bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urbanization and its Impact on Ghana’s Rural Transformation
Authors: Diao Xinshen , Magalhaes Eduardo , Silver Jed 
Published: October 2019

Abstract
Urbanization without industrialization is a major feature in Ghana, as elsewhere in much of Africa. This chapter explores how urbanization in Ghana has affected agricultural development in terms of rural employment, the farm size distribution, and use of modern inputs. In examining these relationships, the authors recognize that there have been distinct spatial patterns of urbanization in Ghana, and urbanization has not affected agriculture equally throughout the country. Therefore, the chapter develops a spatial typology of seven types of districts based on their city population size and location in the north or south of the country and examines the share of households employed in agriculture, nonagriculture, or both across these different district types. The findings illustrate that urbanization is increasing the share of rural households in the nonfarm economy, and contributed to a shift towards more medium-sized farms in the agriculturally important areas of the north. The chapter further tests the induced innovation hypothesis, which predicts that urbanization and associated increases in population density and market access should lead to more intensive farming practices. The findings show though that while there has been substantial uptake of fertilizers, herbicides, and mechanization in recent years, there is only limited support that this has been driven by urbanization.
Developing Agricultural Value Chains
Authors: Kolavalli Shashidhara 
Published: October 2019

Abstract
This chapter asks how can agricultural value chains be further developed in Ghana given prevailing market failure problems that constrain the private sector from playing a greater role. Using first the experience of public interventions in the cocoa subsector through the Ghana Cocoa Board, the chapter evaluates how interventions in three other value chains compare: pineapples, rice, and tomatoes. These latter three crops have under-exploited opportunities because of the inability of farmers to produce sufficient amounts of high-quality farm products that meet urban market, agro-processor, and export demands. This is due to a lack of better seed varieties, an absence of quality control through grading and pricing along value chains, inadequate post-harvest handling, and few large-scale agribusinesses willing or able to take the lead in developing new export markets. The findings reveal opportunities and constraints along the value chains of these commodities, identifies the roles that the public sector should ideally play and, in turn, analyzes whether it has the capacity to feasibly do so.
Vicarious Narratives
Authors: Britton Jeanne M. 
Published: October 2019

Abstract
In 1759, Adam Smith’s Theory of Moral Sentiments defines sympathy as a series of shifts in perspective by which one sees from a different point of view. British and French novels published over the following century redefine sympathy through narrative form—shifting perspectives or “stories within stories” in which one character adopts the voice and perspective of another. Fiction follows Smith’s emphasis on sympathy’s shifting perspectives, but this formal echo coincides with a challenge. For Smith and other Enlightenment philosophers, the experience of sympathy relies on human resemblance. In novels, by contrast, characters who are separated by nationality, race, or species experience a version of sympathy that struggles to accommodate such differences. Encounters between these characters produce shifts in perspective or framed tales as one character sympathizes with another and begins to tell his story, echoing Smith’s definition of sympathy in their form while challenging Enlightenment philosophy’s insistence on human resemblance. Works of sentimental and gothic fiction published between 1750 and 1850 generate a novelistic version of sympathy by manipulating traditional narrative forms (epistolary fiction, embedded tales) and new publication practices (the anthology, the novelistic extract). Second-hand stories transform the vocal mobility, emotional immediacy, and multiple perspectives associated with the declining genre of epistolary fiction into the narrative levels and shifting speakers of nineteenth-century frame tales. Vicarious Narratives argues that fiction redefines sympathy as the struggle to overcome difference through the active engagement with narrative—by listening to, retelling, and transcribing the stories of others.
It is not all about performance: Importance of the funding formula in the allocation of performance-based research funding in England
Authors: Pinar Mehmet 
Published: October 2019

AbstractPerformance-based research funding systems have become popular over the last decades. One of the main reasons for these funding systems is to allow funding bodies to allocate public research funds more effectively based on the assessed quality. However, the performance-based research funding received by higher education institutes (HEIs) not only depends on the quality of research activity carried out but also on the funding formula used by funding bodies. This article examines the funding formula used by Research England (RE) and assesses the effect of this formula on quality-related research (QR) funding allocation using data of mainstream QR funding allocation for the 2017–18 period. RE’s funding formula includes some value judgements by policymakers such as allocation of fourfold QR funding to ‘world-leading’ research compared to ‘internationally-excellent’ research, and the use of different subject cost weights. These value judgements play an important role in the allocation of QR funding beyond the assessed quality of research. This article finds that changes in some of these value judgments such as allocation of threefold (rather than fourfold) QR funding to world-leading research compared to internationally excellent research, or the use of alternative subject cost weights lead to major changes in the allocation of QR funding to different subject areas and HEIs. Results suggest that these value judgments are also important beyond the assessed quality of research, and that consultation of different subject areas and HEIs about these decisions and re-evaluation of some of these value judgements are needed for a more accountable distribution of QR funding.
Direct medical costs of hospitalized patients with idiopathic pulmonary fibrosis in China
Authors: Zheng Xiaofen , Xie Bingbing , Liu Yan , Zhu Ming , Zhang Shu , Ban Chengjun , Geng Jing , Jiang Dingyuan , Ren Yanhong , Dai Huaping , Wang Chen 
Published: October 2019

AbstractBackgroundIdiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrosing interstitial pneumonia of unknown cause. The incidence of IPF is increasing year by year, as well as the mortality rates, which is really a burden both for the family and the society. However few data concerning the economic burden of the patients with IPF is available, especially in China.ObjectiveThis study aimed to examine the direct medical costs of hospitalized patients with IPF and to determine the contributing factors.MethodsThis retrospective analysis used the cost-of-illness framework in order to analyze the direct medical costs of patients with IPF. The study used data from the pneumology department of Beijing Chao-Yang Hospital affiliated to Capital Medical University from year 2012 to 2015. The direct medical costs included drug fee, auxiliary examination fee, treatment fee and other fee. Patients’ characteristics, medical treatment, and the direct medical costs were analyzed by descriptive statistics and multivariable regression.ResultsThere were 219 hospitalized patients meeting the diagnosis of IPF, 91% male. The mean age was 65 years old. For the direct medical costs of hospitalized patients with IPF, the mean(SD) of the total costs per IPF patient per admission was 14882.3 (30975.8)CNY. The largest parts were the examination fee of 6034.5 (15651.2)CNY and the drug fee of 5048.9 (3855.1)CNY. By regression analysis we found that length of stay, emergency treatment, ventilator use and being a Beijing native were significantly (P<0.05) associated with total hospitalization costs, and the length of stay had the biggest impact. Complications or comorbidities contributated to the direct medical costs as follows: respiratory failure with 30898.3CNY (P=0.004), pulmonary arterial hypertension(PAH) with 26898.2CNY (P=0.098), emphysema with 25368.3CNY (P=0.033), and high blood pressure with 24659.4CNY (P=0.026). Using DLCO or DLCO% pred to reflect the severity of IPF, there was no significant correlation between DLCO or DLCO% pred and patients’ direct medical costs. While, the worse the diffusion function, the higher the drug fee.ConclusionThis study showed that IPF has a major impact on the direct medical costs. Thus, appropriate long-term interventions are recommended to lower the economic burden of IPF.Strengths and limitations of this studyIt was the first time in China to discuss the economic burden of diseases and its influencing factors in patients with IPF.The results of this study might be of reference for the establishment of IPF disease-related medical policies in future.The retrospective cross-sectional design does not allow for establishing any causal relationships.It was a a single-center study, resulting a slightly smaller sample size. A large sample of multicenter studies is needed to confirm this.
Increased ultra-rare variant load in an isolated Scottish population impacts exonic and regulatory regions
Authors: Halachev Mihail , Meynert Alison , Taylor Martin S , Vitart Veronique , Kerr Shona M , Klaric Lucija ,   SGP Consortium, Aitman Timothy J , Haley Chris S , Prendergast James G , Pugh Carys , Hume David A , Harris Sarah E , Liewald David C , Deary Ian J , Semple Colin A , Wilson James F 
Published: October 2019

AbstractHuman population isolates provide a snapshot of the impact of historical demographic processes on population genetics. Such data facilitate studies of the functional impact of rare sequence variants on biomedical phenotypes, as strong genetic drift can result in higher frequencies of variants that are otherwise rare. We present the first whole genome sequencing (WGS) study of the VIKING cohort, a representative collection of samples from the isolated Shetland population in northern Scotland, and explore how its genetic characteristics compare to a mainland Scottish population. Our analyses reveal the strong contributions played by the founder effect and genetic drift in shaping genomic variation in the VIKING cohort. About one tenth of all high-quality variants discovered are unique to the VIKING cohort or are seen at frequencies at least ten fold higher than in more cosmopolitan control populations. Multiple lines of evidence also suggest relaxation of purifying selection during the evolutionary history of the Shetland isolate. We demonstrate enrichment of ultra-rare VIKING variants in exonic regions and for the first time we also show that ultra-rare variants are enriched within regulatory regions, particularly promoters, suggesting that gene expression patterns may diverge relatively rapidly in human isolates.Author SummaryPopulation isolates provide a valuable window on the roles of rare genetic variation in human phenotypes, as a result of their unusual evolutionary histories, that often lead to relatively high frequencies of variants that are exceptionally rare elsewhere. Such populations show increased levels of background relatedness among individuals and are often subject to stronger genetic drift, leading to a higher frequency of deleterious variants. Here, for the first time, we present whole genome sequencing data from the Shetland population in Northern Scotland, encompassing 500 individuals, and compare these genomes to the mainland Scottish population. As expected we find the imprint of Shetland population history in the Shetland genome, with strong evidence for founder effects and genetic drift, but we also discover a relaxation of selective constraint across the genome. These influences have combined to endow the Shetland genome with thousands of ultra-rare genetic variants, not observed previously in other populations. Surprisingly these variants are significantly enriched in functional regions including protein coding regions of genes and regulatory elements. Among regulatory regions, promoters are particularly enriched for ultra-rare variants, suggesting the potential for rapid divergence of gene expression in isolates.
CPlantBox, a whole plant modelling framework for the simulation of water and carbon related processes
Authors: Zhou Xiao-Ran , Schnepf Andrea , Vanderborght Jan , Leitner Daniel , Lacointe André , Vereecken Harry , Lobet Guillaume 
Published: October 2019

AbstractThe interaction between carbon and flows within the plant is at the center of most growth and developmental processes. Understanding how these fluxes influence each other, and how they respond to heterogeneous environmental conditions, is important to answer diverse questions in forest, agriculture and environmental sciences. However, due to the high complexity of the plant-environment system, specific tools are needed to perform such quantitative analyses.Here we present CPlantBox, full plant modelling framework based on the root system model CRootBox. CPlantbox is capable of simulating the growth and development of a variety of plant architectures (root and shoot). In addition, the flexibility of CPlantBox enables its coupling with external modeling tools. Here, we connected it to an existing mechanistic model of water and carbon flows in the plant, PiafMunch.The usefulness of the CPlantBox modelling framework is exemplified in four case studies. Firstly, we illustrate the range of plant structures that can be simulated using CPlantBox. In the second example, we simulated diurnal carbon and water flows, which corroborates published experimental data. In the third case study, we simulated impacts of heterogeneous environment on carbon and water flows. Finally, we showed that our modelling framework can be used to fit phloem pressure and flow speed to (published) experimental data.The CPlantBox modelling framework is open-source, highly accessible and flexible. Its aim is to provide a quantitative framework for the understanding of plant-environment interaction.
An integrated platform to systematically identify causal variants and genes for polygenic human traits
Authors: Downes Damien J. , Schwessinger Ron , Hill Stephanie J. , Nussbaum Lea , Scott Caroline , Gosden Matthew E. , Hirschfeld Priscila P. , Telenius Jelena M. , Eijsbouts Chris Q. , McGowan Simon J. , Cutler Antony J. , Kerry Jon , Davies Jessica L. , Dendrou Calliope A. , Inshaw Jamie R.J. , Larke Martin S.C. , Marieke Oudelaar A. , Bozhilov Yavor , King Andrew J. , Brown Richard C. , Suciu Maria C. , Davies James O.J. , Hublitz Philip , Fisher Chris , Kurita Ryo , Nakamura Yukio , Lunter Gerton , Taylor Stephen , Buckle Veronica J. , Todd John A. , Higgs Douglas R. , Hughes Jim R. 
Published: October 2019

ABSTRACTGenome-wide association studies (GWAS) have identified over 150,000 links between common genetic variants and human traits or complex diseases. Over 80% of these associations map to polymorphisms in non-coding DNA. Therefore, the challenge is to identify disease-causing variants, the genes they affect, and the cells in which these effects occur. We have developed a platform using ATAC-seq, DNaseI footprints, NG Capture-C and machine learning to address this challenge. Applying this approach to red blood cell traits identifies a significant proportion of known causative variants and their effector genes, which we show can be validated by direct in vivo modelling.
On the relation of phase separation and Hi-C maps to epigenetics
Authors: Singh Prim B. , Newman Andrew G. 
Published: October 2019

AbstractThe relationship between compartmentalisation of the genome and epigenetics is long and hoary. In 1928 Heitz defined heterochromatin as the largest differentiated chromatin compartment in eukaryotic nuclei. Müller’s (1930) discovery of position-effect variegation (PEV) went on to show that heterochromatin is a cytologically-visible state of heritable (epigenetic) gene repression. Current insights into compartmentalisation have come from a high-throughput top-down approach where contact frequency (Hi-C) maps revealed the presence of compartmental domains that segregate the genome into heterochromatin and euchromatin. It has been argued that the compartmentalisation seen in Hi-C maps is due to the physiochemical process of phase separation. Oddly, the insights provided by these experimental and conceptual advances have remained largely silent on how Hi-C maps and phase separation relate to epigenetics. Addressing this issue directly in mammals, we have made use of a bottom-up approach starting with the hallmarks of constitutive heterochromatin, heterochromatin protein 1 (HP1) and its binding partner the H3K9me2/3 determinant of the histone code. They are key epigenetic regulators in eukaryotes. Both hallmarks are also found outside mammalian constitutive heterochromatin as constituents of larger (0.1-5Mb) heterochromatin-likedomains and smaller (less than 100Kb) complexes. The well-documented ability of HP1 proteins to function as bridges between H3K9me2/3-marked nucleosomes enables cross-linking within and between chromatin fibres that contributes to polymer-polymer phase separation (PPPS) that packages epigenetically-heritable chromatin states during interphase. Contacts mediated by HP1 “bridging” are likely to have been detected in Hi-C maps, as evidenced by the B4 heterochromatic sub-compartment that emerges from contacts between large KRAB-ZNF heterochromatin-likedomains. Further, mutational analyses have revealed a finer, innate, compartmentalisation in Hi-C experiments that likely reflect contacts involving smaller domains/complexes. Proteins that bridge (modified) DNA and histones in nucleosomal fibres – where the HP1-H3K9me2/3 interaction represents the most evolutionarily-conserved paradigm – could drive and generate the fundamental compartmentalisation of the interphase nucleus. This has implications for the mechanism(s) that maintains cellular identity, be it a terminally-differentiated fibroblast or a pluripotent embryonic stem cell.
A sparse observation model to quantify species interactions in time and space
Authors: Ait Kaci Azzou Sadoune , Singer Liam , Aebischer Thierry , Caduff Madleina , Wolf Beat , Wegmann Daniel 
Published: October 2019

SummaryCamera traps and acoustic recording devices are essential tools to quantify the distribution, abundance and behavior of mobile species. Varying detection probabilities among device locations must be accounted for when analyzing such data, which is generally done using occupancy models. We introduce a Bayesian Time-dependent Observation Model for Camera Trap data (Tomcat), suited to estimate relative event densities in space and time.Tomcatallows to learn about the environmental requirements and daily activity patterns of species while accounting for imperfect detection. It further implements a sparse model that deals well will a large number of potentially highly correlated environmental variables. By integrating both spatial and temporal information, we extend the notation of overlap coefficient between species to time and space to study niche partitioning. We illustrate the power ofTomcatthrough an application to camera trap data of eight sympatrically occurring duikerCephalophinaespecies in the savanna - rainforest ecotone in the Central African Republic and show that most species pairs show little overlap. Exceptions are those for which one species is very rare, likely as a result of direct competition.
Transduction of mechanical cellular oscillation by the plasma-membrane mechanosensitive channel MSL10
Authors: Tran Daniel , Girault Tiffanie , Guichard Marjorie , Thomine Sébastien , Leblanc-Fournier Nathalie , Moulia Bruno , de Langre Emmanuel , Allain Jean-Marc , Frachisse Jean-Marie 
Published: October 2019

AbstractThroughout their life, plants are submitted to recurrent cyclic mechanical loading due to wind. The resulting passive oscillation movements of stem and foliage is an important phenomenon for biological and ecological issues such as photosynthesis optimization 1–3 and thermal exchange 4. The induced motions at plant scale are well described and analyzed, with oscillations at typically 1 to 3 Hz in trees 5–10. However, the cellular perception and transduction of such recurring mechanical signals remains an open question. Multimeric protein complexes forming mechanosensitive (MS) channels embedded in the membrane provide an efficient system to rapidly convert mechanical tension into electrical signal 11. Here we show that the plasma membrane mechanosensitive channel MscS-LIKE 10 (MSL10) from the model plant Arabidopsis thaliana responds to pulsed membrane stretching with rapid activation and relaxation kinetics in the range of one second. Under sinusoidal membrane stretching MSL10 presents a greater activity than under static stimulation and behaves as a large bandpass oscillation “follower” without filtering the signal in the range of 0.3 to 3 Hz. With a localization in aerial organs naturally submitted to oscillations, our results suggest that the mechanosensitive channel MSL10 represents a molecular component of a universal system of oscillatory perception in plants.
The BIR2/BIR3-interacting Phospholipase D gamma 1 negatively regulates immunity in Arabidopsis
Authors: Schlöffel Maria A. , Salzer Andrea , Wan Wei-Lin , van Wijk Ringo , Šemanjski Maja , Symeonidi Efthymia , Slaby Peter , Kilian Joachim , Maček Boris , Munnik Teun , Gust Andrea A. 
Published: October 2019

ABSTRACTPlants have evolved effective strategies to defend themselves against pathogen invasion. Starting from the plasma membrane with the recognition of microbe-associated molecular patterns (MAMPs) via pattern recognition receptors, internal cellular signaling pathways are induced to ultimately fend off the attack. Phospholipase D (PLD) hydrolyzes membrane phospholipids to produce phosphatidic acid (PA), which has been proposed to play a second messenger role in immunity. The Arabidopsis PLD family consists of 12 members and for some a specific function in resistance towards a subset of pathogens has been shown. We demonstrate here that Arabidopsis PLDγ1, but not its close homologs PLDγ2 and PLDγ3, is specifically involved in plant immunity. Genetic inactivation of PLDγ1 resulted in increased resistance towards the virulent bacterium Pseudomonas syringae pv. tomato DC3000 and the necrotrophic fungus Botrytis cinerea. As pldγ1 mutant plants responded with elevated levels of reactive oxygen species to MAMP-treatment, a negative regulatory function for this PLD isoform is proposed. Importantly, PA levels in pldγ1 mutants were not affected compared to stressed wild-type plants, suggesting that alterations in PA levels are unlikely the cause for the enhanced immunity in the pldγ1 line. Instead, the plasma-membrane-attached PLDγ1 protein colocalized and associated with the receptor-like kinases BIR2 and BIR3, which are known negative regulators of pattern-triggered immunity. Moreover, complex formation of PLDγ1 and BIR2 was further promoted upon MAMP-treatment. Hence, we propose that PLDγ1 acts as a negative regulator of plant immune responses in complex with immunity-related proteins BIR2 and BIR3.One-sentence summaryA phospholipase D is a novel negative regulator of plant immunity and forms complexes with regulatory receptor-like kinases.