Number Of Different Species Research Articles

Using inventory variables for practical biodiversity assessment in plantation stands

Aim of study: Practically and simply assessing biodiversity by using inventory variables in four types of forest plantation stands (mixed and pure) including species such are chestnut, blue gum and maritime pine.
 Area of study: Northwest Portugal in Vale do Sousa (14,840 ha), which is 97% covered with plantation forests.
 Material and methods: Simulated data, from 90-year stand-level forest management planning, were considered using three indicators: tree species (number of different species and species origin—native or exotic), mean diameter at breast height (DBH), and shrub biomass. Two shrub regeneration types (fully regenerated by seed and fully regenerated by resprouting), and three site quality conditions were also considered.
 Main results: Mean biodiversity scores varied between very low (10.13) in pure blue gum stands on lowest-quality sites with shrub regeneration by seed, and low (29.85) in mixed stands with a dominance of pine, on best-quality sites with shrub regeneration by resprouting. Site quality and shrub regeneration type significantly affected all biodiversity scores in mixed stands dominated by pine and pure chestnut stands, while less affected pure blue gum stands and mixed stands dominated by blue gum.
 Research highlights: The considered biodiversity indicators cover the major biodiversity aspects and allow biodiversity assessment over time. The findings are relevant for biodiversity conservation and fire protection management.

MP25-16 CLINICAL IMPLICATIONS OF THE URINARY DIVERSION MICROBIOME AFTER RADICAL CYSTECTOMY

You have accessJournal of UrologyCME1 May 2022MP25-16 CLINICAL IMPLICATIONS OF THE URINARY DIVERSION MICROBIOME AFTER RADICAL CYSTECTOMY Saum Ghodoussipour, Seyedeh Sanam Ladi Seyedian, David Nusbaum, Shane Pearce, Hiren Patel, Aishani Prem, Wendy Ullmer, Sumeet Bhanvadia, Hooman Djaladat, Anne Schuckman, Gangning Liang, and Siamak Daneshmand Saum GhodoussipourSaum Ghodoussipour More articles by this author , Seyedeh Sanam Ladi SeyedianSeyedeh Sanam Ladi Seyedian More articles by this author , David NusbaumDavid Nusbaum More articles by this author , Shane PearceShane Pearce More articles by this author , Hiren PatelHiren Patel More articles by this author , Aishani PremAishani Prem More articles by this author , Wendy UllmerWendy Ullmer More articles by this author , Sumeet BhanvadiaSumeet Bhanvadia More articles by this author , Hooman DjaladatHooman Djaladat More articles by this author , Anne SchuckmanAnne Schuckman More articles by this author , Gangning LiangGangning Liang More articles by this author , and Siamak DaneshmandSiamak Daneshmand More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002568.16AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: We use bacterial 16S rRNA and fungal ITS sequencing to identify the UD microbiome after radical and clinical implications of taxonomic and microbial diversity differences. METHODS: We enrolled patients who underwent RC and UD with either ileal conduit or neobladder under an IRB-approved protocol. A catheterized urine specimen from the native bladder and a swab of the ileal segment used to create the UD were collected in the operating room. We then collected sequential catheterized specimens from the UD until 1-year after surgery. Preoperative antibiotic prophylaxis was administered according to an institutional ERAS protocol. Microbial 16S rRNA and ITS sequencing and profiling were performed. RESULTS: We included 20 patients (75% male, 30% had neoadjuvant chemotherapy). The 90-day complication rate was 60% (n=12), including infectious in 25% (n=5). The average bacterial count, estimated by gene copy number, was higher in the bowel swab (1.38 x 108 cells/ml) than native bladder (7.23 x 106 cells/ml) as was alpha diversity, which measures the number of different species in each sample (mean species richness = 50 ± 26 in bowel and 29 ± 25 in native bladder). The average UD bacterial count and alpha diversity was high on post-operative day 1 (1.38 x 108 cells/ml and 31 ± 19, respectively), but over time, alpha diversity decreased while bacterial counts tended to increase (11 ± 12 and 4.54 x 108 cells/ml at 1 year, respectively). High fungal cell counts (>1,000 cells/ml) were noted in 7 patients and Candida species were abundant in all but one. Principal coordinate analysis showed microbial profiles of the native bladder and ileum clustering in distinct patterns, but the UD microbiome varied between patients (Figure). Age, gender, receipt of neoadjuvant chemotherapy and type of diversion did not predict similarities in the UD microbiome. There were no significant differences in microbial diversity or bacterial count amongst patients with and without complications. However, a high fungal count was associated with any complication in the first month (p<0.01) and first year (p<0.05). CONCLUSIONS: The UD microbiome differs from the native bladder and ileum and varies widely between patients. High fungal loads are associated with patients having any complication, potentially implicating Candida species as a pathogenic organism. Source of Funding: Zymo Research Corp © 2022 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 207Issue Supplement 5May 2022Page: e434 Advertisement Copyright & Permissions© 2022 by American Urological Association Education and Research, Inc.MetricsAuthor Information Saum Ghodoussipour More articles by this author Seyedeh Sanam Ladi Seyedian More articles by this author David Nusbaum More articles by this author Shane Pearce More articles by this author Hiren Patel More articles by this author Aishani Prem More articles by this author Wendy Ullmer More articles by this author Sumeet Bhanvadia More articles by this author Hooman Djaladat More articles by this author Anne Schuckman More articles by this author Gangning Liang More articles by this author Siamak Daneshmand More articles by this author Expand All Advertisement PDF DownloadLoading ...

Penile Implant Bacterial Biofilm Profiles Vary by Surgery Indication: An Opportunity to Focus on Peri-operative Care

ABSTRACT Introduction The risk for device infection with penile implant revision surgery varies by indication (i.e., mechanical, erosion, infection). Dislodged biofilm from an existing implant is suspected to play a part to the increased risk for infection with revision surgery. An improved understanding of the existing biofilm of commons scenarios may help to guide the selection of peri-operative antibiotics, increase the inclination to replace a compromised device, and potentially lead to improved patient outcomes. Objective To compare bacterial biofilm profiles between implants removed due to mechanical failure, erosion, and infection using 16s rRNA next-generation sequencing (NGS). Methods A retrospective review was performed of 110 patients who underwent penile implant removal with or without replacement. At the time of explant, devices were swabbed with sterile gauze which was sent for NGS testing (MicroGen Diagnostics, Lubbock, TX, USA). NGS involved quantitative PCR and sequencing using Illumina MiSeq technology. Microorganism species identifications and relative abundances were documented. Differences in number of species detected (richness) and species diversity (expressed as the exponential function of the Shannon diversity metric) across samples explained by surgical indication, age, race, diabetes status, or implant duration were assessed using ANOVA. Differences in microbiome compositional profiles among samples were calculated as Bray-Curtis community dissimilarities and Permutational Analysis of Variance was used to test for the effect of the sample variables considered in ANOVA. Statistical analyses were performed using R statistical software. Results Of 110 total implants, 83 had complete data and were included in this study. Indication for device removal included mechanical (n=70), erosion (n=5), and infection (n=8). Species richness and microbiome compositional profiles varied by surgical indication, but not by age, race, diabetes status, or implant duration. The most frequent organisms by mechanical, erosion, and infectious indication for revision surgery were Escherichia coli, Staphylococcus epidermidis, and Pseudomonas aeruginosa, respectively. The highest relative abundant organisms by mechanical, erosion, and infectious indication for revision surgery were E. coli, Corynebacterium Jeikeium, and P. aeruginosa, respectively. Relative abundances of species that were significant through differential abundance testing comparing indication types are exhibited in Figure 1. Antibiotic resistance genes were evaluated with quantitative PCR and detected tetracycline resistance from an infected device and methicillin resistance from an eroded device. Conclusions Bacterial composition of implants varied by indication for surgical removal. Mechanical failure implants had a high presence of E. coli, eroded implants exhibited skin flora, and infected implants demonstrated P. aeruginosa. This information may help to guide optimal peri-operative antibiotic selection. Additional studies will help to further characterize these differences and establish whether common antibiotic combinations for prophylaxis, irrigation, and implant coatings should be altered. Further developments are also needed to help decrease post-operative infection as antibiotic and hydrophilic coatings are not sufficient for sterilizing the implant against biofilm long-term. Disclosure Yes, this is sponsored by industry/sponsor: MicrogenDx Clarification Industry funding only - investigator initiated and executed study

Check of the taxonomy of freshwater fishes of Iraq

Taxonomic studies on freshwater fishes of Iraq were reviewed. Considerable differences in number of species that have been recorded in Iraqi freshwater were noticed, the number ranged from 44 to 70 species. The difference might be due to recording of synonyms or incorrect records. The continuous record of new species on various periods may have contributed to such variation. Thirty eight species, mainly cyprinids, fell into the disagreement category. A final list of the species which have received majority agreement was proposed with a total of 53 species and 12 families.

Comparative Analysis of Microbial Community Diversity and Dynamics on Diseased Tubers During Potato Storage in Different Regions of Qinghai China.

Effective storage of potatoes is very important for the food industry. Given the problems involving rotten potatoes and low quality during storage, harvested potatoes from the main potato-producing areas in the Qinghai Plateau were treated by selection and air drying (Group “A”) and the others were stored directly as controls (Group “C”). Then, the microbial community structure and diversity of diseased potato tubers from four main production areas were analyzed by high-throughput sequencing technology in different storage stages. The results showed that the community composition and diversity of microbes in different regions and storage periods were different, and the dominant fungi in diseased potato tubers were Boeremia in Huangyuan (HY), Maying (MY) and Zhongling (ZL) and Apiotrichum in Huangzhong (HZ) at the genus level. The dominant bacterial genus was Pseudomonas, but its abundance varied in samples from different regions and storage periods. In the analysis of indicator species, there were some common species and endemic species in each region and period, and the period with the largest number of different species was the third period. Among the four storage periods, the region with the largest number of different species was HZ. Some fungi, especially Fusarium and other potato pathogens, were more abundant in control Group “C” than in treatment Group “A.” In the diversity analysis, the α diversity of fungi in Group “C” was higher than that in Group “A,” but the α diversity of bacteria in Group “A” was higher than that in Group “C,” and there was no obvious regularity with storage time. The β diversity varied significantly among different regions. In addition, through functional prediction analysis, it was found that a plant pathogen was one of the main nutritional types of fungi, which indicated that treatment by selection and drying could significantly reduce phytopathogenic microbe and other microorganisms and could be used as an effective measure for potato storage compared with the prevention and control by drugs that can cause environmental pollution. Further analysis of co-occurrence network showed that pathogenic fungi Fusarium was negatively correlated with pathogenic bacteria Erwinia, and there is also a negative correlation between pathogens and antagonistic microorganisms indicated that there were various symbiotic relationships among microorganisms in diseased potatoes. This study may provide a theoretical basis for biological control of potato cellar diseases and the maintenance of potato quality during long-term storage.

Similarities of distributions and feeding habits between Bullet tuna, Auxis rochei, and Pacific bluefin tuna, Thunnus orientalis, larvae in the southern Sea of Japan

Bullet tuna (Auxis rochei: BT) larvae and juveniles are found during summer in the Sea of Japan, where those of Pacific bluefin tuna (Thunnus orientalis: PBF) also occur. However, the ecology of BT larvae and their interactions with the PBF larvae are both unclear. To identify the differences in the spatial distributions and feeding habits between BT and PBF larvae at the larval stages, they were evaluated in the Sea of Japan during the summer. The distributions were assessed using generalized additive models (GAMs) in 2016, 2017, and 2018, and the feeding habits of both species were investigated using a metagenetic technique in 2017 and a morphological technique in 2017 and 2018. The BT and PBF larvae were the only members of the family Scombridae found during the study. The GAMs indicated that BT larvae occur in warm water (>24.3 °C), and PBF larvae are found at similar temperatures (>23.5 °C). BT larvae occurred in more saline conditions than PBF larvae. The ecological niche breadth was estimated with a diversity of environments at which the target species are present, and that of BT was estimated to be greater than that of PBF. Morphologically identified gut contents of BT larvae consisted mainly of copepods and cladocerans, and appendicularians, with sagitta being added to this list through metagenetic identification, and the PBF larvae had the same prey. The breadth of the feeding niche, the diversity of the feeding contents, of the BT larvae were wider than those of the PBF, and their feeding niches highly overlapped. The number of different species in the gut of BT larva was significantly lower than that in PBF larva, suggesting feeding behavior of PBF larvae is superior to that of BT larvae. These results show that PBF larvae are the competitors of BT larvae and may have a competitive advantage; however, environmental characteristics that are unique to the BT larvae are present. These interspecies interactions keep the coexistence of BT and PBF at the juvenile period in the Sea of Japan.

Spatial and Temporal Distribution of Aerobic Denitrification Bacterial Community in Sediments of Gangnan Reservoir

In order to study the spatial and temporal distribution characteristics of aerobic denitrification bacteria in the sediments of Gangnan Reservoir, the aerobic denitrification bacterial community was analyzed using a MiSeq high-throughput sequencing technique based on the napA gene. Moreover, the composition, diversity, difference, and network analysis of the aerobic denitrification bacterial community were investigated. The results showed higher α-diversity (Chao1 index, Observed species index, and Shannon index) in autumn and winter than that in spring and summer; that is, the richness and diversity of sampling sites in autumn and winter were higher. In terms of spatial distribution, the Chao1 index, Observed species index, Shannon index, and Simpson index of the bacterial community in the sampling sites in the transition zone were higher than those in the sampling sites in the inflow area and the main reservoir area, indicating that the richness and diversity of the bacterial community in the sampling sites in the transition zone were the highest. The aerobic denitrifying bacteria in the sediments of Gangnan Reservoir mainly belong to Protebacteria. The first dominant class was β-Proteobacteria, and the first dominant genus was Thauera. A Venn diagram analysis indicated that the community of aerobic denitrification bacteria exhibited significant spatial and temporal differences. At the spatial level, there were higher numbers of different species based on LEfSe analysis than that at the seasonal level. Among the marker species screened by random forest analysis, Comamonas had the highest contribution in all spatial sampling sites, whereas Pectobacterium had the highest contribution in all seasonal sampling sites. Network analysis showed that there were nine modules, including 565 edges of 297 nodes; 47 keystone species were obtained based on the indicator OTUs analysis and network analysis. The principal co-ordinates analysis revealed that keystone species in the spatial distribution exhibited significant differences (Adonis, P<0.001). The results of this study provide scientific basis for the separation and identification of efficient aerobic denitrifying bacteria.

Two sides of one medal: Arable weed vegetation of Europe in phytosociological data compared to agronomical weed surveys

AbstractQuestionsTwo scientific disciplines, vegetation science and weed science, study arable weed vegetation, which has seen a strong diversity decrease in Europe over the last decades. We compared two collections of plot‐based vegetation records originating from these two disciplines. The aim was to check the suitability of the collections for joint analysis and for addressing research questions from the opposing domains. We asked: are these collections complementary? If so, how can they be used for joint analysis?LocationEurope.MethodsWe compared 13 311 phytosociological relevés and 13 328 records from weed science, concerning both data collection properties and the recorded species richness. To deal with bias in the data, we also analysed different subsets (i.e., crops, geographical regions, organic vs conventional fields, center vs edge plots).ResultsRecords from vegetation science have an average species number of 19.0 ± 10.4. Metadata on survey methodology or agronomic practices are rare in this collection. Records from weed science have an average species number of 8.5 ± 6.4. They are accompanied by extensive methodological information. Vegetation science records and the weed science records taken at field edges or from organic fields have similar species numbers. The collections cover different parts of Europe but the results are consistent in six geographical subsets and the overall data set. The difference in species numbers may be caused by differences in methodology between the disciplines, i.e., plot positioning within fields, plot sizes, or survey timing.ConclusionThis comparison of arable weed data that were originally sampled with a different purpose represents a new effort in connecting research between vegetation scientists and weed scientists. Both collections show different aspects of weed vegetation, which means the joint use of the data is valuable as it can contribute to a more complete picture of weed species diversity in European arable landscapes.

Small-scale species richness of plant communities with similar biomass: the influence of habitat types in the context of historical hypothesis (Western Caucasus and Ciscaucasia, Black and Azov Seas, Russia)

We compared the species richness of the plant communities of different habitats on different sites of the biomass gradient. The analysis was based on data on 1089 above-ground biomass samples taken from the sites 0.25 m2 of terrestrial herbaceous communities of the Western Caucasus and Ciscaucasia (30–2800 m a.s.l.) and 317 samples taken from the same sites of the macrophytobenthos of the Black and Azov Seas (0.5–10 m depth). Results showed that a certain amount of biomass, sampled in communities of different types, includes, on average, a significantly different number of species. Thus, among terrestrial plant communities, highmountain communities of the Western Caucasus are characterized by the highest species richness in most ranges of the biomass gradient; communities of herb layer of shaded forests – on the contrary, the lowest richness. The macrophytobenthos of the Black Sea is characterized by lower species richness than most of the terrestrial communities, but higher species richness than the benthic communities of the Azov Sea. We showed that significant difference in the small-scale species richness of these communities can be plausibly explained by the peculiarities of their history.

Automatic construction of accurate bioacoustics workflows under time constraints using a surrogate model

Automated bioacoustics analysis is being increasingly used to describe environmental phenomena such as species abundance and biodiversity. Within this research area, many algorithms have been proposed. These achieve different sub-objectives within bioacoustics processes and can be combined to form workflows. However, these algorithms are typically evaluated in a limited number of scenarios and are rarely evaluated with different combinations of other tasks. This can result in workflows that are not well optimised to serve a given scenario, particularly under resource and time constraints, which ultimately leads to inaccurate bioacoustics analyses. This work examines the problem of bioacoustics workflow construction by searching and ordering combinations of tasks to determine which produce the most accurate output while remaining under user-defined time constraints. Workflow construction is investigated within a scenario where species need to be classified within synthetically generated soundscapes with different numbers of species, noise levels, and densities of species. A search algorithm is created that applies Particle Swarm Optimisation (PSO) to a neural network-based surrogate model. This algorithm is used to efficiently search for candidate workflow structures. This is compared to a random search, a genetic algorithm, and a PSO algorithm without the surrogate model, as well as existing workflows based on previous research. It is found that for all scenarios, the surrogate model-based search method can quickly find effective workflows in a low number of searches. Furthermore, it is found that workflow effectiveness varies depending on the scenarios and recordings used.

Seaweed effects on plant growth and environmental remediation: a review

Seaweeds are plants found in sea that have tremendous applications in the fields of agriculture and environment. It comprises of three giant classes with a large number of different species. their ability to adopt to various conditions qualifies them more applicable to various environmental and agricultural arena. Agriculturally, both three classes Phaeophyta, Rhodophyta and Chlorophyta, have significant roles in promoting plant growth and productivity and soil protection as well as reclamation with class Phaeophyta has highest contribution due to its alginic acid content and other multifaceted components that are higher followed by Rhodophyta and Chlorophyta. Seaweed (living or dead biomass) has ability to phycoremediate environment against heavy toxic metals and lessen the excessiveness of non-metal inorganic elements via physisorption, chemisorption with the aid of binding sites provided by proteins and carbohydrates functional groups existing in their cell walls and secretion of organic acids and intracellular transformation and accumulation. Seaweed is an important factor in environmental remediation and soil restoration processes.

How Soil Invertebrates Deal With Microplastic Contamination

Small animals living in soils, called soil invertebrates, represent a very diverse group of soil inhabitants. They include earthworms, woodlice, spiders, springtails, mites, and some insects. Soil invertebrates feed on dead plants, on fungi and bacteria, or on other soil invertebrates. The many ways soil invertebrates interact with each other, and the large number of different species, make life in soils complex and difficult to understand. Unfortunately, soil invertebrates have been dealing with soil pollution, including contamination with tiny particles of plastic called microplastics for decades now. But are microplastics harmful to these organisms? Can microplastics be passed between soil invertebrates when one feeds on another? Most questions about microplastics and soil invertebrates have been investigated using earthworms, but a few studies on others, like springtails, mites, and nematodes, also exist. In this article, we summarize the effects of microplastics on soil invertebrates.

A new joint species distribution model for faster and more accurate inference of species associations from big community data

Abstract Joint species distribution models (JSDMs) explain spatial variation in community composition by contributions of the environment, biotic associations and possibly spatially structured residual covariance. They show great promise as a general analytical framework for community ecology and macroecology, but current JSDMs, even when approximated by latent variables, scale poorly on large datasets, limiting their usefulness for currently emerging big (e.g. metabarcoding and metagenomics) community datasets. Here, we present a novel, more scalable JSDM (sjSDM) that circumvents the need to use latent variables by using a Monte Carlo integration of the joint JSDM likelihood together with flexible elastic net regularization on all model components. We implemented sjSDM in PyTorch, a modern machine learning framework, which allows making use of both CPU and GPU calculations. Using simulated communities with known species–species associations and different number of species and sites, we compare sjSDM with state‐of‐the‐art JSDM implementations to determine computational runtimes and accuracy of the inferred species–species and species–environment associations. We find that sjSDM is orders of magnitude faster than existing JSDM algorithms (even when run on the CPU) and can be scaled to very large datasets. Despite the dramatically improved speed, sjSDM produces more accurate estimates of species association structures than alternative JSDM implementations. We demonstrate the applicability of sjSDM to big community data using eDNA case study with thousands of fungi operational taxonomic units (OTU). Our sjSDM approach makes the analysis of JSDMs to large community datasets with hundreds or thousands of species possible, substantially extending the applicability of JSDMs in ecology. We provide our method in an R package to facilitate its applicability for practical data analysis.

Multicellularity and sex helped shape the Tree of Life.

Across the Tree of Life, there are dramatic differences in species numbers among groups. However, the factors that explain the differences among the deepest branches have remained unknown. We tested whether multicellularity and sexual reproduction might explain these patterns, since the most species-rich groups share these traits. We found that groups with multicellularity and sexual reproduction have accelerated rates of species proliferation (diversification), and that multicellularity has a stronger effect than sexual reproduction. Patterns of species richness among clades are then strongly related to these differences in diversification rates. Taken together, these results help explain patterns of biodiversity among groups of organisms at the very broadest scales. They may also help explain the mysterious preponderance of sexual reproduction among species (the 'paradox of sex') by showing that organisms with sexual reproduction proliferate more rapidly.

Evolution of Toll, Spatzle and MyD88 in insects: the problem of the Diptera bias

BackgroundArthropoda, the most numerous and diverse metazoan phylum, has species in many habitats where they encounter various microorganisms and, as a result, mechanisms for pathogen recognition and elimination have evolved. The Toll pathway, involved in the innate immune system, was first described as part of the developmental pathway for dorsal-ventral differentiation in Drosophila. Its later discovery in vertebrates suggested that this system was extremely conserved. However, there is variation in presence/absence, copy number and sequence divergence in various genes along the pathway. As most studies have only focused on Diptera, for a comprehensive and accurate homology-based approach it is important to understand gene function in a number of different species and, in a group as diverse as insects, the use of species belonging to different taxonomic groups is essential.ResultsWe evaluated the diversity of Toll pathway gene families in 39 Arthropod genomes, encompassing 13 different Insect Orders. Through computational methods, we shed some light into the evolution and functional annotation of protein families involved in the Toll pathway innate immune response. Our data indicates that: 1) intracellular proteins of the Toll pathway show mostly species-specific expansions; 2) the different Toll subfamilies seem to have distinct evolutionary backgrounds; 3) patterns of gene expansion observed in the Toll phylogenetic tree indicate that homology based methods of functional inference might not be accurate for some subfamilies; 4) Spatzle subfamilies are highly divergent and also pose a problem for homology based inference; 5) Spatzle subfamilies should not be analyzed together in the same phylogenetic framework; 6) network analyses seem to be a good first step in inferring functional groups in these cases. We specifically show that understanding Drosophila’s Toll functions might not indicate the same function in other species.ConclusionsOur results show the importance of using species representing the different orders to better understand insect gene content, origin and evolution. More specifically, in intracellular Toll pathway gene families the presence of orthologues has important implications for homology based functional inference. Also, the different evolutionary backgrounds of Toll gene subfamilies should be taken into consideration when functional studies are performed, especially for TOLL9, TOLL, TOLL2_7, and the new TOLL10 clade. The presence of Diptera specific clades or the ones lacking Diptera species show the importance of overcoming the Diptera bias when performing functional characterization of Toll pathways.

Neuronal Sequence Models for Bayesian Online Inference.

Various imaging and electrophysiological studies in a number of different species and brain regions have revealed that neuronal dynamics associated with diverse behavioral patterns and cognitive tasks take on a sequence-like structure, even when encoding stationary concepts. These neuronal sequences are characterized by robust and reproducible spatiotemporal activation patterns. This suggests that the role of neuronal sequences may be much more fundamental for brain function than is commonly believed. Furthermore, the idea that the brain is not simply a passive observer but an active predictor of its sensory input, is supported by an enormous amount of evidence in fields as diverse as human ethology and physiology, besides neuroscience. Hence, a central aspect of this review is to illustrate how neuronal sequences can be understood as critical for probabilistic predictive information processing, and what dynamical principles can be used as generators of neuronal sequences. Moreover, since different lines of evidence from neuroscience and computational modeling suggest that the brain is organized in a functional hierarchy of time scales, we will also review how models based on sequence-generating principles can be embedded in such a hierarchy, to form a generative model for recognition and prediction of sensory input. We shortly introduce the Bayesian brain hypothesis as a prominent mathematical description of how online, i.e., fast, recognition, and predictions may be computed by the brain. Finally, we briefly discuss some recent advances in machine learning, where spatiotemporally structured methods (akin to neuronal sequences) and hierarchical networks have independently been developed for a wide range of tasks. We conclude that the investigation of specific dynamical and structural principles of sequential brain activity not only helps us understand how the brain processes information and generates predictions, but also informs us about neuroscientific principles potentially useful for designing more efficient artificial neuronal networks for machine learning tasks.

A comparison of passive and active gear in fish community assessments in summer versus winter

Fish populations and communities are monitored using a variety of sampling gears, each with their own inherent biases. Gear biases can arise from a number of factors, such as fish species characteristics (e.g., body shape/size, physiology, and behaviour), species habitat requirements, as well as the abiotic characteristics of sites sampled. Such factors and their effects on gear selectivity are also heavily influenced by seasonality. Consequently, understanding the effects of seasonal changes on gear selectivity is of vital importance, especially during the winter—a season seldom studied in freshwater systems. Here, we compared the selectivity, efficiency, and degree of biodiversity in fish communities sampled using three gear types: minnow traps, Windermere traps, and electrofishing during summer and winter in Hamilton Harbour, ON, Canada. Catch per unit effort was similar among gear types in the summer, whereas in the winter, minnow traps captured the most fish. Electrofishing samples were the most species rich and species diverse, but only during the summer. Additionally, sampling efficiency and the number of different species encountered was highest when all gear types were used in combination, followed by electrofishing alone, Windermere traps alone, and minnow traps alone in both seasons. Each gear type differed in its selectivity for certain species, which was further influenced by seasonality. This resulted in the fish communities caught within each gear type being dissimilar from one another. Our study highlights the importance of understanding gear type selectivity, particularly under different climatic conditions, and outlines the importance of incorporating multiple gear types in ecological assessments of fish populations and communities.

Temporal and geographical comparison of bulk tank milk and water microbiota composition in Brazilian dairy farms

This study investigated the relationship between the bacterial communities of bulk tank milk (BTM) and water used in Brazilian dairy farms. We also explored the association between BTM microbiota and its quality parameters (i.e., somatic cell count [SCC] and total bacteria count [TBC]). Water and BTM samples were collected twice for high throughput metataxonomic characterization. Milk samples were collected for SCCs, TBCs, and antimicrobial residue analysis. Water samples were submitted for physico-chemical and microbiological analyses. Overall, the BTM bacterial community was not influenced by the water microbiota. Furthermore, a higher number of Bacillus spp. and a tendency toward a higher number of Lactococcus spp. was associated with a higher TBC, and consequently could be used as an indicator of milk quality. A higher number of Streptococcus spp. and a tendency toward a higher number of Staphylococcus spp. were associated with a higher SCC. Apart from a variation on the content of the Bacillus taxa, no effect of sampling time on BTM bacterial community was observed. Finally, a negative correlation between the number of different species (richness) on BTM and SCC was found.

Effect of the reaction mechanism on the numerical prediction of the performance of a scramjet combustor at cruise flight 8 Mach number

A numerical investigation of the effect of the hydrogen-air reaction mechanism on the prediction of supersonic combustion was conducted. Different reaction mechanisms with different number of species and reactions were investigated at a Scramjet hypersonic flight trajectory. A generic three-dimensional supersonic combustor was investigated at flight 8 Mach number condition and at an altitude of 30 km. Numerical simulations were performed to determine the influence of the size of the reaction mechanism on the prediction of supersonic lifted flames, in a Scramjet flight trajectory were the combustor inflow conditions are close to the hydrogen-air self-ignition limit. Results showed significant influence of the number of species and reactions involved in the mechanism on the prediction of the ignition length. Shorter ignition delays were obtained with a reduced mechanism. Similarly, combustion efficiency was affected by the reduced mechanism dropping nearly 15%, compared to the reference scheme. On the other hand, no significant influence of the reaction mechanism was observed on the combustor pressure drop. Pressure losses nearly converge to the same values by the exit of the combustor. The present data suggest that the main observed differences are on the different prediction of the location where self-ignition occurred. We show how the ignition delay is affected by the omission of secondary species and steps reactions leading to shorter ignition delays or even attached flames which are not expected to occur at the investigated hypersonic flight condition.

Sampling nearshore Infaunal ‘weeds’ rather than ‘trees’: Does this orthodoxy undervalue importance of sedimentary biomes?

This study compares species composition, abundance, biomass, and several other factors by which sedentary megafaunal and macrofaunal assemblages at depths between 14 m and 55 m on the Hueneme Shelf in southern California, USA, can be characterized. It details fundamental differences between these assemblages in this study area and demonstrates how little we know about a diverse range of attributes that are important in describing and evaluating infaunal assemblages. It provides strong support for a recent claim that: “The soft-sediment seafloor of the open continental shelf is among the least-known biomes on Earth, despite its high diversity and importance to fisheries and biogeochemical cycling” (Tomašových and Kidwell, 2017).Basic and applied research after the 1950s transformed infaunal ecology from a discipline focused primarily on long-lived sedentary megafauna (analogous to ‘trees’ on land) into a field concentrating on opportunistic or ephemeral macrofauna (analogous to ‘weeds’ on land). Based on findings of this study, macrofaunal assemblages play a subordinate role in ecosystem dynamics. Most research in recent decades has overlooked contributions by sedentary megafauna. This focus leads to a poor understanding of the dynamics of these widespread ecosystems, severely undervalues their ecological importance and production, underestimates impacts of anthropogenic activities on unconsolidated sediments as well as the duration of recovery trajectories following disturbances.Sedentary megafaunal and macrofaunal assemblages were quite different in virtually all aspects assessed during this analysis. Although macrofauna in this study had far greater species richness and were far more abundant than sedentary megafauna, conservative estimates for megafaunal biomass and secondary production indicate these organisms contribute substantially more energy to higher trophic levels than macrofauna. In addition, the megafaunal assemblages are characterized by many influential ‘ecosystem engineers’. Consequently, the differences in numbers of species and individuals are irrelevant with regard to determining value to the ecosystem. Megafauna in this area also exhibited more sensitivity in environmental factors. They live substantially longer than macrofauna, likely leading to greater stability in megafaunal assemblages. These differences indicate that current approaches focusing on macrofauna severely undervalue infaunal resources and contributions to higher trophic levels. They imply that studies of megafaunal assemblages should provide considerably greater insight into ecosystem dynamics and secondary production than macrofaunal assemblages and would have greater power to predict or assess environmental degradation or change, and document or predict recovery trajectories.