bluuebunny/crossref_metadata_2025_split huggingface dataset:
Planetary Health, Indigenous Knowledge and Healthcare: a Scoping Review
Authors: Ela Jihae Abou El , Mudgway Mercedes , Harré Niki , Hamill James 
Published: November 2022

AbstractBackgroundPlanetary health is a movement to promote a healthy planet as the most important determinant of human health. Indigenous knowledge often encompasses a holistic view of nature and people in a way more akin to planetary health than to healthcare systems based on people alone. A change in healthcare’s worldview could help it become more environmentally sustainable. The aim of this review was to identify gaps in the literature and opportunities for further research at the nexus of Indigenous knowledge, environmental sustainability and healthcare.MethodsWe searched the databases Web of Science, Medline, and Google Scholar for peer-reviewed publications with terms pertaining to sustainability or planetary health, human healthcare, and indigenous or traditional knowledge. Papers were grouped by theme. Analysis was descriptive.ResultsThe search process resulted in 10 eligible papers. Studies originated from 4 continents including one from Aotearoa New Zealand. Most (8/10) were published since 2020. Methodology included ethnography, discourse, imagery, descriptive, and quantitative analysis. One paper involved a particular healthcare system while all others considered general aspects of human health as related to the environment and Indigenous knowledge. Themes included 1) the importance of indigenous knowledge, 2) conceptual models that incorporate Indigenous approaches to health and the environment, and 3) the implementation of interventions. Within the limitations of the research available, it appears that Indigenous knowledge could make invaluable contributions to more environmentally responsible healthcare systems and can guide interventions to address planetary health problems.ConclusionLiterature on Indigenous knowledge as related to planetary health and healthcare is limited and recent. There is scope for more research from many different Indigenous groups including Māori in Aotearoa, and scope for more collaborative research between healthcare systems and Indigenous peoples.
Tissue Forge: Interactive Biological and Biophysics Simulation Environment
Authors: Sego T.J. , Sluka James P. , Sauro Herbert M. , Glazier James A. 
Published: November 2022

AbstractTissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter physics at multiple scales, from the molecular to the multicellular, using a simple, consistent interface. While Tissue Forge is designed to simplify solving problems in complex subcellular, cellular and tissue biophysics, it supports applications ranging from classic molecular dynamics to agent-based multicellular systems with dynamic populations. Tissue Forge users can build and interact with models and simulations in real-time and change simulation details during execution, or execute simulations off-screen and/or remotely in high-performance computing environments. Tissue Forge provides a growing library of built-in model components along with support for user-specified models during the development and application of custom, agent-based models. Tissue Forge includes an extensive Python API for model and simulation specification via Python scripts, an IPython console and a Jupyter Notebook, as well as C and C++ APIs for integrated applications with other software tools. Tissue Forge supports installations on 64-bit Windows, Linux and MacOS systems and is available for local installation via conda.1Author SummaryTissue Forge is a physics-based modeling and simulation software environment for research problems in physics, chemistry and biology. Tissue Forge supports modeling at a wide range of scales, from as small as the sub-nanometer, to as large as hundreds of micrometers, using particle-based models. It provides rich features for simulation development and application at all stages of model-based research, like real-time simulation visualization and interactivity, and off-screen batch execution, rendering, and GPU acceleration. Users can employ built-in models to represent a wide variety of physical processes, like chemical reactions, fluid convection and intercellular adhesion, or define their own models for agentand rule-based modeling. Tissue Forge is open-source, free and easy to install, supports simulation development in C, C++ and Python programming languages, and can be used as integrated software or in an interactive IPython console and Jupyter Notebook. Tissue Forge also provides a dedicated space for application-specific and user-contributed modeling and simulation features, and developers are welcome to contribute their custom features for distribution in future releases.
The association between type of conception through medically assisted reproduction and childhood cognition: A Danish population-wide cohort study
Authors: Fallesen Peter 
Published: November 2022

AbstractPrevious research has found that children conceived through medically assisted reproduction (MAR) on average has cognitive outcomes on par with or above naturally conceived children. However, previous work has been unable to consider the relationship at a full population level nor consider heterogeneity across type of MAR. We use all Danish live births in the years 2006-2009 (n=259,608) with indicator for MAR conceptions (n=13,554). The dependent variable is the within-year-and-grade standardized test scores carried out in second and third grade in primary schools. We compare the test scores for spontaneously conceived (SC) children and conceived through intrauterine insemination (IUI) and assisted reproductive technologies (ART). We estimate ordinary least squares regressions with a baseline model only adjusted for birthyear and models adjusted for birth-related confounders and socio-demographic family characteristics. At baseline, ART and IUI conceived children performed better in tests than SC peers. After adjusting, ART conceived performed worse than SC peer, and IUI conceived performed as well as SC peers and better than ART conceived. Results likely reflect differences in selection of potential parents into type of MAR as well as consequences of differences in fecundability.
The Impact of War on HIV/AIDS Service Provision: in Rural Health Facilities of Tigray, Northern Ethiopia
Authors: Weledegebriel Migbnesh Gebremedhin , Abebe Haftom Temesgen , Gidey Kidu , Bisrat Haileselassie , Gebru Tekae , Tsegay Niguse , Abera Bisrat Tesfay , Gebremeskel Hailay , Asmerom Demoze , Gebreweld Angesom , Miruts Fikadu , Wasihun Araya Gebreyesus , Hagos Kiflom , Gebrehiwet Tesfay Gebregzabher 
Published: November 2022

AbstractBack groundHIV/AIDS remained among the common public health problems worldwide. Despite the extensive delivery of ART and improved coverage of the service access, still, man-made problems like war have negatively influenced the utilization of antiretroviral treatment services. The war in Tigray Region in the northern Ethiopia broke out in November 2020 and thereby has brought about an extreme damage on most of the infrastructure in Tigray, including the health institutions. The purpose of this study is, therefore, to assess and report the trend of HIV service provision across the war affected rural health facilities in Tigray.MethodsThe study was conducted in 33 rural health facilities during the active war in Tigray. A facility based retrospective cross-sectional study design was conducted among health facilities from July 03 to August 05, 2021.ResultA total of 33 health facilities from 25 rural districts were included in the HIV service delivery assessment. A total of 3274 and 3298 HIV patients were seen during pre-war period in September and October 2020, respectively. The number of follow-up patients during the war period in January remained to be only 847(25%) which is significantly reduced with a P value<0.001. A similar trend was observed during the subsequent months until May. The trend of follow-up patients on ART significantly declined from 1940 in September (pre-war) to 331(16.6%) in May (during the war). This study also revealed a 95.5% reduction of laboratory service provision to HIV/AIDS patients during the war in January and with similar trends thereafter (P<0.001).ConclusionThe war has led to a significant decline of HIV service provision in the rural health facilities and most part of the region during the first eight months of active war in Tigray.
A systematic review and meta-analysis comparing the diagnostic accuracy tests of COVID-19
Authors: Vilca-Alosilla Juan Jeferson , Candia-Puma Mayron Antonio , Coronel-Monje Katiusca , Goyzueta-Mamani Luis Daniel , Galdino Alexsandro Sobreira , Machado-de-Ávila Ricardo Andrez , Giunchetti Rodolfo Cordeiro , Ferraz Coelho Eduardo Antonio , Chávez-Fumagalli Miguel Angel 
Published: November 2022

AbstractIn this work, we report a systematic review and meta-analysis that seeks to analyze the accuracy of diagnostic tests for coronavirus disease 2019 (COVID-19). The objective of this article is to detail the scientific findings based on diagnostic tests of the last years when the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurred. Searches for published studies were carried out in the PubMed database between the years 2020 and 2021 for the diagnosis of COVID-19. Ninety-nine scientific articles that met the criteria were examined and accepted in the meta-analysis, and the diagnostic accuracy was evaluated through specificity and sensitivity. Molecular tests [Reverse transcription polymerase chain reaction (RT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and clustered regularly interspaced short palindromic repeats (CRISPR)] showed better performance in terms of sensitivity and specificity when compared to serological tests [Enzyme-linked immunosorbent assay (ELISA), chemiluminescence immunoassay (CLIA), lateral flow immunoassay (LFIA), chemiluminescent microparticle immunoassays (CMIA), and Fluorescence immunoassay (FIA)], which showed higher specificity, mainly for the detection of IgG antibodies; however, they showed sensitivity <90%. In addition, the antiviral neutralization bioassay (ANB) diagnostic test demonstrated high potential for the diagnosis of COVID-19, since it obtained the highest area under the curve restricted to the false-positive rates (AUCFPR) of 0.984. It is settled that the different diagnostic tests have been efficiently adapted for the detection of SARS-CoV-2; however, their performance still needs to be optimized to control future outbreaks of COVID-19, which will also serve to help the control of future infectious agents.
Echocardiography-Based Deep Learning Model to Differentiate Constrictive Pericarditis and Restrictive Cardiomyopathy
Authors: Chao Chieh-Ju , Jeong Jiwoong , Arsanjani Reza , Kim Kihong , Ayoub Chadi , Grogan Martha , Kane Garvan , Banerjee Imon , Oh Jae K 
Published: November 2022

AbstractBackgroundConstrictive pericarditis (CP) is an uncommon but reversible cause of diastolic heart failure if appropriately identified and treated. Although echocardiography can detect CP based on characteristic cardiac motion and Doppler findings, its diagnosis remains a challenge for clinicians. Artificial intelligence (AI) may enhance identification of CP. We proposed a deep learning approach based on transthoracic echocardiography (TTE) to differentiate CP from restrictive cardiomyopathy (RCM).MethodsPatients with a confirmed diagnosis of CP and cardiac amyloidosis (CA, as the representative disease of RCM) at Mayo Clinic Rochester from 1/2003-12/2021 were identified to extract baseline demographics and the apical 4 chamber (A4C) view from TTE studies. The cases were split into a 60:20:20 ratio for training, validation, and held-out test sets of the ResNet50 deep learning model. The model performance (differentiating CP and CA) was evaluated in the test set with the area under the curve (AUC). GradCAM was used for model interpretation.ResultsA total of 381 patients were identified, including 184 (48.3%) CP, and 197 (51.7%) CA cases. The mean age was 68.7±11.4, and 72.8% were male. ResNet50 had a performance with an AUC to differentiate the 2-class classification task (CP vs. CA, AUC 0.97). The GradCAM heatmap showed activation around the ventricular septal area.ConclusionWith a standard A4C view, our AI model provides a platform for the early and accurate detection of CP, allowing for improved workflow efficiency and prompt referral for more advanced evaluation and intervention of CP.
Structural and Computational Design of a SARS-2 Spike Antigen with Increased Receptor Binding Domain Exposure and Improved Immunogenicity
Authors: Williams James A. , Biancucci Marco , Lessen Laura , Tian Sai , Balsaraf Ankita , Chen Lynn , Chesterman Chelsy , Maruggi Giulietta , Vandepaer Sarah , Huang Ying , Mallett Corey P. , Steff Ann-Muriel , Bottomley Matthew James , Malito Enrico , Wahome Newton , Harshbarger Wayne D. 
Published: November 2022

AbstractEmerging SARS-CoV-2 variants of concern challenge the efficacy of approved vaccines and emphasize the need for improved antigens. Using an evolutionary-based design approach starting from the widely used engineered Spike antigen, S-2P, we sought to increase antigen production levels and the exposure of highly conserved and neutralization sensitive receptor-binding domain (RBD) epitopes. Thirty-six prototypes were generatedin silico, of which fifteen were produced and tested in biochemical assays. Design S2D14, which contains 20 mutations within the Spike S2 domain, showed a 6-fold increase in expression while preserving similar thermal stability and antigenicity as S-2P. Cryo-EM structures indicate that the dominant populations of S2D14 particles have RBDs in exposed states, and analysis of these structures revealed how modifications within the S2 domain balance trimer stability and RBD accessibility through formation and removal of hydrogen bonds and surface charge alterations. Importantly, vaccination of mice with adjuvanted S2D14 resulted in higher levels of neutralizing antibodies than adjuvanted S-2P against SARS-CoV-2 Wuhan strain and four variants of concern. These results can guide the design of next generation vaccines to combat current, and future coronaviruses and the approaches used may be broadly applicable to streamline the successful design of vaccine antigens.
Claspin-dependent and -independent Chk1 activation by a panel of biological stresses
Authors: Hsiao Hao-Wen , Yang Chi-Chun , Masai Hisao 
Published: November 2022

AbstractReplication stress has been suggested to be an ultimate trigger of carcinogenesis. Oncogenic signal, such as overexpression of CyclinE, has been shown to induce replication stress. Here, we show that various biological stresses, including heat, oxidative stress, osmotic stress, LPS, hypoxia, and arsenate induce activation of Chk1, a key effector kinase for replication checkpoint. Some of these stresses indeed reduce the fork rate, inhibiting DNA replication. Analyses of Chk1 activation in the cell population with western analyses showed that Chk1 activation by these stresses is largely dependent on Claspin. On the other hand, single cell analyses with Fucci cells indicated that while Chk1 activation during S phase is dependent on Claspin, that in G1 is mostly independent of Claspin. We propose that various biological stresses activate Chk1 either directly by stalling DNA replication fork or by some other mechanism that does not involve replication inhibition. The former pathway predominantly occurs in S phase and depends on Claspin, while the latter pathway, which may occur throughout the cell cycle, is largely independent of Claspin.Our findings provide evidence for novel links between replication stress checkpoint and other biological stresses and points to the presence of unknown mechanisms of Chk1 activation in mammalian cells.
Spatio-temporal modelling of the effect of selected environmental and land-use factors on species-rich calcareous grasslands: overgrazing and nitrogen deposition
Authors: Damgaard Christian 
Published: November 2022

AbstractThe abundance of sensitive plant species in calcareous grasslands are threatened by agricultural intensification with nutrient addition and increased livestock densities as well as by land abandonment. In order to quantify the effect of selected environmental and land-use factors on the observed variation and changes in the vegetation of calcareous grasslands, large-scale spatial and temporal pin-point plant cover monitoring data are fitted in a structural equation model. The analyzed vegetation data come from 100 Danish sites monitored over an eight year period. The important sources of measurement- and sampling uncertainties have been included using a hierarchical model structure. Furthermore, the measurement- and sampling uncertainties are separated from the process uncertainty, which is important when generating ecological predictions that may feed into local conservation management decisions. There were significant negative effects of grazing and nitrogen deposition on the change in cover of sensitive plant species. Whereas the negative effect of nitrogen deposition on the cover of sensitive species was expected, it was surprising that the model results suggest that the class of sensitive species may be subjected to overgrazing by the grazing regimes that are currently applied at protected Danish calcareous grasslands. The standardized regression coefficients suggest that the effects of both grazing and nitrogen deposition are relatively benign compared to the effects of soil type, soil pH and precipitation. The relatively large effect of precipitation is interesting, since it is predicted that the amount of precipitation and distribution over the season will change due to climate change, and the results suggest that climate change may lead to important species compositional changes in calcareous grasslands. The fitted model may be used to quantify the uncertainties when generating ecological forecasting and local adaptive management plans.
Widespread, depth-dependent cortical microstructure alterations in paediatric focal epilepsy
Authors: Casella Chiara , Vecchiato Katy , Cromb Daniel , Guo Yourong , Winkler Anderson M. , Hughes Emer , Dillon Louise , Green Elaine , Colford Kathleen , Egloff Alexia , Siddiqui Ata , Price Anthony , Grande Lucilio Cordero , Wood Tobias C. , Malik Shaihan , Teixeira Rui Pedro A.G. , Carmichael David W. , O’Muircheartaigh Jonathan 
Published: November 2022

AbstractObjectiveTissue abnormalities in focal epilepsy may extend beyond the presumed focus. The underlying pathophysiology of these broader changes is unclear, and it is not known whether they result from ongoing disease processes, treatment-related side-effects, or whether they emerge earlier. Few studies have focused on the period of onset for most focal epilepsies, childhood. Fewer still have utilised quantitative MRI, which may provide a more sensitive and interpretable measure of tissue microstructural change. Here, we aimed to determine common spatial modes of changes in cortical architecture in children with heterogeneous drug-resistant focal epilepsy and, secondarily, whether changes were related to disease severity.MethodsTo assess cortical microstructure, quantitative T1 and T2 relaxometry (qT1 and qT2) was measured in 43 children with drug-resistant focal epilepsy [age-range=4-18 years] and 46 typically-developing children [age-range=2-18 years]. We assessed depth-dependent qT1 and qT2 values across the neocortex, as well as their gradient of change across cortical depths. We also determined whether global changes seen in group analyses were driven by focal pathologies in individual patients. Finally, as a proof-of-concept, we trained a classifier using qT1 and qT2 gradient maps from patients with radiologically-defined abnormalities (MRI-positive) and healthy controls, and tested if this could classify patients without reported radiological abnormalities (MRI-negative).ResultsWe uncovered depth-dependent qT1 and qT2 increases in widespread cortical areas in patients, likely representing microstructural alterations in myelin or gliosis. Changes did not correlate with disease severity measures, suggesting they may represent antecedent neurobiological alterations. Using a classifier trained with MRI-positive patients and controls, sensitivity was 62% at 100% specificity on held-out MRI-negative patients.SignificanceThese findings suggest the presence of a potential imaging endophenotype of focal epilepsy, detectable irrespective of radiologically-identified abnormalities, and potentially evident pre-symptomatically.Key PointsWe assessed cortical microstructure in children with focal epilepsyQuantitative T1 and T2 relaxometry (qT1 and qT2) was measured in the neocortexPatients showed extensive qT1/qT2 increases and intracortical organization changesAlterations may appear during cerebral development, prior to disease onset
Testing heterochrony: Connecting skull shape ontogeny and evolution of feeding adaptations in baleen whales
Authors: Lanzetti Agnese , Miguez Roberto Portela , Fernandez Vincent , Goswami Anjali 
Published: November 2022

AbstractOntogeny plays a key role in the evolution of organisms, as changes during the complex processes of development can allow for new traits to arise. Identifying changes in ontogenetic allometry – the relationship between skull shape and size during growth – can reveal the processes underlying major evolutionary transformations. Baleen whales (Mysticeti, Cetacea) underwent major morphological changes in transitioning from their ancestral raptorial feeding mode to the three specialised filter feeding modes observed in extant taxa. Heterochronic processes have been implicated in the evolution of these feeding modes, and their associated specialised cranial morphologies, but their role has never been tested with quantitative data. Here, we quantified skull shapes ontogeny and reconstructed ancestral allometric trajectories using 3D geometric morphometrics and phylogenetic comparative methods on sample representing modern mysticetes diversity. Our results demonstrate that Mysticeti, while having a common developmental trajectory, present distinct cranial shapes from early in their ontogeny corresponding to their different feeding ecologies. Size is the main driver of shape disparity across mysticetes. Disparate heterochronic processes are evident in the evolution of the group: skim feeders present accelerated growth relative to the ancestral nodes, while Balaenopteridae have overall slower growth, or paedomorphosis. The grey whale is the only taxon with a relatively faster rate of growth in this group, which might be connected to its unique benthic feeding strategy. Reconstructed ancestral allometries and related skull shapes indicate that extinct taxa used less specialized filter feeding modes, a finding broadly in line with the available fossil evidence.