A Comprehensive Review of Recent Variants and Modifications of Firefly Algorithm

Swarm intelligence (SI) is an emerging field of biologically-inspired artificial intelligence based on the behavioral models of social insects such as ants, bees, wasps, termites etc. Swarm intelligence is the discipline that deals with natural and artificial systems composed of many individuals that coordinate using decentralized control and self-organization. Most SI algorithms have been developed to address stationary optimization problems and hence, they can converge on the (near-) optimum solution efficiently. However, many real-world problems have a dynamic environment that changes over time. In the last two decades, there has been a growing interest of addressing Dynamic Optimization Problems using SI algorithms due to their adaptation capabilities. This paper presents a broad review on two SI algorithms: 1) Firefly Algorithm (FA) 2) Flower Pollination Algorithm (FPA). FA is inspired from bioluminescence characteristic of fireflies. FPA is inspired from the the pollination behavior of flowering plants. This article aims to give a detailed analysis of different variants of FA and FPA developed by parameter adaptations, modification, hybridization as on date. This paper also addresses the applications of these algorithms in various fields. In addition, literatures found that most of the cases that used FA and FPA technique have outperformed compare to other metaheuristic algorithms

Expansion of Metallic Cylinders under Explosive Loading

The behaviour of expanding metallic cylinders under explosive loading was studied. Using ultra high speed photography, the expansion characteristics of aluminium and copper metallic cylinders have been evaluated with different c/m ratio, and by changing the nature of high explosive. The results obtained are comparable to those predicted by the Gurney's energy and momentum balance equations. A cylinder test has been established for comparative to the metal by octol, TNT, PEK-1, baratol and composition B are calculated. The results are in close agreement with those calculated by Kury et al

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

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. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

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

The prevalence and socio-demographic associations of household food insecurity in seven slum sites across Nigeria, Kenya, Pakistan, and Bangladesh. A cross-sectional study

Although the proportion of people living in slums is increasing in low- and middle-income countries and food insecurity is considered a severe hazard for health, there is little research on this topic. This study investigated and compared the prevalence and socio-demographic associations of household food insecurity in seven slum settings across Nigeria, Kenya, Pakistan, and Bangladesh. Data were taken from a cross-sectional, household-based, spatially referenced survey conducted between December 2018 and June 2020. Household characteristics and the extent and distribution of food insecurity across sites was established using descriptive statistics. Multivariable logistic regression of data in a pooled model including all slums (adjusting for slum site) and site-specific analyses were conducted. In total, a sample of 6,111 households were included. Forty-one per cent (2,671) of all households reported food insecurity, with varying levels between the different slums (9-69%). Household head working status and national wealth quintiles were consistently found to be associated with household food security in the pooled analysis (OR: 0·82; CI: 0·69-0·98 & OR: 0·65; CI: 0·57-0·75) and in the individual sites. Households which owned agricultural land (OR: 0·80; CI: 0·69-0·94) were less likely to report food insecurity. The association of the household head's migration status with food insecurity varied considerably between sites. We found a high prevalence of household food insecurity which varied across slum sites and household characteristics. Food security in slum settings needs context-specific interventions and further causal clarification

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. We found 61 somatic copy-number alterations (SCNAs) and 46 significantly mutated genes (SMGs). Eleven SCNAs and 11 SMGs had not been identified in previous TCGA studies of the individual tumor types. We found functionally significant estrogen receptor-regulated long non-coding RNAs (lncRNAs) and gene/lncRNA interaction networks. Pathway analysis identified subtypes with high leukocyte infiltration, raising potential implications for immunotherapy. Using 16 key molecular features, we identified five prognostic subtypes and developed a decision tree that classified patients into the subtypes based on just six features that are assessable in clinical laboratories. By performing molecular analyses of 2,579 TCGA gynecological (OV, UCEC, CESC, and UCS) and breast tumors, Berger et al. identify five prognostic subtypes using 16 key molecular features and propose a decision tree based on six clinically assessable features that classifies patients into the subtypes

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

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. Chiu et al. present a pan-cancer analysis of lncRNA regulatory interactions. They suggest that the dysregulation of hundreds of lncRNAs target and alter the expression of cancer genes and pathways in each tumor context. This implies that hundreds of lncRNAs can alter tumor phenotypes in each tumor context

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

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. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

The Cancer Genome Atlas (TCGA) has catalyzed systematic characterization of diverse genomic alterations underlying human cancers. At this historic junction marking the completion of genomic characterization of over 11,000 tumors from 33 cancer types, we present our current understanding of the molecular processes governing oncogenesis. We illustrate our insights into cancer through synthesis of the findings of the TCGA PanCancer Atlas project on three facets of oncogenesis: (1) somatic driver mutations, germline pathogenic variants, and their interactions in the tumor; (2) the influence of the tumor genome and epigenome on transcriptome and proteome; and (3) the relationship between tumor and the microenvironment, including implications for drugs targeting driver events and immunotherapies. These results will anchor future characterization of rare and common tumor types, primary and relapsed tumors, and cancers across ancestry groups and will guide the deployment of clinical genomic sequencing