bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes
Authors: Eaton Katherine M. , Bernal Moisés A. , Backenstose Nathan J.C. , Krabbenhoft Trevor J. 
Published: June 2020

AbstractLocal adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genusCoregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were amplified for individuals ofC. artedi, C. hoyi, C. kiyi, andC. zenithicus. Comparisons revealed species-specific differences in the coding sequence ofrhodopsin(Tyr261Phe substitution), suggesting local adaptation byC. kiyito the blue-shifted depths of Lake Superior. Parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.
Genetic polymorphisms do not predict inter-individual variability to cathodal transcranial direct current stimulation of the primary motor cortex
Authors: Pellegrini Michael , Zoghi Maryam , Jaberzadeh Shapour 
Published: June 2020

AbstractHigh variability between individuals (i.e. inter-individual variability) in response to transcranial direct current stimulation (tDCS) has become a commonly reported issue in the tDCS literature in recent years. Inherent genetic differences between individuals has been proposed as a contributing factor to observed response variability. This study investigated whether tDCS inter-individual variability was genetically mediated. A large sample-size of sixty-one healthy males received cathodal-tDCS (c-tDCS) and sham-tDCS, of the primary motor cortex at 1mA and 10-minutes via 6×4cm active and 7×5cm return electrodes. Corticospinal excitability (CSE) was assessed via twenty-five single-pulse transcranial magnetic stimulation motor evoked potentials (MEP). Intracortical inhibition (ICI) was assessed via twenty-five 3ms inter-stimulus interval (ISI) paired-pulse MEPs, known as short-interval intracortical inhibition (SICI). Intracortical facilitation (ICF) was assessed via twenty-five 10ms ISI paired-pulse MEPs. Gene variants encoding for excitatory and inhibitory neuroreceptors were determined via saliva samples. Pre-determined thresholds and statistical cluster analyses were used to subgroup individuals. Two distinct subgroups were identified, ‘responders’ reducing CSE following c-tDCS and ‘non-responders’ showing no reduction or even increase in CSE. Differences in CSE between responders and non-responders following c-tDCS were not explained by changes in SICI or ICF. No significant relationships were reported between gene variants and inter-individual variability to c-tDCS suggesting the chosen gene variants did not influence the activity of the neuroreceptors involved in eliciting changes in CSE in responders following c-tDCS. In this largest c-tDCS study of its kind, novel insights were reported into the contribution genetic factors may play in observed inter-individual variability to c-tDCS.
The extent and impact of variation in ADME genes in sub-Saharan African populations
Authors: Rocha Jorge da , Othman Houcemeddine , Botha Gerrit , Cottino Laura , Twesigomwe David , Ahmed Samah , Drögemöller Britt I. , Fadlelmola Faisal M. , Machanick Philip , Mbiyavanga Mamana , Panji Sumir , Wright Galen E.B. , Adebamowo Clement , Matshaba Mogomotsi , Ramsay Michèle , Simo Gustave , Simuunza Martin C. , Tiemessen Caroline T. , Baldwin Sandra , Chiano Mathias , Cox Charles , Gross Annette S. , Thomas Pamela , Gamo Francisco-Javier , Hazelhurst Scott ,   as members of the H3Africa Consortium
Published: June 2020

AbstractInvestigating variation in genes involved in theabsorption, distribution, metabolism, andexcretion(ADME) of drugs are key to characterising pharmacogenomic (PGx) relationships. ADME gene variation is relatively well characterised in European and Asian populations, but African populations are under-studied – which has implications for safe and effective drug use in Africa.The genetic diversity of ADME genes across sub-Saharan African populations is large. The Southern African population cluster is most distinct from that of far West Africa. PGx strategies based on European variants will be of limited use in African populations.Although established variants are important, PGx must take into account the full range of African variation. This work urges further characterisation of variants in African populations includingin vitroandin silicostudies, and to consider the unique African ADME landscape when developing precision medicine guidelines and tools for African populations.Author summaryThe ADME genes are a group of genes that play a key role in absorption, distribution, metabolism and excretion of drugs. Variations in these genes can have a significant impact on drug safety and efficacy. Africa has a high level of genetic variation and is under-studied in drug development, which makes study of variations in these genes in African populations very important. Using a new data set of 458 high-coverage genomes from across Africa, we characterise the extent and impact of variation in the ADME genes, looking at both single nucleotide and copy number variations. We identified 343,368 variants, including 40,692 novel variants, and 930 coding variants which are predicted to have high impact on function. Our discovery curves indicate that there will be considerable value in sequencing more African genomes. Moreover, relatively few of these novel variants are captured on common genotyping arrays. We show that there is considerable diversity within Africa in some important genes, and this will have significant consequences for the emerging field of precision medicine in Africa.
DNA sequence-directed cooperation between nucleoid-associated proteins
Authors: Japaridze Aleksandre , Yang Wayne , Dekker Cees , Nasser William , Muskhelishvili Georgi 
Published: June 2020

AbstractNucleoid associated proteins (NAPs) are a class of highly abundant DNA binding proteins in bacteria and archaea. While the composition and relative abundance of the NAPs change during the bacterial growth cycle, surprisingly little is known about their crosstalk in mutually binding to the bacterial chromosome and stabilising higher-order nucleoprotein complexes. Here, we use atomic force microscopy and solid-state nanopores to investigate long-range nucleoprotein structures formed by the binding of two major NAPs, FIS and H-NS, to DNA molecules with distinct binding-site arrangements. We find that spatial organisation of the protein binding sites can govern the higher-order architecture of the nucleoprotein complexes. Based on sequence arrangement the complexes differed in their global shape and compaction, as well as the extent of FIS and H-NS binding. Our observations highlight the important role the DNA sequence plays in driving structural differentiations within the bacterial chromosome.
Discovery of a novel small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria
Authors: Krauspe Vanessa , Fahrner Matthias , Spät Philipp , Steglich Claudia , Frankenberg-Dinkel Nicole , Macek Boris , Schilling Oliver , Hess Wolfgang R. 
Published: June 2020

AbstractPhycobilisomes are the major pigment-protein antenna complexes that perform photosynthetic light harvesting in cyanobacteria, rhodophyte and glaucophyte algae. Up to 50% of the cellular nitrogen can be stored in their giant structures. Accordingly, upon nitrogen depletion, phycobilisomes are rapidly degraded. This degradation is tightly coordinated, follows a genetic program and involves small proteins serving as proteolysis adaptors. Here, we describe the role of NblD, a novel factor in this process in cyanobacteria. NblD is a cysteine-rich, 66-amino acid small protein that becomes rapidly induced upon nitrogen starvation. Deletion of thenblDgene in the cyanobacteriumSynechocystisprevents the degradation of phycobilisomes, leading to a nonbleaching (nbl) phenotype. Competition experiments provided direct evidence for the physiological importance of NblD. Complementation by a plasmid-localized gene copy fully restored the phenotype of the wild type. Overexpression of NblD under nitrogen-replete conditions showed no effect, in contrast to the unrelated proteolysis adaptors NblA1 and NblA2, which can trigger phycobilisome degradation ectopically. Transcriptome analysis revealed that nitrogen starvation correctly inducesnblA1/2transcription in the ΔnblDstrain implying that NblD does not act as a transcriptional (co-)regulator. However, fractionation and coimmunoprecipitation experiments indicated the presence of NblD in the phycobilisome fraction and identified the β-phycocyanin subunit as its target. These data add NblD as a new factor to the genetically programmed response to nitrogen starvation and demonstrate that it plays a crucial role in the coordinated dismantling of phycobilisomes when nitrogen becomes limiting.Significance StatementDuring genome analysis, genes encoding small proteins are frequently neglected. Accordingly, small proteins have remained underinvestigated in all domains of life. Based on a previous systematic search for such genes, we present the functional analysis of the small protein NblD in a photosynthetic cyanobacterium. We show that NblD plays a crucial role during the coordinated dismantling of phycobilisome light-harvesting complexes. This disassembly is triggered when the cells run low in nitrogen, a condition that frequently occurs in nature. Similar to the NblA proteins that label phycobiliproteins for proteolysis, NblD binds to phycocyanin polypeptides but has a different function. The results show that, even in a well-investigated process, crucial new players can be discovered if small proteins are taken into consideration.
An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution
Authors: Howard Aubrey G.A. , Baker Phillip A. , Ibarra-García-Padilla Rodrigo , Moore Joshua A. , Rivas Lucia J. , Tallman James J. , Singleton Eileen W. , Westheimer Jessa L. , Corteguera Julia A. , Uribe Rosa A. 
Published: June 2020

ABSTRACTNeural crest cells (NCCs) are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here, we utilized single-cell transcriptomic analyses to delineate NCC-derivatives along the posterior developing vertebrate, zebrafish, during the late embryonic to early larval stage, a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC-derived cell-types including mesenchyme, neural crest, neural, neuronal, glial, and pigment, from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages, mesenchyme subtypes, and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorialhoxgene codes, with distinct profiles within neuronal cells. From these analyses, we present a comprehensive cell-type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation.
A Simple Enhancement for Gibson Isothermal Assembly
Authors: Rabe Brian A , Cepko Constance 
Published: June 2020

AbstractGibson Isothermal Assembly has become a widespread cloning method, with a multitude of advantages over traditional cut-and-paste cloning. It allows for scarless assembly of multiple fragments simultaneously and has become widely used for molecular cloning. We have found that a simple change to the formulation of the reaction mix, the addition of a single-stranded DNA binding protein, can substantially improve both the accuracy and efficiency of assembly, especially as the number of fragments being assembled increases. In addition, when creating this Enhanced Gibson Isothermal Assembly reaction mix in-house with homemade DNA ligase, the cost of the reaction can be reduced to less than $10 per milliliter.
Ex-post evaluation of the R&D tax incentive law in Chile
Authors: Mardones Cristian , Madrid Becerra Natalia 
Published: June 2020

PurposeThis study carries out an ex - post evaluation of the Research and Development (R&D) Tax Incentive Law in Chile.Design/methodology/approachA subset of data from the 9th Innovation Survey is chosen, specifically those that were available for the years 2013 and 2014. Then, differences in differences (DID) and matching with differences in differences (MDID) techniques are used to identify the impact of this policy.FindingsThe results obtained allow us to affirm that the use of the R&D Tax Incentive Law had some positive but very low effects on some components of expenditure for innovation. Also, the positive effect of the tax credits on the total expenditure for innovation identified with MDID disappears when only firms that know the R&D Tax Incentive Law are used as a control group.Originality/valueThis work provides new evidence to evaluate innovation policies in Latin America, focusing on tax credits that have been much less studied than subsidy programs. Specifically, it is concluded that there is still a wide margin to improve and reformulate the R&D Tax Incentive Law in Chile.
The future of the circular economy and the circular economy of the future
Authors: Weigend Rodríguez Ricardo , Pomponi Francesco , Webster Ken , D'Amico Bernardino 
Published: June 2020

PurposeThe circular economy (CE) has gained momentum in recent years as a new economic paradigm. While the CE sets a very defined vision for a sustainable future, it still operates in the present. As such, existing guidance on and research into the CE lack a necessary understanding of how to go from the present to the future. What if the future is different from what the CE expects? The CE cannot answer this question adequately and therefore is not capable of developing this understanding alone. To address this shortcoming, this paper proposes futures studies (FS) as a complementary discipline because it offers exactly what CE lacks: methods to explore alternative futures.Design/methodology/approachTo understand the level of interdisciplinary research in the built environment between CE and FS, a systematic literature review is carried out using a bibliometric review and a snowballing technique. This manuscript reviews seminal literature in both fields and their theoretical background.FindingsThis paper demonstrates the lack of collaboration between CE and FS and highlights a systemic failure within CE, which is to consider the future as unknowable. It further provides an initial understanding of where the synergy sits, recommendations on where to start and introduces some of the FS chief methods that could be used by CE in the built environment.Research limitations/implicationsThe authors’ bibliometric review and snowballing approach might have missed out on some literature that still falls within the scope. Such limitations are due, on one hand, to the authors’ bibliometric review approach by selecting publications based on matching keywords. On the other hand, the snowballing approach is affected by the authors’ subjective judgements on which of the publications are worth to explore based mainly just on the title and abstract of the paper.Practical implicationsThe inclusion of Futures Studies will allow a stronger focus on approaching possible futures to be integrated overtly into existing work, research and action within the CE community.Social implicationsIt is more reasonable to expect that by cooperatively creating and implementing constructed futures with FS methods and CE principles, a better future for the built environment be reached. This is why it is so relevant for humanity that these two communities start to interact as soon as possible and maintain and open and productive collaboration in transitioning towards a sustainable society.Originality/valueTo the authors’ knowledge, this research is the first of its kind by considering FS into the CE debate.
What influences consumers to purchase organic food in developing countries?
Authors: Pacho Frida 
Published: June 2020

PurposeThe behavior compelling the consumer’s intention to purchase organic food has received little attention in developing countries. There is limited knowledge concerning the factors that impact consumer’s intention to purchase organic food in these countries. The study empirically examined the impact of attitude, subjective norms, and perceived behavior control on the consumer intention to buy organic food. The study also aimed to explore whether knowledge about organic food and health consciousness has an indirect effect on the relationship between attitude, subjective norms, perceived behavior control and intention to buy.Design/methodology/approachTo accomplish the study’s objectives, the questionnaires were administered to a convenience sample of 730 consumers using a traditional paper and pencil questionnaire interview (PAPI). Confirmatory factor analysis (CFA) was applied to validate the data, and the Structural equation model (SEM) was employed to test the hypotheses.FindingsThe findings showed that subjective norms and attitudes were positively correlated, and they significantly impacted the purchase intention of organic food. The findings also showed that knowledge about organic food and health consciousness has an indirect effect on the relationship between attitude, subjective norms, and intention to buy.Originality/valueThe findings stimulate the momentum to the growing literature, particularly in the developing countries on consumer behaviors regarding organic foods. Also, they will help stakeholders to achieve the marketing strategy for the growth of this sector.
Industry 4.0 and clusters: complementaries or substitutes in firm’s knowledge creation?
Authors: Grashof Nils , Kopka Alexander , Wessendorf Colin , Fornahl Dirk 
Published: June 2020

PurposeThis paper aims to show the interaction effects between clusters and cluster-specific attributes and the industrial internet of things (IoT) knowledge of a firm on the innovativeness of firms. Cluster theory and the concept of key enabling technologies are linked to test their effect on a firm’s incremental and radical knowledge generation.Design/methodology/approachQuantitative approach at the firm-level. By combining several data sources (e.g. ORBIS, PATSTAT and German subsidy catalogue) the paper relies on a unique database encompassing 8,347 firms in Germany. Ordinary least squares (OLS)-regression techniques are used for data analysis.FindingsIndustrial IoT is an important driver of radical patents, mediated positively by firm size. For incremental knowledge, a substitution effect occurs between a cluster and IoT effects, which is bigger for larger firms and dependent on cluster attributes and firms’ outside connections.Research limitations/implicationsThe paper opens up new research paths considering long-term disruptive effects of the industrial IoT compared to short-term effects on the innovativeness of firms within clusters. Additionally, it enables further research enriching the discussion about cluster attributes and how these affect ongoing processes.Practical implicationsLinking cluster theory and policy with Industry 4.0 raises awareness for being considerate in terms of funding and scrutinising one-size-fits-all approaches.Originality/valueConnecting the concepts of a cluster and advanced manufacturing technologies as a proxy for industrial IoT, specifically focussing on both radical and incremental innovations is a new approach. Especially, taking into account the interaction effects between cluster attributes and the influence of industrial IoT on the innovativeness of firms.
Employer branding at armed forces: current and potential employees’ perspective
Authors: Kaur Rajwinder , Shah Reena 
Published: June 2020

Purpose
Drawing from the instrumental and symbolic framework for employer branding, this study aims to explore the perception of the current and potential employees for the Indian armed forces’ employer brand.

Design/methodology/approach
The study is conducted as a mixed-method approach in the form of qualitative and quantitative phases. In the qualitative phase, online reviews of current employees were collected from glassdoor.com and analysis was conducted. While in the quantitative phase, data were collected through questionnaire from 200 potential candidates who were interested in joining the armed forces.[AQ1] Confirmatory factor analysis (CFA) for instrument validity and regression analysis, for finding significant factors, were used for data analysis.

Findings
The qualitative results indicate that the current employee's perception fits the instrumental and symbolic framework. Additionally, variables such as discrimination in positions, risk, stress, confidence and personality development were also identified. The CFA and regression analysis results were found to be significant on the instrumental dimensions – job security and task diversity and symbolic dimensions – competence.

Originality/value
The study emphasizes the important instrumental and symbolic attributes for both current and potential employees. Thus, the armed forces can use these as a base for strategy formulation regarding employer branding.
In liminality: interdisciplinary teams learning through challenges
Authors: Brandshaug Sigrid Westad , Sjølie Ela 
Published: June 2020

PurposeThe aim of this paper is to introduce the concept of liminality as a theoretical lens to explore and discuss how challenges, accompanied by frustrations and confusion, can enable significant learning in a teamwork setting. Student team narratives on how they handle challenges they face working to solve real-world problems are used as the basis for the discussion.Design/methodology/approachThis is a case study using student narratives from an interdisciplinary master course at a Norwegian university.FindingsWe argue that the concept of liminality can support teachers and student teams to understand and handle challenges in ways that enable significant learning and innovation. Practical implications for teachers and facilitators are provided at the end of the paper.Originality/valueThis paper offers new lenses to understand the team- and learning processes in courses where students work with real-world problems. If the teams are able to stay open in the liminality phase it enables significant learning and innovation. This capacity is valuable in a time where teams face complexity and uncertainty is becoming more of a standard than an exception, both in higher education and in working life.