Is there sufficient evidence to support the use of antibiotic holiday just before the second stage of an infected total hip or knee arthroplasty revision surgery?

The practice of implementing an antibiotic holiday before the second stage of hip or knee arthroplasty is currently controversial due to limited evidence for this approach, as per the International Consensus Meeting 2018 on Musculoskeletal Infection. A greater understanding of this issue could augment the quality of Alrayes and Sukeik’s mini-review (2023) on diagnosing, managing, and treating periprosthetic knee infections. However, a significant lack of literature exists concerning the optimal duration for the antibiotic holiday, calling for more research before establishing any clinical guidelines.

A Novel Surgical Treatment Management Algorithm for Elbow Posterolateral Rotatory Instability (PLRI) Based on the Common Extensor Origin Integrity

Background: Here, we introduce a comprehensive treatment algorithm for posterolateral rotatory instability (PLRI) of the elbow, a condition affecting elbow mobility. We outline a diagnostic approach and a novel surgical management plan through the arthroscopic surgeon's point of view. Methods: The central focus of this management approach is the integrity of common extensor origin (CEO). High clinical suspicion must be evident to diagnose PLRI. Special clinical and imaging tests can confirm PLRI but sometimes the final confirmation is established during the arthroscopic treatment. The most appropriate treatment is determined by the degree of CEO integrity. Results: The treatment strategy varies with the CEO's condition: intact or minor tears require arthroscopic lateral collateral ligament imbrication, while extensive tears may need plication reinforced with imbrication or, in cases of retraction, a triceps tendon autograft reconstruction of the lateral ulnar collateral ligament alongside CEO repair. These approaches aim to manage residual instability and are complemented using a tailored rehabilitation protocol to optimize functional outcomes. Conclusion: PLRI is a unique clinical condition and should be treated likewise. This algorithm offers valuable insights for diagnosing and treating PLRI, enhancing therapeutic decision-making.

Septic Tibial Nonunions on Proximal and Distal Metaphysis-A Systematic Narrative Review

BACKGROUND

Infected nonunion of the tibia represents a challenging complication for orthopedic surgeons and poses a major financial burden to healthcare systems. The situation is even more compounded when the nonunion involves the metaphyseal region of long bones, a rare yet demanding complication due to the poor healing potential of infected cancellous bone; this is in addition to the increased likelihood of contamination of adjacent joints. The purpose of this study was to determine the extent and level of evidence in relation to (1) available treatment options for the management of septic tibial metaphyseal nonunions; (2) success rates and bone healing following treatment application; and (3) functional results after intervention.

METHODS

We searched the MEDLINE, Embase, and CENTRAL databases for prospective and retrospective studies through to 25 January 2021. Human-only studies exploring the efficacy of various treatment options and their results in the setting of septic, quiescent, and metaphyseal (distal or proximal) tibia nonunions in the adult population were included. For infection diagnosis, we accepted definitions provided by the authors of source studies. Of note, clinical heterogeneity rendered data pooling inappropriate.

RESULTS

In terms of the species implicated in septic tibial nonunions, staphylococcus aureus was found to be the most commonly isolated microorganism. Many authors implemented the Ilizarov external fixation device with a mean duration of treatment greater than one year. Exceptional or good bone and functional results were recorded in over 80% of patients, although the literature is scarce and possible losses of the follow-up were not recorded.

CONCLUSION

A demanding orthopedic condition that is scarcely studied is infected metaphyseal tibial nonunion. External fixation seems promising, but further research is needed.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO No. CRD42020205781.

Abstract 5427: Improving non-small cell lung cancer segmentation on a challenging dataset

When applied to different datasets, performance of the same deep learning tumor segmentation model can greatly vary. In a non-small cell lung cancer CT scan segmentation study that consists of two datasets, we found that the SwinUNETR model achieves state-of-the-art DICE score on a public dataset NSCLC but performs badly on a private dataset of curated data collected clinically. This performance variation reduces the applicability of such models. To mitigate this gap, through experimentation, we identified a set of techniques and applied them in the following order: (1) normalize a dataset to reduce differences between images. (2) stratify a dataset according to tumor sizes to form a more diverse training set. (3) isolate the lung area before training to help the model focus on the right area. (4) before training, initialize models with self-supervised pre-training weights (5) use a new loss function to give more weights on the cancerous area (6) after a model is trained, perform 3-axis test time flipping augmentation and ensemble the final predictions. In our experiments, our set of techniques improved the test DICE score for both datasets we tested on, where the best improvement was a 53% improvement from 0.32 to 0.49 DICE score.

Citation Format: Yi Wei, Balaji Selvaraj, Mayank Patwari, Qin Li, Meng Xu, Konstantinos Sidiropoulos, Zhenning Zhang, Leon Fedden, Anant Madabhushi, Mohammadhadi Khorrami, Vidya Sankar Viswanathan, Amit Gupta. Improving non-small cell lung cancer segmentation on a challenging dataset. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5427.

Viral infections in orthopedics: A systematic review and classification proposal

BACKGROUND

Although the impact of microbial infections on orthopedic clinical outcomes is well recognized, the influence of viral infections on the musculoskeletal system might have been underestimated.

AIM

To systematically review the available evidence on risk factors and musculoskeletal manifestations following viral infections and to propose a pertinent classification scheme.

METHODS

We searched MEDLINE, Cochrane Central Register of Controlled Trials (CENTRAL), the Reference Citation Analysis (RCA), and Scopus for completed studies published before January 30, 2021, to evaluate risk factors and bone and joint manifestations of viral infection in animal models and patient registries. Quality assessment was performed using SYRCLE's risk of bias tool for animal studies, Moga score for case series, Wylde score for registry studies, and Newcastle-Ottawa Scale for case-control studies.

RESULTS

Six human and four animal studies were eligible for inclusion in the qualitative synthesis. Hepatitis C virus was implicated in several peri- and post-operative complications in patients without cirrhosis after major orthopedic surgery. Herpes virus may affect the integrity of lumbar discs, whereas Ross River and Chikungunya viruses provoke viral arthritis and bone loss.

CONCLUSION

Evidence of moderate strength suggested that viruses can cause moderate to severe arthritis and osteitis. Risk factors such as pre-existing rheumatologic disease contributed to higher disease severity and duration of symptoms. Therefore, based on our literature search, the proposed clinical and pathogenetic classification scheme is as follows: (1) Viral infections of bone or joint; (2) Active bone and joint inflammatory diseases secondary to viral infections in other organs or tissues; and (3) Viral infection as a risk factor for post-surgical bacterial infection.

Network meta-analyses: Methodological prerequisites and clinical usefulness

It is an undeniable fact that systematic reviews play a crucial role in informing clinical practice; however, conventional head-to-head meta-analyses do have limitations. In particular, studies can only be compared in a pair-wise fashion, and conclusions can only be drawn in the light of direct evidence. In contrast, network meta-analyses can not only compare multiple interventions but also utilize indirect evidence which increases their precision. On top of that, they can also rank competing interventions. In this mini-review, we have aimed to elaborate on the principles and techniques governing network meta-analyses to achieve a methodologically sound synthesis, thus enabling safe conclusions to be drawn in clinical practice. We have emphasized the prerequisites of a well-conducted Network Meta-Analysis (NMA), the value of selecting appropriate outcomes according to guidelines for transparent reporting, and the clarity achieved via sophisticated graphical tools. What is more, we have addressed the importance of incorporating the level of evidence into the results and interpreting the findings according to validated appraisal systems (i.e., the Grade of Recommendations, Assessment, Development, and Evaluation system - GRADE). Lastly, we have addressed the possibility of planning future research via NMAs. Thus, we can conclude that NMAs could be of great value to clinical practice.

Which is the optimal minimally invasive treatment for osteoid osteoma of the hip? A systematic review and proportional meta-analysis

BACKGROUND

Osteoid osteomata comprise approximately 10% of benign bone tumours, with 20% of them being located in the proximal femur and 1-3% in the pelvis. In this meta-analysis, we sought to investigate positive and negative outcomes relating to minimally invasive surgery (MIS), which has superseded open resection and conservative measures over the last decades.

METHODS

We searched the PubMed, CENTRAL and grey literature for completed studies published until 10 August 2020. Articles with a minimum of ten patients diagnosed with osteoid osteomata of the proximal femur and/or acetabulum were included. Primary outcomes were success rates, complications and recurrences following treatment. Delays in diagnosis were also recorded. We conducted random effects meta-analysis of success rates for MIS modalities using MedCalc statistical software. Quality was assessed with a modified Delphi checklist.

RESULTS

Sixteen case-series were identified. Success rates for computed-tomography (CT)-guided radiofrequency ablation (RFA), CT-guided percutaneous resection drilling and arthroscopic resection were 98.2% (95% CI 95.8-99.5), p = 0.47; 91.5% (95% CI 81.1-97.9), p = 0.06; and 98% (95% CI 89.3-99.7), p = 0.95, respectively. Both RFA and percutaneous drilling resection were associated with two iatrogenic femoral fractures. Arthroscopic removal was not associated with any complications. Definitive diagnosis was established at least six months after symptom onset in up to 43% of patients.

CONCLUSIONS

RFA could be the most effective treatment options for patients suffering from osteoid osteomata of the hip. Arthroscopy could be potentially as effective as RFA as long as further large-scale studies confirm its efficacy and safety. Reported complications stemming from these modalities were sparse in nature. In order to avoid inordinate diagnostic delays, a high index of suspicion and low threshold for CT scan investigation is required.

The reactome pathway knowledgebase 2022

The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary and acquired disease processes. The processes are annotated as an ordered network of molecular transformations in a single consistent data model. Reactome thus functions both as a digital archive of manually curated human biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. Recent curation work has expanded our annotations of normal and disease-associated signaling processes and of the drugs that target them, in particular infections caused by the SARS-CoV-1 and SARS-CoV-2 coronaviruses and the host response to infection. New tools support better simultaneous analysis of high-throughput data from multiple sources and the placement of understudied ('dark') proteins from analyzed datasets in the context of Reactome's manually curated pathways.

Preventing Staphylococcus aureus stainless steel-associated infections in orthopedics. A systematic review and meta-analysis of animal literature

Surgical site infection in the presence of orthopedic implants poses significant healthcare and socioeconomic burden. To assess the potential of various prevention strategies against Staphylococcus-induced stainless steel-associated infections, a review of animal evidence was designed. The databases of PubMed, Embase, and CENTRAL were searched until March 10, 2020, for articles including animal models with stainless steel instrumentation and techniques to prevent Staphylococcus infection. We conducted a random-effects meta-analysis of standardized mean differences (SMD) with subgroup analysis linked to various protection strategies and we recorded complications. Quality was assessed with the SYRCLE's risk of bias tool. Twenty-five studies were included. Combined active coating (featuring organic antibacterial compound release) and degradable passive finishing (lipid- or polymer-based structure modification reducing bacterial adhesion) was favored over untreated controls (SMDs for methicillin-sensitive Staphylococcus aureus [MSSA] and methicillin-resistant Staphylococcus aureus [MRSA] were -3.46, 95% CI [-4.53 to -2.4], p < .001 [n = 4 head-to-head comparisons]; and -6.67, 95% CI [-10.53 to -3], p < .001 [n = 5 head-to-head comparisons], respectively). Systemic vitamin D supplementation and systemic antibiotic administration with or without local antibiotics demonstrated favorable outcomes against MSSA infection. On the contrary, no benefit was seen following vaccination. Of note, no side effects were documented. On the basis of data gathered from eight studies, which comprised 294 animals, a bioresorbable polymer- or lipid-based surface modification supplemented with organic coating yielded improved infection-related outcomes against MSSA and MRSA stainless steel infections, and therefore, this strategy could be further investigated in human research.

Elastic Intramedullary Nails in the Treatment of Multi-Segmental Humeral Fracture in a Polytrauma Patient

A polytrauma patient with a life-threatening condition is a quite demanding situation due to special considerations regarding the time, the way, and the sequence of the necessary procedures. Elastic intramedullary nails (EIN) could be used under these conditions for adult patients with humeral fractures requiring fixation. Here we present a case of a multi-segmental closed humerus fracture in a polytrauma patient treated by EIN. The general condition of the patient and the need for multiple surgical procedures required the selection of a minimally invasive and time-saving fixation technique. The patient’s follow-up was uneventful with complete healing of the humeral fracture; the functional scores results are excellent at five years post operatively. A review of the literature revealed limited published cases of humeral fractures (128 patients) treated by EIN, despite the fact that the results are quite encouraging. Based on our results and the current literature, we believe that EIN could become an effective treatment choice for multi-level humerus fractures, especially in damage control surgery.

Rationalising animal research synthesis in orthopaedic literature

Systematic reviews in orthopaedic literature are frequently criticised for offering inconsistent conclusions. On top of that, high-quality randomized human evidence on crucial orthopaedic topics is more often than not lacking. In this situation, pooling animal literature could offer an excellent insight into unanswered critical clinical questions, thus potentially improving healthcare. In this paper, we sought to present the rationale and basic principles governing meta-analysis of animal research. More specifically, we elaborated on the available evidence-based methods to achieve a scientifically sound animal data synthesis. In addition, we discussed result interpretation, strength of recommendations and clinical implications based on the results of these meta-analytic modalities.

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis

Pathway analyses are key methods to analyze 'omics experiments. Nevertheless, integrating data from different 'omics technologies and different species still requires considerable bioinformatics knowledge.Here we present the novel ReactomeGSA resource for comparative pathway analyses of multi-omics datasets. ReactomeGSA can be used through Reactome's existing web interface and the novel ReactomeGSA R Bioconductor package with explicit support for scRNA-seq data. Data from different species is automatically mapped to a common pathway space. Public data from ExpressionAtlas and Single Cell ExpressionAtlas can be directly integrated in the analysis. ReactomeGSA greatly reduces the technical barrier for multi-omics, cross-species, comparative pathway analyses.We used ReactomeGSA to characterize the role of B cells in anti-tumor immunity. We compared B cell rich and poor human cancer samples from five of the Cancer Genome Atlas (TCGA) transcriptomics and two of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) proteomics studies. B cell-rich lung adenocarcinoma samples lacked the otherwise present activation through NFkappaB. This may be linked to the presence of a specific subset of tumor associated IgG+ plasma cells that lack NFkappaB activation in scRNA-seq data from human melanoma. This showcases how ReactomeGSA can derive novel biomedical insights by integrating large multi-omics datasets.

Flow characteristics and alkalinity of novel bioceramic root canal sealers

Objective

This study aimed to examine the physical properties (pH and flow) of 2 novel bioceramic sealers.

Materials and Methods

The tested sealers were a calcium hydroxide sealer (Sealapex) and 2 bioceramic sealers (BioRoot RCS and TotalFill BC Sealer). Flow measurements were conducted according to ISO 6876/2012, with a press method of 0.05 mL of sealer. The pH of fresh samples was tested immediately after manipulation, while set samples were stored for 3 times the recommended setting time. The predetermined time intervals ranged from 3 minutes to 24 hours for fresh samples and from 10 minutes to 7 days and 4 weeks for the set samples. Analysis of variance was performed, with p = 0.05 considered indicating significance.

Results

The mean flow values were 26.99 mm for BioRoot, 28.19 for Sealapex, and 30.8 mm for TotalFill BC Sealer, satisfying the ISO standard. In the set samples, BioRoot RCS had higher pH values at 24 hours to 1 week after immersion in distilled water. At 2 weeks, both bioceramic sealers had similar pH values, greater than that of Sealapex. In the fresh samples, the bioceramic sealers had significantly higher initial pH values than Sealapex (p < 0.05). At 24 hours post-immersion, all sealers showed an alkaline pH, with the highest pH observed for TotalFill.

Conclusions

The TotalFill BC Sealer demonstrated the highest flow. The bioceramic sealers initially presented higher alkaline activity than the polymeric calcium hydroxide sealer. However, at 3 and 4 weeks post-immersion, all sealers had similar pH values.

Is coating of titanium implants effective at preventing Staphylococcus aureus infections? A meta-analysis of animal model studies

AIM OF THE STUDY

To assess the effects of the available coating methods against methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) biofilm development on titanium implants.

METHODS

We searched the MEDLINE, Embase, and CENTRAL databases until May 18, 2019, for studies that used animal models of infections to evaluate various titanium implant coating methods to prevent S. aureus infection. Twenty-seven studies were eligible for inclusion in qualitative synthesis. Of those, twenty-three were considered in pair-wise meta-analysis. In addition, subgroup analysis of implant protection strategies relative to uncoated controls was performed, and any adverse events stemming from the coating applications were reported. Quality assessment was performed using SYRCLE's risk of bias tool for animal studies.

RESULTS

Meta-analysis showed that active coating with antibiotics was favoured over uncoated controls (standardised mean differences [SMD] for MRSA and MSSA were - 2.71 [95% CI, - 4.24 to - 1.18], p = 0.0005, and - 2.5 [- 3.79 to - 1.22], p = 0.0001, respectively). Likewise, large effect sizes were demonstrated when a combination of active and conventional non-degradable passive coatings was compared with controls (SMDs for MRSA and MSSA were - 0.62 [95% CI, - 1.15 to - 0.08], p = 0.02, and - 1.93 [95% CI, - 2.87 to - 0.98], p < 0.001, respectively).

DISCUSSION/CONCLUSION

As a standalone prevention method, active titanium coating with antibiotics yielded promising results against both MSSA and MRSA. Combinations between active and non-degradable passive coatings, potentially allowing for sustained antimicrobial substance release, provided consistent hardware infection protection. Thus, we recommend that future research efforts focus on combined coating modalities against S. aureus biofilm infections in the presence of titanium implants.

SYSTEMATIC REVIEW REGISTRATION

CRD42019123462.

Nutritional habits and free grazing regimen of productive animals along with specific ingredients are influential factors for the antioxidant properties of milk: From farm to market

Milk is a fundamental product of animal origin for human health and well-being. It possesses crucial biological properties, which depend on its composition and production methodology. To this end, one of the aims of the present study was to assess the impact of the nutritional and dwelling patterns of productive animals on the antioxidant potency of their generated milk. Thus, samples of sheep milk were collected for 30 consecutive days during the spring months from 5 different farms with different traits and its antioxidant activity was measured. Furthermore, this study aimed to evaluate the antioxidant capacity of 15 commercially available milk samples of different animal origin (i.e., cow and buffalo) and type (i.e., full-fat, light and chocolate) derived from 5 different companies. For all the experiments, the assay that examines the ability of the milk samples to reduce the DPPH• radical was used. It was thus found that the free-grazing regimen of the farm sheep dwelling at high altitude resulted in the production of milk with a greater antioxidant potential. On the other hand, it was also found that the samples of chocolate milk exhibited notably mote potent antioxidant activity than the full-fat and light samples, obviously due to the excessively high composition in antioxidant molecules present in cocoa. From this study that holistically examined the antioxidant properties of milk derived from three different productive animal species, it becomes evident that the nutritional and grazing practices, as well as specific ingredients (i.e., cocoa) lead to the generation of milk with high added biological value.

Reactome and ORCID-fine-grained credit attribution for community curation

Reactome is a manually curated, open-source, open-data knowledge base of biomolecular pathways. Reactome has always provided clear credit attribution for authors, curators and reviewers through fine-grained annotation of all three roles at the reaction and pathway level. These data are visible in the web interface and provided through the various data download formats. To enhance visibility and credit attribution for the work of authors, curators and reviewers, and to provide additional opportunities for Reactome community engagement, we have implemented key changes to Reactome: contributor names are now fully searchable in the web interface, and contributors can ‘claim’ their contributions to their ORCID profile with a few clicks. In addition, we are reaching out to domain experts to request their help in reviewing and editing Reactome pathways through a new ‘Contribution’ section, highlighting pathways which are awaiting community review.

Database URL: https://reactome.org

The reactome pathway knowledgebase

The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consistent data model, an extended version of a classic metabolic map. Reactome functions both as an archive of biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. To extend our ability to annotate human disease processes, we have implemented a new drug class and have used it initially to annotate drugs relevant to cardiovascular disease. Our annotation model depends on external domain experts to identify new areas for annotation and to review new content. New web pages facilitate recruitment of community experts and allow those who have contributed to Reactome to identify their contributions and link them to their ORCID records. To improve visualization of our content, we have implemented a new tool to automatically lay out the components of individual reactions with multiple options for downloading the reaction diagrams and associated data, and a new display of our event hierarchy that will facilitate visual interpretation of pathway analysis results.

Do External Supports Improve Dynamic Balance in Patients with Chronic Ankle Instability? A Network Meta-analysis

BACKGROUND

To improve ankle stability in patients who have experienced an ankle sprain with residual symptoms of instability and/or objective joint laxity, external supports (such as taping, bracing, and orthotic insoles) are used sometimes. However, available randomized trials have disagreed on whether restraints improve balance in those individuals. In this situation, a network meta-analysis can help because it allows for comparing multiple treatments simultaneously, taking advantage not only of direct but also indirect evidence synthesis.

QUESTIONS/PURPOSES

The aim of this network meta-analysis was to assess (1) the impact of taping and orthotic devices on dynamic postural control in individuals with ankle instability and (2) the presence of a placebo effect in participants treated with sham taping and complications resulting from the administered treatments.

METHODS

We searched the PubMed, Scopus, and CENTRAL databases up to February 13, 2019 for completed studies. Randomized trials assessing the results of real and/or sham taping, wait-and-see protocols, ankle bracing, and foot orthotics for ankle instability as determined by one or more ankle sprains followed by ongoing subjective symptoms and/or mechanical laxity were included. We evaluated dynamic postural control in terms of the Star Excursion Balance Test in the posteromedial direction (SEBT-PM), which is considered the most representative of balance deficits in patients with ankle instability. Standardized mean differences were re-expressed to percentage differences in SEBT-PM, with higher scores representing possible improvement. Subsequently, those data were checked against the established minimal detectable change of 14% for this scale to make judgements on clinical importance. We also assessed the presence of a placebo effect by comparing the results of sham taping with no treatment and complications resulting from the administered treatments. Additionally, we judged the quality of trials using the Cochrane risk of bias tool and quality of evidence using the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) approach. A total of 22 trials met our inclusion criteria, 18 of which were deemed to be at a low risk of bias. A network of treatments consisting of 13 studies was created, and the level of evidence was judged to be high. As far as participants' allocation to treatment arms, 85 patients followed a wait-and-see protocol, 29 received placebo taping, 99 were treated with taping, 16 were treated with bracing, 27 were administered insoles, and six individuals were offered a combination of insoles with bracing. Of note, with statistical power set at 80%, a minimum of 16 patients per treatment group was required to provide sufficient statistical power and detect a SEBT-PM percentage difference of 14%.

RESULTS

A network meta-analysis did not demonstrate a benefit of taping or bracing over no treatment (percentage difference in SEBT-PM between taping and bracing versus control: -2.4 [95% CI -6 to 1.1]; p = 0.18, and -7.5 [95% CI -15.9 to 1]; p = 0.08, respectively). This was also the case for sham taping because the measurement increase failed to exceed the minimal detectable change (percentage difference in SEBT-PM between sham taping and untreated control: -1.1 [95% CI -6.9 to 4.7]; p = 0.72). Importantly, there were no reported adverse events after treatment application.

CONCLUSIONS

Evidence of moderate strength indicated that external supports of any type were no more effective than controls in improving dynamic postural control in patients with at least one ankle sprain and residual functional or mechanical deficits. Therefore, implementing those tools as a standalone treatment does not appear to be a viable strategy for the primary management of ankle instability. It is conceivable that combinations of rehabilitation and external supports could be more effective than external supports alone, and future trials should evaluate the potential of such combinations in enhancing not only clinician-reported but also patient-oriented outcomes using long-term follow-up measurements.

LEVEL OF EVIDENCE

Level I, therapeutic study.

The Reactome Pathway Knowledgebase

The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations-an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression profiles or somatic mutation catalogues from tumor cells. To support the continued brisk growth in the size and complexity of Reactome, we have implemented a graph database, improved performance of data analysis tools, and designed new data structures and strategies to boost diagram viewer performance. To make our website more accessible to human users, we have improved pathway display and navigation by implementing interactive Enhanced High Level Diagrams (EHLDs) with an associated icon library, and subpathway highlighting and zooming, in a simplified and reorganized web site with adaptive design. To encourage re-use of our content, we have enabled export of pathway diagrams as 'PowerPoint' files.

Reactome diagram viewer: data structures and strategies to boost performance

Motivation

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community.

Results

The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partitioning data structure minimizes CPU workload, enabling the introduction of new features that further enhance user experience. Through the use of highly optimized data structures and algorithms, Reactome has boosted the performance and usability of the new pathway diagram viewer, providing a robust, scalable and easy-to-integrate solution to pathway visualization. As graph-based visualization of complex data is a frequent challenge in bioinformatics, many of the individual strategies presented here are applicable to a wide range of web-based bioinformatics resources.

Availability and implementation

Reactome is available online at: https://reactome.org. The diagram viewer is part of the Reactome pathway browser (https://reactome.org/PathwayBrowser/) and also available as a stand-alone widget at: https://reactome.org/dev/diagram/. The source code is freely available at: https://github.com/reactome-pwp/diagram.

Supplementary information

Supplementary data are available at Bioinformatics online.

Investigation of the chemical profile and cytotoxicity evaluation of organic components eluted from pit and fissure sealants

The aim of this study was to identify organic components eluted from five resin dental sealants using gas chromatography and mass spectrometry (GC/MS) after 1-day and 40-days storage and the effect of sealants on cell survival of cultured fibroblasts. Five resin materials were studied: BeautiSealant (SHOFU), Clinpro (3M/ESPE), Conseal F (SDI), Grandio Seal (VOCO) and Helioseal Clear (Ivoclar/Vivadent). The organic monomers detected were butylated hydroxytoluene (BHT), bis-phenol-A (BPA), camphoroquinone (CQ), diethylenglycoldimethacrylate (DEGDMA), 4N, N-dimethylaminobenzoic acid butylethoxyester (DMABEE), hydroxyethylmethcrylate (HEMA), hydroquinone monomethylether (MEHQ), triethylene glycol dimethacrylate (TEGDMA), tetrabutylammonium tetrafluoroborate (TBATFB), triphenylstibane (TPSb). The main monomer detected was TEGDMA, whereas BHT and DEGDMA were detected at lower concentrations. Higher monomer concentrations were detected after 40 days storage. The eluting chemical profiles of the tested materials differ qualitative and quantitative. For cytotoxicity evaluation, NIH/3T3 cells were exposed to eluates of sealants and cell viability was assessed by a quantitative technique at two observation periods. Decreased cell viability was observed. The cytotoxicity and the release of monomers from dental materials examined depends on the type of material and the observation time point. Resin-based dental materials have raised public concerns regarding possible adverse biological effects, thus it is essential to evaluate possible side effects for human health.

Reactome enhanced pathway visualization

Motivation

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. Here, we present new developments in the Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users’ own research presentations and publications.

Results

For the higher levels of the hierarchy, Reactome now provides scalable, interactive textbook-style diagrams in SVG format, which are also freely downloadable and editable. Repeated diagram elements like ‘mitochondrion’ or ‘receptor’ are available as a library of graphic elements. Detailed lower-level diagrams are now downloadable in editable PPTX format as sets of interconnected objects.

Availability and implementation

http://reactome.org

Reactome pathway analysis: a high-performance in-memory approach

Background

Reactome aims to provide bioinformatics tools for visualisation, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education. Pathway analysis methods have a broad range of applications in physiological and biomedical research; one of the main problems, from the analysis methods performance point of view, is the constantly increasing size of the data samples.

Results

Here, we present a new high-performance in-memory implementation of the well-established over-representation analysis method. To achieve the target, the over-representation analysis method is divided in four different steps and, for each of them, specific data structures are used to improve performance and minimise the memory footprint. The first step, finding out whether an identifier in the user’s sample corresponds to an entity in Reactome, is addressed using a radix tree as a lookup table. The second step, modelling the proteins, chemicals, their orthologous in other species and their composition in complexes and sets, is addressed with a graph. The third and fourth steps, that aggregate the results and calculate the statistics, are solved with a double-linked tree.

Conclusion

Through the use of highly optimised, in-memory data structures and algorithms, Reactome has achieved a stable, high performance pathway analysis service, enabling the analysis of genome-wide datasets within seconds, allowing interactive exploration and analysis of high throughput data. The proposed pathway analysis approach is available in the Reactome production web site either via the AnalysisService for programmatic access or the user submission interface integrated into the PathwayBrowser. Reactome is an open data and open source project and all of its source code, including the one described here, is available in the AnalysisTools repository in the Reactome GitHub (https://github.com/reactome/).

Open Targets: a platform for therapeutic target identification and validation

We have designed and developed a data integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. The platform is designed to support identification and prioritization of biological targets for follow-up. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources. The platform provides either a target-centric workflow to identify diseases that may be associated with a specific target, or a disease-centric workflow to identify targets that may be associated with a specific disease. Users can easily transition between these target- and disease-centric workflows. The Open Targets Validation Platform is accessible at https://www.targetvalidation.org.

The Reactome pathway Knowledgebase

The Reactome Knowledgebase (www.reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations—an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression pattern surveys or somatic mutation catalogues from tumour cells. Over the last two years we redeveloped major components of the Reactome web interface to improve usability, responsiveness and data visualization. A new pathway diagram viewer provides a faster, clearer interface and smooth zooming from the entire reaction network to the details of individual reactions. Tool performance for analysis of user datasets has been substantially improved, now generating detailed results for genome-wide expression datasets within seconds. The analysis module can now be accessed through a RESTFul interface, facilitating its inclusion in third party applications. A new overview module allows the visualization of analysis results on a genome-wide Reactome pathway hierarchy using a single screen page. The search interface now provides auto-completion as well as a faceted search to narrow result lists efficiently.

Computer-based image analysis system designed to differentiate between low-grade and high-grade laryngeal cancer cases

OBJECTIVE

To design a pattern recognition (PR) system for discriminating between low- and high-grade laryngeal cancer cases, employing immunohistochemically stained, for p63 expression, histopathology images.

STUDY DESIGN

The PR system was designed to assist in the physician's diagnosis for improving patient survival. The material comprised 55 verified cases of laryngeal cancer, 21 of low-grade and 34 of high-grade malignancy. Histopathology images were first processed for automatically segmenting p63 expressed nuclei. Fifty-two features were next extracted from the segmented nuclei, concerning nuclei texture, shape, and physical topology in the image. Those features and the Probabilistic Neural Network classifier were used to design the PR system on the multiprocessors of the Nvidia 580 GTX graphics processing unit (GPU) card using the Compute Unified Device Architecture parallel programming model and C++ programming language.

RESULTS

PR system performance in classifying laryngeal cancer cases as low grade and high grade was 85.7% and 94.1%, respectively. The system's overall accuracy was 90.9%, using 7 features, and its estimated accuracy to "unseen" by the system cases was 80%.

CONCLUSION

Optimum system design was feasible after employing parallel processing techniques and GPU technology. The proposed system was structured so as to function in a clinical environment, as a research tool, and with the capability of being redesigned on site when new verified cases are added to its repository.

Development and evaluation of a PDA-based teleradiology terminal in thyroid nodule diagnosis

We developed a wireless personal digital assistant (PDA)-based teleradiology terminal which allowed a secure connection to the hospital's Picture Archiving and Communication System (PACS) through the DICOM protocol. Ten members of the hospital's medical staff completed a questionnaire about its mobility, usability, stability, performance and diagnostic efficiency in a real health-care environment. There was a high degree of satisfaction with the system's mobility (mean score 4.1, SD 1.0, on a five-point scale), usability (mean score 4.2, SD 1.1), stability (mean score 3.9, SD 0.4) and performance (mean score 4.2, SD 0.6). The system was evaluated as a tool for providing assistance in diagnosing thyroid nodules from ultrasound images. A total of 144 ultrasound images with thyroid nodules were assessed by an expert. Six image quality attributes were evaluated. The physician concluded that the ultrasound thyroid images on the PDA screen were of similar quality to those displayed on a diagnostic visual display unit screen. However, the expert found difficulties in diagnosing microcalcification, internal echo texture and vascularity. The PDA terminal provided rapid, secure and convenient portable access to PACS images and the image quality was sufficient for diagnostic interpretation of ultrasound images of the thyroid.