Otrouha: A Corpus of Arabic ETDs and a Framework for Automatic Subject Classification

Although the Arabic language is spoken by more than 300 million people and is one of the six official languages of the United Nations (UN), there has been less research done on Arabic text data (compared to English) in the realm of machine learning, especially in text classification. In the past decade, Arabic data such as news, tweets, etc. have begun to receive some attention. Although automatic text classification plays an important role in improving the browsability and accessibility of data, Electronic Theses and Dissertations (ETDs) have not received their fair share of attention, in spite of the huge number of benefits they provide to students, universities, and future generations of scholars. There are two main roadblocks to performing automatic subject classification on Arabic ETDs. The first is the unavailability of a public corpus of Arabic ETDs. The second is the linguistic complexity of the Arabic language; that complexity is particularly evident in academic documents such as ETDs. To address these roadblocks, this paper presents Otrouha, a framework for automatic subject classification of Arabic ETDs, which has two main goals. The first is building a Corpus of Arabic ETDs and their key metadata such as abstracts, keywords, and title to pave the way for more exploratory research on this valuable genre of data. The second is to provide a framework for automatic subject classification of Arabic ETDs through different classification models that use classical machine learning as well as deep learning techniques. The first goal is aided by searching the AskZad Digital Library, which is part of the Saudi Digital Library (SDL). AskZad provides other key metadata of Arabic ETDs, such as abstract, title, and keywords. The current search results consist of abstracts of Arabic ETDs. This raw data then undergoes a pre-processing phase that includes stop word removal using the Natural Language Tool Kit (NLTK), and word lemmatization using the Farasa API. To date, abstracts of 518 ETDs across 12 subjects have been collected. For the second goal, the preliminary results show that among the machine learning models, binary classification (one-vs.-all) performed better than multiclass classification. The maximum per subject accuracy is 95%, with an average accuracy of 68% across all subjects. It is noteworthy that the binary classification model performed better for some categories than others. For example, Applied Science and Technology shows 95% accuracy, while the category of Administration shows 36%. Deep learning models resulted in higher accuracy but lower F-measure; their overall performance is lower than machine learning models. This may be due to the small size of the dataset as well as the imbalance in the number of documents per category. Work to collect additional ETDs will be aided by collaborative contributions of data from additional sources

Myopia progression in school children with prolonged screen time during the coronavirus disease confinement

Background: Myopia, the most common refractive error, is a global public health problem with substantial visual impairment if left untreated. Several studies have investigated the association between increased near-work and restricted outdoor activities in children with myopia; however, such studies in children without myopia are scarce. We aimed to monitor the effect of the coronavirus disease-2019 (COVID-19) home confinement and mandatory virtual learning on myopic progression among myopic and non-myopic school-aged children. Methods: We conducted a retrospective chart review of children aged 6 – 12 years attending regular visits to the pediatric ophthalmology clinic in a tertiary eye hospital in Eastern Province, Saudi Arabia. Cycloplegic refraction was determined from three visits at least six months apart: two visits before the start of the COVID-19 pandemic and one during the COVID-19 home confinement. Parents were asked about the time spent in near-work and outdoor activities, the devices used during virtual learning, and the demographic characteristics of the children. Statistical analyses were conducted to compare myopia progression before and during the COVID-19 home confinement. Results: A total of 160 eyes of 80 children were analyzed. The boy (n = 46) to girl (n = 34) ratio was 1.4:1. The hyperopia (n = 131 eyes) to myopia (n = 29 eyes) ratio was 4.5:1. Most eyes exhibited a hyperopic shift before the confinement; however, all eyes displayed a myopic shift during the confinement. When comparing both eyes of the same individual, the more myopic or less hyperopic eye in the same child had a significantly greater myopic shift than the fellow eye (both P < 0.05). Children who used tablets showed a significant myopic shift (P < 0.05). Likewise, children in both age categories (less than or equal to 8 and > 8 years), boys, those living in an apartment, and those having parents with bachelor’s degrees experienced a significant myopic shift during COVID-19 home confinement compared to before (all P < 0.05). The mean myopic shift was greater in children aged > 8 years than in those aged less than or equal to 8 years. Children with and without a family history of myopia had a myopic shift in the mean spherical equivalent during COVID-19 home confinement; however, that of children with no family history was statistically significant (P < 0.05). Conclusions: Progression of myopia accelerated in children during the COVID-19 pandemic. Excessive time spent on digital screen devices at near distances is considered a substantial environmental contributor to myopic shift in children. Further multicenter studies with extended follow-up periods are needed to assess the factors contributing to myopic progression in our population

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

A first update on mapping the human genetic architecture of COVID-19

peer reviewe

Spectral Characterization and Antimicrobial Activity of Chenodeoxycholic Acid Complexes with Zn(II), Mg(II), and Ca(II) Ions

Chenodeoxycholic acid (CA) is a naturally occurring bile acid that is produced in the liver from cholesterol. Three CA complexes using Zn(II), Mg(II), and Ca(II) ions were synthesized to examine the chelation tendencies of CA towards these metal ions. The complexation reaction of CA with the metal ions under investigation was conducted with a 1:1 molar ratio (CA to metal) at 60–70 °C in neutralized media, which consisted of a binary solvent of MeOH and H2O (1:1). The resulting CA complexes were characterized using elemental data (metal, H, C, and Cl analysis) and spectral data (UV–visible, FT-IR, and 1H NMR). The results suggested that CA in anion form utilized oxygen atoms of the carboxylate group (-COO−) to capture Zn(II), Mg(II), and Ca(II) ions. This produced complexes with the general compositions of [Zn(CA)(H2O)Cl], [Mg2(CA)2(H2O)4Cl2], and [Ca2(CA)2(H2O)4Cl2]·2H2O, respectively. The Kirby–Bauer disc diffusion assay was then used to explore the bioactivity of the CA complexes toward three fungal species (Aspergillus niger, Candida albicans, and Penicillium sp.), three Gram-positive bacteria (Staphylococcus aureus, Streptococcus pneumoniae, and Bacillus subtilis), and two Gram-negative bacteria (Pseudomonas aeruginosa and Escherichia coli). The Ca(II) and Mg(II) complexes exhibited marked inhibitory effects on the cell growth of the fungal species Aspergillus niger with potency equal to 127 and 116% of the activity of the positive control, respectively. The Zn(II) and Ca(II) complexes strongly inhibited the growth of Penicillium sp., while the Zn(II) and Mg(II) complexes showed strong growth inhibition towards the Gram-negative species Pseudomonas aeruginosa

Epidemiology and Clinical Characteristics of People with Confirmed SARS-CoV-2 Infection during the Early COVID-19 Pandemic in Saudi Arabia

This study provides epidemiologic and clinical characteristics of 492 consecutive patients diagnosed with SARS-CoV-2 infection at King Faisal Specialist Hospital and Research Centre in Saudi Arabia between March and September 2020. Data were collected from electronic case reports. The cohort was 54% male, with 20.4% aged >60 years, 19.9% aged 31–40 years, and 17% aged 41–50 years. The median incubation period was 16 days, with upper and lower 95% quartiles of 27 and 10 days, respectively. Most patients (79.2%) were symptomatic. Variables significantly different between symptomatic and asymptomatic patients were age, blood oxygen saturation percentage, hemoglobin level, lymphocyte count, neutrophil to lymphocyte (NTL) ratio, and alanine aminotransferase (ALT) and aspartate aminotransferase (AST) level. Asymptomatic patients were mostly younger, with lower body mass index and ALT and AST levels but higher lymphocyte counts, NTL ratio, and CD4, CD8, natural killer cell, IgG, and IgM levels. Factors associated with increased risk of mortality were age (>42 years) and comorbidities, particularly diabetes mellitus and hypertension. Patients who were not given an antiviral regimen were associated with better prognosis than patients who received an antiviral regimen (HR, 0.07; 95% CI, 0.011–0.25). These findings will help clinicians and policymakers adopt best management and treatment options for SARS-CoV-2 infection

Abundant resistome determinants in rhizosphere soil of the wild plant Abutilon fruticosum

Abstract A metagenomic whole genome shotgun sequencing approach was used for rhizospheric soil micribiome of the wild plant Abutilon fruticosum in order to detect antibiotic resistance genes (ARGs) along with their antibiotic resistance mechanisms and to detect potential risk of these ARGs to human health upon transfer to clinical isolates. The study emphasized the potential risk to human health of such human pathogenic or commensal bacteria, being transferred via food chain or horizontally transferred to human clinical isolates. The top highly abundant rhizospheric soil non-redundant ARGs that are prevalent in bacterial human pathogens or colonizers (commensal) included mtrA, soxR, vanRO, golS, rbpA, kdpE, rpoB2, arr-1, efrA and ileS genes. Human pathogenic/colonizer bacteria existing in this soil rhizosphere included members of genera Mycobacterium, Vibrio, Klebsiella, Stenotrophomonas, Pseudomonas, Nocardia, Salmonella, Escherichia, Citrobacter, Serratia, Shigella, Cronobacter and Bifidobacterium. These bacteria belong to phyla Actinobacteria and Proteobacteria. The most highly abundant resistance mechanisms included antibiotic efflux pump, antibiotic target alteration, antibiotic target protection and antibiotic inactivation. antimicrobial resistance (AMR) families of the resistance mechanism of antibiotic efflux pump included resistance-nodulation-cell division (RND) antibiotic efflux pump (for mtrA, soxR and golS genes), major facilitator superfamily (MFS) antibiotic efflux pump (for soxR gene), the two-component regulatory kdpDE system (for kdpE gene) and ATP-binding cassette (ABC) antibiotic efflux pump (for efrA gene). AMR families of the resistance mechanism of antibiotic target alteration included glycopeptide resistance gene cluster (for vanRO gene), rifamycin-resistant beta-subunit of RNA polymerase (for rpoB2 gene) and antibiotic-resistant isoleucyl-tRNA synthetase (for ileS gene). AMR families of the resistance mechanism of antibiotic target protection included bacterial RNA polymerase-binding protein (for RbpA gene), while those of the resistance mechanism of antibiotic inactivation included rifampin ADP-ribosyltransferase (for arr-1 gene). Better agricultural and food transport practices are required especially for edible plant parts or those used in folkloric medicine

Pro106Leu MPL mutation is associated with thrombocytosis and a low risk of thrombosis, splenomegaly and marrow fibrosis

The P106L mutation in the human myeloproliferative leukemia virus oncogene (MPL) was shown to be associated with hereditary thrombocythemia in Arabs. The clinical and bone marrow (BM) features of P106L mutation are unknown. Genetic databases at two tertiary hospitals in Saudi Arabia were searched to identify patients with the MPL P106L mutation. Clinical data were collected retrospectively and the BM aspirates and biopsies were independently reviewed by two hematopathologists. In total, 115 patients were included. Median age was 33 years of which 31 patients were pediatric and 65 were female. The mutation was homozygous in 87 patients. Thrombocytosis was documented in 107 patients, with a median platelet count of 667 × 109/L. The homozygous genotype was associated with a higher platelet count. Thirty-three patients had an evaluable BM and clustering of megakaryocytes was observed in 30/33 patients. At the time of last follow-up, 114 patients were alive. The median follow-up was 7.8 years from the time of thrombocytosis. No patients developed disease progression to myelofibrosis. The P106L mutation was associated with marked thrombocytosis at a younger age and with a low risk of thrombosis, splenomegaly, and marrow fibrosis. The BM demonstrated normal or hypocellular marrow with megakaryocyte clusters

Exploration of genes encoding KEGG pathway enzymes in rhizospheric microbiome of the wild plant Abutilon fruticosum

Abstract The operative mechanisms and advantageous synergies existing between the rhizobiome and the wild plant species Abutilon fruticosum were studied. Within the purview of this scientific study, the reservoir of genes in the rhizobiome, encoding the most highly enriched enzymes, was dominantly constituted by members of phylum Thaumarchaeota within the archaeal kingdom, phylum Proteobacteria within the bacterial kingdom, and the phylum Streptophyta within the eukaryotic kingdom. The ensemble of enzymes encoded through plant exudation exhibited affiliations with 15 crosstalking KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways. The ultimate goal underlying root exudation, as surmised from the present investigation, was the biosynthesis of saccharides, amino acids, and nucleic acids, which are imperative for the sustenance, propagation, or reproduction of microbial consortia. The symbiotic companionship existing between the wild plant and its associated rhizobiome amplifies the resilience of the microbial community against adverse abiotic stresses, achieved through the orchestration of ABA (abscisic acid) signaling and its cascading downstream effects. Emergent from the process of exudation are pivotal bioactive compounds including ATP, D-ribose, pyruvate, glucose, glutamine, and thiamine diphosphate. In conclusion, we hypothesize that future efforts to enhance the growth and productivity of commercially important crop plants under both favorable and unfavorable environmental conditions may focus on manipulating plant rhizobiomes