Search results for: metagenomics profiling

Authors: Erinda Bllaca Ndroqi

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The dilemma with which the monitoring professionals are facing in today’s reality is whether to accept that prisons all over the world constitute a place where not all rights are respected (ethical approach), or widen the scope of monitoring by prioritizing the special needs of people deprived of their liberties (human right approach), despite the context and the level of improved prison condition, staff profiling, more services oriented towards rehabilitation instead of punishment. Such dilemma becomes a concern if taking into consideration the fact that prisoners, due to their powerlessness and 'their lives at the hand of the state', are constantly under the threat of abuse of power and neglect, which in the Albanian case, has never been classified as torture. Scientific research in twenty-four (24) Albanian prisons shows that for some rights, prisoners belonging to 'vulnerable groups' such as mental illness, HIV positive status, sexual orientation, and terminal illness remain quite challenged and do not ensure that their basic rights are being met by the current criminal justice system (despite recommendations set forwards to prison authorities by the European Committee for the Prevention of Torture and Inhuman or Degrading Treatment or Punishment (CPT)). The research orients more discussion about policy and strategic recommendations that would need a thorough assessment of the impact of rehabilitation in special categories of prisoners, including recidivists.

Keywords: prisons, rehabilitation, torture, vulnerability

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Authors: Hyeon Su Kim, Sungjin Park, Hae Ryung Chang, Hae Rim Jung, Young Zoo Ahn, Yon Hui Kim, Seungyoon Nam

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Ependymoma, one of the most common parenchymal spinal cord tumor, represents 3-6% of all CNS tumor. Especially intracranial ependymomas, which are more frequent in childhood, have a more poor prognosis and more malignant than spinal ependymomas. Although there are growing needs to understand pathogenesis, detailed molecular understanding of pathogenesis remains to be explored. A cancer cell is composed of complex signaling pathway networks, and identifying interaction between genes and/or proteins are crucial for understanding these pathways. Therefore, we explored each ependymoma in terms of differential expressed genes and signaling networks. We used Microsoft Excel™ to manipulate microarray data gathered from NCBI’s GEO Database. To analyze and visualize signaling network, we used web-based PATHOME algorithm and Cytoscape. We show HOX family and NEFL are down-regulated but SCL family is up-regulated in cerebrum and posterior fossa cancers over a spinal cancer, and JAK/STAT signaling pathway and Chemokine signaling pathway are significantly different in the both intracranial ependymoma comparing to spinal ependymoma. We are considering there may be an age-dependent mechanism under different histological pathogenesis. We annotated mutation data of each gene subsequently in order to find potential target genes.

Keywords: systems biology, ependymoma, deg, network analysis

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Authors: Muhammad Fiaz, Muhammad Saqlain, Bernard M. Y. Cheung, S. M. Saqlan Naqvi, Ghazala Kaukab Raja

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Background: Association of C allele of rs662799 SNP of APOA5 gene with metabolic syndrome (MetS) has been reported in different populations around the world. A case control study was conducted to explore the relationship of rs662799 variants (T/C) with the MetS and the associated risk phenotypes in a population of Pakistani origin. Methods: MetS was defined according to the IDF criteria. Blood samples were collected from the Pakistan Institute of Medical Sciences, Islamabad, Pakistan for biochemical profiling and DNA extraction. Genotyping of rs662799 was performed using mass ARRAY, iPEX Gold technology. A total of 712 unrelated case and control subjects were genotyped. Data were analyzed using Plink software and SPSS 16.0. Results: The risk allele C of rs662799 showed highly significant association with MetS (OR=1.5, Ρ=0.002). Among risk phenotypes, dyslipidemia, and obesity showed strong association with SNP (OR=1.49, p=0.03; OR =1.46, p=0.01) respectively in models adjusted for age and gender. Conclusion: The rs662799C allele is a significant risk marker for MetS in the local Pakistani population studied. The effect of the SNP is more on dyslipidemia than the other components of the MetS.

Keywords: metabolic syndrome, APOA5, rs662799, dyslipidemia, obesity

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Authors: Ching Kin Keong, Koh Tieng Wei, Abdul Azim Abd. Ghani, Khaironi Yatim Sharif

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Maintaining factory default battery endurance rate over time in supporting huge amount of running applications on energy-restricted mobile devices has created a new challenge for mobile applications developer. While delivering customers’ unlimited expectations, developers are barely aware of efficient use of energy from the application itself. Thus developers need a set of valid energy consumption indicators in assisting them to develop energy saving applications. In this paper, we present a few software product metrics that can be used as an indicator to measure energy consumption of Android-based mobile applications in the early of design stage. In particular, Trepn Profiler (Power profiling tool for Qualcomm processor) has used to collect the data of mobile application power consumption, and then analyzed for the 23 software metrics in this preliminary study. The results show that McCabe cyclomatic complexity, number of parameters, nested block depth, number of methods, weighted methods per class, number of classes, total lines of code and method lines have direct relationship with power consumption of mobile application.

Keywords: battery endurance, software metrics, mobile application, power consumption

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Authors: Jatuporn Juyjingam, Pitak Siriwong

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This paper presents a study of factors effecting the success and failure of social enterprise in Thailand identifying communication as one of the criteria for measuring the social impact of social enterprise. The study focused on the communication driver of the SCALERS model. The research examines how communication is viewed in Thailand social enterprise. The research aims to determine how selected social enterprise uses communication in their operations. More specifically, the study aims to 1) describe the profile of social enterprise in Thailand, 2) identify the different roles of communication in the operation of social enterprise in Thailand, 3) determine Thailand social enterprise concept of communication. The study made use of the case study and cross case study research designs. For the profiling of the social enterprises, the case study was used. The researchers made use of the cross-case research design in identifying trends across the ten social enterprises and in determining the social entrepreneurs’ concept of communication. Key informant interviews were conducted with the heads or representatives of selected social enterprises, a three-part interview schedule was used to facilitate data gathering. The three parts included are 1) Profile of social enterprise in Thailand 2) How social enterprises apply communication in their operations 3) What is the key success in using communication among social enterprise in Thailand. This study is an exploratory research.

Keywords: communication, social entrepreneurship, social enterprise, sustainability development

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Authors: Aliya Grig, Konstantin Sokolov, Igor Shatalin

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The report describes the methodology for collecting data and building an ML model for determining the personality psychotype using profiling and personality traits methods based on several short messages of a user communicating on an arbitrary topic with a chitchat bot. In the course of the experiments, the minimum amount of text was revealed to confidently determine aspects of personality. Model accuracy - 85%. Users' language of communication is English. AI for a personalized communication with a user based on his mood, personality, and current emotional state. Features investigated during the research: personalized communication; providing empathy; adaptation to a user; predictive analytics. In the report, we describe the processes that captures both structured and unstructured data pertaining to a user in large quantities and diverse forms. This data is then effectively processed through ML tools to construct a knowledge graph and draw inferences regarding users of text messages in a comprehensive manner. Specifically, the system analyzes users' behavioral patterns and predicts future scenarios based on this analysis. As a result of the experiments, we provide for further research on training AI models to be empathetic, creating personalized communication for a user

Keywords: AI, empathetic, chatbot, AI models

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Authors: Mashitoh Abd Rahman, Najihah Mohd Hashim, Faiqah Ramli, Syam Mohan, Noraziah Nordin, Hamed Karimian, Hapipah Mohd Ali

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Ovarian cancer is the most lethal gynecological malignancies. HME5, a prenylflavanoid has been isolated from local medicinal plant. This compound has been reported to possess a broad spectrum of biological activities including anticancer property. However, the potential of HME5 as an antiproliferative and cytotoxic agent on an ovarian cancer cells has not yet been investigated. In this present study, we examined the antiproliferative and cytotoxic effect of HME5 on Caov-3 (Human Ovarian Adenocarcinoma) cell line by using 3-[4,5-dimethylthizol-2-y]-2,5-diphenyltetrazolium bromide (MTT) assay, Acridine orange and propidium Iodide (AOPi) and cell cycle analysis study. HME5 has shown to inhibit Caov-3 in a time-dependent manner with the IC50 values of 5µg/ml, 2µg/ml and 1µg/ml after 24h, 48h and 72h treatment, respectively. Morphological study from AOPi analysis showed that HME5 induced apoptosis after 24 and 48h post-treatment. Nevertheless, HME5 exhibited cell cycle arrest at G1 phase as indicated in flow cytometry cell cycle profiling. In conclusion, HME5 inhibited proliferation of Caov-3 through induction of apoptosis and cell cycle arrest at G1 phase.

Keywords: apoptosis, prenylflavanoid, ovarian cancer, HME5

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Authors: Pui Yong Leo, Normy Maziah Mohd Said

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Change of global economy landscape and business environment has led to companies’ decision to go global and enter international markets. As the companies go beyond the comfort zone (i.e. investing in the home country), it is important to ensure a comprehensive risk assessment is carried out. This paper describes a standardized approach for international investment, ensuring identification of risk, risk appetite, risk rating, risk treatment and mitigation plans for respective international investment proposal. The standardized approach is divided into three (3) stages as follows: Stage 1 – Preliminary Risk profiling; with the objective to gauge exposure to countries and high level risk factors as first level assessment. Stage 2 – Risk Parameters; with the objective to define risk appetite for the international investment from the perspective of likelihood and impact. Stage 3 – Detailed Risk Assessments; with the objectives to assess in detail any triggered elements from Stage 1, and project specific risks. The final output will include the mitigation plans for the identified risks for the total investment. Example will be given in this paper to show how comprehensive risk assessment is carried out for an international investment in power energy sector.

Keywords: international investment, mitigation plans, risk appetite, risk assessment

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Authors: Fatma El-Zahraa El-Taher, Ayman Taha, Jane Courtney, Susan Mckeever

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Understanding road networks plays an important role in navigation applications such as self-driving vehicles and route planning for individual journeys. Intersections of roads are essential components of road networks. Understanding the features of an intersection, from a simple T-junction to larger multi-road junctions, is critical to decisions such as crossing roads or selecting the safest routes. The identification and profiling of intersections from satellite images is a challenging task. While deep learning approaches offer the state-of-the-art in image classification and detection, the availability of training datasets is a bottleneck in this approach. In this paper, a labelled satellite image dataset for the intersection recognition problem is presented. It consists of 14,692 satellite images of Washington DC, USA. To support other users of the dataset, an automated download and labelling script is provided for dataset replication. The challenges of construction and fine-grained feature labelling of a satellite image dataset is examined, including the issue of how to address features that are spread across multiple images. Finally, the accuracy of the detection of intersections in satellite images is evaluated.

Keywords: satellite images, remote sensing images, data acquisition, autonomous vehicles

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Authors: Mayowa Philips Ibitola, Abe Oluwaseun Banji, Olorunfemi Akinade-Solomon

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A total of 20 bottom sediment samples were collected from the Lekki Lagoon during the wet and dry season. The study was carried out to determine the textural characteristics, sediment distribution pattern and energy of transportation within the lagoon system. The sediment grain sizes and depth profiling was analyzed using dry sieving method and MATLAB algorithm for processing. The granulometric reveals fine grained sand both for the wet and dry season with an average mean value of 2.03 ϕ and -2.88 ϕ, respectively. Sediments were moderately sorted with an average inclusive standard deviation of 0.77 ϕ and -0.82 ϕ. Skewness varied from strongly coarse and near symmetrical 0.34- ϕ and 0.09 ϕ. The kurtosis average value was 0.87 ϕ and -1.4 ϕ (platykurtic and leptokurtic). Entirely, the bathymetry shows an average depth of 4.0 m. The deepest and shallowest area has a depth of 11.2 m and 0.5 m, respectively. High concentration of fine sand was observed at deep areas compared to the shallow areas during wet and dry season. Statistical parameter results show that the overall sediments are sorted, and deposited under low energy condition over a long distance. However, sediment distribution and sediment transport pattern of Lekki Lagoon is controlled by a low energy current and the down slope configuration of the bathymetry enhances the sorting and the deposition rate in the Lekki Lagoon.

Keywords: Lekki Lagoon, Marine sediment, bathymetry, grain size distribution

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Authors: Salwa A. H. Hamdi, Maha A. M. El-Shazly, Mona Fathi Fol, Hanan S. Mossalem, Mosad A. Ghareeb, Amina M. Ibrahim

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One of the most distinctive and defining features of cephalopods squid, cuttlefish, and Octopus is their inking behavior. Their ink, which is blackened by melanin but also contains other constituents, has been used by humans in various ways for millennia. The present study aims to investigate the chemical profiling of the Octopus vulgaris ink extract and to evaluate its antioxidant, antimicrobial, and anti-schistosomal activities. The present results showed that GC-MS examination of Octopus vulgaris ink comprises 21 compounds. The main detected compounds are (E)-1, 2, 3, 4-Tetra (4-phenylphenyl)-2-butene-1,4-dione, Lipo-3-episapelin A, and 5,10-Dihexyltetrabenzoporphyrin. Results showed that the octopus ink had antioxidant capacity and the capability to mask DPPH free radicals in comparison with ascorbic acid. Octopus Vulgaris ink extract had inhibitory action against three gram-positive bacteria, Streptococcus faecalis, Staphylococcus aureus, and Bacillus subtilis, and three gram-negative bacteria, Neisseria gonorrhoeae, Escherichia coli, and Pseudomonas aeuroginosa. Additionally, the extracted ink revealed antifungal activity against Aspergillus flavus and yeast as Candida albicans. The obtained data indicated the effectiveness of ink extract in pharmaceutical industries as an antioxidant, antimicrobial and antischistosomicidal

Keywords: antimicrobial, antioxidant, ink, octopus vulgaris

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Authors: Olteanu Constanta, Olteanu Lucian

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Researchers note that algebraic reasoning and sense making is essential for building conceptual knowledge in school mathematics. Consequently, pre-service teachers’ own reasoning and sense making are useful in fostering and developing students’ algebraic reasoning and sense making. This article explores the forms of reasoning and sense making that pre-service mathematics teachers exhibit and use in the process of analysing problem-posing tasks with a focus on first-degree equations. Our research question concerns the characteristics of the problem-posing tasks used for reasoning and sense making of first-degree equations as well as the characteristics of pre-service teachers’ reasoning and sense making in problem-posing tasks. The analyses are grounded in a post-structuralist philosophical perspective and variation theory. Sixty-six pre-service primary teachers participated in the study. The results show that the characteristics of reasoning in problem-posing tasks and of pre-service teachers are selecting, exploring, reconfiguring, encoding, abstracting and connecting. The characteristics of sense making in problem-posing tasks and of pre-service teachers are recognition, relationships, profiling, comparing, laddering and verifying. Beside this, the connection between reasoning and sense making is rich in line of flight in problem-posing tasks, while the connection is rich in line of rupture for pre-service teachers.

Keywords: first-degree equations, problem posing, reasoning, rhizomatic assemblage, sense-making, variation theory

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Authors: Rahul Agarwal, Ashutosh Singh

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Cervical cancer is one of the women related cancers which starts from the pre-cancerous cells and a fraction of women with pre-cancers of the cervix will develop cervical cancer. Cervical pre-cancers if treated in pre-invasive stage can prevent almost all true cervical squamous cell carcinoma. The present study investigates the genes and pathways that are involved in the progression of cervical cancer and are responsible in transition from pre-invasive stage to other advanced invasive stages. The study used GDS3292 microarray data to identify the stage specific genes in cervical cancer and further to generate the network of the significant genes. The microarray data GDS3292 consists of the expression profiling of 10 normal cervices, 7 HSILs and 21 SCCs samples. The study identifies 70 upregulated and 37 downregulated genes in HSIL stage while 95 upregulated and 60 downregulated genes in SCC stages. Biological process including cell communication, signal transduction are highly enriched in both HSIL and SCC stages of cervical cancer. Further, the ppi interaction of genes involved in HSIL and SCC stages helps in identifying the interacting partners. This work may lead to the identification of potential diagnostic biomarker which can be utilized for early stage detection.

Keywords: cervical cancer, HSIL, microarray, SCC

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Authors: Dina A. Selim, Eman Shawky, Rasha M. Abu El-Khair

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In the current study, UPLC-MS/MS combined to chemometrics were applied on seven Sri Lankan tea grades; Orange Pekoe, Flowery Pekoe, Broken Orange Pekoe Fannings, Broken Orange Pekoe black tea, green tea, silver tips and golden tips white tea grades for their comprehensive metabolic profiling. Certain metabolites, namely, Theasensinin C and E, theaflavin and theacitrin appeared to be the main chemical markers of black tea type, catechin, epicatechin, epigallocatechin, methyl epigallocatechin were the main discriminatory markers of green tea type, while theanine, oolongotheanine and quercetin glycosides were the main chemical markers of white tea type. Theogalloflavin, epigallocatechin and flavonoid glycosides were the main down-accumulated metabolites while theaflavin gallate, and N-ethyl pyrrolidinone epicatechin were the chief up- accumulated metabolites between whole and broken black tea leave grades while puerin A and C and gallic acid was the main down- accumulated metabolites and N-ethyl pyrrolidinone epicatechin gallate was the main up-accumulated one between broken and fanning black tea grades.

Keywords: tea grading, Sri Lankan tea, chemometrics, metabolomics, chemical markers

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Authors: Hasan Mahmud Reza

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Extensive studies of the human umbilical cord, both basic and translational, over the last three decades have unveiled a plethora of information. The cord lining harbors at least two phenotypically different multipotent stem cells: mesenchymal stem cells (MSCs) and cord lining epithelial stem cells (CLECs). These cells exhibit a mixed genetic profiling of both embryonic and adult stem cells, hence display a broader stem features than cells from other sources. We have observed that umbilical cord-derived cells are immunologically privileged and non-tumorigenic by animal study. These cells are ethically acceptable, thus provides a significant advantage over other stem cells. The high proliferative capacity, viability, differentiation potential, and superior harvest of these cells have made them better candidates in comparison to contemporary adult stem cells. Following 30 replication cycles, these cells have been observed to retain their stemness, with their phenotype and karyotype intact. Transplantation of bioengineered CLEC sheets in limbal stem cell-deficient rabbit eyes resulted in regeneration of clear cornea with phenotypic expression of the normal cornea-specific epithelial cytokeratin markers. The striking features of low immunogenicity protecting self along with co-transplanted allografts from rejection largely define the transplantation potential of umbilical cord-derived stem cells.

Keywords: cord lining epithelial stem cells, mesenchymal stem cell, regenerative medicine, umbilical cord

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Authors: Rorlinda Yusof, Siti Aishah Hassan, Afifah Mohamad Radzi, Mohd Hakimie Zainal Abidin, Amran Rasli, Inderbir Sandhu

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The purpose of this study is to examine the self-identities of gifted and talented students and the relationship between self-identity and academic accomplishment. A random sample of 300 students enrolled in a secondary education programme at the Pusat GENIUS@pintar Negara was chosen as respondents of a 151-item holistic-identity component development tool. The validity of the instrument was assessed using Principal Components Analysis and Factor Analysis via an inter-Item Correlation Matrix (Loading values 0.44 to 0.86), which resulted in the formation of eight dimensions. The Cronbach's Alpha was calculated to determine the instrument's reliability (the overall result was 0.98). The results showed that students' holistic-identity profiles were relatively high (mean=4.09, standard deviation=0.449). In addition, spiritual identity received the greatest mean score (4.34) out of the eight components of identity investigated, while leadership identity received the lowest mean score (3.88). A conceptual framework for Islamic school leadership is recommended to implement spiritual values without differentiation to harmonize spiritual and intellectual intelligence among all the students. Some benchmarking studies with other centres for gifted and talented students are recommended for further research.

Keywords: holistic self-identity, academic achievement, self-development programme, counselling services, gifted and talented students

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Authors: Walaa Al-Maghraby

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Endophytes are organisms that colonize internal plant tissues without causing apparent harm to their host. Almost all groups of microorganisms have been found in endophytic association with plants may be fungi. They stimulate the production of secondary metabolites with a diverse range of biological activities. Leptadenia pyrotechnica is a more or less leafless, erect shrub with straight stems which is highly distributed in Saudi Arabia. Four endophytes fungi were isolated from Leptadenia pyrotechnica and identified using 18S ribosomal RNA sequences, which revealed four fungi genuses, namely Aspergillus terreus; Aspergillus welwitschiae; Aspergillus fumigatus and Aspergillus flavus. In this present study, four endophytic fungi from Leptadenia pyrotechnica were used for obtaining crude aqueous and ethyl acetate extracts for antimicrobial screening against 6 human pathogens, the antibacterial tests presented satisfactory results, where the pathogenic bacteria were inhibited by the four extracts tested, except for Escherichia coli that was inhibited by all extracts except ethyl acetate extract of Aspergillus terreus. Analysis of variance showed that the extract produced by endophyte Leptadenia pyrotechnica was the most effective against all bacteria, either gram-negative or positive. However, the extract was not efficient against pathogenic fungi. Therefore, this study indicates that endophytes from medicinal plant Leptadenia pyrotechnica could be potential sources of antibacterial substances.

Keywords: antimicrobial activity, Aspergillus sp, endophytes, Leptadenia pyrotechnica

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Authors: Silvia Riva, Ezekiel Chinyio

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Introduction: Workers in different sectors are prone to stress at varying levels. They also respond to stress in different ways. An inspiration was to study stress development amongst workers in a work dangerous setting (Construction Industry) as well as how they cope with specific stress incidences. Objective: The overarching objective of the study was to study and correlate between stress and coping strategies. The research was conducted in an organizational industrial setting, and its findings on the coping actions of construction workers are reported in this article. Methods: An online cross-sectional survey was conducted with 80 participants aged 18-62. These were working for three different construction organizations in the West Midland region of the UK. Their coping actions were assessed using the COPE Inventory (Carver, 2013) instrument while the level of stress was assessed by the Perceived Stress Scale (Cohen, 1994). Results: Out of 80 workers (20 female, 25%, mean age 40.66), positive reinterpretation (M=4.15, SD=2.60) and active coping (M=4.18, SD=2.55) were the two most adaptive strategies reported by the workers while the most frequent maladaptive behavior was mental disengagement (M=3.62, SD=2.25). Among the maladaptive tactics, alcohol and drug abuse was a significant moderator in stress reactions (t=6.12, p=.000). Conclusion: Some maladaptive strategies are adopted by construction workers to cope with stress. So, it could be argued that programs of stress prevention and control in the construction industry have a basis to develop solutions that can improve and strengthen effective interventions when workers are stressed or getting stressed.

Keywords: coping, organization, strategies, stress

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Authors: Maxence Queyrel, Edi Prifti, Alexandre Templier, Jean-Daniel Zucker

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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.

Keywords: deep learning, disease prediction, end-to-end machine learning, metagenomics, multiple instance learning, precision medicine

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Authors: Evans Iyamu

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Genes encoding hydrophobins play distinct roles at different stages of the life cycle of fungi, and they foster hyphal attachment to surfaces. The hydrophobin Sc4 is known to provide a hydrophobic membrane lining of the gas channels within Schizophyllum commune fruiting bodies. Here, we cultivated non-fruiting, monokaryotic S. commune 12-43 on glass surfaces that could be verified by micrography. Differential gene expression profiling of nine hydrophobin genes and the hydrophobin-like sc15 gene by quantitative PCR showed significant up-regulation of sc4 when S. commune was attached to glass surfaces, also confirmed with RNA-Seq data analysis. Another silicate, namely quartz sand, was investigated, and induction of sc4 was seen as well. The up-regulation of the hydrophobin gene sc4 may indicate involvement in S. commune hyphal attachment to glass as well as quartz surfaces. We propose that the covering of hyphae by Sc4 allows for direct interaction with the hydrophobic surfaces of silicates and that differential functions of specific hydrophobin genes depend on the surface interface involved. This study could help with the clarification of the biological functions of hydrophobins in natural surroundings, including hydrophobic surface attachment. Therefore, the analysis of growth on glass serves as a basis for understanding S. commune interaction with glass surfaces while providing the possibility to visualize the interaction microscopically.

Keywords: hydrophobin, structured glass surfaces, differential gene expression, quartz sand

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Authors: Daniel Motlhanka, Neo Kerebotswe

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The strong and long history of use of medicinal plants in Botswana to address existing and emerging health threats provides undebatable evidence for their potential as innovative therapeutic tools. The prevalence of emerging health threats, such as COVID-19 and hard-to-treat non-communicable diseases, warrants the scientific community to revisit and exploit ethnopharmacology for its potential as a source of therapeutic tools. Many studies conducted on bioactivity-guided bioassays of ethnobotanical resources have proved a number of health beneficial properties of these plants, such as free radical scavenging, anti-inflammatory, antimicrobial and, most importantly, the capability of medicinal plants to alleviate oxidative stress. In this work, a number of medicinal plants used in Botswana traditional medicine were investigated for both their free radical scavenging capability and total phenolic contents using the Free Radical Scavenging Power (FRSP) and Folin Ciocalteau (FC) method. At 100 micrograms/ml all the studied plants expressed above 90% Scavenging power and expressed total phenolic contents between 5000- 8890 mg/L.GAE. These plants are promising tools for engineering active therapeutic tools against life-threatening diseases of oxidative stress origin.

Keywords: oxidative stress, non-communicable diseases, total phenolics, ethnobotanicals

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Authors: Ashish Kumar Pathak, Ritika Sharma, Vishal Nath, Sudhir Pratap Singh, Rakesh Tuli

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Litchi is a sub-tropical fruit crop with genotypes bearing delicious juicy fruits with variable seed size (bold to rudimentary size). Small seed size is a desirable trait in litchi, as it increases consumer acceptance and fruit processing. The biochemical activities in mid- stage ovules (e.g. 16, 20, 24 and 28 days after anthesis) determine the fate of seed and fruit development in litchi. Comprehensive ovule-specific transcriptome analysis was performed in two litchi genotypes with contrasting seed size to gain molecular insight on determinants of seed fates in litchi fruits. The transcriptomic data was de-novo assembled in 1,39,608 trinity transcripts, out of which 6,325 trinity transcripts were differentially expressed between the two contrasting genotypes. Differential transcriptional pattern was found among ovule development stages in contrasting litchi genotypes. The putative genes for salicylic acid, jasmonic acid and brassinosteroid pathway were down-regulated in ovules of small-seeded litchi. Embryogenesis, cell expansion, seed size and stress related trinity transcripts exhibited altered expression in small-seeded genotype. The putative regulators of seed maturation and seed storage were down-regulated in small-seed genotype.

Keywords: Litchi, seed, transcriptome, defence

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Authors: Joe Modise, Bamidel Joseph Okoli, Nas Molefe, Imelda Ledwaba

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The present study describes the chemical profile and antioxidant potential of the stem bark of Acacia decurrens. The methanol fraction of A. decurrens stem bark gave the highest yield (20 %), while the hexane fraction had the lowest yield (0.2 %). The GC-MS spectra of the hexane, chloroform and ethyl acetate fractions confirm the presence of fifty two major compounds and the ICP-OES analysis of the stem bark was found to contain Co(0.41), Zn(1.75), Mn(3.69), Ca(8.67), Ni(10.54), Mg(12.98), Cr(24.38), K(47.88), Fe(154.62) ppm; which is an indication of hyper-accumulation capacity. The UV-Visible spectra of showed four absorption maxima for hexane fraction at 665 (0.028), 410 (0.116), 335 (0.278) and 250 (0.007) nm, three for chloroform fraction at 665 (0.028), 335 (0.278) and 250 (0.007) nm , three for ethyl acetate fraction at 665 (0.070), 390 (0.648) and 345 (0.663) nm and three for methanol fraction at 385 (0.508), 310 (0.886) and 295 (0.899) nm respectively. Quantitative phytochemical screening indicated that the alkaloid (0.6-3.3) % and saponins (5.1-8.6) % contents of the various fractions were significantly lower than the tannin (30.9-55.8) mg TAE/g, steroid(13.92-41.2) %, phenol (40.6-65.5) mgGAE/g and flavonoids (210.2 -284.9) mg RUE/g contents. The antioxidant activity of the fractions was analysed by different methods and revealed good to moderate antioxidant potential with different IC50 values viz. (42.2-49.6) mg/mL for ABTS and (37.8-75.0) μg/ml for DPPH respectively, compared to standard antioxidants. Based on obtained results, the A.decurrens stem bark fractions can be a source of safe, sustainable natural antioxidant drug and can be exploited as a source of controlled green-heavy metal cleaner.

Keywords: Acacia decurrens, antioxidant, DPPH, ABTS, hyperaccumulation, Menstruum, ICP-OES, GC-MS, UV/visible

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Authors: Saji George, Eng Khuan Seng, Christof Luda

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Nanotechnology has been recognized as an important tool for modern agriculture and has the potential to overcome some of the pressing challenges faced by aquaculture industry. A strategy for optimizing nanotechnology-based therapeutic delivery platform for immunizing farmed fish was developed. Accordingly, a compositional library of nanomaterials of natural chemistry (Halloysite (clay), Chitosan, Hydroxyapatite, Mesoporous Silica and a composite material of clay-chitosan) was screened for their toxicity and efficiency in delivering models antigens in cellular and zebrafish embryo models using high throughput screening platforms. Through multi-parametric optimization, chitosan modified halloysite (clay) nanomaterial was identified as an optimal vaccine delivery platform. Further, studies conducted in juvenile seabass showed the potential of clay-chitosan in delivering outer membrane protein of Tenacibaculum maritimum- TIMA (pathogenic bacteria) to and its efficiency in eliciting immune responses in fish. In short, as exemplified by this work, the strategy of using compositional nanomaterial libraries and their biological profiling using high-throughput screening platform could fasten the discovery process of nanomaterials with potential applications in food and agriculture.

Keywords: nanotechnology, fish-vaccine, drug-delivery, halloysite-chitosan

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Authors: Aqeela Ashraf, Muhammad Imran, Tahir Yaqub, Muhammad Tayyab, Yung Fu Chang

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For the identification of bovine mastitic pathogen, an economical, rapid and sensitive molecular diagnostic assay is developed by PCR multiplexing of gene and pathogenic species specific DNA sequences. The multiplex PCR assay is developed for detecting nine important bacterial pathogens causing mastitis Worldwide. The bacterial species selected for this study are Streptococcus agalactiae, Streptococcus dysagalactiae, Streptococcus uberis, Staphylococcus aureus, Escherichia coli, Staphylococcus haemolyticus, Staphylococcus chromogenes Mycoplasma bovis and Staphylococcus epidermidis. A single reaction assay was developed and validated by 27 reference strains and further tested on 276 bacterial strains obtained from culturing mastitic milk. The multiplex PCR assay developed here is further evaluated by applying directly on genomic DNA isolated from 200 mastitic milk samples. It is compared with bacterial culturing method and proved to be more sensitive, rapid, economical and can specifically identify 9 bacterial pathogens in a single reaction. It has detected the pathogens in few culture negative mastitic samples. Recognition of disease is the foundation of disease control and prevention. This assay can be very helpful for maintaining the udder health and milk monitoring.

Keywords: multiplex PCR, bacteria, mastitis, milk

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Authors: Garima Chaudhary

Abstract:

The gender of an individual in forensic DNA analysis is normally accessed by using the STR multiplexes with the incorporated gender based marker amelogenin or in other words by presence or absence of Y-Chromosome, but it may not be true in all the cases. We hereby report an interesting case of a phenotypic female carrying a male karyotype (46XY). In the alleged murder case, the deceased female with XY genotype was noticed. The expression of 18 Y-linked genes was studied to measure the extent of expression. Expression at 4 loci was observed that might have caused the misinterpretation in forensic casework. This clinical situation of the deceased in this case was diagnosed as testicular feminization syndrome, which characterize a female phenotype with a male karyotype (46, XY). Most of these cases have SRY (testis determining factor). The genetic explanation of this phenomenon is not very clear. Here, we are discussing the impact of such situations of genetic discrepancy in forensic interpretation of results. In the presented murder case of a phenotypic female, sexual assault was also suspected. For confirmation vaginal swabs and micro slides were also sent to us for DNA examination. After DNA analysis using STR markers, Y-chromosome was detected in the samples which supporting the suspicion of sexual assault before murder. When the reference blood sample of the deceased was analyzed, it was found to be case of testicular feminization syndrome. Interesting inferences were made from the results obtained.

Keywords: DNA profiling, forensic case study, Y chromosome, females

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Authors: Musarat Ishaq, Tara Karnezis, Ramin Shayan

Abstract:

Lipedema, a poorly understood chronic disease of adipose hyper-deposition, is often mistaken for obesity and causes significant impairment to mobility and quality-of-life. To identify molecular mechanisms underpinning lipedema, we employed comprehensive omics-based comparative analyses of whole tissue, adipocyte precursors (adipose-derived stem cells (ADSCs)), and adipocytes from patients with or without lipedema. Transcriptional profiling revealed significant differences in lipedema tissue, adipocytes, and ADSCs, with altered levels of mRNAs involved inproliferation and cell adhesion. One highly up-regulated gene in lipedema adipose tissue, adipocytes and ADSCs, ZIC4, encodes Zinc Finger Protein ZIC 4, a class of transcription factor which may be involved in regulating metabolism and adipogenesis. ZIC4 inhibition impaired the adipogenesis of ADSCs into mature adipocytes. Epigenetic regulation study revealed overexpression of ZIC4 is involved in decreased promoter DNA methylation and subsequent decrease in adipogenesis. These epigenetic modifications can alter adipocytes microenvironment and adipocytes differentiation. Our study show that epigenetic events regulate the ability of ADSCs to commit and differentiate into mature adipocytes by modulating ZIC4.

Keywords: lipedema, adipose-derived stem cells, adipose tisue, adipocytes, zinc finger protein, epigenetic

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Authors: Nan Deng, Zhenqiu Liu

Abstract:

Thousands of patients with metastatic tumors were diagnosed with cancers of unknown primary sites each year. The inability to identify the primary cancer site may lead to inappropriate treatment and unexpected prognosis. Nowadays, a large amount of genomics and transcriptomics cancer data has been generated by next-generation sequencing (NGS) technologies, and The Cancer Genome Atlas (TCGA) database has accrued thousands of human cancer tumors and healthy controls, which provides an abundance of resource to differentiate cancer types. Meanwhile, deep convolutional neural networks (CNNs) have shown high accuracy on classification among a large number of image object categories. Here, we utilize 25 cancer primary tumors and 3 normal tissues from TCGA and convert their RNA-Seq gene expression profiling to color images; train, validate and test a CNN classifier directly from these images. The performance result shows that our CNN classifier can archive >80% test accuracy on most of the tumors and normal tissues. Since the gene expression pattern of distant metastases is similar to their primary tumors, the CNN classifier may provide a potential computational strategy on identifying the unknown primary origin of metastatic cancer in order to plan appropriate treatment for patients.

Keywords: bioinformatics, cancer, convolutional neural network, deep leaning, gene expression pattern

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Authors: Daneal Rorke, Gueguim Kana

Abstract:

The shift towards renewable energy sources for biofuel production has received increasing attention. However, the use and pre-treatment of lignocellulosic material are inundated with the generation of fermentation inhibitors which severely impact the feasibility of bioprocesses. This study reports the profiling of all volatile compounds generated during microwave assisted chemical pre-treatment of sorghum leaves. Furthermore, the optimization of reducing sugar (RS) from microwave assisted acid pre-treatment of sorghum leaves was assessed and gave a coefficient of determination (R2) of 0.76, producing an optimal RS yield of 2.74 g FS/g substrate. The development of an intelligent model to predict volatile compound fractions gave R2 values of up to 0.93 for 21 volatile compounds. Sensitivity analysis revealed that furfural and phenol exhibited high sensitivity to acid concentration, alkali concentration and S:L ratio, while phenol showed high sensitivity to microwave duration and intensity as well. These findings illustrate the potential of using an intelligent model to predict the volatile compound fraction profile of compounds generated during pre-treatment of sorghum leaves in order to establish a more robust and efficient pre-treatment regime for biofuel production.

Keywords: artificial neural networks, fermentation inhibitors, lignocellulosic pre-treatment, sorghum leaves

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Authors: Noora Al Muftah, Reda Rawi, Richard Thompson, Halima Bensmail

Abstract:

Clinical responses to anticancer therapies are often restricted to a subset of patients. In some cases, mutated cancer genes are potent biomarkers of response to targeted agents. There is an urgent need to identify biomarkers that predict which patients with are most likely to respond to treatment. Systematic efforts to correlate tumor mutational data with biologic dependencies may facilitate the translation of somatic mutation catalogs into meaningful biomarkers for patient stratification. To identify genomic features associated with drug sensitivity and uncover new biomarkers of sensitivity and resistance to cancer therapeutics, we have screened and integrated a panel of several hundred cancer cell lines from different databases, mutation, DNA copy number, and gene expression data for hundreds of cell lines with their responses to targeted and cytotoxic therapies with drugs under clinical and preclinical investigation. We found mutated cancer genes were associated with cellular response to most currently available Glioma cancer drugs and some frequently mutated genes were associated with sensitivity to a broad range of therapeutic agents. By linking drug activity to the functional complexity of cancer genomes, systematic pharmacogenomic profiling in cancer cell lines provides a powerful biomarker discovery platform to guide rational cancer therapeutic strategies.

Keywords: cancer, gene network, Lasso, penalized regression, P-values, unbiased estimator

Procedia PDF Downloads 409