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.

Paternity testing and other inference about relationships from DNA mixtures.

We present methods for inference about relationships between contributors to a DNA mixture and other individuals of known genotype: a basic example would be testing whether a contributor to a mixture is the father of a child of known genotype. The evidence for such a relationship is evaluated as the likelihood ratio for the specified relationship versus the alternative that there is no relationship. We analyse real casework examples from a criminal case and a disputed paternity case; in both examples part of the evidence was from a DNA mixture. DNA samples are of varying quality and therefore present challenging problems in interpretation. Our methods are based on a recent statistical model for DNA mixtures, in which a Bayesian network (BN) is used as a computational device; the present work builds on that approach, but makes more explicit use of the BN in the modelling. The R code for the analyses presented is freely available as supplementary material. We show how additional information of specific genotypes relevant to the relationship under analysis greatly strengthens the resulting inference. We find that taking full account of the uncertainty inherent in a DNA mixture can yield likelihood ratios very close to what one would obtain if we had a single source DNA profile. Furthermore, the methods can be readily extended to analyse different scenarios as our methods are not limited to the particular genotyping kits used in the examples, to the allele frequency databases used, to the numbers of contributors assumed, to the number of traces analysed simultaneously, nor to the specific hypotheses tested.

Cutaneous manifestations of angioimmunoblastic T-cell lymphoma: clinical and pathological characteristics.

Angioimmunoblastic T-cell lymphoma (AITL), an uncommon variant of peripheral T-cell lymphoma, affects the skin in approximately 50% of cases. Its protean clinical and histopathological cutaneous manifestations pose a challenge in diagnosis, particularly when these precede the diagnosis of AITL on a lymph node biopsy. In this retrospective study, we compared 11 cases of AITL with cutaneous manifestations (mean age 67 years; male:female ratio 1:0.8; 24 skin biopsies) with 20 control cases of inflammatory and non-AITL lymphomatous diseases (mean age 52 years; male:female ratio 1:1.5; 26 skin biopsies). Clinical, histopathological, immunohistochemical, and molecular data were documented. New insights into the clinical evolution of cutaneous involvement by AITL (C-AITL), from early macular, through papular to nodular stages, were observed. Microscopically, a parallel increment in the density of the dermal infiltrate and in the detection of lymphocyte cytological atypia was noted over time. Identification and quantification of follicular T-helper cells (Tfh), the neoplastic lineage, by immunohistochemistry helped to separate cases of C-AITL from inflammatory controls, offering promise as a useful diagnostic adjunct. The presence of T-cell clonality did not have discriminatory value between the 2 groups. Our work suggests that the early maculopapular phase of C-AITL eludes identification on pathological grounds alone and that features such as cytological atypia and high endothelial venules lack diagnostic specificity. In the context of (1) a rash that simulates a drug/viral exanthem or an acute manifestation of a connective tissue disorder, but proves recalcitrant, (2) constitutional abnormalities and/or lymphadenopathy that persist, and (3) a Tfh cell-rich perivascular dermatitis, the diagnosis of early C-AITL can be suspected, but not confirmed, without the benefit of a lymph node biopsy. The later nodular phase of C-AITL occurring in a similar constitutional background, can usually be discerned as lymphomatous, clinically and pathologically. Here a Tfh cell-rich infiltrate is a clue to the specific diagnosis, but confirmation by a nodal evaluation remains mandatory. Despite the difficulty in establishing a diagnosis of C-AITL in its early stages, and speculation that the initial eruptions might be reactive in nature, our sequential data support the concept that these are lymphomatous ab initio. To address the diagnostic challenge presented by this disease, meaningful integration of clinical and pathological data is imperative.

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.

Plasmacytoid dendritic cells in hypertrophic discoid lupus erythematosus: an objective evaluation of their diagnostic value.

BACKGROUND: Hypertrophic discoid lupus erythematosus (HDLE), a rare variant of lupus skin disease, is difficult to distinguish from squamous neoplasms and certain dermatoses microscopically. Recently, recognition of the pathogenetic significance of plasmacytoid dendritic cells (PDCS) in cutaneous lupus erythematosus (LE) and of their patterns of distribution in different manifestations of the disease prompted us to study their diagnostic value in the context of HDLE. METHODS: Using immunohistochemistry (CD123) to label the cells, we examined their quantities and patterns of distribution in 27 tissue samples of HDLE from nine patients compared with 39 inflammatory and neoplastic control samples from 36 patients. RESULTS: Using three parameters pertaining to PDCs: (i) their representation of 10% or more of the inflammatory infiltrate, (ii) their arrangement in clusters of 10 cells or more and (iii) their presence at the dermoepidermal junction, we found them to have significant diagnostic value, with accuracies of 77%, 74% and 71%, respectively. CONCLUSIONS: This study supports the careful descriptive observations of previous authors in the field. It also lends validity to the diagnostic step of mapping, immunohistochemically, the density and distribution of PDCs in suspected cases of HDLE.

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.

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. Treatments included 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.

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.