bluuebunny/crossref_metadata_2025_split huggingface dataset:
DIP/Dpr interactions and the evolutionary design of specificity in protein families
Authors: Sergeeva Alina P. , Katsamba Phinikoula S. , Cosmanescu Filip , Brewer Joshua J. , Ahlsen Goran , Mannepalli Seetha , Shapiro Lawrence , Honig Barry 
Published: January 2020

AbstractDifferential binding affinities among closely related protein family members underlie many biological phenomena, including cell-cell recognition.DrosophilaDIP and Dpr proteins mediate neuronal targeting in the fly through highly specific protein-protein interactions. We show here that DIPs/Dprs segregate into seven specificity subgroups defined by binding preferences between their DIP and Dpr members. We then describe a novel sequence-, structure- and energy-based computational approach, combined with experimental binding affinity measurements, to reveal how specificity is coded on the canonical DIP/Dpr interface. We show that binding specificity of DIP/Dpr subgroups is controlled by “negative constraints”, which interfere with binding. To achieve specificity, each subgroup utilizes a different combination of negative constraints, which are broadly distributed and cover the majority of the protein-protein interface. We discuss the structural origins of negative constraints, and potential general implications for the evolutionary origins of binding specificity in multi-protein families.
USP9X deubiquitinase couples the pluripotency network and cell metabolism to regulate ESC differentiation potential
Authors: de Dieuleveult Maud , Leduc Marjorie , Salataj Eralda , Ransy Céline , Dairou Julien , Homma Kengo , Le Gall Morgane , Bossard Pascale , Lombès Anne , Bouillaud Frédéric , Ferry Laure , Defossez Pierre-Antoine , Cadoret Jean-Charles , Ichijo Hidenori , Wood Stephen A. , Guillonneau François , Dressel Ralf , Miotto Benoit 
Published: January 2020

ABSTRACTEmbryonic stem cells (ESC) have the unique ability to differentiate into all three germ cell layers. ESC transition through different states of pluripotency in response to growth factor signals and environmental cues before becoming terminally differentiated. Here, we demonstrated, by a multi-omic strategy, that the deubiquitinase USP9X regulates the developmental potential of ESC, and their transition from a naive to a more developmentally advance, or primed, state of pluripotency. We show that USP9X facilitates developmental gene expression and induces modifications of the mitochondrial bioenergetics, including decreased routing of pyruvate towards its oxidation and reduced respiration. In addition, USP9X binds to the pluripotency factor ESRRB, regulates its abundance and the transcriptional levels of a subset of its target genes. Finally, under permissive culture conditions, depletion of Usp9X accelerates cell differentiation in all cell lineages. We thus identified a new regulator of naive pluripotency and show that USP9X couples ESRRB pluripotency transcriptional network and cellular metabolism, both of which are important for ESC fate and pluripotency.
New mathematical modelling tools for co-culture experiments: when do we need to explicitly account for signalling molecules?
Authors: Jin Wang , Wang Haolu , Liang Xiaowen , Roberts Michael S , Simpson Matthew J 
Published: January 2020

AbstractMathematical models are often applied to describe cell migration regulated by diffusible signalling molecules. A typical feature of these models is that the spatial and temporal distribution of the signalling molecule density is reported by solving a reaction–diffusion equation. However, the spatial and temporal distributions of such signalling molecules are not often reported or observed experimentally. This leads to a mismatch between the amount of experimental data available and the complexity of the mathematical model used to simulate the experiment. To address this mismatch, we develop a discrete model of cell migration that can be used to describe a new suite of co–culture cell migration assays involving two interacting subpopulations of cells. In this model, the migration of cells from one subpopulation is regulated by the presence of signalling molecules that are secreted by the other subpopulation of cells. The spatial and temporal distribution of the signalling molecules is governed by a discrete conservation statement that is related to a reaction–diffusion equation. We simplify the model by invoking a steady state assumption for the diffusible molecules, leading to a reduced discrete model allowing us to describe how one subpopulation of cells stimulates the migration of the other subpopulation of cells without explicitly dealing with the diffusible molecules. We provide additional mathematical insight into these two stochastic models by deriving continuum limit partial differential equation descriptions of both models. To understand the conditions under which the reduced model is a good approximation of the full model, we apply both models to mimic a set of novel co–culture assays and we systematically explore how well the reduced model approximates the full model as a function of the model parameters.
Beta-3 Adrenoreceptors protect from hypertrophic remodelling through AMP-Activated Protein Kinase and Autophagy
Authors: Dubois-Deruy Emilie , Gelinas Roselle , Beauloye Christophe , Esfahani Hrag , Dessy Chantal , Bertrand Luc , Balligand Jean-Luc 
Published: January 2020

ABSTRACTAimsThe abundance of beta3-adrenergic receptors (β3-ARs) is upregulated in diseased human myocardium. We previously showed that cardiac-specific expression of β3-AR inhibits the hypertrophic response to neurohormonal stimulation. Here, we further analyzed signalling pathways involved in the anti-hypertrophic effect of β3-AR.MethodsIn vitrohypertrophic responses to phenylephrine (PE) were analyzed in neonatal rat ventricular myocytes (NRVM) infected with a recombinant adenovirus expressing the human β3-AR (AdVhβ3). We confirmed results in mice with cardiomyocyte-specific moderate expression of human β3-AR (β3-TG) and WT littermates submitted to thoracic transverse aortic constriction (TAC) for 9 weeks.ResultsWe observed a colocalization of β3-AR with the AMP-activated protein kinase (AMPK) both in neonatal rat andin adult mouse cardiomyocytes. Treatment of NRVM with PE induced hypertrophy and a decrease in phosphorylation of Thr172-AMPK (/2, p=0.0487) and phosphorylation of Ser79- acetyl-CoA carboxylase (ACC) (/2.6, p=0.0317), inducing an increase in phosphorylated Ser235/236 S6 protein (x2.5, p=0.0367) known to be involved in protein synthesis. These effects were reproduced by TAC in WT mice, but restored to basal levels in β3-AR expressing cells/mice. siRNA targeting of AMPK partly abrogated the anti-hypertrophic effect of β3-AR in response to PE in NRVM (x1.3, p<0.0001). Concomitant with hypertrophy, autophagy measured by microtubule-associated protein 1 light chain 3 (LC3)-II/LC3-I ratio and p62 abundance was decreased by PE in NRVM (/2.6, p=0.0010 and x3, p=0.0016, respectively) or TAC in WT mice (/5.4, p=0.0159); and preserved in human β3-AR expressing cells and mice, together with reduced hypertrophy.ConclusionsCardiac-specific moderate expression of β3-AR inhibits the hypertrophic response in part through AMPK activation followed byinhibition of protein synthesis and preservation of autophagy. Activation of the cardiac β3-AR pathway may provide future therapeutic avenues for the modulation of hypertrophic remodelling.
Determinants and overuse of pesticides in grain production
Authors: Sun Shengyang , Zhang Chao , Hu Ruifa 
Published: January 2020

Purpose
The negative externalities of pesticide overuse increasingly concern the public. However, little empirical evidence has been provided for pesticide overuse and the relationship between the governmental agricultural extension system reforms and pesticide use in grain production from a nationwide perspective. The purpose of this paper is to estimate the productive effect and overuse of pesticides, and it also investigates the effect of the governmental agricultural extension system reforms on pesticide expenditure in rice, maize and wheat production in China.

Design/methodology/approach
A two-equation system model consisting of an exponential-specific damage-control production function and a pesticide use function is applied to the provincial-level data during the period 1985–2016.

Findings
While pesticide expenditure significantly increases grain productivity, the actual pesticide expenditure exceeds the economically optimal level. The commercialization reform of the governmental agricultural extension system contributed to the increase in pesticide expenditure. Moreover, the de-commercialization reform of the governmental agricultural extension system plays a limited role in pesticide reduction. Price fluctuations for grain and pesticide also impose significant effects on pesticide expenditure.

Originality/value
This study has two important policy implications for pesticide reduction in China. It is urgent to specify the functions of the governmental agricultural extension system, and encourage the development of the socialized agricultural technology service. More efforts should also be made to remove the bureaucratic intervention on the pricing mechanism of grain product and pesticide.
Post-disaster recovery through the evolution of the lakou, a traditional settlement pattern
Authors: Miller James Patrick 
Published: January 2020

Purpose
Historically, post-disaster reconstruction policies and practice ignore the embedded knowledge of the affected population; the process following the 2010 earthquake in Haiti followed this trend. This paper aims to examine the production of social space in self-settled post-disaster settlements in Leogane and Port-au-Prince, Haiti, the paper demonstrates the role that traditional settlement patterns played in the production of social capital.

Design/methodology/approach
A multi-sited case study approach was implemented to uncover the patterns of the lakou, which is a primary Haitian, traditional settlement pattern reflecting the familial social structure, present in self-settled post-disaster settlements. The study took place between February and June of 2012, two years after the 2010 earthquake across settlements in Leogane and Port-au-Prince. Semi-structured interviews were conducted with 40 inhabitants across the settlements to uncover meanings attached to the creation of space. Together with behavior mapping and participant observations, the interviews were analyzed to validate the reproduction of the lakou.

Findings
This paper demonstrates that endogenous inhabitants create the lakou in post-disaster settlements in Haiti. This case study validates the resilience of the lakou, the inclusive nature of the lakou system, and the important role it plays in the production of social capital within post-disaster communities.

Originality/value
This study demonstrates the importance of traditional settlement patterns in post-disaster community well-being and it demonstrates the need to incorporate traditional settlement patterns into post-disaster planning strategies. Furthermore, the study validates that traditional settlement patterns support the production of social capital within a community.
Assessing the green behaviour of academics
Authors: Fawehinmi Olawole , Yusliza Mohd Yusoff , Mohamad Zaleha , Noor Faezah Juhari , Muhammad Zikri 
Published: January 2020

Purpose
Studies have highlighted concerns about the role of knowledge creation between human resource management practices and employee behaviour. The purpose of this paper is to examine the impact of green human resource management (green HRM) on employee green behaviour (EGB) through the mediation of environmental knowledge of lecturers in public research universities in Malaysia.

Design/methodology/approach
This cross-sectional study examines the mechanism in which green HRM affects the EGB of lecturers through environmental knowledge in Malaysian public research universities. Smart PLS was used to analyse the relationships from 425 valid responses.

Findings
The findings of the study show that green HRM affects EGB through the full mediation of environmental knowledge. This finding gives a theoretical implication in terms of ability, motivation and opportunity theory.

Research limitations/implications
The scope of this study is limited to public research universities in Malaysia. Future studies may explore other variables that could expedite the relationship between green HRM and EGB. Implications include policy making that emphasises on enhancing environmental knowledge of lecturers.

Originality/value
To the best of the authors’ knowledge, no study has been conducted using environmental knowledge as a mediator between green HRM and EGB.
The practices of performance management and low performers in the US Federal Government
Authors: Lee Hyung-Woo , Rhee Dong-Young 
Published: January 2020

PurposeAddressing low performers has been an important issue for government. The purpose of this paper is to examine what practices of performance management are effective in reducing the proportion of low performers in the US federal government.Design/methodology/approachThe authors conducted the binary logit regression analysis and multinomial regression analysis.FindingsAnalyzing the Merit Principle Survey 2016, the authors found that the dismissal of low performing employees and the formal performance improvement plan (PIP) is the most effective in reducing the proportion of low performers. To the contrary, the within-grade-increase did not have a significant influence on the proportion of low performers. Moreover, using the performance appraisal for the purpose of reassigning employees to the position that better match employees’ talent increased the number of low performers in work units.Research limitations/implicationsResearch limitations are as follows. First, the performance measure for this study was the percentage of employees rated as unsuccessful. Second, the pseudo-R2indicated that the proposed model explained only the small, albeit significant, portion of the total variance in employee performance. Lastly, this study used a cross-sectional research design that may impede the validity of inference of causalities.Practical implicationsAccording to a recent news article (Rein, 2018), Trump signed an executive order that limits the stable benefits associated with government employment such as, limiting pay associated with union work and negotiating more stringent union contracts. These measures are largely aimed at eliminating low performing employees rather than attempting to improve their performances through carefully designed training programs. Although removing low performers may be an option, the results indicate that providing assistance in order to develop employee knowledge and skills through the PIP have a comparable impact on reducing low performers.Originality/valueThese findings imply that the use of performance evaluation for developmental or sanctioning purpose is more effective than reassignment or incentive purpose.
KPIs for performance measurement of e-fulfillment systems in multi-channel retailing
Authors: Bressolles Gregory , Lang Gerald 
Published: January 2020

PurposeThe purpose of this paper is to expand existing research on fulfillment systems for multi-channel retailers by combining analysis of customer expectation (CE) with economic performance (EP) aspects.Design/methodology/approachThis exploratory study is based on a literature review of supply chain management and marketing combined with the results of an online questionnaire submitted to French and Chinese multi-channel retailers from two sectors.FindingsThe results enable the authors to identify 13 important key performance indicators (KPIs) used by multi-channel retailers for measuring e-fulfillment system performance and also to determine under which of the EP or CE criteria these KPIs might be linked.Research limitations/implicationsAlthough the sample size is limited, this research is intended to be exploratory, based on the practices of supply chain and marketing managers. Moreover, the results do not address interdependencies among the different KPIs.Practical implicationsE-fulfillment is a major challenge for multi-channel retailers; it is cost intensive and critical for customer satisfaction. The identified set of KPIs enables retailers to choose those relevant to their particular infrastructure.Originality/valueA limited number of scholarly works have explored the operational implications of online retailing in terms of e-fulfillment in a multi-channel context. In order to manage such supply chains efficiently and effectively, traditional measures of supply chain performance need to be adapted. This study expands existing knowledge by developing measurement systems and metrics for the evaluation of supply chain performance in this context.
The hierarchy of resource use for a sustainable circular economy
Authors: Nilsen Heidi Rapp 
Published: January 2020

Purpose
The original principles of the hierarchy of resource use seem to have been forgotten. The purpose of this paper is to address the necessity of these principles in order for a circular economy (CE) to be sustainable.

Design/methodology/approach
This is a general review paper explaining today’s shortcomings in a CE and in the waste hierarchy. Its theoretical contribution is illustrated using the example of marine plastic waste in the Arctic, as well as the EU’s action plan for a CE: “Closing the loop”.

Findings
There is a need to reduce raw materials into the economy directly and not only as a potential result of recycling. This is supported theoretically and by illustrating that the EU’s action plan is closing the loop primarily from the output side.

Research limitations/implications
The theoretical possibility of complete recycling rests on a premise that is now at odds with a sustainable development.

Social implications
The power of existing raw material production cycles must be challenged to allow reduction to be a real option. If not, a CE may exacerbate a moral trade-off by the current generation reducing the safe operating space of future living beings.

Originality/value
The theoretical possibility of recycling everything, also known as the technology-optimist view, has played the role of a safety net for humanity. As we are now exceeding planetary boundaries for a safe and just space for humanity, this theoretical safety net is no longer valid. Instead, we must reinforce the basic principles of the hierarchy of resource use.
Profitability and marketability efficiencies of Vietnam manufacturing firms
Authors: Anh Dao Le Trang , Gan Christopher 
Published: January 2020

PurposeThe purpose of this paper is to measure profitability and marketability efficiencies as well as examine the efficiencies’ determinants of listed manufacturing firms in Vietnam.Design/methodology/approachThis study employs a bootstrap two-stage data envelopment analysis (DEA) approach to investigate the profitability and marketability efficiencies of 102 listed manufacturing firms on Vietnam stock market from 2007 to 2018. The study also applies fractional regression models (FRM) to identify the determinants of Vietnam manufacturing firms’ efficiencies.FindingsThe results reveal that Vietnam manufacturing firms obtain higher average profitability efficiency scores (0.888) than marketability efficiency scores (0.527) from 2007 to 2018. The high-tech firms achieve better profitability and marketability efficiencies than the traditional (resource-intensive and labour-intensive) Vietnam manufacturing firms in recent years (2016–2018). Further, the financial and non-financial factors have heterogeneous impacts on Vietnam manufacturing enterprises’ profit and market valuation efficiencies.Research limitations/implicationsDue to the nature of DEA technique that requires every decision-making unit to have available data of all inputs and outputs, the listed Vietnam manufacturing firms that have incomplete data or go public after 2007 are not included in the data set.Practical implicationsThis study provides a reference for Vietnam manufacturing managers to position their firms competitively in the market as well as make wise operating, financing and management decisions.Originality/valueThis is the first study that attempts to combine bootstrap two-stage DEA and FRM, which are considered advantageous methods for DEA scores’ measurements and determinant evaluations in the current literature.
The effect of regional income inequality and social diversity on the provision of local public goods in Indonesia
Authors: Siburian Matondang Elsa 
Published: January 2020

PurposeThe purpose of this paper is to quantify the effects of regional income disparity and social diversity on local public goods delivery in Indonesia.Design/methodology/approachUsing Indonesian provincial data over the period 2001–2014 and by way of System GMM, this paper circumvents endogeneity and persistence of key variables over time which may bias the estimated impact of the critical variables.FindingsThe result provides no significant evidence on the influence of regional income inequality on the provision of local public goods. The result reveals that ethnic diversity is associated with the more extensive provision of local public goods. A large difference in preferences toward public goods provision in a fragmented society such as Indonesia forces the local government to deliver a greater mixed of public goods to accommodate various preferences for public goods and ensure that each group has equal access to public goods. Political fragmentation within an ethnically heterogeneous society also encourages local politicians to provide a larger provision of public goods to form an inter-ethnic coalition to gain local political access.Practical implicationsThe significant effect of ethnic diversity on public goods provision implies a set of policy recommendation for Indonesian Government in order to maintain peace within the country. The central government should establish a clear-cut standard of local public goods provision for local governments to ensure that that anyone has equal access to public goods regardless of ethnicity. This will mitigate the possibility of ethnic conflict in an ethnically plural society.Originality/valueThis paper extends its analysis using both fractionalization and polarization indexes to measure the social diversity in Indonesia to obtain a comprehensive knowledge regarding the influence of ethnic diversity on the public good provision. This paper proposes a set of policy recommendation for Indonesian Government to manage the effect of social diversity on the provision of local public goods. To the author’s knowledge, this has never been done before for Indonesia.Peer reviewThe peer review history for this article is available at:https://publons.com/publon/10.1108/IJSE-12-2018-0661