bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

ABSTRACT
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

Abstract

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

Abstract
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

AbstractHadarchaeota 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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.