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Recent Submissions

  • Impact of osmotic and thermal isolation barrier on concentration and temperature polarization and energy efficiency in a novel FO-MD integrated module

    Son, Hyuk Soo; Kim, Youngjin; Nawaz, Muhammad Saqib; Al-Hajji, Mohammed Ali; Abu-Ghdaib, Muhannad; Soukane, Sofiane; Ghaffour, NorEddine (Journal of Membrane Science, Elsevier BV, 2020-10-18) [Article]
    In this study, a novel integrated forward osmosis - membrane distillation (FO-MD) module equipped with an isolation barrier carefully placed between the FO and MD membranes is experimentally investigated, and its performance is compared with a conventional hybrid module. The function of the isolation barrier is to osmotically and thermally separate the FO draw solution (DS) and MD feed channels. A systematic approach is adopted to compare the flux through both modules under (i) different and similar hydrodynamic conditions, (ii) different DS concentrations and temperatures, and (iii) different feed solution concentrations. All experiments were performed for 9 h each in batch mode using a custom-made compact module. New FO and MD membrane sheets were mounted for each experiment to ensure similarity in operating conditions. The proposed module design increased the flux by 22.1% using the same module dimensions but different hydrodynamic conditions. The flux increased by 16.6% using the same hydrodynamic conditions but different module dimensions. The FO/MD energy ratio reduced from 0.89 to 0.64 for the novel module, indicating better utilization of energy (primarily from MD). The gain output ratio (GOR) increased on average by 15.8% for the novel module compared to the conventional module, with a maximum increment of 20.7%. The temperature and concentration polarization coefficients in the MD operations showed improvements of 17.4% and 2.6%, respectively. The presence of the isolation barrier inside the integrated module indicated promising improvements of the flux and internal heat recovery, and further significant enhancements are expected for larger scale modules. Additionally, the novel module design offers unprecedented process integration opportunities for FO-MD as well as other membrane hybrid systems.
  • Learning from Scholarly Attributed Graphs for Scientific Discovery

    Akujuobi, Uchenna Thankgod (2020-10-18) [Dissertation]
    Advisor: Zhang, Xiangliang
    Committee members: Moshkov, Mikhail; Hoehndorf, Robert; Zhang, Min
    Research and experimentation in various scientific fields are based on the knowledge and ideas from scholarly literature. The advancement of research and development has, thus, strengthened the importance of literary analysis and understanding. However, in recent years, researchers have been facing massive scholarly documents published at an exponentially increasing rate. Analyzing this vast number of publications is far beyond the capability of individual researchers. This dissertation is motivated by the need for large scale analyses of the exploding number of scholarly literature for scientific knowledge discovery. In the first part of this dissertation, the interdependencies between scholarly literature are studied. First, I develop Delve – a data-driven search engine supported by our designed semi-supervised edge classification method. This system enables users to search and analyze the relationship between datasets and scholarly literature. Based on the Delve system, I propose to study information extraction as a node classification problem in attributed networks. Specifically, if we can learn the research topics of documents (nodes in a network), we can aggregate documents by topics and retrieve information specific to each topic (e.g., top-k popular datasets). Node classification in attributed networks has several challenges: a limited number of labeled nodes, effective fusion of topological structure and node/edge attributes, and the co-existence of multiple labels for one node. Existing node classification approaches can only address or partially address a few of these challenges. This dissertation addresses these challenges by proposing semi-supervised multi-class/multi-label node classification models to integrate node/edge attributes and topological relationships. The second part of this dissertation examines the problem of analyzing the interdependencies between terms in scholarly literature. I present two algorithms for the automatic hypothesis generation (HG) problem, which refers to the discovery of meaningful implicit connections between scientific terms, including but not limited to diseases, drugs, and genes extracted from databases of biomedical publications. The automatic hypothesis generation problem is modeled as a future connectivity prediction in a dynamic attributed graph. The key is to capture the temporal evolution of node-pair (term-pair) relations. Experiment results and case study analyses highlight the effectiveness of the proposed algorithms compared to the baselines’ extension.
  • Dynamic Programming Multi-Objective Combinatorial Optimization

    Mankowski, Michal (2020-10-18) [Dissertation]
    Advisor: Moshkov, Mikhail
    Committee members: Keyes, David E.; Shihada, Basem; Boros, Endre
    In this dissertation, we consider extensions of dynamic programming for combinatorial optimization. We introduce two exact multi-objective optimization algorithms: the multi-stage optimization algorithm that optimizes the problem relative to the ordered sequence of objectives (lexicographic optimization) and the bi-criteria optimization algorithm that simultaneously optimizes the problem relative to two objectives (Pareto optimization). We also introduce a counting algorithm to count optimal solution before and after every optimization stage of multi-stage optimization. We propose a fairly universal approach based on so-called circuits without repetitions in which each element is generated exactly one time. Such circuits represent the sets of elements under consideration (the sets of feasible solutions) and are used by counting, multi-stage, and bi-criteria optimization algorithms. For a given optimization problem, we should describe an appropriate circuit and cost functions. Then, we can use the designed algorithms for which we already have proofs of their correctness and ways to evaluate the required number of operations and the time. We construct conventional (which work directly with elements) circuits without repetitions for matrix chain multiplication, global sequence alignment, optimal paths in directed graphs, binary search trees, convex polygon triangulation, line breaking (text justi cation), one-dimensional clustering, optimal bitonic tour, and segmented least squares. For these problems, we evaluate the number of operations and the time required by the optimization and counting algorithms, and consider the results of computational experiments. If we cannot nd a conventional circuit without repetitions for a problem, we can either create custom algorithms for optimization and counting from scratch or can transform a circuit with repetitions into a so-called syntactical circuit, which is a circuit without repetitions that works not with elements but with formulas representing these elements. We apply both approaches to the optimization of matchings in trees and apply the second approach to the 0/1 knapsack problem. We also brie y introduce our work in operation research with applications to health care. This work extends our interest in the optimization eld from developing new methods included in this dissertation towards the practical application.
  • 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.
  • Spin transport in multilayer graphene away from the charge neutrality point

    He, Xin; Wen, Yan; Zhang, Chenhui; Li, Peng; Zheng, Dongxing; Chen, Aitian; Manchon, Aurelien; Zhang, Xixiang (Carbon, Elsevier BV, 2020-10-17) [Article]
    Graphene is considered as a promising material in spintronics due to its long spin relaxation time and long spin relaxation length. However, its spin transport properties have been studied at low carrier density only, beyond which much is still unknown. In this study, we explore the spin transport and spin precession properties in multilayer graphene at high carrier density using ionic liquid gating. We find that the spin relaxation time is directly proportional to the momentum relaxation time, indicating that the Elliott-Yafet mechanism still dominates the spin relaxation in multilayer graphene away from the charge neutrality point.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

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