gebhart/patrepeval huggingface dataset:
Software design of transperineal prostate needle biopsy robot (2005)

This paper focuses on introducing the software design of a robotic system for accurate and consistent insertion of a percutaneous biopsy needle into the prostate guided by transrectal ultrasound images. A set of software modules in the main computer system is designed to guide the urologist to control the biopsy robot and biopsy process. This system functionally undertakes the control of image acquisition, interaction with the urologist for prostate boundary delineation, puncture point planning and biopsy point definition on 2D image (ultrasound) slices. 3D visualization of the prostate surface, needle, biopsy point and needle trajectory is also performed by the software. The system calculates the required parameters of the needle's trajectory and guides the urologist in maneuvering the robot to perform the biopsy. System performance and experimental results are presented at the end.
The association between research funding status and clinical research papers’ citation impact in Japan: A cross-sectional bibliometric study (2022)

Analysis <i>via</i> multiple indicators including CNCI and the SIGAPS category, which allows for a comparison of the papers' citation impact in different research fields, found a positive relation between research funding status and the citation impact of clinical research papers.
Supplementary Table 2 from Dysfunctional Microvasculature as a Consequence of &lt;i&gt;Shb&lt;/i&gt; Gene Inactivation Causes Impaired Tumor Growth (2023)

Supplementary Table 2 from Dysfunctional Microvasculature as a Consequence of &lt;i&gt;Shb&lt;/i&gt; Gene Inactivation Causes Impaired Tumor Growth
A Tips Scorecard: Are They Accomplishing Their Objectives? (2010)

Treasury Inflation-Protected Securities were developed to provide (1) consumers with assets that permit hedging against real interest rate risk, (2) nominal contract holders a means of hedging against inflation risk, and (3) everyone with an indicator of the term structure of expected inflation. This article evaluates progress toward these objectives.
Modifying the Thioester Linkage Affects the Structure of the Acyl Carrier Protein (2019)

Abstract At the center of many complex biosynthetic pathways, the acyl carrier protein (ACP) shuttles substrates to appropriate enzymatic partners to produce fatty acids and polyketides. Carrier proteins covalently tether their cargo via a thioester linkage to a phosphopantetheine cofactor. Due to the labile nature of this linkage, chemoenzymatic methods have been developed that involve replacement of the thioester with a more stable amide or ester bond. We explored the importance of the thioester bond to the structure of the carrier protein by using solution NMR spectroscopy and molecular dynamics simulations. Remarkably, the replacement of sulfur with other heteroatoms results in significant structural changes, thus suggesting more rigorous selections of isosteric substitutes is needed.
Quantitative determination of release kinetics from fibrous poly(3-hydroxybutyrate) scaffolds (2020)

A fibrous scaffold was prepared from poly(3-hudroxybutirate) (PHB) by wet spinning from chloroform solution. The fibers were precipitated into excess ethanol and they had a regular, cylindrical shape. The diameter of the fibers was regulated by the rate of spinning. A model drug, quercetin, was dissolved in the fiber in various amounts. The rate of drug release could be controlled by the adjustment of fiber diameter. A novel approach is proposed in the paper for the quantitative analysis of release kinetics. The model is based on Fick's laws, and does not use any simplification or introduce empirical constants. The prediction of the new model agreed well with experimental results and proved that the approach offers an exact description of experimental data. Although the method allows the estimation of the diffusion coefficient as well, the value obtained is biased because of the large surface to volume ratio of the scaffold. The comparison of the proposed model to empirical or semi-empirical approaches published earlier showed that the latter are less accurate and predict false results at various stages of the release study. The proposed method of fiber preparation and the model makes possible the prediction and control of the release rate of a drug from fibrous scaffolds.
New matrices and accelerating voltage effects in matrix‐assisted laser desorption/ionization of synthetic polymers (1995)

Abstract Most matrices used in matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) have been selected for their sound performance in the detection of proteins. We evaluated a series of new matrices for the analysis of synthetic polymers and compared their performance to that of conventional ones. Among substituted polycyclic aromatic hydrocarbons 1,4‐dihydroxy‐2‐naphthoic acid, 9‐anthracenecarboxylic acid (9‐ACA), and its mixtures with 5‐methoxysalicylic‐acid (‘super’ 9‐ACA) offered better signal quality for analysis of synthetic polymers. To test the performance of these new matrices, authentic standards of poly(ethylene glycol), poly(propylene glycol), Jeffamine, polybutadiene, poly(methyl methacrylate), poly(dimethyl siloxane), and some of their mixtures were analyzed. By generating mainly [M + Na] + ions, 9‐ACA showed superior performance to most conventional matrices and provided higher effective mass resolution. The ‘super’ 9‐ACA composite matrix was found to be more suitable for larger polymer molecules (&gt;8000 Da). Broader acceptance of MALDI‐MS for synthetic polymer analysis has been delayed by systematic differences observed between MALDI‐MS and gel permeation chromatography (GPC) in terms of oligomer size distributions (R. S. Lehrle and D. S. Sarson, Rapid Commun. Mass Spectrom. ), Vol. 9, p. 91 (1995). We found that part of the discrepancy can be explained by the profound dependence of mass distributions on the accelerating voltage of the time‐of‐flight mass spectrometer. With decreasing accelerating voltage both the ion intensity and the mass resolution decreased, and the high‐mass end of the mass spectrum became truncated. For example, when the accelerating voltage was changed from 30 kV to 18 kV the center of the peak area distribution for poly(methyl‐methacrylate) (PMMA) 6000 shifted to lower values by about 210 Da. At the same time, the skewness of the distribution increased tenfold indicating serious discrimination phenomena. These detrimental effects of lower accelerating voltage were particularly strong for relatively large synthetic polymer molecules.
Gel Formation Driven by Tunable Hydrophobic Domain: Design of Acrylamide Macromonomer with Oligo Hydrophobic Segment (2012)

Nowadays, biomaterials with amphiphilic properties are undergoing remarkable development. Here, we present one such development, in which we prepared amphiphilic graft copolymers, with a main chain composed of hydroxyethyl acrylamide (HEAA), to introduce hydrophilicity, and a side chain composed of poly(trimethylene carbonate) (PTMC) to introduce tunable hydrophobicity. These macromonomers were created with a novel molecular design, which introduced a ring-opening polymerization by the hydroxyl end group of HEAA in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene, and were analyzed by (1)H NMR and gel permeation chromatography. The amphiphilic graft copolymers were shown to form a hydrogel, the swelling ratio of which was greatly influenced by the number of trimethylene carbonate units. These copolymers also exhibited the Tyndall phenomenon in aqueous solution; they aggregated spontaneously due to hydrogen bonding and hydrophobic interactions, and a sodium 8-anilino-1-naphthalenesulfonate (ANS) fluorescence probe was introduced into the hydrophobic domain. The solution property of ANS in the polymer solution was analyzed by fluorescence measurement and (1)H NMR. The maximum fluorescence wavelength of ANS shifted to shorter wavelengths as the degree of polymerization of the hydrophobic PTMC, the composition of the macromonomer, and the concentration of the copolymer increased. The resulting copolymer formed a polymer micelle structure due to the tunable hydrophobic domain formation in selected solvents. Therefore, these amphiphilic graft copolymers containing a PTMC segment are excellent candidates for use as hydrophobic drug delivery carriers.
Template CoMFA: The 3D-QSAR Grail? (2014)

Template CoMFA, a novel alignment methodology for training or test set structures in 3D-QSAR, is introduced. Its two most significant advantages are its complete automation and its ability to derive a single combined model from multiple structural series affecting a biological target. Its only two inputs are one or more "template" structures having 3D coordinates that share some Cartesian space, as may result from X-ray crystallography or pharmacophoric hypothesis, and one or more connectivity-only SAR tables associated with a common target. Template CoMFA also overcomes the major disadvantages of both existing 3D-QSAR alignment methodologies, specifically the tedium and subjectivity of familiar ad hoc approaches, and the awkwardness, occasional physicochemical heresies, and structural scope limitations of the purely topomer approach. The template CoMFA algorithms are described, and two of its application classes are presented. The first class, general models of binding to factor Xa and P38 map kinase, uses crystallographic structures as templates, with the encouraging result that the statistical qualities of each of these two combined models are equivalent to those of their constituent individual series models. The second, 15 data sets originally collected for validation of topomer CoMFA, with arbitrary structures as templates, confirms that the modeling power of template CoMFA resembles that of its predecessors.
Effects of Arylene Diimide Thin Film Growth Conditions on n‐Channel OFET Performance (2008)

Abstract A series of eight perylene diimide (PDI)‐ and naphthalene diimide (NDI)‐based organic semiconductors was used to fabricate organic field‐effect transistors (OFETs) on bare SiO 2 substrates, with the substrate temperature during film deposition ( T d ) varied from 70–130 °C. For the N,N ′‐ n ‐octyl materials that form highly ordered films, the mobility ( µ ) and current on‐off ratio ( I on / I off ) increase slightly from 70 to 90 °C, and remain relatively constant between 90 and 130 °C. I on / I off and µ of dibromo‐PDI‐based OFETs decrease with increasing T d , while films of N,N ′‐1 H ,1 H ‐perfluorobutyl dicyanoperylenediimide (PDI‐FCN 2 ) exhibit dramatic I on / I off and µ enhancements with increasing T d . Increased OFET mobility can be correlated with higher levels of molecular ordering and minimization of film morphology surface irregularities. Additionally, the effects of SiO 2 surface modification with trimethylsilyl and octadecyltrichlorosilyl monolayers, as well as with polystyrene, are investigated for N,N ′‐ n ‐octyl dicyanoperylenediimide (PDI‐8CN 2 ) and PDI‐FCN 2 films deposited at T d = 130 °C. The SiO 2 surface treatments have modest effects on PDI‐8CN 2 OFET mobilities, but modulate the mobility and morphology of PDI‐FCN 2 films substantially. Most importantly, the surface treatments result in substantially increased V th and decreased I off values for the dicyanoperylenediimide films relative to those grown on SiO 2 , resulting in V th &gt; 0.0 V and I on / I off ratios as high as 10 8 . Enhancements in current modulation for these high‐mobility, air‐stable, and solution‐processable n‐type semiconductors, should prove useful in noise‐margin enhancement and further improvements in organic electronics.
A 28.05Gb/s transceiver using quarter-rate triple-speculation hybrid-DFE receiver with calibrated sampling phases in 32nm CMOS (2017)

This paper presents a 28.05Gb/s transceiver in 32nm SOI CMOS technology. The receiver employs a quarterrate triple-speculation architecture. Techniques are introduced to adapt for mismatches in tap weights, gains and sampling phases. Error-free signaling at 28.05Gb/s is demonstrated with the transceiver over a 48dB loss backplane channel. In a four-port configuration, the power consumption at 28.05Gb/s is 484mW/lane, giving a FOM of 0.36mW/Gb/s/dB.
Sensor System Fo4r Buried Waste Containment Sites (2023)

A sensor system for a buried waste containment site having a bottom wall barrier and sidewall barriers, for containing hazardous waste. The sensor system includes one or more sensor devices disposed in one or more of the barriers for detecting a physical parameter either of the barrier itself or of the physical condition of the surrounding soils and buried waste, and for producing a signal representing the physical parameter detected. Also included is a signal processor for receiving signals produced by the sensor device and for developing information identifying the physical parameter detected, either for sounding an alarm, displaying a graphic representation of a physical parameter detected on a viewing screen and/or a hard copy printout. The sensor devices may be deployed in or adjacent the barriers at the same time the barriers are deployed and may be adapted to detect strain or cracking in the barriers, leakage of radiation through the barriers, the presence and leaking through the barriers of volatile organic compounds, or similar physical conditions.
High-Energy Charged Particles for Spatially Fractionated Radiation Therapy (2020)

Spatially fractionated radiotherapy (SFRT) offers a gain in normal tissue sparing with respect to standard seamless irradiations. The beneﬁts of SFRT may be further enhanced by replacing the commonly used photon beams by charged particles. Along this line, proton SFRT has already shown a signiﬁcant widening of the therapeutic window for radioresistant tumors in preclinical studies.The goal of this work was to investigate whether the use of superior energies as compared to the clinical ones, as well as heavy ions could lead to a further improvement of SFRT. New facilities like FAIR, RAON or some others associated to the International Biophysics collaboration will be able to provide very intense high energy ion beams, enabling the experimental evaluation of the Monte Carlo simulations reported in this work. Our results indicate that proton SFRT could beneﬁt from the use of higher beam energies (˜1GeV). Concerning heavy ions, such as carbon or neon, the main advantage would be the possible theragnostic use. Biological experiments are needed to validate these results and they will be the subject of future experimental proposals at those new facilites.
Effect of Chronic Antidepressant Treatment on β-Receptor Coupled Signal Transduction Cascade. Which Effect Matters Most? (2004)

Taken together, the findings reported make it difficult to identify one single component of the beta-receptor coupled signal transduction cascade as common final target of chronic antidepressant treatment.
Annulation Reaction of Vinylaminocarbenes: Characterization of the Tetracarbonyl Vinylcarbene and Metalahexatriene Intermediates (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnnulation Reaction of Vinylaminocarbenes: Characterization of the Tetracarbonyl Vinylcarbene and Metalahexatriene IntermediatesJose Barluenga, Fernando Aznar, Alfredo Martin, Santiago Garcia-Granda, and Enrique Perez-CarrenoCite this: J. Am. Chem. Soc. 1994, 116, 24, 11191–11192Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/ja00103a058https://doi.org/10.1021/ja00103a058research-articleACS PublicationsRequest reuse permissionsArticle Views153Altmetric-Citations49LEARN 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 (3)»Supporting Information Supporting Information Get e-Alerts
Vaccinia Virus Expresses a Novel Profilin with a Higher Affinity for Polyphosphoinositides than Actin (1994)

We expressed in Escherichia coli the vaccinia virus gene for a protein similar to vertebrate profilins, purified the recombinant viral profilin, and characterized its interactions with actin and polyphosphoinositides. Compared with cellular profilins, this viral profilin has a low affinity (Kd > or = 35 microM) for human platelet actin monomers, a weak effect on the exchange of the nucleotide bound to the actin, and no detectable affinity for poly(L-proline). Vaccinia profilin binds to phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 4-monophosphate in micelles and large unilamellar vesicles, but not to phosphatidylserine or phosphatidylcholine. Kinetic analysis by surface plasmon resonance showed that both vaccinia and amoeba profilins bind slowly to polyphosphoinositides, with association rate constants in the range of (1-4) x 10(4) M-1 s-1. The higher affinity of vaccinia profilin for polyphosphoinositides (Kd = 0.2-8.5 microM) than for actin or poly(L-proline) and the concentration of vaccinia profilin expressed in infected HeLa cells (approximately 20 microM) suggest that vaccinia profilin binds preferentially to PIP and PIP2 in vivo. Consequently, vaccinia profilin is more likely to influence phosphoinositide metabolism than actin assembly. Expression of 7-105 microM vaccinia profilin in a Saccharomyces cerevisiae profilin null mutant did not rescue the null phenotype, so that the affinity of vaccinia profilin for phosphoinositides alone is insufficient for normal profilin function in yeast.
PCCI Operation with Early Injection of Conventional Diesel Fuel (2005)

&lt;div class="htmlview paragraph"&gt;In order to further reduce exhaust gas emissions, an investigation was carried out concerning premixed charge compression ignition (PCCI) combustion, which is achieved by the early injection of conventional diesel fuel to the combustion chamber.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The engine used for the experiments was a single cylinder version of a modern passenger car type common rail engine with a displacement of 550(cm&lt;sup&gt;3&lt;/sup&gt;). An injector with a narrower corn angle was used to prevent interaction of the spray and the cylinder liner. Also, the compression ratio was decreased in order to avoid an excessively advanced ignition situation. Additionally, a large degree of cooled exhaust gas recirculation (EGR) was applied.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;These measures led to a significantly reduction in NOX emissions. However, a fuel wall-film, which was formed on the surface of the piston bowl wall, caused increases in soot, HC and CO emissions. Also observed was a reduction in indicated mean effective pressure (IMEP), as well as deteriorate in Coefficient of Variation-IMEP (COV IMEP), both of which result from excessively advanced ignition and the formation of lean air-fuel mixture. A measure, consisting of an EGR increase and a small amount of secondary injection, improved IMEP and COV IMEP. It was also effective in reducing soot.&lt;/div&gt;
Test Point Insertion Methods to Reduce the Number of ATPG Patterns (2003)

The increasing density of LSI chip circuits is causing the execution time of tests based on the full-scan design method to become problematical. In this paper, the authors propose a method of reducing the number of ATPG patterns for a full-scan designed LSI chip by inserting test points. To reduce the number of ATPG patterns, they proposed a test point insertion algorithm based on the improved fault detection probability and a test point insertion algorithm based on the improved value assignment probability. When the authors applied the proposed methods to several actual LSI chips, they were able to reduce the number of ATPG patterns by 48% to 78% compared with the conventional full-scan design by adding test points equivalent to 0.4% to 2.2% of the total number of flip-flops in the LSI chip. © 2006 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 89(5): 54–68, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjb.20267
Palladium‐Catalyzed Allyl Cross‐Coupling Reactions with In Situ Generated Organoindium Reagents (2011)

Inter- and intramolecular palladium-catalyzed allyl cross-coupling reactions, using allylindium generated in situ from allyl halides and indium, is demonstrated. Allylindium compounds may be effective nucleophilic coupling partners in palladium-catalyzed cross-coupling reactions. A variety of allyl halides, such as allyl iodide, allyl bromide, crotyl bromide, prenyl bromide, geranyl bromide, and 3-bromocyclohexene afforded the allylic cross-coupling products in good to excellent yields. Stereochemistry of the double bond is retained in the allylic cross-coupling reactions. Electrophilic cross-coupling partners, such as aryl and vinyl halides, dibromoolefin, alkynyl iodide, and aryl and vinyl triflates participate in these reactions. The presence of various substituents, such as n-butyl, ketal, acetyl, ethoxycarbonyl, nitrile, N-phenylamido, nitro, and chloride groups on the aromatic ring of electrophilic coupling partners showed little effect on the efficiency of the reactions. The present conditions work equally well for not only intermolecular but also intramolecular palladium-catalyzed cross-coupling reactions. These methods provide an efficient synthetic method for the introduction of an allyl group, which can be easily further functionalized to afford an sp(2)- and sp-hybridized carbon. The present method complements existing synthetic methods as a result of advantageous features such as easy preparation and handling, thermal stability, high reactivity and selectivity, operational simplicity, and low toxicity of allylindium reagents.
HER2+ cancer models vary by their dependence on PI3K &lt;i&gt;vs&lt;/i&gt;. MAPK pathways and cellular properties. (2016)

&lt;p&gt;&lt;b&gt;(A)&lt;/b&gt; Relative PI3K/AKT vs. MAPK/ERK dependence (Pathway Bias) across 18 HER2+ cell lines in the presence and absence of exogenous Heregulin (HRG) stimulation. Error bars represent 95% CI. Tissue, genetic status of PI3K-pathway components, and &lt;i&gt;in vitro&lt;/i&gt; proliferation rates (96 hr population doublings; PD) are indicated below for each cell line. &lt;b&gt;(B)&lt;/b&gt; Representative surface responses to AKT and MEK inhibitor combinations in the absence (top) and presence (below) of exogenous HRG for PI3K-dependent, MAPK-dependent, and switching class cells.&lt;/p&gt;