Bioimage informatics in the context of drosophila research

Modern biological research relies heavily on microscopic imaging. The advanced genetic toolkit of drosophila makes it possible to label molecular and cellular components with unprecedented level of specificity necessitating the application of the most sophisticated imaging technologies. Imaging in drosophila spans all scales from single molecules to the entire populations of adult organisms, from electron microscopy to live imaging of developmental processes. As the imaging approaches become more complex and ambitious, there is an increasing need for quantitative, computer-mediated image processing and analysis to make sense of the imagery. Bioimage informatics is an emerging research field that covers all aspects of biological image analysis from data handling, through processing, to quantitative measurements, analysis and data presentation. Some of the most advanced, large scale projects, combining cutting edge imaging with complex bioimage informatics pipelines, are realized in the drosophila research community. In this review, we discuss the current research in biological image analysis specifically relevant to the type of systems level image datasets that are uniquely available for the drosophila model system. We focus on how state-of-the-art computer vision algorithms are impacting the ability of drosophila researchers to analyze biological systems in space and time. We pay particular attention to how these algorithmic advances from computer science are made usable to practicing biologists through open source platforms and how biologists can themselves participate in their further development

ImgLib2-generic image processing in Java

Summary: ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins

Impact evaluation of different cash-based intervention modalities on child and maternal nutritional status in Sindh Province, Pakistan, at 6 mo and at 1 y: A cluster randomised controlled trial

BACKGROUND: Cash-based interventions (CBIs), offer an interesting opportunity to prevent increases in wasting in humanitarian aid settings. However, questions remain as to the impact of CBIs on nutritional status and, therefore, how to incorporate them into emergency programmes to maximise their success in terms of improved nutritional outcomes. This study evaluated the effects of three different CBI modalities on nutritional outcomes in children under 5 y of age at 6 mo and at 1 y. METHODS AND FINDINGS: We conducted a four-arm parallel longitudinal cluster randomised controlled trial in 114 villages in Dadu District, Pakistan. The study included poor and very poor households (n = 2,496) with one or more children aged 6–48 mo (n = 3,584) at baseline. All four arms had equal access to an Action Against Hunger–supported programme. The three intervention arms were as follows: standard cash (SC), a cash transfer of 1,500 Pakistani rupees (PKR) (approximately US$14; 1 PKR = US$0.009543); double cash (DC), a cash transfer of 3,000 PKR; or a fresh food voucher (FFV) of 1,500 PKR; the cash or voucher amount was given every month over six consecutive months. The control group (CG) received no specific cash-related interventions. The median total household income for the study sample was 8,075 PKR (approximately US$77) at baseline. We hypothesized that, compared to the CG in each case, FFVs would be more effective than SC, and that DC would be more effective than SC—both at 6 mo and at 1 y—for reducing the risk of child wasting. Primary outcomes of interest were prevalence of being wasted (weight-for-height z-score [WHZ] < −2) and mean WHZ at 6 mo and at 1 y. The odds of a child being wasted were significantly lower in the DC arm after 6 mo (odds ratio [OR] = 0.52; 95% CI 0.29, 0.92; p = 0.02) compared to the CG. Mean WHZ significantly improved in both the FFV and DC arms at 6 mo (FFV: z-score = 0.16; 95% CI 0.05, 0.26; p = 0.004; DC: z-score = 0.11; 95% CI 0.00, 0.21; p = 0.05) compared to the CG. Significant differences on the primary outcome were seen only at 6 mo. All three intervention groups showed similar significantly lower odds of being stunted (height-for-age z-score [HAZ] < −2) at 6 mo (DC: OR = 0.39; 95% CI 0.24, 0.64; p < 0.001; FFV: OR = 0.41; 95% CI 0.25, 0.67; p < 0.001; SC: OR = 0.36; 95% CI 0.22, 0.59; p < 0.001) and at 1 y (DC: OR = 0.53; 95% CI 0.35, 0.82; p = 0.004; FFV: OR = 0.48; 95% CI 0.31, 0.73; p = 0.001; SC: OR = 0.54; 95% CI 0.36, 0.81; p = 0.003) compared to the CG. Significant improvements in height-for-age outcomes were also seen for severe stunting (HAZ < −3) and mean HAZ. An unintended outcome was observed in the FFV arm: a negative intervention effect on mean haemoglobin (Hb) status (−2.6 g/l; 95% CI −4.5, −0.8; p = 0.005). Limitations of this study included the inability to mask participants or data collectors to the different interventions, the potentially restrictive nature of the FFVs, not being able to measure a threshold effect for the two different cash amounts or compare the different quantities of food consumed, and data collection challenges given the difficult environment in which this study was set. CONCLUSIONS: In this setting, the amount of cash given was important. The larger cash transfer had the greatest effect on wasting, but only at 6 mo. Impacts at both 6 mo and at 1 y were seen for height-based growth variables regardless of the intervention modality, indicating a trend toward nutrition resilience. Purchasing restrictions applied to food-based voucher transfers could have unintended effects, and their use needs to be carefully planned to avoid this

Topoisomerase II inhibitors induce DNA damage-dependent interferon responses circumventing Ebola virus immune evasion

Ebola virus (EBOV) protein VP35 inhibits production of interferon alpha/beta (IFN) by blocking RIG-I-like receptor signaling pathways, thereby promoting virus replication and pathogenesis. A high-throughput screening assay, developed to identify compounds that either inhibit or bypass VP35 IFN-antagonist function, identified five DNA intercalators as reproducible hits from a library of bioactive compounds. Four, including doxorubicin and daunorubicin, are anthracycline antibiotics that inhibit topoisomerase II and are used clinically as chemotherapeutic drugs. These compounds were demonstrated to induce IFN responses in an ATM kinase-dependent manner and to also trigger the DNA-sensing cGAS-STING pathway of IFN induction. These compounds also suppress EBOV replication in vitro and induce IFN in the presence of IFN-antagonist proteins from multiple negative-sense RNA viruses. These findings provide new insights into signaling pathways activated by important chemotherapy drugs and identify a novel therapeutic approach for IFN induction that may be exploited to inhibit RNA virus replication

Magnetic Scanning Tunneling Microscopy with a Two-Terminal Non-Magnetic Tip: Quantitative Results

We report numerical simulation result of a recently proposed \{P. Bruno, Phys. Rev. Lett {\bf 79}, 4593, (1997)\} approach to perform magnetic scanning tunneling microscopy with a two terminal non-magnetic tip. It is based upon the spin asymmetry effect of the tunneling current between a ferromagnetic surface and a two-terminal non-magnetic tip. The spin asymmetry effect is due to the spin-orbit scattering in the tip. The effect can be viewed as a Mott scattering of tunneling electrons within the tip. To obtain quantitative results we perform numerical simulation within the single band tight binding model, using recursive Green function method and Landauer-B\"uttiker formula for conductance. A new model has been developed to take into account the spin-orbit scattering off the impurities within the single-band tight-binding model. We show that the spin-asymmetry effect is most prominent when the device is in quasi-ballistic regime and the typical value of spin asymmetry is about 5%.Comment: 5 pages, Late

Insights from Multimodal Preclinical Imaging in Immunocompetent Nude Mice

Hydrogels based on gelatin have evolved as promising multifunctional biomaterials. Gelatin is crosslinked with lysine diisocyanate ethyl ester (LDI) and the molar ratio of gelatin and LDI in the starting material mixture determines elastic properties of the resulting hydrogel. In order to investigate the clinical potential of these biopolymers, hydrogels with different ratios of gelatin and diisocyanate (3-fold (G10_LNCO3) and 8-fold (G10_LNCO8) molar excess of isocyanate groups) were subcutaneously implanted in mice (uni- or bilateral implantation). Degradation and biomaterial-tissue- interaction were investigated in vivo (MRI, optical imaging, PET) and ex vivo (autoradiography, histology, serum analysis). Multimodal imaging revealed that the number of covalent net points correlates well with degradation time, which allows for targeted modification of hydrogels based on properties of the tissue to be replaced. Importantly, the degradation time was also dependent on the number of implants per animal. Despite local mechanisms of tissue remodeling no adverse tissue responses could be observed neither locally nor systemically. Finally, this preclinical investigation in immunocompetent mice clearly demonstrated a complete restoration of the original healthy tissue