| 151. |
- Poorter, Lourens, et al.
(författare)
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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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Ingår i: Nature Ecology & Evolution. - : Nature Publishing Group. - 2397-334X. ; 3:6, s. 928-934
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Tidskriftsartikel (refereegranskat)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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| 152. |
- Pozdniakova, Tatiana A., et al.
(författare)
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Optimization of a hybrid bacterial/Arabidopsis thaliana fatty acid synthase system II in Saccharomyces cerevisiae
- 2023
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Ingår i: Metabolic Engineering Communications. - 2214-0301. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Fatty acids are produced by eukaryotes like baker's yeast Saccharomyces cerevisiae mainly using a large multifunctional type I fatty acid synthase (FASI) where seven catalytic steps and a carrier domain are shared between one or two protein subunits. While this system may offer efficiency in catalysis, only a narrow range of fatty acids are produced. Prokaryotes, chloroplasts and mitochondria rely instead on a FAS type II (FASII) where each catalytic step is carried out by a monofunctional enzyme encoded by a separate gene. FASII is more flexible and capable of producing a wider range of fatty acid structures, such as the direct production of unsaturated fatty acids. An efficient FASII in the preferred industrial organism S. cerevisiae could provide a platform for developing sustainable production of specialized fatty acids. We functionally replaced either yeast FASI genes (FAS1 or FAS2) with a FASII consisting of nine genes from Escherichia coli (acpP, acpS and fab -A, -B, -D, -F, -G, -H, -Z) as well as three from Arabidopsis thaliana (MOD1, FATA1 and FATB). The genes were expressed from an autonomously replicating multicopy vector assembled using the Yeast Pathway Kit for in-vivo assembly in yeast. Two rounds of adaptation led to a strain with a maximum growth rate (μmax) of 0.19 h−1 without exogenous fatty acids, twice the growth rate previously reported for a comparable strain. Additional copies of the MOD1 or fabH genes resulted in cultures with higher final cell densities and three times higher lipid content compared to the control.
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| 153. |
- Ramos Do Prado, Samira B., et al.
(författare)
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Physiological Degradation of Pectin in Papaya Cell Walls : Release of Long Chains Galacturonans Derived from Insoluble Fractions during Postharvest Fruit Ripening
- 2016
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Papaya (Carica papaya L.) is a fleshy fruit that presents a rapid pulp softening during ripening. However, the timeline on how papaya pectinases act in polysaccharide solubilization and the consequent modification of the cell wall fractions during ripening is still not clear. In this work, the gene expression correlations between, on one hand, 16 enzymes potentially acting during papaya cell wall disassembling and, on the other hand, the monosaccharide composition of cell wall fractions during papaya ripening were evaluated. In order to explain differences in the ripening of papaya samplings, the molecular mass distribution of polysaccharides from water-soluble and oxalate-soluble fractions (WSF and OSF, respectively), as well as the oligosaccharide profiling from the WSF fraction, were evaluated by high performance size exclusion chromatography coupled to a refractive index detector and high performance anion-exchange chromatography coupled to pulse amperometric detection analyses, respectively. Results showed that up-regulated polygalacturonase and β-galactosidase genes were positively correlated with some monosaccharide profiles. In addition, an overall increase in the retention time of high molecular weight (HMW) and low molecular weight (LMW) polysaccharides in WSF and OSF was shown. The apparent disappearance of one HMW peak of the OSF may result from the conversion of pectin that were crosslinked with calcium into more soluble forms through the action of PGs, which would increase the solubilization of polysaccharides by lowering their molecular weight. Thus, the results allowed us to propose a detailed process of papaya cell wall disassembling that would affect sensorial properties and post-harvesting losses of this commercially important fruit.
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| 154. |
- Rodrigues, Gabriel S., et al.
(författare)
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GoalD: A Goal-Driven Deployment Framework for Dynamic and Heterogeneous Computing Environments
- 2019
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Ingår i: Information and Software Technology. - : Elsevier BV. - 0950-5849. ; 111, s. 159-176
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Tidskriftsartikel (refereegranskat)abstract
- Context Emerging paradigms like Internet of Things and Smart Cities utilize advanced sensing and communication infrastructures, where heterogeneity is an inherited feature. Applications targeting such environments require adaptability and context-sensitivity to uncertain availability and failures in resources and their ad-hoc networks. Such heterogeneity is often hard to predict, making the deployment process a challenging task. Objective This paper proposes GoalD as a goal-driven framework to support autonomous deployment of heterogeneous computational resources to fulfill requirements, seen as goals, and their correlated components on one hand, and the variability space of the hosting computing and sensing environment on the other hand. Method GoalD comprises an offline and an online stage to fulfill autonomous deployment by leveraging the use of goals. Deployment configuration strategies arise from the variability structure of the Contextual Goal Model as an underlying structure to guide autonomous planning by selecting available as well as suitable resources at runtime. Results We evaluate GoalD on an existing exemplar from the self-adaptive systems community – the Tele Assistance Service provided by Weyns and Calinescu [1]. Furthermore, we evaluate the scalability of GoalD on a repository consisting of 430,500 artifacts. The evaluation results demonstrate the usefulness and scalability of GoalD in planning the deployment of a system with thousands of components in a few milliseconds. Conclusion GoalD is a framework to systematically tackle autonomous deployment in highly heterogeneous computing environments, partially unknown at design-time following a goal-oriented approach to achieve the user goals in a target environment. GoalD has demonstrated itself able to scale for deployment planning dealing with thousands of components in a few milliseconds.
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| 155. |
- Rongo, Roberto, et al.
(författare)
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Diagnostic criteria for temporomandibular disorders (DC/TMD) for children and adolescents : An international Delphi study—Part 1‐Development of Axis I
- 2021
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Ingår i: Journal of Oral Rehabilitation. - : John Wiley & Sons. - 1365-2842 .- 0305-182X. ; 48:7, s. 836-845
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Tidskriftsartikel (refereegranskat)abstract
- AIM: To develop new instruments and to adapt the diagnostic criteria for temporomandibular disorders (DC/TMD) for the evaluation of TMD in children and adolescents.METHOD: A modified Delphi method was used to seek international consensus among TMD experts. Fourteen clinicians and researchers in the field of orofacial pain and TMD worldwide were invited to participate in a workshop initiated by the International Network for Orofacial Pain and Related Disorders Methodology (INfORM scientific network) at the General Session of the International Association for Dental Research (IADR, London 2018), as the first step in the Delphi process. Participants discussed the protocols required to make physical diagnoses included in the Axis I of the DC/TMD. Thereafter, nine experts in the field were added, and the first Delphi round was created. This survey included 60 statements for Axis I, and the experts were asked to respond to each statement on a five-item Likert scale ranging from "Strongly disagree" to "Strongly agree". Consensus level was set at 80% agreement for the first round, and at 70% for the next.RESULTS: After three rounds of the Delphi process, a consensus among TMD experts was achieved and two adapted DC/TMD protocols for Axis I physical diagnoses for children and adolescents were developed.CONCLUSION: Through international consensus among TMD experts, this study adapted the Axis I of the DC/TMD for use in evaluating TMD in children and adolescents.
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| 156. |
- Rongo, Roberto, et al.
(författare)
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Diagnostic criteria for temporomandibular disorders in children and adolescents: An international Delphi study-Part 2-Development of Axis II
- 2022
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Ingår i: Journal of Oral Rehabilitation. - : WILEY. - 1365-2842 .- 0305-182X. ; 49:5, s. 541-552
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Tidskriftsartikel (refereegranskat)abstract
- Background Unlike the psychosocial assessment established for adults in the Diagnostic Criteria for Temporomandibular Disorders (DC/TMD), a standardised psychosocial assessment for children and adolescents with TMD complaints has not yet been established. Objectives To develop a new standardised instrument set to assess the psychosocial functioning in children and adolescents by adapting the psychosocial status and pain-related disability (Axis II) of the adult DC/TMD and by including new instruments. Methods A modified Delphi method was used to survey 23 international TMD experts and four international experts in pain-related psychological factors for consensus regarding assessment tools for psychosocial functioning and pain-related disability in children and adolescents. The TMD experts reviewed 29 Axis II statements at round 1, 13 at round 2 and 2 at round 3. Agreement was set at 80% for first-round consensus level and 70% for each of the second and third rounds. The psychological experts completed a complementary Delphi survey to reach a consensus on tools to use to assess more complex psychological domains in children and adolescents. For the psychological experts, the first round included 10 open-ended questions on preferred screening tools for depression, anxiety, catastrophising, sleep problems and stress in children (ages 6-9 years old) and adolescents (ages 10-19 years old) as well as on other domains suggested for investigation. In the second round, the psychological experts received a 9-item questionnaire to prioritise the suggested instruments from most to least recommended. Results The TMD experts, after three Delphi rounds, reached consensus on the changes of DC/TMD to create a form to evaluate Axis II in children and adolescents with TMD complaints. The psychological experts added tools to assess depression and anxiety, sleep disorders, catastrophising, stress and resilience. Conclusion Through international expert consensus, this study adapted Axis II of the adult DC/TMD to assess psychosocial functioning and pain-related disability in children and adolescents. The adapted Axis II protocols will be validated in the target populations.
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| 157. |
- Rubin, Adam, et al.
(författare)
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TYPE II SUPERNOVA ENERGETICS AND COMPARISON OF LIGHT CURVES TO SHOCK-COOLING MODELS
- 2016
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 820:1
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Tidskriftsartikel (refereegranskat)abstract
- During the first few days after explosion, Type II supernovae (SNe) are dominated by relatively simple physics. Theoretical predictions regarding early-time SN light curves in the ultraviolet (UV) and optical bands are thus quite robust. We present, for the first time, a sample of 57 R-band SN II light curves that are well-monitored during their rise, with > 5 detections during the first 10 days after discovery, and a well-constrained time of explosion to within 1-3 days. We show that the energy per unit mass (E/M) can be deduced to roughly a factor of five by comparing early-time optical data to the 2011 model of Rabinak & Waxman, while the progenitor radius cannot be determined based on R-band data alone. We find that SN II explosion energies span a range of E/M = (0.2-20) x 10(51) erg/(10 M-circle dot), and have a mean energy per unit mass of < E/M > = 0.85 x 10(51) erg/(10 M-circle dot), corrected for Malmquist bias. Assuming a small spread in progenitor masses, this indicates a large intrinsic diversity in explosion energy. Moreover, E/M is positively correlated with the amount of Ni-56 produced in the explosion, as predicted by some recent models of core-collapse SNe. We further present several empirical correlations. The peak magnitude is correlated with the decline rate (Delta m(15)), the decline rate is weakly correlated with the rise time, and the rise time is not significantly correlated with the peak magnitude. Faster declining SNe are more luminous and have longer rise times. This limits the possible power sources for such events.
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| 158. |
- Salamanova, Evdokiya, et al.
(författare)
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A subset of functional adaptation mutations alter propensity for alpha-helical conformation in the intrinsically disordered glucocorticoid receptor taulcore activation domain
- 2018
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Ingår i: Biochimica et Biophysica Acta - General Subjects. - : ELSEVIER SCIENCE BV. - 0304-4165 .- 1872-8006. ; 1862:6, s. 1452-1461
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Tidskriftsartikel (refereegranskat)abstract
- Background: Adaptive mutations that alter protein functionality are enriched within intrinsically disordered protein regions (IDRs), thus conformational flexibility correlates with evolvability. Pre-structured motifs (PreSMos) with transient propensity for secondary structure conformation are believed to be important for IDR function. The glucocorticoid receptor taulcore transcriptional activation domain (GR taulcore) domain contains three a-helical PreSMos in physiological buffer conditions.Methods: Sixty change-of-function mutants affecting the intrinsically disordered 58-residue GR taulcore were studied using disorder prediction and molecular dynamics simulations.Results: Change-of-function mutations were partitioned into seven clusters based on their effect on IDR predictions and gene activation activity. Some mutations selected from clusters characterized by mutations altering the IDR prediction score, altered the apparent stability of the a-helical form of one of the PreSMos in molecular dynamics simulations, suggesting PreSMo stabilization or destabilization as strategies for functional adaptation. Indeed all tested gain-of-function mutations affecting this PreSMo were associated with increased stability of the a-helical PreSMo conformation, suggesting that PreSMo stabilization may be the main mechanism by which adaptive mutations can increase the activity of this IDR type. Some mutations did not appear to affect PreSMo stability.Conclusions: Changes in PreSMo stability account for the effects of a subset of change-of-function mutants affecting the GR taulcore IDR. General significance: Long IDRs occur in about 50% of human proteins. They are poorly characterized despite much recent attention. Our results suggest the importance of a subtle balance between PreSMo stability and IDR activity, which may provide a novel target for future pharmaceutical intervention.
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| 159. |
- Samudyata, Samudyata, et al.
(författare)
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Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells
- 2019
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Ingår i: Experimental Cell Research. - : Elsevier BV. - 0014-4827 .- 1090-2422. ; 381:1, s. 129-138
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Tidskriftsartikel (refereegranskat)abstract
- Sox2 is a master transcriptional regulator of embryonic development. In this study, we determined the protein interactome of Sox2 in the chromatin and nucleoplasm of mouse embryonic stem (mES) cells. Apart from canonical interactions with pluripotency-regulating transcription factors, we identified interactions with several chromatin modulators, including members of the heterochromatin protein 1 (HP1) family, suggesting a role for Sox2 in chromatin-mediated transcriptional repression. Sox2 was also found to interact with RNA binding proteins (RBPs), including proteins involved in RNA processing. RNA immunoprecipitation followed by sequencing revealed that Sox2 associates with different messenger RNAs, as well as small nucleolar RNA Snord34 and the non-coding RNA 7SK. 7SK has been shown to regulate transcription at gene regulatory regions, which could suggest a functional interaction with Sox2 for chromatin recruitment. Nevertheless, we found no evidence of Sox2 modulating recruitment of 7SK to chromatin when examining 7SK chromatin occupancy by Chromatin Isolation by RNA Purification (ChIRP) in Sox2 depleted mES cells. In addition, knockdown of 7SK in mES cells did not lead to any change in Sox2 occupancy at 7SK-regulated genes. Thus, our results show that Sox2 extensively interacts with RBPs, and suggest that Sox2 and 7SK co-exist in a ribonucleoprotein complex whose function is not to regulate chromatin recruitment, but could rather regulate other processes in the nucleoplasm.
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| 160. |
- Shoukry, Yasser, et al.
(författare)
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SMT-Based Observer Design for Cyber-Physical Systems under Sensor Attacks
- 2016
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Ingår i: 2016 ACM/IEEE 7th International Conference on Cyber-Physical Systems, ICCPS 2016 - Proceedings. - 9781509017720
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Konferensbidrag (refereegranskat)abstract
- We introduce a scalable observer architecture to estimate the states of a discrete-time linear-time-invariant (LTI) system whose sensors can be manipulated by an attacker. Given the maximum number of attacked sensors, we build on previous results on necessary and sufficient conditions for state estimation, and propose a novel multi-modal Luenberger (MML) observer based on efficient Satisfiability Modulo Theory (SMT) solving. We present two techniques to reduce the complexity of the estimation problem. As a first strategy, instead of a bank of distinct observers, we use a family of filters sharing a single dynamical equation for the states, but different output equations, to generate estimates corresponding to different subsets of sensors. Such an architecture can reduce the memory usage of the observer from an exponential to a linear function of the number of sensors. We then develop an efficient SMT-based decision procedure that is able to reason about the estimates of the MML observer to detect at runtime which sets of sensors are attack-free, and use them to obtain a correct state estimate. We provide proofs of convergence for our algorithm and report simulation results to compare its runtime performance with alternative techniques. Our algorithm scales well for large systems (including up to 5000 sensors) for which many previously proposed algorithms are not implementable due to excessive memory and time requirements. Finally, we illustrate the effectiveness of our algorithm on the design of resilient power distribution systems.
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