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Abstract The incidence of gluten-related disorders (GRDs) continues to increase and its global prevalence is estimated at approximately 5% of the population. Celiac disease (CD), dermatitis herpetiformis (DH), gluten ataxia (GA), wheat allergy (WA), and non-celiac gluten sensitivity (NCGS) are the five major GRDs that present with a wide range of clinical manifestations. The diagnosis of GRDs can be challenging because the typical and atypical clinical manifestations of the GRDs overlap. In this review, the current definitions of gluten-related disorders, focusing on their clinical features, diagnostic and therapeutic approaches are presented. We concluded that GRDs are usually diagnosed using a combination of clinical features, serological tests, and histopathological findings. Treatment usually involves dietary modification.

Abstract Background C-reactive protein (CRP) represents a routine diagnostic marker of inflammation. Dissociation of native pentameric CRP (pCRP) into the monomeric structure (mCRP) liberates proinflammatory features, presumably contributing to excessive immune cell activation via unknown molecular mechanisms. Results In a multi-translational study of systemic inflammation, we found a time- and inflammation-dependent pCRP dissociation into mCRP. We were able to confirm that mCRP co-localizes with leukocytes at the site of injury after polytrauma and therefore assessed whether the CRP conformation potentiates neutrophil activation. We found mCRP-induced neutrophil-extracellular trap formation in vitro and ex vivo involving nicotinamide adenine dinucleotide phosphate oxidase activation, p38/mitogen-activated protein kinase signaling, and histone H3 citrullination. Mimicking the trauma milieu in a human ex vivo whole blood model, we found significant mCRP generation as well as NET formation, prevented by blocking pCRP conformational changes. Conclusions Our data provide novel molecular insights how CRP dissociation contributes to neutrophil activation as driver of various inflammatory disorders.

Abstract Building reliable and robust quantitative structure–property relationship (QSPR) models is a challenging task. First, the experimental data needs to be obtained, analyzed and curated. Second, the number of available methods is continuously growing and evaluating different algorithms and methodologies can be arduous. Finally, the last hurdle that researchers face is to ensure the reproducibility of their models and facilitate their transferability into practice. In this work, we introduce QSPRpred, a toolkit for analysis of bioactivity data sets and QSPR modelling, which attempts to address the aforementioned challenges. QSPRpred’s modular Python API enables users to intuitively describe different parts of a modelling workflow using a plethora of pre-implemented components, but also integrates customized implementations in a “plug-and-play” manner. QSPRpred data sets and models are directly serializable, which means they can be readily reproduced and put into operation after training as the models are saved with all required data pre-processing steps to make predictions on new compounds directly from SMILES strings. The general-purpose character of QSPRpred is also demonstrated by inclusion of support for multi-task and proteochemometric modelling. The package is extensively documented and comes with a large collection of tutorials to help new users. In this paper, we describe all of QSPRpred’s functionalities and also conduct a small benchmarking case study to illustrate how different components can be leveraged to compare a diverse set of models. QSPRpred is fully open-source and available at https://github.com/CDDLeiden/QSPRpred . Scientific Contribution QSPRpred aims to provide a complex, but comprehensive Python API to conduct all tasks encountered in QSPR modelling from data preparation and analysis to model creation and model deployment. In contrast to similar packages, QSPRpred offers a wider and more exhaustive range of capabilities and integrations with many popular packages that also go beyond QSPR modelling. A significant contribution of QSPRpred is also in its automated and highly standardized serialization scheme, which significantly improves reproducibility and transferability of models.

Abstract Background Risk scores facilitate the assessment of mortality risk in patients with community-acquired pneumonia (CAP). Despite their utilities, there is a scarcity of evidence comparing the various RS simultaneously. This study aims to evaluate and compare multiple risk scores reported in the literature for predicting 30-day mortality in adult patients with CAP. Methods A retrospective cohort study on patients diagnosed with CAP was conducted across two hospitals in Colombia. The areas under receiver operating characteristic curves (ROC-curves) were calculated for the outcome of survival or death at 30 days using the scores obtained for each of the analyzed questionnaires. Results A total of 7454 potentially eligible patients were included, with 4350 in the final analysis, of whom 15.2% (662/4350) died within 30 days. The average age was 65.4 years (SD: 21.31), and 59.5% (2563/4350) were male. Chronic kidney disease was 3.7% (9.2% vs. 5.5%; p

Abstract Background The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics. Results Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria. Conclusion This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands.

Abstract Background Stereotactic radiotherapy is the preferred treatment for managing patients with fewer than five brain metastases (BMs). However, some lesions recur after irradiation. The purpose of this study was to identify patients who are at a higher risk of failure, which can help in adjusting treatments and preventing recurrence. Methods In this retrospective multicenter study, we analyzed the predictive significance of a set of interpretable morphological features derived from contrast-enhanced (CE) T1-weighted MR images as imaging biomarkers using Kaplan–Meier analysis. The feature sets studied included the total and necrotic volumes, the surface regularity and the CE rim width. Additionally, we evaluated other nonmorphological variables and performed multivariate Cox analysis. Results A total of 183 lesions in 128 patients were included (median age 61 [31–95], 64 men and 64 women) treated with stereotactic radiotherapy (57% single fraction, 43% fractionated radiotherapy). None of the studied variables measured at diagnosis were found to have prognostic value. However, the total and necrotic volumes and the CE rim width measured at the first follow-up after treatment and the change in volume due to irradiation can be used as imaging biomarkers for recurrence. The optimal classification was achieved by combining the changes in tumor volume before and after treatment with the presence or absence of necrosis (p

Abstract Objectives Rice (Oryza sativa) is the most important food for more than two thirds of the world’s population. Bangladesh is the third largest producer and consumer of rice globally. Recently, several symptoms of Bacterial Panicle Blight (BPB) in rice, including seedling blight, sheath rot, floret sterility, and spotted grains, have been detected in the country. In addition, the presence of the most prevalent and virulent causative agent of BPB, Burkholderia glumae, has been confirmed in rice displaying symptoms of the disease. BPB could become one of the next emerging diseases of rice in Bangladesh, and a complete genome of a B. glumae strain from the country will help clarify its origin and devise proper management systems to continue sustainable rice production. Data description We report the first complete genome sequence of a B. glumae strain (BD_21g) isolated from symptomatic rice grains in Bangladesh (Natore District). The genome contains 2 chromosomes (1 and 2, with 3,417,499 and 3,855,283 bp, respectively) and 4 plasmids (1-4, with 123,248, 46,628, 88,744 and 53,064 bp, respectively).

Abstract Background Dental fluorosis (DF) is caused by excessive exposure to fluoride during odontogenesis and leads to various changes in the development of tooth enamel. Some regions in Mexico are considered endemic fluorosis zones due to the high fluoride content in drinking water. The objective of this study was to perform a systematic review and meta-analysis to identify the association between the concentration of fluoride in drinking water and the severity of dental fluorosis in northern and western Mexico. Methods This protocol was registered in the PROSPERO database (ID: CRD42023401519). The search for information was carried out in the PubMed/Medline, Scopus, SpringerLink, and Google Scholar databases between January 2015 and October 2023. The overall relative risk was calculated using the inverse of variance approach with the random effects method. The RoB 2.0 tool was used to construct risk plots. Results Eleven articles were analyzed qualitatively, and most of the included studies presented at least one level of DF severity; six articles were analyzed quantitatively, dividing them into two regions. In North region it was observed a higher prevalence of severe TF cases, corresponding to ≥ TF 5 category (4.78) [3.55, 6.42]. In the West region, most of the included studies presented a higher prevalence of less severe cases, corresponding to ≤ TF 4, in comparison with the North region (0.01) [0.00, 0.52], interpreted as a protective effect. Conclusion The concentrations of fluorides in drinking water are reportedly high in these regions and are directly related to the severity of dental fluorosis experienced by the inhabitants. In the Northern region exists a major concentration of fluoride in drinking water compared with the Western region as well as a prevalence of higher severity cases of dental fluorosis.

Abstract Background Acute leukaemias (AL) are life-threatening blood cancers that can be potentially cured with treatment involving myelosuppressive, multiagent, intensive chemotherapy (IC). However, such treatment is associated with a risk of serious infection, in particular invasive fungal infection (IFI) associated with prolonged neutropenia. Current practice guidelines recommend primary antifungal (AF) prophylaxis to be administered to high-risk patients to reduce IFI incidence. AFs are also used empirically to manage prolonged neutropenic fever. Current strategies lead to substantial overuse of AFs. Galactomannan (GM) and β-D-glucan (BG) biomarkers are also used to diagnose IFI. Combining both biomarkers may enhance the predictability of IFI compared to administering each test alone. Currently, no large-scale randomised controlled trial (RCT) has directly compared a biomarker-based diagnostic screening strategy without AF prophylaxis to AF prophylaxis (without systematic biomarker testing). Methods BioDriveAFS is a multicentre, parallel, two-arm RCT of 404 participants from UK NHS Haematology departments. Participants will be allocated on a 1:1 basis to receive either a biomarker-based antifungal stewardship (AFS) strategy, or a prophylactic AF strategy, which includes existing standard of care (SoC). The co-primary outcomes will be AF exposure in the 12-month post randomisation and the patient-reported EQ-5D-5L measured at 12-month post randomisation. Secondary outcomes will include total AF exposure, probable/proven IFI, survival (all-cause mortality and IFI mortality), IFI treatment outcome, AF-associated adverse effects/events/complications, resource use, episodes of neutropenic fever requiring hospital admission or outpatient management, AF resistance in fungi (non-invasive and invasive) and a Desirability of Outcome Ranking. The trial will have an internal pilot phase during the first 9 months. A mixed methods process evaluation will be integrated in parallel to the internal pilot phase and full trial, aiming to robustly assess how the intervention is delivered. Cost-effectiveness analysis will also be performed. Discussion The BioDriveAFS trial aims to further the knowledge of strategies that will safely optimise AF use through comparison of the clinical and cost-effectiveness of a biomarker-led diagnostic strategy versus prophylactic AF to prevent and manage IFI within acute leukaemia. The evidence generated from the study will help inform global clinical practice and approaches within antifungal stewardship. Trial registration ISRCTN11633399. Registered 24/06/2022.

Abstract Background In Australia, motor vehicle crashes (MVC)-related health data are available from insurance claims and hospitals but not from primary care settings. This study aimed to identify the frequency of MVC-related consultations in Australian general practices, explore the pharmacological management of health conditions related to those crashes, and investigate general practitioners’ (GPs) perceived barriers and enablers in managing these patients. Methods Mixed-methods study. The quantitative component explored annual MVC-related consultation rates over seven years, the frequency of chronic pain, depression, anxiety or sleep issues after MVC, and management with opioids, antidepressants, anxiolytics or sedatives in a sample of 1,438,864 patients aged 16 + years attending 402 Australian general practices (MedicineInsight). Subsequently, we used content analysis of 81 GPs’ qualitative responses to an online survey that included some of our quantitative findings to explore their experiences and attitudes to managing patients after MVC. Results MVC-related consultation rates remained stable between 2012 and 2018 at around 9.0 per 10,000 consultations. In 2017/2018 compared to their peers, those experiencing a MVC had a higher frequency of chronic pain (48% vs. 26%), depression/anxiety (20% vs. 13%) and sleep issues (7% vs. 4%). In general, medications were prescribed more after MVC. Opioid prescribing was much higher among patients after MVC than their peers, whether they consulted for chronic pain (23.8% 95%CI 21.6;26.0 vs. 15.2%, 95%CI 14.5;15.8 in 2017/2018, respectively) or not (15.8%, 95%CI 13.9;17.6 vs. 6.7%, 95% CI 6.4;7.0 in 2017/2018). Qualitative analyses identified a lack of guidelines, local referral pathways and decision frameworks as critical barriers for GPs to manage patients after MVC. GPs also expressed interest in having better access to management tools for specific MVC-related consequences (e.g., whiplash/seatbelt injuries, acute/chronic pain management, mental health issues). Conclusion Chronic pain, mental health issues and the prescription of opioids were more frequent among patients experiencing MVC. This reinforces the relevance of appropriate management to limit the physical and psychological impact of MVC. GPs identified a lack of available resources (e.g. education, checklists and management support tools) for managing MVC-related consequences, and the need for local referral pathways and specific guidelines to escalate treatments.

Abstract Background Mucopolysaccharidosis II (MPS II) is a rare lysosomal storage disease characterized by iduronate-2-sulfatase gene (IDS) deficiency and downstream glycosaminoglycan accumulation. Two-thirds of patients present with neuronopathic disease and evaluating cognitive function in these patients is challenging owing to limitations of currently available tests. During the clinical development of intrathecal idursulfase (idursulfase-IT), regulatory authorities requested qualitative data to further understand the neurocognitive changes observed by the investigators through the clinical trials. Results This qualitative study consisted of semi-structured interviews with all nine of the principal investigators who participated in the idursulfase-IT phase 2/3 (NCT02055118) and extension (NCT02412787) trials. These investigators enrolled the 56 patients with neuronopathic MPS II who qualified for the extension phase of the trial. The investigators were asked to rate the disease status of their patients. Of the 56 patients, 49 (88%) were rated as having disease that was improved/improving, stabilized or slowing progression compared with the expected outcomes with no treatment. Three patients were rated as worsening, while the remaining four patients were considered to have slowing progression or worsening disease. Similar results were demonstrated for patients aged from 3 to under 6 years at baseline, with 33 of 39 patients (85%) rated as having disease that was improved/improving, stabilized or slowing progression. Of the seven patients rated with slowing progression/worsening or worsening disease, five of them had an IDS variant other than missense, while two had a missense class variant. All the assigned improved/improving ratings were in patients receiving idursulfase-IT from the start of the phase 2/3 trial. Moreover, patients under 3 years of age at baseline were all rated as either improved/improving or stabilized disease. In a blinded review of patient profiles, investigators were requested to assign a disease status rating to 18 patients with large IDS deletions; 67% of these patients were rated as improved/improving or stabilized disease. Conclusions This qualitative analysis provides a snapshot of clinicians’ considerations when evaluating treatment in patients with neuronopathic MPS II, compared with the expected decline in cognitive function in the absence of treatment. The results highlight the importance of robust assessment tools in treatment evaluation.

Abstract Background Residual disease following cytoreductive surgery in patients with ovarian cancer has been associated with poorer survival outcomes compared with no residual disease. We performed a meta-analysis to assess the impact of varying levels of residual disease status on survival outcomes in patients with ovarian cancer who have undergone primary cytoreductive surgery or interval cytoreductive surgery in the setting of new therapies for this disease. Methods Medline, Embase, and Cochrane databases (January 2011 – July 2020) and grey literature, bibliographic and key conference proceedings, were searched for eligible studies. Fixed and random-effects meta-analyses compared progression and survival by residual disease level across studies. Heterogeneity between comparisons was explored via type of surgery, disease stage, and type of adjuvant chemotherapy. Results Of 2832 database and 16 supplementary search articles screened, 50 studies were selected; most were observational studies. The meta-analysis showed that median progression-free survival and overall survival decreased progressively with increasing residual disease (residual disease categories of 0 cm, > 0–1 cm and > 1 cm). Compared with no residual disease, hazard ratios (HR) for disease progression increased with increasing residual disease category (1.75 [95% confidence interval: 1.42, 2.16] for residual disease > 0–1 cm and 2.14 [1.34, 3.39] for residual disease > 1 cm), and also for reduced survival (HR versus no residual disease, 1.75 [ 1.62, 1.90] for residual disease > 0–1 cm and 2.32 [1.97, 2.72] for residual disease > 1 cm). All comparisons were significant (p

Abstract Background Approximately two-thirds of patients with mucopolysaccharidosis II (MPS II) have a severe, neuronopathic phenotype, characterized by somatic, cognitive, and behavioral issues. Current standard of care for the treatment of MPS II is enzyme replacement therapy with intravenous recombinant human iduronate-2-sulfatase (idursulfase). To target cognitive manifestations of MPS II, idursulfase has been formulated for intrathecal administration into the cerebrospinal fluid (idursulfase-IT). In accordance with recommendations for patient-focused drug development, semi-structured interviews were conducted to assess caregiver experiences and observations in a 52-week phase 2/3 trial of idursulfase-IT, in addition to intravenous idursulfase in pediatric patients with neuronopathic MPS II, or a substudy which enrolled patients younger than 3 years old, all of whom received idursulfase-IT. Results Overall, 46 caregivers providing care for 50 children (mean [range] age 7.9 [3–17] years at interview) took part in a single 60-min exit interview; six of these children had participated in the substudy. Qualitative and quantitative data were obtained demonstrating the burden of MPS II experienced by caregivers and their families. Following participation in the trials, 39 (78%) of the children were reported by their caregivers to have experienced improvements in the symptoms and impact of disease. Of those with improvements, 37 (95%) experienced cognitive improvements and 26 (67%) experienced emotional/behavioral improvements. Overall, 43 children (86%) were rated by caregivers as having moderate or severe symptoms before the trials; after the trials, 28 children (56%) were considered to have mild or no symptoms. For the six children who participated in the substudy, these proportions were 83% and 100%, respectively. Caregivers’ qualitative descriptions of trial experiences suggested improvements in children’s verbal and non-verbal functioning and spatial and motor skills, as well as a positive impact on family life. Conclusions This study revealed caregiver-reported improvements in children’s MPS II symptoms and the impact of the disease on patients and their families. There was a trend for cognitive improvement and a reduction in severity of MPS II symptoms. After many years of extensive review and regulatory discussions of idursulfase-IT, the clinical trial data were found to be insufficient to meet the evidentiary standard to support regulatory filings.

Abstract Key message Despite been grown under the same climate, oak species are able to correlate with looser, but still identifiable, leaf morphological syndromes, composed by morphological traits with an ecological role in their respective macroclimates. Context Environmental restrictions imposed by climate have been shown to modulate leaf morphology. A reduction of leaf area in hot and dry climates reduces overheating because of a thinner boundary layer. Lobed shapes enhance hydraulic conductivity and faster cooling. Elongated leaves drain more quickly under high precipitation. Trichomes may help to reduce the effects of excessive sun exposure in hot and dry environments. Leaf mass per area (LMA) increases in stressful environments. Aim To assess the influence of global climate and clade on oak leaf syndromes comprising morphological traits with ecological roles. Methods We analyzed seven morphological traits in 141 oak species grown in a botanical garden, characterized into five macroclimates, and explored the partial effects of clade and climate. Results We found significant associations between macroclimate and every morphological trait measured. Temperate species tend to have large, obovate, lobed, malacophyllous leaves. Species occurring in dry habitats usually present small, rounded, pubescent, sclerophyllous leaves. Warm and wet climates induce the development of slender, lanceolate, glabrous leaves with an acuminate apex. Conclusion The functional roles of the different morphological traits are partially confirmed in genus Quercus as a response to the different macroclimates, where different leaf syndromes can be distinguished.

Abstract Given the increasing prevalence of tick-borne diseases, such as Lyme disease, modeling the population and infection dynamics of tick vectors is an important public health tool. These models have applications for testing the effects of control methods or climate change on tick populations. There is an established history of tick population models, but code for them is rarely shared, especially not in a convenient format for others to modify and use. We present an R package, called IxPopDyMod, intended to function as a flexible and consistent framework for reproducible Ixodidae (hard-bodied ticks) population dynamics models. Here we focus on two key parts of the package: a function to create valid model configurations and a function to run a configured model and return the daily population over time. We provide three examples in appendices: one reproducing an existing Ixodes scapularis population model, one providing a novel Dermacentor albipictus model, and one showing Borrelia burgdorferi infection in ticks. Together these examples show the flexibility of the package to model scenarios of interest to tick researches. Graphical Abstract

Abstract Background HIV expansion is controlled by a range of interrelated factors, including the natural history of HIV infection and socio-economical and structural factors. However, how they dynamically interact in particular contexts to drive a transition from concentrated HIV epidemics in vulnerable groups to generalized epidemics is poorly understood. We aim to explore these mechanisms, using Madagascar as a case-study. Methods We developed a compartmental dynamic model using available data from Madagascar, a country with a contrasting concentrated epidemic, to explore the interaction between these factors with special consideration of commercial and transactional sex as HIV-infection drivers. Results The model predicts sigmoidal-like prevalence curves with turning points within years 2020–2022, and prevalence reaching stabilization by 2033 within 9 to 24% in the studied (10 out of 11) cities, similar to high-prevalence regions in Southern Africa. The late/slow introduction of HIV and circumcision, a widespread traditional practice in Madagascar, could have slowed down HIV propagation, but, given the key interplay between risky behaviors associated to young women and acute infections prevalence, mediated by transactional sex, the protective effect of circumcision is currently insufficient to contain the expansion of the disease in Madagascar. Conclusions These results suggest that Madagascar may be experiencing a silent transition from a concentrated to a generalized HIV epidemic. This case-study model could help to understand how this HIV epidemic transition occurs. Graphical abstract

Abstract Background Mucopolysaccharidosis (MPS) II is a rare, X-linked lysosomal storage disease. Approximately two-thirds of patients have central nervous system involvement with some demonstrating progressive cognitive impairment (neuronopathic disease). The natural history of cognitive and adaptive function in patients with MPS II is not well-defined. This 2-year, prospective, observational study evaluated the neurodevelopmental trajectories of boys with MPS II aged ≥ 2 years and 70); between-group differences were nonsignificant. No clear subgroups or patterns were identified for individual changes in VABS-II ABC scores. In total, 49 patients (89.1%) reported ≥ 1 adverse event (AE) and nine patients (16.4%) reported serious AEs. Conclusions Some patients with MPS II had rapid declines in cognitive ability, whereas others remained relatively stable after an initial decline. These insights provide a basis for more detailed analyses of different patient subgroups, which may enhance the definition and understanding of factors that influence cognitive and adaptive function in MPS II. Trial registration ClinicalTrials.gov, NCT01822184. Registered retrospectively: April 2, 2013.

Abstract Key message Among the variety of leaf defensive strategies to counteract herbivory attacks, the oak species analyzed in this study maximize investment in no more than one, with high-LMA oaks developing very tough leaves and low-LMA oaks favoring between high concentrations of condensed tannins or high growth rates. Context Plants develop a variety of defense strategies to counteract herbivory attacks, from physical and chemical defenses to tolerance strategies. Tradeoffs between strategies have been widely assessed from a resource allocation perspective, but there is a need to consider eventual interactions among them. Aim We evaluate the among-species tradeoff between three main constitutive plant defense traits, while considering the leaf mass per area ratio (LMA) as a proxy of leaf construction investment on area basis. Methods Leaf toughness measured as work of fracture, condensed tannins, and relative growth rate (RGR) were analyzed in a set of 19 Quercus L. species with contrasting LMA. Results Most species had low values either in two or in the three traits analyzed. Moreover, the highest values of work of fracture appeared in the species with high LMA; the highest values of condensed tannins were found in the species with the lowest LMA; and high values of RGR were measured in species with intermediate or lower values of LMA. Conclusion Oaks showed a trade-off among leaf defensive strategies influenced by LMA. Oaks with high LMA developed very tough leaves while oaks with low LMA presented lower values of toughness but favored between one of the two other strategies.

Abstract Background Smoke-free housing policies in multiunit housing are increasingly widespread interventions to reduce smoking and secondhand smoke exposure. Little research has identified factors that impede compliance with smoke-free housing policies in low-income multiunit housing and test corresponding solutions. Methods We are using an experimental design to test two compliance support interventions: (A) a “compliance through reduction (via relocation and reduction in personal smoking) and cessation” intervention targets households with smokers and involves support to shift smoking practices to areas beyond the apartment or building setting, reduce personal smoking, and deliver in-residence smoking cessation support services via trained peer educators and (B) a “compliance through resident endorsement” intervention involving voluntary adoption of smoke-free living environments through personal pledges, visible door markers, and/or via social media. We will compare randomly sampled participants in buildings that receive A or B or A plus B to the NYCHA standard approach. Discussion This RCT addresses key gaps in knowledge and capitalizes on key scientific opportunities by (1) leveraging the federal mandate to ban smoking in a public housing system of more than sufficient size to conduct an adequately powered RCT; (2) expanding our understanding of smoke-free policy compliance beyond policy implementation by testing two novel treatments: (a) in-residence smoking cessation and (b) resident endorsement, while (3) addressing population and location-specific tobacco-related disparities. At the conclusion of the study, this RCT will have leveraged a monumental policy shift affecting nearly half a million NYC public housing residents, many of whom disproportionately experience chronic illness and are more likely to smoke and be exposed to secondhand smoke than other city residents. This first-ever RCT will test the effects of much-needed compliance strategies on resident smoking behavior and secondhand smoke exposure in multiunit housing. Trial registration Clinical Trials Registered, NCT05016505. Registered on August 23, 2021.

Abstract Background Due to the Covid-19 pandemic, on-site classroom teaching became limited at most German medical universities. This caused a sudden demand for digital teaching concepts. How the transfer from classroom to digital teaching or digitally assisted teaching was conducted was decided by each university and/or department individually. As a surgical discipline, Orthopaedics and Trauma have a particular focus on hands-on teaching as well as direct contact to patients. Therefore, specific challenges in designing digital teaching concepts were expected to arise. Aim of this study was to evaluate medical teaching at German universities one year into the pandemic as well as to identify potentials and pitfalls in order to develop possible optimization approaches. Methods A questionnaire with 17 items was designed and sent to the professors in charge of organising the teaching in Orthopaedics and Trauma at each medical university. A differentiation between Orthopaedics and Trauma was not made to allow a general overview. We collected the answers and conducted a qualitative analysis. Results We received 24 replies. Each university reported a substantial reduction of their classroom teaching and efforts to transfer their teaching to digital formats. Three sites were able to switch to digital teaching concepts completely, whereas others tried to enable classroom and bedside teaching at least for students of higher edcuational levels. The online platforms used varied depending on the university as well as the format it was supposed to support. Conclusion One year into the pandemic significant differences concerning the proportions of classroom and digital teaching for Orthopaedics and Trauma can be observed. Simultaneously huge differences in concepts used to create digital teaching are present. Since a complete suspense of classroom teaching was never mandatory, several universities developed hygiene concepts to enable hands-on and bedside teaching. Despite these differences, some similarities were observed: the lack of time and personnel to generate adequate teaching material was reported as the leading challenge by all participants of this study.

Abstract Background Although apps are becoming increasingly relevant in healthcare, there is limited knowledge about how healthcare professionals perceive “quality” in this context and how quality principles that can aid them in assessing health-related apps may be prioritised. The objective was to investigate physicians’ views of predefined (general) quality principles for health apps and to determine whether a ranking algorithm applied to the acquired data can provide stable results against various demographic influences and may thus be appropriate for prioritisation. Methods Participants of an online survey of members of two German professional orthopaedics associations conducted between 02/12/2019 and 02/01/2020 were asked about their perception of a set of quality principles for health apps (i.e., “practicality,” “risk adequacy,” “ethical soundness,” “legal conformity,” “content validity,” “technical adequacy,” “usability,” “resource efficiency,” and “transparency”). Structured as a Kano survey, for each principle, there were questions about its perceived relevance and opinions regarding the presence or absence of corresponding characteristics. The available data were evaluated descriptively, and a newly developed method for prioritisation of the principles was applied overall and to different demographic strata (for validation). Results Three hundred eighty-two datasets from 9503 participants were evaluated. Legal conformity, content validity, and risk adequacy filled ranks one to three, followed by practicability, ethical soundness, and usability (ranks 4 to 6). Technical adequacy, transparency, and resource efficiency ranked last (ranks 7 to 9). The ranking based on the proposed method was relatively stable, irrespective of demographic factors. The principles were seen as essential, with one exception (“resource efficiency”). Only those with little to no interest in digitisation (22/382, 5.8%) rated the nine principles indifferently. Conclusions The specified quality principles and their prioritisation can lay a foundation for future assessments of apps in the medical field. Professional societies build upon this to highlight opportunities for digital transformations in medicine and encourage their members to participate.

Abstract Background Long-term follow-up studies in patients with borderline personality disorder (BPD) consistently show persistent impairment in psychosocial adjustment, although symptoms tend to decrease over time. Consequently, it might be better to deemphasize symptom-oriented interventions and instead promote interventions that incorporate patient perspectives on recovery. In this study we aimed to examine the feasibility and acceptability of a novel intervention (dialectical behavioral therapy combined with positive psychology and contextual-based skills) in the clinical treatment of long-lasting BPD difficulties. Methods This was a qualitative study. We developed an initial 8-week group intervention for long-lasting BPD. Upon completion of the 8-week program, the participants were asked to participate in a group discussion to provide feedback. Based on that feedback, the intervention protocol was modified and then offered to a second group of patients, who also provided feedback. The protocol was revised again and administered to a third group. A total of 32 patients participated in the group interventions; of these, 20 provided feedback in the qualitative study. The main outcome measure was acceptability. Results The following overarching themes emerged from the group interviews: helpful, unhelpful and neutral practices; internal/external barriers; facilitators; and effects. Participants reported difficulties in imagining an optimal future and self-compassion. By contrast, positive skills were associated with an increase in positive emotions. The main internal barrier was facing difficult emotions. The main external barriers were language-related issues. The group format was perceived as a facilitator to success. Dropout rates, which were assessed as an additional measure of acceptability, decreased substantially in each successive group, from 60 to 40% and finally 20%. Conclusions The intervention was feasible to implement in the clinical setting and participants rated the final set of skills highly. Most of the skills were considered useful. Participant feedback was invaluable to improve the intervention, as evidenced by the large increase in the retention rate from 40 to 80%. Randomized clinical trials are needed to test the efficacy of this intervention in promoting well-being in participants with long-lasting BPD.

Abstract Background Myocardial strain imaging has gained importance in cardiac magnetic resonance (CMR) imaging in recent years as an even more sensitive marker of early left ventricular dysfunction than left-ventricular ejection fraction (LVEF). fSENC (fast strain encoded imaging) and FT (feature tracking) both allow for reproducible assessment of myocardial strain. However, left-ventricular long axis strain (LVLAS) might enable an equally sensitive measurement of myocardial deformation as global longitudinal or circumferential strain in a more rapid and simple fashion. Methods In this study we compared the diagnostic performance of fSENC, FT and LVLAS for identification of cardiac pathology (ACS, cardiac-non-ACS) in patients presenting with chest pain (initial hscTnT 5–52 ng/l). Patients were prospectively recruited from the chest pain unit in Heidelberg. The CMR scan was performed within 1 h after patient presentation. Analysis of LVLAS was compared to the GLS and GCS as measured by fSENC and FT. Results In total 40 patients were recruited (ACS n = 6, cardiac-non-ACS n = 6, non-cardiac n = 28). LVLAS was comparable to fSENC for differentiation between healthy myocardium and myocardial dysfunction (GLS-fSENC AUC: 0.882; GCS-fSENC AUC: 0.899; LVLAS AUC: 0.771; GLS-FT AUC: 0.740; GCS-FT: 0.688), while FT-derived strain did not allow for differentiation between ACS and non-cardiac patients. There was significant variability between the three techniques. Intra- and inter-observer variability (OV) was excellent for fSENC and FT, while for LVLAS the agreement was lower and levels of variability higher (intra-OV: Pearson > 0.7, ICC > 0.8; inter-OV: Pearson > 0.65, ICC > 0.8; CoV > 25%). Conclusions While reproducibility was excellent for both FT and fSENC, it was only fSENC and the LVLAS which allowed for significant identification of myocardial dysfunction, even before LVEF, and therefore might be used as rapid supporting parameters for assessment of left-ventricular function.

Abstract Background The grazing behaviour of herbivores and their grazing personalities might in part be determined genetically, but there are few studies in beef cattle illustrating this. In this study, we investigated for first time the genetic variation within a candidate ‘grazing gene’, the glutamate metabotropic receptor 5 gene (GRM5), and tested associations between variation in that gene and variation in grazing personality behaviours (GP-behaviours) displayed by free-ranging cows during winter grazing in the steep and rugged rangelands of New Zealand. Mature beef cows (n = 303, from 3 to 10 years of age) were tracked with global positioning system (GPS) and, with 5-minutes (min) relocation frequency, various GP-behaviours were calculated. These included horizontal and vertical distances travelled, mean elevation, elevation range, elevation gain, slope, home range and movement tortuosity, variously calculated using daily relocation trajectories with repeated measurements (i.e., 7 to 24 days (d)) and satellite-derived digital elevation models (DEM). The different GP-behaviours were fitted into mixed models to ascertain their associations with variant sequences and genotypes of GRM5. Results We discovered three GRM5 variants (A, B and C) and identified the six possible genotypes in the cattle studied. The mixed models revealed that A was significantly associated with elevation range, home range and movement tortuosity. Similarly, GRM5 genotypes were associated (P

Abstract Background Corticosteroids are one of the few drugs that have shown a reduction in mortality in coronavirus disease 2019 (COVID-19). In the RECOVERY trial, the use of dexamethasone reduced 28-day mortality compared to standard care in hospitalized patients with suspected or confirmed COVID-19 requiring supplemental oxygen or invasive mechanical ventilation. Evidence has shown that 30% of COVID-19 patients with mild symptoms at presentation will progress to acute respiratory distress syndrome (ARDS), particularly patients in whom laboratory inflammatory biomarkers associated with COVID-19 disease progression are detected. We postulated that dexamethasone treatment in hospitalized patients with COVID-19 pneumonia without additional oxygen requirements and at risk of progressing to severe disease might lead to a decrease in the development of ARDS and thereby reduce death. Methods/design This is a multicenter, randomized, controlled, parallel, open-label trial testing dexamethasone in 252 adult patients with COVID-19 pneumonia who do not require supplementary oxygen on admission but are at risk factors for the development of ARDS. Risk for the development of ARDS is defined as levels of lactate dehydrogenase > 245 U/L, C-reactive protein > 100 mg/L, and lymphocyte count of

Abstract Background Patients with chronic lymphocytic leukemia (CLL) may be more susceptible to COVID-19 related poor outcomes, including thrombosis and death, due to the advanced age, the presence of comorbidities, and the disease and treatment-related immune deficiency. The aim of this study was to assess the risk of thrombosis and bleeding in patients with CLL affected by severe COVID-19. Methods This is a retrospective multicenter study conducted by ERIC, the European Research Initiative on CLL, including patients from 79 centers across 22 countries. Data collection was conducted between April and May 2021. The COVID-19 diagnosis was confirmed by the real-time polymerase chain reaction (RT-PCR) assay for SARS-CoV-2 on nasal or pharyngeal swabs. Severe cases of COVID-19 were defined by hospitalization and the need of oxygen or admission into ICU. Development and type of thrombotic events, presence and severity of bleeding complications were reported during treatment for COVID-19. Bleeding events were classified using ISTH definition. STROBE recommendations were used in order to enhance reporting. Results A total of 793 patients from 79 centers were included in the study with 593 being hospitalized (74.8%). Among these, 511 were defined as having severe COVID: 162 were admitted to the ICU while 349 received oxygen supplementation outside the ICU. Most patients (90.5%) were receiving thromboprophylaxis. During COVID-19 treatment, 11.1% developed a thromboembolic event, while 5.0% experienced bleeding. Thrombosis developed in 21.6% of patients who were not receiving thromboprophylaxis, in contrast to 10.6% of patients who were on thromboprophylaxis. Bleeding episodes were more frequent in patients receiving intermediate/therapeutic versus prophylactic doses of low-molecular-weight heparin (LWMH) (8.1% vs. 3.8%, respectively) and in elderly. In multivariate analysis, peak D-dimer level and C-reactive protein to albumin ratio were poor prognostic factors for thrombosis occurrence (OR = 1.022, 95%CI 1.007‒1.038 and OR = 1.025, 95%CI 1.001‒1.051, respectively), while thromboprophylaxis use was protective (OR = 0.199, 95%CI 0.061‒0.645). Age and LMWH intermediate/therapeutic dose administration were prognostic factors in multivariate model for bleeding (OR = 1.062, 95%CI 1.017–1.109 and OR = 2.438, 95%CI 1.023–5.813, respectively). Conclusions Patients with CLL affected by severe COVID-19 are at a high risk of thrombosis if thromboprophylaxis is not used, but also at increased risk of bleeding under the LMWH intermediate/therapeutic dose administration.

Abstract Background Metabolic activity and environmental energy are two of the most studied putative drivers of molecular evolutionary rates. Their extensive study, however, has resulted in mixed results and has rarely included the exploration of interactions among various factors impacting molecular evolutionary rates across large clades. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with proxies of metabolic demands imposed by flight (wing loading and wing shape) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). Results We found weak evidence of a positive effect of environmental and morphological variables on mitochondrial substitution rates. Additionally, we found that temperature and UV radiation interact to explain molecular rates at nucleotide sites affected by selection and population size (non-synonymous substitutions), contrary to the expectation of their impact on sites associated with mutation rates (synonymous substitutions). We also found a negative interaction between wing shape (as described by the hand-wing index) and body mass explaining mitochondrial molecular rates, suggesting molecular signatures of positive selection or reduced population sizes in small-bodied species with greater flight activity. Conclusions Our results suggest that the demands of flight and environmental energy pose multiple evolutionary pressures on the genome either by driving mutation rates or via their association with natural selection or population size. Data from whole genomes and detailed physiology across taxa will bring a more complete picture of the impact of metabolism, population size, and the environment on avian genome evolution.

Abstract Background An animal model that can mimic the SARS-CoV-2 infection in humans is critical to understanding the rapidly evolving SARS-CoV-2 virus and for development of prophylactic and therapeutic strategies to combat emerging mutants. Studies show that the spike proteins of SARS-CoV and SARS-CoV-2 bind to human angiotensin-converting enzyme 2 (hACE2, a well-recognized, functional receptor for SARS-CoV and SARS-CoV-2) to mediate viral entry. Several hACE2 transgenic (hACE2Tg) mouse models are being widely used, which are clearly invaluable. However, the hACE2Tg mouse model cannot fully explain: (1) low expression of ACE2 observed in human lung and heart, but lung or heart failure occurs frequently in severe COVID-19 patients; (2) low expression of ACE2 on immune cells, but lymphocytopenia occurs frequently in COVID-19 patients; and (3) hACE2Tg mice do not mimic the natural course of SARS-CoV-2 infection in humans. Moreover, one of most outstanding features of coronavirus infection is the diversity of receptor usage, which includes the newly proposed human CD147 (hCD147) as a possible co-receptor for SARS-CoV-2 entry. It is still debatable whether CD147 can serve as a functional receptor for SARS-CoV-2 infection or entry. Results Here we successfully generated a hCD147 knock-in mouse model (hCD147KI) in the NOD-scid IL2Rgammanull (NSG) background. In this hCD147KI-NSG mouse model, the hCD147 genetic sequence was placed downstream of the endogenous mouse promoter for mouse CD147 (mCD147), which creates an in vivo model that may better recapitulate physiological expression of hCD147 proteins at the molecular level compared to the existing and well-studied K18-hACE2-B6 (JAX) model. In addition, the hCD147KI-NSG mouse model allows further study of SARS-CoV-2 in the immunodeficiency condition which may assist our understanding of this virus in the context of high-risk populations in immunosuppressed states. Our data show (1) the human CD147 protein is expressed in various organs (including bronchiolar epithelial cells) in hCD147KI-NSG mice by immunohistochemical staining and flow cytometry; (2) hCD147KI-NSG mice are marginally sensitive to SARS-CoV-2 infection compared to WT-NSG littermates characterized by increased viral copies by qRT-PCR and moderate body weight decline compared to baseline; (3) a significant increase in leukocytes in the lungs of hCD147KI-NSG mice, compared to infected WT-NSG mice. Conclusions hCD147KI-NSG mice are more sensitive to COVID-19 infection compared to WT-NSG mice. The hCD147KI-NSG mouse model can serve as an additional animal model for further interrogation whether CD147 serve as an independent functional receptor or accessory receptor for SARS-CoV-2 entry and immune responses.

Abstract Background To ensure successful medical education despite the COVID-19 pandemic, the demand for online instruction has substantially increased. Fast and efficient teaching in a digital format poses a great challenge for medical students and lecturers as well as the universities. Objective The aim of this study is to capture the readiness of medical students and faculty members to participate in rapidly- evolving online education. Methods This cross-sectional study is based on two questionnaires distributed among medical students and associate deans for education in Germany, Austria and Switzerland. Questions included decision- making questions, categorical questions, and open-ended questions, all addressing the frequency and format of the digital education offered, the perceived quality of digital education, and medical student satisfaction with digital education. Questions about missing content and areas for improvement from the perspectives of medical students were included. The associate deans were asked for their opinions about the impact of the pandemic on teaching, the organizational setup and implementation of digital education by universities, and plans for future initiatives. Results Three thousand and thirty medical students (m = 752 and f = 2245) from 53 universities participated in the study. The study showed that 92% of students were affected by the pandemic, and 19% of the students viewed the changes as entirely negative. 97% of the medical students were able to participate in digital courses, but only 4% were able to learn exclusively online. For 77% of the medical students, digital offerings accounted for over 80% of the education offered. In terms of content, medical students complained about a lack of practical teaching, such as contact with patients, lecturers, fellow medical students, and a poor perceived quality of teaching due to dubbing, frequent changeover of seminars, problem-oriented learning groups and in-person teaching, a lack of interaction possibilities and a lack of technical equipment, such as lecturers’ knowledge and server capacities, at the universities. Overall, almost half of the medical students (42%) rated the implementation of digital teaching at their universities as good or very good. Forty-one of the 53 associate deans responded to the questionnaire, and 35 felt medical education was influenced by the pandemic. The associate deans (80%; 33/41) felt that the digitalization of medical education was negatively influenced by the pandemic. Only 44% (18/41) felt that their universities were well or very well positioned for digital teaching. All the associate deans believe that digital teaching in medicine will continue after the pandemic. Conclusions In the German-speaking world, the rapid conversion of medical teaching to a digital format has been well implemented in many cases. The perceived quality of the implementation of digital education still lacks practical relevance and the use of new digital media, such as learning games, VR, and online question time. The digital format of medical education will likely continue beyond the COVID-19 pandemic.

Abstract Early responses in healthy adult dogs fed grain-free diets with high inclusion of split peas (20%) and lentils (40%) that may lead to canine diet-induced dilated cardiomyopathy (DCM) were investigated. To help understand the clinical relevance of the findings, a survey of electronic health records (EHR) was conducted of dogs with and without suspected DCM for comparison. Control and Test diets were fed to Labrador retriever dogs for 30 days (n = 5 and 6, respectively). Blood and urine samples collected at baseline and days 3, 14 and 28/30 were analyzed for hematology, clinical biochemistry and taurine concentrations. The EHRs of dogs at Banfield® Pet Hospitals in the 2-year period 2018-2019 were surveyed, revealing 420 dogs diagnosed with DCM, which were compared with 420 breed, gender and age-matched healthy control dogs. Compared to baseline values, feeding the Test diet for 28 days caused progressive, significant (p

Abstract Background COVID-19 is a multi-system infection with emerging evidence-based antiviral and anti-inflammatory therapies to improve disease prognosis. However, a subset of patients with COVID-19 signs and symptoms have repeatedly negative RT-PCR tests, leading to treatment hesitancy. We used comparative serology early in the COVID-19 pandemic when background seroprevalence was low to estimate the likelihood of COVID-19 infection among RT-PCR negative patients with clinical signs and/or symptoms compatible with COVID-19. Methods Between April and October 2020, we conducted serologic testing of patients with (i) signs and symptoms of COVID-19 who were repeatedly negative by RT-PCR (‘Probables’; N = 20), (ii) signs and symptoms of COVID-19 but with a potential alternative diagnosis (‘Suspects’; N = 15), (iii) no signs and symptoms of COVID-19 (‘Non-suspects’; N = 43), (iv) RT-PCR confirmed COVID-19 patients (N = 40), and (v) pre-pandemic samples (N = 55). Results Probables had similar seropositivity and levels of IgG and IgM antibodies as propensity-score matched RT-PCR confirmed COVID-19 patients (60.0% vs 80.0% for IgG, p-value = 0.13; 50.0% vs 72.5% for IgM, p-value = 0.10), but multi-fold higher seropositivity rates than Suspects and matched Non-suspects (60.0% vs 13.3% and 11.6% for IgG; 50.0% vs 0% and 4.7% for IgM respectively; p-values

Abstract Background Undergraduate emergency medicine (EM) training is important because all medical graduates are expected to have basic emergency knowledge and skills regardless of their future speciality. EM clerkship should provide opportunities to improve not only knowledge and skills but also the self-efficacy of learners. This study aims to evaluate the expectations, opinions, and self-efficacy beliefs of medical students during a 4-week mandatory EM clerkship. Methods This study used a prospective longitudinal design with quantitative and qualitative survey methods. It includes final year medical students of the 2015–2016 academic year. Voluntary de-identified pre- and post-clerkship surveys included 25 statements. The post-clerkship survey included two open-ended questions asking participants to identify the best and worst three aspects of EM clerkship. Responses were analysed to determine themes or commonalities in participant comments indicative of the EM clerkship learning experiences and environment. Results Sixty-seven out of seventy-nine (85%) students responded to both pre- and post-clerkship surveys. Medical students’ expectations of EM clerkships’ effect on knowledge and skill acquisition were high, and a 4-week mandatory EM clerkship was able to meet their expectations. Medical students had very high expectations of EM clerkships’ educational environment. In most aspects, their experiences significantly exceeded their expectations (p value < 0.001). The only exception was the duration of clerkship, which was deemed insufficient both at the beginning and at the end (p value: 0.92). The students perceived that their self-efficacy improved significantly in the majority of basic EM skills and procedures (p value < 0.001). Emergent qualitative themes in the study also supported these results. Conclusion This study showed that a 4-week mandatory EM clerkship increased medical students' perceived self-efficacy in basic emergency management skills. The EM clerkship met students' expectations on knowledge and skill acquisition, and exceeded students’ expectations on educational environment.

Abstract Background During the COVID-19 crisis it was necessary to generate a specific care network and reconvert operating rooms to attend emergency and high-acuity patients undergoing complex surgery. The aim of this study is to classify postoperative complications and mortality and to assess the impact that the COVID-19 pandemic may have had on the results. Methods this is a non-inferiority retrospective observational study. Two different groups of surgical patients were created: Pre-pandemic COVID and Pandemic COVID. Severity of illness was rated according to the Diagnosis-related Groups (DRG) score. Comparisons were made between groups and between DRG severity score-matched samples. Non-inferiority was set at up to 10 % difference for grade III to V complications according to the Clavien-Dindo classification, and up to 2 % difference in mortality. Results A total of 1649 patients in the PreCOVID group and 763 patients in the COVID group were analysed; 371 patients were matched for DRG severity score 3-4 (236 preCOVID and 135 COVID). No differences were found in relation to re-operation (22.5 % vs. 21.5 %) or late admission to critical care unit (5.1 % vs. 4.5 %). Clavien grade III to V complications occurred in 107 patients (45.3 %) in the PreCOVID group and in 56 patients (41.5 %) in the COVID group, and mortality was 12.7 % and 12.6 %, respectively. During the pandemic, 3 % of patients tested positive for Covid-19 on PCR: 12 patients undergoing elective surgery and 11 emergency surgery; there were 5 deaths, 3 of which were due to respiratory failure following Covid-19-induced pneumonia. Conclusions Although this study has some limitations, it has shown the non-inferiority of surgical outcomes during the COVID pandemic, and indicates that resuming elective surgery is safe. Trial registration Clinicaltrials.gov identifier: NCT04780594 .

Abstract Background To reduce the coronavirus disease burden in England, along with many other countries, the government implemented a package of non-pharmaceutical interventions (NPIs) that have also impacted other transmissible infectious diseases such as norovirus. It is unclear what future norovirus disease incidence is likely to look like upon lifting these restrictions. Methods Here we use a mathematical model of norovirus fitted to community incidence data in England to project forward expected incidence based on contact surveys that have been collected throughout 2020–2021. Results We report that susceptibility to norovirus infection has likely increased between March 2020 and mid-2021. Depending upon assumptions of future contact patterns incidence of norovirus that is similar to pre-pandemic levels or an increase beyond what has been previously reported is likely to occur once restrictions are lifted. Should adult contact patterns return to 80% of pre-pandemic levels, the incidence of norovirus will be similar to previous years. If contact patterns return to pre-pandemic levels, there is a potential for the expected annual incidence to be up to 2-fold larger than in a typical year. The age-specific incidence is similar across all ages. Conclusions Continued national surveillance for endemic diseases such as norovirus will be essential after NPIs are lifted to allow healthcare services to adequately prepare for a potential increase in cases and hospital pressures beyond what is typically experienced.

Abstract Background The use of sequencing and genotyping platforms has undergone dramatic improvements, enabling the generation of a wealth of genomic information. Despite this progress, the availability of high-quality genomic DNA (gDNA) in sufficient concentrations is often a main limitation, especially for third-generation sequencing platforms. A variety of DNA extraction methods and commercial kits are available. However, many of these are costly and frequently give either low yield or low-quality DNA, inappropriate for next generation sequencing (NGS) platforms. Here, we describe a fast and inexpensive DNA extraction method (SILEX) applicable to a wide range of plant species and tissues. Results SILEX is a high-throughput DNA extraction protocol, based on the standard CTAB method with a DNA silica matrix recovery, which allows obtaining NGS-quality high molecular weight genomic plant DNA free of inhibitory compounds. SILEX was compared with a standard CTAB extraction protocol and a common commercial extraction kit in a variety of species, including recalcitrant ones, from different families. In comparison with the other methods, SILEX yielded DNA in higher concentrations and of higher quality. Manual extraction of 48 samples can be done in 96 min by one person at a cost of 0.12 €/sample of reagents and consumables. Hundreds of tomato gDNA samples obtained with either SILEX or the commercial kit were successfully genotyped with Single Primer Enrichment Technology (SPET) with the Illumina HiSeq 2500 platform. Furthermore, DNA extracted from Solanum elaeagnifolium using this protocol was assessed by Pulsed-field gel electrophoresis (PFGE), obtaining a suitable size ranges for most sequencing platforms that required high-molecular-weight DNA such as Nanopore or PacBio. Conclusions A high-throughput, fast and inexpensive DNA extraction protocol was developed and validated for a wide variety of plants and tissues. SILEX offers an easy, scalable, efficient and inexpensive way to extract DNA for various next-generation sequencing applications including SPET and Nanopore among others.

Abstract Background Little is known about whether a more comprehensive health assessment, performed by a general practitioner (GP) during a clinical encounter, could influence patients’ lifestyle. We aimed to investigate whether health assessments, performed by GPs, are more important than the presence of cardiovascular disease (CVD) or cardiometabolic risk factors (obesity, diabetes, hypertension, dyslipidaemia) for engagement in lifestyle change. Methods Cross-sectional, population-based survey conducted in South Australia (September–December 2017) using face-to-face interviews and self-reported data of 2977 individuals aged 15+ years. The main outcome was engagement in four lifestyle changes: 1) increasing fruit/vegetable intake, 2) increasing physical activity level, 3) reducing alcohol consumption, and 4) attempts to stop smoking. Health assessments performed by a GP in the last 12 months included clinical/laboratory investigations (weight/waist circumference, blood pressure, glucose levels, lipid levels) and questions about lifestyle/wellbeing (current diet, physical activity, smoking status, alcohol intake, mental health, sleeping problems). Results were restricted to individuals aged 35+ years because of the low prevalence of CVD or their risk factors among younger participants. Logistic regression was used in all associations, adjusted for sociodemographic, lifestyle, mental health, and clinical variables. Results Of the 2384 investigated adults (mean age 57.3 ± 13.9 years; 51.9% females), 10.2% had CVD and 49.1% at least one cardiometabolic risk factor. Clinical/laboratory assessments performed by the GP were 2–3 times more frequent than assessments of lifestyle, mental health status, or sleeping problems, especially among those with CVD. Individuals with CVD or a cardiometabolic risk factor were no more likely to be increasing their fruit/vegetable consumption (33.6%), physical activity level (40.9%), reducing alcohol consumption (31.1%), or trying to quit smoking (34.0%) than ‘healthy’ participants. However, lifestyle changes were between 30 and 100% more likely when GPs performed three or more health assessments (either clinical/laboratory or questions about lifestyle/wellbeing) than when individuals did not visit the GP or when GPs performed no any assessment during these clinical encounters (p

Abstract Background The logarithmic acid dissociation constant pKa reflects the ionization of a chemical, which affects lipophilicity, solubility, protein binding, and ability to pass through the plasma membrane. Thus, pKa affects chemical absorption, distribution, metabolism, excretion, and toxicity properties. Multiple proprietary software packages exist for the prediction of pKa, but to the best of our knowledge no free and open-source programs exist for this purpose. Using a freely available data set and three machine learning approaches, we developed open-source models for pKa prediction. Methods The experimental strongest acidic and strongest basic pKa values in water for 7912 chemicals were obtained from DataWarrior, a freely available software package. Chemical structures were curated and standardized for quantitative structure–activity relationship (QSAR) modeling using KNIME, and a subset comprising 79% of the initial set was used for modeling. To evaluate different approaches to modeling, several datasets were constructed based on different processing of chemical structures with acidic and/or basic pKas. Continuous molecular descriptors, binary fingerprints, and fragment counts were generated using PaDEL, and pKa prediction models were created using three machine learning methods, (1) support vector machines (SVM) combined with k-nearest neighbors (kNN), (2) extreme gradient boosting (XGB) and (3) deep neural networks (DNN). Results The three methods delivered comparable performances on the training and test sets with a root-mean-squared error (RMSE) around 1.5 and a coefficient of determination (R2) around 0.80. Two commercial pKa predictors from ACD/Labs and ChemAxon were used to benchmark the three best models developed in this work, and performance of our models compared favorably to the commercial products. Conclusions This work provides multiple QSAR models to predict the strongest acidic and strongest basic pKas of chemicals, built using publicly available data, and provided as free and open-source software on GitHub.

Abstract Background Mexico City has one of the highest incidences and mortality rates of acute lymphoblastic leukemia (ALL) in the world and a high frequency of early relapses (17%) and early mortality (15%). Otherwise, childhood overweight and obesity are reaching epidemic proportions. They have been associated with poor outcomes in children with ALL. The aim of present study was to identify if overweight and obesity are predictors of early mortality and relapse in Mexican children with ALL. Methods A multicenter cohort study was conducted. ALL children younger than 15 years old were included and followed-up during the first 24 months after diagnosis. Overweight and obesity were classified according World Health Organization (WHO) and Centers for Disease Control and Prevention (CDC) criteria. Early mortality and early relapses were the main outcomes. Results A total of 1070 children were analyzed. Overweight/obesity at diagnosis were predictors of early mortality (WHO: HR = 1.4, 95%CI:1.0–2.0; CDC: HR = 1.6, 95%CI:1.1–2.3). However, no associations between overweight (WHO: HR = 1.5, 95%CI:0.9–2.5; CDC: HR = 1.0; 95% CI:0.6–1.6) and obesity (WHO: HR = 1.5, 95%CI:0.7–3.2; CDC: HR = 1.4; 95%CI:0.9–2.3) with early relapse were observed. Conclusions Overweight and obese patients embody a subgroup with high risk of dying during leukemia treatment.

Abstract Background Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians. Results A total of 8540 candidate groups of orthologous genes from transcriptomic data of five species of caecilian amphibians and the genome of the frog Xenopus tropicalis were analysed in order to investigate the genetic machinery behind caecilian diversification. We found a total of 168 protein-coding genes with signatures of positive selection at different evolutionary times during the radiation of caecilians. The majority of these genes were related to functional elements of the cell membrane and extracellular matrix with expression in several different tissues. The first colonization of the tropical soils was connected to the largest number of protein-coding genes under positive selection in our analysis. From the results of our study, we highlighted molecular changes in genes involved in perception, reduction-oxidation processes, and aging that likely were involved in the adaptation to different soil strata. Conclusions The genes inferred to have been under positive selection provide valuable insights into caecilian evolution, potentially underpin adaptations of caecilians to their extreme environments, and contribute to a better understanding of fossorial adaptations and molecular evolution in vertebrates.

Abstract Background Inter-observer variability in stroke aetiological classification may have an effect on trial power and estimation of treatment effect. We modelled the effect of misclassification on required sample size in a hypothetical cardioembolic (CE) stroke trial. Methods We performed a systematic review to quantify the reliability (inter-observer variability) of various stroke aetiological classification systems. We then modelled the effect of this misclassification in a hypothetical trial of anticoagulant in CE stroke contaminated by patients with non-cardioembolic (non-CE) stroke aetiology. Rates of misclassification were based on the summary reliability estimates from our systematic review. We randomly sampled data from previous acute trials in CE and non-CE participants, using the Virtual International Stroke Trials Archive. We used bootstrapping to model the effect of varying misclassification rates on sample size required to detect a between-group treatment effect across 5000 permutations. We described outcomes in terms of survival and stroke recurrence censored at 90 days. Results From 4655 titles, we found 14 articles describing three stroke classification systems. The inter-observer reliability of the classification systems varied from ‘fair’ to ‘very good’ and suggested misclassification rates of 5% and 20% for our modelling. The hypothetical trial, with 80% power and alpha 0.05, was able to show a difference in survival between anticoagulant and antiplatelet in CE with a sample size of 198 in both trial arms. Contamination of both arms with 5% misclassified participants inflated the required sample size to 237 and with 20% misclassification inflated the required sample size to 352, for equivalent trial power. For an outcome of stroke recurrence using the same data, base-case estimated sample size for 80% power and alpha 0.05 was n = 502 in each arm, increasing to 605 at 5% contamination and 973 at 20% contamination. Conclusions Stroke aetiological classification systems suffer from inter-observer variability, and the resulting misclassification may limit trial power. Trial registration Protocol available at reviewregistry540.

Abstract Background Hepatitis B (HepB) is a major public health concern in Malaysia yet little is known about knowledge and awareness of this infection in the country. Such information is essential for designing effective intervention strategies for HepB prevention and control. The aim of this study was to characterize knowledge and awareness regarding HepB in Malaysia and to identify their associated sociodemographic determinants. Methods A community-based cross-sectional survey was conducted between January and May 2016 in Selangor state of Malaysia. A two-stage cluster random sampling design was used and one adult member of selected households was interviewed face-to-face. Logistic regression was used to estimate the differences in knowledge and awareness between groups. Results A total of 764 households completed the interviews and were included in the final analysis. Only 36.9 and 38.8% of the participants had good knowledge and awareness, respectively. The factors associated with good knowledge were being in the 35–44 year age group, Malay ethnicity, high educational attainment and high family income. Being Chinese, being older and having high educational attainment were determinants of having good awareness towards HepB. Participants who had good knowledge were 2.5 times more likely to also have good awareness (OR: 2.41, 95% CI: 1.78–3.26, p

Abstract Background Few representative sample studies have reported estimates of bullying and sexual abuse in Australia. By using face-to-face interviews and self-labelling questions, we investigated the prevalence of these forms of abuse and their relationship with current harmful behaviours (smoking dependence, excessive alcohol intake, binge eating), antidepressant use, and the physical (PCS) and mental (MCS) components of health-related quality of life. Methods This study was a population-based survey that investigated 2873 South Australians in 2015 (48.8 ± 18.1 years; 49.3% males). Bullying and sexual abuse (age of onset and duration) and their outcomes were investigated through household interviews. Associations were adjusted for sociodemographic variables by using regression models. Results 45.6% (95% CI 43.3–47.9) of the participants were bullied, and 10.4% (95% CI 9.1–11.9) sexually abused; 7.3% (95% CI 6.2–8.5) reported experiencing both forms of abuse. Moreover, 15.8% of those bullied and 15.0% of those sexually abused suffered from these forms of abuse for > 24 months. Smoking dependence (7.8%) was twice as frequent among those who experienced bullying for > 24 months or when sexual abuse occurred in childhood ( 24 months. Binge eating (8.1%) was more frequent among those bullied or sexually abused in adulthood, but duration did not show a clear pattern. Antidepressant use was up to four times more likely, and PCS or MCS lower among those who were bullied or sexually abused, independent of when these forms of abuse started or their duration. The cumulative adverse relationship of bullying and sexual abuse with the investigated outcomes was more evident for smoking dependence, binge eating, PCS, and MCS than for antidepressant use, but no association was observed with alcohol intake. Conclusions The use of self-labelling questions to investigate sensitive areas such as bullying and sexual abuse in a survey is feasible. Such questions provided estimates that are consistent with findings from studies using more detailed instruments. Bullying and sexual abuse have an additive adverse association with various outcomes. Identifying survivors of both forms of abuse is important to avoid more serious consequences.

Abstract Background The prevalence and distribution of histologically diagnosed breast disease are not well documented in low income countries, Uganda inclusive. Although the greater majority of breast lesions globally are benign, breast cancer is the most frequently diagnosed cancer all over the world. We aimed at documenting the prevalence of different breast diseases histologically diagnosed at the histopathology laboratory of the Department of Pathology of the Makerere University College of Health Sciences (MakCHS Lab) over a decade (2005–2014). We also describe the demographic characteristics of the patients in Uganda diagnosed with breast disease at the MakCHS Lab during the same period. Methods This was a 10 year retrospective study of histologically diagnosed breast disease between 2005 and 2014 inclusive at the MakCHS Lab. We extracted information from hard copies of all 2510 histopathology reports retrieved from archives of the Department of Pathology at the MakCHS Lab. 640 records that were either damaged beyond recognition of key details, were duplicated, were implausible or had no conclusive diagnosis made were excluded. Information to be analyzed was then entered into Epidata (version 3.1) on a password protected laptop. Data analysis was done using SPSS software (v16 for Windows × 64). Results From the 1870 patients’ records eventually analyzed, breast disease was most diagnosed in female patients (97.1%). The overall mean age for breast disease diagnosis was 33 years (S.D ± 16.46) and median age 26 years (IQR: 20–43). Fibroadenoma (40.1%) was the most diagnosed breast disease overall. We noticed steadily increasing frequency of diagnosis of cancerous breast diseases over the last half of the study period. Invasive ductal carcinoma was the most diagnosed breast cancer (326 cases, 55.6%). A high female to male breast cancer ratio of 48:1 was observed. The highest regional breast cancer proportion was from the Western region of the Country. Conclusions There is need for more research into the picture of breast disease in the country, covering various demographic characteristics of the country’s population for all regions and informing about its incidence rates and prevalence and also the breast cancer risk estimate for benign breast disease.

Abstract Background Several mosquito population suppression strategies based on the rearing and release of sterile males have provided promising results. However, the lack of an efficient male selection method has hampered the expansion of these approaches into large-scale operational programmes. Currently, most of these programmes targeting Aedes mosquitoes rely on sorting methods based on the sexual size dimorphism (SSD) at the pupal stage. The currently available sorting methods have not been developed based on biometric analysis, and there is therefore potential for improvement. We applied an automated pupal size estimator developed by Grupo Tragsa with laboratory samples of Anopheles arabiensis, Aedes albopictus, Ae. polynesiensis, and three strains of Ae. aegypti. The frequency distribution of the pupal size was analyzed. We propose a general model for the analysis of the frequency distribution of mosquito pupae in the context of SSD-sorting methods, which is based on a Gaussian mixture distribution functions, thus making possible the analysis of performance (% males recovery) and purity (% males on the sorted sample). Results For the three Aedes species, the distribution of the pupae size can be modeled by a mixture of two Gaussian distribution functions and the proposed model fitted the experimental data. For a given population, each size threshold is linked to a specific outcome of male recovery. Two dimensionless parameters that measure the suitability for SSD-based sorting of a specific batch of pupae are provided. The optimal sorting results are predicted for the highest values of SSD and lowest values of intra-batch variance. Rearing conditions have a strong influence in the performance of the SSD-sorting methods and non-standard rearing can lead to increase pupae size heterogeneity. Conclusions Sex sorting of pupae based on size dimorphism can be achieved with a high performance (% males recovery) and a reasonably high purity (% males on the sorted sample) for the different Aedes species and strains. The purity and performance of a sex sorting operation in the tested Aedes species are linked parameters whose relation can be modeled. The conclusions of this analysis are applicable to all the existing SSD-sorting methods. The efficiency of the SSD-sorting methods can be improved by reducing the heterogeneity of pupae size within rearing containers. The heterogeneity between batches does not strongly affect the quality of the sex sorting, as long as a specific separation threshold is not pre-set before the sorting process. For new developments, we recommend using adaptive and precise threshold selection methods applied individually to each batch or to a mix of batches. Adaptive and precise thresholds will allow the sex-sorting of mixed batches in operational conditions maintaining the target purity at the cost of a reduction in performance. We also recommend a strategy whereby an acceptable level of purity is pre-selected and remains constant across the different batches of pupae while the performance varies from batch to batch to fit with the desired purity.

Abstract Background Mesenchymal stromal cells (MSC) are components of connective tissues and, in vitro, cell entities characterized by cell adhesion and immunophenotyping, although specific markers for their identification are lacking. Currently, MSC derived from either human bone marrow (BM-MSC) or adipose tissue (Ad-MSC) are considered the main sources of MSC for cell therapy. Eph receptors and their ligands, Ephrins, are molecules involved in cell adhesion and migration in several tissues and organs. In the current study, we analyze the pattern of Eph/Ephrin expression in MSC and evaluate the effects of blockade and stimulation of these receptor/ligand pairs on their biology. Methods Eph/Ephrin expression was analyzed in both BM-MSC and Ad-MSC by qRT-PCR. Then, we supplied BM-MSC cultures with either blocking or activating compounds to evaluate their effects on MSC proliferation, survival, and cell cycle by FACS. Changes in cytoskeleton and integrin α5β1 expression were studied in stimulated BM-MSC by immunofluorescence microscopy and FACS, respectively. Results Higher numbers of Eph/Ephrin transcripts occurred in BM-MSC than in Ad-MSC. In addition, the blocking of Eph/Ephrin signaling correlated with decreased numbers of BM-MSC due to increased proportions of apoptotic cells in the cultures but without variations in the cycling cells. Unexpectedly, activation of Eph/Ephrin signaling by clustered Eph/Ephrin fusion proteins also resulted in increased proportions of apoptotic MSC. In this case, MSC underwent important morphological changes, associated with altered cytoskeleton and integrin α5β1 expression, which did not occur under the blocking conditions. Conclusions Taken together, these results suggest that Eph/Ephrin activation affects cell survival through alterations in cell attachment to culture plates, affecting the biology of BM-MSC.

Abstract Asia and its Hindu Kush Himalayan (HKH) region is particularly vulnerable to environmental change, especially climate and land use changes further influenced by rapid population growth, high level of poverty and unsustainable development. Asia has been a hotspot of dengue fever and chikungunya mainly due to its dense human population, unplanned urbanization and poverty. In an urban cycle, dengue virus (DENV) and chikungunya virus (CHIKV) are transmitted by Aedes aegypti and Ae. albopictus mosquitoes which are also competent vectors of Zika virus (ZIKV). Over the last decade, DENV and CHIKV transmissions by Ae. aegypti have extended to the Himalayan countries of Bhutan and Nepal and ZIKV could follow in the footsteps of these viruses in the HKH region. The already established distribution of human-biting Aedes mosquito vectors and a naïve population with lack of immunity against ZIKV places the HKH region at a higher risk of ZIKV. Some of the countries in the HKH region have already reported ZIKV cases. We have documented an increasing threat of ZIKV in Asia and its HKH region because of the high abundance and wide distribution of human-biting mosquito vectors, climate change, poverty, report of indigenous cases in the region, increasing numbers of imported cases and a naïve population with lack of immunity against ZIKV. An outbreak anywhere is potentially a threat everywhere. Therefore, in order to ensure international health security, all efforts to prevent, detect, and respond to ZIKV ought to be intensified now in Asia and its HKH region. To prepare for possible ZIKV outbreaks, Asia and the HKH region can also learn from the success stories and strategies adopted by other regions and countries in preventing ZIKV and associated complications. The future control strategies for DENV, CHIKV and ZIKV should be considered in tandem with the threat to human well-being that is posed by other emerging and re-emerging vector-borne and zoonotic diseases, and by the continuing urgent need to strengthen public primary healthcare systems in the region.