gebhart/patrepeval huggingface dataset:
Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of –1 ribosomal frameshifting (2009)

Many viruses use programmed -1 ribosomal frameshifting to express defined ratios of structural and enzymatic proteins. Pseudoknot structures in messenger RNAs stimulate frameshifting in upstream slippery sequences. The detailed molecular determinants of pseudoknot mechanical stability and frameshifting efficiency are not well understood. Here we use single-molecule unfolding studies by optical tweezers, and frameshifting assays to elucidate how mechanical stability of a pseudoknot and its frameshifting efficiency are regulated by tertiary stem-loop interactions. Mechanical unfolding of a model pseudoknot and mutants designed to dissect specific interactions reveals that mechanical stability depends strongly on triplex structures formed by stem-loop interactions. Combining single-molecule and mutational studies facilitates the identification of pseudoknot folding intermediates. Average unfolding forces of the pseudoknot and mutants ranging from 50 to 22 picoNewtons correlated with frameshifting efficiencies ranging from 53% to 0%. Formation of major-groove and minor-groove triplex structures enhances pseudoknot stem stability and torsional resistance, and may thereby stimulate frameshifting. Better understanding of the molecular determinants of frameshifting efficiency may facilitate the development of anti-virus therapeutics targeting frameshifting.
AAV Vector–mediated RNAi of Mutant Huntingtin Expression Is Neuroprotective in a Novel Genetic Rat Model of Huntington's Disease (2008)

We report the characterization of a new rapid-onset model of Huntington's disease (HD) generated by adeno-associated virus (AAV) vector-mediated gene transfer of N-terminal huntingtin (htt) constructs into the rat striatum. Expression of exon 1 of mutant htt containing 70 CAG repeats rapidly led to neuropathological features associated with HD. In addition, we report novel data relating to neuronal transduction of AAV vectors that modulated the phenotype observed in this model. Quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) revealed that AAV vector-mediated expression in the striatum increased by >100-fold as compared to the endogenous htt level. Moreover, AAV vectors exhibited nonuniform transduction patterns in striatal neuronal populations, as well as axonal transport leading to transduction and neuronal cell death in the globus pallidus and substantia nigra (SN). These findings may inform future studies that utilize AAV vectors for neurodegenerative disease modeling. Further, RNA interference (RNAi) of mutant htt expression mediated by virus vector delivery of short hairpin RNAs (shRNAs) ameliorates early-stage disease phenotypes in transgenic mouse models of HD. However, it has not been reported whether shRNA-mediated knockdown of mutant htt expression is neuroprotective. AAV-shRNA was shown to mediate a dramatic knockdown of HD70 expression, preventing striatal neurodegeneration and concomitant motor behavioral impairment. These results provide further support for the use of AAV vector-mediated RNAi as a therapeutic strategy for HD.
Antizyme protects against abnormal accumulation and toxicity of polyamines in ornithine decarboxylase-overproducing cells. (1994)

Exposure of ornithine decarboxylase (ODC; L-ornithine carboxy-lyase, EC 4.1.1.17)-overproducing mouse FM3A cells to micromolar levels of spermine or spermidine caused abnormal accumulation and toxicity of polyamines. This was apparently due to the inefficiency of negative feedback control of polyamine transport by polyamines in ODC-overproducing cells. Since antizyme is the only protein thus far recognized that can interact with ODC, depletion of free antizyme was regarded as the reason for the abnormal accumulation of polyamines. Accordingly, ODC-overproducing cells were transfected with pMAMneoZ1 possessing rat antizyme cDNA under the control of a glucocorticoid-inducible promoter. In the transfected cells, the addition of dexamethasone caused an increase in the amount of antizyme with an apparent molecular mass of 27 kDa, a decrease in the amount of ODC, a decrease in the polyamine transport activity, and the recovery of growth inhibition or cell death. The results indicate that antizyme can regulate not only the amount of ODC but also the activity of polyamine transport.
Combining multiple sub-apertures for reduced-profile shipboard SATCOM-antenna panels (2002)

In naval SATCOM applications, there are advantages to using multiple antenna panels, each of limited scan range covering only a portion of the required hemisphere. For mechanical steering, the depth of each panel can be reduced by dividing the required aperture into smaller sub apertures at the cost of needing coherent combining. Some aspects of operating such an antenna system are considered. The EIRP, G/T and antenna patterns of combined signals are derived under the assumption of perfect coherent combining. Effects of errors in phase and in time-delay matching are provided in terms of power loss and data rate supported. Practical methods of implementing coherent combining are presented.
Resistance switching in epitaxial SrCoOx thin films (2014)

We observed bipolar switching behavior from an epitaxial strontium cobaltite film grown on a SrTiO3 (001) substrate. The crystal structure of strontium cobaltite has been known to undergo topotactic phase transformation between two distinct phases: insulating brownmillerite (SrCoO2.5) and conducting perovskite (SrCoO3−δ) depending on the oxygen content. The current–voltage characteristics of the strontium cobaltite film showed that it could have a reversible insulator-to-metal transition triggered by electrical bias voltage. We propose that the resistance switching in the SrCoOx thin film could be related to the topotactic phase transformation and the peculiar structure of SrCoO2.5.
Electrophilic aminoalkenylation of aromatics with .alpha.-chloroenamines (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrophilic aminoalkenylation of aromatics with .alpha.-chloroenaminesJacqueline Marchand-Brynaert and Leon GhosezCite this: J. Am. Chem. Soc. 1972, 94, 8, 2869–2870Publication Date (Print):April 1, 1972Publication History Published online1 May 2002Published inissue 1 April 1972https://pubs.acs.org/doi/10.1021/ja00763a061https://doi.org/10.1021/ja00763a061research-articleACS PublicationsRequest reuse permissionsArticle Views427Altmetric-Citations38LEARN 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
Realtime multi-party video conferencing service over information centric network (2015)

Current video conferencing design based on client-server or peer-to-peer architecture do not scale to large number of users. ICN addresses this through network-based multicast built on applications semantics. Considering the pull-based content primitive, scalability is also required to learn the current state of the media names (text, audio, video) of participants considering adhoc join/leave behavior due to variable number of participants, or situations involving mobility. We propose a solution based on an overlay of ICN-based service edge routers (iSER). iSERs being CCN routers allow content multicasting which allows data plane scalability. In [1], we proposed an architecture to sync names using services hosted on the iSER, scalable to large number of conference participants. This paper extends [1] for video conferencing, focussing on a conference participant video production and ingestion, employing (iSER) services to sync conference state among participants, and a controller infrastructure to realize it as a service. We evaluate our design with experiments over a prototype system and share initial results considering several parameters that affect the real-time quality of a video conferencing session in our implementation.
Antimutagenicity and Binding of Lactic Acid Bacteria from a Chinese Cheese to Mutagenic Pyrolyzates (1990)

The microbiological characteristics of Nai Ge Da, a traditional cheese in China, was investigated. The lactic acid bacteria species were identified as Streptococcus cremoris, Streptococcus lactis ssp. diacetylactis, Streptococcus faecalis, and Leuconostoc paramesenteroides, Leuconostoc dextranicum, and Leuconostoc mesenteroides. Streptococcus cremoris, and Leuconostoc paramesenteroides were the dominant strains. The antimutagenicities and binding of strains of S. cremoris and S. lactic ssp. diacetylactis to mutagenic pyrolyzates was investigated. The lyophilized cells of strains showed the highest inhibitory effect on the 3-amino-1,4-dimethyl-[5H]pyrido[4,3-b] indol (Trp-P-1) and 3-amino-1-methyl-[5H]pyrido[4,3-b] indol (Trp-P-2), but many strains had no significant inhibition against 2-amino-6-methyldipyrido[1,2-a:3',2'-d] imidazole (Glu-P-1). The Trp-P-1 and Trp-P-2 were effectively bound to all bacterial cells, but binding of Glu-P-1 to cells was not effective. Among the strains tested, S. cremoris C-25 not only indicated highest binding to Trp-P-1 and Trp-P-2, but it also it had a 25.36% binding ability with Glu-P-1. When all strains were autoclaved for 15 min at 120 degrees C, binding ability to mutagens was reduced by 3 to 19%. The decrease of binding ability of S. cremoris C-25 was much less, being only 2%. After heating at 80 degrees C for 3 h, the binding ability of all strains to mutagenic pyrolyzates was not much different from those of parent viable cells.
A two-level co-design framework for Xputer-based data-driven reconfigurable accelerators (2002)

Presents the parallelizing compilation environment CoDe-X (Co-Design for Xputers) for the simultaneous programming of transputer (Xputer) based accelerators and their hosts. This paper introduces its hardware/software co-design strategies at two levels of partitioning. CoDe-X performs profiling-driven host/accelerator partitioning at the first level, for performance optimization, and resource-driven sequential/structural partitioning of the accelerator source code at the second level, to optimize the utilization of its reconfigurable resources. To stress the significance of this application development methodology, the paper first gives an introduction to the underlying hardware platform.
Generation and Characterization of an Anti-CD19 Single-Chain Fv Immunotoxin Composed of C-Terminal Disulfide-Linked dgRTA (1997)

Our laboratory utilized two methods to produce the anti-CD19 immunotoxin containing a single-chain Fv (scFv) FVS191 and a ricin A chain (RTA). The first method produced the recombinant protein FVS191CDRTA from a fusing gene containing sequences encoding FVS191, catheptsin D proteinase digestion site (CD), and RTA. FVS191CDRTA did not show CD19 antigen binding and cytotoxic activity. The second method generated a disulfide-linked FVS191cys-dgRTA from a FVS191cys, the FVS191 with an additional C-terminal cysteine, and a deglycosylated RTA (dgRTA). The formation of FVS191cys-dgRTA is efficient; up to 70% of the proteins participating in the reaction had formed FVS191cys-dgRTA when the molar ratio of FVS191cys to dgRTA was 1:1. A competitive ELISA assay indicated that FVS191cys-dgRTA and the parental monoclonal antibody B43 possessed comparable CD19 binding abilities. The protein synthesis inhibition assay revealed that FVS191cys-dgRTA was toxic to CD19 positive cell lines, but it was less potent than the intact antibody-conjugated B43-dgRTA, which had an IC50 = 2 x 10(-11) M. 125I-Labeled FVS191 and 125I-labeled B43 were internalized by Nalm-6 cells at 37 degrees C as demonstrated by internalization studies; this result indicates that cross-linking of CD19 antigen is not required for the endocytosis of CD19 and raises the possibility that the lower cytotoxity of FVS191cys-dgRTA is not due to the monovalent binding of CD19 by FVS191cys-dgRTA. Our study with anti-CD19 scFv immunotoxin indicates that the formation of a disulfide-linked scFv immunotoxin is an alternative to the recombinant method of producing scFv immunotoxin.
Evolving Methods in Genetic Epidemiology. III. Gene-Environment Interaction in Epidemiologic Research (1997)

Effects on disease risk Genotype In the absence of envlronmentf No effect, Khoury et al. (24). t R, = disease risk among persons with exposure without genotype, divided by disease risk among persons with no exposure and no susceptible genotype; and R g = disease risk among persons with genotype without exposure, divided by disease risk among persons with no exposure and no susceptible genotype.
pH-Triggered Release from Nonphospholipid LUVs Modulated by the pKa of the Included Fatty Acid (2010)

It has been shown that mixtures of palmitic acid (PA) and cholesterol (Chol) or cholesterol sulfate (Schol) can form fluid bilayers. These bilayers could be extruded using standard extrusion techniques to obtain nonphospholipid large unilamellar vesicles (LUVs). These LUVs displayed a very limited passive permeability, associated with their high sterol content (typically 70 mol %). In addition, they showed a pH-dependent behavior dictated by the electrostatic interfacial interactions, which are drastically modulated by the protonation state of PA. Interestingly, the LUVs prepared with cholesterol were stable at high pH and the release of the content could be triggered by a pH decrease (i.e., the protonation of PA). In contrast, the LUVs including Schol were stable at low pH and a pH increase (leading to the deprotonation of PA) would induce the release. In the present study, we demonstrate that the pH triggering the release in these two systems can be dictated in a predictable manner by selecting a fatty acid with an appropriate pK(a). The pK(a) of the fatty acids was modulated by the presence of an electro-withdrawing group (hydroxyl or fluoro) in the alpha position of the carboxylic function. The fatty acid protonation state is shown to be a critical factor for the modulation of the liposome permeability. The described systems display a remarkable versatility regarding the pH-sensitivity because the nature of the sterol controls the overall pH stability of the LUVs while the fatty acid pK(a) fine-tunes the pH-induced release. Therefore, it is possible to rationally design LUVs with controlled release at a specific pH; this original aspect is beneficial to the use of LUVs for encapsulation, vectorization, and controlled release of active agents.
An International Reference Material for Radiocarbon Dating (1983)

In August 1980, the National Bureau of Standards (NBS) issued, in the form of oxalic acid, a new International Reference Material of contemporary 14 C for use in radiocarbon dating laboratories. This reference material was to replace the 1975 oxalic-acid standard, supplies of which had been practically exhausted in 1978. The preparation of the new oxalic-acid standard was described in a preliminary report, as were, also, the results then available for the activity-concentration ratio of the new to the old standard obtained by a number of leading international laboratories. With the recent completion of the analysis of all results submitted by the participating laboratories, NBS plans to issue these recently calibrated samples of oxalic acid as an NBS Standard Reference Material. There is, however, no significant difference in the reported value of its activity concentration, relative to that of the 1957 standard, from that given provisionally in 1980. Subsequent to our report (Cavallo and Mann, 1980) a further measurement of relative activity concentration was reported by the Radiocarbon Laboratory of Peking University. Their value, and that also for δ 13 C, is insignificantly different from the average value of the results submitted by the eleven laboratories that participated in the international comparison organized by NBS.
Simple Copy Number Determination with Reference Query Pyrosequencing (RQPS) (2010)

The accurate measurement of the copy number (CN) for an allele is often desired. We have developed a simple pyrosequencing-based method, reference query pyrosequencing (RQPS), to determine the CN of any allele in any genome by taking advantage of the fact that pyrosequencing can accurately measure the molar ratio of DNA fragments in a mixture that differ by a single nucleotide. The method involves the preparation of an RQPS probe, which contains two linked DNA fragments that match a reference allele with a known CN and a query allele with an unknown CN. In each fragment, a single nucleotide variation (SNV) is engineered to differentiate it from its genomic counterparts when the probe is mixed with genomic DNA. The ratios of the two pairs of fragments (probe reference vs. genomic reference and probe query vs. genomic query) in the mixture reflect the ratio between the probe and the genomic DNA in a CN-dependent manner. Pyrosequencing can be used to quantify these ratios and thus determine the CN of the query allele. This method could be used to measure the CN of any transgene, differentiate homozygotes from heterozygotes, detect the copy number variation (CNV) of endogenous genes, and screen embryonic stem (ES) cells targeted with bacterial artificial chromosome (BAC) vectors that are not compatible with standard screening methods.
Restriction endonuclease mapping of adenovirus 35, a type isolated from immunocompromised hosts (1985)

The DNA of adenovirus 35 (Ad35), a type recently associated with infections in immunocompromised hosts, was mapped by the use of BamHI, SmaI, PstI, EcoRI, and HpaI restriction endonucleases. In addition to standard mapping procedures, we used the in vitro adenovirus DNA replication system with origins at both physical ends of the linear molecule to determine the terminal fragments. Deletions of single restriction endonuclease sites in a group of closely related adenovirus isolates from patients with acquired immunodeficiency syndrome helped determine the location of some DNA fragments on the genome.
Fludarabine: a new agent with major activity against chronic lymphocytic leukemia (1989)

Fludarabine was used to treat 68 patients with previously treated chronic lymphocytic leukemia (CLL). Nine (13%) patients achieved a complete remission and 30 (44%) a partial remission. The response rates for Rai stages 0 to 2, 3, and 4 were 64%, 58%, and 50% respectively. Seventeen (43%) of the 40 Rai stage 1 to 3 patients and four (19%) of the Rai stage 4 patients returned to Rai stage 0. Survival was strongly correlated with the final Rai stage achieved. The survival of the 11 partial responders with residual disease consisting only of residual bone-marrow nodules was similar to the complete responders (36+ months) and superior to the other partial response patients (16 months). The response to fludarabine was rapid, with 36 (92%) of the 39 responders having achieved at least a partial response following the first three courses. Complete responses occurred in the blood, liver, spleen, and lymph nodes in 48% to 69% of the patients. Eradication of all disease in the bone marrow occurred in only 13% of the cases. Neutropenia and thrombocytopenia occurred in 56% and 25% of evaluable courses. Major infections occurred in 9% of evaluable courses and fevers of unknown origin or minor infections in 12% of courses respectively. Myelosuppression and infection were more common in patients with initial Rai stages 3 and 4 and in nonresponding patients. Other toxicity was mild. No CNS toxicity was noted.
Toxins from bacteria (2010)

Bacterial toxins damage the host at the site of bacterial infection or distant from the site. Bacterial toxins can be single proteins or oligomeric protein complexes that are organized with distinct AB structure-function properties. The A domain encodes a catalytic activity. ADP ribosylation of host proteins is the earliest post-translational modification determined to be performed by bacterial toxins; other modifications include glucosylation and proteolysis. Bacterial toxins also catalyze the non-covalent modification of host protein function or can modify host cell properties through direct protein-protein interactions. The B domain includes two functional domains: a receptor-binding domain, which defines the tropism of a toxin for a cell and a translocation domain that delivers the A domain across a lipid bilayer, either on the plasma membrane or the endosome. Bacterial toxins are often characterized based upon the secretion mechanism that delivers the toxin out of the bacterium, termed types I-VII. This review summarizes the major families of bacterial toxins and also describes the specific structure-function properties of the botulinum neurotoxins.
Design of Raspberry‐Shaped Microcarriers with Adjustable Protrusions and Functional Groups for the Improvement of Lipase Immobilization and Biocatalysis: Environmentally Friendly Esterification of Oleic Acid for Biodiesel (2016)

Abstract The front cover artwork for Issue 16/2016 is provided by researchers from Qiuyu Zhang's group, Northwestern Polytechnical University (P. R. China). The image shows raspberry‐shaped microparticles with adjustable protrusions are designed and synthetized for lipase immobilization to catalyze esterification of oleic acid for biodiesel under mild condition. See the Full Paper itself at http://dx.doi.org/10.1002/cctc.201600413 .
Enzyme-Sensitive Magnetic Resonance Imaging Targeting Myeloperoxidase Identifies Active Inflammation in Experimental Rabbit Atherosclerotic Plaques (2009)

The present study represents a unique approach in the detection of inflammation in atherosclerotic plaques by examining macrophage function and the activity of an effector enzyme to noninvasively provide both anatomic and functional information in vivo.
The relationship between the spleen colony-forming cell and the haemopoietic stem cell. (1978)

Several experimental findings that are inconsistent with the view that the spleen colony-forming cell (CFU-S) is the primary haemopoietic stem cell are reviewed. Recovery of CFU-S, both quantitatively and qualitatively, can proceed differently depending upon the cytotoxic agent or regime used to bring about the depletion. The virtual immortality of the stem cell population is at variance with evidence that the CFU-S population has an 'age-structure' which has been invoked by several workers to explain experimental and clinical observations. To account for these inconsistencies, a hypothesis is proposed in which the stem cell is seen in association with other cells which determine its behaviour. It becomes essentially a fixed tissue cell. Its maturation is prevented and, as a result, its continued proliferation as a stem cell is assured. Its progeny, unless they can occupy a similar stem cell 'niche', are first generation colony-forming cells, which proliferate and mature to acquire a high probability of differentiation, i.e., they have an age-structure. Some of the experimental situations reviewed are discussed in relation to the proposed hypothesis.