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Presents a study which examined a survey of imported dengue fever in university hospitals in France. Patients and methods; Results; Discussion.

BACKGROUND: Bone infection is a common issue in infectiology. The goid standard for evaluating bone infection is the white blood cell (WBC) scan. In our practice the WBC scan is coupied with a bone scan. Discordances in the results of these two examinations are a common occurrence in daily practice. We decided to investigate the meaning of these discordances. Materials and methods: Two hundred and ninety-six 99mTcHMPAO-labelled white blood cells (WBC) and 99mTc-HMDP bone scanning (BS) examinations were performed in our department between 1997 and 2003 for evaluation of bone infection. Out of these 296 examinations, a first rating extracted 54 scans that were considered discordant. These 54 scans were reviewed by three observers. Ciinical and paraciinicai data were obtained for all the cases definitely considered as discordant by all three observers. RESULTS: The observers finally retained-18 cases as discordant from the initiai 296 (6.1%). Thirteen patients were not infected, and five patients were considered infected based on ciinical follow-up or bacterioiogicai and histologicai data. For the 17 patients with WBC-, BS-^, 4 (23.5%) were infected. CONCLUSION: Our study shows that in the vast majority (17 out of 18), discordances consist of a negative WBC scan with a positive bone scan. In these cases the accuracy of the WBC scan is diminished as 23.5% ofthe patients with a negative WBC and a positive bone scan are infected. [ABSTRACT FROM AUTHOR]

The equation of state with light clusters for nuclear and stellar matter is determined using chemical equilibrium constants evaluated from the analysis of the recently published (Xe + Sn) heavy ion data, corresponding to three reactions with different isotopic contents of the emission source. The measured multiplicities are used to extract the thermodynamic properties, and an in-medium correction to the ideal gas internal partition function of the clusters is included in the analysis. This in-medium correction and its respective uncertainty are calculated via a Bayesian analysis, with the unique hypothesis that the different nuclear species in a given sample must correspond to a unique common value for the density of the expanding source. Different parameter sets for the correction are tested, and the effect of the radius of the clusters on the thermodynamics and on the chemical equilibrium constants is also addressed. It is shown that the equilibrium constants obtained are almost independent of the isospin content of the analysed systems. Finally, a comparison with a relativistic mean field model proves that data are consistent with a universal in-medium correction of the scalar σ-meson coupling for nucleons bound in clusters. The obtained value, , is larger than that obtained in a previous study not including in-medium effects in the data analysis. This result implies a smaller effect on the binding energy of the clusters and, as a consequence, larger melting densities, and an increased cluster contribution in supernova matter. [ABSTRACT FROM AUTHOR]

Rheumatoid arthritis (RA) is a progressive, inflammatory autoimmune disease of unknown aetiology. The complex mechanism of aetiopathogenesis, progress and chronicity of the disease involves genetic, epigenetic and environmental factors. To understand the molecular mechanisms underlying disease phenotypes, one has to place implicated factors in their functional context. However, integration and organization of such data in a systematic manner remains a challenging task. Molecular maps are widely used in biology to provide a useful and intuitive way of depicting a variety of biological processes and disease mechanisms. Recent large-scale collaborative efforts such as the Disease Maps Project demonstrate the utility of such maps as versatile tools to organize and formalize disease-specific knowledge in a comprehensive way, both human and machine-readable. We present a systematic effort to construct a fully annotated, expert validated, state-of-the-art knowledge base for RA in the form of a molecular map. The RA map illustrates molecular and signalling pathways implicated in the disease. Signal transduction is depicted from receptors to the nucleus using the Systems Biology Graphical Notation (SBGN) standard representation. High-quality manual curation, use of only human-specific studies and focus on small-scale experiments aim to limit false positives in the map. The state-of-the-art molecular map for RA, using information from 353 peer-reviewed scientific publications, comprises 506 species, 446 reactions and 8 phenotypes. The species in the map are classified to 303 proteins, 61 complexes, 106 genes, 106 RNA entities, 2 ions and 7 simple molecules. The RA map is available online at ramap.elixir-luxembourg.org as an open-access knowledge base allowing for easy navigation and search of molecular pathways implicated in the disease. Furthermore, the RA map can serve as a template for omics data visualization. [ABSTRACT FROM AUTHOR]

High-throughput RNA-sequencing has become the gold standard method for whole-transcriptome gene expression analysis, and is widely used in numerous applications to study cell and tissue transcriptomes. It is also being increasingly used in a number of clinical applications, including expression profiling for diagnostics and alternative transcript detection. However, despite its many advantages, RNA sequencing can be challenging in some situations, for instance in cases of low input amounts or degraded RNA samples. Several protocols have been proposed to overcome these challenges, and many are available as commercial kits. In this study, we systematically test three recent commercial technologies for RNA-seq library preparation (TruSeq, SMARTer and SMARTer Ultra-Low) on human biological reference materials, using standard (1 mg), low (100 ng and 10 ng) and ultra-low (<1 ng) input amounts, and for mRNA and total RNA, stranded and unstranded. The results are analyzed using read quality and alignment metrics, gene detection and differential gene expression metrics. Overall, we show that the TruSeq kit performs well with an input amount of 100 ng, while the SMARTer kit shows decreased performance for inputs of 100 and 10 ng, and the SMARTer Ultra-Low kit performs relatively well for input amounts <1 ng. All the results are discussed in detail, and we provide guidelines for biologists for the selection of an RNA-seq library preparation kit. [ABSTRACT FROM AUTHOR]

Résumé Objectif Comparer l’évolution de densité osseuse, à distance de l’induction thérapeutique, de patients infectés par le VIH, traités avec Ténofovir versus sans Ténofovir. Méthodes Nous avons comparé deux groupes : patients sous Ténofovir versus sans Ténofovir, sélectionnés parmi des patients infectés par le VIH, sous traitement continu depuis plus d’un an, ayant eu au moins deux ostéodensitométries à plus d’un an d’intervalle. Les critères de jugement principaux étaient les variations de densité osseuse lombaire (DOL), de densité osseuse corps entier et la variation osseuse individuelle significative de DOL (perte osseuse quand baisse > 0,04 g/cm 2 ). Différentes variables interférant avec la composition corporelle et la prescription de Ténofovir ont été recueillies via le dossier médical informatisé NADIS. Résultats Notre population comprenait 215 patients, 49 femmes et 166 hommes ; 112 patients sous Ténofovir, 103 patients sans ; suivis trois ans en moyenne. Le groupe sous Ténofovir a eu une perte moyenne de DOL de 0,008 g/cm 2 , contre un gain de 0,009 g/cm 2 pour le groupe sans Ténofovir ( p = 0,01). Un total de 22,7 % des patients sous Ténofovir ont eu une perte osseuse individuelle de DOL, contre 13 % des patients sans Ténofovir ( p = 0,07). En régression logistique multivariée, le fait d’être sous Ténofovir augmentait le risque d’avoir une perte osseuse de DOL, avec un odds ratio de 2,42 (intervalle de confiance à 95 % : 1,03–5,66, p = 0,042). Conclusion Dans notre travail, même à distance de l’induction thérapeutique, la prise de Ténofovir reste associée à une perte de densité osseuse. [ABSTRACT FROM AUTHOR]

Purpose: Cases of fracture-fixation device infection involving Staphylococcus lugdunensis are not frequent. The clinical characteristics and the choice of treatment strategies of these infections are not obviously known to date.Methods: We performed a review of fracture-fixation device infection involving S. lugdunensis managed by our centres.Results: Among the 38 cases of fracture-fixation device infection involving S. lugdunensis, 53% were located in the tibia. Most of our cases (87%) were chronic infections. Purulent discharge, which occurred in 79% of cases, was the most frequent clinical symptom, followed by pain in 63%, local inflammation in 55%, and fever in 37%. Bacteremia and severe sepsis occurred in 10% and 18% of cases, respectively. Four cases (10%) were treated exclusively with antimicrobial treatment alone. Thirty-four cases (89%) were treated with a combination of surgery with antimicrobial therapy including surgical debridement, antibiotics and osteosynthesis device retention in six cases (16%), and osteosynthesis device removal in 27 cases (71%). The mean length of antibiotic treatment was 119 days. The relapse rate was high that was not related to selection of resistant strains. Polymicrobial infection had no impact on clinical outcome. A combination of surgery with antimicrobial therapy was identified as a significant prognostic factor associated with remission (p = 0.042).Conclusions: S. lugdunensis is probably involved in more infections than has been reported. Using appropriate microbiological methods laboratories should routinely identify the species of all coagulase-negative Staphylococci isolates involved in fracture-fixation device infection to better achieve the treatment strategies of fracture-fixation device infection involving S. lugdunensis. [ABSTRACT FROM AUTHOR]

Abstract: Brown algae are important organisms both because of their key ecological roles in coastal ecosystems and because of the remarkable biological features that they have acquired during their unusual evolutionary history. The recent sequencing of the complete genome of the filamentous brown alga Ectocarpus has provided unprecedented access to the molecular processes that underlie brown algal biology. Analysis of the genome sequence, which exhibits several unusual structural features, identified genes that are predicted to play key roles in several aspects of brown algal metabolism, in the construction of the multicellular bodyplan and in resistance to biotic and abiotic stresses. Information from the genome sequence is currently being used in combination with other genomic, genetic and biochemical tools to further investigate these and other aspects of brown algal biology at the molecular level. Here, we review some of the major discoveries that emerged from the analysis of the Ectocarpus genome sequence, with a particular focus on the unusual genome structure, inferences about brown algal evolution and novel aspects of brown algal metabolism. [Copyright &y& Elsevier]

Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further. [ABSTRACT FROM AUTHOR]

We investigated nasopharyngeal carriage of Streptococcus pneumoniae and Staphylococcus aureus among infants and young children with acute otitis media in a country where use of 7-valent pneumococcal conjugate vaccine (PCV7) has been progressively implemented. Among 1783 children enrolled, 60.8% carried S. pneumoniae, and 9% carried S. aureus. Among S. pneumoniae carriers, the rate of S. aureus carriage was 8.4%, compared with 9.9% among S. pneumoniae noncarriers. The rate of S. pneumoniae carriage in the PCV7-vaccinated population was lower (59.8%) than that observed in the nonvaccinated population (66.2%; P < .04). In contrast, in young children (age, <2 years) with acute otitis media, our study suggests that the S. aureus carriage rate is not affected by PCV7 immunization (9.0% in vaccinated children vs. 8.7% in nonvaccinated children). Furthermore, in children aged >1 year, the booster dose induces a sharp reduction in the carriage of vaccine serotypes of S. pneumoniae, without any change in S. aureus carriage. [ABSTRACT FROM AUTHOR]

Study Objective. To determine whether discontinuation of stavudine or protease inhibitor therapy improves human immunodeficiency virus (HIV)-related fat distribution in men. Design. Observational, retrospective study consisting of a cross-sectional (part 1) and a longitudinal (part 2) study. Data Source. Medical records from Purpan University Hospital and La Grave University Hospital, Toulouse, France. Subjects. Eighty men with HIV infection treated with antiretrovirals and 151 healthy male controls matched for age. Measurements and Main Results. In part 1, body composition and fat distribution of the HIV-infected men were compared by dual energy x-ray absorptiometry (DEXA) with those of the controls to determine whether body fat distribution is altered in HIV-infected men. In part 2, we analyzed modifications of body composition and fat distribution in 45 of the 80 patients. These 45 had been exposed to antiretroviral drugs, including stavudine and a protease inhibitor, for at least 5 months before the first of two DEXA assessments. They received three different treatment strategies for several months. In group 1, stavudine was withdrawn; in group 2, protease inhibitor was discontinued, and in group 3, stavudine plus protease inhibitor were continued. Group 1 showed a significant fat gain in the lower extremities 31.7 ± 5.9 months after stavudine discontinuation (p<0.0001). Group 2 did not show any significant modification of total body, lower limb, or trunk fat despite protease inhibitor discontinuation for 35.2 ± 6.6 months. Findings were similar for group 3, who continued receiving stavudine-protease inhibitor therapy for 21.2 ± 12.8 months. Conclusion. These data suggest that long-term withdrawal of stavudine from the antiretroviral therapy regimen may be associated with significant improvement in lipoatrophy in the lower extremities, whereas long-term protease inhibitor withdrawal did not modify fat distribution. [ABSTRACT FROM AUTHOR]

A randomized, open-label trial was performed to study virological and intracellular interactions between stavudine and ribavirin in 30 patients coinfected with human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Patients were randomized to receive either interferon and ribavirin or no treatment for HCV infection for 3 months. Intracellular peripheral blood mononuclear cells' stavudine-triphosphate (TP) concentrations were assessed. Plasma HIV RNA levels did not change significantly between baseline and month 3. There was a nonstatistically significant trend for a lower median residual concentration of intracellular stavudine-TP in the treated group, compared with the control group. The same trend was also observed for peak concentrations. Coprescription of ribavirin and stavudine has no short-term impact on plasma HIV RNA level in HIV-HCV-coinfected patients treated with stavudine as a part of their antiretroviral treatment; this coprescription can be safely used, although an in vivo interaction between ribavirin and stavudine is possible. [ABSTRACT FROM AUTHOR]

The modification of the ground state properties of light atomic nuclei in the nuclear and stellar medium is addressed, using chemical equilibrium constants evaluated from a new analysis of the intermediate energy heavy-ion (Xe+Sn) collision data measured by the INDRA Collaboration. Three different reactions are considered, mainly differing by the isotopic content of the emission source. The thermodynamic conditions of the data samples are extracted from the measured multiplicities allowing for a parametrization of the in-medium modification, determined with the single hypothesis that the different nuclear species in a given sample correspond to a unique common value for the density of the expanding source. We show that this correction, which was not considered in previous analyses of chemical constants from heavy-ion collisions, is necessary, since the observables of the analyzed systems show strong deviations from the expected results for an ideal gas of free clusters. This dataset is further compared to a relativistic mean-field model, and seen to be reasonably compatible with a universal correction of the attractive σ-meson coupling. [ABSTRACT FROM AUTHOR]

Background: Prosthetic joint infection (PJI) caused by Candida spp is a severe complication of arthroplasty. We investigated the outcomes of Candida PJI., Methods: This was a retrospective observational multinational study including patients diagnosed with Candida-related PJI between 2010 and 2021. Treatment outcome was assessed at 2-year follow-up., Results: A total of 269 patients were analyzed. Median age was 73.0 (interquartile range [IQR], 64.0-79.0) years; 46.5% of patients were male and 10.8% were immunosuppressed. Main infection sites were hip (53.0%) and knee (43.1%), and 33.8% patients had fistulas. Surgical procedures included debridement, antibiotics, and implant retention (DAIR) (35.7%), 1-stage exchange (28.3%), and 2-stage exchange (29.0%). Candida spp identified were Candida albicans (55.8%), Candida parapsilosis (29.4%), Candida glabrata (7.8%), and Candida tropicalis (5.6%). Coinfection with bacteria was found in 51.3% of cases. The primary antifungal agents prescribed were azoles (75.8%) and echinocandins (30.9%), administered for a median of 92.0 (IQR, 54.5-181.3) days. Cure was observed in 156 of 269 (58.0%) cases. Treatment failure was associated with age >70 years (OR, 1.811 [95% confidence interval {CI}: 1.079-3.072]), and the use of DAIR (OR, 1.946 [95% CI: 1.157-3.285]). Candida parapsilosis infection was associated with better outcome (OR, 0.546 [95% CI: .305-.958]). Cure rates were significantly different between DAIR versus 1-stage exchange (46.9% vs 67.1%, P = .008) and DAIR versus 2-stage exchange (46.9% vs 69.2%, P = .003), but there was no difference comparing 1- to 2-stage exchanges (P = .777)., Conclusions: Candida PJI prognosis seems poor, with high rate of failure, which does not appear to be linked to immunosuppression, use of azoles, or treatment duration., Competing Interests: Potential conflicts of interest. The authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and clinical questions. DNA methylation analysis bears the particular promise to supplement or replace biochemical and imaging-based tests for the next generation of personalized medicine. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation and hydroxymethylation requiring an additional chemical or enzymatic step to identify hydroxymethylated cytosines. Here, we provide a detailed protocol based on a commercial kit for the preparation of sequencing libraries for the comprehensive whole-genome analysis of DNA methylation and/or hydroxymethylation. The protocol is based on the construction of sequencing libraries from limited amounts of input DNA by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion. For analyses requiring a quantitative distinction between 5-methylcytosine and 5-hydroxymethylcytosines levels, an oxidation step is included in the same workflow to perform oxidative bisulfite sequencing (OxBs-Seq). In this case, two sequencing libraries will be generated and sequenced: a classic methylome following bisulfite conversion and analyzing modified cytosines (not distinguishing between methylated and hydroxymethylated cytosines) and a methylome analyzing only methylated cytosines, respectively. Hydroxymethylation levels are deduced from the differences between the two reactions. We also provide a step-by-step description of the data analysis using publicly available bioinformatic tools. The described protocol has been successfully applied to different human and plant samples and yields robust and reproducible results., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Objectives: Blood-culture-negative infective endocarditis (BCNE) is found in 2 to 48% of cases of infective endocarditis (IE) (Houpikian and Raoult, 2005) [1].IE and vertebral osteomyelitis due to Chlamydia sp. are difficult to diagnose., Patients and Methods: A case report of Chlamydia psittaci IE is provided, associated with a literature review., Results: We report the first case of Chlamydia psittaci IE, revealed by a spondylodiscitis. Questioning of the patient, imaging, serologies and PCR techniques on valves confirmed the diagnosis., Conclusion: C. psittaci IE is rare but probably underdiagnosed. In case of negative blood cultures, questioning patients with IE about their contacts with animals is relevant. PCR techniques are reference tools for diagnosis confirmation when valve or vertebral samples are available., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Masson SAS. All rights reserved.)

Peripheral blood mononuclear cells (PBMCs) are blood cells that are a critical part of the immune system used to fight off infection, defending our bodies from harmful pathogens. In biomedical research, PBMCs are commonly used to study global immune response to disease outbreak and progression, pathogen infections, for vaccine development and a multitude of other clinical applications. Over the past few years, the revolution in single-cell RNA sequencing (scRNA-seq) has enabled an unbiased quantification of gene expression in thousands of individual cells, which provides a more efficient tool to decipher the immune system in human diseases. In this work, we generate scRNA-seq data from human PBMCs at high sequencing depth (>100,000 reads/cell) for more than 30,000 cells, in resting, stimulated, fresh and frozen conditions. The data generated can be used for benchmarking batch correction and data integration methods, and to study the effect of freezing-thawing cycles on the quality of immune cell populations and their transcriptomic profiles., (© 2023. The Author(s).)

The introduction of transcatheter pulmonary valve implantation (TPVI) has greatly benefited the management of right ventricular outflow tract dysfunction. Infective endocarditis (IE) is a feared complication of TPVI that affects valve durability and patient outcomes. Current recommendations provide only limited guidance on the management of IE after TPVI (TPVI-IE). This article, by a group of experts in congenital heart disease in children and adults, interventional cardiology, infectious diseases including IE, and microbiology, provides a comprehensive review of the current evidence on TPVI-IE, including its incidence, risk factors, causative organisms, diagnosis, and treatment. The incidence of TPVI-IE varies from 13-91/1000 person-years for Melody valves to 8-17/1000 person-years for SAPIEN valves. Risk factors include history of IE, DiGeorge syndrome, immunosuppression, male sex, high residual transpulmonary gradient and portal of bacteria entry. Staphylococci and streptococci are the most common culprits, whereas Staphylococcus aureus is associated with the most severe disease. In addition to the modified Duke criteria, a high residual gradient warrants a strong suspicion. Imaging studies are helpful for the diagnosis. Intravenous antibiotics guided by blood culture results are the mainstay of treatment. Invasive re-intervention may be required. TPVI-IE in patients with congenital heart disease exhibits several distinctive features. Whether specific valve types are associated with a higher risk of TPVI-IE requires further investigation. Patient and parent education regarding IE prevention may have a role to play and should be offered to all patients., (Copyright © 2023 Elsevier Masson SAS. All rights reserved.)

Huntington's disease is a fatal neurodegenerative disease characterized by striatal neurodegeneration, aggregation of mutant Huntingtin and the presence of reactive astrocytes. Astrocytes are important partners for neurons and engage in a specific reactive response in Huntington's disease that involves morphological, molecular and functional changes. How reactive astrocytes contribute to Huntington's disease is still an open question, especially because their reactive state is poorly reproduced in experimental mouse models. Here, we show that the JAK2-STAT3 pathway, a central cascade controlling astrocyte reactive response, is activated in the putamen of Huntington's disease patients. Selective activation of this cascade in astrocytes through viral gene transfer reduces the number and size of mutant Huntingtin aggregates in neurons and improves neuronal defects in two complementary mouse models of Huntington's disease. It also reduces striatal atrophy and increases glutamate levels, two central clinical outcomes measured by non-invasive magnetic resonance imaging. Moreover, astrocyte-specific transcriptomic analysis shows that activation of the JAK2-STAT3 pathway in astrocytes coordinates a transcriptional program that increases their intrinsic proteolytic capacity, through the lysosomal and ubiquitin-proteasome degradation systems. This pathway also enhances their production and exosomal release of the co-chaperone DNAJB1, which contributes to mutant Huntingtin clearance in neurons. Together, our results show that the JAK2-STAT3 pathway controls a beneficial proteostasis response in reactive astrocytes in Huntington's disease, which involves bi-directional signalling with neurons to reduce mutant Huntingtin aggregation, eventually improving disease outcomes., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Purpose : The purpose of this study was the clinical and therapeutic assessment of lower-limb osteosynthesis-associated infection (OAI) by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Gram-negative bacteria (GNB), which have been poorly studied to date. Methods : A prospective multicentre observational study was conducted on behalf of ESGIAI (the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group on Implant-Associated Infections). Factors associated with remission of the infection were evaluated by multivariate and Cox regression analysis for a 24-month follow-up period. Results : Patients ( n = 57 ) had a history of trauma (87.7 %), tumour resection (7 %) and other bone lesions (5.3 %). Pathogens included Escherichia coli ( n = 16 ), Pseudomonas aeruginosa ( n = 14 ; XDR 50 %), Klebsiella spp. ( n = 7 ), Enterobacter spp. ( n = 9 ), Acinetobacter spp. ( n = 5 ), Proteus mirabilis ( n = 3 ), Serratia marcescens ( n = 2 ) and Stenotrophomonas maltophilia ( n = 1 ). The prevalence of ESBL (extended-spectrum β -lactamase), fluoroquinolone and carbapenem resistance were 71.9 %, 59.6 % and 17.5 % respectively. Most patients ( n = 37 ; 64.9 %) were treated with a combination including carbapenems ( n = 32 ) and colistin ( n = 11 ) for a mean of 63.3 d. Implant retention with debridement occurred in early OAI (66.7 %), whereas the infected device was removed in late OAI (70.4 %) ( p = 0.008 ). OAI remission was achieved in 29 cases (50.9 %). The type of surgery, antimicrobial resistance and duration of treatment did not significantly influence the outcome. Independent predictors of the failure to eradicate OAI were age > 60  years (hazard ratio, HR, of 3.875; 95 % confidence interval, CI95 %, of 1.540-9.752; p = 0.004 ) and multiple surgeries for OAI (HR of 2.822; CI95 % of 1.144-6.963; p = 0.024 ). Conclusions : Only half of the MDR/XDR GNB OAI cases treated by antimicrobials and surgery had a successful outcome. Advanced age and multiple surgeries hampered the eradication of OAI. Optimal therapeutic options remain a challenge., Competing Interests: At least one of the (co-)authors is a member of the editorial board of . The peer-review process was guided by an independent editor, and the authors also have no other competing interests to declare., (Copyright: © 2022 Efthymia Giannitsioti et al.)

We are at a time of considerable growth in the use and development of transcriptomics studies and subsequent in silico analysis. RNA sequencing is one of the most widely used approaches, now integrated in many studies.  The processing of these data may typically require a noteworthy number of steps, statistical knowledge, and coding skills which is not accessible to all scientists. Despite the undeniable development of software applications over the years to address this concern, it is still possible to improve.  Here we present DEVEA, an R shiny application tool developed to perform differential expression analysis, data visualization and enrichment pathway analysis mainly from transcriptomics data, but also from simpler gene lists with or without statistical values.  Its intuitive and easy-to-manipulate interface facilitates gene expression exploration through numerous interactive figures and tables, statistical comparisons of expression profile levels between groups and further meta-analysis such as enrichment analysis, without bioinformatics expertise. DEVEA performs a thorough analysis from multiple and flexible input data representing distinct analysis stages. From them, it produces dynamic graphs and tables, to explore the expression levels and statistical differential expression analysis results. Moreover, it generates a comprehensive pathway analysis to extend biological insights. Finally, a complete and customizable HTML report can be extracted for further result exploration outside the application. DEVEA is accessible at https://shiny.imib.es/devea/ and the source code is available on our GitHub repository https://github.com/MiriamRiquelmeP/DEVEA., Competing Interests: No competing interests were disclosed., (Copyright: © 2022 Riquelme-Perez M et al.)

Purpose: Staphylococcus aureus (SA) is involved in almost one-third of endocarditis events (known as E-SA) and is frequently associated with unfavorable outcomes compared to infectious endocarditis (IE) caused by other pathogens including coagulase-negative staphylococci (CNS). The aim of this study was to compare the morbidity and mortality of patients with E-SA and endocarditis due to CNS (known as E-CNS)., Methods: A monocentric retrospective cohort analysis was conducted including all patients admitted with IE from January 2010 to December 2017. Lengths of stay, complications, in-hospital and 1-year mortality were described from medical records and compared between E-SA and E-CNS., Results: Among the 428 patients included, 102 had staphylococcus (50 E-SA and 52 E-CNS). Half of the IE events due to staphylococcus occurred in the year following a cardiac procedure [p = 0.029]. A septic embolism occurred in 41% and 48% of patients with E-CNS and E-SA, respectively [p = 0.439]. Cardiac surgery was indicated in 50% of E-SA and 48% of E-CNS cases [p = 0.846]. The intra-hospital and 1-year mortality rates were 25% and 31% for E-CNS and 34% and 45% for E-SA [p = 0.699, p = 0.234]., Conclusion: Embolic complications, surgical management rate and mortality rates of E-SA and E-CNS were comparable, which may suggest a similar morbidity and mortality irrespective of the pathogen involved in IE., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany.)

Aim: Noninvasive biomarkers such as methylated ccfDNA from plasma could help to support the diagnosis of Alzheimer's disease (AD). Methods: A targeted sequencing protocol was developed to identify candidate biomarkers of AD in methylated ccfDNA extracted from plasma. Results: The authors identified differentially methylated CpGs, regions of which were the same as those identified in previous AD studies. Specifically, a differentially methylated CpG of the LHX2 gene previously identified in a plasma study of AD was replicated in the study. The MBP and DUSP22 regions have been identified in other brain studies of AD and in the authors' study. Conclusion: Although these biomarkers must be validated in other cohorts, methylated ccfDNA could be a relevant noninvasive biomarker in AD.

Labelled leucocyte scintigraphy (LS) is regarded as helpful when exploring bone and joint infections. The aim of this study was to evaluate the utility of LS for the diagnosis of chronic periprosthetic joint infections (PJIs) in patients exhibiting arthroplastic loosening. One hundred sixty-eight patients were referred to centres for treatment of complex PJI. One hundred fifty underwent LS using 99m Tc-HMPAO (LLS); 18 also underwent anti-granulocyte scintigraphy (AGS) and 13 additional SPECT with tomodensitometry imaging (SPECT-CT). The LS results were compared with bone scan data. For all, the final diagnoses were determined microbiologically; perioperative samples were cultured. LS values were examined, as well as sensitivity by microorganism, anatomical sites, and injected activity. LS results were also evaluated according to the current use of antibiotics or not. The sensitivity, specificity, and positive predictive value of LLS were 72%, 60%, and 80%, respectively. LLS performed better than did AGS. SPECT-CT revealed the accurate locations of infections. The sensitivity of LS was not significantly affected by the causative pathogen or the injected activity. No correlation was evident between the current antibiotic treatment and the LS value. The test was more sensitive for knee (84%) than hip arthroplasty (57%) but was less specific for knee (52% vs. 75%). Sensitivity and specificity of LLS varied by the location of infection bone scan provide no additional value in PJI diagnosis. Current antibiotic treatment seems to have no influence on LS sensitivity as well as labelling leukocyte activity or pathogens responsible for chronic PJI.

Module network inference is a statistical method to reconstruct gene regulatory networks, which uses probabilistic graphical models to learn modules of coregulated genes and their upstream regulatory programs from genome-wide gene expression and other omics data. Here, we review the basic theory of module network inference, present protocols for common gene regulatory network reconstruction scenarios based on the Lemon-Tree software, and show, using human gene expression data, how the software can also be applied to learn differential module networks across multiple experimental conditions.

The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and disease-associated investigations. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered as the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation and hydroxymethylation requiring an additional chemical or enzymatic step to identify hydroxymethylated cytosines. Here we provide two detailed protocols based on commercial kits for the preparation of sequencing libraries for the comprehensive whole-genome analysis of DNA methylation and/or hydroxymethylation. If only DNA methylation is of interest, sequencing libraries can be constructed from limited amounts of input DNA by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion. For samples with significant levels of hydroxymethylation such as stem cells or brain tissue, we describe the protocol of oxidative bisulfite sequencing (OxBs-seq), which in its current version uses a post-bisulfite adaptor tagging (PBAT) approach. Two methylomes need to be generated: a classic methylome following bisulfite conversion and analyzing both methylated and hydroxymethylated cytosines and a methylome analyzing only methylated cytosines, respectively. We also provide a step-by-step description of the data analysis using publicly available bioinformatic tools. The described protocols have been successfully applied to different human samples and yield robust and reproducible results.

Eighteen hot topics regarding the diagnosis and management of skin and soft-tissue infections (SSTIs) were selected and reviewed by members of the SSTI Working Group of the International Society of Chemotherapy (ISC). Despite the large amount of literature available on the issue selected, there are still many unknowns with regard to many of them and further studies are required to answer these challenging issues that face clinicians on a daily basis., (Copyright © 2016 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.)

Introduction: Streptococcus pneumoniae is the leading cause of bacterial meningitis. Young children, the elderly and those who are immunocompromised or who suffer from chronic diseases have the highest risk of developing pneumococcal meningitis. A 7-valent pneumococcal conjugate vaccine (PCV7) was licensed in 2000 in the US and in 2001 in Europe., Methods: A literature search was performed in PubMed to identify studies assessing the impact of routine childhood PCV7 vaccination on pneumococcal diseases. Here, we report the impact on pneumococcal meningitis., Results: A total of 17 articles reporting impact data on pneumococcal meningitis were included in this review: 11 from Western Europe and 6 from North America. In the post-vaccination period, compared with the pre-vaccination period, a reduction ranging from 59.2% in the US, 1 year after vaccine introduction, to 100% in Belgium, 4 years after vaccine introduction in vaccine-type (VT) pneumococcal meningitis incidence was reported in vaccine-eligible children in seven studies. In addition, the majority of studies reported reductions in VT and all-type pneumococcal meningitis incidence in age groups that were not vaccine-eligible., Conclusions: The results from this review demonstrate that PCV7 has had a significant impact on pneumococcal meningitis across all ages through its use in pediatric immunization programs. With the introduction of 13-valent PCV (PCV13) we can expect to see a reduction in the incidence of pneumococcal meningitis due to the six additional serotypes included, as well as continued protection against pneumococcal meningitis due to PCV7 serotypes. Robust surveillance systems are essential for the evaluation of the impact of PCV13 on all-type pneumococcal meningitis and for monitoring the evolution of non-vaccine serotype pneumococcal meningitis.

Unlabelled: Targeted therapies interfering with specifically one protein activity are promising strategies in the treatment of diseases like cancer. However, accumulated empirical experience has shown that targeting multiple proteins in signaling networks involved in the disease is often necessary. Thus, one important problem in biomedical research is the design and prioritization of optimal combinations of interventions to repress a pathological behavior, while minimizing side-effects. OCSANA (optimal combinations of interventions from network analysis) is a new software designed to identify and prioritize optimal and minimal combinations of interventions to disrupt the paths between source nodes and target nodes. When specified by the user, OCSANA seeks to additionally minimize the side effects that a combination of interventions can cause on specified off-target nodes. With the crucial ability to cope with very large networks, OCSANA includes an exact solution and a novel selective enumeration approach for the combinatorial interventions' problem., Availability: The latest version of OCSANA, implemented as a plugin for Cytoscape and distributed under LGPL license, is available together with source code at http://bioinfo.curie.fr/projects/ocsana.

Introduction: Streptococcus pneumoniae can cause invasive pneumococcal diseases (IPD), such as bacteremic pneumonia, bacteremia, meningitis, and sepsis, and non-IPDs, such as otitis media, nonbacteremic pneumonia, and upper respiratory tract infections. It was estimated in 2000 that, worldwide, S. pneumoniae was responsible for 826,000 deaths annually in children aged between 1 month and 5 years. A 7-valent pneumococcal conjugate vaccine (PCV7) was licensed in 2000 in the USA and in 2001 in Europe., Methods: A literature search was performed in PubMed to identify studies assessing the impact of routine childhood PCV7 vaccination on pneumococcal morbidity and mortality. Here, the impact on IPD is reported., Results: A total of 37 articles reporting impact data on IPD were included in this review: four from Australia, 17 from western Europe, and 16 from North America. In vaccine-eligible children in the postvaccination period, a reduction ranging from 39.9% in Spain to 99.1% in the USA in vaccine-type (VT) IPD incidence, compared with the prevaccination period, was reported in 18 studies. All but one of the 30 studies assessing the impact of PCV7 on all-type IPD reported a reduction ranging from 1.7% in Spain to 76.3% in Australia. In addition, the majority of studies reported reductions in VT and all-type IPD incidence in age groups that were not vaccine eligible., Conclusions: The results from this review illustrate that PCV7 has had a significant impact on IPD across all ages through its use in pediatric immunization programs. With the introduction of 13-valent pneumococcal conjugate vaccine (PCV13) further reductions in the incidence of IPD due to the six additional serotypes included, as well as continued protection against IPD due to PCV7 serotypes may be expected. Robust surveillance systems are essential for the evaluation of the impact of PCV13 on all-type IPD and for monitoring the evolution of non-VT IPD.

The Biological Network Manager (BiNoM) is a software tool for the manipulation and analysis of biological networks. It facilitates the import and conversion of a set of well-established systems biology file formats. It also provides a large set of graph-based algorithms that allow users to analyze and extract relevant subnetworks from large molecular maps. It has been successfully used in several projects related to the analysis of large and complex biological data, or networks from databases. In this tutorial, we present a detailed and practical case study of how to use BiNoM to analyze biological networks.