bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potential of Membranes Surrounding the Fetus as Immunoprotective Cell-Carriers for Allogeneic Transplantations
Authors: Togarrati Padma Priya , Dinglasan Nuntana , Yee Elizabeth , Heitman John W. , Jackman Rachael P. , Geisberg Mark , Norris Philip J. , Bárcena Alicia , Muench Marcus O. 
Published: June 2019

Background.
Membranes surrounding the fetus play a crucial role in providing a physical and immunological barrier between a semiallogeneic fetus and mother during pregnancy. In this study, we tested whether cotransplantation of fetal membranes (FMs) and allogeneic donor cells would improve the retention and function of allografts in mice.

Methods.
Intact and enzyme-digested membranes obtained from E18-E19 pregnant mice were subcutaneously cotransplanted with 10F7MN hybridoma cells that are of BALB/cByJ (Balb) origin and secrete anti-human CD235a antibody. Cells were transplanted into C57BL/6J (B6, allogeneic), Balb (syngeneic), and FVB/NJ (third-party) mice. Serum was collected after 1 and 3 weeks of cell transplantation and tested using flow cytometry for the presence of anti-human CD235a antibody. Immunosuppressive functions of membranes were further investigated by analyzing the cytokine profile of supernatants collected from allo-reactive mixed lymphocyte reactions (MLRs) using a multiplex cytokine assay.

Results.
B6 mice transplanted with 10F7MN cells along with membranes syngeneic to the host had significantly higher levels of CD235a antibody when compared to B6 mice that received cells without membranes, allogenic membranes, or third-party membranes. Syngeneic membranes significantly inhibited T-cell proliferation in the presence of allogeneic stimuli and suppressed the release of Th1-cytokines such as IFNγ, TNFα, and IL-2 in MLRs. Additionally, increases in the levels of Th2-cytokines were found in MLRs containing membrane-derived cells.

Conclusions.
Our study highlights the potential use of syngeneic FMs to act as potent cell-carriers that could improve graft retention as well as graft-specific immunoprotection during allograft transplantation.
Population genomics perspectives on convergent adaptation
Authors: Lee Kristin M. , Coop Graham 
Published: June 2019

Convergent adaptation is the independent evolution of similar traits conferring a fitness advantage in two or more lineages. Cases of convergent adaptation inform our ideas about the ecological and molecular basis of adaptation. In judging the degree to which putative cases of convergent adaptation provide an independent replication of the process of adaptation, it is necessary to establish the degree to which the evolutionary change is unexpected under null models and to show that selection has repeatedly, independently driven these changes. Here, we discuss the issues that arise from these questions particularly for closely related populations, where gene flow and standing variation add additional layers of complexity. We outline a conceptual framework to guide intuition as to the extent to which evolutionary change represents the independent gain of information owing to selection and show that this is a measure of how surprised we should be by convergence. Additionally, we summarize the ways population and quantitative genetics and genomics may help us address questions related to convergent adaptation, as well as open new questions and avenues of research.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
Ecological factors and morphological traits are associated with repeated genomic differentiation between lake and stream stickleback
Authors: Rennison Diana J. , Stuart Yoel E. , Bolnick Daniel I. , Peichel Catherine L. 
Published: June 2019

The repeated evolution of similar phenotypes in independent populations (i.e. parallel or convergent evolution) provides an opportunity to identify genetic and ecological factors that influence the process of adaptation. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model for such studies, as they have repeatedly adapted to divergent habitats across the Northern hemisphere. Here, we use genomic, ecological and morphological data from 16 independent pairs of stickleback populations adapted to divergent lake and stream habitats. We combine a population genomic approach to identify regions of the genome that are likely under selection in these divergent habitats with an association mapping approach to identify regions of the genome that underlie variation in ecological factors and morphological traits. Over 37% of genomic windows are repeatedly differentiated across lake–stream pairs. Similarly, many genomic windows are associated with variation in abiotic factors, diet items and morphological phenotypes. Both the highly differentiated windows and candidate trait windows are non-randomly distributed across the genome and show some overlap. However, the overlap is not significant on a genome-wide scale. Together, our data suggest that adaptation to divergent food resources and predation regimes are drivers of differentiation in lake–stream stickleback, but that additional ecological factors are also important.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
Parallelism and convergence in post-domestication adaptation in cereal grasses
Authors: Woodhouse M. R. , Hufford M. B. 
Published: June 2019

The selection of desirable traits in crops during domestication has been well studied. Many crops share a suite of modified phenotypic characteristics collectively known as the domestication syndrome. In this sense, crops have convergently evolved. Previous work has demonstrated that, at least in some instances, convergence for domestication traits has been achieved through parallel molecular means. However, both demography and selection during domestication may have placed limits on evolutionary potential and reduced opportunities for convergent adaptation during post-domestication migration to new environments. Here we review current knowledge regarding trait convergence in the cereal grasses and consider whether the complexity and dynamism of cereal genomes (e.g., transposable elements, polyploidy, genome size) helped these species overcome potential limitations owing to domestication and achieve broad subsequent adaptation, in many cases through parallel means.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution
Authors: Lamichhaney Sangeet , Card Daren C. , Grayson Phil , Tonini João F. R. , Bravo Gustavo A. , Näpflin Kathrin , Termignoni-Garcia Flavia , Torres Christopher , Burbrink Frank , Clarke Julia A. , Sackton Timothy B. , Edwards Scott V. 
Published: June 2019

Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
Limits in the detection of m6A changes using MeRIP/m6A-seq
Authors: McIntyre Alexa B.R. , Gokhale Nandan S. , Cerchietti Leandro , Jaffrey Samie R. , Horner Stacy M. , Mason Christopher E. 
Published: June 2019

AbstractMany cellular mRNAs contain the modified base m6A, and recent studies have suggested that various stimuli can lead to changes in m6A. The most common method to map m6A and to predict changes in m6A between conditions is methylated RNA immunoprecipitation sequencing (MeRIP-seq), through which methylated regions are detected as peaks in transcript coverage from immunoprecipitated RNA relative to input RNA. Here, we generated replicate controls and reanalyzed published MeRIP-seq data to estimate reproducibility across experiments. We found that m6A peak overlap in mRNAs varies from ∼30 to 60% between studies, even in the same cell type. We then assessed statistical methods to detect changes in m6A peaks as distinct from changes in gene expression. However, from these published data sets, we detected few changes under most conditions and were unable to detect consistent changes across studies of similar stimuli. Overall, our work identifies limits to MeRIP-seq reproducibility in the detection both of peaks and of peak changes and proposes improved approaches for analysis of peak changes.
Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition
Authors: Potok Magdalena E. , Wang Yafei , Xu Linhao , Zhong Zhenhui , Liu Wanlu , Feng Suhua , Naranbaatar Bilguudei , Rayatpisheh Shima , Wang Zonghua , Wohlschlegel James A. , Ausin Israel , Jacobsen Steven E. 
Published: June 2019

AbstractDeposition of the histone variant H2A.Z by the SWI2/SNF2-Related 1 chromatin remodeling complex (SWR1-C) is important for gene regulation in eukaryotes, but the composition of the Arabidopsis SWR1-C has not been thoroughly characterized. Here identify interacting partners of a conserved Arabidopsis SWR1 subunit, ACTIN-RELATED PROTEIN 6 (ARP6). We isolated nine predicted components, and identified additional interactors implicated in histone acetylation and chromatin biology. One of the novel interacting partners, methyl-CpG-binding domain 9 (MBD9), also strongly interacted with the Imitation SWItch (ISWI) chromatin remodeling complex. MBD9 was required for deposition of H2A.Z at a distinct subset of ARP6-dependent loci. MBD9 was preferentially bound to nucleosome-depleted regions at the 5’ ends of genes containing high levels of activating histone marks. These data suggest that MBD9 is a SWR1-C interacting protein required for H2A.Z deposition at a subset of actively transcribing genes.
Metastable neural dynamics underlies cognitive performance across multiple behavioural paradigms
Authors: Alderson Thomas H. , Bokde Arun L.W. , Kelso J.A.Scott. , Maguire Liam , Coyle Damien 
Published: June 2019

AbstractDespite resting state networks being associated with a variety of cognitive abilities, it remains unclear how these local areas act in concert to express particular cognitive operations. Theoretical and empirical accounts indicate that large-scale resting state networks reconcile dual tendencies toward integration and segregation by operating in a metastable regime of their coordination dynamics. One proposal is that metastability confers important behavioural qualities by dynamically binding distributed local areas into large-scale neurocognitive entities. We tested this hypothesis by analysing fMRI data in a large cohort of healthy individuals (N=566) and comparing the metastability of the brain’s large-scale resting network architecture at rest and during the performance of several tasks. Task-based reasoning was principally characterised by high metastability in cognitive control networks and low metastability in sensory processing areas. Although metastability between resting state networks increased during task performance, cognitive ability was more closely linked to spontaneous activity. High metastability in the intrinsic connectivity of cognitive control networks was linked to novel problem solving (or fluid intelligence) but was less important in tasks relying on prior experience (or crystallised intelligence). Crucially, subjects with resting architectures similar or ‘pre-configured’ to a task-general arrangement demonstrated superior cognitive performance. Taken together, our findings support a critical linkage between the spontaneous metastability of the large-scale networks of the cerebral cortex and cognition.
Mitochondria-ER contacts in reactive astrocytes coordinate local perivascular domains to promote vascular remodelling
Authors: Goebel Jana , Engelhardt Esther , Pelzer Patric , Sakthivelu Vignesh , Jahn Hannah M. , Jevtic Milica , Folz-Donahue Kat , Kukat Christian , Schauss Astrid , Frese Christian K. , Giavalisco Patrick , Ghanem Alexander , Conzelmann Karl-Klaus , Motori Elisa , Bergami Matteo 
Published: June 2019

SummaryAstrocytes have emerged for playing important roles in brain tissue repair, however the underlying mechanisms remain poorly understood. We show that acute injury and blood-brain barrier disruption trigger the formation of a prominent mitochondrial-enriched compartment in astrocytic end-feet which enables vascular remodeling. Integrated imaging approaches revealed that this mitochondrial clustering is part of an adaptive response regulated by fusion dynamics. Astrocyte-specific conditional deletion of Mitofusin 2 (Mfn2) suppressed perivascular mitochondrial clustering and disrupted mitochondria-ER contact sites. Functionally, two-photon imaging experiments showed that these structural changes were mirrored by impaired mitochondrial Ca2+ uptake leading to abnormal cytosolic transients within end-feet in vivo. At the tissue level, a compromised vascular complexity in the lesioned area was restored by boosting mitochondrial-ER perivascular tethering in MFN2-deficient astrocytes. These data unmask a crucial role for mitochondrial dynamics in coordinating astrocytic local domains and have important implications for repairing the injured brain.
Chinese consumer trust and preferences for organic labels from different regions
Authors: Chen Mo , Wang Yiqin , Yin Shijiu , Hu Wuyang , Han Fei 
Published: June 2019

Purpose
The organic food sold in China can bear organic labels from different countries/regions. The purpose of this paper is to assess the trust and preferences of consumers for tomatoes carrying these different labels.

Design/methodology/approach
The data came from real choice experiments conducted in Shandong Province, China. A mixed logit model was used to analyze consumer willingness to pay (WTP).

Findings
Results indicated that, among the four organic labels considered in this study, the highest WTP was expressed for organic label from the European Union, followed by Hong Kong’s organic label, Japanese organic label and, lastly, by the Chinese mainland organic label. Consumer trust has a positive effect on their WTPs for the four organic labels. Providing consumers with information on organic can significantly lift their WTPs, and reduce the gaps between WTPs for different organic labels.

Originality/value
This research is of academic value and of value to food suppliers. International food marketers are recommended to equip their products with proper organic labels and initiate additional consumer education.
Phenolic profile of three wild edible mushroom extracts from Ordu, Turkey and their antioxidant properties, enzyme inhibitory activities
Authors: Çol Ayvaz Melek , Aksu Figen , Kır Filiz 
Published: June 2019

PurposeMushrooms have always been treasured and appreciated, thanks to their nutritional as well as medicinal properties. The purpose of this paper is to reveal these properties such as antioxidant activities and enzyme inhibition potentials of three mushroom species from Ordu, Turkey. Furthermore, phenolic profiles which are believed to be source of these properties are investigated.Design/methodology/approachThe assays followed to determine total phenolic, flavonoid and antioxidant contents, antioxidative and enzyme inhibition activities are spectrophotometric methods. Phenolic profiles of mushroom samples were investigated by using the HPLC system.FindingsThe highest phenolic content was found forLactarius deliciosus. Pyrogallol was the major phenolics in all three samples. Total phenolic content values supported that finding. But, total flavonoid content was the maximum forCantharellus cibarius. The magnitude of the antioxidant activities revealed by the different tests varied between species. Furthermore, inhibition potential degrees on acetylcholinesterase, butrylcholinesterase, tyrosinase and urease activities were worth mentioning.Lactarius pyrogalushad anti-tyrosinase activity with a 26.229 percent inhibition rate. IC50values for urease inhibition effect of mushroom samples were in the range of 0.37–0.90 mg/mL.Originality/valueEnzyme inhibitory potentials forL. pyrogaluswas revealed first time. On the other hand, studies on anti-tyrosinase activity of mushrooms are very rare, while almost no studies have been conducted on anti-urease activity. So, the results of present study are very valuable. Thus, the obtained data not only increase the ecological importance of the region but also provide significant contributions to the literature in terms of new sources rich in antioxidants.
Parents’ and kids’ eating away from home cognitions
Authors: Eck Kaitlyn M. , Delaney Colleen , Olfert Melissa D. , Hagedorn Rebecca L. , Leary Miriam P. , Santella Madison E. , Clark Rashel L. , Famodu Oluremi A. , Shelnutt Karla P. , Byrd-Bredbenner Carol 
Published: June 2019

Purpose
Eating away from home frequency is increasing and is linked with numerous adverse health outcomes. The purpose of this paper is to inform the development of health promotion materials for improving eating away from home behaviors by elucidating related parent and child cognitions.

Design/methodology/approach
Parents (n=37) and children (n=35; ages 6–11 years) participated in focus group discussions, based on social cognitive theory. Data were content analyzed to detect themes.

Findings
Many parents were concerned about what children ate away from home, however, others were less concerned because these occasions were infrequent. Lack of time and busy schedules were the most common barriers to eating fewer meals away from home. The greatest barrier to ensuring children ate healthfully away from home was parents were not present to monitor children’s intake. To overcome this, parents supervised what kids packed for lunch, provided caregivers instruction on foods to provide, and taught kids to make healthy choices. Kids understood that frequently eating away from home resulted in less healthful behaviors. Barriers for kids to eat healthy when away from home were tempting foods and eating in places with easy access to less healthy food. Kids reported they could take responsibility by requesting healthy foods and asking parents to help them eat healthfully away from home by providing healthy options and guidance.

Originality/value
This study is one of the first to qualitatively analyze parent and child eating away from home cognitions. It provides insights for tailoring nutrition education interventions to be more responsive to these audiences’ needs.
Off-farm income and food expenditure of rural households in China
Authors: Liu Yuying , Renwick Alan , Fu Xinhong 
Published: June 2019

Purpose
The purpose of this paper is to examine the impact of off-farm income on food expenditure, using survey data of 493 rural households from Gansu, Henan and Shandong provinces in China.

Design/methodology/approach
A two-stage least squares estimator is used to jointly estimate the determinants of off-farm income and the direct impact of off-farm income on food expenditure while controlling for the endogeneity issue associated with off-farm income variable.

Findings
The empirical results show that gender, education of household head, household size, farm size, the presence of children, smartphone use and asset ownership mainly determine off-farm income, and the off-farm income affects food expenditure of rural households significantly. In particular, the results show that a 1,000 yuan increase in per capita off-farm income increases per capita food expenditure by 61 yuan. Further estimations reveal that off-farm income has a larger effect on food expenditure of high-income rural households relative to their low-income counterparts.

Originality/value
Although poverty implications of off-farm income have been well documented, few studies have analysed the effects of off-farm income on food expenditure of rural households. To the best of the authors’ knowledge, there are no studies on this issue that focus on rural China. Therefore, the present study attempts to provide a first insight into the association between off-farm income and food expenditure of rural households in China, with the aim of providing useful evidence for policymakers in their efforts to reduce rural and urban food consumption gap and further increase social welfare.
Nutritional knowledge, attitude, and use of food labels among Indian adults with multiple chronic conditions
Authors: Limbu Yam B. , McKinley Christopher , Gautam Rajesh K. , Ahirwar Ajay K. , Dubey Pragya , Jayachandran C. 
Published: June 2019

Purpose
The purpose of this paper is to examine the indirect effects of nutritional knowledge and attitude toward food label use on food label use through self-efficacy and trust, as well as whether gender moderates this relationship.

Design/methodology/approach
A sample of Indian adults with multiple chronic conditions was surveyed about their nutritional knowledge, attitude, self-efficacy and use of food labels. Hypotheses were tested using Hayes’s (2013) PROCESS macro for SPSS.

Findings
The results show that nutritional knowledge and attitude toward food label use positively predict food label use through self-efficacy and trust. However, these mediation effects are moderated by gender such that the indirect relationship is stronger among men than women.

Practical implications
Food marketers and government agencies engaged in nutrition education campaigns should aim to increase patients’ confidence in comprehending food label information.

Social implications
Since food labels can be a valuable tool to help patients with chronic diseases to make informed decisions about their diet and lifestyle, regulators may consider mandating nutritional labels on foods to help them improve their food or dietary choices.

Originality/value
This study uniquely applies Fisher and Fisher’s (1992) information–motivation–behavioral skills model as a theoretical framework to examine the influence of nutrition knowledge and attitude toward food label use on food label usage of Indian patients with multiple chronic diseases.