bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incidence of thyroid dysfunction following initiation of amiodarone treatment in patients with and without heart failure: a nationwide cohort study
Authors: Ali Sam Aiyad , Ersbøll Mads , Vinding Naja Emborg , Butt Jawad Haider , Rørth Rasmus , Selmer Christian , Westergaard Lucas Malta , Mogensen Ulrik Madvig , Weeke Peter E , Jøns Christian , Gustafsson Finn , Fosbøl Emil , Køber Lars , Kristensen Søren Lund 
Published: December 2022

AbstractAimsThyroid dysfunction is considered the most frequent complication to amiodarone treatment, but data on its occurrence outside clinical trials are sparse. The present study aimed to examine the incidence of thyroid dysfunction following initiation of amiodarone treatment in a nationwide cohort of patients with and without heart failure (HF).Methods and resultsIn Danish registries, we identified all patients with first-time amiodarone treatment during the period 2000–18, without prior thyroid disease or medication. The primary outcome was a composite of thyroid diagnoses and initiation of thyroid drugs. Outcomes were assessed at 1-year follow-up, and for patients free of events in the first year, in a landmark analysis for the subsequent 5 years. We included 43 724 patients with first-time amiodarone treatment, of whom 16 939 (38%) had HF. At 1-year follow-up, the cumulative incidence and adjusted hazard ratio (HR) of the primary outcome were 5.3% and 1.37 (95% confidence interval 1.25–1.50) in patients with a history of HF and 4.2% in those without HF (reference). In the 1-year landmark analysis, the subsequent 5-year cumulative incidences and adjusted HRs of the primary outcome were 5.3% (reference) in patients with 1-year accumulated dose &lt;27.38 g [corresponding to average daily dose (ADD &lt;75 mg)], 14.0% and HR 2.74 (2.46–3.05) for 27.38–45.63 g (ADD 75–125 mg), 20.0% and HR 4.16 (3.77–4.59) for 45.64–63.88 g (ADD 126–175 mg), and 24.5% and HR 5.30 (4.82–5.90) for &gt;63.88 g (ADD &gt;175 mg).ConclusionAmong patients who initiated amiodarone treatment, around 5% had thyroid dysfunction at 1-year follow-up, with a slightly higher incidence in those with HF. A dose–response relationship was observed between the 1-year accumulated amiodarone dose and the subsequent 5-year cumulative incidence of thyroid dysfunction.
Familial atrial fibrillation mutation M1875T-SCN5A increases early sodium current and dampens the effect of flecainide
Authors: O’Reilly Molly , Sommerfeld Laura C , O’Shea C , Broadway-Stringer S , Andaleeb S , Reyat J S , Kabir S N , Stastny D , Malinova A , Delbue D , Fortmueller L , Gehmlich K , Pavlovic D , Skryabin B V , Holmes A P , Kirchhof P , Fabritz L 
Published: December 2022

AbstractAimsAtrial fibrillation (AF) is the most common cardiac arrhythmia. Pathogenic variants in genes encoding ion channels are associated with familial AF. The point mutation M1875T in the SCN5A gene, which encodes the α-subunit of the cardiac sodium channel Nav1.5, has been associated with increased atrial excitability and familial AF in patients.Methods and resultsWe designed a new murine model carrying the Scn5a-M1875T mutation enabling us to study the effects of the Nav1.5 mutation in detail in vivo and in vitro using patch clamp and microelectrode recording of atrial cardiomyocytes, optical mapping, electrocardiogram, echocardiography, gravimetry, histology, and biochemistry. Atrial cardiomyocytes from newly generated adult Scn5a-M1875T+/− mice showed a selective increase in the early (peak) cardiac sodium current, larger action potential amplitude, and a faster peak upstroke velocity. Conduction slowing caused by the sodium channel blocker flecainide was less pronounced in Scn5a-M1875T+/− compared to wildtype atria. Overt hypertrophy or heart failure in Scn5a-M1875T+/− mice could be excluded.ConclusionThe Scn5a-M1875T point mutation causes gain-of-function of the cardiac sodium channel. Our results suggest increased atrial peak sodium current as a potential trigger for increased atrial excitability.
The adjunctive effect for left pulmonary vein isolation of vein of Marshall ethanol infusion in persistent atrial fibrillation
Authors: Huang Lihong , Gao Mingyang , Lai Yiwei , Guo Qi , Li Songnan , Li Changyi , Liu Nian , Wang Wei , Liu Xiaoxia , Zuo Song , Guo Xueyuan , Zhao Xin , Jiang Chenxi , Sang Caihua , Tang Ribo , Long Deyong , Du Xin , Dong Jianzeng , Ma Chang-sheng 
Published: December 2022

AbstractObjectiveThis study sought to assess the effect of ethanol infusion into the vein of Marshall (EIVOM) on the acute success of left pulmonary vein (LPV) isolation in persistent atrial fibrillation (PeAF).Methods and resultsA total of 313 patients with drug-resistant PeAF were enrolled (135 in Group 1 and 178 in Group 2). In Group 1, EIVOM was firstly performed, followed by radiofrequency ablation (RFA) including bilateral pulmonary vein isolation (PVI) and linear ablation at roofline, cavotricuspid isthmus, and mitral isthmus (MI). In Group 2, PVI and linear ablations were completed with RFA. First-pass isolation of the LPV was achieved in 119 (88.1%) and 132 (74.2%) patients in Groups 1 and 2, respectively (P = 0.002). The rate of acute pulmonary vein reconnection (PVR) was significantly lower in Group 1 (9.6% vs. 22.5%, P = 0.003). About half of acute PVR occurred in the carina with or without EIVOM.ConclusionEIVOM is effective in achieving a higher first-pass isolation and a lower acute PVR of LPV in PeAF.
Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam
Authors: Xu Ran , Martelossi Jacopo , Smits Morgan , Iannello Mariangela , Peruzza Luca , Babbucci Massimiliano , Milan Massimo , Dunham Joseph P , Breton Sophie , Milani Liliana , Nuzhdin Sergey V , Bargelloni Luca , Passamonti Marco , Ghiselli Fabrizio 
Published: December 2022

AbstractThe molecular factors and gene regulation involved in sex determination and gonad differentiation in bivalve molluscs are unknown. It has been suggested that doubly uniparental inheritance (DUI) of mitochondria may be involved in these processes in species such as the ubiquitous and commercially relevant Manila clam, Ruditapes philippinarum. We present the first long-read-based de novo genome assembly of a Manila clam, and a RNA-Seq multi-tissue analysis of 15 females and 15 males. The highly contiguous genome assembly was used as reference to investigate gene expression, alternative splicing, sequence evolution, tissue-specific co-expression networks, and sexual contrasting SNPs. Differential expression (DE) and differential splicing (DS) analyses revealed sex-specific transcriptional regulation in gonads, but not in somatic tissues. Co-expression networks revealed complex gene regulation in gonads, and genes in gonad-associated modules showed high tissue specificity. However, male gonad-associated modules showed contrasting patterns of sequence evolution and tissue specificity. One gene set was related to the structural organization of male gametes and presented slow sequence evolution but high pleiotropy, whereas another gene set was enriched in reproduction-related processes and characterized by fast sequence evolution and tissue specificity. Sexual contrasting SNPs were found in genes overrepresented in mitochondrial-related functions, providing new candidates for investigating the relationship between mitochondria and sex in DUI species. Together, these results increase our understanding of the role of DE, DS, and sequence evolution of sex-specific genes in an understudied taxon. We also provide resourceful genomic data for studies regarding sex diagnosis and breeding in bivalves.
Prevalence and characterization of piperaquine, mefloquine and artemisinin derivatives triple-resistant Plasmodium falciparum in Cambodia
Authors: Mairet-Khedim Mélissa , Roesch Camille , Khim Nimol , Srun Sreynet , Bouillon Anthony , Kim Saorin , Ke Sopheakvatey , Kauy Chhayleang , Kloeung Nimol , Eam Rotha , Khean Chanra , Kul Chanvong , Chy Sophy , Leang Rithea , Ringwald Pascal , Barale Jean-Christophe , Witkowski Benoit 
Published: December 2022

Abstract

Background
In early 2016, in Preah Vihear, Northern Cambodia, artesunate/mefloquine was used to cope with dihydroartemisinin/piperaquine-resistant Plasmodium falciparum parasites. Following this policy, P. falciparum strains harbouring molecular markers associated with artemisinin, piperaquine and mefloquine resistance have emerged. However, the lack of a viable alternative led Cambodia to adopt artesunate/mefloquine countrywide, raising concerns about a surge of triple-resistant P. falciparum strains.

Objectives
To assess the prevalence of triple-resistant parasites after artesunate/mefloquine implementation countrywide in Cambodia and to characterize their phenotype.

Methods
For this multicentric study, 846 samples were collected from 2016 to 2019. Genotyping of molecular markers associated with artemisinin, piperaquine and mefloquine resistance was coupled with phenotypic analyses.

Results
Only four triple-resistant P. falciparum isolates (0.47%) were identified during the study period. These parasites combined the pfk13 polymorphism with pfmdr1 amplification, pfpm2 amplification and/or pfcrt mutations. They showed significantly higher tolerance to artemisinin, piperaquine and mefloquine and also to the mefloquine and piperaquine combination.

Conclusions
The use of artesunate/mefloquine countrywide in Cambodia has not led to a massive increase of triple-resistant P. falciparum parasites. However, these parasites circulate in the population, and exhibit clear resistance to piperaquine, mefloquine and their combination in vitro. This study demonstrates that P. falciparum can adapt to more complex drug associations, which should be considered in future therapeutic designs.
A MITE insertion abolishes theAP3-3self-maintenance regulatory loop in apetalous flowers ofNigella damascena
Authors: Conde e Silva Natalia , Leguilloux Martine , Bellec Arnaud , Rodde Nathalie , Aubert Juliette , Manicacci Domenica , Damerval Catherine , Berges Helene , Deveaux Yves 
Published: December 2022

AbstractMADS-box transcription factors are important regulators of floral organ identity through their binding to specific motifs, termed CArG, in the promoter of their target genes. Petal initiation and development depend on class A and B genes, but MADS-box genes of the APETALA3 (AP3) clade are key regulators of this process. In the early diverging eudicot Nigella damascena, an apetalous [T] morph is characterized by the lack of expression of the NdAP3-3 gene, with its expression being petal-specific in the wild-type [P] morph. All [T] morph plants are homozygous for an NdAP3-3 allele with a Miniature Inverted-repeat Transposable Element (MITE) insertion in the second intron of the gene. Here, we investigated to which extent the MITE insertion impairs regulation of the NdAP3-3 gene. We found that expression of NdAP3-3 is initiated in the [T] morph, but the MITE insertion prevents its positive self-maintenance by affecting the correct splicing of the mRNA. We also found specific CArG features in the promoter of the NdAP3-3 genes with petal-specific expression. However, they are not sufficient to drive expression only in petals of transgenic Arabidopsis, highlighting the existence of Nigella-specific cis/trans-acting factors in regulating AP3 paralogs.
Improving machine learning-derived photometric redshifts and physical property estimates using unlabelled observations
Authors: Humphrey A , Cunha P A C , Paulino-Afonso A , Amarantidis S , Carvajal R , Gomes J M , Matute I , Papaderos P 
Published: December 2022

ABSTRACT
In the era of huge astronomical surveys, machine learning offers promising solutions for the efficient estimation of galaxy properties. The traditional, ‘supervised’ paradigm for the application of machine learning involves training a model on labelled data, and using this model to predict the labels of previously unlabelled data. The semi-supervised ‘pseudo-labelling’ technique offers an alternative paradigm, allowing the model training algorithm to learn from both labelled data and as-yet unlabelled data. We test the pseudo-labelling method on the problems of estimating redshift, stellar mass, and star formation rate, using COSMOS2015 broad band photometry and one of several publicly available machine learning algorithms, and we obtain significant improvements compared to purely supervised learning. We find that the gradient-boosting tree methods CatBoost, XGBoost, and LightGBM benefit the most, with reductions of up to ∼15  per cent in metrics of absolute error. We also find similar improvements in the photometric redshift catastrophic outlier fraction. We argue that the pseudo-labelling technique will be useful for the estimation of redshift and physical properties of galaxies in upcoming large imaging surveys such as Euclid and LSST, which will provide photometric data for billions of sources.
Constraining galactic baryon cycle using the galaxy stellar-to-halo mass relations
Authors: Chen Yaoxin , Xu Yingzhong , Kang Xi 
Published: December 2022

ABSTRACT
Galaxies display several well-behaved scaling relations between their properties, such as the star formation rate–stellar mass relation (the main sequence, MS) and the stellar mass–halo mass relation (SHMR). In principle, these scaling relations could imply different star formation histories (SFHs) of galaxies and different constraints on galaxy formation physics. In this paper, we derive the SFHs of galaxies by assuming that they always follow the SHMRs at different redshifts and use an empirical model to constrain key processes in their baryon cycle. It is found that, besides cold accretion due to halo growth, outflow of gas produced by stellar feedback has to be recycled to sustain the derived SFHs of galaxies. The recycled fraction is strongly affected by the baryon fraction in accreted low-mass haloes and the mass loading factor that quantifies the ratio between the galactic outflow rate and star formation rate. Our fiducial model predicts that around 20–60 per cent of outflow is recycled in $\sim 0.5\!-\!4\, \mathrm{Gyr}$, while simulations predict a slightly higher recycle fraction and a lower recycle time. We argue that strong constraints on the baryon cycle process can be obtained from future observation of the circum-galactic medium (CGM) of galaxies, such as the gas cooling rate of CGM. We also find that the implied SFHs from the SHMRs indicate that galaxies stay on the MS only for part of their lifetimes. Our model reproduces the evolution of the mass–metallicity relation as well.
The phase and turbulent properties of Cattail
Authors: Yuen Ka Ho , Chen Avi , Ho Ka Wai , Lazarian Alex 
Published: December 2022

ABSTRACT
A recent publication discovered one of the largest filamentary neutral hydrogen features dubbed Cattail from high-resolution Five-hundred-meter Aperture Spherical radio Telescope observations that might be a new galactic arm of the Milky Way. We evaluate the turbulent and phase properties of Cattail via the newly developed Velocity Decomposition Algorithm and Force Balancing Model. We discover that if there exists a phase transition, then Cattail is unlikely in the cold neutral media phase. We also show that the Cattail is two disjoint features in caustics space, suggesting that the Cattail has two different turbulent systems. We check the spectra of the individual system separated via VDA to confirm this argument. We do not exclude the existence of smaller scale cold media being embedded within this structure.
Simulations of star-forming main-sequence galaxies in Milgromian gravity
Authors: Nagesh Srikanth T , Kroupa Pavel , Banik Indranil , Famaey Benoit , Ghafourian Neda , Roshan Mahmood , Thies Ingo , Zhao Hongsheng , Wittenburg Nils 
Published: December 2022

ABSTRACT
We conduct hydrodynamical MOND simulations of isolated disc galaxies over the stellar mass range M⋆/M⊙ = 107–1011 using the adaptive mesh refinement code phantom of ramses (por), an adaptation of the ramses code with a Milgromian gravity solver. The scale lengths and gas fractions are based on observed galaxies, and the simulations are run for 5 Gyr. The main aim is to see whether the existing sub-grid physics prescriptions for star formation and stellar feedback reproduce the observed main sequence and reasonably match the Kennicutt–Schmidt relation, which captures how the local and global star formation rates relate to other properties. Star formation in the models starts soon after initialization and continues as the models evolve. The initialized galaxies indeed evolve to a state which is on the observed main sequence and the Kennicutt–Schmidt relation. The available formulation of sub-grid physics is therefore adequate and leads to galaxies that largely behave like observed galaxies, grow in radius, and have flat rotation curves – provided we use Milgromian gravitation. Furthermore, the strength of the bars tends to be inversely correlated with the stellar mass of the galaxy, whereas the bar length strongly correlates with the stellar mass. Irrespective of the mass, the bar pattern speed stays constant with time, indicating that dynamical friction does not affect the bar dynamics. The models demonstrate Renzo’s rule and form structures at large radii, much as in real galaxies. In this framework, baryonic physics is thus sufficiently understood to not pose major uncertainties in our modelling of global galaxy properties.
HubPUG: proper motions for local group dwarfs observed with HST utilizing Gaia as a reference frame
Authors: Warfield Jack T , Kallivayalil Nitya , Zivick Paul , Fritz Tobias , Richstein Hannah , Sohn Sangmo Tony , del Pino Andrés , Savino Alessandro , Weisz Daniel R 
Published: December 2022

ABSTRACT
We present the method behind HubPUG, a software tool built for recovering systemic proper motions (PMs) of targets (e.g. clusters or resolved galaxies) in Hubble Space Telescope (HST) fields with two epochs of observations by utilizing stars observed by Gaia as a foreground frame of reference.HST PM experiments have typically relied on the use of distant background galaxies or quasi-stellar objects (QSOs) as stationary sources against which to measure PMs. Without consistent profiles, background galaxies are more difficult to centroid, but benefit on-aggregate from their large numbers. QSOs, though they can be fit with stellar point-spread functions, are sparse, with most fields containing none. Historically, the use of stars as references against which to measure PMs would have been difficult because they have individual PMs of their own. However, Gaia has now provided positions and PMs for over 1.4 billion stars, which are much more likely to be well-imaged in the fields around targets versus background sources, have predictable stellar profiles, and require less observing time per-image for good signal-to-noise. This technique allows us to utilize the power of Gaia to measure the PM of targets too faint for Gaia to observe itself. We have recovered PMs for the Milky Way satellites Sculptor and Draco with comparable uncertainties over HST-only and Gaia-only measurements, limited primarily by the current capabilities of the Gaia data. We also show the promise of this method for satellites of M31 with a new PM measurement for Andromeda VII.
RNA granule-clustered mitochondrial aminoacyl-tRNA synthetases form multiple complexes with the potential to fine-tune tRNA aminoacylation
Authors: Peng Gui-Xin , Mao Xue-Ling , Cao Yating , Yao Shi-Ying , Li Qing-Run , Chen Xin , Wang En-Duo , Zhou Xiao-Long 
Published: December 2022

Abstract
Mitochondrial RNA metabolism is suggested to occur in identified compartmentalized foci, i.e. mitochondrial RNA granules (MRGs). Mitochondrial aminoacyl-tRNA synthetases (mito aaRSs) catalyze tRNA charging and are key components in mitochondrial gene expression. Mutations of mito aaRSs are associated with various human disorders. However, the suborganelle distribution, interaction network and regulatory mechanism of mito aaRSs remain largely unknown. Here, we found that all mito aaRSs partly colocalize with MRG, and this colocalization is likely facilitated by tRNA-binding capacity. A fraction of human mitochondrial AlaRS (hmtAlaRS) and hmtSerRS formed a direct complex via interaction between catalytic domains in vivo. Aminoacylation activities of both hmtAlaRS and hmtSerRS were fine-tuned upon complex formation in vitro. We further established a full spectrum of interaction networks via immunoprecipitation and mass spectrometry for all mito aaRSs and discovered interactions between hmtSerRS and hmtAsnRS, between hmtSerRS and hmtTyrRS and between hmtThrRS and hmtArgRS. The activity of hmtTyrRS was also influenced by the presence of hmtSerRS. Notably, hmtSerRS utilized the same catalytic domain in mediating several interactions. Altogether, our results systematically analyzed the suborganelle localization and interaction network of mito aaRSs and discovered several mito aaRS-containing complexes, deepening our understanding of the functional and regulatory mechanisms of mito aaRSs.
CRISPR/Cas9-Engineered Large Fragment Deletion Mutations in Arabidopsis CEP Peptide–Encoding Genes Reveal Their Role in Primary and Lateral Root Formation
Authors: Huang Aixia , Cui Tingting , Zhang Yan , Ren Xufang , Wang Mengfang , Jia Lingyu , Zhang Yonghong , Wang Guodong 
Published: December 2022

Abstract
C-TERMINALLY ENCODED PEPTIDEs (CEPs) are post-translationally modified peptides that play essential roles in root and shoot development, nitrogen absorption, nodule formation and stress resilience. However, it has proven challenging to determine biological activities of CEPs because of difficulties in obtaining loss-of-function mutants for these small genes. To overcome this challenge, we thus assembled a collection of easily detectable large fragment deletion mutants of Arabidopsis CEP genes through the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9–engineered genome editing. This collection was then evaluated for the usability by functionally analyzing the Arabidopsis growth and development with a focus on the root. Most cep mutants displayed developmental defects in primary and lateral roots showing an increased primary root length and an enhanced lateral root number, demonstrating that the genetic resource provides a useful tool for further investigations into the roles of CEPs.