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Fulltext IntFOLD: an integrated web resource for high performance protein structure and function prediction

McGuffin LJ, Adiyaman R, Maghrabi AHA, Shuid AN, Brackenridge DA, Nealon JO, et al.

Nucleic Acids Res, 2019 07 02;47(W1):W408-W413.
PMID: 31045208 DOI: 10.1093/nar/gkz322

The IntFOLD server provides a unified resource for the automated prediction of: protein tertiary structures with built-in estimates of model accuracy (EMA), protein structural domain boundaries, natively unstructured or disordered regions in proteins, and protein-ligand interactions. The component methods have been independently evaluated via the successive blind CASP experiments and the continual CAMEO benchmarking project. The IntFOLD server has established its ranking as one of the best performing publicly available servers, based on independent official evaluation metrics. Here, we describe significant updates to the server back end, where we have focused on performance improvements in tertiary structure predictions, in terms of global 3D model quality and accuracy self-estimates (ASE), which we achieve using our newly improved ModFOLD7_rank algorithm. We also report on various upgrades to the front end including: a streamlined submission process, enhanced visualization of models, new confidence scores for ranking, and links for accessing all annotated model data. Furthermore, we now include an option for users to submit selected models for further refinement via convenient push buttons. The IntFOLD server is freely available at: http://www.reading.ac.uk/bioinf/IntFOLD/.
Fulltext Fitness level and body composition indices: cross-sectional study among Malaysian adolescent

Hanifah RA, Majid HA, Jalaludin MY, Al-Sadat N, Murray LJ, Cantwell M, et al.

BMC Public Health, 2014;14 Suppl 3:S5.
PMID: 25436933 DOI: 10.1186/1471-2458-14-S3-S5

The importance of fitness level on the well-being of children and adolescent has long been recognised. The aim of this study was to investigate the fitness level of school-going Malaysian adolescent, and its association with body composition indices.
Fulltext The effectiveness of a life style modification and peer support home blood pressure monitoring in control of hypertension: protocol for a cluster randomized controlled trial

Su TT, Majid HA, Nahar AM, Azizan NA, Hairi FM, Thangiah N, et al.

BMC Public Health, 2014;14 Suppl 3:S4.
PMID: 25436830 DOI: 10.1186/1471-2458-14-S3-S4

Death rates due to hypertension in low and middle income countries are higher compared to high income countries. The present study is designed to combine life style modification and home blood pressure monitoring for control of hypertension in the context of low and middle income countries.
Association between self-reported physical activity and indicators of body composition in Malaysian adolescents

Su TT, Sim PY, Nahar AM, Majid HA, Murray LJ, Cantwell MM, et al.

Prev Med, 2014 Oct;67:100-5.
PMID: 25016043 DOI: 10.1016/j.ypmed.2014.07.001

BACKGROUND: Obesity and lack of physical activity are fast becoming a concern among Malaysian adolescents.
OBJECTIVE: This study aims to assess physical activity levels among Malaysian adolescents and investigate the association between physical activity levels and body composition such as body mass index (BMI), waist circumference (WC) and percentage of body fat.
SUBJECTS AND METHODS: 1361 school-going 13 year old multi-ethnic adolescents from population representative samples in Malaysia were involved in our study. Self-reported physical activity levels were assessed using the validated Malay version of the Physical Activity Questionnaire for Older Children (PAQ-C). Height, weight, body fat composition and waist circumference (WC) were measured. Data collection period was from March to May 2012.
RESULTS: 10.8% of the males and 7.4% of the females were obese according to the International Obesity Task Force standards. A majority of the adolescents (63.9%) were physically inactive. There is a weak but significant correlation between physical activity scores and the indicators of obesity. The adjusted coefficient for body fatness was relatively more closely correlated to physical activity scores followed by waist circumference and lastly BMI.
CONCLUSION: This study demonstrates that high physical activity scores were associated with the decreased precursor risk factors of obesity.
Fulltext Prior autoimmune disease and risk of monoclonal gammopathy of undetermined significance and multiple myeloma: a systematic review

McShane CM, Murray LJ, Landgren O, O'Rorke MA, Korde N, Kunzmann AT, et al.

Cancer Epidemiol Biomarkers Prev, 2014 Feb;23(2):332-42.
PMID: 24451437 DOI: 10.1158/1055-9965.EPI-13-0695

BACKGROUND: Several observational studies have investigated autoimmune disease and subsequent risk of monoclonal gammopathy of undetermined significance (MGUS) and multiple myeloma. Findings have been largely inconsistent and hindered by the rarity and heterogeneity of the autoimmune disorders investigated. A systematic review of the literature was undertaken to evaluate the strength of the evidence linking prior autoimmune disease and risk of MGUS/multiple myeloma.
METHODS: A broad search strategy using key terms for MGUS, multiple myeloma, and 50 autoimmune diseases was used to search four electronic databases (PubMed, Medline, Embase, and Web of Science) from inception through November 2011.
RESULTS: A total of 52 studies met the inclusion criteria, of which 32 were suitably comparable to perform a meta-analysis. "Any autoimmune disorder" was associated with an increased risk of both MGUS [n = 760 patients; pooled relative risk (RR) 1.42; 95% confidence interval (CI), 1.14-1.75] and multiple myeloma (n>2,530 patients; RR 1.13, 95% CI, 1.04-1.22). This risk was disease dependent with only pernicious anemia showing an increased risk of both MGUS (RR 1.67; 95% CI, 1.21-2.31) and multiple myeloma (RR 1.50; 95% CI, 1.25-1.80).
CONCLUSIONS: Our findings, based on the largest number of autoimmune disorders and patients with MGUS/multiple myeloma reported to date, suggest that autoimmune diseases and/or their treatment may be important in the etiology of MGUS/multiple myeloma. The strong associations observed for pernicious anemia suggest that anemia seen in plasma cell dyscrasias may be of autoimmune origin.
IMPACT: Underlying mechanisms of autoimmune diseases, general immune dysfunction, and/or treatment of autoimmune diseases may be important in the pathogenesis of MGUS/multiple myeloma.
Fulltext Correction to: The effectiveness of a life style modification and peer support home blood pressure monitoring in control of hypertension: protocol for a cluster randomized controlled trial

Su TT, Majid HA, Nahar AM, Azizan NA, Hairi FM, Thangiah N, et al.

BMC Public Health, 2017 11 06;17(1):864.
PMID: 29110641 DOI: 10.1186/s12889-017-4862-y

After publication of the article [1], it has been brought to our attention that the methodology outlined in the original article was not able to be fully carried out. The article planned a two armed randomized control trial. However, due to a lower response than expected and one housing complex dropping out from the study, the method was changed to pre- and post-intervention with no control group. All other methods were conducted as outlined in the original article.
Fulltext First DNA metabarcoding diet assessment on the critically endangered Tricolour Langur, Presbytischrysomelascruciger

Tingga RCT, Liam J, Deli B, Anuar ML, Ampeng A, Md-Zain BM

Biodivers Data J, 2024;12:e124990.
PMID: 39015797 DOI: 10.3897/BDJ.12.e124990

Presbytischrysomelascruciger or also known as the Tricolour langur-is rare, endemic to Sarawak and Kalimantan in Borneo and classified as a critically endangered subspecies. The current P.c.cruciger population size is uncertain because the numbers are continuously decreasing. At present, there is no comprehensive scientific report on P.c.cruciger in Sarawak, although this subspecies is known to inhabit Maludam area. Recent first sighting of P.c.cruciger in Jemoreng Sarawak presents a research opportunity to study its feeding from a molecular ecology perspective. Herein, we report the first findings on the dietary intake of P.c.cruciger using a high-throughput DNA metabarcoding approach. We emphasise the diet intake of P.c.cruciger from Jemoreng Protected Forest in Sarawak using DNA metabarcoding of the trnL region. Preliminary findings revealed 11 amplicon sequence variants (ASV) classified into one phylum, four classes, four orders, four families, three genera and three plant species. Fibraureatinctoria (akar kuning; Family Menispermaceae), Poikilospermumsuaveolens (akar jangkang; Family Urticaceae) and Litchichinensis (lychee; Family Sapindaceae) were the three main plant species that were consumed by P.c.cruciger. Understanding the dietary intake of P.c.cruciger is of paramount importance for their conservation and management of the habitat areas where their population resides.
Fulltext First Bornean orangutan sighting in Usun Apau National Park, Sarawak

Ampeng A, Liam J, Simpson B, Traelholt C, Md Nor S, Abdan-Saleman MSB, et al.

Biodivers Data J, 2021;9:e60753.
PMID: 33531863 DOI: 10.3897/BDJ.9.e60753

Wildlife surveys were conducted in Usun Apau National Park (UANP), Sarawak from Oct 2017 to Oct 2020. This was the first attempt to document fauna diversity in Usun Apau National Park on the UANP plateau at 1200-1400 m a.s.l. On 17 September 2020, 10 AM, we observed an orangutan individual, Pongo pygmaeus, over a period of one minute at Libut Camp UANP (E: 114039'.546, N: 2052'36.44) at 1,020 m a.s.l. We also recorded four nests and orangutan vocalisation twice. This observation is important for Bornean orangutan conservation as this was the first orangutan sighting in UANP and well outside the species distribution range for in Sarawak.