gebhart/patrepeval huggingface dataset:
Evaluation of Flow Through Simulated Vascular Stenoses with Gradient Echo Magnetic Resonance Imaging (1989)

Magnetic resonance imaging using gradient echo sequences can quickly generate dynamic images of the cardiovascular system. We used a gradient echo sequence (repetition time = 21 milliseconds, echo time = 12 milliseconds, flip angle = 30 degrees) to evaluate how a simulated vascular stenoses affects the signal intensity of flowing fluid. Axial slices were obtained at regular intervals along a plastic tube containing a circular constriction (25%, 51%, or 73% reduction of cross-sectional area). Image data collected at each slice level were used to reconstruct 32 images evenly spaced in time over one cycle of pulsatile flow. Contrast ratios were calculated between signal intensities from tube lumen and surrounding stationary water jacket. Upstream from each stenosis, signal intensity increased during systole and decreased during diastole, paralleling the changes in velocity we measured with a flow probe. However, within the 51% and 73% stenoses and just beyond them, there were consistent decreases in systolic signal intensity. Flow through the 25% constriction had little effect on the signal intensity pattern. These results suggest that the gradient echo pulse sequence may be useful in evaluating disturbed flow associated with vascular stenoses.
Protein recognition motifs: Design of peptidomimetics of helix surfaces (2007)

Helices represent one of the most common recognition motifs in proteins. The design of nonpeptidic scaffolds, such as the 3,2',2''-tris-substituted terphenyl, that can imitate the side-chain orientation along one face of an alpha-helix potentially provides an effective means to modulate helix-recognition functions. Here, based on theoretical arguments, we described novel alpha-helix mimetics which are more effective than the terphenyl at constraining the aryl-aryl torsion angles to those associated with structures suitable for mimicking the alpha-helical twist for side-chain orientation and for superimposing the side chains of residues i, i + 3 or i + 4, i + 7 when compared with the alpha-beta side-chain vectors of the regular alpha-helix with an improved root mean square deviation (RMSD) of approximately 0.5 A. In addition, this study suggests that rotamer distributions around the C(alpha)--C(beta) bonds of these helix mimetics are similar to those of alpha-helices, except that these rotamer distributions show an approximately 60 degrees shift compared to those of alpha-helices when the mimetic axis is superimposed upon the helix axis. This change in rotamer orientation complicates mimicry of the helix surface.
Synthesis of a Bis‐amino Acid that Creates a Sharp Turn. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Assessment of genetic susceptibility to multiple primary cancers through whole-exome sequencing in two large multi-ancestry studies (2022)

Overall, we describe variants and genes that may play a fundamental role in the development of multiple primary cancers and improve our understanding of shared mechanisms underlying carcinogenesis.
Fibroblast Activation Protein Cleaves and Inactivates Fibroblast Growth Factor 21 (2016)

FGF21 is a stress-induced hormone with potent anti-obesity, insulin-sensitizing, and hepatoprotective properties. Although proteolytic cleavage of recombinant human FGF21 in preclinical species has been observed previously, the regulation of endogenously produced FGF21 is not well understood. Here we identify fibroblast activation protein (FAP) as the enzyme that cleaves and inactivates human FGF21. A selective chemical inhibitor, immunodepletion, or genetic deletion of Fap stabilized recombinant human FGF21 in serum. In addition, administration of a selective FAP inhibitor acutely increased circulating intact FGF21 levels in cynomolgus monkeys. On the basis of our findings, we propose selective FAP inhibition as a potential therapeutic approach to increase endogenous FGF21 activity for the treatment of obesity, type 2 diabetes, non-alcoholic steatohepatitis, and related metabolic disorders.
Understanding User Tradeoffs for Search in Encrypted Communication (2018)

End-to-end message encryption is the only way to achieve absolute message privacy. However, searching over end-to-end encrypted messages is complicated. Several popular instant messaging tools (e.g., WhatsApp, iMessage) circumvent this inconvenience by storing the search index locally on the devices. Another approach, called searchable encryption, allows users to search encrypted messages without storing the search index locally. These approaches have inherent tradeoffs between usability and security properties, yet little is known about how general users value these tradeoffs, especially in the context of email rather than instant messaging. In this paper, we systematize these tradeoffs in order to identify key feature differences. We use these differences as the basis for a choice-based conjoint analysis experiment focused on email (n=160), in which participants make a series of choices between email services with competing features. The results allow us to quantify the relative importance of each feature. We find that users indicate high relative importance for increasing privacy and minimizing local storage requirements. While privacy is more important overall, local storage is more important than adding additional marginal privacy after an initial improvement. These results suggest that local indexing, which provides more privacy, may often be appropriate for encrypted email, but that searchable encryption, which limits local storage, may also hold promise for some users.
Fabrication and Characterisation of a Microfluidic Device for Bead-array Analysis by the LIBWE Method (2006)

We have developed a novel design for a microfluidic device incorporating a two-dimensional microbead array by using silica glass plates structured by the laser-micromachining method, Laser-Induced Backside Wet Etching (LIBWE). Surface functionalized borosilicate glass and polymer microbeads 10 m in diameter, which act as detectors, were fixed in etched microstructures and sealed with a polydimethylsiloxane plate to form a microfluidic system. The beads are regularly arranged in a two-dimensional manner without being in contact with any other. Analytes are supplied as a solution flowing in microchannels. The pressure-driven flow in the microchannels was investigated. The successful capture of fluorescein isothiocyanate by amino groups as well as that of biotin by avidin on the beads' surface was confirmed by fluorescence microscopy.
Re: α-Lipoic Acid Treatment Prevents Cystine Urolithiasis in a Mouse Model of Cystinuria (2017)

No AccessJournal of UrologyUrological Survey1 Mar 2018Re: α-Lipoic Acid Treatment Prevents Cystine Urolithiasis in a Mouse Model of Cystinuria Anthony AtalaMD Anthony AtalaAnthony Atala More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2017.11.091AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Re: α-Lipoic Acid Treatment Prevents Cystine Urolithiasis in a Mouse Model of Cystinuria." The Journal of Urology, 199(3), pp. 612–613 © 2018 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 199Issue 3March 2018Page: 612-613 Advertisement Copyright & Permissions© 2018 by American Urological Association Education and Research, Inc.MetricsAuthor Information Anthony Atala More articles by this author Expand All Advertisement PDF downloadLoading ...
ChemInform Abstract: Three New Benzophenone‐Xanthone Dimers from the Root of Garcinia dulcis. (1997)

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.
Development of A CAD Software for Blank Development of Sheet Metal Components (2001)

A software is developed on a CAD platform, CAXA-EB 2000, to calculate the coordinates of points on the blank contours of sheet metal components. The system design is described in this paper.
Photophysics of metal complexes of spheroidal carbon shells (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotophysics of metal complexes of spheroidal carbon shellsF. D. Weiss, J. L. Elkind, S. C. O'Brien, R. F. Curl, and R. E. SmalleyCite this: J. Am. Chem. Soc. 1988, 110, 13, 4464–4465Publication Date (Print):June 1, 1988Publication History Published online1 May 2002Published inissue 1 June 1988https://pubs.acs.org/doi/10.1021/ja00221a085https://doi.org/10.1021/ja00221a085research-articleACS PublicationsRequest reuse permissionsArticle Views369Altmetric-Citations212LEARN 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
Intracellular lactate- and pyruvate-interconversion rates are increased in muscle tissue of non-insulin-dependent diabetic individuals. (1996)

The contribution of muscle tissues of non-insulin-dependent diabetes mellitus (NIDDM) patients to blood lactate appearance remains undefined. To gain insight on intracellular pyruvate/lactate metabolism, the postabsorptive forearm metabolism of glucose, lactate, FFA, and ketone bodies (KB) was assessed in seven obese non-insulin-dependent diabetic patients (BMI = 28.0 +/- 0.5 kg/m2) and seven control individuals (BMI = 24.8 +/- 0.5 kg/m2) by using arteriovenous balance across forearm tissues along with continuous infusion of [3-13C1]-lactate and indirect calorimetry. Fasting plasma concentrations of glucose (10.0 +/- 0.3 vs. 4.7 +/- 0.2 mmol/liter), insulin (68 +/- 5 vs. 43 +/- 6 pmol/liter), FFA (0.57 +/- 0.02 vs. 0.51 +/- 0.02 mmol/liter), and blood levels of lactate (1.05 +/- 0.04 vs. 0.60 +/- 0.06 mmol/liter), and KB (0.48 +/- 0.04 vs. 0.29 +/- 0.02 mmol/liter) were higher in NIDDM patients (P < 0.01). Forearm glucose uptake was similar in the two groups (10.3 +/- 1.4 vs. 9.6 +/ 1.1 micromol/min/liter of forearm tissue), while KB uptake was twice as much in NIDDM patients as compared to control subjects. Lactate balance was only slightly increased in NIDDM patients (5.6 +/- 1.4 vs. 3.3 +/- 1.0 micromol/min/liter; P = NS). A two-compartment model of lactate and pyruvate kinetics in the forearm tissue was used to dissect out the rates of lactate to pyruvate and pyruvate to lactate interconversions. In spite of minor differences in the lactate balance, a fourfold increase in both lactate- (44.8 +/- 9.0 vs. 12.6 +/- 4.6 micromol/min/liter) and pyruvate-(50.4 +/- 9.8 vs. 16.0 +/- 5.0 micromol/min/liter) interconversion rates (both P < 0.01) were found. Whole body lactate turnover, assessed by using the classic isotope dilution principle, was higher in NIDDM individuals (46 +/- 9 vs. 21 +/- 3 micromol/min/kg; P < 0.01). Insights into the physiological meaning of this parameter were obtained by using a whole body noncompartmental model of lactate/pyruvate kinetics which provides a lower and upper bound for total lactate and pyruvate turnover (NIDDM = 46 +/- 9 vs. 108 +/- 31; controls = 21 +/- 3 - 50 +/-13 micromol/min/kg). In conclusion, in the postabsorptive state, despite a trivial lactate release by muscle, lactate- and pyruvate-interconversion rates are greatly enhanced in NIDDM patients, possibly due to concomitant impairment in the oxidative pathway of glucose metabolism. This finding strongly suggest a major disturbance in intracellular lactate/pyruvate metabolism in NIDDM.
Multi-resolution backward video coding (2002)

Hierarchical decomposition of images and their relationship with motion fields continues to be a hotly pursued topic, and the role of backward motion information in coding is beginning to capture the interest of video coding community. This paper simultaneously addresses some of the fundamental issues in multi-resolution and backward motion systems. From a coding viewpoint, a multi-resolution motion hierarchy should be coupled with an estimation system that deals with a maximally subsampled wavelet decomposition of the frames, to avoid redundancy of representation. Given the known difficulties of band-to-band motion compensated estimation in a wavelet domain, we use an alternative approach for estimation of detail bands, using lowpass bands of the anchor frames at higher resolutions. The resulting estimation errors are coded through a zerotree quantizer. Simulations show that a prototype coder of this type is very competitive, with a performance better than conventional forward (block-based) coders.
figure S1 from Visualization of Breast Cancer Metabolism Using Multimodal Nonlinear Optical Microscopy of Cellular Lipids and Redox State (2023)

&lt;p&gt;Figure S1 that contains information about cell metabolic rate during acini formation.&lt;/p&gt;
Introduction (2018)

The field of radiography including the development of contrast media for this diagnostic tool is based on the discovery of X-rays by the physicist Wilhelm Conrad Röntgen. Later on, the rays he discovered came to be called “Roentgen rays” in his honor.
Hardware Trust and Assurance through Reverse Engineering: A Tutorial and Outlook from Image Analysis and Machine Learning Perspectives (2021)

In the context of hardware trust and assurance, reverse engineering has been often considered as an illegal action. Generally speaking, reverse engineering aims to retrieve information from a product, i.e., integrated circuits (ICs) and printed circuit boards (PCBs) in hardware security-related scenarios, in the hope of understanding the functionality of the device and determining its constituent components. Hence, it can raise serious issues concerning Intellectual Property (IP) infringement, the (in)effectiveness of security-related measures, and even new opportunities for injecting hardware Trojans. Ironically, reverse engineering can enable IP owners to verify and validate the design. Nevertheless, this cannot be achieved without overcoming numerous obstacles that limit successful outcomes of the reverse engineering process. This article surveys these challenges from two complementary perspectives: image processing and machine learning. These two fields of study form a firm basis for the enhancement of efficiency and accuracy of reverse engineering processes for both PCBs and ICs. In summary, therefore, this article presents a roadmap indicating clearly the actions to be taken to fulfill hardware trust and assurance objectives.
Metal Deposition Selectivity Based on Photochromism of Diarylethene Film in Intermediate Vacuum (2011)

We report on metal deposition selectivity on a photochromic diarylethene (DAE) surface in intermediate vacuum. Selective deposition means that metal vapor is deposited on colored DAE but not on uncolored. Mg was evaporated on the DAE surfaces at various pressures with the introduction of inert gas. Mg was easy to deposit on the uncolored DAE surface in intermediate vacuum (2×10-1 Torr). The easy-deposition effect in intermediate vacuum was explained by the re-adsorption of Mg atoms desorbed from the DAE surface. Mg cathode patterning of an organic light emitting device on the basis of selective deposition in the intermediate vacuum was successfully demonstrated.
Nano-photonic Supercontinuum Based Mid-Infrared Dual-Comb Spectroscopy (2020)

We demonstrate an approach to dual-comb spectroscopy, based on dispersion engineered and ultra-broadband supercontinuum generation in photonic integrated nonlinear waveguides, and driven by low-noise fiber-laser combs. Both technologies are state-of-the-art and contribute to high-performance mid-infrared spectroscopy.
Thermodynamic and transport properties of carbon dioxide from molecular simulation (2007)

Monte Carlo and molecular dynamics simulations have been used in order to test the ability of a three center intermolecular potential for carbon dioxide to reproduce literature experimental thermophysical values. In particular, both the shear viscosity under supercritical conditions and along the phase coexistence line, as well as the thermal conductivity under supercritical conditions, have been calculated. Together with the already reported excellent agreement for the phase coexistence densities, the authors find that the agreement with experimental values is, in general, good, except for the thermal conductivity at low density. Although extended versions of the model were employed, which include an explicit account of bending and vibrational degrees of freedom, a significant difference was still found with respect to the reported experimental value.
Daughter Ion (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Chiral Macrocyclic Bis(oxazoline) CuI Complexes – Structure/Stereoselectivity Relationships in Catalytic Cyclopropanations (2006)

Abstract The design and synthesis of 18 chiral macrocycles with built in C 2 ‐symmetric bis(oxazoline) units is described and the catalytic properties of their copper(I) complexes in cyclopropanations of styrene with ethyl diazoacetate are assessed. The bridging of two homochiral centers in the bis(oxazoline) unit gives a macrocyclic ligand, which upon binding of Cu I is transformed into a macrocyclic catalytic complex containing a chiral cavity. Such a complex represents a conceptually new type of supramolecular organometallic catalyst, possessing a chiral reaction cavity. A clear relationship between catalyst structures and the stereoselectivity outcome in the catalytic cyclopropanations has been established and it is demonstrated that both the enantioselectivity and the diastereoselectivity can be independently modified by variation of the ligand structural parameters. The Cu I complex of the ligand 3b gave a trans / cis diastereomeric ratio of 94:6 ( de = 88 %), representing the highest diastereoselectivity obtained to date for cyclopropanations catalyzed by the bis(oxazoline) class of complexes. An explanation of the observed relationship between stereochemical outcome and ligand structure is proposed.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
Faulty neuronal determination and cell polarization are reverted by modulating HD early phenotypes (2018)

Increasing evidence suggests that early neurodevelopmental defects in Huntington's disease (HD) patients could contribute to the later adult neurodegenerative phenotype. Here, by using HD-derived induced pluripotent stem cell lines, we report that early telencephalic induction and late neural identity are affected in cortical and striatal populations. We show that a large CAG expansion causes complete failure of the neuro-ectodermal acquisition, while cells carrying shorter CAGs repeats show gross abnormalities in neural rosette formation as well as disrupted cytoarchitecture in cortical organoids. Gene-expression analysis showed that control organoid overlapped with mature human fetal cortical areas, while HD organoids correlated with the immature ventricular zone/subventricular zone. We also report that defects in neuroectoderm and rosette formation could be rescued by molecular and pharmacological approaches leading to a recovery of striatal identity. These results show that mutant huntingtin precludes normal neuronal fate acquisition and highlights a possible connection between mutant huntingtin and abnormal neural development in HD.
Reconstruction of interactions in the ProtoDUNE-SP detector with Pandora (2023)

Abstract The Pandora Software Development Kit and algorithm libraries provide pattern-recognition logic essential to the reconstruction of particle interactions in liquid argon time projection chamber detectors. Pandora is the primary event reconstruction software used at ProtoDUNE-SP, a prototype for the Deep Underground Neutrino Experiment far detector. ProtoDUNE-SP, located at CERN, is exposed to a charged-particle test beam. This paper gives an overview of the Pandora reconstruction algorithms and how they have been tailored for use at ProtoDUNE-SP. In complex events with numerous cosmic-ray and beam background particles, the simulated reconstruction and identification efficiency for triggered test-beam particles is above 80% for the majority of particle type and beam momentum combinations. Specifically, simulated 1 GeV/ c charged pions and protons are correctly reconstructed and identified with efficiencies of 86.1 $$\pm 0.6$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mo>±</mml:mo> <mml:mn>0.6</mml:mn> </mml:mrow> </mml:math> % and 84.1 $$\pm 0.6$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mo>±</mml:mo> <mml:mn>0.6</mml:mn> </mml:mrow> </mml:math> %, respectively. The efficiencies measured for test-beam data are shown to be within 5% of those predicted by the simulation.