Hybridization Sites Research Articles

A many-body quantum model is proposed as the mechanism responsible for accelerating rates of heat uptake by oceans as anthropogenic heat inputs rise

Abstract A recent many-body quantum approach to thermal radiation (1) reveals that the energy capacitance of heated water is about twice its heat capacitance, due to energy stored as local hybrid pairs of photons coupled resonantly to local matter excitations, with pair density weighted by mass density. Energy exchange between photons and localised dipole excitations inside water at steady temperature T, occurs at sites where a hybridisation potential within the Hamiltonian couples local oscillation modes to “free” photon modes. Photon modes in both directions are phase retarded at exit sides of a hybrid site. Optically sharp variations with frequency in the index of refraction n(f) and photon density of states follow. Exit spectral intensities at equilibrium temperature T carry quantum information on the energy density of matter excitations coupled to photons, while occupied hybrid sites are the source of all “free” photons and internal spectral intensities. The matter excitations coupled locally to photons are distinct from those that define specific heat, but in water both arise from molecular oscillations. The energy capacitance CEX(T) of hybrid pairs depends on mass density and is independent of heat capacitance CHT(T) which sets temperature T. CEX(T) is sensitive to T and doubles as a capacitance of energy and of “quantum information”. Expressions for CEX(T) are derived from first principles and applied to water. The density of occupied hybrids is amplified near surfaces by photons reflected off the surface, which create new hybrid pairs, but not extra heat. Energy capacitance CEX(T)+CHT(T) sets dT(t)/dt prior to a new equilibrium state emerging, after input heating rate dQ/dt is switched. Rising atmospheric intensities then raise T, dQ/dt, CEX(T) and CHT(T). The times available to cool overnight are fixed, so that a rising capacitance, adds to energy stored at an accelerating rate. 


Ground Motion Simulation of Scenario Earthquakes in the Nakdonggang Delta Region using a Broadband Hybrid Method and Site Response Analysis

Ground Motion Simulation of Scenario Earthquakes in the Nakdonggang Delta Region using a Broadband Hybrid Method and Site Response Analysis

Predicting candidate miRNAs for targeting begomovirus to induce sequence-specific gene silencing in chilli plants.

The begomoviruses are the most economically damaging pathogens that pose a serious risk to India's chilli crop and have been associated with the chilli leaf curl disease (ChiLCD). Chilli cultivars infected with begomovirus have suffered significant decreases in biomass output, negatively impacting their economic characteristics. We used the C-mii tool to predict twenty plant miRNA families from SRA chilli transcriptome data (retrieved from the NCBI and GenBank databases). Five target prediction algorithms, i.e., C-mii, miRanda, psRNATarget, RNAhybrid, and RNA22, were applied to identify and evaluate chilli miRNAs (microRNAs) as potential therapeutic targets against ten begomoviruses that cause ChiLCD. In this study, the top five chilli miRNAs which were identified by all five algorithms were thoroughly examined. Moreover, we also noted strong complementarities between these miRNAs and the AC1 (REP), AC2 (TrAP) and betaC1 genes. Three computational approaches (miRanda, RNA22, and psRNATarget) identified the consensus hybridization site for CA-miR838 at locus 2052. The top predicted targets within ORFs were indicated by CA-miR2673 (a and b). Through Circos algorithm, we identified novel targets and create the miRNA-mRNA interaction network using the R program. Furthermore, free energy calculation of the miRNA-target duplex revealed that thermodynamic stability was optimal for miR838 and miR2673 (a and b). To the best of our knowledge, this was the first instance of miRNA being predicted from chilli transcriptome information that had not been reported in miRbase previously. Consequently, the anticipated biological results substantially assist in developing chilli plants resistant to ChiLCD.

Elements of a Vanished Space: A Preliminary Study of an Early Eighteenth Century Batavia Castle Residential Hall and its Furnishings

Most depictions of interior spaces in early modern Indonesia lack enough detail to make precise reconstructions. This makes the description and illustration made by Johann Wolfgang Heydt of the Governor General’s residential hall in an early eighteenth century Batavia Castle unique. The illustration, albeit created within a Eurocentric framework, provides relatively detailed furnishing information for a historically important site that has long vanished. This research aims to investigate and specify some of the depicted furnishings — particularly tables, shield lamps, and spittoons — by comparing them with surviving artefacts and accounts of Batavian life. Tables with distinctive Louis XIV style undoubtedly point to the dominance of European taste, but many of them were produced by local Chinese craftsmen rather than brought from Europe. The shield lamps were curious in their provenance and may have been local iterations of Islamic pendant lamps consisting of imported Middle Eastern glass and indigenous metalworks. Spittoons conspicuously displayed in the hall were used to cater to local betel chewing habits that were also adopted by the Dutch inhabitants of the city. These furnishings reveal a hybrid culture where European taste — while still a dominant force within the colonial context — is tempered with the adoption of local customs, materials, and craftsmanship. The analysis of these elements also corroborates a more recent approach to early colonial Batavia as a nuanced, cosmopolitan site of complex social exchange and cultural hybridity.

Carbon stock quantification in a floodplain restoration chronosequence along a Mediterranean-montane riparian corridor

Uncertainty in the global carbon (C) budget has been reduced for most stocks, though it remains incomplete by not considering aquatic and transitional zone carbon stocks. A key issue preventing such complete accounting is a lack of available C data within these aquatic and aquatic-terrestrial transitional ecosystems. Concurrently, quantifiable results produced by restoration practices that explicitly target C stock accumulation and sequestration remain inconsistent or undocumented. To support a more complete carbon budget and identify impacts on C stock accumulation from restoration treatment actions, we investigated C stock values in a Mediterranean-montane riparian floodplain system in California, USA. We quantified the C stock in aboveground biomass, large wood, and litter in addition to the C and total nitrogen in the upper soil profile (5 cm) across 23 unique restoration treatments and remnant old-growth forests. Treatments span 40 years of restoration actions along seven river kilometers of the Cosumnes River, and include process-based (limited intervention), assisted (horticultural planting and other intensive restoration activities), hybrid (a combination of process and assisted actions), and remnant (old-growth forests that were not created with restoration actions) sites. Total C values measured up to 1100 Mg ha−1 and averaged 129 Mg ha−1 with biomass contributing the most to individual plot measurements. From 2012 to 2020, biomass C stock measurements showed an average 32 Mg ha−1 increase across all treatments, though treatment specific values varied. While remnant forest plots held the highest average C values across all stocks (336 Mg ha−1), C values of different stocks varied across treatment type. Process-based restoration treatments held more average biomass C (120 Mg ha−1) than hybrid (23 Mg ha−1) or assisted restoration treatments (50 Mg ha−1), while assisted restoration treatments held more average total C in soil and litter (58 Mg ha−1) than hybrid (35 Mg ha−1) and process-based restoration treatments (37 Mg ha−1). Regardless of treatment type, time was a significant factor for all C stock values. These findings support a more inclusive global carbon budget and provide valuable insight into restoration treatment actions that support C stock accumulation.

A molecular beacon design for a colorimetric loop-mediated isothermal amplification assay.

In this study, a molecular beacon (MB) was designed for colorimetric loop-mediated isothermal amplification (cLAMP). The length of complementary bases on the MB, guanine and cytosine content (GC content), and hybridization sites of complementary bases were investigated as key factors affecting the design of the MB. We designed MBs consisting of 10, 15, and 20 complementary bases located at both ends of the HRPzyme. In the case of the long dumbbell DNA structure amplified from the hlyA gene of Listeria monocytogenes, possessing a flat region (F1c-B1) of 61base pairs (bp), an MB was designed to intercalate into the flat region between the F1c and B1 regions of the LAMP amplicons. In the case of the short dumbbell DNA structure amplified from the bcfD gene of Salmonella species possessing a flat region (F1c-B1) length of 6bp, another MB was designed to intercalate into the LoopF or LoopB regions of the LAMP amplicons. The results revealed that the hybridization site of the MB on the LAMP amplicons was not crucial in designing the MB, but the GC content was an important factor. The highest hybridization efficiencies for LAMP amplicons were obtained from hlyA gene-specific and bcfD gene-specific MBs containing 20- and 15-base complementary sequences, respectively, which exhibited the highest GC content. Therefore, designing MBs with a high GC content is an effective solution to overcome the low hybridization efficiency of cLAMP assays. The results obtained can be used as primary data for designing MBs to improve cLAMP accessibility.

Modulating the electron interaction of Cu-Ni hybrid sites for boosting photocatalytic hydrogen evolution over Al-doped SrTiO3

Cocatalysts play a pivotal role in enhancing the efficiency of photocatalytic water splitting. In this study, we introduced a novel and straightforward pre-impregnation strategy to anchor a CuNi dual cocatalyst onto the surface of Al-doped SrTiO3 (Al-STO), coupled with photodeposition. This approach led to a remarkable 11.07-fold (77.5 µmol/h) increase in hydrogen evolution performance compared to the conventional photodeposition method for decorating with CuNi dual cocatalysts. Not only that, after the 18 h cycle experiment, the catalyst still maintains high activity and high stability similar to that of precious metals, which overcomes the defects of poor stability and short life of non-precious metals. This strategy capitalizes on the pre-adsorption of cocatalyst precursor ions on the Al-STO support via impregnation, enhancing both the adsorption energy and capacity between the precursor ions and the active sites. Detailed characterizations have revealed a strong electronic interaction within the Cu-Ni structure and improved interfacial coupling between CuNi and Al-STO. This not only significantly promotes charge separation and transfer but also provides a plethora of active sites for the photocatalytic generation of H2. Moreover, extensive theoretical calculations have provided deep insights into the reaction mechanism of the CuNi system and elucidated the reasons behind the varying degrees of activity enhancement across different cocatalyst architectural systems.

Comparing Medication History Capture Rates In-Person Versus Hybrid: A Multisite Pilot Study.

Purpose: Medication history is the method many organizations use to adhere to The Joint Commission's (TJC) National Patient Safety Goal (NPSG) to communicate accurate patient medication information. Literature is sparse comparing the number of medication histories completed in-person versus virtually. Methods: This is a single system, multi-site, retrospective observational study. Patients included were admitted through the Emergency Department during October 2022. The primary aim of this study compared the percent capture rates of medication history between 2 hybrid sites to an in-person site within a health-system. Our secondary objective compared the differences in the 'medication history acuity score' (MHAS), defined as the total number of edits, additions, and deletions made during a medication history. Results: The medication history capture rate at the in-person site was 74% and at the hybrid sites were 91% and 80%. There were no differences in total medications on each medication history between in-person and hybrid (11 [5-16] vs 11 [6-16]; P = .252). There were no differences in changes made on medication histories between in-person and hybrid (4 [1-7] vs 3 [1-7]; P = .595). Conclusions: Our study demonstrates that medication history capture rates and MHAS are comparable in both in-person and hybrid environments. This similarity suggests the feasibility of implementing hybrid models for medication history services in diverse healthcare settings, potentially enhancing the capacity of health systems to meet TJC NPSG. These findings indicate that hybrid models could be an effective strategy for healthcare systems to optimize their medication history services, especially in settings with varied patient volumes and site specialties.

Pollinator and habitat-mediated selection as potential contributors to ecological speciation in two closely related species.

In ecological speciation, incipient species diverge due to natural selection that is ecologically based. In flowering plants, different pollinators could mediate that selection (pollinator-mediated divergent selection) or other features of the environment that differ between habitats of 2 species could do so (environment-mediated divergent selection). Although these mechanisms are well understood, they have received little rigorous testing, as few studies of divergent selection across sites of closely related species include both floral traits that influence pollination and vegetative traits that influence survival. This study employed common gardens in sites of the 2 parental species and a hybrid site, each containing advanced generation hybrids along with the parental species, to test these forms of ecological speciation in plants of the genus Ipomopsis. A total of 3 vegetative traits (specific leaf area, leaf trichomes, and photosynthetic water-use efficiency) and 5 floral traits (corolla length and width, anther insertion, petal color, and nectar production) were analyzed for impacts on fitness components (survival to flowering and seeds per flower, respectively). These traits exhibited strong clines across the elevational gradient in the hybrid zone, with narrower clines in theory reflecting stronger selection or higher genetic variance. Plants with long corollas and inserted anthers had higher seeds per flower at the Ipomopsis tenuituba site, whereas selection favored the reverse condition at the Ipomopsis aggregata site, a signature of divergent selection. In contrast, no divergent selection due to variation in survival was detected on any vegetative trait. Selection within the hybrid zone most closely resembled selection within the I. aggregata site. Across traits, the strength of divergent selection was not significantly correlated with width of the cline, which was better predicted by evolvability (standardized genetic variance). These results support the role of pollinator-mediated divergent selection in ecological speciation and illustrate the importance of genetic variance in determining divergence across hybrid zones.

Contribution of the satellitome to the exceptionally large genome of dinoflagellates: The case of the harmful alga Alexandrium minutum

Dinoflagellates are known to possess an exceptionally large genome organized in permanently condensed chromosomes. Focusing on the contribution of satellite DNA (satDNA) to the whole DNA content of genomes and its potential role in the architecture of the chromosomes, we present the characterization of the satellitome of Alexandriun minutum strain VGO577. To achieve this, we analyzed Illumina reads using graph-based clustering and performed complementary bioinformatic analyses. In this way, we discovered 180 satDNAs occupying 17.38 % of the genome. The 12 most abundant satDNAs represent the half of the satellitome but no satDNA is overrepresented, with the most abundant contributing ∼1.56 % of the genome. The largest repeat unit is 517 bp long but more than the half of the satDNAs (101) have repeat units shorter than 20 bp. We used FISH to map a selected set of 26 satDNAs. Although some satDNAs generate discrete hybridization signals at specific chromosomal locations (hybridization sites, HS), our cytological analysis showed that most satDNAs are dispersed throughout the genome, probably forming short arrays. Two satDNAs co-localize with the 45S rDNA. With the exception of telomeric DNA, no other satDNA yields HS on all chromosomes. In addition, we analyzed nine satDNAs yielding HS in VGO577 in four other A. minutum strains. Polymorphism at the intraspecific level was found for the presence/absence and/or abundance of some satDNAs, suggesting the amplification/deletion of these satDNAs following geographic separation or during culture maintenance of the strains. We also discuss how these results contribute to the understanding of chromosome architecture and evolution of dinoflagellate genomes.

Enhanced CO2 Electroreduction Selectivity toward Ethylene on Pyrazolate-Stabilized Asymmetric Ni-Cu Hybrid Sites.

Metal-organic frameworks (MOFs) possess well-defined, designable structures, holding great potential in enhancing product selectivity for electrochemical CO2 reduction (CO2R) through active site engineering. Here, we report a novel MOF catalyst featuring pyrazolate-stabilized asymmetric Ni/Cu sites, which not only maintains structural stability under harsh electrochemical conditions but also exhibits extraordinarily high ethylene (C2H4) selectivity during CO2R. At a cathode potential of -1.3 V versus RHE, our MOF catalyst, denoted as Cu1Ni-BDP, manifests a C2H4 Faradaic efficiency (FE) of 52.7% with an overall current density of 0.53 A cm-2 in 1.0 M KOH electrolyte, surpassing that on prevailing Cu-based catalysts. More remarkably, the Cu1Ni-BDP MOF exhibits a stable performance with only 4.5% reduction in C2H4 FE during 25 h of CO2 electrolysis. A suite of characterization tools─such as high-resolution transmission electron microscopy, X-ray absorption spectroscopy, operando X-ray diffraction, and infrared spectroscopy─and density functional theory calculations collectively reveal that the cubic pyrazolate-metal coordination structure and the asymmetric Ni-Cu sites in the MOF catalyst synergistically facilitate the stable formation of C2H4 from CO2.

Marine hydrokinetic energy potential of Peninsular Malaysia by using hybrid site selection method

The exponential increase in global energy demand is a direct result of the rapid growth of the world's population and technological advancements. However, the use of fossil fuels to meet this demand has led to the issue of CO2 emission and global warming, which prompting nations to undertake mitigation plans for further negative repercussions. Seeing the fact that extensive usage of non-renewable energies is the root cause of these negative effects, renewable energies have become the focus of most research. On top of that too, the implementation of clean energy is urgent to achieve sustainable development. Located in Southeast Asia, Peninsular Malaysia is surrounded by the Strait of Malacca and the South China Sea, making it abundant in the source of hydrokinetic energy. Consequently, researchers have taken a keen interest in exploring marine renewable energy within the region. Coastal regions particularly, can significantly benefit from hydrokinetic energy. Henceforth, this study aims to provide a comprehensive approach to identify the optimal locations for marine hydrokinetic energy extraction in Peninsular Malaysia, considering all essential factors that influence decision-making.

The Bhasa of History—an essay for Dipesh Chakrabarty

ABSTRACT What value does a leading historian of modern South Asia ascribe to bhasa literature? Meant as an introduction to a volume of papers dedicated to Dipesh Chakrabarty, this essay proposes to read through some of his work and draw out a couple of general responses to this central question. The first one concerns Chakrabarty’s larger philosophical engagement with the condition of colonial modernity in India. In his treatment, bhasa literary corpus is a site of difference as well as belonging. He searches for the difference that marks Indian experience of colonial modernity in the literary. The value of bhasa, in this instance, lies in its ability to provide a ground for resistance to the uniform march of enlightenment and capitalist modernity. And, bhasa enables an awareness of historical difference precisely because it provides a sense of belonging. This sense of belongingness is closely tied to a place, a particular location as well as to a sense of everyday intimacy. As the hybrid site of difference as well as belonging, bhasa is then the constitutive cradle of what Chakrabarty calls ‘History 2s’. The second one concerns Chakrabarty’s more specific analysis of the evolution of history as an academic discipline in modern India. He delineates a sharp devaluation in the political worth of the literary that the rise of rational-scientific history writing brought about in the middle decades of the twentieth-century. As he studies the intellectual careers of particular historians, part of his intent is to elaborate on this process of devaluation. The essay situates this reading of Chakrabarty in a larger discursive context. It briefly looks at the work of some other scholars of modern South Asia who share these intellectual concerns, and seeks to create, as it were, a dialogue between Chakrabarty and others. The essay concludes by briefly introducing the papers in the volume. In different ways, they extend Chakrabarty’s preoccupation with the relationship between history and literature, and with the subject of modernity in India at large.

Seismic microzonation mapping of Greater Vancouver based on various site classification metrics

The goal of the multi-year seismic microzonation mapping project for Greater Vancouver, British Columbia, Canada, is to produce seismic hazard maps inclusive of local site effects, in particular seismic hazard specific to one-dimensional site response and three-dimensional Georgia sedimentary basin amplification, as well as liquefaction and landslide hazard potential. We explore the variability in key seismic site characterization measures most often used for seismic microzonation mapping to evaluate the impact on mapping and communication of seismic microzonation of Greater Vancouver. This study focuses on the comparison of seismic microzonation maps of Greater Vancouver based on up to three seismic site term parameters and their associated classification schemes: 1) the time-averaged shear-wave velocity (Vs) of the upper 30 m (Vs30) and associated Canadian National Building Code (NBC) site class; 2) Vs30-based site classification proposed for the updated Eurocode 8; 3) site period (T0) determined from microtremor site amplification spectra; and 4) a hybrid site classification based on T0 and the average Vs and thickness of soil. 810 Vs30 and 2,200 T0 values are determined to evaluate sub-regional differences in these important seismic site parameters in Greater Vancouver. We find that the seismic microzonation of Greater Vancouver depends on the chosen seismic site parameter (Vs30, T0, or a combination of parameters) and that classification schemes with greater class divisions are beneficial to communicating the great variability in seismic site conditions in Greater Vancouver. We recommend that either one hybrid classification map or two classification maps of Vs30 and T0 together are required for effective communication of the seismic microzonation of Greater Vancouver.

Parasite exchange and hybridisation at a wild-feral-domestic interface

Interactions between wild, feral, and domestic animals are of economic and conservation significance. The pigeon Columba livia is a synanthropic species in a feral form, but it also includes the rare Rock Dove. Columba livia is an important player at the wild-domestic interface, acting as a carrier of avian diseases, and the feral form threatens Rock Doves with extinction via hybridisation. Despite its abundance, little is known about drivers of disease prevalence in C. livia, or how disease and hybridisation represent synergistic threats to Rock Doves. We focused on infection by the parasite Trichomonas, first collating prevalence estimates in domestic and free-living populations from relevant studies of C. livia. Second, we characterised variation in the diversity and prevalence of Trichomonas among three C. livia populations in the United Kingdom: a feral, a Rock Dove, and a feral-wild hybrid population. Across multiple continents, free-living pigeons had lower Trichomonas infection than captive conspecifics, but the effect was weak. Environmental factors which could impact Trichomonas infection status did not explain variation in infection among populations. Among the British populations, strain diversity varied, and there was lower parasite prevalence in Rock Doves than feral pigeons. Individual infection status was not explained by the available covariates, including hybrid score and site. The drivers of Trichomonas prevalence are unclear, perhaps due to idiosyncratic local-scale drivers. However, given the population-level variation in both infection prevalence and introgressive hybridisation, the potential combined effects could accelerate the extinction of the Rock Dove. Further study of the synergistic effects of multiple types of biotic interactions at the wild-feral-domestic interface is warranted, especially where vagile, globally distributed and superabundant animals are involved.

Virtual accreditation peer review team visits – higher education accreditations: present and future directions

PurposeThe main objective of the present research is to depict the experience of challenges and opportunities for virtual accreditation peer review team (PRT) visits. COVID-19 has changed higher education delivery. Higher education accreditation and PRT visits have become online. The lockdown forced schools and accreditation agencies to cancel or change visit arrangements. PRT visits could not be stopped during the COVID-19 pandemic, but accrediting agencies needed to review programme quality to meet standards.Design/methodology/approachEight former and present accreditation specialists were interviewed. The researchers described the challenges and opportunities in virtual accreditation visits (VAV). Also, the authors have explained their own experience of coordinating on-site and virtual accreditation visits. Using the NVIVO tool, the experts' replies are transcribed and categorised as challenges and opportunities.FindingsThe findings will help the professionals and academicians better prepare for, plan and execute virtual PRT visits for accreditation agencies and schools. The results revealed that the evaluation and accreditation outcomes are similar for virtual and physical accreditation visits. Finally, the findings suggest that accreditation agencies and schools need to adopt a hybrid site visit model for accreditation visits.Practical implicationsThe school can prepare better for virtual PRT visits by identifying the challenges and opportunities ahead of time. The finding may motivate authorities to schedule meetings in different time zones, prepare document evidence rooms, save money, time, and travel time, and benefit the environment by eliminating paper printing, fuel use, and paper printing.Originality/valueThis research is unique and noteworthy since accreditation organisations, PRT members and schools are uncertain about virtual visits. This may be the first paper in this domain to assist accreditation organisations and institutions review accreditation visits online or in hybrid mode.

Variants in the Sequence of the Probe Hybridization Site May Affect MLPA Performance in Patients with Duchenne/Becker Muscular Dystrophy.

The MLPA (multiplex ligation dependent probe amplification) technique is currently the test most widely used to detect mutations in the Duchenne/Becker muscular dystrophy (DMD) gene in the initial assessment. However, several studies have suggested that MLPA results require implementing other detection methods due to false duplication. Our aim was to evaluate variables that could alter the peak ratio in MLPA in individuals with Duchenne/Becker muscular dystrophy (DMD/BMD) who present sequence variants at the probe hybridization site, such as the location of sequence variants (SVs), melting temperature of the probe, and the type of variant. We analyzed patients with clinical suspicion of DMD/BMD through the MLPA technique. The DMD gene was sequenced in patients with normal results in MLPA. Of 111 patients, 72 had an abnormal MLPA result, of which 10 had a single exon abnormal peak, and 39 had a normal peak ratio. Out of 10 patients, 4 (40%) with a single exon abnormal peak ratio had SV at the hybridization site of the probe. In the other 6, the deletion was confirmed. Out of 39 patients with a normal peak ratio, 11 presented SVs at the hybridization site of the probe, and DMD/BMD was confirmed. In cases of abnormal peak ratio results of MLPA in a single exon, it would be valuable to sequence the DMD gene to assess whether variants in the probe hybridization site might result in a false positive that could be interpreted as an exon deletion.

Ionic Strength and Hybridization Position near Gold Electrodes Can Significantly Improve Kinetics in DNA-Based Electrochemical Sensors.

A variety of electrochemical (EC) biosensors play critical roles in disease diagnostics. More recently, DNA-based EC sensors have been established as promising for detecting a wide range of analyte classes. Since most of these sensors rely on the high specificity of DNA hybridization for analyte binding or structural control, it is crucial to understand the kinetics of hybridization at the electrode surface. In this work, we have used methylene blue-labeled DNA strands to monitor the kinetics of DNA hybridization at the electrode surface with square-wave voltammetry. By varying the position of the double-stranded DNA segment relative to the electrode surface as well as the bulk solution's ionic strength (0.125-1.00 M), we observed significant interferences with DNA hybridization closer to the surface, with more substantial interference at lower ionic strength. As a demonstration of the effect, toehold-mediated strand displacement reactions were slowed and diminished close to the surface, while strategic placement of the DNA binding site improved reaction rates and yields. This work manifests that both the salt concentration and DNA hybridization site relative to the electrode are important factors to consider when designing DNA-based EC sensors that measure hybridization directly at the electrode surface.

Computational Biology and Machine Learning Approaches Identify Rubber Tree (Hevea brasiliensis Muell. Arg.) Genome Encoded MicroRNAs Targeting Rubber Tree Virus 1

Tapping panel dryness (TPD), a complex physiological syndrome associated with the rubber tree (Hevea brasiliensis Muell. Arg.), causes cessation of latex drainage upon tapping and thus threatens rubber production. Rubber tree virus 1 (RTV1) is a novel positive-sense single-stranded RNA virus from the Betaflexiviridae (genus Capillovirus), which has been established to cause TPD. MicroRNAs (miRNAs) play an important role in the interplay between viruses and host cells. In this study, we identified the rubber tree genome-encoded miRNAs and their therapeutic targets against RTV1. We applied computational algorithms to predict target binding sites of rubber tree miRNAs potentially targeting RTV1 RNA genome. Mature rubber-tree miRNAs are retrieved from the miRBase database and are used for hybridization of the RTV1 genome. A total of eleven common rubber-tree miRNAs were identified based on consensus genomic positions. The consensus of four algorithms predicted the hybridization sites of the hbr-miR396a and hbr-miR398 at common genomic loci (6676 and 1840), respectively. A miRNA-regulatory network of rubber tree was constructed with the RTV1— ORFs using Circos, is illustrated to analyze therapeutic targets. Overall, this study provides the first computational evidence of the reliable miRNA–mRNA interaction between specific rubber tree miRNAs and RTV1 genomic RNA transcript. Therefore, the predicted data offer valuable evidence for the development of RTV1-resistant rubber tree in the future. Our work suggests that similar computational host miRNA prediction strategies are warranted for identification of the miRNA targets in the other viral genomes.

Deep Learning for Modeling an Offshore Hybrid Wind–Wave Energy System

The combination of an offshore wind turbine and a wave energy converter on an integrated platform is an economical solution for the electrical power demand in coastal countries. Due to the expensive installation cost, a prediction should be used to investigate whether the location is suitable for these sites. For this purpose, this research presents the feasibility of installing a combined hybrid site in the desired coastal location by predicting the net produced power due to the environmental parameters. For combining these two systems, an optimized array includes ten turbines and ten wave energy converters. The mathematical equations of the net force on the two introduced systems and the produced power of the wind turbines are proposed. The turbines’ maximum forces are 4 kN, and for the wave energy converters are 6 kN, respectively. Furthermore, the comparison is conducted in order to find the optimum system. The comparison shows that the most effective system of desired environmental condition is introduced. A number of machine learning and deep learning methods are used to predict key parameters after collecting the dataset. Moreover, a comparative analysis is conducted to find a suitable model. The models’ performance has been well studied through generating the confusion matrix and the receiver operating characteristic (ROC) curve of the hybrid site. The deep learning model outperformed other models, with an approximate accuracy of 0.96.