Next-generation sequencing of uveal melanoma with clinical and histological correlations: Prognostic value of new mutations in the PI3K/AKT/mTOR pathway.

BACKGROUND: Uveal melanoma (UM) is the eye's most common primary malignancy and there are no effective therapies for disseminated disease. It is important to try to know the patient's prognosis. The aim of this study was to reflect genetic variants, studied using NGS, of a series of 69 cases of UM and its correlation with histopathology and clinical progression. METHODS: We performed targeted NGS using a 519-gene panel. RESULTS: There were selected 28 different mutated genes, showing a total of 231 genetic variants that affected the function of the protein. The most common secondary mutations occurred in SF3B1 (in 26%), followed by BAP1 (in 23%), LRP1B (22%) and FGFR4 (20%). BAP1 mutation was associated with a greater likelihood of metastases and with greater presence of epithelioid cells. LRP1B was also associated with presence of epithelioid cells SF3B1 mutation was significantly associated with a spindle morphology. We found variants in the RAD51B, TOP2A, PTPRD, TSC2, DHX9, PDK1 and MTOR that have not been previously reported in consulted databases. The presence of a mutation in: CHEK2, DHX9 and PDK1 was associated with metastases. CONCLUSIONS: BAP1 is the most solid biomarker of a poor prognosis in UM and mutations can be detected using NGS. SF3B1 is associated with the spindle cell subtype of UM, which gives it probably a favourable prognostic value. Our study suggests that mutations in DHX9 and PDK1 can have prognostic value. These potential biomarkers are related to the PI3K/AKT/mTOR pathway and makes them candidates for developing new directed therapies.

Morphological and Molecular Study of Hybrid Oncocytic/Chromophobe Tumor of the Kidney Associated with Sporadic Renal Oncocytosis and Chronic B-Cell Lymphocytic Leukemia: The Possible Contribution of Lymphoma to Renal Oncocytosis.

Hybrid oncocytic/chromophobe tumor (HOCT) of the kidney arising from a precursor oncocytosis not associated with the Birt-Hogg-Dubé (BHD) syndrome is an unusual and highly interesting neoplasm. Immunohistochemical and molecular findings suggest that HOCT is an entity distinct from both oncocytoma and chromophobe carcinoma. Although uncertainty persists regarding the factors predisposing to the development of HOCT, experimental findings suggest that it may arise due to the effect of toxins or in association with chronic kidney failure. The potential role of prior renal lymphoma in the development of oncocytosis has not hitherto been examined. We present a morphological, immunohistochemical, and molecular analysis of an HOCT arising from renal oncocytosis in conjunction with CLL affecting the kidney. The findings suggest that this tumor belongs to a family of similar neoplasms including oncocytoma, the eosinophilic variant of chromophobe renal-cell carcinoma (CRCC), and low-grade oncocytic tumor, even though these neoplasms may arise from different precursor lesions. HOCT and oncocytosis revealed the same immunohistochemical profile consistent on positivity for epithelial membrane antigen (EMA), cytokeratin 7 (Ck7), E-cadherin, CAM 5.2 and negativity for Pax-8, vimentin, renal-cell carcinoma (RCC) antigen, CD117, racemase, progesterone receptor, and CD10. The Ki-67 proliferation index was <1%. Molecular analysis of the tumor revealed the AKT3 gene mutation variant, classified as probably pathogenic, together with FOS1 gene amplification and no copy number variations (CNVs). Finally, we present a case of HOCT arising from a nonhereditary renal oncocytosis in conjunction with B lymphoma that raises interesting questions regarding pathogenesis.

Diagnostic role of DOG-1, GFAP and B-catenin in Basal cell Adenoma and Cellular Pleomorphic Adenoma of the Salivary Gland.

BACKGROUND: Pleomorphic Adenoma (PA) and Basal cell adenoma (BCA) are benign salivary gland tumors that may pose a diagnostic challenge if typical features are not present. Due to the increased relapse and malignant transformation rate of the former, a correct diagnosis carries relevant prognostic information. Even though immunohistochemistry (IHC) plays a limited role in the diagnosis of these tumors, the use of IHC panels could increase diagnostic accuracy. In the present work, we aimed to demonstrate that the use of an IHC panel consisting of Glial Fibrillary Acid Protein (GFAP), B-Catenin and Discovered On GIST 1 (DOG-1) can aid in the differential diagnosis between PA and BCA. METHODS: We analyzed 18 cases of benign salivary gland tumors (Pleomorphic adenomas and Basal cell adenomas) with overlapping histologic features. First, a head and neck pathologist diagnosed the cases relying on morphology alone. Afterwards, cases were re-evaluated considering the IHC panel results. Inter-observer IHC scoring concordance was evaluated with pre-defined marker cut-off points using Cohen's Kappa scores. RESULTS: Based on morphology alone, 9 cases were classified as PA while the remaining tumors were considered to be BCA. Five out of nine BCA cases showed GFAP staining and absent nuclear B-catenin and DOG-1 positivity. Conversely, 2 PA cases showed absent GFAP and positive nuclear B-catenin with concurrent DOG-1 expression. Therefore, after IHC evaluation, up to 40% of morphologic diagnoses were reconsidered. Overall, the inter-observer concordance for IHC evaluation was good (resulting Kappa Scores between 0.78 and 1). CONCLUSION: Our work supports the use of a concise IHC panel to improve the diagnostic accuracy of benign salivary gland tumors with overlapping histologic features.

An Unusual Case of Desmoplastic Melanoma With Monster Cells Imitating an Atypical Fibroxanthoma.

Numerous cells with very large and irregular nuclei ("monster" cells) have not hitherto been reported in desmoplastic melanoma (DM). Their prognostic significance in melanomas is a matter of debate, although some authors have associated them with more aggressive tumor behavior. We report a mixed DM on the scalp of an 88-year-old woman imitating an atypical fibroxanthoma. Tumor cells stained positive for SOX10, S100, and cyclin D1; BRAF mutation status was negative, and fluorescence in situ hybridization analysis showed copy number gains in 11q13 (cyclin D1) and 6p25 (RREB1), and loss in 6q23 (MYB). Cyclin D1 amplification is associated with poor prognosis in melanoma.

FAIR4Health: Findable, Accessible, Interoperable and Reusable data to foster Health Research.

Due to the nature of health data, its sharing and reuse for research are limited by ethical, legal and technical barriers. The FAIR4Health project facilitated and promoted the application of FAIR principles in health research data, derived from the publicly funded health research initiatives to make them Findable, Accessible, Interoperable, and Reusable (FAIR). To confirm the feasibility of the FAIR4Health solution, we performed two pathfinder case studies to carry out federated machine learning algorithms on FAIRified datasets from five health research organizations. The case studies demonstrated the potential impact of the developed FAIR4Health solution on health outcomes and social care research. Finally, we promoted the FAIRified data to share and reuse in the European Union Health Research community, defining an effective EU-wide strategy for the use of FAIR principles in health research and preparing the ground for a roadmap for health research institutions. This scientific report presents a general overview of the FAIR4Health solution: from the FAIRification workflow design to translate raw data/metadata to FAIR data/metadata in the health research domain to the FAIR4Health demonstrators' performance.

Mitotic count: A need for standardization.

PURPOSE: The mitotic count (MC), number of mitosis per unit area, is a very important parameter frequently used for classification and grading of some tumors. Traditionally, the MC has been expressed in terms of number of mitoses per high power field. The size of the field of view can vary greatly among different microscopes. In order to avoid under or overestimation of mitotic count, a conversion needs to be made. METHODS: A simple formula based on a simple rule of three has been devised to standardize the mitotic count to the reference area by multiplying the number of mitotic figures by a correction factor which has been calculated for the most frequently used microscopes and various common tumors. RESULTS AND CONCLUSIONS: We propose this simple method, which involves only a single multiplication, to standardize the mitotic count to the reference area.

From Raw Data to FAIR Data: The FAIRification Workflow for Health Research.

BACKGROUND: FAIR (findability, accessibility, interoperability, and reusability) guiding principles seek the reuse of data and other digital research input, output, and objects (algorithms, tools, and workflows that led to that data) making them findable, accessible, interoperable, and reusable. GO FAIR - a bottom-up, stakeholder driven and self-governed initiative - defined a seven-step FAIRification process focusing on data, but also indicating the required work for metadata. This FAIRification process aims at addressing the translation of raw datasets into FAIR datasets in a general way, without considering specific requirements and challenges that may arise when dealing with some particular types of data. OBJECTIVES: This scientific contribution addresses the architecture design of an open technological solution built upon the FAIRification process proposed by "GO FAIR" which addresses the identified gaps that such process has when dealing with health datasets. METHODS: A common FAIRification workflow was developed by applying restrictions on existing steps and introducing new steps for specific requirements of health data. These requirements have been elicited after analyzing the FAIRification workflow from different perspectives: technical barriers, ethical implications, and legal framework. This analysis identified gaps when applying the FAIRification process proposed by GO FAIR to health research data management in terms of data curation, validation, deidentification, versioning, and indexing. RESULTS: A technological architecture based on the use of Health Level Seven International (HL7) FHIR (fast health care interoperability resources) resources is proposed to support the revised FAIRification workflow. DISCUSSION: Research funding agencies all over the world increasingly demand the application of the FAIR guiding principles to health research output. Existing tools do not fully address the identified needs for health data management. Therefore, researchers may benefit in the coming years from a common framework that supports the proposed FAIRification workflow applied to health datasets. CONCLUSION: Routine health care datasets or data resulting from health research can be FAIRified, shared and reused within the health research community following the proposed FAIRification workflow and implementing technical architecture.

p73beta-Mediated apoptosis requires p57kip2 induction and IEX-1 inhibition.

Similarly to p53, p73alpha and p73beta induce growth arrest and/or apoptosis in response to DNA damage or when exogenously expressed. However, how they trigger apoptosis remains unresolved. After stable transduction of either p73alpha or p73beta, a greater apoptotic response was observed for p73beta in both primary and tumor cells. Consistently, blocking ectopic and endogenous p73beta expression by specific shRNA significantly decreased apoptotic levels after DNA damage. We found that p73beta targets the apoptotic program at multiple levels: (i) facilitating caspase activation through p53-dependent signals and (ii) inducing p57KIP2, while down-regulating c-IPA1 and IEX1 through a p53-independent mechanism. p73beta-mediated apoptosis was considerably reduced after inhibition of p57(KIP2) by small interfering RNA, IEX-1 overexpression, and in mouse embryo fibroblasts derived from p57-/- mice. Data from this study offer evidence for the apoptotic activity exclusive of p73beta. In the clinical context, these results might have potential therapeutic implications, because p73beta could induce alternative apoptotic responses in tumors harboring p53 mutations.

[Reproductive activity of Strombus gigas (Mesogasteropoda: Strombidae) in differente habitats of Alacranes reef, Yucatán]. / Actividad reproductiva de Strombus gigas (Mesogasteropoda: Strombidae) en diferentes hábitats del Arrecife Alacranes, Yucatán.

The spawning relationships with temperature/photoperiod of Strombus gigas were investigated considering three habitats in Alacranes Reef, Yucatan, between February 1999 and March 2000. The sites were 22 degrees 34'N, 89 degrees 42'W (site 1); 22 degrees 29'N, 89"45'W (site 2) and 22 degrees 22'N, 89 degrees 39'W (site 3). At each site, transects (100 m x 10 m) were done. Different kinds of reproductive behavior of S. gigas was observed: such as copulating and egg-laying. Individuals alone and egg masses were registered as well. The S. gigas shell length and lip thickness were measured. High density of adults was found at site 2 with 87 conchs in one transect of 1000 m2. The mean density per m2 was 0.004 for site 1; 0.035 for site 2; and 0.003 for site 3. The mean shell length was 220 mm and the lip thickness mean was 16 mm (N = 783) for all sites. In February 1999 egg-laying female was found on sand. There was a high reproductive activity at site 2 with 8 egg-laying and 18 egg masses. Minimum reproductive activity was found at site 3 with 2 egg masses. The bottom-water temperature was related positively with copulating pairs (r = 0.723, f = 11.05, p < 0.01) and egg masses (r = 0.736, f = 11.82, p < 0.1). Correlation between photoperiod with copulating pairs (r = 0.857, f = 27.78, p < 0.01) and egg masses (r = 0.782, f = 15.77, p < 0.01) were found as well.

ABA is an essential signal for plant resistance to pathogens affecting JA biosynthesis and the activation of defenses in Arabidopsis.

Analyses of Arabidopsis thaliana defense response to the damping-off oomycete pathogen Pythium irregulare show that resistance to P. irregulare requires a multicomponent defense strategy. Penetration represents a first layer, as indicated by the susceptibility of pen2 mutants, followed by recognition, likely mediated by ERECTA receptor-like kinases. Subsequent signaling of inducible defenses is predominantly mediated by jasmonic acid (JA), with insensitive coi1 mutants showing extreme susceptibility. In contrast with the generally accepted roles of ethylene and salicylic acid cooperating with or antagonizing, respectively, JA in the activation of defenses against necrotrophs, both are required to prevent disease progression, although much less so than JA. Meta-analysis of transcriptome profiles confirmed the predominant role of JA in activation of P. irregulare-induced defenses and uncovered abscisic acid (ABA) as an important regulator of defense gene expression. Analysis of cis-regulatory sequences also revealed an unexpected overrepresentation of ABA response elements in promoters of P. irregulare-responsive genes. Subsequent infections of ABA-related and callose-deficient mutants confirmed the importance of ABA in defense, acting partly through an undescribed mechanism. The results support a model for ABA affecting JA biosynthesis in the activation of defenses against this oomycete.

Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray.

Bacterial transcriptional networks are built on a hierarchy of regulators, on top of which lie the components of the RNA polymerase (in particular the sigma factors) and the global control elements, which play a pivotal role. We have designed a genome-wide oligonucleotide-based DNA microarray for Pseudomonas putida KT2440. In combination with real-time reverse transcription polymerase chain reaction (RT-PCR), we have used it to analyse the expression pattern of the genes encoding the RNA polymerase subunits (the core enzyme and the 24 sigma factors), and various proteins involved in global regulation (Crc, Lrp, Fur, Anr, Fis, CsrA, IHF, HupA, HupB, HupN, BipA and several MvaT-like proteins), during the shift from exponential growth in rich medium into starvation and stress brought about by the entry into stationary phase. Expression of the genes encoding the RNA polymerase core and the vegetative sigma factor decreased in stationary phase, while that of sigma(S) increased. Data obtained for sigma(N), sigma(H), FliA and for the 19 extracytoplasmic function (ECF)-like sigma factors suggested that their mRNA levels change little upon entry into stationary phase. Expression of Crc, BipA, Fis, HupB, HupN and the MvaT-like protein PP3693 decreased in stationary phase, while that of HupA and the MvaT-like protein PP3765 increased significantly. Expression of IHF was indicative of post-transcriptional control. These results provide the first global study of the expression of the transcriptional machinery through the exponential stationary-phase shift in P. putida.

[Rehabilitation in female stress urinary incontinence]. / Tratamiento rehabilitador en la incontinencia urinaria de esfuerzo femenina.

OBJECTIVES: To know the results of a pelvic floor muscle training program in the treatment of female stress urinary incontinence. METHODS: Information phase: patient is informed about the disease, her anatomy, the objectives to be reached and how to perform the exercises. Treatment phase: 6 weeks of visual and auditory biofeedback assisted pelvic floor exercises to develop the pelvic floor muscles. Follow-up phase: one, 3, 6 month and 1 year visits with control for muscle evolution, motivation reinforcement and improvement of the symptoms. RESULTS: 412 Women underwent pelvic floor rehabilitation in a 4 year period, 45.9% were cured, 38.8% improved and 15.3% were treatment failures. CONCLUSIONS: Pelvic floor rehabilitation can cure female urinary stress incontinence and diminishes the number of surgical procedures and hospital costs in the treatment of urinary incontinence.

[Iontophoresis in Peyronie's disease. Our experience]. / Iontoforesis en la enfermedad de Peyronie. Nuestra experiencia.

UNLABELLED: Peyronie's disease is a type of acquired penile incurvation of unknown origin yet, which generates from the difficulty of symmetric expansion of the corpora cavernosum produced by fibrous plaques in the middle line of the albuginea. OBJECTIVES: To define the results of iontophoresis among the wide spectrum of treatments used for this disease. METHODS: 61 patients treated by iontophoresis with orgotein in weekly sessions. RESULTS: Pain improvement 42.6%, incurvation improvement 6.1%, improvement of both 21.3%. CONCLUSIONS: In patients with Peyronie's disease iontophoresis with orgotein diminishes pain with erections, and, to a lesser extent, penile incurvation.

Actividad reproductiva de Strombus gigas (Mesogasteropoda: Strombidae) en diferentes habitats del Arrecife Alacranes, Yucatan / Reproductive activity of Strombus gigas (Mesogasteropoda: Strombidae) in differente habitats of Alacranes reef, Yucatan

The spawning relationships with temperature/photoperiod of Strombus gigas were investigated considering three habitats in Alacranes Reef, Yucatan, between February 1999 and March 2000. The sites were 22 degrees 34'N, 89 degrees 42'W (site 1); 22 degrees 29'N, 89"45'W (site 2) and 22 degrees 22'N, 89 degrees 39'W (site 3). At each site, transects (100 m x 10 m) were done. Different kinds of reproductive behavior of S. gigas was observed: such as copulating and egg-laying. Individuals alone and egg masses were registered as well. The S. gigas shell length and lip thickness were measured. High density of adults was found at site 2 with 87 conchs in one transect of 1000 m2. The mean density per m2 was 0.004 for site 1; 0.035 for site 2; and 0.003 for site 3. The mean shell length was 220 mm and the lip thickness mean was 16 mm (N = 783) for all sites. In February 1999 egg-laying female was found on sand. There was a high reproductive activity at site 2 with 8 egg-laying and 18 egg masses. Minimum reproductive activity was found at site 3 with 2 egg masses. The bottom-water temperature was related positively with copulating pairs (r = 0.723, f = 11.05, p < 0.01) and egg masses (r = 0.736, f = 11.82, p < 0.1). Correlation between photoperiod with copulating pairs (r = 0.857, f = 27.78, p < 0.01) and egg masses (r = 0.782, f = 15.77, p < 0.01) were found as well.