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Objectives: The classic Konno-Rastan procedure may yield different outcomes regarding aortic annulus diameters ≤15 mm and larger. Focusing on the effect of the diameter of the aortic annulus, we described the long-term outcomes of our patients., Methods: The outcomes of paediatric and adult patients who underwent surgery from 2000 to 2021 were studied retrospectively. The patient population was divided into 2 groups with aortic annulus diameters ≤15 mm and >15, and the outcomes were compared between the 2 groups., Results: A total of 48 patients, with a mean age of 12.24 ± 9.42 years (2-53 years) and a median follow-up duration of 8 years (7 months to 20 years) with an IQR of 5.5, were enrolled. The mean peak instantaneous pressure gradient was 78.97 ± 25.29 mmHg, which decreased to 21.43 mmHg (P-value = 0.012). The maximum left ventricular outflow tract gradient at the last follow-up was 28.21 mmHg, with the exception of 1 case with a gradient of 68.45 mmHg. The mean diameter of the aortic annulus was 15.34 ± 3.87 mm (8-23 mm), and the mean prosthetic valve size was 20.31 mm, which was 5 mm (33%) larger than the native annulus diameter. The overall mortality rate was 6.3%, with 1 death in the hospital and 2 in the first year after the surgery. The major complication rate, including mortality, heart block and reintervention, was higher in patients with ≤15 mm annulus (P-value = 0.028.) However, there was no difference between the 2 groups in follow-up. Four (8%) late cardiac reoperations were performed, none of which were related to our surgeries., Conclusions: Kono-Rastan surgery for patients with aortic valve diameter of ≤15 mm can be performed with acceptable long-term outcomes., (© The Author(s) 2023. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery.)

Burn injury is a critical health issue, which is associated with several morbidities and mortalities. Substance abuse, which is an important public health problem in Iran, can affect burn injury outcomes and etiologies in victims. This study was aimed to evaluate different aspects of burn injuries in people who used drug (PWUD) in two referral centers in the south of Iran. This case-control study was conducted on burn victims referred to Amir-al Momenin Hospital and Ghotb-al-din Hospital from 2009 to 2017. Patients with a history of drug consumption were selected from the database and compared to randomly selected burn victims with no history of drug use. Demographics, burn etiology, underlying disease, total body surface area, hospitalization duration, and also the outcomes were collected and recorded in both groups. Data analysis was done by SPSS software. A total of 5912 inpatients were included in this study, of which 2397 of them (40.54%) were female. The mean age of the patients was 26.12 ± 19.18. Drug history was positive in 659 patients (11.15%). Familial issues and mental disorders were significantly higher in the PWUD group compared to the control group (P < .001). Explosion etiology was significantly higher in the PWUD group (P < .001). Psychiatric disorders (P < .001), total body surface area (P = .023), and hospital stay (P < .001) were significantly higher in PWUD; however, the mortality rate had no statistically significant differences between the groups (P = .583). Substance abuse is a risk factor in burn victims, which can affect burn etiology and burn-related morbidities., (© The Author(s) 2022. Published by Oxford University Press on behalf of the American Burn Association. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Objectives: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic. The majority of patients experience asymptomatic to mild self-limited disease, but some cases progress to respiratory and multi-organ failure. However, so far, no approved antiviral therapy has been available for treatment of COVID-19. Sofosbuvir/velpatasvir (SOF/VEL) is an approved anti-HCV drug that is capable of suppressing other families of positive-sense RNA viruses with conserved polymerase and may be effective against SARS-CoV-2. This study was conducted to evaluate the efficacy of the SOF/VEL combination in addition to the national standard of care versus the national standard of care alone (hydroxychloroquine and lopinavir/ritonavir as well as supportive care) in patients with moderate to severe COVID-19 infection., Methods: This single-centre, randomized, open-labelled, prospective clinical trial was done in patients with moderate to severe COVID-19 admitted to Farabi Hospital in Kermanshah Province, Iran. Eligible patients were randomly assigned in a 1:1 ratio to the SOF/VEL arm (SOF/VEL plus the national standard of care) or the control arm (the national standard of care alone). The main outcome of the study was the mortality on Day 28 after randomization. Secondary outcomes were time from the start of medication to clinical improvement, hospital length of stay, need for mechanical ventilation, duration of mechanical ventilation and conversion of RT-PCR results from positive to negative from the time of randomization to discharge. Adverse events were evaluated in all patients who started their assigned treatment., Results: Between 11 April and 8 June 2020, 80 patients were recruited and randomly assigned into the SOF/VEL (n = 40) and control (n = 40) arms. The primary outcome was not significantly different between the two arms (P = 1.00). Secondary outcomes, including time to clinical improvement, hospital length of stay, need for mechanical ventilation, duration of mechanical ventilation and RT-PCR conversion, were not significantly different between arms either (P > 0.05). SOF/VEL treatment and the national standard of care were tolerated similarly., Conclusions: Although treatment with SOF/VEL was safe, adding SOF/VEL to the standard of care did not improve the clinical status or reduce mortality in patients with moderate to severe COVID-19. However, larger randomized clinical trials including more parameters are needed for accurate estimation of the efficacy of SOF/VEL., (© The Author(s) 2021. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Objective: Active Learning (AL) attempts to reduce annotation cost (ie, time) by selecting the most informative examples for annotation. Most approaches tacitly (and unrealistically) assume that the cost for annotating each sample is identical. This study introduces a cost-aware AL method, which simultaneously models both the annotation cost and the informativeness of the samples and evaluates both via simulation and user studies., Materials and Methods: We designed a novel, cost-aware AL algorithm (Cost-CAUSE) for annotating clinical named entities; we first utilized lexical and syntactic features to estimate annotation cost, then we incorporated this cost measure into an existing AL algorithm. Using the 2010 i2b2/VA data set, we then conducted a simulation study comparing Cost-CAUSE with noncost-aware AL methods, and a user study comparing Cost-CAUSE with passive learning., Results: Our cost model fit empirical annotation data well, and Cost-CAUSE increased the simulation area under the learning curve (ALC) scores by up to 5.6% and 4.9%, compared with random sampling and alternate AL methods. Moreover, in a user annotation task, Cost-CAUSE outperformed passive learning on the ALC score and reduced annotation time by 20.5%-30.2%., Discussion: Although AL has proven effective in simulations, our user study shows that a real-world environment is far more complex. Other factors have a noticeable effect on the AL method, such as the annotation accuracy of users, the tiredness of users, and even the physical and mental condition of users., Conclusion: Cost-CAUSE saves significant annotation cost compared to random sampling., (© The Author(s) 2019. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

With the advent of high-throughput technologies leading to big data generation, increasing number of gene signatures are being published to predict various features of diseases such as prognosis and patient survival. However, to use these signatures for identifying therapeutic targets, use of additional bioinformatic tools is indispensible part of research. Here, we have generated a pipeline comprised of nearly 15 bioinformatic tools and enrichment statistical methods to propose and validate a drug combination strategy from already approved drugs and present our approach using published pan-cancer epithelial-mesenchymal transition (EMT) signatures as a case study. We observed that histone deacetylases were critical targets to tune expression of multiple epithelial versus mesenchymal genes. Moreover, SRC and IKBK were the principal intracellular kinases regulating multiple signaling pathways. To confirm the anti-EMT efficacy of the proposed target combination in silico, we validated expression of targets in mesenchymal versus epithelial subtypes of ovarian cancer. Additionally, we inhibited the pinpointed proteins in vitro using an invasive lung cancer cell line. We found that whereas low-dose mono-therapy failed to limit cell dispersion from collagen spheroids in a microfluidic device as a metric of EMT, the combination fully inhibited dissociation and invasion of cancer cells toward cocultured endothelial cells. Given the approval status and safety profiles of the suggested drugs, the proposed combination set can be considered in clinical trials., (© The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

This study assesses the succession of insects on rabbit carcass. The study was conducted in sunny and shaded sites in the west of Iran during four seasons in 2016 and 2017. Based on the results of this study, various factors such as body size, carcass location, and carcass injury could affect the pattern of insect succession on carcass. In this study, we estimated the elapsed time since death (R2 > 0.98, P = 0.00) based on carcass weight loss during the stages of decomposition and the cubic method. Jaccard analysis was performed to determine the similarity of insect taxa during decomposition of rabbit carrion in two different sites during a period of four seasons. Succession pattern analysis for necrophagous insects in both habitats showed a similarity between bloat and decay stages for each habitat. On the other hand, pairwise similarities in taxa were low at the fresh and dry stages, however increased at bloat and decay stages of decomposition. This study shows that succession has some limitations in determining the elapsed time of death. Therefore, the use of source of information such as a weight loss model seems to be essential.

Objective: The Safety Assurance Factors for EHR Resilience (SAFER) guides were released in 2014 to help health systems conduct proactive risk assessment of electronic health record (EHR)- safety related policies, processes, procedures, and configurations. The extent to which SAFER recommendations are followed is unknown., Methods: We conducted risk assessments of 8 organizations of varying size, complexity, EHR, and EHR adoption maturity. Each organization self-assessed adherence to all 140 unique SAFER recommendations contained within 9 guides (range 10-29 recommendations per guide). In each guide, recommendations were organized into 3 broad domains: "safe health IT" (total 45 recommendations); "using health IT safely" (total 80 recommendations); and "monitoring health IT" (total 15 recommendations)., Results: The 8 sites fully implemented 25 of 140 (18%) SAFER recommendations. Mean number of "fully implemented" recommendations per guide ranged from 94% (System Interfaces-18 recommendations) to 63% (Clinical Communication-12 recommendations). Adherence was higher for "safe health IT" domain (82.1%) vs "using health IT safely" (72.5%) and "monitoring health IT" (67.3%)., Conclusions: Despite availability of recommendations on how to improve use of EHRs, most recommendations were not fully implemented. New national policy initiatives are needed to stimulate implementation of these best practices.

Objective: To present user needs and usability evaluations of DataMed, a Data Discovery Index (DDI) that allows searching for biomedical data from multiple sources., Materials and Methods: We conducted 2 phases of user studies. Phase 1 was a user needs analysis conducted before the development of DataMed, consisting of interviews with researchers. Phase 2 involved iterative usability evaluations of DataMed prototypes. We analyzed data qualitatively to document researchers' information and user interface needs., Results: Biomedical researchers' information needs in data discovery are complex, multidimensional, and shaped by their context, domain knowledge, and technical experience. User needs analyses validate the need for a DDI, while usability evaluations of DataMed show that even though aggregating metadata into a common search engine and applying traditional information retrieval tools are promising first steps, there remain challenges for DataMed due to incomplete metadata and the complexity of data discovery., Discussion: Biomedical data poses distinct problems for search when compared to websites or publications. Making data available is not enough to facilitate biomedical data discovery: new retrieval techniques and user interfaces are necessary for dataset exploration. Consistent, complete, and high-quality metadata are vital to enable this process., Conclusion: While available data and researchers' information needs are complex and heterogeneous, a successful DDI must meet those needs and fit into the processes of biomedical researchers. Research directions include formalizing researchers' information needs, standardizing overviews of data to facilitate relevance judgments, implementing user interfaces for concept-based searching, and developing evaluation methods for open-ended discovery systems such as DDIs., (© The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Objective: Finding relevant datasets is important for promoting data reuse in the biomedical domain, but it is challenging given the volume and complexity of biomedical data. Here we describe the development of an open source biomedical data discovery system called DataMed, with the goal of promoting the building of additional data indexes in the biomedical domain., Materials and Methods: DataMed, which can efficiently index and search diverse types of biomedical datasets across repositories, is developed through the National Institutes of Health-funded biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium. It consists of 2 main components: (1) a data ingestion pipeline that collects and transforms original metadata information to a unified metadata model, called DatA Tag Suite (DATS), and (2) a search engine that finds relevant datasets based on user-entered queries. In addition to describing its architecture and techniques, we evaluated individual components within DataMed, including the accuracy of the ingestion pipeline, the prevalence of the DATS model across repositories, and the overall performance of the dataset retrieval engine., Results and Conclusion: Our manual review shows that the ingestion pipeline could achieve an accuracy of 90% and core elements of DATS had varied frequency across repositories. On a manually curated benchmark dataset, the DataMed search engine achieved an inferred average precision of 0.2033 and a precision at 10 (P@10, the number of relevant results in the top 10 search results) of 0.6022, by implementing advanced natural language processing and terminology services. Currently, we have made the DataMed system publically available as an open source package for the biomedical community., (© The Author 2018. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Background: Atopic dermatitis (AD) is a common inflammatory skin disorder, characterized by skin barrier defects and enhanced allergen priming. Null mutations in the filaggrin gene (FLG) are strongly associated with moderate to severe AD, but the pathways linking barrier dysfunction and cutaneous inflammation are still largely unknown., Aim: To assess alteration of endogenous cysteine protease activity in FLG-deficient keratinocytes, and to determine whether the alteration in cysteine protease activity affects epidermal barrier function and associated gene and protein expression., Methods: We established a stable FLG knockdown cell line, and reconstructed epidermal equivalents in vitro. Barrier function of the reconstructed epidermis, the barrier-associated genes and proteins, and the activity of endogenous cysteine proteases were tested. Inhibitors of cysteine proteases were used to further evaluate the role of endogenous cysteine proteases in epidermal barrier function., Results: FLG knockdown induced impaired epidermal barrier function. Microarray, western blotting and fluorescence staining showed reduced expression of K10, ZO-1, E-cadherin, claudin-1 and occludin in FLG knockdown keratinocytes. Compared with cysteine protease activity in control cells, protease activity was dramatically enhanced in FLG knockdown keratinocytes. Furthermore, administration of cysteine protease inhibitors significantly recovered expression of K10 and tight junction proteins, and the barrier defect induced by FLG deficiency., Conclusions: This is the first observation of elevated endogenous cysteine protease activity in FLG-deficient keratinocytes, which may play an important role in impaired barrier function in AD skin. Modulation of cysteine protease activity might be a novel therapeutic approach for AD treatment., (© 2017 British Association of Dermatologists.)

The increasing incidence of type 2 diabetes mellitus globally has increased the incidence of diabetes-associated complications such as nephropathy. DNA damage induced by oxidative stress might be one of the important mechanisms in the pathogenesis of diabetic complications. Two hundred Iranian individuals with the conditions of type 2 diabetes, diabetic nephropathy and nephropathy patients with no sign of diabetes and normal unaffected sex- and age-matched controls (50 in each group) were enrolled in the study. The background and the net levels of micronucleus (MN) formation as well as other cellular damages induced after in vitro treatment with 25 µg/ml of bleomycin (BLM) were evaluated using cytokinesis block MNs cytome assay (CBMN cyt) in peripheral blood lymphocytes. The background and net BLM-induced levels of MNs were significantly higher in all patient groups compared with the control (P < 0.01, P < 0.001, respectively). The frequency of MNs was significantly higher in those patients with prior incidence of nephropathy than those without. A positive association was observed between basal and net MN frequency among study groups and also between net genetic damages and serum creatinine value and duration of diabetes. The rate of basal and net apoptosis was significantly higher in patients with hyperglycemia. Our results indicate that increased genomic instability expressed as MNs is associated with nephropathy in all pathological stages. Therefore, implementation of MN assay in clinical level may potentially enhance the quality of management of patients with diabetes and its complications such as nephropathy., (© The Author 2016. Published by Oxford University Press on behalf of the UK Environmental Mutagen Society. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Studying skin immune cells under various pathophysiological conditions is vital for understanding the nature of cutaneous inflammatory responses. Available methods of isolating cells from the skin have relatively low yield or require in vitro culture. To increase the effective isolation of skin immune cells, we used collagenase P treatment. The number of T cells obtained ex vivo using this technique was dramatically greater than that obtained with conventional methods, without the need for long-term culture. The phenotype and function of isolated cells were comparable with those of cells isolated by EDTA treatment. Collagenase P-based methods will enhance the ability to investigate lymphoid cell function in both healthy and diseased skin., (© 2016 The Authors Clinical and Experimental Dermatology published by John Wiley & Sons Ltd on behalf of British Association of Dermatologists, North American Clinical Dermatologic Society and St Johns Dermatological Society.)

Both dengue NS1 antigen and serum interleukin (IL)-10 levels have been shown to associate with severe clinical disease in acute dengue infection, and IL-10 has also been shown to suppress dengue-specific T cell responses. Therefore, we proceeded to investigate the mechanisms by which dengue NS1 contributes to disease pathogenesis and if it is associated with altered IL-10 production. Serum IL-10 and dengue NS1 antigen levels were assessed serially in 36 adult Sri Lankan individuals with acute dengue infection. We found that the serum IL-10 levels correlated positively with dengue NS1 antigen levels (Spearman's r = 0·47, P < 0·0001), and NS1 also correlated with annexin V expression by T cells in acute dengue (Spearman's r = 0·63, P = 0·001). However, NS1 levels did not associate with the functionality of T cell responses or with expression of co-stimulatory molecules. Therefore, we further assessed the effect of dengue NS1 on monocytes and T cells by co-culturing primary monocytes and peripheral blood mononuclear cells (PBMC), with varying concentrations of NS1 for up to 96 h. Monocytes co-cultured with NS1 produced high levels of IL-10, with the highest levels seen at 24 h, and then declined gradually. Therefore, our data show that dengue NS1 appears to contribute to pathogenesis of dengue infection by inducing IL-10 production by monocytes., (© 2016 British Society for Immunology.)

Background: The role of the epidermis in the immune response is well known. While multiple cytokines are implicated in keratinocyte-mediated infection clearance and wound healing, little is known about the involvement of keratinocytes in promoting resolution of inflammation., Aim: To assess effects of histamine stimulation on keratinocyte function., Methods: We performed a combined microarray/Gene Ontology analysis of histamine-stimulated keratinocytes. Functional changes were tested by apoptosis assessment and scratch assays. Histamine receptor involvement was also assessed by blocking wound closure with specific antagonists., Results: Histamine treatment had extensive effects on keratinocytes, including effects on proinflammatory responses and cellular functions promoting wound healing. At the functional level, there was reduced apoptosis and enhancement of wound healing in vitro. At the receptor level, we identified involvement of all keratinocyte-expressed histamine receptors (HRHs), with HRH1 blockage resulting in the most prominent effect., Conclusions: Histamine activates wound healing and infection clearance-related functions of keratinocytes. While enhancement of histamine-mediated wound healing is mediated predominantly via the HRH1 receptor, other keratinocyte-expressed receptors are also involved. These effects could promote resolution of skin inflammation caused by infection or superficial injury., (© 2014 British Association of Dermatologists.)

Determining previous infecting dengue virus (DENV) serotypes has been difficult due to highly cross-reactive immune responses from previous DENV infections. Determining the correlates of serotype-specific immune responses would be crucial in understanding dengue transmission in the community and would also help to determine the correlates of protective immune responses. Therefore, we set out to define highly conserved, serotype-specific regions of the DENVs. Serotype-specific and highly conserved regions of the four DENV serotypes were identified using Basic Local Alignment Search Tool (BLAST) searches and custom perl scripts. Using ex-vivo and cultured enzyme-linked immunospot (ELISPOT) assays, we identified serotype-specific T cell epitopes within the four DENV serotypes in healthy adult donors from Sri Lanka. We identified T cell responses to 19 regions of the four DENV serotypes. Six peptides were from the NS2A region and four peptides were from the NS4A region. All immune donors responded to peptides of at least two DENV serotypes, suggesting that heterologous infection is common in Sri Lanka. Eight of 20 individuals responded to at least two peptides of DENV-4, despite this serotype not being implicated previously in any of the epidemics in Sri Lanka. The use of these regions to determine past and current infecting DENV serotypes will be of value to characterize further the dynamics of silent dengue transmission in the community. In addition, these T cell responses to these regions could be used to characterize DENV serotype-specific immune responses and thus possibly help us to understand the immune correlates of a protective immune response., (© 2012 The Authors;Clinical and Experimental Immunology © 2012 British Society for Immunology.)

Background: The identification of filaggrin mutations has contributed towards our understanding of hereditary factors associated with epidermal dysfunction observed in individuals with atopic eczema (AE). However, factors that predispose to acquired filaggrin modulation are not well understood. Interleukin (IL)-22 is upregulated in lesional AE tissue, but its effects on filaggrin expression and genes associated with epidermal function have not yet been comprehensively addressed., Objectives: To investigate the effects of IL-22 on expression of filaggrin and genes encoding proteins relevant to epidermal function., Methods: Microarray analysis was performed on IL-22-stimulated HaCaT keratinocytes. Filaggrin protein level was assessed by an intracellular enzyme-linked immunosorbent assay (ELISA) and Western blot in HaCaT cells and the findings were validated in primary keratinocytes., Results: Exposure to IL-22 cytokine resulted in a downregulation of profilaggrin mRNA expression in HaCaT keratinocytes. The expression of genes involved in enzymatic processing of profilaggrin as well as the generation of natural moisturizing factor was also altered. Furthermore, there was an upregulation of many transcripts encoding proteins of the S100 family. Profilaggrin/filaggrin downregulation was detected by intracellular ELISA and Western blot in HaCaT cells. The relevance to the primary setting was confirmed in primary keratinocytes by Western blot., Conclusions: IL-22 downregulates profilaggrin/filaggrin expression in keratinocytes at both mRNA and protein levels and affects genes relevant to epidermal function. This novel pathway may have relevance to the pathogenesis and treatment of atopic and other skin disease., (© 2011 The Authors. BJD © 2011 British Association of Dermatologists.)