A review of big data analysis methods for baleen whale passive acoustic monitoring

Many organizations collect large passive acoustic monitoring (PAM) data sets that need to be efficiently and reliably analyzed. To determine appropriate methods for effective analysis of big PAM data sets, we undertook a literature review of baleen whale PAM analysis methods. Methodologies from 166 studies (published between 2000–2019) were summarized, and a detailed review was performed on the 94 studies that recorded more than 1,000 hr of acoustic data (“big data”). Analysis techniques for extracting baleen whale information from PAM data sets varied depending on the research observed. A spectrum of methodologies was used and ranged from manual analysis of all acoustic data by human experts to completely automated techniques with no manual validation. Based on this assessment, recommendations are provided to encourage robust research methods that are comparable across studies and sectors, achievable across research groups, and consistent with previous work. These include using automated techniques when possible to increase efficiency and repeatability, supplementing automation with manual review to calculate automated detector performance, and increasing consistency in terminology and presentation of results. This work can be used to facilitate discussion for minimum standards and best practices to be implemented in the field of marine mammal PAM.     

Age-of-dam adjustment factors for birth and weaning weight records of beef cattle: a review

Age-of-dam adjustment factors are used to preadjust birth and weaning weight data for national beef cattle genetic evaluations. Adjustments are used in order to make the means of the different age-of-dam subclasses similar so that a fair comparison of animals can be performed. A review was made of various research studies that have estimated age-of-dam adjustment factors for birth weight and weaning weight of beef cattle. In general, birth weight age-of-dam adjustment factors are the same across the sexes, but weaning weight age-of-dam adjustment factors differ across the sexes, with heifer calves receiving smaller adjustments than their male counterparts. Additionally, adjustment factors vary greatly across breeds. Preadjustment of records is difficult to do because a perfect estimate of adjustments is not possible. A more appropriate method for adjusting for age-of-dam is to simultaneously adjust during national genetic evaluations.     

Steroid use and human performance: Lessons for integrative biologists

While recent studies have begun to address how hormones mediate whole-animal performance traits, the field conspicuously lags behind research conducted on humans. Recent studies of human steroid use have revealed that steroid use increases muscle cross-sectional area and mass, largely due to increases in protein synthesis, and muscle fiber hypertrophy attributable to an increased number of satellite cells and myonuclei per unit area. These biochemical and cellular effects on skeletal muscle morphology translate into increased power and work during weight-lifting and enhanced performance in burst, sprinting activities. However, there are no unequivocal data that human steroid use enhances endurance performance or muscle fatigability or recovery. The effects of steroids on human morphology and performance are in general consistent with results found for nonhuman animals, though there are notable discrepancies. However, some of the discrepancies may be due to a paucity of comparative data on how testosterone affects muscle physiology and subsequent performance across different regions of the body and across vertebrate taxa. Therefore, we advocate more research on the basic relationships among hormones, morphology, and performance. Based on results from human studies, we recommend that integrative biologists interested in studying hormone regulation of performance should take into account training, timing of administration, and dosage administered when designing experiments or field studies. We also argue that more information is needed on the long-term effects of hormone manipulation on performance and fitness.     

Proteomics for the discovery of biomarkers and diagnosis of periodontitis: a critical review

Periodontitis is a common chronic and destructive disease whose pathogenetic mechanisms remain unclear. Due to their sensitivity and global scale, proteomics studies offer the opportunity to uncover critical host and pathogen activity indicators and can elucidate clinically applicable biomarkers for improved diagnosis and treatment of the disease. This review summarizes the literature of proteomics studies on periodontitis and comprehensively discusses commonly found candidate biomarkers. Key considerations in the design of an experimental proteomics platform are also outlined. The applicability of protein biomarkers across the progression of periodontitis and unexplored areas of research are highlighted.     

Riparian vegetation research in Mediterranean-climate regions: common patterns, ecological processes, and considerations for management

Riparian corridors in Mediterranean-climate regions (med-regions) are resource-rich habitats within water-limited, larger landscapes. However, little is known about how their plant communities compare functionally and compositionally across med-regions. In recent decades, research on these ecosystems has expanded in both geographic scope and disciplinary depth. We reviewed 286 riparian-vegetation studies across the five med-regions, and identified common themes, including: (1) high levels of plant biodiversity, structural complexity, and cross-region species introductions; (2) strong physical controls on plant demographics and community structure; and (3) intensive human impacts. European and Californian ecosystems were the most represented among the studies reviewed, but Australia, South Africa, and Chile had the greatest proportional increases in articles published since 2000. All med-regions support distinct riparian flora, although many genera have invaded across regions. Plant species in all regions are adapted to multiple abiotic stressors, including dynamic flooding and sediment regimes, seasonal water shortage, and fire. The most severe human impacts are from land-use conversion to agriculture, streamflow regulation, nutrient enrichment, and climate change. Current knowledge gaps and subjects for future research include cumulative impacts to small, ephemeral streams and large, regulated rivers, as well as understudied ecosystems in North Africa, the western Mediterranean basin, and Chile.     

Linking inter-individual variability to endocrine disruptors: insights for epigenetic inheritance

Endocrine disrupting chemicals (EDCs) can induce a myriad of adverse health effects. An area of active investigation is the multi- and transgenerational inheritance of EDC-induced adverse health effects referring to the transmission of phenotypes across multiple generations via the germline. The inheritance of EDC-induced adverse health effects across multiple generations can occur independent of genetics, spurring much research into the transmission of underlying epigenetic mechanisms. Epigenetic mechanisms play important roles in the development of an organism and are responsive to environmental exposures. To date, rodent studies have demonstrated that acquired epigenetic marks, particularly DNA methylation, that are inherited following parental EDC exposure can escape embryonic epigenome reprogramming. The acquired epimutations can lead to subsequent adult-onset diseases. Increasing studies have reported inter-individual variations that occur with epigenetic inheritance. Factors that underlie differences among individuals could reveal previously unidentified mechanisms of epigenetic transmission. In this review, we give an overview of DNA methylation and posttranslational histone modification as the potential mechanisms for disease transmission, and define the requirements for multi- and transgenerational epigenetic inheritance. We subsequently evaluate rodent studies investigating how acquired changes in epigenetic marks especially DNA methylation across multiple generations can vary among individuals following parental EDC exposure. We also discuss potential sources of inter-individual variations and the challenges in identifying these variations. We conclude our review discussing the challenges in applying rodent generational studies to humans.

     

The quest for a mechanistic understanding of biodiversity–ecosystem services relationships

Ecosystem services (ES) approaches to biodiversity conservation are currently high on the ecological research and policy agendas. However, despite a wealth of studies into biodiversity''s role in maintaining ES (B–ES relationships) across landscapes, we still lack generalities in the nature and strengths of these linkages. Reasons for this are manifold, but can largely be attributed to (i) a lack of adherence to definitions and thus a confusion between final ES and the ecosystem functions (EFs) underpinning them, (ii) a focus on uninformative biodiversity indices and singular hypotheses and (iii) top-down analyses across large spatial scales and overlooking of context-dependency. The biodiversity–ecosystem functioning (B–EF) field provides an alternate context for examining biodiversity''s mechanistic role in shaping ES, focusing on species'' characteristics that may drive EFs via multiple mechanisms across contexts. Despite acknowledgements of a need for B–ES research to look towards underlying B–EF linkages, the connections between these areas of research remains weak. With this review, we pull together recent B–EF findings to identify key areas for future developments in B–ES research. We highlight a means by which B–ES research may begin to identify how and when multiple underlying B–EF relationships may scale to final ES delivery and trade-offs.     

Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa

With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependencies, and versions of bioinformatics tools along with a lack of local computational infrastructure and expertise. To address this, H3ABioNet developed a 16S rRNA Microbiome Intermediate Bioinformatics Training course, extending its remote classroom model. The course was developed alongside experienced microbiome researchers, bioinformaticians, and systems administrators, who identified key topics to address. Development of containerised workflows has previously been undertaken by H3ABioNet, and Singularity containers were used here to enable the deployment of a standard replicable software stack across different hosting sites. The pilot ran successfully in 2019 across 23 sites registered in 11 African countries, with more than 200 participants formally enrolled and 106 volunteer staff for onsite support. The pulling, running, and testing of the containers, software, and analyses on various clusters were performed prior to the start of the course by hosting classrooms. The containers allowed the replication of analyses and results across all participating classrooms running a cluster and remained available posttraining ensuring analyses could be repeated on real data. Participants thus received the opportunity to analyse their own data, while local staff were trained and supported by experienced experts, increasing local capacity for ongoing research support. This provides a model for delivering topic-specific bioinformatics courses across Africa and other remote/low-resourced regions which overcomes barriers such as inadequate infrastructures, geographical distance, and access to expertise and educational materials.     

声景生态学研究进展和展望

声景生态学以景观中的声音为研究对象, 探讨其在不同时空维度上的分布和变化模式, 从而揭示自然环境、野生动物和人类活动的相互作用关系。本文通过系统检索声景生态学研究的相关文献, 回顾了该学科的研究框架和研究方法, 总结了目前常用的声学指标, 重点归纳了声景生态学的研究内容, 包括声景组成和各组分间的相互作用, 声景的时空格局, 以及声景生态学在生物多样性监测中的应用。目前, 声景监测中存在的问题主要包括监测的生态系统类型和物种类群有限、声学指标效力有待提高等。建议未来着重推进建立系统性的声景监测网络和数据管理平台, 开发和完善音频数据采集、分析方法和评估指标, 并重视声景数据的采集, 将声景视作一种资源进行研究和保护。     

Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes

Background  

With the growing number of public repositories for high-throughput genomic data, it is of great interest to combine the results produced by independent research groups. Such a combination allows the identification of common genomic factors across multiple cancer types and provides new insights into the disease process. In the framework of the proportional hazards model, classical procedures, which consist of ranking genes according to the estimated hazard ratio or the p-value obtained from a test statistic of no association between survival and gene expression level, are not suitable for gene selection across multiple genomic datasets with different sample sizes. We propose a novel index for identifying genes with a common effect across heterogeneous genomic studies designed to remain stable whatever the sample size and which has a straightforward interpretation in terms of the percentage of separability between patients according to their survival times and gene expression measurements.     

EMG-activated feedback alarms for the treatment of nocturnal bruxism: current status and future directions

This article reviews published research on the use of EMG-activated feedback paradigms to modify nocturnal bruxism. The first three sections review naturalistic trials, laboratory studies, and comparisons of feedback paradigms with alternative treatment/management approaches. The fourth section overviews several sources of theoretical guidance for further research and delineates some substantive directions. The final section identifies major scientific shortcomings that are common in the literature and offers some correctives. The empirical reviews suggest that nocturnal bruxing feedback is beneficial and competitive with other approaches, particularly when the feedback serves to occasion behaviors that require wakefulness. The theoretical overview points to classical learning theories, biofeedback theories, and theories concerning the etiology of bruxism as guideposts for continued research. The methodological narrative calls for adequately detailed scientific reporting, for increased operational commonality across experiments, and for innovative integrations of actuarial and intrasubject research designs.     

Genotype-by-Environment Interactions for Female Mate Choice of Male Cuticular Hydrocarbons in Drosophila simulans

Recent research has highlighted the potential importance of environmental and genotype-by-environment (G×E) variation in sexual selection, but most studies have focussed on the expression of male sexual traits. Consequently, our understanding of genetic variation for plasticity in female mate choice is extremely poor. In this study we examine the genetics of female mate choice in Drosophila simulans using isolines reared across two post-eclosion temperatures. There was evidence for G×Es in female choosiness and preference, which suggests that the evolution of female mate choice behaviour could differ across environments. However, the ranked order of preferred males was consistent across females and environments, so the same males are favoured by mate choice in spite of G×Es. Our study highlights the importance of taking cross-environment perspectives in order to gain a more comprehensive understanding of the operation of sexual selection.     

Weaving animal temperament into food webs: implications for biodiversity

Recent studies into community level dynamics are revealing processes and patterns that underpin the biodiversity and complexity of natural ecosystems. Theoretical food webs have suggested that species‐rich and highly complex communities are inherently unstable, but incorporating certain characteristics of empirical communities, such as allometric body size scaling and non‐random interaction distributions, have been shown to enhance stability and facilitate species coexistence. Incorporating individual level traits and variability into food web theory is seen as a future pathway for this research and our growing knowledge of individual behaviours, in the form of temperament (or personality) traits, can inform the direction of this research. Temperament traits are consistent differences in behaviour between individuals, which are repeatable across time and/or across ecological contexts, such as aggressive or boldness behaviours that commonly differ between individuals of the same species. These traits, under the framework of behavioural reaction norms, show both individual consistency as well as contextual and phenotypic plasticity. This is likely to contribute significantly to the effects of individual trait variability and adaptive trophic behaviour on the structure and dynamics of food webs, which are apparently stabilizing. Exploring the role of temperament in the context of community ecology is a unique opportunity for cross‐pollination between ecological fields, and can provide new insights into community stability and biodiversity.     

Etiology in psychiatry: embracing the reality of poly‐gene‐environmental causation of mental illness

Intriguing findings on genetic and environmental causation suggest a need to reframe the etiology of mental disorders. Molecular genetics shows that thousands of common and rare genetic variants contribute to mental illness. Epidemiological studies have identified dozens of environmental exposures that are associated with psychopathology. The effect of environment is likely conditional on genetic factors, resulting in gene‐environment interactions. The impact of environmental factors also depends on previous exposures, resulting in environment‐environment interactions. Most known genetic and environmental factors are shared across multiple mental disorders. Schizophrenia, bipolar disorder and major depressive disorder, in particular, are closely causally linked. Synthesis of findings from twin studies, molecular genetics and epidemiological research suggests that joint consideration of multiple genetic and environmental factors has much greater explanatory power than separate studies of genetic or environmental causation. Multi‐factorial gene‐environment interactions are likely to be a generic mechanism involved in the majority of cases of mental illness, which is only partially tapped by existing gene‐environment studies. Future research may cut across psychiatric disorders and address poly‐causation by considering multiple genetic and environmental measures across the life course with a specific focus on the first two decades of life. Integrative analyses of poly‐causation including gene‐environment and environment‐environment interactions can realize the potential for discovering causal types and mechanisms that are likely to generate new preventive and therapeutic tools.     

EMG-activated feedback alarms for the treatment of nocturnal bruxism: Current status and future directions

This article reviews published research on the use of EMG-activated feedback paradigms to modify nocturnal bruxism. The first three sections review naturalistic trials, laboratory studies, and comparisons of feedback paradigms with alternative treatment/management approaches. The fourth section overviews several sources of theoretical guidance for further research and delineates some substantive directions. The final section identifies major scientific shortcomings that are common in the literature and offers some correctives. The empirical reviews suggest that nocturnal bruxing feedback is beneficial and competitive with other approaches, particularly when the feedback serves to occasion behaviors that require wakefulness. The theoretical overview points to classical learning theories, biofeedback theories, and theories concerning the etiology of bruxism as guideposts for continued research. The methodological narrative calls for adequately detailed scientific reporting, for increased operational commonality across experiments, and for innovative integrations of actuarial and intrasubject research designs.The authors thank John G. Carlson for commenting on an early draft of the paper.     

A knowledgebase system to enhance scientific discovery: Telemakus

BACKGROUND: With the rapid expansion of scientific research, the ability to effectively find or integrate new domain knowledge in the sciences is proving increasingly difficult. Efforts to improve and speed up scientific discovery are being explored on a number of fronts. However, much of this work is based on traditional search and retrieval approaches and the bibliographic citation presentation format remains unchanged. METHODS: Case study. RESULTS: The Telemakus KnowledgeBase System provides flexible new tools for creating knowledgebases to facilitate retrieval and review of scientific research reports. In formalizing the representation of the research methods and results of scientific reports, Telemakus offers a potential strategy to enhance the scientific discovery process. While other research has demonstrated that aggregating and analyzing research findings across domains augments knowledge discovery, the Telemakus system is unique in combining document surrogates with interactive concept maps of linked relationships across groups of research reports. CONCLUSION: Based on how scientists conduct research and read the literature, the Telemakus KnowledgeBase System brings together three innovations in analyzing, displaying and summarizing research reports across a domain: (1) research report schema, a document surrogate of extracted research methods and findings presented in a consistent and structured schema format which mimics the research process itself and provides a high-level surrogate to facilitate searching and rapid review of retrieved documents; (2) research findings, used to index the documents, allowing searchers to request, for example, research studies which have studied the relationship between neoplasms and vitamin E; and (3) visual exploration interface of linked relationships for interactive querying of research findings across the knowledgebase and graphical displays of what is known as well as, through gaps in the map, what is yet to be tested. The rationale and system architecture are described and plans for the future are discussed.     

Analysis of Rhesus monkey vocalizations: maturation-related sex differences in clear-cell frequency

In the first of two studies six like-sexed pairs of rhesus macaques early in their third year of life were observed for two days, then separated for two days, and finally reunited for two days. In the second, about nine months later, the same animals were paired across sex and were separated in a similar fashion to that in the previous study. The number of distress-related clear calls uttered by females remained stable through both studies, but the males showed a decrease with age in this behavior. The results of these two studies are compared with other research in which maturation-related sex differences have become apparent. These comparisons suggested that decreases in the production of clear calls accompany the onset of puberty. Since the females which were involved in our research reached puberty shortly before the time of our first study and the males did so shortly before the second, the decreases in male clear-call rate which we observed across these two studies appears to have been linked with peri-pubertal influences.     

Group living in squamate reptiles: a review of evidence for stable aggregations

How sociality evolves and is maintained remains a key question in evolutionary biology. Most studies to date have focused on insects, birds, and mammals but data from a wider range of taxonomic groups are essential to identify general patterns and processes. The extent of social behaviour among squamate reptiles is under‐appreciated, yet they are a promising group for further studies. Living in aggregations is posited as an important step in the evolution of more complex sociality. We review data on aggregations among squamates and find evidence for some form of aggregations in 94 species across 22 families. Of these, 18 species across 7 families exhibited ‘stable’ aggregations that entail overlapping home ranges and stable membership in long‐term (years) or seasonal aggregations. Phylogenetic analysis suggests that stable aggregations have evolved multiple times in squamates. We: (i) identify significant gaps in our understanding; (ii) outline key traits which should be the focus of future research; and (iii) outline the potential for utilising reproductive skew theory to provide insights into squamate sociality.