gebhart/patrepeval huggingface dataset:
Proliferation of individual hematopoietic progenitors purified from umbilical cord blood. (1995)

In previous studies, we described long-term cultures of subpopulations of CD34+ cord blood cells that were fractionated using antibodies specific for CD45RA and CD71. In the present study, we plated the most primitive CD34+CD45RAlowCD71low cells individually and analyzed the proliferation and expansion kinetics of the various hematopoietic progenitors included in this subpopulation. The proliferation capacity of single progenitors was assessed by the total number of cells produced, and their expansion capacity was assessed by the production of CD34+ and colony-forming cells. Monolineage progenitors (erythroid, granulocyte, and macrophage progenitors) showed the lowest expansion capacity, which correlated with a relatively short life span (< 37 days) of the generated colonies. Among these cells, erythroid progenitors showed the highest proliferative potential. Based on their relative cell content and proliferation/expansion capacities, two types of both granulomacrophagic (GM) and multipotent (Mix) progenitors were identified. GM progenitors producing colonies with > 70% granulocytes had a low expansion capacity and gave rise to colonies that were sustained for < 42 days. A second type of GM progenitors, giving rise to colonies with > 90% macrophages, had a higher expansion capacity and the colonies they produced were sustained for > 72 days. On the other hand, Mix progenitors producing colonies with > 70% erythroid cells had a lower expansion capacity and life span (< 46 days in culture), than Mix progenitors producing colonies with > 90% myeloid cells (life span of > 72 days). These results demonstrate, at the single-cell level, a correlation between the type of progenitor cell and its expansion capacity. In turn, the expansion capacity of the progenitors was correlated with the life span of the colonies produced. Furthermore, our results suggest that in cord blood, at least two types of bipotential myeloid (GM) progenitors and two types of multipotent (Mix) progenitors can be distinguished, that have respectively low and high proliferative and expansion capacity.
Prostate‐specific antigen concentration in young men: new estimates and review of the literature (2012)

• The PSA estimates, together with those summarized from the literature, provide age- and race-specific PSA reference distributions for young men who might have undergone non-recommended PSA testing. • Comparisons by race could also begin to inform the timing of divergence of prostate cancer risk by race.
Quantification of Large C3 Fragments as an Index ofComplement Activation in Mice (1984)

A method which enables to evaluate the mouse C3 activation has been used to study the activation of the complement system in C57Bl/6 mice injected with cobra venom factor, with Escherichia coli, and with bacterial lipopolysaccharide. It was found that this method was able to detect the complement activation early, at a time when total levels of C3-reacting molecules had not yet decreased.
A new approach to the treatment of filariasis (2001)

The symbiosis of filarial nematodes and intracellular Wolbachia bacteria has recently been exploited as a target for antibiotic therapy of filariasis. Antibiotic treatment of filarial nematodes results in sterility and inhibits larval development and adult worm viability. In the first trial on human onchocerciasis depletion of bacteria following treatment with doxycycline resulted in a complete and long-term block of embryogenesis. Bacteria are unable to repopulate nematode tissues up to 18 months after depletion, suggesting these effects may be permanent. Following ivermectin treatment, individuals given antibiotic therapy showed sustained reductions in skin microfilariae, with the majority of people remaining microfilarial negative 12-18 months after treatment. Since Wolbachia also contribute to the inflammatory pathogenesis of filarial disease, antibiotic therapy could, in addition to effects on worm fertility or viability, prevent the onset or development of filarial pathology.
Colour demosaicking with directional filtering and weighting (2012)

Digital cameras usually use a single sensor covered with a colour filter array which samples only one colour at the location of each pixel. Restoring a full-colour image by the demosaicking technique is a key task in the digital imaging pipeline. This study proposes a novel demosaicking approach based on the existing directional filtering and weighting techniques. The contributions of this study are two-fold. First, the authors analyse the advantages and limitations of the existing directional filtering and weighting techniques, and improve the two existing techniques in order to suppress the common demosaicking artefacts. Second, the authors give a new estimated scheme for the reconstruction of the colour components. The experimental results show that the proposed method outperforms the recent six state-of-the-art demosaicking methods in terms of both subjective and objective measures.
OPS: Optimized Shuffle Management System for Apache Spark (2020)

In recent years, distributed computing frameworks, such as Hadoop MapReduce and Spark, are widely used for big data processing. With the explosive growth of the amount of data, companies tend to store intermediate data of the shuffle phase on disk instead of memory. Therefore, intensive network and disk I/O are both involved in the shuffle phase. To optimize the overhead of the shuffle phase, we propose OPS, an open-source distributed computing shuffle management system based on Spark, which provides an independent shuffle service for Spark. By using early-merge and early-shuffle strategy, OPS alleviates the I/O overhead in the shuffle phase and efficiently schedules the I/O and computing resources. OPS also proposes a slot-based scheduling algorithm to predict and calculate the optimal scheduling result of the reduce task. Besides, OPS provides a taint-redo strategy to ensure the fault tolerance of computing jobs. We evaluated the performance of OPS on a 100-node Amazon AWS EC2 cluster. Overall, OPS optimizes the overhead of shuffle by nearly 50%. In the test cases of HiBench, OPS improves end-to-end completion time by nearly 30% on average.
AutoReplica: Automatic data replica manager in distributed caching and data processing systems (2016)

Nowadays, replication technique is widely used in data center storage systems for large scale Cyber-physical Systems (CPS) to prevent data loss. However, side-effect of replication is mainly the overhead of extra network and I/O traffics, which inevitably downgrades the overall I/O performance of the cluster. To effectively balance the trade-off between I/O performance and fault tolerance, in this paper, we propose a complete solution called “AutoReplica” - a replica manager in distributed caching and data processing systems with SSD-HDD tier storages. In detail, AutoReplica utilizes the remote SSDs (connected by high speed fibers) to replicate local SSD caches to protect data. In order to conduct load balancing among nodes and reduce the network overhead, we propose three approaches (i.e., ring, network, and multiple-SLA network) to automatically setup the cross-node replica structure with the consideration of network traffic, I/O speed and SLAs. To improve the performance during migrations triggered by load balance and failure recovery, we propose the a migrate-on-write technique called “fusion cache” to seamlessly migrate and prefetch among local and remote replicas without pausing the subsystem. Moreover, AutoReplica can also recover from different failure scenarios, while limits the performance downgrading degree. Lastly, AutoReplica supports parallel prefetching from multiple nodes with a new dynamic optimizing streaming technique to improve I/O performance. We are currently in the process of implementing AutoReplica to be easily plugged into commonly used distributed caching systems, and solidifying our design and implementation details.
Five-terminal amorphous silicon thin-film transistor structure (2002)

Hydrogenated amorphous silicon (a-Si:H) thin-film transistors (TFTs) are widely used in large area electronics applications like active-matrix liquid-crystal displays (AMLCDs) or in or X-ray and optical sensors. TFTs often suffer from source and drain series resistances that perturbate the intrinsic channel performance, especially in the cases of poor source and drain contacts or high density of states present in the a-Si:H electronic gap. To accurately evaluate the TFT intrinsic properties without the influence of the parasitic series resistances, we have previously introduced the five-terminal TFT (FT TFT), or gated-four probe TFT (GFP TFT) structure (Chen and Kanicki, 1997 and 1998). This device has two additional electrodes fabricated between the source and drain contacts. Such a structure is expected to allow for evaluation of the potential difference along the conduction channel, assuming that the potential difference is the same at the conduction channel interface (a-Si:H/a-SiN/sub x/:H) and at the back interface (substrate/a-Si:H). We show in this paper that, indeed, FT TFTs can be used to accurately study TFT conduction channel intrinsic properties.
Investigating source and filter contributions, and their interaction, to statistical parametric speech synthesis (2014)

This paper presents an investigation of the separate perceptual degradations introduced by the modelling of source and filter features in statistical parametric speech synthesis. This is achieved using stimuli in which various permutations of natural, vocoded and modelled source and filter are combined, optionally with the addition of filter modifications (e.g. global variance or modulation spectrum scaling). We also examine the assumption of independence between source and filter parameters. Two complementary perceptual testing paradigms are adopted. In the first, we ask listeners to perform “same or different quality” judgements between pairs of stimuli from different configurations. In the second, we ask listeners to give an opinion score for individual stimuli. Combining the findings from these tests, we draw some conclusions regarding the relative contributions of source and filter to the currently rather limited naturalness of statistical parametric synthetic speech, and test whether current independence assumptions are justified.
Significance of Ca-soap formation for calcium absorption in the rat. (1977)

The significance of calcium soap formation in the inhibition of calcium absorption has been studied in rats. 47Ca labelled soaps of fatty acids were introduced into the duodenum and the absorption of calcium measured after four hours in a whole body counter. The absorption of calcium was inversely correlated with the chain length of the fatty acid varying from 1% for Ca-stearate to 60% for Ca-hexanoate. Increasing the degree of unsaturation of the fatty acid was accompanied by increased calcium absorption. The availability of calcium for absorption from the soaps was correlated with their solubility in 1% aqueous Na-tauroglycocholate. The percentages of calcium as soap in the small intestine and the faeces after intragastric administration of calcium and fats were similar, which suggests that the faecal content of calcium soaps is an index of intestinal soap formation. Soap formation was negligible when CaCl2 was given with tristearate, triolaeate, or tridecanoate and no depression of calcium absorption was observed. Calcium absorption was markedly impaired by the addition of phosphates at a Ca/P ratio of 1:1 irrespective of the presence of neutral fats. Stearic acid resulted in significant soap formation and reduced calcium absorption. The degree of Ca-soap formation and the inhibition of calcium absorption were well correlated. The results suggest that, although calcium soap formation may markedly depress calcium absorption in the rat, no significant soap formation takes place when fats are given in the form of triglycerides.
The JEDI event-based infrastructure and its application to the development of the OPSS WFMS (2001)

The development of complex distributed systems demands the creation of suitable architectural styles (or paradigms) and related runtime infrastructures. An emerging style that is receiving increasing attention is based on the notion of event. In an event-based architecture, distributed software components interact by generating and consuming events. An event is the occurrence of some state change in a component of a software system, made visible to the external world. The occurrence of an event in a component is asynchronously notified to any other component that has declared some interest in it. This paradigm (usually called "publish/subscribe", from the names of the two basic operations that regulate the communication) holds the promise of supporting a flexible and effective interaction among highly reconfigurable, distributed software components. In the past two years, we have developed an object-oriented infrastructure called JEDI (Java event-based distributed infrastructure). JEDI supports the development and operation of event-based systems and has been used to implement a significant example of distributed system, namely, the OPSS workflow management system (WFMS). The paper illustrates the main features of JEDI and how we have used them to implement OPSS. Moreover, the paper provides an initial evaluation of our experiences in using the event-based architectural style and a classification of some of the event-based infrastructures presented in the literature.
Improved RJMCMC point process sampler for object detection on images by simulated annealing (2003)

We first recall Geyer and Møller algorithm that allows to sample point processes using a Markov chain. We also recall Green's framework that allows to build samplers on general state spaces by imposing reversibility of the designed Markov chain.Since in our image processing applications, we are interested by sampling highly spatially correlated and non-invariant point processes, we adapt these ideas to improve the exploration ability of the algorithm. In particular, we keep the ability of generating points with non-uniform distributions, and design an updating scheme that allows to generate points in some neighborhood of other points. We first design updating schemes under Green's framework to keep (.) reversibility of the Markov chain and then show that stability properties are not loosed. Using a drift condition we prove that the Markov chain is geometrically ergodic and Harris recurrent.We finally show on experimental results that these kinds of updates are usefull and propose other improvements.
Opt-in method is vital for data sharing (2016)

We agree with van Staa and colleagues on health data, that “The ultimate solution, however, must combine new technologies with clear accountability, transparent operations, and public trust.”1 One method to achieve the necessary confidence is to create an opt-in mechanism for the use of patient identifiable data.2

Building on the Scottish Health Informatics Programme (SHIP) governance mechanisms and …
IgG4-related Lung Disease in a Worker Occupationally Exposed to Asbestos (2010)

A case of IgG4-related lung disease in a worker who had been exposed to asbestos is described. The patient had nocturnal cough and wheeze that responded to inhaled corticosteroid, and the radioallergosorbent test was positive against common allergens, suggesting an association with atopic asthma. IgE elevation is reported in asbestos-exposed workers, and asbestos exposure may cause atopic conditions. Predominance of Th2 cytokines and up-regulation of regulatory T lymphocytes have been reported in IgG4-related disease. IgG4-related disease may occur from hypersensitivity of the regulatory immune system to atopic conditions. Asbestos exposure may be a causal factor of IgG4-related disease.
Characterization of Bax Pore Formation Using Fluorescence Techniques (2007)

Bax is a pro-apoptotic protein believed to permeabilize mitochondria during apoptosis. The mechanism Bax uses is not well understood. In this work, we use fluorescence techniques to shed light on how tBid activates Bax and we examine the topology of the pore-forming domain of Bax. The manner in which tBid promotes apoptosis via Bax activation is not known. Study of tBid and Bax interaction using a new FRET pair showed that the proteins only interacted in the presence ofmembranes. The Bax pore was shown to have a variable size distribution. A fluorescence technique of simultaneously measuring pore formation, Bax insertion and FRET showed that tBid interaction with Bax occurred before all the Bax inserted or formed pores in the liposomes. A chronological order is proposed for Bax pore formation. tBid first binds to liposomes. tBid proceeds to interact with Bax, and Bax inserts into the membrane. After insertion, Bax oligomerizes and forms small pores. More Bax is recruited and the pores become larger. The two central hairpin helices of Bax, helices 5 and 6, are known as the pore-forming domain. We used cysteine scanning with the environment sensitive fluoroprobe NBD to gain insight into the topology of these helices. Fluorescence intensity changes and emission blue shifts showed that residues in these helices undergo conformational reorganization during pore formation. In the activated oligomeric conformation, fluorescence lifetimes showed that helix 5 was more inaccessible to water than helix 6. Cobalt, a cationic NBD quencher, effectively quenched residues in the pore-forming domain, consistent with a pore that is lined with anionic lipid head groups. Quenching with nitroxide groups at various lipid depths showed that residues on helix 6 were most quenched by a shallow quencher, while residues on helix 5 were quenched by deeper quenchers. Compared to beta sheet pore-forming proteins, the data obtained suggests that Bax and possibly other alpha helical pore-forming proteins form a lipidic pore in a dynamic environment. Combined together, the data suggest a model for Bax in which helix 5 spans the bilayer, and helix 6 is buried just below the lipid headgroups of a toroidal pore.
Photochemistry of 4-isobutyl-4-methyl- and 4-(2-methoxyethyl)-4-methyl-2-cyclopentenone. Stereochemical effects in intramolecular abstraction of hydrogen by the .beta.-carbon atom of cyclopentenones (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemistry of 4-isobutyl-4-methyl- and 4-(2-methoxyethyl)-4-methyl-2-cyclopentenone. Stereochemical effects in intramolecular abstraction of hydrogen by the .beta.-carbon atom of cyclopentenonesSemiramis Ayral-Kaloustian, Steven Wolff, and William C. AgostaCite this: J. Am. Chem. Soc. 1977, 99, 18, 5984–5992Publication Date (Print):August 1, 1977Publication History Published online1 May 2002Published inissue 1 August 1977https://pubs.acs.org/doi/10.1021/ja00460a024https://doi.org/10.1021/ja00460a024research-articleACS PublicationsRequest reuse permissionsArticle Views132Altmetric-Citations15LEARN 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
Proteomics Profiling and Risk of New‐Onset Atrial Fibrillation: Framingham Heart Study (2019)

Background Prior studies relating proteomics markers to incident AF screened for limited numbers of proteins. Methods and Results We performed proteomics assays among participants from the Framingham Heart Study Offspring attending their fifth examination. Plasma protein levels (n=1373) were measured by the SOMAscan proteomic profiling platform. We used robust inference for the Cox proportional hazards model to relate each protein level with incident AF. In addition, we examined the association between AF-related genetic loci and levels of proteins associated with AF. Our study included 1885 participants (mean age 55±10 years, 54% women) who had proteomic profiles measured. A total of 349 participants developed AF during follow-up (mean follow-up 18.3 years). We observed that 8 proteins were significantly associated with incident AF after adjusting for age, sex, technical covariates, and correction for multiple testing ( P<0.05/1373=3.6×10<sup>-5</sup>). After additional adjustments for clinical factors associated with AF, ADAMTS13 and N-terminal pro-B-type natriuretic peptide remained significantly associated with the risk of incident AF (hazard ratio, 0.78; 95% CI, 0.70-0.88; and 1.44; 95% CI, 1.22-1.70, respectively; P<3.6×10<sup>-5</sup> for both). None of the 8 proteins were encoded by genes at AF-related genetic loci previously identified by genome-wide association studies. Conclusions We identified 8 proteins associated with risk of incident AF after adjustment for age and sex; 2 proteins were associated with AF after adjustment for AF risk factors. Future studies are needed to replicate our findings, identify whether the markers are mechanistically related to AF development, and whether they are clinically useful for identification of future AF risk.
Nitrogen and chlorine species in the spring Antarctic stratosphere: Comparison of models With Airborne Antarctic Ozone Experiment observations (1989)

The Atmospheric and Environmental Research, Inc., photochemical model has been used to simulate the concentrations and time development of key trace gases in the Antarctic stratosphere before, during, and after the Airborne Antarctic Ozone Experiment (AAOE). The model includes complete gas phase photochemistry and heterogeneous reactions of ClNO 3 (g) and N 2 O 5 (g) with HCl (s) and H 2 O (s). Observations of long‐lived species by the AAOE instruments have been used to constrain the initial conditions in our calculations. We present results from four cases illustrating the evolution of the trace gases for a range of possible initial conditions and duration of heterogeneous activity. The amount of ClO produced by heterogeneous conversion of HCl is determined not only by the initial concentrations of NO x (NO + NO 2 + NO 3 ), N 2 O 5 , and ClNO 3 during winter, but also by the rate at which NO x is resupplied by photolysis of N 2 O 5 and HNO 3 , or by transport. Results from the four cases presented bracket column measurements of HCl, ClNO 3 , and HNO 3 by the Jet Propulsion Laboratory and National Center for Atmospheric Research infrared spectrometers onboard the NASA DC‐8, and in situ measurements of ClO and NO y by instruments aboard the NASA ER‐2. Comparison of results and measurements of HCl and ClO suggests that heterogeneous chemistry was maintained throughout the month of September in 1987. We suggest field observations and kinetic data which would further constrain the photochemistry of the spring Antarctic stratosphere. The behavior of ozone is discussed in a companion paper (Ko et al., this issue).