bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gills are not used for gas exchange in the suspension-feeding hemichordateProtoglossus graveolens
Authors: Sackville Michael A. , Cameron Christopher B. , Brauner Colin J. 
Published: August 2023

AbstractThe gills are hypothesized to play a key role in early vertebrate evolution by replacing the skin as the primary site of gas exchange. In this scenario, water flow across the gills used for suspension feeding in ancestral deuterostomes was coopted for breathing in stem vertebrates to facilitate the evolution of larger, active fishes. This hypothesis is supported by a stem-vertebrate origin for structures that increase gill capacity for breathing. However, these structures might have instead enhanced an already dominant capacity at the gills of invertebrate deuterostomes rather than mark a shift from the skin. To test this, we characterized gill function for gas exchange in the suspension-feeding hemichordate acorn wormProtoglossus graveolens. We measured oxygen uptake and ammonia excretion in whole worms and worm halves with or without gills at 10°C and during an acute thermal challenge at 20°C to maximize gill recruitment. Gills did not enhance oxygen uptake or ammonia excretion, suggesting they are not a primary site of gas exchange. This is the first test of gill function for gas exchange in a suspension-feeding invertebrate deuterostome, and it provides essential support for the long-hypothesized vertebrate origin of breathing at gills and its role in early vertebrate evolution.
Actomyosin-mediated apical constriction promotes physiological germ cell death inC. elegans
Authors: Kohlbrenner Tea , Berger Simon , Aegerter-Wilmsen Tinri , Laranjeira Ana Cristina , deMello Andrew , Hajnal Alex 
Published: August 2023

AbstractGerm cell apoptosis inC. eleganshermaphrodites is a physiological process eliminating around 60% of all cells in meiotic prophase to maintain tissue homeostasis. In contrast to programmed cell death in theC. eleganssoma, the selection of germ cells undergoing apoptosis is stochastic.By live-tracking individual germ cells at the pachytene stage, we found that germ cells smaller than their neighbors are selectively eliminated through apoptosis before differentiating into oocytes. Thus, cell size is a strong predictor of physiological germ cell death. The RAS/MAPK and ECT/RHO/ROCK pathways together regulate germ cell size by controlling actomyosin constriction at the apical rachis bridges, which are cellular openings connecting the syncytial germ cells to a shared cytoplasmic core. Enhancing apical constriction reduces germ cell size and increases the rate of cell death while inhibiting the actomyosin network in the germ cells prevents their death. We propose that actomyosin contractility at the rachis bridges of the syncytial germ cells amplifies intrinsic disparities in cell size. Through this mechanism, animals can adapt the rate of germ cell death and differentiation to changing environmental conditions.
Associations between sex, systemic iron and inflammatory status and subcortical brain iron
Authors: Spence Holly , Mengoa-Fleming Stephanie , Sneddon Alan A. , McNeil Christopher J. , Waiter Gordon D. 
Published: August 2023

AbstractKey PointsDifferences in subcortical brain iron levels were observed between males and femalesFemales exhibited more associations between brain iron and systemic markers for iron than males.Males exhibited more associations between brain iron and systemic markers for inflammation than females.BackgroundBrain iron is increased in several neurodegenerative diseases, with studies demonstrating relationships between increased subcortical iron and disease progression. However, the causes of increased brain iron remain unclear. This study investigates relationships between subcortical iron and systemic iron and inflammatory status to improve our understanding of brain iron accumulation.MethodsBrain MRI scans and blood plasma samples were collected from cognitively healthy females (n=176, mean age = 61.4 ± 4.5 y, age range = 28 - 72 y) andmales (n=152, mean age = 62.0 ± 5.1 y, age range = 32 - 74 y). Quantitative susceptibility mapping was used to quantify regional brain iron. To assess systemic iron, haematocrit, plasma ferritin and plasma soluble transferrin receptor (sTfR) were measured and total body iron index (TBI) was calculated. To assess systemic inflammation, C-reactive protein (CRP), Neutrophil/Lymphocyte ratio (NLR), plasma macrophage colony stimulating factor 1 (MCSF), plasma interleukin 6 (IL6) and plasma interleukin 1β (IL1β) were measured.ResultsFemales exhibited associations between TBI and iron levels in the left and right caudate and right pallidum. Females also exhibited associations between haematocrit and iron levels in the right pallidum and left putamen. However, in males, the only association between brain iron and iron status was a positive correlation between iron in the right caudate and ferritin. In males, positive associations were observed between CRP levels and iron in the right thalamus and between IL6 levels and iron in the right amygdala and right pallidum. Males also exhibited a negative association between IL6 levels and iron in the left caudate. Positive associations between iron in the left thalamus and NLR were observed in both sexes.ConclusionsThis study demonstrates differential relationships between systemic iron and inflammation markers and brain iron in females and males. These results suggest differing iron regulation mechanisms in older age between sexes which could lead towards an understanding of the differences in neurodegenerative disease prevalence in males and females.
The effects of human population density on trophic interactions are contingent upon latitude
Authors: Hernandez-Aguero Juan Antonio , Ruiz-Tapiador Ildefonso , Garibaldi Lucas A. , Kozlov Mikhail V. , Mantyla Elina , Nacif Marcos E. , Salinas Norma , Cayuela Luis 
Published: August 2023

AbstractAim: Studies conducted at a global scale are necessary to make general conclusions on the effect of urbanization on trophic interactions and explore how these effects change along latitudinal gradients. Since biotic interactions are more intense at lower latitudes, we predict that the intensity of trophic interactions will decrease in response to urbanization (quantified by human population density), with higher impacts of urbanization at higher latitudes.Location: Global (881 study sites).Time period: 2000-2021.Major taxa studied: Birds, arthropods and woody plants.Methods: We compiled global data on insect herbivory and bird predation from individual studies using similar methodologies, and fitted generalized linear mixed models to test the effect of human population density, latitude and their interaction on these two response variables.Results: The intensity of herbivory and predation decreased with the increase of human population density at lower latitudes, remained unaffected at intermediate latitudes, and increased at higher latitudes.Main conclusions: The effect of human population density on insect herbivory and bird predation consistently varies across latitudes, with a reversal of the pattern at high versus low latitudes.
Geogenomic predictors of genetree heterogeneity in an Amazonian bird (Thamnophilus aethiops)
Authors: Musher Lukas J. , Del-Rio Glaucia , Marcondes Rafael S. , Brumfield Robb T. , Bravo Gustavo A. , Thom Gregory 
Published: August 2023

AbstractCan knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of four populations of an Amazonian antbird,Thamnophilus aethiops,whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 kya, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered two primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence, and was recovered for the Z chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length, and found that smaller chromosomes experienced higher gene flow. Given that (1) gene-trees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future biogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification.
Predicted Versus Observed Activity of PCB Mixtures Toward the Ryanodine Receptor
Authors: Griffin Justin A. , Li Xueshu , Lehmler Hans-Joachim , Holland Erika B. 
Published: August 2023

ABSTRACTNon-dioxin-like polychlorinated biphenyls (NDL PCBs) alter the activity of the ryanodine receptor (RyR), and this activity is linked to developmental neurotoxicity. Most work to date has focused on the activity of single congeners rather than relevant mixtures. The current study assessed the RyR activity of single congeners or binary, tertiary, and complex PCB mixtures. Observed mixture activity was then compared to the expected activity calculated using the concentration addition (CA) model or a RyR-specific neurotoxic equivalency scheme (rNEQ). The predictions of the CA model were consistent with the observed activity of binary mixtures at the lower portion of the concentration-response curve, supporting the additivity of RyR1 active PCBs. Findings also show that minimally active congeners can compete for the RyR1 binding site, and congeners that do not activate the RyR1 do not interfere with the activity of a full agonist. Complex PCB mixtures that mimic PCB profiles detected in indoor air, fish tissue, and the serum of mothers and children activated the RyR1 and displayed similar efficacy and potency regardless of varying congener profiles. Neither the CA model nor the rNEQ perfectly predicted the observed activity of complex mixtures, but predictions were often within one magnitude of change from the observed response. Importantly, PCB mixtures approximating profiles found in environmental samples or human serum displayed RyR1 activity at concentrations reported in published research. The work presented will aid in the development of risk assessment platforms for NDL PCBs, and similar compounds, towards RyR1 activation and related neurotoxicity.
Macrophage-targeted DNA methyltransferase inhibitor SGI-1027 decreases atherosclerosis in ApoE-null mice
Authors: Márquez-Sánchez Ana Cristina , Manzanares-Guzmán Alejandro , Carriles-Jaimes Ramón , Sánchez-Segura Lino , Colín-Castelán Dannia , Kamen Dan , Koltsova Ekaterina K. , Martínez-Antonio Agustino , Rodríguez-Ríos Dalia , del Carmen Romo-Morales Gloria , Lund Gertrud , Zaina Silvio 
Published: August 2023

AbstractBackground and aimsCorrection of vascular DNA hypermethylation may slow atherogenesis. We tested the anti-inflammatory and anti-atherogenic activity of macrophage-targeted DNA methyltransferase (DNMT) inhibitor SGI-1027.Methods, ResultsSGI-1027 was encapsulated into human serum albumin (HSA) nanoparticles (HSANP) functionalized with the PP1 peptide, a macrophage scavenger receptor 1 ligand, fused to a FLAG epitope (S-HSANP-FLAGPP1). Nanoparticle physico-chemical characteristics predicted good marginalization towards the vascular wall, although SGI-1027 encapsulation efficiency was relatively low (∼23%). S-HSANP-FLAGPP1 were rapidly internalized compared to non-functionalized and, surprisingly, functionalized void controls, and induced a shift towards an anti-inflammatory profile of secreted cytokines in human THP-1 macrophages. S-HSANP-FLAGPP1 colonized the atheroma and induced a significant ∼44% reduction of atherosclerosis burden in the aortic tree of ApoE-null mice compared to controls. A reduction in aortic root atherosclerosis was observed, although primarily induced by HSANP irrespective of loading or functionalization. No alteration of body weight, non-vascular tissue gross histology, plasma glucose, triglyceride or cholesterol were observed. HSA whether free or structured in nanoparticles, induced a 3-4-fold increase in HDL compared to vehicle.ConclusionsWe confirm that DNMT inhibition is anti-atherogenic and provide proof of principle that targeted HSANP are effective carriers for those molecules. SGI-1027 displayed a novel anti-inflammatory activity that is independent of cell proliferation and therefore likely unrelated to DNMT inhibition. HDL elevation may represent an additional advantage of HSA-based nanocarriers.
Spheroid architecture strongly induces miR-221/222 expression and promotes oxidative phosphorylation and survival of mobile tumor cells through a mechanism that includes restriction of miR-9 expression
Authors: Ward Avery S. , Hall Cody N. , Tree Maya O. , Kohtz D. Stave 
Published: August 2023

AbstractTumor cell spheroids are three dimensional multicellular structures that form during the expansive growth of carcinoma cells. Spheroids support tumor metastasis as vehicles of dissemination, promoting growth and survival of bulk tumor and cancer stem cells within the mobile tumor cell population. Deciphering how spheroid architecture affects tumor cell phenotype will be essential for the development of therapeutics to inhibit transperitoneal metastasis and the development of peritoneal carcinomatosis by ovarian cancers. We investigated how spheroid formation directly affects OXPHOS activity and microRNA expression in a cultured ovarian carcinoma cell system. The rate of oxidative phosphorylation/respiration per cell in spheroids was nearly double that of the same cell type growing in suspension as single cells. Cells growing as spheroids showed greatly enhanced expression of miR-221/222, an oncomiR that targets multiple tumor suppressor genes, promotes invasion, as well as reduced expression of miR-9, which targets mitochondrial tRNA-modification enzymes and inhibits OXPHOS. Consistent with the greater efficiency of ATP generation afforded by OXPHOS phosphorylation, tumor cells growing as spheroids injected into the nutrient-poor environment of the murine peritoneum survived longer than the cells growing in suspension as loosely associated aggregates. The data suggest that in addition to the reported effects of spheroid formation on cancer cell growth and phenotype, including promotion of stem cell generation, spheroid architecture increases the OXPHOS activity of constituent tumor cells. During the mobile phase of metastasis, when ovarian tumor cells disperse through nutrient-poor environments such as the peritoneum, enhanced OXPHOS activity afforded by spheroid architecture would enhance survival and thereby contribute to metastatic potential.
Navigational systems in the human brain dynamically code for past, present, and future trajectories
Authors: Cheng You (Lily) , Ling Sam , Stern Chantal E. , Chrastil Elizabeth R. 
Published: August 2023

AbstractNavigational trajectory planning requires the interaction of systems that include spatial orientation and memory. Here, we used a complex navigation task paired with fMRI pattern classification to examine head and travel direction tuning throughout the human brain. Rather than a single, static network, we report multiple simultaneous subnetworks that 1) have strong connections with both allocentric (world-centered) and egocentric (viewer-centered) movement trajectories, 2) change during the course of exploration, 3) code for past and future movements as well as the present direction, and 4) are strongest for individuals who convert their trajectories into egocentric movements once they have learned the environment. These findings shift our understanding of the neural processes underlying navigation from static structure-function relationships to a dynamic understanding of the multiple brain networks that support active navigation. The insights into the nature of individual navigation abilities uncovered here challenge the dominant framework of largely allocentric coding for successful navigation in complex environments, and replace this with a new framework that relies on multiple co-existing dynamic computations.
multiDGD: A versatile deep generative model for multi-omics data
Authors: Schuster Viktoria , Dann Emma , Krogh Anders , Teichmann Sarah A. 
Published: August 2023

AbstractRecent technological advancements in single-cell genomics have enabled joint profiling of gene expression and alternative modalities at unprecedented scale. Consequently, the complexity of multi-omics data sets is increasing massively. Existing models for multi-modal data are typically limited in functionality or scalability, making data integration and downstream analysis cumbersome. We present multiDGD, a scalable deep generative model providing a probabilistic framework to learn shared representations of transcriptome and chromatin accessibility. It shows outstanding performance on data reconstruction without feature selection. We demonstrate on several data sets from human and mouse that multiDGD learns well-clustered joint representations. We further find that probabilistic modelling of sample covatiates enables post-hoc data integration without the need for fine-tuning. Additionally, we show that multiDGD can detect statistical associations between genes and regulatory regions conditioned on the learned representations. multiDGD is available as an scverse-compatible package (https://github.com/Center-for-Health-Data-Science/multiDGD).
Country study on drivers and barriers for employee ownership: the case of MONDRAGON group
Authors: Arando-Lasagabaster Saioa , Herce-Lezeta Beñat 
Published: August 2023

PurposeThis article analyses how the MONDRAGON Group has overcome the barriers that the literature identifies in the creation of employee owned companies (Mygind and Poulsen, 2021), and how it has managed to grow over the last few decades.Design/methodology/approachTo this end, based on an analysis of the legislative framework and the internal documentation of the MONDRAGON Group and its cooperatives, the case of what is often considered the most successful and highly developed network of co-operative firms is studied.FindingsThe study leads us to conclude that MONDRAGON has had sufficient capacity to overcome the barriers faced by worker-owned companies and has known how to adapt to the economic and social demands of each moment, despite the fact that at certain times it has had to act flexibly in its principles.Research limitations/implicationsThe work is limited to the analysis of the Group's internal documentation. It would be interesting to complement this vision with the perceptions of MONDRAGON's partners.Practical implicationsThe MONDRAGON Group's study can show other cooperative experiences what the keys to success are.Originality/valueMONDRAGON has been analysed from different perspectives, but how it has overcome the specific barriers presented by employee-owned companies has not been specifically studied. This perspective makes it possible to identify some of the group's success factors.
The assertion of reproductive and social control in mid‐twentieth‐century US transgender medicine
Authors: Shuster Stef M. 
Published: August 2023

AbstractDrawing on archival materials from the Kinsey Institute, including letters of correspondence between medical professionals and transgender people during the 1950s–1970s, this article demonstrates how scientific and medical communities selectively employed old and new eugenics in their work with trans patients seeking hormonal and/or surgical interventions. Old eugenics helped providers control trans people's reproduction and family formations. New eugenics helped providers maintain social control over trans people's lives and solidify an ‘ideal’ patient who demonstrated their ‘value’ by upholding social fitness standards. This work contributes to histories of trans medicine by analysing this era through the lens of eugenics and expanding understandings of how medical and scientific communities sought to assert reproductive and social control over trans people.
Preoperative automatic reminder systems and impact on quality and compliance with colonoscopy preparation: A multicenter randomized controlled trial
Authors: Chen Bo Ru , Zhang Li Hui , Shi Zhao Hong , Ding Xiang Wu , Liu Yi , Wang Ai Xiang , Chen Zu Fang , Yao Li Wen , Gong Rong Rong , Wang Jun Xiao , Wu Lian Lian , Liu Jun , Yu Hong Gang 
Published: August 2023

ObjectivesTraditional preoperative reminding services have been applied to enhance the quality of bowel preparation for colonoscopy. In this study we aimed to evaluate the effectiveness of an automated electronic reminder system (E‐reminder) on improving bowel preparation and the quality of preoperative education before colonoscopy.MethodsFrom August 2021 to March 2022, 833 outpatients aged 50–75 years who underwent colonoscopy were included and randomly assigned to the E‐reminder group and the control group. While the control group received routine preoperative education. The E‐reminder group received automatic phone call, text message reminders and web services regarding the details of bowel preparation before the colonoscopic examination. The quality of bowel preparation was evaluated by the Boston Bowel Preparation Scale (BBPS) score and the previously validated objective evaluation scale of automatic BBPS (e‐BBPS).ResultsIn manual assessment, the rate of adequate bowel preparation was improved in the E‐reminder group of intention‐to‐treat population using BBPS (60.7% vs 54.5%, P = 0.01). The percentage of objective evaluated adequate bowel preparation using e‐BBPS in the E‐reminder group of per‐protocol population was significantly higher than that in the control group (76.9% vs 69.2%, P = 0.02).ConclusionsE‐reminder was an effective tool to improve the quality of bowel preparation and compliance with medical instructions. It may be regarded as an efficient and convenient education tool, improving the quality of medical service.