bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated Analysis of Patient Networks and Plasmid Genomes to Investigate a Regional, Multispecies Outbreak of Carbapenemase-Producing Enterobacterales Carrying Both blaIMP and mcr-9 Genes
Authors: Wan Yu , Myall Ashleigh C , Boonyasiri Adhiratha , Bolt Frances , Ledda Alice , Mookerjee Siddharth , Weiße Andrea Y , Getino Maria , Turton Jane F , Abbas Hala , Prakapaite Ruta , Sabnis Akshay , Abdolrasouli Alireza , Malpartida-Cardenas Kenny , Miglietta Luca , Donaldson Hugo , Gilchrist Mark , Hopkins Katie L , Ellington Matthew J , Otter Jonathan A , Larrouy-Maumus Gerald , Edwards Andrew M , Rodriguez-Manzano Jesus , Didelot Xavier , Barahona Mauricio , Holmes Alison H , Jauneikaite Elita , Davies Frances 
Published: January 2024

Abstract

Background
Carbapenemase-producing Enterobacterales (CPE) are challenging in healthcare, with resistance to multiple classes of antibiotics. This study describes the emergence of imipenemase (IMP)–encoding CPE among diverse Enterobacterales species between 2016 and 2019 across a London regional network.

Methods
We performed a network analysis of patient pathways, using electronic health records, to identify contacts between IMP-encoding CPE–positive patients. Genomes of IMP-encoding CPE isolates were overlaid with patient contacts to imply potential transmission events.

Results
Genomic analysis of 84 Enterobacterales isolates revealed diverse species (predominantly Klebsiella spp, Enterobacter spp, and Escherichia coli); 86% (72 of 84) harbored an IncHI2 plasmid carrying blaIMP and colistin resistance gene mcr-9 (68 of 72). Phylogenetic analysis of IncHI2 plasmids identified 3 lineages showing significant association with patient contacts and movements between 4 hospital sites and across medical specialties, which was missed in initial investigations.

Conclusions
Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of blaIMPCPE, which remained unidentified during standard investigations. With DNA sequencing and multimodal data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Plasmid-level outbreak analysis reveals that resistance spread may be wider than suspected, allowing more interventions to stop transmission within hospital networks.
Summary
This was an investigation, using integrated pathway networks and genomics methods, of the emergence of imipenemase-encoding carbapenemase-producing Enterobacterales among diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network, which was missed on routine investigations.
Succession of microbial community composition and secondary metabolism during marine biofilm development
Authors: Bech Pernille Kjersgaard , Jarmusch Scott A , Rasmussen Jacob Agerbo , Limborg Morten Tønsberg , Gram Lone , Henriksen Nathalie N Suhr Eiris 
Published: January 2024

Abstract
In nature, secondary metabolites mediate interactions between microorganisms residing in complex microbial communities. However, the degree to which community dynamics can be linked to secondary metabolite potential remains largely unknown. In this study, we address the relationship between community succession and secondary metabolism variation. We used 16S and 18S rRNA gene and adenylation domain amplicon sequencing, genome-resolved metagenomics, and untargeted metabolomics to track the taxons, biosynthetic gene clusters, and metabolome dynamics in situ of microorganisms during marine biofilm succession over 113 days. Two phases were identified during the community succession, with a clear shift around Day 29, where the alkaloid secondary metabolites, pseudanes, were also detected. The microbial secondary metabolite potential changed between the phases, and only a few community members, including Myxococotta spp., were responsible for the majority of the biosynthetic gene cluster potential in the early succession phase. In the late phase, bryozoans and benthic copepods were detected, and the microbial nonribosomal peptide potential drastically decreased in association with a reduction in the relative abundance of the prolific secondary metabolite producers. Conclusively, this study provides evidence that the early succession of the marine biofilm community favors prokaryotes with high nonribosomal peptide synthetase potential. In contrast, the late succession is dominated by multicellular eukaryotes and a reduction in bacterial nonribosomal peptide synthetase potential.
“Candidatus Siderophilus nitratireducens”: a putative nap-dependent nitrate-reducing iron oxidizer within the new order Siderophiliales
Authors: Corbera-Rubio Francesc , Stouten Gerben R , Bruins Jantinus , Dost Simon F , Merkel Alexander Y , Müller Simon , van Loosdrecht Mark C M , van Halem Doris , Laureni Michele 
Published: January 2024

Abstract
Nitrate leaching from agricultural soils is increasingly found in groundwater, a primary source of drinking water worldwide. This nitrate influx can potentially stimulate the biological oxidation of iron in anoxic groundwater reservoirs. Nitrate-dependent iron-oxidizing (NDFO) bacteria have been extensively studied in laboratory settings, yet their ecophysiology in natural environments remains largely unknown. To this end, we established a pilot-scale filter on nitrate-rich groundwater to elucidate the structure and metabolism of nitrate-reducing iron-oxidizing microbiomes under oligotrophic conditions mimicking natural groundwaters. The enriched community stoichiometrically removed iron and nitrate consistently with the NDFO metabolism. Genome-resolved metagenomics revealed the underlying metabolic network between the dominant iron-dependent denitrifying autotrophs and the less abundant organoheterotrophs. The most abundant genome belonged to a new Candidate order, named Siderophiliales. This new species, “Candidatus Siderophilus nitratireducens,” carries genes central genes to iron oxidation (cytochrome c cyc2), carbon fixation (rbc), and for the sole periplasmic nitrate reductase (nap). Using thermodynamics, we demonstrate that iron oxidation coupled to nap based dissimilatory reduction of nitrate to nitrite is energetically favorable under realistic Fe3+/Fe2+ and NO3−/NO2− concentration ratios. Ultimately, by bridging the gap between laboratory investigations and nitrate real-world conditions, this study provides insights into the intricate interplay between nitrate and iron in groundwater ecosystems, and expands our understanding of NDFOs taxonomic diversity and ecological role.
Daily dosing of cannabidiol (CBD) demonstrates a positive effect on measures of stress in dogs during repeated exposure to car travel
Authors: Flint Hannah E , Hunt Alysia B G , Logan Darren W , King Tammie 
Published: January 2024

Abstract
Dogs are routinely exposed to events that may elicit stress and result in negative emotional states which can impact pet dog welfare. One event many dogs living with people are routinely exposed to is car travel, with many dogs displaying behaviors, along with corresponding physiological responses, that are indicative of stress and anxiety. There are a range of management and treatment options that exist from behavior modification, drug therapy, and supplements, often with varying results. The aim of this study was to evaluate whether multiple doses of a tetrahydrocannabinol-free cannabidiol (CBD) distillate over a period of 6 mo could positively influence measures of stress in dogs. In a blinded, parallel design study, dogs (n = 19) underwent a series of short car journeys (test) where a range of physiological and behavioral measures were collected pre, during, and post-test. The car journeys elicited stress in this population of dogs, as indicated by significant changes (P &lt; 0.05) in several stress-related measures (serum cortisol, heart rate, heart rate variability, whining, lip licking, yawning, and qualitative behavioral ratings) observed from baseline to test, which persisted over repeated car travel events. The mitigating effect of CBD treatment varied by measure, with cortisol, whining, lip licking, and qualitative behavioral ratings indicating a significant (P &lt; 0.05) reduction in canine stress compared to the placebo group for at least one time point. Additional research investigating a range of dog populations and stressors is required to fully understand the complex effect of CBD on canine emotional wellbeing.
Zinc status and indicators of intestinal health in enterotoxigenic Escherichia coli F18 challenged newly weaned pigs fed diets with different levels of zinc
Authors: Hansen Sally Veronika , Canibe Nuria , Nielsen Tina Skau , Woyengo Tofuko Awori 
Published: January 2024

Abstract
This study investigated the impact of an enterotoxigenic Escherichia coli (ETEC) F18 challenge on newly weaned pigs when fed one of three Zn levels (150, 1,400, or 2,500 ppm) on performance, Zn status, ETEC shedding, and diarrhea. The ETEC challenge was hypothesized to have a more pronounced negative impact on pigs fed a diet containing 150 ppm Zn compared to 1,400 or 2,500 ppm Zn for 14 d after weaning. The study included 72 ETEC F18 susceptible pigs weaned at ~28 d of age (d 0 of the study). The pigs were distributed according to initial weight and litter to one of the three dietary Zn levels. Half of the pigs were challenged with ETEC on d 1 and 2. The challenge reduced (P ≤ 0.03) feed intake and average daily gain (ADG) during d 3 to 5. Challenged pigs fed 150 ppm Zn had lower (P = 0.01) ADG during d 5 to 7 compared to those fed 1,400 or 2,500 ppm Zn, whereas control pigs’ ADG were not affected by dietary Zn content. Challenged pigs fed 150 ppm Zn also showed lower (P &lt; 0.01) fecal dry matter (DM) on d 5 compared to control pigs fed 150 ppm Zn and challenged pigs fed 1,400 or 2,500 ppm Zn. Challenge increased (P &lt; 0.01) ETEC shedding in all groups, but challenged pigs fed 150 ppm Zn showed higher (P ≤ 0.05) fecal shedding of ETEC and toxins than when fed 1,400 or 2,500 ppm. On d 3, C-reactive protein concentration in plasma was lower (P &lt; 0.03) for pigs fed 1,400 and 2,500 compared to 150 ppm Zn. Plasma haptoglobin and pig major acute phase protein were unaffected by dietary Zn content. On d 0, the serum Zn concentration was 586 ± 36.6 µg/L, which pigs fed 150 ppm Zn maintained throughout the study. The serum Zn concentration increased (P ≤ 0.07) in pigs fed 1,400 or 2,500 ppm Zn. The challenge decreased (P &lt; 0.01) the serum Zn concentration in pigs fed 2,500 ppm Zn. On d 5 and 7, serum Zn concentration was similar for challenged pigs fed 1,400 and 2,500 ppm Zn, while control pigs fed 2,500 ppm Zn had higher (P &lt; 0.01) serum Zn concentration than 1,400 ppm Zn. On d 7, serum Zn concentration tended (P = 0.08) to be lower for pigs with diarrhea (fecal DM ≤ 18%). In summary, these results indicate that newly weaned pigs fed 150 ppm Zn are more susceptible to ETEC F18 colonization and its adverse consequences such as diarrhea and reduced growth, even though challenge did not increase acute phase proteins.
Wnt pathway inhibition with the porcupine inhibitor LGK974 decreases trabecular bone but not fibrosis in a murine model with fibrotic bone
Authors: Lung Hsuan , Wentworth Kelly L , Moody Tania , Zamarioli Ariane , Ram Apsara , Ganesh Gauri , Kang Misun , Ho Sunita , Hsiao Edward C 
Published: January 2024

Abstract
G protein-coupled receptors (GPCRs) mediate a wide spectrum of physiological functions, including the development, remodeling, and repair of the skeleton. Fibrous dysplasia (FD) of the bone is characterized by fibrotic, expansile bone lesions caused by activating mutations in GNAS. There are no effective therapies for FD. We previously showed that ColI(2.3)+/Rs1+ mice, in which Gs-GPCR signaling was hyper-activated in osteoblastic cell lineages using an engineered receptor strategy, developed a fibrotic bone phenotype with trabecularization that could be reversed by normalizing Gs-GPCR signaling, suggesting that targeting the Gs-GPCR or components of the downstream signaling pathway could serve as a promising therapeutic strategy for FD. The Wnt signaling pathway has been implicated in the pathogenesis of FD-like bone, but the specific Wnts and which cells produce them remain largely unknown. Single-cell RNA sequencing on long-bone stromal cells of 9-wk-old male ColI(2.3)+/Rs1+ mice and littermate controls showed that fibroblastic stromal cells in ColI(2.3)+/Rs1+ mice were expanded. Multiple Wnt ligands were up- or downregulated in different cellular populations, including in non-osteoblastic cells. Treatment with the porcupine inhibitor LGK974, which blocks Wnt signaling broadly, induced partial resorption of the trabecular bone in the femurs of ColI(2.3)+/Rs1+ mice, but no significant changes in the craniofacial skeleton. Bone fibrosis remained evident after treatment. Notably, LGK974 caused significant bone loss in control mice. These results provide new insights into the role of Wnt and Gs-signaling in fibrosis and bone formation in a mouse model of Gs-GPCR pathway overactivation.
Brep2Seq: a dataset and hierarchical deep learning network for reconstruction and generation of computer-aided design models
Authors: Zhang Shuming , Guan Zhidong , Jiang Hao , Ning Tao , Wang Xiaodong , Tan Pingan 
Published: January 2024

Abstract
Three-dimensional (3D) reconstruction is a significant research topic in the field of computer-aided design (CAD), which is used to recover editable CAD models from original shapes, including point clouds, voxels, meshes, and boundary representations (B-rep). Recently, there has been considerable research interest in deep model generation due to the increasing potential of deep learning methods. To address the challenges of 3D reconstruction and generation, we propose Brep2Seq, a novel deep neural network designed to transform the B-rep model into a sequence of editable parametrized feature-based modeling operations comprising principal primitives and detailed features. Brep2Seq employs an encoder-decoder architecture based on the transformer, leveraging geometry and topological information within B-rep models to extract the feature representation of the original 3D shape. Due to its hierarchical network architecture and training strategy, Brep2Seq achieved improved model reconstruction and controllable model generation by distinguishing between the primary shape and detailed features of CAD models. To train Brep2Seq, a large-scale dataset comprising 1 million CAD designs is established through an automatic geometry synthesis method. Extensive experiments on both DeepCAD and Fusion 360 datasets demonstrate the effectiveness of Brep2Seq, and show its applicability to simple mechanical components in real-world scenarios. We further apply Brep2Seq to various downstream applications, including point cloud reconstruction, model interpolation, shape constraint generation, and CAD feature recognition.
Joint MR image reconstruction and super-resolution via mutual co-attention network
Authors: Chen Jiacheng , Wu Fei , Wang Wanliang 
Published: January 2024

AbstractIn the realm of medical diagnosis, recent strides in deep neural network-guided magnetic resonance imaging (MRI) restoration have shown promise. Nevertheless, persistent drawbacks overshadow these advancements. Challenges persist in balancing acquisition speed and image quality, while existing methods primarily focus on singular tasks like MRI reconstruction or super-resolution (SR), neglecting the interplay between these tasks. To tackle these challenges, this paper introduces the mutual co-attention network (MCAN) specifically designed to concurrently address both MRI reconstruction and SR tasks. Comprising multiple mutual cooperation attention blocks (MCABs) in succession, MCAN is tailored to maintain consistency between local physiological details and global anatomical structures. The intricately crafted MCAB includes a feature extraction block, a local attention block and a global attention block. Additionally, to ensure data fidelity without compromising acquired data, we propose the channel-wise data consistency block. Thorough experimentation on the IXI and fastMRI dataset showcases MCAN’s superiority over existing state-of-the-art methods. Both quantitative metrics and visual quality assessments validate the enhanced performance of MCAN in MRI restoration. The findings underscore MCAN’s potential in significantly advancing therapeutic applications. By mitigating the trade-off between acquisition speed and image quality while simultaneously addressing both MRI reconstruction and SR tasks, MCAN emerges as a promising solution in the domain of magnetic resonance image restoration.
Does mindless scrolling hamper well-being? Combining ESM and log-data to examine the link between mindless scrolling, goal conflict, guilt, and daily well-being
Authors: de Segovia Vicente David , Van Gaeveren Kyle , Murphy Stephen L , Vanden Abeele Mariek M P 
Published: January 2024

AbstractThis manuscript presents findings from a preregistered mixed-method study involving 67,762 ecological momentary assessments and behavioral smartphone observations from 1,315 adults. The study investigates (a) momentary associations between mindless scrolling, goal conflict, and guilt over smartphone use, and (b) whether guilt experiences during the day culminate into lower well-being. Results indicate that individuals experienced more guilt over their smartphone use when they had mindlessly scrolled for a longer period and that experienced goal conflict partially mediated this relationship. Daily analyses revealed that mindless scrolling was also associated with small negative changes in well-being, and this relationship was partially mediated by guilt experienced over the same day. Individuals with less self-control were more prone to experiencing goal conflict after mindlessly scrolling. These findings indicate that although mindless scrolling may seem a relatively harmless media behavior, it may have both momentary and downstream negative implications for well-being.
Consumer Work and Agency in the Analog Revival
Authors: Beverland Michael B , Fernandez Karen V , Eckhardt Giana M 
Published: January 2024

Abstract
Why do consumers choose difficult analog technologies over their labor-saving digital counterparts? Through ethnographic investigations of three once defunct analog technologies that have experienced a resurgence (vinyl music, film photography, and analog synthesizers), we explore how the act of consumer work enables consumers to experience shifting dimensions of agency. We utilize the theoretical lens of serious leisure to introduce a four-stage work process (novice, apprentice, craft, and design) in which the experience of agency is dependent on the shifting relations between user, object, and context. The four stages are cumulative and conjunctive, representing the development of skills toward mastery while also being connected via three transition mechanisms (contextualization, schematization, and hypothesization) that address agency–alienation tensions. The transition through these mechanisms is necessary to sustain emotional engagement in consumer work. Our contribution lies in demonstrating the myriad of ways in which consumer work as serious leisure generates different experiences of agency and alienation and the ways in which consumers can sustain engagement in their work.
Stability evaluation of candidate reference genes for real-time qPCR normalization in Rhyzopertha dominica (Coleoptera: Bostrycidae)
Authors: Xue Dingrong , Chen Tongtong , Wu Yi 
Published: January 2024

Abstract
Rhyzopertha dominica is a serious stored grain insect pest around the world. Real-time quantitative polymerase chain reaction (RT-qPCR) is a widely used experimental method in molecular biology for detecting the expression of target genes. As appropriate reference genes are essential for normalizing gene expression, the selection of suitable reference genes is the basis of RT-qPCR experiments. In this study, the expression profiles of 7 candidate reference genes of rps3, rps6, rps13, actin, gadph, tubulin, and 18S rRNA were analyzed under 4 different experimental conditions. The expression stability of candidate genes was evaluated using the ΔCt, GeNorm, BestKeeper, NormFinder, and RefFinder methods. The results revealed that different reference genes were suitable for various experiments. Specifically, rps3 and rps6 were appropriate for the developmental stages and all samples: 18S rRNA and rps13 for temperature-related experiments, actin and rps6 for sex-related experiments, and rps6 and gadph for starvation stress. Our results lay essential groundwork for the normalization of RT-qPCR analyses and contribute to genomic and gene functional research of R. dominica.
Social Conflict and the Evolution of Unequal Conventions
Authors: Hwang Sung-Ha , Naidu Suresh , Bowles Samuel 
Published: January 2024

Abstract
We propose a theory of social norms (or conventions) that implement substantial levels of inequality between men and women, ethnic groups, and classes and that persist over long periods of time despite being inefficient and not supported by formal institutions. Consistent with historical cases, we extend the standard asymmetric stochastic evolutionary game model to allow subpopulation sizes to differ and idiosyncratic rejection of a status quo convention to be intentional to some degree (rather than purely random as in the standard evolutionary models). In this setting, if idiosyncratic play is sufficiently intentional and the subordinate class is sufficiently large relative to the elite, then risk-dominated conventions that are both more unequal and inefficient relative to alternative conventions will be stochastically stable and may persist for long periods. We show that the same is true in a general bipartite network of the population if most of the subordinate groups interactions are local, while the elite is more “cosmopolitan”. We apply the model to the evolution of wage conventions on the bipartite network of workers and employers, and find that an unequal monopsonistic wage convention is robust to the idiosyncratic play of workers that otherwise might displace it.
A chromosome-level genome assembly for the dugong (Dugong dugon)
Authors: Baker Dorothy Nevé , Abueg Linelle , Escalona Merly , Farquharson Katherine A , Lanyon Janet M , Le Duc Diana , Schöneberg Torsten , Absolon Dominic , Sims Ying , Fedrigo Olivier , Jarvis Erich D , Belov Katherine , Hogg Carolyn J , Shapiro Beth 
Published: January 2024

Abstract
The dugong (Dugong dugon) is a marine mammal widely distributed throughout the Indo-Pacific and the Red Sea, with a Vulnerable conservation status, and little is known about many of the more peripheral populations, some of which are thought to be close to extinction. We present a de novo high-quality genome assembly for the dugong from an individual belonging to the well-monitored Moreton Bay population in Queensland, Australia. Our assembly uses long-read PacBio HiFi sequencing and Omni-C data following the Vertebrate Genome Project pipeline to reach chromosome-level contiguity (24 chromosome-level scaffolds; 3.16 Gbp) and high completeness (97.9% complete BUSCOs). We observed relatively high genome-wide heterozygosity, which likely reflects historical population abundance before the last interglacial period, approximately 125,000 yr ago. Demographic inference suggests that dugong populations began declining as sea levels fell after the last interglacial period, likely a result of population fragmentation and habitat loss due to the exposure of seagrass meadows. We find no evidence for ongoing recent inbreeding in this individual. However, runs of homozygosity indicate some past inbreeding. Our draft genome assembly will enable range-wide assessments of genetic diversity and adaptation, facilitate effective management of dugong populations, and allow comparative genomics analyses including with other sirenians, the oldest marine mammal lineage.