Deep learning for diagnosis and survival prediction in soft tissue sarcoma

BACKGROUND

Clinical management of soft tissue sarcoma (STS) is particularly challenging. Here, we used digital pathology and deep learning (DL) for diagnosis and prognosis prediction of STS.

PATIENTS AND METHODS

Our retrospective, multicenter study included a total of 506 histopathological slides from 291 patients with STS. The Cancer Genome Atlas cohort (240 patients) served as training and validation set. A second, multicenter cohort (51 patients) served as an additional test set. The use of the DL model (DLM) as a clinical decision support system was evaluated by nine pathologists with different levels of expertise. For prognosis prediction, 139 slides from 85 patients with leiomyosarcoma (LMS) were used. Area under the receiver operating characteristic (AUROC) and accuracy served as main outcome measures.

RESULTS

The DLM achieved a mean AUROC of 0.97 (±0.01) and an accuracy of 79.9% (±6.1%) in diagnosing the five most common STS subtypes. The DLM significantly improved the accuracy of the pathologists from 46.3% (±15.5%) to 87.1% (±11.1%). Furthermore, they were significantly faster and more certain in their diagnosis. In LMS, the mean AUROC in predicting the disease-specific survival status was 0.91 (±0.1) and the accuracy was 88.9% (±9.9%). Cox regression showed the DLM's prediction to be a significant independent prognostic factor (P = 0.008, hazard ratio 5.5, 95% confidence interval 1.56-19.7) in these patients, outperforming other risk factors.

CONCLUSIONS

DL can be used to accurately diagnose frequent subtypes of STS from conventional histopathological slides. It might be used for prognosis prediction in LMS, the most prevalent STS subtype in our cohort. It can also help pathologists to make faster and more accurate diagnoses. This could substantially improve the clinical management of STS patients.

Risk of groundwater contamination widely underestimated because of fast flow into aquifers

Groundwater pollution threatens human and ecosystem health in many regions around the globe. Fast flow to the groundwater through focused recharge is known to transmit short-lived pollutants into carbonate aquifers, endangering the quality of groundwaters where one quarter of the world's population lives. However, the large-scale impact of such focused recharge on groundwater quality remains poorly understood. Here, we apply a continental-scale model to quantify the risk of groundwater contamination by degradable pollutants through focused recharge in the carbonate rock regions of Europe, North Africa, and the Middle East. We show that focused recharge is the primary reason for widespread rapid transport of contaminants to the groundwater. Where it occurs, the concentration of pollutants in groundwater recharge that have not yet degraded increases from <1% to around 20 to 50% of their concentrations during infiltration. Assuming realistic application rates, our simulations show that degradable pollutants like glyphosate can exceed their permissible concentrations by 3 to 19 times when reaching the groundwater. Our results are supported by independent estimates of young water fractions at 78 carbonate rock springs over Europe and a dataset of observed glyphosate concentrations in the groundwater. They imply that in times of continuing and increasing industrial and agricultural productivity, focused recharge may result in an underestimated and widespread risk to usable groundwater volumes.

[Histological subtypes of renal cell carcinoma : Overview and new developments]

BACKGROUND

The classification of renal cell carcinoma (RCC) has changed remarkably in recent years.

OBJECTIVES

This is a short overview of the classification of RCC, focusing on new developments.

MATERIALS AND METHODS

A literature search was performed resulting in an overview of the classification of RCC. Emerging entities were discussed in detail.

RESULTS

Apart from the RCC subtypes in the WHO classification of 2016, several emerging entities came up over the last few years that are characterized by typical morphology, immunophenotype, and especially specific genetic alterations.

CONCLUSION

Precise classification of RCC is the key to better prognostic assessment with potential tumor-specific therapy and plays an important role in the recognition of possible association with hereditary tumor syndromes.

Chocolate ingestion in 156 dogs

OBJECTIVES

To describe the clinical features and outcome of dogs after chocolate ingestion.

MATERIAL AND METHODS

Retrospective evaluation of clinical signs, clinical pathological findings, therapy and outcome of 156 dogs after chocolate ingestion. The concentration of methylxanthines (theobromine, caffeine) was calculated based on the type of chocolate and the amount ingested.

RESULTS

One hundred and twelve dogs had no clinical signs. Forty-four dogs had clinical signs of chocolate intoxication. Twenty-eight of these 44 dogs ingested dark and bitter chocolate. Reasons for presentation were agitation (33), tremor (22), vomiting (21), panting (11), polyuria/polydipsia (seven) and diarrhea (two). Common clinical findings were sinus tachycardia (28), tachypnea/panting (14), hyperthermia (10) and dehydration (seven). Clinical pathological findings in 34 of 44 dogs consisted of hyperlactataemia (23), hypokalaemia (16), mild hyperglycaemia (16) and mild alanine aminotransferase (ALT) and aspartate aminotransferase (AST) elevation (14). After decontamination (apomorphine, activated carbon) and symptomatic treatment (fluid therapy, esmolol, forced diuresis, sedatives), 43 of the 44 dogs survived.

CLINICAL SIGNIFICANCE

In dogs with potential chocolate intoxication, the type and amount of chocolate and the time of ingestion are important factors. Cardiovascular, neurological and gastrointestinal signs are the most common clinical signs. In this case series, the prognosis after decontamination and symptomatic therapy was good, with a mortality rate of less than 3%.

Comprehensive review of genotoxicity data for diclofenac

Diclofenac is a non-steroidal anti-inflammatory drug discovered several decades ago, which has since been used by an estimated one billion patients and has demonstrated an acceptable safety profile. In support of its marketing approval, a comprehensive set of genotoxicity studies were conducted in vitro and in vivo. Despite the fact that these studies preceded both Good Laboratory Practice (GLP) requirements and International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) guidelines on genotoxicity testing, they were conducted using the best scientific principles and are considered appropriate by contemporary standards. In addition to bacterial mutagenicity and mammalian in vitro assays, repeat-dose somatic, germ cell and dominant lethal assays were conducted. These data are made available for the first time to offer researchers an opportunity to review the existing data set that unequivocally demonstrates that diclofenac sodium is not genotoxic. This is further substantiated by long-term bioassay data demonstrating that diclofenac sodium has no carcinogenic potential in rodents. However, more recently, new studies have been published showing a genotoxic potential for diclofenac in novel or modified in vitro test systems. These new publications are discussed in the context of the existing comprehensive data package.

COVID-19 effects on the kidney

Apart from pulmonary disease, acute kidney injury (AKI) is one of the most frequent and most severe organ complications in severe coronavirus disease 2019 (COVID-19). The SARS-CoV‑2 virus has been detected in renal tissue. Patients with chronic kidney disease (CKD) before and on dialysis and specifically renal transplant patients represent a particularly vulnerable population. The increasing number of COVID-19 infected patients with renal involvement led to an evolving interest in the analysis of its pathophysiology, morphology and modes of virus detection in the kidney. Meanwhile, there are ample data from several autopsy and kidney biopsy studies that differ in the quantity of cases as well as in their quality. While the detection of SARS-CoV‑2 RNA in the kidney leads to reproducible results, the use of electron microscopy for visualisation of the virus is difficult and currently critically discussed due to various artefacts. The exact contribution of indirect or direct effects on the kidney in COVID-19 are not yet known and are currently the focus of intensive research.

Association Between Dispatch of Mobile Stroke Units and Functional Outcomes Among Patients With Acute Ischemic Stroke in Berlin

IMPORTANCE

Effects of thrombolysis in acute ischemic stroke are time-dependent. Ambulances that can administer thrombolysis (mobile stroke units [MSUs]) before arriving at the hospital have been shown to reduce time to treatment.

OBJECTIVE

To determine whether dispatch of MSUs is associated with better clinical outcomes for patients with acute ischemic stroke.

DESIGN, SETTING, AND PARTICIPANTS

This prospective, nonrandomized, controlled intervention study was conducted in Berlin, Germany, from February 1, 2017, to October 30, 2019. If an emergency call prompted suspicion of stroke, both a conventional ambulance and an MSU, when available, were dispatched. Functional outcomes of patients with final diagnosis of acute cerebral ischemia who were eligible for thrombolysis or thrombectomy were compared based on the initial dispatch (both MSU and conventional ambulance or conventional ambulance only).

EXPOSURE

Simultaneous dispatch of an MSU (computed tomographic scanning with or without angiography, point-of-care laboratory testing, and thrombolysis capabilities on board) and a conventional ambulance (n = 749) vs conventional ambulance alone (n = 794).

MAIN OUTCOMES AND MEASURES

The primary outcome was the distribution of modified Rankin Scale (mRS) scores (a disability score ranging from 0, no neurological deficits, to 6, death) at 3 months. The coprimary outcome was a 3-tier disability scale at 3 months (none to moderate disability; severe disability; death) with tier assignment based on mRS scores if available or place of residence if mRS scores were not available. Common odds ratios (ORs) were used to quantify the association between exposure and outcome; values less than 1.00 indicated a favorable shift in the mRS distribution and lower odds of higher levels of disability.

RESULTS

Of the 1543 patients (mean age, 74 years; 723 women [47%]) included in the adjusted primary analysis, 1337 (87%) had available mRS scores (primary outcome) and 1506 patients (98%) had available the 3-tier disability scale assessment (coprimary outcome). Patients with an MSU dispatched had lower median mRS scores at month 3 (1; interquartile range [IQR], 0-3) than did patients without an MSU dispatched (2; IQR, 0-3; common OR for worse mRS, 0.71; 95% CI, 0.58-0.86; P < .001). Similarly, patients with an MSU dispatched had lower 3-month coprimary disability scores: 586 patients (80.3%) had none to moderate disability; 92 (12.6%) had severe disability; and 52 (7.1%) had died vs patients without an MSU dispatched: 605 (78.0%) had none to moderate disability; 103 (13.3%) had severe disability; and 68 (8.8%) had died (common OR for worse functional outcome, 0.73, 95% CI, 0.54-0.99; P = .04).

CONCLUSIONS AND RELEVANCE

In this prospective, nonrandomized, controlled intervention study of patients with acute ischemic stroke in Berlin, Germany, the dispatch of mobile stroke units, compared with conventional ambulances alone, was significantly associated with lower global disability at 3 months. Clinical trials in other regions are warranted.

[COVID-19 effects on the kidney]

Bei einer schweren Coronavirus-Erkrankung-2019 (COVID-19) ist neben der Lungenerkrankung selbst das akute Nierenversagen (ANV) eine der häufigsten und schwerwiegendsten Komplikationen. Das SARS-CoV-2-Virus konnte hierbei auch in der Niere nachgewiesen werden. Patienten mit chronischen Nierenerkrankungen (CKD), dialysepflichtige sowie v. a. nierentransplantierte Patienten scheinen eine besonders vulnerable Population darzustellen. Die zunehmende Anzahl SARS-CoV-2-infizierter Patienten hat das Interesse an der genauen Pathophysiologie und Morphologie der Nierenschädigung sowie am direkten Virusnachweis in der Niere geweckt, der im Gegensatz zur Lunge insgesamt schwieriger zu führen ist. Hierzu liegen mittlerweile Daten aus Autopsie- und Nierenbiopsiestudien mit unterschiedlichen Patientenzahlen und von sehr unterschiedlicher Qualität vor. Während der Nachweis von SARS-CoV-2-RNA im Nierengewebe mit gut reproduzierbaren Ergebnissen erfolgt, ist insbesondere der Virusnachweis mittels Elektronenmikroskopie schwierig und wird aufgrund zahlreicher Artefakte derzeit kritisch diskutiert. Die genauen direkten oder indirekten Effekte von SARS-CoV‑2 auf die Niere sind noch nicht im Detail bekannt und derzeit der Fokus intensiver Forschung.

Synaptic processes and immune-related pathways implicated in Tourette syndrome

Tourette syndrome (TS) is a neuropsychiatric disorder of complex genetic architecture involving multiple interacting genes. Here, we sought to elucidate the pathways that underlie the neurobiology of the disorder through genome-wide analysis. We analyzed genome-wide genotypic data of 3581 individuals with TS and 7682 ancestry-matched controls and investigated associations of TS with sets of genes that are expressed in particular cell types and operate in specific neuronal and glial functions. We employed a self-contained, set-based association method (SBA) as well as a competitive gene set method (MAGMA) using individual-level genotype data to perform a comprehensive investigation of the biological background of TS. Our SBA analysis identified three significant gene sets after Bonferroni correction, implicating ligand-gated ion channel signaling, lymphocytic, and cell adhesion and transsynaptic signaling processes. MAGMA analysis further supported the involvement of the cell adhesion and trans-synaptic signaling gene set. The lymphocytic gene set was driven by variants in FLT3, raising an intriguing hypothesis for the involvement of a neuroinflammatory element in TS pathogenesis. The indications of involvement of ligand-gated ion channel signaling reinforce the role of GABA in TS, while the association of cell adhesion and trans-synaptic signaling gene set provides additional support for the role of adhesion molecules in neuropsychiatric disorders. This study reinforces previous findings but also provides new insights into the neurobiology of TS.

Cross-cultural adaptation and psychometric evaluation of the French version of the Gilles de la Tourette Syndrome Quality of Life Scale (GTS-QOL)

INTRODUCTION

The Gilles de la Tourette Syndrome-Quality of Life Scale (GTS-QOL) is a self-rated disease-specific questionnaire to assess health-related quality of life of subjects with GTS. Our aim was to perform the cross-cultural adaptation of the GTS-QOL into French and to assess its psychometric properties.

METHODS

The GTS-QOL was cross-culturally adapted by conducting forward and backward translations, following international guidelines. The psychometric properties of the GTS-QOL-French were assessed in 109 participants aged 16 years and above with regard to factor structure, internal consistency, reliability and convergent validity with the MOVES (Motor tic, Obsessions and compulsions, Vocal tic Evaluation Survey) and the WHOQOL-BREF (World Health Organization Quality of Life Brief).

RESULTS

Exploratory factor analysis of the GTS-QOL-French resulted in a 6-factor solution and did not replicate the original structure in four subscales. The results showed good acceptability (missing values per subscale ranging from 0% to 0.9%), good internal consistency (Cronbach's alpha ranging from 0.68 to 0.94) and good test-retest reliability (intraclass correlation coefficients ranging from 0.70 to 0.81). Convergent validity with the MOVES and WHOQOL-BREF scales showed high correlations.

DISCUSSION

Our study provides evidence of the good psychometric properties of the GTS-QOL-French. The cross-cultural adaptation and validation of this specific instrument will make it possible to assess health-related quality of life in French-speaking subjects with GTS. The GTS-QOL-French could be recommended for use in future research.

Tourette syndrome research highlights from 2019

This is the sixth yearly article in the Tourette Syndrome Research Highlights series, summarizing research from 2019 relevant to Tourette syndrome and other tic disorders. The highlights from 2020 is being drafted on the Authorea online authoring platform; readers are encouraged to add references or give feedback on our selections comments feature on this page. After the calendar year ends, this article is submitted as the annual update for the Tics collection F1000Research.