Analysis of factorial experiments using mixed-effects models: options for estimation, prediction and inference

In linear mixed-effects modelling of experiments, estimation of variance components, prediction of random effects, and computation of denominator degrees of freedom associated with inference on fixed effects, are important elements of the analysis. This thesis investigates alternatives to the likelihoodbased procedures for analysis of factorial experiments with normally distributed observations. Consistent methods, such as the maximum likelihood method, can be disadvantageous in cases where only small samples are available. Moreover, the algorithms used in linear mixed-effects models can be computationally demanding in large datasets. In this thesis, Henderson’s method 3, a non-iterative variance component estimation method, was considered for estimation of the variance components in a two-way mixed linear model with three variance components. The variance component estimator corresponding to one of the random effects was improved by perturbing the standard unbiased estimator. The improved variance component estimator performed better in terms of mean square error. In an application on a quantitative trait loci (QTL) study, the modified estimator was compared to the restricted maximum likelihood estimator on data from European wild boar × domestic pig intercross. The modified estimator was shown to approximate the results obtained from the restricted maximum likelihood (REML) method very closely. For balanced and unbalanced data in two-way with and without interaction models, the generalized prediction intervals for the random effects were derived. The coverage probabilities of the proposed intervals were compared with those based on the REML method and the approximate methods of Satterthwaite (1946) and Kenward and Roger (1997). The coverage of the proposed intervals was closer to the chosen nominal level than coverage of prediction intervals based on the REML method. With focus on Type I error, the implications of the available options in the mixed procedure of SAS and the lmer function of R for the inference on the fixed effects were examined. With the default setting of SAS, the frequency of Type I error was higher than with R. The Type I error rate in SAS was close to the nominal value when negative estimates of the variance components were allowed. Both software packages occasionally produced inaccurate results

Effect of formaldehyde vapor on the blood constituents of male rabbits

The present experimental study was designed to investigate the effect of formaldehyde on blood constituents of rabbit males, Twenty four adult males were randomly subdivided into 3 groups (I, II, III) and exposed to vapour of 10% FD (12 ppm) in cages for the following periods: 2, 4 and 6 months; beside, 8 rabbits were exposed to vapour of distilled water as a control group. Blood parameters examination showed no morphological changes, but with a significant increase in lymphocytes and esonophils percentage. Significant decrease in neutrophil, red blood cell (RBC) and platelets counts was detected. The present study concluded that formaldehyde of such concentration and exposure time have an effect on blood constituents of rabbit males

A Review on the impacts of Azadirachta indica on Multi-drug Resistant Extended Spectrum Beta Lactamase-positive of Escherichia coli and Klebsiella pneumonia

Neem trees have long been considered the holy grail of holistic and nature-based treatments. The medicinal properties that constituents of the trees possess to range from traits that are immunomodulatory to traits combat different disease and infections such as anti-inflammatory and antibacterial effects, to insulating properties that include cardioprotective and hepatoprotective effects. The role of Extended Spectrum Beta-Lactamase positive (ESBL+) bacteria in the occurrence and recurrence of Urinary Tract Infection (UTI) infections, particularly in the Gulf region has been studied extensively. However, suggested treatment methods have had little success due to a variety of factors which include drug resistance, the inability of doctors to calculate the optimal duration for treatment, which has resulted in wrong antibiotic prescriptions, as well as lack of understanding of how UTIs work and thrive in different demographics/ populations which again, results in inappropriate antibiotic treatment of the disease. These discoveries raised the issue of professionals needing better training and education in issues to do with UTIs amongst different demographics of people. In this investigation, the medicinal and pharmacological properties of A. indica from neem leaves were assessed by studying how they affected the activity of ESBL+ bacteria, based on literature from similar studies. The goal and objective of this study were to see if ESBL+ bacteria persisted in the presence of A. Indica from leaf extract, as well as gaining an understanding of the factors that affected the persistence and subsequent treatment of the bacteria using A. indica.Keywords: Azadirachta indica; Neem; UTI; ESBL; E. coli; K. Pneumonia

A Usability Evaluation Framework for

Currently, more than two billions people access the Web for various purposes. The majority are people without programming or modelling background. Part of these people (called end-users) also likes to create their own Web applications to meet their daily needs. Mashup Makers are tools to create such end-user’s Web applications. As such, Mashup Makers could become the dominant environment for end-user development of Web applications. Existing Mashup Makers promise that creating a Web Mashup is very easy and just a matter of a few mouse clicks. However, there is no evidence that this is indeed the case. On the contrary, research has already revealed usability problems with Mashup Makers. Therefore, this thesis concentrates on the usability of Mashup Makers as development environments for Web applications for end-users. Usability is a key issue for the success of software artifacts, and especially if the artifacts are intended for non-technical users. Therefore, we target the achievement of a consolidated approach, model, and framework for the evaluation of the usability of Mashup Makers for end-users. Such a framework will not only allow evaluating the usability of existing Mashup Makers, but it will also provide key issues concerning usability (ie usability impact factors) that developers of Mashup Makers and of other future end-user development tools can take into consideration when developing new tools

Notes on correctness of p-values when analyzing experiments using SAS and R

It is commonly believed that if a two-way analysis of variance (ANOVA) is carried out in R, then reported p-values are correct. This article shows that this is not always the case. Results can vary from non-significant to highly significant, depending on the choice of options. The user must know exactly which options result in correct p-values, and which options do not. Furthermore, it is commonly supposed that analyses in SAS and R of simple balanced experiments using mixed-effects models result in correct p-values. However, the simulation study of the current article indicates that frequency of Type I error deviates from the nominal value. The objective of this article is to compare SAS and R with respect to correctness of results when analyzing small experiments. It is concluded that modern functions and procedures for analysis of mixed-effects models are sometimes not as reliable as traditional ANOVA based on simple computations of sums of squares

cAMP response element binding protein (CREB) activates transcription via two distinct genetic elements of the human glucose-6-phosphatase gene

BACKGROUND: The enzyme glucose-6-phosphatase catalyzes the dephosphorylation of glucose-6-phosphatase to glucose, the final step in the gluconeogenic and glycogenolytic pathways. Expression of the glucose-6-phosphatase gene is induced by glucocorticoids and elevated levels of intracellular cAMP. The effect of cAMP in regulating glucose-6-phosphatase gene transcription was corroborated by the identification of two genetic motifs CRE1 and CRE2 in the human and murine glucose-6-phosphatase gene promoter that resemble cAMP response elements (CRE). RESULTS: The cAMP response element is a point of convergence for many extracellular and intracellular signals, including cAMP, calcium, and neurotrophins. The major CRE binding protein CREB, a member of the basic region leucine zipper (bZIP) family of transcription factors, requires phosphorylation to become a biologically active transcriptional activator. Since unphosphorylated CREB is transcriptionally silent simple overexpression studies cannot be performed to test the biological role of CRE-like sequences of the glucose-6-phosphatase gene. The use of a constitutively active CREB2/CREB fusion protein allowed us to uncouple the investigation of target genes of CREB from the variety of signaling pathways that lead to an activation of CREB. Here, we show that this constitutively active CREB2/CREB fusion protein strikingly enhanced reporter gene transcription mediated by either CRE1 or CRE2 derived from the glucose-6-phosphatase gene. Likewise, reporter gene transcription was enhanced following expression of the catalytic subunit of cAMP-dependent protein kinase (PKA) in the nucleus of transfected cells. In contrast, activating transcription factor 2 (ATF2), known to compete with CREB for binding to the canonical CRE sequence 5'-TGACGTCA-3', did not transactivate reporter genes containing CRE1, CRE2, or both CREs derived from the glucose-6-phosphatase gene. CONCLUSIONS: Using a constitutively active CREB2/CREB fusion protein and a mutant of the PKA catalytic subunit that is targeted to the nucleus, we have shown that the glucose-6-phosphatase gene has two distinct genetic elements that function as bona fide CRE. This study further shows that the expression vectors encoding C2/CREB and catalytic subunit of PKA are valuable tools for the study of CREB-mediated gene transcription and the biological functions of CREB

Applying Agile Software Engineering On Medical Ubiquitous Computing (MUC)

Nowadays, people are involved in using computation capabilities to meet their daily life needs although most of the time they may be unaware as to how this actually happens. Ubiquities Computing is considered the future trend for providing unlimited computing capabilities that handle every service in human life. One of the most crucial implementation of Ubiquities Computing is in Medical and Hospital Service. This is due to their great importance in saving people's lives. The huge amount of data and information delivered by MUC systems draw the attention to the necessity of having a new and modern software engineering methodology; Agile Software engineering methodology is highly considered in the matter. In this paper, we present an implementation of applying agile SWE methodology on MUC System, research related issues are also discussed

Role of basic region leucine zipper transcription factors in controlling gene transcription in mammalian cells

The basic region leucine zipper (bZIP) transcription factors are proteins that bind as dimers to specifc sequences within promoter genes to activate or repress the transcription of these genes. The best known member of the bZIP family is cAMP response element (CRE) binding protein CREB that binds to the CRE 5`-TGACGTCA-3`. To investigate gene regulation by bZIP transcription factors constutively active and dominant-negative bZIP mutants were used. The results show that genes encoding GTP cyclohydrolase I, secretogranin II, tumor necrosis factor alpha and Egr-1 are regulated by CREB and ATF2 via CRE motifs or related sequences. CREB and ATF2 do not heterodimerize but they rather compte for DNA-binding. In contrast, the bZIP proteins CREB2/ATF4, ATF5 and C/EBP heterodimerize with each other but not with CREB or ATF2. CREB2/ATF4, ATF5 and C/EBP transactivate the asparagine synthetase gene but has no or marginal effect on CRE-controlled genes. Furthermore, CREB2/ATF4, ATF5 and C/EBP mediate the activation of the asparagine synthetase gene transcription induced by amino acid deprivation. In a second series of experiments the regulation of the inducible nitric oxide synthase (iNOS) has been investigated as a result of Toll-like receptor stimulation. The results show that stress-activated protein kinases and the bZIP proteins ATF2 and/or c-Jun are involved in the upregulation of iNOS gene following stimulation. Finally the regulation of the c-Jun and c-Fos encoding genes has been investiagted in pituitary cells. Stimulation of the gonadotropin-releasing hormone receptor and the muscarinic acetylcholine receptor type III stimulated c-Jun and c-Fos expression indicating that bZIP transcription factor synthesis is controlled by extracellular signals.Basic Region Leucin Zipper (bZIP) Transkriptionfaktoren sind Proteine, die an spezifische Sequenzen im Promotor binden und dadurch die Transkription dieser Gene entweder aktivieren oder hemmen. Das bekannteste Mitglied der bZIP-Familie is das "cAMP responsive element" (CRE)-bindende Protein CREB, welches an die CRE-Consensussequenz bindet. Um die Gen-Regulation durch bZIP-Transkriptionfaktoren zu untersuchen, wurden konstutiv-aktive und dominant-negative-mutanten verwendet. Die Ergebnisse zeigen, dass die GTP cyclohydrolase I, Sekretogranin II, Tumornekrosefaktor alpha und Egr-1 kodierende Gene durch CREB und ATF2 via CRE-Bindungsmotive oder ähnliche Sequenzen reguliert werden. CREB und ATF2 bilden keine Heterodimere, sonderen konkurrieren um dieselbe DNA-Bindungsstelle. Im Gengensatz dazu bilden die bZIP-Proteine CREB2/ATF4, ATF5 und C/EBP zwar untereinander Heteodimere, jedoch dimersieren sie nicht mit CREB oder ATF2. CREB2/ATF4, ATF5 und C/EBP haben keinen order nur geringen Einfluss auf CRE-regulierte Gene. CREB2/ATF4, ATF5 und C/EBP transaktivieren das Asparaginsynthtasegen und regulieren dessen Transkription nach Entzug von Aminosäuren im Kulturmedium. In einer zweiten Studie wurde die Regulation der induzierbaren Stickstoffmonoxidsynthase (iNOS) untersucht. Die Transkription des iNOS-Gens wird nach Stimulation des "toll-like" Rezeptors 4 aktiviert. Die Ergebnisse zeigen, dass stressaktivierte Proteinkinasen und die bZIP Proteine ATF2 und/oder c-Jun die Aktivierung der iNOS-Gentranskription vermitteln. Schließlich wurde die Regulation von c-Jun und c-Fos kodierenden Genen in pituitary Zellen untersucht. Die Stimulation des "Gonadotropin-Releasing-Hormone Rezeptors" oder des muskarinishen-Acetylcholin-Rezeptors Typ III führte zur Aktivierung des c-Jun und des c-Fos-Gens. Dies zeigt, dass die Biosynthese der bZIP-Proteine c-Jun und c-Fos durch extrazelluläre Stimuli kontrolliert wird

A Case Study on Academic Services Application Using Agile Methodology for Mobile Cloud Computing

Recently, Mobile Cloud Computing reveals many modern development areas in the Information Technology industry. Several software engineering frameworks and methodologies have been developed to provide solutions for deploying cloud computing resources on mobile application development. Agile methodology is one of the most commonly used methodologies in the field. This paper presents the MCCAS a Web and Mobile application that provide feature for the Palestinian higher education/academic institutions. An Agile methodology was used in the development of the MCCAS but in parallel with emphasis on Cloud computing resources deployment. Also many related issues is discussed such as how software engineering modern methodologies (advances) influenced the development process

CD56 expression in breast cancer induces sensitivity to natural killer-mediated cytotoxicity by enhancing the formation of cytotoxic immunological synapse

We examined the potential value of the natural killer (NK) cell line; NK-92, as immunotherapy tool for breast cancer (BC) treatment and searched for biomarker(s) of sensitivity to NK-92-mediated cytotoxicity. The cytotoxic activity of NK-92 cells towards one breast precancerous and nine BC cell lines was analyzed using calcein-AM and degranulation assays. The molecules associated with NK-92-responsiveness were determined by differential gene expression analysis using RNA-sequencing and validated by RT-PCR, immunostaining and flow cytometry. NK-target interactions and immunological synapse formation were assessed by fluorescence microscopy. Potential biomarker expression was determined by IHC in 99 patient-derived BC tissues and 10 normal mammary epithelial tissues. Most (8/9) BC cell lines were resistant while only one BC and the precancerous cell lines were effectively killed by NK-92 lymphocytes. NK-92-sensitive target cells specifically expressed CD56, which ectopic expression in CD56-negative BC cells induced their sensitivity to NK-92-mediated killing, suggesting that CD56 is not only a biomarker of responsiveness but actively regulates NK function. CD56 adhesion molecules which are also expressed on NK cells accumulate at the immunological synapse enhancing NK-target interactions, cytotoxic granzyme B transfer from NK-92 to CD56-expressing target cells and induction of caspase 3 activation in targets. Interestingly, CD56 expression was found to be reduced in breast tumor tissues (36%) with strong inter- and intratumoral heterogeneity in comparison to normal breast tissues (80%). CD56 is a potential predictive biomarker for BC responsiveness to NK-92-cell based immunotherapy and loss of CD56 expression might be a mechanism of escape from NK-immunity. - 2019, The Author(s).We would like to thank Ms Khaoula Errafii, Dr Kumaran Mande and Dr Richard Thompson for technical support in RNA sequencing. This work was supported by the Qatar Biomedical Research Institute (QBRI), Qatar Foundation.Scopu