bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular machinery of auxin synthesis, secretion, and perception in the unicellular chlorophyte algaChlorella sorokinianaUTEX 1230
Authors: Khasin Maya , Cahoon Rebecca R. , Nickerson Kenneth W. , Riekhof Wayne R. 
Published: August 2017

AbstractIndole-3-acetic acid is a ubiquitous small molecule found in all domains of life. It is the predominant and most active auxin in seed plants, where it coordinates a variety of complex growth and development processes. The potential origin of auxin signaling in algae remains a matter of some controversy. In order to clarify the evolutionary context of algal auxin signaling, we undertook a genomic survey to assess whether auxin acts as a signaling molecule in the emerging model chlorophyteChlorella sorokinianaUTEX 1230.C. sorokinianaproduces the auxin indole-3-acetic acid (IAA), which was present in both the cell pellet and in the supernatant at a concentration of ~ 1 nM, and its genome encodes orthologs of genes related to auxin synthesis, transport, and signaling in higher plants. Candidate orthologs for the canonical AUX/IAA signaling pathway were not found; however, auxin-binding protein 1 (ABP1), an alternate auxin receptor, is present and highly conserved at essential auxin binding and zinc coordinating residues. Additionally, candidate orthologs for PIN proteins, responsible for intercellular, vectorial auxin transport in higher plants, were not found, but PILs (PIN-Like) proteins, a recently discovered family that mediates intracellular auxin transport, were identified. The distribution of auxin related gene in this unicellular chlorophyte demonstrates that a core suite of auxin signaling components was present early in the evolution of plants. Understanding the simplified auxin signaling pathways in chlorophytes will aid in understanding phytohormone signaling and crosstalk in seed plants, and in understanding the diversification and integration of developmental signals during the evolution of multicellular plants.
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
Authors: Miao Zhun , Deng Ke , Wang Xiaowo , Zhang Xuegong 
Published: August 2017

AbstractSummaryThe excessive amount of zeros in single-cell RNA-seq data include “real” zeros due to the on-off nature of gene transcription in single cells and “dropout” zeros due to technical reasons. Existing differential expression (DE) analysis methods cannot distinguish these two types of zeros. We developed an R package DEsingle which employed Zero-Inflated Negative Binomial model to estimate the proportion of real and dropout zeros and to define and detect 3 types of DE genes in single-cell RNA-seq data with higher accuracy.Availability and ImplementationThe R package DEsingle is freely available athttps://github.com/miaozhun/DEsingleand is under Bioconductor’s consideration now.Contactzhangxg@tsinghua.edu.cnSupplementary informationSupplementary data are available atbioRxivonline.
Whole exome sequencing of ENU-induced thrombosis modifier mutations in the mouse
Authors: Tomberg Kärt , Westrick Randal J. , Kotnik Emilee N. , Siemieniak David R , Zhu Guojing , Saunders Thomas L. , Cleuren Audrey C. , Ginsburg David 
Published: August 2017

AbstractAlthough the Factor V Leiden (FVL) gene variant is the most prevalent genetic risk factor for venous thrombosis, only 10% of FVL carriers will experience such an event in their lifetime. To identify potential FVL modifier genes contributing to this incomplete penetrance, we took advantage of a perinatal synthetic lethal thrombosis phenotype in mice homozygous for FVL (F5L/L) and haploinsufficient for tissue factor pathway inhibitor (Tfpi+/-) to perform a sensitized dominant ENU mutagenesis screen. Linkage analysis conducted in the 3 largest pedigrees generated from the survivingF5L/LTfpi+/-mice (‘rescues’) using ENU-induced coding variants as genetic markers was unsuccessful in identifying major suppressor loci. Whole exome sequencing was applied to DNA from 107 rescue mice to identify candidate genes enriched for ENU mutations. A total of 3,481 potentially deleterious candidate ENU variants were identified in 2,984 genes. After correcting for gene size and multiple testing,Arl6ip5was identified as the most enriched gene, though not reaching genome-wide significance. Evaluation of CRISPR/Cas9 induced loss of function in the top 6 genes failed to demonstrate a clear rescue phenotype. However, a maternally inherited (not ENU-induced)de novomutation (Plcb4R335Q) exhibited significant co-segregation with the rescue phenotype (p=0.003) in the corresponding pedigree. Thrombosis suppression by heterozygousPlcb4loss of function was confirmed through analysis of an independent, CRISPR/Cas9-inducedPlcb4mutation (p=0.01).Author summaryAbnormal blood clotting in veins (venous thrombosis) or arteries (arterial thrombosis) are major health problems, with venous thrombosis affecting approximately 1 in every thousand individuals annually in the United States. Susceptibility to venous thrombosis is governed by both genes and environment, with approximately 60% of the risk attributed to genetic influences. Though several genetic risk factors are known, >50% of genetic risk remains unexplained. Approximately 5% of people carry the most common known risk factor, Factor V Leiden. However, only 10% of these individuals will develop a blood clot in their lifetime. Mice carrying two copies of the Factor V Leiden mutation together with a mutation in a second gene called tissue factor pathway inhibitor develop fatal thrombosis shortly after birth. To identify genes that prevent this fatal thrombosis, we studied a large panel of mice carrying inactivating gene changes randomly distributed throughout the genome. We identified several genes as potential candidates to alter blood clotting balance in mice and humans with predisposition to thrombosis, and confirmed this protective function for DNA changes in one of these genes (Plcb4).
nextPARS: Parallel probing of RNA structures in Illumina
Authors: Saus Ester , Willis Jesse , Pryszcz Leszek P. , Himmelbauer Heinz , Gabaldón Toni 
Published: August 2017

ABSTRACTRNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining the secondary structures of RNAs is central to understanding their function and evolution. In recent years several sequencing-based approaches have been developed that allow probing structural features of thousands of RNA molecules present in a sample. Here, we describe nextPARS, a novel Illumina-based implementation ofin-vitroparallel probing of RNA structures. Our approach achieves comparable accuracy to previous implementations, while enabling higher throughput and sample multiplexing.
Hundreds of Putative Non-Coding Cis-Regulatory Drivers in Chronic Lymphocytic Leukaemia and Skin Cancer
Authors: Ongen Halit , Delaneau Olivier , Stevens Michael W. , Howald Cedric , Dermitzakis Emmanouil T. 
Published: August 2017

ABSTRACTPerturbations of the coding genome and their role in cancer development have been studied extensively. However, the non-coding genome’s contribution in cancer is poorly understood (1), not only because it is difficult to define the non-coding regulatory regions and the genes they regulate, but also because there is limited power owing to the regulatory regions’ small size. In this study, we try to resolve this issue by defining modules of coordinated non-coding regulatory regions of genes (Cis Regulatory Domains or CRDs). To do so, we use the correlation between histone modifications, assayed by ChIP-seq, in population samples of immortalized B-cells and skin fibroblasts. We screen for CRDs that accumulate an excess of somatic mutations in chronic lymphocytic leukaemia (CLL) and skin cancer, which affect these cell types, after accounting for somatic mutational patterns and biases. At 5% FDR, we find 90 CRDs with significant excess somatic of mutations in CLL, 60 of which regulate 126 genes, and in skin cancer 59 significant CRDs, 25 of which regulate 37 genes. The genes these CRDs regulate include ones already implicated in tumorigenesis, and are enriched in pathways already implicated in the respective cancers, like the B-cell receptor signalling pathway in CLL and the TGFβ signalling pathway in skin cancer. We discover that the somatic mutations in the significant CRDs of CLL are hitting bases more likely to be functional than the mutations in non-significant CRDs. Moreover, in both cancers, mutational signatures observed in the regulatory regions of significant CRDs deviate significantly from their null sequences. Both results indicate selection acting on CRDs during tumorigenesis. Finally, we find that the transcription factor biding sites that are disturbed by the somatic mutations in significant CRDs are enriched for factors known to be involved in cancer development. We are describing a new powerful approach to discover non-coding regions involved in tumorigenesis in CLL and skin cancer and this approach could be generalized to other cancers.
Rhythms of the Body, Rhythms of the Brain: Respiration, Neural Oscillations, and Embodied Cognition
Authors: Varga Somogy , Heck Detlef H. 
Published: August 2017

AbstractIn spite of its importance as a life-defining rhythmic movement and its constant rhythmic contraction and relaxation of the body, respiration has not received attention in Embodied Cognition (EC) literature. Our paper aims to show that (1) respiration exerts significant and unexpected bottom-up influence on cognitive processes, and (2) it does so by modulating neural synchronization that underlies specific cognitive processes. Then, (3) we suggest that the particular example of respiration may function as a model for a general mechanism through which the body influences cognitive functioning. Finally, (4) we work out the implications for embodied cognition, draw a parallel to the role of gesture, and argue that respiration sometimes plays a double, pragmatic and epistemic, role, which reduces the cognitive load. In such cases, consistent with EC, the overall cognitive activity includes a loop-like interaction between neural and non-neural elements. (141 words)
Punishing tax offenders in France and Great Britain: two criminal policies
Authors: Weidenfeld Katia , Spire Alexis 
Published: August 2017

Purpose
Since 2008-2009, the governments in France and Great Britain have encouraged more rigorous penalization of tax evaders. This paper aims to investigate the implementation of these policies on the basis of an important and original empirical material.

Design/methodology/approach
The study done in France relies on interviews conducted with representatives of law enforcement agencies on public statistics and on an innovative database compiled from nearly 600 cases submitted to the judiciary. The comparison with Great Britain is developed through interviews conducted with different participants in the fight against tax fraud and statistical information.

Findings
This paper describes the recent evolution of the machinery for screening tax-related wrongdoings in France and in the UK. It demonstrates that whilst publicly calling for harsh punishment against tax dodgers, in practice, both governments tend to seek a balance between the growing demand for tax equality and the belief that the State should not intervene in the economic realm. This strategy leads to the over-representation of certain categories of taxpayers. Despite the commonalities resulting from the numerous filters before prosecution, the penal strategy takes on two different shapes on either side of the Channel: whereas the British institutions support an “exemplary punitive” system, French regulatory system favours a “quasi-administrative” treatment. The French tax authority continues to use the criminal procedures mainly as a financial instrument for the improved restitution of stolen taxes. The policy of Her Majesty’s Revenue and Customs, supported by the “Sentencing Guidelines”, aims much more at obtaining exemplary convictions.

Originality/value
Based on a large empirical material, this paper highlights the different outcomes of the criminal trials against tax evaders in the two countries.
Develop the recruitment criteria for professionalisation of politicians: a focus to group study
Authors: Ukwatta Wijayantha 
Published: August 2017

Purpose
The purpose of this study is to identify the fundamental elements necessary for formulating criteria to be used when recruiting politicians into the Sri Lankan political system with a view to professionalization. By means of a thorough examination of political practice issues, the paper focuses on the possibility of introducing the concept of political professionalization and endeavors to determine the prerequisite conditions needed to resolve or minimize those issues.

Design/methodology/approach
A total of 27 respondents: academics, clergy and journalists were purposively selected for this study and they were divided into three groups to enable data collection through focus group discussions. A thematic analysis method was used to analyze the data.

Findings
The main political practice problems were bribery and corruption, the misuse of state resources by politicians, the involvement of family in politics, and unscrupulous and unethical political campaigning. The majority of respondents cited greed for political power, low levels of education and an inadequate understanding of the parliamentary process as the leading factors which cause problems to arise in politics as practiced in Sri Lanka. The analysis revealed three main themes: “knowledge”, “skills” and “values”. Respondents recommended policy initiatives for political recruitment.

Originality/value
The findings suggested that the professionalization of political practice should be promoted by introducing knowledge C skills and values as criteria for political recruitment. And it also suggested that the introduction of professional political practice methods is vitally necessary to reduce political practice issues in the current political scenario of Sri Lanka.
Learning disability market position statements, are they fit for purpose?
Authors: Broadhurst Sarah , Landau Keri 
Published: August 2017

Purpose
The purpose of this paper is to review whether current learning disability market position statements (MPS) are actually helping to shape the market and explore their implications for people with learning disabilities and their families.

Design/methodology/approach
Published learning disability MPS were identified via the Institute of Public Care’s MPS database. The quality of the MPS was analysed using a good practice checklist developed by a range of stakeholders.

Findings
Learning disability MPS are not currently fit for purpose. They demonstrate that local authorities are not fully engaging in their market-shaping duties, as required under The Care Act 2014. It is suggested that this is in part due to the lack of recognition that market shaping is a council-wide responsibility and can only be successful if senior officers across the council (and their partners) acknowledge this and are held accountable. Unless this happens, people with learning disabilities will continue to lack the enablers that support them to lead the lives they choose in their communities.

Originality/value
This is the first review of the quality and potential impact of learning disability MPS.
Minority Interest Nation: The Changing Contours of Reporting Scotland on BBC and STV
Authors: Hassan Gerry 
Published: August 2017

AbstractScotland's media has traditionally provided one of the central aspects of Scottish distinctiveness, autonomy and identity. This has often historically been viewed unproblematically and uncritically, but in recent times, the selective discourses of the mainstream media have come under increasing scrutiny and challenge, particularly in the recent independence referendum.This article examines the changing output of BBC and STV, considering in detail the evening news and current affairs programmes of both channels, and charting how they have evolved in media content and output. It also examines wider output and representation by BBC and STV, and concludes by addressing the evolving political and media environment.
Appearance and Textural Properties of Sheared Low Concentration Potato Protein Gels—Impact of Drying Method, pH, and Ionic Strength
Authors: Schmidt Jesper Malling , Larsen Lotte Bach , Hammershøj Marianne 
Published: August 2017

AbstractThe objective was to prepare sheared gels of potato protein concentrate and evaluate the effect of pH (3, ∼4, ∼7), ionic strength (15 or 200 mM) and protein drying conditions (spray or freeze drying) on the final appearance and rheological characteristics. Heat‐set gels 3 % (w/w) at a high ionic strength (200 mM) resulted in an inhomogeneous appearance with presence of clots, while low ionic strength (15 mM) gave homogenous structures. Gels prepared at pH 3 became transparent while preparation above pH 3.0 resulted in high turbidity. Heat treatment and cooling resulted in gelation for all samples except freeze dried powder at pH 3.0. Flow curves during shear from 0.1 to 100 s−1 were fitted by the Herschel–Bulkley model indicating shear thinning behavior for all samples except the freeze dried sample at pH 3 which displayed a Newtonian behavior. Oscillatory measurements after shear indicated viscus behavior (phase angle above 45°) for the spray dried sample at pH 3, and gelled behavior (phase angle above 45°) for the remaining gelled samples. Structure recovery was observed after shear in all samples except at pH 3.0. The data shows potato protein can be used as ingredient in protein beverages.
Optimization of Ripe Olive Processing with a Single Lye Treatment
Authors: Brenes Manuel , Romero Concepción , García‐García Pedro 
Published: August 2017

AbstractThe development of a method for darkening black ripe olives during the washing step with a single NaOH treatment and preservation liquid was studied. Olives of the Hojiblanca cultivar were darkened at pilot plant scale, packed, sterilized, and analyzed after 2 mo of storage at ambient temperature. It was found that the use of a mixture of preservation liquid:water at a ratio of 1:1 during the first washing gave rise to darker olives with slightly better firmness and no effect on sensory quality. However, care must be taken with the concentration of acetic acid in the preservation solution, as a content of this organic acid higher than 25 g/L can cause adverse effects on olive color due to the low pH that can be reached in the flesh of the fruit. Additionally, the re‐use of the preservation solution in the first washing resulted in enrichment in antioxidant compounds of the packed product. Black ripe olives processed with preservation liquid had a total phenolic content of 629 mg/kg, whereas those with only tap water had 376 mg/kg, in particular hydroxytyrosol and hydroxytyrosol‐4‐glucoside. These findings mean that it is possible to get darker olives with higher contents in bioactive substances by reusing the preservation liquid during the darkening step of black ripe olives.
Effects of intrinsic sources of spatial autocorrelation on spatial regression modelling
Authors: Teng Shuqing N. , Xu Chi , Sandel Brody , Svenning Jens‐Christian 
Published: August 2017

Abstract

Detecting and dealing with spatial autocorrelation (SA) are indispensable steps in analyses of geospatial data. Despite consensus that SA originates from both extrinsic factors and intrinsic interactions, previous studies on regression analysis of spatially autocorrelated data have rarely controlled for intrinsic sources in addition to extrinsic ones to assess ceteris paribus (i.e. causal) effects of interest, with the strict exogeneity assumption that errors containing unexplained variance are uncorrelated with explanatory variables for all observations. This assumption becomes invalid when intrinsic SA is not an external process modelled as errors and needs to be controlled for.

Here, we aimed to assess the extent to which not controlling for intrinsic SA negatively affects model performance, specifically in terms of type I error rate and unbiasedness of coefficient estimates, and to identify models that are able to handle these problems. To this end, we applied two categories of regression models that do (intrinsic category) or do not (extrinsic category) explicitly control for intrinsic SA to artificial data generated with both SA sources. These models included the extended spatial Durbin model (ESDM) and its nested models. Four analytic scenarios simulated modelling conditions with increasing complexity of variables omitted during modelling. The two more complex scenarios involved additional violations of strict exogeneity.

We found that intrinsic—just as extrinsic—SA can produce incorrect type I error rates, if not explicitly controlled for. Failing to control for intrinsic SA also generated bias in estimates of ceteris paribus effects. However, ESDM from the intrinsic category exhibited consistently good performance in dealing with intrinsic SA across all the scenarios, but suffered other violations of strict exogeneity.

Overall, model specification should control for both extrinsic and intrinsic processes generating SA in spatial data to provide reliable type I error rates and unbiased estimates of ceteris paribus effects. Given the likely widespread occurrence in observational spatial data of unknown or unmeasurable processes, ESDM should be a generally preferred starting point to explore the optimal model specification for estimating ceteris paribus effects, with due caution to other violations of strict exogeneity.
What constitutes ‘good practice’ in early intervention for psychosis? Analysis of clinical guidelines
Authors: Corsico Paolo , Griffin‐Doyle Michelle , Singh Ilina 
Published: August 2017

BackgroundEarly Intervention in Psychosis (EIP) services have been implemented with the dual aims of preventing harmful outcomes associated with early‐onset psychosis and improving prognosis. However, concerns have been raised regarding the ethical implications of involving young people inEIPservices. One way to ensure high ethical standards and promote good practice inEIPdelivery is through governance of clinical practice. This study aimed to investigate the normative dimensions of good practice inEIPthrough examination of clinical guideline documents published in England over the past 15 years.MethodsA total of 14 clinical guidelines and relevant policy documents forEIPwere retrieved and analysed using a mixed inductive and deductive thematic approach. Themes were derived from the data itself, whereas the development of broader categories was performed through a constant comparison with the scientific literature describing ethical issues inEIP.ResultsEthical touchpoints of good practice inEIPincluded both procedural and substantive factors, which were seen to be interdependent and mutually constitutive. These ethical touchpoints were largely implicit in the documents analysed. Procedural requirements ofEIPservice delivery consisted of norms and rules pertaining toEIPservice structure, adherence to codes of ethics, inclusivity, patient and family centredness and appropriate treatment provision. Substantive factors consisted of moral attributes that should be cultivated by healthcare professionals working inEIP: competency, empathy, sensitivity and trustworthiness.ConclusionsWe argue that, to ensure good practice inEIP, procedural and substantive ethical expectations embedded inEIPguideline documents should be made explicit inEIPservice and care delivery. We suggest that the procedural and substantive factors highlighted in this paper contribute useful dimensions for the eventual evaluation of good practice inEIPservices across England.