Search

The pathogenesis of Alzheimer's disease (AD) depends on environmental and heritable factors, with its molecular etiology still unclear. Here we present a spatial transcriptomic (ST) and single-nucleus transcriptomic survey of late-onset sporadic AD and AD in Down syndrome (DSAD). Studying DSAD provides an opportunity to enhance our understanding of the AD transcriptome, potentially bridging the gap between genetic mouse models and sporadic AD. We identified transcriptomic changes that may underlie cortical layer-preferential pathology accumulation. Spatial co-expression network analyses revealed transient and regionally restricted disease processes, including a glial inflammatory program dysregulated in upper cortical layers and implicated in AD genetic risk and amyloid-associated processes. Cell-cell communication analysis further contextualized this gene program in dysregulated signaling networks. Finally, we generated ST data from an amyloid AD mouse model to identify cross-species amyloid-proximal transcriptomic changes with conformational context., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

Background: Due to the diversity of Shiga toxin-producing Escherichia coli (STEC) isolates, detecting highly pathogenic strains in foodstuffs is challenging. Currently, reference protocols for STEC rely on the molecular detection of eae and the stx1 and/or stx2 genes, followed by the detection of serogroup-specific wzx or wzy genes related to the top 7 serogroups. However, these screening methods do not distinguish between samples in which a STEC possessing both determinants are present and those containing two or more organisms, each containing one of these genes. This study aimed to evaluate ecf1, Z2098, Z2099, and nleA genes as single markers and their combinations (ecf1/Z2098, ecf1/Z2099, ecf1/nleA, Z2098/Z2099, Z2098/nleA, and Z2099/nleA) as genetic markers to detect potentially pathogenic STEC by the polymerase chain reaction (PCR) in 96 animal samples, as well as in 52 whole genome sequences of human samples via in silico PCR analyses., Results: In animal isolates, Z2098 and Z2098/Z2099 showed a strong association with the detected top 7 isolates, with 100% and 69.2% of them testing positive, respectively. In human isolates, Z2099 was detected in 95% of the top 7 HUS isolates, while Z2098/Z2099 and ecf1/Z2099 were detected in 87.5% of the top 7 HUS isolates., Conclusions: Overall, using a single gene marker, Z2098, Z2099, and ecf1 are sensitive targets for screening the top 7 STEC isolates, and the combination of Z2098/Z2099 offers a more targeted initial screening method to detect the top 7 STEC isolates. Detecting non-top 7 STEC in both animal and human samples proved challenging due to inconsistent characteristics associated with the genetic markers studied., (© 2024. The Author(s).)

The study of neurodegenerative diseases, particularly tauopathies like Pick's disease (PiD) and Alzheimer's disease (AD), offers insights into the underlying regulatory mechanisms. By investigating epigenomic variations in these conditions, we identified critical regulatory changes driving disease progression, revealing potential therapeutic targets. Our comparative analyses uncovered disease-enriched non-coding regions and genome-wide transcription factor (TF) binding differences, linking them to target genes. Notably, we identified a distal human-gained enhancer (HGE) associated with E3 ubiquitin ligase (UBE3A), highlighting disease-specific regulatory alterations. Additionally, fine-mapping of AD risk genes uncovered loci enriched in microglial enhancers and accessible in other cell types. Shared and distinct TF binding patterns were observed in neurons and glial cells across PiD and AD. We validated our findings using CRISPR to excise a predicted enhancer region in UBE3A and developed an interactive database (http://swaruplab.bio.uci.edu/scROAD) to visualize predicted single-cell TF occupancy and regulatory networks., Competing Interests: COMPETING FINANCIAL INTERESTS The authors declare no competing interests.

Donkeys (Equus asinus) have been used extensively in agriculture and transportations since their domestication, ca. 5000-7000 years ago, but the increased mechanization of the last century has largely spoiled their role as burden animals, particularly in developed countries. Consequently, donkey breeds and population sizes have been declining for decades, and the diversity contributed by autochthonous gene pools has been eroded. Here, we examined coding-region data extracted from 164 complete mitogenomes and 1392 donkey mitochondrial DNA (mtDNA) control-region sequences to (i) assess worldwide diversity, (ii) evaluate geographical patterns of variation, and (iii) provide a new nomenclature of mtDNA haplogroups. The topology of the Maximum Parsimony tree confirmed the two previously identified major clades, i.e. Clades 1 and 2, but also highlighted the occurrence of a deep-diverging lineage within Clade 2 that left a marginal trace in modern donkeys. Thanks to the identification of stable and highly diagnostic coding-region mutational motifs, the two lineages were renamed as haplogroup A and haplogroup B, respectively, to harmonize clade nomenclature with the standard currently adopted for other livestock species. Control-region diversity and population expansion metrics varied considerably between geographical areas but confirmed North-eastern Africa as the likely domestication center. The patterns of geographical distribution of variation analyzed through phylogenetic networks and AMOVA confirmed the co-occurrence of both haplogroups in all sampled populations, while differences at the regional level point to the joint effects of demography, past human migrations and trade following the spread of donkeys out of the domestication center. Despite the strong decline that donkey populations have undergone for decades in many areas of the world, the sizeable mtDNA variability we scored, and the possible identification of a new early radiating lineage further stress the need for an extensive and large-scale characterization of donkey nuclear genome diversity to identify hotspots of variation and aid the conservation of local breeds worldwide., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Migliore et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In the Summer 2021 a seismic passive survey was carried out at Mefite d'Ansanto (Italy), well-known for the cold non-volcanic and lethal CO 2 emissions. Mefite is located close to that part of Irpinia region hosting the large historical earthquakes' faults, that generated the destructive magnitude 6.8 earthquake of 1980 and have been related to the CO 2 leakage by the scientific community. The survey was conducted by installing a small short-period seismic array with the purpose of determining the wavefield features and detecting the possible signature of the regional stress variations. By analyzing the acquired data, we have determined the properties of the seismic wavefield associated with the emission vents, in the intermediate frequency band, 1-15 Hz, which was found to be composed of a stationary background component and an intermittent higher energy one. Basing on our results, considerations on the medium properties and the deep source available information, we have depicted a schematic model of the shallow seismic source: the background components are linked to the shallower activity of the hydrothermal system, e.g. the bubbling, while the intermittent ones are likely generated by the passage of the overpressured gas, trapped in the first-tens-meters' layers, after overcoming the internal cohesion charge. The characteristics of the wavefield that we have defined, refer to a condition in which no regional earthquakes occurred and could be considered as a basis to identify possible significant variations linked to CO 2 emissions and to the regional stress changes., (© 2024. The Author(s).)

Subtilase exhibits strong cytotoxicity that was first described in O113:H21 strain in Australia as a plasmid- encoded cytotoxin (subAB1). Subsequently, chromosomal variants including subAB2-1, subAB2-2, and subAB2-3 were described. We aimed to investigate the presence of subAB genes in a collection of Shiga toxin-producing Escherichia coli (STEC) strains (n=101) isolated from different sources in Iran. A collection of 101 archived STEC strains isolated from cattle (n=50), goats (n=25), sheep (n=15), wild captive animals (n=8: persian fallow deer, n=3; caspian pony, n=1; Macaca mulatta, n=4), and humans (n=3) during 2007-2016 were analyzed for the detection of different genes encoding the Subtilase variants, plasmidic and chromosomal virulence genes, phylogroups and serogroups. Overall, 57 isolates (56.4%) carried at least one variant of subAB. Most strains from small ruminants including 93% of sheep and 96% of caprine isolates carried at least one chromosomally encoded variant (subAB-2-1 and/or subAb2-2). In contrast, 12 cattle isolates (24%) only harbored the plasmid encoded variant (subAB1). STEC strains from other sources, including deer, pony and humans were positive for subAB-2-1 and/or subAb2-2. Our results reveal the presence of potentially pathogenic genotypes among locus of enterocyte effacement (LEE)-negative isolates, and some host specificity related to Subtilase variants and other virulence markers that may aid in source tracking of STEC during outbreak investigations.

The application of a One Health approach recognizes that human health, animal health, plant health and ecosystem health are intrinsically connected. Tackling complex challenges associated with foodborne zoonoses, antimicrobial resistance, and emerging threats is imperative. Therefore, the One Health European Joint Programme was established within the European Union research programme Horizon 2020. The One Health European Joint Programme activities were based on the development and harmonization of a One Health science-based framework in the European Union (EU) and involved public health, animal health and food safety institutes from almost all EU Member States, the UK and Norway, thus strengthening the cooperation between public, medical and veterinary organizations in Europe. Activities including 24 joint research projects, 6 joint integrative projects and 17 PhD projects, and a multicountry simulation exercise facilitated harmonization of laboratory methods and surveillance, and improved tools for risk assessment. The provision of sustainable solutions is integral to a One Health approach. To ensure the legacy of the work of the One Health European Joint Programme, focus was on strategic communication and dissemination of the outputs and engagement of stakeholders at the national, European and international levels.

Postnatal genomic regulation significantly influences tissue and organ maturation but is under-studied relative to existing genomic catalogs of adult tissues or prenatal development in mouse. The ENCODE4 consortium generated the first comprehensive single-nucleus resource of postnatal regulatory events across a diverse set of mouse tissues. The collection spans seven postnatal time points, mirroring human development from childhood to adulthood, and encompasses five core tissues. We identified 30 cell types, further subdivided into 69 subtypes and cell states across adrenal gland, left cerebral cortex, hippocampus, heart, and gastrocnemius muscle. Our annotations cover both known and novel cell differentiation dynamics ranging from early hippocampal neurogenesis to a new sex-specific adrenal gland population during puberty. We used an ensemble Latent Dirichlet Allocation strategy with a curated vocabulary of 2,701 regulatory genes to identify regulatory "topics," each of which is a gene vector, linked to cell type differentiation, subtype specialization, and transitions between cell states. We find recurrent regulatory topics in tissue-resident macrophages, neural cell types, endothelial cells across multiple tissues, and cycling cells of the adrenal gland and heart. Cell-type-specific topics are enriched in transcription factors and microRNA host genes, while chromatin regulators dominate mitosis topics. Corresponding chromatin accessibility data reveal dynamic and sex-specific regulatory elements, with enriched motifs matching transcription factors in regulatory topics. Together, these analyses identify both tissue-specific and common regulatory programs in postnatal development across multiple tissues through the lens of the factors regulating transcription.

In this work, we studied the selective pressure and evolutionary analysis on the SARS-CoV-2 BF.7 and BQ.1.1 lineages circulating in Italy from July to December 2022. Two different datasets were constructed: the first comprised 694 SARS-CoV-2 BF.7 lineage sequences and the second comprised 734 BQ.1.1 sequences, available in the Italian COVID-19 Genomic (I-Co-Gen) platform and GISAID (last access date 15 December 2022). Alignments were performed with MAFFT v.7 under the Galaxy platform. The HYPHY software was used to study the selective pressure. Four positively selected sites (two in nsp3 and two in the spike ) were identified in the BF.7 dataset, and two (one in ORF8 and one in the spike gene) were identified in the BQ.1.1 dataset. Mutation analysis revealed that R408S and N440K are very common in the spike of the BF.7 genomes, as well as L452R among BQ.1.1. N1329D and Q180H in nsp3 were found, respectively, at low and rare frequencies in BF.7, while I121L and I121T were found to be rare in ORF8 for BQ.1.1. The positively selected sites may have been driven by the selection for increased viral fitness, under circumstances of defined selective pressure, as well by host genetic factors.

Introduction: The BIN1 coding variant rs138047593 (K358R) is linked to Late-Onset Alzheimer's Disease (LOAD) via targeted exome sequencing., Methods: To elucidate the functional consequences of this rare coding variant on brain amyloidosis and neuroinflammation, we generated BIN1 K358R knock-in mice using CRISPR/Cas9 technology. These mice were subsequently bred with 5xFAD transgenic mice, which serve as a model for Alzheimer's pathology., Results: The presence of the BIN1 K358R variant leads to increased cerebral amyloid deposition, with a dampened response of astrocytes and oligodendrocytes, but not microglia, at both the cellular and transcriptional levels. This correlates with decreased neurofilament light chain in both plasma and brain tissue. Synaptic densities are significantly increased in both wild-type and 5xFAD backgrounds homozygous for the BIN1 K358R variant., Discussion: The BIN1 K358R variant modulates amyloid pathology in 5xFAD mice, attenuates the astrocytic and oligodendrocytic responses to amyloid plaques, decreases damage markers, and elevates synaptic densities., Highlights: BIN1 rs138047593 (K358R) coding variant is associated with increased risk of LOAD. BIN1 K358R variant increases amyloid plaque load in 12-month-old 5xFAD mice. BIN1 K358R variant dampens astrocytic and oligodendrocytic response to plaques. BIN1 K358R variant decreases neuronal damage in 5xFAD mice. BIN1 K358R upregulates synaptic densities and modulates synaptic transmission., (© 2024 The Authors. Alzheimer's & Dementia published by Wiley Periodicals LLC on behalf of Alzheimer's Association.)

Drugs of abuse can persistently change the reward circuit in ways that contribute to relapse behavior, partly via mechanisms that regulate chromatin structure and function. Nuclear orphan receptor subfamily4 groupA member2 (NR4A2, also known as NURR1) is an important effector of histone deacetylase 3 (HDAC3)-dependent mechanisms in persistent memory processes and is highly expressed in the medial habenula (MHb), a region that regulates nicotine-associated behaviors. Here, expressing the Nr4a2 dominant negative (Nurr2c) in the MHb blocks reinstatement of cocaine seeking in mice. We use single-nucleus transcriptomics to characterize the molecular cascade following Nr4a2 manipulation, revealing changes in transcriptional networks related to addiction, neuroplasticity, and GABAergic and glutamatergic signaling. The network controlled by NR4A2 is characterized using a transcription factor regulatory network inference algorithm. These results identify the MHb as a pivotal regulator of relapse behavior and demonstrate the importance of NR4A2 as a key mechanism driving the MHb component of relapse., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Mediastinal cysts (MCs) are rare lesions that can arise from embryonic remnants of various mediastinal structures. MCs usually are incidental findings in dogs and cats; however, they can reach a mass-like appearance. The description of MCs on CT in dogs is limited. This retrospective, single-center, descriptive, prevalence study aimed to determine the prevalence of presumed mediastinal cysts (PMCs) in dogs and assess their CT characteristics. Dogs that underwent a thoracic CT scan from January 2019 to August 2021 were included. CT images were evaluated for the presence of PMCs by two diagnostic imaging interns, two last year diagnostic imaging residents, and a board-certified veterinary radiologist. Number, location, margins, shape, volume, size, mass effect, and attenuation values of PMCs were assessed. A total of 866 CT scans were reviewed, and 49 PMCs were identified. The prevalence of PMCs in dogs was 5.66%. English Bulldog and mixed-breed dogs were subjectively overrepresented; however, the possibility of population bias could not be excluded. PMCs were subjectively more frequently observed in male dogs. The PMCs were predominantly round, small, solitary fluid-filled findings localized in the cranioventral mediastinum, with well-defined margins, homogeneous attenuation, and no contrast enhancement. The median attenuation value was 6.32 HU (range: -20.16 to 23.45 HU) precontrast and 7.58 HU (range: -2.45 to 20.79 HU) postcontrast, and the median volume was 1.19 cm 3 (range: 0.02-45.32 cm 3 ). Although the prevalence of PMCs was low in our sample population, findings supported prioritizing a differential diagnosis of incidental PMC for dogs with the above imaging characteristics., (© 2024 American College of Veterinary Radiology.)

Sustainable food systems involve the recycling of biowaste and water. This study characterizes thirty-one top soil improvers of anthropogenic, animal, and green waste origin, along with eleven irrigation waters from rivers, channels, and civil wastewater treatment plants (cWWTPs) for the presence of antimicrobials. Liquid chromatography coupled with hybrid High-Resolution Mass Spectrometry (LC-HRMS/MS) was employed to identify forty-eight drugs belonging to the classes of sulfonamides (11), tetracyclines (7), fluoroquinolones (10), macrolides (12), amphenicols (3), pleuromutilins (2), diaminopyrimidines (1), rifamycins (1) and licosamides (1). Sludge from cWWTPs, animal manure, slurry, and poultry litter exhibited the highest loads for sulfonamides, tetracyclines, fluoroquinolones and macrolides (80, 470, 885, and 4,487 ng g -1 wet weight, respectively) with nor- and ciprofloxacin serving as markers for anthropogenic sources. In compost and digestate, antimicrobials were found to be almost always below the limits of quantification. Reused water from cWWTPs for irrigation in open-field lettuce production were contaminated in the range of 12-221 ng L -1 with sulfonamides, tetracyclines, and fluoroquinolones, compared to very few detected in channels and surface waters. The Antimicrobials Hazard Index (HI), based on the Predicted No Effect Concentration for Antimicrobial Resistance (PNEC AMR ), was significantly >100 in contaminated topsoil improvers from urban and animal sources. Accounting for worst-case inputs from topsoil improvers and irrigation water, as well as dilution factors in amended soil, fluoroquinolones only exhibited an HI around 1 in open fields for lettuce production. The origin of topsoil improvers plays a pivotal role in ensuring safe and sustainable leafy vegetable production, thereby mitigating the risk of Antimicrobial Resistance (AMR) onset in food-borne diseases and the transfer of AMR elements to the human gut flora.

The recycling of biowaste from municipal wastewater treatment plants (WWTPs) in agriculture represents a circular economy-driven source of water and nutrients to support food system sustainability. However, biowaste may represent the source of emerging hazards of anthropogenic and animal origin that can transfer from agricultural soils to related food production, posing a risk to consumers' health, as in the case of outbreaks due to the consumption of ready-to-eat leafy vegetables contaminated with pathogenic E. coli . From this perspective, we propose a combined strategy based on both classical methods and culture-independent metagenomics approaches to identify microbial hazards relevant to foodborne diseases in WWTP-related biowastes. The virulence genes targeted by real-time PCR, performed before and after the enrichment of the raw samples, may represent a proxy for the viability of pathogens, the presence of which is then confirmed via classical microbiological methods. Bioinformatics analysis of shotgun metagenomic sequences could assess the presence of genes associated with resistance to specific antimicrobials followed by phenotypic confirmation via cultivation of the raw samples in the presence of the predicted molecules. Bacterial 16S rDNA analysis supports biowaste traceability based on their taxonomic composition. This strategy would support a "One Health" Action based on a cross-cutting assessment of emerging food-borne risks along the food chain., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Co-published by Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, and American Chemical Society.)

Typical hemolytic uremic syndrome (HUS) is mainly caused by Shiga toxin-producing Escherichia coli (STEC) releasing Shiga toxin 2 (Stx2). Two different structures of this AB5 toxin have been described: uncleaved, with intact B and A chains, and cleaved, with intact B and a nicked A chain consisting of two fragments, A1 and A2, connected by a disulfide bond. Despite having the same toxic effect on sensitive cells, the two forms differ in their binding properties for circulating cells, serum components and complement factors, thus contributing to the pathogenesis of HUS differently. The outcome of STEC infections and the development of HUS could be influenced by the relative amounts of uncleaved or cleaved Stx2 circulating in patients' blood. Cleaved Stx2 was identified and quantified for the first time in four out of eight STEC-infected patients' sera by a method based on the inhibition of cell-free translation. Cleaved Stx2 was present in the sera of patients with toxins bound to neutrophils and in two out of three patients developing HUS, suggesting its involvement in HUS pathogenesis, although in association with other bacterial or host factors.

Introduction: Intervertebral disc protrusion (IVDP) is a neurological disorder commonly observed at the lumbosacral junction of old, medium-to-large breeds, non-chondrodystrophic dogs. Although uncommon, lumbosacral IVDP can also be seen in chondrodystrophic dogs, among them French Bulldogs (FBs) and could be associated with congenital vertebral malformations in this breed. This study aims to evaluate the prevalence, clinical features, and MRI characteristics of lumbosacral IVDP and congenital vertebral malformations in FBs diagnosed with thoracic or lumbar intervertebral disc extrusion (IVDE) and to evaluate the possible interference of the neurologic deficits related to chronic IVDP on neurological examination., Materials and Methods: This is a single-center, retrospective case series. A search for FBs diagnosed with IVDE affecting the thoracic or lumbar regions is done on the database of the AniCura I Portoni Rossi Veterinary Hospital (Zola Predosa, Bologna, Italy). Eligible dogs have a complete medical report and a high-field MRI of the lumbosacral junction. MRIs of the lumbosacral junction are evaluated to determine the position of IVDP, cranial intervertebral foraminal stenosis, and signs of nerve root involvement. Radiographs, when available, are reviewed to identify the presence of lumbosacral congenital vertebral malformations., Results: Eighty FBs are included in the study. The prevalence of lumbosacral IVDP among FBs is 91.3%. Among FBs with lumbosacral IVDP, 45.0% show concurrent cranial intervertebral foraminal stenosis, 28.8% exhibit concurrent nerve root involvement, 56.2% appear to be asymptomatic for lumbosacral changes, while 15.1% manifest a decreased or absent withdrawal reflex as a supposed consequence of chronic lumbosacral IVDP. Congenital vertebral malformations are detected in 10 dogs., Conclusion: The results of this study support the hypothesis that lumbosacral IVDP is frequent in FBs presenting with thoracic or lumbar IVDE. In over half the dogs lumbosacral IVDP appears to be asymptomatic; however, in other cases, chronic lumbosacral IVDP seems to cause neurological deficits that may lead to erroneous localization of acute IVDE, representing a confounding factor for clinicians., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 La Rosa, Morabito, Carloni, Davini, Remelli, Specchi and Bernardini.)

Background: Peripheral nerve sheath tumors (PNSTs) are a group of neoplasms originating from Schwann cells or pluripotent cell of the neural crest. Therapeutic options and prognosis are influenced by their degree of malignancy and location., Hypothesis/objectives: Identify magnetic resonance imaging (MRI) features predictive of PNST histologic grade., Animals: Forty-four dogs with histopathological diagnosis of spinal PNSTs and previous MRI investigation., Methods: A multicenter retrospective study including cases with (a) histopathologic diagnosis of PNST and (b) MRI studies available for review. Histologic slides were reviewed and graded by a board-certified pathologist according to a modified French system (FNCLCC) for grading soft tissue sarcomas. The MRI studies were reviewed by 2 board-certified radiologists blinded to the grade of the tumor and the final decision on the imaging characteristics was reached by consensus. Relationships between tumor grade and histological and MRI findings were assessed using statistical analysis., Results: Forty-four cases met inclusion criteria; 16 patients were PNSTs Grade 1 (low-grade), 19 were PNSTs Grade 2 (medium-grade), and 9 were PNSTs Grade 3 (high-grade). Large volume (P = .03) and severe peripheral contrast enhancement (P = .04) were significantly associated with high tumor grade. Degree of muscle atrophy, heterogeneous signal and tumor growth into the vertebral canal were not associated with grade., Conclusions and Clinical Importance: Grade of malignancy was difficult to identify based on diagnostic imaging alone. However, some MRI features were predictive of high-grade PNSTs including tumor size and peripheral contrast enhancement., (© 2023 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals LLC on behalf of American College of Veterinary Internal Medicine.)

The SARS-CoV-2 Delta variant of concern (VOC) was often associated with serious clinical course of the COVID-19 disease. Herein, we investigated the selective pressure, gene flow and evaluation on the frequencies of mutations causing amino acid substitutions in the Delta variant in three Italian regions. A total of 1500 SARS-CoV-2 Delta genomes, collected in Italy from April to October 2021 were investigated, including a subset of 596 from three Italian regions. The selective pressure and the frequency of amino acid substitutions and the prediction of their possible impact on the stability of the proteins were investigated. Delta variant dataset, in this study, identified 68 sites under positive selection: 16 in the spike (23.5%), 11 in nsp2 (16.2%) and 10 in nsp12 (14.7%) genes. Three of the positive sites in the spike were located in the receptor-binding domain (RBD). In Delta genomes from the three regions, 6 changes were identified as very common (>83.7%), 4 as common (>64.0%), 21 at low frequency (2.1%-25.0%) and 29 rare (≤2.0%). The detection of positive selection on key mutations may represent a model to identify recurrent signature mutations of the virus.

Background: Hypophosphatemia is a common electrolyte disorder in critically ill patients undergoing prolonged kidney replacement therapy (KRT). We evaluated the efficacy and safety of a simplified regional citrate anticoagulation (RCA) protocol for continuous venovenous hemofiltration (CVVH), continuous venovenous hemodiafiltration (CVVHDF) and sustained low-efficiency dialysis filtration (SLED-f). We aimed at preventing KRT-related hypophosphatemia while optimizing acid-base equilibrium., Methods: KRT was performed by the Prismax system (Baxter) and polyacrylonitrile AN69 filters (ST 150, 1.5 m2, Baxter), combining a 18 mmol/L pre-dilution citrate solution (Regiocit 18/0, Baxter) with a phosphate-containing solution (HPO42- 1.0 mmol/L, HCO3- 22.0 mmol/L; Biphozyl, Baxter). When needed, phosphate loss was replaced with sodium glycerophosphate pentahydrate (Glycophos™ 20 mmol/20 mL, Fresenius Kabi Norge AS, Halden, Norway). Serum citrate measurements were scheduled during each treatment. We analyzed data from three consecutive daily 8-h SLED-f sessions, as well as single 72-h CVVH or 72-h CVVHDF sessions. We used analysis of variance (ANOVA) for repeated measures to evaluate differences in variables means (i.e. serum phosphate, citrate). Because some patients received phosphate supplementation, we performed analysis of covariance (ANCOVA) for repeated measures modelling phosphate supplementation as a covariate., Results: Forty-seven patients with acute kidney injury (AKI) or end stage kidney disease (ESKD) requiring KRT were included [11 CVVH, 11 CVVHDF and 25 SLED-f sessions; mean Acute Physiology and Chronic Health Evaluation II (APACHE II) score 25 ± 7.0]. Interruptions for irreversible filter clotting were negligible. The overall incidence of hypophosphatemia (s-P levels <2.5 mg/dL) was 6.6%, and s-P levels were kept in the normality range irrespective of baseline values and the KRT modality. The acid-base balance was preserved, with no episode of citrate accumulation., Conclusions: Our data obtained with a new simplified RCA protocol suggest that it is effective and safe for CVVH, CVVHDF and SLED, allowing to prevent KRT-related hypophosphatemia and maintain the acid-base balance without citrate accumulation., Trial Registration: NCT03976440 (registered 6 June 2019)., (© The Author(s) 2023. Published by Oxford University Press on behalf of the ERA.)

Sepsis-Associated Acute Kidney Injury is a life-threatening condition leading to high morbidity and mortality in critically ill patients admitted to the intensive care unit. Over the past decades, several extracorporeal blood purification therapies have been developed for both sepsis and sepsis-associated acute kidney injury management. Despite the widespread use of extracorporeal blood purification therapies in clinical practice, it is still unclear when to start this kind of treatment and how to define its efficacy. Indeed, several questions on sepsis-associated acute kidney injury and extracorporeal blood purification therapy still remain unresolved, including the indications and timing of renal replacement therapy in patients with septic vs. non-septic acute kidney injury, the optimal dialysis dose for renal replacement therapy modalities in sepsis-associated acute kidney injury patients, and the rationale for using extracorporeal blood purification therapies in septic patients without acute kidney injury. Moreover, the development of novel extracorporeal blood purification therapies, including those based on the use of adsorption devices, raised the attention of the scientific community both on the clearance of specific mediators released by microorganisms and by injured cells and potentially involved in the pathogenic mechanisms of organ dysfunction including sepsis-associated acute kidney injury, and on antibiotic removal. Based on these considerations, the joint commission of the Italian Society of Anesthesiology and Critical Care (SIAARTI) and the Italian Society of Nephrology (SIN) herein addressed some of these issues, proposed some recommendations for clinical practice and developed a common framework for future clinical research in this field., (© 2023. The Author(s).)

Background: Extracorporeal therapies (ET) are increasingly used in pediatric settings as adjuvant therapeutic strategies for overwhelming inflammatory conditions. Although these treatments seem to be effective for removing inflammatory mediators, their influence on antimicrobials pharmacokinetic should not be neglected. Methods: A prospective observational study of children admitted to the pediatric intensive care unit (PICU) with a diagnosis of sepsis/septic shock. All critically ill children received hemoadsorption treatment with CytoSorb (CS) in combination with CKRT. Therapeutic drug monitoring has been performed on 10 critically ill children, testing four antimicrobial molecules: meropenem, ceftazidime, amikacin and levofloxacin. In order to evaluate the total and isolated CKRT and CS contributions to antibiotic removal, blood samples at each circuit point (post-hemofilter, post-CS and in the effluent line) were performed. Therefore, the clearance and mass Removal (MR) of the hemofilter and CS were calculated. Results: Our preliminary report describes a different impact of CS on these target drugs removal: CS clearance was low for amikacine (6-12%), moderate for ceftazidime (43%) and moderate to high for levofloxacine (52-72%). Higher MR and clearance were observed with CKRT compared to CS. To the best of our knowledge, this is the first report regarding pharmacokinetic dynamics in critically ill children treated with CKRT and CS for septic shock.

The Inter European Union Reference Laboratories (EURLs) Working Group on Next Generation Sequencing (NGS) involves eight EURLs for microbiological food and feed hazards and has been working since 2017 to promote the adoption of NGS by the National Reference Laboratories (NRLs) in the European Union. This work illustrates the results of the first 5 years of activity. By working together, the EURLs involved have released guidance documents for assisting NRLs in all the steps of NGS, helping the transition from classical molecular methods towards whole genome sequencing while ensuring harmonization, with the final aim of improving preparedness in the use of NGS to characterize microbial hazards and trace the sources of infection.

Background: Radiotherapy (RT) is an effective treatment for dogs presented with neurologic signs caused by pituitary tumors. However, its impact on the outcome of concurrent pituitary-dependent hypercortisolism (PDH) is controversial., Objectives: Determine whether dogs with PDH have longer survival after pituitary RT compared with dogs with nonhormonally active pituitary masses and to evaluate whether clinical, imaging, and RT variables affect survival., Animals: Ninety-four dogs divided into 2 groups: PDH and non-PDH, based on the presence of hypercortisolism. Forty-seven dogs were allocated to the PDH group and 47 to the non-PDH group., Methods: Retrospective cohort study in which clinical records of dogs undergoing RT for pituitary macroadenomas between 2008 and 2018 at 5 referral centers were retrospectively evaluated., Results: Survival was not statistically different between PDH and non-PDH groups (median survival time [MST], 590 days; 95% confidence interval [CI], 0-830 days and 738 days; 95% CI, 373-1103 days, respectively; P = .4). A definitive RT protocol was statistically associated with longer survival compared with a palliative protocol (MST 605 vs 262 days, P = .05). The only factor statistically associated with survival from multivariate Cox proportional hazard analysis was total radiation dose (Gy) delivered (P < .01)., Conclusions and Clinical Importance: No statistical difference in survival was identified between the PDH and non-PDH groups, and longer survival was associated with higher Gy delivered., (© 2023 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals LLC on behalf of American College of Veterinary Internal Medicine.)

Biological systems are immensely complex, organized into a multi-scale hierarchy of functional units based on tightly regulated interactions between distinct molecules, cells, organs, and organisms. While experimental methods enable transcriptome-wide measurements across millions of cells, popular bioinformatic tools do not support systems-level analysis. Here we present hdWGCNA, a comprehensive framework for analyzing co-expression networks in high-dimensional transcriptomics data such as single-cell and spatial RNA sequencing (RNA-seq). hdWGCNA provides functions for network inference, gene module identification, gene enrichment analysis, statistical tests, and data visualization. Beyond conventional single-cell RNA-seq, hdWGCNA is capable of performing isoform-level network analysis using long-read single-cell data. We showcase hdWGCNA using data from autism spectrum disorder and Alzheimer's disease brain samples, identifying disease-relevant co-expression network modules. hdWGCNA is directly compatible with Seurat, a widely used R package for single-cell and spatial transcriptomics analysis, and we demonstrate the scalability of hdWGCNA by analyzing a dataset containing nearly 1 million cells., Competing Interests: The authors declare no competing interests., (© 2023 The Author(s).)

Pathogen genomics is transforming surveillance of infectious diseases, deepening our understanding of evolution and diffusion of etiological agents, host-pathogen interactions and antimicrobial resistance. This discipline is playing an important role in the development of One Health Surveillance with public health experts of various disciplines integrating methods applied to pathogen research, monitoring, management and prevention of outbreaks. Especially with the notion that foodborne diseases may not be transmitted by food only, the ARIES Genomics project aimed to deliver an Information System for the collection of genomic and epidemiological data to enable genomics-based surveillance of infectious epidemics, foodborne outbreaks and diseases at the animal-human interface. Keeping in mind that the users of the system comprised persons with expertise in a wide variety of domains, the system was expected to be used with a low learning curve directly by the persons target of the analyses' results, keeping the information exchange chains as short as possible. As a result, the IRIDA-ARIES platform (https://irida.iss.it/) provides an intuitive web-based interface for multisectoral data collection and bioinformatic analyses. In practice, the user creates a sample and uploads the Next-generation sequencing reads, then an analysis pipeline is launched automatically performing a series of typing and clustering operations fueling the information flow. Instances of IRIDA-ARIES host the Italian national surveillance system for infections by Listeria monocytogenes (Lm) and the surveillance system for infections by Shigatoxin-producing Escherichia coli (STEC). As of today, the platform does not provide tools to manage epidemiological investigations but serves as an instrument of aggregation for risk monitoring, capable of triggering alarms on possible critical situations that might go unnoticed otherwise., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Knijn, Michelacci, Gigliucci, Tozzoli, Chiani, Minelli, Scavia, Ventola and Morabito.)

Renal replacement therapies (RRT) are essential to support critically ill patients with severe acute kidney injury (AKI), providing control of solutes, fluid balance and acid-base status. To maintain the patency of the extracorporeal circuit, minimizing downtime periods and blood losses due to filter clotting, an effective anticoagulation strategy is required.Regional citrate anticoagulation (RCA) has been introduced in clinical practice for continuous RRT (CRRT) in the early 1990s and has had a progressively wider acceptance in parallel to the development of simplified systems and safe protocols. Main guidelines on AKI support the use of RCA as the first line anticoagulation strategy during CRRT in patients without contraindications to citrate and regardless of the patient's bleeding risk.Experts from the SIAARTI-SIN joint commission have prepared this position statement which discusses the use of RCA in different RRT modalities also in combination with other extracorporeal organ support systems. Furthermore, advise is provided on potential limitations to the use of RCA in high-risk patients with particular attention to the need for a rigorous monitoring in complex clinical settings. Finally, the main findings about the prospective of optimization of RRT solutions aimed at preventing electrolyte derangements during RCA are discussed in detail., (© 2023. The Author(s).)