bluuebunny/crossref_metadata_2025_split huggingface dataset:
Osteopathy modulates brain–heart interaction in chronic pain patients: an ASL study
Authors: Cerritelli Francesco , Chiacchiaretta Piero , Gambi Francesco , Saggini Raoul , Perrucci Mauro Gianni , Ferretti Antonio 
Published: February 2021

AbstractIn this study we used a combination of measures including regional cerebral blood flow (rCBF) and heart rate variability (HRV) to investigate brain–heart correlates of longitudinal baseline changes of chronic low back pain (cLBP) after osteopathic manipulative treatment (OMT). Thirty-two right-handed patients were randomised and divided into 4 weekly session of OMT (N = 16) or Sham (N = 16). Participants aged 42.3 ± 7.3 (M/F: 20/12) with cLBP (duration: 14.6 ± 8.0 m). At the end of the study, patients receiving OMT showed decreased baseline rCBF within several regions belonging to the pain matrix (left posterior insula, left anterior cingulate cortex, left thalamus), sensory regions (left superior parietal lobe), middle frontal lobe and left cuneus. Conversely, rCBF was increased in right anterior insula, bilateral striatum, left posterior cingulate cortex, right prefrontal cortex, left cerebellum and right ventroposterior lateral thalamus in the OMT group as compared with Sham. OMT showed a statistically significant negative correlation between baseline High Frequency HRV changes and rCBF changes at T2 in the left posterior insula and bilateral lentiform nucleus. The same brain regions showed a positive correlation between rCBF changes and Low Frequency HRV baseline changes at T2. These findings suggest that OMT can play a significant role in regulating brain–heart interaction mechanisms.
A novel technology to integrate imaging and clinical markers for non-invasive diagnosis of lung cancer
Authors: Shaffie Ahmed , Soliman Ahmed , Fu Xiao-An , Nantz Michael , Giridharan Guruprasad , van Berkel Victor , Khalifeh Hadil Abu , Ghazal Mohammed , Elmaghraby Adel , El-baz Ayman 
Published: February 2021

AbstractThis study presents a non-invasive, automated, clinical diagnostic system for early diagnosis of lung cancer that integrates imaging data from a single computed tomography scan and breath bio-markers obtained from a single exhaled breath to quickly and accurately classify lung nodules. CT imaging and breath volatile organic compounds data were collected from 47 patients. Spherical Harmonics-based shape features to quantify the shape complexity of the pulmonary nodules, 7th-Order Markov Gibbs Random Field based appearance model to describe the spatial non-homogeneities in the pulmonary nodule, and volumetric features (size) of pulmonary nodules were calculated from CT images. 27 VOCs in exhaled breath were captured by a micro-reactor approach and quantied using mass spectrometry. CT and breath markers were input into a deep-learning autoencoder classifier with a leave-one-subject-out cross validation for nodule classification. To mitigate the limitation of a small sample size and validate the methodology for individual markers, retrospective CT scans from 467 patients with 727 pulmonary nodules, and breath samples from 504 patients were analyzed. The CAD system achieved 97.8% accuracy, 97.3% sensitivity, 100% specificity, and 99.1% area under curve in classifying pulmonary nodules.
CIBERSORT analysis of TCGA and METABRIC identifies subgroups with better outcomes in triple negative breast cancer
Authors: Craven Kelly E. , Gökmen-Polar Yesim , Badve Sunil S. 
Published: February 2021

AbstractStudies have shown that the presence of tumor infiltrating lymphocytes (TILs) in Triple Negative Breast Cancer (TNBC) is associated with better prognosis. However, the molecular mechanisms underlying these immune cell differences are not well delineated. In this study, analysis of hematoxylin and eosin images from The Cancer Genome Atlas (TCGA) breast cancer cohort failed to show a prognostic benefit of TILs in TNBC, whereas CIBERSORT analysis, which quantifies the proportion of each immune cell type, demonstrated improved overall survival in TCGA TNBC samples with increased CD8 T cells or CD8 plus CD4 memory activated T cells and in Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) TNBC samples with increased gamma delta T cells. Twenty-five genes showed mutational frequency differences between the TCGA high and low T cell groups, and many play important roles in inflammation or immune evasion (ATG2B, HIST1H2BC, PKD1, PIKFYVE, TLR3, NOTCH3, GOLGB1, CREBBP). Identification of these mutations suggests novel mechanisms by which the cancer cells attract immune cells and by which they evade or dampen the immune system during the cancer immunoediting process. This study suggests that integration of mutations with CIBERSORT analysis could provide better prediction of outcomes and novel therapeutic targets in TNBC cases.
Enhancement in external quantum efficiency of AlGaInP red μ-LED using chemical solution treatment process
Authors: Jung Byung Oh , Lee Wonyong , Kim Jeomoh , Choi Myungshin , Shin Hui-Youn , Joo Minho , Jung Sukkoo , Choi Yoon-Ho , Kim Moon J. 
Published: February 2021

AbstractTo investigate the effects of their surface recovery and optical properties, extremely small sized (12 µm × 12 µm mesa area) red AlGaInP micro light emitting diodes ($$\upmu$$
μ
LED) were fabricated using a diluted hydrofluoric acid (HF) surface etch treatment. After the chemical treatment, the external quantum efficiencies (EQEs) of $$\upmu$$
μ
-LED at low and high injection current regions have been improved by 35.48% and 12.86%, respectively. The different phenomena of EQEs have a complex relationship between the suppression of non-radiative recombination originating from the etching damage of the surface and the improvement of light extraction of the sidewalls. The constant enhancement of EQE at a high injection current it is attributed to the expansion of the active region’s sidewall surface area by the selective etching of AlInP layers. The improved EQE at a low injection current is related to the minimization of the surface recombination caused by plasma damage from the surface. High-resolution transmission electron microscopy (HR-TEM) revealed physical defects on the sidewall surface, such as plasma-induced lattice disorder and impurity contamination damage, were eliminated using chemical treatment. This study suggests that chemical surface treatment using diluted HF acid can be an effective method for enhancing the $$\upmu$$
μ
-LED performance.
Iohexol plasma clearance simplified by Dried Blood Spot (DBS) sampling to measure renal function in conscious mice
Authors: Rodríguez-Rodríguez Ana Elena , Luis-Lima Sergio , Donate-Correa Javier , Diaz-Martín Laura , Arnau María Rosa , Jiménez-Sosa Alejandro , Gaspari Flavio , Ortiz Alberto , Porrini Esteban 
Published: February 2021

AbstractThere is no simple method to measure glomerular filtration rate (GFR) in mice, which limits the use of mice in models of renal diseases. We aimed at simplifying the plasma clearance of iohexol in mice, using dried blood spot (DBS) sampling in order to reduce the amount of blood taken for analysis. GFR was measured simultaneously by a reference method in total blood—as described before—and tested method using DBS in fifteen male and six female C57BL/6J mice. Total blood extraction was 50 μL for the reference methods and 25μL for the tested methods, distributed in 5 samples. The agreement of GFR values between both methods was analyzed with the concordance correlation coefficient (CCC), total deviation index (TDI) and coverage probability (CP). The agreement between both methods was excellent, showing a TDI = 8.1%, which indicates that 90% of the GFR values obtained with DBS showed an error ranging from − 8 to + 8% of the reference method; a CCC of 0.996 (CI: 0.992), reflecting high precision and accuracy and a CP of 94 (CI: 83), indicating that 6% of the GFR values obtained with DBS had an error greater than 10% of the method in blood. So, both methods are interchangeable. DBS represent a major simplification of GFR measurement in mice. Also, DBS improves animal welfare by reducing the total blood required and refining the procedure.
Immunoinformatic based identification of cytotoxic T lymphocyte epitopes from the Indian isolate of SARS-CoV-2
Authors: Mulpuru Viswajit , Mishra Nidhi 
Published: February 2021

AbstractThe Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has turned into a pandemic with about thirty million confirmed cases worldwide as of September 2020. Being an airborne infection, it can be catastrophic to populous countries like India. This study sets to identify potential cytotoxic T lymphocyte (CTL) epitopes in the SARS-CoV-2 Indian isolate which can act as an effective vaccine epitope candidate for the majority of the Indian population. The immunogenicity and the foreignness of the epitopes towards the human body have to be studied to further confirm their candidacy. The top-scoring epitopes were subjected to molecular docking studies to study their interactions with the corresponding human leukocyte antigen (HLA) system. The CTL epitopes were observed to bind at the peptide-binding groove of the corresponding HLA system, indicating their potency as an epitope candidate. The candidacy was further analyzed using sequence conservation studies and molecular dynamics simulation. The identified epitopes can be subjected to further studies for the development of the SARS-CoV-2 vaccine.
Dispersion as a waste-clearance mechanism in flow through penetrating perivascular spaces in the brain
Authors: Troyetsky Daniel E. , Tithof Jeffrey , Thomas John H. , Kelley Douglas H. 
Published: February 2021

AbstractAccumulation of metabolic wastes in the brain is correlated with several neurodegenerative disorders, including Alzheimer’s disease. Waste transport and clearance occur via dispersion, the combined effect of diffusion and advection by flow of fluid. We examine the relative contributions of diffusion and advection in the perivascular spaces (PVSs) that surround penetrating cortical blood vessels and are filled with cerebrospinal fluid (CSF). To do so, we adapt prior analytic predictions of dispersion to the context of PVSs. We also perform advection-diffusion simulations in PVS-like geometries with parameters relevant to transport of amyloid-$$\beta$$
β
(associated with Alzheimer’s) in a variety of flows, motivated by in vivo measurements. Specifically, we examine solute transport in steady and unsteady Poiseuille flows in an open (not porous) concentric circular annulus. We find that a purely oscillatory flow enhances dispersion only weakly and does not produce significant transport, whereas a steady flow component, even if slow, clears waste more effectively.
Machine learning based predictors for COVID-19 disease severity
Authors: Patel Dhruv , Kher Vikram , Desai Bhushan , Lei Xiaomeng , Cen Steven , Nanda Neha , Gholamrezanezhad Ali , Duddalwar Vinay , Varghese Bino , Oberai Assad A 
Published: February 2021

AbstractPredictors of the need for intensive care and mechanical ventilation can help healthcare systems in planning for surge capacity for COVID-19. We used socio-demographic data, clinical data, and blood panel profile data at the time of initial presentation to develop machine learning algorithms for predicting the need for intensive care and mechanical ventilation. Among the algorithms considered, the Random Forest classifier performed the best with $$\text {AUC} = 0.80$$

AUC
=
0.80

for predicting ICU need and $$\text {AUC} = 0.82$$

AUC
=
0.82

for predicting the need for mechanical ventilation. We also determined the most influential features in making this prediction, and concluded that all three categories of data are important. We determined the relative importance of blood panel profile data and noted that the AUC dropped by 0.12 units when this data was not included, thus indicating that it provided valuable information in predicting disease severity. Finally, we generated RF predictors with a reduced set of five features that retained the performance of the predictors trained on all features. These predictors, which rely only on quantitative data, are less prone to errors and subjectivity.
An asymmetric protoplast fusion and screening method for generating celeriac cybrids
Authors: Bruznican Silvia , Eeckhaut Tom , Van Huylenbroeck Johan , De Keyser Ellen , De Clercq Hervé , Geelen Danny 
Published: February 2021

AbstractCeleriac F1 hybrid seed production is currently complicated due to the instability of cytoplasmic male sterile lines. To develop alternative alloplasmic CMS lines, an asymmetric protoplast fusion and hybrid screening methodology was established. Celeriac suspension cells protoplasts were used as the acceptor and carrot, coriander and white celery mesophyll protoplasts as the donor for protoplast fusion experiments. Acceptor cytoplasmic inheritance was inhibited by iodoacetamide treatment and donor nuclear genome inheritance was prevented by UV exposure. Protoplasts were selectively stained and fused using electroporation and polyethylene glycol, and candidate hybrid shoots were obtained. One chloroplast and three mitochondrial markers that could distinguish acceptor and donors organelles were used to characterize over 600 plants obtained after fusion events, without identifying any cybrid. In order to increase the testing efficiency a high number of micro plantlets were pooled and hence the presence of the carrot specific Atp1 marker in one of the pooled samples was detected. We demonstrated that fusion took place between celeriac and a carrot indicating that the creation of viable hybrids is possible although at a very low frequency. These findings open the path for new cytoplasmic hybridization and the isolation of novel CMS lines of celeriac.
Signatures of white-matter microstructure degradation during aging and its association with cognitive status
Authors: Coelho Ana , Fernandes Henrique M. , Magalhães Ricardo , Moreira Pedro Silva , Marques Paulo , Soares José M. , Amorim Liliana , Portugal-Nunes Carlos , Castanho Teresa , Santos Nadine Correia , Sousa Nuno 
Published: February 2021

AbstractPrevious studies have shown an association between cognitive decline and white matter integrity in aging. This led to the formulation of a “disconnection hypothesis” in the aging-brain, which states that the disruption in cortical network communication may explain the cognitive decline during aging. Although some longitudinal studies have already investigated the changes occurring in white matter microstructure, most focused on specific white matter tracts. Our study aims to characterize the longitudinal whole-brain signatures of white matter microstructural change during aging. Furthermore, we assessed the relationship between distinct longitudinal alterations in white matter integrity and cognition. White matter microstructural properties were estimated from diffusion magnetic resonance imaging, and cognitive status characterized from extensive neurocognitive testing. The same individuals were evaluated at two timepoints, with a mean interval time of 52.8 months (SD = 7.24) between first and last assessment. Our results show that age is associated with a decline in cognitive performance and a degradation in white matter integrity. Additionally, significant associations were found between diffusion measures and different cognitive dimensions (memory, executive function and general cognition). Overall, these results suggest that age-related cognitive decline is related to white matter alterations, and thus give support to the “disconnected hypothesis” of the aging brain.
Comparative genomics of MRSA strains from human and canine origins reveals similar virulence gene repertoire
Authors: Penna Bruno , Silva Marcella B. , Soares André E. R. , Vasconcelos Ana T. R. , Ramundo Mariana S. , Ferreira Fabienne A. , Silva-Carvalho Maria C. , de Sousa Viviane S. , Rabello Renata F. , Bandeira Paula T. , de Souza Viviane S. , Planet Paul J. , Vieira-da-Motta Olney , Botelho Ana M. N. , Figueiredo Agnes M. S. 
Published: February 2021

AbstractMethicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen associated with a wide variety of infections in humans. The ability of MRSA to infect companion animals has gained increasing attention in the scientific literature. In this study, 334 dogs were screened for MRSA in two cities located in Rio de Janeiro State. The prevalence of MRSA in dogs was 2.7%. Genotyping revealed isolates from sequence types (ST) 1, 5, 30, and 239 either colonizing or infecting dogs. The genome of the canine ST5 MRSA (strain SA112) was compared with ST5 MRSA from humans—the main lineage found in Rio de Janeiro hospitals—to gain insights in the origin of this dog isolate. Phylogenetic analysis situated the canine genome and human strain CR14-035 in the same clade. Comparative genomics revealed similar virulence profiles for SA112 and CR14-035. Both genomes carry S. aureus genomic islands νSAα, νSAβ, and νSAγ. The virulence potential of the canine and human strains was similar in a Caenorhabditis elegans model. Together, these results suggest a potential of canine MRSA to infect humans and vice versa. The circulation in community settings of a MRSA lineage commonly found in hospitals is an additional challenge for public health surveillance authorities.
Evolutionary conservation of the DRACH signatures of potential N6-methyladenosine (m6A) sites among influenza A viruses
Authors: Bayoumi Mahmoud , Munir Muhammad 
Published: February 2021

AbstractThe addition of a methyl group to the N6-position of adenosine (m6A) is considered one of the most prevalent internal post-transcriptional modifications and is attributed to virus replication and cell biology. Viral epitranscriptome sequencing analysis has revealed that hemagglutinin (HA) mRNA of H1N1 carry eight m6A sites which are primarily enriched in 5′-DRACH-3′ sequence motif. Herein, a large-scale comparative m6A analysis was conducted to investigate the conservation patterns of the DRACH motifs that corresponding to the reference m6A sites among influenza A viruses. A total of 70,030 complete HA sequences that comprise all known HA subtypes (H1–18) collected over several years, countries, and affected host species were analysed on both mRNA and vRNA strands. The bioinformatic analysis revealed the highest degree of DRACHs conservation among all H1 sequences that clustered largely in the middle and in the vicinity to 3′ end with at least four DRACH motifs were conserved in all mRNA sequences. The major HA-containing subtypes displayed a modest DRACH motif conservation located either in the middle region of HA transcript (H3) or at the 3′ end (H5) or were distributed across the length of HA sequence (H9). The lowest conservation was demonstrated in HA subtypes that infect mostly the wild type avian species and bats. Interestingly, the total number and the conserved DRACH motifs in the vRNA were found to be much lower than those observed in the mRNA. Collectively, the identification of putative m6A topology provides a foundation for the future intervention of influenza infection, replication, and pathobiology in susceptible hosts.
Mechanism of autonomous synchronization of the circadian KaiABC rhythm
Authors: Sasai Masaki 
Published: February 2021

AbstractThe cyanobacterial circadian clock can be reconstituted by mixing three proteins, KaiA, KaiB, and KaiC, in vitro. In this protein mixture, oscillations of the phosphorylation level of KaiC molecules are synchronized to show the coherent oscillations of the ensemble of many molecules. However, the molecular mechanism of this synchronization has not yet been fully elucidated. In this paper, we explain a theoretical model that considers the multifold feedback relations among the structure and reactions of KaiC. The simulated KaiC hexamers show stochastic switch-like transitions at the level of single molecules, which are synchronized in the ensemble through the sequestration of KaiA into the KaiC–KaiB–KaiA complexes. The proposed mechanism quantitatively reproduces the synchronization that was observed by mixing two solutions oscillating in different phases. The model results suggest that biochemical assays with varying concentrations of KaiA or KaiB can be used to test this hypothesis.
Specific domain V reduction of beta-2-glycoprotein I induces protein flexibility and alters pathogenic antibody binding
Authors: Buchholz Ina , McDonnell Thomas , Nestler Peter , Tharad Sudarat , Kulke Martin , Radziszewska Anna , Ripoll Vera M. , Schmidt Frank , Hammer Elke , Toca-Herrera Jose L. , Rahman Anisur , Delcea Mihaela 
Published: February 2021

AbstractBeta-2-glycoprotein I (β2GPI) is a blood protein and the major antigen in the autoimmune disorder antiphospholipid syndrome (APS). β2GPI exists mainly in closed or open conformations and comprises of 11 disulfides distributed across five domains. The terminal Cys288/Cys326 disulfide bond at domain V has been associated with different cysteine redox states. The role of this disulfide bond in conformational dynamics of this protein has not been investigated so far. Here, we report on the enzymatic driven reduction by thioredoxin-1 (recycled by Tris(2-carboxyethyl)phosphine; TCEP) of β2GPI. Specific reduction was demonstrated by Western blot and mass spectrometry analyses confirming majority targeting to the fifth domain of β2GPI. Atomic force microscopy images suggested that reduced β2GPI shows a slightly higher proportion of open conformation and is more flexible compared to the untreated protein as confirmed by modelling studies. We have determined a strong increase in the binding of pathogenic APS autoantibodies to reduced β2GPI as demonstrated by ELISA. Our study is relevant for understanding the effect of β2GPI reduction on the protein structure and its implications for antibody binding in APS patients.
Comparative evaluation of expiratory airflow limitation between patients with COPD and BE using IOS
Authors: dos Santos Daniele Oliveira , Perossi Larissa , Perossi Jéssica , de Souza Simoni Letícia Helena , Holtz Mayara , Moroli Ricardo Grassi , Baddini-Martinez José Antônio , Gastaldi Ada Clarice 
Published: February 2021

AbstractImpulse oscillometry (IOS) allows evaluation of the compartmentalized resistance and reactance of the respiratory system, distinguishing central and peripheral obstruction. The IOS measurements are getting attention in the diagnosis and differentiation of chronic respiratory diseases. However, no data are available in the literature to differentiate between COPD and BE using IOS parameters. We aimed to evaluate the feasibility of IOS in the diagnosis of bronchiectasis non-cystic fibrosis (BE) in comparison to COPD. Whole breath, inspiration, expiration, and inspiratory-expiratory difference (Δ) were evaluated based on the IOS parameters: total resistance (R5), central airway resistance (R20), peripheral airway resistance (R5-R20), reactance (X5), reactance area (AX), and resonance frequency (Fres). Fifty-nine subjects (21 Healthy, 19 BE, and 19 COPD) participated in this study. It was observed a significant difference in the comparison of healthy and pulmonary disease groups (BE and COPD) for total breathing (R5-R20, X5, AX, and Fres), inspiratory phase (R5 and R5-R5), and expiratory phase (R5-R20 and X5). The comparison between BE and COPD groups showed significant difference in the expiratory phase for resistance at 5 and 20 Hz and, ΔR5 and ΔR20. The IOS evidenced an increase of R5, R20 and R5-R20 in patients with BE and COPD when compared to healthy subjects. Expiratory measures of IOS revealed increased airway resistance in COPD compared to BE patients who had similar FEV1 measured by spirometry, however, further studies are needed to confirm these differences.