bluuebunny/crossref_metadata_2025 huggingface dataset:
Navigated Spinal Robotics in Minimally Invasive Spine Surgery, With Preoperative and Intraoperative Workflows: 2-Dimensional Operative Video
Authors: Pham Martin H , Osorio Joseph A , Lehman Ronald A
Published: April 2020

The use of robotic guidance for spinal instrumentation has become promising for its ability to offer the advantages of precision, accuracy, and reproducibility. However, the utilization and adoption of robotic platforms for spine surgery remain limited, especially in comparison to other surgical fields. We present here a case of a 52-yr-old man with a grade 1 L4-5 degenerative spondylolisthesis causing severe claudication and radiculopathy who subsequently underwent a minimally invasive L4-5 transforaminal lumbar interbody fusion with navigated spinal robotic assistance (Mazor X Stealth Edition, Mazor Robotics Ltd, Caesarea, Israel). This platform allows for planning and registration via (1) a preoperative thin-cut computed tomography (CT) scan, or (2) an intraoperative CT “scan-and-plan” method. We show here the preoperative CT method that we use in the majority of our patients. To our knowledge, this is the first video demonstrating the preoperative software and intraoperative surgical registration and instrument workflow of navigated spinal robotic guidance using the Mazor X Stealth Edition for the insertion of pedicle screws in a minimally invasive spine surgery procedure.

There is no identifying information in this video. Patient consent was obtained for the surgical procedure and for publishing of the material included in the video.
High-flow nasal cannula implementation has not reduced intubation rates for bronchiolitis in Canada
Authors: Garland Hilarie , Gunz Anna C , Miller Michael R , Lim Rodrick K
Published: April 2020

Background and Objective

Bronchiolitis is the most common reason for admission to hospital in the first year of life, with increasing hospitalization rates in Canada. Respiratory support with high-flow nasal cannula (HFNC) is being routinely used in paediatric centres, though the evidence of efficacy is continuing to be evaluated. We examined the impact of HFNC on intubation rates, hospital and paediatric critical care unit (PCCU) length of stay (LOS), and PCCU admission rates in paediatric tertiary centres in Canada.

Methods

We conducted a multicentre, interrupted time series analysis to examine intubation rates pre- to postimplementation of HFNC for bronchiolitis. Data were obtained from the Canadian Institute for Health Information database. Paediatric tertiary centres that introduced HFNC between 2009 and 2014 were included, and data were collected from April 2005 to March 2017.

Results

A total of 17,643 patients met inclusion criteria. There was no significant change in intubation rates after the introduction of HFNC. There was a significant increase in PCCU admission, with a decrease in the PCCU LOS following the introduction of HFNC. There was no significant change in average hospital LOS after HFNC was introduced.

Conclusions

This study adds to the evolving evidence showing that overall disease course is not modified by the use of HFNC. The initiation of HFNC in Canadian paediatric centres resulted in no significant change in intubation rates or average LOS in hospital, but had an increase in PCCU admissions. Careful monitoring of new technologies on their clinical impact as well as health care resource utilization is warranted.
Development and initial validation of a composite disease activity score for systemic juvenile idiopathic arthritis
Authors: Tibaldi Jessica , Pistorio Angela , Aldera Elena , Puzone Laura , El Miedany Yasser , Pal Priyankar , Giri Prabhas Prasun , De Hriday , Khubchandani Raju , Chavan Pallavi Pimpale , Vilaiyuk Soamarat , Lerkvaleekul Butsabong , Yamsuwan Jutamas , Sabui Tapas K , Datta Pragati , Pardeo Manuela , Bracaglia Claudia , Sawhney Sujata , Mittal Sumidha , Hassan Waleed A , Elderiny Ghada Farouk , Abu-Zaid Mohammed Hassan , Eissa Mervat , Sztajnbok Flavio , das Neves Sztajnbok Fernanda C , Russo Ricardo , Katsicas María Martha , Cimaz Rolando , Marrani Edoardo , Alexeeva Ekaterina , Dvoryakovskaya Tatyana M , Alsuweiti Motasem O , Alzyoud Ra’ed M , Kostik Mikhail , Chikova Irina , Minoia Francesca , Filocamo Giovanni , Farag Yomna , Lotfy Hala , Nasef Samah Ismail , Al-Mayouf Sulaiman M , Maggio Maria Cristina , Magalhaes Claudia Saad , Gallizzi Romina , Conti Giovanni , Shimizu Masaki , Civino Adele , Felici Enrico , Giancane Gabriella , Ruperto Nicolino , Consolaro Alessandro , Ravelli Angelo
Published: April 2020

Objective

To develop a composite disease activity score for systemic JIA (sJIA) and to provide preliminary evidence of its validity.

Methods

The systemic Juvenile Arthritis Disease Activity Score (sJADAS) was constructed by adding to the four items of the original JADAS a fifth item that aimed to quantify the activity of systemic features. Validation analyses were conducted on patients with definite or probable/possible sJIA enrolled at first visit or at the time of a flare, who had active systemic manifestations, which should include fever. Patients were reassessed 2 weeks to 3 months after baseline. Three versions were examined, including ESR, CRP or no acute-phase reactant.

Results

A total of 163 patients were included at 30 centres in 10 countries. The sJADAS was found to be feasible and to possess face and content validity, good construct validity, satisfactory internal consistency (Cronbach’s alpha 0.64–0.65), fair ability to discriminate between patients with different disease activity states and between those whose parents were satisfied or not satisfied with illness outcome (P < 0.0001 for both), and strong responsiveness to change over time (standardized response mean 2.04–2.58). Overall, these properties were found to be better than those of the original JADAS and of DAS for RA and of Puchot score for adult-onset Still’s disease.

Conclusion

The sJADAS showed good measurement properties and is therefore a valid instrument for the assessment of disease activity in children with sJIA. The performance of the new tool should be further examined in other patient cohorts that are evaluated prospectively.
Determining the Profitability of Reniform Nematode Control Practices in the Mississippi Cotton Production System
Authors: Wilson Bradley R. , Allen Thomas W. , Catchot Angus L. , Krutz L. Jason , Dodds Darrin M.
Published: April 2020

The reniform nematode, Rotylenchulus reniformis, can be damaging in silt loam soils that have predominantly supported cotton (Gossypium hirsutum L.) production in the Mid-Southern United States. The objective of this research was to determine the profitability of integrated nematode management options in Mississippi cotton production in soils naturally infested with the reniform nematode. Experiments were conducted near Hamilton, MS, in 2016 and Oswego and Tchula, MS, in 2017. Commercially available seed treatments included a base seed treatment of azoxystrobin + fludioxonil + mefenoxam and seed-applied nematicides including thiodicarb + imidacloprid and fluopyram. In-furrow nematicides included aldicarb and fluopyram + imidacloprid. Lastly, 1,3-dichloropropene was applied preplant to soil followed by cotton seed with and without treatment. Cotton yield was 40 kg/ha greater when 1,3-dichloropropene was applied, and a base fungicide seed treatment was utilized compared with the base seed treatment alone. Cotton yield was at least 73 kg/ha greater when the base seed treatment was followed by aldicarb or fluopyram + imidacloprid in-furrow compared with seed treatments alone. Economic analyses suggested that seed treatment and in-furrow nematicides without 1,3-dichloropropene provided the greatest return on investment.
Modelling the impact of antibody-dependent enhancement on disease severity of Zika virus and dengue virus sequential and co-infection
Authors: Tang Biao , Xiao Yanni , Sander Beate , Kulkarni Manisha A. , RADAM-LAC Research Team  , Wu Jianhong
Published: April 2020

Human infections with viruses of the genus
Flavivirus
, including dengue virus (DENV) and Zika virus (ZIKV), are of increasing global importance. Owing to antibody-dependent enhancement (ADE), secondary infection with one
Flavivirus
following primary infection with another
Flavivirus
can result in a significantly larger peak viral load with a much higher risk of severe disease. Although several mathematical models have been developed to quantify the virus dynamics in the primary and secondary infections of DENV, little progress has been made regarding secondary infection of DENV after a primary infection of ZIKV, or DENV-ZIKV co-infection. Here, we address this critical gap by developing compartmental models of virus dynamics. We first fitted the models to published data on dengue viral loads of the primary and secondary infections with the observation that the primary infection reaches its peak much more gradually than the secondary infection. We then quantitatively show that ADE is the key factor determining a sharp increase/decrease of viral load near the peak time in the secondary infection. In comparison, our simulations of DENV and ZIKV co-infection (simultaneous rather than sequential) show that ADE has very limited influence on the peak DENV viral load. This indicates pre-existing immunity to ZIKV is the determinant of a high level of ADE effect. Our numerical simulations show that (i) in the absence of ADE effect, a subsequent co-infection is beneficial to the second virus; and (ii) if ADE is feasible, then a subsequent co-infection can induce greater damage to the host with a higher peak viral load and a much earlier peak time for the second virus, and for the second peak for the first virus.
Entropic bonding of the type 1 pilus from experiment and simulation
Authors: Corsetti Fabiano , Alonso-Caballero Alvaro , Poly Simon , Perez-Jimenez Raul , Artacho Emilio
Published: April 2020

The type 1 pilus is a bacterial filament consisting of a long coiled proteic chain of subunits joined together by non-covalent bonding between complementing

β

-strands. Its strength and structural stability are critical for its anchoring function in uropathogenic
Escherichia coli
bacteria. The pulling and unravelling of the FimG subunit of the pilus was recently studied by atomic force microscopy experiments and steered molecular dynamics simulations (Alonso-Caballero
et al.
2018
Nat. Commun
.
9
, 2758. (doi:10.1038/s41467-018-05107-6)). In this work, we perform a quantitative comparison between experiment and simulation, showing a good agreement in the underlying work values for the unfolding. The simulation results are then used to estimate the free energy difference for the detachment of FimG from the complementing strand of the neighbouring subunit in the chain, FimF. Finally, we show that the large free energy difference for the unravelling and detachment of the subunits which leads to the high stability of the chain is entirely entropic in nature.
Morphological diversification has led to inter-specific variation in elastic wing deformation during flight in scarab beetles
Authors: Meresman Y. , Husak J. F. , Ben-Shlomo R. , Ribak G.
Published: April 2020

Insect wing shapes and the internal wing-vein arrangement are remarkably diverse. Although the wings lack intrinsic musculature to adjust shape actively, they elastically deform due to aerodynamic and inertial loads during flapping. In turn, the deformations alter the shape of the wing profile affecting the aerodynamic force. To determine how changes in wing-vein arrangement affect elastic wing deformation during free flight, we compared elastic wing deformations between free-flying rose chafers (Protaetia cuprea) and dung beetles (Scarabaeus puncticollis), complementing the comparison with wing static bending measurements. The broader relevance of the results to scarab beetle divergence was examined in a geometric morphometric (GM) analysis of wing-vein arrangement in 20 species differing in phylogeny and ecology. Despite rose chafers and dung beetles demonstrating similar flapping kinematics and wing size, the rose chafer wings undergo greater elastic deformation during flapping. GM analyses corrected for phylogenetic relatedness revealed that the two beetles represent extremes in wing morphology among the scarab subfamilies. Most of the differences occur at the distal leading edge and the proximal trailing edge of the wing, diversifying the flexibility of these regions, thereby changing the pattern of elastic wing deformation during flapping. Changes to local wing compliance seem to be associated with the diversification of scarab beetles to different food sources, perhaps as an adaptation to meet the demands of diverse flight styles.
Radiation of tropical island bees and the role of phylogenetic niche conservatism as an important driver of biodiversity
Authors: Dorey James B. , Groom Scott V. C. , Freedman Elisha H. , Matthews Cale S. , Davies Olivia K. , Deans Ella J. , Rebola Celina , Stevens Mark I. , Lee Michael S. Y. , Schwarz Michael P.
Published: April 2020

Island biogeography explores how biodiversity in island ecosystems arises and is maintained. The topographical complexity of islands can drive speciation by providing a diversity of niches that promote adaptive radiation and speciation. However, recent studies have argued that phylogenetic niche conservatism, combined with topographical complexity and climate change, could also promote speciation if populations are episodically fragmented into climate refugia that enable allopatric speciation. Adaptive radiation and phylogenetic niche conservatism therefore both predict that topographical complexity should encourage speciation, but they differ strongly in their inferred mechanisms. Using genetic (mitochondrial DNA (mtDNA) and single-nucleotide polymorphism (SNP)) and morphological data, we show high species diversity (22 species) in an endemic clade of Fijian
Homalictus
bees, with most species restricted to highlands and frequently exhibiting narrow geographical ranges. Our results indicate that elevational niches have been conserved across most speciation events, contradicting expectations from an adaptive radiation model but concordant with phylogenetic niche conservatism. Climate cycles, topographical complexity, and niche conservatism could interact to shape island biodiversity. We argue that phylogenetic niche conservatism is an important driver of tropical island bee biodiversity but that this phylogenetic inertia also leads to major extinction risks for tropical ectotherms under future warming climates.
Bacterial community richness shifts the balance between volatile organic compound-mediated microbe–pathogen and microbe–plant interactions
Authors: Raza Waseem , Wang Jianing , Jousset Alexandre , Friman Ville-Petri , Mei Xinlan , Wang Shimei , Wei Zhong , Shen Qirong
Published: April 2020

Even though bacteria are important in determining plant growth and health via volatile organic compounds (VOCs), it is unclear how these beneficial effects emerge in multi-species microbiomes. Here we studied this using a model plant–bacteria system, where we manipulated bacterial community richness and composition and determined the subsequent effects on VOC production and VOC-mediated pathogen suppression and plant growth-promotion. We assembled VOC-producing bacterial communities in different richness levels ranging from one to 12 strains using three soil-dwelling bacterial genera (
Bacillus
,
Paenibacillus
and
Pseudomonas
) and investigated how the composition and richness of bacterial community affect the production and functioning of VOCs. We found that VOC production correlated positively with pathogen suppression and plant growth promotion and that all bacteria produced a diverse set of VOCs. However, while pathogen suppression was maximized at intermediate community richness levels when the relative amount and the number of VOCs were the highest, plant growth promotion was maximized at low richness levels and was only affected by the relative amount of plant growth-promoting VOCs. The contrasting effects of richness could be explained by differences in the amount and number of produced VOCs and by opposing effects of community productivity and evenness on pathogen suppression and plant-growth promotion along the richness gradient. Together, these results suggest that the number of interacting bacterial species and the structure of the rhizosphere microbiome drive the balance between VOC-mediated microbe–pathogen and microbe–plant interactions potentially affecting plant disease outcomes in natural and agricultural ecosystems.
Paenibacillus solisilvae sp. nov., isolated from birch forest soil
Authors: Kong Delong , Zhang Qi , Jiang Xu , Ma Qingyun , Han Xiaoyan , Zhou Yiqing , Xue Huiying , Zhang Yuqin , Zhang Wei , Ruan Zhiyong
Published: April 2020

A Gram-stain-positive, motile, rod-shaped bacterium, designated strain LAM7113T, was isolated from soil sample collected from a birch forest in Xinjiang Uygur Autonomous Region, PR China. Strain LAM7113T grew optimally at pH 8.0, 30 °C and in the presence of 1.0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LAM7113T was closely related to members of the genus

Paenibacillus

, with the highest similarity to

Paenibacillus baekrokdamisoli

Back-11T (96.2 %). The genomic DNA G+C content was 43.4 mol%. The values of average nucleotide identity and DNA–DNA hybridization were 66.1 and 27.0 %, respectively, by comparing the draft genome sequences of strain LAM7113T and

P. baekrokdamisoli

Back-11T. Anteiso-C15 : 0 and iso-C15 : 0 were identified as the major cellular fatty acids. Menaquinone-7 was detected as the predominant respiratory quinone. The major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, three unidentified aminophospholipids, three unidentified glycolipids, one unidentified phospholipid and two unknown polar lipids. Based on its phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM7113T is proposed to represent a novel species of the genus

Paenibacillus

with the name Paenibacillus solisilvae sp. nov. The type strain is LAM7113T (=CGMCC 1.16619T=JCM 32513T).
Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity
Authors: Jia Yong , Shen Gangxu , Nguyen Stephanie , Zhang Yujuan , Huang Keng-Shiang , Ho Hsing-Ying , Hor Wei-Shio , Yang Chih-Hui , Bruning John B , Li Chengdao , Wang Wei-Lung
Published: April 2020

Monitoring the mutation dynamics of SARS-CoV-2 is critical for the development of effective approaches to contain the pathogen. By analyzing 106 SARS-CoV-2 and 39 SARS genome sequences, we provided direct genetic evidence that SARS-CoV-2 has a much lower mutation rate than SARS. Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history. The discrepant phylogenies for the spike protein and its receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARS-CoV-2. Despite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a receptor binding domain mutation that leads to weaker ACE2 binding capability based on in silico simulation, which concerns a SARS-CoV-2 sample collected on 27thJanuary 2020 from India. This represents the first report of a significant SARS-CoV-2 mutant, and requires attention from researchers working on vaccine development around the world.

Highlights

Based on the currently available genome sequence data, we provided direct genetic evidence that the SARS-COV-2 genome has a much lower mutation rate and genetic diversity than SARS during the 2002-2003 outbreak.

The spike (S) protein encoding gene of SARS-COV-2 is found relatively more conserved than other protein-encoding genes, which is a good indication for the ongoing antiviral drug and vaccine development.

Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history.

We confirmed a previously reported rearrangement in the S protein arrangement of SARS-COV-2, and propose that this rearrangement should have occurred between human SARS-CoV and a bat SARS-CoV, at a time point much earlier before SARS-COV-2 transmission to human.

We provided first evidence that a mutated SARS-COV-2 with reduced human ACE2 receptor binding affinity have emerged in India based on a sample collected on 27th January 2020.
Safety of Focused Ultrasound Neuromodulation in Humans with Temporal Lobe Epilepsy
Authors: Stern John M. , Korb Alexander S. , Spivak Norman M. , Becerra Sergio , Kronemyer David , Khanlou Négar , Reyes Samuel D. , Monti Martin M. , Schnakers Caroline , Walshaw Patricia , Kuhn Taylor P. , Cohen Mark S. , Yong William , Fried Itzhak , Jordan Sheldon E. , Engel Jerome , Schafer Mark E. , Bystritsky Alexander
Published: April 2020

Objective

Low-Intensity Focused Ultrasound Pulsations (LIFUP) is a promising new potential neuromodulation tool. However, the safety of LIFUP neuromodulation has not yet been adequately assessed. Patients with refractory temporal lobe epilepsy electing to undergo an anterior temporal lobe resection present a unique opportunity to evaluate the safety and efficacy of LIFUP neuromodulation. Because the brain tissue in these patients will be removed, histological changes in tissue after LIFUP can be examined. Evidence of effective neuromodulation was assessed using functional MRI and EEG, while further potential safety concerns were assessed using neuropsychological testing.

Methods

EEG, functional MRI, and neuropsychology were assessed in six patients before and after focused ultrasound sonication of the temporal lobe at intensities up to 5760 mW/cm2. Using the BrainSonix Pulsar 1002, LIFUP was delivered under MR guidance, using the Siemens Magnetom 3T Prisma scanner. Neuropsychological changes were assessed using various batteries. EEG was recorded using the Electrical Geodesics EGI 256 channel system. Histological changes were assessed using hematoxylin and eosin staining, among others.

Results

LIFUP was not able to modulate the BOLD signal on fMRI in a reliable and consistent manner. The EEG data that was available did not demonstrate a change in activity after LIFUP in all but one subject. Likewise, the neuropsychology testing did not show any statistically significant changes in any test, except for a slight decrease in performance on the one test after LIFUP. Lastly, the histology did not reveal any detectable damage to the tissue, except for one subject for whom the histology findings were inconclusive.

Significance

The safety in the histology was the primary endpoint, and as such, longer exposure at the highest intensity levels will be administered moving forward.

Key Points

LIFUP is a novel brain stimulation technique with not yet fully established safety guidelines.

LIFUP was administered to patients electing to undergo resective brain surgery.

LIFUP does not appear to cause damage to tissue.

Longer exposure times are needed to further show safety at these intensity levels.
Time-Varying COVID-19 Reproduction Number in the United States
Authors: Gunzler Douglas D. , Sehgal Ashwini R.
Published: April 2020

The basic reproduction number is the average number of people to whom an infected person transmits the infection when virtually all individuals in a population are susceptible. We sought to calculate the current reproduction number for COVID-19 for each state in the United States. For the entire United States, the time-varying reproduction number declined from 4.02 to 1.51 between March 17 and April 1, 2020. We also found that the time-varying reproduction number for COVID-19 has declined in most states over the same two week period which suggests that social isolation measures may be having a beneficial effect.
A systematic review protocol for estimation of the prevalence of depression using diagnostic instruments in the elderly population in India, 2000-2019
Authors: Behera Priyamadhaba , Pilania Manju , Yadav Vikas , Bairwa Mohan , Dabar Deepti , Behera Surama Manjari , Poongothai S. , Mohan Viswanathan , Dutt Gupta Shiv
Published: April 2020

Introduction

Depression is a common mental disorder in the elderly population, which significantly impacts their quality of life. However, correct estimates of its magnitude are not available in the elderly in India. The present systematic review and meta-analysis would attempt to estimate the prevalence of depression using diagnostic instruments among elderly persons aged 60 years and above.

Methods and analysis

Searches will be performed in PubMed, Scopus, Embase, Web of Science, CINAHL, and PsycINFO. Community-based cross-sectional and cohort studies (2001 – 9/2019) reporting the prevalence of depression in the elderly; using diagnostic instruments will be included. Studies conducted among chronic disease patients, in-hospital patients, and special groups such as with disaster-stricken populations, and studies reporting the only 1 or 2 subcategories of depression, will be excluded. Disagreements in study selection and data abstraction will be resolved by consensus and arbitration by a third reviewer. AXIS critical appraisal tool will be used for quality assessment of individual studies. Findings of eligible studies will be pooled using fixed-effects or random-effects meta-analysis whichever is appropriate. Heterogeneity between studies will be examined by Cochran’s Q test and quantified by I2statistic. A cumulative meta-analysis will be used to detect temporal trends in the prevalence of depression and the effect of poor-quality studies on the pooled estimate. Publication bias will be assessed by visual inspection of funnel plots and the Egger test.

Ethics and dissemination

No ethical approval will be needed because it will be a systematic review. Data from previously published studies will be retrieved and analyzed. Findings will be disseminated through a peer-reviewed publication in a scientific journal and conferences.

PROSPERO

registration number CRD42019138453.

Strengths and limitations of this study

It is a first-ever systematic review of depression prevalence in India based on diagnostic instruments only.

Meta-analytic techniques such as cumulative meta-analysis, leave-one-out (jack-knife estimation) meta-analysis, and meta-regression will enrich the analysis and provide the estimate of prevalence nearer to the population estimate.

A comprehensive synthesis of all available depression prevalence data in India using a standardized risk of bias tool.

The protocol adheres to Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols guidelines.

Heterogeneity in methodologies, such as diagnostic criteria, study duration, sampling design, and study locations may limit comparison across studies.
Rapid Utilization of Telehealth in a Comprehensive Cancer Center as a Response to COVID-19
Authors: Lonergan Peter E. , Washington Samuel L. , Branagan Linda , Gleason Nathaniel , Pruthi Raj S. , Carroll Peter R. , Odisho Anobel Y.
Published: April 2020

Background

The emergence of the coronavirus disease 2019 (COVID-19) pandemic in March 2020 created unprecedented challenges in the provision of scheduled ambulatory cancer care. As a result, there has been a renewed focus on video consultations as a means to continue ambulatory care.

Objective

To analyze the change in video visit volume at the University of California, San Francisco (UCSF) Comprehensive Cancer Center in response to COVID-19 and compare demographics/appointment data from January 1, 2020 and in the 11 weeks after transition to video visits.

Methods

Patient demographics and appointment data (dates, visit types, and departments) were abstracted from the Electronic Health Record reporting database. Video visits were performed using a HIPAA-compliant video conferencing platform with a pre-existing workflow.

Results

In 17 departments and divisions at the UCSF Cancer Center, 2,284 video visits were performed in the 11 weeks before COVID-19 changes with an average (SD) of 208 (75) per week and 12,946 video visits were performed in the 11 week post-COVID-19 period with an average (SD) of 1,177 (120) per week. The proportion of video visits increased from 7-18% to 54-72%, between the pre- and post-COVID-19 periods without any disparity based on race/ethnicity, primary language, or payor.

Conclusions

In a remarkably brief period of time, we rapidly scaled the utilization of telehealth in response to COVID-19 and maintained access to complex oncologic care at a time of social distancing.
Modifying reusable elastomeric respirators to utilise breathing system filters with 3D printed adapters, a safe alternative to N95 during COVID-19
Authors: Liu D.C.Y. , Koo T.H. , Wong J.K.K. , Wong Y.H. , Fung K.S.C. , Chan Y. , Lim H.S.
Published: April 2020

The COVID-19 pandemic has caused a worldwide shortage of personal protective equipment including N95 and FFP3 respirators. Reusable elastomeric respirators are suitable alternatives when used with compatible filters. These filters may be difficult to source and elastomeric respirators are not recommended for surgical use as the exhaled air is not filtered. Breathing system filters are routinely used in anaesthetic circuits to filter virus and bacteria. In this study, we designed 3D printed adapters that allowed elastomeric respirators to utilise breathing system filters and made simple modifications to the respirators to filter exhaled breaths. We then evaluated the performance and safety of our modified elastomeric respirators with quantitative fit tests.

We recruited 8 volunteers to perform quantitative fit tests. Fit factors, respiratory rate and end-tidal carbon dioxide were recorded before and after wearing the modified respirators for 1 hour. All 8 volunteers obtained fit factors of 200+, the maximum achievable, for all tests exercises in all fit tests. The mean (range) end-tidal carbon dioxide was 4.5 (3.9-5.5) kPa and 4.6 (range 4.1-5.3) kPa before and after 1 hour of usage. The mean (range) respiratory rate was 16.5 (11-24) min-1and 17.4 (15-22) min-1before and after 1 hour of usage. Four (50%) did not experience any subjective discomfort while 2 (25%) reported pressure on the face, 1 (12.5%) reported exhalation resistance and 1 (12.5%) reported transient dizziness with exertion. Breathing system filters combined with properly fitted reusable elastomeric respirators is a safe alternative to N95 during the COVID-19 pandemic.
Covid-19 clinical data analysis using Ball Mapper
Authors: Dlotko Pawel , Rudkin Simon
Published: April 2020

In this note we provide a result of analysis of blood test data from patients with SARS-Cov-2 using Ball Mapper Algorithm. We observe that patients with the virus and in particularly patients who end up in Intensive Care Unit have quite narrow values of those parameters. Please note that this is a preliminary work and it need to be validated on much larger dataset which we are trying to acquire at the moment.
Hospitalization time and outcome in patients with Coronavirus Disease 2019 (COVID-19): analysis data from China
Authors: Chai Songshan , Xiao Dongdong , Cheng Qikai , Huang Shengzhi , Wang Yihao , Qian Jiajia , Wang Jiajing , Li Junjun , Fu Peng , Wang Qiangping , Rao Jing , Zhao Hongyang , Zhang Fangcheng , Xiong Nanxiang
Published: April 2020

Objective

The mean hospitalization time and outcome among patients with coronavirus disease 2019 (COVID-19) was estimated with the purpose of providing evidence for decision-making in medical institutions and governments in epidemic areas.

Method

The data of COVID-19 patients in china were collected from the websites of provincial and municipal health commissions. The mean hospitalization time and mortality in the mild or severe patients and the mean time from severe to mild illness were calculated by Gaussian mixture modeling.

Results

The mean hospitalization time among mild patients in Hubei province, other areas except Hubei province, and the national areas was 20.71± 9.30, 16.86 ± 8.24, and 19.34 ± 9.29 days, respectively. The mean transition time from severe to mild group in the above three areas were 15.00, 17.00, and 14.99 days, respectively. The death rate of mild and severe patients in Hubei province and the national areas were 1.10% and 18.14%, and 1.10% and 17.70%, respectively. Among those patients who died of COVID-19, the mean time from severe transition to death in Hubei province and the national areas was 6.22 ± 5.12 and 6.35 ± 5.27 days, respectively.

Conclusion

There were regional differences in the average length of stay between Hubei province and other regions, which may be related to different medical configurations. For those severe patients who died of COVID-19, the average time from hospitalization to death was about one week, and proper and effective treatments in the first week were critical.
A High-Coverage SARS-CoV-2 Genome Sequence Acquired by Target Capture Sequencing
Authors: Wen Shaoqing , Sun Chang , Zheng Huanying , Wang Ling-xiang , Zhang Huan , Zou Lirong , Liu Zhe , Du Pan-xin , Liang Lijun , Peng Xiaofang , Zhang Wei , Wu Jie , Lei Bo , Ke Changwen , Chen Fang , Zhang Xiao
Published: April 2020

This manuscript is based on the method we developed urgently to deal with the research requirement in the conflict between achieving a complete genome sequence for the evolutionary history of SARS-CoV-2 study and the low viral RNA concentration. Here, in this manuscript, we developed a set of SARS-CoV-2 enrichment probes to increase the sensitivity of sequence-based virus detection and characterization via obtaining the comprehensive genome sequence. Following the CDC health and safety guidelines, we test the concept using the culturing supernatant contain SARS-CoV-2 particles, and its full-length sequence was used for further analysis. The fraction of SARS-CoV-2 endogenous DNA was 93.47% with Cluster Factor about 1.1, which demonstrate that the numbers of mapped reads to SARS-CoV-2 reference sequence significantly increased, compared to metagenomic sequencing technology, following SARS-CoV-2 probe enrichment. Moreover, based on the high-quality sequence, we discussed the heterozygosity and viral expression during replication of coronavirus, and its phylogenetic relationship with other selected high-quality samples from The Genome Variation Map (GVM) (on 2020/03/22). We believe this manuscript is valuable for all the researchers who are interested in using clinical warp samples to obtain the high coverage of SARS-CoV-2 genome sequence with a relatively low concentration of viral particles. This would allow the clinician to correlate the diagnostic data with molecular monitoring in viral evolutional, the most importantly, to track the functional mutation of SARS-CoV-2.
Surveillance by age-class and prefecture for emerging infectious febrile diseases with respiratory symptoms, including COVID-19
Authors: Ueno Tomoaki , Kurita Junko , Sugawara Tamie , Sugishita Yoshiyuki , Ohkusa Yasushi , Kawanohara Hirokazu , Kamei Miwako
Published: April 2020

Object

The COVID-19 outbreak emerged in late 2019 in China, expanding rapidly thereafter. Even in Japan, epidemiological linkage of transmission was probably lost already by February 18, 2020. From that time, it has been necessary to detect clusters using syndromic surveillance.

Method

We identified common symptoms of COVID-19 as fever and respiratory symptoms. Therefore, we constructed a model to predict the number of patients with antipyretic analgesics (AP) and multi-ingredient cold medications (MIC) controlling well-known pediatric infectious diseases including influenza or RS virus infection. To do so, we used the National Official Sentinel Surveillance for Infectious Diseases (NOSSID), even though NOSSID data are weekly data with 10 day delays, on average. The probability of a cluster with unknown febrile disease with respiratory symptoms is a product of the probabilities of aberrations in AP and MIC, which is defined as one minus the probability of the number of patients prescribed a certain type of drug in PS compared to the number predicted using a model. This analysis was conducted prospectively in 2020 using data from October 1, 2010 through 2019 by prefecture and by age-class.

Results

The probability of unknown febrile disease with respiratory symptom cluster was estimated as less than 60% in 2020.

Discussion

The most severe limitation of the present study is that the proposed model cannot be validated. A large outbreak of an unknown febrile disease with respiratory symptoms must be experienced, at which time, practitioners will have to “wing it”. We expect that no actual cluster of unknown febrile disease with respiratory symptoms will occur, but if it should occur, we hope to detect it.
Rapid prototyping and clinical testing of a reusable face shield for health care workers responding to the COVID-19 pandemic
Authors: Mostaghimi Arash , Antonini M.-J. , Plana Deborah , Anderson Philip D. , Beller Brandon , Boyer Edward W. , Fannin Amber , Freake Jacob , Oakley Richard , Sinha Michael S. , Smith Leanne , Van Christopher , Yang Helen , Sorger Peter K. , LeBoeuf Nicole R. , Yu Sherry H.
Published: April 2020

Due to supply chain disruption, the COVID-19 pandemic has caused severe shortages in personal protective equipment (PPE) for health care professionals. Local fabrication based on 3D printing is one way to address this challenge, particularly in the case of simple products such as protective face shields. As a consequence, many public domain designs for face shields have become available. No clear path exists, however, for introducing a locally fabricated and unapproved product into a clinical setting. In a US health care setting, face shields are regulated by the Food and Drug Administration (FDA); similar policies exist in other countries. We describe a research protocol under which rapid iteration on an existing design, coupled with clinical feedback and real-world testing in an emergency department, allowed a face shield to be implemented by the members of the incident command team at a major academic medical center. We describe our design and testing process and provide an overview of regulatory considerations associated with fabrication and testing of face shields and related products. All designs, materials used, testing protocols, and survey results are reported in full to facilitate the execution of similar face shield efforts in other clinical settings. Our work serves as a case study for development of a robust local response to pandemics and other health care emergencies, with implications for healthcare professionals, hospital administrators, regulatory agencies and concerned citizens.
Pregnancy outcomes, Newborn complications and Maternal-Fetal Transmission of SARS-CoV-2 in women with COVID-19: A systematic review of 441 cases
Authors: Gajbhiye Rahul K , Modi Deepak N , Mahale Smita D
Published: April 2020

Objective

The aim of this systematic review was to examine the maternal and fetal outcomes in pregnant women with COVID-19 and also assess the incidence of maternal-fetal transmission of SARS CO-V-2 infection.

Data sources

We searched PUMBED. Medline, Embase, MedRxiv and bioRxiv databases upto 3rdMay 2020 utilizing combinations of word variants for “coronavirus” or “COVID-19” or “severe acute respiratory syndrome” or “SARS-COV-2” and “pregnancy”. We also included data from preprint articles.

Study eligibility criteria

Original case reports and case series on pregnant women with diagnosis of SARS-CoV-2 infection.

Study appraisal and synthesis methods

We included 50 studies reporting the information on 441 pregnant women and 391 neonates. The primary outcome measures were maternal health characteristics and adverse pregnancy outcomes, neonatal outcomes and SARS-CoV-2 infection in neonates was extracted. Treatments given to pregnant women with COVID-19 were also recorded.

Results

Out of 441 women affected by COVID-19 in pregnancy, 387 women have delivered. There are nine maternal deaths reported. In pregnant women with COVID-19, the most common symptoms were fever (56%), cough (43%), myalgia (19%), dyspnea (18%) and diarrhea (6%). Pneumonia was diagnosed by CT scan imaging in 96 % of COVID-19 pregnant women. Pregnancy complications included delivery by cesarean section (80%), preterm labor (26%), fetal distress (8%) and premature rupture of membranes (9%). Six still births (2%) are reported. The most common co-morbidities associated with pregnant women with COVID-19 were hypertensive disorders (10%), diabetes (9%), placental disorders (2%), co-infections (3%), scarred uterus (3%) and hypothyroidism (3%). Amongst the neonates of COVID-19 mothers, preterm birth (25%), respiratory distress syndrome (8%), pneumonia (8%) were reported. There were four neonatal deaths reported. Vertical transmission rate of SARS-CoV-2 is estimated to be 8%.

Conclusion

In pregnant women with COVID-19, hypertensive disorders and diabetes are common comorbidities and there is a risk of preterm delivery and maternal death. Amongst the neonates born to mothers with COVID-19, respiratory distress syndrome and pneumonia are common occurrence. There are reports of still births and neonatal deaths. There is an evidence of vertical transmission of SARS-CoV-2 infection in women with COVID-19.
Discovery of baicalin and baicalein as novel, natural product inhibitors of SARS-CoV-2 3CL proteasein vitro
Authors: Su Haixia , Yao Sheng , Zhao Wenfeng , Li Minjun , Liu Jia , Shang WeiJuan , Xie Hang , Ke Changqiang , Gao Meina , Yu Kunqian , Liu Hong , Shen Jingshan , Tang Wei , Zhang Leike , Zuo Jianping , Jiang Hualiang , Bai Fang , Wu Yan , Ye Yang , Xu Yechun
Published: April 2020

Human infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause coronavirus disease 19 (COVID-19) and there is currently no cure. The 3C-like protease (3CLpro), a highly conserved protease indispensable for replication of coronaviruses, is a promising target for development of broad-spectrum antiviral drugs. To advance the speed of drug discovery and development, we investigated the inhibition of SARS-CoV-2 3CLpro by natural products derived from Chinese traditional medicines. Baicalin and baicalein were identified as the first non-covalent, non-peptidomimetic inhibitors of SARS-CoV-2 3CLpro and exhibited potent antiviral activities in a cell-based system. Remarkably, the binding mode of baicalein with SARS-CoV-2 3CLpro determined by X-ray protein crystallography is distinctly different from those of known inhibitors. Baicalein is perfectly ensconced in the core of the substrate-binding pocket by interacting with two catalytic residues, the crucial S1/S2 subsites and the oxyanion loop, acting as a “shield” in front of the catalytic dyad to prevent the peptide substrate approaching the active site. The simple chemical structure, unique mode of action, and potent antiviral activitiesin vitro, coupled with the favorable safety data from clinical trials, emphasize that baicalein provides a great opportunity for the development of critically needed anti-coronaviral drugs.
Mechanics Of Flight Feathers: Effects Of Captivity?
Authors: Portugal Steven J. , Nudds Robert L. , Green Jonathan A. , Alexander R. McNeil , Butler Patrick J. , Ker Robert F.
Published: April 2020

Feathers act as aerodynamic cantilevers, and to withstand the prolonged cyclical loading that occurs during flight, feathers must be stiff, lightweight and strong. We experimentally tested the differences in feather structure, primarily stiffness and size, between (a) wild and captive Barnacle GeeseBranta leucopsis,and (b) primary feathers dropped during the annual flight feather moult, and those feathers freshly regrown during the moult process. We found that, despite having undergone a 5,000km round-trip migration, flight feathers dropped during moult in the wild geese were stiffer than those measured in the captive geese, both for those dropped during moult and those re-grown. We propose that this may be related to diet or stress in the captive geese.
Identifying flow modules in ecological networks using Infomap
Authors: Farage Carmel , Edler Daniel , Eklöf Anna , Rosvall Martin , Pilosof Shai
Published: April 2020

Analysing how species interact in modules is a fundamental problem in network ecology. Theory shows that a modular network structure can reveal underlying dynamic ecological and evolutionary processes, influence dynamics that operate on the network and affect the stability of the ecological system.

Although many ecological networks describe flows, such as biomass flows in food webs or disease trans-mission, most modularity analyses have ignored network flows, which can hinder our understanding of the interplay between structure and dynamics.

Here we present Infomap, an established method based on network flows to the field of ecological networks. Infomap is a flexible tool that can identify modules in virtually any type of ecological network and is particularly useful for directed, weighted and multilayer networks. We illustrate how Infomap works on all these network types. We also provide a fully documented repository with additional ecological examples. Finally, to help researchers analyse their networks with Infomap, we introduce the open source R package infomapecology.

Analysing flow-based modularity is useful across ecology and transcends to other biological and non-biological disciplines. A dynamic approach for detecting modular structure has strong potential to provide new insights into the organisation of ecological networks.
Triplet-based similarity score for fully multi-labeled trees with poly-occurring labels
Authors: Ciccolella Simone , Bernardini Giulia , Denti Luca , Bonizzoni Paola , Previtali Marco , Della Vedova Gianluca
Published: April 2020

The latest advances in cancer sequencing, and the availability of a wide range of methods to infer the evolutionary history of tumors, have made it important to evaluate, reconcile and cluster different tumor phylogenies.

Recently, several notions of distance or similarities have been proposed in the literature, but none of them has emerged as the golden standard. Moreover, none of the known similarity measures is able to manage mutations occurring multiple times in the tree, a circumstance often occurring in real cases.

To overcome these limitations, in this paper we propose MP3, the first similarity measure for tumor phylogenies able to effectively manage cases where multiple mutations can occur at the same time and mutations can occur multiple times. Moreover, a comparison of MP3 with other measures shows that it is able to classify correctly similar and dissimilar trees, both on simulated and on real data.
Schistosoma mansonieggs modulate the timing of granuloma formation to promote transmission
Authors: Takaki Kevin K. , Rinaldi Gabriel , Berriman Matthew , Pagán Antonio J. , Ramakrishnan Lalita
Published: April 2020

Schistosome eggs provoke the formation of granulomas, organized immune aggregates, around them. For the host, the granulomatous response can be both protective and pathological. Granulomas are also postulated to facilitate egg extrusion through the gut lumen, a necessary step for parasite transmission. We used zebrafish larvae to visualize the granulomatous response toSchistosoma mansonieggs and inert egg-sized beads. Mature eggs rapidly recruit macrophages, which form granulomas within days. Egg-sized inert beads also induce granulomas rapidly, through a foreign body response. Strikingly, immature eggs evade macrophage recruitment altogether, revealing that the eggshell is immunological inert. These findings suggest that the parasite modulates the timing of granuloma formation to its advantage, inhibiting foreign body granuloma formation until it reaches the optimal maturation and location for extrusion. At this point, the parasite secretes specific antigens through the eggshell to trigger granulomas that might facilitate egg extrusion.