Miracle-dz/UniFAR-FTUs huggingface dataset:
Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

Generating the raw data for a de novo genome assembly project for a target eukaryotic species is relatively easy. This democratization of access to large-scale data has allowed many research teams to plan to assemble the genomes of non-model organisms. These new genome targets are very different from the traditional, inbred, laboratory-reared model organisms. They are often small, and cannot be isolated free of their environment – whether ingested food, the surrounding host organism of parasites, or commensal and symbiotic organisms attached to or within the individuals sampled. Preparation of pure DNA originating from a single species can be technically impossible, but assembly of mixed-organism DNA can be difficult, as most genome assemblers perform poorly when faced with multiple genomes in different stoichiometries. This class of problem is common in metagenomic datasets that deliberately try to capture all the genomes present in an environment, but replicon assembly is not often the goal of such programs. Here we present an approach to extracting, from mixed DNA sequence data, subsets that correspond to single species’ genomes and thus improving genome assembly. We use both numerical (proportion of GC bases and read coverage) and biological (best-matching sequence in annotated databases) indicators to aid partitioning of draft assembly contigs, and the reads that contribute to those contigs, into distinct bins that can then be subjected to rigorous, optimized assembly, through the use of taxon-annotated GC-coverage plots (TAGC plots). We also present Blobsplorer, a tool that aids exploration and selection of subsets from TAGC-annotated data. Partitioning the data in this way can rescue poorly assembled genomes, and reveal unexpected symbionts and commensals in eukaryotic genome projects. The TAGC plot pipeline script is available from https://github.com/blaxterlab/blobology, and the Blobsplorer tool from https://github.com/mojones/Blobsplorer.
Domain Analysis and Domain Knowledge : Generation , Representation , and Implementation

Domain analysis is the inference of knowledge, termed domain knowledge, which is implicit in the description of planning problems. For many planning techniques, the use of domain knowledge yields substantial improvements of performance. This paper is concerned with domain analysis in three different ways. Firstly, we propose the domain knowledge exchange language DKEL as a mean to represent domain knowledge and to connect different planning techniques. We then present path reduction, a domain analysis technique, and lastly, we describe a novel approach to implement domain analysis techniques and demonstrate it by its use for path re-
Sodium overload due to a persistent current that attenuates the arrhythmogenic potential of a novel LQT3 mutation

Long QT syndrome (LQTS) is a congenital abnormality of cardiac repolarization that manifests as a prolonged QT interval on 12-lead electrocardiograms (ECGs). The syndrome may lead to syncope and sudden death from ventricular tachyarrhythmias known as torsades de pointes. An increased persistent Na+ current is known to cause a Ca2+ overload in case of ischemia for example. Such increased Na+ persistent current is also usually associated to the LQT3 syndrome. The purpose of this study was to investigate the pathological consequences of a novel mutation in a family affected by LQTS. The impact of biophysical defects on cellular homeostasis are also investigated. Genomic DNA was extracted from blood samples, and a combination of PCR and DNA sequencing of several LQTS-linked genes was used to identify mutations. The mutation was reproduced in vitro and was characterized using the patch clamp technique and in silico quantitative analysis. A novel mutation (Q1476R) was identified on the SCN5A gene encoding the cardiac Na+ channel. Cells expressing the Q1476R mutation exhibited biophysical alterations, including a shift of SS inactivation and a significant increase in the persistent Na+ current. The in silico analysis confirmed the arrhythmogenic character of the Q1476R mutation. It further revealed that the increase in persistent Na+ current causes a frequency-dependent Na+ overload in cardiomyocytes co-expressing WT and mutant Nav1.5 channels that, in turn, exerts a moderating effect on the lengthening of the action potential (AP) duration caused by the mutation. The Q1476R mutation in SCN5A results in a three-fold increase in the window current and a persistent inward Na+ current. These biophysical defects may expose the carrier of the mutation to arrhythmias that occur preferentially in the patient at rest or during tachycardia. However, the Na+ overload counterbalances the gain-of-function of the mutation and is beneficial in that it prevents severe arrhythmias at intermediate heart rates.
Use of colonoscopy to screen asymptomatic adults for colorectal cancer. Veterans Affairs Cooperative Study Group 380.

BACKGROUND AND METHODS The role of colonoscopy in screening for colorectal cancer is uncertain. At 13 Veterans Affairs Medical Centers, we performed colonoscopy to determine the prevalence and location of advanced colonic neoplasms and the risk of advanced proximal neoplasia in asymptomatic patients (age range, 50 to 75 years) with or without distal neoplasia. Advanced colonic neoplasia was defined as an adenoma that was 10 mm or more in diameter, a villous adenoma, an adenoma with high-grade dysplasia, or invasive cancer. In patients with more than one neoplastic lesion, classification was based on the most advanced lesion. RESULTS Of 17,732 patients screened for enrollment, 3196 were enrolled; 3121 of the enrolled patients (97.7 percent) underwent complete examination of the colon. The mean age of the patients was 62.9 years, and 96.8 percent were men. Colonoscopic examination showed one or more neoplastic lesions in 37.5 percent of the patients, an adenoma with a diameter of at least 10 mm or a villous adenoma in 7.9 percent, an adenoma with high-grade dysplasia in 1.6 percent, and invasive cancer in 1.0 percent. Of the 1765 patients with no polyps in the portion of the colon that was distal to the splenic flexure, 48 (2.7 percent) had advanced proximal neoplasms. Patients with large adenomas (> or = 10 mm) or small adenomas (< 10 mm) in the distal colon were more likely to have advanced proximal neoplasia than were patients with no distal adenomas (odds ratios, 3.4 [95 percent confidence interval, 1.8 to 6.5] and 2.6 (95 percent confidence interval, 1.7 to 4.1], respectively). However, 52 percent of the 128 patients with advanced proximal neoplasia had no distal adenomas. CONCLUSIONS Colonoscopic screening can detect advanced colonic neoplasms in asymptomatic adults. Many of these neoplasms would not be detected with sigmoidoscopy.
Induction of Renal 20-Hydroxyeicosatetraenoic Acid by Clofibrate Attenuates High-Fat Diet-Induced Hypertension in Rats

This study compared renal hemodynamics, the expression of CYP4A isoforms [the enzymes for 20-hydroxyeicosatetraenoic acid (20-HETE) production], and tubular sodium transporters in male rats fed a high-fat (HF) or control diet for 10 weeks. We also studied the effect of treatment with clofibrate, a CYP4A inducer, on sodium retention and renal function and on CYP4A expression in HF rats. HF rats had higher blood pressure (BP), renal plasma flow, and glomerular filtration rate (GFR), but no significant change in renal vascular resistance. Reverse transcription-polymerase chain reaction analysis showed that CYP4A1 and CYP4A8 expression was significantly decreased in the renal cortex of HF rats. Western blot analysis showed up-regulation of expression of the α-subunit of the epithelial sodium channel (α-ENaC), the β-subunit of the epithelial sodium channel (β-ENaC), sodium/hydrogen exchanger (NHE)-3, and the renal outer medulla K+ channel (ROMK) in HF rats, whereas expression of the γ-subunit of the epithelial sodium channel and the α1-subunit of Na+-K+-ATPase remained unchanged. Thus, HF treatment caused the reduction of renal CYP4A1 and CYP4A8 expression, whereas the increases in α-ENaC, β-ENaC, NHE-3, and ROMK expression in renal tubules may have contributed sodium retention and hypertension in HF rats. Furthermore, clofibrate treatment (240 mg/kg/day) caused the decrease of BP and GFR and the attenuation of cumulative sodium balance in HF rats. The attenuation of sodium retention by clofibrate treatment is linked to decreased expression of NHE-3 in renal cortex. Clofibrate induction of CYP4A expression occurred in proximal tubules and in the thick ascending limb of the loop of Henle but not in renal microvessels. This induction correlated with the expression of peroxisome proliferator-activated receptor (PPARα) in renal tubules. Therefore, these results suggest that the effects of clofibrate on sodium retention and blood pressure regulation in HF rats may be due to the induction of renal tubular 20-HETE production through the PPARα pathway.
DXR: towards a billion routing lookups per second in software

Can a software routing implementation compete in a field generally reserved for specialized lookup hardware? This paper presents DXR, an IPv4 lookup scheme based on transforming large routing tables into compact lookup structures which easily fit into cache hierarchies of modern CPUs. DXR supports various memory/speed tradeoffs and scales almost linearly with the number of CPU cores. The smallest configuration, D16R, distills a real-world BGP snapshot with 417,000 IPv4 prefixes and 213 distinct next hops into a structure consuming only 782 Kbytes, less than 2 bytes per prefix, and achieves 490 million lookups per second (MLps) in synthetic tests using uniformly random IPv4 keys on a commodity 8-core CPU. Some other DXR configurations exceed 700~MLps at the cost of increased memory footprint. DXR significantly outperforms a software implementation of DIR-24-8-BASIC, has better scalability, and requires less DRAM bandwidth. Our prototype works inside the FreeBSD kernel, which permits DXR to be used with standard APIs and routing daemons such as Quagga and XORP, and to be validated by comparing lookup results against the BSD radix tree.
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
Valor, satisfacción y lealtad en el voluntariado. Aplicación a un megaevento religioso

El presente trabajo tiene como objetivo principal profundizar en el estudio del voluntario como agente esencial en el éxito de cualquier evento, al tiempo que ofrecemos recomendaciones para mejorar la gestión de Megaeventos. Para alcanzar este objetivo proponemos un modelo estructural que analiza la multimensionalidad del valor como antecedente del valor percibido al tiempo que este influye sobre la satisfacción y ésta sobre la lealtad. La población analizada está constituida por los voluntarios que participaron en la Jornada Mundial de la Juventud celebrada en 2011 en Madrid con un total de 1427 casos. Los resultados obtenidos respaldan todas las hipótesis presentadas en el modelo propuesto. De tal forma que se confirma que la multidimensionalidad de la variable valor (espiritualidad, valor social, entretenimiento y eficiencia) es antecedente del valor percibido al tiempo que se confirma la cadena de consecuencias valor-satisfacción-lealtad. El antecedente más importante es el entretenimiento lo que demuestra que el voluntariado es entendido como un divertimento, y no como un trabajo.
Automatic annotation of data extracted from large Web sites

Data extraction from web pages is performed by software modules called wrappers. Recently, some systems for the automatic generation of wrappers have been proposed in the literature. These systems are based on unsupervised inference techniques: taking as input a small set of sample pages, they can produce a common wrapper to extract relevant data. However, due to the automatic nature of the approach, the data extracted by these wrappers have anonymous names. In the framework of our ongoing project RoadRunner, we have developed a prototype, called Labeller, that automatically annotates data extracted by automatically generated wrappers. Although Labeller has been developed as a companion system to our wrapper generator, its underlying approach has a general validity and therefore it can be applied together with other wrapper generator systems. We have experimented the prototype over several real-life web sites obtaining encouraging results.
Identification of the t Complex–encoded Cytoplasmic Dynein Light Chain Tctex1 in Inner Arm I1 Supports the Involvement of Flagellar Dyneins in Meiotic Drive

The cytoplasmic dynein light chain Tctex1 is a candidate for one of the distorter products involved in the non-Mendelian transmission of mouse t haplotypes. It has been unclear, however, how the t-specific mutations in this protein, which is found associated with cytoplasmic dynein in many tissues, could result in a male germ cell–specific phenotype. Here, we demonstrate that Tctex1 is not only a cytoplasmic dynein component, but is also present both in mouse sperm and Chlamydomonas flagella. Genetic and biochemical dissection of the Chlamydomonas flagellum reveal that Tctex1 is a previously undescribed component of inner dynein arm I1. Combined with the recent identification of another putative t complex distorter, Tctex2, within the outer dynein arm, these results support the hypothesis that transmission ratio distortion (meiotic drive) of mouse t haplotypes involves dysfunction of both flagellar inner and outer dynein arms but does not require the cytoplasmic isozyme.
The Essential Role of the N-Terminal Domain of the Orange Carotenoid Protein in Cyanobacterial Photoprotection: Importance of a Positive Charge for Phycobilisome Binding[C][W]

This article provides information about the interaction between the phycobilisomes and the Orange Carotenoid Protein needed for photoprotection. Its red light–activated form has an open structure that allows the interaction of its N-terminal domain, containing the Arg155, with the phycobilisome, permitting a closer interaction between the carotenoid and the phycobilisome chromophores. Most cyanobacteria, under high light conditions, decrease the amount of energy arriving at the reaction centers by increasing thermal energy dissipation at the level of the phycobilisome, the extramembranous antenna. This mechanism is induced by photoactivation of the Orange Carotenoid Protein (OCP). To identify how the activated OCP interacts with phycobilisomes (PBs), several OCP mutants were constructed, and the influence of mutations on photoactivity, stability, and binding to PBs was characterized. The disruption of the salt bridge between Arg155 and Glu244, which stabilizes the interaction between the N- and C-terminal domains, increased the rate of photoactivity and the stability of the photoactivated OCP, suggesting that the activated OCP has an open structure with decreased interdomain interaction. Changing Glu244 to leucine had no effect on OCP binding to PBs. By contrast, substitution of Arg155 with a neutral or a negatively charged amino acid largely decreased OCP binding to the PBs, whereas substitution with a lysine slightly perturbed the interaction. These results strongly suggest that the surface of the N-terminal domain, containing the Arg155, interacts with the PB and that the positive charge of Arg155 plays a key role in photoprotection.
Reaching activity in parietal area V6A of macaque: eye influence on arm activity or retinocentric coding of reaching movements?

Parietal area V6A contains neurons modulated by the direction of gaze as well as neurons able to code the direction of arm movement. The present study was aimed to disentangle the gaze effect from the effect of reaching activity upon single V6A neurons. To this purpose, we used a visuomotor task in which the direction of arm movement remained constant while the animal changed the direction of gaze. Gaze direction modulated reach‐related activity in about two‐thirds of tested neurons. In several cases, modulations were not due to the eye‐position signal per se, the apparent eye‐position modulation being just an epiphenomenon. The real modulating factor was the location of reaching target with respect to the point gazed by the animal, that is, the retinotopic coordinates towards which the action of reaching occurred. Comparison of neural discharge of the same cell during execution of foveated and non‐foveated reaching movements, performed towards the same or different spatial locations, confirmed that in a part of V6A neurons reaching activity is coded retinocentrically. In other neurons, reaching activity is coded spatially, depending on the direction of reaching movement regardless of where the animal was looking at. The majority of V6A reaching neurons use a system that encompasses both of these reference frames. These results are in line with the view of a progressive visuomotor transformation in the dorsal visual stream, that changes the frame of reference from the retinocentric one, typically used by the visual system, to the arm‐centred one, typically used by the motor system.
Controller Design via Nonsmooth Multidirectional Search

We propose an algorithm which combines multidirectional search (MDS) with nonsmooth optimization techniques to solve difficult problems in automatic control. Applications include static and fixed-order output feedback controller design, simultaneous stabilization, $H_2/H_\infty$-synthesis, and much else. We show how to combine direct search techniques with nonsmooth descent steps in order to obtain convergence certificates in the presence of nonsmoothness. Our technique is efficient when small and medium size controllers for plants with large state dimension are sought. Our numerical testing includes several benchmark examples. For instance, our algorithm needs 0.41\,s to compute a static output feedback stabilizing controller for the Boeing 767 flutter benchmark problem [E. E. J. Davison, IFAC Technical Committee Reports, Pergamon Press, Oxford, 1990], a system with 55 states. The first static controller without performance specifications for this system was obtained in [J. Burke, A. Lewis, and M. Overton, SIAM J. Optim. , 15 (2003), pp. 751-779].
Optimal duration of dual antiplatelet therapy after percutaneous coronary intervention with drug eluting stents: meta-analysis of randomised controlled trials

Objective To assess the benefits and risks of short term (<12 months) or extended (>12 months) dual antiplatelet therapy (DAPT) versus standard 12 month therapy, following percutaneous coronary intervention with drug eluting stents. Design Meta-analysis of randomised controlled trials. Data sources PubMed, Embase, Cumulative Index to Nursing and Allied Health Literature, Scopus, Web of Science, Cochrane Library, and major congress proceedings, searched from 1 January 2002 to 16 February 2015. Review methods Trials comparing short term (<12 months) or extended (>12 months) DAPT regimens with standard 12 month duration of therapy. Primary outcomes were cardiovascular mortality, myocardial infarction, stent thrombosis, major bleeding, and all cause mortality. Results 10 randomised controlled trials (n=32 287) were included. Compared to 12 month DAPT, a short term course of therapy was associated with a significant reduction in major bleeding (odds ratio 0.58 (95% confidence interval 0.36 to 0.92); P=0.02) with no significant differences in ischaemic or thrombotic outcomes. Extended versus 12 month DAPT yielded a significant reduction in the odds of myocardial infarction (0.53 (0.42 to 0.66); P<0.001) and stent thrombosis (0.33 (0.21 to 0.51); P<0.001), but more major bleeding (1.62 (1.26 to 2.09); P<0.001). All cause but not cardiovascular death was also significantly increased (1.30 (1.02 to 1.66); P=0.03). Conclusions Compared with a standard 12 month duration, short term DAPT (<12 months) after drug eluting stent implementation yields reduced bleeding with no apparent increase in ischaemic complications, and could be considered for most patients. In selected patients with low bleeding risk and very high ischaemic risk, extended DAPT (>12 months) could be considered. The increase in all cause but not cardiovascular death with extended DAPT requires further investigation.
Cardea: Dynamic Access Control in Distributed Systems

Modern authorization systems span domains of administration, rely on many different authentication sources, and manage complex attributes as part of the authorization process. This . paper presents Cardea, a distributed system that facilitates dynamic access control, as a valuable piece of an inter-operable authorization framework. First, the authorization model employed in Cardea and its functionality goals are examined. Next, critical features of the system architecture and its handling of the authorization process are then examined. Then the S A M L and XACML standards, as incorporated into the system, are analyzed. Finally, the future directions of this project are outlined and connection points with general components of an authorization system are highlighted.
Integrating Discourse, Construction and Objectivity: A Contemporary Realist Approach

In recent developments in the realism-constructionism debate, attempts have been made by individual scholars on both sides to assimilate the other side’s insights into one’s own position. With respect to epistemology, such attempts have so far failed. Situated in this context, this article proposes a general approach in which valid insights from constructionism, discourse theory, and pragmatist critique of realism are integrated into realist epistemology. Discourses are distinguished along two dimensions; interrelating these two dimensions, the interplay between epistemic and extra-discursive factors along them in discursive contention are analyzed under different categories of situations across the entire discursive spectrum. The balance between the determinative effects of epistemic and extra-discursive factors varies from one type of situation to another. Our approach enables the retention of the critical edge of skepticism, shows realist epistemology to be useful in sociological research in ways previously unrealized, and provides heuristic guidelines for conducting sociological research.