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| Open AccessUsing multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data
SARS-CoV-2 genome sequencing data can be used to infer epidemiological parameters, but the impact of the strategy used to select samples on these estimates is rarely considered. Here, the authors produce estimates using different sampling strategies and compare results to those based on case reporting data.
- Rhys P. D. Inward
- , Kris V. Parag
- & Nuno R. Faria
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Article
| Open AccessHousehold transmission of the SARS-CoV-2 Omicron variant in Denmark
In this study, the authors compare the transmission dynamics of the Delta and Omicron SARS-CoV-2 variants using household data from Denmark. They find that Omicron has a higher secondary attack rate, and that the odds of infection with Omicron was higher than with Delta, particularly for vaccinated individuals.
- Frederik Plesner Lyngse
- , Laust Hvas Mortensen
- & Carsten Thure Kirkeby
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Article
| Open AccessTracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA
In this study, the authors develop a method for estimation of SARS-CoV-2 community transmission rates based on a sentinel population of people seeking outpatient testing with recent symptom onset. This method has fewer operational delays than methods based on hospital data, and may be subject to fewer biases.
- Reese Richardson
- , Emile Jorgensen
- & Jaline Gerardin
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Article
| Open AccessSmart soft contact lenses for continuous 24-hour monitoring of intraocular pressure in glaucoma care
Continuous monitoring of intraocular pressure remains a grand challenge in glaucoma care. Here the authors develop smart soft contact lenses for continuous 24-hour monitoring of intraocular pressure in human eyes, even during sleep.
- Jinyuan Zhang
- , Kyunghun Kim
- & Chi Hwan Lee
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Article
| Open AccessA pilot study of neoadjuvant combination of anti-PD-1 camrelizumab and VEGFR2 inhibitor apatinib for locally advanced resectable oral squamous cell carcinoma
In patients with locally advanced resectable oral squamous cell carcinoma (OSCC), the risk of recurrence and metastasis following treatment is high. Here, a phase I clinical trial reports safety and pathological response of neoadjuvant camrelizumab and apatinib in patients with locally advanced resectable OSCC.
- Wu-tong Ju
- , Rong-hui Xia
- & Lai-ping Zhong
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Article
| Open AccessCAR-T cell therapy-related cytokine release syndrome and therapeutic response is modulated by the gut microbiome in hematologic malignancies
The success rate of chimeric antigen receptor T cell therapy is high in blood cancers, yet individual patient characteristics might reduce therapeutic benefit. Here authors show that therapeutic response in multiple myeloma, acute lymphoblastic leukemia and non-Hodgkin lymphoma, and occurrence of severe cytokine release syndrome in multiple myeloma are associated with specific gut microbiome alterations.
- Yongxian Hu
- , Jingjing Li
- & He Huang
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Article
| Open AccessThe impact of repeated rapid test strategies on the effectiveness of at-home antiviral treatments for SARS-CoV-2
Antiviral treatments for SARS-CoV-2 infection are only beneficial when used early in infection, so early case detection is important. Here, the authors assess the frequency of testing needed to achieve population-level benefits and demonstrate the importance of high coverage and short delays from test to treatment.
- Tigist F. Menkir
- & Christl A. Donnelly
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Article
| Open AccessDerivation and validation of an epigenetic frailty risk score in population-based cohorts of older adults
Frailty is associated with an increased risk for negative health outcomes in older populations, and being able to predict frailty could facilitate prevention measures. By performing an epigenome-wide screen, the authors derived a DNA methylation based measure for frailty which can predict both prevalence and longer-term incidence of frailty.
- Xiangwei Li
- , Thomas Delerue
- & Hermann Brenner
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Article
| Open AccessPushing the limits of remote RF sensing by reading lips under the face mask
This study aims to solve the fundamental limitations of camera-based systems by proposing a contactless and privacy-preserving radio frequency-based lip-reading framework, which can recognise lip movements under face masks.
- Hira Hameed
- , Muhammad Usman
- & Qammer H. Abbasi
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Article
| Open AccessGenomic surveillance of SARS-CoV-2 Omicron variants on a university campus
This study presents results from a SARS-CoV-2 genomic surveillance study at a university campus in which ~2,000 samples were sequenced over five months. The authors document the replacement of Delta with Omicron as the dominant variant, and describe clinical characteristics and transmission dynamics.
- Ana A. Weil
- , Kyle G. Luiten
- & Helen Y. Chu
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Article
| Open AccessMsx1+ stem cells recruited by bioactive tissue engineering graft for bone regeneration
Critical-sized bone defects still present clinical challenges. Here the authors show that transplantation of neurotrophic supplement-incorporated hydrogel grafts promote full-thickness regeneration of the calvarium and perform scRNA-seq to reveal contributing stem/progenitor cells, notably a resident Msx1+ skeletal stem cell population.
- Xianzhu Zhang
- , Wei Jiang
- & Hongwei Ouyang
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Article
| Open AccessInterrupted-time-series analysis of the immediate impact of COVID-19 mitigation measures on preterm birth in China
The broader impacts of COVID-19 mitigation measures may include changes in the incidence of preterm birth. Here, the authors use data from ~11.7 million pregnancies in China and find evidence of a small decline in preterm birth rates immediately following the implementation of COVID-19 mitigation measures.
- Yanxia Xie
- , Yi Mu
- & Jun Zhu
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Article
| Open AccessReproducibility of real-world evidence studies using clinical practice data to inform regulatory and coverage decisions
Analyses of real-world evidence from digital clinical practice data provide important insights for healthcare decision makers. Here, authors test reproducibility of 150 peer-reviewed studies, reporting strong reproducibility, which could be further improved through more complete reporting in future original studies
- Shirley V. Wang
- , Sushama Kattinakere Sreedhara
- & Deborah Zarin
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Article
| Open AccessOrganic phosphorescent nanoscintillator for low-dose X-ray-induced photodynamic therapy
Conventional X-ray-induced photodynamic therapy usually requires heavy-metal-containing inorganic scintillators and organic photosensitizers to generate singlet oxygen. Here, the authors develop an organic phosphorescent nanoscintillator for low-dose X-ray-induced photodynamic therapy of deep tumours.
- Xiao Wang
- , Wenjing Sun
- & Wei Huang
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Article
| Open AccessA prospective observational study of post-COVID-19 chronic fatigue syndrome following the first pandemic wave in Germany and biomarkers associated with symptom severity
Some patients experience long-lasting symptoms after coronavirus disease (COVID-19). Here the authors report the clinical and laboratory parameters in patients with post-COVID-19 syndrome from a prospective observational cohort study.
- Claudia Kedor
- , Helma Freitag
- & Carmen Scheibenbogen
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Comment
| Open AccessCall for a unified approach to Monkeypox infection in pregnancy: Lessons from the COVID-19 pandemic
In the current monkeypox outbreak, vaccination and treatment of pregnant women are recommended only if the benefits outweigh risks, but the extremely sparse data available limit evidence-based recommendations. We must facilitate a unified consensus approach to rapidly collect robust data. Two years into the COVID-19 pandemic, monkeypox has emerged as yet another challenge to the mother-fetus dyad, potentially placing both at risk, if exposed.
- Asma Khalil
- , Athina Samara
- & Shamez Ladhani
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Article
| Open AccessIn vivo lentiviral vector gene therapy to cure hereditary tyrosinemia type 1 and prevent development of precancerous and cancerous lesions
Hereditary tyrosinemia type 1 (HT1) is an inborn error of metabolism caused by a deficiency in fumarylacetoacetate hydrolase (FAH). Here, the authors show in an animal model that HT1 can be treated via in vivo portal vein administration of a lentiviral vector carrying the human FAH transgene.
- Clara T. Nicolas
- , Caitlin J. VanLith
- & Joseph B. Lillegard
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Article
| Open AccessInvestigating disparity in access to Australian clinical genetic health services for Aboriginal and Torres Strait Islander people
Globally it is recognised that Indigenous populations should be able to access the benefits of genomics and precision medicine. Here, authors show that there are disparities in access to clinical genetic health services for Aboriginal and/or Torres Strait Islander people in Australia.
- Joanne Luke
- , Philippa Dalach
- & Margaret Kelaher
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Article
| Open AccessMultifunctional nanoparticle potentiates the in situ vaccination effect of radiation therapy and enhances response to immune checkpoint blockade
Radiotherapy can activate an in situ vaccine response and promote response to immune checkpoint inhibitors. Here the authors design a multifunctional nanoparticle to enhance tumor antigen presentation and modulate the tumor immune microenvironment following radiotherapy, showing improved anti-tumor immune responses in radiotherapy-treated tumors when combined with immune checkpoint inhibitors.
- Ying Zhang
- , Raghava N. Sriramaneni
- & Zachary S. Morris
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Article
| Open AccessComparison of the 2021 COVID-19 roadmap projections against public health data in England
The ’Roadmap’ for relaxation of COVID-19 restrictions in England in 2021 was informed by mathematical modelling. Here, the authors perform a retrospective assessment of the accuracy of modelling predictions and identify the main sources of uncertainty that led to observed values deviating from projections.
- Matt J. Keeling
- , Louise Dyson
- & Samuel Moore
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Article
| Open AccessTrends in COVID-19 hospital outcomes in England before and after vaccine introduction, a cohort study
This study investigates trends in mortality and length of stay for people hospitalised with COVID-19 in England until September 2021. It shows that risks were higher for unvaccinated people and those with multiple comorbidities, and that busier hospitals had higher mortality rates at the start of the pandemic but this effect lessened over time.
- Peter D. Kirwan
- , Andre Charlett
- & Anne M. Presanis
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Article
| Open AccessMannose ameliorates experimental colitis by protecting intestinal barrier integrity
New potential therapies for inflammatory bowel disease are needed as not all patients respond to or maintain a response to conventional therapies. Here the authors report that mannose supplementation ameliorates experimental colitis in male mice, potentially via effects on intestinal epithelium lysosomal integrity.
- Lijun Dong
- , Jingwen Xie
- & Daming Zuo
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Article
| Open AccessSecond-dose ChAdOx1 and BNT162b2 COVID-19 vaccines and thrombocytopenic, thromboembolic and hemorrhagic events in Scotland
Here, Simpson et al. analyze data from 3.6 million COVID-19 vaccine second doses (ChAdOx1 and BNT162b2) in Scotland for risk of thrombocytopenic, thromboembolic and hemorrhagic events. Borderline increased risks of immune thrombocytopenic purpura and cerebral venous sinus thrombosis were found for the ChAdOx1 vaccine. These events were rare and usually short-lived.
- Colin R. Simpson
- , Steven Kerr
- & Aziz Sheikh
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Article
| Open AccessSecure human action recognition by encrypted neural network inference
Advanced computer vision technology can provide near real-time home monitoring to support "aging in place” by detecting falls and symptoms related to seizures and stroke. In this paper, the authors propose a strategy that uses homomorphic encryption, which guarantees information confidentiality while retaining action detection.
- Miran Kim
- , Xiaoqian Jiang
- & Shayan Shams
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Article
| Open AccessVaccine effectiveness of CoronaVac against COVID-19 among children in Brazil during the Omicron period
There is limited evidence of the effectiveness of the CoronaVac vaccine for children against the Omicron SARS-CoV-2 variant. Here, the authors use data from Brazil for children aged 6–11 years and estimate effectiveness of 40% against infection and 59% against severe disease at least two weeks after the second dose.
- Pilar T. V. Florentino
- , Flávia J. O. Alves
- & Enny S. Paixão
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Article
| Open AccessEmpirical evidence on the efficiency of backward contact tracing in COVID-19
Backward contact tracing aims to identify individuals who were infected by the same person as infected an index case, and has been shown to be effective in modelling studies of SARS-COV-2. Here, the authors present empirical data of the effectiveness of backward contact tracing from a program amongst university students in Belgium.
- Joren Raymenants
- , Caspar Geenen
- & Emmanuel Andre
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Article
| Open AccessProtection of COVID-19 vaccination and previous infection against Omicron BA.1, BA.2 and Delta SARS-CoV-2 infections
The protection of COVID-19 vaccines against emerging variants needs to be monitored. Here, the authors use community testing data from the Netherlands and find that protection against infection by Omicron subvariants BA.1 and 2 is low and that booster vaccines considerably but temporarily increase protection.
- Stijn P. Andeweg
- , Brechje de Gier
- & Mirjam J. Knol
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Article
| Open AccessSARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings
Air surveillance offers a potential means of monitoring airborne pathogens without the need for individual sampling. Here, the authors perform continuous air sampling in 15 community settings in the US for 29 weeks and demonstrate its feasibility for routine detection of SARS-CoV-2 and other respiratory pathogens.
- Mitchell D. Ramuta
- , Christina M. Newman
- & Shelby L. O’Connor
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Comment
| Open AccessScience in the time of COVID-19: Reflections on the UK Events Research Programme
We reflect on the extent to which the UK Events Research Programme adhered to four principles of design and evaluation in assessing risk of transmission from attending such mass events as football matches and festivals, and lessons learned.
- Theresa M. Marteau
- , Michael J. Parker
- & W. John Edmunds
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Article
| Open AccessA suite of PCR-LwCas13a assays for detection and genotyping of Treponema pallidum in clinical samples
Clinical diagnosis of Treponema pallidum subspecies pallidum (TPA), the causative agent of syphilis, depends upon serological testing, which has reduced sensitivity for some stages of the disease. Accompanying methods to complement serological testing also have distinct limitations. In this work, authors develop an assay that combines PCR with CRISPR-LwCas13a, and demonstrate sensitivity and specificity on clinically confirmed syphilis samples.
- Wentao Chen
- , Hao Luo
- & Heping Zheng
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Article
| Open AccessDynamic actuation enhances transport and extends therapeutic lifespan in an implantable drug delivery platform
Drug delivery implants suffer from diminished release profiles due to fibrous capsule formation over time. Here, the authors use soft robotic actuation to modulate the immune response of the host to maintain drug delivery over the longer-term and to perform controlled release in vivo.
- William Whyte
- , Debkalpa Goswami
- & Ellen T. Roche
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Article
| Open AccessDynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England
The REACT-1 study measures the community prevalence of SARS-CoV-2 in England through repeated cross-sectional surveys. Here, the authors present data from REACT-1 that document the increase in infection prevalence, particularly among children, associated with the Omicron variant in January 2022.
- Paul Elliott
- , Oliver Eales
- & Christl A. Donnelly
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Article
| Open AccessLevels of SARS-CoV-2 antibodies among fully vaccinated individuals with Delta or Omicron variant breakthrough infections
The SARS-CoV-2 Omicron variant is associated with high rates of vaccine breakthrough infections, but the immunological basis for this is not well characterised. Here, the authors show that increased anti-Spike IgG antibody levels are associated with a reduced risk of infection with the Delta variant, but not with Omicron.
- Nina Breinholt Stærke
- , Joanne Reekie
- & Ole Schmeltz Søgaard
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Article
| Open AccessPyro-catalysis for tooth whitening via oral temperature fluctuation
Tooth whitening becoming a common cosmetic treatment has led to the development of catalytic whitening solutions. Here, the authors report upon a thermally triggered, pyrocatalytic, catalyst which can use temperature changes from normal oral activity to breakdown stains and whiten teeth.
- Yang Wang
- , Shuhao Wang
- & Xuliang Deng
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Article
| Open AccessDynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England
This study presents data from the REACT-1 SARS-CoV-2 community sampling study in England from November 2021 to March 2022. They show that the Omicron variant peaked in January with a prevalence of ~7% and that the BA.2 sublineage had a 1.5x higher reproduction number compared to other Omicron sublineages.
- Oliver Eales
- , Leonardo de Oliveira Martins
- & Marc Chadeau-Hyam
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Article
| Open AccessReduction of primary graft dysfunction using cytokine adsorption during organ preservation and after lung transplantation
Lung transplantation is hindered by the scarcity of organs and by mortality following primary graft dysfunction. Here, the authors show that cytokine absorption can be used in donor lungs during ex vivo lung perfusion and post-transplant, and leads to restored lung function and reduced primary graft dysfunction in animal models.
- Haider Ghaidan
- , Martin Stenlo
- & Sandra Lindstedt
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Article
| Open AccessAn analysis of 45 large-scale wastewater sites in England to estimate SARS-CoV-2 community prevalence
Wastewater surveillance could provide a means of monitoring SARS-CoV-2 prevalence that does not rely on testing individuals. Here, the authors report results from England’s national wastewater surveillance program, use it to estimate prevalence, and compare estimates with those from population-based prevalence surveys.
- Mario Morvan
- , Anna Lo Jacomo
- & Leon Danon
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Article
| Open AccessStress-testing the resilience of the Austrian healthcare system using agent-based simulation
As mass quarantines, absences due to sickness, or other shocks thin out patient-physician networks, the system might be pushed to a tipping point where it loses its ability to deliver care. Here, the authors propose a data-driven framework to quantify regional resilience to such shocks via an agent-based model.
- Michaela Kaleta
- , Jana Lasser
- & Peter Klimek
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Article
| Open AccessEmergency triage of brain computed tomography via anomaly detection with a deep generative model
Triage is essential for the early diagnosis and reporting of emergency patients in the emergency department. Here, the authors develop an anomaly detection algorithm with a deep generative model that reprioritizes radiology worklists and provides lesion attention maps for brain CT images with critical findings.
- Seungjun Lee
- , Boryeong Jeong
- & Namkug Kim
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Article
| Open AccessThe Medical Segmentation Decathlon
International challenges have become the de facto standard for comparative assessment of image analysis algorithms. Here, the authors present the results of a biomedical image segmentation challenge, showing that a method capable of performing well on multiple tasks will generalize well to a previously unseen task.
- Michela Antonelli
- , Annika Reinke
- & M. Jorge Cardoso
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Article
| Open AccessGenomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand
Aotearoa New Zealand pursued a COVID-19 elimination strategy until October 2021 when it moved to a suppression strategy. In this genomic surveillance study, the authors describe spread of the virus during the transition between these strategies, with evidence of substantial undetected community transmission.
- Lauren Jelley
- , Jordan Douglas
- & Jemma L. Geoghegan
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Article
| Open AccessThe effect of COVID certificates on vaccine uptake, health outcomes, and the economy
Many countries introduced COVID certificates that were required to access public venues. Here, the authors analyse data from France, Germany, and Italy, and estimate that these policies led to increased vaccine uptake of 6-13 percentage points with subsequent beneficial impacts on health and economic outcomes.
- Miquel Oliu-Barton
- , Bary S. R. Pradelski
- & Guntram B. Wolff
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Article
| Open AccessPopulation genomics of ancient and modern Trichuris trichiura
The whipworm Trichuris trichiura is a soil-transmitted helminth that causes the neglected tropical disease trichuriasis in humans. Here, the authors produce whole genome sequences of modern and ancient samples from humans and non-human primates to characterise the genomic diversity and evolution of this pathogen.
- Stephen R. Doyle
- , Martin Jensen Søe
- & Christian Moliin Outzen Kapel
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Article
| Open AccessInferring the epidemiological benefit of indoor vector control interventions against malaria from mosquito data
Estimating the effectiveness of malaria vector control interventions has typically relied on resource-intensive cluster randomised trials. Here, the authors estimate changes in malaria prevalence using entomological data from experimental hut trials, which may provide an alternative route to approval of interventions in some situations.
- Ellie Sherrard-Smith
- , Corine Ngufor
- & Thomas S. Churcher
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Article
| Open AccessSelf-evolving vision transformer for chest X-ray diagnosis through knowledge distillation
Although deep learning-based computer-aided diagnosis systems have recently achieved expert level performance, developing a robust model requires large, high-quality data with annotations. Here, the authors present a framework which can improve the performance of vision transformer simultaneously with self-supervision and self-training.
- Sangjoon Park
- , Gwanghyun Kim
- & Jong Chul Ye
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Article
| Open AccessRevisiting COVID-19 vaccine hesitancy around the world using data from 23 countries in 2021
Vaccine hesitancy is a public health challenge. Here the authors examine COVID-19 vaccine hesitancy in June 2021 using a survey including individuals from 23 countries, and report differences compared to a year earlier.
- Jeffrey V. Lazarus
- , Katarzyna Wyka
- & Ayman El-Mohandes
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Article
| Open AccessEffect of vaccination on household transmission of SARS-CoV-2 Delta variant of concern
COVID-19 vaccines may reduce the susceptibility of an individual to infection and/or the infectiousness of breakthrough infections. Here, the authors use data from Denmark and estimate that vaccine effectiveness was 61% for susceptibility and 31% for infectiousness during a period of Delta variant dominance.
- Frederik Plesner Lyngse
- , Kåre Mølbak
- & Carsten Thure Kirkeby
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Article
| Open AccessTPGS-based and S-thanatin functionalized nanorods for overcoming drug resistance in Klebsiella pneumonia
Overproduction of efflux pumps represents an important mechanism of Klebsiella pneumonia resistance to tigecycline. Here, the authors design TPGS- and S-thanatin functionalized nanorods loaded with tigecycline to increase drug accumulation inside bacteria and overcome bacterial resistance.
- Xiaojuan Wang
- , Xiaoling Xu
- & Saiping Jiang
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Article
| Open AccessCOVID-19 disease severity in US Veterans infected during Omicron and Delta variant predominant periods
Infection with the SARS-CoV-2 Omicron variant appears to cause milder disease in the general population than infection with Delta. Here the authors use data from the US Department of Veterans Affairs and demonstrate that this also applies to infection in an at-risk population of older age and with more co-morbidities.
- Florian B. Mayr
- , Victor B. Talisa
- & Adeel A. Butt