Analysing olive ripening with digital image RGB histograms.

Digital images are commonly used to monitor processes that are based on colour changes due to their simplicity and easy capture. Colour information in these images can be analysed objectively and accurately using colour histograms. One such process is olive ripening, which is characterized by changes in chemical composition, sensory properties and can be followed by changes in physical appearance, mainly colour. The reference method to quantify the ripeness of olives is the Maturity Index (MI), which is determined by trained experts assigning individual olives into a colour scale through visual inspection. Instead, this study proposes a methodology based on Chemometrics Assisted Colour Histogram-based Analytical Systems (CACHAS) to automatically assess the MI of olives based on R, G, and B colour histograms derived from digital images. The methodology was shown to be easily transferable for routine analysis and capable of controlling the ripening of olives. The study also confirms the high potential of digital images to understand the ripening process of olives (and potentially other fruits) and to predict the MI with satisfactory accuracy, providing an objective and reproducible alternative to visual inspection of trained experts.

Dermoscopy of haemosiderotic/aneurysmal dermatofibroma: A morphological study of 110 cases.

BACKGROUND: Haemosiderotic and aneurysmal dermatofibromas are uncommon and frequently misdiagnosed lesions, which can be considered as different histopathological stages of the same tumour. A dermoscopic diagnosis testing accuracy has not been performed for these tumours to date. OBJECTIVES: To determine the diagnostic significance of dermoscopic structures and patterns associated with haemosiderotic/ aneurysmal dermatofibromas in a large series. METHODS: Dermoscopic images of histopathologically proven cases of 110 haemosiderotic/ aneurysmal dermatofibromas and 501 other tumours were collected. The frequency, sensitivity, specificity, positive predictive value and negative predictive value of the dermoscopic structures and patterns associated with these lesions were calculated. RESULTS: Haemosiderotic/ aneurysmal dermatofibromas are mostly symmetric lesions (86.5%), and a prominent homogeneous area was present in 100% of them. The presence of vascular structures was very common (86.4%), and dotted vessels were predominant (58.2%). Shiny white structures were seen in 85.5% of lesions, while a peripheral delicate pigment network was present in 69.1%. The most significant pattern was the one composed of a prominent homogeneous area and peripheral delicate pigment network, which showed a specificity of 100% with a relatively good sensitivity (69.1%). All the patterns containing a peripheral delicate pigment network showed very good specificities, positive predictive values and negative predictive values. Those patterns without a peripheral delicate pigment network showed the highest sensitivities, but they showed a significant overlap with other tumours, mainly with melanoma. CONCLUSIONS: Dermoscopy is helpful in improving the diagnostic accuracy of haemosiderotic/ aneurysmal dermatofibromas. However, there is a considerable dermoscopic overlap between these tumours and melanoma, specifically when the peripheral delicate pigment network is absent.

Discordant knowing: A social cognitive structure underlying fanaticism.

Examining the epistemic and social-cognitive structures underlying fanaticism, radicalization, and extremism should shed light on how these harmful phenomena develop and can be prevented. In nine studies (N = 3,277), we examined whether discordant knowing-felt knowledge about something that one perceives as opposed by most others-underlies fanaticism. Across multifaceted approaches, experimentally manipulating participants' views to fall under this framework (e.g., "I am certain about X, but most other people think X is unknowable or wrong") heightened indicators of fanaticism, including aggression, determined ignorance, and wanting to join extreme groups in the service of these views. Additional analyses found that this effect occurs via threat-based mechanisms (Studies 1-7), can be intervened on to prevent fanaticism (Study 2), is conditional on the potency of opposition (Study 3), differs from effects on extremism (Study 4), and extends to mental representations of the self (Study 5). Generalizing these findings to real-world contexts, inducing participants with discordant knowledge about the 2020 U.S. Presidential Election and the morality of abortion heightened fanaticism regarding these topics (Studies 6 and 7). Additionally, antivaccine fanatics and followers of a real-world fanatical religious group exhibited greater discordant knowing than nonfanatical individuals (Studies 8 and 9). Collectively, the present studies suggest that a specific epistemic structure-discordant knowing-underlies fanaticism, and further, highlight the potential of investigating constructs like fanaticism from an epistemic social cognitive perspective. (PsycInfo Database Record (c) 2022 APA, all rights reserved).

Dermoscopy of inflamed seborrheic keratosis: A great mimic of malignancy.

BACKGROUND: Clinical and dermoscopic recognition of seborrheic keratoses (SKs) is often straightforward, and biopsy might not be required. However, inflamed SKs (iSKs) can pose a diagnostic challenge. Dermoscopic features of iSKs have not yet been evaluated to date. OBJECTIVES: To assess the diagnostic ability of a group of dermatologists to diagnose iSKs by dermoscopy. To evaluate the dermoscopic findings of a long series of inflamed seborrheic keratoses. METHODS: Clinical and dermoscopic images of 100 difficult-to-diagnose skin tumours, including 29 iSKs, were presented to 33 clinicians (24 dermatologists and 9 dermatology residents), who were blinded to the diagnosis. The dermoscopic features of a series of 219 iSKs were retrospectively analysed. RESULTS: iSKs were correctly identified in a 37.6% of cases. Classic dermoscopic criteria were present in only 47% of iSKs. The most frequent dermoscopic feature in iSKs was the presence of vascularization (91.3%), but only a 44.5% showed predominance of hairpin vessels. A bluish hue was observed in 18.3% of lesions. Seven dermoscopic patterns were identified, based on the dermoscopic similarity to other tumours: seborrheic keratosis-like (28.8%); squamous cell carcinoma-like (25.6%); melanoma-like (17.8%); keratoacanthoma-like (6.8%); basal cell carcinoma-like (5.9%); verruca vulgaris-like (5.9%); nevus-like (2.3%). CONCLUSIONS: The diagnosis of iSKs can be challenging even with dermoscopy. They may behave as authentic mimics of other cutaneous tumours, including squamous cell carcinoma or melanoma. For this reason, histopathological examination should be mandatory in these cases.

The Usefulness of Dermoscopy for the Recognition of Malignant Collision Tumors.

BACKGROUND: Preoperative diagnosis of malignant collision tumors (MCT) is extremely difficult. The value of dermoscopy to improve the correct detection of these tumors has not been previously studied. This study aims to evaluate the diagnostic accuracy of MCT with and without dermoscopy and to describe the dermoscopic features of a large series of MCT. METHODS: Dermoscopic images of 161 MCT were evaluated. Clinical and dermoscopic images of histopathologically proven MCT intermingled with other tumors were randomly presented to clinicians with different levels of experience, blinded to the diagnosis and objective of the study. The clinical and dermoscopic diagnostic accuracies were measured separately. RESULTS: A total of 161 histopathologically proven cases of MCT were collected. The most frequent MCT was basal cell carcinoma-seborrheic keratosis collision tumor (CT; 37.9%), followed by basal cell carcinoma-melanocytic nevus CT (19.9%), and melanoma-seborrheic keratosis CT (6.8%). Diagnostic accuracy among experts on dermoscopy was 71.4%. The study included 119 participants. The percentage of correct diagnoses was 8% by naked eye examination and 36.4% by dermoscopy (p < 0.001). The presence of the malignant component in the cases of MCT was not recognizable in 19.1% of cases by naked eye examination and in 11.8% of cases by dermoscopy (p < 0.001). CONCLUSIONS: The diagnosis of MCT can be assisted and clarified by dermoscopy. However, many of these lesions manifest complex morphologies and continue to be challenging, even for experts on dermoscopy. Atypical, uncertain, or non-classifiable lesions still need a complete excision for the final diagnosis.

Percepciones sobre el uso del condón en migrantes haitianos en la frontera noroeste de México / Perceptions of condom use in Haitian migrants on the northwestern border of México

Resumen Objetivo: Identificar las percepciones sobre el uso de condón en migrantes haitianos en la frontera noroeste de México. Materiales y métodos: Estudio de enfoque cualitativo y diseño etnográfico, en el abordo a siete migrantes haitianos en la zona fronteriza de la ciudad de Mexicali, Baja California, México, con quienes se desarrolló una entrevista semiestructurada, la información fue analizada por el programa NVivo, para comprender frecuencia y estructura de los datos; posteriormente se realizó un proceso de categorización, interpretación y teorización del fenómeno de estudio. De un total de 281 unidades de análisis, se realizó un proceso de categorización, que permitió estructurar dos categorías, seis subcategorías y 12 códigos. Resultados: Se identifica que el uso del condón en migrantes haitianos, es interpretado como un elemento de protección a la salud sexual en la prevención de embarazos no planeados; no obstante, se identifican barreras y consecuencias del uso a nivel personal, cultural y religioso. La construcción de la idea de usarlo, recae en el tipo de relación y nivel de confianza que se tiene de la pareja sexual por lo que estar casado o vivir en concubinato, exime de la obligación o del compromiso social de usar el condón. Así mismo la idea de protección, no refleja la preocupación sobre la transmisión de las ITS. Conclusiones: El condón se percibe como un elemento de importancia para la prevención de embarazos no planeados y del VIH, sin embargo, la presencia de factores personales, sensoriales e ideológicos limitan el uso constante del condón; por lo que el desarrollo de intervenciones culturalmente adaptadas, a la población de migrantes haitianos, en el contexto de la frontera norte de México, pueden fortalecer el uso del condón y la prevención del VIH

Abstract Objective: To identify the perceptions of condom use in Haitian migrants in the northwestern border of Mexico. Materials and methods: Study with a qualitative approach and ethnographic design, on board seven Haitian migrants in the border area of the city of Mexicali, Baja California, Mexico, with whom a semi-structured interview was developed, the information was analyzed by the NVivo program, to understand the frequency and structure of the data; later a process of categorization, interpretation and theorization of the study phenomenon was carried out. Out of a total of 281 units of analysis, a categorization process was carried out, which made it possible to structure two categories, six subcategories and 12 codes. Results: It is identified that the use of condoms in Haitian migrants is interpreted as an element of protection of sexual health in the prevention of unplanned pregnancies; however, barriers and consequences of use are identified on a personal, cultural and religious level. The construction of the idea of using it relies on the type of relationship and level of trust that one has in the sexual partner, so being married or living in a common-law relationship exempts the obligation or social commitment of using the condom. Likewise, the idea of protection does not reflect the concern about the transmission of STIs. Conclusions: The condom is perceived as an important element for the prevention of unintended pregnancies and HIV, however, the presence of personal, sensory and ideological factors limit the constant use of the condom; Therefore, the development of culturally adapted interventions for the Haitian migrant population, in the context of the northern border of Mexico, can strengthen condom use and HIV prevention.

Dermoscopy of Targetoid Hemosiderotic Hemangioma: A Morphological Study of 35 Cases.

BACKGROUND: Targetoid hemosiderotic hemangioma is an uncommon, vascular, benign solitary lesion of lymphatic origin that can be misdiagnosed as other tumors including melanomas. OBJECTIVES: To evaluate the dermoscopic features of a large series of targetoid hemosiderotic hemangiomas. METHODS: Digital dermoscopic images of 35 histopathologically confirmed cases of targetoid hemosiderotic hemangiomas collected from 7 hospitals in Spain and Italy were evaluated for the presence of dermoscopic structures and patterns. RESULTS: The results of our study reveal that the presence of central red and dark lacunae and a peripheral circular reddish-violaceous homogeneous area is the most common dermoscopic pattern in targetoid hemosiderotic hemangioma (71.4%). The targetoid hemosiderotic hemangiomas of our study were correctly diagnosed in 77% of cases. CONCLUSION: Dermoscopy is helpful in improving the diagnosis of targetoid hemosiderotic hemangioma. However, attention must be paid to those cases that dermoscopically may show nontargetoid patterns, which often mimic other lesions, including melanoma.

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data.

MOTIVATION: Because of the advantages of RNA sequencing (RNA-Seq) over microarrays, it is gaining widespread popularity for highly parallel gene expression analysis. For example, RNA-Seq is expected to be able to provide accurate identification and quantification of full-length splice forms. A number of informatics packages have been developed for this purpose, but short reads make it a difficult problem in principle. Sequencing error and polymorphisms add further complications. It has become necessary to perform studies to determine which algorithms perform best and which if any algorithms perform adequately. However, there is a dearth of independent and unbiased benchmarking studies. Here we take an approach using both simulated and experimental benchmark data to evaluate their accuracy. RESULTS: We conclude that most methods are inaccurate even using idealized data, and that no method is highly accurate once multiple splice forms, polymorphisms, intron signal, sequencing errors, alignment errors, annotation errors and other complicating factors are present. These results point to the pressing need for further algorithm development. AVAILABILITY AND IMPLEMENTATION: Simulated datasets and other supporting information can be found at http://bioinf.itmat.upenn.edu/BEERS/bp2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

IVT-seq reveals extreme bias in RNA sequencing.

BACKGROUND: RNA-seq is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the proliferation of library construction methods, understanding the bias it introduces is incomplete but critical to realizing its value. RESULTS: We present a method, in vitro transcription sequencing (IVT-seq), for identifying and assessing the technical biases in RNA-seq library generation and sequencing at scale. We created a pool of over 1,000 in vitro transcribed RNAs from a full-length human cDNA library and sequenced them with polyA and total RNA-seq, the most common protocols. Because each cDNA is full length, and we show in vitro transcription is incredibly processive, each base in each transcript should be equivalently represented. However, with common RNA-seq applications and platforms, we find 50% of transcripts have more than two-fold and 10% have more than 10-fold differences in within-transcript sequence coverage. We also find greater than 6% of transcripts have regions of dramatically unpredictable sequencing coverage between samples, confounding accurate determination of their expression. We use a combination of experimental and computational approaches to show rRNA depletion is responsible for the most significant variability in coverage, and several sequence determinants also strongly influence representation. CONCLUSIONS: These results show the utility of IVT-seq for promoting better understanding of bias introduced by RNA-seq. We find rRNA depletion is responsible for substantial, unappreciated biases in coverage introduced during library preparation. These biases suggest exon-level expression analysis may be inadvisable, and we recommend caution when interpreting RNA-seq results.

CircaDB: a database of mammalian circadian gene expression profiles.

CircaDB (http://circadb.org) is a new database of circadian transcriptional profiles from time course expression experiments from mice and humans. Each transcript's expression was evaluated by three separate algorithms, JTK_Cycle, Lomb Scargle and DeLichtenberg. Users can query the gene annotations using simple and powerful full text search terms, restrict results to specific data sets and provide probability thresholds for each algorithm. Visualizations of the data are intuitive charts that convey profile information more effectively than a table of probabilities. The CircaDB web application is open source and available at http://github.com/itmat/circadb.

The mzIdentML data standard for mass spectrometry-based proteomics results.

We report the release of mzIdentML, an exchange standard for peptide and protein identification data, designed by the Proteomics Standards Initiative. The format was developed by the Proteomics Standards Initiative in collaboration with instrument and software vendors, and the developers of the major open-source projects in proteomics. Software implementations have been developed to enable conversion from most popular proprietary and open-source formats, and mzIdentML will soon be supported by the major public repositories. These developments enable proteomics scientists to start working with the standard for exchanging and publishing data sets in support of publications and they provide a stable platform for bioinformatics groups and commercial software vendors to work with a single file format for identification data.

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

MOTIVATION: A critical task in high-throughput sequencing is aligning millions of short reads to a reference genome. Alignment is especially complicated for RNA sequencing (RNA-Seq) because of RNA splicing. A number of RNA-Seq algorithms are available, and claim to align reads with high accuracy and efficiency while detecting splice junctions. RNA-Seq data are discrete in nature; therefore, with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. The exercise to rigorously compare all viable published RNA-Seq algorithms has not been performed previously. RESULTS: We developed an RNA-Seq simulator that models the main impediments to RNA alignment, including alternative splicing, insertions, deletions, substitutions, sequencing errors and intron signal. We used this simulator to measure the accuracy and robustness of available algorithms at the base and junction levels. Additionally, we used reverse transcription-polymerase chain reaction (RT-PCR) and Sanger sequencing to validate the ability of the algorithms to detect novel transcript features such as novel exons and alternative splicing in RNA-Seq data from mouse retina. A pipeline based on BLAT was developed to explore the performance of established tools for this problem, and to compare it to the recently developed methods. This pipeline, the RNA-Seq Unified Mapper (RUM), performs comparably to the best current aligners and provides an advantageous combination of accuracy, speed and usability. AVAILABILITY: The RUM pipeline is distributed via the Amazon Cloud and for computing clusters using the Sun Grid Engine (http://cbil.upenn.edu/RUM). CONTACT: ggrant@pcbi.upenn.edu; epierce@mail.med.upenn.edu SUPPLEMENTARY INFORMATION: The RNA-Seq sequence reads described in the article are deposited at GEO, accession GSE26248.

Genetic polymorphisms in DNA repair and oxidative stress pathways associated with malignant melanoma susceptibility.

BACKGROUND: Base excision repair (BER) and nucleotide excision repair (NER) pathways eliminate a wide variety of DNA damage, including UV photoproducts. The ability of each individual to repair DNA damage following different causes might explain at least in part the variability in cancer susceptibility. Moreover, inflammatory response to UV exposure may further contribute to skin carcinogenesis by oxidative stress mechanisms. Single nucleotide polymorphisms in genes encoding various DNA-repair enzymes and oxidative stress factors may be candidate low-penetrance variants with a role in susceptibility to different cancers, particularly in those with aetiologies linked to environmental exposure, such as malignant melanoma (MM). METHODS: In this case-control study, 684 Spanish sporadic MM patients and 406 cancer-free control subjects were included and the role of 46 polymorphisms belonging to 16 BER and NER genes as well as 11 genes involved in oxidative stress processes were investigated. RESULTS: One polymorphism was identified to be individually associated with MM in the Spanish population. The variant was found in the NOS1 oxidative stress gene (rs2682826; p-value=0.01). These results suggest a putative role of oxidative stress processes in the genetic predisposition to melanoma. CONCLUSION: To the authors' knowledge, this is the largest DNA repair-related SNP study in melanoma risk conducted in the Spanish population up to now. Furthermore, it also represents a comprehensive genetic study of several oxidative stress polymorphisms tested in relation to MM susceptibility.

A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.

As the incidence of Malignant Melanoma (MM) reflects an interaction between skin colour and UV exposure, variations in genes implicated in pigmentation and tanning response to UV may be associated with susceptibility to MM. In this study, 363 SNPs in 65 gene regions belonging to the pigmentation pathway have been successfully genotyped using a SNP array. Five hundred and ninety MM cases and 507 controls were analyzed in a discovery phase I. Ten candidate SNPs based on a p-value threshold of 0.01 were identified. Two of them, rs35414 (SLC45A2) and rs2069398 (SILV/CKD2), were statistically significant after conservative Bonferroni correction. The best six SNPs were further tested in an independent Spanish series (624 MM cases and 789 controls). A novel SNP located on the SLC45A2 gene (rs35414) was found to be significantly associated with melanoma in both phase I and phase II (P<0.0001). None of the other five SNPs were replicated in this second phase of the study. However, three SNPs in TYR, SILV/CDK2 and ADAMTS20 genes (rs17793678, rs2069398 and rs1510521 respectively) had an overall p-value<0.05 when considering the whole DNA collection (1214 MM cases and 1296 controls). Both the SLC45A2 and the SILV/CDK2 variants behave as protective alleles, while the TYR and ADAMTS20 variants seem to function as risk alleles. Cumulative effects were detected when these four variants were considered together. Furthermore, individuals carrying two or more mutations in MC1R, a well-known low penetrance melanoma-predisposing gene, had a decreased MM risk if concurrently bearing the SLC45A2 protective variant. To our knowledge, this is the largest study on Spanish sporadic MM cases to date.

Letter: Umbilical basal cell carcinoma in a 21-year-old man: Report of an exceptional case and dermatoscopic evaluation.

We report an exceptional case of umbilical basal cell carcinoma (BCC) in a 21-year-old man, whose correct diagnosis was suggested by dermoscopy during initial complete body mole mapping. Although BCC is a common skin tumor, only 7 cases of BCC arising within the umbilicus have been reported previously. To the best of our knowledge, our patient is unique because of his age, being the youngest case of umbilical BCC described in the literature. Complete examination and digital dermoscopic monitoring let us identify an asymptomatic, nonpigmented papule at the umbilicus. Dermoscopy images revealed signs of superficial ulceration and several types of vascular structures, which gave us the clue for the diagnosis and helped us differentiate it from other lesions such as Spitz nevus or amelanotic melanoma. The diagnosis was confirmed with histopathology after excision and there was no evidence of relapse in the following four years.

mzML--a community standard for mass spectrometry data.

Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With the rapid advances in mass spectrometry technology and methods, it has become imperative to provide a standard output format for mass spectrometry data that will facilitate data sharing and analysis. Initially, the efforts to develop a standard format for mass spectrometry data resulted in multiple formats, each designed with a different underlying philosophy. To resolve the issues associated with having multiple formats, vendors, researchers, and software developers convened under the banner of the HUPO PSI to develop a single standard. The new data format incorporated many of the desirable technical attributes from the previous data formats, while adding a number of improvements, including features such as a controlled vocabulary with validation tools to ensure consistent usage of the format, improved support for selected reaction monitoring data, and immediately available implementations to facilitate rapid adoption by the community. The resulting standard data format, mzML, is a well tested open-source format for mass spectrometer output files that can be readily utilized by the community and easily adapted for incremental advances in mass spectrometry technology.

Dermoscopic findings and histological correlation of the acral volar pigmented maculae in Laugier-Hunziker syndrome.

Laugier-Hunziker syndrome (LHS) is an acquired, benign, macular hyperpigmentation of the lips and oral mucosa, often associated with pigmentation of the nails. Volar acral maculae on the palms and fingertips of patients affected by LHS are a typical feature of this rare entity. Dermoscopic examination of these maculae has been described in a previous report, in which authors found a parallel-furrow pattern. We describe two cases in which a parallel-ridge pattern (PRP) was found on the dermoscopic examination of the pigmented acral lesions. Histological examination showed increased melanin in basal keratinocytes, which was most prominent in those located at the crista intermedia profunda, that is, in the epidermal rete ridges underlying the surface ridges. In our study, dermoscopic features of the pigmented maculae found on LHS differed from those previously described. In addition, by means of this case report, the histological features of these lesions are described for the first time, showing an excellent correlation with dermoscopy. The reported cases prove that although the PRP is very specific of melanoma, it is also possible to find it in benign lesions. Therefore, we must be familiar with the differential diagnosis of PRP, and take into consideration the clinical context in which we find it. Further studies are needed to increase our knowledge on the histological and dermoscopic features of acral pigmented maculae of LHS.

The Gene Wiki: community intelligence applied to human gene annotation.

Annotating the function of all human genes is a critical, yet formidable, challenge. Current gene annotation efforts focus on centralized curation resources, but it is increasingly clear that this approach does not scale with the rapid growth of the biomedical literature. The Gene Wiki utilizes an alternative and complementary model based on the principle of community intelligence. Directly integrated within the online encyclopedia, Wikipedia, the goal of this effort is to build a gene-specific review article for every gene in the human genome, where each article is collaboratively written, continuously updated and community reviewed. Previously, we described the creation of Gene Wiki 'stubs' for approximately 9000 human genes. Here, we describe ongoing systematic improvements to these articles to increase their utility. Moreover, we retrospectively examine the community usage and improvement of the Gene Wiki, providing evidence of a critical mass of users and editors. Gene Wiki articles are freely accessible within the Wikipedia web site, and additional links and information are available at http://en.wikipedia.org/wiki/Portal:Gene_Wiki.