Miracle-dz/UniFAR-FTUs huggingface dataset:
Ischemic Preconditioning Confers Epigenetic Repression of Mtor and Induction of Autophagy Through G9a‐Dependent H3K9 Dimethylation

Background Ischemic preconditioning (IPC) protects the heart from prolonged ischemic insult and reperfusion injury through a poorly understood mechanism. Post‐translational modifications of histone residues can confer rapid and drastic switches in gene expression in response to various stimuli, including ischemia. The aim of this study was to investigate the effect of histone methylation in the response to cardiac ischemic preconditioning. Methods and Results We used cardiac biopsies from mice subjected to IPC to quantify global levels of 3 of the most well‐studied histone methylation marks (H3K9me2, H3K27me3, and H3K4me3) with Western blot and found that H3K9me2 levels were significantly increased in the area at risk compared to remote myocardium. In order to assess which genes were affected by the increase in H3K9me2 levels, we performed ChIP‐Seq and transcriptome profiling using microarray. Two hundred thirty‐seven genes were both transcriptionally repressed and enriched in H3K9me2 in the area at risk of IPC mice. Of these, Mtor (Mechanistic target of rapamycin) was chosen for mechanistic studies. Knockdown of the major H3K9 methyltransferase G9a resulted in a significant decrease in H3K9me2 levels across Mtor, increased Mtor expression, as well as decreased autophagic activity in response to rapamycin and serum starvation. Conclusions IPC confers an increase of H3K9me2 levels throughout the Mtor gene—a master regulator of cellular metabolism and a key player in the cardioprotective effect of IPC—leading to transcriptional repression via the methyltransferase G9a. The results of this study indicate that G9a has an important role in regulating cardiac autophagy and the cardioprotective effect of IPC.
Effect of cardiac resynchronization therapy on global and regional oxygen consumption and myocardial blood flow in patients with non-ischaemic and ischaemic cardiomyopathy.

AIMS We studied the effects of cardiac resynchronization therapy (CRT) on global and regional myocardial oxygen consumption (MVO2) and myocardial blood flow (MBF) in non-ischaemic (NICM) and ischaemic dilated cardiomyopathy (ICM). METHODS AND RESULTS Thirty-one NICM and 11 ICM patients, all of them acute responders, were investigated. MVO2 and MBF were obtained by 11C-acetate PET before and after 4 months of CRT. In NICM global MVO2 and MBF did not change during CRT, while the rate pressure product (RPP) normalized MVO2 increased (P=0.03). Before CRT regional MVO2 and MBF were highest in the lateral wall and lowest in the septum. Under therapy, MVO2 and MBF decreased in the lateral wall (P=0.045) and increased in the septum (P=0.045) resulting in a more uniform distribution. In ICM, global MVO2, MBF, and RPP did not change under CRT. Regional MVO2 and MBF showed no significant changes but a similar tendency in the lateral and septal wall to that in NICM. CONCLUSION CRT induces changes of MVO2 and MBF on a regional level with a more uniform distribution between the myocardial walls and improved ventricular efficiency in NICM. Based on the investigated parameters, CRT appears to be more effective in NICM than in ICM.
Support for the Innuitian Ice Sheet in the Canadian High Arctic during the Last Glacial Maximum

The extent of glacier ice in the Canadian High Arctic during the Last Glacial Maximum (LGM) has been debated for decades. One school proposed a regional Innuitian Ice Sheet whereas another proposed a smaller, non-contiguous Franklin Ice Complex. Research throughout western Nares Strait supports coalescent Innuitian and Greenland ice during the LGM, based on widespread glacial and marine deposits dated by 14C and amino acid analyses. This coalescence likely promoted a vigorous regional ice flow westward across Ellesmere Island to Eureka Sound. Post-glacial emergence in Eureka Sound suggests a former ice thickness at least as great as that in Nares Strait (≥ 1 km). Recently, independent field studies elsewhere in the High Arctic also support an Innuitian Ice Sheet during the LGM. Collectively, these studies resolve a long-standing debate, and initiate new opportunities concerning the reconstruction of high-latitude palaeoenvironmental and palaeoclimatic change. © 1998 John Wiley & Sons, Ltd.
Oil and water? High performance garbage collection in Java with MMTk

Increasingly popular languages such as Java and C# require efficient garbage collection. This paper presents the design, implementation, and evaluation of MMTk, a Memory Management Toolkit for and in Java. MMTk is an efficient, composable, extensible, and portable framework for building garbage collectors. MMTk uses design patterns and compiler cooperation to combine modularity and efficiency. The resulting system is more robust, easier to maintain, and has fewer defects than monolithic collectors. Experimental comparisons with monolithic Java and C implementations reveal MMTk has significant performance advantages as well. Performance critical system software typically uses monolithic C at the expense of flexibility. Our results refute common wisdom that only this approach attains efficiency, and suggest that performance critical software can embrace modular design and high-level languages.
Sparse LU factorization for parallel circuit simulation on GPU

Sparse solver has become the bottleneck of SPICE simulators. There has been few work on GPU-based sparse solver because of the high data-dependency. The strong data-dependency determines that parallel sparse LU factorization runs efficiently on shared-memory computing devices. But the number of CPU cores sharing the same memory is often limited. The state of the art Graphic Processing Units (GPU) naturally have numerous cores sharing the device memory, and provide a possible solution to the problem. In this paper, we propose a GPU-based sparse LU solver for circuit simulation. We optimize the work partitioning, the number of active thread groups, and the memory access pattern, based on GPU architecture. On matrices whose factorization involves many floating-point operations, our GPU-based sparse LU factorization achieves 7.90× speedup over 1-core CPU and 1.49× speedup over 8-core CPU. We also analyze the scalability of parallel sparse LU factorization and investigate the specifications on CPUs and GPUs that most influence the performance.
Identity of Two Sympatric Species of Orius (Hemiptera: Heteroptera: Anthocoridae)

Abstract The minute pirate bugs, Orius insidiosus (Say) and Orius pumilio (Champion) (Hemiptera: Heteroptera: Anthocoridae), are closely related species known to be sympatric in north Florida. Here, male and female genitalia, DNA sequences, and the effects of within- and between-species pairings on egg production and egg development were examined to develop a better understanding of the relationship between these two species. Interspecific matings between the two species did not result in viable progeny. Although there were gross similarities in the morphology of the male parameres (external genitalia) between the two species, the cone in O. pumilio was much broader with a greater spiral twist and the flagellum was longer than in O. insidiosus. Correspondingly, there were differences in the morphology of the copulatory tubes of the females of the two species. In O. insidiosus, the organ was somewhat longer than in O. pumilio and oriented parallel to the abdominal midline, while the copulatory tube in O. pumilio tilted slightly towards the midline. Additionally, the copulatory tube for O. pumilio included a sclerotized basal mound that was not present in O. insidiosus. These morphological differences suggest that successful copulation between these species could be difficult. In contrast to conspecific matings, interspecific matings resulted in few or no eggs laid over a period of two weeks and no viable progeny. Comparison of the 18S ribosomal gene ITS-1 sequences between the two species demonstrated only 91% homology. When yolk protein contents were examined to determine whether reproductive physiology had shifted to full egg production, interspecifically mated females contained amounts of yolk protein comparable to that in fed, but unmated females; this was less than 10% of the yolk protein previously found in fed and conspecifically mated females. These findings together confirm that O. insidiosus and O. pumilio are indeed two separate species.
Comparison of Earthquake Scaling Relations Derived from Data of the Instrumental and Preinstrumental Era

Estimates of surface rupture displacement and magnitude for crustal earthquakes from the preinstrumental era (pre-1900) tend to be greater than the corresponding estimates derived from modern scaling relations. We investigate this tendency using an expanded and updated version of the earthquake dataset of Wells and Coppersmith (1994) to fit regression relations of moment magnitude on surface rupture length and rupture area and average surface displacement on surface rupture length. Separate relations are fitted to preinstrumental and instrumental data and the results compared to the equivalent relations of Wells and Coppersmith. We find that our relations for instrumental data remove some, but not all, of the differences between the preinstrumental data and the relations of Wells and Coppersmith. We attribute the remaining differences largely to natural censoring of surface displacements less than about 1 m and surface rupture lengths less than about 5 km from the dataset for the preinstrumental era because regressions constructed from similarly censored instrumental data are indistinguishable from the preinstrumental regressions. Since the regressions for our censored instrumental data (i.e., restricted to moderate to large earthquakes) are different from regressions for our complete dataset of instrumental earthquakes and from the regressions of Wells and Coppersmith (both with a larger proportion of small-to-moderate earthquakes), the results may indicate that large earthquakes have different scaling relationships from those of smaller earthquakes.
Involvement of cathepsin B in the processing and secretion of interleukin‐1β in chromogranin A‐stimulated microglia

Cathepsin B (CB) is a cysteine lysosomal protease implicated in a number of inflammatory diseases. Although it is now evident that caspase‐1, an essential enzyme for maturation of interleukin‐1β (IL‐1β), can be activated through the inflammasome, there is still evidence suggesting the existence of lysosomal‐proinflammatory caspase pathways. In the present study, a marked induction of pro‐IL‐1β, its processing to the mature form and secretion were observed in the primary cultured microglia prepared from wild‐type mice after stimulation with chromogranin A (CGA). Although pro‐IL‐1β also markedly increased in microglia prepared from CB‐deficient mice, CB‐deficiency abrogated the pro‐IL‐1β processing. CA‐074Me, a specific inhibitor for CB, inhibited the pro‐IL‐1β maturation and its release from microglia. Furthermore, the caspase‐1 activation was also inhibited by CA‐074Me and E‐64d, a broad cysteine protease inhibitor. After treatment with CGA, CB was markedly induced at both protein and mRNA levels. The induced pro‐CB was rapidly processed to its mature form. The immunoreactivity for CB co‐localized with both that for caspase‐1 and the cleaved IL‐1β, in the acidic enlarged lysosomes. Inconsistent with these in vitro observations, the immunoreactivity for the cleaved IL‐1β was markedly observed in microglia of the hippocampus from aged wild‐type but not CB‐deficient mice. These observations strongly suggest that CB plays a key role in the pro‐IL‐1β maturationthrough the caspase‐1 activation in enlarged lysosomes ofCGA‐treated microglia. Therefore, either pharmacological or genetic inhibition of CB may provide therapeutic intervention in inflammation‐associated neurological diseases. © 2009 Wiley‐Liss, Inc.
The Effect of Visual Distinctiveness on Multiple Object Tracking Performance

Observers often need to attentively track moving objects. In everyday life, such objects are often visually distinctive. Previous studies have shown that tracking accuracy is increased when the targets contain a visual feature (e.g., a color) not possessed by the distractors. Conversely, a gain in tracking accuracy was not observed when the targets differed from the distractors by only a conjunction of features (Makovski and Jiang, 2009a). In this study we confirm that some conjunction targets have relatively little effect on tracking accuracy, but show that other conjunction targets can significantly aid tracking. For example, tracking accuracy is relatively high when the targets are small red squares and half the distractors are large red squares while the remaining distractors are small green squares. This seems to occur because the targets have a set of features (small and red) not shared by any one distractor. Attending to these features directs attention more to the targets than the distractors, thereby making the targets easier to track. Existing theories of attentive tracking cannot explain these results.
Oseltamivir (Tamiflu) Is a Substrate of Peptide Transporter 1

Oseltamivir, an ester-type prodrug of the neuraminidase inhibitor [3R,4R,5S]-4-acetamido-5-amino-3-(1-ethylpropoxy)-1-cyclohexene-1-carboxylate phosphate (Ro 64-0802), has been developed for the treatment of A and B strains of the influenza virus but has neuropsychiatric and other side effects. In this study, we characterized the transport across intestinal epithelial cells and the absorption of oseltamivir in rats. Uptake by Caco-2 cells (human carcinoma cell line) and HeLa cells transfected with peptide transporter 1 (HeLa/PEPT1) was time- and temperature-dependent and was inhibited by typical PEPT1 inhibitors such as glycyl-sarcosine (Gly-Sar). The uptake by Caco-2 cells and HeLa/PEPT1 was saturable, with similar Km values. Oseltamivir absorption in adult rats was greatly reduced by simultaneous administration of milk, casein, or Gly-Sar. Furthermore, the plasma and brain concentrations of oseltamivir were higher in fasting than in nonfasting rats after oral administration. These results suggest that oseltamivir is a substrate of PEPT1 and that PEPT1 is involved in its intestinal absorption.
Quantifying the Contributions to Dairy Farm Business Risk: Implications for Producer's Risk Management Strategies

The major sources of variability in net farm income on New York dairy farms over the past 10 years are identified using Dairy Farm Business Summary records. The most important source of income variability is the fluctuation in milk prices, followed closely by year-to-year variation in the quantity of purchased feeds. These results suggest that forward pricing of milk and feed purchases may be effective risk reduction strategies. Since a few farms have large cull cow sales, probably due to disease or other production problems, new insurance products to insure against disease may be useful to dairy farmers. It appears that older farmers are more successful in engaging in activities that increase diversification and reduce the variability in reductions in farm income. The same is true for farmers who utilize milking parlors, use recombinant bovine somatotropin, have greater assets per cow, and have engaged in activities to earn income from off-farm sources.
Precipitation Source Inferred from Stable Isotopic Composition of Pleistocene Groundwater and Carbonate Deposits in the Western Desert of Egypt

An Atlantic source of precipitation can be inferred from stable isotopic data (H and O) for fossil groundwaters and uranium-series-dated carbonate spring deposits from oases in the Western Desert of Egypt. In the context of available stable isotopic data for fossil groundwaters throughout North Africa, the observed isotopic depletions (δD −72 to −81‰; δ18O −10.6 to −11.5‰) of fossil (≥32,000 yr B.P.) groundwaters from the Nubian aquifer are best explained by progressive condensation of water vapor from paleowesterly wet oceanic air masses that traveled across North Africa and operated at least as far back as 450,000 yr before the present. The values of δ18O (17.1 to 25.9‰) for 45,000- to >450,000-yr-old tufas and vein-filling calcite deposits from the Kharga and Farafra Oases are consistent with deposition from groundwaters having oxygen isotopic compositions similar to those of fossil groundwaters sampled recently at these locations.
Semantic Relations for Interpreting Dna Microarray Data

The results from microarray experiments, in the form of lists of over-and under-expressed genes, have great potential to support progress in biomedical research. However, results are not easy to interpret. Information about the function of the genes and their relation to other genes is needed, and this information is usually present in vast amounts of biomedical literature. Considerable effort is required to find, read and extract relevant information from the literature. A potential solution is to use computerized text analysis methods to extract relevant information. Our proposal enhances current methods in this regard and uses semantic relations extracted from biomedical text with the SemRep information extraction system. We describe an application that integrates microarray results with semantic relations and discuss its benefits in supporting enhanced access to the relevant literature for interpretation of results. Introduction With the decoding of the human genome and other eukaryotic organisms, molecular biology has entered a new era. High-throughput technologies, such as genomic microarrays can be used to measure the expression levels of essentially all the genes within an entire genome scale simultaneously in a single experiment and can provide information on gene functions and transcriptional networks [1]. However, the successful interpretation of this information for integration into research underpinning biomedical progress is impossible without comparison to the published literature. The exponential growth of the life sciences literature makes it difficult even for experts to absorb all the relevant knowledge in their field of interest. Sophisticated technologies are needed for effective data acquisition. Automatic text mining techniques are increasingly used to help assimilate online textual resources; however, current approaches, based on term co-occurrence in text, do not provide an adequately expressive representation of content to satisfy the needs of biologists in elucidating microarray data. In this paper we propose the use of semantic relations (or predications) for interpreting and exploiting microarray data. We suggest that semantic relations are able to convert textual content into structured information amenable to further computation and that such " executable knowledge " underpins the ability to quickly provide valuable information while interpreting microarray results, such as current knowledge about the disease of interest, genes known to be involved in the etiology of the disease, as well as their relationships (ASSOCIATED_WITH, PREDISPOSES or CAUSES). In addition, information can be determined about the relation between the information determined from the microarray and that in the research literature. We describe the use of …
Exploring defect data from development and customer usage on software modules over multiple releases

Traditional defect analyses of software modules have focused on either identifying error prone modules or predicting the number of faults in a module, based on a set of module attributes such as complexity, lines of code, etc. In contrast to these metrics based modeling studies, the paper explores the relationship of the number of faults per module to the prior history of the module. Specifically, we examine the relationship between: (a) the faults discovered during development of a product release and those escaped to the field; and (b) faults in the current release and faults in previous releases. Based on the actual data from four releases of a commercial application product consisting of several thousand modules, we show that: modules with more defects in development have a higher probability of failure in the field; there is a way to assess the relative quality of software releases without detailed information on the exact release content or code size; and it is sufficient to consider just the previous release for predicting the number of defects during development or field. These results can be used to improve the prediction of quality at the module level of future releases based on the past history.
A delay-based approach using fuzzy logic to improve TCP error detection in ad hoc networks

In recent years, a great deal of effort has been devoted to make the TCP protocol more resilient to the random packet losses inherent in the wireless channels in ad hoc networks. In this paper, we investigate the use of fuzzy logic theory for assisting the TCP error detection mechanism in such networks. An elementary fuzzy logic engine is presented as an intelligent technique for discriminating packet loss due to congestion from packet loss by wireless induced errors. The architecture of the proposed fuzzy-based error detection mechanism is also introduced and discussed. The full approach, for inferring the internal state of the network, relies on round trip time (RTT) measurements only. Hence, this is an end-to-end scheme which requires only end nodes cooperation. Preliminary simulation evaluations show how viable this approach may be.
Fat Absorption Studies in the Diagnosis and Treatment of Pancreatic Fibrosis

The presence of steatorrhoea in pancreatic fibrosis was formerly the cause of its confusion with coeliac disease. This confusion was dispelled by the studies of Blackfan and Wolbach (1933) and of Andersen (1938) who clearly separated pancreatic fibrosis as a separate entity by showing that in this disease there was atrophy of the secretory tissue of the pancreas and that the steatorrhoea resulted from deficiency in pancreatic lipase. Andersen (1945) claimed that, although analysis of single stools or three-day stool collections generally revealed a great increase of faecal fat in pancreatic fibrosis, this was not always found. In the light of recent work, however (Kamer, Bokkel Huinink and Weyers, 1949), it would appear that fat balance studies are necessary for a reliable assessment of fat absorption. In the treatment of pancreatic fibrosis Andersen (1949) stressed the importance of maintaining satisfactory nutrition and claimed that the respiratory involvement, which is such a common feature of this disease, might be secondary to impaired absorption of some substance essential for the normal functioning of the bronchi. The value of pancreatin in improving absorption of food substances in pancreatic fibrosis has been studied by various workers. Shohl, May and Shwachman (1943) found that although pancreatin resulted in a reduction of faecal nitrogen there was no significant decrease in faecal fat, whereas Andersen (1945) using a pancreatin preparation of higher lipase content than that employed by Shohl et al. showed that it produced a considerable decrease in faecal fat. May and Lowe (1949), however, have questioned the usefulness of pancreatin in the treatment of this disease. The object of the present study was to ascertain the magnitude of the fat absorption defect in pancreatic fibrosis by means of fat-balance studies and chylomicrographs, and to compare the findings with those obtained in coeliac disease. From the fat absorption findings in pancreatic fibrosis an attempt was made to estimate the value of pancreatin in treatment and to place dosage on a rational basis.