Identifying rheumatoid arthritis susceptibility genes using high-dimensional methods

Although several genes (including a strong effect in the human leukocyte antigen (HLA) region) and some environmental factors have been implicated to cause susceptibility to rheumatoid arthritis (RA), the etiology of the disease is not completely understood. The ability to screen the entire genome for association to complex diseases has great potential for identifying gene effects. However, the efficiency of gene detection in this situation may be improved by methods specifically designed for high-dimensional data. The aim of this study was to compare how three different statistical approaches, multifactor dimensionality reduction (MDR), random forests (RF), and an omnibus approach, worked in identifying gene effects (including gene-gene interaction) associated with RA. We developed a test set of genes based on previous linkage and association findings and tested all three methods. In the presence of the HLA shared-epitope factor, other genes showed weaker effects. All three methods detected SNPs in PTPN22 and TRAF1-C5 as being important. But we did not detect any new genes in this study. We conclude that the three high-dimensional methods are useful as an initial screening for gene associations to identify promising genes for further modeling and additional replication studies

BOB CAT: a Large-Scale Review and Delphi Consensus for Management of Barrett’s Esophagus With No Dysplasia, Indefinite for, or Low-Grade Dysplasia

OBJECTIVES: Barrett’s esophagus (BE) is a common premalignant lesion for which surveillance is recommended. This strategy is limited by considerable variations in clinical practice. We conducted an international, multidisciplinary, systematic search and evidence-based review of BE and provided consensus recommendations for clinical use in patients with nondysplastic, indefinite, and low-grade dysplasia (LGD). METHODS: We defined the scope, proposed statements, and searched electronic databases, yielding 20,558 publications that were screened, selected online, and formed the evidence base. We used a Delphi consensus process, with an 80% agreement threshold, using GRADE (Grading of Recommendations Assessment, Development and Evaluation) to categorize the quality of evidence and strength of recommendations. RESULTS: In total, 80% of respondents agreed with 55 of 127 statements in the final voting rounds. Population endoscopic screening is not recommended and screening should target only very high-risk cases of males aged over 60 years with chronic uncontrolled reflux. A new international definition of BE was agreed upon. For any degree of dysplasia, at least two specialist gastrointestinal (GI) pathologists are required. Risk factors for cancer include male gender, length of BE, and central obesity. Endoscopic resection should be used for visible, nodular areas. Surveillance is not recommended for <5 years of life expectancy. Management strategies for indefinite dysplasia (IND) and LGD were identified, including a de-escalation strategy for lower-risk patients and escalation to intervention with follow-up for higher-risk patients. CONCLUSIONS: In this uniquely large consensus process in gastroenterology, we made key clinical recommendations for the escalation/de-escalation of BE in clinical practice. We made strong recommendations for the prioritization of future research

Papers, posters, and keynote presented at the 26th Polar Libraries Colloquy, hosted by the University of Alaska Fairbanks, Fairbanks, Alaska, USA 10 – 15 July 2016

Published July 2023 by the University of Alaska Anchorage, UAA/APU Consortium Library, and edited by Daria O. Carle. Copyright in individual papers is held by the contributors. A digital copy of this publication can be found at https://polarlibraries.org/colloquy-proceedings/ and in ScholarWorks, the University of Alaska’s Institutional Repository, https://scholarworks.alaska.edu/. A copy of the 2016 Colloquy program is also available at https://polarlibraries.org/colloquy-proceedings/. Further information on the Polar Libraries Colloquy, including details of membership and upcoming conferences, is available at https://polarlibraries.orgHistory of Polar Information Science / Working in Antarctica: Mapping a Changing Experience through the British Antarctic Survey / Géoindex+: A Geospatial Platform for Northern Historical and Research Data / Establishing Criteria for the Development of the “Northern Collection” at Université Laval’s Library: An Exploratory Approach / Introducing Two New Reserach Platforms: seaiceportal.de and expedition.awi.de (abstract only) / Establishing a Digital Library Service for the Inuvialuit Settlement Region / Changing Patterns of Polar Research / Mapping the Rescue of an Archive / Byrd 1933: Films from the Discovery Lecture Series / History of the Elmer E. Rasmuson Library and Its Rare Books Collection / A Roadmap to Navigate the Range of Polar Libraries, Databases, and Archives Now Available Online / Mapping Change with Finna in an Arctic Research Joint Library (paper not listed in program) / Mapping Chang in a Small Library Environment: From Reading Room to Communications Center (abstract only) / The Continued Evolution of the Cold Regions Bibliography Project: Current Status of the Antarctic Bibliography and the Antarctic Journal of the United States and its Predecessors / Connect the North: The Arctic Connect Project / Languages and Dialects in the Digital Library North (abstract only) / Bridging Arctic Indigenous Knowledge with the Digital World: Sharing Indigenous Ways of Knowing in Partnership with Arctic Communities (abstract only) / The Canadian Consortium for Arctic Data Interoperability (abstract and poster

Global Carbon Budget 2023

Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere in a changing climate is critical to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe and synthesize data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. Fossil CO2 emissions (EFOS) are based on energy statistics and cement production data, while emissions from land-use change (ELUC), mainly deforestation, are based on land-use and land-use change data and bookkeeping models. Atmospheric CO2 concentration is measured directly, and its growth rate (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) is estimated with global ocean biogeochemistry models and observation-based f CO2 products. The terrestrial CO2 sink (SLAND) is estimated with dynamic global vegetation models. Additional lines of evidence on land and ocean sinks are provided by atmospheric inversions, atmospheric oxygen measurements, and Earth system models. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and incomplete understanding of the contemporary carbon cycle. All uncertainties are reported as ±1σ. For the year 2022, EFOS increased by 0.9 % relative to 2021, with fossil emissions at 9.9 ± 0.5 Gt C yr−1 (10.2 ± 0.5 Gt C yr−1 when the cement carbonation sink is not included), and ELUC was 1.2 ± 0.7 Gt C yr−1, for a total anthropogenic CO2 emission (including the cement carbonation sink) of 11.1 ± 0.8 Gt C yr−1 (40.7±3.2 Gt CO2 yr−1). Also, for 2022, GATM was 4.6±0.2 Gt C yr−1 (2.18±0.1 ppm yr−1; ppm denotes parts per million), SOCEAN was 2.8 ± 0.4 Gt C yr−1, and SLAND was 3.8 ± 0.8 Gt C yr−1, with a BIM of −0.1 Gt C yr−1 (i.e. total estimated sources marginally too low or sinks marginally too high). The global atmospheric CO2 concentration averaged over 2022 reached 417.1 ± 0.1 ppm. Preliminary data for 2023 suggest an increase in EFOS relative to 2022 of +1.1 % (0.0 % to 2.1 %) globally and atmospheric CO2 concentration reaching 419.3 ppm, 51 % above the pre-industrial level (around 278 ppm in 1750). Overall, the mean of and trend in the components of the global carbon budget are consistently estimated over the period 1959–2022, with a near-zero overall budget imbalance, although discrepancies of up to around 1 Gt C yr−1 persist for the representation of annual to semi-decadal variability in CO2 fluxes. Comparison of estimates from multiple approaches and observations shows the following: (1) a persistent large uncertainty in the estimate of land-use changes emissions, (2) a low agreement between the different methods on the magnitude of the land CO2 flux in the northern extra-tropics, and (3) a discrepancy between the different methods on the strength of the ocean sink over the last decade. This living-data update documents changes in methods and data sets applied to this most recent global carbon budget as well as evolving community understanding of the global carbon cycle. The data presented in this work are available at https://doi.org/10.18160/GCP-2023 (Friedlingstein et al., 2023)

Single-Incision Single-Instrument Adnexal Surgery in Pediatric Patients

Introduction. Pediatric surgeons often practice pediatric gynecology. The single-incision single-instrument (SISI) technique used for appendectomy is applicable in gynecologic surgery. Methods. We retrospectively analyzed the records of patients undergoing pelvic surgery from 2008 to 2013. SISI utilized a 12 mm transumbilical trocar and an operating endoscope. The adnexa can be detorsed intracorporeally or extracorporealized via the umbilicus for lesion removal. Results. We performed 271 ovarian or paraovarian surgeries in 258 patients. In 147 (54%), the initial approach was SISI; 75 cases (51%) were completed in patients aged from 1 day to 19.9 years and weighing 4.7 to 117 kg. Conversion to standard laparoscopy was due to contralateral oophoropexy, solid mass, inability to mobilize the adnexa, large mass, bleeding, adhesions, or better visualization. When SISI surgery was converted to Pfannenstiel, the principal reason was a solid mass. SISI surgery was significantly shorter than standard laparoscopy. There were no major complications and the overall cohort had an 11% minor complication rate. Conclusion. SISI adnexal surgery is safe, quick, inexpensive, and effective in pediatric patients. SISI was successful in over half the patients in whom it was attempted and offers a scarless result. If unsuccessful, the majority of cases can be completed with standard multiport laparoscopy

Single-Incision Single-Instrument Adnexal Surgery in Pediatric Patients

Introduction. Pediatric surgeons often practice pediatric gynecology. The single-incision single-instrument (SISI) technique used for appendectomy is applicable in gynecologic surgery. Methods. We retrospectively analyzed the records of patients undergoing pelvic surgery from 2008 to 2013. SISI utilized a 12 mm transumbilical trocar and an operating endoscope. The adnexa can be detorsed intracorporeally or extracorporealized via the umbilicus for lesion removal. Results. We performed 271 ovarian or paraovarian surgeries in 258 patients. In 147 (54%), the initial approach was SISI; 75 cases (51%) were completed in patients aged from 1 day to 19.9 years and weighing 4.7 to 117 kg. Conversion to standard laparoscopy was due to contralateral oophoropexy, solid mass, inability to mobilize the adnexa, large mass, bleeding, adhesions, or better visualization. When SISI surgery was converted to Pfannenstiel, the principal reason was a solid mass. SISI surgery was significantly shorter than standard laparoscopy. There were no major complications and the overall cohort had an 11% minor complication rate. Conclusion. SISI adnexal surgery is safe, quick, inexpensive, and effective in pediatric patients. SISI was successful in over half the patients in whom it was attempted and offers a scarless result. If unsuccessful, the majority of cases can be completed with standard multiport laparoscopy

Web processing service for climate impact and extreme weather event analyses. Flyingpigeon (Version 1.0)

Analyses of extreme weather events and their impacts often requires big data processing of ensembles of climate model simulations. Researchers generally proceed by downloading the data from the providers and processing the data files " at home " with their own analysis processes. However, the growing amount of available climate model and observation data makes this procedure quite awkward. In addition, data processing knowledge is kept local, instead of being consolidated into a common resource of reusable code. These drawbacks can be mitigated by using a web processing service (WPS). A WPS hosts services such as data analysis processes that are accessible over the web, and can be installed close to the data archives. We developed a WPS named 'flyingpigeon' that communicates over an HTTP network protocol based on standards defined by the Open Geospatial Consortium (OGC) [23], to be used by climatologists and impact modelers as a tool for analyzing large datasets remotely. Here, we present the current processes we developed in flyingpigeon relating to commonly-used processes (preprocessing steps, spatial subsets at continent, country or region level, and climate indices) as well as methods for specific climate data analysis (weather regimes, analogues of circulation, segetal flora distribution, and species distribution models). We also developed a novel, browser-based interactive data visualization for circulation analogues , illustrating the flexibility of WPS in designing custom outputs. Bringing the software to the data instead of transferring the data to the code is becoming increasingly necessary, especially with the upcoming massive climate datasets

Web processing service for climate impact and extreme weather event analyses. Flyingpigeon (Version 1.0)

International audienceAnalyses of extreme weather events and their impacts often requires big data processing of ensembles of climate model simulations. Researchers generally proceed by downloading the data from the providers and processing the data files " at home " with their own analysis processes. However, the growing amount of available climate model and observation data makes this procedure quite awkward. In addition, data processing knowledge is kept local, instead of being consolidated into a common resource of reusable code. These drawbacks can be mitigated by using a web processing service (WPS). A WPS hosts services such as data analysis processes that are accessible over the web, and can be installed close to the data archives. We developed a WPS named 'flyingpigeon' that communicates over an HTTP network protocol based on standards defined by the Open Geospatial Consortium (OGC) [23], to be used by climatologists and impact modelers as a tool for analyzing large datasets remotely. Here, we present the current processes we developed in flyingpigeon relating to commonly-used processes (preprocessing steps, spatial subsets at continent, country or region level, and climate indices) as well as methods for specific climate data analysis (weather regimes, analogues of circulation, segetal flora distribution, and species distribution models). We also developed a novel, browser-based interactive data visualization for circulation analogues , illustrating the flexibility of WPS in designing custom outputs. Bringing the software to the data instead of transferring the data to the code is becoming increasingly necessary, especially with the upcoming massive climate datasets