bluuebunny/crossref_metadata_2025 huggingface dataset:
Blind spots in global soil biodiversity and ecosystem function research
Authors: Guerra Carlos A. , Heintz-Buschart Anna , Sikorski Johannes , Chatzinotas Antonis , Guerrero-Ramírez Nathaly , Cesarz Simone , Beaumelle Léa , Rillig Matthias C. , Maestre Fernando T. , Delgado-Baquerizo Manuel , Buscot François , Overmann Jörg , Patoine Guillaume , Phillips Helen R. P. , Winter Marten , Wubet Tesfaye , Küsel Kirsten , Bardgett Richard D. , Cameron Erin K. , Cowan Don , Grebenc Tine , Marín César , Orgiazzi Alberto , Singh Brajesh K. , Wall Diana H. , Eisenhauer Nico
Published: September 2019

Soils harbor a substantial fraction of the world’s biodiversity, contributing to many crucial ecosystem functions. It is thus essential to identify general macroecological patterns related to the distribution and functioning of soil organisms to support their conservation and governance. Here we identify and characterize the existing gaps in soil biodiversity and ecosystem function data across soil macroecological studies and >11,000 sampling sites. These include significant spatial, environmental, taxonomic, and functional gaps, and an almost complete absence of temporally explicit data. We also identify the limitations of soil macroecological studies to explore general patterns in soil biodiversity-ecosystem functioning relationships, with only 0.6% of all sampling sites having a non-systematic coverage of both biodiversity and function datasets. Based on this information, we provide clear priorities to support and expand soil macroecological research.
Differential effects of farming practice on cuckoo bumblebee communities in relation to their hosts
Authors: Howard Charlotte E. , Austin Alexander J. , Gilbert James D. J.
Published: September 2019

Bees are important for vital pollination of wild and crop plants, but are in decline worldwide. Intensification of agriculture is a major driver of bee decline. Organic farming practices are designed to limit environmental impacts of agriculture and can increase bee abundance and species diversity. However, studies have been heavily focused towards some guilds of bees, overlooking others. This includes social brood parasites, cuckoo bumblebees, an understudied bee lineage. Little is known about bumblebee host and cuckoo population dynamics, and the effects of farming practice on cuckoo bumblebees have never previously been evaluated.

To compare the effects of farming practice (organic vs conventional) on the abundance, species diversity, and community dissimilarity of cuckoo bumblebees and their hosts, we compared host and cuckoo community metrics across ten matched pairs of organic and conventional farms in Yorkshire, UK.

As found by many previous studies, host bumblebees were more abundant on organic farms than on conventional farms. Despite this, cuckoo bumblebees were equally abundant on both farm types. Contrary to prediction, community dissimilarity and species diversity were unaffected by farm type for both host and cuckoo communities.

Synthesis and applications:Results suggest that cuckoo bumblebee community metrics are not solely driven by host community metrics, and that cuckoos may respond differently from their hosts to differences among farming practices. This could, in turn, indicate that a unified management practice is not sufficient to conserve all bumblebee species.
Single-cell atlas of major haematopoietic tissues sheds light on blood cell formation from embryonic endothelium
Authors: Shvartsman Maya , Pavlovich Polina V. , Oatley Morgan , Ganter Kerstin , McKernan Rachel , Prialgauskaite Radvile , Adamov Artem , Chukreev Konstantin , Descostes Nicolas , Buness Andreas , Cabezas-Wallscheid Nina , Lancrin Christophe
Published: September 2019

The Yolk Sac (YS) and Aorta-Gonad-Mesonephros (AGM) are two major haematopoietic regions during embryonic development. Interestingly, AGM is the only one generating haematopoietic stem cells (HSCs). To identify the difference between AGM and YS, we compared them using single-cell RNA sequencing between 9.5 and 11.5 days of mouse embryonic development and identified cell populations using CONCLUS, a new computational tool. The AGM was the only one containing neurons and a specific mesenchymal population, while the YS major component was an epithelial population expressing liver marker genes. In addition, the YS contained a major endothelial population expressing Stab2, a hyaluronan receptor, also highly expressed by liver endothelium. We demonstrated that the YS haematopoietic potential was restricted to Stab2-negative cells and that ectopic expression of Stab2 could reduce blood cell formation from endothelium. Our results indicate that the AGM is a tissue more favourable to HSCs development than the YS because of its microenvironment and the nature of its endothelial cells.
A multi-seasonal model of plant-nematode interactions and its use to identify optimal plant resistance deployment strategies
Authors: Nilusmas Samuel , Mercat Mathilde , Perrot Thomas , Djian-Caporalino Caroline , Castagnone-Sereno Philippe , Touzeau Suzanne , Calcagno Vincent , Mailleret Ludovic
Published: September 2019

Root-knot nematodes (RKNs) are soil-borne polyphagous pests with major impact on crop yield worlwide. Resistant crops efficiently control avirulent RKNs, but favour the emergence of virulent forms. Virulence being associated with fitness costs, susceptible crops counter-select virulent RKNs. In this study we identify optimal rotation strategies between susceptible and resistant crops to control RKNs and maximize crop yield.

We developed an epidemiological model describing the within-season dynamics of avirulent and virulent RKNs on susceptible or resistant plant root-systems, and their between-season survival. The model was fitted to experimental data and used to predict yield-maximizing rotation strategies, with special attention to the impact of epidemic and genetic parameters.

Crop rotations were found to be efficient under realistic parameter ranges. They were characterised by low ratios of resistant plants, and were robust to parameter uncertainty. Rotations provide significant gain over resistant-only strategies, especially under intermediate fitness costs and severe epidemic contexts.

Switching from the current general deployment of resistant crops to custom rotation strategies could not only maintain or increase crop yield, but also preserve the few and valuable R-genes available to us.
GWAS and Fine-Mapping of Livability and Six Disease Traits in Holstein Cattle
Authors: Freebern Ellen , Santos Daniel JA , Fang Lingzhao , Jiang Jicai , Parker Gaddis Kristen L. , Liu George E. , Vanraden Paul M. , Maltecca Christian , Cole John B. , Ma Li
Published: September 2019

Background

Health traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to identify associated genomic variants and thus reveal insights into the genetic architecture of complex traits and diseases. The objective of this study is to investigate the genetic basis of seven health traits in dairy cattle and to identify potential candidate genes associated with cattle health using GWAS, fine mapping, and analyses of multitissue transcriptome data.

Results

We studied cow livability and six direct disease traits, mastitis, ketosis, hypocalcemia, displaced abomasum, metritis, and retained placenta, using de-regressed breeding values and more than three million imputed DNA sequence variants. After data edits and filtering on reliability, phenotypes for 11,880 to 24,699 Holstein bulls were included in the analyses of the seven traits. GWAS was performed using a mixed-model association test, and a Bayesian fine-mapping procedure was conducted to calculate a posterior probability of causality to each variant and gene in the candidate regions. The GWAS results detected a total of eight genome-wide significant associations for three traits, cow livability, ketosis, and hypocalcemia, including the bovine MHC region associated with livability. Our fine-mapping of associated regions reported 20 candidate genes with the highest posterior probabilities of causality for cattle health. Combined with transcriptome data across multiple tissues in cattle, we further exploited these candidate genes to identify specific expression patterns in disease-related tissues and relevant biological explanations such as the expression ofGCin the liver and association with mastitis as well as theCCDC88Cexpression in CD8 cells and association with cow livability.

Conclusions

Collectively, our analyses report six significant associations and 20 candidate genes of cattle health. With the integration of multi-tissue transcriptome data, our results provide useful information for future functional studies and better understanding of the biological relationship between genetics and disease susceptibility in cattle.
Testosterone secretion varies in a sex- and stage-specific manner: insights on the regulation of competitive traits from a sex-role reversed species
Authors: Lipshutz Sara E. , Rosvall Kimberly A.
Published: September 2019

Testosterone (T) mediates a variety of traits that function in competition for mates, including territorial aggression, ornaments, armaments, and gametogenesis. The link between T and mating competition has been studied mainly in males, but females also face selection pressures to compete for mates. Sex-role reversed species, in which females are the more competitive sex, provide a unique perspective on the role of T in promoting competitive traits. Here, we examine patterns of T secretion in sex-role reversed Northern Jacanas (Jacana spinosa) during breeding, when females are fertile and males are either seeking copulations or conducting parental care. We measured baseline levels of T in circulation along with a suite of behavioral and morphological traits putatively involved in mating competition. We evaluated hypotheses that levels of T track gonadal sex and parental role, and we begin to investigate whether T and competitive traits co-vary in a sex- and stage-specific manner. Although females had higher expression of competitive traits than males at either breeding stage, we found that females and incubating males had similar levels of T secretion, which were lower than those observed in copulating males. T was correlated with wing spur length in females and testes mass in copulating males, but was otherwise uncorrelated with other competitive traits. These findings suggest that levels of T in circulation alone do not predict variation in competitive traits across levels of analysis, including gonadal sex and parental role. Instead, our findings coupled with prior research indicate that selection for female mating competition and male care may generate different physiological regulation of competitive traits in jacanas.

Highlights

In role reversed species, females face stronger competition and males care for offspring

We examine testosterone (T) and competitive traits in female and male jacanas

Circulating T is similar in females and incubating males, but higher in copulating males

Both gonadal sex and parental role shape patterns of T secretion

Physiological regulation of competitive traits may differ in female and male jacanas
Transcriptional changes suggest a major involvement of Gibberellins in Trifolium pratense regrowth after mowing
Authors: Herbert Denise Brigitte , Gross Thomas , Rupp Oliver , Becker Annette
Published: September 2019

Red clover (Trifolium pratense) is used worldwide as a fodder plant due its high nutritional value. In response to mowing, red clover exhibits specific morphological traits to compensate the loss of biomass. The morphological reaction is well described, but knowledge of the underlying molecular mechanisms are still lacking. Here we characterize the molecular genetic response to mowing of red clover by using comparative transcriptomics in greenhouse conditions and agriculturally used field. The analysis of mown and control plants revealed candidate genes possibly regulating crucial steps of the genetic network governing the regrowth reaction. In addition, multiple identified gibberellic acid (GA) related genes suggest a major role for GA in establishing the regrowth morphology of red clover. Mown red clover plants showing this regrowth morphology were partially “rescued” by exogenous GA application, demonstrating the influence of GA during regrowth. Our findings provide insights into the physiological and genetic processes of mowing red clover, to serve as a base for red clover yield improvement.
Effect of integrated health system leading-managing-and-governing for results model on institutional delivery: Team-based quasi-experiment
Authors: Ambelie Yeshambel Agumas , Alene Getu Degu , Gebrekiros Damen Hailemariam
Published: September 2019

Objective

The objective of this study is to examine, based on theory of change, whether integrated leading-managing-and-governing for results model is plausible cause of improved institutional delivery.

Methods

A team-based quasi-experimental study was conducted. One-hundred-thirty-four health facility teams were enrolled in the study. Teams were allocated to intervention and control groups in a 1:1 ratio, non-randomly. End line institutional delivery was the dependent variable while the group (main predictor) and the baseline institutional delivery (covariate) were independent variables. The intervention that was given over six months was integrated leading-managing-and-governing for results model. The institutional deliveries were measured with percentages whilst the group was measured with exposure status (yes or no) to the intervention. Data, from both groups, were collected at baseline and end line. Data were analyzed using analysis of covariance. Statistical significance was determined at (p<.05). The main effect of the intervention was determined by 95% CI, presented in the contrast results.

Results

The adjusted mean institutional deliveries with 95% CI were 47.4 (46.2, 48.6) and 33.4 (32.2, 34.6) in the intervention and control groups, respectively. Contrast results showed that having an intervention group, p = .000, 95% CI (12.2, 15.8), of integrated leading-managing-and governing for results model significantly increased mean institutional delivery compared to having a control group.

Conclusions

This study provides some guidance regarding the plausible causation of integrated leading-managing-and-governing for results model on institutional delivery. It would serve as a baseline in identifying true causation using a randomized design.
A Neural Network Based Algorithm for Dynamically Adjusting Activity Targets to Sustain Exercise Engagement Among People Using Activity Trackers
Authors: Mohammadi Ramin , Centi Amanda Jayne , Atif Mursal , Agboola Stephen , Jethwani Kamal , Kvedar Joseph C , Kamarthi Sagar
Published: September 2019

It is well established that lack of physical activity is detrimental to overall health of an individual. Modern day activity trackers enable individuals to monitor their daily activity to meet and maintain targets and to promote activity encouraging behavior. However, the benefits of activity trackers are attenuated over time due to waning adherence. One of the key methods to improve adherence to goals is to motivate individuals to improve on their historic performance metrics. In this work we developed a machine learning model to dynamically adjust the activity target for the forthcoming week that can be realistically achieved by the activity-tracker users. This model prescribes activity target for the forthcoming week. We considered individual user-specific personal, social, and environmental factors, daily step count through the current week (7 days). In addition, we computed an entropy measure that characterizes the pattern of daily step count for the current week. Data for training the machine learning model was collected from 30 participants over a duration of 9 weeks. The model predicted target daily count with mean absolute error of 1545 steps. The proposed work can be used to set personalized goals in accordance with the individual’s level of activity and thereby improving adherence to fitness tracker.
System-Level Quantification and Phenotyping of Early Embryonic Morphogenesis ofCaenorhabditis elegans
Authors: Guan Guoye , Wong Ming-Kin , Ho Vincy Wing Sze , An Xiaomeng , Chan Lu-Yan , Tian Binghui , Li Zhiyuan , Tang Leihan , Zhao Zhongying , Tang Chao
Published: September 2019

Cell lineage consists of cell division timing, cell migration and cell fate, and is highly conserved during development of nematode species. An outstanding question is how differentiated cells are genetically and physically regulated in order to migrate to their precise destination among individuals. Here, we first generated a reference embryo using time-lapse 3 dimensional images of 222 wild-typeC. elegansembryos at about 1.5-minute interval. This was achieved by automatic tracing and quantitative analysis of cellular phenotypes from 4- to 24-cell stage, including cell cycle duration, division orientation and migration trajectory. We next characterized cell division timing and cell kinematic state, which suggests that eight groups of cells can be clustered based on invariant and distinct division sequence. Cells may still be moving while others start to divide, indicating strong robustness against motional noise in developing embryo. We then devised a system-level phenotyping method for detecting mutant defect in global growth rate, cell cycle duration, division orientation and cell arrangement. A total of 758 genes were selected for perturbation by RNA interference followed by automatic phenotyping, which suggests a cryptic genetic architecture coordinating early morphogenesis spatially and temporally. The high-quality wild-type reference supports a conceptual close-packing model for cell arrangement during 4- to 8-cell stage, implying fundamental mechanical laws regulating the topological structure of earlyC. elegansembryo. Also, we observed a series of remarkable morphogenesis phenomena such as induced defect or recovery from defect in mutant embryo. To facilitate use of this quantification system, we built a software namedSTAR 1.0for visualizing the wild-type reference and mutant phenotype. It also allows automatic phenotyping of new mutant embryo. Taken together, we not only provide a statistical wild-type reference with defined variability, but also shed light on both genetic and physical mechanisms coordinating early embryonic morphogenesis ofC. elegans. The statistical reference permits a sensitive approach for mutant phenotype analysis, with which we phenotype a total of 1818 mutant embryos by depletion of 758 genes.

Highlights & Graphical Abstract

● Spatial-Temporal Wild-Type Reference for Early Embryonic Morphogenesis ofC. elegans

● Variability (Noise) of Division Timing, Division Orientation and Cell Arrangement

● A Conceptual Close-Packing Model for Cell Arrangement Up to 8-Cell Stage

● Quantitative Phenotyping Methods at Embryo and Cellular Level

● Cellular Phenotypes of 1818 Mutant Embryos (758 Genes) Before Gastrulation

● Categorized Phenotypes upon Gene Perturbation
Efficient use of harvest data: An integrated population model for exploited animal populations
Authors: Gamelon Marlène , Baubet Éric , Besnard Aurélien , Gaillard Jean-Michel , Lebreton Jean-Dominique , Touzot Laura , Veylit Lara , Gimenez Olivier
Published: September 2019

Many populations are affected by hunting or fishing. Models designed to assess the sustainability of harvest management require accurate estimates of demographic parameters (e.g. survival, reproduction) hardly estimable with limited data collected on exploited populations. The joint analysis of different data sources with integrated population models (IPM) is an optimal framework to obtain reliable estimates for parameters usually difficult to estimate, while accounting for imperfect detection and observation error. The IPM built so far for exploited populations have integrated count-based surveys and catch-at-age data into ageclass structured population models. But the age of harvested individuals is difficult to assess and often not recorded, and population counts are often not performed on a regular basis, limiting their use for the monitoring of exploited populations.

Here, we propose an IPM that makes efficient use of data commonly collected in exploited marine and terrestrial populations of vertebrates. As individual measures of body mass at both capture and death are often collected in fish and terrestrial game species, our model integrates capture-mark-recapture-recovery data and data collected at death into a body mass-structured population model. It allows the observed number of individuals harvested to be compared with the expected number and provides accurate estimates of demographic parameters.

We illustrate the usefulness of this IPM using an emblematic game species distributed worldwide, the wild boarSus scrofa, as a case study. For this species that has increased in distribution and abundance over the last decades, the model provides accurate and precise annual estimates of key demographic parameters (survival, reproduction, growth) and of population size while accounting for imperfect detection and observation error.

To avoid an overexploitation of declining populations or an under-exploitation of increasing populations, it is crucial to gain a good understanding of the dynamics of exploited populations. When managers or conservationists have limited demographic data, the IPM offers a powerful framework to assess population dynamics. Being highly flexible, the approach is broadly applicable to both terrestrial and marine exploited populations for which measures of body mass are commonly recorded and more generally, to all populations suffering from anthropogenic mortality causes.
Comparisons of the antibody repertoires of a humanized rodent and humans by high throughput sequencing
Authors: Joyce Collin , Burton Dennis R. , Briney Bryan
Published: September 2019

The humanization of animal model immune systems by genetic engineering has shown great promise for antibody discovery, tolerance studies and for the evaluation of vaccines. Assessment of the baseline antibody repertoire of unimmunized model animals will be useful as a benchmark for future immunization experiments. We characterized the heavy chain and kappa chain antibody repertoires of a model animal, the OmniRat, by high throughput antibody sequencing and made use of two novel datasets for comparison to human repertoires. Intra-animal and inter-animal repertoire comparisons reveal a high level of conservation in antibody diversity between the lymph node and spleen and between members of the species. Multiple differences were found in both the heavy and kappa chain repertoires between OmniRats and humans including gene segment usage, CDR3 length distributions, class switch recombination, somatic hypermutation levels and in features of V(D)J recombination. The Inference and Generation of Repertoires (IGoR) software tool was used to model recombination in VH regions which allowed for the quantification of some of these differences. Diversity estimates of the OmniRat heavy chain repertoires almost reached that of humans, around two orders of magnitude less. Despite variation between the species repertoires, a high frequency of OmniRat clonotypes were also found in the human repertoire. These data give insights into the development and selection of humanized animal antibodies and provide actionable information for use in vaccine studies.
Neutrophil-mediated dynamic capillary stalls in ischemic penumbra: persistent traffic jams after reperfusion contribute to injury
Authors: Erdener Şefik Evren , Tang Jianbo , Kılıç Kıvılcım , Postnov Dmitry , Giblin John Thomas , Kura Sreekanth , Chen I-chun Anderson , Vayisoğlu Tuğberk , Sakadžić Sava , Schaffer Chris B. , Boas David A.
Published: September 2019

Ever since the introduction of thrombolysis and the subsequent expansion of endovascular treatments for acute ischemic stroke, it remains to be identified why the actual outcomes are less favorable despite recanalization. Here, by high spatio-temporal resolution imaging of capillary circulation in mice, we introduce the pathological phenomenon of dynamic flow stalls in cerebral capillaries, occurring persistently in the salvageable penumbra after recanalization. These stalls, which are distinct from permanent cellular plugs that can lead to no-flow, were temporarily and repetitively occurring in the capillary network, impairing the overall circulation like small focal traffic jams. In vivo microscopy in the ischemic penumbra revealed leukocytes traveling through capillary lumen or getting stuck, while red blood cell flow was being disturbed in the neighboring segments, within 3 hours after stroke onset. Stall dynamics could be modulated, by injection of an anti-Ly6G antibody specifically targeting neutrophils. By decreasing the number and duration of stalls, we were able to improve the blood flow in the penumbra within 2-24 hours after reperfusion, increase capillary oxygenation, decrease cellular damage and improve functional outcome. Thereby the dynamic microcirculatory stall phenomenon contributes to the ongoing penumbral injury and is a potential hyperacute stage mechanism adding on previous observations of detrimental effects of activated neutrophils in ischemic stroke.

Significance

This work provides in vivo evidence that, even in perfused capillaries, abnormal capillary flow patterns in the form of dynamic stalls can contribute to ongoing tissue injury in the salvageable penumbra in very early hours of cerebral ischemia. These events resembling micro traffic jams in a complex road network, are mediated by passage of neutrophils through the microcirculation and persist despite recanalization of the occluded artery.
Adiponectin and related C1q/TNF-related proteins bind selectively to anionic phospholipids and sphingolipids
Authors: Ye Jessica , Bian Xin , Lim Jaechul , Medzhitov Ruslan
Published: September 2019

Adiponectin (also known as Acrp30) is a well-known adipokine associated with protection from cardiovascular disease, insulin resistance, and inflammation. Though multiple studies have investigated the mechanism of action of adiponectin and its relationship with tissue ceramide levels, several aspects of adiponectin biology remain unexplained, including its high circulating levels, tendency to oligomerize, and marked structural similarity to the opsonin C1q. Given the connection between adiponectin and ceramide metabolism, and the lipid-binding properties of C1q, we hypothesized that adiponectin may function as a lipid binding protein. Indeed, we found that recombinant adiponectin bound to various anionic phospholipids and sphingolipids, including phosphatidylserine, ceramide-1-phosphate, and sulfatide. The globular head-domain of adiponectin was necessary and sufficient for lipid binding. Adiponectin oligomerization was also observed to be critical for efficient lipid binding. In addition to lipids in liposomes, adiponectin bound LDL in an oligomerization-dependent manner. Other C1qTNF-related protein (CTRP) family members Cbln1, CTRP1, CTRP5, and CTRP13 also bound similar target lipids in liposomes. These findings suggest that adiponectin and other CTRP family members may not only function as classical hormones, but also as lipid binding opsonins or carrier proteins.
A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains
Authors: Modi Vivek , Dunbrack Roland L.
Published: September 2019

Studies on the structures and functions of individual kinases have been used to understand the biological properties of other kinases that do not yet have experimental structures. The key factor in accurate inference by homology is an accurate sequence alignment. We present a parsimonious, structure-based multiple sequence alignment (MSA) of 497 human protein kinase domains excluding atypical kinases, even those with related but somewhat different folds. The alignment is arranged in 17 blocks of conserved regions and unaligned blocks in between that contain insertions of varying lengths present in only a subset of kinases. The aligned blocks contain well-conserved elements of secondary structure and well-known functional motifs, such as the DFG and HRD motifs. From pairwise, all-against-all alignment of 272 human kinase structures, we estimate the accuracy of our MSA to be 97%. The remaining inaccuracy comes from a few structures with shifted elements of secondary structure, and from the boundaries of aligned and unaligned regions, where compromises need to be made to encompass the majority of kinases. A new phylogeny of the protein kinase domains in the human genome based on our alignment indicates that ten kinases previously labeled as “OTHER” can be confidently placed into the CAMK group. These kinases comprise the Aurora kinases, Polo kinases, and calcium/calmodulin-dependent kinase kinases.
A novel nuclear speckle factor, USP42, promotes homologous recombination repair by resolving DNA double-strand break induced R-loop
Authors: Matsui Misaki , Sakasai Ryo , Abe Masako , Kimura Yusuke , Kajita Shoki , Torii Wakana , Katsuki Yoko , Ishiai Masamichi , Iwabuchi Kuniyoshi , Takata Minoru , Nishi Ryotaro
Published: September 2019

The nucleus of mammalian cells is highly compartmentalized by nuclear bodies, including nuclear speckles. While nuclear bodies are known to function in regulating gene expression, their involvement in DNA repair has not been actively investigated. Here, our focused screen for nuclear speckle factors involved in homologous recombination (HR), which is a faithful DNA double-strand break (DSB) repair mechanism, revealed that nuclear speckle factors regulating transcription are potentially involved in the regulation of HR. Among the top hits, we provide evidence showing that USP42, which is a deubiquitylating enzyme and a hitherto unidentified nuclear speckles factor, promotes HR by facilitating BRCA1 recruitment to DSB sites and DNA-end resection. We further showed that USP42 localizes to nuclear speckles via an intrinsically disordered region, which is required for efficient HR. Furthermore, we established that USP42 interacts with DHX9, which possesses DNA-RNA helicase activity, and is required for efficient resolution of DSB-induced R-loop. Mechanistically, USP42 antagonizes mono-ubiquitylation of DHX9 that is evoked after DSB induction. In conclusion, our data propose a model in which a novel nuclear speckle factor, USP42, facilitates DSB-induced R-loop resolution, BRCA1 loading to DSB sites and preferential DSB repair by HR, indicating the importance of spatial regulation of DSB repair choice mediated by nuclear bodies.

Significant statement

Defects in the repair of DNA double-strand break (DSB), which is one of the most harmful DNA insults, cause human diseases including cancers. It has been suggested that DSBs generated in the coding region tend to be repaired by homologous recombination (HR) that is error-free DSB repair pathway. To reveal the spatial regulation of HR, in this study, we investigated the potential contribution of nuclear bodies, especially nuclear speckles, to HR, identifying a deubiquitylating enzyme USP42 as a HR promoting factor. We found that USP42 deubiquitylates DHX9, facilitates resolution of DNA-RNA hybrid structure and enhances HR through BRCA1 loading to DSB sites.

Classification

Biological Sciences, Cell Biology
Short paired-end reads trump long single-end reads for expression analysis
Authors: Freedman Adam H. , Gaspar John M. , Sackton Timothy B.
Published: September 2019

Background

Typical experimental design advice for expression analyses using RNA-seq generally assumes that single-end reads provide robust gene-level expression estimates in a cost-effective manner, and that the additional benefits obtained from paired-end sequencing are not worth the additional cost. However, in many cases (e.g., with Illumina NextSeq and NovaSeq instruments), shorter paired-end reads and longer single-end reads can be generated for the same cost, and it is not obvious which strategy should be preferred. Using publicly available data, we test whether short-paired end reads can achieve more robust expression estimates and differential expression results than single-end reads of approximately the same total number of sequenced bases.

Results

At both the transcript and gene levels, 2×40 paired-end reads unequivocally provide expression estimates that are more highly correlated with 2×125 than 1×75 reads; in nearly all cases, those correlations are also greater than for 1×125, despite the greater total number of sequenced bases for the latter. Across an array of metrics, differential expression tests based upon 2×40 consistently outperform those using 1×75.

Conclusion

Researchers seeking a cost-effective approach for gene-level expression analysis should prefer short paired-end reads over a longer single-end strategy. Short paired-end reads will also give reasonably robust expression estimates and differential expression results at the isoform level.
Comparison of a retroviral protease in monomeric and dimeric states
Authors: Wosicki Stanislaw , Gilski Miroslaw , Zabranska Helena , Pichova Iva , Jaskolski Mariusz
Published: September 2019

Retroviral proteases (RPs) are of high interest owing to their crucial role in the maturation process of retroviral particles. RPs are obligatory homodimers, with a pepsin-like active site built around two aspartates (in DTG triads) that activate a water molecule, as the nucleophile, under two flap loops. Mason–Pfizer monkey virus (M-PMV) is unique among retroviruses as its protease is also stable in the monomeric form, as confirmed by an existing crystal structure of a 13 kDa variant of the protein (M-PMV PR) and its previous biochemical characterization. In the present work, two mutants of M-PMV PR, D26N and C7A/D26N/C106A, were crystallized in complex with a peptidomimetic inhibitor and one mutant (D26N) was crystallized without the inhibitor. The crystal structures were solved at resolutions of 1.6, 1.9 and 2.0 Å, respectively. At variance with the previous study, all of the new structures have the canonical dimeric form of retroviral proteases. The protomers within a dimer differ mainly in the flap-loop region, with the most extreme case observed in the apo structure, in which one flap loop is well defined while the other flap loop is not defined by electron density. The presence of the inhibitor molecules in the complex structures was assessed using polder maps, but some details of their conformations remain ambiguous. In all of the presented structures the active site contains a water molecule buried deeply between the Asn26-Thr27-Gly28 triads of the protomers. Such a water molecule is completely unique not only in retropepsins but also in aspartic proteases in general. The C7A and C106A mutations do not influence the conformation of the protein. The Cys106 residue is properly placed at the homodimer interface area for a disulfide cross-link, but the reducing conditions of the crystallization experiment prevented S—S bond formation. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:S2059798319011355.
Evaluation of a compact triangular crinkle-shaped multiband antenna with circular polarized for ITU band based on MADM method
Authors: Beigi Payam , Zehforoosh Yashar , Rezvani Mirhamed , Nourinia Javad
Published: September 2019

Purpose

This paper aims to present a new triangular crinkle-shaped multiband antenna for multiband operation.

Design/methodology/approach

This paper refers to increasing the number of resonance frequency by appending triangular crinkle. Experimental frequency results of the presented antenna are 1.60/2.80/4.00/5.80/7.12/8.32/10.06 GHz.

Findings

The triangular shaped antenna is manufactured on a low-priced FR-4 substrate with small size and tested. The reported antenna with full size 14 × 14 mm2 with a half elliptical ground sheet on the bottom plane of the substrate and a triangular crinkle strip patch in the front of the substrate. The reported antenna has dual polarized, by rectangular slits on the ground sheet can produce the CP radiation on ITU band. The radiation characteristics indicate the mentioned antenna plays good task for multiband structures. Simulation and measured consequences are in desirable agreement and refer to agreeable operation for the introduced antenna.

Originality/value

Also, an evaluation is done based on multiple attribute decision-making method for comparison the proposed monopole antenna with some previously presented multiband monopole antennas.
Employees’ proactive behavior and innovation performance
Authors: Segarra-Ciprés Mercedes , Escrig-Tena Ana , García-Juan Beatriz
Published: September 2019

Purpose

The purpose of this paper is to analyze the degree to which employees’ proactive behavior contributes to innovation performance in firms operating in high-technology sectors. Despite the benefits of these behaviors for individuals and organizations, few studies have analyzed the contextual conditions that enable firms to capture their value in order to improve innovation performance. Drawing on the interactionist perspective, the authors also examine the extent to which informal and formal controls, such as perceived support for innovation and innovation process formalization, can facilitate the contribution of proactive behaviors to improve innovation performance (product and process innovation).

Design/methodology/approach

Based on an empirical study with a sample of 173 firms operating in chemical and information technology service sectors, hierarchical regression analysis was used to test the relationship between employees’ proactive behavior and innovation performance, and the moderating effects of informal and formal controls.

Findings

The results reveal a positive and significant association between proactive behaviors and product and process innovation performance. Both control mechanisms positively moderate the association between proactive behavior and product innovation, but no moderating role was found for process innovation. Moreover, rather than inhibiting innovation performance, innovation process formalization is positively associated with innovation. More specifically, a curvilinear relationship was found, which implies that when the level of formalization is high, it is able to improve product and process innovation.

Practical implications

The findings suggest that managers should consider proactive behavior in selection processes and performance management, and should cultivate a climate to support innovation and establish formal controls for innovation as a way to channel employees’ initiatives into product innovation.

Originality/value

This study contributes to the theoretical and managerial understanding of the extent to which proactive employees and organizational controls are able to enhance innovation in a technologically dynamic context.
Numerical simulation of dissolution of solid particles in fluid flow using the SPH method
Authors: Rahmat Amin , Barigou Mostafa , Alexiadis Alessio
Published: September 2019

Purpose

The purpose of this paper is to numerically study the dissolution of solid particles using the smoothed particle hydrodynamics (SPH) method.

Design/methodology/approach

To implement dissolution, an advection–diffusion mass transport equation is solved over computational particles. Subsequently, these particles disintegrate from the solute when their concentration falls below a certain threshold.

Findings

It is shown that the implementation of dissolution is in good agreement with available data in the literature. The dissolution of solid particles is studied for a wide range of Reynolds and Schmidt numbers. Two-dimensional (2D) results are compared with three-dimensional (3D) cases to identify where 2D results are accurate for modelling 3D dissolution phenomena.

Originality/value

The present numerical model is capable of addressing related problems in pharmaceutical, biochemical, food processing and detergent industries.
Bungee jumping and rocket launching
Authors: Christie Michael , Simon Susan , Graham Wayne , Call Kairen , Farragher Yvonne
Published: September 2019

Purpose

A plethora of principal development programs based on myriad leadership theories currently abounds in many educational jurisdictions globally. Today’s principals, consequently and fortuitously, often feel less isolated and better supported that has been indicated in school leadership research over the past two decades. The purpose of this paper is to discover, however, how principals, through well-designed postgraduate study, can effectively become the transformational leaders, schools regularly require of them.

Design/methodology/approach

Action research involving postgraduate leadership students at an Australian university over a two year period, involved three cycles: identification of leadership learning needs, introduction of innovations to their learning and identification of the transformative learning which contributed to their leadership development.

Findings

Transformative learning impacts significantly on transformational leadership development. This happens when disorienting dilemmas challenge and open minds to possibilities, and paradigmatic assumptions are questioned. The ensuing awareness enables leaders to demonstrate characteristics of transformational leadership especially the dimension of individualised consideration.

Originality/value

Few studies have aligned transformative learning with transformational leadership theory, but this paper found that school leaders benefit from transformative learning in their quest to become such a leader. The scariness of a metaphoric principal bungee-jump could ultimately lead to rocket launching of the most transformative kind.
Application of digital technologies in health insurance for social good of bottom of pyramid customers in India
Authors: Nayak Bishwajit , Bhattacharyya Som Sekhar , Krishnamoorthy Bala
Published: September 2019

Purpose

Social health insurance framework of any country is the national identifier of the country’s policy for taking care of its population which cannot access or afford quality healthcare. The purpose of this paper is to highlight the strategic imperatives of digital technology for the inclusive social health models for the BoP customers.

Design/methodology/approach

A qualitative exploratory study using in-depth personal interviews with 53 Indian health insurance CXOs was conducted with a semi-structured questionnaire. Using MaxQDA software, the interview transcripts were analyzed by means of thematic content analysis technique and patterns identified based on the expert opinions.

Findings

A framework for the strategic imperatives of digital technology in social health insurance emerged from the study highlighting three key themes for technology implementation in the social health insurance sector – analytics for risk management, cost optimization for operations and enhancement of customer experience. The study results provide key insights about how insurers can enhance the coverage of BoP population by leveraging technology.

Social implications

The framework would help health insurers and policymakers to select strategic choices related to technology that would enable creation of inclusive health insurance models for BoP customers.

Originality/value

The absence of specific studies highlighting the strategic digital imperatives in social health insurance creates a unique value proposition for this framework which can help health insurers in developing a convergence in their risk management and customer delight objectives and assist the government in the formulation of a sustainable social health insurance framework.
Understanding the role of social networking platforms in addressing the challenges of Islamic banks
Authors: Naeem Muhammad
Published: September 2019

Purpose

Customers are increasingly interested in reading discussions, experiences, recommendations and reviews on social media platforms related to services and products in which they are highly interested. The purpose of this paper is to find the availability of user-generated content (UGC) in the context of Islamic banks and how it can enhance the level of brand engagement and purchase intention of customers.

Design/methodology/approach

The methodology for this research is designed by following the features of qualitative research methods and a social constructivism approach. Furthermore, non-directive and semi-structured in-depth interviews are constructed to accumulate research data from marketing teams and customers of Islamic banks. The respondents have been carefully chosen on the basis of purposive sampling and their level of awareness related to Islamic banks.

Findings

Islamic banks are more frequently using traditional marketing tools that are unable to enhance levels of information among the targeted population and prove an expensive way of marketing. The findings reveal that Islamic banks lag behind in adopting the latest information exchanging technologies compared to conventional banking systems. A lack of skilled people, reputation and trust, lack of e-marketing strategy and lower levels of investment in social media platforms are major barriers to generate UGC, brand engagement and purchase intention among the targeted market of Islamic banks.

Practical implications

The effective and competent use of various social networking platforms can enhance UGC related to Islamic banking products and services. UGC can generate interactive communication, services reviews, feedbacks, intention to purchase, social influence, social trust and positive customer perception among the targeted population of Islamic banks. The study has summarized and offered practical recommendations to show how Islamic banks can address challenges and enjoy a high level of profitability compared to conventional banking systems.

Originality/value

The present study uncovered the steps that must be taken by the top management of Islamic banks to enhance levels of awareness, online product reviews and recommendations, e-word of mouth and purchase intentions of the targeted market. The study enhanced understanding regarding how a higher level of investment in social networking platforms, safe and secure banking systems and skilled IT professionals can address the challenges of Islamic banks. Furthermore, these factors can create positive UGC, social influence, social brand engagement and purchase intention of customers in Islamic banks. These primary factors must be considered by Islamic banks to compete with conventional banking products and services.
Structure and catalytic performance of Zn-doped TiO2 film
Authors: Yang Mei , Huang Tingyu , Tang Ning , Ou Ben , Zhang Wenhao
Published: September 2019

Purpose

This paper aims to investigate the photocatalytic activity of zinc doped MAO-TiO2 films under the optimum MAO treatment condition.

Design/methodology/approach

The coating was prepared by micro arc oxidation, and the influence of doping on the properties of the coating was also investigated.

Findings

The results show that the BET surface area is 78.25±0.03m2/g, total pore area is 76.32 ± 0.04m2/g, and the total pore volume is 0.2135 ± 0.0004cm3/g. The degradation ratio of the film electrode with Zn-doped in methyl orange solution is up to 94%. When the react circles is 10 times, the degradation ratio is up to more than 85% and remains steady. With the different reaction conditions, these kinetics of the reactions show some different formulas.

Originality/value

A kinetic equation for photocatalytic activity is established.