scholarly journals MixTwice: large-scale hypothesis testing for peptide arrays by variance mixing

2021 ◽  
Author(s):  
Zihao Zheng ◽  
Aisha M Mergaert ◽  
Irene M Ong ◽  
Miriam A Shelef ◽  
Michael A Newton
Keyword(s):  
Large Scale ◽  
Small Sample Size ◽  
Model Fitting ◽  
Small Sample ◽  
Optimization Techniques ◽  
Supplementary Information ◽  
Peptide Arrays ◽  
Serum Samples ◽  
Mixing Distributions ◽  
Variance Parameters

Abstract Summary Peptide microarrays have emerged as a powerful technology in immunoproteomics as they provide a tool to measure the abundance of different antibodies in patient serum samples. The high dimensionality and small sample size of many experiments challenge conventional statistical approaches, including those aiming to control the false discovery rate (FDR). Motivated by limitations in reproducibility and power of current methods, we advance an empirical Bayesian tool that computes local FDR statistics and local false sign rate statistics when provided with data on estimated effects and estimated standard errors from all the measured peptides. As the name suggests, the MixTwice tool involves the estimation of two mixing distributions, one on underlying effects and one on underlying variance parameters. Constrained optimization techniques provide for model fitting of mixing distributions under weak shape constraints (unimodality of the effect distribution). Numerical experiments show that MixTwice can accurately estimate generative parameters and powerfully identify non-null peptides. In a peptide array study of rheumatoid arthritis, MixTwice recovers meaningful peptide markers in one case where the signal is weak, and has strong reproducibility properties in one case where the signal is strong. Availabilityand implementation MixTwice is available as an R software package https://cran.r-project.org/web/packages/MixTwice/. Supplementary information Supplementary data are available at Bioinformatics online.

Phenotypic and Genetic Analyses of a Short Measure of Psychosis-proneness in a Large-scale Australian Twin Study

Twin Research ◽  
2001 ◽  
Vol 4 (1) ◽  
pp. 30-40 ◽  
Author(s):  
David A. Hay ◽  
Nicholas G. Martin ◽  
Debra Foley ◽  
Susan A. Treloar ◽  
Katherine M. Kirk ◽  
...  
Keyword(s):  
Large Scale ◽  
Small Sample Size ◽  
Model Fitting ◽  
Twin Studies ◽  
Small Sample ◽  
Eysenck Personality Questionnaire ◽  
Social Anhedonia ◽  
Genetic Analyses ◽  
Genetic Determination ◽  
Psychosis Proneness

AbstractPrevious genetic analyses of psychosis proneness have been limited by their small sample size. For the purposes of large-scale screening, a 12-item questionnaire was developed through a two-stage process of reduction from the full Chapman and Chapman scales. 3685 individuals (including 1438 complete twin pairs) aged 18–25 years and enrolled in the volunteer Australian Twin Registry returned a mail questionnaire which included this psychosis proneness scale and the Eysenck Personality Questionnaire. Despite the brevity of the questionnaire, item and factor analysis identified four unambiguous and essentially uncorrelated scales. There were (1) Perceptual Aberration – Magical Ideation; (2) Hypomania – Impulsivity/Nonconformity; (3) Social Anhedonia and (4) Physical Anhedonia. Model-fitting analyses showed additive genetic and specific environmental factors were sufficient for three of the four scales, with the Social Anhedonia scale requiring also a parameter for genetic dominance. There was no evidence for the previously hypothesised sex differences in the genetic determination of psychosis-proneness. The potential value of multivariate genetic analysis to examine the relationship between these four scales and dimensions of personality is discussed. The growing body of longitudinal evidence on psychosis-proneness suggests the value of incorporating this brief measure into developmental twin studies.

CONTRIBUTION OF DNA COPY-NUMBER VARIATION (CNV) TO CANCER SUSCEPTIBILITY AND LARGE-SCALE GENOME ALTERATIONS IN OSTEOSARCOMA (OS)

2008 ◽  
Vol 31 (4) ◽  
pp. 19
Author(s):  
I Pasic ◽  
A Shlien ◽  
A Novokmet ◽  
C Zhang ◽  
U Tabori ◽  
...  
Keyword(s):  
Genomic Instability ◽  
Large Scale ◽  
Structural Variation ◽  
Age Of Onset ◽  
Cancer Susceptibility ◽  
Small Sample Size ◽  
Snp Array ◽  
Tumour Suppressor Gene ◽  
Small Sample ◽  
International Hapmap Project

Introduction: OS, a common Li-Fraumeni syndrome (LFS)-associated neoplasm, is a common bone malignancy of children and adolescents. Sporadic OS is also characterized by young age of onset and high genomic instability, suggesting a genetic contribution to disease. This study examined the contribution of novel DNA structural variation elements, CNVs, to OS susceptibility. Given our finding of excessive constitutional DNA CNV in LFS patients, which often coincide with cancer-related genes, we hypothesized that constitutional CNV may also provide clues about the aetiology of LFS-related sporadic neoplasms like OS. Methods: CNV in blood DNA of 26 patients with sporadic OS was compared to that of 263 normal control samples from the International HapMap project, as well as 62 local controls. Analysis was performed on DNA hybridized to Affymetrix genome-wide human SNP array 6.0 by Partek Genomic Suite. Results: There was no detectable difference in average number of CNVs, CNV length, and total structural variation (product of average CNV number and length) between individuals with OS and controls. While this data is preliminary (small sample size), it argues against the presence of constitutional genomic instability in individuals with sporadic OS. Conclusion: We found that the majority of tumours from patients with sporadic OS show CN loss at chr3q13.31, raising the possibility that chr3q13.31 may represent a “driver” region in OS aetiology. In at least one OS tumour, which displays CN loss at chr3q13.31, we demonstrate decreased expression of a known tumour suppressor gene located at chr3q13.31. We are investigating the role ofchr3q13.31 in development of OS.

scholarly journals Review of the Studies in the Use of Biofeedback Therapy in Rehabilitation and Physiatrics of Neurological Patients

Doctor Ru ◽  
2021 ◽  
Vol 20 (9) ◽  
pp. 43-47
Author(s):  
E.Yu. Mozheyko ◽  
◽  
O.V. Petryaeva ◽  
◽  
◽  
...  
Keyword(s):  
Large Scale ◽  
Small Sample Size ◽  
Small Sample ◽  
Healthy Population ◽  
Biofeedback Therapy ◽  
Level Of Evidence ◽  
Double Blind ◽  
Key Points ◽  
Neurological Patients ◽  
Drug Free

Objective of the Review: To collect information, analyse and evaluate previous studies in the use of biofeedback in neurological patients. Key Points. Despite the wide practical application and a lot of available publications, the level of evidence of this method is low because of a small sample size and the challenges with biofeedback mechanism description. A review of various types of biocontrol, its mechanisms and developments shows that drug-free therapy using only patient’s resources (organic, psychological, emotional and volitional) can activate the mechanisms of neuroplasticity, which are poorly studied. Still, it does not prevent from using biocontrol for the therapy of patients and/or prevention of various diseases in healthy population. Conclusion. Biofeedback therapy has proven to be a safe, relatively efficient and easy-to-use method. However, organisation of a large-scale double blind randomized trial is one of the predominant directions in the future. Keywords: biofeedback, biocontrol, neurofeedback, biofeedback therapy.

scholarly journals Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks

2017 ◽  
Author(s):  
Stefano Beretta ◽  
Mauro Castelli ◽  
Ivo Gonçalves ◽  
Ivan Merelli ◽  
Daniele Ramazzotti
Keyword(s):  
Breast Cancer ◽  
Graphical Models ◽  
Protein Interactions ◽  
Large Scale ◽  
Small Sample Size ◽  
Small Sample ◽  
Cancer Data ◽  
Correlation Networks ◽  
Model Complex ◽  
Cancer Networks

AbstractGene and protein networks are very important to model complex large-scale systems in molecular biology. Inferring or reverseengineering such networks can be defined as the process of identifying gene/protein interactions from experimental data through computational analysis. However, this task is typically complicated by the enormously large scale of the unknowns in a rather small sample size. Furthermore, when the goal is to study causal relationships within the network, tools capable of overcoming the limitations of correlation networks are required. In this work, we make use of Bayesian Graphical Models to attach this problem and, specifically, we perform a comparative study of different state-of-the-art heuristics, analyzing their performance in inferring the structure of the Bayesian Network from breast cancer data.

Serum Adsorption Study to Validate the Specificity of a Rapid Test to Detect Strongyloides stercoralis Infection

2021 ◽  
Author(s):  
Rahmah Noordin ◽  
Emelia Osman ◽  
Nor Suhada Anuar ◽  
Nor Mustaiqazah Juri ◽  
Anizah Rahumatullah ◽  
...  
Keyword(s):  
Small Sample Size ◽  
Rapid Test ◽  
High Specificity ◽  
Strongyloides Stercoralis ◽  
Cross Reactivity ◽  
Small Sample ◽  
Polystyrene Microspheres ◽  
Diagnostic Specificity ◽  
Serum Samples ◽  
Rapid Tests

A lateral flow rapid test for strongyloidiasis will greatly facilitate the control and elimination of the disease. Previously SsRapid™ prototype rapid test showed high diagnostic specificity to detect Strongyloides infection, determined using non-Strongyloides sera negative by IgG-ELISAs. Since high specificity is crucial before a test is used for public health control activities, further validation of its specificity is needed. Also, it needs to be ascertained whether non-Strongyloides sera positive by IgG-ELISAs and SsRapid are truly positive for Strongyloides or are cases of cross-reactivity. We performed 84 rapid tests (two types of dipsticks and cassettes) using 34 serum samples. They were divided into four groups based on Strongyloides infection and coinfection with other parasites and the availability of recombinant proteins and rapid tests for the latter. Sera was adsorbed using polystyrene microspheres beads separately coated with four recombinant parasite proteins. The small sample size is a limitation of this study; however, the overall results showed that the sera adsorption procedure was successful, and the SsRapid test is specific.

scholarly journals Copy number variation analysis of twin pairs discordant for cleft lip with or without cleft palate

2019 ◽  
Vol 33 ◽  
pp. 205873841985587
Author(s):  
Luca Scapoli ◽  
Francesco Carinci ◽  
Annalisa Palmieri ◽  
Francesca Cura ◽  
Alessandro Baj ◽  
...  
Keyword(s):  
Cleft Palate ◽  
Copy Number ◽  
Large Scale ◽  
Cleft Lip ◽  
Small Sample Size ◽  
Copy Number Variants ◽  
Monozygotic Twins ◽  
Monozygotic Twin ◽  
Small Sample ◽  
High Level

Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a frequent orofacial malformation. The comparison of concordance rate observed in monozygotic and dizygotic twins supports high level of heritability and a strong genetic component. However, phenotype concordance for orofacial cleft in monozygotic twins is about 50%. The aim of the present investigation was to detect postzygotic events that may account for discordance in monozygotic twins. High-density SNP microarrays hybridization was used to genotype two pairs of monozygotic twins discordant for nsCL/P. Discordant SNP genotypes and copy number variants were analyzed to identify genetic differences responsible of phenotype discrepancy. A number of differences were observed, none involving known nsCL/P candidate genes or genomic regions. Considering the limitation of the study, related to the small sample size and to the large-scale investigation method, the results suggest that the detection of discordant events in other monozygotic twin pairs would be remarkable and warrant further investigations.

Facebook as a platform for co-creating music festival experiences

2016 ◽  
Vol 7 (2) ◽  
pp. 84-99 ◽  
Author(s):  
Emma Hoksbergen ◽  
Andrea Insch
Keyword(s):  
Young Adults ◽  
Large Scale ◽  
Small Sample Size ◽  
Small Sample ◽  
Survey Method ◽  
Future Research ◽  
Content Type ◽  
Music Festival ◽  
Alternative Means ◽  
On Line

Purpose The purpose of this paper is to address the need to understand how younger music festival-goers use and engage with a music festival’s Facebook page, and how they perceive this social networking service (SNS) as a potential on-line platform for value co-creation. Design/methodology/approach Face-to-face in-depth interviews were conducted with 16 young adults who attended an annual New Year’s Eve music festival, Rhythm and Vines, in Gisborne, New Zealand. Findings Analysis of the interview data revealed that the majority of participants did not actively engage with this platform and could be categorised as passive viewers or information-seekers. In addition, participants perceived five types of value from using this SNS: functional, social, emotional, interactive and aesthetic value. Even though participants were not segmented due to the small sample size, patterns in their levels of engagement with Facebook, attendance status, reasons for attending the festival and the combinations of forms of value that they perceived were identified. Research limitations/implications Future research should use a large-scale survey method to obtain a representative sample that is generalisable to a specific population of music festival-goers. Practical implications Dominance of features on Facebook providing festival-goers with functional value suggests they prefer a passive or co-optation approach to value co-creation in this context. Due to the limited extent of participants actively co-creating value on this platform, alternative means of encouraging interaction to co-create value with festival-goers should be investigated. Originality/value This study demonstrates that this SNS provides this group of young adults with a means to connect their real-time festival experience, with their on-line Facebook social network during the year.

scholarly journals Pattern of Coronary Artery Stenosis among Ischaemic Heart Disease Cases in Chittagong

2017 ◽  
Vol 28 (1) ◽  
pp. 30-31
Author(s):  
Abu Tarek Iqbal ◽  
Jalal Uddin ◽  
Dhiman Banik ◽  
Salehuddin ◽  
Hasan Mamun ◽  
...  
Keyword(s):  
Coronary Artery ◽  
Sample Size ◽  
Large Scale ◽  
Resource Constraints ◽  
Coronary Artery Stenosis ◽  
Small Sample Size ◽  
Sampling Technique ◽  
Small Sample ◽  
Artery Stenosis ◽  
Study Results

Many studies were conducted on the topic over the whole world but there is none in Chittagong, Bangladesh. To know the pattern of coronary artery stenosis in Chittagong we have conducted the study because it is important for effective case management. It was an observational study. Convenient sampling technique was used and sample size was fixed to 110 considering resource constraints. All the cases were diagnosed on the basis of history, clinical features and laboratory investigations. Coronary artery angiogram was methodically conducted. All relevant data had been recorded and were managed manually. The findings were validated statistically. Discussion was made with updated literature review and finally conclusion was drawn. Total 110 cases were studied. Stenosis was found in 77(70%) cases. Among them 83% were male and 17% were female. Age range was 30-80 years but 76% cases were of 40-60 years age group. Among the stenosed cases SVD 29%, DVD 20% and TVD 20% only. Only 01% was LMCA. Commonest stenosed vessel was LAD 71%. RCA 60%, LCX 58% and LMCA 6%. 47% of stenosed cases were found with normal ECG. Ejection fraction of 57% stenosed cases was >55%. Study results are not significantly apart from studies in home and abroad. The limitation is small sample size. So, a multicenter study on a large scale cases is hereby advocated for a conclusive opinionMedicine Today 2016 Vol.28(1): 30-31

scholarly journals Educational Stakeholders’ Independent Evaluation of an Artificial Intelligence-Enabled Adaptive Learning System Using Bayesian Network Predictive Simulations

2019 ◽  
Vol 9 (2) ◽  
pp. 110 ◽  
Author(s):  
Meng-Leong HOW ◽  
Wei Loong David HUNG
Keyword(s):  
Artificial Intelligence ◽  
Adaptive Learning ◽  
Large Scale ◽  
Small Sample Size ◽  
Small Sample ◽  
Learning System ◽  
Learning Needs ◽  
Educational Stakeholders ◽  
Independent Evaluation ◽  
Computer Scientists

Artificial intelligence-enabled adaptive learning systems (AI-ALS) are increasingly being deployed in education to enhance the learning needs of students. However, educational stakeholders are required by policy-makers to conduct an independent evaluation of the AI-ALS using a small sample size in a pilot study, before that AI-ALS can be approved for large-scale deployment. Beyond simply believing in the information provided by the AI-ALS supplier, there arises a need for educational stakeholders to independently understand the motif of the pedagogical characteristics that underlie the AI-ALS. Laudable efforts were made by researchers to engender frameworks for the evaluation of AI-ALS. Nevertheless, those highly technical techniques often require advanced mathematical knowledge or computer programming skills. There remains a dearth in the extant literature for a more intuitive way for educational stakeholders—rather than computer scientists—to carry out the independent evaluation of an AI-ALS to understand how it could provide opportunities to educe the problem-solving abilities of the students so that they can successfully learn the subject matter. This paper proffers an approach for educational stakeholders to employ Bayesian networks to simulate predictive hypothetical scenarios with controllable parameters to better inform them about the suitability of the AI-ALS for the students.

scholarly journals Epigenetics and Proteomics Join Transcriptomics in the Quest for Tuberculosis Biomarkers

mBio ◽  
2015 ◽  
Vol 6 (5) ◽  
Author(s):  
Maria M. Esterhuyse ◽  
January Weiner ◽  
Etienne Caron ◽  
Andre G. Loxton ◽  
Marco Iannaccone ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Pilot Study ◽  
Large Scale ◽  
Small Sample Size ◽  
Protein Translation ◽  
Small Sample ◽  
Transcriptional Level ◽  
Content Type ◽  
Dna Methylome ◽  
Large Scale Study

ABSTRACT An estimated one-third of the world's population is currently latently infected with Mycobacterium tuberculosis. Latent M. tuberculosis infection (LTBI) progresses into active tuberculosis (TB) disease in ~5 to 10% of infected individuals. Diagnostic and prognostic biomarkers to monitor disease progression are urgently needed to ensure better care for TB patients and to decrease the spread of TB. Biomarker development is primarily based on transcriptomics. Our understanding of biology combined with evolving technical advances in high-throughput techniques led us to investigate the possibility of additional platforms (epigenetics and proteomics) in the quest to (i) understand the biology of the TB host response and (ii) search for multiplatform biosignatures in TB. We engaged in a pilot study to interrogate the DNA methylome, transcriptome, and proteome in selected monocytes and granulocytes from TB patients and healthy LTBI participants. Our study provides first insights into the levels and sources of diversity in the epigenome and proteome among TB patients and LTBI controls, despite limitations due to small sample size. Functionally the differences between the infection phenotypes (LTBI versus active TB) observed in the different platforms were congruent, thereby suggesting regulation of function not only at the transcriptional level but also by DNA methylation and microRNA. Thus, our data argue for the development of a large-scale study of the DNA methylome, with particular attention to study design in accounting for variation based on gender, age, and cell type. IMPORTANCE DNA methylation modifies the transcriptional program of cells. We have focused on two major populations of leukocytes involved in immune response to infectious diseases, granulocytes and monocytes, both of which are professional phagocytes that engulf and kill bacteria. We have interrogated how DNA methylation, gene expression, and protein translation differ in these two cell populations between healthy individuals and patients suffering from TB. To better understand the underlying biologic mechanisms, we harnessed a statistical enrichment analysis, taking advantage of predefined and well-characterized gene sets. Not only were there clear differences on various levels between the two populations, but there were also differences between TB patients and healthy controls in the transcriptome, proteome, and, for the first time, DNA methylome in these cells. Our pilot study emphasizes the value of a large-scale study of the DNA methylome taking into account our findings.

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