gebhart/patrepeval huggingface dataset:
The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles (2015)

The comprehensive genome mining study described herein has uncovered a myriad of unique TOMM biosynthetic clusters and provides an atlas to guide future discovery efforts. These biosynthetic gene clusters are predicted to produce diverse final products, and the identification of additional combinations of modification enzymes could expand the potential of combinatorial natural product biosynthesis.
Genes Related to Long Polar Fimbriae of Pathogenic <i>Escherichia coli</i> Strains as Reliable Markers To Identify Virulent Isolates (2009)

Lpf (stands for long polar fimbriae) is one of the few adhesive factors of enterohemorrhagic Escherichia coli O157:H7 associated with colonization of the intestine. E. coli O157:H7 strains possess two lpf loci encoding highly regulated fimbrial structures. Database analysis of the genes encoding the major fimbrial subunits demonstrated that they are present in commensal as well as pathogenic (both intestinal and extraintestinal) E. coli strains and in Salmonella strains and that the lpfA1 and lpfA2 genes are highly prevalent among LEE (locus of enterocyte effacement)-positive E. coli strains associated with severe and/or epidemic disease. Further DNA sequence analysis of the lpfA1 and lpfA2 genes from different attaching-and-effacing E. coli strains has led us to the identification of several polymorphisms and the classification of the major fimbrial subunits into distinct variants. Using collections of pathogenic E. coli isolates from Europe and Latin America, we demonstrated that the different lpfA types are associated with the presence of specific intimin (eae) adhesin variants and, most importantly, that they are found in specific E. coli pathotypes. Our results showed that the use of these fimbrial genes as markers, in combination with the different intimin types, resulted in a specific test for the identification of E. coli O157:H7, distinguishing it from other pathogenic E. coli strains.
Lysosomal membrane proteins: life between acid and neutral conditions (2010)

Whereas we have a profound understanding about the function and biogenesis of the protein constituents in the lumen of the lysosomal compartment, much less is known about the functions of proteins of the lysosomal membrane. Proteomic analyses of the lysosomal membrane suggest that, apart from the well-known lysosomal membrane proteins, additional and less abundant membrane proteins are present. The identification of disease-causing genes and the in-depth analysis of knockout mice leading to mutated or absent membrane proteins of the lysosomal membrane have demonstrated the essential role of these proteins in lysosomal acidification, transport of metabolites resulting from hydrolytic degradation and interaction and fusion with other cellular membrane systems. In addition, trafficking pathways of lysosomal membrane proteins are closely linked to the biogenesis of this compartment. This is exemplified by the recent finding that LIMP-2 (lysosomal integral membrane protein type-2) is responsible for the mannose 6-phosphate receptor-independent delivery of newly synthesized β-glucocerebrosidase to the lysosome. Similar to LIMP-2, which could also be linked to vesicular transport processes in certain polarized cell types, the major constituents of the lysosomal membrane, the glycoproteins LAMP (lysosome-associated membrane protein)-1 and LAMP-2 are essential for regulation of lysosomal motility and participating in control of membrane fusion events between autophagosomes or phagosomes with late endosomes/lysosomes. Our recent investigations into the role of these proteins have not only increased our understanding of the endolysosomal system, but also supported their major role in cell physiology and the development of different diseases.
Poly(Malic Acid) Part I— Preparation and Polymerization of Benzyl Malolactonate (1986)

The benzyl ester of the β-lactone of malic acid was synthesized from bromosuccinic acid and polymerized both in bulk and in solution by anionic and cationic initiators and by a heterogeneous catalyst. Anionic polymerization reactions yielded polymers with weight average molecular weights as high as 50,000 as determined by GPC, and with narrow molecular weight distributions. The benzyl ester polymers were readily converted to poly(malic acid) by hydrogenolysis without loss in molecular weight. Poly(malic acid) is being evaluated as a biodegradable, bioresorbable component in drug delivery systems, particularly as a non-toxic, slow release carrier for covalently bound drugs.
[Effects of nebivolol on microcirculation, platelet aggregation and blood viscosity in patients with essential hypertension]. (2002)

In patients with essential hypertension hypotensive action of nebivolol was associated with antiaggregation effect and improvement of blood flow in microvascular networks.
Gonadotropin-releasing Hormone Receptors with Intracellular Carboxyl-terminal Tails Undergo Acute Desensitization of Total Inositol Phosphate Production and Exhibit Accelerated Internalization Kinetics (1998)

The mammalian gonadotropin-releasing hormone receptor (GnRH-R) is the only G-protein-coupled receptor (GPCR) in which the intracellular C-terminal tail is completely absent. In contrast to other GPCRs, the GnRH-R does not show rapid desensitization of total inositol (IP) production, and the rates of internalization are exceptionally slow. We investigated whether the incorporation of a cytoplasmic tail into the C terminus of the GnRH-R affects desensitization events and receptor internalization rates. A GnRH-R/TRH-R chimera was created where the intracellular tail of the rat thyrotropin-releasing hormone receptor (TRH-R) was engineered into the C terminus of the rat GnRH-R. Three different rat GnRH-R cDNA stop codon mutations (one for each reading frame) were also made. The GnRH-stimulated IP production of the wild-type rat GnRH-R expressed in either COS-7 or HEK 293 cells did not desensitize even after prolonged stimulation with GnRH. In contrast, the catfish GnRH-R (which does possess an intracellular tail) and the TRH-R rapidly (<10 min) desensitized following agonist stimulation. The GnRH-R/TRH-R chimera also desensitized following treatment with GnRH, resembling the pattern shown by the TRH-R and the catfish GnRH-R. Two of the stop codon mutants did not show desensitization of IP production, and the third mutant with the longest tail was not functional. Internalization experiments showed that the rat GnRH-R had the slowest endocytosis and recycling rates compared with the TRH-R, the catfish GnRH-R, and the chimeric GnRH/TRH-R. This study demonstrates that the addition of a functional intracellular C-terminal tail to the GnRH-R produces rapid desensitization of IP production and significantly increases internalization rates.
Effects of the chirality and functionality of monomers on the holographic gratings formed in photosensitive films (2003)

Abstract Photosensitive holographic polymer films were fabricated. Instead of liquid crystals, a nonreactive high‐refractive‐index diphenyl sulfide was mixed with several monomers and an initiator for the preparation of the holographic grating films. To investigate the formation of periodic arrays of the photosensitive refractive‐index modulation films and the effects of the chirality and functionality of monomers on the diffraction efficiency, chiral monomeric (−)‐bornyl acrylate, (+)‐bornyl acrylate, and the racemate (±)‐bornyl acrylate were synthesized and copolymerized with various multifunctional monomers. A reasonable schematic of the photosensitive polymerization mechanism was proposed. The effects of the multifunctional monomers, initiator concentrations, and feed monomer concentrations on the diffraction efficiencies were investigated. The morphologies of the polymer matrices were studied with scanning electron microscopy. Pictures of real light diffraction patterns with 15 grating points were obtained. In comparison with those described in the literature, the diffraction efficiency obtained in this investigation was relatively high. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 2246–2254, 2003
Practical performance of planar spiral inductors (2005)

Inductors are essential elements for RF design. For RFIC design, bondwires, planar solenoidal and planar spiral inductors are available. Due to some limitations of bondwires and planar solenoidal inductors, planar spiral inductors are the most popular ones. Designers try to get accurate lumped element models for planar spiral inductors in order to be able to simulate the circuit performance correctly before the integrated circuit is manufactured. Planar spiral inductor measurement methods are discussed, and the comparison between lumped element model simulation results and experimental measurement results are given. The results of this study show that it is possible to model planar spiral inductors with lumped element circuit models, parameters of which can be calculated by basic, but accurate, expressions.
The Role of Learning in Dynamic Portfolio Decisions (1998)

Abstract This paper analyzes the effect of uncertainty about the mean return on the risky asset on the portfolio decisions of an investor who has a long investment horizon. Building on the earlier work of Detemple (1986), Dothan and Feldman (1986), and Gennotte (1986), it is shown that the possibility of future learning about the mean return on the risky asset induces the investor to take a larger or smaller position in the risky asset than she would if there were no learning, the direction of the effect depending on whether the investor is more or less risk tolerant than the logarithmic investor whose portfolio decisions are unaffected by the possibility of future learning. Numerical calculations show that uncertainty about the mean return on the market portfolio has a significant effect on the portfolio decision of an investor with a 20 year horizon if her assessment of the market risk premium is based solely on the Ibbotson and Sinquefield (1995) data.
Heralding single photons without spectral factorability (2010)

Recent efforts to produce single photons via heralding have relied on creating spectrally factorable two-photon states in order to achieve both high purity and high production rate. Through a careful multimode analysis, we find, however, that spectral factorability is not necessary. Utilizing single-mode detection, a similar or better performance can be achieved with nonfactorable states. This conclusion rides on the fact that even when using a broadband filter, a single-mode measurement can still be realized, as long as the coherence time of the triggering photons exceeds the measurement window of the on-off detector.
Development of an Internal Control for Evaluation and Standardization of a Quantitative PCR Assay for Detection of <i>Helicobacter pylori</i> in Drinking Water (2007)

Due to metabolic and morphological changes that can prevent Helicobacter pylori cells in water from growing on conventional media, an H. pylori-specific TaqMan quantitative PCR (qPCR) assay was developed that uses a 6-carboxyfluorescein-labeled probe (A. E. McDaniels, L. Wymer, C. Rankin, and R. Haugland, Water Res. 39:4808-4816, 2005). However, proper internal controls are needed to provide an accurate estimate of low numbers of H. pylori in drinking water. In this study, the 135-bp amplicon described by McDaniels et al. was modified at the probe binding region, using PCR mutagenesis. The fragment was incorporated into a single-copy plasmid to serve as a PCR-positive control and cloned into Escherichia coli to serve as a matrix spike. It was shown to have a detection limit of five copies, using a VIC dye-labeled probe. A DNA extraction kit was optimized that allowed sampling of an entire liter of water. Water samples spiked with the recombinant E. coli cells were shown to behave like H. pylori cells in the qPCR assay. The recombinant E. coli cells were optimized to be used at 10 cells/liter of water, where they were shown not to compete with 5 to 3,000 cells of H. pylori in a duplex qPCR assay. Four treated drinking water samples spiked with H. pylori (100 cells) demonstrated similar cycle threshold values if the chlorine disinfectant was first neutralized by sodium thiosulfate.
Voluntary female sterilization: number one and growing. (1990)

Around 16% of all married women of reproductive age (MWRA) in the world have voluntarily undergone female sterilization which equals about 138 million women (123 million in developing countries). Moreover it has increased 45% since 1984. Researchers estimate that the number of women wishing to be sterilized in developing countries will increase an additional 67 million by 2000. Thus female sterilization is the leading family planning (FP) method in the world. Indeed it leads the list of FP methods used in at least 20 countries. It is also 1 of the fastest growing methods. Expanding safe efficient and convenient services especially in developing countries is the major reason it is the fastest growing method. In Kenya for example female sterilization grew rapidly from about 68 women in 1982 to >11000 women in 1990. IN 1982 physicians at only 2 hospitals in Kenya performed female sterilization but by 1990 health providers performed them at least 50 sites (not including providers in private practice). Of developed countries female sterilization is most prevalent (23% of MWRA) and growing the fastest in the US. A challenge for FP programs is to continue providing safe high quality services to all women wanting to undergo female sterilization. They must also assure voluntarism and informed choice. FP programs should use all channels of communication especially the mass media to clearly and accurately inform the public females sterilization. They should also have well trained staff who can counsel clients objectively and empathetically. Health practitioners should minimize risks by using local anesthesia. They should also be able to perform sterilization in as many places possible for as many women possible thus making sterilization accessible to all women who want it. Finally health professionals must undergo special training and be monitored and supervised frequently.
Breast-cancer risk following long-term oestrogen- and oestrogen-progestin-replacement therapy (1999)

While use of hormone-replacement therapy (HRT) effectively alleviates menopausal symptoms and prevents osteoporosis and possibly cardiovascular disease, there is concern of a detrimental impact on breast-cancer risk. There is a particular lack of data regarding the effect of long-term use of oestrogen-progestin combinations on breast-cancer risk. We conducted a large epidemiological study in Sweden, where combined oestrogen-progestin treatment has been predominant, to examine the influence of different regimens of menopausal hormone therapy on breast-cancer risk. In this population-based case-control study, 3,345 women aged 50 to 74 years with invasive breast cancer (84% of all eligible) and 3,454 controls of similar age (82% of all selected) were included. Mailed questionnaires and telephone interviews were used to collect detailed information on use of hormone replacement and on potential confounding factors. Odds ratios (OR) and 95% confidence intervals (CI) were estimated through multiple logistic regression. There was a trend of increasing breast-cancer risk with duration of oestrogen/oestrogen-progestin use (OR for women treated at least 10 years, 2.43; 95% CI, 1.79-3.30, as compared to never-users), with statistically significant estimates only for women with BMI<27 kg/m2. Excess risks were observed to current use and use that ceased more than 10 years ago (OR for women treated at least 5 years, OR was 2.68, 95% CI, 2.09-3.42, and OR 2.57, 95% CI, 1.28-5.15, as compared with never-users, respectively). A positive association which was noted for use of oestrogen combined with testosterone-derived progestins appeared especially pronounced with continuously combined regimens. Long-term use of replacement oestrogens with or without progestins may substantially increase the incidence of post-menopausal breast cancer, particularly among non-obese women.
Phenotypically and functionally distinct subsets of natural killer cells in human PBMCs (2007)

Human natural killer (NK) cells are one major component of lymphocytes that mediate early protection against viruses and tumor cells, and play an important role in immune regulatory functions. In this study, we demonstrated that human NK cells could be divided into four subsets, CD56hi CD16(-), CD56lo CD16(-), CD56+CD16+ and CD56(-)CD16+, based on the expression of cell surface CD56 and CD16 molecules. Phenotypic analysis of NK cell subsets indicated that the expression of activation markers, adhesion molecules, memory cell markers, inhibitory and activating receptors, and intracellular proteins (granzyme B and perforin) were heterogeneous. Following interleukin (IL)-2 stimulation, interferon-gamma was preferentially produced by CD56+CD16(-) NK cells and this subset showed more proliferative capacity. The cytolytic activity of both CD56+CD16(-) and CD56+/-CD16+ subsets could be augmented in response to IL-2. The data provided a new definition for NK cell subsets demonstrating their phenotypic and functional diversity and possible stage of NK cell differentiation in peripheral blood.
Novel Graphene-Like Electrodes for Capacitive Deionization (2010)

Capacitive deionization (CDI) is a novel technology that has been developed for removal of charged ionic species from salty water, such as salt ions. The basic concept of CDI, as well as electrosorption, is to force charged ions toward oppositely polarized electrodes through imposing a direct electric field to form a strong electrical double layer and hold the ions. Once the electric field disappears, the ions are instantly released back to the bulk solution. CDI is an alternative low-energy consumption desalination technology. Graphene-like nanoﬂakes (GNFs) with relatively high specific surface area have been prepared and used as electrodes for capacitive deionization. The GNFs were synthesized by a modified Hummers' method using hydrazine for reduction. They were characterized by atomic force microscopy, N2 adsorption at 77 K and electrochemical workstation. It was found that the ratio of nitric acid and sulfuric acid plays a vital role in determining the specific surface area of GNFs. Its electrosorption performance was much better than commercial activated carbon (AC), suggesting a great potential in capacitive deionisation application. Further, the electrosorptive performance of GNFs electrodes with different bias potentials, flow rates and ionic strengths were measured and the electrosorption isotherm and kinetics were investigated. The results showed that GNFs prepared by this process had the specific surface area of 222.01 m²/g. The specific electrosorptive capacity of the GNFs was 23.18 µmol/g for sodium ions (Na+) when the initial concentration was at 25 mg/L, which was higher than that of previously reported data using graphene and AC under the same experimental condition. In addition, the equilibrium electrosorption capacity was determined as 73.47 µmol/g at 2.0 V by fitting data through the Langmuir isotherm, and the rate constant was found to be 1.01 min⁻¹ by fitting data through pseudo first-order adsorption. The results suggested that the chemically synthesized GNFs can be used as effective electrode materials in CDI process for brackish water desalination.
Bistable wind-induced vibration energy harvester for self-powered wireless sensors in smart bridge monitoring systems (2019)

Low reliability and high maintenance cost of using power and data cables are two main reasons motivating the application of the self-powered wireless sensors for structural health monitoring (SHM) systems in bridge structures. On the other hand, energy harvesting systems have been introduced as a solution for the current limitations of the batterypowered wireless sensors associated with the finite life-span of batteries and their replacements. The objective in this paper is to propose a new optimized nonlinear energy harvesting concept, namely Bistable Energy Harvesting (BEH) system, for smart SHM of bridge structures. In this study, a dynamic analysis of the energy harvesting system for cablesupported bridges subject to wind-induced vibration is carried out and the feasibility of the energy harvesting device is investigated. This paper presents efficient linear and nonlinear energy harvesting systems for wireless monitoring of long-span cable-supported bridges. It is shown that level of the extracted energy from such energy harvesting system is quite sufficient to supply energy for self-powered sensors of a bridge health monitoring system. This study is to promote the recent line of research on self-powered sensor networks for smart bridge monitoring being performed at the Florida International University.
Characterizations of Aircraft Icing Environments that Include Supercooled Large Drops (2001)

Measurements of aircraft icing environments that include supercooled large drops (SLD) greater than 50 μm in diameter have been made during 38 research flights. These flights were conducted during the First and Third Canadian Freezing Drizzle Experiments. A primary objective of each project was the collection of in situ microphysics data in order to characterize aircraft icing environments associated with SLD. In total there were 2793 30-s averages obtained in clouds with temperatures less than or equal to 0°C, maximum droplet sizes greater than or equal to 50 μm, and ice crystal concentrations less than 1 L−1. The data include measurements from 12 distinct environments in which SLD were formed through melting of ice crystals followed by supercooling in a lower cold layer and from 27 distinct environments in which SLD were formed through a condensation and collision–coalescence process. The majority of the data were collected at temperatures between 0° and −14°C, in stratiform winter clouds associated with warm-frontal or low pressure regions. For in-cloud measurements with temperatures less than or equal to 0°C, the relative fraction of liquid-, mixed-, and glaciated-phase conditions were 0.4, 0.4, and 0.2, respectively. For each 30-s (3 km) measurement, integrated drop spectra that spanned 1–3000 μm were determined using measurements from forward-scattering spectrometer probes and 2D-C and 2D-P probes. The integrated liquid water content (LWC) for each drop spectrum was compared with the LWC measured with a Nevzorov total water content probe and a Rosemount icing detector. The agreement was within the errors expected for such comparisons. This provides confidence in the droplet spectra measurements, particularly in the assessment of extreme conditions. The 99.9th-percentile LWC value was 0.7 g m−3, and the 99th-percentile LWC for drops greater than 50 μm in diameter was 0.2 g m−3. The 99.5th-percentile values of LWC and droplet concentrations are determined for different horizontal length scales and droplet diameter intervals, and are used to characterize the extreme icing conditions observed. The largest median volume diameters (MVD) observed were approximately 1000 μm and represent cases in which the aircraft was flown below cloud base in freezing-rain conditions. In one case, SLD was observed to form at −21°C, and the associated icing was rated as severe. Approximately 3% of the data for which SLD were observed had LWC greater than 0.2 g m−3 and MVD greater than 30 μm. Such conditions are believed to represent conditions that have the largest potential effects on aircraft performance. The analysis is presented in a format that is suitable for several applications within the aviation community, and comparisons are made to four common icing-envelope formulations. The data should be beneficial to regulatory authorities who are currently attempting to assess certification requirements for aircraft that are expected to encounter freezing-precipitation conditions.