bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute postnatal inflammation alters adult microglial responses to LPS that are sex-, region- and timing of postnatal inflammation-dependent
Authors: Nikodemova Maria , Oberto Jose R. , Kaye Ethan L. , Berschel Mackenzie R. , Michaelson Alysha L. , Watters Jyoti J. , Mitchell Gordon S. 
Published: October 2024

Abstract
Background
Adverse events in early life can have impact lasting into adulthood. We investigated the long-term effects of systemic inflammation during postnatal development on adult microglial responses to lipopolysaccharide (LPS) in two CNS regions (cortex, cervical spinal cord) in male and female rats.

Methods
Inflammation was induced in Sprague-Dawley rats by LPS (1 mg/kg) administered intraperitoneally during postnatal development at P7, P12 or P18. As adults (12 weeks of age), the rats received a second LPS dose (1 mg/kg). Control rats received saline. Microglia were isolated 3 h post-LPS followed by gene expression analysis via qRT-PCR for pro-inflammatory (IL-6, iNOS, Ptgs2, C/EBPb, CD14, CXCL10), anti-inflammatory (CD68, Arg-1), and homeostatic genes (P2Y12, Tmemm119). CSF-1 and CX3CL1 mRNAs were analyzed in microglia-free homogenates.

Results
Basal gene expression in adult microglia was largely unaffected by postnatal inflammation. Adult cortical microglial pro-inflammatory gene responses to LPS were either unchanged or attenuated in rats exposed to LPS during postnatal development. Ptgs2, C/EBPb, CXCL10 and Arg-1 were the most affected genes, with expression significantly downregulated vs. rats without postnatal LPS. Spinal microglia were affected most by LPS at P18, with mixed and sometimes opposing effects on proinflammatory genes in males vs. females. Overall, male cortical vs. spinal microglia were more affected by postnatal LPS. Females were affected in both cortex and spinal cord, but the effect was dependent on timing of postnatal LPS. Overall, inflammatory challenge at P18 had greater effect on adult microglia vs. challenge at P12 or P7.

Conclusions
Long-lasting effects of postnatal inflammation on adult microglia depend on postnatal timing, CNS region and sex.
Selective neuronal expression of progranulin is sufficient to provide neuroprotective and anti-inflammatory effects after traumatic brain injury
Authors: Wang Sudena , Weyer Marc-Philipp , Hummel Regina , Wilken-Schmitz Annett , Tegeder Irmgard , Schäfer Michael K. E. 
Published: October 2024

AbstractProgranulin (PGRN), which is produced in neurons and microglia, is a neurotrophic and anti-inflammatory glycoprotein. Human loss-of-function mutations cause frontotemporal dementia, and PGRN knockout (KO) mice are a model for dementia. In addition, PGRN KO mice exhibit severe phenotypes in models of traumatic or ischemic central nervous system (CNS) disorders, including traumatic brain injury (TBI). It is unknown whether restoration of progranulin expression in neurons (and not in microglia) might be sufficient to prevent excessive TBI-evoked brain damage. To address this question, we generated mice with Nestin-Cre-driven murine PGRN expression in a PGRN KO line (PGRN-KONestinGrn) to rescue PGRN in neurons. PGRN expression analysis in primary CNS cell cultures from naïve mice and in (non-) injured brain tissue from PGRN-KONestinGrn revealed expression of PGRN in neurons but not in microglia. After experimental TBI, examination of the structural brain damage at 5 days post-injury (dpi) showed that the TBI-induced loss of brain tissue and hippocampal neurons was exacerbated in PGRN-KOGrnflfl mice (PGRN knockout with the mGrn fl-STOP-fl allele, Cre-negative), as expected, whereas the tissue damage in PGRN-KONestinGrn mice was similar to that in PGRN-WT mice. Analysis of CD68+ immunofluorescent microglia and Cd68 mRNA expression showed that excessive microglial activation was rescued in PGRN-KONestinGrn mice, and the correlation of brain injury with Cd68 expression suggested that Cd68 was a surrogate marker for excessive brain injury caused by PGRN deficiency. The results show that restoring neuronal PGRN expression was sufficient to rescue the exacerbated neuropathology of TBI caused by PGRN deficiency, even in the absence of microglial PGRN. Hence, endogenous microglial PGRN expression was not essential for the neuroprotective or anti-inflammatory effects of PGRN after TBI in this study.
Graphical Abstract
What validated instruments, that measure implementation outcomes, are suitable for use in the Paediatric Intensive Care Unit (PICU) setting? A systematic review of systematic reviews
Authors: Dodds Elizabeth , Redsell Sarah , Timmons Stephen , Manning Joseph C. 
Published: October 2024

Abstract
Background/aims
The measurement of implementation outcomes can establish the success of implementing evidence into practice. However, implementation outcomes are seldom measured in acute healthcare settings, such as Paediatric Intensive Care Units (PICU), and if they are used, are likely to be non-validated, site or intervention-specific measures. To address this literature gap, this systematic review of systematic reviews aims to identify validated instruments to measure implementation outcomes of new EBP interventions in a PICU setting.

Methods
A systematic review of systematic reviews was conducted in two phases. Phase One: Five electronic databases were searched between 06/10/22 and 14/10/22. Systematic reviews were selected using pre-determined eligibility criteria. Methodological quality was assessed using the Critical Appraisal Skills Programme tool and a data extraction table was used to allow further synthesis. Phase Two: Secondary eligibility criteria were used to extract and review instruments from the systematic reviews selected in Phase One. Instruments were analysed and mapped to the Consolidated Framework of Implementation Research (CFIR).

Results
Phase One: Searches resulted in 3195 unique papers. Five systematic reviews were eligible for inclusion. All examined the psychometric properties of each instrument, utilising different methods to do so; three considered their pragmatic or usability properties; and one identified instruments that were transferrable to different settings. Each systematic review identified that most included instruments had limited evidence of their validity or reliability and had poor psychometric properties. Phase two: 93 instruments were screened, and nine were eligible for analysis. After analysis and CFIR mapping, two instruments were identified as potentially adaptable to the PICU setting.

Conclusions
The methodological quality of implementation outcome measurement instruments is inadequate, warranting further validation research. Two instruments were identified that cover multiple CFIR domains and have scope to be adapted for use when implementing evidence-based practice into the PICU. Further work is needed to adapt and further validate an instrument for use in practice.

Trial registration
For transparency of procedures and methods, the protocol for this systematic review was registered with PROSPERO (registration number CRD42022361638L).
Improved detection of methylation in ancient DNA
Authors: Sawyer Susanna , Gelabert Pere , Yakir Benjamin , Llanos-Lizcano Alejandro , Sperduti Alessandra , Bondioli Luca , Cheronet Olivia , Neugebauer-Maresch Christine , Teschler-Nicola Maria , Novak Mario , Pap Ildikó , Szikossy Ildikó , Hajdu Tamás , Moiseyev Vyacheslav , Gromov Andrey , Zariņa Gunita , Meshorer Eran , Carmel Liran , Pinhasi Ron 
Published: October 2024

AbstractReconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA.
Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing
Authors: Henglin Mir , Ghareghani Maryam , Harvey William T. , Porubsky David , Koren Sergey , Eichler Evan E. , Ebert Peter , Marschall Tobias 
Published: October 2024

Abstract
Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce de novo haplotype-resolved assemblies often require either difficult-to-acquire parental data or an intermediate haplotype-collapsed assembly. Here, we present Graphasing, a workflow which synthesizes the global phase signal of Strand-seq with assembly graph topology to produce chromosome-scale de novo haplotypes for diploid genomes. Graphasing readily integrates with any assembly workflow that both outputs an assembly graph and has a haplotype assembly mode. Graphasing performs comparably to trio phasing in contiguity, phasing accuracy, and assembly quality, outperforms Hi-C in phasing accuracy, and generates human assemblies with over 18 chromosome-spanning haplotypes.
Classifying physical activity levels using Mean Amplitude Deviation in adults using a chest worn accelerometer: validation of the Vivalink ECG Patch
Authors: Luckhurst Jim , Hughes Cara , Shelley Benjamin 
Published: October 2024

Abstract
Background
The development of readily available wearable accelerometers has enabled clinicians to objectively monitor physical activity (PA) remotely in the community, a superior alternative to patient self-reporting measures. Critical to the value of these monitors is the ability to reliably detect when patients are undergoing ambulatory activity. Previous studies have highlighted the strength of using mean amplitude deviation (MAD) as a universal measure for analysing raw accelerometery data and defining cut-points between sedentary and ambulatory activities. Currently however there is little evidence surrounding the use of chest-worn accelerometers which can provide simultaneous monitoring of other physiological parameters such as heart rate (HR), RR intervals, and Respiratory Rate alongside accelerometery data. We aimed to calibrate the accelerometery function within the VivaLink ECG patch to determine the cut-point MAD value for differentiating sedentary and ambulatory activities.

Methods
We recruited healthy volunteers to undergo a randomised series of 9 activities that simulate typical free-living behaviours, while wearing a VivaLink ECG Patch (Campbell, California). MAD values were applied to a Generalised Linear Mixed Model to determine cut-points between sedentary and ambulatory activities. We constructed a Receiver Operating Characteristic (ROC) curve to analyse the sensitivity and specificity of the cut-off MAD value.

Results
Eighteen healthy adults volunteered to the study and mean MAD values were collected for each activity. The optimal MAD cut-point between sedentary and ambulatory activities was 47.73mG. ROC curve analysis revealed an area under the curve of 0.99 (p < 0.001) for this value with a sensitivity and specificity of 98% and 100% respectively.

Conclusion
In conclusion, the MAD cut-point determined in our study is very effective at categorising sedentary and ambulatory activities among healthy adults and may be of use in monitoring PA in the community with minimal burden. It will also be useful for future studies aiming to simultaneously monitor PA with other physiological parameters via chest worn accelerometers.
LysoPE mediated by respiratory microorganism Aeromicrobium camelliae alleviates H9N2 challenge in mice
Authors: Yan Qingsong , Xing Junhong , Zou Ruonan , Sun Mingjie , Zou Boshi , Wang Yingjie , Niu Tianming , Yu Tong , Huang Haibin , Yang Wentao , Shi Chunwei , Yang Guilian , Wang Chunfeng 
Published: October 2024

AbstractInfluenza remains a severe respiratory illness that poses significant global health threats. Recent studies have identified distinct microbial communities within the respiratory tract, from nostrils to alveoli. This research explores specific anti-influenza respiratory microbes using a mouse model supported by 16S rDNA sequencing and untargeted metabolomics. The study found that transferring respiratory microbes from mice that survived H9N2 influenza to antibiotic-treated mice enhanced infection resistance. Notably, the levels of Aeromicrobium were significantly higher in the surviving mice. Mice pre-treated with antibiotics and then inoculated with Aeromicrobium camelliae showed reduced infection severity, as evidenced by decreased weight loss, higher survival rates, and lower lung viral titres. Metabolomic analysis revealed elevated LysoPE (16:0) levels in mildly infected mice. In vivo and in vitro experiments indicated that LysoPE (16:0) suppresses inducible nitric oxide synthase (INOS) and cyclooxygenase-2 (COX2) expression, enhancing anti-influenza defences. Our findings suggest that Aeromicrobium camelliae could serve as a potential agent for influenza prevention and a prognostic marker for influenza outcomes.
Mapping stem volume in fast-growing eucalypt plantations: integrating spectral, textural, and temporal remote sensing information with forest inventories and spatial models
Authors: Aló Lívia Lanzi , le Maire Guerric , Thiersch Cláudio Roberto , Mota Thiago Santos , Pinheiro Rafael Costa , de Souza Passos José Raimundo 
Published: October 2024

Abstract
Key message
Accurate volume estimation in Eucalyptus plantation stands was achieved by a linear model using SPOT and Landsat multispectral imagery, specifically texture indices and pixel-scale NDVI time integrals, which reflect the local plantation growth history. Spatial modelling techniques such as Kriging with External Drift and Generalized Additive Model slightly improved predictions by accounting for spatial correlation of volume between sample points.

Context
Forest inventories are widely used to estimate stand production. To capture the inherent spatial variability within stands, spatial modelling techniques such as Kriging with External Drift (KED) and the generalized additive model (GAM) have emerged. These models incorporate information on spatial correlation and auxiliary variables that can be obtained from satellite imagery.

Aims
Our study explored the use of reflectance data from SPOT and Landsat multispectral imagery. We focused on texture indices and temporal integration of vegetation indices as auxiliary variables in KED and GAM to predict stem volume of fast-growing Eucalyptus sp. plantations in Brazil.

Methods
The components extracted from the high-resolution SPOT-6 image included spectral band values, band ratio metrics, key vegetation indices (NDVI, SAVI, and ARVI), texture measurements, and indices derived from texture analysis. Additionally, we included the accumulated NDVI time series acquired from Landsat 5, 7, and 8 satellites between the planting date and the forest inventory measurement date.

Results
The best linear model of stem volume using remotely sensed predictors gave an R-squared value of 0.95 and a Root Mean Square Error (RMSE) of 12.44 m3/ha. The R-squared increased to 0.96 and the RMSE decreased to 10.6 m3/ha when the same predictors were included as auxiliary variables in the KED and GAM spatial models.

Conclusion
The linear model using remotely sensed predictors contributed most to volume prediction, but the addition of spatial coordinates in the KED and GAM spatial models improved local volume predictions.
Fertility outcomes in cows with subclinical endometritis after clinical cure of clinical endometritis
Authors: Barański Wojciech , Zduńczyk Sławomir , Tobolski Dawid , Krupa Milena 
Published: October 2024

AbstractClinical endometritis (CE) is common in post-partum dairy cows and is associated with impaired reproductive performance. The aim of the study was to evaluate the effect of subclinical endometritis (SE) in cows clinically cured of CE on their fertility. The study was performed on 215 Holstein Friesian cows with CE diagnosed by vaginoscopy and ultrasound between 21 and 28 days after parturition. All cows were clinically examined three times at an interval of 2 weeks. Cows without signs of CE were considered cured, and endometrial samples from the uteri were collected by cytobrush to diagnose SE using cytological evaluation of polymorphonuclear neutrophils (PMNs) percentage. The threshold for SE was set at ≥ 5% PMNs. Intervals calving to oestrus and calving to conception, first AI pregnancy rate, pregnancy rate 200 days after artificial insemination (AI), the number of AI per pregnancy (AI/P), pregnancy loss, and culling rate were calculated. SE was diagnosed in 40.9% of cows clinically cured of CE. There were significant differences in the AI/P (3.2 vs. 2.6; p < 0.027) and the pregnancy loss (18.2% vs. 4.7%; p < 0.002) between cows with SE and without SE. Cows with SE showed a tendency towards longer interval calving to conception, lower pregnancy rate 200 days after AI, and higher culling rate. In conclusion, SE after a clinical cure of CE may reduce fertility in dairy cows.
Exploring the co-creation-innovativeness paradox: distance as an ecosystem characteristic of university spin-offs
Authors: Öberg Christina , Grundström Christina 
Published: October 2024

AbstractThrough empirical investigations into university spin-offs (USOs), we discovered innovativeness benefits derived from maintaining both academia and business partners at a distance. Distance should not be misconstrued as isolation; rather, it emphasises specific attributes where partners are maintained at arm’s length, affecting co-creation. Consequently, this paper explores how distance impacts the co-creation and innovativeness of USOs. It presents a longitudinal case study of a Swedish USO and conceptualises various types of distances, including actor-type, industry, supply-chain, geographical and knowledge-related distances. We explore the interplay between these different distance types as antecedents to USOs’ innovativeness and co-creation activities. The paper contributes to the existing literature by introducing the concept of distance as a critical characteristic affecting innovativeness and co-creation. By delineating various types of distances, it refines previous research on the characteristics of firm connections within university and business ecosystems.
Bacillus CotA laccase improved the intestinal health, amino acid metabolism and hepatic metabolic capacity of Pekin ducks fed naturally contaminated AFB1 diet
Authors: Ma Mingxin , Wang Qianqian , Liu Yanrong , Li Guiming , Liu Limeng , Wang Gaigai , Guo Yongpeng , Huang Shimeng , Ma Qiugang , Ji Cheng , Zhao Lihong 
Published: October 2024

Abstract
Background
Aflatoxin B1 (AFB1) is a prevalent contaminant in agricultural products, presenting significant risks to animal health. CotA laccase from Bacillus licheniformis has shown significant efficacy in degrading mycotoxins in vitro test. The efficacy of Bacillus CotA laccase in animals, however, remains to be confirmed. A 2 × 2 factorial design was used to investigate the effects of Bacillus CotA laccase level (0 or 1 U/kg), AFB1 challenge (challenged or unchallenged) and their interactions on ducks. The purpose of this study was to evaluate the efficacy of Bacillus CotA laccase in alleviating AFB1 toxicosis of ducks.

Results
Bacillus CotA laccase alleviated AFB1-induced declines in growth performance of ducks accompanied by improved average daily gain (ADG) and lower feed/gain ratio (F/G). Bacillus CotA laccase ameliorated AFB1-induced gut barrier dysfunctions and inflammation testified by increasing the jejunal villi height/crypt depth ratio (VH/CD) and the mRNA expression of tight junction protein 1 (TJP1) and zonula occluden-1 (ZO-1) as well as decreasing the expression of inflammation-related genes in the jejunum of ducks. Amino acid metabolome showed that Bacillus CotA laccase ameliorated AFB1-induced amino acid metabolism disorders evidenced by increasing the level of glutamic acid in serum and upregulating the expression of amino acid transport related genes in jejunum of ducks. Bacillus CotA laccase ameliorated AFB1-induced liver injury testified by suppressing oxidative stress, inhibiting apoptosis, and downregulating the expression of hepatic metabolic enzyme related genes of ducks. Moreover, Bacillus CotA laccase degraded AFB1 in digestive tract of ducks, resulting in the reduced absorption level of AFB1 across intestinal epithelium testified by the decreased level of AFB1-DNA adduct in the liver, and the reduced content of AFB1 residues in liver and feces of ducks.

Conclusions
Bacillus CotA laccase effectively improved the growth performance, intestinal health, amino acid metabolism and hepatic aflatoxin metabolism of ducks fed AFB1 diets, highlighting its potential as an efficient and safe feed enzyme for AFB1 degradation in animal production.

Graphical Abstract
Modern agriculture and One Health
Authors: Zhang Guangzhi , Qiu Yu , Boireau Pascal , Zhang Yinghui , Ma Xin , Jiang Hui , Xin Ting , Zhang Maodun , Tadesse Zelalem , Wani Nisar Ahmad , Song Junxia , Ding Jiabo 
Published: October 2024

Abstract
Background
The development of modern agriculture has significantly contributed to improving global food security and safety, alleviating poverty, and enhancing human health and livelihoods. However, the rapid advancement of modern agriculture has also brought about various challenges that limit its sustainable development. This commentary aims to discuss these issues through the One Health lens, and provide valuable insights for balancing modern agricultural activities with the need to protect and promote the health of all the sectors.

Main text
This commentary explores the multifaceted impacts of modern agriculture on social development, as well as the associated various health challenges and environmental impacts within the One Health framework. Key issues include ecosystem degradation, increased risk of interspecies disease transmission like zoonoses, reverse zoonoses, and vector-borne diseases, and the escalated threat of antimicrobial resistance due to intensified agricultural production and increased antimicrobial use. To address these challenges, this commentary outlines potential solutions anchored in the development and implementation of modern technologies and good agricultural practices, such as precision farming, integrated pest management, biosecurity measures, vaccination programs, as well as surveillance and early detection of health risks.

Conclusions
Good agricultural practices supported by scientific and technological advancements are essential for aligning productivity with the One Health vision, ensuring the health and resilience of all the sectors. Enhancing stakeholder education, strengthening regulatory frameworks, and providing supportive policies and infrastructure for farmers to adopt sustainable practices are crucial for the long-term viability of agrifood systems. The Food and Agriculture Organization of the United Nations plays a pivotal role in guiding this sustainable transformation through the One Health approach.
Comparison of wall paintings at Ostia Antica by NMR depth profiling
Authors: Urbanek Matea , Bader Jan , Krüger Daniel , Yong Alissa , Becker Hilary , Frick Jürgen , Anders Jens , Del Federico Eleonora , Tomassini Paolo , Blümich Bernhard 
Published: October 2024

Abstract
Painted walls were analyzed at Ostia Antica, the ancient port of Rome, with the aim to trace the evolution of the buildings in the city. Nuclear magnetic resonance (NMR) depth profiles were acquired from walls and mortar fragments to image the stratigraphy of the mortar-layer preparations for the painted surfaces produced over more than five centuries from the second century BC to the third century AD. The profiles are compared in search of similarity to obtain clues suggesting alike workmanship and contemporaneous origin, and to retrace the transformations of execution technique in time.