gebhart/patrepeval huggingface dataset:
Characterization of an Endoprotease (PrpL) Encoded by a PvdS-Regulated Gene in<i>Pseudomonas aeruginosa</i> (2001)

ABSTRACT The expression of many virulence factors in Pseudomonas aeruginosa is dependent upon environmental conditions, including iron levels, oxygen, temperature, and osmolarity. The virulence of P. aeruginosa PAO1 is influenced by the iron- and oxygen-regulated gene encoding the alternative sigma factor PvdS, which is regulated through the ferric uptake regulator (Fur). We observed that overexpression of PvdS in strain PAO1 and a Δ pvdS :: Gm mutant resulted in increased pyoverdine production and proteolytic activity compared to when PvdS was not overexpressed. To identify additional PvdS-regulated genes, we compared extracellular protein profiles from PAO1 and the Δ pvdS :: Gm mutant grown under iron-deficient conditions. A protein present in culture supernatants from PAO1 but not in supernatants from Δ pvdS :: Gm was investigated. Amino acid sequence analysis and examination of the genomic database of PAO1 revealed that the N terminus of this 27-kDa protein is identical to that of protease IV of P. aeruginosa strain PA103-29 and is homologous to an endoprotease produced by Lysobacter enzymogenes. In this study, the gene encoding an endoprotease was cloned from PAO1 and designated prpL (PvdS-regulated endoprotease, lysyl class). All ( n = 41) but one of the strains of P. aeruginosa , including clinical and environmental isolates, examined carry prpL . Moreover, PrpL production among these strains was highly variable. Analysis of RNase protection assays identified the transcription initiation site of prpL and confirmed that its transcription is iron dependent. In the Δ pvdS :: Gm mutant, the level of prpL transcription was iron independent and decreased relative to the level in PAO1. Furthermore, transcription of prpL was independent of PtxR, a PvdS-regulated protein. Finally, PrpL cleaves casein, lactoferrin, transferrin, elastin, and decorin and contributes to PAO1's ability to persist in a rat chronic pulmonary infection model.
Fuzzy Partitioning of a Real Power System for Dynamic Vulnerability Assessment (2009)

Recently, the authors proposed a clustering approach based on the fuzzy C-medoid algorithm (FCMdd), for segregating large power systems into coherent electric areas centered around a representative so-called medoid-bus. This bus was shown to be a natural location for PMU in the context of wide-area measurement system (WAMS) configuration for of dynamic vulnerability assessment (DVA). The method was demonstrated on two test systems. The goal of this companion paper is to extend the approach to an actual grid (Hydro-Quebec) with more realistic characteristics in terms of geography and system dynamics. We start by developing a formulation of the coherency matrix that is recursive in time to enable online grid partitioning. The FCMdd is then implemented and compared with other statistical learning techniques. It is observed that only FCMdd is able to provide an intuitively appealing 7-clusters solution for 429-bus system. It is further demonstrated that medoids-based system-wise indices can forecast the contingencies severity under varying network configurations and loadings.
Characterization by FTIR spectroscopy of the photoreduction of the primary quinone acceptor Q<sub>A</sub> in photosystem II (1990)

Molecular changes associated with the photoreduction of the primary quinone acceptor Qa of photosystem II have been characterized by Fourier transform infrared spectroscopy. This reaction was light-induced at room temperature on photosystem II membranes in the presence of hydroxylamine and diuron. A positive signal at 1478 cm-1 is assigned to the C---O stretching mode of the semiquinone anion, and can be correlated to the negative C=O mode(s) of the neutral QA at 1645 cm-1 and/or 16 cm-1. Analogies with bacterial reaction center are found in the amide I absorption range at 1672 cm-1, 1653 cm-1 and 1630 cm-1. The stabilization of QA- does not result from a large protein conformation change, but involves perturbations of several amino acid vibrations. At 1658 cm-1, a negative feature sensitive to 1H-2H exchange is tentatively assigned to a NH2 histidine mode, while tryptophan D2252 could contribute to the signal at 1560/1550 cm-1.
Green tea catechins decrease oxidative stress in surgical menopause‐induced overactive bladder in a rat model (2012)

Ovariectomy increased oxidative damage, enhanced voiding frequency and decreased bladder compliance. EGCG could restore ovariectomy-induced bladder dysfunction in a dose-dependent fashion through antioxidant, anti-fibrosis and anti-apoptosis effects.
Dictionary Based Secure Provenance Compression for Wireless Sensor Networks (2015)

Due to energy and bandwidth limitations of wireless sensor networks (WSNs), it is crucial that data provenance for these networks be as compact as possible. Even if lossy compression techniques are used for encoding provenance information, the size of the provenance increases with the number of nodes traversed by the network packets. To address such issues, we propose a dictionary based provenance scheme. In our approach, each sensor node in the network stores a packet path dictionary. With the support of this dictionary, a path index instead of the path itself is enclosed with each packet. Since the packet path index is a code word of a dictionary, its size is independent of the number of nodes present in the packet's path. Furthermore, as our scheme binds the packet and its provenance through an AM-FM sketch and uses a secure packet sequence number generation technique, it can defend against most of the known provenance attacks. Through simulation and experimental results, we show that our scheme outperforms other compact provenance schemes with respect to provenance size, robustness, and energy consumption.
Using a Rights-Based Approach to Avoid Harming Health Systems: A Case Study from Papua New Guinea (2013)

Using a Rights-Based Approach to Avoid Harming Health Systems: A Case Study from Papua New Guinea Carmel Williams, Carmel Williams cj.williams@auckland.ac.nz Search for other works by this author on: Oxford Academic Google Scholar Garry Brian Garry Brian Search for other works by this author on: Oxford Academic Google Scholar *Carmel Williams is a Research Fellow in the Centre for Development Studies, University of Auckland, New Zealand. She has worked in international health programme design and management in the Pacific for over 10 years. Garry Brian (grbrian@tpg.com.au) is associated with the Dunedin School of Medicine, University of Otago. He is a population health ophthalmologist with over 20 years' experience working with non-governmental international development organizations in Africa, Asia and the Pacific. Author Notes Journal of Human Rights Practice, Volume 5, Issue 1, March 2013, Pages 177–194, https://doi.org/10.1093/jhuman/hus030 Published: 05 February 2013
Storage characteristics of some vegetables and soft fruits (1975)

SUMMARY Rates of carbon dioxide production, in air and in 3 % 0 2 , over a range of temperatures, were measured for over thirty commodities, and rates of evaporation, under known water vapour pressure deficit, measured for most of them. Optimum storage conditions in air for each commodity were determined. Storage life under these optimum conditions, and under the nearest practical approximation to them, was estimated. In most cases the optimum temperature is o o C, examples of exceptions being runner beans, cucumbers, potatoes, green peppers and tomatoes. The humidity should usually be high, 100 % r.h. often being optimal, particularly for leafy vegetables, provided the temperature is low. Commodities resistant to evaporation, however, such as the onion, may with advantage be stored at lower humidities, thus reducing the microbial hazards.
Versatile Chiral Bidentate Ligands Derived from α-Amino Acids:  Synthetic Applications and Mechanistic Considerations in the Palladium-Mediated Asymmetric Allylic Substitutions (2000)

A new class of chiral amidine-phosphine hybrid ligands 7a,b, which are readily accessible from the corresponding alpha-amino acids, were developed. A versatility for construction of new ligands is desirable, by which a variety of reactions and substrates become applicable. Indeed, a variety of modifications, such as exchange reactions to other amino groups in the amidine skeleton and the production of other types of ligands, are possible using the precursor compounds of 7a. Thus, novel chiral ligands 7c,d, 8, 11, and 13, which provide sterically and electronically different chiral circumstances, were prepared and used for the palladium-mediated asymmetric allylic substitutions of both acyclic and cyclic compounds. In these reactions, high levels of asymmetric induction were achieved for both substrates. A marked advancement of reactivity and enantioselectivity in palladium-catalyzed asymmetric allylations of 1,3-diphenylpropen-2-yl pivalate 14a was attained by examination of electronic substituent effects in a new series of chiral P-N and S-N hybrid ligands 8 and 11. Mechanistic views concerning the enantiodiscriminating step were demonstrated, in which a good correlation between a novel Pr/Mr concept and the absolute configuration of allylation products are discussed for the prediction of enantioselecting direction. The use of ketene silyl acetals as nucleophiles was investigated and compared with the corresponding harder anionic carbon nucleophiles. The former nucleophiles afforded higher enantioselectivity in asymmetric allylic transformations of 14a.
Effect of L. helveticus fermented milk on bone strength in ovariectomized rats. (2009)

In the present study the possible effect of Lactobacillus helveticus-fermented milk on bone was studied in 8 month old SD ovariectomized rats.The ovariectomized rats,which develop an osteoporotic bone disorder with age,were randomized into 6 groups(n=8) receiving milk fermented with L.helveticus and,as reference drinks,water,skim milk,sour milk and L.helveticus fermented milk peptide extract,for 10 weeks.L.helveticus-fermented milk can significantly increases the load of bone and improves the ability of anti-fractured in the long-term feeding of ovariectomized rats.
Reconstitution of Apo-Glucose Dehydrogenase on Pyrroloquinoline Quinone-Functionalized Au Nanoparticles Yields an Electrically Contacted Biocatalyst (2005)

An electrically contacted glucose dehydrogenase (GDH) enzyme electrode is fabricated by the reconstitution of the apo-GDH on pyrroloquinoline quinone (PQQ)-functionalized Au nanoparticles (Au-NPs), 1.4 nm, associated with a Au electrode. The Au-NPs functionalized with a single amine group were attached to the Au surface by 1,4-benzenedithiol bridges, and PQQ was covalently linked to the Au-NPs. The apo-GDH was then reconstituted on the PQQ cofactor sites. The surface coverage of GDH corresponded to 1.4 x 10(-12) mol cm(-2). The reconstituted enzyme revealed direct electrical contact with the electrode surface, and the bioelectrocatalytic oxidation of glucose occurred with a turnover number of 11,800 s(-1). In contrast, a system that included the covalent attachment of GDH to the PQQ-Au-NPs monolayer in a random, nonaligned, configuration revealed lack of electrical communication between the enzyme and the electrode, albeit the enzyme existed in a bioactive structure. The bioelectrocatalytic function of the later system was, however, activated by the diffusional electron mediator 2,6-dichlorophenol-indophenol. The results imply that the alignment of GDH on a Au-NP through the reconstitution process leads to an electrically contacted enzyme-electrode, where the Au-NP acts as a charge-transfer mediator.
Studies on the fate of D-aspartic acid in pineal and pituitary glands of rats after intravenous administration. (1998)

The present study was intended to confirm the idea that D-aspartic acid (Asp) in pineal and pituitary glands could originate from diet as suggested by our previous report [Imai et al. (1997) Proc. Japan Acad. 73B, 48-52]. When the rats were kept under fasting for 2 or 3 days, the levels of D-Asp, but not L-Asp in these glands were significantly lower as compared with those in the rats with diet. The fact suggests that D-Asp in these glands is derived from the exogenous origin. Next, we determined the D- or L-Asp concentration in these glands (at 30min, 3hr and 24hr) and plasma (2min-5hr) following intravenous administration of D- or L-Asp (50mg/kg) into rats. D-Asp concentrations remarkably increased after administration of D-Asp, and the levels were almost constant from 30min to 24hr after administration, indicating that D-Asp was accumulated and deposited in these glands. In contrast, no accumulation of L-Asp was observed in case of L-Asp or D-Asp administration. In plasma, either D- or L-Asp concentration decreased to the normal level at 3hr after the administration of the respective enantiomers, although different half-lives for D- and L-Asp in plasma were obtained; 7.84min for D- and 3.75min for L-Asp. These results indicate that D-Asp incorporated from extracellular fluids into pineal and pituitary glands is difficult to be metabolized and eliminated, and strongly support the idea that the D-Asp in these glands in vivo is derived from the exogenous source, such as dietary D-Asp.
Reaction of Phosphines with 1-Azido-(2-halogenomethyl)benzene Giving Aminophosphonium-Substituted Indazoles (2020)

The reaction between a 1-azido-(2-halogenomethyl)benzene and a phosphine gives different products depending on the nature of the halogen, the phosphine itself, and the solvent employed. While PPh<sub>3</sub> (2 equiv) reacts with the chloro reagent in toluene to give the expected iminophosphorane-phosphonium adduct, trialkylphosphines (PCy<sub>3</sub> and PEt<sub>3</sub>) surprisingly furnish an aminophosphonium substituted by a zwitterionic indazole. The bicyclic product can also form from PPh<sub>3</sub> using the bromo reagent in acetonitrile. A mechanism is proposed for this cyclization based on DFT calculations.
Cotransport of sodium with glutamine, alanine and glucose in the isolated rabbit ileal mucosa. (1992)

To investigate the effect of substrates during oral rehydration therapy, we studied intestinal cation cotransport (ICC) with glutamine (Gln), alanine (Ala) and glucose (Glu). The specific aims were to determine the biological effects of these three different cotransport systems on intestinal function. Isolated rabbit ileal mucosa preparations mounted in Ussing chambers were studied. ICC was determined by measuring short-circuit current (Isc) and potential difference (PD) while monitoring tissue resistance (TR). The data are reported as the mean +/- SEM of 4-6 experiments for each amino acid concentration. Increasing concentrations of Gln (10(-5) to 10(-2) M), Ala (10(-5) to 10(-1) M) and Glu (10(-5) to 10(-2) M) caused a significant (P < 0.05) increase in ICC. Gln (30 mM) and Ala (0.1 M) had a maximal effect (Em(Gln) = 100% and Em(Ala) = 66%, P < 0.05) which was higher than that obtained with 30 mM Glu (Em(Glu) = 35%). When sodium was replaced with choline on the mucosal side, Ringer solution completely abolished the response with Gln, Ala and Glu. The presence of all three substrates (10(-2) M Gln, 10(-1) M Ala, and 10(-2) M Glu) in Ringer solution on the mucosal side caused a significant increase in ICC (delta increase of short circuit current = 111 +/- 43 microA, P < 0.05). These results demonstrate that Gln, Ala and Glu each increased sodium-dependent cation cotransport, and that sodium-dependent intestinal cation cotransport was higher with Gln than with Ala or Glu.
Assessment of vulnerabilities of web applications of Bangladesh: A case study of XSS & CSRF (2016)

In a sophisticated and coordinated cyber-attack $100 million has been stolen from Bangladesh's account. Attackers introduced malicious code remotely into the Bangladesh Bank's server, which allowed them to process and authorize the transactions. Advanced attack techniques poses threats to all web application systems. Cross Site Scripting (XSS) and Cross Site Request Forgery (CSRF) are two vulnerabilities which have techniques that are similar to those of the Bangladesh Bank heist. XSS and CSRF are third and eighth of the top ten web application vulnerabilities on OWASP list from 2013 till now. Both these attacks violate the users trust for the websites and web browsers. Because of the severity of these vulnerabilities, security specialists have always shared their concern and warned the web developers. Yet Bangladesh government's and developers' reluctance to address the severity of the attacks resulted in Bangladesh Bank heist. In this paper, we aim to study and conduct an investigation of the vulnerabilities of similar attacks as these of the Bangladesh Bank heist on web applications of Bangladesh. We would focus on XSS and CSRF vulnerabilities due to their high ranking on the OWASP list. We analyze the data collected during the investigation and provide a summary of the current state and a guideline for the future web developers.
Removal of Toxic Metal Ions from Metal-Finishing Wastewater by Solvent Extraction (1977)

Abstract Solvent extraction procedures are presented for the removal of chromium, cadmium, and zinc from metal-finishing wastewater. The procedures utilize a 25% Alamine 336-xylene solution as the extractant. The three metals can be extracted selectively or simultaneously using a 100 to 1 aqueous phase to organic phase ratio. All three metals can be stripped from the organic phase with better than 99.5% efficiency with 4 M NaOH. The regenerated reagent can be recycled and reused without any loss of extraction efficiency. The procedures are reproducible, rapid, and simple.
Emendation of the genus Acidomonas Urakami, Tamaoka, Suzuki and Komagata 1989 (2004)

The genus Acidomonas and the species Acidomonas methanolica were recharacterized by using the type strain (NRIC 0498 T ), three reference strains and 10 methanol-utilizing bacteria that were isolated from activated sludge from three different sewage-treatment plants in Tokyo. Based on 16S rDNA sequences, all strains formed a single cluster within the Acetobacteraceae that was clearly different from the genera Acetobacter , Gluconobacter , Gluconacetobacter , Asaia and Kozakia . The 14 strains were identified as a single species, Acidomonas methanolica , by DNA–DNA similarities, showed DNA G+C contents that ranged from 62 to 63 mol% and had Q-10 as the major quinone, accounting for >87 % of total ubiquinones. Cells of Acidomonas methanolica had a single polar flagellum (or occasionally polar tuft flagella); this differs from a previous study that described peritrichous flagella. Oxidation of acetate was positive for all strains, but oxidation of lactate was weakly positive and varied with strains. Dihydroxyacetone was not produced from glycerol. Pantothenic acid was an essential requirement for growth. The strains tested grew at mostly the same extent at pH 3·0–8·0. Therefore, Acidomonas methanolica should be regarded as acidotolerant, not acidophilic. The descriptions of the genus Acidomonas and the species Acidomonas methanolica Urakami, Tamaoka, Suzuki and Komagata 1989 are emended with newly obtained data.
Designer Crystals:  Single Crystals with Complex Morphologies (2007)

Biological systems are capable of remarkable control over crystal growth, producing morphologically complex single crystals with curved surfaces. We have previously demonstrated that crystals with identical morphological complexities can be produced synthetically using templating routes. This article provides a detailed investigation into the mechanism of this process, studying the relationship between the chemical environment provided by the template and the structure of the templated particles produced. A range of crystals were precipitated within the confines of macroporous polymer templates whose surface chemistries were varied by oxidation with an oxygen plasma, by modification with adsorbed polyelectrolytes, or by electroless deposition of a thin layer of gold and subsequent functionalization with ω-terminated self-assembled monolayers. The surface chemistry of the template was shown to play a crucial role in determining the structure of templated calcite particles, such that only non-charged surfaces directed the formation of single-crystal particles and polycrystalline particles being produced with negatively charged surfaces. Control of crystal morphologies is clearly fundamental to the development of many new functional materials and devices. This work therefore demonstrates how a templating methodology can provide a general and highly controllable route to synthesizing crystalline materials with defined morphologies and structures.
Improved Kalman filter damage detection approach based on <i>l</i> <sub> <i>p</i> </sub> regularization (2019)

The conventional extended Kalman filter (EKF) for detecting structural damage with measured responses is a dynamic inverse problem. With the increase in size of the extended state vector, EKF suffers from low accuracy and convergence difficulty due to the ill-condition of the inverse problem and increased computational error. To overcome the aforementioned drawbacks, an improved EKF method based on lp regularization (EKF-lp) is proposed in this paper. In the proposed method, the sparse characteristic on the distribution of local damage, as a priori information, is introduced into EKF by the lp regularization technique. Then, the unconstrained optimization problem of EKF becomes the optimization problem with the lp-norm constraint. To obtain a recursive solution of the constrained optimization, a pseudo-measurement equation is used to embed the lp-norm constraint into the recursive EKF steps. In addition, a precise integration method is employed in the time update step to improve the accuracy of state prediction. To select an appropriate p value in the EKF-lp method, a novel L-surface approach is proposed. Finally, the proposed EKF-lp method is compared with the existing EKF with Tikhonov regularization method and EKF with l1 regularization method on a beam example and an experiment of a three-story shear building. It is shown that the proposed method is stable and reliable, and its identification precision is higher than the other methods. Moreover, it requires significant less measurements than conventional methods.
Inductive Behavior of Superconducting Magnets (1963)

The inductive behavior of a closed system of superconductors is investigated with the purpose of attaining high magnetic fields. High-field superconductors do not exhibit the Meissner effect, and the inductive behavior of a system formed of these materials can be predicted fairly accurately from the conservation law of flux linkage which follows from the zero resistivity. Simple flux shielding or trapping is quantitatively analyzed for a tubular geometry. The flux concentration scheme is discussed for several practical configurations. In this scheme, a low field over a large volume (externally applied field) is compressed into a smaller volume to achieve the desired intensification in field strength. The energy of the external magnetic field can be utilized more effectively by flux pumping, but this requires intricate switching sequences.
Understanding Sentiment of People from News Articles: Temporal Sentiment Analysis of Social Events (2007)

Temporal sentiment analysis that analyzes temporal trends of sentiments and topics from a text archive that has timestamps is proposed. The method accepts texts with timestamp such as Weblog and news articles, and produces two kinds of graphs, i.e., (1) topic graph that shows temporal change of topics associated with a sentiment, and (2) sentiment graph that shows temporal change of sentiments associated with a topic. Sample results obtained by applying the method to news articles are described.