gebhart/patrepeval huggingface dataset:
The optimal fixedpoint of recursive programs (1975)

In this paper a new fixedpoint approach towards the semantics of recursive programs is presented. The fixedpoint defined by a recursive program under this semantics contains, in some sense, the maximal amount of “interesting” information which can be extracted from the program. This optimal fixedpoint (which always uniquely exists) may be strictly more defined than the program's least fixedpoint. We consider both the theoretical and the computational aspects of the approach, as well as some techniques for proving properties of the optimal fixedpoint of a given recursive program.
Comparative Peripheral Blood T Cells Analysis Between Adult Deceased Donor Liver Transplantation (DDLT) and Living Donor Liver Transplantation (LDLT) (2017)

BACKGROUND T lymphocytes are an essential component of allograft rejection and tolerance. The aim of the present study was to analyze and compare the characteristics of T cell subsets in patients who underwent deceased donor liver transplantation (DDLT) versus living donor liver transplantation (LDLT). MATERIAL AND METHODS Between April 2013 and June 2014, 64 patients underwent adult liver transplantation. The distribution of peripheral blood T lymphocyte subsets before transplantation and at 4, 8, 12, and 24 weeks post-transplantation were monitored serially. RESULTS In the serial peripheral blood samples, the absolute CD3+ T cell counts in the LDLT group were higher than those in the DDLT group (p=0.037). The CD4+, CD8+, CD4/CD8, Vδ1, Vδ2, and γδ T cell counts did not change significantly over time in either group. The Vδ1/Vδ2 ratio was higher in patients with cytomegalovirus (CMV) infection than in patients without CMV infection (0.12 versus 0.26; p=0.033). The median absolute CD3+ and CD8+ T cell counts in patients with biopsy-proven acute rejection (BPAR) were 884 (range, 305-1,320) and 316 (range, 271-1,077), respectively, whereas they were 320 (range, 8-1,167) and 257 (range, 58-1,472) in patients without BPAR. The absolute CD3+ and CD8 T cell counts were higher in patients with BPAR than in patients without BPAR (p=0.007 and p=0.039, respectively). CONCLUSIONS With the exception of CD3+ T cells, T cell populations did not differ significantly between patients who received DDLT versus LDLT. In liver transplantation patients, CMV infection and BPAR were closely associated with T cell population changes.
First Demonstration of a Staged Optical Injection and Laser Wakefield Acceleration (2005)

A proof-of-principal experiment on staged optical injection and laser acceleration was performed. Electrons created in one gas jet were injected and accelerated to 20 MeV in the plasma wakefield of the second gas jet
Another Great Day for Organometallic Chemistry (2010)

ADVERTISEMENT RETURN TO ISSUEEditor's PageNEXTAnother Great Day for Organometallic ChemistryJohn A. Gladysz, Manfred Bochmann, Dennis L. Lichtenberger, Lanny S. Liebeskind, Tobin J. Marks, and Dwight A. SweigartCite this: Organometallics 2010, 29, 22, 5737Publication Date (Web):October 28, 2010Publication History Received22 October 2010Published online28 October 2010Published inissue 22 November 2010https://pubs.acs.org/doi/10.1021/om101007rhttps://doi.org/10.1021/om101007reditorialACS PublicationsCopyright © 2010 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views2202Altmetric-Citations6LEARN 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 PDF (589 KB) Get e-AlertscloseSUBJECTS:Olefin metathesis,Organometallic chemistry,Pharmaceuticals Get e-Alerts
Modeling of Mitochondria Bioenergetics Using a Composable Chemiosmotic Energy Transduction Rate Law: Theory and Experimental Validation (2011)

Mitochondrial bioenergetic processes are central to the production of cellular energy, and a decrease in the expression or activity of enzyme complexes responsible for these processes can result in energetic deficit that correlates with many metabolic diseases and aging. Unfortunately, existing computational models of mitochondrial bioenergetics either lack relevant kinetic descriptions of the enzyme complexes, or incorporate mechanisms too specific to a particular mitochondrial system and are thus incapable of capturing the heterogeneity associated with these complexes across different systems and system states. Here we introduce a new composable rate equation, the chemiosmotic rate law, that expresses the flux of a prototypical energy transduction complex as a function of: the saturation kinetics of the electron donor and acceptor substrates; the redox transfer potential between the complex and the substrates; and the steady-state thermodynamic force-to-flux relationship of the overall electro-chemical reaction. Modeling of bioenergetics with this rate law has several advantages: (1) it minimizes the use of arbitrary free parameters while featuring biochemically relevant parameters that can be obtained through progress curves of common enzyme kinetics protocols; (2) it is modular and can adapt to various enzyme complex arrangements for both in vivo and in vitro systems via transformation of its rate and equilibrium constants; (3) it provides a clear association between the sensitivity of the parameters of the individual complexes and the sensitivity of the system's steady-state. To validate our approach, we conduct in vitro measurements of ETC complex I, III, and IV activities using rat heart homogenates, and construct an estimation procedure for the parameter values directly from these measurements. In addition, we show the theoretical connections of our approach to the existing models, and compare the predictive accuracy of the rate law with our experimentally fitted parameters to those of existing models. Finally, we present a complete perturbation study of these parameters to reveal how they can significantly and differentially influence global flux and operational thresholds, suggesting that this modeling approach could help enable the comparative analysis of mitochondria from different systems and pathological states. The procedures and results are available in Mathematica notebooks at http://www.igb.uci.edu/tools/sb/mitochondria-modeling.html.
Brush-border-enzyme-mediated intestine-specific drug delivery. Amino acid prodrugs of 5-aminosalicylic acid (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBrush-border-enzyme-mediated intestine-specific drug delivery. Amino acid prodrugs of 5-aminosalicylic acidRoberto Pellicciari, Aaron Garzon-Aburbeh, Benedetto Natalini, Maura Marinozzi, Carlo Clerici, Giorgio Gentili, and Antonio MorelliCite this: J. Med. Chem. 1993, 36, 26, 4201–4207Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://pubs.acs.org/doi/10.1021/jm00078a009https://doi.org/10.1021/jm00078a009research-articleACS PublicationsRequest reuse permissionsArticle Views344Altmetric-Citations14LEARN 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
Gene Amplification of c- myc and N- myc in Small Cell Carcinoma of the Lung (1986)

The relationship of the copy numbers of the c-myc and N-myc oncogenes to tumor formation and progression was studied in small cell carcinoma of the lung. When 96 neoplastic lesions from 45 patients were examined, these lesions could be grouped into three categories: high copy (tumors with greater than 3 copies of the N-myc or c-myc gene per haploid genome), middle copy (1.5 to 3 copies per genome), and normal copy. Fourteen of the patients had middle copy tumors, but this was almost always a result of chromosome duplication rather than the amplification of a small genetic locus. In contrast, five patients had high copy tumors, with the increased copy number in each case due to gene amplification. The amplification did not occur in a heterogeneous fashion within individual patients, since all metastatic lesions from patients with high copy lung tumors were also high copy, while none of 41 metastatic lesions from the other patients were high copy. These data suggest that gene amplification is an important step in neoplastic growth in a subset of patients with small cell carcinoma of the lung and that this genetic event occurs relatively early (before metastasis) in this subset.
DSD: Regularizing Deep Neural Networks with Dense-Sparse-Dense Training Flow. (2016)

Modern deep neural networks have a large number of parameters, making them very powerful machine learning systems. A critical issue for training such large networks on large-scale data-sets is to prevent overfitting while at the same time providing enough model capacity. We propose DSD, a dense-sparse-dense training flow, for regularizing deep neural networks. In the first D step, we train a dense network to learn which connections are important. In the S step, we regularize the network by pruning the unimportant connections and retrain the network given the sparsity constraint. In the final D step, we increase the model capacity by freeing the sparsity constraint, re-initializing the pruned parameters, and retraining the whole dense network. Experiments show that DSD training can improve the performance of a wide range of CNN, RNN and LSTMs on the tasks of image classification, caption generation and speech recognition. On the Imagenet dataset, DSD improved the absolute accuracy of AlexNet, GoogleNet, VGG-16, ResNet50, ResNet-152 and SqueezeNet by a geo-mean of 2.1 points (Top-1) and 1.4 points (Top-5). On the WSJ’92 and WSJ’93 dataset, DSD improved DeepSpeech2 WER by 0.53 and 1.08 points. On the Flickr-8K dataset, DSD improved the NeuralTalk BLEU score by 2.0 points. DSD training flow produces the same model architecture and doesn’t incur any inference overhead.
Comparison of 125I-Insulin Binding and Degradation to Isolated Rat Hepatocytes and Liver Membranes (1975)

(1) Preparation of hepatocytes by collagenase digestion does not appear to alter insulin binding or degradation; (2) studies of liver membranes and isolated hepatocytes obtained from normal rats should yield similar information about insulin-receptor interaction as long as insulin concentrations less than 100 ng./ml. are used; (3) at very high insulin concentrations, some of the radioactivity appears to enter the cells; (4) the kinetics of insulin degradation by hepatocytes and liver membranes are similar; and (5) insulin degradation appears to be primarily a membrane phenomenon.
Peak Force Measurements on a Cylindrical Buoy With Limited Elastic Mooring (2013)

This paper investigates the line force of a moored floating buoy. The experiment was the first experiment made at the Swedish wave energy research site located close to Lysekil on the Swedish west coast. The Lysekil project is run by the Swedish Centre for Renewable Electric Energy Conversion at Uppsala University (Uppsala, Sweden). The experimental setup consists of a cylindrical buoy, with a diameter of 3 m and a height of 0.8 m. The buoy is moored with a line connected to a set of springs in parallel with a rope. The rope in parallel with the springs represents the limited stroke length of a linear-generator-type wave energy converter. The measurement system consists of a force transducer between the buoy and the rope, a three-axis accelerometer inside the buoy, and a remote data logger operated through the Global System for Mobile Communications (GSM) network. The peak forces related to the significant wave height showed a trend of 33 kN/m. Trends were also calculated in 10-kN bins. The data could be used in fatigue simulations of similar devices. The result was very important to set the mechanical design parameters of the first wave energy converter that was deployed at the Lysekil Research Site in March 2006.
Abstract B096: Oncolytic vaccination for HPV induced cancer (2016)

Abstract Oncogenic human papilloma virus (HPV) is directly responsible for 5% of the world's cancer burden. HPV has been etiologically implicated in virtually all cases of cervical carcinoma and is increasingly responsible for head and neck cancers in the developed world with strains 16 and 18 considered high risk. Recently it was estimated that there were over half a million new cases of cervical cancer worldwide and in the same year this disease was projected to claim over 250,00 lives, making it the third most prevalent and fourth most lethal non- skin tumor in women. Current standard of care for advanced cervical carcinoma and head and neck cancers involve chemo-radiation with or without prior surgical resection resulting in significant morbidity without guaranteed cure. Screening programs and prophylactic vaccination are reducing the incidence of some HPV induced tumors, however lack of compliance and unvaccinated populations mean that significant illness and mortality still exists. We therefore sought to develop a novel pre-clinical immunotherapeutic for HPV induced cancers. An oncolytic vaccination strategy utilizing an attenuated Maraba MG1 rhabdovirus expressing inactive HPV antigens based on the E6 and E7 transforming proteins of strains 16 and 18 has been designed (MG1 E6E7). The TC1 cell line, which is a C57BL/6 syngeneic murine HPV cancer model, was acquired. Specific anti-E7 CD8+ T cell responses have been induced after oncolytic vaccination of mice generating sterilizing immunity against future engraftment with TC1 cells. Oncolytic vaccination of tumor free mice has generated between 24 and 50 million, combined blood and splenic CD8+ T cells per mouse, determined by interferon gamma production in response to a single E7 peptide quantified using intracellular staining and flow cytometry. Primed mice, boosted with MG1 E6E7 develop long lasting, marked and specific immunity against E7 and to a lesser extent E6. The prime: boost regimen has therapeutic efficacy against established subcutaneous TC1 tumors (mean volumes of 250 mm3) resulting in durable cures in this model. Depletion of CD8+ T cells impairs the activity of the vaccination protocol supporting the key role of cytotoxic lymphocytes in our treatment regimen. The data generated here support the pre-clinical activity of this oncolytic vaccination and pave the way for future clinical trials for the treatment of advanced metastatic HPV induced carcinomas. Citation Format: Matthew J. Atherton, Kyle B. Stephenson, Yonghong Wan, David F. Stojdl, Brian D. Lichty. Oncolytic vaccination for HPV induced cancer. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr B096.
What Controls the Hybridization Thermodynamics of Spherical Nucleic Acids?* (2020)

The hybridization of free oligonucleotides to densely packed, oriented arrays of DNA modifying the surfaces of spherical nucleic acid (SNA)–gold nanoparticle conjugates occurs with negative cooperativity; that is, each binding event destabilizes subsequent binding events. DNA hybridization is thus an ever-changing function of the number of strands already hybridized to the particle. This chapter quantifies the thermodynamics of binding as a function of the number of pre-hybridized strands. This analysis provides important fundamental insight into the enthalpic and entropic consequences of packing charged DNA strands into a dense monolayer and reveals that SNA binding is regulated by electrostatic effects and collective conformational changes that are analogous to the phenomenon of allostery observed in many regulatory proteins. The chapter draws several important lessons regarding the thermodynamics of oligonucleotide hybridization to SNA–gold nanoparticles conjugates.
Real-time patch sweeping for high-quality depth estimation in 3D video conferencing applications (2011)

In future 3D videoconferencing systems, depth estimation is required to support autostereoscopic displays and even more important, to provide eye contact. Real-time 3D video processing is currently possible, but within some limits. Since traditional CPU centred sub-pixel disparity estimation is computationally expensive, the depth resolution of fast stereo approaches is directly linked to pixel quantization and the selected stereo baseline. In this work we present a novel, highly parallelizable algorithm that is capable of dealing with arbitrary depth resolutions while avoiding texture interpolation related runtime penalties by application of GPU centred design. The cornerstone of our patch sweeping approach is the fusion of space sweeping and patch based 3D estimation techniques. Especially for narrow baseline multi-camera configurations, as commonly used for 3D videoconferencing systems (e.g. [1]), it preserves the strengths of both techniques and avoid their shortcomings at the same time. Moreover, we provide a sophisticated parameterization and quantization scheme that establishes a very good scalability of our algorithm in terms of computation time and depth estimation quality. Furthermore, we present an optimized CUDA implementation for a multi GPU setup in a cluster environment. For each GPU, it performs three pair wise high quality depth estimations for a trifocal narrow baseline camera configuration on a 256x256 image block within real-time.
Methods to Assess the Effect of Dynamic Treatment Regimens Using Electronic Health Records (2020)

Background: Effective management of chronic conditions such as type 2 diabetes requires periodic clinical monitoring and frequent re-evaluation of treatment decisions over the course of the patient’s illness. To optimize and personalize care, the relevant treatment strategies to compare should not only adapt to the patient’s evolving clinical condition but should also integrate the levels of both adherence to treatment and the frequency of clinical monitoring. The comparison of such complex adaptive treatment strategies is particularly relevant to patients and stakeholders concerned with the burden imposed by both daily medication intake and frequent clinical monitoring. Because randomized trials are not well suited to produce such heterogeneous evidence, we need advanced analytic methods that can be applied to real-world observational data and emulate trial inferences. Existing causal inference methods are not well adapted to real-world data that are highly variable in timing and content such as electronic health record (EHR) data. Objectives: To advance and adapt existing causal inference methods so they can not only be adequately applied to real-world observational data but also better inform the impact of both real-world treatment adherence and frequency of clinical monitoring in comparative effectiveness research (CER). Methods: Using both simulated data and existing EHR data from a recent nonrandomized type 2 diabetes study, we will evaluate the applicability and practical performance of new causal inference tools in real-world CER. In particular, we will study their behaviors in studies with relatively small sample sizes and document the conditions under which these methods can provide valid CER evidence. Patient and Stakeholder Engagement: Stakeholders will drive the development, illustration, and dissemination of the proposed methods by identifying areas within chronic disease management with high-priority CER questions. Insights from patients, practicing clinicians, clinical and operational health plan leaders, and CER researchers will help us understand the types of comparative effectiveness questions involving sequences of treatment and monitoring decisions that are of most value to healthcare decision makers, with a focus on the management of chronic diseases and type 2 diabetes. Anticipated Impact: This project will improve the applicability of sophisticated causal methods with EHR data to compare complex treatment strategies that can better inform decision making by clinicians and patients for the management of chronic conditions. It will increase the transparency, relevance, validity, and precision of the evidence generated with these advanced causal inference methods. More on This Project
Publisher Correction: Discordant congenital Zika syndrome twins show differential in vitro viral susceptibility of neural progenitor cells (2018)

The original PDF version of this Article contained errors in the spelling of Luiz Carlos Caires-Júnior, Uirá Souto Melo, Bruno Henrique Silva Araujo, Alessandra Soares-Schanoski, Murilo Sena Amaral, Kayque Alves Telles-Silva, Vanessa van der Linden, Helio van der Linden, João Ricardo Mendes de Oliveira, Nivia Maria Rodrigues Arrais, Joanna Goes Castro Meira, Ana Jovina Barreto Bispo, Esper Abrão Cavalheiro, and Robert Andreata-Santos, which were incorrectly given as Luiz Carlos de Caires Jr., UiráSouto Melo, Bruno Silva Henrique Araujo, Alessandra Soares Schanoski, MuriloSena Amaral, Kayque Telles Alves Silva, Vanessa Van der Linden, Helio Van der Linden, João Mendes Ricardo de Oliveira, Nivia Rodrigues Maria Arrais, Joanna Castro Goes Meira, Ana JovinaBarreto Bispo, EsperAbrão Cavalheiro, and Robert Andreata Santos. Furthermore, in both the PDF and HTML versions of the Article, the top panel of Fig. 3e was incorrectly labeled '10608-1' and should have been '10608-4', and financial support from CAPES and DECIT-MS was inadvertently omitted from the Acknowledgements section. These errors have now been corrected in both the PDF and HTML versions of the Article.