| 1. |
- 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.
|
|
| 2. |
- Liu, Ming, et al.
(författare)
-
Trigger algorithm development on FPGA-based Compute Nodes
- 2009
-
Ingår i: 2009 16th IEEE-NPSS Real Time Conference. - New York : IEEE. - 9781424457960 ; , s. 478-484
-
Konferensbidrag (refereegranskat)abstract
- Based on the ATCA computation architecture and Compute Nodes (CN), investigation and implementation work has been being executed for HADES and PANDA trigger algorithms. We present our designs for HADES track reconstruction processing, Cherenkov ring recognition, Time-Of-Flight processing, electromagnetic shower recognition.. and the PANDA straw tube tracking algorithm. They will appear as co-processors in the uniform system design to undertake the detector-specific computing. The algorithm principles will be explained and hardware designs are described in the paper. The current progress reveals the feasibility to implement these algorithms on FPGAs. Also experimental results demonstrate the performance speedup when compared to alternative software solutions, as well as the potential capability of high-speed parallel/pipelined processing in Data Acquisition and Trigger systems.
|
|
| 3. |
- Wang, Qiang, et al.
(författare)
-
Hardware/Software Co-design of an ATCA-based Computation Platform for Data Acquisition and Triggering
- 2009
-
Ingår i: 16th IEEE NPSS Real Time Conference. - 9781424457960 ; , s. 485-489
-
Konferensbidrag (refereegranskat)abstract
- An ATCA-based computation platform for data acquisition and trigger(TDAQ) applications has been developed for multiple future projects such its PANDA. HADES, and BESIII. Each Compute Node (CN) appears as one (if the fourteen Field Replaceable Units (FRU) in an ATCA shelf, which in total features a high performance of 1890 Clips inter-FPGA on-board channels, 1456 Gbps inter-board backplane connections, 728 Gbps full-duplex optical links, 70 Gbps Ethernet. 140 GBytes DDR2 SDRAM. and all computing resources of 70 Xilinx Virtex-4 FX60 FPGAs. Corresponding to (the system architecture, a hardware/software co-design approach is proposed to ease and accelerate the development for different experiments. In the uniform system design. application-specific computation is to be implemented as customized hardware co-processors, while the embedded PowerPC processor takes charge of flexible slow controls and transmission protocol processing.
|
|
| 4. |
|
|
| 5. |
- de Jong, Roelof S., et al.
(författare)
-
4MOST-4-metre Multi-Object Spectroscopic Telescope
- 2014
-
Ingår i: Ground-based and Airborne Instrumentation for Astronomy V. - : SPIE. - 0277-786X .- 1996-756X. ; 9147
-
Konferensbidrag (refereegranskat)abstract
- 4MOST is a wide-field, high-multiplex spectroscopic survey facility under development for the VISTA telescope of the European Southern Observatory (ESO). Its main science drivers are in the fields of galactic archeology, high-energy physics, galaxy evolution and cosmology. 4MOST will in particular provide the spectroscopic complements to the large area surveys coming from space missions like Gaia, eROSITA, Euclid, and PLATO and from ground-based facilities like VISTA, VST, DES, LSST and SKA. The 4MOST baseline concept features a 2.5 degree diameter field-of-view with similar to 2400 fibres in the focal surface that are configured by a fibre positioner based on the tilting spine principle. The fibres feed two types of spectrographs; similar to 1600 fibres go to two spectrographs with resolution R> 5000 (lambda similar to 390-930 nm) and similar to 800 fibres to a spectrograph with R> 18,000 (lambda similar to 392-437 nm & 515-572 nm & 605-675 nm). Both types of spectrographs are fixed-configuration, three-channel spectrographs. 4MOST will have an unique operations concept in which 5 year public surveys from both the consortium and the ESO community will be combined and observed in parallel during each exposure, resulting in more than 25 million spectra of targets spread over a large fraction of the southern sky. The 4MOST Facility Simulator (4FS) was developed to demonstrate the feasibility of this observing concept. 4MOST has been accepted for implementation by ESO with operations expected to start by the end of 2020. This paper provides a top-level overview of the 4MOST facility, while other papers in these proceedings provide more detailed descriptions of the instrument concept[1], the instrument requirements development[2], the systems engineering implementation[3], the instrument model[4], the fibre positioner concepts[5], the fibre feed[6], and the spectrographs[7].
|
|
| 6. |
- Elmendorf, Sarah C., et al.
(författare)
-
Global assessment of experimental climate warming on tundra vegetation : heterogeneity over space and time
- 2012
-
Ingår i: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 15:2, s. 164-175
-
Forskningsöversikt (refereegranskat)abstract
- Understanding the sensitivity of tundra vegetation to climate warming is critical to forecasting future biodiversity and vegetation feedbacks to climate. In situ warming experiments accelerate climate change on a small scale to forecast responses of local plant communities. Limitations of this approach include the apparent site-specificity of results and uncertainty about the power of short-term studies to anticipate longer term change. We address these issues with a synthesis of 61 experimental warming studies, of up to 20 years duration, in tundra sites worldwide. The response of plant groups to warming often differed with ambient summer temperature, soil moisture and experimental duration. Shrubs increased with warming only where ambient temperature was high, whereas graminoids increased primarily in the coldest study sites. Linear increases in effect size over time were frequently observed. There was little indication of saturating or accelerating effects, as would be predicted if negative or positive vegetation feedbacks were common. These results indicate that tundra vegetation exhibits strong regional variation in response to warming, and that in vulnerable regions, cumulative effects of long-term warming on tundra vegetation and associated ecosystem consequences have the potential to be much greater than we have observed to date.
|
|
| 7. |
- Flory, Stephan, et al.
(författare)
-
How to hit the allergy target: A critical appraisal of intralymphatic immunotherapy with practical recommendations on ultrasound-guided injections
- 2024
-
Ingår i: Allergy. European Journal of Allergy and Clinical Immunology. - : WILEY. - 0105-4538 .- 1398-9995.
-
Tidskriftsartikel (refereegranskat)abstract
- BackgroundIntralymphatic immunotherapy (ILIT) represents a promising novel approach treating allergic diseases. However, no standardized procedures or recommendations have been established or reported, despite the recognized fact that treatment efficacy relies on the ability to inject the allergen intranodally.ObjectiveWe aim to provide a critical appraisal of ILIT as a method of allergen immunotherapy and to deliver practical recommendations for accurate ILIT.MethodsOne hundred and seventy-three ILIT injections were performed in 28 (47%) women and 32 (53%) men with median age of 29 years (21-59). The injections were ultrasound-guided and recorded for retrospective analysis with respect to injection location, needle visibility, medication release, and patient characteristics.ResultsThe results show that the correct positioning of the needle within the lymph node (LN) was most critical. If the whole length of the needle bevel was not inserted into the LN, substance backflush into the interstitium was observed. Selecting a more superficial LN and inserting the needle at a smaller angle towards the LN significantly improved needle visibility in the ultrasound. Longitudinal results showed that continuous practice significantly correlated with improved needle visibility and more accurate ILIT injections.ConclusionBased on our results and practical experience, we propose several recommendations for LN selection and the correct handling of ultrasound probe and needle. We are confident that ILIT standardization and training will be important as to meet the goals of good safety and efficacy of ILIT. Ultrasound-guided ILIT holds promise for treatment of allergy. Correct positioning of the needle within the lymph node is critical for efficacy and safety, and practice correlate with improved needle visibility and more accurate ILIT injections. A guideline is proposed for effective ILIT. Abbreviations: ILIT, intralymphatic immunotherapy; LN, lymph node; SCIT, subcutaneous immunotherapy.image
|
|
| 8. |
- Fuerst, Johannes Jakob, et al.
(författare)
-
Application of a two-step approach for mapping ice thickness to various glacier types on Svalbard
- 2017
-
Ingår i: The Cryosphere. - : Copernicus GmbH. - 1994-0416 .- 1994-0424. ; 11:5, s. 2003-2032
-
Tidskriftsartikel (refereegranskat)abstract
- The basal topography is largely unknown beneath most glaciers and ice caps, and many attempts have been made to estimate a thickness field from other more accessible information at the surface. Here, we present a two-step reconstruction approach for ice thickness that solves mass conservation over single or several connected drainage basins. The approach is applied to a variety of test geometries with abundant thickness measurements including marine-and landterminating glaciers as well as a 2400 km(2) ice cap on Svalbard. The input requirements are kept to a minimum for the first step. In this step, a geometrically controlled, non-local flux solution is converted into thickness values relying on the shallow ice approximation (SIA). In a second step, the thickness field is updated along fast-flowing glacier trunks on the basis of velocity observations. Both steps account for available thickness measurements. Each thickness field is presented together with an error-estimate map based on a formal propagation of input uncertainties. These error estimates point out that the thickness field is least constrained near ice divides or in other stagnant areas. Withholding a share of the thickness measurements, error estimates tend to overestimate mismatch values in a median sense. We also have to accept an aggregate uncertainty of at least 25% in the reconstructed thickness field for glaciers with very sparse or no observations. For Vestfonna ice cap (VIC), a previous ice volume estimate based on the same measurement record as used here has to be corrected upward by 22 %. We also find that a 13% area fraction of the ice cap is in fact grounded below sea level. The former 5% estimate from a direct measurement interpolation exceeds an aggregate maximum range of 6-23% as inferred from the error estimates here.
|
|
| 9. |
- Fuerst, Johannes J., et al.
(författare)
-
The Ice-Free Topography of Svalbard
- 2018
-
Ingår i: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 45:21, s. 11760-11769
-
Tidskriftsartikel (refereegranskat)abstract
- We present a first version of the Svalbard ice-free topography (SVIFT1.0) using a mass conserving approach for mapping glacier ice thickness. SVIFT1.0 is informed by more than 1 million point measurements, totalling more than 8,700 km of thickness profiles. SVIFT1.0 is publicly available and represents the geometric state around the year 2010. Our estimate for the total ice volume is 6,199 km(3), equivalent to 1.5-cm sea level rise. The thickness map suggests that 13% of the glacierized area is grounded below sea level. A complementary map of error estimates comprises uncertainties in the thickness surveys as well as in other input variables. Aggregated error estimates are used to define a likely ice-volume range of 5,200-7,300 km(3). The ice front thickness of marine-terminating glaciers is a key quantity for ice loss attribution because it controls the potential ice discharge by iceberg calving into the ocean. We find a mean ice front thickness of 135 m for the archipelago (likely range 123-158 m). Plain Language Summary Svalbard is an archipelago in the Arctic, north of Norway, which is comparable in size to the New York metropolitan area. Roughly half of it is covered by glacier ice. Yet to this day, the ice volume stored in the many glaciers on Svalbard is not well known. Many attempts have been made to infer a total volume estimate, but results differ substantially. This surprises because of the long research activity in this area. A large record of more than 1 million thickness measurements exists, making Svalbard an ideal study area for the application of a state-of-the-art mapping approach for glacier ice thickness. The mapping approach computes an ice volume that will raise global sea level by more than half an inch if instantaneously melted. If spread over the metropolitan area, New York would be buried beneath a 100-m ice cover. The asset of this approach is that it provides not only a thickness map for each glacier on the archipelago but also an error map that defines the likely local thickness range. Finally, we provide the first well-informed estimate of the ice front thickness of all marine-terminating glaciers that loose icebergs to the ocean. The archipelago-wide mean ice front cliff is 135 m.
|
|
| 10. |
- Hess, Timo, et al.
(författare)
-
Dissecting the genetic heterogeneity of gastric cancer
- 2023
-
Ingår i: EBioMedicine. - : Elsevier. - 2352-3964. ; 92
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Gastric cancer (GC) is clinically heterogenous according to location (cardia/non-cardia) and histopathology (diffuse/intestinal). We aimed to characterize the genetic risk architecture of GC according to its subtypes. Another aim was to examine whether cardia GC and oesophageal adenocarcinoma (OAC) and its precursor lesion Barrett's oesophagus (BO), which are all located at the gastro-oesophageal junction (GOJ), share polygenic risk architecture.Methods: We did a meta-analysis of ten European genome-wide association studies (GWAS) of GC and its subtypes. All patients had a histopathologically confirmed diagnosis of gastric adenocarcinoma. For the identification of risk genes among GWAS loci we did a transcriptome-wide association study (TWAS) and expression quantitative trait locus (eQTL) study from gastric corpus and antrum mucosa. To test whether cardia GC and OAC/BO share genetic aetiology we also used a European GWAS sample with OAC/BO.Findings: Our GWAS consisting of 5816 patients and 10,999 controls highlights the genetic heterogeneity of GC according to its subtypes. We newly identified two and replicated five GC risk loci, all of them with subtype-specific association. The gastric transcriptome data consisting of 361 corpus and 342 antrum mucosa samples revealed that an upregulated expression of MUC1, ANKRD50, PTGER4, and PSCA are plausible GC-pathomechanisms at four GWAS loci. At another risk locus, we found that the blood-group 0 exerts protective effects for non-cardia and diffuse GC, while blood-group A increases risk for both GC subtypes. Furthermore, our GWAS on cardia GC and OAC/BO (10,279 patients, 16,527 controls) showed that both cancer entities share genetic aetiology at the polygenic level and identified two new risk loci on the single-marker level.Interpretation: Our findings show that the pathophysiology of GC is genetically heterogenous according to location and histopathology. Moreover, our findings point to common molecular mechanisms underlying cardia GC and OAC/BO.
|
|
| 11. |
- Hou, Liping, et al.
(författare)
-
Genome-wide association study of 40,000 individuals identifies two novel loci associated with bipolar disorder.
- 2016
-
Ingår i: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 0964-6906. ; 25:15, s. 3383-94
-
Tidskriftsartikel (refereegranskat)abstract
- Bipolar disorder (BD) is a genetically complex mental illness characterized by severe oscillations of mood and behavior. Genome-wide association studies (GWAS) have identified several risk loci that together account for a small portion of the heritability. To identify additional risk loci, we performed a two-stage meta-analysis of >9 million genetic variants in 9,784 bipolar disorder patients and 30,471 controls, the largest GWAS of BD to date. In this study, to increase power we used ∼2,000 lithium-treated cases with a long-term diagnosis of BD from the Consortium on Lithium Genetics, excess controls, and analytic methods optimized for markers on the X-chromosome. In addition to four known loci, results revealed genome-wide significant associations at two novel loci: an intergenic region on 9p21.3 (rs12553324, p=5.87×10(-9); odds ratio=1.12) and markers within ERBB2 (rs2517959, p=4.53×10(-9); odds ratio=1.13). No significant X-chromosome associations were detected and X-linked markers explained very little BD heritability. The results add to a growing list of common autosomal variants involved in BD and illustrate the power of comparing well-characterized cases to an excess of controls in GWAS.
|
|
| 12. |
- Höglinger, Günter U, et al.
(författare)
-
Clinical diagnosis of progressive supranuclear palsy : The movement disorder society criteria
- 2017
-
Ingår i: Movement Disorders. - : Wiley. - 0885-3185. ; 32:6, s. 853-864
-
Tidskriftsartikel (refereegranskat)abstract
- Background: PSP is a neuropathologically defined disease entity. Clinical diagnostic criteria, published in 1996 by the National Institute of Neurological Disorders and Stroke/Society for PSP, have excellent specificity, but their sensitivity is limited for variant PSP syndromes with presentations other than Richardson's syndrome. Objective: We aimed to provide an evidence- and consensus-based revision of the clinical diagnostic criteria for PSP. Methods: We searched the PubMed, Cochrane, Medline, and PSYCInfo databases for articles published in English since 1996, using postmortem diagnosis or highly specific clinical criteria as the diagnostic standard. Second, we generated retrospective standardized clinical data from patients with autopsy-confirmed PSP and control diseases. On this basis, diagnostic criteria were drafted, optimized in two modified Delphi evaluations, submitted to structured discussions with consensus procedures during a 2-day meeting, and refined in three further Delphi rounds. Results: Defined clinical, imaging, laboratory, and genetic findings serve as mandatory basic features, mandatory exclusion criteria, or context-dependent exclusion criteria. We identified four functional domains (ocular motor dysfunction, postural instability, akinesia, and cognitive dysfunction) as clinical predictors of PSP. Within each of these domains, we propose three clinical features that contribute different levels of diagnostic certainty. Specific combinations of these features define the diagnostic criteria, stratified by three degrees of diagnostic certainty (probable PSP, possible PSP, and suggestive of PSP). Clinical clues and imaging findings represent supportive features. Conclusions: Here, we present new criteria aimed to optimize early, sensitive, and specific clinical diagnosis of PSP on the basis of currently available evidence.
|
|
| 13. |
- Keogan, Katharine, et al.
(författare)
-
Global phenological insensitivity to shifting ocean temperatures among seabirds
- 2018
-
Ingår i: Nature Climate Change. - : Springer Science and Business Media LLC. - 1758-678X .- 1758-6798. ; 8:4, s. 313-318
-
Tidskriftsartikel (refereegranskat)abstract
- Reproductive timing in many taxa plays a key role in determining breeding productivity(1), and is often sensitive to climatic conditions(2). Current climate change may alter the timing of breeding at different rates across trophic levels, potentially resulting in temporal mismatch between the resource requirements of predators and their prey(3). This is of particular concern for higher-trophic-level organisms, whose longer generation times confer a lower rate of evolutionary rescue than primary producers or consumers(4). However, the disconnection between studies of ecological change in marine systems makes it difficult to detect general changes in the timing of reproduction(5). Here, we use a comprehensive meta-analysis of 209 phenological time series from 145 breeding populations to show that, on average, seabird populations worldwide have not adjusted their breeding seasons over time (-0.020 days yr(-1)) or in response to sea surface temperature (SST) (-0.272 days degrees C-1) between 1952 and 2015. However, marked between-year variation in timing observed in resident species and some Pelecaniformes and Suliformes (cormorants, gannets and boobies) may imply that timing, in some cases, is affected by unmeasured environmental conditions. This limited temperature-mediated plasticity of reproductive timing in seabirds potentially makes these top predators highly vulnerable to future mismatch with lower-trophic-level resources(2).
|
|
| 14. |
- Liu, Ming, et al.
(författare)
-
ATCA-based Computation Platform for Data Acquisition and Triggering in Particle Physics Experiments
- 2008
-
Ingår i: 2008 INTERNATIONAL CONFERENCE ON FIELD PROGRAMMABLE AND LOGIC APPLICATIONS, VOLS 1 AND 2. ; , s. 287-292
-
Konferensbidrag (refereegranskat)abstract
- An ATCA-based computation platform for data acquisition and trigger applications in nuclear and particle physics experiments has been developed. Each Compute Node (CN) which appears as a Field Replaceable Unit (FRU) in an ATCA shelf, features 5 Xilinx Virtex-4 FX60 FPGAs and up to 10 GBytes DDR2 memory. Connectivity is provided with 8 optical links and 5 Gigabit Ethernet ports, which are mounted on each board to receive data from detectors and forward results to outer shelves or PC farms with attached mass storage. Fast point-to-point on-board interconnections between FPGAs as well as the full-mesh shelf backplane provide flexibility and high bandwidth to partition algorithms and correlate results among them. The system represents a highly reconfigurable and scalable solution for multiple applications.
|
|
| 15. |
- Luederitz, Christopher, et al.
(författare)
-
Learning through Evaluation: A Tentative Evaluative Scheme for Sustainability Transition Experiments
- 2017
-
Ingår i: Journal of Cleaner Production. - 0959-6526. ; 169, s. 61-76
-
Tidskriftsartikel (refereegranskat)abstract
- Transitions towards sustainability are urgently needed to address the interconnected challenges of economic development, ecological integrity, and social justice, from local to global scales. Around the world, collaborative science-society initiatives are forming to conduct experiments in support of sustainability transitions. Such experiments, if carefully designed, provide significant learning opportunities for making progress on transition efforts. Yet, there is no broadly applicable evaluative scheme available to capture this critical information across a large number of cases, and to guide the design of transition experiments. To address this gap, the article develops such a scheme, in a tentative form, drawing on evaluative research and sustainability transitions scholarship, alongside insights from empirical cases. We critically discuss the scheme's key features of being generic, comprehensive, operational, and formative. Furthermore, we invite scholars and practitioners to apply, reflect and further develop the proposed tentative scheme – making evaluation and experiments objects of learning.
|
|
| 16. |
- Mahmoodi, Bakhtawar K., et al.
(författare)
-
Association of Factor V Leiden With Subsequent Atherothrombotic Events A GENIUS-CHD Study of Individual Participant Data
- 2020
-
Ingår i: Circulation. - : Ovid Technologies (Wolters Kluwer Health). - 0009-7322 .- 1524-4539. ; 142:6, s. 546-555
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Studies examining the role of factor V Leiden among patients at higher risk of atherothrombotic events, such as those with established coronary heart disease (CHD), are lacking. Given that coagulation is involved in the thrombus formation stage on atherosclerotic plaque rupture, we hypothesized that factor V Leiden may be a stronger risk factor for atherothrombotic events in patients with established CHD.Methods: We performed an individual-level meta-analysis including 25 prospective studies (18 cohorts, 3 case-cohorts, 4 randomized trials) from the GENIUS-CHD (Genetics of Subsequent Coronary Heart Disease) consortium involving patients with established CHD at baseline. Participating studies genotyped factor V Leiden status and shared risk estimates for the outcomes of interest using a centrally developed statistical code with harmonized definitions across studies. Cox proportional hazards regression models were used to obtain age- and sex-adjusted estimates. The obtained estimates were pooled using fixed-effect meta-analysis. The primary outcome was composite of myocardial infarction and CHD death. Secondary outcomes included any stroke, ischemic stroke, coronary revascularization, cardiovascular mortality, and all-cause mortality.Results: The studies included 69 681 individuals of whom 3190 (4.6%) were either heterozygous or homozygous (n=47) carriers of factor V Leiden. Median follow-up per study ranged from 1.0 to 10.6 years. A total of 20 studies with 61 147 participants and 6849 events contributed to analyses of the primary outcome. Factor V Leiden was not associated with the combined outcome of myocardial infarction and CHD death (hazard ratio, 1.03 [95% CI, 0.92-1.16];I-2=28%;P-heterogeneity=0.12). Subgroup analysis according to baseline characteristics or strata of traditional cardiovascular risk factors did not show relevant differences. Similarly, risk estimates for the secondary outcomes including stroke, coronary revascularization, cardiovascular mortality, and all-cause mortality were also close to identity.Conclusions: Factor V Leiden was not associated with increased risk of subsequent atherothrombotic events and mortality in high-risk participants with established and treated CHD. Routine assessment of factor V Leiden status is unlikely to improve atherothrombotic events risk stratification in this population.
|
|
| 17. |
- Meyer, Nicolas, et al.
(författare)
-
Behavioural responses of breeding arctic sandpipers to ground-surface temperature and primary productivity
- 2021
-
Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 755
-
Tidskriftsartikel (refereegranskat)abstract
- Most birds incubate their eggs, which requires time and energy at the expense of other activities. Birds generally have two incubation strategies: biparental where both mates cooperate in incubating eggs, and uniparental where a single parent incubates. In harsh and unpredictable environments, incubation is challenging due to high energetic demands and variable resource availability. We studied the relationships between the incubation behaviour of sandpipers (genus Calidris) and two environmental variables: temperature and a proxy of primary productivity (i.e. NDVI). We investigated how these relationships vary between incubation strategies and across species among strategies. We also studied how the relationship between current temperature and incubation behaviour varies with previous day's temperature. We monitored the incubation behaviour of nine sandpiper species using thermologgers at 15 arctic sites between 2016 and 2019. We also used thermologgers to record the ground surface temperature at conspecific nest sites and extracted NDVI values from a remote sensing product. We found no relationship between either environmental variables and biparental incubation behaviour. Conversely, as ground-surface temperature increased, uniparental species decreased total duration of recesses (TDR) and mean duration of recesses (MDR), but increased number of recesses (NR). Moreover, small species showed stronger relationships with ground-surface temperature than large species. When all uniparental species were combined, an increase in NDVI was correlated with higher mean duration, total duration and number of recesses, but relationships varied widely across species. Finally, some uniparental species showed a lag effect with a higher nest attentiveness after a warm day while more recesses occurred after a cold day than was predicted based on current temperatures. We demonstrate the complex interplay between shorebird incubation strategies, incubation behaviour, and environmental conditions. Understanding how species respond to changes in their environment during incubation helps predict their future reproductive success.
|
|
| 18. |
- Meyer, Nicolas, et al.
(författare)
-
Nest attentiveness drives nest predation in arctic sandpipers
- 2020
-
Ingår i: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 129:10, s. 1481-1492
-
Tidskriftsartikel (refereegranskat)abstract
- Most birds incubate their eggs to allow embryo development. This behaviour limits the ability of adults to perform other activities. Hence, incubating adults trade off incubation and nest protection with foraging to meet their own needs. Parents can either cooperate to sustain this tradeoff or incubate alone. The main cause of reproductive failure at this reproductive stage is predation and adults reduce this risk by keeping the nest location secret. Arctic sandpipers are interesting biological models to investigate parental care evolution as they may use several parental care strategies. The three main incubation strategies include both parents sharing incubation duties ('biparental'), one parent incubating alone ('uniparental'), or a flexible strategy with both uniparental and biparental incubation within a population ('mixed'). By monitoring the incubation behaviour in 714 nests of seven sandpiper species across 12 arctic sites, we studied the relationship between incubation strategy and nest predation. First, we described how the frequency of incubation recesses (NR), their mean duration (MDR), and the daily total duration of recesses (TDR) vary among strategies. Then, we examined how the relationship between the daily predation rate and these components of incubation behaviour varies across strategies using two complementary survival analysis. For uniparental and biparental species, the daily predation rate increased with the daily total duration of recesses and with the mean duration of recesses. In contrast, daily predation rate increased with the daily number of recesses for biparental species only. These patterns may be attributed to two independent mechanisms: cryptic incubating adults are more difficult to locate than unattended nests and adults departing the nest or feeding close to the nest can draw predators' attention. Our results demonstrate that incubation behaviour as mediated by incubation strategy has important consequences for sandpipers' reproductive success.
|
|
| 19. |
- Patel, Riyaz S., et al.
(författare)
-
Association of Chromosome 9p21 With Subsequent Coronary Heart Disease Events : A GENIUS-CHD Study of Individual Participant Data
- 2019
-
Ingår i: Circulation. - 2574-8300. ; 12:4
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Genetic variation at chromosome 9p21 is a recognized risk factor for coronary heart disease (CHD). However, its effect on disease progression and subsequent events is unclear, raising questions about its value for stratification of residual risk.METHODS: A variant at chromosome 9p21 (rs1333049) was tested for association with subsequent events during follow-up in 103 357 Europeans with established CHD at baseline from the GENIUS-CHD (Genetics of Subsequent Coronary Heart Disease) Consortium (73.1% male, mean age 62.9 years). The primary outcome, subsequent CHD death or myocardial infarction (CHD death/myocardial infarction), occurred in 13 040 of the 93 115 participants with available outcome data. Effect estimates were compared with case/control risk obtained from the CARDIoGRAMplusC4D consortium (Coronary Artery Disease Genome-wide Replication and Meta-analysis [CARDIoGRAM] plus The Coronary Artery Disease [C4D] Genetics) including 47 222 CHD cases and 122 264 controls free of CHD.RESULTS: Meta-analyses revealed no significant association between chromosome 9p21 and the primary outcome of CHD death/myocardial infarction among those with established CHD at baseline (GENIUSCHD odds ratio, 1.02; 95% CI, 0.99-1.05). This contrasted with a strong association in CARDIoGRAMPlusC4D odds ratio 1.20; 95% CI, 1.18-1.22; P for interaction < 0.001 compared with the GENIUS-CHD estimate. Similarly, no clear associations were identified for additional subsequent outcomes, including all-cause death, although we found a modest positive association between chromosome 9p21 and subsequent revascularization (odds ratio, 1.07; 95% CI, 1.04-1.09).CONCLUSIONS: In contrast to studies comparing individuals with CHD to disease-free controls, we found no clear association between genetic variation at chromosome 9p21 and risk of subsequent acute CHD events when all individuals had CHD at baseline. However, the association with subsequent revascularization may support the postulated mechanism of chromosome 9p21 for promoting atheroma development.
|
|
| 20. |
- Patel, Riyaz S., et al.
(författare)
-
Subsequent Event Risk in Individuals With Established Coronary Heart Disease : Design and Rationale of the GENIUS-CHD Consortium
- 2019
-
Ingår i: Circulation. - 2574-8300. ; 12:4
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: The Genetics of Subsequent Coronary Heart Disease (GENIUS-CHD) consortium was established to facilitate discovery and validation of genetic variants and biomarkers for risk of subsequent CHD events, in individuals with established CHD.METHODS: The consortium currently includes 57 studies from 18 countries, recruiting 185 614 participants with either acute coronary syndrome, stable CHD, or a mixture of both at baseline. All studies collected biological samples and followed-up study participants prospectively for subsequent events.RESULTS: Enrollment into the individual studies took place between 1985 to present day with a duration of follow-up ranging from 9 months to 15 years. Within each study, participants with CHD are predominantly of self-reported European descent (38%-100%), mostly male (44%-91%) with mean ages at recruitment ranging from 40 to 75 years. Initial feasibility analyses, using a federated analysis approach, yielded expected associations between age (hazard ratio, 1.15; 95% CI, 1.14-1.16) per 5-year increase, male sex (hazard ratio, 1.17; 95% CI, 1.13-1.21) and smoking (hazard ratio, 1.43; 95% CI, 1.35-1.51) with risk of subsequent CHD death or myocardial infarction and differing associations with other individual and composite cardiovascular endpoints.CONCLUSIONS: GENIUS-CHD is a global collaboration seeking to elucidate genetic and nongenetic determinants of subsequent event risk in individuals with established CHD, to improve residual risk prediction and identify novel drug targets for secondary prevention. Initial analyses demonstrate the feasibility and reliability of a federated analysis approach. The consortium now plans to initiate and test novel hypotheses as well as supporting replication and validation analyses for other investigators.
|
|
| 21. |
- Rehn, Alexandra, et al.
(författare)
-
A methylated lysine is a switch point for conformational communication in the chaperone Hsp90
- 2020
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- Methylation of a conserved lysine in C-terminal domain of the molecular chaperone Hsp90 was shown previously to affect its in vivo function. However, the underlying mechanism remained elusive. Through a combined experimental and computational approach, this study shows that this site is very sensitive to sidechain modifications and crucial for Hsp90 activity in vitro and in vivo. Our results demonstrate that this particular lysine serves as a switch point for the regulation of Hsp90 functions by influencing its conformational cycle, ATPase activity, co-chaperone regulation, and client activation of yeast and human Hsp90. Incorporation of the methylated lysine via genetic code expansion specifically shows that upon modification, the conformational cycle of Hsp90 is altered. Molecular dynamics simulations including the methylated lysine suggest specific conformational changes that are propagated through Hsp90. Thus, methylation of the C-terminal lysine allows a precise allosteric tuning of Hsp90 activity via long distances. Methylation of a lysine residue in Hsp90 is a recently discovered post-translational modification but the mechanistic effects of this modification have remained unknown so far. Here the authors combine biochemical and biophysical approaches, molecular dynamics (MD) simulations and functional experiments with yeast and show that this lysine is a switch point, which specifically modulates conserved Hsp90 functions including co-chaperone regulation and client activation.
|
|
| 22. |
- Respondek, Gesine, et al.
(författare)
-
Which ante mortem clinical features predict progressive supranuclear palsy pathology?
- 2017
-
Ingår i: Movement Disorders. - : Wiley. - 0885-3185. ; 32:7, s. 995-1005
-
Forskningsöversikt (refereegranskat)abstract
- Background: Progressive supranuclear palsy (PSP) is a neuropathologically defined disease presenting with a broad spectrum of clinical phenotypes. Objective: To identify clinical features and investigations that predict or exclude PSP pathology during life, aiming at an optimization of the clinical diagnostic criteria for PSP. Methods: We performed a systematic review of the literature published since 1996 to identify clinical features and investigations that may predict or exclude PSP pathology. We then extracted standardized data from clinical charts of patients with pathologically diagnosed PSP and relevant disease controls and calculated the sensitivity, specificity, and positive predictive value of key clinical features for PSP in this cohort. Results: Of 4166 articles identified by the database inquiry, 269 met predefined standards. The literature review identified clinical features predictive of PSP, including features of the following 4 functional domains: ocular motor dysfunction, postural instability, akinesia, and cognitive dysfunction. No biomarker or genetic feature was found reliably validated to predict definite PSP. High-quality original natural history data were available from 206 patients with pathologically diagnosed PSP and from 231 pathologically diagnosed disease controls (54 corticobasal degeneration, 51 multiple system atrophy with predominant parkinsonism, 53 Parkinson's disease, 73 behavioral variant frontotemporal dementia). We identified clinical features that predicted PSP pathology, including phenotypes other than Richardson's syndrome, with varying sensitivity and specificity. Conclusions: Our results highlight the clinical variability of PSP and the high prevalence of phenotypes other than Richardson's syndrome. The features of variant phenotypes with high specificity and sensitivity should serve to optimize clinical diagnosis of PSP.
|
|
| 23. |
- Schober, Sebastian Johannes, et al.
(författare)
-
No Improvement of Survival for Alveolar Rhabdomyosarcoma Patients After HLA-Matched Versus -Mismatched Allogeneic Hematopoietic Stem Cell Transplantation Compared to Standard-of-Care Therapy
- 2022
-
Ingår i: Frontiers in Oncology. - : Frontiers Media S.A.. - 2234-943X. ; 12
-
Tidskriftsartikel (refereegranskat)abstract
- BackgroundPatients with stage IV alveolar rhabdomyosarcoma (RMA) have a 5-year-survival rate not exceeding 30%. Here, we assess the role of allogeneic hematopoietic stem cell transplantation (allo-HSCT) for these patients in comparison to standard-of-care regimens. We also compare the use of HLA-mismatched vs. HLA-matched grafts after reduced vs. myeloablative conditioning regimens, respectively. Patients and MethodsIn this retrospective analysis, we compare event-free survival (EFS), overall survival (OS), and toxicity of HLA-mismatched vs. -matched transplanted patients in uni- and multivariate analyses (total: n = 50, HLA-matched: n = 15, HLA-mismatched: n = 35). Here, the factors age at diagnosis, age at allo-HSCT, sex, Oberlin score, disease status at allo-HSCT, and HLA graft type are assessed. For 29 primarily transplanted patients, three matched non-transplanted patients per one transplanted patient were identified from the CWS registry. Outcomes were respectively compared for OS and EFS. Matching criteria included sex, age at diagnosis, favorable/unfavorable primary tumor site, and metastatic sites. ResultsMedian EFS and OS did not differ significantly between HLA-mismatched and -matched patients. In the mismatched group, incidence of acute GvHD was 0.87 (grade III-IV: 0.14) vs. 0.80 in HLA-matched patients (grade III-IV: 0.20). Transplant-related mortality (TRM) of all patients was 0.20 and did not differ significantly between HLA-mismatched and -matched groups. A proportion of 0.58 relapsed or progressed and died of disease (HLA-mismatched: 0.66, HLA-matched: 0.53) whereas 0.18 were alive in complete remission (CR) at data collection. Multivariate and competing risk analyses confirmed CR and very good partial response (VGPR) status prior to allo-HSCT as the only decisive predictor for OS (p < 0.001). Matched-pair survival analyses of primarily transplanted patients vs. matched non-transplanted patients also identified disease status prior to allo-HSCT (CR, VGPR) as the only significant predictor for EFS. Here, OS was not affected, however. ConclusionIn this retrospective analysis, only a subgroup of patients with good response at allo-HSCT survived. There was no survival benefit of allo-transplanted patients compared to matched controls, suggesting the absence of a clinically relevant graft-versus-RMA effect in the current setting. The results of this analysis do not support further implementation of allo-HSCT in RMA stage IV patients.
|
|
| 24. |
-
- 2019
-
Tidskriftsartikel (refereegranskat)
|
|
