bluuebunny/crossref_metadata_2025_split huggingface dataset:
Leopard: fast decoding cell type-specific transcription factor binding landscape at single-nucleotide resolution
Authors: Li Hongyang , Guan Yuanfang 
Published: November 2019

AbstractDecoding the cell type-specific transcription factor (TF) binding landscape at single-nucleotide resolution is crucial for understanding the regulatory mechanisms underlying many fundamental biological processes and human diseases. However, limits on time and resources restrict the high-resolution experimental measurements of TF binding profiles of all possible TF-cell type combinations. Previous computational approaches either can not distinguish the cell-context-dependent TF binding profiles across diverse cell types, or only provide a relatively low-resolution prediction. Here we present a novel deep learning approach, Leopard, for predicting TF-binding sites at single-nucleotide resolution, achieving the median area under receiver operating characteristic curve (AUROC) of 0.994. Our method substantially outperformed state-of-the-art methods Anchor and FactorNet, improving the performance by 19% and 27% respectively despite evaluated at a lower resolution. Meanwhile, by leveraging a many-to-many neural network architecture, Leopard features hundred-fold to thousand-fold speedup compared to current many-to-one machine learning methods.
ALTERED MERISTEM PROGRAM1regulates leaf identity independent of miR156-mediated translational repression
Authors: Fouracre Jim P. , Chen Victoria J. , Poethig R. Scott 
Published: November 2019

AbstractInArabidopsis, loss of the carboxypeptidase, ALTERED MERISTEM PROGRAM1 (AMP1), produces an increase in the rate of leaf initiation, an enlarged shoot apical meristem and an increase in the number of juvenile leaves. This phenotype is also observed in plants with reduced levels of miR156-targetedSQUAMOSA PROMOTER BINDING PROTEIN-LIKE(SPL) transcription factors, suggesting that AMP1 may promote SPL activity. However, we found that theamp1phenotype is only partially corrected by elevatedSPLgene expression, and thatamp1has no significant effect onSPLtranscript levels, or on the level or the activity of miR156. Although evidence from a previous study suggests that AMP1 promotes miRNA-mediated translational repression,amp1did not prevent the translational repression of the miR156 target,SPL9, or the miR159 target,MYB33.These results suggest thatAMP1regulates vegetative phase change downstream of, or in parallel to, the miR156/SPLpathway and that it is not universally required for miRNA-mediated translational repression.Summary statementWe show that loss of the carboxypeptidase, AMP1, does not interfere with the function of miR156 or miR159, suggesting that AMP1 is not universally required for miRNA-mediated translational repression inArabidopsis.
Structural characterization of an intermediate reveals a unified mechanism for the CLC Cl−/H+ transport cycle
Authors: Chavan Tanmay S. , Cheng Ricky C. , Jiang Tao , Mathews Irimpan I. , Stein Richard A. , Koehl Antoine , Mchaourab Hassane S. , Tajkhorshid Emad , Maduke Merritt 
Published: November 2019

ABSTRACTAmong coupled exchangers, CLCs uniquely catalyze the exchange of oppositely charged ions (Cl− for H+). Transport-cycle models to describe and explain this unusual mechanism have been proposed based on known CLC structures. While the proposed models harmonize many experimental findings, there have remained gaps and inconsistencies in our understanding. One limitation has been that global conformational change – which occurs in all conventional transporter mechanisms – has not been observed in any high-resolution structure. Here, we describe the 2.6 Å structure of a CLC mutant designed to mimic the fully H+-loaded transporter. This structure reveals a global conformational change to a state that has improved accessibility for the Cl− substrate from the extracellular side and new conformations for two key glutamate residues. Based on this new structure, together with DEER measurements, MD simulations, and functional studies, we propose a unified model of the CLC transport mechanism that reconciles existing data on all CLC-type proteins.
Systems analyses of key metabolic modules of floral and extrafloral nectaries of cotton
Authors: Chatt Elizabeth C. , Mahalim Siti-Nabilla , Mohd-Fadzil Nur-Aziatull , Roy Rahul , Klinkenberg Peter M. , Horner Harry T. , Hampton Marshall , Carter Clay J. , Nikolau Basil J. 
Published: November 2019

AbstractNectar is a primary reward mediating plant-animal mutualisms to improve plant fitness and reproductive success. In Gossypium hirsutum (cotton), four distinct trichomatic nectaries develop, one floral and three extrafloral. The secreted floral and extrafloral nectars serve different purposes, with the floral nectar attracting bees to promote pollination and the extrafloral nectar attracting predatory insects as a means of indirect resistance from herbivores. Cotton therefore provides an ideal system to contrast mechanisms of nectar production and nectar composition between floral and extrafloral nectaries. Here, we report the transcriptome, ultrastructure, and metabolite spatial distribution using mass spectrometric imaging of the four cotton nectary types throughout development. Additionally, the secreted nectar metabolomes were defined and were jointly composed of 197 analytes, 60 of which were identified. Integration of theses datasets support the coordination of merocrine-based and eccrine-based models of nectar synthesis. The nectary ultrastructure supports the merocrine-based model due to the abundance of rough endoplasmic reticulum positioned parallel to the cell walls and profusion of vesicles fusing to the plasma membranes. The eccrine-based model which consist of a progression from starch synthesis to starch degradation and to sucrose biosynthesis was supported by gene expression data. This demonstrates conservation of the eccrine-based model for the first time in both trichomatic and extrafloral nectaries. Lastly, nectary gene expression data provided evidence to support de novo synthesis of amino acids detected in the secreted nectars.One sentence summaryThe eccrine-based model of nectar synthesis and secretion is conserved in both trichomatic and extrafloral nectaries determined by a system-based comparison of cotton (Gossypium hirsutum) nectaries.
Use of financial diaries to understand smallholder investment finance a cross country analysis in Mozambique, Tanzania and Pakistan
Authors: Soria Maria del Puerto , Hernandez Emilio , Ciacci Riccardo 
Published: November 2019

PurposeThe purpose of this paper is to evaluate the relative importance of different sources of finance for agricultural and non-agricultural investments using unique Smallholder Financial Diaries collected by Consultative Group to Assist the Poor (CGAP) in Mozambique, Pakistan and Tanzania at the individual and household level.Design/methodology/approachFollowing the analytical framework of variance decomposition developed in Samphantharak and Townsend (2010), this study develops a method to quantify how much each cash deficit associated to investments and expenses of interest co-move with different financing sources.FindingsThis paper finds that self-finance, rather than formal or informal finance from external providers, is the main financing source for long-term and short-term smallholder agricultural investments. Further, the paper finds that the main source of self-finance varies depending on the economic opportunities faced by smallholders, with non-agricultural income as the dominant financing source for some, while agricultural income dominating for others.Research limitations/implicationsGiven CGAP’s Smallholder Financial Diaries is not nationally representative, research results should be interpreted carefully. However, to the best of the authors’ knowledge, this is the first paper to analyze financing sources for smallholder households making use of high frequency financial data for individuals in developing countries.Practical implicationsThese findings imply that financial inclusion policies specifically targeting smallholders and the agricultural sector would benefit from enabling the development of an ecosystem of diverse financial services that respond simultaneously to both agriculture and non-agriculture needs.Originality/valueThis is paper furthers the authors’ knowledge on how smallholder households are financing their agricultural investments. Moreover, it applies methods in new ways to exploit a unique data set.
Measuring regional differences of construction productive efficiency in China
Authors: Luo Ming , Fan Hongqin , Liu Guiwen 
Published: November 2019

PurposeAs one of the pillar sectors, China’s construction industry (CE) is not efficient in productivity with large regional gaps over the past decades. It is crucial for stakeholders to have insightful information on regional input of resources and output of productive efficiency for making policies and investment decisions. The purpose of this paper is to develop an efficiency measurement for the CE and explore the regional differences of construction productive efficiency across the three regions of China.Design/methodology/approachData envelopment analysis (DEA) is an objective benchmarking methodology used for measuring the performance of construction productivity. Distance friction minimization (DFM) approach, based on DEA model, is applied to identify the causes of inefficiency, sources of growth and the optimal paths to efficient frontier for regional CE. Further studies are conducted to provide insightful information for efficiency improvement, according to DFM modeling results and empirical analysis.FindingsThe results indicate that eastern region leads construction development due to strong performance of coastal provinces. Faced with decreasing supply of skilled workers in developed region, investing more on construction plants and equipment for labor savings is more efficient to the long-term productivity growth of CE in the east. For developing midland region, heavy reliance on cheap manpower should be gradually relieved by allocating more budgets to vocational training and education program to boost quality labor supply, as well as making steady investment on construction equipment and advanced technology. In underdeveloped western region, raising construction labor wages is recommended to attract more workers to meet the market demand and achieve an optimal production efficiency in the CE.Originality/valueThe findings provide insights into the causes of inefficiency, the sources of growth and the best strategies for efficiency improvement in regional CE, recommendations are made for policy making and strategic planning to enhance the overall performance of China’s construction productive efficiency.
Reach out and touch: student training community projects for sustainability - a case study
Authors: De Hooge Ilona E. , van Dam Ynte K. 
Published: November 2019

Purpose
As one of the five concrete actions recommended for implementing sustainable development at universities (internal operations, institutional framework, research, education and capacity building), capacity building has received the least research attention. Although capacity building can be a tangible implementation of outreach that offers empowerment to universities, it is currently unclear how capacity building can be operationalised in concrete activities and which parties represent the university and the community. The purpose of this study is to provide the idea that capacity building can be organised through student training projects.

Design/methodology/approach
To provide support for our suggestion that student training projects can act as an implementation method for capacity building, an illustrative case study is presented. The case study concerns an academic consultancy training project for students in the domain of sustainable development.

Findings
The case study analysis reveals that, as an implementation method, student training projects can provide benefits for both universities and communities. It appears that student training projects do not depend on individual engagement, on individual university staff members or on research grants and that they provide community members with access to resources, expertise and experiences of academics. Moreover, student training projects overcome the major challenges of both power distance and continuity.

Originality/value
To summarise, student training projects may provide a new, promising avenue as an implementation method for capacity building that provides substantial benefits and overcomes the challenges of other methods mentioned in the existing literature.
Vulnerable adults in police custody
Authors: Cummins Ian 
Published: November 2019

Purpose
The purpose of this paper is to discuss the recent National Appropriate Adult Network (NAAN) report on the role of the appropriate adult.

Design/methodology/approach
This paper is based on the NAAN report and a review of relevant policy and research literature.

Findings
There to Help 2 highlights that there are still significant gaps in the provision of appropriate adult schemes across England and Wales. These gaps potentially place vulnerable adults at increased risk.

Originality/value
This paper is a review of recent research.
Supporting wellbeing through scholarship of teaching and learning
Authors: Lawrence Jenny , Herrick Tim 
Published: November 2019

Purpose
The purpose of this paper is to explore the impact and value of a scholarship of teaching and learning-led (SoTL) professional development in higher education (HE), with a focus on practitioner wellbeing.

Design/methodology/approach
The research was a small-scale mixed-methods design, surveying 21 participants and interviewing 3 current students or recent graduates from a UK-based MEd in Teaching and Learning in HE. Data were mapped against an evidence-based framework for wellbeing.

Findings
A SoTL-led form of professional development, an MEd in Teaching in Learning in HE, offers participants opportunity to exercise the “Five Ways to Wellbeing in HE”, which has positive outcomes for staff and students.

Research limitations/implications
The research project was not designed to explore the programme’s impact on wellbeing, but to explore its impact and value on individuals and institutions. Reading data against the “Five Ways to Wellbeing in HE” was retrospective, and individual wellbeing was not measured. However, the theoretical implications are that wellbeing is an additional benefit, which adds to the value of SoTL-led professional development in HE, and that further research is required to explore this more fully.

Practical implications
The wellbeing framework outlined in this research and applied to HE can be used as a model for shaping SoTL-led professional development, to the benefit of the entire learning community.

Originality/value
This paper proposes a connection between wellbeing, SoTL-led professional development and the SOTL.
Financial freedom, market power and bank margins in sub-Saharan Africa
Authors: Sarpong-Kumankoma Emmanuel , Abor Joshua , Aboagye Anthony Quame Q. , Amidu Mohammed 
Published: November 2019

PurposeThis paper examines the effect of financial (banking) freedom and market power on bank net interest margins (NIM).Design/methodology/approachThe study uses data from 11 sub-Saharan African countries over the period, 2006-2012, and the system generalized method of moments to assess how financial freedom affects the relationship between market power and bank NIM.FindingsThe authors find that both financial freedom and market power have positive relationships with bank NIM. However, there is some indication that the impact of market power on bank margins is sensitive to the level of financial freedom prevailing in an economy. It appears that as competition intensifies, margins of banks in freer countries are likely to reduce faster than those in areas with more restrictions.Practical implicationsCompetition policies could be guided by the insight on how financial freedom moderates the effect of market power on bank margins.Originality/valueThis study provides new empirical evidence on how the level of financial freedom affects bank margins and the market power-bank margins relationship.
Lean development evaluation in small Brazilian company
Authors: Hoffmann Davi Laskani , Torres Jr Alvair Silveira 
Published: November 2019

Purpose
The small Brazilian companies are responsible for a large part of national GDP and formal jobs in the country. This expressiveness is contrasted with the specificities of companies of this size possess, including the need to innovate to survive. Research shows that 83 percent of Brazilian SMEs have launched new products and services, obtaining positive results through this innovative process. This competitive advantage is weighted by a great feature of the small organization: resource constraint. The paper aims to discuss this issue.

Design/methodology/approach
Research was carried out in three stages: one qualitative research (by using focal groups) and another two quantitative research works (descriptive and cross-sectional).

Findings
The author identified three factors that are important for teenagers when influencing the purchase of the family car: safety, sportiness and comfort. The identification of these factors shows that the millennial generation tends to emphasize aspects of individual interest, such as status and performance, and family context, such as safety and comfort, rather than social aspects, such as the type of fuel and environmental impact.

Social implications
The authors recommend the development of automobiles that prioritize the three factors mentioned herein in order to reverse the trend of declining car purchase.

Originality/value
The authors presented the relevant attributes in buying decisions of family cars according to teenagers. The authors also indicated which automobile attributes are relevant for a more informed, connected, and with an increasing purchase power generation in contrast with previous generations, whose social context was prior to the emergence of social media.
Financialization and generational differences in the correlates of perceived importance of investment in Hong Kong
Authors: Lee Francis , Tang Gary , Tsang Chung-Kin 
Published: November 2019

PurposeThe purpose of this study is to examine how people’s perceptions of the importance of financial investment relate to their value orientation, societal perceptions and policy attitudes. Tying together insights from theoretical analysis of the financialization of society and Mannheim’s (1972) theory of generation, this study hypothesizes that perceived importance of investment should be less connected to a desire for a wealthy lifestyle and more connected to a critique of social inequality among the young generation. Analysis of survey data (N= 1,020) from Hong Kong, an international financial hub, shows that perceived importance of investment relates positively to consumer materialism, perceptions of social inequality and support for social democratic policies. More importantly, the relationships between the latter variables and perceived importance of investment vary across age groups in ways largely consistent with the expectation. The findings illustrate the changing social significance of financial investment and the reluctant embracement of investment by young people.Design/methodology/approachA representative telephone survey (N= 1,020) was conducted and analyzed.FindingsThe analysis shows that perceived importance of investment relates positively to consumer materialism, perceptions of social inequality and support for social democratic policies. More importantly, the relationships between the latter variables and perceived importance of investment vary across age groups in ways largely consistent with the expectation.Originality/valueThe findings illustrate the changing social significance of financial investment and the reluctant embracement of investment by the young generation. It is, to the authors’ knowledge, the first study in Hong Kong addressing people’s attitudes toward investment in relation to the notion of financialization.
Islamic and Muslim tourism: service quality and theme parks in the UAE
Authors: Lari Lamya Abbas Darwish Abdulla , Iyanna Shilpa , Jabeen Fauzia 
Published: November 2019

PurposeThe purpose of this paper is to identify dimensions of theme park quality from an Islamic perspective and develop a framework to examine the interrelationships between theme park service quality dimensions, visitor delight and visitor loyalty in theme parks in the United Arab Emirates (UAE).Design/methodology/approachThe study is based on a detailed literature review and analysis of visitors’ comments onTripAdvisor.comabout their experience in theme parks in the UAE.FindingsTheme park service quality can be assessed across 4 main dimensions (physical environment, interaction, consumables and access) and 13 sub-dimensions. A relationship is proposed between these dimensions and visitors’ delight, with visitor loyalty a consequence of visitor delight. Nationality is proposed to have a moderating effect on the delight–loyalty relationship.Originality/valueThis study attempts to propose a model for theme park service quality that reflects both traditional dimensions of service quality and dimensions related to Islamic attributes. It is one of very few attempts to investigate theme park visitors’ perception of service quality and its relation to delight and loyalty in the UAE. It is also, as far as the authors are aware, the first study to investigate the moderating effect of nationality on the delight–loyalty relationship.
Cutaneous lupus erythematosus and its association with systemic lupus erythematosus: A nationwide population‐based cohort study in Korea
Authors: Baek Yoo Sang , Park Se Ha , Baek Jinok , Roh Joo Young , Kim Hee Joo 
Published: November 2019

AbstractAlthough lupus erythematosus is known to be more common among women of color, the study populations in previous reports were predominantly Caucasian and there is scarce information on Asian patients. Therefore, we performed a retrospective study using a nationwide population‐based cohort in South Korea. The average annual incidence of cutaneous lupus was 4.36/100 000. Among 634 patients with cutaneous lupus, 20.8% had systemic disease: cutaneous lupus was diagnosed before systemic lupus in 4.26% and after systemic lupus in 8.52%. More female patients than male patients developed systemic lupus erythematosus. The average time to progression to systemic lupus was 1.53 ± 1.46 years.