Hasil untuk "Natural history (General)"

Eleni Adamopoulou, Lefteris Moussiades

Abstract This literature review presents the History, Technology, and Applications of Natural Dialog Systems or simply chatbots. It aims to organize critical information that is a necessary background for further research activity in the field of chatbots. More specifically, while giving the historical evolution, from the generative idea to the present day, we point out possible weaknesses of each stage. After we present a complete categorization system, we analyze the two essential implementation technologies, namely, the pattern matching approach and machine learning. Moreover, we compose a general architectural design that gathers critical details, and we highlight crucial issues to take into account before system design. Furthermore, we present chatbots applications and industrial use cases while we point out the risks of using chatbots and suggest ways to mitigate them. Finally, we conclude by stating our view regarding the direction of technology so that chatbots will become really smart.

L. Judd, H. Akiskal, Pamela J. Schettler et al.

Lei Xu, Lei Xu, Lei Xu et al.

Grasping the genetic structure of marine fish populations is vital for comprehending species connectivity patterns and determining the appropriate spatiotemporal scales for conservation management strategies. Here, we analyzed the population genetics of the Orangefin Ponyfish (Photopectoralis bindus Valenciennes, 1835) by examining a portion of the gene coding for the mitochondrial cytochrome c oxidase subunit I. The aim was to evaluate the haplotype pattern, genetic structure, demographic history, as well as the influence of ecological connectivity through the Qiongzhou Strait on the distribution patterns of this species in the northern South China Sea and the Beibu Gulf. In total, 257 specimens yielded only 13 haplotypes, with the predominant haplotype present at all sampling locations. The analysis revealed a “star-like” haplotype pattern, indicating low levels of both haplotype and nucleotide diversity. Additionally, a small but significant genetic structure was observed between the coastal regions flanking the Leizhou Peninsula. These patterns in the haplotype network and genetic structure may be significantly influenced by contemporary currents, particularly through the connectivity of the Qiongzhou Strait. Tajima’s D and Fu’s Fs demonstrated pronouncedly negative values, along with a unimodal mismatch distribution, suggested a recent demographic expansion of Photopectoralis bindus during the late Pleistocene, likely influenced by fluctuations in sea levels.

Anping Shu, Jiapin Zhu, Baoshan Cui et al.

By offering natural protection along offshore wetlands, mangroves play a crucial role in providing great ecological and economic benefits to local communities. However, mangroves are currently facing an increasing threat of decline worldwide due to widespread human activities and climate change. Recently, eco-friendly wooden fences have been deployed along eroded coasts for mangrove restoration projects, and these fences have the capability to attenuate incoming waves and strengthen sediment deposition in new habitats for mangrove colonization and persistence. However, the design and performance of the fences used can differ substantially among different projects; therefore, it is necessary to study the major factors affecting the wave dissipation performance of these fences and find out a more effective structural design. Thus, we focus on two distinct types of fences with and without porous infill to study the function of infill porosity and frame density, and physical experiments of waves transmission through the fences were carried out in a wave flume, in which nine wooden fences with varied infill porosities (0.60–0.90) and frame densities (0.40 and 0.70) were predetermined to measure the wave transmission, reflection, and wave dissipation. In total, 180 experimental runs were conducted under 18 wave conditions with different wave steepness. The results showed that the fence with a lower infill porosity appears to increase wave transmission coefficient that comes at a cost of a higher reflection coefficient and less wave-energy dissipation inside the fence, and the fence with the highest porosity infills (90%) is nearly equivalent to the fence without any infills but a dense frame in terms of wave damping performance. Moreover, the wave transmission through both fences with and without infill can be remarkably affected by incoming wave steepness. The outcome of the research is not only indicating the importance of the appropriate infill porosity in attenuating incoming waves but also guiding the design of mangrove restoration project in offshore wetlands.

P.J. Stephenson

María Virginia Palchetti, Fernando Zamudio, Sebastián Zeballos et al.

Plants are essential for our lives because they provide food, medicine, fuel, shelter, and immaterial resources. Understanding patterns of plant uses through large-scale plant use analysis may contribute to the development of a biocultural conservation approach. We conducted a systematic review to assess current knowledge of the ethnoflora of Argentina, as well as to identify taxonomic and geographic patterns of ethnobotanical uses of native plants at the large scale. We analyzed 124 articles reporting the use of 1706 species. We found that the most widely studied region and use category were Chaco and medicine, respectively. The number of useful native species within a family was positively related to the total native species in each family at the country level. In general, species of greatest cultural importance at the country level had a wide distribution. Almost 70% of native plants used in one phytogeographic province were exclusive to it, and species with the highest importance were characteristic elements of its vegetation. We found that southern Argentina has an exclusive ethnoflora that differs from that in a large area of central and northern Argentina. Our review highlights that plants used by people are intimately associated with the local environment, and that species with great cultural importance across phytogeographic provinces are frequent in the landscape. We provide the first analysis of ethnobotanical studies and a database of useful native plants across Argentina. This information highlights strengths and gaps in knowledge of useful native species, which is crucial for conservation, sustainability and human well-being.

Bin Wang, Bin Wang, Bin Wang et al.

The summer hypoxia off the Changjiang Estuary is one of the largest coastal hypoxic systems in the world and has displayed spatial heterogeneity in recent years. Based on observation data in the summer of 2014, hypoxia was identified both in the bottom and mid-layers. Except for the typical bottom hypoxia in the submarine canyon, the subsurface oxygen minima (SOM) were captured in the mid-layer of 10~15 m, with lower dissolved oxygen in the mid-layer than at the bottom (30–50 m). This SOM phenomenon was located in the lower boundary of the pycnocline and above the Taiwan warm current (TWC) and Kuroshio subsurface water (KSSW). Due to the southern expansion of Changjiang diluted water (CDW), a high phytoplankton biomass (the maximum chlorophyll a of 25 μg L−1, pH of 8.6, and DO of 11 mg L−1) band occupied the surface area along 123°E. By analyzing the 24-h continuous observation and high-resolution profile data, we revealed that the subsurface oxygen minima were predominantly controlled by remineralization and bottom-flushing effects. Fast local consumption occurred near the pycnocline layer, while the lateral transport of oxygen-rich ambient water replenished the bottom oxygen deficit from south to north. We summarize and contextualize three hot spots of hypoxia into a conceptual diagram and emphasize the influences of advection, mixing, and respiration on their location and severity. Overall, compared with the discussion about the low DO background of TWC/KSSW, this research highlights the flushing effects of TWC/KSSW that will reshape the hypoxia structure and alleviate the hypoxia severity in the south hypoxia area off the Changjiang Estuary.

Javier Montenegro, Allen G. Collins, Russell R. Hopcroft et al.

IntroductionBotrynema, a genus of medusozoans in the trachyline family Halicreatidae, currently contains two species: B. brucei and B. ellinorae, distinguished by the presence or absence, respectively, of an apical knob as a diagnostic character. However, no study has corroborated if these taxonomic diagnoses have a biological and evolutionary basis. Therefore, in this study we attempted to address the question “do the two nominal species in the genus Botrynema represent independent phylogenetic lineages, or two phenotypic variants of a single species?MethodsIn this study we took advantage of legacy collections from different research expeditions across the globe from 2000 to 2021 to study the phylogenetics and taxonomy of the genus Botrynema.ResultsB. brucei and B. ellinorae present partially overlapping vertical distributions in the Arctic and as a whole in the Arctic the genus seems to be limited to the Atlantic water masses. The phylogenetic reconstruction based on the concatenated alignment corroborates the validity of the family Halicreatidae and of genus Botrynema as monophyletic groups. However no clear differentiation was found between the two presently accepted species, B. ellinorae and B. brucei.DiscussionBased on the evidence we gathered, we conclude that while the genus Botrynema does contain at least two species lineages, these lineages are not concordant with current species definitions. The species B. ellinorae is reassigned as a subspecies of B. brucei and diagnostic characters are provided.

Laura Bosco, Laura Bosco, Damaris Siegenthaler et al.

Alternative farming methods must be deployed to mitigate the detrimental impacts of intensive agriculture on climate, biodiversity, and ecosystem services. Organic and biodynamic farming are environmental-friendly practices that progressively replace conventional agriculture. While potential biodiversity benefits of organic vs. conventional farming have been studied repeatedly, the effects of biodynamic farming on biodiversity remain ill-understood. We investigated the effects of these three main management regimes, and their interaction with ground vegetation cover, on vineyard invertebrate communities in SW Switzerland. Invertebrates were sampled three times during the vegetation season in 2016, focusing on ground-dwelling (pitfall traps) and epiphytic (sweep-netting) invertebrates, and their abundance was modelled for single, additive, and interactive influences of management and ground vegetation cover. Overall, organic and, but to a lesser degree, biodynamic vineyards provided better conditions for invertebrate abundance than conventional vineyards. On the one hand, there was a significant interaction between management and ground vegetation cover for epiphytic invertebrates with a positive linear increase in abundance in organic, a positive curvilinear relationship in biodynamic but a negative curvilinear response to vegetation cover in conventional vineyards. The abundance of ground-dwelling invertebrates was primarily affected by the management regime alone, i.e. without any interaction with ground vegetation characteristics, leading to much higher abundances in organic compared to conventional vineyards, while biodynamic did not differ from the other two regimes. We interpret the patterns as follows: organic grape production offers more suitable habitat conditions for invertebrates due to a spatially more heterogenous but also less often disturbed (compared to biodynamic management) or destroyed (compared to conventional) ground vegetation cover, in line with the predictions of the intermediate disturbance hypothesis. Biodynamic and conventional viticultural management regimes often provide a habitat that is either too mineral (conventional: ground vegetation widely eliminated) or subject to soil disturbance happening frequently through ploughing (biodynamic). We conclude that alternative farming methods do promote biodiversity in vineyard agro-ecosystems, especially so organic management.

Zhi Li, Minyu Zhou, Yao Ruan et al.

The Pacific white shrimp Litopenaeus vannamei is an economically important penaeid species worldwide. Under farming conditions, the full ovarian maturation of L. vannamei generally depends on the combination of artificial ablation of unilateral eyestalk and feeding high-quality natural diets, suggesting that nutrient accumulation is important to ovarian maturation. In this study, we aimed to investigate the gene expression related to nutritional accumulation in L. vannamei during ovarian development by transcriptomic analysis. A total of 52.45 Gb of high-quality transcriptome data were obtained from 8 samples from the hepatopancreas and ovaries from shrimp in gonadal developmental stages I-IV. A total of 23,149 expressed genes were detected, of which 19,852 were known genes and 3,297 were novel genes. Our study found that genes related to amino acid, carbohydrate and lipid metabolism were expressed at higher levels in the hepatopancreas than in the ovary. The genes for most lipoproteins and their receptors were predominantly expressed in the hepatopancreas, while vitellogenin receptor (VgR) was specifically expressed in the ovary. Moreover, two vitellogenin (Vg) genes were identified, in which one was specifically expressed in the hepatopancreas and defined as Hp-Vg, and the other was specifically expressed in the ovary and defined as Ov-Vg. In addition, genes related to carotenoid metabolism were enriched in the hepatopancreas. This study provides solid evidence that the hepatopancreas is the major exogenous vitellogenesis site for ovarian maturation of L. vannamei. Two distinct Vg genes perform exogenous and endogenous vitellogenesis in the hepatopancreas and ovary in L. vannamei, respectively. The results of this study also presented some new insights for understanding the nutritional dynamics from the hepatopancreas to ovary during ovarian maturation in penaeids.

Anne Watt, Neil Young, Ruth Haites et al.

Two distinct isolates of the facultative parasite, <i>Tetrahymena rostrata</i> were compared, identifying and utilising markers that are useful for studying clonal variation within the species were identified and utilised. The sequences of mitochondrial genomes and several nuclear genes were determined using Illumina short read sequencing. The two <i>T. rostrata</i> isolates had similar morphology. The linear mitogenomes had the gene content and organisation typical of the <i>Tetrahymena</i> genus, comprising 8 tRNA genes, 6 ribosomal RNA genes and 45 protein coding sequences (CDS), twenty-two of which had known function. The two isolates had nucleotide identity within common nuclear markers encoded within the histone H3 and H4 and small subunit ribosomal RNA genes and differed by only 2–4 nucleotides in a region of the characterised actin genes. Variation was observed in several mitochondrial genes and was used to determine intraspecies variation and may reflect the natural history of <i>T. rostrata</i> from different hosts or the geographic origins of the isolates.

Hun Jun Ha, Ho Kyung Ha

Erosion of cohesive sediments is a ubiquitous phenomenon in estuarine and intertidal environments. Several methods have been proposed to determine the surface erosion threshold (τc0), which are still debatable because of the numerous and uncertain definitions. Based on erosion microcosm experiments, we have compared three different methods using (1) eroded mass (EM), (2) erosion rate (ER), and (3) suspended sediment concentration (SSC), and suggested a suitable method for revealing the variation of erodibility in intertidal sediments. Erosion experiments using a microcosm system were carried out in the Muuido tidal flat, west coast of South Korea. The mean values of τc0 for three methods were: 0.20 ± 0.08 Pa (EM); 0.18 ± 0.07 Pa (ER); and (3) 0.17 ± 0.09 Pa (SSC). The SSC method yielded the lowest τc0, due to the outflow of suspended sediment from the erosion chamber of the microcosm. This was because SSC gradually decreased with time after depleting the erodible sediment at a given bed shear stress (τb). Therefore, the regression between SSC and applied τb might skew an x-intercept, resulting in the underestimation (or “not-determined”) of τc0. The EM method yielded robust and accurate (within the range of τb step at which erosion begins) results. The EM method represents how the erodible depth thickens as τb increases and therefore seems better suited than the SSC and ER methods for representing depth-limited erosion of cohesive sediments. Furthermore, this study identified the spatiotemporal variations of τc0 by EM method in an intertidal flat. The τc0 in mud flat was about two times higher than that in mixed flat. Compared to the end of tidal emersion, the sediment was 10–40% more erodible at the beginning stage.

J. Fernandez-Mendoza, S. Shea, A. Vgontzas et al.

Paulina Bolívar, Laurent Guéguen, Laurent Duret et al.

Abstract Background The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the d N /d S ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and d N /d S are apparently absent. Here we explore the role of GC-biased gene conversion on estimates of substitution rates as a potential driver of these unexpected observations. Results We analyze the relationship between d N /d S estimated from alignments of 47 avian genomes and several proxies for effective population size. To distinguish the impact of GC-biased gene conversion from selection, we use an approach that accounts for non-stationary base composition and estimate d N /d S separately for changes affected or unaffected by GC-biased gene conversion. This analysis shows that the impact of GC-biased gene conversion on substitution rates can explain the lack of correlations between life-history traits and d N /d S . Strong correlations between life-history traits and d N /d S are recovered after accounting for GC-biased gene conversion. The correlations are robust to variation in base composition and genomic location. Conclusions Our study shows that gene sequence evolution across a wide range of avian lineages meets the prediction of the nearly neutral theory, the efficacy of selection increases with effective population size. Moreover, our study illustrates that accounting for GC-biased gene conversion is important to correctly estimate the strength of selection.

Michael Piotrowski

Serial sources such as records, registers, and inventories are the ‘classic’ sources for quantitative history. Unstructured, narrative texts such as newspaper articles or reports were out of reach for historical analyses, both for practical reasons&nbsp;— availability, time needed for manual processing — and for methodological reasons: manual coding of texts is notoriously difficult and hampered by low inter-coder reliability. The recent availability of large amounts of digitized sources allows for the application of natural language processing, which has the potential to overcome these problems. However, the automatic evaluation of large amounts of texts — and historical texts in particular — for historical research also brings new challenges. First of all, it requires a source criticism that goes beyond the individual source and also considers the corpus as a whole. It is a well-known problem in corpus linguistics to determine the ‘balancedness’ of a corpus, but when analyzing the content of texts rather than ‘just’ the language, determining the ‘meaningfulness’ of a corpus is even more important. Second, automatic analyses require operationalizable descriptions of the information you are looking for. Third, automatically produced results require interpretation, in particular, when — as in history — the ultimate research question is qualitative, not quantitative. This, finally, poses the question, whether the insights gained could inform formal, i.e., machine-processable, models, which could serve as foundation and stepping stones for further research.

David J Haw, Derek A T Cummings, Justin Lessler et al.

Infectious disease transmission is an inherently spatial process in which a host's home location and their social mixing patterns are important, with the mixing of infectious individuals often different to that of susceptible individuals. Although incidence data for humans have traditionally been aggregated into low-resolution data sets, modern representative surveillance systems such as electronic hospital records generate high volume case data with precise home locations. Here, we use a gridded spatial transmission model of arbitrary resolution to investigate the theoretical relationship between population density, differential population movement and local variability in incidence. We show analytically that a uniform local attack rate is typically only possible for individual pixels in the grid if susceptible and infectious individuals move in the same way. Using a population in Guangdong, China, for which a robust quantitative description of movement is available (a travel kernel), and a natural history consistent with pandemic influenza; we show that local cumulative incidence is positively correlated with population density when susceptible individuals are more connected in space than infectious individuals. Conversely, under the less intuitively likely scenario, when infectious individuals are more connected, local cumulative incidence is negatively correlated with population density. The strength and direction of correlation changes sign for other kernel parameter values. We show that simulation models in which it is assumed implicitly that only infectious individuals move are assuming a slightly unusual specific correlation between population density and attack rate. However, we also show that this potential structural bias can be corrected by using the appropriate non-isotropic kernel that maps infectious-only code onto the isotropic dual-mobility kernel. These results describe a precise relationship between the spatio-social mixing of infectious and susceptible individuals and local variability in attack rates. More generally, these results suggest a genuine risk that mechanistic models of high-resolution attack rate data may reach spurious conclusions if the precise implications of spatial force-of-infection assumptions are not first fully characterized, prior to models being fit to data.

R. Bradley, Lisa C. Bradley, Heath J. Garner et al.

Sebastian Fraune, Sylvain Foret, Adam Michael Reitzel

The phenotype of an animal cannot be explained entirely by its genes. It is now clear that factors other than the genome contribute to the ecology and evolution of animals. Two fundamentally important factors are the associated microbiota and epigenetic regulations. Unlike the genes and regulatory regions of the genome, epigenetics and microbial composition can be rapidly modified, and may thus represent mechanisms for rapid acclimation to a changing environment. At present, the individual functions of epigenetics, microbiomes, and genomic mutations are largely studied in isolation, particularly for species in marine ecosystems. This single variable approach leaves significant questions open for how these mechanisms intersect in the acclimation and adaptation of organisms in different environments. Here, we propose that the starlet sea anemone, Nematostella vectensis, is a model of choice to investigate the complex interplay between adaptation as well as physiological and molecular plasticity in coastal ecosystems. N. vectensis’ geographic range spans four distinct coastlines, including a wide thermocline along the Atlantic coast of North America. N. vectensis is a particularly powerful invertebrate model for studying genome-environment interactions due to (1) the availability of a well-annotated genome, including preexisting data on genome methylation, histone modifications and miRNAs, (2) an extensive molecular toolkit including well-developed protocols for gene suppression and transgenesis, and (3) the simplicity of culture and experimentation in the laboratory. Taken together, N. vectensis has the tractability to connect the functional relationships between a host animal, microbes, and genome modifications to determine mechanisms underlying phenotypic plasticity and local adaptation.

Robert John Wilson, Michael Heath, Douglas Speirs

The North Atlantic copepods Calanus finmarchicus and C. helgolandicus are moving north in response to rising temperatures. Understanding the drivers of their relative geographic distributions is required in order to anticipate future changes. To explore this, we created a new spatially explicit stage-structured model of their populations throughout the North Atlantic. Recent advances in understanding Calanus biology, including U-shaped relationships between growth and fecundity and temperature, and a new model of diapause duration are incorporated in the model. Equations were identical for both species, but some parameters were species-specific. The model was parameterized using Continuous Plankton Recorder Survey data and tested using time series of abundance and fecundity. The geographic distributions of both species were reproduced by assuming that only known interspecific differences and a difference in the temperature influence on mortality exist. We show that differences in diapause capability are not necessary to explain why C. helgolandicus is restricted to the continental shelf. Smaller body size and higher overwinter temperatures likely make true diapause implausible for C. helgolandicus. Known differences were incapable of explaining why only C. helgolandicus exists southwest of the British Isles. Further, the fecundity of C. helgolandicus in the English Channel is much lower than we predict. We hypothesize that food quality is a key influence on the population dynamics of these species. The modelling framework presented can potentially be extended to further Calanus species.