bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitigating norovirus spread on cruise ships: A model-based assessment of diagnostic timing and isolation
Authors: De Bellis Alfredo , Bizzotto Andrea , Anagnostopoulou Lemonia , Kourentis Leonidas , Marziano Valentina , Mouchtouri Varvara , Merler Stefano , Guzzetta Giorgio 
Published: December 2024

AbstractBackgroundAcute gastroenteritis outbreaks caused by noroviruses are a common public health issue on cruise ships. Understanding the main drivers of sustained outbreaks is critical for evaluating the effectiveness of preventive interventions such as the isolation of infected individuals.MethodsWe analyzed a line-list of 121 cases from a norovirus outbreak on a cruise calling Mediterranean ports (cumulative incidence among passengers 9.7%). We used a Bayesian inference model to reconstruct likely transmission chains, taking into account different transmission settings and the isolation of cases after diagnosis. We then calibrated a branching process model to simulate alternative isolation scenarios and estimate their effectiveness in reducing transmission.ResultsReconstructed transmission chains revealed a high heterogeneity in individual transmission, with 57% (95% CrI: 48%-65%) of secondary cases caused by 10% of infected individuals (here termed “superspreaders”). Superspreaders exhibited longer diagnostic delays (mean 83 hours, 95% CrI: 70-96 hours) compared to other infectors (mean 47 hours, 95% CrI: 44-50 hours) and a halved frequency of vomiting and diarrhea episodes. The 72-hour isolation protocol implemented during the outbreak averted 71% of potential cases compared to a no-intervention scenario, halving the effective reproduction number from 9.8 (95%CrI of the mean: 7.1-12.7) to 4.9 (95%CrI: 3.0-7.1). Reducing diagnostic delays further reduced the effective reproduction number, resulting in lower case numbers and probability of sustained outbreaks.ConclusionsTimely diagnosis and isolation have a remarkable impact on norovirus containment on cruise ship outbreaks. Targeted information campaigns encouraging passengers to seek immediate medical assistance upon gastrointestinal symptoms can significantly improve outbreak management.
Self organisation of invasive breast cancer driven by the interplay of active and passive nematic dynamics
Authors: Gottheil Pablo , Bhattacharyya Saraswat , Lettl Kolya , Friedrich Philip , Roth Kilian , Rivera-Moreno Salvador , Merkel Mario , Aktas Bahriye , Sauer Igor , Daneshgar Assal , Wieland Jonas , Kubitschke Hans , Wegscheider Anne-Sophie , Yeomans Julia M. , Käs Josef A. 
Published: December 2024

AbstractIn invasive breast cancer, cell clusters of varying sizes and shapes are embedded in the fibrous extracellular matrix (ECM). Although the prevailing view attributes this structure to increasing disorder resulting from loss of function and dedifferentiation, our findings reveal that it arises through a process of active self-organization driven by cancer cell motility. Simulations and histological analyses of tumours from over 2,000 breast cancer patients reveal that motile, aligned cancer cells within clusters move as active nematic aggregates through the surrounding highly aligned ECM fibres, which form a confining, passive nematic phase. Cellular motion leads to cluster splitting and coalescence. The degree of cluster activity, combined with heterogeneity in cell motility, is reflected in specific scaling behaviours for cluster shape, size distribution, and the distance between cluster boundaries and nematic defects in ECM alignment. Increased activity estimates correlate with tumour progression and are associated with a poorer prognosis for patients.
To what extent can life history strategies inform species conservation planning?
Authors: Stevenson Emily A. , Lucas Sol , McGowan Philip J. K. , Smallegange Isabel M. , Mair Louise 
Published: December 2024

AbstractGlobal policy aims to prevent species extinctions; to support these aims conservation planners must effectively target interventions to reduce the extinction risk of species. However, there is often a lack of knowledge on the magnitude and direction of species responses to interventions and in turn the extent to which a species extinction risk is reduced. If we can use a species’ life history strategies to predict their responses to interventions, this offers a promising approach to better understand species extinction risks and conservation potential. Here we apply Dynamic Energy Budget Integral Project Models to 23 reptile species to investigate whether their life history traits can be summarised into a life history strategy framework using principal component analysis, and whether species positions along these axes predict their population growth rate, demographic resilience, sensitivity to perturbations and extinction risk. We found that species positions on reproductive and pace of life axes predicted reptile population growth rate and demographic resilience but not sensitivity to perturbations or extinction risk. Our findings show that reptile life history strategies can inform our understanding of reptile species conservation potential and could be applied to influence management decisions such as establishing monitoring timelines.
Matrix Metalloproteinase-2 as a novel regulator of glucose utilization by adipocytes
Authors: Lempicki Melissa D. , Garrigues Ryan J. , Zeczycki Tonya N. , Garcia Brandon L. , Harris Thurl E. , Meher Akshaya K. 
Published: December 2024

ABSTRACTGlucose transporter 4 (GLUT4) expression on white adipocytes is critical for absorbing excess blood glucose, failure of which promotes hyperglycemia. Matrix metalloproteinases (MMPs) play a crucial role in remodeling the white adipose tissue (WAT) during obesity. MMPs have multiple protein substrates, and surprisingly, it is unknown if they can directly target GLUT4 on the adipocyte surface and impair glucose absorption. We identified MMP2 as the highly active gelatinase, a class of MMP, in the gonadal WAT of high-fat diet-induced obese mice.In vitro, metabolic studies in 3T3-L1 adipocytes revealed MMP2 attenuated glucose absorption and glycolysis, which were recovered by an MMP2 inhibitor.In silicostructural analysis using AlphaFold identified a putative MMP2 cleavage site on the extracellular domain of GLUT4. Further, in a substrate competition assay, a peptide mimicking the MMP2 cleavage motif on GLUT4 attenuated the cleavage of an MMP substrate by MMP2. Altogether, our results suggest a novel mechanism of impaired glucose absorption by adipocytes, which may contribute to hyperglycemia during obesity.ARTICLE HIGHLIGHTSIt is unknown if MMPs directly affect adipocyte metabolismviatargeting adipocyte surface proteins.We aimed to determine the highly active gelatinases, a class of MMP, in the white adipose tissue of obese mice, and examined its effect on adipocyte glucose metabolism.MMP2 was the highly active gelatinase in obese adipose tissue and,in vitro, MMP2 reduced adipocyte glucose metabolism, in part, by targeting the GLUT4 receptor.A harmful role of MMP2 is implicated in cardiometabolic diseases and our novel finding on the role of MMP2 on glucose metabolism may add to the pathogenesis of the diseases.
Essential sterols from engineered yeast prevent honeybee colony population decline
Authors: Moore Elynor , de Sousa Raquel T , Felsinger Stella , Arnesen Jonathan A , Dyekjær Jane D , Farman Dudley I , Gonçalves Rui F S , Stevenson Philip C , Borodina Irina , Wright Geraldine A 
Published: December 2024

AbstractHoneybees, the world’s most important crop pollinators, are increasingly facing pollen starvation arising from agricultural intensification and climate change. Frequent flowering dearth periods and high-density rearing conditions weaken colonies, often leading to their demise. Beekeepers provide colonies with pollen substitutes, but these feeds cannot sustain brood production because they lack essential sterols found in pollen. Here, we describe a technological breakthrough in honeybee nutrition with wide-reaching impacts on global food security. We first measured the quantity and proportion of sterols found in honeybee tissues. Using this information, we genetically engineered a strain of the oleaginous yeast,Yarrowia lipolytica, to produce a mixture of essential sterols for bees and incorporated it into an otherwise nutritionally complete diet. Colonies fed exclusively with this diet reared brood for significantly longer than those fed diets without suitable sterols. Incorporating sterol supplements into pollen substitutes using this method will enable beekeepers to rear healthier, longer-lived colonies to meet the growing demands for global crop pollination. It could also reduce competition between bee species for access to natural floral resources, stemming the decline of wild bee populations.
Pol II degradation activates cell death independently from the loss of transcription
Authors: Harper Nicholas W. , Birdsall Gavin A. , Honeywell Megan E. , Pai Athma A. , Lee Michael J. 
Published: December 2024

ABSTRACTPol II-mediated transcription is essential for eukaryotic life. While loss of transcription is thought to be universally lethal, the associated mechanisms promoting cell death are not yet known. Here, we show that death following loss of Pol II is not caused by dysregulated gene expression. Instead, death occurs in response to the loss of Pol II protein itself, specifically loss of the enzymatic subunit, Rbp1. Loss of Pol II exclusively activates apoptosis, and expression of a transcriptionally inactive version of Rpb1 rescues cell viability. Using functional genomics, we identify a previously uncharacterized mechanism that regulates lethality following loss of Pol II, which we call thePol IIDegradation-dependentApoptoticResponse (PDAR). Using the genetic dependencies of PDAR, we identify clinically used drugs that owe their efficacy to a PDAR-dependent mechanism. Our findings unveil a novel apoptotic signaling response that contributes to the efficacy of a wide array of anti-cancer therapies.
The presence of an ESBL-encoding plasmid reported during aKlebsiella pneumoniaenosocomial outbreak in the United Kingdom
Authors: Fordham Stephen Mark Edward , Mantzouratou Anna , Anne Sheridan Elizabeth 
Published: December 2024

AbstractThe presence of extended-spectrum β-lactamase (ESBL) encoding plasmids in bacteria contributes towards rising resistance rates, mortality and healthcare costs in clinical settings. An EBSL-encoding plasmid, pESBL-PH was identified during a nosocomial outbreak ofKlebsiella pneumoniaeST628 at a United Kingdom general district hospital in 2018. A plasmid from the earliest 2018K. pneumoniaestrain discovered during the outbreak was assembled using both Oxford nanopore long reads and illumina short reads, yielding a fully closed plasmid, pESBL-PH-2018. pESBL-PH-2018 was queried against the complete NCBI RefSeq Plasmid Database, comprising 93,823 plasmids, downloaded on July 16, 2024. To identify structurally similar plasmids, strict thresholds were applied: both a shared hash ratio > 0.9 and a mash similarity ≥ 0.98. This returned 61 plasmids belonging to 13 unique sequence types (STs) hosts. The plasmids were detected in 13 unique countries, dating from 2012-2023, associated with a range of infections including bacteremia. Low numbers of single nucleotide polymorphisms (SNPs) were identified between pESBL-PH-2018 and query plasmids, further confirming their relatedness. The AMR region of the plasmids varied; interestingly IS26mediated-tandem amplification of resistance genes, including the ESBLblaCTX-M-15was identified in two independent strains raising their copy number to three. Furthermore, the genomic background of strains carrying a pESBL-PH-2018-like plasmid were analyzed, revealing truncation of the chromosomalompK36porin gene and carbapenemase resistance gene carriage on accessory plasmids in 17.85% and 26.78% of strains with a complete chromosome available. This analysis reveals the widespread dissemination of an ESBL-encoding plasmid in a background of resistance-encoding strains, requiring active surveillance.
Optimization of metagenomic detection method for human breast milk microbiome
Authors: Zhang Qiao , Zhang Yi , Zhu Jianjiang , Gao Yajun , Zeng Wen , Qi Hong 
Published: December 2024

AbstractThis study aims to optimize the metagenomic detection methodology of the human breast milk microbiome and analyze its composition. Twenty-two milk samples were collected from the left and right sides of lactating women during re-examinations at the Haidian Maternal and Child Health Hospital, Beijing. Microbial cell wall disruption parameters were optimized, and a nucleic acid extraction method was developed to construct a microbial DNA/RNA library. Metagenomic next-generation sequencing (mNGS) sequencing was performed, and microbial composition was analyzed using the k- mer Lowest Common Ancestor (LCA) method with a self-generated database constructed via Kraken2 software. Data showed Q20 > 95% and Q30 > 90%, with an average total data volume of 5,567 ± 376.6 Mb and non-human sequence data of 445.1 ± 63.75 Mb, significantly enhancing sequencing efficiency. The microbiome included 21 phyla, 234 genera, and 487 species, with Firmicutes and Proteobacteria as dominant phyla. Predominant genera includedStaphylococcusandStreptococcus, and major species wereStaphylococcus aureus,Streptococcus bradystis, andStaphylococcus epidermidis. Species levels exhibited significant variations among different individuals. Microbial profiles of left- and right-sided milk samples were consistent at the phylum, genus, and species levels. In addition to common bacteria, diverse viral, eukaryotic, and archaeal sequences were detected. This study refined metagenomic detection methods for human breast milk microbiota. Specific flora colonization occurred in healthy breast milk, with the left and right sides exhibiting both correlations and distinct flora environments.ImportanceBreast milk is a vital source of nutrition and immunity for infants, with its microbial composition playing a critical role in shaping the neonatal gut microbiome and supporting early development. However, technical challenges in detecting microorganisms in milk’s complex, lipid-rich environment have limited understanding of the diversity and function of these microbial communities. This study developed an optimized metagenomic sequencing method to analyze the microbial communities in breast milk from healthy mothers, identifying a wide array of bacteria, viruses, eukaryotes, and archaea. Key bacterial genera such asStaphylococcusandStreptococcuswere predominant, with specific flora exhibiting inter-individual variability. Additionally, the study revealed distinct yet correlated microbial environments in the milk from the left and right breasts. These findings advance the understanding of breast milk microbiota and provide a foundation for exploring its implications for maternal and infant health.
Compensatory justice and accountability for First Nations peoples: the Timber Creek case
Authors: Norris Ellie , Kutubi Shawgat , Finau Glenn 
Published: December 2024

PurposeThis paper examines the state’s accountability to its citizens, in particular the First Peoples of settler colonial nations such as Australia, and how these responsibilities may be enacted via a process of compensatory justice in Native Title claims. We focus on the landmark Timber Creek ruling and the impacts of racialized preconceptions on the accountability outcomes of the case.Design/methodology/approachThis study draws on critical race theory to reveal embedded racialised perspectives that perpetuate exclusion and discriminatory outcomes. Court documents including hearing transcripts, case judgements, witness statements, appellant and respondent submissions, expert reports and responses from First Nations leaders, form the basis of our analysis.FindingsThe case highlights how the compensation awarded to Native Title holders was based on racialised assumptions that prioritised neoliberal values, commercial activities and reaching a “socially acceptable” judgement over valuing Aboriginal uses of land. A critical analysis of court documents reveals the pervasiveness of presumed “objectivity” in the use of accounting tools to calculate economic value and the accountability implications of a process based on litigation, not negotiation. These findings reveal the hiding places offered by calculative practices that equate neoliberal priorities with accountability and reaffirm the importance of alternative accountings to resist inequitable distributive outcomes.Originality/valueNovel insights, drawing on First Nations peoples’ connections to land and their perspectives on accountability and justice, are offered in this study. Our analysis of Native Title holders’ submissions to the courts alongside historical and anthropological sources leads to the conclusion that compensation decisions regarding Native Title land must be approached from the perspective of Aboriginal landowners if accountable outcomes are to be achieved.
A 3D printed microfluidic device for centrifugal droplet generation
Authors: Kubicki Wojciech , Thiha Aung , Janisz Tymon , Joseph Karunan , Jamaluddin Nurul Fauzani , Madou Marc , Walczak Rafał , Stojanovic Goran M. , Ibrahim Fatimah 
Published: December 2024

Purpose
This study aims to use an additive process for the first time to develop a microfluidic device that uses centrifugal technique for precise and repeatable generation of microdroplets. Droplets have versatile applications in life sciences, but so far centrifugal devices for their production have been made mainly using standard subtractive techniques. This study focused on evaluating the applicability of 3D printing technology in the development of centrifugal microfluidic devices and investigating their properties and future applications.

Design/methodology/approach
First, the background of this interdisciplinary research, including the principle of droplet microfluidics and the centrifugal technique, is explained. The developed device has the form of a disc (similar to an audio CD), containing an integrated microfluidic system for droplet generation. The disc is rotated at a specific spin profile to induce controlled liquid flow and accurate production of oil-in-water microdroplets. The device was fabricated using material jetting technology. The design, operation principles, printing process parameters and post-processing steps are explained in detail.

Findings
The device was thoroughly characterised, including its mechanical properties, the impact of chemical treatment and the flow measurement of the liquids. The study confirms that the disc can be applied to produce various emulsions using centrifugal force alone. 3D printing technology enables potential mass production and other applications of the device.

Originality/value
The 3D printing process allowed for easy design, fabrication and duplication of the device. Compared to standard PMMA discs, a simpler fabrication protocol and a more flexible and monolithic structure were obtained. The device can be adapted to other microfluidic processes in a lab with high potential for point-of-care applications.
Collagen enhances stability and viability of diced cartilage as an injectable implant: An experimental study in rabbits
Authors: Fei Yanghonghong , Shen Shengxian , Chen Zhao , Lv Wenjia , Lu Haishan , Shi Lina , Hong Xudong , Jin Jian 
Published: December 2024

AbstractThe use of diced cartilage has become increasingly popular in rhinoplasty; however, the viability of the graft can vary. This study aimed to investigate the use of fillers for diced cartilage, evaluate their morphology and viability, and provide a foundation for their clinical use. Six rabbits were used in this experiment. Ear cartilage was excised and diced into pieces and mixed with different fillers, including collagen (COLD), hyaluronic acid (HAD), and normal saline (NSD), or used alone (COND) as a control. They were embedded in the backs of rabbits. After 3 months, the weight and volume of grafts were measured. The cellular viability and morphology were assessed. The HAD group showed the most significant volume change, followed by the NSD group. There was no significant weight change between the COLD and COND groups. Grossly, the COLD group appeared as a smooth block, while the COND and NSD groups appeared rough. Microscopically, fibrous tissue and collagen were arranged regularly in the COLD and HAD groups, and chondrocytes were arranged neatly. By contrast, collagen was less and arranged messily in the NSD and COND groups. There was better cell viability and angiogenesis around cartilage in the COLD group than in the HAD and NSD groups. When mixed with collagen, diced cartilage can maintain its basic shape and smooth appearance, and there is better cell viability and angiogenesis than when mixed with hyaluronic acid or normal saline, or used alone. These findings may provide implications for the clinical use of diced cartilage as injectable implants.
Electrochemical Detection of Carbon Steel Corrosion Induced by Fermentative Bacteria From Natural Gas Transmission Lines
Authors: Davis Joshua A. , Chinthala Sai Prasanna , Monty‐Bromer Chelsea N. , Senko John M. 
Published: December 2024

ABSTRACTThe metabolic potential and corrosive activities of a fermentative bacterial enrichment culture from a natural gas transmission line were characterised. Three metagenome‐assembled genomes (MAGs) attributable to Cytobacillus, Lacrimispora and Staphylococcus spp. were obtained. These MAGs hosted genes involved in the fermentation of carbohydrates to organic acids, which was reflected in the acidification of the growth medium by the culture. To evaluate the corrosive activities of the culture, it was incubated in a split chamber‐zero resistance ammetry (SC‐ZRA) format. This involved deploying carbon steel coupons immersed in liquid medium in opposing chambers of an electrochemical cell. Measurement of current between the coupons indicated the extent and mechanism of corrosion. When the enrichment culture was added to one side of an SC‐ZRA incubation with bicarbonate‐buffered medium, pH change and corrosion were minimal. In bicarbonate‐free medium, the culture acidified the medium, induced electron transfer from the uninoculated chamber to the inoculated chamber, and caused mass loss. These results indicate that fermenter‐induced microbially influenced corrosion (MIC) is due to localised fluid acidification, inducing anodic reactions on the metal surface exposed to the microorganisms and mass loss of the non‐exposed metal.