Miracle-dz/UniFAR-FTUs huggingface dataset:
Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly

Background: The transition to Next Generation sequencing (NGS) sequencing technologies has had numerous applications in Plant, Microbial and Human genomics during the past decade. However, NGS sequencing trades high read throughput for shorter read length, increasing the difficulty for genome assembly. This research presents a comparison of traditional versus Cloud computing-based genome assembly software, using as examples the Velvet and Contrail assemblers and reads from the genome sequence of the zebrafish ( Danio rerio ) model organism. Results: The first phase of the analysis involved a subset of the zebrafish data set (2X coverage) and best results were obtained using K-mer size of 65, while it was observed that Velvet takes less time than Contrail to complete the assembly. In the next phase, genome assembly was attempted using the full dataset of read coverage 192x and while Velvet failed to complete on a 256GB memory compute server, Contrail completed but required 240hours of computation. Conclusion: This research concludes that for deciding on which assembler software to use, the size of the dataset and available computing hardware should be taken into consideration. For a relatively small sequencing dataset, such as microbial or small eukaryotic genome, the Velvet assembler is a good option. However, for larger datasets Velvet requires large-memory compute servers in the order of 1000GB or more. On the other hand, Contrail is implemented using Hadoop, which performs the assembly in parallel across nodes of a compute cluster. Furthermore, Hadoop clusters can be rented on-demand from Cloud computing providers, and therefore Contrail can provide a simple and cost effective way for genome assembly of data generated at laboratories that lack the infrastructure or funds to build their own clusters.
The North American Fetal Therapy Network Registry Data on Outcomes of Radiofrequency Ablation for Twin-Reversed Arterial Perfusion Sequence

Objective: To report the North American Fetal Therapy Network (NAFTNet) Registry data on the outcomes of using radiofrequency ablation to treat twin-reversed arterial perfusion (TRAP). Methods: This was a retrospective review of the records of all patients who underwent percutaneous radiofrequency ablation of an acardiac twin after referral to 12 NAFTNet institutions between 1998 and 2008. Maternal, fetal and neonatal data were analyzed. The primary outcome was neonatal survival to 30 days of age. All participating sites conducted this study under institutional review board approval. Results: Of the 98 patients identified, there were no maternal deaths and no women required blood transfusions. Most women (76 of 98; 78%) stayed in the hospital for ≤1 day after the procedure. Mean gestational age at delivery was 33.4 weeks overall and 36.0 weeks for survivors. Median gestational age at delivery was 37.0 weeks. Survival of the pump twin to 30 days was 80% in the overall cohort. Conclusion: The NAFTNet registry data suggest that radiofrequency ablation of the acardiac twin is an effective treatment for TRAP sequence.
Correlation between Saliva and Plasma Levels of Endothelin Isoforms ET-1, ET-2, and ET-3

Although saliva endothelins are emerging as valuable noninvasive cardiovascular biomarkers, reports on the relationship between isoforms in saliva and plasma remain scarce. We measured endothelins in concurrent saliva and plasma samples (n = 30 males; age 18–63) by HPLC-fluorescence. Results revealed statistically significant positive correlations among all isoforms between saliva and plasma: big endothelin-1 (BET-1, 0.55 ± 0.27 versus 3.35 ± 1.28 pmol/mL; r = 0.38, p = 0.041), endothelin-1 (ET-1, 0.52 ± 0.21 versus 3.45 ± 1.28 pmol/mL; r = 0.53, p = 0.003), endothelin-2 (ET-2, 0.21 ± 0.07 versus 1.63 ± 0.66 pmol/mL; r = 0.51, p = 0.004), and endothelin-3 (ET-3, 0.39 ± 0.19 versus 2.32 ± 1.44 pmol/mL; r = 0.75, p < 0.001). Correlations of BET-1, ET-1, and ET-3 within each compartment were positive in both plasma (p < 0.05) and saliva (p ≤ 0.1), whereas ET-2 was not significantly correlated with other isoforms in either plasma or saliva. For all isoforms, concentrations varied on average fivefold between individuals (90th/10th percentiles); individuals with high plasma endothelin levels generally had high saliva endothelin levels. Our results reveal that salivary ET isoform profiles portray the plasmatic profiles and support the view of coordinated regulation of ET-1 and ET-3, but distinct regulatory pathways for ET-2.
Diffusion-weighted MR imaging: diagnostic accuracy in patients imaged within 6 hours of stroke symptom onset.

PURPOSE To evaluate the diagnostic accuracy of diffusion-weighted magnetic resonance (MR) imaging performed within 6 hours of the onset of stroke symptoms. MATERIALS AND METHODS The authors reviewed the patient records and images from all patients hospitalized in a 10-month period in whom diffusion-weighted imaging was performed within 6 hours of the onset of strokelike symptoms (n = 22). Analyses included comparison of the initial interpretation of the diffusion-weighted images with the final clinical diagnosis; blinded reviews of computed tomographic (CT) scans and conventional and diffusion-weighted images; and determination of lesion contrast-to-noise ratios (CNRs). RESULTS Diffusion-weighted images indicated stroke in 14 patients, all of whom had a final diagnosis of acute stroke. Diffusion-weighted images were negative in eight patients, all of whom had a final clinical diagnosis other than stroke (100% sensitivity, 100% specificity, chi 2 = 23.00, P < .0001). Blinded reviews yielded 100% sensitivity and 86% specificity for diffusion-weighted MR imaging (chi 2 = 15.43, P < .0005); 18% sensitivity and 100% specificity for conventional MR imaging (chi 2 = 2.85, P > .2); and 45% sensitivity and 100% specificity for CT (chi 2 = 4.40, P > .10). Lesion percentage CNRs were 77% for diffusion-weighted imaging, 5.5% for CT, 9.8% for T2-weighted MR imaging, and 3.1% for proton-density-weighted MR imaging (P < .002 for diffusion-weighted imaging vs others). CONCLUSION Diffusion-weighted MR imaging is highly accurate for diagnosing stroke within 6 hours of symptom onset and is superior to CT and conventional MR imaging.
Structured Fisher vector encoding method for human action recognition

This paper presents the structured Fisher vector encoding method, a new video representation which yields an improved model to classical FV for human action recognition. Our proposed representation is based on local structural organization of features by building graphs of trajectories. It preserve more information in feature encoding process by local spatial pooling and refining the representation in the global pooling. Local spatio-temporal information are exploited by presenting the relationships among video trajectories as local graphs of trajectories using a multi-scale Delaunay triangulation. Experiments using the human action recognition datasets (Hollywood2 and HMDB51) show the effectiveness of the proposed approach.
Towards Complex Reasoning Agents for Action Games

The applicability of artificial intelligence techniques to build “believable” characters in computer games is no longer questioned. The techniques that have been effectively applied in most cases, however, are quite simplistic if compared to the most sophisticated techniques produced by the AI research community. We advocate that more ellaborate techniques could bring advantages to game program ming, not only with respect to the performance of the agents being built, but chiefly due to the possibility of allowing agent designers to focus on the appropriate level of abstraction. We illustrate our arguments with a concrete example, namely the endowment of reasoning capabilities for agents in an action game, based on a simplified version of the ATMS.
The Cognitive Ecology of Dolphin Social Engagement

Investigating social cognition in dolphins is a complex, demanding task. Alien in senses, form, and habitat, dolphins are challenging to comprehend and difficult to study. As the previous chapters in this book have made clear, they are also sophisticated, innovative creatures whose cognition we have only just begun to understand. “Cognitive Ecology” (Hutchins, 2010a, 2014) is a transformative new approach that is making exciting inroads in the study of human cognition (Enfield & Levinson, 2006; Goodwin, 2000, 2013; Hutchins, 1995, 2001, 2010a, 2010b; 2014; Malafouris & Renfrew, 2010) Because it provides a way to study social cognition based on observations of naturally-occurring behavior, some researchers working with nonhumans have adopted it as well (e.g. Byrne & Bates, 2014; Forster, 2002; Hirata & Matsuzawa, 2001; Johnson, 2001, 2010; King, 2004; Russon & Andrews, 2011). By outlining how this approach might be applied to the study of social interaction in dolphins, this chapter aims to present a new set of conceptual and methodological tools for studying dolphin communication and cognition (see also Herzing, 2006; Johnson, 2010).
Direct Testing of Gradual PostPeak Softening of Notched Specimens of Fiber Composites Stabilized by Enhanced Stiffness and Mass

Static and dynamic analysis of the fracture tests of fiber composites in hydraulically servo-controlled testing machines currently in use shows that their grips are much too soft and light for observing the postpeak softening. Based on static and dynamic analysis of the test setup, far stiffer and heavier grips are proposed. Tests of compact-tension fracture specimens of woven carbon-epoxy laminates prove this theoretical conclusion. Sufficiently stiff grips allow observation of a stable postpeak, even under load-point displacement control. Dynamic stability analysis further indicates that stable postpeak can be observed under CMOD control provided that a large mass is rigidly attached to the current soft grips. The fracture energy deduced from the area under the measured complete load-deflection curve with stable postpeak agrees closely with the fracture energy deduced from the size effect tests of the same composite. Previous suspicions of dynamic snapback in the testing of composites are dispelled. So is the previous view that fracture mechanics was inapplicable to the fiber-polymer composites.
NIL: attribute selection for matching the task corpus using relative attribute groupings obtained from the test data

The entry presented by the NIL research group of the Universidad Complutense de Madrid adapts existing software previously developed for an application aimed at generating fluent texts for storytelling. The final entry is specifically geared towards system-human match over the challenge corpus. Attributes are selected based on an adaptation of Reiter and Dale’s fast efficient algorithm for referring expression generation, using relative groupings of attributes obtained empirically from the training data to determine the order in which they are considered. The results for the development data indicate that the NIL entry is dealing adequately with issues of identification of referents. Results for systemhuman match are not so good, probably due to the fact that the corpus is a sample of possible references, rather than a selection of ‘ideal’ references.
Effect of Subtherapeutic Antimicrobials on Genetic Diversity of Enterococcus faecium from Chickens

Abstract The effect of growth promotants (bacitracin, virginiamycin, and flavomycin) on the genetic population of Enterococcus faecium isolated from a commercially integrated poultry farm was examined. A total of 551 E. faecium were isolated from chick boxliners (n = 16), litter (n = 334), feed (n = 67), and carcass rinse (n = 134) samples from four chicken houses. Two houses on the farm were control houses and did not use any antimicrobials while two other houses on the farm used flavomycin, virginiamycin, and bacitracin during six different chicken grow outs. BOX-PCR and pulsed-field gel electrophoresis (PFGE) results indicated that E. faecium strains had a high degree of genetic diversity as overall clustering was independent of source, house, or grow out. Similarity of ≥60% for the majority of BOX-PCR genogroups and ≥80% for the majority of PFGE genogroups was observed for a subset of carcass rinse samples (n = 45) examined. Seventy-nine percent (19/24) of isolates in BOX-PCR genogroup 2 also clustered in PFGE genogroup 2, although no association between the isolates and house or grow out was observed. These results suggest that E. faecium from chicken are genetically diverse and that growth-promoting antimicrobials do not affect the genetic population of E. faecium.
Shavenbaby Couples Patterning to Epidermal Cell Shape Control

It is well established that developmental programs act during embryogenesis to determine animal morphogenesis. How these developmental cues produce specific cell shape during morphogenesis, however, has remained elusive. We addressed this question by studying the morphological differentiation of the Drosophila epidermis, governed by a well-known circuit of regulators leading to a stereotyped pattern of smooth cells and cells forming actin-rich extensions (trichomes). It was shown that the transcription factor Shavenbaby plays a pivotal role in the formation of trichomes and underlies all examined cases of the evolutionary diversification of their pattern. To gain insight into the mechanisms of morphological differentiation, we sought to identify shavenbaby's downstream targets. We show here that Shavenbaby controls epidermal cell shape, through the transcriptional activation of different classes of cellular effectors, directly contributing to the organization of actin filaments, regulation of the extracellular matrix, and modification of the cuticle. Individual inactivation of shavenbaby's targets produces distinct trichome defects and only their simultaneous inactivation prevent trichome formation. Our data show that shavenbaby governs an evolutionarily conserved developmental module consisting of a set of genes collectively responsible for trichome formation, shedding new light on molecular mechanisms acting during morphogenesis and the way they can influence evolution of animal forms.
An observational study of seatbelt use among vehicle occupants in Nigeria

Objective The use of seatbelts reduces the likelihood of death and severe injuries to crash-involved vehicle occupants by 45–60%. Several countries, including Nigeria, have laws mandating the use of seatbelts but compliance is not universal. This study was conducted to determine rates of use of seatbelts among vehicle occupants in Ibadan municipality. Design An observational study was conducted. A selected petrol station in each of the five local government areas in Ibadan municipality was used as an observation site. Observations were documented by trained research staff between 08:30 and 18:00 hours over a 6-day period. Results 5757 occupants in 2870 vehicles were observed. Approximately 90% of drivers were men. Driver seatbelts were installed in approximately 90% of vehicles. Overall seatbelt use was 18.7; 31.7% among drivers and 10.3% and 0.4% among front and rear-seated adults, respectively. Only one child (0.7%) was restrained. Significantly more female drivers 47.3% used their seatbelts compared with men, 30.3% (p<0.001). An adult passenger was more likely to be restrained when riding with a female driver (p=0.007) and when the driver was restrained (p=0.000). Conclusions The study showed that seatbelt use among vehicle occupants was low. Further research into reasons for the non-use of restraints needs to be conducted so that these can be incorporated into programmes aimed at improving seatbelt use.
STUDENT PERSONALITY TYPES AND PREDISPOSITIONS TOWARDS DISTANCE EDUCATION.

Most of the distance education debate has focused on either student outcomes or satisfaction with distance learning courses. One significant factor that has been overlooked is the role of student personality characteristics in distance education. This study examines two overall research questions. First, are certain student personality types, as measured by the Myers-Briggs Type Indicator (MBTI) attracted to taking more computer and Internet-based distance learning courses than other personality types? Second, do students, regardless of their own personality types, have a preference for the types of computer and Internet-based courses they would take via distance? The results indicate that MBTI INTP (introverted thinkers with intuition) type students are most attracted to distance learning as a pedagogical method. For the second question, students indicated preferences for courses that emphasize introversion, sensing, and thinking (versus extraversion, intuition, and feeling) characteristics.
Title Stata.com Dfgls — Df-gls Unit-root Test

Syntax Menu Description Options Remarks and examples Stored results Methods and formulas Acknowledgments References Also see Syntax dfgls varname if in , options options Description Main maxlag(#) use # as the highest lag order for Dickey–Fuller GLS regressions notrend series is stationary around a mean instead of around a linear time trend ers present interpolated critical values from Elliott, Rothenberg, and Stock (1996) You must tsset your data before using dfgls; see [TS] tsset. varname may contain time-series operators; see [U] 11.4. 4 Time-series varlists. Description dfgls performs a modified Dickey–Fuller t test for a unit root in which the series has been transformed by a generalized least-squares regression. Options £ £ Main maxlag(#) sets the value of k, the highest lag order for the first-differenced, detrended variable in the Dickey–Fuller regression. By default, dfgls sets k according to the method proposed by Schwert (1989); that is, dfgls sets k max = floor[12{(T + 1)/100} 0.25 ]. notrend specifies that the alternative hypothesis be that the series is stationary around a mean instead of around a linear time trend. By default, a trend is included. ers specifies that dfgls should present interpolated critical values from tables presented by Elliott, Rothenberg, and Stock (1996), which they obtained from simulations. See Critical values under Methods and formulas for details.
26 PFLOPS Stencil Computations for Atmospheric Modeling on Sunway TaihuLight

Stencil computation arises from a broad set of scientific and engineering applications and often plays a critical role in the performance of extreme-scale simulations. Due to the memory bound nature, it is a challenging task to opti- mize stencil computation kernels on modern supercomputers with relatively high computing throughput whilst relatively low data-moving capability. This work serves as a demon- stration on the details of the algorithms, implementations and optimizations of a real-world stencil computation in 3D nonhydrostatic atmospheric modeling on the newly announced Sunway TaihuLight supercomputer. At the algorithm level, we present a computation-communication overlapping technique to reduce the inter-process communication overhead, a locality- aware blocking method to fully exploit on-chip parallelism with enhanced data locality, and a collaborative data accessing scheme for sharing data among different threads. In addition, a variety of effective hardware specific implementation and optimization strategies on both the process- and thread-level, from the fine-grained data management to the data layout transformation, are developed to further improve the per- formance. Our experiments demonstrate that a single-process many-core speedup of as high as 170x can be achieved by using the proposed algorithm and optimization strategies. The code scales well to millions of cores in terms of strong scalability. And for the weak-scaling tests, the code can scale in a nearly ideal way to the full system scale of more than 10 million cores, sustaining 25.96 PFLOPS in double precision, which is 20% of the peak performance.
INTRODUCTION TO MACROECONOMIC DYNAMICS SPECIAL ISSUE: INEQUALITY

This special issue features inequality. This is a subject that rightly draws immediate attention from both the profession and the popular press. The numbers themselves are intrinsically interesting, if not disturbing. There is, on the one hand, great variety in the distribution of earnings and an enormously right-skewed distribution of wealth. On the other hand, there is absolute and relative poverty. In developing countries there are extremes coexisting on both ends of the distribution. But developing economies also feature growth with time-varying levels of inequality. Macroeconomic growth, stability, and social policies seem correlated with poverty reduction in some instances.
Expression, purification, and characterization of histidine-tagged mouse monoglyceride lipase from baculovirus-infected insect cells.

Monoglyceride lipase (MGL) has been produced with the baculovirus-insect cell system. The mouse MGL cDNA was subcloned into a baculovirus transfer vector in frame with a sequence encoding an N-terminal stretch of six histidine residues. Purification to apparent homogeneity was obtained by nickel-chelating chromatography. The final yield was 3 mg of pure enzymatically active MGL per liter of Sf9 cell suspension culture. Analysis by SDS-PAGE and mass spectrometry showed that the recombinant histidine-tagged enzyme had the expected molecular mass. With monoolein as substrate, the specific activity and the apparent K(m) were close to those of rat MGL of adipose tissue.
Child Maturation , Time-Invariant , and Time-Varying Inputs : their Relative Importance in Production of Child Human Capital

We present estimates of a multiple-input, multiple-output directional distance function that relates good and bad inputs from home, school, and environment, to good and bad outputs, measured as children’s cognitive and behavioral development. This household directional distance function is estimated using a balanced panel of 253 families from the National Longitudinal Survey of Youth-Child Sample in two-year intervals from 1994 to 2000. We recover consistent estimates of heretofore-ignored, time-invariant variables from a second-stage estimation process, where the first stage is the within estimator which employs instruments. We then measure productivity growth, technical change, efficiency change, and technical efficiency. We find children’s cognitive/behavioral productivity growth is highest at their youngest age (5 years) and diminishes thereafter. A one percent increase in child age is nearly equal in importance to a one percent improvement in the child’s home environmental quality and is more important than equal percentage changes in other variables, such as maternal cigarette consumption and effective home time. The relative importance of child maturation is consistent with the fundamental principles of the child development literature.
Integrating Techniques for Event-based Business Intelligence Gathering

Gathering news events on companies to provide business intelligence to financial investors and creditors is a challenging problem. With a plethora of online news providers and tens of thousands of companies to monitor, automating the extraction and fusion of events is crucial. We developed an intelligent agent-based component framework to query and extract events from multiple providers. This framework integrates multiple machine learning and natural language processing techniques to down-select articles and extract targeted events. Results indicate that our system is capable of extracting focal events on a variety of topics with effective precision and recall.