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Insulinomas are rare neuroendocrine tumors arising from pancreatic ß cells, characterized by aberrant proliferation and altered insulin secretion, leading to glucose homeostasis failure. With the aim of uncovering the role of noncoding regulatory regions and their aberrations in the development of these tumors, we coupled epigenetic and transcriptome profiling with whole-genome sequencing. As a result, we unraveled somatic mutations associated with changes in regulatory functions. Critically, these regions impact insulin secretion, tumor development, and epigenetic modifying genes, including polycomb complex components. Chromatin remodeling is apparent in insulinoma-selective domains shared across patients, containing a specific set of regulatory sequences dominated by the SOX17 binding motif. Moreover, many of these regions are H3K27me3 repressed in ß cells, suggesting that tumoral transition involves derepression of polycomb-targeted domains. Our work provides a compendium of aberrant cis-regulatory elements affecting the function and fate of ß cells in their progression to insulinomas and a framework to identify coding and noncoding driver mutations.

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By the mid-seventeenth century, images of natural elements that originated in Dutch Brazil circulated in Europe. These were often included in art collections (the Libri Picturati) and natural history treatises (the Historia Naturalis Brasiliae and the India Utriesque re Naturale et Medica, 1658). The plant woodcut images in these books constituted (icono) type specimens and played a significant role in disseminating scientific botanical knowledge. We present a systematic analysis of their origins by cross-referencing the visual and textual sources related to Dutch Brazil. To do so, we used our previous botanical identifications of the portrayed plants, published sources, and digital archival material. The plant woodcuts accounted for 529 images, which corresponded to 426 taxa. We created a PDF booklet to visualize the (dis-) similarities of the woodcuts with the Libri Picturati and other visual sources. Substantial differences in the visual-making methodology exist between the two treatises (1648, 1658). In the first book, most of the images were available from Dutch Brazil and carved into the woodcuts, while most of these woodcuts were reused in the second one. The Indigenous Tupi-based plant names accompanying the images were crucial when arranging the sources, and portraying as much botanical information as possible was commonly the goal. Freshly picked, living plants, dried branches, fruits, and seeds were used to represent the megadiverse Brazilian flora, even when these belonged to species originating from other regions. Despite not being recognized for their contribution, Indigenous Brazilians and enslaved Africans were essential in the visual knowledge-making processes that later resulted in these natural history collections. As several sources remain lost and many histories yet untold, further archival studies and collaborative projects are pertinent to reveal the missing pieces of this conundrum.

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BACKGROUND: Lipids are regulators of insulitis and ß-cell death in type 1 diabetes development, but the underlying mechanisms are poorly understood. Here, we investigated how the islet lipid composition and downstream signaling regulate ß-cell death. METHODS: We performed lipidomics using three models of insulitis: human islets and EndoC-ßH1 ß cells treated with the pro-inflammatory cytokines interlukine-1ß and interferon-γ, and islets from pre-diabetic non-obese mice. We also performed mass spectrometry and fluorescence imaging to determine the localization of lipids and enzyme in islets. RNAi, apoptotic assay, and qPCR were performed to determine the role of a specific factor in lipid-mediated cytokine signaling. RESULTS: Across all three models, lipidomic analyses showed a consistent increase of lysophosphatidylcholine species and phosphatidylcholines with polyunsaturated fatty acids and a reduction of triacylglycerol species. Imaging assays showed that phosphatidylcholines with polyunsaturated fatty acids and their hydrolyzing enzyme phospholipase PLA2G6 are enriched in islets. In downstream signaling, omega-3 fatty acids reduce cytokine-induced ß-cell death by improving the expression of ADP-ribosylhydrolase ARH3. The mechanism involves omega-3 fatty acid-mediated reduction of the histone methylation polycomb complex PRC2 component Suz12, upregulating the expression of Arh3, which in turn decreases cell apoptosis. CONCLUSIONS: Our data provide insights into the change of lipidomics landscape in ß cells during insulitis and identify a protective mechanism by omega-3 fatty acids. Video Abstract.

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OBJECTIVE: The aim of this study was to elucidate the impact of pleural lavage cytology positivity on early recurrence in patients operated on non-small cell lung cancer (NSCLC). METHODS: This is a multicentre prospective cohort study of 684 patients undergoing an anatomical lung resection for NSCLC between October 2015 and October 2017 at 12 national centres. A pleural lavage was performed before and after lung resection. The association between the different predictors of early recurrence and PLC positivity was performed using univariate and multivariate logistic regression models. A propensity score analysis was performed by inverse probability weighting (IPSW) using average treatment effect (ATE) estimation to analyse the impact of PLC positivity on early recurrence. RESULTS: Overall PLC positivity was observed in 15 patients (2.2%). After two years, 193 patients (28.2%) relapsed, 182 (27.2%) with a negative PLC and 11 (73.3%) with a positive PLC (p<0.001). Factors associated to early recurrence were adenocarcinoma histology (OR=1.59, 95%CI 1.06-2.38, p=0.025), visceral pleural invasion (OR=1.59, 95%CI 1.04-2.4, p=0.03), lymph node involvement (OR=1.84, 95%CI 1.14-2.96, p=0.013), advanced pathological stage (OR=2.12, 95%CI 1.27-3.54, p=0.004) and PLC positivity (OR=4.14, 95%CI 1.25-16.36, p=0.028). After IPSW, PLC positivity was associated with an increased risk of early recurrence (OR=3.46, 95%CI 2.25-5.36, p<0.001). CONCLUSIONS: Positive pleural lavage cytology was found to be the strongest predictor of early recurrence.

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Direct lineage reprogramming of one somatic cell into another without transitioning through a progenitor stage has emerged as a strategy to generate clinically relevant cell types. One cell type of interest is the pancreatic insulin-producing ß cell whose loss and/or dysfunction leads to diabetes. To date it has been possible to create ß-like cells from related endodermal cell types by forcing the expression of developmental transcription factors, but not from more distant cell lineages like fibroblasts. In light of the therapeutic benefits of choosing an accessible cell type as the cell of origin, in this study we set out to analyze the feasibility of transforming human skin fibroblasts into ß-like cells. We describe how the timed-introduction of five developmental transcription factors (Neurog3, Pdx1, MafA, Pax4, and Nkx2-2) promotes conversion of fibroblasts toward a ß-cell fate. Reprogrammed cells exhibit ß-cell features including ß-cell gene expression and glucose-responsive intracellular calcium mobilization. Moreover, reprogrammed cells display glucose-induced insulin secretion in vitro and in vivo. This work provides proof-of-concept of the capacity to make insulin-producing cells from human fibroblasts via transcription factor-mediated direct reprogramming.

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BACKGROUND: We evaluated a strategy to shorten the time from admission to surgery in patients with proximal femur fractures on chronic antiplatelet therapy. We reported a 12-month follow-up on complications and quality of life (QoL). METHODS: Multicentre, open-label, randomized, parallel clinical trial. Patients were randomized to either early platelet function-guided surgery (experimental group) or delayed surgery (control group). Medical and surgical complications and QoL (EQ-5D-5L questionnaire) were assessed during the hospital stay, and after hospital discharge at 30 days, and 6 and 12 months. RESULTS: From 156 randomized patients, 143 patients underwent surgery. The mean age was 85.5 (7.8) years and 68.0% were female. After hospital discharge, 5.7% of patients had surgical wound complications and 55.9% had medical complications, with 42.7% having serious adverse events. QoL improved significantly after surgery, with the best scores at the six-month follow-up. The overall mortality was 32.2%. There were no differences between early and delayed surgery groups in any assessed outcomes. CONCLUSION: It seems safe to reduce the time of surgery under neuraxial anaesthesia in patients with hip fractures on chronic antiplatelet therapy by platelet function testing. QoL in particular improves in the first six months after surgery.

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BACKGROUND: Patients with proximal femur fracture on antiplatelet treatment benefit from early surgery. Our goal was to perform early surgery under neuraxial anaesthesia when indicated by the platelet function test. METHODS: We conducted a multicentre randomised open-label parallel clinical trial. Patients were randomised to either early platelet function-guided surgery (experimental group) or delayed surgery (control group). Early surgery was programmed when the functional platelet count (as measured by Plateletworks) was >80 × 109/L. The primary outcome was the emergency admission-to-surgery interval. Secondary outcomes were platelet function, postoperative bleeding, medical and surgical complications, and mortality. RESULTS: A total of 156 patients were randomised, with 78 in each group, with a mean (SD) age of 85.96 (7.9) years, and 67.8% being female. The median (IQR) time to surgery was 2.3 (1.5-3.7) days for the experimental group and 4.9 (4.4-5.6) days for the control group. One-third of patients did not achieve the threshold functional platelet count on the first day of admission, requiring more than one test. There was no difference in clinical outcomes between groups. CONCLUSIONS: A strategy individualised according to the platelet function test shortens the time to proximal femur fracture surgery under neuraxial anaesthesia in patients on chronic antiplatelet treatment. Better powered randomised clinical trials are needed to further evaluate the clinical impact and safety of this strategy.

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In response to liver injury, hepatic stellate cells activate and acquire proliferative and contractile features. The regression of liver fibrosis appears to involve the clearance of activated hepatic stellate cells, either by apoptosis or by reversion toward a quiescent-like state, a process called deactivation. Thus, deactivation of active hepatic stellate cells has emerged as a novel and promising therapeutic approach for liver fibrosis. However, our knowledge of the master regulators involved in the deactivation and/or activation of fibrotic hepatic stellate cells is still limited. The transcription factor GATA4 has been previously shown to play an important role in embryonic hepatic stellate cell quiescence. In this work, we show that lack of GATA4 in adult mice caused hepatic stellate cell activation and, consequently, liver fibrosis. During regression of liver fibrosis, Gata4 was reexpressed in deactivated hepatic stellate cells. Overexpression of Gata4 in hepatic stellate cells promoted liver fibrosis regression in CCl4-treated mice. GATA4 induced changes in the expression of fibrogenic and antifibrogenic genes, promoting hepatic stellate cell deactivation. Finally, we show that GATA4 directly repressed EPAS1 transcription in hepatic stellate cells and that stabilization of the HIF2α protein in hepatic stellate cells leads to liver fibrosis.

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The Libri Picturati includes a collection of plant illustrations from seventeenth century Dutch Brazil that is kept in the Jagiellonian library in Krakow since World War II. While many studies focused on the artistic details and history of these images, we identified the flora depicted. We used contemporary textual sources (e.g., Historia Naturalis Brasiliae), monographs and taxonomist' assessments. We checked origin, life form, domestication and conservation status and the plant parts that are represented. We identified 198 taxa, consisting mostly of wild, native rainforest trees and 35 introduced species. Fertile branches are the most represented, although some loose dry fruits and sterile material were also painted, which sheds light into the collection methods by naturalists in Dutch Brazil. Several species are no longer abundant or have become invasive due to anthropogenic influences since colonialism. Through this botanical iconography, we traced the first records of the sunflower and the Ethiopian pepper in Brazil, as well as the dispersion and assimilation of the flora encountered in the colony by Indigenous, African and European peoples. We emphasized the relevance of combining visual and textual sources when studying natural history collections and we highlighted how digitalization makes these artistic and scientific collections more accessible.

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MOTIVATION: UMI-4C, a technique that combines chromosome conformation capture (4C) and unique molecular identifiers (UMI), is widely used to profile and quantitatively compare targeted chromosomal contact profiles. The analysis of UMI-4C experiments presents several computational challenges, including the removal of the PCR duplication bias and the identification of differential chromatin contacts. RESULTS: We have developed UMI4Cats (UMI-4C Analysis Turned Simple), an R package that facilitates processing, analyzing and visualizing of data obtained by UMI-4C experiments. AVAILABILITY AND IMPLEMENTATION: UMI4Cats is implemented as an R package supported on Linux, MacOS and MS Windows. UMI4Cats is available from Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/UMI4Cats.html) and GitHub (https://github.com/Pasquali-lab/UMI4Cats). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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BACKGROUND: In spite of an increasing number of ethnobotanical market surveys in the past decades, few studies compare changes in plant species trade over time. The open-air market Ver-o-Peso (VOP) in Belém, located near the mouth of the Amazon River in the state of Pará, Brazil, is known for its wide variety of medicinal plants. A survey of VOP was published in 1984, but it remains unknown to what extent its botanical composition changed over 34 years. Furthermore, in northern Brazil, little attention has been given to the origins of the vernacular names of these plants. Our aim is to give an up-to-date overview of the VOP medicinal plant market, concentrating on changes in species composition and vernacular names over time. METHODS: We collected medicinal plants and vernacular names at VOP in August 2018. We identified most plants at the Museo Paraense Emilio Goeldi Herbarium, where we also deposited vouchers and specimen labels. We compared our species composition data to the 1984 inventory by Van den Berg. Furthermore, we investigated the etymologies of the vernacular plant names. RESULTS: We recorded 155 plant specimens and 165 corresponding vernacular names, and collected 146 specimens from the medicinal and ritual stalls of VOP reporting 86 species formerly not recorded at this market. Vernacular names had mostly Portuguese roots, followed by Tupi and African ones. We found 30 species also documented in 1984, and vernacular names that overlapped between both surveys were used for the same botanical species or genus, indicating that vernacular names have changed little in the past decades. Lastly, we found 26 more introduced species sold at VOP compared to 1984. CONCLUSIONS: Forest degradation and deforestation, prevalence of diseases, and methodological factors may play a role in the differences we found in our survey compared to 1984. Of the plants that did overlap between the two surveys, vernacular names of these plants were hardly different. Lastly, the lingual origins of the vernacular names in our survey and the origins of the plant species reflect the history of the intricate syncretism of medicinal plant practices of indigenous, Afro-Brazilian and European origins in Belém.

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Up to 50% of cancer patients and up to 90% of those in terminal stages experience pain associated with disease progression, poor quality of life, and social impact on caregivers. This study aimed to establish standards for the accreditation of oncological pain management in healthcare organizations. A mixed methods approach was used. First, a pragmatic literature review was conducted. Second, consensus between professionals and patients was reached using the Nominal Group and Delphi technique in a step that involved anesthesiologists, oncologists, family physicians, nurses, psychologists, patient representatives, and caregivers. Third, eight hospitals participated in a pilot assessment of the level of fulfillment of each standard. A total of 37 standards were extracted. The Nominal Group produced additional standards, of which 60 were included in Questionnaire 0 that was used in the Delphi Technique. Two Delphi voting rounds were performed to reach a high level of consensus, and involved 64 and 62 participants with response rates of 90% and 87%, respectively. Finally, 39 standards for the management of cancer pain were agreed upon. In the self-evaluation, the average range of compliance was between 56.4% and 100%. The consensus standards of the ACDON Project might improve the monitoring of cancer pain management. These standards satisfied the demands of professionals and patients and could be used for the accreditation of approaches in cancer pain management.

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PURPOSE OF REVIEW: Type 1 diabetes (T1D) develops as a consequence of a combination of genetic predisposition and environmental factors. Combined, these events trigger an autoimmune disease that results in progressive loss of pancreatic ß cells, leading to insulin deficiency. This article reviews the current knowledge on the genetics of T1D with a specific focus on genetic variation in pancreatic islet regulatory networks and its implication to T1D risk and disease development. RECENT FINDINGS: Accumulating evidence suggest an active role of ß cells in T1D pathogenesis. Based on such observation several studies aimed in mapping T1D risk variants acting at the ß cell level. Such studies unravel T1D risk loci shared with type 2 diabetes (T2D) and T1D risk variants potentially interfering with ß-cell responses to external stimuli. The characterization of regulatory genomics maps of disease-relevant states and cell types can be used to elucidate the mechanistic role of ß cells in the pathogenesis of T1D.

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Hemostasis is crucial for reducing bleeding during surgical procedures. The points-of-care based on the platelet function test could be useful to minimize the complications related to chronic antiplatelet therapy during surgery. The present study is aimed at comparing two point-of-care platelet function devices-Platelet Function Analyzer PFA-100® (Siemens Canada, Mississauga, ON, Canada) and Plateletworks®(Helena Laboratories, Beaumont, TX, USA). Our objective is to evaluate if they provide comparable and useful information to manage anti-aggregate patients before surgery. We included patients with a femoral fracture receiving chronic antiplatelet therapy and a median age of 89 years (range from 70 to 98). A platelet function evaluation was performed on all patients before surgery using both devices-Plateletworks® and PFA-100®. The correlation between Plateletworks® and PFA-100® was performed using Cohen's Kappa coefficient. Twenty consecutive patients participated in the trial; 16 patients were under treatment with 75 mg/day of clopidogrel, three with >300 mg/day of acetylsalicylic acid (ASA), and only one was in treatment with both antiplatelet agents. Cohen's Kappa coefficient was 0.327 comparing PFA-100®-ADP (adenosine diphosphate) and Plateletworks® and, 0.200 comparing PFA-100®-EPI (epinephrine) and Plateletworks®. In conclusion, we found a weak concordance comparing PFA-100® and Plateletworks®. This could partially be due to the advanced age of the included patients. However, given the limited sample size, more studies are necessary to confirm these results.

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ETHNOPHARMACOLOGICAL RELEVANCE: Parallelisms between current and historical medicinal practices as described in the seventeenth century treatise Historia Naturalis Brasiliae (HNB) provide us with an overview of traditional plant knowledge transformations. Local markets reflect the actual plant use in urban and rural surroundings, allowing us to trace cross-century similarities of ethnobotanical knowledge. AIMS OF THE STUDY: We aim to verify in how far the HNB, created in seventeenth-century northeastern Brazil, correlates with contemporary plant use in the country by comparing the plant knowledge therein with recent plant market surveys at national level. MATERIALS AND METHODS: We conducted a literature review on ethnobotanical market surveys in Brazil. We used the retrieved data on plant composition and vernacular names, together with our own fieldwork from the Ver-o-Peso market in Belém, to compare each market repertoire with the useful species in the HNB. We analyzed similarities among markets and the HNB with a Detrended Correspondence Analysis and by creating Venn diagrams. We analyzed the methods of the different markets to check whether they influenced our results. RESULTS: Out of the 24 markets reviewed, the greatest similarities with the HNB are seen in northern Brazilian markets, both in plant composition and vernacular names, followed by the northeast. The least overlap is found with markets in the central west and Rio de Janeiro. Most of the shared vernacular names with the HNB belonged to languages of the Tupi linguistic family. CONCLUSION: The similarity patterns in floristic composition among Brazilian markets and the HNB indicate the current wider distribution and trade of the species that Marcgrave and Piso described in 1648 in the northeast. Migration of indigenous groups, environmental changes, globalized and homogenous plant trade, and different market survey methods played a role in these results. The HNB is a reference point in time that captures a moment of colonial cultural transformations.

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Interferon-α (IFNα), a type I interferon, is expressed in the islets of type 1 diabetic individuals, and its expression and signaling are regulated by T1D genetic risk variants and viral infections associated with T1D. We presently characterize human beta cell responses to IFNα by combining ATAC-seq, RNA-seq and proteomics assays. The initial response to IFNα is characterized by chromatin remodeling, followed by changes in transcriptional and translational regulation. IFNα induces changes in alternative splicing (AS) and first exon usage, increasing the diversity of transcripts expressed by the beta cells. This, combined with changes observed on protein modification/degradation, ER stress and MHC class I, may expand antigens presented by beta cells to the immune system. Beta cells also up-regulate the checkpoint proteins PDL1 and HLA-E that may exert a protective role against the autoimmune assault. Data mining of the present multi-omics analysis identifies two compound classes that antagonize IFNα effects on human beta cells.

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The early stages of type 1 diabetes (T1D) are characterized by local autoimmune inflammation and progressive loss of insulin-producing pancreatic ß cells. Here we show that exposure to proinflammatory cytokines reveals a marked plasticity of the ß-cell regulatory landscape. We expand the repertoire of human islet regulatory elements by mapping stimulus-responsive enhancers linked to changes in the ß-cell transcriptome, proteome and three-dimensional chromatin structure. Our data indicate that the ß-cell response to cytokines is mediated by the induction of new regulatory regions as well as the activation of primed regulatory elements prebound by islet-specific transcription factors. We find that T1D-associated loci are enriched with newly mapped cis-regulatory regions and identify T1D-associated variants disrupting cytokine-responsive enhancer activity in human ß cells. Our study illustrates how ß cells respond to a proinflammatory environment and implicate a role for stimulus response islet enhancers in T1D.

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Over the last 20 years, researchers have been mixing qualitative and quantitative approaches, but mixed methods research represents a new movement that arose in response to the currents of qualitative and quantitative research, considered separately. Little has been published on the use of polar coordinate analysis in psychotherapy. This type of analysis can provide detailed information and integrate the qualitative-quantitative analysis. Even less has been published on the analysis of ASD children's behavior. The main aim of this study was to implement this mixed methods methodology to analyze patterns of social behaviors in a group of adolescents with ASD during a group social competence intervention program. Moreover, we wanted to see whether an observational scale could be combined fruitfully with polar coordinate analysis and to investigate whether typical ASD behaviors show similar interrelations (prospective and retrospective sequentialities) as behaviors observed in psychotherapy. We used an adaptation from the Social Skills Training Program (UC Davis, California). We observed that each participant took a unique course, increasing or decreasing the number and quality of their social behaviors. In accordance with previous literature, results suggest some increment in the amount of appropriate social conduct. We did not detect a generalized progress pattern but agreed that there were changes between the beginning and end of the intervention. Therefore, we consider that observational methodology is useful in the field of psychotherapy and ASD, offering detailed information about changes and development that cannot be obtained with other traditional measures, such as questionnaires.