bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2
Authors: Park Sang Woo , Sun Kaiyuan , Abbott Sam , Sender Ron , Bar-on Yinon , Weitz Joshua S. , Funk Sebastian , Grenfell Bryan T. , Backer Jantien A , Wallinga Jacco , Viboud Cecile , Dushoff Jonathan 
Published: July 2022

AbstractEstimating the differences in the incubation-period, serial-interval, and generation-interval distributions of SARS-CoV-2 variants is critical to understanding their transmission and control. However, the impact of epidemic dynamics is often neglected in estimating the timing of infection and transmission—for example, when an epidemic is growing exponentially, a cohort of infected individuals who developed symptoms at the same time are more likely to have been infected recently. Here, we re-analyze incubation-period and serial-interval data describing transmissions of the Delta and Omicron variants from the Netherlands at the end of December 2021. Previous analysis of the same data set reported shorter mean observed incubation period (3.2 days vs 4.4 days) and serial interval (3.5 days vs 4.1 days) for the Omicron variant, but the number of infections caused by the Delta variant decreased during this period as the number of Omicron infections increased. When we account for growth-rate differences of two variants during the study period, we estimate similar mean incubation periods (3.8–4.5 days) for both variants but a shorter mean generation interval for the Omicron variant (3.0 days; 95% CI: 2.7–3.2 days) than for the Delta variant (3.8 days; 95% CI: 3.7–4.0 days). We further note that the differences in estimated generation intervals may be driven by the “network effect”—higher effective transmissibility of the Omicron variant can cause faster susceptible depletion among contact networks, which in turn prevents late transmission (therefore shortening realized generation intervals). Using up-to-date generation-interval distributions is critical to accurately estimating the reproduction advantage of the Omicron variant.SignificanceRecent studies suggest that individuals infected with the Omicron variant develop symptoms earlier (shorter incubation period) and transmit faster (shorter generation interval) than those infected with the Delta variant. However, these studies typically neglect population-level effects: when an epidemic is growing, a greater proportion of current cases were infected recently, biasing us toward observing faster transmission events. Accounting for this dynamical bias, we find that Omicron infections from the Netherlands at the end of December 2021 had similar incubation periods, but shorter generation intervals, compared to Delta infections from the same period. Shorter generation intervals of the Omicron variant might be due to its higher effective reproduction number, which can cause faster local susceptible depletion around the contact network.
The clinical utility and epidemiological impact of self-testing for SARS-CoV-2 using antigen detecting diagnostics: a systematic review and meta-analysis
Authors: Brümmer Lukas E. , Erdmann Christian , Tolle Hannah , McGrath Sean , Olaru Ioana D. , Katzenschlager Stephan , Yerlikaya Seda , Grilli Maurizio , Pollock Nira R. , Erkosar Berra , Mace Aurelien , Ongarello Stefano , Johnson Cheryl C. , Sacks Jilian A. , Denkinger Claudia M. 
Published: July 2022

ABSTRACTIntroductionSelf-testing for COVID-19 (C19ST) based on antigen detecting diagnostics could significantly support controlling the SARS-CoV-2 pandemic. To inform the World Health Organization in developing a C19ST guideline, we performed a systematic review and meta-analysis of the available literature.MethodsWe electronically searched Medline and the Web of Science core collection, performed secondary reference screening, and contacted experts for further relevant publications. Any study published between December 1, 2020 and November 30, 2021 assessing the epidemiological impact and clinical utility of C19ST was included. Study quality was evaluated using the Newcastle Ottawa Scale (NOS). The review was registered on PROSPERO (CRD42022299977).Results11 studies only from high-income countries with an overall low quality (median of 3/9 stars on the NOS) were found. Pooled C19ST positivity was 0.2% (95% CI 0.1% to 0.4%; eight data sets) in populations where otherwise no dedicated testing would have occurred. The impact of self-testing on virus transmission was uncertain. Positive test results mainly resulted in people having to isolate without further confirmation of results (eight data sets). When testing was voluntary by study design, pooled testing uptake was 53.2% (95% CI 36.7% to 68.9%; five data sets. Outside direct health impacts, C19ST reduced quarantine duration and absenteeism from work, and made study participants feel safer. Study participants favored self-testing and were confident that they performed testing and sampling correctly.ConclusionsThe present data suggests that C19ST could be a valuable tool in reducing the spread of COVID-19, as it can achieve good uptake, may identify additional cases, and was generally perceived as positive by study participants. However, data was very limited and heterogenous, and further research especially in low- and middle-income countries is needed to assess the clinical utility and epidemiological impact of C19ST in more detail.CONTRIBUTIONS TO THE LITERATURE- COVID-19 self-testing (C19ST) using antigen detection could conceivably support pandemic control. A current PubMed search found no systematic evidence synthesis of studies assessing the epidemiological impact and clinical utility of C19ST implementation- We systematically reviewed and meta-analyzed 11 studies including more than 1.1 million persons tested- C19ST can achieve good uptake, may identify additional cases, and was general perceived as positive by study participants, suggesting it to be a valuable tool in reducing the spread of SARS-CoV-2- Further data especially from low- and middle-income countries is needed to understand the impact of C19ST in more detail
Oxonium Ion-Guided Ion Mobility-Assisted Glycoproteomics on the timsTOF Pro
Authors: Mukherjee Soumya , Jankevics Andris , Busch Florian , Lubeck Markus , Zou Yang , Kruppa Gary , Heck Albert J. R. , Scheltema Richard A. , Reiding Karli R. 
Published: July 2022

AbstractSpatial separation of ions in the gas-phase, providing information about their size as collisional cross-sections, can readily be achieved through ion mobility. The timsTOF Pro series combines a trapped ion mobility device with a quadrupole, collision-cell and a time-of-flight analyser to enable the analysis of ions at great speed. Here, we show that the timsTOF Pro is capable of physically separating N-glycopeptides from non-modified peptides and producing high-quality fragmentation spectra, both beneficial for glycoproteomics analyses of complex samples. The glycan moieties enlarge the size of glycopeptides compared to non-modified peptides, yielding a clear cluster in the mobilogram that, next to increased dynamic range from the physical separation of glycopeptides and non-modified peptides, can be used to make an effective selection filter for directing the mass spectrometer to analytes of interest. This new approach was applied to selected glycoproteins, human plasma- and neutrophil-derived glycopeptides. We show that the achieved physical separation, combined with the focussing of the mass spectrometer, allows for improved extraction of information from the samples, even at shorter LC gradients of 15 min. We validated our approach on human neutrophil and plasma samples of known make-up, in which we captured the anticipated glycan heterogeneity (paucimannose, phosphomannose, high mannose, hybrid and complex glycans) from plasma and neutrophil samples at the expected abundances. As the method is compatible with off-the-shelve data acquisition routines and data analysis software, it can readily be applied by any laboratory with a timsTOF Pro and is reproducible as demonstrated by a comparison between two laboratories.
Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies
Authors: Chakraborty Mahul , Lara Angelica Guadalupe , Dang Andrew , McCulloch Kyle J. , Rainbow Dylan , Carter David , Ngo Luna Thanh , Solares Edwin , Said Iskander , Corbett-Detig Russ , Gilbert Lawrence E. , Emerson J.J. , Briscoe Adriana D. 
Published: July 2022

AbstractButterflies have photoreceptor cells that are sensitive to the ultraviolet part of the spectrum due to ultraviolet-sensitive rhodopsin (UVRh), a gene that has been duplicated in the Heliconius genus. In individuals expressing UVRh1 and UVRh2, electrophysiological and behavioral studies demonstrate that these opsin proteins enable discrimination of UV wavelengths. This behavioral trait varies between species, being absent in H. melpomene and limited to females in H. erato. To identify the evolutionary origins of this trait, we first examined UV color vision in H. charithonia, a species related to H. erato in the sara/sapho group. We found that this species also has sexually dimorphic UV color vision. To identify the genetic basis of this trait, we built a reference-grade genome assembly of H. charithonia. We discovered that one duplicate, UVRh1, is present on the W chromosome, making it obligately female-specific. We employed gDNA PCR assays of UVRh1 across the Heliconius genus. In species with sexually dimorphic UVRh1 mRNA expression, UVRh1 gDNA is absent in males, whereas in species with sexually monomorphic UVRh1 mRNA expression, UVRh1 gDNA is found in both sexes. The presence or absence of male UVRh1 expression across the Heliconius phylogeny supports a model where sexual dimorphism was acquired early via movement of a gene duplication to the W-chromosome. We used CRISPR-Cas9 to engineer a deletion in the UVRh1 locus in female H. charithonia and use immunohistochemistry to show that UVRh1 protein expression is absent in mutant tissue, similar to that of males. Our results show that a rare behavioral phenotype, sex-specific UV color vision, was acquired via sex chromosome gene traffic of a duplicated UV rhodopsin.
Inside and outside of virus-like particles HBc and HBc/4M2e: a comprehensive study of the structure
Authors: Egorov V.V. , Shvetsov A.V. , Pichkur E.B. , Shaldzhyan A.A. , Zabrodskaya Ya.A. , Vinogradova D.S. , Nekrasov P.A. , Gorshkov A.N. , Garmay Yu.P. , Kovaleva A.A. , Stepanova L.A. , Tsybalova L. M. , Shtam T.A. , Myasnikov A.G. , Konevega A.L. 
Published: July 2022

AbstractThe structure of the core particles of the hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (HBc/4M2e) have been studied using a combination of molecular modeling and cryogenic electron microscopy (cryo-EM). It has also been shown that synthesis of particles occurs inside bacterial cells, but despite the big inner volume of the core shell particle, purified HBc/4M2e do not contain detectable amounts of bacterial proteins. It has been shown that a fragment of the M2e is prone to the formation of amyloid-like fibrils. However, as a part of HBc immunodominant loop M2e domains as repeats, does not exhibit a tendency to aggregation. Full-atom HBc-4M2E model with 3A resolution was obtained by molecular modeling methods based on cryo-EM data.
Comparing children’s night cough with wheeze: phenotypic characteristics, healthcare use and treatment
Authors: Mallet Maria Christina , Mozun Rebeca , Ardura-Garcia Cristina , Pedersen Eva SL , Jurca Maja , Latzin Philipp ,   LUIS study group, Moeller Alexander , Kuehni Claudia E. 
Published: July 2022

AbstractPopulation-based studies of children presenting with dry night cough alone compared with those who also wheeze are few and inconclusive.Luftibus in the school is a population-based study of schoolchildren conducted between 2013–2016 in Zurich, Switzerland. We divided children into four mutually exclusive groups based on reported dry night cough (‘cough’) and wheeze and compared parent-reported symptoms, comorbidities and exposures using multinomial regression, FeNO using quantile regression, spirometry using linear regression and healthcare use and treatments using descriptive statistics.Among 3457 schoolchildren aged 6–17 years, 294 (9%) reported ‘cough’, 181 (5%) reported ‘wheeze’, 100 (3%) reported ‘wheeze and cough’ and 2882 (83%) were ‘asymptomatic.’ Adjusting for confounders in a multinomial regression, children with ‘cough’ reported more frequent colds, rhinitis and snoring than ‘asymptomatic’ children; children with ‘wheeze’ or ‘wheeze and cough’ more often reported hay fever, eczema and parental histories of asthma. FeNO and spirometry were similar among ‘asymptomatic’ and children with ‘cough,’ while children with ‘wheeze’ or ‘wheeze and cough’ had higher FeNO and evidence of bronchial obstruction. Children with ‘cough’ used healthcare less often than those with ‘wheeze,’ and they attended mainly primary care. Twenty-two children (7% of those with ‘cough’) reported a physician diagnosis of asthma and used inhalers. These had similar characteristics as children with wheeze.Our representative population-based study suggests only a small subgroup (7%) of schoolchildren reporting dry night cough without wheeze have features typical of asthma, yet the majority (93%) should be investigated for alternative aetiologies, particularly upper airway disease.Take home messageOur population-based study found children with night cough alone clearly differ from those with wheeze, suggesting different aetiologies and pathophysiology. Yet, a small subgroup (7%) has features of asthma and may benefit from specific work-up.
How long and effective does a mask protect you from an infected person who emits corona virus-laden particles: by implementing physics-based modeling
Authors: Bahrami Flora , Batt Till , Schudel Seraina , Annaheim Simon , He Weidong , Wang Jing , Rossi René M. , Defraeye Thijs 
Published: July 2022

AbstractSARS-CoV-2 spreads via droplets, aerosols, and smear infection. From the beginning of the COVID-19 pandemic, using a facemask in different locations was recommended to slow down the spread of the virus. To evaluate facemasks’ performance, masks’ filtration efficiency is tested for a range of particle sizes. Although such tests quantify the blockage of the mask for a range of particle sizes, the test does not quantify the cumulative amount of virus-laden particles inhaled or exhaled by its wearer. In this study, we quantify the accumulated viruses that the healthy person inhales as a function of time, activity level, type of mask, and room condition using a physics-based model. We considered different types of masks, such as surgical masks and filtering facepieces (FFPs), and different characteristics of public places such as office rooms, buses, trains, and airplanes. To do such quantification, we implemented a physics-based model of the mask. Our results confirm the importance of both people wearing a mask compared to when only one wears the mask. The protection time before the healthy wearer has an infection risk of 50% reduces by 80% if only one wears the facemask instead of both people. The protection time is further reduced if the infected person starts to cough or increases the activity level by 85% and 99%, respectively. Results show the leakage of the mask can considerably affect the performance of the mask. For the surgical mask, the apparent filtration efficiency reduces by 75% with such a leakage, which cannot provide sufficient protection despite the high filtration efficiency of the mask. The facemask model presented provides key input in order to evaluate the protection of masks for different conditions in public places. The physics-based model of the facemask is provided as an online application.
Artificial Intelligence (AI)-based Chatbots in Promoting Health Behavioral Changes: A Systematic Review
Authors: Aggarwal Abhishek , Tam Cheuk Chi , Wu Dezhi , Li Xiaoming , Qiao Shan 
Published: July 2022

AbstractBackgroundArtificial-Intelligence (AI)-based chatbots can offer personalized, engaging, and on-demand health-promotion interventions. This systematic review evaluates the feasibility, efficacy, and intervention characteristics of AI-chatbots in promoting health-behavior change.MethodsA comprehensive search was conducted in seven bibliographic databases (PubMed, IEEE Xplore, ACM Digital Library, PsychoINFO, Web of Science, EMBASE, and JMIR publications) for empirical articles published from 1980 to 2022 that evaluated feasibility and/or efficacy of AI-chatbots for behavioral change. The screening, extraction, and analyses of identified articles followed the PRISMA guidelines.ResultsOf the 15 included studies, majority studies (n=11) reported high usability, acceptability and engagement, and some evidence on feasibility of AI-chatbots. Selected studies demonstrated high efficacy in promoting healthy lifestyles (n=6), smoking cessation (n=4), treatment/medication adherence (n=2), and reduction in substance misuse (n=1). Behavioral change theories and/or expert consultation were used to develop behavioral change strategies of AI-chatbots, including goal setting, monitoring, real-time reinforcement/feedback, and on- demand support. Real-time user-chatbot interaction data, such as user preferences and behavioral performance, were collected on the chatbot platform to identify ways of providing personalized services. The AI-chatbots demonstrated potential for scalability by deployment through accessible devices and platforms (e.g., smartphones and messenger). Participants also reported that AI-chatbots offered a non-judgmental space for communicating sensitive information. However, the reported results need to be interpreted with caution because of moderate to high risk of internal validity, insufficient description of AI-techniques, and limitation for generalizability.ConclusionAI-chatbots have demonstrated efficacy of health-behavior change interventions among large and diverse population; however, future studies need to adopt robust RCTs to establish definitive conclusions.
Parental acceptance of and preferences for administration of routine varicella vaccination in the UK: a study to inform policy
Authors: Sherman Susan M. , Lingley-Heath Nicola , Lai Jasmine , Sim Julius , Bedford Helen 
Published: July 2022

AbstractObjectivesTo explore acceptability of and preferences for the introduction of varicella vaccination to the UK childhood immunisation schedule.DesignWe conducted an online cross-sectional survey exploring parental attitudes towards vaccines in general, and varicella vaccine specifically, and their preferences for how the vaccine should be administered.Participants596 parents (76.3% female, 23.3% male, mean age 33.4 years) whose youngest child was aged 0-5 years.Main outcome measuresWillingness to accept the vaccine for their child and preferences for how the vaccine should be administered (in combination with the MMR vaccine [MMRV], on the same day as the MMR vaccine but as a separate injection [MMR+V], on a separate additional visit).Results74.0% of parents (95% CI 70.2% to 77.5%) were extremely/somewhat likely to accept a varicella vaccine for their child if one became available, 18.3% (95% CI 15.3% to 21.8%) were extremely/somewhat unlikely to accept it and 7.7% (95% CI 5.7% to 10.2%) were neither likely nor unlikely. Reasons provided by parents likely to accept the vaccine included protection from complications of chickenpox, trust in the vaccine/healthcare professionals, and wanting their child to avoid their personal experience of chickenpox. Reasons provided by parents who were unlikely included chickenpox not being a serious illness, concern about side effects, and believing it is preferable to catch chickenpox as a child rather than as an adult. A combined MMRV vaccination or additional visit to the surgery were preferred over an additional injection at the same visit.ConclusionsMost parents would accept a varicella vaccination. These findings highlight parents’ preferences for varicella vaccine administration, information needed to inform vaccine policy and practice and development of a communication strategy.
Discovering and Validating Neoantigens by Mass Spectrometry-based Immunopeptidomics and Deep Learning
Authors: Tran Ngoc Hieu , Peng Chao , Lei Qingyang , Xin Lei , Lang Jingxiang , Zhang Qing , Li Wenting , Miao Haofei , Wu Ping , Qiao Rui , Qin Haiming , Bu Dongbo , Zhang Haicang , Yu Chungong , Liu Xiaolong , Zhang Yi , Shan Baozhen , Li Ming 
Published: July 2022

AbstractNeoantigens are promising targets for cancer immunotherapy but their discovery remains challenging, mainly due to the sensitivity of current technologies to detect them and the specificity of our immune system to recognize them. In this study, we addressed both of those problems and proposed a new approach for neoantigen identification and validation from mass spectrometry (MS) based immunopeptidomics. In particular, we developed DeepNovo Peptidome, ade novosequencing-based search engine that was optimized for HLA peptide identification, especially non-canonical HLA peptides. We also developed DeepSelf, a personalized model for immunogenicity prediction based on the central tolerance of T cells, which could be used to select candidate neoantigens from non-canonical HLA peptides. Both tools were built on deep learning models that were trained specifically for HLA peptides and for the immunopeptidome of each individual patient. To demonstrate their applications, we presented a new MS-based immunopeptidomics study of native tumor tissues from five patients with cervical cancer. We applied DeepNovo Peptidome and DeepSelf to identify and prioritize candidate neoantigens, and then performedin vitrovalidation of autologous neoantigen-specific T cell responses to confirm our results. Our MS-basedde novosequencing approach does not depend on prior knowledge of genome, transcriptome, or proteome information. Thus, it provides an unbiased solution to discover neoantigens from any sources.
Application of Passive Head Motion to Generate Defined Accelerations at the Heads of Rodents
Authors: Maekawa Takahiro , Sakitani Naoyoshi , Ryu Youngjae , Takashima Atsushi , Murase Shuhei , Fink Julius , Nagao Motoshi , Ogata Toru , Shinohara Masahiro , Sawada Yasuhiro 
Published: July 2022

ABSTRACTExercise is widely recognized as effective for various diseases and physical disorders, including those related to brain dysfunction. However, molecular mechanisms behind the beneficial effects of exercise are poorly understood. Many physical workouts, particularly those classified as aerobic exercises such as jogging and walking, produce impulsive forces at the time of foot contact with the ground. Therefore, it was speculated that mechanical impact might be implicated in how exercise contributes to organismal homeostasis. For testing this hypothesis on the brain, a custom-designed passive head motion (hereafter referred to as PHM) system was developed that can generate vertical accelerations with controlled and defined magnitudes and modes and reproduce mechanical stimulation that might be applied to the heads of rodents during treadmill running at moderate velocities, a typical intervention to test the effects of exercise in animals. By using this system, it was demonstrated that PHM recapitulates the serotonin (5-hydroxytryptamine, hereafter referred to as 5-HT) receptor subtype 2A (5-HT2A) signaling in the prefrontal cortex (PFC) neurons of mice. This work provides detailed protocols for applying PHM and measuring its resultant mechanical accelerations at rodents’ heads.SUMMARYThe present protocol describes a custom-designed passive head motion system, which reproduces mechanical accelerations at rodents’ heads generated during their treadmill running at moderate velocities. It allows dissecting mechanical factors/elements from the beneficial effects of physical exercise.