A crowdsourced set of curated structural variants for the human genome.

A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs) is more challenging. In this study, we manually curated 1235 SVs, which can ultimately be used to evaluate SV callers or train machine learning models. We developed a crowdsourcing app-SVCurator-to help GIAB curators manually review large indels and SVs within the human genome, and report their genotype and size accuracy. SVCurator displays images from short, long, and linked read sequencing data from the GIAB Ashkenazi Jewish Trio son [NIST RM 8391/HG002]. We asked curators to assign labels describing SV type (deletion or insertion), size accuracy, and genotype for 1235 putative insertions and deletions sampled from different size bins between 20 and 892,149 bp. 'Expert' curators were 93% concordant with each other, and 37 of the 61 curators had at least 78% concordance with a set of 'expert' curators. The curators were least concordant for complex SVs and SVs that had inaccurate breakpoints or size predictions. After filtering events with low concordance among curators, we produced high confidence labels for 935 events. The SVCurator crowdsourced labels were 94.5% concordant with the heuristic-based draft benchmark SV callset from GIAB. We found that curators can successfully evaluate putative SVs when given evidence from multiple sequencing technologies.

Novel, whisker-dependent texture discrimination task for mice.

Many mammals use their mystacial vibrissae to palpate objects in their environment and encode information such as size, shape and texture. We have developed a novel method to assess the sensitivity with which mice can discriminate textures using their mystacial vibrissae. Our texture discrimination task can be performed within 3 days, requiring approximately 1 h of handling time, per subject, over the entire testing period. No appetitive or aversive training is required. We have demonstrated that this novel texture discrimination task is dependent on intact mystacial vibrissae and can be performed by both young (2-month old) and older (6-month old) C57BL/6 mice. The parameters of the task can be adjusted to assess the sensitivity of mice using a gradient of textures with different roughness. We have developed a novel, efficient method to assess whisker-mediated texture discrimination in mice.

Increased mobility and stem-cell proliferation rate in Dugesia tigrina induced by 880nm light emitting diode.

The therapeutic effects elicited by photobiostimulation in the near infrared range may be associated with increased proliferation rate of particular cell-types. The present study utilized commercial light emitting diodes to investigate the effects of low-level near-infrared radiation on the proliferation rate of stem cells in amputated planarian. Whole and amputated animals were exposed to either ambient diurnal lighting, darkness, white light, red light, or near-infrared (880 nm) light. Irradiation was consistent for the duration of the experiments and was provided using commercial 5mm light emitting diodes (∼1.0 mW/m(2) in power density and ∼0.01 J/cm(2) in radiant exposure). Compared to other groups amputated planarian exposed to near-infrared displayed increased mobility by the 3rd day of exposure (F((4,26))=4.31, p<0.04, η(2)=41%). Higher densities of stem cells were measured in these worms 84 h post injury (F((4,72))=4.78, p<0.01, η(2)=21%). These findings suggest that non-coherent light sources with power-densities about 1000 times lower than contemporary low-power laser settings remain effective in generating photobiostimulation effects and warrants further investigation on stem-cell proliferation induced by near-infrared light emitting diodes.