bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of ductus stent versus surgical systemic-to-pulmonary shunt as initial palliation in patients with univentricular heart
Authors: Grozdanov Dimitrij , Osawa Takuya , Borgmann Kristina , Schaeffer Thibault , Staehler Helena , Di Padua Chiara , Heinisch Paul Philipp , Piber Nicole , Georgiev Stanimir , Hager Alfred , Ewert Peter , Hörer Jürgen , Ono Masamichi 
Published: January 2024

Abstract

OBJECTIVES
In this study, we aimed to compare infants with univentricular hearts who underwent an initial ductus stenting to those receiving a surgical systemic-to-pulmonary shunt (SPS).

METHODS
All infants with univentricular heart and ductal-dependent pulmonary blood flow who underwent initial palliation with either a ductus stenting or a surgical SPS between 2009 and 2022 were reviewed. Outcomes were compared after ductus stenting or SPS including survival, probability of re-interventions and the probability to reach stage II palliations.

RESULTS
A total of 130 patients were evaluated, including 49 ductus stenting and 81 SPSs. The most frequent primary diagnosis was tricuspid atresia in 27, followed by pulmonary atresia with intact ventricular septum in 19 patients. There was comparable hospital mortality (2.0% stent vs 3.7% surgery, P = 0.91) between the groups, but shorter intensive care unit stay (median 1 vs 7 days, P &lt; 0.01) and shorter hospital stay (median 7 vs 17 days, P &lt; 0.01) were observed in patients with initial ductus stenting, compared to those with SPS. However, acute procedure-related complications were more frequently observed in patients with ductus stenting, compared with those with SPS (20.4 vs 6.2%, P = 0.01), and 10 patients needed a shunt procedure after the initial ductus stent. The cumulative incidence of reaching stage II was similar between ductus stenting and SPS (88.0 vs 90.6% at 12 months, P = 0.735). Pulmonary artery (PA) index (median 194 vs 219 mm2/m2, P = 0.93) at stage II was similar between patients with ductus stenting and SPS. However, the ratio of the left to the right PA index [0.69 (0.45–0.95) vs 0.86 (0.51–0.84), P = 0.015] was higher in patients who reached stage II with surgical shunt physiology, compared with patients with ductus stent physiology.

CONCLUSIONS
After initial ductus stenting in infants with univentricular heart, survival is comparable and post-procedural recovery shorter, but more acute stent dysfunctions and lower development of left PA are observed, compared to acute shunt dysfunctions. The less invasive procedure and shorter hospital stay are at the expense of more stent reinterventions.
Up-regulated small-conductance calcium-activated potassium currents contribute to atrial arrhythmogenesis in high-fat feeding mice
Authors: Tsai Wei-Chung , Lin Yi-Hsiung , Kuo Chia-Hao , Jhuo Shih-Jie , Shih Ruo-Yun , Wu Chun-Chieh , Liu I Hsin , Huang Tien-Chi , Liu Ren-Ming , Lin Tsung-Hsien , Su Ho-Ming , Lai Wen-Ter , Lee Chien-Hung , Wu Bin-Nan , Lin Shien-Fong , Lee Hsiang-Chun 
Published: January 2024

Abstract

Aims
Metabolic syndrome (MetS) is associated with arrhythmias and cardiovascular mortality. Arrhythmogenesis in MetS results from atrial structural and electrical remodelling. The small-conductance Ca2+-activated K+ (SK) currents modulate atrial repolarization and may influence atrial arrhythmogenicity. This study investigated the regulation of SK current perturbed by a high-fat diet (HFD) to mimic MetS.

Methods and results
Thirty mice were divided into two groups that were fed with normal chow (CTL) and HFD for 4 months. Electrocardiography and echocardiography were used to detect cardiac electrical and structure remodelling. Atrial action potential duration (APD) and calcium transient duration (CaTD) were measured by optical mapping of Langendorff-perfused mice hearts. Atrial fibrillation (AF) inducibility and duration were assessed by burst pacing. Whole-cell patch clamp was performed in primarily isolated atrial myocytes for SK current density. The SK current density is higher in atrial myocytes from HFD than in CTL mice (P ≤ 0.037). The RNA and protein expression of SK channels are increased in HFD mice (P ≤ 0.041 and P ≤ 0.011, respectively). Action potential duration is shortened in HFD compared with CTL (P ≤ 0.015). The shortening of the atrial APD in HFD is reversed by the application of 100 nM apamin (P ≤ 0.043). Compared with CTL, CaTD is greater in HFD atria (P ≤ 0.029). Calcium transient decay (Tau) is significantly higher in HFD than in CTL (P = 0.001). Both APD and CaTD alternans thresholds were higher in HFD (P ≤ 0.043), along with higher inducibility and longer duration of AF in HFD (P ≤ 0.023).

Conclusion
Up-regulation of apamin-sensitive SK currents plays a partial role in the atrial arrhythmogenicity of HFD mice.
Parent perceptions of school meals and how perceptions differ by race and ethnicity
Authors: Zuercher Monica D , Cohen Juliana F W , Ohri-Vachaspati Punam , Hecht Christina A , Hecht Kenneth , Polacsek Michele , Olarte Deborah A , Read Margaret , Patel Anisha I , Schwartz Marlene B , Chapman Leah E , Orta-Aleman Dania , Ritchie Lorrene D , Gosliner Wendi 
Published: January 2024

Abstract
Parental perceptions of school meals can affect student participation and overall support for school meal policies. Little is known about parental school meal perceptions under universal free school meals (UFSM) policies. We assessed California parents' perceptions of school meals during the COVID-19 emergency response with federally funded UFSM and whether perceptions differed by race/ethnicity. Among 1110 California parents of K–12 students, most reported school meals benefit their families, saving them money (81.6%), time (79.2%), and stress (75.0%). Few reported that their child would be embarrassed to eat school meals (11.7%), but more parents of White students than Hispanic students reported this. Many parents reported that their child likes to eat lunch to be with friends (64.7%); about half felt their child has enough time to eat (54.2%). Fewer parents perceived school lunches to be of good quality (36.9%), tasty (39.6%), or healthy (44.0%). Parents of Hispanic and Asian students had less favorable perceptions of school meal quality, taste, and healthfulness than parents of White students. Parents report that school meals benefit their families, but policy efforts are needed to ensure schools have the resources needed to address cultural appropriateness. Schools should address parental perceptions of meals to optimize participation, nutrition security, and health.
Identification of a Spike-Specific CD8+ T-Cell Epitope Following Vaccination Against the Middle East Respiratory Syndrome Coronavirus in Humans
Authors: Harrer Caroline E , Mayer Leonie , Fathi Anahita , Lassen Susan , Ly My L , Zinser Madeleine E , Wolf Timo , Becker Stephan , Sutter Gerd , Dahlke Christine , Addo Marylyn M ,   for the MVA-MERS-S Study Group, Bartels Etienne , Friedrich Monika , Weskamm Leonie M , Grundlach Swantje , Poetsch Joseph H , Koch Till , Schmiedel Stefan , Haagmanns Bart , Hesterkamp Thomas , Krähling Verena , Volz Asisa , Ditt Vanessa A , Kessler Melanie 
Published: January 2024

Abstract
Licensed vaccines against the Middle East respiratory syndrome coronavirus (MERS-CoV), an emerging pathogen of concern, are lacking. The modified vaccinia virus Ankara vector-based vaccine MVA-MERS-S, expressing the MERS-CoV-spike glycoprotein (MERS-S), is one of 3 candidate vaccines in clinical development and elicits robust humoral and cellular immunity. Here, we identified for the first time a MERS-S–specific CD8+ T-cell epitope in an HLA-A*03:01/HLA-B*35:01-positive vaccinee using a screening assay, intracellular cytokine staining, and in silico epitope prediction. As evidence from MERS-CoV infection suggests a protective role of long-lasting CD8+ T-cell responses, the identification of epitopes will facilitate longitudinal analyses of vaccine-induced T-cell immunity.
Host species and geography impact bee-associated RNA virus communities with evidence for isolation by distance in viral populations
Authors: Robinson Chris R P , Dolezal Adam G , Newton Irene L G 
Published: January 2024

Abstract
Virus symbionts are important mediators of ecosystem function, yet we know little of their diversity and ecology in natural populations. The alarming decline of pollinating insects in many regions of the globe, especially the European honey bee, Apis mellifera, has been driven in part by worldwide transmission of virus pathogens. Previous work has examined the transmission of known honey bee virus pathogens to wild bee populations, but only a handful of studies have investigated the native viromes associated with wild bees, limiting epidemiological predictors associated with viral pathogenesis. Further, variation among different bee species might have important consequences in the acquisition and maintenance of bee-associated virome diversity. We utilized comparative metatranscriptomics to develop a baseline description of the RNA viromes associated with wild bee pollinators and to document viral diversity, community composition, and structure. Our sampling includes five wild-caught, native bee species that vary in social behavior as well as managed honey bees. We describe 26 putatively new RNA virus species based on RNA-dependent RNA polymerase phylogeny and show that each sampled bee species was associated with a specific virus community composition, even among sympatric populations of distinct host species. From 17 samples of a single host species, we recovered a single virus species despite over 600 km of distance between host populations and found strong evidence for isolation by distance in associated viral populations. Our work adds to the small number of studies examining viral prevalence and community composition in wild bees.
Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions
Authors: Schauberger Clemens , Thamdrup Bo , Lemonnier Clarisse , Trouche Blandine , Poulain Julie , Wincker Patrick , Arnaud-Haond Sophie , Glud Ronnie N , Maignien Lois 
Published: January 2024

Abstract
Hadal sediments are hotspots of microbial activity in the deep sea and exhibit strong biogeochemical gradients. But although these gradients are widely assumed to exert selective forces on hadal microbial communities, the actual relationship between biogeochemistry, functional traits, and microbial community structure remains poorly understood. We tested whether the biogeochemical conditions in hadal sediments select for microbes based on their genomic capacity for respiration and carbohydrate utilization via a metagenomic analysis of over 153 samples from the Atacama Trench region (max. depth = 8085 m). The obtained 1357 non-redundant microbial genomes were affiliated with about one-third of all known microbial phyla, with more than half belonging to unknown genera. This indicated that the capability to withstand extreme hydrostatic pressure is a phylogenetically widespread trait and that hadal sediments are inhabited by diverse microbial lineages. Although community composition changed gradually over sediment depth, these changes were not driven by selection for respiratory or carbohydrate degradation capability in the oxic and nitrogenous zones, except in the case of anammox bacteria and nitrifying archaea. However, selection based on respiration and carbohydrate degradation capacity did structure the communities of the ferruginous zone, where aerobic and nitrogen respiring microbes declined exponentially (half-life = 125–419 years) and were replaced by subsurface communities. These results highlight a delayed response of microbial community composition to selective pressure imposed by redox zonation and indicated that gradual changes in microbial composition are shaped by the high-resilience and slow growth of microbes in the seafloor.
Development of a rapid and highly accurate method for 13C tracer-based metabolomics and its application on a hydrogenotrophic methanogen
Authors: Fukuyama Yuto , Shimamura Shigeru , Sakai Sanae , Michimori Yuta , Sumida Tomomi , Chikaraishi Yoshito , Atomi Haruyuki , Nunoura Takuro 
Published: January 2024

Abstract
Microfluidic capillary electrophoresis-mass spectrometry (CE-MS) is a rapid and highly accurate method to determine isotopomer patterns in isotopically labeled compounds. Here, we developed a novel method for tracer-based metabolomics using CE-MS for underivatized proteinogenic amino acids. The method consisting of a ZipChip CE system and a high-resolution Orbitrap Fusion Tribrid mass spectrometer allows us to obtain highly accurate data from 1 μl of 100 nmol/l amino acids comparable to a mere 1 $\times$ 104–105 prokaryotic cells. To validate the capability of the CE-MS method, we analyzed 16 protein-derived amino acids from a methanogenic archaeon Methanothermobacter thermautotrophicus as a model organism, and the mass spectra showed sharp peaks with low mass errors and background noise. Tracer-based metabolome analysis was then performed to identify the central carbon metabolism in M. thermautotrophicus using 13C-labeled substrates. The mass isotopomer distributions of serine, aspartate, and glutamate revealed the occurrence of both the Wood–Ljungdahl pathway and an incomplete reductive tricarboxylic acid cycle for carbon fixation. In addition, biosynthesis pathways of 15 amino acids were constructed based on the mass isotopomer distributions of the detected protein-derived amino acids, genomic information, and public databases. Among them, the presence of alternative enzymes of alanine dehydrogenase, ornithine cyclodeaminase, and homoserine kinase was suggested in the biosynthesis pathways of alanine, proline, and threonine, respectively. To our knowledge, the novel 13C tracer-based metabolomics using CE-MS can be considered the most efficient method to identify central carbon metabolism and amino acid biosynthesis pathways and is applicable to any kind of isolated microbe.
Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum
Authors: Chaumier Timothée , Yang Feng , Manirakiza Eric , Ait-Mohamed Ouardia , Wu Yue , Chandola Udita , Jesus Bruno , Piganeau Gwenael , Groisillier Agnès , Tirichine Leila 
Published: January 2024

Abstract
Diatoms, a prominent group of phytoplankton, have a significant impact on both the oceanic food chain and carbon sequestration, thereby playing a crucial role in regulating the climate. These highly diverse organisms show a wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent a vital source of bioactive compounds that are widely used in biotechnology applications. In the present study, we investigated the genetic and transcriptomic diversity of 17 accessions of the model diatom Phaeodactylum tricornutum including those sampled a century ago as well as more recently collected accessions. The analysis of the data reveals a higher genetic diversity and the emergence of novel clades, indicating an increasing diversity within the P. tricornutum population structure, compared to the previous study and a persistent long-term balancing selection of genes in old and newly sampled accessions. However, the study did not establish a clear link between the year of sampling and genetic diversity, thereby, rejecting the hypothesis of loss of heterozygoty in cultured strains. Transcript analysis identified novel transcript including noncoding RNA and other categories of small RNA such as PiwiRNAs. Additionally, transcripts analysis using differential expression as well as Weighted Gene Correlation Network Analysis has provided evidence that the suppression or downregulation of genes cannot be solely attributed to loss-of-function mutations. This implies that other contributing factors, such as epigenetic modifications, may play a crucial role in regulating gene expression. Our study provides novel genetic resources, which are now accessible through the platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), that offer both ease of use and advanced tools to further investigate microalgae biology and ecology, consequently enriching our current understanding of these organisms.
Rich diversity and active spatial–temporal dynamics ofThalassiosiraspecies revealed by time-series metabarcoding analysis
Authors: Liu Kuiyan , Liu Shuya , Cui Zongmei , Zhao Yongfang , Chen Nansheng 
Published: January 2024

AbstractThalassiosira is a species-rich genus in Bacillariophyta that not only contributes positively as primary producer, but also poses negative impacts on ecosystems by causing harmful algal blooms. Although taxonomical studies have identified a large number of Thalassiosira species, however, the composition of Thalassiosira species and their geographical distribution in marine ecosystems were not well understood due primarily to the lack of resolution of morphology-based approaches used previously in ecological expeditions. In this study, we systematically analyzed the composition and spatial–temporal dynamic distributions of Thalassiosira in the model marine ecosystem Jiaozhou Bay by applying metabarcoding analysis. Through analyzing samples collected monthly from 12 sampling sites, 14 Thalassiosira species were identified, including five species that were not previously reported in Jiaozhou Bay, demonstrating the resolution and effectiveness of metabarcoding analysis in ecological research. Many Thalassiosira species showed prominent temporal preferences in Jiaozhou Bay, with some displaying spring–winter preference represented by Thalassiosira tenera, while others displaying summer–autumn preference represented by Thalassiosira lundiana and Thalassiosira minuscula, indicating that the temperature is an important driving factor in the temporal dynamics. The application of metabarcoding analysis, equipped with appropriate molecular markers with high resolution and high specificity and databases of reference molecular marker sequences for potential all Thalassiosira species, will revolutionize ecological research of Thalassiosira species in Jiaozhou Bay and other marine ecosystems.
Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components
Authors: Duan Changhai , Liu Yang , Liu Ying , Liu Lirui , Cai Mingwei , Zhang Rui , Zeng Qinglu , Koonin Eugene V , Krupovic Mart , Li Meng 
Published: January 2024

Abstract
Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family “Fuxiviridae” harbor an atypical Type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family “Chiyouviridae” encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibit host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.
Wild plant species with broader precipitation niches exhibit stronger host selection in rhizosphere microbiome assembly
Authors: Ma Haikun , Liu Jinming , Mo Lidong , Arias-Giraldo Luisa M , Xiang Meichun , Liu Xingzhong 
Published: January 2024

Abstract
Plants actively recruit microbes from the soil, forming species-specific root microbiomes. However, their relationship with plant adaptations to temperature and precipitation remains unclear. Here we examined the host-selected and conserved microbiomes of 13 native plant species in the Xilingol steppe, Inner Mongolia, a semi-arid region in China. By calculating the global precipitation and temperature niches of these plants, considering plant phylogenetic distances, and analyzing functional traits, we found that these factors significantly influenced the rhizosphere microbiome assembly. We further quantified the strength of host selection and observed that plants with wider precipitation niches exhibited greater host selection strength in their rhizosphere microbiome assembly and higher rhizosphere bacterial diversity. In general, the rhizosphere microbiome showed a stronger link to plant precipitation niches than temperature niches. Haliangium exhibited consistent responsiveness to host characteristics. Our findings offer novel insights into host selection effects and the ecological determinants of wild plant rhizosphere microbiome assembly, with implications for steering root microbiomes of wild plants and understanding plant-microbiome evolution.
Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments
Authors: Zheng Yue , Wang Baozhan , Gao Ping , Yang Yiyan , Xu Bu , Su Xiaoquan , Ning Daliang , Tao Qing , Li Qian , Zhao Feng , Wang Dazhi , Zhang Yao , Li Meng , Winkler Mari-K H , Ingalls Anitra E , Zhou Jizhong , Zhang Chuanlun , Stahl David A , Jiang Jiandong , Martens-Habbena Willm , Qin Wei 
Published: January 2024

Abstract
Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.