gebhart/patrepeval huggingface dataset:
Efficient dynamic verification algorithms for mpi applications (2010)

The Message Passing Interface (MPI) Application Programming Interface (API) is widely used in almost all high performance computing applications. Yet, conventional debugging tools for MPI suffer from two serious drawbacks: they cannot prevent the exponentially growing number of redundant schedules from being explored; and they cannot prevent the processes from being locked into a small subset of schedules, unfortunately often reaching the potentially buggy schedules only when programs are ported to new platforms.
Dynamic verification methods are the natural choice for debugging real world MPI programs when model extraction and maintenance are expensive. While many dynamic verification tools exist for verifying shared memory programs, there are no corresponding tools that support MPI – the lingua franca of parallel programming.
While interleaving reduction suggests the use of dynamic partial order reduction (DPOR), four aspects of MPI make previous DPOR algorithms inapplicable: (i) MPI contains asynchronous calls that can complete out of program order; (ii) MPI has global synchronization operations that have weak semantics; (iii) the runtime of MPI cannot, without intrusive modifications, be forced to pursue a specific interleaving with nondeterministic wildcard receives; and (iv) the progress of MPI operations can depend on platform-dependent runtime buffering, making bugs sometimes appear when resources are added to boost performance. This dissertation provides a formal model for MPI, and introduces a tailor-made notion of Happens-Before ordering for MPI functions. The crucial feature of this Happens-Before relation is that it elegantly solves all these four problems. MPI dynamic analysis is turned into a prioritized scheduling algorithm respecting MPI’s Happens-Before. 
This dissertation contributes three algorithms that have been demonstrated in the context of a practical MPI dynamic verification tool called In-Situ Partial order (ISP). The Partial Order avoiding Elusive Interleavings (POE) algorithm is a simple prioritized execution of the MPI transitions and is guaranteed to find all deadlocks, assertion violations and resource leaks under zero buffering. The POEOPT algorithm avoids many of the redundant interleavings of POE by fully exploiting MPI’s Happens-Before. Finally, the POEMSE algorithm discovers all possible minimal runtime bufferings that guarantee to discover bugs. POEMSE’s slack analysis has minimal overheads, and offers the power of verifying for safe portability by considering all relevant bufferings that might exist in various platforms. In effect, a program is dynamically verified not just with respect to the platform on which the tool is run, but also with respect to all platforms.
Fuzzy c-Means Clustering Based Polarization Assessment in Intelligent Argumentation System for Collaborative Decision Support (2013)

Intelligent argumentation system facilitates stakeholders to exchange dialogue over issues and provides decision support by capturing rationale of the stakeholders through arguments. In argumentation process, stakeholders tend to polarize on their opinions and form polarization groups. A method [1] was developed earlier to identify polarization groups, however, polarization groups tend to overlap to a certain degree and each stakeholder may be a member of multiple polarization groups to varied degrees. Quantifying stakeholders' membership in multiple polarization groups in argumentation for collaborative decision making is not addressed earlier. We present an approach using fuzzy clustering algorithm to address this issue and evaluate the approach using an argumentation tree built by twenty four stakeholders.
Cooperative diversity transmission versus macrodiversity in cellular networks (2005)

This paper studies the potential performance im- provement from cooperative diversity transmission in a cellular network. We consider a simpli ed coopera- tive relaying system which allows the mobile terminals to relay data packets from their partners. We obtain numerical results for the outage probability, taking into account log-distance path loss, spatially corre- lated shadowing and small-scale fading. A compari- son with conventional macrodiversity is performed for various scenarios of interest. The simulation results demonstrate the superiority of cooperative diversity transmission.
Reaction of 1-naphthylhydroxylamine with calf thymus deoxyribonucleic acid. Isolation and synthesis of N-(guanin-C8-yl)-1-naphthylamine. (1981)

A possible activated form of 1-naphthylamine, N-hydroxy-1-naphthylamine, reacted with the C8-position of guanine in deoxyribonucleic acid (DNA). Hydrolysis of the modified DNA with nuclease and acid gave N-(guanin-C8-yl)-1-naphthylamine as a modified base. The C8-position of guanine seems to be a common site of attack on DNA by activated muta-carcinogenic aromatic amines.
4D microscope-integrated intraoperative optical coherence tomography angiography (Conference Presentation) (2017)

Optical coherence tomography (OCT) allows for micron scale imaging of the human retina and cornea. Previous research and commercial intraoperative OCT prototypes have been limited to live B-scan imaging because they were based on previous-generation spectral domain OCT systems. Our group has developed and reported on an intraoperative microscope integrated OCT system based on a 100 kHz commercial swept source laser. This system is capable of live 4D imaging, and with a heads up display allows for dynamic intraoperative visualization of retinal structures, tool tissue interaction, and surgical maneuvers. OCT angiography (OCTA) is an emerging OCT technology that allows for imaging of retinal vasculature without the use of potentially harmful contrast agents. This structural information can provide insights into the state and development of a wide range of ophthalmic pathologies. The addition of OCTA into intraoperative OCT could allow for monitoring of changes in retinal vasculature during surgery and imaging of traditionally non-compliant patients. In this work we provide a brief update of intraoperative 4D MIOCT across a range of pathologies, and demonstrate intraoperative OCTA for the first time. To the best of knowledge, this is the first report of intraoperative OCTA, as well as the first OCTA images ever acquired in an infant.
Polymeric Photoresist Nanoparticles: Light‐Induced Degradation of Hydrophobic Polymers in Aqueous Dispersion (2011)

Nanoparticles consisting of a photoreactive polymer able to radically switch its hydrophobicity are successfully prepared by miniemulsion polymerization. Irradiation with UV light causes degradation of the particles where at complete dissolution is achieved by changing the initial hydrophobic photoresist polymer into hydrophilic poly(methacrylic acid). Incorporation of the fluorescence-sensitive Nile red serves as a solvatochromic probe to study the particle degradation. Diffusion of either Nile red out from or water into the former hard spherical nanoparticles is studied and not only renders the described material an ideal system for applications, where in situ dissolution of nanoparticles may be needed, but also bears the additional advantage of performing controlled burst release.
Rational engineering of lung alveolar epithelium (2023)

Engineered whole lungs may one day expand therapeutic options for patients with end-stage lung disease. However, the feasibility of ex vivo lung regeneration remains limited by the inability to recapitulate mature, functional alveolar epithelium. Here, we modulate multimodal components of the alveolar epithelial type 2 cell (AEC2) niche in decellularized lung scaffolds in order to guide AEC2 behavior for epithelial regeneration. First, endothelial cells coordinate with fibroblasts, in the presence of soluble growth and maturation factors, to promote alveolar scaffold population with surfactant-secreting AEC2s. Subsequent withdrawal of Wnt and FGF agonism synergizes with tidal-magnitude mechanical strain to induce the differentiation of AEC2s to squamous type 1 AECs (AEC1s) in cultured alveoli, in situ. These results outline a rational strategy to engineer an epithelium of AEC2s and AEC1s contained within epithelial-mesenchymal-endothelial alveolar-like units, and highlight the critical interplay amongst cellular, biochemical, and mechanical niche cues within the reconstituting alveolus.
Effect of fluoroalkyl substituents on the reaction of alkylchlorosilanes with silica surfaces (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffect of fluoroalkyl substituents on the reaction of alkylchlorosilanes with silica surfacesC. P. Tripp, R. P. N. Veregin, and M. L. HairCite this: Langmuir 1993, 9, 12, 3518–3522Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://pubs.acs.org/doi/10.1021/la00036a029https://doi.org/10.1021/la00036a029research-articleACS PublicationsRequest reuse permissionsArticle Views403Altmetric-Citations60LEARN 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
3D and 4D Printing of Complex Structures of FeMnSi‐Based Shape Memory Alloy Using Laser Powder Bed Fusion (Adv. Mater. Interfaces 13/2022) (2022)

3D Printed Fe-Shape Memory Alloys In article number 2200171, Dohyung Kim, Irene Ferretto, Christian Leinenbach and Wookjin Lee demonstrate 3D and 4D printing of Fe-based shape memory alloy using laser powder bed fusion technique for the first time. Integrating the material-inherent functionalities into complex 3D structures allows for new functionalities of structures including shape morphing, metal-material behavior, and extraordinary specific strength with shape memory behavior.
Dissolution kinetics of a sodium borosilicate glass in Tris buffer solutions: impact of Tris concentration and acid (HCl/HNO3) identity (2021)

Understanding the corrosion behavior of glasses in near-neutral environments is crucial for many technologies including glasses for regenerative medicine and nuclear waste immobilization. To maintain consistent pH values throughout experiments in the pH = 7 to 9 regime, buffer solutions containing tris(hydroxymethyl)aminomethane ("Tris", or sometimes called THAM) are recommended in ISO standards 10993-14 and 23317 for evaluating biomaterial degradation and utilized throughout glass dissolution behavior literature-a key advantage being the absence of dissolved alkali/alkaline earth cations (i.e. Na+ or Ca2+) that can convolute experimental results due to solution feedback effects. Although Tris is effective at maintaining the solution pH, it has presented concerns due to the adverse artificial effects it produces while studying glass corrosion, especially in borosilicate glasses. Therefore, many open questions still remain on the topic of borosilicate glass interaction with Tris-based solutions. We have approached this topic by studying the dissolution behavior of a sodium borosilicate glass in a wide range of Tris-based solutions at 65 °C with varied acid identity (Tris-HCl vs. Tris-HNO3), buffer concentration (0.01 M to 0.5 M), and pH (7-9). The results have been discussed in reference to previous studies on this topic and the following conclusions have been made: (i) acid identity in Tris-based solutions does not exhibit a significant impact on the dissolution behavior of borosilicate glasses, (ii) ∼0.1 M Tris-based solutions are ideal for maintaining solution pH in the absence of obvious undesirable solution chemistry effects, and (iii) Tris-boron complexes can form in solution as a result of glass dissolution processes. The complex formation, however, exhibits a distinct temperature-dependence, and requires further study to uncover the precise mechanisms by which Tris-based solutions impact borosilicate glass dissolution behavior.
Smartphones as research platform for hearing improvement studies (2017)

This poster presents the development of software tools at the University of Texas at Dallas to turn smartphones into a research platform for hearing improvement studies as part of the newly funded R01 NIH project entitled “Smartphone-Based Open Research Platform for Hearing Improvement Studies.” The challenge in deploying smartphones as a research platform for hearing improvement studies lies in the use of programming languages that researchers are most familiar with. These languages are MATLAB and C. In other words, the challenge to deploy smartphones as a research platform is by not demanding researchers to know the programming languages associated with smartphones (Java for Android smartphones and Objective C for iOS smartphones) in order to turn smartphones into implementation research platforms. This challenge is met in this work by developing software shells that allow signal processing codes that are written in either C or MATLAB to be run on the ARM processors of smartphones/tablets. As part of this poster presentation, demos of the apps that have been generated so far based on these developed software shells will be presented.
A CRISPR-Cas9 Genome Engineering Platform in Primary CD4+ T Cells for the Interrogation of HIV Host Factors (2017)

ABSTRACT CRISPR-Cas9 gene editing strategies have revolutionized our ability to engineer the human genome for robust functional interrogation of complex biological processes. We have recently adapted this technology to primary human T cells to generate a high-throughput platform for analyzing the role of host factors in pathogen infection and lifecycle. Here, we describe applications of this system to investigate HIV pathogenesis in CD4+ T cells. Briefly, CRISPR-Cas9 ribonucleoproteins (crRNPs) are synthesized in vitro and delivered to activated primary human CD4+ T cells by nucleofection. These edited cells are then validated and expanded for use in downstream cellular, genetic, or protein-based assays. Our platform supports the arrayed generation of several gene manipulations in only a few hours’ time and is widely adaptable across culture conditions, infection protocols, and downstream applications. We present detailed protocols for crRNP synthesis, primary T cell culture, 96-well nucleofection, molecular validation, and HIV infection with additional considerations for guide and screen design as well as crRNP multiplexing.
ChemInform Abstract: Comparative Study of the Reactions Between prim., sec., and tert. Germylamines and 3,5‐Di‐tert‐butylorthoquinone by Mono‐Electron Transfer. (1993)

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.
ChemInform Abstract: Cyclic Adenosine 5′‐Diphosphate Ribose Mediated Cellular Signaling: New Insights Using Synthetic Ligands (2000)

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.
Enzymes Inhibiting Lignans from Vitex negundo. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Smartphone Biosensors for Health, Environment, and Food Safety (2014)

This talk will summarize recent developments in the Cunningham Group at Illinois in the utilization of integrated smartphone cameras as a high resolution spectrophotometer that is capable of measuring ELISA assays, label-free photonic crystal biosensor assays, thin film chromatography, and fluorescence spectroscopy
Conceptual design report for the UNI-CAT beam line proposal (1992)

The overall thrusts of UNI-CAT (University-National Laboratory- Industry Collaborative Access Team) are research at the cutting edge of physics, chemistry, biology, materials science, chemical engineering, polymer science, and geology; and education of a new generation of scientists in the use of synchrotron radiation to probe the structure, chemistry, and dynamic behavior of materials. The UNI-CAT proposal is to develop an APS sector that includes a bending magnet beam line and an insertion device beam line. The APS type-A undulator is the preferred choice for the insertion device. 8 figs, 6 refs. (DLC)
JUNO Sensitivity on Proton Decay $p\to \bar\nu K^+$ Searches (2022)

The Jiangmen Underground Neutrino Observatory (JUNO) is a large liquid scintillator detector designed to explore many topics in fundamental physics. In this paper, the potential on searching for proton decay in $p\to \barνK^+$ mode with JUNO is investigated.The kaon and its decay particles feature a clear three-fold coincidence signature that results in a high efficiency for identification. Moreover, the excellent energy resolution of JUNO permits to suppress the sizable background caused by other delayed signals. Based on these advantages, the detection efficiency for the proton decay via $p\to \barνK^+$ is 36.9% with a background level of 0.2 events after 10 years of data taking. The estimated sensitivity based on 200 kton-years exposure is $9.6 \times 10^{33}$ years, competitive with the current best limits on the proton lifetime in this channel.
DOSSIER IMAGERIE ACOUSTIQUE ET OPTIQUE DES MILIEUX BIOLOGIQUES OPTICAL AND ACOUSTICAL IMAGING OF BIOLOGICAL MEDIA Elastography (2001)

We present a concise summary of some of the fundamentals and of our work in the field of elastography over the past 12 years. This summary is not exhaustive, since several recent reviews of this area are available. We begin by presenting some relevant background material from the field of biomechanics, which forms the foundation of this work. We then proceed to discuss the basic principles and limitations that are involved in the production of strain images (elastograms) of biological tissues. Early results as well as current results from biological tissues in vitro and in vivo are shown. We conclude with some thoughts regarding the potential of elastography for medical diagnosis.  2001 Academie des sciences/Editions scientifiques et medicales Elsevier SAS elastography / ultrasound / stress / strain / imaging / elasticity / shear modulus / Young's modulus Elastographie
Design and properties of functional hybrid organic–inorganic membranes for fuel cells (2011)

This critical review presents a discussion on the major advances in the field of organic-inorganic hybrid membranes for fuel cells application. The hybrid organic-inorganic approach, when the organic part is not conductive, reproduces to some extent the behavior of Nafion where discrete hydrophilic and hydrophilic domains are homogeneously distributed. A large variety of proton conducting or non conducting polymers can be combined with various functionalized, inorganic mesostructured particles or an inorganic network in order to achieve high proton conductivity, and good mechanical and chemical properties. The tuning of the interface between these two components and the control over chemical and processing conditions are the key parameters in fabricating these hybrid organic-inorganic membranes with a high degree of reproducibility. This dynamic coupling between chemistry and processing requires the extensive use and development of complementary ex situ measurements with in situ characterization techniques, following in real time the molecular precursor solutions to the formation of the final hybrid organic-inorganic membranes. These membranes combine the intrinsic physical and chemical properties of both the inorganic and organic components. The development of the sol-gel chemistry allows a fine tuning of the inorganic network, which exhibits acid-based functionalized pores (-SO(3)H, -PO(3)H(2), -COOH), tunable pore size and connectivity, high surface area and accessibility. As such, these hybrid membranes containing inorganic materials are a promising family for controlling conductivity, mechanical and chemical properties (349 references).
Chronic Alcohol Consumption Is Associated With an Increased Cytotoxic Profile of Circulating Lymphocytes That May Be Related With the Development of Liver Injury (2010)

Overall, our results suggest that alcoholic patients display different phenotypical and functional changes in circulating PB cytotoxic lymphocytes according to the presence of alcoholic liver disease, which could be related to the development and progress of liver injury.
PIVKA-II is a useful marker in patients with modified UICC T3 stage hepatocellular carcinoma. (2013)

PIVKA-II is useful for determining patient survival and the risk of recurrence in modified UICC T3 stage HCC patients.
Smart design of hollow AuPt nanospheres with a porous shell as superior electrocatalysts for ethylene glycol oxidation (2016)

Hollow AuPt spherical nanoelectrocatalysts for ethylene glycol oxidation were synthesized by a facile and effective method.
Calculation of total scattering from a crystalline structural model based on experimental optics parameters (2020)

Total scattering measurements enable understanding of the structural disorder in crystalline materials by Fourier transformation of the total structure factor, <i>S</i>(<i>Q</i>), where <i>Q</i> is the magnitude of the scattering vector. In this work, the direct calculation of total scattering from a crystalline structural model is proposed. To calculate the total scattering intensity, a suitable <i>Q</i>-broadening function for the diffraction profile is needed because the intensity and the width depend on the optical parameters of the diffraction apparatus, such as the X-ray energy resolution and divergence, and the intrinsic parameters. X-ray total scattering measurements for CeO<sub>2</sub> powder were performed at beamline BL04B2 of the SPring-8 synchrotron radiation facility in Japan for comparison with the calculated <i>S</i>(<i>Q</i>) under various optical conditions. The evaluated <i>Q</i>-broadening function was comparable to the full width at half-maximum of the Bragg peaks in the experimental total scattering pattern. The proposed calculation method correctly accounts for parameters with <i>Q</i> dependence such as the atomic form factor and resolution function, enables estimation of the total scattering factor, and facilitates determination of the reduced pair distribution function for both crystalline and amorphous materials.