bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineered orthogonal quorum sensing systems for synthetic gene regulation
Authors: Tekel Stefan J. , Smith Christina L. , Lopez Brianna , Mani Amber , Connot Christopher , Livingstone Xylaan , Haynes Karmella A. 
Published: December 2018

AbstractGene regulators that are controlled by membrane-permeable compounds called Homoserine lactones (HSLs) have become popular tools for building synthetic gene networks that coordinate behaviors across populations of engineered bacteria. Synthetic HSL-signaling systems are derived from natural DNA and protein elements from microbial quorum signaling pathways. Crosstalk, where a single HSL can activate multiple regulators, can lead to faults in networks composed of parallel signaling pathways. Here, we report an investigation of quorum sensing components to identify synthetic pathways that exhibit little to no crosstalk in liquid and solid cultures. In previous work, we characterized the response of a single regulator (LuxR) to ten distinct HSL-synthase enzymes. Our current study determined the responses of five different regulators (LuxR, LasR, TraR, BjaR, and AubR) to the same set of synthases. We identified two sets of orthogonal synthase-regulator pairs (BjaI/BjaR + EsaI/TraR and LasI/LasR + EsaI/TraR) that show little to no crosstalk when they are expressed in Escherichia coli BL21. These results expand the toolbox of characterized components for engineering microbial communities.
A Deep Learning Genome-Mining Strategy Improves Biosynthetic Gene Cluster Prediction
Authors: Hannigan Geoffrey D. , Prihoda David , Palicka Andrej , Soukup Jindrich , Klempir Ondrej , Rampula Lena , Durcak Jindrich , Wurst Michael , Kotowski Jakub , Chang Dan , Wang Rurun , Piizzi Grazia , Hazuda Daria J. , Woelk Christopher H. , Bitton Danny A. 
Published: December 2018

AbstractNatural products represent a rich reservoir of small molecule drug candidates utilized as antimicrobial drugs, anticancer therapies, and immunomodulatory agents. These molecules are microbial secondary metabolites synthesized by co-localized genes termed Biosynthetic Gene Clusters (BGCs). The increase in full microbial genomes and similar resources has led to development of BGC prediction algorithms, although their precision and ability to identify novel BGC classes could be improved. Here we present a deep learning strategy (DeepBGC) that offers more accurate BGC identification and an improved ability to extrapolate and identify novel BGC classes compared to existing tools. We supplemented this with downstream random forest classifiers that accurately predicted BGC product classes and potential chemical activity. Application of DeepBGC to bacterial genomes uncovered previously undetectable BGCs that may code for natural products with novel biologic activities. The improved accuracy and classification ability of DeepBGC represents a significant step forward forin-silicoBGC identification.
Whole-Cortex Mapping of Common Genetic Influences on Depression and Social Deficits
Authors: Hatoum Alexander S. , Reinberg Andrew E. , Smolker Harry R. , Hewitt John K. , Friedman Naomi P. 
Published: December 2018

AbstractBackgroundSocial processes are associated with depression, particularly understanding and responding to others, deficits in which can manifest as callousness/unemotionality (CU). Thus, CU may reflect some of the genetic risk to depression. Further, this vulnerability likely reflects the neurological substrates of depression, presenting biomarkers to capture genetic vulnerability of depression severity. However, heritability varies within brain regions, so a high-resolution genetic perspective is needed.Method
In a sample of 258 same-sex twin pairs from the Colorado Longitudinal Twin Study (LTS), we developed a toolbox that maps genetic and environmental associations between brain and behavior at high resolution. We used this toolbox to estimate brain areas that are genetically associated with both depressive symptoms and CU. We then overlapped the two maps to generate coordinates that allow for tests of downstream effects of genes influencing our clusters.Results
Genetic variance influencing cortical thickness in the right dorsal lateral prefrontal cortex (DLFPC) sulci and gyri, ventral posterior cingulate cortex (PCC), pre-somatic motor cortex (PreSMA), medial precuneus, left occipital-temporal junction (OTJ), parietal-temporal junction (PTJ), ventral somatosensory cortex (vSMA), and medial and lateral precuneus were genetically associated with both depression and CU. Split-half replication found support for both DLPFC clusters. Meta-analytic term search identified “theory of mind”, “inhibit”, and “pain” as likely functions. Gene and transcript mapping/enrichment analyses implicated calcium channels.ConclusionsCU reflects genetic vulnerability to depression that likely involves executive and social functioning in a distributed process across the cortex. This approach works to unify neuroimaging, neuroinformatics, and genetics to discover pathways to psychiatric vulnerability.
State-dependent geometry of population activity in rat auditory cortex
Authors: Kobak Dmitry , Pardo-Vazquez Jose L. , Valente Mafalda , Machens Christian , Renart Alfonso 
Published: December 2018

AbstractThe accuracy of the neural code depends on the relative embedding of signal and noise in the activity of neural populations. Despite a wealth of theoretical work on population codes, there are few empirical characterisations of the high-dimensional signal and noise subspaces. We studied the geometry of population codes in the rat auditory cortex across brain states along the activation-inactivation continuum, using sounds varying in difference and mean level across the ears. As the cortex becomes more activated, single-hemisphere populations go from preferring contralateral loud sounds to a symmetric preference across lateralisations and intensities, gain-modulation effectively disappears, and the signal and noise subspaces become approximately orthogonal to each other and to the direction corresponding to global activity modulations. Level-invariant decoding of sound lateralisation also becomes possible in the active state. Our results provide an empirical foundation for the geometry and state-dependence of cortical population codes.
Improved representation of sequence Bloom trees
Authors: Harris Robert S. , Medvedev Paul 
Published: December 2018

AbstractAlgorithmic solutions to index and search biological databases are a fundamental part of bioinformatics, providing underlying components to many end-user tools. Inexpensive next generation sequencing has filled publicly available databases such as the Sequence Read Archive beyond the capacity of traditional indexing methods. Recently, the Sequence Bloom Tree (SBT) and its derivatives were proposed as a way to efficiently index such data for queries about transcript presence. We build on the SBT framework to construct the HowDe-SBT data structure, which uses a novel partitioning of information to reduce the construction and query time as well as the size of the index. We evaluate HowDe-SBT by both proving theoretical bounds on its performance and using real RNA-seq data. Compared to previous SBT methods, HowDe-SBT can construct the index in less than 36% the time, and with 39% less space, and can answer small-batch queries at least five times faster. HowDe-SBT is available as a free open source program on https://github.com/medvedevgroup/HowDeSBT.
Exploring the quality of corporate environmental reporting
Authors: Helfaya Akrum , Whittington Mark , Alawattage Chandana 
Published: December 2018

Purpose
The purpose of this paper is to provide a multidimensional model for assessing the quality of corporate environmental reporting (CER) incorporating both preparer- and user-based views.

Design/methodology/approach
As opposed to frequently used researcher-chosen proxies, the authors used an online questionnaire asking preparers and users how they assess the quality of a company’s environmental report.

Findings
The analysis of the responses of 177 users and 86 preparers shows that quantity was not perceived as the most significant element in determining quality. Besides quantity, the respondents also perceived information types, measures used, themes disclosed, adopting reporting guidelines, inclusion of assurance statement and the use of visual tools as significant dimensions/features of reporting quality.

Research limitations/implications
The online questionnaire has some limitations, especially in terms of researcher being absent to clarify meanings and, hence, possibilities that respondents may misinterpret the questionnaire elements.

Practical implications
Considering that robust, reliable measurement of reporting quality is difficult, preparers, standard setters and policy makers need multidimensional quality models that incorporate both users’ perceptions of quality and preparers’ pragmatic understanding of the quality delivery process. These will make the preparers informed of whether their disclosure may be falling short of users’ expectations.

Originality/value
Amid, increasing complexity of CER, the research contributes to the growing body of literature on assessing the quality of CER by developing a less subjective, multidimensional, preparer–user-based quality model. This innovative quality model goes beyond the traditional quality models, subjective author-based quality measures. Focussing on the three dimensions of reporting quality – content, credibility and communication – it also offers a high-level resolution of meaning of CER quality.
Kindness among colleagues; identifying and exploring the gaps in employment contexts
Authors: Gibb Stephen , Rahman Shama 
Published: December 2018

Purpose
The purpose of this study is to model and explore kindness as a factor in employment contexts. “Kindness among colleagues” is a particular context for the scientific study of kindness which has been under-researched. There is scope within the burgeoning study of kindness for research concerned with employment contexts and colleagues, adopting an employment context appropriate construct of kindness, generating and considering evidence that might be evaluated rigorously in the employment context where kindness is both advocated and critiqued.

Design/methodology/approach
The literature review identifies and explores the gaps in kindness research in the employment context. A construct distinguishing a set of antecedents of kindness among colleagues was developed to address these gaps. The relevance and usefulness of the construct was tested in semi-structured interviews among some work colleagues in a specific organization setting.

Findings
The results show that the four antecedents of kindness can be used to capture and explore perceptions and experiences of kindness among colleagues. There is scope for analysis at the levels of individuals, teams and organizations using data about these antecedents which allows for individual and more general workplace dynamics to be described and explored.

Research limitations/implications
The antecedents of kindness construct are validated to an extent by this initial study. The potential of this for describing and analyzing kindness and workplace relevant themes makes it worth further development; to refine and validate an instrument for measuring kindness among colleagues.

Practical implications
Kindness among colleagues, if understood in the nuanced way presented here, can help individuals, teams and organizations review and evaluate themselves in diverse contexts. Contexts can be expected to vary with workforce demographics, leadership style and organization cultures.

Social implications
Kindness is a burgeoning theme and concern across diverse social and cultural contexts for various reasons. The scientific contribution to the advocacy or critique of kindness, in this case kindness among colleagues, provides value in rigor, operationalization and evidencing of the case for and against advocacy of the value of kindness in general.

Originality/value
This is a focused review and study of kindness among colleagues which contributes to the nomological and methodological development of a scientific approach to organizational analysis concerns with this important theme in contemporary times.
Institutional contradiction and BSC implementation: comparative organizational analysis
Authors: Alsharari Nizar Mohammad , Eid Riyad , Assiri Ali 
Published: December 2018

Purpose
This paper aims to explain institutional contradictions in the balanced scorecard (BSC) implementation process between organizations, which successfully implemented BSC. The purpose of this paper is to identify a comprehensive set of potential determinants influencing the successful implementation of BSC.

Design/methodology/approach
This study is an exploratory investigation into the BSC implementation based on a dialectical perspective. It uses the triangulation of data collection including interviews, documents and surveys. This also includes a comprehensive scrutiny of the relevant literature; a comprehensive analysis of case studies of BSC implementations in four organizations; and interviews and documents evidences that have already implemented or are in the process of implementing BSC.

Findings
The BSC was successfully implemented in the organizations, when the accounting systems introduced in these organization had already been institutionalized, that is, accepted and used on day-to-day basis. The dialectical perspective postulates that for change to become institutionalized in the organization, it needs to overcome the problem of embedded agency. This process of change is possible due to the accumulation of institutional contradiction that enables human praxis to introduce change (Seo and Creed, 2002).

Research limitations/implications
There is a need to empirically test and refine the proposed factors and explore relationships among the various variables by collecting data from organizations that have already implemented BSC.

Practical implications
The findings of this study are important and relevant to all the different-sized organizations in the different sectors and industries. This study also makes a significant contribution to society in general.

Originality/value
This paper contributes to the literature on organizational and accounting change that emphasis the crucial role that institutional contradiction plays in the process of BSC implementation. The findings of this study will help management in making crucial decisions and in resource allocations that are required to make the BSC implementation a success.
Playing catch-up: how less developed nations can jump-start technology innovation
Authors: Xu Lu , Kim Seong-Young , Xiong Jie , Yan Jie , Huang Han 
Published: December 2018

Purpose
This study aims to investigate the historical technological catch-up processes with particular attention to the role of windows of opportunity (WoO). As Industry 4.0 becomes the benchmark of many latecomer countries, this paper may provide guidelines to both policymakers and business practitioners. For clarifying how to catch up with the incumbents and leaders, the authors summarize the lessons based on the historical observations to conclude the pathways for latecomers who aim to reduce the gaps to leaders and manage catch-up. This study enriches the literature of catch-up from a holistic view with fresh insights into how and where to catch up.

Design/methodology/approach
The authors analyze the technological catch-up processes emerged in advanced industrial powers, newly industrialized countries (NICs) and emerging economies (EEs). By categorizing the countries into three kinds, they summarize the processes of catch-up along with the industry evolutions. Moreover, they explore how WoO may facilitate the catch-up processes from one stage to the next in above-mentioned categories. Doing so helps to further examine how technological catch-up and WoO interplay and differ among countries. Then, the authors further investigate the latecomers and incumbents and conclude the target choosing, path setting and direction selecting when implementing a catch-up strategy.

Findings
This study shows that technological catch-up emerged first in advanced industrial powers (AIPs), then in NICs and recently in EEs. Technological catch-up processes in AIPs and NICs take longer time than those in EEs. WoO from policy, market and technology usually collaboratively facilitate the technological catch-up processes in AIPs and NICs. However, in EEs, single WoO can lead to a successful catch-up. The authors further summarize the directions and pathways of catch-up: AIPs and NICs are normally considered by some latecomers to catch up with, while EEs are not.

Originality/value
This study is among the first to systematically review the historical developments of industry evolutions by focusing the technological catch-up based on the different categories of countries: AIPs, NICs and EEs. Moreover, the authors are also among the first few integrating the WoO and technological catch-up processes in different kinds of countries. To the best of the authors’ knowledge, they are also one of the pioneers who highlight the directions and pathways of latecomers and target choosing to catch up with. They also explore the possibility of selecting EEs as catch-up targets.
How smaller firms can outperform their peers
Authors: Pett Timothy L. , Errami Youssef , Sié Laurent 
Published: December 2018

Purpose
This paper aims to study the performance of small- and medium-sized enterprises (SMEs) within the French hospitality sector and to determine what firm characteristics (particularly entrepreneurship orientation and strategic initiatives) explain differences in performance. The study is based on data from hotels and differentiates between high- and low-performing businesses. The study examines performance differences relating to entrepreneurial orientation and strategic initiatives. The conclusions indicate that there are differences between high- and low-performing groups, and overall, it seems that there is a relationship between high performance and entrepreneurial, well-planned strategic initiatives.

Design/methodology/approach
This study uses a structured telephone interview procedure to solicit respondents from owner/operators of the hotels throughout the region. The process for gathering data resulted in 66 hotels providing complete responses during interview sessions.

Findings
The primary intent of this study was to examine the relationships between entrepreneurial orientation and strategic initiatives with SME performance. The findings suggest that differences exists. Interestingly, we found that better performing group used more people and tended to see business environment much more favorable compared to low-performing group.

Originality/value
Entrepreneurial orientation research suggest that SMEs firms operate distinct from other ones given different patterns used. These differences come from how SMEs leverage the proactiveness, risk-taking and innovativeness dimensions of entrepreneurial orientation in a firm. Waal and his colleagues suggested that activities associated with creating a high-performing organization using strategic initiatives will lead to subsequent high financial performance. The research found here would also support such an assertion. However, care should be taken in interpreting the generalizability of these results given the limited number of hotels participating in this study; more work is still needed.
Diversity and group performance in a real estate project
Authors: Schrand Liesa , Just Tobias 
Published: December 2018

Purpose
Successful developers need to manage a large number of cooperation partners and find innovative solutions for specific tasks, as each real estate project is somehow unique. Thus, the question arises as to whether intelligent group formation for real estate development calls for more or rather less diverse project groups.

Design/methodology/approach
This paper aims to test the impact of group diversity on overall group performance with a unique data set. The authors collected the results of 150 project assignments from real estate executive education students at the IREBS Real Estate Academy from 2010 until 2016.

Findings
The authors find that group results were impacted positively for groups with disparity in work experience and ability. Differences in sex and age did not yield any measurable impact, neither positive nor negative.

Originality/value
To the best of the authors’ knowledge, this is the first time that the relationship between work group diversity and group performance was tested for real estate educational projects. The authors believe that the results are highly relevant for all university work, for which teams have to cooperate on complex rather than basic assignments and problems. Moreover, they are the first to develop a framework that combines diversity theories with a clear distinction between three diversity concepts.
Evaluation of barriers in the adoption of halal certification: a fuzzy DEMATEL approach
Authors: Khan Shahbaz , Khan Mohd Imran , Haleem Abid 
Published: December 2018

PurposeHigher level of customer satisfaction for halal products can be achieved by the effective adoption of halal certification through assessment and accreditation (HCAA). There are certain issues that seem detrimental towards the adoption of HCAA. The purpose of this paper is to identify the major barriers towards the adoption of HCAA and evaluate inter-relationships among them for developing the strategies to mitigate these barriers.Design/methodology/approachThe barriers towards the adoption of HCAA are identified through an integrative approach of literature review and expert’s opinion. The inter-relationship among the identified barriers is evaluated using fuzzy-based decision-making trial and evaluation laboratory (fuzzy DEMATEL) technique, which categorises them into influential and influenced group.FindingsThe evaluation of inter-relationship among barriers using fuzzy DEMATEL indicates four influencing barriers and six influenced barriers towards the adoption of HCAA. Further, findings suggest an extensive government, and management support is vital in terms of commitment, resources and actions to realise the benefits attributed with HCAA.Research limitations/implicationsThe inter-relationship among barriers is contextual and based on the perception of experts which may be biased as per their background and area of expertise. This study pertains to a specific region and can be extended to the generalised certification system.Originality/valueThe empirical base of the research provides the inter-relationship among the barriers towards the adoption of HCAA which can be effectively used as input in the decision-making process by producers, manufacturers and distributor. The policy maker can analyse the cause group and effect group of barriers to formulate policies that would help in the adoption of HCAA.