Biology subjects

Lai, S.

Publications and source records attributed to Lai, S..

45 records · Page 3Linked to original sources

bioRxiv2019

FoxMask: a new automated tool for animal detection in camera trap images

O_LICamera traps now represent a reliable, efficient and cost-effective technique to monitor wildlife and collect biological data in the field. However, efficiently extracting information from the massive amount of images generated is often extremely time-consuming and may now represent the most rate-limiting step in camera trap studies.\nC_LIO_LITo help overcome this challenge, we developed FoxMask, a new tool performing the automatic detection of animal presence in short sequences of camera trap images. FoxMask uses background estimation and foreground segmentation algorithms to detect the presence of moving objects (most likely, animals) on images.\nC_LIO_LIWe analyzed a sample dataset from camera traps used to monitor activity on arctic fox Vulpes lagopus dens to test the parameter settings and the performance of the algorithm. The shape and color of arctic foxes, their background at snowmelt and during the summer growing season were highly variable, thus offering challenging testing conditions. We compared the automated animal detection performed by FoxMask to a manual review of the image series.\nC_LIO_LIThe performance analysis indicated that the proportion of images correctly classified by FoxMask as containing an animal or not was very high (> 90%). FoxMask is thus highly efficient at reducing the workload by eliminating most false triggers (images without an animal). We provide parameter recommendations to facilitate usage and we present the cases where the algorithm performs less efficiently to stimulate further development.\nC_LIO_LIFoxMask is an easy-to-use tool freely available to ecologists performing camera trap data extraction. By minimizing analytical time, computer-assisted image analysis will allow collection of increased sample sizes and testing of new biological questions.\nC_LI

ecology↗

bioRxiv2019

Tracking progress towards malaria elimination in China: estimates of reproduction numbers and their spatiotemporal variation

China reported zero locally-acquired malaria cases in 2017 and 2018. Understanding the spatio-temporal pattern underlying this decline, especially the relationship between locally-acquired and imported cases, can inform efforts to maintain elimination and prevent re-emergence. This is particularly pertinent in Yunnan province, where the potential for local transmission is highest. Using a geo-located individual-level dataset of cases recorded in Yunnan province between 2011 and 2016, we jointly estimate the case reproduction number, Rc, and the number of unobserved sources of infection. We use these estimates within spatio-temporal geostatistical models to map how transmission varied over time and space, estimate the timeline to elimination and the risk of resurgence. Our estimates suggest that, maintaining current intervention efforts, Yunnan is unlikely to experience sustained local transmission up to 2020. However, even with a mean Rc of 0.005 projected for the year 2019, locally-acquired cases are possible due to high levels of importation.

epidemiology↗

bioRxiv2019

Rehabilitation promotes the recovery of structural and functional features of healthy neuronal networks after stroke

Rehabilitation is the most effective treatment for promoting the recovery of motor deficits after stroke. One of the most challenging experimental goals is to unambiguously link brain rewiring to motor recovery prompted by rehabilitative therapy. Here, we investigated which aspects of cortical remodeling are induced by rehabilitation by combining optical imaging and manipulation tools in a mouse model of stroke. We revealed that the stabilization of peri-infarct synaptic contacts fostered by rehabilitation goes along with increased vascular density induced by angiogenesis. Furthermore, we showed the progressive formation of a new motor representation in the peri-infarct area where temporal and spatial features of cortical activation recovered towards pre-stroke condition. In the same animals we observed the reinforcement of inter-hemispheric connectivity after rehabilitation. The present work provides the first evidences that rehabilitation promotes the combined recovery of structural and functional features distinctive of healthy neuronal networks.

neuroscience↗

bioRxiv2018

Antibody-mediated immobilization of virions in mucus

Antibodies have been shown to hinder the movement of Herpes Simplex Virus (HSV) virions in cervicovaginal mucus (CVM), as well as other viruses in other mucus secretions. However, it has not been possible to directly observe the mechanisms underlying this phenomenon, so the nature of virion-antibody-mucin interactions remain poorly understood. In this work, we analyzed thousands of virion traces from single particle tracking experiments to explicate how antibodies must cooperate to immobilize virions for relatively long time periods. First, using a clustering analysis, we observed a clear separation between two classes of virion behavior: Freely Diffusing and Immobilized. While the proportion of Freely Diffusing virions decreased with antibody concentration, the magnitude of their diffusivity did not, implying an all-or-nothing dichotomy in the pathwise effect of the antibodies. Proceeding under the assumption that all binding events are reversible, we used a novel switch-point detection method to conclude that there are very few, if any, state-switches on the experimental time scale of twenty seconds. To understand this slow state-switching, we analyzed a recently proposed continuous-time Markov chain model for binding kinetics and virion movement. Model analysis implied that virion immobilization requires cooperation by multiple antibodies that are simultaneously bound to the virion and mucin matrix, and that there is an entanglement phenomenon that accelerates antibody-mucin binding when a virion is immobilized. In addition to developing a widely-applicable framework for analyzing multi-state particle behavior, this work substantially enhances our mechanistic understanding of how antibodies can reinforce a mucus barrier against passive invasive species.

immunology↗

bioRxiv2018

Phylogenetic relationships in the genus Avena based on the nuclear Pgk1 gene

The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 3-phosphoglycerate kinase gene(pgk1). A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a major structural divergence between the A and C genomes. Phylogenetic analysis indicated the Cp genome is more closely related to the polyploid species than is the Cv genome. Two haplotypes of pgk1 gene were obtained from most of the AB genome tetraploids. Both types of the barbata group showed a close relationship with the As genome diploid species, supporting the hypothesis that both the A and B genomes are derived from an As genome. Two haplotypes were also detected in A. agadiriana, which showed close relationships with the As genome diploid and the Ac genome diploid, respectively, emphasizing the important role of the Ac genome in the evolution of A. agadiriana. Three homoeologues of thepgK1 gene were detected in five hexaploid accessions. The homoeologues that might represent the D genome were tightly clustered with the tetraploids A. marrocana and A. murphyi, but did not show a close relationship with any extant diploid species.

evolutionary biology↗

bioRxiv2018

Inter-annual variation in seasonal dengue epidemics driven bymultiple interacting factors in Guangzhou, China

Vector-borne diseases display wide inter-annual variation in seasonal epidemic size due to their complex dependence on temporally variable environmental conditions and other factors. In 2014, Guangzhou, China experienced its worst dengue epidemic on record, with incidence exceeding the historical average by two orders of magnitude. To disentangle contributions from multiple factors to inter-annual variation in epidemic size, we fitted a semi-mechanistic model to time series data from 2005-2015 and performed a series of factorial simulation experiments in which seasonal epidemics were simulated under all combinations of year-specific patterns of four time-varying factors: imported cases, mosquito density, temperature, and residual variation in local conditions not explicitly represented in the model. Our results indicate that while epidemics in most years were limited by unfavorable conditions with respect to one or more factors, the epidemic in 2014 was made possible by the combination of favorable conditions for all factors considered in our analysis.

epidemiology↗

bioRxiv2017

Changing geographic patterns and risk factors for avian influenza A(H7N9) infection in China

The 5th epidemic wave in 2016-2017 of avian influenza A(H7N9) virus in China caused more human cases than any previous waves but the factors that may explain the recent range expansion and surge in incidence remain unknown. We investigated the effect of anthropogenic, poultry and wetland information and of market closures on all epidemic waves (1-5). Poultry predictor variables recently became much more important than before, supporting the assumption of much wider H7N9 transmission in the chicken reservoir, that could be linked to increases in pathogenicity. We show that the future range expansion of H7N9 to northern China may translate into a higher risk of coinciding peaks with those of seasonal influenza, leading to a higher risk of reassortments. Live-poultry market closures are showed to be effective in reducing the local incidence rates of H7N9 human cases, but should be paired with other prevention and control measures to prevent transmission.

epidemiology↗

bioRxiv2017

Rehabilitation Restores Cortical Activation Profiles And Stabilizes Synaptic Contacts After Stroke

Rehabilitation is the most effective treatment for promoting the recovery of motor deficits after stroke. Despite its importance, the processes associated with rehabilitative intervention are poorly understood. One of the most challenging experimental goals is to unambiguously link specific circuit changes induced by rehabilitation to improved behavior. Here, we investigate which facets of cortical remodeling are induced by rehabilitation by combining optical imaging and manipulation tools in a mouse model of stroke. We demonstrate the progressive restoration of cortical motor maps and of cortical activity in parallel with the reinforcement of inter-hemispheric connectivity after rehabilitation. Furthermore, we reveal that the increase in vascular density goes along with the stabilization of peri-infarct neural circuitry at synaptic level. The present work provides the first evidences that rehabilitation is sufficient to promote the combined recovery of distinct structural and functional features distinctive of healthy neuronal networks.

neuroscience↗

bioRxiv2017

Mapping Human Hematopoietic Hierarchy At Single Cell Resolution By Microwell-seq

The classical hematopoietic hierarchy, which is mainly built with fluorescence-activated cell sorting (FACS) technology, proves to be inaccurate in recent studies. Single cell RNA-seq (scRNA-seq) analysis provides a solution to overcome the limit of FACS-based cell type definition system for the dissection of complex cellular hierarchy. However, large-scale scRNA-seq is constrained by the throughput and cost of traditional methods. Here, we developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using extremely simple devices. Using Microwell-seq, we constructed a single-cell resolution transcriptome atlas of human hematopoietic differentiation hierarchy by profiling more than 50,000 single cells throughout adult human hematopoietic system. We found that adult human hematopoietic stem and progenitor cell (HSPC) compartment is dominated by progenitors primed with lineage specific regulators. Our analysis revealed differentiation pathways for each cell types, through which HSPCs directly progress to lineage biased progenitors before differentiation. We propose a revised adult human hematopoietic hierarchy independent of oligopotent progenitors. Our study also demonstrates the broad applicability of Microwell-seq technology.

cell biology↗