gebhart/patrepeval huggingface dataset:
Supplemental Treatment for Huntington’s Disease with miR-132 that Is Deficient in Huntington’s Disease Brain (2018)

Huntington's disease (HD) is an intractable neurodegenerative disorder caused by mutant Huntingtin (HTT) proteins that adversely affect various biomolecules and genes. MicroRNAs (miRNAs), which are functional small non-coding RNAs, are also affected by mutant HTT proteins. Here, we show amelioration in motor function and lifespan of HD-model mice, R6/2 mice, by supplying miR-132 to HD brains using a recombinant adeno-associated virus (rAAV) miRNA expression system. miR-132 is an miRNA related to neuronal maturation and function, but the level of miR-132 in the brain of R6/2 mice was significantly lower than that of wild-type mice. Our miR-132 supplemental treatment, i.e., supplying miR-132 to the brain, produced symptomatic improvement or retarded disease progression in R6/2 mice; interestingly, it had little effect on disease-causing mutant HTT mRNA expression and its products. Therefore, the findings suggest that there may be a therapeutic way to treat HD without inhibiting and/or repairing disease-causing HTT genes and gene products. Although miR-132 supplement may not be a definitive treatment for HD, it may become a therapeutic method for relieving HD symptoms and delaying HD progression.
A Protracted and Dynamic Maturation Schedule Underlies Arabidopsis Leaf Development (2008)

Leaf development has been monitored chiefly by following anatomical markers. Analysis of transcriptome dynamics during leaf maturation revealed multiple expression patterns that rise or fall with age or that display age-specific peaks. These were used to formulate a digital differentiation index (DDI) based on a set of selected markers with informative expression during leaf ontogeny. The leaf-based DDI reliably predicted the developmental state of leaf samples from diverse sources and was independent of mitotic cell division transcripts or propensity of specific cell types. When calibrated by informative root markers, the same algorithm accurately diagnosed dissected root samples. We used the DDI to characterize plants with reduced activities of multiple CINCINNATA (CIN)-TCP (TEOSINTE BRANCHED1, CYCLOIDEA, PCF) growth regulators. These plants had giant curled leaves made up of small cells with abnormal shape, low DDI scores, and low expression of mitosis markers, depicting the primary role of CIN-TCPs as promoters of differentiation. Delayed activity of several CIN-TCPs resulted in abnormally large but flat leaves with regular cells. The application of DDI has therefore portrayed the CIN-TCPs as heterochronic regulators that permit the development of a flexible and robust leaf form through an ordered and protracted maturation schedule.
Integrated Modeling Program, Applied Chemical Theory (IMPACT) (2005)

We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanics technologies we include a status report for the fixed charge and polarizable force fields that can be used with the program and illustrate how the force fields, when used together with new atom typing and parameter assignment modules, have greatly expanded the coverage of organic compounds and medicinally relevant ligands. As we discuss in this review, explicit solvent simulations have been used to guide our design of implicit solvent models based on the generalized Born framework and a novel nonpolar estimator that have recently been incorporated into the program. With IMPACT it is possible to use several different advanced conformational sampling algorithms based on combining features of molecular dynamics and Monte Carlo simulations. The program includes two specialized molecular mechanics modules: Glide, a high-throughput docking program, and QSite, a mixed quantum mechanics/molecular mechanics module. These modules employ the IMPACT infrastructure as a starting point for the construction of the protein model and assignment of molecular mechanics parameters, but have then been developed to meet specialized objectives with respect to sampling and the energy function.
From Microporous to Mesoporous Molecular Sieve Materials and Their Use in Catalysis (1997)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFrom Microporous to Mesoporous Molecular Sieve Materials and Their Use in CatalysisAvelino CormaView Author Information Instituto de Tecnología Química, UPV-CSIC, Universidad Politécnica de Valencia, Avda. de los Naranjos s/n, 46022 Valencia, SpainCite this: Chem. Rev. 1997, 97, 6, 2373–2420Publication Date (Web):October 1, 1997Publication History Received7 April 1997Revised16 June 1997Published online1 October 1997Published inissue 1 October 1997https://pubs.acs.org/doi/10.1021/cr960406nhttps://doi.org/10.1021/cr960406nresearch-articleACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views29508Altmetric-Citations5085LEARN 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:Catalysts,Materials,Porous materials,Surfactants,Zeolites Get e-Alerts
Comparison of different antisense strategies in mammalian cells using locked nucleic acids, 2'-O-methyl RNA, phosphorothioates and small interfering RNA (2003)

Locked nucleic acids (LNAs) and double-stranded small interfering RNAs (siRNAs) are rather new promising antisense molecules for cell culture and in vivo applications. Here, we compare LNA-DNA-LNA gapmer oligonucleotides and siRNAs with a phosphorothioate and a chimeric 2'-O-methyl RNA-DNA gapmer with respect to their capacities to knock down the expression of the vanilloid receptor subtype 1 (VR1). LNA-DNA-LNA gapmers with four or five LNAs on either side and a central stretch of 10 or 8 DNA monomers in the center were found to be active gapmers that inhibit gene expression. A comparative co-transfection study showed that siRNA is the most potent inhibitor of VR1-green fluorescent protein (GFP) expression. A specific inhibition was observed with an estimated IC50 of 0.06 nM. An LNA gapmer was found to be the most efficient single-stranded antisense oligonucleotide, with an IC50 of 0.4 nM being 175-fold lower than that of commonly used phosphorothioates (IC50 approximately 70 nM). In contrast, the efficiency of a 2'-O-methyl-modified oligonucleotide (IC50 approximately 220 nM) was 3-fold lower compared with the phosphorothioate. The high potency of siRNAs and chimeric LNA-DNA oligonucleotides make them valuable candidates for cell culture and in vivo applications targeting the VR1 mRNA.
Safeguarding gene drive experiments in the laboratory (2015)

Multiple stringent confinement strategies should be used whenever possible
Expandable intraluminal graft: a preliminary study. Work in progress. (1985)

To overcome the problem of recurrence of stenosis after vascular balloon dilatations, we developed an expandable, intraluminal graft that allows dilatation of the lesion and simultaneous placement of a supportive endoprosthesis to prevent recoil of the arterial wall. The graft is made of continuous, woven, stainless steel wire. The resulting tubular mesh has a wall thickness of 200-450 micron and 80% open surface. The grafts, mounted on angioplasty catheters, are introduced through 8-12-F Teflon sheaths. Eleven grafts of 6, 8, and 10 mm in diameter by 20 mm long were placed in the aorta, common carotid, superior mesenteric, iliac, and renal arteries of dogs. Six grafts showed no stenosis in follow-up studies of up to 8 weeks. Two grafts had moderate stenosis as a result of neointimal hyperplasia. Two partial and one complete graft thrombosis occurred in nonheparinized animals in which the graft outflow was restricted. Anticoagulant was not used on a long-term basis. Light and electron microscopy studies showed complete covering of the graft's inner surface by endothelium at 3 weeks.
Suppression of boron penetration in p-channel MOSFETs using polycrystalline Si/sub 1-x-y/GexCy gate layers (2001)

Boron penetration through thin gate oxides in p-channel MOSFETs with heavily boron-doped gates causes undesirable positive threshold voltage shifts. P-channel MOSFETs with polycrystalline Si/sub 1-x-y/Ge/sub x/C/sub y/ gate layers at the gate-oxide interface show substantially reduced boron penetration and increased threshold voltage stability compared to devices with all poly Si gates or with poly Si/sub 1-x/Ge gate layers. Boron accumulates in the poly Si/sub 1-x-y/Ge/sub x/C/sub y/ layers in the gate, with less boron entering the gate oxide and substrate. The boron in the poly Si/sub 1-x-y/Ge/sub x/C/sub y/ appears to be electrically active, providing similar device performance compared to the poly Si or poly Si/sub 1-x/Ge/sub x/ gated devices.
Leptin Accelerates Autoimmune Diabetes in Female NOD Mice (2002)

We have recently shown that leptin, the product of the obese gene, can directly influence T-cell function. In the work presented here, we explored the role of leptin in the development of spontaneous autoimmunity in the nonobese diabetic (NOD) mouse, an animal model for the study of human insulin-dependent diabetes mellitus (type 1 diabetes). We found that expression of serum leptin increased soon before the onset of hyperglycemia and diabetes in susceptible females. A pathogenetic role of leptin was assessed by administering recombinant leptin to young female and male NOD mice. Intraperitoneal injections of leptin accelerated autoimmune destruction of insulin-producing beta-cells and significantly increased interferon-gamma production in peripheral T-cells. These findings indicate that leptin can favor proinflammatory cell responses and directly influence development of autoimmune disease mediated by Th1 responses.
Further Characterization of the Fate of Human Monoclonal Antibodies in Rhesus Monkeys (1988)

We have shown previously that human monoclonal antibodies are not very immunogenic in rhesus monkeys, with only one monkey out of five mounting an anti-monoclonal antibody response. Two additional monkeys have been injected multiple times with much larger amounts of one human monoclonal antibody. No anti-antibody response has been detected in these monkeys. Structural changes that occur in the monoclonal antibodies over time in vivo have been investigated by Western Blots using anti-idiotypic antisera. Sodium dodecyl sulfate gel electrophoresis reveals that very little antibody has altered molecular weight. Isoelectric focusing patterns change more dramatically. Forms of the antibodies with lower isoelectric points appear in the serum. These forms have a similar in vivo half-life as the freshly prepared antibody. Very low pI forms of the monoclonal antibodies are not detected in the serum. Isoelectric focusing can be used to determine the in vivo or in vitro condition of a monoclonal antibody preparation. Finally, the monkey anti-human IgG that arose in the single monkey studied previously has been further characterized.
A Vaccinia Virus Encoding the Human Sodium Iodide Symporter Facilitates Long-Term Image Monitoring of Virotherapy and Targeted Radiotherapy of Pancreatic Cancer (2012)

GLV-1h153 is a promising oncolytic agent for the treatment, long-term imaging, and monitoring of therapeutic response in a xenograft model of pancreatic cancer. GLV-1h153 provided insight into tumor biologic activity and facilitated enhanced tumor kill when combined with systemic targeted radiotherapy. These results warrant further investigation into parameters and potential synergistic effects of combination therapy.
Related Leucine-based Cytoplasmic Targeting Signals in Invariant Chain and Major Histocompatibility Complex Class II Molecules Control Endocytic Presentation of Distinct Determinants in a Single Protein (1997)

Leucine-based signals in the cytoplasmic tail of invariant chain (Ii) control targeting of newly synthesized major histocompatibility complex class II molecules to the endocytic pathway for acquisition of antigenic peptides. Some protein determinants, however, do not require Ii for effective class II presentation, although endocytic processing is still necessary. Here we demonstrate that a dileucine-based signal in the cytoplasmic tail of the class II beta chain is critical for this Ii-independent presentation. Elimination or mutation of this signal reduces the rate of re-entry of mature surface class II molecules into the endocytic pathway. Antigen presentation controlled by this signal does not require newly synthesized class II molecules and appears to involve determinants requiring only limited proteolysis for exposure, whereas the opposite is true for li-dependent determinants. This demonstrates that related leucine-based trafficking signals in li and class II control the functional presentation of protein determinants with distinct processing requirements, suggesting that the peptide binding sites of newly synthesized versus mature class II molecules are made available for antigen binding in distinct endocytic compartments under the control of these homologous cytoplasmic signals. This permits capture of protein fragments produced optimally under distinct conditions of pH and proteolytic activity.
ChemInform Abstract: Reactions of N‐Acylimidazole with Nucleosides and Nucleotides. (1989)

Abstract Acylation of uridine (I) with the N‐acylimidazoles (II) yields the 3'‐O‐acylribonucleosides (IV) as the main products.
Classification of Text Documents (1998)

The exponential growth of the internet has led to a great deal of interest in developing useful and efficient tools and software to assist users in searching the Web. Document retrieval, categorization, routing and filtering can all be formulated as classification problems. However, the complexity of natural languages and the extremely high dimensionality of the feature space of documents have made this classification problem very difficult. We investigate four different methods for document classification: the naive Bayes classifier, the nearest neighbour classifier, decision trees and a subspace method. These were applied to seven-class Yahoo news groups (business, entertainment, health, international, politics, sports and technology) individually and in combination. We studied three classifier combination approaches: simple voting, dynamic classifier selection and adaptive classifier combination. Our experimental results indicate that the naive Bayes classifier and the subspace method outperform the other two classifiers on our data sets. Combinations of multiple classifiers did not always improve the classification accuracy compared to the best individual classifier. Among the three different combination approaches, our adaptive classifier combination method introduced here performed the best. The best classification accuracy that we are able to achieve on this seven-class problem is approximately 83%, which is comparable to the performance of other similar studies. However, the classification problem considered here is more difficult because the pattern classes used in our experiments have a large overlap of words in their corresponding documents.
Interorgan ammonia, glutamate, and glutamine trafficking in pigs with acute liver failure (2006)

Ammonia reduction is the target for therapy of hepatic encephalopathy, but lack of quantitative data about how the individual organs handle ammonia limits our ability to develop novel therapeutic strategies. The study aims were to evaluate interorgan ammonia metabolism quantitatively in a devascularized pig model of acute liver failure (ALF). Ammonia and amino acid fluxes were measured across the portal drained viscera (PDV), kidneys, hind leg, and lungs in ALF pigs. ALF pigs developed hyperammonemia and increased glutamine levels, whereas glutamate levels were decreased. PDV contributed to the hyperammonemic state mainly through increased shunting and not as a result of increased glutamine breakdown. The kidneys were quantitatively as important as PDV in systemic ammonia release, whereas muscle took up ammonia. Data suggest that the lungs are able to remove ammonia from the circulation during the initial stage of ALF. Our study provides new data supporting the concept of glutamate deficiency in a pig model of ALF. Furthermore, the kidneys are quantitatively as important as PDV in ammonia production, and the muscles play an important role in ammonia removal.
Applications of Platelet‐Rich Plasma in Musculoskeletal and Sports Medicine: An Evidence‐Based Approach (2011)

This article aims to provide a comprehensive review of the current literature that pertains to the therapeutic use of autologous platelet-rich plasma (PRP). The basic science literature regarding the role of growth factors in mediating the healing process and the laboratory data from in vitro and in vivo studies that evaluated PRP are reviewed. Subsequently, the current evidence regarding PRP efficacy from animal models, human surgical studies, and human clinical studies is presented. A critical analysis of the literature follows, and the article concludes with the authors' perspectives on the state of PRP as a potentially efficacious bioregenerative treatment option for musculoskeletal and sports medicine applications. The relevant articles in this review were obtained via PubMed literature searches for PRP publications that pertain to musculoskeletal and sports medicine conditions. This article is not intended to be a formal meta-analysis.
An Improved Method for the Preparation of Organic Monolayers of 1-Alkenes on Hydrogen-Terminated Silicon Surfaces (1999)

The possibility to use dilute alkene solutions for the formation of alkene monolayers with 1-hexadecene on a hydrogen-terminated silicon(100) surface has been investigated for a variety of solvents. The resulting monolayers were analyzed by water contact angles. Anisole, n-butylbenzene, and n-decane were found to be unsuitable solvents for monolayer preparation at all 1-hexadecene concentrations used. At high 1-hexadecene concentrations (25% and 10% (v/v)) well-ordered monolayers were formed in toluene, xylene (mixture of isomers), cumene, tert-butylbenzene, and mesitylene. Only with mesitylene are high-quality monolayers feasible even at significantly lower alkene concentrations (down to 2.5%), making this the solvent of choice. The newly described procedure reduces the amount of alkene needed to form well-ordered monolayers by a factor of 20−40 in comparison with the original procedure that requires neat alkenes.
Guidelines for immunoassay data processing. (1985)

These guidelines outline the minimum requirements for a data-processing package to be used in the immunoassay laboratory. They include recommendations on hardware, software, and program design. We outline the statistical analyses that should be performed to obtain the analyte concentrations of unknown specimens and to ensure adequate monitoring of within- and between-assay errors of measurement.
<title>Phototoxicity, dark-toxicity, and uptake-kinetics of natural hydrophilic and hydrophobic porphyrins in endothelial cells</title> (1996)

The phototoxicity, darktoxicity and uptake kinetics of three natural porphyrins (Uropoprhyrin III; UP III, Coproporphyrin III; CP III and Protoporphyrin IX; PP IX) were investigated in vitro using the BKEz-7 aorta endothelial cells of the calf. The cells were incubated with the porphyrins in different concentrations (0.5 (mu) M PP IX; 50 (mu) M UP III and CP III). After 24 h incubation they were irradiated in the case of PP IX with an Ar<SUP>+</SUP>-dye- laser at 635 nm and in the case of UP III and CP III with a Kr<SUP>+</SUP>-laser at 407 nm: While PP IX was phototoxic at low concentrations (0.5 (mu) M) and low energies (10 J/cm<SUP>2</SUP>), irradiation of UP III and CP III hardly induced phototoxicity even at higher concentrations. The same could be observed for the darktoxicity. PP IX was darktoxic at relatively low concentrations (1 (mu) M). In addition PP IX was taken up much faster and in greater amounts into the endothelial cells than UP III and CP III. These results could be due to the different structures of the sensitizers and/or to different uptake mechanisms. PP IX is a hydrophobic sensitizer while UP III and CP III are both hydrophilic molecules. A different uptake mechanism and accumulation in endothelial cells is quite probable. This hypothesis was confirmed with video-microscopy. In addition to the experiments in vitro, the cellular uptake and distribution of the sensitizers were observed in an appropriate in vivo model of the Chorioallantoismembrane (CAM).
Salvinia molesta D. S. Mitchell (Salviniaceae) (2009)

Salvinia molesta D. S. Mitchell (Salviniaceae) (salvinia) is a floating water fern of tropical and subtropical distribution worldwide. Its center of origin is southeastern Brazil. It is an extremely important invasive species and its biological control is an extraordinary, contemporary, success story.
Low-overhead memory leak detection using adaptive statistical profiling (2004)

Sampling has been successfully used to identify performance optimization opportunities. We would like to apply similar techniques to check program correctness. Unfortunately, sampling provides poor coverage of infrequently executed code, where bugs often lurk. We describe an adaptive profiling scheme that addresses this by sampling executions of code segments at a rate inversely proportional to their execution frequency. To validate our ideas, we have implemented SWAT, a novel memory leak detection tool. SWAT traces program allocations/ frees to construct a heap model and uses our adaptive profiling infrastructure to monitor loads/stores to these objects with low overhead. SWAT reports 'stale' objects that have not been accessed for a 'long' time as leaks. This allows it to find all leaks that manifest during the current program execution. Since SWAT has low runtime overhead (‹5%), and low space overhead (‹10% in most cases and often less than 5%), it can be used to track leaks in production code that take days to manifest. In addition to identifying the allocations that leak memory, SWAT exposes where the program last accessed the leaked data, which facilitates debugging and fixing the leak. SWAT has been used by several product groups at Microsoft for the past 18 months and has proved effective at detecting leaks with a low false positive rate (‹10%).