bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-parametric physiological classification of retinal ganglion cells in the mouse retina
Authors: Jouty Jonathan , Hilgen Gerrit , Sernagor Evelyne , Hennig Matthias H.
Published: September 2018

Retinal ganglion cells, the sole output neurons of the retina, exhibit surprising diversity. A recent study reported over 30 distinct types in the mouse retina, indicating that the processing of visual information is highly parallelised in the brain. The advent of high density multi-electrode arrays now enables recording from many hundreds to thousands of neurons from a single retina. Here we describe a method for the automatic classification of large-scale retinal recordings using a simple stimulus paradigm and a spike train distance measure as a clustering metric. We evaluate our approach using synthetic spike trains, and demonstrate that major known cell types are identified in high-density recording sessions from the mouse retina with around 1000 retinal ganglion cells. A comparison across different retinas reveals substantial variability between preparations, suggesting pooling data across retinas should be approached with caution. As a parameter-free method, our approach is broadly applicable for cellular physiological classification in all sensory modalities.
Accurate Determination of Human CPR Conformational Equilibrium by smFRET using Dual Orthogonal Non-Canonical Amino Acid Labeling
Authors: Quast Robert B. , Fatemi Fataneh , Kranendonk Michel , Margeat Emmanuel , Truan Gilles
Published: September 2018

Conjugation of fluorescent dyes to proteins - a prerequisite for the study of conformational dynamics by single molecule Förster resonance energy transfer (smFRET) - can lead to substantial changes of the dye’s photophysical properties, ultimately biasing the quantitative determination of inter-dye distances. In particular the popular cyanine dyes and their derivatives, which are by far the most used dyes in smFRET experiments, exhibit such behavior. To overcome this, a general strategy to site-specifically equip proteins with FRET pairs by chemo-selective reactions using two distinct non-canonical amino acids simultaneously incorporated through genetic code expansion inEscherichia coliwas developed. Applied to human NADPH- cytochrome P450 reductase (CPR), the importance of homogenously labeled samples for accurate determination of FRET efficiencies was demonstrated. Furthermore, the effect of NADP+ on the ionic strength dependent modulation of the conformational equilibrium of CPR was unveiled. Given its generality and accuracy, the presented methodology establishes a new benchmark to decipher complex molecular dynamics on single molecules.
Temperature-responsive competitive inhibition of CRISPR-Cas9
Authors: Jiang Fuguo , Liu Jun-Jie , Osuna Beatriz A. , Xu Michael , Berry Joel D. , Rauch Benjamin J. , Nogales Eva , Bondy-Denomy Joseph , Doudna Jennifer A.
Published: September 2018

CRISPR–Cas immune systems utilize RNA-guided nucleases to protect bacteria from bacteriophage infection. Bacteriophages have in turn evolved inhibitory ‘anti-CRISPR’ (Acr) proteins, including six inhibitors (AcrIIA1-6) that can block DNA cutting and genome editing by type II-A CRISPR-Cas9 enzymes. We show here that AcrIIA2 and its homologue, AcrIIA2b, prevent Cas9 binding to DNA by occluding protein residues required for DNA binding. Cryo-EM-determined structures of AcrIIA2 or AcrIIA2b bound to S. pyogenes Cas9 reveal a mode of competitive inhibition of DNA binding that is distinct from other known Acrs. Differences in the temperature dependence of Cas9 inhibition by AcrIIA2 and AcrIIA2b arise from differences in both inhibitor structure and the local inhibitor-binding environment on Cas9. These findings expand the natural toolbox for regulating CRISPR-Cas9 genome editing temporally, spatially and conditionally.
Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes
Authors: Haller Benjamin C. , Galloway Jared , Kelleher Jerome , Messer Philipp W. , Ralph Peter L.
Published: September 2018

There is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree-sequence recording method (Kelleher et al., 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward-time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn-in to be constructed extremely efficiently after the fact, using “recapitation”; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a population’s genealogy that can be analyzed in Python using the msprime package. We have implemented the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary simulation software package) and extended it to allow the recording of non-neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modeling and exploration of evolutionary processes.
Strain maps characterize the symmetry of convergence and extension patterns during Zebrafish gastrulation
Authors: Bhattacharya Dipanjan , Zhong Jun , Tavakoli Sahar , Kabla Alexandre , Matsudaira Paul
Published: September 2018

During gastrulation of the zebrafish embryo, the cap of blastoderm cells organizes into the axial body plan of the embryo with left-right symmetry and head-tail, dorsal-ventral polarities. Our labs have been interested in the mechanics of early development and have investigated whether these large-scale cells movements can be described as tissue-level mechanical strain by a tectonics-based approach. The first step is to image the positions of all nuclei from mid-epiboy to early segmentation by digital sheet light microscopy (DSLM), organize the surface of the embryo into multi-cell spherical domains, construct velocity fields from the movements of these domains and extract 3D strain rate maps. Tensile/expansive and compressive strains in the axial and equatorial directions are detected during gastrulation as anterior and posterior expansion along the anterior-posterior axis and medial-lateral compression across the dorsal-ventral axis corresponding to convergence and extension. In later stages in development are represented by localized medial expansion at the onset of segmentation and anterior expansion at the onset of neurulation. Symmetric patterns of rotation are first detected in the animal hemispheres at mid-epiboly and then the vegetal hemispheres by the end of gastrulation. By analysing the temporal sequence of large scale movements, deformations across the embryo can be attributed to a combination of epiboly and dorsal convergence-extension.

Significance

Strain is an emergent property of tissues that originates from the mechanical coupling of cell-cell and cell-substrate interactions, individual cell shape changes, and cell level forces. By imaging the positions of nuclei from mid-epiboly to early segmentation of the zebrafish embryo we are able to calculate three types of strain maps by a plate tectonics based method. The regions of expansive and compressive axial and equatorial strain correspond to areas undergoing convergence and extension, a major step in the formation of the embryonic body plan as well as the formation of somite and head structures. The most striking signatures of strain are: 1. the bilateral symmetry of linear strain across the anterior-posterior, dorsal-ventral axis during gastrulation, 2. the complementary counter-rotational strains or curl in the animal hemisphere at mid epiboly, and 3. a divergence or saddle point in the region of the dorsal organizer, head-trunk boundary. These strains represent a general method to describe large-scale tissue-level mechanics not only of embryonic development but also tissue homeostasis and disease.
Bayesian coalescent inference of in-host evolution using Next Generation Sequencing
Authors: Leen Gayle , Baguelin Marc
Published: September 2018

Within an infected individual, influenza virus exists as a heterogeneous population of variants. When representing the viral population as a consensus sequence, information about minority variants is lost. However, using next generation sequencing (NGS), it is possible to identify nucleotide substitutions which segregate at low frequencies in the viral population, and can give insight into the within-host processes that drive the virus’s evolution, and is a step towards understanding the dynamics of the disease. During the course of an infection, mutations may occur, and at each segregating site, the frequency of the derived allele in the population will fluctuate. We develop a method which can use information about the relative frequencies of mutations in NGS data from a viral population sampled at multiple time points, to infer past population dynamics with a Bayesian skyline model. By using coalescent theory, we analytically derive the joint allele frequency spectrum for a population across multiple time points, and relate this to the coalescent intervals generated from the skyline model. We demonstrate the model on data taken from populations of equine influenza virus sampled during an infection, and show that it is possible to infer a posterior distribution of effective viral population size through time. We also show how the model can be used to infer the probability that a mutation occurred within-host, as opposed to being an ancestral mutation which occurred prior to infection.

Author Summary

When a host is infected by a virus, many particles of the infecting agent enter the body of the host. This viral population is composed of many closely related viruses that continue diversifying by mutating while reproducing in the host. New sequencing technologies allow the quantifying of the proportion of the different variants present in the host at a particular time. Unfortunately, the data resulting from such sequencing techniques are difficult to interpret as they consist of many unlinked copies of relatively small fragments of genetic code distributed along the genome of the virus.

We designed a method combining models of virus genealogies and frequency of mutations appearing in the data to reconstruct the variation of the viral population inside the host. It also allows us to time the apparition of particular variants. This could be useful to detect if a particular mutation (e.g. providing drug resistance) has appeared in host or was circulating before. We applied our method to data of within-host evolution of equine influenza.
Iron and Heme Coordinate Erythropoiesis through HRI-Mediated Regulation of Protein Translation and Gene Expression
Authors: Zhang Shuping , Macias-Garcia Alejandra , Ulirsch Jacob C. , Velazquez Jason , Butty Vincent L. , Levine Stuart S. , Sankaran Vijay G. , Chen Jane-Jane
Published: September 2018

Iron and heme play central roles in red blood cell production. However, the mechanisms by which iron and heme levels coordinate erythropoiesis remain incompletely understood. HRI is a heme-regulated kinase that controls translation by phosphorylating eIF2α. Here, we investigate the global impact of iron, heme and HRI on protein translation in vivo in murine primary erythroblasts using ribosome profiling. By defining the underlying changes in translation during iron and HRI deficiencies, we validate known regulators of this process, including Atf4, and identify novel pathways such as co-regulation of ribosomal protein mRNA translation. Surprisingly, we found that heme and HRI pathways, but not iron-regulated pathways, mediate the major protein translational and transcriptional responses to iron deficiency in erythroblasts in vivo and thereby identify previously unappreciated regulators of erythropoiesis. Our genome-wide study uncovers the major impact of the HRI-mediated integrated stress response for the adaptation to iron deficiency anemia.
Streaming histogram sketching for rapid microbiome analytics
Authors: Rowe Will P. M. , Carrieri Anna Paola , Alcon-Giner Cristina , Caim Shabhonam , Shaw Alex , Sim Kathleen , Kroll J Simon , Hall Lindsay J. , Pyzer-Knapp Edward O. , Winn Martyn D.
Published: September 2018

Motivation

The growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research; allowing for the design of new studies, augmentation of novel datasets and reanalysis of published works. This vast amount of microbiome data, as well as the widespread proliferation of microbiome research and the looming era of clinical metagenomics, means there is an urgent need to develop analytics that can process huge amounts of data in a short amount of time.

To address this need, we propose a new method for the compact representation of microbiome sequencing data using similarity-preserving sketches of streaming k-mer spectra. These sketches allow for dissimilarity estimation, rapid microbiome catalogue searching, and classification of microbiome samples in near real-time.

Results

We apply streaming histogram sketching to microbiome samples as a form of dimensionality reduction, creating a compressed ‘histosketch’ that can be used to efficiently represent microbiome k-mer spectra. Using public microbiome datasets, we show that histosketches can be clustered by sample type using pairwise Jaccard similarity estimation, consequently allowing for rapid microbiome similarity searches via a locality sensitive hashing indexing scheme. Furthermore, we show that histosketches can be used to train machine learning classifiers to accurately label microbiome samples. Specifically, using a collection of 108 novel microbiome samples from a cohort of premature neonates, we trained and tested a Random Forest Classifier that could accurately predict whether the neonate had received antibiotic treatment (95% accuracy, precision 97%) and could subsequently be used to classify microbiome data streams in less than 12 seconds.

We provide our implementation, Histosketching Using Little K-mers (HULK), which can histosketch a typical 2GB microbiome in 50 seconds on a standard laptop using 4 cores, with the sketch occupying 3000 bytes of disk space.

Availability

Our implementation (HULK) is written in Go and is available at: https://github.com/will-rowe/hulk (MIT License)
Spider mites escape bacterial infection by avoiding contaminated food
Authors: Zélé Flore , Santos-Matos Gonçalo , Figueiredo Alexandre , Eira Cátia , Pinto Catarina , Laurentino Telma , Sucena Élio , Magalhães Sara
Published: September 2018

To fight infection, arthropods rely on the deployment of an innate immune response but also upon physical/chemical barriers and avoidance behaviours. However, most studies focus on immunity, with other defensive mechanisms being relatively overlooked.

We have previously shown that the spider mite Tetranychus urticae does not mount an induced immune response towards systemic bacterial infections, entailing very high mortality rates. Therefore, we hypothesized that other defence mechanisms may be operating to minimize infection risk. Here, we test (a) if spider mites are also highly susceptible to other infection routes - spraying and feeding - and (b) if they display avoidance behaviours towards infected food. Individuals sprayed with or fed on Escherichia coli or Pseudomonas putida survived less than the control, pointing to a deficient capacity of the gut epithelium, and possibly of the cuticle, to contain bacteria. Additionally, we found that spider mites prefer uninfected food to food contaminated with bacteria, a choice that probably does not rely on olfactory cues.

Our results suggest that spider mites may rely mostly on avoidance behaviours to minimize bacterial infection and highlight the multi-layered nature of immune strategies present in arthropods.
Topological Reinforcement as a Principle of Modularity Emergence in Brain Networks
Authors: Damicelli Fabrizio , Hilgetag Claus C. , Hütt Marc-Thorsten , Messé Arnaud
Published: September 2018

Modularity is a ubiquitous topological feature of structural brain networks at various scales. While a variety of potential mechanisms have been proposed, the fundamental principles by which modularity emerges in neural networks remain elusive. We tackle this question with a plasticity model of neural networks derived from a purely topological perspective. Our topological reinforcement model acts enhancing the topological overlap between nodes, iteratively connecting a randomly selected node to a non-neighbor with the highest topological overlap, while pruning another network link at random. This rule reliably evolves synthetic random networks toward a modular architecture. Such final modular structure reflects initial ‘proto-modules’, thus allowing to predict the modules of the evolved graph. Subsequently, we show that this topological selection principle might be biologically implemented as a Hebbian rule. Concretely, we explore a simple model of excitable dynamics, where the plasticity rule acts based on the functional connectivity between nodes represented by co-activations. Results produced by the activity-based model are consistent with the ones from the purely topological rule, showing a consistent final network configuration. Our findings suggest that the selective reinforcement of topological overlap may be a fundamental mechanism by which brain networks evolve toward modular structure.
The essential genome of the crenarchaeal model Sulfolobus islandicus
Authors: Zhang Changyi , Phillips Alex P. R. , Wipfler Rebecca L. , Olsen Gary J. , Whitaker Rachel J.
Published: September 2018

Sulfolobus islandicus is a model experimental system in the TACK superphylum of the Archaea, a key lineage in the evolutionary history of cell biology. Here we report a genome-wide identification of the repertoire of genes essential to S. islandicus growth in culture. We confirm previous targeted gene knockouts, uncover the non-essentiality of functions assumed to be essential to the Sulfolobus cell, including the proteinaceous S-layer, and highlight key essential genes whose functions are yet to be determined. Phyletic distributions illustrate the potential transitions that have occurred during the evolution of this contemporary archaeal cell and highlight the sets of genes that may have been associated with each transition. We use this comparative context as a lens to focus future research on archaea-specific uncharacterized essential genes for which future functional data would provide valuable insights into the evolutionary history of the contemporary cell.
Modulating CRISPR gene drive activity through nucleocytoplasmic localization of Cas9 in S. cerevisiae
Authors: Goeckel Megan E. , Basgall Erianna M. , Lewis Isabel C. , Goetting Samantha C. , Yan Yao , Halloran Megan , Finnigan Gregory C.
Published: September 2018

The bacterial CRISPR/Cas genome editing system has provided a major breakthrough in molecular biology. One use of this technology is within a nuclease-based gene drive. This type of system can install a genetic element within a population at unnatural rates. Combatting of vector-borne diseases carried by metazoans could benefit from a delivery system that bypasses traditional Mendelian laws of segregation. Recently, laboratory studies in fungi, insects, and even mice, have demonstrated successful propagation of CRISPR gene drives and the potential utility of this type of mechanism. However, current gene drives still face challenges including evolved resistance, containment, and the consequences of application in wild populations. In this study, we use an artificial gene drive system in budding yeast to explore mechanisms to modulate nuclease activity of Cas9 through its nucleocytoplasmic localization. We examine non-native nuclear localization sequences on Cas9 fusion proteins in vivo and demonstrate that appended signals can titrate gene drive activity and serve as a potential molecular safeguard.
Simultaneous SNP selection and adjustment for population structure in high dimensional prediction models
Authors: Bhatnagar Sahir R , Yang Yi , Lu Tianyuan , Schurr Erwin , Loredo-Osti JC , Forest Marie , Oualkacha Karim , Greenwood Celia MT
Published: September 2018

Complex traits are known to be influenced by a combination of environmental factors and rare and common genetic variants. However, detection of such multivariate associations can be compromised by low statistical power and confounding by population structure. Linear mixed effects models (LMM) can account for correlations due to relatedness but have not been applicable in high-dimensional (HD) settings where the number of fixed effect predictors greatly exceeds the number of samples. False positives or false negatives can result from two-stage approaches, where the residuals estimated from a null model adjusted for the subjects’ relationship structure are sub-sequently used as the response in a standard penalized regression model. To overcome these challenges, we develop a general penalized LMM with a single random effect calledggmixfor simultaneous SNP selection and adjustment for population structure in high dimensional prediction models.We develop a blockwise coordinate descent algorithm with automatic tuning parameter selection which is highly scalable, computationally efficient and has theoretical guarantees of convergence. Through simulations and three real data examples, we show thatggmixleads to more parsimonious models compared to the two-stage approach or principal component adjustment with better prediction accuracy. Our method performs well even in the presence of highly correlated markers, and when the causal SNPs are included in the kinship matrix.ggmixcan be used to construct polygenic risk scores and select instrumental variables in Mendelian randomization studies.Our algorithms are available in an R package (https://github.com/greenwoodlab/ggmix).

1

Author Summary

This work addresses a recurring challenge in the analysis and interpretation of genetic association studies: which genetic variants can best predict and are independently associated with a given phenotype in the presence of population structure ? Not controlling confounding due to geographic population structure, family and/or cryptic relatedness can lead to spurious associations. Much of the existing research has therefore focused on modeling the association between a phenotype and a single genetic variant in a linear mixed model with a random effect. However, this univariate approach may miss true associations due to the stringent significance thresholds required to reduce the number of false positives and also ignores the correlations between markers. We propose an alternative method for fitting high-dimensional multivariable models, which selects SNPs that are independently associated with the phenotype while also accounting for population structure. We provide an efficient implementation of our algorithm and show through simulation studies and real data examples that our method outperforms existing methods in terms of prediction accuracy and controlling the false discovery rate.
Assessing the digital library research output: bibliometric analysis from 2002 to 2016
Authors: Ahmad Khurshid , Jian Ming Zheng , Rafi Muhammad
Published: September 2018

Purpose

The purpose of this bibliometric analysis is to quantify the prominence and impact of published literature within the field. The research has been conducted with the intent of obtaining the expansion and characteristics of the literature on digital library.

Design/methodology/approach

More than 4,206 documents found in the period of 2002-2016 were collected from the ISI Web of Science and were analyzed to explore the annual productivity, yearly citation, most cited articles, prolific authors, eminent journals of the subject, productivity of institutes and contribution of countries. These results are based on the types of documents (articles, reviews, proceedings papers, book reviews, editorial materials and book chapters).

Findings

The core findings are that the most productive year of publication was 2016, and the growth of citation increased rapidly; the top source of title is electronic library. The result shows that the USA dominates in the research output, with Illinois University securing the first position; the most prolific author is Fourie I from South Africa. In the document types category, the most cited sources are research articles.

Originality/value

This research is useful for the researchers interested in the field of bibliometrics as it postulates an inclusive indication of provenance in the field of library and information science.
A cylindrical insert for parabolic trough solar collector
Authors: Bellos Evangelos , Daniil Ilias , Tzivanidis Christos
Published: September 2018

Purpose

The purpose of this paper is to investigate a cylindrical flow insert for a parabolic trough solar collector. Centrally placed and eccentric placed inserts are investigated in a systematic way to determine which configuration leads to the maximum thermal enhancement.

Design/methodology/approach

The analysis is performed in SolidWorks Flow Simulation with a validated computational fluid dynamics model. Moreover, the useful heat production and the pumping work demand increase are evaluated using the exergy and the overall efficiency criteria. The different scenarios are compared for inlet temperature of 600 K, flow rate of 100 L/min and Syltherm 800 as the working fluid. Moreover, the inlet temperature is examined from 450 to 650 K, and the diameter of the insert is investigated up to 50 mm.

Findings

According to the final results, the use of a cylindrical insert of 30 mm diameter is the most sustainable choice which leads to 0.56 per cent thermal efficiency enhancement. This insert was examined in various eccentric positions, and it is found that the optimum location is 10 mm over the initial position in the vertical direction. The thermal enhancement, in this case, is about 0.69 per cent. The pumping work demand was increased about three times with the insert of 30 mm, but the absolute values of this parameter are too low compared to the useful heat production. So, it is proved that the increase in the pumping work is not able to eliminate the useful heat production increase. Moreover, the thermal enhancement is found to be greater at higher temperature levels and can reach up to 1 per cent for an inlet temperature of r650 K.

Originality/value

The present work is a systematic investigation of the cylindrical flow insert in a parabolic trough collector. Different diameters of this insert, as well as different positions in two dimensions, are examined using a parametrization of angle-radius. To the authors’ knowledge, there is no other study in the literature that investigates the presented many cases systematically with the followed methodology on parabolic trough collectors. Moreover, the results of this work are evaluated with various criteria (thermal, exergy and overall efficiency), something which is not found in the literature.
Approach to activity engagement and differences in activity participation in chronic pain: A five‐day observational study
Authors: Andrews Nicole E. , Strong Jenny , Meredith Pamela J. , Branjerdporn Grace S.
Published: September 2018

Background/aim

Activity pacing is one of the most widely endorsed interventions used by occupational therapists to assist clients to manage chronic pain conditions. It targets two behaviours that are thought to be maladaptive: activity avoidance and overactivity (activity engagement that severely aggravates pain). However, in more recent years, the potential for activity pacing to negatively impact activity participation has been recognised which deters habitually overactive individuals from adopting the self‐management strategy. The main aim of this study was to evaluate if variances in activity participation can be explained by how individuals approach activity engagement when in pain.

Methods

Sixty‐eight adults with chronic pain completed a demographic questionnaire, the Pain and Activity Relations Questionnaire (PARQ), and recorded their participation in activities for five days using a paper diary. Two of the authors independently coded the recorded activities into one of three time‐use categories: rest, productivity or leisure/social. A MANCOVA model was produced to examine differences in time use across four ‘approach to activity engagement’ categories which were determined by scores on the PARQ.

Results

A significant multivariate effect was found. Univariate comparisons revealed that ‘overactives’ (high overactivity, low avoidance) and ‘pacers’ (low overactivity, low avoidance) spent a similar amount of time resting over the five‐day period. ‘Overactives’ spent the most amount of time on productive tasks and the least amount of time on social/leisure activities out of the four subgroups.

Conclusion

Results suggest that activity pacing does not negatively impact on activity participation in chronic pain populations. ‘Pacers’ spent a similar amount of time resting, and had a slightly better balance between productive tasks and leisure/social activities, when compared to ‘overactives’. The results of this study can be incorporated into patient education and highlight potential treatment avenues for individuals with chronic pain who are habitually overactive.
Arthropod biodiversity in olive groves under two soil management systems: presence versus absence of herbaceous cover crop
Authors: Carpio Antonio J. , Castro Jesús , Tortosa Francisco S.
Published: September 2018

Agricultural intensification has greatly affected biodiversity in recent decades. One common and recent transformation that has taken place in Mediterranean countries is olive grove intensification, although its effects on biodiversity have rarely been studied.

In the present study, we investigated the effect of soil management practices, with versus without soil cover crops, on the arthropod abundance, richness, diversity and species composition in Andalusia olive groves, South Spain.

The results obtained show that these soil cover crops positively affect the diversity of arthropods, along with other variables such as the diversity of the plant community and Shannon index of the landscape. By contrast, the number of arthropods was higher in olive groves with bare ground as a result of the abundance of two families (Entomobryidae and Aeolothripidae), which comprised more than 50% of all the individuals collected.

Rank abundance diagrams and multivariate analyses showed differences between the two types of soil management systems with respect to the composition of families.

In conclusion, soil cover crops strongly improve the diversity of arthropods in olive orchards, which helps to maintain biodiversity in these intensive agroecosystems at the same time as improving other ecosystems services, such as soil fertility and the prevention of soil erosion.
Remoteness, urbanization, and child nutrition in sub‐Saharan Africa
Authors: Headey Derek , Stifel David , You Liangzhi , Guo Zhe
Published: September 2018

Rural populations face a much higher burden of child undernutrition than urban populations, especially in sub‐Saharan Africa, a continent where many households still live in remote rural areas. Despite this, relatively little research has analyzed nutrition differences across rural and urban populations, or across gradients of rural remoteness. In this article, we study these differences in sub‐Saharan Africa by linking spatial data on travel times to urban centers with 20,000 or more people as our measure of remoteness to Demographic Health Survey data covering 74,398 children from 10,900 communities in 23 countries. We find that children in rural communities have much worse linear growth and dietary outcomes than urban children, but that children in more remote rural communities face only a small nutritional penalty compared to children from less remote communities. Moreover, the harmful effects of remoteness and rural living largely disappear once we control for education, wealth, and social/infrastructural services. This implies that the key nutritional disadvantages faced by rural populations stem chiefly from social and economic poverty. Combating these problems requires a combination of innovative cost‐effective mechanisms for extending basic services to isolated rural communities and facilitating welfare‐enhancing migration to urban areas.
The Contested Legacies of Indigenous Debt Bondage in Southeast Asia: Indebtedness in the Vietnamese Sex Sector
Authors: Lainez Nicolas
Published: September 2018

The modern‐slavery paradigm promotes analogies between contemporary trafficking and the transatlantic, white, and indigenous slave trade. The analogy some scholars use to address debt bondage in past and present Southeast Asia prompted me to consider the hypothesis that the debts incurred by Vietnamese sex workers with moneylenders, procurers, and migration brokers are a remnant of indigenous slavery. However, the ethnographic and legalistic study of debt in the Vietnamese sex sector across Southeast Asia in relation to debt‐bondage traditions provides limited support to the transhistorical thesis. Nonetheless, it throws light on the creditor–debtor relationship and shows that sex workers need credit to finance production and social reproduction in a region undergoing rapid capitalist development, and that because of their exclusion from financial, labor, and labor migration markets, they access it through personalized arrangements that generate strong obligations and dependencies with the potential for restrictions of freedom, in a social structure that promotes patronage, vertical bonding, and dependency. [debt, (modern) slavery, trafficking, sex work, migration, Vietnam, Cambodia, Singapore]
Dietary soyasaponin attenuates 2,4-dinitrofluorobenzene-induced contact hypersensitivity via gut microbiota in mice
Authors: Nagano T , Katase M , Tsumura K
Published: September 2018

Soyasaponins (SSs) are abundant in soybeans and display inhibitory activity against contact hypersensitivity (CHS), which is often used as a mouse model for allergic contact dermatitis (ACD); however, their therapeutic mechanisms remain unknown. Here, we attempted to clarify the role of gut microbiota in the inhibition of CHS by dietary soyasaponins. For antibiotic treatment, mice were administered a mixture of ciprofloxacin and metronidazole or vancomycin. These antibiotics and SSs were given to mice via drinking water 3-weeks prior to CHS induction with 2,4-dinitrofluorobenzene, and the mice were analysed for ear swelling, tissue oedema, infiltration of Gr-1-positive immune cells, the composition of faecal microbiota and regulatory T (Treg) cells. The soyasaponin diets attenuated ear swelling and tissue oedema, and reduced the number of Gr-1-positive cells infiltrating ear tissues. CHS caused changes in the structure of the gut microbiota, but dietary SSs blocked the changes in the microbiota composition. Ciprofloxacin and metronidazole treatments significantly enhanced the severity of CHS symptoms, whereas vancomycin treatment blocked the suppressive effect of dietary SSs on CHS. These antibiotic treatments differed in their effects on the gut microbiota composition. Treg cells in auricular lymph node and spleen increased under SS-enriched diets, but this increase was blocked by vancomycin treatment. These results suggest that dietary SSs exert their inhibitory activity on CHS via the gut microbiota in mice, suggesting that dietary supplementation with SSs may have beneficial effects on ACD patients, but that the gut microbiota is a critical determinant of the therapeutic value of dietary SSs.
Safety of calcium and vitamin D supplements, a randomized controlled trial
Authors: Aloia John F. , Katumuluwa Subhashini , Stolberg Alexandra , Usera Gianina , Mikhail Mageda , Hoofnagle Andrew N. , Islam Shahidul
Published: September 2018

Objective

It is anticipated that an intake of vitamin D found acceptable by Endocrine Society Guidelines (10 000 IU/day) with co‐administered calcium supplements may result in frequent hypercalciuria and hypercalcaemia. This combination may be associated with kidney stones. The objective of this study was to compare the episodes of hypercalciuria and hypercalcaemia from calcium supplements co‐administered with 10 000 IU or 600 IU vitamin D daily. This design allows a comparison of the Institute of Medicine recommendation for the RDA of vitamin D along with the upper limit of calcium intake with the high intake of vitamin D suggested by the Endocrine Society.

Context

Harms of currently recommended high intake of vitamin D have not been studied.

Design

The design was a randomized controlled trial with 2 groups with evaluation every 3 months for one year: (a) CaCO3 1200 mg/day with 10 000 IU vitamin D3/day or (b) CaCO3 1200 mg/day with 600 IU vitamin D3/day.

Patients

This study was conducted in an ambulatory research centre in healthy, white postmenopausal women.

Measurements

Serum and 24‐hour urine calcium were measured.

Results

Hypercalcaemia and hypercalciuria occurred in both groups. At the final visit, 19/48 in the high dose D group had hypercalciuria. The odds of developing hypercalciuria were 3.6 [OR = 3.6(1.39, 9.3)] times higher in the high dose D group. The odds of developing hypercalcaemia did not differ between groups.

Conclusions

The safe upper level of vitamin D recommended by the Endocrine Society when accompanied by calcium supplements results in frequent hypercalciuria. The risk of kidney stones at these levels should be investigated.
Qualitative exploration of supporting figures in the lives of emerging adults who left care compared with their noncare‐leaving peers
Authors: Sulimani‐Aidan Yafit
Published: September 2018

Studies on youth leaving care have emphasized their limited social support and their need for continuing support after emancipation. However, less is known about the nature of their existing social networks after emancipation and their roles during their transition to adulthood compared with their noncare‐leaving peers. With this in mind, 32 young adults aged 18 to 25 participated in semi‐structured interviews regarding their current support figures in order to learn whether they were congruent with their needs after emancipation. Thematic analysis revealed four main features of the two groups' social networks: (a) stability versus uncertainty as to the lasting presence of the supportive figure, (b) reliance on parents as main supportive figures versus relying on different supportive figures, (c) confidence versus uncertainty in the supportive figures' ability to help, and (d) holistic versus fragmented support of the young adults' needs. The discussion addresses the unique characteristics of care leavers in emerging adulthood and the implications of their social networks' features for their adjustment after emancipation. One of the study's recommendations is to proactively connect them to new supportive figures such as professionals or mentors by offering them mentoring programs cognizant of the instrumental and developmental tasks of emerging adulthood.
A quantitative appraisal of African Americans’ decisions to become registered organ donors at the driver’s license office
Authors: DuBay Derek A. , Ivankova Nataliya V. , Herbey Ivan , Redden David T. , Holt Cheryl , Siminoff Laura , Fouad Mona N. , Su Zemin , Morinelli Thomas A. , Martin Michelle Y.
Published: September 2018

African American (AA) organ donation registration rates fall short of national objectives. The goal of the present study was to utilize data acquired from a quantitative telephone survey to provide information for a future Department of Motorized Vehicles (DMV) intervention to increase AA organ donor registration at the DMV. AAs (n = 20 177) that had visited an Alabama DMV office within a 3‐month period were recruited via direct mailing to participate in a quantitative phone survey. Data from 155 respondents that participated in the survey were analyzed. Of those respondents deciding to become a registered organ donor (ROD; n = 122), one‐third made that decision at the time of visiting the DMV. Of those who chose not to become a ROD (n = 33), one‐third made the decision during the DMV visit. Almost 85% of all participants wanted to learn more about organ donation while waiting at the DMV, preferably via TV messaging (digital signage), with the messaging delivered from organ donors, transplant recipients, and healthcare experts. Altruism, accurate organ donation information, and encouragement from family and friends were the most important educational topics to support AAs becoming a ROD. These data provide a platform to inform future interventions designed to increase AAs becoming a ROD at the DMV.
Diagnostik blasenbildender Autoimmundermatosen
Authors: van Beek Nina , Zillikens Detlef , Schmidt Enno
Published: September 2018

Blasenbildende Autoimmundermatosen (BAIDs) sind eine heterogene Gruppe seltener Erkrankungen, die klinisch durch Erosionen und/oder Blasen an Haut und Schleimhäuten charakterisiert sind. BAIDs können in zwei Gruppen eingeteilt werden: Pemphigus‐Erkrankungen, die durch intraepidermale Blasenbildung und Autoantikörper gegen desmosomale Proteine wie Desmoglein (Dsg) 1, Dsg3 und Mitglieder der Plakin‐Familie charakterisiert sind, sowie subepidermale BAIDs, die Pemphigoid‐Erkrankungen und die Dermatitis herpetiformis umfassen. Bei der Dermatitis herpetiformis greifen die Autoantikörper die Transglutaminasen 2 und 3 an, während sie bei Pemphigoid‐Erkrankungen gegen Strukturproteine der dermoepidermalen Junktionszone gerichtet sind. Die Analyse einer periläsionalen Biopsie mittels direkter Immunfluoreszenzmikroskopie (IF‐Mikroskopie) stellt zwar nach wie vor den diagnostischen Goldstandard dar, mittlerweile sind jedoch verschiedene Tests allgemein verfügbar, die eine serologische Diagnosefindung für den Großteil der Patienten ermöglichen. Zur serologischen Standarddiagnostik gehört die indirekte IF auf Affenösophagus und NaCl‐separierter Spalthaut. Die Spezifität der Autoantikörper kann mit ELISA‐Systemen, die auf rekombinanten Formen der immundominanten Regionen der Zielantigene basieren, sowie indirekter IF‐Mikroskopie anhand multivarianter Tests mit mehreren multivariate näher charakterisiert werden. Diese serologischen Tests werden durch verschiedene hauseigene Immunoblotting‐ und ELISA‐Systeme ergänzt, die nur in spezialisierten Laboratorien verfügbar sind. In diesem Review geben wir einen Überblick über neue Entwicklungen bei der Diagnose von BAIDs und beschreiben moderne Diagnoseverfahren für diese Krankheitsgruppe.
Phototherapy
Authors: Singer Sebastian , Berneburg Mark
Published: September 2018

The efficacy of phototherapy is based on the interaction between ultraviolet (UV) radiation and the skin. The photobiological effects thus achieved depend on the wavelengths used. Targeted use of UVA and UVB, where indicated in combination with a photosensitizer such as psoralen, provides the dermatologist with a broad armamentarium for the treatment of a multitude of skin diseases. The spectrum of indications ranges from superficial dermatitis, psoriasis, and malignancies, such as cutaneous T‐cell lymphoma, to deep sclerosing conditions such as morphea. The objective of the present review is to highlight the photobiological effects of the various types of UV radiation as well as the resultant clinical indications for phototherapy.
Evaluation of the effects of dapagliflozin, a sodium‐glucose co‐transporter‐2 inhibitor, on hepatic steatosis and fibrosis using transient elastography in patients with type 2 diabetes and non‐alcoholic fatty liver disease
Authors: Shimizu Masanori , Suzuki Kunihiro , Kato Kanako , Jojima Teruo , Iijima Toshie , Murohisa Toshimitsu , Iijima Makoto , Takekawa Hidehiro , Usui Isao , Hiraishi Hideyuki , Aso Yoshimasa
Published: September 2018

Aims

To investigate the effects of dapagliflozin on liver steatosis and fibrosis evaluated in patients with type 2 diabetes and non‐alcoholic fatty liver disease (NAFLD).

Materials and methods

In a randomized, active‐controlled, open‐label trial, 57 patients with type 2 diabetes and NAFLD were randomized to a dapagliflozin group (5 mg/d; n = 33) or a control group (n = 24) and were treated for 24 weeks. Hepatic steatosis and fibrosis were assessed using transient elastography to measure controlled attenuation parameter (CAP) and liver stiffness, respectively.

Results

Baseline liver stiffness measurement (LSM) was positively correlated with several markers and scoring systems for liver fibrosis. In week 24, there was a significant decrease in CAP from 314 ± 61 to 290 ± 73 dB/m (P = 0.0424) in the dapagliflozin group, while there was no significant change in the control group. In addition, LSM tended to decrease from 9.49 ± 6.05 to 8.01 ± 5.78 kPa in the dapagliflozin group. In 14 patients from this group with LSM values ≥8.0 kPa, indicating significant liver fibrosis, LSM decreased significantly from 14.7 ± 5.7 to 11.0 ± 7.3 kPa (P = 0.0158). Furthermore, serum alanine aminotransferase and γ‐glutamyltranspeptidase levels decreased in the dapagliflozin group, but not in the control group, and visceral fat mass was significantly reduced in the dapagliflozin group.

Conclusions

Based on these findings, the sodium‐glucose co‐transporter‐2 inhibitor dapagliflozin improves liver steatosis in patients with type 2 diabetes and NAFLD, and attenuates liver fibrosis only in patients with significant liver fibrosis, although the possibility cannot be excluded that a reduction in body weight or visceral adipose tissue by dapagliflozin may be associated with a decrease of liver steatosis or fibrosis.
From body‐on‐frame to unibody constructions and designs mimicking biological structures – an overview
Authors: Vallittu Pekka K. , Durgesh Bangalore H. , AlKheraif AbdulAziz A. , Hjerppe Jenni
Published: September 2018

In dentistry, isotropic materials, such as metals, ceramics, and polymers, are used. Their properties are not related to any specific direction of the material microstructure. There is a trend toward non‐metallic, adhesive, and minimally invasive dentistry. This is in line with the conceptual change seen in the automobile industry, in which the basis of car structures has changed from body‐on‐frame designs to unibody designs. In unibody designs, all structural parts of the body of the car mechanically form a single structural entity. In modern adhesive dentistry, remaining tooth substance and the dental material form unibody designs, enabling preservation of tooth substance. Biological structures are created to withstand loading and are light in weight. The structural designs of elements in these biological materials are, to a large extent, based on fibrous material. More attention has been paid to mimicking fibrous structures of dental hard tissues by synthetic fiber‐reinforced composites. This overview reports key features of natural fibrous elements and how they are utilized in dentistry. Special emphasis is placed on the aspects of interfacial adhesion of restorative materials, especially ceramics to resin‐based materials and their role in the unibody design of the tooth‐restoration system.