Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel parallel QR algorithm for hybrid distributed memory HPC systems 1

A novel variant of the parallel QR algorithm for solving dense nonsymmetric eigenvalue problems on hybrid distributed high performance computing (HPC) systems is presented. For this purpose, we introduce the concept of multi-window bulge chain chasing and parallelize aggressive early deflation. The multi-window approach ensures that most computations when chasing chains of bulges are performed in level 3 BLAS operations, while the aim of aggressive early deflation is to speed up the convergence of the QR algorithm. Mixed MPI-OpenMP coding techniques are utilized for porting the codes to distributed memory platforms with multithreaded nodes, such as multicore processors. Numerous numerical experiments confirm the superior performance of our parallel QR algorithm in comparison with the existing ScaLAPACK code, leading to an implementation that is one to two orders of magnitude faster for sufficiently large problems, including a number of examples from applications.
Examining the Double-Deficit Hypothesis in an Orthographically Consistent Language

We examined the double-deficit hypothesis in Finnish. One hundred five Finnish children with high familial risk for dyslexia and 90 children with low family risk were followed from the age of 3½ years until Grade 3. Children's phonological awareness, rapid naming speed, text reading, and spelling were assessed. A deficit in rapid automatized naming (RAN) predicted slow reading speed across time and spelling difficulties after Grade 1. A deficit in phonological awareness predicted difficulties in spelling, but only in the familial risk sample. The effect of familial risk was significant in the development of phonological awareness, RAN, reading, and spelling. Our findings suggest that the basic premise of the double-deficit hypothesis—that RAN and phonological awareness are separable deficits with different effects on reading and spelling outcomes—holds also in a consistent orthography.
Monitoring native vegetation on an urban groundwater supply mound using airborne digital imagery

High spatial resolution airborne imagery has been acquired at anniversary dates and processed to produce monitoring information for vegetation on the Gnangara Mound. The Mound, located north of Perth Western Australia, is of great importance to the city's water supply and retains significant biodiversity values. An effective monitoring system for vegetation is a priority for multiple agencies concerned with management and regulation of the Mound. Individual tree deaths and spatial patterns across the area were detected using the image sequences. Spatial analysis showed no associations with borefield pumping, but active disease processes were identified. Methods and results are presented.
TNF- (cid:2) expression in neutrophils and its regulation by glycogen synthase kinase-3: A potentiating role for lithium expression in and a

Glycogen synthase kinase 3 (GSK-3) is associated with several cellular systems, including immune response. Lithium, a widely used pharmacological treatment for bipolar disorder, is a GSK-3 inhibitor. GSK-3 (cid:2) is the predominant isoform in human neutrophils. In this study, we examined the effect of GSK-3 inhibition on the production of TNF- (cid:2) by neutrophils. In the murine air pouch model of inﬂammation, lithium chloride (LiCl) ampliﬁed TNF- (cid:2) release. In lipopoly-saccharide-stimulated human neutrophils, GSK-3 inhibitors mimicked the effect of LiCl, each potentiating TNF- (cid:2) release after 4 h, in a concentration-dependent fashion, by up to a 3-fold increase (ED 50 of 1 mM for lithium). LiCl had no signiﬁcant effect on cell viability. A positive association was revealed between GSK-3 inhibition and prolonged activation of the p38/MNK1/eIF4E pathway of mRNA translation. Using lysine and arginine labeled with stable heavy isotopes followed by quantitative mass spectrometry, we determined that GSK-3 inhibition markedly increases (by more than 3-fold) de novo TNF- (cid:2) protein synthesis. ﬁndings light a novel mechanism synthase kinase-3: potentiating
National population-based study comparing treatment-related toxicity in men who received Intensity-Modulated versus 3D-Conformal Radical Radiotherapy for prostate cancer

Purpose There has been a rapid adoption of Intensity-modulated radiotherapy (IMRT) despite a lack of robust evidence demonstrating superiority over 3D-Conformal radiotherapy (3D-CRT). The aim of this national population-based study was to compare severe genitourinary (GU) and gastrointestinal (GI) toxicity in patients with prostate cancer who were treated with radical IMRT or 3D-CRT. We developed a A competing comparing and following and and treatment competing event. We adjusted for year of radiotherapy, age, RCS Charlson comorbidity score, socioeconomic deprivation status, prostate cancer risk group, and radiotherapy treatment region. Results are reported as adjusted hazard ratios (HR) with 95% confidence intervals (95%CI). A p-value smaller than 0.05 was considered statistically significant. P-values were based on the Wald test or the likelihood ratio test, as appropriate. who received 3D-CRT. Our study used a transparent coding system that was specifically developed to identify only severe complications. This coding system can be used to provide a performance indicator for service evaluation and quality assessment. Furthermore, it can be used for comparative effectiveness research using existing administrative data to capture GU and GI toxicity following pelvic-based radiotherapy of other tumours such as cervical cancer.
Freshwater transport at Fimbulisen, Antarctica

[1] The intricate near-circumpolar system of fronts and currents surrounding Antarctica isolates much of Earth's freshwater from the saline oceans immediately north. The Antarctic Slope Front sustains bathymetrically steered flow at the shelf break, whereas the shallow Coastal Current travels rapidly alongside the ice front. A hydrographic survey of the southeastern Weddell Sea finds these two features to have merged near the narrow (<40 km wide) continental shelf at Fimbulisen. On the prime meridian, its Trolltunga ice tongue overshoots the shelf break northward into this slope current. Observations on either side of the ice tongue demonstrate its retarding effect on the westward-flowing waters it overhangs and its contribution to the poorly understood freshwater budget. From oxygen isotope ratio measurements and referenced geostrophic shears, we find the combined glacial meltwater and sea ice melt transport upstream of Trolltunga at 0.6°E to account for 18.0 ± 5.8 mSv of the total 1.6 ± 0.2 Sv westward transport (Sv = 106 m3 s−1). In Trolltunga's lee and downstream at 2.8°W, we find this figure to ultimately increase to 23.8 ± 15.5 mSv of a total 2.8 ± 0.4 Sv transport. Each of these sections was impeded by sea ice cover, so these estimates of westward transport are probably lower limits. The westward glacial ice meltwater transport of 10 ± 3 mSv at 2.8°W highlights the role that Fimbulisen plays in preconditioning shelf waters before they reach broad continental shelves in the southwestern Weddell Sea where they transform to bottom waters.
Glacial cycles and solar insolation: the role of orbital, seasonal, and spatial variations

Abstract. We use a statistical model, the cointegrated vector autoregressive model, to evaluate the relative roles that orbital, seasonal, and spatial variations in solar insolation play in glacial cycles during the late Quaternary (390kyr – present). To do so, we estimate models of varying complexity and compare the accuracy of their in-sample simulations. Results indicate that variations in solar insolation associated with changes in Earth's orbit have the greatest explanatory power and that obliquity, precession, and eccentricity are needed to generate an accurate simulation of glacial cycles. Seasonal variations in insolation play a lesser role, while cumulative summer-time insolation has little explanatory power. Finally, solar insolation in the Northern Hemisphere generates the more accurate in-sample simulation of surface temperature while ice volume is simulated most accurately by solar insolation in the Southern Hemisphere.
Performance modeling of single-inlet aerosol sampling cyclones

A technical basis has been developed which justifies using two nondimensional parameters: the ratio of the cutpoint particle diameter to the cyclone diameter, (D 0.5 /D c ) and the flow Reynolds numbers, Ref. An improved method has also been developed for the design of single-inlet aerosol sampling cyclones using these parameters in a semiempirical functional relation. This allows predictions to be made of aerodynamic equivalent particle (AED) cutpoint diameter for a Stairmand cyclone which has had an alteration to its outlet tube diameter. The correlation coefficient for the functional relationship is r 2 >0.99. Using a particular cyclone, a designer can hold the airflow rate constant and then predict how the particle cutpoint will change as the outlet tube diameter is changed
Well-being Among Australian Children: A Review of Frameworks and Measures

This paper provides a review of the literature related to the theoretical frameworks and measurement issues that surround the study of child well-being and has been conducted in order to provide the basis for the development of small area level child well-being indicators in Australia . We identify three basic sets of frameworks used to conceptualise child well-being: those that originate from a health/well-being perspective, those that have come from a disadvantage perspective and those that focus on the child’s perspective. As well as giving an overview of selected Australian and international studies that have emerged from these perspectives, we cover a range of measurement issues related to child well-being, including the development of indicators and the rationale behind measuring well-being at a small area level. We summarise the range of domains used in recent studies of child well-being, demonstrating areas of consensus and divergence.
Intradural Extramedullary Spinal Cord Tumors: A Retrospective Study of Tumor Types, Locations, and Surgical Outcomes

Introduction: Intradural extramedullary spinal cord tumors (IESCT) account for approximately two thirds of all intraspinal neoplasms. The purpose of this report was to determine short-and long-term outcomes of surgical patients with IESCT, and to examine clinical features that could be helpful in management of patients with these lesions. Methods: A retrospective review of 67 operative IESCT cases between 1974 and 2001 was performed. Outcomes were scored at one month and at mean follow-up of 8.5 months postoperatively. In addition, patient demographics, tumor types and locations were also collected. Statistical analysis was conducted utilizing Chi-square and Student's t-tests. Results: There were 31 men and 36 women (mean age 48 y/o, range 18-87 y/o). Men presented at a younger age than women (44 vs 53 y/o, P<0.02). Fifty-seven (85%) patients presented with severe radiculopathy and/or myelopathy. The remaining 10 (15%) had symptoms typical of disc herniation. Mean duration of symptoms prior to diagnosis was 11 months. Schwannomas (36 patients) had the longest mean duration of symptoms (14.9 months), followed by meningiomas (21 patients, 8.4 months), and ependymomas (10 patients, 2 months). Sixty-three (94%) of patients demonstrated significant improvement at one-month and 62 (92%) at 8.5-month mean follow-up as compared to the index exam. Only 13/67 (19.4%) patients had residual focal deficits on long term follow-up. Conclusions: Surgery for IESCT should be expected to produce significant and dramatic improvement in great majority of patients. Demographic, tumor-specific and anatomic considerations may be clinically useful when approaching IESCT.
Vibration and Sound Response of Glass-Fiber-Reinforced Polyamide 6 Using Microcellular-Foaming-Process-Applied Injection Molding Process

In this study, the vibration and sound response characteristics of composites produced via injection molding applied with a microcellular foaming process (MCPs) were improved. The study was conducted using PA6 and glass fiber composites, which are representative thermoplastic engineering plastics. Two types of specimens were used: a plate specimen to confirm the basic sound and vibration characteristics, and a large roof-rack specimen from an actual vehicle with a complex shape. The frequency response function curve was calculated by conducting an impact test, and natural frequency and damping ratio were measured based on the curve. The results confirmed that, in the case of a specimen manufactured through the injection molding process to which MCPs were applied, the natural frequency was lowered, and the damping ratio decreased. The degree of change in the natural frequency and damping ratio was confirmed. To determine the cause of the change in the natural frequency and damping ratio, the mode shape at the natural frequency of each specimen was measured and the relationship was confirmed by measuring the density and the elastic modulus of the composite. In addition, the usability of the specimens to which MCPs were applied was verified by conducting impact strength and tensile strength tests.
Mapping cellular response to destabilized transthyretin reveals cell- and amyloidogenic protein-specific signatures

Abstract Background In ATTR amyloidosis, transthyretin (TTR) protein is secreted from the liver and deposited as toxic aggregates at downstream target tissues. Despite recent advancements in treatments for ATTR amyloidosis, the mechanisms underlying misfolded TTR-mediated cellular damage remain elusive. Methods In an effort to define early events of TTR-associated stress, we exposed neuronal (SH-SY5Y) and cardiac (AC16) cells to wild-type and destabilized TTR variants (TTRV122I (p.V142I) and TTRL55P (p.L70P)) and performed transcriptional (RNAseq) and epigenetic (ATACseq) profiling. We subsequently compared TTR-responsive signatures to cells exposed to destabilized antibody light chain protein associated with AL amyloidosis as well as ER stressors (thapsigargin, heat shock). Results In doing so, we observed overlapping, yet distinct cell type- and amyloidogenic protein-specific signatures, suggesting unique responses to each amyloidogenic variant. Moreover, we identified chromatin level changes in AC16 cells exposed to mutant TTR that resolved upon pre-incubation with kinetic stabilizer tafamidis. Conclusions Collectively, these data provide insight into the mechanisms underlying destabilized protein-mediated cellular damage and provide a robust resource representing cellular responses to aggregation-prone proteins and ER stress.
Surveying Campus GIS and GPS Users to Determine Role and Level of Library Services

This survey was created by The University of Tennessee (UT) Libraries to assess the need for providing geographic information system (GIS) and global positioning system (GPS) services to the UT Knoxville, community. In the past few years, the UT Libraries have seen an increase in the number of students and faculty who need help with GIS-related technologies (GIS and GPS). To meet these needs, the library has expanded virtual training and begun to collaborate with other departments on campus to assist users with GIS needs. This survey attempts to answer the question: Where does the library fit into campus GIS-related services? Graduate students and faculty who participated in the survey agreed that the library should play a central role in offering GIS-related services. However, the survey results show that there is not enough training available with GIS-related technologies on campus. If the library is to play a central role, then additional resources should be considered to support GIS-related services in the library and across campus.
Remote sensing of aerosol properties over oceans using the MODIS/EOS spectral radiances

Spectral radiances measured at the top of the atmosphere in a wide spectral range (0.55–2.13 μm) are used to monitor the aerosol optical thickness and the aerosol size distribution (integrated on the vertical column) of the ambient (undisturbed) aerosol over the oceans. Even for the moderate resolution imaging spectrometer (MODIS) wide spectral range, only three parameters that describe the aerosol loading and size distribution can be retrieved. These three parameters are not always unique. For instance, the spectral radiance of an aerosol with a bilognormal size distribution can be simulated very well with a single lognormal aerosol with an appropriate mean radius and width of distribution. Preassumptions on the general structure of the size distribution are therefore required in the inversion of MODIS data. The retrieval of the aerosol properties is performed using lookup table computations. The volume size distribution in the lookup table is described with two lognormal modes: a single mode to describe the accumulation mode particles (radius 1.0 μm). Note that two accumulation modes may be present, one dominated by gas phase processes and a second dominated by cloud phase processes. The coarse mode can also be split into several partially overlapping modes describing maritime salt particles and dust. The aerosol parameters we expect to retrieve are η, the fractional contribution of the accumulation mode to scattering; τ, the spectral optical thickness; and rm, the mean particle size of the dominant mode. Additional radiative quantities such as asymmetry parameter and effective radius are derived subsequently. The impact of the surface conditions, wind speed and chlorophyll content on the retrieval is estimated, the impact of potential sources of error like the calibration of the instrument is also tested. The algorithm has been applied successfully to actual data sets provided by the Thematic Mapper on Landsat 5 and by the MODIS airborne simulator on the ER-2 and tested against ground and airborne measurements. A first estimate of the general accuracy is Δτ = ±0.05±0.05τ (at 550 nm), Δrm = 0.3rm, Δη = ±0.25.
Geochemistry of heavy metals in the surficial sediments of mangroves of the south west coast of India

The distribution and speciation of Fe, Mn and Cu in six geographically different mangroves of the south west coast of India have been examined. The metal concentrations in sediments ranged from 0.53–95.44 mg/g for iron, 12.16–325.98 μg/g for manganese and 0.13–243.32 μg/g for copper. The metal levels in sediments were comparable with those from similar aquatic systems. Speciation of metals in sediments and principal component analysis (PCA) of the speciation data indicates that ultimate storage of iron is in the inorganic pyrite form. Manganese and copper exhibit temporary storage by associations with organic matter.
diverse protein families Genome-scale phylogenetic function annotation of large and Material Supplemental

The Statistical Inference of Function Through Evolutionary Relationships (SIFTER) framework uses a statistical graphical model that applies phylogenetic principles to automate precise protein function prediction (Engelhardt et al., 2005, 2006). Here we present a significant revision of the approach (SIFTER version 2.0) that allows annotations to be made on a genomic scale. We confirm that SIFTER 2.0 produces equivalently precise predictions to the earlier version of SIFTER on a carefully studied family and on a collection of one hundred protein families with limited functional diversity. We have added an approximation method to SIFTER 2.0, and show a 500-fold improvement in speed with minimal impact on prediction results in the functionally diverse sulfotransferase protein family. On the Nudix protein family, which was previously inaccessible to the SIFTER framework because of the 66 possible molecular functions, SIFTER achieved 47.4% accuracy on experimental data (where BLAST achieved 34.0%). Finally, we used SIFTER to annotate all of the Schizosaccharomyces pombe proteins with experimental functional characterizations, based on annotations from proteins in 46 complete fungal genomes. SIFTER precisely predicted molecular function for 45.5% of the characterized proteins in this genome, as compared with four current function prediction methods that precisely predicted function for 62.6%, 30.6%, 6.0% and 5.7% of these same proteins. We use both precision-recall curves and ROC analyses to compare these genome-scale predictions across the different methods and to assess performance on different types of applications. SIFTER 2.0 is now capable of predicting protein molecular function for large and functionally diverse protein families using an approximate statistical model, enabling phylogenetics-based protein function prediction for genome-wide analyses. The code for SIFTER and protein family data are available for download at http://sifter.berkeley. edu. Cold Spring Harbor Laboratory Press on July 28, 2011 Published by genome.cshlp. org Downloaded from
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes

data Supplementary http://www.genome. org/cgi/content/full/gr.6593807/DC1 12 Genomes" Drosophila " References http://www.genome. org/cgi/content/abstract/gr.6593807v1#otherarticles Article cited in: P<P Published online November 7, 2007 in advance of the print journal. service Email alerting click here top right corner of the article or Receive free email alerts when new articles cite this article sign up in the box at the