bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic and non-genetic factors affecting the expression of COVID-19 relevant genes in the large airway epithelium
Authors: Kasela Silva , Ortega Victor E , Martorella Molly , Garudadri Suresh , Nguyen Jenna , Ampleford Elizabeth , Pasanen Anu , Nerella Srilaxmi , Buschur Kristina L , Barjaktarevic Igor Z , Barr R Graham , Bleecker Eugene R , Bowler Russell P , Comellas Alejandro P , Cooper Christopher B , Couper David J , Criner Gerard J , Curtis Jeffrey L , Han MeiLan K , Hansel Nadia N , Hoffman Eric A , Kaner Robert J , Krishnan Jerry A , Martinez Fernando J , McDonald Merry-Lynn N , Meyers Deborah A , Paine Robert , Peters Stephen P , Castro Mario , Denlinger Loren C , Erzurum Serpil C , Fahy John V , Israel Elliot , Jarjour Nizar N , Levy Bruce D , Li Xingnan , Moore Wendy C , Wenzel Sally E , Zein Joe ,   NHLBI SubPopulations and InteRmediate Outcome Measures In COPD Study (SPIROMICS),   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Langelier Charles , Woodruff Prescott G , Lappalainen Tuuli , Christenson Stephanie A
Published: October 2020

Introductory paragraph

Particular host and environmental factors influence susceptibility to severe COVID-19. We analyzed RNA-sequencing data from bronchial epithelial brushings - a relevant tissue for SARS-CoV-2 infection - obtained from three cohorts of uninfected individuals, and investigated how non-genetic and genetic factors affect the regulation of host genes implicated in COVID-19. We found thatACE2expression was higher in relation to active smoking, obesity, and hypertension that are known risk factors of COVID-19 severity, while an association with interferon-related inflammation was driven by the truncated, non-bindingACE2isoform. We discovered that expression patterns of a suppressed airway immune response to early SARS-CoV-2 infection, compared to other viruses, are similar to patterns associated with obesity, hypertension, and cardiovascular disease, which may thus contribute to a COVID-19-susceptible airway environment. eQTL mapping identified regulatory variants for genes implicated in COVID-19, some of which had pheWAS evidence for their potential role in respiratory infections. These data provide evidence that clinically relevant variation in the expression of COVID-19-related genes is associated with host factors, environmental exposures, and likely host genetic variation.
Evaluation of the accuracy, ease of use and limit of detection of novel, rapid, antigen-detecting point-of-care diagnostics for SARS-CoV-2
Authors: Krüger L.J. , Gaeddert M. , Köppel L. , Brümmer L. E. , Gottschalk C. , Miranda I.B. , Schnitzler P. , Kräusslich H.G. , Lindner A.K. , Nikolai O. , Mockenhaupt F.P. , Seybold J. , Corman V.M. , Drosten C. , Pollock N.R. , Cubas-Atienzar A.I. , Kontogianni K. , Collins A. , Wright A. H. , Knorr B. , Welker A. , de Vos M. , Sacks J.A. , Adams E.R. , Denkinger C.M. ,   for the study team
Published: October 2020

Background

Reliable point-of-care (POC) diagnostics not requiring laboratory infrastructure could be a game changer in the COVID-19 pandemic, particularly in the Global South. We assessed performance, limit of detection and ease-of-use of three antigen-detecting, rapid POC tests (Ag-RDT) for SARS-CoV-2.

Methods

This prospective, multi-centre diagnostic accuracy study recruited participants suspected to have SARS-CoV-2 in Germany and the UK. Paired nasopharyngeal swabs (NP) or NP and/or oropharyngeal swabs (OP) were collected from participants (one for clinical RT-PCR and one for Ag-RDT). Performance of each of three Ag-RDTs was compared to RT-PCR overall, and according to predefined subcategories e.g. cycle threshold (CT)-value, days from symptoms onset, etc. In addition, limited verification of the analytical limit-of-detection (LOD) was determined. To understand the usability a System Usability Scale (SUS) questionnaire and ease-of-use (EoU) assessment were performed.

Results

Between April 17th and August 25th, 2020, 2417 participants were enrolled, with 70 (3.0%) testing positive by RT-PCR. The best-performing test (SD Biosensor, Inc. STANDARD Q) was 76×6% (95% Confidence Interval (CI) 62×8-86×4) sensitive and 99×3% (CI 98×6-99×6) specific. A sub-analysis showed all samples with RT-PCR CT-values <25 were detectable by STANDARD Q. The test was considered easy-to-use (SUS 86/100) and suitable for POC. Bioeasy and Coris showed specificity of 93×1% (CI 91×0%-94×8%) and 95×8% (CI 93×4%-97×4%), respectively, not meeting the predefined target of ≥98%.

Conclusion

There is large variability in performance of Ag-RDT with SD Biosensor showing promise. Given the usability at POC, this test is likely to have impact despite imperfect sensitivity; however further research and modelling are needed.
COVID-19 Pandemic in University Hospital: Impact on Medical Training of Medical Interns
Authors: Lim WeiHonn , Teoh Li Ying , Seevalingam Kanesh Kumaran A/L , Kuppusamy Shanggar
Published: October 2020

Introduction

Coronavirus 2019 (COVID-19) has strike all nations hard since the end of year 2019, Malaysia unable to escape the fate as well. Healthcare system, financial growth, industrial development and educational programme are stunted. Inevitably, professional training and education are affected which include the medical training of medical interns.

Methods

This is a cross-sectional, pilot study to determine the impact of the pandemic on University Malaya Medical Centre (UMMC) medical interns. A survey which comprises 37-items was used. Data are analysed by Ordinal Logistic Regression Analysis.

Results

Medical interns feel that they lack clinical skills (p = 0.005) and need more exposure in surgical operations (p =0.029). Some are satisfied with the introduction of triage (p = 0.024), online teaching (p = 0.005) and bedside teaching (p=0.023). Most of them think they are fit and ready to handle the pandemic (p = 0.012 and 0.025 respectively) except first year medical interns (p = 0.029). Some feel like their time are wasted (p <0.05) as they are involved in many non-clinical activities (p = 0.003).

Conclusion

In summary, COVID-19 has a great impact on medical training amongst medical interns. Alternative measures should be taken to minimize the interruption in training of our future leaders in medical field.
Factors associated with access to virtual care in older adults: A cross-sectional study
Authors: Liu Laura , Goodarzi Zahra , Jones Aaron , Posno Ron , Straus Sharon , Watt Jennifer
Published: October 2020

Background

During the COVID-19 pandemic, virtual care (i.e. telephone or videoconference) has played a critical role. However, concerns were raised regarding equitable access for older adults, in particular, given potential advantages of videoconference-as opposed to telephone-based assessment. Our objective was to describe patient-specific factors associated with different modes of virtual healthcare.

Methods

We reviewed medical records of all patients assessed virtually in the geriatric medicine clinic at St. Michael’s Hospital, Toronto, Canada, between March 17 and July 13, 2020. We derived adjusted odds ratios (OR), risk differences (RD), and marginal and predicted probabilities, with 95% confidence intervals, from a multivariable logistic regression model, which tested the association between having a videoconference assessment (vs. a telephone assessment) and patient age, sex, ability to use a computer, education, frailty (measured on the Clinical Frailty Scale), history of cognitive impairment, and immigration history; language of assessment, and caregiver involvement in assessment.

Results

Our study included 330 patients (227 telephone and 103 videoconference assessments). Frailty (adjusted OR 0.62, 0.45 to 0.85; adjusted RD -0.08, -0.09 to -0.06) and absence of a caregiver (adjusted OR 0.12, 0.06 to 0.24; adjusted RD -0.35, -0.43 to -0.26) were associated with lower odds of videoconference assessment. For example, an 80-year-old woman with mild frailty who immigrated to Canada, speaks English, attained a post-secondary education, does not have cognitive impairment, and uses a computer had a 60% (39% to 80%) predicted probability of videoconference assessment if a caregiver was present compared to 15% (3% to 26%) without a caregiver. Only 32 of 98 (32.7%) patients who could independently use a computer participated in videoconference assessments.

Conclusion

Given the recent expansion of virtual care, we must urgently implement and evaluate strategies that optimise equitable access to videoconference-based virtual care for older adults.
Prognostic accuracy of MALDI mass spectrometric analysis of plasma in COVID-19
Authors: Lazari Lucas Cardoso , De Rose Ghilardi Fabio , Rosa-Fernandes Livia , Assis Diego M , Nicolau José Carlos , Santiago Veronica Feijoli , Dalçóquio Talia Falcão , Angeli Claudia B. , Bertolin Adriadne Justi , Marinho Claudio R. F. , Wrenger Carsten , Durigon Edison Luiz , Siciliano Rinaldo Focaccia , Palmisano Giuseppe
Published: October 2020

Purpose

SARS-CoV-2 infection poses a global public health problem. There is a critical need for improvements in the noninvasive prognosis of COVID-19. We hypothesized that matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF MS) analysis combined with bottom-up proteomic analysis of plasma proteins might identify features to predict high and low risk cases of COVID-19.

Patients and Methods

We used MALDI-TOF MS to analyze plasma small proteins and peptides isolated using C18 micro-columns from a cohort containing a total of 117 cases of high (hospitalized) and low risk (outpatients) cases split into training (n = 88) and validation sets (n= 29). The plasma protein/peptide fingerprint obtained was used to train the algorithm before validation using a blinded test cohort.

Results

Several sample preparation, MS and data analysis parameters were optimized to achieve an overall accuracy of 85%, sensitivity of 90%, and specificity of 81% in the training set. In the blinded test set, this signature reached an overall accuracy of 93.1%, sensitivity of 87.5%, and specificity of 100%. From this signature, we identified two distinct regions in the MALDI-TOF profile belonging to the same proteoforms. A combination of 1D SDS-PAGE and quantitative bottom-up proteomic analysis allowed the identification of intact and truncated forms of serum amyloid A-1 and A-2 proteins. Conclusions: We found a plasma proteomic profile that discriminates against patients with high and low risk COVID-19. Proteomic analysis of C18-fractionated plasma may have a role in the noninvasive prognosis of COVID-19. Further validation will consolidate its clinical utility.

Key message

What is the key question?

Do individuals infected with SARS-CoV-2 harboring different degree of disease severity have a plasma protein profile that differentiate them and predict the COVID-19 outcome?

What is the bottom line?

In a series of 117 patients with COVID-19 divided in hospitalized (60) and outpatients (57), differential expression of serum amyloid A-1 (SAA1) and A-2 (SAA2) predict their outcome.

Why read on?

The high mortality rate in SARS-CoV-2 infected individuals requires accurate markers for predicting COVID-19 severity. Plasma levels of SAA1 and SAA2 indicate higher risk of hospitalization and can be used to improve COVID-19 monitoring and therapy.
A Mechanism for Severity of Disease in Older Patients with COVID-19: The Nexus between Telomere Length and Lymphopenia
Authors: Benetos Athanase , Lai Tsung-Po , Toupance Simon , Labat Carlos , Verhulst Simon , Gautier Sylvie , Ungeheuer Marie-Noelle , Perret-Guillaume Christine , Levy Daniel , Susser Ezra , Aviv Abraham
Published: October 2020

Background

Lymphopenia due to a plummeting T-cell count is a major feature of severe COVID-19. T-cell proliferation is telomere length (TL)-dependent and TL shortens with age. Older persons are disproportionally affected by severe COVID-19, and we hypothesized that those with short TL have less capacity to mount an adequate T-cell proliferative response to SARS-CoV-2. This hypothesis predicts that among older patients with COVID-19, shorter telomeres of peripheral blood mononuclear cells (PBMCs) will be associated with a lower lymphocyte count.

Methods

Our sample comprised 17 COVID-19 and 21 non-COVID-19 patients, aged 87 ± 8 (mean ± SD) and 87 ± 9 years, respectively. We measured TL by the Telomere Shortest Length Assay, a novel method that measures and tallies the short telomeres directly relevant to telomere-mediated biological processes. The primary analysis quantified TL as the proportion of telomeres shorter than 2 kilobases. For comparison, we also quantified TL by Southern blotting, which measures the mean length of telomeres.

Results

Lymphocyte count (109/L) was 0.91 ± 0.42 in COVID-19 patients and 1.50 ± 0.50 in non-COVID-19 patients (P < 0.001). In COVID-19 patients, but not in non-COVID-19 patients, lymphocyte count was inversely correlated with the proportion of telomeres shorter than 2 kilobases (P = 0.005) and positively correlated with the mean of telomeres measured by TeSLA (P = 0.03). Lymphocyte counts showed no statistically significant correlations with Southern blotting results in COVID-19 or non-COVID-19 patients.

Conclusions

These results support the hypothesis that a compromised TL-dependent T-cell proliferative response contributes to lymphopenia and the resulting disproportionate severity of COVID-19 among old adults. We infer that infection with SARS-CoV-2 uncovers the limits of the TL reserves of older persons.
A broad-based probe-free qPCR assay for detection and discrimination of three human herpes viruses
Authors: Gupta Anshu , Lawrence Shelley M. , Fraley Stephanie I.
Published: October 2020

Human cytomegalovirus (HCMV) and herpes simplex viruses (HSV) 1 and 2 are double stranded DNA viruses that establish lifetime latency in a host upon initial infection. Primary infection or reactivation of latent virus during pregnancy can transmit the virusin uteroor during natural childbirth to the fetus. The majority of these infections are asymptomatic at birth but may present later with potentially lethal disseminated infection or meningitis (HSV), or long-term neurodevelopmental sequelae including sensorineural hearing loss or neurodevelopmental impairments (HCMV). Unfortunately, early signs and symptoms of disseminated viral infections may be misdiagnosed as bacterial sepsis. Therefore, immediate testing for viral etiologies may not be ordered or even considered by skilled clinicians. In asymptomatic HCMV infections, early detection is necessary to monitor for and treat future neurologic sequelae. In acutely ill-appearing infants, specific detection of viruses against other disease-causing agents is vital to inform correct patient management, including early administration of the correct antimicrobial(s). An ideal test should be rapid, inexpensive, require low sample volumes, and demonstrate efficacy in multiple tissue matrices to aid in timely clinical decision-making for neonatal infections. This work discusses the development of a rapid probe-free qPCR assay for HSV and HCMV that enables early and specific detection of these viruses in neonates. The assay’s probe free chemistry would allow easier extension to a broad-based multiplexed pathogenic panel as compared to assays utilizing sequence-specific probes or nested PCR.
A multi-scale integrated analysis identifies KRT8 as a pan-cancer early biomarker
Authors: Scott Madeleine K. D. , Ozawa Michael G. , Chu Pauline , Limaye Maneesha , Nair Viswam S. , Schaffert Steven , Koong Albert C. , West Robert , Khatri Purvesh
Published: October 2020

An early biomarker would transform our ability to screen and treat patients with cancer. The large amount of multi-scale molecular data in public repositories from various cancers provide unprecedented opportunities to find such a biomarker. However, despite identification of numerous molecular biomarkers using these public data, fewer than 1% have proven robust enough to translate into clinical practice1. One of the most important factors affecting the successful translation to clinical practice is lack of real-world patient population heterogeneity in the discovery process. Almost all biomarker studies analyze only a single cohort of patients with the same cancer using a single modality. Recent studies in other diseases have demonstrated the advantage of leveraging biological and technical heterogeneity across multiple independent cohorts to identify robust disease biomarkers. Here we analyzed 17149 samples from patients with one of 23 cancers that were profiled using either DNA methylation, bulk and single-cell gene expression, or protein expression in tumor and serum. First, we analyzed DNA methylation profiles of 9855 samples across 23 cancers from The Cancer Genome Atlas (TCGA). We then examined the gene expression profile of the most significantly hypomethylated gene, KRT8, in 6781 samples from 57 independent microarray datasets from NCBI GEO. KRT8 was significantly over-expressed across cancers except colon cancer (summary effect size=1.05; p < 0.0001). Further, single-cell RNAseq analysis of 7447 single cells from lung tumors showed that genes that significantly correlated with KRT8 (p < 0.05) were involved in p53-related pathways. Immunohistochemistry in tumor biopsies from 294 patients with lung cancer showed that high protein expression of KRT8 is a prognostic marker of poor survival (HR = 1.73, p = 0.01). Finally, detectable KRT8 in serum as measured by ELISA distinguished patients with pancreatic cancer from healthy controls with an AUROC=0.94. In summary, our analysis demonstrates that KRT8 is (1) differentially expressed in several cancers across all molecular modalities and (2) may be useful as a biomarker to identify patients that should be further tested for cancer.
Delay and bias in PubMed medical subject heading (MeSH®) indexing of respiratory journals
Authors: Hadfield Ruth M.
Published: October 2020

Introduction

PubMed is a primary global open-access literature research database. Articles on PubMed are indexed manually with medical subject headings (MeSH®) to facilitate more complete literature searches. We aimed to determine the length of delay from publication to MeSH® indexing for key respiratory journals and to investigate whether delays are increasing over time and whether there are country or impact-factor specific biases in indexing.

Methods

PubMed was searched for the keyword ‘asthma’ for the 10 year period June 2009 to June 2019. MEDLINE fields including journal title, publication date, PubMed entrez date and MeSH® indexing date were extracted and delay in indexing was calculated in days.

Results

Twenty-nine respiratory journals had delay from publication to MeSH® indexing ranging from an average of 153.6 days to 409.9 days; 5/29 (17.2%) had never been indexed for PubMed. There was a significantly longer delay in MeSH® indexing for UK-based publications (mean delay of 281.7 days) compared to USA-based publications (mean delay of 214.9 days; mean difference 66.8 days, 95% CI 60.8, 72.8, P < 0.0001). Delays in MeSH® indexing increased over time.

Conclusion

There are long and increasing delays in PubMed MeSH® indexing of respiratory journals. All PubMed users should be aware that systematic literature searches that rely on MeSH® search terms or utilise PubMed filters are likely to exclude recent research and citations from key journals. Researchers and clinicians need to be aware of these delays and biases to ensure their literature searches are both up-to-date and complete.
RT qLAMP--Direct Detection of SARS-CoV-2 in Raw Sewage
Authors: Ongerth Jerry E. , Danielson Richard E.
Published: October 2020

The project purpose was to examine ability of a loop-mediated isothermal amplification (LAMP) assay to quantify SARS-CoV-2 in raw sewage, directly, using no preliminary sample processing for virus concentration and RNA extraction. An objective was to take advantage of extensive recently published work to facilitate process development, principally primer selection, and to use readily available off the shelf materials with conventional lab procedure and equipment. Well-developed and referenced primers for ORF1a, E, and N-gene targets were selected and applied, using commercially available synthetic RNA standards, and raw sewage from a local wastewater agency serving 650,000. County health department monitoring provided current COVID-19 data. Testing defined performance characteristics for each primer set, with significant differences between them. Specific amplification of SARS-CoV-2 RNA was observed using each of the primer sets, with E-gene and N-gene primers most effective. Positive analysis results from all raw sewage samples corresponded to calculated concentrations of virus in 5-10 μL raw sewage aliquots for 25 μL reactions. Results show that even at low reported case rates e.g. 1-10/100,000, SARS-CoV-2 is present in raw sewage at > 1-5/ μL, permitting direct LAMP-based detection. Use of RT qLAMP will facilitate wastewater-based epidemiology as an important component for COVID-19 control.
Analysis of serum trace elements, macro-minerals, antioxidants, malondialdehyde and immunoglobulins in seborrheic dermatitis patients: A case-control investigation
Authors: Jahan Ishrat , Islam Md. Rabiul , Islam Md. Reazul , Ali Rubaiya , Rahman S. M. Matiur , Nahar Zabun , Hasnat Abul , Islam Md. Saiful
Published: October 2020

Background

There are many theories abound; the exact mechanism for the pathophysiology of seborrheic dermatitis (SD) remains unknown. Neuropsychiatric disorders, stress, weakened or irregular immune responses, fungal infections, etc. are thought to be associated with the development of SD. The present study aimed to determine the serum levels of trace elements (TEs), macro-minerals (MMs), antioxidant vitamins, malondialdehyde (MDA), and immunoglobulins in SD patients to explore their role in the disease progression.

Methods

This prospective case-control study recruited 75 SD patients and 76 healthy controls (HCs) matched by age and gender. Serum TEs and MMs were analyzed by the flame atomic absorption spectroscopy and graphite furnace atomic absorption spectrometry. RP-HPLC was used to determine the serum levels of vitamin A and E. Serum MDA levels were measured by UV spectrophotometry as a marker of lipid peroxidation, whereas the turbidimetric method was used to quantify the serum levels of immunoglobulins.

Results

We found significantly higher concentrations of serum copper, manganese, and iron, calcium, and magnesium in SD patients compared to HCs. Serum levels of vitamin E significantly decreased and serum levels of MDA significantly increased in SD patients. Besides, the lower concentrations of immunoglobulin A, G, and M were observed in SD patients when compared to HCs. The present study also found a positive correlation between serum Zn and Ca levels (r = 0.365, p = 0.009) in SD patients; whereas a negative relation was detected between serum Cu and Ca levels (r = -0.298, p = 0.035).

Conclusions

The present study suggests that increased levels of TEs, MMs, MDA, and decreased levels of immunoglobulins and vitamin E are strongly associated with the pathophysiology of SD. Moreover, these alterations may provide a predictive tool for the assessment and management of SD patients.
Transposon-insertion sequencing in a clinical isolate ofLegionella pneumophilaidentifies essential genes and determinants of natural transformation
Authors: Hardy Léo , Juan Pierre-Alexandre , Coupat-Goutaland Bénédicte , Charpentier Xavier
Published: October 2020

Legionella pneumophilais a Gram-negative bacterium ubiquitous in freshwater environments which, if inhaled, can cause a severe pneumonia in humans. The emergence ofL. pneumophilais linked to several traits selected in the environment, the acquisition of some of which involved intra- and interkingdown horizontal gene transfer events. Transposon-insertion sequencing (TIS) is a powerful method to identify the genetic basis of selectable traits as well as to identify fitness determinants and essential genes, possible antibiotic targets. TIS has not yet been used to its full power inL. pneumophila, possibly because of difficulty to obtain a high-saturation transposon insertion library. Indeed, we found that ST1 isolates, to which belong the commonly used laboratory strains, are poorly permissive to saturating mutagenesis by conjugation-mediated transposon delivery. In contrast, we obtained high-saturation libraries in non-ST1 clinical isolates, offering the prospect of using TIS on unalteredL. pneumophilastrains. Focusing on one of them, we therefore used TIS to identify essential genes inL. pneumophila. We also revealed that TIS could be used to identify genes controlling vertical transmission of mobile genetic elements. We then applied TIS to identify all the genes required forL. pneumophilato develop competence and undergo natural transformation, defining the set of major and minor Type IV pilins that are engaged in DNA uptake. This work paves the way for the functional exploration of theL. pneumophilagenome by TIS and the identification of the genetic basis of other life traits of this species.

Importance

Legionella pneumophilais the etiologic agent of a severe form of nosocomial and community-acquired pneumonia in humans.L. pneumophilais found in man-made and freshwater environments which are the causing source of the infection. The environmental life traits ofL. pneumophila, such as its abilities to form biofilms, resist biocides and unicellular predators, are essential to its ability to accidentally infect humans. A comprehensive identification of the genetic basis of these life traits could be obtained through the use of transposon-insertion sequencing. Yet, this powerful approach, had not been fully implemented inL. pneumophila. Here we described the successful implementation of the transposon-sequencing approach in a clinical isolate ofL. pneumophila. We identify essential genes, potential drug targets, and genes required for horizontal gene transfer by natural transformation. This work represents an important step towards identifying the genetic basis of the many life traits of this environmental and pathogenic species.
Development, evaluation, and validation of machine learning models for COVID-19 detection based on routine blood tests
Authors: Federico Cabitza , Andrea Campagner , Davide Ferrari , Chiara Di Resta , Daniele Ceriotti , Eleonora Sabetta , Alessandra Colombini , Elena De Vecchi , Giuseppe Banfi , Massimo Locatelli , Anna Carobene
Published: October 2020

Background

The rRT-PCR test, the current gold standard for the detection of coronavirus disease (COVID-19), presents with known shortcomings, such as long turnaround time, potential shortage of reagents, false-negative rates around 15–20%, and expensive equipment. The hematochemical values of routine blood exams could represent a faster and less expensive alternative.

Methods

Three different training data set of hematochemical values from 1,624 patients (52% COVID-19 positive), admitted at San Raphael Hospital (OSR) from February to May 2020, were used for developing machine learning (ML) models: the complete OSR dataset (72 features: complete blood count (CBC), biochemical, coagulation, hemogasanalysis and CO-Oxymetry values, age, sex and specific symptoms at triage) and two sub-datasets (COVID-specific and CBC dataset, 32 and 21 features respectively). 58 cases (50% COVID-19 positive) from another hospital, and 54 negative patients collected in 2018 at OSR, were used for internal-external and external validation.

Results

We developed five ML models: for the complete OSR dataset, the area under the receiver operating characteristic curve (AUC) for the algorithms ranged from 0.83 to 0.90; for the COVID-specific dataset from 0.83 to 0.87; and for the CBC dataset from 0.74 to 0.86. The validations also achieved good results: respectively, AUC from 0.75 to 0.78; and specificity from 0.92 to 0.96.

Conclusions

ML can be applied to blood tests as both an adjunct and alternative method to rRT-PCR for the fast and cost-effective identification of COVID-19-positive patients. This is especially useful in developing countries, or in countries facing an increase in contagions.
Impact of COVID-19-lockdown and vulnerability factors on cognitive functioning and mental health in Italian population
Authors: Fiorenzato Eleonora , Zabberoni Silvia , Costa Alberto , Cona Giorgia
Published: October 2020

The COVID-19 outbreak and its associated restrictive measures, such as lockdown, exposed most individuals to an unprecedented stressful situation, increasing worldwide the prevalence of mental health disorders.

Here, we aimed at exploring for the first time the effect of COVID-19-lockdown on subjective cognitive functioning as well as mental health, in terms of its prevalence and clinical severity. In addition, potential risk factors characterizing more vulnerable groups were investigated. A nationwide cross-sectional online-survey was conducted during the final phase of lockdown in Italy (after 7-10 weeks of home confinement), leading to a sample of 1215 participants.

We found lockdown can have a severe impact on subjective cognitive functioning, along with mental health disorders. Namely, under restrictions, cognitive complaints were mostly perceived in everyday tasks involving attention, temporal orientation and executive functions; while no changes in language abilities were reported. Conversely, a paradoxical effect was observed in memory domain, with people experiencing a reduction of memory failures compared to pre-lockdown times.

Further, higher severity and prevalence of depression, anxiety disorders and of other psychological issues (involving sleep, appetite, libido and hypochondria) were observed – with a prevalence of mild-to-severe depression and anxiety rising up to 32.30% and 35.72% respectively, under restrictions.

Being female, young (<45 years), repeatedly exposed to COVID-19-media, working from home or being unemployed were identified as relevant risk factors for experiencing cognitive worsening and mental health disorders, related to the COVID-19 lockdown. Being resident in high infection-prevalence areas was related to higher level of depression and health anxiety. As lockdown and quarantine measures could be reimposed, health officials have to carefully consider these more vulnerable groups in their decision-making process, to develop an effective global and long-term response to the mental health challenges of this pandemic as well as to implement psychological interventions and specific guidelines, particularly about COVID-19-media exposure.
Pitfalls in EEG analysis in patients with non-convulsive status epilepticus
Authors: Wang Ying , Zibrandtsen Ivan C , Lazeron Richard HC , van Dijk Johannes P , Long Xi , Aarts Ronald M , Wang Lei , Arends Johan BAM
Published: October 2020

Objective

Electroencephalography (EEG) interpretations through visual (by human raters) and automated (by computer technology) analysis are still not reliable for the diagnosis of non-convulsive status epilepticus (NCSE). This study aimed to identify typical pitfalls in the EEG analysis and make suggestions as to how those pitfalls might be avoided.

Methods

We analyzed the EEG recordings of individuals who had clinically confirmed or suspected NCSE. Epileptiform EEG activity during seizures (ictal discharges) were visually analyzed by two independent raters. We investigated whether unreliable EEG visual interpretations quantified by low inter-rater agreement can be predicted by the characteristics of ictal discharges and individuals’ clinical data. In addition, the EEG recordings were automatically analyzed by in-house algorithms. To further explore the causes of unreliable EEG interpretations, two epileptologists analyzed EEG patterns most likely misinterpreted as ictal discharges based on the differences between the EEG interpretations through the visual and automated analysis.

Results

Short ictal discharges with a gradual onset (developing over 3 seconds in length) were liable to be misinterpreted. An extra 2 minutes of ictal discharges contributed to an increase in the kappa statistics of > 0.1. Other problems were the misinterpretation of abnormal background activity (slow wave activities, other abnormal brain activity, and the ictal-like movement artifacts), continuous interictal discharges, and continuous short ictal discharges.

Conclusion

A longer duration criterion for NCSE-EEGs than 10 seconds that commonly used in NCSE working criteria is needed. Using knowledge of historical EEGs, individualized algorithms, and context-dependent alarm thresholds may also avoid the pitfalls.
A patient-designed tissue-engineered model of the infiltrative glioblastoma microenvironment
Authors: Cornelison R. C. , Yuan J. X. , Tate K. M. , Petrosky A. , Beeghly G. F. , Bloomfield M. , Schwager S. C. , Berr A. L. , Cimini D. , Bafakih F. F. , Mandell J. W. , Purow B. W. , Horton B. J. , Munson J. M.
Published: October 2020

Glioblastoma is an aggressive brain cancer characterized by diffuse infiltration. Infiltrated glioma cells persist in the brain post-resection where they interact with glial cells and experience interstitial fluid flow. We recreate this infiltrative microenvironmentin vitrobased on resected patient tumors and examine malignancy metrics (invasion, proliferation, and stemness) in the context of cellular and biophysical factors and therapies. Our 3D tissue-engineered model comprises patient-derived glioma stem cells, human astrocytes and microglia, and interstitial fluid flow. We found flow contributes to all outcomes across seven patient-derived lines, and glial effects are driven by CCL2 and differential glial activation. We conducted a six-drug screen using four outcomes and find expression of putative stemness marker CD71, opposed to viability IC50, significantly predicts murine xenograft survival. Our results dispute the paradigm of viability as predictive of drug efficacy. We posit this patient-centric, infiltrative tumor model is a novel advance towards translational personalized medicine.
Optimal versus approximate channel selection methods for EEG decoding with application to topology-constrained neuro-sensor networks
Authors: Mundanad Narayanan Abhijith , Patrinos Panagiotis , Bertrand Alexander
Published: October 2020

Channel selection or electrode placement for neural decoding is a commonly encountered problem in electroencephalography (EEG). Since evaluating all possible channel combinations is usually infeasible, one usually has to settle for heuristic methods or convex approximations without optimality guarantees. To date, it remains unclear how large the gap is between the selection made by these approximate methods and the truly optimal selection. The goal of this paper is to quantify this optimality gap for several state-of-the-art channel selection methods in the context of least-squares based neural decoding. To this end, we reformulate the channel selection problem as a mixed-integer quadratic program (MIQP), which allows the use of efficient MIQP solvers to find the optimal channel combination in a feasible computation time for up to 100 candidate channels. As this reveals the exact solution to the combinatorial problem, it allows to quantify the performance losses when using state-of-the-art sub-optimal (yet faster) channel selection methods. In a context of auditory attention decoding, we find that a greedy channel selection based on the utility metric does not show a significant optimality gap compared to optimal channel selection, whereas other state-of-the-art greedy orl1-norm penalized methods do show a significant loss in performance. Furthermore, we demonstrate that the MIQP formulation also provides a natural way to incorporate topology constraints in the selection, e.g., for electrode placement in neuro-sensor networks with galvanic separation constraints. Furthermore, a combination of this utility-based greedy selection with an MIQP solver allows to perform a topology constrained electrode placement, even in large scale problems with more than 100 candidate positions.
Simulating digital micromirror devices for patterning coherent excitation light in structured illumination microscopy
Authors: Lachetta Mario , Sandmeyer Hauke , Sandmeyer Alice , Schulte am Esch Jan , Huser Thomas , Müller Marcel
Published: October 2020

Digital micromirror devices (DMDs) are spatial light modulators that employ the electro-mechanical movement of miniaturized mirrors to steer and thus modulate the light reflected of a mirror array. Their wide availability, low cost and high speed make them a popular choice both in consumer electronics such as video projectors, and scientific applications such as microscopy.

High-end fluorescence microscopy systems typically employ laser light sources, which by their nature provide coherent excitation light. In super-resolution microscopy applications that use light modulation, most notably structured illumination microscopy (SIM), the coherent nature of the excitation light becomes a requirement to achieve optimal interference pattern contrast. The universal combination of DMDs and coherent light sources, especially when working with multiple different wavelengths, is unfortunately not straight forward. The substructure of the tilted micromirror array gives rise to ablazed grating, which has to be understood and which must be taken into account when designing a DMD-based illumination system.

Here, we present a set of simulation frameworks that explore the use of DMDs in conjunction with coherent light sources, motivated by their application in SIM, but which are generalizable to other light patterning applications. This framework provides all the tools to explore and compute DMD-based diffraction effects and to simulate possible system alignment configurations computationally, which simplifies the system design process and provides guidance for setting up DMD-based microscopes.
Arabidopsisinositol polyphosphate kinase activities regulate COP9 deneddylation functions in phosphate-homeostasis
Authors: Walia Yashika , Noopur Medha , Sahoo Bhaskar Chandra , Bhattacharya Ishana , Kasera Mritunjay , Pullagurla Naga Jyothi , Saxena Shobhita , Liu Guizhen , Schaaf Gabriel , Jessen Henning , Laha Debabrata , Bhattacharjee Souvik , Bhattacharjee Saikat
Published: October 2020

Plant Cullin RING Ubiquitin E3 ligases (CRLs) facilitate targeted protein degradation during physiological development and adaptation to stress. The deneddylase activity of COP9 signalosome (CSN) regulates cellular ratios of neddylated cullins available for the continuum of CRL functions. While selective inositol polyphosphates (InsPs) function as co-factors in plant responses involving the ubiquitylation of negative regulators, a relationship to CSN-CRL activities has not yet been established. Here, we show that the twoArabidopsis thalianaInsP-kinases IPK1 and ITPK1 physically interact and metabolically connect with the CSN holo-complex to modulate cullin deneddylation efficiency. Specifically, functional deficiency of ITPK1 lowers cullin deneddylation rates and disrupts the dissociation equilibrium of CSN5, the deneddylase catalytic subunit, and CUL1 with the holo-complex. Our results identify a novel auto-regulatory switch of CSN functions, defined by deneddylation activity. We further demonstrate that phosphate starvation response (PSR), which is induced in Pi-starved wild-type plants and constitutive in the above InsP-kinase mutants, is orchestrated in part by reduced deneddylation rates that, in turn, affect the stability of SPX4, a key negative regulator of PSR. Pharmacological inhibition of cullin neddylation stabilizes SPX4 and impairs PSR, thus linking CSN-CRL dynamics to phosphate (Pi)-sensing. Conversely, when exposed to compounds that inhibit CSN5 deneddylase activity, wild-type plants display phenotypes similar to the above InsP-kinase mutants. Overall, our data reveal that the regulation of plant Pi-starvation responses by specific InsP-kinases is caused by a direct role of these kinases in balancing coordination between CRL-CSN activities.
Derivation of Isogenic Mesodermal and Ectomesodermal Chondrocytes from Human Induced Pluripotent Stem Cells for Articular Cartilage Regeneration
Authors: Lee Ming-Song , Stebbins Matthew J. , Jiao Hongli , Huang Hui-Ching , Walzack Brian E. , Palecek Sean P. , Shusta Eric V. , Li Wan-Ju
Published: October 2020

Generating phenotypic chondrocytes from human pluripotent stem cells through driving developmental lineage-specific differentiation remains to be of great interest in the field of cartilage regeneration. In this study, we derived chondrocytes from human induced pluripotent stem cells (hiPSCs) along the mesodermal or ectomesodermal lineages to prepare isogenic mesodermal cell-derived chondrocytes (MC-Chs) or neural crest cell-derived chondrocytes (NCC-Chs), respectively, and further evaluated differences in their cellular and molecular characteristics and cartilage repair capabilities. Our results showed that both lineage-derived chondrocytes expressed hyaline cartilage-associated markers and were capable of forming hyaline cartilage-like tissue ectopically and at joint defects. Moreover, NCC-Chs showed the absence of markers of hypertrophic chondrocytes and revealed a closer morphological resemblance to articular chondrocytes and a greater capability of producing glycosaminoglycans and collagen type 2 at cartilage defects compared to MC-Chs. It was found that the profile of global transcript expression of NCC-Chs more closely resembled that of native chondrocytes (NCs) than that of MC-Chs. Induced by additional growth factors identified through the analysis of transcriptome comparison to NCs, both MC-Chs and NCC-Chs showed a further increase in the phenotype of hyaline cartilage chondrocytes. Results of this study reveal differences in cellular and molecular characteristics and cartilage repair capabilities between isogenic hiPSC-derived MC-Chs and NCC-Chs and demonstrate that chondrocytes derived from hiPSCs along the ectomesodermal lineage are a potential cell source for articular cartilage regeneration.
Lipid interactions of an actinoporin pore-forming oligomer
Authors: Sepehri A. , Nepal B. , Lazaridis T.
Published: October 2020

The actinoporins are cytolytic toxins produced by sea anemones. Upon encountering a membrane, preferably containing sphingomyelin, they oligomerize and insert their N-terminal helix into the membrane, forming a pore. Whether sphingomyelin is specifically recognized by the protein or simply induces phase coexistence in the membrane has been debated. Here, we perform multimicrosecond molecular dynamics simulations of an octamer of fragaceatoxin C, a member of the actinoporin family, in lipid bilayers containing either pure 1,2-Dioleoyl-sn-Glycero-3-Phosphocholine (DOPC) or a 1:1 mixture of DOPC and palmitoyl sphingomyelin (PSM). The complex is highly stable in both environments, with only slight fraying of the inserted helices near their N-termini. Analyzing the structural parameters of the mixed membrane in the course of the simulation we see signs of a phase transition for PSM in the inner leaflet of the bilayer. In both leaflets, cross-interactions between lipids of different type decrease over time. Surprisingly, the aromatic loop thought to be responsible for sphingomyelin recognition interacts more with DOPC than PSM by the end of the simulation. These results support the notion that the key membrane property that actinoporins recognize is lipid phase coexistence.

SIGNIFICANCE STATEMENT

The mechanism of selectivity of naturally produced toxins for their target membranes is not well understood. For example, actinoporins, toxins produced by sea anemones, have been reported to selectively target sphingomyelin-containing membranes. Whether they bind this lipid preferentially or recognize the phase coexistence that sphingomyelin induces is not clear. This work examines this issue by long computer simulations of an actinoporin oligomer embedded in lipid bilayers and finds no preferential interactions of the protein with sphingomyelin. Instead, the simulations show signs of phase separation, suggesting that phase coexistence is the key property that actinoporins recognize.
Longitudinal in vivo micro-CT-based approach allows spatio-temporal characterization of fracture healing patterns and assessment of biomaterials in mouse femur defect models
Authors: Wehrle Esther , Tourolle né Betts Duncan C , Kuhn Gisela A , Floreani Erica , Nambiar Malavika H , Schroeder Bryant J , Hofmann Sandra , Müller Ralph
Published: October 2020

Thorough preclinical evaluation of functionalized biomaterials for treatment of large bone defects is essential prior to clinical application. Using in vivo micro-computed tomography (micro-CT) and mouse femoral defect models with different defect sizes, we were able to detect spatio-temporal healing patterns indicative of physiological and impaired healing in three defect sub-volumes and the adjacent cortex. The time-lapsed in vivo micro-CT-based approach was then applied to evaluate the bone regeneration potential of functionalized biomaterials using collagen and BMP-2. Both collagen and BMP-2 treatment led to distinct changes in bone turnover in the different healing phases. Despite increased periosteal bone formation, 87.5% of the defects treated with collagen scaffolds resulted in non-unions. Additional BMP-2 application significantly accelerated the healing process and increased the union rate to 100%. This study further shows potential of time-lapsed in vivo micro-CT for capturing spatio-temporal deviations preceding non-union formation and how this can be prevented by application of functionalized biomaterials.

This study therefore supports the application of longitudinal in vivo micro-CT for discrimination of normal and disturbed healing patterns and for the spatio-temporal characterization of the bone regeneration capacity of functionalized biomaterials.
Fast recovery of disrupted tip links induced by mechanical displacement of hair bundles
Authors: Alonso R. G. , Tobin M. , Martin P. , Hudspeth A. J.
Published: October 2020

Hearing and balance rely on the capacity of mechanically sensitive hair bundles to transduce vibrations into electrical signals that are forwarded to the brain. Hair bundles possess tip links that interconnect the mechanosensitive stereocilia and convey force to the transduction channels. A dimer of dimers, each of these links comprises two molecules of protocadherin 15 (PCDH15) joined to two of cadherin 23 (CDH23). The “handshake” that conjoins the four molecules can be disruptedin vivoby intense stimulation andin vitroby exposure to Ca2+chelators. Using hair bundles from the rat’s cochlea and the bullfrog’s sacculus, we observed that extensive recovery of mechanoelectrical transduction, hair-bundle stiffness, and spontaneous bundle oscillation can occur within seconds after Ca2+chelation, especially if hair bundles are deflected towards their short edges. Investigating the phenomenon in a two-compartment ionic environment that mimics natural conditions, we combined iontophoretic application of a Ca2+chelator to selectively disrupt the tip links of individual frog hair bundles with displacement clamping to control hair-bundle motion and measure forces. Our observations suggest that, after the normal Ca2+concentration has been restored, mechanical stimulation facilitates the reconstitution of functional tip links.

Significance Statement

Each of the sensory receptors responsible for hearing or balance—a hair cell—has a mechanosensitive hair bundle. Mechanical stimuli pull upon molecular filaments—the tip links—that open ionic channels in the hair bundle. Loud sounds can damage hearing by breaking the tip links; recovery by replacement of the constituent proteins then requires several hours. We disrupted the tip linksin vitroby removing the calcium ions that stabilize them, then monitored the electrical response or stiffness of hair bundles to determine whether the links could recover. We found that tip links recovered within seconds if their ends were brought back into contact. This form of repair might occur in normal ears to restore sensitivity after damage.