bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ubiquity and Origins of Structural Maintenance of Chromosomes (SMC) Proteins in Eukaryotes
Authors: Yoshinaga Mari , Inagaki Yuji 
Published: November 2021

Abstract
Structural maintenance of chromosomes (SMC) protein complexes are common in Bacteria, Archaea, and Eukaryota. SMC proteins, together with the proteins related to SMC (SMC-related proteins), constitute a superfamily of ATPases. Bacteria/Archaea and Eukaryotes are distinctive from one another in terms of the repertory of SMC proteins. A single type of SMC protein is dimerized in the bacterial and archaeal complexes, whereas eukaryotes possess six distinct SMC subfamilies (SMC1–6), constituting three heterodimeric complexes, namely cohesin, condensin, and SMC5/6 complex. Thus, to bridge the homodimeric SMC complexes in Bacteria and Archaea to the heterodimeric SMC complexes in Eukaryota, we need to invoke multiple duplications of an SMC gene followed by functional divergence. However, to our knowledge, the evolution of the SMC proteins in Eukaryota had not been examined for more than a decade. In this study, we reexamined the ubiquity of SMC1–6 in phylogenetically diverse eukaryotes that cover the major eukaryotic taxonomic groups recognized to date and provide two novel insights into the SMC evolution in eukaryotes. First, multiple secondary losses of SMC5 and SMC6 occurred in the eukaryotic evolution. Second, the SMC proteins constituting cohesin and condensin (i.e., SMC1–4), and SMC5 and SMC6 were derived from closely related but distinct ancestral proteins. Based on the above-mentioned findings, we discuss how SMC1–6 have diverged from the archaeal homologs.
Evolutionary Dynamics of Asexual Hypermutators Adapting to a Novel Environment
Authors: Ho Wei-Chin , Behringer Megan G , Miller Samuel F , Gonzales Jadon , Nguyen Amber , Allahwerdy Meriem , Boyer Gwyneth F , Lynch Michael 
Published: November 2021

Abstract
How microbes adapt to a novel environment is a central question in evolutionary biology. Although adaptive evolution must be fueled by beneficial mutations, whether higher mutation rates facilitate the rate of adaptive evolution remains unclear. To address this question, we cultured Escherichia coli hypermutating populations, in which a defective methyl-directed mismatch repair pathway causes a 140-fold increase in single-nucleotide mutation rates. In parallel with wild-type E. coli, populations were cultured in tubes containing Luria-Bertani broth, a complex medium known to promote the evolution of subpopulation structure. After 900 days of evolution, in three transfer schemes with different population-size bottlenecks, hypermutators always exhibited similar levels of improved fitness as controls. Fluctuation tests revealed that the mutation rates of hypermutator lines converged evolutionarily on those of wild-type populations, which may have contributed to the absence of fitness differences. Further genome-sequence analysis revealed that, although hypermutator populations have higher rates of genomic evolution, this largely reflects strong genetic linkage. Despite these linkage effects, the evolved population exhibits parallelism in fixed mutations, including those potentially related to biofilm formation, transcription regulation, and mutation-rate evolution. Together, these results are generally inconsistent with a hypothesized positive relationship between the mutation rate and the adaptive speed of evolution, and provide insight into how clonal adaptation occurs in novel environments.
Long-term impacts of coal mine fire-emitted PM2.5 on hospitalisation: a longitudinal analysis of the Hazelwood Health Study
Authors: Xu Rongbin , Gao Caroline X , Dimitriadis Christina , Smith Catherine L , Carroll Matthew T C , Ikin Jillian F , Johnston Fay H , Sim Malcolm R , Abramson Michael J , Guo Yuming 
Published: November 2021

Abstract

Background
Little is known about the long-term health impacts of exposures to landscape fire smoke. We aimed to evaluate the association between exposure to coal mine fire-related particulate matter 2.5 μm or less in diameter (PM2.5) and hospitalisation in the 5 years following the 6-week Hazelwood coal mine fire in Australia in 2014.

Methods
We surveyed 2725 residents (mean age: 58.3 years; 54.3% female) from an exposed and a comparison town. Individual PM2.5 exposures during the event were estimated using modelled PM2.5 concentrations related to the coal mine fire and self-reported location data. The individual exposure and survey data were linked with hospitalisation records between January 2009 and February 2019. Recurrent event survival analysis was used to evaluate relationships between PM2.5 exposure and hospitalisation following mine fire, adjusting for important covariates.

Results
Each 10-µg/m3 increase in mine fire-related PM2.5 was associated with a 9% increased hazard [hazard ratio (HR) = 1.09; 95% confidence interval (CI): 1.01, 1.17] of respiratory hospitalisation over the next 5 years, with stronger associations observed for females (HR = 1.16; 95% CI: 1.06, 1.27) than males (HR = 0.99; 95% CI: 0.89, 1.11). In particular, increased hazards were observed for hospitalisations for asthma (HR = 1.43; 95% CI: 1.19, 1.73) and chronic obstructive pulmonary disease (HR = 1.14; 95% CI: 1.02, 1.28). No such association was found for hospitalisations for cardiovascular diseases, mental illness, injuries, type 2 diabetes, renal diseases or neoplasms.

Conclusions
A 6-week exposure to coal mine fire-related PM2.5 was associated with increased hazard of respiratory hospitalisations over the following 5 years, particularly for females.
Long-term adjustable gastric band with resultant megaoesophagus causing cardiac compression
Authors: De Silva Ramesh , Pham My , Devadas Michael , Kiat Hosen 
Published: November 2021

Abstract
Oesophageal dilatation following laparoscopic-assisted gastric banding (LAGB) is a well-described complication reported in up to 80% of LAGB patients [ 1, 2]. Severe oesophageal dilatation in addition to aperistalsis is known as megaoesophagus. Symptomatic compression cardiac compression from oesophageal dilatation as a complication of LAGB is an extremely rare complication and is presented in this case report.
Enzymatic deamination of the epigenetic nucleosideN6-methyladenosine regulates gene expression
Authors: Jiang Zhuoran , Wang Chao , Wu Zixin , Chen Kun , Yang Wei , Deng Hexiang , Song Heng , Zhou Xiang 
Published: November 2021

AbstractN6-methyladenosine (m6A) modification is the most extensively studied epigenetic modification due to its crucial role in regulating an array of biological processes. Herein, Bsu06560, formerly annotated as an adenine deaminase derived from Bacillus subtilis 168, was recognized as the first enzyme capable of metabolizing the epigenetic nucleoside N6-methyladenosine. A model of Bsu06560 was constructed, and several critical residues were putatively identified via mutational screening. Two mutants, F91L and Q150W, provided a superiorly enhanced conversion ratio of adenosine and N6-methyladenosine. The CRISPR-Cas9 system generated Bsu06560-knockout, F91L, and Q150W mutations from the B. subtilis 168 genome. Transcriptional profiling revealed a higher global gene expression level in BS-F91L and BS-Q150W strains with enhanced N6-methyladenosine deaminase activity. The differentially expressed genes were categorized using GO, COG, KEGG and verified through RT-qPCR. This study assessed the crucial roles of Bsu06560 in regulating adenosine and N6-methyladenosine metabolism, which influence a myriad of biological processes. This is the first systematic research to identify and functionally annotate an enzyme capable of metabolizing N6-methyladenosine and highlight its significant roles in regulation of bacterial metabolism. Besides, this study provides a novel method for controlling gene expression through the mutations of critical residues.
Coordinated glucocorticoid receptor and MAFB action induces tolerogenesis and epigenome remodeling in dendritic cells
Authors: Morante-Palacios Octavio , Ciudad Laura , Micheroli Raphael , de la Calle-Fabregat Carlos , Li Tianlu , Barbisan Gisela , Houtman Miranda , Edalat Sam G , Frank-Bertoncelj Mojca , Ospelt Caroline , Ballestar Esteban 
Published: November 2021

Abstract
Glucocorticoids (GCs) exert potent anti-inflammatory effects in immune cells through the glucocorticoid receptor (GR). Dendritic cells (DCs), central actors for coordinating immune responses, acquire tolerogenic properties in response to GCs. Tolerogenic DCs (tolDCs) have emerged as a potential treatment for various inflammatory diseases. To date, the underlying cell type-specific regulatory mechanisms orchestrating GC-mediated acquisition of immunosuppressive properties remain poorly understood. In this study, we investigated the transcriptomic and epigenomic remodeling associated with differentiation to DCs in the presence of GCs. Our analysis demonstrates a major role of MAFB in this process, in synergy with GR. GR and MAFB both interact with methylcytosine dioxygenase TET2 and bind to genomic loci that undergo specific demethylation in tolDCs. We also show that the role of MAFB is more extensive, binding to thousands of genomic loci in tolDCs. Finally, MAFB knockdown erases the tolerogenic properties of tolDCs and reverts the specific DNA demethylation and gene upregulation. The preeminent role of MAFB is also demonstrated in vivo for myeloid cells from synovium in rheumatoid arthritis following GC treatment. Our results imply that, once directly activated by GR, MAFB plays a critical role in orchestrating the epigenomic and transcriptomic remodeling that define the tolerogenic phenotype.
Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq
Authors: Engel Krysta L , Lo Hei-Yong G , Goering Raeann , Li Ying , Spitale Robert C , Taliaferro J Matthew 
Published: November 2021

Abstract
Thousands of RNA species display nonuniform distribution within cells. However, quantification of the spatial patterns adopted by individual RNAs remains difficult, in part by a lack of quantitative tools for subcellular transcriptome analysis. In this study, we describe an RNA proximity labeling method that facilitates the quantification of subcellular RNA populations with high spatial specificity. This method, termed Halo-seq, pairs a light-activatable, radical generating small molecule with highly efficient Click chemistry to efficiently label and purify spatially defined RNA samples. We compared Halo-seq with previously reported similar methods and found that Halo-seq displayed a higher efficiency of RNA labeling, indicating that it is well suited to the investigation of small, precisely localized RNA populations. We then used Halo-seq to quantify nuclear, nucleolar and cytoplasmic transcriptomes, characterize their dynamic nature following perturbation, and identify RNA sequence features associated with their composition. Specifically, we found that RNAs containing AU-rich elements are relatively enriched in the nucleus. This enrichment becomes stronger upon treatment with the nuclear export inhibitor leptomycin B, both expanding the role of HuR in RNA export and generating a comprehensive set of transcripts whose export from the nucleus depends on HuR.
A randomized controlled trial of two dialysate sodium concentrations in hospitalized hemodialysis patients
Authors: Causland Finnian R Mc , Ravi Katherine Scovner , Curtis Katherine A , Kibbelaar Zoé A , Short Samuel A P , Singh Anika T , Correa Simon , Waikar Sushrut S 
Published: November 2021

ABSTRACT

Background
Several large dialysis organizations have lowered the dialysate sodium concentration (DNa) in an effort to ameliorate hypervolemia. The implications of lower DNa on intra-dialytic hypotension (IDH) during hospitalizations of hemodialysis (HD) patients is unclear.

Methods
In this double-blind, single center, randomized controlled trial (RCT), hospitalized maintenance HD patients were randomized to receive higher (142 mmol/L) or lower (138 mmol/L) DNa for up to six sessions. Blood pressure (BP) was measured in a standardized fashion pre-HD, post-HD and every 15 min during HD. The endpoints were: (i) the average decline in systolic BP (pre-HD minus lowest intra-HD, primary endpoint) and (ii) the proportion of total sessions complicated by IDH (drop of ≥20 mmHg from the pre-HD systolic BP, secondary endpoint).

Results
A total of 139 patients completed the trial, contributing 311 study visits. There were no significant differences in the average systolic blood pressure (SBP) decline between the higher and lower DNa groups (23 ± 16 versus 26 ± 16 mmHg; P = 0.57). The proportion of total sessions complicated by IDH was similar in the higher DNa group, compared with the lower DNa group [54% versus 59%; odds ratio 0.72; 95% confidence interval (95% CI) 0.36–1.44; P = 0.35]. In post hoc analyses adjusting for imbalances in baseline characteristics, higher DNa was associated with 8 mmHg (95% CI 2–13 mmHg) less decline in SBP, compared with lower DNa. Patient symptoms and adverse events were similar between the groups.

Conclusions
In this RCT for hospitalized maintenance of HD patients, we found no difference in the absolute SBP decline between those who received higher versus lower DNa in intention-to-treat analyses. Post hoc adjusted analyses suggested a lower risk of IDH with higher DNa; thus, larger, multi-center studies to confirm these findings are warranted.
Trends in Cigar Sales and Prices, by Product and Flavor Type—the United States, 2016–2020
Authors: Wang Xu , Kim Yoonsang , Borowiecki Mateusz , Tynan Michael A , Emery Sherry , King Brian A 
Published: November 2021

Abstract

Introduction
Cigar smoking has increased in recent decades as the cigar product landscape has diversified. This study assessed trends in US cigar sales during 2016–2020.

Aims and Methods
Unit sales and average unit price for cigars were assessed during January 3, 2016–June 13, 2020, overall and by product and flavor type, for the 48 contiguous US states and D.C. Assessed cigar types were large cigars, little cigars, and cigarillos; assessed flavor types were tobacco/unflavored, candy/sweets, fruit, menthol, alcohol, coffee, other flavors, and no flavor stated. A joinpoint regression model was used to assess the magnitude and significance of sales trends.

Results
During January 3, 2016–June 13, 2020, unit sales of cigarillos increased (average monthly percentage change [AMPC] = 0.7%, p &lt; .001), while unit sales of large cigars (AMPC = −0.8%, p &lt; .001) and little cigars decreased (AMPC = −0.2%, p &lt; .001). The average price of cigarillos gradually decreased since mid-August 2017 (AMPC = −0.1%, p &lt; .001), and the average price of little cigars decreased from mid-June 2016 to mid-June 2019 (AMPC = −0.3%, p &lt; .001). In contrast, the average price of large cigars increased during the entire study period (AMPC = 0.6%, p &lt; .001). Irrespective of cigar type, tobacco-flavored/unflavored products were the most commonly sold cigars during the assessed period; however, sales of other flavors varied by cigar type.

Conclusions
Cigar sales and price vary by type over time in the United States, including sales of cigarillos (94.2% of unit sales) increasing as their prices have decreased in recent years. Public health strategies are warranted to address the full scope of cigar types being used in the United States.

Implications
Surveillance of cigar sales data, including product characteristics, can provide a timely complement to self-reported survey data of cigar use. This study assessed trends in US cigar sales during 2016–2020, including by product and flavor type. The findings indicate that sales of cigarillos, which comprise most cigar sales in the United States during the assessed period, increased as their prices decreased. Sales of certain flavors, such as candy/sweet cigarillos and coffee large cigars, increased significantly. These findings reinforce the importance of evidence-based strategies, including increasing price and restricting flavors, to reduce the affordability and consumption of cigars in the United States.
Serum Concentrations of Cotinine and Trans-3′-Hydroxycotinine in US Adults: Results From Wave 1 (2013–2014) of the Population Assessment of Tobacco and Health Study
Authors: Sosnoff Connie S , Caron Kevin , Akins J Ricky , Dortch Kristin , Hunter Ronald E , Pine Brittany N , Feng June , Blount Benjamin C , Li Yao , van Bemmel Dana M , Kimmel Heather L , Edwards Kathryn C , Goniewicz Maciej L , Hatsukami Dorothy K , de Castro B Rey , Bernert John T , Arnstein Stephen , Borek Nicolette , Deng-Bryant Ying , Mishina Elena , Lawrence Charles , Hyland Andrew , Hecht Stephen S , Conway Kevin P , Pirkle James L , Wang Lanqing 
Published: November 2021

Abstract

Introduction
The Population Assessment of Tobacco and Health (PATH) Study is a nationally representative cohort of tobacco product users and nonusers. The study’s main purpose is to obtain longitudinal epidemiologic data on tobacco use and exposure among the US population.

Aims and Methods
Nicotine biomarkers—cotinine (COT) and trans-3′-hydroxycotinine (HCT)—were measured in blood samples collected from adult daily tobacco users and nonusers during Wave 1 of the PATH Study (2013–2014; n = 5012; one sample per participant). Participants’ tobacco product use and exposure to secondhand smoke were categorized based on questionnaire responses. Nonusers were subdivided into never users and recent former users. Daily tobacco users were classified into seven tobacco product use categories: exclusive users of cigarette, smokeless tobacco, electronic cigarette, cigar, pipe, and hookah, as well as polyusers. We calculated sample-weighted geometric mean (GM) concentrations of cotinine, HCT, and the nicotine metabolite ratio (NMR) and evaluated their associations with tobacco use with adjustment for potential confounders.

Results
The GMs (95% confidence intervals) of COT and HCT concentrations for daily tobacco users were 196 (184 to 208) and 72.5 (67.8 to 77.4) ng/mL, and for nonusers they were 0.033 (0.028 to 0.037) and 0.021 (0.018 to 0.023) ng/mL. Exclusive smokeless tobacco users had the highest COT concentrations of all user groups examined. The GM NMR in daily users was 0.339 (95% confidence interval: 0.330 to 0.350).

Conclusions
These nationally representative estimates of serum nicotine biomarkers could be the basis for reference ranges characterizing nicotine exposure for daily tobacco users and nonusers in the US adult population.

Implications
This report summarizes the serum nicotine biomarker measurements in Wave 1 of the PATH Study. We are reporting the first estimates of HCT in serum for daily tobacco users and nonusers in the noninstitutionalized, civilian US adult population; the first nationally representative serum COT estimates for daily exclusive users of different tobacco products and daily polyusers; and the first nationally representative estimate of the serum NMR in daily tobacco users by age, race/ethnicity, and sex.
The emerging contours of a post-Brexit Britain
Authors: Adam Christopher 
Published: November 2021

Abstract:This paper introduces a set of papers analysing the likely economic impact of Brexit across key aspects of the UK economy as the country comes to the end of its first full year outside the European Union. The Brexit vote in 2016 was not just a vote on the UK’s relations with the institutions of the European Union but was also a referendum on the fractured state of the UK as a nation. The resulting conflation of Brexit with domestic economic policy debates is reflected in this issue. A first cluster of papers focuses on the consequences of choosing to abandon the ‘four freedoms’ enshrined in the Treaty of Europe, the free movement of goods, services, capital, and labour across the EU, and a second is concerned with the indirect effects of Brexit in those areas of domestic policy that have been opened up by the Brexit decision. The economic consequences of Brexit are only just emerging, but these papers provide an informed perspective on the state of debate, and the likely implications of Brexit across a range of policy areas, both international and domestic.
Changes in phytoplankton composition hinder the recovery from eutrophication in a perialpine lake (Lake Lugano, Switzerland and Italy)
Authors: Lepori Fabio , Capelli Camilla , Foresti Danilo 
Published: November 2021

AbstractWe investigated the factors shaping the response of summer phytoplankton biomass to declining phosphorus (P) concentrations in a lake undergoing restoration (South basin of Lake Lugano, Switzerland and Italy). During 1989–2019, summer P concentrations declined from values typical of eutrophic lakes (&gt;30 μg L−1) to values typical of mesotrophic lakes (10–30 μg L−1). Contrary to expectations, this decline was not followed by a decline in phytoplankton biomass. Instead, phytoplankton biomass showed the highest values in summers with lowest P concentrations. This paradoxical effect was associated with a change in phytoplankton composition. Higher P concentrations were associated with higher relative biomass of green algae, lower P concentrations with higher biomass of cyanobacteria and diatoms. We interpreted this change as a shift from edible and P-demanding phytoplankton to inedible and P-efficient phytoplankton, leading to different trophic structures. The pattern observed may be prompted by the particular conditions of deep lakes approaching mesotrophy, including occurrence of deep-water P reserves and high N concentrations, which can benefit inedible metalimnetic cyanobacteria. To attain reductions in summer phytoplankton biomass, restoration efforts may need to further reduce P concentrations and, possibly, address N enrichment.
A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations
Authors: Gerlin Léo , Cottret Ludovic , Escourrou Antoine , Genin Stéphane , Baroukh Caroline 
Published: November 2021

Abstract
Predicting and understanding plant responses to perturbations require integrating the interactions between nutritional sources, genes, cell metabolism, and physiology in the same model. This can be achieved using metabolic modeling calibrated by experimental data. In this study, we developed a multi-organ metabolic model of a tomato (Solanum lycopersicum) plant during vegetative growth, named Virtual Young TOmato Plant (VYTOP) that combines genome-scale metabolic models of leaf, stem and root and integrates experimental data acquired from metabolomics and high-throughput phenotyping of tomato plants. It is composed of 6,689 reactions and 6,326 metabolites. We validated VYTOP predictions on five independent use cases. The model correctly predicted that glutamine is the main organic nutrient of xylem sap. The model estimated quantitatively how stem photosynthetic contribution impacts exchanges between the different organs. The model was also able to predict how nitrogen limitation affects vegetative growth and the metabolic behavior of transgenic tomato lines with altered expression of core metabolic enzymes. The integration of different components, such as a metabolic model, physiological constraints, and experimental data, generates a powerful predictive tool to study plant behavior, which will be useful for several other applications, such as plant metabolic engineering or plant nutrition.