bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transposable elements contribute to the establishment of the glycine shuttle in Brassicaceae species
Authors: Triesch Sebastian , Denton Alisandra K. , Bouvier Jacques W. , Buchmann Jan P. , Reichel-Deland Vanessa , Martins Guerreiro Ricardo Nuno Ferreira , Busch Noah , Schlüter Urte , Stich Benjamin , Kelly Steven , Weber Andreas P.M. 
Published: December 2022

AbstractC3-C4intermediate photosynthesis has evolved at least five times convergently in the Brassicaceae, despite this family lackingbona fideC4species. The establishment of this carbon concentrating mechanism is known to require a complex suite of ultrastructural modifications as well as changes in spatial expression patterns, which are both thought to be underpinned by a reconfiguration of existing gene-regulatory networks. However, to date, the mechanisms which underpin the reconfiguration of these gene networks are largely unknown. In this study, we used a pan-genomic association approach to identify genomic features that could confer differential gene expression toward the C3-C4 intermediate state by analysing eight C3 species and seven C3-C4 species from five independent origins in the Brassicaceae. We found a strong correlation between transposable element (TE) insertions incis-regulatory regions and the C3-C4intermediacy. Specifically, our study revealed 113 gene models in which presence of a TE within a gene correlates with C3-C4intermediate photosynthesis. In this set, genes involved in the photorespiratory glycine shuttle are enriched, including the glycine decarboxylase P-protein whose expression domain undergoes a spatial shift during the transition to C3-C4photosynthesis. When further interrogating this gene, we discovered independent TE insertions in its upstream region which we conclude to be responsible for causing the spatial shift inGLDP1gene expression. Our findings hint at a pivotal role of TEs in the evolution of C3-C4intermediacy, especially in mediating differential spatial gene expression.
metaDMG – A Fast and Accurate Ancient DNA Damage Toolkit for Metagenomic Data
Authors: Michelsen Christian , Pedersen Mikkel Winther , Fernandez-Guerra Antonio , Zhao Lei , Petersen Troels C. , Korneliussen Thorfinn Sand 
Published: December 2022

AbstractMotivationUnder favourable conditions DNA molecules can persist for hundreds of thousands of years. Such genetic remains make up invaluable resources to study past assemblages, populations, and even the evolution of species. However, DNA is subject to degradation, and hence over time decrease to ultra low concentrations which makes it highly prone to contamination by modern sources. Strict precautions are therefore necessary to ensure that DNA from modern sources does not appear in the final data is authenticated as ancient. The most generally accepted and widely applied authenticity for ancient DNA studies is to test for elevated deaminated cytosine residues towards the termini of the molecules: DNA damage. To date, this has primarily been used for single organisms and recently for read assemblies, however, these methods are not applicable for estimating DNA damage for ancient metagenomes with tens and even hundreds of thousands of species.MethodsWe presentmetaDMG, a novel framework and toolkit that allows for the estimation, quantification and visualization of postmortem damage for single reads, single genomes and even metagenomic environmental DNA by utilizing the taxonomic branching structure. It bypasses any need for initial classification, splitting reads by individual organisms, and realignment. We have implemented a Bayesian approach that combines a modified geometric damage profile with a beta-binomial model to fit the entire model to the individual misincorporations at all taxonomic levels.ResultsWe evaluated the performance using both simulated and published environmental DNA datasets and compared to existing methods when relevant. We findmetaDMGto be an order of magnitude faster than previous methods and more accurate – even for complex metagenomes. Our simulations show thatmetaDMGcan estimate DNA damage at taxonomic levels down to 100 reads, that the estimated uncertainties decrease with increased number of reads and that the estimates are more significant with increased number of C to T misincorporations.ConclusionmetaDMGis a state-of-the-art program for aDNA damage estimation and allows for the computation of nucleotide misincorporation, GC-content, and DNA fragmentation for both simple and complex ancient genomic datasets, making it a complete package for ancient DNA damage authentication.
Optimisation of immunocytochemistry methodology for the detection of endogenous eIF2B localised foci
Authors: de Oliveira Madalena I. Ribeiro , Hanson Filipe M. , Hodgson Rachel E. , Cross Alison K , Campbell Susan G. , Allen K. Elizabeth 
Published: December 2022

AbstractThe multisubunit eukaryotic initiation factor 2B (eIF2B), a guanine nucleotide exchange factor (GEF) for eIF2, is an essential regulator of translation initiation. Activation of the cellular integrated stress response (ISR) by factors such as endoplasmic reticulum stress leads to phosphorylation of eIF2α and inhibition of eIF2B GEF activity. Cytoplasmic bodies containing eIF2B subunits, termed eIF2B bodies, have been shown to alter in subunit composition and fluorescence recovery after photobleaching activity in response to the ISR. Analysis of the subunit composition of endogenous eIF2B bodies is dependent on accurate detection of each protein in a cellular context via immunocytochemistry (ICC). We describe bioinformatic techniques to optimize the ICC detection of eIF2B foci in U373 cells. The screening of commercially available primary antibodies against predicted epitopes enhanced measurements of the number, size and fluorescence intensity of eIF2B bodies. A consistent and reproducible ICC analysis of endogenous eIF2B bodies will aid characterisation of eIF2B bodies during the ISR or under disease conditions.SummaryeIF2B is a housekeeping protein and localised eIF2B foci, named eIF2B bodies, can be detected through immunocytochemistry. Here, we discuss the use of immunoinformatics to optimise eIF2B localisation detection.
A liver-specific mitochondrial carrier that controls gluconeogenesis and energy expenditure
Authors: Yook Jin-Seon , Taxin Zachary H. , Yuan Bo , Oikawa Satoshi , Auger Christopher , Mutlu Beste , Puigserver Pere , Hui Sheng , Kajimura Shingo 
Published: December 2022

ABSTRACTMitochondria provide essential metabolites and ATP for the regulation of energy homeostasis. For instance, liver mitochondria are a vital source of gluconeogenic precursors under a fasted state. However, the regulatory mechanisms at the level of mitochondrial membrane transport are not fully understood. Here, we report a liver-specific mitochondrial inner-membrane carrier, SLC25A47, which is required for hepatic gluconeogenesis and energy homeostasis. Genome-wide association studies found significant associations betweenSLC25A47and fasting glucose, HbA1c, and cholesterol levels in humans. In mice, we demonstrated that liver-specific deletion ofSlc25a47impaired hepatic gluconeogenesis selectively from lactate, while significantly enhancing whole-body energy expenditure and the hepatic expression of FGF21. These metabolic changes were not a consequence of general liver dysfunction because acute SLC25A47 deletion in adult mice was sufficient to enhance hepatic FGF21 production, pyruvate tolerance, and insulin tolerance independent of liver damage and mitochondrial dysfunction. Mechanistically, SLC25A47 loss leads to impaired hepatic pyruvate flux and malate accumulation in the mitochondria, thereby restricting hepatic gluconeogenesis. Together, the present study identified a crucial node in the mitochondrial inner-membrane that regulates fasting-induced gluconeogenesis and energy homeostasis.SIGNIFICANCEGiven the impenetrable nature of the mitochondrial inner-membrane, most of the known metabolite carrier proteins, including SLC25A family members, are ubiquitously expressed in mammalian tissues. One exception is SLC25A47 which is selectively expressed in the liver. The present study showed that depletion of SLC25A47 reduced mitochondrial pyruvate flux and hepatic gluconeogenesis under a fasted state, while activating energy expenditure. The present work offers a liver-specific target through which we can restrict hepatic gluconeogenesis, which is often in excess under hyperglycemic and diabetic conditions.
A high-quality reference genome for the fission yeastSchizosaccharomyces osmophilus
Authors: Jia Guo-Song , Zhang Wen-Cai , Liang Yue , Liu Xi-Han , Rhind Nicholas , Pidoux Alison , Brysch-Herzberg Michael , Du Li-Lin 
Published: December 2022

AbstractFission yeasts are an ancient group of fungal species that diverged from each other from tens to hundreds of million years ago. Among them is the preeminent model organismSchizosaccharomyces pombe, which has significantly contributed to our understandings of molecular mechanisms underlying fundamental cellular processes. The availability of the genomes ofS. pombeand three other fission yeast speciesS. japonicus,S. octosporus, andS. cryophilushas enabled cross-species comparisons that provide insights into the evolution of genes, pathways, and genomes. Here, we performed genome sequencing on the type strain of the recently identified fission yeast speciesS. osmophilusand obtained a complete mitochondrial genome and a nuclear genome assembly with gaps only at rRNA gene arrays. A total of 5098 protein-coding nuclear genes were annotated and orthologs for more than 95% of them were identified. Genome-based phylogenetic analysis showed thatS. osmophilusis most closely related toS. octosporusand these two species diverged around 16 million years ago. To demonstrate the utility of thisS. osmophilusreference genome, we conducted cross-species comparative analyses of centromeres, telomeres, transposons, the mating-type region, Cbp1 family proteins, and mitochondrial genomes. These analyses revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of two types of repeats, delineated relationships among Tf1/sushi group retrotransposons, characterized the evolutionary origins and trajectories of Cbp1 family domesticated transposases, and discovered signs of interspecific transfer of two types of mitochondrial selfish elements.
Pediatric critical care capacity in Canada: a national cross-sectional study
Authors: Ganesan Saptharishi Lalgudi , Garros Daniel , Foster Jennifer , Genova Tanya Di , Fontela Patricia S. , Murthy Srinivas ,   the Canadian Critical Care Trials Group (CCCTG)
Published: December 2022

AbstractBackgroundPediatric intensive care unit (PICU) capacity is a current and future health system challenge in Canada. Despite experiencing two pandemics over the last 15 years and surges in PICU admissions every winter, the bed capacity of Canadian PICUs and their ability to accommodate surges in demand are unknown.MethodsWe conducted an internet-based cross-sectional survey to gather information from Canadian PICUs regarding PICU characteristics, medical staffing, therapies provided, and anticipated challenges related to surge management. The survey was completed by a representative of each PICU and validated by PICU Directors. Quantitative survey results were summarized as counts, proportions, and ratios while qualitative response was analyzed using inductive content analysis.ResultsRepresentatives from all19 PICUslocated in17 hospitalscompleted the survey and reported having275(217level 3 &58level 2) funded beds with298physical bed spaces. Two PICUs representing47beds (35Level 3 &12Level 2) are specialized cardiac ICUs. Roughly13385, 13419, 11430 and 12315Canadian children were admitted to these PICUs in the years 2018, 2019, 2020 & 2021, respectively. During a surge, PICUs reported being able to add5.9 ± 3.4 (range: 0 – 14)beds per unit and a total of108temporary surge beds. Several barriers for the successful implementation of surge plans were identified.InterpretationCanadian pediatric critical care capacity is comparable to other high-income countries, though our ability to respond to a pandemic/epidemic surge with significant pediatric critical illness may be limited.
Characteristics of head and neck alignment and function of deep cervical flexor muscles in patients with nonspecific neck pain
Authors: Kawasaki Tomoko , Ohji Shunsuke , Aizawa Junya , Sakai Tomoko , Hirohata Kenji , Koseki Taiichi , Kuruma Hironobu , Okawa Atsushi , Jinno Tetsuya 
Published: December 2022

AbstractObjectiveTo compare forward head posture (FHP) in natural and corrected head postures between patients with nonspecific neck pain (NSNP) and controls, and to clarify the relationship between natural- and corrected-head posture angle differences and deep cervical flexor function.DesignSurvey studySettingPatients with NSNP were outpatients at an orthopedic clinic; the controls were community volunteers.ParticipantsThirty-eight patients were divided into the NSNP and control groups (n=19 each), including patients reporting a numerical rating pain score of 3-7 for at least 3 months and those with no neck pain within 12 months previously, respectively.InterventionsTo evaluate FHP, the cranial rotation and vertical angles were measured using lateral photographs of the head and neck. The craniocervical flexion test was used to evaluate deep cervical flexor activation and endurance.Main outcome measuresWe evaluated the head and neck alignment in natural and corrected head postures and the relationship between the degree of change and deep cervical flexor function.ResultsThe FHP in the natural head posture did not differ significantly between the groups. For corrected head posture, the FHP was significantly smaller in the NSNP group than in the control group. In the NSNP group, the cranial rotation and vertical angles were significantly different between natural and corrected head postures, and the angle difference between these postures was significantly correlated with deep cervical flexor function.ConclusionsIn patients with NSNP, hypercorrection in the corrected head posture was shown and may be correlated with dysfunction of the deep cervical flexors. Further investigation into the causal relationship between hypercorrection, deep neck flexor dysfunction, and neck pain is required.
Long-term air pollution exposure and markers of cardiometabolic health in the National Longitudinal Study of Adolescent to Adult Health (Add Health) Study
Authors: Bravo Mercedes A. , Fang Fang , Hancock Dana B. , Johnson Eric O. , Harris Kathleen Mullan 
Published: December 2022

ABSTRACTBackgroundAir pollution exposure is associated with cardiovascular morbidity and mortality. Although exposure to air pollution early in life may represent a critical window for development of cardiovascular disease risk factors, few studies have examined associations of long-term air pollution exposure with markers of cardiovascular and cardiometabolic health in young adults.ObjectivesBy combining health data from the National Longitudinal Study of Adolescent to Adult Health (Add Health) with air pollution data from the Fused Air Quality Surface using Downscaling (FAQSD) archive, we: (1) calculated multi-year estimates of exposure to ozone (O3) and particulate matter with an aerodynamic diameter ≤2.5μm (PM2.5) for Add Health participants; and (2) estimated associations between air pollution exposures and multiple markers of cardiometabolic health.MethodsAdd Health is a nationally representative longitudinal cohort study of over 20,000 adolescents aged 12–19 in the United States (US) in 1994–95 (Wave I). Participants have been followed through adolescence and into adulthood with five in-home interviews. Estimated daily concentrations of O3and PM2.5at census tracts were obtained from the FAQSD archive and used to generate tract-level annual averages of O3and PM2.5concentrations. We estimated associations between average O3and PM2.5exposures from 2002–07 and markers of cardiometabolic health measured at Wave IV (2008–09), including hypertension, hyperlipidemia, body mass index (BMI), diabetes, C-reactive protein, and metabolic syndrome.ResultsThe final sample size was 11,259 individual participants. The average age of participants at Wave IV was 28.4 years (range: 24–34 years). In models adjusting for age, race/ethnicity, and sex, long-term O3exposure (2002–07) was associated with elevated odds of hypertension, with an odds ratio (OR) of 1.015 (95% confidence interval [CI]: 1.011, 1.029); obesity (1.022 [1.004, 1.040]); diabetes (1.032 [1.009,1.054]); and metabolic syndrome (1.028 [1.014, 1.041]); PM2.5exposure (2002–07) was associated with elevated odds of hypertension (1.022 [1.001, 1.045]).ConclusionFindings suggest that long-term ambient air pollution exposure, particularly O3exposure, is associated with cardiometabolic health in early adulthood.
Linked Patient and Provider Impressions of Outpatient Teleneurology Encounters
Authors: James Justin G. , Park Jane , Oliver Alexandria , Xie Sharon X. , Siderowf Andrew , Spindler Meredith , Wechsler Lawrence , Tropea Thomas F. 
Published: December 2022

AbstractBackground and ObjectivesTeleneurology is common in clinical practice partly due to the SARS CoV-2 pandemic. Impressions about teleneurology from patients and providers alike are generally favorable; some of the reported benefits include ease of access to specialized healthcare, savings of time and money, and similar quality of care as an in-person visit. However, comparisons between patient and provider impressions about the same teleneurology encounter have not been described. Here we describe patient impressions about a teleneurology encounter and evaluate concordance with provider impressions about the same encounter.MethodsPatients and providers at the University of Pennsylvania Hospital Neurology Department were surveyed about their impressions of teleneurology between April 27thand June 16th, 2020. A convenience sample of patients, whose providers completed a questionnaire, were contacted by telephone to solicit their impressions the same encounter. Unique questionnaires for patients and providers focused on similar themes, such as adequacy of technology, assessment of history obtained, and overall quality of the visit. Summaries of patient responses are reported with the raw percent agreement between patients and providers for similar questions.ResultsOne hundred thirty-seven patients completed the survey; 64 (47%) were male and 73 were (53%) female. Sixty-six (47%) patients had a primary diagnosis of PD, 42 (30%) a non-PD movement disorder, and 29 (21%) a non-movement disorder neurological disease. One hundred one (76%) were established patient visits and 36 (26%) were new patient visits. Provider responses from 8 different physicians were included. The majority of patients responded that the ease of joining their visit, their comfort engaging with their physicians during their visit, understanding their plan of care after their visit, and the quality of care from their teleneurology visit were satisfactory. Patients and providers agreed about their impressions of the quality of the history obtained (87% agreement), patient-provider relationship (88% agreement), and overall quality of their experience (70% agreement).DiscussionPatients had favorable impressions about their clinical experience with teleneurology and expressed an interest in incorporating telemedicine visits into their ongoing care. Patients and providers were highly concordant for the history obtained, patient-provider relationship, and overall quality.
COMORBIDITY OF PULMONARY TUBERCULOSIS AND BACTERIAL PNEUMONIA IN PATIENTS WITH LATE STAGES OF HIV-INFECTION WITH IMMUNODEFICIENCY
Authors: Mishina A.V. , Mishin V.Yu. , Shashenkov I. V. 
Published: December 2022

AbstractPurposeTo study specifics of diagnostics and clinics of comorbidity of pulmonary tuberculosis and bacterial pneumonia in patients with HIV-infection with immunodeficiency.Materials and methodsNinety-three first-time diagnosed patients with pulmonary tuberculosis and 4B stage of HIV-infection in the advanced phase in the absence of antiretroviral therapy were examined. The patients were divided into 3 groups. The 1stgroup included 31 patient with pulmonary tuberculosis and pneumonia associated withStreptococcus pneumoniae, the 2ndgroup included 31 patient with pulmonary tuberculosis and pneumonia associated withStaphylococcus aureus. The 3rdgroup included 31 patient without bacterial pneumonia selected by a copy-pair principle. Statistical treatment of the data was performed using Microsoft Office Excel 2019 with calculation of the mean parameter in the group and the standard error of the mean confidence interval (CI).ResultsComorbidity of pulmonary tuberculosis and pneumonia associated withS. pneumoniaeorS. aureusin patients with 4B stage of HIV-infection with immunodeficiency in the advance phase with absence of antiretroviral treatment is characterized with generalization of tuberculosis and development of opportunistic infections of the lungs with severe clinical picture, high level of drug resistance ofM. tuberculosisand the agents of bacterial pneumonia. At computed tomography of the chest a focal dissemination is revealed in the lungs as well as an intrathoracic lymphadenopathy and changes of the lung pattern, which almost does not differ in patients with bacterial pneumonia.ConclusionClinical signs and X-ray changes in combination of pulmonary tuberculosis and pneumonia associated withS. pneumoniaeorS. aureusand pulmonary tuberculosis with bacterial pneumonia at the late stages of HIV-infection with immunodeficiency have the same type of character that can be diagnosed only with special microbiological viral and molecular genetic studies of abnormal material from the respiratory system and other organs with obligatory determination of drug resistance to the antituberculosis drug products and the antibacterial agents of wide spectrum.
The rate of adaptive molecular evolution in wild and domesticatedSaccharomyces cerevisiaepopulations
Authors: Raas Maximilian W. D. , Dutheil Julien Y. 
Published: December 2022

AbstractThrough its fermentative capacities,Saccharomyces cerevisiaewas central in the development of civilization during the Neolithic period, and the yeast remains of importance in industry and biotechnology giving rise tobona fidedomesticated populations. Here, we conduct a population genomic study of domesticated and wild populations ofS. cerevisiae. Using coalescent analyses, we report that the effective population size of yeast populations decreased since the divergence withS. paradoxus. We fitted models of distribution of fitness effects to infer the rate of adaptive (ωa) and non-adaptive (ωna) non-synonymous substitutions in protein-coding genes. We report an overall limited contribution of positive selection toS. cerevisiaeprotein evolution, albeit with higher rates of adaptive evolution in wild compared to domesticated populations. Our analyses revealed the signature of background selection and possibly Hill-Robertson interference, as recombination was found to be negatively correlated withωnaand positively correlated withωa. However, the effect of recombination onωawas found to be labile, as it is only apparent after removing the impact of codon usage bias on the synonymous site frequency spectrum and disappears if we control for the correlation withωna, suggesting it could be an artefact of the decreasing population size. Furthermore, the rate of adaptive non-synonymous substitutions is significantly correlated with the residue solvent exposure, a relation that cannot be explained by the population’s demography. Together, our results provide a detailed characterization of adaptive mutations in protein-coding genes acrossS. cerevisiaepopulations.