gebhart/patrepeval huggingface dataset:
Molecular Manipulations of the Catalytic RNAs from the Human Hepatitis Delta Virus (2003)

Hepatitis delta virus (HDV) is an infectious, subviral, pathogen that is associated with a high incidence of fulminant hepatitis in humans. It consists of a closed-circular, single-stranded, RNA genome of about 1700 nucleotides in length that is replicated by a rolling-circle mechanism (reviewed by refs. and ). There is no DNA intermediate. The infectious genomic strand is a template for an RNA-dependent RNA polymerase (most likely a modified activity of the host’s RNA polymerase II) that generates linear single-stranded multimers of the antigenomic sense. These linear multimers are site-specifically cleaved and ligated to form the closed-circular antigenomic RNAs, which are likewise templates for rolling-circle replication. The linear genomic multimers are also site-specifically cleaved and ligated, and the resulting circular RNAs are subsequently encapsulated to form new infectious particles.
Three dimensional culture of HepG2 liver cells on a rat decellularized liver matrix for pharmacological studies (2015)

Three-dimensional in vitro tumor models are needed to obtain more information about drug behavior in tumors. The aim of this study is to establish a new model for hepatocellular carcinoma (HCC) using decellularized rat livers. After generating the rat liver scaffolds, HepG2 liver cancer cells were perfused via the portal vein and placed in a bioreactor for 10 days. Histology was performed to analyze cell distribution within the scaffolds. Function and tumor-related gene expression were examined by polymerase chain reaction (PCR). We evaluated the function of HepG2 cells grown on scaffolds in the presence of a well-known anti-cancer drug to investigate the potential application of our system for drug screening. The scaffolds were devoid of cellular materials and preserved extracellular matrix components. HepG2 cells grew well on the scaffolds. The PCR results showed that the cells maintained function and invasion ability at significantly higher levels than cells grown on two-dimensional (2-D) dishes or spheroids on Matrigel. Unlike the 2-D cultures, albumin secretion and alpha-fetoprotein expression in three-dimensional cultures were less susceptible to lower concentrations of the drug. Cells grown in scaffolds seemed to respond to the drug in an analogous manner to its known activity in vivo. These findings strengthen the potential use of rat liver scaffolds for screening HCC drugs.
The 9- cis -epoxycarotenoid cleavage reaction is the key regulatory step of abscisic acid biosynthesis in water-stressed bean (1999)

Abscisic acid (ABA), a cleavage product of carotenoids, is involved in stress responses in plants. A well known response of plants to water stress is accumulation of ABA, which is caused by de novo synthesis. The limiting step of ABA biosynthesis in plants is presumably the cleavage of 9-cis-epoxycarotenoids, the first committed step of ABA biosynthesis. This step generates the C(15) intermediate xanthoxin and C(25)-apocarotenoids. A cDNA, PvNCED1, was cloned from wilted bean (Phaseolus vulgaris L.) leaves. The 2, 398-bp full-length PvNCED1 has an ORF of 615 aa and encodes a 68-kDa protein. The PvNCED1 protein is imported into chloroplasts, where it is associated with the thylakoids. The recombinant protein PvNCED1 catalyzes the cleavage of 9-cis-violaxanthin and 9'-cis-neoxanthin, so that the enzyme is referred to as 9-cis-epoxycarotenoid dioxygenase. When detached bean leaves were water stressed, ABA accumulation was preceded by large increases in PvNCED1 mRNA and protein levels. Conversely, rehydration of stressed leaves caused a rapid decrease in PvNCED1 mRNA, protein, and ABA levels. In bean roots, a similar correlation among PvNCED1 mRNA, protein, and ABA levels was observed. However, the ABA content was much less than in leaves, presumably because of the much smaller carotenoid precursor pool in roots than in leaves. At 7 degrees C, PvNCED1 mRNA and ABA were slowly induced by water stress, but, at 2 degrees C, neither accumulated. The results provide evidence that drought-induced ABA biosynthesis is regulated by the 9-cis-epoxycarotenoid cleavage reaction and that this reaction takes place in the thylakoids, where the carotenoid substrate is located.
Molecular Basis for Hematopoietic/Mesenchymal Interaction during Initiation of Peyer's Patch Organogenesis (2001)

Mice deficient in lymphotoxin beta receptor (LTbetaR) or interleukin 7 receptor alpha (IL-7Ralpha) lack Peyer's patches (PPs). Deficiency in CXC chemokine receptor 5 (CXCR5) also severely affects the development of PPs. A molecular network involving these three signaling pathways has been implicated in PP organogenesis, but it remains unclear how they are connected during this process. We have shown that PP organogenesis is initiated at sites containing IL-7Ralpha(+) lymphoid cells and vascular cell adhesion molecule (VCAM)-1/intercellular adhesion molecule (ICAM)-1 expressing nonlymphoid elements. Here we characterize these lymphoid and nonlymphoid components in terms of chemokine signals. The lymphoid population expresses CXCR5 and has a strong chemotactic response to B lymphocyte chemoattractant (BLC). Importantly, chemokines produced by VCAM-1(+)ICAM-1(+) nonlymphoid cells mediate the recruitment of lymphoid cells. Furthermore, we show that these VCAM-1(+)ICAM-1(+) cells are mesenchymal cells that are activated by lymphoid cells through the LTbetaR to express adhesion molecules and chemokines. Thus, promotion of PP development relies on mutual interaction between mesenchymal and lymphoid cells.
Identification of two proteins associated with virulence of Streptococcus suis type 2 (1991)

The protein profiles of various cell fractions of 180 strains of Streptococcus suis type 2, which were isolated from diseased pigs, from healthy pigs when they were slaughtered, and from human patients, were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting. The isolates from diseased pigs contained two proteins that were absent in most of the isolates from healthy pigs. One of these proteins was a 136-kDa protein that was previously identified as the muramidase-released protein (MRP). This protein was predominantly detected in protoplast supernatants and culture supernatants. The second protein was a 110-kDa protein that was detected only in culture supernatants and therefore was provisionally called extracellular factor (EF). Three phenotypes of S. suis type 2 strains were recognized. Isolates from organs of diseased pigs mainly belonged to the MRP+ EF+ phenotype (77%), while isolates from tonsils of healthy pigs mainly had the MRP- EF- phenotype (86%). Most of the isolates from human patients contained MRP (89%); 74% had the MRP+ EF- phenotype. These findings confirm the results of previous investigations which demonstrated that S. suis type 2 strains differ in virulence. Monoclonal antibodies raised against the 110-kDa EF recognized proteins with higher molecular weights in culture supernatants of all of the strains with the MRP+ EF- phenotype. However, none of the strains with the MRP+ EF+ phenotype produced these high-molecular-weight proteins. Our results demonstrate that MRP and EF are associated with virulence. This suggests that one or both of these proteins are virulence factors that play a role in the pathogenesis of S. suis type 2 infections in pigs and human patients.
Stereoselective hydrolysis of triglycerides by animal and microbial lipases (1993)

In the present paper, a study on the stereoselectivity of 25 lipases of animal and microbial origin towards homogeneous prochiral triglycerides is presented. All the lipases tested catalyse the hydrolysis of the chemically alike but sterically nonequivalent ester groups in trioctanoin and triolein with different degrees of stereobias, depending on the fatty acyl chain length of the substrate (Rogalska et al., J. Biol. Chem. 256:20271-20276, 1990). Hydrolysis of the sn-2 ester group is catalysed by very few lipases and only Candida antarctica A shows a clear preference for this position. Most of the lipases investigated (12 with trioctanoin and 16 with triolein) showed a preference for the sn-1 position. Using trioctanoin as substrate we observed a total stereoselectivity for position sn-1 with Pseudomonas sp. and Pseudomonas aeruginosa and for position sn-3 with Candida antarctica B. This was not the case with triolein as substrate. Among the 23 lipases studied here and the other two lipases described previously (Rogalska et al., J. Biol. Chem. 256:20271-20276, 1990), 17 show a higher stereoselectivity with trioctanoin than with triolein. With guinea pig pancreatic lipase and with three mold lipases (Geotrichum candidum M, Geotrichum candidum A, and Candida antarctica B), the preference switches from sn-3 to sn-1 when the acyl chain length increases from eight to 18 carbon atoms. The main conclusion to emerge from the present study is that the specific stereopreference of each lipase for a given substrate under given lipolytic conditions can be said to be its fingerprint.
Genetic analysis of osmotic and cold stress signal transduction in Arabidopsis: interactions and convergence of abscisic acid-dependent and abscisic acid-independent pathways. (1997)

To dissect genetically the complex network of osmotic and cold stress signaling, we constructed lines of Arabidopsis plants displaying bioluminescence in response to low temperature, drought, salinity, and the phytohormone abscisic acid (ABA). This was achieved by introducing into Arabidopsis plants a chimeric gene construct consisting of the firefly luciferase coding sequence (LUC) under the control of the stress-responsive RD29A promoter. LUC activity in the transgenic plants, as assessed by using in vivo luminescence imaging, faithfully reports the expression of the endogenous RD29A gene. A large number of cos (for constitutive expression of osmotically responsive genes), los (for low expression of osmotically responsive genes), and hos (for high expression of osmotically responsive genes) mutants were identified by using a high-throughput luminescence imaging system. The los and hos mutants were grouped into 14 classes according to defects in their responses to one or a combination of stress and ABA signals. Based on the classes of mutants recovered, we propose a model for stress signaling in higher plants. Contrary to the current belief that ABA-dependent and ABA-independent stress signaling pathways act in a parallel manner, our data reveal that these pathways cross-talk and converge to activate stress gene expression.
ZooKeeper: wait-free coordination for internet-scale systems (2010)

In this paper, we describe ZooKeeper, a service for coordinating processes of distributed applications. Since ZooKeeper is part of critical infrastructure, ZooKeeper aims to provide a simple and high performance kernel for building more complex coordination primitives at the client. It incorporates elements from group messaging, shared registers, and distributed lock services in a replicated, centralized service. The interface exposed by Zoo-Keeper has the wait-free aspects of shared registers with an event-driven mechanism similar to cache invalidations of distributed file systems to provide a simple, yet powerful coordination service. The ZooKeeper interface enables a high-performance service implementation. In addition to the wait-free property, ZooKeeper provides a per client guarantee of FIFO execution of requests and linearizability for all requests that change the ZooKeeper state. These design decisions enable the implementation of a high performance processing pipeline with read requests being satisfied by local servers. We show for the target workloads, 2:1 to 100:1 read to write ratio, that ZooKeeper can handle tens to hundreds of thousands of transactions per second. This performance allows ZooKeeper to be used extensively by client applications. 1
Chemotactic and Anaphylatoxic Fragment Cleaved from the Fifth Component of Guinea Pig Complement (1968)

The fifth component of guinea pig complement, with a sedimentation coefficient 7.8S, is cleaved by sensitized sheep erythrocytes treated with the first four components of complement into two fragments with sedimentation coefficients of 7.4S and 1.5S. The smaller fragment, with a molecular weight of about 15,000, possesses chemotactic activity for rabbit polymorphonuclear leukocytes, as well as anaphylatoxic activity for guinea pig ileum.
Poly(amido‐amine)s and poly(ester‐amine)s based on aromatic amines containing carboxyl groups (1995)

Abstract The preparation of poly(amido‐amine)s and poly(ester‐amine)s via polyaddition between aromatic amines containing free or esterified carboxyl groups and compounds with activated double bounds [ N , N ′‐methylenebis(acrylamide), 1,4‐diacryloylpiperazine and 1,3‐propanediyl diacrylate] is described. The products obtained are typical polyelectrolytes, their solutions exhibiting anomalous viscosity behaviour.
A Clinical Inflammatory Syndrome Attributable to Aerosolized Lipid–DNA Administration in Cystic Fibrosis (2001)

Immunologic reactivity to lipid-DNA conjugates has traditionally been viewed as less of an issue than with viral vectors. We performed a dose escalation safety trial of aerosolized cystic fibrosis transmembrane conductance regulator (CFTR) cDNA to the lower airways of eight adult cystic fibrosis patients, and monitored expression by RT-PCR. The cDNA was complexed to a cationic lipid amphiphile (GL-67) consisting of a cholesterol anchor linked to a spermine head group. CFTR transgene was detected in three patients at 2-7 days after gene administration. Four of the eight patients developed a pronounced clinical syndrome of fever (maximum of 103.3EF), myalgias, and arthralgia beginning within 6 hr of gene administration. Serum IL-6 but not levels of IL-8, IL-1, TNF-alpha, or IFN-gamma became elevated within 1-3 hr of gene administration. No antibodies to the cationic liposome or plasmid DNA were detected. We found that plasmid DNA by itself elicited minimal proliferation of peripheral blood mononuclear cells taken from study patients, but led to brisk immune cell proliferation when complexed to a cationic lipid. Lipid and DNA were synergistic in causing this response. Cellular proliferation was also seen with eukaryotic DNA, suggesting that at least part of the immunologic response to lipid-DNA conjugates is independent of unmethylated (E. coli-derived) CpG sequences that have previously been associated with innate inflammatory changes in the lung.
Jini Specification (1999)

From the Publisher:
This book contains the formal specification for the Jini technology. It offers a review of distributed computing fundamentals, an overview of the Jini architecture, and an introduction to the key concepts that are the source of the technology's simplicity and powerremote objects, leasing, distributed events, and a two-phase commit protocol. The formal specification provides the definitive description of every element of the Jini architecture, including detailed information on such topics as: 
Jini Discovery and Join protocols Jini Entry usage and the AbstractEntry class Jini Distributed Leasing concepts Jini Distributed Event programming model Jini Transaction model and semantics Jini Lookup service and lookup attribute schema Jini device architecture 


As networks continue to pervade our personal and professional lives, there is an urgent call for the flexible and robust network infrastructure that Jini represents.
Elevated levels of tumour endothelial marker-8 in human breast cancer and its clinical significance (2006)

Tumour endothelial marker-8 (TEM-8) belongs to a family of endothelial markers that are raised during tumour angiogenesis. We have recently reported aberrant expression of TEMs at the mRNA level in human breast cancer. This study sought to examine the level of TEM-8 expression at the protein and mRNA level in human breast cancer tissue, and in a panel of human breast cancer cell lines. We also wished to determine if TEM-8 can be used as a suitable marker for identifying tumour associated micro-vessels. At the mRNA level more tumours showed positive TEM-8 expression compared to normal background tissue. TEM-8 was detected in a variety of breast cancer cell lines, endothelial cells (HECV) and in a human fibroblast cell line (MRC5) at both the mRNA and protein level. Using immunohistochemistry the distribution of TEM-8 staining was more widespread in invasive breast cancer tissue compared to normal background tissue. Furthermore, the TEM-8 marker was found to be more discriminatory in identifying micro-vessels in tumour endothelium (2.8+/-0.83 vs. normal 1.66+/-0.52; P<0.011), compared to the vWFA marker (1.61+/-0.54 vs. normal 2.71+/-0.76; P<0.009). Raised levels of TEM-8 were associated with shorter survival outcome, but were not correlated to disease-free survival as shown by Kaplan-Meier and Cox regression analysis. We conclude that TEM-8 is a useful marker for identifying tumour associated micro-vessels and that elevated levels are associated with disease progression, which may have some bearing on the prognostic outcome in breast cancer.
Safety and Tumor Responses with Lambrolizumab (Anti–PD-1) in Melanoma (2013)

In patients with advanced melanoma, including those who had had disease progression while they had been receiving ipilimumab, treatment with lambrolizumab resulted in a high rate of sustained tumor regression, with mainly grade 1 or 2 toxic effects. (Funded by Merck Sharp and Dohme; ClinicalTrials.gov number, NCT01295827.).
Nanocomposites with Polymer Grafted Nanoparticles (2013)

A recurring challenge in the field of nanocomposites is to control the spatial distribution of nanoparticles (NPs) in a polymer matrix. This issue is of critical importance since it is now well-established that a specific NP dispersion state is necessary to optimize a desired property of polymer nanocomposites (PNCs). This Perspective focuses on one particular approach to controlling NP spatial dispersion, and hence the properties of polymer-based nanocomposites: the use of polymer-grafted NPs. Novel developments over the past decade in synthesis techniques allow us to controllably functionalize NPs with polymer chains. This has ignited considerable interest in this field, leading to significant advances in creating nanocomposites with tunable physical properties. We begin by briefly outlining the various synthetic strategies for functionalizing NPs and then discuss various methods for controllably dispersing them in a polymer matrix. The consequences of having states with controlled NP dispersion on nanocomposite properties, primarily the mechanical and optical properties, will then be discussed. In every section of this Perspective, we have an explicit discussion of unresolved issues and critical questions which need to be addressed for continuing progress, especially as it relates to current and potential applications of this class of materials.
Semaphorins and cell migration (2001)

Les semaphorines ont ete initialement decrites dans le systeme nerveux central pour leurs proprietes repulsives sur le guidage axonal. Il s'agit d'une famille de molecules caracterisees par la presence d'un domaine dit Sema dans leur region extracellulaire. La decouverte de nombreux membres a conduit a la classification en sept sous-familles. Il est apparu que des semaphorines pouvaient aussi exercer un effet attractif sur les axones conferant a ces molecules une place importante dans la regulation de la migration des cellules nerveuses. De facon interessante, des semaphorines ont egalement ete identifiees hors du systeme nerveux. C'est ainsi le cas pour CD100 decouverte initialement pour ses proprietes dans l'activation lymphocytaire humaine puis identifiee comme semaphorine apres clonage du gene correspondant. Il existe egalement des semaphorines virales et l'expression d'un certain nombre de genes de semaphorine a ete correlee a certaines pathologies comme des cancers ou des pathologies inflammatoires. Il semble que ces semaphorines « non-nerveuses » puissent participer a la regulation de la migration dans le systeme immunitaire. Certaines modifient les capacites adherentes des cellules (comme CD100 ou la semaphorine de vaccine), d'autres paraissent influer plus directement sur le phenomene de migration avec en particulier un effet inhibiteur de CD100. L'integration de ces stimuli par rapport aux autres signaux chimiotactiques reste a determiner.
Multifunctional interventional devices for MRI: A combined electrophysiology/MRI catheter (2002)

The design and application of a two-wire electrophysiology (EP) catheter that simultaneously records the intracardiac electrogram and receives the MR signal for active catheter tracking is described. The catheter acts as a long loop receiver, allowing for visualization of the entire catheter length while simultaneously behaving as a traditional two-wire EP catheter, allowing for intracardiac electrogram recording and ablation. The application of the device is demonstrated by simultaneously tracking the catheter and recording the intracardiac electrogram in canine models using 7 and 10 frame/sec real-time imaging sequences. Using solely MR imaging, the entire catheter was visualized and guided from the jugular vein into the cardiac chambers, where the intracardiac electrogram was recorded. By combining several functions in a single, simple structure, the excellent tissue contrast and functional imaging capabilities of MR can be used to improve the efficacy of EP interventions. This catheter will facilitate MR-guided interventions and demonstrates the design of multifunctional interventional devices for use in MRI.
Flexible, solid-state, ion-conducting membrane with 3D garnet nanofiber networks for lithium batteries (2016)

Beyond state-of-the-art lithium-ion battery (LIB) technology with metallic lithium anodes to replace conventional ion intercalation anode materials is highly desirable because of lithium's highest specific capacity (3,860 mA/g) and lowest negative electrochemical potential (∼3.040 V vs. the standard hydrogen electrode). In this work, we report for the first time, to our knowledge, a 3D lithium-ion-conducting ceramic network based on garnet-type Li6.4La3Zr2Al0.2O12 (LLZO) lithium-ion conductor to provide continuous Li(+) transfer channels in a polyethylene oxide (PEO)-based composite. This composite structure further provides structural reinforcement to enhance the mechanical properties of the polymer matrix. The flexible solid-state electrolyte composite membrane exhibited an ionic conductivity of 2.5 × 10(-4) S/cm at room temperature. The membrane can effectively block dendrites in a symmetric Li | electrolyte | Li cell during repeated lithium stripping/plating at room temperature, with a current density of 0.2 mA/cm(2) for around 500 h and a current density of 0.5 mA/cm(2) for over 300 h. These results provide an all solid ion-conducting membrane that can be applied to flexible LIBs and other electrochemical energy storage systems, such as lithium-sulfur batteries.
Oral R115866 in the treatment of moderate to severe facial acne vulgaris: an exploratory study (2007)

The current data indicate that treatment with oral R115866 1 mg once daily for 12 weeks in patients with moderate to severe facial acne vulgaris is efficacious and well tolerated and merits further investigation.
Multiple priority, per flow, dual GCRA rate controller for ATM switches (2002)

We propose a rate controller for ATM switches. The rate controller supports multiple priorities, and dual leaky bucket (GCRA) traffic descriptors (such as VBR). While regulating each stream independently, our rate controller requires relatively modest computation bandwidth so that it can be implemented without any additional special-purpose hardware. It also enjoys the important advantage of being decoupled from the link schedulers. We study what is the best way to allocate resources to rate controllers along the path of connection, and demonstrate the effectiveness of aggressive shaping at the network ingress.