| 1. |
|
|
| 2. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
|
|
| 3. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 4. |
-
- 2019
-
Tidskriftsartikel (refereegranskat)
|
|
| 5. |
- Bentham, James, et al.
(författare)
-
A century of trends in adult human height
- 2016
-
Ingår i: eLIFE. - 2050-084X. ; 5
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 6. |
- Bentham, James, et al.
(författare)
-
A century of trends in adult human height
- 2016
-
Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 5
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 7. |
|
|
| 8. |
- Kattge, Jens, et al.
(författare)
-
TRY plant trait database - enhanced coverage and open access
- 2020
-
Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 9. |
- Danaei, Goodarz, et al.
(författare)
-
Effects of diabetes definition on global surveillance of diabetes prevalence and diagnosis: a pooled analysis of 96 population-based studies with 331288 participants
- 2015
-
Ingår i: The Lancet Diabetes & Endocrinology. - 2213-8595 .- 2213-8587. ; 3:8, s. 624-637
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 10. |
- Erzurumluoglu, A. Mesut, et al.
(författare)
-
Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci
- 2020
-
Ingår i: Molecular Psychiatry. - : Nature Publishing Group. - 1359-4184 .- 1476-5578. ; 25:10, s. 2392-2409
-
Tidskriftsartikel (refereegranskat)abstract
- Smoking is a major heritable and modifiable risk factor for many diseases, including cancer, common respiratory disorders and cardiovascular diseases. Fourteen genetic loci have previously been associated with smoking behaviour-related traits. We tested up to 235,116 single nucleotide variants (SNVs) on the exome-array for association with smoking initiation, cigarettes per day, pack-years, and smoking cessation in a fixed effects meta-analysis of up to 61 studies (up to 346,813 participants). In a subset of 112,811 participants, a further one million SNVs were also genotyped and tested for association with the four smoking behaviour traits. SNV-trait associations with P < 5 × 10-8 in either analysis were taken forward for replication in up to 275,596 independent participants from UK Biobank. Lastly, a meta-analysis of the discovery and replication studies was performed. Sixteen SNVs were associated with at least one of the smoking behaviour traits (P < 5 × 10-8) in the discovery samples. Ten novel SNVs, including rs12616219 near TMEM182, were followed-up and five of them (rs462779 in REV3L, rs12780116 in CNNM2, rs1190736 in GPR101, rs11539157 in PJA1, and rs12616219 near TMEM182) replicated at a Bonferroni significance threshold (P < 4.5 × 10-3) with consistent direction of effect. A further 35 SNVs were associated with smoking behaviour traits in the discovery plus replication meta-analysis (up to 622,409 participants) including a rare SNV, rs150493199, in CCDC141 and two low-frequency SNVs in CEP350 and HDGFRP2. Functional follow-up implied that decreased expression of REV3L may lower the probability of smoking initiation. The novel loci will facilitate understanding the genetic aetiology of smoking behaviour and may lead to the identification of potential drug targets for smoking prevention and/or cessation.
|
|
| 11. |
- Richards, Stephen, et al.
(författare)
-
Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
-
Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
-
Tidskriftsartikel (refereegranskat)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
|
|
| 12. |
- Ruilope, LM, et al.
(författare)
-
Design and Baseline Characteristics of the Finerenone in Reducing Cardiovascular Mortality and Morbidity in Diabetic Kidney Disease Trial
- 2019
-
Ingår i: American journal of nephrology. - : S. Karger AG. - 1421-9670 .- 0250-8095. ; 50:5, s. 345-356
-
Tidskriftsartikel (refereegranskat)abstract
- <b><i>Background:</i></b> Among people with diabetes, those with kidney disease have exceptionally high rates of cardiovascular (CV) morbidity and mortality and progression of their underlying kidney disease. Finerenone is a novel, nonsteroidal, selective mineralocorticoid receptor antagonist that has shown to reduce albuminuria in type 2 diabetes (T2D) patients with chronic kidney disease (CKD) while revealing only a low risk of hyperkalemia. However, the effect of finerenone on CV and renal outcomes has not yet been investigated in long-term trials. <b><i>Patients and</i></b> <b><i>Methods:</i></b> The Finerenone in Reducing CV Mortality and Morbidity in Diabetic Kidney Disease (FIGARO-DKD) trial aims to assess the efficacy and safety of finerenone compared to placebo at reducing clinically important CV and renal outcomes in T2D patients with CKD. FIGARO-DKD is a randomized, double-blind, placebo-controlled, parallel-group, event-driven trial running in 47 countries with an expected duration of approximately 6 years. FIGARO-DKD randomized 7,437 patients with an estimated glomerular filtration rate ≥25 mL/min/1.73 m<sup>2</sup> and albuminuria (urinary albumin-to-creatinine ratio ≥30 to ≤5,000 mg/g). The study has at least 90% power to detect a 20% reduction in the risk of the primary outcome (overall two-sided significance level α = 0.05), the composite of time to first occurrence of CV death, nonfatal myocardial infarction, nonfatal stroke, or hospitalization for heart failure. <b><i>Conclusions:</i></b> FIGARO-DKD will determine whether an optimally treated cohort of T2D patients with CKD at high risk of CV and renal events will experience cardiorenal benefits with the addition of finerenone to their treatment regimen. Trial Registration: EudraCT number: 2015-000950-39; ClinicalTrials.gov identifier: NCT02545049.
|
|
| 13. |
- Zhou, Bin, et al.
(författare)
-
Worldwide trends in diabetes since 1980: A pooled analysis of 751 population-based studies with 4.4 million participants
- 2016
-
Ingår i: The Lancet. - : Elsevier B.V.. - 0140-6736 .- 1474-547X. ; 387:10027, s. 1513-1530
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 14. |
- Abbafati, Cristiana, et al.
(författare)
-
- 2020
-
Tidskriftsartikel (refereegranskat)
|
|
| 15. |
|
|
| 16. |
|
|
| 17. |
|
|
| 18. |
|
|
| 19. |
|
|
| 20. |
|
|
| 21. |
|
|
| 22. |
|
|
| 23. |
|
|
| 24. |
|
|
| 25. |
|
|
| 26. |
|
|
| 27. |
|
|
| 28. |
|
|
| 29. |
- Aaltonen, T., et al.
(författare)
-
Evidence for a Particle Produced in Association with Weak Bosons and Decaying to a Bottom-Antibottom Quark Pair in Higgs Boson Searches at the Tevatron
- 2012
-
Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 109:7, s. 071804-
-
Tidskriftsartikel (refereegranskat)abstract
- We combine searches by the CDF and D0 Collaborations for the associated production of a Higgs boson with a W or Z boson and subsequent decay of the Higgs boson to a bottom-antibottom quark pair. The data, originating from Fermilab Tevatron p (p) over bar collisions at root s = 1.96 TeV, correspond to integrated luminosities of up to 9.7 fb(-1). The searches are conducted for a Higgs boson with mass in the range 100-150 GeV/c(2). We observe an excess of events in the data compared with the background predictions, which is most significant in the mass range between 120 and 135 GeV/c(2). The largest local significance is 3.3 standard deviations, corresponding to a global significance of 3.1 standard deviations. We interpret this as evidence for the presence of a new particle consistent with the standard model Higgs boson, which is produced in association with a weak vector boson and decays to a bottom-antibottom quark pair.
|
|
| 30. |
- Alanwar, Amr, et al.
(författare)
-
Enhancing Data-Driven Reachability Analysis using Temporal Logic Side Information
- 2022
-
Ingår i: Proceedings. - : Institute of Electrical and Electronics Engineers Inc..
-
Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- This paper presents algorithms for performingdata-driven reachability analysis under temporal logic sideinformation. In certain scenarios, the data-driven reachablesets of a robot can be prohibitively conservative due to theinherent noise in the robot’s historical measurement data. Inthe same scenarios, we often have side information about therobot’s expected motion (e.g., limits on how much a robotcan move in a one-time step) that could be useful for furtherspecifying the reachability analysis. In this work, we showthat if we can model this side information using a signaltemporal logic (STL) fragment, we can constrain the datadriven reachability analysis and safely limit the conservatismof the computed reachable sets. Moreover, we provide formalguarantees that, even after incorporating side information, thecomputed reachable sets still properly over-approximate therobot’s future states. Lastly, we empirically validate the practicality of the over-approximation by computing constrained,data-driven reachable sets for the Small-Vehicles-for-Autonomy(SVEA) hardware platform in two driving scenarios.
|
|
| 31. |
- Alanwar, Amr, et al.
(författare)
-
Logical Zonotopes : A Set Representation for the Formal Verification of Boolean Functions
- 2023
-
Ingår i: 2023 62nd IEEE Conference on Decision and Control, CDC 2023. - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 60-66
-
Konferensbidrag (refereegranskat)abstract
- A logical zonotope, which is a new set representation for binary vectors, is introduced in this paper. A logical zonotope is constructed by XORing a binary vector with a combination of other binary vectors called generators. Such a zonotope can represent up to 2γ binary vectors using only γ generators. It is shown that logical operations over sets of binary vectors can be performed on the zonotopes' generators and, thus, significantly reduce the computational complexity of various logical operations (e.g., XOR, NAND, AND, OR, and semi-tensor products). Similar to traditional zonotopes' role in the formal verification of dynamical systems over real vector spaces, logical zonotopes can efficiently analyze discrete dynamical systems defined over binary vector spaces. We illustrate the approach and its ability to reduce the computational complexity in two use cases: (1) encryption key discovery of a linear feedback shift register and (2) safety verification of a road traffic intersection protocol.
|
|
| 32. |
- Alimena, Juliette, et al.
(författare)
-
Searching for long-lived particles beyond the Standard Model at the Large Hadron Collider
- 2020
-
Ingår i: Journal of Physics G. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 47:9
-
Tidskriftsartikel (refereegranskat)abstract
- Particles beyond the Standard Model (SM) can generically have lifetimes that are long compared to SM particles at the weak scale. When produced at experiments such as the Large Hadron Collider (LHC) at CERN, these long-lived particles (LLPs) can decay far from the interaction vertex of the primary proton-proton collision. Such LLP signatures are distinct from those of promptly decaying particles that are targeted by the majority of searches for new physics at the LHC, often requiring customized techniques to identify, for example, significantly displaced decay vertices, tracks with atypical properties, and short track segments. Given their non-standard nature, a comprehensive overview of LLP signatures at the LHC is beneficial to ensure that possible avenues of the discovery of new physics are not overlooked. Here we report on the joint work of a community of theorists and experimentalists with the ATLAS, CMS, and LHCb experiments-as well as those working on dedicated experiments such as MoEDAL, milliQan, MATHUSLA, CODEX-b, and FASER-to survey the current state of LLP searches at the LHC, and to chart a path for the development of LLP searches into the future, both in the upcoming Run 3 and at the high-luminosity LHC. The work is organized around the current and future potential capabilities of LHC experiments to generally discover new LLPs, and takes a signature-based approach to surveying classes of models that give rise to LLPs rather than emphasizing any particular theory motivation. We develop a set of simplified models; assess the coverage of current searches; document known, often unexpected backgrounds; explore the capabilities of proposed detector upgrades; provide recommendations for the presentation of search results; and look towards the newest frontiers, namely high-multiplicity 'dark showers', highlighting opportunities for expanding the LHC reach for these signals.
|
|
| 33. |
- Block, Keith I., et al.
(författare)
-
Designing a broad-spectrum integrative approach for cancer prevention and treatment
- 2015
-
Ingår i: Seminars in Cancer Biology. - : Academic Press. - 1044-579X .- 1096-3650. ; 35, s. S276-S304
-
Forskningsöversikt (refereegranskat)abstract
- Targeted therapies and the consequent adoption of "personalized" oncology have achieved notable successes in some cancers; however, significant problems remain with this approach. Many targeted therapies are highly toxic, costs are extremely high, and most patients experience relapse after a few disease-free months. Relapses arise from genetic heterogeneity in tumors, which harbor therapy-resistant immortalized cells that have adopted alternate and compensatory pathways (i.e., pathways that are not reliant upon the same mechanisms as those which have been targeted). To address these limitations, an international task force of 180 scientists was assembled to explore the concept of a low-toxicity "broadspectrum" therapeutic approach that could simultaneously target many key pathways and mechanisms. Using cancer hallmark phenotypes and the tumor microenvironment to account for the various aspects of relevant cancer biology, interdisciplinary teams reviewed each hallmark area and nominated a wide range of high-priority targets (74 in total) that could be modified to improve patient outcomes. For these targets, corresponding low-toxicity therapeutic approaches were then suggested, many of which were phytochemicals. Proposed actions on each target and all of the approaches were further reviewed for known effects on other hallmark areas and the tumor microenvironment Potential contrary or procarcinogenic effects were found for 3.9% of the relationships between targets and hallmarks, and mixed evidence of complementary and contrary relationships was found for 7.1%. Approximately 67% of the relationships revealed potentially complementary effects, and the remainder had no known relationship. Among the approaches, 1.1% had contrary, 2.8% had mixed and 62.1% had complementary relationships. These results suggest that a broad-spectrum approach should be feasible from a safety standpoint. This novel approach has potential to be relatively inexpensive, it should help us address stages and types of cancer that lack conventional treatment, and it may reduce relapse risks. A proposed agenda for future research is offered. (C) 2015 The Authors. Published by Elsevier Ltd.
|
|
| 34. |
|
|
| 35. |
- Chen, Xiao, et al.
(författare)
-
Safe Intersection Coordination with Mixed Traffic : From Estimation to Control
- 2023
-
Konferensbidrag (refereegranskat)abstract
- In this paper, we propose an integrated framework for safe intersection coordination of connected and automated vehicles (CAVs) in mixed traffic. An intelligent intersection is introduced as a central node to orchestrate state data sharing among connected agents and enable CAV to acknowledge the presence of human-driven vehicles (HDVs) beyond the line of sight of onboard sensors. Since state data shared between agents might be uncertain or delayed, we design the intelligent intersection to safely compensate for these uncertainties and delays using robust set estimation and forward reachability analysis. When the intersection receives state data from an agent, it first generates a zonotope to capture the possible measurement noise in the state estimate. Then, to compensate for communication and processing delays, it uses forward reachability analysis to enlarge the set to capture all the possible states the agent could have occupied throughout the delays. Finally, using the resulting set as the initial condition, a distributed model predictive control onboard the CAV will plan an invariant safe motion by considering the worst-case behavior of human drivers. As a result, the vehicle is guaranteed to be safe while driving through the intersection. A prototype of our proposed framework is implemented using.
|
|
| 36. |
- Elsik, Christine G., et al.
(författare)
-
The Genome Sequence of Taurine Cattle : A Window to Ruminant Biology and Evolution
- 2009
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 324:5926, s. 522-528
-
Tidskriftsartikel (refereegranskat)abstract
- To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
|
|
| 37. |
- Evangelou, Evangelos, et al.
(författare)
-
Meta-analysis of genome-wide association studies confirms a susceptibility locus for knee osteoarthritis on chromosome 7q22
- 2011
-
Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 1468-2060 .- 0003-4967. ; 70:2, s. 349-355
-
Tidskriftsartikel (refereegranskat)abstract
- Objectives Osteoarthritis (OA) is the most prevalent form of arthritis and accounts for substantial morbidity and disability, particularly in older people. It is characterised by changes in joint structure, including degeneration of the articular cartilage, and its aetiology is multifactorial with a strong postulated genetic component. Methods A meta-analysis was performed of four genome-wide association (GWA) studies of 2371 cases of knee OA and 35 909 controls in Caucasian populations. Replication of the top hits was attempted with data from 10 additional replication datasets. Results With a cumulative sample size of 6709 cases and 44 439 controls, one genome-wide significant locus was identified on chromosome 7q22 for knee OA (rs4730250, p = 9.2 x 10(-9)), thereby confirming its role as a susceptibility locus for OA. Conclusion The associated signal is located within a large (500 kb) linkage disequilibrium block that contains six genes: PRKAR2B (protein kinase, cAMP-dependent, regulatory, type II, beta), HPB1 (HMG-box transcription factor 1), COG5 (component of oligomeric golgi complex 5), GPR22 (G protein-coupled receptor 22), DUS4L (dihydrouridine synthase 4-like) and BCAP29 (B cell receptor-associated protein 29). Gene expression analyses of the (six) genes in primary cells derived from different joint tissues confirmed expression of all the genes in the joint environment.
|
|
| 38. |
- Fang, Evandro F., et al.
(författare)
-
A research agenda for ageing in China in the 21st century (2nd edition): Focusing on basic and translational research, long-term care, policy and social networks.
- 2020
-
Ingår i: Ageing Research Reviews. - : Elsevier BV. - 1568-1637. ; 64
-
Tidskriftsartikel (refereegranskat)abstract
- One of the key issues facing public healthcare is the global trend of an increasingly ageing society which continues to present policy makers and caregivers with formidable healthcare and socio-economic challenges. Ageing is the primary contributor to a broad spectrum of chronic disorders all associated with a lower quality of life in the elderly. In 2019, the Chinese population constituted 18 % of the world population, with 164.5 million Chinese citizens aged 65 and above (65+), and 26 million aged 80 or above (80+). China has become an ageing society, and as it continues to age it will continue to exacerbate the burden borne by current family and public healthcare systems. Major healthcare challenges involved with caring for the elderly in China include the management of chronic non-communicable diseases (CNCDs), physical frailty, neurodegenerative diseases, cardiovascular diseases, with emerging challenges such as providing sufficient dental care, combating the rising prevalence of sexually transmitted diseases among nursing home communities, providing support for increased incidences of immune diseases, and the growing necessity to provide palliative care for the elderly. At the governmental level, it is necessary to make long-term strategic plans to respond to the pressures of an ageing society, especially to establish a nationwide, affordable, annual health check system to facilitate early diagnosis and provide access to affordable treatments. China has begun work on several activities to address these issues including the recent completion of the of the Ten-year Health-Care Reform project, the implementation of the Healthy China 2030 Action Plan, and the opening of the National Clinical Research Center for Geriatric Disorders. There are also societal challenges, namely the shift from an extended family system in which the younger provide home care for their elderly family members, to the current trend in which young people are increasingly migrating towards major cities for work, increasing reliance on nursing homes to compensate, especially following the outcomes of the ‘one child policy’ and the ‘empty-nest elderly’ phenomenon. At the individual level, it is important to provide avenues for people to seek and improve their own knowledge of health and disease, to encourage them to seek medical check-ups to prevent/manage illness, and to find ways to promote modifiable health-related behaviors (social activity, exercise, healthy diets, reasonable diet supplements) to enable healthier, happier, longer, and more productive lives in the elderly. Finally, at the technological or treatment level, there is a focus on modern technologies to counteract the negative effects of ageing. Researchers are striving to produce drugs that can mimic the effects of ‘exercising more, eating less’, while other anti-ageing molecules from molecular gerontologists could help to improve ‘healthspan’ in the elderly. Machine learning, ‘Big Data’, and other novel technologies can also be used to monitor disease patterns at the population level and may be used to inform policy design in the future. Collectively, synergies across disciplines on policies, geriatric care, drug development, personal awareness, the use of big data, machine learning and personalized medicine will transform China into a country that enables the most for its elderly, maximizing and celebrating their longevity in the coming decades. This is the 2nd edition of the review paper (Fang EF et al., Ageing Re. Rev. 2015).
|
|
| 39. |
- Gao, Yulong, et al.
(författare)
-
Reachability-based Human-in-the-Loop Control with Uncertain Specifications
- 2020
-
Ingår i: IFAC PAPERSONLINE. - : Elsevier BV. - 2405-8963. ; , s. 1880-1887
-
Konferensbidrag (refereegranskat)abstract
- We propose a shared autonomy approach for implementing human operator decisions onto an automated system during multi-objective missions, while guaranteeing safety and mission completion. A mission is specified as a set of linear temporal logic (LTL) formulae. Then, using a novel correspondence between LTL and reachability analysis, we synthesize a set of controllers for assisting the human operator to complete the mission, while guaranteeing that the system maintains specified spatial and temporal properties. We assume the human operator's exact preference of how to complete the mission is unknown. Instead, we use a datadriven approach to infer and update the automated system's internal belief of which specified objective the human intends to complete. If, while the human is operating the system, she provides inputs that violate any of the invariances prescribed by the LTL formula, our verified controller will use its internal belief of the human operator's intended objective to guide the operator back on track. Moreover, we show that as long as the specifications are initially feasible, our controller will stay feasible and can guide the human to complete the mission despite some unexpected human errors. We illustrate our approach with a simple, but practical, experimental setup where a remote operator is parking a vehicle in a parking lot with multiple parking options. In these experiments, we show that our approach is able to infer the human operator's preference over parking spots in real-time and guarantee that the human will park in the spot safely.
|
|
| 40. |
- Gao, Yulong, et al.
(författare)
-
Risk-Aware Optimal Control for Automated Overtaking With Safety Guarantees
- 2021
-
Ingår i: IEEE Transactions on Control Systems Technology. - : Institute of Electrical and Electronics Engineers Inc.. - 1063-6536 .- 1558-0865. ; , s. 1-13
-
Tidskriftsartikel (refereegranskat)abstract
- This article proposes a solution to the overtaking control problem where an automated vehicle tries to overtake another vehicle with uncertain motion. Our solution allows the automated vehicle to robustly overtake a human-driven vehicle under certain assumptions. Uncertainty in the predicted motion makes the automated overtaking problem hard to solve due to feasibility issues that arise from the fact that the overtaken vehicle (e.g., a vehicle driven by an aggressive driver) may accelerate to prevent the overtaking maneuver. To counteract them, we introduce the weak assumption that the predicted velocity of the overtaken vehicle respects a supermartingale, meaning that its velocity is not increasing in expectation during the maneuver. We show that this formulation presents a natural notion of risk. Based on the martingale assumption, we perform a risk-aware reachability analysis by analytically characterizing the predicted collision probability. Then, we design a risk-aware optimal overtaking algorithm with guaranteed levels of collision avoidance. Finally, we illustrate the effectiveness of the proposed algorithm with a simulated example.
|
|
| 41. |
- Gao, Yulong, et al.
(författare)
-
Stochastic Modeling and Optimal Control for Automated Overtaking
- 2019
-
Ingår i: Proceedings of the IEEE Conference on Decision and Control. - : Institute of Electrical and Electronics Engineers Inc.. - 9781728113982 ; , s. 1273-1278
-
Konferensbidrag (refereegranskat)abstract
- This paper proposes a solution to the overtaking problem where an automated vehicle tries to overtake a human-driven vehicle, which may not be moving at a constant velocity. Using reachability theory, we first provide a robust time-optimal control algorithm to guarantee that there is no collision throughout the overtaking process. Following the robust formulation, we provide a stochastic reachability formulation that allows a trade-off between the conservative overtaking time and the allowance of a small collision probability. To capture the stochasticity of a human driver's behavior, we propose a new martingale-based model where we classify the human driver as aggressive or nonaggressive. We show that if the human driver is nonaggressive, our stochastic time-optimal control algorithm can provide a shorter overtaking time than our robust algorithm, whereas if the human driver is aggressive, the stochastic algorithm will act on a collision probability of zero, which will match the robust algorithm. Finally, we detail a simulated example that illustrates the effectiveness of the proposed algorithms.
|
|
| 42. |
- Gao, Yulong, et al.
(författare)
-
Temporal Logic Trees for Model Checking and Control Synthesis of Uncertain Discrete-time Systems
- 2021
-
Ingår i: IEEE Transactions on Automatic Control. - : Institute of Electrical and Electronics Engineers (IEEE). - 0018-9286 .- 1558-2523. ; , s. 1-1
-
Tidskriftsartikel (refereegranskat)abstract
- We propose algorithms for performing model checking and control synthesis for discrete-time uncertain systems under linear temporal logic (LTL) specifications. We construct temporal logic trees (TLT) from LTL formulae via reachability analysis. In contrast to automaton-based methods, the construction of the TLT is abstraction-free for infinite systems, that is, we do not construct discrete abstractions of the infinite systems. Moreover, for a given transition system and an LTL formula, we prove that there exist both a universal TLT and an existential TLT via minimal and maximal reachability analysis, respectively. We show that the universal TLT is an underapproximation for the LTL formula and the existential TLT is an overapproximation. We provide sufficient conditions and necessary conditions to verify whether a transition system satisfies an LTL formula by using the TLT approximations. As a major contribution of this work, for a controlled transition system and an LTL formula, we prove that a controlled TLT can be constructed from the LTL formula via control-dependent reachability analysis. Based on the controlled TLT, we design an online control synthesis algorithm, under which a set of feasible control inputs can be generated at each time step. We also prove that this algorithm is recursively feasible. We illustrate the proposed methods for both finite and infinite systems and highlight the generality and online scalability with two simulated examples.
|
|
| 43. |
- Gasperetti, Alessio, et al.
(författare)
-
Efficacy of Catheter Ablation for Atrial Arrhythmias in Patients with Arrhythmogenic Right Ventricular Cardiomyopathy - A Multicenter Study
- 2021
-
Ingår i: Journal of Clinical Medicine. - : MDPI. - 2077-0383. ; 10:21
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Atrial arrhythmias are present in up to 20% of patients with arrhythmogenic right ventricular cardiomyopathy (ARVC). Catheter ablation (CA) is an effective treatment for atrial arrhythmias in the general population. Data regarding CA for atrial arrhythmias in ARVC are scarce. Objective: To assess the safety and efficacy of CA for atrial arrhythmias in patients with ARVC. Methods: In this international collaborative effort, all patients with a definite diagnosis of ARVC undergoing CA for atrial fibrillation (AF), focal atrial tachycardia (AT), or cavotricuspid isthmus (CTI)-dependent atrial flutter (AFl) were extracted from twelve ARVC registries. Demographic, periprocedural, and long-term arrhythmic outcome data were collected. Results: Thirty-seven patients were enrolled in the study (age 50.2 & PLUSMN; 16.6 years, male 84%, CHA(2)DS(2)VASc 1 (1,2), HAS-BLED 0 (0-2)). The arrhythmia leading to CA was AF in 23 (62%), focal left AT in 5 (14%), and CTI-dependent AFl in 9 (24%). Acute procedural success was achieved in all procedures but one (n = 1 focal left AT; 97% acute success). The median follow-up period was 27 (13-67) months, and 96%, 74%, and 61% of patients undergoing AF ablation were free from any atrial arrhythmia recurrence after a single procedure at 6 months, 12 months, and last follow-up, respectively. After focal AT ablation, freedom from atrial arrhythmia recurrence was 80%, 80%, and 60% at 6 months, 12 months, and last follow-up, respectively. All patients undergoing CTI ablation were free from atrial arrhythmia recurrences at 6 months, with 89% single-procedural arrhythmic freedom at last follow-up. One major complication (2.7%; PV stenosis requiring PV stenting) occurred. Conclusions: CA is safe and effective in managing atrial arrhythmias in patients with ARVC, with success rates comparable to the general population.
|
|
| 44. |
- Goossens, Maria E., et al.
(författare)
-
International pooled study on diet and bladder cancer : the bladder cancer, epidemiology and nutritional determinants (BLEND) study: design and baseline characteristics
- 2016
-
Ingår i: Archives of Public Health. - : BMC. - 0778-7367 .- 2049-3258. ; 74
-
Tidskriftsartikel (refereegranskat)abstract
- Background: In 2012, more than 400,000 urinary bladder cancer cases occurred worldwide, making it the 7th most common type of cancer. Although many previous studies focused on the relationship between diet and bladder cancer, the evidence related to specific food items or nutrients that could be involved in the development of bladder cancer remains inconclusive. Dietary components can either be, or be activated into, potential carcinogens through metabolism, or act to prevent carcinogen damage. Methods/design: The BLadder cancer, Epidemiology and Nutritional Determinants (BLEND) study was set up with the purpose of collecting individual patient data from observational studies on diet and bladder cancer. In total, data from 11,261 bladder cancer cases and 675,532 non-cases from 18 case-control and 6 cohort studies from all over the world were included with the aim to investigate the association between individual food items, nutrients and dietary patterns and risk of developing bladder cancer. Discussion: The substantial number of cases included in this study will enable us to provide evidence with large statistical power, for dietary recommendations on the prevention of bladder cancer.
|
|
| 45. |
- Grasse, Patricia, et al.
(författare)
-
GEOTRACES inter-calibration of the stable silicon isotope composition of dissolved silicic acid in seawater
- 2017
-
Ingår i: Journal of Analytical Atomic Spectrometry. - : Royal Society of Chemistry (RSC). - 0267-9477 .- 1364-5544. ; 32:3, s. 562-578
-
Tidskriftsartikel (refereegranskat)abstract
- The first inter-calibration study of the stable silicon isotope composition of dissolved silicic acid in seawater, delta Si-30(OH)(4), is presented as a contribution to the international GEOTRACES program. Eleven laboratories from seven countries analyzed two seawater samples from the North Pacific subtropical gyre (Station ALOHA) collected at 300 m and at 1000 m water depth. Sampling depths were chosen to obtain samples with a relatively low (9 mmol L-1, 300 m) and a relatively high (113 mmol L-1, 1000 m) silicic acid concentration as sample preparation differs for low- and highconcentration samples. Data for the 1000 m water sample were not normally distributed so the median is used to represent the central tendency for the two samples. Median delta Si-30(OH)(4) values of +1.66& for the low-concentration sample and +1.25& for the high-concentration sample were obtained. Agreement among laboratories is overall considered very good; however, small but statistically significant differences among the mean isotope values obtained by different laboratories were detected, likely reflecting inter-laboratory differences in chemical preparation including pre-concentration and purification methods together with different volumes of seawater analyzed, and the use of different mass spectrometers including the Neptune MC-ICP-MS (Thermo Fisher (TM), Germany), the Nu Plasma MC-ICP-MS (Nu Instruments (TM), Wrexham, UK), and the Finnigan (TM) (now Thermo Fisher (TM), Germany) MAT 252 IRMS. Future studies analyzing delta Si-30(OH)(4) in seawater should also analyze and report values for these same two reference waters in order to facilitate comparison of data generated among and within laboratories over time.
|
|
| 46. |
- Grasse, P., et al.
(författare)
-
GEOTRACES Intercalibration of the Stable Silicon Isotope Composition of Dissolved Silicic Acid in Seawater
- 2017
-
Ingår i: Journal of Analytical Atomic Spectrometry. - London. - 0267-9477. ; 32, s. 562-578
-
Tidskriftsartikel (refereegranskat)abstract
- The first inter-calibration study of the stable silicon isotope composition of dissolved silicic acid in seawater, d30Si(OH)4, is presented as a contribution to the international GEOTRACES program. Eleven laboratories from seven countries analyzed two seawater samples from the North Pacific subtropical gyre (Station ALOHA) collected at 300 m and at 1000 m water depth. Sampling depths were chosen to obtain samples with a relatively low (9 mmol L-1, 300 m) and a relatively high (113 mmol L-1, 1000 m) silicic acid concentration as sample preparation differs for low- and high concentration samples. Data for the 1000 m water sample were not normally distributed so the median is used to represent the central tendency for the two samples. Median d30Si(OH)4 values of +1.66‰ for the low-concentration sample and +1.25‰ for the high-concentration sample were obtained. Agreement among laboratories is overall considered very good; however, small but statistically significant differences among the mean isotope values obtained by different laboratories were detected, likely reflecting inter-laboratory differences in chemical preparation including preconcentration and purification methods together with different volumes of seawater analyzed, andthe use of different mass spectrometers including the Neptune MC-ICP-MS (Thermo Fisher™, Germany), the Nu Plasma MC-ICP-MS (Nu Instruments™, Wrexham, UK), and the Finnigan™ (now Thermo Fisher™, Germany) MAT 252 IRMS. Future studies analyzing d30Si(OH)4 in seawater should also analyze and report values for these same two reference waters in order to facilitate comparison of data generated among and within laboratories over time.
|
|
| 47. |
|
|
| 48. |
|
|
| 49. |
- Hudson, Thomas J., et al.
(författare)
-
International network of cancer genome projects
- 2010
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7291, s. 993-998
-
Tidskriftsartikel (refereegranskat)abstract
- The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
|
|
| 50. |
- Jiang, Bin, et al.
(författare)
-
Predator species related adaptive changes in larval growth and digestive physiology
- 2019
-
Ingår i: Journal of insect physiology. - : Elsevier BV. - 0022-1910 .- 1879-1611. ; 114, s. 23-29
-
Tidskriftsartikel (refereegranskat)abstract
- Prey species are often non-randomly distributed along predator gradients but according to how they trade off growth against predation risk. The foraging-mediated growth/predation risk trade-off is well established, with increased foraging accelerating growth but also increasing predator induced mortality. While adaptations in digestive physiology may partly modify the relationship between foraging and growth in response to predation risk, studies exploring the impact of digestive physiology on growth in prey subjected to predation risk are still scarce. Larvae of the dragonfly genus Leucorrhinia segregate at the species level between lakes either being dominated by predatory fish (fish-lakes) or predatory invertebrates (dragonfly-lakes). Predators of these two lake types differ dramatically in their hunting style like searching and pursuing mode causing different selection pressure on prey traits including foraging. In a laboratory experiment we estimated growth rate, digestive physiology (ingested food, growth efficiency, assimilation efficiency, conversion efficiency) and metabolic rate (oxygen consumption) in the presence and absence of predator cues. Whereas fish-lake and dragonfly-lake Leucorrhinia species did not differ in growth rate, they evolved different pathways of digestive physiology to achieve similar growth rate. Because fish-lake species expressed a higher metabolic rate than dragonfly-lake species, we assume energy to be differently allocated and used for metabolic demands between species of both predator environments. Further, growth rate, but not digestive physiology was plastic in response to the presence of predator cues. Our results highlight the impact of digestive physiology in shaping the foraging-mediated growth/predation risk trade-off, with digestive physiology contributing to species distribution patterns along predator gradients.
|
|
