bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hybrid assembly of the genome of the entomopathogenic nematodeSteinernema carpocapsaeidentifies the X-chromosome
Authors: Serra Lorrayne , Macchietto Marissa , Macias-Muñoz Aide , McGill Cassandra Joan , Rodriguez Isaryhia Maya , Rodriguez Bryan , Murad Rabi , Mortazavi Ali 
Published: March 2019

AbstractEntomopathogenic nematodes from the genusSteinernemaare lethal insect parasites that quickly kill their insect hosts with the help of their symbiotic bacteria.Steinernema carpocapsaeis one of the most studied entomopathogens due to its broad lethality to diverse insect species and its effective commercial use as a biological control agent for insect pests, as well as a genetic model for studying parasitism, pathogenesis, and symbiosis. In this study, we used long-reads from the Pacific Biosciences platform and BioNano Genomics Irys system to assemble the best genome ofS. carpocapsaeALL strain to date, comprising 84.5 Mb in 16 scaffolds, with an N50 of 7.36Mb. The largest scaffold, with 20.9Mb, was identified as chromosome X based on sex-specific genome sequencing. The high level of contiguity allowed us to characterize gene density, repeat content, and GC content. RNA-seq data from 17 developmental stages, spanning from embryo to adult, were used to predict 30,957 gene models. Using this new genome, we performed a macrosyntenic analysis toCaenorhabditis elegansandPristionchus pacificusand foundS. carpocapsae’schromosome X to be primarily orthologous toC. elegans’andP. pacificus’chromosome II and IV. We also investigated the expansion of protein families and gene expression differences between male and female stage nematodes. This new genome and more accurate set of annotations provide a foundation for new comparative genomic and gene expression studies within theSteinernemaclade and across the Nematoda phylum.Article SummaryThe insect killing worms Steinernema carpocapsae is a model organism for parasitism and symbiosis. The authors have used long reads and optical mapping to generate substantially contiguous assembly and a new set of gene annotations. They have identified the X chromosome as well as expansions in specific family proteases found in the venom of this worm. A macrosyntenic analysis withC. elegansshows a broad conservation of ancestral chromosomes with the exception of chromosome X. This new assembly will be useful to theSteinernemacommunity and the broader nematode genomics community.
Fenestrae-associated protein Plvap regulates the rate of blood-borne proteins passage into the hypophysis
Authors: Gordon Ludmila , Blechman Janna , Shimoni Eyal , Gur Dvir , Anand-Apte Bela , Levkowitz Gil 
Published: March 2019

SummaryTo maintain body homeostasis, endocrine systems must detect and integrate a multitude of blood-borne peripheral signals. This is mediated by specialized permeable pores in the endothelial membrane, dubbed fenestrae. Plasmalemma vesicles-associated protein (Plvap) is located in the fenestral diaphragm and is thought play a role in the selective passage of proteins through the fenestrae. However, this suggested function has yet to be demonstrated directly. Here, we studied the development of fenestrated capillaries in a major neuroendocrine interface between the blood and brain, namely the hypophysis. Using a transgenic permeability biosensor to visualize the vascular excretion of a genetically tagged plasma protein (DBP-EGFP), we show that the developmental acquisition of vascular permeability is associated with differential expression of zebrafish plvap orthologs in the hypophysis versus brain. Ultrastructural analysis of the hypophyseal vasculature revealed that plvapb mutants display deficiencies in fenestral and stomatal diaphragms as well as increased density of fenestrae, but not of caveolae. Measurements of DBP-EGFP dynamics in live plvapb mutant larvae provided a direct proof that Plvap limits the rate of blood-borne protein passage through fenestrated endothelia. Overall, we present the regulatory role of Plvap in the development of blood-borne protein detection machinery in a major neuroendocrine interface between the brain and the general circulation.
Autologous adipose-derived stem cell transplantation enhances healing of wound with exposed bone in a rat model
Authors: Hamada Tomo , Matsubara Hidenori , Yoshida Yasuhisa , Ugaji Shuhei , Nomura Issei , suchiya Hiroyuki T 
Published: March 2019

AbstractObjectivesSoft tissue wounds with exposed bone often require extended healing times and can be associated with severe complications. We describe the ability of artificial dermis with autogenic adipose-derived stem cells (ADSCs) to promote the healing of wounds with exposed bone in a rat model.MethodsAdipose tissues harvested from the bilateral inguinal regions of Wistar rats were used as ADSCs. Rats were randomly divided into control and ADSC groups to investigate the efficacy of ADSC transplantation for wound healing (n=20 per group). Soft tissue defects were created on the heads of the rats and were covered with artificial dermis with or without the seeded ADSCs. Specimens from these rats were evaluated using digital image analysis, histology, immunohistochemistry, cell labeling, and real-time reverse-transcription polymerase chain reaction (Real-time RT-PCR).ResultsThe average global wound area was significantly smaller in the ADSC group than in the control group on days 3, 7, and 14 after surgery (p<0.05). After 14 days, the blood vessel density in the wound increased by 1.6-fold in the ADSC group compared with that in the control group (p<0.01). Real-time RT-PCR results showed higherFgfbandVegfexpression levels at all time points, and higherTgfb1andTgfb3expression levels until 14 days after surgery, in the ADSC group than in the control group (p<0.05).ConclusionsIn wounds with exposed bone, autogenic ADSCs can promote vascularization and wound healing. Use of this cell source has multiple benefits, including convenient clinical application and lack of ethical concerns.
Effect of topical soluble epoxide hydrolase inhibition in a preclinical diabetic wound healing model
Authors: Reisdorf William C. , Rajpal Neetu , Gehman Andrew J. , Jain Piyush , Burgert Mark E. , Sonti Sujatha , Agarwal Pankaj , Rajpal Deepak K. 
Published: March 2019

AbstractThe objective of this study was to test a topical formulation of EPHX2 inhibitor, GSK2256294, in a dermal wound diabetic (db/db) mouse model. Comparisons were made between groups treated with EPHX2 inhibitor, matching vehicle control and a currently approved treatment for diabetic ulcers, becaplermin/Regranex, as a positive control which is highly efficacious in this model. Leptin receptor-deficient (db/db) male mice were sequentially assigned to treatment groups (N=10 per group) based on blood glucose levels and body weight. Mice were given a single 8 mm diameter full thickness wound on the back. Wounds were photographed and traced, and fresh test materials applied periodically with fresh dressing. Of ten mice treated with GSK2256294, three had completely healed wounds at the study conclusion, and 8/10 mice reached at least 50% closure. In the vehicle group, no mice achieved complete closure, and only 6/10 reached at least 50% closure by the study conclusion. Nine of ten wounds achieved complete closure in the positive control group by 21 days. Although the EPHX2 inhibitor results were indicative of efficacy, the single-sided p-value criterion of 0.05 was not met in this study.
The Gag Protein PEG10 Binds to RNA and Regulates Trophoblast Stem Cell Lineage Specification
Authors: Abed Mona , Verschueren Erik , Budayeva Hanna , Liu Peter , Kirkpatrick Donald S. , Reja Rohit , Kummerfeld Sarah K. , Webster Joshua D. , Gierke Sarah , Reichelt Mike , Anderson Keith R. , Newman Robert J , Roose-Girma Merone , Modrusan Zora , Pektas Hazal , Maltepe Emin , Newton Kim , Dixit Vishva M. 
Published: March 2019

ABSTRACTPeg10(paternally expressed gene 10) is an imprinted gene that is essential for placental development. It is thought to derive from a Ty3-gyspy LTR (long terminal repeat) retrotransposon and retains Gag and Pol-like domains. Here we show that the Gag domain of PEG10 can promote vesicle budding similar to the HIV p24 Gag protein. Expressed in a subset of mouse endocrine organs in addition to the placenta, PEG10 was identified as a substrate of the deubiquitinating enzyme USP9X. Consistent with PEG10 having a critical role in placental development, PEG10-deficient trophoblast stem cells (TSCs) exhibited impaired differentiation into placental lineages. PEG10 expressed in wild-type, differentiating TSCs was bound to many cellular RNAs includingHbegf(Heparin-binding EGF-like growth factor), which is known to play an important role in placentation. Expression ofHbegfwas reduced in PEG10-deficient TSCs suggesting that PEG10 might bind to and stabilize RNAs that are critical for normal placental development.
Obtaining tertiary protein structures by the ab-initio interpretation of small angle X-ray scattering data
Authors: Prior Christopher , Davies Owen R , Bruce Daniel , Pohl Ehmke 
Published: March 2019

ABSTRACTSmall angle X-ray scattering (SAXS) has become an important tool to investigate the structure of proteins in solution. In this paper we present a novel ab-initio method to represent polypeptide chains as discrete curves that can be used to derive a meaningful three-dimensional model from only the primary sequence and experimental SAXS data. High resolution crystal structures were used to generate probability density functions for each of the common secondary structural elements found in proteins. These are used to place realistic restraints on the model curve’s geometry. To evaluate the quality of potential models and demonstrate the efficacy of this novel technique we developed a new statistic to compare the entangled geometry of two open curves, based on mathematical techniques from knot theory. The chain model is coupled with a novel explicit hydration shell model in order derive physically meaningful 3D models by optimizing configurations against experimental SAXS data using a monte-caro based algorithm. We show that the combination of our ab-initio method with spatial restraints based on contact predictions successfully derives a biologically plausible model of the coiled–coil component of the human synaptonemal complex central element protein.SIGNIFICANCESmall-angle X-ray scattering allows for structure determination of biological macromolecules and their complexes in aqueous solution. Using a discrete curve representation of the polypeptide chain and combining it with empirically determined constraints and a realistic solvent model we are now able to derive realistic ab-initio 3-dimensional models from BioSAXS data. The method only require a primary sequence and the scattering data form the user.
Brand forgiveness
Authors: Fetscherin Marc , Sampedro Alexandra 
Published: March 2019

Purpose
This paper aims to explore and discuss the concept of brand forgiveness. It empirically assesses the relationships among three types of brand transgressions, brand forgiveness and three consumer coping strategies.

Design/methodology/approach
A 3 × 2 research design is used to evaluate the effects of three types of brand transgression (performance, image and value) and two degrees of severity (high vs low) for brand forgiveness. Then, this paper use a 2 × 3 research design, evaluating two degrees of brand forgiveness (high vs low) together with their effects on three different consumer coping strategies (switching, attacking and purchasing again). Using a representative sample of 472 US consumers, various hypotheses related to these research designs are tested.

Findings
The results show that almost half (48 per cent) of the consumers are unlikely or very unlikely to forgive a brand compared to about a third (32 per cent) who are likely or very likely to forgive. The results of ANOVA show the more severe the brand transgression, the less likely the forgiveness. Consumers who are more likely to forgive are less likely to avoid the brand or engage in attacking behaviors; they are also more likely to purchase the brand again. The results of regression analyses show that consumers witnessing a performance-based brand transgression are more likely to forgive the brand than in the case of image- or value-based brand transgressions.

Originality/value
This paper explores and outlines the brand forgiveness construct, both theoretically and empirically.
Climate change, responsible leadership and organizational commitment
Authors: Mousa Mohamed , Puhakka Vesa , Abdelgaffar Hala A. 
Published: March 2019

Purpose
The purpose of this paper is to focus on physicians in the four public hospitals located in the October province of Egypt in an attempt to explore the effect of climate change on physicians’ affective, continuance and normative commitment with and without mediating the role of responsible leadership.

Design/methodology/approach
A total of 360 physicians were contacted and all of them received a set of questionnaires. After two follow-ups, a total of 240 responses were collected with a response rate of 66.67 percent. Multiple regressions were employed to show how much variation in affective, continuance and normative commitment can be explained by climate change with and without the mediation of responsible leadership.

Findings
The findings show a statistically negative effect for climate change on physicians’ three approaches of organizational commitment (affective, continuance and normative). Furthermore, the statistical analysis proved that having responsible leaders in hospitals has a negligible effect on the relationship between climate change and the affective, continuance and normative commitment.

Originality/value
This paper contributes by filling a gap in environment and organization literature, in which empirical studies on the relationship between climate change and organizational commitment have been limited until now.
Pathways from flexible work arrangements to financial performance
Authors: Kotey Bernice Adei , Sharma Bishnu 
Published: March 2019

Purpose
The purpose of this paper is to investigate the direct and indirect effects of flexible working arrangements (FWAs) on return on labour (ROL).

Design/methodology/approach
Data from 4,204 employees and their employers were used to construct regression models to assess separately, the direct relationships between the FWAs and ROL and also the indirect relationships, with job satisfaction and staff turnover as mediating variables, applying Baron and Kenny’s (1986) mediation rules.

Findings
Flexible work hours significantly and directly increased ROL and indirectly through reduction in staff turnover, while the negative direct effect of job sharing on ROL was indirectly reduced by its positive effect on job satisfaction. Time in lieu of overtime (TOIL) and working from home reduced ROL with the direct negative effects of TOIL on ROL worsened by a reduction in job satisfaction.

Practical implications
The results suggest that not all FWAs increase ROL and that the direct effects of FWAs on ROL emanate from the efficacy with which work is reallocated in FWA negotiations. The indirect effects derive from employees’ reciprocation of FWAs through improved job satisfaction and turnover. The onus is therefore, on employers to maximise returns from FWAs through efficient work reallocation during negotiations.

Originality/value
The study makes a contribution by examining the direction of effects of FWAs on ROL and the pathways (direct and indirect) by which the effects occur. Research in this area has hitherto considered subjective and qualitative performance measures. FWAs, such as job sharing and TOIL, which are rarely considered in the literature, are covered in the study.
Wildlife differentially affect tree and liana regeneration in a tropical forest: An 18‐year study of experimental terrestrial defaunation versus artificially abundant herbivores
Authors: Luskin Matthew Scott , Ickes Kalan , Yao Tze Leong , Davies Stuart J. 
Published: March 2019

Abstract

Hunting and land use change modify native herbivore abundances and cause cascading effects in natural ecosystems. The outcomes for vegetation depend on changes to specific plant–animal interactions, such as seed dispersal or predation, or physical disturbances.

We experimentally manipulated terrestrial wildlife populations in a primary lowland forest in Malaysia over an 18‐year period (1996–2014) to understand how artificially high or low animal densities affect tree and liana regeneration. Our study site retains a diverse wildlife community and artificially high densities of native wild pigs (Sus scrofa) that are sustained by crop raiding in distant oil palm plantations. We used fencing that excluded terrestrial animals >1 kg to experimentally simulate conditions similar to those in defaunated forests. These two treatments – abnormally high pig abundances and megafauna loss from hunting – represent common outcomes in disturbed Southeast Asian forests and are characteristic of many forests globally. We focused on trees and lianas because they are the two dominant woody life‐forms in tropical forests and crucial determinants of forest structure and function.

We found that liana sapling abundances (30–100 cm height) increased by 86% in unfenced control plots with wildlife but were stable in exclosures. In contrast, tree abundances did not change in unfenced control plots but increased by 83% in exclosures without wildlife. Evidence of scaring on surviving stems suggested that these inverted outcomes were driven by selective use of tree saplings for wild pig nests. Lianas may also have greater tolerance to wildlife disturbances like nest building. By the end of the study, lianas comprised 38% of all saplings in unfenced controls but just 14% in exclosures.

Synthesis and applications. We conclude that artificially abundant wildlife, such as crop‐raiding wild pigs, may shift tropical forest understories towards lianas while defaunation may shift it towards trees. These results highlight that ecological cascades from hunting or land use change can alter plant functional types and reshape to long‐term patterns of forest succession and change. Managing unnatural wild boar populations may be required to conserve native plant communities in both their native and exotic ranges.
How Much Do Investors Pay for Houses?
Authors: Bracke Philippe 
Published: March 2019

AbstractI combine housing sales from the England and Wales Land Registry with online rental listings from property portal Zoopla to identify buy‐to‐rent transactions—known as buy‐to‐let (BTL) in the UK. These sales are procyclical, concentrated in areas where the housing market is performing well, and more common for small dwellings. Comparing these transactions against all other housing sales in 2009–2014, I show that BTL investors pay less than other buyers for the same properties. The heterogeneity of discounts across regions and property types is consistent with a simple theoretical framework that emphasizes the drivers of investors' and homeowners' demand for houses.
Prognosis for residual islet β‐cell secretion function in young patients with newly diagnosed type 1 diabetes
Authors: Miao Haitao , Zhang Juanjuan , Gu Bin , Gao Aibo , Hong Jie , Zhang Yifei , Gu Weiqiong 
Published: March 2019

AbstractBackgroundThis study investigated possible predictors of residual islet β‐cell function (RBF) in young patients with newly diagnosed type 1 diabetes (T1D).MethodsAfter analyzing RBF in 443 patients with T1D according to age at diagnosis and disease duration, 110 were followed‐up over 18‐60 months. A nomogram was developed by logistic regression to explore factors associated with long‐term RBF.ResultsOf the 443 T1D patients (mean [±SD] age 20.28 ± 5.50 years; mean [±SD] diabetes duration 28.5 ± 14.6 months), RBF was preserved in 64.3%. Independent predictors for poor RBF outcome among the 110 patients in the follow‐up cohort were age at onset (odds ratio [OR] 0.82; 95% confidence interval [CI] 0.73‐0.92; P < 0.001), high‐risk human leukocyte antigen (HLA) status (OR 4.73; CI 1.28‐17.52; P = 0.020), female sex (OR 3.39; CI 1.03‐11.22; P = 0.045), and a history of diabetic ketoacidosis (DKA; OR 8.71; CI 2.31‐32.83; P < 0.001). Baseline glutamic acid decarboxylase (GAD) antibody, family history of diabetes, body mass index, insulin dosage, and C‐peptide and HbA1c levels were not associated with poor RBF outcome. Intensive glycemic control after T1D diagnosis may improve RBF within a mean (±SD) follow‐up of 35.1 ± 13.8 months. The calibration plot for the probability of 2‐, 3‐, and 4‐year RBF showed optimal agreement between nomogram‐predicted and actual observed probabilities.ConclusionsYounger age of onset, female sex, higher HLA risk status, and a history of DKA were the main factors predicting long‐term poor preserved β‐cell function. Glycemic control could improve RBF during the course of diabetes. The nomogram provides an individualized risk estimate of RBF in patients with newly diagnosed T1D within Chinese Han populations.
Interleukin‐6 and interleukin‐17 are related to depression in patients with rheumatoid arthritis
Authors: Li Ya‐Chi , Chou Yu‐Ching , Chen Hsiang‐Cheng , Lu Chun‐Chi , Chang Deh‐Ming 
Published: March 2019

AbstractAimMood disorders are a serious issue for patients with rheumatoid arthritis (RA) because poor mental health can exacerbate the disease course. This study aimed to identify the effect of proinflammatory cytokines on the mood of patients with RA.MethodsThis study was conducted at a rheumatology clinic in Northern Taiwan. In total, 113 patients with RA and 42 healthy controls were assessed for anxiety and depression symptoms using Hospital Anxiety and Depression Scale (HADS). RA was assessed using the Disease Activity Score of 28 joints (DAS28). Serum proinflammatory cytokine levels, including interleukin (IL)‐1β, IL‐6, IL‐17 and tumor necrosis factor alpha (TNF‐α) were measured and compared between different patient groups according to disease activity and pain level.ResultsSerum IL‐1β, IL‐6, IL‐17 and TNF‐α levels were significantly higher in patients with RA than in healthy controls, as were the mean anxiety and depression subscale scores. In patients with RA who had different disease activities, pain severity correlated with both anxiety and depression symptoms. When HADS scores were analyzed according to pain levels, age was correlated with depression in the severe pain group. In the mild pain group, patients with higher IL‐6 or higher IL‐17 had a higher risk of depression. There was no correlation between mood symptoms and cytokine levels in healthy controls.ConclusionElevated serum IL‐6 and IL‐17 levels in patients with RA induce arthritis and cause mood symptoms, especially depression symptoms.