gebhart/patrepeval huggingface dataset:
Triple Trans-Splicing Adeno-Associated Virus Vectors Capable of Transferring the Coding Sequence for Full-Length Dystrophin Protein into Dystrophic Mice (2013)

Recombinant adeno-associated virus (rAAV) vectors have been shown to permit very efficient widespread transgene expression in skeletal muscle after systemic delivery, making these increasingly attractive as vectors for Duchenne muscular dystrophy (DMD) gene therapy. DMD is a severe muscle-wasting disorder caused by DMD gene mutations leading to complete loss of dystrophin protein. One of the major issues associated with delivery of the DMD gene, as a therapeutic approach for DMD, is its large open reading frame (ORF; 11.1 kb). A series of truncated microdystrophin cDNAs (delivered via a single AAV) and minidystrophin cDNAs (delivered via dual-AAV trans-spliced/overlapping reconstitution) have thus been extensively tested in DMD animal models. However, critical rod and hinge domains of dystrophin required for interaction with components of the dystrophin-associated protein complex, such as neuronal nitric oxide synthase, syntrophin, and dystrobrevin, are missing; these dystrophin domains may still need to be incorporated to increase dystrophin functionality and stabilize membrane rigidity. Full-length DMD gene delivery using AAV vectors remains elusive because of the limited single-AAV packaging capacity (4.7 kb). Here we developed a novel method for the delivery of the full-length DMD coding sequence to skeletal muscles in dystrophic mdx mice using a triple-AAV trans-splicing vector system. We report for the first time that three independent AAV vectors carrying "in tandem" sequential exonic parts of the human DMD coding sequence enable the expression of the full-length protein as a result of trans-splicing events cojoining three vectors via their inverted terminal repeat sequences. This method of triple-AAV-mediated trans-splicing could be applicable to the delivery of any large therapeutic gene (≥11 kb ORF) into postmitotic tissues (muscles or neurons) for the treatment of various inherited metabolic and genetic diseases.
The Effects of Proactive Release Behaviors During Human-Robot Handovers (2019)

Most research on human-robot handovers focuses on how the robot should approach human receivers and notify them of the readiness to take an object; few studies have investigated the effects of different release behaviors. Not releasing an object when a person desires to take it breaks handover fluency and creates a bad handover experience. In this paper, we investigate the effects of different release behaviors. Specifically, we study the benefits of a proactive release, during which the robot actively detects a human grasp effort pattern. In a 36-participant user study <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sup> The study is ready to reproduce with a Baxter robot. The code and environment setup is available at https://github.com/umhan35/handover_moveit, results suggest proactive release is more efficient than rigid release (which only releases when the robot is fully stopped) and passive release (the robot detects pulling by checking if a threshold value is reached). Subjectively, the overall handover experience is improved: the proactive release is significantly better in terms of handover fluency and ease-of-taking.
Epitaxial grain growth in thin metal films (1990)

Epitaxial alignment has been obtained by means of grain growth in polycrystalline films deposited on single-crystal substrates. A theory for epitaxial grain growth is outlined and results given for experiments on Au, Al, Cu, and Ag films on vacuum-cleaved NaCl, KBr, KCl, or mica. Epitaxial grain growth provides a fundamentally different alternative to conventional epitaxy, and can lead to very thin films with improved continuity and crystalline perfection, as well as non-lattice-matched orientations.
Efficient multiplication-free arithmetic codes (1995)

Arithmetic coding is a powerful lossless data compression technique that has attracted much attention. It provides more flexibility and better efficiency than Huffman coding does. However, the multiplications needed in its encoding and decoding algorithms are very undesirable. Rissanen and Mohiuddin (1989) have proposed a simple scheme to avoid the multiplications. The present authors found that the performance of their proposed scheme might degrade significantly in some cases. They propose a multiplication-free multialphabet arithmetic code which can be shown to have minor performance degradation in all cases. In the proposed scheme, each multiplication is replaced by a single shift-and-add. The authors prove, by both theoretical analysis and simulation results, that the degradation of the proposed multiplication-free scheme is always several times (2-7 times in the present experiments) smaller than that of the Rissanen-Mohiuddin's scheme.
Certification assays for HIV-1-based vectors: frequent passage of gag sequences without evidence of replication-competent viruses (2003)

A principal concern regarding the safety of HIV-1-based vectors is replication-competent lentivirus (RCL). We have developed two PCR assays for detecting RCL; the first detects recombination between gag regions in the transfer vector and the packaging construct (sensitivity of detection approximately 10-100 copies of target sequence). The second assay uses real-time PCR to detect vesicular stomatitis virus glycoprotein (VSVG) envelope DNA (sensitivity approximately 5-50 VSVG sequences). In an attempt to amplify any RCL, test vectors were used to transduce C8166 and 293 cells, which were then screened weekly for 3 weeks. Psi-gag recombinants were routinely detected (20 of 21 analyses) in four transductions using the RRL-CMV-GFP vector. In contrast, VSVG sequences were detected only once in 21 analyses. Interestingly, p24 levels (as measured by ELISA) were occasionally detectable after 3 weeks of culture. To determine if a true RCL was present, 21-day cell-free medium was used to transduce naïve cells. No evidence of psi-gag or VSVG transfer was detected, indicating that the recombination events were insufficient to reconstitute a true RCL. These findings have important implications for the design and safety of HIV-1-based vectors intended for clinical applications.
Asymmetric Alcoholysis of Cyclic Anhydrides (2003)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAsymmetric Alcoholysis of Cyclic AnhydridesYonggang Chen, Paul McDaid, and Li DengView Author Information Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110 Cite this: Chem. Rev. 2003, 103, 8, 2965–2984Publication Date (Web):July 29, 2003Publication History Received27 February 2003Published online29 July 2003Published inissue 1 August 2003https://pubs.acs.org/doi/10.1021/cr020037xhttps://doi.org/10.1021/cr020037xresearch-articleACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views3792Altmetric-Citations197LEARN 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,Desymmetrization,Kinetic resolution,Organic compounds,Stereoselectivity Get e-Alerts
Cardiovascular risk: its assessment in clinical practice. (2001)

Cardiovascular disease is one of the major causes of mortality and morbidity in Western industrialised countries. Many factors impact on the likelihood of an individual suffering a stroke or heart attack. One of the greatest challenges facing clinicians today is how best to identify those individuals at increased risk, to prevent them becoming tomorrow's patients. Risk assessment tools can provide useful frameworks to support the identification of individuals who may benefit from therapeutic intervention; however, such tools should be used with care, as they do not include all the factors that contribute to future disease risk, and they are subject to an age bias. Nonetheless, they provide a systematic, evidence-based approach to the delivery of preventative healthcare services.
Signal Transducers and Activators of Transcription (STATs): Novel Targets of Chemopreventive and Chemotherapeutic Drugs (2006)

A family of latent cytoplasmic transcription factors, signal transducers and activators of transcription (STATs), mediates the responsiveness of cells to several cytokines and growth factors. Although mutations of STATs have not been described in human tumors, the activity of several members of the family, such as STAT1, STAT3 and STAT5, is deregulated in a variety of human tumors. STAT3 and STAT5 acquire oncogenic potential through constitutive phosphorylation on tyrosine, and their activity has been shown to be required to sustain a transformed phenotype. Disruption of STAT3 and STAT5 signaling in transformed cells therefore represents an excellent opportunity for targeted cancer therapy. In contrast to STAT3 and STAT5, STAT1 negatively regulates cell proliferation and angiogenesis and thereby inhibits tumor formation. Consistent with its tumor suppressive properties, STAT1 and its downstream targets have been shown to be reduced in a variety of human tumors and STAT1 deficient mice are highly susceptible to tumor formation. In recent years we have gained mechanistic understanding of the pathways whereby STATs convey signals from the cytoplasm to the nucleus. In addition, several endogenous regulators of the JAK/STAT pathway have been described - and their mechanism of action revealed - that profoundly affect signaling by STATs. Both should greatly facilitate the design of drugs with potential to modulate STAT signaling and to restore the homeostasis in tissues where STATs have gone awry.
DNA methylation in stem cell renewal and multipotency (2011)

Owing to their potential for differentiation into multiple cell types, multipotent stem cells extracted from many adult tissues are an attractive stem cell resource for the replacement of damaged tissues in regenerative medicine. The requirements for cellular differentiation of an adult stem cell are a loss of proliferation potential and a gain of cell-type identity. These processes could be restricted by epigenetic modifications that prevent the risks of lineage-unrelated gene expression or the undifferentiated features of stem cells in adult somatic cells. In this review, we focus on the role of DNA methylation in controlling the transcriptional activity of genes important for self-renewal, the dynamism of CpG methylation of tissue-specific genes during several differentiation programs, and whether the multilineage potential of adult stem cells could be imposed early in the original precursor stem cells through CpG methylation. Additionally, we draw attention to the role of DNA methylation in adult stem cell differentiation by reviewing the reports on spontaneous differentiation after treatment with demethylating agents and by considering the evidence provided by reprogramming of somatic cells into undifferentiated cells (that is, somatic nuclear transfer or generation of induced pluripotent cells). It is clear from the evidence that DNA methylation is necessary for controlling stem cell proliferation and differentiation, but their exact contribution in each lineage program is still unclear. As a consequence, in a clinical setting, caution should be exerted before employing adult stem cells or their derivatives in regenerative medicine and appropriate tests should be applied to ensure the integrity of the genome and epigenome.
Protein arginine methyltransferase 5 regulates multiple signaling pathways to promote lung cancer cell proliferation (2016)

Our data provide the molecular basis by which PRMT5 and p44 regulate cell growth and lay a foundation for further investigation of their role in lung tumor initiation.
Monotonicity testing over general poset domains (2002)

The field of property testing studies algorithms that distinguish, using a small number of queries, between inputs which satisfy a given property, and those that are 'far' from satisfying the property. Testing properties that are defined in terms of monotonicity has been extensively investigated, primarily in the context of the monotonicity of a sequence of integers, or the monotonicity of a function over the n-dimensional hypercube {1,…,m}n. These works resulted in monotonicity testers whose query complexity is at most polylogarithmic in the size of the domain.We show that in its most general setting, testing that Boolean functions are close to monotone is equivalent, with respect to the number of required queries, to several other testing problems in logic and graph theory. These problems include: testing that a Boolean assignment of variables is close to an assignment that satisfies a specific 2-CNF formula, testing that a set of vertices is close to one that is a vertex cover of a specific graph, and testing that a set of vertices is close to a clique.We then investigate the query complexity of monotonicity testing of both Boolean and integer functions over general partial orders. We give algorithms and lower bounds for the general problem, as well as for some interesting special cases. In proving a general lower bound, we construct graphs with combinatorial properties that may be of independent interest.
Formation of High-Temperature Lutetium Disilicate from Lutetium-Saturated Aluminosilicates in Mild Conditions. Incorporation of Si and Al XAS Techniques to the Study of These Systems (1996)

The formation of lutetium disilicate from lutetium-saturated montmorillonite induced by hydrothermal treatments in mild conditions has been studied. Changes in the silicate lattice and in the species located in the interlayer space have been examined by using XRD, MAS-NMR, and Lu LIII EXAFS techniques, as well as soft-energy XANES of Al and Si, the main silicate constituents. Results obtained showed that the Lu2Si2O7 phase was formed to a considerable extent at 300 °C and that the reaction started at a temperature as low as 200 °C. These results imply that the previously reported higher temperature, 400 °C, is not a thermodynamic barrier for the solid-state reaction and offer an effective mechanism to immobilize these ions. Capabilities of soft XAFS techniques in the study of complex systems such as aluminosilicate minerals are shown.
Na<sub>3</sub>V<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub>@C core–shell nanocomposites for rechargeable sodium-ion batteries (2014)

Na<sub>3</sub>V<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub>@C core–shell nanocomposites were synthesized and applied as electrode materials in rechargeable sodium batteries, showing remarkable rate capability and cyclability.
Novel engine concepts for multi fuel military vehicles (2012)

The paper considers different options to design a multi fuel engine retaining the power densities and efficiencies of the latest Diesel heavy duty truck engines while operating with various other fuels. In a first option, an igniting Diesel fuel is coupled to a main fuel that may have any Cetane or octane number in a design where every engine cylinder accommodates a direct Diesel injector, a glow plug and the multi fuel direct injector in a bowl-in-piston combustion chamber configuration. Alternatively, an igniting gasoline fuel replaces the Diesel fuel in a design where every engine cylinder accommodates a gasoline direct injector, the multi fuel direct injector and a jet ignition pre chamber also with a bowl-in-piston combustion chamber configuration. Both these designs permit load control by changing the amount of fuel injected and Diesel-like, gasoline-like and mixed Diesel/gasoline-like modes of operation modulating the amount of the multi fuel that burn premixed or diffusion. The paper only covers engine performance simulations for operation Diesel-like and gasoline/HHCI-like, being the simulations of the mixed Diesel/gasoline-like modes currently not available. The new designs have the potential to deliver even better than current heavy duty truck Diesel fuel conversion efficiency both part load and full load operating with variable quality fuels.
Molecular modelling of the ORL1 receptor and its complex with nociceptin (1998)

The opioid receptor like (ORL1) receptor is a G-protein coupled receptor superfamily, and regulates a plethora of neurophysiological functions. The structural requirements for receptor activation by its endogenous agonist, nociceptin (FGGFTGARKSARKLANQ), differ markedly from those of the kappa-opioid receptor and its putative peptide agonist, dynorphin A (YGGFLRRIRPKLKWDNQ). In order to probe the functional architecture of the ORL1 receptor, a molecular model of the receptor has been built, including the TM domain and the extra- and intracellular loops. An extended binding site able to accommodate nociceptin-(1-13), the shortest fully active analogue of nociceptin, has been characterized. The N-terminal FGGF tetrapeptide is proposed to bind in a highly conserved region, comprising two distinct hydrophobic pockets in a cavity formed by TM helices 3, 5, 6 and 7, capped by the acidic second extracellular (EL2) loop controlling access to the TM elements of the peptide binding site. The nociceptin conformation provides for the selective preference of the ORL1 receptor for nociceptin over dynorphin A, conferred by residue positions 5 and 6 (TG versus LR), and the favourable interaction of its highly positively charged core (residues 8-13) with the EL2 loop, thought to mediate receptor activation. The functional roles of the EL2 loop and the conserved N-terminal tetrapeptide opioid 'message' binding site are discussed in the context of the different structural requirements of the ORL1 and kappa-opioid receptors for activation.
The Extra Cytoplasmic Function Sigma Factor σ <sup>E</sup> Is Essential for <i>Mycobacterium tuberculosis</i> Virulence in Mice (2004)

The virulence of a Mycobacterium tuberculosis H37Rv sigE mutant was studied in immunodeficient and immunocompetent mice. The mutant was strongly attenuated in both animal models and induced formation of granulomas with different characteristics than those induced by the wild-type strain.
Wide Area Technical Report Service (1995)

Wide Area Technical Report Service (WATERS) is a distributed database of computer science technical reports. Contributors are departments of computer science that make their reports, stored locally at their sites, available through World-Wide Web and a WAIS search engine. By using WATERS, anyone with access to the Internet can, using a client such as Mosaic browse, search, obtain abstract and bibliographic information, and retrieve technical reports online. The latter assumes that the user's WWW client is set up to launch viewers such as ghostview for Postscript files, xdvi for dvi files, and xtiff for TIFF page images.
I/O guided detection of list catamorphisms (2010)

Inductive programming (IP), usually defined as a search in a space of candidate programs, is an inherent exponentially complex problem. To constrain the search space, program templates have ever been one of the first choices. In previous approaches to incorporate program schemes, either an (often very well) informed expert user has to provide a template in advance, or templates are used simply on suspicion, regardless whether they are target-aiming or not. Instead of rather fit the data to the template, we present an approach to fit a template to the data. We propose to utilise universal properties of higher-order functions to detect the appropriateness of a certain template in the input/output examples. We use this technique to introduce catamorphisms on lists in our IP system Igor2.
A thin liquid layer on the surface of mercury as a matrix of a flow-mediated two-dimensional assembly of proteins (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA thin liquid layer on the surface of mercury as a matrix of a flow-mediated two-dimensional assembly of proteinsMariko Yamaki, Keiko Matsubara, and Kuniaki NagayamaCite this: Langmuir 1993, 9, 11, 3154–3158Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/la00035a067https://doi.org/10.1021/la00035a067research-articleACS PublicationsRequest reuse permissionsArticle Views139Altmetric-Citations30LEARN 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
An Alternative Route to Aryloxymethylphosphonates and Phosphinates via Fluoride Ion Displacement from Activated Aromatic Substrates (1994)

Dialkyl aryloxymethylphosphonates and phosphinates can be prepared in a single step by the reaction of activated fluorobenzenes with dialkyl hydroxymethylphosphonates or phosphinates.
Advanced Photon Source accelerator ultrahigh vacuum guide (1994)

In this document the authors summarize the following: (1) an overview of basic concepts of ultrahigh vacuum needed for the APS project, (2) a description of vacuum design and calculations for major parts of APS, including linac, linac waveguide, low energy undulator test line, positron accumulator ring (PAR), booster synchrotron ring, storage ring, and insertion devices, and (3) cleaning procedures of ultrahigh vacuum (UHV) components presently used at APS.