Search results for: predictive coding

Authors: Amr A. El Hanafy, Muhammad I. Qureshi, Jamal Sabir, Mohamed Mutawakil, Mohamed M. Ahmed, Hassan El Ashmaoui, Hassan Ramadan, Mohamed Abou-Alsoud, Mahmoud Abdel Sadek

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β-Lactoglobulin (β-LG) is the dominant non-casein whey protein found in bovine milk and of most ruminants. The amino acid sequence of β-LG along with its 3-dimensional structure illustrates linkage with the lipocalin superfamily. Preliminary studies in goats indicated that milk yield can be influenced by polymorphism in genes coding for whey proteins. The aim of this study is to identify and evaluate the incidence of functional polymorphisms in the exonic and intronic portions of β-LG gene in native Saudi goat breeds (Ardi, Habsi, and Harri). Blood samples were collected from 300 animals (100 for each breed) and genomic DNA was extracted using QIAamp DNA extraction Kit. A fragment of the β-LG gene from exon 7 to 3’ flanking region was amplified with pairs of specific primers. Subsequent digestion with Sac II restriction endonuclease revealed two alleles (A and B) and three different banding patterns or genotypes i.e. AA, AB and BB. The statistical analysis showed that β-LG AA genotype had higher milk yield than β-LG AB and β-LG BB genotypes. Nucleotide sequencing of the selected β-LG fragments was done and submitted to GenBank NCBI (Accession No. KJ544248, KJ588275, KJ588276, KJ783455, KJ783456 and KJ874959). Two already established SNPs in exon 7 (+4601 and +4603) and one fresh SNP in the 3’ UTR region were detected in the β-LG fragments with designated AA genotype. The polymorphisms in exon 7 did not produce any amino acid change. Phylogenetic analysis on the basis of nucleotide sequences of native Saudi goats indicated evolutional similarity with the GenBank reference sequences of goat, Bubalus bubalis and Bos taurus.

Keywords: β-Lactoglobulin, Saudi goats, PCR-RFLP, functional polymorphism, nucleotide sequencing, phylogenetic analysis

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Authors: Abdolghani Ebrahimi, Diego Klabjan, Chenxi Ge, Daniela Ladner, Parker Stride

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In this work, we use machine learning and novel data analysis techniques to predict the one-year mortality of cirrhotic patients. Data from 2,322 patients with liver cirrhosis are collected at a single medical center. Different machine learning models are applied to predict one-year mortality. A comprehensive feature space including demographic information, comorbidity, clinical procedure and laboratory tests is being analyzed. A temporal pattern mining technic called Frequent Subgraph Mining (FSM) is being used. Model for End-stage liver disease (MELD) prediction of mortality is used as a comparator. All of our models statistically significantly outperform the MELD-score model and show an average 10% improvement of the area under the curve (AUC). The FSM technic itself does not improve the model significantly, but FSM, together with a machine learning technique called an ensemble, further improves the model performance. With the abundance of data available in healthcare through electronic health records (EHR), existing predictive models can be refined to identify and treat patients at risk for higher mortality. However, due to the sparsity of the temporal information needed by FSM, the FSM model does not yield significant improvements. To the best of our knowledge, this is the first work to apply modern machine learning algorithms and data analysis methods on predicting one-year mortality of cirrhotic patients and builds a model that predicts one-year mortality significantly more accurate than the MELD score. We have also tested the potential of FSM and provided a new perspective of the importance of clinical features.

Keywords: machine learning, liver cirrhosis, subgraph mining, supervised learning

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Authors: Suwapitch Chalongkulasak, Teerasak E-Kobon, Pramote Chumnanpuen

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Acne vulgaris is a common skin disease mainly caused by the Gram–positive pathogenic bacterium, Propionibacterium acnes. This bacterium stimulates inflammation process in human sebaceous glands. Giant African snail (Achatina fulica) is alien species that rapidly reproduces and seriously damages agricultural products in Thailand. There were several research reports on the medical and pharmaceutical benefits of this snail mucus peptides and proteins. This study aimed to in silico predict multifunctional bioactive peptides from A. fulica mucus peptidome using several bioinformatic tools for determination of antimicrobial (iAMPpred), anti–biofilm (dPABBs), cytotoxic (Toxinpred), cell membrane penetrating (CPPpred) and anti–quorum sensing (QSPpred) peptides. Three candidate peptides with the highest predictive score were selected and re-designed/modified to improve the required activities. Structural and physicochemical properties of six anti–P. acnes (APA) peptide candidates were performed by PEP–FOLD3 program and the five aforementioned tools. All candidates had random coiled structure and were named as APA1–ori, APA2–ori, APA3–ori, APA1–mod, APA2–mod and APA3–mod. To validate the APA activity, these peptide candidates were synthesized and tested against six isolates of P. acnes. The modified APA peptides showed high APA activity on some isolates. Therefore, our biomimetic mucus peptides could be useful for preventing acne vulgaris and further examined on other activities important to medical and pharmaceutical applications.

Keywords: Propionibacterium acnes, Achatina fulica, peptidomes, antibacterial peptides, snail mucus

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Authors: I. Boroňová, J. Bernasovská, J. Kmec, E. Petrejčíková

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Dilated cardiomyopathy (DCM) is a primary myocardial disease, it is characterized by progressive systolic dysfunction due to cardiac chamber dilatation and inefficient myocardial contractility with estimated prevalence of 37 in 100 000 people. It is the most frequent cause of heart failure and cardiac transplantation in young adults. About one-third of all patients have a suspected familial disease indicating a genetic basis of DCM. Many candidate gene studies in humans have tested the association of single nucleotide polymorphisms (SNPs) in various genes coding for proteins with a known cardiovascular function. In our study we present the results of ZBTB17 gene rs10927875 polymorphism genotyping in relation to dilated cardiomyopathy in Slovak population. The study included 78 individuals, 39 patients with DCM and 39 healthy control persons. The mean age of patients with DCM was 50.7±11.5 years; the mean age of individuals in control group was 51.3±9.8 years. Risk factors detected at baseline in each group included age, sex, body mass index, smoking status, diabetes and blood pressure. Genomic DNA was extracted from leukocytes by a standard methodology and screened for rs10927875 polymorphism in intron of ZBTB17 gene using Real-time PCR method (Step One Applied Biosystems). The distribution of investigated genotypes for rs10927875 polymorphism in the group of patients with DCM was as follows: CC (89.74%), CT (10.26%), TT (0%), and the distribution in the control group: CC (92.31%), CT (5.13%), and TT (2.56%). Using the chi-square (χ2) test we compared genotype and allele frequencies between patients and controls. There was no difference in genotype or allele frequencies in ZBTB17 gene rs10927875 polymorphism between patients and control group (χ2=3.028, p=0.220; χ2=0.264, p=0.608). Our results represent an initial study, it can be considered as preliminary and first of its kind in Slovak population. Further studies of ZBTB17 gene polymorphisms of more numerous files and additional functional investigations are needed to fully understand the role of genetic associations.

Keywords: dilated cardiomyopathy, SNP polymorphism, ZBTB17 gene, bioscience

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Authors: Bernard Igoche Igoche, Olumuyiwa Matthew, Peter Bednar, Alexander Gegov

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This study presents an ontology-driven approach for knowledge discovery and validation from admission databases in Nigerian polytechnic institutions. The research aims to address the challenges of extracting meaningful insights from vast amounts of admission data and utilizing them for decision-making and process improvement. The proposed methodology combines the knowledge discovery in databases (KDD) process with a structural causal model (SCM) ontological framework. The admission database of Benue State Polytechnic Ugbokolo (Benpoly) is used as a case study. The KDD process is employed to mine and distill knowledge from the database, while the SCM ontology is designed to identify and validate the important features of the admission process. The SCM validation is performed using the conditional independence test (CIT) criteria, and an algorithm is developed to implement the validation process. The identified features are then used for machine learning (ML) modeling and prediction of admission status. The results demonstrate the adequacy of the SCM ontological framework in representing the admission process and the high predictive accuracies achieved by the ML models, with k-nearest neighbors (KNN) and support vector machine (SVM) achieving 92% accuracy. The study concludes that the proposed ontology-driven approach contributes to the advancement of educational data mining and provides a foundation for future research in this domain.

Keywords: admission databases, educational data mining, machine learning, ontology-driven knowledge discovery, polytechnic education, structural causal model

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Authors: Md. Najiur Rahman

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This hypothesis reveals a profound and symmetrical connection that goes beyond the boundaries of quantum physics and cosmology, revolutionizing our understanding of the fundamental building blocks of the cosmos, given its name ‘The Theory of the Mystery’. This theory has an elegantly simple equation, “R = ∆r / √∆m” which establishes a beautiful and well-crafted relationship between the radius (R) of an elementary particle or galaxy, the relative change in radius (∆r), and the mass difference (∆m) between related entities. It is fascinating to note that this formula presents a super synchronization, one which involves the convergence of every basic particle and any single celestial entity into perfect alignment with its respective mass and radius. In addition, we have a Supporting equation that defines the mass-radius connection of an entity by the equation: R=√m/N, where N is an empirically established constant, determined to be approximately 42.86 kg/m, representing the proportionality between mass and radius. It provides precise predictions, collects empirical evidence, and explores the far-reaching consequences of theories such as General Relativity. This elegant symmetry reveals a fundamental principle that underpins the cosmos: each component, whether small or large, follows a precise mass-radius relationship to exert gravity by a universal law. This hypothesis represents a transformative process towards a unified theory of physics, and the pursuit of experimental verification will show that each particle and galaxy is bound by gravity and plays a unique but harmonious role in shaping the universe. It promises to reveal the great symphony of the mighty cosmos. The predictive power of our hypothesis invites the exploration of entities at the farthest reaches of the cosmos, providing a bridge between the known and the unknown.

Keywords: unified theory, quantum gravity, mass-radius relationship, dark matter, uniform gravity

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Authors: Alanoud Moraya Aldalan, Abdulaziz Almaleh

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A crucial component of maintaining a customer-oriented business as in the telecom industry is understanding the reasons and factors that lead to customer churn. Competition between telecom companies has greatly increased in recent years. It has become more important to understand customers’ needs in this strong market of telecom industries, especially for those who are looking to turn over their service providers. So, predictive churn is now a mandatory requirement for retaining those customers. Machine learning can be utilized to accomplish this. Churn Prediction has become a very important topic in terms of machine learning classification in the telecommunications industry. Understanding the factors of customer churn and how they behave is very important to building an effective churn prediction model. This paper aims to predict churn and identify factors of customers’ churn based on their past service usage history. Aiming at this objective, the study makes use of feature selection, normalization, and feature engineering. Then, this study compared the performance of four different machine learning algorithms on the Orange dataset: Logistic Regression, Random Forest, Decision Tree, and Gradient Boosting. Evaluation of the performance was conducted by using the F1 score and ROC-AUC. Comparing the results of this study with existing models has proven to produce better results. The results showed the Gradients Boosting with feature selection technique outperformed in this study by achieving a 99% F1-score and 99% AUC, and all other experiments achieved good results as well.

Keywords: machine learning, gradient boosting, logistic regression, churn, random forest, decision tree, ROC, AUC, F1-score

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Authors: Khaled Barkaoui

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Research on second-language (L2) learning tends to focus on comparing students with different levels of proficiency at one point in time. However, to understand L2 development, we need more longitudinal research. In this study, we adopt a longitudinal approach to examine changes in three indicators of L2 ability, complexity, accuracy, and fluency (CAF), as reflected in the writing of L2 learners when writing on different tasks before and after a period L2 instruction. Each of 85 Chinese learners of English at three levels of English language proficiency responded to two writing tasks (independent and integrated) before and after nine months of English-language study in China. Each essay (N= 276) was analyzed in terms of numerous CAF indices using both computer coding and human rating: number of words written, number of errors per 100 words, ratings of error severity, global syntactic complexity (MLS), complexity by coordination (T/S), complexity by subordination (C/T), clausal complexity (MLC), phrasal complexity (NP density), syntactic variety, lexical density, lexical variation, lexical sophistication, and lexical bundles. Results were then compared statistically across tasks, L2 proficiency levels, and time. Overall, task type had significant effects on fluency and some syntactic complexity indices (complexity by coordination, structural variety, clausal complexity, phrase complexity) and lexical density, sophistication, and bundles, but not accuracy. L2 proficiency had significant effects on fluency, accuracy, and lexical variation, but not syntactic complexity. Finally, fluency, frequency of errors, but not accuracy ratings, syntactic complexity indices (clausal complexity, global complexity, complexity by subordination, phrase complexity, structural variety) and lexical complexity (lexical density, variation, and sophistication) exhibited significant changes after instruction, particularly for the independent task. We discuss the findings and their implications for assessment, instruction, and research on CAF in the context of L2 writing.

Keywords: second language writing, Fluency, accuracy, complexity, longitudinal

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Authors: Muhammet Baldan, Emel Timuçin

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Molecular solubility prediction plays a crucial role in various fields, such as drug discovery, environmental science, and material science. In this study, we compare the performance of five machine learning algorithms—linear regression, support vector machines (SVM), random forests, gradient boosting machines (GBM), and neural networks—for predicting molecular solubility using the AqSolDB dataset. The dataset consists of 9981 data points with their corresponding solubility values. MACCS keys (166 bits), RDKit properties (20 properties), and structural properties(3) features are extracted for every smile representation in the dataset. A total of 189 features were used for training and testing for every molecule. Each algorithm is trained on a subset of the dataset and evaluated using metrics accuracy scores. Additionally, computational time for training and testing is recorded to assess the efficiency of each algorithm. Our results demonstrate that random forest model outperformed other algorithms in terms of predictive accuracy, achieving an 0.93 accuracy score. Gradient boosting machines and neural networks also exhibit strong performance, closely followed by support vector machines. Linear regression, while simpler in nature, demonstrates competitive performance but with slightly higher errors compared to ensemble methods. Overall, this study provides valuable insights into the performance of machine learning algorithms for molecular solubility prediction, highlighting the importance of algorithm selection in achieving accurate and efficient predictions in practical applications.

Keywords: random forest, machine learning, comparison, feature extraction

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Authors: S. S. Singh, A. Bhattacharya, S. Bhattacharya

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The eukaryotic exosome complex plays a pivotal role in RNA biogenesis, maturation, surveillance and differential expression of various RNAs in response to varying environmental signals. The exosome is composed of evolutionary conserved nine core subunits and the associated exonucleases Rrp6 and Rrp44. Rrp6p is crucial for the processing of rRNAs, other non-coding RNAs, regulation of polyA tail length and termination of transcription. Rrp6p, a 3’-5’ exonuclease is required for degradation of 5’-external transcribed spacer (ETS) released from the rRNA precursors during the early steps of pre-rRNA processing. In the parasitic protist Entamoeba histolytica in response to growth stress, there occurs the accumulation of unprocessed pre-rRNA and 5’ ETS sub fragment. To understand the processes leading to this accumulation, we looked for Rrp6 and the exosome subunits in E. histolytica, by in silico approaches. Of the nine core exosomal subunits, seven had high percentage of sequence similarity with the yeast and human. The EhRrp6 homolog contained exoribonuclease and HRDC domains like yeast but its N- terminus lacked the PMC2NT domain. EhRrp6 complemented the temperature sensitive phenotype of yeast rrp6Δ cells suggesting conservation of biological activity. We showed 3’-5’ exoribonuclease activity of EhRrp6p with in vitro-synthesized appropriate RNAs substrates. Like the yeast enzyme, EhRrp6p degraded unstructured RNA, but could degrade the stem-loops slowly. Furthermore, immunolocalization revealed that EhRrp6 was nuclear-localized in normal cells but was diminished from nucleus during serum starvation, which could explain the accumulation of 5’ETS during stress. Our study shows functional conservation of EhRrp6p in E.histolytica, an early-branching eukaryote, and will help to understand the evolution of exosomal components and their regulatory function.

Keywords: entamoeba histolytica, exosome complex, rRNA processing, Rrp6

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Authors: Bummo Ahn

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Palpation is widely used to measure soft tissue firmness or stiffness in the living condition in order to apply detection, diagnosis, and treatment of tumors, scar tissue, abnormal muscle tone, or muscle spasticity. Since these methods are subjective and depend on the proficiency level, it is concluded that there are other diagnoses depending on the condition of the experts and the results are not objective. The mechanical property obtained by using the elasticity of the tissue is important to calculate a predictive variable for monitoring abnormal tissues. If the mechanical load such as reaction force on the foot increases in the same region under the same conditions, the mechanical property of the tissue is changed. Therefore, objective diagnosis is possible not only for experts but also for patients using this quantitative information. Furthermore, the portable system also allows non-experts to easily diagnose at home, not in hospitals or institutions. In this paper, we introduce a portable palpation system that can be used to measure the mechanical properties of human tissue, which can be applied to monitor diabetic foot ulceration patients with measuring the mechanical property change of foot tissue. The system was designed to be smaller and portable in comparison with the conventional palpation systems. It is consists of the probe, the force sensor, linear actuator, micro control unit, the display module, battery, and housing. Using this system, we performed validation experiments by applying different palpations (3 and 5 mm) to soft tissue (silicone rubber) and measured reaction forces. In addition, we estimated the elastic moduli of the soft tissue against different palpations and compare the estimated elastic moduli that show similar value even if the palpation depths are different.

Keywords: palpation probe, portable, diabetic foot ulceration, monitoring, mechanical property

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Authors: Shahad Nagoor, Lucy Hederman, Kevin Koidl, Annalina Caputo

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Doctors’ notes reflect their impressions, attitudes, clinical sense, and opinions about patients’ conditions and progress, and other information that is essential for doctors’ daily clinical decisions. Despite their value, clinical notes are insufficiently researched within the language processing community. Automatically extracting information from unstructured text data is known to be a difficult task as opposed to dealing with structured information such as vital physiological signs, images, and laboratory results. The aim of this research is to investigate how Natural Language Processing (NLP) techniques and machine learning techniques applied to clinician notes can assist in doctors’ decision-making in Intensive Care Unit (ICU) for coronavirus disease 2019 (COVID-19) patients. The hypothesis is that clinical outcomes like survival or mortality can be useful in influencing the judgement of clinical sentiment in ICU clinical notes. This paper introduces two contributions: first, we introduce COVID_ICU_BERT, a fine-tuned version of clinical transformer models that can reliably predict clinical sentiment for notes of COVID patients in the ICU. We train the model on clinical notes for COVID-19 patients, a type of notes that were not previously seen by clinicalBERT, and Bio_Discharge_Summary_BERT. The model, which was based on clinicalBERT achieves higher predictive accuracy (Acc 93.33%, AUC 0.98, and precision 0.96 ). Second, we perform data augmentation using clinical contextual word embedding that is based on a pre-trained clinical model to balance the samples in each class in the data (survived vs. deceased patients). Data augmentation improves the accuracy of prediction slightly (Acc 96.67%, AUC 0.98, and precision 0.92 ).

Keywords: BERT fine-tuning, clinical sentiment, COVID-19, data augmentation

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Authors: Anthony I. Otuonye, Juliet N. Odii, Perpetual N. Ibe

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The obvious challenges faced by most commercial bank customers while using the services of ATMs (Automated Teller Machines) across developing countries have triggered the need for an improved system with better security features. Current ATM systems are password-based, and research has proved the vulnerabilities of these systems to heinous attacks and manipulations. We have discovered by research that the security of current ATM-assisted banking services in most developing countries of the world is easily broken and maneuvered by fraudsters, majorly because it is quite difficult for these systems to identify an impostor with privileged access as against the authentic bank account owner. Again, PIN (Personal Identification Number) code passwords are easily guessed, just to mention a few of such obvious limitations of traditional ATM operations. In this research work also, we have developed a system of fingerprint biometrics with PIN code Authentication that seeks to improve the security features of traditional ATM installations as well as other Banking Services. The aim is to ensure better security at all ATM installations and raise the confidence of bank customers. It is hoped that our system will overcome most of the challenges of the current password-based ATM operation if properly applied. The researchers made use of the OOADM (Object-Oriented Analysis and Design Methodology), a software development methodology that assures proper system design using modern design diagrams. Implementation and coding were carried out using Visual Studio 2010 together with other software tools. Results obtained show a working system that provides two levels of security at the client’s side using a fingerprint biometric scheme combined with the existing 4-digit PIN code to guarantee the confidence of bank customers across developing countries.

Keywords: fingerprint biometrics, banking operations, verification, ATMs, PIN code

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Authors: Ahmad Rasyadan Arshad, A. Rahman A. Jamal, N. Mohamed Ibrahim, Nor Azian Abdul Murad

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Introduction: Parkinson’s disease (PD) is a complex and asymptomatic disease where patients are usually diagnosed at late stage where about 70% of the dopaminergic neurons are lost. Therefore, identification of molecular biomarkers is crucial for early diagnosis of PD. MicroRNA (miRNA) is a short nucleotide non-coding small RNA which regulates the gene expression in post-translational process. The involvement of these miRNAs in neurodegenerative diseases includes maintenance of neuronal development, necrosis, mitochondrial dysfunction and oxidative stress. Thus, miRNA could be a potential biomarkers for diagnosis of PD. Objective: This study aim to identify the miRNA involved in Late Onset PD (LOPD) and Early Onset PD (EOPD) compared to the controls. Methods: This is a case-control study involved PD patients in the Chancellor Tunku Muhriz Hospital at the UKM Medical Centre. miRNA samples were extracted using miRNeasy serum/plasma kit from Qiagen. The quality of miRNA extracted was determined using Agilent RNA 6000 Nano kit in the Bioanalyzer. miRNA expression was performed using GeneChip miRNA 4.0 chip from Affymetrix. Microarray was performed in EOPD (n= 7), LOPD (n=9) and healthy control (n=11). Expression Console and Transcriptomic Analyses Console were used to analyze the microarray data. Result: miR-129-5p was significantly downregulated in EOPD compared to LOPD with -4.2 fold change (p = <0.050. miR-301a-3p was upregulated in EOPD compared to healthy control (fold = 10.3, p = <0.05). In LOPD versus healthy control, miR-486-3p (fold = 15.28, p = <0.05), miR-29c-3p (fold = 12.21, p = <0.05) and miR-301a-3p (fold = 10.01, p =< 0.05) were upregulated. Conclusion: Several miRNA have been identified to be differentially expressed in EOPD compared to LOPD and PD versus control. These miRNAs could serve as the potential biomarkers for early diagnosis of PD. However, these miRNAs need to be validated in a larger sample size.

Keywords: early onset PD, late onset PD, microRNA (miRNA), microarray

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Authors: Garima Joshi, Pratap Sharan, V. Sreenivas, Nand Kumar, Kameshwar Prasad, Ashima N. Wadhawan

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Schizophrenia is a debilitating disorder and is marked by cognitive impairment, which deleteriously impacts the social and professional functioning along with the quality of life of the patients and the caregivers. Often the cognitive symptoms are in their prodromal state and worsen as the illness progresses; they have proven to have a good predictive value for the prognosis of the illness. It has been shown that intensive cognitive rehabilitation (CR) leads to improvements in the healthy as well as cognitively-impaired subjects. As the majority of population in India falls in the lower to middle socio-economic status and have low education levels, using the existing packages, a majority of which are developed in the West, for cognitive rehabilitation becomes difficult. The use of technology is also restricted due to the high costs involved and the limited availability and familiarity with computers and other devices, which pose as an impedance for continued therapy. Cognitive rehabilitation in India uses a plethora of retraining methods for the patients with schizophrenia targeting the functions of attention, information processing, executive functions, learning and memory, and comprehension along with Social Cognition. Psychologists often have to follow an integrative therapy approach involving social skills training, family therapy and psychoeducation in order to maintain the gains from the cognitive rehabilitation in the long run. This paper reviews the methodologies and cognitive retaining programs used in India. It attempts to elucidate the evolution and development of methodologies used, from traditional paper-pencil based retraining to more sophisticated neuroscience-informed techniques in cognitive rehabilitation of deficits in schizophrenia as home-based or supervised and guided programs for cognitive rehabilitation.

Keywords: schizophrenia, cognitive rehabilitation, neuropsychological interventions, integrated approached to rehabilitation

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Authors: V. Konjik, J. Schwartz, R. Sandhoff, M. Mack

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The rising number of multi-resistant pathogens demands the development of new antibiotics in order to reduce the lethal risk of infections. Here, we investigate roseoflavin, a vitamin B2 analogue which is produced by Streptomyces davawensis and Streptomyces cinnabarinus. We consider roseoflavin to be a 'Trojan horse' compound. Its chemical structure is very similar to riboflavin but in fact it is a toxin. Furthermore, it is a clever strategy with regard to the delivery of an antibiotic to its site of action but also with regard to the production of this chemical: The producer cell has only to convert a vitamin (which is already present in the cytoplasm) into a vitamin analog. Roseoflavin inhibits the activity of Flavin depending proteins, which makes up to 3.5 % of predicted proteins in organisms sequenced so far. We sequentially knocked out gene clusters and later on single genes in order to find the ones which are involved in the roseoflavin biosynthesis. Consequently, we identified the gene rosB, coding for the protein carrying out the first step of roseoflavin biosynthesis, starting form Flavin mononucleotide. Here we show, that the protein RosB has so far unknown features. It is per se an oxidoreductase, a decarboxylase and an aminotransferase, all rolled into one enzyme. A screen of cofactors revealed needs of oxygen, NAD+, thiamine and glutamic acid to carry out its function. Surprisingly, thiamine is not only needed for the decaboxylation step, but also for the oxidation of 8-demethyl-8-formyl Flavin mononucleotide. We had managed to isolate three different Flavin intermediates with different oxidation states, which gave us a mechanistic insight of RosB functionality. Our work points to a so far new function of thiamine in Streptomyces davawensis. Additionally, RosB could be extremely useful for chemical synthesis. Careful engineering of RosB may allow the site-specific replacement of methyl groups by amino groups in polyaromatic compounds of commercial interest. Finally, the complete clarification of the roseoflavin biosynthesis opens the possibility of engineering cost-effective roseoflavin producing strains.

Keywords: antibiotic, flavin analogue, roseoflavin biosynthesis, vitamin B2

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Authors: Larissa Burruano, Sergey Grabovyj, Irina Nguen

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The study aimed to assess the level of adherence to anti retroviral therapy (ART) and to examine the relationship between adherence and risk behavior factor (drug use) among patients infected with HIV. The patients with newly diagnosed or established HIV infection under follow-up at the Sumskij Regional Centre for AIDS Prevention in Ukraine were eligible for this study. Medical records were used to measure the patient’s adherence to medication. Measurements were obtained at month 6 and at month 12 to calculate the number of medication omission during the past 30 days: (on a 2-point scale – once until three in a month – were considered adherent, three and more in a month – were considered non-adherent). Of the 50 study participants, 27 (54.0%) were men and 23 (46.0%) women. The mean age is 35.2 years (SD= 5.1). A majority of the patients (82.0%) is in the age group of 25-30 years. The main level of adherence was 74.0% and 66.0% at 6 and 12 months, respectively. The main routes of HIV transmission were drug injection among men 12 (44.4%) and sexual contact among women 11 (47.8%). Univariate analyses indicated that patients who had lower level of education were more likely to have been non-adherent at month 6- (X2 =5.1, n=50, p < .05) and at month 12 (X2 = 4.34, n=50, p < .05). Multivariate tests showed that only age (OR= 1.163 [95% CI 0.98–1.370]) was significant independent predictor of treatment adherence, while gender, education, employment status were not predictive for the risk of developing non-compliance. There was not a significant interaction between non-adherence and intravenous drug use. Consistent with these findings, younger people were more likely to have missed a dose of their medication because they had a greater sense of invulnerability than older patients. The study indicates that the socio demographic characteristic should be taken into an account in the future research regarding adherence in the case of HIV infection. If the patient anti retroviral adherence can be improved by qualitatively better medical care in all regions of the Ukraine, behavioral changes in the population can to be expected in the long term.

Keywords: HIV, antiretroviral therapy, adherence, Ukraine, Eastern Europe

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Authors: Soheila Sadeghi

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Accurate forecasting of project performance metrics is crucial for successfully managing and delivering urban road reconstruction projects. Traditional methods often rely on static baseline plans and fail to consider the dynamic nature of project progress and external factors. This research proposes a machine learning-based approach to forecast project performance metrics, such as cost variance and earned value, for each Work Breakdown Structure (WBS) category in an urban road reconstruction project. The proposed model utilizes time series forecasting techniques, including Autoregressive Integrated Moving Average (ARIMA) and Long Short-Term Memory (LSTM) networks, to predict future performance based on historical data and project progress. The model also incorporates external factors, such as weather patterns and resource availability, as features to enhance the accuracy of forecasts. By applying the predictive power of machine learning, the performance forecasting model enables proactive identification of potential deviations from the baseline plan, which allows project managers to take timely corrective actions. The research aims to validate the effectiveness of the proposed approach using a case study of an urban road reconstruction project, comparing the model's forecasts with actual project performance data. The findings of this research contribute to the advancement of project management practices in the construction industry, offering a data-driven solution for improving project performance monitoring and control.

Keywords: project performance forecasting, machine learning, time series forecasting, cost variance, earned value management

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Authors: Yong Chen

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To understand the detailed molecular mechanisms of memory formation in engram cells is one of the most fundamental questions in neuroscience. Recent single-cell RNA-seq (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) techniques have allowed us to explore the sparsely activated engram ensembles, enabling access to the molecular mechanisms that underlie experience-dependent memory formation and consolidation. However, the absence of specific and powerful computational methods to detect memory-related genes (modules) and their regulatory relationships in the sc/snRNA-seq datasets has strictly limited the analysis of underlying mechanisms and memory coding principles in mammalian brains. Here, we present a deep-learning method named SCENTBOX, to detect memory-related gene modules and causal regulatory relationships among themfromsc/snRNA-seq datasets. SCENTBOX first constructs codifferential expression gene network (CEGN) from case versus control sc/snRNA-seq datasets. It then detects the highly correlated modules of differential expression genes (DEGs) in CEGN. The deep network embedding and attention-based convolutional neural network strategies are employed to precisely detect regulatory relationships among DEG genes in a module. We applied them on scRNA-seq datasets of TRAP; Ai14 mouse neurons with fear memory and detected not only known memory-related genes, but also the modules and potential causal regulations. Our results provided novel regulations within an interesting module, including Arc, Bdnf, Creb, Dusp1, Rgs4, and Btg2. Overall, our methods provide a general computational tool for processing sc/snRNA-seq data from case versus control studie and a systematic investigation of fear-memory-related gene modules.

Keywords: sc/snRNA-seq, memory formation, deep learning, gene module, causal inference

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Authors: Junyu Chen, Peng Xu

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In the context of global efforts to enhance building energy efficiency, accurate thermal load forecasting is crucial for both device sizing and predictive control. Variable Refrigerant Flow (VRF) systems are widely used in buildings around the world, yet VRF zonal load prediction has received limited attention. Due to differences between VRF zones in building-level prediction methods, zone-level load forecasting could significantly enhance accuracy. Given that modern VRF systems generate high-quality data, this paper introduces transfer learning to leverage this data and further improve prediction performance. This framework also addresses the challenge of predicting load for building zones with no historical data, offering greater accuracy and usability compared to pure white-box models. The study first establishes an initial variable set of VRF zonal building loads and generates a foundational white-box database using EnergyPlus. Key variables for VRF zonal loads are identified using methods including SRRC, PRCC, and Random Forest. XGBoost and LSTM are employed to generate pre-trained black-box models based on the white-box database. Finally, real-world data is incorporated into the pre-trained model using transfer learning to enhance its performance in operational buildings. In this paper, zone-level load prediction was integrated with transfer learning, and a framework was proposed to improve the accuracy and applicability of VRF zonal load prediction.

Keywords: zonal load prediction, variable refrigerant flow (VRF) system, transfer learning, energyplus

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Authors: Manar Makhoul, Buthainah Alsalamah, Salam Lawand, Hassan Azzam

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The major storage proteins in endosperm of 33 cultivated and wild barley genotypes (H.vulgare, H. spontaneum, H. bulbosum, H. murinum, H. marinum) were analyzed to demonstrate the variation in the hordein polypeptides encoded by multigene families in grains. The SDS-PAGE revealed 13 and 17 alleles at the Hor1 and the Hor2 loci respectively, with frequencies from 0.83 to 14 and 0.56 to 13.41% respectively, while seven alleles at the Hor3 locus with frequencies from 3.63 to 30.91% were recognized. The phylogenetic analysis indicated to relevance of the polymorphism in hordein patterns as successful tool in identifying the individual genotypes and discriminating the species according to genome type. We also reported in this research complete nucleotide sequence B-hordein genes of seven wild and cultivated barley genotypes. A 152bp upstream sequence of B-hordein promoter contained a TATA box, CATC box, AAAG motif, N-motif and E-motif. In silico analysis of B-Hordein sequences demonstrated that the coding regions were not interrupted by any intron, and included the complete ORF which varied between 882 and 906 bp, and encoded mature proteins with 293-301 residues characterized by high contents of glutamine (29%), and proline (18%). Comparison of the predicted polypeptide sequences with the published ones suggested that all S-rich prolamins genes are descended from common ancestor. The sequence started at N-terminal with a signal peptide, and then followed directly by two domains; a repetitive one based on the repetition of the repeat unit PQQPFPQQ and C-terminal domain. Also, it was found that positions of the eight cysteine residues were highly conserved in all the B-hordein sequences, but Hordeum bulbosum had additional unpaired one. The phylogenetic tree of B-hordein polypeptide separated the genotypes in distinct seven subgroups. In general, the high homology between B-hordeins and LMW glutenin subunits suggests similar bread-making influences for these B-hordeins.

Keywords: hordeum, phylogenetic tree, sequencing, storage protein

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Authors: Yohannes Bisa Biramo

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This study examined the meditational role of surface acting and deep acting on the relationship between calling orientation and work engagement of teachers in secondary schools of Wolaita Zone, Wolaita, Ethiopia. A predictive non-experimental correlational design was performed among 300 secondary school teachers. Stratified random sampling followed by a systematic random sampling technique was used as the basis for selecting samples from the target population. To analyze the data, Structural Equation Modeling (SEM) was used to test the association between the independent variables and the dependent variables. Furthermore, the goodness of fit of the study variables was tested using SEM to see and explain the path influence of the independent variable on the dependent variable. Confirmatory factor analysis (CFA) was conducted to test the validity of the scales in the study and to assess the measurement model fit indices. The analysis result revealed that calling was significantly and positively correlated with surface acting, deep acting and work engagement. Similarly, surface acting was significantly and positively correlated with deep acting and work engagement. And also, deep acting was significantly and positively correlated with work engagement. With respect to mediation analysis, the result revealed that surface acting mediated the relationship between calling and work engagement and also deep acting mediated the relationship between calling and work engagement. Besides, by using the model of the present study, the school leaders and practitioners can identify a core area to be considered in recruiting and letting teachers teach, in giving induction training for newly employed teachers and in performance appraisal.

Keywords: calling, surface acting, deep acting, work engagement, mediation, teachers

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Authors: Yuexin Liu, Gordon B. Mills, Russell R. Broaddus, John N. Weinstein

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The lethality of endometrioid endometrial cancer (EEC) is primarily attributable to the high-stage diseases. However, there are no available biomarkers that predict EEC patient staging at the time of diagnosis. We aim to develop a predictive scheme to help in this regards. Using reverse-phase protein array expression profiles for 210 EEC cases from The Cancer Genome Atlas (TCGA), we constructed a Protein Scoring of EEC Staging (PSES) scheme for surgical stage prediction. We validated and evaluated its diagnostic potential in an independent cohort of 184 EEC cases obtained at MD Anderson Cancer Center (MDACC) using receiver operating characteristic curve analyses. Kaplan-Meier survival analysis was used to examine the association of PSES score with patient outcome, and Ingenuity pathway analysis was used to identify relevant signaling pathways. Two-sided statistical tests were used. PSES robustly distinguished high- from low-stage tumors in the TCGA cohort (area under the ROC curve [AUC]=0.74; 95% confidence interval [CI], 0.68 to 0.82) and in the validation cohort (AUC=0.67; 95% CI, 0.58 to 0.76). Even among grade 1 or 2 tumors, PSES was significantly higher in high- than in low-stage tumors in both the TCGA (P = 0.005) and MDACC (P = 0.006) cohorts. Patients with positive PSES score had significantly shorter progression-free survival than those with negative PSES in the TCGA (hazard ratio [HR], 2.033; 95% CI, 1.031 to 3.809; P = 0.04) and validation (HR, 3.306; 95% CI, 1.836 to 9.436; P = 0.0007) cohorts. The ErbB signaling pathway was most significantly enriched in the PSES proteins and downregulated in high-stage tumors. PSES may provide clinically useful prediction of high-risk tumors and offer new insights into tumor biology in EEC.

Keywords: endometrial carcinoma, protein, protein scoring of EEC staging (PSES), stage

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Authors: Zixuan Zhao, Lingbin Du, Le Wang, Youqing Wang, Yi Yang, Jingjun Chen, Hengjin Dong

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Objectives: Few results from public attitudes for lung cancer screening are available both in China and abroad. This study aimed to identify preferred lung cancer screening modalities in a Chinese population and predict uptake rates of different modalities. Materials and Methods: A discrete choice experiment questionnaire was administered to 392 Chinese individuals aged 50–74 years who were at high risk for lung cancer. Each choice set had two lung screening options and an option to opt-out, and respondents were asked to choose the most preferred one. Both mixed logit analysis and stepwise logistic analysis were conducted to explore whether preferences were related to respondent characteristics and identify which kinds of respondents were more likely to opt out of any screening. Results: On mixed logit analysis, attributes that were predictive of choice at 1% level of statistical significance included the screening interval, screening venue, and out-of-pocket costs. The preferred screening modality seemed to be screening by low-dose computed tomography (LDCT) + blood test once a year in a general hospital at a cost of RMB 50; this could increase the uptake rate by 0.40 compared to the baseline setting. On stepwise logistic regression, those with no endowment insurance were more likely to opt out; those who were older and housewives/househusbands, and those with a health check habit and with commercial endowment insurance were less likely to opt out from a screening programme. Conclusions: There was considerable variance between real risk and self-perceived risk of lung cancer among respondents, and further research is required in this area. Lung cancer screening uptake can be increased by offering various screening modalities, so as to help policymakers further design the screening modality.

Keywords: lung cancer, screening, China., discrete choice experiment

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Authors: Harini Chakkera

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Background: Inpatient hyperglycemia is an established independent risk factor among several patient cohorts with hospital readmission. This has not been studied after kidney transplantation. Nearly one-third of patients who have undergone a kidney transplant reportedly experience 30-day readmission. Methods: Data on first-time solitary kidney transplantations were retrieved between September 2015 to December 2018. Information was linked to the electronic health record to determine a diagnosis of diabetes mellitus and extract glucometeric and insulin therapy data. Univariate logistic regression analysis and the XGBoost algorithm were used to predict 30-day readmission. We report the average performance of the models on the testing set on five bootstrapped partitions of the data to ensure statistical significance. Results: The cohort included 1036 patients who received kidney transplantation, and 224 (22%) experienced 30-day readmission. The machine learning algorithm was able to predict 30-day readmission with an average AUC of 77.3% (95% CI 75.30-79.3%). We observed statistically significant differences in the presence of pretransplant diabetes, inpatient-hyperglycemia, inpatient-hypoglycemia, and minimum and maximum glucose values among those with higher 30-day readmission rates. The XGBoost model identified the index admission length of stay, presence of hyper- and hypoglycemia and recipient and donor BMI values as the most predictive risk factors of 30-day readmission. Additionally, significant variations in the therapeutic management of blood glucose by providers were observed. Conclusions: Suboptimal glucose metrics during hospitalization after kidney transplantation is associated with an increased risk for 30-day hospital readmission. Optimizing the hospital blood glucose management, a modifiable factor, after kidney transplantation may reduce the risk of 30-day readmission.

Keywords: kidney, transplant, diabetes, insulin

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Authors: Shraddha Jain Sharma, Ratnalata Gupta

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Predicting stock movements in the financial market is both difficult and rewarding. Analysts and academics are increasingly using advanced approaches such as machine learning techniques to anticipate stock price patterns, thanks to the expanding capacity of computing and the recent advent of graphics processing units and tensor processing units. Stock market prediction is a type of time series prediction that is incredibly difficult to do since stock prices are influenced by a variety of financial, socioeconomic, and political factors. Furthermore, even minor mistakes in stock market price forecasts can result in significant losses for companies that employ the findings of stock market price prediction for financial analysis and investment. Soft computing techniques are increasingly being employed for stock market prediction due to their better accuracy than traditional statistical methodologies. The proposed research looks at the need for soft computing techniques in stock market prediction, the numerous soft computing approaches that are important to the field, past work in the area with their prominent features, and the significant problems or issue domain that the area involves. For constructing a predictive model, the major focus is on neural networks and fuzzy logic. The stock market is extremely unpredictable, and it is unquestionably tough to correctly predict based on certain characteristics. This study provides a complete overview of the numerous strategies investigated for high accuracy prediction, with a focus on the most important characteristics.

Keywords: stock market prediction, artificial intelligence, artificial neural networks, fuzzy logic, accuracy, deep learning, machine learning, stock price, trading volume

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Authors: Ivan Potapov

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Background: The aim of this paper is to investigate poly code texts in the communication of youth antisocial groups. Nowadays, the notion of a text has numerous interpretations. Besides all the approaches to defining a text, we must take into account semiotic and cultural-semiotic ones. Rapidly developing IT, world globalization, and new ways of coding of information increase the role of the cultural-semiotic approach. However, the development of computer technologies leads also to changes in the text itself. Polycode texts play a more and more important role in the everyday communication of the younger generation. Therefore, the research of functional and pragmatic aspects of both verbal and non-verbal content is actually quite important. Methods and Material: For this survey, we applied the combination of four methods of text investigation: not only intention and content analysis but also semantic and syntactic analysis. Using these methods provided us with information on general text properties, the content of transmitted messages, and each communicants’ intentions. Besides, during our research, we figured out the social background; therefore, we could distinguish intertextual connections between certain types of polycode texts. As the sources of the research material, we used 20 public channels in the popular messenger Telegram and data extracted from smartphones, which belonged to arrested members of antisocial groups. Findings: This investigation let us assert that polycode texts can be characterized as highly intertextual language unit. Moreover, we could outline the classification of these texts based on communicants’ intentions. The most common types of antisocial polycode texts are a call to illegal actions and agitation. What is more, each type has its own semantic core: it depends on the sphere of communication. However, syntactic structure is universal for most of the polycode texts. Conclusion: Polycode texts play important role in online communication. The results of this investigation demonstrate that in some social groups using these texts has a destructive influence on the younger generation and obviously needs further researches.

Keywords: text, polycode text, internet linguistics, text analysis, context, semiotics, sociolinguistics

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Authors: Thewodros K. Geberemariam

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The rapid physical expansion of urbanization coupled with aging infrastructure presents a unique decision and management challenges for many big city municipalities. Cities must therefore upgrade and maintain the existing aging urban drainage infrastructure systems to keep up with the demands. Given the overall contribution of assets to municipal revenue and the importance of infrastructure to the success of a livable city, many municipalities are currently looking for a robust and smart urban drainage infrastructure asset management solution that combines management, financial, engineering and technical practices. This robust decision-making shall rely on sound, complete, current and relevant data that enables asset valuation, impairment testing, lifecycle modeling, and forecasting across the multiple asset portfolios. On this paper, predictive computational intelligence (CI) and multi-class machine learning (ML) coupled with online, offline, and historical record data that are collected from an array of multi-parameter sensors are used for the extraction of different operational and non-conforming patterns hidden in structured and unstructured data to determine and produce actionable insight on the current and future states of the network. This paper aims to improve the strategic decision-making process by identifying all possible alternatives; evaluate the risk of each alternative, and choose the alternative most likely to attain the required goal in a cost-effective manner using historical and near real-time urban drainage infrastructure data for urban drainage infrastructures assets that have previously not benefited from computational intelligence and machine learning advancements.

Keywords: computational intelligence, machine learning, urban drainage infrastructure, machine learning, classification, prediction, asset management space

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Authors: Nouira Mariem, Ennigrou Samir

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Background and aims: Healthcare-associated infections (HAI) represent a major public health problem worldwide. They represent one of the most serious adverse events in health care. The objectives of our study were to estimate the prevalence of HAI at the Charles Nicolle Hospital (CNH) and to identify the main associated factors as well as to estimate the frequency of antibiotic use. Methods: It was a cross-sectional study at the CNH with a unique passage per department (October-December 2018). All patients present at the wards for more than 48 hours were included. All patients from outpatient consultations, emergency, and dialysis departments were not included. The site definitions of infections proposed by the Centers for Disease Control and Prevention (CDC) were used. Only clinically and/or microbiologically confirmed active HAIs were included. Results: A total of 318 patients were included, with a mean age of 52 years and a sex ratio (female/male) of 1.05. A total of 41 patients had one or more active HAIs, corresponding to a prevalence of 13.1% (95% CI: 9.3%-16.9%). The most frequent site infections were urinary tract infections and pneumonia. Multivariate analysis among adult patients (>=18 years) (n=261) revealed that infection on admission (p=0.01), alcoholism (p=0.01), high blood pressure (p=0.008), having at least one invasive device inserted (p=0.004), and history of recent surgery (p=0.03), increased the risk of HAIs significantly. More than 1 of 3 patients (35.4%) were under antibiotics on the day of the survey, of which more than half (57.4%) were under two or more types of antibiotics. Conclusion: The prevalence of HAIs and antibiotic prescriptions at the CNH were considerably high. An infection prevention and control committee, as well as the development of an antibiotic stewardship program with continuous monitoring using repeated prevalence surveys, must be implemented to limit the frequency of these infections effectively.

Keywords: prevalence, healthcare associated infection, antibiotic, Tunisia

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Authors: Osama Zayed

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Aim of the work: The aim of this study is to assess the predictors of pelvic vascular injuries in patients with pelvic fractures from major blunt trauma. Methods: This study was conducted as a tool-assessment study. Forty six patients with pelvic fractures from major blunt trauma will be recruited to the study arriving to department of emergency, Suez Canal University Hospital. Data were collected from questionnaire including; personal data of the studied patients and full medical history, clinical examinations, outcome measures (The Physiological and Operative Severity Score for enumeration of Mortality and morbidity (POSSUM), laboratory and imaging studies. Patients underwent surgical interventions or further investigations based on the conventional standards for interventions. All patients were followed up during conservative, operative and post-operative periods in the hospital for interpretation the predictive scores of vascular injuries. Results: Significant predictors of vascular injuries according to computed tomography (CT) scan include age, male gender, lower Glasgow coma (GCS) scores, occurrence of hypotension, mortality rate, higher physical POSSUM scores, presence of ultrasound collection, type of management, higher systolic blood pressure (SBP) and diastolic blood pressure (DBP) POSSUM scores, presence of abdominal injuries, and poor outcome. Conclusions: There was higher frequency of males than females in the studied patients. There were high probability of morbidity and low probability of mortality among patients. Our study demonstrates that POSSUM score can be used as a predictor of vascular injury in pelvis fracture patients.

Keywords: predictors, pelvic vascular injuries, pelvic fractures, major blunt trauma, POSSUM

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