Miracle-dz/UniFAR-FTUs huggingface dataset:
Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits

Mitochondrial dysfunction has been observed in skeletal muscle of people with diabetes and insulin-resistant individuals. Furthermore, inherited mutations in mitochondrial DNA can cause a rare form of diabetes. However, it is unclear whether mitochondrial dysfunction is a primary cause of the common form of diabetes. To date, common genetic variants robustly associated with type 2 diabetes (T2D) are not known to affect mitochondrial function. One possibility is that multiple mitochondrial genes contain modest genetic effects that collectively influence T2D risk. To test this hypothesis we developed a method named Meta-Analysis Gene-set Enrichment of variaNT Associations (MAGENTA; http://www.broadinstitute.org/mpg/magenta). MAGENTA, in analogy to Gene Set Enrichment Analysis, tests whether sets of functionally related genes are enriched for associations with a polygenic disease or trait. MAGENTA was specifically designed to exploit the statistical power of large genome-wide association (GWA) study meta-analyses whose individual genotypes are not available. This is achieved by combining variant association p-values into gene scores and then correcting for confounders, such as gene size, variant number, and linkage disequilibrium properties. Using simulations, we determined the range of parameters for which MAGENTA can detect associations likely missed by single-marker analysis. We verified MAGENTA's performance on empirical data by identifying known relevant pathways in lipid and lipoprotein GWA meta-analyses. We then tested our mitochondrial hypothesis by applying MAGENTA to three gene sets: nuclear regulators of mitochondrial genes, oxidative phosphorylation genes, and ∼1,000 nuclear-encoded mitochondrial genes. The analysis was performed using the most recent T2D GWA meta-analysis of 47,117 people and meta-analyses of seven diabetes-related glycemic traits (up to 46,186 non-diabetic individuals). This well-powered analysis found no significant enrichment of associations to T2D or any of the glycemic traits in any of the gene sets tested. These results suggest that common variants affecting nuclear-encoded mitochondrial genes have at most a small genetic contribution to T2D susceptibility.
Making Music Together: An Exploration of Amateur and Pro-Am Grime Music Production

This novel research presents the results of an ethnographic study, which focused upon the production of an EP created by an amateur and a pro-amateur producer. The research presents their production practices across the production workflow, from inception and ideation through to completion. The paper describes the distinct processes that occur when collaborating on the production of the EP. The exploration here discusses the use of software systems to facilitate production of a series of music tracks. We further explicate the use of technologies in the production settings, and these range from mobile devices (smartphones) through to digital audio workstations. Further to this, we start to map out how the technology used affords and supports collaboration and communication across a distributed context. We respond to our findings by presenting a series of design implications that address the research.
Malignant gastrointestinal stromal tumor: distribution, imaging features, and pattern of metastatic spread.

PURPOSE To investigate and describe the anatomic distribution, imaging features, and pattern of metastatic spread of malignant gastrointestinal stromal tumors (GISTs). MATERIALS AND METHODS The medical records of all patients at our institution with a histologic diagnosis of GIST were reviewed. Two radiologists with knowledge of the diagnosis reviewed the radiologic findings by means of consensus. Sixty-seven patients underwent computed tomography, and scans of the primary tumor were available in 38 patients. RESULTS One hundred sixteen patients with malignant GISTs were identified (76 men and 40 women; mean age, 54.6 years +/- 13.5 [SD]). The primary tumor locations in descending order of frequency were the small bowel (n = 49), stomach (n = 43), colon (n = 7), rectum (n = 6), other (n = 3), and not specified (n = 8). Mean primary tumor size was 13 cm +/- 6. Tumors were typically well defined (31 of 36 [86%]), with a heterogeneous rim of soft tissue with lower signal intensity than that of the contrast material-enhanced liver. Central fluid attenuation was seen in 24 of 36 (67%) patients. Metastases were seen in 23 of 38 (61%) patients at presentation and in 53 of 61 (87%) patients during follow-up. Spread was usually to the liver or peritoneum. Visceral obstruction rarely occurred, even in the presence of extensive peritoneal metastatic disease. Ascites was an unusual finding. CONCLUSION Malignant GISTs are typically large, well-circumscribed, heterogeneous, centrally necrotic tumors that arise in the wall of the small bowel or stomach. They rarely obstruct viscera, despite their large size and propensity to metastasize to the liver and peritoneum.
Comparison of Scheduling Algorithms for Domain Specific Web Crawler

Domain-specific Web crawlers are effective tools for acquiring information from the Web. One of the most crucial factors influencing the efficiency of domain crawlers is choice of crawling strategy. This article describes and compares several strategies for domain specific Web crawling. It concentrates particularly on scheduling algorithms which determine order of crawling URLs collected by the crawler. The objective of these strategies is to download the most relevant Web pages in an early stage of the crawl. In the paper there are presented four different algorithms which are compared using several metrics.
Cannabinoids with a Propyl Side Chain in Cannabis: Occurrence and Chromatographic Behavior

Neutral cannabinoids with a pentyl side chain—for example, cannabidiol, tetrahydrocannabinol, and cannabinol—are generally accompanied by homologs with a propyl side chain, of which at least one has psychotropic activity. Samples of hashish and marihuana from Asia especially sometimes have abundant amounts of propyl cannabinoids, the quantities being of the same order as that of the accompanying pentyl cannabinoids. Detection and identification of the propyl and pentyl cannabinoids in gas chromatography and thin-layer chromatography is discussed.
An improved algorithm for radio broadcast

We show that for every radio network <i>G</i> = (<i>V</i>, <i>E</i>) and source <i>s</i> ∈ <i>V</i>, there exists a radio broadcast schedule for <i>G</i> of length <i>Rad</i>(<i>G</i>, <i>s</i>) + <i>O</i>(&sqrt;<i>Rad</i>(<i>G</i>, <i>s</i>) ṡlog<sup>2</sup> <i>n</i>) = <i>O</i>(<i>Rad</i>(<i>G</i>, <i>s</i>) + log<sup>4</sup> <i>n</i>), where <i>Rad</i>(<i>G</i>, <i>s</i>) is the radius of the radio network <i>G</i> with respect to the source <i>s</i>. This result improves the previously best-known upper bound of <i>O</i>(<i>Rad</i>(<i>G</i>, <i>s</i>) + log<sup>5</sup> <i>n</i>) due to Gaber and Mansour [1995]. For graphs with small genus, particularly for <i>planar</i> graphs, we provide an even better upper bound of <i>Rad</i>(<i>G</i>, <i>S</i>) + <i>O</i>(&sqrt;<i>Rad</i>(<i>G</i>,<i>s</i>) ṡ log <i>n</i> + log<sup>3</sup> <i>n</i>) = <i>O</i>(<i>Rad</i>(<i>G</i>, <i>s</i>) + log<sup>3</sup> <i>n</i>).
A Neural Mechanism for Time-Window Separation Resolves Ambiguity of Adaptive Coding

The senses of animals are confronted with changing environments and different contexts. Neural adaptation is one important tool to adjust sensitivity to varying intensity ranges. For instance, in a quiet night outdoors, our hearing is more sensitive than when we are confronted with the plurality of sounds in a large city during the day. However, adaptation also removes available information on absolute sound levels and may thus cause ambiguity. Experimental data on the trade-off between benefits and loss through adaptation is scarce and very few mechanisms have been proposed to resolve it. We present an example where adaptation is beneficial for one task—namely, the reliable encoding of the pattern of an acoustic signal—but detrimental for another—the localization of the same acoustic stimulus. With a combination of neurophysiological data, modeling, and behavioral tests, we show that adaptation in the periphery of the auditory pathway of grasshoppers enables intensity-invariant coding of amplitude modulations, but at the same time, degrades information available for sound localization. We demonstrate how focusing the response of localization neurons to the onset of relevant signals separates processing of localization and pattern information temporally. In this way, the ambiguity of adaptive coding can be circumvented and both absolute and relative levels can be processed using the same set of peripheral neurons.
Methods for Domain-Independent Information Extraction from the Web: An Experimental Comparison

Our KNOWITALL system aims to automate the tedious process of extracting large collections of facts (e.g., names of scientists or politicians) from the Web in an autonomous, domain-independent, and scalable manner. In its first major run, KNOWITALL extracted over 50,000 facts with high precision, but suggested a challenge: How can we improve KNOWITALL's recall and extraction rate without sacrificing precision? This paper presents three distinct ways to address this challenge and evaluates their performance. Rule Learning learns domain-specific extraction rules. Subclass Extraction automatically identifies sub-classes in order to boost recall. List Extraction locates lists of class instances, learns a "wrapper" for each list, and extracts elements of each list. Since each method bootstraps from KNOWITALL's domain-independent methods, no hand-labeled training examples are required. Experiments show the relative coverage of each method and demonstrate their synergy. In concert, our methods gave KNOWITALL a 4-fold to 19-fold increase in recall, while maintaining high precision, and discovered 10,300 cities missing from the Tipster Gazetteer.
The Benefits, Costs, and Paradox of Revenge

In this article, we examine the psychology of revenge. We begin by discussing challenges associated with defining revenge. We then review the relative costs and benefits associated with taking revenge. Although revenge can deter future harm, promote cooperation, and restore avengers’ self-worth and power, it can also contribute to conflict escalation and adverse psychological outcomes for avengers, such as depression and reduced life satisfaction. Next, we examine the prevalence of revenge. In distinguishing between the desire for revenge and act of revenge, we challenge the notion that the act of revenge is an automatic or pervasive response to injustice. We highlight four factors that influence whether victims of injustice choose to take revenge: the persistence of anger, perceptions of the costs of revenge, cultural and religious values regarding revenge, and the presence of external systems that can restore justice on behalf of victims. ‘‘Prompted to my revenge by heaven and hell’’ ‐ Hamlet Act 2, Scene 2
Piezo1 and Piezo2 Are Essential Components of Distinct Mechanically Activated Cation Channels

Mechanical Responders Identified Although many cells appear to respond to mechanical stimulation through increased conductance of ion channels in the plasma membrane, the actual channels that mediate these effects—which are important in diverse processes from hearing and touch to control of blood pressure—have remained elusive. Coste et al. (p. 55, published online 2 September) used RNA interference to decrease expression of candidate genes systematically in a mouse neuroblastoma cell line and identified two genes that encode proteins, Piezo1 and Piezo2, which are required for mechanically stimulated cation conductance in these cells and in cultured dorsal root ganglion neurons. Similar proteins are expressed in a range of species from protozoa to vertebrates. The proteins are not similar to known pore-forming proteins and thus could be unusual channels or regulatory components of a channel complex. Cation channel genes encode for a transducer molecule that converts mechanical stimuli into cell signaling. Mechanical stimuli drive many physiological processes, including touch and pain sensation, hearing, and blood pressure regulation. Mechanically activated (MA) cation channel activities have been recorded in many cells, but the responsible molecules have not been identified. We characterized a rapidly adapting MA current in a mouse neuroblastoma cell line. Expression profiling and RNA interference knockdown of candidate genes identified Piezo1 (Fam38A) to be required for MA currents in these cells. Piezo1 and related Piezo2 (Fam38B) are vertebrate multipass transmembrane proteins with homologs in invertebrates, plants, and protozoa. Overexpression of mouse Piezo1 or Piezo2 induced two kinetically distinct MA currents. Piezos are expressed in several tissues, and knockdown of Piezo2 in dorsal root ganglia neurons specifically reduced rapidly adapting MA currents. We propose that Piezos are components of MA cation channels.
The design and implementation of scalable information services in a grid environment

This paper proposes an Extensible Monitoring and Discovery Service for grid environment MASSIVE (MEMDS). The MASSIVE project focuses on developing a multidisciplinary applications-oriented simulation and visualization environment. In the MEMDS, appropriate mechanisms make custom information services established and deployed easily, and the developed APIs simplify the access to the MDS and provide a uniform interface for programmers. Corresponding practices show that the MEMDS improves the extensibility and flexibility of the grid information service.
Autoimmunity and pulmonary hypertension: a perspective

The association between autoimmunity and pulmonary arterial hypertension (PAH) has been appreciated for >40 yrs, but how autoimmune injury might contribute to the pathogenesis of this disease has only been examined in a case-specific manner. It is becoming increasingly clear that a variety of diverse clinical diseases, ranging from viral infections to connective tissue disorders, can culminate in pulmonary vascular pathology that is indistinguishable. Is there a hitherto unappreciated biology that unites these seemingly unrelated conditions? The answer to this question may come from the increasing body of evidence concerned with the central importance of regulatory T-cells in preventing inappropriate B-cell activity. Two striking similarities between conditions associated with severe angioproliferative pulmonary hypertension are a defect in the CD4 T-cell compartment and auto-antibody production. Pathogenic auto-antibodies targeting endothelial cells are capable of inducing vascular endothelial apoptosis and may initiate the development of PAH. The present review will focus on what is known about autoimmune phenomena in pulmonary arterial hypertension patients, in order to better consider whether an early loss of self-tolerance followed by autoimmune injury could influence the early development of severe angioproliferative pulmonary hypertension.
Selective plating of nickel ceramic composite films for MEMS applications

A simple, selective and CMOS-compatible deposition method for nickel ceramic composite films has been demonstrated. Using an electroless plating technique, two types of nickel ceramic composite thin films, nickel-cordierite and nickel-iron (II, III) oxide, have been successfully deposited and characterized on silicon substrates. The incorporation of an appropriate amount of cordierite particles into a nickel matrix is shown to significantly reduce the thermal expansion mismatch between nickel and silicon, yet maintain the Young's modulus, Berkovich hardness and electrical resistivity at approximately 167 GPa, 7.6 GPa and 9.4 /spl mu//spl Omega/-cm, respectively, values which correspond closely to electroless nickel. On the other hand, the addition of iron (II, III) oxide instead of cordierite can also increase the coercivity of electroless nickel up to 170 Oe, thereby significantly enhancing its ferromagnetic properties.
Aldosterone Nongenomically Produces NADPH Oxidase–Dependent Reactive Oxygen Species and Induces Myocyte Apoptosis

The roles of aldosterone in the progression of heart failure have not been fully elucidated. This study examined whether aldosterone nongenomically activates reactive oxygen species (ROS) production, causing myocyte apoptosis. Addition of aldosterone to neonatal rat cardiac myocytes caused the activation of NADPH oxidase and intracellular ROS production in a dose-dependent manner (10−9−10−7 mol/L). NADPH oxidase activation was evident as soon as 5 min after aldosterone treatment. Neither an inhibitor for nuclear transcription (actinomycin D) nor an inhibitor of new protein synthesis (cycloheximide) blocked this rapid activation, and specific binding of aldosterone to plasma membrane fraction was inhibited by eplerenone, suggesting a nongenomic mechanism. Aldosterone did not affect the mRNA or protein levels of NOX2, which is a major subunit of NADPH oxidase in myocytes, after 48 h. Nuclear staining with DAPI showed that aldosterone (10−7 mol/L) increased the myocyte apoptosis (2.3 fold, p<0.001), coincident with the activation of caspase-3 (1.4 fold, p<0.05), compared with the serum-deprived control after 48 h. Aldosterone also induced phosphorylation of apoptosis signal–regulating kinase 1 (ASK1). These effects of aldosterone on myocyte ROS accumulation, ASK1 activation, and apoptosis were abolished by eplerenone, a mineralocorticoid receptor (MR) antagonist, apocynin, an inhibitor of NADPH oxidase activation, and tempol, a free radical scavenger, but by neither RU486, a glucocorticoid receptor antagonist, nor butylated hydroxyanisol (BHA), a mitochondrial ROS scavenger. In conclusion, aldosterone-mediated ROS production is blocked by eplerenone and induced by the nongenomic activation of NADPH oxidase, leading to myocyte apoptosis associated with ASK1 activation. These proapoptotic actions of aldosterone may play a role in the progression of heart failure.
Spatiotemporal mining in microblogs

Recently, microblogging services are getting increasing attention from the research community. A main cause of this trend is their inherent spatial and temporal information, which can find several uses, such as identifying local trends and events, detecting emergency situations, predicting and monitoring natural phenomena, etc. The growing demand of location based services for the purpose of user profiling, marketing, advertising and recommending, adds even more applications to this movement. In this survey we group microblog spatiotemporal mining into three main categories: i) user location estimation, ii) topic, event, and trend detection, and iii) correlation between topics and locations. The state of the art approaches for those problems span the fields of natural language processing, information retrieval, machine learning, text mining and database management. We present and analyze several of those techniques, in order to gain a better understanding of their underlying mechanisms.
Driver’s mental workload assessment using EEG data in a dual task paradigm

The integration of physiological monitoring into the human-machine interface holds great promise both for real-time assessment of operator status and for providing a mean to allocate tasks between machines and humans based on the operator status. Our group, aiming to provide a new human-machine interface to improve traffic safety using brain signals, has conducted a number of researches for the driver states monitoring based on EEG data in recent years. This article presents our study for the representation of mental workload using EEG data. A simulated driving task - the Lane Change Task (LCT), combined with a secondary auditory task - the Paced Auditory Addition Serial Task (PASAT), was adopted to simulate the situation of in-vehicle conversations. Participants were requested to perform the lane change task under three task conditions - primary LCT, LCT with a slow PASAT and LCT with a fast PASAT. The EEG recordings combined with performance data from LCT and PASAT provided plenty information for comprehensive understanding of driver's workload. The analysis of event-related potentials (ERP) revealed that LCT evoked cognitive responses, such as P2, N2, P3b, CNV, and the amplitudes of P3b decreased with the task load. A crucial benefit of these findings is that the increase or decrease of amplitudes of ERP components can be directly used for representing driver's mental workload. The full text of this paper may be found at: http://www-nrd.nhtsa. dot.gov/pdf/esv/esv21/09-0250.pdf For the covering abstract see ITRD E145407.
Directed Feedback Vertex Set Problem is FPT

To decide if the parameterized feedback vertex set problem in directed graph is fixed-parameter tractable is a long standing open problem. In this paper, we prove that the parameterized feed- back vertex set in directed graph is fixed-parameter tractable and give the first FPT algorithm of running time O((1.48k) k n O(1) ) for it. As the feedback arc set problem in directed graph can be transformed to a feedback vertex set problem in directed graph, hence we also show that the parameterized feedback arc set problem can be solved in
Prevalence and risk factors for transmission of infection among children in household contact with adults having pulmonary tuberculosis

Aims: To study the prevalence of tuberculosis infection among children in household contact with adults having pulmonary tuberculosis, and identify the possible risk factors. Methods: Children under the age of 5 years who were in household contact with 200 consecutive adults with pulmonary tuberculosis underwent tuberculin skin testing. Transverse induration of greater than 10 mm was defined as positive tuberculin test suggestive of tubercular infection. Infected children underwent chest radiography and analysis of gastric lavage fluid or induced sputum for detection of acid fast bacilli. Results: Tuberculin test was positive in 95 of 281 contacts (33.8%), of which 65 were contacts of sputum positive patients, while 30 were contacts of sputum negative patients. Nine of these children were diagnosed as having tuberculosis based on clinical features and/or recovery of acid fast bacilli; seven were in contact with sputum positive adults. The important risk factors for transmission of infection were younger age, severe malnutrition, absence of BCG vaccination, contact with an adult who was sputum positive, and exposure to environmental tobacco smoke. Conclusion: The prevalence of tuberculosis infection and clinical disease among children in household contact with adult patients is higher than in the general population, and risk is significantly increased by contact with sputum positive adults.