gebhart/patrepeval huggingface dataset:
Finite-element analysis of aortic valve-sparing: influence of graft shape and stiffness (2001)

Aortic valve incompetence due to aortic root dilation may be surgically corrected by resuspension of the native valve within a vascular graft. This study was designed to examine the effect of graft shape and material properties on aortic valve function, using a three-dimensional finite-element model of the human aortic valve and root. First, the normal root elements in the model were replaced with graft elements, in either a cylindrical or a "pseudosinus" shape. Next, the elements were assigned the material properties of either polyethylene terephthalate, expanded polytetrafluoroethylene, or polyurethane. Diastolic pressures were applied, and stresses, strains, and coaptation were recorded for the valve, root, and graft. Regarding shape, the cylindrical graft models increased the valve stresses by up to 173%, whereas the root-shaped graft model increased valve stresses by up to 40% as compared to normal. Regarding material properties, the polyurethane models demonstrated valve stress, strain, and coaptation values closest to normal, for either root shape. Graft shape had a greater effect on the simulated valve function than did the material property of the graft. Optimizing the shape and material design of the graft may result in improved longevity of the spared valve if a normal environment is restored.
Managing vitamin D deficiency in inflammatory bowel disease (2019)

Management of inflammatory bowel disease (IBD), including ulcerative colitis and Crohn's disease, is generally cumbersome for patients and is a massive health-economic burden. In recent years, the immunomodulating effects of vitamin D have gained a huge interest in its possible pathogenic influence on the pathophysiology of IBD. Vitamin D deficiency is frequent among patients with IBD. Several clinical studies have pointed to a critical role for vitamin D in ameliorating disease outcomes. Although causation versus correlation unfortunately remains an overwhelming issue in the illusive chicken versus egg debate regarding vitamin D and IBD, here we summarise the latest knowledge of the immunological effects of vitamin D in IBD and recommend from available evidence that physicians regularly monitor serum 25(OH)D levels in patients with IBD. Moreover, we propose an algorithm for optimising vitamin D status in patients with IBD in clinical practice. Awaiting well-powered controlled clinical trials, we consider vitamin D supplementation to be an affordable and widely accessible therapeutic strategy to ameliorate IBD clinical outcomes.
Role of DNA topology in altering the site/sequence specificity of cleavage of DNA by bleomycin and talisomycin (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRole of DNA topology in altering the site/sequence specificity of cleavage of DNA by bleomycin and talisomycinChristopher K. Mirabelli, Cheng Hsiung Huang, and Stanley T. CrookeCite this: Biochemistry 1983, 22, 2, 300–306Publication Date (Print):January 18, 1983Publication History Published online1 May 2002Published inissue 18 January 1983https://pubs.acs.org/doi/10.1021/bi00271a011https://doi.org/10.1021/bi00271a011research-articleACS PublicationsRequest reuse permissionsArticle Views21Altmetric-Citations21LEARN 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
Optimized small‐molecule pull‐downs define MLBP1 as an acyl‐lipid‐binding protein (2019)

Abscisic acid (ABA) receptors belong to the START domain superfamily, which encompasses ligand-binding proteins present in all kingdoms of life. START domain proteins contain a central binding pocket that, depending on the protein, can couple ligand binding to catalytic, transport or signaling functions. In Arabidopsis, the best characterized START domain proteins are the 14 PYR/PYL/RCAR ABA receptors, while the other members of the superfamily do not have assigned ligands. To address this, we used affinity purification of biotinylated proteins expressed transiently in Nicotiana benthamiana coupled to untargeted LC-MS to identify candidate binding ligands. We optimized this method using ABA-PYL interactions and show that ABA co-purifies with wild-type PYL5 but not a binding site mutant. The K<sub>d</sub> of PYL5 for ABA is 1.1 μm, which suggests that the method has sufficient sensitivity for many ligand-protein interactions. Using this method, we surveyed a set of 37 START domain-related proteins, which resulted in the identification of ligands that co-purified with MLBP1 (At4G01883) or MLP165 (At1G35260). Metabolite identification and the use of authentic standards revealed that MLBP1 binds to monolinolenin, which we confirmed using recombinant MLBP1. Monolinolenin also co-purified with MLBP1 purified from transgenic Arabidopsis, demonstrating that the interaction occurs in a native context. Thus, deployment of this relatively simple method allowed us to define a protein-metabolite interaction and better understand protein-ligand interactions in plants.
Sustained release of neurotrophin‐3 via calcium phosphate‐coated sutures promotes axonal regeneration after spinal cord injury (2016)

Because of the dynamics of spinal cord injury (SCI), the optimal treatment will almost certainly be a combination approach to control the environment and promote axonal growth. This study uses peripheral nerve grafts (PNGs) as scaffolds for axonal growth while delivering neurotrophin-3 (NT-3) via calcium phosphate (CaP) coatings on surgical sutures. CaP coating was grown on sutures, and NT-3 binding and release were characterized in vitro. Then, the NT-3-loaded sutures were tested in a complete SCI model. Rats were analyzed for functional improvement and axonal growth into the grafts. The CaP-coated sutures exhibited a burst release of NT-3, followed by a sustained release for at least 20 days. Functionally, the rats with PNGs + NT-3-loaded sutures and the rats treated with PNGs scored significantly higher than controls on day 56 postoperatively. However, functional scores in rats treated with PNGs + NT-3-loaded suture were not significantly different from those of rats treated with PNGs alone. Cholera toxin subunit B (CTB) labeling rostral to the graft was not observed in any controls, but CTB labeling rostral to the graft was observed in almost all rats that had had a PNG. Neurofilament labeling on transverse sections of the graft revealed that the rats treated with the NT-3-loaded sutures had significantly more axons per graft than rats treated with an NT-3 injection and rats without NT-3. These data demonstrate that PNGs serve as scaffolds for axonal growth after SCI and that CaP-coated sutures can efficiently release NT-3 to increase axonal regeneration. © 2016 Wiley Periodicals, Inc.
<title>Controlling a robot task using external redundant sensors</title> (1994)

Industry may potentially benefit a lot from the use of robots since they permit us to perform tasks that humans can not possibly do (in hostile environment, heavy devices to move...) with a better accuracy and an increased productivity. It is the same for surgical applications where robots are used as physical interfaces between computerized data and the real world for the execution of complex and/or accurate interventions. In this paper, we present a low-cost system whose purpose is to improve the safety by a redundant control when using robots. This system is based on a continuous monitoring of the position of a collection of passive markers by a set of standard video cameras. Since the task has been planned, the position of visible markers in the images can be predicted and can be verified with a limited image processing. Any significant discrepancy between the predicted position of a marker and the real one results in an emergency stop of the robot. The calibration procedures are presented and experimental results are described.
Blood donor exposome and impact of common drugs on red blood cell metabolism (2020)

Abstract Computational models based on recent maps of the red blood cell proteome suggest that mature erythrocytes may harbor targets for common drugs. This prediction is relevant to red blood cell storage in the blood bank, in which the impact of small molecule drugs or other xenometabolites deriving from dietary, iatrogenic or environmental exposures (“exposome”) may alter erythrocyte energy and redox metabolism and, in so doing, affect red cell storage quality and post-transfusion efficacy. To test this prediction, here we provide a comprehensive characterization of the blood donor exposome, including the detection of common prescription and off-the-counter drugs in 250 units donated by healthy volunteers from the REDS-III RBC Omics study. Based on high-throughput drug screenings of 1,366 FDA-approved drugs, we report a significant impact of ∼65% of the tested drugs on erythrocyte metabolism. Machine learning models built using metabolites as predictors were able to accurately predict drugs for several drug classes/targets (bisphosphonates, anticholinergics, calcium channel blockers, adrenergics, proton-pump inhibitors, antimetabolites, selective serotonin reuptake inhibitors, and mTOR) suggesting that these drugs have a direct, conserved, and significant impact on erythrocyte metabolism. We then focused on ranitidine – a common antiacid – as a representative drug with the potential to improve human erythrocyte storage quality and post-transfusion performances in mice. By combining tracing experiments with 1,2,3- 13 C 3 -glucose, proteome integral solubility alteration assays, genetic ablation of S1P synthesis capacity, in silico docking and 1D NMR, we show that ranitidine triggers metabolic mechanisms involving sphingosine 1-phosphate (S1P)-dependent modulation of erythrocyte glycolysis and/or direct binding to hemoglobin. Graphical Abstract RBC exposome from the REDS III study revealed that blood from a subset of donors contains traces of the most common drugs in the United States. RBCs can uptake these drugs, in some cases can metabolize them to their bioactive metabolites and in others the drug can directly impact RBC metabolism during storage. Key points Blood donor exposomes include metabolites of environmental exposure, traces of common prescription or off-the-counter drugs; 65% of 1366 FDA- approved drug significantly affect RBC metabolism. Ranitidine significantly impacts glycolysis and S1P metabolism.
Nonstereogenic α‐aminoisobutyryl‐glycyl dipeptidyl unit nucleates type I′ β‐turn in linear peptides in aqueous solution (2007)

The use of alpha,alpha-disubstituted amino acids represents a valuable strategy to exercise conformational control in peptides. Incorporation of the nonstereogenic alpha-aminoisobutyryl-glycyl (Aib-Gly) dipeptidyl sequence into i+1 and i+2 positions of an acyclic peptide sequence, originally designed and investigated by Gellman and coworkers, [H-Arg-Tyr-Val-Glu-Val-Yyy-Xxx-Orn-Lys-Ile-Leu-Gln-NH2] nucleates a stable [2:4] left-handed type I' beta-turn in water. NMR spectra show that this newly designed beta-hairpin does not aggregate in water up to a concentration of approximately 1 mM, and that its backbone conformation is superimposable on corresponding hairpins containing the DPro-Gly (literature) and Aib-DAla (this work) sequences. The Aib-Gly turn-inducer sequence eliminates complications because of cis-trans isomerization of Zzz-Pro bonds, and constitutes an attractive alternative to the proteogenic Asn-Gly and nonproteogenic DPro-Gly motifs previously suggested as turn-inducer sequences. These design principles could be exploited to prepare water-soluble beta-hairpin peptides with robust structures and novel function.
H-Bonding as a Control Element in Stereoselective Ru-Catalyzed Olefin Metathesis (2009)

H-bonding interactions have been exploited extensively in the design of catalysts for stereoselective synthesis but have rarely been utilized in the development of metal-catalyzed processes. Studies described herein demonstrate that intramolecular H-bonding interactions can significantly increase the rate and levels of stereochemical control in Ru-catalyzed olefin metathesis reactions. The utility of H-bonding in catalytic olefin metathesis is elucidated through development of exceptionally facile and highly diastereoselective ring-opening/cross-metathesis (DROCM) reactions, involving achiral Ru catalysts and enantiomerically enriched allylic alcohols. Transformations proceed to completion readily (> 98% conversion, up to 87% yield), often within minutes, in the presence of < or = 2 mol % of an achiral catalyst to afford synthetically versatile products of high stereochemical purity (up to > 98:2 dr and 11:1 E:Z).
Human motion tracking and gait analysis: a brief review of current sensing systems and integration with intelligent environments (2008)

Human motion tracking and gait analysis is becoming a topic of great interest in everyday applications generating a large amount of research into systems that can provide this information in real time at a low cost and with the smallest intrusion level possible. In this line different approaches have been proposed following distinct philosophies usually related to the final application of the system. This paper is aimed on one hand at providing a review of non vision based current systems highlighting how distinct and oriented towards particular applications they are. On the other this paper deals with the problem of integrating such different elements into efficient environmental intelligence applications that can be used as a base for home rehabilitation or automatic elderly assistance. This is addressed by implementing a specific device access layer within a novel distributed agent based ambient intelligence architecture called HI <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> .
Is Document Frequency important for PRF? (2012)

Abstract. We introduce in this paper a new heuristic constraint for PRF models, referred to as the Document Frequency (DF) constraint, which is validated through a series of experiments with an oracle. We then analyze, from a theoretical point of view, state-of-the-art PRF models according to their relation with this constraint. This analysis reveals that the standard mixture model for PRF in the language modeling family does not satisfy the DF constraint on the contrary to several recently proposed models. Lastly, we perform tests, which further validate the constraint, with a simple family of tf-idf functions based on a parameter controlling the satisfaction of the DF constraint. 1
Role of interleukin-1 in the pulmonary immune response duringPseudomonas aeruginosapneumonia (2002)

Pneumonia is associated with elevated concentrations of the proinflammatory cytokine interleukin (IL)-1 in the pulmonary compartment. To study the role of IL-1 in the pathogenesis of Pseudomonas pneumonia, IL-1 receptor type 1 gene-deficient (IL-1R -/-) mice and wild-type mice were intranasally inoculated with Pseudomonas aeruginosa. The absence of the IL-1 signal attenuated the outgrowth of Pseudomonas in lungs, as reflected by an increasing number of colony-forming units (cfu) during Pseudomonas pneumonia in wild-type mice and a concurrently decreasing number of cfu during pulmonary infection in IL-1R -/- mice (P < 0.05, IL-1R -/- mice vs. wild-type mice). Influx of neutrophils was decreased in bronchoalveolar lavage fluids in IL-1R -/- mice compared with wild-type mice. Similarly, lung levels of cytokines (tumor necrosis factor-alpha, IL-6) and chemokines (macrophage inflammatory protein-2 and KC) were lower in IL-1R -/- mice 24 h postinoculation. Consistent with results obtained in IL-1R -/- mice, treatment of wild-type mice with IL-1R antagonist also diminished outgrowth of Pseudomonas when compared with wild-type mice treated with vehicle (P < 0.05). These results demonstrate that an absence or reduction in endogenous IL-1 activity improves host defense against Pseudomonas pneumonia while suppressing the inflammatory response.
Strategy for monitoring T cell responses to NY-ESO-1 in patients with any HLA class I allele (2000)

NY-ESO-1 elicits frequent antibody responses in cancer patients, accompanied by strong CD8(+) T cell responses against HLA-A2-restricted epitopes. To broaden the range of cancer patients who can be assessed for immunity to NY-ESO-1, a general method was devised to detect T cell reactivity independent of prior characterization of epitopes. A recombinant adenoviral vector encoding the full cDNA sequence of NY-ESO-1 was used to transduce CD8-depleted peripheral blood lymphocytes as antigen-presenting cells. These modified antigen-presenting cells were then used to restimulate memory effector cells against NY-ESO-1 from the peripheral blood of cancer patients. Specific CD8(+) T cells thus sensitized were assayed on autologous B cell targets infected with a recombinant vaccinia virus encoding NY-ESO-1. Strong polyclonal responses were observed against NY-ESO-1 in antibody-positive patients, regardless of their HLA profile. Because the vectors do not cross-react immunologically, only responses to NY-ESO-1 were detected. The approach described here allows monitoring of CD8(+) T cell responses to NY-ESO-1 in the context of various HLA alleles and has led to the definition of NY-ESO-1 peptides presented by HLA-Cw3 and HLA-Cw6 molecules.
From Short- to Long-Term Effects of C-Section Delivery on Microbiome Establishment and Host Health (2021)

The establishment of gut microbiota has been proven to be impacted by several factors during pregnancy, delivery, and neonate periods. The body of evidence describing C-section delivery (CSD) as one of the most disruptive events during early life has expanded in recent years, concluding that CSD results in a drastic change in microbiota establishment patterns. When comparing the gut microbiota composition of CSD babies with vaginally delivered (VD) babies, the former show a microbiome that closely resembles that found in the environment and the mother's skin, while VD babies show a microbiome more similar to the vaginal microbiome. Although these alterations of normal gut microbiota establishment tend to disappear during the first months of life, they still affect host health in the mid-long term since CSD has been correlated with a higher risk of early life infections and non-transmissible diseases, such as inflammatory diseases, allergies, and metabolic diseases. In recent years, this phenomenon has also been studied in other mammals, shedding light on the mechanisms involved in the effects of a CSD on host health. In addition, strategies to revert the disruptions in gut microbiomes caused by a CSD are currently in the process of development and evaluation. In this review, we discuss the recent advances in CSD research, from the alteration of gut microbiota establishment to the possible effects on host health during early life and development.
Introduction (2020)

This chapter sets the scene for the book by introducing the significance of narrative and its mediations for the experience of a global public health emergency. It provides some necessary detail on the swine flu pandemic of 2009 to help the reader situate the empirical material to come in following chapters. The chapter also introduces “Cameron’s infection story” to explain how we use narrative in this book and make links with narrative theory in the social sciences. Cameron’s story also helps to locate the book in the lived experience of everyday people in 2009 and foregrounds the focus of this book on the stories of individuals affected in different ways by the pandemic.
Ionic Liquids for Propene‐Propane Separation (2009)

Abstract This paper presents an extensive study on the feasibility of ionic liquids (IL) for the extractive distillation of propene‐propane mixtures. A new experimental method for express screening of non‐volatile entrainers was elaborated. A series of ILs and their mixtures were screened at ambient temperature and low pressures. The screening results show that every tested IL turns a low boiler propene into a high boiler and the alkene‐to‐alkane separation factor can be as low as 0.28. The solubility and separation efficiency can be tuned by adjusting the chemical structures of the ions forming the IL. It was found that shortening of the alkyl substituents of the imidazolium ions leads to a decrease in capacity and to an increase in the separation factor. Interestingly, ILs containing nitrile functionalities in either the cation or the anion showed, in our experiments, enhanced separation ability combined with still good capacities. From our thermodynamic measurements, [EMIM][[B(CN) 4 ] was proved to be the most promising candidate. Binary mixtures of ILs were also tested and resulted in separation factors and capacities between the values for the individual ILs. For the most promising candidates, also autoclave measurements at elevated temperatures and pressures were carried out. These experiments indicate that the separation ability decreases with growing temperature and loading. In general, our study definitely proves the high potential of ILs to act as entrainers in the extractive distillation of propene‐propane mixtures or for the separation of any other low‐boiling alkene‐alkane mixture.