bluuebunny/crossref_metadata_2025_split huggingface dataset:
Initial refinement of data from video-based single-cell tracking
Authors: Suárez Korsnes Mónica , Korsnes Reinert 
Published: May 2022

AbstractBackgroundVideo recording of cells offers a straightforward way to gain valuable information from their response to treatments. An indispensable step in obtaining such information involves tracking individual cells from the recorded data. A subsequent step is reducing such data to represent essential biological information. This can help to compare various single-cell tracking data providing a novel source of information. The vast array of potential data sources highlights the significance of methodologies prioritizing simplicity, robustness, transparency, affordability, sensor independence, and freedom from reliance on specific software or online services.MethodsThe provided data presents single-cell tracking of clonal (A549) cells as they grow in two-dimensional (2D) monolayers over 94 hours, spanning several cell cycles. The cells are exposed to three different concentrations of yessotoxin (YTX). The data treatments showcase the parametrization of population growth curves, as well as other statistical descriptions. These include the temporal development of cell speed in family trees with and without cell death, correlations between sister cells, single-cell average displacements, and the study of clustering tendencies.ResultsVarious statistics obtained from single-cell tracking reveal patterns suitable for data compression and parametrization. These statistics encompass essential aspects such as cell division, movements, and mutual information between sister cells.ConclusionThis work presents practical examples that highlight the abundant potential information within large sets of single-cell tracking data. Data reduction is crucial in the process of acquiring such information which can be relevant for phenotypic drug discovery and therapeutics, extending beyond standardized procedures. Conducting meaningful big data analysis typically necessitates a substantial amount of data, which can stem from standalone case studies as an initial foundation.
Cortical response variability is driven by local excitability changes with somatotopic organization
Authors: Stephani T. , Nierula B. , Villringer A. , Eippert F. , Nikulin V.V. 
Published: May 2022

AbstractIdentical sensory stimuli can lead to different neural responses depending on the instantaneous brain state. Specifically, neural excitability in sensory areas may shape the brain’s response already from earliest cortical processing onwards. However, whether these dynamics affect a given sensory domain globally or occur on a spatially local level is largely unknown. We studied this in the somatosensory domain of 38 human participants with EEG, presenting stimuli to the median and tibial nerves alternatingly, and testing the co-variation of initial cortical responses in hand and foot areas, as well as their relation to pre-stimulus oscillatory states. We found that amplitude fluctuations of initial cortical responses to hand and foot stimulation – the N20 and P40 components of the somatosensory evoked potential (SEP), respectively – were not related, indicating local excitability changes in primary sensory regions. In addition, effects of pre-stimulus alpha (8-13 Hz) and beta (18-23 Hz) band amplitude on hand-related responses showed a robust somatotopic organization, thus further strengthening the notion of local excitability fluctuations. However, for foot-related responses, the spatial specificity of pre-stimulus effects was less consistent across frequency bands, with beta appearing to be more foot-specific than alpha. Connectivity analyses in source space suggested this to be due to a somatosensory alpha rhythm that is primarily driven by activity in hand regions while beta frequencies may operate in a more hand-region-independent manner. Altogether, our findings suggest spatially distinct excitability dynamics within the primary somatosensory cortex, yet with the caveat that frequency-specific processes in one sub-region may not readily generalize to other sub-regions.
Coupling of NOD2 to GIV is Required for Bacterial Sensing
Authors: Katkar Gajanan D. , Anandachar Mahitha Shree , Sinha Saptarshi , Ibeawuchi Stella-Rita , Espinoza Celia R. , Coates Jane , Malhotra Yashaswat S. , Mullick Madhubanti , Castillo Vanessa , Vo Daniella T. , Sahoo Debashis , Ghosh Pradipta 
Published: May 2022

ABSTRACT/SUMMARYSensing of pathogens by Nucleotide oligomerization domain (NOD)-like 2 receptor (NOD2) induces a protective inflammatory response that coordinates bacterial clearance. Polymorphisms in NOD2 impair bacterial clearance, leading to chronic gut inflammation in Crohn’s disease (CD) via mechanisms that remain incompletely understood. We identify GIV/Girdin (CCDC88A) as a NOD2-interactor that shapes bacterial sensing-and-signaling in macrophages. Myeloid-specific GIV depletion exacerbated and protracted infectious colitis and abolished the protective effect of muramyl dipeptide (MDP) in both chemical colitis and severe sepsis. In the presence of GIV, macrophages enhance anti-bacterial pathways downstream of NOD2, clear microbes rapidly and concomitantly suppress inflammation. GIV’s actions are mediated via its C-terminus, which directly binds the terminal leucine-rich repeat (LRR#10) of NOD2; binding is augmented by MDP and ATP, precedes receptor oligomerization, and is abolished by the1007fsCD-risk variant which lacks LRR#10. Findings illuminate mechanisms that underlie protective NOD2 signaling and loss of function in the major1007fsvariant.In briefThis work reveals a mechanism by which macrophages use their innate immune sensor, NOD2, to protect the host against overzealous inflammation during bacterial infections, and the consequences of its loss, as occurs in the most important Crohn’s disease-risk variant.GRAPHIC ABSTRACTHIGHLIGHTSGIV is a functional and direct interactor of the terminal LRR repeat of NOD2Mice lacking MФ GIV develop dysbiosis, protracted ileocolitis and sepsisMDP/NOD2-dependent protective host responses require GIVCD-risk NOD21007fsvariant lacking the terminal LRR#10 cannot bind GIV
Effectiveness of influenza vaccination against SARS-CoV-2 infection among healthcare workers in Qatar
Authors: Tayar Elias , Abdeen Sami , Alah Muna Abed , Chemaitelly Hiam , Bougmiza Iheb , Ayoub Houssein H. , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Al-Romaihi Hamad Eid , Al-Thani Mohamed H. , Bertollini Roberto , Abu-Raddad Laith J. , Al-Khal Abdullatif 
Published: May 2022

AbstractA number of studies reported that influenza vaccination is associated with lower risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and/or coronavirus disease 2019 (COVID-19) morbidity and mortality. We conducted a matched, test-negative, case-control study to estimate effectiveness of influenza vaccination, using Abbott’s quadrivalent Influvac Tetra vaccine, against SARS-CoV-2 infection and against severe COVID-19. The study was implemented on a population of 30,774 healthcare workers (HCWs) in Qatar during the 2020 annual influenza vaccination campaign, between September 17, 2020 and December 31, 2020, before introduction of COVID-19 vaccination. The median age in the matched samples was 36 years (interquartile range (IQR), 32-44) for cases and 35 years (IQR, 32-42) for controls. The median duration between influenza vaccination and the PCR test was 43 days (IQR, 29-62). The estimated effectiveness of influenza vaccination against SARS-CoV-2 infection >14 days after receiving the vaccine was 29.7% (95% CI: 5.5-47.7%). The estimated effectiveness of influenza vaccination against any severe, critical, or fatal COVID-19 was 88.9% (95% CI: 4.1-98.7%). Sensitivity analyses confirmed main analysis results. Recent influenza vaccination is associated with an appreciable reduction in the risk of SARS-CoV-2 infection and COVID-19 severity.
Smoking trajectories over the first year of the pandemic in UK middle-aged adults: evidence from the UKHLS COVID-19 study
Authors: Gagné Thierry 
Published: May 2022

ABSTRACTBackgroundThe COVID-19 pandemic has altered the conditions leading people to smoke. Multiple studies have examined changes in population levels of smoking at the start of the pandemic. However, conclusions remain mixed due to the high proportion of studies with poor methods and short follow-up periods.MethodsThis study used longitudinal data from the UKHLS COVID-19 study to derive smoking trajectories among 4,130 UK adults aged 35-64 across four time points over the first year of the pandemic (2018-19, April 2020, September 2020, and January 2021). Random-effects models were used to examine subject-specific changes across time points.ResultsBetween the pre-pandemic estimate and January 2021, there was a significant decline in smoking from 14.8% to 13.1% (PR = 0.89, 95%CI 0.83-0.95). The number of cigarettes smoked per day among smokers increased in April 2020 (B = 0.5, 95%CI 0.0, 1.0) and September 2020 (B = 1.0, 95%CI 0.4, 1.5), but declined back to pre-pandemic levels in January 2021 (B = 0.3, 95%CI -0.3, 0.8). These changes did not vary by sex, ethnicity, relationship status, education, occupation, or household income.ConclusionAmong UK adults aged 35-64, there has been a slight decrease in smoking which was maintained up to January 2021. Whereas there was an increase in cigarette consumption among smokers at the start of the pandemic, this was no longer observable in January 2021. The findings support the argument that the first year of the pandemic is unlikely to have had a negative effect of most middle-aged adult smokers’ trajectory.
Physical activity, respiratory physiotherapy practices, and nutrition among people with primary ciliary dyskinesia in Switzerland
Authors: Lam Yin Ting , Pedersen Eva SL , Schreck Leonie D , Hüsler Leonie , Koppe Helena , Belle Fabiën N , Clarenbach Christian , Latzin Philipp ,   Swiss PCD research group, Kuehni Claudia E , Goutaki Myrofora 
Published: May 2022

SummaryAims of the studyWe know little about the level of physical activity, respiratory physiotherapy practices, and nutritional status of people with primary ciliary dyskinesia (PCD), although these are important aspects of patients with chronic respiratory disease. We assessed physical activity, respiratory physiotherapy practices, and nutritional status among people with PCD in Switzerland, investigated how these vary by age, and identified factors associated with regular physical activity.MethodsWe sent a postal questionnaire survey to people with PCD enrolled in the Swiss PCD registry (CH-PCD), based on the standardised FOLLOW-PCD patient questionnaire. We collected information about physical activity, physiotherapy, respiratory symptoms, and nutritional status. We calculated the metabolic equivalent (MET) to better reflect the intensity of the reported physical activities. To assess nutritional status, we extracted information from CH-PCD and calculated participants’ body mass index (BMI).ResultsOf the 86 questionnaires we sent, 74 (86% response rate) were returned from 24 children and 50 adults. The median age at survey completion was 23 years [IQR (interquartile range) 15–51], and 51% were female. Among all 74 participants, 48 (65%) performed sports regularly. Children were vigorously active (median MET 9.1; IQR 7.9–9.6) and adults were moderately active (median MET 5.5; IQR 4.3-6.9). 59 participants (80%) reported performing some type of respiratory physiotherapy. However, only 30% of adults saw a professional physiotherapist compared with 75% of children. Half of the participants had normal BMI; one child (4%) and two adults (4%) were underweight. People who were regularly physically active reported seeing a physiotherapist more often.ConclusionsOur study is the first to provide patient-reported data about physical activity, respiratory physiotherapy, and nutrition among people with PCD. Our results highlight that professional respiratory physiotherapy, exercise recommendations, and nutritional advice are often not implemented in the care of people with PCD in Switzerland. Multidisciplinary care in specialised centres by teams including physiotherapists and nutrition consultants could improve the quality of life of people with PCD.
A systematic review of ontology-based clinical decision support system rules: usage, management, and interoperability
Authors: Jing Xia , Min Hua , Gong Yang , Sittig Dean F. , Biondich Paul , Robinson David , Law Tim , Wright Adam , Nøhr Christian , Faxvaag Arild , Rennert Lior , Hubig Nina , Gimbel Ronald 
Published: May 2022

AbstractObjectiveClinical decision support systems (CDSS) have a critical role in improving the quality and safety of health care delivery. CDSS rules direct the behavior of CDSS. However, the CDSS rules have not been routinely shared and reused, and ontology can promote the reusing of CDSS rules. We systematically screened literature to elaborate on the current status of ontology applied in CDSS rule management.MethodsWe searched PubMed, the Association for Computing Machinery (ACM) Digital Library, and the Nursing & Allied Health Database for publications focusing on ontology, clinical decision support, and rules. Grounded theory and PRISMA 2020 guidelines were followed. One author started the screening and literature analysis, and two authors validated the processes and results. Inclusion and exclusion criteria were developed and refined iteratively.ResultsAmong 81 included publications, the identified CDSS were mainly applied to managing chronic conditions, alerts for medication prescriptions, reminders for immunizations and preventive services, diagnoses, and treatment recommendations. The CDSS rules were presented in Semantic Web Rule Language, Jess, or Jena formats. Despite ontology was used to supply medical knowledge, CDSS rules, and terminologies to CDSS, ontology has not been used in CDSS rule management.ConclusionsAlthough ontology can facilitate the reuse, management, and maintenance of CDSS rules, CDSS ontology remains unavailable indicating that more efforts are needed to improve the reusability and interoperability of CDSS rules.
High-speed MRI recordings of eyeball lifting, retraction and compression during blinks
Authors: Kirchner Johannes , Watson Tamara , Bauer Jochen , Lappe Markus 
Published: May 2022

AbstractBlinks occur frequently in normal life and have increasingly been linked to perceptual and cognitive effects. However, the oculomechanics of blink-related eye movements are much less researched than other types of eye movements. While it has been observed that the eye is being pulled back into its socket during a blink, possibly due to co-contraction of extraocular muscles, this elusive eye motion has not been studied in detail due to the technical difficulties that go along with a closed eyelid. Here we use dynamic magnetic resonance imaging (MRI) to obtain videos of this motion and analyse the kinematics with the recently developed MREyeTrack algorithm. We show that the eye is not only retracted but also lifted up during a blink. For some participants we observed eyeball lifting by up to 3 mm, far exceeding the amount of translation believed to occur during natural eye movements. Slow blinks can be accompanied by large tonic rotations of up to 15°. Furthermore, we collected evidence that the co-contraction of extraocular muscles leads to a slight compression of the eyeball. These findings demonstrate the surprising complexity of ocular motility and offer new opportunities to study orbital mechanics in health and disease.
Phenotypic and genetic factors are associated with absence of cardiomyopathy symptoms in PLN c.40_42delAGA carriers
Authors: Lopera-Maya Esteban A. , Li Shuang , de Brouwer Remco , Nolte Ilja M. , van Breen Justin ,   The Netherlands ACM registry,   Lifelines Cohort study, Jongbloed Jan D.H. , Swertz Morris A. , Snieder Harold , Franke Lude , Wijmenga Cisca , de Boer Rudolf A. , Deelen Patrick , van der Zwaag Paul A. , Sanna Serena 
Published: May 2022

AbstractThe c.40_42delAGA variant in the phospholamban gene (PLN) has been associated with dilated and arrhythmogenic cardiomyopathy, with up to 70% of carriers experiencing a major cardiac event by age 70. However, other carriers remain asymptomatic or show only mild symptoms in old age. To understand the mechanisms behind this incomplete penetrance, we evaluated potential phenotypic and genetic modifiers in 74 PLN c.40_42delAGA carriers identified in 36,339 participants of the Lifelines population cohort. Asymptomatic carriers (N=48) showed shorter QRS duration (−5.73 ms, p-value=0.001) compared to asymptomatic non-carriers and symptomatic carriers (N=26), and we replicated this in different subset of 21,771 participants from the Lifelines cohort (−3.87 ms, p-value=0.028) and in 592 carriers from the Arrhythmogenic Cardiomyopathy (ACM) patient registry (−6.91 ms, p-value=0.0002). Furthermore, symptomatic carriers showed a higher correlation between genetic predisposition to higher QRS duration (PGSQRS) and QRS (p-value=1.98×10-8), suggesting that symptomatic PLN c.40_42delAGA carriers may have an increased sensitivity to the effect of genetic variation in cardiac rhythm. Our results may help improve risk prediction models for cardiac outcomes for future studies, while our approach could guide studies on genetic diseases with incomplete penetrance.
Sociodemographic inequalities and excess non-COVID-19 mortality during the COVID-19 pandemic: A data-driven analysis of 1,069,174 death certificates in Mexico
Authors: Antonio-Villa Neftali Eduardo , Fermín-Martínez Carlos A. , Aburto José Manuel , Fernández-Chirino Luisa , Ramírez-García Daniel , Pisanty-Alatorre Julio , González-Díaz Armando , Vargas-Vázquez Arsenio , Seiglie Jacqueline A. , Barquera Simón , Gutiérrez-Robledo Luis Miguel , Bello-Chavolla Omar Yaxmehen 
Published: May 2022

ABSTRACTBACKGROUNDIn 2020, Mexico experienced one of the highest rates of excess mortality globally. However, the extent to which non-COVID deaths contributed to excess mortality, its regional characterization, and the association between municipal-and individual-level sociodemographic inequality has not been characterized.METHODSWe conducted a retrospective municipal an individual-level study using death certificate data in Mexico from 2016-2020. We analyzed mortality related to COVID-19 and to non-COVID-19 causes using ICD-10 codes to identify cause-specific mortality. Excess mortality was estimated as the increase in deaths in 2020 compared to the average of 2016-2019, disaggregated by primary cause of death, death setting (in-hospital and out-of-hospital) and geographical location. We evaluated correlates of non-COVID-19 mortality at the individual level using mixed effects logistic regression and correlates of non-COVID-19 excess mortality in 2020 at the municipal level using negative binomial regression.RESULTSWe identified 1,069,174 deaths in 2020 (833.5 per 100,000 inhabitants), which was 49% higher compared to the 2016-2019 average (557.38 per 100,000 inhabitants). Overall excess mortality (276.11 deaths per 100,000 inhabitants) was attributable in 76.1% to COVID-19; however, non-COVID-19 causes comprised one-fifth of excess deaths. COVID-19 deaths occurred primarily in-hospital, while excess non-COVID-19 deaths decreased in this setting and increased out-of-hospital. Excess non-COVID-19 mortality displayed geographical heterogeneity linked to sociodemographic inequalities with clustering in states in southern Mexico. Municipal-level predictors of non-COVID-19 excess mortality included levels of social security coverage, higher rates of COVID-19 hospitalization, and social marginalization. At the individual level, lower educational attainment, blue collar workers, and lack of medical care assistance were associated with non-COVID-19 mortality during 2020.CONCLUSIONNon-COVID-19 causes of death, largely chronic cardiometabolic conditions, comprised up to one-fifth of excess deaths in Mexico during 2020. Non-COVID-19 excess deaths occurred disproportionately out-of-hospital and were associated with both individual-and municipal-level sociodemographic inequalities. These findings should prompt an urgent call to action to improve healthcare coverage and access to reduce health and sociodemographic inequalities in Mexico to reduce preventable mortality in situations which increase the stress of healthcare systems, including the ongoing COVID-19 pandemic.
Post COVID-19 condition of the Omicron variant of SARS-CoV-2
Authors: Morioka Shinichiro , Tsuzuki Shinya , Suzuki Michiyo , Terada Mari , Akashi Masako , Osanai Yasuyo , Kuge Chika , Sanada Mio , Tanaka Keiko , Maruki Taketomo , Takahashi Kozue , Saito Sho , Hayakawa Kayoko , Teruya Katsuji , Hojo Masayuki , Ohmagari Norio 
Published: May 2022

AbstractBackgroundNo epidemiological data on post coronavirus disease (COVID-19) condition due to Omicron variant has been reported yet.MethodsThis was as a single-center, cross-sectional study, that interviewed via telephone the patients who recovered from Omicron COVID-19 infection (Omicron group), and surveyed via self-reporting questionnaire those patients infected with other strains (control group). Data on patients’ characteristics, information regarding the acute-phase COVID-19, as well as presence and duration of COVID-19-related symptoms were obtained. Post COVID-19 condition in this study was defined as a symptom that lasted at least 2 months within 3 months since the onset of COVID-19. We investigated and compared the prevalence of post COVID-19 condition in both groups after performing propensity score matching.ResultsWe conducted interviews for 53 out of 128 patients with Omicron, and obtained 502 responses in the control group. After matching, 18 patients each in Omicron and control group had improved covariate balance of the older adult, female sex, obese patients, and vaccination status. There were no significant differences in the prevalence of each post-acute COVID-19 symptoms between the two groups. The numbers of patients with at least one post-acute COVID-19 symptom in the Omicron and the control group were 1 (5.6%) and 10 (55.6%) (p=0.003), respectively.ConclusionThe prevalence of post Omicron COVID-19 conditions was less than that of the other strains. Further research with more participants is needed to investigate the precise epidemiology of post COVID-19 condition of Omicron, and its impact on health-related quality of life and social productivity.