both normal and faulted unbalanced distribution systems. Based on a hybrid compensation method, the proposed methodology has three distinguishable enhancements compared with the existing algorithms. First, the internal impedance of power source is discussed in detail, and a revised power flow algorithm is introduced accordingly. Second, various types of single or multiple faults are simulated in a complete uniform model without any extra processing for a certain fault. At the same time, both direct short circuits and faults through impedance are under full considerations. Third, a novel Thevenin equivalent is developed when the source transformer is ungrounded. In addition, the influence of shunt capacitance of lines is studied, which is especially important for single line-to-ground faults in an ungrounded system. A computer program has been developed based on this methodology. Numerical tests on a Chinese large real distribution system verify the validity and efficiency of the presented algorithm.
Brain retraction injury (2003)

This paper reviews the literature of the brain retraction injury during the last century. The review focused on the instrument characteristic as well as the physiopathological and histopathological damage of the brain induced by brain retraction. It was found that lesions were induced by cerebral ischemia. We conclude that a better monitoring system needs to be developed to avoid brain injury.
Antiapoptotic Role for Ornithine Decarboxylase during Oocyte Maturation (2009)

Ornithine decarboxylase (ODC), the rate-limiting enzyme in polyamine biosynthesis, is a nonredundant and essential gene in all eukaryotes. During the mitotic cell cycle, ODC exhibits two activity peaks: one at the G(1)/S transition and one during the G(2)/M transition. The physiological role of this cell cycle-dependent ODC activity dynamic is not clear. Previous studies have reported a significant elevation of ODC activity during Xenopus oocyte maturation, which resembles mitotic G(2)/M transition. In order to study the roles of ODC activity in the oocytes, we utilized antisense morpholino (xODC mo) oligonucleotides to inhibit ODC translation. We report here that xODC mo abolished ODC activity increase during oocyte maturation. xODC mo-injected oocytes underwent germinal vesicle breakdown, emitted the first polar body, and reached metaphase II, thus completing nuclear maturation. However, the metaphase II oocytes exhibited high levels of reactive oxygen species and became apoptotic. When transferred to host frogs and subsequently ovulated, these eggs were fertilized but exhibited embryo fragmentation. Translation of ODC is therefore integral to cytoplasmic maturation, protecting metaphase II oocytes from reactive oxygen species-induced apoptosis.
A neural network model of causality (1994)

This paper proposes a model for commonsense causal reasoning, based on the basic idea of neural networks. After an analysis of the advantages and limitations of existing accounts of causality, a fuzzy logic based formalism FEL is proposed that takes into account the inexactness and the cumulative evidentiality of commonsense causal reasoning, overcoming the limitations of existing accounts. Analyses concerning how FEL handles various aspects of commonsense causal reasoning are performed, in an abstract way. FEL can be implemented (naturally) in a neural (connectionist) network. This work also serves to link rule-based reasoning with neural network models, in that a rule-encoding scheme (FEL) is equated directly to a neural network model.
Moderate Intense Physical Activity Depends on Selected Metabolic Equivalent of Task (MET) Cut-Off and Type of Data Analysis (2013)

MVPA varies upon the selected physical activity guideline/targets and bouts versus non-bouts analysis. Accelerometry measured MVPA non-bouts target of 80 min*day⁻¹, using a 3 METs MVPA threshold, is associated to the commonly-used MVPA bout target of 30 min*day⁻¹.
Alternatives to Conventional Food Processing (2010)

This multi-authored book is edited by an expert in the field and includes chapters from international contributors. It is fully cross disciplinary relating green principles to the food industry, covering legal and policy issues, engineering, food processing and food science. It addresses the alternatives to conventional food processing that have reduced energy requirements or solvent use and how they affect final food quality. Initially, the principles of green chemistry and technologies are outlined to provide a justification and basis for the processing methods that are addressed. This is followed by a discussion of legal and policy issues in both the EU and the US which provide further justification for the need for such technologies and the constraints and benefits of current policies and regulations. The major green technologies available to the food industry are discussed, outlining the main principles and applications of each. The degree to which they are already in commercial use and developments needed to extend their use further are also covered.
A stochastic multicriteria model for evidence‐based decision making in drug benefit‐risk analysis (2011)

Drug benefit-risk (BR) analysis is based on firm clinical evidence regarding various safety and efficacy outcomes. In this paper, we propose a new and more formal approach for constructing a supporting multi-criteria model that fully takes into account the evidence on efficacy and adverse drug reactions. Our approach is based on the stochastic multi-criteria acceptability analysis methodology, which allows us to compute the typical value judgments that support a decision, to quantify decision uncertainty, and to compute a comprehensive BR profile. We construct a multi-criteria model for the therapeutic group of second-generation antidepressants. We assess fluoxetine and venlafaxine together with placebo according to incidence of treatment response and three common adverse drug reactions by using data from a published study. Our model shows that there are clear trade-offs among the treatment alternatives.
Formation of shallow silicide contacts of high Schottky barrier on Si: Alloying Pd and Pt with W versus alloying Pd and Pt with Si (1982)

The contact reaction of a Si substrate with codeposited Pd-W and Pt-W alloy films has been compared to that with codeposited Pd-Si and Pt-Si alloy films. Effects of alloy composition and heat treatment on component redistribution, reaction product, temperature of silicide formation, and morphological changes have been analyzed by ion backscattering, x-ray diffraction, and scanning electron microscopy and correlated with earlier current-voltage measurements of change of Schottky barrier height. The advantage and disadvantage of using alloys of near noble and refractory metals and of using alloys of near noble metal and Si for the formation of shallow contacts of high Schottky barrier height (0.87–0.74 eV) are reviewed.
Thromboxane Synthetase Inhihitors. I. Synthesis of Some Imidazolylarylmethanols and Their Inhihitory Activity on Platelet Aggregation (1989)

Several imidazolylpyridinemethanols and imidazolylbenzenemethanols were prepared and evaluated for an inhibitory activity against arachidonic acid-induced platelet aggregation. The result shows that the arylmethanol moiety is essential for the activity and may correspond to the 15-OH group of prostagrandin H2 (PGH2). Among the compounds tested, 4-[alpha-hydroxy-5-(1-imidazolyl)-2-methylbenzyl]-3,5-dimethylbenzoic acid (XV) was found to have a potent inhibitory activity and a long duration of action. Structure-activity relationships are also discussed briefly.
Modification of the Mycobacterium bovis extracellular protein MPB70 with fluorescein for rapid detection of specific serum antibodies by fluorescence polarization (1996)

The principle of fluorescence polarization described by Perrin (F. Perrin, J. Phys. Radium 7:390-401, 1926) was applied to the development of a novel assay that used fluorescein-labeled Mycobacterium bovis secretory protein MPB70 for rapid detection of anti-MPB70 antibodies in selected sera from three M. bovis-infected species (elk, Ilama, and bison). Labeling of purified MPB70 with fluorescein isothiocyanate resulted in the incorporation of 0.96 +/- 0.08 (mean +/- standard deviation; n = 3) fluorescein group per MPB70 molecule. The labeled protein fluoresced strongly with an emission maximum at 518 nm when excited with light of a wavelength near 493 nm, and its immunoreactivity with anti-MPB70 monoclonal antibody 4C3/17 was not altered by modification with fluorescein. The fluorescence polarization assay protocol was optimized for analysis of serum samples by incorporating into the assay buffer 0.05% lithium dodecyl sulfate, which prevents the occurrence of some nonspecific interactions. Sera from M. bovis-infected animals, selected on the basis of exhibiting the presence of anti-MPB70 antibodies, as detected by enzyme-linked immunosorbent assay (ELISA), reacted with fluorescein-labeled MPB70, resulting in an increase in polarization of up to 330 milli-polarization units, in contrast to the values for noninfected sera (167 to 178 mP), which were close to that obtained in the absence of specific antibodies (164.7 +/- 3.3 mP; n = 6). These results demonstrated the feasibility of using fluorescein-labeled MPB70 to detect anti-MPB70 antibodies by fluorescence polarization and suggested that the assay described here can be an alternative to ELISA or other antibody assay systems. The advantages of this original methodology and its general applicability to the diagnosis of infectious diseases are discussed.
Transferrin-mediated tumor delivery of contrast media for optical imaging and magnetic resonance imaging (1999)

Many tumor cells are characterized by the overexpression of highly specific transferrin receptors. Transferrin is bound to its receptor, which is followed by rapid internalization into intracellular compartments; it can thus be used for the specific delivery of coupled contrast agents in to tumor cells. The aim of our study was to investigate the tumor- specificity of transferrin-modified contrast agents for optical imaging and magnetic resonance imaging (MRI). Indotricarbocyanine, a near-IR absorbing dye, and ultrasmall superparamagnetic iron oxide particles, a contrast material for MRI, were covalently coupled to transferrin and examined in vitro and in vivo for their potential as tumor-specific contrast agents. CEll culture experiments using HT29 and A431 tumor cells showed specific uptake of transferrin- modified contrast agents by the cells at 37 degrees C, while uptake was inhibited at 4 degrees C or in the presence of an excess of unlabeled transferrin. Optical imaging of tumor- bearing nude mice after intravenous injection of transferrin-ICC resulted in pronounced tumor fluorescence. Tumor specificity was also observe in MRI, where transferrin-USPIO accumulated in SMT2A tumor-bearing rats. We conclude that transferrin-modified contrast agents for optical imaging and MRI can be specifically delivered to tumor tissue by use of transferrin receptor pathways.
Enumeration of potentially pathogenic bacteria from sewage sludges (1980)

To ascertain the health risks that may be posed by the land application of sewage sludges, a scheme was devised to determine the types and numbers of pathogenic and potentially pathogenic bacteria present in sludges. A processing treatment was adapted to sludge to give a homogenate which yielded the greatest numbers of viable bacteria. Conventional methods were successful in enumerating Klebsiella, Staphylococcus, gram-negative enteric bacteria, and commonly used indicator organisms. Modifications of conventional methods improved the enumeration of Salmonella, Mycobacterium sp., fluorescent Pseudomonas sp., and Clostridium perfringens. However, Shigella methodology yielded only one isolate. Utilizing the proposed scheme, the population densities of these organisms were estimated in three domestic wastewater sludges. In light of these results, the potential impact of land application of sewage sludges is discussed.
The failure of nisoldipine to prevent the hypertensive response to cyclosporine A infusion in sheep (1990)

Hypertension and nephrotoxicity are major clinical problems associated with cyclosporine A administration. Sheep rapidly develop hypertension after intravenous administration of cyclosporine A at 6 mg/kg per day over 5 days, and this is associated with a rise in peripheral resistance. Nephrotoxicity is not a feature of cyclosporine A-induced hypertension in this species. This study reports the use of nisoldipine to investigate the role of Ca2(+)-induced smooth muscle contraction in cyclosporine A-induced hypertension in conscious sheep. After 3 control days, nisoldipine at 24 mg/day was infused intravenously alone for 24h (E1), followed by 5 days of nisoldipine plus cyclosporine A (6 mg/kg per day; E2-E6). After 24 h of nisoldipine alone, mean arterial pressure (MAP) was unchanged, heart rate rose from a control value of 60 +/- 2 beats/min to 102 +/- 9 beats/min (P less than or equal to 0.001), calculated total peripheral resistance (CTPR) fell from 15.8 +/- 0.5 to 11.7 +/- 0.5 mmHg/l per min (P less than or equal to 0.001) and stroke volume fell from 73 +/- 4 ml/beat to 60 +/- 5 ml/beat (P less than or equal to 0.01).(ABSTRACT TRUNCATED AT 250 WORDS)
Magnetic domain observation of induced anisotropy around scratches in Mn-Zn ferrites using SEM (1976)

The (001) plane Mn-Zn single-crystal ferrite specimen was scratched by a pyramidal diamond at an interfacial angle of 120° along the [010] direction. Around the scratch groove, [100] domains were induced and enclosed with zigzag-shaped walls, on which they are bounded by the main sample domains in the [010] direction. These domains have fine structure and could result from the induced anisotropy of the inverse magnetostriction effect caused by the residual stress around the scratch groove.