gebhart/patrepeval huggingface dataset:
Genome Sequence of a Nephritogenic and Highly Transformable M49 Strain ofStreptococcus pyogenes (2008)

The 1,815,783-bp genome of a serotype M49 strain of Streptococcus pyogenes (group A streptococcus [GAS]), strain NZ131, has been determined. This GAS strain (FCT type 3; emm pattern E), originally isolated from a case of acute post-streptococcal glomerulonephritis, is unusually competent for electrotransformation and has been used extensively as a model organism for both basic genetic and pathogenesis investigations. As with the previously sequenced S. pyogenes genomes, three unique prophages are a major source of genetic diversity. Two clustered regularly interspaced short palindromic repeat (CRISPR) regions were present in the genome, providing genetic information on previous prophage encounters. A unique cluster of genes was found in the pathogenicity island-like emm region that included a novel Nudix hydrolase, and, further, this cluster appears to be specific for serotype M49 and M82 strains. Nudix hydrolases eliminate potentially hazardous materials or prevent the unbalanced accumulation of normal metabolites; in bacteria, these enzymes may play a role in host cell invasion. Since M49 S. pyogenes strains have been known to be associated with skin infections, the Nudix hydrolase and its associated genes may have a role in facilitating survival in an environment that is more variable and unpredictable than the uniform warmth and moisture of the throat. The genome of NZ131 continues to shed light upon the evolutionary history of this human pathogen. Apparent horizontal transfer of genetic material has led to the existence of highly variable virulence-associated regions that are marked by multiple rearrangements and genetic diversification while other regions, even those associated with virulence, vary little between genomes. The genome regions that encode surface gene products that will interact with host targets or aid in immune avoidance are the ones that display the most sequence diversity. Thus, while natural selection favors stability in much of the genome, it favors diversity in these regions.
Removal of Cu and Ni by free and immobilized microalgae. (1992)

The present investigation evaluated the effectiveness of Chlorella cells in concentrating Cu and Ni in their cells and thereby removing the two metals from solution. The removal efficiency of the two metals by free and immobilized algal cells were further studied. (1) Four types of Chlorella cells, namely Chlorella pyrenoidosa (26) (from Carolina Biological Supplies Company), Chlorella HKBC-1 and-2 (isolated from a polluted stream receiving wastewater from several electroplating factories) and Chlorella HKBC-3 (from a clean water pond) were subjected to different concentrations of Cu and Ni accordingly. It was revealed that Chlorella HKBC-1 was the most tolerant species to Cu and Ni as reflected by their highest values of 48 h and 96 h "Highest no effect concentrations" (The highest concentration of the tested substance that does not inhibit the growth rate of the alga: Cu 2 and Ni 10 mg/l at 48 h, Cu 2 and Ni 5 at 96 h). This was followed by C. pyrenoidosa (26) and then C. HKBC-2 while C. HKBC-3 had the lowest tolerance to the two metals (Cu 0.5 and Ni 2 at 48 h; Cu 0.5 and Ni 1 mg/l at 96 h). (2) It was further revealed that C. HKBC-1 had higher concentration factors and removal efficiencies of Ni (734-963 mg/l, 16.3-18.7%) and C. HKBC-2 had higher concentration factors and removal efficiencies of Cu (2316-2839 mg/l, 53.7-66%) when exposed to lower concentrations of Cu (0.5, 1 and 2 mg/l) and Ni (5, 10 and 13 mg/l). (3) By treating the free and immobilized algal cells (algal cells entrapped in alginate beads) with different concentrations of Cu and Ni, it was observed that free cells had higher concentration factors and removal efficiencies when compared with immobilized cells (free cells: Cu 1577-3056 mg/l, 24.2-71.4%; Ni 355-849 mg/l, 4.8-18.7%; immobilized cells: Cu 453-935 mg/l, 13.9-53.2%; Ni 244-486 mg/l, 3.2-11.9%).
Hemoglobin regulates the migration of glioma cells along poly(ε‐caprolactone)‐aligned nanofibers (2014)

Aligned fibers have been shown to facilitate cell migration in the direction of fiber alignment while oxygen (O2 )-carrying solutions improve the metabolism of cells in hypoxic culture. Therefore, U251 aggregate migration on poly(ε-caprolactone) (PCL)-aligned fibers was studied in cell culture media supplemented with the O2 storage and transport protein hemoglobin (Hb) obtained from bovine, earthworm and human sources at concentrations ranging from 0 to 5 g/L within a cell culture incubator exposed to O2 tensions ranging from 1 to 19% O2 . Individual cell migration was quantified using a wound healing assay. In addition, U251 cell aggregates were developed and aggregate dispersion/cell migration quantified on PCL-aligned fibers. The results of this work show that the presence of bovine or earthworm Hb improved individual cell viability at 1% O2 , while human Hb adversely affected cell viability at increasing Hb concentrations and decreasing O2 levels. The control data suggests that decreasing the O2 tension in the incubator from 5 to 1% O2 decreased aggregate dispersion on the PCL-aligned fibers. However, the addition of bovine Hb at 5% O2 significantly improved aggregate dispersion. At 19% O2 , Hb did not impact aggregate dispersion. Also at 1% O2 , aggregate dispersion appeared to increase in the presence of earthworm Hb, but only at the latter time points. Taken together, these results show that Hb-based O2 carriers can be utilized to improve O2 availability and the migration of glioma spheroids on nanofibers.
Gender in transition (2002)

The objective of this report is to help put gender on the map of policymaking in the region formed by the transition countries of Europe and Central Asia by raising awareness of the gender implications of the social and economic changes experienced by these countries during the 1990s. The report draws on existing and new empirical evidence from administrative and survey data to evaluate the gender consequences of developments in key areas that affect people's livelihoods and welfare--labor markets, nonlabor income and poverty, education, life expectancy and health, and non-income dimensions of vulnerabiity. It shows that the transition process has not been gender neutral. However, the ways in which reforms have affected men, women, and gender relations have varied considerably across countries. While women's welfare appears to have declined relative to men's in Central Asia, the burden of transformation has fallen disproportionately on men in the European countries in the former Soviet Union. The Central and Eastern European countries (CEE) present a more mixed picture, with no obvious patterns in gender inequality emerging over the last decade.
Localization of the cellular‐fibronectin‐specific epitope recognized by the monoclonal antibody IST‐9 using fusion proteins expressed in E. coli (1987)

Here we report on a monoclonal antibody (IST-9) which distinguishes between human cellular and plasma fibronectin. Using beta-galactosidase-fibronectin fusion proteins expressed in E. coli we have demonstrated that this monoclonal antibody is specific for a fibronectin segment (ED) which can be included or omitted from the molecule depending on the pattern of splicing of the mRNA precursors. Furthermore, using the same fusion proteins we have been able to localize precisely the epitopes of two other monoclonal antibodies (IST-1 and IST-2), specific for the heparin-binding domain 5 of fibronectin.
Molecular cloning, sequencing, chromosomal localization and expression of mouse p21 (Waf1). (1994)

The recent discovery that expression of Waf1 (p21), an inhibitor of cyclin-dependent kinases, is induced by the tumor suppressor p53 provides an important linkage between growth suppression and the cell cycle. We report here the cloning and sequencing of a mouse p21 cDNA that contains the entire coding region. Hybridization of the mouse p21 probe in Southern blot analyses confirms that p21 is a single-copy gene and that the corresponding locus, Waf1, lies proximal to H-2 on mouse chromosome 17. In northern analyses, the expression of p21 is found in most normal mouse tissues, but a surprising lack of correlation is found between mRNA levels of p21 and p53. In order to determine which regions of p21 are most evolutionarily conserved, we have compared the cDNA sequences for the entire p21 coding region in 13 different mouse strains or species and the human p21 sequence. We conclude that two regions (corresponding to human codons 21-60 and 130-164) are strongly conserved in p21 and that these regions may represent domains that are especially critical to a functional p21 protein.
Local work function analysis of Pt/TiO2photocatalyst by a Kelvin probe force microscope (2007)

Nanometre-sized Pt clusters were prepared on a TiO2(110)-(1 × 1) surface, and the lateral distribution of work function was examined by using a Kelvin probe force microscope. Local work function on the Pt clusters was smaller than that on the surrounding TiO2 surface. Assuming that the dipole moments which perturb the work function are produced by uneven electron distribution, the decrease of the work function indicates electron transfer from the clusters to the TiO2 surface. After decomposition of pivalate anions on the surfaces by UV irradiation, the work function increased on some Pt clusters. It is known that holes photoexcited in TiO2 attach to pivalate anions to cause a decomposition reaction. Hence the increase of the observed work function by UV irradiation can be ascribed to the trapping of the accompanying electrons to the Pt clusters.
Virtual Exploration of Underwater Archaeological Sites: Visualization and Interaction in Mixed Reality Environments (2008)

This paper describes the ongoing developments in Photogrammetry and Mixed Reality for the Venus European project (Virtual ExploratioN of Underwater Sites, http://www.venus-project.eu). The main goal of the project is to provide archaeologists and the general public with virtual and augmented reality tools for exploring and studying deep underwater archaeological sites out of reach of divers. These sites have to be reconstructed in terms of environment (seabed) and content (artifacts) by performing bathymetric and photogrammetric surveys on the real site and matching points between geolocalized pictures. The base idea behind using Mixed Reality techniques is to offer archaeologists and general public new insights on the reconstructed archaeological sites allowing archaeologists to study directly from within the virtual site and allowing the general public to immersively explore a realistic reconstruction of the sites. Both activities are based on the same VR engine but drastically differ in the way they present information. General public activities emphasize the visually and auditory realistic aspect of the reconstruction while archaeologists activities emphasize functional aspects focused on the cargo study rather than realism which leads to the development of two parallel VR demonstrators. This paper will focus on several key points developed for the reconstruction process as well as both VR demonstrators (archaeological and general public) issues. The first developed key point concerns the densification of seabed points obtained through photogrammetry in order to obtain high quality terrain reproduction. The second point concerns the development of the Virtual and Augmented Reality (VR/AR) demonstrators for archaeologists designed to exploit the results of the photogrammetric reconstruction. And the third point concerns the development of the VR demonstrator for general public aimed at creating awareness of both the artifacts that were found and of the process with which they were discovered by recreating the dive process from ship to seabed.
SPT Genes: Key Players in the Regulation of Transcription, Chromatin Structure and Other Cellular Processes (2001)

Suppressor of Ty (SPT) genes were originally identified through a genetic screen for mutations in the yeast Saccharomyces cerevisiae that restore gene expression disrupted by the insertion of the transposon Ty. Classic members of the SPT gene family, SPT11, SPT12, and SPT15, encode for the histones H2A and H2B, and for TATA-binding protein (TBP), respectively. Over the past few years, molecular complexes and cellular functions in which other SPT gene products involve have been discovered through genetic and biochemical studies in yeast and several other organisms: Key regulators of transcription and chromatin structure, such as DSIF, SAGA, and FACT, all contain SPT gene products as essential subunits. In addition, accumulating evidence suggests that SPT gene products play more diverse roles, including roles in DNA replication, DNA recombination and developmental regulation. Here we review the current understanding of the functions and roles of the SPT genes, with special emphasis on the role of SPT5 in transcript elongation and in neuronal development in vertebrates.
Frequency tracking in acoustic trapping for improved performance stability and system surveillance (2013)

This work proposes and demonstrates an acoustic trapping system where the trapping frequency is automatically determined and can be used to analyse changes in the acoustic trap. Critical for the functionality of this system is the use of a kerfed transducer that removes spurious resonances. This makes it possible to determine the optimal trapping frequency by analysing electrical impedance. It is demonstrated that the novel combination of a kerfed transducer and acoustic trapping in glass capillaries creates a high Q-value resonator. This narrows the frequency bandwidth but allows excellent performance, as confirmed by a ten-fold increase in the flow retention speed when compared to previously reported values. Importantly, the use of automatic frequency tracking allows the use of such a narrow bandwidth resonator without compromising system stability. As changes in temperature, buffer-properties, and the amount of captured particles will affect the properties of the acoustic resonator, corresponding changes in resonance frequency will occur. It is shown that such frequency changes can be accurately tracked using the setup. Therefore, monitoring the frequency over time adds a new feature to acoustic trapping, where experimental progress can be monitored and the amount of trapped material can be quantified.
Effects of Low‐Dose Morphine on Gastric Emptying in Healthy Volunteers (1998)

Appropriate preoperative pain therapy for patients undergoing surgery may be withheld due to the fear that opioids will inhibit gastric emptying and increase the risk of aspiration. Previously, doses of 5 to 10 mg of morphine have been shown to delay gastric emptying time. However, the effect of lower doses of morphine on gastric emptying in humans has not been reported. In this study, the effects of intravenous morphine 0.05 mg/kg-3.5 mg for 70-kg body weight, a dose that can cause analgesia--on gastric emptying were evaluated in a double-blind, randomized, placebo-controlled study in 15 healthy human volunteers using the acetaminophen test. Our data indicated that this low dose of morphine significantly prolonged the gastric emptying time. Thus, even small doses of morphine inhibit gastric emptying. This effect may be important in patients undergoing surgery, in patients receiving other oral medications after surgery in ambulatory settings, and in instances of patient-controlled analgesia.
Highly selective isolation of human DNAs from rodent–human hybrid cells as circular yeast artificial chromosomes by transformation-associated recombination cloning (1996)

Transformation-associated recombination (TAR) can be exploited in yeast to clone human DNAs. TAR cloning was previously accomplished using one or two telomere-containing vectors with a common human repeat(s) that could recombine with human DNA during transformation to generate yeast artificial chromosomes (YACs). On basis of the proposal that broken DNA ends are more recombinogenic than internal sequences, we have investigated if TAR cloning could be applied to the generation of circular YACs by using a single centromere vector containing various human repeats at opposite ends. Transformation with these vectors along with human DNA led to the efficient isolation of circular YACs with a mean size of approximately 150 kb. The circular YACs are stable and they can be easily separated from yeast chromosomes or moved into bacterial cells if the TAR vector contains an Escherichia coli F-factor cassette. More importantly, circular TAR cloning enabled the selective isolation of human DNAs from monochromosomal human-rodent hybrid cell lines. Although < 2% of the DNA in the hybrid cells was human, as much as 80% of transformants had human DNA YACs when a TAR cloning vector contained Alu repeats. The level of enrichment of human DNA was nearly 3000-fold. A comparable level of enrichment was demonstrated with DNA isolated from a radiation hybrid cell line containing only 5 Mb of human DNA. A high selectivity of human DNA cloning was also observed for linear TAR cloning with two telomere vectors. No human-rodent chimeras were detected among YACs generated by TAR cloning. The results with a circular TAR cloning vector or two vectors differed from results with a single-telomere vector in that the latter often resulted in a series of terminal deletions in linear YACs. This could provide a means for physical mapping of cloned material.
Inhibition of NF-κB-Dependent T Cell Activation Abrogates Acute Allograft Rejection (2001)

Using a heterotopic model of transplantation, we investigated the role of T cell activation in vivo during allograft rejection in I-kappaB(DeltaN)-transgenic mice that express a transdominant inhibitor of NF-kappaB in T cells. Our results show indefinite prolongation of graft survival in the I-kappaB(DeltaN)-transgenic recipients. Interestingly, at the time of rejection of grafts in wild-type recipients, histology of grafts in the I-kappaB(DeltaN)-transgenic recipients showed moderate rejection; nevertheless, grafts in the I-kappaB(DeltaN) recipients survived >100 days. Analysis of acute phase cytokines, chemokine, chemokine receptors, and immune responses shows that the blockade of NF-kappaB activation in T cells inhibits up-regulation of many of these parameters. Interestingly, our data also suggest that the T cell component of the immune response exerted positive feedback regulation on the expression of multiple chemokines that are produced predominantly by non-T cells. In conclusion, our studies indicate NF-kappaB activation in T cells is necessary for acute allograft rejection.
Formulation of solid dispersion of rebamipide evaluated in a rat model for improved bioavailability and efficacy (2011)

A solid dispersion of rebamipide was successfully formulated using the spray-drying method. Bioavailability and efficacy of rebamipide were increased significantly by solubility enhancement of the drug.
Positioning tolerances for phase plates compensating aberrations of the human eye (2000)

The positioning tolerances for phase plates used to compensate human eye aberrations are analyzed. Lateral displacements, in-plane rotations, and axial translations are considered, describing analytic and numerical procedures to compute the maximum degree of compensation achievable in each case. The compensation loss is found to be dependent both on the kind and the amount of misalignment and on the particular composition of the aberration pattern of each subject in terms of Zernike polynomials. We applied these procedures to a set of human eye aberrations measured with the laser ray-tracing method. The general trend of results suggests that lateral positioning, followed by angular positioning, are the key factors affecting compensation performance in practical setups, whereas axial positioning has far less stringent requirements.
Dialogue between skin microbiota and immunity (2014)

Human skin, the body's largest organ, functions as a physical barrier to bar the entry of foreign pathogens, while concomitantly providing a home to myriad commensals. Over a human's life span, keratinized skin cells, immune cells, and microbes all interact to integrate the processes of maintaining skin's physical and immune barrier under homeostatic healthy conditions and also under multiple stresses, such as wounding or infection. In this Review, we explore the intricate interactions of microbes and immune cells on the skin surface and within associated appendages to regulate this orchestrated maturation in the context of both host physiological changes and environmental challenges.
Comparison of potato varieties between seasons and their potential for acrylamide formation (2007)

Abstract BACKGROUND: Acrylamide is a probable human carcinogen produced during food preparation, including frying of potato products. The aim of this study was to investigate the impact of seasonal variation on tuber composition and its acrylamide generation potential. RESULTS: The chemical composition of potato varieties used respectively for French fry (Bintje and Ramos) and crisp (Lady Rosetta and Saturna) production was studied throughout a storage period of 9 months during two growing seasons (2003 and 2004), in addition to their acrylamide generation potential during preparation of French fries. A significant impact of variable climatological conditions on the reducing sugar, dry matter, total free amino acid and free asparagine contents of tubers was observed. Exceptionally warm summers gave rise to a lower reducing sugar content (expressed on a dry matter basis) and thus a lower susceptibility to acrylamide generation during frying. CONCLUSION: It cannot be excluded that potato growers and the potato‐processing industry are confronted with some harvests that are more prone to acrylamide generation than others owing to climatological variability, thus confirming the importance of a multifactorial approach to mitigate acrylamide generation in potato products. Copyright © 2007 Society of Chemical Industry
Temperature-Sensitive Mutant of Escherichia coli K-12 with an Impaired d -Alanine: d -Alanine Ligase (1973)

The temperature-sensitive Escherichia coli mutant strain ST-640 lyses at the restrictive temperature except when an osmotic stabilizer or a high concentration of d-alanine is present. The presence of dl-alanyl-dl-alanine does not prevent lysis. The rate of murein synthesis, followed in a wall medium, is decreased at both 30 and 42 C. d-Alanyl-d-alanine and uridine diphosphate-N-acetyl-muramyl (UDP-MurNAc)-pentapeptide are synthesized in decreased amounts, accompanied by accumulation of UDP-MurNAc-tripeptide at 42 C but not at 30 C. Uridine nucleotide precursors leak into the medium, especially out of the mutant cells. This leakage is prevented when NaCl is present. The d-alanine: d-alanine ligase (ADP) (EC 6.3.2.4) of the mutant strain, assayed in crude extracts, is temperature sensitive. The impaired ligase is relatively resistant to d-cycloserine and other inhibitors of the enzyme. Combined genetic and enzymatic results show that the low ligase activity is due to a mutation in the ddl gene, the structural gene for d-alanine: d-alanine ligase.