bluuebunny/crossref_metadata_2025 huggingface dataset:
Yoga for Preventive Health: A Holistic Approach
Authors: Madan Shobhit , Sembhi Jasraj , Khurana Navpreet , Makkar Kanika , Byati Priya
Published: January 2022

Yoga has been prevalent for over 5000 years; it originated in India and has become an essential lifestyle ingredient for achieving optimal health. The goal of this article in lifestyle modification is to increase awareness about the benefits of yoga and how its practice can reduce the overall risk of chronic diseases. Yoga has been proven to be therapeutic for enhancing immunity and support management of chronic diseases such as cardiovascular, respiratory, endocrine disorders, obesity, cancer, and metabolic syndrome. Yoga techniques called asanas, such as pranayama for breathing regulation and dhyana for meditation, boost innate immune response, interrupt inflammation, and thereby prevent the manifestation of chronic diseases. Yoga also provides symptomatic relief for chronic arthritis by increasing joint flexibility and microcirculation. Yoga and meditation regulate neurotransmitters, neuropeptides, hormones, and cytokines that mediate interactions between the central nervous system and the immune system. These techniques reduce the psychological and physiological effects of chronic stress. Serotonin, oxytocin, and melatonin released directly due to practicing yoga have been shown to better manage anxiety and fear, especially during the pandemic. We believe the current trends of chronic disease management will become more effective with the implementation of lifestyle changes using yoga.
Layout analysis of compressed air and hydraulic energy storage systems for vehicles
Authors: Yi Tong , Jin Chun , Hong Jichao , Liu Yanbo
Published: January 2022

The compressed air energy storage system has a better energy density, while the widely used hydraulic one is superior in power performance. Therefore, they are suitable for different hybrid vehicles, which require a comparative study on the performances and vehicle applicability of the broad pressure energy storage system layouts. In this paper, an integrated mathematical model of four basic pressure layouts is presented for characteristic analysis and applicability discussion. Results show that the open volume layout achieves the best power performance with the flow specific power of 13.92 MJ/m3, thus it is suitable for heavy hybrid trucks and mobile machinery. The open mass layout achieves the best energy performance with the energy density of 124.35 MJ/m3, which can be used in light new energy passenger vehicles. And the performance of the closed volume layout is close to the open volume layout with the flow specific power of 9.78 MJ/m3, so it could be applied to middle and light hybrid trucks. This research provides a basis for the hybrid method of pressure energy storage system layouts for vehicles, and could be applied in the design and research of non-electric hybrid vehicles in the near future.
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.
Unicorn: Anomalous Double Ostium Left Main Coronary Artery With Intra-Mural Connection - Diagnosed with Multi-Modality Imaging
Authors: Horne David , Mohsin Hina , P. Chen Robert
Published: January 2022

Case report of a unicorn: anomalous double ostium left main coronary artery with common intra-mural connection. Three-dimensional virtual endo-luminal angioscopy and catheter-based imaging confirmed the diagnosis, subsequently avoiding cardiac surgical intervention.
Shaping Organizational Citizenship Behavior of New Employees: Effects of Mentoring Functions and Supervisor Need for Achievement
Authors: Chang Han Cheng , Uen Jin Feng
Published: January 2022

In this study, we explored the relationship among mentoring functions (MFs), direct supervisor need for achievement (DSNFA), and employee organizational citizenship behavior (OCB) from the perspective of conservation of resources (COR) theory. A sample of 242 dyads was selected from new employees and direct supervisors employed in four- and five-star hotels in Taiwan. The results revealed that MFs and DSNFA were positively related to new-employee OCB. However, DSNFA negatively moderated the relationship between MFs and new-employee OCB. That is, low DSNFA positively moderated the relationship between MFs and OCB more than high DSNFA did. The results were explained using COR theory, which states that the development of positive personality traits is limited to in specific circumstances. Organizations in the hospitality industry that emphasize on OCB should examine their human resource activities to optimize performance.
Evaluation of and Policy Measures for the Sustainable Development of National Experimental Teaching Demonstration Centers in Chinese Universities and Colleges
Authors: Qian Hui , Ye Min , Liu Jingjiang , Gao Dongfeng
Published: January 2022

The establishment of national experimental teaching demonstration centers (NETDCs) in China has played an important role in improving the experimental teaching level in universities and colleges, promoting scientific research, and cultivating innovative talents for national- and region-level innovations. However, how to promote the sustainable development of NETDCs in China is becoming a critical issue. This paper constructs a new theoretical model for evaluating the sustainable development of NETDCs in China. This model consists of 5 dimensions (i.e., environmental, structural, human, teaching, and output entropies), 11 primary indicators, and 34 secondary indicators. A multidimensional scale for evaluating the sustainable development of NETDCs was developed and validated based on 24,483 questionnaires from 895 NETDCs in China. The results show that the development level and overall level of NETDCs in China for all 11 primary indicators are uneven. Policy measures for promoting the sustainable development of NETDCs are proposed and discussed.
Factors Impacting Mobile Banking in India: Empirical Approach Extending UTAUT2 with Perceived Value and Trust
Authors: Sankaran Raja , Chakraborty Shibashish
Published: January 2022

The aim of this research is to study the factors impacting usage of mobile banking (mBanking) by consumers in India. The study adopts the Extended Unified Theory of Acceptance and Use of Technology (UTAUT2) with Social Value (SV), Monetary Value (MV), Emotional Value (EV), Quality Value (QV), Trust and the moderation effect of gender. Online and offline survey methods were used to collect primary data from 457 Indian consumers using mBanking. SPSS AMOS was utilized to empirically validate the conceptual model, test research hypothesis and moderation effect. The factors effort expectancy (EE), monetary value (MV), emotional value (EV), quality value (QV) and trust (TR) were found to be significant on behavioural intent (BI), whereas performance expectancy (PE) and social value (SV) were not found to be significant. Banking organizations can formulate strategies to attract new consumers and continue to engage in retaining consumers in using these influencing factors to adopt mBanking and other related mobile financial services (MFS). The study integrates perceived value components and trust with UTAUT2 to form a comprehensive model for examining mBanking adoption.
Why Rotationplasty? A Qualitative Study of Decision-Making by Families of Patients With Primary Bone Sarcoma
Authors: Chan Chung M , Lindsay Adam D. , Spiguel Andre R V , Parker Gibbs C. , Scarborough Mark T
Published: January 2022

Rotationplasty is an established technique that is indicated as part of the surgical reconstruction for certain patients with primary bone tumors around the knee who undergo tumor resection. There is considerable variation in the application of rotationplasty by surgeons as well as acceptance of the procedure by patients who may be candidates for this procedure. We qualitatively studied the decision-making process of families of patients who had undergone rotationplasty by interviewing 4 patients and their families using semi-structured interviews. Thematic analysis identified the following themes that were important in the decision-making process: (1) the desire for good information sources, (2) finding value in meeting with other patients who had been faced with a similar decision, (3) prioritizing function over cosmesis, (4) a desire to limit the need for revision surgeries, and (5) accepting that a return to normalcy is not an option with a surgery. Physicians and patients faced with a similar decision can benefit from a better understanding of the process, and by the normalization of anxieties and concerns that they may experience.
Rural Patients’ Perceptions of Their Potentially Preventable Hospitalisation: A Qualitative Study
Authors: Ridge Andrew , Peterson Gregory M , Seidel Bastian M , Anderson Vinah , Nash Rosie
Published: January 2022

Potentially preventable hospitalisations (PPHs) occur when patients receive hospital care for a condition that could have been more appropriately managed in the primary healthcare setting. It is anticipated that the causes of PPHs in rural populations may differ from those in urban populations; however, this is understudied. Semi-structured interviews with 10 rural Australian patients enabled them to describe their recent PPH experience. Reflexive thematic analysis was used to identify the common factors that may have led to their PPH. The analysis revealed that most participants had challenges associated with their health and its optimal self-management. Self-referral to hospital with the belief that this was the only treatment option available was also common. Most participants had limited social networks to call on in times of need or ill health. Finally, difficulty in accessing primary healthcare, especially urgently or after-hours, was described as a frequent cause of PPH. These qualitative accounts revealed that patients describe nonclinical risk factors as contributing to their recent PPH and reinforces that the views of patients should be included when designing interventions to reduce PPHs.
Diagnosis and monitoring of systemic sclerosis-associated interstitial lung disease using high-resolution computed tomography
Authors: Khanna Dinesh , Distler Oliver , Cottin Vincent , Brown Kevin K , Chung Lorinda , Goldin Jonathan G , Matteson Eric L , Kazerooni Ella A , Walsh Simon LF , McNitt-Gray Michael , Maher Toby M
Published: January 2022

Patients with systemic sclerosis are at high risk of developing systemic sclerosis–associated interstitial lung disease. Symptoms and outcomes of systemic sclerosis–associated interstitial lung disease range from subclinical lung involvement to respiratory failure and death. Early and accurate diagnosis of systemic sclerosis–associated interstitial lung disease is therefore important to enable appropriate intervention. The most sensitive and specific way to diagnose systemic sclerosis–associated interstitial lung disease is by high-resolution computed tomography, and experts recommend that high-resolution computed tomography should be performed in all patients with systemic sclerosis at the time of initial diagnosis. In addition to being an important screening and diagnostic tool, high-resolution computed tomography can be used to evaluate disease extent in systemic sclerosis–associated interstitial lung disease and may be helpful in assessing prognosis in some patients. Currently, there is no consensus with regards to frequency and scanning intervals in patients at risk of interstitial lung disease development and/or progression. However, expert guidance does suggest that frequency of screening using high-resolution computed tomography should be guided by risk of developing interstitial lung disease. Most experienced clinicians would not repeat high-resolution computed tomography more than once a year or every other year for the first few years unless symptoms arose. Several computed tomography techniques have been developed in recent years that are suitable for regular monitoring, including low-radiation protocols, which, together with other technologies, such as lung ultrasound and magnetic resonance imaging, may further assist in the evaluation and monitoring of patients with systemic sclerosis–associated interstitial lung disease. A video abstract to accompany this article is available at: https://www.globalmedcomms.com/respiratory/Khanna/HRCTinSScILD
The private rental housing market before and during the COVID-19 pandemic: A submarket analysis in Cracow, Poland
Authors: Tomal Mateusz , Helbich Marco
Published: January 2022

How the COVID-19 pandemic has altered the segmentation of residential rental markets is largely unknown. We therefore assessed rental housing submarkets before and during the pandemic in Cracow, Poland. We used geographically and temporally weighted regression to investigate the marginal prices of housing attributes over space–time. The marginal prices were further reduced to a few principal components per time period and spatially clustered to identify housing submarkets. Finally, we applied the adjusted Rand index to evaluate the spatiotemporal stability of the housing submarkets. The results revealed that the pandemic outbreak significantly lowered rents and modified the relevance of some housing characteristics for rental prices. Proximity to the university was no longer among the residential amenities during the pandemic. Similarly, the virus outbreak diminished the effect of a housing unit’s proximity to the city center. The market partitioning showed that the number of Cracow’s residential rental submarkets increased significantly as a result of the COVID-19 pandemic, as it enhanced the spatial variation in the marginal prices of covariates. Our findings suggest that the emergence of the coronavirus reshaped the residential rental market in three ways: Rents were decreased, the underlying rental price-determining factors changed, and the spatiotemporal submarket structure was altered.
Effects of family risk on early attachment security: Gender-specific susceptibility and mediation by parenting behavior
Authors: Gerlach Jennifer , Fößel Judith M. , Vierhaus Marc , Sann Alexandra , Eickhorst Andreas , Zimmermann Peter , Spangler Gottfried
Published: January 2022

Growing up in high-risk environments is detrimental to children’s development of attachment security. Parenting behavior is hypothesized to be the mechanism through which risks exert their influence. However, risk influences can vary between individuals by gender. Aim of this study was to explore specific pathways of family risk on early attachment security and additionally examine the transmission via parenting behavior. The sample consisted of 197 children and their primary caregivers. Children’s age ranged between 10 and 21 months ( M = 15.25, SD = 3.59). Data assessment included 21 distal and proximal family risk factors, children’s attachment security, and parental responsivity and supportive presence. Whereas distal risk factors had an adverse effect only on girls’ attachment security, proximal risks negatively affected only boys’ attachment security. Additionally, patterns of risk factors occurring in our sample were analyzed using an exploratory principal component analysis. Regardless of the child’s gender, a low socio- economic status was negatively related to attachment security of all children. Migration and crowding and a high emotional load of the primary caregiver both negatively predicted girls’ but not boys’ attachment security. However, the attachment security of boys was affected by a negative family climate. Most of the adverse risk effects on attachment security were mediated by parental responsivity and supportive presence so that the transmission of risk occurs through parenting behavior. Results revealed a different susceptibility of family risks for girls and boys. The consideration of a gender-sensitive approach in developmental psychopathology and interventions of developmental child welfare services is recommended.
An evaluation of the question types used by criminal justice professionals with complainants in child sexual assault trials
Authors: Powell Martine B. , Goodman-Delahunty Jane , Deck Sarah L. , Bearman Madeleine , Westera Nina
Published: January 2022

The way that complainants of child sexual assault are questioned about their experiences can profoundly influence the accuracy, credibility, and consistency of their evidence. This is the case for all people, but especially children whose language, social, and cognitive capacity is still developing. In this study, we examined the questions used by a representative sample of Australian prosecutors, defense lawyers, and judges/magistrates to determine if this is an area that warrants improvement. Our focus was the type of questions used by the different professionals and how (if at all) these varied across complainant age groups (children, adolescents, and adults, total N = 63). Our findings revealed that each complainant group was questioned in a manner known to heighten misunderstanding and error (e.g., complex and leading questions were used frequently by all professional groups). There was also little indication of question adaption according to age (e.g., prosecutors asked children more complex questions than they asked adults). When the results are considered in the context of the broader literature on the impact of different question styles, they suggest that professional development in questioning would improve the quality of trial advocacy and judicial rulings.
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

This 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

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

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

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

Motivation

Protein 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.

Results

The 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.

Availability

SAP4SS 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

Cellular 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

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

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

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.
Urogenital Microbiota:Potentially Important Determinant of PD-L1 Expression in Male Patients with Non-muscle Invasive Bladder Cancer
Authors: Chen Chunxiao , Huang Zehai , Huang Pengcheng , Li Kun , Zeng Jiarong , Wen Yuehui , Li Biao , Zhao Jie , Wu Peng
Published: January 2022

Background

Urogenital microbiota may be associated with the recurrence of bladder cancer, but the underlying mechanism remains unclear. The notion that microbiota can upregulate PD-L1 expression in certain epithelial tumors to promote immune escape has been demonstrated. Thus, we hypothesized that the urogenital microbiota may be involved in the recurrence and progression of non-muscle invasive bladder cancer (NMIBC) by upregulating the PD-L1 expression. To test this hypothesis, we investigated the relationship between urogenital microbial community and PD-L1 expression in male patients with NMIBC.

Results

16S rRNA gene sequencing was performed to analyse the composition of urogenital microbiota, and the expression of PD-L1 in cancerous tissues was detected by immunohistochemistry. The subjects (aged 43–79 years) were divided into PD-L1-positive group (Group P, n = 9) and PD-L1-negative group (Group N, n = 19) respectively based on their PD-L1 immunohistochemical results. No statistically significant differences were found in the demographic characteristics between group P and N. We observed that group P exhibited higher species richness (based on Observed species and Ace index, both P < 0.05). Furthermore, subgroup analysis showed that the increase in number of PD-L1 positive cells was accompanied by increased richness of urogenital microbiota. Significantly different composition of urogenital microbiota was found between group P and group N (based on weighted Unifrac and unweighted Unifrac distances metric, both P < 0.05). Enrichment of some bacterial genera (e.g., Leptotrichia, Roseomonas, and Propionibacterium) and decrease of some bacterial genera (e.g., Prevotella and Massilia) were observed in group P as compared with group N. These findings indicated that these genera may affect the expression of PD-L1 through some mechanisms to be studied.

Conclusion

Our study provided for the first time an overview of the association between urogenital microbiota and PD-L1 expression in male patients with NMIBC, indicating that urogenital microbiota was an important determinant of PD-L1 expression in male NMIBC patients.
Biochemical and transcriptomic analyses of the symbiotic interaction between Cremastra appendiculata and the mycorrhizal fungus Coprinellus disseminatus
Authors: Gao Yanyan , Ji Jun , Zhang Yujin , Yang Ningxian , Zhang Mingsheng
Published: January 2022

Background

Cremastra appendiculata is a rare terrestrial orchid with a high market value as an ornamental and medicinal plant. However, the species depends entirely on fungi for seed germination under natural conditions. In a previous study, we have successfully isolated and identified the mycorrhizal fungus Coprinellus disseminatus which was able to induce the germination of C. appendiculata seeds. We then speculated that C. disseminatus may do so by breaking the testa imposed dormancy of the seeds. In this study, biochemical and transcriptomic analyses were used to characterize the germination of C. appendiculata seeds, collected at different stages of germination, as affected by C. disseminatus.

Results

The lignocellulose in the seeds coat of C. appendiculata was degraded by the mycorrhizal fungus resulting in facilitated absorption of water. The rate of decline in lignin content was 67 and 73% at 6 and 12 days after sowing, respectively. The water content increased from 13 to 90% during symbiosis. A total of 15,382 genes showing significantly different levels of expression (log2 FPKM≥2.0, Qvalue≤0.05) were successfully identified among all libraries, where the highest number of DEGs was shared between 6 days versus 0 day after symbiotic germination. Gene annotation results suggested that 15 key genes related water-status, such as DHN gene family and Xero 1 were down-regulated. The genes zeaxanthin epoxidase ZEP, 9-cis-epoxycarotenoid dioxygenase NCED3 and β-carotene hydroxylase involved in the biosynthesis of abscisic acid (ABA) were significantly down-regulated in 6 days as compared to 0 day after symbiotic germination.

Conclusions

This work demonstrates that mycorrhizal fungus C. disseminatus can stimulate C. appendiculata seeds germination through a mechanism of breaking the testa imposed dormancy and inducing water absorption of the embryo.
Intervention and in-hospital pharmacoterapies in octogenarian with acute coronary syndrome: a 10-year retrospective analysis of the Malaysian National Cardiovascular Database (NCVD) registry
Authors: Suki Siti Z. , Zuhdi Ahmad S. M. , Yahya ‘ Abqariyah A. , Zaharan Nur L.
Published: January 2022

Background

Octogenarians and beyond have often been neglected in the populational study of disease despite being at the highest point of non-modifiable disease risk burden and the fastest-growing age group for the past decade. This study examined the characteristics and in-hospital management of octogenarian patients with acute coronary syndrome (ACS) in a multi-ethnic, middle-income country in South East Asia.

Method

This retrospective study utilised the Malaysian National Cardiovascular Disease- ACS (NCVD-ACS) registry. Consecutive patient data of those ≥80 years old admitted with ACS at 24 participating hospitals from 2008 to 2017 (n = 3162) were identified. Demographics, in-hospital intervention, and evidence-based pharmacotherapies over the 10-years were examined and compared across groups of interests using the Chi-square test. Multivariate logistic regression was used to calculate the adjusted odds ratio of receiving individual therapies according to patients’ characteristics.

Results

Octogenarians made up 3.8% of patients with ACS in the NCVD-ACS registry (mean age = 84, SD ± 3.6) from 2008 until 2017. The largest ethnic group was Chinese (44%). Most octogenarians (95%) have multiple cardiovascular risk factors, with hypertension (82%) being the main. Non-ST-elevation myocardial infarction (NSTEMI) predominated (38%, p < 0.001). Within the 10-year, there were positive increments in cardiovascular intervention and pharmacotherapies. Only 10% of octogenarians with ACS underwent percutaneous coronary intervention (PCI), the majority being STEMI patients (17.5%; p < 0.05). More than 80% were prescribed aspirin (91.3%) either alone or combined, dual antiplatelet therapy (DAPT) (83.3%), anticoagulants (89.7%) and statins (89.6%), while less being prescribed angiotensin-converting enzyme inhibitors/angiotensin receptor blockers (47.6%) and beta-blockers (43.0%). Men were more likely to receive PCI than women (adjusted Odds Ratio (aOR): 0.698; 95% CI: 0.490–0.993). NSTEMI (aOR = 0.402, 95% CI: 0.278–0.583) and unstable angina (UA) (aOR = 0.229, 95% CI: 0.143–0.366) were less likely to receive PCI but more likely given anticoagulants (NSTEMI, aOR = 1.543, 95% CI: 1.111–2.142; UA, aOR = 1.610, 95% CI: 1.120–2.314) than STEMI. The presence of cardiovascular risk factors and comorbidities influences management.

Conclusion

Octogenarians with ACS in this country were mainly treated with cardiovascular pharmacotherapies. As the number of octogenarians with ACS will continue to increase, the country needs to embrace the increasing use of PCI in this group of patients.