Transcriptomic profiles and diagnostic biomarkers in the Mediterranean seagrasses Posidonia oceanica and Cymodocea nodosa reveal mechanistic insights of adaptative strategies upon desalination brine stress

Seawater desalination by reverse osmosis is growing exponentially due to water scarcity. Byproducts of this process (e.g. brines), are generally discharged directly into the coastal ecosystem, causing detrimental effects, on benthic organisms. Understanding the cellular stress response of these organisms (biomarkers), could be crucial for establishing appropriate salinity thresholds for discharged brines. Early stress biomarkers can serve as valuable tools for monitoring the health status of brine-impacted organisms, enabling the prediction of long-term irreversible damage caused by the desalination industry. In this study, we conducted laboratory-controlled experiments to assess cellular and molecular biomarkers against brine exposure in two salinity-sensitive Mediterranean seagrasses: Posidonia oceanica and Cymodocea nodosa. Treatments involved exposure to 39, 41, and 43 psu, for 6 h and 7 days. Results indicated that photosynthetic performance remained unaffected across all treatments. However, under 43 psu, P. oceanica and C. nodosa exhibited lipid oxidative damage, which occurred earlier in P. oceanica. Additionally, P. oceanica displayed an antioxidant response at higher salinities by accumulating phenolic compounds within 6 h and ascorbate within 7 d; whereas for C. nodosa the predominant antioxidant mechanisms were phenolic compounds accumulation and total radical scavenging activity, which was evident after 7 d of brines exposure. Finally, transcriptomic analyses in P. oceanica exposed to 43 psu for 7 days revealed a poor up-regulation of genes associated with brassinosteroid response and abiotic stress response, while a high down-regulation of genes related to primary metabolism was detected. In C. nodosa, up-regulated genes were involved in DNA repair, cell cycle regulation, and reproduction, while down-regulated genes were mainly associated with photosynthesis and ribosome assembly. Overall, these findings suggest that 43 psu is a critical salinity-damage threshold for both seagrasses; and despite the moderate overexpression of several transcripts that could confer salt tolerance, genes involved in essential biological processes were severely downregulated.

Neurogenic appendicopathy: A rare differential diagnosis of acute appendicitis

AIM OF THE STUDY

In histologically non-inflamed but clinically suspect appendices, changes described as neurogenic appendicopathy with fibrous or fibrolipomatous obliterations can be observed. The purpose of this study was to analyse the incidence of these entities of the appendix in a longitudinal patient cohort.

PATIENTS AND METHODS

This is a retrospective single-centre study of 457 patients undergoing laparoscopic appendectomy from 2017 to 2020 due to suspected acute appendicitis.

RESULTS

In 72 patients (15.8%) with clinically suspected acute appendicitis, the appendix showed no distinct signs of acute inflammation during the procedure. In 43 patients, histological analysis revealed neurogenic appendicopathy or fibrous and fibrolipomatous obliteration. Female gender (P=0.088), younger age (P<0.0001), longer pain duration (P<0.0001) and repetitive pain episodes were more frequent in these patients than in those with acute appendicitis. Inflammation markers were also decreased in the group of patients with neurogenic appendicopathy (leukocytes 9.8±3.5 vs. 13.0±4.5 G/L and C-reactive protein 38.7±60.7 vs. 59.4±70.5mg/L).

CONCLUSION

Neurogenic appendicopathy with fibrous/fibrolipomatous obliteration is a differential diagnosis of acute appendicitis that can only be confirmed by pathology. Female gender, young age, prolonged duration with repetitive episodes of pain, and relatively low inflammatory markers are evocative of this diagnosis.

Informal sale of antibiotics in Guatemalan convenience stores before and after implementation of federal antibiotic dispensing legislation

BACKGROUND

Convenience stores in Guatemala provide essential consumer goods in communities, but many dispense antibiotics illegally. Federal legislation, passed in August of 2019, requires prescriptions for antibiotic purchase at pharmacies but it is unclear if this legislation is enforced or if it has any impact on unlawful sales of antibiotics.

METHODS

To determine if antibiotic availability changed in convenience stores, we carried out a repeated measures study collecting antibiotic availability data before and after implementation of the dispensing regulation.

RESULTS

There was no statistical difference in the proportion of convenience stores that sold antibiotics before and after antibiotic regulations [66.6% (295/443) and 66.7% (323/484), respectively, P>0.96], nor in the number of stores selling amoxicillin [55.5% (246/443) and 52.3% (253/484), respectively, P>0.96], but fewer stores (20%) sold tetracycline capsules after regulation was passed (P<0.05). For stores visited both before and after passage of legislation (n=157), 15% stopped selling antibiotics while 25% started selling antibiotics. Antibiotics from convenience stores were reportedly sold for use in people and animals.

CONCLUSIONS

Antibiotics remain widely available in convenience stores consistent with no significant change in the informal sector after implementation of prescription requirements for pharmacies. Importantly, effects from regulatory change could have been masked by potential changes in antibiotic use during the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic.

[Microbiota in food allergy: prebiotics, probiotics and synbiotics]

The close relationship between the microbiota and allergic diseases has been known for several years, particularly food allergy. Although the best studied microbiota is that related to bacteria, viruses, parasites and fungi are also constituents of this, although their role is not definitively clarified. The microbial world interacts with the human body constantly, we are in daily contact with an infinite and innumerable number of varieties of microbes in our environment, some of them can pass through the body without causing any harm, while others generate undesirable risk for the body. health. Alteration of the original composition of the microbiota (dysbiosis) is associated with food allergy. This dysbiosis is related to changes in habits, method of termination of pregnancy (birth or cesarean section), replacement of breastfeeding or interruption at an early age; decrease in family size; loss of contact with farm animals or pets; inappropriate prescription or abuse of antibiotics. The transition from a diet based exclusively on milk to one with solid foods is associated with a drastic increase in microbial diversity. Immunomodulatory components of the microbiota (cell surface polysaccharides), dietary factors (vitamin A), and production of secondary metabolites (short-chain fatty acids and secondary bile acid metabolites) promote differentiation of the RORγt+ cell population Treg. ILC3 produces IL-2, which plays a decisive role in maintaining intestinal homeostasis.

Is unicentric familial papillary thyroid microcarcinoma different from multicentric?

BACKGROUND

Familial papillary thyroid microcarcinoma (FPTMC) appears to be more aggressive than sporadic papillary thyroid microcarcinoma (SPTMC). However, there are authors who indicate that unicentric FPTMC has a similar prognosis to SPTMC. The objective is to analyze whether unicentric FPTMC has a better prognosis than multicentric FPTMC.

DESIGN AND METHODS

Type of study: National multicenter longitudinal analytical observational study.

STUDY POPULATION

Patients with FPTMC.

STUDY GROUPS

Two groups were compared: Group A (unicentric FPTMC) vs. Group B (multicentric FPTMC).

STUDY VARIABLES

It is analyzed whether between the groups there are: a) differentiating characteristics; and b) prognostic differences.

STATISTICAL ANALYSIS

Cox regression analysis and survival analysis.

RESULTS

Ninety-four patients were included, 44% (n = 41) with unicentric FPTMC and 56% (n = 53) with multicentric FPTMC. No differences were observed between the groups according to socio-familial, clinical or histological variables. In the group B a more aggressive treatment was performed, with higher frequency of total thyroidectomy (99 vs. 78%; p = 0.003), lymph node dissection (41 vs. 15%; p = 0.005) and therapy with radioactive iodine (96 vs. 73%; p = 0.002). Tumor stage was similar in both groups (p = 0.237), with a higher number of T3 cases in the group B (24 vs. 5%; p = 0.009). After a mean follow-up of 90 ± 68.95 months, the oncological results were similar, with a similar disease persistence rate (9 vs. 5%; p = 0.337), disease recurrence rate (21 vs. 8%; p = 0.159) and disease-free survival (p = 0.075).

CONCLUSIONS

Unicentric FPTMC should not be considered as a SPTMC due to its prognosis is similar to multicentric FPTMC.

Protocolization of multicenter clinical studies in the digital era. Is useful data centralization by a data-manager?

INTRODUCTION

In multicenter studies, the protocolization of data is a critical phase that can generate biases.The objective is to analyze the concordance and reliability of the data obtained in a clinical multicenter study between the protocolization in the center of origin and the centralized protocolization of the data by a data -manager.

METHODS

National multicenter clinical study about an infrequent carcinoma. A double protocolization of the data is carried out: (a) center of origin; and (b) centralized by a data manager: The concordance between the data is analyzed for the global data and for the two groups of the project: (a) study group (Familiar carcinoma, 30 researchers protocolize); (b) control group (Sporadic carcinoma, 4 people protocolize). Interobserver variability is evaluated using Cohen's kappa coefficient.

RESULTS

The study includes a total of 689 patients with carcinoma, 252 in the study group and 437 in the control group. Regarding the concordance analysis of the tumor stage, 2.5% of disagreements were observed and the concordance between people who protocolize was near perfect (Kappa = 0.931). Regarding the evaluation of the recurrence risk, disagreements occurred in 7% of the cases and the concordance was near perfect (Kappa = 0.819). Regarding the sonography evaluation (TIRADS), the disagreements were 6.9% and the concordance was near perfect (Kappa = 0.922). Also, 4.6% of transcription errors were detected.

CONCLUSIONS

In multicenter clinical studies, the centralized data protocolization o by a data-manager seems to present similar results to the direct protocolization in the database in the center of origin.

Single cell transcriptomic analysis of Graves' disease thyroid glands reveals the broad immunoregulatory potential of thyroid follicular and stromal cells and implies a major re-interpretation of the role of aberrant HLA class II expression in autoimmunity

The study of the immune response in thyroid autoimmunity has been mostly focused on the autoantibodies and lymphocytes, but there are indications that intrinsic features of thyroid tissue cells may play a role in disrupting tolerance that needs further investigation. The overexpression of HLA and adhesion molecules by thyroid follicular cells (TFC) and our recent demonstration that PD-L1 is also moderately expressed by TFCs in autoimmune thyroid indicates that TFCs they may activate but also inhibit the autoimmune response. Intriguingly, we have recently found that in vitro cultured TFCs are able to suppress the proliferation of autologous lymphocyte T in a contact-dependent manner which is independent of the PD-1/PD-L1 signaling pathway. To get a more comprehensive picture of TFC activating and inhibitory molecules/pathways driving the autoimmune response in the thyroid glands, preparations of TFCs and stromal cells from five Graves' disease (GD) and four control thyroid glands were compared by scRNA-seq. The results confirmed the previously described interferon type I and type II signatures in GD TFCs and showed unequivocally that they express the full array of genes that intervene in the processing and presentation of endogenous and exogeneous antigens. GD TFCs lack however expression of costimulatory molecules CD80 and CD86 required for priming T cells. A moderate overexpression of CD40 by TFCs was confirmed. GD Fibroblasts showed widespread upregulation of cytokine genes. The results from this first single transcriptomic profiling of TFC and thyroid stromal cells provides a more granular view of the events occurring in GD. The new data point at an important contribution of stromal cells and prompt a major re-interpretation of the role of MHC over-expression by TFC, from deleterious to protective. Most importantly this re-interpretation could also apply to other tissues, like pancreatic beta cells, where MHC over-expression has been detected in diabetic pancreas.

Update meta-analysis on the efficacy and safety issues of fexofenadine

Background

Fexofenadine emerged as one of the most representative second generation histamine H1 antagonist drugs since the 1990s, with an outstanding efficacy and appreciable safety for the treatment of allergic patients. While allergic rhino-conjunctivitis represents the most frequent atopic disease globally, an update of fexofenadine efficacy and safety on this entity was proposed as a surrogate of allergic condition.

Methods

Double blind, placebo controlled, randomized clinical trials investigating the efficacy and safety of fexofenadine for the treatment of Allergic Rhinitis were searched in 5 major global databases. Eligibility criteria and characteristics, risk of bias, and validity assessment, data extraction and heterogeneity evaluation are described. Primary outcome selected corresponded to 12-reflective and instantaneous total symptom scores (TSS), besides morning instantaneous TSS and the frequency of reported adverse events (AEs); analysis was planned on the intention-to-treat population.Standardized mean differences of scoring systems were analyzed, and Cochran's Q statistic test and the I2 test were assessed for heterogeneity.

Results

From the initial 83 identified records, 12 eligible studies were selected. In the evaluated patients, individuals receiving fexofenadine (1910) showed a significant reduction of TSS compared with those who received placebo (1777), change from baseline: standardized mean difference (SMD) -0.33; 95% CI-0.47 to -0.18, p < 0.0001. Morning instantaneous TSS also demonstrated lower symptoms (change from baseline: SMS -1.42; 95% CI -2.22 to -0.62, p = 0.0005). Heterogeneity was found across selected studies.Frequency of AEs was similar compared to placebo (OR = 1.04; 0.88-1.21), with no detection of heterogeneity across these 12 studies.

Conclusions

According to this new evidence, fexofenadine maintains its beneficial profile on signs and symptoms of patients with allergic conditions, as well as its attributes as one of the major candidates for an ideal antihistamine medication (including special conditions such as pregnancy and pre-school age), providing support to its over-the-counter condition in several countries.

Integrated View of Baseline Protein Expression in Human Tissues

The availability of proteomics datasets in the public domain, and in the PRIDE database, in particular, has increased dramatically in recent years. This unprecedented large-scale availability of data provides an opportunity for combined analyses of datasets to get organism-wide protein abundance data in a consistent manner. We have reanalyzed 24 public proteomics datasets from healthy human individuals to assess baseline protein abundance in 31 organs. We defined tissue as a distinct functional or structural region within an organ. Overall, the aggregated dataset contains 67 healthy tissues, corresponding to 3,119 mass spectrometry runs covering 498 samples from 489 individuals. We compared protein abundances between different organs and studied the distribution of proteins across these organs. We also compared the results with data generated in analogous studies. Additionally, we performed gene ontology and pathway-enrichment analyses to identify organ-specific enriched biological processes and pathways. As a key point, we have integrated the protein abundance results into the resource Expression Atlas, where they can be accessed and visualized either individually or together with gene expression data coming from transcriptomics datasets. We believe this is a good mechanism to make proteomics data more accessible for life scientists.

SelectBCM tool: a batch evaluation framework to select the most appropriate batch-correction methods for bulk transcriptome analysis

Bulk transcriptomes are an essential data resource for understanding basic and disease biology. However, integrating information from different experiments remains challenging because of the batch effect generated by various technological and biological variations in the transcriptome. Numerous batch-correction methods to deal with this batch effect have been developed in the past. However, a user-friendly workflow to select the most appropriate batch-correction method for the given set of experiments is still missing. We present the SelectBCM tool that prioritizes the most appropriate batch-correction method for a given set of bulk transcriptomic experiments, improving biological clustering and gene differential expression analysis. We demonstrate the applicability of the SelectBCM tool on analyses of real data for two common diseases, rheumatoid arthritis and osteoarthritis, and one example to characterize a biological state, where we performed a meta-analysis of the macrophage activation state. The R package is available at https://github.com/ebi-gene-expression-group/selectBCM.

Thyroid cells from normal and autoimmune thyroid glands suppress T lymphocytes proliferation upon contact revealing a new regulatory inhibitory type of interaction independent of PD1/PDL1

Immune Checkpoint Receptors include a number of inhibitory receptors that limit tissue damage during immune responses; blocking PD-1/PD-L1 checkpoint receptor axis led to a paradigm shift in cancer immunotherapy but also to autoimmune adverse effects, prominently thyroid autoimmunity. Although PD-L1 is known to be expressed on thyroid follicular cells (TFCs) of autoimmune glands the role on PD-1/PD-L1 in the interaction between T cells and thyroid cells in the tissue has not been investigated. Here we report that autologous primary TFCs, but not transformed TFCs, inhibit CD4 and CD8 T cell proliferation but no cytokine production. This effect is not, however, mediated by PD-1/PD-L1 nor locally produced cytokines. Beta galactosidase analysis excluded culture-induced senescence as an explanation. High resolution flow cytometry demonstrated that autologous TFC/T cells co-culture induced the expansion of several clusters of double negative (DN) T cells characterized by high expression of activation markers and negative immune checkpoints. Single cell transcriptomic profiling demonstrated that dissociated TFC express numerous candidate molecules for mediating this suppressive activity, including CD40, E-Cadherin and TIGIT ligands. These ligands directly or through the generation of a suppressor population of DN T cells, and not the PD-1/PD-L1 axis, are most likely the responsible of TFC immunosuppressive activity. These results contribute to reveal the complex network of inhibitory mechanism that operate at the tissue level to restrain autoimmunity but also point to pathways, other that PD-1/PD-L1, that can contribute to tumor evasion.

Biological behavior of familial papillary thyroid microcarcinoma: Spanish multicenter study

PURPOSE

Familial papillary thyroid microcarcinoma (FPTMC) can present a more aggressive behavior than the sporadic microcarcinoma. However, few studies have analyzed this situation. The objective is to analyze the recurrence rate of FPTMC and the prognostic factors which determine that recurrence in Spain.

METHODS

Spanish multicenter longitudinal analytical observational study was conducted. Patients with FPTMC received treatment with curative intent and presented cure criteria 6 months after treatment. Recurrence rate and disease-free survival (DFS) were analyzed. Two groups were analyzed: group A (no tumor recurrence) vs. group B (tumor recurrence).

RESULTS

Ninety-four patients were analyzed. During a mean follow-up of 73.3 ± 59.3 months, 13 recurrences of FPTMC (13.83%) were detected and mean DFS was 207.9 ± 11.5 months. There were multifocality in 56%, bilateral thyroid involvement in 30%, and vascular invasion in 7.5%; that is to say, they are tumors with histological factors of poor prognosis in a high percentage of cases. The main risk factors for recurrence obtained in the multivariate analysis were the tumor size (OR: 2.574, 95% CI 1.210-5.473; p = 0.014) and the assessment of the risk of recurrence of the American Thyroid Association (ATA), both intermediate risk versus low risk (OR: 125, 95% CI 10.638-1000; p < 0.001) and high risk versus low risk (OR: 45.454, 95% CI 5.405-333.333; p < 0.001).

CONCLUSION

FPTMC has a recurrence rate higher than sporadic cases. Poor prognosis is mainly associated with the tumor size and the risk of recurrence of the ATA.

Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas

The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets.

Expression Atlas update: gene and protein expression in multiple species

The EMBL-EBI Expression Atlas is an added value knowledge base that enables researchers to answer the question of where (tissue, organism part, developmental stage, cell type) and under which conditions (disease, treatment, gender, etc) a gene or protein of interest is expressed. Expression Atlas brings together data from >4500 expression studies from >65 different species, across different conditions and tissues. It makes these data freely available in an easy to visualise form, after expert curation to accurately represent the intended experimental design, re-analysed via standardised pipelines that rely on open-source community developed tools. Each study's metadata are annotated using ontologies. The data are re-analyzed with the aim of reproducing the original conclusions of the underlying experiments. Expression Atlas is currently divided into Bulk Expression Atlas and Single Cell Expression Atlas. Expression Atlas contains data from differential studies (microarray and bulk RNA-Seq) and baseline studies (bulk RNA-Seq and proteomics), whereas Single Cell Expression Atlas is currently dedicated to Single Cell RNA-Sequencing (scRNA-Seq) studies. The resource has been in continuous development since 2009 and it is available at https://www.ebi.ac.uk/gxa.

Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses

Several single-cell RNA sequencing (scRNA-seq) studies analyzing immune response to COVID-19 infection have been recently published. Most of these studies have small sample sizes, which limits the conclusions that can be made with high confidence. By re-analyzing these data in a standardized manner, we validated 8 of the 20 published results across multiple datasets. In particular, we found a consistent decrease in T-cells with increasing COVID-19 infection severity, upregulation of type I Interferon signal pathways, presence of expanded B-cell clones in COVID-19 patients but no consistent trend in T-cell clonal expansion. Overall, our results show that the conclusions drawn from scRNA-seq data analysis of small cohorts of COVID-19 patients need to be treated with some caution.

Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19

The coronavirus disease 2019 (COVID-19) pandemic caused by the new coronavirus (SARS-CoV-2) is currently responsible for more than 3 million deaths in 219 countries across the world and with more than 140 million cases. The absence of FDA-approved drugs against SARS-CoV-2 has highlighted an urgent need to design new drugs. We developed an integrated model of the human cell and SARS-CoV-2 to provide insight into the virus' pathogenic mechanism and support current therapeutic strategies. We show the biochemical reactions required for the growth and general maintenance of the human cell, first, in its healthy state. We then demonstrate how the entry of SARS-CoV-2 into the human cell causes biochemical and structural changes, leading to a change of cell functions or cell death. A new computational method that predicts 20 unique reactions as drug targets from our models and provides a platform for future studies on viral entry inhibition, immune regulation, and drug optimisation strategies. The model is available in BioModels (https://www.ebi.ac.uk/biomodels/MODEL2007210001) and the software tool, findCPcli, that implements the computational method is available at https://github.com/findCP/findCPcli.

ISA API: An open platform for interoperable life science experimental metadata

BACKGROUND

The Investigation/Study/Assay (ISA) Metadata Framework is an established and widely used set of open source community specifications and software tools for enabling discovery, exchange, and publication of metadata from experiments in the life sciences. The original ISA software suite provided a set of user-facing Java tools for creating and manipulating the information structured in ISA-Tab-a now widely used tabular format. To make the ISA framework more accessible to machines and enable programmatic manipulation of experiment metadata, the JSON serialization ISA-JSON was developed.

RESULTS

In this work, we present the ISA API, a Python library for the creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats by using a common data model engineered as Python object classes. We describe the ISA API feature set, early adopters, and its growing user community.

CONCLUSIONS

The ISA API provides users with rich programmatic metadata-handling functionality to support automation, a common interface, and an interoperable medium between the 2 ISA formats, as well as with other life science data formats required for depositing data in public databases.

UCSC Cell Browser: Visualize Your Single-Cell Data

Summary

As the use of single-cell technologies has grown, so has the need for tools to explore these large, complicated datasets. The UCSC Cell Browser is a tool that allows scientists to visualize gene expression and metadata annotation distribution throughout a single-cell dataset or multiple datasets.

Availability and implementation

We provide the UCSC Cell Browser as a free website where scientists can explore a growing collection of single-cell datasets and a freely available python package for scientists to create stable, self-contained visualizations for their own single-cell datasets. Learn more at https://cells.ucsc.edu.

Supplementary information

Supplementary data are available at Bioinformatics online.

Differential Behavior of 25(OH)D and f25(OH)D3 in Patients with Morbid Obesity After Bariatric Surgery

BACKGROUND

Total 25-OH-vitamin D (25(OH)D) levels are decreased in patients with obesity, but few data exist regarding free-vitamin D3 (f25(OH)D3) concentrations. We aimed to evaluate the effect of bariatric surgery on 25(OH)D and f25(OH)D3 in a cohort of patients with morbid obesity.

METHODS

Twenty-four patients submitted to sleeve gastrectomy (SG) (mean age 48 years, body mass index (BMI) 48.16±10.73k/m²) were evaluated before and 1 year after surgery. Anthropometric data, parathormone (PTH), calcium, alkaline phosphatase, 25(OH)D, and f25(OH)D3 were recorded.

RESULTS

25(OH)D and f25(OH)D3 correlated well before and after SG. Baseline determinations did not correlate with BMI, but they inversely correlated with BMI 1 year after surgery (r_s=-0.46, p=0.02 and r_s=-0.60, p=0.002, respectively). Post-surgery % total body weight loss (%TBWL) was 27.4±13.8 %; f25(OH)D3 concentrations increased significantly (5.28±2.29 pg/mL vs 6.64±2.25 pg/mL; p=0.03), whereas 25(OH)D did not change. Patients who achieved a BMI <35 kg/m² 1 year after surgery had significantly higher concentrations of f25(OH)D3 (7.9±1 pg/mL vs 4.8±1.1, p<0.001) and 25(OH)D (30.9±9.4 ng/mL vs 22.3±13.4; p=0.03) compared to those who remained with BMI >35 kg/m².

CONCLUSION

There is a significant inverse relationship between BMI and both f25(OH)D3 and 25(OH)D 1 year after surgery. Only f25(OH)D3 concentrations increased 1 year after surgery, which could be explained by a greater f25(OH)D3 sequestration before SG in the adipose tissue, potentially due to the more liposoluble nature of f25(OH)D3 than the protein-bound form 25(OH)D.

BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

BioContainers is an open-source project that aims to create, store, and distribute bioinformatics software containers and packages. The BioContainers community has developed a set of guidelines to standardize software containers including the metadata, versions, licenses, and software dependencies. BioContainers supports multiple packaging and container technologies such as Conda, Docker, and Singularity. The BioContainers provide over 9000 bioinformatics tools, including more than 200 proteomics and mass spectrometry tools. Here we introduce the BioContainers Registry and Restful API to make containerized bioinformatics tools more findable, accessible, interoperable, and reusable (FAIR). The BioContainers Registry provides a fast and convenient way to find and retrieve bioinformatics tool packages and containers. By doing so, it will increase the use of bioinformatics packages and containers while promoting replicability and reproducibility in research.

Optimal treatment sequencing of abiraterone acetate plus prednisone and enzalutamide in patients with castration-resistant metastatic prostate cancer: A systematic review and meta-analysis

PURPOSE

To evaluate the impact of the hormonal treatment sequencing including abiraterone acetate plus prednisone (AAP) and enzalutamide (ENZ) in mCRPC, and determine which sequence provides more benefits for patients.

METHODS

Studies published in English between 1 January 2013 and 30 September 2017 were identified in PubMed and EMBASE electronic databases. Studies assessing the efficacy of treatment sequences, based on AAP and ENZ, in mCRPC patients, were eligible for analysis.

RESULTS

Seventeen studies met the inclusion criteria. Two assessed both treatment sequences AAP → ENZ and ENZ → AAP; it was found that sequence of AAP → ENZ showed a statistically significantly longer PSA-PFS than the observed in ENZ → AAP (pooled HR: 0,54; 95% CI; 0,36-0,82; p < 0,05). The nine studies analysing Doc → AAP → ENZ sequence, revealed favourable results in terms of PFS. The 5 studies which analysed AAP → ENZ sequence, show a decrease in PSA levels ≥ 50% in 11-41% of patients treated with enzalutamide after previous treatment with AAP. In the two studies that analysed the Doc → ENZ → AAP sequence, PSA response rates were much lower than those reported with Doc → AAP → ENZ, with decreases in PSA ≥ 30 of 3-18% and PSA ≥ 50 of 8-11%.

CONCLUSION

Significant clinical efficacy of AAP administered as the first-line treatment in mCRPC patients followed by enzalutamide, delaying disease progression, compared with the ENZ → AAP sequence. However, more studies and randomized trials are needed, to validate the best treatment sequencing.

[Allergic rhinitis' treatment in children in Argentina. Update]

Allergic rhinitis (AR) is the most frequent allergic disease. Prevalence in children and teenagers in Argentina ranges between 22.3% and 34.9%. Given this situation, members of the scientific committees of Pediatrics and Rhinitis of the Argentinian Association of Allergy and Clinical Immunology (AAAeIC) have reviewed scientific evidence in order to update the therapeutic regulations of this pathology in the pediatric population. The classification and categorization of AR are currently in full review all around the world. It is necessary to make a differential diagnosis with other non-allergic types of rhinitis in children, and to confirm AR based on the clinical history, physical examination, determination of bio-markers, and/or skin tests. Non-pharmacological treatment includes education and guidelines of environmental control for allergens such as dust mites, anemophilous fungi, animal epithelium, and pollens. Step pharmacological therapy is proposed according to the control of the disease. Second-generation, non-sedating anti-histamines are the first line of therapy. The association with oral decongestants is not recommended in children under 4 years of age. Inhaled corticosteroids are the first choice for both moderate and severe forms. This document warns pediatricians about the importance of an early diagnosis, the rational use of step pharmacological therapy, and specific immunotherapy in children.

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

Background

The vast ecosystem of single-cell RNA-sequencing tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatics community leans once more towards the large computing requirements and the statistically driven methods needed to process and understand these ever-growing datasets.

Results

Here we outline several Galaxy workflows and learning resources for single-cell RNA-sequencing, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The Galaxy reproducible bioinformatics framework provides tools, workflows, and trainings that not only enable users to perform 1-click 10x preprocessing but also empower them to demultiplex raw sequencing from custom tagged and full-length sequencing protocols. The downstream analysis supports a range of high-quality interoperable suites separated into common stages of analysis: inspection, filtering, normalization, confounder removal, and clustering. The teaching resources cover concepts from computer science to cell biology. Access to all resources is provided at the singlecell.usegalaxy.eu portal.

Conclusions

The reproducible and training-oriented Galaxy framework provides a sustainable high-performance computing environment for users to run flexible analyses on both 10x and alternative platforms. The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy community provide a means for users to learn, publish, and teach single-cell RNA-sequencing analysis.

Long-term results of a randomized study comparing parathyroidectomy with cinacalcet for treating tertiary hyperparathyroidism

Tertiary hyperparathyroidism is a common cause of hypercalcemia after kidney transplantation (KT) and has been associated with renal dysfunction, bone mineral density loss, and increased risk of fracture and cardiovascular events. In a previous 12-month clinical trial, we demonstrated that subtotal parathyroidectomy was more effective than cinacalcet for controlling hypercalcemia. In the current study, we retrospectively evaluate whether this effect is maintained after 5 years of follow-up. In total, 24 patients had data available at 5 years, 13 in the cinacalcet group and 11 in the parathyroidectomy group. At 5 years, 7 of 11 patients (64%) in the parathyroidectomy group and 6 of 13 patients (46%) in the cinacalcet group (P = .44) showed normocalcemia. However, recurrence of hypercalcemia was only observed in the cinacalcet group (P = .016). Subtotal parathyroidectomy retained a greater reduction in intact parathyroid hormone (iPTH) compared with cinacalcet group. No differences were observed in kidney function and incidence of fragility fractures between both groups. Cinacalcet was discontinued in 5 out of 13 patients. In conclusion, in kidney transplant patients with tertiary hyperparathyroidism recurrence of hypercalcemia after 5-year follow-up is more frequent in cinacalcet than after subtotal parathyroidectomy.

P1748PARATHYROIDECTOMY REMAINS EFFECTIVE FOR TREATING TERTIARY HYPERPARATHYROIDISM: LONG-TERM RESULTS OF A RANDOMIZED STUDY

Background and Aims

Tertiary hyperparathyroidism is a common cause of hypercalcemia after kidney transplant (KT) and has been associated with renal dysfunction, loss bone mineral density and increased risk of fracture, vascular calcification, and increased risk of cardiovascular events. Long clinical management remains controversial. The aim of this study is to evaluate the long-term effectiveness and safety of parathyroidectomy versus cinacalcet in patients with persistent hyperparathyroidism.

Method

A 12-month prospective, multicenter, randomized study demonstrated than subtotal parathyroidectomy is more effective than cinacalcet for controlling hypercalcemia. Now, we evaluate in the same cohort of patients if this effect is maintained after 5 years of follow-up. Laboratory assessment included serum calcium, serum phosphate, intact parathyroid hormone (iPTH), calcidiol levels, estimated glomerular filtration rate and proteinuria at 2, 3, 4 and 5 year follow-up. Therapeutic details about the use of vitamin D, calcium supplementation and phosphate binders were compiled. Fragility fractures were also collected.

Results

In total, 24 patients had data available at 5 years, 13 in the cinacalcet group and 11 in the parathyroidectomy group. At 5 years, six of 13 patients in the cinacalcet group and ten of 11 patients in the parathyroidectomy group (p=0.015) showed normocalcemia (Figure 1). Subtotal parathyroidectomy retained a greater reduction of iPTH compared with cinacalcet group (Figure 2). No differences were observed in kidney function and incidence of fragility fractures between both groups. In relation of treatment, 8 of 13 patients in cinacalcet group maintained treatment with cinacalcet after 5 years follow-up.

Conclusion

Subtotal parathyroidectomy is more effective in long term to maintain normal serum calcium and iPTH compared with cinacalcet in kidney transplant patients with tertiary hyperparathyroidism.

Expression Atlas update: from tissues to single cells

Expression Atlas is EMBL-EBI's resource for gene and protein expression. It sources and compiles data on the abundance and localisation of RNA and proteins in various biological systems and contexts and provides open access to this data for the research community. With the increased availability of single cell RNA-Seq datasets in the public archives, we have now extended Expression Atlas with a new added-value service to display gene expression in single cells. Single Cell Expression Atlas was launched in 2018 and currently includes 123 single cell RNA-Seq studies from 12 species. The website can be searched by genes within or across species to reveal experiments, tissues and cell types where this gene is expressed or under which conditions it is a marker gene. Within each study, cells can be visualized using a pre-calculated t-SNE plot and can be coloured by different features or by cell clusters based on gene expression. Within each experiment, there are links to downloadable files, such as RNA quantification matrices, clustering results, reports on protocols and associated metadata, such as assigned cell types.

Laser-Induced Periodic Surface Structuring of Poly(trimethylene terephthalate) Films Containing Tungsten Disulfide Nanotubes

We report the study of the formation of Laser Induced Periodic Surface Structures (LIPSS), with UV femtosecond laser pulses (λ = 265 nm), in free-standing films of both Poly(trimethylene terephthalate) (PTT) and the composite PTT/tungsten disulfide inorganic nanotubes (PTT-WS2). We characterized the range of fluences and number of pulses necessary to induce LIPSS formation and measured the topography of the samples by Atomic Force Microscopy, the change in surface energy and contact angle using the sessile drop technique, and the modification in both Young's modulus and adhesion force values with Peak Force-Quantitative Nanomechanical Mapping. LIPSS appeared parallel to the laser polarization with a period close to its wavelength in a narrow fluence and number of pulses regime, with PTT-WS2 needing slightly larger fluence than raw PTT due to its higher crystallinity and heat diffusion. Little change was found in the total surface energy of the samples, but there was a radical increase in the negative polar component (γ-). Besides, we measured small variations in the samples Young's modulus after LIPSS formation whereas adhesion is reduced by a factor of four. This reduction, as well as the increase in γ-, is a result of the modification of the surface chemistry, in particular a slight oxidation, during irradiation.

Laparoscopy versus open adrenalectomy in patients with solid tumor metastases: results of a multicenter European study

Background

The outcome of adrenalectomy carried out by laparoscopy or open surgery for solid tumor metastases was assessed.

Methods

A total of 317 patients with histologically confirmed adrenal metastatic disease collected from 30 centres in Europe underwent adrenalectomy by laparoscopy (n=146) or open laparotomy (n=171). Differences between laparoscopic and open adrenalectomy were assessed by a single Cox analysis for both procedures.

Results

The median overall survival was 24.0 [95% confidence interval (CI): 21.4-26.6] months for open adrenalectomy and 45.0 (95% CI: 22.6-67.4) for laparoscopic adrenalectomy (P=0.008). Survival rates were 68%, 49%, 35% and 29% at 1, 2, 3 and 5 years for open surgery vs. 88%, 62%, 52% and 46% for laparoscopy, respectively. In the subgroup of R0 resections, the difference in survival in favor of laparoscopy (median 46 vs. 27 months) was marginally significant (P=0.073). Renal cancer [hazard ratio (HR) 0.42; 95% CI: 0.23-0.76, P=0.005], surgery of the primary tumor (HR 0.33; 95% CI: 0.19-0.54), and use of chemotherapy (HR 0.62; 95% CI: 0.43-0.88) were associated with a better survival, whereas type of resection (R1/R2 vs. R0) was associated with a worse prognosis (HR 2.29; 95% CI: 1.52-3.44, P<0.001).

Conclusions

Laparoscopic adrenalectomy patients showed a longer survival than open adrenalectomy individuals, as minimally invasive approach was attempted more common in less advanced disease which led to higher number of R0 resections.

Laparoscopy versus open adrenalectomy in patients with solid tumor metastases: results of a multicenter European study

BACKGROUND

The outcome of adrenalectomy carried out by laparoscopy or open surgery for solid tumor metastases was assessed.

METHODS

A total of 317 patients with histologically confirmed adrenal metastatic disease collected from 30 centres in Europe underwent adrenalectomy by laparoscopy (n=146) or open laparotomy (n=171). Differences between laparoscopic and open adrenalectomy were assessed by a single Cox analysis for both procedures.

RESULTS

The median overall survival was 24.0 [95% confidence interval (CI): 21.4-26.6] months for open adrenalectomy and 45.0 (95% CI: 22.6-67.4) for laparoscopic adrenalectomy (P=0.008). Survival rates were 68%, 49%, 35% and 29% at 1, 2, 3 and 5 years for open surgery vs. 88%, 62%, 52% and 46% for laparoscopy, respectively. In the subgroup of R0 resections, the difference in survival in favor of laparoscopy (median 46 vs. 27 months) was marginally significant (P=0.073). Renal cancer [hazard ratio (HR) 0.42; 95% CI: 0.23-0.76, P=0.005], surgery of the primary tumor (HR 0.33; 95% CI: 0.19-0.54), and use of chemotherapy (HR 0.62; 95% CI: 0.43-0.88) were associated with a better survival, whereas type of resection (R1/R2 vs. R0) was associated with a worse prognosis (HR 2.29; 95% CI: 1.52-3.44, P<0.001).

CONCLUSIONS

Laparoscopic adrenalectomy patients showed a longer survival than open adrenalectomy individuals, as minimally invasive approach was attempted more common in less advanced disease which led to higher number of R0 resections.

Using a Novel Diagnostic Nomogram to Differentiate Malignant from Benign Parathyroid Neoplasms

We sought to develop an immunohistochemical (IHC) tool to support the diagnosis of parathyroid carcinoma (PC) and help differentiate it from atypical parathyroid neoplasms (atypical) and benign adenomas. Distinguishing PC from benign parathyroid neoplasms can be challenging. Many cases of PC are histopathologically borderline for definitive malignancy. Recently, individual IHC biomarkers have been evaluated to aid in discrimination between parathyroid neoplasms. PC, atypical parathyroid neoplasms, and parathyroid adenomas treated at our institution from 1997 to 2014 were studied retrospectively. IHC analysis was performed to evaluate parafibromin, retinoblastoma (RB), protein gene product 9.5 (PGP9.5), Ki67, galectin-3, and E-cadherin expression. Receiver operating characteristic (ROC) analysis and multivariable logistic regression model for combinations of biomarkers were evaluated to classify patients as PC or atypical/adenoma. A diagnostic nomogram using 5 biomarkers was created for PC. Sixty-three patients were evaluated. The percent staining of parafibromin (p < 0.0001), RB (p = 0.04), Ki67 (p = 0.02), PGP9.5 (p = 0.04), and Galectin-3 (p = 0.01) differed significantly in the three diagnostic groups. ROC analysis demonstrated that parafibromin had the best performance in discriminating PC from atypical/adenoma; area under the curve (AUC) was 81% (cutoff, 92.5%; sensitivity rate, 64%; specificity rate, 87%). We created a diagnostic nomogram using a combination of biomarkers; AUC was 84.9% (95% confidence interval, 73.4-96.4%). The optimism-adjusted AUC for this model was 80.5% (mean absolute error, 0.043). A diagnostic nomogram utilizing an immunoexpression, a combination of immunohistochemical biomarkers, can be used to help differentiate PC from other parathyroid neoplasms, thus potentially improving diagnostic classification.

Interoperable and scalable data analysis with microservices: applications in metabolomics

MOTIVATION

Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed using the Kubernetes container orchestrator.

RESULTS

We developed a Virtual Research Environment (VRE) which facilitates rapid integration of new tools and developing scalable and interoperable workflows for performing metabolomics data analysis. The environment can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry, one nuclear magnetic resonance spectroscopy and one fluxomics study. We showed that the method scales dynamically with increasing availability of computational resources. We demonstrated that the method facilitates interoperability using integration of the major software suites resulting in a turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, statistics and identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science.

AVAILABILITY AND IMPLEMENTATION

The PhenoMeNal consortium maintains a web portal (https://portal.phenomenal-h2020.eu) providing a GUI for launching the Virtual Research Environment. The GitHub repository https://github.com/phnmnl/ hosts the source code of all projects.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

p13CMFA: Parsimonious 13C metabolic flux analysis

Deciphering the mechanisms of regulation of metabolic networks subjected to perturbations, including disease states and drug-induced stress, relies on tracing metabolic fluxes. One of the most informative data to predict metabolic fluxes are ¹³C based metabolomics, which provide information about how carbons are redistributed along central carbon metabolism. Such data can be integrated using ¹³C Metabolic Flux Analysis (¹³C MFA) to provide quantitative metabolic maps of flux distributions. However, ¹³C MFA might be unable to reduce the solution space towards a unique solution either in large metabolic networks or when small sets of measurements are integrated. Here we present parsimonious ¹³C MFA (p¹³CMFA), an approach that runs a secondary optimization in the ¹³C MFA solution space to identify the solution that minimizes the total reaction flux. Furthermore, flux minimization can be weighted by gene expression measurements allowing seamless integration of gene expression data with ¹³C data. As proof of concept, we demonstrate how p¹³CMFA can be used to estimate intracellular flux distributions from ¹³C measurements and transcriptomics data. We have implemented p¹³CMFA in Iso2Flux, our in-house developed isotopic steady-state ¹³C MFA software. The source code is freely available on GitHub (https://github.com/cfoguet/iso2flux/releases/tag/0.7.2).

¹³C Metabolic Flux Analysis (¹³C MFA) is a well-established technique that has proven to be a valuable tool in quantifying the metabolic flux profile of central carbon metabolism. When a biological system is incubated with a ¹³C-labeled substrate, ¹³C propagates to metabolites throughout the metabolic network in a flux and pathway-dependent manner. ¹³C MFA integrates measurements of ¹³C enrichment in metabolites to identify the flux distributions consistent with the measured ¹³C propagation. However, there is often a range of flux values that can lead to the observed ¹³C distribution. Indeed, either when the metabolic network is large or a small set of measurements are integrated, the range of valid solutions can be too wide to accurately estimate part of the underlying flux distribution. Here we propose to use flux minimization to select the best flux solution in the¹³C MFA solution space. Furthermore, this approach can integrate gene expression data to give greater weight to the minimization of fluxes through enzymes with low gene expression evidence in order to ensure that the selected solution is biologically relevant. The concept of using flux minimization to select the best solution is widely used in flux balance analysis, but it had never been applied in the framework of ¹³C MFA. We have termed this new approach parsimonious ¹³C MFA (p¹³CMFA).

Automated structure prediction of trans-acyltransferase polyketide synthase products

Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are among the most complex known enzymes from secondary metabolism and are responsible for the biosynthesis of highly diverse bioactive polyketides. However, most of these metabolites remain uncharacterized, since trans-AT PKSs frequently occur in poorly studied microbes and feature a remarkable array of non-canonical biosynthetic components with poorly understood functions. As a consequence, genome-guided natural product identification has been challenging. To enable de novo structural predictions for trans-AT PKS-derived polyketides, we developed the trans-AT PKS polyketide predictor (TransATor). TransATor is a versatile bio- and chemoinformatics web application that suggests informative chemical structures for even highly aberrant trans-AT PKS biosynthetic gene clusters, thus permitting hypothesis-based, targeted biotechnological discovery and biosynthetic studies. We demonstrate the applicative scope in several examples, including the characterization of new variants of bioactive natural products as well as structurally new polyketides from unusual bacterial sources.

Results of a nationwide survey on multidisciplinary teams on thyroid cancer in Spain

AIM

There is an important lack of knowledge as to the functioning of multidisciplinary teams on thyroid cancer in current clinical practice. We aimed to retrieve data on the composition, structure, and procedures developed by the multidisciplinary units of thyroid cancer in Spain.

METHODS

A nationwide survey consisting of questions about composition, structure, and functioning of multidisciplinary teams was designed. It was available online from November 15, 2017 to February 15, 2018.

RESULTS

Seventy-two multidisciplinary units responded to our survey. Of these, 15 (20.8%) focused only in thyroid cancer, while 57 (79.2%) included other endocrine disorders or non-endocrine tumors. The median (interquartile range) of members of the teams was 11 (9-14). The most frequent medical specialties in the units were endocrinology (100%), surgery (94.4%), pathology (80.6%), radiology (75.0%), nuclear medicine (73.6%), and medical oncology (55.6%). The annual number of patients reviewed by the teams was 40 (20-74). 56.9% of the multidisciplinary teams have elaborated clinical protocols for local use. Apart from clinical case discussions in the meetings, 45.8% of the units included educational activities and 36.1% research subjects. Quality indicators were developed by 22% of the teams.

CONCLUSIONS

These results suggest that there are some hopeful signs that international recommendations of having multidisciplinary approach to patients with thyroid cancer are being followed in Spain. This gives us the opportunity to proceed with further studies to analyze the real impact of this high standard of care on patient outcomes.

PhenoMeNal: processing and analysis of metabolomics data in the cloud

BACKGROUND

Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution.

FINDINGS

PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm.

CONCLUSIONS

PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and 'omics research domains.

Characteristics of professionalism of specialists and advantages of multidisciplinary teams in thyroid cancer: results of a national opinion survey

INTRODUCTION

The opinion of professionals about multidisciplinary teams (MDT) in thyroid cancer has not been studied in Spain. This study was intended to ascertain the opinion of specialists about the characteristics of the professionals and the advantages provided by these teams.

METHODS

A survey was designed to assess the opinion about the characteristics of professionalism and the advantages of MDT for patients, professionals, and the health care system. The survey was posted online from November 15, 2017 to February 15, 2018.

RESULTS

A total of 226 surveys were evaluated. The ability for teamwork was considered the most important characteristic to be met by professionals by 37.2% of respondents, while scientific competence was the most important indicator of professionalism for 37.6%. More than two thirds of specialists felt that MDTs improve the choice of treatments and diagnostic procedures, decrease clinical variability, facilitate implementation of clinical guidelines, improve ongoing training, and increase patient satisfaction and hospital prestige. The degree of agreement with the advantages of MDTs was significantly higher among specialists who had a MDT at their hospitals.

CONCLUSIONS

The overall opinion of professionals on the MDT model is highly favorable. Hospital managers and health care authorities should take these facts into account in order to encourage and support implementation of these teams.

High-Definition Analysis of Host Protein Stability during Human Cytomegalovirus Infection Reveals Antiviral Factors and Viral Evasion Mechanisms

Human cytomegalovirus (HCMV) is an important pathogen with multiple immune evasion strategies, including virally facilitated degradation of host antiviral restriction factors. Here, we describe a multiplexed approach to discover proteins with innate immune function on the basis of active degradation by the proteasome or lysosome during early-phase HCMV infection. Using three orthogonal proteomic/transcriptomic screens to quantify protein degradation, with high confidence we identified 35 proteins enriched in antiviral restriction factors. A final screen employed a comprehensive panel of viral mutants to predict viral genes that target >250 human proteins. This approach revealed that helicase-like transcription factor (HLTF), a DNA helicase important in DNA repair, potently inhibits early viral gene expression but is rapidly degraded during infection. The functionally unknown HCMV protein UL145 facilitates HLTF degradation by recruiting the Cullin4 E3 ligase complex. Our approach and data will enable further identifications of innate pathways targeted by HCMV and other viruses.

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Multiplexed viral screens uncover host proteins targeted by early HCMV infection

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Finding host proteins targeted for degradation by HCMV reveals immune evasion strategies

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A screen of HCMV deletion mutants discovers viral factors that target >250 host proteins

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HLTF is an antiviral restriction factor that is targeted for degradation by HCMV UL145

Validation of a Visual-Spatial Secondary Task to Assess Automaticity in Laparoscopic Skills

INTRODUCTION

Our objective was to assess reliability and validity of a visual-spatial secondary task (VSST) as a method to measure automaticity on a basic simulated laparoscopic skill model. In motor skill acquisition, expertise is defined by automaticity. The highest level of performance with less cognitive and attentional resources characterizes this stage, allowing experts to perform multiple tasks. Conventional validated parameters as operative time, objective assessment skills scales (OSATS), and movement economy, are insufficient to distinguish if an individual has reached the more advanced learning phases, such as automaticity. There is literature about using a VSST as an attention indicator that correlates with the automaticity level.

METHODS

Novices with completed and approved Fundamentals of Laparoscopic Surgery course, and laparoscopy experts were enrolled for an experimental study and measured under dual tasks conditions. Each participant performed the test giving priority to the primary task while at the same time they responded to a VSST. The primary task consisted of 4 interrupted laparoscopic stitches (ILS) on a bench-model. The VSST was a screen that showed different patterns that the surgeon had to recognize and press a pedal while doing the stitches (PsychoPsy software, Python, MacOS). Novices were overtrained on ILS until they reach at least 100 repetitions and then were retested. Participants were video recorded and then assessed by 2 blinded evaluators who measured operative time and OSATS. These scores were considered indicators of quality for the primary task. The VSST performance was measured by the detectability index (DI), which is a ratio between correct and wrong detections. A reliable evaluation was defined as two measures of DI with less than 10% of difference, maintaining the cutoff scores for performance on the primary task (operative time <110 seg and OSATS >17 points).

RESULTS

Novices (n = 11) achieved reliable measure of the test after 2 (2-5) repetitions on the preassessment and 3.75 (2-5) on the postassessment (p = 0.04); whereas laparoscopy experts (n = 4) did it after 3.5 (3-4) repetitions. Proficiency cutoff scores for the primary task were achieved on every measure for novices (prepost overtraining) and experts. Expert performance on VSST was DI 0.78 (0.69-0.87). Novice performance was significantly better on postassessment (DI-pre 0.48 [0.06-0.71] vs DI-post 0.78 [0.48-0.95], p = 0.003). Overtraining consisted in 140 (100-210) repetitions of ILS for all novices, made in 8 hours (3-15). By categorizing DI based on expert performance, novices with DI-post >0.65 achieved better OSATS score and less operative time than novices with DI-post<0.65 (p = 0.007 y, p = 0.089, respectively).

CONCLUSION

Measuring automaticity is feasible using a VSST. This instrument is reliable and has a face, content and construct validity. A DI over 0.65 may be a cutoff point correlated with high standard performance on the primary task. This instrument measures performance on laparoscopic skills, and along with conventional indicators, would better define advance levels of expertise. More studies are required applying this VSST to achieve external validity by reproducing our results.

Recommendations for the packaging and containerizing of bioinformatics software

Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. However, containers and software packages should be produced under certain rules and standards in order to be reusable, compatible and easy to integrate into pipelines and analysis workflows. Here, we presented a set of recommendations developed by the BioContainers Community to produce standardized bioinformatics packages and containers. These recommendations provide practical guidelines to make bioinformatics software more discoverable, reusable and transparent.  They are aimed to guide developers, organisations, journals and funders to increase the quality and sustainability of research software.

Recommendations for the packaging and containerizing of bioinformatics software

Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. However, containers and software packages should be produced under certain rules and standards in order to be reusable, compatible and easy to integrate into pipelines and analysis workflows. Here, we presented a set of recommendations developed by the BioContainers Community to produce standardized bioinformatics packages and containers. These recommendations provide practical guidelines to make bioinformatics software more discoverable, reusable and transparent.  They are aimed to guide developers, organisations, journals and funders to increase the quality and sustainability of research software.

Automated assembly of species metabolomes through data submission into a public repository

Following similar global efforts to exchange genomic and other biomedical data, global databases in metabolomics have now been established. MetaboLights, the first general purpose, publically available, cross-species, cross-application database in metabolomics, has become the fastest growing data repository at the European Bioinformatics Institute in terms of data volume. Here we present the automated assembly of species metabolomes in MetaboLights, a crucial reference for chemical biology, which is growing through user submissions.

BioContainers: an open-source and community-driven framework for software standardization

Motivation

BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters).

Availability and Implementation

The software is freely available at github.com/BioContainers/.

Functional SNP allele discovery (fSNPd): an approach to find highly penetrant, environmental-triggered genotypes underlying complex human phenotypes

BACKGROUND

Significant human diseases/phenotypes exist which require both an environmental trigger event and a genetic predisposition before the disease/phenotype emerges, e.g. Carbamazepine with the rare SNP allele of rs3909184 causing Stevens Johnson syndrome, and aminoglycosides with rs267606617 causing sensory neural deafness. The underlying genotypes are fully penetrant only when the correct environmental trigger(s) occur, otherwise they are silent and harmless. Such diseases/phenotypes will not appear to have a Mendelian inheritance pattern, unless the environmental trigger is very common (>50% per lifetime). The known causative genotypes are likely to be protein-altering SNPs with dominant/semi-dominant effect. We questioned whether other diseases and phenotypes could have a similar aetiology.

METHODS

We wrote the fSNPd program to analyse multiple exomes from a test cohort simultaneously with the purpose of identifying SNP alleles at a significantly different frequency to that of the general population. fSNPd was tested on trial cohorts, iteratively improved, and modelled for performance against an idealised association study under mutliple parameters. We also assessed the seqeuncing depath of all human exons to determine which were sufficiently well sequenced in an exome to be sued by fSNPd - by assessing forty exomes base by base.

RESULTS

We describe a simple methodology for the detection of SNPs capable of causing a phenotype triggered by an environmental event. This uses cohorts of relatively small size (30-100 individuals) with the phenotype being investigated, their exomes, and thence seeks SNP allele frequencies significantly different from expected to identify potentially clinically important, protein altering SNP alleles. The strengths and weaknesses of this approach for discovering significant genetic causes of human disease are comparable to Mendelian disease mutation detection and Association Studies.

CONCLUSIONS

The fSNPd methodology is another approach, and has potentially significant advantage over Association studies in needing far fewer individuals, to detect genes involved in the pathogenesis of a diseases/phenotypes. Furthermore, the SNP alleles identified alter amino acids, potentially making it easier to devise functional assays of protein function to determine pathogenicity.

Efficacy of extended thrombo-prophylaxis in major abdominal surgery: What does the evidence show?

Venous thromboembolism (VTE) is a frequent complication following major abdominal surgery. The use of low-molecular-weight heparins (LMWH) to prevent thrombotic events in these patients is a common and well documented practice. However, there is some controversy surrounding the duration of the prophylaxis, as it has been suggested that the risk persists for several weeks after surgery.The objective of this meta-analysis is to systematically review the clinical studies that compared safety and efficacy of extended use of LMWH (for three to four weeks after surgery) versus conventional in-hospital prophylaxis. An electronic data base search was performed. Only randomized, controlled studies were eligible. Data on the incidence of deep vein thrombosis (DVT), VTE and bleeding were extracted. Only three studies fulfilled the inclusion criteria. The indication for surgery was neoplastic disease in 70.6% (780/1104) of patients. The administration of extended LMWH prophylaxis significantly reduced the incidence of VTE, 5.93% (23/388) versus 13.6% (55/405), RR 0.44 (CI 95% 0.28 – 0.7); DVT 5.93% (23/388) versus 12.9% (52/402), RR 0.46 (CI 95% 0,29 – 0,74); proximal DVT 1% (4/388) versus 4.72% (19/402), RR 0.24 (CI 95% 0.09 – 0,67). We found no significant difference in major or minor bleeding between the two groups: 3.85% (21/545) in the extended thrombo-prophylaxis (ETP) group versus 3.48% (19/559) in the conventional prophylaxis group; RR 1.12 (CI 95% 0.61 – 2.06). There was no heterogeneity between the studies. We conclude that ETP with LMWH should be considered as a safe and useful strategy to prevent VTE in high-risk major abdominal surgery.