gebhart/patrepeval huggingface dataset:
Identification of a bacterial pectin acetyl esterase in <i>Erwinia chrysanthemi</i> 3937 (1997)

Erwinia chrysanthemi causes soft-rot diseases of various plants by enzymatic degradation of the pectin in plant cell walls. The structural complexity of pectin requires the combined action of several pectinases for its efficient breakdown. Three types of pectinases have so far been identified in E. chrysanthemi: two pectin methyl esterases (PemA, PemB), a polygalacturonase (PehX), and eight pectate lyases (PelA, PelB, PelC, PelD, PelE, PelL, PelZ, PelX). We report in this paper the analysis of a novel enzyme, the pectin acetyl esterase encoded by the paeY gene. No bacterial form of pectin acetyl esterases has been described previously, while plant tissues and some pectinolytic fungi were found to produce similar enzymes. The paeY gene is present in a cluster of five pectinase-encoding genes, pelA-pelE-pelD-paeY-pemA. The paeY open reading frame is 1650 bases long and encodes a 551-residue precursor protein of 60704Da, including a 25-amino-acid signal peptide. PaeY shares one region of homology with a rhamnogalacturonan acetyl esterase of Aspergillus aculeatus. To characterize the enzyme, the paeY gene was overexpressed and its protein product was purified. PaeY releases acetate from sugar-beet pectin and from various synthetic substrates. Moreover, the enzyme was shown to act in synergy with other pectinases. The de-esterification rate by PaeY increased after previous demethylation of the pectins by PemA and after depolymerization of the pectin by pectate lyases. In addition, the degradation of sugar-beet pectin by pectate lyases is favoured after the removal of methyl and acetyl groups by PemA and PaeY, respectively. The paeY gene was first identified on the basis of its regulation, which shares several characteristics with that of other pectinases. Analysis of the paeY transcription, using gene fusions, revealed that it is induced by pectic catabolic products and is affected by growth phase, oxygen limitation and catabolite repression. Regulation of paeY expression appears to be dependent on the KdgR repressor, which controls all the steps of pectin catabolism, and on the catabolite regulatory protein (CRP), the global activator of sugar catabolism. The contiguous pelD, paeY and pemA genes are transcribed as an operon from a promoter proximal to pelD which allows the regulation by KdgR and CRP. However, transcription can be interrupted at the intra-operon Rho-independent terminator situated between pelD and paeY. The paeY mutant inoculated into Saintpaulia plants was less invasive than the wild-type E. chrysanthemi strain 3937, demonstrating the important role of PaeY in the soft-rot disease.
ASYMPTOMATIC BACTERIURIA IN SCHOOL GIRLS (1975)

The short-term prognosis of 116 school girls with asymptomatic bacteriuria (ABU) treated or left untreated is reported. In untreated girls a spontaneous remission was obtained in 11% within one year. A short course of nitrofurantoin eliminated the bacteriuria in 93% of the girls in the treatment group. The recurrence rate was 30% in one year in the patients that became abacteriuric spontaneously, after a bladder washout test or after treatment with penicillin or nitrofurantoin. The first recurrence occurred withn 3 months in 79% (19/24). Nineteen of the 24 patients with recurrences (79%) had a third infection within 9 months. In patients with parenchymal reduction or reflux the renal concentrating capacity increased significantly after treatment of the bacteriuria. All the girls left untreated had normal renal concentrating capacity on detection and this remained unchanged during the year of follow-up. One of 28 untreated girls attracted a symptomatic pyelonephritis caused by a strain different from that at detection of ABU. Of 81 girls cured from the bacteriuria 24 recurred, 5 with a symptomatic pyelonephritis and 3 with cystitis. It is concluded that strains isolated from girls with ABU do not commonly cause symptomatic pyelonephritis.
Expression of the Molecular Chaperone Hsp70 in Detergent-resistant Microdomains Correlates with Its Membrane Delivery and Release (2003)

Accumulating evidence suggests that some heat shock proteins (Hsps), in particular the 72-kDa inducible Hsp70, associate to the cell membrane and might be secreted through an unknown mechanism to exert important functions in the immune response and signal transduction. We speculated that specialized structures named lipid rafts, known as important platforms for the delivery of proteins to the cell membrane, might be involved in the unknown mechanism ensuring membrane association and secretion of Hsp70. Lipid rafts are sphingolipid-cholesterol-rich structures that have been mainly characterized in polarized epithelial cells and can be isolated as detergent-resistant microdomains (DRMs). Analysis of soluble and DRM fractions prepared from unstressed Caco-2 epithelial cells revealed that Hsp70, and to a lesser extent calnexin, were present in DRM fractions. Increased expression of Hsps, through heat shock or by using drugs acting on protein trafficking or intracellular calcium level, induced an efficient translocation to DRM. We also found that Hsp70 was released by epithelial Caco-2 cells, and this release dramatically increased after heat shock. Drugs known to block the classical secretory pathway were unable to reduce Hsp70 release. By contrast, release of the protein was affected by the raft-disrupting drug methyl-beta-cyclodextrin. Our data suggest that lipid rafts are part of a mechanism ensuring the correct functions of Hsps and provide a rational explanation for the observed membrane association and release of Hsp70.
El abuso de posición dominante en la defensa de la competencia (2005)

Es una publicacion realizada por el Departamento de Derecho Empresario de la Universidad Austral.
[Stimulation of induction or inhibition of crown-gall tumor development by RNA-fragments U2. Interference by auxin]. (1979)

RNA-fragments U2 obtained by mild degradation with RNase U2 of ribosomal RNA containing A and G nucleotides in excess are capable of exhibiting either a stimulatory effect on the induction of Crown-gall tumors or an inhibitory action on their subsequent development. These different effects are dependent on the moment at which RNA-fragments were introduced into wounded Pea seedlings infected by Agrobacterium tumefaciens B6. The results obtained in vitro and in vivo suggest that an interaction between auxin and RNA-fragments U2 may take place, either increasing the tumor induction or inhibiting the proliferation of tumourous cells.
Galanin : a new multifunctional peptide in the neuro-endocrine system (1991)

This is the first-ever book dedicated solely to Galanin. It covers Galanin's biochemistry, distribution, receptors, neuro-endocrinology and functions within the nervous system
Introduction to Statistical Reasoning (1999)

Displaying data summarizing data producing data explaining data estimation hypothesis tests comparing two samples using ANOVA to compare several means chi-square tests for categorical data simple regression.
The <i>Arabidopsis thaliana REDUCED EPIDERMAL FLUORESCENCE1</i> Gene Encodes an Aldehyde Dehydrogenase Involved in Ferulic Acid and Sinapic Acid Biosynthesis (2004)

Recent research has significantly advanced our understanding of the phenylpropanoid pathway but has left in doubt the pathway by which sinapic acid is synthesized in plants. The reduced epidermal fluorescence1 (ref1) mutant of Arabidopsis thaliana accumulates only 10 to 30% of the sinapate esters found in wild-type plants. Positional cloning of the REF1 gene revealed that it encodes an aldehyde dehydrogenase, a member of a large class of NADP(+)-dependent enzymes that catalyze the oxidation of aldehydes to their corresponding carboxylic acids. Consistent with this finding, extracts of ref1 leaves exhibit low sinapaldehyde dehydrogenase activity. These data indicate that REF1 encodes a sinapaldehyde dehydrogenase required for sinapic acid and sinapate ester biosynthesis. When expressed in Escherichia coli, REF1 was found to exhibit both sinapaldehyde and coniferaldehyde dehydrogenase activity, and further phenotypic analysis of ref1 mutant plants showed that they contain less cell wall-esterified ferulic acid. These findings suggest that both ferulic acid and sinapic acid are derived, at least in part, through oxidation of coniferaldehyde and sinapaldehyde. This route is directly opposite to the traditional representation of phenylpropanoid metabolism in which hydroxycinnamic acids are instead precursors of their corresponding aldehydes.
Current and future trends in immunization against meningitis (1993)

The progress in vaccines for Haemophilus influenzae type b infection is followed; it is the disadvantages of pure polysaccharide vaccines that have stimulated the development of the present generation of polysaccharide-protein conjugated vaccines. From extensive clinical trials it is apparent that these are very effective in preventing disease in children. Conjugated haemophilus vaccines were introduced into the routine immunization schedules in the UK in Autumn 1992. Meningococcal A and C polysaccharide vaccines, effective for epidemic disease, are only now being developed in a protein conjugated form with the prospect of protecting young children and producing durable immunity Group B outer membrane-based meningococcal vaccines produce only a low degree of protection and much further work is needed before even the optimum vaccine constituents of this organism can be identified. Vaccines to replace multivalent pneumococcal polysaccharide mixtures are only in the very earliest stages of development.
Structural features of the apelin receptor N-terminal tail and first transmembrane segment implicated in ligand binding and receptor trafficking (2013)

G-protein coupled receptors (GPCRs) comprise a large family of membrane proteins with rich functional diversity. Signaling through the apelin receptor (AR or APJ) influences the cardiovascular system, central nervous system and glucose regulation. Pathophysiological involvement of apelin has been shown in atherosclerosis, cancer, human immunodeficiency virus-1 (HIV-1) infection and obesity. Here, we present the high-resolution nuclear magnetic resonance (NMR) spectroscopy-based structure of the N-terminus and first transmembrane (TM) segment of AR (residues 1-55, AR55) in dodecylphosphocholine micelles. AR55 consists of two disrupted helices, spanning residues D14-K25 and A29-R55(1.59). Molecular dynamics (MD) simulations of AR built from a hybrid of experimental NMR and homology model-based restraints allowed validation of the AR55 structure in the context of the full-length receptor in a hydrated bilayer. AR55 structural features were functionally probed using mutagenesis in full-length AR through monitoring of apelin-induced extracellular signal-regulated kinase (ERK) phosphorylation in transiently transfected human embryonic kidney (HEK) 293A cells. Residues E20 and D23 form an extracellular anionic face and interact with lipid headgroups during MD simulations in the absence of ligand, producing an ideal binding site for a cationic apelin ligand proximal to the membrane-water interface, lending credence to membrane-catalyzed apelin-AR binding. In the TM region of AR55, N46(1.50) is central to a disruption in helical character. G42(1.46), G45(1.49) and N46(1.50), which are all involved in the TM helical disruption, are essential for proper trafficking of AR. In summary, we introduce a new correlative NMR spectroscopy and computational biochemistry methodology and demonstrate its utility in providing some of the first high-resolution structural information for a peptide-activated GPCR TM domain.
An RNA-Seq atlas of gene expression in mouse and rat normal tissues (2017)

Gene functionality is closely connected to its expression specificity across tissues and cell types. RNA-Seq is a powerful quantitative tool to explore genome wide expression. The aim of this study is to provide a comprehensive RNA-Seq dataset across the same 13 tissues for mouse and rat, two of the most relevant species for biomedical research. The dataset provides the transcriptome across tissues from three male C57BL6 mice and three male Han Wistar rats. We also describe our bioinformatics pipeline to process and technically validate the data. Principal component analysis shows that tissue samples from both species cluster similarly. We show by comparative genomics that many genes with high sequence identity with respect to their human orthologues also have a highly correlated tissue distribution profile and are in agreement with manually curated literature data for human. In summary, the present study provides a unique resource for comparative genomics and will facilitate the analysis of tissue specificity and cross-species conservation in higher organisms.
Effect of various techniques of tetracycline hydrochloride demineralization on root dentin surface: A scanning electron microscopic study (2011)

Aim : To evaluate the in-vitro effect of various techniques of Tetracycline Hydrochloride application on root dentin surface at different magnifications of scanning electron microscopic (SEM). Materials and Methods : Twenty human teeth were collected and stored in distilled water after soft tissue removal using hand instruments. The apical third of each root was removed remaining mid-third region was sectioned longitudinally through the root canal following removal of its cementum with a tapered fissure bur. The dentin blocks were divided into 4 groups having 5 samples in each group. A tetracycline hydrochloride solution was prepared by adding the contents of one 500 mg capsule to 5 ml of distilled water. The application time of the tetracycline hydrochloride was 5 minutes. After the treatment of the root surfaces, the samples were fixed in 2.5% glutaraldehyde prepared in phosphate buffer (pH 7.3) for 24 hours at 4°C and prepared for SEM. Mean and standard deviation were estimated from the samples for each study group. Mean values were compared by either ONE-WAY ANOVA with Tukey - HSD procedure. Results : All technique of tetracycline application shows removal of smear layer and exposure of dentinal tubule orifices. Burnishing technique showed significant difference than immersion technique and saturation technique. Conclusion : In view of these present findings, tetracycline hydrochloride as a root conditioner may be evaluated in vivo studies. It is reasonable to expect lesser tissue destruction and better regeneration of periodontal tissues if it is used as a root conditioner during periodontal regeneration procedures.
An antenna switch MMIC using E/D mode p-HEMT for GSM/DCS/PCS/WCDMA bands application (2003)

A monolithic antenna switch IC using enhancement and depletion (E/D) -mode AlGaAs/InGaAs pseudomorphic high electron mobility transistors (p-HEMTs) has been developed for GSM/DCS/PCS/WCDMA band digital mobile communication systems. This antenna switch MMIC achieves a low insertion loss and small chip size using a single pole double throw (SPDT) switch for GSM and single pole 4 throw (SP4T) switch for other band configurations, as well as internal logic circuits with an E/D mode p-HEMTs process. This MMIC achieves an insertion loss of 0.21 dB at 915 MHz and 0.53 dB at 1785 MHz. The isolation to the RX ports is more than 30 dB, and the input power at 0.1 dB compression is over 36 dBm at +2.7 V operation.
Supermeres are functional extracellular nanoparticles replete with disease biomarkers and therapeutic targets (2021)

Extracellular vesicles and exomere nanoparticles are under intense investigation as sources of clinically relevant cargo. Here we report the discovery of a distinct extracellular nanoparticle, termed supermere. Supermeres are morphologically distinct from exomeres and display a markedly greater uptake in vivo compared with small extracellular vesicles and exomeres. The protein and RNA composition of supermeres differs from small extracellular vesicles and exomeres. Supermeres are highly enriched with cargo involved in multiple cancers (glycolytic enzymes, TGFBI, miR-1246, MET, GPC1 and AGO2), Alzheimer's disease (APP) and cardiovascular disease (ACE2, ACE and PCSK9). The majority of extracellular RNA is associated with supermeres rather than small extracellular vesicles and exomeres. Cancer-derived supermeres increase lactate secretion, transfer cetuximab resistance and decrease hepatic lipids and glycogen in vivo. This study identifies a distinct functional nanoparticle replete with potential circulating biomarkers and therapeutic targets for a host of human diseases.
Participation of complement in host defense against capsule-deficient Haemophilus influenzae (1983)

To investigate the role of complement in immunity to capsule-deficient Haemophilus influenzae, rats were depleted of C3 with cobra venom factor and challenged with three different strains of capsule-deficient H. influenzae. Two of them (Rd and U1) did not elaborate type b capsular antigen, whereas the other (S2) elaborated 0.16% of the amount made by its type b parent strain. Depletion of C3 significantly enhanced early intravascular bacterial survival after intravenous inoculation and strikingly increased the susceptibility of rats to infection with capsule-deficient H. influenzae. After intraperitoneal inoculation with strain Rd or U1, C3-depleted rats developed bacteremia, whereas control rats did not; challenge with strain S2 resulted in transient bacteremia in normal rats and in death in C3-depleted animals. To determine whether the greater virulence of strain S2, as compared with strain Rd or U1, was accounted for by the small amounts of capsular antigen it elaborated, we also compared its relative virulence to that of three genetically closely related capsule-deficient variants elaborating either small amounts of type b capsule or producing no detectable b antigen. No difference in virulence was observed among these four variants; all C3-depleted rats inoculated developed bacteremia of similar magnitude followed by similar mortality rates. These studies demonstrate a significant role for complement in host defense mechanisms against capsule-deficient H. influenzae and suggest that interstrain differences of virulence are not attributable to residual elaboration of small amounts of type b capsule.
3',3'-Difluoro-3'-deoxythymidine: comparison of anti-HIV activity to 3'-fluoro-3'-deoxythymidine (1992)

3',3'-Difluoro-3'-deoxythymidine (3) has been synthesized in four steps from thymidine, and characterized by 1H NMR and NOE experiments. The JHF coupling constants support a conformation in solution that is predominantly 2'-endo (S). Although conformationally and sterically nucleoside 3 may resemble other thymidine analogs which are active against HIV-1, 3 is virtually inactive.
Protective Effect of Pseudomonas Fluorescens as a Probiotic in Controlling Fish Pathogens (2014)

The use of Pseudomonas fluorscens isolates as biological control agents against two fish pathogens; Pseudomonas angulliseptica and Streptococcus faecium in Nile tilapia were investigated in vivo and vitro. Pseudomonas fluorscens biovars I, II & III were tested in vitro using the agar diffusion method and showed effectiveness in inhibiting growth of P. angulliseptica and Strep. faecium. Pseudomonas fluorscens biovar II was the most effective with largest inhibition zones against both pathogens. For oral administration, P. fluorscens biovars were incorporated into the mixed feed diet. A significant reduction in mortality rate and a significant increase in hematological parameters, total protein, and globulin in fish groups fed Pseudomonas fluorscens incorporated diet following challenge by P. angulliseptica and Strep. faecium. It could be concluded that P. fluorescens has a protective effect against different Nile Tilapia pathogens and could be used as a probiotic bacteria and an eco-friendly alternative measure to chemical antimicrobials and further research studies to clarify its protective mechanisms on cellular and molecular levels.
Galectin-3 and cancer (Review). (2004)

Galectin-3 is a pleiotropic carbohydrate-binding protein involved in a variety of normal and pathological biological processes. Its carbohydrate-binding properties constitute the basis for cell-cell and cell-matrix interactions and cancer progression. Modulation of galectin-3 expression in cancer cells has indeed been reported. These observations lead to the recognition of galectin-3 as a diagnostic/prognostic marker for specific cancer types, such as thyroid and prostate. This review discusses the expression and cellular localization of galectin-3 in cancer cells, as well as its numerous functions in cancer cell biology, including cell-cell adhesion, cell-matrix interactions, growth regulation, apoptosis, angiogenesis and mRNA splicing.
Continuous Separation of High Molecular Weight Compounds Using a Microliter Volume Free-Flow Electrophoresis Microstructure (1996)

A microliter volume free-flow electrophoresis microstructure (μ-FFE) was used to perform a continuous separation of high molecular weight compounds. The μ-FFE microstructure had a separation bed volume of 25 μL and was fabricated from silicon using standard micromachining technology. Laser-induced fluorescence was used to detect the sample components, which were labeled with fluorescein isothiocyanate (FITC) prior to analysis. The continuous separation of human serum albumin (HSA), bradykinin, and ribonuclease A demonstrated that only 25 V/cm was required to isolate HSA from bradykinin and ribonuclease A, while 100 V/cm was needed for the separation of bradykinin from ribonuclease A. Comparison of the observed band broadening with the theoretical variance indicated that dispersion due to the initial bandwidth, diffusion, and hydrodynamic broadening were the main contributors to the band broadening of HSA and bradykinin. However, the band broadening for ribonuclease A could not be sufficiently accounted for using the above contributors. Adsorption was found to be a possible contributor to the overall variance for ribonuclease A. Calculation of the theoretical variance due to Joule heating indicated that broadening due to Joule heating effects was insignificant. This was likely due to the narrow cross-sectional area of the device, which facilitated efficient cooling. Electrohydrodynamic distortion was observed for HSA as it migrated toward the side bed. Studies of the resolution of bradykinin and ribonuclease A as a function of field strength at various sample and carrier flow rates indicated that, for maximum throughput, high field strengths and high flow rates were required. However, no optimal conditions were found. The μ-FFE device has a peak capacity of ∼8 bands/cm, while for a typical separation of proteins using a commercial system, a peak capacity of 10 bands/cm is obtained. Thus, the resolving power of the μ-FFE device is similar to those of conventional systems. The continuous separation of tryptic digests of mellitin and cytochrome c demonstrated the ability to continuously separate more complex mixtures. Finally, modifications were made to the microstructure to facilitate fraction collection, and the fractionation of whole rat plasma was performed. Off-line analysis of the resulting fractions indicated that the complete isolation of serum albumin and globulins was possible using a field strength of 25 V/cm.
On a fast pitch search of CELP type vocoder using decimation technique (2002)

Code excited linear prediction (CELP) vocoders exhibit good performance at data rates below 4.8 kbps. The major drawback of CELP type coders is a large amount of computation. In this paper, we propose a new pitch searching method that preserves the quality of the CELP vocoder and reduces computational complexity. The basic idea is to grasp preliminary pitches using major formant for speech signal and perform pitch search only about the preliminary pitches. Applying the proposed method to the CELP vocoder, we can reduce complexity by an average 41% in the pitch search.