gebhart/patrepeval huggingface dataset:
Identification of Novel Pathogenicity Loci in Clostridium perfringens Strains That Cause Avian Necrotic Enteritis (2010)

Type A Clostridium perfringens causes poultry necrotic enteritis (NE), an enteric disease of considerable economic importance, yet can also exist as a member of the normal intestinal microbiota. A recently discovered pore-forming toxin, NetB, is associated with pathogenesis in most, but not all, NE isolates. This finding suggested that NE-causing strains may possess other virulence gene(s) not present in commensal type A isolates. We used high-throughput sequencing (HTS) technologies to generate draft genome sequences of seven unrelated C. perfringens poultry NE isolates and one isolate from a healthy bird, and identified additional novel NE-associated genes by comparison with nine publicly available reference genomes. Thirty-one open reading frames (ORFs) were unique to all NE strains and formed the basis for three highly conserved NE-associated loci that we designated NELoc-1 (42 kb), NELoc-2 (11.2 kb) and NELoc-3 (5.6 kb). The largest locus, NELoc-1, consisted of netB and 36 additional genes, including those predicted to encode two leukocidins, an internalin-like protein and a ricin-domain protein. Pulsed-field gel electrophoresis (PFGE) and Southern blotting revealed that the NE strains each carried 2 to 5 large plasmids, and that NELoc-1 and -3 were localized on distinct plasmids of sizes approximately 85 and approximately 70 kb, respectively. Sequencing of the regions flanking these loci revealed similarity to previously characterized conjugative plasmids of C. perfringens. These results provide significant insight into the pathogenetic basis of poultry NE and are the first to demonstrate that netB resides in a large, plasmid-encoded locus. Our findings strongly suggest that poultry NE is caused by several novel virulence factors, whose genes are clustered on discrete pathogenicity loci, some of which are plasmid-borne.
A study of communication resource allocation in a distributed system (2002)

The authors introduce two techniques for allocating and managing buffers in support of distributed system operation and evaluate the resulting system behavior. For this evaluation a methodology that permits the development of an analytic model is introduced. With the help of this model, it becomes possible to fine-tune the buffer allocation policies in realistic system configurations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The effects of antidepressants on the cerebrospinal fluid homovanillic acid/5-hydroxyindoleacetic acid ratio (1987)

Dopamine and serotonin systems are morphologically interconnected in the midbrain. Several studies have also demonstrated a functional relationship between these two monoamine systems. Concentrations of their metabolites, 5-hydroxyindoleacetic acid (5HIAA) and homovanillic acid (HVA), consistently correlate with one another in human cerebrospinal fluid. Previous studies of the effects of antidepressants on the dopamine and serotonin systems have focused on the two systems in isolation without considering the interactions between the two. One way of taking this interaction into account may be to form a ratio of dopamine and serotonin measures. The present study measured HVA and 5HIAA in cerebrospinal fluid of 31 patients with depression and 12 patients with Alzheimer's disease before and after treatment with a variety of antidepressant drugs. The ratio of HVA/5HIAA was able to discriminate much more powerfully between effects of different drugs than HVA or 5HIAA examined separately.
Effect of initial immunosuppression on long-term kidney transplant outcome in immunological low-risk patients (2018)

These results suggest that in immunological low-risk patients excellent long-term kidney graft survival can be achieved irrespective of the type of initial immunosuppressive therapy (CsA or TAC; with or without MMF), despite differences in 1-year rejection-free survival.
Crystal structure of Bi4Ti3O12 (1972)

The crystal structure of Bi4Ti3O12 has been determined from x-ray and neutron diffraction patterns. Physical properties indicate monoclinic symmetry, but the diffraction data are consistent with a polar orthorhombic structure, space group B2cb, with a = 5.448(2), b = 5.411(2), c = 32,83(1) Å, and Z = 4. Integrated intensities of 2500 x-ray reflections were measured using an automated diffractometer, and the intensities of 28 neutron peaks were obtained from powder patterns. Final R-factors between the refined structure and the x-ray and neutron data were 0.07 and 0.09, respectively. Titanium is the principal contributor to polarization along a, shifting an average of 0.32 Å from the octahedron centers. The spontaneous polarization, calculated on the basis of point charges on the ions, is 28 μC/cm2 along a, somewhat smaller than the observed value of 50 ± 5 μC/cm2. The bismuth bonding is very asymmetric, causing rotations of the octahedra about a and c. A model involving the correlated reorientation of lone-pair electrons is offered as a possible explanation of the monoclinic behavior, accounting satisfactorily for the small (4 μC/cm2) component of P, along c.
Corrole Chelated Metal Complexes for HER and Oer (2017)

We have recently introduced corrole metal complexes (metallocorroles) as catalysts for various energy-relevant reactions. This includes those that are of prime importance for the electrochemical splitting of water into its elements, the hydrogen and oxygen evolution reactions. Tuning of the redox potentials, M(I)/M(II) for HER and M(III)/M(IV) for OER (M= Fe, Co, or Mn), is achieved via variations of substituents on the corrole ligand. These hypothesis-driven changes allow for the highly desired shifting of electrocatalytic onset potentials. On top of the already published results listed below, new approaches and novel catalysts will be disclosed. REFERENCES “Cobalt Corrole Catalyst for Efficient Hydrogen Evolution Reaction from H 2 O under Ambient Conditions: Reactivity, Spectroscopy and DFT Calculations”, Inorg. Chem. 2013 , 52 , 3381-3387. "The Cobalt Corrole Catalyzed Hydrogen Evolution Reaction: Surprising Electronic Effects and Characterization of Key Reaction Intermediates" Chem. Commun. 2014 , 50 , 2725-2727. "Metallocorroles as photocatalysts for driving endergonic reactions, exemplified by bromide to bromine conversion", Angew. Chem. 2015 , 54 , 12370 –12373. "Metallocorroles as Non-Precious Metal Catalysts for Oxygen Reduction", Angew. Chem. 2015 , 54, 14080 –14084. “Metallocorroles as Non-Precious Metal Electrocatalysts for Highly Efficient Oxygen Reduction in Alkaline Media" ChemCatChem 2016 , 8 , 2832-2837. “Metallocorroles as Electrocatalysts for the Oxygen Reduction Reaction (ORR)", Israel J. Chem. 2016 , 56 , 756– 762. “Dioxygen bound Cobalt Corroles”, Chem. Commun. 2017 , in press.
Pressure overload and neurohumoral activation differentially affect the myocardial proteome (2005)

Treatment with monocrotaline causes pulmonary hypertension in rats. This results in severe pressure overload-induced hypertrophy of the right ventricles, whilst the normally loaded left ventricles do not hypertrophy. Both ventricles are affected by enhanced neuroendocrine stimulation in this model. We analyzed in this model load-induced and catecholamine-induced changes of right and left ventricular proteome by two-dimensional gel electrophoresis, tryptic in-gel digest, and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. All analyzed animals showed right ventricular hypertrophy without signs of heart failure. Changes of 27 proteins in the right and 21 proteins in the left ventricular myocardium were found. Given the hemodynamic features of this animal model, proteome changes restricted to the right ventricle are caused by pressure overload. We describe for the first time a potentially novel pathway (BRAP2/BRCA1) that is involved in myocardial hypertrophy. Furthermore, we demonstrate that increased afterload-induced hypertrophy leads to striking changes in the energy metabolism with down-regulation of pyruvate dehydrogenase (subunit beta E1), isocitrate dehydrogenase, succinyl coenzyme A ligase, NADH dehydrogenase, ubiquinol-cytochrome C reductase, and propionyl coenzyme A carboxylase. These changes go in parallel with alterations of the thin filament proteome (troponin T, tropomyosin), probably associated with Ca(2+) sensitization of the myofilaments. In contrast, neurohumoral stimulation of the left ventricle increases the abundance of proteins relevant for energy metabolism. This study represents the first in-depth analysis of global proteome alterations in a controlled animal model of pressure overload-induced myocardial hypertrophy.
Transition-Metal Catalyzed Cross-Coupling Reactions of Functionalized Organometallic Reagents, Nickel-Catalyzed Amination of Aryl Chlorides and Preparation and Reactions of Organozinc Reagents (2009)

BrNEt 2 + Bu 3 Sn-NEt 2 Bu 3 Sn-Br + [(o-Tol) 3 P] 2 PdCl 2(1 mol%) toluene, 100 C, 3 h 1 2 3 : 81 % Scheme 1.First palladium-catalyzed arylaminantion using tributyltin amides.These limitations were overcome by the pioneering work of Buchwald and Hartwig in 1995. 20 Both groups independently reported the palladium-catalyzed amination of aryl bromides (4) 11
CD21-Dependent Infection of an Epithelial Cell Line, 293, by Epstein-Barr Virus (1999)

Epstein-Barr virus (EBV) is invariably present in undifferentiated nasopharyngeal carcinomas, is found sporadically in other carcinomas, and replicates in the differentiated layer of the tongue epithelium in lesions of oral hairy leukoplakia. However, it is not clear how frequently or by what mechanism EBV infects epithelial cells normally. Here, we report that a human epithelial cell line, 293, can be stably infected by EBV that has been genetically marked with a selectable gene. We show that 293 cells express a relatively low level of CD21, that binding of fluorescein-labeled EBV to 293 cells can be detected, and that both the binding of virus to cells and infection can be blocked with antibodies specific for CD21. Two proteins known to form complexes with CD21 on the surface of lymphoid cells, CD35 and CD19, could not be detected at the surface of 293 cells. All infected clones of 293 cells exhibited tight latency with a pattern of gene expression similar to that of type II latency, but productive EBV replication and release of infectious virus could be induced inefficiently by forced expression of the lytic transactivators, R and Z. Low levels of mRNA specific for the transforming membrane protein of EBV, LMP-1, as well as for LMP-2, were detected; however, LMP-1 protein was either undetectable or near the limit of detection at less than 5% of the level typical of EBV-transformed B cells. A slight increase in expression of the receptor for epidermal growth factor, which can be induced in epithelial cells by LMP-1, was detected at the cell surface with two EBV-infected 293 cell clones. These results show that low levels of surface CD21 can support infection of an epithelial cell line by EBV. The results also raise the possibility that in a normal infection of epithelial cells by EBV, the LMP-1 protein is not expressed at levels that are high enough to be oncogenic and that there might be differences in the cells of EBV-associated epithelial cancers that have arisen to allow for elevated expression of LMP-1.
Oxidized Linoleic Acid Interacts With Gut Microbiota to Promote Colitis and Colorectal Cancer (2021)

Abstract Background: Emerging human studies support that a high intake of linoleic acid (LA), which is an essential fatty acid and the most abundant polyunsaturated fatty acid (PUFA) in human diet, is associated with increased risks of developing inflammatory bowel disease (IBD). As a PUFA, LA is highly prone to oxidation; to date, it remains unknown whether the observed IBD-enhancing effect of dietary LA is caused by LA itself (un-oxidized LA) or oxidized LA. Answering this question will help us to identify the exact risk factor of IBD and to develop targeted strategies to reduce the risks of IBD; in addition, the obtained information could have important implications for optimizing dietary recommendations. Results: Here we show that oxidized LA, rather than LA itself, exacerbates colitis and colorectal tumorigenesis, via gut microbiota- and microbial receptor Toll-like receptor 4 (TLR4)-dependent mechanisms. Administration of a diet containing oxidized LA, at low human-consumption levels, increases the severity of colitis and exaggerates the development of colorectal tumorigenesis in mice. In addition, oxidized LA alters gut microbiota and fails to promote colitis in antibiotic-treated mice. Finally, oxidized LA activates TLR4 signaling in vivo and fails to promote colitis in Tlr4-/- mice. Conclusions: Overall, these results support that oxidized LA could be a risk factor of IBD and associated diseases, highlighting the need to develop novel strategies to further control oxidation of dietary LA and potentially update policies regulating the levels of oxidized LA in food products.
Comparative actinomycete diversity in marine sediments (2008)

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 52:1-11 (2008) - DOI: https://doi.org/10.3354/ame01211 Comparative actinomycete diversity in marine sediments Alejandra Prieto-Davó, William Fenical, Paul R. Jensen* Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, 92093-0204, USA *Corresponding author. Email: pjensen@ucsd.edu ABSTRACT: The diversity of cultured actinomycete bacteria was compared between near- and off-shore marine sediments. Strains were tested for the effects of seawater on growth and analyzed for 16S rRNA gene sequence diversity. In total, 623 strains representing 6 families in the order Actinomycetales were cultured. These strains were binned into 16 to 63 operational taxonomic units (OTUs) over a range of 97 to 100% sequence identity. The majority of the OTUs were closely related (>98% sequence identity) to strains previously reported from non-marine sources, indicating that most are not restricted to the sea. However, new OTUs averaged 96.6% sequence identity with previously cultured strains and ca. one-third of the OTUs were marine-specific, suggesting that sediment communities include considerable actinomycete diversity that does not occur on land. Marine specificity did not increase at the off-shore sites, indicating high levels of terrestrial influence out to 125 km from shore. The requirement of seawater for growth was observed among <6% of the strains, while all members of 9 OTUs possessed this trait, revealing a high degree of marine adaptation among some lineages. Statistical analyses predicted greater OTU diversity at the off-shore sites and provided a rationale for expanded exploration of deep-sea samples. A change in community composition was observed, with the number of Micromonospora OTUs increasing in the off-shore samples. UniFrac (see http://bmf2.colorado.edu/unifrac) statistics support a difference in community composition between near- and off-shore locations. Overall, 123 of 176 strains had distinct 16S rRNA gene sequences, indicating a high level of actinomycete diversity in marine sediments. KEY WORDS: Marine actinomycetes · Marine sediments · Bacterial diversity · Seawater requirements · Phylogeny Full text in pdf format NextCite this article as: Prieto-Davó A, Fenical W, Jensen PR (2008) Comparative actinomycete diversity in marine sediments. Aquat Microb Ecol 52:1-11. https://doi.org/10.3354/ame01211 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 52, No. 1. Online publication date: June 19, 2008 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2008 Inter-Research.
16 Minimally Invasive Glaucoma Surgery and Valves (2019)

The chapter describes various types of minimally invasive glaucoma surgery and the different devices used for the minimally invasive glaucoma surgery (MIGS) procedure along with the mechanism of the pathway of function.
Epigenetic Modifications: Therapeutic Potential in Cancer (2015)

Epigenetic modifications and alterations in chromatin structure and function contribute to the cumulative changes observed as normal cells undergo malignant transformation. These modifications and enzymes (DNA methyltransferases, histone deacetylases, histone methyltransferases, and demethylases) related to them have been deeply studied to develop new drugs, epigenome-targeted therapies and new diagnostic tools. Epigenetic modifiers aim to restore normal epigenetic modification patterns through the inhibition of epigenetic modifier enzymes. Four of them (azacitidine, decitabine, vorinostat and romidepsin) are approved by the U.S. Food and Drug Administration. This article provides an overview about the known functional roles of epigenetic enzymes in cancer development.
Spatial confinement of surface phonons in micro-resonators (2017)

International audience
AURP: An AUV-Aided Underwater Routing Protocol for Underwater Acoustic Sensor Networks (2012)

Deploying a multi-hop underwater acoustic sensor network (UASN) in a large area brings about new challenges in reliable data transmissions and survivability of network due to the limited underwater communication range/bandwidth and the limited energy of underwater sensor nodes. In order to address those challenges and achieve the objectives of maximization of data delivery ratio and minimization of energy consumption of underwater sensor nodes, this paper proposes a new underwater routing scheme, namely AURP (AUV-aided underwater routing protocol), which uses not only heterogeneous acoustic communication channels but also controlled mobility of multiple autonomous underwater vehicles (AUVs). In AURP, the total data transmissions are minimized by using AUVs as relay nodes, which collect sensed data from gateway nodes and then forward to the sink. Moreover, controlled mobility of AUVs makes it possible to apply a short-range high data rate underwater channel for transmissions of a large amount of data. To the best to our knowledge, this work is the first attempt to employ multiple AUVs as relay nodes in a multi-hop UASN to improve the network performance in terms of data delivery ratio and energy consumption. Simulations, which are incorporated with a realistic underwater acoustic communication channel model, are carried out to evaluate the performance of the proposed scheme, and the results indicate that a high delivery ratio and low energy consumption can be achieved.
Regioselective halogenation and palladium-catalysed couplings on 5,15-diphenylporphyrin (2000)

5,15-Diphenylporphyrin was regiospecifically halogenated in high yield to give 5-iodo-15-bromo-10,20-diphenylporphyrin, which was then subjected to Heck and Stille-type coupling reactions to form unsymmetrically substituted porphyrins. The regioselectivity of the iodination of diphenylporphyrins and subsequent formation of amphiphilic porphyrins via palladium-based methodology was also studied. The utility of this method for the synthesis of photodynamic sensitisers has been demonstrated on AR4-2J rat pancreatic carcinoma cells.
Distributed simulation in manufacturing: EPOCHS: integrated commercial off-the-shelf software for agent-based electric power and communication simulation (2003)

This paper reports on the development of the Electric Power and Communication Synchronizing Simulator (EPOCHS), a distributed simulation environment. Existing electric power simulation tools accurately model power systems of the past, which were controlled as large regional power pools without significant communication elements. However, as power systems increasingly turn to protection and control systems that make use of computer networks, these simulators are less and less capable of predicting the likely behavior of the resulting power grids. Similarly, the tools used to evaluate new communication protocols and systems have been developed without attention to the roles they might play in power scenarios. EPOCHS utilizes multiple research and commercial off-the-shelf (COTS) systems to bridge the gap. EPOCHS is also notable for allowing users to transparently encapsulate complex system behavior that bridges multiple domains through the use of a simple agent-based framework.
A visualization instrument to investigate the mechanical-electro properties of high temperature superconducting tapes under multi-fields (2016)

We construct a visible instrument to study the mechanical-electro behaviors of high temperature superconducting tape as a function of magnetic field, strain, and temperature. This apparatus is directly cooled by a commercial Gifford-McMahon cryocooler. The minimum temperature of sample can be 8.75 K. A proportion integration differentiation temperature control is used, which is capable of producing continuous variation of specimen temperature from 8.75 K to 300 K with an optional temperature sweep rate. We use an external loading device to stretch the superconducting tape quasi-statically with the maximum tension strain of 20%. A superconducting magnet manufactured by the NbTi strand is applied to provide magnetic field up to 5 T with a homogeneous range of 110 mm. The maximum fluctuation of the magnetic field is less than 1%. We design a kind of superconducting lead composed of YBa2Cu3O7-x coated conductor and beryllium copper alloy (BeCu) to transfer DC to the superconducting sample with the maximum value of 600 A. Most notably, this apparatus allows in situ observation of the electromagnetic property of superconducting tape using the classical magnetic-optical imaging.
28.3: A High‐Resolution Full Color TFT‐LCD on Transparent Plastic (2003)

Abstract We developed a 93 DPI full color TFT‐LCD (2.2 inch) on transparent plastic (PES) using hydrogenated amorphous silicon thin film transistor (a‐Si:H TFT). The low temperature process (&lt;150) and the island formation of inorganic layers give a stress‐free AMLCD on PES.
XRCC1 haploinsufficiency in mice has little effect on aging, but adversely modifies exposure-dependent susceptibility (2011)

Oxidative DNA damage plays a role in disease development and the aging process. A prominent participant in orchestrating the repair of oxidative DNA damage, particularly single-strand breaks, is the scaffold protein XRCC1. A series of chronological and biological aging parameters in XRCC1 heterozygous (HZ) mice were examined. HZ and wild-type (WT) C57BL/6 mice exhibit a similar median lifespan of ~26 months and a nearly identical maximal life expectancy of ~37 months. However, a number of HZ animals (7 of 92) showed a propensity for abdominal organ rupture, which may stem from developmental abnormalities given the prominent role of XRCC1 in endoderm and mesoderm formation. For other end-points evaluated-weight, fat composition, blood chemistries, condition of major organs, tissues and relevant cell types, behavior, brain volume and function, and chromosome and telomere integrity-HZ mice exhibited by-and-large a normal phenotype. Treatment of animals with the alkylating agent azoxymethane resulted in both liver toxicity and an increased incidence of precancerous lesions in the colon of HZ mice. Our study indicates that XRCC1 haploinsufficiency in mammals has little effect on chronological longevity and many key biological markers of aging in the absence of environmental challenges, but may adversely affect normal animal development or increase disease susceptibility to a relevant genotoxic exposure.