Nationwide comprehensive gastro-intestinal cancer cohorts: the 3P initiative

Background: The increasing sub-classification of cancer patients due to more detailed molecular classification of tumors, and limitations of current trial designs, require innovative research designs. We present the design, governance and current standing of three comprehensive nationwide cohorts including pancreatic, esophageal/gastric, and colorectal cancer patients (NCT02070146). Multidisciplinary collection of clinical data, tumor tissue, blood samples, and patient-reported outcome (PRO) measures with a nationwide coverage, provides the infrastructure for future and novel trial designs and facilitates research to improve outcomes of gastrointestinal cancer patients. Material and methods: All patients aged ≥18 years with pancreatic, esophageal/gastric or colorectal cancer are eligible. Patients provide informed consent for: (1) reuse of clinical data; (2) biobanking of primary tumor tissue; (3) collection of blood samples; (4) to be informed about relevant newly identified genomic aberrations; (5) collection of longitudinal PROs; and (6) to receive information on new interventional studies and possible participation in cohort multiple randomized controlled trials (cmRCT) in the future. Results: In 2015, clinical data of 21,758 newly diagnosed patients were collected in the Netherlands Cancer Registry. Additional clinical data on the surgical procedures were registered in surgical audits for 13,845 patients. Within the first two years, tumor tissue and blood samples were obtained from 1507 patients; during this period, 1180 patients were included in the PRO registry. Response rate for PROs was 90%. The consent rate to receive information on new interventional studies and possible participation in cmRCTs in the future was >85%. The number of hospitals participating in the cohorts is steadily increasing. Conclusion: A comprehensive nationwide multidisciplinary gastrointestinal cancer cohort is feasible and surpasses the limitations of classical study designs. With this initiative, novel and innovative studies can be performed in an efficient, safe, and comprehensive setting

Nationwide comprehensive gastro-intestinal cancer cohorts: the 3P initiative

Background: The increasing sub-classification of cancer patients due to more detailed molecular classification of tumors, and limitations of current trial designs, require innovative research designs. We present the design, governance and current standing of three comprehensive nationwide cohorts including pancreatic, esophageal/gastric, and colorectal cancer patients (NCT02070146). Multidisciplinary collection of clinical data, tumor tissue, blood samples, and patient-reported outcome (PRO) measures with a nationwide coverage, provides the infrastructure for future and novel trial designs and facilitates research to improve outcomes of gastrointestinal cancer patients. Material and methods: All patients aged ≥18 years with pancreatic, esophageal/gastric or colorectal cancer are eligible. Patients provide informed consent for: (1) reuse of clinical data; (2) biobanking of primary tumor tissue; (3) collection of blood samples; (4) to be informed about relevant newly identified genomic aberrations; (5) collection of longitudinal PROs; and (6) to receive information on new interventional studies and possible participation in cohort multiple randomized controlled trials (cmRCT) in the future. Results: In 2015, clinical data of 21,758 newly diagnosed patients were collected in the Netherlands Cancer Registry. Additional clinical data on the surgical procedures were registered in surgical audits for 13,845 patients. Within the first two years, tumor tissue and blood samples were obtained from 1507 patients; during this period, 1180 patients were included in the PRO registry. Response rate for PROs was 90%. The consent rate to receive information on new interventional studies and possible participation in cmRCTs in the future was >85%. The number of hospitals participating in the cohorts is steadily increasing. Conclusion: A comprehensive nationwide multidisciplinary gastrointestinal cancer cohort is feasible and surpasses the limitations of classical study designs. With this initiative, novel and innovative studies can be performed in an efficient, safe, and comprehensive setting

Data from: Limiting burrowing activity and overland dispersal of the invasive alien red swamp crayfish Procambarus clarkii by sophisticated design of watercourses

<p>Two datasets belonging to the paper "Limiting burrowing activity and overland dispersal of the invasive alien red swamp crayfish <i>Procambarus clarkii</i> by sophisticated design of watercourses" published in Ecological Engineering (https://doi.org/10.1016/j.ecoleng.2022.106787), are provided here. </p><p> </p><p>The first dataset "Burrow data from Limiting burrowing activity and overland dispersal P. clarkii.csv" contains data from an inventory of crayfish burrows in three watercourses in the municipality of Horssen (Province of Gelderland), the Netherlands. These data were collected during a lowering of the water level in these watercourses, which takes place annually in the winter period to prevent nuisance from excessively high phreatic groundwater in agricultural areas. The sites were located up to 5 km apart. On each bank, red swamp crayfish burrows with tunnel openings in banks below the shoreline were counted from the opposite bank of the watercourse using binoculars. This field survey was performed in March 2019 when the water level was lowered for the maintenance of the watercourses. The chance of overlooking burrows was very low as the vegetation cover was low in this period. Three sites with 'natural-like' banks (banks rehabilitated to a natural profile during rehabilitation projects, in the dataset referred to as 'natural' banks) were chosen in the area with a lowered water level and presence of red swamp crayfish. At site 1, 2 and 3, a total of 125, 46 and 18 bank transects respectively, each one 10 metres long, were surveyed. Banks were categorized as follows: (a) non-natural (steep, <i>viz</i>. > 40°, and barely vegetated; n = 77), (b) semi-natural (steep with some vegetation; n = 50), and (c) natural (gentle sloping, <i>viz</i>. < 25°, with a diverse, well-developed submerged and emergent vegetation; n = 62). See the paper for schematic cross-sections of three bank types.</p><p>The second dataset "Inclination experiment data from Limiting burrowing activity and overland dispersal P. clarkii.csv" contains data of an inclination experiment to relate frequencies of overland movement of the red swamp crayfish to several inclinations and substrate types. For this purpose, a wooden plate of 120 x 180 cm with a 10 cm thick layer of soil was used as a base on which three lanes of 40 cm wide and 180 cm long were constructed with one substrate type each: a) bare sandy soil, b), species-poor grassland with low (2-5 cm) vegetation and c) tall (40-50 cm) herbaceous-rich grassland. Inclinations applied for this experiment were 0°, 10°, 20° and 30°. Individuals were randomly selected for each treatment and placed in the middle of a lane and oriented perpendicular to the lane. After each trial, the crayfish was placed back in the water container and replaced by another crayfish. There was a minimum period of at least one hour between each trial for each crayfish. Each crayfish was used once for each substrate type and inclination test, and the treatment order was randomised for each animal. A crayfish was placed in the middle of the lane and could freely move around for a period of three minutes. Hereafter, by the change of its position on the lane after 3 minutes it was recorded whether an individual moved up (or left in case of 0°), down (or right in case of 0°), or did not move. In total, 273 trials were conducted. Trial numbers differ between treatments due to mortality of three animals during storage.</p><p> </p><p>Abstract</p><p> </p><p>Invasive alien crayfish species pose major ecological and hydrological risks globally. The red swamp crayfish (<i>Procambarus clarkii</i>) is one of the most widespread crayfish species worldwide. Its impacts arise from burrowing activities and lead to mobilization of soil nutrients, water safety risks by instability of dikes and erosion of banks. Increased sediment load demands additional dredging of drainage ditches and canals to ensure their water discharge capacity. Sustainable methods for limiting burrowing in banks and dispersal behaviour of crayfish were not yet available. Therefore, a field study was performed to determine whether the number of burrows and overland movement of crayfish were related to a particular bank type. Burrows were counted in three watercourses during a water-level decline. The number of burrows was significantly lower in natural banks than in non-natural and semi-natural banks. The construction of natural-like banks along watercourses may significantly reduce sediment load, erosion and the collapse of banks by burrowing activities of crayfish. An inclination experiment mimicking various types of terrestrial dispersal barriers elucidated that steepness, soil type and vegetation structure of small embankments near watercourses were significant factors for manipulating overland movement of crayfish. Crayfish were taken out of the water for this purpose and placed on small experimental embankments varying in slope and types of vegetation. The lowest frequencies of upward movement were recorded at inclinations of 20° and 30° on bare sandy soil and short and species-poor grassland substrates. This implies that crayfish crawling out of the water will return to the watercourse when encountering such a dispersal barrier. Therefore, a sophisticated design of embankments along watercourses can be a tool to reduce colonization risk of nearby located, hydrologically isolated water bodies with high nature values. </p&gt

The Genomics of Isolated Populations of Gampsocleis glabra (Orthoptera : Tettigoniidae) in Central and Western Europe

Habitat destruction and fragmentation are among the major current threats to global biodiversity. Fragmentation may also affect species with good dispersal abilities. We study the heath bushcricket Gampsocleis glabra, a specialist of steppe-like habitats across Europe that are highly fragmented, investigating if these isolated populations can be distinguished using population genomics and if there are any traces of admixture or dispersal among them. We try to answer these questions using genome-wide SNP data generated with ddRAD sequencing. We calculated F-statistics and visualized differentiation using STRUCTURE plots. While limited by the difficulty of sampling this threatened species, our results show that all populations except one that was represented by a singleton were clearly distinct, with pairwise FST values between 0.010 and 0.181. STRUCTURE indicated limited but visible admixture across most populations and probably also an exchange of individuals between populations of Germany and The Netherlands. We conclude that in G. glabra, a certain amount of gene flow has persisted, at least in the past, also among populations that are isolated today. We also detect a possibly more recent dispersal event between a population in The Netherlands and one in Germany, which may be human aided. We suggest that the conservation of larger populations should be maintained, that efforts should be taken to restore abandoned habitat, that the preservation even of small habitat fragments may be beneficial for the conservation of this species, and that these habitats should be regularly monitored for possible (re-)colonization

The Genomics of Isolated Populations of Gampsocleis glabra (Orthoptera : Tettigoniidae) in Central and Western Europe

Habitat destruction and fragmentation are among the major current threats to global biodiversity. Fragmentation may also affect species with good dispersal abilities. We study the heath bushcricket Gampsocleis glabra, a specialist of steppe-like habitats across Europe that are highly fragmented, investigating if these isolated populations can be distinguished using population genomics and if there are any traces of admixture or dispersal among them. We try to answer these questions using genome-wide SNP data generated with ddRAD sequencing. We calculated F-statistics and visualized differentiation using STRUCTURE plots. While limited by the difficulty of sampling this threatened species, our results show that all populations except one that was represented by a singleton were clearly distinct, with pairwise FST values between 0.010 and 0.181. STRUCTURE indicated limited but visible admixture across most populations and probably also an exchange of individuals between populations of Germany and The Netherlands. We conclude that in G. glabra, a certain amount of gene flow has persisted, at least in the past, also among populations that are isolated today. We also detect a possibly more recent dispersal event between a population in The Netherlands and one in Germany, which may be human aided. We suggest that the conservation of larger populations should be maintained, that efforts should be taken to restore abandoned habitat, that the preservation even of small habitat fragments may be beneficial for the conservation of this species, and that these habitats should be regularly monitored for possible (re-)colonization

Life-history traits and potential invasiveness of introduced pumpkinseed Lepomis gibbonus populations in northwestern Europe

Contains fulltext : 76077.pdf (publisher's version ) (Open Access)Special Issue10 p

The effects of shifting vegetation mosaics on habitat suitability for coastal dune fauna—a case study on sand lizards (lacerta agilis)

Contains fulltext : 92455.pdf (publisher's version ) (Closed access)12 p