gebhart/patrepeval huggingface dataset:
Aminoacrylate Intermediates in the Reaction of <i>Citrobacter freundii</i> Tyrosine Phenol-Lyase (2006)

Tyrosine phenol-lyase (TPL) from Citrobacter freundii is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the reversible hydrolytic cleavage of l-Tyr to give phenol and ammonium pyruvate. The proposed reaction mechanism for TPL involves formation of an external aldimine of the substrate, followed by deprotonation of the alpha-carbon to give a quinonoid intermediate. Elimination of phenol then has been proposed to give an alpha-aminoacrylate Schiff base, which releases iminopyruvate that ultimately undergoes hydrolysis to yield ammonium pyruvate. Previous stopped-flow kinetic experiments have provided direct spectroscopic evidence for the formation of the external aldimine and quinonoid intermediates in the reactions of substrates and inhibitors; however, the predicted alpha-aminoacrylate intermediate has not been previously observed. We have found that 4-hydroxypyridine, a non-nucleophilic analogue of phenol, selectively binds and stabilizes aminoacrylate intermediates in reactions of TPL with S-alkyl-l-cysteines, l-tyrosine, and 3-fluoro-l-tyrosine. In the presence of 4-hydroxypyridine, a new absorption band at 338 nm, assigned to the alpha-aminoacrylate, is observed with these substrates. Formation of the 338 nm peaks is concomitant with the decay of the quinonoid intermediates, with good isosbestic points at approximately 365 nm. The value of the rate constant for aminoacrylate formation is similar to k(cat), suggesting that leaving group elimination is at least partially rate limiting in TPL reactions. In the reaction of S-ethyl-l-cysteine in the presence of 4-hydroxypyridine, a subsequent slow reaction of the alpha-aminoacrylate is observed, which may be due to iminopyruvate formation. Both l-tyrosine and 3-fluoro-l-tyrosine exhibit kinetic isotope effects of approximately 2-3 on alpha-aminoacrylate formation when the alpha-(2)H-labeled substrates are used, consistent with the previously reported internal return of the alpha-proton to the phenol product. These results are the first direct spectroscopic observation of alpha-aminoacrylate intermediates in the reactions of TPL.
Neural Transplantation (1995)

Cell transplantation is now being explored as a new therapeutic strategy to restore function in the diseased human central nervous system. Neural grafts show long-term survival and function in patients with Parkinson's disease but the symptomatic relief needs to be increased. Cell transplantation seems justified in patients with Huntington's disease and, at a later stage, possibly also in demyelinating disorders. The further development in this research field will require systematic studies in animal experiments but also well-designed clinical trials in small groups of patients.
Stimulation of 16-dehydroprogesterone and progesterone reductases of Eubacterium sp. strain 144 by hemin and hydrogen or pyruvate (1985)

Suspensions of Eubacterium sp. strain 144, prepared from cells grown with 16-dehydroprogesterone, catalyzed the reduction of this steroid to 17-isoprogesterone at a very low rate. Modifications of the assay to optimize the pH (5.5) and increase the steroid solubility (10% [vol/vol] methanol) did not significantly enhance the reaction. However, growth of strain 144 in the presence of hemin was found to stimulate 16-dehydroprogesterone reductase during the initial 30 min of incubation, giving a biphasic time course. These biphasic kinetics could be eliminated by providing the cells with an exogenous electron donor. Strain 144 used either H2 or pyruvate for this purpose, and 17-isoprogesterone formation was nearly complete after 20 to 30 min of incubation. However, under these conditions, strain 144 further converted 17-isoprogesterone to products which lacked UV absorbance (254 nm). When progesterone was used as a substrate, it was found that strain 144 could reduce the C4-C5 double bond of this steroid by a progesterone reductase to give mostly 5 beta-pregnadione and some 5 alpha-pregnadione. Furthermore, the 3-keto group of 5 beta-pregnadione steroid was also reduced to a hydroxy function. The maximum activities of both 16-dehydroprogesterone and progesterone reductases in cell suspensions required the growth of strain 144 with hemin and 16-dehydroprogesterone and the presence of H2 or pyruvate.
The genetic analysis of mitosis in <i>Aspergillus nidulans</i> (1989)

We describe here recent work on the molecular genetics of mitosis in the filamentous fungus Aspergillus nidulans. Aspergillus is one of three simple eukaryotes with powerful genetic systems that have been used to analyze mitosis. The modern molecular biological techniques available with this organism have made it possible to use mutations to identify genes and proteins that play an important role in mitosis. Three Aspergillus genes that affect mitosis are described. One gene, nimA, is specifically expressed late in the cell cycle and codes for a putative protein kinase that induces mitosis, even in cells blocked in S-phase. The second gene, bimG, codes for a putative phosphatase that interacts functionally with the nimA kinase. The third gene, bimE, codes for a protein that suppresses mitosis during interphase, apparently by keeping nimA turned off. None of these genes appear to be similar to any of the genes affecting mitosis that have been characterized in other eukaryotes, but rather appear to be elements of a system that prevents mitosis from occurring during interphase.
Studies on Tolerance of the Y Chromosome Antigen in Mice (1960)

Summary The principle of immunologic tolerance has been employed to study the isoantigen—usually referred to as the Y-factor—that is responsible for the rejection of male skin isografts by female mice of many different inbred strains. Various lines of evidence are presented that lend strong support to the view that this antigen is determined by a locus on the Y chromosome and that it behaves in all respects like the tissue transplantation antigens responsible for the destruction of tissue homografts. Tolerance of male skin isografts, like tolerance of skin homografts, can be abolished by transfer of normal or sensitized lymphoid cells from a genetically appropriate donor. Exactly the same Y antigen appears to be present in all male mice, irrespective of their strain of origin, as evidenced by the fact that C57 female mice could be made tolerant of subsequent male skin isografts by inoculation at birth with male cells derived from any one of four different and unrelated donor strains. The tolerance-responsive period of C57 female mice to this fairly weak antigen was found to be of the order of 17 days. Because of the very high degree of toleranceresponsiveness of C57 females to the Y antigen, this simple tolerance system has been employed to investigate several fundamental aspects of transplantation immunology. For example, it has been found possible to render female mice tolerant of male skin isografts by repeated inoculations with high dosages of a cell-free extract of male lymphoid cells. Highly suggestive evidence has also been obtained that persistence of tolerance of the Y antigen does not require persistence of the antigen.
Implementing One Health approaches to confront emerging and re-emerging zoonotic disease threats: lessons from PREDICT (2020)

Recurring outbreaks of emerging and re-emerging zoonoses, such as Ebola virus disease, avian influenza, and Nipah virus, serve as a reminder that the health of humans, animals, and the environment are interconnected and that early response to emerging zoonotic pathogens requires a coordinated, interdisciplinary, cross-sectoral approach. As our world becomes increasingly connected, emerging diseases pose a greater threat, requiring coordination at local, regional, and global levels. One Health is a multisectoral, transdisciplinary, and collaborative approach promoted to more effectively address these complex health threats. Despite strong advocacy for One Health, challenges for practical implementation remain. Here we discuss the value of the One Health approach for addressing global health challenges. We also share strategies applied to achieve successful outcomes through the USAID Emerging Pandemic Threats Program PREDICT project, which serve as useful case studies for implementing One Health approaches. Lastly, we explore methods for promoting more formal One Health implementation to capitalize on the added value of shared knowledge and leveraged resources.
Survey of IIR adaptive filtering algorithms (1982)

Several adaptive algorithms for IIR filters have been presented in recent years. These algorithms can be categorized as gradient search or non-gradient search. We present here an example in which a non-quadratic, multimodal error surface is possible. In particular, a case is presented which models a fourth-order FIR plant with a two-pole adaptive IIR filter. The resulting error surface has three distinct minima. Using this example, we compare the NRLMS (gradient search) algorithm with the Genetic (non-gradient search) Algorithm. A combination of the two algorithms is then presented which has improved performance over the individual algorithms.
Rescue of biosynthesis of nicotinamide adenine dinucleotide protects the heart in cardiomyopathy caused by lamin A/C gene mutation (2018)

Cardiomyopathy caused by lamin A/C gene (LMNA) mutations (hereafter referred as LMNA cardiomyopathy) is an anatomic and pathologic condition associated with muscle and electrical dysfunction of the heart, often leading to heart failure-related disability. There is currently no specific therapy available for patients that target the molecular pathophysiology of LMNA cardiomyopathy. Recent studies suggested that nicotinamide adenine dinucleotide (NAD+) cellular content could be a critical determinant for heart function. Biosynthesis of NAD+ from vitamin B3 (known as salvage pathways) is the primary source of NAD+. We showed here that NAD+ salvage pathway was altered in the heart of mouse and human carrying LMNA mutation, leading to an alteration of one of NAD+ co-substrate enzymes, PARP-1. Oral administration of nicotinamide riboside, a natural NAD+ precursor and a pyridine-nucleoside form of vitamin B3, leads to a marked improvement of the NAD+ cellular content, an increase of PARylation of cardiac proteins and an improvement of left ventricular structure and function in a model of LMNA cardiomyopathy. Collectively, our results provide mechanistic and therapeutic insights into dilated cardiomyopathy caused by LMNA mutations.
Multi-Grained Level of Detail for Rendering Complex Meshes Using a Hierarchical Seamless Texture Atlas (2006)

Previous algorithms for view-dependent level of detail provide local mesh refinements either at the finest granularity or at a fixed, coarse granularity. The former provides triangle-level adaptation, often at the expense of heavy CPU usage and low triangle rendering throughput; the latter improves CPU usage and rendering throughput by operating on groups of triangles. We present a new multiresolution hierarchy and associated algorithms that provide adaptive granularity. This multi-grained hierarchy allows independent control of the number of hierarchy nodes processed on the CPU and the number of triangles to be rendered on the GPU. We employ a seamless texture atlas style of geometry image as a GPU-friendly data organization, enabling efficient rendering and GPU-based stitching of patch borders. We demonstrate our approach on both large triangle meshes and terrains with up to billions of vertices.
Iterative application of the Chase algorithm on Reed-Solomon product codes (2002)

This work proposes a new iterative application of the Chase algorithm on Reed-Solomon (RS) product codes. Reliability information of bit positions is calculated only once. Although the bit error rates (BER) achieved are not as good as the results obtained with the recent turbo product decoding (TPD) algorithm, decoding complexity is far less. Simulation results are presented for a communications system using binary phase shift keying (BPSK) on an additive white Gaussian noise (AWGN) channel for both hard and soft decoding iterations and their performances are compared with turbo product decoding.
Assessment of Salt Loading on Well Casings (2002)

Abstract In the next decade significant new oil field developments will be brought on-stream in the deep water Gulf of Mexico. A large number of these wells will be drilled through salt. Assuring the integrity of these wells over the life of the field is a major drilling engineering challenge, as the consequences of well failures may result in billions of dollars remedial costs and lost production. To address these challenges for BP's deepwater developments, advanced numerical finite element analyses of salt / casing interaction were undertaken by Sandia National Laboratories using state-of-the-art computational modeling developed as part of extensive research supporting the Strategic Petroleum Reserve (SPR) and the Waste Isolation Pilot Plant (WIPP) projects. The paper summarizes, briefly, the salient features of salt mechanical behavior of relevance to well integrity. The results of numerical modeling of casing loading are presented which focus on the importance of assessing the possibility of both uniform and non-uniform loading by the salt; and the impact that production-induced heating of the salt has on the rate and magnitude of casing loading. Based on the findings of these analyses, strategies for minimizing the magnitude of loading on well casings are discussed. The relative merits of cementing the annulus through salt are compared with the option of leaving the annulus open in order to defer the time at which salt loading occurs.
Optical coherent tomography (OCT) bio-imaging using 3D scanning micromirror (2007)

Design and development of a 3D scanning MEMS micromirror integrated miniaturized optical probe has been presented in this article. The probe is designed to be less than 2 mm in diameter and has dynamic scanning modality for larger field of view. Scanning is achieved using 3D micromirror device, which has 16º out of plane and 360º beam rotation capability. Initial target of 45º out of plane deflection is yet to be achieved. The probe being developed currently would have scanning capability in one quarter of 360º full rotation. The field of view would still be very large and multiple optical biopsies would be possible for planned cancer model diagnostics. The feasibility of using scanning mirror into an optical probe was demonstrated using scanning repeatability and OCT imaging tests. Geometrical optics and package design using silicon optical bench have been established. Miniaturized 3D scanning micromirror have been designed and developed with 16º out of plane deflection demonstrated. Probe package integration and optical testing are carried out.
New York Public Library Acquisitions June 1955-July 1956 (1957)

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Toward a Software Architecture for Quantum Computing Design Tools (2004)

Compilers and computer-aided design tools will be essential for quantum computing. We present a computer-aided design flow that transforms a highlevel language program representing a quantum computing algorithm into a technology-specific implementation. We trace the significant steps in this flow and illustrate the transformations to the representation of the quantum program. The focus of this paper is on the languages and transformations needed to represent and optimize a quantum algorithm along the design flow.
Co-refinement of multiple-contrast neutron/X-ray reflectivity data using<i>MOTOFIT</i> (2006)

The contrast-variation technique is employed in multiple-contrast neutron/X-ray reflectometry experiments to highlight scattering from different structural components that are present at a surface or interface. The advantage of this technique is that the structural model used to describe the interfacial scattering length density profile must apply to all the contrasts measured. A new reflectivity analysis package, MOTOFIT , which runs in the IGOR Pro environment (http://www.wavemetrics.com), has been created to aid the simultaneous fitting (with the same structural model) of these multiple-contrast data, using an intuitive graphical user interface, which most co-refinement packages do not possess. MOTOFIT uses a slab-model approach with the Abeles matrix method, and extensions for surface roughness to perform non-linear least-squares regression on the experimental reflectivity curves. Other features, such as the ability to create complicated interparameter constraints or analyse reflectivity from multilayers, simulated annealing, etc. , make MOTOFIT a powerful reflectometry analysis package
Secretory IgA-mediated protection against<i>V. cholerae</i>and heat-labile enterotoxin-producing enterotoxigenic<i>Escherichia coli</i>by rice-based vaccine (2010)

Cholera and enterotoxigenic Escherichia coli (ETEC) are among the most common causes of acute infantile gastroenteritis globally. We previously developed a rice-based vaccine that expressed cholera toxin B subunit (MucoRice-CTB) and had the advantages of being cold chain-free and providing protection against cholera toxin (CT)-induced diarrhea. To advance the development of MucoRice-CTB for human clinical application, we investigated whether the CTB-specific secretory IgA (SIgA) induced by MucoRice-CTB gives longstanding protection against diarrhea induced by Vibrio cholerae and heat-labile enterotoxin (LT)-producing ETEC (LT-ETEC) in mice. Oral immunization with MucoRice-CTB stored at room temperature for more than 3 y provided effective SIgA-mediated protection against CT- or LT-induced diarrhea, but the protection was impaired in polymeric Ig receptor-deficient mice lacking SIgA. The vaccine gave longstanding protection against CT- or LT-induced diarrhea (for > or = 6 months after primary immunization), and a single booster immunization extended the duration of protective immunity by at least 4 months. Furthermore, MucoRice-CTB vaccination prevented diarrhea in the event of V. cholerae and LT-ETEC challenges. Thus, MucoRice-CTB is an effective long-term cold chain-free oral vaccine that induces CTB-specific SIgA-mediated longstanding protection against V. cholerae- or LT-ETEC-induced diarrhea.
Hyperbranched Polyglycerol as a Colloid in Cold Organ Preservation Solutions (2015)

Hydroxyethyl starch (HES) is a common colloid in organ preservation solutions, such as in University of Wisconsin (UW) solution, for preventing graft interstitial edema and cell swelling during cold preservation of donor organs. However, HES has undesirable characteristics, such as high viscosity, causing kidney injury and aggregation of erythrocytes. Hyperbranched polyglycerol (HPG) is a branched compact polymer that has low intrinsic viscosity. This study investigated HPG (MW-0.5 to 119 kDa) as a potential alternative to HES for cold organ preservation. HPG was synthesized by ring-opening multibranching polymerization of glycidol. Both rat myocardiocytes and human endothelial cells were used as an in vitro model, and heart transplantation in mice as an in vivo model. Tissue damage or cell death was determined by both biochemical and histological analysis. HPG polymers were more compact with relatively low polydispersity index than HES in UW solution. Cold preservation of mouse hearts ex vivo in HPG solutions reduced organ damage in comparison to those in HES-based UW solution. Both size and concentration of HPGs contributed to the protection of the donor organs; 1 kDa HPG at 3 wt% solution was superior to HES-based UW solution and other HPGs. Heart transplants preserved with HPG solution (1 kDa, 3%) as compared with those with UW solution had a better functional recovery, less tissue injury and neutrophil infiltration in syngeneic recipients, and survived longer in allogeneic recipients. In cultured myocardiocytes or endothelial cells, significantly more cells survived after cold preservation with the HPG solution than those with the UW solution, which was positively correlated with the maintenance of intracellular adenosine triphosphate and cell membrane fluidity. In conclusion, HPG solution significantly enhanced the protection of hearts or cells during cold storage, suggesting that HPG is a promising colloid for the cold storage of donor organs and cells in transplantation.
Extraction, integration and analysis of crowdsourced points of interest from multiple web sources (2014)

The amount of user-generated geospatial content on the Web is constantly increasing, making it a valuable source of information for enabling, enriching and enhancing geospatial applications and services. However, this content is highly heterogeneous and diverse, varying significantly in quality and accuracy. Extracting, integrating, and mining these crowdsourced geospatial data from the Web is far from trivial. Among the main challenges are to retrieve data from multiple sources, each one providing its own access methods and restrictions, to deal with different schemas and taxonomies, and to find matching entities across multiple sources. In this paper, we present our work for retrieving and integrating crowdsourced Points of Interest (POIs) from popular Web sources. We retrieve POIs from different Web sources and we describe the steps taken for mapping the source categories to a common schema, detecting duplicate POIs, and eventually clustering them to identify hotspots. We present the results of this process applied to six major Web sources to retrieve and integrate POIs located in the metropolitan areas of three European capital cities.
Correlation of Cytokine Elaboration with Mononuclear Cell Adhesion to Platelet Storage Bag Plastic Polymers: a Pilot Study (1999)

The basis for many febrile nonhemolytic transfusion reactions associated with platelet transfusion therapy is cytokine elaboration and accumulation in the storage bag, which correlate with the leukocyte content and the length of platelet storage. We propose that a possible additional variable in the elaboration and accumulation of cytokines is the differential adhesion of mononuclear cells to the plastic substrate of the platelet storage bag. We hypothesize that mononuclear cell adhesion-induced cytokine release is greater in random-donor platelet bags composed of the polyolefin polymer compared to the single-donor apheresis platelet bags composed of the polyvinyl chloride polymer with the tri-(2-ethylhexyl) trimellitate (TEHTM) plasticizer. For four blood donors, we demonstrate preferential mononuclear cell adhesion, in vitro, to discs of polyolefin polymer versus discs of polyvinyl chloride polymer with the TEHTM plasticizer. Scanning electron microscopy corroborates this. In addition, proinflammatory cytokine (interleukin 1beta [IL-1beta] and tumor necrosis factor alpha [TNF-alpha]) levels are greater in culture wells containing discs of polyolefin polymer than in those containing discs of polyvinyl chloride polymer with the TEHTM plasticizer, and even more so in storage bags containing polyolefin polymer versus polyvinyl chloride polymer with the TEHTM plasticizer (IL-1beta, TNF-alpha, IL-6, and IL-8). This study suggests, for the first time, that differential plastic substrate mononuclear cell adhesion may contribute to cytokine release during platelet storage. This may represent an additional variable in the pathophysiology of febrile nonhemolytic transfusion reactions in patients receiving stored platelet units.