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PurposeThis study aims to compare the performance of two nature-inspired metaheuristics inside Grasshopper in optimizing daylighting and energy performance against brute force in terms of the resemblance to ideal solution and calculation time.Design/methodology/approachThe simulation-based optimization process was controlled using two population-based metaheuristic algorithms, namely, the genetic algorithm (GA) and particle swarm optimization (PSO). The objectives of the optimization routine were optimizing daylighting and energy consumption of a standard reference office while varying the urban context configuration in Alexandria, Egypt.FindingsThe results from the GA and PSO were compared to those from brute force. The GA and PSO demonstrated much faster performance to converge to design solution after conducting only 25 and 43% of the required simulation runs, respectively. Also, the average proportion of the resulted weighted sum optimization (WSO) per case using the GA and PSO to that from brute force algorithm was 85 and 95%, respectively.Originality/valueThe work of this paper goes beyond the current practices for showing that the performance of the optimization algorithm can differ by changing the urban context configuration while solving the same problem under the same design variables and objectives.

Objective: This study was designated to evaluate postoperative pain in irreversible symptomatic teeth after different irrigation activation methods using visual analogue scale. Materials and Methods:78 Patients having symptomatic irreversible pulpitis in mandibular first molar (vital pulp) with no periapical involvement were involved in the study. Cases were classified into three groups according to the the final irrigation agitation method used, twenty-six patients each group (n=26). Group A: Root canals were irrigated using NaOCl2* 2.6% with NaviTip (31-gauge 27mm) with double side port irrigator tip (SVN). Group B: Root canals were irrigated using 2.6% NaOCl with manual dynamic agitation using master cone for 60 seconds. Group C: Root canals were irrigated using 2.6% NaOCl with mechanical agitation using ultrasonic device ultra-x for 60 seconds. Postoperative pain was evaluated after 6,12,24, 48, and 72 hours and 1 week. Data were explored for normality using Kolmogorov-Smirnov and Shapiro-Wilk tests and showed parametric (normal) distribution. Statistical analysis was performed with IBM® SPSS® Statistics Version 20 for Windows. Results: Severity of postoperative pain was more intense at 6- 12and 24-hour time intervals in group 2 patients than those patients in groups 1and 3 (P < .05). There was no significant difference among the groups at the other time intervals (P > .05). Severity of postoperative pain in all groups decreased over time. Conclusion: After endodontic therapy in lower molars with acute pulpitis manual dynamic agitation caused greater postoperative pain in comparison with the other methods in the first 24 hours.

The identification of Standardized Regression Coefficients (SRCs) can be used to aid designers in identifying the most influential design variables affecting building performance. Nevertheless, multicollinearity can nullify the reliability of SRCs. This study aims to develop a method for estimating reliable SRCs of design variables in daylighting and energy performance of buildings in the face of multicollinearity. A parametric model is developed, then, daylight and energy simulations are commenced, next, Principal Component Analysis (PCA) is performed and the extracted Principal Components (PCs) are interpreted to meaningful factors, finally, the SRCs of the extracted PCs in daylighting and energy performance were calculated. The method was applied to a standard office, where the quantitative performance of (3564) different cases were predicted in terms of twelve urban context configurations against nine variables. Four PCs out of nine variables were extracted, namely, PC1: window geometry, PC2: glazing properties, PC3: opposing building paint, and PC4: building paint. The generated SRCs charts of the extracted PCs described the behaviors of the PCs in daylighting and energy performance. The Horizontal Obstruction Angle (HOA) affected the PCs’ behavior for all performance metrics, Annual Sunlight Exposure (ASE) was not affected by PC3 and PC4, PC1 had an inverse relationship with Lighting Energy (LE), whilst, the contribution of PC3 on LE was increased dramatically when a steep HOA existed. Total Energy Consumption (TEC) showed the same trend as Cooling Energy (CE). The resulted behaviors were consistent with the literature and confirmed the efficiency of the proposed method.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19. SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control its life cycle remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively the cellular and viral RBPs that are involved in SARS-CoV-2 infection. We reveal that SARS-CoV-2 infection profoundly remodels the cellular RNA-bound proteome, which includes wide-ranging effects on RNA metabolic pathways, non-canonical RBPs and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Amongst them, several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19., Graphical Abstract, Kamel, Noerenberg, Cerikan and colleagues apply a multi-omic approach to identify the RNA-binding proteins that regulate SARS-CoV-2 infection. They discovered that the complement of RNA-binding proteins heavily remodels upon SARS-CoV-2 infection. They also show that the viral RNA interacts with dozens of cellular and six viral RNA-binding proteins. These host-virus interactions are fundamental for SARS-CoV-2 infection and have great potential for new therapeutic approaches against COVID-19.

RNA viruses interact with a wide range of cellular RNA-binding proteins (RBPs) during their life cycle. The prevalence of these host-virus interactions has been highlighted by new methods that elucidate the composition of viral ribonucleoproteins (vRNPs). Applied to 11 viruses so far, these approaches have revealed hundreds of cellular RBPs that interact with viral (v)RNA in infected cells. However, consistency across methods is limited, raising questions about methodological considerations when designing and interpreting these studies. Here, we discuss these caveats and, through comparing available vRNA interactomes, describe RBPs that are consistently identified as vRNP components and outline their potential roles in infection. In summary, these novel approaches have uncovered a new universe of host-virus interactions holding great therapeutic potential.

The expansion of tropical mosquito habitats and associated arboviruses is a risk for human health, and it thus becomes fundamental to identify new antiviral strategies. In this study we employ a new approach to elucidate the composition of the ribonucleoproteins (RNPs) of a prototypical arbovirus called Sindbis (SINV). SINV RNPs contain 453 cellular and 6 viral proteins, many of these proteins are nuclear in uninfected cells and redistribute to the cytoplasm upon infection. These findings suggest that SINV RNAs act as ’spiderwebs’, capturing host factors required for viral replication and gene expression in the cytoplasm. Functional perturbation of several of these host proteins causes profound effects in virus infection, as illustrated here with the tRNA ligase complex. Moreover, inhibition of viral RNP components with available drugs hampers the infection of a wide range of viruses, opening new avenues for the development of broad-spectrum therapies.Research highlightsSINV RNA interactome includes 453 cellular and 6 viral proteins.Nuclear RBPs that interact with SINV RNA are selectively redistributed to the cytoplasm upon infectionThe tRNA ligase complex plays major regulatory roles in SINV and SARS-CoV- 2 replicationThe SINV RNA interactome is enriched in pan-viral regulators with therapeutic potential.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19. SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control SARS-CoV-2 infection remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively which cellular and viral RBPs are involved in SARS-CoV-2 infection. We reveal that the cellular RNA-bound proteome is remodelled upon SARS-CoV-2 infection, having widespread effects on RNA metabolic pathways, non-canonical RBPs and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Amongst them, several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.

Interactions between RNA-binding proteins (RBPs) and RNAs are critical to cell biology. However, methods to comprehensively and quantitatively assess these interactions within cells were lacking. RNA interactome capture (RIC) uses in vivo UV crosslinking, oligo(dT) capture, and proteomics to identify RNA-binding proteomes. Recent advances have empowered RIC to quantify RBP responses to biological cues such as metabolic imbalance or virus infection. Enhanced RIC exploits the stronger binding of locked nucleic acid (LNA)-containing oligo(dT) probes to poly(A) tails to maximize RNA capture selectivity and efficiency, profoundly improving signal-to-noise ratios. The subsequent analytical use of SILAC and TMT proteomic approaches, together with high-sensitivity sample preparation and tailored statistical data analysis, substantially improves RIC’s quantitative accuracy and reproducibility. This optimized approach is an extension of the original RIC protocol. It takes 3 d plus 2 weeks for proteomics and data analysis and will enable the study of RBP dynamics under different physiological and pathological conditions. This protocol extension describes an improved method for global profiling of poly(A) RNA-binding proteins (RBPs) and quantitative analysis of RBP dynamics in response to biological and pharmacological cues that uses UV crosslinking, capture with LNA-modified oligo-dT probes, and proteomics.

Nature and culture have always offered a variety of resources for tourism in different areas. Furthermore, the fact that these assets are key for choice makers whatsoever, levels on aggravate suitable arrangements for the enhancing of ecotourism. As per the World Tourism Organization, ecotourism has been estimated to account between 10% to 15% of all international travel expenditures, it seems to be even faster than the tourism industry, as it represents 20% of the world travel market. Research assumes that despite large portions of vernacular dwells exist in Egypt, (but desired) to package vernacular architecture traditions and quantitative design knowledge to modern building designers. The aim of this study is to develop and preserve the identity of vernacular architecture in ecotourism sectors in Nubia, Egypt so that they could develop the economy and urban texture as well, and to outline the role of natural and cultural Egyptian rural communities to protect and preserve their heritage and their ecotourism resources as well. This study will assess and analyse six different international, national and local ecotourism rating manuals and certifications as well to seek the common ecotourism criteria to preserve vernacular architecture, then outline preservation vernacular-ecotourism Guidelines passed on ecotourism criteria and indicators, then validate it with efficient scale like Likert scale to be easy to use by decision makers. The research main findings based on the performance of selected vernacular-ecotourism case studies in Nubia, Egypt, were the criteria of vernacular ecotourism preservation. The research will accentuate that the Nubian building technology could be useful for redesign ecotourism resorts in rural community in Egypt. Sustainable architecture planning is a capable apparatus for making ecotourism offices that encourage aware and widening social exchanges.

The rapid increase in vehicular use due to human activities in urban areas has been leading to a worsening in air quality, thus negatively affect the exposure of inhabitants to polluted air and also harms the environment. This work studies the contribution of traffic flow on CO and NO2 concentration. The field measurement of both pollutants was considered in a roughly isolated street canyon. In addition, the meteorological parameters of the studied location were collected parallel with traffic flow data. There have been days in which the study location was affected by traffic flow and some others were not affected. In particular, statistical tests and data analysis were applied to the collected dataset after splitting it into two groups. One with zero traffic flow and the other with a significant variation in traffic flow. Also, the effect of meteorological parameters such as wind speed, wind direction, ambient temperature, and relative humidity on pollutant concentrations was considered. Moreover, the multivariate linear regression models were developed for both pollutants to address the contribution of each factor. As a result, the positive effect of traffic flow and the negative effect of the wind directions highly improves the prediction of the near-road traffic-related pollutant concentration.

Newcastle disease (ND) causes severe economic losses in poultry production. Despite the intensive vaccination regimes of NDV in Egypt, many outbreaks are being reported. The present study focused on the preparation and evaluation of inactivated velogenic Newcastle disease virus vaccine (genotype VII) isolated from Egyptian broiler chicken during 2015-2016. Fifty-five tissue samples including trachea, lung, liver, proventriculus, intestine, and kidney collected from commercial broiler chickens were used for virus isolation in specific pathogen-free embryonated chicken eggs (ECE) and identified using RT-PCR and sequencing. The isolates were classified by sequencing as velogenic NDV genotype VIId containing F0 protein cleavage site motifs (112RRQKRF117). A selected isolate was served as a master seed for the preparation of inactivated NDV vaccine with or without Montanide ISA70 adjuvant and evaluated in SPF chicks. Nine NDV isolates were isolated on ECE and the highest infectivity titer of the virus was 7.50 log10 EID50 mL-1 by the 5th passage. Vaccinated chicks with NDV-Montanide ISA70 adjuvanted vaccine exhibited antibody titer of 5.20 log2 at the 3rd-week-post-vaccination (WPV) with the highest titer (8.90 log2 mL-1) at the 6th-WPV. Protective antibodies values were persisted to 12th WPV followed by a gradual decrease to the end of the experiment (16th weeks). Vaccination of chicks with inactivated NDV isolate without adjuvant failed to induce protective HI antibodies all over the experiment. Chickens vaccinated with the ISA70 adjuvant vaccine were passed homologous challenge tests with 100% protective efficiency, while the unadjuvanted vaccine could not provide any protective efficiency. In conclusion, the preparation of inactivated oil adjuvant vaccine from NDV field circulating strains was efficient in controlling the disease in Egypt.

Fish represent a worldwide significant source of animal protein. In order to investigate the prevalence of MRSA in catfish as well as the inhibitory effect of Sidr honey on virulence genes of MRSA, fish were collected from Bahr Elbaker canal at Sharkia Governorate, Egypt. Swab samples were collected under complete aseptic conditions from internal organs (pancreas, liver, kidney and intestine), gills and skin then subjected to bacteriological examination. A total of 70 S. aureus strains were isolated from catfish, out of them 15 (21.42%) strains were identified as MRSA as a first record in Egypt. PCR was used for detection of meca, coa and spa genes in the isolated MRSA strains before and after the exposure to sidr honey. Before exposure to sider honey, all the selected MRSA strains showed positive results for meca, coa and spa genes with specific amplicon size of 310 bp, 430 bp and 226 bp, respectively. After exposure to sidr honey, MRSA strains showed inhibition of coa and spa genes, but has no effect on meca gene. In addition, scanning electron microscopy was used for detection of the morphological characters of MRSA strains before and after treatment with sidr honey. After exposure of MRSA strains to 30% (w/v) Sidr honey for 48 hours, cells surfaces were observable irregular with the appearance of cell debris. In conclusion, MRSA strains could be isolated from fresh water catfish in Egypt which may be attributed to the contamination of water and fish food. Sider honey showed a significant inhibitory effect on the growth of isolated MRSA strains. Moreover, it could inhibit spa and coa genes. SEM is a valuable tool revealing the abnormal morphological changes that take place in MRSA strains after exposure to Sidr honey.

Nevertheless to say that Energy consumption has a negative significant impact on the environment. In this context, the buildings sector accounts for around a percentage of 30% of the world energy total consumption. Consequently, building designers should consider energy savings strategies in their designs to achieve a low level of energy consumption while maintaining their design goals. On the other hand, building energy performance assessments face difficult challenges. The main target of such paper is to evolve a newly easy-to-use integrated BIM-based framework to support decision making at the conceptual stage, which is considered the most critical phase of the design. This framework empowers designers to investigate more design options while achieving the high level of the energy performance. Utilizing the power of visual programming to set the key-parameters that have significant effects on the performance like building orientation and form, and with using the appropriate BIM tools to easily transfer the design from the conceptual phase to the schematic phase of the project. A case study was applied to showcase the implementation of this workflow. Designers with limited programming experience may use this workflow to perform a broad variety of design options analysis, take the conscious design decision and easily implement it with their BIM-based workflow which will effectively reduce the time of design, improve the collaboration between teams, cause a significant energy saving in the building, and inevitably reduce life-cycle cost of the building.

Here we show that the adenovirus major late promoter produces a 31-nucleotide transcriptional start site small RNA (MLP-TSS-sRNA) that retains the 7-methylguanosine (m7G)-cap and is incorporated onto Ago2-containing RNA-induced silencing complexes (RISC) in human adenovirus-37 infected cells. RNA polymerase II CLIP (UV-cross linking immunoprecipitation) experiments suggest that the MLP-TSS-sRNA is produced by promoter proximal stalling/termination of RNA polymerase II transcription at the site of the small RNA 3′ end. The MLP-TSS-sRNA is highly stable in cells and functionally active, down-regulating complementary targets in a sequence and dose-dependent manner. The MLP-TSS-sRNA is transcribed from the opposite strand to the adenoviral DNA polymerase and preterminal protein mRNAs, two essential viral replication proteins. We show that the MLP-TSS-sRNA act in trans to reduce DNA polymerase and preterminal protein mRNA expression. As a consequence of this, the MLP-TSS-sRNA has an inhibitory effect on the efficiency of viral DNA replication. Collectively, our results suggest that this novel sRNA may serve a regulatory function controlling viral genome replication during a lytic and/or persistent adenovirus infection in its natural host.

The direction towards sustainable development challenges the designers to explore energy-efficient designs to provide adequate levels of natural daylighting. Indeed, using computational simulations can offer valuable performance predictions; still, exploring all possible combinations of design variables is a tedious and time-consuming task. This type of problems also doesn’t yield straightforward mathematical forms, and using black-box optimizations is more useful. This paper presented reviews, methodological tools and measures to help designers evaluating the potential contribution of simulation-based metaheuristics to optimize the design of façades in such obstructed contexts. The tested metaheuristics algorithms showed promising potential to attain optimum solutions, though the results confirmed that Genetic Algorithm is not sensitive to population size for optimizing façade design problems, as it obtained optimum designs only after conducting several runs of simulations. In contrast, Particle Swarm Optimization exhibited a higher sensitivity towards swarm sizes, where it converged much faster with larger swarm sizes; and a better performance could be achieved when the swarm size was 10 times the number of design variables alongside 0.2 particle’s velocity. This implies that metaheuristics optimization can be used along with simulations as accelerated tools in the early stages of design to rapidly predict building performances in obstructed environments.

Adenovirus type 5 encodes two short, highly structured noncoding RNAs, the virus-associated (VA) RNAI and VA RNAII. These RNAs are expressed in large amounts late during a lytic infection. Early studies established an important role for VA RNAI in maintaining efficient translation in late virus-infected cells by blocking activation of the key interferon-induced PKR protein kinase. More recent studies have demonstrated that the VA RNAs also target the RNAi/miRNA pathway. Collectively, available data suggest that the VA RNAs are multifunctional RNAs suppressing the activity of three dsRNA-sensing enzyme systems in human cells. Here, the known functions of the VA RNAs are summarized and the interplay between VA RNA expression and the activity of the interferon and RNAi pathways are discussed in more detail.

At late times during a lytic infection human adenovirus type 5 produces ∼10(8) copies per cell of virus-associated RNA I (VA RNAI). This short highly structured RNA polymerase III transcript has previously been shown to be essential for lytic virus growth. A fraction of VA RNAI is processed by Dicer into small RNAs, so-called mivaRNAIs, which are efficiently incorporated into the RNA-induced silencing complex. Here, we constructed recombinant adenoviruses with mutations in the seed sequence of both the 5'- and the 3'-strand of the mivaRNAI duplex. The results showed that late viral protein synthesis, as well as new virus progeny formation, was essentially unaffected by the seed sequence mutations under lytic replicative conditions in HeLa or HEK293 cells. Collectively, our results suggest that either strand of the mivaRNAI duplex does not have target mRNA interactions that are critical for the establishment of virus growth under lytic conditions. Further, by depletion of protein kinase R (PKR) in HEK293 cells, we show that the suppressive effect of VA RNAI on the interferon-induced PKR pathway is most critical for late gene expression.

Human adenoviruses (HAdVs) encode for multifunctional non-coding virus-associated (VA) RNAs, which function as powerful suppressors of the cellular interferon (IFN) and RNA interference (RNAi) systems. In this study we tested the ability of various plant and animal virus encoded RNAi and IFN suppressor proteins to functionally substitute for the HAdV-5 VA RNAI. Our results revealed that only the Vaccinia virus (VACV) E3L protein was able to substitute for the HAdV-5 VA RNAI functions in virus-infected cells. Interestingly, the E3L protein rescues the translational defect but does not stimulate viral capsid mRNA accumulation observed with VA RNA. We further show that the E3L C-terminal region containing the dsRNA-binding domain is needed to enhance VA RNAI mutant virus replication. Additionally, we show that the HAdV-4 and HAdV-37 VA RNAI are more effective than the HAdV-5 VA RNAI in rescuing virus replication.

Cytochrome P450 family member CYP51A1 is a key enzyme in cholesterol biosynthesis whose deregulation is implicated in numerous diseases, including retinal degeneration. Here we describe that HAdV-37 infection leads to downregulation of CYP51A1 expression and overexpression of its antisense non-coding Alu element (AluCYP51A1) in retinal pigment epithelium (RPE) cells. This change in gene expression is associated with a reversed accumulation of a positive histone mark at the CYP51A1 and AluCYP51A1 promoters. Further, transient AluCYP51A1 RNA overexpression correlates with reduced CYP51A1 mRNA accumulation. Collectively, our data suggest that AluCYP51A1 might control CYP51A1 gene expression in HAdV-37-infected RPE cells.