bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strain-level characterization of health-associated bacterial consortia that colonize the human gut during infancy
Authors: Minot Samuel S. , Mayer-Blackwell Koshlan , Fiore-Gartland Andrew , Johnson Andrew , Self Steven , Bhatti Parveen , Yao Lena , Liu Lili , Sun Xin , Jinfa Yi , Kublin James 
Published: December 2023

AbstractBackgroundThe human gut microbiome develops rapidly during infancy, a key window of development coinciding with maturation of the adaptive immune system. However, little is known of the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n=94) from a cohort of infants (n=15) at monthly intervals in the first six months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants.ResultsStrain-levelde novoanalysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a cohort of infants with cystic fibrosis identified one such novel consortium of diverseEnterobacteraleswhich was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual.ConclusionBy augmenting published metagenomic datasets with data from a newly established cohort we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.
Rumen protozoa are a hub for diverse hydrogenotrophic functions
Authors: Toyber Ido , Kumar Raghawendra , Jami Elie 
Published: December 2023

AbstractCiliate protozoa are an integral part of the rumen microbial community involved in a variety of metabolic processes. These processes are thought to be in part the outcome of interactions with their associated prokaryotic community. For example, methane production is facilitated by interspecies hydrogen transfer between protozoa and archaea. We hypothesize that ciliate protozoa are host to a stable prokaryotic community dictated by specific functions they carry. Here we modify the microbial community by varying the forage to concentrate ratios and show that, despite major changes in the prokaryotic community, several taxa remain stably associated with ciliate protozoa. By quantifying genes belonging to various known reduction pathways in the rumen, we find that the bacterial community associated with protozoa is enriched in genes belonging to hydrogen utilization pathways and that these genes correspond to the same taxonomic affiliations seen enriched in protozoa. Our results show that ciliate protozoa in the rumen may serve as a hub for various hydrogenotrophic functions and a better understanding of the processes driven by different protozoa may unveil potential role of ciliates in shaping rumen metabolism.
Actin dynamics switches two distinct modes of endosomal fusion in yolk sac visceral endoderm cells
Authors: Koike Seiichi , Tachikawa Masashi , Tsutsumi Motosuke , Okada Takuya , Nemoto Tomomi , Keino-Masu Kazuko , Masu Masayuki 
Published: December 2023

AbstractMembranes undergo various patterns of deformation during vesicle fusion, but how this membrane deformation is regulated and contributes to fusion remains unknown. In this study, we developed a new method of observing the fusion of individual late endosomes and lysosomes by using yolk sac visceral endoderm cells that have huge endocytic vesicles. We found that there were two distinct fusion modes that were differently regulated. In homotypic fusion, two late endosomes fused quickly, whereas in heterotypic fusion they fused to lysosomes slowly. Mathematical modeling showed that vesicle size is a critical determinant of these fusion types and that membrane fluctuation forces can overcome the vesicle size effects. We found that actin filaments were bound to late endosomes and forces derived from dynamic actin remodeling were necessary for quick fusion during homotypic fusion. Furthermore, cofilin played a role in endocytic fusion by regulating actin turnover. These data suggest that actin promotes vesicle fusion for efficient membrane trafficking in visceral endoderm cells.
Identification of the mode of evolution in incomplete carbonate successions
Authors: Hohmann Niklas , Koelewijn Joël R , Burgess Peter , Jarochowska Emilia 
Published: December 2023

AbstractBackgroundThe fossil record provides the unique opportunity to observe evolution over millions of years, but is known to be incomplete. While incompleteness varies spatially and is hard to estimate for empirical sections, computer simulations of geological processes can be used to examine the effects of the incompletenessin silico. We combine simulations of different modes of evolution (stasis, (un)biased random walks) with deposition of carbonate platforms strata to examine how well the mode of evolution can be recovered from fossil time series, and how test results vary between different positions in the carbonate platform and multiple stratigraphic architectures generated by different sea level curves.ResultsStratigraphic architecture and position along an onshore-offshore gradient has only a small influence on the mode of evolution recovered by statistical tests. For simulations of random walks, support for the correct mode decreases with time series length. Visual examination of trait evolution in lineages shows that rather than stratigraphic incompleteness, maximum hiatus duration determines how much fossil time series differ from the original evolutionary process. Gradual directional evolution is more susceptible to stratigraphic effects, turning it into punctuated evolution. In contrast, stasis remains unaffected.ConclusionsFossil time series favor the recognition of both stasis and complex, punctuated modes of evolution.Not stratigraphic incompleteness, but the presence of rare, prolonged gaps has the largest effect on trait evolution. This suggests that incomplete sections with regular hiatus frequency and durations can potentially preserve evolutionary history without major biases. Understanding external controls on stratigraphic architectures such as sea level fluctuations is crucial for distinguishing between stratigraphic effects and genuine evolutionary process.
Persistent enrichment of multidrug resistantKlebsiellain oral and nasal communities during long-term starvation
Authors: Liu Jett , Spencer Nell , Utter Daniel R. , Grossman Alex , Santos Nídia C.D. , Shi Wenyuan , Baker Jonathon L. , Hasturk Hatice , He Xuesong , Bor Batbileg 
Published: December 2023

AbstractThe human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission within human populations via the environment, and they routinely possess a clinically-significant antibiotic-resistance genes. Among these opportunistic pathogens, theKlebsiellagenus stands out as a notable example, with its members frequently linked to nosocomial infections and multidrug resistance. As with many colonizing opportunistic pathogens, howKlebsiellatransitions from an asymptomatic colonizer to a pathogen remains unclear. Here, we explored a possible explanation by investigating the ability of oral and nasalKlebsiellato outcompete their native microbial community members underin vitrostarvation conditions, which could be analogous to external hospital environments. WhenKlebsiellawas present within a healthy human oral or nasal sample, the bacterial community composition shifted dramatically under starvation conditions and typically became dominated byKlebsiella. Furthermore, introducingK. pneumoniaeexogenously into a native microbial community lackingK. pneumoniae, even at low inoculum, led to repeated dominance under starvation.K.pneumoniaestrains isolated from healthy individuals’ oral and nasal cavities also exhibited resistance to multiple classes of antibiotics and were genetically similar to clinical and gut isolates. In addition, we found that in the absence ofKlebsiella, other understudied opportunistic pathogens, such asPeptostreptococcus, dominate under starvation conditions. Our findings establish an environmental circumstance that allows for the outgrowth ofKlebsiellaand other opportunistic pathogens. The ability to outcompete other commensal bacteria and to persist under harsh environmental conditions may contribute to the colonization-to-infection transition of these opportunistic pathogens.
Integrated Hfq-interacting RNAome and transcriptomic analysis reveals complex regulatory networks of nitrogen fixation in root-associatedPseudomonas stutzeriA1501
Authors: Lv Fanyang , Zhan Yuhua , Feng Haicao , Sun Wenyue , Yin Changyan , Han Yueyue , Shao Yahui , Xue Wei , Jiang Shanshan , Ma Yiyuan , Hu Haonan , Jinfeng Wei , Yan Yongliang , Lin Min 
Published: December 2023

ABSTRACTThe RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated diazotrophs; however, its target RNAs and the mechanisms underlying nitrogen fixation remain largely unknown. Here, we used enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing (eCLIP-seq) to identify hundreds of Hfq-binding RNAs probably involved in nitrogen fixation, carbon substrate utilization, biofilm formation, and other functions. Collectively, these processes endow strain A1501 with the requisite capabilities to thrive in the highly competitive rhizosphere. Our findings revealed a previously uncharted landscape of Hfq target genes. Notable among these isnifM, encoding an isomerase necessary for nitrogenase reductase solubility;amtB,encoding an ammonium transporter;oprB,encoding a carbohydrate porin; andcheZ,encoding a chemotaxis protein. Furthermore, we identified more than one hundred genes of unknown function, which expands the potential direct regulatory targets of Hfq in diazotrophs. Our data showed that Hfq directly interacts with regulatory proteins (RsmA, AlgU, NifA), regulatory ncRNA RsmY, and other potential targets, thus revealing the mechanistic links in nitrogen fixation and other metabolic pathways.IMPORTANCENumerous experimental approaches often face challenges in distinguishing between direct and indirect effects of Hfq-mediated regulation. New technologies based on high-throughput sequencing are increasingly providing insight into the global regulation of Hfq in gene expression. Here, enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing (eCLIP-seq) was employed to identify the Hfq-binding sites and potential targets in the root-associatedP. stutzeriA1501, and identify hundreds of novel Hfq-binding RNAs that are predicted to be involved in metabolism, environmental adaptation, and nitrogen fixation. In particular, we have shown that Hfq interactions with various regulatory proteins and their potential targets at both the protein and RNA levels. This study not only enhances our understanding of Hfq regulation but, importantly, also provides a framework for addressing integrated regulatory network underlying root-associated nitrogen fixation.
Moving wall effect on normal shock wave–turbulent boundary layer interaction on an airfoil
Authors: Szulc Oskar , Doerffer Piotr , Flaszynski Pawel , Braza Marianna 
Published: December 2023

Purpose
This paper aims to describe a proposal for an innovative method of normal shock wave–turbulent boundary layer interaction (SBLI) and shock-induced separation control.

Design/methodology/approach
The concept is based on the introduction of a tangentially moving wall upstream of the shock wave and in the interaction region. The SBLI control mechanism may be implemented as a closed belt floating on an air cushion, sliding over two cylinders and forming the outer skin of the suction side of the airfoil. The presented exploratory numerical study is conducted with SPARC solver (steady 2D RANS). The effect of the moving wall is presented for the NACA 0012 airfoil operating in transonic conditions.

Findings
To assess the accuracy of obtained solutions, validation of the computational model is demonstrated against the experimental data of Harris, Ladson & Hill and Mineck & Hartwich (NASA Langley). The comparison is conducted not only for the reference (impermeable) but also for the perforated (permeable) surface NACA 0012 airfoils. Subsequent numerical analysis of SBLI control by moving wall confirms that for the selected velocity ratios, the method is able to improve the shock-upstream boundary layer and counteract flow separation, significantly increasing the airfoil aerodynamic performance.

Originality/value
The moving wall concept as a means of normal shock wave–turbulent boundary layer interaction and shock-induced separation control has been investigated in detail for the first time. The study quantified the necessary operational requirements of such a system and practicable aerodynamic efficiency gains and simultaneously revealed the considerable potential of this promising idea, stimulating a new direction for future investigations regarding SBLI control.
Influence of human capital and social capital on MSME access to finance: assessing the mediating role of financial literacy
Authors: Hj Talip Siti Nor Suriana , Wasiuzzaman Shaista 
Published: December 2023

PurposeThe authors investigate the role of financial literacy in influencing the relationship between human capital and social capital, with access to finance of micro, small and medium enterprises (MSMEs).Design/methodology/approachData were gathered from 337 MSMEs in Brunei Darussalam, and analysis on the data was carried out using a number of statistical methods. The relationships between human capital, social capital, financial literacy and access to finance were analyzed using PLS-SEM.FindingsThe results show that human capital does influence access to finance but contrary to previous studies, the influence is negative. Financial literacy is an important element in the relationship between human capital, social capital and access to finance, although it plays a greater role in the relationship between social capital and access to finance. Further analysis shows that financial knowledge is significant in moderating the relationships between human and social capital with access to finance. Financial skills is found to only moderate the relationship between social capital and access to finance.Originality/valueTo the authors' knowledge, this study is the first that integrates the human capital, social capital, financial literacy and access to finance in a single model. The authors also highlight the importance of enhancing the financial literacy of MSMEs so that the problem of access to finance can be alleviated, especially in developing countries.
Gender bias in university student mobility: a cohort analysis in Italy
Authors: Sulis Isabella , Barbieri Barbara , Salaris Luisa , Melis Gabriella , Porcu Mariano 
Published: December 2023

PurposeThis paper aims to assess gender bias in Italian university student mobility controlling for the field of study. It uses data from the Italian National Student Archive (Anagrafe Nazionale degli Studenti – ANS) for the cohort of freshmen enrolled in the 2017 academic year. The macro-regional comparison unfolds across the following areas: North and Centre, Southern Italy and main Islands (Sicily and Sardinia).Design/methodology/approachThe analysis is firstly carried out at the national level, and secondly, it focusses on macro-geographical areas. University mobility choices are thus investigated from a gender perspective, conditioning upon other theoretically relevant characteristics collected for the prospective first-year university student population enrolled in 2017. The authors analyse data in a regression setting (logit models) within the multilevel framework, which considers students at level 1 and the field of study at level 2. Gender differences in the propensity to be a mover – conditional upon the choice of the field of study – were captured by introducing random intercepts to account for clustering of students in fields of study and random slopes to allow the gender effect to differ among them.FindingsFindings show that university student mobility in Italy leads evidence of gender bias. This has been detected using a multilevel random slope approach that allowed the authors to jointly estimate a slope parameter for gender within each field of study. Moreover, using a regression setting allowed the authors to control for heterogeneity in geographical, educational and socio-demographic characteristics across students. In line with previous empirical findings, the authors' data highlight the presence of a relevant mobility flow of university students from the South toward the North-Centre of Italy and lower mobility of female students compared to male students from the South and Islands.Originality/valueTo the best of the authors' knowledge, there are no studies in Italy, which investigate if families' investment in higher education in terms of selection of no-local universities are affected by gender bias and if geographical differences in this behaviour between macro-areas are in place. Thus, investigating students' choices in tertiary education allows the authors to shed light on the presence of gender bias in families' education strategies addressed to increase the endowment of students' assets for future job opportunities.
Sustainable lean manufacturing as long-term strategy: performance framework development and prioritization
Authors: Gama Mariana da Silva Barbosa , Bonamigo Andrei 
Published: December 2023

PurposeIn response to mounting global concerns about climate change and scarcity of natural resources, manufacturers have been pressured to develop strategies and enhance their sustainability performance. The integration of sustainable lean manufacturing (SLM) during value chain processes could balance environmental, social and economic concerns into their decision-making, which not only ensures responsible practices but also drives efficiency and success. This paper aims to identify, measure and prioritize metrics to develop a performance measurement system that assesses the multi-dimensional performance of SLM.Design/methodology/approachStrategic decision-making has some conflicting criteria and objectives to be considered simultaneously. The Multi-Criteria Decision Making provides a foundation for selecting, sorting and prioritizing these strategies with the determination of drivers and indicator weight.FindingsThe performance model enables the decision-makers to consistently evaluate the level of sustainability through a multidimensional framework, which could support the assessment of the existing sustainability of a manufacturing process and analyze opportunities for improvement. This study divided the performance into five drivers: Quality, Operational, Finance, Environment, Safety and People and selected 17 KPIs for assessing the multi-dimensional performance of SLM organizations. The research results revealed an organization's perspective transition from strategies focused on operational and economic performance to a more sustainable ideal with greater importance for social and environmental directions.Originality/valueThis framework will be facilitated by the selection of the most significant drivers and the development of strategic plans for the successful adoption of sustainable manufacturing. The practices support implementation, pursue competitive advantages and sustain manufacturing, meeting strategic requirements of suitable and lean performance. With the limited resources of the organizations, the framework proposed will guide the priorities and actions to be taken toward the SLM.
The disclosure of climate-related risks and opportunities in financial statements: the UK’s FTSE 100
Authors: Borghei Zahra , Linnenluecke Martina , Bui Binh 
Published: December 2023

Purpose
This paper aims to explore current trends in how companies disclose climate-related risks and opportunities in their financial statements. As part of the authors’ analysis, they examine: whether forward-looking assumptions and judgements are typically considered in reporting climate-related risks/opportunities; whether there are differences in the reporting practices of firms in carbon-intensive industries versus non-carbon-intensive industries; and whether negative media reports have an influence on the levels of disclosure a firm makes.

Design/methodology/approach
The authors chose content analysis as their methodology and examined the financial statements published by firms listed on the UK’s FTSE 100 between 2016 and 2020. This analysis is framed by Suchman’s three dimensions of legitimacy, being pragmatic, cognitive and moral.

Findings
Climate-related disclosures in the notes and financial accounts of these firms did increase over the period. Yet, overall, the level the disclosures was inadequate and the quality was inconsistent. From this, the authors conclude that pragmatic legitimacy is not a particularly strong driving factor in compelling organisations to disclose climate-related information. The firms in carbon-intensive industries do provide greater levels of disclosure, including both qualitative and quantitative (monetary) content, which is consistent with cognitive legitimacy. However, from a moral legitimacy perspective, this study finds that firms did not adapt responsively to negative media coverage as a way of reflecting their accountability to broader public norms and values. Overall, this analysis suggests that regulatory enforcement and a systematic reporting framework with adequate guidance is going to be critical to developing transparent climate-related reporting in future.

Originality/value
This paper contributes to existing studies on climate-related disclosures, which have mainly examined the ‘front-half’ of annual reports. Conversely, this study aims to shed light on these practices in the “back-half” of these reports, exploring the underlying reasons for reporting climate-related risks and opportunities in financial accounts. The authors’ insights into the current disclosure practices make a theoretical contribution to the literature. Practitioners can also draw on these insights to improve how they report on climate-related risks and opportunities in their financial statements.