gebhart/patrepeval huggingface dataset:
Porcine Encephalomyocarditis Virus Persists in Pig Myocardium and Infects Human Myocardial Cells (2001)

Recent advances toward using pig tissues in human transplantation have made it necessary to determine the risk of transmitting zoonotic viruses from pigs to humans or vice versa. We investigated the suitability of the porcine encephalomyocarditis virus (EMCV) model for such studies by determining its ability to persist in pigs, escape detection by routine serological methods, and infect human cells. Intraperitoneal inoculation of 5-week-old pigs with EMCV-30, a strain isolated from commercial pigs, resulted in acute cellular degeneration, infiltration of lymphocytes, and apoptosis in myocardium in 13 of 15 (86.7%) pigs during the acute phase of disease (3 to 21 days postinfection), followed by less-severe lymphocytic infiltration and apoptosis in 5 of 10 (50%) pigs during the chronic phase of the disease (day 45 to 90 postinfection). In the brain, lymphocytic infiltration, neuronal degeneration, and gliosis were observed in 26 to 33% of pigs in the acute phase of disease whereas perivascular cuffing was the predominant feature during chronic disease. EMCV antigens and RNA were demonstrated in the myocardium and brain during the chronic phase of disease. Analysis of 100 commercial pigs that were negative for EMCV antibodies identified two pig hearts positive for EMCV RNA. Porcine EMCV productively infected primary human cardiomyocytes as demonstrated by immunostaining using a monoclonal antibody specific for EMCV RNA polymerase, which is expressed only in productively infected cells, and by a one-step growth curve that showed production of 100 to 1,000 PFU of virus per cell within 6 h. The findings that porcine EMCV can persist in pig myocardium and can infect human myocardial cells make it an important infectious agent to screen for in pig-to-human cardiac transplants and a good model for xenozoonosis.
Elucidating the Mechanism of Action of the Immunosuppressant 15-Deoxyspergualin (1995)

15-Deoxyspergualin (DSG) is an immunosuppressive agent currently in Phase I/II clinical trials. We have previously shown that DSG specifically interacts with Hsc70, a member of the heat shock protein 70 family. In this article we show that DSG appears to bind either kinetically or to a different site on Hsc70 from that of peptides. In addition, we show that DSG inhibits the localization of Hsp70 into the nucleus in response to heat shock. Finally, data are presented showing that there is a correlation between decreases in the transcription factor nuclear factor kappa B and kappa light chain expression in response to varying doses of DSG.
Poster discussion session report (1998)

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Use Case API - design pattern for shared data (2018)

The paper explores aspect of exposing data for public usage from technical point of view. The main aim of this paper is to consider and propose the way of exposing read-only APIs, where state management is minor or no issue, but in the same case, domain complexity can reach high levels. In the paper, the authors propose complete approach to the process of API exposing, from use-case definition and description, to usage of proposed architectural design pattern for read-only API exposure. The paper encompasses the following aspects which were taken into account in proposed design pattern: API usability, developer experience, unit and integration testing, architecture constraints. Moreover, the authors summarize the paper and outline directions for further work.
ResourceExchange: Latency-Aware Scheduling in Virtualized Environments with High Performance Fabrics (2011)

Virtualized infrastructures have seen strong acceptance in data center systems and applications, but have not yet seen adoptance for latency-sensitive codes which require I/O to arrive predictability, or response times to be generated within certain timeliness guarantees. Examples of such applications include certain classes of parallel HPC codes, server systems performing phonecall or multimedia delivery, or financial services in electronic trading platforms, like ICE and CME. In this paper, we argue that the use of high-performance, VMM-bypass capable devices can help create the virtualized infrastructures needed for the latency-sensitive applications listed above. However, to enable consolidation, problems to be solved go beyond efficient I/O virtualization, and include dealing with the shared use of I/O and compute resource, in ways that minimize or eliminate interference. Toward this end, we describe ResEx -- a resource management approach for virtualized RDMA-based platforms which incorporates concepts from supply-demand theory and congestion pricing to dynamically control the allocation of CPU and I/O resources of guest VMs. ResEx and its mechanisms and abstractions allow multiple 'pricing policies' to be deployed on these types of virtualized platforms, including such which reduce interference and enhance isolation by identifying and taxing VMs responsible for resource congestion. While the main ideas behind ResEx are more general, the design presented in this paper is specific for InfiniBand RDMA-based virtualized platforms due to the use of asynchronous monitoring needed to determine the VMs' I/O usage, and the methods to establish the trading rate for the underlying CPU and I/O resources. The latter is particularly necessary since the hypervisor's only mechanism to control I/O usage is by making appropriate adjustments in the VM's CPU resources. The experimental evaluation of our solution uses InfiniBand platforms virtualized with the open source Xen hyper visor, and an RDMA-based latency-sensitive benchmark, BenchEx, based on a model of a financial trading platform. The results demonstrate the utility of the ResEx approach in making RDMA-based virtualized platforms more manageable and better suited for hosting even latency-sensitive workloads. ResEx can reduce the latency interference by as much as 30% in some cases as shown.
Superresolution vibrational imaging by simultaneous detection of Raman and hyper-Raman scattering (2011)

We have developed a superresolution vibrational imaging method by simultaneous detection of Raman and hyper-Raman scattering. Raman and hyper-Raman images obtained with the same laser spot carry independent information on the sample spatial distribution, owing to different signal dependence (linear in Raman and quadratic in hyper-Raman) on the incident light intensity. This information can be quantitatively analyzed to recover the incident light intensity distribution at the focal plane. A superresolution vibrational image is then derived by the constrained deconvolution of the images by the obtained incident light intensity distribution. This method has been applied to a TiO₂ nanostructure and the obtained superresolution image was compared with a scanning electron microscopy image. The spatial resolution achieved by the present method is evaluated to be 160 nm, which is more than twice better than the diffraction limited resolution.
Automating Abstract Syntax Tree Construction for Context Free Grammars (2012)

In most of the compilers or programming languages tools, parsers are used for transforming human readable code into Parse Trees or Abstract Syntax Trees (AST). A popular method to create parsers is to use a parser generator. Advanced parser generators (e.g. ANTLR, SDF) are able to generate directly ASTs if the grammar is annotated with AST generation rules. These annotations are typically done manually, by adding to each grammar rule a constructor and associating an AST component to each constructor. This might be inconvenient for people with little experience in writing grammars or for those who already have a grammar for their language. In this paper, we present a generic method for inferring such AST generation rules and a tool which automatically generates the annotated grammar. Assuming you have a grammar for a language, some input programs and their corresponding ASTs, the tool will infer the rules for constructing the AST. If the input programs cover the whole range of the language syntax constructs then the parser corresponding to the generated annotated grammar is able to parse and transform into an AST any program of the given language.
Characterization of a lung epithelium specific E-cadherin knock-out model: Implications for obstructive lung pathology (2018)

The airway epithelium regulates responses to aeroallergens, acting as a physical and immunological barrier. In asthma, epithelial barrier function and the expression of adherens junction protein E-cadherin is compromised, but it is unknown whether this is cause or consequence of the disease. We hypothesized that airway epithelial loss of E-cadherin is a critical step in the development of manifestations of asthma. We generated a transgenic mouse model with conditional loss of E-cadherin in lung epithelial cells at birth and onwards. We observed normal lung development at the time of birth in mice lacking E-cadherin in the lung epithelium. However, E-cadherin deficiency led to progressive epithelial damage in mice growing into adulthood, as evidenced by airway epithelial denudation, decreased zonula occludens (ZO)-1 expression, loss of ciliated cells, and enlarged alveolar spaces. In addition, spontaneous goblet cell metaplasia with mucus production was observed. These epithelial changes were accompanied by elevated levels of the epithelial-derived chemokine CCL17, infiltration of eosinophils and dendritic cells, and mucus production. In conclusion, loss of E-cadherin induces features in the lung reminiscent of those observed in asthma, indicating that the disruption of E-cadherin-mediated cell-cell contacts may play a key role in the development of asthma manifestations.
Antibodies for all: The case for genome‐wide affinity reagents (2012)

For more than 30 years, the production of research antibodies has been dominated by hybridoma technologies, while modern recombinant technologies have lagged behind. Here I discuss why this situation must change if we are to generate reliable, comprehensive reagent sets on a genome-wide scale, and I describe how a cultural shift in the research community could revolutionize and modernize the affinity reagent field. In turn, such a revolution would pay huge dividends by closing the gap between basic research and therapeutic development, thus enabling the development of myriad new therapies for unmet medical needs.
A corpus-based approach for automated LOINC mapping (2013)

This study showed that a rich corpus of local terms mapped to LOINC contains collective knowledge that can help map terms from other institutions. Using freely available software tools, we developed a data-driven automated approach that operates on term descriptions from existing mappings in the corpus. Accurate and efficient automated mapping methods can help to accelerate adoption of vocabulary standards and promote widespread health information exchange.
Irreversible inhibition of aspartate aminotransferase by 2-amino-3-butenoic acid (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIrreversible inhibition of aspartate aminotransferase by 2-amino-3-butenoic acidRobert R. RandoCite this: Biochemistry 1974, 13, 19, 3859–3863Publication Date (Print):September 1, 1974Publication History Published online1 May 2002Published inissue 1 September 1974https://pubs.acs.org/doi/10.1021/bi00716a006https://doi.org/10.1021/bi00716a006research-articleACS PublicationsRequest reuse permissionsArticle Views350Altmetric-Citations76LEARN 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
Evaluation of thymosin α 1 in nonclinical models of the immune-suppressing indications melanoma and sepsis (2015)

All three models demonstrated a benefit after treatment with Ta1, with no evidence of toxicity. These initial pilot studies support the hypothesis that immune-suppressive indications, including sepsis and melanoma, may be treated with Ta1 alone or by Ta1 in combination with other immunotherapies.
The stringdist Package for Approximate String Matching (2014)

Comparing text strings in terms of distance functions is a common and fundamental task in many statistical text-processing applications. Thus far, string distance functionality has been somewhat scattered around R and its extension packages, leaving users with inconistent interfaces and encoding handling. The stringdist package was designed to offer a low-level interface to several popular string distance algorithms which have been re-implemented in C for this purpose. The package offers distances based on counting q-grams, edit-based distances, and some lesser known heuristic distance functions. Based on this functionality, the package also offers inexact matching equivalents of R's native exact matching functions match and %in%.
Abstract 2757: NT5C2 single nucleotide polymorphisms affects survival and response in <i>de novo</i> AML patients with normal karyotype (2010)

Abstract The nucleoside analog cytosine arabinoside (Cytosar®, AraC) is one of the corner stones in the treatment of acute myeloid leukemia (AML). Activated AraC is metabolized to inactive compounds by several intracellular enzymes. The levels of some of these enzymes have been correlated to effect of AraC and clinical outcome in patients with AML. This study was designed to evaluate if single nucleotide polymorphisms (SNPs) in genes coding for enzymes involved in the inactivation of AraC affects the therapeutic response in AML-patients treated with AraC in combination with anthracyclines. Three SNPs were investigated in 96 de novo AML patients with normal karyotype and correlated to response and overall survival. Two SNPs were located in the cytidine deaminase gene (CDA, A79C, rs2072671 and C-451T, rs532545), deaminating and inactivating AraC to its corresponding uridine derivative, AraU. The third SNP (A7G, rs10883841) was in the NT5C2 gene coding for the cytosolic 5′-nucleotidase II (cN-II), responsible for dephosphorylation and hence inactivation of AraC monophosphate. All SNPs were in Hardy-Weinberg equilibrium and the allele frequencies were 34.4, 34.4 and 18.8% for CDA A79C and C-451T, and NT5C2 A7G, respectively. Patients that were wild type (A/A) for NT5C2 A7G were found to have a borderline significant higher response rate (51 complete responders of 60 patients with A/A vs 20 complete responders of 30 with A/G or G/G, p=0.06) and longer survival (median survival 1.66 years compared to 0.87 years, log-rank p=0.08) compared to the rest of the patients. The two CDA SNPs (A79C, C-451T) were found to be in linkage disequilibrium. Although statistically not significant, patients that were found to be homozygous for the alternate genetic variant of the CDA SNP had a shorter survival compared to patients carrying the wild type or heterozygous genetic variants. In conclusion, our findings suggest that certain NT5C2 (cN-II) genotypes might affect the survival after chemotherapy and may provide useful information for treatment strategies, classification and individualized chemotherapy, and eventually used as prognostic marker. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2757.
Graphical Models and Exponential Families (2013)

We provide a classification of graphical models according to their representation as subfamilies of exponential families. Undirected graphical models with no hidden variables are linear exponential families (LEFs), directed acyclic graphical models and chain graphs with no hidden variables, including Bayesian networks with several families of local distributions, are curved exponential families (CEFs) and graphical models with hidden variables are stratified exponential families (SEFs). An SEF is a finite union of CEFs satisfying a frontier condition. In addition, we illustrate how one can automatically generate independence and non-independence constraints on the distributions over the observable variables implied by a Bayesian network with hidden variables. The relevance of these results for model selection is examined.
Ethylenation of secondary and tertiary alkyllithiums. I. Conditions and limits of the reaction (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEthylenation of secondary and tertiary alkyllithiums. I. Conditions and limits of the reactionPaul D. Bartlett, Stephen J. Tauber, and William P. WeberCite this: J. Am. Chem. Soc. 1969, 91, 23, 6362–6366Publication Date (Print):November 1, 1969Publication History Published online1 May 2002Published inissue 1 November 1969https://pubs.acs.org/doi/10.1021/ja01051a030https://doi.org/10.1021/ja01051a030research-articleACS PublicationsRequest reuse permissionsArticle Views326Altmetric-Citations67LEARN 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
The effects of baseline heart rate recovery normality and exercise training protocol on heart rate recovery in patients with heart failure (2014)

HRR1 did not improve after training. HRR2 improved only in the IT group. Both HRRs in patients with abnormal baseline values improved after both exercise protocols. IT might be superior to CT in improving HRR2. Baseline HRR might play a role in its response to exercise.
The remarkable basicity of 1,8-bis(dimethylamino)naphthalene (1968)

R. W. Alder, P. S. Bowman, W. R. S. Steele and D. R. Winterman, Chem. Commun. (London), 1968, 723 DOI: 10.1039/C19680000723
Detecting stop consonants in continuous speech (2002)

The problem of implementing a detector for stop consonants in continuously spoken speech is considered. The problem is posed as one of finding an optimal filter (linear or nonlinear) that operates on a particular appropriately chosen representation, and ideally outputs a 1 when a stop occurs and 0 otherwise. The performance of several variants of a canonical stop detector is discussed and its implications for human and machine speech recognition is considered.
Nonlinear Attosecond Metrology by Intense Isolated Attosecond Pulses (2015)

For the future progress of nonlinear attosecond science, one of the most important issues is the development of high-energy isolated attosecond pulse sources. In this paper, we review our research on the energy-scaling method for isolated attosecond pulse generation, which combines infrared two-color gating and an energy-scaling method of high-order harmonic generation. By establishing the robust energy-scaling method, the maximum pulse energy of the isolated attosecond pulse reaches 1.3 μJ/pulse in the XUV region, which is almost 100-fold higher than the values ever reported before. The pulse duration of this isolated attosecond pulse is directly measured to be 500 as by the autocorrelation method using the nonlinear interaction of N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> . This nonlinear experiment clearly shows that our developed isolated attosecond pulse has enough pulse energy to make a breakthrough for nonlinear attosecond metrology as well as for attosecond-pump/attosecond-probe experiments investigating electronic processes. In addition, we further extend the high-energy harmonic continuum by using the infrared two-color gating method up to the soft-x-ray region. With the aim to temporally characterize an isolated attosecond pulse in the soft-x-ray region, we demonstrate the first observation of above-threshold ionization of He with two-photon absorption of multiple higher harmonics in the soft-x-ray region.
A Note on an Adaptive Hypersphere Decision Boundary (1966)

Supplementing earlier papers, this note treats two topics: nonsupervised adaptation to the optimum hypersphere for normal distributions, and supervised estimation of the shape parameter m for Pearson probability distributions.
MicroRNA-221-3p Regulates Angiopoietin-Like 8 (ANGPTL8) Expression in Adipocytes (2017)

The inflammation-induced miR-221-3p regulates ANGPTL8 expression in adipocytes. This miRNA impact may become especially prominent under pathologic conditions such as morbid obesity, putatively contributing to the impaired AT lipid metabolism in metabolic disease.
THE EFFECTS OF DIETARY ELECTROLYTE BALANCE ON THE PERFORMANCE AND SPECIFIC BLOOD PARAMETERS OF GROWING PIGS (2001)

D×Y×L cross breed pigs weighing about 20kg were fed a basic diet with 6 levels of electrolyte balance(EB) (50,150,200,250,300,and 400meq/kg,respectively) under an environment at 34.6℃ or 28.4℃ air temperatures.The blood K+ of Na+ concentration,diarrhea rate or performance of pigs were not affected by dietary EB levels,but water consumption significantly increased when dietary BE was higher than 300meq/kg(P≤0.01).The pig's blood HCO3- concentration (P≤0.05),base excess(P≤0.01),and pH(P≤0.01) increased linearly (R2=0.89～0.94) or quadratically (R2=0.95～0.98) to the peak when dietary EB changing from 50 to 300meq/kg,after that there was no significantly change observed(P0.1).Serum urea nitrogen and blood CO2 pressure decreased quadratically (R2=0.89～0.93) or triply (R2=0.96～1.00) to the valley bottoms when dietary EB changing from 50 to 300meq/kg(P≤0.1),after that they tended to increase.It was concluded that at high ambient temperature,there was no effect of dietary EB levels on the blood K+ or Na+ concentration or performance of growing pigs.But blood acid-base status and nitrogen metabolism was significantly affected by dietary EB levels.The blood buffering capacity and nitrogen deposition of growing pigs were superior,when the dietary EB was about 300meq/kg.
The Syntheses of Carbamates from Reactions of Primary and Secondary Aliphatic Amines with Dimethyl Carbonate in Ionic Liquids. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.