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Orthography-phonology consistency in English: Theory- and data-driven measures and their impact on auditory vs. visual word recognition

Lim A, O'Brien B, Onnis L

Behav Res Methods, 2024 Mar;56(3):1283-1313.
PMID: 37553536 DOI: 10.3758/s13428-023-02094-5

Research on orthographic consistency in English words has selectively identified different sub-syllabic units in isolation (grapheme, onset, vowel, coda, rime), yet there is no comprehensive assessment of how these measures affect word identification when taken together. To study which aspects of consistency are more psychologically relevant, we investigated their independent and composite effects on human reading behavior using large-scale databases. Study 1 found effects on adults' naming responses of both feedforward consistency (orthography to phonology) and feedback consistency (phonology to orthography). Study 2 found feedback but no feedforward consistency effects on visual and auditory lexical decision tasks, with the best predictor being a composite measure of consistency across grapheme, rime, OVC, and word-initial letter-phoneme. In Study 3, we explicitly modeled the reading process with forward and backward flow in a bidirectionally connected neural network. The model captured latent dimensions of quasi-regular mapping that explain additional variance in human reading and spelling behavior, compared to the established measures. Together, the results suggest interactive activation between phonological and orthographic word representations. They also validate the role of computational analyses of language to better understand how print maps to sound, and what properties of natural language affect reading complexity.

Matched MeSH terms: Reading
Fulltext Shewanella phage encoding a putative anti-CRISPR-like gene represents a novel potential viral family

Wang H, Zheng K, Wang M, Ma K, Ren L, Guo R, et al.

Microbiol Spectr, 2024 Feb 06;12(2):e0336723.
PMID: 38214523 DOI: 10.1128/spectrum.03367-23

Shewanella is a prevalent bacterial genus in deep-sea environments including marine sediments, exhibiting diverse metabolic capabilities that indicate its significant contributions to the marine biogeochemical cycles. However, only a few Shewanella phages were isolated and deposited in the NCBI database. In this study, we report the isolation and characterization of a novel Shewanella phage, vB_SbaS_Y11, that infects Shewanella KR11 and was isolated from the sewage in Qingdao, China. Transmission electron microscopy revealed that vB_SbaS_Y11 has an icosahedral head and a long tail. The genome of vB_SbaS_Y11 is a linear, double-stranded DNA with a length of 62,799 bp and a G+C content of 46.9%, encoding 71 putative open reading frames. No tRNA genes or integrase-related feature genes were identified. An uncharacterized anti-CRISPR AcrVA2 gene was detected in its genome. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analyses indicate that vB_SbaS_Y11 has a novel genomic architecture and shares low similarity to Pseudomonas virus H66 and Pseudomonas phage F116. vB_SbaS_Y11 represents a potential new family-level virus cluster with eight metagenomic assembled viral genomes named Ranviridae.IMPORTANCEThe Gram-negative Shewanella bacterial genus currently includes about 80 species of mostly aquatic Gammaproteobacteria, which were isolated around the globe in a multitude of environments, such as freshwater, seawater, coastal sediments, and the deepest trenches. Here, we present a Shewanella phage vB_SbaS_Y11 that contains an uncharacterized anti-CRISPR AcrVA2 gene and belongs to a potential virus family, Ranviridae. This study will enhance the knowledge about the genome, diversity, taxonomic classification, and global distribution of Shewanella phage populations.

Matched MeSH terms: Open Reading Frames
Fulltext Characterization and genomic analysis of a novel lytic phage vB_PstM_ZRG1 infecting Stutzerimonas stutzeri, representing a new viral genus, Elithevirus

Chen Y, Guo R, Liang Y, Luo L, Han Y, Wang H, et al.

Virus Res, 2023 Sep;334:199183.
PMID: 37499764 DOI: 10.1016/j.virusres.2023.199183

Stutzerimonas stutzeri is an opportunistic pathogen widely distributed in the environment and displays diverse metabolic capabilities. In this study, a novel lytic S. stutzeri phage, named vB_PstM_ZRG1, was isolated from the seawater in the East China Sea (29°09'N, 123°39'E). vB_PstM_ZRG1 was stable at temperatures ranging from -20°C to 65°C and across a wide range of pH values from 3 to 10. The genome of vB_PstM_ZRG1 was determined to be a double-stranded DNA with a genome size of 52,767 bp, containing 78 putative open reading frames (ORFs). Three auxiliary metabolic genes encoded by phage vB_PstM_ZRG1 were predicted, including Toll/interleukin-1 receptor (TIR) domain, proline-alanine-alanine-arginine (PAAR) protein and SGNH (Ser-Gly-Asn-His) family hydrolase, especially TIR domain is not common in isolated phages. Phylogenic and network analysis showed that vB_PstM_ZRG1 has low similarity to other phage genomes in the GenBank and IMG/VR database, and might represent a novel viral genus, named Elithevirus. Additionally, the distribution map results indicated that vB_PstM_ZRG1 could infect both extreme colds- and warm-type hosts in the marine environment. In summary, our finding provided basic information for further research on the relationship between S. stutzeri and their phages, and expanded our understanding of genomic characteristics, phylogenetic diversity and distribution of Elithevirus.

Matched MeSH terms: Open Reading Frames
Unearth of small open reading frames (sORFs) in drought stress transcriptome of Oryza sativa subsp. indica

Ong SN, Tan BC, Hanada K, Teo CH

Gene, 2023 Aug 20;878:147579.
PMID: 37336274 DOI: 10.1016/j.gene.2023.147579

Drought is a major abiotic stress that influences rice production. Although the transcriptomic data of rice against drought is widely available, the regulation of small open reading frames (sORFs) in response to drought stress in rice is yet to be investigated. Different levels of drought stress have different regulatory mechanisms in plants. In this study, drought stress was imposed on four-leaf stage rice, divided into two treatments, 40% and 30% soil moisture content (SMC). The RNAs of the samples were extracted, followed by the RNA sequencing analysis on their sORF expression changes under 40%_SMC and 30%_SMC, and lastly, the expression was validated through NanoString. A total of 122 and 143 sORFs were differentially expressed (DE) in 40%_SMC and 30%_SMC, respectively. In 40%_SMC, 69 sORFs out of 696 (9%) DEGs were found to be upregulated. On the other hand, 69 sORFs out of 449 DEGs (11%) were significantly downregulated. The trend seemed to be higher in 30%_SMC, where 112 (12%) sORFs were found to be upregulated from 928 significantly upregulated DEGs. However, only 8% (31 sORFs out of 385 DEGs) sORFs were downregulated in 30%_SMC. Among the identified sORFs, 110 sORFs with high similarity to rice proteome in the PsORF database were detected in 40%_SMC, while 126 were detected in 30%_SMC. The Gene Ontology (GO) enrichment analysis of DE sORFs revealed their involvement in defense-related biological processes, such as defense response, response to biotic stimulus, and cellular homeostasis, whereas enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that DE sORFs were associated with tryptophan and phenylalanine metabolisms. Several DE sORFs were identified, including the top five sORFs (OsisORF_3394, OsisORF_0050, OsisORF_3007, OsisORF_6407, and OsisORF_7805), which have yet to be characterised. Since these sORFs were responsive to drought stress, they might hold significant potential as targets for future climate-resilient rice development.

Matched MeSH terms: Open Reading Frames/genetics
Fulltext Psychrobacter Phage Encoding an Antibiotics Resistance Gene Represents a Novel Caudoviral Family

Wang H, Ren L, Liang Y, Zheng K, Guo R, Liu Y, et al.

Microbiol Spectr, 2023 Aug 17;11(4):e0533522.
PMID: 37272818 DOI: 10.1128/spectrum.05335-22

Psychrobacter is an important bacterial genus that is widespread in Antarctic and marine environments. However, to date, only two complete Psychrobacter phage sequences have been deposited in the NCBI database. Here, the novel Psychrobacter phage vB_PmaS_Y8A, infecting Psychrobacter HM08A, was isolated from sewage in the Qingdao area, China. The morphology of vB_PmaS_Y8A was characterized by transmission electron microscopy, revealing an icosahedral head and long tail. The genomic sequence of vB_PmaS_Y8A is linear, double-stranded DNA with a length of 40,226 bp and 44.1% G+C content, and encodes 69 putative open reading frames. Two auxiliary metabolic genes (AMGs) were identified, encoding phosphoadenosine phosphosulfate reductase and MarR protein. The first AMG uses thioredoxin as an electron donor for the reduction of phosphoadenosine phosphosulfate to phosphoadenosine phosphate. MarR regulates multiple antibiotic resistance mechanisms in Escherichia coli and is rarely found in viruses. No tRNA genes were identified and no lysogeny-related feature genes were detected. However, many similar open reading frames (ORFs) were found in the host genome, which may indicate that Y8A also has a lysogenic stage. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis indicate that vB_PmaS_Y8A contains a novel genomic architecture similar only to that of Psychrobacter phage pOW20-A, although at a low similarity. vB_PmaS_Y8A represents a new family-level virus cluster with 22 metagenomic assembled viral genomes, here named Minviridae. IMPORTANCE Although Psychrobacter is a well-known and important bacterial genus that is widespread in Antarctic and marine environments, genetic characterization of its phages is still rare. This study describes a novel Psychrobacter phage containing an uncharacterized antibiotic resistance gene and representing a new virus family, Minviridae. The characterization provided here will bolster current understanding of genomes, diversity, evolution, and phage-host interactions in Psychrobacter populations.

Matched MeSH terms: Open Reading Frames
Fulltext Characterization and Genomic Analysis of ssDNA Vibriophage vB_VpaM_PG19 within Microviridae, Representing a Novel Viral Genus

Guo R, Zheng K, Luo L, Liu Y, Shao H, Guo C, et al.

Microbiol Spectr, 2022 Aug 31;10(4):e0058522.
PMID: 35862991 DOI: 10.1128/spectrum.00585-22

Vibrio parahaemolyticus, a widespread marine bacterium, is responsible for a variety of diseases in marine organisms. Consumption of raw or undercooked seafood contaminated with V. parahaemolyticus is also known to cause acute gastroenteritis in humans. While numerous dsDNA vibriophages have been isolated so far, there have been few studies of vibriophages belonging to the ssDNA Microviridae family. In this study, a novel ssDNA phage, vB_VpaM_PG19 infecting V. parahaemolyticus, with a 5,572 bp ssDNA genome with a G+C content of 41.31% and encoded eight open reading frames, was isolated. Genome-wide phylogenetic analysis of the total phage isolates in the GenBank database revealed that vB_VpaM_PG19 was only related to the recently deposited vibriophage vB_VpP_WS1. The genome-wide average nucleotide homology of the two phages was 89.67%. The phylogenetic tree and network analysis showed that vB_VpaM_PG19 was different from other members of the Microviridae family and might represent a novel viral genus, together with vibriophage vB_VpP_WS1, named Vimicrovirus. One-step growth curves showed that vB_VpaM_PG19 has a short incubation period, suggesting its potential as an antimicrobial agent for pathogenic V. parahaemolyticus. IMPORTANCE Vibriophage vB_VpaM_PG19 was distant from other isolated microviruses in the phylogenetic tree and network analysis and represents a novel microviral genus, named Vimicrovirus. Our report describes the genomic and phylogenetic features of vB_VpaM_PG19 and provides a potential antimicrobial candidate for pathogenic V. parahaemolyticus.

Matched MeSH terms: Open Reading Frames
Fulltext Genome and Ecology of a Novel Alteromonas Podovirus, ZP6, Representing a New Viral Genus, Mareflavirus

Wang Z, Zhang F, Liang Y, Zheng K, Gu C, Zhang W, et al.

Microbiol Spectr, 2021 10 31;9(2):e0046321.
PMID: 34643440 DOI: 10.1128/Spectrum.00463-21

Alteromonas is a ubiquitous, abundant, copiotrophic and phytoplankton-associated marine member of the Gammaproteobacteria with a range extending from tropical waters to polar regions and including hadal zones. Here, we describe a novel Alteromonas phage, ZP6, that was isolated from surface coastal waters of Qingdao, China. ZP6 contains a linear, double-stranded, 38,080-bp DNA molecule with 50.1% G+C content and 47 putative open reading frames (ORFs). Three auxiliary metabolic genes were identified, encoding metal-dependent phosphohydrolase, diaminopurine synthetase, and nucleotide pyrophosphohydrolase. The first two ORFs facilitate the replacement of adenine (A) by diaminopurine (Z) in phage genomes and help phages to evade attack from host restriction enzymes. The nucleotide pyrophosphohydrolase enables the host cells to stop programmed cell death and improves the survival rate of the host in a nutrient-depleted environment. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis revealed that ZP6 is most closely related to Enhodamvirus but with low similarity (shared genes, <30%, and average nucleotide sequence identity, <65%); it is distinct from other bacteriophages. Together, these results suggest that ZP6 could represent a novel viral genus, here named Mareflavirus. Combining its ability to infect Alteromonas, its harboring of a diaminopurine genome-biosynthetic system, and its representativeness of an understudied viral group, ZP6 could be an important and novel model system for marine virus research. IMPORTANCE Alteromonas is an important symbiotic bacterium of phytoplankton, but research on its bacteriophages is still at an elementary level. Our isolation and genome characterization of a novel Alteromonas podovirus, ZP6, identified a new viral genus of podovirus, namely, Mareflavirus. The ZP6 genome, with a diaminopurine genome-biosynthetic system, is different from those of other isolated Alteromonas phages and will bring new impetus to the development of virus classification and provide important insights into novel viral sequences from metagenomic data sets.

Matched MeSH terms: Open Reading Frames
Fulltext House building tips (HBT) corpus dataset as a resource to discover Malay architectural ingenuity and identity

Zaini MF, Sarudin A, Muhammad MM, Osman Z, Mohamed Redzwan HF, Al-Muhsin MA

Data Brief, 2021 Jun;36:107013.
PMID: 33898671 DOI: 10.1016/j.dib.2021.107013

House Building Tips is the title of a classic text containing historical information on early house construction in Malay communities. These tips were written by a scholar with knowledge of house construction through observation of the surrounding environment. In Malaysia, written sources or records of house construction are scarce and underexposed. As such, this research was conducted to guarantee the written legacy of the construction of Malay houses. The purpose of this paper is to introduce a statistical data source of house building tips that is laden with Malay ingenuity and identity. The wordlists generated from this study can become a source of reference for the field of Malay architecture. Accordingly, this study utilises the quantitative method by applying the Linguistic Corpus Statistical Approach; these data utilise specific corpus development procedures, beginning with text collection, scanning and cleaning processes, text annotation, and data storing in plain text. Next, the data analysis procedure utilises a corpus software, LancsBox, to generate specialised wordlists. The bubble graphs are developed based on these wordlists through the Tableau software, and illustrate the most used lexical items with the raw and relative frequency values. This facilitates searches for, and the reading of, architectural words and architectural word references. These data represent written sources that need to be preserved and become points of reference concerning Malay architectural ingenuity and identity.

Matched MeSH terms: Reading
Membrane-bound Δ12 fatty acid desaturase (FAD12); From Brassica napus to E. coli expression system

Halim NFAA, Ali MSM, Leow ATC, Rahman RNZRA

Int J Biol Macromol, 2021 Jun 01;180:242-251.
PMID: 33737181 DOI: 10.1016/j.ijbiomac.2021.03.072

Fatty acid desaturase catalyzes the desaturation reactions by insertion of double bonds into the fatty acyl chain, producing unsaturated fatty acids. Though soluble fatty acid desaturases have been studied widely in advanced organisms, there are very limited studies of membrane fatty acid desaturases due to the difficulty of generating recombinant desaturase. Brassica napus is a rapeseed, which possesses a range of different membrane-bound desaturases capable of producing fatty acids including Δ3, Δ4, Δ8, Δ9, Δ12, and Δ15 fatty acids. The 1155 bp open reading frame of Δ12 fatty acid desaturase (FAD12) from Brassica napus codes for 383 amino acid residues with a molecular weight of 44 kDa. It was expressed in Escherichia coli at 37 °C in soluble and insoluble forms when induced with 0.5 mM IPTG. Soluble FAD12 has been purified using Ni2+-Sepharose affinity chromatography with a total protein yield of 0.728 mg/mL. Gas chromatography-mass spectrometry (GC-MS) analysis revealed that desaturase activity of FAD12 could produce linoleic acid from oleic acid at a retention time of 17.6 with a conversion rate of 47%. Characterization of purified FAD12 revealed the optimal temperature of FAD12 was 50 °C with 2 mM preferred substrate concentration of oleic acid. Analysis of circular dichroism (CD) showed FAD12 was made up of 47.3% and 0.9% of alpha-helix and β-sheet secondary structures. The predicted Tm value was 50.2 °C.

Matched MeSH terms: Open Reading Frames
Feasibility of manual bronchial branch reading technique in navigating conventional rEBUS bronchoscopy in the evaluation of peripheral pulmonary lesion

Kho SS, Nyanti LE, Chai CS, Chan SK, Tie ST

Clin Respir J, 2021 Jun;15(6):595-603.
PMID: 33113256 DOI: 10.1111/crj.13297

BACKGROUND: Although radial endobronchial ultrasound (rEBUS) is an important verification tool in guided bronchoscopy, a navigational route was not provided. Manual airway mapping allows the bronchoscopist to translate the bronchial branching in computed tomography (CT) into a comparable bronchoscopic road map. We aimed to explore the feasibility of this technique in navigating conventional rEBUS bronchoscopy in the localisation of peripheral pulmonary lesion by determining navigation success and diagnostic yield.
METHODS: Retrospective review of consecutive rEBUS bronchoscopy performed with a 6.2 mm conventional bronchoscope navigated via manual bronchial branch reading technique over 18 months.
RESULTS: Ninety-eight target lesions were included. Median lesion size was 2.67 cm (IQR 2.22-3.38) with 96.9% demonstrating positive CT bronchus sign. Majority (86.7%) of lesions were situated in between the third and fifth airway generations. Procedure was performed with endotracheal intubation in 43.9% and fluoroscopy in 72.4%. 98.9% of lesions were successfully navigated and verified by rEBUS following the pre-planned airway road map. Bidirectional guiding device was employed in 29.6% of cases. Clinical diagnosis was secured in 88.8% of cases, majority of which were malignant disease. The discrepancy between navigation success and diagnostic yield was 10.1%. Target PPL located within five airway generations was associated with better diagnostic yield (95.1% vs. 58.8%, P

Matched MeSH terms: Reading
Fulltext Complete mitochondrial genomes and phylogenetic relationships of the genera Nephila and Trichonephila (Araneae, Araneoidea)

Yong HS, Song SL, Chua KO, Wayan Suana I, Eamsobhana P, Tan J, et al.

Sci Rep, 2021 May 21;11(1):10680.
PMID: 34021208 DOI: 10.1038/s41598-021-90162-1

Spiders of the genera Nephila and Trichonephila are large orb-weaving spiders. In view of the lack of study on the mitogenome of these genera, and the conflicting systematic status, we sequenced (by next generation sequencing) and annotated the complete mitogenomes of N. pilipes, T. antipodiana and T. vitiana (previously N. vitiana) to determine their features and phylogenetic relationship. Most of the tRNAs have aberrant clover-leaf secondary structure. Based on 13 protein-coding genes (PCGs) and 15 mitochondrial genes (13 PCGs and two rRNA genes), Nephila and Trichonephila form a clade distinctly separated from the other araneid subfamilies/genera. T. antipodiana forms a lineage with T. vitiana in the subclade containing also T. clavata, while N. pilipes forms a sister clade to Trichonephila. The taxon vitiana is therefore a member of the genus Trichonephila and not Nephila as currently recognized. Studies on the mitogenomes of other Nephila and Trichonephila species and related taxa are needed to provide a potentially more robust phylogeny and systematics.

Matched MeSH terms: Open Reading Frames
Fulltext Knowledge of cardiovascular disease risk in rheumatoid arthritis patients before and after educational intervention from a Southeast Asia country: Malaysia

Teoh BC, Syed Sulaiman SA, Tan BE

Arch Rheumatol, 2021 Mar;36(1):63-71.
PMID: 34046570 DOI: 10.46497/ArchRheumatol.2021.7726

Objectives: This study aims to improve knowledge on cardiovascular disease (CVD) risk among rheumatoid arthritis (RA) patients using a multi- language leaflet tailored to our multi-ethnic patient population.
Patients and methods: This was a prospective study conducted in Hospital Pulau Pinang, Malaysia, between March 2015 and June 2015. Educational intervention was provided to 96 patients (11 males, 85 females; mean age 52.4±12.9 years; range, 20 to 83 years) who fulfilled the inclusion/exclusion criteria. Questionnaires to assess knowledge of CVD risk were given to patients to be answered before reading the informative leaflet, after one hour of intervention, and during their next follow-up three months from the intervention. Both the informative leaflet and questionnaires were prepared in English and then translated into Malay and Chinese languages to suit the need of local patients.
Results: Our results showed that RA patients had good knowledge at baseline regarding risk of smoking, hypertension, and hyperlipidemia on increasing CVD risk and that exercise would not damage their joints. However, they had low knowledge at baseline regarding the amount of exercise needed for lower CVD risks and risk of CVD with use of anti-inflammatory drugs in RA. Total knowledge score increased significantly from baseline immediately after educational intervention. However, total knowledge score decreased after three months compared to immediate post- intervention phase while it was still significantly higher compared to baseline. The improvement was most obvious for knowledge regarding anti- inflammatory drugs and CVD risk and knowledge regarding the number of flares and CVD risk. Our study did not find any significant association between demographic characteristics and traditional cardiovascular risk factors with knowledge of CVD risk.
Conclusion: Rheumatoid arthritis patients have low knowledge regarding their CVD risk related to their disease. The intervention of providing an informative leaflet effectively improved the knowledge of this group of patients on CVD risk particularly in the field related to RA-specific risk.

Matched MeSH terms: Reading
Fulltext MILLENIAL’S BEHAVIOUR AND ATTITUDE TOWARDS NATURAL COSMETICS: A CASE STUDY IN UNIVERSITI MALAYSIA TERENGGANU

SITI DIANA KAMILA NADIM, JARINA MOHD JANI

UMT Journal of Undergraduate Research, 2021;3(1):63-74.
MyJurnal

Investing in natural cosmetics contributes to the sustainability of natural resources in two ways – the emission of less harmful by-products, and the conservation of ecosystems through sustainable harvesting of resources. Therefore, studying students’ (millennials’) behaviour and attitude towards these products may help improve awareness-raising approaches on their benefits for local market acceptance. A study was conducted in Universiti Malaysia Terengganu (UMT), Malaysia with the aim to understand the current perception and habits of UMT students towards natural cosmetics and their readiness to convert to natural cosmetics. 521 responses were collected through an online survey that focused on three themes: Stage of Change, Decisional Balance Inventory, and Product Knowledge and Perception. The study found that most of the respondents (79%) claim to be using natural cosmetics, while only nine percent are not considering at all. Eighty-six percent of those users practice label reading habits although most respondents could not distinguish natural cosmetics from synthetic ones if solely based on personal knowledge and appearance of product. This proves that product design does influence customers’ purchasing behaviours. Moreover, results indicate that existing natural cosmetic users are quite likely to maintain the habit, while others are still indecisive. Meanwhile, label reading habits are quite likely to be maintained by many respondents. Hence, based on results, businesses should acknowledge that there is a demand in natural cosmetics among Malaysian millennials, and should increase their promotional activities, improve product design and affordability in order to grab consumers’ attention to switch from synthetic to natural cosmetics.

Matched MeSH terms: Reading
Emergency department discharge instruction for mild traumatic brain injury: Evaluation on readability, understandability, actionability and content

Abdul Rahman N', Nurumal MS, Awang MS, Mohd Shah ANS

Australas Emerg Care, 2020 Dec;23(4):240-246.
PMID: 32713770 DOI: 10.1016/j.auec.2020.06.005

INTRODUCTION: Emergency departments (EDs) routinely provide discharge instructions due to a large number of patients with mild traumatic brain injury (mTBI) being discharged home directly from ED. This study aims to evaluate the quality of available mTBI discharge instructions provided by EDs of Malaysia government hospitals.
METHODS: All 132 EDs were requested for a copy of written discharge instruction given to the patients. The mTBI discharge instructions were evaluated using the Patient Education Materials Assessment-Printable Tool (PEMAT-P) for understandability and actionability. Readability was measured using an online readability tool of Malay text. The content was compared against the discharge instructions recommended by established guidelines.
RESULTS: 49 articles were eligible for the study. 26 of the articles met the criteria of understandability, and 3 met the criteria for actionability. The average readability level met the ability of average adult. Most of the discharge instructions focused on emergency symptoms, and none contained post-concussion features.
CONCLUSION: Majority of the discharge instructions provided were appropriate for average people to read but difficult to understand and act upon. Important information was neglected in most discharge instructions. Thus, revision and future development of mTBI discharge instruction should consider health literacy demand and cognitive ability to process such information.

Matched MeSH terms: Reading
Complete genome sequences of two novel dicistroviruses detected in yellow crazy ants (Anoplolepis gracilipes)

Lee CC, Lin CY, Hsu HW, Yang CS

Arch Virol, 2020 Nov;165(11):2715-2719.
PMID: 32776255 DOI: 10.1007/s00705-020-04769-2

We report two novel RNA viruses from yellow crazy ants, (Anoplolepis gracilipes) detected using next-generation sequencing. The complete genome sequences of the two viruses were 10,662 and 8,238 nucleotides in length, respectively, with both possessing two open reading frames with three conserved protein domains. The genome organization is characteristic of members of the genus Triatovirus in the family Dicistroviridae. The two novel viruses were tentatively named "Anoplolepis gracilipes virus 1" and "Anoplolepis gracilipes virus 2" (AgrV-1 and AgrV-2). Phylogenetic analyses based on amino acid sequences of the non-structural polyprotein (ORF1) suggest that the two viruses are triatovirus-like viruses. This is the first report on the discovery of novel triatovirus-like viruses in yellow crazy ants with a description of their genome structure (two ORFs and conserved domains of RNA helicase, RNA-dependent RNA polymerase, and capsid protein), complete sequences, and viral prevalence across the Asia-Pacific region.

Matched MeSH terms: Open Reading Frames
Fulltext A Novel RNA Virus, Macrobrachium rosenbergii Golda Virus (MrGV), Linked to Mass Mortalities of the Larval Giant Freshwater Prawn in Bangladesh

Hooper C, Debnath PP, Biswas S, van Aerle R, Bateman KS, Basak SK, et al.

Viruses, 2020 10 02;12(10).
PMID: 33023199 DOI: 10.3390/v12101120

Mass mortalities of the larval stage of the giant freshwater prawn, Macrobrachium rosenbergii, have been occurring in Bangladesh since 2011. Mortalities can reach 100% and have resulted in an 80% decline in the number of hatcheries actively producing M. rosenbergii. To investigate a causative agent for the mortalities, a disease challenge was carried out using infected material from a hatchery experiencing mortalities. Moribund larvae from the challenge were prepared for metatranscriptomic sequencing. De novo virus assembly revealed a 29 kb single‑stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in the Nidovirales order. Primers were designed against the novel virus and used to screen cDNA from larvae sampled from hatcheries in the South of Bangladesh from two consecutive years. Larvae from all hatcheries screened from both years were positive by PCR for the novel virus, including larvae from a hatchery that at the point of sampling appeared healthy, but later experienced mortalities. These screens suggest that the virus is widespread in M. rosenbergii hatchery culture in southern Bangladesh, and that early detection of the virus can be achieved by PCR. The hypothesised protein motifs of Macrobrachium rosenbergii golda virus (MrGV) suggest that it is likely to be a new species within the Nidovirales order. Biosecurity measures should be taken in order to mitigate global spread through the movement of post-larvae within and between countries, which has previously been linked to other virus outbreaks in crustacean aquaculture.

Matched MeSH terms: Open Reading Frames
Quality and Readability of Web-based Arabic Health Information on Denture Hygiene: An Infodemiology Study

Alhajj MN, Mashyakhy M, Ariffin Z, Ab-Ghani Z, Johari Y, Salim NS

J Contemp Dent Pract, 2020 Sep 01;21(9):956-960.
PMID: 33568578

AIM: This study aimed to assess the quality and readability of the available health information on the net regarding denture hygiene.
MATERIALS AND METHODS: Three search engines (Google, Yahoo!, and Bing) were searched. The first 20 consecutive websites from each engine were obtained and checked for eligibility. For the quality of the websites, the Health on the Net Foundation Code of Conduct (HONcode), the DISCERN tool, the Journal of the American Medical Association (JAMA) Benchmarks, and Google PageRank were used for the assessment of the included websites. For readability, an online web tool was used, including well-known analyzing indices [Flesch Kincaid grade level (FKGL), Simple Measure of Gobbledygook (SMOG), and Flesch Reading Ease (FRE)]. The acceptable readability level was set to be ≥80.0 for the FRE and <7 for the FKGL and SMOG. The data were presented in frequencies and percentages.
RESULTS: Out of the 60 screened websites, 14 websites were eligible for analysis. There was only one (7.1%) website that had the HONcode seal. The mean score of all websites based on the DISCERN tool was 29.6 ± 12.1, with no website achieved the high score (≥65). Only one (7.1%) website scored >5 based on Google PageRank. Regarding JAMA benchmarks, all websites achieved a mean score of 2.57 ± 1.1. The mean grade level based on the FKGL was 8.4 ± 6.3. All websites had a score of <7 according to the SMOG index. The mean score of the readability ease index was 90.5 ± 16.4.
CONCLUSION: Most of the dental health information on denture hygiene available on the Arabic websites did not have the required level of quality, regardless of being readable and comprehensible by most of the general people.
CLINICAL SIGNIFICANCE: Directing the patients to the appropriate websites related to their cases is the responsibility of the dentists.

Matched MeSH terms: Reading*
Fulltext Knockdown of Tousled‑like kinase 1 inhibits survival of glioblastoma multiforme cells

Ibrahim K, Abdul Murad NA, Harun R, Jamal R

Int J Mol Med, 2020 Aug;46(2):685-699.
PMID: 32468002 DOI: 10.3892/ijmm.2020.4619

Glioblastoma multiforme (GBM) is an aggressive type of brain tumour that commonly exhibits resistance to treatment. The tumour is highly heterogenous and complex kinomic alterations have been reported leading to dysregulation of signalling pathways. The present study aimed to investigate the novel kinome pathways and to identify potential therapeutic targets in GBM. Meta‑analysis using Oncomine identified 113 upregulated kinases in GBM. RNAi screening was performed on identified kinases using ON‑TARGETplus siRNA library on LN18 and U87MG. Tousled‑like kinase 1 (TLK1), which is a serine/threonine kinase was identified as a potential hit. In vitro functional validation was performed as the role of TLK1 in GBM is unknown. TLK1 knockdown in GBM cells significantly decreased cell viability, clonogenicity, proliferation and induced apoptosis. TLK1 knockdown also chemosensitised the GBM cells to the sublethal dose of temozolomide. The downstream pathways of TLK1 were examined using microarray analysis, which identified the involvement of DNA replication, cell cycle and focal adhesion signalling pathways. In vivo validation of the subcutaneous xenografts of stably transfected sh‑TLK1 U87MG cells demonstrated significantly decreased tumour growth in female BALB/c nude mice. Together, these results suggested that TLK1 may serve a role in GBM survival and may serve as a potential target for glioma.

Matched MeSH terms: Open Reading Frames/genetics
Fulltext Positioning and Utilization of Information and Communication Technology in Community Pharmacies of Selangor, Malaysia: Cross-Sectional Study

Kc B, Lim D, Low CC, Chew C, Blebil AQ, Dujaili JA, et al.

JMIR Med Inform, 2020 Jul 08;8(7):e17982.
PMID: 32463787 DOI: 10.2196/17982

BACKGROUND: Information and communication technology (ICT) is an essential element of modern "smart" cities. These smart cities have integrated housing, marketplace, public amenities, services, business, and transportation via ICT. ICT is also now widely used in urban health care delivery.
OBJECTIVE: The aim of this study was to determine the positioning and roles of ICT in community pharmacies in the state of Selangor, Malaysia.
METHODS: A cross-sectional study was conducted from November 2018 to January 2019 across 9 different subdistricts in the state of Selangor, including Subang Jaya, Cheras, Puchong, Port Klang, Kota Kemuning, Selayang, Chow Kit, Ampang, and Seri Kembangan. A total of 90 community pharmacists were approached from the 9 subdistricts and invited to participate in the study.
RESULTS: Of the 90 community pharmacies approached, 60 agreed to participate in the study, representing a response rate of 67%. The majority (36/60, 60%) of the respondents were women, and more than half (32/60, 53%) of the community pharmacies were run by young adults (ie, 30 years old and younger). More than three-quarters of the community pharmacies (46/60, 77%) used electronic health records. Half of the community pharmacies used online social media platforms for advertising and promoting their pharmacies. The vast majority of the community pharmacies (55/60, 92%) were using modern electronic payment systems, and some were also using other new electronic payment methods. Moreover, most of the community pharmacies (41/60, 68%) were using software and programs for accounting and logistics purposes. In addition, 47/60 (78%) of the community pharmacies used a barcode reading system for medicines/health products, and 16/60 (27%) of the pharmacies had online stores, and consumers could buy medicines and health products from these pharmacies via their online portal. In addition, 20/60 (33%) of the community pharmacies used at least one of the common online business platforms available in Southeast Asia to sell products/medicines. The telephone was the most commonly used means of communication with patients, although some pharmacies also used email, WhatsApp, SMS text messaging, and other communication platforms.
CONCLUSIONS: This study showed that the majority of community pharmacies in Selangor, Malaysia are using ICT for different purposes. However, there is still limited use of mobile apps to provide health services. Overall, community pharmacies have been adopting ICT apps for pharmacy services but the rate of adoption is relatively slower than that in other sectors of Malaysia.

Matched MeSH terms: Reading
The effects of gender and academic achievement on reading fluency among Year 2 Malaysian school children

Abd Ghani A, Muslim NH, Zakaria MN

Int J Pediatr Otorhinolaryngol, 2020 May;132:109907.
PMID: 32018165 DOI: 10.1016/j.ijporl.2020.109907

OBJECTIVE: Language disorders can affect reading skills contributing to poor academic achievements. As such, it is vital for speech language pathologists to identify the potential language-based reading problems among children. To achieve this, specific reading assessments should be developed and studied. Thus, the present study aimed to determine the effects of gender and academic achievement on oral reading fluency (ORF) and silent reading fluency (SRF) among Year 2 Malaysian children.
METHODS: In this study that employed a comparative design, fifty-nine typically developing Malaysian children (24 boys, aged from 8 years, 0 months to 8 years, 11 months) were enrolled. They were chosen from three different classrooms (consisting of high achieving, medium achieving and low achieving students, respectively) in a primary school. Their ORF and SRF skills were assessed according to the established methods.
RESULTS: As revealed by two-way ANOVA results, both ORF and SRF scores were found to be comparable between boys and girls (p > 0.05). In contrast, ORF and SRF results between the three classrooms were significantly different from each other (p

Matched MeSH terms: Reading*

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