Category: Statistics

J Neurointerv Surg. 2021 Aug 23:neurintsurg-2021-017858. doi: 10.1136/neurintsurg-2021-017858. Online ahead of print.

ABSTRACT

BACKGROUND: Delivery of acute stroke endovascular intervention can be challenging because it requires complex coordination of patient and staff across many different locations. In this proof-of-concept paper we (a) examine whether WiFi fingerprinting is a feasible machine learning (ML)-based real-time location system (RTLS) technology that can provide accurate real-time location information within a hospital setting, and (b) hypothesize its potential application in streamlining acute stroke endovascular intervention.

METHODS: We conducted our study in a comprehensive stroke care unit in Melbourne, Australia that offers a 24-hour mechanical thrombectomy service. ML algorithms including K-nearest neighbors, decision tree, random forest, support vector machine and ensemble models were trained and tested on a public WiFi dataset and the study hospital WiFi dataset. The hospital dataset was collected using the WiFi explorer software (version 3.0.2) on a MacBook Pro (AirPort Extreme, Broadcom BCM43x×1.0). Data analysis was implemented in the Python programming environment using the scikit-learn package. The primary statistical measure for algorithm performance was the accuracy of location prediction.

RESULTS: ML-based WiFi fingerprinting can accurately predict the different hospital zones relevant in the acute endovascular intervention workflow such as emergency department, CT room and angiography suite. The most accurate algorithms were random forest and support vector machine, both of which were 98% accurate. The algorithms remain robust when new data points, which were distinct from the training dataset, were tested.

CONCLUSIONS: ML-based RTLS technology using WiFi fingerprinting has the potential to streamline delivery of acute stroke endovascular intervention by efficiently tracking patient and staff movement during stroke calls.

PMID:34426539 | DOI:10.1136/neurintsurg-2021-017858

Eur J Hosp Pharm. 2021 Sep;28(5):271-275. doi: 10.1136/ejhpharm-2018-001673. Epub 2019 Aug 24.

ABSTRACT

OBJECTIVES: To improve the disinfection methods for materials with a non-sterile surface to be used in aseptic handling.

METHODS: The surface bioburden on ampoules (A) and injection vials (IV) is determined by contact plates and total immersion. The occurrence of spore-forming bacteria is determined by strain colouring and matrix-assisted laser desorption ionisation-time of flight mass spectrometry. The disinfection procedures of non-sterile materials in 10 hospital pharmacies are judged by observing.

RESULTS: After wiping according to local disinfection methods, the mean surface bioburden determined by contact plates in 10 hospital pharmacies is 0.36 (plastic A), 0.50 (glass A) and 0.29 colony-forming unit (cfu) (IV). The observers found great differences in accuracy of wiping and degree of wetting the sterile gauzes.After improved wiping with commercially available alcohol impregnated sterile wipes and a two-towel technique (one-step TT disinfection), the mean surface bioburden determined by contact plates is 0.03 (plastic A), 0.2 (glass A) and 0.13 cfu (IV). Further improvement can be reached by submerging A and IV in ethanol 70% followed by improved wiping (two-step TT disinfection), but still micro-organisms will remain (mean surface bioburden determined by total immersion is 0 (plastic A) and 0.3 cfu (IV); glass A not determined). Two-step TT disinfection is more labour intensive. Spilling of alcohol is another disadvantage. However, we presume one-step TT disinfection is effective enough in daily practice. Routine surface bioburden determinations have to prove this.The effectiveness of the combination of spray and wipe is not examined because we observed a quick disappearance of alcohols from vertical as well as horizontal surfaces, which shortens the contact time to far below the advised 2 min.Spore-forming bacteria disappear as quickly as other micro-organisms during disinfection by alcohols.

CONCLUSION: Local disinfection procedures can be improved. Complete removal of micro-organisms from materials with a non-sterile surface, even after two-step TT disinfection, is impossible. Routine surface bioburden determinations have to prove if one-step TT disinfection is effective enough.

PMID:34426480 | DOI:10.1136/ejhpharm-2018-001673

Proc Natl Acad Sci U S A. 2021 Aug 31;118(35):e2105482118. doi: 10.1073/pnas.2105482118.

ABSTRACT

Observational knowledge of the epidemic intensity, defined as the number of deaths divided by global population and epidemic duration, and of the rate of emergence of infectious disease outbreaks is necessary to test theory and models and to inform public health risk assessment by quantifying the probability of extreme pandemics such as COVID-19. Despite its significance, assembling and analyzing a comprehensive global historical record spanning a variety of diseases remains an unexplored task. A global dataset of historical epidemics from 1600 to present is here compiled and examined using novel statistical methods to estimate the yearly probability of occurrence of extreme epidemics. Historical observations covering four orders of magnitude of epidemic intensity follow a common probability distribution with a slowly decaying power-law tail (generalized Pareto distribution, asymptotic exponent = -0.71). The yearly number of epidemics varies ninefold and shows systematic trends. Yearly occurrence probabilities of extreme epidemics, P_y, vary widely: P_y of an event with the intensity of the “Spanish influenza” (1918 to 1920) varies between 0.27 and 1.9% from 1600 to present, while its mean recurrence time today is 400 y (95% CI: 332 to 489 y). The slow decay of probability with epidemic intensity implies that extreme epidemics are relatively likely, a property previously undetected due to short observational records and stationary analysis methods. Using recent estimates of the rate of increase in disease emergence from zoonotic reservoirs associated with environmental change, we estimate that the yearly probability of occurrence of extreme epidemics can increase up to threefold in the coming decades.

PMID:34426498 | DOI:10.1073/pnas.2105482118

BMJ Open. 2021 Aug 23;11(8):e050795. doi: 10.1136/bmjopen-2021-050795.

ABSTRACT

OBJECTIVES: Adequate risk adjustment for factors beyond the control of the healthcare system contributes to the process of transparent and equitable benchmarking of trauma outcomes. Current risk adjustment models are not optimal in terms of the number and nature of predictor variables included in the model and the treatment of missing data. We propose a statistically robust and parsimonious risk adjustment model for the purpose of benchmarking.

SETTING: This study analysed data from the multicentre Australia New Zealand Trauma Registry from 1 July 2016 to 30 June 2018 consisting of 31 trauma centres.

OUTCOME MEASURES: The primary endpoints were inpatient mortality and length of hospital stay. Firth logistic regression and robust linear regression models were used to study the endpoints, respectively. Restricted cubic splines were used to model non-linear relationships with age. Model validation was performed on a subset of the dataset.

RESULTS: Of the 9509 patients in the model development cohort, 72% were male and approximately half (51%) aged over 50 years . For mortality, cubic splines in age, injury cause, arrival Glasgow Coma Scale motor score, highest and second-highest Abbreviated Injury Scale scores and shock index were significant predictors. The model performed well in the validation sample with an area under the curve of 0.93. For length of stay, the identified predictor variables were similar. Compared with low falls, motor vehicle occupants stayed on average 2.6 days longer (95% CI: 2.0 to 3.1), p<0.001. Sensitivity analyses did not demonstrate any marked differences in the performance of the models.

CONCLUSION: Our risk adjustment model of six variables is efficient and can be reliably collected from registries to enhance the process of benchmarking.

PMID:34426470 | DOI:10.1136/bmjopen-2021-050795

BMJ Open. 2021 Aug 23;11(8):e051977. doi: 10.1136/bmjopen-2021-051977.

ABSTRACT

OBJECTIVE: To describe the accuracy of coding of ethnicity in National Health Service (NHS) administrative hospital records compared with self-declared records in maternity booking systems, and to assess the potential impact of misclassification bias.

DESIGN: Secondary analysis of data from records of women giving birth in England (2015-2017).

SETTING: NHS Trusts in England participating in a national audit programme.

PARTICIPANTS: 1 237 213 women who gave birth between 1 April 2015 and 31 March 2017. PRIMARY AND SECONDARY OUTCOME MEASURES: (1) Proportion of women with complete ethnicity; (2) agreement on coded ethnicity between maternity (maternity information systems (MIS)) and administrative hospital (Hospital Episode Statistics (HES)) records; (3) rates of caesarean section and obstetric anal sphincter injury by ethnic group in MIS and HES.

RESULTS: 91.3% of women had complete information regarding ethnicity in HES. Overall agreement between data sets was 90.4% (κ=0.83); 94.4% when collapsed into aggregate groups of white/South Asian/black/mixed/other (κ=0.86). Most disagreement was seen in women coded as mixed in either data set. Rates of obstetrical events and complications by ethnicity were similar regardless of data set used, with the most differences seen in women coded as mixed.

CONCLUSIONS: Levels of accuracy in ethnicity coding in administrative hospital records support the use of ethnicity collapsed into groups (white/South Asian/black/mixed/other), but findings for mixed and other groups, and more granular classifications, should be treated with caution. Robustness of results of analyses for associations with ethnicity can be improved by using additional primary data sources.

PMID:34426472 | DOI:10.1136/bmjopen-2021-051977

Br J Ophthalmol. 2021 Aug 23:bjophthalmol-2021-319574. doi: 10.1136/bjophthalmol-2021-319574. Online ahead of print.

ABSTRACT

BACKGROUND/AIMS: To investigate the relationship between the foveal avascular zone (FAZ) parameters assessed by optical coherence tomography angiography (OCTA) and central visual field parameters in glaucoma and healthy subjects.

METHODS: One hundred and eighty-eight subjects (248 eyes), including 24 healthy (38 eyes), 37 glaucoma suspect (42 eyes, and 127 primary open angle glaucoma (POAG) patients (168 eyes), underwent imaging using OCTA and standard automated perimetry using the 24-2 and 10-2 Swedish Interactive Thresholding Algorithm. OCTA-based and OCT-based FAZ parameters (superficial FAZ area, FAZ circumference), foveal vessel density (FD300) and foveal thickness were measured. The correlation between FAZ parameters and visual field parameters was assessed using linear mixed model.

RESULTS: Axial length adjusted-FAZ area was not different among the three groups (mean (95% CI)): in healthy 0.31 (0.27 to 0.36) mm², glaucoma suspect 0.29 (0.26 to 0.31) mm² and POAG eyes 0.28 (0.27 to 0.30) mm² (p=0.578). FD300 was lower in glaucoma suspect 49.1% (47.9% to 50.4%) and POAG eyes 48.7% (48.1% to 49.4%) than healthy eyes 50.5% (49.3% to 51.7%) though the difference was not statistically significant (p=0.071). Lower FD300 was associated with worse 24-2 and 10-2 visual field mean deviation and foveal threshold in multivariable linear mixed models (all p<0.05). In addition, a smaller FAZ area was associated with lower intraocular pressure (IOP) (p=0.026).

CONCLUSIONS: The FD300, but not the FAZ area was correlated with 10° central visual field mean deviation and foveal threshold in healthy, glaucoma suspect and POAG eyes. In contrast, a smaller FAZ area was associated with lower IOP.

PMID:34426401 | DOI:10.1136/bjophthalmol-2021-319574

BMJ Glob Health. 2021 Aug;6(8):e006216. doi: 10.1136/bmjgh-2021-006216.

ABSTRACT

Health management information systems (HMIS) are a crucial source of timely health statistics and have the potential to improve reporting in low-income countries. However, concerns about data quality have hampered their widespread adoption in research and policy decisions. This article presents results from a data verification study undertaken to gain insights into the quality of HMIS data in Ethiopia. We also provide recommendations for working with HMIS data for research and policy translation. We linked the HMIS to the 2016 Emergency Obstetric and Newborn Care Assessment, a national census of all health facilities that provided maternal and newborn health services in Ethiopia. We compared the number of visits for deliveries and caesarean sections (C-sections) reported in the HMIS in 2015 (January-December) to those found in source documents (paper-based labour and delivery and operating theatre registers) in 2425 facilities across Ethiopia. We found that two-thirds of facilities had ‘good’ HMIS reporting for deliveries (defined as reporting within 10% of source documents) and half had ‘very good’ reporting (within 5% of source documents). Results were similar for reporting on C-section deliveries. We found that good reporting was more common in urban areas (OR: 1.30, 95% CI 1.06 to 1.59), public facilities (OR: 2.95, 95% CI 1.38 to 6.29) and in hospitals compared with health centres (OR: 1.71, 95% CI 1.13 to 2.61). Facilities in the Somali and Afar regions had the lowest odds of good reporting compared with Addis Ababa and were more likely to over-report deliveries in the HMIS. Further work remains to address remaining discrepancies in the Ethiopian HMIS. Nonetheless, our findings corroborate previous data verification exercises in Ethiopia and support greater use and uptake of HMIS data for research and policy decisions (particularly, greater use of HMIS data elements (eg, absolute number of services provided each month) rather than coverage indicators). Increased use of these data, combined with feedback mechanisms, is necessary to maintain data quality.

PMID:34426404 | DOI:10.1136/bmjgh-2021-006216

Sci Total Environ. 2021 Aug 11;800:149626. doi: 10.1016/j.scitotenv.2021.149626. Online ahead of print.

ABSTRACT

Modeling studies project that in the future surface waters in the northeast US will continue to recover from acidification over decades following reductions in atmospheric sulfur dioxide and nitrogen oxides emissions. However, these studies generally assume stationary climatic conditions over the simulation period and ignore the linkages between soil and surface water recovery from acid deposition and changing climate, despite fundamental impacts to watershed processes and comparable time scales for both phenomena. In this study, the integrated biogeochemical model PnET-BGC was applied to two montane forest watersheds in the Adirondack region of New York, USA to evaluate the recovery of surface waters from historical acidification in response to possible future changes in climate and atmospheric sulfur and nitrogen deposition. Statistically downscaled climate scenarios on average project warmer temperatures and greater precipitation for the Adirondack by the end of the century. Model simulations suggest under constant climate, acid-sensitive Buck Creek would gain 12.8 μeq L^-1 of acid neutralizing capacity (ANC) by 2100 from large reductions in deposition, whereas acid insensitive Archer Creek is projected to gain 7.9 μeq L^-1 of ANC. However, climate change could limit those improvements in acid-base status. Under climate change, a negative offset relative to the ANC increases with no climate change are projected for both streams by 2100. In acid-insensitive Archer Creek the negative offset (-8.5 μeq L^-1) was large enough that ANC is projected to decrease by -0.6 μeq L^-1, whereas in acid-sensitive Buck Creek, the negative offset (-0.4 μeq L^-1) resulted in a slight decline of the projected future ANC increase to 12.4 μeq L^-1. Calculated target loads for 2150 for both sites decreased when future climate change was considered in model simulations, which suggests further reductions in acid deposition may be necessary to restore ecosystem structure and function under a changing climate.

PMID:34426327 | DOI:10.1016/j.scitotenv.2021.149626

Ann Rheum Dis. 2021 Aug 23:annrheumdis-2021-220687. doi: 10.1136/annrheumdis-2021-220687. Online ahead of print.

ABSTRACT

OBJECTIVE: Alteration of the gut microbiome has been linked to the pathogenesis of systemic lupus erythematosus (SLE). However, a comprehensive view of the gut microbiome in SLE and its interaction with the host remains to be revealed. This study aimed to reveal SLE-associated changes in the gut microbiome and its interaction with the host by a comprehensive metagenome-wide association study (MWAS) followed by integrative analysis.

METHODS: We performed a MWAS of SLE based on shotgun sequencing of the gut microbial DNA from Japanese individuals (N _case=47, N _control=203). We integrated the result of the MWAS with the genome-wide association study (GWAS) data and plasma metabolite data.

RESULTS: Via species level phylogenetic analysis, we identified and validated increases of Streptococcus intermedius and Streptococcus anginosus in the patients with SLE. Microbial gene analysis revealed increases of Streptococcus-derived genes including one involved in redox reaction. Additionally, microbial pathways related to sulfur metabolism and flagella assembly were altered in the patients with SLE. We identified an overlap in the enriched biological pathways between the metagenome and the germline genome by comparing the result of the MWAS and the GWAS of SLE (ie, MWAS-GWAS interaction). α-diversity and β-diversity analyses provided evidence of dysbiosis in the metagenome of the patients with SLE. Microbiome-metabolome association analysis identified positive dosage correlation of acylcarnitine with Streptococcus intermedius, an SLE-associated taxon.

CONCLUSION: Our MWAS followed by integrative analysis revealed SLE-associated changes in the gut microbiome and its interaction with the host, which contribute to our understanding of the relationship between the microbiome and SLE.

PMID:34426398 | DOI:10.1136/annrheumdis-2021-220687

Sci Total Environ. 2021 Aug 4;799:149472. doi: 10.1016/j.scitotenv.2021.149472. Online ahead of print.

ABSTRACT

The systematic and scientific assessments on heavy metal pollutions and water quality characteristics are greatly important to protecting the river and coastal eco-environment. In this paper, sediment size, organic matter, total nitrogen, total phosphorus, and heavy metal contents were analyzed by collecting surface sediments and surface water in the reservoir control reach of the middle Han River. Besides, sediment enrichment factor and sediment pollution index were used to evaluate the heavy metal pollution, and enrichment analysis and redundancy analysis were applied to analyze the sources of heavy metals in sediments. The results show a low heavy metal content in the surface water, and the water quality is graded as a Good level. The average enrichment factor of Cd in surface sediments reached 4.63. Zn and Cu also showed significant enrichment in the tributary sediments, whose content far exceeded the background value of soil elements. Thus, the potential ecological risk of heavy metals was at a medium level. Statistical analysis and enrichment factors showed that the accumulation of heavy metals in sediments was affected by pollutant input and reservoir regulation, and it was urgent to conduct an integrated regulation of the heavy metals in river sediment. This study provided an insight into the understanding of feasible assessment for heavy metal contaminated sediment.

PMID:34426303 | DOI:10.1016/j.scitotenv.2021.149472