The SAR group (Stramenopila, Alveolata, Rhizaria) is one of the largest clades in the tree of eukaryotes and includes a great number of parasitic lineages. Rhizarian parasites are obligate and have devastating effects on commercially important plants and animals but despite this fact, our knowledge of their biology and evolution is limited. Here, we present rhizarian transcriptomes from all major parasitic lineages in order to elucidate their evolutionary relationships using a phylogenomic approach. Our results suggest that Ascetosporea, parasites of marine invertebrates, are sister to the novel clade Apofilosa. The phytomyxean plant parasites branch sister to the vampyrellid algal ectoparasites in the novel clade Phytorhiza. They also show that Ascetosporea + Apofilosa + Retaria + Filosa + Phytorhiza form a monophyletic clade, although the branching pattern within this clade is difficult to resolve and appears to be model-dependent. Our study does not support the monophyly of the rhizarian parasitic lineages (Endomyxa), suggesting independent origins for rhizarian animal and plant parasites.

BackgroundFive-aminolevulinic acid (Gliolan, medac, Wedel, Germany, 5-ALA) is approved for fluorescence-guided resections of adult malignant gliomas. Case reports indicate that 5-ALA can be used for children, yet no prospective study has been conducted as of yet. As a basis for a study, we conducted a survey among certified European Gliolan users to collect data on their experiences with children.MethodsInformation on patient characteristics, MRI characteristics of tumors, histology, fluorescence qualities, and outcomes were requested. Surgeons were further asked to indicate whether fluorescence was “useful”, i.e., leading to changes in surgical strategy or identification of residual tumor. Recursive partitioning analysis (RPA) was used for defining cohorts with high or low likelihoods for useful fluorescence.ResultsData on 78 patients <18 years of age were submitted by 20 centers. Fluorescence was found useful in 12 of 14 glioblastomas (85 %), four of five anaplastic astrocytomas (60 %), and eight of ten ependymomas grades II and III (80 %). Fluorescence was found inconsistently useful in PNETs (three of seven; 43 %), gangliogliomas (two of five; 40 %), medulloblastomas (two of eight, 25 %) and pilocytic astrocytomas (two of 13; 15 %). RPA of pre-operative factors showed tumors with supratentorial location, strong contrast enhancement and first operation to have a likelihood of useful fluorescence of 64.3 %, as opposed to infratentorial tumors with first surgery (23.1 %).ConclusionsOur survey demonstrates 5-ALA as being used in pediatric brain tumors. 5-ALA may be especially useful for contrast-enhancing supratentorial tumors. These data indicate controlled studies to be necessary and also provide a basis for planning such a study.

The diagnostic criteria and management of this condition continue to be a topic of debate in the literature. The term definitive symptomatic LOVA (longstanding overt ventriculomegaly in adults) is applied to patients that fulfil a series of diagnostic criteria,which are reviewed in our paper. The main subject of our study is to propose a rearrangement of the criteria for the diagnosis of this entity and adjusted treatment strategies. We present our data evaluating the role of endoscopy in this pathology. This descriptive and analytical study comprised 27 adult patients with LOVA who underwent endoscopic third ventriculostomy (ETV). Data regarding age, gender and onset of symptoms, a previously implanted shunt, clinical examination and radiological findings at the time of diagnosis, and the intracranial pressure (ICP) recordings in some cases, were carefully retrospectively reviewed. ETV success was determined based on clinical state and radiological criteria. ETV was performed in all 27 cases. Mean follow up period was 4.2 years (6 months to 8 years). 2/27 patients (7.40%) were lost to follow-up. The overall success rate for ETV was 76% (21/25 patients). ETV resulted in shunt independency in two of the three patients with a previous shunt. Based on our results, we believe that ETV must be considered as the treatment of choice for patients with symptomatic LOVA.

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Aerial photogrammetry by Unmanned Aerial Vehicles (UAVs) is a widespread method to perform mapping tasks with high-resolution to reconstruct three-dimensional (3D) building and façade models. However, the survey of Ground Control Points (GCPs) represents a time-consuming task, while the use of Real-Time Kinematic (RTK) drones allows for one to collect camera locations with an accuracy of a few centimeters. DJI Phantom 4 RTK (DJI-P4RTK) combines this with the possibility to acquire oblique images in stationary conditions and it currently represents a versatile drone widely used from professional users together with commercial Structure-from-Motion software, such as Agisoft Metashape. In this work, we analyze the architectural application of this drone to the photogrammetric modeling of a building with particular regard to metric survey specifications for cultural heritage for 1:20, 1:50, 1:100, and 1:200 scales. In particular, we designed an accuracy assessment test signalizing 109 points, surveying them with total station and adjusting the measurements through a network approach in order to achieve millimeter-level accuracy. Image datasets with a designed Ground Sample Distance (GSD) of 2 mm were acquired in Network RTK (NRTK) and RTK modes in manual piloting and processed both as single façades (S–F) and as an overall block (4–F). Subsequently, we compared the results of photogrammetric models generated in Agisoft Metashape to the Signalized Point (SP) coordinates. The results highlight the importance of processing an overall photogrammetric block, especially whenever part of camera locations exhibited a poorer accuracy due to multipath effects. No significant differences were found between the results of network real-time kinematic (NRTK) and real-time kinematic (RTK) datasets. Horizontal residuals were generally comparable to GNSS accuracy in NRTK/RTK mode, while vertical residuals were found to be affected by an offset of about 5 cm. We introduced an external GCP or used one SP per façade as GCP, assuming a poorer camera location accuracy at the same time, in order to fix this issue and comply with metric survey specifications for the widest architectural scale range. Finally, both S–F and 4–F projects satisfied the metric survey requirements of a scale of 1:50 in at least one of the approaches tested.

Here, we present the draft genome sequence of Komagatabaeicter rhaeticus strain AF1, which was isolated from Kombucha tea and is capable of producing high levels of cellulose.

Background The increasing amounts of genomics data have helped in the understanding of the molecular dynamics of complex systems such as plant and animal diseases. However, transcriptional regulation, although playing a central role in the decision-making process of cellular systems, is still poorly understood. In this study, we linked expression data with mathematical models to infer gene regulatory networks (GRN). We present a simple yet effective method to estimate transcription factors’ GRNs from transcriptional data. Method We defined interactions between pairs of genes (edges in the GRN) as the partial mutual information between these genes that takes into account time and possible lags in time from one gene in relation to another. We call this method Gene Regulatory Networks on Transfer Entropy (GRNTE) and it corresponds to Granger causality for Gaussian variables in an autoregressive model. To evaluate the reconstruction accuracy of our method, we generated several sub-networks from the GRN of the eukaryotic yeast model, Saccharomyces cerevisae . Then, we applied this method using experimental data of the plant pathogen Phytophthora infestans . We evaluated the transcriptional expression levels of 48 transcription factors of P. infestans during its interaction with one moderately resistant and one susceptible cultivar of yellow potato ( Solanum tuberosum group Phureja), using RT-qPCR . With these data, we reconstructed the regulatory network of P. infestans during its interaction with these hosts. Results We first evaluated the performance of our method, based on the transfer entropy (GRNTE), on eukaryotic datasets from the GRNs of the yeast S. cerevisae. Results suggest that GRNTE is comparable with the state-of-the-art methods when the parameters for edge detection are properly tuned. In the case of P. infestans, most of the genes considered in this study, showed a significant change in expression from the onset of the interaction (0 h post inoculum - hpi) to the later time-points post inoculation. Hierarchical clustering of the expression data discriminated two distinct periods during the infection: from 12 to 36 hpi and from 48 to 72 hpi for both the moderately resistant and susceptible cultivars. These distinct periods could be associated with two phases of the life cycle of the pathogen when infecting the host plant: the biotrophic and necrotrophic phases. Conclusions Here we presented an algorithmic solution to the problem of network reconstruction in time series data. This analytical perspective makes use of the dynamic nature of time series data as it relates to intrinsically dynamic processes such as transcription regulation, were multiple elements of the cell (e.g., transcription...

Here, we present the draft genome sequence of Komagataeibacter intermedius strain AF2, which was isolated from Kombucha tea and is capable of producing cellulose, although at lower levels compared to another bacterium from the same environment, K. rhaeticus strain AF1.