gebhart/patrepeval huggingface dataset:
Natural Products and Synthetic Biology (2014)

ADVERTISEMENT RETURN TO ISSUEPREVViewpointNEXTNatural Products and Synthetic BiologyMohammad R. Seyedsayamdost and Jon Clardy*View Author Information Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States*Ph: 1-617-432-2845. Fax: 1-617-432-6424. E-mail: [email protected]Cite this: ACS Synth. Biol. 2014, 3, 10, 745–747Publication Date (Web):January 7, 2014Publication History Received10 March 2013Published online7 January 2014Published inissue 17 October 2014https://doi.org/10.1021/sb400025pCopyright © 2014 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views5106Altmetric-Citations28LEARN 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 (331 KB) Get e-AlertscloseSUBJECTS:Antimicrobial agents,Metabolism,Molecules,Pharmaceuticals,Synthetic biology Get e-Alerts
Indium−Tin Oxide Coated Microfabricated Device for the Injection of a Single Cell into a Fused Silica Capillary for Chemical Cytometry (2010)

A microfabricated device is described for the capture and injection of a single mammalian cell into a fused silica capillary for subsequent analysis by chemical cytometry. The device consists of a 500 μm diameter well made from polydimethylsiloxane on an indium-tin oxide coated microscope slide. The bottom of the well contains a 2 μm high aperture, which was designed to block passage of cells. A cellular suspension was allowed to settle on the device, and aspiration through the aperture was used to trap a single NG-108 cell. Untrapped cells were washed from the device, and a 150 μm outer diameter and 50 μm inner diameter capillary was placed in the well. To inject a cell, voltage was applied to the indium-tin oxide while simultaneously applying vacuum at the distal end of the capillary.
Work safety (1995)

Employers, it seems, are still not getting the message. Despite advances in lifting aids, the promotion of safe handling techniques and legislation to ensure tasks are assessed and risks reduced, injuries are still occurring. Some employers condone techniques that transgress the basic rules of lifting. Indeed, some are still being taught.
End-user feature engineering in the presence of class imbalance (2009)

Intelligent user interfaces, such as recommender systems and email classifiers, use machine learning algorithms to customize their behavior to the preferences of an end user. Although these learning systems are somewhat reliable, they are not perfectly accurate. Traditionally, end users who need to correct these learning systems can only provide more labeled training data. In this paper, we focus on incorporating new features suggested by the end user into machine learning systems. To investigate the effects of user-generated features on accuracy we developed an autocoding application that enables end users to assist a machine-learned program in coding a transcript by adding custom features. Our results show that adding usergenerated features to the machine learning algorithm can result in modest improvements to its F1 score. Further improvements are possible if the algorithm accounts for class imbalance in the training data and deals with lowquality user-generated features that add noise to the learning algorithm. We show that addressing class imbalance improves performance to an extent but improving the quality of features brings about the most beneficial change. Finally, we discuss changes to the user interface that can help end users avoid the creation of lowquality features.
Engineering of a Chimeric RB69 DNA Polymerase Sensitive to Drugs Targeting the Cytomegalovirus Enzyme (2009)

Detailed structural and biochemical studies with the human cytomegalovirus (HCMV UL54) DNA polymerase are hampered by difficulties to obtain this enzyme in large quantities. The crystal structure of the related RB69 DNA polymerase (gp43) is often used as a model system to explain mechanisms of inhibition of DNA synthesis and drug resistance. However, here we demonstrate that gp43 is approximately 400-fold less sensitive to the pyrophosphate analog foscarnet, when compared with UL54. The RB69 enzyme is also able to discriminate against the nucleotide analog inhibitor acyclovir. In contrast, the HCMV polymerase is able to incorporate this compound with similar efficiency as observed with its natural counterpart. In an attempt to identify major determinants for drug activity, we replaced critical regions of the nucleotide-binding site of gp43 with equivalent regions of the HCMV enzyme. We show that chimeric gp43-UL54 enzymes that contain residues of helix N and helix P of UL54 are resensitized against foscarnet and acyclovir. Changing a region of three amino acids of helix N showed the strongest effects, and changes of two segments of three amino acids in helix P further contributed to the reversal of the phenotype. The engineered chimeric enzyme can be produced in large quantities and may therefore be a valuable surrogate system in drug development efforts. This system may likewise be used for detailed structural and biochemical studies on mechanisms associated with drug action and resistance.
The crystal and molecular structures of 1-naphthylphenyliodonium tetrafluoroborate and 1-naphthylphenyliodonium tetrakis(pentafluorophenyl)gallate (2002)

The X-ray structures of 1-naphthylphenyliodonium tetrafluoroborate 1 and 1-naphthylphenyliodonium tetrakis(pentafluorophenyl)gallate 2 are reported. Crystals of 1 are monoclinic, space group P2(1)/c, with unit cell dimensions a = 11.8914(11), b = 8.8699(9), c = 14.4445 (13) Å, β = 90.944(4)°, Z = 4, and R = 0.0596 for 8286 unique observed reflections. Crystals of 2 are monoclinic, space group P2(1)/c, with unit cell dimensions a = 15.003(5), b = 18.287(6), c = 14.738(6) Å, β = 115.436(13)°, Z = 4, and R = 0.0222 for 8063 unique observed reflections. The iodonium cations of 1 exist as π-stacked dimers; however, those of 2 are monomeric.
Determination of the absolute configuration of six-membered-ring ketones by carbon-13 NMR (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of the absolute configuration of six-membered-ring ketones by carbon-13 NMRG. L. Lemiere, R. A. Dommisse, J. A. Lepoivre, F. C. Alderweireldt, H. Hiemstra, H. Wynberg, J. B. Jones, and E. J. TooneCite this: J. Am. Chem. Soc. 1987, 109, 5, 1363–1370Publication Date (Print):March 1, 1987Publication History Published online1 May 2002Published inissue 1 March 1987https://pubs.acs.org/doi/10.1021/ja00239a013https://doi.org/10.1021/ja00239a013research-articleACS PublicationsRequest reuse permissionsArticle Views223Altmetric-Citations39LEARN 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
New Particulate Filter Concept to Reduce Particle Number Emissions (2011)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Gasoline Direct Injection (GDI) engines achieve better fuel economy but have the drawback of increased Particulate Matter (PM) emissions. As known from diesel engine applications particulate filters are an effective PM reduction device which is expected to be effective for reduction of particulates emitted by GDI engines as well. For this investigation new filter concepts especially designed for GDI applications are proposed. Filtration efficiency, pressure drop and regeneration performance were verified by cold flow bench and engine and chassis dynamometer testing. The experimental data were used to discuss the validity of these new filter design concepts.&lt;/div&gt;&lt;/div&gt;
Effect of evaporation and condensation on a thermoacoustic engine: A Lagrangian simulation approach (2017)

Acoustic oscillations of a fluid (a mixture of gas and vapor) parcel in a wet stack of a thermoacoustic engine are numerically simulated with a Lagrangian approach taking into account Rott equations and the effect of non-equilibrium evaporation and condensation of water vapor at the stack surface. In a traveling-wave engine, the volume oscillation amplitude of a fluid parcel always increases by evaporation and condensation. As a result, pV work done by a fluid parcel is enhanced, which means enhancement of acoustic energy in a thermoacoustic engine. On the other hand, in a standing-wave engine, the volume oscillation amplitude sometimes decreases by evaporation and condensation, and pV work is suppressed. Presence of a tiny traveling-wave component, however, results in the enhancement of pV work by evaporation and condensation.
Toward Predicting Distributed Systems Dynamics (2015)

Systems of "building block" algorithms can guarantee that self-organizing systems eventually converge to a predictable state, but what of their dynamical behavior in environments with ongoing changes? To begin to address this challenge, we analyze a commonly used distributed distance estimation algorithm from a stability theory perspective, identifying key properties of monotonicity and dynamical behavior envelope. This allows standard stability theory analysis to be applied to predict the behavior of the algorithm in response to persistent perturbation, both in isolation and as part of a composite system, as demonstrated both analytically and in simulation.
Chemical class specificity using self-assembled monolayers on SAW devices: Effects of adsorption time and substrate grain size (1997)

The authors report selectivity and sensitivity for 97-MHz SAW (surface acoustic wave) sensors functionalized with (COO{sup {minus}}){sub 2}/Cu{sup 2+}-terminated, organomercaptan-based, self-assembled monolayers (SAMs). Responses were obtained as a function of SAM formation time on thin Au films of controlled grain size. The authors find that the SAM films (1) preferentially adsorb classes of organic analytes according to simple chemical interaction concepts, (2) reversibly adsorb multilayers of some analytes well below their saturation vapor pressure, (3) adsorb more diisopropylmethylphosphonate (DIMP) at a given partial pressure as SAM solution-phase adsorption time increases, and (4) adsorb more DIMP at a given partial pressure as the grain size of the supporting Au film decreases.
Separator for Lithium Batteries (2016)

Lithium ion batteries have been utilized in portable devices and electric vehicles. In this report, a separator for lithium ion batteries is described from the point of view of battery performance. Some of characteristics of separator are introduced, in addition, a newly developed separator and a three dimensionally structured separator are described in this report, in detail.
Inherited complement deficiency states: implications for immunity and immunological disease (1990)

The study of complement deficiency states and their influence on immune function has generated new insights and still provides a challenge to continued investigation. The association of classical pathway deficiencies (C1, C4, C2 or C3) with immunological diseases such as SLE and glomerulonephritis has contributed to current knowledge concerning complement-dependent immune complex handling and elimination. Susceptibility to systemic infection with encapsulated bacteria is encountered in most forms of inherited complement deficiency. Recurrent neisserial infection is the only clinical manifestation clearly associated with defects of the membranolytic sequence C5-C9, while deficiency of properdin, a component of the alternative activation pathway, appears to predispose to nonrecurrent meningococcal disease. Inherited complement deficiency is rare, but the perspective is widened by the more common occurence of acquired defects in immunological diseases, and the apparent requirement for efficient complement recruitment in host defense. Another aspect is the possibility that complement deficiency might alleviate or prevent inflammatory symptoms. Notably, complement deficiency has not been reported in classical rheumatoid arthritis. Considerations of this kind would be refuted or modified by findings of complement deficiency in single patients.
SAR Probing of KX2-391 Provided Analogues With Juxtaposed Activity Profile Against Major Oncogenic Kinases (2022)

Tirbanibulin (KX2-391, KX-01), a dual non-ATP (substrate site) Src kinase and tubulin-polymerization inhibitor, demonstrated a universal anti-cancer activity for variety of cancer types. The notion that KX2-391 is a highly selective Src kinase inhibitor have been challenged by recent reports on the activities of this drug against FLT3-ITD mutations in some leukemic cell lines. Therefore, we hypothesized that analogues of KX2-391 may inhibit oncogenic kinases other than Src. A set of 4-aroylaminophenyl-<i>N</i>-benzylacetamides were synthesized and found to be more active against leukemia cell lines compared to solid tumor cell lines. <i>N</i>-(4-(2-(benzylamino)-2-oxoethyl)phenyl)-4-chlorobenzamide (<b>4e</b>) exhibited activities at IC<sub>50</sub> 0.96 µM, 1.62 µM, 1.90 µM and 4.23 µM against NB4, HL60, MV4-11 and K562 leukemia cell lines, respectively. We found that underlying mechanisms of <b>4e</b> did not include tubulin polymerization or Src inhibition. Such results interestingly suggested that scaffold-hopping of KX2-391 may change the two main underlying cytotoxic mechanisms (Src and tubulin). Kinase profiling using two methods revealed that <b>4e</b> significantly reduces the activities of some other potent oncogenic kinases like the MAPK member ERK1/2 (>99%) and it also greatly upregulates the pro-apoptotic c-Jun kinase (84%). This research also underscores the importance of thorough investigation of total kinase activities as part of the structure-activity relationship studies.
Effect of Adhesive Nanoparticle Enrichment on Static Load Transfer Capacity and Failure Mode of Bonded Steel–Magnesium Single Lap Joints (2015)

An experimental procedure and test setup are used for investigating effect of using nanoparticle additives to the adhesive on the load transfer capacity (LTC) of bonded magnesium (Mg)–steel (St) single lap joints (SLJ). Investigated variables include the nanopowder material (alumina versus silica), particulate size (20 nm versus 80 nm), and concentration in the adhesive (2.5 wt.% versus 5.0 wt.%). Two different levels of surface roughness on the bonded area are used, namely, sanding the bond area with G60 or G180 sand paper. Test data and scanning electron microscopy (SEM) failure mode analysis are provided.
Riboflavin Depletion Promotes Longevity and Metabolic Hormesis in Caenorhabditis elegans (2022)

Summary Riboflavin is an essential cofactor in many enzymatic processes and in the production of flavin adenine dinucleotide (FAD). Here we report that the partial depletion of riboflavin through knockdown of the C. elegans riboflavin transporter 1 ( rft-1 ) promotes metabolic health by reducing intracellular flavin concentrations. Knockdown of rft-1 significantly increases lifespan in a manner dependent on FOXO/ daf-16 , AMP-activated protein kinase (AMPK)/ aak-2 , the mitochondrial unfolded protein response, and mTOR complex 2 (mTORC2). Riboflavin depletion promotes altered energetic and redox states and increases adiposity, independent of lifespan genetic dependencies. Riboflavin depleted animals also exhibit activation of caloric restriction reporters without a reduction in TORC1 signaling. Our findings indicate that riboflavin depletion activates an integrated, hormetic response that promotes lifespan and healthspan in C. elegans.
Low leakage current AlGaN/GaN on Si-based Schottky barrier diode with bonding-pad electrode mesa etching (2015)

Bonding-pad electrode-area-etched AlGaN/GaN on a Si-based Schottky barrier diode (SBD) is fabricated. Electrode mesa etching leads to reverse bias leakage current about one order of magnitude lower than that of SBD without electrode mesa etching, but forward currents do not vary greatly, compared with that in conventional SBD, which has no electrode mesa etching.
Capturing spatially resolved kinetic data and coking of Ga–Pt supported catalytically active liquid metal solutions during propane dehydrogenationin situ (2020)

Supported liquid phase catalysis has great potential to unify the advantages from both homogeneous and heterogeneous catalysis. Recently, we reported supported catalytically active liquid metal solutions (SCALMS) as a new class of liquid phase catalysts. SCALMS enable high temperature application due to the high thermal stability of liquid metals when compared to supported molten salts or ionic liquids. The highly dynamic liquid metal/gas interface of SCALMS allows for catalysis over single atoms of an active metal atom within a matrix of liquid gallium. In the present study, kinetic data is acquired along the catalyst bed in a compact profile reactor during propane dehydrogenation (PDH) over gallium-platinum SCALMS. The reactor design allows for the analysis of the temperature and gas phase composition along the catalyst bed with a high spatial resolution using a sampling capillary inside the reactor. The concentration profiles suggest enhanced deactivation of the catalyst at the end of the bed with a deactivation front moving from the end to the beginning of the catalyst bed over time on stream. Only minor amounts of side products, formed via cracking of propane, were identified, supporting previously reported high selectivity of SCALMS during alkane dehydrogenation. The acquired data is supported by in situ high-resolution thermogravimetry coupled with mass spectrometry to monitor the activity and coking behaviour of SCALMS during PDH. The results strongly suggest an enhanced formation of coke over Al<sub>2</sub>O<sub>3</sub>-supported SCALMS when compared to using SiO<sub>2</sub> as the support material.
A Cascaded Feedback Control Scheme for Trajectory Tracking of Robot Manipulator Systems WITH Actuator Dynamics (2007)

In the case of control for nonlinear mechanical systems, which have complex actuator dynamics, the total system becomes high-order and nonlinear. Generally speaking, it is not easy to tune feedback gains for state feedback. In this paper, we propose a feedback control scheme for motion control of nonlinear high-order systems. We prove that the proposed scheme can improve the trajectory tracking performance of a robot manipulator system with actuator dynamics. Moreover, some simulation results demonstrate the effectiveness of the proposed control scheme.
Supplementary Figure 3 from Dual mTORC1/2 and HER2 Blockade Results in Antitumor Activity in Preclinical Models of Breast Cancer Resistant to Anti-HER2 Therapy (2023)

&lt;p&gt;PDF file, 714KB, Combination index (CI) of the combination of lapatinib and INK-128 in resistant cell lines.&lt;/p&gt;
Plasma-nitrided silicon-rich oxide as an extension to ultrathin nitrided oxide gate dielectrics (2005)

We have investigated the mechanism of N incorporation, during plasma nitridation, in thermally grown ultrathin (&amp;lt;2nm)SiO2 films and deposited silicon-rich oxide films. X-ray photoelectron spectroscopy analysis indicates that N atoms exchange mainly with O to bond with Si atoms in ultrathin plasma-nitrided oxides. Based on this understanding, we were able to increase the amount of N that can be incorporated in plasma-nitrided silicon oxides by increasing the silicon content in these films. This was achieved by depositing ultrathin substoichiometric silicon-rich oxide films. We demonstrate an increase of almost twice as much N in these ultrathin plasma-nitrided silicon-rich oxide films yielding lower gate leakage current for a given thickness.
Frequency-Shaped Randomized Sampling (2007)

This paper explores the use of discrete-time randomized sampling as a method to mitigate the effects of aliasing. Two distinct sampling architectures are presented along with second-order characterizations of the resulting sampling error. In the first, denoted simple randomized sampling, non-white sampling processes are shown to frequency-shape the error spectrum, so that its power is minimized in the band of interest. The design of non-white binary processes for use in randomized sampling is considered. In the second model, denoted filtered randomized sampling, a pre-filter, post-filter, and the sampling process are used to achieve a similar effect. In both cases, optimal mean-squared-error solutions are derived. Results from simulation are shown.
The impact of sequence divergence and DNA mismatch repair on homeologous recombination in Arabidopsis (2006)

We examined the effects of substrate divergence and DNA mismatch repair (MMR) on recombination in Arabidopsis thaliana. Relative to the frequency observed in plants with a homologous construct (0% divergence), recombination was decreased 4.1-, 9.6-, 11.7- or 20.3-fold, respectively, in lines with constructs containing 0.5%, 2%, 4% or 9% divergence between the recombination substrates. To evaluate the contribution of the MMR system in this decrease, 12 independent reporter lines (two or three lines per reporter construct) were crossed to an AtMSH2 T-DNA insertional mutant. We examined the recombination frequency in progeny homozygous for a reporter T-DNA and homozygous either for the wild type or the mutant allele of AtMSH2. The loss of MMR activity led to a two- to ninefold increase in homeologous recombination and the size of the increase did not seem to correlate with the amount of divergence. Inversely, complementation of the insertional mutant with a wild-type cDNA of AtMSH2 reduced recombination. Our results demonstrate clearly that sequence divergence can dramatically reduce the recombination frequency in plants and that the MMR system plays a part in this decrease.