Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel high performance metagenome-derived alkali-thermostable endo-β-1,4-glucanase for lignocellulosic biomass hydrolysis in the harsh conditions

Background: Lignocellulosic biomass, is a great resource for the production of bio-energy and bio-based material since it is largely abundant, inexpensive and renewable. The requirement of new energy sources has led to a wide search for novel effective enzymes to improve the exploitation of lignocellulose, among which the importance of thermostable and halotolerant cellulase enzymes with high pH performance is significant. Results: The primary aim of this study was to discover a novel alkali-thermostable endo-β-1,4-glucanase from the sheep rumen metagenome. Using a multi-step in-silico analysis, primary candidates with desired properties were found and subjected to cloning, expression, and purification followed by functional and structural characterization. The enzymes' kinetic parameters, including V max , Km, and specific activity, were calculated. The PersiCel4 demonstrated its optimum activity at pH 8.5 and a temperature of 85°C and was able to retain more than 70% of its activity after 150 hours of storage at 85°C. Furthermore, this enzyme was able to maintain its catalytic activity in the presence of different concentrations of NaCl, MgCl 2 , CaCl 2 , and MnCl 2 . Our results showed that treatment with MnCl 2 could enhance the enzyme’s activity by 89%. PersiCel4 was ultimately used for enzymatic hydrolysis of autoclave pretreated rice straw, the most abundant agricultural waste with rich cellulose content. In autoclave treated rice straw, enzymatic hydrolysis with the PersiCel4 increased the release of reducing sugar up to 260% after 72 hours in the harsh condition ( T= 85°C, pH = 8.5). Conclusion: Considering the urgent demand for stable cellulases that are operational on extreme temperature and pH conditions and due to several proposed distinctive characteristics of PersiCel4, it can be used in the harsh condition for bioconversion of lignocellulosic biomass.
A 3.4 Angstrom cryo-EM structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles

Human coronavirus NL63 (HCoV-NL63) is an enveloped pathogen of the family Coronaviridae that spreads worldwide and causes up to 10% of all annual respiratory diseases. HCoV-NL63 is typically associated with mild upper respiratory symptoms in children, elderly and immunocompromised individuals. It has also been shown to cause severe lower respiratory illness. NL63 shares ACE2 as a receptor for viral entry with SARS-CoV and SARS-CoV-2. Here we present the in situ structure of HCoV-NL63 spike (S) trimer at 3.4-A resolution by single-particle cryo-EM imaging of vitrified virions without chemical fixative. It is structurally homologous to that obtained previously from the biochemically purified ectodomain of HCoV-NL63 S trimer, which displays a 3-fold symmetric trimer in a single conformation. In addition to previously proposed and observed glycosylation sites, our map shows density at other amino acid positions as well as differences in glycan structures. The domain arrangement within a protomer is strikingly different from that of the SARS-CoV-2 S and may explain their different requirements for activating binding to the receptor. This structure provides the basis for future studies of spike proteins with receptors, antibodies, or drugs, in the native state of the coronavirus particles.
TBLT IN PRACTICE: BRINGING TASKS TO ENGLISH CLASSROOM IN THE CURRICULUM 2013

Task-based language teaching (TBLT) has been one of an approaches used in EFL classrooms due to its effectiveness. It focuses on the authentic language of students in doing meaningful task using the target language. This study investigates the application of TBLT in EFL classroom in the Curriculum 2013. It examines the kind of tasks that can be applied to scaffold students‟ writing ability and its effectiveness in scaffolding students‟ writing ability. Classroom action research was used in conducting the research in which qualitative data was obtained through observation, interview and documentation. The site of the study was in one of Junior High Schools in Bogor in which class 8 grade was selected. The findings revealed that TBLT can be implemented in the Curriculum 2013 by using different kind of tasks. This study suggests that English teachers may find, modify, and create various kinds of tasks to be implemented in their own classes using TBLT approach.
Restoration and Enhancement of Underwater Under-Exposure Images with Detail-Preserving

Underwater images have great practical value in many fields such as underwater archeology, seabed mining, and underwater exploration. Due to the complex underwater environment, there are problems such as poor light, low contrast, and color degradation. Traditional underwater image processing methods cannot well achieve the goal of clear display under extreme conditions. This paper proposes a method for restoration and enhancement of underwater under-exposure images that protects edge details and enhances image color. Firstly, the underwater image was preprocessed, denoising with improved wavelet threshold function, defogging with the Multi-Scale Retinex Color Restoration (MSRCR) and guided filter method. Then, the method of adaptive exposure graph is used to enhance the under-exposure image. Finally, the deep learning algorithm combined with the Non-Subsampled Contour Transform (NSCT) technology is used to solve the problem of color degradation and edge texture weakening. Experiments show that compared with other underwater image processing methods, this method greatly improves the clarity of the image, enhances the color saturation and the edge texture details of the image, and has a better visual effect.
PREVENTIVE STRATEGIES OF SSI: NURSES’ KNOWLEDGE IN PRE-OPERATIVE AND POST-OPERATIVE SURGICAL SITE CARE

Some patients’ condition occasionally necessitates medical surgical operations. However, in some cases, the proper care of such resultant surgical sites fails to meet the professional standards due to diverse reasons and knowledge inadequacy. As such, infections are prone to manifest. Nonetheless, many researchers across the globe have sought to determine best nursing practices and ways of preventing such surgical site infections. Hence, this review purposed to detail the current prevention strategies of the surgical site infections and the subsequent improvement approaches within the hospital setups. The previous literature was thus obtained from three major journal databases; CINAHL, PubMed and Medline. Subsequently, the resultant journal articles from the previous researchers consistently confirm the need for strict adherence to the standard operation protocols for the prevention of both pre-operative and post-operative infections. Other measures revolve around hygiene; hand cleaning using antiseptic substances, use of sterile wound dressing materials, use of antiseptic soaps to clean surface. Some studies also confirm the need to remove the wound dressing materials between 24 and 48 hours. Nonetheless, studies also confirm that essence of training to bolster nurses’ knowledge about the prevention strategies of the surgical site infections. Based on such empirical data, it becomes apparent that the prevention measures rotate around the adherence to policies, inculcating strict hygiene and also improving nurses’ knowledge. Keywords: Surgical site infection; Nurses’ Knowledge; SSI; Pre-operative; Post-operative; Preventive Strategies of SSI Cite as: AbuAlkishik, S. Y. , Amin, R. A. & Aung, M. M. T. (2020). Preventive strategies of SSI: nurses’ knowledge in pre-operative and post-operative surgical site care. Journal of Qualitative Social Sciences, 2(1), 7-11.
Premarital sexual practice and its associated factors in Ethiopia. A systematic review and meta-analysis

Background Globally, large numbers of adolescents engage in premarital sexual practice. Youths who begin early sexual activity are more likely to be exposed for high-risk of having multiple sexual partners, infection with Human Immune Deficiency Virus (HIV) and other sexual transmitted diseases. There are pocket studies which reported meager and fragmented evidences across different parts of Ethiopia related with this issue, hence the aim of this review was also to estimate those meager evidences and come up with concrete information at the national level.Methods articles were retrived through search engines such as: PubMed/MEDLINE, EMBASE, CINAHL, Google Scholar, HINARI portal, and Cochrane Library using the preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA-P) guidelines. Joanna Briggs Institute Meta-Analysis of Statistics Assessment and Review Instrument (JBI-MAStARI) was used for critical appraisal of the included articles. Random effect model analysis technique was considered to estimate the pooled prevalence of premarital sexual practice with their respective odds ratio (OR) and 95% confidence interval (CI). Cochran’s Q statistic, Egger’s and Begg’s test and meta regression were carried out to assess heterogeneity, publication bias and to identify associated factors respectively.Results Exactly 24 articles with total sample size 14,872 individuals were included for this review. The pooled estimate of premarital sexual practice at the national level was 30.98% (95% CI: 26.74, 35.21). Being female sex (OR=1.55: 95% CI; 1.01, 2.37), age >18yrs (OR=2.39: 95% CI; 1.29, 4.42), being alcohol abuser with (OR=3.47; 95% CI; 1.94, 6.19) and exposed to pornography (OR=3.24:95% CI; 1.95, 5.38) were the associated factors of premarital sexual practice in Ethiopia.Conclusion The pooled prevalence of premarital sexual practice in Ethiopia was high in comparison with other countries. So that it is the strong recommendations of the authors’ to provide an integrated youth’s reproductive and sexual health services on the local context to decrease their exposure for premarital sexual practices and its negative impact on future life opportunities. Keywords: Pooled; Premarital; Sexual; Practice; Prevalence; Ethiopia .
Electromagnetic and Mechanical Perturbations of Photonic Crystal Slab Sensors

Electromagnetic and Mechanical Perturbations of Photonic Crystal Slab Sensors Cory Rewcastle Master of Applied Science Graduate Department of Electrical and Computer Engineering University of Toronto 2017 Modifications to existing two dimensional photonic crystal slabs (PCS) are designed, to perturb device properties for benefits in refractive index and optoacoustic sensing. Sub-wavelength metal features are added to dielectric PCS devices, providing a method of control of the electromagnetic near-field. These designs suffer a quality factor / sensitivity trade-off, while maintaining detection limits on the same order of magnitude as standard PCS and localized surface plasmon based refractive index sensors. The use of a thinned substrate under all-dielectric PCS devices is examined for the purpose of creating acoustically sensitive, single component optical resonators. Tested samples demonstrate system limited sub-MPa detection limits, flat bandwidth responses in the low MHz range, and microsecond event separations. Future applications and avenues of research are discussed.
Worldwide version-controlled database of glacier thickness observations

Abstract. Although worldwide inventories of glacier area have been coordinated internationally for several decades, a similar effort for glacier ice thicknesses was only initiated in 2013. Here, we present the third version of the Glacier Thickness Database (GlaThiDa v3), which includes 3 854 279 thickness measurements distributed over roughly 3000 glaciers worldwide. Overall, 14 % of global glacier area is now within 1 km of a thickness measurement (located on the same glacier) – a significant improvement over GlaThiDa v2, which covered only 6 % of global glacier area and only 1100 glaciers. Improvements in measurement coverage increase the robustness of numerical interpolations and model extrapolations, resulting in better estimates of regional to global glacier volumes and their potential contributions to sea-level rise. In this paper, we summarize the sources and compilation of glacier thickness data and the spatial and temporal coverage of the resulting database. In addition, we detail our use of open-source metadata formats and software tools to describe the data, validate the data format and content against this metadata description, and track changes to the data following modern data management best practices. Archived versions of GlaThiDa are available from the World Glacier Monitoring Service (e.g., v3.1.0, from which this paper was generated: https://doi.org/10.5904/wgms-glathida-2020-10; GlaThiDa Consortium, 2020), while the development version is available on GitLab (https://gitlab.com/wgms/glathida, last access: 9 November 2020).
Infrastructure Megaprojects as Enablers of Digital Innovation Transitions

Innovation refers to the development of a new product, service or process (Abernathy and Clark, 1985). Novelty and innovations are often observed in projects (Shenhar and Dvir, 2007). Innovations are highly context-dependent and rely on good projects (Shenhar and Dvir, 2007). Infrastructure megaprojects have a particularly close relationship with innovation (Davies et al., 2009). This relation between innovation and its context, such as infrastructure megaprojects. is important for understanding innovation. Digital innovation is differentiated from other innovations as it is highly pervasive and systemic (Egyedi and Sherif, 2008). This chapter increases our understanding of digital innovation and its relation to institutional contexts, especially infrastructure megaprojects. Focusing on the relation between digital innovation and infrastructure megaprojects, such as London Heathrow and Crossrail (Davies et al., 2009; Dodgson et al., 2015), shows how these infrastructure megaprojects influenced institutions through standardisation to promote digital innovation.
Almost Famous: The Short- and Long-Term Effects of Housing Wealth Shocks on Career Decisions

Using a novel data set of career histories in the film industry, we study the effect of housing wealth shocks on the quality of jobs that individuals pursue. Homeowners facing greater local house price declines reduce their participation in high-quality projects, such as big-budget films and productions with award-winning talent, while increasing their involvement in low-quality films. Importantly, differences in local labor demand do not explain these results. Consistent with individuals relying on home equity extraction during job searches, these negative shocks have a greater impact on lower-equity and less-wealthy homeowners. These short-term wealth shocks also affect long-term career trajectories.
Dynamic and Scalable Deep Neural Network Verification Algorithm

Deep neural networks have widely used for dealing with complex real-world problems. However, a major concern in applying them to safety-critical systems is the great difficulty in providing formal guarantees about their behavior. Verifying its behavior means study the evolution of its outputs depending on the variation of its inputs. This verification is crucial in an uncertain environment where neural network inputs are noisy. In this paper, we propose an efficient technique for verifying feed-forward neural networks properties. In order to quantify the behavior of the proposed algorithm, we introduce different neural network scenarios to highlight the robustness according to predefined metrics and constraints. The proposed technique is based on the linearization of the non-convex Rectified Linear Unit (ReLU) activation function using the Big-M optimization approach. Moreover, we contribute by an iterative process to find the largest input range verifying (and then defining) the neural network proprieties of neural networks.
Genomic prediction of yield and deep root growth in wheat using a semi-field phenotyping system with a water availability gradient

Background Deeper roots can help plants to take up available resources in deep soil ensuring better growth and higher yields under conditions of limited water supply. The objective was to explore the possibility of genomic prediction for grain-related and root traits of winter wheat measured in a semi-field root phenotyping facility allowing for a water availability gradient and interaction of genomic by water availability gradient. Genotyped winter wheat lines were grown as rows within two subunits of the semi-field facility. Along each row, a water availability gradient was applied by varying the depth distance to a subsurface-irrigation system. Root data were collected based on images taken from a minirhizotron tube below each row in one side of each bed. Results The analysis comprised four grain-related traits: grain yield (GY), protein concentration (PC), total nitrogen content (NC), and thousand kernel weight (TKW) measured on each half row along the water gradient. In addition, two root traits, total root length between 1.2 m and 2 m depth (TRL) and root length in four intervals (IRL) on each tube were analyzed. Two sets of models with or without the effect of neighbors from both sides of each row were applied. Variance components of all effects in the models were estimated. Predictive ability (PA) was measured as the correlation between mean phenotypes corrected for fixed effects and predicted genomic breeding values for each line. Estimated heritabilities ( ) ranged from 0.263 to 0.680 for grain-related traits and from 0.030 to 0.055 for root traits. No interaction of genomic by water availability gradient was found. The relative amount of genetic variance was similar for grain-related and root traits. The PA ranged from 0.246 to 0.477 for grain-related traits and from 0.057 to 0.062 for root traits. Including neighbor effects in the model increased the and the PA for GY and NC. Conclusions In conclusion, it is possible to do genomic prediction for grain-related and root traits in the semi-field facility. Accuracy of root records is low using the current evaluation system due to large environmental variance, and more accurate root records are needed.
MAVEN Deliverable 6.4: Integration Final Report

This document presents the work that has been performed in WP6 after D6.3, and therefore focussing on the integration sprints 3-6. It describes which parts of the system are implemented and how they are put together. To do so, it builds upon the deliverables created so far, esp. D6.3 and all other deliverables of the underlying work packages 3, 4 and 5. Another important aspect for understanding the content of this deliverable is D2.1 [4] for the scenario definition of the whole MAVEN project, and the deliverables D6.1 [5] and D6.2 [6], which give an overview on the existing infrastructure and vehicles used in MAVEN.
LCLS-II: Status, Issues and Plans

The Linac Coherent Light Source II (LCLS-II) project requires the assembly, test, and installation of 37 cryomodules (CM) in order to deliver a 4 GeV CW electron beam to the FEL undulators for production of both hard and soft X-ray pulses at a repetition rate of up to 1 MHz. SRF cavity performance in the 30+ tested CM exceeds gradient and cryogenic dynamic heat-load requirements (set at 16 MV/m and 10 W resp). In this talk we present microphonics, shipping, magnetic-flux exclusion, and field emission performance. The US funding agency, DOE, has recently approved an additional 20 CM for the extension of LCLS-II to 8 GeV. This paper will also include initial cavity and heat-load performance results for the extension project, LCLS-II-HE.
Effect of silver fluoride on micro-ecology of plaque from extensive caries of primary teeth - in vitro study

Background The action mechanism of silver diammine fluoride (SDF) on plaque micro-ecology was seldom studied. This study investigated micro-ecological changes in dental plaque on extensive carious cavity of deciduous teeth after topical SDF treatment. Methods Deciduous teeth with extensive caries freshly removed from school children were collected in clinic. After initial plaque collection, each cavity was topically treated with 38% SDF in vitro. Repeated plaque collections were done at 24 hours and 1 week post-intervention. Post-intervention micro-ecological changes including microbial diversity, microbial metabolism function as well as inter-microbial connections were analyzed and compared after Pyrosequencing of the DNA from the plaque sample using Illumina MiSeq platform. Results After SDF application, microbial diversity decreased (p>0.05). Microbial community composition post-intervention was obviously different from that of supragingival and pre-intervention plaque as well as saliva. At 1 week post-intervention, the relative content of Pseudomonas , Fusobacterium and Pseudoramibacter was obviously higher than before, while most of the other bacteria was obviously reduced, although not statistically significant (P>0.05). The inter-microbial connections became more complex, with positive connections overcame negative ones. Carbohydrate transportation and metabolic functions in the plaque were significantly reduced at 24 hours and 1 week post-intervention. Conclusions SDF has extensive antimicrobial effect on dental plaque, which may reduce carbohydrate metabolism in dental plaque and help promote new balance of the plaque flora.
Build a Bioinformatics Analysis Platform and Apply it to Routine Analysis of Microbial Genomics and Comparative Genomics

Genomics and comparative genomics have been increasingly used as routine methods for general microbiological researches. However, it is usually necessary to call several tools or even write some scripts to complete some simple analysis, which is complicated for most biological researchers. To simplify the operation process, especially for the convenience of microbiologists in the analysis, here we have developed PGCGAP, a comprehensive, malleable and easily-installed prokaryotic genomics and comparative genomics analysis pipeline, which implements genome assembly, gene prediction and annotation, average nucleotide identity (ANI) calculation, phylogenetic analysis, COG annotation, pan-genome analysis, inference of orthologous gene groups, variants calling and annotation and screening for antimicrobial and virulence genes. Although we have tried our best to simplify the installation and usage of PGCGAP, it may be difficult for non-bioinformatician users to master it. So, a protocol was created to help microbiologists without any experience in bioinformatics to establish their own bioinformatics platform and perform routine analysis. This protocol shows how to choose equipment, to install a Linux subsystem on a laptop with windows 10 system, to install PGCGAP and perform all analysis with an example dataset. The protocol requires a basic understanding of Linux, so an additional web page was written to help uninitiated users learn Linux and whole-genome sequencing (http://bcam.hzau.edu.cn/linuxwgs.php).