Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability.

Microsatellite instability in colorectal cancer predicts favorable outcomes. However, the mechanistic relationship between microsatellite instability, tumor-infiltrating immune cells, Immunoscore, and their impact on patient survival remains to be elucidated. We found significant differences in mutational patterns, chromosomal instability, and gene expression that correlated with patient microsatellite instability status. A prominent immune gene expression was observed in microsatellite-instable (MSI) tumors, as well as in a subgroup of microsatellite-stable (MSS) tumors. MSI tumors had increased frameshift mutations, showed genetic evidence of immunoediting, had higher densities of Th1, effector-memory T cells, in situ proliferating T cells, and inhibitory PD1-PDL1 cells, had high Immunoscores, and were infiltrated with mutation-specific cytotoxic T cells. Multivariate analysis revealed that Immunoscore was superior to microsatellite instability in predicting patients' disease-specific recurrence and survival. These findings indicate that assessment of the immune status via Immunoscore provides a potent indicator of tumor recurrence beyond microsatellite-instability staging that could be an important guide for immunotherapy strategies.

The neural signature of the decision value of future pain.

Pain is a primary driver of action. We often must voluntarily accept pain to gain rewards. Conversely, we may sometimes forego potential rewards to avoid associated pain. In this study, we investigated how the brain represents the decision value of future pain. Participants (n = 57) performed an economic decision task, choosing to accept or reject offers combining various amounts of pain and money presented visually. Functional MRI (fMRI) was used to measure brain activity throughout the decision-making process. Using multivariate pattern analyses, we identified a distributed neural representation predicting the intensity of the potential future pain in each decision and participants' decisions to accept or avoid pain. This neural representation of the decision value of future pain included negative weights located in areas related to the valuation of rewards and positive weights in regions associated with saliency, negative affect, executive control, and goal-directed action. We further compared this representation to future monetary rewards, physical pain, and aversive pictures and found that the representation of future pain overlaps with that of aversive pictures but is distinct from experienced pain. Altogether, the findings of this study provide insights on the valuation processes of future pain and have broad potential implications for our understanding of disorders characterized by difficulties in balancing potential threats and rewards.

Neural representations of vicarious rewards are linked to interoception and prosocial behaviour.

Every day we constantly observe other people receiving rewards. Theoretical accounts posit that vicarious reward processing might be linked to people's sensitivity to internal body states (interoception) and facilitates a tendency to act prosocially. However, the neural processes underlying the links between vicarious reward processing, interoception, and prosocial behaviour are poorly understood. Previous research has linked vicarious reward processing to the anterior cingulate gyrus (ACCg) and the anterior insula (AI). Can we predict someone's propensity to be prosocial or to be aware of interoceptive signals from variability in how the ACCg and AI process rewards? Here, participants monitored rewards being delivered to themselves or a stranger during functional magnetic resonance imaging. Later, they performed a task measuring their willingness to exert effort to obtain rewards for others, and a task measuring their propensity to be aware and use interoceptive respiratory signals. Using multivariate similarity analysis, we show that people's willingness to be prosocial is predicted by greater similarity between self and other representations in the ACCg. Moreover, greater dissimilarity in self-other representations in the AI is linked to interoceptive propensity. These findings highlight that vicarious reward is linked to bodily signals in AI, and foster prosocial tendencies through the ACCg.

Variomes: a high recall search engine to support the curation of genomic variants.

MOTIVATION: Identification and interpretation of clinically actionable variants is a critical bottleneck. Searching for evidence in the literature is mandatory according to ASCO/AMP/CAP practice guidelines; however, it is both labor-intensive and error-prone. We developed a system to perform triage of publications relevant to support an evidence-based decision. The system is also able to prioritize variants. Our system searches within pre-annotated collections such as MEDLINE and PubMed Central. RESULTS: We assess the search effectiveness of the system using three different experimental settings: literature triage; variant prioritization and comparison of Variomes with LitVar. Almost two-thirds of the publications returned in the top-5 are relevant for clinical decision-support. Our approach enabled identifying 81.8% of clinically actionable variants in the top-3. Variomes retrieves on average +21.3% more articles than LitVar and returns the same number of results or more results than LitVar for 90% of the queries when tested on a set of 803 queries; thus, establishing a new baseline for searching the literature about variants. AVAILABILITY AND IMPLEMENTATION: Variomes is publicly available at https://candy.hesge.ch/Variomes. Source code is freely available at https://github.com/variomes/sibtm-variomes. SynVar is publicly available at https://goldorak.hesge.ch/synvar. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Systematic Review of In Vitro Antimicrobial Susceptibility Testing for Bacillus anthracis, 1947-2019.

Bacillus anthracis, the causative agent of anthrax, is a high-consequence bacterial pathogen that occurs naturally in many parts of the world and is considered an agent of biowarfare or bioterrorism. Understanding antimicrobial susceptibility profiles of B. anthracis isolates is foundational to treating naturally occurring outbreaks and to public health preparedness in the event of an intentional release. In this systematic review, we searched the peer-reviewed literature for all publications detailing antimicrobial susceptibility testing of B. anthracis. Within the set of discovered articles, we collated a subset of publications detailing susceptibility testing that followed standardized protocols for Food and Drug Administration-approved, commercially available antimicrobials. We analyzed the findings from the discovered articles, including the reported minimal inhibitory concentrations. Across the literature, most B. anthracis isolates were reported as susceptible to current first-line antimicrobials recommended for postexposure prophylaxis and treatment. The data presented for potential alternative antimicrobials will be of use if significant resistance to first-line antimicrobials arises, the strain is bioengineered, or first-line antimicrobials are not tolerated or available.

Circulating DNA changes are predictive of disease progression after transarterial chemoembolization.

Transarterial chemoembolization (TACE) is used to treat patients with unresectable hepatocellular carcinoma (HCC). We evaluated the clinical impact of a-fetoprotein (AFP) and circulating cell-free and tumor DNA (cfDNA and ctDNA) changes around the TACE procedure. Our prospective monocentric study enrolled consecutive patients treated with TACE, with samples collected at baseline (D - 1), Day 2 (D + 2) and 1 month (M + 1) after TACE. cfDNA was quantified by the fluorometric method, and ctDNA was quantified by digital polymerase chain reaction designed for two hotspot TERT mutations. Computerized tomography scans or magnetic resonance imaging were performed at M + 1 every 3 months following TACE and independently reviewed. The objective was to identify thresholds of cfDNA, ctDNA and AFP changes associated with progressive disease (PD) using receiver operating characteristic curves. Thirty-eight patients were included from March 2018 to March 2019. All markers significantly increased from D - 1 to D + 2 (P < .005), and cfDNA and ctDNA significantly decreased from D + 2 to M + 1 (P < .0001). The analysis of changes from D - 1 to M + 1 identified thresholds at +31.4% for cfDNA and 0% for ctDNA that were significantly associated with PD at M + 1 (44.4% [>+31.4%] vs 3.8% [≤+31.4%] and 50.0% [>0%] vs 5.0% [≤0%], respectively). No significant threshold was identified for AFP. Using a score combining cfDNA and ctDNA, the patients were classified into high- or low-risk PD groups at M + 1, with PD rates of 80.0% vs 4.3% (P = .001) and median progression-free survival times of 1.3 vs 10.3 months (P = .002). Our study suggests that cfDNA and ctDNA increases around the TACE procedure and are associated with therapeutic failure.

Beam Spray Thresholds in ICF-Relevant Plasmas.

Beam spray measurements suggest thresholds that are a factor of ≈2 to 15× less than expected based on the filamentation figure of merit often quoted in the literature. In this moderate-intensity regime, the relevant mechanism is forward stimulated Brillouin scattering. Both weak ion acoustic wave damping and thermal enhancement of ion acoustic waves contribute to the low thresholds. Forward stimulated Brillouin scattering imparts a redshift to the transmitted beam. Regarding the specific possibility of beam spray occurring outside the laser entrance holes of an indirectly driven hohlraum, this shift may be the most concerning feature owing to the high sensitivity of crossed-beam energy transfer to the interacting beam wavelengths in the subsequent overlap region.

SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts.

Thanks to recent efforts by the text mining community, biocurators have now access to plenty of good tools and Web interfaces for identifying and visualizing biomedical entities in literature. Yet, many of these systems start with a PubMed query, which is limited by strong Boolean constraints. Some semantic search engines exploit entities for Information Retrieval, and/or deliver relevance-based ranked results. Yet, they are not designed for supporting a specific curation workflow, and allow very limited control on the search process. The Swiss Institute of Bioinformatics Literature Services (SIBiLS) provide personalized Information Retrieval in the biological literature. Indeed, SIBiLS allow fully customizable search in semantically enriched contents, based on keywords and/or mapped biomedical entities from a growing set of standardized and legacy vocabularies. The services have been used and favourably evaluated to assist the curation of genes and gene products, by delivering customized literature triage engines to different curation teams. SIBiLS (https://candy.hesge.ch/SIBiLS) are freely accessible via REST APIs and are ready to empower any curation workflow, built on modern technologies scalable with big data: MongoDB and Elasticsearch. They cover MEDLINE and PubMed Central Open Access enriched by nearly 2 billion of mapped biomedical entities, and are daily updated.

The neXtProt knowledgebase in 2020: data, tools and usability improvements.

The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe the incorporation of three new data sets that provide expression, function, protein-protein binary interaction, post-translational modifications (PTM) and variant information. New SPARQL query examples illustrating uses of the new data were added. neXtProt has continued to develop tools for proteomics. We have improved the peptide uniqueness checker and have implemented a new protein digestion tool. Together, these tools make it possible to determine which proteases can be used to identify trypsin-resistant proteins by mass spectrometry. In terms of usability, we have finished revamping our web interface and completely rewritten our API. Our SPARQL endpoint now supports federated queries. All the neXtProt data are available via our user interface, API, SPARQL endpoint and FTP site, including the new PEFF 1.0 format files. Finally, the data on our FTP site is now CC BY 4.0 to promote its reuse.

A shift from phenol to silica-based leaf defences during long-term soil and ecosystem development.

The resource availability hypothesis predicts that plants adapted to infertile soils have high levels of anti-herbivore leaf defences. This hypothesis has been mostly explored for secondary metabolites such as phenolics, whereas it remains underexplored for silica-based defences. We determined leaf concentrations of total phenols and silicon (Si) in plants growing along the 2-million-year Jurien Bay chronosequence, exhibiting an extreme gradient of soil fertility. We found that nitrogen (N) limitation on young soils led to a greater expression of phenol-based defences, whereas old, phosphorus (P)-impoverished soils favoured silica-based defences. Both defence types were negatively correlated at the community and individual species level. Our results suggest a trade-off among these two leaf defence strategies based on the strength and type of nutrient limitation, thereby opening up new perspectives for the resource availability hypothesis and plant defence research. This study also highlights the importance of silica-based defences under low P supply.

CEA, CA19-9, circulating DNA and circulating tumour cell kinetics in patients treated for metastatic colorectal cancer (mCRC).

BACKGROUND: We previously reported that CEA kinetics are a marker of progressive disease (PD) in metastatic colorectal cancer (mCRC). This study was specifically designed to confirm CEA kinetics for predicting PD and to evaluate CA19-9, cell-free DNA (cfDNA), circulating tumour DNA (ctDNA) and circulating tumour cell (CTC) kinetics. METHODS: Patients starting a chemotherapy (CT) with pre-treatment CEA > 5 ng/mL and/or CA19.9 > 30 UI/mL were prospectively included. Samples were collected from baseline to cycle 4 for CEA and CA19-9 and at baseline and the sixth week for other markers. CEA kinetics were calculated from the first to the third or fourth CT cycle. RESULTS: A total of 192 mCRC patients were included. CEA kinetics based on the previously identified >0.05 threshold was significantly associated with PD (p < 0.0001). By dichotomising by the median value, cfDNA, ctDNA and CA19-9 were associated with PD, PFS and OS in multivariate analysis. A circulating scoring system (CSS) combining CEA kinetics and baseline CA19-9 and cfDNA values classified patients based on high (n = 58) and low risk (n = 113) of PD and was independently associated with PD (ORa = 4.6, p < 0.0001), PFS (HRa = 2.07, p < 0.0001) and OS (HRa = 2.55, p < 0.0001). CONCLUSIONS: CEA kinetics alone or combined with baseline CA19-9 and cfDNA are clinically relevant for predicting outcomes in mCRC. TRIAL REGISTRATION NUMBER: NCT01212510.

The Feature-Viewer: a visualization tool for positional annotations on a sequence.

SUMMARY: The Feature-Viewer is a lightweight library for the visualization of biological data mapped to a protein or nucleotide sequence. It is designed for ease of use while allowing for a full customization. The library is already used by several biological data resources and allows intuitive visual mapping of a full spectra of sequence features for different usages. AVAILABILITY AND IMPLEMENTATION: The Feature-Viewer is open source, compatible with state-of-the-art development technologies and responsive, also for mobile viewing. Documentation and usage examples are available online.

Nonlinear polarization transfer and control of two laser beams overlapping in a uniform nonlinear medium.

A scheme for polarization control using two laser beams in a non-linear optical medium is studied using both co- and counter-propagating beam geometries. In particular, we show that under certain conditions it is possible for two laser beams to exchange their polarization states. A model accounting for a more realistic, 2D propagation geometry is presented. The 2D model produces drastically different results (compared to the 1D propagation geometry), creating difficulties for implementing polarization control in a realistic setting. A proposal for overcoming these difficulties by reducing the non-linear optical medium to a thin slab is presented.

Socio-cognitive processing in people with eating disorders: Computerized tests of mentalizing, empathy and imitation skills.

OBJECTIVE: Eating disorders are psychiatric illnesses characterized by extreme eating behaviors, such as sustained food restriction or loss of control over eating. Symptoms are thought to be maintained by a variety of mechanisms, one of which may be the socio-cognitive impairments associated with eating disorders. While some previous work has addressed socio-cognitive impairments in eating disorders, this work has relied mostly on self-report data. METHOD: Here we employed computerized tests of (a) mentalizing (ability to infer the mental states of others); (b) empathy (the degree to which the emotional states of others can be identified and the degree to which the states of others impact one's own emotional state); and (c) imitation (the degree to which observation of another's actions prompts the performance of those actions); in a group of 78 women with an eating disorder and a matched control group of 66 healthy women. RESULTS: People with eating disorders showed both hyper- and hypo-mentalizing and reduced accuracy of emotional and cognitive mental state inference. They displayed less imitation of observed actions, but no differences in empathy compared to healthy controls. Although anxiety and depressive symptoms had significant effects on mentalizing, most of the observed inter-group differences persisted. DISCUSSION: Women with eating disorders have difficulties mentalizing and imitating observed actions despite intact non-social automatic imitation, compared to healthy controls. These findings provide an indication that intervention modules to strengthen specific areas of social cognition might be helpful to improve patients' social skills.

What is the Best Therapeutic Strategy for Metachronous Resectable Colorectal Liver Metastases After Adjuvant Oxaliplatin-Based Chemotherapy? A Multidisciplinary Inter-Group Survey.

BACKGROUND: To report the current clinical practice of French physicians for metachronous resectable liver metastasis (LM) occurring after a FOLFOX adjuvant chemotherapy for primary cancer. METHODS: Twenty four clinical situations were proposed to a panel of experts via 4 learned societies. Clinical situations varied according time of recurrence (early between 6 and 12 month or > 12 month), extension of LM (limited ≤ 2 or extended > 2 lesions), presence of a neuropathy or not, and of a RAS or BRAF mutation. RESULTS: A total of 157 physicians participated in this study. A consensus was reached in 17 (71%) clinical situations. For an early limited recurrence, whatever presence of neuropathy, the preferred therapeutic approach (45%) was upfront surgery. For an early extended recurrence, whatever presence of neuropathy, there was a consensus (64%) for a preoperative chemotherapy by FOLFIRI + biologic agent. For a late recurrence without neuropathy, there was a consensus (50%) for a preoperative FOLFOX chemotherapy, whatever the extension of LM. For a late recurrence with neuropathy, upfront surgery was chosen (52%) for limited LM, and preoperative chemotherapy by FOLFIRI + biologic agent (73%) for extended LM. No response was influenced by the RAS mutation status. There was a strong consensus for intensified preoperative chemotherapy in all clinical situations for BRAF-mutated LM. CONCLUSIONS: This national survey provides an overview of the practice patterns in the treatment of LM occurring after adjuvant FOLFOX for primary. It could be a basis to establish expert's recommendations for the clinical practice.

Aminotransferases disorders associated with venous thromboembolic events in patients infected with COVID-19.

INTRODUCTION AND OBJECTIVES: Since the outbreak of the COVID-19 pandemic, increasing evidence suggests that infected patients present a high incidence of venous thromboembolic (VTE) events and elevated aminotransferases (AT).The objective of this work was to evaluate the incidence of aminotransferases disorders in patients infected with COVID-19 and to manage the VTE events associated with elevated AT. PATIENTS OR MATERIALS AND METHODS: We report a retrospective study of 46 patients admitted for COVID-19 infection. Venous duplex ultrasound of lower limbs was performed in all patients at Day 0 and Day 5. All patients had antithrombotic-prophylaxis upon admission using low molecular weight heparin with Enoxaparin. Demographics, comorbidities and laboratory parameters were collected and analyzed. RESULTS: Elevated AT were reported in 28 patients (61%). 10 had acute VTE events of which eight (17.4%) had aminotransferases disorders. They had been treated with curative Enoxaparin. After a follow-up of 15 and/or 30 days, six of them were controlled, and treated with direct oral anticoagulant (DOACs) after normalization of aminotransferases. CONCLUSIONS: The incidence of aminotransferases disorders associated with acute VTE events in patients infected with COVID-19 is significant. The use of DOACs appear pertinent in these patients. Monitoring of the liver balance should therefore be considered at a distance from the acute episode in the perspective of DOACs relay.

A filter approach for feature selection in classification: application to automatic atrial fibrillation detection in electrocardiogram recordings.

BACKGROUND: In high-dimensional data analysis, the complexity of predictive models can be reduced by selecting the most relevant features, which is crucial to reduce data noise and increase model accuracy and interpretability. Thus, in the field of clinical decision making, only the most relevant features from a set of medical descriptors should be considered when determining whether a patient is healthy or not. This statistical approach known as feature selection can be performed through regression or classification, in a supervised or unsupervised manner. Several feature selection approaches using different mathematical concepts have been described in the literature. In the field of classification, a new approach has recently been proposed that uses the [Formula: see text]-metric, an index measuring separability between different classes in heart rhythm characterization. The present study proposes a filter approach for feature selection in classification using this [Formula: see text]-metric, and evaluates its application to automatic atrial fibrillation detection. METHODS: The stability and prediction performance of the [Formula: see text]-metric feature selection approach was evaluated using the support vector machine model on two heart rhythm datasets, one extracted from the PhysioNet database and the other from the database of Marseille University Hospital Center, France (Timone Hospital). Both datasets contained electrocardiogram recordings grouped into two classes: normal sinus rhythm and atrial fibrillation. The performance of this feature selection approach was compared to that of three other approaches, with the first two based on the Random Forest technique and the other on receiver operating characteristic curve analysis. RESULTS: The [Formula: see text]-metric approach showed satisfactory results, especially for models with a smaller number of features. For the training dataset, all prediction indicators were higher for our approach (accuracy greater than 99% for models with 5 to 17 features), as was stability (greater than 0.925 regardless of the number of features included in the model). For the validation dataset, the features selected with the [Formula: see text]-metric approach differed from those selected with the other approaches; sensitivity was higher for our approach, but other indicators were similar. CONCLUSION: This filter approach for feature selection in classification opens up new methodological avenues for atrial fibrillation detection using short electrocardiogram recordings.

Rapid Nanopore Whole-Genome Sequencing for Anthrax Emergency Preparedness.

Human anthrax cases necessitate rapid response. We completed Bacillus anthracis nanopore whole-genome sequencing in our high-containment laboratory from a human anthrax isolate hours after receipt. The de novo assembled genome showed no evidence of known antimicrobial resistance genes or introduced plasmid(s). Same-day genomic characterization enhances public health emergency response.

Withholding the Introduction of Anti-Epidermal Growth Factor Receptor: Impact on Outcomes in RAS Wild-Type Metastatic Colorectal Tumors: A Multicenter AGEO Study (the WAIT or ACT Study).

BACKGROUND: Patients with RAS wild-type (WT) nonresectable metastatic colorectal cancer (mCRC) may receive either bevacizumab or an anti-epidermal growth factor receptor (EGFR) combined with first-line, 5-fluorouracil-based chemotherapy. Without the RAS status information, the oncologist can either start chemotherapy with bevacizumab or wait for the introduction of the anti-EGFR. Our objective was to compare both strategies in a routine practice setting. MATERIALS AND METHODS: This multicenter, retrospective, propensity score-weighted study included patients with a RAS WT nonresectable mCRC, treated between 2013 and 2016 by a 5-FU-based chemotherapy, with either delayed anti-EGFR or immediate anti-vascular endothelial growth factor (VEGF). Primary criterion was overall survival (OS). Secondary criteria were progression-free survival (PFS) and objective response rate (ORR). RESULTS: A total of 262 patients (129 in the anti-VEGF group and 133 in the anti-EGFR group) were included. Patients receiving an anti-VEGF were more often men (68% vs. 56%), with more metastatic sites (>2 sites: 15% vs. 9%). The median delay to obtain the RAS status was 19 days (interquartile range: 13-26). Median OS was not significantly different in the two groups (29 vs. 30.5 months, p = .299), even after weighting on the propensity score (hazard ratio [HR] = 0.86, 95% confidence interval [CI], 0.69-1.08, p = .2024). The delayed introduction of anti-EGFR was associated with better median PFS (13.8 vs. 11.0 months, p = .0244), even after weighting on the propensity score (HR = 0.74, 95% CI, 0.61-0.90, p = .0024). ORR was significantly higher in the anti-EGFR group (66.7% vs. 45.6%, p = .0007). CONCLUSION: Delayed introduction of anti-EGFR had no deleterious effect on OS, PFS, and ORR, compared with doublet chemotherapy with anti-VEGF. IMPLICATIONS FOR PRACTICE: For RAS/RAF wild-type metastatic colorectal cancer, patients may receive 5-fluorouracil-based chemotherapy plus either bevacizumab or an anti-epidermal growth factor receptor (EGFR). In daily practice, the time to obtain the RAS status might be long enough to consider two options: to start the chemotherapy with bevacizumab, or to start without a targeted therapy and to add the anti-EGFR at reception of the RAS status. This study found no deleterious effect of the delayed introduction of an anti-EGFR on survival, compared with the introduction of an anti-vascular endothelial growth factor from cycle 1. It is possible to wait one or two cycles to introduce the anti-EGFR while waiting for RAS status.

The Day after Tomorrow: How Should We Address Health System Organization to Treat Cancer Patients after the Peak of the COVID-19 Epidemic?

On March 11, 2020, the WHO director general declared COVID-19 a pandemic. This pandemic evolves in successive phases, i.e., phase 1 (the start phase), phase 2 ("the storm"), and phase 3 (the recession). To date, oncology and surgery groups have only given instructions for addressing phases 1 and 2. To prevent excess cancer mortality, health care systems (HCS) need to be restructured. Our aim is to detail the specificities of each epidemic phase and discuss several methods of organization to optimize cancer patient flow during the COVID-19 pandemic, particularly during phase 3. Hospitals must be reorganized in order to create a cancer hub that is free of infection, allowing for the safe treatment of patients. Hospital structures are different, but all allow for the creation of virus-free areas. Screening programs are critical and need to be applied to all people entering the virus-free zone, including health care workers. Some reorganization proposals are internal to a hospital, while others require interhospital collaboration. The heterogeneity and complexity of HCS will make interhospital management difficult. The ministry of health has an important role in managing the cancer crisis. Cancer management should be declared a priority. Oncological and surgical societies must coordinate their efforts to facilitate this prioritization. The anticipation of oncological management during phase 3 of the pandemic is necessary because it requires a complete readjustment of HCS. This adaptation should allow for the continuation of cancer care to prevent excess cancer mortality, as the virus will still be present for a currently undetermined period of time.