Understanding environmental microbiomes is central to furthering strategies for the restoration of polluted habitats. Such studies allow us to gather important information on the native microbiota, as well as possible microbial responses to remediation procedures. In recent years, metagenomics has emerged as a reliable method to enable the holistic characterization of diverse microbiomes including those from soil, oceans, lakes, and animal gut, among others. Indeed, metagenomics has been used to identify microbial proxies from contaminated environments and elaborate taxonomic and functional changes in microbial communities during pollution events. Coupled with continually decreasing sequencing costs, metagenomics, and associated bioinformatic tools/pipelines now constitute routinely used methods in laboratories worldwide. This necessitates an adequate understanding of metagenomic shotgun sequencing and various other related sequencing applications, as well as the constantly evolving bioinformatic milieu, to ensure proper interpretation of microbiome data. To this end, we review the various massively parallel sequencing-based applications for studying microbiomes in this chapter and discuss the bioinformatic tools, strategies, and approaches available to analyze the sequencing data generated. To provide context, we additionally discuss studies where next-generation sequencing-based applications have been employed in investigating contaminated environments.
Diabetes is a considerate metabolic disorder that can lead to a series of complications, involving the malfunctioning of the reproductive system of males. It has been observed that there is a gradual rise in male diabetic patients and almost half of the diabetic males have low semen quality and decrease reproductive function. In diabetic conditions, prolonged hyperglycemia leads to oxidative stress, diabetic neuropathy, and insulin resistance. Insulin resistance and its deficiency can impair the hypothalamus, pituitary gland, gonads, and perigonads. This causes a decrease in the secretion of gonadal steroids such as GnRH (gonadotropin-releasing hormone), FSH (follicle-stimulating hormone), LH (luteinizing hormone), and Testosterone. Moreover, it also causes damage to the testicles, spermatogenic and stromal cells, seminiferous tubules, and various structural injuries to male reproductive organs. During spermatogenesis, glucose metabolism plays an important role, because the fundamental activities of cells and their specific features, such as motility and mature sperm fertilization activity, are maintained by glucose metabolism. All these activities can influence the fertility and reproductive health of males. But the glucose metabolism is primarily disrupted in diabetic conditions. Until now, there has been no medicine focusing on the reproductive health of diabetic people. In this chapter, we review the consequences of diabetes on the reproductive system of males and all the pathways involved in the dysfunction of the reproductive system. This will help interpret the effects of DM on male reproductive health.
Background Health-related data are collected from a variety of sources for different purposes, including secondary use for population health monitoring (HM) and health system performance assessment (HSPA). Most of these data sources are not included in databases of international organizations (e.g., WHO, OECD, Eurostat), limiting their use for research activities and policy making. This study aims at identifying and describing collection methods, quality assessment procedures, availability and accessibility of health data across EU Member States (MS) for HM and HSPA. Methods A structured questionnaire was developed and administered through an online platform to partners of the InfAct consortium form EU MS to investigate data collections applied in HM and HSPA projects, as well as their methods and procedures. A descriptive analysis of the questionnaire results was performed. Results Information on 91 projects from 18 EU MS was collected. In these projects, data were mainly collected through administrative sources, population health interview or health examination surveys and from electronic medical records. Tools and methods used for data collection were mostly mandatory reports, self-administered questionnaires, or record linkage of various data sources. One-third of the projects shared data with EU research networks and less than one-third performed quality assessment of their data collection procedures using international standardized criteria. Macrodata were accessible via open access and reusable in 22 projects. Microdata were accessible upon specific request and reusable in 15 projects based on data usage licenses. Metadata was available for the majority of the projects, but followed reporting standards only in 29 projects. Overall, compliance to FAIR Data principles (Findable, Accessible, Interoperable, and Reusable) was not optimal across the EU projects. Conclusions Data collection and exchange procedures differ across EU MS and research data are not always available, accessible, comparable or reusable for further research and evidence-based policy making. There is a need for an EU-level health information infrastructure and governance to promote and facilitate sharing and dissemination of standardized and comparable health data, following FAIR Data principles, across the EU.
Background Research networks offer multidisciplinary expertise and promote information exchange between researchers across Europe. They are essential for the European Union’s (EU) health information system as providers of health information and data. The aim of this mapping exercise was to identify and analyze EU research networks in terms of health data collection methods, quality assessment, availability and accessibility procedures. Methods A web-based search was performed to identify EU research networks that are not part of international organizations (e.g., WHO-Europe, OECD) and are involved in collection of data for health monitoring or health system performance assessment. General characteristics of the research networks (e.g., data sources, representativeness), quality assessment procedures, availability and accessibility of health data were collected through an ad hoc extraction form. Results Fifty-seven research networks, representative at national, international or regional level, were identified. In these networks, data are mainly collected through administrative sources, health surveys and cohort studies. Over 70% of networks provide information on quality assessment of their data collection procedures. Most networks share macrodata through articles and reports, while microdata are available from ten networks. A request for data access is required by 14 networks, of which three apply a financial charge. Few networks share data with other research networks (8/49) or specify the metadata-reporting standards used for data description (9/49). Conclusions Improving health information and availability of high quality data is a priority in Europe. Research networks could play a major role in tackling health data and information inequalities by enhancing quality, availability, and accessibility of health data and data sharing across European networks.
Background Non-Communicable diseases (NCD) are the main contributors to mortality and burden of disease. There is no infrastructure in Europe that could provide health information (HI) on Public Health monitoring and Health Systems Performance (HSP) for research and evidence-informed decision-making. Moreover, there was no EU and European Economic Area Member States (EU/EEA MSs) general consensus, on developing this initiative and guarantee its sustainability. The aim of this study is to analyze the integration of technical and political views made by the Joint Action on Health Information (InfAct; Information for Action) and the results obtained from those activities, in terms of advice and national and institutional support to develop an integrated and sustainable European Distributed Infrastructure on Population Health (DIPoH) for research and evidence-informed policy-making. Methods InfAct established two main boards, the Technical Dialogues (TDs) and the Assembly of Members (AoM), to provide a platform for discussion with EU/EEA MSs to establish a sustainable infrastructure for HI: 1) The TDs were composed by national technical experts (NTE) with the aim to discuss and provide feedback about scientific aspects, feasibility and EU-added value of the infrastructure proposed by InfAct. 2) The AoM gathered country representatives from Ministries of Health and Research at the highest political level, with the aim of providing policy-oriented advice for the future political acceptance, support, implementation, and development of InfAct’s outcomes including DIPoH. The documentation provided for the meetings consisted in Fact-Sheets, where the main results, new methods and proposals were clearly exposed for discussion and assessment; altogether with more extended information of the DIPoH. The documentation was provided to national representatives within one more before each TD and AoM meeting. The Agenda and methodological approaches for each TD and AoM meeting consisted in the presentations of the InfAct outcomes extending the information provided in the Fact-Sheets; followed by a non-structured interaction, exchange of information, discussion and suggestions by the MSs representatives. The outcomes of the non-structured discussions were collected in Minutes of the TD and AoM meetings, and the final version was obtained with the consensus of all participants. Additionally, structured letters of political support were provided to the AoM representatives, for them to consider providing their MS written support for DIPoH. Results NTE, within the TDs, considered that DIPoH was useful for technical mutual learning and cooperation among and within countries; although they considered that the technical feasibility to uptake InfAct deliverables at the national and EU level was complex. The AoM focused on political support, resources, and expected MSs returns. The AoM representatives agreed in the interest of setting up an integrated and sustainable HI infrastructure and they considered DIPoH to be well-articulated and defined; although, some of them, expressed some barriers for providing DIPoH political support. The AoM representatives stated that the AoM is the most suitable way to inform EU MSs/ACs about future advances of DIPoH. Both boards provided valuable feedback to develop this infrastructure. Eleven countries and sixteen institutions supported the proposal, either by letters of political support or by signing the Memorandum of Understandings (MoU) and three countries, additionally, provided expression of financial commitment, for DIPoH to be added to the ESFRI 2021 roadmap. Conclusions TDs and AoM were key forums to develop, advise, advocate and provide support for a sustainable European research infrastructure for Population Health.
Background Circulating tumor cells (CTCs) are responsible for the metastatic dissemination of colorectal cancer (CRC) to the liver, lungs and lymph nodes. CTCs rarity and heterogeneity strongly limit the elucidation of their biological features, as well as preclinical drug sensitivity studies aimed at metastasis prevention. Methods We generated organoids from CTCs isolated from an orthotopic CRC xenograft model. CTCs-derived organoids (CTCDOs) were characterized through proteome profiling, immunohistochemistry, immunofluorescence, flow cytometry, tumor-forming capacity and drug screening assays. The expression of intra- and extracellular markers found in CTCDOs was validated on CTCs isolated from the peripheral blood of CRC patients. Results CTCDOs exhibited a hybrid epithelial-mesenchymal transition (EMT) state and an increased expression of stemness-associated markers including the two homeobox transcription factors Goosecoid and Pancreatic Duodenal Homeobox Gene-1 (PDX1), which were also detected in CTCs from CRC patients. Functionally, CTCDOs showed a higher migratory/invasive ability and a different response to pathway-targeted drugs as compared to xenograft-derived organoids (XDOs). Specifically, CTCDOs were more sensitive than XDOs to drugs affecting the Survivin pathway, which decreased the levels of Survivin and X-Linked Inhibitor of Apoptosis Protein (XIAP) inducing CTCDOs death. Conclusions These results indicate that CTCDOs recapitulate several features of colorectal CTCs and may be used to investigate the features of metastatic CRC cells, to identify new prognostic biomarkers and to devise new potential strategies for metastasis prevention.
Background In Europe, data on population health is fragmented, difficult to access, project-based and prone to health information inequalities in terms of availability, accessibility and especially in quality between and within countries. This situation is further exacerbated and exposed by the recent COVID-19 pandemic. The Joint Action on Health Information (InfAct) that builds on previous works of the BRIDGE Health project, carried out collaborative action to set up a sustainable infrastructure for health information in the European Union (EU). The aim of this paper is to present InfAct’s proposal for a sustainable research infrastructure, the Distributed Infrastructure on Population Health (DIPoH), which includes the setup of a Health Information Portal on population health to be maintained beyond InfAct’s time span. Methods The strategy for the proposal was based on three components: scientific initiatives and proposals to improve Health Information Systems (HIS), exploration of technical acceptability and feasibility, and finally obtaining high-level political support.. The technical exploration (Technical Dialogues—TD) was assumed by technical experts proposed by the countries, and political guidance was provided by the Assembly of Members (AoM), which gathered representatives from Ministries of Health and Science of EU/EEA countries. The results from the AoM and the TD were integrated in the sustainability plan compiling all the major outputs of InfAct. Results The InfAct sustainability plan was organized in three main sections: a proposal of a new research infrastructure on population health (the DIPoH), new health information tools and innovative proposals for HIS, and a comprehensive capacity building programme. These activities were carried out in InfAct and are being further developed in the Population Health Information Research Infrastructure (PHIRI). PHIRI is a practical rollout of DIPoH facilitating and generating the best available evidence for research on health and wellbeing of populations as impacted by COVID-19. Conclusions The sustainability plan received wide support from Member States and was recognized to have an added value at EU level. Nevertheless, there were several aspects which still need to be considered for the near future such as: (i) a commitment of stable financial and political support by Member States (MSs), (ii) the availability of resources at regional, national and European level to deal with innovations, and (iii) a more direct involvement from EU and international institutions such as the European Centre for Disease Prevention and Control (ECDC), the World Health Organization (WHO) and the Organisation for Economic Cooperation and Development OECD for providing support and sustainable contributions.
Aesthetic aspects of drinking water, such as Taste and Odor (T&O), have significant effects on consumer perceptions and acceptability. Solving unpleasant water T&O episodes in water supplies is challenging, since it requires expertise and know-how in diagnosis, evaluation of impacts and implementation of control measures. We present gaps, challenges and perspectives to advance water T&O science and technology, by identifying key areas in sensory and chemical analysis, risk assessment and water treatment, as articulated by WaterTOP (COST Action CA18225), an interdisciplinary European and international network of researchers, experts, and stakeholders.
Introduction The aim of the study was to evaluate, in a regulated generics market, the effect of the number of manufacturers of generic drugs on the amplitude of off-patent products price reduction and the price evolution of originators and generics after the patent expiry of pharmaceuticals dispensed by community pharmacies and reimbursed by the Italian National Health Service (INHS). Methods The AIFA “transparency list” was utilized to select unbranded and branded off-patent drug dispensed by community pharmacies and reimbursed by the Italian National Health Service between 2012 and 2018. The unbranded drug entry in the transparency list database was considered as a proxy of its patent expiry. Results A total of 42 different active ingredients were included in the analysis. The relative price per dose at time t of unbranded and branded drugs, considering as common denominator the price per dose a year before the patent expiry, ( t-1 ) decreased with the increase of unbranded manufacturers. At the time of the patent expiry, the price of unbranded drugs was almost 50% less than that of branded drugs at t-1 and the price of branded drugs started to decrease before the first unbranded entry. Conclusion An inverse relation between the number of generic drug entrants and the price of generics and originators was detected. The patent expiry determines a price decline, more concentrated in the first year of patent expiry.
Objective: The objective of this review is to evaluate the effectiveness of transitional care interventions for seriously ill patients and their caregivers. Introduction: Seriously ill patients and their caregivers may have complex health and social care needs that require services from numerous providers across multiple sectors. Transitional care interventions have been designed to enhance a collaborative approach among providers to facilitate the care transition process. However, the effectiveness of transitional care interventions for seriously ill patients, their caregivers, and the effects of such interventions on their outcomes remain unclear. Inclusion criteria: Randomized controlled trials with adult patients (≥18 y old) with serious illness and their caregivers involved in transitional care programs will be considered for inclusion. The patients' outcomes will include mortality and/or survival, symptoms (eg, pain, nausea), and health-related quality of life. The caregivers' outcomes will include caregiver burden, preparedness, and well-being. Methods: The JBI methodology for systematic reviews of effectiveness evidence will be followed. The search strategy aims to locate published and unpublished studies. Electronic databases, including PubMed, Embase, CINAHL, and the Cochrane Central Register of Controlled Trials, will be systematically searched from 2003 to the present. Studies in English, Italian, Spanish, French, and German will be included. Critical appraisal and data extraction will be conducted using standardized tools. Quantitative data will be pooled in statistical meta-analysis or, if statistical pooling is not possible, the findings will be reported narratively. Certainty of the evidence will be assessed using the Grading of Recommendations Assessment, Development and Evaluation (GRADE). Systematic review registration number: PROSPERO CRD42022319848.
Background Most SARS-CoV-2 rapid antigen detection tests (RADTs) validation studies have been performed on specimens from COVID-19 patients and negative controls or from mostly symptomatic individuals. Herein we evaluated the diagnostic accuracy of AFIAS COVID-19 Ag, hereinafter denominated as AFIAS, during a COVID-19 screening program surveillance testing conducted among personnel of an Italian military airport. Methods Nasopharyngeal swabs (NPSs) were collected from study participants and were analysed by both AFIAS and RT-PCR assay. A questionnaire collecting demographic and exposure data were administered to all participants. AFIAS accuracy parameters including Cohen’s kappa (K) were determined. Results Overall, from November 2020 to April 2021, 1294 (NPSs) were collected from 1183 participants (88.6% males, 11.4% females; mean age were 41.3, median age 42). Forty-nine NPSs (3.78%) were positive by RT-PCR, while 54 NPSs were positive by AFIAS. Overall baseline sensitivity, specificity, positive and negative predictive values were 0.633, 0.981, 0.574, 0.985, respectively and K was 0.585 (moderate). AFIAS sensitivity tended to be higher for NPSs with higher viral load. A higher sensitivity (0.944) compared to the overall baseline sensitivity (0.633) was also found for NPSs from participants with COVID-19 compatible symptoms, for which K was 0.891 (almost perfect). Instead, AFIAS sensitivity was quite poor for NPSs from asymptomatic participants. Most false negative NPSs in this group had moderate viral load. Conclusion Overall, AFIAS showed high specificity but only moderate sensitivity, mainly because of the high proportion of asymptomatic participants. However, AFIAS showed good sensitivity for NPSs with high viral load and nearly optimal accuracy parameters for NPSs from participants with COVID-19 compatible symptoms. Thus, taking into consideration its performance features, this test can be useful for COVID-19 case identification and management as well as for infection control.
Background The introduction of the prion Real-Time Quaking-Induced Conversion assay (RT-QuIC) has led to a revision of the diagnostic criteria for sporadic Creutzfeldt-Jakob disease (sCJD). Validation studies are needed for the amended criteria, especially for their diagnostic value in the clinical setting. Methods We studied 1250 patients with suspected CJD referred for diagnosis to two Italian reference centres between 2010 and 2020. Focusing on the first diagnostic assessment, we compared the diagnostic value of the old and the amended criteria and that of different combinations of clinical variables and biomarker results. Results The studied cohort comprised 850 participants with CJD (297 definite sCJD, 151 genetic CJD, 402 probable sCJD) and 400 with non-CJD (61 with neuropathology). At first clinical evaluation, the sensitivity of the old criteria (76.8%) was significantly lower than that of the amended criteria (97.8%) in the definite CJD cohort with no difference between definite and probable sCJD cases. Specificity was ~94% for both criteria against the non-CJD cohort (82.0% against definite non-CJD group). Cerebrospinal fluid (CSF) RT-QuIC was highly sensitive (93.9%) and fully specific against definite non-CJD patients. Limiting the criteria to a positive RT-QuIC or/and the combination of a clinical course compatible with possible CJD with a positive MRI (Q-CM criteria) provided higher diagnostic accuracy than both the old and amended criteria, overcoming the suboptimal specificity of ancillary test results (ie, CSF protein 14-3-3). Conclusions CSF RT-QuIC is highly sensitive and specific for diagnosing CJD in vitam. The Q-CM criteria provide a high diagnostic value for CJD.
The neglected zoonosis cystic echinococcosis affects mainly pastoral and rural communities in both low-income and upper-middle-income countries. In Europe, it should be regarded as an orphan and rare disease. Although human cystic echinococcosis is a notifiable parasitic infectious disease in most European countries, in practice it is largely under-reported by national health systems. To fill this gap, we extracted data on the number, incidence, and trend of human cases in Europe through a systematic review approach, using both the scientific and grey literature and accounting for the period of publication from 1997 to 2021. The highest number of possible human cases at the national level was calculated from various data sources to generate a descriptive model of human cystic echinococcosis in Europe. We identified 64 745 human cystic echinococcosis cases from 40 European countries. The mean annual incidence from 1997 to 2020 throughout Europe was 0·64 cases per 100 000 people and in EU member states was 0·50 cases per 100 000 people. Based on incidence rates and trends detected in this study, the current epicentre of cystic echinococcosis in Europe is in the southeastern European countries, whereas historical endemic European Mediterranean countries have recorded a decrease in the number of cases over the time.
Polybrominated diphenyl ethers (PBDEs) are persistent organic chemicals implied as flame retardants. Humans are mainly exposed to BDE-47, -99, and -209 congeners by diet. PBDEs are metabolic disruptors with the liver as the main target organ. To investigate their mode of action at a human-relevant concentration, we exposed HepG2 cells to these congeners and their mixture at 1 nM, analyzing their transcriptomic and proteomic profiles. KEGG pathways and GSEA Hallmarks enrichment analyses evidenced that BDE-47 disrupted the glucose metabolism and hypoxia pathway; all the congeners and the MIX affected lipid metabolism and signaling Hallmarks regulating metabolism as mTORC1 and PI3K/AKT/MTOR. These results were confirmed by glucose secretion depletion and increased lipid accumulation, especially in BDE-47 and -209 treated cells. These congeners also affected the EGFR/MAPK signaling; further, BDE-47 enriched the estrogen pathway. Interestingly, BDE-209 and the MIX increased ERα gene expression, whereas all the congeners and the MIX induced ERβ and PPARα. We also found that PBDEs modulated several lncRNAs and that HNRNAP1 represented a central hub in all the four interaction networks. Overall, the PBDEs investigated affected glucose and lipid metabolism with different underlying modes of action, as highlighted by the integrated omics analysis, at a dietary relevant concentration. These results may support the mechanism-based risk assessment of these compounds in relation to liver metabolism disruption.
Background Breast implants are biomaterials eliciting a physiological and mandatory foreign body response. Objectives We designed an animal study to investigate the impact of different implant surfaces on the formation of the perirprosthetic capsule, the inflammatory response and the cellular composition. Methods We implanted 1 scaled-down version of breast implants by different manufactures on 70 female Sprague Dawley rats. Animals were divided into five groups of 14 animals. Group A received a smooth implant (Ra≈0.5µm) according to the ISO 14607-2018 classification, Group B smooth implant (Ra≈3.2µm), Group C smooth implant (Ra≈5µm), Group D macrotextured implant (Ra≈62µm) and Group E macrotextured implant (Ra≈75µm). At 60 days, all animals received a magnetic resonance imaging (MRI) and 35 animals were sacrificed and their capsules sent for histology (capsule thickness, inflammatory infiltrate) and immunohistochemistry analysis (cellular characterization). The remaining animals repeated the MRI at 120 days and were sacrificed following the same protocol. Results MRI showed a thinner capsule in the smooth implants (Group A, B, C) at 60 days (p < 0.001) but not at 120 days (p = 0.039), confirmed with histology both at 60 days (p = 0.005) and 120 days (p < 0.001). Smooth implants (Group A, B, C) presented a mild inflammatory response at 60 days that was maintained at 120 days and a high M2-Macrophage concentration (anti-inflammatory). Conclusions Our study confirms that smooth implants form a thinner capsule, inferior inflammatory infiltrate and a cellular composition that indicates a mild host inflammatory response. A new host inflammatory response classification is elaborated classifying breast implants into mild, moderate, and high.
Hepatitis B virus (HBV) infection is a serious global health problem. Patients with autoimmune diseases, such as Lupus Erythematosus, are exposed to a higher risk of acquiring infections. In this study, a molecular characterization, genomic investigation of the Hepatitis B virus, polymerase (P) and surface (S) genes, from a patient affected by Cutaneous Lupus Erythematosus (CLE), was presented. Viral DNA was extracted from 200 μL of serum, and the HBV-DNA was amplified by real-time polymerase chain reaction (PCR) with the Platinum Taq DNA Polymerase. The PCR products were purified and sequencing reactions were performed. A phylogenetic analysis was performed through maximum likelihood and Bayesian approaches. The HBV CLE isolate was classified as sub-genotype D3 and related to other Italian HBV D3 genomes, and some from foreign countries. No drug resistant mutations were identified. One mutation (a.a. 168 M) was located in the last part of the major hydrophilic region (MHR) of the surface antigen (HBsAg). Moreover, three sites (351G, 526Y, 578C) in the polymerase were exclusively present in the CLE patient. The mutations identified exclusively in the HBsAg of our CLE patient may have been selected because of the Lupus autoantibodies, which are characteristic in the Lupus autoimmune disease, using a possible molecular mimicry mechanism.
The urban overheating phenomenon in Mediterranean cities is a societal challenge with vast implications for the protection of public health. An additional analysis of the pilot TEMP randomized 2 × 2 cross-over trial was set up, using wearable sensor-based skin temperature measurements (n = 14). The study objectives were to: (i) assess the recurrence patterns of skin temperature measurements in individuals spending time in two climatologically contrasting settings (urban versus mountainous), and (ii) evaluate the association between the diurnal nonlinear recurrence quantification analysis (RQA) metrics and metabolic hormone levels. The intervention was a short-term stay (5–7 days) in a mountainous, climate-cooler setting (range 600–900 m altitude), which is about a 1 h drive from the main urban centres of Cyprus. The RQA analysis showed a blunting phenomenon on the nonlinear temporal dynamics of skin temperature time series observed in the urban setting. Compared with the mountainous setting, a more stable (and thus less adaptive) profile of skin temperature dynamics in the urban setting appeared, being less deterministic and with a smaller degree of complexity. No significant (p > 0.05) associations were observed between the leptin or cortisol and any of the skin temperature dynamical descriptors. However, there were marginal associations between the adiponectin and laminarity (beta = 0.24, 95%CI: −0.02, 0.50, p = 0.07) and with determinism (beta = 0.23, 95%CI: −0.037, 0.50, p = 0.09). We found dysregulations in skin temperature temporal dynamics of the study population while residing in the urban setting when compared with the cooler mountainous setting; these dysregulations took the form of reduced cycle duration and complexity, while skin temperature dynamics became less responsive to perturbations and less regular in magnitude. More research is needed to better understand heat stress temporal dynamics and their influence on human health. Trial registration: This trial is registered with ClinicalTrials.gov; number: NCT03625817.
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