Displaying publications 41 - 60 of 82 in total

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  1. Wengert PC, Wong NH, Barton HA, Gan HM, Hudson AO, Savka MA
    BMC Res Notes, 2021 May 08;14(1):175.
    PMID: 33964980 DOI: 10.1186/s13104-021-05589-6
    OBJECTIVES: To characterize the bacterial community of Wind Cave's Madison aquifer through whole-genome sequencing, and to better understand the bacterial ecology by identifying genes involved in acyl-homoserine lactone (AHL) based quorum-sensing (QS) systems.

    RESULTS: Genome-based taxonomic classification revealed the microbial richness present in the pristine Madison aquifer. The strains were found to span eleven genera and fourteen species, of which eight had uncertain taxonomic classifications. The genomes of strains SD129 and SD340 were found to contain the archetypical AHL QS system composed of two genes, luxI and luxR. Surprisingly, the genomes of strains SD115, SD129, SD274 and SD316 were found to contain one to three luxR orphans (solos). Strain SD129, besides possessing an archetypical AHL QS luxI-luxR pair, also contained two luxR solos, while strain SD316 contained three LuxR solos and no luxI-luxR pairs. The ligand-binding domain of two LuxR solos, one each from strains SD129 and SD316, were found to contain novel substitutions not previously reported, thus may represent two LuxR orphans that detection and response to unknown self-produced signal(s), or to signal(s) produced by other organisms.

  2. Mahmood H, Habib M, Aslam W, Khursheed S, Fatima S, Aziz S, et al.
    BMC Res Notes, 2021 Sep 10;14(1):354.
    PMID: 34507605 DOI: 10.1186/s13104-021-05768-5
    OBJECTIVE: Diffuse Large B Cell Lymphoma (DLBCL) is the most common type of Non-Hodgkin Lymphoma (NHL). The aim of this study was to assess the clinico pathological characteristics of DLBCL specifically, among the affected individuals residing in Northern areas of Pakistan who had not been previously included in major lymphoma studies due to their remote location.

    RESULTS: Mean age of the patients was 49.7 years. Male: female ratio was 1.5:1. Primary site was lymph node in 99 (71.74%) patients, out of which, 36 (26.09%) patients had B symptoms and 19 (13.77%) patients had stage IV disease. 39 (28.26%) patients had primary extra nodal involvement, 4 (2.90%) patients had B symptoms and 3 (2.17%) had stage IV disease. Extra nodal sites involved in primary extra nodal DLBCL were gastrointestinal tract (GIT) 19 (48.72%), tonsils 6 (15.38%), spine 4 (10.26%), soft tissue swelling 3 (7.69%), parotid gland 2 (5.13%), thyroid 2 (5.13%) central nervous system (CNS) 1 (2.56), breast 1 (2.56%) and bone marrow 1 (2.56%). Our study revealed increased percentage of patients with nodal DLBCL in stage IV and with B symptoms. Few patients with primary extra nodal DLBCL had B symptoms and stage IV disease at presentation. GIT was the most common site of involvement in primary extra nodal DLBCL.

  3. Akita H, Kimura ZI, Yusoff MZM, Nakashima N, Hoshino T
    BMC Res Notes, 2017 Jul 06;10(1):249.
    PMID: 28683814 DOI: 10.1186/s13104-017-2565-1
    OBJECTIVE: A lignin-degrading bacterium, Burkholderia sp. CCA53, was previously isolated from leaf soil. The purpose of this study was to determine phenotypic and biochemical features of Burkholderia sp. CCA53.

    RESULTS: Multilocus sequence typing (MLST) analysis based on fragments of the atpD, gltD, gyrB, lepA, recA and trpB gene sequences was performed to identify Burkholderia sp. CCA53. The MLST analysis revealed that Burkholderia sp. CCA53 was tightly clustered with B. multivorans ATCC BAA-247T. The quinone and cellular fatty acid profiles, carbon source utilization, growth temperature and pH were consistent with the characteristics of B. multivorans species. Burkholderia sp. CCA53 was therefore identified as B. multivorans CCA53.

  4. Loch A, Bewersdorf JP, Kofink D, Ismail D, Abidin IZ, Veriah RS
    BMC Res Notes, 2017 Jul 17;10(1):291.
    PMID: 28716156 DOI: 10.1186/s13104-017-2617-6
    BACKGROUND: In a world of ever increasing health care costs, generic drugs represent a major opportunity to ensure access to essential medicines for people who otherwise would be unable to afford them. However, some clinicians and patients are still questioning the safety and effectiveness of generic formulations compared to the proprietary drugs necessitating further systematic research analyzing the generic drugs' efficacy. Our objective was to compare the lipid lowering effects of generic and branded atorvastatin.

    METHODS: This cross-sectional, retrospective cohort study was conducted at the University of Malaya Medical Centre from 1 May 2013 until 30 May 2013. We analyzed the lipid profiles (total cholesterol, LDL-cholesterol, HDL-cholesterol, triglycerides) of 629 patients before and at least 3 months after switching them from proprietary atorvastatin (Lipitor®) to generic atorvastatin (atorvastatin calcium from Ranbaxy Laboratories, Inc.). We also investigated if there was any difference in the effectiveness of both atorvastatin formulations in various ethnic groups.

    RESULTS: 266 patients were included in this study. When comparing the median values we found no statistically significant differences (Wilcoxon signed-rank test; p 

  5. Kho SS, Chan SK, Yong MC, Tie ST
    BMC Res Notes, 2017 Jul 21;10(1):304.
    PMID: 28732541 DOI: 10.1186/s13104-017-2635-4
    BACKGROUND: Massive hemoptysis is a common encounter in respiratory medicine. Bronchoscopy plays an important role in localizing the origin of bleeding, as well as endoscopic treatment of centrally located lesions. Endobronchial embolization is a novel technique enabling the management of hemoptysis arising even from peripheral lesions, via occlusion of the culprit bronchus, thereby securing the airway. Endobronchial Watanabe Spigot had been advocate in the treatment of bronchopleural fistula and the use of this novel technique had since then been expanded into the management of massive hemoptysis. To the best of our knowledge, this is the first reported case in Malaysia.

    CASE PRESENTATION: 78-year-old lady who presented with life-threatening hemoptysis leading rapidly to cardiac arrest upon arrival. Spontaneous circulation was restored after resuscitation with an urgent thoracic computed tomography angiogram revealed bleeding likely from the posterior basal segment of left lower lobe, with bronchiectatic changes. Urgent flexible bronchoscopy revealed airway flooding, with bleeding originating from the lingular and posterior-basal segment of the left lower lobe. Airway toileting was performed and two 7 mm Endobronchial Watanabe Spigots were plugged into the culprit bronchi. Urgent bronchial artery embolization was then attempted, but was unsuccessful. She was managed conservatively, as surgical resection was deemed high risk. The spigots were removed 4 days later uneventfully. There was no recurrence of hemoptysis, and patient remained well during 1-month follow up.

    CONCLUSIONS: The utmost priority in managing life-threatening hemoptysis is to prevent airway flooding. Endobronchial embolization with Endobronchial Watanabe Spigot is useful as a temporary measure before definitive therapy, or can itself be the main therapeutic player in the hemoptysis armament for high-risk patients.

  6. Abdullah NL, Gunasekaran R, Mohd-Zin SW, Lim BH, Maniam P, Mohd-Salleh AS, et al.
    BMC Res Notes, 2018 Jul 16;11(1):475.
    PMID: 30012199 DOI: 10.1186/s13104-018-3593-1
    OBJECTIVES: The Neural Tube Defects Research Group of University of Malaya was approached to analyze a tablet named TELSE, which may have resulted in a baby born with central nervous system malformation at the University of Malaya Medical Centre. In this animal experimental study, we investigated the content of TELSE and exposure of its contents that resulted in failure of primary neurulation.

    RESULTS: Liquid Chromatography Tandem Mass spectrophotometry analysis of the TELSE tablet confirmed the presence of trimethoprim as the active compound. The TELSE tablet-treated females produced significant numbers of embryos with exencephaly (n = 8, 36.4%, *P 

  7. Chew KS, van Merriënboer J, Durning SJ
    BMC Res Notes, 2016 Sep 17;9(1):445.
    PMID: 27639851 DOI: 10.1186/s13104-016-2249-2
    Although a clinician may have the intention of carrying out strategies to reduce cognitive errors, this intention may not be realized especially under heavy workload situations or following a period of interruptions. Implementing strategies to reduce cognitive errors in clinical setting may be facilitated by a portable mnemonic in the form of a checklist.
  8. Bunawan H, Yen CC, Yaakop S, Noor NM
    BMC Res Notes, 2017 Jan 26;10(1):67.
    PMID: 28126013 DOI: 10.1186/s13104-017-2379-1
    The chloroplastic trnL intron and the nuclear internal transcribed spacer (ITS) region were sequenced for 11 Nepenthes species recorded in Peninsular Malaysia to examine their phylogenetic relationship and to evaluate the usage of trnL intron and ITS sequences for phylogenetic reconstruction of this genus.
  9. Hii SYF, Ahmad N, Hashim R, Liow YL, Abd Wahab MA, Mohd Khalid MKN
    BMC Res Notes, 2018 Oct 25;11(1):760.
    PMID: 30359301 DOI: 10.1186/s13104-018-3868-6
    OBJECTIVE: There is a lack of study in Corynebacterium diphtheriae isolates in Malaysia. The alarming surge of cases in year 2016 lead us to evaluate the local clinical C. diphtheriae strains in Malaysia. We conducted single nucleotide polymorphism phylogenetic analysis on the core and pan-genome as well as toxin and diphtheria toxin repressor (DtxR) genes of Malaysian C. diphtheriae isolates from the year 1986-2016.

    RESULTS: The comparison between core and pan-genomic comparison showed variation in the distribution of C. diphtheriae. The local isolates portrayed a heterogenous trait and a close relationship between Malaysia's and Belarus's, Africa's and India's strains were observed. A toxigenic C. diphtheriae clone was noted to be circulating in the Malaysian population for nearly 30 years and from our study, the non-toxigenic and toxigenic C. diphtheriae strains can be differentiated significantly into two large clusters, A and B respectively. Analysis against vaccine strain, PW8 portrayed that the amino acid composition of toxin and DtxR in Malaysia's local strains are well-conserved and there was no functional defect noted. Hence, the change in efficacy of the currently used toxoid vaccine is unlikely to occur.

  10. Mohd Hanafiah K, Garcia ML, Barnes NC, Anderson DA
    BMC Res Notes, 2018 Oct 01;11(1):688.
    PMID: 30285838 DOI: 10.1186/s13104-018-3799-2
    OBJECTIVE: To conduct a proof-of-concept study on preferential binding of polymeric IgA (pIgA) using a novel recombinant rabbit/human chimeric secretory component (cSC) and preliminary assessment of the diagnostic potential of virus-specific pIgA in discriminating acute hepatitis A, E, and C (HAV, HEV, HCV) patients and uninfected controls using an indirect enzyme-linked immunoassay.

    RESULTS: cSC binds > 0.06 μg/ml of purified human and mouse pIgA with negligible cross-reactivity against IgM and IgA. Virus-specific pIgA was significantly higher in serum of acute HAV (n = 6) and HEV (n = 12) patients than uninfected samples (HEV: p 

  11. Ja'afar JN, Bhore SJ, Phua KK
    BMC Res Notes, 2018 Oct 29;11(1):766.
    PMID: 30373642 DOI: 10.1186/s13104-018-3870-z
    OBJECTIVE: Identification of Salmonella Typhi by conventional culture techniques is labour-intensive, time consuming, and lack sensitivity and specificity unlike high-throughput epidemiological markers that are highly specific but are not affordable for low-resource settings. SCAR, obtained from RAPD technique, is an affordable, reliable and reproducible method for developing genetic markers. Hence, this study investigated the use of SCAR as an alternative molecular epidemiological marker for easy identification of S. Typhi in low-resource settings.

    RESULTS: One hundred and twenty RAPD primers were screened through RAPD-PCR against a panel of common enterobacteriaceae for the best RAPD band pattern discrimination to develop SCAR primers that were used to develop a RAPD-SCAR PCR. Of this number, 10 were selected based on their calculated indices of discrimination. Four RAPD primers, SBSA02, SBSA03, SBSD08 and SBSD11 produced suitable bands ranging from 900 to 2500 bp. However, only SBSD11 was found to be specific for S. Typhi, and was cloned, sequenced and used to design new SCAR primers. The primers were used to amplify a panel of organisms to evaluate its specificity. However, the amplified regions were similar to other non-Typhi genomes denoting a lack of specificity of the primers as a marker for S. Typhi.

  12. Hajissa K, Muhajir AEMA, Eshag HA, Alfadel A, Nahied E, Dahab R, et al.
    BMC Res Notes, 2018 Oct 31;11(1):779.
    PMID: 30382901 DOI: 10.1186/s13104-018-3871-y
    OBJECTIVE: Schistosomiasis remains one of the most common parasitic diseases worldwide. This is a cross-sectional study aimed to determine the prevalence of schistosomiasis and its associated risk factors among primary school children in Um-Asher area. The study was conducted among 170 primary school students in Um-Asher area from November 2017 to February 2018. Urine and stool samples were collected and examined for schistosomiasis infections. Moreover, data on sociodemographic characteristics and associated risk factors were obtained using a questionnaire.

    RESULTS: The overall prevalence of Schistosoma haematobium was 12.9%, whereas that of Schistosoma mansoni was 2.95%. Additionally, the males had higher prevalence (60%) of S. mansoni than females (40%). However, both gender were equally infected with S. haematobium (50%). With regard to risk factors, distance of residence from water source and source of drinking water are relatively associated with the infection.

  13. Chew KS, Liaw SY, Ahmad Zahedi AZ, Wong SSL, Singmamae N, Kaushal DN, et al.
    BMC Res Notes, 2019 Oct 21;12(1):670.
    PMID: 31639035 DOI: 10.1186/s13104-019-4698-x
    OBJECTIVES: This paper describes the development and translation of a questionnaire purported to measure (1) the perception of the placement strategy of automated external defibrillator, (2) the perception on the importance of bystander cardiopulmonary resuscitation and automated external defibrillator (3) the perception on the confidence and willingness to apply these two lifesaving interventions as well as (4) the fears and concerns in applying these two interventions. For construct validation, exploratory factor analysis was performed using principal axis factoring and promax oblique rotation and confirmatory factor analysis performed using partial least square.

    RESULTS: Five factors with eigenvalue > 1 were identified. Pattern matrix analysis showed that all items were loaded into the factors with factor loading > 0.4. One item was subsequently removed as Cronbach's alpha > 0.9 which indicates redundancy. Confirmatory factor analysis demonstrated acceptable factor loadings except for one item which was subsequently removed. Internal consistency and discriminant validity was deemed acceptable with no significant cross-loading.

  14. Basabaeen AA, Abdelgader EA, BaHashwan OS, Babekir EA, Abdelateif NM, Bamusa SA, et al.
    BMC Res Notes, 2019 May 23;12(1):282.
    PMID: 31122288 DOI: 10.1186/s13104-019-4319-8
    OBJECTIVE: To investigate the ZAP-70 and CD38 expressions and their combined expressions in Sudanese B-CLL patients and their relationships with clinical and hematological characteristics as well as the disease staging at presentation.

    RESULTS: In the present cross-sectional descriptive study, analysis of ZAP-70 expression showed that 36/110 (32.7%) patients positively expressed ZAP-70 and insignificant higher presentation in intermediate and at advanced stages as well as no correlation was seen with hematological parameters and clinical features compared with negatively ZAP-70, on the other hand, 41/110 (37.3%) were CD38+ and no significant correlation was shown with the stage at presentation, clinical characteristics (except Splenomegaly, P = 0.02) and hematological parameters. However, in combined expressions of both ZAP-70 and CD38 together, 20/110 (18.2%) were concordantly ZAP-70+/CD38+, 53/110 (48.2%) concordantly ZAP-70-/CD38- and 37/110 (33.6%) either ZAP-70+ or CD38+, and these three groups showed insignificant correlation with clinical (except Splenomegaly, P = 0.03) and hematological parameters, and the stage at presentation. Our data showed the combined analysis of these two markers, lead to classify our patients into three subgroups (either concordant positive, negative or discordant expressions) with statistically insignificant correlation with clinical presentation (except Splenomegaly), hematological parameters and stage at presentation of B-CLL patients.

  15. Gan IN, Tan HS
    BMC Res Notes, 2019 Feb 21;12(1):97.
    PMID: 30791948 DOI: 10.1186/s13104-019-4124-4
    OBJECTIVES: Shigella is a human pathogen that causes shigellosis, an acute invasive intestinal infection. Recent studies in the model bacterium Escherichia coli (E. coli) provided evidence that small regulatory RNAs (sRNAs) can contribute to antimicrobial resistance or susceptibility. One of the sRNAs is SdsR, which increases sensitivity of E. coli against fluoroquinolone by repressing the drug efflux pump, TolC. However, no reports exist about the effect of SdsR on fluoroquinolone resistance in Shigella sonnei (S. sonnei). In this study, we established the effect of SdsR on the sensitivity of S. sonnei to norfloxacin.

    DATA DESCRIPTION: We tested the effects of SdsR and SdsRv2 on fluoroquinolone resistance in S. sonnei in vivo. SdsRv2 is a synthetic version which promotes higher binding stability to tolC mRNA. Overexpression of either SdsR or SdsRv2 lowers the expression of tolC mRNA. Interestingly, SdsR and SdsRv2 promote the growth of S. sonnei in the presence of a sub-inhibitory concentration of norfloxacin. Mutant carrying SdsRv2 showed the highest growth advantage. This phenotype is opposite to the effect of SdsR reported in E. coli. This study is an example that demonstrates the difference in the phenotypic effect of a highly conserved sRNA in two closely related bacteria.

  16. Mad' Atari MFB, Folta KM
    BMC Res Notes, 2019 Mar 15;12(1):144.
    PMID: 30876440 DOI: 10.1186/s13104-019-4117-3
    OBJECTIVE: The treatment of plant tissue with Agrobacterium tumefaciens is often a critical first step to both stable and transient plant transformation. In both applications bacterial suspensions are oftentimes physically introduced into plant tissues using hand-driven pressure from a needleless syringe. While effective, this approach has several drawbacks that limit reproducibility. Pressure must be provided with the syringe perfectly perpendicular to the tissue surface. The researcher must also attempt to provide even and consistent pressure, both within and between experimental replicates. These factors mean that the procedures do not always translate well between research groups or biological replicates.

    RESULTS: We have devised a method to introduce Agrobacterium suspensions into plant leaves with greater reproducibility. Using a decommissioned dissecting microscope as an armature, a syringe body with the bacterial suspension is mounted to the nosepiece. Gentle, even pressure is applied by rotating the focus knob. The treatment force is measured using a basic kitchen scale. The development of the Standardized Pressure Agrobacterium Infiltration Device (SPAID) provides a means to deliver consistent amounts of bacterial suspensions into plant tissues with the goal of increasing reproducibility between replicates and laboratories.

  17. Mohd Abd Razak MR, Norahmad NA, Md Jelas NH, Jusoh B, Muhammad A, Mohmad Misnan N, et al.
    BMC Res Notes, 2019 Apr 03;12(1):206.
    PMID: 30944031 DOI: 10.1186/s13104-019-4242-z
    OBJECTIVE: The purpose of this study was to profile and identify the endothelial cell biology related genes that are affected by dengue virus infection in the liver tissue of AG129 mice, with and without Carica papaya leaf juice treatment.

    RESULTS: The dengue fever mouse model was established by intraperitoneal inoculation of dengue virus, New Guinea C strain at 2 × 106 PFU. Daily oral administration of 1000 mg/kg freeze-dried C. papaya leaf juice (FCPLJ) was done starting from day 1 to day 3 post infection. The RNA was extracted from liver tissues harvested on day 4 post infection. The expression levels of 84 genes related to mouse endothelial cell biology were determined by qRT-PCR technique. Dengue virus infection upregulated 15 genes and downregulated two genes in the liver of AG129 mice. The FCPLJ treatment upregulated monocyte chemoattractant protein 1 and downregulated intercellular adhesion molecule 1, integrin beta 3 and fibronectin 1 genes during dengue virus infection. The data showed the potential effect of FCPLJ treatment on the expression profile of endothelial cell biology related genes in the liver of dengue virus infected-AG129 mice. Further proteomic studies are needed to determine the functional roles of the genes affected by FCPLJ treatment.

  18. Mussa A, Talib M, Mohamed Z, Hajissa K
    BMC Res Notes, 2019 Jun 11;12(1):334.
    PMID: 31186056 DOI: 10.1186/s13104-019-4361-6
    OBJECTIVE: Rapid diagnostic tests (RDTs) play a crucial role in the management and control of malaria infection. The histidine-rich protein 2 (PfHRP-2) based RDTs are the most commonly used RDTs for malaria diagnosis in Sudan. Deletion of pfhrp2 in Plasmodium falciparum genome affect the accuracy of PfHRP-2 based RDT kits. This study aimed to identify molecular variation of pfhrp2 among suspected malaria patients from different clinics in Omdurman, Sudan.

    RESULTS: A noticeable variation between the RDT (Alltest Biotech, China) and nPCR results was observed, for RDT 78% (46/59) were P. falciparum positive, 6.8% (4/59) were co-infected with both P. falciparum and Plasmodium vivax, 15.3% (9/59) were negative by the RDT. However, when the nPCR was applied only 44.1% (26/59) and 55.9% (33/59) was P. falciparum positive and negative respectively. The pfhrp2 was further amplified form all nPCR positive samples. Only 17 DNA samples were positive from the 26 positive P. falciparum, interestingly, variation in band sizes was observed and further confirmed by DNA sequencing, and sequencing analysis revealed a high-level of genetic diversity of the pfhrp2 gene in the parasite population from the study area. However, despite extreme sequence variation, diversity of PfHRP2 does not appear to affect RDT performance.

  19. Osman HA, Hamid MMA, Ahmad RB, Saleem M, Abdallah SA
    BMC Res Notes, 2020 Feb 10;13(1):65.
    PMID: 32041645 DOI: 10.1186/s13104-020-4933-5
    OBJECTIVE: Alpha-thalassemia is a genetic disorder characterized by deletions of one or more α globin genes that result in deficient of α globin chains reducing haemoglobin concentration. The study aimed to screen 97 patients with microcytosis and hypochromasia for the 3.7 and 4.2 alpha thalassemia deletion mutations.

    RESULTS: Out of 97 patients screened, only 7 were carriers for the 3.7 deletion and all patients were negative for the 4.2 deletion. The 3.7 deletion was found in Foor, Hawsa and Rezagat Sudanese tribes. In the carriers of the 3.7 deletion, Red Blood Cells and Haematocrit were significantly increased. The Red Blood Cells were 7.23 ± 0.78 × 1012/L in adult males and 7.21 ± 0.67 × 1012/L in adult females while in children were 5.07 ± 0.87 × 1012/L. The mean cell volume and mean cell haemoglobin were significantly decreased, but the mean cell haemoglobin concentration slightly decreased. Haemoglobin levels didn't revealed statistically significant decrease in adult males (11.7 ± 0.57 g/dL) and adult females (11.25 ± 0.64 g/dL), while in children were (11.6 ± 2.95 g/dL). Haemoglobin electrophoresis revealed two patients of the 3.7 and 4.2 negative were carriers for β-thalassemia. The study concluded that α3.7 deletion has frequency of 0.07 in Sudanese with hypochromasia and microcytosis.

  20. Kee QT, Abd Rahman MH, Mohamad Fadzil N, Mohammed Z, Shahar S
    BMC Res Notes, 2021 Oct 24;14(1):395.
    PMID: 34689826 DOI: 10.1186/s13104-021-05813-3
    OBJECTIVE: Near visual impairment (VI) is a common disability in an aging population. Near vision is crucial in activity of daily living including reading, smartphone and computer use and meal preparation. This study was conducted to determine the association between near visual acuity (VA) and contrast sensitivity (CS) with activity of daily living (ADL) among visually impaired older adults.

    RESULTS: A total of 208 participants aged  ≥  60 were recruited from the population-based longitudinal study on neuroprotective model for healthy longevity. Habitual near VA and CS were measured using Lighthouse near VA chart and Pelli-Robson CS chart, respectively. Lawton instrumental activities of daily living (IADL) was used to assess ADL. There are 41.8% participants with near visual impairment and 28.7% among them had IADL disability. Independent t test showed significant lower mean IADL score among visually impaired participants [t(206)  =  2.03, p  =  0.04]. IADL score significantly correlated with near VA (r  =   - 0.21, p  =  0.05) but not with CS (r  =   - 0.14, p = 0.21). Near VA (B  =   - 0.44, p  =  0.03) and age (B  =   - 0.07, p  =  0.01) significantly predicted IADL. The findings show poorer VA renders higher IADL disability, which may necessitate interventions to improve ADL among visually impaired older adults.

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