Enhancing speed and scalability of the ParFlow simulation code

Regional hydrology studies are often supported by high resolution simulations of subsurface flow that require expensive and extensive computations. Efficient usage of the latest high performance parallel computing systems becomes a necessity. The simulation software ParFlow has been demonstrated to meet this requirement and shown to have excellent solver scalability for up to 16,384 processes. In the present work we show that the code requires further enhancements in order to fully take advantage of current petascale machines. We identify ParFlow's way of parallelization of the computational mesh as a central bottleneck. We propose to reorganize this subsystem using fast mesh partition algorithms provided by the parallel adaptive mesh refinement library p4est. We realize this in a minimally invasive manner by modifying selected parts of the code to reinterpret the existing mesh data structures. We evaluate the scaling performance of the modified version of ParFlow, demonstrating good weak and strong scaling up to 458k cores of the Juqueen supercomputer, and test an example application at large scale.Comment: The final publication is available at link.springer.co

Scalable parallel simulation of variably saturated flow

In this thesis we develop highly accurate simulation tools for variably saturated flow through porous media able to take advantage of the latest supercomputing resources. Hence, we aim for parallel scalability to very large compute resources of over 105 CPU cores. Our starting point is the parallel subsurface flow simulator ParFlow. This library is of widespread use in the hydrology community and known to have excellent parallel scalability up to 16k processes. We first investigate the numerical tools this library implements in order to perform the simulations it was designed for. ParFlow solves the governing equation for subsurface flow with a cell centered finite difference (FD) method. The code targets high performance computing (HPC) systems by means of distributed memory parallelism. We propose to reorganize ParFlow's mesh subsystem by using fast partitioning algorithms provided by the parallel adaptive mesh refinement (AMR) library p4est. We realize this in a minimally invasive manner by modifying selected parts of the code to reinterpret the existing mesh data structures. Furthermore, we evaluate the scaling performance of the modified version of ParFlow, demonstrating excellent weak and strong scaling up to 458k cores of the Juqueen supercomputer at the Jülich Supercomputing Centre. The above mentioned results were obtained for uniform meshes and hence without explicitly exploiting the AMR capabilities of the p4est library. A natural extension of our work is to activate such functionality and make ParFlow a true AMR application. Enabling ParFlow to use AMR is challenging for several reasons: It may be based on assumptions on the parallel partition that cannot be maintained with AMR, it may use mesh-related metadata that is replicated on all CPUs, and it may assume uniform meshes in the construction of mathematical operators. Additionally, the use of locally refined meshes will certainly change the spectral properties of these operators. In this work, we develop an algorithmic approach to activate the usage of locally refined grids in ParFlow. AMR allows meshes where elements of different size neighbor each other. In this case, ParFlow may incur erroneous results when it attempts to communicate data between inter-element boundaries. We propose and discuss two solutions to this issue operating at two different levels: The first manipulates the indices of the degrees of freedom, While the second operates directly on the degrees of freedom. Both approaches aim to introduce minimal changes to the original ParFlow code. In an AMR framework, the FD method taken by ParFlow will require modifications to correctly deal with different size elements. Mixed finite elements (MFE) are on the other hand better suited for the usage of AMR. It is known that the cell centered FD method used in ParFlow might be reinterpreted as a MFE discretization using Raviart-Thomas elements of lower order. We conclude this thesis presenting a block preconditioner for saddle point problems arising from a MFE on locally refined meshes. We evaluate its robustness with respect to various classes of coefficients for uniform and locally refined meshes

Lutzomyia longipalpis s.l. in Brazil and the impact of the Sao Francisco River in the speciation of this sand fly vector

Lutzomyia longipalpis s.l. (Diptera: Psychodidae) is the principal vector of Leishmania infantum chagasi in the Americas, and constitutes a complex of species. Various studies have suggested an incipient speciation process based on behavioral isolation driven by the chemotype of male sexual pheromones. It is well known that natural barriers, such as mountains and rivers can directly influence population divergence in several organisms, including insects. In this work we investigated the potential role played by the Sao Francisco River in eastern Brazil in defining the current distribution of Lu. longipalpis s.l. Our studies were based on analyses of polymorphisms of the cytochrome b gene (cyt b) sequences from Lu. longipalpis s.l. available in public databases, and from additional field-caught individuals. Altogether, 9 distinct populations and 89 haplotypes were represented in the analyses. Lu. longipalpis s.l. populations were grouped according to their distribution in regards to the 10°S parallel: north of 10°S (<10°S); and south of 10°S (>10°S). Our results suggest that although no polymorphisms were fixed, moderate genetic divergences were observed between the groups analyzed (i.e., FST = 0.184; and Nm = 2.22), and were mostly driven by genetic drift. The population divergence time estimated between the sand fly groups was about 0.45 million years (MY), coinciding with the time of the change in the course of the Sao Francisco River, during the Mindel glaciation. Overall, the polymorphisms on the cyt b haplotypes and the current speciation process detected in Lu. longipalpis s.l. with regards to the distribution of male sexual pheromones suggest a role of the Sao Francisco River as a significant geographical barrier in this process

Differentiation Between Women With Vulvovaginal Symptoms Who are Positive or Negative for Candida Species by Culture

Objective: To investigate whether clinical criteria could differentiate between women with vulvovaginitis who were culture positive or negative for vaginal Candida species. Methods: Vulvovaginal specimens were obtained from 501 women with a vaginal discharge and/or pruritis. Clinical information and wet mount microscopy findings were obtained. All specimens were sent to a central laboratory for species identification. Results: A positive culture for Candida species was obtained from 364 (72.7%) of the specimens. C. albicans was identified in 86.4% of the positive cultures, followed by C. glabrata in 4.5%, C. parapsilosis in 3.9%, C. tropicalis in 2.7% and other Candida species in 1.4%.Women with a positive Candida culture had an increased utilization of oral contraceptives (26.1% vs. 16.8%, p = 0.02) and antibiotics (8.2% vs. 0.7%, p = 0.001), and were more likely to be pregnant (9.1% vs. 3.6%, p = 0.04) than the culture-negative women. Dyspareunia was more frequent in women without Candida (38.0% vs. 28.3%, p = 0.03) while vaginal erythema (p = 0.01) was more common in women with a positive Candida culture. Conclusions: Although quantitative differences were observed, the presence of vaginal Candida vulvovaginitis cannot be definitively identified by clinical criteria

Variação espacial da resistividade elétrica em terraços agrícolas: correlação estatística entre TRE e algoritmos de direção de fluxos = Electrical resistivity spatial variation in agriculture terraces : statistical correlation with ERT and flow direction algorithms

The construction of terraces, in the Douro Region, with earthen embankments rises aset of problems related to the hydrological processes. The main objective of this study is the evaluation of the electrical resistivity spatial variation in agriculture terraces atDouro valley (Portugal).To achieve this objective two variables are analysed, the soil electrical resistivity andthe flow direction algorithms. In field survey, 13 electrical resistivity profiles wererecorded. The contributing area calculated with the algorithms D (DeterminiscInfinity Flow) and MFD (Multiple Flow Direction), are the base of the internal runoffmodelling, both supported by the digital elevation model with a special resolution of1m2.Was stablished a correlation between the spatial variation of the soil electrical resistivityrepresented by standard deviation electrical resistivity of each profile and the averagevalue of contributing area coincident with each profile.The electrical resistivity standard deviation seems to be moderately good correlated forthe D algorithm at about 1m of depth and has a good correlaon at 1,5m to 2m ofdepth with the MFD algorithm. The results analysis shows a significant positivestatistical correlation between electrical resistivity standard deviation and thecontributing areas (MFD and D) depending on the soil depths

MeerKLASS: MeerKAT Large Area Synoptic Survey

We discuss the ground-breaking science that will be possible with a wide area survey, using the MeerKAT telescope, known as MeerKLASS (MeerKAT Large Area Synoptic Survey). The current specifications of MeerKAT make it a great fit for science applications that require large survey speeds but not necessarily high angular resolutions. In particular, for cosmology, a large survey over $\sim 4,000 \, {\rm deg}^2$ for $\sim 4,000$ hours will potentially provide the first ever measurements of the baryon acoustic oscillations using the 21cm intensity mapping technique, with enough accuracy to impose constraints on the nature of dark energy. The combination with multi-wavelength data will give unique additional information, such as exquisite constraints on primordial non-Gaussianity using the multi-tracer technique, as well as a better handle on foregrounds and systematics. Such a wide survey with MeerKAT is also a great match for HI galaxy studies, providing unrivalled statistics in the pre-SKA era for galaxies resolved in the HI emission line beyond local structures at z > 0.01. It will also produce a large continuum galaxy sample down to a depth of about 5\,$\mu$Jy in L-band, which is quite unique over such large areas and will allow studies of the large-scale structure of the Universe out to high redshifts, complementing the galaxy HI survey to form a transformational multi-wavelength approach to study galaxy dynamics and evolution. Finally, the same survey will supply unique information for a range of other science applications, including a large statistical investigation of galaxy clusters as well as produce a rotation measure map across a huge swathe of the sky. The MeerKLASS survey will be a crucial step on the road to using SKA1-MID for cosmological applications and other commensal surveys, as described in the top priority SKA key science projects (abridged).Comment: Larger version of the paper submitted to the Proceedings of Science, "MeerKAT Science: On the Pathway to the SKA", Stellenbosch, 25-27 May 201

Physical literacy in older adults: a scoping review protocol

Population aging is a prominent phenomenon worldwide. The increase in physical inactivity and co-morbid diseases poses a major challenge to current community health policies. Physical activity guidelines recommended for older people have not been met by this population group. For this reason, a new model, physical literacy, is being innovated and has gained global attention and has emerged as an effective and innovative active aging strategy to improve physical activity participation of this vulnerable group. However, the evidence on physical literacy in the older adult so far is brief and diffuse. Therefore, the aim was to conduct a scoping review protocol to identify and map physical literacy in older people. This scoping review protocol was based on the Joanna Briggs Institute Method. The search will be performed on Embase, IBSS ProQuest, Medline OVID, PsycINFO Ebsco, PubMed, ScienceDirect, Scopus, SPORTDiscus, Social Services Abstracts ProQuest, Sociological Abstracts ProQuest, Web of Science ISI, Wiley Online Library, Cochrane Library, and ERIC Ebsco databases. All types of studies published since 2001 in English, Spanish, and Portuguese examining physical literacy over the lifespan of older adults were included. Two independent reviewers will organize and select studies according to the objectives and questions of the scoping review. The selected publications will be organized and summarized using a checklist proposed by the PRISMA-ScR. Qualitative data analysis (thematic analysis) will be performed to identify meanings and patterns to answer the research question. The final scoping review will present the main evidence available, key concepts/definitions, research conducted, and knowledge gaps related to physical literacy in older adults, leading to strategies to improve the community health of this population, as well as health literacy

Effectiveness and long-term retention of anti-tumour necrosis factor treatment in juvenile and adult patients with juvenile idiopathic arthritis: data from Reuma.pt

Methods. We prospectively collected patient and disease characteristics from patients with JIA who started biological therapy. Adverse events were collected during the follow-up period. Predictors of response at 1 year and drug retention rates were assessed at 4 years of treatment for the first biologic agent.Results. A total of 812 JIA patients [65% females, mean age at JIA onset 6.9 years (s.d. 4.7)], 227 received biologic therapy; 205 patients (90.3%) were treated with an anti-TNF as the first biologic. All the parameters used to evaluate disease activity, namely number of active joints, ESR and Childhood HAQ/HAQ, decreased significantly at 6 months and 1 year of treatment. The mean reduction in Juvenile Disease Activity Score 10 (JADAS10) after 1 year of treatment was 10.4 (s.d. 7.4). According to the definition of improvement using the JADAS10 score, 83.3% respond to biologic therapy after 1 year. Fourteen patients discontinued biologic therapies due to adverse events. Retention rates were 92.9% at 1 year, 85.5% at 2 years, 78.4% at 3 years and 68.1% at 4 years of treatment. Among all JIA subtypes, only concomitant therapy with corticosteroids was found to be univariately associated with withdrawal of biologic treatment (P = 0.016).Conclusion. Biologic therapies seem effective and safe in patients with JIA. In addition, the retention rates for the first biologic agent are high throughout 4 years

Effects of ezetimibe on markers of synthesis and absorption of cholesterol in high-risk patients with elevated C-reactive protein

AbstractAimsHigh-risk subjects with elevated C-reactive protein (CRP) are at high risk for cardiovascular events and frequently require potent statins or combined lipid-lowering therapy to achieve lipid targets and decrease inflammation. Our study aimed at evaluating the effects of three lipid-modifying therapies on LDL-cholesterol, CRP levels and markers of cholesterol absorption and synthesis.Main methodsA prospective intervention study was performed in high cardiovascular risk individuals receiving atorvastatin 10mg daily for four weeks. Those with CRP≥2.0mg/L were randomized to another four-week treatment period with atorvastatin 40mg, ezetimibe 10mg or the combination of atorvastatin 40mg / ezetimibe 10mg. Lipids, markers of cholesterol absorption (campesterol and β-sitosterol), and synthesis (desmosterol), as well as CRP were quantified at baseline and end of study.Key findingsOne hundred and twenty two individuals were included. Atorvastatin alone or combined with ezetimibe reduced both LDL-cholesterol and CRP (P<0.002 vs. baseline; Wilcoxon); ezetimibe did not modify CRP. Ezetimibe-based therapies reduced absorption markers and their ratios to cholesterol (P<0.0001 vs. baseline, for all; Wilcoxon), whereas atorvastatin alone increased campesterol/cholesterol and β-sitosterol/cholesterol ratios (P<0.05 vs. baseline; Wilcoxon). In addition, ezetimibe also increased desmosterol and desmosterol/cholesterol ratio (P<0.0001 vs. baseline; Wilcoxon).SignificanceThese results contribute to understanding the link between cellular cholesterol homeostasis, inflammation and lipid-modifying therapies. Our findings highlight the broader benefit of combined therapy with a potent statin and ezetimibe decreasing inflammation, and preventing increase in cholesterol biosynthesis, an effect not observed with ezetimibe alone