bluuebunny/crossref_metadata_2025 huggingface dataset:
Spillover of Early Extubation Practices From the Pediatric Heart Network Collaborative Learning Study*
Authors: Witte Madolin K. , Mahle William T. , Pasquali Sara K. , Nicolson Susan C. , Shekerdemian Lara S. , Wolf Michael J. , Zhang Wenying , Donohue Janet E. , Gaies Michael
Published: December 2020

Objectives:

The Pediatric Heart Network Collaborative Learning Study used collaborative learning strategies to implement a clinical practice guideline that increased rates of early extubation after infant repair of tetralogy of Fallot and coarctation of the aorta. We assessed early extubation rates for infants undergoing cardiac surgeries not targeted by the clinical practice guideline to determine whether changes in extubation practices spilled over to care of other infants.

Design:

Observational analyses of site’s local Society of Thoracic Surgeons Congenital Heart Surgery Database and Pediatric Cardiac Critical Care Consortium Registry.

Setting:

Four Pediatric Heart Network Collaborative Learning Study active-site hospitals.

Patients:

Infants undergoing ventricular septal defect repair, atrioventricular septal defect repair, or superior cavopulmonary anastomosis (lower complexity), and arterial switch operation or isolated aortopulmonary shunt (higher complexity).

Interventions:

None.

Measurements and Main Results:

Aggregate outcomes were compared between the 12 month pre-clinical practice guideline and 12 months after study completion (Follow Up). In infants undergoing lower complexity surgeries, early extubation increased during Follow Up compared with Pre-Clinical Practice Guideline (30.2% vs 18.8%, p = 0.006), and hours to initial postoperative extubation decreased. We observed variation in these outcomes by surgery type, with only ventricular septal defect repair associated with a significant increase in early extubation during Follow Up compared with Pre-Clinical Practice Guideline (47% vs 26%, p = 0.006). Variation by study site was also seen, with only one hospital showing an increase in early extubation. In patients undergoing higher complexity surgeries, there was no difference in early extubation or hours to initial extubation between the study eras.

Conclusions:

We observed spillover of extubation practices promoted by the Collaborative Learning Study clinical practice guideline to lower complexity operations not included in the original study that was sustainable 1 year after study completion, though this effect differed across sites and operation subtypes. No changes in postoperative extubation outcomes following higher complexity surgeries were seen. The significant variation in outcomes by site suggests that center-specific factors may have influenced spillover of clinical practice guideline practices.
Comparison of the Postoperative Outcomes of Posterior Layer Advancement and Modified Iliff Suturing to Correct Involutional Lower Lid Entropion
Authors: Kinoshita Shinsuke , Ukyo Hisaki , Masuda Naonori , Osawa Shunsuke
Published: December 2020

Involutional lower lid entropion is treated surgically with either incision or rotational suturing. The authors have obtained good results with the modified Iliff suture (MIS) procedure. Here, the authors compare the efficacy and postoperative outcomes of MIS and posterior layer advancement. This study included Japanese patients with a normal snap-back test, who underwent primary surgery for correcting involutional lower lid entropion, performed by the same surgeon, from April 2009 to March 2017, and who were followed up for at least 24 months postoperatively. Posterior layer advancement was performed on 50 eyelids of 48 patients (19 men, 29 women; mean age 74.1 ± 8.7 years) and MIS was performed on 50 eyelids of 40 patients (16 men, 24 women; mean age 77.3 ± 7.5 years). The authors compared the postoperative follow-up duration, recurrence rate, and operating time between groups. Postoperative follow-up duration was 34.5 ± 7.4 months in the posterior layer advancement and 32.3 ± 8.1 months in the MIS group (P = 0.180). Recurrence rate was 6% (3 cases) in the posterior layer advancement group and 4% (2 cases) in the MIS group (P > 0.999). Operating time was significantly shorter in the MIS group (5.8 ± 1.1 minutes) than in the posterior layer advancement group (31.6 ± 4.1 minutes, P < 0.001). Modified Iliff suture is less invasive than posterior layer advancement and has similar postoperative outcomes; thus, it is useful for treating involutional lower lid entropion.
Navigation-Assisted Resection and Fibula Free-Flap Reconstruction of an Extensive Maxillary Tumor
Authors: Zavattero Emanuele , Ramieri Guglielmo , Volpe Fabio , Borbon Claudia
Published: December 2020

Objective:

Tumor resection and reconstruction as a one-step procedure requires accurate definition of the intended safety margins, precise location of osteotomy lines and reliable individual rehabilitation.

In recent years, the role of image-guided surgery in the maxillofacial region has increased significantly. As this technology allows the surgeon to track the actual position of each instrument during the operation in real-time, it makes it possible to perform extensive bone structure resections and reconstructions in anatomically distorted or complex areas, such as the head and neck region, without unnecessarily damaging vital structures.

The authors described a case of a 26-year-old woman presented to our Clinic with an extensive maxillary squamous cell carcinoma involving the infratemporal fossa. The patient underwent single-step navigation-guided en bloc resection of the tumor and defect reconstruction.

The aim of this study is describe and discuss the unusual surgical planning and the challenging operative technique adding a new case to the currently limited scientific literature on the computer-assisted head and neck oncologic surgery.
Model Experimental Study of Man-Machine Interactive Robot-Assisted Craniotomy
Authors: Aung Zin Mar , Chen Xiaojun , Xu Cheng , Sun Mengzhe , Lin Li , Xie Le , Xu Haisong , Han Dong , Chai Gang
Published: December 2020

To evaluate the feasibility, safety, and accuracy of the new man-machine interactive robotic system in model experiment. The implantation of the 8 to 10 bone screws over the skull model obtained from real patient's digital imaging and communications in medicine (DICOM), three-dimensional spiral computed tomography (CT) scans were taken. The end of the robotic arm was replaced with standard parts (including marker ball) for cone beam computed tomography (CBCT) scanning. The marker ball and marker pin were segmented and marked and exported via txt format. The position of the robotic end and model was obtained through the conversion of spacious position of standard parts and the executive end was replaced eventually. The water balloon was placed inside the skull model to imitate the dura mater and the destruction was documented for the system's safety. The system accuracy was evaluated by the error between the actual drilling position and the virtual plan and selection of 14 points of the skull window of milling pathway, monitored intraoperatively via Micron Tracker system and the overall skull window overlapped percentage via Mimics. Five model experiments were successfully performed with the average registration time of 3 minutes without destruction of balloon. The error of the outer table was 0.85 ± 0.45 mm, the inner table was 0.78 ± 0.49 mm, the line segment error of milling cutter was 0.93 ± 0.50 mm and the overall skull window overlapped percentage was 97.37% ± 0.78%. The system shows safety, accuracy, and reliability which can be an optional assistant method for craniotomy in the future.
Predicting Trainee Clinical Success From Performance at Simulated Endotracheal Intubation
Authors: Hastings Randolph H. , Tapia Viridiana J. , Lurie Benjamin , Hallare Jericho A. , Dinescu A. Teodora , Gabriel Rodney A. , Delson Nathan , Suresh Preetham J.
Published: December 2020

Introduction

Multiple attempts and failure at endotracheal intubation (ETI) are common for inexperienced practitioners and can cause patient morbidity. A test to predict a provider's likelihood of success at patient ETI could assist decisions about training. This project investigated whether trainees' performance at laryngoscopy on airway mannequins predicted their laryngoscopy outcomes in patients.

Methods

Twenty-one consenting first-year anesthesiology residents, emergency medicine residents, and medical students enrolled in this prospective, observational study. They performed laryngoscopy and ETI with a curved laryngoscope on 4 airway mannequins. Metrics included peak dental force, procedure duration, esophageal intubation, laryngeal view, and first-pass ETI success on the mannequins. Trainee data from 203 patient ETIs were collected over a roughly 2-month period centered around the simulation test. Multivariable logistic regression analyzed the relationship of mannequin metrics, participant experience, and a patient difficult airway score with trainee ETI outcomes in patients.

Results

Median trainee first-pass success rate at patient ETI was 63%, the rate of ETI problems was 16%, and the esophageal intubation rate was 6%. Laryngoscopy peak dental force, first-pass ETI success, and duration on individual mannequins were significant predictors of patient ETI first-pass success. Metrics from 2 of the 4 mannequins predicted ETI problems.

Discussion

Performance metrics from simulated laryngoscopy predicted trainee outcomes during patient ETI. First-pass success and ETI problems affect patient safety and are related to trainee skill. Mannequin laryngoscopy tests could identify trainees who would benefit from additional practice. The metrics could be surrogate end points in research to optimize simulated laryngoscopy training.
Co-constructive Patient Simulation
Authors: Martin Andrés , Weller Indigo , Amsalem Doron , Duvivier Robbert , Jaarsma Debbie , de Carvalho Filho Marco Antonio
Published: December 2020

Introduction

In simulation sessions using standardized patients (SPs), it is the instructors, rather than the learners, who traditionally identify learning goals. We describe co-constructive patient simulation (CCPS), an experiential method in which learners address self-identified goals.

Methods

In CCPS, a designated learner creates a case script based on a challenging clinical encounter. The script is then shared with an actor who is experienced working as an SP in medical settings. An instructor with experience in the model is involved in creating, editing, and practicing role play of the case. After co-creation of the case, learners with no prior knowledge of the case (peers or a supervisor) interview the SP. The clinical encounter is followed by a group debriefing session.

Results

We conducted 6 CCPS sessions with senior trainees in child and adolescent psychiatry. Topics that are difficult to openly talk about may be especially appropriate for the CCPS model—without overt guidance or solicitation, the scripts developed by learners for this series involved: medical errors and error disclosure; racial tensions, including overt racism; interprofessional conflict; transphobia; patient-on-provider violence; sexual health; and the sharing of vulnerability and personal imperfections in the clinical setting.

Conclusions

Co-constructive patient simulation provides an alternative multistage and multimodal approach to traditional SP simulation sessions that can adapt iteratively and in real time to new clinical vicissitudes and challenges This learner-centered model holds promise to enrich simulation-based education by fostering autonomous, meaningful, and relevant experiences that are in alignment with trainees' self-identified learning goals.
Safety Considerations for In Situ Simulation in Closed SARS-CoV-2 Units
Authors: Jafri Farrukh N. , Shah Sharan , Yang Christina J. , Restivo Andrew , Singh Maninder , Yoon Andrew , Ahmed Sadia T.
Published: December 2020

Summary Statement

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic placed a tremendous strain on the healthcare system, which led to the deployment of new personnel into acute care settings, early graduation of medical students, and development of new treatment spaces. Education teams at the Montefiore Health System and New York Health and Hospitals/Jacobi Medical Center found simulation, both laboratory-based and in situ, critical to the training of medical staff and investigation of latent safety threats. Through our experience, we encountered unique infection control concerns based on in situ sessions, which prompted us to redesign our programs for the treatment of SARS-CoV-2. Using this experience, we outline our rationale for the use of in situ simulation for newly developed SARS-CoV-2 spaces along with recommendations on safety checks to consider before starting.
Pleurectomy Decortication in the Treatment of Malignant Pleural Mesothelioma
Authors: Lapidot Moshe , Gill Ritu R. , Mazzola Emanuele , Freyaldenhoven Samuel , Swanson Scott J. , Jaklitsch Michael T. , Sugarbaker David J. , Bueno Raphael
Published: December 2020

Objective:

We report a series of 355 consecutive patients treated over 9 years in a single institution with intended PDC.

Background:

Surgery for MPM has shifted from extra-pleural pneumonectomy to PDC with the goal of MCR.

Methods:

Clinical and outcome data were reviewed. Kaplan-Meier estimators and log rank test were used to compare the overall survival, and logistic regression models were used.

Results:

MCR was achieved in 304. There were 223 males, median age was 69 and histology was epithelioid in 184. The 30 and 90-day mortality were 3.0% and 4.6%.

Most complications were low grade. Prolonged air leak in 141, deep venous thrombosis in 64, Atrial fibrillation in 42, chylothorax in 24, Empyema in 23, pneumonia in 21, Hemothorax in 12 and pulmonary embolus in 8. Median/5-year survival were 20.7 months/17.9% in the intent-to-treat cohort and 23.2months/21.2% in the MCR group. The survivals were best for patients with Tlstage and epithelioid histology (69.8months/54.1%). In a multivariable analysis, factors that were found to be associated with longer patient overall survival included epithelioid histology, T stage, quantitative clinical stage/tumor volume staging, adjuvant chemotherapy, intraoperative heated chemo, female sex, and length of stay shorter than 14 days.

Conclusions:

PDC is feasible with low mortality and is associated with manageable complication rates. 5-year survival of patients undergoing PDC with MCR in multi-modality setting is approaching 25% depending on quantitative and clinical stage, sex and histological subtype and is better than PDC without- MCR.
Imaging Tolerance Induction in Neonatal Mice: Hierarchical Interplay Between Allogeneic Adult and Neonatal Immune Cells
Authors: Bascom Roger A. , Tao KeSheng , West Lori J.
Published: December 2020

Background.

In Medawar’s murine neonatal tolerance model, injection of adult semiallogeneic lymphohematopoietic cells (spleen cells [SC] and bone marrow cells [BMC]) tolerizes the neonatal immune system. An eventual clinical application would require fully allogeneic (allo) cells, yet little is known about the complex in vivo/in situ interplay between those cells and the nonconditioned neonatal immune system.

Methods.

To this end, labeled adult SC and BMC were injected into allogeneic neonates; interactions between donor and host cells were analyzed and modulated by systematic depletion/inactivation of specific donor and host immune effector cell types.

Results.

Consistent with effector cell compositions, allo-SC and allo-SC/BMC each induced lethal acute graft-versus-host disease, whereas allo-BMC alone did so infrequently. CD8 T cells from SC inoculum appeared naïve, while those of BMC were more memory-like. Age-dependent, cell-type dominance defined the interplay between adult donor cells and the neonatal host immune system such that if the dominant adult effector type was removed, then the equivalent neonatal one became dominant. Depletion of donor/host peripheral T cells protected against acute graft-versus-host disease and prolonged heart allograft survival; peripheral CD8 T-cell depletion together with CD4 T cell–costimulation blockade induced more robust tolerance.

Conclusions.

This comprehensive study provides direct observation of the cellular interplay between allogeneic donor and host immune systems, adds to our previous work with semiallogeneic donor cells, and provides important insights for robust tolerance induction. Induction of transplant tolerance in neonates will likely require “crowd sourcing” of multiple tolerizing cell types and involve depletion of immune effector cells with costimulation blockade.
Serum Glycomics on Postoperative Day 7 Are Associated With Graft Loss Within 3 Months After Liver Transplantation Regardless of Early Allograft Dysfunction
Authors: Verhelst Xavier , Geerts Anja , Colman Roos , Vanlander Aude , Degroote Helena , Abreu de Carvalho Luis , Meuris Leander , Berrevoet Frederik , Rogiers Xavier , Callewaert Nico , Van Vlierberghe Hans
Published: December 2020

Background.

Prediction of outcome after liver transplantation (LT) is limited by the lack of robust predictors of graft failure. In this prospective study, we aimed to define a serum glycomic signature in the first week after LT that is associated with graft loss at 3 mo after LT.

Methods.

Patients were included between January 1, 2011, and February 28, 2017. Glycomic analysis was performed using DNA sequencer-associated fluorophore-associated capillary electrophoresis on a serum sample 1 wk after LT. Making use of Lasso regression, an optimal glycomic signature was identified associated with 3-mo graft survival.

Results.

In this cohort of 131 patients, graft loss at 3 mo occurred in 14 patients (11.9%). The optimal mode, called the GlycoTransplantTest, yielded an area under the curve of 0.95 for association with graft loss at 3 mo. Using an optimized cutoff for this biomarker, sensitivity was 86% and specificity 89%. Negative predictive value was 98%. Odds ratio for graft loss at 3 mo was 70.211 (P < 0.001; 95% confidence interval, 10.876-453.231).

Conclusions.

A serum glycomic signature is highly associated with graft loss at 3 mo. It could support decision making in early retransplantation.
Real-world Site Experiences With GeneMatch
Authors: Bardach Shoshana H. , Langbaum Jessica B. , Kebodeaux Carey S. , Jicha Gregory A.
Published: December 2020

Background:

Registries have been proposed as a novel way to accelerate targeted recruitment for Alzheimer disease prevention clinical trials. However, there are limited data regarding registry effectiveness at accelerating recruitment and enrollment in research opportunities. This manuscript explores one site’s experience with GeneMatch, a novel genetic registry for Alzheimer disease research.

Methods:

Referrals from GeneMatch to the site were tracked to understand the demographics of those referred and ultimate research enrollment outcomes. Referrals were cross-referenced with the site’s existing recruitment database, to better understand the role of GeneMatch in the context of existing recruitment efforts.

Results:

GeneMatch referred 86 individuals to the site, resulting in 54 individuals coming into the site to pursue research involvement further. The majority of referrals (52/86, 60.47%) did not have prior contact with the site about research engagement, and having prior site contact did not significantly relate to engaging in on-site research.

Conclusions:

GeneMatch helped identify new individuals for participation in Alzheimer disease prevention studies. Results highlight the value of continuing local site-level efforts while also taking advantage of registries to enhance research recruitment. Ongoing efforts to further develop these and other novel strategies for outreach and engagement are much needed.
The prevalence of pilus islets in Streptococcus pneumoniae isolates from healthy children in Indonesia
Authors: Safari Dodi , Valentiya Feby , Salsabila Korrie , Paramaiswari Wisiva Tofriska , Tafroji Wisnu , Hammerschmidt Sven , Hadinegoro Sri Rezeki
Published: December 2020

Streptococcus pneumoniae

produces pili that function as adherence factors to bind to epithelial cells in the human upper respiratory tract. In this study, we investigated the prevalence of pilus islets (PIs) in

S. pneumoniae

strains carried by healthy children below 5 years of age prior to pneumococcal vaccination in 2012 in Lombok Island, Indonesia. In all, 347 archived

S. pneumoniae

isolates were screened using polymerase chain reactions for the presence of rrgC and pitB genes representing pilus islet 1 (PI-1) and pilus islet 2 (PI-2), respectively. We found that 40 isolates (11.5 %) contained the PI genes: 5.2% carried both PI-1 and PI-2, and 3.5 and 2.9% carried PI-1 and PI-2, respectively. Furthermore, we found that most of the strains carrying either of the PIs belonged to the vaccine serotypes 19F and 19A and were less susceptible to chloramphenicol and tetracycline.
Streptomyces gossypiisoli sp. nov., isolated from cotton soil in Xinjiang, PR China
Authors: Zhang Qiao-Yan , Qin Song , Luo Xiao-Xia , Xia Zhan-Feng
Published: December 2020

A novel actinobacterium, designated TRM 44567T, was isolated from cotton soil in Xinjiang Uygur Autonomous Region, northwest PR China. Growth occurred at 16–45 °C, pH 5.0–9.0, and 0–7 % (w/v) NaCl, with optimum growth at 37 °C, pH 7.0–8.0 and 1 % (w/v) NaCl, respectively. Comparative 16S rRNA gene sequence analysis indicated that strain TRM 44567T was phylogenetically most closely related to

Streptomyces chromofuscus

NBRC 12851T (98.48 % sequence similarity); however, the average nucleotide identity between strain TRM 44567T and

S. chromofuscus

NBRC 12851T was only 83.77 %. Strain TRM 44567T possessed ll-diaminopimelic acid as the diagnostic cell-wall diamino acid. The predominant menaquinones were MK-9(H10), MK-9(H6) and MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were iso-C16 : 0, C16 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C14 : 0 and iso-C15 : 0. The genomic DNA G+C content was 70.8 mol%. Strain TRM 44567T represents a novel species of the genus

Streptomyces

, for which the name Streptomyces gossypiisoli sp. nov. is proposed. The type strain is TRM 44567T (=KCTC 39957 T=CCTCC AA 2017011T).
Tn1 transposition in the course of natural transformation enables horizontal antibiotic resistance spread in Acinetobacter baylyi
Authors: Kloos Julia , Johnsen Pål J. , Harms Klaus
Published: December 2020

Transposons are genetic elements that change their intracellular genomic position by transposition and are spread horizontally between bacteria when located on plasmids. It was recently discovered that transposition from fully heterologous DNA also occurs in the course of natural transformation. Here, we characterize the molecular details and constraints of this process using the replicative transposon Tn1 and the naturally competent bacterium

Acinetobacter baylyi

. We find that chromosomal insertion of Tn1 by transposition occurs at low but detectable frequencies and preferably around the

A. baylyi

terminus of replication. We show that Tn1 transposition is facilitated by transient expression of the transposase and resolvase encoded by the donor DNA. RecA protein is essential for the formation of a circular, double-stranded cytoplasmic intermediate from incoming donor DNA, and RecO is beneficial but not essential in this process. Absence of the recipient RecBCD nuclease stabilizes the double-stranded intermediate. Based on these results, we suggest a mechanistic model for transposition during natural transformation.
Clinical Characteristics and Risk Factors for Myocardial Injury and Arrhythmia in COVID-19 patients
Authors: Ren Hong Gang , Guo Xingyi , Tu Lei , Hu Qinyong , Blighe Kevin , Safdar Luqman Bin , Stebbing Justin , Weiner Shepard D , Willis Monte S , Rosendaal Frits R , Xu Guogang , Cao Feng , Wang Dao Weng
Published: December 2020

The authors have withdrawn this manuscript because of a lack of novelty of results and, with that, a lack of intention to publish in a peer reviewed journal. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Razor: annotation of signal peptides from toxins
Authors: Bhandari Bikash K. , Gardner Paul P. , Lim Chun Shen
Published: December 2020

Motivation

Signal peptides are responsible for protein transport and secretion and are ubiquitous to all forms of life. The annotation of signal peptides is important for understanding protein translocation and toxin secretion and evolution.

Results

Here we explore the features of these signal sequences from eukaryotic proteins. Strikingly, we find that the signal peptides from secretory toxins have common features across kingdoms, supporting the idea of horizontal gene transfer or convergence of toxin genes across kingdoms. We leverage these features to build Razor, a simple yet powerful tool specialised in identifying signal peptides from toxins using the first 23 N-terminal residues. We demonstrate the usability of Razor by analysing all the sequences reviewed by UniProt. Indeed, Razor is able to identify toxins using their N-terminal sequences only. Strikingly, we also discover that many defensive proteins across kingdoms harbour a toxin-like signal peptide; some of these defensive proteins have emerged through convergent evolution, e.g. defensin and defensin-like protein families, and phospholipase families. In sum, Razor uses an approach independent of homology search to identify novel and known toxin classes across species using N-terminal residues.

Availability and implementation

Razor is available as a web application (https://tisigner.com/razor) and a command-line tool (https://github.com/Gardner-BinfLab/Razor).
To the canopy and beyond: Air samples reveal wind dispersal as a driver of ubiquitous protistan pathogen assembly in tree canopies
Authors: Jauss Robin-Tobias , Nowack Anne , Walden Susanne , Wolf Ronny , Schaffer Stefan , Schellbach Barbara , Bonkowski Michael , Schlegel Martin
Published: December 2020

We analyzed air dispersal of the protistan phyla Cercozoa and Oomycota with an air sampler near the ground (~2 m) and in tree crowns (~25 m) of three tree species (oak, linden and ash) in a temperate floodplain forest in March (before leafing) and May (after leaf unfolding) with a cultivation-independent high throughput metabarcoding approach. Both, Cercozoa and Oomycota, contain important pathogens of forest trees and other vegetation. We found a high diversity of Cercozoa and Oomycota in air samples with 122 and 81 OTUs, respectively. Especially oomycetes showed a high temporal variation in beta diversity between both sampling dates. Differences in community composition between air samples in tree canopies and close to the ground were however negligible, and also tree species identity did not affect communities in air samples, indicating that the distribution of protistan propagules through the air was not spatially restricted in the forest ecosystem. OTUs of plant pathogens, whose host species that did not occur in the forest, demonstrate wind dispersal of propagules from outside the forest biome. Overall, our results lead to a better understanding of the stochastic processes of wind dispersal of protists and protistan pathogens, a prerequisite to understand the mechanisms of their community assembly in forest ecosystems.

Importance

Wind dispersal has been shown to play a crucial role in protistan community assembly. The protistan taxa Cercozoa and Oomycota contain important plant parasites with a major ecologic and economic impact. However, comprehensive assessments of cercozoan and oomycete diversity in forest air samples were lacking. Using a cultivation-independent high throughput metabarcoding approach, we analyzed cercozoan and oomycete air dispersal in forest floors and the canopy region – a potential filter for microbial propagules. Our study provides insights into the diversity and community assembly of protists within the air, contributing to a better understanding which factors drive the distribution of plant pathogens within forest ecosystems.
A Novel COVID-19 Early Warning Tool: Moore Swab Method for Wastewater Surveillance at an Institutional Level
Authors: Liu Pengbo , Ibaraki Makoto , VanTassell Jamie , Geith Kelly , Cavallo Matthew , Kann Rebecca , Moe Christine
Published: December 2020

SARS-CoV-2 is a respiratory virus but it is also detected in a significant proportion of fecal samples of COVID-19 cases. Recent studies have shown that wastewater surveillance can be a low-cost tool for management of COVID-19 pandemic and tracking COVID-19 outbreaks in communities but most studies have been focusing on sampling from wastewater treatment plants. Institutional level of wastewater surveillance may serve well for early warning purposes since cases can be tracked and immediate action can be executed in the event of positive signal. In this study, a novel Moore swab method was developed and used for wastewater surveillance of COVID-19 at institutional level. Among the 219 swab samples tested, 28 (12.8%) swabs collected from the three campuses and two buildings were positive for SARS-CoV-2. Further individual clinical diagnosis validated the wastewater results and indicated that this method was sensitive enough to detect 1-2 cases in a building. In addition, comparison between grab and Moore swab methods from the hospital sewage line indicated that Moore swab method was more sensitive than the grab sampling method. These results suggest that the Moore swab is a sensitive, practical, and easy to use early warning tool for COVID-19 surveillance especially in low-resource settings and at an early stage of infection in communities.
Protocol for a Feasibility study incorporating a Randomised Pilot Trial with an Embedded Process Evaluation and Feasibility Economic Analysis of ThinkCancer!: A primary care intervention to expedite cancer diagnosis in Wales
Authors: Disbeschl Stefanie , Surgey Alun , Roberts Jessica L , Hendry Annie , Lewis Ruth , Goulden Nia , Hoare Zoe , Williams Nefyn , Anthony Bethany Fern , Edwards Rhiannon Tudor , Law Rebecca-Jane , Hiscock Julia , Carson-Stevens Andrew , Neal Richard D , Wilkinson Clare
Published: December 2020

Background

Relative to the rest of Europe, the UK has relatively poor cancer outcomes, with late diagnosis and a slow referral process being major contributors. General practitioners (GPs) are often faced with patients presenting with a multitude of non-specific symptoms that could be cancer. Safety netting can be used to manage diagnostic uncertainty by ensuring patients with vague symptoms are appropriately monitored, which is now even more crucial due to the ongoing Covid-19 pandemic and its major impact on cancer referrals. The ThinkCancer! Workshop is an educational behaviour change intervention aimed at the whole general practice team, designed to improve primary care approaches to ensure timely diagnosis of cancer. The workshop will consist of teaching and awareness sessions, the appointment of a Safety Netting Champion and the development of a bespoke Safety Netting Plan, and has been adapted so it can be delivered remotely. This study aims to assess the feasibility of the ThinkCancer! Intervention for a future definitive randomised controlled trial.

Methods

The ThinkCancer! study is a randomised, multisite feasibility trial, with an embedded process evaluation and feasibility economic analysis. Twenty-three to 30 general practices will be recruited across Wales, randomised in a ratio of 2:1 of intervention versus control who will follow usual care. The workshop will be delivered by a GP educator and will be adapted iteratively throughout the trial period. Baseline practice characteristics will be collected via questionnaire. We will also collect Primary Care Intervals (PCI), Two Week Wait (2WW) referral rates, conversion rates and detection rates at baseline and six months post-randomisation. Participant feedback, researcher reflections and economic costings will be collected following each workshop. A process evaluation will assess implementation using an adapted Normalisation Measure Development (NoMAD) questionnaire and qualitative interviews. An economic feasibility analysis will inform a future economic evaluation.

Discussion

This study will allow us to test and further develop a novel evidenced-based complex intervention aimed at general practice teams to expedite the diagnosis of cancer in primary care. The results from this study will inform the future design of a full-scale definitive phase III trial.

Trial registratio

intended registry: clinicaltrials.gov
The Impact of Coronavirus Disease 2019 Pandemic on People with Diabetes in Indonesia: A Cross Sectional National Scale Web-Survey
Authors: Kshanti Ida Ayu , Epriliawati Marina , Mokoagow Md Ikhsan , Nasarudin Jerry , Magfira Nadya
Published: December 2020

Background

As the country with the 7th largest number of People with Diabetes (PWD) in the world, the COVID-19 pandemic, and the Large Social Scale Restriction (LSSR) policy taken by the Indonesian government to reduce the number of COVID-19 transmissions is estimated to interfere diabetes management and will increase the incidence of diabetes complications. This study aims to determine the difficulties of diabetes management and its impact on diabetes morbidity during the COVID-19 pandemic in Indonesia.

Methodology

This study is a cross-sectional study using a national scale web survey. This research was conducted in Indonesia enrolling 1,124 PWD aged 18 years or older. Diabetes complications are defined as any incidence of hypoglycaemia, or Diabetic Foot Ulcer (DFU), or hospital admission experienced by PWD in Indonesia during the COVID-19 pandemic. The correlation between diabetes management difficulties and diabetes-related complications was measured using a modified cox regression test.

Results

Diabetes management difficulties were experienced by 69.8% of PWD in Indonesia. The difficulties include attending diabetes consultation 30.1%, access to diabetes medication 12.4%, checking blood sugar levels 9.5%, controlling diet 23.8%, and performing regular exercise 36.5%. Diabetes-related complications occurred in 24.6% of subjects. Those who had diabetes management difficulties during the COVID-19 pandemic are prone to have diabetes complications by 1.4 times greater (PR: 1.41, 95% CI: 1.09-1.83) than those who did not.

Conclusion

The COVID-19 pandemic and LSSR have a substantial impact on diabetes management and indirectly increased diabetes morbidity in Indonesia.
Correlation between adult tobacco smoking prevalence and mortality of Coronavirus Disease-19 across the world
Authors: Magfira Nadya , Helda
Published: December 2020

Background and aim

Coronavirus disease 2019 (COVID-19) is a global pandemic spreading worldwide. Limited studies showed that smokers were at higher risk of having severe complications and higher mortality. This study aims to analyze the possible correlation between adult tobacco smoking prevalence and COVID-19 mortality all over the world.

Methods

This is a correlation study, we conducted a linear regression to analyse the correlation between smoking prevalence data in adults and COVID-19 Case Fatality Ratio (CFR) in countries with 1000 confirmed COVID-19 cases on May 3, 2020.

Results

Seventy-five country included with median CFR 3.66%. There are no relationships between adult male or female smoking prevalence with COVID-19 mortality in all over the countries. The multivariate analysis showed p-values of 0.823 and 0.910 for male and female smoking prevalence respectively. However, in lower-middle-income countries (LMIC), there is a positive correlation between the prevalence of adult male smoking with the lethality of COVID-19. Each percentage point increase in adult male smoking prevalence caused a CFR of COVID-19 increase by 0.08% (95% CI 0.00%-0.15%, p=0.041).

Conclusions

A correlation was found between the prevalence of adult male smoking and the CFR of COVID-19 in lower middle-income countries. Based on these findings, strengthening tobacco control policies is needed to reduce the impact of the COVID-19 pandemic especially in LMIC. Further researches are still needed.
Which COVID policies are most effective? A Bayesian analysis of COVID-19 by jurisdiction
Authors: Wibbens Phebo , Koo Wesley Wu-Yi , McGahan Anita M.
Published: December 2020

This paper reports the results of a Bayesian analysis on large-scale empirical data to assess the effectiveness of eleven types of COVID-control policies that have been implemented at various levels of intensity in 40 countries and U.S. states since the onset of the pandemic. The analysis estimates the marginal impact of each type and level of policy as implemented in concert with other policies. The purpose is to provide policymakers and the general public with an estimate of the relative effectiveness of various COVID-control strategies. We find that a set of widely implemented core policies reduces the spread of virus but not by enough to contain the pandemic except in a few highly compliant jurisdictions. The core policies include the cancellation of public events, restriction of gatherings to fewer than 100 people, recommendation to stay at home, recommended restrictions on internal movement, implementation of a partial international travel ban, and coordination of information campaigns. For the median jurisdiction, these policies reduce growth rate in new infections from an estimated 270% per week to approximately 49% per week, but this impact is insufficient to prevent eventual transmission throughout the population because containment occurs only when a jurisdiction reduces growth in COVID infection to below zero. Most jurisdictions must also implement additional policies, each of which has the potential to reduce weekly COVID growth rate by 10 percentage points or more. The slate of these additional high-impact policies includes targeted or full workplace closings for all but essential workers, stay-at-home requirements, and targeted school closures.
High efficacy of saliva in detecting SARS-CoV-2 by RT-PCR in adults and children
Authors: Huber Michael , Schreiber Peter W. , Scheier Thomas , Audigé Annette , Buonomano Roberto , Rudiger Alain , Braun Dominique L. , Eich Gerhard , Keller Dagmar I. , Hasse Barbara , Böni Jürg , Berger Christoph , Günthard Huldrych F. , Manrique Amapola , Trkola Alexandra
Published: December 2020

Background

RT-PCR of nasopharyngeal swabs (NPS) is the acknowledged gold standard for the detection of SARS-CoV-2 infection. Rising demands for repetitive screens and mass-testing necessitate, however, the development of additional test strategies. Saliva may serve as an alternative to NPS as its collection is simple, non-invasive and amenable for mass- and home-testing but rigorous validation of saliva particularly in children is missing.

Methods

We conducted a large-scale head-to-head comparison of SARS-CoV-2 detection by RT-PCR in saliva and nasopharyngeal swab (NPS) of 1270 adults and children reporting to outpatient test centers and an emergency unit for an initial SARS-CoV-2 screen. The saliva collection strategy developed utilizes common, low-cost plastic tubes, does not create biohazard waste at collection and was tailored for self-collection and suitability for children.

Results

In total, 273 individuals were tested SARS-CoV-2 positive in either NPS or saliva. SARS-CoV-2 RT-PCR results in the two specimens showed a high agreement (Overall Percent Agreement = 97.8%). Despite lower viral loads in saliva of both adults and children, detection of SARS-CoV-2 in saliva compared well to NPS (Positive Percent Agreement = 92.5%). Importantly, in children, SARS-CoV-2 infections were more often detected in saliva than NPS (Positive Predictive Value = 84.8%), underlining that NPS sampling in children can be challenging.

Conclusions

The comprehensive parallel analysis reported here establishes saliva as a generally reliable specimen for the detection of SARS-CoV-2 with particular advantages for testing children that is readily applicable to increase and facilitate repetitive and mass-testing in adults and children.

Article Summary Main Points

Comparison with nasopharyngeal swabs in a large test center-based study confirms that saliva is a reliable and convenient material for the detection of SARS-CoV-2 by RT-PCR in adults and increases detection efficacy in children.
Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater
Authors: Whitney Oscar N. , Kennedy Lauren C. , Fan Vinson , Hinkle Adrian , Kantor Rose , Greenwald Hannah , Crits-Christoph Alexander , Al-Shayeb Basem , Chaplin Mira , Maurer Anna C. , Tjian Robert , Nelson Kara L.
Published: December 2020

Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastewater RNA extraction methods’ sensitivity, speed, and reduce reliance on often expensive commercial reagents to make wastewater-based epidemiology more accessible. We present a kit-free wastewater RNA extraction method, titled “Sewage, Salt, Silica and SARS-CoV-2” (4S), that employs the abundant and affordable reagents sodium chloride (NaCl), ethanol and silica RNA capture matrices to recover 6-fold more SARS-CoV-2 RNA from wastewater than an existing ultrafiltration-based method. The 4S method concurrently recovered pepper mild mottle virus (PMMoV) and human 18S ribosomal subunit rRNA, both suitable as fecal concentration controls. The SARS-CoV-2 RNA concentrations measured in three sewersheds corresponded to the relative prevalence of COVID-19 infection determined via clinical testing. Lastly, controlled experiments indicate that the 4S method prevented RNA degradation during storage of wastewater samples, was compatible with heat pasteurization, and could be performed in approximately 3 hours. Overall, the 4S method is promising for effective, economical, and accessible wastewater-based epidemiology for SARS-CoV-2, providing another tool to fight the global pandemic.

SYNOPSIS

The 4S method for measuring SARS-CoV-2 in wastewater is promising for effective, economical, and accessible wastewater-based epidemiology.

ABSTRACT ART
Designing and validating a Markov model for hospital-based addiction consult service impact on 12-month drug and non-drug related mortality
Authors: King Caroline A. , Englander Honora , Korthuis P. Todd , Barocas Joshua A. , McConnell K. John , Morris Cynthia D. , Cook Ryan
Published: December 2020

Introduction

Addiction consult services (ACS) engage hospitalized patients with opioid use disorder (OUD) in care and help meet their goals for substance use treatment. Little is known about how ACS affect mortality for patients with OUD. The objective of this study was to design and validate a model that estimates the impact of ACS care on 12-month mortality among hospitalized patients with OUD.

Methods

We developed a Markov model of referral to an ACS, post-discharge engagement in SUD care, and 12-month drug-related and non-drug related mortality among hospitalized patients with OUD. We populated our model using Oregon Medicaid data and validated it using international modeling standards.

Results

There were 6,654 patients with OUD hospitalized from April 2015 through December 2017. There were 114 (1.7%) drug-related deaths and 408 (6.1%) non-drug related deaths at 12 months. Bayesian logistic regression models estimated four percent (4%, 95% CI= 2%, 6%) of patients were referred to an ACS. Of those, 47% (95% CI= 37%, 57%) engaged in post-discharge OUD care, versus 20% not referred to an ACS (95% CI= 16%, 24%). The risk of drug-related death at 12 months among patients in post-discharge OUD care was 3% (95% CI= 0%, 7%) versus 6% not in care (95% CI = 2%, 10%). The risk of non-drug related death was 7% (95% CI =1%, 13%) among patients in post-discharge OUD treatment, versus 9% not in care (95% CI= 5%, 13%).

Discussion

Our novel Markov model reflects trajectories of care and survival for patients hospitalized with OUD. This model can be used to evaluate the impact of other clinical and policy changes to improve patient survival.
Implications of delayed reopening in controlling the COVID-19 surge in Southern and West-Central USA
Authors: Dandekar Raj , Wang Emma , Barbastathis George , Rackauckas Chris
Published: December 2020

1

In the wake of the rapid surge in the Covid-19 infected cases seen in Southern and West-Central USA in the period of June-July 2020, there is an urgent need to develop robust, data-driven models to quantify the effect which early reopening had on the infected case count increase. In particular, it is imperative to address the question: How many infected cases could have been prevented, had the worst affected states not reopened early? To address this question, we have developed a novel Covid-19 model by augmenting the classical SIR epidemiological model with a neural network module. The model decomposes the contribution of quarantine strength to the infection timeseries, allowing us to quantify the role of quarantine control and the associated reopening policies in the US states which showed a major surge in infections. We show that the upsurge in the infected cases seen in these states is strongly co-related with a drop in the quarantine/lockdown strength diagnosed by our model. Further, our results demonstrate that in the event of a stricter lockdown without early reopening, the number of active infected cases recorded on 14 July could have been reduced by more than 40% in all states considered, with the actual number of infections reduced being more than 100, 000 for the states of Florida and Texas. As we continue our fight against Covid-19, our proposed model can be used as a valuable asset to simulate the effect of several reopening strategies on the infected count evolution; for any region under consideration.
Low-cost, Smartphone-based Specular Imaging and Automated Analysis of the Corneal Endothelium
Authors: Mantena Sreekar , Chandra Jay , Pecyna Eryk , Zhang Andrew , Garrity Dominic , Tone Stephan Ong , Sastry Srinivas , Uddaraju Madhu , Jurkunas Ula V.
Published: December 2020

Purpose

Specular and confocal microscopes are important tools to monitor the health of the corneal endothelium (CE), but their high costs significantly limit accessibility in low-resource environments. In our study, we developed and validated a low-cost, fully automated method to quantitatively evaluate the CE using smartphone-based specular microscopy.

Methods

A OnePlus 7 Pro smartphone attached to a Topcon SL-D701 slit-lamp was used to image normal the central corneal endothelium using the specular reflection technique. Images were automatically processed on-device and endothelial cell density (ECD), percentage of hexagonal cells (HEX), and coefficient of variation (CV) values were determined using our novel image analysis algorithm. The morphometric parameters generated from the images taken by Tomey EM-4000 specular microscope were compared between the testing modalities.

Results

No significant differences in ECD (2799 ± 156 cells/mm2 vs 2779 ± 166 cells/mm2; p=0.28) and HEX (52 ± 6% vs 53 ± 6%; p=0.50) computed by smartphone-based specular imaging and specular microscope, respectively, were found. A statistically significant difference in CV (34 ± 3% vs 30 ± 3%; p<0.01) was found between the two methods. The concordance achieved between the smartphone-based method and the Tomey specular microscope is very similar to the concordance between two specular microscopes reported in the literature.

Conclusions

Smartphone-based specular imaging and automated analysis is a low-cost method to quantitatively evaluate the CE with accuracy comparable to the clinical standard.

Translational Relevance

This tool can be used to screen the CE in low-resource regions and reveal the need for further investigation of suspected corneal endotheliopathies.