gebhart/patrepeval huggingface dataset:
Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field (2021)

We present a methodology for defining and optimizing a general force field for classical molecular simulations, and we describe its use to derive the Open Force Field 1.0.0 small-molecule force field, codenamed Parsley. Rather than using traditional atom typing, our approach is built on the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism, which handles increases in the diversity and specificity of the force field definition without needlessly increasing the complexity of the specification. Parameters are optimized with the ForceBalance tool, based on reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These quantum reference data are computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. In this initial application of the method, we present essentially a full optimization of all valence parameters and report tests of the resulting force field against compounds and data types outside the training set. These tests show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields, as is accuracy on binding free energies. We find that this initial Parsley force field affords accuracy similar to that of other general force fields when used to calculate relative binding free energies spanning 199 protein-ligand systems. Additionally, the resulting infrastructure allows us to rapidly optimize an entirely new force field with minimal human intervention.
Characterization of the subtypes of cell motility in ageing human skin fibroblasts (1990)

Previous studies have noted alterations in cell migration during wound healing with age. Both intracellular and extracellular factors alter cell migration. In an effort to clarify the relationship between ageing and cell motility we have utilized time-lapse videomicroscopy to quantitatively and qualitatively study the various subtypes of cell motility including membrane ruffling, lamellapodal extension and cell translocation of ageing human fibroblasts in culture. We demonstrate a global decline in all types of cell motility of human fibroblasts with increasing donor age. Furthermore, we demonstrate that this decrease in cell motility with ageing is independent of chemotactic gradients.
Clinical Measurements of Cement Injection Pressure During Vertebroplasty (2005)

High injection pressures approaching 20 atmospheres are reached during conventional vertebroplasty. Widening the syringe tip diameter did not significantly change injection pressures, whereas elapsed time did. Further research is needed to improve injection equipment and materials for vertebroplasty.
Single-mode Large-aperture Vertical Cavity Surface Emitting Laser (1993)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text C. J. CHANG-HASNAIN, Y. A. WU, and R. NABIEV, "Single-mode Large-aperture Vertical Cavity Surface Emitting Laser," Optics & Photonics News 4(12), 26-26 (1993) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
A Realization of Motion Acquisition System Based on Interaction Mode Control (2007)

Recently, skill preservation of an expert has been a serious problem of the medical or production fields. This paper proposes a motion acquisition and reproduction of human motion by bilateral motion control. The proposed skill preservation system is composed of two modes; acquisition mode and reproduction mode. In the acquisition mode, the control system is based on bilateral control. Since a touching motion is subject to the “law of action and reaction”, it is possible to decompose the force information into action force and reaction force by using the bilateral control. Furthermore, human motion is acquired in decoupled modal space by using the quarry matrix. The decoupled modes correspond to “moving”, “yawing”, “grasping” tasks, and so on. Thus the skilled motion by a human is easily obtained and analyzed in the modal space. In the reproduction mode, the acquired human motion is reproduced in the modal space by the interaction mode control.The proposed skill preservation system is applied for grasping motion by three fingers. As a result, both grasping force and moving position are well reproduced automatically. The experimental results show viability of the proposed method.
Sesquiterpenoids from the Rhizomes of <i>Curcuma phaeocaulis</i> and Their Inhibitory Effects on LPS-Induced TLR4 Activation (2016)

Two new guaiane-type (2, 6) and one new furanogermacrane-type (11) sesquiterpenoids have been isolated along with twelve known compounds from an EtOAc-soluble extract of Curcuma phaeocaulis rhizomes. The structures of the isolated compounds were elucidated using a combination of NMR, MS, and circular dichroism (CD) spectra. The inhibitory effects of each compound on lipopolysaccharide (LPS)-induced Toll-like receptor 4 (TLR4) activation in THP-1-Blue cells were assessed, and compound 4 showed more potent inhibitory activity against LPS-stimulated TLR4 activation.
A Lewis acid-mediated version of the Nicholas reaction: Synthesis of syn-alkylated products and cobalt-complexed cycloalkynes (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Lewis acid-mediated version of the Nicholas reaction: Synthesis of syn-alkylated products and cobalt-complexed cycloalkynesStuart L. Schreiber, Tarek. Sammakia, and William E. CroweCite this: J. Am. Chem. Soc. 1986, 108, 11, 3128–3130Publication Date (Print):May 1, 1986Publication History Published online1 May 2002Published inissue 1 May 1986https://pubs.acs.org/doi/10.1021/ja00271a066https://doi.org/10.1021/ja00271a066research-articleACS PublicationsRequest reuse permissionsArticle Views1377Altmetric-Citations152LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Formation and coordination modes of the C4E4 moiety (E = COOMe) bound to two palladium(ii) moieties (2011)

The transmetallation of the palladacyclopentadiene complex Pd{C(COOMe)C(COOMe)C(COOMe)C(COOMe)}(bipy) with the dicationic Pd(II) complex [Pd(bipy)(CH(3)CN)(2)][BF(4)](2) afforded a terminally σ-palladated diene complex [Pd(2){μ-η(1):η(1)-C(COOMe)C(COOMe)C(COOMe)C(COOMe)}(bipy)(2)(CH(3)CN)(2)][BF(4)](2). It was revealed by X-ray crystallographic analysis that replacement of the acetonitrile ligands in a terminally σ-palladated diene complex with PPh(3) ligands resulted in the conformation change of the σ-palladated diene moiety from skewed s-cis to planar s-trans. Treatment of a bis-triphenylphosphine dipalladium complex [Pd(2)(PPh(3))(2)(CH(3)CN)(4)][PF(6)](2) with dimethoxyacetylene dicarboxylate (DMAD) (1 equiv.) in acetonitrile resulted in the insertion of DMAD to the Pd-Pd bond to afford [Pd(2){μ-η(1):η(1)-C(COOMe)C(COOMe)}(PPh(3))(2)(CH(3)CN)(4)][PF(6)](2). Addition of the second DMAD gave the ylide-type complex [Pd(2){μ-η(2):η(3)-C(COOMe)C(COOMe)C(COOMe)C(COOMe)(PPh(3))}(PPh(3))(2)(CH(3)CN)(3)][PF(6)](2) of which the structure was determined by X-ray crystallographic analysis.
ChemInform Abstract: α‐Sulfinyl‐Substituted Radicals. Part 2. Stereoselective Interand Intramolecular Addition Reactions of Acyclic α‐Sulfinyl Radicals. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Table Legends from Personalized <i>In Vitro</i> and <i>In Vivo</i> Cancer Models to Guide Precision Medicine (2023)

&lt;p&gt;Supplementary Table Legends&lt;/p&gt;
Separation and detection of phospholipid hydroperoxides in the low nanomolar range by a high performance liquid chromatography/irothiocyanate assay (1990)

A new method for the detection of phospholipid hydroperoxides in the low nanomolar range has been developed by using a high performance liquid chromatography system combined with a post-column reaction. The detection is based on the oxidation of Fe(II) to Fe(III) by hydroperoxides and the subsequent formation of an ironthiocyanate complex, which can be determined spectrophotometrically at 505 nm. By this method it is possible to separate and quantitate phosphatidylethanolamine hydroperoxide and phosphatidylcholine hydroperoxide formed in erythrocyte ghost membranes during photooxidation.
The authors reply (2012)

Department of Emergency Medicine, Carolinas Medical Center, Charlotte, NC (Puskarich, Kline) University of Mississippi Medical Center, Jackson, MS (Jones)
Extra-Cellular Matrix in the Craniofacial Complex (2006)

The extracellular matrix (ECM) constitutes the solid-phase microenvironment of cells and harbors a myriad of structural proteins whose complex functions are now beginning to be unraveled. The papers presented in this issue reveal novel concepts about the role of the ECM in controlling the structure, strength and function of the head and face. Empha
MPC for coupled station keeping, attitude control, and momentum management of GEO satellites using on-off electric propulsion (2017)

This paper develops a model predictive control (MPC) policy for simultaneous station keeping, attitude control, and momentum management of a nadir-pointing geostationary satellite equipped with three reaction wheels and four on-off electric thrusters mounted on two boom assemblies attached to the anti-nadir face of the satellite. A closed-loop pulse-width modulation (PWM) scheme is implemented in conjunction with the MPC policy in order to generate on-off commands to the thrusters. The MPC policy is shown to satisfy all station keeping and attitude constraints while managing stored momentum, enforcing thruster constraints, and minimizing required delta-v.
Cell Cycle Withdrawal Promotes Myogenic Induction of Akt, a Positive Modulator of Myocyte Survival (1999)

During myogenesis, proliferating myoblasts withdraw from the cell cycle, acquire an apoptosis-resistant phenotype, and differentiate into myotubes. Previous studies indicate that myogenic induction of the cyclin-dependent kinase inhibitor p21 results in an inhibition of apoptotic cell death in addition to its role as a negative cell cycle regulator. Here we demonstrate that the protein encoded by the Akt proto-oncogene is induced in C2C12 cells during myogenic differentiation with a corresponding increase in kinase activity. In differentiating cultures, expression of dominant-negative forms of Akt increase the frequency of cell death whereas expression of wild-type Akt protects against death, indicating that Akt is a positive modulator of myocyte survival. Antisense oligonucleotides against p21 block cell cycle withdrawal, inhibit Akt induction, and enhance cell death in differentiating myocyte cultures. Adenovirus-mediated transfer of wild-type or constitutively active Akt constructs confer partial resistance to cell death under conditions where cell cycle exit is blocked by the antisense oligonucleotides. Collectively, these data indicate that cell cycle withdrawal facilitates the induction of Akt during myogenesis, promoting myocyte survival.
Predicting asthma morbidity in children using proposed markers of Th2‐type inflammation (2015)

Assessment of both local and systemic Th2-mediated inflammation by the analysis of easily attainable biomarkers such as exhaled NO and blood eosinophils has a high predictive value for the identification of children with the highest asthma morbidity. Adjusting FeNO values according to the individual child's height increases the clinical usefulness of this biomarker.
Synthesis of a Novel Oligo(p-phenylene) Ladder by Sulfide and Sulfonio Groups (1999)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTSynthesis of a Novel Oligo(p-phenylene) Ladder by Sulfide and Sulfonio GroupsAgus Haryono, Kenji Miyatake, Junichiro Natori, and Eishun TsuchidaView Author Information Department of Polymer Chemistry, Advanced Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan Cite this: Macromolecules 1999, 32, 9, 3146–3149Publication Date (Web):April 15, 1999Publication History Received16 November 1998Revised23 February 1999Published online15 April 1999Published inissue 1 May 1999https://pubs.acs.org/doi/10.1021/ma9817774https://doi.org/10.1021/ma9817774brief-reportACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views1484Altmetric-Citations46LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alkyls,Infrared light,Oligomers,Oxides,Sulfides Get e-Alerts
Visualizing polarization singularities in Bessel-Poincaré beams (2015)

We demonstrate that an annulus of light whose polarization is linear at each point, but the plane of polarization gradually rotates by π radians can be used to generate Bessel-Poincaré beams. In any transverse plane this beam exhibits concentric rings of polarization singularities in the form of L-lines, where the polarization is purely linear. Although the L-lines are invisible in terms of light intensity variations, we present a simple way to visualize them as dark rings around a sharp peak of intensity in the beam center. To do this we use a segmented polarizer whose transmission axes are oriented differently in each segment. The radius of the first L-line is always smaller than the radius of the central disk of the zero-order Bessel beam that would be produced if the annulus were homogeneously polarized and had no phase circulation along it.
A practical approach to creating environment maps using digital images (2003)

Conventional panoramic stereo camera heads have a horizontal displacement structure. When a camera head is used in generating a spatial panorama, it may encounter occlusion inconsistency in the overlap region of two adjacent viewing angles; that is, occlusion may occur from one viewing angle, but not from an adjacent angle. Also, computing spatial panorama may become unnecessarily complex. This paper reports a solution to the above problems by using a dual camera head with the two cameras being displaced vertically with parallel optical axes, and by letting the rotation axis pass through the focal points of the two cameras.
Alzheimer's disease: evaluation using label-free, stainless, fluorescence of tryptophan metabolites and the kynurenine pathway (2018)

Under stress conditions, pro-inflammatory cytokines, such as tumor necrosis factor-alpha, interleukin-1 beta, interleukin 6 and interferon gamma are released. It is known that these cytokines stimulate indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO), which increase tryptophan metabolism through the kynurenine pathway, and that this can cause increased production of neurotoxic compounds. Brain tissues from Alzheimer’s disease patients and agematched controls were investigated using label-free fluorescence spectroscopy. Tryptophan (exc. 280/ em. 340 nm) and its metabolites (N-formyl-L-kynurenine (exc. 325/em. 434 nm), kynurenine (exc. 365/em. 480 nm) and kynurenic acid (exc. 330/em. 390 nm)) have distinct spectral profiles. Preliminary results show a difference in the optical signatures in three important areas of the brain (hippocampus, BA 9, BA 17) between patients with Alzheimer’s disease and agedmatched controls (normal), and a marked relative increase in tryptophan in the Alzheimer’s patients. Thus determinations of tryptophan to tryptophan metabolite ratios could potentially be used to measure IDO and TDO activity and the degree of inflammation in the brain. This label-free optical technique may be useful in the study of Alzheimer’s and other neurodegenerative diseases.
A Review of Recent Studies On the Sources of Hazardous Compounds Emitted From Solid Waste Landfills: a U.S. Experience (1993)

Municipal solid waste landfills operating in the United States receive a large variety of materials generated by an industrialized, "throwaway" society. As a result, liquid and gas emissions (produced during the normal decomposition processes occurring within the landfill) are often contaminated with hazardous compounds. The presence of hazardous pollutants in liquid and gaseous emissions is well documented, however, the source of these pollutants is not always apparent. Potential sources of these hazardous contaminants in municipal solid waste landfills may include small quantity generators of hazardous wastes, household hazardous wastes, wastes disposed prior to the 1980 enactment of U.S. hazardous waste disposal legislation, and biological and chemical transformation products of buried refuse. Source identification will facilitate characterization and quantification of emissions necessary for the design and operation of leachate gas collection and treatment facilities.
Simultaneous Targeting of PARP1 and RAD52 Triggers Dual Synthetic Lethality in BRCA-Deficient Tumor Cells (2018)

PARP inhibitors (PARPis) have been used to induce synthetic lethality in BRCA-deficient tumors in clinical trials with limited success. We hypothesized that RAD52-mediated DNA repair remains active in PARPi-treated BRCA-deficient tumor cells and that targeting RAD52 should enhance the synthetic lethal effect of PARPi. We show that RAD52 inhibitors (RAD52is) attenuated single-strand annealing (SSA) and residual homologous recombination (HR) in BRCA-deficient cells. Simultaneous targeting of PARP1 and RAD52 with inhibitors or dominant-negative mutants caused synergistic accumulation of DSBs and eradication of BRCA-deficient but not BRCA-proficient tumor cells. Remarkably, Parp1-/-;Rad52-/- mice are normal and display prolonged latency of BRCA1-deficient leukemia compared with Parp1-/- and Rad52-/- counterparts. Finally, PARPi+RAD52i exerted synergistic activity against BRCA1-deficient tumors in immunodeficient mice with minimal toxicity to normal cells and tissues. In conclusion, our data indicate that addition of RAD52i will improve therapeutic outcome of BRCA-deficient malignancies treated with PARPi.
Laser performance of neodymium-doped lanthanum tungstate crystals (2001)

We demonstrated the laser oscillation of neodymium-doped lanthanum tungstate (Nd:LWO) crystals. The crystals with Nd concentration up to 20 at. % were grown using the micro-pulling-down method. Oscillation was observed using uncoated samples under pulsed laser pumping. Minimum threshold of 5.9 mW was exhibited for 1.8 at. %-doped sample. Maximum slope efficiency of 35 % was achieved for 3.2 at. %-doped sample. This crystal had high receptivity for Nd and low concentration quenching.
Large genome deletions reveal gene effects on ethanol tolerance in Saccharomyces cerevisiae (2019)

The yeast Saccharomyces cerevisiae, which is a model system for biological research, has been widely used as an industrial host. Using the mazF-mediated deletion system, we made large deletions, including both terminal and internal regions of the chromosome. We obtained 12 deletion strains with different sizes of the deleted genome region(s), varying from 20 kb to 80 kb. Each deletion removed a cluster of nonessential genes, as deduced by an online prediction program. Phenotype analysis of the mutants with large deletions showed that genome regions YOR124C/YOR134W and YOL020W/YOL011W appeared to be related to ethanol tolerance and high salinity sensitivity, respectively. The loss of CAT5, ADE2, or RGA1 reduced the ethanol tolerance of yeast. Dispensable genes or interactions among non-essential genes were involved in the functional effects of genome deletions.
Wireless Bioelectronic Nanosystems for Intracellular Communication (2018)

&lt;p&gt; &lt;i&gt;In order for the field of bioelectronics to make an impact on healthcare&lt;/i&gt;&lt;i&gt;,&lt;/i&gt;&lt;i&gt; there is an urgent requirement for the development of “wireless” electronic systems to both sense and actuate cell behaviour. Herein we report the first example of an innovative intracellular wireless electronic communication system. We demonstrate that chemistry can&lt;/i&gt;&lt;i&gt; &lt;/i&gt;&lt;i&gt;be electrically modulated in a “wireless” manner on the nanoscale at the surface of conductive nanoparticles&lt;/i&gt;&lt;i&gt; &lt;/i&gt;&lt;i&gt;uptaken by cells at unreported low potentials. The system is made functional by modifying gold nanoparticles incorporating&lt;/i&gt;&lt;i&gt; &lt;/i&gt;&lt;i&gt;a Zn-porphyrin, which&lt;/i&gt;&lt;i&gt; &lt;/i&gt;&lt;i&gt;are&lt;/i&gt;&lt;i&gt; &lt;/i&gt;&lt;i&gt;taken up by cells and are shown to be biocompatible. It is demonstrated the redox state of Zn-porphyrin modified gold nanoparticles is modulated and reported on fluorescently when applying an external electrical potential. This provides an attractive new “wireless” approach to develop novel bioelectronic devices for modulating and sensing cellular behaviour using intracellular monitoring&lt;/i&gt;&lt;i&gt;.&lt;/i&gt; &lt;i&gt;&lt;/i&gt;&lt;/p&gt;