bluuebunny/crossref_metadata_2025_split huggingface dataset:
Associations and recovery dynamics of the nasopharyngeal microbiota during influenza-like illness in the aging population
Authors: Shetty Sudarshan A. , van Beek Josine , Bijvank Elske , Groot James , Kuiling Sjoerd , Bosch Thijs , van Baarle Debbie , Fuentes Susana 
Published: September 2021

AbstractBackgroundOlder adults are more susceptible to respiratory pathogens, several of which have been associated with an altered respiratory microbiota. Influenza-like illness (ILI), a disease caused by respiratory pathogens including but not exclusively by influenza virus, is a major health concern in this population. However, there is little information on changes in the nasopharyngeal (NP) microbiota of older adults associated with respiratory infections identified by/ reported as ILI, as well as its dynamics during recovery. Here, we compared the NP microbiota in older adults who presented with ILI (n= 240) to the NP microbiota in older adults not reporting an ILI event (n= 157) during the 2014-2015 influenza season. To investigate the dynamics of the microbiota from the acute phase to the recovery phase of the infection, participants reporting an ILI event were sampled at onset of infection (<72 hours), at 14 days and at 7-9 weeks after infection (recovery sample).ResultsCross-sectional analysis of the microbiota at the different time-points showed no differences in alpha diversity between the groups. A small but significant effect of the ILI was observed on the microbiota community and structure when compared to controls and recovery samples. Furthermore, the NP microbiota exhibited inter-individual differences in dynamics from onset of ILI to recovery.Corynebacterium, one of the keystone species in the upper respiratory tract, was negatively associated with ILI and its abundance increased after recovery. Potential pathobionts such asHaemophilus, PorphyromonasandGemellahad higher abundances during acute-ILI. Stability and changes in the NP microbial community showed individual dynamics. Key core genera,Corynebacterium, MoraxellaandDolosigranulumexhibited higher inter-individual variability in acute-ILI, but showed comparable variability to controls after recovery. Participants in the ILI group with higher core microbiota abundances at the acute phase showed higher microbiota stability after recovery.ConclusionsOur findings demonstrate that acute-ILI is associated with small but significant alterations in the phylogenetic structure of the NP microbiota in older adults. The observed variation in the core microbiota suggests potential imbalances in the ecosystem, which could play a role in the recovery of the NP microbiota after an ILI event.
MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data
Authors: Noecker Cecilia , Eng Alexander , Borenstein Elhanan 
Published: September 2021

AbstractMotivationRecent technological developments have facilitated an expansion of microbiome-metabolome studies, in which a set of microbiome samples are assayed using both genomic and metabolomic technologies to characterize the composition of microbial taxa and the concentrations of various metabolites. A common goal of many of these studies is to identify microbial features (species or genes) that contribute to differences in metabolite levels across samples. Previous work indicated that integrating these datasets with reference knowledge on microbial metabolic capacities may enable more precise and confident inference of such microbe-metabolite links.ResultsWe present MIMOSA2, an R package and web application for model-based integrative analysis of microbiome-metabolome datasets. MIMOSA2 uses reference databases to construct a community metabolic model based on microbiome data and uses this model to predict differences in metabolite levels across samples. These predictions are compared with metabolomics data to identify putative microbiome-governed metabolites and specific taxonomic contributors to metabolite variation. MIMOSA2 supports various input data types and can be customized to incorporate user-defined metabolic pathways. We demonstrate MIMOSA2’s ability to identify ground truth microbial mechanisms in simulation datasets, and compare its results with experimentally inferred mechanisms in a dataset describing honeybee gut microbiota. Overall, MIMOSA2 combines reference databases, a validated statistical framework, and a user-friendly interface to facilitate modeling and evaluating relationships between members of the microbiota and their metabolic products.Availability and ImplementationMIMOSA2 is implemented in R under the GNU General Public License v3.0 and is freely available as a web server and R package fromwww.borensteinlab.com/software_MIMOSA2.html.
A network approach to genetic circuit designs
Authors: Crowther Matthew , Wipat Anil , Goñi-Moreno Ángel 
Published: September 2021

AbstractAs genetic circuits become more sophisticated, the size and complexity of data about their designs increases. This data captured goes beyond monolithic genetic sequences and towards circuit modularity and functional details, which are beneficial for analyzing circuit performance and establishing design automation techniques. However, the accessibility, visualisation and usability of design data (and metadata) have received relatively little attention to date. Here, we present a method to turn circuit designs into networks and showcase its potential to enhance the utility of design data. Since networks are dynamic structures, initial graphs can be interactively shaped into sub-networks of relevant information based on requirements such as abstraction, hierarchy and protein interactions. Additionally, several visual changes can be applied, such as colouring or clustering nodes based on types (e.g., genes or promoters), resulting in easier comprehension from a user perspective. This approach allows circuit designs to be coupled to other networks, such as metabolic pathways or implementation protocols captured in graph-like formats. Therefore, we advocate using networks to structure, access and improve synthetic biology information.
Elevated phosphorylation of EGFR in NSCLC due to mutations in PTPRH
Authors: Swiatnicki Matthew R. , Rennhack Jonathan P. , Hollern Daniel P. , Perry Ashlee V. , Kubiak Rachel , Riveria Riveria Sarai M. , O’Reilly Sandra , Andrechek Eran R. 
Published: September 2021

AbstractThe role of EGFR in lung cancer is well described with numerous activating mutations that result in phosphorylation and tyrosine kinase inhibitors that target EGFR. While the role of the EGFR kinase in non-small cell lung cancer (NSCLC) is appreciated, control of EGFR signaling pathways through dephosphorylation by phosphatases is not as clear. In recent work we identified mutations in Protein Tyrosine Phosphatase Receptor Type H (Ptprh, also known as SAP-1) as being associated with elevated phosphorylation of EGFR in a mouse model of breast cancer. We have examined a series of tumors from this mouse model, revealing conserved V483MPtprhmutations within the FVB background, but a series of varied mutations in other backgrounds. Despite the variedPtprhmutations in other background strains, matched primary and metastatic tumors largely shared mutational profiles. Profiling the downstream events ofPtprhmutant tumors revealed AKT activation, suggesting a key target of PTPRH was EGFR tyrosine 1197. Given the role of EGFR in lung cancer, we explored TCGA data which revealed that a subset ofPTPRHmutant tumors shared gene expression profiles withEGFRmutant tumors, but thatEGFRmutations andPTPRHmutations were mutually exclusive. Generation of a PTPRH knockout NSCLC cell line resulted in Y1197 phosphorylation of EGFR, and a rescue with expression of wild type PTPRH returned EGFR phosphorylation to parental line values while a rescue with a D986A catalytically dead mutant PTPRH did not, demonstrating that PTPRH targets EGFR. As expected with active EGFR, the knockout of PTPRH was associated with increased growth rate. Moreover, a dose response curve illustrated that two human NSCLC lines that had naturally occurringPTPRHmutations responded to EGFR tyrosine kinase inhibition. Injection of one of the NSCLC human lines into mice resulted in tumors, and Osimertinib treatment resulted in a reduction of tumor volume relative to vehicle controls. Consistent with prior literature from breast cancer,PTPRHmutation resulted in nuclear pEGFR as seen in immunohistochemistry, suggesting that there may also be a role for EGFR as a transcriptional co-factor. Other roles for PTPRH were explored through a receptor tyrosine kinase array, noting elevated phosphorylation of FGFR1. Knockout of PTPRH in NSCLC cell lines resulted in elevated phosphorylated FGFR1 relative to controls, indicating that PTPRH has a number of targets that may be aberrantly activated in NSCLC with mutations in PTPRH. Together these data suggest that mutations in PTPRH in NSCLC may result in clinically actionable alterations using existing therapies.
Variance of allele balance calculated from low coverage sequencing data infers departure from a diploid state
Authors: Fletcher Kyle , Han Rongkui , Smilde Diederik , Michelmore Richard 
Published: September 2021

AbstractMotivationPolyploidy and heterokaryosis are common and consequential genetic phenomena that increase the number of haplotypes in an organism and complicate whole-genome sequence analysis. Allele balance has been used to infer polyploidy and heterokaryosis in diverse organisms using read sets sequenced to greater than 50x whole-genome coverage. However, Sequencing to adequate depth is costly if applied to multiple individuals or large genomes.ResultsWe developed VCFvariance.pl to utilize the variance of allele balance to infer polyploidy and/or heterokaryosis at low sequence coverage. This analysis requires as little as 10x whole-genome coverage and reduces the allele balance profile down to a single value, which can be used to determine if an individual has two or more haplotypes. This approach was validated on simulated, synthetic, and authentic read sets from an oomycete, fungus, and plant. The approach was deployed to ascertain the genome status of multiple isolates of Bremia lactucae and Phytophthora infestans.Availability and implementationVCFvariance.pl is a Perl script available at https://github.com/kfletcher88/VCFvariance.
Seeking transparency makes one blind: how to rethink disclosure, account for nature and make corporations sustainable
Authors: Quattrone Paolo 
Published: September 2021

PurposeFinancial and nonfinancial disclosures are still anchored to conventional notions of transparency, whereby corporations “push” information out to various stakeholders. Such information is now “pulled” from various sources and addresses aspects of corporate behavior that go well beyond those envisioned by the disclosure framework. This shift makes notions of values, measurement and accountability more fragmented, complex and difficult. The paper aims to bring the accounting scholarly debate back to what and how transparency can be achieved especially in relation to issues of social inequality and sustainability.Design/methodology/approachAfter an analysis of the limitations of current approaches to disclosure, the paper proposes a shift toward normative policies that profit of years of critique of positivism.FindingsDrawing on the notion of value-added, the paper ends with a new income statement design, labeled as Value-Added Statement for Nature, which recognizes Nature as a further stakeholder and forces human stakeholders to give voice, or at least acknowledge the lack of voice, for non-human actors.Originality/valueThe author proposes a shift in the perspective, practice and institutional arrangements in which disclosure occurs. Measurement and transparency need to happen in communication exercises, which do not presuppose what needs to be made transparent once and for good but define procedures on how to make fragmented, complex, multiple and volatile notions of value transparent. Income statements and accounting more in general is to be reconceived as a platform where stakeholders will have to continuously negotiate what counts as the common good in the interest of all, including Nature.
Research on automatic parking system based on linear quadratic regulator
Authors: Qian Yan , Wang Zhaoqiang , Liang Wei , Lu Chenhui 
Published: September 2021

PurposeThe purpose of this study is to solve the problem of path planning and path tracking in the automatic parking assistant system.Design/methodology/approachThis paper first uses the method of reverse driving to confirm few control points based on the constraints of the construction of the vehicle and the environment information, then a reference path with free-collision and continuous curvature is designed based on the Bézier curve. According to the principle of the discrete linear quadratic regulator (LQR), a tracking controller that combines feedforward control and feedback control is designed.FindingsFinally, simulation analysis are carried out in Simulink and CARSIM. The results show that the proposed method can obtain a better path tracking effect when the parking space size is appropriate.Originality/valueAccording to the principle of the discrete LQR, a tracking controller that combines feedforward control and feedback control is designed.
Cooperation for innovation: more is not necessarily merrier
Authors: Temel Serdal , Mention Anne-Laure , Yurtseven Alp Eren 
Published: September 2021

PurposeEmbracing a large set of innovation objectives and collaborating with diverse partners have been promoted as a means to improve innovation performance. However, empirical evidence on the relationships between breadth of objectives, breadth of cooperation and innovation performance is limited, particularly in the context of emerging economies. A larger number of objectives and cooperation partners inevitably increases the complexity in organizational alignment, and cooperation eventually leads to diminishing returns. This study adds to the debate on the costs and benefits of cooperation for innovation. Understanding the optimal levels of the breadth of objectives and cooperation supports managerial decision-making and productivity in the practice of cooperation for innovation.Design/methodology/approachOperationalizing breadth of innovation objectives and cooperation via the Turkish Community Innovation Survey data, self-reports reflecting 5,863 firm-level responses between 2006 and 2008 are analysed using tobit and probit models. The maximum likelihood estimator is used to find the optimal levels for breadth of objectives and cooperation.FindingsFirms with greater breadth of innovation objectives experience higher innovation performance; those with greater breadth of cooperation also experience higher innovation performance, but our results indicate the existence of optimal levels of breadth for both innovation objectives and cooperation.Research limitations/implicationsThe authors extend the logic that there is no safety in numbers in cooperation for innovation. If the aim is to enhance innovation performance, managers and policymakers need to pay attention to the number of innovation objectives and the amount of cooperation pursued by firms. However, innovation success may be closely associated with a firm's dynamic capabilities and ability to mobilize its resources. Drawing on organizational learning theories, future research could explore why a lower than maximum level of cooperation may be more conducive to reaching levels of enhanced innovation performance and whether this level is influenced by cognitive processes.Originality/valueThe authors draw attention to the ideal number of innovation objectives and number of cooperating partners required to enhance innovation performance, thus contributing to the debate on the complex relationships between innovation, performance and cooperation in the unique setting of a large developing economy.
Toward collaborative networking among innovation laboratories: a conceptual framework
Authors: Memon Atia Bano , Meyer Kyrill , Tunio Muhammad Nawaz 
Published: September 2021

PurposeThe purpose of this paper is to suggest a conceptual framework of collaborative networking among structurally and functionally varying types of Innovation Laboratories, which will enable them to leverage upon diverse competencies of each other and thereby facilitate their clients (business organizations) throughout the innovation process.Design/methodology/approachThe conceptual framework proposed herein is oriented around design science research, whereby the important constructs underpinning the development of framework are identified from existing literature. The framework is based upon two constructs, service-based categorization of extant Innovation Laboratories, and concepts of horizontal and vertical modes of inter-InnoLab collaboration (collaboration among Innovation Laboratories). The framework is subsequently developed in iterations based on experts’ views and discussions.FindingsThe conceptual framework presents eight different opportunities of interconnection among Innovation Laboratories including the four horizontal collaboration possibilities as network of mentors, network of process intermediaries, network of resource providers and network of network coordinators which are followed by four subsequent vertical collaboration possibilities among these horizontal collaboration networks. The proposed collaborative network of Innovation Laboratories enables undertaking of complete innovation process with four possible entry and four possible exit points for business organizations.Originality/valueThe conceptual framework proposed herein is first of its kind to suggest a worldwide collaborative networking among Innovation Laboratories. The applicability and usefulness of the framework is supported by the existingad hoctype individual collaborative activities being exercised by different kinds of Innovation Laboratories as reported by Innovation Laboratory facilitators and observed in practical field.
Peri-urban territories and rural water community governance in Chile
Authors: Duarte Vera Alejandra , Vanhulst Julien , Letelier Araya Eduardo Antonio 
Published: September 2021

PurposeRural drinking water services in Chile are managed by Rural Drinking Water Associations (RDWAs) with a community governance model. However, urban growth and a neoliberal institutional setting tend to favor market-style governance, both in terms of territorial planning and drinking water supply, placing stress on the community governance model of RDWA. The authors seek to understand these processes and identify the position of RDWA actors facing socio-territorial and environmental transformations experienced in peri-urban sectors of the city of Talca (Chile).Design/methodology/approachThe authors used georeferenced data, participant and non-participant observation and semi-structured interviews. With these data, the authors analyzed the positions and discourses of water governance actors in relation to socio-territorial transformations in the peri-urban areas of the city, as well as for tensions between community and market governance.FindingsThe authors identified a growth tendency of RDWA users around the city of Talca due to a sharp drinking water demand increase in peri-urban territories. As such, the authors describe and contrast RWDA managers and governmental regulators' discourses regarding environmental and socio-territorial transformations. In these discourses, the authors found three critical topics: (1) land liberalization blurring urban territory borders; (2) Law #20998, a poorly financed reform which raises the specter of RDWA privatization, jeopardizing historic community drinking water management; and (3) the consequences of declining community commitment to RDWAs.Practical implicationsOne key implication of these findings is the need to modify RDWA pricing policies to deal with new rural inhabitant lifestyles and drinking water demands and to fulfill water basic needs of rural families, avoiding privatization risks. This change could help not only dealing with growing scarcity during global climate change, but could also provide financial resources to face new technical and administrative requirements of SSR Law.Originality/valueThe originality of the study comes from using a framework of governance tensions applied to water governance in peri-urban areas in a neoliberal institutional setting.
Intensifying effects of COVID-19 on economic growth, logistics performance, environmental sustainability and quality management: evidence from Asian countries
Authors: Ikram Muhammad , Shen Yichen , Ferasso Marcos , D’Adamo Idiano 
Published: September 2021

Purpose
This study aims to explore the effects of the COVID-19 outbreak on exports of goods and services, logistics performance, environmental management system (ISO 14001) certification and quality management system (ISO 9001) certification in top affected Asian countries of India, Iran, Indonesia, Philippines, Bangladesh and Pakistan.

Design/methodology/approach
A novel grey relational analysis models’ approach is used to examine the inter-relationship between COVID-19 economic growth and environmental performance. Moreover, the authors applied a conservative (maximin) model to investigate which countries have the least intensifying affected among all of the top affected COVID-19 Asian countries based on the SS degree of grey relation values. The data used in this study was collected from multiple databases during 2020 for analysis.

Findings
Results indicate that the severity of COVID-19 shows a strong negative association and influence of COVID-19 on the exportation of goods and services, logistics performance, ISO 9001 and ISO 14001 certifications in all the six highly affected countries during a pandemic outbreak. Although the adverse effects of COVID-19 in exporting countries persisted until December 31, 2020, their magnitude decreased over time in Indonesia and Pakistan. During the COVID-19 outbreak, Pakistan showed comparatively better performance among the six top highly affected Asian countries due to its smart locked down strategy and prevents its economy from severe damages. While India and Iran export drastically go down due to a rapid increase in the number of COVID-19 cases and deaths.

Research limitations/implications
The research findings produce much-required policy suggestions for leaders, world agencies and governments to take corrective measures on an emergent basis to prevent the economies from more damages and improve their logistics, environmental and quality performance during the pandemic of COVID-19.

Originality/value
This study develops a framework and investigates the intensifying effects of COVID-19 effects on economic growth, logistics performance, environmental performance and quality production processes.