Abstract: The primary tool currently used to pre-process 10X chromium single-cell ATAC-seq data is Cell Ranger, which can take very long to run on standard datasets. To facilitate rapid pre-processing that enables reproducible workflows, we present a suite of tools called scATAK for pre-processing single-cell ATAC-seq data that is 15 to 18 times faster than Cell Ranger on mouse and human samples. Our tool can also calculate chromatin interaction potential matrices and generate open chromatin signal and interaction traces for cell groups. We use scATAK tool to explore the chromatin regulatory landscape of a healthy adult human brain and unveil cell-type specific features, and show that it provides a convenient and computational efficient approach for pre-processing single-cell ATAC-seq data.
Abstract: Parallel Job Shop Scheduling Problem (JSSP) is a multi-objective and multi constrains NP-optimization problem. Traditional Artificial Intelligence techniques have been widely used; however, they could be trapped into the local minimum without reaching the optimum solution. Thus, we propose a hybrid Artificial Intelligence (AI) model with Discrete Breeding Swarm (DBS) added to traditional AI to avoid this trapping. This model is applied in the cost minimization of the Car Sequencing and Operator Allocation (CSOA) problem. The practical experiment shows that our model outperforms other techniques in cost minimization.
Abstract: Analysis of the human microbiome using metagenomic
sequencing data has demonstrated high ability in discriminating
various human diseases. Raw metagenomic sequencing data require
multiple complex and computationally heavy bioinformatics steps
prior to data analysis. Such data contain millions of short sequences
read from the fragmented DNA sequences and stored as fastq files.
Conventional processing pipelines consist in multiple steps including
quality control, filtering, alignment of sequences against genomic
catalogs (genes, species, taxonomic levels, functional pathways,
etc.). These pipelines are complex to use, time consuming and
rely on a large number of parameters that often provide variability
and impact the estimation of the microbiome elements. Training
Deep Neural Networks directly from raw sequencing data is a
promising approach to bypass some of the challenges associated with
mainstream bioinformatics pipelines. Most of these methods use the
concept of word and sentence embeddings that create a meaningful
and numerical representation of DNA sequences, while extracting
features and reducing the dimensionality of the data. In this paper
we present an end-to-end approach that classifies patients into disease
groups directly from raw metagenomic reads: metagenome2vec. This
approach is composed of four steps (i) generating a vocabulary of
k-mers and learning their numerical embeddings; (ii) learning DNA
sequence (read) embeddings; (iii) identifying the genome from which
the sequence is most likely to come and (iv) training a multiple
instance learning classifier which predicts the phenotype based on
the vector representation of the raw data. An attention mechanism
is applied in the network so that the model can be interpreted,
assigning a weight to the influence of the prediction for each genome.
Using two public real-life data-sets as well a simulated one, we
demonstrated that this original approach reaches high performance,
comparable with the state-of-the-art methods applied directly on
processed data though mainstream bioinformatics workflows. These
results are encouraging for this proof of concept work. We believe
that with further dedication, the DNN models have the potential to
surpass mainstream bioinformatics workflows in disease classification
tasks.
Abstract: There is an increasing interest in introducing computational thinking at an early age. Computational thinking, like mathematical thinking, engineering thinking, and scientific thinking, is a kind of analytical thinking. Learning computational thinking skills is not only to improve technological literacy, but also allows learners to equip with practicable skills such as problem-solving skills. As people realize the importance of computational thinking, the field of educational technology faces a problem: how to choose appropriate tools and activities to help students develop computational thinking skills. Robots are gradually becoming a popular teaching tool, as robots provide a tangible way for young children to access to technology, and controlling a robot through programming offers them opportunities to engage in developing computational thinking. This study explores whether the introduction of flowcharts into the robotics programming courses can help children convert natural language into a programming language more easily, and then to better cultivate their computational thinking skills. An experimental study was adopted with a sample of children ages six to seven (N = 16) participated, and a one-meter-tall humanoid robot was used as the teaching tool. Results show that children can master basic programming concepts through robotic courses. Children's computational thinking has been significantly improved. Besides, results suggest that flowcharts do have an impact on young children’s computational thinking skills development, but it only has a significant effect on the "sequencing" and "correspondence" skills. Overall, the study demonstrates that the humanoid robot and flowcharts have qualities that foster young children to learn programming and develop computational thinking skills.
Abstract: The increasing generation of saline wastewater through various industrial activities is becoming a global concern for activated sludge (AS) based biological treatment which is widely applied in wastewater treatment plants (WWTPs). As for the AS process, an increase in wastewater salinity has negative impact on its overall performance. The advent of conventional aerobic granular sludge (AGS) or bacterial AGS biotechnology has gained much attention because of its superior performance. The development of algal-bacterial AGS could enhance better nutrients removal, potentially reduce aeration cost through symbiotic algae-bacterial activity, and thus, can also reduce overall treatment cost. Nonetheless, the potential of salt stress to decrease biomass growth, microbial activity and nutrient removal exist. Up to the present, little information is available on saline wastewater treatment by algal-bacterial AGS. To the authors’ best knowledge, a comparison of the two AGS systems has not been done to evaluate nutrients removal capacity in the context of salinity increase. This study sought to figure out the impact of salinity on the algal-bacterial AGS system in comparison to bacterial AGS one, contributing to the application of AGS technology in the real world of saline wastewater treatment. In this study, the salt concentrations tested were 0 g/L, 1 g/L, 5 g/L, 10 g/L and 15 g/L of NaCl with 24-hr artificial illuminance of approximately 97.2 µmol m¯²s¯¹, and mature bacterial and algal-bacterial AGS were used for the operation of two identical sequencing batch reactors (SBRs) with a working volume of 0.9 L each, respectively. The results showed that salinity increase caused no apparent change in the color of bacterial AGS; while for algal-bacterial AGS, its color was progressively changed from green to dark green. A consequent increase in granule diameter and fluffiness was observed in the bacterial AGS reactor with the increase of salinity in comparison to a decrease in algal-bacterial AGS diameter. However, nitrite accumulation peaked from 1.0 mg/L and 0.4 mg/L at 1 g/L NaCl in the bacterial and algal-bacterial AGS systems, respectively to 9.8 mg/L in both systems when NaCl concentration varied from 5 g/L to 15 g/L. Almost no ammonia nitrogen was detected in the effluent except at 10 g/L NaCl concentration, where it averaged 4.2 mg/L and 2.4 mg/L, respectively, in the bacterial and algal-bacterial AGS systems. Nutrients removal in the algal-bacterial system was relatively higher than the bacterial AGS in terms of nitrogen and phosphorus removals. Nonetheless, the nutrient removal rate was almost 50% or lower. Results show that algal-bacterial AGS is more adaptable to salinity increase and could be more suitable for saline wastewater treatment. Optimization of operation conditions for algal-bacterial AGS system would be important to ensure its stably high efficiency in practice.
Abstract: Water plays a major role in maintaining life on earth, but it can also serve as a matrix for pathogenic organisms, posing substantial health threats to humans. Although, outbreaks of diseases attributable to drinking water may not be common in industrialized countries, they still occur and can lead to serious acute, chronic, or sometimes fatal health consequences. The analysis of drinking water samples from different regions of Kuwait was performed in this study for bacterial and viral contaminations. Drinking tap water samples were collected from 15 different locations of the six Kuwait governorates. All samples were analyzed by confocal microscopy for the presence of bacteria. The samples were cultured in vitro to detect cultivable organisms. DNA was isolated from the cultured organisms and the identity of the bacteria was determined by sequencing the bacterial 16S rRNA genes, followed by BLAST analysis in the database of NCBI, USA. RNA was extracted from water samples and analyzed by real-time PCR for the detection of viruses with potential health risks, i.e. Astrovirus, Enterovirus, Norovirus, Rotavirus, and Hepatitis A. Confocal microscopy showed the presence of bacteria in some water samples. The 16S rRNA gene sequencing of culture grown organisms, followed by BLAST analysis, identified the presence of several non-pathogenic bacterial species. However, one sample had Acinetobacter baumannii, which often causes opportunistic infections in immunocompromised people, but none of the studied viruses could be detected in the drinking water samples analyzed. The results indicate that drinking water samples analyzed from various locations in Kuwait are relatively safe for drinking and do not contain many harmful pathogens.
Abstract: Graphene material has found tremendous applications
in water desalination, DNA sequencing and energy storage. Multiple
nanopores are etched to create opening for water desalination and
energy storage applications. The nanopores created are of the order
of 3-5 nm allowing multiple ions to transport through the pore. In
this paper, we present for the first time, molecular dynamics study of
single ion transport, where only one ion passes through the graphene
nanopore. The diameter of the graphene nanopore is of the same
order as the hydration layers formed around each ion. Analogous to
single electron transport resulting from ionic transport is observed
for the first time. The current-voltage characteristics of such a device
are similar to single electron transport in quantum dots. The current
is blocked until a critical voltage, as the ions are trapped inside a
hydration shell. The trapped ions have a high energy barrier compared
to the applied input electrical voltage, preventing the ion to break free
from the hydration shell. This region is called “Coulomb blockade
region”. In this region, we observe zero transport of ions inside the
nanopore. However, when the electrical voltage is beyond the critical
voltage, the ion has sufficient energy to break free from the energy
barrier created by the hydration shell to enter into the pore. Thus, the
input voltage can control the transport of the ion inside the nanopore.
The device therefore acts as a binary storage unit, storing 0 when
no ion passes through the pore and storing 1 when a single ion
passes through the pore. We therefore postulate that the device can
be used for fluidic computing applications in chemistry and biology,
mimicking a computer. Furthermore, the trapped ion stores a finite
charge in the Coulomb blockade region; hence the device also acts
a super capacitor.
Abstract: Synthetic domestic wastewater was treated via combining treatment methods, including electrochemical oxidation, adsorption, and sequencing batch reactor (SBR). In the upper part of the reactor, an anode and a cathode (Ti/RuO2-IrO2) were organized in parallel for the electrochemical oxidation procedure. Sodium sulfate (Na2SO4) with a concentration of 2.5 g/L was applied as the electrolyte. The voltage and current were fixed on 7.50 V and 0.40 A, respectively. Then, 15% working value of the reactor was filled by activated sludge, and 85% working value of the reactor was added with synthetic wastewater. Powdered cockleshell, 1.5 g/L, was added in the reactor to do ion-exchange. Response surface methodology was employed for statistical analysis. Reaction time (h) and pH were considered as independent factors. A total of 97.0% biochemical oxygen demand, 99.9% phosphorous and 88.6% cadmium were eliminated at the optimum reaction time (80.0 min) and pH (6.4).
Abstract: Industry employers require new graduates to bring with them a range of knowledge, skills and abilities which mean these new employees can immediately make valuable work contributions. These will be a combination of discipline and professional knowledge, skills and abilities which give graduates the technical capabilities to solve practical problems whilst interacting with a range of stakeholders. Underpinning the development of these disciplines and professional knowledge, skills and abilities, are “enabling” knowledge, skills and abilities which assist students to engage in learning. These are academic and learning skills which are essential to common starting points for both the learning process of students entering the course as well as forming the foundation for the fully developed graduate knowledge, skills and abilities. This paper reports on a project created to introduce and strengthen these enabling skills into the first semester of a Bachelor of Information Technology degree in an Australian polytechnic. The project uses an action research approach in the context of ongoing continuous improvement for the course to enhance the overall learning experience, learning sequencing, graduate outcomes, and most importantly, in the first semester, student engagement and retention. The focus of this is implementing the new curriculum in first semester subjects of the course with the aim of developing the “enabling” learning skills, such as literacy, research and numeracy based knowledge, skills and abilities (KSAs). The approach used for the introduction and embedding of these KSAs, (as both enablers of learning and to underpin graduate attribute development), is presented. Building on previous publications which reported different aspects of this longitudinal study, this paper recaps on the rationale for the curriculum redevelopment and then presents the quantitative findings of entering students’ reading literacy and numeracy knowledge and skills degree as well as their perceived research ability. The paper presents the methodology and findings for this stage of the research. Overall, the cohort exhibits mixed KSA levels in these areas, with a relatively low aggregated score. In addition, the paper describes the considerations for adjusting the design and delivery of the new subjects with a targeted learning experience, in response to the feedback gained through continuous monitoring. Such a strategy is aimed at accommodating the changing learning needs of the students and serves to support them towards achieving the enabling learning goals starting from day one of their higher education studies.
Abstract: Bioremediation technology is now used for treatment instead of traditional metal removal methods. A strain was isolated from Marsa Alam, Red sea, Egypt showed high resistance to high lead concentration and was identified by the 16S rRNA gene sequencing technique as Halomonas sp. ES015. Medium optimization was carried out using Plackett-Burman design, and the most significant factors were yeast extract, casamino acid and inoculums size. The optimized media obtained by the statistical design raised the removal efficiency from 84% to 99% from initial concentration 250 ppm of lead. Moreover, Box-Behnken experimental design was applied to study the relationship between yeast extract concentration, casamino acid concentration and inoculums size. The optimized medium increased removal efficiency to 97% from initial concentration 500 ppm of lead. Immobilized Halomonas sp. ES015 cells on sponge cubes, using optimized medium in loop bioremediation column, showed relatively constant lead removal efficiency when reused six successive cycles over the range of time interval. Also metal removal efficiency was not affected by flow rate changes. Finally, the results of this research refer to the possibility of lead bioremediation by free or immobilized cells of Halomonas sp. ES015. Also, bioremediation can be done in batch cultures and semicontinuous cultures using column technology.
Abstract: The role and relative importance of intrinsic and extrinsic factors in the development of complex diseases such as cancer still remains a controversial issue. Determining the amount of variation explained by these factors needs experimental data and statistical models. These models are nevertheless based on the occurrence and accumulation of random mutational events during stem cell division, thus rendering cancer development a stochastic outcome. We demonstrate that not only individual genome sequencing is uninformative in determining cancer risk, but also assigning a unique genome sequence to any given individual (healthy or affected) is not meaningful. Current whole-genome sequencing approaches are therefore unlikely to realize the promise of personalized medicine. In conclusion, since genome sequence differs from cell to cell and changes over time, it seems that determining the risk factor of complex diseases based on genome sequence is somewhat unrealistic, and therefore, the resulting data are likely to be inherently uninformative.
Abstract: In this paper, the flow of different classes of patients
into a hospital is modelled and analyzed by using the queueing
network analyzer (QNA) algorithm and discrete event simulation.
Input data for QNA are the rate and variability parameters of the
arrival and service times in addition to the number of servers in each
facility. Patient flows mostly match real flow for a hospital in Egypt.
Based on the analysis of the waiting times, two approaches are
suggested for improving performance: Separating patients into
service groups, and adopting different service policies for sequencing
patients through hospital units. The separation of a specific group of
patients, with higher performance target, to be served separately from
the rest of patients requiring lower performance target, requires the
same capacity while improves performance for the selected group of
patients with higher target. Besides, it is shown that adopting the
shortest processing time and shortest remaining processing time
service policies among other tested policies would results in,
respectively, 11.47% and 13.75% reduction in average waiting time
relative to first come first served policy.
Abstract: In this study, raw coffee wastewater (CWW) was used as a complex substrate for anaerobic digestion. The inoculum adaptation stage, microbial diversity analysis and biomethane potential (BMP) tests were performed. A fast inoculum adaptation stage was used by the replacement of vinasse to CWW in an anaerobic sequential batch reactor (AnSBR) operated at mesophilic conditions. Illumina MiSeq sequencing was used to analyze the microbial diversity. While, BMP tests using inoculum adapted to CWW were carried out at different inoculum to substrate (I/S) ratios (2:1, 3:1 and 4:1, on a VS basis). Results show that the adaptability percentage was increased gradually until it reaches the highest theoretical value in a short time of 10 d; with a methane yield of 359.10 NmL CH4/g COD-removed; Methanobacterium beijingense was the most abundant microbial (75%) and the greatest specific methane production was achieved at I/S ratio 4:1, whereas the lowest was obtained at 2:1, with BMP values of 320 NmL CH4/g VS and 151 NmL CH4/g VS, respectively. In conclusion, gradual replacement of substrate was a feasible method to adapt the inoculum in a short time even using complex raw substrates, whereas in the BMP tests, the specific methane production was proportional to the initial amount of inoculum.
Abstract: To be sure about the effective and less effective/ineffective approaches to course instruction, we hold the opinion that the faculty members need regular feedback from their students in order to be aware of how well or unwell their teaching styles have worked when instructing the courses. It can be confirmed without a slightest hesitation that undergraduate students’ motivated-ness can be sustained when continually improving the quality of teaching and properly sequencing the academic courses both, in the curricula and timetables. At Estonian Aviation Academy, four different forms of feedback are used: Lecture monitoring, questionnaires for all students, study information system subject monitoring and direct feedback received by the lecturer. Questionnaires for all students are arranged once during a study year and separately for the first year and senior students. The results are discussed in academic departments together with student representatives, analyzed with the teaching staff and, if needed, improvements are suggested. In addition, a monitoring system is planned where a lecturer acts in both roles – as an observer and as the lecturer. This will foster better exchange of experience and through this help to make the whole study process more interesting.
Abstract: Wilson’s disease (WD) is an autosomal recessive disorder of the copper metabolism, which is caused by a mutation in the copper-transporting P-type ATPase (ATP7B). The mechanism of this disease is the failure of hepatic excretion of copper to bile, and leads to copper deposits in the liver and other organs. The ATP7B gene is located on the long arm of chromosome 13 (13q14.3). This study aimed to investigate the gene mutation in the Vietnamese patients with WD, and make a presymptomatic diagnosis for their familial members. Forty-three WD patients and their 65 siblings were identified as having ATP7B gene mutations. Genomic DNA was extracted from peripheral blood samples; 21 exons and exon-intron boundaries of the ATP7B gene were analyzed by direct sequencing. We recognized four mutations ([R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G) in the sum of 20 detectable mutations, accounting for 87.2% of the total. Mutation S105* was determined to have a high rate (32.6%) in this study. The hotspot regions of ATP7B were found at exons 2, 16, and 8, and intron 14, in 39.6 %, 11.6 %, 9.3%, and 7 % of patients, respectively. Among nine homozygote/compound heterozygote siblings of the patients with WD, three individuals were determined as asymptomatic by screening mutations of the probands. They would begin treatment after diagnosis. In conclusion, 20 different mutations were detected in 43 WD patients. Of this number, four novel mutations were explored, including [R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G. The mutation S105* is the most prevalent and has been considered as a biomarker that can be used in a rapid detection assay for diagnosis of WD patients. Exons 2, 8, and 16, and intron 14 should be screened initially for WD patients in Vietnam. Based on risk profile for WD, genetic testing for presymptomatic patients is also useful in diagnosis and treatment.
Abstract: This study was performed to optimise the react time (RT) and study its effects on the removal rates of nitrogen compounds in a sequencing batch reactor (SBR) treating synthetic industrial wastewater. The results showed that increasing the RT from 4 h to 10, 16 and 22 h significantly improved the nitrogen compounds’ removal efficiency, it was increased from 69.5% to 95%, 75.7 to 97% and from 54.2 to 80.1% for NH3-N, NO3-N and NO2-N respectively. The results obtained from this study showed that the RT of 22 h was the optimum for nitrogen compounds removal efficiency.
Abstract: Enzymes are the biocatalysts which catalyze the biochemical processes and thus have a wide variety of applications in the industrial sector. β-Galactosidase (E.C. 3.2.1.23) also known as lactase, is one of the prime enzymes, which has significant potential in the dairy and food processing industries. It has the capability to catalyze both the hydrolytic reaction for the production of lactose hydrolyzed milk and transgalactosylation reaction for the synthesis of prebiotics such as lactulose and galactooligosaccharides. These prebiotics have various nutritional and technological benefits. Although, the enzyme is naturally present in almonds, peaches, apricots and other variety of fruits and animals, the extraction of enzyme from these sources increases the cost of enzyme. Therefore, focus has been shifted towards the production of low cost enzyme from the microorganisms such as bacteria, yeast and fungi. As compared to yeast and bacteria, fungal β-galactosidase is generally preferred as being extracellular and thermostable in nature. Keeping the above in view, the present study was carried out for the isolation of the β-galactosidase producing fungal strain from the food as well as the agricultural wastes. A total of more than 100 fungal cultures were examined for their potential in enzyme production. All the fungal strains were screened using X-gal and IPTG as inducers in the modified Czapek Dox Agar medium. Among the various isolated fungal strains, the strain exhibiting the highest enzyme activity was chosen for further phenotypic and genotypic characterization. The strain was identified as Rhizomucor pusillus on the basis of 5.8s RNA gene sequencing data.
Abstract: Handwriting is essential to academic success; however, the current literature is limited in the identification of pre-handwriting skills. The purpose of this study was to identify the pre-handwriting skills, which occupational therapy practitioners deem important to handwriting success, as well as those which aid in intervention planning. The online survey instrument consisted of 33 questions that assessed various skills related to the development of handwriting, as well as captured demographic information. Both occupational therapists and occupational therapy assistants were included in the survey study. The survey found that the respondents were in agreement that purposeful scribbling, the ability of a child to copy (vertical/horizontal lines, circle, squares, and triangles), imitating an oblique cross, cognitive skills (attention, praxis, self-regulation, sequencing), grasp patterns, hand dominance, in hand manipulation skills (shift, translation, rotation), bilateral integration, stabilization of paper, crossing midline, and visual perception were important indicators of handwriting readiness. The results of the survey support existing research regarding the skills necessary for the successful development of handwriting in children.
Abstract: Approximately 10,000 different types of dyes and
pigments are being used in various industrial applications yearly,
which include the textile and printing industries. However, these dyes
are difficult to degrade naturally once they enter the aquatic system.
Their high persistency in natural environment poses a potential health
hazard to all form of life. Hence, there is a need for alternative dye
removal strategy in the environment via bioremediation. In this study,
fungi laccase is investigated via commercial agar dyes plates and
submerged fermentation to explore the application of fungi laccase in
textile dye wastewater treatment. Two locally isolated basidiomycetes
were screened for laccase activity using media added with commercial
dyes such as 2, 2-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid
(ABTS), guaiacol and Remazol Brillant Blue R (RBBR). Isolate TBB3
(1.70±0.06) and EL2 (1.78±0.08) gave the highest results for ABTS
plates with the appearance of greenish halo on around the isolates.
Submerged fermentation performed on Isolate TBB3 with the
productivity 3.9067 U/ml/day, whereas the laccase activity for Isolate
EL2 was much lower (0.2097 U/ml/day). As isolate TBB3 showed
higher laccase production, it was subjected to molecular
characterization by DNA isolation, PCR amplification and sequencing
of ITS region of nuclear ribosomal DNA. After being compared with
other sequences in National Center for Biotechnology Information
(NCBI database), isolate TBB3 is probably from species Trametes
hirsutei. Further research work can be performed on this isolate by
upscale the production of laccase in order to meet the demands of the
requirement for higher enzyme titer for the bioremediation of textile
dyes.
Abstract: Gastric Cancer (GC) has high morbidity and fatality
rate in various countries. It is still one of the most frequent and
deadly diseases. Gastrokine1 (GKN1) and gastrokine2 (GKN2) genes
are highly expressed in the normal stomach epithelium and play
important roles in maintaining the integrity and homeostasis of
stomach mucosal epithelial cells. In this study, 47 paired samples that
were grouped according to the types of gastric cancer and the clinical
characteristics of the patients, including gender and average of age.
They were investigated with gene expression analysis and mutation
screening by monitoring RT-PCR, SSCP and nucleotide sequencing
techniques. Both GKN1 and GKN2 genes were observed significantly
reduced found by (Wilcoxon signed rank test; p