Billespears9824

8%) of these tumors were diagnosed radiographically. Incidence was higher in children aged 01-09 years compared to older children. Whites had a higher incidence compared to Blacks. However, the risk of death was higher among Blacks and Other race compared to Whites. There was no difference in survival by sex.

We report the most comprehensive incidence and survival data on these lethal brainstem HGGs. Incidence and survival among patients with brainstem HGGs differed significantly by race, ethnicity, age-groups and grade.

We report the most comprehensive incidence and survival data on these lethal brainstem HGGs. Incidence and survival among patients with brainstem HGGs differed significantly by race, ethnicity, age-groups and grade.

Knowledge on management of pediatric spinal cord low-grade glioma (LGG) is scarce.

We analyzed clinical datasets of 128 pediatric patients with spinal LGG followed within the prospective multicenter trials HIT-LGG 1996 (n=36), SIOP-LGG 2004 (n=56) and the subsequent LGG-Interim registry (n=36).

Spinal LGG, predominantly pilocytic astrocytomas (76%), harbored KIAA1549-BRAF fusion in 14/35 patients (40%) and FGFR1-TACC1 fusion in 3/26 patients (12%), as well as BRAFV600E mutation in 2/66 patients (3%). 10-year overall survival (OS) and event-free survival (EFS) was 93±2% and 38±5%, respectively. Disseminated disease (n=16) was associated with inferior OS and EFS, while age ≥11 years and total resection were favorable factors for EFS. We observed 117 patients following total (n=24) or subtotal/partial resection (n=74), biopsy (n=16), or radiologic diagnosis only (n=3). Eleven patients were treated first with chemotherapy (n=9) or irradiation (n=2). Up to 20.8 years after diagnosis/initial intervention 73/128 patients experienced one (n=43) or up to six (n=30) radiological/clinical disease progressions. Tumor resections were repeated in 36 patients (range, 2-6) and 47 patients required non-surgical treatment (chemotherapy, n=20; radiotherapy, n=10; multiple treatment lines, n=17). Long-term disease control for a median of 6.5 (range, 0.02-20) years was achieved in 73/77 patients following one (n=57) or repeated (n=16) resections, and in 35/47 patients after non-surgical treatment.

The majority of patients experienced disease progression, even after years. Multiple interventions were required for more than a third, yet multimodal treatment enabled long-term disease control. Molecular testing may reveal therapeutic targets.

The majority of patients experienced disease progression, even after years. Multiple interventions were required for more than a third, yet multimodal treatment enabled long-term disease control. Molecular testing may reveal therapeutic targets.

Analysis of genetic sequences is usually based on finding similar parts of sequences, e.g. DNA reads and/or genomes. For big data, this is typically done via "seeds" simple similarities (e.g. exact matches) that can be found quickly. For huge data, sparse seeding is useful, where we only consider seeds at a subset of positions in a sequence.

Here we study a simple sparse-seeding method using seeds at positions of certain "words" (e.g. ac, at, gc, or gt). Sensitivity is maximized by using words with minimal overlaps. That is because, in a random sequence, minimally-overlapping words are anti-clumped. We provide evidence that this is often superior to acclaimed "minimizer" sparse-seeding methods. Our approach can be unified with design of inexact (spaced and subset) seeds, further boosting sensitivity. Thus, we present a promising approach to sequence similarity search, with open questions on how to optimize it.

Software to design and test minimally-overlapping words is freely available at https//gitlab.com/mcfrith/noverlap.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.

Pre-existing conditions interfere with cancer diagnosis by offering diagnostic alternatives, competing for clinical attention or through patient surveillance.

To investigate associations between oesophagogastric cancer stage and pre-existing conditions.

Retrospective cohort study using Clinical Practice Research Datalink (CPRD) data, with English cancer registry linkage. Participants aged ≥40 years had consulted primary care in the year before their incident diagnosis of oesophagogastric cancer in 01/01/2010-31/12/2015. CPRD records pre-diagnosis were searched for codes denoting clinical features of oesophagogastric cancer and for pre-existing conditions, including those providing plausible diagnostic alternatives for those features. Logistic regression analysed associations between stage and multimorbidity (≥2 conditions; reference category no multimorbidity) and having 'diagnostic alternative(s)', controlling for age, sex, deprivation and cancer site.

Of 2444 participants provided, 695 (28%) were excluded for missing stage, leaving 1749 for analysis (1265/1749, 72.3% had advanced-stage disease). Multimorbidity was associated with stage [odds ratio 0.63, 95% confidence interval (CI) 0.47-0.85, P = 0.002], with moderate evidence of an interaction term with sex (1.76, 1.08-2.86, P = 0.024). There was no association between alternative explanations and stage (odds ratio 1.18, 95% CI 0.87-1.60, P = 0.278).

In men, multimorbidity is associated with a reduced chance of advanced-stage oesophagogastric cancer, to levels seen collectively for women.

In men, multimorbidity is associated with a reduced chance of advanced-stage oesophagogastric cancer, to levels seen collectively for women.

The complex role of urbanisation in heat-mortality risk has not been fully studied. Japan has experienced a rapid population increase and densification in metropolitan areas since the 2000s; we investigated the effects of population concentration in metropolitan areas on heat-mortality risk using nationwide data.

We collected time-series data for mortality and weather variables for all 47 prefectures in Japan (1980-2015). The prefectures were classified into three sub-areas based on population size lowest (<1500000), intermediate (1500000 to 3000000), and highest (>3000000; i.e. metropolitan areas). Regional indicators associated with the population concentration of metropolitan areas were obtained.

Since the 2000s, the population concentration intensified in the metropolitan areas, with the highest heat-mortality risk in prefectures with the highest population. Higher population density and apartment % as well as lower forest area and medical services were associated with higher heat-mortality risk; these associations have generally become stronger since the 2000s.

Population concentration in metropolitan areas intensified interregional disparities in demography, living environments, and medical services in Japan; these disparities were associated with higher heat-mortality risk. Our results can contribute to policies to reduce vulnerability to high temperatures.

Population concentration in metropolitan areas intensified interregional disparities in demography, living environments, and medical services in Japan; these disparities were associated with higher heat-mortality risk. Our results can contribute to policies to reduce vulnerability to high temperatures.

While over 150 thousand genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2.

Galaxy http//corgat.cloud.ba.infn.it/galaxy; software https//github.com/matteo14c/CorGAT/tree/Revision_V1; docker https//hub.docker.com/r/laniakeacloud/galaxy_corgat.

Supplementary data are available at Bioinformatics online.

Supplementary data are available at Bioinformatics online.

The COVID-19 pandemic has prompted an impressive, worldwide response by the academic community. 4-Methylumbelliferone nmr In order to support text mining approaches as well as data description, linking and harmonization in the context of COVID-19, we have developed an ontology representing major novel coronavirus (SARS-CoV-2) entities. The ontology has a strong scope on chemical entities suited for drug repurposing, as this is a major target of ongoing COVID-19 therapeutic development.

The ontology comprises 2.270 classes of concepts and 38.987 axioms (2622 logical axioms and 2434 declaration axioms). It depicts the roles of molecular and cellular entities in virus-host interactions and in the virus life cycle, as well as a wide spectrum of medical and epidemiological concepts linked to COVID-19. The performance of the ontology has been tested on Medline and the COVID-19 corpus provided by the Allen Institute.

COVID-19 Ontology is released under a Creative Commons 4.0 License and shared via https//github.com/covid-19-ontology/covid-19. The ontology is also deposited in BioPortal at https//bioportal.bioontology.org/ontologies/COVID-19.

COVID-19 Ontology is released under a Creative Commons 4.0 License and shared via https//github.com/covid-19-ontology/covid-19. The ontology is also deposited in BioPortal at https//bioportal.bioontology.org/ontologies/COVID-19.

Unbiased detection of protein-protein and protein-RNA interactions within ribonucleoprotein complexes are enabled through crosslinking followed by mass spectrometry. Yet, different methods detect different types of molecular interactions and therefore require the usage of different software packages with limited compatibility. We present crisscrosslinkeR, an R package that maps both protein-protein and protein-RNA interactions detected by different types of approaches for crosslinking with mass spectrometry. crisscrosslinkeR produces output files that are compatible with visualization using popular software packages for the generation of publication-quality figures.

crisscrosslinkeR is a free and open-source package, available through GitHub github.com/egmg726/crisscrosslinker.

Workflows are available at https//egmg726.github.io/crisscrosslinker/.

Workflows are available at https//egmg726.github.io/crisscrosslinker/.The prediction of epitope recognition by T-cell receptors (TCRs) has seen many advancements in recent years, with several methods now available that can predict recognition for a specific set of epitopes. However, the generic case of evaluating all possible TCR-epitope pairs remains challenging, mainly due to the high diversity of the interacting sequences and the limited amount of currently available training data. In this work, we provide an overview of the current state of this unsolved problem. First, we examine appropriate validation strategies to accurately assess the generalization performance of generic TCR-epitope recognition models when applied to both seen and unseen epitopes. In addition, we present a novel feature representation approach, which we call ImRex (interaction map recognition). This approach is based on the pairwise combination of physicochemical properties of the individual amino acids in the CDR3 and epitope sequences, which provides a convolutional neural network with the combined representation of both sequences.