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Pediatric burn injuries can alter the trajectory of the survivor's entire life. Patient-centered outcome measures are helpful to assess unique physical and psychosocial needs and long-term recovery. This study aimed to develop a conceptual framework to measure pediatric burn outcomes in survivors aged 5 to 12 years as a part of the School-Aged Life Impact Burn Recovery Evaluation Computer Adaptive Test (SA-LIBRE5-12 CAT) development. This study conducted a systematic literature review guided by the WHO International Classification of Functioning-Child and Youth and domains in the American Burn Association/Shriners Hospitals for Children Burn Outcomes Questionnaire5-18. Interviews with eight parents and seven clinicians were conducted to identify important domains in child recovery. One clinician focus group with four clinicians was completed to identify gaps in the preliminary framework, and semiweekly expert consensus meetings were conducted with three experts to solidify the framework. Qualitative data were analyzed by grounded theory methodology. Three major thematic outcome domains emerged: 1) Physical Functioning: fine motor and upper extremity, gross motor and lower extremity, pain, skin symptoms, sleep and fatigue, and physical resilience; 2) Psychological Functioning: cognitive, behavioral, emotional, resilience, and body image; and 3) Family and Social Functioning: family relationships, and parental satisfaction, school, peer relations, and community participation. The framework will be used to develop item banks for a CAT-based assessment of school-aged children's health and developmental outcomes, which will be designed for clinical and research use to optimize interventions, personalize care, and improve long-term health outcomes for burned children.

Modern, reliable, and valid outcome measures are essential to understanding the health needs of young children with burn injuries. Burn-specific and age-appropriate legacy assessment tools exist for this population but are hindered by the limitations of existing paper-based instruments. The purpose of this study was to develop item pools comprised of questions appropriate for children aged 1-5 with burn injuries. Item development was based on a framework provided by previous work to develop the Preschool Life Impact Burn Recovery Evaluation (LIBRE) Conceptual Model. The Preschool LIBRE Conceptual Model work established four sub-domains of functioning for children with burns aged 1-5. Item development involved a systematic literature review, a qualitative item review process with clinical experts, and parent cognitive interviews. Four item pools were established: (1) communication and language development; (2) physical functioning; (3) psychological functioning and (4) social functioning for preschool-aged children with burn injuries. We selected and refined candidate items, recall periods, survey instructions, and response option choices through clinical and parental feedback during the qualitative review and cognitive interview processes. Item pools are currently being field-tested as part of the process to calibrate and validate the Preschool1-5 LIBRE Computer Adaptive Test (CAT) Profile.

Analysis of the different methods of teaching English has become increasingly important as the subject of global Englishes receives greater attention. In Asia, more educators have been using textbooks that are culturally specific in their design; however, a limited number of studies have been conducted that demonstrate their practical efficacy. Building on a preliminary study into the effectiveness of culturally familiar materials in EFL education in Japan, a crossover study using both quantitative and qualitative methods was conducted to examine the influence of cultural familiarity on university students' reading comprehension, vocabulary retention, and interest in the texts. Seventy-eight lower-intermediate level EFL students from four intact classes were divided into two groups with equivalent vocabulary proficiency. Participants read four simplified newspaper articles that contained culturally familiar or unfamiliar proper nouns allocated using a crossover design. Pre- and post-lesson tests were used to gauge the effectiveness of culturally familiar proper nouns on reading comprehension, vocabulary retention, and interest of each article. The results revealed that students who read the culturally familiar version of the articles scored higher in reading comprehension and vocabulary retention, and generally reported greater interest and engagement. These findings provide important insights to EFL educators, learners and material designers.

Due to the rapid developmental growth in preschool-aged children, more precise measurement of the effects of burns on child health outcomes is needed. Expanding upon the Shriners Hospitals for Children/American Burn Association Burn Outcome Questionnaire 0 to 5 (BOQ0-5), we developed a conceptual framework describing domains important in assessing recovery from burn injury among preschool-aged children (1-5 years). We developed a working conceptual framework based on the BOQ0-5, the National Research Council and Institute of Medicines Model of Child Health, and the World Health Organizations International Classification of Functioning, Disability, and Health for Children and Youth. We iteratively refined our framework based on a literature review, focus groups, interviews, and expert consensus meetings. Data were qualitatively analyzed using methods informed by grounded theory. We reviewed 95 pediatric assessments, conducted two clinician focus groups and six parent interviews, and consulted with 23 clinician experts. Three child health outcome domains emerged from our analysis: symptoms, functioning, and family. The symptoms domain describes parents perceptions of their childs pain, skin-related discomfort, and fatigue. The functioning domain describes childrens physical functioning (gross and fine motor function), psychological functioning (internalizing, externalizing, and dysregulation behavior; trauma; toileting; resilience), communication and language development (receiving and producing meaning), and social functioning (connecting with family/peers, friendships, and play). The family domain describes family psychological and routine functioning outcomes.

Due to the rapid developmental growth in preschool-aged children, more precise measurement of the effects of burns on child health outcomes is needed. Expanding upon the Shriners Hospitals for Children/American Burn Association Burn Outcome Questionnaire 0 to 5 (BOQ0-5), we developed a conceptual framework describing domains important in assessing recovery from burn injury among preschool-aged children (1-5 years). We developed a working conceptual framework based on the BOQ0-5, the National Research Council and Institute of Medicine's Model of Child Health, and the World Health Organization's International Classification of Functioning, Disability, and Health for Children and Youth. We iteratively refined our framework based on a literature review, focus groups, interviews, and expert consensus meetings. Data were qualitatively analyzed using methods informed by grounded theory. We reviewed 95 pediatric assessments, conducted two clinician focus groups and six parent interviews, and consulted with 23 clinician experts. Three child health outcome domains emerged from our analysis: symptoms, functioning, and family. The symptoms domain describes parents' perceptions of their child's pain, skin-related discomfort, and fatigue. The functioning domain describes children's physical functioning (gross and fine motor function), psychological functioning (internalizing, externalizing, and dysregulation behavior; trauma; toileting; resilience), communication and language development (receiving and producing meaning), and social functioning (connecting with family/peers, friendships, and play). The family domain describes family psychological and routine functioning outcomes.

Despite the vast extent of the English vocabulary, it has been estimated that only around 2400 high frequency word families, which are found on Browne, Culligan, and Phillips' (2013) "New General Service List" (NGSL), make up over 92% of most general English texts. Several studies have shown that a word must be encountered anywhere from six (Saragi, Nation, & Meister, 1978; Rott, 1999) to 20 times (Herman, Anderson, Pearson, & Nagy, 1987) for a learner to acquire it. Unfortunately, many EFL textbooks do not adequately recycle high frequency vocabulary and learners may not have enough encounters with these critical words in their language classes (Nation, 1993). This raises the question of how teachers can ensure learners encounter high frequency vocabulary on a regular basis. In this paper, we describe how learner made vocabulary cards help students initially learn the lexical items found on the NGSL and other important special purpose vocabulary lists. We then present a variety of engaging cooperative learning activities that reinforce the learning of these lexical items, thereby overcoming the lack of recycling in most EFL textbooks. These exciting activities have been well received by learners across levels in a variety of EFL contexts.

Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, and microRNAs in 5,185 TCGA tumors and 1,019 ENCODE assays. Our predictions included hundreds of candidate onco- and tumor-suppressor lncRNAs (cancer lncRNAs) whose somatic alterations account for the dysregulation of dozens of cancer genes and pathways in each of 14 tumor contexts. To demonstrate proof of concept, we showed that perturbations targeting OIP5-AS1 (an inferred tumor suppressor) and TUG1 and WT1-AS (inferred onco-lncRNAs) dysregulated cancer genes and altered proliferation of breast and gynecologic cancer cells. Our analysis indicates that, although most lncRNAs are dysregulated in a tumor-specific manner, some, including OIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergistically dysregulate cancer pathways in multiple tumor contexts.

Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA), and we identified 119 splicing factor genes with significant non-silent mutation patterns, including mutation over-representation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). Furthermore, RNA sequencing analysis revealed altered splicing events associated with selected splicing factor mutations. In addition, we were able to identify common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of genes involved in the RNA-splicing process is common in cancer and may represent an underappreciated hallmark of tumorigenesis.

Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atlas, we perform comprehensive molecular characterization of 929 ubiquitin-related genes and 95 deubiquitinase genes. Among them, we systematically identify top somatic driver candidates, including mutated FBXW7 with cancer-type-specific patterns and amplified MDM2 showing a mutually exclusive pattern with BRAF mutations. Ubiquitin pathway genes tend to be upregulated in cancer mediated by diverse mechanisms. By integrating pan-cancer multiomic data, we identify a group of tumor samples that exhibit worse prognosis. These samples are consistently associated with the upregulation of cell-cycle and DNA repair pathways, characterized by mutated TP53, MYC/TERT amplification, and APC/PTEN deletion. Our analysis highlights the importance of the ubiquitin pathway in cancer development and lays a foundation for developing relevant therapeutic strategies.

We characterized the epigenetic landscape of genes encoding long noncoding RNAs (lncRNAs) across 6,475 tumors and 455 cancer cell lines. In stark contrast to the CpG island hypermethylation phenotype in cancer, we observed a recurrent hypomethylation of 1,006 lncRNA genes in cancer, including EPIC1 (epigenetically-induced lncRNA1). Overexpression of EPIC1 is associated with poor prognosis in luminal B breast cancer patients and enhances tumor growth in vitro and in vivo. Mechanistically, EPIC1 promotes cell-cycle progression by interacting with MYC through EPIC1's 129-283 nt region. EPIC1 knockdown reduces the occupancy of MYC to its target genes (e.g., CDKN1A, CCNA2, CDC20, and CDC45). MYC depletion abolishes EPIC1's regulation of MYC target and luminal breast cancer tumorigenesis in vitro and in vivo.

The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on "chromatin-state" to explain their interplay. Integrating eQTL, mRNA co-expression, and Hi-C data analysis, we developed a computational method to infer causal enhancer-gene interactions, revealing enhancers of clinically actionable genes. Having identified an enhancer ∼140 kb downstream of PD-L1, a major immunotherapy target, we validated it experimentally. This study provides a systematic view of enhancer activity in diverse tumor contexts and suggests the clinical implications of enhancers.

Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression of proliferation genes. Aneuploidy was anti-correlated with expression of immune signaling genes, due to decreased leukocyte infiltrates in high-aneuploidy samples. Chromosome arm-level alterations show cancer-specific patterns, including loss of chromosome arm 3p in squamous cancers. We applied genome engineering to delete 3p in lung cells, causing decreased proliferation rescued in part by chromosome 3 duplication. This study defines genomic and phenotypic correlates of cancer aneuploidy and provides an experimental approach to study chromosome arm aneuploidy.

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumor-infiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy.

Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may respond. The transcriptome of these "hidden responders" may reveal responsive molecular states. We describe and evaluate a machine-learning approach to classify aberrant pathway activity in tumors, which may aid in hidden responder identification. The algorithm integrates RNA-seq, copy number, and mutations from 33 different cancer types across The Cancer Genome Atlas (TCGA) PanCanAtlas project to predict aberrant molecular states in tumors. Applied to the Ras pathway, the method detects Ras activation across cancer types and identifies phenocopying variants. The model, trained on human tumors, can predict response to MEK inhibitors in wild-type Ras cell lines. We also present data that suggest that multiple hits in the Ras pathway confer increased Ras activity. The transcriptome is underused in precision oncology and, combined with machine learning, can aid in the identification of hidden responders.

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale.

Restorative sleep is an important component of quality of life. Disturbances in sleep after burn injury were reported but all based on uncontrolled or nonstandardized data. The occurrence and the effect of long-term sleep problems in young adult burn survivors have not been well defined. This 5-year (2003-2008) prospective multicenter longitudinal study included adults with burn injuries ages 19 to 30 years who completed the Young Adult Burn Outcome Questionnaire (YABOQ) up to 36 months after injury. The items measured 15 patient-reported outcomes including physical, psychological, and social statuses and symptoms such as itch and pain. Scores of these 15 YABOQ outcome domains were standardized to a mean of 50 and a SD of 10 based on an age-matched nonburned reference group of young adults. Sleep quality was assessed using the item 'How satisfied are you now with your sleep,' rated by a 5-point Likert scale. Patients responding with very and somewhat dissatisfied were classified as having sleep dissatisfaction and the remaining as less or not dissatisfied. The associations between sleep dissatisfaction (yes/no) and YABOQ outcome domains were analyzed longitudinally using mixed-effect generalized linear models, adjusted for %TBSA burned, age, gender, and race. Generalized estimating equations were used to take into account correlated error resulting from repeated surveys on each patient over time. One hundred and fifty-two burn survivors participated in the YABOQ survey at baseline and during the follow-up who had at least one survey with a response to the sleep item. Among them, sleep dissatisfaction was twice as prevalent (76/152, 50%) when compared with the nonburned reference group (29/112, 26%). The likelihood of a burn survivor being dissatisfied with sleep was reduced over time after the burn injury. Sleep dissatisfaction following burns was significantly associated, in a dose-dependent manner, with increasing burn size (P = .001). Better sleep was associated with better outcomes in all domains (P < .05) except Fine Motor Function, and this association was significantly more apparent in the longer term compared with the shorter term with the same domains (P < .05). Dissatisfaction with sleep is highly prevalent following burn injuries in young adults. Lower satisfaction with sleep is associated with poorer scores in nearly all quality of life measures. Satisfaction with sleep should be addressed during the long-term clinical follow-up of young adults with burn injuries. Further research should be undertaken to understand the components of sleep quality that are important to burn survivors and which ones might be modified and tested in future intervention studies.

The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is 'web ready': written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components.Availability and implementationThe MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/Supplementary information: Supplementary data are available at Bioinformatics online.Contactmsa@bio.sh.

With the growing importance of the United Nations' SDGs, many EFL textbooks addressing the goals have been developed. However, these textbooks generally discuss the applicability of the SDGs in Global South countries, and for university students in Japan, this has resulted in "SDG burnout," as they study the topic but often fail to find meaningful connections to the materials. This article builds on previous research into the efficacy of culturally familiar materials, and it takes SDG education in a new direction through the creation of materials in dialogue with social justice issues. Four lessons were created by the researchers, and as part of the post-reading assignment, learners had the autonomy to choose between culturally familiar or unfamiliar activities related to either the news or popular culture. A 6-point Likert scale was used to gauge student interest, which indicated that the inclusion of social justice issues may positively affect interest. A series of binomial tests revealed that learners preferred culturally familiar activities and activities related to the news. These findings provide important implications for teaching the SDGs as they suggest learners might be most receptive to culturally familiar materials that are based on the news and connected to issues of social justice. [ABSTRACT FROM AUTHOR]