bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibodies against malondialdehyde among 60-year-olds: prediction of cardiovascular disease
Authors: Samal Shailesh Kumar , Leander Karin , Vikström Max , Griesbaum Lena , de Faire Ulf , Frostegård Johan 
Published: September 2023

AbstractMalondialdehyde (MDA) is generated in oxidized LDL. It forms covalent protein adducts, and is recognized by antibodies (anti-MDA). We previously studied IgM anti-MDA, and here we focus on IgG, IgG1 and IgG2 anti-MDA in predicting cardiovascular disease (CVD). We determined, by ELISA, anti-MDA in a 7-year follow-up of 60-year-old men and women from Stockholm County (2039 men, 2193 women). We identified 210 incident CVD cases (defined as new events of myocardial infarction (MI), and hospitalization for angina pectoris) and ischemic stroke, and 620 age- and sex-matched controls. IgG anti-MDA was not associated with CVD. Median values only differed significantly for IgG1 anti-MDA among men, with lower levels among cases than controls (p = 0.039). High IgG1 anti-MDA (above 75th percentile) was inversely associated with CVD risk after adjustment for smoking, body mass index, type 2 diabetes, hyperlipidemia, and hypertension, (OR and 95% CI: 0.59; 0.40–0.89). After stratification by sex, this association emerged in men (OR and 95% CI: 0.46; 0.27–0.77), but not in women. IgG2 anti-MDA were associated with protection in the whole group and among men though weaker than IgG1 anti-MDA. IgG2 anti-MDA above the 75th percentile was associated with an increased risk of MI/angina in women (OR and 95% CI: 2.57; (1.08–6.16)). IgG1 and less so IgG2 anti-MDA are protection markers for CVD and MI/angina in the whole group and among men. However, IgG2 anti-MDA was a risk marker for MI/angina among women. These findings could have implications for both prediction and therapy.
An inspired microenvironment of cell replicas to induce stem cells into keratocyte-like dendritic cells for corneal regeneration
Authors: Fallah Tafti Mahsa , Aghamollaei Hossein , Moosazadeh Moghaddam Mehrdad , Jadidi Khosrow , Faghihi Shahab 
Published: September 2023

AbstractCorneal stromal disorders due to the loss of keratocytes can affect visual impairment and blindness. Corneal cell therapy is a promising therapeutic strategy for healing corneal tissue or even enhancing corneal function upon advanced disorders, however, the sources of corneal keratocytes are limited for clinical applications. Here, the capacity of cell-imprinted substrates fabricated by molding human keratocyte templates to induce differentiation of human adipose-derived stem cells (hADSCs) into keratocytes, is presented. Keratocytes are isolated from human corneal stroma and grown to transmit their ECM architecture and cell-like topographies to a PDMS substrate. The hADSCs are then seeded on cell-imprinted substrates and their differentiation to keratocytes in DMEM/F12 (with and without chemical factors) are evaluated by real-time PCR and immunocytochemistry. The mesenchymal stem cells grown on patterned substrates present gene and protein expression profiles similar to corneal keratocytes. In contrast, a negligible expression of myofibroblast marker in the hADSCs cultivated on the imprinted substrates, is observed. Microscopic analysis reveals dendritic morphology and ellipsoid nuclei similar to primary keratocytes. Overall, it is demonstrated that biomimetic imprinted substrates would be a sufficient driver to solely direct the stem cell fate toward target cells which is a significant achievement toward corneal regeneration.
Metabolomics profiling in predicting of post-herpetic neuralgia induced by varicella zoster
Authors: Lu Lina , Mei Lihong , Li Xushuo , Lin Yanhua , Wang Hongfeng , Yang Gao 
Published: September 2023

AbstractTo explore potential metabolomics biomarkers in predicting post-herpetic neuralgia (PHN) induced by herpes zoster (HZ). A total of 90 eligible patients were prospectively enrolled and assigned into an acute pain (ACP) group and a PHN group. Serum samples were collected before clinical intervention to perform metabolomics profiling analyses using gas chromatography mass spectrometry (GC–MS). Key metabolites were identified using partial least squares discriminant analysis (PLS-DA). A binary logistic regression was used to build a combined biomarker model to predict PHN from ACP. The discriminating efficiency of the combined biomarker model was investigated and validated by internal validation. Six metabolites were identified as the key metabolites related to PHN. All these metabolites (N-Acetyl-5-hydroxytryptaMine, glucose, dehydroascorbic acid, isopropyl-beta-d-thiogalactopyranoside, 1,5-anhydro-d-sorbitol, and glutamic acid) were found elevated in the PHN group. Pathway analyses showed that glucose-alanine cycle, tryptophan metabolism, tyrosine metabolism, lactose degradation, malate-aspartate shuttle were top five metabolic pathways evolved in PHN. The AUC was 0.85 (95% CI 0.76–0.93) for the combined biomarker model, and was 0.91 (95% CI 0.84–1.00) for the internal validation data set to predict PHN. Metabolomics analyses of key metabolites could be used to predict PHN induced by HZ.
High risk clear cell renal cell carcinoma microenvironments contain protumour immunophenotypes lacking specific immune checkpoints
Authors: Raghubar Arti M. , Matigian Nicholas A. , Crawford Joanna , Francis Leo , Ellis Robert , Healy Helen G. , Kassianos Andrew J. , Ng Monica S. Y. , Roberts Matthew J. , Wood Simon , Mallett Andrew J. 
Published: September 2023

AbstractPerioperative immune checkpoint inhibitor (ICI) trials for intermediate high-risk clear cell renal cell carcinoma (ccRCC) have failed to consistently demonstrate improved patient outcomes. These unsuccessful ICI trials suggest that the tumour infiltrating immunophenotypes, termed here as the immune cell types, states and their spatial location within the tumour microenvironment (TME), were unfavourable for ICI treatment. Defining the tumour infiltrating immune cells may assist with the identification of predictive immunophenotypes within the TME that are favourable for ICI treatment. To define the immunophenotypes within the ccRCC TME, fresh para-tumour (pTME, n = 2), low-grade (LG, n = 4, G1-G2) and high-grade (HG, n = 4, G3-G4) tissue samples from six patients with ccRCC presenting at a tertiary referral hospital underwent spatial transcriptomics sequencing (ST-seq). Within the generated ST-seq datasets, immune cell types and states, termed here as exhausted/pro-tumour state or non-exhausted/anti-tumour state, were identified using multiple publicly available single-cell RNA and T-cell receptor sequencing datasets as references. HG TMEs revealed abundant exhausted/pro-tumour immune cells with no consistent increase in expression of PD-1, PD-L1 and CTLA4 checkpoints and angiogenic genes. Additional HG TME immunophenotype characteristics included: pro-tumour tissue-resident monocytes with consistently increased expression of HAVCR2 and LAG3 checkpoints; an exhausted CD8+ T cells sub-population with stem-like progenitor gene expression; and pro-tumour tumour-associated macrophages and monocytes within the recurrent TME with the expression of TREM2. Whilst limited by a modest sample size, this study represents the largest ST-seq dataset on human ccRCC. Our study reveals that high-risk ccRCC TMEs are infiltrated by exhausted/pro-tumour immunophenotypes lacking specific checkpoint gene expression confirming that HG ccRCC TME are immunogenic but not ICI favourable.
Discovery of l-threonine transaldolases for enhanced biosynthesis of beta-hydroxylated amino acids
Authors: Jones Michaela A. , Butler Neil D. , Anderson Shelby R. , Wirt Sean A. , Govil Ishika , Lyu Xinyi , Fang Yinzhi , Kunjapur Aditya M. 
Published: September 2023

AbstractBeta-hydroxy non-standard amino acids (β-OH-nsAAs) have utility as small molecule drugs, precursors for beta-lactone antibiotics, and building blocks for polypeptides. While the L-threonine transaldolase (TTA), ObiH, is a promising enzyme for β-OH-nsAA biosynthesis, little is known about other natural TTA sequences. We ascertained the specificity of the TTA enzyme class more comprehensively by characterizing 12 candidate TTA gene products across a wide range (20-80%) of sequence identities. We found that addition of a solubility tag substantially enhanced the soluble protein expression level within this difficult-to-express enzyme family. Using an optimized coupled enzyme assay, we identified six TTAs, including one with less than 30% sequence identity to ObiH that exhibits broader substrate scope, two-fold higher L-Threonine (L-Thr) affinity, and five-fold faster initial reaction rates under conditions tested. We harnessed these TTAs for first-time bioproduction of β-OH-nsAAs with handles for bio-orthogonal conjugation from supplemented precursors during aerobic fermentation of engineered Escherichia coli, where we observed that higher affinity of the TTA for L-Thr increased titer. Overall, our work reveals an unexpectedly high level of sequence diversity and broad substrate specificity in an enzyme family whose members play key roles in the biosynthesis of therapeutic natural products that could benefit from chemical diversification.
Insights from multi-omics integration into seed germination of Taxus chinensis var mairei
Authors: Chen Lulu , Qin Liang , Zhang Yawen , Xu Hualei , Bu Yufen , Wu Ran , Liu Haiqiang , Hao Qichen , Hu Hao , Zhou Yijun , Feng Jinchao , Jing Yanping , Han Jun , Wang Xiaodong 
Published: September 2023

AbstractThe transition from deep dormancy to seed germination is essential for the life cycle of plants, but how this process occurs in the gymnosperm Chinese yew (Taxus chinensis var mairei), the natural source of the anticancer drug paclitaxel, remains unclear. Herein, we analyse the transcriptome, proteome, spatial metabolome, and spatial lipidome of the Chinese yew and present the multi-omics profiles of dormant and germinating seeds. Our results show that abscisic acid and gibberellic acid 12 homoeostasis is closely associated with gene transcription and protein translation, and the balance between these phytohormones thereby determines if seeds remain dormant or germinate. We find that an energy supply of carbohydrates from glycolysis and the TCA cycle feed into the pentose phosphate pathway during seed germination, and energy supplied from lipids are mainly derived from the lipolysis of triacylglycerols. Using mass spectrometry imaging, we demonstrate that the spatial distribution of plant hormones and phospholipids has a remarkable influence on embryo development. We also provide an atlas of the spatial distribution of paclitaxel C in Chinese yew seeds for the first time. The data from this study enable exploration of the germination mechanism of Chinese yew seeds across several omics levels.
A self-supervised deep learning method for data-efficient training in genomics
Authors: Gündüz Hüseyin Anil , Binder Martin , To Xiao-Yin , Mreches René , Bischl Bernd , McHardy Alice C. , Münch Philipp C. , Rezaei Mina 
Published: September 2023

AbstractDeep learning in bioinformatics is often limited to problems where extensive amounts of labeled data are available for supervised classification. By exploiting unlabeled data, self-supervised learning techniques can improve the performance of machine learning models in the presence of limited labeled data. Although many self-supervised learning methods have been suggested before, they have failed to exploit the unique characteristics of genomic data. Therefore, we introduceSelf-GenomeNet, a self-supervised learning technique that is custom-tailored for genomic data.Self-GenomeNetleverages reverse-complement sequences and effectively learns short- and long-term dependencies by predicting targets of different lengths.Self-GenomeNetperforms better than other self-supervised methods in data-scarce genomic tasks and outperforms standard supervised training with ~10 times fewer labeled training data. Furthermore, the learned representations generalize well to new datasets and tasks. These findings suggest thatSelf-GenomeNetis well suited for large-scale, unlabeled genomic datasets and could substantially improve the performance of genomic models.
Molecular control of endurance training adaptation in male mouse skeletal muscle
Authors: Furrer Regula , Heim Barbara , Schmid Svenia , Dilbaz Sedat , Adak Volkan , Nordström Karl J. V. , Ritz Danilo , Steurer Stefan A. , Walter Jörn , Handschin Christoph 
Published: September 2023

AbstractSkeletal muscle has an enormous plastic potential to adapt to various external and internal perturbations. Although morphological changes in endurance-trained muscles are well described, the molecular underpinnings of training adaptation are poorly understood. We therefore aimed to elucidate the molecular signature of muscles of trained male mice and unravel the training status-dependent responses to an acute bout of exercise. Our results reveal that, even though at baseline an unexpectedly low number of genes define the trained muscle, training status substantially affects the transcriptional response to an acute challenge, both quantitatively and qualitatively, in part associated with epigenetic modifications. Finally, transiently activated factors such as the peroxisome proliferator-activated receptor-γ coactivator 1α are indispensable for normal training adaptation. Together, these results provide a molecular framework of the temporal and training status-dependent exercise response that underpins muscle plasticity in training.
Impact of supplementary sensory feedback on the control and embodiment in human movement augmentation
Authors: Pinardi Mattia , Longo Matthew R. , Formica Domenico , Strbac Matija , Mehring Carsten , Burdet Etienne , Di Pino Giovanni 
Published: September 2023

AbstractIn human movement augmentation, the number of controlled degrees of freedom could be enhanced by the simultaneous and independent use of supernumerary robotic limbs (SRL) and natural ones. However, this poses several challenges, that could be mitigated by encoding and relaying the SRL status. Here, we review the impact of supplementary sensory feedback on the control and embodiment of SRLs. We classify the main feedback features and analyse how they improve control performance. We report the feasibility of pushing body representation beyond natural human morphology and suggest that gradual SRL embodiment could make multisensory incongruencies less disruptive. We also highlight shared computational bases between SRL motor control and embodiment and suggest contextualizing them within the same theoretical framework. Finally, we argue that a shift towards long term experimental paradigms is necessary for successfully integrating motor control and embodiment.
Potential of nanostructured carbon materials for iodine detection in realistic environments revealed by first-principles calculations
Authors: Zhour Kazem , Daouli Ayoub , Postnikov Andrei , Hasnaoui Abdellatif , Badawi Michael 
Published: September 2023

In the context of effective detection of iodine species (I2, CH3I) formed in nuclear power plants and nuclear fuel reprocessing facilities, we perform a comparative study of potential sensing performance of 8-Pmmn borophene, BC3, C3N, and BC6N.
Accumulated Secretions and Associated Aerodigestive Function in Patients With Dysphagia
Authors: Hunting Alexandra , Steffanoni Belinda , Jacques Angela , Miles Anna 
Published: September 2023

Purpose:
Accumulated pharyngo-laryngeal secretions are associated with dysphagia, aspiration, and poor health outcomes. Despite ongoing developments in the evaluation of pharyngo-laryngeal secretions, understanding of the underlying mechanisms is limited. Pathophysiology associated with accumulated secretions is needed to guide tailored, targeted treatment pathways. This study reports the prevalence of accumulated pharyngo-laryngeal secretions in a large acute care caseload and explores the relationship between secretions and aerodigestive function.

Method:

Consecutive inpatients (
N
= 222) referred for flexible endoscopic evaluation of swallow (FEES) with suspected dysphagia following assessment by a speech-language pathologist were recruited (43% neurological, 22% neurosurgical, 20% critical care, 15% other), and 250 standardized FEES were completed (222 first FEES, 28 repeat FEES). The assessment protocol included secretion assessment using the New Zealand Secretion Scale (NZSS), pharyngeal squeeze maneuver, laryngeal motor and sensory assessment, Penetration-Aspiration Scale, and Yale Pharyngeal Residue Severity Rating Scale. Urge-to-clear ratings were collected during endoscopy. Cough peak expiratory flow and swallow frequency measures were also collected, as well as clinical outcomes at time of discharge.

Results:

There was a high incidence of accumulated secretions, with 77% of inpatients having elevated NZSS (
Mdn
= 3, range: 0–7) and 37% with pooled laryngeal secretions. Accumulated secretions were associated with reduced swallow frequency, reduced laryngeal adductor reflex, impaired pharyngeal squeeze maneuver, and peak expiratory flow. NZSS scores also correlated with swallow measures (Penetration-Aspiration Scale and Yale Pharyngeal Residue Severity Rating Scale) and patient outcomes including diet recommendations at discharge and pneumonia during admission.

Conclusions:
This large study contributes to evidence associating both sensory and motor impairments with secretion accumulation and aspiration risk. Further exploration of the key physiological mechanisms contributing to accumulated secretions will serve as markers to provide proof of principle for targets for secretion management protocols.

Supplemental Material:

https://doi.org/10.23641/asha.24101667
5G supporting digital servitization in manufacturing: An exploratory survey
Authors: Cimini Chiara , Lagorio Alexandra , Pinto Roberto , Pezzotta Giuditta , Adrodegari Federico , Cavalieri Sergio 
Published: September 2023

AbstractDigital servitization is a business model transformation process enabled by the use of digital technologies to create or improve industrial services and product‐service offerings by creating value and competitive advantage increasing customer satisfaction and loyalty as well as company revenue streams. 5G networks can enable digital servitization of manufacturing by providing faster, more secure, and more reliable communications between machines, devices, and humans. This paper explores the impact of adopting 5G technologies on servitization and identifies the services that can benefit most from 5G networks. The research consists of two parts: a literature review of the technologies currently used in the design and provision of industrial services that could benefit from 5G networks and an exploratory survey involving manufacturing companies that have started the digital servitization journey. The main results emerging from the research suggest that 5G can profoundly impact services supported by Augmented Reality, Cloud computing, and Cyber‐physical systems, mainly concerning maintenance, workforce training, machine diagnosis and monitoring.
Research on seamless image stitching based on fast marching method
Authors: Pan Weidong , Li Anhu , Wu Yusheng , Deng Zhaojun , Liu Xingsheng 
Published: September 2023

AbstractImage stitching is an important way to achieve large‐field high‐resolution imaging. The inconsistencies in brightness and structure and defects in ghosting, blurring and misalignment between images, which are inevitable and difficult to eliminate, make a challenge to image stitching, due to the external lighting environment and changes in camera pose and parameters. Here, a novel method is proposed to search for the optimal seamline based on the fast marching method, which can stitch large parallax images with high quality. A feature weight map is first formed based on the similarity in colour, edge, texture and saliency of the images. Then it is used as the cost value of the seamline to search for the optimal seamline by fast marching method. The results show that this new method is more efficient to reduce defects, such as ghosting, misalignment and chromatic aberration, and realize high quality image stitching compared with traditional stitching tools and methods, which provides a new perspective for image stitching technology.
Three-dimensional relation between coronal dimming, filament eruption, and CME
Authors: Chikunova Galina , Podladchikova Tatiana , Dissauer Karin , Veronig Astrid M. , Dumbović Mateja , Temmer Manuela , Dickson Ewan C. M. 
Published: September 2023

Context.Coronal dimmings are localized regions of reduced emission in the extreme-ultraviolet (EUV) and soft X-rays formed as a result of the expansion and mass loss by coronal mass ejections (CMEs) low in the corona. Distinct relations have been established between coronal dimmings (intensity, area, magnetic flux) and key characteristics of the associated CMEs (mass and speed) by combining coronal and coronagraphic observations from different viewpoints in the heliosphere.Aims.We investigate the relation between the spatiotemporal evolution of the dimming region and both the dominant direction of the filament eruption and CME propagation for the 28 October 2021 X1.0 flare/CME event observed from multiple viewpoints in the heliosphere by Solar Orbiter, STEREO-A, SDO, and SOHO.Methods.We present a method for estimating the dominant direction of the dimming development based on the evolution of the dimming area, taking into account the importance of correcting the dimming area estimation by calculating the surface area of a sphere for each pixel. To determine the propagation direction of the flux rope during early CME evolution, we performed 3D reconstructions of the white-light CME by graduated cylindrical shell modeling (GCS) and 3D tie-pointing of the eruptive filament.Results.The dimming evolution starts with a radial expansion and later propagates more to the southeast. The orthogonal projections of the reconstructed height evolution of the prominent leg of the erupting filament onto the solar surface are located in the sector of the dominant dimming growth, while the orthogonal projections of the inner part of the GCS reconstruction align with the total dimming area. The filament reaches a maximum speed of ≈250 km s−1at a height of about ≈180 Mm before it can no longer be reliably followed in the EUV images. Its direction of motion is strongly inclined from the radial direction (64° to the east, 32° to the south). The 3D direction of the CME and the motion of the filament leg differ by 50°. This angle roughly aligns with the CME half-width obtained from the CME reconstruction, suggesting a relation between the reconstructed filament and the associated leg of the CME body.Conclusions.The dominant propagation of the dimming growth reflects the direction of the erupting magnetic structure (filament) low in the solar atmosphere, though the filament evolution is not directly related to the direction of the global CME expansion. At the same time, the overall dimming morphology closely resembles the inner part of the CME reconstruction, validating the use of dimming observations to obtain insight into the CME direction.