Performance enhancement of a GIS-based facility location problem using desktop grid infrastructure

This paper presents the integration of desktop grid infrastructure with GIS technologies, by proposing a parallel resolution method in a generic distributed environment. A case study focused on a discrete facility location problem, in the biomass area, exemplifies the high amount of computing resources (CPU, memory, HDD) required to solve the spatial problem. A comprehensive analysis is undertaken in order to analyse the behaviour of the grid-enabled GIS system. This analysis, consisting of a set of the experiments on the case study, concludes that the desktop grid infrastructure is able to use a commercial GIS system to solve the spatial problem achieving high speedup and computational resource utilization. Particularly, the results of the experiments showed an increase in speedup of fourteen times using sixteen computers and a computational efficiency greater than 87 % compared with the sequential procedure.This work has been developed under the support of the program Formacion de Personal Investigador, grants number BFPI/2009/103 and BES-2007-17019, from the Conselleria d'Educacio of the Generalitat Valenciana and the Spanish Ministry of Science and Technology.García García, A.; Perpiñá Castillo, C.; Alfonso Laguna, CD.; Hernández García, V. (2013). Performance enhancement of a GIS-based facility location problem using desktop grid infrastructure. Earth Science Informatics. 6(4):199-207. https://doi.org/10.1007/s12145-013-0119-1S19920764Anderson D (2004) Boinc: a system for public-resource computing and storage. Proceedings of the 5th IEEE/ACM International Workshop on Grid Computing. IEEE Computer Society, Washington DC, pp 4–10Available scripts webpage: http://personales.upv.es/angarg12/Campos I et al (2012) Modelling of a watershed: a distributed parallel application in a grid framework. Comput Informat 27(2):285–296Church RL (2002) Geographical information systems and location science. Comput Oper Res 29:541–562Clarke KC (1986) Advances in geographic information systems, computers. Environ Urban Syst 10:175–184Dowers S, Gittings BM, Mineter MJ (2000) Towards a framework for high-performance geocomputation: handling vector-topology within a distributed service environment. Comput Environ Urban Syst 24:471–486Geograma SL (2009). Teleatlas. http://www.geograma.com . Accessed September 2009GRASS Development Team (2012) GRASS GIS. http://grass.osgeo.org/Hoekstra AG, Sloot PMA (2005) Introducing grid speedup: a scalability metric for parallel applications on the grid, EGC 2005, LNCS 3470, pp. 245–254Hu Y et al. (2004) Feasibility study of geo-spatial analysis using grid computing. Computational Science-ICCS. Springer Berlin Heidelberg, 956–963Huang Z et al (2009) Geobarn: a practical grid geospatial database system. Adv Electr Comput Eng 9:7–11Huang F et al (2011) Explorations of the implementation of a parallel IDW interpolation algorithm in a Linux cluster-based parallel GIS. Comput Geosci 37:426–434Laure E et al (2006) Programming the grid with gLite. CMST 12(1):33–45Li WJ et al (2005) The Design and Implementation of GIS Grid Services. In: Zhuge H, Fox G (eds) Grid and Cooperative Computing. Vol. 3795 of Lecture Notes in Computer Science 10. Springer, Berlin, pp 220–225National Geographic Institute (2010) BCN25: numerical cartographic database. http://www.ign.es/ign/main/index.do . Accessed April 2010Open Geospatial Consortium, Inc (2012) Open GIS Specification Model, http://www.opengeospatial.org/Openshaw S, Turton I (1996) A parallel Kohonen algorithm for the classification of large spatial datasets. Comput Geosci 22:1019–1026Perpiñá C, Alfonso D, Pérez-Navarro A (2007) BIODER project: biomass distributed energy resources assessment and logistic strategies for sitting biomass plants in the Valencia province (Spain), 17th European Biomass Conference and Exhibition Proceedings, Hamburg, Germany, pp. 387–393Perpiñá C et al (2008) Methodology based on Geographic Information Systems for biomass logistics and transport optimization. Renew Energ 34:555–565Shen Z et al (2007) Distributed computing model for processing remotely sensed images based on grid computing. Inf Sci 177:504–518Spanish Ministry of Agriculture, fisheries and food (2009). http://www.magrama.gob.es/es/ . Accessed March 2009Spanish Ministry of Environment (2008). http://www.magrama.gob.es/es/ . Accessed May 2008University of California. List of BOINC projects. http://boinc.berkeley.edu/projects.phpXiao N, Fu W (2003) SDPG: Spatial data processing grid. J Comput Sci Technol 18:523–53

Lead Optimization of 3,5-Disubstituted-7-Azaindoles for the Treatment of Human African Trypanosomiasis

Neglected tropical diseases such as human African trypanosomiasis (HAT) are prevalent primarily in tropical climates and among populations living in poverty. Historically, the lack of economic incentive to develop new treatments for these diseases has meant that existing therapeutics have serious shortcomings in terms of safety, efficacy, and administration, and better therapeutics are needed. We now report a series of 3,5-disubstituted-7-azaindoles identified as growth inhibitors of Trypanosoma brucei, the parasite that causes HAT, through a high-throughput screen. We describe the hit-to-lead optimization of this series and the development and preclinical investigation of 29d, a potent antitrypanosomal compound with promising pharmacokinetic (PK) parameters. This compound was ultimately not progressed beyond in vivo PK studies due to its inability to penetrate the blood-brain barrier (BBB), critical for stage 2 HAT treatments

Structural Basis for Specificity of Propeptide-Enzyme Interaction in Barley C1A Cysteine Peptidases

C1A cysteine peptidases are synthesized as inactive proenzymes. Activation takes place by proteolysis cleaving off the inhibitory propeptide. The inhibitory capacity of propeptides from barley cathepsin L and B-like peptidases towards commercial and barley cathepsins has been characterized. Differences in selectivity have been found for propeptides from L-cathepsins against their cognate and non cognate enzymes. Besides, the propeptide from barley cathepsin B was not able to inhibit bovine cathepsin B. Modelling of their three-dimensional structures suggests that most propeptide inhibitory properties can be explained from the interaction between the propeptide and the mature cathepsin structures. Their potential use as biotechnological tools is discussed

An in vitro model of early anteroposterior organization during human development.

The body plan of the mammalian embryo is shaped through the process of gastrulation, an early developmental event that transforms an isotropic group of cells into an ensemble of tissues that is ordered with reference to three orthogonal axes1. Although model organisms have provided much insight into this process, we know very little about gastrulation in humans, owing to the difficulty of obtaining embryos at such early stages of development and the ethical and technical restrictions that limit the feasibility of observing gastrulation ex vivo2. Here we show that human embryonic stem cells can be used to generate gastruloids-three-dimensional multicellular aggregates that differentiate to form derivatives of the three germ layers organized spatiotemporally, without additional extra-embryonic tissues. Human gastruloids undergo elongation along an anteroposterior axis, and we use spatial transcriptomics to show that they exhibit patterned gene expression. This includes a signature of somitogenesis that suggests that 72-h human gastruloids show some features of Carnegie-stage-9 embryos3. Our study represents an experimentally tractable model system to reveal and examine human-specific regulatory processes that occur during axial organization in early development

Longitudinal multi-centre brain imaging studies: guidelines and practical tips for accurate and reproducible imaging endpoints and data sharing

Abstract Background Research involving brain imaging is important for understanding common brain diseases. Study endpoints can include features and measures derived from imaging modalities, providing a benchmark against which other phenotypical data can be assessed. In trials, imaging data provide objective evidence of beneficial and adverse outcomes. Multi-centre studies increase generalisability and statistical power. However, there is a lack of practical guidelines for the set-up and conduct of large neuroimaging studies. Methods We address this deficit by describing aspects of study design and other essential practical considerations that will help researchers avoid common pitfalls and data loss. Results The recommendations are grouped into seven categories: (1) planning, (2) defining the imaging endpoints, developing an imaging manual and managing the workflow, (3) performing a dummy run and testing the analysis methods, (4) acquiring the scans, (5) anonymising and transferring the data, (6) monitoring quality, and (7) using structured data and sharing data. Conclusions Implementing these steps will lead to valuable and usable data and help to avoid imaging data wastage

Prevalence and socio-demographic correlates of physical activity levels among South African adults in Cape Town and Mount Frere communities in 2008-2009

BACKGROUND: Physical activity has been linked to reduced risk of various cardiometabolic disease, cancer, and premature mortality. We investigated the prevalence and socio-demographic correlates of physical activity among adults in urban and rural communities in South Africa. METHODS: This was a cross-sectional survey comprising 1733 adults aged ?35 years from the Cape Town (urban) and Mount Frere (rural) sites of the Prospective Urban Rural Epidemiology study. Physical activity was assessed using the validated International Physical Activity Questionnaire. Multinomial logistic regressions were used to relate physical activity with socio-demographic characteristics. RESULTS: Overall, 74% of participants engaged in moderate-to-vigorous physical activity. In the adjusted regression models, women were 34% less likely to engage in vigorous physical activity (OR =0.66, 95%-CI = 0.47-0.93). Physical activity decreased with age, varied with marital status, education and occupation, always in differential ways between urban and rural participants (all interactions p ? 0.047). For instance, in urban settings, those with secondary education were more likely to engage in moderate physical activity (OR = 2.06, 95%-CI = 1.08-3.92) than those with tertiary education. Single people were more likely to engage in high physical activity (OR = 2.10, 95%-CI = 1.03-4.28) than divorced. Overall, skilled participants were more likely to engage in vigorous physical activity (OR = 2.07, 95%-CI = 1.41-3.05) driven by significant effect in rural area (OR = 2.70, 95%-CI = 1.51-4.83). Urban participants were more likely to engage in moderate physical activity (OR = 1.67, 95%-CI = 1.31-2.13) than rural participants. CONCLUSIONS: To prevent chronic diseases among South Africans, attention should be paid to specific policies and interventions aimed at promoting PA among young adults in rural and urban setting, and across the social-economic diversity

Salt intake and gastric cancer: a pooled analysis within the Stomach cancer Pooling (StoP) Project

Purpose: Previous studies show that consuming foods preserved by salting increases the risk of gastric cancer, while results on the association between total salt or added salt and gastric cancer are less consistent and vary with the exposure considered. This study aimed to quantify the association between dietary salt exposure and gastric cancer, using an individual participant data meta-analysis of studies participating in the Stomach cancer Pooling (StoP) Project. Methods: Data from 25 studies (10,283 cases and 24,643 controls) from the StoP Project with information on salt taste preference (tasteless, normal, salty), use of table salt (never, sometimes, always), total sodium intake (tertiles of grams/day), and high-salt and salt-preserved foods intake (tertiles of grams/day) were used. A two-stage approach based on random-effects models was used to pool study-specific adjusted (sex, age, and gastric cancer risk factors) odds ratios (aORs), and the corresponding 95% confidence intervals (95% CI). Results: Gastric cancer risk was higher for salty taste preference (aOR 1.59, 95% CI 1.25–2.03), always using table salt (aOR 1.33, 95% CI 1.16–1.54), and for the highest tertile of high-salt and salt-preserved foods intake (aOR 1.24, 95% CI 1.01–1.51) vs. the lowest tertile. No significant association was observed for the highest vs. the lowest tertile of total sodium intake (aOR 1.08, 95% CI 0.82–1.43). The results obtained were consistent across anatomic sites, strata of Helicobacter pylori infection, and sociodemographic, lifestyle and study characteristics. Conclusion: Salty taste preference, always using table salt, and a greater high-salt and salt-preserved foods intake increased the risk of gastric cancer, though the association was less robust with total sodium intake. © 2022, The Author(s), under exclusive licence to Springer Nature Switzerland AG.This study was funded by national funds from the Foundation for Science and Technology—FCT (Portuguese Ministry of Science, Technology and Higher Education), under the Unidade de Investigação em Epidemiologia—Instituto de Saúde Pública da Universidade do Porto (EPIUnit; UIDB/04750/2020), by the Associazione Italiana per la Ricerca sul Cancro (AIRC), Project no. 21378 (Investigator Grant), and the Agency for Management of University and Research Grants (AGAUR) of the Catalan Government (Grant 2017SGR723). AC and SM were funded under the scope of the project "NEON-PC—Neuro-oncological complications of prostate cancer: longitudinal study of cognitive decline" (POCI-01-0145-FEDER-032358; ref. PTDC/SAU-EPI/32358/2017). SM was also funded under EPIUnit—Junior Research—Prog Financing (UIDP/04750/2020). An individual grant attributed to NA (SFRH/BD/119390/2016) was funded by FCT and the ‘Programa Operacional Capital Humano’ (POCH/FSE). The authors thank the European Cancer Prevention (ECP) Organization for providing support for the project meetings, all MCC-Spain study collaborators (CIBERESP, ISCIII, ISGlobal, ICO, University of Huelva, University of Oviedo, University of Cantabria, University of León, ibs. Granada, Instituto Salud Pública de Navarra, FISABIO, Murcia Regional Health Authority and cols). The funding sources had no role in the study design; collection, analysis, and interpretation of data; in the writing of the report; and in the decision to submit the article for publication

Comparison of the efficacy and safety of rosuvastatin 10 mg and atorvastatin 20 mg in high-risk patients with hypercholesterolemia – Prospective study to evaluate the Use of Low doses of the Statins Atorvastatin and Rosuvastatin (PULSAR)

BACKGROUND: Many patients at high risk of cardiovascular disease do not achieve recommended low-density lipoprotein cholesterol (LDL-C) goals. This study compared the efficacy and safety of low doses of rosuvastatin (10 mg) and atorvastatin (20 mg) in high-risk patients with hypercholesterolemia. METHODS: A total of 996 patients with hypercholesterolemia (LDL-C ≥ 3.4 and < 5.7 mmol/L [130 and 220 mg/dL]) and coronary heart disease (CHD), atherosclerosis, or a CHD-risk equivalent were randomized to once-daily rosuvastatin 10 mg or atorvastatin 20 mg. The primary endpoint was the percentage change from baseline in LDL-C levels at 6 weeks. Secondary endpoints included LDL-C goal achievement (National Cholesterol Education Program Adult Treatment Panel III [NCEP ATP III] goal < 100 mg/dL; 2003 European goal < 2.5 mmol/L for patients with atherosclerotic disease, type 2 diabetes, or at high risk of cardiovascular events, as assessed by a Systematic COronary Risk Evaluation (SCORE) risk ≥ 5% or 3.0 mmol/L for all other patients), changes in other lipids and lipoproteins, cost-effectiveness, and safety. RESULTS: Rosuvastatin 10 mg reduced LDL-C levels significantly more than atorvastatin 20 mg at week 6 (44.6% vs. 42.7%, p < 0.05). Significantly more patients achieved NCEP ATP III and 2003 European LDL-C goals with rosuvastatin 10 mg compared with atorvastatin 20 mg (68.8% vs. 62.5%, p < 0.05; 68.0% vs. 63.3%, p < 0.05, respectively). High-density lipoprotein cholesterol was increased significantly with rosuvastatin 10 mg versus atorvastatin 20 mg (6.4% vs. 3.1%, p < 0.001). Lipid ratios and levels of apolipoprotein A-I also improved more with rosuvastatin 10 mg than with atorvastatin 20 mg. The use of rosuvastatin 10 mg was also cost-effective compared with atorvastatin 20 mg in both a US and a UK setting. Both treatments were well tolerated, with a similar incidence of adverse events (rosuvastatin 10 mg, 27.5%; atorvastatin 20 mg, 26.1%). No cases of rhabdomyolysis, liver, or renal insufficiency were recorded. CONCLUSION: In high-risk patients with hypercholesterolemia, rosuvastatin 10 mg was more efficacious than atorvastatin 20 mg at reducing LDL-C, enabling LDL-C goal achievement and improving other lipid parameters. Both treatments were well tolerated