bluuebunny/crossref_metadata_2025 huggingface dataset:
Volumetric Accuracy Analysis of Virtual Safety Barriers for Cooperative-Control Robotic Mastoidectomy
Authors: Ding Andy S. , Capostagno Sarah , Razavi Christopher R. , Li Zhaoshuo , Taylor Russell H. , Carey John P. , Creighton Francis X.
Published: July 2021

Hypothesis:

Virtual fixtures can be enforced in cooperative-control robotic mastoidectomies with submillimeter accuracy.

Background:

Otologic procedures are well-suited for robotic assistance due to consistent osseous landmarks. We have previously demonstrated the feasibility of cooperative-control robots (CCRs) for mastoidectomy. CCRs manipulate instruments simultaneously with the surgeon, allowing the surgeon to control instruments with robotic augmentation of motion. CCRs can also enforce virtual fixtures, which are safety barriers that prevent motion into undesired locations. Previous studies have validated the ability of CCRs to allow a novice surgeon to safely complete a cortical mastoidectomy. This study provides objective accuracy data for CCR-imposed safety barriers in cortical mastoidectomies.

Methods:

Temporal bone phantoms were registered to a CCR using preoperative computed tomography (CT) imaging. Virtual fixtures were created using 3D Slicer, with 2D planes placed along the external auditory canal, tegmen, and sigmoid, converging on the antrum. Five mastoidectomies were performed by a novice surgeon, moving the drill to the limit of the barriers. Postoperative CT scans were obtained, and Dice coefficients and Hausdorff distances were calculated.

Results:

The average modified Hausdorff distance between drilled bone and the preplanned volume was 0.351 ± 0.093 mm. Compared with the preplanned volume of 0.947 cm3, the mean volume of bone removed was 1.045 cm3 (difference of 0.0982 cm3 or 10.36%), with an average Dice coefficient of 0.741 (range, 0.665–0.802).

Conclusions:

CCR virtual fixtures can be enforced with a high degree of accuracy. Future studies will focus on improving accuracy and developing 3D fixtures around relevant surgical anatomy.
Exploring the Charge Nurse Role Transition
Authors: Doherty Dennis P. , Hunter Revell Susan M. , McCurry Mary , Asselin Marilyn E.
Published: July 2021

The novice charge nurse role transition is not well understood. This article reports on a qualitative descriptive study of the novice charge nurse role transition. Rubin and Rubin’s responsive interviewing was used. Fourteen novice charge nurses participated in Zoom interviews. Thematic analysis revealed three phases: taxiing to the runway, takeoff, and reaching cruising altitude, each with distinct themes. Nursing professional development practitioners can use these findings to better understand and support new charge nurses through this transition.
Mycoplasma genitalium Infection Is Not Associated With Genital Tract Inflammation Among Adolescent and Young Adult Women in Baltimore, Maryland
Authors: Wang Runzhi , Trent Maria E. , Bream Jay H. , Nilles Tricia L. , Gaydos Charlotte A. , Carson Kathryn A. , Coleman Jenell S.
Published: July 2021

Background

Mycoplasma genitalium (MG) is a prevalent sexually transmitted infection, but little is known about the associated inflammatory signatures in the genital tract of adolescents and young adult women.

Methods

Adolescents and young adult women aged 13 to 24 years were recruited. Demographic information, sexual behavior history, and medical history were collected. Vaginal swab samples were tested for MG, Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, bacterial vaginosis, and measurement of 13 cytokines, chemokines, and antimicrobial proteins. Vaginal cytokine concentrations were compared by MG infection status. The strength of associations between multiple factors and MG infection was evaluated.

Results

Of 215 participants, 16.7% (95% confidence interval [CI], 12.0%–22.4%) had MG infection. Inflammation was not associated with MG infection (P > 0.05). M. genitalium infection was associated with C. trachomatis infection (adjusted prevalence ratio [aPrR], 3.02; 95% CI, 1.69–5.39), bisexual behavior in the past 3 months (aPrR, 2.07; 95% CI, 1.18–3.64), genitourinary symptoms (aPrR, 2.06; 95% CI, 1.22–3.49), and self-reported Black race (aPrR, 3.53; 95% CI, 1.11–11.18).

Conclusions

Higher levels of genital tract cytokines were not associated with MG infection. C. trachomatis infection, bisexual behavior, self-reported Black race, and genitourinary symptoms were associated with an increased likelihood of MG infection.
HMGA2-WIF1 Rearrangements Characterize a Distinctive Subset of Salivary Pleomorphic Adenomas With Prominent Trabecular (Canalicular Adenoma-like) Morphology
Authors: Agaimy Abbas , Ihrler Stephan , Baněčková Martina , Costés Martineau Valérie , Mantsopoulos Konstantinos , Hartmann Arndt , Iro Heinrich , Stoehr Robert , Skálová Alena
Published: July 2021

Most of salivary gland neoplasms (benign and malignant) are characterized by recurrent gene fusions. Pleomorphic adenoma (PA), the most frequent salivary gland tumor, is driven by chromosomal rearrangements involving PLAG1 mapped to 8q12 and HMGA2 mapped to 12q13-15 in most cases. Multiple fusion partners have been identified including CTNNB1, FGFR1, LIFR, CHCHD7 and TCEA for PLAG1 fusions and NFIB, WIF1 and FHIT for HMGA2 fusions. To date, no data exist on the morphology of the few reported HMGA2-WIF1-rearranged PAs. We present 28 major salivary gland adenomas displaying distinctive trabecular and canalicular morphology associated with recurrent genotype. Patients were 15 females and 13 males aged 43 to 87 (median: 65). All tumors originated from the parotid. Their size range was 1 to 4 cm (mean: 2.3). Histologically, all tumors showed elongated or columnar cells arranged into bilayered to multilayered communicating and branching strands and trabeculae in a manner similar to canalicular adenoma of minor salivary glands or trabecular myoepithelioma with variable solid confluent intercalated duct-like areas. Fifteen tumors were exclusively canalicular/trabecular while 13 had intermingled or well-demarcated conventional (chondromyxoid) PA component comprising 5 to >50% of the tumor. The monomorphic areas expressed uniformly CK7 (28/28), vimentin (21/21), S100 (24/24), SOX10 (16/17) and variably p63 (8/21) and mammaglobin (6/16) but were negative with p40 (0/24), smooth muscle actin (0/24) and MUC4 (0/16). Targeted RNA sequencing revealed HMGA2 fusions in 14/16 (87%) assessable cases. Fusion partner was WIF1 (12), RPSAP52 (1) and HELB (1). Separate testing of the 2 components in 1 hybrid tumor showed same HMGA2/WIF1 fusion. HMGA2 immunohistochemistry was homogeneously positive in all cases including the 2 fusion-negative cases. A control cohort of 12 genuine canalicular adenomas revealed no HMGA2 fusions (0/4) and lacked HMGA2 immunoreactivity (0/12). This study highlights a distinctive variant in the spectrum of PA characterized by prominent trabecular and canalicular adenoma-like morphology. Our data confirm that canalicular adenomas in major salivary glands (either monomorphic or part of hybrid tumors) are distinct from canalicular adenoma of minor salivary glands. Their uniform genotype irrespective of presence or absence of a conventional PA component argues for classifying those tumors lacking a conventional PA component as “monomorphic variants of PA” rather than canalicular/basal cell adenomas, intercalated duct adenoma, trabecular myoepithelioma or true hybrid tumors.
Increased infectious-cause hospitalization among infants who are HIV-exposed uninfected compared with HIV-unexposed
Authors: Anderson Kim , Kalk Emma , Madlala Hlengiwe P. , Nyemba Dorothy C. , Kassanjee Reshma , Jacob Nisha , Slogrove Amy , Smith Mariette , Eley Brian S. , Cotton Mark F. , Muloiwa Rudzani , Spittal Graeme , Kroon Max , Boulle Andrew , Myer Landon , Davies Mary-Ann
Published: July 2021

Objectives:

Increased risk of morbidity and hospitalization has been observed in children who are HIV-exposed uninfected (HEU) compared with HIV-unexposed uninfected (HUU). Studies in the era of universal maternal antiretroviral treatment (ART) are limited.

Design:

Prospective cohort.

Methods:

We investigated hospitalization between 29 days and 12 months of life in a South African cohort of infants born between February 2017 and January 2019 (HEU = 455; HUU = 458). All mothers known with HIV during pregnancy received ART. We reviewed hospital records and classified and graded infectious diagnoses using a standardized tool. We examined factors associated with infectious-cause hospitalization using mixed-effects Poisson regression.

Results:

Infants HEU vs. HUU had higher all-cause and infectious-cause hospitalization (13 vs. 7%, P = 0.004 and 10 vs. 6%, P = 0.014, respectively). Infectious causes accounted for most hospitalizations (77%). More infants HEU were hospitalized with severe or very severe infections than those HUU (9 vs. 6%; P = 0.031). Mortality (<1%) did not differ between groups. HIV exposure was a significant risk factor for infectious-cause hospitalization [adjusted incidence rate ratios (aIRRs) = 2.8; 95% confidence interval (CI) 1.5–5.4]. Although increased incidence of preterm birth (14 vs. 10%; P < 0.05) and shorter duration of breastfeeding (44 vs. 68% breastfed for ≥3 months, P < 0.001) among infants HEU vs. HUU contributed to increased hospitalization, they did not account for all the increased risk.

Conclusion:

Infectious-cause hospitalization incidence was higher among infants HEU vs. HUU, likely partly because of higher incidence of preterm birth and lower breastfeeding rates among infants HEU. The increased infectious disease burden in HEU infants has important implications for health services in sub-Saharan Africa.
Low-Density Granulocytes and Neutrophil Extracellular Traps as Biomarkers of Disease Activity in Adult Inflammatory Myopathies
Authors: Torres-Ruiz Jiram , Carrillo-Vázquez Daniel Alberto , Leal-Alanis Araceli , Zentella-Dehesa Alejandro , Tapia-Rodríguez Miguel , Maravillas-Montero Jose Luis , Nuñez-Álvarez Carlos Alberto , Carazo-Vargas Edgar Rafael , Romero-Hernández Izamar , Juárez-Vega Guillermo , Alcocer-Varela Jorge , Gómez-Martín Diana
Published: July 2021

Background/Objective

Biomarkers for disease activity and damage accrual in idiopathic inflammatory myopathies (IIMs) are currently lacking. The purpose of this cross-sectional study is to analyze the relationship among low-density granulocytes (LDGs), neutrophil extracellular traps (NETs), and clinical and immunological features of patients with IIM.

Methods

We assessed disease activity, damage accrual, amount of LDGs, NETs, expression of LL-37, and serum cytokines in 65 adult patients with IIM. Differences between groups and correlations were assessed by Kruskal-Wallis, Mann-Whitney U, and Spearman ρ tests. The association between LDGs, NETs, disease activity, calcinosis, and cutaneous ulcers was assessed by logistic regression. To address the capacity of LDGs and NETs to diagnose disease activity, we used receiving operating characteristic curves.

Results

Low-density granulocytes were higher in patients with active disease, ulcers, calcinosis, and anti–MDA5 antibodies, which correlated with serum levels of IL-17A and IL-18. Neutrophil extracellular traps were higher in patients with calcinosis, elevated titers of antinuclear antibodies, and positive anti-PM/Scl75 tests. The combination of a high proportion of both total LDGs and NETs was associated with the presence of calcinosis and cutaneous ulcers. LL-37 was higher in NETs originating from LDGs. Normal-density neutrophils were elevated in patients with active dermatomyositis.

Conclusions

Low-density granulocytes and NETs containing LL-37 are increased in patients with IIM and active disease, and correlate with proinflammatory cytokines. Both total and CD10+ LDGs are potential biomarkers for disease activity and, in combination with NETs, have the potential to detect patients who are at risk for cutaneous ulcers and calcinosis.
Patterns of adverse childhood experiences and associations with prenatal substance use and poor infant outcomes in a multi-country cohort of mothers: A Latent Class Analysis
Authors: Hemady Chad Lance , Speyer Lydia Gabriela , Murray Aja Louise , Brown Ruth Harriet , Meinck Franziska , Fry Deborah , Do Huyen , Sikander Siham , Madrid Bernadette , Fernando Asvini , Walker Susan , Dunne Michael , Foley Sarah , Hughes Claire , Osafo Joseph , Baban Adriana , Taut Diana , Ward Catherine L. , Thang Vo Van , Fearon Pasco , Tomlinson Mark , Valdebenito Sara , Eisner Manuel
Published: July 2021

Aims This paper explores the number and characterization of latent classes of adverse childhood experiences across the Evidence for Better Lives Study cohort and investigates how the various typologies link to prenatal substance use (i.e., smoking, alcohol, and illicit drugs) and poor infant outcomes (i.e., infant prematurity and low birth weight). Participants and setting A total of 1,189 mother-infant dyads residing in eight diverse low- and middle-income countries (LMICs) were recruited. Methods Latent class analysis using the Bolck, Croon, and Hagenaars (BCH) 3-step method with auxiliary multilevel logistic regressions with distal outcomes were performed. Results The LCA identified three high-risk classes and one low-risk class, namely: (1) highly maltreated (7%, n = 89), (2) emotionally and physically abused with intra-familial violence exposure (13%, n = 152), (3), emotionally abused (40%, n = 474), and (4) low household dysfunction and abuse (40%, n = 474). Overall, across all latent classes, there were low probabilities of prenatal substance use and poor infant outcomes. However, pairwise comparisons between classes indicate that class 1 and 3 had higher probabilities of prenatal illicit drug use compared to class 4. Additionally, class 2 had higher probability of low birth weight compared to the three remaining classes. Conclusion The results further our understanding of the dynamic and multifaceted nature of ACEs. More research grounded on LMICs is warranted with more attention to various parameters of risk exposure (i.e., severity, duration, chronicity).
Assessing the Effects of Behavioral Circadian Rhythm Disruption in Shift-Working Police Academy Trainees
Authors: Erickson Melissa L. , Wang Will , Counts Julie , Redman Leanne M. , Parker Daniel , Huebner Janet L. , Dunn Jessilyn , Kraus William E.
Published: July 2021

Night shift work, characterized by behavioral circadian disruption, increases cardiometabolic disease risk. Our long-term goal is to develop a novel methodology to quantify behavioral circadian disruption in field-based settings and to explore relations to four metabolic salivary biomarkers of circadian rhythm. This pilot study enrolled 36 police academy trainees to test the feasibility of using wearable activity trackers to assess changes in behavioral patterns. Using a two-group observational study design, participants completed in-class training during dayshift for six weeks followed by either dayshift or nightshift field-training for six weeks. We developed a novel data-post processing step that improves sleep detection accuracy of sleep episodes that occur during daytime. We next assessed changes to resting heart rate (RHR) and sleep regularity index (SRI) during dayshift versus nightshift field training. Secondarily, we examined changes in field-based assessments of salivary cortisol, uric acid, testosterone, and melatonin during dayshift versus nightshift. Compared to dayshift, nightshift workers experienced larger changes to resting heart rate, sleep regularity index (indicating reduced sleep regularity), and alternations to sleep/wake activity patterns accompanied by blunted salivary cortisol. Salivary uric acid, testosterone, and melatonin did not change. These findings show that nightshift work—a form of behavioral circadian rhythm disruption—was detectable in police trainees using activity trackers alone and in combination with a specialized data analysis methodology.

KEY POINTS

Night shift work increases cardiometabolic disease risk and this may be a consequence of behavioral circadian misalignment.

To advance this hypothesis, methodologies to quantify behavioral irregularities during nightshift in field-based settings are needed.

In this pilot study, commercially available activity trackers combined with a novel data processing step were used to assess alterations in sleep/wake patterns in police trainees during dayshift versus nightshift.

We also explored relations with four metabolic salivary biomarkers of circadian rhythm during dayshift versus nightshift.

Compared to dayshift, nightshift resulted in larger perturbations of resting heart rate, sleep regularity index (indicating reduced regularity), and alterations in sleep and activity patterns; this was accompanied by blunted cortisol.

This novel data processing step extends commercially available technology for successful application in real-world shift work settings.
Machine Learning Applied to Routine Blood Tests and Clinical Metadata to Identify and Classify Heart failure
Authors: James Nick , Gerrish Lianna , Rokotyan Nikita , Gladding Patrick A.
Published: July 2021

Introduction

We applied machine learning (ML) to routine bloods, then to advanced haematology data from a full blood count (rawFBC) plus biochemistry, to build predictive models for heart failure, which were then used at population scale.

Methods

Routine blood results from 8,031 patients with heart failure, with equal number of controls, were used in ML training and testing datasets (Split 80:20). NT-proBNP was used for diagnostic comparison. rawFBC metadata was used in a dataset of 698 patients, 314 of whom had heart failure, to train and test ML models (Split 70:30) from rawFBC, rawFBC plus biochemistry and routine bloods. The rawFBC model was used to predict heart failure in a validation dataset of 69,492 FBCs (2.3% heart failure prevalence).

Results

Heart failure was predicted from rawFBC and biochemistry versus rawFBC AUROC 0.93 versus 0.91, 95% CI -0.023 to 0.048, P = 0.5, and predicted from routine bloods and NT-proBNP, AUROC 0.87 versus 0.81, 95% CI 0.004 to 0.097, P = 0.03. In the validation cohort heart failure was predicted from rawFBC with AUROC 0.83, 95% CI 0.83 to 0.84, P < 0.001, sensitivity 75%, specificity 76%, PPV 7%, NPV 99.2% (Figure 2). Elevated NT-proBNP (≥ 34 pmol/L) was predicted from rawFBC with AUROC 0.97, 95% CI 0.93 to 0.99, P < 0.0001. Common predictive features included markers of erythropoiesis (red cell distribution width, haemoglobin, haematocrit).

Conclusion

Heart failure can be predicted from routine bloods with accuracy equivalent to NT-proBNP. Predictive features included markers of erythropoiesis, with therapeutic monitoring implications.
Prognostic accuracy of triage tools for adults with suspected COVID-19 in a pre-hospital setting: an observational cohort study
Authors: Marincowitz Carl , Sutton Laura , Stone Tony , Pilbery Richard , Campbell Richard , Thomas Benjamin , Turner Janette , Bath Peter A. , Bell Fiona , Biggs Katie , Hasan Madina , Hopfgartner Frank , Mazumdar Suvodeep , Petrie Jennifer , Goodacre Steve
Published: July 2021

Study Objective

Tools proposed to triage patient acuity in COVID-19 infection have only been validated in hospital populations. We estimated the accuracy of five risk-stratification tools recommended to predict severe illness and compare accuracy to existing clinical decision-making in a pre-hospital setting.

Methods

An observational cohort study using linked ambulance service data for patients attended by EMS crews in the Yorkshire and Humber region of England between 18th March 2020 and 29th June 2020 was conducted to assess performance of the PRIEST tool, NEWS2, the WHO algorithm, CRB-65 and PMEWS in patients with suspected COVID-19 infection. The primary outcome was death or need for organ support.

Results

Of 7549 patients in our cohort, 17.6% (95% CI:16.8% to 18.5%) experienced the primary outcome. The NEWS2, PMEWS, PRIEST tool and WHO algorithm identified patients at risk of adverse outcomes with a high sensitivity (>0.95) and specificity ranging from 0.3 (NEWS2) to 0.41 (PRIEST tool). The high sensitivity of NEWS2 and PMEWS was achieved by using lower thresholds than previously recommended. On index assessment, 65% of patients were transported to hospital and EMS decision to transfer patients achieved a sensitivity of 0.84 (95% CI 0.83 to 0.85) and specificity of 0.39 (95% CI 0.39 to 0.40).

Conclusion

Use of NEWS2, PMEWS, PRIEST tool and WHO algorithm could improve sensitivity of EMS triage of patients with suspected COVID-19 infection. Use of the PRIEST tool would improve sensitivity of triage without increasing the number of patients conveyed to hospital.
Excess morbidity and mortality among survivors of childhood acute lymphoblastic leukaemia: 25 years of follow-up from the United Kingdom Childhood Cancer Study (UKCCS)
Authors: Kane Eleanor , Kinsey Sally , Bonaventure Audrey , Johnston Tom , Simpson Jill , Howell Debra , Smith Alexandra , Roman Eve
Published: July 2021

Objectives

To examine morbidity and mortality in survivors of childhood acute lymphoblastic leukaemia (ALL) across their teenage and young adult (TYA) years; comparing the patterns observed with individually matched general population controls.

Design

Case-control study with follow-up linkage to administrative healthcare databases for up to 25 years.

Setting

The study population comprises all children (0-14 years) registered for primary care with the National Health Service (NHS) in England 1992-1996.

Participants

1082 five-year survivors of ALL diagnosed <15 years of age, and 2018 age- and sex-matched population-based controls; followed to 15 March 2020.

Main outcome measures

Associations with hospital activity, cancer, and mortality were assessed using incidence rate ratios and absolute risk difference.

Results

Mortality 5-25 years after diagnosis was 20 times higher in cases than controls (Rate Ratio 21.3, 95% Confidence Interval 11.2-45.6), and cancer incidence 10 time higher (IRR 9.9 95% CI 4.1-29.1). Hospital activity was increased for many clinical specialties, the strongest effects being for endocrinology; outpatient IRR 36.7, 95% CI 17.3-93.4 and inpatient 19.7, 95% CI 1.9-25.5 for males, and 11.0, 95% CI 6.2-21.1 and 6.2 95% CI 3.1-13.5 respectively for females. Notable excesses were also evident for cardiology, neurology, ophthalmology, respiratory medicine and general medicine. Males were also more likely to attend gastroenterology, ENT (ear, nose and throat), urology, and dermatology; while females were more likely to be seen in plastic surgery and less likely in midwifery.

Conclusions

Adding to a large excess risk of death and cancer, survivors of childhood ALL experience excess outpatient and inpatient activity across their TYA years. Involving most clinical specialties, the observed effects are striking, showing no signs of diminishing over the first 25 years of follow-up. These findings underscore the need to take prior ALL drug and/or radiation treatment into account when interpreting seemingly unrelated symptoms in later life.
Science in School: Transforming K-12 Outreach through Scientist Teacher Partnerships
Authors: Abramowitz Brian , Ennes Megan , Killingsworth Stephanie , Antonenko Pavlo , MacFadden Bruce , Ivory Alan
Published: July 2021

The Scientist in Every Florida School (SEFS) program was started in 2019 with a long-term vision to connect Earth systems scientists with public K-12 schools in Florida and therefore create long-term scientist-teacher partnerships. SEFS fulfills personalized requests to create meaningful and impactful interactions to support teacher pedagogy and student learning. We have as part of our mission a focus on mainstream public schools, and in particular, those that are Title I. We also are committed to working with at-risk teachers. The major components of our program include the scientist-teacher partnerships, focused professional development workshops on Florida’s Earth systems (air, water, land, and life), classroom visits, and other web-based activities. Although still only in its first few years, the project and its more than 600 scientists have a wide reach with over 850 teachers and 53,000 students participating in our programs, which were delivered virtually in the 2020-2021 school year covering about 60% of Florida’s 67 counties. In this article, we describe our programmatic features as well as recommendations for those who could implement similar programs.
Benefits and Challenges of Using Virtual Primary Care During the COVID-19 Pandemic: From Key Lessons to a Framework for Implementation
Authors: Li Edmond , Tsopra Rosy , Gimenez Geronimo Larrain , Serafini Alice , Gusso Gustavo , Lingner Heidrun , Fernandez Maria Jose , Irving Greg , Petek Davorina , Hoffman Robert , Lazic Vanja , Ensieh Memarian , Koskela Tuomas , Collins Claire , Espitia Sandra Milena , Clavería Ana , Nessler Katarzyna , O’Neill Braden Gregory , Hoedebecke Kyle , Ungan Mehmet , Laranjo Liliana , Ghafur Saira , Fontana Gianluca , Majeed Azeem , Car Josip , Darzi Ara , Neves Ana Luisa
Published: July 2021

Background

With the onset of COVID-19, general practitioners (GPs) and patients worldwide swiftly transitioned from face-to-face to digital remote consultations. There is a need to evaluate how this global shift has impacted patient care, healthcare providers, patient and carer experience, and health systems.

Objective

We explored GPs’ perspectives on the main benefits and challenges of using digital remote care.

Methods

GPs across 20 countries completed an online questionnaire between June – September 2020. GPs’ perceptions on main barriers and challenges were explored using free-text questions. Thematic analysis was used to analyse the data.

Results

1,605 respondents participated in our survey. The benefits identified included reducing COVID-19 transmission risks, guaranteeing access and continuity of care, improved efficiency, faster access to care, improved convenience and communication with patients, greater work flexibility for providers, and hastening the digital transformation of primary care and the accompanying legal frameworks.

Main challenges included patient’s preference for face-to-face consultations, digital exclusion, lack of physical examinations, clinical uncertainty, delays in diagnosis and treatment, overuse and misuse of digital remote care, and unsuitability for certain types of consultations. Other challenges include the lack of formal guidance, higher workloads, remuneration issues, organisational culture, technical difficulties, implementation and financial issues, and regulatory weaknesses.

Conclusion

At the frontline of care delivery, GPs can provide important insights on what worked well, why, and how. Lessons learned during the emergency phase can be used to inform the stable adoption of virtual care solutions, and co-design processes and platforms that are technologically robust, secure, and supported by a strategic long-term plan.
Genomic epidemiologic assessment implicates prolonged silent carriage, virulence factors and transmission between staff and patients in a NICU outbreak of MRSA
Authors: Madera Sharline , McNeil Nicole , Serpa Paula Hayakawa , Kamm Jack , Pak Christy , Caughell Carolyn , Nichols Amy , Dynerman David , Li Lucy M. , Sanchez-Guerrero Estella , Phelps Maira , Detweiler Angela M. , Neff Norma , Reyes Helen , Miller Steve , Yokoe Deborah , DeRisi Joseph L. , Ramirez-Avila Lynn , Langelier Charles R.
Published: July 2021

Introduction

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen in neonatal intensive care units (NICU) that carries significant morbidity and mortality. Improving our understanding of MRSA transmission dynamics, especially among high risk patients, is an infection prevention priority.

Methods

We investigated a cluster of clinical MRSA cases in the NICU using a combination of epidemiologic review and whole genome sequencing (WGS) of isolates from clinical and surveillance cultures obtained from patients and healthcare personnel (HCP).

Results

Phylogenetic analysis identified two genetically distinct phylogenetic clades and revealed multiple silent transmission events between HCP and infants. The predominant outbreak strain harbored multiple virulence factors. Epidemiologic investigation and genomic analysis identified a HCP colonized with the dominant MRSA outbreak strain who cared for the majority of NICU patients who were infected or colonized with the same strain, including one NICU patient with severe infection seven months before the described outbreak. These results guided implementation of infection prevention interventions that prevented further transmission events.

Conclusion

Silent transmission of MRSA between HCP and NICU patients likely contributed to a NICU outbreak involving a virulent MRSA strain. WGS enabled data-driven decision making to inform implementation of infection control policies that mitigated the outbreak. Prospective WGS coupled with epidemiologic analysis can be used to detect transmission events and prompt early implementation of control strategies.

Whole genome sequencing identified a NICU outbreak of MRSA preceded by silent transmission between health care personnel and patients seven months prior to outbreak detection. This study suggests prospective genomic analysis may identify isolates with high virulence potential, offering an early opportunity for intervention.
CRISPR-Cas9 Screen Reveals PSMB3 Contributes to Gliomagenesis Through Proteasome-Dependent and Independent Mechanisms
Authors: Baisiwala Shivani , Budhiraja Shreya , Zolp Andrew J , Nandoliya Khizar , Chen Li , Park Cheol H. , Perrault Ella N , Saathoff Miranda R , Dmello Crismita , Shireman Jack M , Lin Peiyu , Dara Gabriel , McCortney Katy , Horbinski Craig , Sonabend Adam M , Ahmed Atique U
Published: July 2021

Glioblastoma (GBM) is the most common adult malignant brain tumor, with a median survival of 21 months and a 100% recurrence rate. Even though many of the critical oncogenic drivers for GBM have been identified, the basis of gliomagenesis is still under investigation. To identify novel genes that contribute to GBM progression, we performed a genome-wide CRISPR-Cas9 knockout screen. We identified four previously unstudied genes – PSMB3, CHCHD4, SPDYE5, HSPA1 – which had elevated expression in cancer and demonstrated a significant positive correlation with respect to GBM growth and patient survival in vivo and patient datasets. Furthermore, overexpression of PSMB3 and HSPA5 in neural stem cells resulted in transformation to a cancer phenotype. Further investigation of PSMB3, a subunit of the proteasome, allowed us to identify both ubiquitin-mediated and non-ubiquitin-mediated mechanisms of oncogenesis. Ultimately, the data from our CRISPR screens suggests that these genes drive tumor progression, making them promising therapeutic targets for GBM.
Killer Knots: Molecular evolution of Inhibitor Cystine Knot toxins in wandering spiders (Araneae: Ctenidae)
Authors: Cole T. Jeffrey , Brewer Michael S.
Published: July 2021

Venom expressed by the nearly 50,000 species of spiders on Earth largely remains an untapped reservoir of a diverse array of biomolecules with potential for pharmacological and agricultural applications. A large fraction of the noxious components of spider venoms are a functionally diverse family of structurally related polypeptides with an inhibitor cystine knot (ICK) motif. The cysteine-rich nature of these toxins makes structural elucidation difficult, and most studies have focused on venom components from the small handful of medically relevant spider species such as the highly aggressive Brazilian wandering spider Phoneutria nigriventer. To alleviate difficulties associated with the study of ICK toxins in spiders, we devised a comprehensive approach to explore the evolutionary patterns that have shaped ICK functional diversification using venom gland transcriptomes and proteomes from phylogenetically distinct lineages of wandering spiders and their close relatives. We identified 626 unique ICK toxins belonging to seven topological elaborations. Phylogenetic tests of episodic diversification revealed distinct regions between cysteine residues that demonstrated differential evidence of positive or negative selection, which may have structural implications towards the specificity and efficacy of these toxins. Increased taxon sampling and whole genome sequencing will provide invaluable insights to further understand the evolutionary processes that have given rise to this diverse class of toxins.
Functional Inference of Gene Regulation using Single-Cell Multi-Omics
Authors: Kartha Vinay K. , Duarte Fabiana M. , Hu Yan , Ma Sai , Chew Jennifer G. , Lareau Caleb A. , Earl Andrew , Burkett Zach D. , Kohlway Andrew S. , Lebofsky Ronald , Buenrostro Jason D.
Published: July 2021

Cells require coordinated control over gene expression when responding to environmental stimuli. Here, we apply scATAC-seq and scRNA-seq in resting and stimulated human blood cells. Collectively, we generate ∼91,000 single-cell profiles, allowing us to probe the cis-regulatory landscape of immunological response across cell types, stimuli and time. Advancing tools to integrate multi-omic data, we develop FigR - a framework to computationally pair scATAC-seq with scRNA-seq cells, connect distal cis-regulatory elements to genes, and infer gene regulatory networks (GRNs) to identify candidate TF regulators. Utilizing these paired multi-omic data, we define Domains of Regulatory Chromatin (DORCs) of immune stimulation and find that cells alter chromatin accessibility prior to production of gene expression at time scales of minutes. Further, the construction of the stimulation GRN elucidates TF activity at disease-associated DORCs. Overall, FigR enables the elucidation of regulatory interactions across single-cell data, providing new opportunities to understand the function of cells within tissues.
Single cell analysis of endometriosis reveals a coordinated transcriptional program driving immunotolerance and angiogenesis across eutopic and ectopic tissues
Authors: Tan Yuliana , Flynn William F. , Sivajothi Santhosh , Luo Diane , Bozal Suleyman B. , Luciano Anthony A. , Robson Paul , Luciano Danielle E. , Courtois Elise T.
Published: July 2021

Endometriosis is characterized by growth of endometrial-like tissue outside of the uterus affecting many women in their reproductive age, causing years of pelvic pain and potential infertility. Its pathophysiology remains largely unknown, limiting diagnosis and treatment. We characterized peritoneal and ovarian lesions at single-cell transcriptome resolution and compared to matched eutopic endometrium, control endometrium, and organoids derived from these tissues, generating data on over 100,000 cells across 12 individuals. We spatially localized many of the cell types using imaging mass cytometry. We identify a perivascular mural cell unique to the peritoneal lesions with dual roles in angiogenesis promotion and immune cell trafficking. We define an immunotolerant peritoneal niche, fundamental differences in eutopic endometrium and between lesions microenvironments, and a novel progenitor-like epithelial cell subpopulation. Altogether, this study provides a holistic view of the endometriosis microenvironment representing the first comprehensive cell atlas of the disease, essential information for advancing therapeutics and diagnostics.
The epithelial-specific ER stress sensor IRE1β enables host-microbiota crosstalk to affect colon goblet cell development
Authors: Grey Michael J. , Luca Heidi De , Ward Doyle V. , Kreulen Irini A. M. , Foley Sage E. , Thiagarajah Jay R. , McCormick Beth A. , Turner Jerrold R. , Lencer Wayne I.
Published: July 2021

Epithelial cells lining mucosal surfaces of the gastrointestinal and respiratory tracts uniquely express IRE1β (Ern2), a paralogue of the most evolutionarily conserved endoplasmic reticulum stress sensor IRE1α. How IRE1β functions at the host-environment interface and why a second IRE1 paralogue evolved remain incompletely understood. Using conventionally raised and germ-freeErn2-/-mice, we found that IRE1β was required for microbiota-induced goblet cell maturation and mucus barrier assembly in the colon. This occurred only after colonization of the alimentary tract with normal gut microflora, which induced IRE1β expression. IRE1β acted by splicingXbp1mRNA to expand ER function and prevent ER stress in goblet cells. Although IRE1α can also spliceXbp1mRNA, it did not act redundantly to IRE1β in this context. By regulating assembly of the colon mucus layer, IRE1β further shaped the composition of the gut microbiota. Mice lacking IRE1β had a dysbiotic microbial community that failed to induce goblet cell development when transferred into germ-free wild type mice. These results show that IRE1β evolved at mucosal surfaces to mediate crosstalk between gut microbes and the colonic epithelium required for normal homeostasis and host defense.
Patient-derived gene and protein expression signatures of NGLY1 deficiency
Authors: Rauscher Benedikt , Mueller William F. , Clauder-Münster Sandra , Jakob Petra , Saiful Islam M. , Sun Han , Ghidelli-Disse Sonja , Boesche Markus , Bantscheff Marcus , Pflaumer Hannah , Collier Paul , Haase Bettina , Chen Songjie , Wang Guangwen , Benes Vladimir , Snyder Michael , Drewes Gerard , Steinmetz Lars M.
Published: July 2021

N-Glycanase 1 (NGLY1) deficiency is a rare and complex genetic disorder. Although recent studies have shed light on the molecular underpinnings of NGLY1 deficiency, a systematic characterization of gene and protein expression changes in patient-derived cells has been lacking. Here, we performed RNA-sequencing and mass spectrometry to determine the transcriptomes and proteomes of 66 cell lines representing 4 different cell types derived from 14 NGLY1 deficient patients and 17 controls. While gene and protein expression levels agreed well with each other, expression differences were more pronounced at the protein level. Although NGLY1 protein levels were up to 9.5-fold downregulated in patients compared to parent controls, depending on the genotype, NGLY1 protein was still detectable in all patient-derived lymphoblastoid cell lines. Consistent with the role of NGLY1 as a regulator of the transcription factor Nrf1, we observed a cell type-independent downregulation of proteasomal genes in NGLY1 deficient cells. In contrast, genes involved in ribosomal mRNA processing were upregulated in multiple cell types. In addition, we observed cell type-specific effects. For example, genes and proteins involved in glutathione synthesis, such as the glutamate-cystein ligase subunits GCLC and GCLM, were downregulated specifically in lymphoblastoid cells. We provide a web application that enables access to all results generated in this study at https://apps.embl.de/ngly1browser. This resource will guide future studies of NGLY1 deficiency in directions that are most relevant to patients.
Transparency in peer review: Exploring the content and tone of reviewers’ confidential comments to editors
Authors: O’Brien Bridget C. , Artino Anthony R. , Costello Joseph A. , Driessen Erik , Maggio Lauren A.
Published: July 2021

Purpose

Recent calls to improve transparency in peer review have prompted examination of many aspects of the peer review process. Peer review systems often allow confidential comments to editors that could reduce transparency to authors, yet this option has escaped scrutiny. Our study explores 1) how reviewers use the confidential comments section and 2) alignment between comments to the editor and comments to authors with respect to content and tone.

Methods

Our dataset included 358 reviews of 168 manuscripts submitted between January 1, 2019 and August 24, 2020 to a health professions education journal with a single blind review process. We first identified reviews containing comments to the editor. Then, for the reviews with comments, we used procedures consistent with conventional and directed qualitative content analysis to develop a coding scheme and code comments for content, tone, and section of the manuscript. For reviews in which the reviewer recommended “reject,” we coded for alignment between reviewers’ comments to the editor and to authors. We report descriptive statistics.

Results

49% of reviews contained comments to the editor (n=176). Most of these comments summarized the reviewers’ impression of the article (85%), which included explicit reference to their recommended decision (44%) and suitability for the journal (10%). The majority of comments addressed argument quality (56%) or research design/methods/data (51%). The tone of comments tended to be critical (40%) or constructive (34%). For the 48 reviews recommending “reject,” the majority of comments to the editor contained content that also appeared in comments to the authors (65%); additional content tended to be irrelevant to the manuscript. Tone frequently aligned (85%).

Conclusion

Findings indicate variability in how reviewers use the confidential comments to editor section in online peer review systems, though generally the way they use them suggests integrity and transparency to authors.
Developmentally-regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome
Authors: Kaneko Keisuke , Currin Christopher B. , Goff Kevin M. , Somarowthu Ala , Vogels Tim P. , Goldberg Ethan M.
Published: July 2021

Dravet syndrome (DS) is a neurodevelopmental disorder defined by epilepsy, intellectual disability, and sudden death, due to heterozygous variants in SCN1A with loss of function of the sodium channel subunit Nav1.1. Nav1.1-expressing parvalbumin GABAergic interneurons (PV-INs) from pre-weanling Scn1a+/− mice show impaired action potential generation. A novel approach assessing PV-IN function in the same mice at two developmental time points showed that, at post-natal day (P) 16-21, spike generation was impaired all mice, deceased prior or surviving to P35. However, synaptic transmission was selectively dysfunctional in pre-weanling mice that did not survive. Spike generation in surviving mice normalized by P35, yet we again identified abnormalities in synaptic transmission. We conclude that combined dysfunction of PV-IN spike generation and synaptic transmission drives disease severity, while ongoing dysfunction of synaptic transmission contributes to chronic pathology. Modeling revealed that PV-IN axonal propagation is more sensitive to decreases in sodium conductance than spike generation.
Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer
Authors: Kim Yang Joon , Rhee Kaitlin , Liu Jonathan , Jeammet Paul , Turner Meghan , Small Stephen , Garcia Hernan G.
Published: July 2021

A challenge in quantitative biology is to predict output patterns of gene expression from knowledge of input transcription factor patterns and from the arrangement of binding sites for these transcription factors on regulatory DNA. We tested whether widespread thermodynamic models could be used to infer parameters describing simple regulatory architectures that inform parameter-free predictions of more complex enhancers in the context of transcriptional repression by Runt in the early fruit 2y embryo. By modulating the number and placement of Runt binding sites within an enhancer, and quantifying the resulting transcriptional activity using live imaging, we discovered that thermodynamic models call for higher-order cooperativity between multiple molecular players. This higher-order cooperativity capture the combinatorial complexity underlying eukaryotic transcriptional regulation and cannot be determined from simpler regulatory architectures, highlighting the challenges in reaching a predictive understanding of transcriptional regulation in eukaryotes and calling for approaches that quantitatively dissect their molecular nature.
Ethanol pre-exposure enhances alcohol-seeking behavior at cellular level by chemoattraction and exhibits bleb-driven cellular stress response in uniform ethanol concentration
Authors: Kar Neelakshi , Bellare Jayesh
Published: July 2021

This study investigates the effect of ethanol and its pre-exposure on cell migration. Here, fibroblast cells were first pre-treated with ethanol, and their migratory behavior was tested in both chemotaxis and chemokinesis setup. 1% ethanol was taken as a potential chemotactic agent. The study reveals that in presence of ethanol gradient cells display migration towards ethanol, and pre-exposure further augments this migratory behavior by altering their chemotactic responsiveness. In uniform ethanol concentration, cells first undergo three staged adaptations to the new environment: shrinking, blebbing, and recovery, where cells use bleb-driven cell protection machinery to adapt. Thus, migration is initially stalled. But once the cells resume locomotion, no significant difference in migratory parameters is observed. Overall, this study establishes ethanol as a chemoattractant for fibroblasts, with cells showing enhanced alcohol-seeking behavior upon pre-exposure. Such behavior is reminiscent of seeking and tolerance exhibited by alcohol-dependent addictive behavior in higher organisms including humans.
4D live-cell imaging of microgametogenesis in the human malaria parasite Plasmodium falciparum
Authors: Yahiya Sabrina , Jordan Sarah , Smith Holly X. , Gaboriau David C. A. , Famodimu Mufuliat T. , Dahalan Farah A. , Churchyard Alisje , Ashdown George W. , Baum Jake
Published: July 2021

Formation of gametes in the malaria parasite occurs in the midgut of the mosquito and is critical to onward parasite transmission. Transformation of the male gametocyte into microgametes, called microgametogenesis, is an explosive cellular event and one of the fastest eukaryotic DNA replication events known. The transformation of one microgametocyte into eight flagellated microgametes requires reorganisation of the parasite cytoskeleton, replication of the 22.9 Mb genome, axoneme formation and host erythrocyte egress, all of which occur simultaneously in <20 minutes. Whilst high-resolution imaging has been a powerful tool for defining stages of microgametogenesis, it has largely been limited to fixed parasite samples, given the speed of the process and parasite photosensitivity. Here, we have developed a live-cell fluorescence imaging workflow that captures the explosive dynamics of microgametogenesis in full. Using the most virulent human malaria parasite, Plasmodium falciparum, our live-cell approach combines three-dimensional imaging through time (4D imaging) and covers early microgametocyte development through to microgamete release. Combining live-cell stains for DNA, tubulin and the host erythrocyte membrane, 4D imaging enables definition of the positioning of newly replicated and segregated DNA. It also shows the microtubular cytoskeleton, location of newly formed basal bodies and elongation of axonemes, as well as behaviour of the erythrocyte membrane, including its specific perforation prior to microgamete egress. 4D imaging was additionally undertaken in the presence of known transmission-blocking inhibitors and the untested proteasomal inhibitor bortezomib. Here, for the first time we find that bortezomib inhibition results in a clear block of DNA replication, full axoneme nucleation and elongation. These data not only define a framework for understanding microgametogenesis in general but also suggest that the process is critically dependent on proteasomal activity, helping to identify potentially novel targets for transmission-blocking antimalarial drug development.