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1.	Beal, Jacob, et al. (author) Robust estimation of bacterial cell count from optical density 2020 In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1 Journal article (peer-reviewed)abstract Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
2.	Klionsky, Daniel J, et al. (author) Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). 2016 In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 12:1, s. 1-222 Journal article (peer-reviewed)
3.	Azevedo, Flavio, et al. (author) Social and moral psychology of COVID-19 across 69 countries 2023 In: Scientific Data. - : NATURE PORTFOLIO. - 2052-4463. ; 10:1 Journal article (peer-reviewed)abstract The COVID-19 pandemic has affected all domains of human life, including the economic and social fabric of societies. One of the central strategies for managing public health throughout the pandemic has been through persuasive messaging and collective behaviour change. To help scholars better understand the social and moral psychology behind public health behaviour, we present a dataset comprising of 51,404 individuals from 69 countries. This dataset was collected for the International Collaboration on Social & Moral Psychology of COVID-19 project (ICSMP COVID-19). This social science survey invited participants around the world to complete a series of moral and psychological measures and public health attitudes about COVID-19 during an early phase of the COVID-19 pandemic (between April and June 2020). The survey included seven broad categories of questions: COVID-19 beliefs and compliance behaviours; identity and social attitudes; ideology; health and well-being; moral beliefs and motivation; personality traits; and demographic variables. We report both raw and cleaned data, along with all survey materials, data visualisations, and psychometric evaluations of key variables.
4.	Dantonello, Tobias M, et al. (author) Embryonal rhabdomyosarcoma with metastases confined to the lungs : Report from the CWS Study Group. 2011 In: Pediatric Blood & Cancer. - : Wiley. - 1545-5009 .- 1545-5017. ; 56:5, s. 725-732 Journal article (peer-reviewed)abstract BACKGROUND: Embryonal rhabdomyosarcoma [RME] is the most common pediatric soft tissue sarcoma. Whereas the prognosis of localized rhabdomyosarcoma has improved, it remains poor for metastatic disease. METHODS: We analyzed RME-patients with isolated pulmonary metastases [PRME] treated in four consecutive CWS-trials. Treatment included multiagent chemotherapy and local treatment of the primary tumor. Therapy of lung metastases after induction chemotherapy depended on response and individual decisions. RESULTS: Twenty-nine patients <21 years had PRME. Their median age was six years, the median follow-up nine years. Twenty-eight children had their primary tumor located in an unfavorable site and 22 of the primaries were >5 cm. In addition to conventional chemotherapy, seven patients received high-dose treatment and eight patients oral metronomic chemotherapy. The lung metastases were in remission after induction chemotherapy in 22 individuals. 19 patients received no local treatment of metastases; 3 patients had pulmonary metastasectomy and lung radiation was administered to 9 individuals. In total, 24/29 patients achieved a complete remission [CR]. Actuarial 5-year event-free and overall survival for all patients was 37.9 ± 18% and 48.7 ± 18%, respectively; it was 45.8 ± 20% and 58.3 ± 20% for the 24 patients who achieved a CR. Local treatment of metastases had no impact on the failure pattern. Younger age, good response, achievement of CR and maintenance-treatment were favorable prognostic factors in univariate analysis. CONCLUSIONS: Children with PRME have a fair prognosis. Local treatment of metastases did not improve outcome in our sample. Metronomic treatment may be an attractive option for PREM-patients. [correction made here after initial online publication].
5.	Menkveld, Albert J., et al. (author) Nonstandard Errors 2024 In: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390 Journal article (peer-reviewed)abstract In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
6.	Van Bavel, Jay J., et al. (author) National identity predicts public health support during a global pandemic 2022 In: Nature Communications. - : Nature Portfolio. - 2041-1723. ; 13:1 Journal article (peer-reviewed)abstract Understanding collective behaviour is an important aspect of managing the pandemic response. Here the authors show in a large global study that participants that reported identifying more strongly with their nation reported greater engagement in public health behaviours and support for public health policies in the context of the pandemic. Changing collective behaviour and supporting non-pharmaceutical interventions is an important component in mitigating virus transmission during a pandemic. In a large international collaboration (Study 1, N = 49,968 across 67 countries), we investigated self-reported factors associated with public health behaviours (e.g., spatial distancing and stricter hygiene) and endorsed public policy interventions (e.g., closing bars and restaurants) during the early stage of the COVID-19 pandemic (April-May 2020). Respondents who reported identifying more strongly with their nation consistently reported greater engagement in public health behaviours and support for public health policies. Results were similar for representative and non-representative national samples. Study 2 (N = 42 countries) conceptually replicated the central finding using aggregate indices of national identity (obtained using the World Values Survey) and a measure of actual behaviour change during the pandemic (obtained from Google mobility reports). Higher levels of national identification prior to the pandemic predicted lower mobility during the early stage of the pandemic (r = -0.40). We discuss the potential implications of links between national identity, leadership, and public health for managing COVID-19 and future pandemics.
7.	Abelev, Betty, et al. (author) Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV 2013 In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41 Journal article (peer-reviewed)abstract Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
8.	Abelev, Betty, et al. (author) Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV 2012 In: Journal of High Energy Physics. - 1029-8479. ; :11 Journal article (peer-reviewed)abstract The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
9.	Abelev, Betty, et al. (author) Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC 2012 In: Journal of High Energy Physics. - 1029-8479. ; :7 Journal article (peer-reviewed)abstract We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
10.	Alexakis, Alexandros Efraim, et al. (author) Modification of CNF‐Networks by the Addition of Small Amounts of Well‐Defined Rigid Cationic Nanolatexes 2022 In: Macromolecular Chemistry and Physics. - : Wiley. - 1022-1352 .- 1521-3935. ; 224:1, s. 2200249-2200249 Journal article (peer-reviewed)abstract Cellulose nanofibril (CNF)-networks are modified by the addition of small amounts (below 10 wt%) of well-defined cationic nanolatexes synthesized through reversible addition–fragmentation chain-transfer-mediated polymerization-induced self-assembly (PISA). Minute amounts of nanolatex inclusions lead to increased tensile and shear moduli, indicating that nanolatexes can act as bridging-points between CNFs. At higher nanolatex content, this stiffening effect is lost, likely due to interactions between nanolatexes leading to plasticization. The influence of nanolatex content and size on interparticle distance is discussed and is used as a tool to understand the effects observed in macroscopic properties. Upon annealing, the stiffening effect is lost due to the softening of the nanolatexes, indicating that the core–shell morphology is a prerequisite for this effect. These systems form a versatile platform to develop fundamental insights into complex condensed colloidal systems, to ultimately aid in the development of new sustainable material concepts.
11.	Bolin, Sara, 1988-, et al. (author) Dormant SOX9-positive cells behind MYC-driven medulloblastoma recurrence Journal article (peer-reviewed)abstract Tumor recurrence is a slow biological process involving therapy resistance, immune escape, and metastasis and is the leading cause of death in medulloblastoma, the most frequent malignant pediatric brain tumor. By studying paired primary-recurrent patient samples and patient-derived xenografts we identified a significant accumulation of SOX9-positive cells in relapses and metastases. They exist as rare, quiescent cells in Group 3 and Group 4 patients that constitute two-thirds of medulloblastoma. To follow relapse at the single-cell level we developed an inducible dual Tet model of MYC-driven MB, where MYC can be directed from treatment-sensitive bulk cells to resistant, dormant SOX9-positive cells by doxycycline. SOX9 promoted immune es-cape, DNA repair suppression and was essential for recurrence. Tumor cell dormancy was non-hierarchical, migratory, and depended on MYC suppression by SOX9 to promote relapse. By using computational modeling and treatment we further showed how doxorubicin and MGMT inhibitors are specifically targeting relapsing cells.
12.	Bomholt, Tobias, et al. (author) The Use of HbA1c, Glycated Albumin and Continuous Glucose Monitoring to Assess Glucose Control in the Chronic Kidney Disease Population Including Dialysis. 2021 In: Nephron. Clinical practice. - : S. Karger AG. - 1660-8151 .- 2235-3186. ; 145:1, s. 14-19 Journal article (peer-reviewed)abstract BACKGROUND: Glycated haemoglobin A1c (HbA1c) has limitations as a glycemic marker for patients with diabetes and CKD and for those receiving dialysis. Glycated albumin is an alternative glycemic marker, and some studies have found that glycated albumin more accurately reflects glycemic control than HbA1c in these groups. However, several factors are known to influence the value of glycated albumin including proteinuria. Continuous glucose monitoring (CGM) is another alternative to HbA1c. CGM allows one to assess mean glucose, glucose variability, and the time spent in hypo-, normo-, and hyperglycemia. Currently, several different CGM models are approved for use in patients receiving dialysis; CKD (not on dialysis) is not a contraindication in any of these models. Some devices are for blind recording, while others provide real-time data to patients. Small studies suggest that CGM could improve glycemic control in hemodialysis patients, but this has not been studied for individual CKD stages.SUMMARY: Glycated albumin and CGM avoid the pitfalls of HbA1c in CKD and dialysis populations. However, the value of glycated albumin may be affected by several factors. CGM provides a precise estimation of the mean glucose. Here, we discuss the strengths and limitations for using HbA1c, glycated albumin, or CGM in CKD and dialysis population. Key Messages: Glycated albumin is an alternative glycemic marker but is affected by proteinuria. CGM provides a precise estimation of mean glucose and glucose variability. It remains unclear if CGM improves glycemic control in the CKD and dialysis populations.
13.	Borgenvik, Anna, 1987-, et al. (author) Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma 2022 In: Cancer Research. - : AMER ASSOC CANCER RESEARCH. - 0008-5472 .- 1538-7445. ; 82:24, s. 4586-4603 Journal article (peer-reviewed)abstract Relapse is the leading cause of death in patients with medulloblas-toma, the most common malignant pediatric brain tumor. A better understanding of the mechanisms underlying recurrence could lead to more effective therapies for targeting tumor relapses. Here, we observed that SOX9, a transcription factor and stem cell/glial fate marker, is limited to rare, quiescent cells in high-risk medulloblastoma with MYC amplification. In paired primary-recurrent patient samples, SOX9-positive cells accumulated in medulloblastoma relapses. SOX9 expression anti-correlated with MYC expression in murine and human medulloblastoma cells. However, SOX9-positive cells were plastic and could give rise to a MYC high state. To follow relapse at the single-cell level, an inducible dual Tet model of medulloblastoma was developed, in which MYC expression was redirected in vivo from treatment-sensitive bulk cells to dormant SOX9-positive cells using doxycycline treatment. SOX9 was essential for relapse initiation and depended on suppression of MYC activity to promote therapy resistance, epithelial-mesenchymal transition, and immune escape. p53 and DNA repair pathways were downregulated in recurrent tumors, whereas MGMT was upregulated. Recurrent tumor cells were found to be sensitive to treatment with an MGMT inhibitor and doxorubicin. These findings suggest that recurrence-specific targeting coupled with DNA repair inhibition comprises a potential therapeutic strategy in patients affected by medulloblastoma relapse.Significance: SOX9 facilitates therapy escape and recurrence in medulloblastoma via temporal inhibition of MYC/MYCN genes, revealing a strategy to specifically target SOX9-positive cells to prevent tumor relapse.
14.	Bussy, Aurélie, et al. (author) Cerebellar and subcortical atrophy contribute to psychiatric symptoms in frontotemporal dementia 2023 In: Human Brain Mapping. - : Wiley. - 1065-9471 .- 1097-0193. ; 44:7, s. 2684-2700 Journal article (peer-reviewed)abstract Recent studies have reported early cerebellar and subcortical impact in the disease progression of genetic frontotemporal dementia (FTD) due to microtubule-associated protein tau (MAPT), progranulin (GRN) and chromosome 9 open reading frame 72 (C9orf72). However, the cerebello-subcortical circuitry in FTD has been understudied despite its essential role in cognition and behaviors related to FTD symptomatology. The present study aims to investigate the association between cerebellar and subcortical atrophy, and neuropsychiatric symptoms across genetic mutations. Our study included 983 participants from the Genetic Frontotemporal dementia Initiative including mutation carriers and noncarrier first-degree relatives of known symptomatic carriers. Voxel-wise analysis of the thalamus, striatum, globus pallidus, amygdala, and the cerebellum was performed, and partial least squares analyses (PLS) were used to link morphometry and behavior. In presymptomatic C9orf72 expansion carriers, thalamic atrophy was found compared to noncarriers, suggesting the importance of this structure in FTD prodromes. PLS analyses demonstrated that the cerebello-subcortical circuitry is related to neuropsychiatric symptoms, with significant overlap in brain/behavior patterns, but also specificity for each genetic mutation group. The largest differences were in the cerebellar atrophy (larger extent in C9orf72 expansion group) and more prominent amygdalar volume reduction in the MAPT group. Brain scores in the C9orf72 expansion carriers and MAPT carriers demonstrated covariation patterns concordant with atrophy patterns detectable up to 20 years before expected symptom onset. Overall, these results demonstrated the important role of the subcortical structures in genetic FTD symptom expression, particularly the cerebellum in C9orf72 and the amygdala in MAPT carriers.
15.	Böhlen, Till Tobias, et al. (author) Effect of Conventional and Ultrahigh Dose Rate FLASH Irradiations on Preclinical Tumor Models : A Systematic Analysis 2023 In: International Journal of Radiation Oncology Biology Physics. - 0360-3016. ; 117:4, s. 1007-1017 Journal article (peer-reviewed)abstract Purpose: Compared with conventional dose rate irradiation (CONV), ultrahigh dose rate irradiation (UHDR) has shown superior normal tissue sparing. However, a clinically relevant widening of the therapeutic window by UHDR, termed “FLASH effect”, also depends on the tumor toxicity obtained by UHDR. Based on a combined analysis of published literature, the current study examined the hypothesis of tumor isoefficacy for UHDR versus CONV and aimed to identify potential knowledge gaps to inspire future in vivo studies. Methods and Materials: A systematic literature search identified publications assessing in vivo tumor responses comparing UHDR and CONV. Qualitative and quantitative analyses were performed, including combined analyses of tumor growth and survival data. Results: We identified 66 data sets from 15 publications that compared UHDR and CONV for tumor efficacy. The median number of animals per group was 9 (range 3-15) and the median follow-up period was 30.5 days (range 11-230) after the first irradiation. Tumor growth assays were the predominant model used. Combined statistical analyses of tumor growth and survival data are consistent with UHDR isoefficacy compared with CONV. Only 1 study determined tumor-controlling dose (TCD50) and reported statistically nonsignificant differences. Conclusions: The combined quantitative analyses of tumor responses support the assumption of UHDR isoefficacy compared with CONV. However, the comparisons are primarily based on heterogeneous tumor growth assays with limited numbers of animals and short follow-up, and most studies do not assess long-term tumor control probability. Therefore, the assays may be insensitive in resolving smaller response differences, such as responses of radioresistant tumor subclones. Hence, tumor cure experiments, including additional TCD50 experiments, are needed to confirm the assumption of isoeffectiveness in curative settings.
16.	Cristal, Adrian, et al. (author) LEGaTO: First Steps Towards Energy-Efficient Toolset for Heterogeneous Computing 2018 In: ACM International Conference Proceeding Series. - New York, NY, USA : ACM. ; , s. 210-217 Conference paper (peer-reviewed)abstract LEGaTO is a three-year EU H2020 project which started in December 2017. The LEGaTO project will leverage task-based programming models to provide a software ecosystem for Made-in-Europe heterogeneous hardware composed of CPUs, GPUs, FPGAs and dataflow engines. The aim is to attain one order of magnitude energy savings from the edge to the converged cloud/HPC.
17.	Cristal, Adrian, et al. (author) LEGaTO: Towards Energy-Efficient, Secure, Fault-tolerant Toolset for Heterogeneous Computing 2018 In: Proceedings of the 15th ACM International Conference on Computing Frontiers. - New York, NY, USA : ACM. - 9781450357616 ; , s. 276-278 Conference paper (peer-reviewed)abstract LEGaTO is a three-year EU H2020 project which started in December 2017. The LEGaTO project will leverage task-based programming models to provide a software ecosystem for Made-in-Europe heterogeneous hardware composed of CPUs, GPUs, FPGAs and dataflow engines. The aim is to attain one order of magnitude energy savings from the edge to the converged cloud/HPC.
18.	Dulio, Valeria, et al. (author) The NORMAN Association and the European Partnership for Chemicals Risk Assessment (PARC) : let’s cooperate! 2020 In: Environmental Sciences Europe. - : Springer. - 2190-4707 .- 2190-4715. ; 32:1 Journal article (peer-reviewed)abstract The Partnership for Chemicals Risk Assessment (PARC) is currently under development as a joint research and innovation programme to strengthen the scientific basis for chemical risk assessment in the EU. The plan is to bring chemical risk assessors and managers together with scientists to accelerate method development and the production of necessary data and knowledge, and to facilitate the transition to next-generation evidence-based risk assessment, a non-toxic environment and the European Green Deal. The NORMAN Network is an independent, well-established and competent network of more than 80 organisations in the field of emerging substances and has enormous potential to contribute to the implementation of the PARC partnership. NORMAN stands ready to provide expert advice to PARC, drawing on its long experience in the development, harmonisation and testing of advanced tools in relation to chemicals of emerging concern and in support of a European Early Warning System to unravel the risks of contaminants of emerging concern (CECs) and close the gap between research and innovation and regulatory processes. In this commentary we highlight the tools developed by NORMAN that we consider most relevant to supporting the PARC initiative: (i) joint data space and cutting-edge research tools for risk assessment of contaminants of emerging concern; (ii) collaborative European framework to improve data quality and comparability; (iii) advanced data analysis tools for a European early warning system and (iv) support to national and European chemical risk assessment thanks to harnessing, combining and sharing evidence and expertise on CECs. By combining the extensive knowledge and experience of the NORMAN network with the financial and policy-related strengths of the PARC initiative, a large step towards the goal of a non-toxic environment can be taken.
19.	Farzaneh, Amirfarrokh, et al. (author) A Kinetic Study of CO2 and Steam Gasification of Char from Lignin Produced in the SEW Process 2014 In: BioResources. - : BioResources. - 1930-2126. ; 9:2, s. 3052-3063 Journal article (peer-reviewed)abstract The reaction kinetics of gasification are important for the design of gasifiers using biomass feedstocks, such as lignin, produced in biorefinery processes. Condensed and uncondensed lignin samples used in the present study were prepared using the SEW (SO2-ethanol-water) fractionation process applied to spruce wood chips: the dissolved lignin is precipitated during the recovery of SO2 and ethanol from the spent fractionation liquor. The gasification of char made from condensed and uncondensed SEW lignin was investigated using thermogravimetric analysis (TGA) at atmospheric pressure using either CO2 or steam. The main aim of this study was to quantify the reaction rate during the gasification process, which was found to be best described as zero-order. All experiments were performed at constant temperatures between 700 and 1050 °C to obtain the necessary information for describing the reaction rate equation in an Arrhenius form; the heating rate was 20 °C/min for both samples. The experiments led to almost similar results for both samples. The activation energies of CO2 gasification were approximately 160 kJ/mol and 170 kJ/mol for uncondensed and condensed lignin char, respectively. The activation energies of steam gasification were approximately 90 kJ/mol and 100 kJ/mol for uncondensed and condensed lignin char, respectively.
20.	Grüning, Björn, et al. (author) Bioconda: A sustainable and comprehensive software distribution for the life sciences 2017 Other publication (other academic/artistic)abstract We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
21.	Hoffman, Joel, et al. (author) Mapping the availability of translated versions of posttraumatic stress disorder screening questionnaires for adults : A scoping review 2022 In: European Journal of Psychotraumatology. - : Informa UK Limited. - 2000-8198 .- 2000-8066. ; 13:2 Research review (peer-reviewed)abstract Background: The most used questionnaires for PTSD screening in adults were developed in English. Although many of these questionnaires were translated into other languages, the procedures used to translate them and to evaluate their reliability and validity have not been consistently documented. This comprehensive scoping review aimed to compile the currently available translated and evaluated questionnaires used for PTSD screening, and highlight important gaps in the literature.Objective: This review aimed to map the availability of translated and evaluated screening questionnaires for posttraumatic stress disorder (PTSD) for adults.Methods: All peer-reviewed studies in which a PTSD screening questionnaire for adults was translated, and which reported at least one result of a qualitative and /or quantitative evaluation procedure were included. The literature was searched using Embase, MEDLINE, and APA PsycInfo, citation searches and contributions from study team members. There were no restrictions regarding the target languages of the translations. Data on the translation procedure, the qualitative evaluation, the quantitative evaluation (dimensionality of the questionnaire, reliability, and performance), and open access were extracted.Results: A total of 866 studies were screened, of which 126 were included. Collectively, 128 translations of 12 different questionnaires were found. Out of these, 105 (83.3%) studies used a forward and backward translation procedure, 120 (95.2%) assessed the reliability of the translated questionnaire, 60 (47.6%) the dimensionality, 49 (38.9%) the performance, and 42 (33.3%) used qualitative evaluation procedures. Thirty-four questionnaires (27.0%) were either freely available or accessible on request.Conclusions: The analyses conducted and the description of the methods and results varied substantially, making a quality assessment impractical. Translations into languages spoken in middle- or low-income countries were underrepresented. In addition, only a small proportion of all translated questionnaires were available. Given the need for freely accessible translations, an online repository was developed.
22.	Islar, Mine, et al. (author) Diverse values of nature for sustainability 2022 In: Nature. - 0028-0836 .- 1476-4687. ; 620, s. 813-823 Journal article (peer-reviewed)abstract Twenty-five years since foundational publications on valuing ecosystem services for human well-being1,2, addressing the global biodiversity crisis3 still implies confronting barriers to incorporating nature’s diverse values into decision-making. These barriers include powerful interests supported by current norms and legal rules such as property rights, which determine whose values and which values of nature are acted on. A better understanding of how and why nature is (under)valued is more urgent than ever4. Notwithstanding agreements to incorporate nature’s values into actions, including the Kunming-Montreal Global Biodiversity Framework (GBF)5 and the UN Sustainable Development Goals6, predominant environmental and development policies still prioritize a subset of values, particularly those linked to markets, and ignore other ways people relate to and benefit from nature7. Arguably, a ‘values crisis’ underpins the intertwined crises of biodiversity loss and climate change8, pandemic emergence9 and socio-environmental injustices10. On the basis of more than 50,000 scientific publications, policy documents and Indigenous and local knowledge sources, the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES) assessed knowledge on nature’s diverse values and valuation methods to gain insights into their role in policymaking and fuller integration into decisions7,11. Applying this evidence, combinations of values-centred approaches are proposed to improve valuation and address barriers to uptake, ultimately leveraging transformative changes towards more just (that is, fair treatment of people and nature, including inter- and intragenerational equity) and sustainable futures.
23.	Kemp, John P, et al. (author) Does bone resorption stimulate periosteal expansion? A cross sectional analysis of β-C-telopeptides of type I collagen (CTX), genetic markers of the RANKL pathway, and periosteal circumference as measured by pQCT. 2014 In: Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research. - : Wiley. - 1523-4681. ; 29:4, s. 1015-1024 Journal article (peer-reviewed)abstract We hypothesised that bone resorption acts to increase bone strength through stimulation of periosteal expansion. Hence, we examined whether bone resorption, as reflected by serum β-C-telopeptides of type I collagen (CTX), is positively associated with periosteal circumference (PC), in contrast to inverse associations with parameters related to bone remodelling such as cortical bone mineral density (BMDC ). CTX and mid-tibial pQCT scans were available in 1130 adolescents (mean age 15.5 years) from the Avon Longitudinal Study of Parents and Children (ALSPAC). Analyses were adjusted for age, gender, time of sampling, tanner stage, lean mass, fat mass and height. CTX was positively related to PC [β= 0.19 (0.13, 0.24)] (coefficient=SD change per SD increase in CTX, 95% CI)], but inversely associated with BMDC [β= -0.46 (-0.52,-0.40)] and cortical thickness [β= -0.11 (-0.18, -0.03)]. CTX was positively related to bone strength as reflected by the strength-strain index (SSI) [β= 0.09 (0.03, 0.14)]. To examine the causal nature of this relationship, we then analysed whether SNPs within key osteoclast regulatory genes, known to reduce areal/cortical BMD, conversely increase PC. Fifteen such genetic variants within or proximal to genes encoding RANK, RANKL and OPG were identified by literature search. Six of the 15 alleles that were inversely related to BMD were positively related to CTX (P<0.05 cut-off) (n=2379). Subsequently, we performed a meta-analysis of associations between these SNPs and PC in ALSPAC (n=3382), Gothenburg Osteoporosis and Obesity Determinants (GOOD) (n=938) and the Young Finns Study (YFS) (n=1558). Five of the 15 alleles that were inversely related to BMD were positively related to PC (P<0.05 cut-off). We conclude that despite having lower BMD, individuals with a genetic predisposition to higher bone resorption have greater bone size, suggesting that higher bone resorption is permissive for greater periosteal expansion.
24.	Klionsky, Daniel J., et al. (author) Guidelines for the use and interpretation of assays for monitoring autophagy 2012 In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544 Research review (peer-reviewed)abstract In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
25.	McMillan, Hilary, et al. (author) Panta Rhei 2013-2015 : global perspectives on hydrology, society and change 2016 In: Hydrological Sciences Journal. - : Taylor & Francis Group. - 0262-6667 .- 2150-3435. ; 61:7, s. 1174-1191 Journal article (peer-reviewed)abstract In 2013, the International Association of Hydrological Sciences (IAHS) launched the hydrological decade 2013-2022 with the theme "Panta Rhei: Change in Hydrology and Society". The decade recognizes the urgency of hydrological research to understand and predict the interactions of society and water, to support sustainable water resource use under changing climatic and environmental conditions. This paper reports on the first Panta Rhei biennium 2013-2015, providing a comprehensive resource that describes the scope and direction of Panta Rhei. We bring together the knowledge of all the Panta Rhei working groups, to summarize the most pressing research questions and how the hydrological community is progressing towards those goals. We draw out interconnections between different strands of research, and reflect on the need to take a global view on hydrology in the current era of human impacts and environmental change. Finally, we look back to the six driving science questions identified at the outset of Panta Rhei, to quantify progress towards those aims.
26.	Paternoster, Lavinia, et al. (author) Genetic determinants of trabecular and cortical volumetric bone mineral densities and bone microstructure. 2013 In: PLoS genetics. - : Public Library of Science (PLoS). - 1553-7404 .- 1553-7390. ; 9:2 Journal article (peer-reviewed)abstract Most previous genetic epidemiology studies within the field of osteoporosis have focused on the genetics of the complex trait areal bone mineral density (aBMD), not being able to differentiate genetic determinants of cortical volumetric BMD (vBMD), trabecular vBMD, and bone microstructural traits. The objective of this study was to separately identify genetic determinants of these bone traits as analysed by peripheral quantitative computed tomography (pQCT). Separate GWA meta-analyses for cortical and trabecular vBMDs were performed. The cortical vBMD GWA meta-analysis (n=5,878) followed by replication (n=1,052) identified genetic variants in four separate loci reaching genome-wide significance (RANKL, rs1021188, p=3.6×10⁻¹⁴; LOC285735, rs271170, p=2.7×10⁻¹²; OPG, rs7839059, p=1.2×10⁻¹⁰; and ESR1/C6orf97, rs6909279, p=1.1×10⁻⁹). The trabecular vBMD GWA meta-analysis (n=2,500) followed by replication (n=1,022) identified one locus reaching genome-wide significance (FMN2/GREM2, rs9287237, p=1.9×10⁻⁹). High-resolution pQCT analyses, giving information about bone microstructure, were available in a subset of the GOOD cohort (n=729). rs1021188 was significantly associated with cortical porosity while rs9287237 was significantly associated with trabecular bone fraction. The genetic variant in the FMN2/GREM2 locus was associated with fracture risk in the MrOS Sweden cohort (HR per extra T allele 0.75, 95% confidence interval 0.60-0.93) and GREM2 expression in human osteoblasts. In conclusion, five genetic loci associated with trabecular or cortical vBMD were identified. Two of these (FMN2/GREM2 and LOC285735) are novel bone-related loci, while the other three have previously been reported to be associated with aBMD. The genetic variants associated with cortical and trabecular bone parameters differed, underscoring the complexity of the genetics of bone parameters. We propose that a genetic variant in the RANKL locus influences cortical vBMD, at least partly, via effects on cortical porosity, and that a genetic variant in the FMN2/GREM2 locus influences GREM2 expression in osteoblasts and thereby trabecular number and thickness as well as fracture risk.
27.	Paternoster, Lavinia, et al. (author) Genome-Wide Association Meta-Analysis of Cortical Bone Mineral Density Unravels Allelic Heterogeneity at the RANKL Locus and Potential Pleiotropic Effects on Bone 2010 In: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 6:11, s. e1001217- Journal article (peer-reviewed)abstract Previous genome-wide association (GWA) studies have identified SNPs associated with areal bone mineral density (aBMD). However, this measure is influenced by several different skeletal parameters, such as periosteal expansion, cortical bone mineral density (BMDC) cortical thickness, trabecular number, and trabecular thickness, which may be under distinct biological and genetic control. We have carried out a GWA and replication study of BMDC, as measured by peripheral quantitative computed tomography (pQCT), a more homogenous and valid measure of actual volumetric bone density. After initial GWA meta-analysis of two cohorts (ALSPAC n = 999, aged similar to 15 years and GOOD n = 935, aged similar to 19 years), we attempted to replicate the BMDC associations that had p<1 x 10(-5) in an independent sample of ALSPAC children (n = 2803) and in a cohort of elderly men (MrOS Sweden, n = 1052). The rs1021188 SNP (near RANKL) was associated with BMDC in all cohorts (overall p = 2 x 10(-14), n = 5739). Each minor allele was associated with a decrease in BMDC of similar to 0.14SD. There was also evidence for an interaction between this variant and sex (p = 0.01), with a stronger effect in males than females (at age 15, males -6.77mg/cm(3) per C allele, p = 2 x 10(-6); females -2.79 mg/cm(3) per C allele, p = 0.004). Furthermore, in a preliminary analysis, the rs1021188 minor C allele was associated with higher circulating levels of sRANKL (p<0.005). We show this variant to be independent from the previously aBMD associated SNP (rs9594738) and possibly from a third variant in the same RANKL region, which demonstrates important allelic heterogeneity at this locus. Associations with skeletal parameters reflecting bone dimensions were either not found or were much less pronounced. This finding implicates RANKL as a locus containing variation associated with volumetric bone density and provides further insight into the mechanism by which the RANK/RANKL/OPG pathway may be involved in skeletal development.
28.	Pommery, Yannick, et al. (author) Dentition and feeding in Placodontia : tooth replacement in Henodus chelyops 2021 In: BMC Ecology and Evolution. - : BioMed Central (BMC). - 2730-7182. ; 21 Journal article (peer-reviewed)abstract Background: Placodontia is a Triassic sauropterygian reptile group characterized by flat and enlarged crushing teeth adapted to a durophagous diet. The enigmatic placodont Henodus chelyops has numerous autapomorphic character states, including extreme tooth count reduction to only a single pair of palatine and dentary crushing teeth. This renders the species unusual among placodonts and challenges identification of its phylogenetic position.Results: The skulls of two Henodus chelyops specimens were visualized with synchrotron tomography to investigate the complete anatomy of their functional and replacement crushing dentition in 3D. All teeth of both specimens were segmented, measured, and statistically compared to reveal that H. chelyops teeth are much smaller than the posterior palatine teeth of other cyamodontoid placodonts with the exception of Parahenodus atancensis from the Iberian Peninsula. The replacement teeth of this species are quite similar in size and morphology to the functional teeth.Conclusion: As other placodonts, Henodus chelyops exhibits vertical tooth replacement. This suggests that vertical tooth replacement arose relatively early in placodont phylogeny. Analysis of dental morphology in H. chelyops revealed a concave shape of the occlusal surface and the notable absence of a central cusp. This dental morphology could have reduced dental wear and protected against failure. Hence, the concave teeth of H. chelyops appear to be adapted to process small invertebrate items, such as branchiopod crustaceans. Small gastropods were encountered in the matrix close to both studied skulls.
29.	Rendo, Verónica, et al. (author) Exploiting loss of heterozygosity for allele-selective colorectal cancer chemotherapy 2020 In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11 Journal article (peer-reviewed)abstract Allelic losses occurring in cancer cells have been suggested as potential targets for therapy. Here, the authors show how recurring loss of heterozygosity of a drug metabolic gene in colorectal cancers can be exploited using a low molecular weight compound. Cancer chemotherapy targeting frequent loss of heterozygosity events is an attractive concept, since tumor cells may lack enzymatic activities present in normal constitutional cells. To find exploitable targets, we map prevalent genetic polymorphisms to protein structures and identify 45 nsSNVs (non-synonymous small nucleotide variations) near the catalytic sites of 17 enzymes frequently lost in cancer. For proof of concept, we select the gastrointestinal drug metabolic enzyme NAT2 at 8p22, which is frequently lost in colorectal cancers and has a common variant with 10-fold reduced activity. Small molecule screening results in a cytotoxic kinase inhibitor that impairs growth of cells with slow NAT2 and decreases the growth of tumors with slow NAT2 by half as compared to those with wild-type NAT2. Most of the patient-derived CRC cells expressing slow NAT2 also show sensitivity to 6-(4-aminophenyl)-N-(3,4,5-trimethoxyphenyl)pyrazin-2-amine (APA) treatment. These findings indicate that the therapeutic index of anti-cancer drugs can be altered by bystander mutations affecting drug metabolic genes.
30.	Ruggeri, Kai, et al. (author) The globalizability of temporal discounting 2022 In: Nature Human Behaviour. - : Springer Nature. - 2397-3374. ; 6:10, s. 1386-1397 Journal article (peer-reviewed)abstract Economic inequality is associated with preferences for smaller, immediate gains over larger, delayed ones. Such temporal discounting may feed into rising global inequality, yet it is unclear whether it is a function of choice preferences or norms, or rather the absence of sufficient resources for immediate needs. It is also not clear whether these reflect true differences in choice patterns between income groups. We tested temporal discounting and five intertemporal choice anomalies using local currencies and value standards in 61 countries (N = 13,629). Across a diverse sample, we found consistent, robust rates of choice anomalies. Lower-income groups were not significantly different, but economic inequality and broader financial circumstances were clearly correlated with population choice patterns. Ruggeri et al. find in a study of 61 countries that temporal discounting patterns are globally generalizable. Worse financial environments, greater inequality and high inflation are associated with extreme or inconsistent long-term decisions.
31.	Rydgren, Tobias, 1973- (author) Experimental Studies Aiming to Prevent Type 1 Diabetes Mellitus 2007 Doctoral thesis (other academic/artistic)abstract Type 1 diabetes mellitus (T1DM) is an autoimmune disease in which T-cells and macrophages invade the islets of Langerhans and selectively destroy the insulin producing β-cells, either directly or through the secretion of e.g. cytokines and nitric oxide (NO). This thesis has studied possible strategies to prevent T1DM. In β-cells and macrophages, NO is produced by inducible nitric oxide synthase (iNOS). In the first study, we found that 1400W, a highly selective inhibitor of iNOS could prevent interleukin (IL)-1β induced suppression of rat islet function in vitro, but not diabetes induced by multiple low dose streptozotocin (MLDS), a well established animal model for autoimmune diabetes, in vivo. Next, we wanted to test a new type of high affinity blocker of IL-1 action, called IL-1 trap, in vitro. Here we found that an IL-1 trap could prevent the suppressive effects by IL-1β on rat pancreatic islet function. Also, it was sufficient to block the action of IL-1β to prevent islet cell death induced by a combination of IL-1β, tumor necrosis factor-α and interferon-γ.In study III, a murine IL-1 trap was found to prolong islet graft survival in the recurrence of disease (ROD) model, a T1DM model that involves syngeneic transplantation of healthy pancreatic islets to diabetic nonobese diabetic mice. Mice treated with IL-1 trap displayed an increased mRNA level of the cytokine IL-4 in isolated spleen cells. This suggests a shift towards Th2-cytokine production, which in part could explain the results. Finally, simvastatin an anti-hypercholesterolemic drug that possesses anti-inflammatory properties e.g. by interfering with transendothelial migration of leukocytes to sites of inflammation was studied. We found that the administration of simvastatin could delay, and in some mice prevent, the onset of MLDS-diabetes, and prolong islet graft survival in the ROD model.
32.	Stanaway, Jeffrey D., et al. (author) Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990-2017: A systematic analysis for the Global Burden of Disease Study 2017 2018 In: The Lancet. - 1474-547X .- 0140-6736. ; 392:10159, s. 1923-1994 Journal article (peer-reviewed)abstract Background The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 comparative risk assessment (CRA) is a comprehensive approach to risk factor quantification that offers a useful tool for synthesising evidence on risks and risk-outcome associations. With each annual GBD study, we update the GBD CRA to incorporate improved methods, new risks and risk-outcome pairs, and new data on risk exposure levels and risk- outcome associations. Methods We used the CRA framework developed for previous iterations of GBD to estimate levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (DALYs), by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017. This study included 476 risk-outcome pairs that met the GBD study criteria for convincing or probable evidence of causation. We extracted relative risk and exposure estimates from 46 749 randomised controlled trials, cohort studies, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. Using the counterfactual scenario of theoretical minimum risk exposure level (TMREL), we estimated the portion of deaths and DALYs that could be attributed to a given risk. We explored the relationship between development and risk exposure by modelling the relationship between the Socio-demographic Index (SDI) and risk-weighted exposure prevalence and estimated expected levels of exposure and risk-attributable burden by SDI. Finally, we explored temporal changes in risk-attributable DALYs by decomposing those changes into six main component drivers of change as follows: (1) population growth; (2) changes in population age structures; (3) changes in exposure to environmental and occupational risks; (4) changes in exposure to behavioural risks; (5) changes in exposure to metabolic risks; and (6) changes due to all other factors, approximated as the risk-deleted death and DALY rates, where the risk-deleted rate is the rate that would be observed had we reduced the exposure levels to the TMREL for all risk factors included in GBD 2017.
33.	Steffan, Adrian, et al. (author) Validation of an open source, remote web-based eye-tracking method (WebGazer) for research in early childhood 2024 In: Infancy. - 1525-0008 .- 1532-7078. ; 29:1 Journal article (peer-reviewed)abstract Measuring eye movements remotely via the participant's webcam promises to be an attractive methodological addition to in-person eye-tracking in the lab. However, there is a lack of systematic research comparing remote web-based eye-tracking with in-lab eye-tracking in young children. We report a multi-lab study that compared these two measures in an anticipatory looking task with toddlers using WebGazer.js and jsPsych. Results of our remotely tested sample of 18-27-month-old toddlers (N=125) revealed that web-based eye-tracking successfully captured goal-based action predictions, although the proportion of the goal-directed anticipatory looking was lower compared to the in-lab sample (N=70). As expected, attrition rate was substantially higher in the web-based (42%) than the in-lab sample (10%). Excluding trials based on visual inspection of the match of time-locked gaze coordinates and the participant's webcam video overlayed on the stimuli was an important preprocessing step to reduce noise in the data. We discuss the use of this remote web-based method in comparison with other current methodological innovations. Our study demonstrates that remote web-based eye-tracking can be a useful tool for testing toddlers, facilitating recruitment of larger and more diverse samples; a caveat to consider is the larger drop-out rate.
34.	The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data 2022 In: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2 Journal article (peer-reviewed)abstract This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
35.	Usino, David, et al. (author) Primary interactions of biomass components during fast pyrolysis 2021 In: Journal of Analytical and Applied Pyrolysis. - : Elsevier BV. - 0165-2370 .- 1873-250X. ; 159 Journal article (peer-reviewed)abstract Fast pyrolysis is an industrially attractive method to produce fuels and chemicals from biomass; however, to gain better control over the process, the reactions and interactions between the components and decomposition products need elucidation. This study investigated primary reactions during fast pyrolysis of biomass. Pyrolysis of the three main biomass components (cellulose, hemicellulose and lignin) and their blends was carried out with a micro-pyrolyser connected to a Gas Chromatograph-Mass Spectrometer/Flame Ionisation Detector (GC–MS/FID). The blends of the individual components were prepared in similar proportions to that of native biomass (birchwood) and were pyrolysed at 600 °C for 2 s. The results showed that the two-component blends decrease the production of saccharides to a large extent. This was especially noticeable for levoglucosan when cellulose was mixed with either hemicellulose or lignin. Similarly, in the presence of cellulose, the formation of phenolic compounds from lignin was inhibited by 62 %. However, no differences were found in yields of the main products for the xylan-lignin blend compared to those from the individual components. The yields of volatile products from the cellulose-xylan blend were promoted for a majority of the product categories and were most pronounced for the aldehydes. Furthermore, while the formation of the phenols and saccharides was slightly inhibited for the three-component blend, the aldehydes, ketones and furans showed an increased production compared to the weighed sum of products expected, based on the pyrolysis of the individual components. The native biomass showed a similar trend as the three-component blend in all product categories except for the saccharides, which were inhibited to a large extent. This study provides a better understanding of the interactions occurring between different components during fast pyrolysis of biomass.
36.	van Hilst, Jony, et al. (author) Minimally invasive versus open distal pancreatectomy for pancreatic ductal adenocarcinoma (DIPLOMA) : study protocol for a randomized controlled trial 2021 In: Trials. - : BMC. - 1745-6215. ; 22:1 Journal article (peer-reviewed)abstract Background: Recently, the first randomized trials comparing minimally invasive distal pancreatectomy (MIDP) with open distal pancreatectomy (ODP) for non-malignant and malignant disease showed a 2-day reduction in time to functional recovery after MIDP. However, for pancreatic ductal adenocarcinoma (PDAC), concerns have been raised regarding the oncologic safety (i.e., radical resection, lymph node retrieval, and survival) of MIDP, as compared to ODP. Therefore, a randomized controlled trial comparing MIDP and ODP in PDAC regarding oncological safety is warranted. We hypothesize that the microscopically radical resection (R0) rate is non-inferior for MIDP, as compared to ODP. Methods/design: DIPLOMA is an international randomized controlled, patient- and pathologist-blinded, non-inferiority trial performed in 38 pancreatic centers in Europe and the USA. A total of 258 patients with an indication for elective distal pancreatectomy with splenectomy because of proven or highly suspected PDAC of the pancreatic body or tail will be randomly allocated to MIDP (laparoscopic or robot-assisted) or ODP in a 1:1 ratio. The primary outcome is the microscopically radical resection margin (R0, distance tumor to pancreatic transection and posterior margin >= 1 mm), which is assessed using a standardized histopathology assessment protocol. The sample size is calculated with the following assumptions: 5% one-sided significance level (alpha), 80% power (1-beta), expected R0 rate in the open group of 58%, expected R0 resection rate in the minimally invasive group of 67%, and a non-inferiority margin of 7%. Secondary outcomes include time to functional recovery, operative outcomes (e.g., blood loss, operative time, and conversion to open surgery), other histopathology findings (e.g., lymph node retrieval, perineural- and lymphovascular invasion), postoperative outcomes (e.g., clinically relevant complications, hospital stay, and administration of adjuvant treatment), time and site of disease recurrence, survival, quality of life, and costs. Follow-up will be performed at the outpatient clinic after 6, 12, 18, 24, and 36 months postoperatively. Discussion: The DIPLOMA trial is designed to investigate the non-inferiority of MIDP versus ODP regarding the microscopically radical resection rate of PDAC in an international setting.
37.	Villanueva Perez, Pablo, et al. (author) Megahertz X-ray Multi-projection imaging 2023 In: arXiv.org. - 2331-8422. Journal article (other academic/artistic)abstract X-ray time-resolved tomography is one of the most popular X-raytechniques to probe dynamics in three dimensions (3D). Recent developments in time-resolved tomography opened the possibility of recordingkilohertz-rate 3D movies. However, tomography requires rotating thesample with respect to the X-ray beam, which prevents characterization of faster structural dynamics. Here, we present megahertz (MHz)X-ray multi-projection imaging (MHz-XMPI), a technique capable ofrecording volumetric information at MHz rates and micrometer resolution without scanning the sample. We achieved this by harnessing theunique megahertz pulse structure and intensity of the European X-rayFree-electron Laser with a combination of novel detection and reconstruction approaches that do not require sample rotations. Our approachenables generating multiple X-ray probes that simultaneously record several angular projections for each pulse in the megahertz pulse burst.We provide a proof-of-concept demonstration of the MHz-XMPI technique’s capability to probe 4D (3D+time) information on stochasticphenomena and non-reproducible processes three orders of magnitudefaster than state-of-the-art time-resolved X-ray tomography, by generating 3D movies of binary droplet collisions. We anticipate that MHz-XMPIwill enable in-situ and operando studies that were impossible before,either due to the lack of temporal resolution or because the systemswere opaque (such as for MHz imaging based on optical microscopy).
38.	Vinkler, Michal, et al. (author) Understanding the evolution of immune genes in jawed vertebrates 2023 In: Journal of Evolutionary Biology. - : John Wiley & Sons. - 1010-061X .- 1420-9101. ; 36:6, s. 847-873 Research review (peer-reviewed)abstract Driven by co-evolution with pathogens, host immunity continuously adapts to optimize defence against pathogens within a given environment. Recent advances in genetics, genomics and transcriptomics have enabled a more detailed investigation into how immunogenetic variation shapes the diversity of immune responses seen across domestic and wild animal species. However, a deeper understanding of the diverse molecular mechanisms that shape immunity within and among species is still needed to gain insight into-and generate evolutionary hypotheses on-the ultimate drivers of immunological differences. Here, we discuss current advances in our understanding of molecular evolution underpinning jawed vertebrate immunity. First, we introduce the immunome concept, a framework for characterizing genes involved in immune defence from a comparative perspective, then we outline how immune genes of interest can be identified. Second, we focus on how different selection modes are observed acting across groups of immune genes and propose hypotheses to explain these differences. We then provide an overview of the approaches used so far to study the evolutionary heterogeneity of immune genes on macro and microevolutionary scales. Finally, we discuss some of the current evidence as to how specific pathogens affect the evolution of different groups of immune genes. This review results from the collective discussion on the current key challenges in evolutionary immunology conducted at the ESEB 2021 Online Satellite Symposium: Molecular evolution of the vertebrate immune system, from the lab to natural populations.
39.	Wikström, Hanna, 1970, et al. (author) Låt de hungerstrejkande palestinierna stanna 2014 In: SVT Opinion. ; 2014-10-11 Journal article (other academic/artistic)
40.	Zheng, Hou-Feng, et al. (author) Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture 2015 In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 526:7571, s. 112- Journal article (peer-reviewed)abstract The extent to which low-frequency (minor allele frequency (MAF) between 1-5%) and rare (MAF <= 1%) variants contribute to complex traits and disease in the general population is mainly unknown. Bone mineral density (BMD) is highly heritable, a major predictor of osteoporotic fractures, and has been previously associated with common genetic variants(1-8), as well as rare, population specific, coding variants(9). Here we identify novel non-coding genetic variants with large effects on BMD (n(total) = 53,236) and fracture (n(total) = 508,253) in individuals of European ancestry from the general population. Associations for BMD were derived from whole-genome sequencing (n = 2,882 from UK10K (ref. 10); a population-based genome sequencing consortium), whole-exome sequencing (n = 3,549), deep imputation of genotyped samples using a combined UK10K/1000 Genomes reference panel (n = 26,534), and de novo replication genotyping (n = 20,271). We identified a low-frequency non-coding variant near a novel locus, EN1, with an effect size fourfold larger than the mean of previously reported common variants for lumbar spine BMD8 (rs11692564(T), MAF51.6%, replication effect size510.20 s.d., P-meta = 2 x 10(-14)), which was also associated with a decreased risk of fracture (odds ratio = 0.85; P = 2 x 10(-11); ncases = 98,742 and ncontrols = 409,511). Using an En1cre/flox mouse model, we observed that conditional loss of En1 results in low bone mass, probably as a consequence of high bone turnover. We also identified a novel low frequency non-coding variant with large effects on BMD near WNT16 (rs148771817(T), MAF = 1.2%, replication effect size +10.41 s.d., P-meta = 1 x 10(-11)). In general, there was an excess of association signals arising from deleterious coding and conserved non-coding variants. These findings provide evidence that low-frequency non-coding variants have large effects on BMD and fracture, thereby providing rationale for whole-genome sequencing and improved imputation reference panels to study the genetic architecture of complex traits and disease in the general population.
41.	Zheng, Hou-Feng, et al. (author) WNT16 influences bone mineral density, Cortical bone thickness, bone strength, and Osteoporotic fracture risk 2012 In: PLoS genetics. - SAN FRANCISCO, USA : PUBLIC LIBRARY SCIENCE. - 1553-7404. ; 8:7, s. e1002745- Journal article (peer-reviewed)abstract We aimed to identify genetic variants associated with cortical bone thickness (CBT) and bone mineral density (BMD) by performing two separate genome-wide association study (GWAS) meta-analyses for CBT in 3 cohorts comprising 5,878 European subjects and for BMD in 5 cohorts comprising 5,672 individuals. We then assessed selected single-nucleotide polymorphisms (SNPs) for osteoporotic fracture in 2,023 cases and 3,740 controls. Association with CBT and forearm BMD was tested for ∼2.5 million SNPs in each cohort separately, and results were meta-analyzed using fixed effect meta-analysis. We identified a missense SNP (Thr>Ile; rs2707466) located in the WNT16 gene (7q31), associated with CBT (effect size of -0.11 standard deviations [SD] per C allele, P = 6.2×10(-9)). This SNP, as well as another nonsynonymous SNP rs2908004 (Gly>Arg), also had genome-wide significant association with forearm BMD (-0.14 SD per C allele, P = 2.3×10(-12), and -0.16 SD per G allele, P = 1.2×10(-15), respectively). Four genome-wide significant SNPs arising from BMD meta-analysis were tested for association with forearm fracture. SNP rs7776725 in FAM3C, a gene adjacent to WNT16, was associated with a genome-wide significant increased risk of forearm fracture (OR = 1.33, P = 7.3×10(-9)), with genome-wide suggestive signals from the two missense variants in WNT16 (rs2908004: OR = 1.22, P = 4.9×10(-6) and rs2707466: OR = 1.22, P = 7.2×10(-6)). We next generated a homozygous mouse with targeted disruption of Wnt16. Female Wnt16(-/-) mice had 27% (P<0.001) thinner cortical bones at the femur midshaft, and bone strength measures were reduced between 43%-61% (6.5×10(-13)

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