bluuebunny/crossref_metadata_2025 huggingface dataset:
COVID-19 Associated Pulmonary Aspergillosis: Systematic Review and Patient-Level Meta-analysis
Authors: Kariyawasam Ruwandi M. , Dingle Tanis C. , Kula Brittany E. , Sligl Wendy I. , Schwartz Ilan S.
Published: May 2021

Rationale

Pulmonary aspergillosis may complicate COVID-19 and contribute to excess mortality in intensive care unit (ICU) patients. The incidence is unclear because of discordant definitions across studies.

Objective

We sought to review the incidence, diagnosis, treatment, and outcomes of COVID-19-associated pulmonary aspergillosis (CAPA), and compare research definitions.

Methods

We systematically reviewed the literature for ICU cohort studies and case series including ≥ patients with CAPA. We calculated pooled incidence. Patients with sufficient clinical details were reclassified according to 4 standardized definitions (Verweij, White, Koehler, and Bassetti).

Measurements

Correlations between definitions were assessed with Spearman’s rank test. Associations between antifungals and outcome were assessed with Fisher’s Exact test.

Main Results

38 studies (35 cohort studies and 3 case series) were included. Among 3,297 COVID-19 patients in ICU cohort studies, 313 were diagnosed with CAPA (pooled incidence 9.5%). 197 patients had patient-level data allowing reclassification. Definitions had limited correlation with one another (ρ=0.330 to 0.621, p<0.001). 38.6% of patients reported to have CAPA did not fulfil any research definitions. Patients were diagnosed after a median of 9 days (interquartile range 5-14) in ICUs. Tracheobronchitis occured in 5.3% of patients examined with bronchoscopy. The mortality rate (50.0%) was high, irrespective of antifungal use (p=0.28); this remained true even when the analysis was restricted to patients meeting standardized definitions for CAPA.

Conclusions

The reported incidence of CAPA is exaggerated by use of non-standard definitions. Further research should focus on identifying patients likely to benefit from antifungals.
Combining serological assays and official statistics to describe the trajectory of the COVID-19 pandemic: results from the EPICOVID19-RS study in Rio Grande do Sul (Southern Brazil)
Authors: Hartwig Fernando P. , Vidaletti Luís Paulo , Barros Aluísio J. D. , Victora Gabriel D. , Menezes Ana M. B. , Mesenburg Marilia A. , Horta Bernardo L. , Silveira Mariângela F. , Victora Cesar G. , Hallal Pedro C. , Struchiner Claudio J.
Published: May 2021

Background

The EPICOVID19-RS study conducted 10 population-based surveys in Rio Grande do Sul (Southern Brazil), starting early in the epidemic. The sensitivity of the rapid point-of-care test used in the first eight surveys has been shown to decrease over time after some phases of the study were concluded. The 9th survey used both the rapid test and an enzyme-linked immunosorbent assay (ELISA) test, which has a higher and stable sensitivity.

Methods

We provide a theoretical justification for a correction procedure of the rapid test estimates, assess its performance in a simulated dataset and apply it to empirical data from the EPICOVID19-RS study. COVID-19 deaths from official statistics were used as an indicator of the temporal distribution of the epidemic, under the assumption that fatality is constant over time. Both the indicator and results from the 9th survey were used to calibrate the temporal decay function of the rapid test’s sensitivity from a previous validation study, which was used to estimate the true sensitivity in each survey and adjust the rapid test estimates accordingly.

Results

Simulations corroborated the procedure is valid. Corrected seroprevalence estimates were substantially larger than uncorrected estimates, which were substantially smaller than respective estimates from confirmed cases and therefore clearly underestimate the true infection prevalence.

Conclusion

Correcting biased estimates requires a combination of data and modelling assumptions. This work illustrates the practical utility of analytical procedures, but also the critical need for good quality, populationally-representative data for tracking the progress of the epidemic and substantiate both projection models and policy making.
Evaluation of mRNA-1273 against SARS-CoV-2 B.1.351 Infection in Nonhuman Primates
Authors: Corbett Kizzmekia S. , Werner Anne P. , O’ Connell Sarah , Gagne Matthew , Lai Lilin , Moliva Juan I. , Flynn Barbara , Choi Angela , Koch Matthew , Foulds Kathryn E. , Andrew Shayne F. , Flebbe Dillon R. , Lamb Evan , Nurmukhambetova Saule T. , Provost Samantha J. , Bock Kevin W. , Minai Mahnaz , Nagata Bianca M. , Van Ry Alex , Flinchbaugh Zackery , Johnston Timothy S. , Mokhtari Elham Bayat , Mudvari Prakriti , Henry Amy R. , Laboune Farida , Chang Becky , Porto Maciel , Wear Jaclyn , Alvarado Gabriela S. , Boyoglu-Barnum Seyhan , Todd John-Paul M. , Bart Bridget , Cook Anthony , Dodson Alan , Pessaint Laurent , Steingrebe Katelyn , Elbashir Sayda , Andersen Hanne , Wu Kai , Edwards Darin K. , Kar Swagata , Lewis Mark G. , Bortiz Eli , Moore Ian N. , Carfi Andrea , Suthar Mehul S. , McDermott Adrian , Roederer Mario , Nason Martha C. , Sullivan Nancy J. , Douek Daniel C. , Graham Barney S. , Seder Robert A.
Published: May 2021

Background

Vaccine efficacy against the B.1.351 variant following mRNA-1273 vaccination in humans has not been determined. Nonhuman primates (NHP) are a useful model for demonstrating whether mRNA-1273 mediates protection against B.1.351.

Methods

Nonhuman primates received 30 or 100 µg of mRNA-1273 as a prime-boost vaccine at 0 and 4 weeks, a single immunization of 30 µg at week 0, or no vaccine. Antibody and T cell responses were assessed in blood, bronchioalveolar lavages (BAL), and nasal washes. Viral replication in BAL and nasal swabs were determined by qRT-PCR for sgRNA, and histopathology and viral antigen quantification were performed on lung tissue post-challenge.

Results

Eight weeks post-boost, 100 µg x2 of mRNA-1273 induced reciprocal ID50 neutralizing geometric mean titers against live SARS-CoV-2 D614G and B.1.351 of 3300 and 240, respectively, and 430 and 84 for the 30 µg x2 group. There were no detectable neutralizing antibodies against B.1351 after the single immunization of 30 µg. On day 2 following B.1.351 challenge, sgRNA in BAL was undetectable in 6 of 8 NHP that received 100 µg x2 of mRNA-1273, and there was a ∼2-log reduction in sgRNA in NHP that received two doses of 30 µg compared to controls. In nasal swabs, there was a 1-log10 reduction observed in the 100 µg x2 group. There was limited inflammation or viral antigen in lungs of vaccinated NHP post-challenge.

Conclusions

Immunization with two doses of mRNA-1273 achieves effective immunity that rapidly controls lower and upper airway viral replication against the B.1.351 variant in NHP.
Evidence for Deleterious Antigenic Imprinting in SARS-CoV-2 Immune Response
Authors: Sen Sanjana R. , Sanders Emily C. , Santos Alicia M. , Bhuvan Keertna , Tang Derek Y. , Gelston Aidan A. , Miller Brian M. , Ricks-Oddie Joni L. , Weiss Gregory A.
Published: May 2021

A previous report demonstrated the strong association between the presence of antibodies binding to an epitope region from SARS-CoV-2 nucleocapsid, termed Ep9, and COVID-19 disease severity. Patients with anti-Ep9 antibodies (Abs) had hallmarks of antigenic imprinting (AIM), including early IgG upregulation and cytokine-associated injury. Thus, the immunological memory of a previous infection was hypothesized to drive formation of suboptimal anti-Ep9 Abs in severe COVID-19 infections. This study identifies a putative primary antigen capable of stimulating production of cross-reactive, anti-Ep9 Abs. Binding assays with patient blood samples directly show cross-reactivity between Abs binding to Ep9 and only one bioinformatics-derived, homologous potential antigen, a sequence derived from the neuraminidase protein of H3N2 Influenza A virus. This cross-reactive binding is highly influenza strain specific and sensitive to even single amino acid changes in epitope sequence. The neuraminidase protein is not present in the influenza vaccine, and the anti-Ep9 Abs likely resulted from the widespread influenza infection in 2014. Therefore, AIM from a previous infection could underlie some cases of COVID-19 disease severity.

Importance

Infections with SARS-COV-2 result in diverse disease outcomes, ranging from asymptomatic to fatal. The mechanisms underlying different disease outcomes remain largely unexplained. Previously, our laboratory identified a strong association between the presence of an antibody and increased disease severity in a subset of COVID-19 patients. Here, we report that this severity-associated antibody cross-reacts with viral proteins from an influenza A viral strain from 2014. Therefore, we speculate that antibodies generated against previous infections, like the 2014 influenza A, play a significant role in directing some peoples’ immune responses against SARS-COV-2. Such understanding of the sources and drivers of COVID-19 disease severity can help early identification and pre-emptive treatment.
Smartwatch Facilitated Remote Health Care for Patients Undergoing Transcatheter Aortic Valve Replacement Amid COVID-19 Pandemic
Authors: Liu Xianbao , Fan Jiaqi , Guo Yuchao , Dai Hanyi , Xu Jianguo , Wang Lihan , Hu Po , Lin Xinping , Li Cheng , Zhou Dao , Li Huajun , Wang Jian’an
Published: May 2021

BACKGROUND

The novel coronavirus disease-2019 (COVID-19 Pandemic) has brought difficulties to the management of patients undergoing transcatheter aortic valve replacement (TAVR).

OBJECTIVES

This prospective, observational cohort study sought to evaluate the feasibility of a novel, virtual, and remote health care strategy for TAVR patients with smart wearable devices.

METHODS

A total of 100 consecutive severe aortic stenosis patients who underwent elective transfemoral TAVR were enrolled and each received a HUAWEI smartwatch at least one day before TAVR. Vital signs were continuously tracked and recorded. Single lead electrocardiogram (ECG) was recorded periodically after TAVR. A designated heart team member was to provide remote data-assisted health care to address the medical demand.

RESULTS

Thirty-eight cardiac events were reported in 34 patients after discharge, with most of the events (76.0%) were detected and confirmed by the smartwatch. Six patients were advised and readmitted to the hospital for arrhythmia events, among whom, four received pacemaker implantations. The remaining 28 (82.4%) patients received telemedicine monitoring instead of face-to-face clinical visits, and three of them received new medication treatment under a doctor’s online guidance of doctors. New-onset LBBB was found in 48 patients with transient and recovered spontaneously in 30 patients, while new-onset atrial fibrillation in 4 patients. There were no significant differences in the average weekly heart rates, the ratio of abnormal or low oxygen saturation when compared with the baseline. The average daily steps increased over time significantly (baseline, 870±1353 steps; first week, 1986±2406 steps; second week, 2707±2716 steps; third week, 3059±3036 steps; fourth week, 3678±3485 steps, p < 0.001).

CONCLUSIONS

Smartwatch can facilitate remote health care for patients undergoing TAVR during COVID-19 and enables a novel remote follow-up strategy. The majority of cardiac clinical events that occurred within 30-day follow-up were detected by the smartwatch, mainly due to the record of conduction abnormality. (SMART Watch Facilitated Early Discharge in Patients undergoing Transcatheter Aortic Valve Replacement, NCT04454177).
Dynamic magnetic resonance imaging of muscle contraction in facioscapulohumeral muscular dystrophy
Authors: Deligianni Xeni , Santini Francesco , Paoletti Matteo , Solazzo Francesca , Bergsland Niels , Savini Giovanni , Faggioli Arianna , Germani Giancarlo , Monforte Mauro , Ricci Enzo , Tasca Giorgio , Pichiecchio Anna
Published: May 2021

Background

Quantitative muscle MRI (water-T2 and fat mapping) is being increasingly used to assess disease involvement in muscle disorders, while imaging techniques for assessment of the dynamic and elastic muscle properties have not been translated yet into clinics.

Methods

Here, we quantitatively characterized muscle deformation (strain) in patients affected by facioscapulohumeral muscular dystrophy (FSHD), a prevalent muscular dystrophy, by applying dynamic MRI synchronized with neuromuscular electrical stimulation (NMES). We evaluated the quadriceps muscles in 34 ambulatory patients and 12 healthy controls, at 6 month intervals.

Results

We found that while a subgroup of patients behaved similarly to controls, for another subgroup the strain significantly decreased over time (50% over 1.5 years). Dynamic MRI parameters did not correlate with quantitative MRI.

Conclusions

In conclusion, our results suggest that the evaluation of muscle ability to contract by NMES-MRI could be used to explore the elastic properties and monitor muscle involvement in FSHD and other neuromuscular disorders.
Emergence of SARS-CoV-2 variants of concern in the pediatric population of the United States
Authors: Bard Jennifer Dien , Bootwalla Moiz , Leber Amy , Planet Paul , Moustafa Ahmed M. , Harris Rebecca , Chen Pei Ying , Shen Lishuang , Ostrow Dejerianne , Maglinte Dennis , Flores Jessica , Somak Roy , Ranganathan Sarangarajan , Perlman Elizabeth , Zheng Xiaotian , Selvarangan Rangaraj , Banerjee Dithi , Delaney Meghan , Campos Joseph , Michael Drew G. , Vilain Eric , LoTempio Jonathan , Dunn James , Jung Sarah , Dominguez Samuel R. , Judkins Alexander R. , Gai Xiaowu
Published: May 2021

The evolution of SARS-CoV2 virus has led to the emergence of variants of concern (VOC). Children, particularly <12 years old not yet eligible for vaccines, continue to be important reservoirs of SARS-CoV-2 yet VOC prevalence data in this population is lacking. We report data from a genomic surveillance program that includes 9 U.S. children’s hospitals. Analysis of SARS-CoV-2 genomes from 2119 patients <19 years old between 03/20 to 04/21 identified 252 VOCs and 560 VOC signature mutations, most from 10/20 onwards. 75.00% of the VOC signature mutations detected were in children <12 years old, including 32 cases of B.1.1.7 and 346 of B.1.419/B.1417. From 02/21 to 04/21, B.1.1.7 prevalence increased from 1.28% to 72.22% corresponding with the decline of B.1419/B.1417 from 52.57% to 5.56% at one institution. There continues to be a need for ongoing genomic surveillance, particularly among young children who will be the last groups to be vaccinated.
MLC Seq: De novo sequencing of full-length tRNA isoforms by mass ladder complementation
Authors: Yuan Xiaohong , Su Yue , Zhang Xudong , Turkel Spencer J. , Shi Shundi , Wang Xuanting , Choi Eun-Jin , Wu Wenzhe , Liu Haichuan , Viner Rosa , Russo James J. , Li Wenjia , Bao Xiaoyong , Chen Qi , Zhang Shenglong
Published: May 2021

tRNAs can exist in distinct isoforms because of different chemical modifications, which confounds attempts to accurately sequence individual tRNA species using next generation sequencing approaches or to quantify different RNA modifications at specific sites on a tRNA strand. Herein, we develop a mass spectrometric (MS) ladder complementation sequencing (MLC-Seq), allowing for direct and simultaneous sequencing of full-length tRNA molecules, including those with low abundance. MLC-seq is achieved by improved instrumentation, and advanced algorithms that identify each tRNA species and related isoforms in an RNA mixture, and assemble full MS ladders from partial ladders with missing ladder components. Using MLC-Seq, we successfully obtained the sequence of tRNA-Phe from yeast and tRNA-Glu from mouse hepatocytes, and simultaneously revealed new tRNA isoforms derived from nucleotide modifications. Importantly, MLC-Seq pinpointed the location and stoichiometry changes of RNA modifications in tRNA-Glu upon the treatment of dealkylated enzyme AlkB, which confirmed its known enzymatic activity and suggested previously unidentified effects in RNA editing.
Genetic Dissection of the RNA Polymerase II Transcription Cycle
Authors: Chou Shao-Pei , Alexander Adriana K. , Rice Edward J. , Choate Lauren A , Cohen Paula E , Danko Charles G.
Published: May 2021

How DNA sequence affects the dynamics and position of RNA Polymerase II (Pol II) during transcription remains poorly understood. Here we used naturally occurring genetic variation in F1 hybrid mice to explore how DNA sequence differences affect the genome-wide distribution of Pol II. We measured the position and orientation of Pol II in eight organs collected from heterozygous F1 hybrid mice using ChRO-seq. Our data revealed a strong genetic basis for the precise coordinates of transcription initiation and promoter proximal pause, allowing us to redefine molecular models of core transcriptional processes. Our results implicate the strength of base pairing between A-T or G-C dinucleotides as key determinants to the position of Pol II initiation and pause. We report evidence that initiation site selection follows a stochastic process similar to brownian motion along the DNA template. We found widespread differences in the position of transcription termination, which impact the primary structure and stability of mature mRNA. Finally, we report evidence that allelic changes in transcription often affect mRNA and ncRNA expression across broad genomic domains. Collectively, we reveal how DNA sequences shape core transcriptional processes at single nucleotide resolution in mammals.
TIR signaling promotes the interactions between EDS1/PAD4 and ADR1-L1 and oligomerization of ADR1-L1
Authors: Wu Zhongshou , Tian Lei , Liu Xueru , Zhang Yuelin , Li Xin
Published: May 2021

Both plants and animals use nucleotide-binding leucine-rich repeat (NLR) immune receptors to perceive pathogens and trigger immunity. Toll/interleukin-1 receptor (TIR)-type plant NLRs (TNLs) require the lipase-like protein family members Enhanced Disease Susceptibility 1 (EDS1)/ Phytoalexin Deficient 4 (PAD4)/ Senescence-Associated Gene 101 (SAG101) and helper NLRs (hNLRs) for downstream signaling, the biochemical mechanisms of which remain unclear. Here, we report that TIR signaling promotes the association of EDS1 and PAD4 with hNLR ACTIVATED DISEASE RESISTANCE 1-Like 1 (ADR1-L1), and the oligomerization of ADR1-L1s for downstream immune activation and cell death.
Presynaptic HCN channels constrain GABAergic synaptic transmission in pyramidal cells of the medial prefrontal cortex
Authors: Cai Wei , Liu Shu-Su , Li Bao-Ming , Zhang Xue-Han
Published: May 2021

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are widely expressed in neurons in the central nervous system. It has been documented that HCN channels regulate the intrinsic excitability of pyramidal cells in the medial prefrontal cortex (mPFC) of rats. Here, we report that HCN channels limited GABAergic transmission onto pyramidal cells in the mPFC. Pharmacological block of HCN channels resulted in a significant increase in the frequency of both spontaneous and miniature inhibitory postsynaptic currents (IPSCs) in mPFC pyramidal cells. Such facilitation effect on mIPSCs required presynaptic Ca2+ influx and reversed by high-dose cAMP. Such facilitation did not exist in the presence of the T-type Ca2+ channel selective blockers. Immunofluorescence staining revealed that HCN channels expressed in presynaptic GABAergic terminals, as well as in both soma and neurite of parvalbumin-expressing (PV-expressing) basket cells in the mPFC. The present results indicate that HCN channels in GABAergic interneurons, most likely PV-expressing basket cells, constrain inhibitory control over layer 5-6 pyramidal cells through restricting presynaptic Ca2+ entry.
Positive Selection and Heat-Response Transcriptomes Reveal Adaptive Features of the Brassicaceae Desert Model, Anastatica hierochuntica
Authors: Eshel Gil , Duppen Nick , Wang Guannan , Oh Dong-Ha , Kazachkova Yana , Herzyk Pawel , Amtmann Anna , Gordon Michal , Chalifa-Caspi Vered , Oscar Michelle Arland , Bar-David Shirli , Marshall-Colon Amy , Dassanayake Maheshi , Barak Simon
Published: May 2021

Plant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat-tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts.

We generated an A. hierochuntica reference transcriptome and pinpointed extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat and identifying positively selected genes in A. hierochuntica.

The two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat “stress-ready” state. Furthermore, the A. hierochuntica global transcriptome as well as heat-responsive orthologs, display a lower basal and higher heat-induced expression than in A. thaliana. Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV-B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod-insensitive, early-flowering phenotype.

We suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle.
Hippocampal TRPV1 channels in the modulation of contextual fear conditioning
Authors: Iglesias Lia P. , Fernandes Heliana B. , de Miranda Aline S. , Sorgi Carlos A. , Moreira Fabrício A.
Published: May 2021

Psychiatric disorders have been linked to impairments in fear memory circuitry. Thus, pharmacological approaches that impair aversive memories have been investigated as new treatments. The TRPV1 channel modulates biological processes related to memory consolidation and retrieval. However, TRPV1 seems involved in memories generated by high intense conditioning. Anandamide (AEA), the main endocannabinoid, is an agonist of both, TRPV1 channels and CB1 receptors which are colocalized in several brain structures. Remarkably, AEA has twenty-times more affinity for CB1 than for TRPV1, which may be involved in the intensity-dependent recruitment of this channel. In order to evaluate the role of intensity of the conditioning in the recruitment of TRPV1, the animals were submitted to the contextual fear conditioning (CFC) and conditioned with low, moderate or high intensity. Before the retrieval a TRPV1 blocker was administered into the dorsal hippocampus (dHPC). The levels of AEA were quantified by Mass Spectrometry. The RNA levels of Arc, Zif and Trkb, involved in memory and plasticity, were quantified by PCR. Our results showed that TRPV1 blockers impair the retrieval of memory in animals conditioned with moderate and high intensity but not low ones. As revealed by Mass Spectrometry, this different recruitment among intensities seems to be associated with the levels of AEA released. Moreover, the impairment in freezing induced by blocking TRPV1 was prevented by a subeffective dose of the cannabinoid receptor CB1 antagonist which suggest that TRPV1 blockers act increasing AEA availability in the synaptic cleft to act through CB1 receptors. Despite blocking TRPV1 channels impairs freezing in moderate and high intensities, it increases the RNA levels of Arc, Zif and Trkb only in animals conditioned with the moderate intensity. In accordance, the treatment impairs retrieval in both intensities but only in the moderate intensity is able to prevent the reinstatement. Summarizing, our results suggested that intensity of the conditioning modulates AEA levels which in turns determines if TRPV1 will be recruited at the retrieval and which molecular pathways will be engaged due to TRPV1 blocking.
Automated detection of artefacts in neonatal EEG with residual neural networks
Authors: Webb Lachlan , Kauppila Minna , Roberts James A. , Vanhatalo Sampsa , Stevenson Nathan
Published: May 2021

Background and Objective

To develop a computational algorithm that detects and identifies different artefact types in neonatal electroencephalography (EEG) signals.

Methods

As part of a larger algorithm, we trained a Residual Deep Neural Network on expert human annotations of EEG recordings from 79 term infants recorded in a neonatal intensive care unit (112 h of 18-channel recording). The network was trained using 10 fold cross validation in Matlab. Artefact types included: device interference, EMG, movement, electrode pop, and non-cortical biological rhythms. Performance was assessed by prediction statistics and further validated on a separate independent dataset of 13 term infants (143 h of 3-channel recording). EEG pre-processing steps, and other post-processing steps such as averaging probability over a temporal window, were also included in the algorithm.

Results

The Residual Deep Neural Network showed high accuracy (95%) when distinguishing periods of clean, artefact-free EEG from any kind of artefact, with a median accuracy for individual patient of 91% (IQR: 81%-96%). The accuracy in identifying the five different types of artefacts ranged from 57%-92%, with electrode pop being the hardest to detect and EMG being the easiest. This reflected the proportion of artefact available in the training dataset. Misclassification as clean was low for each artefact type, ranging from 1%-11%. The detection accuracy was lower on the validation set (87%). We used the algorithm to show that EEG channels located near the vertex were the least susceptible to artefact.

Conclusion

Artefacts can be accurately and reliably identified in the neonatal EEG using a deep learning algorithm. Artefact detection algorithms can provide continuous bedside quality assessment and support EEG review by clinicians or analysis algorithms.

Highlights

We applied a Residual Deep Neural Network as part of an artefact detection algorithm in neonatal electroencephalograms.

The algorithm shows high accuracy in identifying artefactual data in general and for specific artefact types.

EEG channels near the top of the head are less prone to artefact.
EVALUATION OF A RAPID ANTIGEN TEST FOR SARS-COV-2 IN SYMPTOMATIC PATIENTS AND THEIR CONTACTS: A MULTICENTER STUDY
Authors: Thirion-Romero Ireri , Guerrero-Zúñiga Selene , Arias-Mendoza Alexandra , Cornejo-TJuárez Dora Patricia , Meza-Meneses Patricia , Torres-Erazo Darwin Stalin , Hernández Thierry , Galindo-Fraga Arturo , Villegas-Mota Isabel , Sepúlveda-Delgado Jesús , Ávila Ríos Santiago , Becerril-Vargas Eduardo , Fernández-Plata Rosario , Midori Pérez-Kawabe TIT , Vázquez Pérez Joel Armando , Kawa Karasik Simón , Terán Gustavo Reyes , Pérez-Padilla José Rogelio ,   Rapid COVID-19 Antigen Test Group
Published: May 2021

BACKGROUND

Point-of-care rapid tests to identify SARS-CoV-2 can be of great help because, in principle, they allow decisions to be made at the site of care for treatment, or for the separation of cohorts avoiding cross-infection, especially in emergency situations.

METHODS

A cross sectional study in adults requesting care in Emergency Rooms (ER), or the outpatient clinics of referral hospitals for COVID-19, to define the diagnostic characteristics of a rapid antigen test for SARS-CoV-2 (the Abbott Panbio™) having as a gold standard the RT-PCR for SARS-CoV-2. Health personnel in a routine situation within an active pandemic in several cities of Mexico performed the tests.

RESULTS

A total of 1,069 participants with a mean age of 47 years (SD 16 years), 47% with a self-reported comorbidity, and an overall prevalence of a positive RT-PCR test of 45%, were recruited from eight hospitals in Mexico. Overall sensitivity of the Panbio test was 54.4% (95%CI 51-57) with a positive likelihood ratio of 35.7, a negative likelihood ratio of 0.46 and a Receiver-Operating Characteristics curve area of 0.77.

Positivity for the rapid test depended strongly on an estimate of the viral load (Cycle threshold of RT-PCR, Ct), and the days of symptoms. With a Ct≤25, sensitivity of the rapid test was 0.82 (95%CI, 0.76-0.87). For patients during the first week of symptoms sensitivity was 69.6% (95%CI 66-73). On the other hand, specificity of the rapid test was above 97.8% in all groups.

CONCLUSIONS

The Panbio™ rapid antigen test for SARS-CoV-2 has a good specificity, but due to low and heterogeneous sensitivity in real life, a negative test in a person with suggestive symptoms at a time of community transmission of SARS-CoV-2 requires confirmation with RT-PCR, and after the first week of symptoms, sensitivity decreases considerably.
Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria
Authors: Balakrishnan Rohan , Mori Matteo , Segota Igor , Zhang Zhongge , Aebersold Ruedi , Ludwig Christina , Hwa Terence
Published: May 2021

Bacteria allocate their proteome to cellular functions differently in different growth conditions. It is largely unknown how such allocation arises from known mechanisms of gene regulation while constrained by limited translation capacity and fixed protein density. Here, we performed absolute transcriptomic and proteomic analysis forE. coliacross many conditions, obtaining a plethora of results on promoters and mRNAs characteristics that clash with conventional expectations: the majority of mRNAs exhibit similar translational efficiencies, while the promoter strengths are vastly different across genes. These characteristics prescribe two principles of gene regulation guiding bacteria to attain the desired protein allocation under global constraints: Total transcriptional output is tightly coordinated with ribosomal activity, and the concentrations of individual proteins are largely set by transcription. These two principles lead to a quantitative formulation of Central Dogma which unravels the complex relationship between gene regulatory activities and mRNA/protein concentrations across conditions. The knowledge obtained will be invaluable for accurately inferring gene regulatory interactions from ‘omics data, as well as for guiding the design of genetic circuits for synthetic biology applications inE. coliand other organisms.
ZNF146/OZF and ZNF507 target LINE-1 sequences
Authors: Creamer Kevin M. , Larsen Eric C. , Lawrence Jeanne B.
Published: May 2021

Repetitive sequences including transposable elements (TEs) and transposon-derived fragments account for nearly half of the human genome. While transposition-competent TEs must be repressed to maintain genomic stability, mutated and fragmented TEs comprising the bulk of repetitive sequences can also contribute to regulation of host gene expression and broader genome organization. Here we analyzed published ChIP-seq data sets to identify proteins broadly enriched on TEs in the human genome. We show two of the proteins identified, C2H2 zinc finger-containing proteins ZNF146 (also known as OZF) and ZNF507, are targeted to distinct sites within LINE-1 ORF2 at thousands of locations in the genome. ZNF146 binding sites are found at old and young LINE-1 elements. In contrast, ZNF507 preferentially binds at young LINE-1 sequences correlated to sequence changes in LINE-1 elements at ZNF507’s binding site. To gain further insight into ZNF146 and ZNF507 function, we disrupt their expression in HEK293 cells using CRISPR/Cas9 and perform RNA sequencing, finding modest gene expression changes in cells where ZNF507 has been disrupted. We further identify a physical interaction between ZNF507 and PRMT5, suggesting ZNF507 may target arginine methylation activity to LINE-1 sequences.
Dynamic trajectories of connectome state transitions are heritable
Authors: Jun Suhnyoung , Alderson Thomas H. , Altmann Andre , Sadaghiani Sepideh
Published: May 2021

The brain’s functional connectome is dynamic, constantly reconfiguring in an individual-specific manner. However, which characteristics of such reconfigurations are subject to genetic effects, and to what extent, is largely unknown. Here, we identified heritable dynamic features, quantified their heritability, and determined their association with cognitive phenotypes. In resting-state fMRI, we obtained multivariate features, each describing a temporal or spatial characteristic of connectome dynamics jointly over a set of connectome states. We found strong evidence for heritability of temporal features, particularly fractional occupancy (FO) and transition probability (TP), describing the trajectory of state transitions. Genetic effects explained a substantial proportion of phenotypic variance of these features (h2=.39, 95% CI= [.24,.54] for FO; h2=.43, 95% CI=[.29,.57] for TP). Moreover, these temporal phenotypes were associated with cognitive performance. Contrarily, we found no robust evidence for heritability of spatial features of the dynamic states (i.e., states’ Modularity and connectivity pattern). Genetic effects may therefore primarily contribute to how the connectome transitions across states, rather than the precise spatial instantiation of the states in individuals. In sum, genetic effects impact the duration spent in each connectivity configuration and the frequency of shifting between configurations, and such temporal features may act as endophenotypes for cognitive abilities.
Quantifying brain state transition cost via Schrödinger bridge
Authors: Kawakita Genji , Kamiya Shunsuke , Sasai Shuntaro , Kitazono Jun , Oizumi Masafumi
Published: May 2021

Quantifying brain state transition cost is a fundamental problem in systems neuroscience. Previous studies utilized network control theory to measure the cost by considering a neural system as a deterministic dynamical system. However, this approach does not capture the stochasticity of neural systems, which is important for accurately quantifying brain state transition cost. Here, we propose a novel framework based on optimal control in stochastic systems. In our framework, we quantify the transition cost as the Kullback-Leibler divergence from an uncontrolled transition path to the optimally controlled path, which is known as Schrödinger bridge. To test its utility, we applied this framework to functional magnetic resonance imaging data from the Human Connectome Project and computed the brain state transition cost in cognitive tasks. We demonstrate correspondence between brain state transition cost and the difficulty of tasks. The results suggest that our framework provides a general theoretical tool for investigating cognitive functions from the viewpoint of transition cost.

Author Summary

In our daily lives, we perform numerous tasks with different kinds and levels of cognitive demand. To successfully perform these tasks, the brain needs to modulate its spontaneous activity to reach an appropriate state for each task. Previous studies utilized optimal control in deterministic systems to measure cost for brain state transition. However, there has not been a unified framework for quantifying brain state transition cost that takes account of stochasticity of neural activities. Here, we propose a novel framework for measuring brain state transition cost, utilizing the idea of optimal control in stochastic systems. We assessed the utility of our framework for quantifying the cost of transitioning between various cognitive tasks. Our framework can be applied to very diverse settings due to its generality.
Kinetic Monitoring Of Neuronal Stress Response To Proteostasis Dysfunction
Authors: Santiago-Lopez Angel J. , Berglund Ken , Gross Robert E. , Gutekunst Claire-Anne N.
Published: May 2021

Proteostasis dysfunction and activation of the unfolded protein response (UPR) are characteristic of all major neurodegenerative diseases. Nevertheless, although the UPR and proteostasis dysfunction has been studied in great detail in model organisms like yeast and mammalian cell lines, it has not yet been examined in neurons. In this study, we applied a viral vector-mediated expression of a reporter protein based on a UPR transcription factor, ATF4, and time-lapse fluorescent microscopy to elucidate how mouse primary neurons respond to pharmacological and genetic perturbations to neuronal proteostasis. In in vitro models of endoplasmic reticulum (ER) stress and proteasome inhibition, we used the ATF4 reporter to reveal the time course of the neuronal stress response relative to neurite degeneration and asynchronous cell death. We showed how potential neurodegenerative disease co-factors, ER stress and mutant α-synuclein overexpression, impacted neuronal stress response and overall cellular health. This work therefore introduces a viral vector-based reporter that yields a quantifiable readout suitable for non-cell destructive kinetic monitoring of proteostasis dysfunction in neurons by harnessing ATF4 signaling as part of the UPR activation.
Crystal structures of two camelid nanobodies raised against GldL, a component of the type IX secretion system fromFlavobacterium johnsoniae
Authors: Trinh Thi Trang Nhung , Gaubert Anaïs , Melani Pauline , Cambillau Christian , Roussel Alain , Leone Philippe
Published: May 2021

GldL is an inner-membrane protein that is essential for the function of the type IX secretion system (T9SS) inFlavobacterium johnsoniae. The complex that it forms with GldM is supposed to act as a new rotary motor involved in the gliding motility of the bacterium. In the context of structural studies of GldL to gain information on the assembly and function of the T9SS, two camelid nanobodies were selected, produced and purified. Their interaction with the cytoplasmic domain of GldL was characterized and their crystal structures were solved. These nanobodies will be used as crystallization chaperones to help in the crystallization of the cytoplasmic domain of GldL and could also help to solve the structure of the complex using molecular replacement.
The influence of second language learning motivation on students' understandability of textbooks
Authors: Zhang Yuqian , De Zoysa Anura , Jagoda Kalinga
Published: May 2021

Purpose

The purpose of this study is to examine the relationship between the understandability of an accounting textbooks written in English and the language learning motivation of international students. Previous research assumed that native speakers of a language and second-language speakers would understand a given accounting text similarly and little attempt has been made to ascertain any individual differences in users’ capacity to read and understand a foreign language.

Design/methodology/approach

The 107 participants in this study comprised of full-time English as a Second Language postgraduate commerce students studying at a major Australian university. The authors used two-part questionnaire to examine the motivation of participants and the understandability of an accounting textbook using the Cloze test.

Findings

The results suggest that most international students have difficulty in understanding the textbook narratives used in this study. Furthermore, the results show that students’ motivation to learn a foreign language impacts on the understandability of an accounting textbook.

Practical implications

This study will help the educators, textbook publishers and students to understand the needs of ESL students. It is expected to provide guidance for authors and instructors to enhance the effectiveness of the accounting courses.

Originality/value

The accounting literature shows that there have been efforts by accounting researchers to measure the understandability of accounting texts or narratives. This research provided valuable insights of the learning challenges of international students and valuable recommendations to educators and publishers to enhance the delivery.
Solution of the 3D Helmholtz equation using barycentric Lagrange interpolation collocation method
Authors: Yang Miaomiao , Du Xinkun , Ge Yongbin
Published: May 2021

Purpose

This meshless collocation method is applicable not only to the Helmholtz equation with Dirichlet boundary condition but also mixed boundary conditions. It can calculate not only the high wavenumber problems, but also the variable wave number problems.

Design/methodology/approach

In this paper, the authors developed a meshless collocation method by using barycentric Lagrange interpolation basis function based on the Chebyshev nodes to deduce the scheme for solving the three-dimensional Helmholtz equation. First, the spatial variables and their partial derivatives are treated by interpolation basis functions, and the collocation method is established for solving second order differential equations. Then the differential matrix is employed to simplify the differential equations which is on a given test node. Finally, numerical experiments show the accuracy and effectiveness of the proposed method.

Findings

The numerical experiments show the advantages of the present method, such as less number of collocation nodes needed, shorter calculation time, higher precision, smaller error and higher efficiency. What is more, the numerical solutions agree well with the exact solutions.

Research limitations/implications

Compared with finite element method, finite difference method and other traditional numerical methods based on grid solution, meshless method can reduce or eliminate the dependence on grid and make the numerical implementation more flexible.

Practical implications

The Helmholtz equation has a wide application background in many fields, such as physics, mechanics, engineering and so on.

Originality/value

This meshless method is first time applied for solving the 3D Helmholtz equation. What is more the present work not only gives the relationship of interpolation nodes but also the test nodes.
The mutual impact of university president’s leadership and organizational justice on knowledge sharing: the mediating effect of communication
Authors: Kim Soo Jung , Jang Youjin , Yoo Myunghyun , Song Ji Hoon
Published: May 2021

Purpose

The purpose of this study is to empirically examine the mediating effect of organizational communication in the relationships among transformational leadership, organizational justice and knowledge sharing within the higher education setting in South Korea.

Design/methodology/approach

A sample of 321 university employees, including 151 faculty members and 170 administrative staff members, from a representative private university, participated in the survey as part of a consulting project for university innovation. Structural equation modeling (SEM) was mainly used for data analysis to identify the structural relationship among the research variables.

Findings

The results of this study confirmed that transformational leadership positively influences organizational justice and knowledge sharing. However, the influence of organizational justice on knowledge sharing was not statistically significant. The mediating effect of organizational communication among those relationships to increase the members’ knowledge sharing behavior was statistically significant.

Originality/value

In this study, holistic aspects of the organization, including leadership, organizational culture and organizational strategy, were examined for encouraging employees’ knowledge sharing behavior while an organization undergoes innovational changes. More practically, this study suggested that organizational communication could be used as one of the critical strategies in the process of university innovation.
High-performance work system: a systematic review of literature
Authors: Kaushik Dilip , Mukherjee Ujjal
Published: May 2021

Purpose

This paper aims to review the existing body of knowledge on high-performance work systems (HPWS) with a special focus on the recent developments that strengthen its prevalence. Considering the current business ecosystem, the author proposes two more characteristics of HPWS which will add value to the literature. It also aims to propose several gaps in the literature considering the role of HPWS in the organization.

Design/methodology/approach

This paper uses a systematic literature review methodology to strengthen the concept, its connection with people and organization, theoretical underpinnings and intervening mechanisms that have not received much attention. The information collected from various studies was analyzed thematically and synthesized to assess the existing body of literature. For a better understanding of HPWS, the review is organized under the following subthemes: definition and meaning, conceptualization, technology infusion, relationship with people and organization, theories commonly used and positives and negative consequences of HPWS.

Findings

This study identifies and describes key characteristics of HPWS such as system, synergistic effect, performance and proposes two new characteristics – agility and adoption of technology. Further findings of this study indicate that HPWS has both positive and negative influences on employee outcomes. The positive outcome helps in the development of human capital that provides a competitive advantage to the organization. The study also underlines some negative influences of HPWS on employee behavior due to the misalignment of HR practices. Scope for further research is also provided for future researchers.

Originality/value

The paper adds the recent developments in the area of HPWS literature and proposes research directions for future researchers.
A literature review exploring the role of technology in business survival during the Covid-19 lockdowns
Authors: Abed Salma S.
Published: May 2021

Purpose

The Covid-19 pandemic has affected every aspect of human life. Even though the pandemic length was not too long, a huge volume of research relating to Covid-19 has been published in different contexts. This paper aims to review the literature investigating the impact of Covid −19 on businesses generally and explore studies examining the technology role of business survival during the Covid-19 lockdowns specifically.

Design/methodology/approach

This study implemented the concept of a systematic review approach to review the literature that has been conducted in the business field during the Covid-19 crisis in general. Additionally, it looks into the research examining the role of technology in business survival in the Covid-19 crisis specifically. All studies were conducted in 2020. A total of 53 studies were identified and categorised into different themes. The research methods, theories and locations have also been analysed.

Findings

It was found that Covid-19 pandemic has affected all business sectors in several ways. Technology adoption has a critical role for business survival during the Covid-19 crises especially with small businesses. Very limited research has been conducted on the adoption of different technologies during the Covid-19 lockdowns.

Originality/value

This study presents the most frequent themes and topics that have been explored in the literature during the Covid-19 crisis in the business field. It highlights the methods used in addition to the theories and research locations present in this literature. Finally, it proposes the possible implications of this literature review.