Posterior corneal surface stability after femtosecond laser-assisted in situ keratomileusis in patients with myopia and myopic astigmatism.

Purpose: To evaluate the variation and stability of the posterior cornea surface parameters (posterior cornea curvature [PCC], posterior cornea astigmatism [PCA], and posterior cornea elevation [PCE]) after femtosecond laser-assisted in situ keratomileusis (LASIK) in patients with myopia and myopic astigmatism over a period of 6 months or longer.

Methods: This retrospective study comprised 284 right eyes. Patients aged 18 years or older with myopia up to -12.

SIEVE: One-stop differential expression, variability, and skewness analyses using RNA-Seq data.

Motivation: RNA-Seq data analysis is commonly biased towards detecting differentially expressed genes and insufficiently conveys the complexity of gene expression changes between biological conditions. This bias arises because discrete models of RNA-Seq count data cannot fully characterize the mean, variance, and skewness of gene expression distribution using independent model parameters. A unified framework that simultaneously tests for differential expression, variability, and skewness is needed to realize the full potential of RNA-Seq data analysis in a systems biology context.

Diverse impacts of red palm olein, extra virgin coconut oil and extra virgin olive oil on cardiometabolic risk markers in individuals with central obesity: a randomised trial.

Purpose: Dietary fats with an abundance of phytonutrients have garnered public attention beyond fatty acids per se. This study was set to investigate the impact of consuming diets with red palm olein (RPOO), extra virgin coconut oil (EVCO) and extra virgin olive oil (EVOO, as a control) on cardiometabolic risk biomarkers and lipid profile.

Methods: We recruited a total of 156 individuals with central obesity, aged 25-45 years, with waist circumference ≥ 90 cm for men and ≥ 80 cm for women in a parallel single-blind 3-arm randomised controlled trial.

clrDV: a differential variability test for RNA-Seq data based on the skew-normal distribution.

Background: Pathological conditions may result in certain genes having expression variance that differs markedly from that of the control. Finding such genes from gene expression data can provide invaluable candidates for therapeutic intervention. Under the dominant paradigm for modeling RNA-Seq gene counts using the negative binomial model, tests of differential variability are challenging to develop, owing to dependence of the variance on the mean.

Size-age population structure of an endangered and anthropogenically introgressed northern Adriatic population of marble trout ( Cuv.): insights for its conservation and sustainable exploitation.

Salmonid species are main actors in the Italian socio-ecological landscape of inland fisheries. We present novel data on the size-age structure of one of the remnant Italian populations of the critically endangered marble trout , which co-occurs with other stocked non-native salmonids in a large glacial river of the Lake Maggiore basin (Northern Italy-Southern Switzerland). Like other Italian native trout populations, the Toce River marble trout population is affected by anthropogenic introgression with the non-native brown trout .

On the classification of simple and complex biological images using Krawtchouk moments and Generalized pseudo-Zernike moments: a case study with fly wing images and breast cancer mammograms.

In image analysis, orthogonal moments are useful mathematical transformations for creating new features from digital images. Moreover, orthogonal moment invariants produce image features that are resistant to translation, rotation, and scaling operations. Here, we show the result of a case study in biological image analysis to help researchers judge the potential efficacy of image features derived from orthogonal moments in a machine learning context.

Ocular surface disease in psoriatic patients in a developing country.

Purpose: To evaluate ocular surface changes among patients with psoriasis in Malaysia, a developing country in Southeast Asia.

Methods: An interdisciplinary case-control study (60 psoriasis patients and 40 control subjects) to look at the differences in ocular surface manifestations between patients with psoriasis and a group of age-, gender- and ethnicity-matched healthy controls.

Results: One hundred and twenty eyes of 60 patients with psoriasis and 80 eyes of 40 healthy controls without psoriasis were included in the study.

Random forests for predicting species identity of forensically important blow flies (Diptera: Calliphoridae) and flesh flies (Diptera: Sarcophagidae) using geometric morphometric data: Proof of concept.

Wing shape variation has been shown to be useful for delineating forensically important fly species in two Diptera families: Calliphoridae and Sarcophagidae. Compared to DNA-based identification, the cost of geometric morphometric data acquisition and analysis is relatively much lower because the tools required are basic, and stable softwares are available. However, to date, an explicit demonstration of using wing geometric morphometric data for species identity prediction in these two families remains lacking.

Linking the effects of helminth infection, diet and the gut microbiota with human whole-blood signatures.

Helminth infection and dietary intake can affect the intestinal microbiota, as well as the immune system. Here we analyzed the relationship between fecal microbiota and blood profiles of indigenous Malaysians, referred to locally as Orang Asli, in comparison to urban participants from the capital city of Malaysia, Kuala Lumpur. We found that helminth infections had a larger effect on gut microbial composition than did dietary intake or blood profiles.

Enrichment of gut-derived Fusobacterium is associated with suboptimal immune recovery in HIV-infected individuals.

We explored the gut microbiota profile among HIV-infected individuals with diverse immune recovery profiles following long-term suppressive ART and investigated the relationship between the altered bacteria with markers of immune dysfunction. The microbiota profile of rectal swabs from 26 HIV-infected individuals and 20 HIV-uninfected controls were examined. Patients were classified as suboptimal responders, sIR (n = 10, CD4 T-cell <350 cells/ul) and optimal responders, oIR (n = 16, CD4 T-cell >500 cells/ul) after a minimum of 2 years on suppressive ART.

Esophageal squamous cell carcinomas in a Malaysian cohort show a lack of association with human papillomavirus.

Objective: With an age-standardized incidence rate of 2 per 100 000, esophageal cancer is not common among Malaysians, but they are nevertheless important due to its poor prognosis. The study is to clarify whether the human papillomavirus (HPV) is associated with esophageal cancer in Malaysians as there has been no report to date on this in Malaysians and other South East Asians.

Methods: Altogether 67 esophageal squamous cell carcinomas histologically diagnosed between 1 January 2004 and 31 December 2014 at the Department of Pathology, University of Malaya Medical Center, Malaysia were considered for HPV analysis using two commercially available methods, polymerase chain reaction with flow-through hybridization (21 HPV GenoArray Diagnostic Kit) and multiplex real-time polymerase chain reaction (Anyplex II HPV28 Detection).

Dosage-dependent reduction of macular pigment optical density in female breast cancer patients receiving tamoxifen adjuvant therapy.

It is now increasingly common for breast cancer patients to receive adjuvant tamoxifen therapy for a period of up to 10 years. As survival rate increases, managing tamoxifen ocular toxicities is important for patients' quality of life. Macular pigments in photoreceptor cells protect against free radical damage, which can cause macular degeneration.

CORNAS: coverage-dependent RNA-Seq analysis of gene expression data without biological replicates.

Background: In current statistical methods for calling differentially expressed genes in RNA-Seq experiments, the assumption is that an adjusted observed gene count represents an unknown true gene count. This adjustment usually consists of a normalization step to account for heterogeneous sample library sizes, and then the resulting normalized gene counts are used as input for parametric or non-parametric differential gene expression tests. A distribution of true gene counts, each with a different probability, can result in the same observed gene count.

DeSigN: connecting gene expression with therapeutics for drug repurposing and development.

Background: The drug discovery and development pipeline is a long and arduous process that inevitably hampers rapid drug development. Therefore, strategies to improve the efficiency of drug development are urgently needed to enable effective drugs to enter the clinic. Precision medicine has demonstrated that genetic features of cancer cells can be used for predicting drug response, and emerging evidence suggest that gene-drug connections could be predicted more accurately by exploring the cumulative effects of many genes simultaneously.

Germline APOBEC3B deletion is associated with breast cancer risk in an Asian multi-ethnic cohort and with immune cell presentation.

Background: APOBEC3B is a cytosine deaminase implicated in immune response to viral infection, cancer predisposition and carcinogenesis. Germline APOBEC3B deletion is more common in East Asian women and confers a modest risk to breast cancer in both East Asian and Caucasian women. Analysis of tumour samples from women of European descent has shown that germline APOBEC3B deletion is associated with an increased propensity to develop somatic mutations and with an enrichment for immune response-related gene sets.

Monogenean anchor morphometry: systematic value, phylogenetic signal, and evolution.

Background. Anchors are one of the important attachment appendages for monogenean parasites. Common descent and evolutionary processes have left their mark on anchor morphometry, in the form of patterns of shape and size variation useful for systematic and evolutionary studies.

Getting the most out of RNA-seq data analysis.

Background. A common research goal in transcriptome projects is to find genes that are differentially expressed in different phenotype classes. Biologists might wish to validate such gene candidates experimentally, or use them for downstream systems biology analysis.

Gross mismatch between thermal tolerances and environmental temperatures in a tropical freshwater snail: climate warming and evolutionary implications.

The relationship between acute thermal tolerance and habitat temperature in ectotherm animals informs about their thermal adaptation and is used to assess thermal safety margins and sensitivity to climate warming. We studied this relationship in an equatorial freshwater snail (Clea nigricans), belonging to a predominantly marine gastropod lineage (Neogastropoda, Buccinidae). We found that tolerance of heating and cooling exceeded average daily maximum and minimum temperatures, by roughly 20°C in each case.

Spectral-domain optical coherence tomography evaluation of postoperative cystoid macular oedema following phacoemulsification with intraoperative complication.

Background: To report the rate of cystoid macular oedema (CMO) as detected by spectral-domain optical coherence tomography (SD-OCT) after intraoperative complication during phacoemulsification. The secondary objectives include comparing mean macular thickness and best-corrected visual acuity (BCVA) between those who developed postoperative CMO against those who did not.

Methods: This is a prospective cohort study conducted in a tertiary hospital between July 2009 and June 2010.

A phylogenomic approach to bacterial subspecies classification: proof of concept in Mycobacterium abscessus.

Background: Mycobacterium abscessus is a rapidly growing mycobacterium that is often associated with human infections. The taxonomy of this species has undergone several revisions and is still being debated. In this study, we sequenced the genomes of 12 M.

Comparative analysis of viral genomes from acute and chronic hepatitis B reveals novel variants associated with a lower rate of chronicity.

Infection with the hepatitis B virus (HBV) may lead to an acute or chronic infection. It is generally accepted that the clinical outcome of infection depends on the balance between host immunity and viral survival strategies. In order to persist, the virus needs to have a high rate of replication and some immune-escape capabilities.

An age-adjusted seroprevalence study of Toxoplasma antibody in a Malaysian ophthalmology unit.

Toxoplasma gondii is a public health risk in developing countries, especially those located in the tropics. Widespread infection may inflict a substantial burden on state resources, as patients can develop severe neurological defects and ocular diseases that result in lifelong loss of economic independence. We tested sera for IgG antibody from 493 eye patients in Malaysia.

Plasma, aqueous and vitreous homocysteine levels in proliferative diabetic retinopathy.

Background/aims: To compare homocysteine (Hcy) concentration in the blood plasma, vitreous and aqueous of eyes with proliferative diabetic retinopathy (PDR) against control, and to investigate associations between Hcy concentration in blood plasma with that of aqueous and vitreous in these two groups.

Methods: Blood plasma, aqueous and vitreous samples were collected during combined cataract and pars plana vitrectomy from 20 eyes with PDR and 21 eyes of patients without diabetes mellitus. Hcy concentration in the samples was determined by chemiluminescent microparticle immunoassay.