bluuebunny/crossref_metadata_2025_split huggingface dataset:
Serial infection with SARS-CoV-2 Omicron BA.1 and BA.2 following three-dose COVID-19 vaccination
Authors: Lapointe Hope R. , Mwimanzi Francis , Cheung Peter K. , Sang Yurou , Yaseen Fatima , Kalikawe Rebecca , Datwani Sneha , Waterworth Rachel , Umviligihozo Gisele , Ennis Siobhan , Young Landon , Dong Winnie , Kirkby Don , Burns Laura , Leung Victor , Holmes Daniel T. , DeMarco Mari L. , Simons Janet , Matic Nancy , Montaner Julio S.G. , Brumme Chanson J. , Prystajecky Natalie , Niikura Masahiro , Lowe Christopher F. , Romney Marc G. , Brockman Mark A. , Brumme Zabrina L. 
Published: May 2022

ABSTRACTSARS-CoV-2 Omicron infections are common among individuals who are vaccinated or have recovered from prior variant infection, but few reports have documented serial Omicron infections. We characterized SARS-CoV-2 humoral responses in a healthy young person who acquired laboratory-confirmed Omicron BA.1.15 ten weeks after a third dose of BNT162b2, and BA.2 thirteen weeks later. Responses were compared to those of 124 COVID-19 naive vaccinees. One month after the second and third vaccine doses, the participant’s wild-type and BA.1-specific IgG, ACE2 competition and virus neutralization activities were average for a COVID-19 naive triple-vaccinated individual. BA.1 infection boosted the participant’s responses to the cohort ≥95th percentile, but even this strong “hybrid” immunity failed to protect against BA.2. Moreover, reinfection increased BA.1 and BA.2-specific responses only modestly. Results illustrate the risk of Omicron infection in fully vaccinated individuals and highlight the importance of personal and public health measures as vaccine-induced immune responses wane.
The role of healthcare cost accounting in pricing and reimbursement in low- and middle-income countries
Authors: Guinness Lorna , Ghosh Srobana , Mehndiratta Abha , Shah Hiral Anil 
Published: May 2022

AbstractBackgroundProgress towards universal health coverage requires evidence based policy and good quality cost data systems. Establishing these systems, can be complex, resource intensive and take time. Synthesising information on the experiences of low-and-middle income countries (LMICs) in trying to institutionalize cost data systems provides lessons for other settings.MethodsWe performed a scoping literature review, screening for publicly available peer-reviewed English-language publications alongside a grey literature search, focussing on national level health system costing in LMICs, and used a narrative synthesis approach to document experience of costing and how costing evidence is used to inform tariffs.ResultsA total of 484 papers were initially identified of which 30 papers were considered eligible. Fourteen papers reported on primary cost data collection for price-setting purposes; 18 papers provided an explanation of how cost evidence informs tariff-setting. Documented experience is largely focussed in the Asia region (n = 22) with countries at different stages of developing cost systems to inform tariff setting. Country experiences on healthcare cost accounting tend to showcase country costing experiences, methods and implementation. There is little documentation of how cost data has been incorporated into decision making and price setting. Where cost data, cost systems and costing has been used, improved transparency in decision making alongside increased service provision efficiency has followed.ConclusionsWhile there are accepted and widely used methods for generating cost information, countries need to build sustainable cost systems appropriate to their settings and budgets and adopt transparent processes and methodologies for translating costs into prices.
Depiction of cell atlas and analysis of microenvironment alterations in human meniscus degeneration using single-cell transcriptomic
Authors: Fu Weili , Chen Sijie , Yang Runze , Gao Haoxiang , Li Jian , Zhang Xuegong 
Published: May 2022

AbstractBackgroundMusculoskeletal tissue degeneration impairs the life quality and function of many people. Meniscus degeneration is a major origin of knee osteoarthritis and a common threat to athletic ability, but its cellular mechanism remains elusive.MethodsWe built a cell atlas of healthy/degenerated human meniscus using scRNA-seq to investigate meniscal microenvironment homeostasis and its changes in the degeneration process and verified findings with immunofluorescent imaging.ResultsWe identified and localized cell types in inner and outer meniscus, found new chondrocyte subtypes contributing to degeneration, and revealed how cellular compositions, functions, and interactions participated in degeneration.We found that ECM disassembly, angiogenesis, and inflammation form a positive feedback loop driving the degeneration. Comparison of cellular interactions between different degenerative states identified each cell type’s functions in the loop.ConclusionsThe study revealed changes in the meniscal microenvironment during degeneration and discovered new cell subtypes as potential therapeutic targets. The observed mechanism could also be a general model for other joint degenerations.FundingThe National Natural Science Foundation of China (81972123, 82172508, 62050178, 61721003) and the National Key Research and Development Program of China (2021YFF1200901).
How should job crafting interventions be implemented to make their effects last? Study protocol of group concept mapping
Authors: Roczniewska Marta , Rundgren Emma Hedberg , Hasson Henna , Bakker Arnold B. , von Thiele Schwarz Ulrica 
Published: May 2022

AbstractBy means of job crafting (JC) employees shape and customize their job design to align it with their preferences. Research has so far shown that such bottom-up proactivity can be stimulated via JC interventions. While the overall effectiveness behind these interventions has been supported, it is unclear how to implement these interventions to make their effects lasting. The overall aim of this project will be to investigate how to implement JC interventions with lasting effects. We will apply a group concept mapping (GCM) methodology, which is a mixed methods approach for engaging stakeholder groups in a structured conceptualization process. As part of concept mapping procedures, brainstorming sessions will be conducted with experts in job crafting to identify factors expected to make job crafting intervention effects lasting. These factors will be sorted by similarity and rated by each participant in regard to their perceived importance and feasibility to ensure lasting, sustainable effects. The data will be analyzed using multidimensional scaling (MDS), hierarchical cluster analysis, descriptive and inferential statistics, resulting in a visual representation of conceptually distinguished clusters representing the factors influencing sustainability of JC interventions. In the final step of the GCM methodology, a workshop will be conducted with the participants to facilitate interpretation of the results. This study will provide knowledge relevant to organizational practitioners and scholars who want to implement JC interventions with lasting effects.
Spectrum of Adverse Event Following COVID-19 Immunization in High Altitude, Nepal
Authors: Gurung Minani , Lama Tashi , Rajbhandari Bibek , Shilpakar Olita , Maharjan Ashmita , Nepal Sujita , Gajmer Dev , Lama Kailash , Poudel Lisasha 
Published: May 2022

ABSTRACTIntroductionNepal started vaccinating frontline workers against COVID-19, in January 2021.Side effects of the vaccine are still unknown in high altitude regions. Poor surveillance and the lack of health workers in remote places to take care of people in case of vaccination side-effects could prove to be a challenge in the drive, especially in high altitudes like Humla district, Nepal. High altitude regions are harder to access and also mobilization of vaccines and manpower is strenuous due to harsh weather conditions and complex geography. We aimed to study the spectrum of Adverse Event Following COVID-19 Immunization among the front liners of Humla district.MethodsThis is a cross-sectional study conducted in Humla district, Nepal. COVID-19 Immunization vaccine recipients were contacted through a phone call within 5 days of vaccination to record the adverse effects. Patterns and distribution of adverse effects were analyzed in high altitude settings. Ethical approval was taken from Nepal Health Research Council.ResultsOf total respondents, 84.1% (95% C.I: 80.9 to 86.9) had shown symptoms after vaccination. The average time for the appearance of symptoms was 1.27 +_ 0.60 days. For systemic effects, tenderness was the side effect seen after vaccination (63.8%) followed by other side effects like pain (58.5%), Pyrexia (37.4%), Chills (29.8%), Myalgia (28.9%) and Malaise (15.2%) while for localized effects, the symptoms such as Arthralgia (16.6%) and Bruising (16.1%) were the most common effects.ConclusionsSerious and life threatening adverse effects following immunization were not seen in our study site which was of altitude 2500 meter and above. Our study shows a similar type of side effect pattern as that of the lower altitude regions.
Covid-19 Vaccine Acceptance Among People Incarcerated in Connecticut State Jails
Authors: Lind Margaret L. , Kennedy Byron S. , Nieto Murilo Dorion , Houde Amy J. , Sosensky Peri , Borg Ryan , Cummings Derek A.T. , Ko Albert I. , Richeson Robert P. 
Published: May 2022

AbstractObjectiveTo assess the Connecticut Department of Correction’s (DOC) COVID-19 vaccine program within jails.MethodsWe conducted a retrospective cohort analysis among people who were incarcerated in a DOC-operated jail between February 2 and November 8, 2021, and were eligible for vaccination at the time of incarceration (intake). We compared the vaccination rates before and after incarceration using an age-adjusted survival analysis with a time-varying exposure of incarceration and an outcome of vaccination.ResultsDuring the study period, 3,716 people spent ≥1 night in jail and were eligible for vaccination at intake. Of these residents, 136 were vaccinated prior to incarceration, 2,265 had a recorded vaccine offer, and 476 were vaccinated while incarcerated. The age-adjusted hazard of vaccination following incarceration was significantly higher than prior to incarceration (12.5; 95% CI: 10.2-15.3).ConclusionsWe found that residents were more likely to become vaccinated in jail than the community. Though these findings highlight the utility of vaccination programs within jails, the low level of vaccination in this population speaks to the need for additional program development within jails and the community.
A comparative study of structural variant calling strategies using the Alzheimer’s Disease Sequencing Project’s whole genome family data
Authors: Malamon John S. , Farrell John J. , Xia Li Charlie , Dombroski Beth A. , Lee Wan-Ping , Das Rueben G. , Vardarajan Badri N. , Way Jessica , Kuzma Amanda B. , Valladares Otto , Leung Yuk Yee , Scanlon Allison J. , Barrera Lopez Irving Antonio , Brehony Jack , Worley Kim C. , Zhang Nancy R. , Wang Li-San , Farrer Lindsay A. , Schellenberg Gerard D. 
Published: May 2022

ABSTRACTBackgroundReliable detection and accurate genotyping of structural variants (SVs) and insertion/deletions (indels) from whole-genome sequence (WGS) data is a significant challenge. We present a protocol for variant calling, quality control, call merging, sensitivity analysis, in silico genotyping, and laboratory validation protocols for generating a high-quality deletion call set from whole genome sequences as part of the Alzheimer’s Disease Sequencing Project (ADSP). This dataset contains 578 individuals from 111 families.MethodsWe applied two complementary pipelines (Scalpel and Parliament) for SV/indel calling, break-point refinement, genotyping, and local reassembly to produce a high-quality annotated call set. Sensitivity was measured in sample replicates (N=9) for all callers using in silico variant spike-in for a wide range of event sizes. We focused on deletions because these events were more reliably called. To evaluate caller specificity, we developed a novel metric called the D-score that leverages deletion sharing frequencies within and outside of families to rank recurring deletions. Assessment of overall quality across size bins was measured with the kinship coefficient. Individual callers were evaluated for computational cost, performance, sensitivity, and specificity. Quality of calls were evaluated by Sanger sequencing of predicted loss-of-function (LOF) variants, variants near AD candidate genes, and randomly selected genome-wide deletions ranging from 2 to 17,000 bp.ResultsWe generated a high-quality deletion call set across a wide range of event sizes consisting of 152,301 deletions with an average of 263 per genome. A total of 114 of 146 predicted deletions (78.1%) were validated by Sanger sequencing. Scalpel was more accurate in calling deletions ≤100 bp, whereas for Parliament, sensitivity was improved for deletions > 900 bp. We validated 83.0% (88/106) and 72.5% (37/51) of calls made by Scalpel and Parliament, respectively. Eleven deletions called by both Parliament and Scalpel in the 101-900 bin were tested and all were confirmed by Sanger sequencing.ConclusionsWe developed a flexible protocol to assess the quality of deletion detection across a wide range of sizes. We also generated a truth set of Sanger sequencing validated deletions with precise breakpoints covering a wide spectrum of sizes between 1 and 17,000 bp.
Processing of task-irrelevant sounds during typical everyday activities in children
Authors: Debnath Ranjan , Wetzel Nicole 
Published: May 2022

AbstractOur ability to focus on a task and ignore task-irrelevant stimuli is critical for efficient cognitive functioning. Attention control is especially required in the auditory modality as sound has privileged access to perception and consciousness. Despite this important function, little is known about auditory attention during typical everyday activities in childhood. We investigated the impact of task-irrelevant sounds on attention during three everyday activities – playing a game, reading a book, watching a movie. During these activities, environmental novel sounds were presented within a sequence of standard sounds to 7–8-year-old children and adults. We measured ERPs reflecting early sound processing and attentional orienting and theta power evoked by standard and novel sounds during these activities. Playing a game vs. reading or watching reduced early encoding of sounds in children and affected ongoing information processing and attention allocation in both groups. In adults, theta power was reduced during playing at mid-central brain areas. Results show a pattern of immature neuronal mechanisms underlying perception and attention of task-irrelevant sounds in 7–8-year-old children. While the type of activity affected the processing of irrelevant sounds in both groups, early stimulus encoding processes were more sensitive to the type of activities in children.
Model-based intensification of CHO cell cultures: one-step strategy from fed-batch to perfusion
Authors: Richelle Anne , Corbett Brandon , Agarwal Piyush , Vernersson Anton , Trygg Johan , McCready Chris 
Published: May 2022

ABSTRACTThere is a growing interest in continuous processing of the biopharmaceutical industry. However, the technology transfer from traditional batch-based processes is considered a challenge as protocol and tools still remain to be established for their usage at the manufacturing scale. Here, we present a model-based approach to design optimized perfusion cultures of CHO cells using only the knowledge captured during small-scale fed-batch experiments. The novelty of the proposed model lies in the simplicity of its structure. Thanks to the introduction of a new catch-all variable representing a bulk of by-products secreted by the cells during their cultivation, the model was able to successfully predict cellular behavior under different operating modes without changes in its formalism. To our knowledge, this is the first experimentally validated model capable, with a single set of parameters, to capture culture dynamic under different operating modes and at different scales.
Population estimate, natural history and conservation of the melanisticIguana Iguanapopulation on Saba, Caribbean Netherlands
Authors: van den Burg Matthijs P. , Madden Hannah , Debrot Adolphe O. 
Published: May 2022

AbstractIntraspecific diversity is among the most important biological variables, although still poorly understood for most species.Iguana iguanais a Neotropical lizard known from Central and South America, including from numerous Caribbean islands. Despite the presence of native melanisticI. iguanapopulations in the Lesser Antilles, these have received surprisingly little research attention. Here we assessed population size, distribution, degree of melanism, and additional morphological and natural history characteristics for the melanistic iguanas of Saba, Caribbean Netherlands based on a one-month fieldwork visit. Using Distance sampling from a 38-transect dataset we estimate the population size at 8233 ±2205 iguanas. Iguanas mainly occurred on the southern and eastern sides of the island, between 180-390 m (max altitude 530 m), with highest densities both in residential and certain natural areas. Historically, iguanas were relatively more common at higher altitudes, probably due to more extensive forest clearing for agricultural reasons. No relationship was found between the degree of melanism and elevation, and few animals were completely melanistic. Furthermore, we found that body-ratio data collection through photographs is biased and requires physical measuring instead. Although the population size appears larger than previously surmised, the limited nesting sites and extremely low presence of juvenile and hatchling iguanas (2.4%), is similarly worrying as the situation forI. delicatissimaon neighboring St. Eustatius. The island’s feral cat and large goat population are suspected to impact nest site quality, nest success, and hatchling survival. These aspects require urgent future research to guide necessary conservation management.
Scalable power analysis and effect size exploration of microbiome community differences with Evident
Authors: Rahman Gibraan , McDonald Daniel , Gonzalez Antonio , Vázquez-Baeza Yoshiki , Jiang Lingjing , Casals-Pascual Climent , Peddada Shyamal , Hakim Daniel , Dilmore Amanda Hazel , Nowinski Brent , Knight Rob 
Published: May 2022

AbstractDifferentiating microbial communities among samples is a major objective in biomedicine. Quantifying the effect size of these differences allows researchers to understand the factors most associated with communities and to optimize the design and clinical resources required to address particular research questions. Here, we present Evident, a package for effect size calculations and power analysis on microbiome data and show that Evident scales to large datasets with numerous metadata covariates.
Detection of outlier methylation from bisulfite sequencing data with novel Bioconductor package BOREALIS
Authors: Oliver Gavin R. , Jenkinson Garrett , Olson Rory J. , Schultz-Rogers Laura E. , Klee Eric W. 
Published: May 2022

AbstractDNA sequencing results in genetic diagnosis of 18-40% of previously unsolved cases, while the incorporation of RNA-Seq analysis has more recently been shown to generate significant numbers of previously unattainable diagnoses. Multiple inborn diseases resulting from disorders of genomic imprinting are well characterized and a growing body of literature suggest the causative or correlative role of aberrant DNA methylation in diverse rare inherited conditions. Therefore, the systematic application of genomic-wide methylation-based sequencing for undiagnosed cases of rare disease is a logical progression from current testing paradigms. Following the rationale previously exploited in RNA-based studies of rare disease, we can assume that disease-associated methylation aberrations in an individual will demonstrate significant differences from individuals with unrelated phenotypes. Thus, aberrantly methylated sites will be outliers from a heterogeneous cohort of individuals.Based on this rationale, we present BOREALIS: Bisulfite-seq OutlieR MEthylation At SingLe-SIte ReSolution. BOREALIS uses a beta binomial model to identify outlier methylation at single CpG site resolution from bisulfite sequencing data. This method addresses a need unmet by standard differential methylation analyses based on case-control groups. Utilizing a heterogeneous cohort of 94 rare disease patients undiagnosed following DNA-based testing we show that BOREALIS can successfully identify outlier methylation linked to phenotypically relevant genes, providing a new avenue of exploration in the quest for increased diagnostic rates in rare disease patients. We highlight the case of a patient with previously undetected hypermethylation patterns that are informing clinical decision-making. BOREALIS is implemented in R and is freely available as a Bioconductor package.
Convolutions are competitive with transformers for protein sequence pretraining
Authors: Yang Kevin K. , Fusi Nicolo , Lu Alex X. 
Published: May 2022

AbstractPretrained protein sequence language models have been shown to improve the performance of many prediction tasks, and are now routinely integrated into bioinformatics tools. However, these models largely rely on the Transformer architecture, which scales quadratically with sequence length in both run-time and memory. Therefore, state-of-the-art models have limitations on sequence length. To address this limitation, we investigated if convolutional neural network (CNN) architectures, which scale linearly with sequence length, could be as effective as transformers in protein language models. With masked language model pretraining, CNNs are competitive to and occasionally superior to Transformers across downstream applications while maintaining strong performance on sequences longer than those allowed in the current state-of-the-art Transformer models. Our work suggests that computational efficiency can be improved without sacrificing performance simply by using a CNN architecture instead of a Transformer, and emphasizes the importance of disentangling pretraining task and model architecture.