The Future of OA A large-scale analysis projecting Open Access publication and readership, bioRxiv, 2019-10-09
Understanding the growth of open access (OA) is important for deciding funder policy, subscription allocation, and infrastructure planning. This study analyses the number of papers available as OA over time. The models includes both OA embargo data and the relative growth rates of different OA types over time, based on the OA status of 70 million journal articles published between 1950 and 2019. The study also looks at article usage data, analyzing the proportion of views to OA articles vs views to articles which are closed access. Signal processing techniques are used to model how these viewership patterns change over time. Viewership data is based on 2.8 million uses of the Unpaywall browser extension in July 2019. We found that Green, Gold, and Hybrid papers receive more views than their Closed or Bronze counterparts, particularly Green papers made available within a year of publication. We also found that the proportion of Green, Gold, and Hybrid articles is growing most quickly. In 2019- 31% of all journal articles are available as OA. - 52% of article views are to OA articles. Given existing trends, we estimate that by 2025 - 44% of all journal articles will be available as OA. - 70% of article views will be to OA articles. The declining relevance of closed access articles is likely to change the landscape of scholarly communication in the years to come.
biorxiv scientific-communication-and-education 200-500-users 2019A proximity biotinylation map of a human cell, bioRxiv, 2019-10-08
Compartmentalization is an essential characteristic of eukaryotic cells, ensuring that cellular processes are partitioned to defined subcellular locations. High throughput microscopy1 and biochemical fractionation coupled with mass spectrometry2-6 have helped to define the proteomes of multiple organelles and macromolecular structures. However, many compartments have remained refractory to such methods, partly due to lysis and purification artefacts and poor subcompartment resolution. Recently developed proximity-dependent biotinylation approaches such as BioID and APEX provide an alternative avenue for defining the composition of cellular compartments in living cells (e.g. 7-10). Here we report an extensive BioID-based proximity map of a human cell, comprising 192 markers from 32 different compartments that identifies 35,902 unique high confidence proximity interactions and localizes 4,145 proteins expressed in HEK293 cells. The recall of our localization predictions is on par with or better than previous large-scale mass spectrometry and microscopy approaches, but with higher localization specificity. In addition to assigning compartment and subcompartment localization for many previously unlocalized proteins, our data contain fine-grained localization information that, for example, allowed us to identify proteins with novel roles in mitochondrial dynamics. As a community resource, we have created humancellmap.org, a website that allows exploration of our data in detail, and aids with the analysis of BioID experiments.
biorxiv molecular-biology 200-500-users 2019Natural image reconstruction from brain waves a novel visual BCI system with native feedback, bioRxiv, 2019-10-02
AbstractHere we hypothesize that observing the visual stimuli of different categories trigger distinct brain states that can be decoded from noninvasive EEG recordings. We introduce an effective closed-loop BCI system that reconstructs the observed or imagined stimuli images from the co-occurring brain wave parameters. The reconstructed images are presented to the subject as a visual feedback. The developed system is applicable to training BCI-naïve subjects because of the user-friendly and intuitive way the visual patterns are employed to modify the brain states.
biorxiv neuroscience 200-500-users 2019Molecular Cross-Validation for Single-Cell RNA-seq, bioRxiv, 2019-10-01
Single-cell RNA sequencing enables researchers to study the gene expression of individual cells. However, in high-throughput methods the portrait of each individual cell is noisy, representing thousands of the hundreds of thousands of mRNA molecules originally present. While many methods for denoising single-cell data have been proposed, a principled procedure for selecting and calibrating the best method for a given dataset has been lacking. We present “molecular cross-validation,” a statistically principled and data-driven approach for estimating the accuracy of any denoising method without the need for ground-truth. We validate this approach for three denoising methods—principal component analysis, network diffusion, and a deep autoencoder—on a dataset of deeply-sequenced neurons. We show that molecular cross-validation correctly selects the optimal parameters for each method and identifies the best method for the dataset.
biorxiv bioinformatics 200-500-users 2019Molecular Atlas of the Adult Mouse Brain, bioRxiv, 2019-09-28
AbstractBrain maps are essential for integrating information and interpreting the structure-function relationship of circuits and behavior. We aimed to generate a systematic classification of the adult mouse brain organization based on unbiased extraction of spatially-defining features. Applying whole-brain spatial transcriptomics, we captured the gene expression signatures to define the spatial organization of molecularly discrete subregions. We found that the molecular code contained sufficiently detailed information to directly deduce the complex spatial organization of the brain. This unsupervised molecular classification revealed new area- and layer-specific subregions, for example in isocortex and hippocampus, and a new division of striatum. The whole-brain molecular atlas further supports the identification of the spatial origin of single neurons using their gene expression profile, and forms the foundation to define a minimal gene set - a brain palette – that is sufficient to spatially annotate the adult brain. In summary, we have established a new molecular atlas to formally define the identity of brain regions, and a molecular code for mapping and targeting of discrete neuroanatomical domains.
biorxiv neuroscience 200-500-users 2019Hackflex low cost Illumina sequencing library construction for high sample counts, bioRxiv, 2019-09-23
ABSTRACTWe developed Hackflex, a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 11 times more libraries for high-throughput Illumina sequencing to be generated at a fixed cost. We call this new method Hackflex. Quality of library preparation was tested by constructing libraries from E. coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. We demonstrated that Hackflex can produce high quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. Using Hackflex, we were able to achieve a per sample reagent cost of library prep of A$8.66, which is 8.23 times lower than the Standard Nextera Flex protocol at advertised retail price. An additional simple modification to the protocol enables a further price reduction of up to 11 fold or about A$6.50sample. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programs where sequencing large numbers of libraries is beneficial.
biorxiv genomics 200-500-users 2019