Extracting Axial Depth and Trajectory Trend Using Astigmatism, Gaussian Fitting, and CNNs for Protein Tracking

Accurate analysis of vesicle trafficking in live cells is challenging for a number of reasons: varying appearance, complex protein movement patterns, and imaging conditions. To allow fast image acquisition, we study how employing an astigmatism can be utilized for obtaining additional information that could make tracking more robust. We present two approaches for measuring the z position of individual vesicles. Firstly, Gaussian curve fitting with CNN-based denoising is applied to infer the absolute depth around the focal plane of each localized protein. We demonstrate that adding denoising yields more accurate estimation of depth while preserving the overall structure of the localized proteins. Secondly, we investigate if we can predict using a custom CNN architecture the axial trajectory trend. We demonstrate that this method performs well on calibration beads data without the need for denoising. By incorporating the obtained depth information into a trajectory analysis, we demonstrate the potential improvement in vesicle tracking

lncRNA requirements for mouse acute myeloid leukemia and normal differentiation

A substantial fraction of the genome is transcribed in a cell type-specific manner, producing long non-coding RNAs (lncRNAs), rather than protein-coding transcripts. Here we systematically characterize transcriptional dynamics during hematopoiesis and in hematological malignancies. Our analysis of annotated and de novo assembled lncRNAs showed many are regulated during differentiation and mis-regulated in disease. We assessed lncRNA function via an in vivo RNAi screen in a model of acute myeloid leukemia. This identified several lncRNAs essential for leukemia maintenance, and found that a number act by promoting leukemia stem cell signatures. Leukemia blasts show a myeloid differentiation phenotype when these lncRNAs were depleted, and our data indicates that this effect is mediated via effects on the c-MYC oncogene. Bone marrow reconstitutions showed that a lncRNA expressed across all progenitors was required for the myeloid lineage, whereas the other leukemia-induced lncRNAs were dispensable in the normal setting

A digital intake approach in specialized mental health care : study protocol of a cluster randomised controlled trial

Background: Enhancing patient participation is becoming increasingly important in mental health care as patients use to have a dependent, inactive role and nonadherence to treatment is a regular problem. Research shows promising results of initiatives stimulating patient participation in partnership with their clinicians. However, few initiatives targeting both patients’ and clinicians’ behaviour have been evaluated in randomised trials (RCT). Therefore, in GGz Breburg, a specialized mental health institution, a digital intake approach was developed aimed at exploring treatment needs, expectations and preferences of patients intended to prepare patients for the intake consultations. Subsequently, patients and clinicians discuss this information during intake consultations and make shared decisions about options in treatment. The aim of this trial is to test the efficacy of this new digital intake approach facilitated by Routine Outcome Monitoring (ROM), peer support and training of clinicians as compared to the intake as usual. The primary outcome is decisional conflict about choices in treatment. Secondary outcomes focus on patient participation, shared decision making, working alliance, adherence to treatment and clinical outcomes. Methods: This article presents the study protocol of a cluster-randomised controlled trial in four outpatient departments for adults with depression, anxiety and personality disorders, working in two different regions. Randomisation is done between two similar intake-teams within each department. In the four intervention teams the new intake approach is implemented. The four control teams apply the intake as usual and will implement the new approach after the completion of the study. In total 176 patients are projected to participate in the study. Data collection will be at baseline, and at two weeks and two months after the intake. Discussion: This study will potentially demonstrate the efficacy of the new digital intake approach in mental health care in terms of the primary outcome the degree of decisional conflict about choices in treatment. The findings of this study may contribute to the roll out of such eHealth initiatives fostering patient involvement in decision making about their treatment

THE ROLE OF MINERAL NUTRITION ON YIELDS AND FRUIT QUALITY IN GRAPEVINE, PEAR AND APPLE

ABSTRACT Fertilization of temperate fruit trees, such as grapevine ( Vitis spp.), apple ( Malus domestica), and pear ( Pyrus communis) is an important tool to achive maximum yield and fruit quality. Fertilizers are provided when soil fertility does not allow trees to express their genetic potential, and time and rate of application should be scheduled to promote fruit quality. Grapevine berries, must and wine quality are affected principally by N, that regulate the synthesis of some important compounds, such as anthocyanins, which are responsible for coloring of the must and the wine. Fermenation of the must may stop in grapes with low concentration of N because N is requested in high amount by yeasts. An N excess may increase the pulp to peel ratio, diluting the concentration of anthocyanins and promoting the migration of anthocyanins from berries to the growing plant organs; a decrease of grape juice soluble solid concentration is also expected because of an increase in vegetative growth. Potassium is also important for wine quality contributing to adequate berry maturation, concentration of sugars, synthesis of phenols and the regulation of pH and acidity. In apple and pear, Ca and K are important for fruit quality and storage. Potassium is the most important component of fruit, however, any excess should be avoided and an adequate K:Ca balance should be achieved. Adequate concentration of Ca in the fruit prevents pre- and post-harvest fruit disorders and, at the same time, increases tolerance to pathogens. Although N promotes adequate growth soil N availability should be monitored to avoid excessive N uptake that may decrease fruit skin color and storability