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We present TreeFrog, a massively parallel halo merger tree builder that is capable comparing different halo catalogues and producing halo merger trees. The code is written in c++11, use the MPI and OpenMP API’s for parallelisation, and includes python tools to read/manipulate the data products produced. The code correlates binding energy sorted particle ID lists between halo catalogues, determining optimal descendant/progenitor matches using multiple snapshots, a merit function that maximises the number of shared particles using pseudo-radial moments, and a scheme for correcting halo merger tree pathologies. Focusing on VELOCIraptor catalogues for this work, we demonstrate how searching multiple snapshots spanning a dynamical time significantly reduces the number of stranded halos, those lacking a descendant or a progenitor, critically correcting poorly resolved halos. We present a new merit function that improves the distinction between primary and secondary progenitors, reducing tree pathologies. We find FOF accretion rates and merger rates show similar mass ratio dependence. The model merger rates from Poole, et al. [2017, 472, 3659] agree with the measured net growth of halos through mergers.
Facial transplantation is emerging as a therapeutic option for self-inflicted gunshot wounds. The self-inflicted nature of this injury raises questions about the appropriate role of self-harm in determining patient eligibility. Potential candidates for facial transplantation undergo extensive psychosocial screening. The presence of a self-inflicted gunshot wound warrants special attention to ensure that a patient is prepared to undergo a demanding procedure that poses significant risk, as well as stringent lifelong management. Herein, we explore the ethics of considering mechanism of injury in the patient selection process, referring to the precedent set forth in solid organ transplantation. We also consider the available evidence regarding outcomes of individuals transplanted for self-inflicted mechanisms of injury in both solid organ and facial transplantation. We conclude that while the presence of a self-inflicted gunshot wound is significant in the overall evaluation of the candidate, it does not on its own warrant exclusion from consideration for a facial transplantation.
Hermaphroditism is thought to be an advantageous strategy common in marine molluscs that exhibit simultaneous, sequential or alternating hermaphroditism. Several species of patellid limpets have previously been shown to be protandrous hermaphrodites. The present study aimed to confirm whether this phenomenon occurs in Patella piperata. Transitional forms of simultaneous protandrous hermaphroditism were found in intermediate size classes of P. piperata, in Madeira (North-eastern Atlantic). Sequential hermaphroditism was confirmed after histological analysis. The overall sex-ratio was biased towards females but approached similar proportions in the larger size classes. Analysis of size at sex change showed that at a shell length of 36 mm 50% of the population probably have changed sex. The results reported confirm the occurrence of sequential hermaphroditism. These findings are of utmost importance to the understanding of the reproductive biology of this species with direct effect on management and conservation of this traditionally harvested limpet.
To determine the association between excess body fat, assessed by skinfold thickness, and the incidence of type 2 diabetes mellitus (T2DM) and hypertension (HT).
Data from the ongoing PERU MIGRANT Study were analysed. The outcomes were T2DM and HT, and the exposure was skinfold thickness measured in bicipital, tricipital, subscapular and suprailiac areas. The Durnin–Womersley formula and SIRI equation were used for body fat percentage estimation. Risk ratios and population attributable fractions (PAF) were calculated using Poisson regression.
Rural (Ayacucho) and urban shantytown district (San Juan de Miraflores, Lima) in Peru.
Adults (n 988) aged ≥30 years (rural, rural-to-urban migrants, urban) completed the baseline study. A total of 785 and 690 were included in T2DM and HT incidence analysis, respectively.
At baseline, age mean was 48·0 (sd 12·0) years and 47 % were males. For T2DM, in 7·6 (sd 1·3) years, sixty-one new cases were identified, overall incidence of 1·0 (95 % CI 0·8, 1·3) per 100 person-years. Bicipital and subscapular skinfolds were associated with 2·8-fold and 6·4-fold risk of developing T2DM. On the other hand, in 6·5 (sd 2·5) years, overall incidence of HT was 2·6 (95 % CI 2·2, 3·1) per 100 person-years. Subscapular and overall fat obesity were associated with 2·4- and 2·9-fold risk for developing HT. The PAF for subscapular skinfold was 73·6 and 39·2 % for T2DM and HT, respectively.
We found a strong association between subscapular skinfold thickness and developing T2DM and HT. Skinfold assessment can be a laboratory-free strategy to identify high-risk HT and T2DM cases.
We present VELOCIraptor, a massively parallel galaxy/(sub)halo finder that is also capable of robustly identifying tidally disrupted objects and separate stellar halos from galaxies. The code is written in C++11, use the Message Passing Interface (MPI) and OpenMP Application Programming Interface (API) for parallelisation, and includes python tools to read/manipulate the data products produced. We demonstrate the power of the VELOCIraptor (sub)halo finder, showing how it can identify subhalos deep within the host that have negligible density contrasts to their parent halo. We find a subhalo mass-radial distance dependence: large subhalos with mass ratios of ≳10−2 are more common in the central regions than smaller subhalos, a result of dynamical friction and low tidal mass loss rates. This dependence is completely absent in (sub)halo finders in common use, which generally search for substructure in configuration space, yet is present in codes that track particles belonging to halos as they fall into other halos, such as hbt+. VELOCIraptor largely reproduces the dependence seen without tracking, finding a similar radial dependence to hbt+ in well-resolved halos from our limited resolution fiducial simulation.
The Roosevelt–Rondon Expedition marmoset Mico marcai was first collected in 1914 and all information on this primate previously came from three skins brought back by this expedition. As a result, M. marcai is categorized as Data Deficient on the IUCN Red List. As the presumed range of M. marcai lies on the path of the advancing arc of deforestation in Brazil, the collection of relevant data to assess the conservation status of this Amazonian species is of some urgency. Here we present the first field data on the distribution and population size of, and threats to, M. marcai, to reassess the species’ conservation status. During 2012–2015 we surveyed the species in the Marmelos–Aripuanã interfluve, and estimated its density using distance sampling. We also used spatial predictive modelling to estimate forest loss within the species range under two deforestation scenarios. We found the marmoset in 13 localities and estimated its extent of occurrence to be 31,073 km2. We estimated the species’ density to be 8.31 individuals/km2 and extrapolated this to estimate a total population of 258,218 individuals (CI 150,705–441,860). Under a business-as-usual deforestation scenario, c. 10,000 km2 of forest, comprising 33% of the species’ range, would be lost in three marmoset generations (c. 18 years), and we, therefore, recommend that M. marcai be categorized as Vulnerable on the IUCN Red List based on criterion A3c. Other Amazonian marmosets require similar reassessment as their ranges also fall in the path of the arc of deforestation.
In 2017, dicamba-resistant (DR) soybean was commercially available to farmers in the United States. In August and September of 2017, a survey of 312 farmers from 60 Nebraska soybean-producing counties was conducted during extension field days or online. The objective of this survey was to understand farmers’ adoption and perceptions regarding DR soybean technology in Nebraska. The survey contained 16 questions and was divided in three parts: (1) demographics, (2) dicamba application in DR soybean, and (3) dicamba off-target injury to sensitive soybean cultivars. According to the results, 20% of soybean hectares represented by the survey were planted to DR soybean in 2017, and this number would probably double in 2018. Sixty-five percent of survey respondents own a sprayer and apply their own herbicide programs. More than 90% of respondents who adopted DR soybean technology reported significant improvement in weed control. Nearly 60% of respondents used dicamba alone or glyphosate plus dicamba for POST weed control in DR soybean; the remaining 40% added an additional herbicide with an alternative site of action (SOA) to the POST application. All survey respondents used one of the approved dicamba formulations for application in DR soybean. Survey results indicated that late POST dicamba applications (after late June) were more likely to result in injury to non-DR soybean compared to early POST applications (e.g., May and early June) in 2017. According to respondents, off-target dicamba movement resulted both from applications in DR soybean and dicamba-based herbicides applied in corn. Although 51% of respondents noted dicamba injury on non-DR soybean, 7% of those who noted injury filed an official complaint with the Nebraska Department of Agriculture. Although DR soybean technology allowed farmers to achieve better weed control during 2017 than previous growing seasons, it is apparent that off-target movement and resistance management must be addressed to maintain the viability and effectiveness of the technology in the future.
Although the Near Threatened jaguar Panthera onca ranges from the south-west USA to central Argentina, populations outside Amazonia are generally small and isolated. One such area, the Sierra Madre de Chiapas in the state of Chiapas, Mexico, is potentially an important area for jaguar conservation but information on the species in this region is limited and its conservation status is unknown. In this study we documented the occurrence and abundance of jaguars in the Sierra Madre de Chiapas complex. We compiled all available records of the species within the region and conducted a camera-trap survey during August 2015–December 2016. Interviews were conducted to determine the perception of the jaguar by cattle owners and to obtain information on any livestock predation. We found that jaguars still occur throughout the Sierra Madre de Chiapas landscape, including the plains on the Pacific Coast of Chiapas, but its abundance in the region is low. On the basis of our findings we have incorporated the Sierra Madre de Chiapas in Mexico's National Jaguar Conservation Strategy, and recommend that international organizations include this area in their priorities for jaguar conservation. To improve coexistence between jaguars and the communities of the Sierra Madre de Chiapas, strategies need to be developed, in collaboration with the local communities, to improve livestock practices for reduction of predation by jaguars, to strengthen government conservation policies and to implement educational and communication programmes about the importance of this species in the region.
The aim of this study was to re-examine the chronic effect (>7 d) of fructose consumption on postprandial TAG, in adolescents and adults. The research was carried out in March 2017 and used different electronic databases, such as Medline® (Pubmed®), Embase® and Cochrane. The review considered clinical trials (parallel or crossed) that evaluated the effect of fructose consumption for a period longer than 7 d, in humans. Two investigators independently performed data extraction. The outcome was the absolute delta of TAG concentration in a 4-h postprandial period. The results were presented with delta mean difference between treatments with 95 % CI. The calculations were made based on random-effect models. Statistical heterogeneity of treatment effects between studies was assessed by Cochrane’s ‘Q Test’ and ‘I2’ inconsistency test. The meta-analysis of the twelve selected interventions (n 318) showed that fructose generated larger variation (δ) of TAG concentrations during the postprandial period, compared with other carbohydrates (mean difference: 8·02 (95 % CI 0·46, 15·58) mg/dl (0·09 (95 % CI 0·01, 0·18) mmol/l); I2: 74 %). High heterogeneity was generated almost exclusively by one study, and its withdrawal did not alter the result. We concluded that chronic consumption of fructose (>7 d) has a negative role on postprandial TAG in healthy adolescents and adults, as well as in overweight/obese individuals, but not in diabetics.
We show that on-off intermittency in solar and stellar cycles is a result of amplitude-phase synchronization in multiscale interactions in solar/stellar dynamos or magnetorotational instability which leads to the formation of kinematic and magnetic coherent structures, and the novel techniques of Lagrangian coherent structures can detect transport barriers and vortices such as magnetic flux tubes/ropes in solar and stellar turbulence with high accuracy.
One of the Leishmania species known to be non-infective to humans is Leishmania (Mundinia) enriettii whose vertebrate host is the guinea pig Cavia porcellus. It is a good model for cutaneous leishmaniasis, chemotherapeutic and molecular studies. In the last years, an increased interest has emerged concerning the L. (Mundinia) subgenus after the finding of Leishmania (M.) macropodum in Australia and with the description of other new/putative species such as L. (M.) martiniquensis and ‘L. (M.) siamensis’. This review focused on histopathology, glycoconjugates and innate immunity. The presence of Leishmania RNA virus and shedding of extracellular vesicles by the parasite were also evaluated.
Traditionally, personalised nutrition was delivered at an individual level. However, the concept of delivering tailored dietary advice at a group level through the identification of metabotypes or groups of metabolically similar individuals has emerged. Although this approach to personalised nutrition looks promising, further work is needed to examine this concept across a wider population group. Therefore, the objectives of this study are to: (1) identify metabotypes in a European population and (2) develop targeted dietary advice solutions for these metabotypes. Using data from the Food4Me study (n 1607), k-means cluster analysis revealed the presence of three metabolically distinct clusters based on twenty-seven metabolic markers including cholesterol, individual fatty acids and carotenoids. Cluster 2 was identified as a metabolically healthy metabotype as these individuals had the highest Omega-3 Index (6·56 (sd 1·29) %), carotenoids (2·15 (sd 0·71) µm) and lowest total saturated fat levels. On the basis of its fatty acid profile, cluster 1 was characterised as a metabolically unhealthy cluster. Targeted dietary advice solutions were developed per cluster using a decision tree approach. Testing of the approach was performed by comparison with the personalised dietary advice, delivered by nutritionists to Food4Me study participants (n 180). Excellent agreement was observed between the targeted and individualised approaches with an average match of 82 % at the level of delivery of the same dietary message. Future work should ascertain whether this proposed method could be utilised in a healthcare setting, for the rapid and efficient delivery of tailored dietary advice solutions.
Preschoolers’ vocabulary acquisition sets the stage for later reading ability and school achievement. This study examined the role of socioeconomic status (SES) and the quality of the home environment of seventy-seven Chilean majority and Mapuche minority families from low and lower-middle-class backgrounds in explaining individual differences in vocabulary acquisition of their three-and-a-half-year-old children. Additionally, we investigated whether the relation between SES and receptive and expressive vocabulary was mediated by the quality of the home environment as the Family Investment Model suggests. The quality of the home environment significantly predicted receptive and expressive vocabulary above and beyond ethnicity, SES, parental caregiver status, and quantity of daycare. Furthermore, the quality of the home environment mediated the relation between SES and expressive and receptive vocabulary acquisition.
, along with their rotations, play an important role among those functions that are harmonic and orientation-preserving and map the unit disc onto a convex domain. The main theorem in this paper generalises results in recent literature by showing that convex combinations of functions in
Spring tillage is a component of an integrated weed management strategy for control of early emerging glyphosate-resistant weeds such as common ragweed; however, the effect of tillage on common ragweed emergence pattern is unknown. The objectives of this study were to evaluate whether spring tillage during emergence would influence the emergence pattern or stimulate additional emergence of common ragweed and to characterize common ragweed emergence in southeast Nebraska. A field experiment was conducted for three years (2014 to 2016) in Gage County, Nebraska in a field naturally infested with glyphosate-resistant common ragweed. Treatments consisted of a no-tillage control and three spring tillage timings. The Soil Temperature and Moisture Model (STM2) software was used to estimate soil temperature and moisture at a 2-cm depth. The Weibull function was fit to total common ragweed emergence (%) with day of year (DOY), thermal time, and hydrothermal time as independent variables. Tillage treatments and year had no effect on total common ragweed emergence (P=0.88 and 0.35, respectively) and time to 10, 25, 50, 75, and 90% emergence (P=0.31). However, emergence pattern was affected by year (P=<0.001) with 50% total emergence reached on May 5 in 2014, April 20 in 2015, and April 2 in 2016 and 90% total emergence reached on May 12, 2014, May 8, 2015, and April 30, 2016. According to the corrected information-theoretic model comparison criterion (AICc), the Weibull function with thermal time and base temperature of 3 C best explained the emergence pattern over three years. This study concludes that spring tillage does not stimulate additional emergence; therefore, after the majority of the common ragweed has emerged and before the crop has been planted, tillage could be used as an effective component of an integrated glyphosate-resistant common ragweed management program in Nebraska.
The IUCN Red List is widely used to guide conservation policy and practice. However, in most cases the evaluation of a species using IUCN Red List criteria takes into account only the global status of the species. Although subpopulations may be assessed using the IUCN categories and criteria, this rarely occurs, either because it is difficult to identify subpopulations or because of the effort involved. Using the jaguar Panthera onca as a model we illustrate that wide-ranging species that are assigned a particular category of threat based on the IUCN Red List criteria may display considerable heterogeneity within individual taxa in terms of the level of risk they face. Using the information available on the conservation status of the species, we evaluated the jaguar's current geographical range and its subpopulations. We identified the most threatened subpopulations, using the extent of occurrence, area of occupancy, population size and the level of threat to each subpopulation. The main outcome of this analysis was that although a large subpopulation persists in Amazonia, virtually all others are threatened because of their small size, isolation, deficient protection and the high human population density. Based on this approach, future conservation efforts can be prioritized for the most threatened subpopulations. Based on our findings we recommend that for future Red List assessments assessors consider the value of undertaking assessments at the subpopulation level. For the jaguar, sub-global assessments should be included on the Red List as a matter of urgency.
Traditional breeding has been used to develop grain sorghum germplasm that is tolerant to acetolactate synthase (ALS)-inhibiting herbicides (Inzen Technology, DuPont). Inzen sorghum carries a double mutation in the ALS gene (Val560Ile and Trp574Leu), which confers high level of tolerance to ALS-inhibiting herbicides. Overreliance on ALS-inhibiting herbicides for weed control during the 1990s resulted in the evolution of ALS inhibitor–resistant shattercane populations in Nebraska. According to a survey conducted in 2013, ALS inhibitor–resistant weedy Sorghum populations persist in Nebraska. The objectives of this research were to determine whether the ALS mutations present in Inzen sorghum were present in the ALS inhibitor–resistant shattercane and johnsongrass populations detected in Nebraska and northern Kansas, and whether these populations evolved ALS resistance independently. Primers specific to the Val560 and Trp574 region of the ALS gene were used to screen the populations with PCR. The Trp574Leu mutation was present in one ALS inhibitor–resistant johnsongrass population. The Val560Ile was detected in three ALS inhibitor–resistant shattercane, one susceptible shattercane, one ALS inhibitor–resistant johnsongrass, and one susceptible johnsongrass population. Moreover, Val560Ile was present in resistant and/or susceptible individuals within johnsongrass and shattercane populations that were segregating for ALS resistance, indicating that by itself the Val560Ile mutation does not confer resistance to ALS-inhibiting herbicides. None of the populations presented both mutations simultaneously, as does Inzen sorghum. A shattercane population containing the Ser653Thr mutation was also detected. This research indicates that the ALS mutations present in Inzen sorghum already exist individually in weedy sorghum populations. Moreover, our results present strong evidence that ALS resistance in these populations evolved independently. Thus, widespread overreliance on ALS-inhibiting herbicides prior to adoption of glyphosate-tolerant crops in the 1990s exerted sufficient selective pressure on shattercane and johnsongrass populations for resistance to evolve multiple times in the Midwest. Finally, a survey of the 5′ portion of the ALS gene in more diverse wild and weedy Sorghum species was hampered by limited coverage in genomic resequencing surveys, suggesting that refined PCR-based methods will be needed to assess SNP variation in this gene region, which includes the Ala122, Pro197, and Ala205 codons known to confer ALS resistance in other species.
Molluscs are subjected to intense harvesting in many areas around the world. Conservation measures have been developed to preserve populations of an overexploited gastropod species, the abalone Haliotis tuberculata coccinea. This species was surveyed in subtidal localities throughout coastal Tenerife, Canary Islands over the last two decades (1994–2014). A clear indicator of non-recovery was observed in the decrease of mean size throughout the last two decades, even after the inclusion of this species in the Regional Catalogue of Endangered Species. The mean size of abalones decreased from 33.5 mm (1994) to 28–29 mm (2002 and 2014), corresponding to sub-adult individuals. The structure of size classes was typical of an overexploited species, with reduced occurrence of large individuals (>50 mm). Several factors might explain this pattern such as illegal harvesting, proliferation of featureless benthos and a decrease of suitable habitats for colonization and settlement. Complementary conservation actions are urgently needed to preserve this species in the area studied.