jimnoneill/paper-to-field-training huggingface dataset:
Alternative Ways to Die5Epac1 deletion prevents cardiomyocyte apoptosis during ischemia/reperfusion6Subcellular redistribution of mitogen and stress activated kinase 1 (MSK1) contributes to protection against oxidative stress- induced apoptosis in cardiac myocytes7Excessive ROS production in mitochondria switches off protective mitochondrial kinase signaling

&lt;b&gt;Introduction:&lt;/b&gt; Early coronary reperfusion has been established as the best therapeutic strategy to limit infarct size and improve prognosis. Therefore, elucidating the mechanisms underlying cardiomyocyte death may yield novel therapeutic targets to limit ischemia reperfusion (I/R) injury. I/R is accompanied and influenced by perturbations of the β-adrenergic receptor pathway which acts through cAMP dependent signaling cascade to modulate cardiac function and remodeling. &lt;b&gt;Purpose:&lt;/b&gt; Although the involvement of the cAMP-binding protein Epac1 in cardiac hypertrophy and arrhythmia has been recently described, its role in I/R induced-cardiomyocyte death has not yet been investigated. &lt;b&gt;Methods:&lt;/b&gt; Isolated adult cardiomyocytes from Epac1 knock-out (Epac1-/-) mice or wild-type (WT) littermates were exposed to hypoxia (HX) for 4h and 2h of reoxygenation period (HX+R). Cell death was determined by Trypan blue staining and LDH release. The mitochondrial permeability transition pore (mPTP) opening was monitored by the calcein loading CoCl(2)-quenching technique. The area at risk was examined by Evans blue and infarct size was evaluated by TTC staining. &lt;b&gt;Results:&lt;/b&gt; Our data showed that HX+R-induced cardiomyocyte death were significantly prevented in adult cardiomyocytes isolated from Epac1-/- mice. In addition, we found that the increased expression of apoptotic markers (Bax, cleaved Caspase-9,Caspase-3) during HX+R conditions were also inhibited in Epac1-/- cardiomyocytes compared to WT cells. Interestingly, HX+R induced a decrease in calcein fluorescence corresponding to mPTP opening (56%±1.1 vs control cells set at 100%) in WT cardiomyocytes while genetic deletion of Epac1 prevented mPTP opening in HX+R conditions. Concomitantly, we found that the infarct size was significantly reduced in the Epac1-/- mice compared to the WT animals (53±4 % vs 33±4%, p&lt;0.01) despite the same area at risk. &lt;b&gt;Conclusion:&lt;/b&gt; Epac1 deletion confers resistance to I/R injury via the inhibition of a mitochondrial death signaling. Our study shed light the therapeutic potential of the inhibition of Epac1 and, the development of Epac1 inhibitors as new drugs to treat I/R injury.

Topic: Cardiac Ischemia and Reperfusion
Subfield: Pathology and Forensic Medicine
Field: Medicine
Domain: Health Sciences
Effects of a synthetic precocene on late embryos and subsequent development of the cockroach <i>Diploptera punctata</i>

Precocene III (PIII, 7-ethoxy-precocene II), dissolved in acetone, was applied to eggs in the brood sac of Diploptera punctata females, at 55–56 days or 62–63 days (about 83.5 ± 1.0% or 95.5 ± 1.0% of the gestation period, respectively) after the mother's ecdysis to adult. Controls received acetone alone or no treatment. Acetone itself induced abortion in many instances and reduced the number of surviving progeny from those females that did give birth. These lethal effects were more pronounced after PIII treatment. A portion of the surviving nymphs that had been treated as eggs with PIII developed normally up to the fourth stadium, although the duration of this development, especially that of the first stadium, was longer than in the controls. In contrast, another portion of the nymphs that had hatched from precocene-treated eggs exhibited disturbed development. Treatment of the eggs in 55- to 56-day-old mothers with the highest dose still permitting hatching (40 μg of PIII in 2 μL of acetone, into the brood sac) yielded the highest proportion of disturbed development. In almost all instances of such disturbed development, the moult from the second to the third stadium was greatly delayed and the insects died in or shortly after an unsuccessful ecdysis, some of them exhibiting slightly prothetelic wings. No sign of precocious metamorphosis was observed in the first or second stadium. These results are compared with those in the literature on the effects of surgical allatectomy of the second and later instars of D. punctata. The morphogenetic role of the juvenile hormone in the early part of postembryonic development is also discussed.

Topic: Insect and Arachnid Ecology and Behavior
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Copy number variation detection workflow using next generation sequencing data

In the last decade, discovery of copy number variations (CNVs) have dramatically changed our understanding of differences between individuals. CNVs include both additional copies of sequence (duplications) and loss of genetic material (deletions) and provide an alternate paradigm for the genetic basis of human diseases. Genome-wide CNV detection is now possible using high-throughput, low-cost next generation sequencing (NGS) methods. Nature of NGS data demands various preprocessing and pretreatment steps before extracting any meaningful information. Among the plethora of variant calling methods available, R-based methods offer flexible environment, facilitating choice of various methods depending on the type of data or type of analysis to be performed. Here we give a pipeline for various steps involved in CNV detection in NGS data using R-based algorithms and packages.

Topic: Genomic variations and chromosomal abnormalities
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Seymour Fractures: A Retrospective Review of Infection Rates, Treatment and Timing of Antibiotic Administration.

Early administration of antibiotics within 24 hours of injury is associated with a reduction in the development of infections. Patients with delayed antibiotic administration may be at high risk for early superficial infection or osteomyelitis. This study highlights the importance of early identification and appropriate treatment of Seymour fractures including the prompt administration of antibiotics following injury.

Topic: Hermeneutics and Narrative Identity
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
Enhancing Positioning of Photovoltaic Panels Using 3D Geographic Information

As the national mapping agency of Great Britain, Ordnance Survey (OS) is looking to launch a new generation of 3D products over the next few years and are keen to test and validate the value of 3D models, in particular with photovoltaic (PV) suitability assessments (Ordnance Survey 2012). Current desktop methods to assess a property for PV suitability are crude, unreliable and mostly two-dimensional. The argument presented in this paper concerns the capacity of 3D geographic information (GI) to enhance the desktop evaluation assessment of property suitability for photovoltaic panels. Qualitative interviews were used to gather data on potential users, forming a specification of their needs which consequently framed the development of a prototype solar panel positioning tool. The resulting tool presented an alternative, robust and 3D method of assessing a property for PV suitability, demonstrating the analytical potential of OS 3D data. This study offers an unconventional approach to PV analysis which could be incorporated into a wider renewable technology suitability assessment toolkit. This paper presents the results from the interviews and the prototype solar panel positioning tool.

Topic: 3D Modeling in Geospatial Applications
Subfield: Building and Construction
Field: Engineering
Domain: Physical Sciences
Statins and risk of decompensation in hepatitis B virus–related and hepatitis C virus–related cirrhosis: Methodological issues

Potential conflict of interest: Nothing to report. TO THE EDITOR: We read the article by Chang et al.,1 in which the authors used a nationwide database and reported that statin use is associated with lower decompensation rates in both hepatitis B virus–related and hepatitis C virus–related cirrhosis. Their findings support the use of statins in the prevention of decompensation in patients with cirrhosis. However, several methodological issues need to be clarified before extrapolating their results to patients with hepatitis B virus–related or hepatitis C virus–related cirrhosis. First, the authors adopted the method of new user design in their work and arbitrarily defined the date of first statin prescription as the index date for the statin users. In contrast, statin nonusers were followed up from the date of cirrhosis diagnosis. Although this approach can avoid misclassified immortal time, excluded immortal time may introduce selection bias (another form of immortal time bias).2 It has been shown that results can be biased toward a protective effect of treatment by either misclassified immortal time or excluded immortal time.3 They also did not report the mean interval between the date of diagnosis of cirrhosis and the date of first statin prescription, which would influence the magnitude of bias. Second, hepatotoxicity is a concern in the prescription of statins in patients with chronic liver disease. In real‐world practice, many physicians are reluctant to initiate statins in patients with an out‐of‐range liver enzyme value.4 Statin users in this study may just represent groups with better liver function reserve and slower progression of fibrosis compared to statin nonusers. Although propensity score matching was used to minimized confounding by indication of statin and the authors included 14 covariates in their logistic regression model to calculate propensity scores, some of the confounding mentioned above may still exist between statin users and nonusers due to a lack of important laboratory data such as liver enzyme and bilirubin levels in their database. We agree that statin use may be beneficial in patients with liver cirrhosis; however, the results of this study may amplify the advantage of these drugs due to selection bias and incomplete control over the confounding factors between statin users and nonusers.

Topic: Liver Disease Diagnosis and Treatment
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
Processing and Recognition of Facial Affect in Schizophrenia

A deficit in the recognition of facial affect has been well documented in people with schizophrenia. Our 1995 research with normal subjects showed that hemispheric bias for processing facial affect is related to accuracy of recognition of facial affect. We tested whether this relationship holds in a sample of 25 people with schizophrenia who completed tasks of identification of facial affect and chimeric facial affect. Subjects with a left visual-field bias were significantly more accurate in identifying one facial emotion (sad) than were other subjects. Individual differences in hemispheric advantage for processing affect appears to be an important variable related to functional br capacity within different populations.

Topic: Face Recognition and Perception
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
A new chlorobenzoate derivative from the red alga <i>Solieria</i> sp.

A new chlorobenzoate derivative, solieriate (<b>1</b>), together with six known compounds (<b>2-7</b>), were isolated from the red alga <i>Solieria</i> sp. The structures of <b>1-7</b> were determined by comprehensive spectroscopic methods and X-ray diffraction analysis. Compound <b>1</b> is the first example of halogenated derivative isolated from this genus. In addition, <b>1</b> exhibited moderate antibacterial activity on <i>A. baumannii</i> with MIC value of 64 μg/ml.

Topic: Seaweed-derived Bioactive Compounds
Subfield: Aquatic Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Establishment of an integrated clinical network and comprehensive data warehouse for the conduct of comparative effectiveness research in COPD

Background: Chronic obstructive pulmonary disease (COPD) affects many millions worldwide and is increasing in incidence, morbidity, and mortality. Efficacy trials can guide COPD care, but an infrastructure for comparative effectiveness research (CER) across diverse settings are needed to more fully evaluate commonly used therapies in clinical practice. Methods: We created an inter-disciplinary and multi-institutional network for CER named COPD Outcomes-based Network for Clinical Effectiveness and Research Translation (CONCERT). We developed a platform for comprehensive interoperable clinical data upload and synthesis across diverse outpatient and hospital practice settings to create a comprehensive COPD data warehouse (COPD DataHub) and have begun populating it thru inclusion pathways designed to maximize identification of COPD patients from 2006 through 2008. Results: The COPD DataHub was designed to be flexible to incorporate data from seven varied health care settings including university-affiliated medical centers, a community medical center, a health maintenance organization and a government-operated veteran medical center. It includes a total of 146,240 unique patients, 58.3% female at non-veteran sites, whites 68.4%, blacks 14.3% and other races 17.3%, average patient age 61.8 years (S.D. 13.5). Conclusions: We demonstrated the feasibility of developing a rich CER data repository by linking COPD patients across diverse health care settings. CONCERT has successfully created a multi-institutional platform to pursue observational CER studies and identify patients with COPD for enrollment into prospective pragmatic clinical trials.

Topic: Chronic Obstructive Pulmonary Disease (COPD) Research
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
A Microfluidic Model of Microbubble Lodging in Small Arteriole Bifurcations

Lodging of cardiovascular gas bubbles is investigated in a microfluidic model of small arteriole bifurcations. This work is motivated by a novel gas embolotherapy technique for the potential treatment of cancer by tumor infarction and by air embolism. The experimental model arteriole bifurcations were constructed from a transparent elastomer, poly(dimethylsiloxane), using soft lithography. A single air bubble was suspended in water within the parent tube of the bifurcation and a specified driving pressure was imposed via constant elevation reservoirs that were open to atmospheric pressure. The driving pressure and bubble size were varied, and their effects on the bubble lodging were assessed. These findings may be useful in developing strategies for microbubble delivery in gas embolotherapy.

Topic: Ultrasound and Hyperthermia Applications
Subfield: Biomedical Engineering
Field: Engineering
Domain: Physical Sciences
PENGARUH KONSENTRASI EKSTRAK DAUN KELOR (Moringa oleifera L.) TERHADAP MORTALITAS Sitophilus zeamais Motsch.

Corn is the strategic commodity in Indonesia. The quality of many domestic corn does not meet feed factory standards. High yield losses icause of damage due to warehouse pests. Sitophilus zeamais Motsch or powder beetle is a warehouse pest that causes seeds to become hollow, break quickly and disintegrate into flour. Sitophilus zeamais Motsch pest control still relies on synthetic pesticides. The use of synthetic pesticides will cause various negative impacts such as pest resistance, residue, resurgencies, high costs and environmental pollution. One alternative for controlling Sitophilus zeamais Motsch is to use natural ingredients, namely Moringa. Moringa leaves contain phenol, hydroquinone, flavonoids, steroids, triterpenoids, tannins, alkaloids and saponins. The experiment began by drying 10 grams of Moringa leaves. then puree using a blender and continue with maceration. 200, 400, 600, 800, and 1000 mg of Moringa leaf powder were dissolved in 1 L of distilled water solution and left for 24 hours. After 24 hours, the solution was filtered 3 times so that all the substances contained in the Moringa leaves are extracted. The insecticide was tested by observing the number of S. zeamais pests that died when given Moringa leaf extract. The mortality data that was obtained was analyzed using ANOVA, if there was a real effect then continued using the 5% DMRT test. Determination of LC50 using a probit test. Moringa extract can function as a vegetable insecticide for S.zeamais. The higher concentration of Moringa leaf extract can increase the mortality of S.zeamais

Topic: Moringa oleifera research and applications
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Asymptomatic Demyelinated Plaque

A clinically silent multiple sclerosis (MS) plaque in the midcervical spinal cord was found unexpectedly at autopsy in a 66-year-old man who died of bronchogenic carcinoma. The patient's history revealed a transient episode of neurological symptoms compatible with an attack of MS more than 30 years prior to death, with no appreciable residual deficits. The discrete anatomical location of this plaque with well-preserved axons emphasizes that the retention of functional integrity of demyelinated axons may be an important factor underlying the poor clinicopathologic correlation in MS.

Topic: Peripheral Neuropathies and Disorders
Subfield: Neurology
Field: Medicine
Domain: Health Sciences
The Formulation of the Declaration of Rights

After a period of comparative neglect, historians are re-examining the English Revolution of 1688 with revived interest and revised interpretation. In the past few decades numerous works have carefully re-investigated and often reinterpreted the roles played by such disparate groups as the Whigs, die nobility, the common people, and die urban mob, as well as by such leading individuals as die Earl of Sunderland, James II, and William of Orange. They have broadened our perspective of the Revolution by placing it in die wider context of European affairs and have persuasively demonstrated that die replacement of James II by William and Mary was justified most frequently and effectively not by John Locke's Two Treatises of Government , which was indeed composed prior to 1688, but by mat old relic from James I's reign, divine right of kings.

Topic: American Constitutional Law and Politics
Subfield: Political Science and International Relations
Field: Social Sciences
Domain: Social Sciences
The nuclear sulfenome of Arabidopsis: spotlight on histone acetyltransferase GCN5 regulation through functional thiols

Abstract In aerobic life forms, reactive oxygen species (ROS) are produced by the partial reduction of oxygen during energy-generating metabolic processes. In plants, ROS production increases during periods of both abiotic and biotic stress, severely overloading the antioxidant systems. Hydrogen peroxide (H2O2) plays a central role in cellular redox homeostasis and signalling by oxidizing crucial cysteines to sulfenic acid, which is considered a biologically relevant post-translational modification (PTM). Until now, the impact of the nucleus on cellular redox homeostasis has been relatively unexplored. The regulation of histone-modifying enzymes by oxidative PTMs at redox-sensitive cysteine or tyrosine residues is particularly intriguing because it allows the integration of redox signalling mechanisms with chromatin control of transcriptional activity. One of the most extensively studied histone acetyltransferases is the conserved GENERAL CONTROL NONDEPRESSIBLE 5 (GCN5) complex. This study investigated the nuclear sulfenome in Arabidopsis thaliana by expressing a nuclear variant of the Yeast Activation Protein-1 (YAP1) probe and identified 225 potential redox-active proteins undergoing S-sulfenylation. Mass spectrometry analysis further confirmed the S-sulfenylation of GCN5 at Cys293, Cys368, and Cys400, and their functional significance and impact on the GCN5 protein–protein interaction network were assessed using cysteine-to-serine mutagenesis.

Topic: Redox biology and oxidative stress
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Defluorinative functionalization of perfluoroalkyl alkenes with ureas: synthesis of <i>C</i>4-perfluoroalkenyl 2-imidazolones

A defluorinative 1,2,3,4-tetrafunctionalization of perfluoroalkyl alkenes with readily available ureas via multi-bond interconversion at four carbon sites has been developed for the synthesis of perfluoroalkenyl 2-imidazolones.

Topic: Fluorine in Organic Chemistry
Subfield: Pharmaceutical Science
Field: Pharmacology, Toxicology and Pharmaceutics
Domain: Life Sciences
EFFICACY OF THREE MERIDIAN FORMULATIONS AGAINST JAPANESE BEETLE, 2001

This trial was conducted on a lawn at Campbell's Scottish Highlands Golf Course, Salem, NH.Test plots were 49 ft 2 , replicated five times, in an RCB design.All treatments were applied 18 Jul.The dry granular treatment was applied using large saltshakers.Liquid treatments were applied using a 7-ft boom on a twowheel bicycle-type sprayer, equipped with four 8005 nozzles, fitted with 50-mesh screens.The volume of water and insecticide mix was 2 gal/1,000ft 2 , delivered with CO 2 at 40psi.All treatments were hand watered to approximately 1/4 inch; the lawn was mowed every 3 days at 7/8 inch.There was no precipitation 24 h before or after application.Weather conditions at time of application were as follows: sky, cloudy; wind, less than 5 mph; air temperature, 64.4°F.Soil composition and conditions were as follows: texture, sandy loam; sand, 62%; silt, 31%; clay, 7%; pH, 6.6; organic matter, 7.6%; thatch depth, 0.38 inch; soil moisture, 18.4%; soil surface temperature, 71.6°F; at 1-inch depth, 70.5°F; at 2-inch depth, 69.3°F.The trial was rated for live grubs, 1-ft 2 section per plot, on 19 Sep.A Ryan sod cutter was used to cut the sod 12 inches wide and 2 inches deep.All grubs were identified to species; only JB grubs (the predominant species) were analyzed.

Topic: Hemiptera Insect Studies
Subfield: Ecology, Evolution, Behavior and Systematics
Field: Agricultural and Biological Sciences
Domain: Life Sciences
The evolution of CD4+ T cell cytometry in perspective: challenges for resource poor settings.

CD4+ T cell cytometry antedated the Human Immunodeficiency Virus (HIV) epidemic. However it was in the wake of the HIV scourge that CD4+ T cell counting technology gradually evolved from a pure cellular research assay technique into a routine clinical diagnostic test. In the more than two and half decades of the HIV/AIDS pandemic, this cell based diagnostic test has undergone several phases of technological improvements in the efforts to produce cheaper and more robust equipment for the monitoring of patients. The evolution however, is still very much in progress. Resource poor countries that remain the worst hit by the scourge of HIV/AIDS are paradoxically usually the last to benefit from the impact of the technological advancements in CD4+ T cell cytometry. This review highlights the progress and the scientific milestones so far attained in the development of improved techniques for CD4+ T cells count as a major cornerstone of patient care, as well as the emerging future directions in the evolution of this important cellular diagnostic test. Some of the challenges for developing economies are highlighted.

Topic: HIV Research and Treatment
Subfield: Virology
Field: Immunology and Microbiology
Domain: Life Sciences