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Young children not only need to learn how to perform isolated actions, but also temporally and spatially coordinated actions such as using a knife and fork. Routes to learning such coordinated actions include imitation and participation in joint action. However, little is known about the mechanisms guiding transmission of coordinated actions through observation and joint action performance. This paper reports an experiment comparing children’s tendency to imitate multiple, coordinated actions following demonstration by a single model acting bimanually (Bimanual Observation condition), two models performing the same actions jointly with one performing each hand action (Joint Observation condition) and a condition in which the child actively takes part in the joint action demonstration by performing one part in coordination with a partner (Joint Action condition). When children were subsequently left alone to perform the task independently, they were more likely to imitate both coordinated actions in the two observation conditions than in the Joint Action condition, with no difference between performance in Bimanual and Joint Observation conditions. It is argued that this is due to children being more able to form a global representation of both actions and the relations between the two when observing from a distance than when actively involved in the task. [ABSTRACT FROM AUTHOR]

Human social interaction is often intermittent. Two acquainted persons can have extended periods without social interaction punctuated by periods of repeated interaction. In this case, the repeated interaction can be characterized by a seed initiative by either of the persons and a number of follow-up interactions. The tendency to initiate social interaction plays an important role in the formation of social networks and is in general not symmetric between persons. In this paper, we study the dynamics of initiative by analysing and modeling a detailed call and text message network sampled from a group of 700 individuals. We show that in an average relationship between two individuals, one part is almost twice as likely to initiate communication compared to the other part. The asymmetry has social consequences and ultimately might lead to the discontinuation of a relationship. We explain the observed asymmetry by a positive feedback mechanism where individuals already taking initiative are more likely to take initiative in the future. In general, people with many initiatives receive attention from a broader spectrum of friends than people with few initiatives. Lastly, we compare the likelihood of taking initiative with the basic personality traits of the five factor model. [ABSTRACT FROM AUTHOR]

A new method is introduced allowing seamless assembly of independent, functionally tested, blunt-end double strand nucleic acid (DNA fragments not supplied in vectors such as plasmids) into more complex biological (e.g. protein expression vectors) and higher order multi-device (e.g. biochemical pathways). Individual parts include bacterial selection markers and origins of replication, promoters useful in a variety of species, transcription terminators, shuttle sequences and a variety of “N” and “C” terminal solubility/affinity protein tags. Parts are not subjected to pre-assembly manipulation with nucleic acid modifying enzymes. Instead, they are simply mixed in appropriate pre-defined combinations and concentrations and then seamlessly linked into devices employing a specialized thermostable enzyme blend. Combinatorial assembly of parts is an inherent time-saving feature of the new method, in contrast to hierarchical binary assembly (“one part at a time”) methods. This feature substantially simplifies and speeds optimization of device and system development. The versatility and functionality of the new method was shown by combinatorial assembly of parts into vector devices, one of which optimally expressed protein from a model gene. Also, a four-enzyme biosynthetic pathway system was re-created by combinatorial construction from parts and devices. Concepts discussed in this paper provide synthetic biologists, chemists and bio-engineers with improved and expanded capability to create novel biological molecules and systems. [ABSTRACT FROM AUTHOR]

Once in the ocean, plastics are rapidly colonized by complex microbial communities. Factors affecting the development and composition of these communities are still poorly understood. Additionally, whether there are plastic-type specific communities developing on different plastics remains enigmatic. We determined the development and succession of bacterial communities on different plastics under ambient and dim light conditions in the coastal Northern Adriatic over the course of two months using scanning electron microscopy and 16S rRNA gene analyses. Plastics used were low- and high-density polyethylene (LDPE and HDPE, respectively), polypropylene (PP) and polyvinyl chloride with two typical additives (PVC DEHP and PVC DINP). The bacterial communities developing on the plastics clustered in two groups; one group was found on PVC and the other group on all the other plastics and on glass, which was used as an inert control. Specific bacterial taxa were found on specific surfaces in essentially all stages of biofilm development and in both ambient and dim light conditions. Differences in bacterial community composition between the different plastics and light exposures were stronger after an incubation period of one week than at the later stages of the incubation. Under both ambient and dim light conditions, one part of the bacterial community was common on all plastic types, especially in later stages of the biofilm development, with families such as Flavobacteriaceae, Rhodobacteraceae, Planctomycetaceae and Phyllobacteriaceae presenting relatively high relative abundances on all surfaces. Another part of the bacterial community was plastic-type specific. The plastic-type specific fraction was variable among the different plastic types and was more abundant after one week of incubation than at later stages of the succession. [ABSTRACT FROM AUTHOR]

Background and aim: Self-medication (SM) is one part of self-care which is known to contribute to primary health care. If practiced appropriately, it has major benefits for the consumers such as self-reliance and decreased expense. However, inappropriate practice can have potential dangers such as incorrect self-diagnosis, dangerous drug-drug interactions, incorrect manner of administration, incorrect dosage, incorrect choice of therapy, masking of a severe disease, and/or risk of dependence and abuse. The main objective of this study was to assess the prevalence and determinants of the self-medication practice (SMP) in Addis Ababa. Methodology: A community based cross-sectional study was conducted among selected households in Addis Ababa from April 2016 to May 2016, with a recall period of two months before its conduction. Trained data collectors were employed to collect the data from the 604 sampled participants using pre-tested and validated questionnaires. Result: Among the 604 participants involved in this study, 422 (69.9%) were female and 182 (30.1%) were male and there was a mean age of 41.04 (± 13.45) years. The prevalence of SM in this study was 75.5%. The three most frequently reported ailments were headache 117 (25.7%), abdominal pain 59 (12.9%) and cough 54 (11.8%). The two main reasons for SM were mildness of illness 216 (47.4%) and previous knowledge about the drug 106 (23.2%). The two most frequently consumed medications were paracetamol 92 (20.2%) and traditional remedies 73 (16.0%), while drug retail outlets 319 (83.3%) were the main source of drugs. The two most frequently reported source of drug information were health professionals 174 (45.4%) and experience from previous treatment 82 (21.4%). Moreover, there were statistically significant differences among respondents who reported practicing SM based on income and knowledge about appropriate SMP. Conclusion and recommendation: Self-medication was practiced with a range of drugs from the conventional paracetamol and NSAIDs to antimicrobials. Being that the practice of SM is inevitable, health authorities and professionals are highly demanded to educate the public not only on the advantages and disadvantages of SM but on its proper use. [ABSTRACT FROM AUTHOR]

Even among isogenic cells, the time to progress through the cell cycle, or the intermitotic time (IMT), is highly variable. This variability has been a topic of research for several decades and numerous mathematical models have been proposed to explain it. Previously, we developed a top-down, stochastic drift-diffusion+threshold (DDT) model of a cell cycle checkpoint and showed that it can accurately describe experimentally-derived IMT distributions [Leander R, Allen EJ, Garbett SP, Tyson DR, Quaranta V. Derivation and experimental comparison of cell-division probability densities. J. Theor. Biol. 2014;358:129–135]. Here, we use the DDT modeling approach for both descriptive and predictive data analysis. We develop a custom numerical method for the reliable maximum likelihood estimation of model parameters in the absence of a priori knowledge about the number of detectable checkpoints. We employ this method to fit different variants of the DDT model (with one, two, and three checkpoints) to IMT data from multiple cell lines under different growth conditions and drug treatments. We find that a two-checkpoint model best describes the data, consistent with the notion that the cell cycle can be broadly separated into two steps: the commitment to divide and the process of cell division. The model predicts one part of the cell cycle to be highly variable and growth factor sensitive while the other is less variable and relatively refractory to growth factor signaling. Using experimental data that separates IMT into G1 vs. S, G2, and M phases, we show that the model-predicted growth-factor-sensitive part of the cell cycle corresponds to a portion of G1, consistent with previous studies suggesting that the commitment step is the primary source of IMT variability. These results demonstrate that a simple stochastic model, with just a handful of parameters, can provide fundamental insights into the biological underpinnings of cell cycle progression. [ABSTRACT FROM AUTHOR]

We investigated soluble carbohydrate transport in trees that differed in their phloem loading strategies in order to better understand the transport of photosynthetic products into the roots and the rhizosphere as this knowledge is needed to better understand the respiratory processes in the rhizosphere. We compared beech, which is suggested to use mainly passive loading of transport sugars along a concentration gradient into the phloem, with ash that uses active loading and polymer trapping of raffinose family oligosaccharides (RFOs). We pulse-labeled 20 four-year old European beech and 20 four-year old ash trees with 13CO2 and tracked the fate of the label within different plant compartments. We extracted soluble carbohydrates from leaves, bark of stems and branches, and fine roots, measured their amount and isotopic content and calculated their turnover times. In beech one part of the sucrose was rapidly transported into sink tissues without major exchange with storage pools whereas another part of sucrose was strongly exchanged with unlabeled possibly stored sucrose. In contrast the storage and allocation patterns in ash depended on the identity of the transported sugars. RFO were the most important transport sugars that had highest turnover in all shoot compartments. However, the turnover of RFOs in the roots was uncoupled from the shoot. The only significant relation between sugars in the stem base and in the roots of ash was found for the amount (r2 = 0.50; p = 0.001) and isotopic content (r2 = 0.47; p = 0.01) of sucrose. The negative relation of the amounts suggested an active transport of sucrose into the roots of ash. Sucrose concentration in the root also best explained the concentration of RFOs in the roots suggesting that RFO in the roots of ash may be resynthesized from sucrose. Our results interestingly suggest that in both tree species only sucrose directly entered the fine root system and that in ash RFOs are transported indirectly into the fine roots only. The direct transport of sucrose might be passive in beech but active in ash (sustained active up- and unloading to co-cells), which would correspond to the phloem loading strategies. Our results give first hints that the transport of carbohydrates between shoot and root is not necessarily continuous and involves passive (beech) and active (ash) transport processes, which may be controlled by the phloem unloading. [ABSTRACT FROM AUTHOR]

Many challenging engineering problems are regular, meaning solutions to one part of a problem can be reused to solve other parts. Evolutionary algorithms with indirect encoding perform better on regular problems because they reuse genomic information to create regular phenotypes. However, on problems that are mostly regular, but contain some irregularities, which describes most real-world problems, indirect encodings struggle to handle the irregularities, hurting performance. Direct encodings are better at producing irregular phenotypes, but cannot exploit regularity. An algorithm called HybrID combines the best of both: it first evolves with indirect encoding to exploit problem regularity, then switches to direct encoding to handle problem irregularity. While HybrID has been shown to outperform both indirect and direct encoding, its initial implementation required the manual specification of when to switch from indirect to direct encoding. In this paper, we test two new methods to improve HybrID by eliminating the need to manually specify this parameter. Auto-Switch-HybrID automatically switches from indirect to direct encoding when fitness stagnates. Offset-HybrID simultaneously evolves an indirect encoding with directly encoded offsets, eliminating the need to switch. We compare the original HybrID to these alternatives on three different problems with adjustable regularity. The results show that both Auto-Switch-HybrID and Offset-HybrID outperform the original HybrID on different types of problems, and thus offer more tools for researchers to solve challenging problems. The Offset-HybrID algorithm is particularly interesting because it suggests a path forward for automatically and simultaneously combining the best traits of indirect and direct encoding. [ABSTRACT FROM AUTHOR]

Colony Collapse Disorder (CCD) has become a global problem for beekeepers and for the crops that depend on bee pollination. While many factors are known to increase the risk of colony collapse, the ectoparasitic mite Varroa destructor is considered to be the most serious one. Although this mite is unlikely to cause the collapse of hives itself, it is the vector for many viral diseases which are among the likely causes for Colony Collapse Disorder. The effects of V. destructor infestation differ from one part of the world to another, with greater morbidity and higher colony losses in European honey bees (EHB) in Europe, Asia and North America. Although this mite has been present in Brazil for many years, there have been no reports of colony losses amongst Africanized Honey Bees (AHB). Studies carried out in Mexico have highlighted different behavioral responses by the AHB to the presence of the mite, notably as far as grooming and hygienic behavior are concerned. Could these explain why the AHB are less susceptible to Colony Collapse Disorder? In order to answer this question, we have developed a mathematical model of the infestation dynamics to analyze the role of resistance behavior by bees in the overall health of the colony, and as a consequence, its ability to face epidemiological challenges. [ABSTRACT FROM AUTHOR]

Reliable and real-time information on soil and crop properties is important for the development of management practices in accordance with the requirements of a specific soil and crop within individual field units. This is particularly the case in salt-affected agricultural landscape where managing the spatial variability of soil salinity is essential to minimize salinization and maximize crop output. The primary objectives were to use linear mixed-effects model for soil salinity and crop yield calibration with horizontal and vertical electromagnetic induction (EMI) measurements as ancillary data, to characterize the spatial distribution of soil salinity and crop yield and to verify the accuracy of spatial estimation. Horizontal and vertical EMI (type EM38) measurements at 252 locations were made during each survey, and root zone soil samples and crop samples at 64 sampling sites were collected. This work was periodically conducted on eight dates from June 2012 to May 2013 in a coastal salt-affected mud farmland. Multiple linear regression (MLR) and restricted maximum likelihood (REML) were applied to calibrate root zone soil salinity (ECe) and crop annual output (CAO) using ancillary data, and spatial distribution of soil ECe and CAO was generated using digital soil mapping (DSM) and the precision of spatial estimation was examined using the collected meteorological and groundwater data. Results indicated that a reduced model with EMh as a predictor was satisfactory for root zone ECe calibration, whereas a full model with both EMh and EMv as predictors met the requirement of CAO calibration. The obtained distribution maps of ECe showed consistency with those of EMI measurements at the corresponding time, and the spatial distribution of CAO generated from ancillary data showed agreement with that derived from raw crop data. Statistics of jackknifing procedure confirmed that the spatial estimation of ECe and CAO exhibited reliability and high accuracy. A general increasing trend of ECe was observed and moderately saline and very saline soils were predominant during the survey period. The temporal dynamics of root zone ECe coincided with those of daily rainfall, water table and groundwater data. Long-range EMI surveys and data collection are needed to capture the spatial and temporal variability of soil and crop parameters. Such results allowed us to conclude that, cost-effective and efficient EMI surveys, as one part of multi-source data for DSM, could be successfully used to characterize the spatial variability of soil salinity, to monitor the spatial and temporal dynamics of soil salinity, and to spatially estimate potential crop yield. [ABSTRACT FROM AUTHOR]

Studies of marine viromes (viral metagenomes) have revealed that DNA viruses are highly diverse and exhibit biogeographic patterns. However, little is known about the diversity of RNA viruses, which are mostly composed of eukaryotic viruses, and their biogeographic patterns in the oceans. A growth in global commerce and maritime traffic may accelerate spread of diverse and non-cosmopolitan DNA viruses and potentially RNA viruses from one part of the world to another. Here, we demonstrated through metagenomic analyses that failure to comply with mid-ocean ballast water exchange regulation could result in movement of viromes including both DNA viruses and RNA viruses (including potential viral pathogens) unique to geographic and environmental niches. Furthermore, our results showed that virus richness (known and unknown viruses) in ballast water is associated with distance between ballast water exchange location and its nearest shoreline as well as length of water storage time in ballast tanks (voyage duration). However, richness of only known viruses is governed by local environmental conditions and different viral groups have different responses to environmental variation. Overall, these results identified ballast water as a factor contributing to ocean virome transport and potentially increased exposure of the aquatic bioshpere to viral invasion. [ABSTRACT FROM AUTHOR]

Purpose: To examine the associations between overweight/obesity and occupation among Hispanics/Latinos, the largest minority population in the U.S. Methods: This study included 7,409 employed individuals in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), a prospective study of Hispanic/Latino individuals aged 18–74 in four communities in the U.S. We independently examined the relationships between BMI, Occupational Activity (OA), and Total Hours Worked, quantified via self-reported hours worked per week and occupation-assigned Metabolic Equivalents (METs). Results: More than three quarters of the participants were either overweight (39.3%) or obese (37.8%). Individuals with a primary occupation and those employed in a secondary occupation worked an average of 36.8 and 14.6 hrs/wk, respectively. The overall adjusted odds for being obese compared to normal weight were 3.2% (AOR = 1.03, 95% CI 1.01, 1.05) and 14.4% (AOR = 1.14 95% Cl 1.07, 1.23) greater for each 10 MET•hrs/wk unit of increased OA, and each 10-hrs/wk unit of Total Hours Worked, respectively. Conclusion: This study presents the first findings on the association between OA with overweight/obesity among Hispanic/Latino individuals in the U.S. Increasing OA and Total Hours Worked per week were independently associated with increasing odds of overweight/obesity suggesting that the workplace is only one part of the overall energy expenditure dynamic. Our findings point to the need to emphasize engaging employed individuals in greater levels of PA outside of the work environment to impact overweight/obesity. [ABSTRACT FROM AUTHOR]

Human observers are remarkably proficient at recognizing expressions of emotions and at readily grouping them into distinct categories. When morphing one facial expression into another, the linear changes in low-level features are insufficient to describe the changes in perception, which instead follow an s-shaped function. Important questions are, whether there are single diagnostic regions in the face that drive categorical perception for certain parings of emotion expressions, and how information in those regions interacts when presented together. We report results from two experiments with morphed fear-anger expressions, where (a) half of the face was masked or (b) composite faces made up of different expressions were presented. When isolated upper and lower halves of faces were shown, the eyes were found to be almost as diagnostic as the whole face, with the response function showing a steep category boundary. In contrast, the mouth allowed for a substantially lesser amount of accuracy and responses followed a much flatter psychometric function. When a composite face consisting of mismatched upper and lower halves was used and observers were instructed to exclusively judge either the expression of mouth or eyes, the to-be-ignored part always influenced perception of the target region. In line with experiment 1, the eye region exerted a much stronger influence on mouth judgements than vice versa. Again, categorical perception was significantly more pronounced for upper halves of faces. The present study shows that identification of fear and anger in morphed faces relies heavily on information from the upper half of the face, most likely the eye region. Categorical perception is possible when only the upper face half is present, but compromised when only the lower part is shown. Moreover, observers tend to integrate all available features of a face, even when trying to focus on only one part. [ABSTRACT FROM AUTHOR]

Existing estimates of fish and consumer biomass in the world’s oceans are disparate. This creates uncertainty about the roles of fish and other consumers in biogeochemical cycles and ecosystem processes, the extent of human and environmental impacts and fishery potential. We develop and use a size-based macroecological model to assess the effects of parameter uncertainty on predicted consumer biomass, production and distribution. Resulting uncertainty is large (e.g. median global biomass 4.9 billion tonnes for consumers weighing 1 g to 1000 kg; 50% uncertainty intervals of 2 to 10.4 billion tonnes; 90% uncertainty intervals of 0.3 to 26.1 billion tonnes) and driven primarily by uncertainty in trophic transfer efficiency and its relationship with predator-prey body mass ratios. Even the upper uncertainty intervals for global predictions of consumer biomass demonstrate the remarkable scarcity of marine consumers, with less than one part in 30 million by volume of the global oceans comprising tissue of macroscopic animals. Thus the apparently high densities of marine life seen in surface and coastal waters and frequently visited abundance hotspots will likely give many in society a false impression of the abundance of marine animals. Unexploited baseline biomass predictions from the simple macroecological model were used to calibrate a more complex size- and trait-based model to estimate fisheries yield and impacts. Yields are highly dependent on baseline biomass and fisheries selectivity. Predicted global sustainable fisheries yield increases ≈4 fold when smaller individuals (< 20 cm from species of maximum mass < 1kg) are targeted in all oceans, but the predicted yields would rarely be accessible in practice and this fishing strategy leads to the collapse of larger species if fishing mortality rates on different size classes cannot be decoupled. Our analyses show that models with minimal parameter demands that are based on a few established ecological principles can support equitable analysis and comparison of diverse ecosystems. The analyses provide insights into the effects of parameter uncertainty on global biomass and production estimates, which have yet to be achieved with complex models, and will therefore help to highlight priorities for future research and data collection. However, the focus on simple model structures and global processes means that non-phytoplankton primary production and several groups, structures and processes of ecological and conservation interest are not represented. Consequently, our simple models become increasingly less useful than more complex alternatives when addressing questions about food web structure and function, biodiversity, resilience and human impacts at smaller scales and for areas closer to coasts. [ABSTRACT FROM AUTHOR]

Developing generalisations of invasive species is an important part of invasion biology. However, trends and generalisations from one part of the world may not necessarily hold elsewhere. We present the first inventory and analysis of all Hymenoptera alien to New Zealand, and compare patterns from New Zealand with those previously published from Europe (DAISIE). Between the two regions there was broad correlation between families with the highest number of alien species (Braconidae, Encyrtidae, Pteromalidae, Eulophidae, Formicidae, Aphelinidae). However, major differences also existed. The number of species alien to New Zealand is higher than for Europe (334 vs 286), and major differences include: i) the much lower proportion of intentionally released species in New Zealand (21% vs 63% in Europe); and ii) the greater proportion of unintentionally introduced parasitoids in New Zealand (71.2% vs 22.6%). The disharmonic ‘island’ nature of New Zealand is shown, as a high proportion of families (36%) have no native representatives, and alien species also represent >10% of the native fauna for many other families. A much larger proportion of alien species are found in urban areas in New Zealand (60%) compared to Europe (~30%), and higher numbers of alien species were present earlier in New Zealand (especially <1950). Differences in the origins of alien species were also apparent. Unlike Europe, the New Zealand data reveals a change in the origins of alien species over time, with an increasing dominance of alien species from Australasia (a regional neighbour) during the past 25 years. We recommend that further effort be made towards the formation, and analysis, of regional inventories of alien species. This will allow a wider range of taxa and regions to be examined for generalisations, and help assess and prioritise the risk posed by certain taxa towards the economy or environment. [ABSTRACT FROM AUTHOR]

Phenotypic mosaic trees offer an ideal system for studying differential gene expression. We have investigated two mosaic eucalypt trees from two closely related species (Eucalyptus melliodora and E. sideroxylon), which each support two types of leaves: one part of the canopy is resistant to insect herbivory and the remaining leaves are susceptible. Driving this ecological distinction are differences in plant secondary metabolites. We used these phenotypic mosaics to investigate genome wide patterns of foliar gene expression with the aim of identifying patterns of differential gene expression and the somatic mutation(s) that lead to this phenotypic mosaicism. We sequenced the mRNA pool from leaves of the resistant and susceptible ecotypes from both mosaic eucalypts using the Illumina HiSeq 2000 platform. We found large differences in pathway regulation and gene expression between the ecotypes of each mosaic. The expression of the genes in the MVA and MEP pathways is reflected by variation in leaf chemistry, however this is not the case for the terpene synthases. Apart from the terpene biosynthetic pathway, there are several other metabolic pathways that are differentially regulated between the two ecotypes, suggesting there is much more phenotypic diversity than has been described. Despite the close relationship between the two species, they show large differences in the global patterns of gene and pathway regulation. [ABSTRACT FROM AUTHOR]

The need for interfacing structural biology and biophysics to molecular evolution is being increasingly recognized. One part of the big problem is to understand how physics and chemistry shape the sequence space available to functional proteins, while satisfying the needs of biology. Here we present a quantitative, structure-based analysis of a high-resolution map describing the tolerance to all substitutions in all positions of a functional enzyme, namely a TEM lactamase previously studied through deep sequencing of mutants growing in competition experiments with selection against ampicillin. Substitutions are rarely observed within 7 Å of the active site, a stringency that is relaxed slowly and extends up to 15–20 Å, with buried residues being especially sensitive. Substitution patterns in over one third of the residues can be quantitatively modeled by monotonic dependencies on amino acid descriptors and predictions of changes in folding stability. Amino acid volume and steric hindrance shape constraints on the protein core; hydrophobicity and solubility shape constraints on hydrophobic clusters underneath the surface, and on salt bridges and polar networks at the protein surface together with charge and hydrogen bonding capacity. Amino acid solubility, flexibility and conformational descriptors also provide additional constraints at many locations. These findings provide fundamental insights into the chemistry underlying protein evolution and design, by quantitating links between sequence and different protein traits, illuminating subtle and unexpected sequence-trait relationships and pinpointing what traits are sacrificed upon gain-of-function mutation. [ABSTRACT FROM AUTHOR]

In epidemiologic studies, measurement error in dietary variables often attenuates association between dietary intake and disease occurrence. To adjust for the attenuation caused by error in dietary intake, regression calibration is commonly used. To apply regression calibration, unbiased reference measurements are required. Short-term reference measurements for foods that are not consumed daily contain excess zeroes that pose challenges in the calibration model. We adapted two-part regression calibration model, initially developed for multiple replicates of reference measurements per individual to a single-replicate setting. We showed how to handle excess zero reference measurements by two-step modeling approach, how to explore heteroscedasticity in the consumed amount with variance-mean graph, how to explore nonlinearity with the generalized additive modeling (GAM) and the empirical logit approaches, and how to select covariates in the calibration model. The performance of two-part calibration model was compared with the one-part counterpart. We used vegetable intake and mortality data from European Prospective Investigation on Cancer and Nutrition (EPIC) study. In the EPIC, reference measurements were taken with 24-hour recalls. For each of the three vegetable subgroups assessed separately, correcting for error with an appropriately specified two-part calibration model resulted in about three fold increase in the strength of association with all-cause mortality, as measured by the log hazard ratio. Further found is that the standard way of including covariates in the calibration model can lead to over fitting the two-part calibration model. Moreover, the extent of adjusting for error is influenced by the number and forms of covariates in the calibration model. For episodically consumed foods, we advise researchers to pay special attention to response distribution, nonlinearity, and covariate inclusion in specifying the calibration model. [ABSTRACT FROM AUTHOR]

Recently, high-resolution magnetometry surveys have led to the discovery of a special category of buildings–so-called ‘mega-structures’–situated in highly visible positions in the public space of Tripolye giant-settlements of the late 5th and first half of the 4th millennium BCE. In this paper we explore what these buildings actually are and how they can contribute to the understanding of the development of social space in Tripolye giant-settlements. For this investigation, we linked newly obtained excavation data from the giant-settlement Maidanetske, Ukraine, with a much larger sample of such buildings from magnetic plans obtained in the region between the Carpathian foothills and the Dnieper River. Accordingly, Tripolye mega-structures represent a particular kind of integrative building documented in many non-ranked ethnographic contexts. Based on our results we are interpreting that these buildings were used for various ritual and non-ritual activities, joint decision-making, and the storage and consumption of surplus. In Tripolye giant-settlements at least three different categories of mega-structures could be identified which most likely represent different levels of socio-political integration and decision-making. The emergence of this hierarchical system of high-level integrative buildings for the whole community and different low-level integrative architectures for certain segments of local communities was related to the rise of Tripolye mega-sites. The presence of different integrative levels most likely reflects the fusion of different previously independent communities in the giant-settlements. Later in the mega-site development, we observe how low-level integrative buildings increasingly lose their importance indicated by shrinking size and, finally, their disappearance. This observation might indicate that the power which was previously distributed across the community was transferred to a central institution. It is argued that the non-acceptance of this concentration of power and the decline of lower decision-making levels might be a crucial factor for the disintegration of Tripolye giant-settlements around 3600 BCE. [ABSTRACT FROM AUTHOR]

Implantation failure and early pregnancy loss have been reported to be closely related to the quality of mammalian oocytes; however, the pregnant outcome of embryos from in-vitro matured (IVM) oocytes remains unknown. In this study we examined spindle assembly and chromosome segregation during differentiation, and the duration of IVM of mouse oocytes. The resulting implantation and pregnancy outcomes were analyzed to clarify the relationship between the spindle and chromosomes of IVM oocytes and implantation and early pregnancy. Cumulus-enclosed germinal vesicle oocytes were collected and randomly cultured in IVM medium with different IVM durations. One part of IVM oocytes were analyzed the spindle and chromosome morphology by immunofluorescence method, and the other part of them were fertilized by intracytoplasmic sperm injection. The resulting embryos were transferred into pseudo-pregnant female mice, and the post-implantation and full term development was observed. The chromosome aberrations and incorrect spindle assembly seems not affect the early development and blastocyst cell number derived from IVM oocytes, however the development potential of the resulting embryos after implantation were significant decreased with the ratio increasing of chromosome aberrations and incorrect spindle assembly. Accordingly, the full-term development was also decreased. In conclusion, the present study showed the spindle assembly of in vitro-matured oocytes was one of the most important factors that affected the implantation and ongoing pregnancy rates of IVM oocytes, and the improvement by an appropriate duration of maturation in vitro will enhance the post-implantation development potential of the resulting embryos, and decrease implantation failure and early pregnancy loss. [ABSTRACT FROM AUTHOR]

Introduction: To combat the AIDS epidemic and increase HIV treatment access, the South African government implemented a nurse-based, doctor-supported model of care that decentralizes administration of antiretroviral treatment (ART) for HIV positive patients through nurse initiated and managed ART. Médecins Sans Frontières (MSF) implemented a mentorship programme to ensure successful task-shifting, subsequently assessing the quality of clinical care provided by nurses. Methods: A before-after cross-sectional study was conducted on nurses completing the mentorship programme in Khayelitsha, South Africa, from February 2011-September 2012. Routine clinical data from 229 patient folders and 21 self-assessment questionnaires was collected to determine the number of patients initiated on ART by nurses; quality of ART management before-after mentorship; patient characteristics for doctor and nurse ART initiations; and nurse self-assessments after mentorship. Results: Twenty one nurses were authorized by one nurse mentor with one part-time medical officer's support, resulting in nurses initiating 77% of ART eligible patients. Improvements in ART management were found for drawing required bloods (91% vs 99%, p = 0.03), assessing adherence (50% vs 78%, p<0.001) and WHO staging (63% vs 91%, p<0.001). Nurse ART initiation indicators were successfully completed at 95–100% for 11 of 16 indicators: clinical presentation; patient weight; baseline blood work (CD4, creatinine, haemoglobin); STI screening; WHO stage, correlating medical history; medications prescribed appropriately; ART start date; and documented return date. Doctors initiated more patients with TB/HIV co-infection and WHO Stage 3 and 4 disease than nurses. Nurse confidence improved for managing HIV-infected children and pregnant women, blood result interpretation and long-term side effects. Conclusions: Implementation of a clinical mentorship programme in Khayelitsha led to nurse initiation of a majority of eligible patients, enabling medical officers to manage complex cases. As mentorship can increase clinical confidence and enhance professional development, it should be considered essential for universal ART access in resource limited settings. [ABSTRACT FROM AUTHOR]

Background: The most distinguishing genetic feature of hepatitis C virus (HCV) is its remarkable diversity and variation. To understand this feature, we previously performed genetic analysis of HCV in the long-term culture of human hepatoma HuH-7-derived HCV RNA-replicating cell lines. On the other hand, we newly established HCV RNA-replicating cell lines using human hepatoma Li23 cells, which were distinct from HuH-7 cells. Methodology/Principal Findings: Li23-derived HCV RNA-replicating cells were cultured for 4 years. We performed genetic analysis of HCVs recovered from these cells at 0, 2, and 4 years in culture. Most analysis was performed in two separate parts: one part covered from the 5′-terminus to NS2, which is mostly nonessential for RNA replication, and the other part covered from NS3 to NS5B, which is essential for RNA replication. Genetic mutations in both regions accumulated in a time-dependent manner, and the mutation rates in the 5′-terminus-NS2 and NS3-NS5B regions were 4.0–9.0×10−3 and 2.7–4.0×10−3 base substitutions/site/year, respectively. These results suggest that the variation in the NS3-NS5B regions is affected by the pressure of RNA replication. Several in-frame deletions (3–105 nucleotides) were detected in the structural regions of HCV RNAs obtained from 2-year or 4-year cultured cells. Phylogenetic tree analyses clearly showed that the genetic diversity of HCV was expanded in a time-dependent manner. The GC content of HCV RNA was significantly increased in a time-dependent manner, as previously observed in HuH-7-derived cell systems. This phenomenon was partially due to the alterations in codon usages for codon optimization in human cells. Furthermore, we demonstrated that these long-term cultured cells were useful as a source for the selection of HCV clones showing resistance to anti-HCV agents. Conclusions/Significance: Long-term cultured HCV RNA-replicating cells are useful for the analysis of evolutionary dynamics and variations of HCV and for drug-resistance analysis. [ABSTRACT FROM AUTHOR]

Recent years have seen a growing consensus that events during one part of an animal's annual cycle can detrimentally affect its future fitness. Notably, migratory species have been shown to commonly display such carry-over effects, facing severe time constraints and physiological stresses that can influence events across seasons. However, to date, no study has examined a full annual cycle to determine when these carry-over effects arise and how long they persist within and across years. Understanding when carry-over effects are created and how they persist is critical to identifying those periods and geographic locations that constrain the annual cycle of a population and determining how selection is acting upon individuals throughout the entire year. Using three consecutive years of migration tracks and four consecutive years of breeding success data, we tested whether carry-over effects in the form of timing deviations during one migratory segment of the annual cycle represent fitness costs that persist or accumulate across the annual cycle for a long-distance migratory bird, the Hudsonian godwit, Limosa haemastica. We found that individual godwits could migrate progressively later than population mean over the course of an entire migration period, especially southbound migration, but that these deviations did not accumulate across the entire year and were not consistently detected among individuals across years. Furthermore, neither the accumulation of lateness during previous portions of the annual cycle nor arrival date at the breeding grounds resulted in individuals suffering reductions in their breeding success or survival. Given their extreme life history, such a lack of carry-over effects suggests that strong selection exists on godwits at each stage of the annual cycle and that carry-over effects may not be able to persist in such a system, but also emphasizes that high-quality stopover and wintering sites are critical to the maintenance of long-distance migratory populations. [ABSTRACT FROM AUTHOR]

Background: Multiple biomarker testing is necessary to facilitate individualized treatment of lung cancer patients. More than 80% of lung cancers are diagnosed based on very small tumor samples. Often there is not enough tissue for molecular analysis. We compared three minimal invasive sampling methods with respect to RNA quantity for molecular testing. Methods: 106 small biopsies were prospectively collected by three different methods forceps biopsy, endobronchial ultrasound (EBUS) guided transbronchial needle aspiration (TBNA), and CT-guided core biopsy. Samples were split into two halves. One part was formalin fixed and paraffin embedded for standard pathological evaluation. The other part was put in RNAlater for immediate RNA/DNA extraction. If the pathologist confirmed the diagnosis of non-small cell lung cancer(NSCLC), the following molecular markers were tested: EGFR mutation, ERCC1, RRM1 and BRCA1. Results: Overall, RNA-extraction was possible in 101 out of 106 patients (95.3%). We found 49% adenocarcinomas, 38% squamouscarcinomas, and 14% non-otherwise-specified(NOS). The highest RNA yield came from endobronchial ultrasound guided needle aspiration, which was significantly higher than bronchoscopy (37.74±41.09 vs. 13.74±15.53 ng respectively, P = 0.005) and numerically higher than CT-core biopsy (37.74±41.09 vs. 28.72±44.27 ng respectively, P = 0.244). EGFR mutation testing was feasible in 100% of evaluable patients and its incidence was 40.8%, 7.9% and 14.3% in adenocarcinomas, squamouscarcinomas and NSCLC NOS subgroup respectively. There was no difference in the feasibility of molecular testing between the three sampling methods with feasibility rates for ERCC1, RRM1 and BRCA1 of 91%, 87% and 81% respectively. Conclusion: All three methods can provide sufficient tumor material for multiple biomarkers testing from routinely obtained small biopsies in lung cancer patients. In our study EBUS guided needle aspiration provided the highest amount of tumor RNA compared to bronchoscopy or CT guided core biopsy. Thus EBUS should be considered as an acceptable option for tissue acquisition for molecular testing. [ABSTRACT FROM AUTHOR]

Background: Atrial fibrosis, as a hallmark of atrial structure remodeling, plays an important role in maintenance of chronic atrial fibrillation, but interrelationship of atrial fibrosis and atrial fibrillation is uncertain. Label-free proteomics can implement high throughput screening for finding and analyzing pivotal proteins related to the disease.. Therefore, we used label-free proteomics to explore and analyze differentially proteins in chronic atrial fibrillation patients with mitral valve disease. Methods: Left and right atrial appendages obtained from patients with mitral valve disease were both in chronic atrial fibrillation (CAF, AF≥6 months, n = 6) and in sinus rhythm (SR, n = 6). One part of the sample was used for histological analysis and fibrosis quantification; other part were analyzed by label-free proteomic combining liquid chromatography with mass spectrometry (LC-MS), we utilized bioinformatics analysis to identify differential proteins. Results: Degree of atrial fibrosis was higher in CAF patients than that of SR patients. 223 differential proteins were detected between two groups. These proteins mainly had vital functions such as cell proliferation, stress response, focal adhesion apoptosis. We evaluated that serine/threonine protein kinase N2 (PKN2), dermatopontin(DP), S100 calcium binding protein B(S100B), protein tyrosine kinase 2(PTK2) and discoidin domain receptor tyrosine kinase 2(DDR2) played important roles in fibrotic process related to atrial fibrillation. Conclusion: The study presented differential proteins responsible for atrial fibrosis in chronic atrial fibrillation patients through label-free proteomic analysis. We assessed some vital proteins including their characters and roles. These findings may open up new realm for mechanism research of atrial fibrillation. [ABSTRACT FROM AUTHOR]

Usually, the origin of a within-cohort bimodal size distribution is assumed to be caused by initial size differences or by one discrete period of accelerated growth for one part of the population. The aim of this study was to determine if more continuous pathways exist allowing shifts from the small to the large fraction within a bimodal age-cohort. Therefore, a Eurasian perch population, which had already developed a bimodal size-distribution and had differential resource use of the two size-cohorts, was examined. Results revealed that formation of a bimodal size-distribution can be a continuous process. Perch from the small size-cohort were able to grow into the large size-cohort by feeding on macroinvertebrates not used by their conspecifics. The diet shifts were accompanied by morphological shape changes. Intra-specific competition seemed to trigger the development towards an increasing number of large individuals. A stage-structured matrix model confirmed these assumptions. The fact that bimodality can be a continuous process is important to consider for the understanding of ecological processes and links within ecosystems. [ABSTRACT FROM AUTHOR]

Typical data in a microbiome study consist of the operational taxonomic unit (OTU) counts that have the characteristic of excess zeros, which are often ignored by investigators. In this paper, we compare the performance of different competing methods to model data with zero inflated features through extensive simulations and application to a microbiome study. These methods include standard parametric and non-parametric models, hurdle models, and zero inflated models. We examine varying degrees of zero inflation, with or without dispersion in the count component, as well as different magnitude and direction of the covariate effect on structural zeros and the count components. We focus on the assessment of type I error, power to detect the overall covariate effect, measures of model fit, and bias and effectiveness of parameter estimations. We also evaluate the abilities of model selection strategies using Akaike information criterion (AIC) or Vuong test to identify the correct model. The simulation studies show that hurdle and zero inflated models have well controlled type I errors, higher power, better goodness of fit measures, and are more accurate and efficient in the parameter estimation. Besides that, the hurdle models have similar goodness of fit and parameter estimation for the count component as their corresponding zero inflated models. However, the estimation and interpretation of the parameters for the zero components differs, and hurdle models are more stable when structural zeros are absent. We then discuss the model selection strategy for zero inflated data and implement it in a gut microbiome study of > 400 independent subjects. [ABSTRACT FROM AUTHOR]

Aphids exhibit a form of phenotypic plasticity, called polyphenism, in which genetically identical females reproduce sexually during one part of the life cycle and asexually (via parthenogenesis) during the remainder of the life cycle. The molecular basis for aphid parthenogenesis is unknown. Cytological observations of aphid parthenogenesis suggest that asexual oogenesis evolved either through a modification of meiosis or from a mitotic process. As a test of these alternatives, we assessed the expression levels and expression patterns of canonical meiotic recombination and germline genes in the sexual and asexual ovaries of the pea aphid, Acyrthosiphon pisum. We observed expression of all meiosis genes in similar patterns in asexual and sexual ovaries, with the exception that some genes encoding Argonaute-family members were not expressed in sexual ovaries. In addition, we observed that asexual aphid tissues accumulated unspliced transcripts of Spo11, whereas sexual aphid tissues accumulated primarily spliced transcripts. In situ hybridization revealed Spo11 transcript in sexual germ cells and undetectable levels of Spo11 transcript in asexual germ cells. We also found that an obligately asexual strain of pea aphid produced little spliced Spo11 transcript. Together, these results suggest that parthenogenetic oogenesis evolved from a meiosis-like, and not a mitosis-like, process and that the aphid reproductive polyphenism may involve a modification of Spo11 gene activity. [ABSTRACT FROM AUTHOR]

'Huangguogan' (Citrus reticulata × C. sinensis) is a new cultivar of mandarin citrus in China, and the research on fertilization of 'Huangguogan' is very limited. In this study, the effect of N fertilization on 'Huangguogan' fruit quality was determined at ripening. Sugars (sucrose, fructose, and glucose), organic acids (pyruvic, oxalic, citric acid, etc.), and vitamin components were measured at six stages of fruit development, and eight enzymes related to the glycolytic and Krebs cycle were assessed. The 1.81 kg N y-1 treatment group showed the highest total soluble solids concentration and total soluble solids/titratable acidity ratio but the lowest titratable acidity (acid content) at ripening, while the N1 treatment (0 kg N y-1) showed the opposite trend. Sucrose and citric acid accumulated to the largest extent during fruit development. Sucrose and ascorbic acid content increased (8.46 to 50.97 mg g-1 and 8.16 to 27.39 mg g-1, respectively), while citric acid content decreased (90.81 to 0.02 mg g-1). Aconitase was the key enzyme responsible for the observed changes in citric acid. The N concentrations in ripening fruit ranged from 2.25% to 4.15%. Curve estimation and principal component analysis revealed that fruit N was positively correlated with the sugars and vitamin components and negatively correlated with the organic acids. The accumulation of these metabolites seemed closely related to the dynamic changes in fruit N concentration at the five N levels tested. In conclusion, we suggest that the 1.81 kg N y-1 treatment represents the most suitable N fertilizer treatment for 'Huangguogan' citrus fruit. [ABSTRACT FROM AUTHOR]

Background: Physical inactivity is high within the Qatari population, particularly within females, and school-based environments, contributing to increased morbidity and mortality. School-based physical activity (PA) outcomes may be mediated by physical self-concept. Low physical self-concept may negatively impact PA engagement, compromising childhood and adolescent physical fitness, which may translate into adulthood. Normative physical fitness data for the Qatari population is unavailable. Stratifying normative physical fitness appears prudent, to not only allow comparisons to be made worldwide, but enable informed decisions for public health policy and future interventions in the Qatari population. Purpose: To establish the physical fitness of young adults in Qatar, and examine differences between males and females for physical self-concept, and engagement in school-based and extra-curricular PA. Method: 186 (females n = 85) healthy participants [median (minimum—maximum) age: males = 21 (18–26), females = 21 (18–24) y; height: males = 1.74 (1.57–1.99), females = 1.61 (1.46–1.76) m; body mass: males = 71.9 (49.3–145.0), females = 56.8 (35.7–96.4) kg] completed the ALPHA-FIT test battery for adults (one leg stand, figure of eight run, handgrip strength, jump and reach, modified push-up, dynamic sit-up and 2 km walk), physical self-description questionnaire (measuring physical self-concept), and were asked to answer 'yes' or 'no' to whether they participated in school-based and extra-curricular PA. Results: Data is reported as effect size; ±90% confidence limit. Males compared to females most likely performed better for dynamic sit-up (2.2; ±0.76), very likely better for the figure of eight run (0.86; ±0.42) and likely better for handgrip strength (2.1; ±0.75). Males likely had higher physical self-concept for coordination (0.78; ±0.37) and endurance (0.66; ±0.27) compared to females. There were no differences for school-based PA (p ≥ 0.78) or for extra-curricular PA for males (p ≥ 0.26) or females (p ≥ 0.21). Conclusion: The data suggests that the young Qatari adult population has variable, yet generally low, physical fitness traits compared to individuals worldwide, likely due to their low PA. The precise aetiology for this is not well documented, yet such data may be prudent to evidence-inform strategies to improve physical fitness through increased PA (synergistic relationship), given the strong association between physical activity/fitness and morbidity/mortality. [ABSTRACT FROM AUTHOR]

Background: Evidence indicates that human circadian rhythm is affected by the intestinal microbiota, and establishment of the circadian rhythm begins during fetal development. However, the relationship between maternal fermented food intake and infant sleep duration has not been previously investigated. In this study, we examined whether dietary consumption of fermented food during pregnancy is associated with infant sleep duration at 1 year of age. Methods: This birth cohort study used data from a nationwide government-funded study called The Japan Environment and Children’s Study (JECS). After exclusions from a dataset comprising 104,065 JECS records, we evaluated 72,624 mother-child pairs where the child was 1 year old. We investigated the association between dietary intake of fermented foods during pregnancy and infant sleep duration of less than 11 h at 1 year of age. Results: Multivariable logistic regression showed that maternal intake of fermented food, especially miso, during the pregnancy was independently associated with reduced risk of infant sleep duration of less than 11 h. Conclusions: Further research, including interventional studies, is warranted to confirm the association between consumption of fermented foods during pregnancy and sufficient infant sleep duration. Trial registration: . [ABSTRACT FROM AUTHOR]

The development of ICU-acquired sodium disturbances is not fully understood. Alterations in non-osmotic skin sodium storage, hypothetically inflammation-driven, could play a role. To investigate this in critically ill patients we conducted a patient-control study with skin punch biopsies in patients with sepsis (n = 15), after coronary artery bypass grafting (CABG, n = 15) and undergoing total hip arthroplasty (THA-controls, n = 15) respectively, together representing a range in severity of systemic inflammation. Biopsies were taken within 24 hours (sepsis) and within 2 hours (CABG) after ICU-admission, and prior to arthroplasty. Biopsies were analysed for sodium content. In addition immunostainings and quantitative real time PCR were performed. The primary aim of this study was to detect possible differences in amounts of cutaneous sodium. The secondary aims were to quantify inflammation and lymphangiogenesis with concomitant markers. The highest amounts of both water and sodium were found in patients with sepsis, with slightly lower values after CABG and the lowest amounts in THA-controls. Correlation between water and sodium was 0.5 (p<0.01). In skin biopsies in all groups comparable amounts of macrophages, T-cells and lymph vessels were found. In all groups comparable expression of inflammation markers were found. However, higher mRNA transcript expression levels of markers of lymphangiogenesis were found in patients with sepsis and after CABG. The conjoint accumulation of water and sodium points towards oedema formation. However, the correlation coefficient of 0.5 leaves room for alternative explanations, including non-osmotic sodium storage. No signs of dermal inflammation were found, but upregulation of markers of lymphangiogenesis could indicate future lymphangiogenesis. [ABSTRACT FROM AUTHOR]

Microliths–small, retouched, often-backed stone tools–are often interpreted to be the product of composite tools, including projectile weapons, and efficient hunting strategies by modern humans. In Europe and Africa these lithic toolkits are linked to hunting of medium- and large-sized game found in grassland or woodland settings, or as adaptations to risky environments during periods of climatic change. Here, we report on a recently excavated lithic assemblage from the Late Pleistocene cave site of Fa-Hien Lena in the tropical evergreen rainforest of Sri Lanka. Our analyses demonstrate that Fa-Hien Lena represents the earliest microlith assemblage in South Asia (c. 48,000–45,000 cal. years BP) in firm association with evidence for the procurement of small to medium size arboreal prey and rainforest plants. Moreover, our data highlight that the lithic technology of Fa-Hien Lena changed little over the long span of human occupation (c. 48,000–45,000 cal. years BP to c. 4,000 cal. years BP) indicating a successful, stable technological adaptation to the tropics. We argue that microlith assemblages were an important part of the environmental plasticity that enabled Homo sapiens to colonise and specialise in a diversity of ecological settings during its expansion within and beyond Africa. The proliferation of diverse microlithic technologies across Eurasia c. 48–45 ka was part of a flexible human ‘toolkit’ that assisted our species’ spread into all of the world’s environments, and the development of specialised technological and cultural approaches to novel ecological situations. [ABSTRACT FROM AUTHOR]

In the present report, we used highly elongated Drosophila bristle cells to dissect the role of dynein heavy chain (Dhc64C) in Golgi organization. We demonstrated that whereas in the bristle "somal" region Golgi units are composed of cis-, medial, and trans-Golgi compartments (“complete Golgi”), the bristle shaft contains Golgi satellites that lack the trans-Golgi compartment (hereafter referred to as “incomplete Golgi”) and which are static and localized at the base area. However, in Dhc64C mutants, the entire bristle shaft was filled with complete Golgi units containing ectopic trans-Golgi components. To further understand Golgi bristle organization, we tested the roles of microtubule (MT) polarity and the Dhc-opposing motor, kinesin heavy chain (Khc). For our surprise, we found that in Khc and Ik2Dominant-negative (DN) flies in which the polarized organization of MTs is affected, the bristle shaft was filled with complete Golgi, similarly to what is seen in Dhc64C flies. Thus, we demonstrated that MTs and the motor proteins Dhc and Khc are required for bristle Golgi organization. However, the fact that both Dhc64C and Khc flies showed similar Golgi defects calls for an additional work to elucidate the molecular mechanism describing why these factors are required for bristle Golgi organization. [ABSTRACT FROM AUTHOR]

Tremendous amounts of nitrogen (N) fertilizer have been added to arable lands, often resulting in substantial effects on terrestrial ecosystems, including soil acidification, altered enzyme activities and changes in microbial community composition. Soil microbes are the major drivers of soil carbon (C) and N cycling; therefore, understanding the response of microbial communities to elevated N inputs is of significant importance. This study was carried out to investigate the influences of different N fertilization rates (0, 182, and 225 kg ha-1 representing control, low, and high N supply for each crop season for summer maize and winter wheat) on soil biochemical attributes, extracellular enzyme activities, and the microbial community composition in a winter wheat-summer maize rotation cropping system in north-central China. The results showed that N addition significantly decreased the soil pH in both the wheat and maize seasons. Microbial biomass N (MBN) decreased following N fertilization in the wheat season, while the opposite trend in MBN was observed in the maize season. Response ratio analysis showed that the activities of enzymes involved in C, N, and phosphorus cycling were significantly enhanced under N enrichment in both the wheat and maize seasons, and higher enzyme activities were noted in the high N addition treatment than in the low N addition treatment. A linear increase in fungal abundance with the N addition gradient was observed in the wheat season, whereas the fungal abundance increased and then decreased in the maize season. The bacterial abundance showed an increased and then decreased trend in response to the N addition gradient in both the wheat and maize crop seasons. Moreover, the partial least squares path model (PLS-PM) analysis showed that soil pH and soil organic carbon (SOC) were the most important soil variables, causing shifts in the soil bacteria. Furthermore, compared with the N-cycling enzymes, the C-cycling enzymes were significantly affected by the soil pH and SOC. Taken together, these results suggest that the effect of N addition on enzyme activities was consistent in both crop seasons, while the effects on MBN and microbial community composition to N addition were highly variable in the two crop seasons. Moreover, N fertilization-induced changes in the soil chemical properties such as soil acidity and SOC played a substantial role in shaping the microbial community. [ABSTRACT FROM AUTHOR]

Background: An increasing number of people with stroke live in their communities, yet the understanding of how their reintegration into society can best be facilitated is incomplete. If needs are not sufficiently met and difficulties overcome, it may result in limited participation and decreased life satisfaction for this group. We aimed to understand life after stroke through the lens of participants’ cameras, and hence their views and experiences guided this study. Methods: By the means of photovoice, an action research method, this study was conducted in a collaborative format with six women and five men after stroke. Participants photographed in everyday life for up to four weeks and then met to discuss all images in a focus group setting. Subsequently, participants gave feedback on the method and discussed the upcoming photography exhibition. All photos and the three focus group discussions were analyzed using a thematic analysis with an inductive approach. Results: In the focus group discussions, life after stroke were conceptualized through five main themes: a driving force to participate in society; managing everyday life through inventiveness and persistent training; insufficient healthcare and rehabilitation in the long-term perspective; finding meaningful relationships and activities in daily life. Participants’ voices are made clear through selected photos, which aim to present each theme and make results easier to understand. Conclusions: Participants found new ways to approach everyday life situations and had thereby regained a sense of control in life. However, it was evident that psychological processes towards adaptation were hindered by depression and that some individuals felt alone in an ongoing struggle. Additionally, available interventions a long time after stroke were not flexible enough to address all participants’ needs. [ABSTRACT FROM AUTHOR]

In this study, the spatial distribution of the transient pressure and the slipstream caused by a 1/10 scaled metro train passing through a tunnel was studied with moving model test. We hereby investigate the mechanism underlying the mitigation of the transient pressure on both the train surface and tunnel wall, as well as that of the slipstream in the tunnel. Experimental results showed that the airshaft at different locations in a tunnel had different pressure relief effects. The most significant pressure amplitude decreased by 36.0% with the airshaft locating in the middle of the tunnel. Meanwhile, the slipstream speed was also relieved from 0.45 to 0.36 after an airshaft. We also assessed and analyzed the impact of train speed on the transient pressures and slipstream. It was found that the increase of the train speed would increase the transient pressure and slipstream speed, but it did not effect their spatial distribution. [ABSTRACT FROM AUTHOR]

Potential environmental risks of genetically modified (GM) crops have raised concerns. To better understand the effect of transgenic rice on the bacterial community in paddy soil, a field experiment was carried out using pairs of rice varieties from two subspecies (indica and japonica) containing bar transgene with herbicide resistance and their parental conventional rice. The 16S rRNA gene of soil genomic DNA from different soil layers at the maturity stage was sequenced using high-throughput sequencing on the Illumina MiSeq platform to explore the microbial community diversity among different rice soils. There were no significant differences in diversity indices between transgenic japonica rice and its sister conventional rice (japonica pair) among different soil layers, but, significant differences was observed between transgenic indica rice and its conventional rice (indica pair) in the topsoil layer around concentrated rice roots according to the ace diversity index. Though the japonica rice soil and indica rice soil were shared several key genera, including Rivibacter, Anaeromyxobacter, Roseomonas, Geobacter, Thiobacillus, Clostridium, and Desulfobulbus, the primary bacterial genera in indica rice soil were different from those in japonica rice. Synechococcus and Dechloromonas were present in japonica rice samples, while Chloronema, Flexibacter, and Blastocatella were observed in indica rice soil. Moreover, the abundance of genera between GM and non-GM varieties in japonica rice was significantly different from indica rice, and several bacterial communities influenced these differences. Anaerovorax was more abundant in transgenic japonica rice soil than conventional rice soil, while it was deficient in transgenic indica rice soil compared to conventional rice soil, and opposite responses to Deferrisoma were in that of indica rice. Thus, we concluded that transgenic indica and japonica rice had different effects on soil bacteria compared with their corresponding sister conventional rice. However, these composition and abundance difference only occurred for a few genera but had no effect on the primary genera and soil characteristics were mainly contributed to these differences. Thus, differences in bacterial community structure can be ignored when evaluating the impacts of transgenic rice in the complex soil microenvironment. [ABSTRACT FROM AUTHOR]

Physicochemical properties of water molecules as the main compositions of the freezing media can be affected by the electromagnetic fled. The purpose of this study was to apply extremely low repetition rate electromagnetic fields (ELEFs) to change the molecular network of water molecules existing in freezing media used for human sperm cryopreservation. First, different time periods and pulsed electromagnetic fields were used to evaluate the physiochemical properties of water. The lowest rate of cluster size, surface tension, viscosity, and density was observed for water samples exposed to 1000 Hz ELEF for 60 min (P < 0.05) that could be results in small ice crystal formation. Therefore, this treatment was selected for further evaluations in human sperm freezing because there was minimal probability of amorphous ice crystallization in this group. To assess fertilizing potential, human semen samples were subjected to ELEF (1000 Hz) water-made freezing medium and cryopreserved. The highest percentage of total motility, progressive motility, viability, membrane integrity, mitochondrial membrane potential, DNA integrity, and TAC were obtained in frozen ELEF as compared to other groups. The percentage of viable spermatozoa (Annexin V-/PI-) in frozen ELEF was significantly higher than in frozen control. The level of ROS was significantly lower in frozen ELEF when compared to frozen control. It can be concluded that the modification of physicochemical properties of water existing in cryopreservation media by ELEF is a suitable strategy to improve the outcome of cryopreservation. [ABSTRACT FROM AUTHOR]

Our previous single-cell based gene expression analysis pointed out significant variations of LDHA level during erythroid differentiation. Deeper investigations highlighted that a metabolic switch occurred along differentiation of erythroid cells. More precisely we showed that self-renewing progenitors relied mostly upon lactate-productive glycolysis, and required LDHA activity, whereas differentiating cells, mainly involved mitochondrial oxidative phosphorylation (OXPHOS). These metabolic rearrangements were coming along with a particular temporary event, occurring within the first 24h of erythroid differentiation. The activity of glycolytic metabolism and OXPHOS rose jointly with oxgene consumption dedicated to ATP production at 12-24h of the differentiation process before lactate-productive glycolysis sharply fall down and energy needs decline. Finally, we demonstrated that the metabolic switch mediated through LDHA drop and OXPHOS upkeep might be necessary for erythroid differentiation. We also discuss the possibility that metabolism, gene expression and epigenetics could act together in a circular manner as a driving force for differentiation. [ABSTRACT FROM AUTHOR]

Background: Active living approaches seek to promote physical activity and reduce sedentary time across different domains, including through active travel. However, there is little information on how movement behaviours in different domains relate to each other. We used compositional data analysis to explore associations between active commuting and patterns of movement behaviour during discretionary time. Methods and findings: We analysed cross-sectional and longitudinal data from the UK Biobank study. At baseline (2006–2010) and follow up (2009–2013) participants reported their mode of travel to work, dichotomised as active (walking, cycling or public transport) or inactive (car). Participants also reported activities performed during discretionary time, categorised as (i) screen time; (ii) walking for pleasure; and (iii) sport and do-it-yourself (DIY) activities, summed to produce a total. We applied compositional data analysis to test for associations between active commuting and the composition and total amount of discretionary time, using linear regression models adjusted for covariates. Adverse events were not investigated in this observational analysis. The survey response rate was 5.5%. In the cross-sectional analysis (n = 182,406; mean age = 52 years; 51% female), active commuters engaged in relatively less screen time than those who used inactive modes (coefficient -0.12, 95% confidence interval [CI] -0.13 to -0.11), equating to approximately 60 minutes less screen time per week. Similarly, in the longitudinal analysis (n = 4,323; mean age = 51 years; 49% female) there were relative reductions in screen time in those who used active modes at both time points compared with those who used inactive modes at both time points (coefficient -0.15, 95% confidence interval [CI] -0.24 to -0.06), equating to a difference between these commute groups of approximately 30 minutes per week at follow up. However, as exposures and outcomes were measured concurrently, reverse causation is possible. Conclusions: Active commuting was associated with a more favourable pattern of movement behaviour during discretionary time. Active commuters accumulated 30–60 minutes less screen time per week than those using inactive modes. Though modest, this could have a cumulative effect on health over time. [ABSTRACT FROM AUTHOR]

Vector tile technology is developing rapidly and has received increasing attention in recent years. Compared to the raster tile, the vector tile has shown incomparable advantages, such as flexible map styles, suitability for high-resolution screens and ease of interaction. Recent studies on vector tiles have mostly focused on improving the efficiency on the server side and have overlooked the efficiency on the client side, which affects user experience. Parallel computing provides solutions to this issue. Parallel visualization of vector tiles is a typical example of embarrassing parallelism; thus, estimating the computing times of each tile accurately and decomposing the workload into multiple computing units evenly are key to the parallel visualization of vector tiles. This article adopts mainstream parallel computing and proposes an efficient tile-based parallel method for accelerating geographical feature visualization by building computational weight functions (CWFs) of geographical feature visualizations. The computing time of each vector tile is estimated by the CWF, and an effective workload decomposition strategy is proposed such that the efficiency of vector tile visualization is improved on the client side. Furthermore, a tile-based reconstruction scheme for geographical features is also proposed. Experiments show that the R-squared value of the estimated computing times of vector tiles is 0.914 and that the computational efficiency of the parallel visualization of vector tiles with the proposed workload decomposition strategy is 18.6% higher than that of common parallel visualization. Finally, users can obtain the entire set of features effectively and accurately based on the proposed reconstruction scheme. [ABSTRACT FROM AUTHOR]

Air pollution is closely associated with the development of respiratory illness. Behavioral adaptations of people to air pollution may influence its impact, yet this has not been investigated in the literature. Our hypothesis is that people experience and learn the underlying air quality to decide their adaptation, and they have a stronger incentive to behaviorally adapt to the air quality as it deteriorates. We tested our hypothesis on a sample of approximately 25,700 individuals from South Korea from 2002 to 2013 that contained information on daily doctor’s visits due to respiratory disease. We matched individuals to the mean of the past seven-day concentration of the particulate matter of size between 2.5 and 10 micrometers (PM10) in their county of residence. We examined whether people living in counties with greater air pollution suffer less from respiratory disease when the concentration increases. For the analysis, we separated counties into quintiles based on their mean seven-day PM10, and regressed the binary indicator of a daily doctor’s visit with a resulting diagnosis of respiratory disease on the seven-day PM10 concentration of the county of residence interacted with the quintile dummies. The key findings are that a 1-standard-deviation increase in the seven-day PM10 concentration in the two lowest quintiles is associated with an increase of 0.054 percentage points in the likelihood of a doctor’s visit with a resulting diagnosis of respiratory disease, which is about 40% larger than the effect in higher quintiles, and the size of 1-standard-deviation gradually increases from 0.037 percentage points in the third quintile to 0.040 percentage points in the fifth quintile. The smaller increase in the likelihood of respiratory disease in more polluted locations can be explained by the behavioral adaptation to the environment, but the effectiveness of the adaptation seems limited among the highly polluted locations. [ABSTRACT FROM AUTHOR]

Aim: The aim of this systematic review was to summarize and critically appraise the quality of published literature on measurement properties of questionnaires assessing Cognitive Reserve (CR) in adults (>18 years). Methods: We systematically searched for published studies on MEDLINE, PsycINFO, and Web of Science through August 2018. We evaluated the methodological quality of the included studies and the results on measurement properties based on a consensus-based standard checklist. Results: The search strategy identified 991 publications, of which 37 were selected evaluating the measurement properties of six different questionnaires. Construct validity of the Cognitive Reserve Index questionnaire was most extensively evaluated, while evaluation of the remaining measurement properties of this questionnaire was scarce. Measurement properties of the Cognitive Reserve Questionnaire and the Cognitive Reserve Scale were assessed more completely. While the Lifetime of Experience Questionnaire seems to be the most thorough instrument, a finale recommendation for one specific questionnaire cannot be drawn, since about half of the measurement properties for each questionnaire were poorly or not assessed at all. Conclusions: There is a need of high quality methodological studies assessing measurement properties of CR questionnaires, especially regarding content validity, structural validity, and responsiveness. Trial registration: PROSPERO Registration number . [ABSTRACT FROM AUTHOR]

Emplaced health promotion interventions, delivered by community health workers are increasingly being used internationally. However, the application of epidemiological risk knowledge to individuals within such communities is not straightforward and creates tensions for community health workers who are part of the communities that they are serving. Situated qualitative interview data were co-produced with community health workers employed in a superdiverse, deprived, post-industrial region of the United Kingdom, using photo-voice methods, to develop an account of how they made sense of the challenges of their work. The analysis draws on and develops theories of risk work and resilience work, which draw on practice theory. The key findings were that, first, being a critical insider enabled community health workers to make sense of the diverse constraints on health and lifestyles within their community. Second, they understood their own public health role as limited by operating within this context, so they articulated their occupational identity as focused on supporting clients to make small but sustainable changes to their own and their families’ lifestyles. Third, the uncertainties of translating population based risk information to individual clients were (at least partially) resolved at an embodied level, with the community health workers identifying as accessible and trusted role models for the value of changed lifestyles. The article is important for policy and practice as it provides a critique of a rapidly evolving new mode of delivery of public health services, and insights on the development of this new public health workforce. [ABSTRACT FROM AUTHOR]

Background: Despite the criticality of adherence to tuberculosis treatment, there is paucity of rigorous experimental research exploring the efficacy of interventions to promote adherence and a greater lack of inquiry addressing the integral role of adherence behaviour. The aim of this formative study was to examine the way in which the Wisepill evriMED Medication Event Reminder Monitor (MERM) was used among outpatients with drug susceptible pulmonary tuberculosis. Methods: In depth interviews were conducted with 20 outpatients receiving treatment from two public healthcare facilities in Thanh Hoa, a rural province in northern Viet Nam. Patients had been enrolled in a randomized controlled trial evaluating the effect of using the MERM device upon adherence for between 1–3 months. The control group used the device without an alert, while the intervention group used the device with a daily alert and scheduled dosing history review. Findings: All 20 patients interviewed were supportive of using the MERM device. Those able to be at home at the time that their treatment was due (50%) used the device as intended. Patients who worked all reported separating the time when the box was opened from the time at which they ingested their medication. Patients expressed fidelity to the prescribed medication taking time and concerns regarding the portability of the device. Limitations of the study surround the inclusion of a small sample population that did not experience factors that further compromise adherence. Conclusions: Data recorded by the box did not always accurately reflect usage patterns. The alert in the intervention arm was able to support adherence only in patients who did not work while completing their treatment. MERM implementation can be improved by better aligning prescriber instructions with patients’ daily routines, and increasing the use of adherence data to guide adherence support practices. Healthcare staff need to be aware of potential barriers to optimal use of MERM devices. A rigorous qualitative approach to formative assessment is essential to inform the scale up of new digital technologies. [ABSTRACT FROM AUTHOR]

Canine Visceral Leishmaniasis (CVL) prevalence, spatial distribution and associated factors were assessed in four locations in Iguazú department in 2014 and in Puerto Iguazú city again in 2018. The city areas were divided into a grid of 400x400m cells. All cells were sampled in 2014 and a random subsampling was developed in 2018. In each cell, five dogs clustered in a ‘critical scenario’ (prone to have vectors) were sampled. A rapid immunochromatographic dipstick was used to detect antibodies against Leishmania infantum, confirming by lymph node smears observation and PCR. For Puerto Iguazú, Generalized Linear Models (GLMs) were constructed considering environmental, dog and clinical variables. Pearson's Chi square and Fisher's exact tests were employed to evaluate the association between CVL, dog clinical signs and infestation with other parasites. Cartographic outputs were made and Moran's I indices were calculated as spatial autocorrelation indicators. CVL prevalence rates were 26.18% in 2014 and 17.50% in 2018. No associations were established in environmental models, but dog age and repellent use were significant when running 2014 dog models. Clinical models showed significant associations between seropositive dogs and ophthalmological, dermal signs and onychogryphosis in 2014. In 2018, only adenomegaly was associated. The results of global Moran´s I were not significant but regarding local analysis, six sites in 2014 and one in 2018 presented autocorrelation with neighboring sites. The decrease in CVL prevalence may be associated to transmission stabilization, which could explain the lack of associations with dog-related variables. Further, spatial distribution of CVL is a poor evidence for design of transmission control measures but could be important in case of intensive parasite circulation or when the first autochthonous cases appear. For control success, sensitivity of diagnostic methods, political will and adequate material resources remain critical. Modeling of multiple variables will be required to identify factors that drive disease stabilization/destabilization. [ABSTRACT FROM AUTHOR]

Ecoregionalization is the process by which a territory is classified in similar areas according to specific environmental and climatic factors. The climate and the environment strongly influence the presence and distribution of vectors responsible for significant human and animal diseases worldwide. In this paper, we developed a map of the eco-climatic regions of Italy adopting a data-driven spatial clustering approach using recent and detailed spatial data on climatic and environmental factors. We selected seven variables, relevant for a broad set of human and animal vector-borne diseases (VBDs): standard deviation of altitude, mean daytime land surface temperature, mean amplitude and peak timing of the annual cycle of land surface temperature, mean and amplitude of the annual cycle of greenness value, and daily mean amount of rainfall. Principal Component Analysis followed by multivariate geographic clustering using the k-medoids technique were used to group the pixels with similar characteristics into different ecoregions, and at different spatial resolutions (250 m, 1 km and 2 km). We showed that the spatial structure of ecoregions is generally maintained at different spatial resolutions and we compared the resulting ecoregion maps with two datasets related to Bluetongue vectors and West Nile Disease (WND) outbreaks in Italy. The known characteristics of Culicoides imicola habitat were well captured by 2/22 specific ecoregions (at 250 m resolution). Culicoides obsoletus/scoticus occupy all sampled ecoregions, according to its known widespread distribution across the peninsula. WND outbreak locations strongly cluster in 4/22 ecoregions, dominated by human influenced landscape, with intense cultivations and complex irrigation network. This approach could be a supportive tool in case of VBDs, defining pixel-based areas that are conducive environment for VBD spread, indicating where surveillance and prevention measures could be prioritized in Italy. Also, ecoregions suitable to specific VBDs vectors could inform entomological surveillance strategies. [ABSTRACT FROM AUTHOR]

The objective of the study was to find out the prophylactic efficacy of Quercetin in ameliorating the hypoxia induced vascular leakage in lungs of rats. Male SD rats received different doses of quercetin @ 25mg, 50mg, 100mg and 200mg/Kg BW, 1h prior to hypobaric hypoxia exposure (7,620m, for 6h). Quercetin 50 mg/kg BW supplemented orally 1h prior to hypoxia exposure was considered to be the optimum dose, due to significant reduction (p<0.001) in lung water content and lung transvascular leakage compared to control (hypoxia, 6h). Further, biochemical analysis (ROS, MDA, GSH, GPx, LDH, and albumin) and differential expressions of proteins (IKK-α/β, NFĸB, Nrf-2,TNF-α, ICAM-1, VCAM, P-selectin, Hif-1α, VEGF, TNF-α, TGF-β, INF-γ and IL-4) were determined by western blotting and ELISA. Changes in lung parenchyma were assessed by histopathology. Quercetin (50 mg/kg BW) prophylaxis under hypoxia showed significant reduction in oxidative stress (ROS and MDA), concomitant increase in antioxidants (GSH, GPx and SOD) followed by decreased LDH and albumin extravasation in BAL fluid over hypoxia. Quercetin prophylaxis significantly down regulated hypoxia induced increase in IKKα/β and NFĸB expressions leading to reduction in the levels of pro-inflammatory cytokines (TNF-α and INF-γ) followed by up regulation of anti-inflammatory cytokines (IL-4 and INF-γ) in lungs. Further, hypoxia mediated increase in HIF-1α was stabilized and VEGF levels in lungs were significantly down regulated by quercetin supplementation, leading to reduction in vascular leakage in lungs of rats under hypoxia. However, Quercetin has also enacted as Nrf-2 activator which significantly boosted up the synthesis of GSH under hypoxic condition compared to hypoxia. Histopathological observations further confirmed that quercetin preconditioning has an inhibitory effect on progression of oxidative stress and inflammation via attenuation of NFκB and stabilization HIF-1α in lungs of rats under hypoxia.These studies indicated that quercetin prophylaxis abrogates the possibility of hypobaric hypoxia induced pulmonary edema in rats. [ABSTRACT FROM AUTHOR]