| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Bentham, James, et al.
(author)
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A century of trends in adult human height
- 2016
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In: eLIFE. - 2050-084X. ; 5
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Journal article (peer-reviewed)abstract
- Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.522.7) and 16.5 cm (13.319.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
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| 3. |
- Bentham, James, et al.
(author)
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A century of trends in adult human height
- 2016
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In: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 5
-
Journal article (peer-reviewed)abstract
- Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5–22.7) and 16.5 cm (13.3– 19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8– 144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries.
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| 4. |
- Bernal, Ximena E., et al.
(author)
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Empowering Latina scientists
- 2019
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 363:6429, s. 825-826
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Journal article (other academic/artistic)
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| 5. |
- Danaei, Goodarz, et al.
(author)
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Effects of diabetes definition on global surveillance of diabetes prevalence and diagnosis: a pooled analysis of 96 population-based studies with 331288 participants
- 2015
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In: The Lancet Diabetes & Endocrinology. - 2213-8595 .- 2213-8587. ; 3:8, s. 624-637
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Journal article (peer-reviewed)abstract
- Background Diabetes has been defined on the basis of different biomarkers, including fasting plasma glucose (FPG), 2-h plasma glucose in an oral glucose tolerance test (2hOGTT), and HbA(1c). We assessed the effect of different diagnostic definitions on both the population prevalence of diabetes and the classification of previously undiagnosed individuals as having diabetes versus not having diabetes in a pooled analysis of data from population-based health examination surveys in different regions. Methods We used data from 96 population-based health examination surveys that had measured at least two of the biomarkers used for defining diabetes. Diabetes was defined using HbA(1c) (HbA(1c) >= 6 . 5% or history of diabetes diagnosis or using insulin or oral hypoglycaemic drugs) compared with either FPG only or FPG-or-2hOGTT definitions (FPG >= 7 . 0 mmol/L or 2hOGTT >= 11 . 1 mmol/L or history of diabetes or using insulin or oral hypoglycaemic drugs). We calculated diabetes prevalence, taking into account complex survey design and survey sample weights. We compared the prevalences of diabetes using different definitions graphically and by regression analyses. We calculated sensitivity and specificity of diabetes diagnosis based on HbA1c compared with diagnosis based on glucose among previously undiagnosed individuals (ie, excluding those with history of diabetes or using insulin or oral hypoglycaemic drugs). We calculated sensitivity and specificity in each survey, and then pooled results using a random-effects model. We assessed the sources of heterogeneity of sensitivity by meta-regressions for study characteristics selected a priori. Findings Population prevalence of diabetes based on FPG- or-2hOGTT was correlated with prevalence based on FPG alone (r= 0 . 98), but was higher by 2-6 percentage points at different prevalence levels. Prevalence based on HbA(1c) was lower than prevalence based on FPG in 42 . 8% of age-sex-survey groups and higher in another 41 . 6%; in the other 15 . 6%, the two definitions provided similar prevalence estimates. The variation across studies in the relation between glucose-based and HbA(1c)-based prevalences was partly related to participants' age, followed by natural logarithm of per person gross domestic product, the year of survey, mean BMI, and whether the survey population was national, subnational, or from specific communities. Diabetes defined as HbA(1c) 6 . 5% or more had a pooled sensitivity of 52 . 8% (95% CI 51 . 3-54 . 3%) and a pooled specificity of 99 . 74% (99 . 71-99 . 78%) compared with FPG 7 . 0 mmol/L or more for diagnosing previously undiagnosed participants; sensitivity compared with diabetes defined based on FPG-or-2hOGTT was 30 . 5% (28 . 7-32 . 3%). None of the preselected study-level characteristics explained the heterogeneity in the sensitivity of HbA(1c) versus FPG. Interpretation Different biomarkers and definitions for diabetes can provide different estimates of population prevalence of diabetes, and differentially identify people without previous diagnosis as having diabetes. Using an HbA(1c)-based definition alone in health surveys will not identify a substantial proportion of previously undiagnosed people who would be considered as having diabetes using a glucose-based test.
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| 6. |
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| 7. |
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| 8. |
- Santangelo, James S., et al.
(author)
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Global urban environmental change drives adaptation in white clover
- 2022
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 375
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Journal article (peer-reviewed)abstract
- Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural dines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.
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| 9. |
- Zhou, Bin, et al.
(author)
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Worldwide trends in diabetes since 1980: A pooled analysis of 751 population-based studies with 4.4 million participants
- 2016
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In: The Lancet. - : Elsevier B.V.. - 0140-6736 .- 1474-547X. ; 387:10027, s. 1513-1530
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Journal article (peer-reviewed)abstract
- Background: One of the global targets for non-communicable diseases is to halt, by 2025, the rise in the age standardised adult prevalence of diabetes at its 2010 levels. We aimed to estimate worldwide trends in diabetes, how likely it is for countries to achieve the global target, and how changes in prevalence, together with population growth and ageing, are aff ecting the number of adults with diabetes.Methods: We pooled data from population-based studies that had collected data on diabetes through measurement of its biomarkers. We used a Bayesian hierarchical model to estimate trends in diabetes prevalence-defined as fasting plasma glucose of 7.0 mmol/L or higher, or history of diagnosis with diabetes, or use of insulin or oral hypoglycaemic drugs-in 200 countries and territories in 21 regions, by sex and from 1980 to 2014. We also calculated the posterior probability of meeting the global diabetes target if post-2000 trends continue.Findings: We used data from 751 studies including 4372000 adults from 146 of the 200 countries we make estimates for. Global age-standardised diabetes prevalence increased from 4.3% (95% credible interval 2.4-17.0) in 1980 to 9.0% (7.2-11.1) in 2014 in men, and from 5.0% (2.9-7.9) to 7.9% (6.4-9.7) in women. The number of adults with diabetes in the world increased from 108 million in 1980 to 422 million in 2014 (28.5% due to the rise in prevalence, 39.7% due to population growth and ageing, and 31.8% due to interaction of these two factors). Age-standardised adult diabetes prevalence in 2014 was lowest in northwestern Europe, and highest in Polynesia and Micronesia, at nearly 25%, followed by Melanesia and the Middle East and north Africa. Between 1980 and 2014 there was little change in age-standardised diabetes prevalence in adult women in continental western Europe, although crude prevalence rose because of ageing of the population. By contrast, age-standardised adult prevalence rose by 15 percentage points in men and women in Polynesia and Micronesia. In 2014, American Samoa had the highest national prevalence of diabetes (>30% in both sexes), with age-standardised adult prevalence also higher than 25% in some other islands in Polynesia and Micronesia. If post-2000 trends continue, the probability of meeting the global target of halting the rise in the prevalence of diabetes by 2025 at the 2010 level worldwide is lower than 1% for men and is 1% for women. Only nine countries for men and 29 countries for women, mostly in western Europe, have a 50% or higher probability of meeting the global target.Interpretation: Since 1980, age-standardised diabetes prevalence in adults has increased, or at best remained unchanged, in every country. Together with population growth and ageing, this rise has led to a near quadrupling of the number of adults with diabetes worldwide. The burden of diabetes, both in terms of prevalence and number of adults aff ected, has increased faster in low-income and middle-income countries than in high-income countries.
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| 10. |
- Abolfathi, Bela, et al.
(author)
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The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
-
In: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
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Journal article (peer-reviewed)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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| 11. |
- Angelstam, Per, et al.
(author)
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Maintaining natural and traditional cultural green infrastructures across Europe: learning from historic and current landscape transformations
- 2021
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In: Landscape Ecology. - : Springer Publishing Company. - 0921-2973 .- 1572-9761. ; 36:2, s. 637-663
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Journal article (peer-reviewed)abstract
- Context Maintaining functional green infrastructures (GIs) require evidence-based knowledge about historic and current states and trends of representative land cover types. Objectives We address: (1) the long-term loss and transformation of potential natural forest vegetation; (2) the effects of site productivity on permanent forest loss and emergence of traditional cultural landscapes; (3) the current management intensity; and (4) the social-ecological contexts conducive to GI maintenance . Methods We selected 16 case study regions, each with a local hotspot landscape, ranging from intact forest landscapes, via contiguous and fragmented forest covers, to severe forest loss. Quantitative open access data were used to estimate (i) the historic change and (ii) transformation of land covers, and (iii) compare the forest canopy loss from 2000 to 2018. Qualitative narratives about each hotspot landscape were analysed for similarities (iv). Results While the potential natural forest vegetation cover in the 16 case study regions had a mean of 86%, historically it has been reduced to 34%. Higher site productivity coincided with transformation to non-forest land covers. The mean annual forest canopy loss for 2000-2018 ranged from 0.01 to 1.08%. The 16 case studies represented five distinct social-ecological contexts (1) radical transformation of landscapes, (2) abuse of protected area concepts, (3) ancient cultural landscapes (4) multi-functional forests, and (5) intensive even-aged forest management, of which 1 and 4 was most common. Conclusions GIs encompass both forest naturalness and traditional cultural landscapes. Our review of Pan-European regions and landscapes revealed similarities in seemingly different contexts, which can support knowledge production and learning about how to sustain GIs.
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| 12. |
- Blanton, Michael R., et al.
(author)
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Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
- 2017
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In: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
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Journal article (peer-reviewed)abstract
- We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
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| 13. |
- Carpintero, Guillermo, et al.
(author)
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Interconnection challenges on integrated terahertz photonic systems
- 2021
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In: OPTICAL INTERCONNECTS XXI. - : SPIE-Intl Soc Optical Eng.
-
Conference paper (peer-reviewed)abstract
- We present the current challenges for high frequency interconnects, especially for calibrated measures of the frequency response of components operating above 100 GHz. This is the challenge addressed by the TERAmeasure Future and Emerging Technologies project, aiming to combine photonics and electronics to develop new paradigm in the millimetre and Terahertz frequency ranges, overcoming the current obstacles to better measurements, eliminating the frequency banded nature of rectangular waveguides and providing metrology-grade results across the full frequency range.
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| 14. |
- Colomé, Núria, et al.
(author)
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Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis
- 2022
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In: Journal of Proteomics. - : Elsevier. - 1874-3919 .- 1876-7737. ; 251
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Journal article (peer-reviewed)abstract
- Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.
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| 15. |
- Corzo-Bacallao, Julio Adolfo, et al.
(author)
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Influence of tree shade on the growth and chlorophyll content of Arabica coffee plants established in an agroforestry system at southern Manabí, Ecuador
- 2023
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In: Sarhad Journal of Agriculture. - : ResearchersLinks Ltd. - 1016-4383 .- 2224-5383. ; 39:Specialissue 2, s. 37-47
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Journal article (peer-reviewed)abstract
- The experiment was developed under production conditions on a farm in the Santa Ana city, south-central region of the province of Manabí, Ecuador, in a mountainous area of approximately 300 meters above sea level. Coffee (Coffea arabica, sp.) production is carried out in a context of peasant family agriculture, with an agroforestry system with coffee trees of the Sarchimor variety planted at 1.5 x 1.5 m, interspersed with tree species typical of the dry forest. The system involves manual weed control, without fertilization, irrigation, phytosanitary control, or shade regulation. In this scenario, and during an experimental period of 90 days (03/08/2022 - 26/10/2022), phenological variables of coffee trees maintained in a study area of 50 x 50 m at a high (S1: 51-70%) and low (S3: 1-30%) shade level was compared with those obtained at an intermediate shade level considered as standard (S2: 31-50%). The phenological variables related to vegetative development (Total Branches) of coffee plants showed higher values in S2 compared to S1 and S3. These results are related to the higher photosynthetic activity associated with the higher intensity of incident solar radiation, although the relationship is not linear. In our results, flowering and fruiting were not affected by the level of shade, nor were their precursors, such as nodes per productive branch and productive nodes per productive branch. On the other hand, coffee plants at full sun exposure in S1, without shade, decreased chlorophyll measured in SPAD units, as a possible compensation for the increase in photosynthetically active uptake in that condition.
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| 16. |
- Ferrando, Carlos, et al.
(author)
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Effects of oxygen on post-surgical infections during an individualised perioperative open-lung ventilatory strategy : a randomised controlled trial
- 2020
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In: British Journal of Anaesthesia. - : ELSEVIER SCI LTD. - 0007-0912 .- 1471-6771. ; 124:1, s. 110-120
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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.
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| 17. |
- Kattge, Jens, et al.
(author)
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TRY plant trait database - enhanced coverage and open access
- 2020
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In: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Journal article (peer-reviewed)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 18. |
- Kehoe, Laura, et al.
(author)
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Make EU trade with Brazil sustainable
- 2019
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Journal article (other academic/artistic)
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| 19. |
- Muñoz, Felipe, et al.
(author)
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Unique features of β-cell metabolism are lost in type 2 diabetes
- 2024
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In: Acta Physiologica. - 1748-1708.
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Research review (peer-reviewed)abstract
- Pancreatic β cells play an essential role in the control of systemic glucose homeostasis as they sense blood glucose levels and respond by secreting insulin. Upon stimulating glucose uptake in insulin-sensitive tissues post-prandially, this anabolic hormone restores blood glucose levels to pre-prandial levels. Maintaining physiological glucose levels thus relies on proper β-cell function. To fulfill this highly specialized nutrient sensor role, β cells have evolved a unique genetic program that shapes its distinct cellular metabolism. In this review, the unique genetic and metabolic features of β cells will be outlined, including their alterations in type 2 diabetes (T2D). β cells selectively express a set of genes in a cell type-specific manner; for instance, the glucose activating hexokinase IV enzyme or Glucokinase (GCK), whereas other genes are selectively “disallowed”, including lactate dehydrogenase A (LDHA) and monocarboxylate transporter 1 (MCT1). This selective gene program equips β cells with a unique metabolic apparatus to ensure that nutrient metabolism is coupled to appropriate insulin secretion, thereby avoiding hyperglycemia, as well as life-threatening hypoglycemia. Unlike most cell types, β cells exhibit specialized bioenergetic features, including supply-driven rather than demand-driven metabolism and a high basal mitochondrial proton leak respiration. The understanding of these unique genetically programmed metabolic features and their alterations that lead to β-cell dysfunction is crucial for a comprehensive understanding of T2D pathophysiology and the development of innovative therapeutic approaches for T2D patients.
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| 20. |
- Muñoz Medina, Felipe, et al.
(author)
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Employees Perceptions of Job Insecurity and Performance : A Qualitative Approach
- 2022
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In: International Journal of Environmental Research and Public Health. - : MDPI AG. - 1661-7827 .- 1660-4601. ; 19:24
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Journal article (peer-reviewed)abstract
- The purpose of this article is to understand the experience of workers’ perceptions of job insecurity and its relation to performance. To this end, we conducted semi-structured interviews with 38 workers in the retail, services, education, financial, construction, and pharmaceutical industries in Chile. Using content analysis based on workers’ accounts of their own experience, we identified two main categories: (a) the experience of job insecurity viewed in relation to the context of the COVID-19 pandemic and emotional aspects of job insecurity, and (b) the relation between job insecurity and performance. The possibility of job loss expresses itself in experiences and emotions that are related to the performance of workers in different ways. These findings are discussed in terms of stress theory and the motivation to preserve jobs.
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| 21. |
- Munoz, William Armando, et al.
(author)
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Insulator to semimetallic transition in conducting polymers
- 2016
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In: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 94:20
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Journal article (peer-reviewed)abstract
- We report a multiscale modeling of electronic structure of a conducting polymer poly(3,4-ethylenedioxythiopehene) (PEDOT) based on a realistic model of its morphology. We show that when the charge carrier concentration increases, the character of the density of states (DOS) gradually evolves from the insulating to the semimetallic, exhibiting a collapse of the gap between the bipolaron and valence bands with the drastic increase of the DOS between the bands. The origin of the observed behavior is attributed to the effect of randomly located counterions giving rise to the states in the gap. These results are discussed in light of recent experiments. The method developed in this work is general and can be applied to study the electronic structure of other conducting polymers.
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| 22. |
- Poorter, Lourens, et al.
(author)
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Functional recovery of secondary tropical forests
- 2021
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 118:49, s. e2003405118-e2003405118
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Journal article (peer-reviewed)abstract
- One-third of all Neotropical forests are secondary forests that regrow naturally after agricultural use through secondary succession. We need to understand better how and why succession varies across environmental gradients and broad geographic scales. Here, we analyze functional recovery using community data on seven plant characteristics (traits) of 1,016 forest plots from 30 chronosequence sites across the Neotropics. By analyzing communities in terms of their traits, we enhance understanding of the mechanisms of succession, assess ecosystem recovery, and use these insights to propose successful forest restoration strategies. Wet and dry forests diverged markedly for several traits that increase growth rate in wet forests but come at the expense of reduced drought tolerance, delay, or avoidance, which is important in seasonally dry forests. Dry and wet forests showed different successional pathways for several traits. In dry forests, species turnover is driven by drought tolerance traits that are important early in succession and in wet forests by shade tolerance traits that are important later in succession. In both forests, deciduous and compound-leaved trees decreased with forest age, probably because microclimatic conditions became less hot and dry. Our results suggest that climatic water availability drives functional recovery by influencing the start and trajectory of succession, resulting in a convergence of community trait values with forest age when vegetation cover builds up. Within plots, the range in functional trait values increased with age. Based on the observed successional trait changes, we indicate the consequences for carbon and nutrient cycling and propose an ecologically sound strategy to improve forest restoration success.
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| 23. |
- Poorter, Lourens, et al.
(author)
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Wet and dry tropical forests show opposite successional pathways in wood density but converge over time
- 2019
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In: Nature Ecology & Evolution. - : Nature Publishing Group. - 2397-334X. ; 3:6, s. 928-934
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Journal article (peer-reviewed)abstract
- Tropical forests are converted at an alarming rate for agricultural use and pastureland, but also regrow naturally through secondary succession. For successful forest restoration, it is essential to understand the mechanisms of secondary succession. These mechanisms may vary across forest types, but analyses across broad spatial scales are lacking. Here, we analyse forest recovery using 1,403 plots that differ in age since agricultural abandonment from 50 sites across the Neotropics. We analyse changes in community composition using species-specific stem wood density (WD), which is a key trait for plant growth, survival and forest carbon storage. In wet forest, succession proceeds from low towards high community WD (acquisitive towards conservative trait values), in line with standard successional theory. However, in dry forest, succession proceeds from high towards low community WD (conservative towards acquisitive trait values), probably because high WD reflects drought tolerance in harsh early successional environments. Dry season intensity drives WD recovery by influencing the start and trajectory of succession, resulting in convergence of the community WD over time as vegetation cover builds up. These ecological insights can be used to improve species selection for reforestation. Reforestation species selected to establish a first protective canopy layer should, among other criteria, ideally have a similar WD to the early successional communities that dominate under the prevailing macroclimatic conditions.
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| 24. |
- Ruiz Muñoz, Juan Felipe, 1986-
(author)
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Problems in Problem-Based Design Engineering Education : Towards a Multidisciplinary Designerly Educational Approach
- 2024
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Doctoral thesis (other academic/artistic)abstract
- Modern industry faces complex and 'wicked' problems that require engineering professionals to go beyond traditional natural science-based linear problem-solving approaches and adopt collaborative, multidisciplinary, and iterative problem-solving strategies. To tackle these kinds of problems, organizations are increasingly turning to design problem- solving methods based on the designer’s way of thinking, acting, and doing. Designers have a distinctive ability to deal with poorly defined, ambiguous, or "wicked" problems by emphasizing iterative exploration of both the problem and the solution spaces. They do this through design reasoning patterns that involve constant iteration and temporary solutions. This shift towards designerly ways of problem-solving has, in turn, had an effect on engineering education, where there has been a significant shift towards educational models that utilize design methodologies to engage students in immersive problem-solving experiences. One challenge for educators who utilize models based on designerly thinking is to create structures that actually support the learning objectives, and the development of student skills that are rooted in design reasoning and acting, and not merely in design tools. Another challenge is to support collaboration across multiple areas that traditionally had clear boundaries.This thesis studies practices utilized by educators in problem-based designerly education to understand the underlying mechanisms and theoretical underpinnings of problem exploration in multidisciplinary education. Additionally, this thesis aims to explore and discuss the same processes and methods in the context of multidisciplinary education and design objects that can support collaboration across boundaries.This thesis's key contributions are the exploration and discussion of aspects of problem exploration, framing, and reframing in a designerly problem-based multidisciplinary educational environment, as well as the challenges and difficulties that educators and students encounter in the process of exploring problems and collaborating and crossing disciplinary boundaries with participants from multiple disciplines. To do so, this thesis first explores the importance that (the framing of the) design brief has in the problem-solving process. Furthermore, the design briefs are discussed as boundary objects that serve a crucial role in negotiation, communication, and coordination tools between stakeholders. Second, the importance of the reflective process that follows the idea generation and prototype-building activities are discussed as an aspect of an educational model that allows participants to explore problems and avoid design fixation. Moreover, these objects are discussed based on their function as disciplinary boundary crossing objects and as an aid in negotiation, and collaboration objects in problem exploration. Thirdly, methods and processes for assessment of student characteristics and skills are discussed, where tensions and trade-offs between self-reporting and observer-based methods are studied and explored. These methods then serve as boundary objects in the discussions between teaching teams in the student team formation process. Furthermore, team building and specifically the process of trust-building and objects that aid in boundary-crossing collaboration and communication to develop trust between students are also discussed.
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| 25. |
- Ruiz Muñoz, Juan Felipe
(author)
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The Problem of Formulating Design Problems : A Typology of Design Briefs
- 2020
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Licentiate thesis (other academic/artistic)abstract
- It is common for a design team to be handed a problem to solve for others. The handing over is normally referred to as a ‘briefing’ process, and the documentation of the starting point and what is to be done is known as a ‘brief’. It is known that the way we frame and understand a problem influences what paths we see to potential solutions. The aim of this thesis is to understand what makes a good design brief and to do so in order to create an empirically informed, and theoretically underpinned, typology of design briefs and the kind of search processes they are disposed to induce.Different bodies of literature have tried to grasp how design solves problems in order to understand designer’s behavior and ultimately facilitate or improve it. Distinctions can, and have been made, between different kinds of problem formulations, as well as different problem-solving approaches. This thesis aims to integrate two previously distinct literatures, search process from the organizational perspective developed by James G. March, Herbert A. Simon, Richard Cyert and others and Design and the Design Process from the perspectives of authors such as Donald Schön, Kees Dorst and Nigel Cross among others, to propose a typology of design briefs in order to ultimately facilitate problem formulation and subsequently facilitate the design process.The simple and immediate answer to the question of what makes a good design brief is: ‘that depends’. It depends on the design process to be followed (if there is one), it depends on the kind of goals that should be achieved, the time available, and it also depends on how much and what is known about the problem and potential solutions. Based on this, four ideal types of design briefs are articulated, including the expected associated search behavior and challenges of design teams.
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| 26. |
- Ruiz Muñoz, Juan Felipe, et al.
(author)
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What is your (freaking) Problem? Prototypes for problem exploration on early stages of design
- 2023
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In: From Abstractness to Concreteness – experiential knowledge and the role of prototypes in design research. - : Politecnico di MIlano. - 9788894167436 ; , s. 702-715
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Conference paper (peer-reviewed)abstract
- Prototyping is a crucial element of the design activity. Prototypes serve as temporary and incomplete embodiments of design ideas with which designers explore the design problem as well as propose and refine possible solutions to the problem. Given its deep connection to solutions, prototyping has been typically associated with the later stages of design. A stage in which the problem has been sufficiently mapped that a solution can be proposed and refined based on the discovery of requirements. Yet the question of what it means to prototype for problem exploration remains. To provide an answer to this question, first we take a quick look at what the role of prototypes is in design and more specifically what their role might be in the early stages of design. And later we discuss from the perspective of the reflective conversation that the designer has with the artifact it has created and what we reflect on when dealing with problem exploration. Subsequently some illustrative examples are presented of unintentional problem exploration prototyping from student design projects. To conclude, a reflection of the importance of design education in preparing practitioners to better deal with different types of prototyping beyond solution refinement.
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| 27. |
- Santana, Felipe A., et al.
(author)
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Final Targeting Strategy for the SDSS-IV APOGEE-2S Survey
- 2021
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In: Astronomical Journal. - : American Astronomical Society. - 1538-3881 .- 0004-6256. ; 162:6
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Journal article (peer-reviewed)abstract
- APOGEE is a high-resolution (R similar to 22,000), near-infrared, multi-epoch, spectroscopic survey of the Milky Way. The second generation of the APOGEE project, APOGEE-2, includes an expansion of the survey to the Southern Hemisphere called APOGEE-2S. This expansion enabled APOGEE to perform a fully panoramic mapping of all of the main regions of the Milky Way; in particular, by operating in the H band, APOGEE is uniquely able to probe the dust-hidden inner regions of the Milky Way that are best accessed from the Southern Hemisphere. In this paper we present the targeting strategy of APOGEE-2S, with special attention to documenting modifications to the original, previously published plan. The motivation for these changes is explained as well as an assessment of their effectiveness in achieving their intended scientific objective. In anticipation of this being the last paper detailing APOGEE targeting, we present an accounting of all such information complete through the end of the APOGEE-2S project; this includes several main survey programs dedicated to exploration of major stellar populations and regions of the Milky Way, as well as a full list of programs contributing to the APOGEE database through allocations of observing time by the Chilean National Time Allocation Committee and the Carnegie Institution for Science. This work was presented along with a companion article, Beaton et al. (2021), presenting the final target selection strategy adopted for APOGEE-2 in the Northern Hemisphere.
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| 28. |
- Testoni, Giorgia, et al.
(author)
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Lack of Glycogenin Causes Glycogen Accumulation and Muscle Function Impairment
- 2017
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In: Cell Metabolism. - : Cell Press. - 1550-4131 .- 1932-7420. ; 26:1, s. 256-266
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Journal article (peer-reviewed)abstract
- Glycogenin is considered essential for glycogen synthesis, as it acts as a primer for the initiation of the polysaccharide chain. Against expectations, glycogenin-deficient mice (Gyg KO) accumulate high amounts of glycogen in striated muscle. Furthermore, this glycogen contains no covalently bound protein, thereby demonstrating that a protein primer is not strictly necessary for the synthesis of the polysaccharide in vivo. Strikingly, in spite of the higher glycogen content, Gyg KO mice showed lower resting energy expenditure and less resistance than control animals when subjected to endurance exercise. These observations can be attributed to a switch of oxidative myofibers toward glycolytic metabolism. Mice overexpressing glycogen synthase in the muscle showed similar alterations, thus indicating that this switch is caused by the excess of glycogen. These results may explain the muscular defects of GSD XV patients, who lack glycogenin-1 and show high glycogen accumulation in muscle.
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| 29. |
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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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In: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
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Journal article (peer-reviewed)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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