bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrodynamic and anthropogenic disturbances co-shape microbiota rhythmicity and community assembly within intertidal groundwater-surface water continuum
Authors: Zhao Ze , Zhang Lu , Zhang Guoqing , Gao Han , Chen Xiaogang , Li Ling , Ju Feng 
Published: November 2022

AbstractTidal hydrodynamics drive the groundwater-seawater exchange and shifts in microbiota structure in the coastal zone. However, how the coastal water microbiota structure and assembly patterns respond to periodic tidal fluctuations and anthropogenic disturbance remain unexplored in the intertidal groundwater-surface water (GW-SW) continuum, although it affects biogeochemical cycles and coastal water quality therein. Here, through hourly time-series sampling in the saltmarsh tidal creek, rhythmic patterns of microbiota structure in response to daily and monthly tidal fluctuations in intertidal surface water are disentangled for the first time. The similarity in archaeal community structures between groundwater and ebb-tide surface water (R2=0.06,p=0.2) demonstrated archaeal transport through groundwater discharge, whereas multi-source transport mechanisms led to unique bacterial biota in ebb-tide water. Homogeneous selection (58.6%-69.3%) dominated microbiota assembly in the natural intertidal GW-SW continuum and the presence of 157 rhythmic ASVs identified at ebb tide and 141 at flood tide could be attributed to different environmental selection between groundwater and seawater. For intertidal groundwater in the tidal creek affected by anthropogenically contaminated riverine inputs, higher microbial diversity and shift in community structure were primarily controlled by increased co-contribution of dispersal limitation and drift (jointly 57.8%) and enhanced microbial interactions. Overall, this study fills the knowledge gaps in the tide-driven water microbial dynamics in coastal transition zone and the response of intertidal groundwater microbiota to anthropogenic pollution of overlying waters. It also highlights the potential of microbiome analysis in enhancing coastal water quality monitoring and identifying anthropogenic pollution sources (e.g., aquaculture pathogenicVibrio) through the detection of rhythmic microbial variances associated with intertidal groundwater discharge and seawater intrusion.
A method to adjust for the uncertainty of predicted expression in transcriptome-wide association study
Authors: Majumdar Arunabha , Haldar Tanushree 
Published: November 2022

AbstractTranscriptome-wide association study (TWAS) is a powerful approach to identifying novel genes associated with complex phenotypes. Standard TWAS approaches build a prediction model for the genetic component of expression based on reference transcriptome data. Next, an outcome is regressed on the predicted expression in separate GWAS data. The traditional TWAS approach disregards the uncertainty of predicted expression, which can lead to unreliable inference on gene-phenotype associations. We propose a novel approach to adjust for the uncertainty of predicted expression in TWAS. We adapt techniques from measurement error theory and implement bootstrapping algorithms for penalized regression to explicitly obtain an adjustment factor that needs to be incorporated in the unadjusted TWAS. We base the framework on adaptive Lasso. We use extensive simulations to show that the traditional TWAS inflates the type I error rate, whereas the adjusted TWAS adequately controls it. At the expense of an inflated false positive rate, the unadjusted TWAS offers a limited increase in power than the adjusted TWAS, which is statistically unjustified. Our approach produces more accurate estimates of the gene’s effect size than a traditional approach. We demonstrate the merits of the adjusted approach by conducting TWAS for height and lipid phenotypes, LDL, HDL, and triglycerides while integrating the Geuvadis transcriptome and UK Biobank GWAS data.
Whole-cortex in situ sequencing reveals peripheral input-dependent cell type-defined area identity
Authors: Chen Xiaoyin , Fischer Stephan , Rue Mara CP , Zhang Aixin , Mukherjee Didhiti , Kanold Patrick O , Gillis Jesse , Zador Anthony M 
Published: November 2022

AbstractThe cortex is composed of neuronal types with diverse gene expression that are organized into specialized cortical areas. These areas, each with characteristic cytoarchitecture (Brodmann 1909; Vogt and Vogt 1919; Von Bonin 1947), connectivity (Zingg et al. 2014; Harris et al. 2019), and neuronal activity (Schwarz et al. 2008; Ferrarini et al. 2009; He et al. 2009; Meunier et al. 2010; Bertolero et al. 2015), are wired into modular networks (Zingg et al. 2014; Harris et al. 2019; Huang et al. 2020). However, it remains unclear whether cortical areas and their modular organization can be similarly defined by their transcriptomic signatures and how such signatures are established in development. Here we used BARseq, a high-throughputin situsequencing technique, to interrogate the expression of 104 cell type marker genes in 10.3 million cells, including 4,194,658 cortical neurons over nine mouse forebrain hemispheres at cellular resolution.De novoclustering of gene expression in single neurons revealed transcriptomic types that were consistent with previous single-cell RNAseq studies(Yao et al. 2021a; Yao et al. 2021b). Gene expression and the distribution of fine-grained cell types vary along the contours of cortical areas, and the composition of transcriptomic types are highly predictive of cortical area identity. Moreover, areas with similar compositions of transcriptomic types, which we defined as cortical modules, overlap with areas that are highly connected, suggesting that the same modular organization is reflected in both transcriptomic signatures and connectivity. To explore how the transcriptomic profiles of cortical neurons depend on development, we compared the cell type distributions after neonatal binocular enucleation. Strikingly, binocular enucleation caused the cell type compositional profiles of visual areas to shift towards neighboring areas within the same cortical module, suggesting that peripheral inputs sharpen the distinct transcriptomic identities of areas within cortical modules. Enabled by the high-throughput, low-cost, and reproducibility of BARseq, our study provides a proof-of-principle for using large-scalein situsequencing to reveal brain-wide molecular architecture and to understand its development.
A novel pathway of functional microRNA uptake and mitochondria delivery
Authors: Liu Jiachen , Li Weili , Li Jianfeng , Song Eli , Liang Hongwei , Rong Weiwei , Jiang Xinli , Xu Nuo , Wang Wei , Qu Shuang , Zhang Yujing , Zhang Chen-Yu , Zen Ke 
Published: November 2022

AbstractExtracellular miRNAs serve as signal molecules in the recipient cells. Uptake of extracellular miRNAs by the recipient cells and their intracellular transport, however, remains elusive. Here we show RNA phase separation as a novel pathway of miRNA uptake. In the presence of serum, synthetic miRNAs rapidly self-assembly into ∼110nm discrete nanoparticles which enable miRNAs’ entry into different cells. Depleting serum cationic proteins prevents the formation of such nanoparticles and thus blocks miRNA uptake. Different from lipofectamine-mediated miRNA transfection in which the majority of miRNAs are in lysosomes of transfected cells, nanoparticles-mediated miRNA uptake predominantly delivers miRNAs into mitochondria in a polyribonucleotide nucleotidyltransferase 1-dependent manner. Functional assays further show that the internalized miR-21 via miRNA phase separation enhances mitochondrial translation of Cytochrome b, leading to increase in ATP and ROS reduction in HEK293T cells. Our findings reveal a previously unrecognized mechanism for uptaking and delivering functional extracellular miRNAs into mitochondria.SynopsisRNA phase separation-based extracellular miRNA uptake and PNPT1-mediated mitochondrial delivery of internalized miRNAsmiRNAs can self-assembly into ∼110nm nanoparticles to enter various cells in the presence of serummiRNA phase separation is mediated by serum cationic proteinsInternalized miRNAs via this nanoparticle pathway are predominantly delivered to mitochondriaMitochondrial delivery of the internalized miRNAs is mediated by PNPT1
ShigellaipaA mediates actin bundling through diffusible vinculin oligomers with activation imprint
Authors: Valencia-Gallardo Cesar , Aguilar-Salvador Daniel-Isui , Khakzad Hamed , Cocom-Chan Benjamin , Bou-Nader Charles , Velours Christophe , Zarrouk Yosra , Le Clainche Christophe , Malosse Christian , Lima Diogo Borges , Quenech’Du Nicole , Mazhar Bilal , Essid Sami , Fontecave Marc , Asnacios Atef , Chamot-Rooke Julia , Malmström Lars , Van Nhieu Guy Tran 
Published: November 2022

AbstractUpon activation, vinculin reinforces cytoskeletal anchorage during cell adhesion. Activating ligands classically disrupt intramolecular interactions between the vinculin head and tail domain that binds to actin filaments. Here, we show thatShigellaIpaA triggers major allosteric changes in the head domain leading to vinculin homo-oligomerization. Through the cooperative binding of its three vinculin-binding sites (VBSs), IpaA induces a striking reorientation of the D1 and D2 head subdomains associated with vinculin oligomerization. IpaA thus acts as a catalyst producing vinculin clusters that bundle actin at a distance from the activation site and trigger the formation of highly stable adhesions resisting the action of actin relaxing drugs. Unlike canonical activation, vinculin homo-oligomers induced by IpaA appear to keep a persistent imprint of the activated state in addition to their bundling activity, accounting for stable cell adhesion independent of force transduction and relevant to bacterial invasion.
Human cerebrospinal fluid sample preparation and annotation for integrated lipidomics and metabolomics profiling studies
Authors: Hooshmand Kourosh , Xu Jin , Simonsen Anja Hviid , Wretlind Asger , de Zawadzki Andressa , Sulek Karolina , Hasselbalch Steen Gregers , Legido-Quigley Cristina 
Published: November 2022

AbstractObjectiveMass spectrometry (MS)-based lipidomics and metabolomics approaches play an essential role in identifying molecular profiles and relevant clinical biomarkers associated with diseases. Cerebrospinal fluid (CSF) is a metabolically diverse biofluid and a key specimen for exploring biochemical changes in neurodegenerative diseases because its composition reflects brain metabolic activity. CSF lipidomics is receiving increasing attention owing to the importance of lipids in brain molecular signaling and their association with several neurological diseases. Detecting lipid species in CSF using MS-based techniques remains challenging because lipids are highly complex in structure and their concentrations span over a broad dynamic range. This work aimed to develop a robust lipidomics and metabolomics method based on commonly used two-phase extraction systems from human CSF samples.MethodsPrioritizing lipid detection, biphasic extraction methods, Folch, Bligh & Dyer (B&D), Matyash and acidified Folch and B&D (aFolch and aB&D), were compared using 150 μl of human CSF samples (n=6) for the simultaneous extraction of lipids and metabolites with a wide range of polarity in a single extraction. Multiple chromatographical separation approaches, including reversed-phase liquid chromatography (RPLC), hydrophilic interaction liquid chromatography (HILIC), and gas chromatography (GC), were utilized to characterize human CSF metabolome through MS-based untargeted approaches.ResultsA total of 219 lipids across 12 lipid subclasses were identified in CSF samples using RPLC-MS/MS. The aB&D method was found as the most reproducible technique (RSD <15%) for lipid extraction. We found remarkable differences in extraction efficiencies among the five different procedures. The aB&D and B&D yielded the highest peak intensities for targeted lipid internal standards and displayed superior extracting power for major endogenous lipid classes. A total of 674 unique metabolites with a wide polarity range were annotated in CSF using, combining RPLC-MS/MS (n=219), HILIC-MS/MS (n=304) and GC-QTOF MS (n=151).ConclusionsOverall, our findings show that the aB&D extraction method provided suitable lipid coverage, reproducibility, and extraction efficiency for global lipidomics profiling of human CSF samples. In combination with RPLC-MS/MS lipidomics, complementary screening approaches enabled a comprehensive metabolite signature that can be employed in an array of clinical studies.
Adoption of modern technologies for implementing industry 4.0: an integrated MCDM approach
Authors: Javaid Mohd , Khan Shahbaz , Haleem Abid , Rab Shanay 
Published: November 2022

PurposeModern technologies are seen as an essential component of the fourth industrial revolution (industry 4.0) and their adoption is vital to transform the existing manufacturing system into industry 4.0-based manufacturing system. Therefore, the primary objective of this research explores the barriers of modern technology adoption and their mitigating solutions in order to align with Industry 4.0 objectives.Design/methodology/approachBarriers to adopting modern technologies and respective mitigating solutions are identified from the available literature. Further, these barriers are ranked with the help of expert opinions by using the BWM method appropriately. The identified solutions are ranked using the combined compromise solution (CoCoSo) method.FindingsSeveral modern technologies and their capabilities are recognised to support the industry 4.0-based manufacturing systems. This study identifies 22 barriers to the effective adoption of modern technologies in manufacturing and 14 solutions to overcome these barriers. Change management, the high initial cost of technology and appropriate support infrastructure are the most significant barriers. The most prominent solutions to overcome the most considerable barriers are ‘supportive research, development and commercialisation environment’, ‘updated policy and effective implementation’ and ‘capacity building through training’ that are the top three solutions that need to be addressed.Research limitations/implicationsThe barriers and solutions of modern technology adoption are obtained through a comprehensive literature review, so there is a chance to ignore some significant barriers and their solutions. Furthermore, ranking barriers and solutions is done with expert opinion, which is not free from biases.Practical implicationsThis identification and prioritisation of barriers will help managers to understand the barriers so they can better prepare themselves. Furthermore, the suggested solutions to overcome these barriers are helpful for the managers and could be strategically adopted through optimal resource utilisation.Originality/valueThis study proposes a framework to identify and analyse the significant barriers and solutions to adopting modern technologies in the manufacturing system. It might be helpful for manufacturing organisations that are willing to transform their manufacturing system into industry 4.0.
Do different dimensions of corporate social responsibility disclosure have different economic consequence: multi-approaches for profitability examination
Authors: Alshurafat Hashem , Ananzeh Husam , Al-Hazaima Huthaifa , Al Shbail Mohannad Obeid 
Published: November 2022

PurposeThis study examines the impact of Corporate Social Responsibility Disclosure (hereafter CSRD) on the Corporate Economic Performance (hereafter CEP) of a group of public shareholding companies in Jordan.Design/methodology/approachThis study uses different proxies to examine the impact of CSRD on companies’ financial and economic value. The data were collected from a sample of 94 companies listed on the Amman Stock Exchange from 2010 to 2016. Based on a checklist of 41 indicators, this study employed the manual content analysis technique to collect and analyse CSRD data. A statistical analysis technique was also used to examine the hypothesized relationships between collected data on CSRD and profitability.FindingsThe findings indicate that CSRD is value-relevant. It is positively and statistically associated with firm value proxied by Tobin’s Q. In addition, it is positively and statistically associated with firm financial performance proxied by ROE and ROA.Research limitations/implicationsThis study contributes to the research debate on the relationship between CSRD and CEP, particularly in developing nations. The study draws attention to the need for information on different dimensions of CSR, including human resource, environmental, product responsibility, and community participation, as disclosure on such dimensions is positively associated with profitability.Practical implicationsThe findings provide important implications for Jordanian corporate managers to maintain CSRD in their best interest. With more emphasis on disclosing stand-alone CSR reports, corporate managers can present more information on different dimensions of CSR, attracting the attention of stakeholders such as investors, the government, media, and humanitarian activists and enhancing overall corporate goodwill.Originality/valueCSRD activities reflect a positive impact on CEP. Due to the dearth of relevant research conducted in developing countries, this study provides empirical evidence on the positive relationship between CSRD and CEP in an emerging economy, with more emphasis on specific dimensions of CSR, including human resources, environmental, product responsibility, and community participation. Since multiple proxies exist to measure profitability, this study uses multi-approaches for profitability examination proxied by Tobin’s Q, ROE, and ROA. Moreover, the issue of CSR is original and interesting to be examined in the Jordanian context, where the listed firms have reported a homogeneous perception of CSR.
Managerial control systems and innovation partnership success: an empirical analysis in Italian firms
Authors: Pistoni Anna , Arcari Anna , Gigliarano Chiara 
Published: November 2022

PurposeThis study analyses the link between product/service innovation, partnerships and Managerial Control System (MCS). Particularly, it aims to analyse empirically the role of MCS in supporting the innovation partnership successful functioning and management.Design/methodology/approachThe sample of this study consists of 106 Italian manufacturing firms belonging to the sectors of the Italian economy with the largest number of registered patents according to the European trend chart on innovation.FindingsThe results show that MCS may play a key role in reducing risks and lowering the likelihood of failure of innovation partnerships. Particularly, the authors found a positive correlation between the use of informal control mechanisms and a partnership’s successful performance. Moreover, among informal control, the findings show that trust is the only true informal mechanism that can guarantee a successful collaboration. The results of this study may offer relevant implications for practitioners. With regard to the control of the partnership’s activities, the initiatives and creativity of those who are actively involved in the innovation process should not be inhibited; therefore, stifling them with strict rules and procedures would be ineffective but if a firm is not willing to give up formal control mechanisms altogether because it does not believe that a trust-based coordination is sufficiently reassuring, it should opt for “weak”, albeit formal, control mechanisms based on a shared production and management of plans and reports, thus ensuring a perfect information symmetry among different partners.Originality/valueNotwithstanding the different opportunities provided by partnerships and strategic alliances to support there is a growing body of evidence of a high failure rate in such organisational forms. One of the causes cited in the literature is the high level of risk associated with alliances as compared to internal development of innovation. The risks mainly arise from the difficulties to obtain cooperation with partners that might have different objectives, and from the potential opportunistic behaviour of some of the partners. This is particularly true in innovation networks where the uncertainty of producing an interesting result is very high and the investments that the partners make are considerable. In this context, MCS could play a relevant role in reducing the risks and decreasing the likelihood of failure.
PFSA-ID: an annotated Indonesian corpus and baseline model of public figures statements attributions
Authors: Purnomo W.P. Yohanes Sigit , Kumar Yogan Jaya , Zulkarnain Nur Zareen 
Published: November 2022

Purpose
By far, the corpus for the quotation extraction and quotation attribution tasks in Indonesian is still limited in quantity and depth. This study aims to develop an Indonesian corpus of public figure statements attributions and a baseline model for attribution extraction, so it will contribute to fostering research in information extraction for the Indonesian language.

Design/methodology/approach
The methodology is divided into corpus development and extraction model development. During corpus development, data were collected and annotated. The development of the extraction model entails feature extraction, the definition of the model architecture, parameter selection and configuration, model training and evaluation, as well as model selection.

Findings
The Indonesian corpus of public figure statements attribution achieved 90.06% agreement level between the annotator and experts and could serve as a gold standard corpus. Furthermore, the baseline model predicted most labels and achieved 82.026% F-score.

Originality/value
To the best of the authors’ knowledge, the resulting corpus is the first corpus for attribution of public figures’ statements in the Indonesian language, which makes it a significant step for research on attribution extraction in the language. The resulting corpus and the baseline model can be used as a benchmark for further research. Other researchers could follow the methods presented in this paper to develop a new corpus and baseline model for other languages.
A systematic literature review on supply chain resilience in SMEs: learnings from COVID-19 pandemic
Authors: Mishra Ruchi , Singh Rajesh Kumar 
Published: November 2022

PurposeThe study aims to review state-of-art literature on supply chain resilience in SMEs in the context of the coronavirus (COVID-19) pandemic and provides a comprehensive view of insights gained, gaps identified and suggests potential areas of future research.Design/methodology/approachUsing a thorough search strategy, 46 articles were found relevant for this study. Each of these articles was further reviewed, classified and analysed to highlight the development of literature in this field and identify the significant focal area of research in this domain.FindingsThe classification of studies indicates a growing number of articles in the last two years with a significant focus on multiple industries and survey-based research design. The study's findings suggest that literature on supply chain resilience in SMEs falls into four categories: supply chain resilience principle, impact of COVID-19 pandemic on SMEs, strategies for developing supply chain resilience and role of Industry 4.0 technologies in supply chain resilience. We also identified knowledge gaps and suggested directions for future research to catalyse studies at the interface of supply chain resilience, SMEs and COVID-19 pandemic.Research limitations/implicationsThe generalisability of this study can be limited to a specific population of online databases and selected time periods chosen for a particular period.Originality/valueThe study provides a structured literature review on studies published between 2012 and 2022 for the use of academicians and practitioners. Findings will be of great value for SMEs to improve their resilience during the uncertain business environment.