bluuebunny/crossref_metadata_2025 huggingface dataset:
Defective Assistive Device Involvement in Older Adult Emergency Department Visits
Authors: Restrepo Felipe , Mali Namrata , Sands Laura P , Abrahams Alan , Goldberg David M , Gruss Richard , Zaman Nohel , Shields Wendy , Omaki Elise , Ehsani Johnathon , Ractham Peter , Kaewkitipong Laddawan
Published: January 2024

Background and Objectives

Many older adults adopt equipment to address physical limitations and reduce dependence on others to complete basic activities of daily living. Although a few prior studies have considered injuries associated with assistive devices for older adults, those studies focused on older adults’ health and functional risks for injury. There is limited analysis of older adult injuries involving defective or malfunctioning assistive devices.

Research Design and Methods

Data from this study are from the National Electronic Surveillance System All Injury Program which collected data on consumer product-related injuries from a probability sample of 66 hospital Emergency Departments across the United States. Data from 30 776 older adult Emergency Department (ED) injury narratives from 2016 to 2020 were coded according to the assistive device involved and whether malfunctioning led to the injury. The study team manually examined all narratives in which the assistive device was coded to have malfunctioned.

Results

A total of 10 974 older adult ED cases were treated for 12 488 injuries involving a defective device. Injuries included 4 212 head and neck injuries (eg, concussion), 4 317 trunk injuries (eg, hip fractures), and 3 959 arm or leg injuries (eg, leg fracture). Of these patients, 4 586 were admitted to a hospital ward for further evaluation and treatment. Seventy percent of these patients were injured while using a walker; in contrast, wheelchairs were implicated in only 4% of the above cases. Design flaws were identified in 8 158 cases and part breakage/decoupling incidents in 2 816 cases.

Discussion and Implications

Our findings provide evidence that assistive devices are actively involved in older adult injuries. Further research is needed to reduce injuries associated with assistive devices by educating patients and their careproviders about device use and assembly and developing effective methods for informing manufacturers about malfunctioning devices.
Transcriptome Dynamics and Cell Dialogs Between Oocytes and Granulosa Cells in Mouse Follicle Development
Authors: Liu Wenju , Chen Chuan , Gao Yawei , Cui Xinyu , Zhang Yuhan , Gu Liang , He Yuanlin , Li Jing , Gao Shaorong , Gao Rui , Jiang Cizhong
Published: January 2024

The development and maturation of follicles is a sophisticated and multistage process. The dynamic gene expression of oocytes and their surrounding somatic cells and the dialogs between these cells are critical to this process. In this study, we accurately classified the oocyte and follicle development into nine stages and profiled the gene expression of mouse oocytes and their surrounding granulosa cells and cumulus cells. The clustering of the transcriptomes showed the trajectories of two distinct development courses of oocytes and their surrounding somatic cells. Gene expression changes precipitously increased at Type 4 stage and drastically dropped afterward within both oocytes and granulosa cells. Moreover, the number of differentially expressed genes between oocytes and granulosa cells dramatically increased at Type 4 stage, most of which persistently passed on to the later stages. Strikingly, cell communications within and between oocytes and granulosa cells became active from Type 4 stage onward. Cell dialogs connected oocytes and granulosa cells in both unidirectional and bidirectional manners. TGFB2/3, TGFBR2/3, INHBA/B, and ACVR1/1B/2B of TGF-β signaling pathway functioned in the follicle development. NOTCH signaling pathway regulated the development of granulosa cells. Additionally, many maternally DNA methylation- or H3K27me3-imprinted genes remained active in granulosa cells but silent in oocytes during oogenesis. Collectively, Type 4 stage is the key turning point when significant transcription changes diverge the fate of oocytes and granulosa cells, and the cell dialogs become active to assure follicle development. These findings shed new insights on the transcriptome dynamics and cell dialogs facilitating the development and maturation of oocytes and follicles.
Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses
Authors: Shan Ke-Jia , Wu Changcheng , Tang Xiaolu , Lu Roujian , Hu Yaling , Tan Wenjie , Lu Jian
Published: January 2024

The monkeypox virus (mpox virus, MPXV) epidemic in 2022 has posed a significant public health risk. Yet, the evolutionary principles of MPXV remain largely unknown. Here, we examined the evolutionary patterns of protein sequences and codon usage in MPXV. We first demonstrated the signal of positive selection in OPG027, specifically in the Clade I lineage of MPXV. Subsequently, we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 outbreak. Furthermore, we showed strong epistasis between amino acid substitutions located in different genes. The codon adaptation index (CAI) analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes, and the CAI decreased over time and diverged between clades, with Clade I > IIa and IIb-A > IIb-B. While the decrease in fatality rate among the three groups aligned with the CAI pattern, it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality rates. This study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.
Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products
Authors: Yu Tao , Luo Yingfeng , Tan Xinyu , Zhao Dahe , Bi Xiaochun , Li Chenji , Zheng Yanning , Xiang Hua , Hu Songnian
Published: January 2024

Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. Here, by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiomes. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes, which represent 1895 species spanning 105 phyla. In addition, beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences potentially encode novel natural products, with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.
DVsc: An Automated Framework for Efficiently Detecting Viral Infection from Single-cell Transcriptomics Data
Authors: Leng Fei , Mei Song , Zhou Xiaolin , Liu Xuanshi , Yuan Yefeng , Xu Wenjian , Hao Chongyi , Guo Ruolan , Hao Chanjuan , Li Wei , Zhang Peng
Published: January 2024

Single-cell RNA sequencing (scRNA-seq) has emerged as a valuable tool for studying cellular heterogeneity in various fields, particularly in virological research. By studying the viral and cellular transcriptomes, the dynamics of viral infection can be investigated at a single-cell resolution. However, limited studies have been conducted to investigate whether RNA transcripts from clinical samples contain substantial amounts of viral RNAs, and a specific computational framework for efficiently detecting viral reads based on scRNA-seq data has not been developed. Hence, we introduce DVsc, an open-source framework for precise quantitative analysis of viral infection from single-cell transcriptomics data. When applied to approximately 200 diverse clinical samples that were infected by more than 10 different viruses, DVsc demonstrated high accuracy in systematically detecting viral infection across a wide array of cell types. This innovative bioinformatics pipeline could be crucial for addressing the potential effects of surreptitiously invading viruses on certain illnesses, as well as for designing novel medicines to target viruses in specific host cell subsets and evaluating the efficacy of treatment. DVsc supports the FASTQ format as an input and is compatible with multiple single-cell sequencing platforms. Moreover, it could also be applied to sequences from bulk RNA sequencing data. DVsc is available at http://62.234.32.33:5000/DVsc.
TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning
Authors: Yeh Shan-Ju , Paithankar Shreya , Chen Ruoqiao , Xing Jing , Sun Mengying , Liu Ke , Zhou Jiayu , Chen Bin
Published: January 2024

Gene expression profiling of new or modified cell lines becomes routine today; however, obtaining comprehensive molecular characterization and cellular responses for a variety of cell lines, including those derived from underrepresented groups, is not trivial when resources are minimal. Using gene expression to predict other measurements has been actively explored; however, systematic investigation of its predictive power in various measurements has not been well studied. Here, we evaluated commonly used machine learning methods and presented TransCell, a two-step deep transfer learning framework that utilized the knowledge derived from pan-cancer tumor samples to predict molecular features and responses. Among these models, TransCell had the best performance in predicting metabolite, gene effect score (or genetic dependency), and drug sensitivity, and had comparable performance in predicting mutation, copy number variation, and protein expression. Notably, TransCell improved the performance by over 50% in drug sensitivity prediction and achieved a correlation of 0.7 in gene effect score prediction. Furthermore, predicted drug sensitivities revealed potential repurposing candidates for new 100 pediatric cancer cell lines, and predicted gene effect scores reflected BRAF resistance in melanoma cell lines. Together, we investigated the predictive power of gene expression in six molecular measurement types and developed a web portal (http://apps.octad.org/transcell/) that enables the prediction of 352,000 genomic and cellular response features solely from gene expression profiles.
Rethinking pragmatism through the lens of Michel Foucault: governance of bilateral relations
Authors: Chowdhury Suban Kumar
Published: January 2024

Pragmatism, responding to the call for ‘decentring International Relations’, fosters analytical eclecticism for resolving inter-paradigmatic disputes. John Dewey's pragmatism aligns seamlessly with constructivism, offering nuanced insights. However, in bilateral relations, pragmatism is often confined within realist frameworks, lacking analytical rigor for understanding governmentality. In this article, the author challenges this by emphasizing relational power dynamics and non-neutral knowledge, introducing ‘balancing pragmatism’ rooted in ‘bricolage’ for nuanced governance. Leveraging Foucauldian insights, the author reconceptualizes governance pragmatism within the power-knowledge interplay, illustrated by the India–Bangladesh Land Boundary Agreement (LBA). The LBA's success challenges realist power paradigms, recognizing the pivotal role of Foucauldian dynamics in enhancing pragmatic balancing. This enriches the constructivist paradigm with discerning governance. Interpreting pragmatism through a Foucauldian lens in the LBA underscores implications for bilateral governance, highlighting analytical eclecticism and adaptability within a Foucauldian framework to address geopolitical challenges. It advocates for a more inclusive analytical approach in international relations. Understanding ‘balancing pragmatism’ is crucial for practitioners, challenging the state-centric paradigm and emphasizing nuanced governance through the transformative intersection of power and knowledge. Interpreting pragmatism as a Foucauldian-informed balancing act, as seen in the LBA, holds broad implications for IR, urging scholars to integrate Foucault's dynamics for nuanced global analyses of pragmatic balancing.
Imagining Collective Reincorporation: Perceptions of Colombia’s Novel Approach to Peacebuilding
Authors: O’Brien Colleen Alena
Published: January 2024

In Colombia, the FARC and the Colombian government have adopted a new term, ‘reincorporation,’ to refer to the FARC’s simultaneous and collective transition into society, in contrast to past programmes in which ex-combatants individually transitioned back into civilian society (generally known as ‘reintegration’). This collectivist approach is unprecedented in postconflict societies. In this Note from the Field, I seek to offer observations about this collective process of reintegration based on ethnographic fieldwork and suggest how ethnography can reveal new imaginaries for DDR scenarios.
Gut Microbiota Alterations and Circulating Imidazole Propionate Levels Are Associated With Obstructive Coronary Artery Disease in People With HIV
Authors: Trøseid Marius , Molinaro Antonio , Gelpi Marco , Vestad Beate , Kofoed Klaus Fuglsang , Fuchs Andreas , Køber Lars , Holm Kristian , Benfield Thomas , Ueland Per M , Hov Johannes R , Nielsen Susanne Dam , Knudsen Andreas Dehlbæk
Published: January 2024

Background

The impact of gut microbiota and its metabolites on coronary artery disease (CAD) in people with human immunodeficiency virus (PWH) is unknown. Emerging evidence suggests that imidazole propionate (ImP), a microbial metabolite, is linked with cardiometabolic diseases.

Methods

Fecal samples from participants of the Copenhagen Comorbidity in HIV infection (COCOMO) study were processed for 16S rRNA sequencing and ImP measured with liquid chromatography-tandem mass spectrometry. CAD severity was investigated by coronary computed tomography-angiography, and participants grouped according to obstructive CAD (n = 60), nonobstructive CAD (n = 80), or no CAD (n = 114).

Results

Participants with obstructive CAD had a gut microbiota with lower diversity and distinct compositional shift, with increased abundance of Rumiococcus gnavus and Veillonella, known producers of ImP. ImP plasma levels were associated with this dysbiosis, and significantly elevated in participants with obstructive CAD. However, gut dysbiosis but not plasma ImP was independently associated with obstructive CAD after adjustment for traditional and HIV-related risk factors (adjusted odds ratio, 2.7; 95% confidence interval, 1.1–7.2; P = .048).

Conclusions

PWH with obstructive CAD displays a distinct gut microbiota profile and increased circulating ImP plasma levels. Future studies should determine whether gut dysbiosis and related metabolites such as ImP are predictive of incident cardiovascular events.
Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets
Authors: Mazel Florent , Pitteloud Camille , Guisan Antoine , Pellissier Loïc
Published: January 2024

Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont communities are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e. harbor host specificity) and host phylogeny (i.e. harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g. endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g. most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e. hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. Although elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher host specificity in endosymbionts corroborates the idea that—everything else being equal—vertically transmitted microbes harbor stronger host specificity signal, but the absence of phylosymbiosis suggests that host specificity changes quickly on evolutionary time scales.
Anaerobic hexadecane degradation by a thermophilic Hadarchaeon from Guaymas Basin
Authors: Benito Merino David , Lipp Julius S , Borrel Guillaume , Boetius Antje , Wegener Gunter
Published: January 2024

Hadarchaeota inhabit subsurface and hydrothermally heated environments, but previous to this study, they had not been cultured. Based on metagenome-assembled genomes, most Hadarchaeota are heterotrophs that grow on sugars and amino acids, or oxidize carbon monoxide or reduce nitrite to ammonium. A few other metagenome-assembled genomes encode alkyl-coenzyme M reductases (Acrs), β-oxidation, and Wood-Ljungdahl pathways, pointing toward multicarbon alkane metabolism. To identify the organisms involved in thermophilic oil degradation, we established anaerobic sulfate-reducing hexadecane-degrading cultures from hydrothermally heated sediments of the Guaymas Basin. Cultures at 70°C were enriched in one Hadarchaeon that we propose as Candidatus Cerberiarchaeum oleivorans. Genomic and chemical analyses indicate that Ca. C. oleivorans uses an Acr to activate hexadecane to hexadecyl-coenzyme M. A β-oxidation pathway and a tetrahydromethanopterin methyl branch Wood–Ljungdahl (mWL) pathway allow the complete oxidation of hexadecane to CO2. Our results suggest a syntrophic lifestyle with sulfate reducers, as Ca. C. oleivorans lacks a sulfate respiration pathway. Comparative genomics show that Acr, mWL, and β-oxidation are restricted to one family of Hadarchaeota, which we propose as Ca. Cerberiarchaeaceae. Phylogenetic analyses further indicate that the mWL pathway is basal to all Hadarchaeota. By contrast, the carbon monoxide dehydrogenase/acetyl-coenzyme A synthase complex in Ca. Cerberiarchaeaceae was horizontally acquired from Bathyarchaeia. The Acr and β-oxidation genes of Ca. Cerberiarchaeaceae are highly similar to those of other alkane-oxidizing archaea such as Ca. Methanoliparia and Ca. Helarchaeales. Our results support the use of Acrs in the degradation of petroleum alkanes and suggest a role of Hadarchaeota in oil-rich environments.
Dynamic nitrogen fixation in an aerobic endophyte of Populus
Authors: Sher Andrew W , Aufrecht Jayde A , Herrera Daisy , Zimmerman Amy E , Kim Young-Mo , Munoz Nathalie , Trejo Jesse B , Paurus Vanessa L , Cliff John B , Hu Dehong , Chrisler William B , Tournay Robert J , Gomez-Rivas Emma , Orr Galya , Ahkami Amir H , Doty Sharon L
Published: January 2024

Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte–poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant–endophyte interactions.
Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics
Authors: Yu Xiaoqian Annie , McLean Craig , Hehemann Jan-Hendrik , Angeles-Albores David , Wu Fuqing , Muszyński Artur , Corzett Christopher H , Azadi Parastoo , Kujawinski Elizabeth B , Alm Eric J , Polz Martin F
Published: January 2024

Members of microbial communities can substantially overlap in substrate use. However, what enables functionally redundant microorganisms to coassemble or even stably coexist remains poorly understood. Here, we show that during unstable successional dynamics on complex, natural organic matter, functionally redundant bacteria can coexist by partitioning low-concentration substrates even though they compete for one simple, dominant substrate. We allowed ocean microbial communities to self-assemble on leachates of the brown seaweed Fucus vesiculosus and then analyzed the competition among 10 taxonomically diverse isolates representing two distinct stages of the succession. All, but two isolates, exhibited an average of 90% ± 6% pairwise overlap in resource use, and functional redundancy of isolates from the same assembly stage was higher than that from between assembly stages, leading us to construct a simpler four-isolate community with two isolates from each of the early and late stages. We found that, although the short-term dynamics of the four-isolate communities in F. vesiculosus leachate was dependent on initial isolate ratios, in the long term, the four isolates stably coexist in F. vesiculosus leachate, albeit with some strains at low abundance. We therefore explored the potential for nonredundant substrate use by genomic content analysis and RNA expression patterns. This analysis revealed that the four isolates mainly differed in peripheral metabolic pathways, such as the ability to degrade pyrimidine, leucine, and tyrosine, as well as aromatic substrates. These results highlight the importance of fine-scale differences in metabolic strategies for supporting the frequently observed coexistence of large numbers of rare organisms in natural microbiomes.
Biocontrol in built environments to reduce pathogen exposure and infection risk
Authors: Gottel Neil R , Hill Megan S , Neal Maxwell J , Allard Sarah M , Zengler Karsten , Gilbert Jack A
Published: January 2024

The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.
Predominant heterotrophic diazotrophic bacteria are involved in Sargassum proliferation in the Great Atlantic Sargassum Belt
Authors: Léger-Pigout Matéo , Navarro Elisabeth , Ménard Frédéric , Ruitton Sandrine , Le Loc’h François , Guasco Sophie , Munaron Jean-Marie , Thibault Delphine , Changeux Thomas , Connan Solène , Stiger-Pouvreau Valérie , Thibaut Thierry , Michotey Valérie
Published: January 2024

Since 2011, the Caribbean coasts have been subject to episodic influxes of floating Sargassum seaweed of unprecedented magnitude originating from a new area “the Great Atlantic Sargassum Belt” (GASB), leading in episodic influxes and mass strandings of floating Sargassum. For the biofilm of both holopelagic and benthic Sargassum as well as in the surrounding waters, we characterized the main functional groups involved in the microbial nitrogen cycle. The abundance of genes representing nitrogen fixation (nifH), nitrification (amoA), and denitrification (nosZ) showed the predominance of diazotrophs, particularly within the GASB and the Sargasso Sea. In both location, the biofilm associated with holopelagic Sargassum harboured a more abundant proportion of diazotrophs than the surrounding water. The mean δ15N value of the GASB seaweed was very negative (−2.04‰), and lower than previously reported, reinforcing the hypothesis that the source of nitrogen comes from the nitrogen-fixing activity of diazotrophs within this new area of proliferation. Analysis of the diversity of diazotrophic communities revealed for the first time the predominance of heterotrophic diazotrophic bacteria belonging to the phylum Proteobacteria in holopelagic Sargassum biofilms. The nifH sequences belonging to Vibrio genus (Gammaproteobacteria) and Filomicrobium sp. (Alphaproteobacteria) were the most abundant and reached, respectively, up to 46.0% and 33.2% of the community. We highlighted the atmospheric origin of the nitrogen used during the growth of holopelagic Sargassum within the GASB and a contribution of heterotrophic nitrogen-fixing bacteria to a part of the Sargassum proliferation.
Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria
Authors: Luo Zhen-Hao , Li Qi , Xie Yuan-Guo , Lv Ai-Ping , Qi Yan-Ling , Li Meng-Meng , Qu Yan-Ni , Liu Ze-Tao , Li Yu-Xian , Rao Yang-Zhi , Jiao Jian-Yu , Liu Lan , Narsing Rao Manik Prabhu , Hedlund Brian P , Evans Paul N , Fang Yuan , Shu Wen-Sheng , Huang Li-Nan , Li Wen-Jun , Hua Zheng-Shuang
Published: January 2024

Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts on the biogeochemical cycles of carbon and nitrogen. In contrast to these well-studied ammonia-oxidizing archaea (AOA), deep-branching non-AOA within this class remain poorly characterized because of a low number of genome representatives. Here, we reconstructed 128 Nitrososphaeria metagenome-assembled genomes from acid mine drainage and hot spring sediment metagenomes. Comparative genomics revealed that extant non-AOA are functionally diverse, with capacity for carbon fixation, carbon monoxide oxidation, methanogenesis, and respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested that the common ancestor of Nitrososphaeria was likely an aerobic thermophile. We further surmise that the functional differentiation of Nitrososphaeria was primarily shaped by oxygen, pH, and temperature, with the acquisition of pathways for carbon, nitrogen, and sulfur metabolism. Our study provides a more holistic and less biased understanding of the diversity, ecology, and deep evolution of the globally abundant Nitrososphaeria.
CRISPR-Cas in Pseudomonas aeruginosa provides transient population-level immunity against high phage exposures
Authors: Watson Bridget N J , Capria Loris , Alseth Ellinor O , Pons Benoit J , Biswas Ambarish , Lenzi Luca , Buckling Angus , van Houte Stineke , Westra Edze R , Meaden Sean
Published: January 2024

The prokaryotic adaptive immune system, CRISPR-Cas (clustered regularly interspaced short palindromic repeats; CRISPR-associated), requires the acquisition of spacer sequences that target invading mobile genetic elements such as phages. Previous work has identified ecological variables that drive the evolution of CRISPR-based immunity of the model organism Pseudomonas aeruginosa PA14 against its phage DMS3vir, resulting in rapid phage extinction. However, it is unclear if and how stable such acquired immunity is within bacterial populations, and how this depends on the environment. Here, we examine the dynamics of CRISPR spacer acquisition and loss over a 30-day evolution experiment and identify conditions that tip the balance between long-term maintenance of immunity versus invasion of alternative resistance strategies that support phage persistence. Specifically, we find that both the initial phage dose and reinfection frequencies determine whether or not acquired CRISPR immunity is maintained in the long term, and whether or not phage can coexist with the bacteria. At the population genetics level, emergence and loss of CRISPR immunity are associated with high levels of spacer diversity that subsequently decline due to invasion of bacteria carrying pilus-associated mutations. Together, these results provide high resolution of the dynamics of CRISPR immunity acquisition and loss and demonstrate that the cumulative phage burden determines the effectiveness of CRISPR over ecologically relevant timeframes.
Megataxonomy and global ecology of the virosphere
Authors: Koonin Eugene V , Kuhn Jens H , Dolja Valerian V , Krupovic Mart
Published: January 2024

Nearly all organisms are hosts to multiple viruses that collectively appear to be the most abundant biological entities in the biosphere. With recent advances in metagenomics and metatranscriptomics, the known diversity of viruses substantially expanded. Comparative analysis of these viruses using advanced computational methods culminated in the reconstruction of the evolution of major groups of viruses and enabled the construction of a virus megataxonomy, which has been formally adopted by the International Committee on Taxonomy of Viruses. This comprehensive taxonomy consists of six virus realms, which are aspired to be monophyletic and assembled based on the conservation of hallmark proteins involved in capsid structure formation or genome replication. The viruses in different major taxa substantially differ in host range and accordingly in ecological niches. In this review article, we outline the latest developments in virus megataxonomy and the recent discoveries that will likely lead to reassessment of some major taxa, in particular, split of three of the current six realms into two or more independent realms. We then discuss the correspondence between virus taxonomy and the distribution of viruses among hosts and ecological niches, as well as the abundance of viruses versus cells in different habitats. The distribution of viruses across environments appears to be primarily determined by the host ranges, i.e. the virome is shaped by the composition of the biome in a given habitat, which itself is affected by abiotic factors.
The Aesthetic Analysis of a Garden
Authors: Fenner David
Published: January 2024

Offering aesthetic judgments of gardens is common. These judgments follow an evidentiary structure that is common to the evaluation of other aesthetic objects: summary judgments evidenced by the attribution of narrow formal aesthetic properties, “formal-adjacent” aesthetic properties, and relevant contextual relations. Yet, in a garden, these evidencing properties and relations take on forms that are different from those of other aesthetic and/or art objects. In this article, I consider these differences and consider whether aesthetic analyses of gardens rest on one or more conceptual mistakes. In the end, I conclude that we can meet all challenges.
Integrated microbiomics and metabolomics analysis reveals the influence of gut microbiota on the growth and metabolism of sea cucumber seedlings
Authors: Jia Airong , Niu Xinyan , Zhang Miansong , Liu Xue , Cui Tingting , Liu Changheng , Bai Xinfeng
Published: January 2024

Aims

This study explores the impact of gut microbiota on body metabolites and the growth rate of sea cucumber seedlings.

Methods and results

A comprehensive analysis using metabolomics and microbiomics was conducted to ascertain the gut microbiota and body metabolites in sea cucumber seedlings exhibiting varying growth rates. Distinct changes in the intestinal flora were observed in correlation with different growth rates of sea cucumber seedlings. The microbial communities of faster-growing seedlings exhibited greater diversity and evenness of taxa. For example, the abundance of genera Rhodococcus, Woeseia, Lysobacter, Desulfuromonadia_Sva1033, and Flavobacteriaceae_NS5_marine_group was more than 24 times higher in the fast-growing group compared to the slow-growing group. Metabolomics analysis revealed an association between high growth rates of cucumber seedlings and discrepancies in metabolites, such as amino acids, lipids, and carbohydrates. Isorenieratene, possibly synthesized by Rhodococcus, was more than 2.5 times more abundant in the fast-growing group than the slow-growing group. Slow-growing seedlings showed considerable enrichment of environmental pollutants, such as antibiotics and drugs, while their colonies were devoid of bacteria capable of degrading such pollutants. In addition, significant differences were observed between groups in the biosynthesis of amino acids, metabolism of arginine and proline, biosynthesis of unsaturated fatty acids, and metabolism of linoleic acid. Moreover, significant correlations between the microbial genera and sea cucumber metabolites were identified through correlation analysis.

Conclusions

Significant differences exist in the gut microbiota and metabolite composition among seedlings with varying growth rates. Microbes residing in the gut have the potential to influence the growth of seedlings through modulation of their metabolism.
Impaired muscle parameters in adults with mild to severe types of osteogenesis imperfecta: a cross-sectional study
Authors: Coussens Marie , Lapauw Bruno , De Wandele Inge , Malfait Fransiska , Pocovi Natasha C , Pacey Verity , Calders Patrick
Published: January 2024

Impaired muscle parameters may further compromise the already compromised skeleton in individuals with OI. This cross-sectional study aimed to compare muscle function and body composition in adults with various OI types and healthy controls. Sixty-eight adults with OI (mean age 42.2 yr; 27 men) and 68 healthy age- and sex-matched controls were recruited. Maximal isometric muscle force was assessed by handheld dynamometry (hand grip, hip flexors, shoulder abductors, and ankle dorsiflexors), muscle endurance by posture maintenance tests (shoulder abduction, hip flexion, and wall sit), and functional lower limb strength by 30-s chair rise test. In a sub cohort, dynamic muscle function (peak power and force) was assessed by a ground reaction force plate, and lean and fat mass, muscle and fat cross-sectional area (CSA), and muscle density by dual-energy X-ray absorptiometry and peripheral quantitative computed tomography. Multiple linear regression models were fitted with group (OI type I, III, IV/V, or controls), country, sex, and age in the fixed effects part. Overall, adults with various types of OI had lower isometric, endurance, and functional muscle strength (mean difference [MD] = OI type I: 19–43%, OI type IV/V: 25–68%, OI type III: 20–72%) compared to controls. Furthermore, adults with OI type I had lower dynamic muscle function (peak force [MD = 25–29%] and power [MD = 18–60%]), lean mass (MD = 10–17%), muscle CSA (MD = 9–21%), and muscle density (MD = 2–3%) but higher adiposity indices (MD = 24–42%) compared to controls. Functional lower limb strength and maximal muscle force were significantly different between OI types, whereas muscle endurance was not.

To conclude, adults with OI present with markedly impaired muscle function which may partially be explained by their altered body composition. Our findings emphasize the need for proper assessment of various muscle parameters and (research into) appropriate and safe muscle strengthening approaches in this population.
Influence of vitamin D supplementation on bone mineral content, bone turnover markers, and fracture risk in South African schoolchildren: multicenter double-blind randomized placebo-controlled trial (ViDiKids)
Authors: Middelkoop Keren , Micklesfield Lisa K , Walker Neil , Stewart Justine , Delport Carmen , Jolliffe David A , Mendham Amy E , Coussens Anna K , van Graan Averalda , Nuttall James , Tang Jonathan C Y , Fraser William D , Cooper Cyrus , Harvey Nicholas C , Hooper Richard L , Wilkinson Robert J , Bekker Linda-Gail , Martineau Adrian R
Published: January 2024

Randomized controlled trials (RCTs) to determine the influence of vitamin D on BMC and fracture risk in children of Black African ancestry are lacking. We conducted a sub-study (n = 450) nested within a phase 3 RCT of weekly oral supplementation with 10 000 IU vitamin D3 vs placebo for 3 yr in HIV-uninfected Cape Town schoolchildren aged 6–11 yr. Outcomes were BMC at the whole body less head (WBLH) and LS and serum 25-hydroxyvitamin D3 (25(OH)D3), PTH, alkaline phosphatase, C-terminal telopeptide, and PINP. Incidence of fractures was a secondary outcome of the main trial (n = 1682). At baseline, mean serum 25(OH)D3 concentration was 70.0 nmol/L (SD 13.5), and 5.8% of participants had serum 25(OH)D3 concentrations <50 nmol/L. Among sub-study participants, end-trial serum 25(OH)D3 concentrations were higher for participants allocated to vitamin D vs placebo (adjusted mean difference [aMD] 39.9 nmol/L, 95% CI, 36.1 to 43.6) and serum PTH concentrations were lower (aMD −0.55 pmol/L, 95% CI, −0.94 to −0.17). However, no interarm differences were seen for WBLH BMC (aMD −8.0 g, 95% CI, −30.7 to 14.7) or LS BMC (aMD −0.3 g, 95% CI, −1.3 to 0.8) or serum concentrations of bone turnover markers. Fractures were rare among participants in the main trial randomized to vitamin D vs placebo (7/755 vs 10/758 attending at least 1 follow-up; adjusted odds ratio 0.70, 95% CI, 0.27 to 1.85). In conclusion, a 3-yr course of weekly oral vitamin D supplementation elevated serum 25(OH)D3 concentrations and suppressed serum PTH concentrations in HIV-uninfected South African schoolchildren of Black African ancestry but did not influence BMC or serum concentrations of bone turnover markers. Fracture incidence was low, limiting power to detect an effect of vitamin D on this outcome.
On the Relationship Between German International Criminal Law and Counter-terrorism Criminal Law
Authors: Geneuss Julia
Published: January 2024

In many cases, and, in particular, in cases concerning crimes committed in the Syrian conflict, an overlap can be identified between international criminal law and counter-terrorism criminal law. The reason for this is the approximative and normative intertwining of these two areas in German criminal law. By way of counter-terrorism criminal law, Germany implemented an organizational crime of membership in an organization whose objective or activities are directed towards the commission of, inter alia, genocide, crimes against humanity, and war crimes, as well as murder. As a consequence, non-state armed groups active in a non-international armed conflict are considered terrorist groups. While this allows for cumulative prosecution, charging, and conviction, in this article an argument will be made that the increasing intertwining of German international criminal law and counter-terrorism criminal law has a problematic side. It blurs the historical, conceptual, and normative differences between the two areas of criminal law. Eventually, this further deepens the asymmetry in the prosecution of state and non-state actors for international crimes.
TGFβ macrophage reprogramming: a new dimension of macrophage plasticity
Authors: Oliver Mary A , Davis Xenia D , Bohannon Julia K
Published: January 2024

The August 2023 article in Science Signaling, “TGF-β uncouples glycolysis and inflammation in macrophages and controls survival during sepsis,” challenges the traditional M1/M2 macrophage classification by investigating the impact of transforming growth factor β on macrophage metabolism and function. Despite its conventional anti-inflammatory role, transforming growth factor β–treated macrophages exhibit a distinct phenotype marked by heightened glycolysis, suppressed proinflammatory cytokines, and increased coagulation factor expression. The study identifies phosphofructokinase, liver type as a crucial glycolytic enzyme regulated by transforming growth factor β via the mTOR–c-MYC pathway. Epigenetic changes induced by transforming growth factor β, such as increased Smad3 activation and reduced proinflammatory transcription factor motif enrichment, contribute to the anti-inflammatory profile. The research extends its implications to sepsis, revealing the role of transforming growth factor β in exacerbating coagulation and reducing survival in mouse models. This effect involves upregulation of coagulation factor F13A1, dependent on phosphofructokinase, liver type activity and glycolysis in macrophages. Connections to COVID-19 pathology are drawn, as transforming growth factor β–treated macrophages and SARS-CoV-2 E protein-exposed cells display similar metabolic profiles. Bioinformatic analysis of COVID-19 patient data suggests correlations between myeloid expression of TGFβR1, PFKL, and F13A1 with disease severity. The study challenges the M1/M2 classification, emphasizing the complexity of macrophage responses influenced by transforming growth factor β, proposing transforming growth factor β as a potential therapeutic target for conditions like sepsis and COVID-19 where dysregulated coagulation is significant. Overall, the research provides valuable insights into transforming growth factor β–mediated immunometabolic regulation, paving the way for future investigations and potential therapeutic interventions.
Integrated Behavioral Health Prevention for Infants in Pediatric Primary Care: A Mixed-Methods Pilot Study
Authors: Ammerman Robert T , Rybak Tiffany M , Herbst Rachel B , Mara Constance A , Zion Cynthia , Patel Meera A , Burstein Emma , Lauer Brea A , Fiat Aria E , Jordan Phoebe , Burkhardt Mary Carol , McClure Jessica M , Stark Lori J
Published: January 2024

Objective

Pediatric primary care is a promising setting in which to deliver preventive behavioral health services to young children and their families. Integrated behavioral health care models typically emphasize treatment rather than prevention. This pilot study examined the efficacy of an integrated behavioral health preventive (IBH-P) intervention delivered by psychologists and focused on supporting parenting in low-income mothers of infants as part of well-child visits in the first 6 months of life.

Methods

Using a mixed-methods approach that included a pilot randomized clinical trial and post-intervention qualitative interviews, 137 mothers were randomly assigned to receive IBH-P or usual care. Self-report measures of parenting, child behavior, and stress were obtained at pre- and/or post-intervention. Direct observation of mother–infant interactions was conducted at post-intervention.

Results

No differences between groups were found on maternal attunement, knowledge of child development, nurturing parenting, or infant behavior. A secondary analysis on a subsample with no prior exposure to IBH-P with older siblings found that mothers in IBH-P reported increased self-efficacy relative to controls. In the qualitative interviews, mothers stated that they valued IBH-P, learning about their baby, liked the integration in primary care, and felt respected and comfortable with their provider.

Conclusions

Findings are discussed in terms of the next steps in refining IBH-P approaches to prevention in primary care.
Pushchino multibeams pulsar search – III. Drift periods of pulsars from summed power spectra method
Authors: Smirnova T V , Tyul’bashev S A , Kitaeva M A , Malofeev V M
Published: January 2024

The drift periods P2 and P3 were searched for using the summed power spectra of 41 pulsars observed at declinations from −9° to +42°. The power spectra of pulses with a given period, pulse width, and drift behaviour have been simulated, the applicability of such a method for estimating drift parameters is shown. For most pulsars, the distribution of harmonic amplitudes in the power spectra corresponds to the expected distribution for these pulsars without drift. At the same time, it was found that for a number of sources, the summed power spectra accumulated over a long period of time give the same drift parameters as those determined by other methods. For 11 pulsars we have defined or redefined the drift period P2. For eight sources the drift period P3 has been determined or redefined. The drift direction of subpulses was redefined for them.
Gas phase ions in protoplanetary discs from collisions of solids
Authors: Penner Jakob , Wurm Gerhard , Teiser Jens
Published: January 2024

Ionization is important for magnetohydrodynamics and chemistry in protoplanetary discs but known ionization sources are often weak along the mid-plane. We present, for the first time, data from a laboratory experiment, where we measure ions from colliding mm-basalt grains emitted into the surrounding gas phase. This positive detection implies that very basic collisions in early phases of planet formation are sources of ionization. The mid-plane of protoplanetary discs might be ionized despite the lack of intense radiation sources.