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PloS One 2020Acute infections of the middle ear are the most commonly treated childhood diseases. Because complications affect children's language learning and cognitive processes,...
Acute infections of the middle ear are the most commonly treated childhood diseases. Because complications affect children's language learning and cognitive processes, it is essential to diagnose these diseases in a timely and accurate manner. The prevailing literature suggests that it is difficult to accurately diagnose these infections, even for experienced ear, nose, and throat (ENT) physicians. Advanced care practitioners (e.g., nurse practitioners, physician assistants) serve as first-line providers in many primary care settings and may benefit from additional guidance to appropriately determine the diagnosis and treatment of ear diseases. For this purpose, we designed a content-based image retrieval (CBIR) system (called OtoMatch) for normal, middle ear effusion, and tympanostomy tube conditions, operating on eardrum images captured with a digital otoscope. We present a method that enables the conversion of any convolutional neural network (trained for classification) into an image retrieval model. As a proof of concept, we converted a pre-trained deep learning model into an image retrieval system. We accomplished this by changing the fully connected layers into lookup tables. A database of 454 labeled eardrum images (179 normal, 179 effusion, and 96 tube cases) was used to train and test the system. On a 10-fold cross validation, the proposed method resulted in an average accuracy of 80.58% (SD 5.37%), and maximum F1 score of 0.90 while retrieving the most similar image from the database. These are promising results for the first study to demonstrate the feasibility of developing a CBIR system for eardrum images using the newly proposed methodology.
Topics: Adult; Algorithms; Child; Databases as Topic; Deep Learning; Humans; Image Processing, Computer-Assisted; Information Storage and Retrieval; Reproducibility of Results; Tympanic Membrane
PubMed: 32413096
DOI: 10.1371/journal.pone.0232776 -
Journal of Medical Internet Research Oct 2021Electronic health records (EHRs, such as those created by an anesthesia management system) generate a large amount of data that can notably be reused for clinical audits...
BACKGROUND
Electronic health records (EHRs, such as those created by an anesthesia management system) generate a large amount of data that can notably be reused for clinical audits and scientific research. The sharing of these data and tools is generally affected by the lack of system interoperability. To overcome these issues, Observational Health Data Sciences and Informatics (OHDSI) developed the Observational Medical Outcomes Partnership (OMOP) common data model (CDM) to standardize EHR data and promote large-scale observational and longitudinal research. Anesthesia data have not previously been mapped into the OMOP CDM.
OBJECTIVE
The primary objective was to transform anesthesia data into the OMOP CDM. The secondary objective was to provide vocabularies, queries, and dashboards that might promote the exploitation and sharing of anesthesia data through the CDM.
METHODS
Using our local anesthesia data warehouse, a group of 5 experts from 5 different medical centers identified local concepts related to anesthesia. The concepts were then matched with standard concepts in the OHDSI vocabularies. We performed structural mapping between the design of our local anesthesia data warehouse and the OMOP CDM tables and fields. To validate the implementation of anesthesia data into the OMOP CDM, we developed a set of queries and dashboards.
RESULTS
We identified 522 concepts related to anesthesia care. They were classified as demographics, units, measurements, operating room steps, drugs, periods of interest, and features. After semantic mapping, 353 (67.7%) of these anesthesia concepts were mapped to OHDSI concepts. Further, 169 (32.3%) concepts related to periods and features were added to the OHDSI vocabularies. Then, 8 OMOP CDM tables were implemented with anesthesia data and 2 new tables (EPISODE and FEATURE) were added to store secondarily computed data. We integrated data from 5,72,609 operations and provided the code for a set of 8 queries and 4 dashboards related to anesthesia care.
CONCLUSIONS
Generic data concerning demographics, drugs, units, measurements, and operating room steps were already available in OHDSI vocabularies. However, most of the intraoperative concepts (the duration of specific steps, an episode of hypotension, etc) were not present in OHDSI vocabularies. The OMOP mapping provided here enables anesthesia data reuse.
Topics: Anesthesia; Data Science; Databases, Factual; Electronic Health Records; Hospitals; Humans; Medical Informatics
PubMed: 34714250
DOI: 10.2196/29259 -
Data in Brief Dec 2022The summary data presented in this paper describes beekeeping practices, use of natural resources and economic attributes associated with honey bee products, native...
A survey dataset to better understand the honey bee industry, use and value of natural resources and challenges for beekeepers in Western Australia: A beekeepers' perspective.
The summary data presented in this paper describes beekeeping practices, use of natural resources and economic attributes associated with honey bee products, native flora and environmental challenges relating to apiary sites. Despite being a well-established industry, information and data about productivity and the behavior of beekeepers, particularly those who migrate across the state of Western Australia, is lacking. We developed an online quantitative survey, the Natural Resources for Beekeepers Questionnaire (Western Australia) 2020-21, the first comprehensive, spatially referenced survey of beekeepers in Western Australia since 1990. It is also the first survey of small-scale amateur beekeepers that estimates their supply to the local honey market. For commercial beekeepers, a focus of the survey was to estimate the value of apiary sites and the productivity of migratory beekeepers. The data gives measures related to the production system and profitability of the Western Australian beekeeping industry, focusing on the 2019-2020 season and historical production. It includes tables describing memberships and certification; years beekeeping; hive types; apiary site availability, productivity, use, exchange and value; logistics; pollination services; honey bee products, sales and distribution; yields by season and site; targeted flora and commercial significance; recovery after bush fire and logging; labour details; operating costs; and asset values. The dataset in this paper is a subset of the survey results as aggregated summary statistics, categorized by type of beekeeper (Backyard, Hobbyist-Amateur and Commercial) and across eight regions (IBRA7 - Interim Biogeographic Regionalization for Australia). The online survey questionnaire is provided with this paper. Access to the survey offers the opportunity for reproducibility of a complex online questionnaire in the future and/or for other regions. This dataset will allow a more comprehensive assessment of the implications of natural resource management decisions in the future and the potential for strategic development of the beekeeping industry.
PubMed: 36425993
DOI: 10.1016/j.dib.2022.108639 -
The Cochrane Database of Systematic... Mar 2021Retained placenta is a common complication of pregnancy affecting 1% to 6% of all births. If a retained placenta is left untreated, spontaneous delivery of the placenta... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Retained placenta is a common complication of pregnancy affecting 1% to 6% of all births. If a retained placenta is left untreated, spontaneous delivery of the placenta may occur, but there is a high risk of bleeding and infection. Manual removal of the placenta (MROP) in an operating theatre under anaesthetic is the usual treatment, but is invasive and may have complications. An effective non-surgical alternative for retained placenta would potentially reduce the physical and psychological trauma of the procedure, and costs. It could also be lifesaving by providing a therapy for settings without easy access to modern operating theatres or anaesthetics. Injection of uterotonics into the uterus via the umbilical vein and placenta is an attractive low-cost option for this. This is an update of a review last published in 2011.
OBJECTIVES
To assess the use of umbilical vein injection (UVI) of saline solution with or without uterotonics compared to either expectant management or with an alternative solution or other uterotonic agent for retained placenta.
SEARCH METHODS
For this update, we searched Cochrane Pregnancy and Childbirth's Trials Register, ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform (14 June 2020), and reference lists of retrieved studies.
SELECTION CRITERIA
Randomised controlled trials (RCTs) comparing UVI of saline or other fluids (with or without uterotonics), either with expectant management or with an alternative solution or other uterotonic agent, in the management of retained placenta. We considered quasi-randomised, cluster-randomised, and trials reported only in abstract form.
DATA COLLECTION AND ANALYSIS
Two review authors independently assessed trials for inclusion and risk of bias, extracted data, and checked them for accuracy. We assessed the certainty of the evidence using the GRADE approach. We calculated pooled risk ratios (RRs) and mean differences (MDs) with 95% confidence intervals (CIs), and presented results using 'Summary of findings' tables.
MAIN RESULTS
We included 24 trials (n = 2348). All included trials were RCTs, one was quasi-randomised, and none were cluster-randomised. Risk of bias was variable across the included studies. We assessed certainty of evidence for four comparisons: saline versus expectant management, oxytocin versus expectant management, oxytocin versus saline, and oxytocin versus plasma expander. Evidence was moderate to very-low certainty and downgraded for risk of bias of included studies, imprecision, and inconsistency of effect estimates. Saline solution versus expectant management There is probably little or no difference in the incidence of MROP between saline and expectant management (RR 0.93, 95% CI 0.80 to 1.10; 5 studies, n = 445; moderate-certainty evidence). Evidence for the following remaining primary outcomes was very-low certainty: severe postpartum haemorrhage 1000 mL or greater, blood transfusion, and infection. There were no events reported for maternal mortality or postpartum anaemia (24 to 48 hours postnatal). No studies reported addition of therapeutic uterotonics. Oxytocin solution versus expectant management UVI of oxytocin solution might slightly reduce in the need for manual removal compared with expectant management (mean RR 0.73, 95% CI 0.56 to 0.95; 7 studies, n = 546; low-certainty evidence). There may be little to no difference between the incidence of blood transfusion between groups (RR 0.81, 95% CI 0.47 to 1.38; 4 studies, n = 339; low-certainty evidence). There were no maternal deaths reported (2 studies, n = 93). Evidence for severe postpartum haemorrhage of 1000 mL or greater, additional uterotonics, and infection was very-low certainty. There were no events for postpartum anaemia (24 to 48 hours postnatal). Oxytocin solution versus saline solution UVI of oxytocin solution may reduce the use of MROP compared with saline solution, but there was high heterogeneity (RR 0.82, 95% CI 0.69 to 0.97; 14 studies, n = 1370; I² = 54%; low-certainty evidence). There were no differences between subgroups according to risk of bias or oxytocin dose for the outcome MROP. There may be little to no difference between groups in severe postpartum haemorrhage of 1000 mL or greater, blood transfusion, use of additional therapeutic uterotonics, and antibiotic use. There were no events for postpartum anaemia (24 to 48 hours postnatal) (very low-certainty evidence) and there was only one event for maternal mortality (low-certainty evidence). Oxytocin solution versus plasma expander One small study reported UVI of oxytocin compared with plasma expander (n = 109). The evidence was very unclear about any effect on MROP or blood transfusion between the two groups (very low-certainty evidence). No other primary outcomes were reported. For other comparisons there were little to no differences for most outcomes examined. However, there was some evidence to suggest that there may be a reduction in MROP with prostaglandins in comparison to oxytocin (4 studies, n = 173) and ergometrine (1 study, n = 52), although further large-scale studies are needed to confirm these findings.
AUTHORS' CONCLUSIONS
UVI of oxytocin solution is an inexpensive and simple intervention that can be performed when placental delivery is delayed. This review identified low-certainty evidence that oxytocin solution may slightly reduce the need for manual removal. However, there are little or no differences for other outcomes. Small studies examining injection of prostaglandin (such as dissolved misoprostol) into the umbilical vein show promise and deserve to be studied further.
Topics: Anti-Bacterial Agents; Bias; Blood Transfusion; Female; Humans; Injections, Intravenous; Oxytocics; Oxytocin; Placenta, Retained; Plasma Substitutes; Pregnancy; Prostaglandins; Randomized Controlled Trials as Topic; Sodium Chloride; Umbilical Veins
PubMed: 33705565
DOI: 10.1002/14651858.CD001337.pub3 -
Bioinformatics (Oxford, England) Aug 2020Accurate 3D modelling of protein-protein interactions (PPI) is essential to compensate for the absence of experimentally determined complex structures. Here, we present...
SUMMARY
Accurate 3D modelling of protein-protein interactions (PPI) is essential to compensate for the absence of experimentally determined complex structures. Here, we present a new set of commands within the ModelX toolsuite capable of generating atomic-level protein complexes suitable for interface design. Among these commands, the new tool ProteinFishing proposes known and/or putative alternative 3D PPI for a given protein complex. The algorithm exploits backbone compatibility of protein fragments to generate mutually exclusive protein interfaces that are quickly evaluated with a knowledge-based statistical force field. Using interleukin-10-R2 co-crystalized with interferon-lambda-3, and a database of X-ray structures containing interleukin-10, this algorithm was able to generate interleukin-10-R2/interleukin-10 structural models in agreement with experimental data.
AVAILABILITY AND IMPLEMENTATION
ProteinFishing is a portable command-line tool included in the ModelX toolsuite, written in C++, that makes use of an SQL (tested for MySQL and MariaDB) relational database delivered with a template SQL dump called FishXDB. FishXDB contains the empty tables of ModelX fragments and the data used by the embedded statistical force field. ProteinFishing is compiled for Linux-64bit, MacOS-64bit and Windows-32bit operating systems. This software is a proprietary license and is distributed as an executable with its correspondent database dumps. It can be downloaded publicly at http://modelx.crg.es/. Licenses are freely available for academic users after registration on the website and are available under commercial license for for-profit organizations or companies.
CONTACT
[email protected] or [email protected].
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Algorithms; Proteins; Software
PubMed: 32437555
DOI: 10.1093/bioinformatics/btaa533 -
Frontiers in Veterinary Science 2022Good calf health is crucial for a successfully operating farm business and animal welfare on dairy farms. To evaluate calf health on farms and to identify potential...
Benchmarking calf health: Assessment tools for dairy herd health consultancy based on reference values from 730 German dairies with respect to seasonal, farm type, and herd size effects.
Good calf health is crucial for a successfully operating farm business and animal welfare on dairy farms. To evaluate calf health on farms and to identify potential problem areas, benchmarking tools can be used by farmers, herd managers, veterinarians, and other advisory persons in the field. However, for calves, benchmarking tools are not yet widely established in practice. This study provides hands-on application for on-farm benchmarking of calf health. Reference values were generated from a large dataset of the "PraeRi" study, including 730 dairy farms with a total of 13,658 examined preweaned dairy calves. At herd level, omphalitis (O, median 15.9%) was the most common disorder, followed by diarrhea (D, 15.4%) and respiratory disease (RD, 2.9%). Abnormal weight bearing (AWB) was rarely detected (median, 0.0%). Calves with symptoms of more than one disorder at the same time (multimorbidity, M) were observed with a prevalence of 2.3%. The enrolled farms varied in herd size, farm operating systems, and management practices and thus represented a wide diversity in dairy farming, enabling a comparison with similar managed farms in Germany and beyond. To ensure comparability of the data in practice, the reference values were calculated for the whole data set, clustered according to farm size (1-40 dairy cows ( = 130), 41-60 dairy cows ( = 99), 61-120 dairy cows ( = 180), 121-240 dairy cows ( = 119) and farms with more than 240 dairy cows ( = 138), farm operating systems (conventional ( = 666), organic ( = 64)) and month of the year of the farm visit. There was a slight tendency for smaller farms to have a lower prevalence of disorders. A statistically significant herd-size effect was detected for RD ( = 0.008) and D ( < 0.001). For practical application of these reference values, tables, diagrams, and an Excel (Microsoft) based calf health calculator were developed as tools for on-farm benchmarking (https://doi.org/10.6084/m9.figshare.c.6172753). In addition, this study provides a detailed description of the colostrum, feeding and housing management of preweaned calves in German dairy farms of different herd sizes and farm type (e.g., conventional and organic).
PubMed: 36213417
DOI: 10.3389/fvets.2022.990798 -
Sensors (Basel, Switzerland) Nov 2022The occurrence of landslides has been increasing in recent years due to intense and prolonged rainfall events. Lowering the groundwater in natural and man-made slopes...
The occurrence of landslides has been increasing in recent years due to intense and prolonged rainfall events. Lowering the groundwater in natural and man-made slopes can help to mitigate the hazards. Subsurface drainage systems equipped with pumps have traditionally been regarded as a temporary remedy for lowering the groundwater in geosystems, whereas long-term usage of pumping-based techniques is uncommon due to the associated high operational costs in labor and energy. This study investigates the intelligent control of groundwater in slopes enabled by deep reinforcement learning (DRL), a subfield of machine learning for automated decision-making. The purpose is to develop an autonomous geosystem that can minimize the operating cost and enhance the system's safety without introducing human errors and interventions. To prove the concept, a seepage analysis model was implemented using a partial differential equation solver, FEniCS, to simulate the geosystem (i.e., a slope equipped with a pump and subjected to rainfall events). A Deep Q-Network (i.e., a DRL learning agent) was trained to learn the optimal control policy for regulating the pump's flow rate. The objective is to enable intermittent control of the pump's flow rate (i.e., 0%, 25%, 50%, 75%, and 100% of the pumping capacity) to keep the groundwater close to the target level during rainfall events and consequently help to prevent slope failure. A comparison of the results with traditional proportional-integral-derivative-controlled and uncontrolled water tables showed that the geosystem integrated with DRL can dynamically adapt its response to diverse weather events by adjusting the pump's flow rate and improve the adopted control policy by gaining more experience over time. In addition, it was observed that the DRL control helped to mitigate slope failure during rainfall events.
Topics: Humans; Groundwater; Machine Learning
PubMed: 36366203
DOI: 10.3390/s22218503 -
Frontiers in Surgery 2022Video-Assisted and Robotic-Assisted techniques become constantly more prominent practice in thoracic surgery for lung cancer. Furthermore, the increased frequency in... (Review)
Review
BACKGROUND
Video-Assisted and Robotic-Assisted techniques become constantly more prominent practice in thoracic surgery for lung cancer. Furthermore, the increased frequency in detection of small lung cancers makes the intra-operative identification of these cancers even more challenging. Indocyanine Green (ICG) is one of the most commonly used dyes that assists surgeons identify small lung cancers intra-operatively. Our study aimed to evaluate the effectiveness and safety of ICG in lung cancer detection.
METHODS
We performed a systematic review of the literature by screening the databases of MEDLINE, EMBASE, CENTRAL and Scopus until 30th April 2022 and the first 300 articles of Google Scholar for any suitable grey literature. We included any study that investigated the effectiveness of ICG in lung cancer detection. We excluded studies that explored the use of ICG only in identification of intersegmental planes, lymph node mapping, case reports and non-English articles. We aimed to perform a meta-analysis on test accuracy studies using hierarchical summary receiver operating characteristic (HSROC) and the bivariate random-effects models. In cases where the data for a localization technique was not sufficient for that analysis, it was presented with tables with narrative purposes. Each study was assessed for Risk of Bias (RoB) and Applicability using the QUADAS-2 tool.
RESULTS
We found 30 eligible studies that included a total of 1,776 patients who underwent ICG localization of pulmonary nodules. We identified three ICG localization techniques: CT-guided, endobronchial and intravenous. From the 30 studies, 13 investigated CT-guided localization, 12 explored an endobronchial method while 8 studies administered ICG intravenously the median reported success rate was 94.3% (IQR: 91.4%-100%) and 98.3% (IQR: 94%-100%) for the first two techniques respectively. Intravenous ICG lung cancer localization showed Sensitivity of 88% (95% CI: 59%-0.97%) and Specificity of 25% (95% CI: 0.04%-0.74%). There were 15.2% (150/989) patients who experienced complications from CT guided ICG localization. No ICG-related complications were reported in endobronchial or intravenous techniques.
CONCLUSION
Our study provides a comprehensive review of the literature on ICG localization techniques for lung cancer. Current evidence suggests that ICG is boh effective and safe. Further prospective research with standardized protocols across multiple thoracic units is required in order to accurately validate these findings.
PubMed: 35959126
DOI: 10.3389/fsurg.2022.967897 -
International Journal of Environmental... Feb 2023As a means of enhancing food security, efficient agricultural processing and the maintenance of a smooth supply chain are essential for ensuring food quality and...
As a means of enhancing food security, efficient agricultural processing and the maintenance of a smooth supply chain are essential for ensuring food quality and reducing food wastage. Agricultural enterprises play a crucial role in the processing and transportation of food from farms to dinner tables. Operating income growth plays the vital role of ensuring that agricultural enterprises function in a stable manner while also indicating the quantity and quality of market food supply. Therefore, the objective of this study is to explore the impact of digital inclusive finance on food security by analyzing the effect of digital inclusive finance on the operating income of agricultural enterprises in China. By applying pooled OLS analysis to Chinese agricultural enterprises that are listed in the National Equities Exchange and Quotations, this study finds that digital inclusive finance can help improve agricultural operating income. The results reveal that digital inclusive finance can facilitate the promotion of agricultural operating income by increasing the supply of financing, accelerating inventory liquidity, and supporting investment in research and development. In addition, this study concludes that digital inclusive finance is more effective for increasing agricultural operating income as a result of its wider coverage and deeper utilization. Furthermore, the development of traditional finance is still necessary for the digitization of digital inclusive finance to be effective.
Topics: Agriculture; Farms; China; Meals; Food Security; Economic Development
PubMed: 36833648
DOI: 10.3390/ijerph20042956 -
Journal of Orthopaedics and... Nov 2022Synovial fluid markers (synovial leukocyte count and differential) have been shown to be most accurate in diagnosing prosthetic joint infection (PJI). An inverse...
BACKGROUND
Synovial fluid markers (synovial leukocyte count and differential) have been shown to be most accurate in diagnosing prosthetic joint infection (PJI). An inverse correlation for synovial leukocyte count and synovial pH is known assuming that leukocyte metabolism causes synovial fluid acidosis. This study's purpose is to analyze the use of synovial pH as a potential diagnostic marker for PJI.
MATERIALS AND METHODS
92 patients who presented with painful total joint arthroplasty (TJA) of the hip (THA; n = 25) or knee (TKA, n = 67) were prospectively investigated. In our cohort 33% (30/92) had PJI and 67% (62/92) were diagnosed non-infected based on the modified Musculoskeletal Infection Society (MSIS) criteria of 2018. Receiver operating curves and the Youden's index were used to define an ideal cut-off value for synovial pH and the sensitivity and specificity were calculated using cross-tables. Additionally, the sensitivity and specificity were calculated for synovial white blood cell (WBC) count (cut-off > 3000 leukocytes) and percentage of neutrophils (PMN%, cut-off > 80%).
RESULTS
The median synovial pH level was significantly lower in the group with chronic PJI compared to implants with aseptic failure (7.09 vs. 7.27; p < 0.001). The calculated optimal cut-off value was 7.11 (AUC 0.771) with a sensitivity of 53% and specificity of 89%. However, the sensitivity and specificity of synovial WBC count were 90% and 88% and for synovial PMN% 73% and 98%, respectively.
CONCLUSION
Synovial pH may be a useful adjunct parameter in the diagnosis of chronic PJI after hip or knee arthroplasty, but showed low sensitivity in this preliminary cohort. Future studies with larger numbers are needed.
LEVEL OF EVIDENCE
2a, diagnostic study. Trial registration German Clinical Trials Register (Registration number: DRKS00021038).
Topics: Humans; Synovial Fluid; Prosthesis-Related Infections; Arthritis, Infectious; Leukocyte Count; Arthroplasty, Replacement, Knee; Hydrogen-Ion Concentration
PubMed: 36402933
DOI: 10.1186/s10195-022-00672-5