Now showing items 1-20 of 21338

    • High summer temperatures amplify functional differences between coral- and algae-dominated reef communities

      Roth, Florian; Rädecker, Nils; Carvalho, Susana; Duarte, Carlos M.; Saderne, Vincent; Anton Gamazo, Andrea; Silva, Luis; Calleja Cortes, Maria de Lluch; Moran, Xose Anxelu G.; Voolstra, Christian R.; Kürten, Benjamin; Jones, Burton; Wild, Christian (Ecology, Wiley, 2020-10-17) [Article]
      Shifts from coral to algal dominance are expected to increase in tropical coral reefs as a result of anthropogenic disturbances. The consequences for key ecosystem functions such as primary productivity, calcification, and nutrient recycling are poorly understood, particularly under changing environmental conditions. We used a novel in situ incubation approach to compare functions of coral- and algae-dominated communities in the central Red Sea bi-monthly over an entire year. In situ gross and net community primary productivity, calcification, dissolved organic carbon fluxes, dissolved inorganic nitrogen fluxes, and their respective activation energies were quantified to describe the effects of seasonal changes. Overall, coral-dominated communities exhibited 30% lower net productivity and 10 times higher calcification than algae-dominated communities. Estimated activation energies indicated a higher thermal sensitivity of coral-dominated communities. In these communities, net productivity and calcification were negatively correlated with temperature (>40% and >65% reduction, respectively, with +5°C increase from winter to summer), while carbon losses via respiration and dissolved organic carbon release were more than doubled at higher temperatures. In contrast, algae-dominated communities doubled net productivity in summer, while calcification and dissolved organic carbon fluxes were unaffected. These results suggest pronounced changes in community functioning associated with phase shifts. Algae-dominated communities may outcompete coral-dominated communities due to their higher productivity and carbon retention to support fast biomass accumulation while compromising the formation of important reef framework structures. Higher temperatures likely amplify these functional differences, indicating a high vulnerability of ecosystem functions of coral-dominated communities to temperatures even below coral bleaching thresholds. Our results suggest that ocean warming may not only cause but also amplify coral-algal phase shifts in coral reefs.
    • Diatom modulation of select bacteria through use of two unique secondary metabolites

      Shibl, Ahmed A.; Isaac, Ashley; Ochsenkühn, Michael A.; Cardenas, Anny; Fei, Cong; Behringer, Gregory; Arnoux, Marc; Drou, Nizar; Santos, Miraflor P.; Gunsalus, Kristin C.; Voolstra, Christian R.; Amin, Shady A. (Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, 2020-10-17) [Article]
      Unicellular eukaryotic phytoplankton, such as diatoms, rely on microbial communities for survival despite lacking specialized compartments to house microbiomes (e.g., animal gut). Microbial communities have been widely shown to benefit from diatom excretions that accumulate within the microenvironment surrounding phytoplankton cells, known as the phycosphere. However, mechanisms that enable diatoms and other unicellular eukaryotes to nurture specific microbiomes by fostering beneficial bacteria and repelling harmful ones are mostly unknown. We hypothesized that diatom exudates may tune microbial communities and employed an integrated multiomics approach using the ubiquitous diatom Asterionellopsis glacialis to reveal how it modulates its naturally associated bacteria. We show that A. glacialis reprograms its transcriptional and metabolic profiles in response to bacteria to secrete a suite of central metabolites and two unusual secondary metabolites, rosmarinic acid and azelaic acid. While central metabolites are utilized by potential bacterial symbionts and opportunists alike, rosmarinic acid promotes attachment of beneficial bacteria to the diatom and simultaneously suppresses the attachment of opportunists. Similarly, azelaic acid enhances growth of beneficial bacteria while simultaneously inhibiting growth of opportunistic ones. We further show that the bacterial response to azelaic acid is numerically rare but globally distributed in the world’s oceans and taxonomically restricted to a handful of bacterial genera. Our results demonstrate the innate ability of an important unicellular eukaryotic group to modulate select bacteria in their microbial consortia, similar to higher eukaryotes, using unique secondary metabolites that regulate bacterial growth and behavior inversely across different bacterial populations.
    • Bulk and Interfacial Properties of the Decane + Water System in the Presence of Methane, Carbon Dioxide, and Their Mixture

      Yang, Yafan; Nair, Arun Kumar Narayanan; Anwari Che Ruslan, Mohd Fuad; Sun, Shuyu (The Journal of Physical Chemistry B, American Chemical Society (ACS), 2020-10-16) [Article]
      Molecular dynamics simulations are carried out to study the two-phase behavior of the n-decane + water system in the presence of methane, carbon dioxide, and their mixture under reservoir conditions. The simulation studies were complemented by theoretical modeling using the perturbed-chain statistical associating fluid theory (PC-SAFT) equation of state (EoS) and density gradient theory. Our results show that the presence of methane and carbon dioxide decreases the interfacial tension (IFT) of the decane + water system. In general, the IFT increases with increasing pressure and decreasing temperature for the methane + decane + water and carbon dioxide + decane + water systems, similar to what has been found for the corresponding decane + water system. The most important finding of this study is that the presence of carbon dioxide decreases the IFT of the methane + decane + water system. The atomic density profiles provide evidence of the local accumulation of methane and carbon dioxide at the interface, in most of the studied systems. The results of this study show the preferential dissolution in the water-rich phase and enrichment at the interface for carbon dioxide in the methane + carbon dioxide + decane + water system. This indicates the preferential interaction of water with carbon dioxide relative to methane and decane. Notably, there is an enrichment of the interface by decane at high mole fractions of methane in the methane/decane-rich or methane/carbon dioxide/decane-rich phase. Overall, the solubility of methane and carbon dioxide in the water-rich phase increases with increasing pressure and temperature. Additionally, we find that the overall performance of the PC-SAFT EoS and the cubic-plus-association EoS is similar with respect to the calculation of bulk and interfacial properties of these systems.
    • Guest Editorial Special Issue on “Wireless Networks Empowered by Reconfigurable Intelligent Surfaces”

      Di Renzo, Marco; Debbah, Merouane; Alouini, Mohamed-Slim; Yuen, Chau; Marzetta, Thomas; Zappone, Alessio (IEEE Journal on Selected Areas in Communications, Institute of Electrical and Electronics Engineers (IEEE), 2020-10-16) [Article]
      Future wireless networks will be as pervasive as the air we breathe, not only connecting us but embracing us through a web of systems that support personal and societal well-being. That is, the ubiquity, speed and low latency of such networks will allow currently disparate devices and services to become a distributed intelligent communications, sensing, and computing platform.
    • Pan-regional marine benthic cryptobiome biodiversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures.

      Pearman, John K.; Chust, G; Aylagas, E; Villarino, E; Watson, J R; Chenuil, A; Borja, A; Cahill, A E; Carugati, L; Danovaro, R; David, R; Irigoien, X; Mendibil, I; Moncheva, S; Rodríguez-Ezpeleta, N; Uyarra, M C; Carvalho, Susana (Molecular ecology, Wiley, 2020-10-16) [Article]
      Autonomous Reef Monitoring Structures (ARMS) have been applied worldwide to characterize the critical yet frequently overlooked biodiversity patterns of marine benthic organisms. In order to disentangle the relevance of environmental factors in benthic patterns, here, through standardized metabarcoding protocols, we analyze sessile and mobile (
    • Total alkalinity production in a mangrove ecosystem reveals an overlooked Blue Carbon component

      Saderne, Vincent; Fusi, Marco; Thomson, Timothy; Dunne, Aislinn; Mahmud, Fatima; Roth, Florian; Carvalho, Susana; Duarte, Carlos M. (Limnology and Oceanography Letters, Wiley, 2020-10-16) [Article]
      Mangroves have the capacity to sequester organic carbon (Corg) in their sediments permanently. However, the carbon budget of mangroves is also affected by the total alkalinity (TA) budget. Principally, TA emitted from carbonate sediment dissolution is a perennial sink of atmospheric CO2. The assessment of the TA budget of mangrove carbonate sediments in the Red Sea revealed a large TA emission of 403 ± 17 mmol m−2 d−1, independent of light, seasons, or the presence of pneumatophores, compared to −36 ± 10 mmol m−2 d−1 in lagoon sediment. We estimate the TA emission from carbonate dissolution in Red Sea mangroves supported a CO2 uptake of 345 ± 15 gC m−2 yr−1, 23-fold the Corg burial rate of 15 gC m−2 yr−1. The focus on Corg burial in sediments may substantially underestimate the role of mangroves in CO2 removal. Quantifying the role of mangroves in climate change mitigation requires carbonate dissolution to be included in assessments.
    • Metagrating-Based Terahertz Polarization Beam Splitter Designed by Simplified Modal Method

      Ma, Xinyu; Li, Yanfeng; Lu, Yongchang; Han, Jiaguang; Zhang, Xixiang; Zhang, Weili (Frontiers in Physics, Frontiers Media SA, 2020-10-15) [Article]
      Terahertz waves are finding important applications in diverse fields, and meanwhile the manipulation of terahertz waves calls for the development of various functional devices. Here, we have designed and fabricated a metagrating-based polarization beam splitter for terahertz waves using the simplified modal method. By only considering two propagation modes and treating the grating as a Mach-Zehnder interferometer, the method can greatly simplify the reverse grating design process. The parameters of the grating are first obtained under the guidance of the simplified modal method and then improved upon by the finite element method. The fabricated device is finally experimentally demonstrated with a terahertz time-domain spectroscopy system. The diffraction efficiencies of the polarization beam splitter at 0.9 THz are measured to be 69 and 63% for TE and TM waves relative to that of a silicon plate, respectively. The corresponding extinction ratios are 12 and 17 dB for TE and TM waves, respectively. The experiment results agree well with the simulations.
    • Ion-Exchange Materials for Membrane Capacitive Deionization

      McNair, Robert; Szekely, Gyorgy; Dryfe, Robert A. W. (ACS ES&T Water, ACS, 2020-10-14) [Article]
      The scarcity of clean water is a problem affecting large parts of the world. In fact, the World Health Organization/UNICEF Joint Monitoring Programme for Water Supply, Sanitation and Hygiene (2019) estimates that up to 2.2 billion people lack access to safely managed drinking water services. To address this, desalination techniques such as reverse osmosis, flash distillation, and electrodialysis have been utilized to convert the plentiful amounts of salt water into consumable water supplies for the general population. In the past 15 years, membrane capacitive deionization (MCDI) has emerged as an alternative desalination technique that has since received extensive research attention. MCDI has sought to challenge benchmark methods such as reverse osmosis, removing salt by application of a voltage between two electrodes covered with ion-exchange membranes, all under ambient conditions. The incorporation of ion-exchange materials over electrodes in MCDI has been shown to maximize the desalination performance in terms of salt removal and energy efficiency. This review provides a comprehensive assessment of the developments relating to ion-exchange materials in MCDI. The fabrication and characterization methods of the materials have been outlined and compared with those of commercially available ion-exchange membranes where possible. A critical comparison of the ion-exchange materials has been conducted, and the commercial viability of the technologies has been evaluated. In light of the findings of the review, the authors have indicated future directions and action points the field should look to address in the coming years. It is hoped that the findings of this review can contribute to the large-scale commercialization and application of MCDI, which can improve aspects of water treatment and quality, contaminant removal, and sanitation on a global scale.
    • Survey of energy-autonomous solar cell receivers for satellite–air–ground–ocean optical wireless communication

      Kong, Meiwei; Kang, Chun Hong; Alkhazragi, Omar; Sun, Xiaobin; Guo, Yujian; Sait, Mohammed; Holguin Lerma, Jorge Alberto; Ng, Tien Khee; Ooi, Boon S. (Progress in Quantum Electronics, Elsevier BV, 2020-10-14) [Article]
      With the advent of the Internet of Things, energy- and bandwidth-related issues are becoming increasingly prominent in the context of supporting the massive connectivity of various smart devices. To this end, we propose that solar cells with the dual functions of energy harvesting and signal acquisition are critical for alleviating energy-related issues and enabling optical wireless communication (OWC) across the satellite–air–ground–ocean (SAGO) boundaries. Moreover, we present the first comprehensive survey on solar cell-based OWC technology. First, the historical evolution of this technology is summarized, from its beginnings to recent advances, to provide the relative merits of a variety of solar cells for simultaneous energy harvesting and OWC in different application scenarios. Second, the performance metrics, circuit design, and architectural design for energy-autonomous solar cell receivers are provided to help understand the basic principles of this technology. Finally, with a view to its future application to SAGO communication networks, we note the challenges and future trends of research related to this technology in terms of channel characterization, light source development, photodetector development, modulation and multiplexing techniques, and network implementations.
    • Organic carbon export and loss rates in the Red Sea

      Kheireddine, Malika; Dall'Olmo, Giorgio; Ouhssain, Mustapha; Krokos, Georgios; Claustre, Hervé; Schmechtig, Catherine; Poteau, Antoine; Zhan, Peng; Hoteit, Ibrahim; Jones, Burton (Global Biogeochemical Cycles, American Geophysical Union (AGU), 2020-10-14) [Article]
      The export and fate of organic carbon in the mesopelagic zone are still poorly understood and quantified due to lack of observations. We exploited data from a BGC-Argo float that was deployed in the Red Sea to study how a warm and hypoxic environment can affect the fate of the organic carbon in the ocean’s interior. We observed that only 10% of the particulate organic carbon (POC) exported survived at depth due to remineralization processes in the upper mesopelagic zone. We also found that POC exported was rapidly degraded in a first stage and slowly in a second one, which may be dependent on the palatability of the organic matter. We observed that AOU-based loss rates (a proxy of the remineralization of total organic matter) were significantly higher than the POC-based loss rates, likely because changes in AOU are mainly attributed to changes in dissolved organic carbon. Finally, we showed that POC- and AOU-based loss rates could be expressed as a function of temperature and oxygen concentration. These findings advance our understanding of the biological carbon pump and mesopelagic ecosystem.
    • Analogue neuro-memristive convolutional dropout nets

      Krestinskaya, O.; James, Alex P. (Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, The Royal Society, 2020-10-14) [Article]
      Randomly switching neurons ON/OFF while training and inference process is an interesting characteristic of biological neural networks, that potentially results in inherent adaptability and creativity expressed by human mind. Dropouts inspire from this random switching behaviour and in the artificial neural network they are used as a regularization techniques to reduce the impact of over-fitting during the training. The energy-efficient digital implementations of convolutional neural networks (CNN) have been on the rise for edge computing IoT applications. Pruning larger networks and optimization for performance accuracy has been the main direction of work in this field. As opposed to this approach, we propose to build a near-sensor analogue CNN with high-density memristor crossbar arrays. Since several active elements such as amplifiers are used in analogue designs, energy efficiency becomes a main challenge. To address this, we extend the idea of using dropouts in training to also the inference stage. The CNN implementations require a subsampling layer, which is implemented as a mean pooling layer in the design to ensure lower energy consumption. Along with the dropouts, we also investigate the effect of non-idealities of memristor and that of the network.
    • Interleukin-26 activates macrophages and facilitates killing of Mycobacterium tuberculosis

      Hawerkamp, Heike C.; van Geelen, Lasse; Korte, Jan; Di Domizio, Jeremy; Swidergall, Marc; Momin, Afaque Ahmad Imtiyaz; Guzmán-Vega, Francisco J.; Arold, Stefan T.; Ernst, Joachim; Gilliet, Michel; Kalscheuer, Rainer; Homey, Bernhard; Meller, Stephan (Scientific Reports, Springer Science and Business Media LLC, 2020-10-14) [Article]
      Abstract Tuberculosis-causing Mycobacterium tuberculosis (Mtb) is transmitted via airborne droplets followed by a primary infection of macrophages and dendritic cells. During the activation of host defence mechanisms also neutrophils and T helper 1 (TH1) and TH17 cells are recruited to the site of infection. The TH17 cell-derived interleukin (IL)-17 in turn induces the cathelicidin LL37 which shows direct antimycobacterial effects. Here, we investigated the role of IL-26, a TH1- and TH17-associated cytokine that exhibits antimicrobial activity. We found that both IL-26 mRNA and protein are strongly increased in tuberculous lymph nodes. Furthermore, IL-26 is able to directly kill Mtb and decrease the infection rate in macrophages. Binding of IL-26 to lipoarabinomannan might be one important mechanism in extracellular killing of Mtb. Macrophages and dendritic cells respond to IL-26 with secretion of tumor necrosis factor (TNF)-α and chemokines such as CCL20, CXCL2 and CXCL8. In dendritic cells but not in macrophages cytokine induction by IL-26 is partly mediated via Toll like receptor (TLR) 2. Taken together, IL-26 strengthens the defense against Mtb in two ways: firstly, directly due to its antimycobacterial properties and secondly indirectly by activating innate immune mechanisms.
    • Biofilm removal efficacy using direct electric current in cross-flow ultrafiltration processes for water treatment

      Kerdi, Sarah; Qamar, Adnan; Vrouwenvelder, Johannes S.; Ghaffour, NorEddine (Journal of Membrane Science, Elsevier BV, 2020-10-14) [Article]
      Biofouling of membranes in water treatment is considered as one of the major practical problems. A novel and an efficient approach for cleaning biofilm grown on the membrane surface is proposed by applying a direct electric current (124 mA, 90 s) through platinum electrodes inside a cross-flow ultrafiltration channel. Depending on the electrochemical reactions occurring at the electrodes, either chlorine or hydrogen-producing configuration is realized by interchanging the current polarity. Baseline determination of the amount of chlorine generated and change in pH is assessed as a function of current intensity, linear cross-flow velocity, and duration of applied current. The efficiency of the proposed method is determined by investigating electrically treated biofilm through bacterial inactivation using Confocal Laser Scanning Microscopy (CLSM), bacterial cell structure changes through Scanning Electron Microscopy (SEM), and by estimating the amount of biomass removal through Optical Coherence Tomography (OCT). When a chlorine-producing electrode is placed at the inlet of the flow cell, 68% of bacterial inactivation is achieved without any modification of bacterial cell shape. Furthermore, a high and near-complete biomass removal is achieved (99%) after a subsequent forward flush of the electrically treated biofilm. However, placing a hydrogen-producing electrode at the inlet reveals a slightly lower bacterial inactivation (65%) and lower biomass removal (77%). Additional systematic experiments using individually sodium hydroxide (NaOH), sodium hypochlorite (NaOCl), or gas microbubbles enabled to elucidate the cause of biofilm removal, synergic effect of caustic agent NaOH and microbubbles.
    • A Comprehensive Subcellular Atlas of the Toxoplasma Proteome via hyperLOPIT Provides Spatial Context for Protein Functions.

      Barylyuk, Konstantin; Koreny, Ludek; Ke, Huiling; Butterworth, Simon; Crook, Oliver M; Lassadi, Imen; Gupta, Vipul; Tromer, Eelco; Mourier, Tobias; Stevens, Tim J; Breckels, Lisa M; Pain, Arnab; Lilley, Kathryn S; Waller, Ross F (Cell host & microbe, Elsevier BV, 2020-10-14) [Article]
      Apicomplexan parasites cause major human disease and food insecurity. They owe their considerable success to highly specialized cell compartments and structures. These adaptations drive their recognition, nondestructive penetration, and elaborate reengineering of the host's cells to promote their growth, dissemination, and the countering of host defenses. The evolution of unique apicomplexan cellular compartments is concomitant with vast proteomic novelty. Consequently, half of apicomplexan proteins are unique and uncharacterized. Here, we determine the steady-state subcellular location of thousands of proteins simultaneously within the globally prevalent apicomplexan parasite Toxoplasma gondii. This provides unprecedented comprehensive molecular definition of these unicellular eukaryotes and their specialized compartments, and these data reveal the spatial organizations of protein expression and function, adaptation to hosts, and the underlying evolutionary trajectories of these pathogens.
    • Flexible Cross-Modal Hashing

      Yu, Guoxian; Liu, Xuanwu; Wang, Jun; Domeniconi, Carlotta; Zhang, Xiangliang (IEEE Transactions on Neural Networks and Learning Systems, Institute of Electrical and Electronics Engineers (IEEE), 2020-10-14) [Article]
      Hashing has been widely adopted for large-scale data retrieval in many domains due to its low storage cost and high retrieval speed. Existing cross-modal hashing methods optimistically assume that the correspondence between training samples across modalities is readily available. This assumption is unrealistic in practical applications. In addition, existing methods generally require the same number of samples across different modalities, which restricts their flexibility. We propose a flexible cross-modal hashing approach (FlexCMH) to learn effective hashing codes from weakly paired data, whose correspondence across modalities is partially (or even totally) unknown. FlexCMH first introduces a clustering-based matching strategy to explore the structure of each cluster and, thus, to find the potential correspondence between clusters (and samples therein) across modalities. To reduce the impact of an incomplete correspondence, it jointly optimizes the potential correspondence, the crossmodal hashing functions derived from the correspondence, and a hashing quantitative loss in a unified objective function. An alternative optimization technique is also proposed to coordinate the correspondence and hash functions and reinforce the reciprocal effects of the two objectives. Experiments on public multimodal data sets show that FlexCMH achieves significantly better results than state-of-the-art methods, and it, indeed, offers a high degree of flexibility for practical cross-modal hashing tasks.
    • Predicting Candidate Genes From Phenotypes, Functions, And Anatomical Site Of Expression.

      Chen, Jun; Althagafi, Azza Th.; Hoehndorf, Robert (Bioinformatics (Oxford, England), Oxford University Press (OUP), 2020-10-14) [Article]
      MOTIVATION:Over the past years, many computational methods have been developed to incorporate information about phenotypes for disease gene prioritization task. These methods generally compute the similarity between a patient's phenotypes and a database of gene-phenotype to find the most phenotypically similar match. The main limitation in these methods is their reliance on knowledge about phenotypes associated with particular genes, which is not complete in humans as well as in many model organisms such as the mouse and fish. Information about functions of gene products and anatomical site of gene expression is available for more genes and can also be related to phenotypes through ontologies and machine learning models. RESULTS:We developed a novel graph-based machine learning method for biomedical ontologies which is able to exploit axioms in ontologies and other graph-structured data. Using our machine learning method, we embed genes based on their associated phenotypes, functions of the gene products, and anatomical location of gene expression. We then develop a machine learning model to predict gene-disease associations based on the associations between genes and multiple biomedical ontologies, and this model significantly improves over state of the art methods. Furthermore, we extend phenotype-based gene prioritization methods significantly to all genes which are associated with phenotypes, functions, or site of expression. AVAILABILITY:Software and data are available at https://github.com/bio-ontology-research-group/DL2Vec.
    • Extended field-of-view ultrathin microendoscopes for high-resolution two-photon imaging with minimal invasiveness

      Fellin, Tommaso; Antonini, Andrea; Sattin, Andrea; Moroni, Monica; Bovetti, Serena; Moretti, Claudio; Succol, Francesca; Forli, Angelo; Vecchia, Dania; Rajamanickam, Vijayakumar Palanisamy; Bertoncini, Andrea; Panzeri, Stefano; Liberale, Carlo (eLife, eLife Sciences Publications, Ltd, 2020-10-13) [Article]
      Imaging neuronal activity with high and homogeneous spatial resolution across the field-of-view (FOV) and limited invasiveness in deep brain regions is fundamental for the progress of neuroscience, yet is a major technical challenge. We achieved this goal by correcting optical aberrations in gradient index lens-based ultrathin (< 500 μm) microendoscopes using aspheric microlenses generated through 3D-microprinting. Corrected microendoscopes had extended FOV (eFOV) with homogeneous spatial resolution for two-photon fluorescence imaging and required no modification of the optical set-up. Synthetic calcium imaging data showed that, compared to uncorrected endoscopes, eFOV-microendoscopes led to improved signal-to-noise ratio and more precise evaluation of correlated neuronal activity. We experimentally validated these predictions in awake head-fixed mice. Moreover, using eFOV-microendoscopes we demonstrated cell-specific encoding of behavioral state-dependent information in distributed functional subnetworks in a primary somatosensory thalamic nucleus. eFOV-microendoscopes are, therefore, small-crosssection ready-to-use tools for deep two-photon functional imaging with unprecedentedly high and homogeneous spatial resolution.
    • Unlocking the relationships among population structure, plant architecture, growing season, and environmental adaptation in Henan wheat cultivars.

      Yang, Jian; Zhou, Yanjie; Hu, Weiguo; Zhang, Yu'e; Zhou, Yong; Chen, Yongxing; Wang, Xicheng; Zhao, Hong; Cao, Tingjie; Liu, Zhiyong (BMC plant biology, Springer Science and Business Media LLC, 2020-10-13) [Article]
      BACKGROUND:Ecological environments shape plant architecture and alter the growing season, which provides the basis for wheat genetic improvement. Therefore, understanding the genetic basis of grain yield and yield-related traits in specific ecological environments is important. RESULTS:A structured panel of 96 elite wheat cultivars grown in the High-yield zone of Henan province in China was genotyped using an Illumina iSelect 90 K SNP assay. Selection pressure derived from ecological environments of mountain front and plain region provided the initial impetus for population divergence. This determined the dominant traits in two subpopulations (spike number and spike percentage were dominance in subpopulation 2:1; thousand-kernel weight, grain filling rate (GFR), maturity date (MD), and fertility period (FP) were dominance in subpopulation 2:2), which was also consistent with their inheritance from the donor parents. Genome wide association studies identified 107 significant SNPs for 12 yield-related traits and 10 regions were pleiotropic to multiple traits. Especially, GY was co-located with MD/FP, GFR and HD at QTL-ple5A, QTL-ple7A.1 and QTL-ple7B.1 region. Further selective sweep analysis revealled that regions under selection were around QTLs for these traits. Especially, grain yield (GY) is positively correlated with MD/FP and they were co-located at the VRN-1A locus. Besides, a selective sweep signal was detected at VRN-1B locus which was only significance to MD/FP. CONCLUSIONS:The results indicated that extensive differential in allele frequency driven by ecological selection has shaped plant architecture and growing season during yield improvement. The QTLs for yield and yield components detected in this study probably be selectively applied in molecular breeding.
    • Semantic similarity and machine learning with ontologies.

      Kulmanov, Maxat; Smaili, Fatima Z.; Gao, Xin; Hoehndorf, Robert (Briefings in bioinformatics, Oxford University Press (OUP), 2020-10-13) [Article]
      Ontologies have long been employed in the life sciences to formally represent and reason over domain knowledge and they are employed in almost every major biological database. Recently, ontologies are increasingly being used to provide background knowledge in similarity-based analysis and machine learning models. The methods employed to combine ontologies and machine learning are still novel and actively being developed. We provide an overview over the methods that use ontologies to compute similarity and incorporate them in machine learning methods; in particular, we outline how semantic similarity measures and ontology embeddings can exploit the background knowledge in ontologies and how ontologies can provide constraints that improve machine learning models. The methods and experiments we describe are available as a set of executable notebooks, and we also provide a set of slides and additional resources at https://github.com/bio-ontology-research-group/machine-learning-with-ontologies.
    • Stability theory of nano-fluid over an exponentially stretching cylindrical surface containing microorganisms.

      Ferdows, M; Hossan, Amran; Bangalee, M Z I; Sun, Shuyu; Alzahrani, Faris (Scientific reports, Springer Science and Business Media LLC, 2020-10-13) [Article]
      This research is emphasized to describe the stability analysis in the form of dual solution of the flow and heat analysis on nanofluid over an exponential stretching cylindrical surface containing microorganisms. The research is also implemented to manifest the dual profiles of velocity, temperature and nanoparticle concentration in the effect of velocity ratio parameter ([Formula: see text]). Living microorganisms' cell are mixed into the nanofluid to neglect the unstable condition of nano type particles. The governing equations are transformed to non-linear ordinary differential equations with respect to pertinent boundary conditions by using similarity transformation. The significant differential equations are solved using build in function bvp4c in MATLAB. It is seen that the solution is not unique for vertical stretching sheet. This research is reached to excellent argument when found results are compared with available result. It is noticed that dual results are obtained demanding on critical value ([Formula: see text]), the meanings are indicated at these critical values both solutions are connected and behind these critical value boundary layer separates thus the solution are not stable.