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In the field of transmission electron microscopy, data interpretation often lags behind acquisition methods, as image processing methods often have to be manually tailored to individual datasets. Machine learning offers a promising approach for fast, accurate analysis of electron microscopy data. Here, we demonstrate a flexible two-step pipeline for the analysis of high-resolution transmission electron microscopy data, which uses a U-Net for segmentation followed by a random forest for the detection of stacking faults. Our trained U-Net is able to segment nanoparticle regions from the amorphous background with a Dice coefficient of 0.8 and significantly outperforms traditional image segmentation methods. Using these segmented regions, we are then able to classify whether nanoparticles contain a visible stacking fault with 86% accuracy. We provide this adaptable pipeline as an open-source tool for the community. The combined output of the segmentation network and classifier offer a way to determine statistical distributions of features of interest, such as size, shape, and defect presence, enabling the detection of correlations between these features.
Concerns persist regarding possible false-negative results that may compromise COVID-19 containment. Although obtaining a true false-negative rate is infeasible, using real-life observations, the data suggest a possible false-negative rate of ˜2.3%. Use of a sensitive, amplified RNA platform should reassure healthcare systems.
Investigate an outbreak of coronavirus disease 2019 (COVID-19) among operating room staff utilizing contact tracing, mass testing for severe acute respiratory coronavirus virus 2 (SARS-CoV-2), and environmental sampling.
Operating room staff with positive SARS-CoV-2 molecular testing.
Epidemiologic and environmental investigations were conducted including contact tracing, environmental surveys, and sampling and review of the operating room schedule for staff-to-staff, staff-to-patient, and patient-to-staff SARS-CoV-2 transmission.
In total, 24 healthcare personnel (HCP) tested positive for SARS-CoV-2, including nurses (29%), surgical technologists (25%), and surgical residents (16%). Moreover, 19 HCP (79%) reported having used a communal area, most commonly break rooms (75%). Overall, 20 HCP (83%) reported symptomatic disease. In total, 72 environmental samples were collected from communal areas for SARS-CoV-2 genomic testing; none was positive. Furthermore, 236 surgical cases were reviewed for transmission: 213 (90%) had negative preoperative SARS-CoV-2 testing, 21 (9%) had a positive test on or before the date of surgery, and 2 (<1%) did not have a preoperative test performed. In addition, 40 patients underwent postoperative testing (mean, 13 days to postoperative testing), and 2 returned positive results. Neither of these 2 cases was linked to our outbreak.
Complacency in infection control practices among staff during peak community transmission of SARS-CoV-2 is believed to have driven staff-to-staff transmission. Prompt identification of the outbreak led to rapid interventions, ultimately allowing for uninterrupted surgical service.
In recent years, a variety of efforts have been made in political science to enable, encourage, or require scholars to be more open and explicit about the bases of their empirical claims and, in turn, make those claims more readily evaluable by others. While qualitative scholars have long taken an interest in making their research open, reflexive, and systematic, the recent push for overarching transparency norms and requirements has provoked serious concern within qualitative research communities and raised fundamental questions about the meaning, value, costs, and intellectual relevance of transparency for qualitative inquiry. In this Perspectives Reflection, we crystallize the central findings of a three-year deliberative process—the Qualitative Transparency Deliberations (QTD)—involving hundreds of political scientists in a broad discussion of these issues. Following an overview of the process and the key insights that emerged, we present summaries of the QTD Working Groups’ final reports. Drawing on a series of public, online conversations that unfolded at www.qualtd.net, the reports unpack transparency’s promise, practicalities, risks, and limitations in relation to different qualitative methodologies, forms of evidence, and research contexts. Taken as a whole, these reports—the full versions of which can be found in the Supplementary Materials—offer practical guidance to scholars designing and implementing qualitative research, and to editors, reviewers, and funders seeking to develop criteria of evaluation that are appropriate—as understood by relevant research communities—to the forms of inquiry being assessed. We dedicate this Reflection to the memory of our coauthor and QTD working group leader Kendra Koivu.1
Background: Hospitalists play a critical role in antimicrobial stewardship as the primary antibiotic prescriber for many inpatients. We sought to describe antibiotic prescribing variation among hospitalists within a healthcare system. Methods: We created a novel metric of hospitalist-specific antibiotic prescribing by linking hospitalist billing data to hospital medication administration records in 4 hospitals (two 500-bed academic (AMC1 and AMC2), one 400-bed community (CH1), and one 100-bed community (CH2)) from January 2016 to December 2018. We attributed dates that a hospitalist electronically billed for a given patient as billed patient days (bPD) and mapped an antibiotic day of therapy (DOT) to a bPD. Each DOT was classified according to National Healthcare Safety Network antibiotic categories: broad-spectrum hospital-onset (BS-HO), broad-spectrum community-onset (BS-CO), anti-MRSA, and highest risk for Clostridioides difficile infection (CDI). DOT and bPD were pooled to calculate hospitalist-specific DOT per 1,000 bPD. Best subsets regression was performed to assess model fit and generate hospital and antibiotic category-specific models adjusting for patient-level factors (eg, age ≥65, ICD-10 codes for comorbidities and infections). The models were used to calculate predicted hospitalist-specific DOT and observed-to-expected ratios (O:E) for each antibiotic category. Kruskal-Wallis tests and pairwise Wilcoxon rank-sum tests were used to determine significant differences between median DOT per 1,000 bPD and O:E between hospitals for each antibiotic category. Results: During the study period, 116 hospitalists across 4 hospitals contributed a total of 437,303 bPD. Median DOT per 1,000 bPD varied between hospitals (BS-HO range, 46.7–84.2; BS-CO range, 63.3–100; anti-MRSA range, 48.4–65.4; CDI range, 82.0–129.4). CH2 had a significantly higher median DOT per 1,000 bPD compared to the academic hospitals (all antibiotic categories P < .001) and CH1 (BS-HO, P = .01; anti-MRSA, P = .02) (Fig. 1A). The 4 antibiotic groups at 4 hospitals resulted in 16 models, with good model fit for CH2 (R2 > 0.55 for all models), modest model fit for AMC2 (R2 = 0.46–0.55), fair model fit for CH1 (R2 = 0.19–0.35), and poor model fit for AMC1 (R2 < 0.12 for all models). Variation in hospitalist-specific O:E was moderate (IQR, 0.9–1.1). AMC1 showed greater variation than other hospitals, but we detected no significant differences in median O:E between hospitals (all antibiotic categories P > .10) (Fig. 1B). Conclusions: Adjusting for patient-level factors significantly reduced much of the variation in hospitalist-specific DOT per 1,000 bPD in some but not all hospitals, suggesting that unmeasured factors may drive antibiotic prescribing. This metric may represent a target for stewardship intervention, such as hospitalist-specific feedback of antibiotic prescribing practices.
Disclosures: Scott Fridkin, consulting fee - vaccine industry (various) (spouse)
Background: Certain nursing home (NH) resident care tasks have a higher risk for multidrug-resistant organisms (MDRO) transfer to healthcare personnel (HCP), which can result in transmission to residents if HCPs fail to perform recommended infection prevention practices. However, data on HCP-resident interactions are limited and do not account for intrafacility practice variation. Understanding differences in interactions, by HCP role and unit, is important for informing MDRO prevention strategies in NHs. Methods: In 2019, we conducted serial intercept interviews; each HCP was interviewed 6–7 times for the duration of a unit’s dayshift at 20 NHs in 7 states. The next day, staff on a second unit within the facility were interviewed during the dayshift. HCP on 38 units were interviewed to identify healthcare personnel (HCP)–resident care patterns. All unit staff were eligible for interviews, including certified nursing assistants (CNAs), nurses, physical or occupational therapists, physicians, midlevel practitioners, and respiratory therapists. HCP were asked to list which residents they had cared for (within resident rooms or common areas) since the prior interview. Respondents selected from 14 care tasks. We classified units into 1 of 4 types: long-term, mixed, short stay or rehabilitation, or ventilator or skilled nursing. Interactions were classified based on the risk of HCP contamination after task performance. We compared proportions of interactions associated with each HCP role and performed clustered linear regression to determine the effect of unit type and HCP role on the number of unique task types performed per interaction. Results: Intercept-interviews described 7,050 interactions and 13,843 care tasks. Except in ventilator or skilled nursing units, CNAs have the greatest proportion of care interactions (interfacility range, 50%–60%) (Fig. 1). In ventilator and skilled nursing units, interactions are evenly shared between CNAs and nurses (43% and 47%, respectively). On average, CNAs in ventilator and skilled nursing units perform the most unique task types (2.5 task types per interaction, Fig. 2) compared to other unit types (P < .05). Compared to CNAs, most other HCP types had significantly fewer task types (0.6–1.4 task types per interaction, P < .001). Across all facilities, 45.6% of interactions included tasks that were higher-risk for HCP contamination (eg, transferring, wound and device care, Fig. 3). Conclusions: Focusing infection prevention education efforts on CNAs may be most efficient for preventing MDRO transmission within NH because CNAs have the most HCP–resident interactions and complete more tasks per visit. Studies of HCP-resident interactions are critical to improving understanding of transmission mechanisms as well as target MDRO prevention interventions.
Funding: Centers for Disease Control and Prevention (grant no. U01CK000555-01-00)
Disclosures: Scott Fridkin, consulting fee, vaccine industry (spouse)
To investigate the molecular epidemiology of methicillin-susceptible Staphylococcus aureus (MSSA) in infants in a neonatal intensive care unit (NICU) using whole-genome sequencing.
Investigation of MSSA epidemiology in a NICU.
Single-center, level IV NICU.
Universal S. aureus screening was done using a single swab obtained from the anterior nares, axilla, and groin area of infants in the NICU on a weekly basis. Core genome multilocus sequence type (cgMLST) analysis was performed on MSSA isolates detected over 1 year (2018–2019).
In total, 68 MSSA-colonized infants were identified, and cgMLSTs of 67 MSSA isolates were analyzed. Overall, we identified 11 cgMLST isolate groups comprising 39 isolates (58%), with group sizes ranging from 2 to 10 isolates, and 28 isolates (42%) were unrelated to each other or any of the isolate groups. Cases of infants colonized by MSSA were scattered throughout the 1-year study period, and isolates belonging to the same cgMLST group were typically detected contemporaneously, over a few weeks or a few months. Overall, 13 infants (19.7%) developed MSSA infections: bacteremia (n = 3), wound infection (n = 5), conjunctivitis (n = 4), and cellulitis (n = 1). We detected no association between these clinically manifest infections and specific cgMLST groups.
Although MSSA isolates in infants in a NICU showed high diversity, most were related to other isolates, albeit within small groups. cgMLST facilitates an understanding of the complex transmission dynamics of MSSA in NICUs, and these data can be used to inform better control strategies.
Placements within high secure forensic hospitals consist of wards providing various different levels of relational security. They should form a coherent pathway through secure care, based on individual patient risks and needs. Moves to less secure wards within high secure forensic hospitals and moves on to lower secure hospital settings have rarely been systematically studied.
The aim of this study was to ascertain if placements within Broadmoor High Secure Hospital and moves from Broadmoor to medium secure hospitals corresponded to measures of violence risk, programme completion and recovery.
A 13-month prospective cohort study was completed. Patients (n = 142) were rated at baseline for violence risk (Historical, Clinical and Risk – 20), therapeutic programme completion and recovery (DUNDRUM tool) and overall functioning (Global Assessment of Functioning). Placements on the care pathway and moves on to medium secure hospitals were observed.
Placements on the care pathway within the high secure hospital were associated with dynamic violence risk (F = 16.324, P<0.001), therapeutic programme completion (F = 4.167, P = 0.003), recovery (F = 2.440, P = 0.050) with better scores on these measures being found in the rehabilitation wards and the poorest scores on the highest levels of dependency. Moves to medium secure hospitals were associated with better scores on dynamic risk of violence (F = 33.199, P<0.001), therapeutic programme completion (F = 9.237 P<0.001), recovery (F = 6.863, P = 0.001).
Placements within Broadmoor Hospital formed a coherent pathway through high secure care. Moves to less secure places were influenced by more than reduction in violence risk. Therapeutic programme completion and recovery in a broad sense were also important.
The COVID-19 pandemic has created a high demand on personal protective equipment, including disposable N95 masks. Given the need for mask reuse, we tested the feasibility of vaporized hydrogen peroxide (VHP), ultraviolet light (UV), and ethanol decontamination strategies on N95 mask integrity and the ability to remove the infectious potential of SARS-CoV-2.
Disposable N95 masks, including medical grade (1860, 1870+) and industrial grade (8511) masks, were treated by VHP, UV, and ethanol decontamination. Mask degradation was tested using a quantitative respirator fit testing. Pooled clinical samples of SARS-CoV-2 were applied to mask samples, treated, and then either sent immediately for real-time reverse transcriptase–polymerase chain reaction (RT-PCR) or incubated with Vero E6 cells to assess for virucidal effect.
Both ethanol and UV decontamination showed functional degradation to different degrees while VHP treatment showed no significant change after two treatments. We also report a single SARS-CoV-2 virucidal experiment using Vero E6 cell infection in which only ethanol treatment eliminated detectable SARS-CoV-2 RNA.
We hope our data will guide further research for evidenced-based decisions for disposable N95 mask reuse and help protect caregivers from SARS-CoV-2 and other pathogens.
Euthanasia and assisted suicide (EAS) based on a psychiatric disorder (psychiatric EAS) continue to pose ethical and policy challenges, even in countries where the practice has been allowed for years. We conducted a systematic review of reasons, a specific type of review for bioethical questions designed to inform rational policy-making. Our aims were twofold: (1) to systematically identify all published reasons for and against the practice (2) to identify current gaps in the debate and areas for future research.
Following the PRISMA guidelines, we performed a search across seven electronic databases to include publications focusing on psychiatric EAS and providing ethical reasons. Reasons were grouped into domains by qualitative content analysis.
We included 42 articles, most of which were written after 2013. Articles in favor and against were evenly distributed. Articles in favor were mostly full-length pieces written by non-clinicians, with articles against mostly reactive, commentary-type pieces written by clinicians. Reasons were categorized into eight domains: (1) mental and physical illness and suffering (2) decisional capacity (3) irremediability (4) goals of medicine and psychiatry (5) consequences for mental health care (6) psychiatric EAS and suicide (7) self-determination and authenticity (8) psychiatric EAS and refusal of life-sustaining treatment. Parity- (or discrimination-) based reasons were dominant across domains, mostly argued for by non-clinicians, while policy reasons were mostly pointed to by clinicians.
The ethical debate about psychiatric EAS is relatively young, with prominent reasons of parity. More direct engagement is needed to address ethical and policy considerations.
To assess the nutritional quality of Australian supermarket own brand chilled convenience foods (SOBCCF), for example, ready meals, pizza, pies and desserts.
Two large supermarkets (Coles and Woolworths) in Perth, Western Australia were audited in February 2017.
Data were extracted from photographic images of 291 SOBCCF, including front-of-pack information (i.e. product name, description and nutrition labels including Health Star Rating (HSR)) and back-of-pack information (i.e. nutrition information panel and ingredients list). SOBCCF were classified as healthy or unhealthy consistent with principles of the Australian Guide to Healthy Eating (AGTHE), NOVA classification of level of food processing and HSR score.
Fifty-four percentage of SOBCCF were classified as unhealthy according to AGTHE principles, 94 % were ultra-processed foods using NOVA and 81 % scored a HSR of ≥2·5, implying that they were a healthy choice. Some convenience food groups comprised more healthy choices overall including prepared vegetables, salad kits and bowls, soups and vegetarian food. A significantly larger proportion of SOBCCF from Coles were classified as unhealthy compared with Woolworths (70 v. 44 %, P < 0·05) using the AGTHE.
The findings suggest there is potential for Australian supermarkets to improve the nutritional quality of their SOBCCF and highlights the differences between supermarkets in applying their corporate social responsibility policies. Policies to assist consumers to select healthier foods should address difficulties in identifying healthy convenience foods. The findings reveal misclassification of unhealthy SOBCCF as healthy by the HSR suggesting that its algorithm should be reformed to align with recommendations of the AGTHE.
To determine the effect of an electronic medical record (EMR) nudge at reducing total and inappropriate orders testing for hospital-onset Clostridioides difficile infection (HO-CDI).
An interrupted time series analysis of HO-CDI orders 2 years before and 2 years after the implementation of an EMR intervention designed to reduce inappropriate HO-CDI testing. Orders for C. difficile testing were considered inappropriate if the patient had received a laxative or stool softener in the previous 24 hours.
Four hospitals in an academic healthcare network.
All patients with a C. difficile order after hospital day 3.
Orders for C. difficile testing in patients administered a laxative or stool softener in <24 hours triggered an EMR alert defaulting to cancellation of the order (“nudge”).
Of the 17,694 HO-CDI orders, 7% were inappropriate (8% prentervention vs 6% postintervention; P < .001). Monthly HO-CDI orders decreased by 21% postintervention (level-change rate ratio [RR], 0.79; 95% confidence interval [CI], 0.73–0.86), and the rate continued to decrease (postintervention trend change RR, 0.99; 95% CI, 0.98–1.00). The intervention was not associated with a level change in inappropriate HO-CDI orders (RR, 0.80; 95% CI, 0.61–1.05), but the postintervention inappropriate order rate decreased over time (RR, 0.95; 95% CI, 0.93–0.97).
An EMR nudge to minimize inappropriate ordering for C. difficile was effective at reducing HO-CDI orders, and likely contributed to decreasing the inappropriate HO-CDI order rate after the intervention.