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A 53-year-old lady with dysfunctional renal transplant and post-surgical hypoparathyroidism with phosphocalcic metabolism impairment was admitted to hospital because of long-lasting epigastric pain and nausea. An esophagogastroduodenoscopy was performed, visualising a nodular lesion of 1 cm diameter with a depressed and ulcerated base. Microscopically the lesion was in relation with a metastatic calcinosis ulcer. Pantoprazole was initiated and serum phosphocalcic levels adjusted, achieving symptom remission. In the follow-up esophagogastroduodenoscopy, the lesion was healing with a fibrinous base and the histopathological report diagnosed superficial gastritis.

The prognosis of patients with advanced high-grade (G3) digestive neuroendocrine neoplasms (NENs) is rather poor. The addition of immune checkpoint inhibition to platinum-based chemotherapy may improve survival. NICE-NEC (NCT03980925) is a single-arm, phase II trial that recruited chemotherapy-naive, unresectable advanced or metastatic G3 NENs of gastroenteropancreatic (GEP) or unknown origin. Patients received nivolumab 360 mg intravenously (iv) on day 1, carboplatin AUC 5 iv on day 1, and etoposide 100 mg/m 2 /d iv on days 1-3, every 3 weeks for up to six cycles, followed by nivolumab 480 mg every 4 weeks for up to 24 months, disease progression, death or unacceptable toxicity. The primary endpoint was the 12-month overall survival (OS) rate (H 0 50%, H 1 72%, β 80%, α 5%). Secondary endpoints were objective response rate (ORR), duration of response (DoR), progression-free survival (PFS), and safety. From 2019 to 2021, 37 patients were enrolled. The most common primary sites were the pancreas (37.8%), stomach (16.2%) and colon (10.8%). Twenty-five patients (67.6%) were poorly differentiated carcinomas (NECs) and/or had a Ki67 index >55%. The ORR was 56.8%. Median PFS was 5.7 months (95%CI: 5.1-9) and median OS 13.9 months (95%CI: 8.3-Not reached), with a 12-month OS rate of 54.1% (95%CI: 40.2-72.8) that did not meet the primary endpoint. However, 37.6% of patients were long-term survivors (>2 years). The safety profile was consistent with previous reports. There was one treatment-related death. Nivolumab plus platinum-based chemotherapy was associated with prolonged survival in over one-third of chemonaïve patients with G3 GEP-NENs, with a manageable safety profile., (© 2024. The Author(s).)

Background: Liver transplantation is an increasingly frequent surgical procedure, with elevated rates of postoperative incisional hernias ranging from 5% to 46%. There are numerous known risk factors for incisional hernia, including the type of incision, patient sex, and presence of comorbidities such as diabetes, ascites, older age, and the use of steroids. Most studies on the treatment of incisional hernias in patients who have undergone liver transplantation have shown consistently high rates of complications. Consequently, we propose the use of nonvascular fascia for the symptomatic treatment of incisional hernias in patients with concomitant liver transplantation., Methods: We performed our new technique on 8 patients, who had previously undergone liver transplantation, between January 2019 and January 2023. The patients were examined using imaging techniques during the follow-up period., Results: Of the 8 patients, 7 were liver transplant recipients and 1 was a combined liver-kidney transplant patient. The median donor age was 57 y (5-66 y), whereas the mean recipient age was 58 y (31-66 y). The median patient height and weight were 163 cm (117-185 cm) and 76 kg (17-104 kg), respectively. Immunosuppression did not change in fascia recipients. The median time between transplantation and hernia repair surgery was 41 mo (5-116 mo). The sizes of the aponeurotic defects varied from 6 × 6 to 25 × 20 cm. Two patients experienced complications: one experienced bulging that required reintervention and the other experienced surgical site seroma. There was no mortality related to the use of the technique, and none were reported during follow-up., Conclusions: With its promising results, nonvascularized fascial transplantation can be a successful treatment for incisional hernias in patients who had previously received a liver transplant., Competing Interests: The authors declare no funding or conflicts of interest., (Copyright © 2024 The Author(s). Transplantation Direct. Published by Wolters Kluwer Health, Inc.)

Neuroendocrine neoplasms (NENs) are mutationally quiet (low number of mutations/Mb), and epigenetic mechanisms drive their development and progression. We aimed at comprehensively characterising the microRNA (miRNA) profile of NENs, and exploring downstream targets and their epigenetic modulation. In total, 84 cancer-related miRNAs were analysed in 85 NEN samples from lung and gastroenteropancreatic (GEP) origin, and their prognostic value was evaluated by univariate and multivariate models. Transcriptomics (N = 63) and methylomics (N = 30) were performed to predict miRNA target genes, signalling pathways and regulatory CpG sites. Findings were validated in The Cancer Genome Atlas cohorts and in NEN cell lines. We identified a signature of eight miRNAs that stratified patients in three prognostic groups (5-year survival of 80%, 66% and 36%). Expression of the eight-miRNA gene signature correlated with 71 target genes involved in PI3K-Akt and TNFα-NF-kB signalling. Of these, 28 were associated with survival and validated in silico and in vitro. Finally, we identified five CpG sites involved in the epigenetic regulation of these eight miRNAs. In brief, we identified an 8-miRNA signature able to predict survival of patients with GEP and lung NENs, and identified genes and regulatory mechanisms driving prognosis in NEN patients., (© 2023 The Authors. Molecular Oncology published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.)

Pancreatic cancer and biliary tract cancer have a poor prognosis. In recent years, the development of new diagnostic techniques has enabled the identification of the main genetic alterations involved in the development of these tumours. Multiple studies have assessed the ability to predict response to treatment of certain biomarkers, such as BRCA in pancreatic cancer, IDH1 or FGFR2 in biliary tract cancer and microsatellite instability or NTRK fusions in an agnostic tumour fashion. In this consensus, a group of experts selected by the Spanish Society of Medical Oncology (SEOM) and the Spanish Society of Pathology (SEAP) reviewed the role played by these mutations in the process of carcinogenesis and their clinical implications. Based on their results, a series of recommendations are made to optimize the determination of these biomarkers and thus help standardize the diagnosis and treatment of these tumours., (Copyright © 2022 Sociedad Española de Anatomía Patológica. Publicado por Elsevier España, S.L.U. All rights reserved.)

Pancreatic cancer and biliary tract cancer have a poor prognosis. In recent years, the development of new diagnostic techniques has enabled the identification of the main genetic alterations involved in the development of these tumours. Multiple studies have assessed the ability of certain biomarkers, such as BRCA in pancreatic cancer, IDH1 or FGFR2 in biliary tract cancer and microsatellite instability or NTRK fusions in an agnostic tumour fashion, to predict response to treatment.In this consensus, a group of experts selected by the Spanish Society of Medical Oncology (SEOM) and the Spanish Society of Pathology (SEAP) reviewed the role played by these mutations in the process of carcinogenesis and their clinical implications. As a result, this article proposes a series of recommendations to optimize the determination of these biomarkers to help standardize the diagnosis and treatment of these tumours., (© 2022. The Author(s).)

Pembrolizumab, a programmed cell death receptor (PD-1) inhibitor, have improved the prognosis in several types of cancer. Despite the important clinical benefits, checkpoint inhibition have been associated with inflammatory and immune-related side effects (irAE).

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the "big picture" of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic process of workflow development than we know today. We believe that this can lead to more robust, reusable, and sustainable workflows in the future., Competing Interests: No competing interests were disclosed., (Copyright: © 2021 Lamprecht AL et al.)

Introduction: The hepatic cystic tumour is a very rare neoplasm, representing about 5% of all cystic liver neoplasms. The preoperative diagnosis is difficult and can lead to confusion. The aim of this study is to analyze a number of cases operated at our centre with an histologic diagnosis of liver cystic neoplasms and also to describe the sintomathology, diagnosis and management as per the recent classification., Methods: A retrospective analysis was performed including all the cystic liver neoplasms operated between January 2000 and December 2019. The study was performed based on the pre-existing pathology archives. The 2010 previous cases were reclassified following the new 2010 OMS classification., Results: The study sample was of 10 patients, identifying 6 of them as mucinous cystic liver neoplasms, and the other 4 as intraductal papillary biliary neoplasms. The majority of the patients were women (8/10) and the median age was 47 years. Regarding the treatment, 3 hepatectomy and 7 enucleations were performed. Frozen section intraoperatively was not required in any case. In one case, variable cellular atypia with areas of adenocarcinoma was observed, and the patient received neoadyuvant chemotherapy with taxol and carboplatin. In all cases the resection margins were negative., Conclusion: Cystic liver neoplasms are infrequent tumours with a difficult differential diagnosis. Therefore, with a high radiological suspicious, the treatment should be a complete resection to avoid recurrences and malignancies., (Copyright © 2020 AEC. Publicado por Elsevier España, S.L.U. All rights reserved.)

This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of "big data" (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA's activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors.

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Benchmark challenges, such as the Critical Assessment of Structure Prediction (CASP) and Dialogue for Reverse Engineering Assessments and Methods (DREAM) have been instrumental in driving the development of bioinformatics methods. Typically, challenges are posted, and then competitors perform a prediction based upon blinded test data. Challengers then submit their answers to a central server where they are scored. Recent efforts to automate these challenges have been enabled by systems in which challengers submit Docker containers, a unit of software that packages up code and all of its dependencies, to be run on the cloud. Despite their incredible value for providing an unbiased test-bed for the bioinformatics community, there remain opportunities to further enhance the potential impact of benchmark challenges. Specifically, current approaches only evaluate end-to-end performance; it is nearly impossible to directly compare methodologies or parameters. Furthermore, the scientific community cannot easily reuse challengers' approaches, due to lack of specifics, ambiguity in tools and parameters as well as problems in sharing and maintenance. Lastly, the intuition behind why particular steps are used is not captured, as the proposed workflows are not explicitly defined, making it cumbersome to understand the flow and utilization of data. Here we introduce an approach to overcome these limitations based upon the WINGS semantic workflow system. Specifically, WINGS enables researchers to submit complete semantic workflows as challenge submissions. By submitting entries as workflows, it then becomes possible to compare not just the results and performance of a challenger, but also the methodology employed. This is particularly important when dozens of challenge entries may use nearly identical tools, but with only subtle changes in parameters (and radical differences in results). WINGS uses a component driven workflow design and offers intelligent parameter and data selection by reasoning about data characteristics. This proves to be especially critical in bioinformatics workflows where using default or incorrect parameter values is prone to drastically altering results. Different challenge entries may be readily compared through the use of abstract workflows, which also facilitate reuse. WINGS is housed on a cloud based setup, which stores data, dependencies and workflows for easy sharing and utility. It also has the ability to scale workflow executions using distributed computing through the Pegasus workflow execution system. We demonstrate the application of this architecture to the DREAM proteogenomic challenge.

Background and Aims: endoscopic submucosal dissection (ESD) in the Western setting remains a challenge. Therefore, other simplified techniques such as knife-assisted snare resection (KAR) have been reported to overcome this issue., Methods: patients who underwent an ESD for the treatment of gastrointestinal neoplasms were included in a retrospective cross-sectional observational study. Factors associated with the end of ESD as a salvage p-KAR were identified and a logistic regression model was developed., Results: a total of 136 lesions in 133 patients were analyzed. Operator experience of under 50 cases and the combination of lesion size > 30 mm and colorectal location were independent predictive factors for switching to a salvage p-KAR according to the multivariate logistic regression analysis. We developed a risk scoring system based on these four variables (experience, size, location and the combination of size and location) with a receiver operating characteristic curve of 0.81 (95% CI: 0.74-0.89). The diagnostic accuracy of the score for a cut-off point ≥ 5 had a sensitivity of 0.79 (95% CI: 0.66-0.93) and a specificity of 0.71 (95% CI: 0.61-0.80)., Conclusion: a simple predictive score system that includes four preoperative factors accurately predicts ESD to finish as a p-KAR. A careful selection of cases considering these variables could be useful to achieve better outcomes in the Western setting.

Intraductal papillary neoplasm of the bile duct (IPNB) or biliary papillomatosis (BP) is a premalignant entity with high risk of malignant transformation. When the disease extends widely from the intrahepatic to the extrahepatic biliary tree, liver transplantation (LT) is the only option available. We present the case of a 43-year-old male who was admitted in our hospital with an acute cholangitis. He was diagnosed of diffuse biliary and pancreatic papillomatosis. Firstly, we performed a cephalic pancreaticoduodenectomy, then we completed a total pancreatectomy, and finally, after confirming the absence of foci of carcinoma infiltration or lymph nodes involvement, a LT was performed. Foci of carcinoma infiltration or lymph nodes involvement in the liver were not found. After a two-year follow-up the patient developed liver recurrence and the biopsy showed a biliary adenocarcinoma. In 2010, Vibert et al. published a series of three cases concluding that in the absence of invasive carcinoma and positive lymph nodes, LT can be performed with success. The present case is the first to describe recurrence of the disease after LT in the absence of invasive carcinoma and positive lymph nodes in the literature. When the disease affects widely the entire biliary duct, small micro-invasive foci may not be detected. Nevertheless, although we know that it is a recurrent entity, the pathogenesis is unknown, and we do not know if it is possible that papillomatosis recurs over the new liver.

Scientific collaborations involving multiple institutions are increasingly commonplace. It is not unusual for publications to have dozens or hundreds of authors, in some cases even a few thousands. Gathering the information for such papers may be very time consuming, since the author list must include authors who made different kinds of contributions and whose affiliations are hard to track. Similarly, when datasets are contributed by multiple institutions, the collection and processing details may also be hard to assemble due to the many individuals involved. We present our work to date on automatically generating author lists and other portions of scientific papers for multi-institutional collaborations based on the metadata created to represent the people, data, and activities involved. Our initial focus is ENIGMA, a large international collaboration for neuroimaging genetics.

Congenital diarrheal disorders are a group of rare enteropathies that often present with life-threatening diarrhea in the first weeks of life. Enteric anendocrinosis, characterized by a lack of intestinal enteroendocrine cells due to recessively inherited mutations in the Neurogenin-3 ( NEUROG3 ) gene, has been described as a cause of congenital malabsorptive diarrhea. Diabetes mellitus also is typically associated with NEUROG3 mutations, be it early onset or a later presentation. Here we report a case of a 16-year-old male patient with severe malabsorptive diarrhea from birth, who was parenteral nutrition dependent and who developed diabetes mellitus at 11 years old. To the best of our knowledge, only 9 cases of recessively inherited NEUROG3 mutations have been reported in the literature to date. Our patient presents with several remarkable differences compared with previously published cases. This report can contribute by deepening our knowledge on new aspects of such an extremely rare disease., Competing Interests: POTENTIAL CONFLICT OF INTEREST: The authors have indicated they have no potential conflicts of interest to disclose., (Copyright © 2017 by the American Academy of Pediatrics.)

Objective: We sought to identify possible diseases associated with bloodstream infections caused by new species of S. bovis group isolated in blood cultures and by studying patient records, Methods: Forty-four consecutive blood culture isolates initially designated S. bovis were further characterised using phenotypic methods Patient records were examined., Results: We identified 15 Streptococcus gallolyticus subsp. gallolyticus, 24 Streptococcus gallolyticus subsp. pasteurianus, and 5 Streptococcus infantarius isolates in 44 BSI episodes., Conclusions: The association between S. bovis bacteraemia and endocarditis and/or colon carcinoma is highly dependent on the causative species. Streptococcus gallolyticus subsp. gallolyticus is a surrogate for endocarditis and/or bowel disease, whereas Streptococcus gallolyticus subsp. pasteurianus is a surrogate for hepato-biliary disease., (Copyright © 2011 Elsevier España, S.L. All rights reserved.)

Introduction: Susceptibility testing for non-fermenting gram-negative rods (NFGNR) is problematic; valid methods are needed for this purpose., Methods: In this study, 228 NFGNR clinical isolates were evaluated, including 85 Acinetobacter spp., 80 Stenotrophomonas maltophilia, 50 Pseudomonas aeruginosa, and 13 other species (8 Ralstonia pickettii and 5 Burkholderia cepacia). Agar dilution was used as the reference method, and results were compared with those obtained by disk diffusion, Etest, and microdilution performed with the VITEK 2 Compact System., Results: The disk method was unacceptable for S. maltophilia and P. aeruginosa, in the latter organism, mainly because of poor agreement in the colistin results. Nonetheless, the disk method is valid for Acinetobacter spp. and the remaining NFGNRs. The VITEK 2 Compact System yielded poor results for piperacillin-tazobactam, tigecycline, and ceftazidime in S. maltophilia. There were minor discrepancies with the VITEK 2 Compact system and the Etest for tigecycline in Acineobacter spp. and S. maltophilia, likely because of the differing composition of the Muller-Hinton agar lots. Hence, Etest results should be interpreted with caution., Conclusion: The disk diffusion method is inadequated for S. maltophilia. This method is unacceptable for testing colistin in P. aeruginosa. The methods Vitek 2 Compact System and Etest show minor discrepancies for testing S. maltophilia and Acinetobacter spp. for tigecycline.

Data analysis processes in scientific applications can be expressed as coarse-grain workflows of complex data processing operations with data flow dependencies between them. Performance optimization of these workflows can be viewed as a search for a set of optimal values in a multi-dimensional parameter space. While some performance parameters such as grouping of workflow components and their mapping to machines do not a ect the accuracy of the output, others may dictate trading the output quality of individual components (and of the whole workflow) for performance. This paper describes an integrated framework which is capable of supporting performance optimizations along multiple dimensions of the parameter space. Using two real-world applications in the spatial data analysis domain, we present an experimental evaluation of the proposed framework.

Background: Myxoinflammatory fibroblastic sarcoma (MFS) is a distinct neoplasm that usually arises in the acral zones of distalextremities. We report, for the first time, the preoperative fine needle a,spiration cytology (FNAC) findings of an MFS case that was confirmed after surgical excision., Case: An 81-year-old woman presented with a multinodular tumor in the distal right extremity that had been present for 1 year. FNA C of the lesion was performed and followed by local excision. The fine needle aspiration smears contained 2 of the 3 types of neoplastic cells that have been observed in MFS: spindled and ganglionlike cells. The background was myxoid, with a prominent inflammatory infiltrate. Histopathologic examination of the surgical specimen confirmed the diagnosis of MFS., Conclusion: Although the cytologic diagnosis was "pleomorphic sarcoma," MFS was considered and local excision recommended, given the reported low grade nature of this entity. However, the need for extreme caution in the diagnosis of soft tissue lesions on cytologic grounds alone cannot be overemphasized.