bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes
Authors: Sun Jin , Li Runsheng , Chen Chong , Sigwart Julia D. , Kocot Kevin M. 
Published: April 2021

Choosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations. Significant recent progress in long-read sequencing technologies such as PacBio and Oxford Nanopore Technologies (ONT) has also brought about a large variety of assemblers. Although these have been extensively tested on model species such asHomo sapiensandDrosophila melanogaster, such benchmarking has not been done in Mollusca, which lacks widely adopted model species. Molluscan genomes are notoriously rich in repeats and are often highly heterozygous, making their assembly challenging. Here, we benchmarked 10 assemblers based on ONT raw reads from two published molluscan genomes of differing properties, the gastropodChrysomallon squamiferum(356.6 Mb, 1.59% heterozygosity) and the bivalveMytilus coruscus(1593 Mb, 1.94% heterozygosity). By optimizing the assembly pipeline, we greatly improved both genomes from previously published versions. Our results suggested that 40–50X of ONT reads are sufficient for high-quality genomes, with Flye being the recommended assembler for compact and less heterozygous genomes exemplified byC. squamiferum, while NextDenovo excelled for more repetitive and heterozygous molluscan genomes exemplified byM. coruscus. A phylogenomic analysis using the two updated genomes with 32 other published high-quality lophotrochozoan genomes resulted in maximum support across all nodes, and we show that improved genome quality also leads to more complete matrices for phylogenomic inferences. Our benchmarking will ensure efficiency in future assemblies for molluscs and perhaps also for other marine phyla with few genomes available.This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
Molluscan phylogenomics requires strategically selected genomes
Authors: Sigwart Julia D. , Lindberg David R. , Chen Chong , Sun Jin 
Published: April 2021

The extraordinary diversity in molluscan body plans, and the genomic mechanisms that enable it, remains one of the great questions of evolution. The eight distinct living taxonomic classes of molluscs are each unambiguously monophyletic; however, significant controversy remains about the phylogenetic relationships among those eight branches. Molluscs are the second-largest animal phylum, with over 100 000 living species with broad biological, economic and medical interest. To date, only around 53 genome assemblies have been accessioned to NCBI GenBank covering only four of the eight living molluscan classes. Furthermore, the molluscan taxa where partial or whole-genome assemblies are available are often aberrantly fast evolving or recently derived lineages. Characteristic adaptations provide interesting targets for whole-genome projects, in animals like the scaly-foot snail or octopus, but without basal-branching lineages for comparison, the context of recently derived features cannot be assessed. The currently available genomes also create a non-optimal set of taxa for resolving deeper phylogenetic branches: they are a small sample representing a large group, and those that are available come primarily from a rarefied pool. Thoughtful selection of taxa for future projects should focus on the blank areas of the molluscan tree, which are ripe with opportunities to delve into peculiarities of genome evolution, and reveal the biology and evolutionary history of molluscs.
This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
Sticky problems: extraction of nucleic acids from molluscs
Authors: Adema Coen M. 
Published: April 2021

Traditional molecular methods and omics-techniques across molluscan taxonomy increasingly inform biology of Mollusca. Recovery of DNA and RNA for such studies is challenged by common biological properties of the highly diverse molluscs. Molluscan biomineralization, adhesive structures and mucus involve polyphenolic proteins and mucopolysaccharides that hinder DNA extraction or copurify to inhibit enzyme-catalysed molecular procedures. DNA extraction methods that employ the detergent hexadecyltrimethylammoniumbromide (CTAB) to remove these contaminants importantly facilitate molecular-level study of molluscs. Molluscan pigments may stain DNA samples and interfere with spectrophotometry, necessitating gel electrophoresis or fluorometry for accurate quantification. RNA can reliably be extracted but the ‘hidden break’ in 28S rRNA of molluscs (like most protostomes) causes 18S and 28S rRNA fragments to co-migrate electrophoretically. This challenges the standard quality control based on the ratio of 18S and 28S rRNA, developed for deuterostome animals. High-AT content in molluscan rRNA prevents the effective purification of polyadenylated mRNA. Awareness of these matters aids the continuous expansion of molecular malacology, enabling work also with museum specimens and next-generation sequencing, with the latter imposing unprecedented demands on DNA quality. Alternative methods to extract nucleic acids from molluscs are available from literature and, importantly, from communications with others who study the molecular biology of molluscs.This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
Mobilizing molluscan models and genomes in biology
Authors: Davison Angus , Neiman Maurine 
Published: April 2021

Molluscs are among the most ancient, diverse, and important of all animal taxa. Even so, no individual mollusc species has emerged as a broadly applied model system in biology. We here make the case that both perceptual and methodological barriers have played a role in the relative neglect of molluscs as research organisms. We then summarize the current application and potential of molluscs and their genomes to address important questions in animal biology, and the state of the field when it comes to the availability of resources such as genome assemblies, cell lines, and other key elements necessary to mobilising the development of molluscan model systems. We conclude by contending that a cohesive research community that works together to elevate multiple molluscan systems to ‘model’ status will create new opportunities in addressing basic and applied biological problems, including general features of animal evolution.This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
Extensive genome-wide duplications in the eastern oyster (Crassostrea virginica)
Authors: Modak Tejashree H. , Literman Robert , Puritz Jonathan B. , Johnson Kevin M. , Roberts Erin M. , Proestou Dina , Guo Ximing , Gomez-Chiarri Marta , Schwartz Rachel S. 
Published: April 2021

Genomic structural variation is an important source of genetic and phenotypic diversity, playing a critical role in evolution. The recent availability of a high-quality reference genome for the eastern oyster,Crassostrea virginica, and whole-genome sequence data of samples from across the species range in the USA, provides an opportunity to explore structural variation across the genome of this species. Our analysis shows significantly greater individual-level duplications of regions across the genome than that of most model vertebrate species. Duplications are widespread across all ten chromosomes with variation in frequency per chromosome. The eastern oyster shows a large interindividual variation in duplications as well as particular chromosomal regions with a higher density of duplications. A high percentage of duplications seen inC. virginicalie completely within genes and exons, suggesting the potential for impacts on gene function. These results support the hypothesis that structural changes may play a significant role in standing genetic variation inC. virginica, and potentially have a role in their adaptive and evolutionary success. Altogether, these results suggest that copy number variation plays an important role in the genomic variation ofC. virginica.This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
Inference of DNA methylation patterns in molluscs
Authors: Männer Lisa , Schell Tilman , Provataris Panagiotis , Haase Martin , Greve Carola 
Published: April 2021

Mollusca are the second largest and arguably most diverse phylum of the animal kingdom. This is in sharp contrast to our very limited knowledge concerning epigenetic mechanisms including DNA methylation in this invertebrate group. Here, we inferred DNA methylation patterns by analysing the normalized dinucleotide CG content in protein-coding sequences and identified DNA methyltransferases (DNMT1 and 3) in published transcriptomes and genomes of 140 species across all eight classes of molluscs. Given the evolutionary age and morphological diversity of molluscs, we expected to find evidence for diverse methylation patterns. Our inferences suggest that molluscs possess substantial levels of DNA methylation in gene bodies as a rule. Yet, we found deviations from this general picture with regard to (i) the CpG observed/expected distributions indicating a reduction in DNA methylation in certain groups and (ii) the completeness of the DNMT toolkit. Reductions were evident in Caudofoveata, Solenogastres, Polyplacophora, Monoplacophora, as well as Scaphopoda. Heterobranchia and Oegopsida were remarkable as they lacked DNMT3, usually responsible for de novo methylation, yet showed signs of DNA methylation. Our survey may serve as guidance for direct empirical analyses of DNA methylation in molluscs.
This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
Potential of genomic technologies to improve disease resistance in molluscan aquaculture
Authors: Potts Robert W. A. , Gutierrez Alejandro P. , Penaloza Carolina S. , Regan Tim , Bean Tim P. , Houston Ross D. 
Published: April 2021

Molluscan aquaculture is a major contributor to global seafood production, but is hampered by infectious disease outbreaks that can cause serious economic losses. Selective breeding has been widely used to improve disease resistance in major agricultural and aquaculture species, and has clear potential in molluscs, albeit its commercial application remains at a formative stage. Advances in genomic technologies, especially the development of cost-efficient genomic selection, have the potential to accelerate genetic improvement. However, tailored approaches are required owing to the distinctive reproductive and life cycle characteristics of molluscan species. Transgenesis and genome editing, in particular CRISPR/Cas systems, have been successfully trialled in molluscs and may further understanding and improvement of genetic resistance to disease through targeted changes to the host genome. Whole-organism genome editing is achievable on a much greater scale compared to other farmed species, making genome-wide CRISPR screening approaches plausible. This review discusses the current state and future potential of selective breeding, genomic tools and genome editing approaches to understand and improve host resistance to infectious disease in molluscs.This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.
Estimated durations of asymptomatic, symptomatic, and care-seeking phases of tuberculosis disease
Authors: Ku Chu-Chang , MacPherson Peter , Khundi McEwen , Nzawa Rebecca , Feasey Helena RA. , Nliwasa Marriott , Horton Katherine C. , Corbett Elizabeth L. , Dodd Peter J. 
Published: April 2021

AbstractRatios of bacteriologically-positive tuberculosis prevalence to notification rates are used to characterise typical durations of tuberculosis disease, but have not accounted for asymptomatic periods prior to care-seeking. We developed novel statistical models to estimate progression from initial bacteriological-positivity including smear conversion, symptom onset and initial care-seeking and fitted them to tuberculosis prevalence survey and notification data (one subnational and 11 national datasets) within a Bayesian framework. Asymptomatic tuberculosis duration was in the range 4 – 8 months for African countries; three countries in Asia showed longer durations of > 1 year. Care-seeking typically began half-way between symptom onset and notification. Our method also estimated smear progression rates and case-detection ratios. We found evidence for higher case-detection ratios and much shorter durations of tuberculosis for people living with HIV. To eradicate tuberculosis transmission, greater gains may be achieved by proactively screening people without symptoms through active case finding interventions.
Comprehensive assessment of humoral response after Pfizer BNT162b2 mRNA Covid-19 vaccination: a three-case series
Authors: Danese Elisa , Montagnana Martina , Salvagno Gian Luca , Gelati Matteo , Peserico Denise , Pighi Laura , De Nitto Simone , Henry Brandon M. , Porru Stefano , Lippi Giuseppe 
Published: April 2021

AbstractBackgroundSince universal vaccination is a pillar against coronavirus disease 2019 (COVID-19), monitoring anti-SARS-CoV-2 neutralizing antibodies is essential for deciphering post-vaccination immune response.MethodsThree healthcare workers received 30 μg BNT162b2 mRNA Covid-19 Vaccine, followed by a second identical dose, 21 days afterwards. Venous blood was drawn at baseline and at serial intervals, up to 63 days afterwards, for assessing total immunoglobulins (Ig) anti-RBD (receptor binding domain), IgG anti-S1/S2, IgG anti-RBD, IgM anti-RBD, IgM anti-N/S1 and IgA anti-S1.ResultsAll subjects were SARS-CoV-2 seronegative at baseline. Total Ig anti-RBD, IgG anti-S1/S2 and IgG anti-RBD levels increased between 91-368 folds until 21 days after the first vaccine dose, then reached a plateau. The levels raised further after the second dose (by ∼30-, ∼8- and ∼8-fold, respectively), peaking at day 35, but then slightly declining and stabilizing ∼50 days after the first dose. IgA anti-S1 levels increased between 7-11 days after the first dose, slightly declined before the second dose, after which levels augmented by ∼24-fold from baseline. The anti-RBD and anti-N/S1 IgM kinetics were similar to that of anti-S1 IgA, though displaying substantially weaker increases and modest peaks, only 4 to 7-fold higher than baseline. Highly significant inter-correlation was noted between total Ig anti-RBD, anti-S1/S2 and anti-RBD IgG (all r=0.99), whilst other anti-SARS-CoV-2 antibodies displayed lower, though still significant, correlations. Serum spike protein concentration was undetectable at all time points.ConclusionsBNT162b2 mRNA vaccination generates a robust humoral immune response, especially involving IgG and IgA, magnified by the second vaccine dose.
Subpopulation-specific Machine Learning Prognosis for Underrepresented Patients with Double Prioritized Bias Correction
Authors: Afrose Sharmin , Song Wenjia , Nemeroff Charles B. , Lu Chang , Yao Danfeng (Daphne) 
Published: April 2021

AbstractBackgroundMany clinical datasets are intrinsically imbalanced, dominated by overwhelming majority groups. Off-the-shelf machine learning models that optimize the prognosis of majority patient types (e.g., healthy class) may cause substantial errors on the minority prediction class (e.g., disease class) and demographic subgroups (e.g., Black or young patients). In the typical one-machine-learning-model-fits-all paradigm, racial and age disparities are likely to exist, but unreported. In addition, some widely used whole-population metrics give misleading results.MethodsWe design a double prioritized (DP) bias correction technique to mitigate representational biases in machine learning-based prognosis. Our method trains customized machine learning models for specific ethnicity or age groups, a substantial departure from the one-model-predicts-all convention. We compare with other sampling and reweighting techniques in mortality and cancer survivability prediction tasks.ResultsWe first provide empirical evidence showing various prediction deficiencies in a typical machine learning setting without bias correction. For example, missed death cases are 3.14 times higher than missed survival cases for mortality prediction. Then, we show DP consistently boosts the minority class recall for underrepresented groups, by up to 38.0%. DP also reduces relative disparities across race and age groups, e.g., up to 88.0% better than the 8 existing sampling solutions in terms of the relative disparity of minority class recall. Cross-race and cross-age-group evaluation also suggests the need for subpopulation-specific machine learning models.ConclusionsBiases exist in the widely accepted one-machine-learning-model-fits-all-population approach. We invent a bias correction method that produces specialized machine learning prognostication models for underrepresented racial and age groups. This technique may reduce life-threatening prediction mistakes for minority populations.Plain Language SummaryThis work aims to improve the prediction accuracy of machine learning models in medical applications, e.g., estimating the likelihood of a patient dying in an emergency room visit or surviving cancer. Inaccurate prediction may produce life-threatening consequences. We first examine how biases in training data impact prediction outcomes, in particular how underrepresented patients (e.g., young patients or patients of color) are impacted. Then, we design a double prioritized (DP) bias correction technique. It allows one to train machine learning models for specific demographic groups, e.g., one machine learning model for Black patients and another model for Asian patients. Our results confirm the need for training subpopulation-specific machine learning models. Our work helps improve the medical care of minority patients in the age of digital health.
Retrospective feasibility study of Mycobacterium tuberculosis modified lipoprotein as a potential biomarker for TB detection in children
Authors: Yang Xinxin , Wipperman Matthew F. , Nachman Sharon , Sampson Nicole S. 
Published: April 2021

AbstractBackgroundCurrent TB diagnostic methods available have been developed for adults and development efforts have neglected the differences in disease and sampling that occur between adults and children. Diagnostic challenges are even greater in HIV co-infected children and infants.Methods and resultsWe established a sandwich ELISA assay to detect Mycobacterium tuberculosis modified lipoprotein (TLP) ex vivo in plasma. The study population contains plasma samples from 21 patients with active TB and 24 control samples with no TB, collected in the International Maternal Pediatric Adolescent AIDS Clinical Trails (IMPAACT) P1041 study. Retrospective analysis was performed and the result demonstrate that TLP level is associated with TB disease.ConclusionsPlasma levels of TLP associate with active TB disease in HIV positive subjects and can be used as an indicator for TB detection in children.
Comparison of post-COVID depression and major depressive disorder
Authors: Perlis Roy H. , Santillana Mauricio , Ognyanova Katherine , Green Jon , Druckman James , Lazer David , Baum Matthew A. 
Published: April 2021

AbstractBackgroundDuring the COVID-19 pandemic rates of depressive symptoms are markedly elevated, particularly among survivors of infection. Understanding whether such symptoms are distinct among those with prior SARS-CoV-2 infection, or simply a nonspecific reflection of elevated stress, could help target interventions.MethodWe analyzed data from multiple waves of a 50-state survey that included questions about COVID-19 infection as well as the Patient Health Questionnaire examining depressive and anxious symptoms. We utilized multiple logistic regression to examine whether sociodemographic features associated with depression liability differed for those with or without prior COVID-19, and then whether depressive symptoms differed among those with or without prior COVID-19.ResultsAmong 91,791 respondents, in regression models, age, gender, race, education, and income all exhibited an interaction with prior COVID-19 in risk for moderate or greater depressive symptoms (p<0.0001 in all cases), indicating differential risk in the two subgroups. Among those with such symptoms, levels of motoric symptoms and suicidality were significantly greater among those with prior COVID-19 illness. Depression risk increased with greater interval following acute infection.DiscussionOur results suggest that major depressive symptoms observed among individuals with prior COVID-19 illness may not reflect typical depressive episodes, and merit more focused neurobiological investigation.
Whole-Body Muscle MRI Characteristics of LAMA2 Gene Mutation Congenital Muscular Dystrophy Children
Authors: Sakr Hossam M. , Fahmy Nagia , Elsayed Nermine S. , Abdulhady Hala , El-Sobky Tamer A. , Saadawy Amr M. , Beroud Christophe , Udd Bjarne 
Published: April 2021

AbstractMerosin-deficient or LAMA2-related congenital muscular dystrophy (CMD) belongs to a group of muscle diseases with an overlapping diagnostic spectrum. MRI plays an important role in the diagnosis and disease-tracking of muscle diseases. Whole-body MRI is ideal for describing patterns of muscle involvement. Our purpose is to analyze the pattern of muscle involvement in merosin-deficient CMD children employing whole-body muscle MRI. Ten children with merosin-deficient CMD underwent whole-body muscle MRI. We used a control group of other hereditary muscle diseases, which included 13 children. Overall, 37 muscles were graded for fatty infiltration using Mercuri scale modified by Fischer et al 2008. The results showed a fairly consistent pattern of muscle fatty infiltration in index group, which differed from that in control group. There was a highly statistically significant difference between the two groups in regard to the fatty infiltration of the neck, serratus anterior, rotator cuff, deltoid, forearm, gluteus maximus, gluteus medius, gastrocnemius and soleus muscles. Additionally, results showed relative sparing of the brachialis, biceps brachii, gracilis, sartorius, semitendinosus and extensor muscles of the ankle in index group. There is evidence to suggest that whole-body muscle MRI can become a useful contributor to the differential diagnosis of merosin deficient CMD.Study HighlightsWhole-body muscle MRI is a useful contributor to the differential diagnosis of merosin-deficient (LAMA2-related) congenital muscular dystrophy.The study demonstrated the presence of a fairly characteristic pattern of whole-body muscle MRI in children with merosin-deficient CMD in terms of sensitivity and specificity.The study may be considered as a preliminary step of arriving at an MRI classification system for children with merosin-deficient CMD.