| 1. |
- Saunois, M., et al.
(author)
-
The global methane budget 2000–2012
- 2016
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In: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 8:2, s. 697-751
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Journal article (peer-reviewed)abstract
- The global methane (CH4) budget is becoming an increasingly important component for managing realistic pathways to mitigate climate change. This relevance, due to a shorter atmospheric lifetime and a stronger warming potential than carbon dioxide, is challenged by the still unexplained changes of atmospheric CH4 over the past decade. Emissions and concentrations of CH4 are continuing to increase, making CH4 the second most important human-induced greenhouse gas after carbon dioxide. Two major difficulties in reducing uncertainties come from the large variety of diffusive CH4 sources that overlap geographically, and from the destruction of CH4 by the very short-lived hydroxyl radical (OH). To address these difficulties, we have established a consortium of multi-disciplinary scientists under the umbrella of the Global Carbon Project to synthesize and stimulate research on the methane cycle, and producing regular (∼ biennial) updates of the global methane budget. This consortium includes atmospheric physicists and chemists, biogeochemists of surface and marine emissions, and socio-economists who study anthropogenic emissions. Following Kirschke et al. (2013), we propose here the first version of a living review paper that integrates results of top-down studies (exploiting atmospheric observations within an atmospheric inverse-modelling framework) and bottom-up models, inventories and data-driven approaches (including process-based models for estimating land surface emissions and atmospheric chemistry, and inventories for anthropogenic emissions, data-driven extrapolations). For the 2003–2012 decade, global methane emissions are estimated by top-down inversions at 558 Tg CH4 yr−1, range 540–568. About 60 % of global emissions are anthropogenic (range 50–65 %). Since 2010, the bottom-up global emission inventories have been closer to methane emissions in the most carbon-intensive Representative Concentrations Pathway (RCP8.5) and higher than all other RCP scenarios. Bottom-up approaches suggest larger global emissions (736 Tg CH4 yr−1, range 596–884) mostly because of larger natural emissions from individual sources such as inland waters, natural wetlands and geological sources. Considering the atmospheric constraints on the top-down budget, it is likely that some of the individual emissions reported by the bottom-up approaches are overestimated, leading to too large global emissions. Latitudinal data from top-down emissions indicate a predominance of tropical emissions (∼ 64 % of the global budget, < 30° N) as compared to mid (∼ 32 %, 30–60° N) and high northern latitudes (∼ 4 %, 60–90° N). Top-down inversions consistently infer lower emissions in China (∼ 58 Tg CH4 yr−1, range 51–72, −14 %) and higher emissions in Africa (86 Tg CH4 yr−1, range 73–108, +19 %) than bottom-up values used as prior estimates. Overall, uncertainties for anthropogenic emissions appear smaller than those from natural sources, and the uncertainties on source categories appear larger for top-down inversions than for bottom-up inventories and models. The most important source of uncertainty on the methane budget is attributable to emissions from wetland and other inland waters. We show that the wetland extent could contribute 30–40 % on the estimated range for wetland emissions. Other priorities for improving the methane budget include the following: (i) the development of process-based models for inland-water emissions, (ii) the intensification of methane observations at local scale (flux measurements) to constrain bottom-up land surface models, and at regional scale (surface networks and satellites) to constrain top-down inversions, (iii) improvements in the estimation of atmospheric loss by OH, and (iv) improvements of the transport models integrated in top-down inversions. The data presented here can be downloaded from the Carbon Dioxide Information Analysis Center (http://doi.org/10.3334/CDIAC/GLOBAL_METHANE_BUDGET_2016_V1.1) and the Global Carbon Project.
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| 2. |
- Saunois, M., et al.
(author)
-
Variability and quasi-decadal changes in the methane budget over the period 2000–2012
- 2017
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In: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 17:18, s. 11135-11161
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Journal article (peer-reviewed)abstract
- Following the recent Global Carbon Project (GCP) synthesis of the decadal methane (CH4) budget over 2000–2012 (Saunois et al., 2016), we analyse here the same dataset with a focus on quasi-decadal and inter-annual variability in CH4 emissions. The GCP dataset integrates results from top-down studies (exploiting atmospheric observations within an atmospheric inverse-modelling framework) and bottom-up models (including process-based models for estimating land surface emissions and atmospheric chemistry), inventories of anthropogenic emissions, and data-driven approaches. The annual global methane emissions from top-down studies, which by construction match the observed methane growth rate within their uncertainties, all show an increase in total methane emissions over the period 2000–2012, but this increase is not linear over the 13 years. Despite differences between individual studies, the mean emission anomaly of the top-down ensemble shows no significant trend in total methane emissions over the period 2000–2006, during the plateau of atmospheric methane mole fractions, and also over the period 2008–2012, during the renewed atmospheric methane increase. However, the top-down ensemble mean produces an emission shift between 2006 and 2008, leading to 22 [16–32] Tg CH4 yr−1 higher methane emissions over the period 2008–2012 compared to 2002–2006. This emission increase mostly originated from the tropics, with a smaller contribution from mid-latitudes and no significant change from boreal regions. The regional contributions remain uncertain in top-down studies. Tropical South America and South and East Asia seem to contribute the most to the emission increase in the tropics. However, these two regions have only limited atmospheric measurements and remain therefore poorly constrained. The sectorial partitioning of this emission increase between the periods 2002–2006 and 2008–2012 differs from one atmospheric inversion study to another. However, all top-down studies suggest smaller changes in fossil fuel emissions (from oil, gas, and coal industries) compared to the mean of the bottom-up inventories included in this study. This difference is partly driven by a smaller emission change in China from the top-down studies compared to the estimate in the Emission Database for Global Atmospheric Research (EDGARv4.2) inventory, which should be revised to smaller values in a near future. We apply isotopic signatures to the emission changes estimated for individual studies based on five emission sectors and find that for six individual top-down studies (out of eight) the average isotopic signature of the emission changes is not consistent with the observed change in atmospheric 13CH4. However, the partitioning in emission change derived from the ensemble mean is consistent with this isotopic constraint. At the global scale, the top-down ensemble mean suggests that the dominant contribution to the resumed atmospheric CH4 growth after 2006 comes from microbial sources (more from agriculture and waste sectors than from natural wetlands), with an uncertain but smaller contribution from fossil CH4 emissions. In addition, a decrease in biomass burning emissions (in agreement with the biomass burning emission databases) makes the balance of sources consistent with atmospheric 13CH4 observations. In most of the top-down studies included here, OH concentrations are considered constant over the years (seasonal variations but without any inter-annual variability). As a result, the methane loss (in particular through OH oxidation) varies mainly through the change in methane concentrations and not its oxidants. For these reasons, changes in the methane loss could not be properly investigated in this study, although it may play a significant role in the recent atmospheric methane changes as briefly discussed at the end of the paper.
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| 3. |
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| 4. |
- Anastasopoulos, M., et al.
(author)
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Multi-Grid detector for neutron spectroscopy : Results obtained on time-of-flight spectrometer CNCS
- 2017
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In: Journal of Instrumentation. - : IOP PUBLISHING LTD. - 1748-0221. ; 12:4
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Journal article (peer-reviewed)abstract
- The Multi-Grid detector technology has evolved from the proof-of-principle and characterisation stages. Here we report on the performance of the Multi-Grid detector, the MG.CNCS prototype, which has been installed and tested at the Cold Neutron Chopper Spectrometer, CNCS at SNS. This has allowed a side-by-side comparison to the performance of 3He detectors on an operational instrument. The demonstrator has an active area of 0.2 m2. It is specifically tailored to the specifications of CNCS. The detector was installed in June 2016 and has operated since then, collecting neutron scattering data in parallel to the He-3 detectors of CNCS. In this paper, we present a comprehensive analysis of this data, in particular on instrument energy resolution, rate capability, background and relative efficiency. Stability, gamma-ray and fast neutron sensitivity have also been investigated. The effect of scattering in the detector components has been measured and provides input to comparison for Monte Carlo simulations. All data is presented in comparison to that measured by the 3He detectors simultaneously, showing that all features recorded by one detector are also recorded by the other. The energy resolution matches closely. We find that the Multi-Grid is able to match the data collected by 3He, and see an indication of a considerable advantage in the count rate capability. Based on these results, we are confident that the Multi-Grid detector will be capable of producing high quality scientific data on chopper spectrometers utilising the unprecedented neutron flux of the ESS.
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| 5. |
- Gaetani, L., et al.
(author)
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A new enzyme-linked immunosorbent assay for neurofilament light in cerebrospinal fluid: analytical validation and clinical evaluation
- 2018
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In: Alzheimers Research & Therapy. - : Springer Science and Business Media LLC. - 1758-9193. ; 10
-
Journal article (peer-reviewed)abstract
- Background: Cerebrospinal fluid (CSF) neurofilament light (NfL) is a reliable marker of neuro-axonal damage in different neurological disorders that is related to disease severity. To date, all recent studies performed in human CSF have used the same enzyme-linked immunosorbent assay (ELISA). To confirm the large body of evidence for NfL, we developed a new ELISA method and here we present the performance characteristics of this new ELISA for CSF NfL in different neurological disorders. Methods: We produced two monoclonal antibodies (NfL21 and NfL23) directed against the NfL core domain, and developed a novel sandwich ELISA method that we evaluated in patients with: 1) inflammatory demyelinating diseases (IDD; n = 97), including multiple sclerosis (MS; n = 59), clinically isolated syndrome (CIS; n = 32), and radiologically isolated syndrome (RIS; n = 6); 2) Alzheimer's disease (AD; n = 72), including mild cognitive impairment due to AD (MCI-AD, n = 36) and probable AD dementia (AD-dem; n = 36); 3) Parkinson's disease (PD; n = 30); and 4) other neurological noninflammatory and non-neurodegenerative diseases (OND; n = 30). Results: Our new NfL ELISA showed a good analytical performance (inter-plate coefficient of variation (CV) < 13%), with no cross-reactivity with neurofilament medium and heavy (NfM and NfH). With respect to the other available ELISAs, CSF NfL showed the same range of values with a strong correlation (r = 0.9984, p < 0.001) between the two methods. CSF NfL levels were significantly higher in MCI-AD/AD-dem and IDD patients as compared with both PD and OND patients. The highest discriminative power was obtained between IDD and OND patients (area under the curve (AUC) 0.87, 95% confidence interval (CI) 0.80-0.95). Within the IDD group, CSF NfL positively correlated with several clinical and radiological disease severity parameters. Conclusions: These results show a good analytical performance of the new ELISA for quantification of NfL concentrations in the CSF. CSF NfL is confirmed to be a reliable marker in AD and MS, and a disease-severity marker in MS patients.
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| 6. |
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| 7. |
- Höglund, Arja, et al.
(author)
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Associations between fluctuations in daytime sleepiness and motor and non-motor symptoms in Parkinson's disease
- 2021
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In: Movement Disorders Clinical Practice. - 2330-1619. ; 8:1, s. 44-50
-
Journal article (peer-reviewed)abstract
- Abstract Background Non-motor fluctuations (NMF) are a major concern in Parkinson's disease (PD), and they have been categorised into neuropsychiatric, autonomic and sensory fluctuations. However, this categorisation does not include sleep and sleep-related features, and the association between daytime sleepiness and other motor and/or non-motor fluctuations in PD remains to be elucidated. Objective To investigate the relationship between daytime sleepiness and other non-motor and motor fluctuations in people with PD. Methods A three-day home diary recording daytime sleepiness, mood, anxiety, and motor symptoms was used along with the Karolinska Sleepiness Scale (KSS) and six days of accelerometer (Parkinson's KinetiGraph?; PKG?) registration to detect motor fluctuations among people with a DaTSCAN verified clinical PD diagnosis (32 men; mean PD duration, 8.2?years). Participants were categorised as motor fluctuators or non-fluctuators according to the UPDRS part IV and/or the presence of motor and non-motor fluctuations. Results Fifty-two people with PD participated. Daytime sleepiness correlated significantly with motor symptoms, mood and anxiety among those classified as motor fluctuators (n = 28). Motor fluctuators showed stronger correlations between the individual mean level of all diary variables (daytime sleepiness, anxiety, mood and motor symptoms) when compared to the non-fluctuators (n = 24). Stronger positive within-individual correlations were found among fluctuators in comparison to non-fluctuators. In general, PKG data did not correlate with diary data. Conclusion Episodes of daytime sleepiness, as reported by home diaries, were associated with other self-reported non-motor and motor fluctuations, but were not supported by PKG data.
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| 8. |
- Papaevangelou, T., et al.
(author)
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ESS nBLM : Beam loss monitors based on fast neutron detection
- 2018
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In: HB2018 - Proceedings of the 61st ICFA Advanced Beam Dynamics Workshop on High-Intensity and High-Brightness Hadron Beams. - 9783954502028 ; , s. 404-409
-
Conference paper (peer-reviewed)abstract
- A new type of Beam Loss Monitor (BLM) system is being developed for use in the European Spallation Source (ESS) linac, primarily aiming to cover the low energy part (proton energies between 3-100 MeV). In this region of the linac, typical BLM detectors based on charged particle detection (i.e. Ionization Chambers) are not appropriate because the expected particle fields will be dominated by neutrons and photons. Another issue is the photon background due to the RF cavities, which is mainly due to field emission from the electrons from the cavity walls, resulting in bremsstrahlung photons. The idea for the ESS neutron sensitive BLM system (ESS nBLM) is to use Micromegas detectors specially designed to be sensitive to fast neutrons and insensitive to low energy photons (X and gammas). In addition, the detectors must be insensitive to thermal neutrons, because those neutrons may not be directly correlated to beam losses. The appropriate configuration of the Micromegas operating conditions will allow excellent timing, intrinsic photon background suppression and individual neutron counting, extending thus the dynamic range to very low particle fluxes.
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| 9. |
- Bereczki, E., et al.
(author)
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Synaptic proteins in CSF relate to Parkinson's disease stage markers
- 2017
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In: Npj Parkinsons Disease. - : Springer Science and Business Media LLC. - 2373-8057. ; 3
-
Journal article (peer-reviewed)abstract
- Recent findings of morphological and functional changes in Parkinson's disease brains have shown altered synapse formation, but their role in cognitive decline is still an area under exploration. Here we measured the concentration of three key synaptic proteins, Rab3A, SNAP25 and neurogranin by enzyme-linked immunosorbent assay, in cerebrospinal fluid from a total of 139 participants (87 controls and 52 Parkinson's disease patients out of which 30 were drug-naive) and explored their associations with motor and cognitive symptoms. Associations with motor disease stage (assessed by Hoehn and Yahr scale) and cognitive performance (assessed by the Montreal Cognitive Assessment scores) were explored. An overall increase in the concentration of SNAP25 was found in Parkinson's disease patients (p = 0.032). Increased neurogranin levels were found in the drug naive patients subgroup (p = 0.023). Significant associations were observed between increased concentration of neurogranin and cognitive impairment in total Parkinson's disease group (p = 0.017), as well as in the drug naive (p = 0.021) and with motor disease stage (p = 0.041). There were no significant disease-driven changes observed in the concentration of Rab3a. Concentrations SNAP25 and neurogranin were increased in cerebrospinal fluid of Parkinson's disease patients in a disease specific manner and related to cognitive and motor symptom severity. Future longitudinal studies should explore whether cerebrospinal fluid synaptic proteins can predict cognitive decline in Parkinson's disease.
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| 10. |
- Fernberg, P., et al.
(author)
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Time Trends in Risk and Risk Determinants of Non-Hodgkin Lymphoma in Solid Organ Transplant Recipients
- 2011
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In: American Journal of Transplantation. - : Elsevier BV. - 1600-6135 .- 1600-6143. ; 11:11, s. 2472-2482
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Journal article (peer-reviewed)abstract
- Organ transplantation increases risk of non-Hodgkin lymphoma (NHL), but long-term risk and time trends have seldom been evaluated. Immunosuppressive drug load is an important risk determinant, but the details are unclear. We studied NHL risk in a nationwide Swedish cohort of 11 081 graft recipients transplanted 1970-2008. Relative risks (RRs) were estimated within the cohort and versus the general population by age, sex, follow-up time and calendar period. NHL risk was also assessed by cumulative and average doses of immunosuppressive treatments in a nested case-control design throughout 1997 using conditional logistic regression. We observed 153 NHL cases during 97 853 years of follow-up. Compared with the general population, NHL risk was eightfold increased (RR 7.9; 95% confidence interval [CI] 6.6-9.4), and increased risks persisted after >= 15 years of follow-up among kidney (6.1; 95% CI 3.5-10) and nonkidney recipients (44; 14-103). Among nonkidney recipients, NHL risk was lower in the 2000s compared with the 1990s (0.5; 95% CI 0.3-1.0; p = 0.04). A high average dose of antithymocyte immunoglobulin (ATG) conferred an eightfold increased risk of NHL (OR 8.5; 95% CI 1.9-38). To conclude, posttransplant NHL risk decreased during the last decade among nonkidney recipients, possibly because of a more careful use of ATG, the introduction of new drugs, or both.
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| 11. |
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| 12. |
- Gisselsson, D, et al.
(author)
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A case of dermatofibrosarcoma protuberans with a ring chromosome 5 and a rearranged chromosome 22 containing amplified COL1A1 and PDGFB sequences
- 1998
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In: Cancer Letters. - 0304-3835 .- 1872-7980. ; 133:2, s. 34-129
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Journal article (peer-reviewed)abstract
- Dermatofibrosarcoma protuberans (DFSP) is a cutaneous tumour of borderline malignancy, the cytogenetic features of which include the translocation t(17;22)(q22;q13) or, more commonly, supernumerary ring chromosomes containing material from 17q22 and 22q13. These rearrangements result in the COL1A1/PDGFB fusion gene. Here, we describe a case of DFSP displaying a ring chromosome 5 together with a large marker chromosome composed of chromosome 22 alphoid DNA, material from distal 12q and amplified COL1A1 and PDGFB sequences. This is the first case of DFSP with multiple copies of COL1A1 and PDGFB not confined to ring chromosomes, showing that DFSP is similar to other borderline malignant mesenchymal tumours, where rings and giant markers are alternative vehicles for amplified material.
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| 13. |
- Henneberger, P K, et al.
(author)
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The occupational contribution to severe exacerbation of asthma.
- 2010
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In: The European respiratory journal : official journal of the European Society for Clinical Respiratory Physiology. - : European Respiratory Society (ERS). - 1399-3003 .- 0903-1936. ; 36:4, s. 743-50
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Journal article (peer-reviewed)abstract
- The goal of this study was to identify occupational risk factors for severe exacerbation of asthma and estimate the extent to which occupation contributes to these events. The 966 participants were working adults with current asthma who participated in the follow-up phase of the European Community Respiratory Health Survey. Severe exacerbation of asthma was defined as self-reported unplanned care for asthma in the past 12 months. Occupations held in the same period were combined with a general population job-exposure matrix to assess occupational exposures. 74 participants reported having had at least one severe exacerbation event, for a 1-yr cumulative incidence of 7.7%. From regression models that controlled for confounders, the relative risk (RR) was statistically significant for low (RR 1.7, 95% CI 1.1-2.6) and high (RR 3.6, 95% CI 2.2-5.8) biological dust exposure, high mineral dust exposure (RR 1.8, 95% CI 1.02-3.2), and high gas and fumes exposure (RR 2.5, 95% CI 1.2-5.5). The summary category of high dust, gas, or fumes exposure had RR 3.1 (95% CI 1.9-5.1). Based on this RR, the population attributable risk was 14.7% among workers with current asthma. These results suggest occupation contributes to approximately one in seven cases of severe exacerbation of asthma in a working population, and various agents play a role.
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| 14. |
- Hoffmann, V S, et al.
(author)
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Treatment and outcome of 2904 CML patients from the EUTOS population-based registry
- 2017
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In: Leukemia. - : Springer Science and Business Media LLC. - 0887-6924 .- 1476-5551. ; 31:3, s. 593-601
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Journal article (peer-reviewed)abstract
- The European Treatment and Outcome Study (EUTOS) population-based registry includes data of all adult patients newly diagnosed with Philadelphia chromosome-positive and/or BCR-ABL1+ chronic myeloid leukemia (CML) in 20 predefined countries and regions of Europe. Registration time ranged from 12 to 60 months between January 2008 and December 2013. Median age was 55 years and median observation time was 29 months. Eighty percent of patients were treated first line with imatinib, and 17% with a second-generation tyrosine kinase inhibitor, mostly according to European LeukemiaNet recommendations. After 12 months, complete cytogenetic remission (CCyR) and major molecular response (MMR) were achieved in 57% and 41% of patients, respectively. Patients with high EUTOS risk scores achieved CCyR and MMR significantly later than patients with low EUTOS risk. Probabilities of overall survival (OS) and progression-free survival for all patients at 12, 24 and 30 months was 97%, 94% and 92%, and 95%, 92% and 90%, respectively. The new EUTOS long-term survival score was validated: the OS of patients differed significantly between the three risk groups. The probability of dying in remission was 1% after 24 months. The current management of patients with tyrosine kinase inhibitors resulted in responses and outcomes in the range reported from clinical trials. These data from a large population-based, patient sample provide a solid benchmark for the evaluation of new treatment policies.Leukemia advance online publication, 23 September 2016; doi:10.1038/leu.2016.246.
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| 15. |
- Ingvar, A., et al.
(author)
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No association between infections, HLA type and other transplantrelated factors and risk of cutaneous squamous cell carcinoma in solid organ transplant recipients
- 2012
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In: Acta Dermato-Venereologica. - : Medical Journals Sweden AB. - 0001-5555 .- 1651-2057. ; 92:6, s. 609-614
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Journal article (peer-reviewed)abstract
- Recipients of solid organ transplants are at a markedly increased risk of cutaneous squamous cell carcinoma (SCC). We investigated potential associations between post-transplant infections, HLA type, and other transplant-related factors and risk of SCC, taking immunosuppressive treatment into account. A population-based case-control study was conducted. All patients who developed SCC during follow-up (1970-1997) were eligible as cases (n = 207). Controls (n = 189) were individually matched to the cases on age and calendar period of transplantation. Detailed exposure information was collected through an extensive, blinded review of medical records. Odds ratios were computed with conditional logistic regression. There were no significant associations with any infectious agents, or with number and timing of infections, specific HLA-type, donor characteristics, or other transplant characteristics and risk of post-transplant SCC. These results suggest that risk of post-transplant SCC is neither closely related to specific post-transplant infectious disorders, nor to the infectious load or specific HLA types.
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| 16. |
- Kamoun, Aurélie, et al.
(author)
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A Consensus Molecular Classification of Muscle-invasive Bladder Cancer
- 2020
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In: European Urology. - : Elsevier BV. - 0302-2838. ; 77:4, s. 420-433
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Journal article (peer-reviewed)abstract
- Background: Muscle-invasive bladder cancer (MIBC) is a molecularly diverse disease with heterogeneous clinical outcomes. Several molecular classifications have been proposed, but the diversity of their subtype sets impedes their clinical application. Objective: To achieve an international consensus on MIBC molecular subtypes that reconciles the published classification schemes. Design, setting, and participants: We used 1750 MIBC transcriptomic profiles from 16 published datasets and two additional cohorts. Outcome measurements and statistical analysis: We performed a network-based analysis of six independent MIBC classification systems to identify a consensus set of molecular classes. Association with survival was assessed using multivariable Cox models. Results and limitations: We report the results of an international effort to reach a consensus on MIBC molecular subtypes. We identified a consensus set of six molecular classes: luminal papillary (24%), luminal nonspecified (8%), luminal unstable (15%), stroma-rich (15%), basal/squamous (35%), and neuroendocrine-like (3%). These consensus classes differ regarding underlying oncogenic mechanisms, infiltration by immune and stromal cells, and histological and clinical characteristics, including outcomes. We provide a single-sample classifier that assigns a consensus class label to a tumor sample's transcriptome. Limitations of the work are retrospective clinical data collection and a lack of complete information regarding patient treatment. Conclusions: This consensus system offers a robust framework that will enable testing and validation of predictive biomarkers in future prospective clinical trials. Patient summary: Bladder cancers are heterogeneous at the molecular level, and scientists have proposed several classifications into sets of molecular classes. While these classifications may be useful to stratify patients for prognosis or response to treatment, a consensus classification would facilitate the clinical use of molecular classes. Conducted by multidisciplinary expert teams in the field, this study proposes such a consensus and provides a tool for applying the consensus classification in the clinical setting.
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| 17. |
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| 18. |
- Mauri, G., et al.
(author)
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Neutron reflectometry with the Multi-Blade B-10-based detector
- 2018
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In: Proceedings of the Royal Society. Mathematical, Physical and Engineering Sciences. - : The Royal Society. - 1364-5021 .- 1471-2946. ; 474:2216
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Journal article (peer-reviewed)abstract
- The Multi-Blade is a boron-10-based gaseous detector developed for neutron reflectometry instruments at the European Spallation Source in Sweden. The main challenges for neutron reflectometry detectors are the instantaneous counting rate and spatial resolution. The Multi-Blade has been tested on the CRISP reflectometer at the ISIS Neutron and Muon Source in the UK. A campaign of scientific measurements has been performed to study the Multi-Blade response in real instrumental conditions. The results of these tests are discussed in this paper.
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| 19. |
- Onatsu, J., et al.
(author)
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Serum Neurofilament Light Chain Concentration Correlates with Infarct Volume but Not Prognosis in Acute Ischemic Stroke
- 2019
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In: Journal of Stroke & Cerebrovascular Diseases. - : Elsevier BV. - 1052-3057. ; 28:8, s. 2242-2249
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Journal article (peer-reviewed)abstract
- Background and Purpose: We studied serum neurofilaments diagnostic value in patients with acute ischemic stroke (AIS) or TIA and evaluated any correlation with symptom severity, cerebral infarction volume, aetiology, and clinical outcome. Methods: One hundred and thirty-six patients (101 with AIS, and 35 with TIA) were included. Acute-phase serum neurofilament light chain (sNfL) was analyzed with a novel ultrasensitive single molecule array (Simoa). Cerebral infarction volume was measured from brain computed tomography in the subacute phase (> 2 days). Stroke aetiology was defined by trial of ORG 10172 in acute stroke treatment classification, severity by National Institute of Health stroke scale (NIHSS) and the degree of disability by the Modified Rankin Scale (mRS) after 90 days. Results: sNfL was markedly higher in patients with AIS (89.5 pg/mL [IQR: 44.7-195.3]) than with TIA (25.2 pg/mL [IQR: 14.6-48.0]), P = <. 001), also after adjusting for age, NIHSS, and stroke volume (P=.003). In receiver operating characteristic analysis, sNfL concentration greater than or equal to 49 pg/mL proved to be the best cut-off value to differentiate between patients with stroke and those with TIA (sensitivity of 73% and specificity of 80%). sNfL concentration significantly correlated with cerebral infarction volume (r = .413, P = < .001), this association remained significant after adjusting for established predictors (P=.019). Patients with AIS due to cardioembolism or large artery atherosclerosis had the highest sNfL concentrations. NIHSS on admission (r = .343, P =< .001) and mRS scores after 3 months (r = .306, P = .004) correlated with sNfL concentration, however functional outcome 3 months after stroke was not associated with sNfL after adjusting for potential confounders. Conclusions: Cases with stroke were distinguishable from those with TIA following the determination of sNfL in the blood samples. The presence and amount of axonal damage estimated by sNfL correlated with the final cerebral infarction volume but was not predictive of degree of disability.
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| 20. |
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| 21. |
- Piscitelli, F., et al.
(author)
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Characterization of the Multi-Blade 10B-based detector at the CRISP reflectometer at ISIS for neutron reflectometry at ESS
- 2018
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In: Journal of Instrumentation. - : IOP PUBLISHING LTD. - 1748-0221. ; 13:5
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Journal article (peer-reviewed)abstract
- The Multi-Blade is a Boron-10-based gaseous thermal neutron detector developed to face the challenge arising in neutron reflectometry at neutron sources. Neutron reflectometers are challenging instruments in terms of instantaneous counting rate and spatial resolution. This detector has been designed according to the requirements given by the reflectometers at the European Spallation Source (ESS) in Sweden. The Multi-Blade has been installed and tested on the CRISP reflectometer at the ISIS neutron and muon source in U.K.. The results on the detailed detector characterization are discussed in this manuscript.
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| 22. |
- Piscitelli, Francesco, et al.
(author)
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Neutron reflectometry on highly absorbing films and its application to (B4C)-B-10-based neutron detectors
- 2016
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In: Royal Society of London. Proceedings A. Mathematical, Physical and Engineering Sciences. - : The Royal Society. - 1364-5021 .- 1471-2946. ; 472:2185
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Journal article (peer-reviewed)abstract
- Neutron reflectometry is a powerful tool used for studies of surfaces and interfaces. The absorption in the typical studied materials is neglected and this technique is limited only to the reflectivity measurement. For strongly absorbing nuclei, the absorption can be directly measured by using the neutron-induced fluorescence technique which exploits the prompt particle emission of absorbing isotopes. This technique is emerging from soft matter and biology where highly absorbing nuclei, in very small quantities, are used as a label for buried layers. Nowadays, the importance of absorbing layers is rapidly increasing, partially because of their application in neutron detection; a field that has become more active also due to the He-3-shortage. We extend the neutron-induced fluorescence technique to the study of layers of highly absorbing materials, in particular (B4C)-B-10. The theory of neutron reflectometry is a commonly studied topic; however, when a strong absorption is present the subtle relationship between the reflection and the absorption of neutrons is not widely known. The theory for a general stack of absorbing layers has been developed and compared to measurements. We also report on the requirements that a (B4C)-B-10 layer must fulfil in order to be employed as a converter in neutron detection.
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| 23. |
- Shankar, P. Gowri, et al.
(author)
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King or royal family? : Testing for species boundaries in the King Cobra, Ophiophagus hannah (Cantor, 1836), using morphology and multilocus DNA analyses
- 2021
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In: Molecular Phylogenetics and Evolution. - : Elsevier. - 1055-7903 .- 1095-9513. ; 165
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Journal article (peer-reviewed)abstract
- In widespread species, the diverse ecological conditions in which the populations occur, and the presence of many potential geographical barriers through their range are expected to have created ample opportunities for the evolution of distinct, often cryptic lineages. In this work, we tested for species boundaries in one such widespread species, the king cobra, Ophiophagus hannah (Cantor, 1836), a largely tropical elapid snake distributed across the Oriental realm. Based on extensive geographical sampling across most of the range of the species, we initially tested for candidate species (CS) using Maximum-Likelihood analysis of mitochondrial genes. We then tested the resulting CS using both morphological data and sequences of three single-copy nuclear genes. We used snapclust to determine the optimal number of clusters in the nuclear dataset, and Bayesian Phylogenetics and Phylogeography (BPP) to test for likely species status. We used non-metric multidimensional scaling (nMDS) analysis for discerning morphological separation. We recovered four independently evolving, geographically separated lineages that we consider Confirmed Candidate Species: (1) Western Ghats lineage; (2) Indo-Chinese lineage (3) Indo-Malayan lineage; (4) Luzon Island lineage, in the Philippine Archipelago. We discuss patterns of lineage divergence, particularly in the context of low morphological divergence, and the conservation implications of recognizing several endemic king cobra lineages.
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| 24. |
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| 25. |
- Sternberg-Simon, M., et al.
(author)
-
Natural killer cell inhibitory receptor expression in humans and mice : A closer look
- 2013
-
In: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 4:March, s. 65-
-
Journal article (peer-reviewed)abstract
- The Natural Killer (NK) cell population is composed of subsets of varying sizes expressing different combinations of inhibitory receptors for MHC class I molecules. Genes within the NK gene complex, including the inhibitory receptors themselves, seem to be the primary intrinsic regulators of inhibitory receptor expression, but the MHC class I background is an additional Modulating factor. In this paper, we have performed a parallel study of the inhibitory receptor repertoire in inbred mice of the C57Bl/6 background and in a cohort of 44 humans. Deviations of subset frequencies from the "product rule (PR)," i.e., differences between observed and expected frequencies of NK cells, were used to identify MHC-independent and MHC-dependent control of receptor expression frequencies. Some deviations from the PR were similar in mice and humans, such as the decreased presence of NK cell subset lacking inhibitory receptors. Others were different, including a role for NKG2A in determining over- or under-representation of specific subsets in humans but not in mice. Thus, while human and murine inhibitory receptor repertoires differed in details, there may also be shared principles governing NK cell repertoire formation in these two species.
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| 26. |
- Andersen, Ken, et al.
(author)
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B-10 multi-grid proportional gas counters for large area thermal neutron detectors
- 2013
-
In: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - : Elsevier BV. - 0167-5087 .- 0168-9002 .- 1872-9576. ; 720, s. 116-121
-
Journal article (peer-reviewed)abstract
- He-3 was a popular material in neutrons detectors until its availability dropped drastically in 2008. The development of techniques based on alternative convertors is now of high priority for neutron research institutes. Thin films of B-10 or (B4C)-B-10 have been used in gas proportional counters to detect neutrons, but until now, only for small or medium sensitive area. We present here the multi-grid design, introduced at the ILL and developed in collaboration with ESS for LAN (large area neutron) detectors. Typically thirty (B4C)-B-10 films of 1 mu m thickness are used to convert neutrons into ionizing particles which are subsequently detected in a proportional gas counter. The principle and the fabrication of the multi-grid are described and some preliminary results obtained with a prototype of 200 cm x 8 cm are reported; a detection efficiency of 48% has been measured at 2.5 angstrom with a monochromatic neutron beam line, showing the good potential of this new technique. (C) 2013 Elsevier B.V. All rights reserved.
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| 27. |
- Andersson, Anna, et al.
(author)
-
Paired multiplex reverse-transcriptase polymerase chain reaction (PMRT-PCR) analysis as a rapid and accurate diagnostic tool for the detection of MLL fusion genes in hematologic malignancies
- 2001
-
In: Leukemia. - 1476-5551. ; 15:8, s. 1293-1293
-
Journal article (peer-reviewed)abstract
- The MLL gene in chromosome band 11q23 is frequently rearranged in acute lymphoblastic and acute myeloid leukemias. To date, more than 50 different chromosomal regions are known to participate in translocations involving 11q23, many of which affect MLL. The pathogenetically important outcome of these rearrangements is most likely the creation of a fusion gene consisting of the 5' part of the MLL gene and the 3' end of the partner gene. Although abnormalities of the MLL gene as such are generally associated with poor survival, recent data suggest that the prognostic impact varies among the different fusion genes generated. Hence, detection of the specific chimeric gene produced is important for proper prognostication and clinical decision making. We have developed a paired multiplex reverse-transcriptase polymerase chain reaction analysis to facilitate a rapid and accurate detection of the most frequent MLL fusion genes in adult and childhood acute leukemias. To increase the specificity, two sets of primers were designed for each fusion gene, and these paired primer sets were run in parallel in two separate multiplex one-step PCR reactions. Using the described protocol, we were able to amplify successfully, in one single assay, the six clinically relevant fusion genes generated by the t(4;11)(q21;q23) [MLL/AF4], t(6;11)(q27;q23) [MLL/AF6], t(9;11)(p21-22;q23) [MLL/AF9], t(10;11)(p11-13;q23) [MLL/AF10], t(11;19)(q23;p13.1) [MLL/ELL], and t(11;19)(q23; p13.3) [MLL/ENL] in cell lines, as well as in patient material.
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| 28. |
- Andersson, Claes, et al.
(author)
-
Psychosocial dysfunction is associated with recidivism in crime in paroled offenders
- 2013
-
In: Alcoholism. - : John Wiley & Sons. - 0145-6008 .- 1530-0277. ; 37:s2, s. 260A-260A
-
Journal article (other academic/artistic)abstract
- The objective of this research was to study whether automated telephony could be used in paroled offenders to perform daily assessment of variables associated with recidivismin crime, and whether there are grounds for studying the effects of a brief intervention based on these assessments during 30 days following probation. The design included a randomized controlled trial using automated daily assessments and feedback interventions based on Interactive Voice Response (IVR). Participants included paroled offenders (N = 108) during their first 30 days after leaving prison. All subjects were called daily and answered assessment questions. Based on the content of their daily assessments, the subjects in the intervention group received immediate feedback and a recommendation by IVR, and their probation officers also received a daily report by email. Main outcomemeasures (assessed daily) included Stress (Arnetz and Hasson Stress Questionnaire and a revised version of Daily Assessment of Daily Experience), Mood (SCL-8D measuring depression and anxiety), and Use and Urge to Use Alcohol and Drugs (revised version of the Alcohol Urge Questionnaire). Participants were also asked to rate the severity of their most stressful event that day. The outcome variables were analyzed using linear mixed models, presented as group differences between means, 95%CI. Results indicated that the intervention group showed greater improvement than the control group in stress (9.6, 0.5; 18.7, p = 0.038), depression/anxiety (4.6, 0.2; 9.0, p = 0.042), alcohol use (0.8, 0.1; 1.4, p = 0.031), drug use (1.0, 0.5; 1.6, p = 0.000), and in the severity of themost stressful daily event (1.9, 1.1; 2.7, p = 0.000). There were no differences between the groups in the Stress scale and in craving for alcohol and drugs. Overall, the research suggests that in paroled offenders, automated telephony is an effective technology thatmay be used to follow up and to give interventions, resulting in reduced stress and drug use.
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| 29. |
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| 30. |
- Andrén, Lennart, 1946, et al.
(author)
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Diltiazem in hypertensive patients with type II diabetes mellitus.
- 1988
-
In: The American journal of cardiology. - : Elsevier BV. - 0002-9149. ; 62:11
-
Journal article (peer-reviewed)abstract
- Twenty-three patients with essential hypertension and diabetes mellitus type II were treated with the calcium antagonist diltiazem (120 to 180 mg twice daily). The mean dose was 307 mg/day. The study was a double-blind, placebo-controlled, crossover design. All measurements were performed 12 to 14 hours after drug intake. Blood pressure, heart rate and forearm blood flow were measured noninvasively. Platelet function was studied by measuring adenosine diphosphate-induced platelet aggregation and the platelet specific proteins, beta thromboglobulin and platelet factor 4. Thromboxane B2 formation in serum and the plasma concentration of diltiazem and its metabolites N-demethyldiltiazem, deacetyldiltiazem and N-demethyldeacetyldiltiazem were measured both during placebo and diltiazem treatment. Diabetic control was evaluated by following HbA1C, fasting blood glucose and urinary glucose. Diltiazem reduced both systolic and diastolic (supine and standing) blood pressure significantly. Forearm blood flow was significantly increased by 32%, p less than 0.05. Supine heart rate decreased significantly, while no such change was seen in the standing position. No significant changes were observed in platelet function during diltiazem treatment. There was no relation between the observed blood pressure reduction and the plasma concentration of diltiazem or its metabolites. A positive correlation between the change in heart rate and the metabolite N-demethyldeacetyldiltiazem was observed (r = 0.647, p = 0.005). Three patients were excluded during diltiazem treatment (skin exanthema, headache and atrial fibrillation) and 1 during placebo treatment (angina pectoris). No negative effect on diabetes control was observed. Thus, diltiazem could be used for treatment of hypertension in diabetic patients.
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| 31. |
- Ashton, Nicholas J., et al.
(author)
-
An update on blood-based biomarkers for non-Alzheimer neurodegenerative disorders.
- 2020
-
In: Nature Reviews Neurology. - : Springer Science and Business Media LLC. - 1759-4766 .- 1759-4758. ; 16, s. 265-284
-
Research review (peer-reviewed)abstract
- Cerebrospinal fluid analyses and neuroimaging can identify the underlying pathophysiology at the earliest stage of some neurodegenerative disorders, but do not have the scalability needed for population screening. Therefore, a blood-based marker for such pathophysiology would have greater utility in a primary care setting and in eligibility screening for clinical trials. Rapid advances in ultra-sensitive assays have enabled the levels of pathological proteins to be measured in blood samples, but research has been predominantly focused on Alzheimer disease (AD). Nonetheless, proteins that were identified as potential blood-based biomarkers for AD, for example, amyloid-β, tau, phosphorylated tau and neurofilament light chain, are likely to be relevant to other neurodegenerative disorders that involve similar pathological processes and could also be useful for the differential diagnosis of clinical symptoms. This Review outlines the neuropathological, clinical, molecular imaging and cerebrospinal fluid features of the most common neurodegenerative disorders outside the AD continuum and gives an overview of the current status of blood-based biomarkers for these disorders.
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| 32. |
- Bereczki, E., et al.
(author)
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Synaptic proteins predict cognitive decline in Alzheimer's disease andLewy body dementia
- 2016
-
In: Alzheimer's & Dementia. - : Wiley. - 1552-5260 .- 1552-5279. ; 12:11, s. 1149-1158
-
Journal article (peer-reviewed)abstract
- Introduction Our objective was to compare the levels of three synaptic proteins involved in different steps of the synaptic transmission: Rab3A, SNAP25, and neurogranin, in three common forms of dementia: Alzheimer's disease (AD), dementia with Lewy bodies (DLB), and Parkinson's disease dementia. Methods A total of 129 postmortem human brain samples were analyzed in brain regional specific manner exploring their associations with morphologic changes and cognitive decline. Results We have observed robust changes reflecting synaptic dysfunction in all studied dementia groups. There were significant associations between the rate of cognitive decline and decreased levels of Rab3 in DLB in the inferior parietal lobe and SNAP25 in AD in the prefrontal cortex. Of particular note, synaptic proteins significantly discriminated between dementia cases and controls with over 90% sensitivity and specificity. Discussion Our findings suggest that the proposition that synaptic markers can predict cognitive decline in AD, should be extended to Lewy body diseases. © 2016 The Alzheimer's Association
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| 33. |
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| 34. |
- Bergman, ASF, et al.
(author)
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Diltiazem infusion for renal protection in cardiac surgical patients with preexisting renal dysfunction
- 2002
-
In: Journal of Cardiothoracic and Vascular Anesthesia. - : Elsevier BV. - 1532-8422 .- 1053-0770. ; 16:3, s. 294-299
-
Journal article (peer-reviewed)abstract
- Objective: To evaluate if the calcium channel blocker diltiazem protects postoperatively renal function in cardiac surgical patients with preexisting mild-to-moderate renal dysfunction. Design: Prospective, randomized, placebo-controlled, double-blind, clinical study. Setting: Cardiothoracic anesthesia department at a university hospital. Participants: Adult patients undergoing elective cardiac surgery using cardiopulmonary bypass, with a preoperatively elevated serum creatinine level (n = 24). Interventions: Randomized infusions of diltiazem (bolus 0.25 mg/kg followed by a continuous infusion of 1.7 pg/kg/min) (DTZ, n = 12) or placebo (C, n = 12) were started 30 minutes before induction of anesthesia and continued for 24 hours. Measurements and Main Results: Median plasma concentrations of diltiazem (DTZ group) were 79 mug/L before cardiopulmonary bypass, 67 mug/L at the end of cardiopulmonary bypass, and 164 mug/L at 24 hours postoperatively. Serum creatinine levels; on postoperative days 1, 3, and 5; and 3 weeks postoperatively were similar between groups. lohexol clearance did not differ between the groups on day 5 but was higher in the DTZ group than in the placebo group 3 weeks after surgery (median, 51 v 40 mL/min/1.73 m(2); p < 0.05). Urinary N-acetyl-β-glucosamidase concentrations were similar between the groups during the study but were increased from baseline on days 2 and 4 and 3 weeks postoperatively. Conclusion: Diltiazem can be safely used in patients who have mild-to-moderate renal dysfunction and undergo cardiac surgery using cardiopulmonary bypass. Within the limits of this study, the data suggest that addition of prophylactic diltiazem may prevent further glomerular damage resulting from cardiopulmonary bypass and may improve glomerular function 3 weeks after cardiac surgery.
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| 35. |
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| 36. |
- Birch, Jens, et al.
(author)
-
(B4C)-B-10 Multi-Grid as an Alternative to He-3 for Large Area Neutron Detectors
- 2013
-
In: IEEE Transactions on Nuclear Science. - 0018-9499 .- 1558-1578. ; 60:2, s. 871-878
-
Journal article (peer-reviewed)abstract
- Despite its present shortage, He-3 continues to be the most common neutron converter for detectors in neutron scattering science. However, it is obvious that the development of large area neutron detectors based on alternative neutron converters is rapidly becoming a matter of urgency. In the technique presented here, grids each comprising 28 (B4C)-B-10 layers ( each 1 mu m thick) are used to convert neutrons into ionizing particles which are subsequently detected in proportional gas counters. The total active area of the prototype is 8 cm x 200 cm. To instrument this detector 4.6 m(2) of B-10-enriched boron carbide were coated onto aluminium blades using a DC magnetron sputtering machine. Characterization of the prototype showed neutron efficiency to be epsilon(n) = 46.8% for 2.5 angstrom neutrons, which is in line with expectations from MC simulation. This result demonstrates the potential of this technique as alternative to He-3-based position sensitive detectors.
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| 37. |
- Birch, Jens, et al.
(author)
-
In-beam test of the Boron-10 Multi-Grid neutron detector at the IN6 time-of-flight spectrometer at the ILL
- 2014
-
In: INTERNATIONAL WORKSHOP ON NEUTRON OPTICS AND DETECTORS (NOPandD 2013). - : IOP Publishing: Conference Series / Institute of Physics (IoP).
-
Conference paper (peer-reviewed)abstract
- A neutron detector concept based on solid layers of boron carbide enriched in 1 B has been in development for the last few years as an alternative for He-3 by collaboration between the ILL, ESS and Linkoping University. This Multi-Grid detector uses layers of aluminum substrates coated with (B4C)-B-10 on both sides that are traversed by the incoming neutrons. Detection is achieved using a gas counter readout principle. By segmenting the substrate and using multiple anode wires, the detector is made inherently position sensitive. This development is aimed primarily at neutron scattering instruments with large detector areas, such as time-of-flight chopper spectrometers. The most recent prototype has been built to be interchangeable with the He-3 detectors of IN6 at ILL. The 1 B detector has an active area of 32 x 48 cm(2). It was installed at the IN6 instrument and operated for several weeks, collecting data in parallel with the regularly scheduled experiments, thus providing the first side-by-side comparison with the conventional He-3 detectors. Results include an efficiency comparison, assessment of the in-detector scattering contribution, sensitivity to gamma-rays and the signal-to-noise ratio in time-of-flight spectra. The good expected performance has been confirmed with the exception of an unexpected background count rate. This has been identified as natural alpha activity in aluminum. New convertor substrates are under study to eliminate this source of background.
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| 38. |
- Birch, J, et al.
(author)
-
Investigation of background in large-area neutron detectors due to alpha emission from impurities in aluminium
- 2015
-
In: Journal of Instrumentation. - : IOP PUBLISHING LTD. - 1748-0221. ; 10
-
Journal article (peer-reviewed)abstract
- Thermal neutron detector based on films of (B4C)-B-10 have been developed as an alternative to He-3 detectors. In particular, The Multi-Grid detector concept is considered for future large area detectors for ESS and ILL instruments. An excellent signal-to-background ratio is essential to attain expected scientific results. Aluminium is the most natural material for the mechanical structure of of the Multi-Grid detector and other similar concepts due to its mechanical and neutronic properties. Due to natural concentration of alpha emitters, however, the background from alpha particles misidentified as neutrons can be unacceptably high. We present our experience operating a detector prototype affected by this issue. Monte Carlo simulations have been used to confirm the background as alpha particles. The issues have been addressed in the more recent implementations of the Multi-Grid detector by the use of purified aluminium as well as Ni-plating of standard aluminium. The result is the reduction in background by two orders of magnitude. A new large-area prototype has been built incorporating these modifications.
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| 39. |
- Birch, J., et al.
(author)
-
Multi-Grid boron-10 detector for time-of-flight spectrometers in neutron scattering science
- 2015
-
In: 2015 IEEE Nuclear Science Symposium and Medical Imaging Conference, NSS/MIC 2015. - : Institute of Electrical and Electronics Engineers (IEEE). - 9781467398626
-
Conference paper (peer-reviewed)abstract
- The Multi-Grid (MG) detector has been introduced at ILL and developed by a collaboration between ILL, ESS and Linkoping University. This detector design addresses the severely decreased availability of He3, in particular for neutron scattering instruments with large-area detectors, such as time-of-flight neutron spectrometers at ESS and other facilities. The MG detector is based on thin converter films of boron-10 carbide arranged in layers orthogonal to the incoming neutrons. The design of the detector provides position resolution, efficiency competitive with He3 and a strong gamma rejection capability. This paper presents the MG large-area (2.4m2) demonstrator and the progress made in order to meet the needs of production of B4C-coated layers, mechanical parts and assembly on a scale similar to that of the final detectors for ESS. A particular effort was made to produce aluminium detector parts with a low alpha background, successfully reducing the background rate to acceptable levels. Following the IN5 demonstrator, a compact prototype has been designed in order to finalise the electronic readout to be used at the ESS instruments equipped with the MG.
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| 40. |
- Boström, Henrik, et al.
(author)
-
Explaining multivariate time series forecasts : An application to predicting the Swedish GDP?
- 2020
-
In: CEUR Workshop Proceedings. - : CEUR-WS.
-
Conference paper (peer-reviewed)abstract
- Various approaches to explaining predictions of black box models have been proposed, including model-agnostic techniques that measure feature importance (or effect) by presenting modified test instances to the underlying black-box model. These modifications rely on choosing feature values from the complete range of observed values. However, when applying machine learning algorithms to the task of forecasting from multivariate time-series, it is suggested that the temporal aspect should be taken into account when analyzing the feature effect. A modification of individual conditional expectation (ICE) plots is proposed, called ICE-T plots, which displays the prediction change for temporally ordered feature values. Results are presented from a case study on predicting the Swedish gross domestic product (GDP) based on a comprehensive set of indicator and prognostic variables. The effect of calculating feature effect with and without temporal constraints is demonstrated, as well as the impact of transformations and forecast horizons on what features are found to have a large effect, and the use of ICE-T plots as a complement to ICE plots.
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| 41. |
- Branström, J., et al.
(author)
-
Compression wood in knots and the effect on surface roughness.
- 2005
-
In: proceedings from IMPC 2005.
-
Conference paper (other academic/artistic)abstract
- The microstructural and ultrastructural characteristics of knot wood were examined and related to paper properties. Norway spruce (Picea abies) chips were laboratory fractionated and sorted into a knot containing assortment and a non knot containing reference assortment. The proportions of compression wood in these two assortments were then assessed and the two chip assortments refined in pilot refiners. The knot containing portion was divided into wood from the upper branch, wood from the lower branch compression wood and wood surrounding the branch. Fibres from the three knotwood portions and the reference chips were extracted and measurements were made of fibre properties including fibre length, fibre width and cell wall thickness. The two chip assortments were refined in a pilot plant and the surface properties of laboratory sheets were measured. The knot containing chips had adverse effects on several paper properties. However, no clear relationship was established between surface roughness and the presence of compression wood fibres in knot wood. (6 fig, 12 ref)
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| 42. |
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| 43. |
- Choi, Woonyoung, et al.
(author)
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Genetic Alterations in the Molecular Subtypes of Bladder Cancer : Illustration in the Cancer Genome Atlas Dataset
- 2017
-
In: European Urology. - : Elsevier BV. - 0302-2838 .- 1873-7560. ; 72:3, s. 354-365
-
Research review (peer-reviewed)abstract
- Context: Recent whole genome mRNA expression profiling studies revealed that bladder cancers can be grouped into molecular subtypes, some of which share clinical properties and gene expression patterns with the intrinsic subtypes of breast cancer and the molecular subtypes found in other solid tumors. The molecular subtypes in other solid tumors are enriched with specific mutations and copy number aberrations that are thought to underlie their distinct progression patterns, and biological and clinical properties. Objective: The availability of comprehensive genomic data from The Cancer Genome Atlas (TCGA) and other large projects made it possible to correlate the presence of DNA alterations with tumor molecular subtype membership. Our overall goal was to determine whether specific DNA mutations and/or copy number variations are enriched in specific molecular subtypes. Evidence: We used the complete TCGA RNA-seq dataset and three different published classifiers developed by our groups to assign TCGA's bladder cancers to molecular subtypes, and examined the prevalence of the most common DNA alterations within them. We interpreted the results against the background of what was known from the published literature about the prevalence of these alterations in nonmuscle-invasive and muscle-invasive bladder cancers. Evidence synthesis: The results confirmed that alterations involving RB1 and NFE2L2 were enriched in basal cancers, whereas alterations involving FGFR3 and KDM6A were enriched in luminal tumors. Conclusions: The results further reinforce the conclusion that the molecular subtypes of bladder cancer are distinct disease entities with specific genetic alterations. Patient summary: Our observation showed that some of subtype-enriched mutations and copy number aberrations are clinically actionable, which has direct implications for the clinical management of patients with bladder cancer. We analyzed the prevalence of the most common genomic alterations in the bladder cancer molecular subtypes. The results have important implications for our understanding of bladder cancer etiology and the development of molecular subtype-specific therapies.
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| 44. |
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| 45. |
- Cortazar-Chinarro, Maria, et al.
(author)
-
Association between the skin microbiome and MHC class II diversity in an amphibian
- 2024
-
In: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 33:1
-
Journal article (peer-reviewed)abstract
- Microbiomes play an important role in determining the ecology and behaviour of their hosts. However, questions remain pertaining to how host genetics shape microbiomes, and how microbiome composition influences host fitness. We explored the effects of geography, evolutionary history and host genetics on the skin microbiome diversity and structure in a widespread amphibian. More specifically, we examined the association between bacterial diversity and composition and the major histocompatibility complex class II exon 2 diversity in 12 moor frog (Rana arvalis) populations belonging to two geographical clusters that show signatures of past and ongoing differential selection. We found that while bacterial alpha diversity did not differ between the two clusters, MHC alleles/supertypes and genetic diversity varied considerably depending on geography and evolutionary history. Bacterial alpha diversity was positively correlated with expected MHC heterozygosity and negatively with MHC nucleotide diversity. Furthermore, bacterial community composition showed significant variation between the two geographical clusters and between specific MHC alleles/supertypes. Our findings emphasize the importance of historical demographic events on hologenomic variation and provide new insights into how immunogenetic host variability and microbial diversity may jointly influence host fitness with consequences for disease susceptibility and population persistence.
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| 46. |
- Ekblom, Robert, et al.
(author)
-
Female choice and male humoral immune response in the lekking great snipe (Gallinago media)
- 2005
-
In: Behavioral Ecology. - : Oxford University Press (OUP). - 1045-2249 .- 1465-7279. ; 16:2, s. 346-351
-
Journal article (peer-reviewed)abstract
- Parasites and diseases constitute major evolutionary forces in many natural populations, and thus having an efficient immune defense to resist infections is crucial for many organisms. Properties of the immune response may also influence mate choice decisions in many animals. Theory predicts several advantages for females when choosing males with superior immune systems. These benefits can be both direct (e.g. increased paternal care and reduced disease transmission) and indirect (good genes). We have investigated female choice with respect to antibody response to two novel antigens in males of a lekking bird, the great snipe (Gallinago media). Because of the lek mating system, female choice probably mainly incurs indirect (genetic) rather than direct benefits. Males responded to vaccination with diphtheria and tetanus toxoids by producing specific antibodies to both antigens. Triggering the immune system had no negative impact on display activities or survival. Males that were chosen by females as mates had on average higher antibody response to the tetanus antigen than their neighbors. We did not, however, find any covariance between the strength of the antibody response and male mating success.
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| 47. |
- Fernström, Erik, et al.
(author)
-
Cerebrospinal fluid markers of extracellular matrix remodelling, synaptic plasticity and neuroinflammation before and after cranial radiotherapy
- 2018
-
In: Journal of Internal Medicine. - : Wiley. - 0954-6820. ; 284:2, s. 211-225
-
Journal article (peer-reviewed)abstract
- Background Advances in the treatment of brain tumours have increased the number of long-term survivors, but at the cost of side effects following cranial radiotherapy ranging from neurocognitive deficits to outright tissue necrosis. At present, there are no tools reflecting the molecular mechanisms underlying such side effects, and thus no means to evaluate interventional effects after cranial radiotherapy. Therefore, fluid biomarkers are of great clinical interest. Objective Cerebrospinal fluid (CSF) levels of proteins involved in inflammatory signalling, synaptic plasticity and extracellular matrix (ECM) integrity were investigated following radiotherapy to the brain. Methods Patients with small-cell lung cancer (SCLC) eligible for prophylactic cranial irradiation (PCI) were asked to participate in the study. PCI was prescribed either as 2 Gy/fraction to a total dose of 30 Gy (limited disease) or 4 Gy/fraction to 20 Gy (extensive disease). CSF was collected by lumbar puncture at baseline, 3 months and 1 year following PCI. Protein concentrations were measured using immunobased assays or mass spectrometry. Results The inflammatory markers IL-15, IL-16 and MCP-1/CCL2 were elevated in CSF 3 months following PCI compared to baseline. The plasticity marker GAP-43 was elevated 3 months following PCI, and the same trend was seen for SNAP-25, but not for SYT1. The investigated ECM proteins, brevican and neurocan, showed a decline following PCI. There was a strong correlation between the progressive decline of soluble APP and brevican levels. Conclusion To our knowledge, this is the first time ECM-related proteins have been shown to be affected by cranial radiotherapy in patients with cancer. These findings may help us to get a better understanding of the mechanisms behind side effects following radiotherapy.
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| 48. |
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| 49. |
- Fisher, Matthew C., et al.
(author)
-
Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi
- 2018
-
In: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 8
-
Journal article (peer-reviewed)abstract
- Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to researchers as part of the BiodivERsA project RACE; here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been applied across 5 continents, 23 countries and in 62 amphibian species. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this group of emerging pathogens.
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| 50. |
- Foiani, M. S., et al.
(author)
-
Searching for novel cerebrospinal fluid biomarkers of tau pathology in frontotemporal dementia: An elusive quest
- 2019
-
In: Journal of Neurology, Neurosurgery and Psychiatry. - : BMJ. - 0022-3050 .- 1468-330X. ; 90:7, s. 740-746
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Journal article (peer-reviewed)abstract
- Background: Frontotemporal dementia (FTD) is a pathologically heterogeneous neurodegenerative disorder associated usually with tau or TDP-43 pathology, although some phenotypes such as logopenic variant primary progressive aphasia are more commonly associated with Alzheimer's disease pathology. Currently, there are no biomarkers able to diagnose the underlying pathology during life. In this study, we aimed to investigate the potential of novel tau species within cerebrospinal fluid (CSF) as biomarkers for tau pathology in FTD. Methods: 86 participants were included: 66 with a clinical diagnosis within the FTD spectrum and 20 healthy controls. Immunoassays targeting tau fragments N-123, N-mid-region, N-224 and X-368, as well as a non-phosphorylated form of tau were measured in CSF, along with total-tau (T-tau) and phospho-tau (P-tau (181) ). Patients with FTD were grouped based on their Aβ 42 level into those likely to have underlying Alzheimer's disease (AD) pathology (n=21) and those with likely frontotemporal lobar degeneration (FTLD) pathology (n=45). The FTLD group was then subgrouped based on their underlying clinical and genetic diagnoses into those with likely tau (n=7) or TDP-43 (n=18) pathology. Results: Significantly higher concentrations of tau N-mid-region, tau N-224 and non-phosphorylated tau were seen in both the AD group and FTLD group compared with controls. However, none of the novel tau species showed a significant difference between the AD and FTLD groups, nor between the TDP-43 and tau pathology groups. In a subanalysis, normalising for total-tau, none of the novel tau species provided a higher sensitivity and specificity to distinguish between tau and TDP-43 pathology than P-tau (181) /T-tau, which itself only had a sensitivity of 61.1% and specificity of 85.7% with a cut-off of <0.109. Conclusions: Despite investigating multiple novel CSF tau fragments, none show promise as an FTD biomarker and so the quest for in vivo markers of FTLD-tau pathology continues. © Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY. Published by BMJ.
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