bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seroprevalence of anti-SARS-CoV-2 specific antibodies in vaccinated and vaccine naïve adult Nigerians
Authors: Onifade Abdulfattah Adekunle , Fowotade Adeola , Rahamon Sheu Kadiri , Edem Victory Fabian , Yaqub Surajudeen Adebayo , Akande Olatunji Kadri , Arinola Olatunbosun Ganiyu 
Published: July 2022

AbstractBackgroundReports on the evaluation of immune responses to different COVID-19 vaccines are limited. Similarly, effects of age and gender have not been well explored as variables that could impact on the vaccine-induced antibody response. Therefore, seroprevalence of anti-SARS-CoV-2 specific antibodies in vaccinated and vaccine naïve adult Nigerians was determined in this study.MethodologyA total of 141 adults were enrolled into this study. Presence or absence of SARS-CoV-2 infection was confirmed by real-time reverse-transcriptase polymerase-chain reaction (RT-PCR) assay on nasopharyngeal and oropharyngeal swab specimens. Anti-SARS-CoV-2 Specific IgG and IgM antibodies were qualitatively detected using a Rapid Diagnostic Test kit.ResultsPre-vaccination, 77% of the study participants had never had PCR-confirmed COVID-19 test yet 66.7% of them were seropositive for SARS-CoV-2 antibodies. Of 111 COVID-19 vaccinated participants, 69.2% and 73.8% of them had SARS-CoV-2 specific IgG post-first and second doses of COVID-19 vaccine respectively. However, 23.1% and 21.4% of the participants who have had first and second doses respectively had no detectable anti-SARS-CoV-2 antibodies. The proportion of participants with SARS-CoV-2 specific IgG was insignificantly higher in those between the ages of 18 – 40 years and 41 – 59 years compared with individuals aged ≥60 years. No significant association was observed between gender and seropositivity for SARS-CoV-2 antibodies.ConclusionThere is high SARS-CoV-2 antibody seroprevalence among Nigerian adults who never had PCR-confirmed COVID-19. Also, there is the need for anti-SARS-CoV-2 antibodies screening post vaccination as this could be essential in achieving herd immunity. Age and gender do not seem to have significant association with seropositivity.
Estimating the prevalence of LAMA2 congenital muscular dystrophy using population genetic databases
Authors: Lake Nicole J. , Phua Joel , Liu Wei , Moors Tristen , Axon Steven , Lek Monkol 
Published: July 2022

AbstractBACKGROUNDRecessive pathogenic variants in LAMA2 resulting in complete or partial loss of laminin α2 protein cause congenital muscular dystrophy (LAMA2 CMD). The prevalence of LAMA2 CMD has been estimated by epidemiological studies to lie between 1.36 - 20 cases per million. However, prevalence estimates from epidemiological studies are vulnerable to inaccuracies owing to challenges with studying rare diseases. Population genetic databases offer an alternative method for estimating prevalence.OBJECTIVEWe aim to use population allele frequency data for reported and predicted pathogenic variants to estimate the birth prevalence of LAMA2 CMD.METHODSA list of reported pathogenic LAMA2 variants was compiled from public databases, and supplemented with predicted loss of function (LoF) variants in genome aggregation database (gnomAD). gnomAD allele frequencies for 273 reported pathogenic and predicted LoF LAMA2 variants were used to calculate disease prevalence using a Bayesian methodology.RESULTSThe world-wide birth prevalence of LAMA2 CMD was estimated to be 8.3 per million (95% confidence interval (CI) 6.27 – 10.5 per million). The prevalence estimates for each population in gnomAD varied, ranging from 1.79 per million in East Asians (95% CI 0.63 – 3.36) to 10.1 per million in Europeans (95% CI 6.74 – 13.9). These estimates were generally consistent with those from epidemiological studies, where available.CONCLUSIONSWe provide robust world-wide and population-specific birth prevalence estimates for LAMA2 CMD, including for non-European populations in which LAMA2 CMD prevalence hadn’t been studied. This work will inform the design and prioritization of clinical trials for promising LAMA2 CMD treatments.
SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern
Authors: Aggarwal Anupriya , Akerman Anouschka , Milogiannakis Vanessa , Silva Mariana Ruiz , Walker Gregory , Kidinger Andrea , Angelovich Thomas , Waring Emily , Amatayakul-Chantler Supavadee , Roth Nathan , Coppola Germano , Yeang Malinna , Jean Tyra , Foster Charles , Hoppe Alexandra Carey , Ling Munier C. Mee , Darley David , Churchill Melissa , Starck Damian , Christ Daniel , Matthews Gail , Rawlinson William , Kelleher Anthony D. , Turville Stuart 
Published: July 2022

AbstractGenetically distinct viral variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been recorded since January 2020. Over this time global vaccine programs have been introduced, contributing to lower COVID-19 hospitalisation and mortality rates, particularly in developed countries. In late 2021, the Omicron BA.1 variant emerged, with substantially different genetic differences and clinical effects from other variants of concern (VOC). This variant demonstrated higher numbers of polymorphisms in the gene encoding the Spike (S) protein, and it has displaced the previously dominant Delta variant. Shortly after dominating global spread in early 2022, BA.1 was supplanted by the genetically distinct Omicron lineage BA.2. A sub-lineage of BA.2, designated BA.5 has now started to dominate globally, with the potential to supplant BA.2. To address the relative threat of BA.5, we determined infectivity to particle ratios in primary nasopharyngeal samples and expanded low passage isolates in a well characterised, genetically engineered ACE2/TMPRSS2 cell line. We then assessed the impact of BA.5 infection on humoral neutralisation in vitro, in vaccinated and convalescent cohorts, using concentrated human IgG pooled from thousands of plasma donors, and licensed monoclonal antibody therapies. The infectivity of virus in primary swabs and expanded isolates revealed that whilst BA.1 and BA.2 are attenuated through ACE2/TMPRSS2, BA.5 infectivity is equivalent to that of an early 2020 circulating clade and has greater sensitivity to the TMPRSS2 inhibitor Nafamostat. As with BA.1, we observed BA.5 to significantly reduce neutralisation titres across all donors. Concentrated pooled human IgG from convalescent and vaccinated donors had greater breadth of neutralisation, although the potency was still reduced 7-fold with BA.5. Of all therapeutic antibodies tested, we observed a 14.3-fold reduction using Evusheld and 16.8-fold reduction using Sotrovimab when neutralising a Clade A versus BA.5 isolate. These results have implications for ongoing tracking and management of Omicron waves globally.
Assessing the impact of SARS-CoV-2 lineages and mutations on patient survival
Authors: Loucera Carlos , Perez-Florido Javier , Casimiro-Soriguer Carlos S. , Ortuño Francisco M. , Carmona Rosario , Bostelmann Gerrit , Martínez-González L. Javier , Muñoyerro-Muñiz Dolores , Villegas Román , Rodriguez-Baño Jesus , Romero-Gomez Manuel , Lorusso Nicola , Garcia-León Javier , Navarro-Marí Jose M. , Camacho-Martinez Pedro , Merino-Diaz Laura , de Salazar Adolfo , Viñuela Laura ,   The Andalusian COVID-19 sequencing initiative, Lepe Jose A , Garcia Federico , Dopazo Joaquin 
Published: July 2022

AbstractAfter more than two years of COVID-19 pandemic, SARS-CoV-2 still remains a global public health problem. Successive waves of infection have produced new SARS-CoV-2 variants with new mutations whose impact on COVID-19 severity and patient survival is uncertain. A total of 764 SARS-CoV-2 genomes sequenced from COVID-19 patients, hospitalized from 19th February 2020 to 30st April 2021, along with their clinical data, were used for survival analysis. A significant association of B.1.1.7, the alpha lineage, with patient mortality (Log Hazard ratio LHR=0.51, C.I.=[0.14,0.88]) was found upon adjustment by all the covariates known to affect COVID-19 prognosis. Moreover, survival analysis of mutations in the SARS-CoV-2 genome rendered 27 of them significantly associated with higher mortality of patients. Most of these mutations were located in the S, ORF8 and N proteins. This study illustrates how a combination of genomic and clinical data provide solid evidence on the impact of viral lineage on patient survival.
PET/CT and SPECT/CT imaging of 90Y hepatic radioembolization at therapeutic and diagnostic activity levels: anthropomorphic phantom study
Authors: Budzyńska A , Kubik A , Kacperski K , Szubstarska P , Kuć M , Piasecki P , Konior M , Gryziński M , Dziuk M , Iller E 
Published: July 2022

AbstractPurposePrior to 90Y radioembolization procedure a pretherapy simulation using 99mTc-MAA is performed. Alternatively, a small dosage of 90Y microspheres could be used. We aimed to assess the accuracy of lung shunt fraction (LSF) estimation in both high activity 90Y posttreatment and pretreatment scans with isotope activity of ∼100 MBq, using different imaging techniques. Additionally, we assessed the feasibility of visualising hot and cold hepatic tumours in PET/CT and Bremsstrahlung SPECT/CT images.Materials and MethodsAnthropomorphic phantom including liver (with two spherical tumours) and lung inserts was filled with 90Y chloride to simulate an LSF of 9.8%. The total initial activity in the liver was 1451 MBq, including 19.4 MBq in the hot sphere. Nine measurement sessions including PET/CT, SPECT/CT, and planar images were acquired at activities in the whole phantom ranging from 1618 MBq down to 43 MBq.The visibility of the tumours was appraised based on independent observers’ scores. Quantitatively, contrast-to-noise ratio (CNR) was calculated for both spheres in all images.ResultsLSF estimation: For high activity in the phantom, PET reconstructions slightly underestimated the LSF; absolute difference was <1.5pp (percent point). For activity <100 MBq, the LSF was overestimated. Both SPECT and planar scintigraphy overestimated the LSF for all activities.Foci visibility: For SPECT/CT the cold tumour proved too small to be discernible (CNR <0.5) regardless of the 90Y activity in the liver, while hot sphere was visible for activity >200 MBq (CNR>4). For PET/CT, the cold tumour was only visible with the highest 90Y activity (CNR>4), whereas the hot one was seen for activity >100 MBq (CNR>5).ConclusionsPET/CT may accurately estimate the LSF in a 90Y posttreatment procedure. However, at low activities of about 100 MBq it seems to provide unreliable estimations. PET imaging provided better visualisation of both hot and cold tumours.
Monkeypox caused less worry than COVID-19 among the general population during the first month of the WHO Monkeypox alert
Authors: Temsah Mohamad-Hani , Aljamaan Fadi , Alenezi Shuliweeh , Alhasan Khalid , Saddik Basema , Al-Barag Ahmad , Alhaboob Ali , Bahabri Nezar , Alshahrani Fatimah , Alrabiaah Abdulkarim , Alaraj Ali , Bahkali Feras , Alkriadees Khaled , Jamal Amr , Halwani Rabih , AlZamil Fahad , Al-Subaie Sarah , Barry Mazin , Memish Ziad A , Al-Tawfiq Jaffar A. 
Published: July 2022

AbstractBackgroundMonkeypox re-emerged in May 2022 as another global health threat. This study assessed the public’s perception, worries, and vaccine acceptance for Monkeypox and COVID-19 during the first month of WHO announcement.MethodsA national cross-sectional survey was conducted between May 27 and June 5, 2022, in Saudi Arabia. Data were collected on sociodemographic characteristics, previous infection with COVID-19, worry levels regarding Monkeypox compared to COVID-19, awareness, and perceptions of Monkeypox, and vaccine acceptance.ResultsAmong the 1546 participants, most respondents (62%) were more worried about COVID-19 than Monkeypox. Respondents aged 45 years and above and those with a university degree or higher had lower odds of agreement with Monkeypox vaccination (OR .871, p-value .006, OR .719, p-value <0.001), respectively. Respondents with moderate to a high level of self and family commitment to infection control precautionary measures and those who expressed self and family worry of Monkeypox infection had significantly higher odds of vaccination agreement (OR 1.089 p-value=0.047, OR1.395 p-value=0.003) respectively. On the other hand, respondents who previously developed COVID-19 were significantly more worried about the Monkeypox disease (1.30 times more, p-value=0.020).ConclusionWorry levels amongst the public are higher from COVID-19 than Monkeypox. Perception of Monkeypox as a dangerous and virulent disease, worry from contracting the disease, and high commitment to infection precautionary measures were predictors of agreement with Monkeypox vaccination. While advanced age and high education level are predictors of low agreement with vaccination.
COVID-19 in non-hospitalised adults caused by either SARS-CoV-2 sub-variants Omicron BA.1, BA.2, BA.5 or Delta associates with similar illness duration, symptom severity and viral kinetics, irrespective of vaccination history
Authors: Townsley Hermaleigh , Gahir Joshua , Russell Timothy W , Carr Edward J , Dyke Matala , Adams Lorin , Miah Murad , Clayton Bobbi , Smith Callie , Miranda Mauro , Mears Harriet V , Bailey Chris , Black James RM , Fowler Ashley S , Crawford Margaret , Wilkinson Katalin , Hutchinson Matthew , Harvey Ruth , O’Reilly Nicola , Kelly Gavin , Goldstone Robert , Beale Rupert , Papineni Padmasayee , Corrah Tumena , Gilson Richard , Caidan Simon , Nicod Jerome , Gamblin Steve , Kassiotis George , Libri Vincenzo , Williams Bryan , Gandhi Sonia , Kucharski Adam J , Swanton Charles , Bauer David LV , Wall Emma C 
Published: July 2022

AbstractBackgroundSARS-CoV-2 variant Omicron rapidly evolved over 2022, causing three waves of infection due to sub-variants BA.1, BA.2 and BA.4/5. We sought to characterise symptoms and viral loads over the course of COVID-19 infection with these sub-variants in otherwise-healthy, vaccinated, non-hospitalised adults, and compared data to infections with the preceding Delta variant of concern (VOC).MethodsIn a prospective, observational cohort study, healthy vaccinated UK adults who reported a positive PCR or lateral flow test, self-swabbed on alternate days until day 10. We compared symptoms and viral load trajectories between infections caused by VOCs Delta and Omicron (sub-variants BA.1, BA.2 and BA.4/5), and tested for relationships between vaccine dose, symptoms and PCR Ct value as a proxy for viral load.Results555 infection episodes were reported among 483 participants. Across VOCs, symptom burden and duration were similar, however symptom profiles differed among infections caused by Delta compared to Omicron sub-variants; symptoms of all Omicron sub-variants BA.1, BA.2 and BA.4/5 were very similar. Anosmia was reported in 7-13% of participants with Omicron sub-variants, compared to 25/60 (42%) with Delta infection (P= 1.31e-08 or 1.03e-05 or 5.63e-05; χ2test d2+Delta vs. Omicron BA.1 or vs. BA.2, or BA.5, respectively), fever was more common with Omicron BA.5 (30/55, 55%) than Delta (20/60, 33%) (p 0.03). Amongst infections with all Omicron sub-variants, symptoms of coryza, fatigue, cough and myalgia predominated. Viral load trajectories and peaks did not differ between Delta, and Omicron, irrespective of symptom severity (including asymptomatic participants), VOC or vaccination status. Ct values were negatively associated with time since vaccination in participants infected with BA.1; however, this trend was not observed in BA.2/BA.4/5 infections.ConclusionOur study emphasises both the changing symptom profile of COVID-19 infections in the Omicron era, and ongoing transmission risk of Omicron sub-variants in vaccinated adults.Trial registrationNCT04750356
Modeling the impact of the Omicron infection wave in Germany
Authors: Maier Benjamin F. , Burdinski Angelique , Wiedermann Marc , Rose Annika H. , der Heiden Matthias an , Wichmann Ole , Harder Thomas , Schlosser Frank , Brockmann Dirk 
Published: July 2022

BACKGROUNDIn November 2021, the first case of SARS-CoV-2 “variant of concern” (VOC) B.1.1.529 (“Omicron”) was reported in Germany, alongside global reports of reduced vaccine efficacy against infections with this variant. The potential threat posed by the rapid spread of this variant in Germany remained, at the time, elusive.METHODSWe developed a variant-dependent population-averaged susceptible-exposed-infected-recovered (SEIR) infectious disease model. The model was calibrated on the observed fixation dynamics of the Omicron variant in December 2021, and allowed us to estimate potential courses of upcoming infection waves in Germany, focusing on the corresponding burden on intensive care units (ICUs) and the efficacy of contact reduction strategies.RESULTSA maximum median incidence of approximately 300 000 (50% PI in 1000: [181,454], 95% PI in 1000: [55,804]) reported cases per day was expected with the median peak occurring in the mid of February 2022, reaching a cumulative Omicron case count of 16.5 million (50% PI in mio: [11.4, 21.3], 95% PI in mio: [4.1, 27.9]) until Apr 1, 2022. These figures were in line with the actual Omicron waves that were subsequently observed in Germany with respective peaks occurring in mid February (peak: 191k daily new cases) and mid March (peak: 230k daily new cases), cumulatively infecting 14.8 million individuals during the study period. The model peak incidence was observed to be highly sensitive to variations in the assumed generation time and decreased with shorter generation time. Low contact reductions were expected to lead to containment. Early, strict, and short contact reductions could have led to a strong “rebound” effect with high incidences after the end of the respective non-pharmaceutical interventions. Higher vaccine uptake would have led to a lower outbreak size. To ensure that ICU occupancy remained below maximum capacity, a relative risk of requiring ICU care of 10%–20% was necessary (after infection with Omicron vs. infection with Delta).CONCLUSIONSWe expected a large cumulative number of infections with the VOC Omicron in Germany with ICU occupancy likely remaining below capacity nevertheless, even without additional non-pharmaceutical interventions. Our estimates were in line with the retrospectively observed waves. The results presented here informed legislation in Germany. The methodology developed in this study might be used to estimate the impact of future waves of COVID-19 or other infectious diseases.
Cohort-mean measured macromolecules lead to more robust linear-combination modeling than parameterized and subject-specific ones
Authors: Zöllner Helge J. , Davies-Jenkins Christopher W. , Murali-Manohar Saipavitra , Gong Tao , Hui Steve C. N. , Song Yulu , Chen Weibo , Wang Guangbin , Edden Richard A. E. , Oeltzschner Georg 
Published: July 2022

AbstractExpert consensus recommends linear-combination modeling (LCM) of 1H MR spectra with sequence-specific simulated metabolite basis function and experimentally derived macromolecular (MM) basis functions. Measured MM basis functions have been derived from metabolite-nulled spectra averaged across a small cohort. The use of subject-specific instead of cohort-averaged measured MM basis functions has not been studied. Furthermore, measured MM basis functions are not widely available to non-expert users, who commonly rely on parameterized MM signals internally simulated by LCM software. To investigate the impact of the choice of MM modeling, this study, therefore, compares metabolite level estimates between different MM modeling strategies (cohort-mean measured; subject-specific measured; parameterized) in a lifespan cohort and characterizes its impact on metabolite-age associations.100 conventional (TE = 30 ms) and metabolite-nulled (TI = 650 ms) PRESS datasets, acquired from the medial parietal lobe in a lifespan cohort (20-70 years of age), were analyzed in Osprey. Short-TE spectra were modeled in Osprey using six different strategies to consider the macromolecular baseline. Fully tissue- and relaxation-corrected metabolite levels were compared between MM strategies. Model performance was evaluated by model residuals, the Akaike information criterion (AIC), and the impact on metabolite-age associations.The choice of MM strategy had a significant impact on the mean metabolite level estimates and no major impact on variance. Correlation analysis revealed moderate-to-strong agreement between different MM strategies (r > 0.6). The lowest relative model residuals and AIC values were found for the cohort-mean measured MM. Metabolite-age associations were consistently found for two major singlet signals (tCr, tCho) for all MM strategies, however, findings for highly J-coupled metabolites it was depended on the MM strategy. A variance partition analysis indicated that up to 44% of the total variance was related to the choice of MM strategy. Additionally, the variance partition analysis reproduced the metabolite-age association for tCr and tCho found in the simpler correlation analysis.In summary, the inclusion of a single high-SNR MM basis function (cohort-mean) leads to more robust metabolite estimation (lower model residuals and AIC values) compared to MM strategies with more degrees of freedom (Gaussian parametrization) or subject-specific MM information. Integration of multiple LCM analyses into a single statistical model potentially improves the robustness in the detection of underlying effects (e.g. metabolite vs age), reduces algorithm-based bias, and estimates algorithm-related variance.
Ethanol Exposure Perturbs Sea Urchin Development and Disrupts Developmental Timing
Authors: Rodríguez-Sastre Nahomie , Shapiro Nicholas , Hawkins Dakota Y. , Lion Alexandra T. , Peyreau Monique , Correa Andrea E. , Dionne Kristin , Bradham Cynthia A. 
Published: July 2022

AbstractEthanol is a known vertebrate teratogen that causes craniofacial defects as a component of fetal alcohol syndrome (FAS). Our results show that sea urchin embryos treated with ethanol similarly show broad skeletal patterning defects, potentially analogous to the defects associated with FAS. The sea urchin larval skeleton is a simple patterning system that involves only two cell types: the primary mesenchymal cells (PMCs) that secrete the calcium carbonate skeleton and the ectodermal cells that provide migratory, positional, and differentiation cues for the PMCs. Perturbations in RA biosynthesis and Hh signaling pathways are thought to be causal for the FAS phenotype in vertebrates. Surprisingly, our results indicate that these pathways are not functionally relevant for the teratogenic effects of ethanol in developing sea urchins. We found that developmental morphology as well as the expression of ectodermal and PMC genes was delayed by ethanol exposure. Temporal transcriptome analysis revealed significant impacts of ethanol on signaling and metabolic gene expression, and a disruption in the timing of GRN gene expression that includes both delayed and precocious gene expression throughout the specification network. We conclude that the skeletal patterning perturbations in ethanol-treated embryos likely arise from a loss of temporal synchrony within and between the instructive and responsive tissues.