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Deep learning (DL) is one of the fastest-growing topics in materials data science, with rapidly emerging applications spanning atomistic, image-based, spectral, and textual data modalities. DL allows analysis of unstructured data and automated identification of features. The recent development of large materials databases has fueled the application of DL methods in atomistic prediction in particular. In contrast, advances in image and spectral data have largely leveraged synthetic data enabled by high-quality forward models as well as by generative unsupervised DL methods. In this article, we present a high-level overview of deep learning methods followed by a detailed discussion of recent developments of deep learning in atomistic simulation, materials imaging, spectral analysis, and natural language processing. For each modality we discuss applications involving both theoretical and experimental data, typical modeling approaches with their strengths and limitations, and relevant publicly available software and datasets. We conclude the review with a discussion of recent cross-cutting work related to uncertainty quantification in this field and a brief perspective on limitations, challenges, and potential growth areas for DL methods in materials science.

Organ fibroblasts are essential components of homeostatic and diseased tissues. They participate in sculpting the extracellular matrix, sensing the microenvironment, and communicating with other resident cells. Recent studies have revealed transcriptomic heterogeneity among fibroblasts within and between organs. To dissect the basis of interorgan heterogeneity, we compare the gene expression of murine fibroblasts from different tissues (tail, skin, lung, liver, heart, kidney, and gonads) and show that they display distinct positional and organ-specific transcriptome signatures that reflect their embryonic origins. We demonstrate that expression of genes typically attributed to the surrounding parenchyma by fibroblasts is established in embryonic development and largely maintained in culture, bioengineered tissues and ectopic transplants. Targeted knockdown of key organ-specific transcription factors affects fibroblast functions, in particular genes involved in the modulation of fibrosis and inflammation. In conclusion, our data reveal that adult fibroblasts maintain an embryonic gene expression signature inherited from their organ of origin, thereby increasing our understanding of adult fibroblast heterogeneity. The knowledge of this tissue-specific gene signature may assist in targeting fibrotic diseases in a more precise, organ-specific manner.

PURPOSE: We sought to investigate clinical outcomes of relapsed medulloblastoma and to compare molecular features between patient-matched diagnostic and relapsed tumors. METHODS: Children and infants enrolled on either SJMB03 (NCT00085202) or SJYC07 (NCT00602667) trials who experienced medulloblastoma relapse were analyzed for clinical outcomes, including anatomic and temporal patterns of relapse and postrelapse survival. A largely independent, paired molecular cohort was analyzed by DNA methylation array and next-generation sequencing. RESULTS: A total of 72 of 329 (22%) SJMB03 and 52 of 79 (66%) SJYC07 patients experienced relapse with significant representation of Group 3 and wingless tumors. Although most patients exhibited some distal disease (79%), 38% of patients with sonic hedgehog tumors experienced isolated local relapse. Time to relapse and postrelapse survival varied by molecular subgroup with longer latencies for patients with Group 4 tumors. Postrelapse radiation therapy among previously nonirradiated SJYC07 patients was associated with long-term survival. Reirradiation was only temporizing for SJMB03 patients. Among 127 patients with patient-matched tumor pairs, 9 (7%) experienced subsequent nonmedulloblastoma CNS malignancies. Subgroup (96%) and subtype (80%) stabilities were largely maintained among the remainder. Rare subgroup divergence was observed from Group 4 to Group 3 tumors, which is coincident with genetic alterations involving MYC, MYCN, and FBXW7. Subgroup-specific patterns of alteration were identified for driver genes and chromosome arms. CONCLUSION: Clinical behavior of relapsed medulloblastoma must be contextualized in terms of up-front therapies and molecular classifications. Group 4 tumors exhibit slower biological progression. Utility of radiation at relapse is dependent on patient age and prior treatments. Degree and patterns of molecular conservation at relapse vary by subgroup. Relapse tissue enables verification of molecular ta

Purpose: SJMB03 (ClinicalTrials.gov identifier: NCT00085202) was a phase III risk-adapted trial that aimed to determine the frequency and clinical significance of biological variants and genetic alterations in medulloblastoma. Patients and Methods: Patients 3-21 years old were stratified into average-risk and high-risk treatment groups based on metastatic status and extent of resection. Medulloblastomas were molecularly classified into subgroups (Wingless [WNT], Sonic Hedgehog [SHH], group 3, and group 4) and subtypes based on DNA methylation profiles and overlaid with gene mutations from next-generation sequencing. Coprimary study end points were (1) to assess the relationship between ERBB2 protein expression in tumors and progression-free survival (PFS), and (2) to estimate the frequency of mutations associated with WNT and SHH tumors. Clinical and molecular risk factors were evaluated, and the most robust were used to model new risk-classification categories. Results: Three hundred thirty eligible patients with medulloblastoma were enrolled. Five-year PFS was 83.2% (95% CI, 78.4 to 88.2) for average-risk patients (n = 227) and 58.7% (95% CI, 49.8 to 69.1) for high-risk patients (n = 103). No association was found between ERBB2 status and PFS in the overall cohort (P = .74) or when patients were stratified by clinical risk (P = .71). Mutations in CTNNB1 (96%), DDX3X (37%), and SMARCA4 (24%) were most common in WNT tumors and PTCH1 (38%), TP53 (21%), and DDX3X (19%) in SHH tumors. Methylome profiling classified 53 WNT (17.4%), 48 SHH (15.7%), 65 group 3 (21.3%), and 139 group 4 (45.6%) tumors. A comprehensive clinicomolecular risk factor analysis identified three low-risk groups (WNT, low-risk SHH, and low-risk combined groups 3 and 4) with excellent (5-year PFS > 90%) and two very high-risk groups (high-risk SHH and high-risk combined groups 3 and 4) with poor survival (5-year PFS < 60%). CONCLUSION These results establish a new risk stratification for future medu

Fertility preservation in the cancer setting, known as oncofertility, is a field that requires cross-disciplinary interaction between physicians, basic scientists, clinical researchers, ethicists, lawyers, educators, and religious leaders. Funded by the National Institutes of Health, the Oncofertility Consortium (OC) was formed to be a scientifically grounded, transparent, and altruistic resource, both intellectual and monetary, for building this new field of practice capable of addressing the unique needs of young patients with cancer. The OC has expanded its attention to include other nonmalignant conditions that can threaten fertility, and the work of the OC now extends around the globe, involving partners who together have created a community of shared effort, resources, and practices. The OC creates materials that are translated, disseminated, and amended by all participants in the field, and local programs of excellence have developed worldwide to accelerate the pace and improve the quality of oncofertility research and practice. Here we review the global oncofertility programs and the capacity building activities that strengthen these research and clinical programs, ultimately improving patient care.

Purpose: Sun-exposure can cause health problems, including melanoma and nonmelanoma skin cancer, especially in Australia where the incidence of skin cancer is particularly high. Childhood cancer survivors (CCSs) have an augmented risk due to previous cancer history and treatment. Despite recommendations advising sun protection, CCSs may be placing themselves at risk. We considered daily summer sun-exposure in an Australian cohort of CCSs and in community reference groups, and identified factors associated with sun-exposure in these populations. Methods: Summer sun-exposure data were collected on 471 CCSs (119 parents of survivors aged < 16, and 352 survivors aged ≥16) and a reference group of 470 participants from the community (155 parents of children aged < 16, and 355 adults aged ≥16). Survivors completed paper questionnaires and the reference groups completed an online survey. Medical records confirmed survivors’ clinical information. Ordinal logistic regressions identified factors associated with daily summer sun-exposure. Results: More daily summer sun-exposure was reported by both parents reporting for the young survivors (U = 5,522.5, P < .001; U = 31,412, P < .001) and by older survivors (U = 5,039.5, P < .001; U = 29,913, P < .001). Among younger participants greater sun-exposure was associated with being a CCS, while in older participants, greater sun-exposure was associated with being a CCS, a male, smoker/ex- smoker and was also increased in those with more sensitive skin reaction to sunlight. Focusing only on the CCSs, when treatments were considered, none statistically predicted sun-exposure in young CCSs while older CCSs who received radiotherapy were less likely to spend excess time in the sun. Conclusion: CCSs have sun-exposure at times of day when sun-related skin damage is highest, despite advice to avoid highest risk times. This data can inform sun-protection programs and lifestyle advice aimed at ameliorating the potential inc

Estimates of the number of childhood cancers with a genetic basis range from 5–8.5% found in germline samples to 29% based on clinical criteria. Family history-taking practice is a fundamental first step in detecting at risk individuals and families. This study focused on Li-Fraumeni Syndrome (LFS), a highly penetrant cancer syndrome. Reported family history in a cohort of 648 of cancer survivor cohort (CCS) was examined. Eligible CCS were: (i) aged up to 14 years at diagnosis; (ii) more than 5 years postdiagnosis; (iii) treated for a childhood cancer at the study hospitals in NSW, Australia; (iv) in remission for more than 3 years. CCS completed self-administered questionnaires. Medical records confirmed diagnosis and treatment-related information. Our findings reveal an increased cancer risk among sibling and relatives of CCS. 91% of siblings diagnosed with cancer were diagnosed under the age of 40 and about 30% diagnosed under the aged of 15 revealing a 5- (RR = 5.1; 95% CI, 3.3–7.9) and 44-fold (RR = 44.6; 95% CI, 18.4–108.3) increased risked of cancer compared with the Australian population, respectively. About 2% of CCS reported that they had been diagnosed with a genetic cancer syndrome. However, 11% of survivors described a family history pattern which met Chompret criteria for screening for TP53 mutations associated with LFS. Our data suggests that familial cancer predispositions may be initially overlooked. Aperiodic and accurate ascertainment of family cancer history of childhood cancer patients and survivors is therefore recommended.

Objective: Many survivors are disengaged from follow-up, mandating alternative models of survivorship-focused care for late effects surveillance. We explored survivors' barriers to accessing, and preferences for survivorship care. Methods: We invited Australian and New Zealand survivors of childhood cancer from three age groups: <16 years (represented by parents), 16-25 years (adolescent and young adults (AYAs)) and >25 years (older survivors'). Participants completed questionnaires and optional interviews. Results: 633 survivors/parents completed questionnaires: 187 parents of young survivors (mean age: 12.4 years), 251 AYAs (mean age: 20.6 years) and 195 older survivors (mean age: 32.5 years). Quantitative data were complemented by 151 in-depth interviews. Most participants, across all age groups, preferred specialised follow-up (ie, involving oncologists, nurses or a multidisciplinary team; 86%-97%). Many (36%-58%) were unwilling to receive community-based follow-up. More parents (75%) than AYAs (58%) and older survivors (30%) were engaged in specialised follow-up. While follow-up engagement was significantly lower in older survivors, survivors' prevalence of late effects increased. Of those attending a follow-up clinic, 34%-56% were satisfied with their care, compared with 14%-15% of those not receiving cancer-focused care (p<0.001). Commonly reported barriers included lack of awareness about follow-up availability (67%), followed by logistical (65%), care-related beliefs (59%) and financial reasons (57%). Older survivors (p<0.001), living outside major cities (p=0.008), and who were further from diagnosis (p=0.014) reported a higher number of barriers. Conclusions: Understanding patient-reported barriers, and tailoring care to survivors' follow-up preferences, may improve engagement with care and ensure that the survivorship needs of this population are met.

Background: Despite international evidence about fertility preservation (FP), several barriers still prevent the implementation of equitable FP practice. Currently, oncofertility competencies do not exist. The aim of this study was to develop an oncofertility competency framework that defines the key components of oncofertility care, develops a model for prioritizing service development, and defines the roles that health care professionals (HCPs) play. Materials and Method: A quantitative modified Delphi methodology was used to conduct two rounds of an electronic survey, querying and synthesizing opinions about statements regarding oncofertility care with HCPs and patient and family advocacy groups (PFAs) from 16 countries (12 high and 4 middle income). Statements included the roles of HCPs and priorities for service development care across ten domains (communication, oncofertility decision aids, age-appropriate care, referral pathways, documentation, oncofertility training, reproductive survivorship care and fertility-related psychosocial support, supportive care, and ethical frameworks) that represent 33 different elements of care. Results: The first questionnaire was completed by 457 participants (332 HCPs and 125 PFAs). One hundred and thirty-eight participants completed the second questionnaire (122 HCPs and 16 PFAs). Consensus was agreed on 108 oncofertility competencies and the roles HCPs should play in oncofertility care. A three-tier service development model is proposed, with gradual implementation of different components of care. A total of 92.8% of the 108 agreed competencies also had agreement between high and middle income participants. Conclusion: FP guidelines establish best practice but do not consider the skills and requirements to implement these guidelines. The competency framework gives HCPs and services a structure for the training of HCPs and implementation of care, as well as defining a model for prioritizing oncofertility service development

© The Author(s) 2018. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. BACKGROUND: Fertility preservation (FP) is an important quality of life issue for cancer survivors of reproductive age. Despite the existence of broad international guidelines, the delivery of oncofertility care, particularly amongst paediatric, adolescent and young adult patients, remains a challenge for healthcare professionals (HCPs). The quality of oncofertility care is variable and the uptake and utilization of FP remains low. Available guidelines fall short in providing adequate detail on how oncofertility models of care (MOC) allow for the real-world application of guidelines by HCPs. OBJECTIVE AND RATIONALE: The aim of this study was to systematically review the literature on the components of oncofertility care as defined by patient and clinician representatives, and identify the barriers, facilitators and challenges, so as to improve the implementation of oncofertility services. SEARCH METHODS: A systematic scoping review was conducted on oncofertility MOC literature published in English between 2007 and 2016, relating to 10 domains of care identified through consumer research: communication, oncofertility decision aids, age-appropriate care, referral pathways, documentation, training, supportive care during treatment, reproductive care after cancer treatment, psychosocial support and ethical practice of oncofertility care. A wide range of electronic databases (CINAHL, Embase, PsycINFO, PubMed, AEIPT, Education Research Complete, ProQuest and VOCED) were searched in order to synthesize the evidence around delivery of oncofertility care. Related citations and reference lists were searched. The review was undertaken following registration (International prospective register of systematic reviews (PROSPERO) registration number CRD42017055837) and guidelines of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRI