Clustering Algorithms: Their Application to Gene Expression Data

Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Therefore, the use of clustering techniques is a first step toward addressing these challenges, which is essential in the data mining process to reveal natural structures and iden-tify interesting patterns in the underlying data. The clustering of gene expression data has been proven to be useful in making known the natural structure inherent in gene expression data, understanding gene functions, cellular processes, and subtypes of cells, mining useful information from noisy data, and understanding gene regulation. The other benefit of clustering gene expression data is the identification of homology, which is very important in vaccine design. This review examines the various clustering algorithms applicable to the gene expression data in order to discover and provide useful knowledge of the appropriate clustering technique that will guarantee stability and high degree of accuracy in its analysis procedure

Human infection challenge in the pandemic era and beyond, HIC-Vac annual meeting report, 2022

HIC-Vac is an international network of researchers dedicated to developing human infection challenge studies to accelerate vaccine development against pathogens of high global impact. The HIC-Vac Annual Meeting (3rd and 4th November 2022) brought together stakeholders including researchers, ethicists, volunteers, policymakers, industry partners, and funders with a strong representation from low- and middle-income countries. The network enables sharing of research findings, especially in endemic regions. Discussions included pandemic preparedness and the role of human challenge to accelerate vaccine development during outbreak, with industry speakers emphasising the great utility of human challenge in vaccine development. Public consent, engagement, and participation in human challenge studies were addressed, along with the role of embedded social science and empirical studies to uncover social, ethical, and regulatory issues around human infection challenge studies. Study volunteers shared their experiences and motivations for participating in studies. This report summarises completed and ongoing human challenge studies across a variety of pathogens and demographics, and addresses other key issues discussed at the meeting

The global burden of cancer attributable to risk factors, 2010–19: a systematic analysis for the Global Burden of Disease Study 2019

BACKGROUND: Understanding the magnitude of cancer burden attributable to potentially modifiable risk factors is crucial for development of effective prevention and mitigation strategies. We analysed results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 to inform cancer control planning efforts globally. METHODS: The GBD 2019 comparative risk assessment framework was used to estimate cancer burden attributable to behavioural, environmental and occupational, and metabolic risk factors. A total of 82 risk–outcome pairs were included on the basis of the World Cancer Research Fund criteria. Estimated cancer deaths and disability-adjusted life-years (DALYs) in 2019 and change in these measures between 2010 and 2019 are presented. FINDINGS: Globally, in 2019, the risk factors included in this analysis accounted for 4·45 million (95% uncertainty interval 4·01–4·94) deaths and 105 million (95·0–116) DALYs for both sexes combined, representing 44·4% (41·3–48·4) of all cancer deaths and 42·0% (39·1–45·6) of all DALYs. There were 2·88 million (2·60–3·18) risk-attributable cancer deaths in males (50·6% [47·8–54·1] of all male cancer deaths) and 1·58 million (1·36–1·84) risk-attributable cancer deaths in females (36·3% [32·5–41·3] of all female cancer deaths). The leading risk factors at the most detailed level globally for risk-attributable cancer deaths and DALYs in 2019 for both sexes combined were smoking, followed by alcohol use and high BMI. Risk-attributable cancer burden varied by world region and Socio-demographic Index (SDI), with smoking, unsafe sex, and alcohol use being the three leading risk factors for risk-attributable cancer DALYs in low SDI locations in 2019, whereas DALYs in high SDI locations mirrored the top three global risk factor rankings. From 2010 to 2019, global risk-attributable cancer deaths increased by 20·4% (12·6–28·4) and DALYs by 16·8% (8·8–25·0), with the greatest percentage increase in metabolic risks (34·7% [27·9–42·8] and 33·3% [25·8–42·0]). INTERPRETATION: The leading risk factors contributing to global cancer burden in 2019 were behavioural, whereas metabolic risk factors saw the largest increases between 2010 and 2019. Reducing exposure to these modifiable risk factors would decrease cancer mortality and DALY rates worldwide, and policies should be tailored appropriately to local cancer risk factor burden

Safety with laser during retinal therapy : an electroretinographic study

Studies of the retinal sensitivity, as reflected in the ERG records, have been made, before, during, and after exposure of the eye to an argon laser beam ( > = 488 nm ; intensity 1 mW/cm2 ; durations 0.12 and 0.25 sec). The applied retinal load thus was similar as that during retinal treatments. The ERG records were carried out at different temperatures (10 - 30°C) for both light and dark adapted eyes. The aim of this study was to assess the best suitable conditions for retinal laser treatments without affecting other retinal tissues. The obtained results showed that the argon laser therapy causes some damage to the eye which is paralleled by a noticeable change in the b-wave amplitude (Ab) of the electroretinogram. This damage recovers faster when the laser dose and the eye temperature are reduced. Also it was preferable to perform these treatments in dark adapted eyes rather than in light adapted eyes. Simple calculations of the changes in the external K+ concentration, ΔK, induced by light stimulation were performed, before and after laser treatment, using Nernst equation modified by Miller relating Ab to the logarithm of the external K+ concentration. This led to the conclusion that laser treatment has an indirect effect on the eye through its direct effects on the pigment epithelium and photoreceptor membrane permeabilities to K+. Moreover, calculations of the repair-damage ratio represented by Ab variations, after laser exposure, helped for optimizing the laser conditions during treatments. This indicated that the ERG is a sensitive tool for studying the effects on the eye during treatments

Adaptive protection coordination scheme for distribution network with distributed generation using ABC

This paper presents an adaptive protection coordination scheme for optimal coordination of DOCRs in interconnected power networks with the impact of DG, the used coordination technique is the Artificial Bee Colony (ABC). The scheme adapts to system changes; new relays settings are obtained as generation-level or system-topology changes. The developed adaptive scheme is applied on the IEEE 30-bus test system for both single- and multi-DG existence where results are shown and discussed

Structural Changes, Electrophoretic Pattern, and Quality Attributes of Camel Meat Treated with Fresh Ginger Extract and Papain Powder

Camel is a valuable source of meat for African and Asian countries; however, the most important problem associated with camel meat is its extreme toughness. This toughness has been attributed to its contents of connective tissue, which become more crossly linked in old animals. The toughness of camel meat decreases the consumer acceptance of this meat and reduces its chances of being utilized as a raw material for further processing into meat products. Ginger and papain were used in the current study as tenderizing enzymes, and the structural changes, electrophoretic pattern, physicochemical characteristics, and sensory scores of the treated meat were examined. The treatment of camel meat with ginger and papain resulted in marked destructive changes in the connective tissue and myofibers, and a reduction in the protein bands, with a consequent improvement in its tenderness. All the enzyme-treated samples exhibited significant increases in the protein solubility, with significant decreases in the shear-force values. Moreover, an improvement in the sensory scores of the raw and cooked meat and a reduction in the bacterial counts after the treatments were recorded. Ginger and papain induced a significant improvement in the physicochemical characteristics, sensory attributes, and bacterial counts of the camel meat; therefore, these materials can be utilized by meat processors to boost the consumer acceptance of this meat, and to increase its suitability as a raw material for further meat processing

Removal of toxic pollutants from produced water by phytoremediation: Applications and mechanistic study

Elsevier Ltd In this study, a greenhouse experiment of complete randomized design with three replications was conducted to investigate the potential of Medicago sativa, Zea mays, Helianthus annus, Sorghum bicolor, Phragmites australis and Caroxylon imbricatum in the removal of toxic pollutants from a produced water (PW). The collected local oil-refinery wastewater was also characterized physically and chemically. The concentration of the total dissolved solids (TDS), chloride, sodium, boron ions and sodium adsorption ratio were 300 g/L, 122 g/L, 61 g/L, 0.038 g/L and 139.9 meq/L, respectively. Results showed that except M. sativa, tolerated up to 10% diluted PW with a 30% decrease in length and biomass compared to control treatment, all other plants could not survive. However, Caroxylon imbricatum tolerated up to 20% diluted PW without any significant differences in the morphological characteristics. The Fourier transform infrared (FTIR) results for C. imbricatum tissues showed that cellulose structure had the greatest role in the metal adsorption and transportation inside the plant tissue. This conclusion is verified by the shifting or disappearance in transmission bands at 1028, 1334, 2852 and 2921 cm−1. After PW treatment, the soil with sandy-loam texture used in this study showed a huge accumulation of sodium ions up to 17.6 × 103 mg/Kg. The organic contents of the PW were below the detection limits of the gas chromatography (GC) and ultra-performance liquid chromatography (UPLC) instruments. The results of polycyclic aromatic hydrocarbons (PAHs) extraction showed accumulation of less polar PAHs in 30% irrigated soil

The role of customized vestibular rehabilitation with visual desensitization in the management of visual vertigo syndrome

Objectives: The objective of this study is to assess the benefits of customized vestibular rehabilitation with visual desensitization in the management of visual vertigo (VV). Methods: This retrospective study included 65 patients suffering from VV with situational characteristic questionnaire more than 0.9. Patients who did not complete the follow up in the VV clinic were not included in the analysis. Patients underwent customized vestibular rehabilitation using graded and progressive gaze stabilization exercises without background followed by introduction of visual stimulation (e.g. patterned wallpaper) and optokinetic DVD for home training to promote visual desensitization. The Situational Characteristic Questionnaire (SCQ), Hospital Anxiety and Depression Scale (HADS), the Nijmegen Questionnaire and Dizziness Handicap Inventory (DHI) were used to assess patient symptoms before and after the vestibular rehabilitation. Results: Seventy-five per cent of subjects in the study had statistically significant improvement in the SCQ from 2.31 ± 0.73 to 1.89 ± 0.88 after the rehabilitation. Sixty-three per cent of patients had statistically significant improvement in the Nijmegen questionnaire from 27.03 ± 9.94 to 24.75 ± 11.88 after the rehabilitation. There was statistically insignificant difference in the HADS score from 9.69 ± 4.28 to 9.76 ± 5.21 after the rehabilitation. Although there was improvement in the total DHI score as well (from 53.87 ± 16.289 to 50.10 ± 20.413), this was statistically insignificant. However, there was statistically significant improvement in the DHI some subgroups (physical and functional scores) and statistically non-significant improvement in other subgroups (emotional score and total score). The mean duration of rehabilitation was 6.8 ± 5 months. Correlation analysis between SCQ score and other questionnaire scores after the rehabilitation shows significant positive correlation between the post-rehabilitation SCQ questionnaire and other questionnaires. Conclusions: Customized vestibular rehabilitation incorporating visual desensitization exercises with optokinetic DVD results in significant improvement in VV symptoms

Experimental challenge models for Johne's disease: A review and proposed international guidelines

An international committee of Johne's disease (JD) researchers was convened to develop guidelines for JD challenge studies in multiple animal species. The intent was to develop and propose international standard guidelines for models based on animal species that would gain acceptance worldwide. Parameters essential for the development of long-term and short-term infection models were outlined and harmonized to provide a “best fit” JD challenge model for cattle, goats, sheep, cervids, and mice. These models will be useful to study host–pathogen interactions, host immunity at the local and systemic level, and for evaluating vaccine candidates and therapeutics. The consensus guidelines herein list by animal species strains of Mycobacterium avium subsp. paratuberculosis used, challenge dose, dose frequency, age of challenge, route of challenge, preparation of inoculum, experimental animal selection, quality control, minimal experimental endpoints and other parameters