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Neotropical fishes exhibit remarkable karyotype diversity, whose evolution is poorly understood. Here, we studied genetic differences in 60 individuals, from 11 localities of one species, the wolf fish Hoplias malabaricus, from populations that include six different "karyomorphs". These differ in Y-X chromosome differentiation, and, in several cases, by fusions with autosomes that have resulted in multiple sex chromosomes. Other differences are also observed in diploid chromosome numbers and morphologies. In an attempt to start understanding how this diversity was generated, we analyzed within- and between-population differences in a genome-wide sequence data set. We detect clear genotype differences between karyomorphs. Even in sympatry, samples with different karyomorphs differ more in sequence than samples from allopatric populations of the same karyomorph, suggesting that they represent populations that are to some degree reproductively isolated. However, sequence divergence between populations with different karyomorphs is remarkably low, suggesting that chromosome rearrangements may have evolved during a brief evolutionary time. We suggest that the karyotypic differences probably evolved in allopatry, in small populations that would have allowed rapid fixation of rearrangements, and that they became sympatric after their differentiation. Further studies are needed to test whether the karyotype differences contribute to reproductive isolation detected between some H. malabaricus karyomorphs., (© 2024. The Author(s), under exclusive licence to The Genetics Society.)

Background and Aims: Biogeographical relationships between the Canary Islands and north-west Africa are often explained by oceanic dispersal and geographical proximity. Sister-group relationships between Canarian and eastern African/Arabian taxa, the 'Rand Flora' pattern, are rare among plants and have been attributed to the extinction of north-western African populations. Euphorbia balsamifera is the only representative species of this pattern that is distributed in the Canary Islands and north-west Africa; it is also one of few species present in all seven islands. Previous studies placed African populations of E. balsamifera as sister to the Canarian populations, but this relationship was based on herbarium samples with highly degraded DNA. Here, we test the extinction hypothesis by sampling new continental populations; we also expand the Canarian sampling to examine the dynamics of island colonization and diversification., Methods: Using target enrichment with genome skimming, we reconstructed phylogenetic relationships within E. balsamifera and between this species and its disjunct relatives. A single nucleotide polymorphism dataset obtained from the target sequences was used to infer population genetic diversity patterns. We used convolutional neural networks to discriminate among alternative Canary Islands colonization scenarios., Key Results: The results confirmed the Rand Flora sister-group relationship between western E. balsamifera and Euphorbia adenensis in the Eritreo-Arabian region and recovered an eastern-western geographical structure among E. balsamifera Canarian populations. Convolutional neural networks supported a scenario of east-to-west island colonization, followed by population extinctions in Lanzarote and Fuerteventura and recolonization from Tenerife and Gran Canaria; a signal of admixture between the eastern island and north-west African populations was recovered., Conclusions: Our findings support the Surfing Syngameon Hypothesis for the colonization of the Canary Islands by E. balsamifera, but also a recent back-colonization to the continent. Populations of E. balsamifera from northwest Africa are not the remnants of an ancestral continental stock, but originated from migration events from Lanzarote and Fuerteventura. This is further evidence that oceanic archipelagos are not a sink for biodiversity, but may be a source of new genetic variability., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company.)

Competing Interests: There are no conflicts of interest.

The N-terminal tails of eukaryotic histones are frequently posttranslationally modified. The role of these modifications in transcriptional regulation is well-documented. However, the extent to which the enzymatic processes of histone posttranslational modification might affect metabolic regulation is less clear. Here, we investigated how histone methylation might affect metabolism using metabolomics, proteomics, and RNA-seq data from cancer cell lines, primary tumour samples and healthy tissue samples. In cancer, the expression of histone methyltransferases (HMTs) was inversely correlated to the activity of NNMT, an enzyme previously characterised as a methyl sink that disposes of excess methyl groups carried by the universal methyl donor S-adenosyl methionine (SAM or AdoMet). In healthy tissues, histone methylation was inversely correlated to the levels of an alternative methyl sink, PEMT. These associations affected the levels of multiple histone marks on chromatin genome-wide but had no detectable impact on transcriptional regulation. We show that HMTs with a variety of different associations to transcription are co-regulated by the Retinoblastoma (Rb) tumour suppressor in human cells. Rb-mutant cancers show increased total HMT activity and down-regulation of NNMT. Together, our results suggest that the total activity of HMTs affects SAM metabolism, independent of transcriptional regulation., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Perez, Sarkies. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than threefold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed the best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone., Competing Interests: ML, MC, GG, NP, GT, SB, VC, JC, IE, BH, AH, XH, LI, EN, JO, VP, AP, DP, MP, MR, CS, JS, AT, ST, PU, JV, RW, AW, YW, FB, RC, GG, RG, JK, AK, AR, PR, DS, IG No competing interests declared, AG is an employee of Embark Veterinary, Inc. The author declares that no other competing interests exist, JA is an employee of Ancestry DNA. The author declares that no other competing interests exist, AB is an employee of 54Gene, Inc. The author declares that no other competing interests exist, (© 2023, Lauterbur et al.)

Rationale: Electronic (e)-cigarettes are popular among youth and cigarette smokers attempting to quit. Studies to date have focused on the utility of e-cigarettes as a smoking cessation tool, but the biological effects are largely unknown., Objectives: To identify transcriptomic differences in the blood and sputum of e-cigarette users compared to conventional cigarettes smokers and healthy controls and describe biological pathways affected by these tobacco products., Methods: Cross-sectional analysis of whole blood and sputum RNA-sequencing data from 8 smokers, 9 e-cigarette users (e-cigs) and 4 controls. Weighted gene co-network analysis (WGCNA) identified gene module associations. Ingenuity Pathway Analysis (IPA) identified canonical pathways associated with tobacco products., Main Results: In blood, a three-group comparison showed 16 differentially expressed genes (DEGs); pair-wise comparison showed 7 DEGs between e-cigs and controls, 35 DEGs between smokers and controls, and 13 DEGs between smokers and e-cigs. In sputum, 438 DEGs were in the three-group comparison. In pair-wise comparisons, there were 2 DEGs between e-cigs and controls, 270 DEGs between smokers and controls, and 468 DEGs between smokers and e-cigs. Only 2 genes in the smokers vs. control comparison overlapped between blood and sputum. Most gene modules identified through WGCNA associated with tobacco product exposures also were associated with cotinine and exhaled CO levels. IPA showed more canonical pathways altered by conventional cigarette smoking than by e-cigarette use., Conclusion: Cigarette smoking and e-cigarette use led to transcriptomic changes in both blood and sputum. However, conventional cigarettes induced much stronger transcriptomic responses in both compartments., (© 2023. The Author(s).)

Premise: Pilosocereus (Cactaceae) is an important dry forest element in all subregions and transitional zones of the neotropics, with the highest diversity in eastern Brazil. The genus is subdivided into informal taxonomic groups; however, most of these are not supported by recent molecular phylogenetic inferences. This lack of confidence is probably due to the use of an insufficient number of loci and the complexity of cactus diversification. Here, we explored the species relationships in Pilosocereus in more detail, integrating multilocus phylogenetic approaches with the assessment of the ancestral range and the effect of geography on diversification shifts., Methods: We used 28 nuclear, plastid, and mitochondrial loci from 54 plant samples of 31 Pilosocereus species for phylogenetic analyses. We used concatenated and coalescent phylogenetic trees and Bayesian models to estimate the most likely ancestral range and diversification shifts., Results: All Pilosocereus species were clustered in the same branch, except P. bohlei. The phylogenetic relationships were more associated with the geographic distribution than taxonomic affinities among taxa. The genus began diversifying during the Plio-Pleistocene transition in the Caatinga domain and experienced an increased diversification rate during the Calabrian age., Conclusions: We recovered a well-supported multispecies coalescent phylogeny. Our results refine the pattern of rapid diversification of Pilosocereus species across neotropical drylands during the Pleistocene and highlight the need for taxonomic rearrangements in the genus. We recovered a pulse of diversification during the Pleistocene that was likely driven by multiple dispersal and vicariance events within and among the Caatinga, Cerrado, and Atlantic Forest domains., (© 2023 Botanical Society of America.)

Allopatry is generally considered to be one of the main contributors to the remarkable Neotropical biodiversity. However, the role of chromosomal rearrangements including neo-sex chromosomes for genetic diversity is still poorly investigated and understood. Here, we assess the genetic divergence in five Pyrrhulina species using population genomics and combined the results with previously obtained cytogenetic data, highlighting that molecular genetic diversity is consistent with their chromosomal features. The results of a principal coordinate analysis (PCoA) indicated a clear difference among all species while showing a closer relationship of the ones located in the same geographical region. This was also observed in genetic structure analyses that only grouped P. australis and P. marilynae , which were also recovered as sister species in a species tree analysis. We observed a contradictory result for the relationships among the three species from the Amazon basin, as the phylogenetic tree suggested P. obermulleri and P. semifasciata as sister species, while the PCoA showed a high genetic difference between P. semifasciata and all other species. These results suggest a potential role of sex-related chromosomal rearrangements as reproductive barriers between these species., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Ferreira, Souza, de Moraes, Perez, Sassi, Viana, Feldberg, Ezaz, Liehr, Bertollo and Cioffi.)

Quaternary climatic oscillations had a large impact on European biogeography. Alternation of cold and warm stages caused recurrent glaciations, massive vegetation shifts, and large-scale range alterations in many species. The Eurasian steppe biome and its grasslands are a noteworthy example; they underwent climate-driven, large-scale contractions during warm stages and expansions during cold stages. Here, we evaluate the impact of these range alterations on the late Quaternary demography of several phylogenetically distant plant and insect species, typical of the Eurasian steppes. We compare three explicit demographic hypotheses by applying an approach combining convolutional neural networks with approximate Bayesian computation. We identified congruent demographic responses of cold stage expansion and warm stage contraction across all species, but also species-specific effects. The demographic history of the Eurasian steppe biota reflects major paleoecological turning points in the late Quaternary and emphasizes the role of climate as a driving force underlying patterns of genetic variance on the biome level., (© 2022. The Author(s).)

Delimiting species boundaries is a major goal in evolutionary biology. An increasing volume of literature has focused on the challenges of investigating cryptic diversity within complex evolutionary scenarios of speciation, including gene flow and demographic fluctuations. New methods based on model selection, such as approximate Bayesian computation, approximate likelihoods, and machine learning are promising tools arising in this field. Here, we introduce a framework for species delimitation using the multispecies coalescent model coupled with a deep learning algorithm based on convolutional neural networks (CNNs). We compared this strategy with a similar ABC approach. We applied both methods to test species boundary hypotheses based on current and previous taxonomic delimitations as well as genetic data (sequences from 41 loci) in Pilosocereus aurisetus, a cactus species complex with a sky-island distribution and taxonomic uncertainty. To validate our method, we also applied the same strategy on data from widely accepted species from the genus Drosophila. The results show that our CNN approach has a high capacity to distinguish among the simulated species delimitation scenarios, with higher accuracy than ABC. For the cactus data set, a splitter hypothesis without gene flow showed the highest probability in both CNN and ABC approaches, a result agreeing with previous taxonomic classifications and in line with the sky-island distribution and low dispersal of P. aurisetus. Our results highlight the cryptic diversity within the P. aurisetus complex and show that CNNs are a promising approach for distinguishing complex evolutionary histories, even outperforming the accuracy of other model-based approaches such as ABC., (© 2021 John Wiley & Sons Ltd.)

Diversity found in Neotropical freshwater fish is remarkable. It can even hinder a proper delimitation of many species, with the wolf fish Erythrinus erythrinus (Teleostei, Characiformes) being a notable example. This nominal species shows remarkable intra-specific variation, with extensive karyotype diversity found among populations in terms of different diploid chromosome numbers (2 n ), karyotype compositions and sex chromosome systems. Here, we analyzed three distinct populations (one of them cytogenetically investigated for the first time) that differed in terms of their chromosomal features (termed karyomorphs) and by the presence or absence of heteromorphic sex chromosomes. We combined cytogenetics with genomic approaches to investigate how the evolution of multiple sex chromosomes together with allopatry is linked to genetic diversity and speciation. The results indicated the presence of high genetic differentiation among populations both from cytogenetic and genomic aspects, with long-distance allopatry potentially being the main agent of genetic divergence. One population showed a neo-X 1 X 2 Y sexual chromosome system and we hypothesize that this system is associated with enhanced inter-population genetic differentiation which could have potentially accelerated speciation compared to the effect of allopatry alone.

Background: Mitochondria are ancient endosymbiotic organelles crucial to eukaryotic growth and metabolism. The mammalian mitochondrial genome encodes for 13 mitochondrial proteins, and the remaining mitochondrial proteins are encoded by the nuclear genome. Little is known about how coordination between the expression of the two sets of genes is achieved., Results: Correlation analysis of RNA-seq expression data from large publicly available datasets is a common method to leverage genetic diversity to infer gene co-expression modules. Here we use this method to investigate nuclear-mitochondrial gene expression coordination. We identify a pitfall in correlation analysis that results from the large variation in the proportion of transcripts from the mitochondrial genome in RNA-seq data. Commonly used normalisation techniques based on total read counts, such as FPKM or TPM, produce artefactual negative correlations between mitochondrial- and nuclear-encoded transcripts. This also results in artefactual correlations between pairs of nuclear-encoded genes, with important consequences for inferring co-expression modules beyond mitochondria. We show that these effects can be overcome by normalizing using the median-ratio normalisation (MRN) or trimmed mean of M values (TMM) methods. Using these normalisations, we find only weak and inconsistent correlations between mitochondrial and nuclear-encoded mitochondrial genes in the majority of healthy human tissues from the GTEx database., Conclusions: We show that a subset of healthy tissues with high expression of NF-κB show significant coordination, suggesting a role for NF-κB in ensuring balanced expression between mitochondrial and nuclear genes. Contrastingly, most cancer types show robust coordination of nuclear and mitochondrial OXPHOS gene expression, identifying this as a feature of gene regulation in cancer., (© 2021. The Author(s).)

Diamante Lake located at 4589 m.a.s.l. in the Andean Puna constitutes an extreme environment. It is exposed to multiple extreme conditions such as an unusually high concentration of arsenic (over 300 mg L -1 ) and low oxygen pressure. Microorganisms thriving in the lake display specific genotypes that facilitate survival, which include at least a multitude of plasmid-encoded resistance traits. Hence, the genetic information provided by the plasmids essentially contributes to understand adaptation to different stressors. Though plasmids from cultivable organisms have already been analyzed to the sequence level, the impact of the entire plasmid-borne genetic information on such microbial ecosystem is not known. This study aims at assessing the plasmidome from Diamante Lake, which facilitates the identification of potential hosts and prediction of gene functions as well as the ecological impact of mobile genetic elements. The deep-sequencing analysis revealed a large fraction of previously unknown DNA sequences of which the majority encoded putative proteins of unknown function. Remarkably, functions related to the oxidative stress response, DNA repair, as well as arsenic- and antibiotic resistances were annotated. Additionally, all necessary capacities related to plasmid replication, mobilization and maintenance were detected. Sequences characteristic for megaplasmids and other already known plasmid-associated genes were identified as well. The study highlights the potential of the deep-sequencing approach specifically targeting plasmid populations as it allows to evaluate the ecological impact of plasmids from (cultivable and non-cultivable) microorganisms, thereby contributing to the understanding of the distribution of resistance factors within an extremophilic microbial community., (© 2021. The Author(s).)

Study Design: Prospective clinical pilot study and cadaveric study., Objective: The aim of this study was to evaluate the spread of an ultrasound-guided interfascial plane blocks (UGIPBs) and its potential efficacy for cervical radiculopathy., Summary of Background Data: Cervical radiculopathy is a common disorder, potentially leading to severe pain and disability. Conservative treatment with cervical epidural steroid injections (ESI) is limited by concerns regarding their safety. UGIPBs are used in cervical surgical procedures as part of the multimodal postoperative analgesia regimen however, were not described for cervical radiculopathy., Methods: Twelve patients with acute cervical radicular pain who failed conservative treatment and were candidates for surgery were offered a cervical retrolaminar injection. A solution of 4 mL lidocaine 0.5% and 10 mg dexamethasone was injected, assisted by ultrasound guidance, at the posterior aspect of the cervical lamina corresponding to the compressed nerve root level. Additionally, a cadaver study was carried to evaluate the contrast spread and infiltration into near structures, both anatomically and radiographically., Results: Twelve patients underwent the procedure, with a mean follow-up time of 14.5 weeks. Average numerical rating scale improved from 7.25 at baseline to 2.83 following the injection (P < 0.001). Three patients received 2 to 3 injections without significant improvement and were eventually operated. No adverse events were reported.In the cadaver study, fluoroscopy demonstrated contrast spread between T1 and T3 caudally, C2 to C5 cranially and facet joints laterally. Anatomically, the dye spread was demonstrated up to C2 cranially, T1 caudally, the articular pillars of C4 to C7, and the neural foramen of C6 laterally., Conclusion: A solution injected into the cervical retrolaminar plane can diffuse in the cranial-caudal axis to C2-T3 and laterally to the facet joints and the cervical neural foramen. Our pilot study confirmed the feasibility of our study protocol. Future studies are needed to support our early results.Level of Evidence: 4., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

An old and controversial question in biology is whether information perceived by the nervous system of an animal can "cross the Weismann barrier" to alter the phenotypes and fitness of their progeny. Here, we show that such intergenerational transmission of sensory information occurs in the model organism, C. elegans, with a major effect on fitness. Specifically, that perception of social pheromones by chemosensory neurons controls the post-embryonic timing of the development of one tissue, the germline, relative to others in the progeny of an animal. Neuronal perception of the social environment thus intergenerationally controls the generation time of this animal., Competing Interests: Declaration of interests The authors report no competing interests., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Asthma is a heterogeneous disease characterized by inflammation in the respiratory airways which manifests clinically with wheezing, cough, and episodic periods of chest tightness; if left untreated it can lead to permanent obstruction or death. In the US, asthma affects all ages and genders, and individuals from racial and ethnic minority groups are disproportionately burdened by this disease. The financial cost of asthma exceeds $81 billion every year and despite all the resources invested, asthma is responsible for over 3,500 deaths annually in the nation. In this overview, we highlight important factors associated with health disparities in asthma. While they are complex and overlap, we group these factors in five domains: biological, behavioral, socio-cultural, built environment, and health systems. We review the biological domain in detail, which traditionally has been best studied. We also acknowledge that implicit and explicit racism is an important contributor to asthma disparities and responsible for many of the socio-environmental factors that worsen outcomes in this disease., (Copyright ©2021, Yale Journal of Biology and Medicine.)

Despite decades of cytogenetic and genomic research of dynamic sex chromosome evolution in teleost fishes, multiple sex chromosomes have been largely neglected. In this review, we compiled available data on teleost multiple sex chromosomes, identified major trends in their evolution and suggest further trajectories in their investigation. In a compiled dataset of 440 verified records of fish sex chromosomes, we counted 75 multiple sex chromosome systems with 60 estimated independent origins. We showed that male-heterogametic systems created by Y-autosome fusion predominate and that multiple sex chromosomes are over-represented in the order Perciformes. We documented a striking difference in patterns of differentiation of sex chromosomes between male and female heterogamety and hypothesize that faster W sex chromosome differentiation may constrain sex chromosome turnover in female-heterogametic systems. We also found no significant association between the mechanism of multiple sex chromosome formation and percentage of uni-armed chromosomes in teleost karyotypes. Last but not least, we hypothesized that interaction between fish populations, which differ in their sex chromosomes, can drive the evolution of multiple sex chromosomes in fishes. This underlines the importance of broader inter-population sampling in studies of fish sex chromosomes. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.

Systematic revisions of South American marsupials have contributed to our knowledge about genus and species diversity in the last decades, including studies of the most recently described genus Cryptonanus (Didelphidae), currently comprising four recognized species. Herein we provide the first phylogeny for these mouse opossums based on comprehensive sampling, including representatives from all nominal taxa, encompassing most of the geographic distribution of the genus while also extending its known range. The taxonomic status of Cryptonanus species was explored by analyses of multiple mitochondrial and nuclear DNA markers to assess phylogenetic relationships and to provide divergence time estimates, species delimitations and biogeographical hypotheses. Cryptonanus monophyly remained highly supported despite the inclusion of abundant new data from more than a hundred specimens, comprising 10 independent evolutionary lineages. Species-complexes within valid nominal taxa reveal higher species richness in the genus. Based on divergence estimates from a dated phylogeny, we suggest that Cryptonanus diversified along the Quaternary, with speciation events occurring well into the Pleistocene. The best supported biogeographical hypothesis endorses speciation by vicariance and subset speciation across open formations in shaping the evolutionary history of this didelphid genus, strongly associated with dry tropical landscapes of South America., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Purpose: Rhinoplasty is one of the most common and challenging plastic surgery procedures. Facial analysis is a crucial step in planning. Utilizing three-dimensional (3D) model of a patient's face is an emerging way of performing facial analysis. This paper evaluates the agreement and reliability of facial measurements taken using a web app, located at digitized-rhinoplasty.com, that utilizes 3D models of the patient's face., Methods: Eleven measurements were calculated on 16 human subjects. Three methods of measurements were performed: direct measurements on human subjects' faces, measurements on 2D photographs, and measurements on 3D models of face scans. The Bland-Altman plot is used for testing the agreement between the web app and the well-known Blender 3D modeling software. Intra-rater and inter-rater reliability was calculated and compared for 2D and 3D methods using the intraclass correlation coefficient (ICC) method. The statistical analysis methods were checked for the normality and homoscedasticity assumptions., Results: The results indicate that the web app and Blender software show agreement within 95% confidence limits. The web app performs well in intra-rater and inter-rater reliability statistical analysis. The web app's reliability scores are consistently better than facial analysis software which was found highly reliable in a previous study. We also compare the methods of measurements in terms of time, ease of use, and cost., Conclusion: The utilization of 3D computer modeling for facial analysis has its advantages and started to become more common due to recent advances in technology. The web app utilizes 3D face scans for pre-operative planning and post-operative evaluation of facial surgeries. The web app performs well in agreement and inter-/intra-reliability analysis and performs consistently better than software that works utilizing 2D photographs. The web app provides accurate, repeatable, affordable, and fast facial measurements for facial analysis when compared to direct and 2D methods., (© 2021. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)

Young adult never cigarette smokers with disabilities may be at particular risk for adopting e-cigarettes, but little attention has been paid to these people. This study examines the associations between different types of disability and e-cigarette use in this population. Young adult never-smokers from the 2016-2017 Behavioral Risk Factor Surveillance System (BRFSS) survey who were either never or current e-cigarette users ( n = 79,177) were selected for the analysis. The Least Absolute Shrinkage and Selection Operator (LASSO) algorithm was used to select confounders for multivariable logistic regression models. Multivariable logistic regression models were used to determine the associations between current e-cigarette use and different types of disability after incorporating BRFSS survey design and adjusting for confounders. Young adult never-smokers who reported any disability had increased odds (OR 1.44, 95% CI 1.18-1.76) of e-cigarette use compared to those who reported no disability. Young adult never-smokers who reported self-care, cognitive, vision, and independent living disabilities had higher odds of e-cigarette use compared to those who reported no disability. There was no statistically significant difference in the odds of e-cigarette use for those reporting hearing and mobility disabilities compared to those who reported no disability. This study highlights the need for increased public education and cessation programs for this population.

Background: Electronic cigarettes (e-cigarettes) generally have a more favorable toxicant profile than conventional cigarettes; however, limited information exists for women of reproductive age (WRA). Our aim was to compare biomarkers of toxicant exposure, inflammation, and oxidative stress among WRA who self-report exclusive e-cigarette use, exclusive cigarette smoking, or never tobacco use (controls). Methods: Multivariable linear regression models were used to compare the geometric means of urinary biomarkers of toxicant exposure and their metabolites, serum markers of inflammation [highly sensitive C-reactive protein, soluble intercellular adhesion molecule (sICAM), interleukin 6, fibrinogen], and a measurement of oxidative stress [prostaglandin F2a-8-isoprostane (F2PG2a)] among WRA from the Population Assessment of Tobacco and Health survey. Results: E-cigarette users had higher levels of lead, tobacco-specific nitrosamines, nicotine metabolites, and some volatile organic compounds (VOCs) than controls. Except for cadmium and lead, e-cigarette users had lower levels of the analyzed urinary toxicant biomarkers compared with cigarette smokers. Cigarette smokers had higher levels of all the biomarkers of toxicant exposure than controls. There were no significant differences in the levels of markers of inflammation and oxidative stress between e-cigarette users and controls. E-cigarette users and controls had lower levels of sICAM and F2PG2a than cigarette smokers. Conclusion: WRA who use e-cigarettes had lower levels of some of the evaluated urinary biomarkers of toxicant exposure and serum biomarkers of inflammation and oxidative stress than those who smoke cigarettes, but higher lead, nicotine metabolites, and some VOCs than controls, which can increase health risks.

In the fish genus Hoplias , two major general groups can be found, one of which is formed by the "common trahiras" ( Hoplias malabaricus group) and the other by the "giant trahiras" ( Hoplias lacerdae group, in addition to Hoplias aimara ), which usually comprises specimens of larger body size. Previous investigations from the giant trahiras group recovered 2n = 50 meta/submetacentric chromosomes and no sex chromosome differentiation, indicating a probable conservative pattern for their karyotype organization. Here, we conducted comparative cytogenetic studies in six giant trahiras species, two of them for the first time. We employed standard and advanced molecular cytogenetics procedures, including comparative genomic hybridization (CGH), as well as genomic assessments of diversity levels and phylogenetic relationships among them. The results strongly suggest that the giant trahiras have a particular and differentiated evolutionary pathway inside the Hoplias genus. While these species share the same 2n and karyotypes, their congeneric species of the H. malabaricus group show a notable chromosomal diversity in number, morphology, and sex chromosome systems. However, at the same time, significant changes were characterized at their inner chromosomal level, as well as in their genetic diversity, highlighting their current relationships resulting from different evolutionary histories.

Methods: We conducted a cross-sectional study of adults between 18 and 55 years old. Inclusion criteria were: exclusive e-cigarette use or cigarette smoking for ≥ 1 year or no history of tobacco use. Participants with a history of pulmonary illness, atopy, medications (except birth control pills), marijuana, and illegal substance use were excluded. Custom Multiplex ELISA was used to measure YKL-40 and other biomarker levels in the serum and induced sputum of the participants. Multivariable linear regression was used to compare the levels of YLK-40 in healthy participants, e-cigarette, and cigarette users after adjusting for age, sex, and BMI., Results: We recruited 20 healthy controls, 23 cigarette smokers, and 22 exclusive e-cigarette users. Serum YKL-40 (ng/ml) was significantly higher in e-cigarette users (Median 21.2 [IQR 12.1-24.0] ng/ml) when compared to controls (12.2 [IQR 8.7-18.1] ng/ml, p = 0.016) but comparable to cigarette smokers (21.6 [IQR 11.62-51.7] ng/ml, p = 0.31). No significant differences were found in the serum or sputum of the other biomarkers tested., Conclusion: The inflammatory biomarker, YKL-40 is elevated in the serum but not the sputum of e-cigarette users with no reported pulmonary disease. Further research is necessary to characterize this association.

Purpose: Rhinoplasty is one of the most common and challenging plastic surgery procedures. The results of the operation have a significant impact on the facial appearance. The planning is critical for successful rhinoplasty surgery. In this paper, we present a web application designed for preoperative rhinoplasty surgery planning., Methods: The application uses the three-dimensional (3D) model of a patient's face and facilitates marking of an extensive number of facial features and auto-calculation of facial measurements to develop a numerical plan of the surgery. The web application includes definitions, illustrations, and formulas to describe the features and measurements. In addition to the existing measurements, the user can calculate the distance between any two points, the angle between any three points, and the ratio of any two distances. We conducted a survey among experienced rhinoplasty surgeons to get feedback about the web application and to understand their attitude toward utilizing 3D models for preoperative planning., Results: The web application can be accessed and used through any web browser at digitized-rhinoplasty.com. The web application was utilized in our tests and also by the survey participants. The users successfully marked the facial features on the 3D models and reviewed the auto-calculated measurements. The survey results show that the experienced surgeons who tried the web application found it useful for preoperative planning and they also think that utilizing 3D models is beneficial., Conclusions: The web application introduced in this paper helps analyzing the patient's face in details utilizing 3D models and provides numeric outputs to be used in the rhinoplasty operation planning. The experienced rhinoplasty surgeons that participated to our survey agree that the web app would be a beneficial tool for rhinoplasty surgeons. We aim to further improve the web application with more functionality to help surgeons for preoperative planning of rhinoplasty.

E-cigarette use is increasing among young adult never smokers of conventional cigarettes, but the awareness of the factors associated with e-cigarette use in this population is limited. The goal of this work was to use machine learning (ML) algorithms to determine the factors associated with current e-cigarette use among US young adult never cigarette smokers. Young adult (18-34 years) never cigarette smokers from the 2016 and 2017 Behavioral Risk Factor Surveillance System (BRFSS) who reported current or never e-cigarette use were used for the analysis ( n = 79,539). Variables associated with current e-cigarette use were selected by two ML algorithms (Boruta and Least absolute shrinkage and selection operator (LASSO)). Odds ratios were calculated to determine the association between e-cigarette use and the variables selected by the ML algorithms, after adjusting for age, gender and race/ethnicity and incorporating the BRFSS complex design. The prevalence of e-cigarette use varied across states. Factors previously reported in the literature, such as age, race/ethnicity, alcohol use, depression, as well as novel factors associated with e-cigarette use, such as disabilities, obesity, history of diabetes and history of arthritis were identified. These results can be used to generate further hypotheses for research, increase public awareness and help provide targeted e-cigarette education.

Fungal rots are one of the main causes of large economic losses and deterioration in the quality and nutrient composition of fruits during the postharvest stage. The yeast Clavispora lusitaniae 146 has previously been shown to efficiently protect lemons from green mold caused by Penicillium digitatum . In this work, the effect of yeast concentration and exposure time on biocontrol efficiency was assessed; the protection of various citrus fruits against P. digitatum by C. lusitaniae 146 was evaluated; the ability of strain 146 to degrade mycotoxin patulin was tested; and the effect of the treatment on the sensory properties of fruits was determined. An efficient protection of lemons was achieved after minimum exposure to a relatively low yeast cell concentration. Apart from lemons, the yeast prevented green mold in grapefruits, mandarins, oranges, and tangerines, implying that it can be used as a broad-range biocontrol agent in citrus. The ability to degrade patulin indicated that strain 146 may be suitable for the control of further Penicillium species. Yeast treatment did not alter the sensory perception of the aroma of fruits. These results corroborate the potential of C. lusitaniae 146 for the control of postharvest diseases of citrus fruits and indicate its suitability for industrial-scale fruit processing.

Mobile genetic elements, including plasmids, drive the evolution of prokaryotic genomes through the horizontal transfer of genes allowing genetic exchange between bacteria. Moreover, plasmids carry accessory genes, which encode functions that may offer an advantage to the host. Thus, it is expected that in a certain ecological niche, plasmids are enriched in accessory functions, which are important for their hosts to proliferate in that niche. Puquio de Campo Naranja is a high-altitude lake from the Andean Puna exposed to multiple extreme conditions, including high UV radiation, alkalinity, high concentrations of arsenic, heavy metals, dissolved salts, high thermal amplitude and low O 2 pressure. Microorganisms living in this lake need to develop efficient mechanisms and strategies to cope under these conditions. The aim of this study was to characterize the plasmidome of microbialites from Puquio de Campo Naranja, and identify potential hosts and encoded functions using a deep-sequencing approach. The potential ecological impact of the plasmidome, including plasmids from cultivable and non-cultivable microorganisms, is described for the first time in a lake representing an extreme environment of the Puna. This study showed that the recovered genetic information for the plasmidome was novel in comparison to the metagenome derived from the same environment. The study of the total plasmid population allowed the identification of genetic features typically encoded by plasmids, such as resistance and virulence factors. The resistance genes comprised resistances to heavy metals, antibiotics and stress factors. These results highlight the key role of plasmids for their hosts and impact of extrachromosomal elements to thrive in a certain ecological niche., (Copyright © 2020 Perez, Kurth, Farías, Soria, Castillo Villamizar, Poehlein, Daniel and Dib.)

Background: Stethoscope hygiene is rarely done despite guideline recommendations. We wanted to determine whether demonstrating what is growing on the stethoscopes of providers via culture or bioluminescence technology alters perceptions and improves compliance., Methods: Providers were given the opportunity to (1) culture their stethoscopes before and after disinfection with alcohol pads, alcohol-based hand rub, or hydrogen peroxide disinfectant wipes and (2) swab stethoscopes for bioluminescence-based adenosine triphosphate testing before and after disinfection. Outcomes were observed for hand and stethoscope hygiene rates and before and after intervention survey responses. The bacteria that were isolated, colony-forming units (CFU), and bioluminescence scores were tracked., Results: A total of 1,245 observed hand hygiene opportunities showed that compliance improved from 72.5%-82.3% (P < .001). In addition, 590 observed patient-provider encounters revealed no significant change in stethoscope hygiene rates of 10% initially and 5% afterward (P = .08), although self-reported rates trended from 56%- 67% postintervention (P = .06). Perceptions regarding stethoscope hygiene importance improved (8.5/10 to 9.3/10; P = .04). Disinfection with alcohol pads, alcohol-based hand rub, and hydrogen peroxide disinfectant wipes were equivalent in CFU reduction (P = .21)., Conclusions: Showing providers what is growing on their stethoscopes via cultures and bioluminescence technology before and after disinfection improved "buy in" regarding stethoscope hygiene importance. Both methods were rated as having an equal impact, however, objective observations failed to show improvement., (Copyright © 2019. Published by Elsevier Inc.)

Background: The use of e-cigarettes is increasing in the US but there is still a paucity of research on the metabolic effects of e-cigarette use. The goal of this work was to determine the association between e-cigarette use and self-reported prediabetes in adult never cigarette smokers., Method: The 2017 cross sectional Behavioral Risk Factor Surveillance System (BRFSS) survey data was used for the analysis. Current e-cigarette users reported daily or someday use of e-cigarettes and former e-cigarette users reported no current use of e-cigarettes. Participants who reported a history of diabetes, gestational prediabetes/ diabetes were excluded. Odds ratios were calculated to determine the association between e-cigarette use and self-reported prediabetes in never cigarette smokers after adjusting for potential confounders., Results: There were a total of 154,404 participants that met the inclusion criteria. Of those participants, there were 143,952 never, 1339 current and 7625 former e-cigarette users. Current e-cigarette users had an increased odds of reporting a diagnosis of prediabetes 1.97 (95% CI 1.25-3.10) compared to never e-cigarette users. After stratifying by gender, men and women had an increased odds ratio of reporting a diagnosis of prediabetes 2.36 (95% CI 1.26-4.40) and 1.88 (95% CI 1.00-3.53) respectively when compared to never e-cigarette users. There was no association between former e-cigarette use and a self-reported diagnosis of prediabetes., Conclusion: Our findings show that e-cigarette use may be associated with self-reported prediabetes. Further evaluation is needed in prospective studies., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Introduction: Atypical antipsychotics are commonly used in patients with psychiatric conditions and dementia. They are also frequently used in patients being admitted with pneumonia; however, there are few safety data. The purpose of this study was to examine whether atypical antipsychotic use prior to admission is associated with increased mortality in patients with pneumonia., Methods: We conducted a retrospective cohort study of hospitalised patients with pneumonia over a 10-year period. We included patients 65 years or older and hospitalised with pneumonia. For our primary analysis, we used propensity score matching to balance confounders between atypical antipsychotic users and nonusers., Results: There were 102 897 patients and 5977 were taking atypical antipsychotics. After matching there were 5513 users and 5513 nonusers. Atypical antipsychotic use was associated with increased odds of 30-day (OR 1.20, 95% CI 1.11-1.31) and 90-day mortality (1.19, 1.09-1.30)., Conclusion: In patients 65 years or older that are hospitalised with pneumonia, we found an association between atypical antipsychotic use and increased odds of mortality. This was particularly pronounced for patients with pre-existing psychiatric or cardiac conditions. We suggest closely monitoring patients who use these medications and minimising their use in older adult patients., Competing Interests: Conflict of interest: Z. Boivin has nothing to disclose. Conflict of interest: M.F. Perez has nothing to disclose. Conflict of interest: N.C. Atuegwu has nothing to disclose. Conflict of interest: M. Metersky has nothing to disclose. Conflict of interest: C.A. Alvarez has nothing to disclose. Conflict of interest: A. Anzueto has nothing to disclose. Conflict of interest: E.M. Mortensen has nothing to disclose., (Copyright ©ERS 2019.)

The use of electronic cigarettes (e-cigarettes) has increased in the US, but little is known about the effects of these products on lung health. The main purpose of this study was to examine the association between e-cigarette use and a participant's report of being diagnosed with chronic obstructive pulmonary disease (COPD) in a nationally representative sample of adults. Methods: The first wave of the Population Assessment of Tobacco and Health (PATH) survey adult data was used ( N = 32,320). Potential confounders between e-cigarette users and non-users were balanced using propensity score matching. Odds ratios (OR) were calculated to examine the association between e-cigarette use and COPD in the propensity-matched sample, the entire sample, different age groups, and in nonsmokers. Replicate weights and balanced repeated replication methods were utilized to account for the complex survey design. Results: Of the 3642 participants who met the criteria for e-cigarette use, 2727 were propensity matched with 2727 non e-cigarette users. In the propensity-matched sample, e-cigarette users were more likely to report being diagnosed with COPD (OR 1.43, 95% confidence interval [CI] 1.12-1.85) than non-e-cigarette users after adjusting for confounders. The result was similar in the entire sample and in the different age subgroups. Among nonsmokers, the odds of reporting a COPD diagnosis were even greater among e-cigarette users (OR 2.94, 95% CI 1.73-4.99) compared to non-e-cigarette users. Conclusion: Our findings demonstrate that e-cigarette use was associated with a reported diagnosis of COPD among adults in the US. Further research is necessary to characterize the nature of this association and on the long-term effects of using e-cigarettes.

The South American arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum ) are emblematic species widely distributed in the Amazon and surrounding basins. Arowana species are under strong anthropogenic pressure as they are extensively exploited for ornamental and food purposes. Until now, limited genetic and cytogenetic information has been available, with only a few studies reporting to their genetic diversity and population structure. In the present study, cytogenetic and DArTseq-derived single nucleotide polymorphism (SNP) data were used to investigate the genetic diversity of the two Osteoglossum species, the silver arowana O. bicirrhosum , and the black arowana O. ferreirai . Both species differ in their 2n (with 2n = 54 and 56 for O. ferreirai and O. bicirrhosum , respectively) and in the composition and distribution of their repetitive DNA content, consistent with their taxonomic status as different species. Our genetic dataset was coupled with contemporary and paleogeographic niche modeling, to develop concurrent demographic models that were tested against each other with a deep learning approach in O. bicirrhosum . Our genetic results reveal that O. bicirrhosum colonized the Tocantins-Araguaia basin from the Amazon basin about one million years ago. In addition, we highlighted a higher genetic diversity of O. bicirrhosum in the Amazon populations in comparison to those from the Tocantins-Araguaia basin., Competing Interests: None of the authors has any conflicts of interest in the manuscript.

Arowanas (Osteoglossinae) are charismatic freshwater fishes with six species and two genera ( Osteoglossum and Scleropages ) distributed in South America, Asia, and Australia. In an attempt to provide a better assessment of the processes shaping their evolution, we employed a set of cytogenetic and genomic approaches, including i) molecular cytogenetic analyses using C- and CMA 3 /DAPI staining, repetitive DNA mapping, comparative genomic hybridization (CGH), and Zoo-FISH, along with ii) the genotypic analyses of single nucleotide polymorphisms (SNPs) generated by diversity array technology sequencing (DArTseq). We observed diploid chromosome numbers of 2 n = 56 and 54 in O. bicirrhosum and O. ferreirai , respectively, and 2 n = 50 in S. formosus, while S. jardinii and S. leichardti presented 2 n = 48 and 44, respectively. A time-calibrated phylogenetic tree revealed that Osteoglossum and Scleropages divergence occurred approximately 50 million years ago (MYA), at the time of the final separation of Australia and South America (with Antarctica). Asian S. formosus and Australian Scleropages diverged about 35.5 MYA, substantially after the latest terrestrial connection between Australia and Southeast Asia through the Indian plate movement. Our combined data provided a comprehensive perspective of the cytogenomic diversity and evolution of arowana species on a timescale., Competing Interests: The authors declare no conflict of interest.

Vitellogenins are a family of yolk proteins that are by far the most abundant among oviparous animals. In the model nematode Caenorhabditis elegans , the 6 vitellogenins are among the most highly expressed genes in the adult hermaphrodite intestine, which produces copious yolk to provision eggs. In this article we review what is known about the vitellogenin genes and proteins in C. elegans , in comparison with vitellogenins in other taxa. We argue that the primary purpose of abundant vitellogenesis in C. elegans is to support post-embryonic development and fertility, rather than embryogenesis, especially in harsh environments. Increasing vitellogenin provisioning underlies several post-embryonic phenotypic alterations associated with advancing maternal age, demonstrating that vitellogenins can act as an intergenerational signal mediating the influence of parental physiology on progeny. We also review what is known about vitellogenin regulation - how tissue-, sex- and stage-specificity of expression is achieved, how vitellogenins are regulated by major signaling pathways, how vitellogenin expression is affected by extra-intestinal tissues and how environmental experience affects vitellogenesis. Lastly, we speculate whether C. elegans vitellogenins may play other roles in worm physiology.

Electronic nicotine product use is increasing in the U.S., but few studies have addressed its effects on oral health. The goal of this work was to determine the association between electronic nicotine product use and periodontal disease. Population Assessment of Tobacco and Health adult survey data from 2013⁻2016 (waves 1, 2 and 3) was used for the analysis. Longitudinal electronic nicotine product users used electronic nicotine products regularly every day or somedays in all three waves. Participants with new cases of gum disease reported no history of gum disease in wave 1 but reported being diagnosed with gum disease in waves 2 or 3. Odds ratios (OR) were calculated to determine the association between electronic nicotine product use and new cases of gum disease after controlling for potential cofounders. Compared to never users, longitudinal electronic nicotine product users had increased odds of being diagnosed with gum disease (OR 1.76, 95% Confidence Interval (CI) 1.12⁻2.76) and bone loss around teeth (OR 1.67, 95% CI 1.06⁻2.63). These odds were higher for participants with a history of marijuana and a history of illicit or non-prescribed drug use. Our findings show that e-cigarettes may be harmful to oral health.