Correction to "Insights into the Effects of Violating Statistical Assumptions for Dimensionality Reduction for Chemical "-omics" Data with Multiple Explanatory Variables"

[This corrects the article DOI: 10.1021/acsomega.3c01613.].

Using Artificial Intelligence as a Melanoma Screening Tool in Self-Referred Patients

INTRODUCTION

Early detection of melanoma requires timely access to medical care. In this study, we examined the feasibility of using artificial intelligence (AI) to flag possible melanomas in self-referred patients concerned that a skin lesion might be cancerous.

METHODS

Patients were recruited for the study through advertisements in 2 hospitals in Halifax, Nova Scotia, Canada. Lesions of concern were initially examined by a trained medical student and if the study criteria were met, the lesions were then scanned using the FotoFinder System®. The images were analyzed using their proprietary computer software. Macroscopic and dermoscopic images were evaluated by 3 experienced dermatologists and a senior dermatology resident, all blinded to the AI results. Suspicious lesions identified by the AI or any of the 3 dermatologists were then excised.

RESULTS

Seventeen confirmed malignancies were found, including 10 melanomas. Six melanomas were not flagged by the AI. These lesions showed ambiguous atypical melanocytic proliferations, and all were diagnostically challenging to the dermatologists and to the dermatopathologists. Eight malignancies were seen in patients with a family history of melanoma. The AI's ability to diagnose malignancy is not inferior to the dermatologists examining dermoscopic images.

CONCLUSION

AI, used in this study, may serve as a practical skin cancer screening aid. While it does have technical and diagnostic limitations, its inclusion in a melanoma screening program, directed at those with a concern about a particular lesion would be valuable in providing timely access to the diagnosis of skin cancer.

Insights into the Effects of Violating Statistical Assumptions for Dimensionality Reduction for Chemical "-omics" Data with Multiple Explanatory Variables

Biological volatilome analysis is inherently complex due to the considerable number of compounds (i.e., dimensions) and differences in peak areas by orders of magnitude, between and within compounds found within datasets. Traditional volatilome analysis relies on dimensionality reduction techniques which aid in the selection of compounds that are considered relevant to respective research questions prior to further analysis. Currently, compounds of interest are identified using either supervised or unsupervised statistical methods which assume the data residuals are normally distributed and exhibit linearity. However, biological data often violate the statistical assumptions of these models related to normality and the presence of multiple explanatory variables which are innate to biological samples. In an attempt to address deviations from normality, volatilome data can be log transformed. However, whether the effects of each assessed variable are additive or multiplicative should be considered prior to transformation, as this will impact the effect of each variable on the data. If assumptions of normality and variable effects are not investigated prior to dimensionality reduction, ineffective or erroneous compound dimensionality reduction can impact downstream analyses. It is the aim of this manuscript to assess the impact of single and multivariable statistical models with and without the log transformation to volatilome dimensionality reduction prior to any supervised or unsupervised classification analysis. As a proof of concept, Shingleback lizard (Tiliqua rugosa) volatilomes were collected across their species distribution and from captivity and were assessed. Shingleback volatilomes are suspected to be influenced by multiple explanatory variables related to habitat (Bioregion), sex, parasite presence, total body volume, and captive status. This work determined that the exclusion of relevant multiple explanatory variables from analysis overestimates the effect of Bioregion and the identification of significant compounds. The log transformation increased the number of compounds that were identified as significant, as did analyses that assumed that residuals were normally distributed. Among the methods considered in this work, the most conservative form of dimensionality reduction was achieved through analyzing untransformed data using Monte Carlo tests with multiple explanatory variables.

Acute onset of blisters in an infant with acrodermatitis enteropathica: A case report

We represent a pediatric case of the congenital disorder caused by zinc malabsorption, acrodermatitis enteropathica, presenting with acute onsetof blisters. Although blisters can be seen in this condition, it is not always a key feature and can therefore be overlooked when considering a differential diagnosis of acute blistering in infancy. We therefore review the common and less common features of this cutaneous eruption as well as provide an extensive differential diagnosis for acute blistering in infancy. We also emphasize the importance of lifelong treatment with zinc supplementation in these children.

Casework applications of probabilistic genotyping methods for DNA mixtures that allow relationships between contributors

In both criminal cases and civil cases there is an increasing demand for the analysis of DNA mixtures involving relationships. The goal might be, for example, to identify the contributors to a DNA mixture where the unknown donors may be related, or to infer the relationship between individuals based on a DNA mixture. This paper applies a new approach to modelling and computation for DNA mixtures involving contributors with arbitrarily complex relationships to two real cases from the Spanish Forensic Police.

Analysis of grouped data using conjugate generalized linear mixed models

This article concerns a class of generalized linear mixed models for two-level grouped data, where the random effects are uniquely indexed by groups and are independent. We derive necessary and sufficient conditions for the marginal likelihood to be expressed in explicit form. These models are unified under the conjugate generalized linear mixed models framework, where conjugate refers to the fact that the marginal likelihood can be expressed in closed form, rather than implying inference via the Bayesian paradigm. The proposed framework allows simultaneous conjugacy for Gaussian, Poisson and gamma responses, and thus can accommodate both unit- and group-level covariates. Only group-level covariates can be incorporated for the binomial distribution. In a simulation of Poisson data, our framework outperformed its competitors in terms of computational time, and was competitive in terms of robustness against misspecification of the random effects distributions.

Prevention of alopecia in medical and interventional chemotherapy patients

BACKGROUND

Chemotherapy-induced alopecia is one of the most distressing side effects of cancer treatment. Although there have been a number of investigated strategies to reduce this, there is no standard of care for treatment.

OBJECTIVE

This review aims to summarize the relevant evidence for the treatments available for chemotherapy-induced alopecia.

METHODS

A literature search using PubMed and the MEDLINE subengine was completed. The terms "chemotherapy," "alopecia," "quality of life," and "strategies" were used, and articles from the last 10 years were considered. The pediatric population was not investigated.

RESULTS

Physical therapies for alopecia prevention have shown some promise but range from insufficient to detrimental depending on the type of cancer. Cold caps may be more effective than tourniquets and may be associated with fewer metastatic events. Pharmacologic therapies, both immunomodulators and growth factors, have stood the test of several trials to date. In particular, cyclosporine has been shown either to prevent alopecia or promote hair growth during a chemotherapy regimen.

CONCLUSION

Although the evidence is not yet overwhelming, it is becoming clear that a combination of mechanical and chemical interventions may help compensate for the downfalls of either therapy alone.

Favre-Racouchot syndrome in a 39-year old female following radiation therapy

BACKGROUND

Favre-Racouchot syndrome is a cutaneous disease characterized by nodules, cysts, and comedones that typically develops on sun-exposed areas of the face. This syndrome most commonly affects white males between the ages of 40 and 60 years and is frequently associated with chronic sun exposure and, more recently, chronic cigarette smoking.

OBJECTIVE

We report a case of Favre-Racouchot syndrome in a 39-year-old female who received 6 weeks of radiation therapy to treat a grade 3 oligodendroglioma.

RESULTS AND CONCLUSION

Although there have been previously reported cases of Favre-Racouchot syndrome following radiation therapy, this case is unique given the young age of the patient and extent of involvement.

Discussion of ‘Beyond mean regression’

Methodology for regression beyond the mean has been a goal of researchers for many years. This discussion provides some additional context for the important ideas in the present paper, by recounting some of the historical background to the GAMLSS approach and pointing to the power and appeal of fully probabilistic regression analysis in the setting of Bayesian nonparametrics.

LOGICOIL--multi-state prediction of coiled-coil oligomeric state

MOTIVATION

The coiled coil is a ubiquitous α-helical protein-structure domain that directs and facilitates protein-protein interactions in a wide variety of biological processes. At the protein-sequence level, the coiled coil is readily recognized via a conspicuous heptad repeat of hydrophobic and polar residues. However, structurally coiled coils are more complicated, existing in a wide range of oligomer states and topologies. As a consequence, predicting these various states from sequence remains an unmet challenge.

RESULTS

This work introduces LOGICOIL, the first algorithm to address the problem of predicting multiple coiled-coil oligomeric states from protein-sequence information alone. By covering >90% of the known coiled-coil structures, LOGICOIL is a net improvement compared with other existing methods, which achieve a predictive coverage of ∼31% of this population. This leap in predictive power offers better opportunities for genome-scale analysis, and analyses of coiled-coil containing protein assemblies.

AVAILABILITY

LOGICOIL is available via a web-interface at http://coiledcoils.chm.bris.ac.uk/LOGICOIL. Source code, training sets and supporting information can be downloaded from the same site.

Hypertrophic and Ulcerated Discoid Lupus Erythematosus

Background:

Hypertrophic lupus is an uncommon clinical variant of chronic cutaneous lupus that remains a challenge to treat. A 45-year-old female day-care worker with long-standing lupus presented with hypertrophic cutaneous involvement on the dorsal hand, elbow, and toe of 6 years' duration. Treatmentsincluded monotherapy with either hydroxychloroquine or chloroquine and potent topical and intralesional steroid injection. Systemic chemotherapy with R–CHOP chemotherapy for stage IIA diffuse large B-cell lymphoma did not clear the skin findings.

Objective:

To review the clinical presentation and treatment of hypertrophic lupus. This report documents clinical improvement in refractory hypertrophic lupus with a regimen of acitretin and combination antimalarial therapy.

Methods:

The available published literature on the treatment of hypertrophic lupus was reviewed. There is limited published experience combining retinoids and antimalarials for the treatment of refractory lupus. Combination therapy with two antimalarials (ie, quinacrine with either hydroxychloroquine or chloroquine) provides therapeutic benefit for resistant cutaneous disease. In this case, triple therapy with two antimalarials and an oral retinoid achieved clinical clearance relatively rapidly, and this effect was maintained over a year.

Results:

This article reports successful treatment of refractory hypertrophic discoid lupus with combination therapy that included chloroquine 250 mg/d, quinacrine 100 mg/d, and actitretin 25 mg/d.

Conclusion:

This report suggests that combination therapy using two antimalarials and an oral retinoid is a consideration for refractory hypertrophic lupus, but further study is warranted.

Contexte:

Le lupus hypertrophique est une variante clinique rare du lupus cutané chronique, une affection difficile à traiter. Une travailleuse des services de garderie souffrant de lupus depuis longtemps a consulté pour la présence de lésions cutanées hypertrophiques sur le dos de la main, le coude et les orteils, et ce, depuis 6 ans. Plusieurs traitements ont été tentés, notamment l'hydroxychloroquine ou la chloroquine en monothérapie, de puissants médicaments topiques, et des injections intralésionnelles de stéroïde; la chimiothérapie R-CHOP par voie générale, pour les lymphomes diffus, à grandes cellules B, de stade IIA, n'est pas venu à bout des lésions cutanées.

Objectif:

L'étude avait pour objectif de passer en revue le tableau clinique et le traitement du lupus hypertrophique. Le présent rapport fait état d'une atténuation clinique du lupus hypertrophique réfractaire, par un traitement composé d'acitrétine et d'une association d'antipaludiques.

Méthode:

Nous avons passé en revue la documentation publiée, accessible sur le traitement du lupus hypertrophique. Les rapports publiés d'expériences associant les rétinoïdes et les antipaludiques dans le traitement du lupus réfractaire étaient peu nombreux. L'association de deux antipaludiques, soit la quinacrine avec l'hydroxychloroquine ou la chloroquine, procure un soulagement thérapeutique dans les cas de maladie cutanée rebelle. Dans le présent cas, la trithérapie, composée de deux antipaludiques et d'un rétinoïde oral, a produit, dans un temps relativement court, la disparition clinique des lésions, et l'effet s'est maintenu sur une période de 1 an.

Résultats:

Le présent rapport fait état du traitement réussi du lupus discoïde hypertrophique réfractaire, composé de chloroquine, 250 mg/j; de quinacrine, 100 mg/j, et d'acitrétine, 25 mg/j.

Conclusion:

D'après le rapport, le traitement d'association, composé de deux antipaludiques et d'un rétinoïde oral, peut être envisagé dans le lupus hypertrophique réfractaire, mais une étude approfondie s'impose.

Behavioral plasticity in honey bees is associated with differences in brain microRNA transcriptome

Small, non-coding microRNAs (miRNAs) have been implicated in many biological processes, including the development of the nervous system. However, the roles of miRNAs in natural behavioral and neuronal plasticity are not well understood. To help address this we characterized the microRNA transcriptome in the adult worker honey bee head and investigated whether changes in microRNA expression levels in the brain are associated with division of labor among honey bees, a well-established model for socially regulated behavior. We determined that several miRNAs were downregulated in bees that specialize on brood care (nurses) relative to foragers. Additional experiments showed that this downregulation is dependent upon social context; it only occurred when nurse bees were in colonies that also contained foragers. Analyses of conservation patterns of brain-expressed miRNAs across Hymenoptera suggest a role for certain miRNAs in the evolution of the Aculeata, which includes all the eusocial hymenopteran species. Our results support the intriguing hypothesis that miRNAs are important regulators of social behavior at both developmental and evolutionary time scales.

Etanercept-induced cutaneous and pulmonary sarcoid-like granulomas resolving with adalimumab

A 59-year-old female with rheumatoid arthritis on etanercept therapy presented with a 7-cm-large subcutaneous forearm mass. Multiple smaller nodules subsequently developed on the upper and lower extremities. Except for a new cough, the patient was systemically well. Biopsy of the mass showed sarcoidal type granulomatous inflammation with nodular aggregations of non-necrotizing epithelioid histiocytes in the subcutis. A chest computed tomography (CT) scan showed mediastinal adenopathy consistent with pulmonary sarcoidosis. Etanercept was discontinued, and the patient was started on adalimumab for rheumatoid arthritis control. The cutaneous nodules fully resolved in 6 months with no additional treatment. A 4-month follow-up CT scan showed significant regression of mediastinal adenopathy. The patient has since been maintained on adalimumab therapy for 2 years with no recurrence of sarcoid-like manifestations. Biologic response modifiers targeting tumor necrosis factor alpha (TNFα) are effective treatments of chronic inflammatory conditions such as rheumatoid arthritis and psoriasis. TNFα represents a major cytokine in granuloma formation, and TNFα inhibitors are sometimes efficacious in the treatment of sarcoidosis. Paradoxically, there is a small volume of literature implicating TNFα inhibitors in the development of sarcoid-like disease. We present this case to promote the recognition of TNFα inhibitor-induced sarcoidosis and to illustrate the wide clinicopathologic differential of sarcoidal type granulomas.

SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences

MOTIVATION

The coiled coil is a ubiquitous α-helical protein structure domain that directs and facilitates protein-protein interactions in a wide variety of biological processes. At the protein-sequence level, coiled coils are quite straightforward and readily recognized via the conspicuous heptad repeats of hydrophobic and polar residues. However, structurally they are more complicated, existing in a range of oligomer states and topologies. Here, we address the issue of predicting coiled-coil oligomeric state from protein sequence.

RESULTS

The predominant coiled-coil oligomer states in Nature are parallel dimers and trimers. Here, we improve and retrain the first-published algorithm, SCORER, that distinguishes these states, and test it against the current standard, MultiCoil. The SCORER algorithm has been revised in two key respects: first, the statistical basis for SCORER is improved markedly. Second, the training set for SCORER has been expanded and updated to include only structurally validated coiled coils. The result is a much-improved oligomer state predictor that outperforms MultiCoil, particularly in assigning oligomer state to short coiled coils, and those that are diverse from the training set.

AVAILABILITY

SCORER 2.0 is available via a web interface at http://coiledcoils.chm.bris.ac.uk/Scorer. Source code, training sets and Supporting Information can be downloaded from the same site.

Cocaine-related retiform purpura: evidence to incriminate the adulterant, levamisole

The term 'cocaine-induced pseudovasculitis' was coined to encompass a constellation of clinical and laboratory findings which mimics a systemic vasculitis but lacks confirmatory evidence of vasculitis on biopsy. Antineutrophil cytoplasmic antibodies reacting with human neutrophil elastase (HNE) have been reported to distinguish the cocaine-related syndrome from a true autoimmune vasculitis. Published cases of retiform purpura related to cocaine use are rare and an etiologic role for levamisole, a common adulterant of cocaine, has been postulated. We describe two female patients aged 39 and 49 years with cocaine-related retiform purpura, mainly affecting the legs. The initial clinical and serological profile in case 1 led to a suspicion of anti-phospholipid syndrome and in case 2 to Wegener's granulomatosis with an unexplained associated neutropenia. Skin biopsies revealed a mixed pattern of leukocytoclastic vasculitis and microvascular thrombosis in case 1 and pure microvascular thrombosis in case 2. Identification of anti-HNE antibodies in both patients linked their disease to cocaine. The mixed vasculopathic pattern in case 1 and the associated neutropenia in case 2, both known adverse effects of levamisole, point to this as the true etiologic agent. Urine toxicology shortly after a binge of cocaine use in each case was positive for levamisole.

Novel Case of Generalized Multinucleate Cell Angiohistiocytoma

Background:

Multinucleate cell angiohistiocytoma is a rare benign fibrohistiocytic and vascular proliferation, typically characterized by the development of solitary papules, in an acral distribution in otherwise healthy late middle-aged to elderly women.

Objective:

Our objectives are to present a novel case of generalized multinucleate cell angiohistiocytoma and to review the current literature regarding the clinical and histologic findings in this condition, as well as its potential causes and treatments.

Observations:

We describe a 35-year-old man who presented with generalized asymptomatic firm violaceous papules. Histopathology revealed dermal vascular proliferation; a perivascular infiltrate of lymphocytes, histiocytes, neutrophils, and plasma cells; thickened surrounding collagen bundles; and characteristic multinucleate cells with scalloped borders.

Conclusion:

Our patient is one of three patients reported to date with generalized lesions of multinucleate cell angiohistiocytoma who were all in a younger age group (20–40 years old) than previously reported for solitary lesions.

Granulomatous vasculitis in Crohn's disease: a clinicopathologic correlate of two unusual cases

Cutaneous complications occur not uncommonly in patients with Crohn's disease (CD). Gastrointestinal CD often shows non-caseating granulomas and a rare cutaneous finding in CD is a sterile granulomatous infiltrate not contiguous with the GI tract, termed extraintestinal CD (ECD). The clinical presentation of ECD is diverse. The most common histopathological presentation is a superficial and deep granulomatous infiltrate that often accompanies a mixed perivascular infiltrate. Here we report two patients with CD and skin lesions characterized on microscopy by granulomatous vasculitis. A 29-year-old female presented with papules and ulcerated nodules above the ankle. The biopsy showed dermal and superficial subcutaneous involvement by a vasocentric infiltrate of mononuclear and multinucleated histiocytes as well as mural fibrin deposition. A 35-year-old male presented with two tender indurated erythematous plaques with punched-out centers on the lower leg. Histopathologically, a granulomatous vasculitis of small and medium-sized vessels in the dermis and subcutis was evident. These two cases represent the rarely described phenomenon of cutaneous granulomatous vasculitis in CD. Previously reported examples of this entity are reviewed.

Enumerating the decomposable neighbours of a decomposable graph under a simple perturbation scheme

Given a decomposable graph, we characterize and enumerate the set of pairs of vertices whose connection or disconnection results in a new graph that is also decomposable. We discuss the relevance of this results to Markov chain Monte Carlo methods that sample or optimize over the space of decomposable graphical models according to probabilities determined by a posterior distribution given observed multivariate data.

Enumerating the junction trees of a decomposable graph

We derive methods for enumerating the distinct junction tree representations for any given decomposable graph. We discuss the relevance of the method to estimating conditional independence graphs of graphical models and give an algorithm that, given a junction tree, will generate uniformly at random a tree from the set of those that represent the same graph. Programs implementing these methods are included as supplemental material.

Inference from genome-wide association studies using a novel Markov model

In this paper we propose a Bayesian modeling approach to the analysis of genome-wide association studies based on single nucleotide polymorphism (SNP) data. Our latent seed model combines various aspects of k-means clustering, hidden Markov models (HMMs) and logistic regression into a fully Bayesian model. It is fitted using the Markov chain Monte Carlo stochastic simulation method, with Metropolis-Hastings update steps. The approach is flexible, both in allowing different types of genetic models, and because it can be easily extended while remaining computationally feasible due to the use of fast algorithms for HMMs. It allows for inference primarily on the location of the causal locus and also on other parameters of interest. The latent seed model is used here to analyze three data sets, using both synthetic and real disease phenotypes with real SNP data, and shows promising results. Our method is able to correctly identify the causal locus in examples where single SNP analysis is both successful and unsuccessful at identifying the causal SNP.

Sub-optimal doses of human recombinant erythropoietin markedly lower serum ferritin

Human recombinant erythropoietin in full dose substantially raises the haemoglobin in patients with end stage renal disease on dialysis. In lower doses no or little rise in haemoglobin is achieved but the ferritin, often very high before treatment, is disproportionately lowered. The hormone therefore may be useful in reducing iron overload in other situations.

Which tests are most useful in distinguishing between reactive thrombocytosis and the thrombocytosis of myeloproliferative disease?

In an attempt to distinguish between thrombocytosis in myeloproliferative disease (MPD) and reactive thrombocytosis (RT) the following aspects of platelet structure and function were evaluated: platelet size, platelet aggregation and adhesion, dense granule and alpha granule components. In addition plasma fibrinogen and von Willebrand factor antigen (vWFag) were measured. In all parameters measured there was a significant difference between normals and both categories of thrombocytosis, however there was considerable overlap between MPD and RT. Plasma fibrinogen emerged as the best single test to discriminate between MPD and RT, levels of less than 5.0 g/l indicating MPD and greater than 5.0 g/l indicating RT.

miRNAs in the Plant Genome: All Things Great and Small

Plants produce two major types of small RNAs that are 21 to 24 nucleotides in size. Small interfering RNAs (siRNAs) are typically involved in transcriptional gene silencing that results from the targeting of genomic DNA and triggering of histone modifications or DNA methylation. Deep sequencing experiments have demonstrated that thousands of loci, usually repetitive sequences, generate these siRNAs. In contrast, microRNAs (miRNAs) are encoded by perhaps just several hundred loci per genome that generate Pol II-derived single stranded precursors which are processed into specific miRNAs. miRNAs act in a post-transcriptional manner to regulate gene function. Recent work has focused on the identification and classification of small RNA-producing loci, as well as understanding small RNA targeting and function, and the evolution of this relatively recently discovered class of regulatory molecules.

Von Willebrand's disease and angiodysplasia treated with thalidomide

A 54-year-old man with type IIB VWD and severe angiodysplasia had such a large blood loss from the bowel that it was difficult to keep up with transfusion requirements. Treatment with factor eight concentrate barely slowed the loss. D.D.A.V.P., Octreotide, and recombinant activated Factor VII, tried separately, were ineffective. The use of Thalidomide at a dose of 150 mg daily has rendered him free from blood loss for the last six months and we suggest would be worth a trial in similar cases.

Audit of correction of high INR in an anticoagulation clinic

Examination of the ways in which staff in the anticoagulation clinic dealt with high International Normalized Ratio (INR) results, not dosed by the computer programme, revealed an unacceptable variation in dosage change. Our aim has been to produce a protocol for either manual use and/or transfer to the computer, which would safely correct INR above the upper limit of the therapeutic range, 4.5 to a maximum of 8.0 within 7 days. We collected a large number of results (4.095) and arranged them in four INR groups (4.6-5.0, 5.1-6.0, 6.1-7.0 and 7.1-8.0) and three dosage classes (<3, 3-8 and >8 mg) in order to analyse the effects of the regimens used. This has enabled us to construct a protocol partly empirically and partly by use of a graph correlating dosage change with reduction in the INR, which will now be tested in the clinic. This protocol will deal with all INR up to a maximum of 7.0 as we have decided to contact patients with higher results. Putting this protocol onto the computer should reduce manual dosing by 15%.

BGX: a fully Bayesian integrated approach to the analysis of Affymetrix GeneChip data

We present Bayesian hierarchical models for the analysis of Affymetrix GeneChip data. The approach we take differs from other available approaches in two fundamental aspects. Firstly, we aim to integrate all processing steps of the raw data in a common statistically coherent framework, allowing all components and thus associated errors to be considered simultaneously. Secondly, inference is based on the full posterior distribution of gene expression indices and derived quantities, such as fold changes or ranks, rather than on single point estimates. Measures of uncertainty on these quantities are thus available. The models presented represent the first building block for integrated Bayesian Analysis of Affymetrix GeneChip data: the models take into account additive as well as multiplicative error, gene expression levels are estimated using perfect match and a fraction of mismatch probes and are modeled on the log scale. Background correction is incorporated by modeling true signal and cross-hybridization explicitly, and a need for further normalization is considerably reduced by allowing for array-specific distributions of nonspecific hybridization. When replicate arrays are available for a condition, posterior distributions of condition-specific gene expression indices are estimated directly, by a simultaneous consideration of replicate probe sets, avoiding averaging over estimates obtained from individual replicate arrays. The performance of the Bayesian model is compared to that of standard available point estimate methods on subsets of the well known GeneLogic and Affymetrix spike-in data. The Bayesian model is found to perform well and the integrated procedure presented appears to hold considerable promise for further development.

Genetics of the DST-mediated mRNA decay pathway using a transgene-based selection

mRNA sequences that control abundance, localization and translation initiation have been identified, yet the factors that recognize these sequences are largely unknown. In this report, a transgene-based strategy designed to isolate mutants of Arabidopsis thaliana that fail to recognize these sequences is described. In this strategy, a selectable gene and a screenable marker gene are put under the control of the sequence element being analysed and mutants are selected with altered abundance of the corresponding marker RNAs. The selection of mutants deficient in recognition of the DST (downstream) mRNA degradation signal is used as a test-case to illustrate some of the technical aspects that have facilitated success. Using this strategy, we report the isolation of a new mutant, dst3, deficient in the DST-mediated mRNA decay pathway. The targeted genetic strategy described circumvents certain technical limitations of biochemical approaches. Hence, it provides a means to investigate a variety of other mechanisms responsible for post-transcriptional regulation.