Assessing the Potential of Multi-spectral and Multi-temporal Satellite Images for Classification and Mapping of Plant Communities in a Temperate Region

Classification and mapping of plant communities is an essential step for conservation and management of ecosystems and biodiversity. We adopt the Genus-Physiognomy-Ecosystem (GPE) system developed in previous study for satellite-based classification of plant communities. This paper assesses the potential of multi-spectral and multi-temporal images collected by Sentinel-2 satellites. This research was conducted in five representative study sites in a temperate region. It consists of 44 types of plant communities including a few land cover types as well. The plant community types were enumerated in the study sites and ground truth data were prepared with reference to extant vegetation surveys, visual interpretation of high-resolution images, and onsite field observations. We acquired all Sentinel-2 Level-1C product images available for the study sites between 2017-2019 and generated monthly median composite images consisting of ten spectral and twelve spectral-indices. Gradient Boosting Decision Trees (GBDT) classifier was employed as an efficient and distributed gradient boosting technique for the supervised classification of big datasets involved in the research. The cross-validation accuracy in terms of kappa coefficient varied from 87% in Oze site with 41 land cover and plant community types to 95% in Hakkoda site with 19 land cover and plant community types; with average performance of 91% across all sites. In addition, the resulting maps demonstrated a clear distribution of plant community types involved in all sites, highlighting the potential of Sentinel-2 multi-spectral and multi-temporal images with GPE classification system for operational and broad-scale mapping of land cover and plant communities.

Herbicide Efficacy of Spot Spraying Systems in Fallow and Postharvest in the Pacific Northwest Dryland Wheat Production Region

Real-time spot spraying technology has the potential to reduce herbicide costs and slow herbicide resistance. However, few studies exist on the efficacy of this technology in the Pacific Northwest (PNW). This research compared the herbicide efficacy (reduction in weed density and cover) of WEED-IT and WeedSeeker spot spraying systems to uniform spraying in fallow and postharvest in 2019 and 2020. Weed community types included naturally occurring weeds, natural + Russian thistle (Salsola tragus L.), or natural + kochia (Bassia scoparia (L.) A. J. Scott). Herbicides included glyphosate or the pre-mix bromoxynil + pyrasulfotole. Additionally, herbicide efficacy was studied with short stubble (~10 cm), tall stubble (~25 cm), and normal stubble (~20 cm) with chaff and straw removed. In fallow, herbicide efficacy was 1.5 times higher for uniform applications than for WEED-IT or WeedSeeker in 2019 and 2020. Herbicide efficacy was also 1.9 times higher for uniform applications in postharvest in 2019 but no differences were found in 2020. The weed community impacted herbicide efficacy but herbicide efficacy did not differ between residue management treatments. Finally, WEED-IT and WeedSeeker used 53% less herbicide volume in comparison to uniform applications. This research demonstrated that spot spraying technology can be efficacious and economical for growers in the PNW.

Feasibility Study Examining the Association between Gut Microbiota and Immune Response to Seasonal Influenza Vaccination in Healthy Adults

<p>Research into the effect of the gut microbiota on host immune response is continuing to shed new light on the underappreciated role of the microbiota in human health. Recent research using mice has shown that the microbiota is critical to the host immune response to influenza infection. Whilst there is great variation in the human gut microbiota, classifications called stool community types can be used to classify individuals based on the abundance of major bacterial taxa. The primary objective of this study was to investigate the feasibility of using the study protocol for a large randomised controlled trial. Healthy adult participants (n=125) aged 18 to 64 were recruited from the general population and vaccinated with the seasonal trivalent influenza vaccine. Participants were followed up over a period of six months, during which time, both stool and blood samples were collected. Blood samples were collected at Day Zero, Three, Seven, 28 and 180 to measure immune response. The immune response to vaccination was measured by HAI antibody titres at Day Zero and Day 28. Stool samples were collected at Day Zero and Day 28 to assign participants to one of the four stool community types and assess stability over time. Stool samples were assigned to stool community types using the proportions of major taxa present. The association between stool community type and either post vaccination HAI titre, seroconversion rates or seroprotection rates was also assessed. The results obtained in this study supported the feasibility of a large randomised controlled trial using the study protocol. The study demonstrated a high participant retention rate (97.6%; 95% CI = 93.1% to 99.5%), as well as high participant adherence to the study protocol and good success obtaining the required blood and stool samples.</p>

Feasibility Study Examining the Association between Gut Microbiota and Immune Response to Seasonal Influenza Vaccination in Healthy Adults

<p>Research into the effect of the gut microbiota on host immune response is continuing to shed new light on the underappreciated role of the microbiota in human health. Recent research using mice has shown that the microbiota is critical to the host immune response to influenza infection. Whilst there is great variation in the human gut microbiota, classifications called stool community types can be used to classify individuals based on the abundance of major bacterial taxa. The primary objective of this study was to investigate the feasibility of using the study protocol for a large randomised controlled trial. Healthy adult participants (n=125) aged 18 to 64 were recruited from the general population and vaccinated with the seasonal trivalent influenza vaccine. Participants were followed up over a period of six months, during which time, both stool and blood samples were collected. Blood samples were collected at Day Zero, Three, Seven, 28 and 180 to measure immune response. The immune response to vaccination was measured by HAI antibody titres at Day Zero and Day 28. Stool samples were collected at Day Zero and Day 28 to assign participants to one of the four stool community types and assess stability over time. Stool samples were assigned to stool community types using the proportions of major taxa present. The association between stool community type and either post vaccination HAI titre, seroconversion rates or seroprotection rates was also assessed. The results obtained in this study supported the feasibility of a large randomised controlled trial using the study protocol. The study demonstrated a high participant retention rate (97.6%; 95% CI = 93.1% to 99.5%), as well as high participant adherence to the study protocol and good success obtaining the required blood and stool samples.</p>

Characterization of the Ovine Vaginal Microbiome and Inflammation Patterns as an Improved Testing Model of Human Vaginal Irritation

The development of therapies targeted to improve the health of women has utilized direct vaginal delivery as a more effective and less toxic method of protection from HIV and other pathogens. Vaginal applicants and delivery devices that provide sustained effects have been met with increasing acceptability, but the efficacy and toxicity outcomes have not been successfully predicted by preclinical in vitro studies and animal modeling. We have explored the utilization of sheep as a model for testing the safety of vaginal applicants and devices based on spatial and structural similarities to the human vagina. As recently noted by the FDA, an additional safety measure is an impact on the vaginal microbiome (VMB) that is known to contribute to vaginal health and influence pathogen susceptibility and drug metabolism. To advance the utility of the sheep vaginal model, we completed a thorough molecular characterization of the ovine VMB utilizing both next-generation sequencing (NGS) and PCR methods. The process also created a custom PCR array to quantify ovine VMB community profiles in an affordable, higher throughput fashion. The results from vaginal swabs (&gt;475 samples) collected from non-pregnant crossbred Dorset and Merino ewes treated with selected vaginal applicants or collected as sham samples established 16 VMB community types (VMB CTs). To associate VMB CTs with eubiosis or dysbiosis, we also completed custom ELISAs for six cytokines identifying IL1B, IL8, TNFa, and CXCL10 as useful markers to support the characterization of ovine vaginal inflammation. The results indicated that Pasteurella, Actinobacillus, Pseudomonas, Bacteroides, Leptotrichia, and E. coli were common markers of eubiosis (low inflammatory marker expression), and that Haemophilus, Ureaplasma, and Corynebacterium were associated with dysbiosis (high cytokine levels). Utilizing the optimized workflow, we also confirmed the utility of three commonly used vaginal applicants for impact on the VMB and inflammatory state, producing a dataset that supports the recommendation for the use of sheep for testing of vaginal applicants and devices as part of preclinical pipelines.

AQUATIC AND MARSHY VEGETATION IN THE CENTER OF THE LOWER PLAIN OF SOMES RIVER: GENERAL CHARACTERISATION

Aiming to a larger study of vegetation of the lower Some Plain (Romania), this short paper summarises the outcome of the floristic inventories performed in aquatic and marshy vegetation, which was dominant in the area until about three centuries ago when the extended wetland drainage has started. By using the phytosociological method, 20 plant associations assigned to four vegetation classes were distinguished. Without presenting phytosociological tables at this first stage, the syntaxonomical framework, distribution and species composition of the revealed plant communities are briefly discussed by reference to the process of wetland drying and successional change as well as to newly formed anthropogenic lakes. The conservative value of some plant community types is emphasized by mentioning the presence of several endangered species that are included in the European-level Habitats Directive and various regional or national red lists/books.

Niche difference determines coexistence and similar underlying processes in four ecological groups

Understanding how species interactions affect community composition is an important objective in ecology. Yet, the multitude of methods to study coexistence has hampered cross-community comparisons. Here, we standardized niche and fitness differences across 1018 species pairs to compare the processes driving composition and outcomes, among four community types (annual plant, perennial plant, phytoplankton, and bacteria/yeast). First, we show that niche differences are more important drivers of coexistence than fitness differences. Second, in all community types negative frequency dependence is the most frequent process. Finally, the outcome of species interactions differs among community types. Coexistence was the most frequent outcome for perennial plants and phytoplankton, while competitive exclusion was the most prevalent outcome in annual plants and bacteria/yeasts. Overall, our results show that niche and fitness differences can be used as a common currency that allow cross community comparisons to understand species coexistence.

Stratification of the Gut Microbiota Composition Landscape Across the Alzheimer's Disease Continuum in a Turkish Cohort

Alzheimer's disease (AD) is a heterogeneous neurodegenerative disorder that spans over a continuum with multiple phases including preclinical, mild cognitive impairment, and dementia. Unlike most other chronic diseases there are limited number of human studies reporting on AD gut microbiota in the literature. These published studies suggest that the gut microbiota of AD continuum patients varies considerably throughout the disease stages, raising expectations for existence of multiple microbiota community types. However, the community types of AD gut microbiota were not systematically investigated before, leaving important research gap for diet-based intervention studies and recently initiated precision nutrition approaches aiming at stratifying patients into distinct dietary subgroups. Here, we comprehensively assessed the community types of gut microbiota across the AD continuum. We analyze 16S rRNA amplicon sequencing of stool samples from 27 mild cognitive patients, 47 AD, and 51 non-demented control subjects using tools compatible with compositional nature of microbiota. To characterize gut microbiota community types, we applied multiple machine learning techniques including partitioning around the medoid clustering, fitting probabilistic Dirichlet mixture model, Latent Dirichlet Allocation model, and performed topological data analysis for population scale microbiome stratification based on Mapper algorithm. These four distinct techniques all converge on Prevotella and Bacteroides partitioning of the gut microbiota across AD continuum while some methods provided fine scale resolution in partitioning the community landscape. The Signature taxa and neuropsychometric parameters together robustly classify the heterogenous groups within the cohort. Our results provide a framework for precision nutrition approaches and diet-based intervention studies targeting AD cohorts.