bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites
Authors: Jiao Shihu , Ye Xiucai , Ao Chunyan , Sakurai Tetsuya , Zou Quan , Xu Lei 
Published: October 2023

Abstract

Motivation
The rapid and extensive transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an unprecedented global health emergency, affecting millions of people and causing an immense socioeconomic impact. The identification of SARS-CoV-2 phosphorylation sites plays an important role in unraveling the complex molecular mechanisms behind infection and the resulting alterations in host cell pathways. However, currently available prediction tools for identifying these sites lack accuracy and efficiency.

Results
In this study, we presented a comprehensive biological function analysis of SARS-CoV-2 infection in a clonal human lung epithelial A549 cell, revealing dramatic changes in protein phosphorylation pathways in host cells. Moreover, a novel deep learning predictor called PSPred-ALE is specifically designed to identify phosphorylation sites in human host cells that are infected with SARS-CoV-2. The key idea of PSPred-ALE lies in the use of a self-adaptive learning embedding algorithm, which enables the automatic extraction of context sequential features from protein sequences. In addition, the tool uses multihead attention module that enables the capturing of global information, further improving the accuracy of predictions. Comparative analysis of features demonstrated that the self-adaptive learning embedding features are superior to hand-crafted statistical features in capturing discriminative sequence information. Benchmarking comparison shows that PSPred-ALE outperforms the state-of-the-art prediction tools and achieves robust performance. Therefore, the proposed model can effectively identify phosphorylation sites assistant the biomedical scientists in understanding the mechanism of phosphorylation in SARS-CoV-2 infection.

Availability and implementation
PSPred-ALE is available at https://github.com/jiaoshihu/PSPred-ALE and Zenodo (https://doi.org/10.5281/zenodo.8330277).
Evaluation of haplotype-aware long-read error correction with hifieval
Authors: Guo Yujie , Feng Xiaowen , Li Heng 
Published: October 2023

Abstract

Summary
The PacBio High-Fidelity (HiFi) sequencing technology produces long reads of &gt;99% in accuracy. It has enabled the development of a new generation of de novo sequence assemblers, which all have sequencing error correction (EC) as the first step. As HiFi is a new data type, this critical step has not been evaluated before. Here, we introduced hifieval, a new command-line tool for measuring over- and under-corrections produced by EC algorithms. We assessed the accuracy of the EC components of existing HiFi assemblers on the CHM13 and the HG002 datasets and further investigated the performance of EC methods in challenging regions such as homopolymer regions, centromeric regions, and segmental duplications. Hifieval will help HiFi assemblers to improve EC and assembly quality in the long run.

Availability and implementation
The source code is available at https://github.com/magspho/hifieval.
Struct2GO: protein function prediction based on graph pooling algorithm and AlphaFold2 structure information
Authors: Jiao Peishun , Wang Beibei , Wang Xuan , Liu Bo , Wang Yadong , Li Junyi 
Published: October 2023

Abstract

Motivation
In recent years, there has been a breakthrough in protein structure prediction, and the AlphaFold2 model of the DeepMind team has improved the accuracy of protein structure prediction to the atomic level. Currently, deep learning-based protein function prediction models usually extract features from protein sequences and combine them with protein–protein interaction networks to achieve good results. However, for newly sequenced proteins that are not in the protein–protein interaction network, such models cannot make effective predictions. To address this, this article proposes the Struct2GO model, which combines protein structure and sequence data to enhance the precision of protein function prediction and the generality of the model.

Results
We obtain amino acid residue embeddings in protein structure through graph representation learning, utilize the graph pooling algorithm based on a self-attention mechanism to obtain the whole graph structure features, and fuse them with sequence features obtained from the protein language model. The results demonstrate that compared with the traditional protein sequence-based function prediction model, the Struct2GO model achieves better results.

Availability and implementation
The data underlying this article are available at https://github.com/lyjps/Struct2GO.
Leucine-rich repeat kinase 2 promotes the development of experimental severe acute pancreatitis
Authors: Otsuka Yasuo , Hara Akane , Minaga Kosuke , Sekai Ikue , Kurimoto Masayuki , Masuta Yasuhiro , Takada Ryutaro , Yoshikawa Tomoe , Kamata Ken , Kudo Masatoshi , Watanabe Tomohiro 
Published: October 2023

Abstract
Translocation of gut bacteria into the pancreas promotes the development of severe acute pancreatitis (SAP). Recent clinical studies have also highlighted the association between fungal infections and SAP. The sensing of gut bacteria by pattern recognition receptors promotes the development of SAP via the production of proinflammatory cytokines; however, the mechanism by which gut fungi mediate SAP remains largely unknown. Leucine-rich repeat kinase 2 (LRRK2) is a multifunctional protein that regulates innate immunity against fungi via Dectin-1 activation. Here, we investigated the role of LRRK2 in SAP development and observed that administration of LRRK2 inhibitors attenuated SAP development. The degree of SAP was greater in Lrrk2 transgenic (Tg) mice than in control mice and was accompanied by an increased production of nuclear factor-kappaB-dependent proinflammatory cytokines. Ablation of the fungal mycobiome by anti-fungal drugs inhibited SAP development in Lrrk2 Tg mice, whereas the degree of SAP was comparable in Lrrk2 Tg mice with or without gut sterilization by a broad range of antibiotics. Pancreatic mononuclear cells from Lrrk2 Tg mice produced large amounts of IL-6 and TNF-α upon stimulation with Dectin-1 ligands, and inhibition of the Dectin-1 pathway by a spleen tyrosine kinase inhibitor protected Lrrk2 Tg mice from SAP. These data indicate that LRRK2 activation is involved in the development of SAP through proinflammatory cytokine responses upon fungal exposure.
Outcomes of patients with early calcific aortic valve disease detected by clinically indicated echocardiography
Authors: Moore Matthew K , Jones Gregory T , Whalley Gillian , Prendergast Bernard , Williams Michael J A , Coffey Sean 
Published: October 2023

Abstract

Aims
Previous studies have demonstrated relatively slow rates of progression of early calcific aortic valve disease (CAVD), which encompasses aortic sclerosis (ASc) and mild aortic stenosis (AS). The potential evolution to clinically significant AS is unclear, and we therefore examined the long-term outcomes of patients with ASc and mild AS detected at the time of clinically indicated echocardiography.

Methods and results
Data from initial clinically indicated echocardiograms performed between 2010 and 2018 in patients aged ≥18 years were extracted and linked to nationally collected outcome data. Those with impaired right or left systolic ventricular function or other significant left-sided valve disease were excluded. A time to first event analysis was performed with a composite primary outcome of cardiovascular death and aortic valve intervention (AVI). Of the 13 313 patients, 8973 had no CAVD, 3436 had ASc, and 455 had mild AS. The remainder had moderate or worse stenosis. Over a median follow-up period of 4.2 (interquartile range 1.8–6.7) years (and after adjustment for age and sex), those with ASc were at greater risk of the primary outcome [hazard ratio (HR) 2.9, 95% confidence interval (CI) 2.1–4.0] and need for AVI (HR 26.8, 95% CI 9.1–79.1) compared with those with no CAVD. Clinical event rates accelerated after ∼5 years in those with mild AS.

Conclusion
Patients with ASc are &gt;25 times more likely to require AVI than those with no CAVD, and follow-up echocardiography should be considered within 3–4 years in those with mild AS.
Blood pressure control in hypertensive sleep apnoea patients of the European Sleep Apnea Database cohort - effects of positive airway pressure and antihypertensive medication
Authors: Svedmyr Sven , Hedner Jan , Bailly Sebastien , Fanfulla Francesco , Hein Holger , Lombardi Carolina , Ludka Ondrej , Mihaicuta Stefan , Parati Gianfranco , Pataka Athanasia , Schiza Sophia , Tasbakan Sezai , Testelmans Dries , Zou Ding , Grote Ludger ,   European Sleep Apnea Database (ESADA) study group, P Steiropoulos , J Verbraecken , E Petiet , Trakada Georgia , I Fietze , T Penzel , Ludka Ondrej , I Bouloukaki , S Schiza , W T McNicholas , S Ryan , R L Riha , J A Kvamme , L Grote , J Hedner , D Zou , Hertegonne Katrien , Pevernagie Dirk , S Bailly , J L Pépin , R Tamisier , H Hein , O K Basoglu , M S Tasbakan , J Buskova , P Joppa , R Staats , Testelmans Dries , Gouveris Haralampos , K Ludwig , C Lombardi , G Parati , M R Bonsignore , Fanfulla Francesco , M Drummond , M van Zeller , W Randerath , Treml Marcel , Z Dogas , R Pecotic , A Pataka , U Anttalainen , T Saaresranta , P Sliwinski 
Published: October 2023

Abstract

Aims
We analysed longitudinal blood pressure (BP) data from hypertensive obstructive sleep apnoea (OSA) patients in the European Sleep Apnea Database cohort. The study investigated the interaction between positive airway pressure (PAP)-induced BP change and antihypertensive treatment (AHT).

Methods and results
Hypertensive patients with AHT [monotherapy/dual therapy n = 1283/652, mean age 59.6 ± 10.7/60.6 ± 10.3 years, body mass index (BMI) 34.2 ± 6.5/34.8 ± 7.0 kg/m2, apnoea–hypopnoea index 46 ± 25/46 ± 24 n/h, proportion female 29/26%, respectively] started PAP treatment. Office BP at baseline and 2- to 36-month follow-up were assessed. The interaction between AHT drug classes and PAP on BP was quantified and the influences of age, gender, BMI, co-morbidities, BP at baseline, and study site were evaluated. Following PAP treatment (daily usage, 5.6 ± 1.6/5.7 ± 1.9 h/day), systolic BP was reduced by −3.9 ± 15.5/−2.8 ± 17.7 mmHg in mono/dual AHT and diastolic BP by −3.0 ± 9.8/−2.7 ± 10.8 mmHg, respectively, all P &lt; 0.0001. Systolic and diastolic BP control was improved following PAP treatment (38/35% to 54/46% and 67/67% to 79/74%, mono/dual AHT, respectively). PAP treatment duration predicted a larger BP improvement in the monotherapy group. Intake of renin–angiotensin blockers [angiotensin converting enzyme inhibitor (ACEI)/angiotensin receptor blocker (ARB)] alone or in any AHT combination was associated with better BP control. The AHT-dependent BP improvement was independent of confounders.

Conclusion
In this pan-European OSA patient cohort, BP control improved following initiation of PAP. Longer PAP treatment duration, was associated with a favourable effect on BP. Our study suggests that ACEI/ARB, alone or in combination with other drug classes, provides a particularly strong reduction of BP and better BP control when combined with PAP in OSA.
Future burden of myocardial infarction in Australia: impact on health outcomes between 2019 and 2038
Authors: Abebe Tamrat Befekadu , Morton Jedidiah I , Ilomaki Jenni , Ademi Zanfina 
Published: October 2023

Abstract

Background
Myocardial infarction (MI) remains a major health burden in Australia. Yet the future burden of MI has not been extensively studied for the Australian population.

Methods and results
A multistate lifetable model was constructed to estimate the lifetime risk of MI and project the health burden of MI for the Australian population aged between 40 and 100 years over a 20-year period (2019–2038). Data for the model were primarily sourced from the Victorian-linked dataset and supplemented with other national data. The lifetime risk of MI at age 40 was estimated as 24.4% for males and 13.2% for females in 2018. From 2019 to 2038, 891 142 Australians were projected to develop incident MI. By 2038, the model estimated there would be 702 226 people with prevalent MI, 51 262 incident non-fatal MI, and 3717 incident fatal MI; these numbers represent a significant increase compared to the 2019 estimates, with a 27.0% (148 827), 62.0% (19 629), and 104.7% (1901) rise, respectively. Projected years of life lived (YLL) (5% discount) accrued by the Australian population was 174 795 232 (84 356 304 in males and 90 438 928 in females), with 7 657 423 YLL among people with MI (4 997 009 in males and 2 660 414 in females).

Conclusion
The burden of MI was projected to increase between 2019 and 2038 in Australia. The outcomes of the model provide important information for decision-makers to prioritize population-wide prevention strategies to reduce the burden of MI.
Three-dimensional changes in the cranial base associated with soft-diet feeding
Authors: Murata Yuka , Tanikawa Chihiro , Shiraishi Yuki , Inubushi Toshihiro , Kono Kana , Kamioka Hiroshi , Yamashiro Takashi 
Published: October 2023

Summary

Background
Masticatory activity affects the morphology of the maxillo-mandibular complex, however, its influence on the cranial base remains to be elucidated. The recent integration of quantitative morphometric analysis with 3D imaging enabled a comprehensive and high-resolution morphological characterization of the craniofacial complex. We aimed to investigate the influence of masticatory activity on the morphology of the growing cranial base by three-dimensional (3D) geometric morphometric approach using micro-CT.

Methods
The micro-CT data was reanalyzed to illustrate the 3D shape of the cranial base, and wireframe models were generated by connecting landmarks on the images. In the original study, mice were fed a soft diet (SD) of powdered pellets or a conventional hard diet (HD) for 6 weeks from 3 to 9 weeks of age, immediately after weaning. A principal component (PC) analysis analyzed shape variations and assessed their significance, while canonical variate (CV) analysis facilitated the comparison and differentiation of groups based on shape, unveiling meaningful shape distinctions.

Results
Three PCs were extracted that significantly separated the SD and HD groups among those explaining variations in shape. These PCs were related to the length of the sphenoid bone, the width of the anterior part of the sphenoid bone, and the length of the cranial base. Furthermore, one CV effectively distinguished SD from HD, and CV analysis showed that the sphenoid was shortened in the length and narrowed at the border of the temporal bone in SD mice.

Conclusions
Masticatory loading affects the skeletal development of the cranial base. The morphology of the sphenoid bone was affected in both the sagittal and transverse axes.
simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods
Authors: Kanduri Chakravarthi , Scheffer Lonneke , Pavlović Milena , Rand Knut Dagestad , Chernigovskaya Maria , Pirvandy Oz , Yaari Gur , Greiff Victor , Sandve Geir K 
Published: October 2023

Abstract

Background
Machine learning (ML) has gained significant attention for classifying immune states in adaptive immune receptor repertoires (AIRRs) to support the advancement of immunodiagnostics and therapeutics. Simulated data are crucial for the rigorous benchmarking of AIRR-ML methods. Existing approaches to generating synthetic benchmarking datasets result in the generation of naive repertoires missing the key feature of many shared receptor sequences (selected for common antigens) found in antigen-experienced repertoires.

Results
We demonstrate that a common approach to generating simulated AIRR benchmark datasets can introduce biases, which may be exploited for undesired shortcut learning by certain ML methods. To mitigate undesirable access to true signals in simulated AIRR datasets, we devised a simulation strategy (simAIRR) that constructs antigen-experienced-like repertoires with a realistic overlap of receptor sequences. simAIRR can be used for constructing AIRR-level benchmarks based on a range of assumptions (or experimental data sources) for what constitutes receptor-level immune signals. This includes the possibility of making or not making any prior assumptions regarding the similarity or commonality of immune state–associated sequences that will be used as true signals. We demonstrate the real-world realism of our proposed simulation approach by showing that basic ML strategies perform similarly on simAIRR-generated and real-world experimental AIRR datasets.

Conclusions
This study sheds light on the potential shortcut learning opportunities for ML methods that can arise with the state-of-the-art way of simulating AIRR datasets. simAIRR is available as a Python package: https://github.com/KanduriC/simAIRR.
Elucidation of bacterial trehalose-degrading trehalase and trehalose phosphorylase: physiological significance and its potential applications
Authors: Shrestha Prasansah , Karmacharya Jayram , Han So-Ra , Lee Jun Hyuck , Oh Tae-Jin 
Published: October 2023

Abstract
Bacteria possess diverse metabolic and genetic processes, resulting in the inability of certain bacteria to degrade trehalose. However, some bacteria do have the capability to degrade trehalose, utilizing it as a carbon source, and for defense against environmental stress. Trehalose, a disaccharide, serves as a carbon source for many bacteria, including some that are vital for pathogens. The degradation of trehalose is carried out by enzymes like trehalase (EC 3.2.1.28) and trehalose phosphorylase (EC 2.4.1.64/2.4.1.231), which are classified under the glycoside hydrolase families GH37, GH15, and GH65. Numerous studies and reports have explored the physiological functions, recombinant expression, enzymatic characteristics, and potential applications of these enzymes. However, further research is still being conducted to understand their roles in bacteria. This review aims to provide a comprehensive summary of the current understanding of trehalose degradation pathways in various bacteria, focusing on three key areas: (i) identifying different trehalose-degrading enzymes in Gram-positive and Gram-negative bacteria, (ii) elucidating the mechanisms employed by trehalose-degrading enzymes belonging to the glycoside hydrolases GH37, GH15, and GH65, and (iii) discussing the potential applications of these enzymes in different sectors. Notably, this review emphasizes the bacterial trehalose-degrading enzymes, specifically trehalases (GH37, GH15, and GH65) and trehalose phosphorylases (GH65), in both Gram-positive and Gram-negative bacteria, an aspect that has not been highlighted before.
SMRT–AgRenSeq-d in potato (Solanum tuberosum) as a method to identify candidates for the nematode resistance Gpa5
Authors: Wang Yuhan , Brown Lynn H , Adams Thomas M , Cheung Yuk Woon , Li Jie , Young Vanessa , Todd Drummond T , Armstrong Miles R , Neugebauer Konrad , Kaur Amanpreet , Harrower Brian , Oome Stan , Wang Xiaodan , Bayer Micha , Hein Ingo 
Published: October 2023

Abstract
Potato is the third most important food crop in the world. Diverse pathogens threaten sustainable crop production but can be controlled, in many cases, through the deployment of disease resistance genes belonging to the family of nucleotide-binding, leucine-rich-repeat (NLR) genes. To identify effective disease resistance genes in established varieties, we have successfully established SMRT–AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR–AgRenSeq-d. The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score. Using a SMRT–RenSeq-based sequence representation of the NLRome from the cultivar Innovator, SMRT–AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1, Rpi-R2-like, Rpi-R3a, and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations. All benchmark genes were identified with an F1 score of 1, which indicates absolute linkage in the panel. This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode (PCN) species Globodera pallida (pathotypes Pa2/3). Assuming that NLRs are involved in controlling many types of resistances, SMRT–AgRenSeq-d can readily be applied to diverse crops and pathogen systems.
Pulmonary valve reconstruction for acquired pulmonary regurgitation in patients with treated congenital heart disease
Authors: Jussli-Melchers Jill , Hansen Jan Hinnerk , Scheewe Jens , Attmann Tim , Eide Martin , Logoteta Jana , Dütschke Peter , Salehi Ravesh Mona , Uebing Anselm , Voges Inga 
Published: October 2023

Abstract

OBJECTIVES
Pulmonary valve regurgitation is a common problem after relief of right ventricular outflow tract (RVOT) obstruction with a transannular patch. Pulmonary valve replacement with a homograft or xenograft is the routine treatment. Longevity of biological valves and the availability of homografts are limited. Alternatives to restore RVOT competence are evaluated. The goal of this study was to present intermediate-term results for pulmonary valve reconstruction (PVr) in patients with severe regurgitation.

METHODS
PVr was performed in 24 patients (August 2006‒July 2018). We analysed perioperative data, pre- and postoperative cardiac magnetic resonance (CMR) imaging studies, freedom from valve replacement and risk factors for pulmonary valve dysfunction.

RESULTS
The underlying diagnoses were tetralogy of Fallot (n = 18, 75%), pulmonary stenosis (n = 5, 20.8%) and the double outlet right ventricle post banding procedure (n = 1, 4.2%). The median age was 21.5 (14.8–23.7) years. Main (n = 9, 37.5%) and branch pulmonary artery procedures (n = 6, 25%) and surgery of the RVOT (n = 16, 30.2%) were often part of the reconstruction. The median follow-up after the operation was 8.0 (4.7–9.7) years. Freedom from valve failure was 96% at 2 and 90% at 5 years. The mean longevity of the reconstructive surgery was 9.9 years (95% confidence interval: 8.8–11.1 years). CMR before and 6 months after surgery showed a reduction in the regurgitation fraction [41% (33–55) vs 20% (18–27) P = 0.00] and of the indexed right ventricular end-diastolic volume [156 ml/m2 (149–175) vs 116 ml/m2 (100–143), P = 0.004]. Peak velocity across the pulmonary valve (determined by CMR) half a year after surgery was 2.0, unchanged.

CONCLUSIONS
PVr can be achieved with acceptable intermediate-term results and may delay pulmonary valve replacement.