Search results for: molecular data

Authors: M. Gowri, E. K. Girija, V. Ganesh

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Background and Significance: Among the dental infections, inflammation and infection of the root canal are common among all age groups. Currently, the management of root canal infections involves cleaning the canal with powerful irrigants followed by intracanal medicament application. Though these treatments have been in vogue for a long time, root canal failures do occur. Treatment for root canal infections is limited due to the anatomical complexity in terms of small micrometer volumes and poor penetration of drugs. Thus, infections of the root canal seem to be a challenge that demands development of new agents that can eradicate C. albicans. Methodology: In the present study, we synthesized and screened silver-curcumin nanoparticle against Candida albicans. Detailed molecular studies were carried out with silver-curcumin nanoparticle on C. albicans pathogenicity. Morphological cell damage and antibiofilm activity of silver-curcumin nanoparticle on C. albicans was studied using scanning electron microscopy (SEM). Biochemical evidence for membrane damage was studied using flow cytometry. Further, the antifungal activity of silver-curcumin nanoparticle was evaluated in an ex vivo dentinal tubule infection model. Results: Screening data showed that silver-curcumin nanoparticle was active against C. albicans. Silver-curcumin nanoparticle exerted time kill effect and post antifungal effect. When used in combination with fluconazole or nystatin, silver-curcumin nanoparticle revealed a minimum inhibitory concentration (MIC) decrease for both drugs used. In-depth molecular studies with silver-curcumin nanoparticle on C. albicans showed that silver-curcumin nanoparticle inhibited yeast to hyphae (Y-H) conversion. Further, SEM images of C. albicans showed that silver-curcumin nanoparticle caused membrane damage and inhibited biofilm formation. Biochemical evidence for membrane damage was confirmed by increased propidium iodide (PI) uptake in flow cytometry. Further, the antifungal activity of silver-curcumin nanoparticle was evaluated in an ex vivo dentinal tubule infection model, which mimics human tooth root canal infection. Confocal laser scanning microscopy studies showed eradication of C. albicans and reduction in colony forming unit (CFU) after 24 h treatment in the infected tooth samples in this model. Conclusion: The results of this study can pave the way for developing new antifungal agents with well deciphered mechanisms of action and can be a promising antifungal agent or medicament against root canal infection.

Keywords: C. albicans, ex vivo dentine model, inhibition of biofilm formation, root canal infection, yeast to hyphae conversion inhibition

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Authors: Lesley Northrop, Justin DeGrazia, Jessica Greenwood

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ASPIRA Labs now offers an en-suit and ready-to-implement technology transfer solution to enable labs and hospitals that lack the resources to build it themselves to offer in-house genetic testing. This unique platform employs a patented Molecular Inversion Probe (MIP) technology that combines the specificity of a hybrid capture protocol with the ease of an amplicon-based protocol and utilizes an advanced bioinformatics analysis pipeline based on machine learning. To demonstrate its efficacy, two independent genetic tests were validated on this technology transfer platform: expanded carrier screening (ECS) and hereditary cancer testing (HC). The analytical performance of ECS and HC was validated separately in a blinded manner for calling three different types of variants: SNVs, short indels (typically, <50 bp), and large indels/CNVs defined as multi-exonic del/dup events. The reference set was constructed using samples from Coriell Institute, an external clinical genetic testing laboratory, Maine Molecular Quality Controls Inc. (MMQCI), SeraCare and GIAB Consortium. Overall, the analytical performance showed a sensitivity and specificity of >99.4% for both ECS and HC in detecting SNVs. For indels, both tests reported specificity of 100%, and ECS demonstrated a sensitivity of 100%, whereas HC exhibited a sensitivity of 96.5%. The bioinformatics pipeline also correctly called all reference CNV events resulting in a sensitivity of 100% for both tests. No additional calls were made in the HC panel, leading to a perfect performance (specificity and F-measure of 100%). In the carrier panel, however, three additional positive calls were made outside the reference set. Two of these calls were confirmed using an orthogonal method and were re-classified as true positives leaving only one false positive. The pipeline also correctly identified all challenging carrier statuses, such as positive cases for spinal muscular atrophy and alpha-thalassemia, resulting in 100% sensitivity. After confirmation of additional positive calls via long-range PCR and MLPA, specificity for such cases was estimated at 99%. These performance metrics demonstrate that this tech-transfer solution can be confidently internalized by clinical labs and hospitals to offer mainstream ECS and HC as part of their test catalog, substantially increasing access to quality germline genetic testing for labs of all sizes and resources levels.

Keywords: clinical genetics, genetic testing, molecular genetics, technology transfer

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Authors: Djamila Benhaddouche, Abdelkader Benyettou

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In this paper, we used data mining to extract biomedical knowledge. In general, complex biomedical data collected in studies of populations are treated by statistical methods, although they are robust, they are not sufficient in themselves to harness the potential wealth of data. For that you used in step two learning algorithms: the Decision Trees and Support Vector Machine (SVM). These supervised classification methods are used to make the diagnosis of thyroid disease. In this context, we propose to promote the study and use of symbolic data mining techniques.

Keywords: biomedical data, learning, classifier, algorithms decision tree, knowledge extraction

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Authors: Usama Ahmed

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Data mining is the process of analyze data which are used to predict helpful information. It is the field of research which solve various type of problem. In data mining, classification is an important technique to classify different kind of data. Diabetes is most common disease. This paper implements different classification technique using Waikato Environment for Knowledge Analysis (WEKA) on diabetes dataset and find which algorithm is suitable for working. The best classification algorithm based on diabetic data is Naïve Bayes. The accuracy of Naïve Bayes is 76.31% and take 0.06 seconds to build the model.

Keywords: data mining, classification, diabetes, WEKA

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Authors: Asifa Amara, Prachi Singh, Kanishka, Debargho Pathak, Akshat Kumar, Jayakumar Eravelly

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Today's generation is totally dependent on technology that uses data as its fuel. The present study is all about innovations and developments in data science and gives an idea about how efficiently to use the data provided. This study will help to understand the core concepts of data science. The concept of artificial intelligence was introduced by Alan Turing in which the main principle was to create an artificial system that can run independently of human-given programs and can function with the help of analyzing data to understand the requirements of the users. Data science comprises business understanding, analyzing data, ethical concerns, understanding programming languages, various fields and sources of data, skills, etc. The usage of data science has evolved over the years. In this review article, we have covered a part of data science, i.e., machine learning. Machine learning uses data science for its work. Machines learn through their experience, which helps them to do any work more efficiently. This article includes a comparative study image between human understanding and machine understanding, advantages, applications, and real-time examples of machine learning. Data science is an important game changer in the life of human beings. Since the advent of data science, we have found its benefits and how it leads to a better understanding of people, and how it cherishes individual needs. It has improved business strategies, services provided by them, forecasting, the ability to attend sustainable developments, etc. This study also focuses on a better understanding of data science which will help us to create a better world.

Keywords: data science, machine learning, data analytics, artificial intelligence

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Authors: Mohd Adil, Rosina Khan, Asad U. Khan, Vasantha Rupasinghe HP

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The study examined the effects of Syzygium aromaticum extracts on the virulence properties of Streptococcus mutans. The activity of glucosyltransferases in the presence of crude and diethylether fraction was reduced to 80% at concentration 78.12μg/ml and 39.06μg/ml respectively. The glycolytic pH drop by S. mutans cells was also disrupted by these extracts without affecting the bacterial viability. Microscopic analysis revealed morphological changes of the S. mutans biofilms, indicating that these plant extracts at sub-MICs could significantly affect the ability of S. mutans to form biofilm with distorted extracellular matrix. Furthermore, with the help of quantitative RT-PCR, the expression of different genes involved in adherence, quorum sensing, in the presence of these extracts were down regulated. The crude and active fractions were found effective in preventing caries development in rats. The data showed that S. aromaticum holds promise as a naturally occurring source of compounds that may prevent biofilm-related oral diseases.

Keywords: biofilm, quorum sensing, Streptococcus mutans, Syzygium aromaticum extract

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Authors: Nayeli Camacho, Fernanda Lara-Perez, Carolina Ortega-Portilla, Diego G. Espinosa-Arbelaez, Juan M. Alvarado-Orozco, Guillermo C. Mondragon-Rodriguez

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Ultra-high molecular weight polyethylene (UHMWPE) has been the gold standard material for total knee replacements for almost five decades. Wear damage to UHMWPE articulating surface is inevitable due to the natural sliding and rolling movements of the knee. This generates a considerable amount of wear debris, which results in mechanical instability of the joint, reduces joint mobility, increases pain with detrimental biologic responses, and causes component loosening. The presence of wear particles has been closely related to adverse reactions in the knee joint surrounding tissue, especially for particles in the range of 0.3 to 2 μm. Carbon-based materials possess excellent mechanical properties and have shown great promise in tribological applications. In this study, diamond-like carbon coatings (DLC) and carbon nanotubes (CNTs) were used to decrease the wear rate of ultra-high molecular weight polyethylene. A titanium doped DLC (Ti-DLC) was deposited by magnetron sputtering on stainless steel precision spheres while CNTs were used as a second phase reinforcement in UHMWPE at a concentration of 1.25 wt.%. A comparative tribological analysis of the wear of UHMWPE and UHMWPE-CNTs with a stainless steel counterpart with and without Ti-DLC coating is presented. The experimental wear testing was performed on a pin-on-disc tribometer under dry conditions, using a reciprocating movement with a load of 1 N at a frequency of 2 Hz for 100,000 and 200,000 cycles. The wear tracks were analyzed with high-resolution scanning electron microscopy to determine wear modes and observe the size and shape of the wear debris. Furthermore, profilometry was used to study the depth of the wear tracks and to map the wear of the articulating surface. The wear tracks at 100,000 and 200,000 cycles on all samples were relatively shallow, and they were in the range of average roughness. It was observed that the Ti-DLC coating decreases the mass loss in the UHMWPE and the depth of the wear track. The combination of both carbon-based materials decreased the material loss compared to the system of stainless steel and UHMWPE. Burnishing of the surface was the predominant wear mode observed with all the systems, more subtle for the systems with Ti-DLC coatings. Meanwhile, in the system composed of stainless steel-UHMWPE, the intrinsic surface roughness of the material was completely replaced by the wear tracks.

Keywords: CNT reinforcement, self-lubricating materials, Ti-DLC, UHMWPE tribological performance

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Authors: Suruchi Shukla, Shantanu Prakash, Amita Jain

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Introduction: Arboviral diseases are one of the most common causes of viral hemorrhagic fever (VHF). Of which, Dengue and Chikungunya pose a significant health problem in India. Arbovirus has a tendency to cross the territories and emerge in the new region. Considering the above issues, in the current study active surveillance was conducted among viral hemorrhagic fever (VHF) cases reported from Uttar Pradesh (UP), India. We studied the arboviral etiology of VHF; mainly Dengue, Chikungunya, and ZIKA. Methods: Clinical samples of 465 suspected VHF cases referred to tertiary care referral center of UP, India were enrolled in the study during a period from 15th May 2016 to 9th March 2018. Serum specimens were collected and analyzed for the presence of Dengue, Chikungunya, and ZIKA either by serology and/or by molecular assays. Results: Of all tested, 165 (35.4%) cases were positive for either Dengue or Chikungunya. Dengue (21.2%) was found to be the most prevalent, followed by Chikungunya, (6.6%). None of the cases tested positive for ZIKA virus. Serum samples of 35 (7.5%) cases were positive for both Dengue and Chikungunya. DEN-2 serotype was the most predominant serotype. Phylogenetic and sequence analysis of DEN-2 strains showed 100% clustering with the Cosmopolitan genotype strain. Bleeding from several sites, jaundice, abdominal pain, arthralgia, haemoconcentration, and thrombocytopenia were significantly higher in dengue hemorrhagic cases. However, the rash was significantly more common in Chikungunya patients. Most of the Dengue and Chikungunya positive cases (Age group 6-40 years) were seen in post monsoon season (September to November). Conclusion: Only one-third of total VHF cases are positive for either Dengue/Chikungunya or both. This necessitates the screening of other etiologies capable of causing hemorrhagic manifestations.

Keywords: viral hemorrhagic fever, dengue, chikungunya, zika, India

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Authors: Azadeh Bashiri

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Introduction: Lack of proper diagnosis and inadequate treatment of asthma leads to physical and financial complications. This study aimed to use data mining techniques and creating a neural network intelligent system for diagnosis of asthma. Methods: The study population is the patients who had visited one of the Lung Clinics in Tehran. Data were analyzed using the SPSS statistical tool and the chi-square Pearson's coefficient was the basis of decision making for data ranking. The considered neural network is trained using back propagation learning technique. Results: According to the analysis performed by means of SPSS to select the top factors, 13 effective factors were selected, in different performances, data was mixed in various forms, so the different models were made for training the data and testing networks and in all different modes, the network was able to predict correctly 100% of all cases. Conclusion: Using data mining methods before the design structure of system, aimed to reduce the data dimension and the optimum choice of the data, will lead to a more accurate system. Therefore, considering the data mining approaches due to the nature of medical data is necessary.

Keywords: asthma, data mining, Artificial Neural Network, intelligent system

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Authors: Khashayar Nasrifar

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Ionic liquids (ILs) exhibit particular properties exemplified by extremely low vapor pressure and high thermal stability. The properties of ILs can be tailored by proper selection of cations and anions. As such, ILs are appealing as potential solvents to substitute traditional solvents with high vapor pressure. One of the IL properties required in chemical and process design is density. In developing corresponding state liquid density correlations, scaling hypothesis is often used. The hypothesis expresses the temperature dependence of saturated liquid densities near the vapor-liquid critical point as a function of reduced temperature. Extending the temperature dependence, several successful correlations were developed to accurately correlate the densities of normal liquids from the triple point to a critical point. Applying mixing rules, the liquid density correlations are extended to liquid mixtures as well. ILs are not molecular liquids, and they are not classified among normal liquids either. Also, ILs are often used where the condition is far from equilibrium. Nevertheless, in calculating the properties of ILs, the use of corresponding state correlations would be useful if no experimental data were available. With well-known generalized saturated liquid density correlations, the accuracy in predicting the density of ILs is not that good. An average error of 4-5% should be expected. In this work, a data bank was compiled. A simplified and concise corresponding state saturated liquid density correlation is proposed by phenomena-logically modifying reduced temperature using the temperature-dependence for an interacting parameter of the Soave-Redlich-Kwong equation of state. This modification improves the temperature dependence of the developed correlation. Parametrization was next performed to optimize the three global parameters of the correlation. The correlation was then applied to the ILs in our data bank with satisfactory predictions. The correlation of IL density applied at 0.1 MPa and was tested with an average uncertainty of around 2%. No adjustable parameter was used. The critical temperature, critical volume, and acentric factor were all required. Methods to extend the predictions to higher pressures (200 MPa) were also devised. Compared to other methods, this correlation was found more accurate. This work also presents the chronological order of developing such correlations dealing with ILs. The pros and cons are also expressed.

Keywords: correlation, corresponding state principle, ionic liquid, density

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Authors: Christopher Muhawe, Masooda Bashir

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With increased Internet Communication Technology(ICT), the virtual world has become the new normal. At the same time, there is an unprecedented collection of massive amounts of data by both private and public entities. Unfortunately, this increase in data collection has been in tandem with an increase in data misuse and data breach. Regrettably, the majority of data breach and data misuse claims have been unsuccessful in the United States courts for the failure of proof of direct injury to physical or economic interests. The requirement to express data privacy harms from an economic or physical stance negates the fact that not all data harms are physical or economic in nature. The challenge is compounded by the fact that data breach harms and risks do not attach immediately. This research will use a descriptive and normative approach to show that not all data harms can be expressed in economic or physical terms. Expressing privacy harms purely from an economic or physical harm perspective negates the fact that data insecurity may result into harms which run counter the functions of privacy in our lives. The promotion of liberty, selfhood, autonomy, promotion of human social relations and the furtherance of the existence of a free society. There is no economic value that can be placed on these functions of privacy. The proposed approach addresses data harms from a psychological and social perspective.

Keywords: data breach and misuse, economic harms, privacy harms, psychological harms

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

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Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: synthetic gene network, network identification, optimization, nonlinear modeling

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Authors: Chandra Prayaga, Aaron Wade, Lakshmi Prayaga, Gopi Shankar Mallu

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This paper presents the use of machine learning algorithms to predict the success of students in an introductory physics course. Data having 140 rows pertaining to the performance of two batches of students was used. The lack of sufficient data to train robust machine learning models was compensated for by generating synthetic data similar to the real data. CTGAN and CTGAN with Gaussian Copula (Gaussian) were used to generate synthetic data, with the real data as input. To check the similarity between the real data and each synthetic dataset, pair plots were made. The synthetic data was used to train machine learning models using the PyCaret package. For the CTGAN data, the Ada Boost Classifier (ADA) was found to be the ML model with the best fit, whereas the CTGAN with Gaussian Copula yielded Logistic Regression (LR) as the best model. Both models were then tested for accuracy with the real data. ROC-AUC analysis was performed for all the ten classes of the target variable (Grades A, A-, B+, B, B-, C+, C, C-, D, F). The ADA model with CTGAN data showed a mean AUC score of 0.4377, but the LR model with the Gaussian data showed a mean AUC score of 0.6149. ROC-AUC plots were obtained for each Grade value separately. The LR model with Gaussian data showed consistently better AUC scores compared to the ADA model with CTGAN data, except in two cases of the Grade value, C- and A-.

Keywords: machine learning, student success, physics course, grades, synthetic data, CTGAN, gaussian copula CTGAN

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Authors: Sharon N. Nuñal, May Flor S. Muegue, Nizzy Hope N. Cartago, Raymund B. Parcon, Sheina B. Logronio

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The antioxidant and anti-inflammatory potentials of Perna Viridis, Modiolus philippinarum, and Mytella charruana found in the Philippines were assessed. Mussel protein samples were hydrolyzed using trypsin, maturase, alcalase and pepsin at 1% and 2% concentrations and then fractionated through membrane filtration (<10 kDa and <30 kDa). Antioxidant assays showed that pepsin hydrolysate at 2% enzyme concentration exhibited the maximum activities for both 2,2-Diphenyl-1-picrylhydrazyl (DPPH) Radical Scavenging Activity (155-176 µM TE/mg protein) and 2,2-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) radical scavenging (67-68 µM TE/mg protein) assays while trypsin hydrolysate dominated the Ferric Reducing Antioxidant Power (FRAP) for the three mussel species. Lower molecular weight peptide fractions at <10 kDa exhibited better antioxidant activities than the higher molecular weight fractions. The anti-inflammatory activities of M. philippinarum and M. charruana showed comparable protein denaturation inhibition potentials with the highest in P. Viridis samples (98.93%). The 5-Lipoxygenase (5-LOX) inhibitory activities of mussel samples showed no significant difference with inhibition exceeding 70%. P. Viridis demonstrated the highest inhibition against Cyclooxygenase-2 (COX-2) at 56.19%, while the rest showed comparable activities. This study showed that the three mussel species are potential sources of bioactive peptides and lipids with antioxidant and anti-inflammatory properties.

Keywords: anti-inflammatory, antioxidant, bioactive properties, mussel

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Authors: Chuping Lo

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This paper presents a simple model demonstrating that ceteris paribus countries with lower barriers to accessing global data tend to earn higher incomes than other countries. Therefore, large countries that inherently have greater data resources tend to have higher incomes than smaller countries, such that the former may be more hesitant than the latter to liberalize cross-border data flows to maintain this advantage. Furthermore, countries with higher artificial intelligence (AI) intensity in production technologies tend to benefit more from economies of scale in data aggregation, leading to higher income and more trade as they are better able to utilize global data.

Keywords: digital intensity, digital divide, international trade, scale of economics

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Authors: Soheil Zorofchian Moghadamtousi, Habsah Abdul Kadir, Mohammadjavad Paydar, Elham Rouhollahi, Hamed Karimian

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The present study was designed to evaluate the molecular mechanisms of Annona muricata leaves ethyl acetate extract (AMEAE) against lung cancer A549 cells. Cell viability analysis revealed the selective cytotoxic effect of AMEAE towards A549 cells. Treatment of A549 cells with AMEAE significantly elevated the reactive oxygen species formation, followed by attenuation of mitochondrial membrane potential via upregulation of Bax and downregulation of Bcl-2, accompanied by cytochrome c release to the cytosol. The released cytochrome c triggered the activation of caspase-9 followed by caspase-3. In addition, AMEAE-induced apoptosis was accompanied by cell cycle arrest at G1 phase. Our data showed for the first time that AMEAE inhibited the proliferation of A549 cells, leading to cell cycle arrest and programmed cell death through activation of the mitochondrial-mediated signaling pathway.

Keywords: Annona muricata, lung cancer, apoptosis, mitochondria

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Authors: G. R. Navaneesh, E. Nagarajan, C. H. Rajam Raju

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Nowadays the multimedia data are used to store some secure information. All previous methods allocate a space in image for data embedding purpose after encryption. In this paper, we propose a novel method by reserving space in image with a boundary surrounded before encryption with a traditional RDH algorithm, which makes it easy for the data hider to reversibly embed data in the encrypted images. The proposed method can achieve real time performance, that is, data extraction and image recovery are free of any error. A secure transmission process is also discussed in this paper, which improves the efficiency by ten times compared to other processes as discussed.

Keywords: secure communication, reserving room before encryption, least significant bits, image encryption, reversible data hiding

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Authors: Fuad M. Alkoot

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DNA data have been used in forensics for decades. However, current research looks at using the DNA as a biometric identity verification modality. The goal is to improve the speed of identification. We aim at using gene data that was initially used for autism detection to find if and how accurate is this data for identification applications. Mainly our goal is to find if our data preprocessing technique yields data useful as a biometric identification tool. We experiment with using the nearest neighbor classifier to identify subjects. Results show that optimal classification rate is achieved when the test set is corrupted by normally distributed noise with zero mean and standard deviation of 1. The classification rate is close to optimal at higher noise standard deviation reaching 3. This shows that the data can be used for identity verification with high accuracy using a simple classifier such as the k-nearest neighbor (k-NN). 

Keywords: biometrics, genetic data, identity verification, k nearest neighbor

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Authors: R Palson Kennedy, P.Kiran Sai

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This article introduces machine learning (ML) researchers to the hurdles that geoscience problems present, as well as the opportunities for improvement in both ML and geosciences. This article presents a review from the data life cycle perspective to meet that need. Numerous facets of geosciences present unique difficulties for the study of intelligent systems. Geosciences data is notoriously difficult to analyze since it is frequently unpredictable, intermittent, sparse, multi-resolution, and multi-scale. The first half addresses data science’s essential concepts and theoretical underpinnings, while the second section contains key themes and sharing experiences from current publications focused on each stage of the data life cycle. Finally, themes such as open science, smart data, and team science are considered.

Keywords: Data science, intelligent system, machine learning, big data, data life cycle, recent development, geo science

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Authors: Caroline Mendes, Mary McNamara, Orla Howe

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For chemotherapy, a drug delivery system should be able to specifically target cancer cells and deliver the therapeutic dose without affecting normal cells. Folate receptors (FR) can be considered key targets since they are commonly over-expressed in cancer cells and they are the molecular marker used in this study. Here, cyclodextrin (CD) has being studied as a vehicle for delivering the chemotherapeutic drug, methotrexate (MTX). CDs have the ability to form inclusion complexes, in which molecules of suitable dimensions are included within the CD cavity. In this study, β-CD has been modified using folic acid so as to specifically target the FR molecular marker. Thus, the system studied here for drug delivery consists of β-CD, folic acid and MTX (CDEnFA:MTX). Cellular uptake of folic acid is mediated with high affinity by folate receptors while the cellular uptake of antifolates, such as MTX, is mediated with high affinity by the reduced folate carriers (RFCs). This study addresses the gene (mRNA) and protein expression levels of FRs and RFCs in the cancer cell lines CaCo-2, SKOV-3, HeLa, MCF-7, A549 and the normal cell line BEAS-2B, quantified by real-time polymerase chain reaction (real-time PCR) and flow cytometry, respectively. From that, four cell lines with different levels of FRs, were chosen for cytotoxicity assays of MTX and CDEnFA:MTX using the MTT assay. Real-time PCR and flow cytometry data demonstrated that all cell lines ubiquitously express moderate levels of RFC. These experiments have also shown that levels of FR protein in CaCo-2 cells are high, while levels in SKOV-3, HeLa and MCF-7 cells are moderate. A549 and BEAS-2B cells express low levels of FR protein. FRs are highly expressed in all the cancer cell lines analysed when compared to the normal cell line BEAS-2B. The cell lines CaCo-2, MCF-7, A549 and BEAS-2B were used in the cell viability assays. 48 hours treatment with the free drug and the complex resulted in IC50 values of 93.9 µM ± 9.2 and 56.0 µM ± 4.0 for CaCo-2 for free MTX and CDEnFA:MTX respectively, 118.2 µM ± 10.8 and 97.8 µM ± 12.3 for MCF-7, 36.4 µM ± 6.9 and 75.0 µM ± 8.5 for A549 and 132.6 µM ± 12.1 and 288.1 µM ± 16.3 for BEAS-2B. These results demonstrate that MTX is more toxic towards cell lines expressing low levels of FR, such as the BEAS-2B. More importantly, these results demonstrate that the inclusion complex CDEnFA:MTX showed greater cytotoxicity than the free drug towards the high FR expressing CaCo-2 cells, indicating that it has potential to target this receptor, enhancing the specificity and the efficiency of the drug.

Keywords: cyclodextrins, cancer treatment, drug delivery, folate receptors, reduced folate carriers

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Authors: Marc Bachelet, Abhijit Kumar Chatterjee, José Manuel Avila

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Data quality is a key component of any data-driven organization. Without data quality, organizations cannot effectively make data-driven decisions, which often leads to poor business performance. Therefore, it is important for an organization to ensure that the data they use is of high quality. This is where the concept of data mesh comes in. Data mesh is an organizational and architectural decentralized approach to data management that can help organizations improve the quality of data. The concept of data mesh was first introduced in 2020. Its purpose is to decentralize data ownership, making it easier for domain experts to manage the data. This can help organizations improve data quality by reducing the reliance on centralized data teams and allowing domain experts to take charge of their data. This paper intends to discuss how a set of elements, including data mesh, are tools capable of increasing data quality. One of the key benefits of data mesh is improved metadata management. In a traditional data architecture, metadata management is typically centralized, which can lead to data silos and poor data quality. With data mesh, metadata is managed in a decentralized manner, ensuring accurate and up-to-date metadata, thereby improving data quality. Another benefit of data mesh is the clarification of roles and responsibilities. In a traditional data architecture, data teams are responsible for managing all aspects of data, which can lead to confusion and ambiguity in responsibilities. With data mesh, domain experts are responsible for managing their own data, which can help provide clarity in roles and responsibilities and improve data quality. Additionally, data mesh can also contribute to a new form of organization that is more agile and adaptable. By decentralizing data ownership, organizations can respond more quickly to changes in their business environment, which in turn can help improve overall performance by allowing better insights into business as an effect of better reports and visualization tools. Monitoring and analytics are also important aspects of data quality. With data mesh, monitoring, and analytics are decentralized, allowing domain experts to monitor and analyze their own data. This will help in identifying and addressing data quality problems in quick time, leading to improved data quality. Data culture is another major aspect of data quality. With data mesh, domain experts are encouraged to take ownership of their data, which can help create a data-driven culture within the organization. This can lead to improved data quality and better business outcomes. Finally, the paper explores the contribution of AI in the coming years. AI can help enhance data quality by automating many data-related tasks, like data cleaning and data validation. By integrating AI into data mesh, organizations can further enhance the quality of their data. The concepts mentioned above are illustrated by AEKIDEN experience feedback. AEKIDEN is an international data-driven consultancy that has successfully implemented a data mesh approach. By sharing their experience, AEKIDEN can help other organizations understand the benefits and challenges of implementing data mesh and improving data quality.

Keywords: data culture, data-driven organization, data mesh, data quality for business success

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Authors: Kan Yu, Khui Hung Lee, Eben Afrifa-Yamoah, Jing Guo, Katrina Harrison, Jack Goldblatt, Nicholas Pachter, Jitian Xiao, Guicheng Brad Zhang

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Background and Significance of the Study: Congenital Heart Defects (CHDs) are the most common malformation at birth and one of the leading causes of infant death. Although the exact etiology remains a significant challenge, epigenetic modifications, such as DNA methylation, are thought to contribute to the pathogenesis of congenital heart defects. At present, no existing DNA methylation biomarkers are used for early detection of CHDs. The existing CHD diagnostic techniques are time-consuming and costly and can only be used to diagnose CHDs after an infant was born. The present study employed a machine learning technique to analyse genome-wide methylation data in children with and without CHDs with the aim to find methylation biomarkers for CHDs. Methods: The Illumina Human Methylation EPIC BeadChip was used to screen the genome‐wide DNA methylation profiles of 24 infants diagnosed with congenital heart defects and 24 healthy infants without congenital heart defects. Primary pre-processing was conducted by using RnBeads and limma packages. The methylation levels of top 600 genes with the lowest p-value were selected and further investigated by using a random forest approach. ROC curves were used to analyse the sensitivity and specificity of each biomarker in both training and test sample sets. The functionalities of selected genes with high sensitivity and specificity were then assessed in molecular processes. Major Findings of the Study: Three genes (MIR663, FGF3, and FAM64A) were identified from both training and validating data by random forests with an average sensitivity and specificity of 85% and 95%. GO analyses for the top 600 genes showed that these putative differentially methylated genes were primarily associated with regulation of lipid metabolic process, protein-containing complex localization, and Notch signalling pathway. The present findings highlight that aberrant DNA methylation may play a significant role in the pathogenesis of congenital heart defects.

Keywords: biomarker, congenital heart defects, DNA methylation, random forest

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Authors: Alma Khasenovna Zhakina, Arnt Oxana Vasilievna, Vasilets Evgeny Petrovich

Abstract:

The aim of this project is to develop methods for obtaining new molecularly imprinted polymers from coal waste to study their structure, structural and morphological features and properties. Recently, the development of molecularly imprinted polymers has become one of the hot topics for researchers. Modern research indicates the broad prospects of rapidly developing molecular imprinting technologies for creating a new generation of sorption materials. The attractiveness of this area of research lies in the fact that the use of imprinted polymers is not limited to scientific research; they are already being introduced in the chemical, pharmaceutical and biotechnological industries, primarily at the stages of purification of the final product. For the use of molecularly imprinted polymers in the development of sorption material, their ability to selectively remove pollutants, including trace concentrations, is of fundamental importance, and the exceptional stability of polymeric materials under harsh conditions makes it possible to simplify the process of water purification as a whole. The scientific and technical effect is associated with the development of technologies for the production of new molecularly imprinted polymers, the establishment of optimal conditions for their production and the creation of effective imprinted sorbents on their basis for wastewater treatment from heavy metals. The social effect is due to the fact that the use of coal waste as a feedstock for the production of imprinted sorbents will make it possible in the future to create new industries with additional jobs and obtain competitive multi-purpose products. The economic and multiplier effect is associated with the low cost of the final product due to the involvement of local coal waste in the production, reduction of transport, customs and other costs.

Keywords: imprinted polymers, coal waste, polymerization, template, customized sorbents

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Authors: Chi-Ching Lee, Po-Jung Huang, Kuo-Yang Huang, Petrus Tang

Abstract:

Background: Recent advances in high-throughput research technologies such as new-generation sequencing and multi-dimensional liquid chromatography makes it possible to dissect the complete transcriptome and proteome in a single run for the first time. However, it is almost impossible for many laboratories to handle and analysis these “BIG” data without the support from a bioinformatics team. We aimed to provide a web-based analysis platform for users with only limited knowledge on bio-computing to study the functional genomics and proteomics. Method: We use NCI-60 as an example dataset to demonstrate the power of the web-based analysis platform and data delivering system: C-eXpress takes a simple text file that contain the standard NCBI gene or protein ID and expression levels (rpkm or fold) as input file to generate a distribution map of gene/protein expression levels in a heatmap diagram organized by color gradients. The diagram is hyper-linked to a dynamic html table that allows the users to filter the datasets based on various gene features. A dynamic summary chart is generated automatically after each filtering process. Results: We implemented an integrated database that contain pre-defined annotations such as gene/protein properties (ID, name, length, MW, pI); pathways based on KEGG and GO biological process; subcellular localization based on GO cellular component; functional classification based on GO molecular function, kinase, peptidase and transporter. Multiple ways of sorting of column and rows is also provided for comparative analysis and visualization of multiple samples.

Keywords: cancer, visualization, database, functional annotation

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Authors: Doaa Hashad, Amany Elyamany, Perihan Salem

Abstract:

Introduction: Hepatitis C virus infection (HCV) constitutes a serious dilemma that has an impact on the health of millions of Egyptians. Hepatitis C virus related hepatocellular carcinoma (HCV-HCC) is a crucial consequence of HCV that represents the third cause of cancer-related deaths worldwide. Aim of the study: assess the use of mitochondrial DNA (mtDNA) content as a non-invasive molecular biomarker in hepatitis c virus related hepatocellular carcinoma (HCV-HCC). Methods: A total of 135 participants were enrolled in the study. Volunteers were assigned to one of three groups equally; a group of HCV related cirrhosis (HCV-cirrhosis), a group of HCV-HCC and a control group of age- and sex- matched healthy volunteers with no evidence of liver disease. mtDNA was determined using a quantitative real-time PCR technique. Results: mtDNA content was lowest in HCV-HCC cases. No statistically significant difference was observed between the group of HCV-cirrhosis and the control group as regards mtDNA level. HCC patients with multi-centric hepatic lesions had significantly lower mtDNA content. On using receiver operating characteristic curve analysis, a cutoff of 34 was assigned for mtDNA content to distinguish between HCV-HCC and HCV-cirrhosis patients who are not yet complicated by malignancy. Lower mtDNA was associated with greater HCC risk on using healthy controls, HCV-cirrhosis, or combining both groups as a reference group. Conclusions: mtDNA content might constitute a non-invasive molecular biomarker that reflects tumor burden in HCV-HCC cases and could be used as a predictor of HCC risk in patients of HCV-cirrhosis. In addition, the non significant difference of mtDNA level between HCV-cirrhosis patients and healthy controls could eliminate the grey zone created by the use of AFP in some cirrhotic patients.

Keywords: DNA copy number, HCC, HCV, mitochondrial

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Authors: Ji Eun Shin, Byung Ho Jung, Dong Hoon Lim

Abstract:

It is almost impossible to store or analyze big data increasing exponentially with traditional technologies. Hadoop is a new technology to make that possible. R programming language is by far the most popular statistical tool for big data analysis based on distributed processing with Hadoop technology. With RHadoop that integrates R and Hadoop environment, we implemented parallel multiple regression analysis with different sizes of actual data. Experimental results showed our RHadoop system was much faster as the number of data nodes increases. We also compared the performance of our RHadoop with lm function and big lm packages available on big memory. The results showed that our RHadoop was faster than other packages owing to paralleling processing with increasing the number of map tasks as the size of data increases.

Keywords: big data, Hadoop, parallel regression analysis, R, RHadoop

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Authors: Haojie Wang, Xun Li, Rui Yin

Abstract:

In order to solve the memorization overfitting in the meta-learning MAML algorithm, a method of generating mutually exclusive tasks based on data augmentation is proposed. This method generates a mutex task by corresponding one feature of the data to multiple labels, so that the generated mutex task is inconsistent with the data distribution in the initial dataset. Because generating mutex tasks for all data will produce a large number of invalid data and, in the worst case, lead to exponential growth of computation, this paper also proposes a key data extraction method, that only extracts part of the data to generate the mutex task. The experiments show that the method of generating mutually exclusive tasks can effectively solve the memorization overfitting in the meta-learning MAML algorithm.

Keywords: data augmentation, mutex task generation, meta-learning, text classification.

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Authors: Sifat Rahman Ahona, Rifat Tasnim, Naima Hassan

Abstract:

Data aggregation is a helpful technique for reducing the data communication overhead in wireless sensor network. One of the important tasks of data aggregation is positioning of the aggregator points. There are a lot of works done on data aggregation. But, efficient positioning of the aggregators points is not focused so much. In this paper, authors are focusing on the positioning or the placement of the aggregation points in wireless sensor network. Authors proposed an algorithm to select the aggregators positions for a scenario where aggregator nodes are more powerful than sensor nodes.

Keywords: aggregation point, data communication, data aggregation, wireless sensor network

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Authors: Jamal S. M. Sabir, Edward C. Theriot, Schonna R. Manning, Abdulrahman L. Al-Malki, Mohammad, Mumdooh J. Sabir, Dwight K. Romanovicz, Nahid H. Hajrah, Robert K. Jansen, Matt P. Ashworth

Abstract:

The diatom Phaeodactylum tricornutum has been used as a model for cell biologists and ecologists for over a century. We have incorporated several new raphid pennates into a three-gene phylogenetic dataset (SSU, rbcL, psbC), and recover Gomphonemopsis sp. as sister to P. tricornutum with 100% BS support. This is the first time a close relative has been identified for P. tricornutum with robust statistical support. We test and reject a succession of hypotheses for other relatives. Our molecular data are statistically significantly incongruent with placement of either or both species among the Cymbellales, an order of diatoms with which both have been associated. We believe that further resolution of the phylogenetic position of P. tricornutum will rely more on increased taxon sampling than increased genetic sampling. Gomphonemopsis is a benthic diatom, and its phylogenetic relationship with P. tricornutum is congruent with the hypothesis that P. tricornutum is a benthic diatom with specific adaptations that lead to active recruitment into the plankton. We hypothesize that other benthic diatoms are likely to have similar adaptations and are not merely passively recruited into the plankton.

Keywords: benthic, diatoms; ecology, Phaeodactylum tricornutum, phylogeny, tychoplankton

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Authors: Paula Simões, Isabel Natário

Abstract:

This paper reviews a number of theoretical aspects for implementing an explicit spatial perspective in econometrics for modelling non-continuous data, in general, and count data, in particular. It provides an overview of the several spatial econometric approaches that are available to model data that are collected with reference to location in space, from the classical spatial econometrics approaches to the recent developments on spatial econometrics to model count data, in a Bayesian hierarchical setting. Considerable attention is paid to the inferential framework, necessary for structural consistent spatial econometric count models, incorporating spatial lag autocorrelation, to the corresponding estimation and testing procedures for different assumptions, to the constrains and implications embedded in the various specifications in the literature. This review combines insights from the classical spatial econometrics literature as well as from hierarchical modeling and analysis of spatial data, in order to look for new possible directions on the processing of count data, in a spatial hierarchical Bayesian econometric context.

Keywords: spatial data analysis, spatial econometrics, Bayesian hierarchical models, count data

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