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  • 2019  (17)
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  • 2019  (17)
  • 1
    Language: English
    In: Hydrology and Earth System Sciences Discussions, 05/17/2019, pp.1-24
    ISSN: Hydrology and Earth System Sciences Discussions
    E-ISSN: 1812-2116
    Source: CrossRef
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  • 2
    In: European Journal of Soil Science, May 2019, Vol.70(3), pp.454-465
    Description: Soil structural traits provide links between soil structure and ecosystem functioning. The size and stability of soil aggregates are assumed to provide information on aggregate formation and turnover. A standard method to analyse these traits is to determine the mass distribution on sieves. The major drawback of this method is the small size resolution because of a small number of size classes. A promising, yet still unexplored, method for size distribution analysis in soil science, is dynamic image analysis, which foremost allows a much larger diameter resolution and the assessment of both size and shape distributions. The aim of our study was to validate the applicability of dynamic digital image analysis in combination with sonication to characterize the size and shape distribution and the stability of aggregates. We used two different heterogeneous reference materials and three different soil samples with different aggregate stabilities to test this method. The soil samples were chosen based on increasing clay, humus and calcium carbonate contents. The method yielded reproducible results for diameter and shape distributions for both reference materials and soil samples. The most important improvement compared to well‐established methods was the extremely large size resolution. This allows specification of the pattern of diameter‐dependent breakup curves by relating them to specific soil properties. The information on sphericity adds supplementary information on the aggregates released. We found much lower sphericity of 1‐mm aggregates mobilized from topsoil samples formed from the activity of living organisms than aggregates mobilized from subsoil samples formed mainly by physicochemical processes. Highlights Our aim was to validate dynamic digital image analysis to characterize soil aggregates.Dynamic image analysis allows high resolution and shape analysis compared to established methods.The method yielded reproducible results for diameter and shape distributions.We established high‐resolution disruption patterns of aggregates enabling new approaches in future research.
    Keywords: Aggregate Breakdown Dynamics ; Particle‐Size Distribution ; Ultrasonic Dispersion
    ISSN: 1351-0754
    E-ISSN: 1365-2389
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  • 3
    Language: English
    In: Journal of Hydrology X, 01/2019, Vol.2, C, p.100014
    ISSN: 25899155
    Source: Elsevier (via CrossRef)
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  • 4
    Language: English
    In: Forests, 01 August 2019, Vol.10(9), p.726
    Description: The compaction of forest soils can deteriorate soil aeration, leading to decreased CH4 uptake and increased N2O efflux. Black alder (Alnus glutinosa) may accelerate soil structure regeneration as it can grow roots under anaerobic soil conditions. However, symbiotic nitrogen fixation by alder can have undesirable side-effects on greenhouse gas (GHG) fluxes. In this study, we evaluated the possible trade-off between alder-mediated structure recovery and GHG emissions. We compared two directly adjacent 15-year old beech (Fagus sylvatica) and alder stands (loamy texture, pH 5−6), including old planted skid trails. The last soil trafficking on the skid trails took place in 1999. GHG fluxes were measured over one year. Undisturbed plots with beech had a moderately higher total porosity and were lower in soil moisture and soil organic carbon than undisturbed alder plots. No differences in mineral nitrogen were found. N2O emissions in the undisturbed beech stand were 0.4 kg ha−1 y−1 and 3.1 kg ha−1 y−1 in the undisturbed alder stand. CH4 uptake was 4.0 kg ha−1 y−1 and 1.5 kg ha−1 y−1 under beech and alder, respectively. On the beech planted skid trail, topsoil compaction was still evident by reduced macro porosity and soil aeration; on the alder planted skid trail, soil structure of the uppermost soil layer was completely recovered. Skid trail N2O fluxes under beech were five times higher and CH4 oxidation was 0.6 times lower compared to the adjacent undisturbed beech stand. Under alder, no skid-trail-effects on GHG fluxes were evident. Multiple regression modelling revealed that N2O and CH4 emissions were mainly governed by soil aeration and soil temperature. Compared to beech, alder considerably increased net fluxes of GHG on undisturbed plots. However, for skid trails we suggest that black alder improves soil structure without deterioration of the stand's greenhouse gas balance, when planted only on the compacted areas.
    Keywords: Soil Compaction ; Skid Trails ; Black Alder ; Alnus Glutinosa ; Greenhouse Gas Fluxes ; Soil Structure Recovery ; Forestry
    E-ISSN: 1999-4907
    Source: Directory of Open Access Journals (DOAJ)
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  • 5
    Language: English
    In: Agricultural and Forest Meteorology, 15 February 2019, Vol.265, pp.424-434
    Description: Molecular diffusion is commonly assumed as main physical process of gas transport in soils. However, non-diffusive gas transport processes like the so-called pressure-pumping effect can affect soil gas transport significantly. The pressure-pumping effect has only been detected indirectly and the underlying mechanisms remain unclear. Using a novel method the soil gas transport at a conifer forest site was monitored over a seven-week period. Airflow and air pressure were simultaneously measured above and below the forest canopy and air pressure was also measured in the soil. During episodes of high above-canopy wind speed, the effective soil gas diffusivity temporarily increased due to pressure-pumping. The enhancement of the gas transport rate in the topsoil reached up to 30%. We found that the best meteorological proxy explaining this effect was related to air pressure fluctuations measured at soil surface and not the mean wind speed directly above ground. While sub-canopy wind speeds continuously decreased from the bottom of the tree crown to the soil surface, amplitudes of the air pressure fluctuations were nearly constant in the whole sub-canopy profile and in the soil. We hypothesize that the air pressure fluctuations responsible for pressure-pumping are related to characteristics of above-canopy airflow rather than to airflow directly above the soil surface.
    Keywords: Pressure-Pumping ; Soil Gas Transport ; Air Pressure Fluctuations ; Tracer Gas ; Agriculture ; Meteorology & Climatology
    ISSN: 0168-1923
    E-ISSN: 1873-2240
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  • 6
    Language: English
    In: Journal of Hydrology X, 01 January 2019, Vol.2
    Description: The choice of uranine (UR) and sulforhodamine B (SRB) as hydrological tracers has recently been questioned since they might interact with the soil or become degraded. In this context, microbiological degradation of UR and SRB and the factors influencing it remain poorly studied. Here, we conducted a long-term mesocosm experiment where the effects of plants and hydrologic conditions on the dissipation and degradation of UR and SRB was separately investigated. Mass balances were combined with excitation emission matrix (EEM) fluorescence spectroscopy to characterize microbially-derived organic matter. Results revealed that most of SRB accumulated in the sand while UR was mainly found in the pore water. The estimated degradation of UR and SRB was greater in the treatments with plants and under unsaturated conditions. Overall, UR exhibited higher presumable degradation than SRB. Two components were identified by parallel factor analysis of the EEMs in addition to the UR-related component (U), one humic-like of high molecular weight primarily derived from terrestrial or soil organic matter sources (A + C) and a second humic-like of lower molecular weight related to recent microbial activity (M). A high positive correlation (Spearman’s rho = 0.74, p 〈 0.001) between M and U suggested a possible link, in which the presence of UR fostered microbial processes, thus supporting the hypothesis of biodegradation of UR, which seemed independent of the presence of plants, whereas it was not possible to point out such a correlation for SRB. These results show for the first time that plants and the alternation of oxic and anoxic conditions are favourable to increase degradation of UR and SRB and that microbiological degradation can be involved and dominant in UR dissipation. Keywords: Hydrological tracers, Wetland mesocosm, Degradation, Sorption, Excitation-emission matrix fluorescence spectroscopy
    ISSN: 2589-9155
    Source: Directory of Open Access Journals (DOAJ)
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  • 7
    In: Movement Disorders, January 2019, Vol.34(1), pp.67-77
    Description: Objectives The objectives of this study were to investigate (1) the annual rate of progression of motor and cognitive symptoms and (2) baseline predictors of different modalities for this progression in early Parkinson's disease (PD) when compared with healthy controls. Methods A total of 135 de novo PD and 109 healthy controls (of the De Novo Parkinson cohort) were investigated at baseline and after 24 and 48 months. To delineate motor progression and cognitive decline, the Movement Disorder Society‐Unified Parkinson's Disease Rating Scale part III (MDS‐UPDRS III) and the Mini‐Mental Status Examination (MMSE) were selected. Baseline variables used to predict progression included sociodemographic factors, comorbidities, motor/nonmotor symptoms, polysomnography, MRI, and laboratory biomarkers in serum and CSF. Results Symptoms worsened over 4 years in PD with an annual change of 1.8 points on the MDS‐UPDRS III and 0.2 points on the MMSE. Baseline predictors of worse progression of motor symptoms in PD included male sex, orthostatic blood pressure drop, diagnosis of coronary artery disease, arterial hypertension, elevated serum uric acid, and CSF neurofilament light chain. Predictors of cognitive decline in PD included previous heavy alcohol abuse, current diagnoses of diabetes mellitus, arterial hypertension, elevated periodic limb movement index during sleep, decreased hippocampal volume by MRI, higher baseline levels of uric acid, C‐reactive protein, high density lipoprotein (HDL) cholesterol, and glucose levels. Conclusion Cardiovascular risk factors, deregulated blood glucose, uric acid metabolism, and inflammation were identified as risk markers for faster disease progression. Our panel of risk parameters needs validation during our continuing follow‐up and also in independent patient cohorts. © 2018 International Parkinson and Movement Disorder Society
    Keywords: Cohort Studies ; Outcome Research ; Parkinson'S Disease/Parkinsonism
    ISSN: 0885-3185
    E-ISSN: 1531-8257
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  • 8
    Language: English
    In: Bone marrow transplantation, August 2019, Vol.54(Suppl 2), pp.743-748
    Description: We review current approaches in HLA-haploidentical hematopoietic stem cell transplantation (haplo-HSCT) for pediatric patients with hemoglobinopathies with a focus on recent developments using TCRα/β+/CD19+ depleted grafts in patients with β-thalassemia major (TM) or sickle cell disease (SCD) in two European transplant units. Eleven TM and three SCD patients (Roma cohort) received a preparative regimen consisting of busulfan/thiotepa/cyclophosphamide/ATG preceded by fludarabine/hydroxyurea/azathioprine. The preparative regimen for 5 SCD patients included treosulfan/thiotepa/fludarabine/ATG (Berlin pilot cohort). All grafts were PBSC engineered by TCR-α/β+/CD19+ depletion. In both cohorts, rates for graft failure, treatment related mortality (TRM) and GvHD were encouraging. Overall survival (OS) and disease-free survival (DFS) in the Roma cohort were 84 and 69%, respectively, while OS and DFS are 100% in the Berlin cohort. Immune reconstitution was satisfactory. Although asymptomatic viral reactivation was common, no severe viral infection occured. These data confirm that TCR-α/β+/CD19+ depletion is a well-suited haplo-HSCT strategy for children with hemoglobinopathies. We discuss the results in the context of additional optimization strategies and introduce our concepts for multicenter trial protocols in Germany.
    Keywords: Activation ; Transplantation ; Rejection ; Transplants & Implants ; Grafts ; Cyclophosphamide ; Survival ; Stem Cells ; Busulfan ; Graft-Versus-Host Reaction ; Pediatrics ; Depletion ; Hematopoietic Stem Cells ; Thalassemia ; Hemopoiesis ; Cd19 Antigen ; Optimization ; Treosulfan ; T-Cell Receptor ; Depletion ; Stem Cell Transplantation ; Histocompatibility Antigen HLA ; Grafting ; Stem Cells ; Optimization ; Hydroxyurea ; Fludarabine ; Transplantation ; Azathioprine ; Patients ; Stem Cells ; Survival ; Sickle Cell Disease ; Immune Reconstitution ; Grafts;
    ISSN: 02683369
    E-ISSN: 1476-5365
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  • 9
    In: International Journal of Cancer, 01 June 2019, Vol.144(11), pp.2782-2794
    Description: Primary liver cancer (PLC) ranks among the most lethal solid cancers worldwide due to lack of effective biomarkers for early detection and limited treatment options in advanced stages. Development of primary culture models that closely recapitulate phenotypic and molecular diversities of PLC is urgently needed to improve the patient outcome. Long‐term cultures of 7 primary liver cancer cell lines of hepatocellular and cholangiocellular origin were established using defined culture conditions. Morphological and histological characteristics of obtained cell lines and xenograft tumors were analyzed and compared to original tumors. Time course analyses of transcriptomic and genomic changes were performed using next‐generation sequencing (NGS). Key oncogenic alterations were identified by targeted NGS and cell lines carrying potentially actionable mutations were treated with corresponding specific inhibitors. PDCL fully resembled morphological features of the primary cancers and over extended period in culture. Genomic alterations as well as transcriptome profiles showed high similarity with primary tumors and remained stable during long‐term culturing. Targeted‐NGS confirmed that key oncogenic mutations such as TP53, KRAS, CTNNB1 as well as actionable mutations (e.g. MET, cKIT, KDR) were highly conserved in PDCL and amenable for individualized therapeutic approaches. Integrative genomic and transcriptomic approaches further demonstrated that PDCL more closely resemble molecular and prognostic features of PLC than established cell lines and are valuable tool for direct target evaluation. Our integrative analysis demonstrates that PDCL represents refined model for discovery of relevant molecular subgroups and exploration of precision medicine approaches for the treatment of this deadly disease. What's new? More and more people are affected by primary liver cancer but therapeutic progress is hampered by the phenotypic and molecular diversity within the tumor. To tackle this issue, the authors established multiple patient‐specific cell lines from freshly resected liver tumors and showed that they retained key oncogenic mutations, copy number alterations and gene expression signatures from the primary tumor. These cell lines facilitate direct exploration of therapeutic targets and may expedite drug discovery and individualized approaches to liver cancer treatment.
    Keywords: Primary Liver Cancer ; Patient‐Derived Cell Lines ; Primary Culture ; Drug Discovery ; Molecular Targets
    ISSN: 0020-7136
    E-ISSN: 1097-0215
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  • 10
    Language: English
    In: NATURE COMMUNICATIONS, 2019
    Description: The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca's large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for 〉60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.
    Keywords: Androgen Receptor ; Breast-Cancer ; Gene ; Cell ; Inhibition ; Resistance ; Pathway ; Mutations ; Landscape ; Resource
    ISSN: 2041-1723
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