bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ventricular arrhythmias and sudden death in heart failure
Authors: Trancuccio Alessandro , Latini Alessia Chiara , Arnò Carlo , Kukavica Deni , Mazzanti Andrea , Priori Silvia G 
Published: December 2023

Abstract
Ventricular arrhythmias (VAs) are highly prevalent in patients with heart failure (HF) and range from isolated premature ventricular complexes (PVCs) to more severe arrhythmias such as non-sustained or sustained ventricular tachycardia (VTns and VTs, respectively) and, lastly, to ventricular fibrillation (VF). The clinical relevance of VAs, which may cause sudden cardiac death (SCD), is related to the fact that they represent an important competing cause of morbidity and mortality in patients with HF. Considering the epidemiology, progressive and degenerative nature of the disease, elevated socioeconomic costs of HF, as well overall cost-effectiveness of implantable cardioverter defibrillator (ICD), appropriate and periodic risk stratification represents a crucial moment in the management of patients with HF. This chapter reviews the current knowledge on the clinical impact of VA, most relevant arrhythmic mechanisms from the cellular level to the organ level, providing mechanistic insights for the treatment and management of VA, and highlight the state-of-the-art approaches to the prevention of the occurrence of SCD.
Diabetes, prediabetes, and heart failure
Authors: Rosano Giuseppe , Butler Javed , Seferović Petar M , Seferović Jelena , Cosentino Francesco 
Published: December 2023

Abstract
Type 2 diabetes mellitus (T2DM) and prediabetes confer an increased risk of developing heart failure (HF). In patients with known HF, concomitant T2DM and prediabetes are associated with worse symptoms and functional status, greater risk of complications and hospitalization for worsening HF, and greater cardiovascular and total mortality. Furthermore, patients with HF appear to be at a higher risk of developing T2DM. The underlying mechanisms of the bidirectional relationship between T2DM and HF have been intensively researched and include multiple, complex alterations at cellular, myocardial, and systemic levels. This chapter reviews the epidemiology, risk factors, and underlying mechanisms, and summarizes clinical presentation, complications, and outcomes of patients with concomitant T2DM and HF. It provides an overview of the contemporary management of HF and T2DM and highlights interventions to improve clinical outcomes in this population.
Pregnancy and heart failure
Authors: Bauersachs Johann , Hilfiker-Kleiner Denise , Sliwa Karen 
Published: December 2023

Abstract
Patients with pre-existing heart failure, or developing heart failure during pregnancy, are at elevated, and sometimes high, risk for adverse outcomes, including death of the mother and the child. Here we summarize the physiology and pathophysiology of the cardiovascular system and heart failure during/after pregnancy. We provide information on pre-pregnancy counselling of women at risk, or with pre-existing heart failure, and give advice for diagnosis and management of women who present with (de novo or previously unknown) heart failure during or after pregnancy. Sub-chapters include specific cardiomyopathies such as peripartum, hypertrophic dilated and restrictive cardiomyopathy, as well as left ventricular non-compaction, arrhythmogenic right ventricular cardiomyopathy, and Takotsubo syndrome. Patients in need of specific assessment and advice around pregnancy include those with adult congenital heart disease and those with a history of chemo-/radiotherapy for cancer or haematological malignancies.
First Light and Reionization Epoch Simulations (flares) – XIV. The Balmer/4000 Å breaks of distant galaxies
Authors: Wilkins Stephen M , Lovell Christopher C , Irodotou Dimitrios , Vijayan Aswin P , Vikaeus Anton , Zackrisson Erik , Caruana Joseph , Stanway Elizabeth R , Conselice Christopher J , Seeyave Louise T C , Roper William J , Chworowsky Katherine , Finkelstein Steven L 
Published: December 2023

ABSTRACT
With the successful launch and commissioning of JWST we are now able to routinely spectroscopically probe the rest-frame optical emission of galaxies at z &gt; 6 for the first time. Among the most useful spectral diagnostics used in the optical is the Balmer/4000 Å break; this is, in principle, a diagnostic of the mean ages of composite stellar populations. However, the Balmer break is also sensitive to the shape of the star formation history, the stellar (and gas) metallicity, the presence of nebular continuum emission, and dust attenuation. In this work, we explore the origin of the Balmer/4000 Å break using the synthesizer synthetic observations package. We then make predictions of the Balmer/4000 Å break using the First Light and Reionization Epoch Simulations at 5 &lt; z &lt; 10. We find that the average break strength weakly correlates with stellar mass and rest-frame far-ultraviolet luminosity, but that this is predominantly driven by dust attenuation. We also find that break strength provides a weak diagnostic of the age but performs better as a means to constrain star formation and stellar mass, alongside the ultraviolet and optical luminosity, respectively.
Dark-ages reionization and galaxy formation simulation – XXI. Constraining the evolution of the ionizing escape fraction
Authors: Mutch Simon J , Greig Bradley , Qin Yuxiang , Poole Gregory B , Wyithe J Stuart B 
Published: December 2023

ABSTRACT
The fraction of ionizing photons that escape their host galaxies to ionize hydrogen in the intergalactic medium (IGM) is a critical parameter in analyses of the reionization era. In this paper, we use the meraxes semi-analytic galaxy formation model to infer the mean ionizing photon escape fraction and its dependence on galaxy properties through joint modelling of the observed high redshift galaxy population and existing constraints on the reionization history. Using a Bayesian framework, and under the assumption that escape fraction is primarily related to halo mass, we find that the joint constraints of the ultraviolet luminosity function, cosmic microwave background optical depth, and the Ly α forest require an escape fraction of $(18\pm 5)$ per cent for galaxies within haloes of M ≲ 109 M⊙ and $(5\pm 2)$ per cent for more massive haloes. In terms of galaxy properties, this transition in escape fraction occurs at stellar masses of M⋆ ∼ 107 M⊙, nearly independent of redshift. As a function of redshift, reionization is dominated by the smaller M⋆ ≲ 107 M⊙ galaxies with high escape fractions at z ≳ 6 and by the larger M⋆ ≳ 107 M⊙ galaxies with lower escape fractions at z ≲ 6. Galaxies with star formation rates of 10−2.5 M⊙yr−1 to 10−1.5 M⊙yr−1 provide the dominant source of ionizing photons throughout reionization. Our results are consistent with recent direct measurements of a $\sim 5~{{\ \rm per\ cent}}$ escape fraction from massive galaxies at the end of reionization and support the picture of low mass galaxies being the dominant sources of ionizing photons during reionization.
Parasitoid Serpins Evolve Novel Functions to Manipulate Host Homeostasis
Authors: Wu Zhiwei , Yuan Ruizhong , Gu Qijuan , Wu Xiaotong , Gu Licheng , Ye Xiqian , Zhou Yuenan , Huang Jianhua , Wang Zhizhi , Chen Xuexin 
Published: December 2023

Abstract
Parasitoids introduce various virulence factors when parasitism occurs, and some taxa generate teratocytes to manipulate the host immune system and metabolic homeostasis for the survival and development of their progeny. Host-parasitoid interactions are extremely diverse and complex, yet the evolutionary dynamics are still poorly understood. A category of serpin genes, named CvT-serpins, was discovered to be specifically expressed and secreted by the teratocytes of Cotesia vestalis, an endoparasitoid of the diamondback moth Plutella xylostella. Genomic and phylogenetic analysis indicated that the C. vestalis serpin genes are duplicated and most of them are clustered into 1 monophyletic clade. Intense positive selection was detected at the residues around the P1–P1′ cleavage sites of the Cv-serpin reactive center loop domain. Functional analyses revealed that, in addition to the conserved function of melanization inhibition (CvT-serpins 1, 16, 18, and 21), CvT-serpins exhibited novel functions, i.e. bacteriostasis (CvT-serpins 3 and 5) and nutrient metabolism regulation (CvT-serpins 8 and 10). When the host-parasitoid system is challenged with foreign bacteria, CvT-serpins act as an immune regulator to reprogram the host immune system through sustained inhibition of host melanization while simultaneously functioning as immune effectors to compensate for this suppression. In addition, we provided evidence that CvT-serpin8 and 10 participate in the regulation of host trehalose and lipid levels by affecting genes involved in these metabolic pathways. These findings illustrate an exquisite tactic by which parasitoids win out in the parasite–host evolutionary arms race by manipulating host immune and nutrition homeostasis via adaptive gene evolution and neofunctionalization.
Exonic splicing code and coordination of divalent metals in proteins
Authors: Bakhtiar Dara , Vondraskova Katarina , Pengelly Reuben J , Chivers Martin , Kralovicova Jana , Vorechovsky Igor 
Published: December 2023

Abstract
Exonic sequences contain both protein-coding and RNA splicing information but the interplay of the protein and splicing code is complex and poorly understood. Here, we have studied traditional and auxiliary splicing codes of human exons that encode residues coordinating two essential divalent metals at the opposite ends of the Irving–Williams series, a universal order of relative stabilities of metal–organic complexes. We show that exons encoding Zn2+-coordinating amino acids are supported much less by the auxiliary splicing motifs than exons coordinating Ca2+. The handicap of the former is compensated by stronger splice sites and uridine-richer polypyrimidine tracts, except for position –3 relative to 3′ splice junctions. However, both Ca2+ and Zn2+ exons exhibit close-to-constitutive splicing in multiple tissues, consistent with their critical importance for metalloprotein function and a relatively small fraction of expendable, alternatively spliced exons. These results indicate that constraints imposed by metal coordination spheres on RNA splicing have been efficiently overcome by the plasticity of exon–intron architecture to ensure adequate metalloprotein expression.
Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR
Authors: Baldoni Pedro L , Chen Yunshun , Hediyeh-zadeh Soroor , Liao Yang , Dong Xueyi , Ritchie Matthew E , Shi Wei , Smyth Gordon K 
Published: December 2023

Abstract
Differential expression analysis of RNA-seq is one of the most commonly performed bioinformatics analyses. Transcript-level quantifications are inherently more uncertain than gene-level read counts because of ambiguous assignment of sequence reads to transcripts. While sequence reads can usually be assigned unambiguously to a gene, reads are very often compatible with multiple transcripts for that gene, particularly for genes with many isoforms. Software tools designed for gene-level differential expression do not perform optimally on transcript counts because the read-to-transcript ambiguity (RTA) disrupts the mean-variance relationship normally observed for gene level RNA-seq data and interferes with the efficiency of the empirical Bayes dispersion estimation procedures. The pseudoaligners kallisto and Salmon provide bootstrap samples from which quantification uncertainty can be assessed. We show that the overdispersion arising from RTA can be elegantly estimated by fitting a quasi-Poisson model to the bootstrap counts for each transcript. The technical overdispersion arising from RTA can then be divided out of the transcript counts, leading to scaled counts that can be input for analysis by established gene-level software tools with full statistical efficiency. Comprehensive simulations and test data show that an edgeR analysis of the scaled counts is more powerful and efficient than previous differential transcript expression pipelines while providing correct control of the false discovery rate. Simulations explore a wide range of scenarios including the effects of paired vs single-end reads, different read lengths and different numbers of replicates.
Risk of Severe Maternal Morbidity Associated With Severe Acute Respiratory Syndrome Coronavirus 2 Infection During Pregnancy
Authors: Regan Annette K , Arah Onyebuchi A , Fell Deshayne B , Sullivan Sheena G 
Published: December 2023

Abstract

Background
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection during pregnancy increases the risk of adverse fetal and neonatal outcomes, but the contribution to severe maternal morbidity (SMM) has been less frequently documented.

Methods
We conducted a national cohort study of 93 624 deliveries occurring between 11 March 2020 and 1 July 2021 using medical claims information from the OptumLabs Data Warehouse. SARS-CoV-2 infection was identified from diagnostic and laboratory testing claims records. We identified 21 SMM conditions using International Classification of Diseases, Tenth Revision, Clinical Modification and procedure codes and compared SMM conditions by SARS-CoV-2 status using Poisson regression with robust variance, adjusting for maternal sociodemographic and health factors, onset of labor, and week of conception.

Results
Approximately 5% of deliveries had a record of SARS-CoV-2 infection: 27.0% &lt;7 days before delivery, 13.5% within 7–30 days of delivery, and 59.5% earlier in pregnancy. Compared to uninfected pregnancies, the adjusted risk of SMM was 2.22 times higher (95% confidence interval [CI], 1.97–2.48) among those infected &lt;7 days before delivery and 1.66 times higher (95% CI, 1.23–2.08) among those infected 7–30 days before delivery. The highest risks were observed for acute respiratory distress syndrome (adjusted risk ratio [aRR], 13.24 [95% CI, 12.86–13.61]) and acute renal failure (aRR, 3.91 [95% CI, 3.32–4.50]).

Conclusions
COVID-19 is associated with increased rates of SMM.
A Systematic Literature Review to Identify Diagnostic Gaps in Managing Immunocompromised Patients With Cancer and Suspected Infection
Authors: Hill Joshua A , Park Sarah Y , Gajurel Kiran , Taplitz Randy 
Published: December 2023

Abstract
Patients with cancer are increasingly vulnerable to infections, which may be more severe than in the general population. Improvements in rapid and timely diagnosis to optimize management are needed. We conducted a systematic literature review to determine the unmet need in diagnosing acute infections in immunocompromised patients with cancer and identified 50 eligible studies from 5188 records between 1 January 2012 and 23 June 2022. There was considerable heterogeneity in study designs and parameters, laboratory methods and definitions, and assessed outcomes, with limited evaluation of diagnostic impact on clinical outcomes. Culture remains the primary diagnostic strategy. Fewer studies employing molecular technologies exist, but emerging literature suggests that pathogen-agnostic molecular tests may add to the diagnostic armamentarium. Well-designed clinical studies using standardized methodologies are needed to better evaluate performance characteristics and clinical and economic impacts of emerging diagnostic techniques to improve patient outcomes.
Increasing marsh bird abundance in coastal wetlands of the Great Lakes, 2011–2021, likely caused by increasing water levels
Authors: Tozer Douglas C , Bracey Annie M , Fiorino Giuseppe E , Gehring Thomas M , Gnass Giese Erin E , Grabas Greg P , Howe Robert W , Lawrence Gregory J , Niemi Gerald J , Wheelock Bridget A , Ethier Danielle M 
Published: December 2023

AbstractWetlands of the Laurentian Great Lakes of North America (i.e., lakes Superior, Michigan, Huron, Erie, and Ontario) provide critical habitat for marsh birds. We used 11 years (2011–2021) of data collected by the Great Lakes Coastal Wetland Monitoring Program at 1,962 point-count locations in 792 wetlands to quantify the first-ever annual abundance indices and trends of 18 marsh-breeding bird species in coastal wetlands throughout the entire Great Lakes. Nine species (50%) increased by 8–37% per year across all of the Great Lakes combined, whereas none decreased. Twelve species (67%) increased by 5–50% per year in at least 1 of the 5 Great Lakes, whereas only 3 species (17%) decreased by 2–10% per year in at least 1 of the lakes. There were more positive trends among lakes and species (n = 34, 48%) than negative trends (n = 5, 7%). These large increases are welcomed because most of the species are of conservation concern in the Great Lakes. Trends were likely caused by long-term, cyclical fluctuations in Great Lakes water levels. Lake levels increased over most of the study, which inundated vegetation and increased open water-vegetation interspersion and open water extent, all of which are known to positively influence abundance of most of the increasing species and negatively influence abundance of all of the decreasing species. Coastal wetlands may be more important for marsh birds than once thought if they provide high-lake-level-induced population pulses for species of conservation concern. Coastal wetland protection and restoration are of utmost importance to safeguard this process. Future climate projections show increases in lake levels over the coming decades, which will cause “coastal squeeze” of many wetlands if they are unable to migrate landward fast enough to keep pace. If this happens, less habitat will be available to support periodic pulses in marsh bird abundance, which appear to be important for regional population dynamics. Actions that allow landward migration of coastal wetlands during increasing lake levels by removing or preventing barriers to movement, such as shoreline hardening, will be useful for maintaining marsh bird breeding habitat in the Great Lakes.
Two ARGONAUTE proteins loaded with transposon-derived small RNAs are associated with the reproductive cell lineage in Arabidopsis
Authors: Bradamante Gabriele , Nguyen Vu Hoang , Incarbone Marco , Meir Zohar , Bente Heinrich , Donà Mattia , Lettner Nicole , Scheid Ortrun Mittelsten , Gutzat Ruben 
Published: December 2023

Abstract
In sexually propagating organisms, genetic, and epigenetic mutations are evolutionarily relevant only if they occur in the germline and are hence transmitted to the next generation. In contrast to most animals, plants are considered to lack an early segregating germline, implying that somatic cells can contribute genetic information to progeny. Here we demonstrate that 2 ARGONAUTE proteins, AGO5 and AGO9, mark cells associated with sexual reproduction in Arabidopsis (Arabidopsis thaliana) throughout development. Both AGOs are loaded with dynamically changing small RNA populations derived from highly methylated, pericentromeric, long transposons. Sequencing of single stem cell nuclei revealed that many of these transposons are co-expressed within an AGO5/9 expression domain in the shoot apical meristem (SAM). Co-occurrence of transposon expression and specific ARGONAUTE (AGO) expression in the SAM is reminiscent of germline features in animals and supports the existence of an early segregating germline in plants. Our results open the path to investigating transposon biology and epigenome dynamics at cellular resolution in the SAM stem cell niche.
Transcription factor OsMYB30 increases trehalose content to inhibit α-amylase and seed germination at low temperature
Authors: Yu Huihui , Teng Zhenning , Liu Bohan , Lv Jiahan , Chen Yinke , Qin Zhonge , Peng Yan , Meng Shuan , He Yuchi , Duan Meijuan , Zhang Jianhua , Ye Nenghui 
Published: December 2023

Abstract
Low-temperature germination (LTG) is an important agronomic trait for direct-seeding cultivation of rice (Oryza sativa). Both OsMYB30 and OsTPP1 regulate the cold stress response in rice, but the function of OsMYB30 and OsTPP1 in regulating LTG and the underlying molecular mechanism remains unknown. Employing transcriptomics and functional studies revealed a sugar signaling pathway that regulates seed germination in response to low temperature (LT). Expression of OsMYB30 and OsTPP1 was induced by LT during seed germination, and overexpressing either OsMYB30 or OsTPP1 delayed seed germination and increased sensitivity to LT during seed germination. Transcriptomics and qPCR revealed that expression of OsTPP1 was upregulated in OsMYB30-overexpressing lines but downregulated in OsMYB30-knockout lines. In vitro and in vivo experiments revealed that OsMYB30 bound to the promoter of OsTPP1 and regulated the abundance of OsTPP1 transcripts. Overaccumulation of trehalose (Tre) was found in both OsMYB30- and OsTPP1-overexpressing lines, resulting in inhibition of α-amylase 1a (OsAMY1a) gene during seed germination. Both LT and exogenous Tre treatments suppressed the expression of OsAMY1a, and the osamy1a mutant was not sensitive to exogenous Tre during seed germination. Overall, we concluded that OsMYB30 expression was induced by LT to activate the expression of OsTPP1 and increase Tre content, which thus inhibited α-amylase activity and seed germination. This study identified a phytohormone-independent pathway that integrates environmental cues with internal factors to control seed germination.
Causalized convergent cross-mapping and its approximate equivalence with directed information in causality analysis
Authors: Deng Jinxian , Sun Boxin , Scheel Norman , Renli Alina B , Zhu David C , Zhu Dajiang , Ren Jian , Li Tongtong , Zhang Rong 
Published: December 2023

Abstract
Convergent cross-mapping (CCM) has attracted increased attention recently due to its capability to detect causality in nonseparable systems under deterministic settings, which may not be covered by the traditional Granger causality. From an information-theoretic perspective, causality is often characterized as the directed information (DI) flowing from one side to the other. As information is essentially nondeterministic, a natural question is: does CCM measure DI flow? Here, we first causalize CCM so that it aligns with the presumption in causality analysis—the future values of one process cannot influence the past of the other, and then establish and validate the approximate equivalence of causalized CCM (cCCM) and DI under Gaussian variables through both theoretical derivations and fMRI-based brain network causality analysis. Our simulation result indicates that, in general, cCCM tends to be more robust than DI in causality detection. The underlying argument is that DI relies heavily on probability estimation, which is sensitive to data size as well as digitization procedures; cCCM, on the other hand, gets around this problem through geometric cross-mapping between the manifolds involved. Overall, our analysis demonstrates that cross-mapping provides an alternative way to evaluate DI and is potentially an effective technique for identifying both linear and nonlinear causal coupling in brain neural networks and other settings, either random or deterministic, or both.