bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance Evaluation of the Verily Numetric Watch sleep suite for digital sleep assessment against in-lab polysomnography
Authors: Nelson Benjamin W. , Saeb Sohrab , Barman Poulami , Verma Nishant , Allen Hannah , de Zambotti Massimiliano , Baker Fiona C. , Arra Nicole , Sridhar Niranjan , Sullivan Shannon S. , Plowman Scooter , Rainaldi Erin , Kapur Ritu , Shin Sooyoon 
Published: September 2024

AbstractThe goal was to evaluate the performance of a multi-sensor wrist-worn wearable device for generating 12 sleep measures in a diverse cohort. Our study technology was the sleep suite of the Verily Numetric Watch (VNW), using polysomnography (PSG) as reference during 1-night simultaneous recording in a sample of N=41 (18 male, age range: 18-78 years). We performed epoch-by-epoch comparisons for all measures. Key specific analyses were: core accuracy metrics for sleep vs wake classification; bias for continuous measures (Bland-Altman); Cohen’s kappa and accuracy for sleep stage classifications; and mean count difference and linearly weighted Cohen’s kappa for count metric. In addition, we performed subgroup analyses by sex, age, skin tone, body mass index, and arm hair density. Sensitivity and specificity (95% CI) of sleep versus wake classification were 0.97 (0.96, 0.98) and 0.66 (0.61, 0.71), respectively. Mean total sleep time bias was 14.55 minutes (1.61, 27.16); wake after sleep onset, −11.77 minutes (−23.89, 1.09); sleep efficiency, 3.15% (0.68, 5.57); sleep onset latency, −3.24 minutes (−9.38, 3.57); light-sleep duration, 3.78 minutes (−7.04, 15.06); deep-sleep duration, 3.91 minutes (−4.59, 12.60); rapid eye movement-sleep duration, 6.94 minutes (0.57, 13.04). Median difference for number of awakenings, 0.00 (0.00, 1.00); and overall accuracy of sleep stage classification, 0.78 (0.51, 0.88). Most measures showed statistically significant proportional biases and/or heteroscedasticity. Subgroup results appeared largely consistent with the overall group, although small samples preclude strong conclusions. These results support the use of VNW’s in classifying sleep versus wake, sleep stages, and for related overnight sleep measures.
Hypoxia impedes differentiation of cranial neural crest cells into derivatives relevant for craniofacial development
Authors: Schmid Theresa , Rodrian Gabriele , Kohler Alexander , Wegner Michael , Gölz Lina , Weider Matthias 
Published: September 2024

ABSTRACTOrofacial clefts are the second-most prevalent congenital malformation. Risk factors are multifactorial and include genetic components but also environmental factors. One environmental factor is hypoxia during pregnancy, caused for instance by tobacco smoking, medication or living at high altitudes. Knowledge about the molecular link between hypoxia and orofacial clefts is at large. We here show that hypoxia has only modest effects on proliferating cranial neural crest cells, but dramatically influences their differentiation potential. We detected massive perturbations in their differentiation to chondrocytes, osteoblasts and smooth muscle cells. The transcriptional induction of the majority of regulated genes during each of these processes was grossly impaired by hypoxic conditions, as evidenced by genome-wide transcriptomic analyses. Bioinformatic analyses pointed to cytoskeletal organization and amino acid metabolism as two main processes compromised during all three differentiation pathways, and several orofacial cleft risk genes were among the genes with impaired induction during hypoxia. Our analyses reveal a drastic influence of hypoxia on the differentiation potential of cranial neural crest cells as a possible source for the occurrence of orofacial clefts.
MICROBIOTA DRIVES THE SEXUALLY DIMORPHIC INFECTION OUTCOMES IN MEALWORM BEETLES
Authors: Seal Srijan , Kumar Devashish , Thunga Pavankumar , Khangar Pawan , Gupta Manisha , Basu Dipendra Nath , Raychoudhury Rhitoban , Khan Imroze 
Published: September 2024

ABSTRACTSexually dimorphic responses to pathogenic infections in animals may stem from sex-specific differences in their life history and immune investment. Recent evidence highlights that such sex-specific variations in immune responses can also be critically regulated by microbiota. However, direct experiments to test how microbiota jointly impacts sex-specific immunity and vulnerability to pathogens are still limited. To this end, we usedTenebrio molitorbeetles to first establish that sexes appear to differ in their microbiota composition and infection responses. Females were more vulnerable to bacterial infections and carried a higher bacterial load than males. When we depleted the microbiome, only females improved their post-infection survival, leading to a loss of sex-specific infection outcomes. Males, on the other hand, remained unaffected. Microbiota reconstitution (via feeding on faecal matter) of microbiota-depleted females increased their susceptibility to infection again, restoring the sexual dimorphism. We thus found a causal association between microbiome and infection responses. We also found reduced expression of an antimicrobial peptide tenecin 1 in females, which could be associated with their higher infection susceptibility, but such immune gene-vs-phenotypic associations were not consistent across microbiota manipulations. Immune strategies that are required to mediate the causal links between microbiome and infection response might thus vary with microbiota manipulations, warranting future investigations.
High-coverage, massively parallel sequencing of single-cell genomes with CAP-seq
Authors: Li Mengzhen , Zhai Xuanpei , Li Jie , Li Shiyan , Du Yanan , Zhang Jian , Zhang Rong , Luo Yuan , Wei Wu , Liu Yifan 
Published: September 2024

AbstractMicroorganisms dominate Earth’s ecosystems in both abundance and diversity. Studying these organisms relies on their genome information, but obtaining high-quality genomes has long been challenging due to technical limitations in genomic sequencing. Traditional genome sequencing methods are limited by the need to culture isolated strains, excluding unculturable taxa and restricting the study of complex communities. Metagenomics bypasses this but lacks single-cell resolution and often misses rare, critical species. Droplet-based single-cell genomics offers high-throughput genome library preparation but faces challenges like requiring complex microfluidic setups and low genome coverage. To address these challenges, we introduce CAP-seq, a high-throughput single-cell genomic sequencing method with markedly improved genome coverage and ease of use. CAP-seq employs semi-permeable compartments that allow reagent exchange while retaining large DNA fragments, enabling efficient genome processing. This innovation results in higher-quality single amplified genomes (SAGs) and significantly improves resolution. In validation tests with simple and complex microbial communities, CAP-seq yielded high-quality SAGs with over 50% genome coverage, capturing rare taxa more accurately and providing detailed insights into strain-level variation. CAP-seq thus offers a scalable, high-resolution solution for microbial genomic analysis, overcoming the limitations of droplet-based single-cell genomics and enhancing the study of complex microbial ecosystems.
A Comprehensive Atlas of AAV Tropism in the Mouse
Authors: Walkey Christopher J. , Snow Kathy J. , Bulcha Jote , Cox Aaron R. , Martinez Alexa E. , Ljungberg M. Cecilia , Lanza Denise G. , Giorgi Marco De , Chuecos Marcel A. , Alves-Bezerra Michele , Suarez Carlos Flores , Hartig Sean M. , Hilsenbeck Susan G. , Hsu Chih-Wei , Saville Ethan , Gaitan Yaned , Duryea Jeff , Hannigan Seth , Dickinson Mary E. , Mirochnitchenko Oleg , Wang Dan , Lutz Cathleen M. , Heaney Jason D. , Gao Guangping , Murray Stephen A. , Lagor William R. 
Published: September 2024

SummaryGene therapy with Adeno-Associated Viral (AAV) vectors requires knowledge of their tropism within the body. Here we analyze the tropism of ten naturally occurring AAV serotypes (AAV3B, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAVrh8, AAVrh10 and AAVrh74) following systemic delivery into male and female mice. A transgene expressing ZsGreen and Cre recombinase was used to identify transduction in a cell-dependent manner based on fluorescence. Cre-driven activation of tdTomato fluorescence offered superior sensitivity for transduced cells. All serotypes except AAV3B and AAV4 had high liver tropism. Fluorescence activation revealed transduction of unexpected tissues, including adrenals, testes and ovaries. Rare transduced cells within tissues were also readily visualized. Biodistribution of AAV genomes correlated with fluorescence, except in immune tissues. AAV4 was found to have a pan-endothelial tropism while also targeting pancreatic beta cells. This public resource enables selection of the best AAV serotypes for basic science and preclinical applications in mice.
A stable 15-member bacterial SynCom promotesBrachypodiumgrowth under drought stress
Authors: Yadav Archana , Chen Mingfei , Acharya Shwetha M. , Yang Yuguo , Zhao Tiffany Z. , Chakraborty Romy 
Published: September 2024

AbstractRhizosphere microbiomes are known to drive soil nutrient cycling and influence plant fitness during adverse environmental conditions. Field-derived robust Synthetic Communities (SynComs) of microbes that mimic the diversity of rhizosphere microbiomes can greatly advance a deeper understanding of such processes. However, assembling stable, genetically tractable, reproducible, and scalable SynComs remains challenging. Here, we present a systematic approach using a combination of network analysis and cultivation-guided methods to construct a 15-member SynCom from the rhizobiome ofBrachypodium distachyon. This SynCom incorporates diverse strains from five bacterial phyla and demonstrates strong stability bothin vitroandin planta. Genomic analysis of the individual strains revealed that they encode multiple plant growth-promoting traits, some of which were validated by laboratory phenotypic assays. Additionally, most strains encoded genes both for the synthesis of osmoprotectants (trehalose and betaine) and Na+/K+transporters. These traits likely enabled the resilience ofBrachypodiumto drought stress where plants amended with SynCom recovered better than without. We further observed preferential colonization of SynCom strains around root tips under stress, likely due to active interactions between plant root metabolites and bacteria. Our results represent significant progress towards building and testing stable model SynComs for a better understanding of plant-microbe interactions.
Robinow SyndromeDVL1variants disrupt morphogenesis and appendage formation in a Drosophila disease model
Authors: Akarsu Gamze , MacCharles Katja R. , Lam Wong Kenneth Kin , Richman Joy M. , Verheyen Esther M. 
Published: September 2024

AbstractRobinow Syndrome is a rare developmental syndrome caused by variants in numerous genes involved in Wnt signaling pathways. We previously showed that expression of patient variants in Drosophila and a chicken model disrupts the balance of canonical and non-canonical/PCP Wnt signaling. We also noted neomorphic effects that warranted further investigation. In this study, we examine morphological changes that occur as a result of one variant, DVL11519ΔT, that serves as a prototype for the other pathogenic variants. We show that epithelial imaginal disc development is disrupted in legs and wings. Shortened leg segments are reminiscent of shortened limb bones seen in RS patients. We find that imaginal disc development is disrupted and accompanied by increased cell death, without changes in cell proliferation. Furthermore, we find altered dynamics of basement membrane components and modulators. Notably we find increased MMP1 expression and tissue distortion, which is dependent on JNK signaling. We also find enhanced collagen IV (Viking) secreted from cells expressing DVL11519ΔT. Through these studies we have gained more insight into developmental consequences of DVL1 variants implicated in autosomal dominant Robinow Syndrome.
Ki-67 and CDK1 Control the Dynamic Association of Nuclear Lipids with Mitotic Chromosomes
Authors: Hu Hsiao-Tang , Wang Ueh-Ting Tim , Chen Bi-Chang , Hsueh Yi-Ping , Wang Ting-Fang 
Published: September 2024

AbstractNuclear lipids play roles in regulatory processes such as signaling, transcriptional regulation, and DNA repair. In this report, we demonstrate that nuclear lipids may contribute to Ki-67-regulated chromosome integrity during mitosis. In COS-7 cells, nuclear lipids are enriched at the perichromosomal layer and excluded from intrachromosomal regions during early mitosis, but are then detected in intrachromosomal regions during late mitosis, as revealed by TT-ExM, an improved expansion microscopy technique that enables high-sensitivity, super-resolution imaging of proteins, lipids, and nuclear DNA. The nuclear non-histone protein Ki-67 acts as a surfactant to form a repulsive molecular brush around fully condensed sister chromatids in early mitosis, preventing the diffusion or penetration of nuclear lipids into intrachromosomal regions. Ki-67 is phosphorylated during mitosis by cyclin-dependent kinase 1 (CDK1), the best-known master regulator of the cell cycle. Both Ki-67 knockdown and reduced Ki-67 phosphorylation by CDK1 inhibitors allow nuclear lipids to penetrate chromosomal regions. Thus, both Ki-67 protein level and phosphorylation status during mitosis appear to influence the perichromosomal distribution of nuclear lipids. Ki-67 knockdown and CDK1 inhibition also lead to uneven chromosome disjunction between daughter cells, highlighting the critical role of this regulatory mechanism in ensuring accurate chromosome segregation. Given that Ki-67 has been proposed to promote chromosome individualization during open mitosis in vertebrates, our results reveal that nuclear lipid enrichment at the perichromosomal layer enhances Ki-67’s ability to form a protective chromosomal envelope, which is critical for correct chromosome segregation and maintenance of genome integrity during mitosis.
EB-SUN, a New Microtubule Plus-End Tracking Protein inDrosophila
Authors: Kim Sun K. , Rogers Stephen L. , Lu Wen , Lee Brad S. , Gelfand Vladimir I. 
Published: September 2024

AbstractMicrotubule (MT) regulation is essential for oocyte development. InDrosophila, MT stability, polarity, abundance, and orientation undergo dynamic changes across developmental stages. In our effort to identify novel microtubule-associated proteins (MAPs) that regulate MTs in theDrosophilaovary, we identified a previously uncharacterized gene, CG18190, encoding a novel MT end-binding (EB) protein, which we propose to name EB-SUN. We show that EB-SUN colocalizes with EB1 at growing microtubule plus-ends inDrosophilaS2 cells. Tissue-specific and developmental expression profiles from Paralog Explorer reveal that EB-SUN is predominantly expressed in the ovary and early embryos, while EB1 is ubiquitously expressed. Furthermore, as early as oocyte determination, EB-SUN comets are highly concentrated in oocytes during oogenesis. EB-SUN knockout (KO) results in a decrease in MT density at the onset of mid-oogenesis (Stage 7) and delays oocyte growth during late mid-oogenesis (Stage 9). Combining EB-SUN KO with EB1 knockdown (KD) in germ cells significantly further reduced MT density at Stage 7. Notably, all eggs from EB-SUN KO/EB1 KD females fail to hatch, unlike single gene depletion, suggesting a functional redundancy between these two EB proteins during embryogenesis. Our findings indicate that EB-SUN and EB1 play distinct roles during early embryogenesis.Significance StatementOur study identified a novel microtubule end-binding (EB) protein, which is highly expressed in theDrosophilaovary, and we propose to name it EB-SUN.We demonstrate the functional redundancy of EB-SUN and EB1 during oocyte development, while highlighting their distinct roles in early embryogenesis.Given the high conservation of MT-dependent mechanisms in oogenesis and EB proteins across species, these findings provide insights into the differential regulation and tissue-specific functions of the EB family, usingDrosophilaas a model system, potentially benefiting future research on MT regulation in higher organisms.
Do returnee executives influence firms’ relative exploratory innovation focus? The moderating role of economic policy uncertainty
Authors: Ren Ge , Zeng Ping , Zhong Xi 
Published: September 2024

PurposeBased on upper echelon theory and signaling theory, we aim to examine the impact of returnee executives on firms’ relative exploratory innovation focus and the moderating effect of economic policy uncertainty on this relationship.Design/methodology/approachUsing panel data of Chinese listed companies from 2009 to 2020, we obtained empirical evidence to support our arguments.FindingsReturnee executives positively influence firms’ relative exploratory innovation focus. This means that firms with returnee executives will shift the focus of their innovation activities toward exploratory innovation more than exploitative innovation. In addition, we find that economic policy uncertainty strengthens this relationship.Originality/valueFirst, by showing how returnee executives positively influence firms’ shift in focus to exploratory rather than exploitative innovation, we expand our understanding of firms’ trade-offs between exploratory and exploitative innovation. Second, this study examines how returnee executives influence the relative importance that firms place on exploratory and exploitative innovation, allowing us to build a realistic and nuanced view of how returnee executives influence firms’ strategic choices. Finally, this study expands the strategic leadership literature and responds directly to the call for studies focusing on how institutional environmental conditions and executive characteristics work together to shape firm outcomes.
Contribution of university curriculum, work and life experience to work readiness: perspectives of individuals transitioning from university to physiotherapy practice
Authors: Lawton Vidya , Pacey Verity , Jones Taryn M. , Dean Catherine M. 
Published: September 2024

PurposeAustralian physiotherapy programs incorporate work-integrated learning within curriculum, with the aim to produce work-ready graduates. Recent research in physiotherapy has identified six domains of work readiness. The purpose of this study was to examine the association between university performance, paid work and work readiness, and explore the perceived contributions of university curriculum, work and life experiences to work readiness in those individuals transitioning into practice.Design/methodology/approachA mixed-methods design was used incorporating an online survey, and linked university performance data of completing students and recent graduates. The survey included personal and work data, a work readiness scale and Likert scales measuring perceived contributions to work readiness from university curriculum (academic and clinical), work and life experiences. University performance was calculated as the Course Weighted Average Mark. Correlation analysis examined the relationship between university performance, paid work and work readiness. Perceived contributions from university curriculum, and work and life experiences for work readiness domains were calculated as percentages of each Likert response.FindingsAnalysis included 129 surveys (51 completing students and 78 recent graduates). There was no association between university performance, work (paid and unpaid) and perceived work readiness (all p-values > 0.05). There was a high consistent trend that university academic curriculum (range 71–97%), clinical curriculum (range 89–99%) and work and life experiences (range 67–94%) contributed to all work readiness domains.Originality/valueThis study highlights the significant influence of university curriculum, work and life experiences on perceived readiness for practice.
Agri-food supply chain concentration and financial growth: configuration and congruence approaches
Authors: Xu Jiawei , Zhang Baofeng , Lu Jianjun , Yu Yubing , Chen Haidong , Zhou Jie 
Published: September 2024

PurposeThe importance of the agri-food supply chain in both food production and distribution has made the issue of its development a critical concern. Based on configuration theory and congruence theory, this research investigates the complex impact of supply chain concentration on financial growth in agri-food supply chains.Design/methodology/approachThe cluster analysis and response surface methodology are employed to analyse the data collected from 207 Chinese agri-food companies from 2010 to 2022.FindingsThe results indicate that different combination patterns of supply chain concentration can lead to different levels of financial growth. We discover that congruent supplier and customer concentration is beneficial for companies’ financial growth. This impact is more pronounced when the company is in the agricultural production stage of agri-food supply chains. Post-hoc analysis indicates that there exists an inverted U-shaped relationship between the overall levels of supply chain concentration and financial growth.Practical implicationsOur research uncovers the complex interplay between supply chain base and financial outcomes, thereby revealing significant ramifications for agri-food supply chain managers to optimise their strategies for exceptional financial growth.Originality/valueThis study proposes a combined approach of cluster analysis and response surface analysis for analysing configuration issues in supply chain management.