gebhart/patrepeval huggingface dataset:
The Phytoalexin-Inducible Multidrug Efflux Pump AcrAB Contributes to Virulence in the Fire Blight Pathogen, Erwinia amylovora (2004)

The enterobacterium Erwinia amylovora causes fire blight on members of the family Rosaceae, with economic importance on apple and pear. During pathogenesis, the bacterium is exposed to a variety of plant-borne antimicrobial compounds. In plants of Rosaceae, many constitutively synthesized isoflavonoids affecting microorganisms were identified. Bacterial multidrug efflux transporters which mediate resistance toward structurally unrelated compounds might confer tolerance to these phytoalexins. To prove this hypothesis, we cloned the acrAB locus from E. amylovora encoding a resistance nodulation division-type transport system. In Escherichia coli, AcrAB of E. amylovora conferred resistance to hydrophobic and amphiphilic toxins. An acrB-deficient E. amylovora mutant was impaired in virulence on apple rootstock MM 106. Furthermore, it was susceptible toward extracts of leaves of MM 106 as well as to the apple phytoalexins phloretin, naringenin, quercetin, and (+)-catechin. The expression of acrAB was determined using the promoterless reporter gene egfp. The acrAB operon was up-regulated in vitro by the addition of phloretin and naringenin. The promoter activity of acrR, encoding a regulatory protein involved in acrAB expression, was increased by naringenin. In planta, an induction of acrAB was proved by confocal laser scanning microscopy. Our results strongly suggest that the AcrAB transport system plays an important role as a protein complex required for virulence of E. amylovora in resistance toward apple phytoalexins and that it is required for successful colonization of a host plant.
Homogeneous chemiluminescent measurement of nitric oxide with ozone. Implications for continuous selective monitoring of gaseous air pollutants (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHomogeneous chemiluminescent measurement of nitric oxide with ozone. Implications for continuous selective monitoring of gaseous air pollutantsArthur. Fontijn, Alberto J. Sabadell, and Richard J. RoncoCite this: Anal. Chem. 1970, 42, 6, 575–579Publication Date (Print):May 1, 1970Publication History Published online1 May 2002Published inissue 1 May 1970https://pubs.acs.org/doi/10.1021/ac60288a034https://doi.org/10.1021/ac60288a034research-articleACS PublicationsRequest reuse permissionsArticle Views1393Altmetric-Citations335LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Double trans-chromosomic mice: Maintenance of two individual human chromosome fragments containing Ig heavy and κ loci and expression of fully human antibodies (2000)

The use of a human chromosome or its fragment as a vector for animal transgenesis may facilitate functional studies of large human genomic regions. We describe here the generation and analysis of double trans-chromosomic (Tc) mice harboring two individual human chromosome fragments (hCFs). Two transmittable hCFs, one containing the Ig heavy chain locus (IgH, approximately 1.5 Mb) and the other the kappa light chain locus (Igkappa, approximately 2 Mb), were introduced into a mouse strain whose endogenous IgH and Igkappa loci were inactivated. In the resultant double-Tc/double-knockout mice, substantial proportion of the somatic cells retained both hCFs, and the rescue in the defect of Ig production was shown by high level expression of human Ig heavy and kappa chains in the absence of mouse heavy and kappa chains. In addition, serum expression profiles of four human Ig gamma subclasses resembled those seen in humans. They mounted an antigen-specific human antibody response upon immunization with human serum albumin, and human serum albumin-specific human monoclonal antibodies with various isotypes were obtained from them. These results represent a generation of mice with "humanized" loci by using the transmittable hCFs, which suggest that the Tc technology may allow for the humanization of over megabase-sized, complex loci in mice or other animals. Such animals may be useful not only for studying in vivo functions of the human genome but also for obtaining various therapeutic products.
Recent progress in Erbium-doped waveguide amplifiers. (2000)

We will describe Er-doped aluminosilicate waveguide amplifiers integrated with 980nm/1550nm WDM on Silicon Optical Bench and report on their performance. Recent progress in Er-doped waveguide amplifiers will be reviewed.
Expression of CCR5 Is Increased in Human Monocyte-Derived Macrophages and Alveolar Macrophages in the Course of in Vivo and in Vitro Mycobacterium tuberculosis Infection (1999)

Human immunodeficiency virus (HIV) replicates more efficiently in Mycobacterium tuberculosis (MTB)-infected macrophages than in uninfected controls. We investigated whether this may be partly explained by changes in expression of CCR5 in the course of mycobacterial infection, as this molecule has been shown to be a coreceptor for HIV entry. Since the lung is the preferential organ of HIV replication in the course of tuberculosis, we preliminarily analyzed beta-chemokine receptor expression in alveolar macrophages from patients with active tuberculosis, using flow cytometry based on an MIP-1alpha ligand-biotin/avidin-FITC detection system. Increased MIP-1alpha receptor (MIP-1alphaR) expression in alveolar macrophages from infected patients was observed whereas no detectable expression could be revealed in uninfected controls. Since MIP-la can also bind CCR1 and CCR4, the presence of CCR5 mRNA was investigated in bronchoalveolar lavage (BAL) cells and detected in alveolar macrophages from tuberculosis patients only. The study was then extended to in vitro MTB-infected macrophages. Monocyte-derived macrophages (MDMs) were left to differentiate for 7 days before MTB H37Rv infection, and CCR5 expression was monitored, by using a specific monoclonal antibody, on days 1, 6, and 11 after infection. Increased CCR5 expression in MTB-infected macrophages was observed, with a peak on day 6 (64% in MTB-infected versus 33% in control cultures) and a decrease by day 11 (25% in MTB infected versus 13% in control cultures). These results show that CCR5 expression is enhanced in the course of in vitro MTB infection and during active pulmonary tuberculosis.
Sol−Gel Synthesis of Free-Standing Ferroelectric Lead Zirconate Titanate Nanoparticles (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSol−Gel Synthesis of Free-Standing Ferroelectric Lead Zirconate Titanate NanoparticlesChao Liu, Bingsuo Zou, Adam J. Rondinone, and Z. John ZhangView Author Information School of Chemistry & Biochemistry Georgia Institute of Technology, Atlanta, Georgia 30332-0400 Cite this: J. Am. Chem. Soc. 2001, 123, 18, 4344–4345Publication Date (Web):April 17, 2001Publication History Received1 June 2000Revised22 January 2001Published online17 April 2001Published inissue 1 May 2001https://pubs.acs.org/doi/10.1021/ja001893yhttps://doi.org/10.1021/ja001893yrapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views3153Altmetric-Citations138LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Nanoparticles,Perovskites,Physical and chemical processes,Polarization,Precursors Get e-Alerts
Fast approximate energy minimization via graph cuts (1999)

In this paper we address the problem of minimizing a large class of energy functions that occur in early vision. The major restriction is that the energy function's smoothness term must only involve pairs of pixels. We propose two algorithms that use graph cuts to compute a local minimum even when very large moves are allowed. The first move we consider is an /spl alpha/-/spl beta/-swap: for a pair of labels /spl alpha/,/spl beta/, this move exchanges the labels between an arbitrary set of pixels labeled a and another arbitrary set labeled /spl beta/. Our first algorithm generates a labeling such that there is no swap move that decreases the energy. The second move we consider is an /spl alpha/-expansion: for a label a, this move assigns an arbitrary set of pixels the label /spl alpha/. Our second algorithm, which requires the smoothness term to be a metric, generates a labeling such that there is no expansion move that decreases the energy. Moreover, this solution is within a known factor of the global minimum. We experimentally demonstrate the effectiveness of our approach on image restoration, stereo and motion.
Editorial [Suppression of Premature Stop Codons for the Treatment of a Subset of Patients with Genetic Disorders] (2009)

The concept of personalized medicine has been extended to recognize the fact that variations in the genetic makeup of individuals can greatly alter their responsiveness to drug treatments for a variety of disorders. An important corollary to this concept is that patients may have one of a number of different genetic diseases due to the same type of mutation in the disease-causing gene. This creates the possibility of a very different paradigm within personalized medicine, in which a drug can be designed to treat a specific genetic mutation, rather than a specific disease. The first example of this paradigm is drug-based suppression of a premature stop codon. There are a large number of individuals collectively afflicted by genetic disorders resulting form premature stop codons. Development of a drug-based therapy that can suppress this class of mutations could allow treatment of subsets of patients across a large number of genetic disorders, and thus address a substantial unmet medical need.
The simian virus 40 small-t intron, present in many common expression vectors, leads to aberrant splicing. (1990)

Polymerase chain reaction analysis was used to identify aberrant splicing of the simian virus 40 small-t intron present in pRSVcat. We examined factors governing the selection and relative use of aberrant 5' splice sites derived from the chloramphenicol acetyltransferase-coding region. Our results indicated that transcripts from virtually any cDNA positioned upstream of the small-t intron could contain alternative 5' splice sites and therefore be subject to deletions within the protein-coding region.
[Synergistic effect of organic solvents and tobacco smoke on the indicators of humoral immunity in humans]. (1991)

Medical examinations were performed among 49 non-smokers, 47 workers who had been smoking for more than 10 years, 19 non-smokers exposed to organic solvents and 41 smoking persons occupationally exposed to organic solvents. Both cigarette smoking and the action of organic solvents. decreased the levels of IgA, AgG, IgM and that of lysozyme. In persons exposed to the actions of both cigarette smoking and benzol and its homologues, more significant decreases of IgA, AgG, IgM and lysozyme concentrations were revealed as compared to those affected by one of the factors. The same concerned the IgD level. The contributors proposed that cigarette smoking should be taken into account when evaluating the immunotoxic properties of industrial factors.
An investigative pharmacology study of a GDF‐8 (myostatin) inhibitor, ACE‐031, in the Common Marmoset (Callithrix Jacchus) (2008)

ACE‐031 is a biotherapeutic based on the activin receptor type IIB under investigation for treatment of diseases involving loss of muscle mass, strength and function. ACE‐031 has demonstrated increased skeletal muscle mass and strength in rodent models of ALS and muscular dystrophy. The purpose of this study was to evaluate the pharmacologic effects of ACE‐031 administered once weekly for 13 weeks to marmosets via subcutaneous injection. Marmosets (n=6/sex) were randomized into groups receiving 3 mg/kg of ACE‐031 or vehicle. Body composition analysis using Dual Energy X‐ray Absorptiometry (DXA) or EchoMRI TM was performed at baseline then twice monthly for the duration of the study. DEXA scans were performed with a Lunar scanner for calculation of regional body composition. Whole body composition analysis was performed using EchoMRI TM technology. Animals were euthanized following last dose and subjected to complete histopathology evaluation. Skeletal muscle was subjected to fiber type analysis. Preliminary data suggest that ACE‐031 demonstrates pharmacologic changes in body composition in the marmoset, consistent with that observed in rodents. These data provide a basis for future functional studies in this species. Demonstration of activity in nonhuman primates greatly enhances our confidence in the clinical potential of this product, thereby offering hope for otherwise untreatable conditions.
A preliminary pathological study on human allotransplantation. (2003)

The rejection in deep tissues should be monitored in controlling the rejection of hand allograft.
Human T cell hybridomas producing cytotoxic lymphokines: induction of lymphotoxin release and killer cell activity by anti-CD3 monoclonal antibody or lectins and phorbol ester. (1986)

Human T cell hybrids were constructed between lectin-activated peripheral blood lymphocytes and CEM.TET1, a variant of the CEM T lymphoblastoid cell line. Hybrids were screened for their ability to produce cytotoxic lymphokines and interleukin-2 (IL-2) following lectin activation. Five hybrids were identified that released significant levels (greater than 75 units/ml) of cytotoxic activity that was detected on the murine L929 target cells; three hybrids were identified that produced IL-2. Cell surface phenotype of the T cell hybrids did not correlate with their ability to produce these lymphokines. The II-23 hybrid (CD3+;4+) produced an inducible cytotoxic activity that was fully neutralized by anti-lymphotoxin antibodies. The release of lymphotoxin (LT) rapidly attained maximum levels 12 hrs to 24 hrs after lectin activation; IL-2 production was maximum at 48 hrs. The induction of LT and IL-2 release required similar membrane stimulating agents. The phorbol ester, phorbol 12-myristate 13-acetate (PMA) in combination with phytohemagglutinin or concanavalin A, were required for maximal release of LT and IL-2. Anti-CD3 monoclonal antibodies coupled to agarose, but not anti-T200-agarose, induced the release of high levels of LT and IL-2. Soluble anti-CD3 was not sufficient to induce IL-2 or LT release from the II-23 hybrid; however, soluble anti-CD3 combined with PMA was a strong stimulus for lymphotoxin and IL-2 release. The II-23 hybrid also functioned as a cytotoxic T cell line in a 51Chromium release assay. Induction of killer cell function required similar perturbation of Ti/CD3 complex. This human T cell hybrid line offers an inducible model system for the simultaneous study of the molecular events regulating the production of growth inhibitory/cytotoxic (LT) and growth promoting (IL-2) lymphokines and cytotoxic T cell function.
Multiple fundamental frequency estimation based on harmonicity and spectral smoothness (2003)

A new method for estimating the fundamental frequencies of concurrent musical sounds is described. The method is based on an iterative approach, where the fundamental frequency of the most prominent sound is estimated, the sound is subtracted from the mixture, and the process is repeated for the residual signal. For the estimation stage, an algorithm is proposed which utilizes the frequency relationships of simultaneous spectral components, without assuming ideal harmonicity. For the subtraction stage, the spectral smoothness principle is proposed as an efficient new mechanism in estimating the spectral envelopes of detected sounds. With these techniques, multiple fundamental frequency estimation can be performed quite accurately in a single time frame, without the use of long-term temporal features. The experimental data comprised recorded samples of 30 musical instruments from four different sources. Multiple fundamental frequency estimation was performed for random sound source and pitch combinations. Error rates for mixtures ranging from one to six simultaneous sounds were 1.8%, 3.9%, 6.3%, 9.9%, 14%, and 18%, respectively. In musical interval and chord identification tasks, the algorithm outperformed the average of ten trained musicians. The method works robustly in noise, and is able to handle sounds that exhibit inharmonicities. The inharmonicity factor and spectral envelope of each sound is estimated along with the fundamental frequency.
Number of A β Inoculations in APP+PS1 Transgenic Mice Influences Antibody Titers, Microglial Activation, and Congophilic Plaque Levels (2001)

There have been several reports on the use of beta-amyloid (Abeta ) vaccination in different mouse models of Alzheimer's disease (AD) and its effects on pathology and cognitive function. In this report, the histopathologic findings in the APP+PS1 doubly transgenic mouse were compared after three, five, or nine Abeta inoculations. The number of inoculations influenced the effects of vaccination on Congo red levels, microglia activation, and anti-Abeta antibody titers. After three inoculations, the antibody titer of transgenic mice was substantially lower than that found in nontransgenic animals. However, after nine inoculations, the levels were considerably higher in both genotypes and no longer distinguishable statistically. The number of inoculations influenced CD45 expression, an indicator of microglial activation. There was an initial upregulation, which was significant after five inoculations, but by nine inoculations, the extent of microglial activation was equivalent to that in mice given control vaccinations. Along with this increased CD45 expression, there was a correlative reduction in staining by Congo red, which stains compact plaques. When data from the mice from all groups were combined, there was a significant correlation between activation of microglia and Congo red levels, suggesting that microglia play a role in the clearance of compact plaque.
Polymerase Evolution:  Efforts toward Expansion of the Genetic Code (2005)

Genetic information is encoded by, but potentially not limited to, a four-letter alphabet. A variety of predominantly hydrophobic nucleobase analogues that form self-pairs in DNA have been examined as third base pair candidates. For example, the PICS self-pair is both stable in duplex DNA and synthesized by some wild-type polymerases with reasonable efficiency. These efforts to expand the genetic code are expected to be facilitated by optimizing both the unnatural nucleobase analogues and the polymerases that replicate them. Here, we report the use of an activity-based selection system to evolve a DNA polymerase that more efficiently replicates DNA containing the PICS self-pair. The selection system is based on the co-display on phage of DNA polymerase libraries and a DNA substrate containing the self-pair. Only polymerases that accept the unnatural substrate incorporate a biotin-dUTP to the attached primer and may then be isolated on a streptavidin solid support. A mutant of Sf polymerase, P2, was evolved which both inserts dPICSTP opposite dPICS in the template and extends the unnatural primer terminus by incorporation of the next correct natural dNTP, where the parental enzyme catalyzes neither step at detectable rates. P2 was found to be a triple mutant of Sf, with the mutations F598I, I614F, and Q489H. The evolved properties of P2, as well as the observed mutations, are consistent with an increased affinity for the DNA primer-template containing the self-pair.
Lipid accumulation in rabbit aortic intima 2 hours after bolus infusion of low density lipoprotein. A deep-etch and immunolocalization study of ultrarapidly frozen tissue. (1991)

The intima from aortas of normal New Zealand White rabbits was studied 2 hours after infusion of 320 mg human low density lipoprotein (LDL), resulting in a plasma concentration of at least five times and maximally 20 times the values found in normal rabbit serum. The following techniques were used: 1) ultrarapid freezing without chemical fixation, followed by freeze-etching; 2) immunofluorescence microscopy; and 3) postembedding immunogold-labeling electron microscopy. In the latter two methods MB47, a murine monoclonal antibody against human apolipoprotein B, was used as the primary antibody. Control rabbits were infused with the same volume of buffer only. Rotary-shadowed replicas of samples from the LDL-injected rabbits showed the deposition of lipidlike particles in the subendothelial-intimal space that were the size of the injected LDL (23 nm). In focal areas of the intima, groups of 23-nm-sized lipidlike particles and larger lipidlike structures were found enmeshed in the extracellular matrix. Control replicas were essentially free of lipid deposition. Immunofluorescence microscopy of frozen aortic cross sections showed an overall increase in apolipoprotein B in the intima of the LDL-injected rabbits. The presence of apolipoprotein B in the intima was also confirmed by immunoelectron microscopy. These in vivo results show that clustering of LDL-sized particles occurs in the intima within 2 hours of excessive LDL uptake. It also demonstrates the interaction of these LDL-sized particles with the filaments of the extracellular matrix. The clustering of the LDL-sized particles supports the possibility that LDL self-aggregation may occur in vivo and that components of the extracellular matrix are involved in this process.