bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Architecture of Sponge Choanocyte Chambers Maximizes Mechanical Pumping Efficiency
Authors: Ogawa Takumi , Koyama Shuji , Omori Toshihiro , Kikuchi Kenji , de Maleprade Hélène , Goldstein Raymond E. , Ishikawa Takuji 
Published: March 2024

AbstractSponges, the basalmost members of the animal kingdom, exhibit a range of complex architectures in which microfluidic channels connect multitudes of spherical chambers lined with choanocytes, flagellated filter-feeding cells. Choanocyte chambers can possess scores or even hundreds of such cells, which drive complex flows entering through porous walls and exiting into the sponge channels. One of the mysteries of the choanocyte chamber is its spherical shape, as it seems inappropriate for inducing directional transport since many choanocyte flagella beat in opposition to such a flow. Here we combine direct imaging of choanocyte chambers in living sponges with computational studies of many-flagella models to understand the connection between chamber architecture and directional flow. We find that those flagella that beat against the flow play a key role in raising the pressure inside the choanocyte chamber, with the result that the mechanical pumping efficiency, calculated from the pressure rise and flow rate, reaches a maximum at a small outlet opening angle. Comparison between experimental observations and the results of numerical simulations reveal that the chamber diameter, flagellar wave number and the outlet opening angle of the freshwater spongeE. muelleri, as well as several other species, are related in a manner that maximizes the mechanical pumping efficiency. These results indicate the subtle balances at play during morphogenesis of choanocyte chambers, and give insights into the physiology and body design of sponges.
Admixture with cultivated sunflower likely facilitated establishment and spread of wild sunflower (H. annuus) in Argentina
Authors: Hernández Fernando , Vercellino Román B. , Todesco Marco , Bercovich Natalia , Alvarez Daniel , Brunet Johanne , Presotto Alejandro , Rieseberg Loren H. 
Published: March 2024

ABSTRACTA better understanding of the genetic and ecological factors underlying successful invasions is critical to mitigate the negative impacts of invasive species. Here, we study the invasion history ofHelianthus annuuspopulations from Argentina, with particular emphasis on the role of post-introduction admixture with cultivated sunflower (alsoH. annuus) and climate adaptation driven by large haploblocks. We conducted genotyping-by-sequencing of samples of wild populations as well as Argentinian cultivars and compared them with wild (including related annualHelianthusspecies) and cultivated samples from the native range. We also characterized samples for 11 known haploblocks associated with environmental variation in native populations to test whether haploblocks contributed to invasion success. Population genomics analyses supported two independent geographic sources for Argentinian populations, the central United States and Texas, but no significant contribution of related annualHelianthusspecies. We found pervasive admixture with cultivated sunflower, likely as result of post-introduction hybridization. Genomic scans between invasive populations and their native sources identified multiple genomic regions with evidence of selection in the invaded range. These regions significantly overlapped between the two native-invasive comparisons and showed disproportionally high crop ancestry, suggesting that crop alleles contributed to invasion success. We did not find evidence of climate adaptation mediated by haploblocks, yet outliers of genome scans were enriched in haploblock regions and, for at least two haploblocks, the cultivar haplotype was favored in the invaded range. Our results show that admixture with cultivated sunflower played a major role in the establishment and spread ofH. annuuspopulations in Argentina.
Application of Cancer Cell Line Encyclopedia for Measuring Correlation Between Transcriptomics and Proteomics as a Guide for System-level Insights
Authors: Williams Blake , Perry Darryl , Aspesi Peter , Parker Jefferson , Johnson Ted , Su Wendy , Tabacman Eduardo , Delisle Kirk , Avishan Kayvon , Myer Vic , Mapa Felipa , Hinterberg Michael , Williams Alan , Jennings Lori , Janjic Nebojsa , Loureiro Joseph 
Published: March 2024

AbstractRobust and reliable proteome measurements provide mechanistic insights in biomedical research. SOMAmer (Slow Off-rate Modified Aptamer) reagents are modified, DNA-based, affinity reagents that measure defined target proteins with reproducibility and accuracy similar to monoclonal antibodies. Applying SOMAmer reagent technology, we developed SomaScan, a clinical proteome profiling platform with capability to measure 7,523 proteoforms for 6,594 human proteins by UniprotID in small sample volumes (e.g., 55μl plasma or serum). We evaluated the platform by profiling the proteome of a panel of well characterized Cell Line Encyclopedia (CCLE) cancer models. Unsupervised machine learning analyses demonstrate the SomaScan assay distinguishing cell lines on the basis of their proteome signatures, and identifying both tissue-specific and oncogenic pathways. The proteome measured by SomaScan correlates with published CCLE transcriptome at a level comparable to other published transcript to proteome studies. Taken together, we demonstrate that the SomaScan platform is a technically reproducible system suitable for biomedical and clinical applications that reliably illuminates underlying biomolecular mechanisms.
Targeting students of nonhealth academic fields for basic life support: they need to know why, what and how to do CPR
Authors: Sugimoto PN , Gouvêa GB , Salles IC , Carvalho HB , Aikawa P , Azi LMTA , Silva LFF , Macchione M , Semeraro F , Lockey A , Greif RT , Carmona MJC , Böttiger BW , Nakagawa NK 
Published: March 2024

ABSTRACTEducation in basic life support is widely proposed to increase survival and quality-of-life in out-of-hospital sudden cardiac arrest. We aimed to assess knowledge, skills and attitudes regarding acute myocardial infarction and sudden cardiac arrest among university students of all fields of knowledge.MethodsThe local Ethical Research Committee approved this cross-sectional study. An electronic survey “KIDS SAVE LIVES BRAZIL” was sent to 58,862 students of 82 disciplines in three universities, aged ≥ 18 years. The survey covered three categories: knowledge, skills, and attitude. Each category was graded between 0 and 10 points (the highest).ResultsAmong university students, 4,803 undergraduates (8.2 %) answered the survey, and were divided in three groups of disciplines: medicine (219, ∼21.7 years, 38% male), other-health-care (n=1,058; ∼22.9 years; 36% male), and nonhealth-care (n=3,526; ∼22.9 years; 35% male). All three groups showed significant differences between them (p<0.001). The nonhealth-care compared with medicine and other-health-care group showed, respectively, the lowest (p<0.001) median scores (25-75%) in knowledge [4.0 (0.0-9.3), 4.0 (4.0-8.0), and 4.0 (4.0-4.7)], skills [2.4 (1.2-3.3), 6.4 (4.0-8.3), 4.0 (2.4-6.2], and attitude [5.9 (5.9-6.8), 7.3 (5.9-7.3), and 7.3 (5.9-7.3)].ConclusionUniversity students have the willingness to help victims suffering from acute myocardial infarction or sustaining sudden cardiac arrest. However, nonhealth-care students markedly lack knowledge and skills to perform cardiopulmonary resuscitation and automated external defibrillation. Our findings reveal a stark difference in basic life support competencies between students in health-care related fields and those in nonhealthy-care fields, emphasizing the need for universal basic life support training.KEY MESSAGES1. Our findings reveal a stark difference in basic life support competencies between students in health-care related fields and those in nonhealth fields, emphasizing the need for universal basic life support training.2. An action for curriculum modification to include basic life support training for all students is timely and practical, given the global burden of heart disease and the proven benefits of early intervention in sudden cardiac arrest cases.3. Our study contributes significantly to the ongoing discussion about public health education and the role of nonhealth professionals in emergency medical response. It may serve as a catalyst for policy changes within educational institutions and among healthcare policymakers, aiming to create a more resilient and responsive community in the face of out-of-hospital medical emergencies.
Factors that affect enrollment into a community-based health insurance scheme among households in Arba Minch Zuria District, Gamo Zone, Southern Ethiopia, 2023: A community-based unmatched case-control Study
Authors: Bujitie Silas Bukuno , daud Yusuf Haji 
Published: March 2024

AbstractBackgroundMany low-and middle-income countries are affected by catastrophic health expenditures as out-of-pocket payments exceed the World Health Organization’s (WHO) 10% threshold level. The government of Ethiopia has been working to reduce out-of-pocket payments from 37% to less than 15% in its health sector transformation plan II; however, the scheme was marked by a low membership and dropout rate. The aim of the study was to identify determinants of enrolment into a community-based health insurance scheme (CBHIS) in Arba Minch Zuria District of Gamo Zone, Southern Ethiopia.MethodsUnmatched case-control study was employed from February 8, 2023, to March 9, 2023, among 327 participants (109 cases and 218 controls to community-based health insurance (CBHI) scheme) in a 1:2 proportions. Multi-stage sampling technique was used to draw the study participants. Data were collected by using structured interviewer administered questionnaire and then entered into Epi-data and exported to SPSS for analysis. Bivariable and multivariable analysis was carried out using binary logistic regression. Significance was declared by using an adjusted odds ratio (AOR) with 95% confidence interval (CIs) and a p value of <0.05.ResultsA total of 327 participants (109 enrolled and 218 non-enrolled) were interviewed, resulting in a response rate of 100%. Family size (AOR=1.66; 95% CI: 1.00–2.73), wealth index (AOR=2.29; 95% CI: 1.25–4.19), awareness level of the community based health insurance scheme (AOR=3.78; 95% CI: 1.09–13.18), and perceived quality of health care (AOR=1.67; 95% CI: 1.02-2.75) were found to be determinant factors of enrollment in the scheme.ConclusionStrengthening community awareness activities, focusing on families of poor households, and improving the quality of health service delivery are highly recommended to improve enrollment in the scheme.
The transition from a non-westernized to westernized gut microbiome in Indian-Immigrants and Indo-Canadians is associated with dietary acculturation
Authors: D’Aloisio Leah D. , Ballal Mamatha , Ghosh Sanjoy , Haskey Natasha , Abulizi Nijiati , Karimianghadim Ramin , Liu Chuyi , Sruthi Pacha , Nagarajan Lakshmipriya , Vasudevan Sudha , Shetty Vignesh , Purandare Mrudgandha , Bhaumik Ushasi , Howlader Debaki Ranjan , Pakpour Sepideh , Barnett Jacqueline , Gibson Deanna L. 
Published: March 2024

BackgroundIndian immigration to westernized countries has surged in recent years, with this demographic facing a higher risk of Inflammatory Bowel Disease (IBD) after migration. Studying the gut microbiome is crucial to understanding the factors contributing to IBD, yet Indians remain underrepresented in microbiome research,ObjectiveThis study investigates the gut microbiome of Indians residing in India, Indian immigrants in Canada, and Canadians of Indian ancestry to understand the impact of westernization on their gut. Given the higher risk of IBD among Indo-Canadians, these results provide insight into how westernization of the gut microbiome may influence incidence of IBD. Stool samples were collected from healthy Indians in India, Indian Immigrants in Canada, Indo-Canadians, plus Canadian-borne individuals with European descent and Euro-Immigrants as non-Indian/westernized controls (N= 174). 16S rRNA gene and shotgun sequencing compared microbial taxa and functional profiles across groups. Dietary and demographic data were collected to assess lifestyle patterns.ResultsIndians and Indo-Immigrants had distinct gut microbiotas from westernized groups, with high abundances ofPrevotellaspp. and a CAZyme profile reflecting their traditional high complex carbohydrate diet. The Indian microbiome also showed characteristics of high bacterial cell turnover, pathogenic potential, and stress tolerance, indicating their gut may be better primed to handle stressors on the gut. Indo-Canadians displayed a transitional microbiome towards westernization, which followed a pattern of increasing dietary acculturation.ConclusionsThe shift from a non-westernized to westernized microbiome in Indo-Canadians highlights the significant influence that westernization and dietary acculturation has on the gut microbiome. Given that 44% of the Canadian population is made up of first- and second-generation immigrants and westernized practices are being adopted worldwide, future research should investigate the health implications that such microbiome transitions have on immigrant populations and newly industrialized nations.
Liebenberg syndrome severity arises from variations inPitx1locus topology and ectopically transcribing cells
Authors: Bompadre Olimpia , Rouco Raquel , Darbellay Fabrice , Rauseo Antonella , Guerard-Millet Fanny , Gentile Claudia , Kmita Marie , Andrey Guillaume 
Published: March 2024

AbstractEnhancer hijacking, a common cause of gene misregulation linked to disease, occurs when non-matching enhancers and promoters interact ectopically. This interaction is made possible by genetic changes that alter the arrangement or insulation of gene regulatory landscapes. While the concept of enhancer hijacking is well understood, the specific reasons behind the variation in phenotypic severity or the point at which those phenotypes become evident remain unexplored. In this work, we expand on the ectopic activation of the hindlimb-specific transcription factorPitx1by one of its own enhancers,Pen, in forelimb tissues that causes the Liebenberg syndrome. We combine a previously developedin-embryocell-tracing approach to a series of inversions and relocations to show that reduction inPitx1-Penrelative genomic positioning leads to increased proportions ofPitx1forelimb-expressing cells and more severe phenotypical outcomes. We demonstrate that thePitx1locus assumes an active topology when enhancer-promoter contacts are required for transcription and that its promoter generates consistent transcription levels across different alleles. Finally, we show that changes in 3D chromatin structure and enhancer-promoter contacts are not the result ofPitx1transcriptional activity. In summary, our work shows that variation in enhancer-promoter interactions can lead to pathogenic locus activation in variable proportions of cells which, in turn, define phenotypic severity.
Preference-Independent Encoding of Visual Saliency Within but Not Cross Features in the Mouse Superior Colliculus
Authors: Wu Ruixiang , Xu Jinhuai , Li Chunpeng , Zhang Zhaoji , Li Ling-yun , Li Ya-tang 
Published: March 2024

AbstractDetecting conspicuous stimuli in a visual scene is crucial for animal survival, yet it remains debated how the brain encodes visual saliency. Here we investigate how visual saliency is represented in the superficial superior colliculus (sSC) of awake mice using two-photon calcium imaging. We report on a preference-independent saliency map in the sSC. Specifically, salient stimuli evoke stronger responses in both excitatory and inhibitory neurons compared to uniform stimuli, with similar encoding patterns observed in both neuron types. The largest response occurs when a salient stimulus is positioned at the receptive field center, with contextual effects extending ∼40° away from the center. The response amplitude correlates well with the saliency strength of stimuli and is not influenced by the orientation or motion direction preferences of neurons. However, saliency encoding does depend on specific visual features. Furthermore, neurons involved in saliency encoding exhibit weak orientation or direction selectivity, suggesting a complementary relationship between the saliency map and the feature map.
RGS10 deficiency facilitates distant metastasis by inducing epithelial-mesenchymal transition in breast cancer
Authors: Liu Yang , Jiang Yi , Qiu Peng , Ma Tie , Bai Yang , Bu Jiawen , Hu Yueting , Jin Ming , Zhu Tong , Gu Xi 
Published: March 2024

AbstractDistant metastasis is the major cause of death in patients with breast cancer. Epithelial–mesenchymal transition (EMT) contributes to breast cancer metastasis. Regulator of G protein-signaling (RGS) proteins modulate metastasis in various cancers. This study identified a novel role for RGS10 in EMT and metastasis in breast cancer. RGS10 protein levels were significantly lower in breast cancer tissues compared to normal breast tissues, and deficiency in RGS10 protein predicted a worse prognosis in patients with breast cancer. RGS10 protein levels were lower in the highly aggressive cell line MDA-MB-231 than in the poorly aggressive, less invasive cell lines MCF7 and SKBR3. Silencing RGS10 in SKBR3 cells enhanced EMT and caused SKBR3 cell migration and invasion. The ability of RGS10 to suppress EMT and metastasis in breast cancer was dependent on lipocalin-2 and miR-539-5p. These findings identify RGS10 as a tumor suppressor, prognostic biomarker, and potential therapeutic target for breast cancer.
Past, present, and future spatial distributions of deep-sea coral and sponge microbiomes revealed by predictive models
Authors: Busch Kathrin , Murillo Francisco Javier , Lirette Camille , Wang Zeliang , Kenchington Ellen 
Published: March 2024

AbstractKnowledge of the spatial distribution patterns of biodiversity in the ocean is key to evaluate and ensure ocean integrity and resilience. Especially for the deep ocean, wherein situmonitoring requires sophisticated instruments and considerable ﬁnancial investments, modelling approaches are crucial to move from scattered data points to predictive continuous maps. Those modelling approaches are commonly run on the macrobial level, but spatio-temporal predictions of host-associated microbiomes are not being targeted. This is especially problematic as previous research has highlighted that host-associated microbes (microbiomes) may display distribution patterns that are not perfectly correlated with host animal biogeographies, but also with other factors such as prevailing environmental conditions. We here establish a new simulation approach and present predicted spatio-temporal distribution patterns of deep-sea sponge and coral microbiomes, making use of a combination of environmental data, host data and microbiome data to advance our understanding of deep-sea microbiomes. This approach allows predictions of microbiome spatio-temporal distribution patterns on scales that are currently not covered by classical sampling approaches at sea. This includes both predictions in space within regional oceanic provinces off eastern North America, and also in time, with predictions into the past and future, covering a time span of 214 years. In summary, our presented predictions allow (i) identiﬁcation of microbial biodiversity hotspots in the past, present, and future, (ii) evaluation of microbial-macrobial connections at case-study sites through trait-based predictions, and (iii) identiﬁcation of shifts in microbial community composition (key taxa) across environmental gradients and shifting environmental conditions.
Deciphering Oxygen Distribution and Hypoxia Profiles in the Tumor Microenvironment: A Data-Driven Mechanistic Modeling Approach
Authors: Kumar P. , Lacroix M. , Dupré P. , Arslan J. , Fenou L. , Orsetti B. , Le Cam L. , Racoceanu D. , Radulescu O. 
Published: March 2024

AbstractThe distribution of hypoxia within tissues plays a critical role in tumor diagnosis and prognosis. Recognizing the significance of tumor oxygenation and hypoxia gradients, we introduce mathematical frameworks grounded in mechanistic modeling approaches for their quantitative assessment within a tumor microenvironment. Our approach provides a non-invasive method to measure and predict hypoxia using known blood vasculature. Formulating a reaction-diffusion model for oxygen distribution, we apply it to derive the corresponding hypoxia profile. The modeling and simulations successfully replicate the observed inter- and intra-tumor heterogeneity in experimentally obtained hypoxia profiles across various tumor tissues (breast, ovarian, and pancreatic) in our dataset. Employing a data-driven approach, we propose a method to deduce partial differential equation (PDE) models with spatially dependent parameters, enabling us to comprehend the variability of hypoxia profiles within a tissue. The versatility of our framework lies not only in capturing diverse and dynamic behaviors of tumor oxygenation but also in categorizing states of vascularization. These categories are distinguished based on the dynamics of oxygen molecules, as identified by the model parameters.
Pawpaws prevent predictability: A locally-dominant tree alters understory beta-diversity and community assembly
Authors: Wassel Anna C. , Myers Jonathan A. 
Published: March 2024

AbstractWhile dominant species are known to be important in ecosystem functioning and community assembly, biodiversity responses to the presence of dominant species can be highly variable. Dominant species can increase the importance of deterministic community assembly by competitively excluding species in a consistent way across local communities, resulting in low site-to-site variation in community composition (beta-diversity) and non-random community structure. In contrast, dominant species could increase the importance of stochastic community assembly by reducing the total number of individuals in local communities (community size), resulting in high beta-diversity and more random community structure. We tested these hypotheses in a large, temperate oak-hickory forest plot containing a locally-dominant tree species, pawpaw (Asimina triloba; Annonaceae), an understory tree species that occurs in dense, clonal patches in forests throughout the east-central United States. We determined how the presence of pawpaw influences local species diversity, community size, and beta-diversity by measuring the abundance of all vascular plant species in 1x1-m plots both inside and outside pawpaw patches. To test whether the presence of pawpaw influences local assembly processes, we compared observed patterns of beta-diversity inside and outside patches to a null model of random assembly. We found lower local species diversity, lower community size, and higher observed beta-diversity inside pawpaw patches than outside pawpaw patches. Moreover, standardized effect sizes of beta-diversity from the null model were lower inside pawpaw patches than outside pawpaw patches, indicating more random community composition inside pawpaw patches. Together these results suggest that pawpaw increases the importance of stochastic relative to deterministic community assembly at local scales, likely by decreasing overall numbers of individuals, and increasing random local extinctions inside patches. Our findings provide insights into the ecological processes by which locally-dominant tree species shape the assembly and diversity of understory plant communities at different spatial scales.