bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community-based Reconstruction and Simulation of a Full-scale Model of Region CA1 of Rat Hippocampus
Authors: Romani Armando , Antonietti Alberto , Bella Davide , Budd Julian , Giacalone Elisabetta , Kurban Kerem , Sáray Sára , Abdellah Marwan , Arnaudon Alexis , Boci Elvis , Colangelo Cristina , Courcol Jean-Denis , Delemontex Thomas , Ecker András , Falck Joanne , Favreau Cyrille , Gevaert Michael , Hernando Juan B. , Herttuainen Joni , Ivaska Genrich , Kanari Lida , Kaufmann Anna-Kristin , King James Gonzalo , Kumbhar Pramod , Lange Sigrun , Lu Huanxiang , Lupascu Carmen Alina , Migliore Rosanna , Petitjean Fabien , Planas Judit , Rai Pranav , Ramaswamy Srikanth , Reimann Michael W. , Riquelme Juan Luis , Guerrero Nadir Román , Shi Ying , Sood Vishal , Sy Mohameth François , Van Geit Werner , Vanherpe Liesbeth , Freund Tamás F. , Mercer Audrey , Muller Eilif , Schürmann Felix , Thomson Alex M. , Migliore Michele , Káli Szabolcs , Markram Henry 
Published: May 2023

AbstractThe CA1 region of the hippocampus is one of the most studied regions of the rodent brain, thought to play an important role in cognitive functions such as memory and spatial navigation. Despite a wealth of experimental data on its structure and function, it has been challenging to reconcile information obtained from diverse experimental approaches. To address this challenge, we present a community-driven, full-scalein silicomodel of the rat CA1 that integrates a broad range of experimental data, from synapse to network, including the reconstruction of its principal afferents, the Schaffer collaterals, and a model of the effects that acetylcholine has on the system. We tested and validated each model component and the final network model, and made input data, assumptions, and strategies explicit and transparent. The unique flexibility of the model allows scientists to address a range of scientific questions. In this article, we describe the methods used to set up simulations that reproduce and extendin vitroandin vivoexperiments. Among several applications in the article, we focus on theta rhythm, a prominent hippocampal oscillation associated with various behavioral correlates and use our computer model to reproduce and reconcile experimental findings. Finally, we make data, code and model available through the hippocampushub.eu portal, which also provides an extensive set of analyses of the model and a user-friendly interface to facilitate adoption and usage. This neuroscience community-driven model represents a valuable tool for integrating diverse experimental data and provides a foundation for further research into the complex workings of the hippocampal CA1 region.
Bacteriophage populations mirror those of bacterial pathogens at sites of infection
Authors: Haddock NL , Barkal LJ , Bollyky PL 
Published: May 2023

AbstractBacteriophages, viruses that parasitize bacteria, are known to be abundant at sites of bacterial colonization but the relationship between phages and bacteria at sites of infection is unclear. Bacteriophage are highly specific to their bacterial host species and so we hypothesize that phage populations would mirror those of bacterial pathogens within infected tissues. To test this, here we study publicly-available cell-free DNA generated using next generation sequencing of infected bodily fluids, including urine, joint fluid, peritoneal fluid, bronchoalveolar lavage fluid, cerebrospinal fluid, and abscess fluid as well as uninfected control samples. These were analyzed using a computational pipeline for identifying bacteriophage sequences in cfDNA. We find that bacteriophage sequences are present in both infected and uninfected bodily fluids and represent a variety of bacteriophage morphologies and bacterial hosts. Additionally, phages fromE. coli, Streptococcus, andS. aureusare overrepresented both in terms of proportion and diversity in fluids infected with these same pathogens. These data indicate that phages reflect the relative abundance of their bacterial hosts at sites of infection. Bacteriophage sequences may help inform future investigative and diagnostic approaches that utilize cell-free DNA to study the microbiome within infected tissues.ImportanceBacteriophages are an active area of investigation in microbiome research but most studies have focused on phage populations at sites of bacterial colonization. Little is known about bacteriophage ecology at sites of active infection. To address this gap in knowledge, we utilized a publicly available dataset to study bacteriophage populations in cell free DNA collected from sites of infection. We find that phages reflect the relative abundance of their bacterial hosts at sites of infection. These studies may lead to future investigative and diagnostic approaches that incorporate phages as well as bacterial cell free DNA.
Neural Tracking Measures of Speech Intelligibility: Manipulating Intelligibility while Keeping Acoustics Unchanged
Authors: Karunathilake I.M Dushyanthi , Kulasingham Joshua P. , Simon Jonathan Z. 
Published: May 2023

AbstractNeural speech tracking has advanced our understanding of how our brains rapidly map an acoustic speech signal onto linguistic representations and ultimately meaning. It remains unclear, however, how speech intelligibility is related to the corresponding neural responses. Many studies addressing this question vary the level of intelligibility by manipulating the acoustic waveform, but this makes it difficult to cleanly disentangle effects of intelligibility from underlying acoustical confounds. Here, using magnetoencephalography (MEG) recordings, we study neural measures of speech intelligibility by manipulating intelligibility while keeping the acoustics strictly unchanged. Acoustically identical degraded speech stimuli (three-band noise vocoded, ∼20 s duration) are presented twice, but the second presentation is preceded by the original (non-degraded) version of the speech. This intermediate priming, which generates a ‘pop-out’ percept, substantially improves the intelligibility of the second degraded speech passage. We investigate how intelligibility and acoustical structure affects acoustic and linguistic neural representations using multivariate Temporal Response Functions (mTRFs). As expected, behavioral results confirm that perceived speech clarity is improved by priming. TRF analysis reveals that auditory (speech envelope and envelope onset) neural representations are not affected by priming, but only by the acoustics of the stimuli (bottom-up driven). Critically, our findings suggest that segmentation of sounds into words emerges with better speech intelligibility, and most strongly at the later (∼400 ms latency) word processing stage, in prefrontal cortex (PFC), in line with engagement of top-down mechanisms associated with priming. Taken together, our results show that word representations may provide some objective measures of speech comprehension.Significance StatementElectrophysiological studies have shown that brain tracks different speech features. How these neural tracking measures are modulated by speech intelligibility, however, remained elusive. Using noise-vocoded speech and a priming paradigm, we disentangled the neural effects of intelligibility from the underlying acoustical confounds. Neural intelligibility effects are analyzed at both acoustic and linguistic level using multivariate Temporal Response Functions. Here, we find evidence for an effect of intelligibility and engagement of top-down mechanisms, but only in responses to lexical structure of the stimuli, suggesting that lexical responses are strong candidates for objective measures of intelligibility. Auditory responses are not influenced by intelligibility but only by the underlying acoustic structure of the stimuli.
The cholesterol pathway of the Golgi stress response induces cell death and transcription of Golgi-related genes through metabolic dysregulation of phosphatidylinositol-4-phosphate
Authors: Sasaki Kanae , Adachi Takuya , Morishita Fumi , Toide Marika , Watanabe Yuto , Sakurai Hajime Tajima , Wakabayashi Sadao , Kusumi Satoshi , Yamaji Toshiyuki , Sakurai Kaori , Koga Daisuke , Hanada Kentaro , Yohda Masafumi , Yoshida Hiderou 
Published: May 2023

AbstractThe Golgi stress response is an important cytoprotective system that enhances Golgi function in response to cellular demand, while cells damaged by prolonged Golgi stress undergo cell death to ensure the survival of organisms. OSW-1, a natural compound with anticancer activity, acts as a potent inhibitor of OSBP that transports cholesterol and phosphatidylinositol-4-phosphate (PI4P) at contact sites between the endoplasmic reticulum and the Golgi apparatus. Previously, we reported that OSW-1 induces the Golgi stress response, resulting in Golgi stress-induced transcription and cell death. However, the underlying molecular mechanism has been unknown. To reveal the mechanism of a novel pathway of the Golgi stress response regulating transcriptional induction and cell death (the cholesterol pathway), we performed a genome-wide knockout screen and found that transcriptional induction as well as cell death induced by OSW-1 was repressed in HeLa cells deficient in factors involved in the PI4P metabolism, such as PITPNB and PI4KB genes. Our data indicate that OSW-1 induces Golgi stress-dependent transcriptional induction and cell death through dysregulation of the PI4P metabolism in the Golgi apparatus.
Myeloid Cell Derived IL1β Contributes to Pulmonary Vascular Remodeling in Heart Failure with Preserved Ejection Fraction
Authors: Agrawal Vineet , Kropski Jonathan A. , Gokey Jason J. , Kobeck Elizabeth , Murphy Matthew , Murray Katherine T. , Fortune Niki L. , Moore Christy S. , Meoli David F. , Monahan Ken , Su Yan Ru , Blackwell Thomas , Gupta Deepak K. , Talati Megha H. , Gladson Santhi , Carrier Erica J. , West James D. , Hemnes Anna R. 
Published: May 2023

ABSTRACTBackgroundPulmonary hypertension (PH) in heart failure with preserved ejection fraction (HFpEF) is a common and highly morbid syndrome, but mechanisms driving PH-HFpEF are not well understood. We sought to determine whether a well-accepted murine model of HFpEF also displays features of PH in HFpEF, and we sought to identify pathways that might drive early remodeling of the pulmonary vasculature in HFpEF.MethodsEight week old male and female C57/BL6J mice were given either L-NAME and high fat diet (HFD) or control water/diet for 2,5, and 12 weeks. Bulk RNA sequencing and single cell RNA sequencing was performed to identify early and cell-specific pathways that might regulate pulmonary vascular remodeling in PH-HFpEF. Finally, clodronate liposome and IL1β antibody treatments were utilized to deplete macrophages or IL1β, respectively, to assess their impact on pulmonary vascular remodeling in HFpEF.ResultsMice given L-NAME/HFD developed PH, small vessel muscularization, and right heart dysfunction after 2 weeks of treatment. Inflammation-related gene ontologies were over-represented in bulk RNA sequencing analysis of whole lungs, with an increase in CD68+ cells in both murine and human PH-HFpEF lungs. Cytokine profiling of mouse lung and plasma showed an increase in IL1β, which was confirmed in plasma from patients with HFpEF. Single cell sequencing of mouse lungs also showed an increase in M1-like, pro-inflammatory populations of Ccr2+ monocytes and macrophages, and transcript expression of IL1β was primarily restricted to myeloid-type cells. Finally, clodronate liposome treatment prevented the development of PH in L-NAME/HFD treated mice, and IL1β antibody treatment also attenuated PH in L-NAME/HFD treated mice.ConclusionsOur study demonstrated that a well-accepted model of HFpEF recapitulates features of pulmonary vascular remodeling commonly seen in patients with HFpEF, and we identified myeloid cell derived IL1β as an important contributor to PH in HFpEF.
Understanding the effects of personality traits on the quality of individual ideas on open innovation platforms: a mediated empirical investigation
Authors: Zhou Lixin , Zhang Zhenyu , Zhao Laijun , Yang Pingle 
Published: May 2023

PurposeOnline open innovation platforms provide opportunities for product users to participate in the innovation process and contribute their ideas to the platform. Nonetheless, they also present a significant challenge for platform managers, who select high-quality innovations from a massive collection of information with diverse quality.Design/methodology/approachIn this study, the authors employed a machine learning method to automatically collect a real dataset of 2,276 innovations and 30,004 detailed comments from the online platform of IdeaExchange and then conducted empirical experiments to verify the study hypothesis.FindingsResults show that extraversion, conscientiousness and openness to experience positively and directly influenced the quality of their innovation. Furthermore, an individual's social network position mediated among extraversion, neuroticism, conscientiousness and openness to experience and the quality of an innovation.Research limitations/implicationsResults showed that extraversion, conscientiousness and openness to experience positively and directly influenced the quality of their innovation. Furthermore, an individual's social network position mediated among extraversion, neuroticism, conscientiousness, openness to experience and the quality of innovations.Originality/valueThis study combined the Big Five personality traits theory and social network theory to examine the association between user intrinsic personality traits, social network position and the quality of their innovative ideas in the context of online innovation platforms. Additionally, the findings provide new insights for platform managers on how to select high-quality innovation information by considering user personality traits and their social network position.
Barriers to environmental impact assessment implementation for construction projects in Nigeria
Authors: Osuizugbo Innocent Chigozie , Nnodu Chinedu Valerie 
Published: May 2023

PurposeEnvironmental impact assessment (EIA) is one of the best approaches to identifying, preventing, minimising, compensating for any unfavourable impacts on the environment and also encouraging sustainability. This paper aims to investigate the barriers to EIA implementation for construction projects in Nigeria.Design/methodology/approachThe study adopted a survey research technique. The snowball sampling approach was adopted to identify key stakeholders in EIA practice for the administration of questionnaire. A total of 187 questionnaires were administered and a response rate of 60% (113 questionnaires were adequately filled and returned) was achieved. Descriptive and inferential statistics were utilised in analysing elicited data.FindingsThe results from data analysis showed that, “failure to influence the decision-making process/multiple conflicting decision-making”, “unstable regulatory regime”, “lack of available, accessible and fit-for purpose data”, “inadequate public knowledge of legal issues” and “poor provision of information” were the top most five barriers to EIA implementation for construction projects in Nigeria. Also, the results from the research show a statistically significant degree of agreement on the rankings by the groups of key stakeholders in EIA concerning the barriers to EIA implementation for construction projects.Originality/valueThis paper contributed to more effective EIA studies by drawing attentions to barriers to EIA implementation for construction projects. An understanding of these barriers can help key stakeholders in the construction industry of developing countries such as Nigeria to facilitate development of methods required in reducing barriers to EIA implementation in the construction sector.
A fuzzy AHP study of barriers for circularity in the wine sector in Bulgaria
Authors: Dimitrova Vesselina , Gallucci Teodoro , Marinov Georgi , Boshnakov Petyo 
Published: May 2023

PurposeIdentifying the barriers that hinder the circularity in the wine industry in Bulgaria and proposing a preliminary circular economy (CE) index for ranking in order of importance the barriers for providing a suitable and replicable model through the contextualization of the study applied at the territorial level.Design/methodology/approachThe article adopts a Fuzzy AHP methodology based on 6 main barriers and 19 sub-barriers to find the weights of the barriers and rank them. The study was conducted in Bulgaria, and it consists of a questionnaire with pairwise comparisons to ask for expert opinions of members of the Executive Board of the National Association of Bulgarian Vinegrowers and additional members of the regional vine and winegrowing chambers.FindingsThe study identifies training and education and environmental barriers as the most important among the main barriers whereas, economic barriers are assessed as low impact. Considering the sub-barriers, lack of consumer awareness and interest, unclear taxation for CE, lack of knowledge about environmental emissions (carbon, water etc.) within the supply chains, and lack of digital trends are determined as the most significant sub-barriers.Research limitations/implicationsThe preliminary CE index can be practically used and tested, when necessary, by each winemaker according to their understanding and opinion of CE barriers and sub-barriers. The ranking within the CE index can lead winemakers also to decisions related to the company's social policy.Originality/valueThe study uses the Fuzzy AHP methodology with expert opinions to analyze and weigh the main barriers to achieving CE at the micro-level.
A non-parametric synthesis measure for board quality: empirical evidence from Indian banks
Authors: Singh Rohit Kumar , Sharma Supran Kumar 
Published: May 2023

PurposeThe paper aims to craft a non-parametric composite value for the board quality of Indian banks where the weights can be assigned endogenously.Design/methodology/approachThe study employed a non-parametric data envelopment analysis (DEA)-based novel extension known as the benefit of doubt approach. To measure the strength of the Indian bank corporate board in terms of board efficiency (BEF), the study used a mixed approach, i.e. first, the study calculates the percentile ranks of the five attributes that the study assumes are the characteristics of the strong board including board size, number of outside directors, frequency of meetings, non-duality leadership and board gender diversity. Thereafter, the study performs the benefit-to-doubt approach to finally measure the efficiency of the board.FindingsThe findings of the study establish that the methodological framework present in the study to measure the strength of the board in terms of BEF has been a much superior method over the other weighted and non-weighted linear average methods.Practical implicationsThis methodology aids the shareholders, investors and regulatory bodies in rating the Indian banks based on their strength in terms of better monitoring boards and ensuring a smooth agent–owner relationship.Originality/valueThe benefit of doubt approach has been a unique and novel methodology to craft the composite value for any multidimensional phenomenon. One of the major benefits of using this approach is that it assigns the weights endogenously to each dimension and thereafter collectively determines the efficiency of such a phenomenon.
Impact of COVID-19 on logistics sector companies
Authors: Vilko Jyri , Hallikas Jukka 
Published: May 2023

PurposeThe scale and measure of the impact of the coronavirus disease 2019 (COVID-19) on economic development has been a popular topic in the literature. The global pandemic has posed challenges to the supply chains and logistics in many countries, causing delays and disrupting supply chains and decreasing the volume of logistics flows. To ensure economic growth in the future, it is essential to acknowledge the impact the COVID-19 in order to increase the accuracy of anticipating changes during widespread pandemic. In this study, the linkage between economic development and the COVID-19 estimated and real impact is illustrated in a case study comparison between the Finnish and German logistic companies' viewpoints. The study shows how the international COVID-19 pandemic has affected to logistics organization perceptions on the changes in operational environment and continuity of business.Design/methodology/approachThe empirical part of the study relies on mixed methods approach using panel data from logistics companies and expert group discussion. The panel data participants were logistics sector actors and the data was collected through a questionnaire. Numerous sources found from the literature are used to gain a holistic understanding of the attributes and impact of change in the logistics field.FindingsThis study provides an important, yet sparsely addressed viewpoint to the supply chain management literature by illustrating the changes caused be a widespread pandemic can cause to the logistics sector companies. Furthermore, the findings illustrate how different roles in supply chain actors perceived the COVID-19 in their operations, before and during the pandemic. The findings of the paper illustrate how drastic uncertainty and changes in the operational environment is seen in the logistics organizations. The findings suggest that increased uncertainty and changes in the operational environment can cause significant drop in expectations of the business development in the logistics sector depending on the actor’s role in the supply chain and international perspective.Originality/valueThis paper contributes to the supply chain management and logistics literature with insights into how widespread pandemic is perceived in different roles of the supply chain as well as in different countries where the pandemic has spread in different pace. Analyzing the differences between the expected and realized impact from the business environment can give valuable information for academics and managers in the field, and thus give insights to improve the planning and decision-making in logistics field during a global pandemic.
The nexus between economic policy uncertainty and access to finance: a study of developing countries
Authors: Farooq Omar , Jabbouri Imad , Naili Maryem 
Published: May 2023

PurposeThis paper attempts to document the effect of economic uncertainty on financing constraints faced by private firms.Design/methodology/approachOrdered logistic regression is used to analyze the data of private firms from 101 developing countries. The data was provided by the World Bank's Enterprise Surveys and was gathered during the period between 2006 and 2019.FindingsThe findings show that firms headquartered in countries with high economic uncertainty face more financing constraints than firms headquartered in countries with low economic uncertainty. The authors argue that the increase in economic uncertainty allows capital providers to adjust their lending decisions by reducing the provision of capital to firms. The paper also shows that firms headquartered in countries with strong institutional infrastructure and well-functioning firms are less likely to be affected by economic uncertainty while accessing finance.Practical implicationsThe findings would help managers, investors, regulators, and policymakers better understand the implication of economic policy uncertainty on the real economy. This study also sheds the light on the importance of minimizing volatility, ambiguity, and randomness in governmental decisions and policies. Regardless of the pertinence of these policies, arbitrariness surrounding their development and communication can limit their effectiveness and produce unwanted effects.Originality/valueThis paper is closely related to prior literature that documents the behavior of credit providers and investors (the supply side) during the periods of economic uncertainty. The authors differ from this strand of literature by taking the perspective of firms – the demand side.