bluuebunny/crossref_metadata_2025 huggingface dataset:
COVID-19 (Coronavirus Disease) Outbreak Prediction Using a Susceptible-Exposed-Symptomatic Infected-Recovered-Super Spreaders-Asymptomatic Infected-Deceased-Critical (SEIR-PADC) Dynamic Model
Authors: Sedaghat Ahmad , Mosavi Amir
Published: December 2020

Extension of SIR type models has been reported in a number of publications in mathematics community. But little is done on validation of these models to fit adequately with multiple clinical data of an infectious disease. In this paper, we introduce SEIR-PAD model to assess susceptible, exposed, infected, recovered, super-spreader, asymptomatic infected, and deceased populations. SEIR-PAD model consists of 7-set of ordinary differential equations with 8 unknown coefficients which are solved numerically in MATLAB using an optimization algorithm to fit 4-set of COVID-19 clinical data consist of cumulative populations of infected, deceased, recovered, and susceptible. Trends of COVID-19 in Trends in Gulf Cooperation Council (GCC) countries are successfully predicted using available data from outbreak until 23rd June 2020. Promising results of SEIR-PAD model provide insight into better management of COVID-19 pandemic in GCC countries.
Predicting intention to receive COVID-19 vaccine among the general population using the Health Belief Model and the Theory of Planned Behavior Model
Authors: Shmueli Liora
Published: December 2020

Background

A novel coronavirus (COVID-19) was declared a global pandemic by the World Health Organization (WHO) in March, 2020. Until such time as a vaccine becomes available, it is important to identify the determining factors that influence the intention of the general public to accept a future COVID-19 vaccine. Consequently, we aim to explore behavioral-related factors predicting intention to receive COVID-19 vaccine among the general population using the Health Belief Model (HBM) and the Theory of Planned Behavior (TPB) model.

Methods

An online survey was conducted among adults aged 18 years and older from May 24 to June 24, 2020. The survey included socio-demographic and health-related questions, questions related to the HBM and TPB dimensions, and intention to receive COVID-19 vaccine. Associations between questionnaire variables and COVID-19 vaccination intention were assessed by univariate and multivariate analyses.

Results

Eighty percent of 398 eligible respondents stated their willingness to receive COVID-19 vaccine. A unified model including HBM and TPB covariates as well as demographic and health-related factors, proved to be a powerful predictor of intention to receive COVID-19 vaccine, explaining 78% of the variance (adjusted R2 = 0.78). Men (OR=4.35, 95% CI 1.58–11.93), educated respondents (OR=3.54, 95% CI 1.44–8.67) and respondents who had received the seasonal influenza vaccine in the previous year (OR=3.31, 95% CI 1.22–9.00) stated higher intention to receive COVID-19 vaccine. Participants were more likely to be willing to get vaccinated if they reported higher levels of perceived benefits of COVID-19 vaccine (OR=4.49, 95% CI 2.79–7.22), of perceived severity of COVID-19 infection (OR=2.36, 95% CI 1.58–3.51) and of cues to action (OR=1.99, 95% CI 1.38–2.87), according to HBM, and if they reported higher levels of subjective norms (OR=3.04, 95% CI 2.15–4.30) and self-efficacy (OR=2.05, 95% CI 1.54–2.72) according to TPB. Although half of the respondents reported they had not received influenza vaccine last year, 40% of them intended to receive influenza vaccine in the coming winter and 66% of them intended to receive COVID-19 vaccine.

Conclusions

Providing data on the public perspective and predicting intention for COVID-19 vaccination using HBM and TPB is important for health policy makers and healthcare providers and can help better guide compliance as the COVID-19 vaccine becomes available to the public.
Bortezomib abrogates temozolomide-induced autophagic flux through an ATG5 dependent pathway
Authors: Rahman Mohummad Aminur , Engelsen Agnete , Sarowar Shahin , Bindesbøll Christian , Birkeland Even , Lotsberg Maria L. , Knappskog Stian , Simonsen Anne , Chekenya Martha
Published: December 2020

Glioblastoma (GBM) is invariably resistant to temozolomide (TMZ) chemotherapy. Inhibiting the proteasomal pathway is an emerging strategy to accumulate damaged proteins and inhibit their lysosomal degradation. We hypothesized that bortezomib (BTZ) might sensitize GBM cells to TMZ. We examined change in autophagic flux after drug treatments and in combination with pharmacological inhibitors or CRISPR cas9 knockout of autophagy-related genes -5 and -7 (ATG5 and ATG7, respectively). Autophagic flux was increased in temozolomide resistant GBM cells as indicated by diminished levels of the autophagy markers LC3A/B-II and p62(SQSTM1), increased localisation of LC3A/B-II with STX17, higher long-lived protein degradation and no induction of apoptosis. In contrast, BTZ treatment abrogated autophagic flux by accumulation of LC3A/B-II and p62(SQSTM1) positive autophagosomes that did not fuse with lysosomes and reduced degradation of long-lived proteins. BTZ synergistically enhanced TMZ efficacy by attenuating cell proliferation, increased DNA damage and apoptosis. CRISPR CasATG5knockout reversed BTZ-induced autophagy blockade and rescued the GBM treated cells from death. We conclude that bortezomib abrogates temozolomide induced autophagy through ATG5 dependent pathway.
Occupational exposures associated with being a COVID-19 case; evidence from three case-controls studies
Authors: Hiironen Iina , Saavedra-Campos Maria , Panitz Jennifer , Ma Thomas , Nsonwu Olisaeloka , Charlett Andre , Hughes Gareth , Oliver Isabel
Published: December 2020

Background

The evidence on risk factors for transmission of SARS-CoV-2 in community settings is sparse, yet this information is key to inform public health action. We investigated factors associated with being a COVID-19 case using data collected through contact tracing.

Methods

We conducted three retrospective, frequency-matched case-control studies between August 2020 and October 2020 using case data from the NHS Test and Trace programme. Controls were obtained through Market Research Panels. Multivariable analyses provided adjusted odds ratios (aORs) for multiple community exposure settings. We analysed the results in meta-analyses using random effects models to obtain pooled odds ratios (pORs).

Results

Across all study periods, there was strong statistical evidence that working in healthcare (pOR 2.87, aOR range 2.72-3.08), social care (pOR 4.15, aOR range 2.46-5.41) or hospitality (pOR 2.36, aOR range 2.01-2.63) were associated with increased odds of being a COVID-19 case. There was also evidence that working in warehouse setting was associated with increased odds (pOR 3.86, aOR range 1.06-14.19), with a substantial increase in odds observed over the study periods. A similar pattern was also observed in education and construction.

Conclusions

The studies indicate that some workplace settings are associated with increased odds of being a case. However, it is not possible to determine how much of the transmission of SARS-CoV-2 took place within the workplace, and how much was associated with social, household or transport exposures.
Transmission risk of SARS-CoV-2 on airplanes and high-speed trains
Authors: Hu Maogui , Wang Jinfeng , Lin Hui , Ruktanonchai Corrine W , Xu Chengdong , Meng Bin , Zhang Xin , Carioli Alessandra , Feng Yuqing , Yin Qian , Floyd Jessica R , Ruktanonchai Nick W , Li Zhongjie , Yang Weizhong , Tatem Andrew J , Lai Shengjie
Published: December 2020

Modern transportation plays a key role in the long-distance and rapid spread of SARS-CoV-2. However, little is known about the transmission risk of SARS-CoV-2 on confined vehicles, such as airplanes and trains. Based on the itinerary and epidemiological data of COVID-19 cases and close contacts among 9,265 airline passengers on 291 airplanes and 29,335 passengers on 830 high-speed trains in China from December 20, 2019 to March 17, 2020, we estimated that the upper bound of overall attack rate of COVID-19 among passengers was 0.60% (95% confidence interval: 0.43%-0.84%) for airplanes and 0.35% (0.28%-0.44%) for trains departing from Wuhan before its lockdown, respectively. The reproduction number during travel ranged from 0.12 to 0.19 on airplanes and from 0.07 to 0.12 on trains, with the risk varying by seat distance from the index case and joint travel time, but the difference in risk was not significant between the types of aircraft and train. Overall, the risk of SARS-CoV-2 transmission on planes and high-speed trains with high efficiency air filtration devices was relatively low. Our findings improve understanding of COVID-19 spread during travel and may inform response efforts, such as lifting travel restrictions, and resuming transportation in the pandemic.
Estimating the risk of incident SARS-CoV-2 infection among healthcare workers in quarantine hospitals: the Egyptian example
Authors: Jijón Sofía , Shafie Ahmad Al , Hassan Essam ,   EMAE-MESuRS working group on nosocomial SARS-CoV-2 modeling, Temime Laura , Jean Kévin , El-Kassas Mohamed
Published: December 2020

In response to the COVID-19 epidemic, Egypt established a unique care model based on quarantine hospitals where only externally-referred confirmed COVID-19 patients were admitted, and healthcare workers resided continuously over 1-to 2-week working shifts. While the COVID-19 risk for HCWs has been widely reported in standard healthcare settings, it has not been evaluated yet in quarantine hospitals.

Here, we relied on longitudinal data, including results of routine RT-PCR tests, collected within three quarantine hospitals located in Cairo and Fayoum, Egypt. Using a model-based approach that accounts for the time-since-exposure variation in false-negative rates of RT-PCR tests, we computed the incidence of SARS-CoV-2 infection among HCWs. Over a total follow-up of 6,064 person-days (PD), we estimated an incidence rate (per 100 PD) of 1.05 (95% CrI: 0.58–1.65) at Hospital 1, 1.92 (95% CrI: 0.93–3.28) at Hospital 2 and 7.62 (95% CrI: 3.47–13.70) at Hospital 3. The probability for an HCW to be infected at the end of a shift was 13.7% (95% CrI: 7.8%–20.8%) and 23.8% (95% CrI: 12.2%–37.3%) for a 2-week shift at Hospital 1 and Hospital 2, respectively, which lies within the range of risk levels previously documented in standard healthcare settings, whereas it was >3-fold higher for a 7-day shift at Hospital 2 (42.6%, 95%CrI: 21.9%–64.4%). Our model-based estimates unveil a proportion of undiagnosed infections among HCWs of 46.4% (95% CrI: 18.8%–66.7%), 45.0% (95% CrI: 5.6%–70.8%) and 59.2% (95% CrI: 34.8%–78.8%), for Hospitals 1 to 3, respectively.

The large variation in SARS-CoV-2 incidence we document here suggests that HCWs from quarantine hospitals may face a high occupational risk of infection, but that, with sufficient anticipation and infection control measures, this risk can be brought down to levels similar to those observed in standard healthcare settings.

WHAT THIS PAPER ADDS

What is already known on this topic

Previous studies conducted in standard care settings have documented that frontline healthcare workers (HCWs) face high risk of COVID-19. Whether risk levels differ in alternative care models, such as COVID-19 quarantine hospitals in Egypt where HCWs resided in the hospital days and nights for various durations, is unknown.

What this study adds

COVID-19 risk for HCWs in quarantine hospitals varies substantially between facilities, from risk levels that are in the range of those documented in standard healthcare settings to levels that were approximatively 3 times higher.

How this study might affect research, practice or policy

With sufficient anticipation and infection control measures, occupational COVID-19 risk for HCWs working in quarantine hospitals can be brought down to levels similar to those observed in standard healthcare settings.
Population risk factors for severe disease and mortality in COVID-19: A global systematic review and meta-analysis
Authors: Booth Adam , Reed Angus Bruno , Ponzo Sonia , Yassaee Arrash , Aral Mert , Plans David , Labrique Alain , Mohan Diwakar
Published: December 2020

Aim

COVID-19 clinical presentation is heterogeneous, ranging from asymptomatic to severe cases. While there are a number of early publications relating to risk factors for COVID-19 infection, low sample size and heterogeneity in study design impacted consolidation of early findings. There is a pressing need to identify the factors which predispose patients to severe cases of COVID-19. For rapid and widespread risk stratification, these factors should be easily obtainable, inexpensive, and avoid invasive clinical procedures. The aim of our study is to fill this knowledge gap by systematically mapping all the available evidence on the association of various clinical, demographic, and lifestyle variables with the risk of specific adverse outcomes in patients with COVID-19.

Methods

The systematic review was conducted using standardized methodology, searching three electronic databases (PubMed, Embase, and Web of Science) for relevant literature published between 1st January 2020 and 9th July 2020. Included studies reported characteristics of patients with COVID-19 while reporting outcomes relating to disease severity. In the case of sufficient comparable data, meta-analyses were conducted to estimate risk of each variable.

Results

Seventy-six studies were identified, with a total of 17,860,001 patients across 14 countries. The studies were highly heterogeneous in terms of the sample under study, outcomes, and risk measures reported. A large number of risk factors were presented for COVID-19. Commonly reported variables for adverse outcome from COVID-19 comprised patient characteristics, including age >75 (OR = 2.65 (1.81–3.90)), male sex (OR = 2.05(1.39–3.04)) and severe obesity (OR = 2.57 (1.31–5.05)). Active cancer (OR = 1.46 (1.04–2.04)) was associated with increased risk of severe outcome. A number of common symptoms and vital measures (respiratory rate and SpO2) also suggested elevated risk profiles.

Conclusions

Based on the findings of this study, a range of easily assessed parameters are valuable to predict elevated risk of severe illness and mortality as a result of COVID-19, including patient characteristics and detailed comorbidities, alongside the novel inclusion of real-time symptoms and vital measurements.
Indoor residual spraying practises against Triatoma infestans in the Bolivian Chaco: contributing factors to suboptimal insecticide delivery to treated households
Authors: Gonçalves Raquel , Logan Rhiannon A.E. , Ismail Hanafy M. , Paine Mark J.I. , Bern Caryn , Courtenay Orin
Published: December 2020

Background

Indoor Residual Spraying (IRS) of insecticides is a key method to reduce transmission by Triatoma infestans, vector of Chagas disease in a large part of South America. However, the successes of IRS in the Gran Chaco region straddling Bolivia, Argentina and Paraguay, have not equalled those in other Southern Cone countries.

Aims

This study evaluated routine IRS practises and insecticide quality control in a typical endemic community in the Bolivian Chaco.

Methods

Alpha-cypermethrin active ingredient (a.i.) concentrations captured onto filter papers fitted to sprayed wall surfaces, and in prepared spray tank solutions, were measured using an adapted Insecticide Quantification Kit (IQK™). The results were analysed by negative binomial GLM regression in relation to the time (minutes) spray teams spent treating houses, spray rates (surface area to spray [m2/minute]), householder compliance to empty houses for IRS delivery, and the visual presence/absence of filter papers. The IQK™ assays developed for these samples were validated against HPLC quantification methods. Results: Substantial variations in the delivered a.i. concentrations were observed; only 10.4% (50/480) of filter papers, and 8.8% (5/57) of houses received the target concentration. The delivered concentrations were not related to those in the matched spray tank solutions. The sedimentation of a.i. in the surface solution of prepared spray tanks was rapid, resulting in a 29% loss of a.i. content within 5 minutes, and 48.5% after 15 minutes. The delivered concentrations were positively associated with the time spent spraying the house, and inversely related to the spray rate, but showed weak correlations in both cases. The influence of householder compliance on spray rates were significant, though associated differences in delivered concentrations were not detected. No differences were observed in spray rates between houses fitted with filter papers and houses without.

Conclusions

Suboptimal delivery of IRS is partially attributed to the insecticide physical characteristics, and the need for revision of insecticide delivery methods, which includes training of IRS teams and community education to encourage compliance. The IQK™ is a necessary field-friendly tool to improve IRS quality, and to facilitate health worker training and decision making by the Chagas disease vector control managers.
Adverse Cardiovascular Complications Following Prescription of Programmed Cell Death 1 (PD-1) and Programmed Cell Death Ligand 1 (PD-L1) Inhibitors: A Propensity-Score Matched Cohort Study with Competing Risk Analysis
Authors: Zhou Jiandong , Lee Sharen , Lakhani Ishan , Yang Lei , Liu Tong , Zhang Yuhui , Xia Yunlong , Wong Wing Tak , Bao Kelvin King Hei , Wong Ian Chi Kei , Tse Gary , Zhang Qingpeng
Published: December 2020

Background

Programmed death-1 (PD-1) and programmed death-ligand 1 (PD-L1) inhibitors, such as pembrolizumab, nivolumab and atezolizumab, are major classes of immune checkpoint inhibitors that are increasingly used for cancer treatment. However, their use is associated with adverse cardiovascular events. We examined the incidence of new-onset cardiac complications in patients receiving PD-1 or PD-L1 inhibitors.

Methods

Patients receiving PD-1 or PD-L1 inhibitors since their launch up to 31stDecember 2019 at publicly funded hospitals of Hong Kong, China, without pre-existing cardiac complications were included. The primary outcome was a composite of incident heart failure, acute myocardial infarction, atrial fibrillation or atrial flutter with the last follow-up date of 31stDecember 2020. Propensity score matching between PD-L1 inhibitor use and PD-1 inhibitor use with a 1:2 ratio for patient demographics, past comorbidities and non-PD-1/PD-L1 medications was performed.

Results

A total of 1959 patients were included. Over a median follow-up of 247 days (interquartile range [IQR]: 72-506), 320 (incidence rate [IR]: 16.31%) patients met the primary outcome after PD-1/PD-L1 treatment: 244 (IR: 12.57%) with heart failure, 38 (IR: 1.93%) with acute myocardial infarction, 54 (IR: 2.75%) with atrial fibrillation, 6 (IR: 0.31%) with atrial flutter. Compared with PD-1 inhibitor treatment, PD-L1 inhibitor treatment was significantly associated with lower risks of the composite outcome both before (hazard ratio [HR]: 0.32, 95% CI: [0.18-0.59], P value=0.0002) and after matching (HR: 0.34, 95% CI: [0.18-0.65], P value=0.001), and lower all-cause mortality risks before matching (HR: 0.77, 95% CI: [0.64-0.93], P value=0.0078) and after matching (HR: 0.80, 95% CI: [0.65-1.00], P value=0.0463). Patients who developed cardiac complications had shorter average readmission intervals and a higher number of hospitalizations after treatment with PD-1/PD-L1 inhibitors in both the unmatched and matched cohorts (P value<0.0001). Competing risk analysis with cause-specific and subdistribution hazard models and multiple approaches based on the propensity score all confirmed these observations.

Conclusions

Compared with PD-1 treatment, PD-L1 treatment was significantly associated with lower risk of new onset cardiac complications and all-cause mortality both before and after propensity score matching.
The EEG multiverse of schizophrenia
Authors: Gordillo Dario , Ramos da Cruz Janir , Chkonia Eka , Lin Wei-Hsiang , Favrod Ophélie , Brand Andreas , Figueiredo Patrícia , Roinishvili Maya , Herzog Michael H.
Published: December 2020

Research on schizophrenia typically focuses on one paradigm, for which clear-cut differences between patients and controls are established. Great care is taken to understand the underlying genetical, neurophysiological, and cognitive mechanism, which eventually may explain the clinical outcome. One tacit assumption of these deep rooting approaches is that paradigms tap into common and representative aspects of the disorder. Here, we analyzed the resting-state electroencephalogram (EEG) of 121 schizophrenia patients and 75 controls. Using multiple signal processing methods, we extracted 194 EEG features. Sixty-nine out of the 194 EEG features showed a significant difference between patients and controls indicating that these features detect an important aspect of schizophrenia. Surprisingly, the correlations between these features were very low, suggesting that each feature picks up a different aspect of the disorder. We propose that complementing deep with shallow rooting approaches, where many roughly independent features are extracted from one paradigm (or several paradigms), will strongly improve diagnosis and potential treatment of schizophrenia.
SARS-CoV-2 testing of 11,884 healthcare workers at an acute NHS hospital trust in England: a retrospective analysis
Authors: Hanrath Aidan T. , Schim van der Loeff Ina , Lendrem Dennis W. , Baker Kenneth F. , Price David A. , McDowall Peter , McDowall Kiera , Cook Sue , Towns Peter , Schwab Ulrich , Evans Adam , Dixon Jill , Collins Jennifer , Burton-Fanning Shirelle , Saunders David , Harwood Jayne , Samuel Julie , Schmid Matthias L. , Pareja-Cebrian Lucia , Hunter Ewan , Murphy Elizabeth , Taha Yusri , Payne Brendan A. I. , Duncan Christopher J.A.
Published: December 2020

Healthcare workers (HCWs) are known to be at increased risk of infection with SARS-CoV-2, although whether these risks are equal across all roles is uncertain. Here we report a retrospective analysis of a large real-world dataset obtained from 10 March to 6 July 2020 in an NHS Foundation Trust in England with 17,126 employees. 3,338 HCWs underwent symptomatic PCR testing (14.4% positive, 2.8% of all staff) and 11,103 HCWs underwent serological testing for SARS-CoV-2 IgG (8.4% positive, 5.5% of all staff). Seropositivity was lower than other hospital settings in England but higher than community estimates. Increased test positivity rates were observed in HCWs from BAME backgrounds and residents in areas of higher social deprivation. A logistic regression model adjusting for these factors showed significant increases in the odds of testing positive in certain occupational groups, most notably domestic services staff, nurses and health-care assistants. PCR testing of symptomatic HCWs appeared to underestimate overall infection levels, probably due to asymptomatic seroconversion. Clinical outcomes were reassuring, with only a small minority of HCWs with COVID-19 requiring hospitalisation (2.3%) or ICU management (0.7%) and with no deaths. Despite a relatively low level of HCW infection compared to other UK cohorts, there were nevertheless important differences in test positivity rates between occupational groups, robust to adjustment for demographic factors such as ethnic background and social deprivation. Quantitative and qualitative studies are needed to better understand the factors contributing to this risk. Robust informatics solutions for HCW exposure data are essential to inform occupational monitoring.
When months matter; modelling the impact of the COVID-19 pandemic on the diagnostic pathway of Motor Neurone Disease (MND)
Authors: Burchill Ella , Rawji Vishal , Styles Katy , Rooney Siobhan , Stone Patrick , Astin Ronan , Sharma Nikhil
Published: December 2020

Background

A diagnosis of MND takes an average 10-16 months from symptom onset. Early diagnosis is important to access supportive measures to maximise quality of life. The COVID-19 pandemic has caused significant delays in NHS pathways; the majority of GP appointments now occur online with subsequent delays in secondary care assessment. Given the rapid progression of MND, patients may be disproportionately affected resulting in late stage new presentations. We used Monte Carlo simulation to model the pre-COVID-19 diagnostic pathway and then introduced plausible COVID-19 delays.

Methods

The diagnostic pathway was modelled using gamma distributions of time taken: 1) from symptom onset to GP presentation, 2) for specialist referral, and 3) for diagnosis reached after neurology appointment. We incorporated branches to simulate delays: when patients did not attend their GP and when the GP consultation did not result in referral. An emergency presentation was triggered when diagnostic pathway time was within 30 days of projected median survival. Total time-to-diagnosis was calculated over 100,000 iterations. The pre-COVID-19 model was estimated using published data and the Improving MND Care Survey 2019. We estimated COVID-19 delays using published statistics.

Results

The pre-COVID model reproduced known features of the MND diagnostic pathway, with a median time to diagnosis of 399 days and predicting 5.2% of MND patients present as undiagnosed emergencies. COVID-19 resulted in diagnostic delays from 558 days when only primary care was 25% delayed, to 915 days when both primary and secondary care were 75%. The model predicted an increase in emergency presentations ranging from 15.4%-44.5%.

Interpretations

The model suggests the COVID-19 pandemic will result in later-stage diagnoses and more emergency presentations of undiagnosed MND. Late-stage presentations may require rapid escalation to multidisciplinary care. Proactive recognition of acute and late-stage disease with altered service provision will optimise care for people with MND.

Funding

This research was supported and funded by a grant from the Reta Lila Weston Trust. NS was supported by the National Institute for Health Research University College London Hospitals Biomedical Research Centre.
Wnt signaling recruits KIF2A to the spindle to ensure chromosome congression and alignment during mitosis
Authors: Bufe Anja , del Arco Ana García , Hennecke Magdalena-Isabell , Ostermaier Matthias , de Jaime-Soguero Anchel , Lin Yu-Chih , Ciprianidis Anja , Engel Ulrike , Beli Petra , Bastians Holger , Acebrón Sergio P.
Published: December 2020

Canonical Wnt signaling plays critical roles in development and tissue renewal by regulating β-catenin target genes. Recent evidence showed that β-catenin-independent Wnt signaling is also required for faithful execution of mitosis. This mitotic Wnt signaling functions through Wnt-dependent stabilization of proteins (Wnt/STOP), as well as through components of the LRP6 signalosome. However, the targets and specific functions of mitotic Wnt signaling still remain uncharacterized. Using phosphoproteomics, we identified that Wnt signaling regulates the microtubule depolymerase KIF2A during mitosis. We found that Dishevelled recruits KIF2A via its N-terminal and motor domains, which is further promoted upon LRP6 signalosome formation during mitosis. We show that Wnt signaling modulates KIF2A interaction with PLK1, which is critical for KIF2A localization at the spindle. Accordingly, Wnt signaling promotes chromosome congression and alignment by monitoring KIF2A protein levels at the spindle poles both in somatic cells and in pluripotent stem cells. Our findings highlight a novel function of Wnt signaling during cell division, which could have important implications for genome maintenance, notably in stem cells.

SIGNIFICANCE

Wnt signaling plays essential roles in embryonic patterning, stem cell renewal, and cell cycle progression from G1 to S phase via the regulation ofβ-catenin target genes. Here, we show that Wnt signaling also promotes faithful execution of mitosis by ensuring chromosome congression and alignment before cell division, including in pluripotent stem cells. We demonstrate that the Wnt signaling transducer Dishevelled recruits the mitotic kinesin KIF2A, and mediates its binding to the spindle. KIF2A is a microtubule depolymerase that controls chromosome alignment and congression during mitosis. Consequently, we found that inhibition of Wnt signaling leads to KIF2A-dependent chromosome congression and alignment defects.
Evolutionary tracking of SARS-CoV-2 genetic variants highlights an intricate balance of stabilizing and destabilizing mutations
Authors: Jacob Jobin John , Vasudevan Karthick , Pragasam Agila Kumari , Gunasekaran Karthik , Veeraraghavan Balaji , Mutreja Ankur
Published: December 2020

The currently ongoing COVID-19 pandemic caused by SARS-CoV-2 has accounted for millions of infections and deaths across the globe. Genome sequences of SARS-CoV-2 are being published daily in public databases and the availability of this genome datasets has allowed unprecedented access into the mutational patterns of SARS-CoV-2 evolution. We made use of the same genomic information for conducting phylogenetic analysis and identifying lineage-specific mutations. The catalogued lineage defining mutations were analysed for their stabilizing or destabilizing impact on viral proteins. We recorded persistence of D614G, S477N, A222V V1176F variants and a global expansion of the PANGOLIN variant B.1. In addition, a retention of Q57H (B.1.X), R203K/G204R (B.1.1.X), T85I (B.1.2-B.1.3), G15S+T428I (C.X) and I120F (D.X) variations was observed. Overall, we recorded a striking balance between stabilizing and destabilizing mutations, therefore well-maintained protein structures. With selection pressures in the form of newly developed vaccines and therapeutics to mount soon in coming months, the task of mapping of viral mutations and recording of their impact on key viral proteins would be crucial to pre-emptively catch any escape mechanism that SARS-CoV-2 may evolve for.

STUDY IMPORTANCE

As large numbers of the SARS CoV-2 genome sequences are shared in publicly accessible repositories, it enables scientists a detailed evolutionary analysis since its initial isolation in Wuhan, China. We investigated the evolutionarily associated mutational diversity overlaid on the major phylogenetic lineages circulating globally, using 513 representative genomes. We detailed phylogenetic persistence of key variants facilitating global expansion of the PANGOLIN variant B.1, including the recent, fast expanding, B.1.1.7 lineage. The stabilizing or destabilizing impact of the catalogued lineage defining mutations on viral proteins indicates their possible involvement in balancing the protein function and structure. A clear understanding of this mutational profile is of high clinical significance to catch any vaccine escape mechanism, as the same proteins make crucial components of vaccines recently approved and in development. In this direction, our study provides an imperative framework and baseline data upon which further analysis could be built as newer variants of SARS-CoV-2 continue to appear.
Computational prediction of CRISPR-impaired non-coding regulatory regions
Authors: Baumgarten Nina , Schmidt Florian , Wegner Martin , Hebel Marie , Kaulich Manuel , Schulz Marcel H.
Published: December 2020

Genome-wide CRISPR screens are becoming more widespread and allow the simultaneous interrogation of thousands of genomic regions. Although recent progress has been made in the analysis of CRISPR screens, it is still an open problem how to interpret CRISPR mutations in non-coding regions of the genome. Most of the tools concentrate on the interpretation of mutations introduced in gene coding regions. We introduce a computational pipeline that uses epigenomic information about regulatory elements for the interpretation of CRISPR mutations in non-coding regions. We illustrate our approach on the analysis of a genome-wide CRISPR screen in hTERT-RPE-1 cells and reveal novel regulatory elements that mediate chemoresistance against doxorubicin in these cells. We infer links to established and to novel chemoresistance genes. Our approach is general and can be applied on any cell type and with different CRISPR enzymes.
Hidden dynamics of ubiquitin-mediated autoregulation of human 26S proteasome during substrate degradation
Authors: Wu Zhaolong , Chen Enbo , Zou Shitao , Hou Yanzhen , Zhang Shuwen , Wang Wei Li , Dong Yuanchen , Mao Youdong
Published: December 2020

The 26S proteasome regulates proteostasis and myriad cellular processes. Here we reconstitute the hidden dynamics of human 26S proteasome during protein degradation using cryo-EM data-driven deep learning, which identified 64 proteasomal conformers. These conformers revealed substrate-dependent conformational entanglement of two 19S regulatory particles in the doubly capped holocomplexes. The rate-limiting step in single-nucleotide exchange dynamics of the AAA-ATPase motor is ATPase re-engagement with the substrate, while the rate-limiting step in proteasomal degradation is the initiation of substrate unfolding by the AAA-ATPase motor following deubiquitylation. Nine rare conformers delineated novel ubiquitin-binding sites on the RPN2 and α5 subunits, along with a ubiquitylation site on RPN10, which were verified using site-directed mutagenesis and liquid chromatography-tandem mass spectrometry. Opening of the 20S core particle gate was found to upregulate proteolytic activity by allosterically promoting nucleophilic attack on the scissile peptide bond. Our systematic analyses illuminate a grand hierarchical allostery underlying ubiquitin-mediated proteasome autoregulation.
Estradiol enhances ethanol stimulation of ventral tegmental area dopamine neuron firing without limiting ethanol inhibition onto those neurons
Authors: Lambeth Philip S. , Lasek Amy W. , Mangieri Regina A.
Published: December 2020

Females can progress to alcohol and other substance use disorders more quickly than males. The ovarian hormone 17β-estradiol (E2) contributes to sex differences observed in drug use and abuse and may be a principal driver of these differences. However, it is not entirely clear how E2 acts to affect processing of ethanol reward, and several brain regions and mechanisms are implicated. We sought to clarify the role of E2 in modulating the response of ventral tegmental area dopamine neurons to ethanol. To this end, we recorded spontaneous action potentials and inhibitory post synaptic currents from dopaminergic neurons in acute horizontal brain slices from ovariectomized (OVX) dopamine neuron reporter mice (Pitx3-eGFP) treated with either vehicle (VEH) or E2. On the basis of prior work, we hypothesized that E2 administration would cause dopamine cells from OVX+E2 animals to show a more substantial ethanol-induced increase in firing rate compared to control animals. Our data confirmed that ethanol stimulation of the firing rate of dopamine neurons from OVX+E2 mice was greater than that of OVX+VEH animals. Further, we hypothesized that the firing rate increase would be accompanied by a concomitant decrease in ethanol stimulated inhibition onto those same neurons. We found that although ethanol caused the expected increase in GABAAreceptor-mediated synaptic inhibition in both groups, there was no difference in this response between OVX+E2 and OVX+VEH animals. Our findings lend additional support for the ability of E2 to enhance ventral tegmental area dopamine neuron responses to ethanol and suggest that this effect is not mediated by an E2-elicited suppression of synaptic inhibition.
No support for white matter microstructural properties and connectivity differences in the combined and inattentive adhd presentations
Authors: Saad Jacqueline F. , Griffiths Kristi R. , Kohn Michael R. , Braund Taylor A , Clarke Simon , Williams Leanne M. , Korgaonkar Mayuresh S.
Published: December 2020

Evidence from functional neuroimaging studies support neural differences between the Attention Deficit Hyperactivity Disorder (ADHD) presentation types. It remains unclear if these neural deficits also manifest at the structural level. We have previously shown that the ADHD combined, and ADHD inattentive types demonstrate differences in graph properties of structural covariance suggesting an underlying difference in neuroanatomical organization. The goal of this study was to examine and validate white matter brain organization between the two subtypes using both scalar and connectivity measures of brain white matter. We used both tract-based spatial statistical (TBSS) and tractography analyses with network-based Statistics (NBS) and graph-theoretical analyses in a cohort of 35 ADHD participants (aged 8-17 years) defined using DSM-IV criteria as combined (ADHD-C) type (n=19) or as predominantly inattentive (ADHD-I) type (n=16), and 28 matched neurotypical controls. We performed TBSS analyses on scalar measures of fractional anisotropy (FA), mean (MD), radial (RD), and axial (AD) diffusivity to assess differences in WM between ADHD types and controls. NBS and graph theoretical analysis of whole brain inter-regional tractography examined connectomic differences and brain network organization, respectively. None of the scalar measures significantly differed between ADHD types or relative to controls. Similarly, there were no tractography connectivity differences between the two subtypes and relative to controls using NBS. Global and regional graph measures were also similar between the groups. A single significant finding was observed for nodal degree between the ADHD-C and controls, in the right insula (corrected p=.029). Our result of no white matter differences between the subtypes is consistent with most previous findings. These findings together might suggest that the white matter structural architecture is largely similar between the DSM-based ADHD presentations.
Experimental warming influences species abundances in aDrosophilahost community through direct effects on species performance rather than altered competition and parasitism
Authors: Thierry Mélanie , Pardikes Nicholas A. , Lue Chia-Hua , Lewis Owen T. , Hrček Jan
Published: December 2020

Current global warming trends are expected to have direct effects on species through their sensitivity to temperature, as well as on their biotic interactions, with cascading indirect effects on species, communities, and entire ecosystems. To predict the community-level consequences of global change we need to understand the relative roles of both the direct and indirect effects of warming. We used a laboratory experiment to investigate how warming affects a tropical community of three species ofDrosophilahosts interacting with two species of parasitoids over a single generation. Our experimental design allowed us to distinguish between the direct effects of temperature on host species performance, and indirect effects through altered biotic interactions (competition among hosts and parasitism by parasitoid wasps). Although experimental warming significantly decreased parasitism for all host-parasitoid pairs, the effects of parasitism and competition on host communities did not vary across temperatures. Instead, effects on host relative abundances were species-specific, with one host species dominating the community at warmer temperatures, independently of parasitism and competition treatments. Our results show that temperature shaped aDrosophilahost community directly through differences in species’ thermal performance, and not via its influences on biotic interactions.
Dissecting human skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses
Authors: He Jian , Yan Jing , Wang Jianfang , Zhao Liangyu , Xin Qian , Zeng Yang , Sun Yuxi , Zhang Han , Bai Zhijie , Li Zongcheng , Ni Yanli , Gong Yandong , Li Yunqiao , He Han , Bian Zhilei , Lan Yu , Ma Chunyu , Bian Lihong , Zhu Heng , Liu Bing , Yue Rui
Published: December 2020

Human skeletal stem cells (SSCs) have been discovered in fetal and adult bones. However, the spatiotemporal ontogeny of human SSCs during embryogenesis has been elusive. Here we map the transcriptional landscape of human embryonic skeletogenesis at single-cell resolution to address this fundamental question. We found remarkable heterogeneity within human limb bud mesenchyme and epithelium, as well as the earliest osteo-chondrogenic progenitors. Importantly, embryonic SSCs (eSSCs) were found in the perichondrium of human long bones, which self-renew and generate osteochondral lineage cells, but not adipocytes or hematopoietic stroma. eSSCs are marked by the adhesion molecule CADM1 and highly enrich FOXP1/2 transcriptional network. Interestingly, neural crest-derived cells with similar phenotypic markers and transcriptional network were also found in the sagittal suture of human embryonic calvaria. Taken together, this study revealed the cellular heterogeneity and lineage hierarchy during human embryonic skeletogenesis, and identified distinct skeletal stem/progenitor cells that orchestrate endochondral and intramembranous ossification.
A WDR35-dependent coatomer transports ciliary membrane proteins from the Golgi to the cilia
Authors: Quidwai Tooba , Hall Emma A. , Keighren Margaret A. , Leng Weihua , Kiesel Petra , Wells Jonathan N. , Murphy Laura C. , Marsh Joseph A. , Pigino Gaia , Mill Pleasantine
Published: December 2020

Intraflagellar transport (IFT) is a highly conserved mechanism for motor-driven transport of cargo within cilia, but how this cargo is selectively transported to cilia and across the diffusion barrier is unclear. WDR35/IFT121 is a component of the IFT-A complex best known for its role in ciliary retrograde transport. In the absence of WDR35, small mutant cilia form but fail to enrich in diverse classes of ciliary membrane proteins. InWdr35mouse mutants, the IFT-A peripheral components are degraded and core components accumulate at the transition zone. We reveal deep sequence homology and structural similarity of WDR35 and other IFT-As to the coatomer COPI proteinsaandβ′, and demonstrate an accumulation of ‘coat-less’ vesicles which fail to fuse withWdr35mutant cilia. Our data provides the firstin situevidence of a novel coatomer function for WDR35 likely with other IFT-A proteins in delivering ciliary membrane cargo from the Golgi necessary for cilia elongation.
CRISPR-based functional genomics in human dendritic cells
Authors: Jost Marco , Jacobson Amy N. , Hussmann Jeffrey A. , Cirolia Giana , Fischbach Michael A. , Weissman Jonathan S.
Published: December 2020

Dendritic cells (DCs) regulate processes ranging from antitumor and antiviral immunity to host-microbe communication at mucosal surfaces. It remains difficult, however, to genetically manipulate human DCs, limiting our ability to probe how DCs elicit specific immune responses. Here, we develop a CRISPR/Cas9 genome editing method for human monocyte-derived DCs (moDCs) that mediates knockouts with a median efficiency of >93% across >300 genes. Using this method, we perform genetic screens in moDCs, identifying mechanisms by which DCs tune responses to lipopolysaccharides from the human microbiome. In addition, we reveal donor-specific responses to lipopolysaccharides, underscoring the importance of assessing immune phenotypes in donor-derived cells, and identify genes that control this specificity, highlighting the potential of our method to pinpoint determinants of inter-individual variation in immune responses. Our work sets the stage for a systematic dissection of the immune signaling at the host-microbiome interface and for targeted engineering of DCs for neoantigen vaccination.
Atomic Force Microscopy Reveals Distinct Protofilament-scale Structural Dynamics in Depolymerizing Microtubule Arrays
Authors: Wijeratne Sithara S. , Marchan Michelle F. , Tresback Jason S. , Subramanian Radhika
Published: December 2020

The dynamic reorganization of microtubule-based cellular structures, such as the spindle and the axoneme, fundamentally depends on the dynamics of individual polymers within multimicrotubule arrays. A major class of enzymes, implicated in both the complete demolition and fine size control of microtubule-based arrays, are depolymerizing kinesins. How different depolymerases differently remodel microtubule arrays is poorly understood. A major technical challenge in addressing this question is that existing optical or electron-microscopy methods lack the spatial-temporal resolution to observe the dynamics of individual microtubules within larger arrays. Here we use Atomic Force Microscopy (AFM) to image depolymerizing arrays at single microtubule and protofilament resolution. We discover previously unseen modes of microtubule array destabilization by conserved depolymerases. We find that the kinesin-13 MCAK mediates asynchronous protofilament depolymerization and lattice-defect propagation, whereas the kinesin-8 Kip3p promotes synchronous protofilament depolymerization. Unexpectedly, MCAK can depolymerize the highly stable axonemal doublets, but Kip3p cannot. We propose that distinct protofilament-level activities underlie the functional dichotomy of depolymerases, resulting in either large-scale destabilization or length regulation of microtubule arrays. Our work establishes AFM as a powerful strategy to visualize microtubule dynamics within arrays and reveals how nanometer-scale substrate specificity leads to differential remodeling of micron-sized cytoskeletal structures.

SIGNIFICANCE STATEMENT

One cannot help but marvel at the precise organization of microtubule polymers in cellular structures such as the axoneme and the spindle. However, our understanding of the biochemical mechanisms that sculpt these arrays comes largely from in vitro experiments with a small number (one or two) of microtubules. This is somewhat akin to studying the architecture of multilane highways by studying one-lane streets. Here we directly visualize depolymerizing microtubule arrays at individual microtubule and protofilament resolution using Atomic Force Microscopy. Our results reveal differences in microtubule depolymerase activity and provide insights into how these differences in enzymatic activity on the nanometer scale can result in the differential remodeling of multi-microtubule arrays on the micron-length scale.
Identifying and testing marker-trait associations for growth and phenology in three pine species: implications for genomic prediction
Authors: Perry Annika , Wachowiak Witold , Beaton Joan , Iason Glenn , Cottrell Joan , Cavers Stephen
Published: December 2020

In tree species, genomic prediction offers the potential to forecast mature trait values in early growth stages, if robust marker-trait associations can be identified. Here we apply a novel multispecies approach using genotypes from a new genotyping array, based on 20,795 SNPs from three closely related pine species (Pinus sylvestris, Pinus uncinataandPinus mugo), to test for associations with growth and phenology data from a common garden study. Predictive models constructed using significantly associated SNPs were then tested and applied to an independent multisite field trial ofP. sylvestrisand the capability to predict trait values was evaluated. One hundred and eighteen SNPs showed significant associations with the traits in the pine species. Common SNPs (MAF > 0.05) associated with bud set were only found in genes putatively involved in growth and development, whereas those associated with growth and budburst were also located in genes putatively involved in response to environment and, to a lesser extent, reproduction. At one of the two independent sites, the model we developed produced highly significant correlations between predicted values and observed height data (YA, height 2020: r = 0.376,p< 0.001). Predicted values estimated with our budburst model were weakly but positively correlated with duration of budburst at one of the sites (GS, 2015: r = 0.204,p= 0.034; 2018: r = 0.205,p= 0.034-0.037) and negatively associated with budburst timing at the other (YA: r = -0.202,p= 0.046). Genomic prediction resulted in the selection of sets of trees whose mean height was taller than the average for each site. Our results provide tentative support for the capability of prediction models to forecast trait values in trees, while highlighting the need for caution in applying them to trees grown in different environments.