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  • 2017
  • swepub:Mat__t
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2.
  • Kanai, M, et al. (author)
  • 2023
  • swepub:Mat__t
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  • Bouyoucef, S E, et al. (author)
  • Poster Session 2 : Monday 4 May 2015, 08
  • 2015
  • In: European Heart Journal Cardiovascular Imaging. - : Oxford University Press (OUP). - 2047-2404 .- 2047-2412. ; 16 Suppl 1
  • Journal article (peer-reviewed)
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6.
  • Namkoong, H, et al. (author)
  • DOCK2 is involved in the host genetics and biology of severe COVID-19
  • 2022
  • In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 609:7928, s. 754-
  • Journal article (peer-reviewed)abstract
    • Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge1–5. Here we conducted a genome-wide association study (GWAS) involving 2,393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3,289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target.
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  • Wang, QBS, et al. (author)
  • The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force
  • 2022
  • In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 4830-
  • Journal article (peer-reviewed)abstract
    • Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection.
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  • Katayama, S, et al. (author)
  • Antisense transcription in the mammalian transcriptome
  • 2005
  • In: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 309:5740, s. 1564-1566
  • Journal article (peer-reviewed)abstract
    • Antisense transcription (transcription from the opposite strand to a protein-coding or sense strand) has been ascribed roles in gene regulation involving degradation of the corresponding sense transcripts (RNA interference), as well as gene silencing at the chromatin level. Global transcriptome analysis provides evidence that a large proportion of the genome can produce transcripts from both strands, and that antisense transcripts commonly link neighboring “genes” in complex loci into chains of linked transcriptional units. Expression profiling reveals frequent concordant regulation of sense/antisense pairs. We present experimental evidence that perturbation of an antisense RNA can alter the expression of sense messenger RNAs, suggesting that antisense transcription contributes to control of transcriptional outputs in mammals.
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  • Evangelou, Evangelos, et al. (author)
  • Meta-analysis of genome-wide association studies confirms a susceptibility locus for knee osteoarthritis on chromosome 7q22
  • 2011
  • In: Annals of the Rheumatic Diseases. - : BMJ. - 1468-2060 .- 0003-4967. ; 70:2, s. 349-355
  • Journal article (peer-reviewed)abstract
    • Objectives Osteoarthritis (OA) is the most prevalent form of arthritis and accounts for substantial morbidity and disability, particularly in older people. It is characterised by changes in joint structure, including degeneration of the articular cartilage, and its aetiology is multifactorial with a strong postulated genetic component. Methods A meta-analysis was performed of four genome-wide association (GWA) studies of 2371 cases of knee OA and 35 909 controls in Caucasian populations. Replication of the top hits was attempted with data from 10 additional replication datasets. Results With a cumulative sample size of 6709 cases and 44 439 controls, one genome-wide significant locus was identified on chromosome 7q22 for knee OA (rs4730250, p = 9.2 x 10(-9)), thereby confirming its role as a susceptibility locus for OA. Conclusion The associated signal is located within a large (500 kb) linkage disequilibrium block that contains six genes: PRKAR2B (protein kinase, cAMP-dependent, regulatory, type II, beta), HPB1 (HMG-box transcription factor 1), COG5 (component of oligomeric golgi complex 5), GPR22 (G protein-coupled receptor 22), DUS4L (dihydrouridine synthase 4-like) and BCAP29 (B cell receptor-associated protein 29). Gene expression analyses of the (six) genes in primary cells derived from different joint tissues confirmed expression of all the genes in the joint environment.
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  • Nishida, Masahiro, et al. (author)
  • Evaluation of dynamic compressive properties of PLA polymer blends using split Hopkinson pressure bar
  • 2009
  • In: DYMAT 2009, 9th International conferense on the mechanical and physical behaviour of materials under dynamic loading. - Les Ulis : EDP Sciences. - 9782759804726 ; , s. 909-915
  • Conference paper (peer-reviewed)abstract
    • Poly(lactic acid) (PLA) has been used as a biomaterial for bone fixation devices in oral and orthopedic surgery because of good biocompatibility and bioabsorbability. Because Poly(e-Caprolactone) (PCL) is a ductile, bioabsorbable and biodegradable polymer, many types of PLA/ PCL polymer blends have been developed to improve its material strength and impact resistance. The stress-strain curves of PLA and PLA/PCL polymer blends were measured using a split Hopkinson pressure bar (Kolsky bar) method and a universal testing machine. The effect of PCL content on Young's modulus and yield stress was examined. The values of constants in Cowper-Symonds equation with respect to yield stress were determined for PLA and PLA/PCL polymer blend specimens. PLA/PCL specimens were observed using a scanning electron microscope.
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  • Ohshima, M., et al. (author)
  • TGF-beta Signaling in Gingival Fibroblast-Epithelial Interaction
  • 2010
  • In: Journal of Dental Research. - : SAGE Publications. - 0022-0345 .- 1544-0591. ; 89:11, s. 1315-1321
  • Journal article (peer-reviewed)abstract
    • The underlying mechanism and the therapeutic regimen for the transition of reversible gingivitis to irreversible periodontitis are unclear. Since transforming growth factor (TGF)-beta has been implicated in differentially regulated gene expression in gingival fibroblasts, we hypothesized that TGF-beta signaling is activated in periodontitis-affected gingiva, along with enhanced collagen degradation, that is reversed by TGF-beta inhibition. A novel three-dimensional (3D) gel-culture system consisting of primary human gingival fibroblasts (GF) and gingival epithelial (GE) cells in collagen gels was applied. GF populations from patients with severe periodontitis degraded collagen gels, which was reduced by TGF-beta-receptor kinase inhibition. Up-regulation of TGF-beta-responsive genes was evident in GF/GE cocultures. Furthermore, the TGF-beta downstream transducer Smad3C was highly phosphorylated in periodontitis-affected gingiva and 3D cultures. These results imply that TGF-beta signaling is involved in fibroblast-epithelial cell interaction in periodontitis, and suggest that the 3D culture system is a useful in vitro model for therapeutic drug screening for periodontitis.
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  • Romanov, Michael N., et al. (author)
  • Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor
  • 2014
  • In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 15, s. 1060-
  • Journal article (peer-reviewed)abstract
    • Background: The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. Results: Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra-and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. Conclusions: Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.
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  • Zhang, Shidong, et al. (author)
  • Simple and complex polymer electrolyte fuel cell stack models : A comparison
  • 2018. - 13
  • In: ECS Transactions. - : The Electrochemical Society. - 1938-6737 .- 1938-5862. - 9781607685395 ; 86, s. 287-300
  • Conference paper (peer-reviewed)abstract
    • In this paper, two distinct polymer electrolyte fuel cell stack models are constructed: a detailed numerical model (DNM) employing a fine-scale computational mesh and a coarse-mesh approach based on a distributed resistance analogy (DRA) where diffusion terms in the transport equations are replaced by rate terms. Both methods are applied to a 5-cell, high-temperature polymer electrolyte fuel cell stack with an active area of 200 cm2 per cell. The polarization curve and local current density distributions from both the DRA and DNM are compared with experimental data, finding good agreement. Temperature, pressure, Nernst potential, and species distributions are also exhibited. The DNM displays details of fine-scale local extrema not captured by the DRA; however, the latter requires orders of magnitude less computer processor power and memory for execution. Both methods provide much finer-scale results than present experimental techniques.
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  • Barrenäs, Fredrik, et al. (author)
  • Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control
  • 2019
  • In: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 10
  • Journal article (peer-reviewed)abstract
    • Natural hosts of simian immunodeficiency virus (SIV) avoid AIDS despite lifelong infection. Here, we examined how this outcome is achieved by comparing a natural SIV host, African green monkey (AGM) to an AIDS susceptible species, rhesus macaque (RM). To asses gene expression profiles from acutely SIV infected AGMs and RMs, we developed a systems biology approach termed Conserved Gene Signature Analysis (CGSA), which compared RNA sequencing data from rectal AGM and RM tissues to various other species. We found that AGMs rapidly activate, and then maintain, evolutionarily conserved regenerative wound healing mechanisms in mucosal tissue. The wound healing protein fibronectin shows distinct tissue distribution and abundance kinetics in AGMs. Furthermore, AGM monocytes exhibit an embryonic development and repair/regeneration signature featuring TGF-beta and concomitant reduced expression of inflammatory genes compared to RMs. This regenerative wound healing process likely preserves mucosal integrity and prevents inflammatory insults that underlie immune exhaustion in RMs.
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  • Craig, O. E., et al. (author)
  • Earliest evidence for the use of pottery
  • 2013
  • In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 496:7445, s. 351-354
  • Journal article (peer-reviewed)abstract
    • Pottery was a hunter-gatherer innovation that first emerged in East Asia between 20,000 and 12,000 calibrated years before present(1,2) (cal BP), towards the end of the Late Pleistocene epoch, a period of time when humans were adjusting to changing climates and new environments. Ceramic container technologies were one of a range of late glacial adaptations that were pivotal to structuring subsequent cultural trajectories in different regions of the world, but the reasons for their emergence and widespread uptake are poorly understood. The first ceramic containers must have provided prehistoric hunter-gatherers with attractive new strategies for processing and consuming foodstuffs, but virtually nothing is known of how early pots were used. Here we report the chemical analysis of food residues associated with Late Pleistocene pottery, focusing on one of the best-studied prehistoric ceramic sequences in the world, the Japanese Jomon. We demonstrate that lipids can be recovered reliably from charred surface deposits adhering to pottery dating from about 15,000 to 11,800 cal BP (the Incipient Jomon period), the oldest pottery so far investigated, and that in most cases these organic compounds are unequivocally derived from processing freshwater and marine organisms. Stable isotope data support the lipid evidence and suggest that most of the 101 charred deposits analysed, from across the major islands of Japan, were derived from high-trophic-level aquatic food. Productive aquatic ecotones were heavily exploited by late glacial foragers(3), perhaps providing an initial impetus for investment in ceramic container technology, and paving the way for further intensification of pottery use by hunter-gatherers in the early Holocene epoch. Now that we have shown that it is possible to analyse organic residues from some of the world's earliest ceramic vessels, the subsequent development of this critical technology can be clarified through further widespread testing of hunter-gatherer pottery from later periods.
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  • Djebien, S., et al. (author)
  • Strain Rate and Notch Radius Effects on Evaluating the Stress–Strain Relations Using the Stepwise Modeling Method
  • 2024
  • In: Journal of Dynamic Behavior of Materials. - : Springer. - 2199-7446 .- 2199-7454. ; 10, s. 26-39
  • Journal article (peer-reviewed)abstract
    • Accurate computer simulations require the selection of suitable material models and precise prediction of their parameters. In the fields of impact engineering and plastic working, stress–strain relations that include the post-necking regime up to fracture are crucial for predicting the behavior correctly. However, obtaining suitable stress–strain relations after necking requires some form of correction and adjustment for stress and/or strain. This study applies a stepwise modeling method for post-necking characterization that only utilizes the local strain field obtained from tensile experiments to precisely measure stress–strain relations at high strain rates. The effects of the notch radius of specimens on stress–strain relations were examined to measure stress–strain relations with large strain near the stress triaxiality of 1/3. The study also discusses adequate resolution for precise stress–strain measurements. Subsequently, specimens with suitable notch radius were used to measure stress–strain relations of plate specimens of aluminum alloy 2024-T3 at high strain rates. The study also examined the effects of strain rate on the flow stress and fracture strain of aluminum alloy 2024-T3.
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  • Jordan, Richard W., et al. (author)
  • Observations on the morphological diversity and distribution of two siliceous nannoplankton genera, Hyalolithus and Petasaria
  • 2015
  • In: Micropaleontology. - 0026-2803 .- 1937-2795. ; 61:6, s. 439-455
  • Journal article (peer-reviewed)abstract
    • Scale-bearing siliceous nannoplankton are occasionally encountered in surface seawater samples, but are rarely identified or illustrated. In this study, the morphological diversity of the haptophyte Hyalolithus neolepis and the enigmatic Petasaria heterolepis are investigated in scanning and transmission electron microscopes using materials from around the world. Results show that H. neolepis scales exhibit variation in the width of the marginal hyaline area, but intermediate specimens make separation of the two morphologies difficult. Petasaria heterolepis scales also show differences, in the presence of tubercle rows in the hyaline area and degree of hyaline areal coverage, but separation into discrete varieties is difficult at present. However, specimens with scales bearing a protuberance are considered to be distinct enough to warrant the erection of a new species, Petasaria protuberans Jordan,Malinverno, Å upraha, Thomsen et Young sp. nov.
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  • Nakanishi, Miharu, et al. (author)
  • e-learning and web-based tools for psychosocial interventions addressing neuropsychiatric symptoms of dementia during the covid-19 pandemic in tokyo, japan : Quasi-experimental study
  • 2021
  • In: JMIR Medical Education. - : JMIR Publications Inc.. - 2369-3762. ; 7:4
  • Journal article (peer-reviewed)abstract
    • Background: Concern has been raised that the COVID-19 pandemic and consequent social distancing measures may increase neuropsychiatric symptoms in people with dementia. Thus, we developed and delivered an e-learning training course to professional caregivers on using a web-based tool for psychosocial interventions for people with dementia. Objective: The aim of our study was to evaluate the feasibility and efficacy of an e-learning course in combination with a web-based tool in addressing neuropsychiatric symptoms of dementia. Methods: A quasi-experimental design was used in Tokyo, Japan. The e-learning course was delivered three times to professional caregivers between July and December 2020. Caregivers who completed the course assessed the level of neuropsychiatric symptoms in people with dementia using the total score from the Neuropsychiatric Inventory (NPI) via a web-based tool. The primary outcome measures were the number of caregivers who implemented follow-up NPI evaluations by March 2021 and the change in NPI scores from baseline to their most recent follow-up evaluations. As a control group, information was also obtained from professional caregivers who completed a face-to-face training course using the same web-based tool between July 2019 and March 2020. Results: A total of 268 caregivers completed the e-learning course in 2020. Of the 268 caregivers, 56 (20.9%) underwent follow-up evaluations with 63 persons with dementia. The average NPI score was significantly reduced from baseline (mean 20.4, SD 16.2) to the most recent follow-up evaluations (mean 14.3, SD 13.4). The effect size was assumed to be medium (Cohen drm [repeated measures]=0.40). The control group consisted of 252 caregivers who completed a face-to-face training course. Of the 252 caregivers, 114 (45.2%) underwent follow-up evaluations. Compared to the control group, caregivers who completed the e-learning course were significantly less likely to implement follow-up evaluations (χ2 1=52.0, P<.001). The change in NPI scores did not differ according to the type of training course (baseline-adjusted difference=-0.61, P=.69). Conclusions: The replacement of face-to-face training with e-learning may have provided professionals with an opportunity to participate in the dementia behavior analysis and support enhancement (DEMBASE) program who may not have participated in the program otherwise. Although the program showed equal efficacy in terms of the two training courses, the feasibility was suboptimal with lower implementation levels for those receiving e-learning training. Thus, further strategies should be developed to improve feasibility by providing motivational triggers for implementation and technical support for care professionals. Using online communities in the program should also be investigated.
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  • Nishida, Jun, et al. (author)
  • Structural dynamics inside a functionalized metal-organic framework probed by ultrafast 2D IR spectroscopy
  • 2014
  • In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 111:52, s. 18442-18447
  • Journal article (peer-reviewed)abstract
    • The structural elasticity of metal-organic frameworks (MOFs) is a key property for their functionality. Here, we show that 2D IR spectroscopy with pulse-shaping techniques can probe the ultrafast structural fluctuations of MOFs. 2D IR data, obtained from a vibrational probe attached to the linkers of UiO-66 MOF in low concentration, revealed that the structural fluctuations have time constants of 7 and 670 ps with no solvent. Filling the MOF pores with dimethylformamide (DMF) slows the structural fluctuations by reducing the ability of the MOF to undergo deformations, and the dynamics of the DMF molecules are also greatly restricted. Methodology advances were required to remove the severe light scattering caused by the macroscopic-sizedMOF particles, eliminate interfering oscillatory components from the 2D IR data, and address Forster vibrational excitation transfer.
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  • Nishida, Masahiro, et al. (author)
  • Determination of dynamic material properties for poly(L-lactic acid)/poly(e-caprolactone) blends : Experiments and simulation using split Hopkinson pressure bars
  • 2012
  • In: EPJ Web of Conferences. - Les Ulis : EDP Sciences. - 2100-014X. - 9782759807574 ; , s. 3001-
  • Conference paper (peer-reviewed)abstract
    • Coefficients of Cowper-Symonds constitutive equation for PLLA/PCL = 80/20 were determined using the results of compressive tests at high and low strain rates. The simulation of split Hopkinson pressure bar using the coefficients was carried out under the same condition as the experiments. The diameter and thickness of specimens were measured by a high-speed video camera. The stress and strain histories of specimens, the thickness and the diameter in the simulations at high strain rate were compared with those in the experiments
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  • Nishida, T., et al. (author)
  • Optical sum-frequency emission from Langmuir-Blodgett films of variable thickness : Effects of the substrate and polar orientation of fatty acids in the films
  • 2006
  • In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 96:7
  • Journal article (peer-reviewed)abstract
    • The nonlinear optical response arising from a model multilayer structure, i.e., Langmuir-Blodgett (LB) films comprised of different numbers of per-protonated (H) and per-deuterated (D) fatty acid layers on solid substrates, has been evaluated by sum-frequency generation (SFG) spectroscopy. The SFG signals depend significantly on the absolute polar orientation of the fatty acids in the individual layers and on the nonlinear optical response of the substrate. The SFG spectra on gold and fused quartz substrates demonstrate a totally different dependence on the number of the contributing H layers, which it is possible to analyze quantitatively. The results provide important information for understanding the origin of the nonlinear optical responses from ordered systems composed of multiple interfaces and therefore for extracting exact structural information about each interface from the observed SFG signals.
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  • Romieu, Isabelle, et al. (author)
  • Energy balance and obesity : what are the main drivers?
  • 2017
  • In: Cancer Causes and Control. - : Springer Science and Business Media LLC. - 0957-5243 .- 1573-7225. ; 28:3, s. 247-258
  • Journal article (peer-reviewed)abstract
    • Purpose: The aim of this paper is to review the evidence of the association between energy balance and obesity. Methods: In December 2015, the International Agency for Research on Cancer (IARC), Lyon, France convened a Working Group of international experts to review the evidence regarding energy balance and obesity, with a focus on Low and Middle Income Countries (LMIC). Results: The global epidemic of obesity and the double burden, in LMICs, of malnutrition (coexistence of undernutrition and overnutrition) are both related to poor quality diet and unbalanced energy intake. Dietary patterns consistent with a traditional Mediterranean diet and other measures of diet quality can contribute to long-term weight control. Limiting consumption of sugar-sweetened beverages has a particularly important role in weight control. Genetic factors alone cannot explain the global epidemic of obesity. However, genetic, epigenetic factors and the microbiota could influence individual responses to diet and physical activity. Conclusion: Energy intake that exceeds energy expenditure is the main driver of weight gain. The quality of the diet may exert its effect on energy balance through complex hormonal and neurological pathways that influence satiety and possibly through other mechanisms. The food environment, marketing of unhealthy foods and urbanization, and reduction in sedentary behaviors and physical activity play important roles. Most of the evidence comes from High Income Countries and more research is needed in LMICs.
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