Measurement invariance of the SF-12 among different demographic groups: The HELIUS study

AIM

To investigate whether items of the SF-12, widely used to assess health outcome in clinical practice and public health research, provide unbiased measurements of underlying constructs in different demographic groups regarding gender, age, educational level and ethnicity.

METHODS

We included 23,146 men and women aged 18-70 of Dutch, South-Asian Surinamese, African Surinamese, Ghanaian, Turkish, or Moroccan origin from the HELIUS study. Both multiple group confirmatory factor analyses (MGCFA), with increasingly stringent model constraints (i.e. assessing Configural, Metric, Strong and Strict measurement invariance (MI)), and regression analysis were conducted to establish comparability of SF-12 items across demographic groups.

RESULTS

MI regarding gender, age and education was tested in the ethnic Dutch group (N = 4,615). In each subsequent step of testing MI, change in goodness-of-fit measures did not exceed 0.010 (RMSEA) or 0.004 (CFI). Moreover, goodness-of-fit indices showed good fit for strict invariance models: RMSEA<0.055; CFI>0.97. Regarding ethnicity, RMSEA values of metric and subsequent models fell above 0.055, indicating violation of measurement invariance in factor loadings, thresholds and residual variances. Regression analysis revealed possible age-, education- and ethnicity-related DIF. Adjustment for this DIF had little impact on the magnitude of age and educational differences in physical and mental health, but ethnic inequalities in physical health-and to a lesser extent mental health-were reduced after DIF adjustment.

CONCLUSIONS

We found no evidence of violation of measurement invariance of the SF-12 regarding gender, age and educational level. If minor DIF would remain undetected in our MGCFA analyses, we showed that this would have negligible effect on the magnitude of demographic health inequalities. Regarding ethnicity, the SF-12 was not measurement invariant. After accounting for DIF, we observed a reduction of ethnic inequalities in health, in particular in physical health. Caution is warranted when comparing SF-12 scores across population groups with various ethnic backgrounds.

Predominant Golgi Residency of the Plant K/HDEL Receptor Is Essential for Its Function in Mediating ER Retention

Accumulation of soluble proteins in the endoplasmic reticulum (ER) of plants is mediated by a receptor termed ER RETENTION DEFECTIVE2 (ERD2) or K/HDEL receptor. Using two gain-of-function assays and by complementing loss of function in Nicotiana benthamiana, we discovered that compromising the lumenal N terminus or the cytosolic C terminus with fluorescent fusions abolishes its biological function and profoundly affects its subcellular localization. Based on the confirmed asymmetrical topology of ERD2, we engineered a new fluorescent ERD2 fusion protein that retains biological activity. Using this fusion, we show that ERD2 is exclusively detected at the Golgi apparatus, unlike nonfunctional C-terminal fusions, which also label the ER. Moreover, ERD2 is confined to early Golgi compartments and does not show ligand-induced redistribution to the ER. We show that the cytosolic C terminus of ERD2 plays a crucial role in its function. Two conserved leucine residues that do not correspond to any known targeting motifs for ER-Golgi trafficking were shown to be essential for both ERD2 Golgi residency and its ability to mediate ER retention of soluble ligands. The results suggest that anterograde ER to Golgi transport of ERD2 is either extremely fast, well in excess of the bulk flow rate, or that ERD2 does not recycle in the way originally proposed.

Extent of third-order linkage disequilibrium in a composite line of Iberian pigs

BACKGROUND

Previous studies on linkage disequilibrium have investigated second order linkage disequilibrium in animal and plant populations. The objective of this paper was to investigate the genome-wide levels of third order linkage disequilibrium in a composite line founded by admixture of four Iberian pig strains. A model for the generation of third order linkage disequilibrium by population admixture is proposed. A computer Expectation-Maximization algorithm is developed and applied to the estimation of third order linkage disequilibrium at inter- and intra-chromosomal level using 26,347 SNPs typed in 306 sows. The relationship of third order linkage disequilibrium with physical distance was investigated over 35 million triplets in SSC12. Basic and normalized estimates of inter and intra-chromosomal third order linkage disequilibrium are reported.

RESULTS

Genome-wide analyses revealed that third order linkage disequilibrium is rather common among linked loci in this Iberian pig line. It is shown that population admixture of multiple populations may explain the observed levels of third order linkage disequilibrium although it could be generated by genetic drift. Third order linkage disequilibrium decreases rapidly up to 4 Mb and then declines slowly. The short distances between consecutive markers explain the maintenance of the observed third order linkage disequilibria levels when using a model incorporating the break-up of disequilibrium by recombination. Genome-wide testing also revealed that only 3.6% of the normalized estimates were different from 1, - 1, 0, or from a not well-defined situation in which there is only one possible value for the third order linkage disequilibrium parameter, given allele frequencies and pairwise linkage disequilibria parameters.

CONCLUSIONS

Third order linkage disequilibrium is common among linked markers in the analyzed pig line and may have been generated by population admixture of multiple populations or by genetic drift. As with second order linkage disequilibrium, the absolute value of the third order linkage disequilibrium decreases with physical distance. Normalization of third order linkage disequilibrium should be avoided for closely linked bi-allelic loci.

Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns

BACKGROUND

Anisakis simplex sensu stricto and Anisakis pegreffii are sibling species of nematodes parasitic on marine mammals. Zoonotic human infection with third stage infective larvae causes anisakiasis, a debilitating and potentially fatal disease. These 2 species show evidence of hybridisation in geographical areas where they are sympatric. How the species and their hybrids differ is still poorly understood.

RESULTS

Third stage larvae of Anisakis simplex s.s., Anisakis pegreffii and hybrids were sampled from Merluccius merluccius (Teleosti) hosts captured in waters of the FAO 27 geographical area. Specimens of each species and hybrids were distinguished with a diagnostic genetic marker (ITS). RNA was extracted from pools of 10 individuals of each taxon. Transcriptomes were generated using Illumina RNA-Seq, and assembled de novo. A joint assembly (here called merged transcriptome) of all 3 samples was also generated. The inferred transcript sets were functionally annotated and compared globally and also on subsets of secreted proteins and putative allergen families. While intermediary metabolism appeared to be typical for nematodes in the 3 evaluated taxa, their transcriptomes present strong levels of differential expression and enrichment, mainly of transcripts related to metabolic pathways and gene ontologies associated to energy metabolism and other pathways, with significant presence of excreted/secreted proteins, most of them allergens. The allergome of the 2 species and their hybrids has also been thoroughly studied; at least 74 different allergen families were identified in the transcriptomes.

CONCLUSIONS

A. simplex s.s., A. pegreffi and their hybrids differ in gene expression patterns in the L3 stage. Strong parent-of-origin effects were observed: A. pegreffi alleles dominate in the expression patterns of hybrids albeit the latter, and A. pegreffii also display significant differences indicating that hybrids are intermediate biological entities among their parental species, and thus of outstanding interest in the study of speciation in nematodes. Analyses of differential expression based on genes coding for secreted proteins suggests that co-infections presents different repertoires of released protein to the host environment. Both species and their hybrids, share more allergen genes than previously thought and are likely to induce overlapping disease responses.

Examination of performance of the Center for Epidemiologic Studies Depression Scale Short Form 10 among African youth in poor, rural households

BACKGROUND

Youth mental health has emerged as a pressing global issue. However, to advance research gaps in low-income settings, we need valid measures of common mental health disorders. Using primary data collected in five countries (Kenya, Malawi, Tanzania, Zambia, and Zimbabwe), this study aims to assess the psychometric properties of the commonly used 10-item Center for Epidemiological Studies Depression (CES-D 10) scale among poor, disadvantaged youth populations in sub-Saharan African (SSA).

METHODS

Youth samples from each country (sample sizes ranging from 651 to 2098) come from large household surveys with youth modules, collected for impact evaluations of cash transfer programs targeted to poor families. For each sample, we assessed internal consistency (alpha), conducted factor analysis, and then examined construct validity and measurement invariance. We performed both exploratory (EFA) and confirmatory factor analysis (CFA) to examine and confirm the structure of the CES-D 10 for each country and then used multigroup CFA to assess measurement invariance across gender and age. Multivariate analyses were conducted to assess construct validity via test of the relationship between CES-D 10 and background characteristics.

RESULTS

Results show the CES-D 10 had strong psychometric properties and was a reliable measure of depressive symptoms among disadvantaged youth in SSA. Across countries, there was high internal consistency (Cronbach alphas = 0.70-0.76) and the traditional two-factor solution showed good model fit. Full measurement invariance of the CES-D 10 was supported across gender. Consistent with previous literature on risk factors for depressive symptoms, the CES-D 10 was associated with increasing age, and female gender and being out of school in some locations.

CONCLUSIONS

Results from this study support broad use of the CES-D 10 among poor youth populations in SSA. Between one-third and two-thirds of our samples demonstrated depressive symptoms as classified by recommended cut-offs for the CES-D 10, indicating a high burden of mental illness in disadvantaged youth populations. This tool can be used in future efforts to study prevalence and dynamics of depressive symptoms in this population, as well as effectiveness of policies and interventions to improve the mental health of youth in SSA.

Genetic profile of scrapie codons 146, 211 and 222 in the PRNP gene locus in three breeds of dairy goats

Polymorphisms at PRNP gene locus have been associated with resistance against classical scrapie in goats. Genetic selection on this gene within appropriate breeding programs may contribute to the control of the disease. The present study characterized the genetic profile of codons 146, 211 and 222 in three dairy goat breeds in Greece. A total of 766 dairy goats from seven farms were used. Animals belonged to two indigenous Greek, Eghoria (n = 264) and Skopelos (n = 287) and a foreign breed, Damascus (n = 215). Genomic DNA was extracted from blood samples from individual animals. Polymorphisms were detected in these codons using Real-Time PCR analysis and four different Custom TaqMan® SNP Genotyping Assays. Genotypic, allelic and haplotypic frequencies were calculated based on individual animal genotypes. Chi-square tests were used to examine Hardy-Weinberg equilibrium state and compare genotypic distribution across breeds. Genetic distances among the three breeds, and between these and 30 breeds reared in other countries were estimated based on haplotypic frequencies using fixation index FST with Arlequin v3.1 software; a Neighbor-Joining tree was created using PHYLIP package v3.695. Level of statistical significance was set at P = 0.01. All scrapie resistance-associated alleles (146S, 146D, 211Q and 222K) were detected in the studied population. Significant frequency differences were observed between the indigenous Greek and Damascus breeds. Alleles 222K and 146S had the highest frequency in the two indigenous and the Damascus breed, respectively (ca. 6.0%). The studied breeds shared similar haplotypic frequencies with most South Italian and Turkish breeds but differed significantly from North-Western European, Far East and some USA goat breeds. Results suggest there is adequate variation in the PRNP gene locus to support breeding programs for enhanced scrapie resistance in goats reared in Greece. Genetic comparisons among goat breeds indicate that separate breeding programs should apply to the two indigenous and the imported Damascus breeds.

Sequencing conjugated polymers by eye

The solid-state microstructure of a conjugated polymer is the most important parameter determining its properties and performance in (opto)-electronic devices. A huge amount of research has been dedicated to tuning and understanding how the sequence of monomers, the nature and frequency of defects, the exact backbone conformation, and the assembly and crystallinity of conjugated polymers affect their basic photophysics and charge transporting properties. However, because of the lack of reliable high-resolution analytical techniques, all the structure-property relations proposed in the literature are based either on molecular modeling or on indirect experimental data averaged on polydisperse samples. We show that a combination of electrospray vacuum deposition and high-resolution scanning tunneling microscopy allows the imaging of individual conjugated polymers with unprecedented detail, thereby unraveling structural and self-assembly characteristics that have so far been impossible to determine.

Binding of sulphonylureas to plasma proteins - A KATP channel perspective

Sulphonylurea drugs stimulate insulin secretion from pancreatic β-cells primarily by inhibiting ATP sensitive potassium (K_ATP) channels in the β-cell membrane. The effective sulphonylurea concentration at its site of action is significantly attenuated by binding to serum albumin, which makes it difficult to compare in vitro and in vivo data. We therefore measured the ability of gliclazide and glibenclamide to inhibit K_ATP channels and stimulate insulin secretion in the presence of serum albumin. We used this data, together with estimates of free drug concentrations from binding studies, to predict the extent of sulphonylurea inhibition of K_ATP channels at therapeutic concentrations in vivo. K_ATP currents from mouse pancreatic β-cells and Xenopus oocytes were measured using the patch-clamp technique. Gliclazide and glibenclamide binding to human plasma were determined in spiked plasma samples using an ultrafiltration-mass spectrometry approach. Bovine serum albumin (60g/l) produced a mild, non-significant reduction of gliclazide block of K_ATP currents in pancreatic β-cells and Xenopus oocytes. In contrast, glibenclamide inhibition of recombinant K_ATP channels was dramatically suppressed by albumin (predicted free drug concentration <0.1%). Insulin secretion was also reduced. Free concentrations of gliclazide and glibenclamide in the presence of human plasma measured in binding experiments were 15% and 0.05%, respectively. Our data suggest the free concentration of glibenclamide in plasma is too low to account for the drug’s therapeutic effect. In contrast, the free gliclazide concentration in plasma is high enough to close K_ATP channels and stimulate insulin secretion.

Specific serum and CSF microRNA profiles distinguish sporadic behavioural variant of frontotemporal dementia compared with Alzheimer patients and cognitively healthy controls

Information on circulating miRNAs in frontotemporal lobar degeneration is very limited and conflicting results have complicated an interpretation in Alzheimer's disease thus far. In the present study we I) collected samples from multiple clinical centers across Germany, II) defined 3 homogenous patient groups with high sample sizes (bvFTD n = 48, AD n = 48 and cognitively healthy controls n = 44), III) compared expression levels in both CSF and serum samples and IV) detected a limited set of miRNAs by using a MIQE compliant protocol based on SYBR-green miRCURY assays that have proven reliable to generate reproducible results. We included several quality controls that identified and reduced technical variation to increase the reliability of our data. We showed that the expression levels of circulating miRNAs measured in CSF did not correlate with levels in serum. Using cluster analysis we found expression pattern in serum that, in part, reflects the genomic organization and affiliation to a specific miRNA family and that were specifically altered in bvFTD, AD, and control groups. Applying factor analysis we identified a 3-factor model characterized by a miRNA signature that explained 80% of the variance classifying healthy controls with 97%, bvFTD with 77% and AD with 72% accuracy. MANOVA confirmed signals like miR-320a and miR-26b-5p at BH corrected significance that contributed most to discriminate bvFTD cases with 96% sensitivity and 90% specificity and AD cases with 89% sensitivity and specificity compared to healthy controls, respectively. Correlation analysis revealed that miRNAs from the 3-factor model also correlated with levels of protein biomarker amyloid-beta1-42 and phosphorylated neurofilament heavy chain, indicating their potential role in the monitoring of progressive neuronal degeneration. Our data show that miRNAs can be reproducibly measured in serum and CSF without pre-amplification and that serum includes higher expressed signals that demonstrate an overall better ability to classify bvFTD, AD and healthy controls compared to signals detected in CSF.

Domestication affects exploratory behaviour of pikeperch (Sander lucioperca L.) during the transition to pelleted food

Genetic selection for body size during domestication of animal species can inadvertently affect a number of physiological and behavioural traits. The pace-of-life syndrome (POLS) hypothesis predicts that domestication in an artificial environment lacking predators and providing abundant resources prefers proactive individuals with strong feeding motivation, high levels of aggression and risk taking, with low hypothalamus-pituitary-adrenal (HPA) axis responsiveness. In the present experiment we weaned fingerling pike-perch from live feed and habituated them to formulated feed. We recorded the number of weeks needed for the fish to accept pellets, their body length at the age of 100 days, their boldness in a novel object test and their HPI axis responsiveness. Individuals accepting the artificial feed within the first week grew larger than fish habituating later; therefore early weaners would be kept and bred in routine aquaculture procedures. Contrary to predictions of POLS hypothesis, fish weaning earlier and thus growing faster were less bold and had higher HPI axis responsiveness than fish accepting the pellets later or never. As live feed is preferred to artificial pellets, less competitive individuals may switch to pellets earlier. Inadvertent selection for stress sensitive fish may have an effect on production in aquaculture as well as on natural population after intensive restocking.

Live-cell imaging of conidial anastomosis tube fusion during colony initiation in Fusarium oxysporum

Fusarium oxysporum exhibits conidial anastomosis tube (CAT) fusion during colony initiation to form networks of conidial germlings. Here we determined the optimal culture conditions for this fungus to undergo CAT fusion between microconidia in liquid medium. Extensive high resolution, confocal live-cell imaging was performed to characterise the different stages of CAT fusion, using genetically encoded fluorescent labelling and vital fluorescent organelle stains. CAT homing and fusion were found to be dependent on adhesion to the surface, in contrast to germ tube development which occurs in the absence of adhesion. Staining with fluorescently labelled concanavalin A indicated that the cell wall composition of CATs differs from that of microconidia and germ tubes. The movement of nuclei, mitochondria, vacuoles and lipid droplets through fused germlings was observed by live-cell imaging.

Prediction of clamp-derived insulin sensitivity from the oral glucose insulin sensitivity index

AIMS/HYPOTHESIS

The euglycaemic-hyperinsulinaemic clamp is the gold-standard method for measuring insulin sensitivity, but is less suitable for large clinical trials. Thus, several indices have been developed for evaluating insulin sensitivity from the oral glucose tolerance test (OGTT). However, most of them yield values different from those obtained by the clamp method. The aim of this study was to develop a new index to predict clamp-derived insulin sensitivity (M value) from the OGTT-derived oral glucose insulin sensitivity index (OGIS).

METHODS

We analysed datasets of people that underwent both a clamp and an OGTT or meal test, thereby allowing calculation of both the M value and OGIS. The population was divided into a training and a validation cohort (n = 359 and n = 154, respectively). After a stepwise selection approach, the best model for M value prediction was applied to the validation cohort. This cohort was also divided into subgroups according to glucose tolerance, obesity category and age.

RESULTS

The new index, called PREDIcted M (PREDIM), was based on OGIS, BMI, 2 h glucose during OGTT and fasting insulin. Bland-Altman analysis revealed a good relationship between the M value and PREDIM in the validation dataset (only 9 of 154 observations outside limits of agreement). Also, no significant differences were found between the M value and PREDIM (equivalence test: p < 0.0063). Subgroup stratification showed that measured M value and PREDIM have a similar ability to detect intergroup differences (p < 0.02, both M value and PREDIM).

CONCLUSIONS/INTERPRETATION

The new index PREDIM provides excellent prediction of M values from OGTT or meal data, thereby allowing comparison of insulin sensitivity between studies using different tests.

Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis

Phenomics is the comprehensive study of phenotypes at every level of biology: from metabolites to organisms. With high throughput technologies increasing the scope of biological discoveries, the field of phenomics has been developing rapid and precise methods to collect, catalog, and analyze phenotypes. Such methods have allowed phenotypic data to be widely used in medical applications, from assisting clinical diagnoses to prioritizing genomic diagnoses. To channel the benefits of phenomics into the field of inborn errors of metabolism (IEM), we have recently launched IEMbase, an expert-curated knowledgebase of IEM and their disease-characterizing phenotypes. While our efforts with IEMbase have realized benefits, taking full advantage of phenomics requires a comprehensive curation of IEM phenotypes in core phenomics projects, which is dependent upon contributions from the IEM clinical and research community. Here, we assess the inclusion of IEM biochemical phenotypes in a core phenomics project, the Human Phenotype Ontology. We then demonstrate the utility of biochemical phenotypes using a text-based phenomics method to predict gene-disease relationships, showing that the prediction of IEM genes is significantly better using biochemical rather than clinical profiles. The findings herein provide a motivating goal for the IEM community to expand the computationally accessible descriptions of biochemical phenotypes associated with IEM in phenomics resources.

Worldwide assessment of healthcare personnel dealing with lymphoedema

BACKGROUND

Lymphoedema is a pandemic with about 250 million people suffering from this condition worldwide. Lymphatic diseases have considerable public health significance, but yet few professionals are specialised in their management causing a substantial burden on health resources.

AIMS AND OBJECTIVES

This study aims to give an overview of the approximate number of medical professionals, professional societies, institutions and companies dealing with lymphoedema in various countries. Concepts of improvement for current human resources are considered.

METHODS

An online database analysis (Google search engine and PubMed) was carried out for each country of the world. Additionally, relevant congress participant lists as well as member lists of significant medical societies and reports of the World Health Organisation were analysed.

RESULTS

Overall distribution of tertiary level professionals specialised in this field is heterogenous. A decrescent gradient of professionals can be seen between developed and developing countries and between urban and rural areas. Countries in general do not seem to have yet met the current demand for specialists at tertiary level in this field.

CONCLUSIONS

This study intends to draw attention to the current medical coverage gaps due to a low number of lymphoedema specialists at tertiary level. It wishes to start a discussion about structured reimbursement and certification of knowledge and skills that are essential incentives for experts to act as multiplicators and change the lack of care in the mid-term. Current fail prescriptions and evitable disability and sick certificates represent a high financial burden that could be reinvested in a correct management. Policy makers must focus in the two above mentioned essential measures. Medical training and the consequent development of the industry will then naturally take place, as it was the case for other professional groups in the past.

Assembly of Synthetic Functional Cellulosomal Structures onto the Cell Surface of Lactobacillus plantarum, a Potent Member of the Gut Microbiome

Heterologous display of enzymes on microbial cell surfaces is an extremely desirable approach, since it enables the engineered microbe to interact directly with the plant wall extracellular polysaccharide matrix. In recent years, attempts have been made to endow noncellulolytic microbes with genetically engineered cellulolytic capabilities for improved hydrolysis of lignocellulosic biomass and for advanced probiotics. Thus far, however, owing to the hurdles encountered in secreting and assembling large, intricate complexes on the bacterial cell wall, only free cellulases or relatively simple cellulosome assemblies have been introduced into live bacteria. Here, we employed the "adaptor scaffoldin" strategy to compensate for the low levels of protein displayed on the bacterial cell surface. That strategy mimics natural elaborated cellulosome architectures, thus exploiting the exponential features of their Lego-like combinatorics. Using this approach, we produced several bacterial consortia of Lactobacillus plantarum, a potent gut microbe which provides a very robust genetic framework for lignocellulosic degradation. We successfully engineered surface display of large, fully active self-assembling cellulosomal complexes containing an unprecedented number of catalytic subunits all produced in vivo by the cell consortia. Our results demonstrate that the enzyme stability and performance of the cellulosomal machinery, which are superior to those seen with the equivalent secreted free enzyme system, and the high cellulase-to-xylanase ratios proved beneficial for efficient degradation of wheat straw.IMPORTANCE The multiple benefits of lactic acid bacteria are well established in health and industry. Here we present an approach designed to extensively increase the cell surface display of proteins via successive assembly of interactive components. Our findings present a stepping stone toward proficient engineering of Lactobacillus plantarum, a widespread, environmentally important bacterium and potent microbiome member, for improved degradation of lignocellulosic biomass and advanced probiotics.

Asthma and COPD overlap (ACO) is related to a high burden of sleep disturbance and respiratory symptoms: Results from the RHINE and Swedish GA2LEN surveys

Background

The term Asthma and COPD Overlap (ACO) describes a condition where asthma and COPD overlap. We aimed to investigate associations between ACO and insomnia and respiratory symptoms, and to investigate the prevalence of ACO and the characteristics of subjects with ACO in two Northern European population studies.

Methods

The study comprised 25 429 subjects aged ≥ 40 years who participated in one of two Northern European general population surveys. Both surveys included questions on asthma, COPD, respiratory and sleep-related symptoms, including difficulty initiating sleep, difficulty maintaining sleep, early-morning awakening, and excessive daytime sleepiness. ACO was defined as having both self-reported asthma and COPD.

Results

The prevalence of ACO was 1.0%. The group with ACO had a higher prevalence of both insomnia and respiratory symptoms than subjects with only asthma or COPD. Having ACO was independently associated with a 2–3 times higher probability of having sleep-related symptoms as compared with the group without asthma or COPD, after adjustment for age, sex, BMI, smoking history and educational level (adjusted odds ratio 2.14–3.36, 95% CI).

Conclusion

Subjects with ACO have a high prevalence of insomnia and respiratory symptoms. To our knowledge, this is the first study to assess the association between sleep-related symptoms and ACO.

Guns, germs, and trees determine density and distribution of gorillas and chimpanzees in Western Equatorial Africa

We present a range-wide assessment of sympatric western lowland gorillas Gorilla gorilla gorilla and central chimpanzees Pan troglodytes troglodytes using the largest survey data set ever assembled for these taxa: 59 sites in five countries surveyed between 2003 and 2013, totaling 61,000 person-days of fieldwork. We used spatial modeling to investigate major drivers of great ape distribution and population trends. We predicted density across each taxon's geographic range, allowing us to estimate overall abundance: 361,900 gorillas and 128,700 chimpanzees in Western Equatorial Africa-substantially higher than previous estimates. These two subspecies represent close to 99% of all gorillas and one-third of all chimpanzees. Annual population decline of gorillas was estimated at 2.7%, maintaining them as Critically Endangered on the International Union for Conservation of Nature and Natural Resources (IUCN) Red List. We quantified the threats to each taxon, of which the three greatest were poaching, disease, and habitat degradation. Gorillas and chimpanzees are found at higher densities where forest is intact, wildlife laws are enforced, human influence is low, and disease impacts have been low. Strategic use of the results of these analyses could conserve the majority of gorillas and chimpanzees. With around 80% of both subspecies occurring outside protected areas, their conservation requires reinforcement of anti-poaching efforts both inside and outside protected areas (particularly where habitat quality is high and human impact is low), diligent disease control measures (including training, advocacy, and research into Ebola virus disease), and the preservation of high-quality habitat through integrated land-use planning and implementation of best practices by the extractive and agricultural industries.

History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology

Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are well-known acquired immunity systems that are widespread in archaea and bacteria. The RNA-guided nucleases from CRISPR-Cas systems are currently regarded as the most reliable tools for genome editing and engineering. The first hint of their existence came in 1987, when an unusual repetitive DNA sequence, which subsequently was defined as a CRISPR, was discovered in the Escherichia coli genome during an analysis of genes involved in phosphate metabolism. Similar sequence patterns were then reported in a range of other bacteria as well as in halophilic archaea, suggesting an important role for such evolutionarily conserved clusters of repeated sequences. A critical step toward functional characterization of the CRISPR-Cas systems was the recognition of a link between CRISPRs and the associated Cas proteins, which were initially hypothesized to be involved in DNA repair in hyperthermophilic archaea. Comparative genomics, structural biology, and advanced biochemistry could then work hand in hand, not only culminating in the explosion of genome editing tools based on CRISPR-Cas9 and other class II CRISPR-Cas systems but also providing insights into the origin and evolution of this system from mobile genetic elements denoted casposons. To celebrate the 30th anniversary of the discovery of CRISPR, this minireview briefly discusses the fascinating history of CRISPR-Cas systems, from the original observation of an enigmatic sequence in E. coli to genome editing in humans.

The Phosphate Fast-Responsive Genes PECP1 and PPsPase1 Affect Phosphocholine and Phosphoethanolamine Content

Phosphate starvation-mediated induction of the HAD-type phosphatases PPsPase1 (AT1G73010) and PECP1 (AT1G17710) has been reported in Arabidopsis (Arabidopsis thaliana). However, little is known about their in vivo function or impact on plant responses to nutrient deficiency. The preferences of PPsPase1 and PECP1 for different substrates have been studied in vitro but require confirmation in planta. Here, we examined the in vivo function of both enzymes using a reverse genetics approach. We demonstrated that PPsPase1 and PECP1 affect plant phosphocholine and phosphoethanolamine content, but not the pyrophosphate-related phenotypes. These observations suggest that the enzymes play a similar role in planta related to the recycling of polar heads from membrane lipids that is triggered during phosphate starvation. Altering the expression of the genes encoding these enzymes had no effect on lipid composition, possibly due to compensation by other lipid recycling pathways triggered during phosphate starvation. Furthermore, our results indicated that PPsPase1 and PECP1 do not influence phosphate homeostasis, since the inactivation of these genes had no effect on phosphate content or on the induction of molecular markers related to phosphate starvation. A combination of transcriptomics and imaging analyses revealed that PPsPase1 and PECP1 display a highly dynamic expression pattern that closely mirrors the phosphate status. This temporal dynamism, combined with the wide range of induction levels, broad expression, and lack of a direct effect on Pi content and regulation, makes PPsPase1 and PECP1 useful molecular markers of the phosphate starvation response.

Experimental study of isolas in nonlinear systems featuring modal interactions

The objective of the present paper is to provide experimental evidence of isolated resonances in the frequency response of nonlinear mechanical systems. More specifically, this work explores the presence of isolas, which are periodic solutions detached from the main frequency response, in the case of a nonlinear set-up consisting of two masses sliding on a horizontal guide. A careful experimental investigation of isolas is carried out using responses to swept-sine and stepped-sine excitations. The experimental findings are validated with advanced numerical simulations combining nonlinear modal analysis and bifurcation monitoring. In particular, the interactions between two nonlinear normal modes are shown to be responsible for the creation of the isolas.

Epidemiological and histological findings implicate matrix Gla protein in diastolic left ventricular dysfunction

OBJECTIVES

A novel paradigm of diastolic left ventricular (LV) dysfunction proposes involvement of the cardiac microvasculature. Vitamin K dependent matrix Gla protein (MGP) plays a role in preserving microcirculatory integrity. We hypothesized that LV filling pressure-a measure of diastolic LV dysfunction-increases with higher plasma level of inactive desphospho-uncarboxylated MGP (dp-ucMGP). We also studied the distribution of active and inactive MGP in human myocardium.

METHODS

We measured echocardiographic diastolic LV function and plasma dp-ucMGP (ELISA) in 668 Flemish and for replication in 386 Swiss.

RESULTS

Among Flemish and Swiss, E/e' (6.78 vs. 6.73) and dp-ucMGP (3.94 μg/L vs. 4.20 μg/L) were similarly distributed. In multivariable-adjusted models, for each doubling of dp-ucMGP, E/e' increased by 0.26, 0.33 and 0.31 in Flemish, Swiss and both cohorts combined (P≤0.026); the odds ratios for having E/e' ≥ 8.5 were 1.99, 3.29 and 2.36, respectively (P≤0.017). Cardiac biopsies from patients with ischemic or dilated cardiomyopathy and healthy hearts (n = 4 for each) were stained with conformation-specific MGP antibodies. In diseased compared with normal hearts, uncarboxylated inactive MGP was more prevalent (P≤0.004) in the perivascular matrix and interstitium (204.4 vs. 8.6 μm2 per field) and phosphorylated active MGP in and around capillaries and interstitial cells (31.3 vs. 6.6 number of positive capillaries and cells per field).

CONCLUSIONS

Our study supports a role of activated MGP in maintaining myocardial integrity and diastolic LV performance and can potentially be translated into new strategies for managing diastolic LV dysfunction and preventing its progression to heart failure.

Worldwide Protein Data Bank validation information: usage and trends

Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrendsDB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

Validation of ligands in macromolecular structures determined by X-ray crystallography

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) play a crucial role in structure-guided drug discovery and design, and also provide atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. The quality with which small-molecule ligands have been modelled in Protein Data Bank (PDB) entries has been, and continues to be, a matter of concern for many investigators. Correctly interpreting whether electron density found in a binding site is compatible with the soaked or co-crystallized ligand or represents water or buffer molecules is often far from trivial. The Worldwide PDB validation report (VR) provides a mechanism to highlight any major issues concerning the quality of the data and the model at the time of deposition and annotation, so the depositors can fix issues, resulting in improved data quality. The ligand-validation methods used in the generation of the current VRs are described in detail, including an examination of the metrics to assess both geometry and electron-density fit. It is found that the LLDF score currently used to identify ligand electron-density fit outliers can give misleading results and that better ligand-validation metrics are required.

Tumor-infiltrating immune cells as potential biomarkers predicting response to treatment and survival in patients with metastatic melanoma receiving ipilimumab therapy

Monoclonal antibodies targeting immune checkpoints are gaining ground in the treatment of melanoma and other cancers, and considerable effort is made to identify biomarkers predicting the efficacy of these therapies. Our retrospective study was performed on surgical tissue samples (52 lymph nodes and 34 cutaneous/subcutaneous metastases) from 30 patients with metastatic melanoma treated with ipilimumab. Using a panel of 11 antibodies against different immune cell types, intratumoral immune cell densities were determined and evaluated in relation to response to ipilimumab treatment and disease outcome. For most markers studied, median immune cell densities were at least two times higher in lymph node metastases compared to skin/subcutaneous ones; therefore, the prognostic and predictive associations of immune cell infiltration were evaluated separately in the two groups of metastases as well as in all samples as a whole. Higher prevalence of several immune cell types was seen in lymph node metastases of the responders compared to non-responders, particularly FOXP3+ cells and CD8+ T lymphocytes. In subcutaneous or cutaneous metastases, on the other hand, significant difference could be observed only in the case of CD16 and CD68. Associations of labeled cell densities with survival were also found for most cell types studied in nodal metastases, and for CD16+ and CD68+ cells in skin/s.c. metastatic cases. Our results corroborate the previous findings suggesting an association between an immunologically active tumor microenvironment and response to ipilimumab treatment, and propose new potential biomarkers for predicting treatment efficacy and disease outcome.

Incorporating threat in hotspots and coldspots of biodiversity and ecosystem services

Spatial prioritization could help target conservation actions directed to maintain both biodiversity and ecosystem services. We delineate hotspots and coldspots of two biodiversity conservation features and five regulating and cultural services by incorporating an indicator of 'threat', i.e. timber harvest profitability for forest areas in Telemark (Norway). We found hotspots, where high values of biodiversity, ecosystem services and threat coincide, ranging from 0.1 to 7.1% of the area, depending on varying threshold levels. Targeting of these areas for conservation follows reactive conservation approaches. In coldspots, high biodiversity and ecosystem service values coincide with low levels of threat, and cover 0.1-3.4% of the forest area. These areas might serve proactive conservation approaches at lower opportunity cost (foregone timber harvest profits). We conclude that a combination of indicators of biodiversity, ecosystem services and potential threat is an appropriate approach for spatial prioritization of proactive and reactive conservation strategies.

Sequence-based prediction of permissive stretches for internal protein tagging and knockdown

BACKGROUND

Internal tagging of proteins by inserting small functional peptides into surface accessible permissive sites has proven to be an indispensable tool for basic and applied science. Permissive sites are typically identified by transposon mutagenesis on a case-by-case basis, limiting scalability and their exploitation as a system-wide protein engineering tool.

METHODS

We developed an apporach for predicting permissive stretches (PSs) in proteins based on the identification of length-variable regions (regions containing indels) in homologous proteins.

RESULTS

We verify that a protein's primary structure information alone is sufficient to identify PSs. Identified PSs are predicted to be predominantly surface accessible; hence, the position of inserted peptides is likely suitable for diverse applications. We demonstrate the viability of this approach by inserting a Tobacco etch virus protease recognition site (TEV-tag) into several PSs in a wide range of proteins, from small monomeric enzymes (adenylate kinase) to large multi-subunit molecular machines (ATP synthase) and verify their functionality after insertion. We apply this method to engineer conditional protein knockdowns directly in the Escherichia coli chromosome and generate a cell-free platform with enhanced nucleotide stability.

CONCLUSIONS

Functional internally tagged proteins can be rationally designed and directly chromosomally implemented. Critical for the successful design of protein knockdowns was the incorporation of surface accessibility and secondary structure predictions, as well as the design of an improved TEV-tag that enables efficient hydrolysis when inserted into the middle of a protein. This versatile and portable approach can likely be adapted for other applications, and broadly adopted. We provide guidelines for the design of internally tagged proteins in order to empower scientists with little or no protein engineering expertise to internally tag their target proteins.

White Matter Microstructure of the Human Mirror Neuron System is Related to Symptom Severity in Adults with Autism

Mirror neuron system (MNS) dysfunctions might underlie deficits in autism spectrum disorders (ASD). Diffusion tensor imaging based probabilistic tractography was conducted in 15 adult ASD patients and 13 matched, healthy controls. Fractional anisotropy (FA) was quantified to assess group differences in tract-related white matter microstructure of both the classical MNS route (mediating "emulation") and the alternative temporo-frontal route (mediating "mimicry"). Multiple linear regression was used to investigate structure-function relationships between MNS connections and ASD symptom severity. There were no significant group differences in tract-related FA indicating an intact classical MNS in ASD. Direct temporo-frontal connections could not be reconstructed challengeing the concept of multiple routes for imitation. Tract-related FA of right-hemispheric parieto-frontal connections was negatively related to autism symptom severity.

How will climate change pathways and mitigation options alter incidence of vector-borne diseases? A framework for leishmaniasis in South and Meso-America

The enormous global burden of vector-borne diseases disproportionately affects poor people in tropical, developing countries. Changes in vector-borne disease impacts are often linked to human modification of ecosystems as well as climate change. For tropical ecosystems, the health impacts of future environmental and developmental policy depend on how vector-borne disease risks trade off against other ecosystem services across heterogeneous landscapes. By linking future socio-economic and climate change pathways to dynamic land use models, this study is amongst the first to analyse and project impacts of both land use and climate change on continental-scale patterns in vector-borne diseases. Models were developed for cutaneous and visceral leishmaniasis in the Americas-ecologically complex sand fly borne infections linked to tropical forests and diverse wild and domestic mammal hosts. Both diseases were hypothesised to increase with available interface habitat between forest and agricultural or domestic habitats and with mammal biodiversity. However, landscape edge metrics were not important as predictors of leishmaniasis. Models including mammal richness were similar in accuracy and predicted disease extent to models containing only climate and land use predictors. Overall, climatic factors explained 80% and land use factors only 20% of the variance in past disease patterns. Both diseases, but especially cutaneous leishmaniasis, were associated with low seasonality in temperature and precipitation. Since such seasonality increases under future climate change, particularly under strong climate forcing, both diseases were predicted to contract in geographical extent to 2050, with cutaneous leishmaniasis contracting by between 35% and 50%. Whilst visceral leishmaniasis contracted slightly more under strong than weak management for carbon, biodiversity and ecosystem services, future cutaneous leishmaniasis extent was relatively insensitive to future alternative socio-economic pathways. Models parameterised at narrower geographical scales may be more sensitive to land use pattern and project more substantial changes in disease extent under future alternative socio-economic pathways.

Documenting and explaining the HIV decline in east Zimbabwe: the Manicaland General Population Cohort

PURPOSE

The Manicaland cohort was established to provide robust scientific data on HIV prevalence and incidence, patterns of sexual risk behaviour and the demographic impact of HIV in a sub-Saharan African population subject to a generalised HIV epidemic. The aims were later broadened to include provision of data on the coverage and effectiveness of national HIV control programmes including antiretroviral therapy (ART).

PARTICIPANTS

General population open cohort located in 12 sites in Manicaland, east Zimbabwe, representing 4 major socioeconomic strata (small towns, agricultural estates, roadside settlements and subsistence farming areas). 9,109 of 11,453 (79.5%) eligible adults (men 17-54 years; women 15-44 years) were recruited in a phased household census between July 1998 and January 2000. Five rounds of follow-up of the prospective household census and the open cohort were conducted at 2-year or 3-year intervals between July 2001 and November 2013. Follow-up rates among surviving residents ranged between 77.0% (over 3 years) and 96.4% (2 years).

FINDINGS TO DATE

HIV prevalence was 25.1% at baseline and had a substantial demographic impact with 10-fold higher mortality in HIV-infected adults than in uninfected adults and a reduction in the growth rate in the worst affected areas (towns) from 2.9% to 1.0%pa. HIV infection rates have been highest in young adults with earlier commencement of sexual activity and in those with older sexual partners and larger numbers of lifetime partners. HIV prevalence has since fallen to 15.8% and HIV incidence has also declined from 2.1% (1998-2003) to 0.63% (2009-2013) largely due to reduced sexual risk behaviour. HIV-associated mortality fell substantially after 2009 with increased availability of ART.

FUTURE PLANS

We plan to extend the cohort to measure the effects on the epidemic of current and future HIV prevention and treatment programmes. Proposals for access to these data and for collaboration are welcome.

A combination of plasma phospholipid fatty acids and its association with incidence of type 2 diabetes: The EPIC-InterAct case-cohort study

BACKGROUND

Combinations of multiple fatty acids may influence cardiometabolic risk more than single fatty acids. The association of a combination of fatty acids with incident type 2 diabetes (T2D) has not been evaluated.

METHODS AND FINDINGS

We measured plasma phospholipid fatty acids by gas chromatography in 27,296 adults, including 12,132 incident cases of T2D, over the follow-up period between baseline (1991-1998) and 31 December 2007 in 8 European countries in EPIC-InterAct, a nested case-cohort study. The first principal component derived by principal component analysis of 27 individual fatty acids (mole percentage) was the main exposure (subsequently called the fatty acid pattern score [FA-pattern score]). The FA-pattern score was partly characterised by high concentrations of linoleic acid, stearic acid, odd-chain fatty acids, and very-long-chain saturated fatty acids and low concentrations of γ-linolenic acid, palmitic acid, and long-chain monounsaturated fatty acids, and it explained 16.1% of the overall variability of the 27 fatty acids. Based on country-specific Prentice-weighted Cox regression and random-effects meta-analysis, the FA-pattern score was associated with lower incident T2D. Comparing the top to the bottom fifth of the score, the hazard ratio of incident T2D was 0.23 (95% CI 0.19-0.29) adjusted for potential confounders and 0.37 (95% CI 0.27-0.50) further adjusted for metabolic risk factors. The association changed little after adjustment for individual fatty acids or fatty acid subclasses. In cross-sectional analyses relating the FA-pattern score to metabolic, genetic, and dietary factors, the FA-pattern score was inversely associated with adiposity, triglycerides, liver enzymes, C-reactive protein, a genetic score representing insulin resistance, and dietary intakes of soft drinks and alcohol and was positively associated with high-density-lipoprotein cholesterol and intakes of polyunsaturated fat, dietary fibre, and coffee (p < 0.05 each). Limitations include potential measurement error in the fatty acids and other model covariates and possible residual confounding.

CONCLUSIONS

A combination of individual fatty acids, characterised by high concentrations of linoleic acid, odd-chain fatty acids, and very long-chain fatty acids, was associated with lower incidence of T2D. The specific fatty acid pattern may be influenced by metabolic, genetic, and dietary factors.

The 'experimental public' in longitudinal health research: views of local leaders and service providers in rural South Africa

BACKGROUND

The concept of 'experimental public' has been recently applied to publics involved in clinical trials. This term could also be applied to publics involved in longitudinal research such as health and demographic surveillance systems. The ethics of practice and public engagement with these experimental publics are of key importance and include issues of informed consent, confidentiality, collection of body tissue samples and fair local benefit.

METHODS

Individual (n = 11) and focus group (n = 5) qualitative semi-structured interviews were conducted with 56 local leaders and service providers regarding their views about research activities in a longitudinal health research study site run by the MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt) in rural South Africa. Deductive and inductive thematic analysis was undertaken using NVivo software to identify the emergent themes.

RESULTS

There was an understanding of the usefulness of collecting demographic data, but reasons for gathering other contextual data such as on food security, as well as the reasons for collection of blood was less clear. While appreciation was expressed for feedback of individual results such as blood pressure levels during home-based data collection, there were requests for more results from biomarkers, and for these to be given at home, rather than at the clinic. There were reports of indirect refusals, and offers by leaders to assist in reducing refusal rates. There were concerns about confidentiality, especially in the publication of results. Some leaders would have liked to receive more individual level data for planning of services, although they understood this would breach confidentiality. Service providers were concerned about the withdrawal of some services post intervention trials.

CONCLUSIONS

This experimental public has, over time, developed a nuanced understanding of the reasons for research and the procedures undertaken. Discussions concerning fair benefit ranged from requests for more individual clinically-relevant results for participants, to understanding how research results could assist in planning of public health services at local and national levels. The concerns illustrate the complexity of the ethics of practice which has implications for policy, practice and governance for those working in longitudinal health research sites globally.

A phase transition caught in mid-course: independent and concomitant analyses of the monoclinic and triclinic structures of (nBu4N)[Co(orotate)2(bipy)]·3H2O

The preparation and characterization of the nBu4N+ salts of two bis-orotate(2-) complexes of cobalt, namely bis(tetra-n-butylammonium) diaquabis(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-ide-6-carboxylato-κ2N1,O6)cobalt(II) 1.8-hydrate, (C16H36N)2[Co(C5H2N2O4)2(H2O)2]·1.8H2O, (1), and tetra-n-butylammonium (2,2'-bipyridine-κ2N,N')bis(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-ide-6-carboxylato-κ2N1,O6)cobalt(III) trihydrate, (C16H36N)[Co(C5H2N2O4)2(C10H8N2)]·3H2O, (2), are reported. The CoIII complex, (2), which is monoclinic at room temperature, presents a conservative single-crystal-to-single-crystal phase transition below 200 K, producing a triclinic twin. The transition, which involves a conformational change in one of the nBu groups of the cation, is reversible and can be cycled. Both end phases have been characterized structurally and the system was also characterized structurally in a two-phase intermediate state, using single-crystal diffraction techniques, with both the monoclinic and triclinic phases present. Thermal analysis allows a rough estimate of the small energy content, viz. 0.25 kJ mol-1, for both the monoclinic-to-triclinic transformation and the reverse transition, in agreement with the nature of the structural changes involving only the nBu4N+ cation.

The intensive care delirium research agenda: a multinational, interprofessional perspective

Delirium, a prevalent organ dysfunction in critically ill patients, is independently associated with increased morbidity. This last decade has witnessed an exponential growth in delirium research in hospitalized patients, including those critically ill, and this research has highlighted that delirium needs to be better understood mechanistically to help foster research that will ultimately lead to its prevention and treatment. In this invited, evidence-based paper, a multinational and interprofessional group of clinicians and researchers from within the fields of critical care medicine, psychiatry, pediatrics, anesthesiology, geriatrics, surgery, neurology, nursing, pharmacy, and the neurosciences sought to address five questions: (1) What is the current standard of care in managing ICU delirium? (2) What have been the major recent advances in delirium research and care? (3) What are the common delirium beliefs that have been challenged by recent trials? (4) What are the remaining areas of uncertainty in delirium research? (5) What are some of the top study areas/trials to be done in the next 10 years? Herein, we briefly review the epidemiology of delirium, the current best practices for management of critically ill patients at risk for delirium or experiencing delirium, identify recent advances in our understanding of delirium as well as gaps in knowledge, and discuss research opportunities and barriers to implementation, with the goal of promoting an integrated research agenda.

The association between car accident fatalities and children's fears: A study in seven EU countries

Children's fear of a car accident occurring to parents or themselves has been used as a concrete example to illustrate one of the symptoms of anxiety disorders such as separation anxiety and generalized anxiety. However, its usage across countries may be questionable where the prevalence of this specific type of injury differs. This cross-sectional study compares samples from seven diverse European countries (Bulgaria, Germany, Italy, Lithuania, Netherlands, Romania, Turkey) to see if an environmental exposure, car accident death rate per 100,000 people (country-wide from WHO data), is associated with children's self-report of car accident fears. In this study, 6-11 year-old children were surveyed by a diagnostic instrument (Dominic Interactive) about several situations and asked if they believed they were similar to a fictional child depicted in said situations. Mothers were surveyed for additional sociodemographic information. Multivariable logistic regression was used to adjust for covariates including mother's age, mother's education, single parenting, and mother's professional inactivity. We report a monotonic relationship between higher car accident death rates and the prevalence of children reporting fear of parent's or own accident. Relative to a reference of 3.9 deaths per 100,000 people, children's odds of reporting fear of parent's accident ranged from 1.99 (95% CI 1.51-2.61) times to 4.84 (95% CI 3.68-6.37) times as the risk of death by car accident increased across countries. A similar result arose from fear of child's own accident, with significant ORs ranging from 1.91 (95% CI 1.53-2.40) to 2.68 (95% CI 2.07-3.47) alongside increased death rates. Given that reporting of these fears accompanies correspondingly high accident death rates, the pertinence of using fear of car accidents as an illustration for some diagnostic item for mental disorders cross-nationally appears to be an issue.

A molecular quantum spin network controlled by a single qubit

Scalable quantum technologies require an unprecedented combination of precision and complexity for designing stable structures of well-controllable quantum systems on the nanoscale. It is a challenging task to find a suitable elementary building block, of which a quantum network can be comprised in a scalable way. We present the working principle of such a basic unit, engineered using molecular chemistry, whose collective control and readout are executed using a nitrogen vacancy (NV) center in diamond. The basic unit we investigate is a synthetic polyproline with electron spins localized on attached molecular side groups separated by a few nanometers. We demonstrate the collective readout and coherent manipulation of very few (≤ 6) of these S = 1/2 electronic spin systems and access their direct dipolar coupling tensor. Our results show that it is feasible to use spin-labeled peptides as a resource for a molecular qubit-based network, while at the same time providing simple optical readout of single quantum states through NV magnetometry. This work lays the foundation for building arbitrary quantum networks using well-established chemistry methods, which has many applications ranging from mapping distances in single molecules to quantum information processing.

Neighbourhood immigrant concentration effects on migrant and native youth's educational commitments, an enquiry into personality differences

In the literature examining neighbourhood effects on educational outcomes, the socialisation mechanism is usually investigated by looking at the association between neighbourhood characteristics and educational attainment. The step in between, that adolescents actually internalise educational norms held by residents, is often assumed. We attempt to fill this gap by looking at how the internalisation of educational norms (commitments) is influenced by neighbourhoods' immigrant concentration. We investigate this process for both migrant and native youth, as both groups might be influenced differently by immigrant concentrations. To test our hypothesis we used longitudinal panel data with five waves (N = 4255), combined with between-within models which control for a large portion of potential selection bias. These models have an advantage over naïve OLS models in that they predict the effect of change in neighbourhood characteristics on change in educational commitment, and therefore offer a more dynamic approach to modelling neighbourhood effects. Our results show that living in neighbourhoods with higher proportions of immigrants increases the educational commitments of migrant youth compared to living in neighbourhoods with lower proportions. Besides, we find that adolescents with a resilient personality experience less influence of the neighbourhood context on educational commitments than do adolescents with non-resilient personalities.

TRACMIT: An effective pipeline for tracking and analyzing cells on micropatterns through mitosis

The use of micropatterns has transformed investigations of dynamic biological processes by enabling the reproducible analysis of live cells using time-lapse fluorescence microscopy. With micropatterns, thousands of individual cells can be efficiently imaged in parallel, rendering the approach well suited for screening projects. Despite being powerful, such screens remain challenging in terms of data handling and analysis. Typically, only a fraction of micropatterns is occupied in a manner suitable to monitor a given phenotypic output. Moreover, the presence of dying or otherwise compromised cells complicates the analysis. Therefore, focusing strictly on relevant cells in such large time-lapse microscopy dataset poses interesting analysis challenges that are not readily met by existing software packages. This motivated us to develop an image analysis pipeline that handles all necessary image processing steps within one open-source platform to detect and analyze individual cells seeded on micropatterns through mitosis. We introduce a comprehensive image analysis pipeline running on Fiji termed TRACMIT (pipeline for TRACking and analyzing cells on micropatterns through MITosis). TRACMIT was developed to rapidly and accurately assess the orientation of the mitotic spindle during metaphase in time-lapse fluorescence microscopy of human cells expressing mCherry::histone 2B and plated on L-shaped micropatterns. This solution enables one to perform the entire analysis from the raw data, avoiding the need to save intermediate images, thereby decreasing data volume and thus reducing the data that needs to be processed. We first select micropatterns containing a single cell and then identify anaphase figures in the time-lapse recording. Next, TRACMIT tracks back in time until metaphase, when the angle of the mitotic spindle with respect to the micropattern is assessed. We designed the pipeline to allow for manual validation of selected cells with a simple user interface, and to enable analysis of cells plated on micropatterns of different shapes. For ease of use, the entire pipeline is provided as a series of Fiji/ImageJ macros, grouped into an ActionBar. In conclusion, the open source TRACMIT pipeline enables high-throughput analysis of single mitotic cells on micropatterns, thus accurately and efficiently allowing automatic determination of spindle positioning from time-lapse recordings.

Effects of the EQUIP quasi-experimental study testing a collaborative quality improvement approach for maternal and newborn health care in Tanzania and Uganda

BACKGROUND

Quality improvement is a recommended strategy to improve implementation levels for evidence-based essential interventions, but experience of and evidence for its effects in low-resource settings are limited. We hypothesised that a systemic and collaborative quality improvement approach covering district, facility and community levels, supported by report cards generated through continuous household and health facility surveys, could improve the implementation levels and have a measurable population-level impact on coverage and quality of essential services.

METHODS

Collaborative quality improvement teams tested self-identified strategies (change ideas) to support the implementation of essential maternal and newborn interventions recommended by the World Health Organization. In Tanzania and Uganda, we used a plausibility design to compare the changes over time in one intervention district with those in a comparison district in each country. Evaluation included indicators of process, coverage and implementation practice analysed with a difference-of-differences and a time-series approach, using data from independent continuous household and health facility surveys from 2011 to 2014. Primary outcomes for both countries were birth in health facilities, breastfeeding within 1 h after birth, oxytocin administration after birth and knowledge of danger signs for mothers and babies. Interpretation of the results considered contextual factors.

RESULTS

The intervention was associated with improvements on one of four primary outcomes. We observed a 26-percentage-point increase (95% CI 25-28%) in the proportion of live births where mothers received uterotonics within 1 min after birth in the intervention compared to the comparison district in Tanzania and an 8-percentage-point increase (95% CI 6-9%) in Uganda. The other primary indicators showed no evidence of improvement. In Tanzania, we saw positive changes for two other outcomes reflecting locally identified improvement topics. The intervention was associated with an increase in preparation of clean birth kits for home deliveries (31 percentage points, 95% CI 2-60%) and an increase in health facility supervision by district staff (14 percentage points, 95% CI 0-28%).

CONCLUSIONS

The systemic quality improvement approach was associated with improvements of only one of four primary outcomes, as well as two Tanzania-specific secondary outcomes. Reasons for the lack of effects included limited implementation strength as well a relatively short follow-up period in combination with a 1-year recall period for population-based estimates and a limited power of the study to detect changes smaller than 10 percentage points.

TRIAL REGISTRATION

Pan African Clinical Trials Registry: PACTR201311000681314.

Multi-scale ancient DNA analyses confirm the western origin of Michelsberg farmers and document probable practices of human sacrifice

In Europe, the Middle Neolithic is characterized by an important diversification of cultures. In northeastern France, the appearance of the Michelsberg culture has been correlated with major cultural changes and interpreted as the result of the settlement of new groups originating from the Paris Basin. This cultural transition has been accompanied by the expansion of particular funerary practices involving inhumations within circular pits and individuals in “non-conventional” positions (deposited in the pits without any particular treatment). If the status of such individuals has been highly debated, the sacrifice hypothesis has been retained for the site of Gougenheim (Alsace). At the regional level, the analysis of the Gougenheim mitochondrial gene pool (SNPs and HVR-I sequence analyses) permitted us to highlight a major genetic break associated with the emergence of the Michelsberg in the region. This genetic discontinuity appeared to be linked to new affinities with farmers from the Paris Basin, correlated to a noticeable hunter-gatherer legacy. All of the evidence gathered supports (i) the occidental origin of the Michelsberg groups and (ii) the potential implication of this migration in the progression of the hunter-gatherer legacy from the Paris Basin to Alsace / Western Germany at the beginning of the Late Neolithic. At the local level, we noted some differences in the maternal gene pool of individuals in "conventional" vs. "non-conventional" positions. The relative genetic isolation of these sub-groups nicely echoes both their social distinction and the hypothesis of sacrifices retained for the site. Our investigation demonstrates that a multi-scale aDNA study of ancient communities offers a unique opportunity to disentangle the complex relationships between cultural and biological evolution.

Diversity of inland valleys and opportunities for agricultural development in Sierra Leone

Inland valleys are becoming increasingly important agricultural production areas for rural households in sub-Saharan Africa due to their relative high and secure water availability and soil fertility. In addition, inland valleys are important as water buffer and biodiversity hot spots and they provide local communities with forest, forage, and fishing resources. As different inland-valley ecosystem functions may conflict with agricultural objectives, indiscriminate development should be avoided. This study aims to analyze the diversity of inland valleys in Sierra Leone and to develop guidelines for more precise interventions. Land use, biophysical and socio-economic data were analyzed on 257 inland valleys using spatial and multivariate techniques. Five cluster groups of inland valleys were identified: (i) semi-permanently flooded with high soil organic carbon (4.2%) and moderate available phosphorus (10.2 ppm), mostly under natural vegetation; (ii) semi-permanently flooded with low soil organic carbon (1.5%) and very low available phosphorus (3.1 ppm), abandoned by farmers; (iii) seasonally flooded with moderate soil organic carbon (3.1%) and low available phosphorus (8.3 ppm), used for rainfed rice and off-season vegetables produced without fertilizer application for household consumption and market; (iv) well drained with moderate soil organic carbon (3.8%) and moderate available phosphorus (10.0 ppm), used for rainfed rice and off-season vegetables produced with fertilizer application for household consumption and market; and (v) well drained with moderate soil organic carbon (3.6%) and moderate available phosphorus (11 ppm), used for household consumption without fertilizer application. Soil organic carbon, available phosphorus, hydrological regime, physical accessibility and market opportunity were the major factors affecting agricultural intensification of inland valleys. Opening up the areas in which inland valleys occur through improved roads and markets, and better water control through drainage infrastructures along with an integrated nutrient management would promote the sustainable agricultural use of inland valleys.

When do traumatic experiences alter risk-taking behavior? A machine learning analysis of reports from refugees

Exposure to traumatic stressors and subsequent trauma-related mental changes may alter a person's risk-taking behavior. It is unclear whether this relationship depends on the specific types of traumatic experiences. Moreover, the association has never been tested in displaced individuals with substantial levels of traumatic experiences. The present study assessed risk-taking behavior in 56 displaced individuals by means of the balloon analogue risk task (BART). Exposure to traumatic events, symptoms of posttraumatic stress disorder and depression were assessed by means of semi-structured interviews. Using a novel statistical approach (stochastic gradient boosting machines), we analyzed predictors of risk-taking behavior. Exposure to organized violence was associated with less risk-taking, as indicated by fewer adjusted pumps in the BART, as was the reported experience of physical abuse and neglect, emotional abuse, and peer violence in childhood. However, civil traumatic stressors, as well as other events during childhood were associated with lower risk taking. This suggests that the association between global risk-taking behavior and exposure to traumatic stress depends on the particular type of the stressors that have been experienced.

Investigation of DNA repair-related SNPs underlying susceptibility to papillary thyroid carcinoma reveals MGMT as a novel candidate gene in Belarusian children exposed to radiation

BACKGROUND

Genetic factors may influence an individual's sensitivity to ionising radiation and therefore modify his/her risk of developing papillary thyroid carcinoma (PTC). Previously, we reported that common single nucleotide polymorphisms (SNPs) within the DNA damage recognition gene ATM contribute to PTC risk in Belarusian children exposed to fallout from the Chernobyl power plant accident. Here we explored in the same population the contribution of a panel of DNA repair-related SNPs in genes acting downstream of ATM.

METHODS

The association of 141 SNPs located in 43 DNA repair genes was examined in 75 PTC cases and 254 controls from the Gomel region in Belarus. All subjects were younger than 15 years at the time of the Chernobyl accident. Conditional logistic regressions accounting for radiation dose were performed with PLINK using the additive allelic inheritance model, and a linkage disequilibrium (LD)-based Bonferroni correction was used for correction for multiple testing.

RESULTS

The intronic SNP rs2296675 in MGMT was associated with an increased PTC risk [per minor allele odds ratio (OR) 2.54 95% CI 1.50, 4.30, P per allele = 0.0006, P corr.= 0.05], and gene-wide association testing highlighted a possible role for ERCC5 (P Gene = 0.01) and PCNA (P Gene = 0.05) in addition to MGMT (P Gene = 0.008).

CONCLUSIONS

These findings indicate that several genes acting in distinct DNA repair mechanisms contribute to PTC risk. Further investigation is needed to decipher the functional properties of the methyltransferase encoded by MGMT and to understand how alteration of such functions may lead to the development of the most common type of thyroid cancer.

Rapid forest clearing in a Myanmar proposed national park threatens two newly discovered species of geckos (Gekkonidae: Cyrtodactylus)

Myanmar’s recent transition from military rule towards a more democratic government has largely ended decades of political and economic isolation. Although Myanmar remains heavily forested, increased development in recent years has been accompanied by exceptionally high rates of forest loss. In this study, we document the rapid progression of deforestation in and around the proposed Lenya National Park, which includes some of the largest remaining areas of lowland evergreen rainforest in mainland Southeast Asia. The globally unique forests in this area are rich in biodiversity and remain a critical stronghold for many threatened and endangered species, including large charismatic fauna such as tiger and Asian elephant. We also conducted a rapid assessment survey of the herpetofauna of the proposed national park, which resulted in the discovery of two new species of bent-toed geckos, genus Cyrtodactylus. We describe these new species, C. lenyasp. nov. and C. payarhtanensissp. nov., which were found in association with karst (i.e., limestone) rock formations within mature lowland wet evergreen forest. The two species were discovered less than 35 km apart and are each known from only a single locality. Because of the isolated nature of the karst formations in the proposed Lenya National Park, these geckos likely have geographical ranges restricted to the proposed protected area and are threatened by approaching deforestation. Although lowland evergreen rainforest has vanished from most of continental Southeast Asia, Myanmar can still take decisive action to preserve one of the most biodiverse places on Earth.

The mouse genome displays highly dynamic populations of KRAB-zinc finger protein genes and related genetic units

KRAB-containing poly-zinc finger proteins (KZFPs) constitute the largest family of transcription factors encoded by mammalian genomes, and growing evidence indicates that they fulfill functions critical to both embryonic development and maintenance of adult homeostasis. KZFP genes underwent broad and independent waves of expansion in many higher vertebrates lineages, yet comprehensive studies of members harbored by a given species are scarce. Here we present a thorough analysis of KZFP genes and related units in the murine genome. We first identified about twice as many elements than previously annotated as either KZFP genes or pseudogenes, notably by assigning to this family an entity formerly considered as a large group of Satellite repeats. We then could delineate an organization in clusters distributed throughout the genome, with signs of recombination, translocation, duplication and seeding of new sites by retrotransposition of KZFP genes and related genetic units (KZFP/rGUs). Moreover, we harvested evidence indicating that closely related paralogs had evolved through both drifting and shifting of sequences encoding for zinc finger arrays. Finally, we could demonstrate that the KAP1-SETDB1 repressor complex tames the expression of KZFP/rGUs within clusters, yet that the primary targets of this regulation are not the KZFP/rGUs themselves but enhancers contained in neighboring endogenous retroelements and that, underneath, KZFPs conserve highly individualized patterns of expression.

Investigation of bacterial communities within the digestive organs of the hydrothermal vent shrimp Rimicaris exoculata provide insights into holobiont geographic clustering

Prokaryotic communities forming symbiotic relationships with the vent shrimp, Rimicaris exoculata, are well studied components of hydrothermal ecosystems at the Mid-Atlantic Ridge (MAR). Despite the tight link between host and symbiont, the observed lack of spatial genetic structure seen in R. exoculata contrasts with the geographic differentiation detected in specific bacterial ectosymbionts. The geographic clustering of bacterial lineages within a seemingly panmictic host suggests either the presence of finer scale restriction to gene flow not yet detected in the host, horizontal transmission (environmental selection) of its endosymbionts as a consequence of unique vent geochemistry, or vertically transmitted endosymbionts that exhibit genetic differentiation. To identify which hypothesis best fits, we tested whether bacterial assemblages exhibit differentiation across sites or host populations by performing a 16S rRNA metabarcoding survey on R. exoculata digestive prokaryote samples (n = 31) taken from three geochemically distinct vents across MAR: Rainbow, Trans-Atlantic Geotraverse (TAG) and Logatchev. Analysis of communities across two organs (digestive tract, stomach), three molt colors (white, red, black) and three life stages (eggs, juveniles, adults) also provided insights into symbiont transmission mode. Examining both whole communities and operational taxonomic units (OTUs) confirmed the presence of three main epibionts: Epsilonproteobacteria, Mollicutes and Deferribacteres. With these findings, we identified a clear pattern of geographic segregation by vent in OTUs assigned to Epsilonproteobacteria. Additionally, we detected evidence for differentiation among all communities associated to vents and life stages. Overall, results suggest a combination of environmental selection and vertical inheritance of some of the symbiotic lineages.

APP, PSEN1, and PSEN2 mutations in early-onset Alzheimer disease: A genetic screening study of familial and sporadic cases

BACKGROUND

Amyloid protein precursor (APP), presenilin-1 (PSEN1), and presenilin-2 (PSEN2) mutations cause autosomal dominant forms of early-onset Alzheimer disease (AD-EOAD). Although these genes were identified in the 1990s, variant classification remains a challenge, highlighting the need to colligate mutations from large series.

METHODS AND FINDINGS

We report here a novel update (2012-2016) of the genetic screening of the large AD-EOAD series ascertained across 28 French hospitals from 1993 onwards, bringing the total number of families with identified mutations to n = 170. Families were included when at least two first-degree relatives suffered from early-onset Alzheimer disease (EOAD) with an age of onset (AOO) ≤65 y in two generations. Furthermore, we also screened 129 sporadic cases of Alzheimer disease with an AOO below age 51 (44% males, mean AOO = 45 ± 2 y). APP, PSEN1, or PSEN2 mutations were identified in 53 novel AD-EOAD families. Of the 129 sporadic cases screened, 17 carried a PSEN1 mutation and 1 carried an APP duplication (13%). Parental DNA was available for 10 sporadic mutation carriers, allowing us to show that the mutation had occurred de novo in each case. Thirteen mutations (12 in PSEN1 and 1 in PSEN2) identified either in familial or in sporadic cases were previously unreported. Of the 53 mutation carriers with available cerebrospinal fluid (CSF) biomarkers, 46 (87%) had all three CSF biomarkers-total tau protein (Tau), phospho-tau protein (P-Tau), and amyloid β (Aβ)42-in abnormal ranges. No mutation carrier had the three biomarkers in normal ranges. One limitation of this study is the absence of functional assessment of the possibly and probably pathogenic variants, which should help their classification.

CONCLUSIONS

Our findings suggest that a nonnegligible fraction of PSEN1 mutations occurs de novo, which is of high importance for genetic counseling, as PSEN1 mutational screening is currently performed in familial cases only. Among the 90 distinct mutations found in the whole sample of families and isolated cases, definite pathogenicity is currently established for only 77%, emphasizing the need to pursue the effort to classify variants.

Delivery of iron-fortified yoghurt, through a dairy value chain program, increases hemoglobin concentration among children 24 to 59 months old in Northern Senegal: A cluster-randomized control trial

Background

Innovative strategies are needed to enhance the nutritional impact of agriculture. Value chain approaches, which use supply chains to add value (usually economic) to products as they move from producers to consumers, can be used to increase access to nutritious foods and improve nutritional status. This study tested whether a dairy value chain could be used to distribute a micronutrient-fortified yoghurt (MNFY) (conditional upon the producer supplying a minimum amount of cow milk/day) to improve hemoglobin and reduce anemia among preschool children in a remote area in Northern Senegal.

Methods

A cluster randomized control trial was used to compare 204 children (24 to 59 months of age at baseline) from households who received the MNFY coupled to a behavior change communication (BCC) campaign focusing on anemia prevention to 245 children from a control group (receiving BCC only) after one year. Randomization was done at the level of the family concession (households from the same family) (n = 321). Eligible households had a child of the target age and were willing to deliver milk to the dairy factory. Changes in anemia and hemoglobin between groups were assessed using mixed regression models.

Key findings

Anemia prevalence was very high at baseline (80%) and dropped to close to 60% at endline, with no differences between intervention groups. Hemoglobin increased by 0.55 g/dL, 95%CI (0.27; 0.84) more in the intervention compared to the control group after one year, in models that controlled for potentially confounding factors. The impact was greater (0.72 g/dL, 95%CI (0.34; 1.12)) for boys, compared to girls (0.38 g/dL, 95%CI (-0.03; 0.80)).

Conclusion

The dairy value chain was a successful strategy to distribute MNFY among pastoralists in Northern Senegal, and increase Hb concentrations among their children. This study is one of the first proofs of concept showing that a nutrition-sensitive agriculture value chain approach can contribute to improved child nutrition in a remote pastoralist population.

Trial registration

ClinicalTrials.gov NCT02079961

B1-insensitive T2 mapping of healthy thigh muscles using a T2-prepared 3D TSE sequence

Purpose

To propose a T2-prepared 3D turbo spin echo (T2prep 3D TSE) sequence for B1-insensitive skeletal muscle T2 mapping and compare its performance with 2D and 3D multi-echo spin echo (MESE) for T2 mapping in thigh muscles of healthy subjects.

Methods

The performance of 2D MESE, 3D MESE and the proposed T2prep 3D TSE in the presence of transmit B1 and B0 inhomogeneities was first simulated. The thigh muscles of ten young and healthy subjects were then scanned on a 3 T system and T2 mapping was performed using the three sequences. Transmit B1-maps and proton density fat fraction (PDFF) maps were also acquired. The subjects were scanned three times to assess reproducibility. T2 values were compared among sequences and their sensitivity to B1 inhomogeneities was compared to simulation results. Correlations were also determined between T2 values, PDFF and B1.

Results

The left rectus femoris muscle showed the largest B1 deviations from the nominal value (from 54.2% to 92.9%). Significant negative correlations between T2 values and B1 values were found in the left rectus femoris muscle for 3D MESE (r = -0.72, p<0.001) and 2D MESE (r = -0.71, p<0.001), but not for T2prep 3D TSE (r = -0.32, p = 0.09). Reproducibility of T2 expressed by root mean square coefficients of variation (RMSCVs) were equal to 3.5% in T2prep 3D TSE, 2.6% in 3D MESE and 2.4% in 2D MESE. Significant differences between T2 values of 3D sequences (T2prep 3D TSE and 3D MESE) and 2D MESE were found in all muscles with the highest values for 2D MESE (p<0.05). No significant correlations were found between PDFF and T2 values.

Conclusion

A strong influence of an inhomogeneous B1 field on the T2 values of 3D MESE and 2D MESE was shown, whereas the proposed T2prep 3D TSE gives B1-insensitive and reproducible thigh muscle T2 mapping.

Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome

The continuous integration of experimental data into coherent models of the brain is an increasing challenge of modern neuroscience. Such models provide a bridge between structure and activity, and identify the mechanisms giving rise to experimental observations. Nevertheless, structurally realistic network models of spiking neurons are necessarily underconstrained even if experimental data on brain connectivity are incorporated to the best of our knowledge. Guided by physiological observations, any model must therefore explore the parameter ranges within the uncertainty of the data. Based on simulation results alone, however, the mechanisms underlying stable and physiologically realistic activity often remain obscure. We here employ a mean-field reduction of the dynamics, which allows us to include activity constraints into the process of model construction. We shape the phase space of a multi-scale network model of the vision-related areas of macaque cortex by systematically refining its connectivity. Fundamental constraints on the activity, i.e., prohibiting quiescence and requiring global stability, prove sufficient to obtain realistic layer- and area-specific activity. Only small adaptations of the structure are required, showing that the network operates close to an instability. The procedure identifies components of the network critical to its collective dynamics and creates hypotheses for structural data and future experiments. The method can be applied to networks involving any neuron model with a known gain function.

Beyond opportunity costs: who bears the implementation costs of reducing emissions from deforestation and degradation?

Reducing Emissions from Deforestation and Degradation (REDD+) in developing countries is based on the premise that conserving tropical forests is a cost-effective way to reduce carbon emissions and therefore can be fully funded by international actors with obligations or interests in reducing emissions. However, concerns have repeatedly been raised about whether stakeholders in REDD+ host countries will actually end up bearing the costs of REDD+. Most prior analyses of the costs of REDD+ have focused on the opportunity costs of foregone alternative uses of forest land. We draw on a pan-tropical study of 22 subnational REDD+ initiatives in five countries to explore patterns in implementation costs, including which types of organizations are involved and which are sharing the costs of implementing REDD+. We find that many organizations involved in the implementation of REDD+, particularly at the subnational level and in the public sector, are bearing implementation costs not covered by the budgets of the REDD+ initiatives. To sustain this level of cost-sharing, REDD+ must be designed to deliver local as well as global forest benefits.