Incorporating 2D tree-ring data in 3D laser scans of coarse-root systems

In times of global change biomass calculations and the carbon cycle is gaining in importance. Forests act as carbon sinks and hence, play a crucial role in worlds and forests carbon budgets. Unfortunately, growth models and biomass calculations existing so far mainly concentrate on the above-ground part of trees. For this reason, the aim of the present study is to develop an annually resolved 3D growth model for tree roots, which allows for reliable biomass calculations and can later be combined with above-ground models. A FARO scan arm was used to measure the surface of a tree-root segment. In addition, ring-width measurements were performed manually on sampled cross sections using WinDENDRO. The main goal of this study is to model root growth on an annual scale by combining these data sets. In particular, a laser scan arm was tested as a device for the realistic reproduction of tree-root architecture, although the first evaluation has been performed for a root segment rather than for an entire root system. Deviations in volume calculations differed between 5% and 7% from the actual volume and varied depending on the used modeling technique. The model with the smallest deviations represented the structure of the root segment in a realistic way and distances and diameter of cross sections were acceptable approximations of the real values. However, the volume calculations varied depending on object complexity, modeling technique and order of modeling steps. In addition, it was possible to merge tree-ring borders as coordinates into the surface model and receive age information in connection with the spatial allocation. The scan arm was evaluated as an innovative and applicable device with high potential for root modeling. Nevertheless, there are still many problems connected with the scanning technique which have an influence on the accuracy of the model but are expected to improve with technical progress.     

RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics,March 2011

Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interactions and progress, especially building on successes at establishing data standards by the GSC and by the biodiversity and ecological communities. Until recently, the contribution of microbial life to the biomass and biodiversity of the biosphere was largely overlooked (because it was resistant to systematic study). Now, emerging genomic and metagenomic tools are making investigation possible. Initial research findings suggest that major advances are in the offing. Although different research communities share some overlapping concepts and traditions, they differ significantly in sampling approaches, vocabularies and workflows. Likewise, their definitions of ‘fitness for use’ for data differ significantly, as this concept stems from the specific research questions of most importance in the different fields. Nevertheless, there is little doubt that there is much to be gained from greater coordination and integration. As a first step toward interoperability of the information systems used by the different communities, participants agreed to conduct a case study on two of the leading data standards from the two formerly disparate fields: (a) GSC’s standard checklists for genomics and metagenomics and (b) TDWG’s Darwin Core standard, used primarily in taxonomy and systematic biology.     

Recruitment Kinetics of DNA Repair Proteins Mdc1 and Rad52 but Not 53BP1 Depend on Damage Complexity

The recruitment kinetics of double-strand break (DSB) signaling and repair proteins Mdc1, 53BP1 and Rad52 into radiation-induced foci was studied by live-cell fluorescence microscopy after ion microirradiation. To investigate the influence of damage density and complexity on recruitment kinetics, which cannot be done by UV laser irradiation used in former studies, we utilized 43 MeV carbon ions with high linear energy transfer per ion (LET = 370 keV/µm) to create a large fraction of clustered DSBs, thus forming complex DNA damage, and 20 MeV protons with low LET (LET  = 2.6 keV/µm) to create mainly isolated DSBs. Kinetics for all three proteins was characterized by a time lag period T₀ after irradiation, during which no foci are formed. Subsequently, the proteins accumulate into foci with characteristic mean recruitment times τ₁. Mdc1 accumulates faster (T₀ = 17±2 s, τ₁ = 98±11 s) than 53BP1 (T₀ = 77±7 s, τ₁ = 310±60 s) after high LET irradiation. However, recruitment of Mdc1 slows down (T₀ = 73±16 s, τ₁ = 1050±270 s) after low LET irradiation. The recruitment kinetics of Rad52 is slower than that of Mdc1, but exhibits the same dependence on LET. In contrast, the mean recruitment time τ₁ of 53BP1 remains almost constant when varying LET. Comparison to literature data on Mdc1 recruitment after UV laser irradiation shows that this rather resembles recruitment after high than low LET ionizing radiation. So this work shows that damage quality has a large influence on repair processes and has to be considered when comparing different studies.     

Comparison of the orthonasal and retronasal detection thresholds for carbon dioxide in humans

Several studies have investigated the orthonasal detection threshold for carbon dioxide (CO(2)) in humans. The aim of current study was to investigate whether 24 healthy young subjects exhibited differences of CO(2) detection thresholds during orthonasal or retronasal stimulation. As nasal mucosa is believed to desensitize to CO(2) concentrations at or below 4% (v/v) during expiration, the second aim of the study was to explore the influence during nasal versus oral breathing on the detection thresholds. CO(2) stimuli of varying concentrations and a duration of 1000 ms were applied with an air-dilution olfactometer in either the anterior nasal cavity or the nasopharynx during nasal respectively oral breathing. In these 4 conditions, the mean CO(2) detection thresholds using the staircase forced-choice procedure were between 3.9% and 5.3% (v/v). Statistical analysis revealed a significant difference between orthonasal and retronasal stimulation. The CO(2) detection threshold was lower in retronasal stimulation. The nasopharyngeal mucosa is more sensitive to perithreshold CO(2) stimuli than the nasal mucosa. The breathing route had no influence on the detection thresholds. The results of this study indicate that the natural contact of the nasal mucosa with approximately 4% (v/v) CO(2) during nasal expiration does not influence CO(2) detection thresholds.     

Nuclear calcium-VEGFD signaling controls maintenance of dendrite arborization necessary for memory formation

The role of neuronal dendrites is to receive and process synaptic inputs. The geometry of the dendritic arbor can undergo neuronal activity-dependent changes that may impact the cognitive abilities of the organism. Here we show that vascular endothelial growth factor D (VEGFD), commonly known as an angiogenic mitogen, controls the total length and complexity of dendrites both in cultured hippocampal neurons and in the adult mouse hippocampus. VEGFD expression is dependent upon basal neuronal activity and requires nuclear calcium-calmodulin-dependent protein kinase IV (CaMKIV) signaling. Suppression of VEGFD expression in the mouse hippocampus by RNA interference causes memory impairments. Thus, nuclear calcium-VEGFD signaling mediates the effect of neuronal activity on the maintenance of dendritic arbors in the adult hippocampus and is required for cognitive functioning. These results suggest that caution be employed in the clinical use of blockers of VEGFD signaling for antiangiogenic cancer therapy.     

Psoriasis carries an increased risk of venous thromboembolism: a Danish nationwide cohort study

Background

Psoriasis is an immunoinflammatory disease associated with cardiovascular risk factors, atherothrombotic events, and hypercoagulability. Venous thromboembolism (VTE) is potentially lethal and shares risk factors with psoriasis, but the risk of VTE associated with psoriasis is unknown. The present study investigated the potential association between psoriasis and VTE.

Methods and Findings

Information from nationwide prospectively recorded registers of hospitalization, drug dispensing from pharmacies, socio-economic data, and causes of death was linked on an individual level. In an unselected nationwide cohort, we used multivariate Poisson regression models controlling for age, gender, comorbidity, concomitant medication, socio-economic data, and calendar year, to assess the risk of VTE associated with psoriasis. A total of 35,138 patients with mild and 3,526 patients with severe psoriasis were identified and compared with 4,126,075 controls. Patients with psoriasis had higher incidence rates per 1000 person-years of VTE than controls (1.29, 1.92, and 3.20 for controls, mild psoriasis, and severe psoriasis, respectively). The rate ratio (RR) of VTE was elevated in all patients with psoriasis with RR 1.35 (95% confidence interval [CI] 1.21–1.49) and RR 2.06 (CI 1.63–2.61) for mild and severe psoriasis, respectively. Exclusion of patients with malignancies, and censoring of patients undergoing surgery did not alter the results.

Conclusion

This nationwide cohort study indicates that patients with psoriasis are at increased risk of VTE. The risk was highest in young patients with severe psoriasis. Physicians should be aware that patients with psoriasis may be at increased risk of both venous and arterial thromboembolic events.     

Cognition after malignant media infarction and decompressive hemicraniectomy - a retrospective observational study

Background

The Multiple Sclerosis International Quality Of Life (MusiQoL) questionnaire, a 31-item, multidimensional, self-administrated questionnaire that is available in 14 languages including Spanish, has been validated using a large international sample. We investigated the validity and reliability of the Spanish version of MusiQoL in Spain.

Methods

Consecutive patients with different types and severities of multiple sclerosis (MS) were recruited from 22 centres across Spain. All patients completed the MusiQoL questionnaire, the 36-Item Short Form (SF-36) health survey, and a symptoms checklist at baseline and 21 days later. External validity, internal consistency, reliability and reproducibility were tested.

Results

A total of 224 Spanish patients were evaluated. Dimensions of MusiQoL generally demonstrated a high internal consistency (Cronbach's alpha: 0.70-0.92 for all but two MusiQoL domain scores). External validity testing revealed that the MusiQoL index score correlated significantly with all SF-36 dimension scores (Pearson's correlation: 0.46-0.76), reproducibility was satisfactory (intraclass correlation coefficient: 0.60-0.91), acceptability was high, and the time taken to complete the 31-item questionnaire was reasonable (mean [standard deviation]: 9.8 [11.8] minutes).

Conclusions

The Spanish version of the MusiQoL questionnaire appears to be a valid and reliable instrument for measuring quality of life in patients with MS in Spain and constitutes a useful instrument to measure health-related quality of life in the clinical setting.