Using demographics toward efficient data classification in citizen science: a Bayesian approach

Public participation in scientific activities, often called citizen science, offers a possibility to collect and analyze an unprecedentedly large amount of data. However, diversity of volunteers poses a challenge to obtain accurate information when these data are aggregated. To overcome this problem, we propose a classification algorithm using Bayesian inference that harnesses diversity of volunteers to improve data accuracy. In the algorithm, each volunteer is grouped into a distinct class based on a survey regarding either their level of education or motivation to citizen science. We obtained the behavior of each class through a training set, which was then used as a prior information to estimate performance of new volunteers. By applying this approach to an existing citizen science dataset to classify images into categories, we demonstrate improvement in data accuracy, compared to the traditional majority voting. Our algorithm offers a simple, yet powerful, way to improve data accuracy under limited effort of volunteers by predicting the behavior of a class of individuals, rather than attempting at a granular description of each of them

The role of social attraction and its link with boldness in the collective movements of three-spined sticklebacks.

Social animals must time and coordinate their behaviour to ensure the benefits of grouping, resulting in collective movements and the potential emergence of leaders and followers. However, individuals often differ consistently from one another in how they cope with their environment, a phenomenon known as animal personality, which may affect how individuals use coordination rules and requiring them to compromise. Here we tracked the movements of pairs of three-spined sticklebacks, Gasterosteus aculeatus, separated by a transparent partition that allowed them to observe and interact with one another in a context containing cover. Individuals differed consistently in their tendency to approach their partner's compartment during collective movements. The strength of this social attraction was positively correlated with the behavioural coordination between members of a pair but was negatively correlated with an individual's tendency to lead. Social attraction may form part of a broader behavioural syndrome as it was predicted by the boldness of an individual, measured in isolation prior to the observation of pairs, and by the boldness of the partner. We found that bolder fish, and those paired with bolder partners, tended to approach their partner's compartment less closely. These findings provide important insights into the mechanisms that govern the dynamics and functioning of social groups and the emergence and maintenance of consistent behavioural differences.This study was supported by a BBSRC scholarship to J.W.J. and a fellowship from the Humboldt-Universit€at zu Berlin Postdoc Fellowship under the Excellence of Initiative to S.N.This is the final published version. It first appeared at http://www.sciencedirect.com/science/article/pii/S000334721400414X#

Comparing spatial patterns of marine vessels between vessel-tracking data and satellite imagery

Monitoring marine use is essential to effective management but is extremely challenging, particularly where capacity and resources are limited. To overcome these limitations, satellite imagery has emerged as a promising tool for monitoring marine vessel activities that are difficult to observe through publicly available vessel-tracking data. However, the broader use of satellite imagery is hindered by the lack of a clear understanding of where and when it would bring novel information to existing vessel-tracking data. Here, we outline an analytical framework to (1) automatically detect marine vessels in optical satellite imagery using deep learning and (2) statistically contrast geospatial distributions of vessels with the vessel-tracking data. As a proof of concept, we applied our framework to the coastal regions of Peru, where vessels without the Automatic Information System (AIS) are prevalent. Quantifying differences in spatial information between disparate datasets—satellite imagery and vessel-tracking data—offers insight into the biases of each dataset and the potential for additional knowledge through data integration. Our study lays the foundation for understanding how satellite imagery can complement existing vessel-tracking data to improve marine oversight and due diligence

Initiative, Personality and Leadership in Pairs of Foraging Fish

Studies of coordinated movement have found that, in many animal species, bolder individuals are more likely to initiate movement and shyer individuals to follow. Here, we show that in pairs of foraging stickleback fish, leadership is not merely a passive consequence of temperamental differences. Instead, the act of initiating a joint foraging trip out of cover itself brings about a change in the role that an individual plays throughout the subsequent trip, and success in recruiting a partner affects an individual's tendency to initiate the next trip. On each joint trip, whichever fish took the initiative in leading out of cover gains greater influence over its partner's behaviour, which persists even after several changes in position (i.e. termination attempts and re-joining). During any given trip, the initiator is less responsive to its partner's movements than during trips initiated by the partner. An individual's personality had an important effect on its response to failure to recruit a partner: while bold fish were unaffected by failures to initiate a joint trip, shy individuals were less likely to attempt another initiation after a failure. This difference provides a positive feedback mechanism that can partially stabilise social roles within the pair, but it is not strong enough to prevent occasional swaps, with individuals dynamically adjusting their responses to one another as they exchange roles

Rights and representation support justice across aquatic food systems

Injustices are prevalent in food systems, where the accumulation of vast wealth is possible for a few, yet one in ten people remain hungry. Here, for 194 countries we combine aquatic food production, distribution and consumption data with corresponding national policy documents and, drawing on theories of social justice, explore whether barriers to participation explain unequal distributions of benefits. Using Bayesian models, we find economic and political barriers are associated with lower wealth-based benefits; countries produce and consume less when wealth, formal education and voice and accountability are lacking. In contrast, social barriers are associated with lower welfare-based benefits; aquatic foods are less affordable where gender inequality is greater. Our analyses of policy documents reveal a frequent failure to address political and gender-based barriers. However, policies linked to more just food system outcomes centre principles of human rights, specify inclusive decision-making processes and identify and challenge drivers of injustice

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

Intraspecific competition among early life stages and the optimal spawning strategy of red drum (Sciaenops ocellatus)

textThis collection of studies was designed to understand the mechanisms and consequences of competition among early life stages of red drum (Sciaenops ocellatus), with a special attention to asymmetric competition and multiple-breeding strategy of parents. The overall hypotheses were that (1) red drum larvae show behavioral interactions, and the magnitude of these interactions is explained by the sizes of the competing individuals, (2) red drum larvae compete for food and habitat use, and the competition is asymmetric as determined by size and behavioral interactions, and (3) the parents can reduce negative effects of competition among larvae and increase larval survival by altering their multiple-spawning traits. The laboratory experiments showed the existence of sociality in red drum larvae. The magnitudes of aggressive behavior, vigilant behavior and shoaling behavior were explained by a combination of absolute and relative phenotypes of competing individuals, such as body lengths and body condition. A new method of combining the laboratory experiments and the foraging theory disentangled interference competition for food from exploitative competition, revealing that both absolute and relative body lengths of competing individuals influence feeding efficiencies. In addition, vigilant behavior decreased feeding efficiency regardless of body sizes. The competitor size and behavioral interactions between individuals had different effects on competition for habitat use: the existence of larger individuals prevented the newly settled larvae from entering preferred habitats, whereas the aggressive behavior from the occupants of preferred habitats moved newly settled larvae to the unpreferred habitats. Finally, computer simulations using an individual-based model revealed that as interference competition among larvae increased, the number of spawning events and the spawning interval of the parents increased to lessen competition and maximize total survival of offspring.Marine Scienc