bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-scale Genomic Survey of Non-typhoidalSalmonella entericaserovar Minnesota Strains in Chicken Products Reveals the Emergence of Multidrug Resistant Clones
Authors: Huang Jiayi , Alzahrani Khaloud O. , Zhou Ge , Alsalman Shahad A. , Almansour Ayidh M. , Alhadlaq Meshari A. , Alhussain Shaykhah , Alajlan Abdullah A. , Al-Akeel Saleh I. , Al Rashidy Malfi S. , Alzauhair Abdulrahman , AlReshoodi Fahad M. , Alsufyani Amani T. , Alotaibi Nourah M. , Althubaiti Afnan , Alshdokhi Elaf , Alhamed Ashwaq , Almusa Manal , Almadi Talah , Almutairi Nouf , Mukhtar Lenah E. , AlHarbi Abdulmohsen L. , Banzhaf Manuel , Milner Mathew , AlArawi Mohammad , Alajel Sulaiman , Moradigaravand Danesh 
Published: July 2024

AbstractBackgroundSalmonella entericaserovar Minnesota (S. Minnesota) is an emerging serovar of non-typhoidalSalmonella, known to persist in the food chain and distribution systems, potentially leading to outbreaks ofSalmonellainfections in human settings. Understanding the population genomics and dynamics of this pathogen is key to designing preventative measures and containing its spread within the poultry production chain.MethodsIn this study, we conducted a large-scale study onS. Minnesota outbreak by fully characterizing population diversity and dynamics of a systematic collection from the poultry production chain in the Kingdom of Saudi Arabia (KSA). We sequenced 260S. Minnesota strains from the western, eastern, and central regions of the country. We analyzed sequencing data to decipher the population diversity and dynamics of multidrug resistant strains and characterize the genetic basis of resistance and virulence. A hybrid long- and short-read sequencing approach was employed to analyze the population diversity of plasmids carrying antimicrobial resistance and virulence factors.ResultsOur results indicate the rise of four clones (Bayesian Analysis of Population Structure; BAPS groups) in Saudi Arabia, three of which were mixed with global strains. The clones emerged over the past five to ten years and exhibited circulation between countries. The transmission analysis shows evidence of the spread of strains across cities, between countries, and mixing of strains from different suppliers, on epidemiological time scales. The emerging clones also harbored a higher resistance and virulence level than ancestral clones, owing to the acquisition of multiple plasmids, most importantly the IncC plasmid. The IncC plasmid was a mosaic plasmid, which carried antimicrobial resistance islands withblaCMY-2, ESBLblaCTX-M, aminoglycoside, and tetracycline resistance genes, as well as a hyperpathogenicity island with yersiniabactin genes. The plasmidome analysis revealed a high level of dynamics in the IncC plasmid structures with various configurations of resistance genes.ConclusionTaken together, our results demonstrate a dynamic population and the emergence of multidrug-resistant clones inS. Minnesota. The results also highlight the role of plasmid acquisition and genomic variations in driving the concurrent evolution of pathogenicity and resistance inS. Minnesota.
Senescent fibroblasts in the tumor stroma rewire lung cancer metabolism and plasticity
Authors: Lee Jin Young , Reyes Nabora , Woo Sang-Ho , Goel Sakshi , Stratton Fia , Kuang Chaoyuan , Mansfield Aaron S. , LaFave Lindsay M. , Peng Tien 
Published: July 2024

SummarySenescence has been demonstrated to either inhibit or promote tumorigenesis. Resolving this paradox requires spatial mapping and functional characterization of senescent cells in the native tumor niche. Here, we identified senescentp16Ink4a+ cancer-associated fibroblasts with a secretory phenotype that promotes fatty acid uptake and utilization by aggressive lung adenocarcinoma driven by Kras and p53 mutations. Furthermore, rewiring of lung cancer metabolism byp16Ink4a+ cancer- associated fibroblasts also altered tumor cell identity to a highly plastic/dedifferentiated state associated with progression in murine and human LUAD. Ourex vivosenolytic screening platform identified XL888, a HSP90 inhibitor, that clearedp16Ink4a+ cancer- associated fibroblastsin vivo. XL888 administration after establishment of advanced lung adenocarcinoma significantly reduced tumor burden concurrent with the loss of plastic tumor cells. Our study identified a druggable component of the tumor stroma that fulfills the metabolic requirement of tumor cells to acquire a more aggressive phenotype.
Investigating digitization and digital preservation strategies for theses and dissertations: a case study of Quaid-I-Azam university, Pakistan
Authors: Arif Muhammad , Mirza Khalid Bashir , Hamid Muhammad 
Published: July 2024

Purpose
The purpose of this study is to outline the process, procedures and techniques used for digitization and digital preservation of theses and dissertations (TDs) collection at the Central Library of Quaid-I-Azam University, Pakistan.

Design/methodology/approach
Since the phenomenon under investigation is exploratory in nature, a case study qualitative paradigm was used to conduct this study.

Findings
The findings of the study offer a brief overview of the cost-effective solution that leveraged in-house expertise for the digital preservation of TDs. This led to the establishment of a knowledge repository hosting a substantial collection of approximately 25,857 electronic theses and dissertations, accessible online since August 2023. This project digitally preserved approximately 9,387 TDs on CDs/DVDs, and scanned about 15,000 print TDs, comprising around 1,399,244 pages. The cost incurred per page, including labor and rent of a photocopy machine, was just Rs 0.548 making it a cost-effective technique. The total cost incurred for this process was just 0.768m Pakistani rupees (equivalent to $2,509.55). The findings revealed key challenges, including administrative, financial, technical and copyright issues, that impede the effective execution of the project.

Research limitations/implications
This case study is limited to one Pakistani public sector university library. This case study holds significance in terms of practical insights and implications for academic institutions and library administrators in other developing countries like Pakistan, which have similar economic, social and technical circumstances.

Originality/value
To the best of the authors’ knowledge, this is the first-ever study conducted to elucidate the cost-effective strategy adopted for digitally preserved TDs without additional financial and human resources while creating a knowledge repository.
Gender gap in agricultural productivity: evidence from Burkina Faso
Authors: Valea Aristide Bonsdaouêndé , Noufé Tiatité 
Published: July 2024

PurposeWomen make a major contribution to the agricultural sector, especially in developing countries. Despite this, women still face many obstacles in carrying out their agricultural activities. These obstacles have a negative impact on their productivity and create a gender gap. This paper analyses the difference in agricultural productivity between male-headed and female-headed households in Burkina Faso.Design/methodology/approachUsing data from the Permanent Agricultural Survey (EPA), we applied the Blinder-Oaxaca decomposition method to determine the size of the gender gap and identify the variables explaining this gap. In this study, we used the value of production per farm worker as a measure of productivity.FindingsThe results indicate a gender gap of 43.8 percentage points in favor of male-headed households. Around 131% of this difference is explained by differences in observable household characteristics. The factor that most explains this difference in productivity is the difference in the total area of land available to households.Practical implicationsThis finding calls for women’s access to land to be considered in the design and implementation of agricultural development policies.Originality/valueOne of the main contributions of this article in relation to previous studies lies in the unit of analysis. Rather than focusing on individual producers, as in previous studies, we have instead considered the household as the unit of analysis, since in developing countries such as Burkina Faso, production decisions are taken at household level. It contributes to inform economic policy decisions by providing decision-makers with the factors on which they can act to bring about an increase in agricultural productivity by reducing the gap between male-headed households and female-headed households.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-11-2023-0923
Nylon dyeing with reactive dyes by intermittent exposure to microwave irradiations to improve leveling
Authors: Irfan Mohammad , Gao Aiqin , Hou Aiqin 
Published: July 2024

Purpose
Reactive dyes are believed to have great potential for nylon dyeing, but these anionic dyes tend to rush toward the nylon at the beginning of the process, resulting in uneven dyeing. Achieving uniformity gets even harder when the dyeing is performed under exposure to eco-friendly technique microwave irradiations. This study aims to achieve rapid and homogenous results by intermittent shaking and non-continuous exposure to microwave.

Design/methodology/approach
A set of reactive red dyes, based on the same chromophore and different substituents in the auxochrome part, was applied to the nylon fabric without any leveling agent. A series of experiments were designed to investigate the effect of different dye structures, exhaustion pH, liquor ratio, exhaustion time and fixation time to obtain an optimum recipe under the microwave dyeing technique.

Findings
Dyeing performance was characterized based on the color strength, exhaustion and fixation percentages and color fastness values. The characterization showed that better results can be achieved at a liquor ratio of 1:15 at exhaustion pH 2.7 which is also the isoelectric point of nylon, with 5.5 to 7 min of exhaustion and 6 to 8 min of fixation time for different dyes. Microwave dyed samples secured higher color strength values and provided better exhaustion and fixation than the conventional dye samples. Furthermore, the X-ray diffraction results verified that there was no considerable difference in the morphological structure of nylon with microwave exposure.

Originality/value
An applied technique is disclosed in this work to achieve uniform dyeing on nylon 66 with reactive dyes without any leveling agent under exposure to eco-friendly rapid heating microwave irradiations.
Constrained simultaneous recovery of the depth to basement and lateral susceptibility variation
Authors: Liu Zhuo , Li Yaoguo , Xu Kaijun 
Published: July 2024

AbstractThe basin environment is a widely studied subject in both geology and geophysics for its economic significance in energy and mineral explorations. However, the estimation of the basement depth is often a challenging task given the complexity of the basement relief and lateral physical property change. Previous works simplify the problem by only inverting for the depth to the basement, and more recent studies have suggested the need to incorporate the variation of physical properties to improve basement structure imaging. In this study, we develop an inversion method with the associated workflow to simultaneously recover both the depth to a magnetic basement and a laterally varying magnetic susceptibility in the basement rock. To achieve this, we employ a set of constraints on the inverse problem. Particularly, both the recovered susceptibility and basement depth models are bounded below a possible maximum value, and the depth model is guided by a few depth points obtained from the resistivity models that are obtained from the one‐dimensional blocky inversions of magnetotelluric (MT) data. In addition, we apply the fuzzy C‐means (FCM) clustering to the susceptibility model during the inversion and use the inverted cluster centers to differentiate for different geological units in the basement. To show the effectiveness of our work, we compare the existing approaches and our method using two test inversions on one synthetic model resembling the basin–basement environment before demonstrating our method on a field data example with magnetic data collected by the U.S. Geological Survey (USGS) over the Illinois Basin. Our results show improved recovery in both basement relief and susceptibility in the basement rock, and inversion with field data is able to identify three different susceptibility zones in basement rock below the Illinois Basin.
Fecal bacterial communities of the platypus (Ornithorhynchus anatinus) reflect captivity status—Implications for conservation and management
Authors: DUNGAN Ashley M. , THOMAS Jessica L. 
Published: July 2024

AbstractThe duck‐billed platypus (Ornithorhynchus anatinus) is currently listed as near‐threatened. A key part of the conservation strategy for this species is its captive maintenance; however, captive animals often have dysbiotic gut bacterial microbiomes. Here, for the first time, we characterize the gut microbiome of wild platypus via fecal samples using high‐throughput sequencing of the bacterial 16S rRNA gene and identify microbial biomarkers of captivity in this species. At the phylum level, Firmicutes (50.4%) predominated among all platypuses, followed by Proteobacteria (28.7%), Fusobacteria (13.4%), and Bacteroidota (6.9%), with 21 “core” bacteria identified. Captive individuals did not differ in their microbial α‐diversity compared to wild platypus but had significantly different community composition (β‐diversity) and exhibited higher abundances of Enterococcus, which are potential pathogenic bacteria. Four taxa were identified as biomarkers of wild platypus, including Rickettsiella, Epulopiscium, Clostridium, and Cetobacterium. This contrast in gut microbiome composition between wild and captive platypus is an essential insight for guiding conservation management, as the rewilding of captive animal microbiomes is a new and emerging tool to improve captive animal health, maximize captive breeding efforts, and give reintroduced or translocated animals the best chance of survival.
Climate cycling did not affect haplotype distribution in an abundant Southern African avian habitat generalist species, the familiar chat (Oenanthe familiaris)
Authors: VOELKER Gary , WOGAN Guinevere O.U. , HUNTLEY Jerry W. , KALIBA Potiphar M. , DE SWARDT Dawie H. , BOWIE Rauri C. K. 
Published: July 2024

AbstractAvian species diversity in Southern Africa is remarkably high, yet the mechanisms responsible for that diversity are poorly understood. While this is particularly true with respect to species endemic to the subregion, it is unclear as to how more broadly distributed African species may have colonized southern Africa. One process that may in part account for the high bird species diversity in southern Africa is a “species pump” model, wherein the region was repeatedly colonized by lineages from areas further north: a pattern related to climate cycling and the eastern African arid corridor. Once occupying southern Africa, with its many varied biomes, it is possible that climate cycling further affected lineages by generating genetic diversity in multiple refugia, a pattern recently shown for several southern African bird species. Here, we used mtDNA to address these questions in a widespread, sedentary habitat generalist bird species, the familiar chat (Oenanthe familiaris). The phylogenetic structure suggests a north‐to‐south colonization pattern, supporting the “species pump” model. Haplotype diversity was partitioned into two distinct clusters: southern Africa and Malawi (East Africa). Southern African haplotypes were not geographically partitioned, and we hypothesize that this pattern has arisen because this species is a habitat generalist, and as such resilient to habitat‐altering climate perturbations. Based on our phylogenetic results, we discuss the validity of currently recognized subspecies.
Exploring the secrets of marine microorganisms: Unveiling secondary metabolites through metagenomics
Authors: Wang Shaoyu , Li Xinyan , Yang Weiqin , Huang Ranran 
Published: July 2024

AbstractMarine microorganisms are increasingly recognized as primary producers of marine secondary metabolites, drawing growing research interest. Many of these organisms are unculturable, posing challenges for study. Metagenomic techniques enable research on these unculturable microorganisms, identifying various biosynthetic gene clusters (BGCs) related to marine microbial secondary metabolites, thereby unveiling their secrets. This review comprehensively analyses metagenomic methods used in discovering marine microbial secondary metabolites, highlighting tools commonly employed in BGC identification, and discussing the potential and challenges in this field. It emphasizes the key role of metagenomics in unveiling secondary metabolites, particularly in marine sponges and tunicates. The review also explores current limitations in studying these metabolites through metagenomics, noting how long‐read sequencing technologies and the evolution of computational biology tools offer more possibilities for BGC discovery. Furthermore, the development of synthetic biology allows experimental validation of computationally identified BGCs, showcasing the vast potential of metagenomics in mining marine microbial secondary metabolites.
Advances in Aureobasidium research: Paving the path to industrial utilization
Authors: Xiao Difan , Driller Marielle , Dielentheis‐Frenken Marie , Haala Frederick , Kohl Philipp , Stein Karla , Blank Lars M. , Tiso Till 
Published: July 2024

AbstractWe here explore the potential of the fungal genus Aureobasidium as a prototype for a microbial chassis for industrial biotechnology in the context of a developing circular bioeconomy. The study emphasizes the physiological advantages of Aureobasidium, including its polyextremotolerance, broad substrate spectrum, and diverse product range, making it a promising candidate for cost‐effective and sustainable industrial processes. In the second part, recent advances in genetic tool development, as well as approaches for up‐scaled fermentation, are described. This review adds to the growing body of scientific literature on this remarkable fungus and reveals its potential for future use in the biotechnological industry.
Burning question: Rethinking organohalide degradation strategy for bioremediation applications
Authors: Lu Qihong , Liang Qi , Wang Shanquan 
Published: July 2024

AbstractOrganohalides are widespread pollutants that pose significant environmental hazards due to their high degree of halogenation and elevated redox potentials, making them resistant to natural attenuation. Traditional bioremediation approaches, primarily relying on bioaugmentation and biostimulation, often fall short of achieving complete detoxification. Furthermore, the emergence of complex halogenated pollutants, such as per‐ and polyfluoroalkyl substances (PFASs), further complicates remediation efforts. Therefore, there is a pressing need to reconsider novel approaches for more efficient remediation of these recalcitrant pollutants. This review proposes novel redox‐potential‐mediated hybrid bioprocesses, tailored to the physicochemical properties of pollutants and their environmental contexts, to achieve complete detoxification of organohalides. The possible scenarios for the proposed bioremediation approaches are further discussed. In anaerobic environments, such as sediment and groundwater, microbial reductive dehalogenation coupled with fermentation and methanogenesis can convert organohalides into carbon dioxide and methane. In environments with anaerobic‐aerobic alternation, such as paddy soil and wetlands, a synergistic process involving reduction and oxidation can facilitate the complete mineralization of highly halogenated organic compounds. Future research should focus on in‐depth exploration of microbial consortia, the application of ecological principles‐guided strategies, and the development of bioinspired‐designed techniques. This paper contributes to the academic discourse by proposing innovative remediation strategies tailored to the complexities of organohalide pollution.
What's different about digital? A qualitative interview study exploring experiences of adapting in‐person behaviour change interventions for digital delivery
Authors: Cooney Eva , Toomey Elaine , Ryan Kathleen , Meade Oonagh , McSharry Jenny 
Published: July 2024

AbstractObjectivesDigital health behaviour change interventions may be adapted from in‐person interventions, without appropriate consideration of how the digital context might differ. Drawing on the wider literature on behaviour change intervention development, this research aims to explore the digital adaptation process of health behaviour change interventions and the specific considerations for digital modes of delivery.DesignA qualitative interview study.MethodsInterviews with 15 intervention developers/facilitators were analysed using inductive thematic analysis.ResultsFindings highlight a continuum of digitalization, where variation in technology available and human support influences considerations for digital adaptation. ‘What vs how: “trying to do the impossible”’ describes the balance between retaining the intervention's active ingredients while modifying for digital delivery. Through ‘Trial and error’, participants described an iterative process based on experience of delivery. ‘Creating connection and engagement’ emphasizes the importance of social support and the challenges of replicating this.ConclusionsSeveral considerations for digital adaptations are proposed including the involvement of end‐users (facilitators and recipients) during adaptation, the need to understand the original intervention and new context for use, and the different motivational needs of digital intervention recipients.
Comprehensive immune modulation mechanisms of Angong Niuhuang Wan in ischemic stroke: Insights from mass cytometry analysis
Authors: Yao Yang , Ni Weihua , Feng Liangshu , Meng Jihong , Tan Xiaomu , Chen Hansen , Shen Jiangang , Zhao Heng 
Published: July 2024

AbstractBackgroundAngong Niuhuang Wan (AGNHW, 安宫牛黄丸), is a classical medicinal formula in Traditional Chinese Medicine (TCM) that has been appreciated for its neuroprotective properties in ischemic cerebral injuries, yet its intricate mechanisms remain only partially elucidated.AimsThis study leverages advanced Mass cytometry (CyTOF) to analyze AGNHW's multifaceted immunomodulation effects in‐depth, emphasizing previously underexplored areas.ResultsAGNHW mitigated monocyte‐derived macrophages (MoDM) infiltration in the brain, distinguishing its effects on those from microglia. While the vehicle group exhibited elevated inflammatory markers like CD4, CD8a, and CD44 in ischemic brains, the AGNHW‐treated group attenuated their expressions, indicating AGNHW's potential to temper the post‐ischemic inflammatory response. Systemically, AGNHW modulated fundamental immune cell dynamics, notably augmenting CD8+ T cells, B cells, monocytes, and neutrophil counts in the peripheral blood under post‐stroke conditions. Intracellularly, AGNHW exhibited its targeted modulation of the signaling pathways, revealing a remarked inhibition of key markers like IκBα, indicating potential suppression of inflammatory responses in ischemic brain injuries.ConclusionThis study offers a comprehensive portrait of AGNHW's immunomodulation effects on ischemic stroke, illuminating its dual sites of action—both cerebral and systemic—and its nuanced modulation of cellular and molecular dynamics.