bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploration of whole genome amplification generated chimeric sequences in long-read sequencing data
Authors: Lu Na , Qiao Yi , An Pengfei , Luo Jiajian , Bi Changwei , Li Musheng , Lu Zuhong , Tu Jing 
Published: August 2023

Abstract

Motivation
Multiple displacement amplification (MDA) has become the most commonly used method of whole genome amplification, generating a vast amount of DNA with higher molecular weight and greater genome coverage. Coupling with long-read sequencing, it is possible to sequence the amplicons of over 20 kb in length. However, the formation of chimeric sequences (chimeras, expressed as structural errors in sequencing data) in MDA seriously interferes with the bioinformatics analysis but its influence on long-read sequencing data is unknown.

Results
We sequenced the phi29 DNA polymerase-mediated MDA amplicons on the PacBio platform and analyzed chimeras within the generated data. The 3rd-ChimeraMiner has been constructed as a pipeline for recognizing and restoring chimeras into the original structures in long-read sequencing data, improving the efficiency of using TGS data. Five long-read datasets and one high-fidelity long-read dataset with various amplification folds were analyzed. The result reveals that the mis-priming events in amplification are more frequently occurring than widely perceived, and the propor tion gradually accumulates from 42% to over 78% as the amplification continues. In total, 99.92% of recognized chimeric sequences were demonstrated to be artifacts, whose structures were wrongly formed in MDA instead of existing in original genomes. By restoring chimeras to their original structures, the vast majority of supplementary alignments that introduce false-positive structural variants are recycled, removing 97% of inversions on average and contributing to the analysis of structural variation in MDA-amplified samples. The impact of chimeras in long-read sequencing data analysis should be emphasized, and the 3rd-ChimeraMiner can help to quantify and reduce the influence of chimeras.

Availability and implementation
The 3rd-ChimeraMiner is available on GitHub, https://github.com/dulunar/3rdChimeraMiner.
Genesis-DB: a database for autonomous laboratory systems
Authors: Reder Gabriel K , Gower Alexander H , Kronström Filip , Halle Rushikesh , Mahamuni Vinay , Patel Amit , Hayatnagarkar Harshal , Soldatova Larisa N , King Ross D 
Published: August 2023

Abstract

Summary
Artificial intelligence (AI)-driven laboratory automation—combining robotic labware and autonomous software agents—is a powerful trend in modern biology. We developed Genesis-DB, a database system designed to support AI-driven autonomous laboratories by providing software agents access to large quantities of structured domain information. In addition, we present a new ontology for modeling data and metadata from autonomously performed yeast microchemostat cultivations in the framework of the Genesis robot scientist system. We show an example of how Genesis-DB enables the research life cycle by modeling yeast gene regulation, guiding future hypotheses generation and design of experiments. Genesis-DB supports AI-driven discovery through automated reasoning and its design is portable, generic, and easily extensible to other AI-driven molecular biology laboratory data and beyond.

Availability and implementation
Genesis-DB code and installation instructions are available at the GitHub repository https://github.com/TW-Genesis/genesis-database-system.git. The database use case demo code and data are also available through GitHub (https://github.com/TW-Genesis/genesis-database-demo.git). The ontology can be downloaded here: https://github.com/TW-Genesis/genesis-ontology/releases/download/v0.0.23/genesis.owl. The ontology term descriptions (including mappings to existing ontologies) and maintenance standard operating procedures can be found at: https://github.com/TW-Genesis/genesis-ontology.
BERTrand—peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing
Authors: Myronov Alexander , Mazzocco Giovanni , Król Paulina , Plewczynski Dariusz 
Published: August 2023

Abstract

Motivation
The advent of T-cell receptor (TCR) sequencing experiments allowed for a significant increase in the amount of peptide:TCR binding data available and a number of machine-learning models appeared in recent years. High-quality prediction models for a fixed epitope sequence are feasible, provided enough known binding TCR sequences are available. However, their performance drops significantly for previously unseen peptides.

Results
We prepare the dataset of known peptide:TCR binders and augment it with negative decoys created using healthy donors’ T-cell repertoires. We employ deep learning methods commonly applied in Natural Language Processing to train part a peptide:TCR binding model with a degree of cross-peptide generalization (0.69 AUROC). We demonstrate that BERTrand outperforms the published methods when evaluated on peptide sequences not used during model training.

Availability and implementation
The datasets and the code for model training are available at https://github.com/SFGLab/bertrand.
Fast and flexible inference for joint models of multivariate longitudinal and survival data using integrated nested Laplace approximations
Authors: Rustand Denis , van Niekerk Janet , Krainski Elias Teixeira , Rue Håvard , Proust-Lima Cécile 
Published: August 2023

Abstract
Modeling longitudinal and survival data jointly offers many advantages such as addressing measurement error and missing data in the longitudinal processes, understanding and quantifying the association between the longitudinal markers and the survival events, and predicting the risk of events based on the longitudinal markers. A joint model involves multiple submodels (one for each longitudinal/survival outcome) usually linked together through correlated or shared random effects. Their estimation is computationally expensive (particularly due to a multidimensional integration of the likelihood over the random effects distribution) so that inference methods become rapidly intractable, and restricts applications of joint models to a small number of longitudinal markers and/or random effects. We introduce a Bayesian approximation based on the integrated nested Laplace approximation algorithm implemented in the R package R-INLA to alleviate the computational burden and allow the estimation of multivariate joint models with fewer restrictions. Our simulation studies show that R-INLA substantially reduces the computation time and the variability of the parameter estimates compared with alternative estimation strategies. We further apply the methodology to analyze five longitudinal markers (3 continuous, 1 count, 1 binary, and 16 random effects) and competing risks of death and transplantation in a clinical trial on primary biliary cholangitis. R-INLA provides a fast and reliable inference technique for applying joint models to the complex multivariate data encountered in health research.
Behavior of higher trophic levels associated with an invasive plant varies among populations
Authors: Ismail Mohannad , Siemann Evan , Ding Jianqing 
Published: August 2023

Abstract
Invasive plants from their native and introduced ranges differ in their interactions with herbivores but it is not known whether they also vary in their interactions with herbivore natural enemies. Here, we used olfactometer bioassays and cage experiments to investigate how foraging behaviors of 2 parasitoid and 1 hyperparasitoid species depended on plant population origin. Triadica sebifera (Euphorbiaceae) is native to China but invasive in the United States. In China, it is fed on by a specialist noctuid Gadirtha fusca (Lepidoptera: Nolidae), which hosts a parasitoid Apanteles sp. (Hymenoptera: Microgastinae) and hyperparasitoid (Hymenoptera: Eurytomidae) plus a generalist aphid Toxoptera odinae (Homoptera: Aphidiidae) parasitized by Lysiphlebus confusus (Hymenoptera: Aphidiinae). Both parasitoids preferred plants infested by their host over herbivore-free plants in olfactometer bioassays. Apanteles sp. and Eurytomid wasps preferred G. fusca infested plants from China populations over those from US populations in olfactometer bioassays but L. confusus wasps did not discriminate between T. odinae infested plants from China vs. US populations. Similarly, G. fusca caterpillars on China population plants were more likely to be parasitized than ones on US population plants when they were in the same cage but odds of parasitism for T. odinae did not differ for those on China vs. US population plants. These results suggest that populations from the native and introduced ranges may differ in traits that impact higher trophic levels. This may have implications for successful control of invasive plants as biocontrol agents are introduced or herbivores begin to feed on them in their introduced ranges.
Genetic determinants of thyroid function in children
Authors: Mulder Tessa A , Campbell Purdey J , Taylor Peter N , Peeters Robin P , Wilson Scott G , Medici Marco , Dayan Colin , Jaddoe Vincent V W , Walsh John P , Martin Nicholas G , Tiemeier Henning , Korevaar Tim I M 
Published: August 2023

AbstractObjectiveGenome-wide association studies in adults have identified 42 loci associated with thyroid stimulating hormone (TSH) and 21 loci associated with free thyroxine (FT4) concentrations. While biologically plausible, age-dependent effects have not been assessed. We aimed to study the association of previously identified genetic determinants of TSH and FT4 with TSH and FT4 concentrations in newborns and (pre)school children.MethodsWe selected participants from three population-based prospective cohorts with data on genetic variants and thyroid function: Generation R (N = 2169 children, mean age 6 years; N = 2388 neonates, the Netherlands), the Avon Longitudinal Study of Parents and Children (ALSPAC; N = 3382, age 7.5 years, United Kingdom), and the Brisbane Longitudinal Twin Study (BLTS; N = 1680, age 12.1 years, Australia). The association of single nucleotide polymorphisms (SNPs) with TSH and FT4 concentrations was studied with multivariable linear regression models. Weighted polygenic risk scores (PRSs) were defined to combine SNP effects.ResultsIn childhood, 30/60 SNPs were associated with TSH and 11/31 SNPs with FT4 after multiple testing correction. The effect sizes for AADAT, GLIS3, TM4SF4, and VEGFA were notably larger than in adults. The TSH PRS explained 5.3%-8.4% of the variability in TSH concentrations; the FT4 PRS explained 1.5%-4.2% of the variability in FT4 concentrations. Five TSH SNPs and no FT4 SNPs were associated with thyroid function in neonates.ConclusionsThe effects of many known thyroid function SNPs are already apparent in childhood and some might be notably larger in children as compared to adults. These findings provide new knowledge about genetic regulation of thyroid function in early life.
Clinical presentation of calmodulin mutations: the International Calmodulinopathy Registry
Authors: Crotti Lia , Spazzolini Carla , Nyegaard Mette , Overgaard Michael T , Kotta Maria-Christina , Dagradi Federica , Sala Luca , Aiba Takeshi , Ayers Mark D , Baban Anwar , Barc Julien , Beach Cheyenne M , Behr Elijah R , Bos J Martijn , Cerrone Marina , Covi Peter , Cuneo Bettina , Denjoy Isabelle , Donner Birgit , Elbert Adrienne , Eliasson Håkan , Etheridge Susan P , Fukuyama Megumi , Girolami Francesca , Hamilton Robert , Horie Minoru , Iascone Maria , Jaimez Juan Jiménez , Jensen Henrik Kjærulf , Kannankeril Prince J , Kaski Juan P , Makita Naomasa , Muñoz-Esparza Carmen , Odland Hans H , Ohno Seiko , Papagiannis John , Porretta Alessandra Pia , Prandstetter Christopher , Probst Vincent , Robyns Tomas , Rosenthal Eric , Rosés-Noguer Ferran , Sekarski Nicole , Singh Anoop , Spentzou Georgia , Stute Fridrike , Tfelt-Hansen Jacob , Till Jan , Tobert Kathryn E , Vinocur Jeffrey M , Webster Gregory , Wilde Arthur A M , Wolf Cordula M , Ackerman Michael J , Schwartz Peter J 
Published: August 2023

Abstract

Aims
Calmodulinopathy due to mutations in any of the three CALM genes (CALM1–3) causes life-threatening arrhythmia syndromes, especially in young individuals. The International Calmodulinopathy Registry (ICalmR) aims to define and link the increasing complexity of the clinical presentation to the underlying molecular mechanisms.

Methods and results
The ICalmR is an international, collaborative, observational study, assembling and analysing clinical and genetic data on CALM-positive patients. The ICalmR has enrolled 140 subjects (median age 10.8 years [interquartile range 5–19]), 97 index cases and 43 family members. CALM-LQTS and CALM-CPVT are the prevalent phenotypes. Primary neurological manifestations, unrelated to post-anoxic sequelae, manifested in 20 patients. Calmodulinopathy remains associated with a high arrhythmic event rate (symptomatic patients, n = 103, 74%). However, compared with the original 2019 cohort, there was a reduced frequency and severity of all cardiac events (61% vs. 85%; P = .001) and sudden death (9% vs. 27%; P = .008). Data on therapy do not allow definitive recommendations. Cardiac structural abnormalities, either cardiomyopathy or congenital heart defects, are present in 30% of patients, mainly CALM-LQTS, and lethal cases of heart failure have occurred. The number of familial cases and of families with strikingly different phenotypes is increasing.

Conclusion
Calmodulinopathy has pleiotropic presentations, from channelopathy to syndromic forms. Clinical severity ranges from the early onset of life-threatening arrhythmias to the absence of symptoms, and the percentage of milder and familial forms is increasing. There are no hard data to guide therapy, and current management includes pharmacological and surgical antiadrenergic interventions with sodium channel blockers often accompanied by an implantable cardioverter–defibrillator.
Dietary fruits and vegetables and risk of cardiovascular diseases in elderly Chinese
Authors: Wang Kang , Chen Zhangling , Shen Maoqi , Chen Pengfei , Xiao Yichao , Fang Zhenfei , Hu Xinqun , Tang Jianjun , Liu Qiming , Zhou Shenghua 
Published: August 2023

Abstract

Background
Evidence regarding the potential effect of fruit and vegetable consumption on cardiovascular diseases (CVD) was limited and inconsistent among Asian people.

Methods
We prospectively examined associations of fruit and vegetable consumption with the risk of CVD among 9740 participants aged 65 years and older (mean baseline age: 88 years) in the Chinese Longitudinal Healthy Longevity Survey (CLHLS) (2008–2018). Dietary data were collected using a validated food frequency questionnaire.

Results
During 37 366 person-years of follow-up, a total of 3738 CVD cases were recorded. After adjusting for demographics, dietary, lifestyle and economical social factors, higher intakes of total fruits and vegetables were associated with lower risk of CVD [comparing with extreme quintiles, hazard ratio and 95% confidence interval: 0.84 (0.74, 0.95)]. The inverse association was mainly driven by vegetable consumption [0.86 (0.77, 0.95)]. Furthermore, the inverse association was stronger for the risk of hypertension [0.84 (0.72, 0.98)]. These associations were consistent across age, sex, body mass index, residence, exercise status, smoking, drinking, meat intake, modified hPDI and health status.

Conclusions
This study suggests higher intakes of total fruits and vegetables are associated with a lower risk of CVD among elderly Chinese people, supporting the current recommendations of increasing fruit and vegetable consumption as part of a healthy diet for the prevention of CVD.
Effectiveness of primary care interventions in conjointly treating comorbid chronic pain and depression: a systematic review and meta-analysis
Authors: Patel Krishna H , Chrisinger Benjamin 
Published: August 2023

Abstract

Background
Chronic pain and depression are highly comorbid, but the lack of consensus on the best treatment strategies puts patients at high risk of suboptimal care-coordination as well as health and social complications. Therefore, this study aims to quantitatively assesses how effective different primary care interventions have been in treating the comorbid state of chronic pain and depression. In particular, this study evaluates both short-term outcomes—based specifically on measures of chronic pain and depression during an intervention itself—and long-term outcomes or measures of pain and depression in the months after conclusion of the formal study intervention.

Methods
This study is a systematic review and meta-analysis of randomised-controlled trials (RCTs) enrolling patients with concurrent chronic pain and depression. Intensity and severity of pain and depression symptoms were the primary outcomes. The main inclusion criteria were RCTs that: (i) enrolled patients diagnosed with depression and chronic pain, (ii) occurred in primary care settings, (iii) reported baseline and post-intervention outcomes for chronic pain and depression, (iv) lasted at least 8 weeks, and (v) used clinically validated outcome measures. Risk of bias was appraised with the Risk of Bias 2 tool, and GRADE guidelines were used to evaluate the quality of evidence.

Results
Of 692 screened citations, 7 multicomponent primary care interventions tested across 891 patients were included. Meta-analyses revealed significant improvements in depression at post-intervention (SMD = 0.44, 95% CI [0.17, 0.71], P = 0.0014) and follow-up (SMD = 0.41, 95% CI [0.01, 0.81], P = 0.0448). Non-significant effects were observed for chronic pain at post-intervention (SMD = 0.27, 95% CI [−0.08, 0.61], P = 0.1287) and follow-up (SMD = 0.13, 95% CI [−0.3, 0.56], P = 0.5432).

Conclusions
Based on the results of the meta-analysis, primary care interventions largely yielded small to moderate positive effects for depressive symptoms and no significant effects on pain. In one study, stepped-care to be more effective in treatment of comorbid chronic pain and depression than other interventions both during the intervention and upon post-intervention follow-up. As such, depression appears more amenable to treatment than pain, but the number of published RCTs assessing both conditions is limited. More research is needed to further develop optimal treatment strategies.
Histology, physiology, and transcriptomic and metabolomic profiling reveal the developmental dynamics of annual shoots in tree peonies (Paeonia suffruticosa Andr.)
Authors: Tong Ningning , Shu Qingyan , Wang Baichen , Peng Liping , Liu Zheng'an 
Published: August 2023

Abstract
The development of tree peony annual shoots is characterized by “withering”, which is related to whether there are bud points in the leaf axillaries of annual shoots. However, the mechanism of “withering” in tree peony is still unclear. In this study, Paeonia ostii ‘Fengdan’ and P. suffruticosa ‘Luoyanghong’ were used to investigate dynamic changes of annual shoots through anatomy, physiology, transcriptome, and metabolome. The results demonstrated that the developmental dynamics of annual shoots of the two cultivars were comparable. The withering degree of P. suffruticosa ‘Luoyanghong’ was higher than that of P. ostii ‘Fengdan’, and their upper internodes of annual flowering shoots had a lower degree of lignin deposition, cellulose, C/N ratio, showing no obvious sclerenchyma, than the bottom ones and the whole internodes of vegetative shoot, which resulted in the “withering” of upper internodes. A total of 36 phytohormone metabolites were detected, of which 33 and 31 were detected in P. ostii ‘Fengdan’ and P. suffruticosa ‘Luoyanghong’, respectively. In addition, 302 and 240 differentially expressed genes related to lignin biosynthesis, carbon and nitrogen metabolism, plant hormone signal transduction, and zeatin biosynthesis were screened from the two cultivars. Furtherly, 36 structural genes and 40 transcription factors associated with the development of annual shoots were highly co-expressed, and eight hub genes involved in this developmental process were identified. Consequently, this study explained the developmental dynamic on the varied annual shoots through multi-omics, providing a theoretical foundation for germplasm innovation and the mechanized harvesting of tree peony annual shoots.
Motivational Interviewing and Chronic Care Management Using the Transtheoretical Model of Change
Authors: Wood Angela R , Ross Levi , Wood Ralph J 
Published: August 2023

Abstract
The number of Americans living with chronic health conditions has steadily increased. Chronic diseases are the leading causes of death and disability in the United States and cost the healthcare system an estimated $4.1 trillion dollars a year. The role of social workers in assisting patients in the management of their chronic diseases is vital. The behavioral health changes often required of chronic care management (CCM) patients require support and intervention by professionals to help the patient improve self-management of their chronic health conditions. Motivational interviewing (MI) is an evidence-based practice that helps people change by paying attention to the language patients use as they discuss their change goals and behaviors. Applying the principles and strategies of MI within the stages of change model (transtheoretical model of change) can help social workers better understand and assist patients receiving CCM. This article outlines specific strategies the social worker can use to address motivation at different stages of change.
Genomics of Marine Larval Evolution and Development
Authors: Zakas Christina , Martín-Durán José M 
Published: August 2023

Synopsis
Functional and ecological genomics in emerging marine models is shaping our views on new and fundamental biological questions. Representing a wealth of morphological, behavioral, and developmental adaptations, marine organisms are a key group for studying ancestral and shared body plan patterns, as well as some of the most intriguing novelties in animals. Here, we outline key questions, resources, and approaches to advance our understanding of marine larva biology and evolution that were covered in the recent symposium “Genomics of marine larval evolution and development.” Over 2 days, researchers from multiple continents, career stages, and research interests, covering a range of taxonomic diversity, contributed to three emerging topics: (1) Understanding the genetic basis of larval morphology and behaviors; (2) Finding the genomic basis for body plan development and novel morphologies; and (3) Constructing genomic tools in development for comparative insights. In this short piece, we highlight some of the most relevant findings on how different developmental modes and larval forms evolve.
Innovation on technological “islands”: domain contrast, boundary spanning, knowledge depth and breadth
Authors: Ubisch Sverre , Wang Pengfei 
Published: August 2023

Abstract
Prior literature has long examined innovation as a recombination process within or across the boundaries of technological domains. However, limited attention is paid to boundaries per se. Building upon recent development of categorical contrast, this study distinguishes domains with crisp boundaries from those with fuzzy boundaries and examines their effects on innovation outputs. Analyzing a large sample of US patents, we find that spanning crisp boundaries is more likely to generate impactful inventions but at the same time leads to significantly higher recombinant uncertainty. We continue to explore what types of inventors are better able to span such types of domain boundaries. Focusing specifically on the role of inventors’ knowledge expertise, we find that while both knowledge depth and breadth enhance the impact of technologies that span crisp boundaries, knowledge breadth is also found to escalate the associated uncertainty. Our emphasis on the contrast of technological domains contributes to the literature on recombinative innovation and boundary spanning.