Firewood extraction affects carbon pools and nutrients in remnant fragments of temperate forests at the Mexican Transvolcanic Belt

Globally, remnant fragments of forests represent the main carbon reservoir of terrestrial ecosystems, but they suffer strong degradation due to uncontrolled wood extraction mainly by tree cut for household fuel use and charcoal production. The present study evaluates the degradation caused by wood extraction on carbon pools and soil nutrient dynamics in temperate forests distributed in remnant fragments located in central Mexico. Four sites with different intensity of wood extraction were chosen for measuring carbon pools and nutrient fluxes during two years. Both, aboveground carbon biomass and soil organic carbon values decreased with the intensity of forest degradation. The degraded forest (DF) showed total carbon content 55 % lower than that shown by the seminatural forest (SF). Additionally, litterfall production was reduced in DF as compared to SF; the decomposition rate of standing litter was higher in the latter site. As a consequence, DF had lower organic matter inputs to the soil than that presented by SF. Soil extractable ammonium and microbial biomass-carbon and -nitrogen were lower in DF than in SF. It was concluded that the uncontrolled wood extraction in these remnants of temperate forest in Mexico significantly reduced the carbon pools, carbon and nutrient fluxes through litterfall and consequently, the soil nutrient dynamics were disrupted

On the benefits of tasking with OpenMP

Tasking promises a model to program parallel applications that provides intuitive semantics. In the case of tasks with dependences, it also promises better load balancing by removing global synchronizations (barriers), and potential for improved locality. Still, the adoption of tasking in production HPC codes has been slow. Despite OpenMP supporting tasks, most codes rely on worksharing-loop constructs alongside MPI primitives. This paper provides insights on the benefits of tasking over the worksharing-loop model by reporting on the experience of taskifying an adaptive mesh refinement proxy application: miniAMR. The performance evaluation shows the taskified implementation being 15–30% faster than the loop-parallel one for certain thread counts across four systems, three architectures and four compilers thanks to better load balancing and system utilization. Dynamic scheduling of loops narrows the gap but still falls short of tasking due to serial sections between loops. Locality improvements are incidental due to the lack of locality-aware scheduling. Overall, the introduction of asynchrony with tasking lives up to its promises, provided that programmers parallelize beyond individual loops and across application phases.Peer ReviewedPostprint (author's final draft

Does posterior capsule opacification affect the results of diagnostic technologies to evaluate the retina and the optic disc?

The visual outcome obtained after cataract removal may progressively decline because of posterior capsular opacification (PCO). This condition can be treated by creating an opening in the posterior lens capsule by Nd:YAG laser capsulotomy. PCO optical imperfections cause several light reflection, refraction, and diffraction phenomena, which may interfere with the functional and structural tests performed in different ocular locations for the diagnosis and follow-up of ocular disease, like macular and optic nerve diseases. Some parameters measured by visual field examinations, scanning laser polarimetry, and optical coherence tomography (OCT) have changed after PCO removal. Imaging quality also changes following capsulotomy. Consequently, the results of ancillary tests in pseudophakic eyes for studying ocular diseases like glaucoma or maculopathies should be correlated with other clinical examinations, for example, slit-lamp biomicroscopy or funduscopy. If PCO is clinically significant, a new baseline should be set for future comparisons following capsulotomy when using automated perimetry and scanning laser polarimetry. To perform OCT in the presence of PCO, reliable examinations (considering signal strength) apparently guarantee that measurements are not influenced by PCO

GOPHER, an HPC framework for large scale graph exploration and inference

Biological ontologies, such as the Human Phenotype Ontology (HPO) and the Gene Ontology (GO), are extensively used in biomedical research to investigate the complex relationship that exists between the phenome and the genome. The interpretation of the encoded information requires methods that efficiently interoperate between multiple ontologies providing molecular details of disease-related features. To this aim, we present GenOtype PHenotype ExplOrer (GOPHER), a framework to infer associations between HPO and GO terms harnessing machine learning and large-scale parallelism and scalability in High-Performance Computing. The method enables to map genotypic features to phenotypic features thus providing a valid tool for bridging functional and pathological annotations. GOPHER can improve the interpretation of molecular processes involved in pathological conditions, displaying a vast range of applications in biomedicine.This work has been developed with the support of the Severo Ochoa Program (SEV-2015-0493); the Spanish Ministry of Science and Innovation (TIN2015- 65316-P); and the Joint Study Agreement no. W156463 under the IBM/BSC Deep Learning Center agreement.Peer ReviewedPostprint (author's final draft

Relation between Epidural Analgesia and severe perineal laceration in childbearing women in Catalonia

Our objectives were to study the association between epidural analgesia and risk of severe perineal laceration (SPL), and identify additional risk factors for SPL. This multicentre study consisted of an analysis of data from the MidconBirth Phase I Database, on the use of EA and perineal results during childbirth. (World Health Organization, International Clinical Trials Registry Platform, 2016: http://apps.who.int/trialsearch/Trial2.aspx?TrialID=ISRCTN17833269). We conducted a prospective study of pregnant women at term between July 2016 and July 2017 in 30 public maternity hospitals in Catalonia, Spain. Inclusion criteria were an uncomplicated singleton pregnancy, in cephalic presentation and vaginal birth. Data was analysed separately for instrumental births and spontaneous vaginal births, as the former is more frequently associated with episiotomy and more perineal lacerations. Risk factors as well as protective factors in each cohort of women (instrumental and spontaneous vaginal birth), were identified. Multivariate logistic regression model was performed to study the association between epidural analgesia and SPL to identify potential confounders. Odds ratios (OR), using 95% confidence intervals (CI) were constructed. During the study period, 5497 eligible women gave birth, 77.46% of them received epidural analgesia. SPL occurred in 1.63% of births. The univariate analysis showed births with epidural analgesia had significantly higher rates of inductions, augmentation of labour, lithotomy position for birth and episiotomy. However, this association disappeared when the variable "type of vaginal birth" was introduced. In multivariate logistic regression, nulliparity was the major predictor for SPL (OR: 0.17; CI 95%: 0.08-0.34, p: 0.000). Epidural analgesia was not associated with SPL once confounding factors were included. Other interesting factors associated with SPL were identified. This paper identifies important practice areas which contribute to SPL and which have the potential to be rectified. It offers evidence on the role that EA plays on pelvic floor injuries and it adds to existing evidence about the disadvantages of using the lithotomy position for birth, especially in relation to SPL. It highlights the need for practice change in Catalonia from what can be considered a medical model of care to one more aligned with the midwifery philosophy of care through the development of clinical guidelines. It also signals the need to provide women with evidence base upon which to make informed choices on the use of EA, specifically in relation to SPL. [Abstract copyright: Copyright © 2018 Elsevier Ltd. All rights reserved.

Genetic variation in the TLL1 gene is not associated with fibrosis in patients with metabolic associated fatty liver disease

Metabolic associated fatty liver disease (MAFLD) is the most prevalent liver disease in Western nations, with high heritability. A recent study of Japanese patients with the disease suggested that TLL1 rs17047200 is associated with fibrosis; whether a similar association is observed in Caucasian patients with MAFLD is unknown. We investigated the association of the TLL1 rs17047200 polymorphism with liver fibrosis in a cohort of Caucasian patients with MAFLD (n = 728). We also investigated whether TLL1 expression is altered during liver injury in humans, in murine models of fibrosis, and in in-vitro. While TLL1 expression is upregulated in the liver of humans with MAFLD and in mice, the rs17047200 variant was not associated with fibrosis or any other histological features, or with hepatic TLL1 expression. In conclusion, the TLL1 rs17047200 variant is not a risk variant for fibrosis in Caucasian patients with MAFLD. However, TLL1 could be involved in the pathogenesis of liver fibrosis

Copy number variation and expression of exportin-4 associates with severity of fibrosis in metabolic associated fatty liver disease

Background: Liver fibrosis risk is a heritable trait, the outcome of which is the net deposition of extracellular matrix by hepatic stellate cell-derived myofibroblasts. Whereas nucleotide sequence variations have been extensively studied in liver fibrosis, the role of copy number variations (CNV) in which genes exist in abnormal numbers of copies (mostly due to duplication or deletion) has had limited exploration. Methods: The impact of the XPO4 CNV on histological liver damage was examined in a cohort comprised 646 Caucasian patients with biopsy-proven MAFLD and 170 healthy controls. XPO4 expression was modulated and function was examined in human and animal models. Findings: Here we demonstrate in a cohort of 816 subjects, 646 with biopsy-proven metabolic associated liver disease (MAFLD) and 170 controls, that duplication in the exportin 4 (XPO4) CNV is associated with the severity of liver fibrosis. Functionally, this occurs via reduced expression of hepatic XPO4 that maintains sustained activation of SMAD3/SMAD4 and promotes TGF-β1-mediated HSC activation and fibrosis. This effect was mediated through termination of nuclear SMAD3 signalling. XPO4 demonstrated preferential binding to SMAD3 compared to other SMADs and led to reduced SMAD3-mediated responses as shown by attenuation of TGFβ1 induced SMAD transcriptional activity, reductions in the recruitment of SMAD3 to target gene promoters following TGF-β1, as well as attenuation of SMAD3 phosphorylation and disturbed SMAD3/SMAD4 complex formation. Interpretation: We conclude that a CNV in XPO4 is a critical mediator of fibrosis severity and can be exploited as a therapeutic target for liver fibrosis. Funding: ME and JG are supported by the Robert W. Storr Bequest to the Sydney Medical Foundation, University of Sydney; a National Health and Medical Research Council of Australia (NHMRC) Program Grant (APP1053206) and Project and ideas grants (APP2001692, APP1107178 and APP1108422). AB is supported by an Australian Government Research Training Program (RTP) scholarship. EB is supported by Horizon 2020 under grant 634413 for the project EPoS

Hypoglycemia in Type 1 Diabetic Pregnancy: Role of preconception insulin aspart treatment in a randomized study

Objective: A recent randomized trial compared prandial insulin aspart (IAsp) with human insulin in type 1 diabetic pregnancy. The aim of this exploratory analysis was to investigate the incidence of severe hypoglycemia during pregnancy and compare women enrolled preconception with women enrolled during early pregnancy. Research design and methods: IAsp administered immediately before each meal was compared with human insulin administered 30 min before each meal in 99 subjects (44 to IAsp and 55 to human insulin) randomly assigned preconception and in 223 subjects (113 for IAsp and 110 for human insulin) randomly assigned in early pregnancy (<10 weeks). NPH insulin was the basal insulin. Severe hypoglycemia (requiring third-party assistance) was recorded prospectively preconception (where possible), during pregnancy, and postpartum. Relative risk (RR) of severe hypoglycemia was evaluated with a gamma frailty model. Results: Of the patients, 23% experienced severe hypoglycemia during pregnancy with the peak incidence in early pregnancy. In the first half of pregnancy, the RR of severe hypoglycemia in women randomly assigned in early pregnancy/preconception was 1.70 (95% CI 0.91–3.18, P = 0.097); the RR in the second half of pregnancy was 1.35 (0.38–4.77, P = 0.640). In women randomly assigned preconception, severe hypoglycemia rates occurring before and during the first and second halves of pregnancy and postpartum for IAsp versus human insulin were 0.9 versus 2.4, 0.9 versus 2.4, 0.3 versus 1.2, and 0.2 versus 2.2 episodes per patient per year, respectively (NS). Conclusions: These data suggest that initiation of insulin analog treatment preconception rather than during early pregnancy may result in a lower risk of severe hypoglycemia in women with type 1 diabetes