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1.	Anel-López, Luis, et al. (author) Reduced glutathione and Trolox (vitamin E) as extender supplements in cryopreservation of red deer epididymal spermatozoa 2012 In: Animal Reproduction Science. - : Elsevier. - 0378-4320 .- 1873-2232. ; 135:1-4, s. 37-46 Journal article (peer-reviewed)abstract The use of assisted reproductive techniques in cervids is increasing as the commercial use of these species increase. We have tested the suitability of the antioxidants Trolox and reduced glutathione (GSH) for freezing red deer epididymal spermatozoa, aiming at improving post-thawing quality. Samples from 19 stags were frozen in a TES-Tris-fructose extender (20% egg yolk, 8% glycerol), with 1 or 5 mM of antioxidant. Motility (CASA), lipoperoxidation (malondialdehyde -MDA- production), membrane status, mitochondrial activity, acrosomal status (flow cytometry) and chromatin status (SCSA: %DFI and %HDS; flow cytometry) were assessed after thawing and after 6 h at 39°C. There were few differences between treatments after thawing, with Trolox reducing MDA production in a dose-response manner. After the incubation, sperm quality decreased and %DFI increased moderately, with no change for MDA. GSH improved motility, kinematic parameters and mitochondrial status, with a slight increase in %HDS. GSH 5 mM also increased moderately MDA production and %DFI, possibly due to enhanced metabolic activity and reducing power. Trolox maintained MDA low, but was detrimental to sperm quality. Trolox might not be appropriate for the cryopreservation of red deer epididymal spermatozoa, at least at the millimolar range. GSH results are promising, especially regarding motility improvement after the post-thawing incubation, and should be selected for future fertility trials.
2.	Klionsky, Daniel J, et al. (author) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). 2016 In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 12:1, s. 1-222 Journal article (peer-reviewed)
3.	Arndt, D. S., et al. (author) State of the Climate in 2016 2017 In: Bulletin of The American Meteorological Society - (BAMS). - 0003-0007 .- 1520-0477. ; 98:8, s. S1-S280 Journal article (peer-reviewed)abstract In 2016, the dominant greenhouse gases released into Earth's atmosphere-carbon dioxide, methane, and nitrous oxide-continued to increase and reach new record highs. The 3.5 +/- 0.1 ppm rise in global annual mean carbon dioxide from 2015 to 2016 was the largest annual increase observed in the 58-year measurement record. The annual global average carbon dioxide concentration at Earth's surface surpassed 400 ppm (402.9 +/- 0.1 ppm) for the first time in the modern atmospheric measurement record and in ice core records dating back as far as 800000 years. One of the strongest El Nino events since at least 1950 dissipated in spring, and a weak La Nina evolved later in the year. Owing at least in part to the combination of El Nino conditions early in the year and a long-term upward trend, Earth's surface observed record warmth for a third consecutive year, albeit by a much slimmer margin than by which that record was set in 2015. Above Earth's surface, the annual lower troposphere temperature was record high according to all datasets analyzed, while the lower stratospheric temperature was record low according to most of the in situ and satellite datasets. Several countries, including Mexico and India, reported record high annual temperatures while many others observed near-record highs. A week-long heat wave at the end of April over the northern and eastern Indian peninsula, with temperatures surpassing 44 degrees C, contributed to a water crisis for 330 million people and to 300 fatalities. In the Arctic the 2016 land surface temperature was 2.0 degrees C above the 1981-2010 average, breaking the previous record of 2007, 2011, and 2015 by 0.8 degrees C, representing a 3.5 degrees C increase since the record began in 1900. The increasing temperatures have led to decreasing Arctic sea ice extent and thickness. On 24 March, the sea ice extent at the end of the growth season saw its lowest maximum in the 37-year satellite record, tying with 2015 at 7.2% below the 1981-2010 average. The September 2016 Arctic sea ice minimum extent tied with 2007 for the second lowest value on record, 33% lower than the 1981-2010 average. Arctic sea ice cover remains relatively young and thin, making it vulnerable to continued extensive melt. The mass of the Greenland Ice Sheet, which has the capacity to contribute similar to 7 m to sea level rise, reached a record low value. The onset of its surface melt was the second earliest, after 2012, in the 37-year satellite record. Sea surface temperature was record high at the global scale, surpassing the previous record of 2015 by about 0.01 degrees C. The global sea surface temperature trend for the 21st century-to-date of +0.162 degrees C decade(-1) is much higher than the longer term 1950-2016 trend of +0.100 degrees C decade(-1). Global annual mean sea level also reached a new record high, marking the sixth consecutive year of increase. Global annual ocean heat content saw a slight drop compared to the record high in 2015. Alpine glacier retreat continued around the globe, and preliminary data indicate that 2016 is the 37th consecutive year of negative annual mass balance. Across the Northern Hemisphere, snow cover for each month from February to June was among its four least extensive in the 47-year satellite record. Continuing a pattern below the surface, record high temperatures at 20-m depth were measured at all permafrost observatories on the North Slope of Alaska and at the Canadian observatory on northernmost Ellesmere Island. In the Antarctic, record low monthly surface pressures were broken at many stations, with the southern annular mode setting record high index values in March and June. Monthly high surface pressure records for August and November were set at several stations. During this period, record low daily and monthly sea ice extents were observed, with the November mean sea ice extent more than 5 standard deviations below the 1981-2010 average. These record low sea ice values contrast sharply with the record high values observed during 2012-14. Over the region, springtime Antarctic stratospheric ozone depletion was less severe relative to the 1991-2006 average, but ozone levels were still low compared to pre-1990 levels. Closer to the equator, 93 named tropical storms were observed during 2016, above the 1981-2010 average of 82, but fewer than the 101 storms recorded in 2015. Three basins-the North Atlantic, and eastern and western North Pacific-experienced above-normal activity in 2016. The Australian basin recorded its least active season since the beginning of the satellite era in 1970. Overall, four tropical cyclones reached the Saffir-Simpson category 5 intensity level. The strong El Nino at the beginning of the year that transitioned to a weak La Nina contributed to enhanced precipitation variability around the world. Wet conditions were observed throughout the year across southern South America, causing repeated heavy flooding in Argentina, Paraguay, and Uruguay. Wetter-than-usual conditions were also observed for eastern Europe and central Asia, alleviating the drought conditions of 2014 and 2015 in southern Russia. In the United States, California had its first wetter-than-average year since 2012, after being plagued by drought for several years. Even so, the area covered by drought in 2016 at the global scale was among the largest in the post-1950 record. For each month, at least 12% of land surfaces experienced severe drought conditions or worse, the longest such stretch in the record. In northeastern Brazil, drought conditions were observed for the fifth consecutive year, making this the longest drought on record in the region. Dry conditions were also observed in western Bolivia and Peru; it was Bolivia's worst drought in the past 25 years. In May, with abnormally warm and dry conditions already prevailing over western Canada for about a year, the human-induced Fort McMurray wildfire burned nearly 590000 hectares and became the costliest disaster in Canadian history, with $3 billion (U.S. dollars) in insured losses.
4.	Breznau, Nate, et al. (author) Observing many researchers using the same data and hypothesis reveals a hidden universe of uncertainty 2022 In: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:44 Journal article (peer-reviewed)abstract This study explores how researchers analytical choices affect the reliability of scientific findings. Most discussions of reliability problems in science focus on systematic biases. We broaden the lens to emphasize the idiosyncrasy of conscious and unconscious decisions that researchers make during data analysis. We coordinated 161 researchers in 73 research teams and observed their research decisions as they used the same data to independently test the same prominent social science hypothesis: that greater immigration reduces support for social policies among the public. In this typical case of social science research, research teams reported both widely diverging numerical findings and substantive conclusions despite identical start conditions. Researchers expertise, prior beliefs, and expectations barely predict the wide variation in research outcomes. More than 95% of the total variance in numerical results remains unexplained even after qualitative coding of all identifiable decisions in each teams workflow. This reveals a universe of uncertainty that remains hidden when considering a single study in isolation. The idiosyncratic nature of how researchers results and conclusions varied is a previously underappreciated explanation for why many scientific hypotheses remain contested. These results call for greater epistemic humility and clarity in reporting scientific findings.
5.	Chappell, E, et al. (author) Malignancies among children and young people with HIV in Western and Eastern Europe and Thailand 2021 In: AIDS (London, England). - 1473-5571. ; 35:12, s. 1973-1985 Journal article (peer-reviewed)
6.	Crichton, S, et al. (author) Height and timing of growth spurt during puberty in young people living with vertically acquired HIV in Europe and Thailand 2019 In: AIDS (London, England). - 1473-5571. ; 33:12, s. 1897-1910 Journal article (peer-reviewed)
7.	Cruz, Raquel, et al. (author) Novel genes and sex differences in COVID-19 severity 2022 In: Human Molecular Genetics. - : Oxford University Press. - 0964-6906 .- 1460-2083. ; 31:22, s. 3789-3806 Journal article (peer-reviewed)abstract Here, we describe the results of a genome-wide study conducted in 11 939 coronavirus disease 2019 (COVID-19) positive cases with an extensive clinical information that were recruited from 34 hospitals across Spain (SCOURGE consortium). In sex-disaggregated genome-wide association studies for COVID-19 hospitalization, genome-wide significance (P < 5 × 10−8) was crossed for variants in 3p21.31 and 21q22.11 loci only among males (P = 1.3 × 10−22 and P = 8.1 × 10−12, respectively), and for variants in 9q21.32 near TLE1 only among females (P = 4.4 × 10−8). In a second phase, results were combined with an independent Spanish cohort (1598 COVID-19 cases and 1068 population controls), revealing in the overall analysis two novel risk loci in 9p13.3 and 19q13.12, with fine-mapping prioritized variants functionally associated with AQP3 (P = 2.7 × 10−8) and ARHGAP33 (P = 1.3 × 10−8), respectively. The meta-analysis of both phases with four European studies stratified by sex from the Host Genetics Initiative (HGI) confirmed the association of the 3p21.31 and 21q22.11 loci predominantly in males and replicated a recently reported variant in 11p13 (ELF5, P = 4.1 × 10−8). Six of the COVID-19 HGI discovered loci were replicated and an HGI-based genetic risk score predicted the severity strata in SCOURGE. We also found more SNP-heritability and larger heritability differences by age (<60 or ≥60 years) among males than among females. Parallel genome-wide screening of inbreeding depression in SCOURGE also showed an effect of homozygosity in COVID-19 hospitalization and severity and this effect was stronger among older males. In summary, new candidate genes for COVID-19 severity and evidence supporting genetic disparities among sexes are provided.
8.	Goetghebuer, T, et al. (author) Time to Switch to Second-line Antiretroviral Therapy in Children With Human Immunodeficiency Virus in Europe and Thailand 2018 In: Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. - : Oxford University Press (OUP). - 1537-6591. ; 66:4, s. 594-603 Journal article (peer-reviewed)
9.	Mata-Campuzano, María, et al. (author) Effect of several antioxidants on thawed ram spermatozoa submitted to 37°C up to four hours. 2012 In: Reproduction in domestic animals. - : Blackwell Verlag. - 0936-6768 .- 1439-0531. ; 47:6, s. 907-914 Journal article (peer-reviewed)abstract Thawed ram spermatozoa were incubated at 37°C in the presence of dehydroascorbic acid (DHA), TEMPOL (TPL), N-acetyl-cysteine (NAC) and rutin (RUT), at 0.1 and 1 mm, in order to test their effects on sperm physiology. Cryopreserved spermatozoa from four rams were thawed, pooled, washed and incubated in TALP-Hepes with 1 mm or 0.1 mm of each antioxidant, performing a replicate with induced oxidative stress (Fe(2+) /ascorbate). Motility (CASA), viability and mitochondrial membrane potential (flow cytometry) were analysed at 2 and 4 h. Lipoperoxidation (MDA production), intracellular reactive oxygen species (ROS) and DNA status (TUNEL) were analysed at 4 h. Antioxidants, except DHA 0.1 mm, decreased motility and kinematic parameters, but had little effect on viability or mitochondrial activity. Except 1 mm DHA, the antioxidants reduced ROS at 4 h. Moreover, NAC 1 mm, rutin and TEMPOL reduced ROS and DNA damage in the presence of oxidative stress. N-acetyl-cysteine, rutin 1 mm and TEMPOL reduced lipoperoxidation in the presence of oxidative stress. However, DHA did not affect lipoperoxidation. At 1 mm, DHA increased DNA damage in the absence of oxidative stress. Dehydroascorbic acid effects could arise from spermatozoa having a low capacity for reducing it to ascorbic acid, and it may be tested in the presence of other antioxidants or reducing power. Future research should focus in testing whether the inhibition of motility observed for NAC, rutin and TEMPOL is reversible. These antioxidants might be useful at lower temperatures (refrigerated storage or cryopreservation) when their protective effects could be advantageous.
10.	Abazajian, Kevork, et al. (author) CMB-S4 : Forecasting Constraints on Primordial Gravitational Waves 2022 In: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 926:1 Journal article (peer-reviewed)abstract CMB-S4—the next-generation ground-based cosmic microwave background (CMB) experiment—is set to significantly advance the sensitivity of CMB measurements and enhance our understanding of the origin and evolution of the universe. Among the science cases pursued with CMB-S4, the quest for detecting primordial gravitational waves is a central driver of the experimental design. This work details the development of a forecasting framework that includes a power-spectrum-based semianalytic projection tool, targeted explicitly toward optimizing constraints on the tensor-to-scalar ratio, r, in the presence of Galactic foregrounds and gravitational lensing of the CMB. This framework is unique in its direct use of information from the achieved performance of current Stage 2–3 CMB experiments to robustly forecast the science reach of upcoming CMB-polarization endeavors. The methodology allows for rapid iteration over experimental configurations and offers a flexible way to optimize the design of future experiments, given a desired scientific goal. To form a closed-loop process, we couple this semianalytic tool with map-based validation studies, which allow for the injection of additional complexity and verification of our forecasts with several independent analysis methods. We document multiple rounds of forecasts for CMB-S4 using this process and the resulting establishment of the current reference design of the primordial gravitational-wave component of the Stage-4 experiment, optimized to achieve our science goals of detecting primordial gravitational waves for r > 0.003 at greater than 5σ, or in the absence of a detection, of reaching an upper limit of r < 0.001 at 95% CL.
11.	Ade, Peter, et al. (author) The Simons Observatory : science goals and forecasts 2019 In: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :2 Journal article (peer-reviewed)abstract The Simons Observatory (SO) is a new cosmic microwave background experiment being built on Cerro Toco in Chile, due to begin observations in the early 2020s. We describe the scientific goals of the experiment, motivate the design, and forecast its performance. SO will measure the temperature and polarization anisotropy of the cosmic microwave background in six frequency bands centered at: 27, 39, 93, 145, 225 and 280 GHz. The initial con figuration of SO will have three small-aperture 0.5-m telescopes and one large-aperture 6-m telescope, with a total of 60,000 cryogenic bolometers. Our key science goals are to characterize the primordial perturbations, measure the number of relativistic species and the mass of neutrinos, test for deviations from a cosmological constant, improve our understanding of galaxy evolution, and constrain the duration of reionization. The small aperture telescopes will target the largest angular scales observable from Chile, mapping approximate to 10% of the sky to a white noise level of 2 mu K-arcmin in combined 93 and 145 GHz bands, to measure the primordial tensor-to-scalar ratio, r, at a target level of sigma(r) = 0.003. The large aperture telescope will map approximate to 40% of the sky at arcminute angular resolution to an expected white noise level of 6 mu K-arcmin in combined 93 and 145 GHz bands, overlapping with the majority of the Large Synoptic Survey Telescope sky region and partially with the Dark Energy Spectroscopic Instrument. With up to an order of magnitude lower polarization noise than maps from the Planck satellite, the high-resolution sky maps will constrain cosmological parameters derived from the damping tail, gravitational lensing of the microwave background, the primordial bispectrum, and the thermal and kinematic Sunyaev-Zel'dovich effects, and will aid in delensing the large-angle polarization signal to measure the tensor-to-scalar ratio. The survey will also provide a legacy catalog of 16,000 galaxy clusters and more than 20,000 extragalactic sources.
12.	Ademuyiwa, Adesoji O., et al. (author) Determinants of morbidity and mortality following emergency abdominal surgery in children in low-income and middle-income countries 2016 In: BMJ Global Health. - : BMJ Publishing Group Ltd. - 2059-7908. ; 1:4 Journal article (peer-reviewed)abstract Background: Child health is a key priority on the global health agenda, yet the provision of essential and emergency surgery in children is patchy in resource-poor regions. This study was aimed to determine the mortality risk for emergency abdominal paediatric surgery in low-income countries globally.Methods: Multicentre, international, prospective, cohort study. Self-selected surgical units performing emergency abdominal surgery submitted prespecified data for consecutive children aged <16 years during a 2-week period between July and December 2014. The United Nation's Human Development Index (HDI) was used to stratify countries. The main outcome measure was 30-day postoperative mortality, analysed by multilevel logistic regression.Results: This study included 1409 patients from 253 centres in 43 countries; 282 children were under 2 years of age. Among them, 265 (18.8%) were from low-HDI, 450 (31.9%) from middle-HDI and 694 (49.3%) from high-HDI countries. The most common operations performed were appendectomy, small bowel resection, pyloromyotomy and correction of intussusception. After adjustment for patient and hospital risk factors, child mortality at 30 days was significantly higher in low-HDI (adjusted OR 7.14 (95% CI 2.52 to 20.23), p<0.001) and middle-HDI (4.42 (1.44 to 13.56), p=0.009) countries compared with high-HDI countries, translating to 40 excess deaths per 1000 procedures performed.Conclusions: Adjusted mortality in children following emergency abdominal surgery may be as high as 7 times greater in low-HDI and middle-HDI countries compared with high-HDI countries. Effective provision of emergency essential surgery should be a key priority for global child health agendas.
13.	Ajileye, Adebisi, et al. (author) Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDRsl Assays 2017 In: Antimicrobial Agents and Chemotherapy. - : AMER SOC MICROBIOLOGY. - 0066-4804 .- 1098-6596. ; 61:4 Journal article (peer-reviewed)abstract In this study, using the Hain GenoType MTBDRsl assays (versions 1 and 2), we found that some nonsynonymous and synonymous mutations in gyrA in Mycobacterium tuberculosis result in systematic false-resistance results to fluoroquinolones by preventing the binding of wild-type probes. Moreover, such mutations can prevent the binding of mutant probes designed for the identification of specific resistance mutations. Although these mutations are likely rare globally, they occur in approximately 7% of multidrug-resistant tuberculosis strains in some settings.
14.	Alvarez, Alberto, 1992-, et al. (author) Assessing the Effects of Interacting with MAP-Elites 2021 In: Proceedings of the seventeenth {AAAI} Conference on Artificial Intelligence and Interactive Digital Entertainment. - : Association for the Advancement of Artificial Intelligence. - 9781577358718 ; , s. 124-131 Conference paper (peer-reviewed)abstract MAP-Elites has been successfully applied to the generation of game content and robot behaviors. However, its behavior and performance when interacted with in co-creative systems is underexplored. This paper analyzes the implications of synthetic interaction for the stability and adaptability of MAP-Elites in such scenarios. We use pre-recorded human-made level design sessions with the Interactive Constrained MAP-Elites (IC MAP-Elites). To analyze the effect of each edition step in the search space over time using different feature dimensions, we introduce Temporal Expressive Range Analysis (TERA). With TERAs, MAP-Elites is assessed in terms of its adaptability and stability to generate diverse and high-performing individuals. Our results show that interactivity, in the form of design edits and MAP-Elites adapting towards them, directs the search process to previously unexplored areas of the fitness landscape and points towards how this could improve and enrich the co-creative process with quality-diverse individuals.
15.	Alvarez, Alberto, 1992-, et al. (author) Empowering Quality Diversity in Dungeon Design with Interactive Constrained MAP-Elites 2019 Conference paper (peer-reviewed)abstract We propose the use of quality-diversity algorithms for mixed-initiative game content generation. This idea is implemented as a new feature of the Evolutionary Dungeon Designer, a system for mixed-initiative design of the type of levels you typically find in computer role playing games. The feature uses the MAP-Elites algorithm, an illumination algorithm which divides the population into a number of cells depending on their values along several behavioral dimensions. Users can flexibly and dynamically choose relevant dimensions of variation, and incorporate suggestions produced by the algorithm in their map designs. At the same time, any modifications performed by the human feed back into MAP-Elites, and are used to generate further suggestions.
16.	Alvarez, Alberto, 1992- (author) Exploring Game Design through Human-AI Collaboration 2022 Doctoral thesis (other academic/artistic)abstract Game design is a hard and multi-faceted task that intertwines different gameplay mechanics, audio, level, graphic, and narrative facets. Games' facets are developed in conjunction with others with a common goal that makes games coherent and interesting. These combinations result in plenty of games in diverse genres, which usually require a collaboration of a diverse group of designers. Collaborators can take different roles and support each other with their strengths resulting in games with unique characteristics. The multi-faceted nature of games and their collaborative properties and requirements make it an exciting task to use Artificial Intelligence (AI). The generation of these facets together requires a holistic approach, which is one of the most challenging tasks within computational creativity. Given the collaborative aspect of games, this thesis approaches their generation through Human-AI collaboration, specifically using a mixed-initiative co-creative (MI-CC) paradigm. This paradigm creates an interactive and collaborative scenario that leverages AI and human strengths with an alternating and proactive initiative to approach a task. However, this paradigm introduces several challenges, such as Human and AI goal alignment or competing properties.In this thesis, game design and the generation of game facets by themselves and intertwined are explored through Human-AI collaboration. The AI takes a colleague's role with the designer, arising multiple dynamics, challenges, and opportunities. The main hypothesis is that AI can be incorporated into systems as a collaborator, enhancing design tools, fostering human creativity, and reducing workload. The challenges and opportunities that arise from this are explored, discussed, and approached throughout the thesis. As a result, multiple approaches and methods such as quality-diversity algorithms and designer modeling are proposed to generate game facets in tandem with humans, create a better workflow, enhance the interaction, and establish adaptive experiences.
17.	Alvarez, Alberto, 1992- (author) Exploring the Dynamic Properties of Interaction in Mixed-Initiative Procedural Content Generation 2020 Licentiate thesis (other academic/artistic)abstract As AI develops, grows, and expands, the more benefits we can have from it. AI is used in multiple fields to assist humans, such as object recognition, self-driving cars, or design tools. However, AI could be used for more than assisting humans in their tasks. It could be employed to collaborate with humans as colleagues in shared tasks, which is usually described as Mixed-Initiative (MI) paradigm. This paradigm creates an interactive scenario that leverage on AI and human strengths with an alternating and proactive initiative to approach a task. However, this paradigm introduces several challenges. For instance, there must be an understanding between humans and AI, where autonomy and initiative become negotiation tokens. In addition, control and expressiveness need to be taken into account to reach some goals. Moreover, although this paradigm has a broader application, it is especially interesting for creative tasks such as games, which are mainly created in collaboration. Creating games and their content is a hard and complex task, since games are content-intensive, multi-faceted, and interacted by external users. Therefore, this thesis explores MI collaboration between human game designers and AI for the co-creation of games, where the AI's role is that of a colleague with the designer. The main hypothesis is that AI can be incorporated in systems as a collaborator, enhancing design tools, fostering human creativity, reducing their workload, and creating adaptive experiences. Furthermore, This collaboration arises several dynamic properties such as control, expressiveness, and initiative, which are all central to this thesis. Quality-Diversity algorithms combined with control mechanisms and interactions for the designer are proposed to investigate this collaboration and properties. Designer and Player modeling is also explored, and several approaches are proposed to create a better workflow, establish adaptive experiences, and enhance the interaction. Through this, it is demonstrated the potential and benefits of these algorithms and models in the MI paradigm.
18.	Alvarez, Alberto, 1992-, et al. (author) Interactive Constrained MAP-Elites : Analysis and Evaluation of the Expressiveness of the Feature Dimensions 2022 In: IEEE Transactions on Games. - : IEEE. - 2475-1502 .- 2475-1510. ; 14:2, s. 202-211 Journal article (peer-reviewed)abstract We propose the Interactive Constrained MAP-Elites, a quality-diversity solution for game content generation, implemented as a new feature of the Evolutionary Dungeon Designer (EDD): a mixed-initiative co-creativity tool for designing dungeons. The feature uses the MAP-Elites algorithm, an illumination algorithm that segregates the population among several cells depending on their scores with respect to different behavioral dimensions. Users can flexibly and dynamically alternate between these dimensions anytime, thus guiding the evolutionary process in an intuitive way, and then incorporate suggestions produced by the algorithm in their room designs. At the same time, any modifications performed by the human user will feed back into MAP-Elites, closing a circular workflow of constant mutual inspiration. This paper presents the algorithm followed by an in-depth evaluation of the expressive range of all possible dimension combinations in several scenarios, and discusses their influence in the fitness landscape and in the overall performance of the procedural content generation in EDD.
19.	Alvarez, Alberto, 1992-, et al. (author) Story Designer: Towards a Mixed-Initiative Tool to Create Narrative Structures 2022 In: FDG '22: Proceedings of the 17th International Conference on the Foundations of Digital Games. - New York, NY, USA : ACM Digital Library. - 9781450397957 Conference paper (peer-reviewed)abstract Narratives are a predominant part of games, and their design poses challenges when identifying, encoding, interpreting, evaluating, and generating them. One way to address this would be to approach narrative design in a more abstract layer, such as narrative structures. This paper presents Story Designer, a mixed-initiative co-creative narrative structure tool built on top of the Evolutionary Dungeon Designer (EDD) that uses tropes, narrative conventions found across many media types, to design these structures. Story Designer uses tropes as building blocks for narrative designers to compose complete narrative structures by interconnecting them in graph structures called narrative graphs. Our mixed-initiative approach lets designers manually create their narrative graphs and feeds an underlying evolutionary algorithm with those, creating quality-diverse suggestions using MAP-Elites. Suggestions are visually represented for designers to compare and evaluate and can then be incorporated into the design for further manual editions. At the same time, we use the levels designed within EDD as constraints for the narrative structure, intertwining both level design and narrative. We evaluate the impact of these constraints and the system’s adaptability and expressiveness, resulting in a potential tool to create narrative structures combining level design aspects with narrative.
20.	Alvarez, Alberto, 1992-, et al. (author) Toward Designer Modeling Through Design Style Clustering 2022 In: IEEE Transactions on Games. - : IEEE. - 2475-1502 .- 2475-1510. ; 14:4, s. 676-686 Journal article (peer-reviewed)abstract We propose modeling designer style in mixed-initiative game content creation tools as archetypical design traces. These design traces are formulated as transitions between design styles; these design styles are in turn found through clustering all intermediate designs along the way to making a complete design. This method is implemented in the Evolutionary Dungeon Designer, a research platform for mixed-initiative systems to create adventure and dungeon crawler games. We present results both in the form of design styles for rooms, which can be analyzed to better understand the kind of rooms designed by users, and in the form of archetypical sequences between these rooms, i.e., Designer Personas.
21.	Alvarez, E. M., et al. (author) The global burden of adolescent and young adult cancer in 2019: a systematic analysis for the Global Burden of Disease Study 2019 2022 In: Lancet Oncology. - : Elsevier BV. - 1470-2045. ; 23:1, s. 27-52 Journal article (peer-reviewed)abstract Background In estimating the global burden of cancer, adolescents and young adults with cancer are often overlooked, despite being a distinct subgroup with unique epidemiology, clinical care needs, and societal impact. Comprehensive estimates of the global cancer burden in adolescents and young adults (aged 15-39 years) are lacking. To address this gap, we analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019, with a focus on the outcome of disability-adjusted life-years (DALYs), to inform global cancer control measures in adolescents and young adults. Methods Using the GBD 2019 methodology, international mortality data were collected from vital registration systems, verbal autopsies, and population-based cancer registry inputs modelled with mortality-to-incidence ratios (MIRs). Incidence was computed with mortality estimates and corresponding MIRs. Prevalence estimates were calculated using modelled survival and multiplied by disability weights to obtain years lived with disability (YLDs). Years of life lost (YLLs) were calculated as age-specific cancer deaths multiplied by the standard life expectancy at the age of death. The main outcome was DALYs (the sum of YLLs and YLDs). Estimates were presented globally and by Socio-demographic Index (SDI) quintiles (countries ranked and divided into five equal SDI groups), and all estimates were presented with corresponding 95% uncertainty intervals (UIs). For this analysis, we used the age range of 15-39 years to define adolescents and young adults. Findings There were 1.19 million (95% UI 1.11-1.28) incident cancer cases and 396 000 (370 000-425 000) deaths due to cancer among people aged 15-39 years worldwide in 2019. The highest age-standardised incidence rates occurred in high SDI (59.6 [54.5-65.7] per 100 000 person-years) and high-middle SDI countries (53.2 [48.8-57.9] per 100 000 person-years), while the highest age-standardised mortality rates were in low-middle SDI (14.2 [12.9-15.6] per 100 000 person-years) and middle SDI (13.6 [12.6-14.8] per 100 000 person-years) countries. In 2019, adolescent and young adult cancers contributed 23.5 million (21.9-25.2) DALYs to the global burden of disease, of which 2.7% (1.9-3.6) came from YLDs and 97.3% (96.4-98.1) from YLLs. Cancer was the fourth leading cause of death and tenth leading cause of DALYs in adolescents and young adults globally. Interpretation Adolescent and young adult cancers contributed substantially to the overall adolescent and young adult disease burden globally in 2019. These results provide new insights into the distribution and magnitude of the adolescent and young adult cancer burden around the world. With notable differences observed across SDI settings, these estimates can inform global and country-level cancer control efforts. Copyright (C) 2021 The Author(s). Published by Elsevier Ltd.
22.	Alvarez, EM, et al. (author) The global burden of adolescent and young adult cancer in 2019: a systematic analysis for the Global Burden of Disease Study 2019 2022 In: The Lancet. Oncology. - 1474-5488. ; 23:1, s. 27-52 Journal article (peer-reviewed)
23.	Alvarez, Ines, et al. (author) Comparing Admission Control Architectures for Real-Time Ethernet 2020 In: IEEE Access. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 2169-3536. ; 8, s. 136260-136260 Journal article (peer-reviewed)abstract Industry 4.0 and Autonomous Driving are emerging resource-intensive distributed application domains that deal with open and evolving environments. These systems are subject to stringent resource, timing, and other non-functional constraints, as well as frequent reconfiguration. Thus, real-time behavior must not preclude operational flexibility. This combination is motivating ongoing efforts within the Time Sensitive Networking (TSN) standardization committee to define admission control mechanisms for Ethernet. Existing mechanisms in TSN, like those of AVB, its predecessor, follow a distributed architecture that favors scalability. Conversely, the new mechanisms envisaged for TSN (IEEE 802.1Qcc) follow a (partially) centralized architecture, favoring short reconfiguration latency. This paper shows the first quantitative comparison between distributed and centralized admission control architectures concerning reconfiguration latency. Here, we compare AVB against a dynamic real-time reconfigurable Ethernet technology with centralized management, namely HaRTES. Our experiments show a significantly lower latency using the centralized architecture. We also observe the dependence of the distributed architecture in the end nodes & x2019; performance and the benefit of having a protected channel for the admission control transactions.
24.	Alvarez, Ines, et al. (author) Comparing Admission Control Architectures for Real-Time Ethernet (vol 8, pg 105521, 2020) 2020 In: IEEE Access. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 2169-3536. ; 8, s. 136260-136260 Journal article (other academic/artistic)
25.	Alvarez Vadillo, Ines, et al. (author) Implementing a First CNC for Scheduling and Configuring TSN Networks 2022 In: IEEE International Conference on Emerging Technologies and Factory Automation, ETFA. - : Institute of Electrical and Electronics Engineers Inc.. - 9781665499965 Conference paper (peer-reviewed)abstract Novel industrial applications are leading to important changes in industrial systems. One of the most important changes is the need for systems that are capable to adapt to changes in the environment or the system itself. Because of their nature many of these applications are distributed, and their network infrastructure is key to guarantee the correct operation of the overall system. Furthermore, in order for a distributed system to be able to adapt, its network must be flexible enough to support changes in the traffic during runtime. The Time-Sensitive Networking (TSN) Task Group has proposed a series of standards that aim at providing deterministic real-time communications over Ethernet. TSN also provides centralised online configuration and control architectures which enable the online configuration of the network. A key part in TSN's centralised architectures is the Centralised Network Configuration element (CNC). In this work we present a first implementation of a CNC capable of scheduling time-triggered traffic and deploying such configuration in the network using the Network Configuration (NETCONF) protocol. We also assess the correctness of our implementation using an industrial use case provided by Volvo Construction Equipment.
26.	Bott, Lukas Thomas, et al. (author) Coulomb dissociation of O-16 into He-4 and C-12 2023 In: NUCLEAR PHYSICS IN ASTROPHYSICS - X, NPA-X 2022. - : EDP Sciences. - 2100-014X. ; 279 Conference paper (peer-reviewed)abstract We measured the Coulomb dissociation of O-16 into He-4 and C-12 within the FAIR Phase-0 program at GSI Helmholtzzentrum fur Schwerionenforschung Darmstadt, Germany. From this we will extract the photon dissociation cross section O-16(alpha,gamma)C-12, which is the time reversed reaction to C-12(alpha,gamma)O-16. With this indirect method, we aim to improve on the accuracy of the experimental data at lower energies than measured so far. The expected low cross section for the Coulomb dissociation reaction and close magnetic rigidity of beam and fragments demand a high precision measurement. Hence, new detector systems were built and radical changes to the (RB)-B-3 setup were necessary to cope with the high-intensity O-16 beam. All tracking detectors were designed to let the unreacted O-16 ions pass, while detecting the C-12 and He-4.
27.	Bujosa Mateu, Daniel, et al. (author) CSRP : An Enhanced Protocol for Consistent Reservation of Resources for AVB/TSN 2021 In: IEEE Transactions on Industrial Informatics. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 1551-3203 .- 1941-0050. ; 17:5, s. 3640-3650 Journal article (peer-reviewed)abstract The IEEE Audio Video Bridging (AVB) Task Group (TG) was created to provide Ethernet with soft real-time guarantees. Later on, the TG was renamed to Time-Sensitive Networking (TSN) and its scope broadened to support hard real-time and critical applications. The Stream Reservation Protocol (SRP) is a key work of the TGs as it allows reserving resources in the network, guaranteeing the required quality of service. AVB's SRP is based on a distributed architecture, whereas TSN's is based on centralized ones. The distributed version of SRP is supported and used in TSN. Nevertheless, it was not designed to provide properties that are important for critical applications. In this article, we model SRP using UPPAAL and we study the termination and consistency. We verify that SRP does not provide such properties. Furthermore, we propose an improved protocol called Consistent Stream Reservation Protocol (CSRP) and we formally verify its correctness using UPPAAL.
28.	Ebrahimi-Fakhari, Darius, et al. (author) Defining the clinical, molecular and imaging spectrum of adaptor protein complex 4-associated hereditary spastic paraplegia 2020 In: Brain. - OXFORD ENGLAND : Oxford University Press (OUP). - 0006-8950 .- 1460-2156. ; 143:10, s. 2929-2944 Journal article (peer-reviewed)abstract Bi-allelic loss-of-function variants in genes that encode subunits of the adaptor protein complex 4 (AP-4) lead to prototypical yet poorly understood forms of childhood-onset and complex hereditary spastic paraplegia: SPG47 (AP4B1), SPG50 (AP4M1), SPG51 (AP4E1) and SPG52 (AP4S1). Here, we report a detailed cross-sectional analysis of clinical, imaging and molecular data of 156 patients from 101 families. Enrolled patients were of diverse ethnic backgrounds and covered a wide age range (1.0-49.3 years). While the mean age at symptom onset was 0.8 +/- 0.6 years [standard deviation (SD), range 0.2-5.0], the mean age at diagnosis was 10.2 +/- 8.5 years (SD, range 0.1-46.3). We define a set of core features: early-onset developmental delay with delayed motor milestones and significant speech delay (50% non-verbal); intellectual disability in the moderate to severe range; mild hypotonia in infancy followed by spastic diplegia (mean age: 8.4 +/- 5.1 years, SD) and later tetraplegia (mean age: 16.1 +/- 9.8 years, SD); postnatal microcephaly (83%); foot deformities (69%); and epilepsy (66%) that is intractable in a subset. At last follow-up, 36% ambulated with assistance (mean age: 8.9 +/- 6.4 years, SD) and 54% were wheelchair-dependent (mean age: 13.4 +/- 9.8 years, SD). Episodes of stereotypic laughing, possibly consistent with a pseudobulbar affect, were found in 56% of patients. Key features on neuroimaging include a thin corpus callosum (90%), ventriculomegaly (65%) often with colpocephaly, and periventricular white-matter signal abnormalities (68%). Iron deposition and polymicrogyria were found in a subset of patients. AP4B1-associated SPG47 and AP4M1-associated SPG50 accounted for the majority of cases. About two-thirds of patients were born to consanguineous parents, and 82% carried homozygous variants. Over 70 unique variants were present, the majority of which are frameshift or nonsense mutations. To track disease progression across the age spectrum, we defined the relationship between disease severity as measured by several rating scales and disease duration. We found that the presence of epilepsy, which manifested before the age of 3 years in the majority of patients, was associated with worse motor outcomes. Exploring genotype-phenotype correlations, we found that disease severity and major phenotypes were equally distributed among the four subtypes, establishing that SPG47, SPG50, SPG51 and SPG52 share a common phenotype, an 'AP-4 deficiency syndrome'. By delineating the core clinical, imaging, and molecular features of AP-4-associated hereditary spastic paraplegia across the age spectrum our results will facilitate early diagnosis, enable counselling and anticipatory guidance of affected families and help define endpoints for future interventional trials.
29.	Feldmann, Daneil C., et al. (author) Investigation of multiple populations highlight VEGFA polymorphisms to modulate anterior cruciate ligament injury 2022 In: Journal of Orthopaedic Research. - : John Wiley & Sons. - 0736-0266 .- 1554-527X. ; 40:7, s. 1604-1612 Journal article (peer-reviewed)abstract Polymorphisms in VEGFA and KDR encoding proteins have been associated with anterior cruciate ligament (ACL) injury risk. We leveraged a collective sample from Sweden, Poland, and Australia to investigate the association of functional polymorphisms in VEGFA and KDR with susceptibility to ACL injury risk. Using a case–control genetic association approach, polymorphisms in VEGFA and KDR were genotyped and haplotypes inferred from 765 controls, and 912 cases clinically diagnosed with ACL rupture. For VEGFA, there was a significant overrepresentation of the rs2010963 CC genotype (p = 0.0001, false discovery rate [FDR]: p = 0.001, odds ratio [OR]: 2.16, 95% confidence interval [CI]: 1.47–3.19) in the combined ACL group (18%) compared to the combined control group (11%). The VEGFA (rs699947 C/A, rs1570360 G/A, rs2010963 G/C) A-A-G haplotype was significantly (p = 0.010, OR: 0.85, 95% CI: 0.69–1.05) underrepresented in the combined ACL group (23%) compared to the combined control group (28%). In addition, the A-G-G construct was significantly (p = 0.036, OR: 0.81, 95% CI: 0.64–1.02) underrepresented in the combined ACL group (12%) compared to the combined CON group (16%). Our findings support the association of the VEGFA rs2010963 CC genotype with increased risk and (ii) the VEGFA A-A-G haplotype with a reduced risk, and are in alignment with the a priori hypothesis. Collectively identifying a genetic interval within VEGFA to be implicated in ACL risk modulation and highlight further the importance of vascular regulation in ligament biology.
30.	Ferrando, Carlos, et al. (author) Effects of oxygen on post-surgical infections during an individualised perioperative open-lung ventilatory strategy : a randomised controlled trial 2020 In: British Journal of Anaesthesia. - : ELSEVIER SCI LTD. - 0007-0912 .- 1471-6771. ; 124:1, s. 110-120 Journal article (peer-reviewed)abstract Background: We aimed to examine whether using a high fraction of inspired oxygen (FIO2) in the context of an individualised intra- and postoperative open-lung ventilation approach could decrease surgical site infection (SSI) in patients scheduled for abdominal surgery. Methods: We performed a multicentre, randomised controlled clinical trial in a network of 21 university hospitals from June 6, 2017 to July 19, 2018. Patients undergoing abdominal surgery were randomly assigned to receive a high (0.80) or conventional (0.3) FIO2 during the intraoperative period and during the first 3 postoperative hours. All patients were mechanically ventilated with an open-lung strategy, which included recruitment manoeuvres and individualised positive end-expiratory pressure for the best respiratory-system compliance, and individualised continuous postoperative airway pressure for adequate peripheral oxyhaemoglobin saturation. The primary outcome was the prevalence of SSI within the first 7 postoperative days. The secondary outcomes were composites of systemic complications, length of intensive care and hospital stay, and 6-month mortality. Results: We enrolled 740 subjects: 371 in the high FIO2 group and 369 in the low FIO2 group. Data from 717 subjects were available for final analysis. The rate of SSI during the first postoperative week did not differ between high (8.9%) and low (9.4%) FIO2 groups (relative risk [RR]: 0.94; 95% confidence interval [CI]: 0.59-1.50; P=0.90]). Secondary outcomes, such as atelectasis (7.7% vs 9.8%; RR: 0.77; 95% CI: 0.48-1.25; P=0.38) and myocardial ischaemia (0.6% [n=2] vs 0% [n=0]; P=0.47) did not differ between groups. Conclusions: An oxygenation strategy using high FIO2 compared with conventional FIO2 did not reduce postoperative SSIs in abdominal surgery. No differences in secondary outcomes or adverse events were found.
31.	Jones, Benedict C, et al. (author) To which world regions does the valence-dominance model of social perception apply? 2021 In: Nature Human Behaviour. - : Springer Science and Business Media LLC. - 2397-3374. ; 5:1, s. 159-169 Journal article (peer-reviewed)abstract Over the past 10 years, Oosterhof and Todorov's valence-dominance model has emerged as the most prominent account of how people evaluate faces on social dimensions. In this model, two dimensions (valence and dominance) underpin social judgements of faces. Because this model has primarily been developed and tested in Western regions, it is unclear whether these findings apply to other regions. We addressed this question by replicating Oosterhof and Todorov's methodology across 11 world regions, 41 countries and 11,570 participants. When we used Oosterhof and Todorov's original analysis strategy, the valence-dominance model generalized across regions. When we used an alternative methodology to allow for correlated dimensions, we observed much less generalization. Collectively, these results suggest that, while the valence-dominance model generalizes very well across regions when dimensions are forced to be orthogonal, regional differences are revealed when we use different extraction methods and correlate and rotate the dimension reduction solution. PROTOCOL REGISTRATION: The stage 1 protocol for this Registered Report was accepted in principle on 5 November 2018. The protocol, as accepted by the journal, can be found at https://doi.org/10.6084/m9.figshare.7611443.v1 .
32.	Jover, Mateu, et al. (author) Migrating Legacy Ethernet-Based Traffic with Spatial Redundancy to TSN networks 2022 In: IEEE International Conference on Emerging Technologies and Factory Automation, ETFA. - : Institute of Electrical and Electronics Engineers Inc.. - 9781665499965 Conference paper (peer-reviewed)abstract Distributed Control Systems (DCSs) for emerging industrial control applications impose new communication requirements that cannot be satisfied by current Industrial Ethernet protocols. As a result, industry is pushing the Time-Sensitive Networking (TSN) standards as the de-facto Ethernet-based linklayer to fulfill these requirements. Adequate roadmaps are needed to support a smooth transition from Industrial-Ethernet-based legacy systems to TSN-based ones. In this context some works propose mechanisms to migrate, i.e. map, route and schedule, legacy traffic to TSN. However none of them considers traffic including streams with spatial redundancy requirements and, thus, they cannot be used to migrate legacy highly-reliable DCSs. The present work extends a previous toolchain to migrate, for the first time, legacy critical traffic that includes spatially redundant streams. Particularly, since redundancy is costly, this work proposes and compares two routing methods that consider one redundant stream per traffic.
33.	Kassebaum, Nicholas J., et al. (author) Global, regional, and national disability-adjusted life-years (DALYs) for 315 diseases and injuries and healthy life expectancy (HALE), 1990-2015 : a systematic analysis for the Global Burden of Disease Study 2015 2016 In: The Lancet. - 0140-6736 .- 1474-547X. ; 388:10053, s. 1603-1658 Journal article (peer-reviewed)abstract 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.
34.	Martinez-Madrid, Belen, et al. (author) Immunolocalisation of aquaporins 3, 7, 9 and 10 in the epididymis of three wild ruminant species (Iberian ibex, mouflon and chamois) and sperm cryoresistance 2023 In: Reproduction, Fertility and Development. - : CSIRO PUBLISHING. - 1031-3613 .- 1448-5990. ; 35:16, s. 708-721 Journal article (peer-reviewed)abstract Context In the epididymis, epithelial cells manage changes in the luminal environment for proper sperm maturation. Moreover, aquaglyceroporins, a subgroup of aquaporins (AQP), modulate the transport of water, glycerol and other small molecules in epithelial cells.AimsWe aim to characterise the lining epithelium, quantify its cell composition and immunolocalise the aquaglyceroporins AQP3, AQP7, AQP9 and AQP10 alongside the epididymal ductus of three wild ruminant species, and to determine if species-specific differences could be associated with cauda sperm cryoresistance variations.MethodsEpididymides from Iberian ibex (n = 5), mouflon (n = 5) and chamois (n = 6) were obtained. Cauda spermatozoa were collected and sperm parameters were analysed before and after freezing. Histology and immunohistochemistry of AQP3, 7, 9, 10 and T-CD3 were performed in the caput, corpus and cauda epididymal regions.Key resultsThis work first describes the lining epithelium in Iberian ibex, mouflon and chamois epididymis along the three anatomical regions, consisting of principal, basal, apical, clear and halo cells. However, the percentage of each cell type differed in ibex compared to mouflon and chamois. The positive T-CD3 immunolabeling of all the halo cells confirmed their T-lymphocyte nature. Aquaglyceroporin expression patterns were similar among species, except for differences in AQP7 and AQP10 immunolocalisation in ibex. Species-specific differences in epididymal sperm cryoresistance were confirmed.ConclusionsThe epididymal epithelium of the three wild ruminants differ in their relative number of cell types and AQP immunolocalisation, which ultimately appears to affect cauda epidydimal spermatozoa cryoresistance.ImplicationsOur study provides information on the relevance of the quantitative composition and AQP pattern expression in epididymal lining epithelium on sperm cryoresistance. This work describes the lining epithelium and expression patterns of aquaglyceroporins (AQP3, AQP7, AQP9 and AQP10) in the Iberian ibex, mouflon and chamois epididymis. Species-specific differences in cauda epididymal sperm cryoresistance were confirmed. Differences among the three wild ruminant epididymides in the relative number of epithelial cell types and the immunolocalisation of AQP7 and AQP10 appear to affect the cryoresistance of cauda epididymal spermatozoa.
35.	Mavaddat, Nasim, et al. (author) Prediction of Breast Cancer Risk Based on Profiling With Common Genetic Variants 2015 In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 1460-2105 .- 0027-8874. ; 107:5, s. 036-036 Journal article (peer-reviewed)abstract Background: Data for multiple common susceptibility alleles for breast cancer may be combined to identify women at different levels of breast cancer risk. Such stratification could guide preventive and screening strategies. However, empirical evidence for genetic risk stratification is lacking. Methods: We investigated the value of using 77 breast cancer-associated single nucleotide polymorphisms (SNPs) for risk stratification, in a study of 33 673 breast cancer cases and 33 381 control women of European origin. We tested all possible pair-wise multiplicative interactions and constructed a 77-SNP polygenic risk score (PRS) for breast cancer overall and by estrogen receptor (ER) status. Absolute risks of breast cancer by PRS were derived from relative risk estimates and UK incidence and mortality rates. Results: There was no strong evidence for departure from a multiplicative model for any SNP pair. Women in the highest 1% of the PRS had a three-fold increased risk of developing breast cancer compared with women in the middle quintile (odds ratio [OR] = 3.36, 95% confidence interval [CI] = 2.95 to 3.83). The ORs for ER-positive and ER-negative disease were 3.73 (95% CI = 3.24 to 4.30) and 2.80 (95% CI = 2.26 to 3.46), respectively. Lifetime risk of breast cancer for women in the lowest and highest quintiles of the PRS were 5.2% and 16.6% for a woman without family history, and 8.6% and 24.4% for a woman with a first-degree family history of breast cancer. Conclusions: The PRS stratifies breast cancer risk in women both with and without a family history of breast cancer. The observed level of risk discrimination could inform targeted screening and prevention strategies. Further discrimination may be achievable through combining the PRS with lifestyle/environmental factors, although these were not considered in this report.
36.	OBrien, Emma, et al. (author) Sperm freezability is neither associated with the expression of aquaporin 3 nor sperm head dimensions in dromedary camel (Camelus dromedarius) 2022 In: Theriogenology. - : ELSEVIER SCIENCE INC. - 0093-691X .- 1879-3231. ; 189, s. 230-236 Journal article (peer-reviewed)abstract The expression of aquaglyceroporin 3 (AQP-3) has been demonstrated in the spermatozoa of several mammalian species and its role has been associated with cryotolerance. Post-thaw sperm quality from individual dromedary males with different response to freezing-thawing process was evaluated through sperm head morphometry. In order to understand the cellular mechanisms affected by cryoinjury we have explored the presence and distribution of sperm AQP-3 using western blotting and immunocyto-chemistry. WB showed different intensity of the specific signal bands at 28 kDa. Immunofluorescence assessments allowed us to identify five different and clear AQP-3 distribution patterns of labelling in the sperm plasma membrane; acrosome, post-acrosome, mid-piece, and principal and final tail. Although expression of AQP-3 varied among male ejaculates, the individual sperm response to freeze-thawing was not associated with AQP-3 expression. Thus, AQP3 expressions do not seem like a reliable predictor of sperm response to freeze-thawing process in this species. This work is the first to describe the morphometric characteristics of the heads of dromedary spermatozoa. No correlation was found be-tween sperm head dimensions and sperm quality variables after freeze-thawing suggesting that dromedary camel sperm head morphometry is also not a reliable predictor of cryosurvival.
37.	Papp, Zoltan, et al. (author) Levosimendan Efficacy and Safety : 20 Years of SIMDAX in Clinical Use 2020 In: Journal of Cardiovascular Pharmacology. - : Ovid Technologies (Wolters Kluwer Health). - 0160-2446 .- 1533-4023. ; 76:1, s. 4-22 Journal article (peer-reviewed)abstract Levosimendan was first approved for clinical use in 2000, when authorization was granted by Swedish regulatory authorities for the hemodynamic stabilization of patients with acutely decompensated chronic heart failure (HF). In the ensuing 20 years, this distinctive inodilator, which enhances cardiac contractility through calcium sensitization and promotes vasodilatation through the opening of adenosine triphosphate-dependent potassium channels on vascular smooth muscle cells, has been approved in more than 60 jurisdictions, including most of the countries of the European Union and Latin America. Areas of clinical application have expanded considerably and now include cardiogenic shock, takotsubo cardiomyopathy, advanced HF, right ventricular failure, pulmonary hypertension, cardiac surgery, critical care, and emergency medicine. Levosimendan is currently in active clinical evaluation in the United States. Levosimendan in IV formulation is being used as a research tool in the exploration of a wide range of cardiac and noncardiac disease states. A levosimendan oral form is at present under evaluation in the management of amyotrophic lateral sclerosis. To mark the 20 years since the advent of levosimendan in clinical use, 51 experts from 23 European countries (Austria, Belgium, Croatia, Cyprus, Czech Republic, Estonia, Finland, France, Germany, Greece, Hungary, Italy, the Netherlands, Norway, Poland, Portugal, Russia, Slovenia, Spain, Sweden, Switzerland, the United Kingdom, and Ukraine) contributed to this essay, which evaluates one of the relatively few drugs to have been successfully introduced into the acute HF arena in recent times and charts a possible development trajectory for the next 20 years.
38.	Pequeno, Belen, et al. (author) Cooling rate modifies the location of aquaporin 3 in spermatozoa of sheep and goat 2024 In: Theriogenology. - : ELSEVIER SCIENCE INC. - 0093-691X .- 1879-3231. ; 223, s. 29-35 Journal article (peer-reviewed)abstract The freeze-thawing process induces osmotic changes that may affect the membrane domain location of aquaporins' (AQP) in spermatozoa. Recent studies suggest that changes in AQP3 localization allows better sperm osmo-adaptation, improving the cryoresistance. Ultra-rapid freezing is an alternative cryopreservation technique that requires less equipment than conventional freezing, and it is faster, simpler and can be used in the field. This study aimed to determine the influence of freezing-thawing rates (slow (control) vs. ultra-rapid) on AQP3 expression and location in the spermatozoa from small ruminants (sheep and goats) and its relationship with sperm cryo-damage. Spermatozoa were collected from 10 Merino rams and 10 Murciano-Granadina bucks. The presence and distribution of AQP3 were assessed by Western blotting and immunocytochemistry (ICC), employing a commercial rabbit polyclonal antibody. Sperm motility was CASA system-analyzed, and membrane and acrosome integrity assessed by fluorescence (PI/PNA-FITC). Western blotting did not detect a significant effect of freezing-thawing rate on the amount of AQP3 while ICC found freezing-thawing rate affecting AQP3 location (P < 0.05). In both species, the percentages of spermatozoa showing AQP3 in the post-acrosome region, mid-piece, and principal piece of the tail were greater in samples cryopreserved by slow freezing-thawing (control) than ultra-rapid freezing-thawing rates (P < 0.05). Spermatozoa cryopreserved using ultra-rapid freezing-thawing showed decrease motility, plasma membrane, and acrosome integrity (P < 0.05), which might be related, at least in part, to a lower expression of AQP3. In conclusion, the cooling rate modifies the location of AQP3 in spermatozoa of sheep and goat, which might be associated with sperm cryosurvival.
39.	Pequeno, Belen, et al. (author) Variation of existence and location of aquaporin 3 in relation to cryoresistance of ram spermatozoa 2023 In: Frontiers in Veterinary Science. - : FRONTIERS MEDIA SA. - 2297-1769. ; 10 Journal article (peer-reviewed)abstract Introduction and objectiveOsmotic changes during the process of freeze-thawing involve changes in the location of aquaporins (AQPs) in membrane domains of spermatozoa. Some AQPs, like aquaporin 3 (AQP3), are linked to sperm cryotolerance in the porcine species. Conspicuous individual variability exists between rams and their ejaculates, which may be classified as displaying good freezability (GFE) or poor freezability (PFE), depending on several endogenous and environmental factors. The present work aimed to examine whether differences in freezability could even involve changes in location and expression of AQP3 in ram spermatozoa. MethodsThirty ejaculates from 10 rams (three of each) were evaluated and subsequently classified as GFE (n = 13) or PFE (n = 17) through a principal component analysis (PCA) and k-means cluster analysis. Spermatozoa were examined for the presence, abundance and distribution of AQP3 by western blot and immunocytochemistry, employing a commercial rabbit polyclonal antibody (AQP3 - ab125219). Results and discussionAlthough AQP3 was found in the sperm acrosome, midpiece, principal and end piece of the tail in both fresh and after frozen-thawed samples, its highest immunolabeling was found in the mid- and principal piece. In the GFE group, the expression of AQP3 in the mid- and principal piece was greater (P < 0.05) in frozen-thawed samples than in fresh specimens while such differences were not detected in the PFE group. Sperm cryotolerance relates to changes in AQP3 expression and thus AQP3 could be used as a biomarker for cryotolerance. ConclusionA greater capacity of AQP3 localization in mid- and principal piece of the spermatozoa could be linked to an increase the osmo-adaptative capacity of ejaculates with better capacity to withstand freeze-thawing processes.
40.	Peris-Frau, Patricia, et al. (author) Comparative evaluation of DNA integrity using sperm chromatin structure assay and Sperm-Ovis-Halomax during in vitro capacitation of cryopreserved ram spermatozoa 2019 In: Reproduction in domestic animals. - : WILEY. - 0936-6768 .- 1439-0531. ; 54, s. 46-49 Journal article (peer-reviewed)abstract This study aimed to compare the ability of sperm chromatin structure assay (SCSA (R)) and Sperm-Ovis-Halomax (R) to detect DNA fragmentation in frozen-thawed ram spermatozoa incubated under capacitating conditions in synthetic oviductal fluid (SOF) supplemented with oestrous sheep serum (SOF-ESS) at multiple time points (0-240 min). Incubation in SOF-ESS had no significant effects on SCSA (R) parameters while the percentage of spermatozoa with fragmented DNA measured by Sperm-Ovis-Halomax (R) increased after 180 min of incubation. In addition, no correlation or agreement was found between the techniques, suggesting that SCSA (R) and Sperm-Ovis-Halomax (R) may quantify different types of DNA damage in ram spermatozoa under these experimental conditions.
41.	Peris-Frau, Patricia, et al. (author) Unravelling how in vitro capacitation alters ram sperm chromatin before and after cryopreservation 2021 In: Andrology. - : WILEY. - 2047-2919 .- 2047-2927. ; 9:1, s. 414-425 Journal article (peer-reviewed)abstract Background Sperm chromatin structure provides valuable information for the prediction of male fertility and can be altered during different procedures. Previous studies have shown that sperm chromatin condensation decreased during in vitro capacitation. Moreover, cryopreservation can affect sperm DNA integrity and chromatin compaction. Objectives This study aimed to investigate dynamic modifications produced in the chromatin structure of ram spermatozoa during in vitro capacitation before and after cryopreservation. Materials and methods Chromatin decondensation (AB+), DNA methylation, DNA fragmentation index (%DFI) and high DNA stainability (HDS) were evaluated in fresh and frozen-thawed ram spermatozoa incubated under capacitating (CAP) conditions at 1, 5, 15, 30, 60, 120, 180 and 240 minutes and under non-capacitating (NC) conditions at 0, 15 and 240 minutes. Results Incubation in NC conditions did not induce significant changes in chromatin condensation (P > .05; AB + and HDS). However, incubation of fresh and cryopreserved ram spermatozoa under CAP conditions significantly increased chromatin decondensation (P < .05), reaching the highest percentage of AB + and HDS from 180 to 240 minutes in fresh samples and from 5 to 30 minutes in cryopreserved samples. Both variables (HDS and AB+) were positively correlated with tyrosine phosphorylation, total motility, progressive motility, curvilinear velocity and amplitude of lateral head displacement, as well as between them under CAP conditions in fresh and cryopreserved spermatozoa. DNA methylation significantly increased in cryopreserved spermatozoa (P < .05), but only after extended incubation under CAP conditions (60-240 minutes), while the %DFI, albeit higher in cryopreserved samples, remained constant under CAP and NC conditions in both types of sample (P > .05). Discussion and conclusions Our results suggest that sperm chromatin condensation decreased progressively during in vitro capacitation of ram spermatozoa, while sperm DNA integrity remained intact. Such changes in chromatin condensation appeared faster after sperm cryopreservation.
42.	Poláková, Silvia, et al. (author) Formation of new chromosomes as a virulence mechanism in yeast Candida glabrata. 2009 In: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 106:8, s. 2688-2693 Journal article (peer-reviewed)abstract In eukaryotes, the number and rough organization of chromosomes is well preserved within isolates of the same species. Novel chromosomes and loss of chromosomes are infrequent and usually associated with pathological events. Here, we analyzed 40 pathogenic isolates of a haploid and asexual yeast, Candida glabrata, for their genome structure and stability. This organism has recently become the second most prevalent yeast pathogen in humans. Although the gene sequences were well conserved among different strains, their chromosome structures differed drastically. The most frequent events reshaping chromosomes were translocations of chromosomal arms. However, also larger segmental duplications were frequent and occasionally we observed novel chromosomes. Apparently, this yeast can generate a new chromosome by duplication of chromosome segments carrying a centromere and subsequently adding novel telomeric ends. We show that the observed genome plasticity is connected with antifungal drug resistance and it is likely an advantage in the human body, where environmental conditions fluctuate a lot.
43.	Przeslawski, Rachel, et al. (author) Implications of sponge biodiversity patterns for the management of a marine reserve in northern Australia 2015 In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:11 Journal article (peer-reviewed)abstract Marine reserves are becoming progressively more important as anthropogenic impacts continue to increase, but we have little baseline information for most marine environments. In this study, we focus on the Oceanic Shoals Commonwealth Marine Reserve (CMR) in northern Australia, particularly the carbonate banks and terraces of the Sahul Shelf and Van Diemen Rise which have been designated a Key Ecological Feature (KEF). We use a species-level inventory compiled from three marine surveys to the CMR to address several questions relevant to marine management: 1) Are carbonate banks and other raised geomorphic features associated with biodiversity hotspots? 2) Can environmental (depth, substrate hardness, slope) or biogeographic (east vs west) variables help explain local and regional differences in community structure? 3) Do sponge communities differ among individual raised geomorphic features? Approximately 750 sponge specimens were collected in the Oceanic Shoals CMR and assigned to 348 species, of which only 18% included taxonomically described species. Between eastern and western areas of the CMR, there was no difference between sponge species richness or assemblages on raised geomorphic features. Among individual raised geomorphic features, sponge assemblages were significantly different, but species richness was not. Species richness showed no linear relationships with measured environmental factors, but sponge assemblages were weakly associated with several environmental variables including mean depth and mean backscatter (east and west) and mean slope (east only). These patterns of sponge diversity are applied to support the future management and monitoring of this region, particularly noting the importance of spatial scale in biodiversity assessments and associated management strategies.
44.	Salazar-Alvarez, German, et al. (author) Tunable High-Field Magnetization in Strongly Exchange-Coupled Freestanding Co/CoO Core/Shell Coaxial Nanowires 2016 In: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 8:34, s. 22477-22483 Journal article (peer-reviewed)abstract The exchange bias properties of Co/CoO coaxial core/shell nanowires were investigated with cooling and applied fields perpendicular to the wire axis. This configuration leads to unexpected exchange-bias effects. First, the magnetization value at high fields is found to depend on the field-cooling conditions. This effect arises from the competition between the magnetic anisotropy and the Zeeman energies for cooling fields perpendicular to the wire axis. This allows imprinting predefined magnetization states to the antiferromagnetic (AFM) shell, as corroborated by micromagnetic simulations. Second, the system exhibits a high-field magnetic irreversibility, leading to open hysteresis loops attributed to the AFM easy axis reorientation during the reversal (effect similar to athermal training). A distinct way to manipulate the high-field magnetization in exchange-biased systems, beyond the archetypical effects, was thus experimentally and theoretically demonstrated.
45.	Santiago-Moreno, Julian, et al. (author) Expression of Aquaglyceroporins in Spermatozoa from Wild Ruminants Is Influenced by Photoperiod and Thyroxine Concentrations 2022 In: International Journal of Molecular Sciences. - : MDPI. - 1661-6596 .- 1422-0067. ; 23:6 Journal article (peer-reviewed)abstract This work identified the presence of AQPs in frozen-thawed sperm of wild ruminants and assessed the influence of the interaction between photoperiod and thyroxine on AQP expression, and on testosterone secretion. Thyroxine and melatonin were administered to ibexes. In a second experiment, performed in mouflons, circulating thyroxine was reduced via treatment with propylthiouracil (PTU), and an artificial long day (LD) photoperiod established. In the ibexes, the melatonin treatment increased the blood plasma testosterone concentration, reduced the cryoresistance ratio (CR) for sperm viability and the presence of an intact acrosome, and increased the percentage of sperm with AQP7 in the acrosome and of AQP3 and AQP10 in the midpiece. In the mouflons, neither the PTU treatment, the LD, nor the combination of both affected the CR of any sperm variable. The percentage of sperm with AQP3 increased in the post-acrosome region but decreased in the tail in the LD+PTU group. The percentage of sperm with AQP10 in the principal piece and endpiece was lower in the PTU+LD group than in the control and LD groups. The influence of photoperiod/melatonin on AQP expression might be indirectly exerted through changes in the testosterone concentration, and thus ultimately affect sperm cryoresistance.
46.	Schwarz, Maria, et al. (author) Excessive copper impairs intrahepatocyte trafficking and secretion of selenoprotein P. 2023 In: Nature communications. - 2041-1723. ; 14:1 Journal article (peer-reviewed)abstract Selenium homeostasis depends on hepatic biosynthesis of selenoprotein P (SELENOP) and SELENOP-mediated transport from the liver to e.g. the brain. In addition, the liver maintains copper homeostasis. Selenium and copper metabolism are inversely regulated, as increasing copper and decreasing selenium levels are observed in blood during aging and inflammation. Here we show that copper treatment increased intracellular selenium and SELENOP in hepatocytes and decreased extracellular SELENOP levels. Hepatic accumulation of copper is a characteristic of Wilson's disease. Accordingly, SELENOP levels were low in serum of Wilson's disease patients and Wilson's rats. Mechanistically, drugs targeting protein transport in the Golgi complex mimicked some of the effects observed, indicating a disrupting effect of excessive copper on intracellular SELENOP transport resulting in its accumulation in the late Golgi. Our data suggest that hepatic copper levels determine SELENOP release from the liver and may affect selenium transport to peripheral organs such as the brain.
47.	Wang, Haidong, et al. (author) Estimates of global, regional, and national incidence, prevalence, and mortality of HIV, 1980-2015 : the Global Burden of Disease Study 2015. 2016 In: The lancet. HIV. - : Elsevier. - 2352-3018. ; 3:8, s. e361-e387 Journal article (peer-reviewed)abstract BACKGROUND: Timely assessment of the burden of HIV/AIDS is essential for policy setting and programme evaluation. In this report from the Global Burden of Disease Study 2015 (GBD 2015), we provide national estimates of levels and trends of HIV/AIDS incidence, prevalence, coverage of antiretroviral therapy (ART), and mortality for 195 countries and territories from 1980 to 2015.METHODS: For countries without high-quality vital registration data, we estimated prevalence and incidence with data from antenatal care clinics and population-based seroprevalence surveys, and with assumptions by age and sex on initial CD4 distribution at infection, CD4 progression rates (probability of progression from higher to lower CD4 cell-count category), on and off antiretroviral therapy (ART) mortality, and mortality from all other causes. Our estimation strategy links the GBD 2015 assessment of all-cause mortality and estimation of incidence and prevalence so that for each draw from the uncertainty distribution all assumptions used in each step are internally consistent. We estimated incidence, prevalence, and death with GBD versions of the Estimation and Projection Package (EPP) and Spectrum software originally developed by the Joint United Nations Programme on HIV/AIDS (UNAIDS). We used an open-source version of EPP and recoded Spectrum for speed, and used updated assumptions from systematic reviews of the literature and GBD demographic data. For countries with high-quality vital registration data, we developed the cohort incidence bias adjustment model to estimate HIV incidence and prevalence largely from the number of deaths caused by HIV recorded in cause-of-death statistics. We corrected these statistics for garbage coding and HIV misclassification.FINDINGS: Global HIV incidence reached its peak in 1997, at 3·3 million new infections (95% uncertainty interval [UI] 3·1-3·4 million). Annual incidence has stayed relatively constant at about 2·6 million per year (range 2·5-2·8 million) since 2005, after a period of fast decline between 1997 and 2005. The number of people living with HIV/AIDS has been steadily increasing and reached 38·8 million (95% UI 37·6-40·4 million) in 2015. At the same time, HIV/AIDS mortality has been declining at a steady pace, from a peak of 1·8 million deaths (95% UI 1·7-1·9 million) in 2005, to 1·2 million deaths (1·1-1·3 million) in 2015. We recorded substantial heterogeneity in the levels and trends of HIV/AIDS across countries. Although many countries have experienced decreases in HIV/AIDS mortality and in annual new infections, other countries have had slowdowns or increases in rates of change in annual new infections.INTERPRETATION: Scale-up of ART and prevention of mother-to-child transmission has been one of the great successes of global health in the past two decades. However, in the past decade, progress in reducing new infections has been slow, development assistance for health devoted to HIV has stagnated, and resources for health in low-income countries have grown slowly. Achievement of the new ambitious goals for HIV enshrined in Sustainable Development Goal 3 and the 90-90-90 UNAIDS targets will be challenging, and will need continued efforts from governments and international agencies in the next 15 years to end AIDS by 2030.
48.	Wang, Haidong, et al. (author) Global, regional, and national life expectancy, all-cause mortality, and cause-specific mortality for 249 causes of death, 1980-2015 : a systematic analysis for the Global Burden of Disease Study 2015 2016 In: The Lancet. - 0140-6736 .- 1474-547X. ; 388:10053, s. 1459-1544 Journal article (peer-reviewed)abstract BACKGROUND: Improving survival and extending the longevity of life for all populations requires timely, robust evidence on local mortality levels and trends. The Global Burden of Disease 2015 Study (GBD 2015) provides a comprehensive assessment of all-cause and cause-specific mortality for 249 causes in 195 countries and territories from 1980 to 2015. These results informed an in-depth investigation of observed and expected mortality patterns based on sociodemographic measures.METHODS: We estimated all-cause mortality by age, sex, geography, and year using an improved analytical approach originally developed for GBD 2013 and GBD 2010. Improvements included refinements to the estimation of child and adult mortality and corresponding uncertainty, parameter selection for under-5 mortality synthesis by spatiotemporal Gaussian process regression, and sibling history data processing. We also expanded the database of vital registration, survey, and census data to 14 294 geography-year datapoints. For GBD 2015, eight causes, including Ebola virus disease, were added to the previous GBD cause list for mortality. We used six modelling approaches to assess cause-specific mortality, with the Cause of Death Ensemble Model (CODEm) generating estimates for most causes. We used a series of novel analyses to systematically quantify the drivers of trends in mortality across geographies. First, we assessed observed and expected levels and trends of cause-specific mortality as they relate to the Socio-demographic Index (SDI), a summary indicator derived from measures of income per capita, educational attainment, and fertility. Second, we examined factors affecting total mortality patterns through a series of counterfactual scenarios, testing the magnitude by which population growth, population age structures, and epidemiological changes contributed to shifts in mortality. Finally, we attributed changes in life expectancy to changes in cause of death. We documented each step of the GBD 2015 estimation processes, as well as data sources, in accordance with Guidelines for Accurate and Transparent Health Estimates Reporting (GATHER).FINDINGS: Globally, life expectancy from birth increased from 61·7 years (95% uncertainty interval 61·4-61·9) in 1980 to 71·8 years (71·5-72·2) in 2015. Several countries in sub-Saharan Africa had very large gains in life expectancy from 2005 to 2015, rebounding from an era of exceedingly high loss of life due to HIV/AIDS. At the same time, many geographies saw life expectancy stagnate or decline, particularly for men and in countries with rising mortality from war or interpersonal violence. From 2005 to 2015, male life expectancy in Syria dropped by 11·3 years (3·7-17·4), to 62·6 years (56·5-70·2). Total deaths increased by 4·1% (2·6-5·6) from 2005 to 2015, rising to 55·8 million (54·9 million to 56·6 million) in 2015, but age-standardised death rates fell by 17·0% (15·8-18·1) during this time, underscoring changes in population growth and shifts in global age structures. The result was similar for non-communicable diseases (NCDs), with total deaths from these causes increasing by 14·1% (12·6-16·0) to 39·8 million (39·2 million to 40·5 million) in 2015, whereas age-standardised rates decreased by 13·1% (11·9-14·3). Globally, this mortality pattern emerged for several NCDs, including several types of cancer, ischaemic heart disease, cirrhosis, and Alzheimer's disease and other dementias. By contrast, both total deaths and age-standardised death rates due to communicable, maternal, neonatal, and nutritional conditions significantly declined from 2005 to 2015, gains largely attributable to decreases in mortality rates due to HIV/AIDS (42·1%, 39·1-44·6), malaria (43·1%, 34·7-51·8), neonatal preterm birth complications (29·8%, 24·8-34·9), and maternal disorders (29·1%, 19·3-37·1). Progress was slower for several causes, such as lower respiratory infections and nutritional deficiencies, whereas deaths increased for others, including dengue and drug use disorders. Age-standardised death rates due to injuries significantly declined from 2005 to 2015, yet interpersonal violence and war claimed increasingly more lives in some regions, particularly in the Middle East. In 2015, rotaviral enteritis (rotavirus) was the leading cause of under-5 deaths due to diarrhoea (146 000 deaths, 118 000-183 000) and pneumococcal pneumonia was the leading cause of under-5 deaths due to lower respiratory infections (393 000 deaths, 228 000-532 000), although pathogen-specific mortality varied by region. Globally, the effects of population growth, ageing, and changes in age-standardised death rates substantially differed by cause. Our analyses on the expected associations between cause-specific mortality and SDI show the regular shifts in cause of death composition and population age structure with rising SDI. Country patterns of premature mortality (measured as years of life lost [YLLs]) and how they differ from the level expected on the basis of SDI alone revealed distinct but highly heterogeneous patterns by region and country or territory. Ischaemic heart disease, stroke, and diabetes were among the leading causes of YLLs in most regions, but in many cases, intraregional results sharply diverged for ratios of observed and expected YLLs based on SDI. Communicable, maternal, neonatal, and nutritional diseases caused the most YLLs throughout sub-Saharan Africa, with observed YLLs far exceeding expected YLLs for countries in which malaria or HIV/AIDS remained the leading causes of early death.INTERPRETATION: At the global scale, age-specific mortality has steadily improved over the past 35 years; this pattern of general progress continued in the past decade. Progress has been faster in most countries than expected on the basis of development measured by the SDI. Against this background of progress, some countries have seen falls in life expectancy, and age-standardised death rates for some causes are increasing. Despite progress in reducing age-standardised death rates, population growth and ageing mean that the number of deaths from most non-communicable causes are increasing in most countries, putting increased demands on health systems.

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