bluuebunny/crossref_metadata_2025_split huggingface dataset:
A structural equation model for imaging genetics using spatial transcriptomics
Authors: Huisman Sjoerd M.H. , Mahfouz Ahmed , Batmanghelich Nematollah K. , Lelieveldt Boudewijn P.F. , Reinders Marcel J.T. 
Published: January 2018

AbstractAlzheimer’s disease is a neurodegenerative disorder that causes changes in the structure of the brain, observable with MRI scans, and that has a strong heritable component, reflected in the DNA. Imaging genetics deals with such relationships between genetic variation and imaging variables, often in a disease context. The complex relationships between brain volumes and genetic variants have been explored both with dimension reduction methods and model based approaches. However, these models usually do not make use of the extensive knowledge of the spatio-anatomical patterns of gene activity. We present a method for integrating genetic markers (single nucleotide polymorphisms) and imaging features, which is based on a causal model and, at the same time, uses the power of dimension reduction. We use structural equation models to find latent variables that explain brain volume changes in a disease context, and which are in turn affected by genetic variants. We make use of publicly available spatial transcriptome data from the Allen Human Brain Atlas to specify the model structure, which reduces noise and improves interpretability. The model is tested in a simulation setting, and applied on a case study of the Alzheimer’s Disease Neuroimaging Initiative.
Loss of mCHH islands in maize chromomethylase and DDM1-type nucleosome remodeler mutants
Authors: Fu Fang-Fang , Dawe R. Kelly , Gent Jonathan I. 
Published: January 2018

ABSTRACTPlants make use of three types of DNA methylation, each characterized by distinct DNA methyltransferases. One type, RNA-directed DNA methylation (RdDM), is guided by siRNAs to the edges of transposons that are close to genes, areas called mCHH islands in maize. Another type, chromomethylation, is guided by histone H3 lysine 9 methylation to heterochromatin across the genome. We examined DNA methylation and small RNA expression in plant tissues that were mutant for both copies of the genes encoding chromomethylases as well as mutants for both copies of the genes encoding DDM1-type nucleosome remodelers, which facilitate chromomethylation. Both sets of double mutants were nonviable but produced embryos and endosperm. RdDM was severely compromised in the double mutant embryos, both in terms of DNA methylation and siRNAs. Loss of 24nt siRNA from mCHH islands was coupled with a gain of 21, 22, and 24nt siRNAs in heterochromatin. These results reveal a requirement for both chromomethylation and DDM1-type nucleosome remodeling for RdDM in mCHH islands, which we hypothesize is due to dilution of RdDM components across the genome when heterochromatin is compromised.
PIN7 auxin carrier is a terminator of radial root expansion inArabidopsis thaliana
Authors: Ruiz Rosquete Michel , Kleine-Vehn Jürgen 
Published: January 2018

AbstractDirectional growth of lateral roots is critical for radial expansion and soil coverage. Despite its importance, almost nothing is known about its molecular determinants. Initially, young lateral roots (LRs) grow away from the parental root maintaining the angle acquired shortly after emergence. A second downwards bending response to gravity terminates the so-called plateau phase and thereby limits the radial root expansion. Here we show that the exit from the plateau phase correlates with an increase in auxin signalling at the tip of LRs. Moreover, the increase in auxin levels induces the termination of the plateau phase, which requires PIN auxin efflux carriers. Our data suggests that the developmental increase of auxin triggers the preferential de-repression of PIN7 in gravity-sensing columella cells. The subsequent polarization of PIN7 heralds the bending towards gravity and, hence, the exit from the plateau phase. This developmental framework reveals the distinct roles of PIN auxin efflux carriers in controlling the radial growth of root systems.
Conditional Upregulation of KCC2 selectively enhances neuronal inhibition during seizures
Authors: Goulton CS , Watanabe M , Cheung DL , Wang KW , Oba T , Khoshaba A , Lai D , Inada H , Eto K , Nakamura K , Power JM , Lewis TM , Housley GD , Wake H , Nabekura J , Moorhouse AJ 
Published: January 2018

Abstract/SummaryEfficacious neuronal inhibition is sustained by the neuronal K+Cl- co-transporter KCC2, and loss of KCC2 function through injury or mutation is associated with altered GABAergic signalling and neuronal seizures. Here we report a transgenic mouse with conditional KCC2 overexpression that results in increased membrane transport function. Increased KCC2 has little impact on behavioural and in vitro assays of neuronal excitability and GABAA receptor responses under resting conditions. In contrast, increased KCC2 imparts resistance to seizure-like neuronal activity in hippocampal slices and prevents the progression of mice into behavioural status epilepticus following multiple kainic acid doses. Our results demonstrate a transgenic mouse to facilitate investigations into the role of KCC2 in brain function, and provide a proof of principle that targeting KCC2 may be an effective way to selectively enhance neuronal inhibition to mitigate against diseases that involve an imbalance between excitation and inhibition.
Patterns of microsatellite distribution reflect the evolution of biological complexity
Authors: Srivastava Surabhi , Avvaru Akshay Kumar , Sowpati Divya Tej , Mishra Rakesh K 
Published: January 2018

AbstractMicrosatellites, also known as Simple Sequence Repeats (SSRs), are evolutionarily conserved repeat elements distributed non-randomly in all genomes. Many studies have investigated their pattern of occurrence in order to understand their role, but their identification has largely been non-exhaustive and limited to a few related species or model organisms. Here, we identify ~685 million microsatellites from 719 eukaryotes and analyze their evolutionary trends from protists to mammals. We document novel patterns uniquely demarcating closely related species, including in pathogens like Leishmania as well as in higher organisms such as Drosophila, birds, primates, and cereal crops. The distribution of SSRs in coding and non-coding regions reveals taxon-specific variations in their exonic, intronic and intergenic densities. We also show that specific SSRs accumulate at longer lengths in higher organisms indicating an evolutionary selection pressure. In general, we observe greater constraints in the SSR composition of multicellular organisms with complex cell types, while simpler organisms show more diversity. The conserved microsatellite trends and species-specific signatures identified in this study closely mirror phylogenetic relationships and we hypothesize that SSRs are integral components in speciation and the evolution of organismal complexity. The microsatellite dataset generated in this work provides a large number of candidates for functional analysis and unparalleled scope for understanding their roles across the evolutionary landscape.
Assembly and validation of conserved long non-coding RNAs in the ruminant transcriptome
Authors: Bush Stephen J. , Muriuki Charity , McCulloch Mary E. B. , Farquhar Iseabail L. , Clark Emily L. , Hume David A. 
Published: January 2018

AbstractmRNA-like long non-coding RNAs (lncRNA) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. In many cases, therefore, lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNA, we comparedde novoassembled lncRNA derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNA assembled in cattle and human. Few lncRNA could be reproducibly assembled from a single dataset, even with deep sequencing of the same tissues from multiple animals. Furthermore, there was little sequence overlap between lncRNA assembled from pooled RNA-seq data. We combined positional conservation (synteny) with cross-species mapping of candidate lncRNA to identify a consensus set of ruminant lncRNA and then used the RNA-seq data to demonstrate detectable and reproducible expression in each species. The majority of lncRNA were encoded by single exons, and expressed at < 1 TPM. In sheep, 20-30% of lncRNA had expression profiles significantly correlated with neighbouring protein-coding genes, suggesting association with enhancers. Alongside substantially expanding the ruminant lncRNA repertoire, the outcomes of our analysis demonstrate that stochastic sampling can be partly overcome by combining RNA-seq datasets from related species. This has practical implications for the future discovery of lncRNA in other species.
Core Proteome and Architecture of COPI Vesicles
Authors: Rhiel Manuel , Hessling Bernd , Gao Qi , Hellwig Andrea , Adolf Frank , Wieland Felix T. 
Published: January 2018

AbstractRetrieval of escaped ER-residents and intra-Golgi transport is facilitated by coat protein complex I (COPI)-coated vesicles. Their formation requires the activated small GTPase ADP-ribosylation factor (Arf) and the coat complex coatomer. Here we assess the protein composition of COPI vesicles by combining stable isotope labeling with amino acids in cell culture (SILAC) within vitroreconstitution of COPI vesicles from semi-intact cells (SIC) using the minimal set of recombinant coat proteins. This approach yields an unbiased picture of the proteome of these carriers. We define a set of ~40 proteins common to COPI vesicles produced from different human as well as murine cell lines. Almost allbona fideCOPI vesicle proteins are either ER-Golgi cycling proteins or Golgi-residents, while only a minor portion of secreted proteins was found. Moreover, we have investigated a putative role of γ- and ζ-COP as well as Arf isoforms in sorting and recruitment of specific proteins into COPI vesicles. As opposed to the related COPII system, all isoforms of coatomer and all COPI-forming isoforms of the small GTPase Arf produce COPI-coated vesicles with strikingly similar protein compositions. We present a model for the core architecture of COPI vesicles.
Ecological feedback on diffusion dynamics
Authors: Park Hye Jin , Gokhale Chaitanya S. 
Published: January 2018

AbstractSpatial patterns are ubiquitous across different scales of organization. Animal coat pattern, spatial organization of insect colonies, and vegetation in arid areas are prominent examples from such diverse ecologies. Typically, pattern formation has been described by reaction-diffusion equations, which considers individuals dispersing between sub-populations of a global pool. This framework applied to public goods game nicely showed the endurance of populations via diffusion and generation of spatial patterns. However, how the spatial characteristics, such as diffusion, are related to the eco-evolutionary process as well as the nature of the feedback from evolution to ecology and vice versa, has been so far neglected. We present a thorough analysis of the ecologically driven evolutionary dynamics in a spatially extended version of ecological public goods games. We show how these evolutionary dynamics feedback into shaping the ecology thus together determining the fate of the system.
Reduced-nutrient leachates in cash cover crop-soybean systems
Authors: Thom Matthew D. , Forcella Frank , Eberle Carrie A. , Matthees Heather L. , Weyers Sharon L. , Gesch Russ W. , Ott Matthew A. , Feyereisen Gary W. , Strock Jeffrey S. , Wyse Don 
Published: January 2018

AbstractOver-wintering crops are known to reduce nutrients in soil leachate in spring, but little economic incentive is available to grow these crops in the Upper Midwest. New oilseed-bearing cash cover crops, such as winter camelina and pennycress, may provide the needed incentives. However, the abilities of these crops to sequester labile soil nutrients are unknown. We used lysimeters buried at 30, 60, and 100 cm to examine nitrate and soil reactive phosphorus (SRP) in six soybean cropping system treatments: clean till, no-till, and autumn-seeded radish, winter rye, pennycress, and winter camelina. Radish winter-killed naturally, winter rye was killed with a glyphosate, and pennycress and winter camelina were allowed to mature naturally after relay sowing of soybean. Leachate chemistry was studied for the autumn, spring, and summer periods over two growing season. In autumn, leachates under radish and winter rye tended to have the lowest nitrate levels. In spring, differences among nitrate levels across treatments were greater than at any other time period, with values much lower under pennycress and winter camelina treatments than other treatments. In summer, nitrate levels were more uniform, with the lowest values occurring where soybean grew best. In general, cash cover crops like pennycress and winter camelina provide both environmental and economic resources to growers in that they represent cash-generating grain crops that sequester labile soil nutrients, especially in spring, and protect and promote soil health from autumn through early summer.
Xylanase B fromClostridium cellulovorans743B: overexpression, purification, crystallization and X-ray diffraction analysis
Authors: Nakajima Daichi , Nagano Akihiko , Shibata Toshiyuki , Tanaka Reiji , Kuroda Kouichi , Ueda Mitsuyoshi , Miyake Hideo 
Published: January 2018

Clostridium cellulovoransproduces multi-enzyme complexes called cellulosomes capable of efficiently degrading cellulosic biomass. There are three xylanase genes containing a sequence corresponding to a dockerin domain that are necessary for constructing cellulosomes in the genome. Among the xylanases encoded by these genes, xylanase B (XynB) contains a catalytic domain belonging to glycoside hydrolase family 10 and a carbohydrate-binding module (CBM) at the N-terminus, making it a member of CBM family 22. In this study, XynB was cloned, overexpressed, purified and crystallized. XynB was crystallized using the hanging-drop vapour-diffusion method in the presence of 0.2 Msodium acetate trihydrate, 0.1 MTris–HCl pH 8.5, 32%(w/v) PEG 4000 at 293 K. X-ray diffraction analysis revealed that the crystal diffracted to 1.95 Å resolution and belonged to space groupP212121, with unit-cell parametersa = 74.28,b= 77.55,c= 88.20 Å, α = β = γ = 90°. The data-evaluation statistics revealed high quality of the collected data, thereby establishing a solid basis for determination of the structure of cellulosomal xylanase fromC. cellulovorans.
Destination website quality, users’ attitudes and the willingness to participate in online co-creation experiences
Authors: Jiménez-Barreto Jano , Campo-Martínez Sara 
Published: January 2018

PurposeAn official destination website (ODW) is a key component for tourist’s decision-making processes. ODW acts as a direct channel where users may share experiences and opinions about previous or future travels. At the same time, it drives user participation in destination branding activities. In this context, it is crucial to identify how the destination website, using Web 2.0 technologies, could motivate user’s participation with the brand. The purpose of this paper is to propose and evaluate a model that posits the destination website quality as a determinant factor to predict users’ attitudes toward the website and their willingness to participate in co-creation experiences.Design/methodology/approachUsing a combined qualitative and quantitative method, this paper provides an exploratory research that examines the role of destination website quality on attitudes toward the website and the willingness to participate in online co-creation experiences.FindingsFindings confirm that there is a direct and significant relationship between website quality, attitudes toward the website and willingness to participate in online co-creation experiences. Moreover, attitudes toward the website partially mediate relationships between destination website quality and willingness to participate in online co-creation experiences.Originality/valueThe literature of value co-creation is trying to identify which factors drive consumer’s participation with brands across different consumption contexts. This study provides evidence that confirms, from a tourism destination website point of view, that website quality is one of these key factors that motives user’s co-creation with a destination.
Constructing an index to examine house price misalignment with fundamentals in Malta
Authors: Micallef Brian 
Published: January 2018

Purpose
The purpose of this paper is to compute an aggregate misalignment index using a multiple indicator approach to identify under- or over-valuation of house prices in Malta based on fundamentals.

Design/methodology/approach
A total of six indicators are used that capture households, investors and system-wide factors: the house price-to-Retail Price Index ratio, the price-to-hypothetical borrowing volume ratio, price-to-construction costs ratio, price-to-rent ratio, dwelling investment-to-GDP ratio and the loan bearing capacity. The weights are derived using principal component analysis. The analysis is performed using both the house price indices of the National Statistics Office (NSO) and the Central Bank of Malta (CBM), which are based on contract and advertised prices, respectively.

Findings
House prices in Malta were overvalued by around 20 to 25 per cent in the pre-crisis boom. This disequilibrium started to be corrected following the decline in house prices, with the CBM and NSO house price cycles reaching a trough in 2013 and 2014, respectively. At the trough, house prices were undervalued by around 10 to 15 per cent. Since then, house prices started to recover although the recovery in advertised prices was more pronounced compared to that based on contract prices. In mid-2017, advertised house prices were slightly overvalued, while contract prices still have to reach their equilibrium level. The dynamics from the misalignment index, including its peaks and troughs, are remarkably similar to the range derived from statistical filters.

Practical implications
Estimates of house price misalignment have both economic and financial stability implications.

Originality/value
This paper allows for a decomposition of the house price cycle, tailored for the particular characteristics of the Maltese housing market. It also takes into account the relationship between house prices and private sector rents, which in recent years have been buoyed, among other factors, by the high inflow of foreign workers and changing patterns in the tourism industry.
Health promotion in a prison setting: an exploratory study on why and how to do it
Authors: de Castro Rodrigues Andreia , Jólluskin Glória , Silva Isabel 
Published: January 2018

Purpose
Developing interventions in challenging contexts should imply proper discussion from its theoretical framework to implementation details. The purpose of this paper is to examine health promotion in prison settings as a mean of improving inmates’ rights concerning physical/emotional well-being, empowering inmates both to reclusion and re-entry challenges.

Design/methodology/approach
The development of a health promotion program, implemented in a prison setting with an initial group of 11 inmates, is described. The program design followed professionals’ and inmates’ inputs and previous similar interventions taking a peer education, community-based and participative approach.

Findings
Although some prison settings present major constraints to interventions’ development, the authors were able to perform the program and reinforced the idea that prisons can and should be health-promoting contexts. The authors found several specific needs that must be addressed when people are under custody, if we want imprisonment to be developmental instead of detrimental experiences.

Research limitations/implications
As a single-year-funded program, its replication and valid evaluation were enabled. Being external to the system also complicated the process agility, and conditioned inmates’ selection and compliance.

Practical implications
This paper promotes a best-practices forum in this issue; it addresses prison health agents’ training, who may assume an institutional essential role; it concerns inmates’ rehabilitation and ultimately, community health and safety.

Originality/value
The use of a peer education approach in these contexts is an innovative feature, since it has been developed in other institutional contexts and social groups. Nevertheless, the authors maintain the strong adequacy of this methodology to work with inmates and inside prison settings.
Dayah collectively as a social movement
Authors: Hanafiah Hanafiah 
Published: January 2018

Purpose
The purpose of this paper is to explore, find and formulate a mechanism and strategy in social process in Dayah, which can be developed to be a model of new social process applied in public school.

Design/methodology/approach
The main objective of this research was to examine the strategy and mechanism of social reproduction in Dayah. The strategy and mechanism of social reproduction in public schools were also observed for comparison. The public schools were high school or vocational high school equivalent to the class in Dayah Mudi Mesra. The selected high schools as the object of comparison were SMAN 1 Samalanga and SMAN 2 Tanjungan, Samalanga. The selected public schools were public schools with similar sociological and psychological background and culture with Dayah Samalanga. This study is a social study using a qualitative approach with phenomenological design. The method used is the case study method; case studies are used as a comprehensive explanation related to the various aspects of a person, group, organization, program, or community situation that is studied, attempted and explored as deeply as possible.

Findings
Dayah with Islamic culture promises an effective social movement in Acehnese society. Dayah potential power was on the agents or social actor as the initiators of the idea of the creation of a network of social movements among Dayahs in Aceh. The stages of the creation of a social movement until movement crystallization can be modelled by utilizing their expert elite agents that are owned by Dayah in Aceh which is the intellectual elites and clerical elites. In addition, Dayah is a form of Acehnese local wisdom in education and religion that enables social movements to walk more naturally, democratically and educationally. Dayah ability related to Islamic culture as a broader social movement even has been tested at the level of the state and the nation of Indonesia. It is indicated by the creation of democratic process in Indonesia, which is activated by a community of Islam with democratic values as religion doctrine. As social movements, religious communities are able to construct perceptions, thoughts and attitudes in the lower class in response to the post-Suharto democratic change. Collins mentioned that social movements, which are derived from Islamic organizations, are able to show their presence at the local and national level.

Originality/value
The sociological wisdom is its unique social process. Based on preliminary studies, social processes in Dayah are closely related to the cosmopolitan value of Islam. This cosmopolitan value appears in the social order in the Dayah subculture, which appears to be more open to the role of the individual in society as an agent who can achieve a new social class. In this case, Dayah education can be a counter attack against negative social reproduction trends in general education.