Browsing by Subject "COMPRESSION"

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  • Byggmästar, Jesper Johan André; Nagel, Morten Jesper; Albe, Karsten; Henriksson, Krister Olof Edvin; Nordlund, Kai Henrik (2019)
    We present an analytical bond-order potential for the Fe-O system, capable of reproducing the basic properties of wustite as well as the energetics of oxygen impurities in alpha-iron. The potential predicts binding energies of various small oxygen-vacancy clusters in alpha-iron in good agreement with density functional theory results, and is therefore suitable for simulations of oxygen-based defects in iron. We apply the potential in simulations of the stability and structure of Fe/FeO interfaces and FeO precipitates in iron, and observe that the shape of FeO precipitates can change due to formation of well-defined Fe/FeO interfaces. The interface with crystalline Fe also ensures that the precipitates never become fully amorphous, no matter how small they are.
  • Gagie, Travis; Hoobin, Christopher; Puglisi, Simon J. (2017)
    Motivated by the rapidly increasing size of genomic databases, code repositories and versioned texts, several compression schemes have been proposed that work well on highly-repetitive strings and also support fast random access: e.g., LZ-End, RLZ, GDC, augmented SLPs, and block graphs. Block graphs have good worst-case bounds but it has been an open question whether they are practical. We describe an implementation of block graphs that, for several standard datasets, provides better compression and faster random access than competing schemes.
  • Karppinen, Helena; Pitkala, Kaisu H.; Kautiainen, Hannu; Tilvis, Reijo S.; Valvanne, Jaakko; Yoder, Kathe; Strandberg, Timo E. (2017)
    Objective: To explore changes in self-reported disabilities, health, comorbidities and psychological wellbeing (PWB) in aged cohorts over two decades. Design, setting and subjects: Cross-sectional cohort studies with postal surveys were conducted among community-dwelling people aged 75, 80, 85, 90 and 95 years in 1989 (n = 660), 1999 (n = 2598) and 2009 (n = 1637) in Helsinki, Finland. Main outcome measures: Self-reported items on disability, self-rated health (SRH), diagnoses and PWB were compared between cohorts of the same age. Standardized mortality ratios (SMRs) were calculated for each study year to explore the representativeness of the samples compared to general population of same age. Results: A significantly lower proportion of the 75-85-year-olds of the later study years reported going outdoors daily, although this group had improvements in both SRH and PWB scores. The number of comorbidities increased over time among 75-85-year-olds. The only significant change that could be verified among 90- and 95-year-olds between 1999 and 2009, was the lower proportion of participants going outdoors daily. The trend of leveling-off in disabilities was not explained by the SMRs (0.90, 0.71 and 0.60 for 1989, 1999 and 2009). Conclusions: The latest older people's cohorts showed an end to previously reported improvements in disabilities, despite having favorable trends in SRH and PWB. Primary care may be faced with increasing need of appropriate services for their senior members.
  • Kassebaum, Nicholas J.; Arora, Megha; Barber, Ryan M.; Bhutta, Zulfigar A.; Carter, Austin; Casey, Daniel C.; Charlson, Fiona J.; Coates, Matthew M.; Coggeshall, Megan; Cornaby, Leslie; Dandona, Lalit; Dicker, Daniel J.; Erskine, Holly E.; Ferrari, Alize J.; Fitzmaurice, Christina; Foreman, Kyle; Forouzanfar, Mohammad H.; Fullman, Nancy; Gething, Peter W.; Goldberg, Ellen M.; Graetz, Nicholas; Haagsma, Juanita A.; Johnson, Catherine; Kemmer, Laura; Khalil, Ibrahim A.; Kinfu, Yohannes; Kutz, Michael J.; Kyu, Hmwe H.; Leung, Janni; Liang, Xiaofeng; Lim, Stephen S.; Lim, Stephen S.; Lozano, Rafael; Mensah, George A.; Mikesell, Joe; Mokdad, Ali H.; Mooney, Meghan D.; Naghavi, Mohsen; Nguyen, Grant; Nsoesie, Elaine; Pigott, David M.; Pinho, Christine; Rankin, Zane; Reinig, Nikolas; Salomon, Joshua A.; Sandar, Logan; Lallukka, Tea; Meretoja, Atte; Meretoja, Tuomo J.; Weiderpass, Elisabete; GBD 2015 DALY & HALE (2016)
    Background Healthy life expectancy (HALE) and disability-adjusted life-years (DALYs) provide summary measures of health across geographies and time that can inform assessments of epidemiological patterns and health system performance, help to prioritise investments in research and development, and monitor progress toward the Sustainable Development Goals (SDGs). We aimed to provide updated HALE and DALYs for geographies worldwide and evaluate how disease burden changes with development. Methods We used results from the Global Burden of Diseases, Injuries, and Risk Factors Study 2015 (GBD 2015) for all-cause mortality, cause-specific mortality, and non-fatal disease burden to derive HALE and DALYs by sex for 195 countries and territories from 1990 to 2015. We calculated DALYs by summing years of life lost (YLLs) and years of life lived with disability (YLDs) for each geography, age group, sex, and year. We estimated HALE using the Sullivan method, which draws from age-specific death rates and YLDs per capita. We then assessed how observed levels of DALYs and HALE differed from expected trends calculated with the Socio-demographic Index (SDI), a composite indicator constructed from measures of income per capita, average years of schooling, and total fertility rate. Findings Total global DALYs remained largely unchanged from 1990 to 2015, with decreases in communicable, neonatal, maternal, and nutritional (Group 1) disease DALYs off set by increased DALYs due to non-communicable diseases (NCDs). Much of this epidemiological transition was caused by changes in population growth and ageing, but it was accelerated by widespread improvements in SDI that also correlated strongly with the increasing importance of NCDs. Both total DALYs and age-standardised DALY rates due to most Group 1 causes significantly decreased by 2015, and although total burden climbed for the majority of NCDs, age-standardised DALY rates due to NCDs declined. Nonetheless, age-standardised DALY rates due to several high-burden NCDs (including osteoarthritis, drug use disorders, depression, diabetes, congenital birth defects, and skin, oral, and sense organ diseases) either increased or remained unchanged, leading to increases in their relative ranking in many geographies. From 2005 to 2015, HALE at birth increased by an average of 2.9 years (95% uncertainty interval 2.9-3.0) for men and 3.5 years (3.4-3.7) for women, while HALE at age 65 years improved by 0.85 years (0.78-0.92) and 1.2 years (1.1-1.3), respectively. Rising SDI was associated with consistently higher HALE and a somewhat smaller proportion of life spent with functional health loss; however, rising SDI was related to increases in total disability. Many countries and territories in central America and eastern sub-Saharan Africa had increasingly lower rates of disease burden than expected given their SDI. At the same time, a subset of geographies recorded a growing gap between observed and expected levels of DALYs, a trend driven mainly by rising burden due to war, interpersonal violence, and various NCDs. Interpretation Health is improving globally, but this means more populations are spending more time with functional health loss, an absolute expansion of morbidity. The proportion of life spent in ill health decreases somewhat with increasing SDI, a relative compression of morbidity, which supports continued efforts to elevate personal income, improve education, and limit fertility. Our analysis of DALYs and HALE and their relationship to SDI represents a robust framework on which to benchmark geography-specific health performance and SDG progress. Country-specific drivers of disease burden, particularly for causes with higher-than-expected DALYs, should inform financial and research investments, prevention efforts, health policies, and health system improvement initiatives for all countries along the development continuum. Copyright (C) The Author(s). Published by Elsevier Ltd.
  • Almeida, Joao R.; Pinho, Armando J.; Oliveira, Jose L.; Fajarda, Olga; Pratas, Diogo (2020)
    Next-generation sequencing triggered the production of a massive volume of publicly available data and the development of new specialised tools. These tools are dispersed over different frameworks, making the management and analyses of the data a challenging task. Additionally, new targeted tools are needed, given the dynamics and specificities of the field. We present GTO, a comprehensive toolkit designed to unify pipelines in genomic and proteomic research, which combines specialised tools for analysis, simulation, compression, development, visualisation, and transformation of the data. This toolkit combines novel tools with a modular architecture, being an excellent platform for experimental scientists, as well as a useful resource for teaching bioinformatics enquiry to students in life sciences. GTO is implemented in C language and is available, under the MIT license, at https://bioinformatics.ua.pt/gto. (C) 2020 The Authors. Published by Elsevier B.V.
  • Tanner, Timo; Antikainen, Osmo; Ehlers, Henrik; Yliruusi, Jouko (2017)
    With modern tableting machines large amounts of tablets are produced with high output. Consequently, methods to examine powder compression in a high-velocity setting are in demand. In the present study, a novel gravitation-based method was developed to examine powder compression. A steel bar is dropped on a punch to compress microcrystalline cellulose and starch samples inside the die. The distance of the bar is being read by a high-accuracy laser displacement sensor which provides a reliable distance-time plot for the bar movement. In-die height and density of the compact can be seen directly from this data, which can be examined further to obtain information on velocity, acceleration and energy distribution during compression. The energy consumed in compact formation could also be seen. Despite the high vertical compression speed, the method was proven to be cost-efficient, accurate and reproducible. (C) 2017 Elsevier B.V. All rights reserved.
  • Hosseini, Morteza; Pratas, Diogo; Morgenstern, Burkhard; Pinho, Armando J. (2020)
    Background: The development of high-throughput sequencing technologies and, as its result, the production of huge volumes of genomic data, has accelerated biological and medical research and discovery. Study on genomic rearrangements is crucial owing to their role in chromosomal evolution, genetic disorders, and cancer. Results: We present Smash++, an alignment-free and memory-efficient tool to find and visualize small- and large-scale genomic rearrangements between 2 DNA sequences. This computational solution extracts information contents of the 2 sequences, exploiting a data compression technique to find rearrangements. We also present Smash++ visualizer, a tool that allows the visualization of the detected rearrangements along with their self- and relative complexity, by generating an SVG (Scalable Vector Graphics) image. Conclusions: Tested on several synthetic and real DNA sequences from bacteria, fungi, Aves, and Mammalia, the proposed tool was able to accurately find genomic rearrangements. The detected regions were in accordance with previous studies, which took alignment-based approaches or performed FISH (fluorescence in situ hybridization) analysis. The maximum peak memory usage among all experiments was similar to 1 GB, which makes Smash++ feasible to run on present-day standard computers.
  • Lehti, T. E.; Öhman, H.; Knuutila, M.; Kautiainen, H.; Karppinen, H.; Tilvis, R.; Strandberg, T.; Pitkälä, K. H. (2021)
    Background Changes in older people's symptoms across recent decades have not been investigated. Aims We analyzed temporal trends in symptom burden by comparing data from independent, cross-sectional cohorts retrieved in 1989, 1999, 2009, and 2019. Furthermore, we compared the association between symptom burden and psychological wellbeing (PWB) in older men and women. Methods The Helsinki Aging Study recruited a random sample of people aged 75, 80, and 85 in 1989, and random samples aged 75, 80, 85, 90, and 95 in 1999, 2009, and 2019 (four study waves). Altogether, 6263 community-dwelling people answered the questions concerning symptoms in the questionnaire surveys. The symptoms inquired in all study waves were dizziness, back pain, joint pain, chest pain, shortness of breath, and loss of appetite. Symptom burden was calculated according to the number of symptoms and their frequency (score range: 0-6). PWB and the Charlson comorbidity index were calculated. Results Symptom burden decreased in both men and women aged 75 and 80 from 1989 to 2019. Changes in cohorts aged 85 + were nonsignificant. There was a significant difference in symptom burden between men and women in all ages with men having fewer symptoms. PWB decreased with increasing symptom burden. Men had greater PWB than women up to severe levels of symptom burden. Conclusions Symptom burden decreased from 1989 to 2019 in cohorts aged 75-80, whereas changes remained nonsignificant in cohorts aged 85 +. To our knowledge, this is the first study to examine temporal trends in symptom burden.
  • van Raalte, Alyson A.; Sasson, Isaac; Martikainen, Pekka (2018)