• Curcumin as an anticancer agent in malignant mesothelioma: A review

      Baldi, A; De Luca, A; Maiorano, P; D’angelo, C; Giordano, A; Giordano, Antonio|0000-0002-5959-016X (2020-03-01)
      © 2020 by the authors. Licensee MDPI, Basel, Switzerland. Malignant mesothelioma is an infrequent tumor that initiates from the mesothelial cells lining of body cavities. The great majority of mesotheliomas originate in the pleural cavity, while the remaining cases initiate in the peritoneal cavity, in the pericardial cavity or on the tunica vaginalis. Usually, mesotheliomas grow in a diffuse pattern and tend to enclose and compress the organs in the various body cavities. Mesothelioma incidence is increasing worldwide and still today, the prognosis is very poor, with a reported median survival of approximately one year from presentation. Thus, the development of alternative and more effective therapies is currently an urgent requirement. The aim of this review article was to describe recent findings about the anti-cancer activity of curcumin and some of its derivatives on mesotheliomas. The potential clinical implications of these findings are discussed.
    • Decision aids that facilitate elements of shared decision making in chronic illnesses: A systematic review

      Wieringa, TH; Rodriguez-Gutierrez, R; Spencer-Bonilla, G; De Wit, M; Ponce, OJ; Sanchez-Herrera, MF; Espinoza, NR; Zisman-Ilani, Y; Kunneman, M; Schoonmade, LJ; Montori, VM; Snoek, FJ (2019-05-20)
      © 2019 The Author(s). Background: Shared decision making (SDM) is a patient-centered approach in which clinicians and patients work together to find and choose the best course of action for each patient's particular situation. Six SDM key elements can be identified: situation diagnosis, choice awareness, option clarification, discussion of harms and benefits, deliberation of patient preferences, and making the decision. The International Patient Decision Aid Standards (IPDAS) require that a decision aid (DA) support these key elements. Yet, the extent to which DAs support these six key SDM elements and how this relates to their impact remain unknown. Methods: We searched bibliographic databases (from inception until November 2017), reference lists of included studies, trial registries, and experts for randomized controlled trials of DAs in patients with cardiovascular, or chronic respiratory conditions or diabetes. Reviewers worked in duplicate and independently selected studies for inclusion, extracted trial, and DA characteristics, and evaluated the quality of each trial. Results: DAs most commonly clarified options (20 of 20; 100%) and discussed their harms and benefits (18 of 20; 90%; unclear in two DAs); all six elements were clearly supported in 4 DAs (20%). We found no association between the presence of these elements and SDM outcomes. Conclusions: DAs for selected chronic conditions are mostly designed to transfer information about options and their harms and benefits. The extent to which their support of SDM key elements relates to their impact on SDM outcomes could not be ascertained. Systematic review registration: PROSPERO registration number: CRD42016050320.
    • Developing a community-based genetic nomenclature for anole lizards

      Kusumi, K; Kulathinal, RJ; Abzhanov, A; Boissinot, S; Crawford, NG; Faircloth, BC; Glenn, TC; Janes, DE; Losos, JB; Menke, DB; Poe, S; Sanger, TJ; Schneider, CJ; Stapley, J; Wade, J; Wilson-Rawls, J; Kulathinal, Rob|0000-0003-1907-2744 (2011-11-11)
      Background: Comparative studies of amniotes have been hindered by a dearth of reptilian molecular sequences. With the genomic assembly of the green anole, Anolis carolinensis available, non-avian reptilian genes can now be compared to mammalian, avian, and amphibian homologs. Furthermore, with more than 350 extant species in the genus Anolis, anoles are an unparalleled example of tetrapod genetic diversity and divergence. As an important ecological, genetic and now genomic reference, it is imperative to develop a standardized Anolis gene nomenclature alongside associated vocabularies and other useful metrics.Results: Here we report the formation of the Anolis Gene Nomenclature Committee (AGNC) and propose a standardized evolutionary characterization code that will help researchers to define gene orthology and paralogy with tetrapod homologs, provide a system for naming novel genes in Anolis and other reptiles, furnish abbreviations to facilitate comparative studies among the Anolis species and related iguanid squamates, and classify the geographical origins of Anolis subpopulations.Conclusions: This report has been generated in close consultation with members of the Anolis and genomic research communities, and using public database resources including NCBI and Ensembl. Updates will continue to be regularly posted to new research community websites such as lizardbase. We anticipate that this standardized gene nomenclature will facilitate the accessibility of reptilian sequences for comparative studies among tetrapods and will further serve as a template for other communities in their sequencing and annotation initiatives. © 2011 Kusumi et al; licensee BioMed Central Ltd.
    • Development of the uncinate fasciculus: Implications for theory and developmental disorders

      Olson, IR; Heide, RJVD; Alm, KH; Vyas, G (2015-07-03)
      © 2015 The Authors. Abstract The uncinate fasciculus (UF) is a long-range white matter tract that connects limbic regions in the temporal lobe to the frontal lobe. The UF is one of the latest developing tracts, and continues maturing into the third decade of life. As such, individual differences in the maturational profile of the UF may serve to explain differences in behavior. Indeed, atypical macrostructure and microstructure of the UF have been reported in numerous studies of individuals with developmental and psychiatric disorders such as social deprivation and maltreatment, autism spectrum disorders, conduct disorder, risk taking, and substance abuse. The present review evaluates what we currently know about the UF's developmental trajectory and reviews the literature relating UF abnormalities to specific disorders. Additionally, we take a dimensional approach and critically examine symptoms and behavioral impairments that have been demonstrated to cluster with UF aberrations, in an effort to relate these impairments to our speculations regarding the functionality of the UF. We suggest that developmental disorders with core problems relating to memory retrieval, reward and valuation computation, and impulsive decision making may be linked to aberrations in uncinate microstructure.
    • Disparities in the completion of steps to kidney transplantation: Protocol for a systematic review

      Traino, HM; Nonterah, CW; Cyrus, JW; Gillespie, A; Urbanski, M; Adair-Kriz, M; Gardiner, Heather Marie|0000-0003-2017-991X (2015-01-01)
      Introduction: Disparities in access to transplantation have been well documented. The extant literature, however, focuses largely on disparities and related barriers for African-American patients and none has used the steps to transplantation as a guiding framework. This review will catalogue disparities in the steps to transplantation as well as the barriers and facilitators to completion of each step identified in the extant literature. The results of the review will be used to generate recommendations for future research to improve equity in access to kidney transplantation. Methods and analysis: Standard procedures will be used in the conduct of the review. Searches will be performed using the following electronic databases: PubMed/Medline, PsycINFO, CINHAL, EMBASE, Cochrane library and Web of Science. Reports of original research will be eligible for inclusion if they are published from 2005 to present, written or available in English language, performed in the USA, enrol adult participants (18 years of age or more), and employ descriptive or observational designs. Two authors will independently screen retrieved articles for inclusion. MaxQDA will be used for data analysis and management. All included reports will be coded for article characteristics; disparities identified; barriers and motivators of completion of steps to transplantation; and proposed solutions to disparities and barriers. Each report will be coded independently by two authors and discrepancies resolved by discussion among the full team. A qualitative approach to data analysis is planned. Risk of bias will be assessed using standard procedures. Ethics and dissemination: The findings will provide crucial information on the current status of disparities in access to transplantation. PRISMA guidelines will be followed in reporting the results of the review. It is anticipated that these results will inform research which seeks to increase parity in access to transplantation.
    • Editorial: Global Education of Health Management

      Evashwick, CJ; Aaronson, WE (2019-01-01)
    • Editorial: Modeling Play in Early Infant Development

      Shaw, P; Lee, M; Shen, Q; Hirsh-Pasek, K; Adolph, KE; Oudeyer, PY; Popp, J (2020-08-06)
    • Editorial: Obesity Science and Practice (Feb 2018)

      Sarwer, DB; Sarwer, David B|0000-0003-1033-5528 (2018-02-01)
    • Effect of deinstitutionalisation for adults with intellectual disabilities on costs: A systematic review

      May, P; Lombard Vance, R; Murphy, E; O'Donovan, MA; Webb, N; Sheaf, G; McCallion, P; Stancliffe, R; Normand, C; Smith, V; McCarron, M; Mccallion, Philip|0000-0001-5129-6399 (2019-01-01)
      © 2019 Author(s). Objective To review systematically the evidence on the costs and cost-effectiveness of deinstitutionalisation for adults with intellectual disabilities. Design Systematic review. Population Adults (aged 18 years and over) with intellectual disabilities. Intervention Deinstitutionalisation, that is, the move from institutional to community settings. Primary and secondary outcome measures Studies were eligible if evaluating within any cost-consequence framework (eg, cost-effectiveness analysis, cost-utility analysis) or resource use typically considered to fall within the societal viewpoint (eg, cost to payers, service-users, families and informal care costs). Search We searched MEDLINE, PsycINFO, CENTRAL, CINAHL, EconLit, Embase and Scopus to September 2017 and supplemented this with grey literature searches and handsearching of the references of the eligible studies. We assessed study quality using the Critical Appraisals Skills Programme suite of tools, excluding those judged to be of poor methodological quality. Results Two studies were included; both were cohort studies from the payer perspective of people leaving long-stay National Health Service hospitals in the UK between 1984 and 1992. One study found that deinstitutionalisation reduced costs, one study found an increase in costs. Conclusion A wide-ranging literature review found limited evidence on costs associated with deinstitutionalisation for people with intellectual disabilities. From two studies included in the review, the results were conflicting. Significant gaps in the evidence base were observable, particularly with respect to priority populations in contemporary policy: older people with intellectual disabilities and serious medical illness, and younger people with very complex needs and challenging behaviours. PROSPERO registration number CRD42018077406
    • Embodied cognition and STEM learning: overview of a topical collection in CR:PI

      Weisberg, SM; Newcombe, NS (2017-12-01)
      © 2017, The Author(s). Embodied learning approaches emphasize the use of action to support pedagogical goals. A specific version of embodied learning posits an action-to-abstraction transition supported by gesture, sketching, and analogical mapping. These tools seem to have special promise for bolstering learning in science, technology, engineering, and mathematics (STEM) disciplines, but existing efforts need further theoretical and empirical development. The topical collection in Cognitive Research: Principles includes articles aiming to formalize and test the effectiveness of embodied learning in STEM. The collection provides guideposts, staking out the terrain that should be surveyed before larger-scale efforts are undertaken. This introduction provides a broader context concerning mechanisms that can support embodied learning and make it especially well suited to the STEM disciplines.
    • Enhancer of zeste homolog 2 (EZH2) in pediatric soft tissue sarcomas: First implications

      Ciarapica, R; Miele, L; Giordano, A; Locatelli, F; Rota, R; Giordano, Antonio|0000-0002-5959-016X (2011-05-25)
      Soft tissue sarcomas of childhood are a group of heterogeneous tumors thought to be derived from mesenchymal stem cells. Surgical resection is effective only in about 50% of cases and resistance to conventional chemotherapy is often responsible for treatment failure. Therefore, investigations on novel therapeutic targets are of fundamental importance. Deregulation of epigenetic mechanisms underlying chromatin modifications during stem cell differentiation has been suggested to contribute to soft tissue sarcoma pathogenesis. One of the main elements in this scenario is enhancer of zeste homolog 2 (EZH2), a methyltransferase belonging to the Polycomb group proteins. EZH2 catalyzes histone H3 methylation on gene promoters, thus repressing genes that induce stem cell differentiation to maintain an embryonic stem cell signature. EZH2 deregulated expression/function in soft tissue sarcomas has been recently reported. In this review, an overview of the recently reported functions of EZH2 in soft tissue sarcomas is given and the hypothesis that its expression might be involved in soft tissue sarcomagenesis is discussed. Finally, the therapeutic potential of epigenetic therapies modulating EZH2-mediated gene repression is considered. © 2011 Ciarapica et al; licensee BioMed Central Ltd.
    • Enhancer trapping in zebrafish using the Sleeping Beauty transposon

      Balciunas, D; Davidson, AE; Sivasubbu, S; Hermanson, SB; Welle, Z; Ekker, SC; Balciunas, Darius|0000-0003-1938-3243 (2004-09-03)
      Background: Among functional elements of a metazoan gene, enhancers are particularly difficult to find and annotate. Pioneering experiments in Drosophila have demonstrated the value of enhancer "trapping" using an invertebrate to address this functional genomics problem. Results: We modulated a Sleeping Beauty transposon-based transgenesis cassette to establish an enhancer trapping technique for use in a vertebrate model system, zebrafish Danio rerio. We established 9 lines of zebrafish with distinct tissue- or organ-specific GFP expression patterns from 90 founders that produced GFP-expressing progeny. We have molecularly characterized these lines and show that in each line, a specific GFP expression pattern is due to a single transposition event. Many of the insertions are into introns of zebrafish genes predicted in the current genome assembly. We have identified both previously characterized as well as novel expression patterns from this screen. For example, the ET7 line harbors a transposon insertion near the mkp3 locus and expresses GFP in the midbrain-hindbrain boundary, forebrain and the ventricle, matching a subset of the known FGF8-dependent mkp3 expression domain. The ET2 line, in contrast, expresses GFP specifically in caudal primary motoneurons due to an insertion into the poly(ADPribose) glycohydrolase (PARG) locus. This surprising expression pattern was confirmed using in situ hybridization techniques for the endogenous PARG mRNA, indicating the enhancer trap has replicated this unexpected and highly localized PARG expression with good fidelity. Finally, we show that it is possible to excise a Sleeping Beauty transposon from a genomic location in the zebrafish germline. Conclusions: This genomics tool offers the opportunity for large-scale biological approaches combining both expression and genomic-level sequence analysis using as a template an entire vertebrate genome. © 2004 Balciunas et al; licensee BioMed Central Ltd.
    • Epidural Electrical Stimulation: A Review of Plasticity Mechanisms That Are Hypothesized to Underlie Enhanced Recovery From Spinal Cord Injury With Stimulation

      Eisdorfer, JT; Smit, RD; Keefe, KM; Lemay, MA; Smith, GM; Spence, AJ; Spence, Andrew|0000-0001-7352-0128; Lemay, Michel|0000-0002-5636-0297 (2020-09-02)
      © Copyright © 2020 Eisdorfer, Smit, Keefe, Lemay, Smith and Spence. Spinal cord injury (SCI) often results in life-long sensorimotor impairment. Spontaneous recovery from SCI is limited, as supraspinal fibers cannot spontaneously regenerate to form functional networks below the level of injury. Despite this, animal models and humans exhibit many motor behaviors indicative of recovery when electrical stimulation is applied epidurally to the dorsal aspect of the lumbar spinal cord. In 1976, epidural stimulation was introduced to alleviate spasticity in Multiple Sclerosis. Since then, epidural electrical stimulation (EES) has been demonstrated to improve voluntary mobility across the knee and/or ankle in several SCI patients, highlighting its utility in enhancing motor activation. The mechanisms that EES induces to drive these improvements in sensorimotor function remain largely unknown. In this review, we discuss several sensorimotor plasticity mechanisms that we hypothesize may enable epidural stimulation to promote recovery, including changes in local lumbar circuitry, propriospinal interneurons, and the internal model. Finally, we discuss genetic tools for afferent modulation as an emerging method to facilitate the search for the mechanisms of action.
    • Erratum to: E-GRASP: An integrated evolutionary and GRASP resource for exploring disease associations

      Karim, S; Nour Eldin, HF; Abusamra, H; Salem, N; Alhathli, E; Dudley, J; Sanderford, M; Scheinfeldt, LB; Chaudhary, AG; Al-Qahtani, MH; Kumar, S; Kumar, Sudhir|0000-0002-9918-8212 (2017-04-06)
      © 2017 The Author(s). This article [1] unfortunately published with an author deleted in the author list. The correct author list is presented above.
    • Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia

      Hughes, T; Ekman, D; Ardawatia, H; Elofsson, A; Liberles, DA; Liberles, David A|0000-0003-3487-8826 (2007-05-22)
      The high retention of duplicate genes in the genome of Paramecium tetraurelia has led to the hypothesis that most of the retained genes have persisted because of constraints due to gene dosage. This and other possible mechanisms are discussed in the light of expectations from population genetics and systems biology. © 2007 BioMed Central Ltd.
    • Evolution and structure of proteins and proteomes

      Liberles, DA; Teufel, AI; Liberles, David A|0000-0003-3487-8826 (2018-12-01)
      <jats:p>This themed issue centered on the evolution and structure of proteins and proteomes is comprised of seven published manuscripts. [...]</jats:p>
    • Evolutionary sequence analysis of complete eukaryote genomes

      Blair, JE; Shah, P; Hedges, SB (2005-03-11)
      Background: Gene duplication and gene loss during the evolution of eukaryotes have hindered attempts to estimate phylogenies and divergence times of species. Although current methods that identify clusters of orthologous genes in complete genomes have helped to investigate gene function and gene content, they have not been optimized for evolutionary sequence analyses requiring strict orthology and complete gene matrices. Here we adopt a relatively simple and fast genome comparison approach designed to assemble orthologs for evolutionary analysis. Our approach identifies single-copy genes representing only species divergences (panorthologs) in order to minimize potential errors caused by gene duplication. We apply this approach to complete sets of proteins from published eukaryote genomes specifically for phylogeny and time estimation. Results: Despite the conservative criterion used, 753 panorthologs (proteins) were identified for evolutionary analysis with four genomes, resulting in a single alignment of 287,000 amino acids. With this data set, we estimate that the divergence between deuterostomes and arthropods took place in the Precambrian, approximately 400 million years before the first appearance of animals in the fossil record. Additional analyses were performed with seven, 12, and 15 eukaryote genomes resulting in similar divergence time estimates and phylogenies. Conclusion: Our results with available eukaryote genomes agree with previous results using conventional methods of sequence data assembly from genomes. They show that large sequence data sets can be generated relatively quickly and efficiently for evolutionary analyses of complete genomes. © 2005 Blair et al; licensee BioMed Central Ltd.
    • Examining Adolescence as a Sensitive Period for High-Fat, High-Sugar Diet Exposure: A Systematic Review of the Animal Literature

      Murray, S; Chen, EY (2019-10-25)
      © Copyright © 2019 Murray and Chen. Animal studies suggest that poor nutrition (e.g., high-fat, high-sugar diets) may lead to impairments in cognitive functioning. Accumulating evidence suggests that the deleterious effects of these diets appear more pronounced in animals maintained on this diet early in life, consistent with the notion that the developing brain may be especially vulnerable to environmental insults. The current paper provides the first systematic review of studies comparing the effects of high-fat, high-sugar diet exposure during adolescence and adulthood on memory performance. The majority of studies (7/8) identified here report diet-induced memory problems when diet exposure began in adolescence but not adulthood. These findings lend support to the hypothesis that adolescence is a sensitive period during which palatable diets may contribute to negative neurocognitive effects. The current review explores putative mechanisms involved in diet-induced cognitive dysfunction and highlights promising areas for further research.
    • Extracting functional trends from whole genome duplication events using comparative genomics

      Hermansen, RA; Hvidsten, TR; Sandve, SR; Liberles, DA; Liberles, David A|0000-0003-3487-8826 (2016-05-10)
      © 2016 Hermansen et al. Background: The number of species with completed genomes, including those with evidence for recent whole genome duplication events has exploded. The recently sequenced Atlantic salmon genome has been through two rounds of whole genome duplication since the divergence of teleost fish from the lineage that led to amniotes. This quadrupoling of the number of potential genes has led to complex patterns of retention and loss among gene families. Results: Methods have been developed to characterize the interplay of duplicate gene retention processes across both whole genome duplication events and additional smaller scale duplication events. Further, gene expression divergence data has become available as well for Atlantic salmon and the closely related, pre-whole genome duplication pike and methods to describe expression divergence are also presented. These methods for the characterization of duplicate gene retention and gene expression divergence that have been applied to salmon are described. Conclusions: With the growth in available genomic and functional data, the opportunities to extract functional inference from large scale duplicates using comparative methods have expanded dramatically. Recently developed methods that further this inference for duplicated genes have been described.
    • Feasibility of muscle synergy outcomes in clinics, robotics, and sports: A systematic review

      Taborri, J; Agostini, V; Artemiadis, PK; Ghislieri, M; Jacobs, DA; Roh, J; Rossi, S (2018-01-01)
      Copyright © 2018 Juri Taborri et al. In the last years, several studies have been focused on understanding how the central nervous system controls muscles to perform a specific motor task. Although it still remains an open question, muscle synergies have come to be an appealing theory to explain the modular organization of the central nervous system. Even though the neural encoding of muscle synergies remains controversial, a large number of papers demonstrated that muscle synergies are robust across different tested conditions, which are within a day, between days, within a single subject, and between subjects that have similar demographic characteristics. Thus, muscle synergy theory has been largely used in several research fields, such as clinics, robotics, and sports. The present systematical review aims at providing an overview on the applications of muscle synergy theory in clinics, robotics, and sports; in particular, the review is focused on the papers that provide tangible information for (i) diagnosis or pathology assessment in clinics, (ii) robot-control design in robotics, and (iii) athletes' performance assessment or training guidelines in sports.