bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intraoperative Positioning in Maxillofacial Trauma Patients With Cervical Spine Injury – Is It Safe? Radiological Simulation in a Healthy Volunteer
Authors: Pepper Thomas , Spiers Harry , Weller Alex , Schilling Clare 
Published: January 2022

Study Design Observational. Objective To investigate the effects on the cervical spine of positioning patients for maxillofacial procedures by simulating intraoperative positions for common maxillofacial procedures. Methods Magnetic resonance imaging was used to assess the effects of head position in common intraoperative configurations – neutral (anterior mandible position), extended (tracheostomy position) and laterally rotated (mandibular condyle position) on the C-spine of a healthy volunteer. Results In the tracheostomy position, maximal movement occurred in the sagittal plane between the cervico-occipital junction and C4–C5, as well as at the cervico-thoracic junction. Minimal movement occurred at C2 (on C3), C5 (on C6) and C6 (on C7). In the mandibular condyle position, C-spine movements occurred in both rotational and sagittal planes. Maximal movement occurred above the level of C4, concentrated at atlanto-occipital and atlanto-axial (C1–2) joints. Conclusions Neck extension is likely to be relatively safe in injuries that are stable in flexion and extension, such as odontoid peg fracture and fractures between C5 and C7. Head rotation is likely to be relatively safe in fractures below C4, as well as vertebral body fractures, and laminar fractures without disc disruption. Early dialogue with the neurosurgical team remains a central tenet of safe management of patients with combined maxillofacial and C-spine injuries.
Infectious risk in multiple sclerosis patients treated with disease-modifying therapies: A three-year observational cohort study
Authors: Zingaropoli Maria Antonella , Pasculli Patrizia , Iannetta Marco , Perri Valentina , Tartaglia Matteo , Crisafulli Sebastiano Giuseppe , Merluzzo Chiara , Baione Viola , Mazzochi Lorenzo , Taglietti Ambra , Pauri Flavia , Frontoni Marco , Altieri Marta , Gaeta Aurelia , Antonelli Guido , Conte Antonella , Mastroianni Claudio Maria , Ciardi Maria Rosa 
Published: January 2022

Background The disease-modifying therapies (DMTs) largely used in multiple sclerosis (MS) may result in higher infectious risk. Objective We aimed to investigate the infectious risk in DMT-treated MS patients. Methods MS patients were evaluated for infectious risk before starting, switching or during DMT. Results In this three-year observational cohort study 174 MS patients were enrolled. Among them, 18 patients were anti-HBc + and 19 patients were QuantiFERON®-TB Gold In-Tube (QFT)  +  . No patients with anti-HBc + showed a detectable HBV-DNA and all started DMT. Among QTB + patients, 17 latent TB infections (LTBIs) and 2 active TB infections (TBIs) were identified. After one month of LTBI prophylaxis or TB treatment, respectively, all patients started DMTs. Overall, 149 started DMTs. During DMTs, one ocrelizumab-treated patient with anti-HBc + developed HBV reactivation and six patients (3 on natalizumab, 2 on ocrelizumab and 1 on IFN-β) showed reactivation of HSV-1, with detectable plasma DNA. Finally, 1 cladribine-treated patient experienced VZV reactivation. All the reactivations of latent infections have been successfully treated. Conclusion Screening of infectious diseases in DMT candidate MS patients helps to mitigate the infectious risk. During DMTs, a regular assessment of infectious risk allows to avoid discontinuing MS therapy and guarantees a higher degree of safety.
An experimental study on changes in sound absorption capability of spruce (Picea sitchensis), Douglas fir (Pseudotsuga menziesii), and larch (Larix kaempferi) after microwave treatment
Authors: Jang Eun-Suk , Kang Chun-Won 
Published: January 2022

AbstractThis study investigated changes in the sound absorption coefficients of three anatomical sections of cubed spruce (Picea sitchensis), Douglas fir (Pseudotsuga menziesii), and larch (Larix kaempferi) after microwave treatment. Microwave treatment at 1000 W and 2.4 GHz for 20 min increased the sound absorption coefficients (at 2000–5000 Hz) of spruce by 6.9% in the transverse section, 20.0% in the radial section, and 31.7% in the tangential section. The sound absorption coefficients of Douglas fir increased by 28.9% in the transverse section, 19.1% in the radial section, and 50.0% in the tangential section. Larch coefficients increased by 16.7% in the transverse section, 37.2% in the radial section, and 38.8% in the tangential section. The sound absorption coefficients of the softwoods differed according to species and anatomical plane after microwave treatment. It was concluded that changes in the measured sound absorption coefficient indicate alteration in the pore structure of wood, which can affect in turn wood permeability and impregnation. These data will be helpful for predicting the permeability and impregnation of wood after microwave treatment.
Non-homogeneous dispersion of graphene in polyacrylonitrile substrates induces a migrastatic response and epithelial-like differentiation in MCF7 breast cancer cells
Authors: Diban Nazely , Mantecón-Oria Marián , Berciano María T. , Puente-Bedia Alba , Rivero María J. , Urtiaga Ane , Lafarga Miguel , Tapia Olga 
Published: January 2022

Abstract
Background
Recent advances from studies of graphene and graphene-based derivatives have highlighted the great potential of these nanomaterials as migrastatic agents with the ability to modulate tumor microenvironments. Nevertheless, the administration of graphene nanomaterials in suspensions in vivo is controversial. As an alternative approach, herein, we report the immobilization of high concentrations of graphene nanoplatelets in polyacrylonitrile film substrates (named PAN/G10) and evaluate their potential use as migrastatic agents on cancer cells.

Results
Breast cancer MCF7 cells cultured on PAN/G10 substrates presented features resembling mesenchymal-to-epithelial transition, e.g., (i) inhibition of migratory activity; (ii) activation of the expression of E-cadherin, cytokeratin 18, ZO-1 and EpCAM, four key molecular markers of epithelial differentiation; (iii) formation of adherens junctions with clustering and adhesion of cancer cells in aggregates or islets, and (iv) reorganization of the actin cytoskeleton resulting in a polygonal cell shape. Remarkably, assessment with Raman spectroscopy revealed that the above-mentioned events were produced when MCF7 cells were preferentially located on top of graphene-rich regions of the PAN/G10 substrates.

Conclusions
The present data demonstrate the capacity of these composite substrates to induce an epithelial-like differentiation in MCF7 breast cancer cells, resulting in a migrastatic effect without any chemical agent-mediated signaling. Future works will aim to thoroughly evaluate the mechanisms of how PAN/G10 substrates trigger these responses in cancer cells and their potential use as antimetastatics for the treatment of solid cancers.

Graphical Abstract
Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT
Authors: Elangovan Aparna , Li Yuan , Pires Douglas E. V. , Davis Melissa J. , Verspoor Karin 
Published: January 2022

Abstract
Motivation
Protein-protein interactions (PPIs) are critical to normal cellular function and are related to many disease pathways. A range of protein functions are mediated and regulated by protein interactions through post-translational modifications (PTM). However, only 4% of PPIs are annotated with PTMs in biological knowledge databases such as IntAct, mainly performed through manual curation, which is neither time- nor cost-effective. Here we aim to facilitate annotation by extracting PPIs along with their pairwise PTM from the literature by using distantly supervised training data using deep learning to aid human curation.

Method
We use the IntAct PPI database to create a distant supervised dataset annotated with interacting protein pairs, their corresponding PTM type, and associated abstracts from the PubMed database. We train an ensemble of BioBERT models—dubbed PPI-BioBERT-x10—to improve confidence calibration. We extend the use of ensemble average confidence approach with confidence variation to counteract the effects of class imbalance to extract high confidence predictions.

Results and conclusion
The PPI-BioBERT-x10 model evaluated on the test set resulted in a modest F1-micro 41.3 (P =5 8.1, R = 32.1). However, by combining high confidence and low variation to identify high quality predictions, tuning the predictions for precision, we retained 19% of the test predictions with 100% precision. We evaluated PPI-BioBERT-x10 on 18 million PubMed abstracts and extracted 1.6 million (546507 unique PTM-PPI triplets) PTM-PPI predictions, and filter $$\approx 5700$$

≈
5700

(4584 unique) high confidence predictions. Of the 5700, human evaluation on a small randomly sampled subset shows that the precision drops to 33.7% despite confidence calibration and highlights the challenges of generalisability beyond the test set even with confidence calibration. We circumvent the problem by only including predictions associated with multiple papers, improving the precision to 58.8%. In this work, we highlight the benefits and challenges of deep learning-based text mining in practice, and the need for increased emphasis on confidence calibration to facilitate human curation efforts.
Machine learning-based predictions of dietary restriction associations across ageing-related genes
Authors: Vega Magdaleno Gustavo Daniel , Bespalov Vladislav , Zheng Yalin , Freitas Alex A. , de Magalhaes Joao Pedro 
Published: January 2022

Abstract
Background
Dietary restriction (DR) is the most studied pro-longevity intervention; however, a complete understanding of its underlying mechanisms remains elusive, and new research directions may emerge from the identification of novel DR-related genes and DR-related genetic features.

Results
This work used a Machine Learning (ML) approach to classify ageing-related genes as DR-related or NotDR-related using 9 different types of predictive features: PathDIP pathways, two types of features based on KEGG pathways, two types of Protein–Protein Interactions (PPI) features, Gene Ontology (GO) terms, Genotype Tissue Expression (GTEx) expression features, GeneFriends co-expression features and protein sequence descriptors. Our findings suggested that features biased towards curated knowledge (i.e. GO terms and biological pathways), had the greatest predictive power, while unbiased features (mainly gene expression and co-expression data) have the least predictive power. Moreover, a combination of all the feature types diminished the predictive power compared to predictions based on curated knowledge. Feature importance analysis on the two most predictive classifiers mostly corroborated existing knowledge and supported recent findings linking DR to the Nuclear Factor Erythroid 2-Related Factor 2 (NRF2) signalling pathway and G protein-coupled receptors (GPCR).
We then used the two strongest combinations of feature type and ML algorithm to predict DR-relatedness among ageing-related genes currently lacking DR-related annotations in the data, resulting in a set of promising candidate DR-related genes (GOT2, GOT1, TSC1, CTH, GCLM, IRS2 and SESN2) whose predicted DR-relatedness remain to be validated in future wet-lab experiments.

Conclusions
This work demonstrated the strong potential of ML-based techniques to identify DR-associated features as our findings are consistent with literature and recent discoveries. Although the inference of new DR-related mechanistic findings based solely on GO terms and biological pathways was limited due to their knowledge-driven nature, the predictive power of these two features types remained useful as it allowed inferring new promising candidate DR-related genes.
Secondary structure specific simpler prediction models for protein backbone angles
Authors: Newton M. A. Hakim , Mataeimoghadam Fereshteh , Zaman Rianon , Sattar Abdul 
Published: January 2022

AbstractMotivationProtein backbone angle prediction has achieved significant accuracy improvement with the development of deep learning methods. Usually the same deep learning model is used in making prediction for all residues regardless of the categories of secondary structures they belong to. In this paper, we propose to train separate deep learning models for each category of secondary structures. Machine learning methods strive to achieve generality over the training examples and consequently loose accuracy. In this work, we explicitly exploit classification knowledge to restrict generalisation within the specific class of training examples. This is to compensate the loss of generalisation by exploiting specialisation knowledge in an informed way.ResultsThe new method named SAP4SS obtains mean absolute error (MAE) values of 15.59, 18.87, 6.03, and 21.71 respectively for four types of backbone angles$$\phi$$ϕ,$$\psi$$ψ,$$\theta$$θ, and$$\tau$$τ. Consequently, SAP4SS significantly outperforms existing state-of-the-art methods SAP, OPUS-TASS, and SPOT-1D: the differences in MAE for all four types of angles are from 1.5 to 4.1% compared to the best known results.AvailabilitySAP4SS along with its data is available fromhttps://gitlab.com/mahnewton/sap4ss.
Sensei: how many samples to tell a change in cell type abundance?
Authors: Liang Shaoheng , Willis Jason , Dou Jinzhuang , Mohanty Vakul , Huang Yuefan , Vilar Eduardo , Chen Ken 
Published: January 2022

AbstractCellular heterogeneity underlies cancer evolution and metastasis. Advances in single-cell technologies such as single-cell RNA sequencing and mass cytometry have enabled interrogation of cell type-specific expression profiles and abundance across heterogeneous cancer samples obtained from clinical trials and preclinical studies. However, challenges remain in determining sample sizes needed for ascertaining changes in cell type abundances in a controlled study. To address this statistical challenge, we have developed a new approach, named Sensei, to determine the number of samples and the number of cells that are required to ascertain such changes between two groups of samples in single-cell studies. Sensei expands the t-test and models the cell abundances using a beta-binomial distribution. We evaluate the mathematical accuracy of Sensei and provide practical guidelines on over 20 cell types in over 30 cancer types based on knowledge acquired from the cancer cell atlas (TCGA) and prior single-cell studies. We provide a web application to enable user-friendly study design viahttps://kchen-lab.github.io/sensei/table_beta.html.
Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages
Authors: Cao Xingwei , Xu Xingye , Dong Jie , Xue Ying , Sun Lilian , Zhu Yafang , Liu Tao , Jin Qi 
Published: January 2022

Abstract
Background
Circular RNAs (circRNAs) are a group of noncoding RNAs that participate in gene expression regulation in various pathways. The essential roles of circRNAs have been revealed in many species. However, knowledge of circRNAs in fungi is still not comprehensive.

Results
Trichophyton rubrum (T. rubrum) is considered a model organism of human pathogenic filamentous fungi and dermatophytes. In this study, we performed a genome-wide investigation of circRNAs in T. rubrum based on high-throughput sequencing and ultimately identified 4254 circRNAs. Most of these circRNAs were specific to the conidial or mycelial stage, revealing a developmental stage-specific expression pattern. In addition, 940 circRNAs were significantly differentially expressed between the conidial and mycelial stages. PCR experiments conducted on seven randomly selected differentially expressed (DE-) circRNAs confirmed the circularized structures and relative expression levels of these circRNAs. Based on their genome locations, most circRNAs originated from intergenic regions, unlike those in plants and animals. Furthermore, we constructed circRNA-miRNA-mRNA regulatory networks that included 661 DE-circRNAs targeting 140 miRNAs and further regulating 2753 mRNAs. The relative expression levels of two randomly selected circRNA-miRNA-mRNA axes were investigated by qRT-PCR, and the competing endogenous RNA (ceRNA) network theory was validated. Functional enrichment analysis of the target genes suggested that they were significantly involved in posttranscriptional processes and protein synthesis as well as some small-molecule metabolism processes. CircRNAs are relatively more conserved in closely related dermatophytes but rarely conserved in distantly related species. Tru_circ07138_001 is a highly conserved circRNA that was conserved in all ten dermatophytes analyzed in our study and three distantly related species. Its host gene TERG_07138 was also highly conserved in two of these distantly related species Gallus gallus and Caenorhabditis elegans. The specific role of this circRNA deserves further exploration.

Conclusions
Our study is the first to provide a global profile of circRNAs in T. rubrum as well as dermatophytes. These results could serve as valuable resources for research on circRNA regulatory mechanisms in fungi and reveal new insights for further investigation of the physical characteristics of these significant human fungal pathogens.
Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum
Authors: Deneweth Jan , Van de Peer Yves , Vermeirssen Vanessa 
Published: January 2022

Abstract
Background
Transposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution. Several TEs can contribute to gene regulation by influencing expression of nearby genes as stress-responsive regulatory motifs. To delineate TE-mediated plant stress regulatory networks, we took a 2-step computational approach consisting of identifying TEs in the proximity of stress-responsive genes, followed by searching for cis-regulatory motifs in these TE sequences and linking them to known regulatory factors. Through a systematic meta-analysis of RNA-seq expression profiles and genome annotations, we investigated the relation between the presence of TE superfamilies upstream, downstream or within introns of nearby genes and the differential expression of these genes in various stress conditions in the TE-poor Arabidopsis thaliana and the TE-rich Solanum lycopersicum.

Results
We found that stress conditions frequently expressed genes having members of various TE superfamilies in their genomic proximity, such as SINE upon proteotoxic stress and Copia and Gypsy upon heat stress in A. thaliana, and EPRV and hAT upon infection, and Harbinger, LINE and Retrotransposon upon light stress in S. lycopersicum. These stress-specific gene-proximal TEs were mostly located within introns and more detected near upregulated than downregulated genes. Similar stress conditions were often related to the same TE superfamily. Additionally, we detected both novel and known motifs in the sequences of those TEs pointing to regulatory cooption of these TEs upon stress. Next, we constructed the regulatory network of TFs that act through binding these TEs to their target genes upon stress and discovered TE-mediated regulons targeted by TFs such as BRB/BPC, HD, HSF, GATA, NAC, DREB/CBF and MYB factors in Arabidopsis and AP2/ERF/B3, NAC, NF-Y, MYB, CXC and HD factors in tomato.

Conclusions
Overall, we map TE-mediated plant stress regulatory networks using numerous stress expression profile studies for two contrasting plant species to study the regulatory role TEs play in the response to stress. As TE-mediated gene regulation allows plants to adapt more rapidly to new environmental conditions, this study contributes to the future development of climate-resilient plants.
Administration of Human Derived Upper gut Commensal Prevotella histicola delays the onset of type 1 diabetes in NOD mice
Authors: Marietta Eric , Horwath Irina , Meyer Stephanie , Khaleghi-Rostamkolaei Shahryar , Norman Eric , Luckey David , Balakrishnan Baskar , Mangalam Ashutosh , Choung Rok Seon , Taneja Veena , Murray Joseph A. 
Published: January 2022

Abstract
Background
Type 1 diabetes (T1D) is an autoimmune disease that is increasing in prevalence worldwide. One of the contributing factors to the pathogenesis of T1D is the composition of the intestinal microbiota, as has been demonstrated. in T1D patients, with some studies demonstrating a deficiency in their levels of Prevotella. We have isolated a strain of Prevotella histicola from a duodenal biopsy that has anti-inflammatory properties, and in addition, alters the development of autoimmune diseases in mouse models. Therefore, our hypothesis is that the oral administration of P. histicola might delay the development of T1D in the non-obese diabetic (NOD) mice. To assess this, we used the following materials and methods. Female NOD mice (ages 5–8 weeks) were administered every other day P. histicola that was cultured in-house. Blood glucose levels were measured every other week. Mice were sacrificed at various time points for histopathological analysis of the pancreas. Modulation of immune response by the commensal was tested by analyzing regulatory T-cells and NKp46+ cells using flow cytometry and intestinal cytokine mRNA transcript levels using quantitative RT-PCR. For microbial composition, 16 s rRNA gene analysis was conducted on stool samples collected at various time points.

Results
Administration of P. histicola in NOD mice delayed the onset of T1D. Beta diversity in the fecal microbiomes demonstrated that the microbial composition of the mice administered P. histicola was different from those that were not treated. Treatment with P. histicola led to a significant increase in regulatory T cells with a concomitant decrease in NKp46+ cells in the pancreatic lymph nodes as compared to the untreated group after 5 weeks of treatment.

Conclusions
These observations suggest that P. histicola treatment delayed onset of diabetes by increasing the levels of regulatory T cells in the pancreatic lymph nodes. This preliminary work supports the rationale that enteral exposure to a non pathogenic commensal P. histicola be tested as a future therapy for T1D.