gebhart/patrepeval huggingface dataset:
Multiplex single-molecule kinetics of nanopore-coupled polymerases (2020)

Abstract DNA polymerases have revolutionized the biotechnology field due to their ability to precisely replicate stored genetic information. Screening variants of these enzymes for unique properties gives the opportunity to identify polymerases with novel features. We have previously developed a single-molecule DNA sequencing platform by coupling a DNA polymerase to a α-hemolysin pore on a nanopore array. Here, we use this approach to demonstrate a single-molecule method that enables rapid screening of polymerase variants in a multiplex manner. In this approach, barcoded DNA strands are complexed with polymerase variants and serve as templates for nanopore sequencing. Nanopore sequencing of the barcoded DNA reveals both the barcode identity and kinetic properties of the polymerase variant associated with the cognate barcode, allowing for multiplexed investigation of many polymerase variants in parallel on a single nanopore array. Further, we develop a robust classification algorithm that discriminates kinetic characteristics of the different polymerase mutants. As a proof of concept, we demonstrate the utility of our approach by screening a library of ~100 polymerases to identify variants for potential applications of biotechnological interest. We anticipate our screening method to be broadly useful for applications that require polymerases with unique or altered physical properties.
Document summarisation using combination and reduction of extracted sentences (2009)

An ideal summariser should produce a summary which contains all the crucial information present in the original text, while conforming to the size of the summary. We propose a novel method to perform single-document summarisation of the English text. We start by combining semantically related sentences using a rule-based approach to avoid loss of important information and maintain coherence in the resulting summary. The rules for combination rely on surface indicators present in the sentence i.e., cue-phrases. Then we extract important text from the combined sentences using lexical chains. This is followed by a sentence-reduction step involving removal of superfluous phrases from the extracted sentences using a rule-based approach. The rules for sentence pruning use discourse trees generated using the intra-sentential rhetorical relations. The summaries produced by our system were agreed by human subjects to be more concise and coherent than extraction-based summaries for the same documents.
Direct evidence of Mg diffusion through threading mixed dislocations in GaN p–n diodes and its effect on reverse leakage current (2019)

Mg diffusion is a common problem in GaN devices with p–n junctions. Although this impurity diffusion is reported to occur through threading dislocations (TDs), no direct evidence has yet been obtained. Therefore, we tried the direct observation of Mg diffusion by atom probe tomography (APT) analysis. The n-type drift layer of the fabricated p–n diode was exposed, and etch pits were formed on the drift layer to identify the TD position. The APT analysis around TDs was carried out by lifting out the drift layer around specific etch pits using a focused ion beam to include TDs. The relationship between the etch pit shape and the TD type was confirmed by cross-sectional scanning transmission electron microscopy observation. The APT analysis of two types of etch pits formed on the mixed dislocations was performed, and Mg diffusion was clearly observed through the mixed dislocations. In this work, we show direct evidence of Mg diffusion via mixed dislocations in GaN p–n diodes and its effect on reverse leakage current.
Novel Conotoxins from Conus striatus and Conus kinoshitai Selectively Block TTX-Resistant Sodium Channels (2006)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionNovel Conotoxins from Conus striatus and Conus kinoshitai Selectively Block TTX-Resistant Sodium ChannelsGrzegorz Bulaj, Peter J. West, James E. Garrett, Maren Watkins, Min-Min Zhang, Raymond S. Norton, Brian J. Smith, Doju Yoshikami, and Baldomero M. OliveraCite this: Biochemistry 2006, 45, 9, 3116Publication Date (Web):February 8, 2006Publication History Published online8 February 2006Published inissue 1 March 2006https://pubs.acs.org/doi/10.1021/bi068001chttps://doi.org/10.1021/bi068001ccorrectionACS PublicationsCopyright © 2006 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views318Altmetric-Citations-LEARN 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 PDF (5 KB) Get e-Alertsclose Get e-Alerts
Abstract 2996: Systemic depletion of L-methionine with an engineered human enzyme for the treatment of melanoma (2019)

Abstract Metastatic melanoma is an aggressive form of cancer responsible for the majority of skin cancer related deaths. While treatment for metastatic melanoma has improved in recent years with the introduction of targeted therapies and immunotherapies, the five-year survival rate for stage IV melanoma remains only 15-20%. To address the need for alternative options for melanoma treatment, we have begun exploring use of an engineered human enzyme called methionine-gamma-lyase (hMGL). Many cancers, including melanoma, have a high requirement for methionine in comparison with non-cancerous cells. The hMGL enzyme works to exploit this difference by degrading extracellular L-methionine resulting in cancer cell starvation. The hypothesis tested in this research is that the systemic depletion of L-methionine using hMGL will provide significant benefits for melanoma treatment alone or in combination with other therapeutic agents. Treatment of several melanoma cell lines (A375, Hs294T, Skmel28, and B16F10) with various concentrations of hMGL demonstrated that L-methionine depletion reduced survival and led to a G2 cell cycle arrest. To investigate the mechanism of action, analyses of melanoma cells treated with hMGL have shown that signal transducer and activator of transcription 3 (STAT3) tyrosine phosphorylation is significantly reduced. Additionally, hMGL treatment leads to activation of the uncharged tRNA amino acid sensing pathway as shown by an increase in p-eIF2α and Sestrin 2 and an increase in autophagy shown by a decrease in p-ULKSer757 and an increase in cleaved LC3B. Because L-methionine depletion affects levels of glutathione through reduction of cysteine synthesis, preliminary experiments were conducted to evaluate hMGL treatment combined with a thioredoxin reductase inhibitor. This combination, targeting two different intracellular antioxidant pathways, resulted in synergistic inhibition of survival in multiple melanoma cell lines. The current data support the hypothesis that L-methionine depletion using hMGL may have therapeutic efficacy either alone or in combinations for melanoma treatment. Research funded by CPRIT grant RP180590. Citation Format: Carly S. Wilder, Achinto Saha, George Georgiou, Everett Stone, John DiGiovanni. Systemic depletion of L-methionine with an engineered human enzyme for the treatment of melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2996.
Structure and dynamics of the Arabidopsis O-fucosyltransferase SPINDLY (2023)

SPINDLY (SPY) in Arabidopsis thaliana is a novel nucleocytoplasmic protein O-fucosyltransferase (POFUT), which regulates diverse developmental processes. Sequence analysis indicates that SPY is distinct from ER-localized POFUTs and contains N-terminal tetratricopeptide repeats (TPRs) and a C-terminal catalytic domain resembling the O-linked-N-acetylglucosamine (GlcNAc) transferases (OGTs). However, the structural feature that determines the distinct enzymatic selectivity of SPY remains unknown. Here we report the cryo-electron microscopy (cryo-EM) structure of SPY and its complex with GDP-fucose, revealing distinct active-site features enabling GDP-fucose instead of UDP-GlcNAc binding. SPY forms an antiparallel dimer instead of the X-shaped dimer in human OGT, and its catalytic domain interconverts among multiple conformations. Analysis of mass spectrometry, co-IP, fucosylation activity, and cryo-EM data further demonstrates that the N-terminal disordered peptide in SPY contains trans auto-fucosylation sites and inhibits the POFUT activity, whereas TPRs 1-5 dynamically regulate SPY activity by interfering with protein substrate binding.
Path following for mechanical systems: Experiments and examples (2011)

This paper concerns the design of path following controllers for mechanical systems. Our method is to find a coordinate and feedback transformation that puts the mechanical system in a convenient form for path following control design. In this form, linear and controllable subsystems govern motions toward and along the path. We choose a particular "virtual output" to perform input-output feedback linearization, and characterize when this virtual output can be used. We apply this technique to a planar five-bar linkage robot, and implement it experimentally, highlighting behaviour fundamentally different from standard tracking control. In simulation, we further illustrate our approach on an underactuated five-bar robot with a flexible link.
Correlative dynamic contrast MRI and microscopic assessments of tumor vascularity in RIP‐tag2 transgenic mice (2009)

The purpose of this study was to define the feasibility of dynamic contrast-enhanced magnetic resonance imaging (MRI) to estimate the vascular density and leakiness of spontaneous islet cell tumors in RIP-Tag2 transgenic mice. Dynamic T(1)-weighted spoiled gradient echo (SPGR) imaging at 2.0 T was performed in 17 RIP-Tag2 mice using a prototype blood pool macromolecular contrast medium (MMCM), albumin-(Gd-DTPA)(35). Kinetic analysis of the dynamic enhancement responses based on a two-compartment model was used to estimate fractional plasma volume (fPV) and the coefficient of endothelial permeability (K(PS)) for each tumor. The MRI estimate of fPV was correlated on a tumor-by-tumor basis with corresponding microscopic measurements of vascular density. The fPV assays by MMCM-enhanced imaging ranged from 2.4%-14.1% of tissue volume. Individual tumor fPV values correlated significantly (r = 0.79, P < 0.001) with the corresponding microscopic estimates of vascularity consisting of the combined area densities of lectin-perfused microvessels plus erythrocyte-stained blood lakes. A biotinylated derivative of the albumin-based MMCM confirmed extravasation of the contrast agent from some tumor blood vessels and accumulation in 25% of blood lakes. The K(PS) values ranged from 0 (no detectable leak) to 0.356 mL/min/100 cm(3). Dynamic MMCM-enhanced MRI is feasible in RIP-Tag2 pancreatic tumors, yielding estimates of vascular permeability and microscopically validated measurements of vascular richness.
Effectiveness of Germicidal UV Radiation for Reducing Fungal Contamination within Air-Handling Units (2001)

Levels of fungi growing on insulation within air-handling units (AHUs) in an office building and levels of airborne fungi within AHUs were measured before the use of germicidal UV light and again after 4 months of operation. The fungal levels following UV operation were significantly lower than the levels in control AHUs.
Viral subversion of immunogenic cell death (2009)

While physiological cell death is non-immunogenic, pathogen induced cell death can be immunogenic and hence stimulate an immune response against antigens that derive from dying cells and are presented by dendritic cells (DCs). The obligate immunogenic "eat-me" signal generated by dying cells consists in the exposure of calreticulin (CRT) at the cell surface. This particular "eat-me" signal, which facilitates engulfment by DCs, can only be found on cells that succumb to immunogenic apoptosis, while it is not present on cells dying in an immunologically silent fashion. CRT normally resides in the lumen of the endoplasmic reticulum (ER), yet can translocate to the plasma membrane surface through a complex pathway that involves elements of the ER stress response (e.g., the eIF2alpha-phosphorylating kinase PERK), the apoptotic machinery (e.g., caspase-8 and its substrate BAP31, Bax, Bak), the anterograde transport from the ER to the Golgi apparatus, and SNARE-dependent exocytosis. A large panoply of viruses encodes proteins that inhibit eIF2alpha kinases, catalyze the dephosphorylation of eIF2alpha, bind to caspase-8, Bap31, Bax or Bak, or perturb exocytosis. We therefore postulate that obligate intracellular pathogens have developed a variety of strategies to subvert CRT exposure, thereby avoiding immunogenic cell death.
Use of Broad Biological Profiling as a Relevant Descriptor to Describe and Differentiate Compounds: Structure– In Vitro (Pharmacology–ADME)– In Vivo (Safety) Relationships (2008)

This chapter contains sections titled: Introduction Biological Profiling/Fingerprints and Drug Discovery Applications Polypharmacology of Drugs The BioPrint® Approach BioPrint® General BioPrint® Assay Selection and Profile Description Compounds in BioPrint® BioPrint® In Vivo Data sets Compound Details ADR Data Pharmacokinetics Toxicity Data Structure–In Vitro Relationships Similarity, Chemotypes – What Is a Biologically Relevant Descriptor? Using Biological Fingerprints as a Meaningful Descriptor for Drug Leads and Candidates Differentiation of Leads Analysis of Attrited Compounds Structural versus Experimental Differentiation – Dependence on Structure-Derived Descriptor Used Predictive Models from Pharmacological Data Predictive Models from ADME Data – BioPrint® Learnings Chemogenomic Analysis – Target–Target Relationships In Vitro–In Vivo Relationships – Placing Drug Candidates in the Context of BioPrint® Analyzing Potential ADR Liabilities Based on Individual Hits Analyzing Potential ADR Liabilities Based on Profile Similarity A Perspective for the Future References
Method of characterization of effective shrinkage in reflection holograms (2004)

A method is described to evaluate plane-wave volume hologram fringe inclination and spacing, as well as the recording material average refraction index. This evaluation allows us to estimate changes in the hologram parameters due to recording material shrinkage. The method is based on measurements of the incident and diffracted beam Bragg angles for two different wavelengths. The conditions for minimizing measurement errors are obtained. The experimental data are in good agreement with the calculated data.
Numerical study of annihilation processes in electrically pumped organic semiconductor laser diodes (2006)

We examine the influence of various annihilation processes on the laser threshold current density of organic semiconductor laser diode structures. A three-layer laser diode structure is systematically investigated by means of numerical simulations. Our self consistent model treats the dynamics of electrons, holes and singlet as well as triplet excitons in the framework of a drift-diffusion model. The resulting particle distributions enter into the optical model. In our approach, we consider the actual waveguide structure and solve the resulting laser rate equation. The various annihilation processes are included as reactions between the different species in the device. We systematically vary the device dimensions and parameters of our singlet exciton annihilation model to identify the dominating quenching process in order to deduce design rules for potential organic laser diode structures. A standard material with typical material properties and annihilation rate coefficients is investigated. Singlet exciton quenching by polarons is identified as the main loss channel. The laser threshold in three layer devices is found to be very sensitive to the thickness of the emission layer.
The Role of Antioxidation and Immunomodulation in Postnatal Multipotent Stem Cell-Mediated Cardiac Repair (2013)

Oxidative stress and inflammation play major roles in the pathogenesis of coronary heart disease including myocardial infarction (MI). The pathological progression following MI is very complex and involves a number of cell populations including cells localized within the heart, as well as cells recruited from the circulation and other tissues that participate in inflammatory and reparative processes. These cells, with their secretory factors, have pleiotropic effects that depend on the stage of inflammation and regeneration. Excessive inflammation leads to enlargement of the infarction site, pathological remodeling and eventually, heart dysfunction. Stem cell therapy represents a unique and innovative approach to ameliorate oxidative stress and inflammation caused by ischemic heart disease. Consequently, it is crucial to understand the crosstalk between stem cells and other cells involved in post-MI cardiac tissue repair, especially immune cells, in order to harness the beneficial effects of the immune response following MI and further improve stem cell-mediated cardiac regeneration. This paper reviews the recent findings on the role of antioxidation and immunomodulation in postnatal multipotent stem cell-mediated cardiac repair following ischemic heart disease, particularly acute MI and focuses specifically on mesenchymal, muscle and blood-vessel-derived stem cells due to their antioxidant and immunomodulatory properties.
Thermal Design Analysis of Free Space Optical Interconnect (FSOI) Package Module (2001)

Abstract A detailed thermal analysis for the FSOI (Free Space Optical Interconnect) technology incorporating VCSEL (Vertical Cavity Surface Emitting Laser) devices is performed using commercially available software. FSOI is one of the latest technologies used to transmit information at high-speed to/from a microprocessor to memory device via photons. Due to large heat dissipation and compact packaging design, temperature and associated thermal strain/stress could reach high values in the FSOI assembly, causing serious reliability and quality problems. Several design options are investigated in order to provide optimal thermal management for the FSOI module, and maintain VCSEL temperatures within reasonable limits. Convective cooling results for both organic and ceramic boards are investigated. For designs with organic boards and without any thermal enhancement, the VCSEL temperature is well above the acceptable limit of 85°C at an ambient temperature of 30°C. The sequential inclusion of pedestals, board thermal vias, conductive rings between the optical modules, and metallic (Al) rods will significantly enhance the module thermal performance and reduce VCSEL temperature to 46°C. The presence of thermal vias in the organic board is critical; however, if the copper area percentage in the via block vs. the die area is above 3%, the VCSEL temperatures will remain constant. The ceramic boards provide a good thermal solution, as VCSEL temperatures remain below the upper limit without including any thermal vias in the board. The comparison between the effect of convective air speed on FSOI with ceramic versus organic boards reveals that the VCSEL temperature is slightly higher (less than 2°C) for the case incorporating a ceramic board. However, the ceramic board has no thermal vias, compared to the 100% copper via block in the organic board. Hence, the same results are accomplished with much less complexity in the ceramic substrate design alternative. This option is suggested for manufacturing purposes, with improved thermal performances.
Poly(vinyl acetate) and Poly(vinyl acetate-co-ethylene) Latexes via Dispersion Polymerizations in Carbon Dioxide (1998)

The preparation of stable dispersions of poly(vinyl acetate) or ethylene/vinyl acetate copolymers via dispersion polymerizations in a carbon dioxide continuous phase has been investigated. The effectiveness of stabilizers of various chemical compositions and architectures was compared. Both fluorinated and siloxane-based stabilizers including homopolymers, block copolymers, and reactive macromonomers were employed. Effects of variations in the reaction temperature, pressure, stabilizer composition, stabilizer concentration, and use of cosolvents on the resulting product were investigated. A turbidimetry technique was used successfully to monitor dispersed-phase volume fractions, particle sizes, and number densities during the polymerizations and to give the final particle sizes at the end of the polymerizations. The fluorinated stabilizers gave rise to smaller particles and more stable latexes when compared to the siloxane-based stabilizers.
Correction to “Extraordinary Dielectric Properties at Heterojunctions of Amorphous Ferroelectrics” (2019)

RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCorrection to “Extraordinary Dielectric Properties at Heterojunctions of Amorphous Ferroelectrics”M. Helena Braga*M. Helena BragaMore by M. Helena Braga, Joana E. OliveiraJoana E. OliveiraMore by Joana E. Oliveira, Tianhan KaiTianhan KaiMore by Tianhan Kaihttp://orcid.org/0000-0001-5667-1426, Andrew J. MurchisonAndrew J. MurchisonMore by Andrew J. Murchison, Allen J. BardAllen J. BardMore by Allen J. Bardhttp://orcid.org/0000-0002-8517-0230, and John B. Goodenough*John B. GoodenoughMore by John B. Goodenoughhttp://orcid.org/0000-0001-9350-3034Cite this: J. Am. Chem. Soc. 2019, 141, 31, 12419Publication Date (Web):July 24, 2019Publication History Published online24 July 2019Published inissue 7 August 2019https://doi.org/10.1021/jacs.9b06973Copyright © 2019 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views2072Altmetric-Citations-LEARN 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 InReddit PDF (235 KB) Get e-Alerts Get e-Alerts