Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences

The Ocean Biogeographic Information System (OBIS) is the world's most comprehensive online, open-access database of marine species distributions. OBIS grows with millions of new species observations every year. Contributions come from a network of hundreds of institutions, projects and individuals with common goals: to build a scientific knowledge base that is open to the public for scientific discovery and exploration and to detect trends and changes that inform society as essential elements in conservation management and sustainable development. Until now, OBIS has focused solely on the collection of biogeographic data (the presence of marine species in space and time) and operated with optimized data flows, quality control procedures and data standards specifically targeted to these data. Based on requirements from the growing OBIS community to manage datasets that combine biological, physical and chemical measurements, the OBIS-ENV-DATA pilot project was launched to develop a proposed standard and guidelines to make sure these combined datasets can stay together and are not, as is often the case, split and sent to different repositories. The proposal in this paper allows for the management of sampling methodology, animal tracking and telemetry data, biological measurements (e.g., body length, percent live cover, ...) as well as environmental measurements such as nutrient concentrations, sediment characteristics or other abiotic parameters measured during sampling to characterize the environment from which biogeographic data was collected. The recommended practice builds on the Darwin Core Archive (DwC-A) standard and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of a DwC Event Core in combination with a DwC Occurrence Extension and a proposed enhancement to the DwC MeasurementOrFact Extension. This new structure enables the linkage of measurements or facts - quantitative and qualitative properties - to both sampling events and species occurrences, and includes additional fields for property standardization. We also embrace the use of the new parentEventID DwC term, which enables the creation of a sampling event hierarchy. We believe that the adoption of this recommended practice as a new data standard for managing and sharing biological and associated environmental datasets by IODE and the wider international scientific community would be key to improving the effectiveness of the knowledge base, and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean, and on land.Fil: De Pooter, Daphnis. Flanders Marine Institute; BélgicaFil: Appeltans, Ward. UNESCO-IOC; BélgicaFil: Bailly, Nicolas. Hellenic Centre for Marine Research, MedOBIS; GreciaFil: Bristol, Sky. United States Geological Survey; Estados UnidosFil: Deneudt, Klaas. Flanders Marine Institute; BélgicaFil: Eliezer, Menashè. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Fujioka, Ei. University Of Duke. Nicholas School Of Environment. Duke Marine Lab; Estados UnidosFil: Giorgetti, Alessandra. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Goldstein, Philip. University of Colorado Museum of Natural History, OBIS; Estados UnidosFil: Lewis, Mirtha Noemi. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; ArgentinaFil: Lipizer, Marina. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Mackay, Kevin. National Institute of Water and Atmospheric Research; Nueva ZelandaFil: Marin, Maria Rosa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; ArgentinaFil: Moncoiffé, Gwenaëlle. British Oceanographic Data Center; Reino UnidoFil: Nikolopoulou, Stamatina. Hellenic Centre for Marine Research, MedOBIS; GreciaFil: Provoost, Pieter. UNESCO-IOC; BélgicaFil: Rauch, Shannon. Woods Hole Oceanographic Institution; Estados UnidosFil: Roubicek, Andres. CSIRO Oceans and Atmosphere; AustraliaFil: Torres, Carlos. Universidad Autonoma de Baja California Sur; MéxicoFil: van de Putte, Anton. Royal Belgian Institute for Natural Sciences; BélgicaFil: Vandepitte, Leen. Flanders Marine Institute; BélgicaFil: Vanhoorne, Bart. Flanders Marine Institute; BélgicaFil: Vinci, Mateo. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Wambiji, Nina. Kenya Marine and Fisheries Research Institute; KeniaFil: Watts, David. CSIRO Oceans and Atmosphere; AustraliaFil: Klein Salas, Eduardo. Universidad Simon Bolivar; VenezuelaFil: Hernandez, Francisco. Flanders Marine Institute; Bélgic

Local immune response to food antigens drives meal-induced abdominal pain

Up to 20% of people worldwide develop gastrointestinal symptoms following a meal1, leading to decreased quality of life, substantial morbidity and high medical costs. Although the interest of both the scientific and lay communities in this issue has increased markedly in recent years, with the worldwide introduction of gluten-free and other diets, the underlying mechanisms of food-induced abdominal complaints remain largely unknown. Here we show that a bacterial infection and bacterial toxins can trigger an immune response that leads to the production of dietary-antigen-specific IgE antibodies in mice, which are limited to the intestine. Following subsequent oral ingestion of the respective dietary antigen, an IgE- and mast-cell-dependent mechanism induced increased visceral pain. This aberrant pain signalling resulted from histamine receptor H1-mediated sensitization of visceral afferents. Moreover, injection of food antigens (gluten, wheat, soy and milk) into the rectosigmoid mucosa of patients with irritable bowel syndrome induced local oedema and mast cell activation. Our results identify and characterize a peripheral mechanism that underlies food-induced abdominal pain, thereby creating new possibilities for the treatment of irritable bowel syndrome and related abdominal pain disorders

An indigestion or a viral gastritis, or not?

Case report: An 18 mth old boy was sent to the Emergency Room of the Jessa Hospital (Hasselt, Belgium) because of persistent vomiting. The clinical examination was without particularities, except for a runny nose. The diagnosis of indigestion or (viral) gastritis was made. Patient was sent home. He was represented at the ER five days later. He stopped vomiting for 3 consecutive days after his first hospital visit, but started to vomit again the last 2 days, the last night even two times with bilious vomiting. His appetite was decreased since one week. The infant was not comfortable during abdominal palpation. This finding led to the decision for further investigations. An abdominal ultrasound showed air superposition in the epi- and mesogastrium. There were no signs of intussusception. An abdominal X-ray was performed (fig 1). Answer and discussion: The abdominal X-ray showed a corpus alienum, presumably magnets, in the mesogastrium and free air under the right diaphragm (fig. 1). An abdominal CT-scan could not visualise whether the magnets were situated in- or outside the intestinal lumen. At laparoscopy, clitted small intestinal loops with multiple perforation sites were detected as well as a purulent peritonitis in the left fossa iliaca (fig. 2). Magnets were removed. Perforations were sutured. Postoperatively augmentin was given. Patient recovered completly.</jats:p

Laparoscopic common bile duct exploration for common bile duct stones after gastric surgery

Background Gallstone disease is common after gastric surgery and especially after weight loss from bariatric surgery. In patients with normal gastroduodenal anatomy, treatment of common bile duct stones (CBS) generally consists of, endoscopic retrograde cholangiopancreaticography (ERCP) and endoscopic sphincterotomy (ES), followed by cholecystectomy in a second stage. However, after gastric surgery the papilla may not be easily accessible endoscopically. The aim of our study was to evaluate the therapeutic success of single-stage laparoscopic cholecystectomy and common bile duct exploration (LCBDE) after previous gastric surgery. Methods In this observational cohort study, all LCBDE in patients with previous gastric surgery between January 2014 and July 2022 were retrospectively reviewed. Gastric surgery consisted of Roux-en-Y gastric bypass, BII subtotal gastrectomy, total gastrectomy and subtotal gastrectomy with Roux-en-Y reconstruction. Outcomes of interest consisted of successful duct clearance, postoperative adverse events and CBS recurrence. Results Forty-four patients (M/F: 22/22) underwent LCBDE after previous gastric surgery, in which simultaneous cholecystectomy was performed in 38 cases. Median (range) age 68 (25-90) years. Presence of CBS was confirmed in 38 patients (85%), a choledochal polyp in one patient (2%) and recurrence of gastric cancer in another (2%). Duct clearance was successful in 37 out of 38 patients (97%). Median (range) length of stay after LCBDE was 1 (0-12) day(s). Eight patients developed a postoperative adverse event, of which three Clavien-Dindo > 3a complications. Three patients were readmitted. At a median (range) follow-up of 60 (24-120) months, no CBS recurrences were observed. Conclusions LCBDE is a safe technique, with a high rate of successful duct clearance after previous gastric surgery, even after previous cholecystectomy. In experienced centers, LCBDE provides a valid alternative for complex interventional endoscopy, omitting the need for the creation of a gastro-gastric fistula

Magnets and children: a dangerous combination

Background Accidental ingestion of foreign bodies is a common problem in children. Fortunately, the gastrointestinal tract is quite resilient to foreign bodies. On the other hand, the ingestion of magnets can result in enormous morbidity. Because of their natural tendency to firmly adhere they can cause intestinal obstruction, pressure necrosis, fistula formation or perforation. With this case report, we aim to raise awareness of the risks that these magnets pose to children. Methods We describe a case of intestinal perforation caused by the separate ingestion of multiple magnets from a children's toy (buckyballs, Neodymium spheres) by a two-year-old boy. A search in the Pubmed database showed some publications and varied management guidelines. Results The boy was treated with an exploratory laparoscopy converted to a mini-laparotomy. We removed the four magnets through separate enterotomies. Postoperative recovery was uneventful. The boy was discharged on a postoperative day five and had no complications at three months follow-ups. Conclusion Accidental ingestion of multiple magnets is rare but can create a life-threatening situation in children. If the magnets are still in the stomach, endoscopic retrieval is needed. If they are beyond the stomach, in asymptomatic cases close clinical and radiographic vigilance is mandatory. When symptomatic we advise urgent removal. If treated on time, the surgical outcome is good and fast recovery is expected