bluuebunny/crossref_metadata_2025_split huggingface dataset:
Porphyromonas spp., Fusobacterium spp., and Bacteroides spp. dominate microbiota in the course of macropod progressive periodontal disease
Authors: Yip Sabine , Dehcheshmeh Manijeh Mohammadi , McLelland David J. , Boardman Wayne S. J. , Saputra Sugiyono , Ebrahimie Esmaeil , Weyrich Laura S. , Bird Philip S. , Trott Darren J. 
Published: September 2021

AbstractMacropod progressive periodontal disease (MPPD) is a necrotizing, polymicrobial, inflammatory disease commonly diagnosed in captive macropods. MPPD is characterized by gingivitis associated with dental plaque formation, which progresses to periodontitis and then to osteomyelitis of the mandible or maxilla. However, the underlying microbial causes of this disease remain poorly understood. In this study, we collected 27 oral plaque samples and associated clinical records from 22 captive Macropodidae and Potoroidae individuals that were undergoing clinical examination at Adelaide and Monarto Zoos in South Australia (15 healthy, 7 gingivitis and 5 periodontitis-osteomyelitis samples). The V3-V4 region of the 16S ribosomal RNA gene was sequenced using an Illumina Miseq to explore links between MPPD and oral bacteria in these animals. Compositional differences were detected between the microbiota of periodontitis-osteomyelitis cases compared to healthy samples (p-value with Bonferroni correction < 0.01), as well as gingivitis cases compared to healthy samples (p-value with Bonferroni correction < 0.05) using Permutational Multivariate Analysis of Variance (PERMANOVA). An overabundance of Porphyromonas, Fusobacterium, and Bacteroides taxa was also identified in animals with MPPD compared to healthy individuals using linear discriminant analysis effect size (LEfSe; p =  < 0.05). An increased abundance of Desulfomicrobium also was detected in MPPD samples (LEfSe; p < 0.05), which could potentially reflect differences in disease progression. This is the first microbiota analysis of MPPD in captive macropods, and these results support a polymicrobial pathogenesis of MPPD, suggesting that the microbial interactions underpinning MPPD may be more complex than previously documented.
Reciprocal regulation of endothelial–mesenchymal transition by MAPK7 and EZH2 in intimal hyperplasia and coronary artery disease
Authors: Vanchin Byambasuren , Sol Marloes , Gjaltema Rutger A. F. , Brinker Marja , Kiers Bianca , Pereira Alexandre C. , Harmsen Martin C. , Moonen Jan-Renier A. J. , Krenning Guido 
Published: September 2021

AbstractEndothelial–mesenchymal transition (EndMT) is a form of endothelial dysfunction wherein endothelial cells acquire a mesenchymal phenotype and lose endothelial functions, which contributes to the pathogenesis of intimal hyperplasia and atherosclerosis. The mitogen activated protein kinase 7 (MAPK7) inhibits EndMT and decreases the expression of the histone methyltransferase Enhancer-of-Zeste homologue 2 (EZH2), thereby maintaining endothelial quiescence. EZH2 is the catalytic subunit of the Polycomb Repressive Complex 2 that methylates lysine 27 on histone 3 (H3K27me3). It is elusive how the crosstalk between MAPK7 and EZH2 is regulated in the endothelium and if the balance between MAPK7 and EZH2 is disturbed in vascular disease. In human coronary artery disease, we assessed the expression levels of MAPK7 and EZH2 and found that with increasing intima/media thickness ratio, MAPK7 expression decreased, whereas EZH2 expression increased. In vitro, MAPK7 activation decreased EZH2 expression, whereas endothelial cells deficient of EZH2 had increased MAPK7 activity. MAPK7 activation results in increased expression of microRNA (miR)-101, a repressor of EZH2. This loss of EZH2 in turn results in the increased expression of the miR-200 family, culminating in decreased expression of the dual-specificity phosphatases 1 and 6 who may repress MAPK7 activity. Transfection of endothelial cells with miR-200 family members decreased the endothelial sensitivity to TGFβ1-induced EndMT. In endothelial cells there is reciprocity between MAPK7 signaling and EZH2 expression and disturbances in this reciprocal signaling associate with the induction of EndMT and severity of human coronary artery disease.
Genotypes of informative loci from 1000 Genomes data allude evolution and mixing of human populations
Authors: Padakanti Sridevi , Tiong Khong-Loon , Chen Yan-Bin , Yeang Chen-Hsiang 
Published: September 2021

AbstractPrincipal Component Analysis (PCA) projects high-dimensional genotype data into a few components that discern populations. Ancestry Informative Markers (AIMs) are a small subset of SNPs capable of distinguishing populations. We integrate these two approaches by proposing an algorithm to identify necessary informative loci whose removal from the data deteriorates the PCA structure. Unlike classical AIMs, necessary informative loci densely cover the genome, hence can illuminate the evolution and mixing history of populations. We conduct a comprehensive analysis to the genotype data of the 1000 Genomes Project using necessary informative loci. Projections along the top seven principal components demarcate populations at distinct geographic levels. Millions of necessary informative loci along each PC are identified. Population identities along each PC are approximately determined by weighted sums of minor (or major) alleles over the informative loci. Variations of allele frequencies are aligned with the history and direction of population evolution. The population distribution of projections along the top three PCs is recapitulated by a simple demographic model based on several waves of founder population separation and mixing. Informative loci possess locational concentration in the genome and functional enrichment. Genes at two hot spots encompassing dense PC 7 informative loci exhibit differential expressions among European populations. The mosaic of local ancestry in the genome of a mixed descendant from multiple populations can be inferred from partial PCA projections of informative loci. Finally, informative loci derived from the 1000 Genomes data well predict the projections of an independent genotype data of South Asians. These results demonstrate the utility and relevance of informative loci to investigate human evolution.
Nanopore sequencing and de novo assembly of a misidentified Camelpox vaccine reveals putative epigenetic modifications and alternate protein signal peptides
Authors: Saud Zack , Hitchings Matthew D. , Butt Tariq M. 
Published: September 2021

AbstractDNA viruses can exploit host cellular epigenetic processes to their advantage; however, the epigenome status of most DNA viruses remains undetermined. Third generation sequencing technologies allow for the identification of modified nucleotides from sequencing experiments without specialized sample preparation, permitting the detection of non-canonical epigenetic modifications that may distinguish viral nucleic acid from that of their host, thus identifying attractive targets for advanced therapeutics and diagnostics. We present a novel nanopore de novo assembly pipeline used to assemble a misidentified Camelpox vaccine. Two confirmed deletions of this vaccine strain in comparison to the closely related Vaccinia virus strain modified vaccinia Ankara make it one of the smallest non-vector derived orthopoxvirus genomes to be reported. Annotation of the assembly revealed a previously unreported signal peptide at the start of protein A38 and several predicted signal peptides that were found to differ from those previously described. Putative epigenetic modifications around various motifs have been identified and the assembly confirmed previous work showing the vaccine genome to most closely resemble that of Vaccinia virus strain Modified Vaccinia Ankara. The pipeline may be used for other DNA viruses, increasing the understanding of DNA virus evolution, virulence, host preference, and epigenomics.
Studying the distribution patterns, dynamics and influencing factors of city functional components by gradient analysis
Authors: Liu Shun , Yang Guofu , Wu Zhaoping , Mao Feng , Qu Zelong , Ge Ying , Chang Jie 
Published: September 2021

AbstractUnderstanding the spatial distribution characteristics and formation mechanism of urban facilities (city functional components) constitutes the basis of urban layout optimization. Currently, research on the overall distribution of the various types of city functional components is lacking. In this study, by applying the gradient analysis method common in ecology, we considered 13 types of city functional components (80,214 individuals in total) in large, medium and small Chinese cities (9 cities in total) to carry out quantitative analysis of the distribution of components along urban–rural gradients through density distribution curves. The results indicated that: (1) a higher density of city functional components near the city centre revealed an obvious aggregated distribution; (2) the spatial distribution dynamics of city functional components were related to the city size, providing a reference for the rational distribution of components in cities of different sizes; (3) the distribution of city functional components was affected by their ecosystem services. This study offers a new perspective for the application of ecological methods in the examination of the distribution of city functional components.
Treatment of moderate to severe respiratory COVID-19: a cost-utility analysis
Authors: Congly Stephen E. , Varughese Rhea A. , Brown Crystal E. , Clement Fiona M. , Saxinger Lynora 
Published: September 2021

AbstractDespite COVID-19’s significant morbidity and mortality, considering cost-effectiveness of pharmacologic treatment strategies for hospitalized patients remains critical to support healthcare resource decisions within budgetary constraints. As such, we calculated the cost-effectiveness of using remdesivir and dexamethasone for moderate to severe COVID-19 respiratory infections using the United States health care system as a representative model. A decision analytic model modelled a base case scenario of a 60-year-old patient admitted to hospital with COVID-19. Patients requiring oxygen were considered moderate severity, and patients with severe COVID-19 required intubation with intensive care. Strategies modelled included giving remdesivir to all patients, remdesivir in only moderate and only severe infections, dexamethasone to all patients, dexamethasone in severe infections, remdesivir in moderate/dexamethasone in severe infections, and best supportive care. Data for the model came from the published literature. The time horizon was 1 year; no discounting was performed due to the short duration. The perspective was of the payer in the United States health care system. Supportive care for moderate/severe COVID-19 cost $11,112.98 with 0.7155 quality adjusted life-year (QALY) obtained. Using dexamethasone for all patients was the most-cost effective with an incremental cost-effectiveness ratio of $980.84/QALY; all remdesivir strategies were more costly and less effective. Probabilistic sensitivity analyses showed dexamethasone for all patients was most cost-effective in 98.3% of scenarios. Dexamethasone for moderate-severe COVID-19 infections was the most cost-effective strategy and would have minimal budget impact. Based on current data, remdesivir is unlikely to be a cost-effective treatment for COVID-19.
A potential role for the adrenal gland in autism
Authors: Al-Zaid Felwah S. , Alhader Abdel Fattah A. , Al-Ayadhi Laila Y. 
Published: September 2021

AbstractAndrogens have been implicated in autism pathophysiology as recently, prenatal exposure to elevated androgens has been proposed as risk factor. However, published data on postnatal sex hormone levels in autistic children are controversial and the source of prenatal androgen exposure in autism remains unknown. Therefore, this study investigated postnatal sex hormone levels and dehydroepiandrosterone (DHEA) to shed light on a potential role for the adrenal gland in autism pathophysiology. A case-control study investigating estradiol (E2), DHEA, follicle-stimulating hormone (FSH) and luteinizing hormone (LH) levels was conducted with 31 Saudi males with autism and 28 healthy, age-matched boys plasma. Moreover, correlation analysis with measured hormones and previously measured total testosterone (TT) and free testosterone (FT) in the same group of autism was conducted. DHEA was significantly higher (p < 0.05) in the autism group compared to controls. DHEA positively correlated with previously measured TT (r = + 0.79, p < 0.001) and FT (r = + 0.72, p < 0.001) levels in the same autism group. FSH levels were also significantly higher in the autism group than in the control group (p < 0.01). To the best of our knowledge, this is the first study to report a strong positive correlation between TT, FT and DHEA, suggesting an adrenal source for elevated androgen levels.
Dynamics of SARS-CoV-2 mutations reveals regional-specificity and similar trends of N501 and high-frequency mutation N501Y in different levels of control measures
Authors: Justo Arevalo Santiago , Zapata Sifuentes Daniela , J. Huallpa César , Landa Bianchi Gianfranco , Castillo Chávez Adriana , Garavito-Salini Casas Romina , Uribe Calampa Carmen Sofia , Uceda-Campos Guillermo , Pineda Chavarría Roberto 
Published: September 2021

AbstractCoronavirus disease 2019 (COVID-19) is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This disease has spread globally, causing more than 161.5 million cases and 3.3 million deaths to date. Surveillance and monitoring of new mutations in the virus’ genome are crucial to our understanding of the adaptation of SARS-CoV-2. Moreover, how the temporal dynamics of these mutations is influenced by control measures and non-pharmaceutical interventions (NPIs) is poorly understood. Using 1,058,020 SARS-CoV-2 from sequenced COVID-19 cases from 98 countries (totaling 714 country-month combinations), we perform a normalization by COVID-19 cases to calculate the relative frequency of SARS-CoV-2 mutations and explore their dynamics over time. We found 115 mutations estimated to be present in more than 3% of global COVID-19 cases and determined three types of mutation dynamics: high-frequency, medium-frequency, and low-frequency. Classification of mutations based on temporal dynamics enable us to examine viral adaptation and evaluate the effects of implemented control measures in virus evolution during the pandemic. We showed that medium-frequency mutations are characterized by high prevalence in specific regions and/or in constant competition with other mutations in several regions. Finally, taking N501Y mutation as representative of high-frequency mutations, we showed that level of control measure stringency negatively correlates with the effective reproduction number of SARS-CoV-2 with high-frequency or not-high-frequency and both follows similar trends in different levels of stringency.
A simple method to describe the COVID-19 trajectory and dynamics in any country based on Johnson cumulative density function fitting
Authors: Ćmiel Adam M. , Ćmiel Bogdan 
Published: September 2021

AbstractA simple method is utilised to study and compare COVID-19 infection dynamics between countries based on curve fitting to publicly shared data of confirmed COVID-19 infections. The method was tested using data from 80 countries from 6 continents. We found that Johnson cumulative density functions (CDFs) were extremely well fitted to the data (R2 > 0.99) and that Johnson CDFs were much better fitted to the tails of the data than either the commonly used normal or lognormal CDFs. Fitted Johnson CDFs can be used to obtain basic parameters of the infection wave, such as the percentage of the population infected during an infection wave, the days of the start, peak and end of the infection wave, and the duration of the wave’s increase and decrease. These parameters can be easily interpreted biologically and used both for describing infection wave dynamics and in further statistical analysis. The usefulness of the parameters obtained was analysed with respect to the relation between the gross domestic product (GDP) per capita, the population density, the percentage of the population infected during an infection wave, the starting day and the duration of the infection wave in the 80 countries. We found that all the above parameters were significantly associated with GDP per capita, but only the percentage of the population infected was significantly associated with population density. If used with caution, this method has a limited ability to predict the future trajectory and parameters of an ongoing infection wave.
Melanoma cells adopt features of both mesenchymal and amoeboid migration within confining channels
Authors: Gabbireddy Sairisheel R. , Vosatka Karl W. , Chung Aram J , Logue Jeremy S. 
Published: September 2021

AbstractFor metastasis to occur, cancer cells must traverse a range of tissue environments. In part, this is accomplished by cells adjusting their migration mode to one that is best suited to the environment. Melanoma cells have been shown to be particularly plastic, frequently using both mesenchymal and amoeboid (bleb-based) modes of migration. It has been demonstrated that 2D confinement will promote the transition from mesenchymal to bleb-based migration. However, if melanoma cells similarly transition to bleb-based migration in response to 3D confinement, such as within narrow channels, is unknown. Here, using micro-fabricated channels, we demonstrate that metastatic, A375-M2, melanoma cells adopt features of both mesenchymal and bleb-based migration. In narrow (8 µm; height and width) channels coated with fibronectin, ~ 50% of melanoma cells were found to use either mesenchymal or bleb-based migration modes. In contrast, the inhibition of Src family kinases or coating channels with BSA, completely eliminated any features of mesenchymal migration. Detailed comparisons of migration parameters revealed that blebbing cells, particularly in the absence of adhesions, were faster than mesenchymal cells. In contrast to what has been previously shown under conditions of 2D confinement, pharmacologically inhibiting Arp2/3 promoted a fast filopodial-based mode of migration. Accordingly, we report that melanoma cells adopt a unique range of phenotypes under conditions of 3D confinement.
Gravity-induced phase phenomena in plate-rod colloidal mixtures
Authors: Eckert Tobias , Schmidt Matthias , de las Heras Daniel 
Published: September 2021

AbstractGravity can affect colloidal suspensions since for micrometer-sized particles gravitational and thermal energies can be comparable over vertical length scales of a few millimeters. In mixtures, each species possesses a different buoyant mass, which can make experimental results counter-intuitive and difficult to interpret. Here, we revisit from a theoretical perspective iconic sedimentation-diffusion-equilibrium experiments on colloidal plate-rod mixtures by van der Kooij and Lekkerkerker. We reproduce their findings, including the observation of five different mesophases in a single cuvette. Using sedimentation path theory, we incorporate gravity into a microscopic theory for the bulk of a plate-rod mixture. We also show how to disentangle the effects of gravity from sedimentation experiments to obtain the bulk behavior and make predictions that can be experimentally tested. These include changes in the sequence by altering the sample height. We demonstrate that both buoyant mass ratio and sample height form control parameters to study bulk phase behavior.
Sustainability of emerging energy and transportation technologies is impacted by the coexistence of minerals in nature
Authors: Elshkaki Ayman 
Published: September 2021

AbstractWind power and electric vehicles can help reduce carbon dioxide emissions and improve air quality. However, these technologies rely on rare metals whose extraction requires large amounts of energy and water and are high in carbon emissions. Here we consider the sustainability of both technologies and the impacts of rare earth elements co-extraction. We use a global dynamic material flow-stock model and several scenarios for rare earth elements demand and supply. Cumulative carbon dioxide equivalent emissions associated with rare earth metals oversupply was between 5.5 and 6.4 times the emissions associated with dysprosium and neodymium production when dysprosium demand was increased. Carbon dioxide equivalent emissions associated with metals extraction and production were equivalent to between 10% and 29% of carbon dioxide emissions reduction through electric vehicle use. Targeting metal rich deposits and increased material efficiency and recycling reduced carbon dioxide emissions by 78%, 39% and 35%, and combined by 90%. Our findings highlight the role of resource efficiency and recycling in enhancing clean energy technologies.
Cognitive and Physiological Measures of Listening Effort During Degraded Speech Perception: Relating Dual-Task and Pupillometry Paradigms
Authors: Colby Sarah , McMurray Bob 
Published: September 2021

Purpose
Listening effort is quickly becoming an important metric for assessing speech perception in less-than-ideal situations. However, the relationship between the construct of listening effort and the measures used to assess it remains unclear. We compared two measures of listening effort: a cognitive dual task and a physiological pupillometry task. We sought to investigate the relationship between these measures of effort and whether engaging effort impacts speech accuracy.

Method

In Experiment 1, 30 participants completed a dual task and a pupillometry task that were carefully matched in stimuli and design. The dual task consisted of a spoken word recognition task and a visual match-to-sample task. In the pupillometry task, pupil size was monitored while participants completed a spoken word recognition task. Both tasks presented words at three levels of listening difficulty (unmodified, eight-channel vocoding, and four-channel vocoding) and provided response feedback on every trial. We refined the pupillometry task in Experiment 2 (
n
= 31); crucially, participants no longer received response feedback. Finally, we ran a new group of subjects on both tasks in Experiment 3 (
n
= 30).

Results
In Experiment 1, accuracy in the visual task decreased with increased signal degradation in the dual task, but pupil size was sensitive to accuracy and not vocoding condition. After removing feedback in Experiment 2, changes in pupil size were predicted by listening condition, suggesting the task was now sensitive to engaged effort. Both tasks were sensitive to listening difficulty in Experiment 3, but there was no relationship between the tasks and neither task predicted speech accuracy.

Conclusions
Consistent with previous work, we found little evidence for a relationship between different measures of listening effort. We also found no evidence that effort predicts speech accuracy, suggesting that engaging more effort does not lead to improved speech recognition. Cognitive and physiological measures of listening effort are likely sensitive to different aspects of the construct of listening effort.

Supplemental Material

https://doi.org/10.23641/asha.16455900