bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters
Authors: Yan Wei , Hall A. Brantley , Jiang Xiaofang 
Published: January 2022

AbstractAntibiotic-resistance genes (ARGs) regulated by invertible promoters can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of these ARGs regulated by invertible promoters remains poorly understood. Here, we sought to assess the threat posed by ARGs regulated by invertible promoters by systematically searching for ARGs regulated by invertible promoters in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified ARGs regulated by invertible promoters and categorized them into three classes based on the invertase-regulating phase variation. In the human gut microbiome, ARGs regulated by invertible promoters are exclusively found in Bacteroidales species. Through genomic analysis, we observed that ARGs regulated by invertible promoters have convergently originated from ARG insertions into glycan-synthesis loci that were regulated by invertible promoters at least three times. Moreover, all three classes of invertible promoters regulating ARGs are located within integrative conjugative elements (ICEs). Therefore, horizontal transfer via ICEs could explain the wide taxonomic distribution of ARGs regulated by invertible promoters. Overall, these findings reveal that glycan-synthesis loci regulated by invertible promoters in Bacteroidales species are an important hotspot for the emergence of clinically-relevant ARGs regulated by invertible promoters.
Thalamic white matter macrostructure and subnuclei volumes in Parkinson’s disease depression
Authors: Bhome R. , Zarkali A. , Thomas G. E. C. , Iglesias J. E. , Cole J. H. , Weil R. S. 
Published: January 2022

AbstractDepression is a common non-motor feature of Parkinson’s disease (PD) which confers significant morbidity and is challenging to treat. The thalamus is a key component in the basal ganglia-thalamocortical network critical to the pathogenesis of PD and depression but the precise thalamic subnuclei involved in PD depression have not been identified. We performed structural and diffusion-weighted imaging (DWI) on 76 participants with PD to evaluate the relationship between PD depression and grey and white matter thalamic subnuclear changes. We used a thalamic segmentation method to divide the thalamus into its 50 constituent subnuclei (25 each hemisphere). Fixel-based analysis was used to calculate mean fibre cross-section (FC) for white matter tracts connected to each subnucleus. We assessed volume and FC at baseline and 14–20 months follow-up. A generalised linear mixed model was used to evaluate the relationship between depression, subnuclei volume and mean FC for each thalamic subnucleus. We found that depression scores in PD were associated with lower right pulvinar anterior (PuA) subnucleus volume. Antidepressant use was associated with higher right PuA volume suggesting a possible protective effect of treatment. After follow-up, depression scores were associated with reduced white matter tract macrostructure across almost all tracts connected to thalamic subnuclei. In conclusion, our work implicates the right PuA as a relevant neural structure in PD depression and future work should evaluate its potential as a therapeutic target for PD depression.
Specific immune status in Parkinson’s disease at different ages of onset
Authors: Tian Jun , Dai Shao-Bing , Jiang Si-Si , Yang Wen-Yi , Yan Yi-Qun , Lin Zhi-Hao , Dong Jia-Xian , Liu Yi , Zheng Ran , Chen Ying , Zhang Bao-Rong , Pu Jia-Li 
Published: January 2022

AbstractRecent evidence suggests that innate and adaptive immunity play a crucial role in Parkinson’s disease (PD). However, studies regarding specific immune cell classification in the peripheral blood in PD remain lacking. Therefore, we aimed to explore the different immune status in patients with PD at different ages of onset. We included 22 patients; among them were 10 who had early-onset PD (EOPD) and 12 had late-onset PD (LOPD) and 10 young healthy controls (YHCs) and 8 elder HCs (EHCs). Mass cytometry staining technology was used to perform accurate immunotyping of cell populations in the peripheral blood. Motor symptoms and cognitive function were assessed using the Unified Parkinson’s Disease Rating Scale (UPDRS) III score and Mini-mental State Examination (MMSE) score, respectively.Ttest and ANOVA statistical analysis were performed on the frequency of annotated cell population. Linear regression model was used to analyze the correlation between clusters and clinical symptoms. We characterized 60 cell clusters and discovered that the immune signature of PD consists of cluster changes, including decreased effector CD8+T cells, lower cytotoxicity natural killer (NK) cells and increased activated monocytes in PD patients. In summary, we found that CD8+T cells, NK cells, and monocytes were associated with PD. Furthermore, there may be some differences in the immune status of patients with EOPD and LOPD, suggesting differences in the pathogenesis between these groups.
Biallelic expansion in RFC1 as a rare cause of Parkinson’s disease
Authors: Kytövuori Laura , Sipilä Jussi , Doi Hiroshi , Hurme-Niiranen Anri , Siitonen Ari , Koshimizu Eriko , Miyatake Satoko , Matsumoto Naomichi , Tanaka Fumiaki , Majamaa Kari 
Published: January 2022

AbstractAn intronic expansion (AAGGG)exp in the RFC1 gene has recently been shown to cause recessively inherited cerebellar ataxia, neuropathy, and vestibular areflexia syndrome and, furthermore, a few patients with ataxia and parkinsonism have been reported. We investigated 569 Finnish patients with medicated parkinsonism for RFC1 and found biallelic (AAGGG)exp in three non-consanguineous patients with clinically confirmed Parkinson’s disease without ataxia suggesting that RFC1-related disorders include Parkinson’s disease as well.
Confirming the trilinear form of the optical magnetoelectric effect in the polar honeycomb antiferromagnet Co2Mo3O8
Authors: Reschke S. , Farkas D. G. , Strinić A. , Ghara S. , Guratinder K. , Zaharko O. , Prodan L. , Tsurkan V. , Szaller D. , Bordács S. , Deisenhofer J. , Kézsmárki I. 
Published: January 2022

AbstractMagnetoelectric phenomena are intimately linked to relativistic effects and also require the material to break spatial inversion symmetry and time-reversal invariance. Magnetoelectric coupling can substantially affect light–matter interaction and lead to non-reciprocal light propagation. Here, we confirm on a fully experimental basis, without invoking either symmetry-based or material-specific assumptions, that the optical magnetoelectric effect in materials with non-parallel magnetization (M) and electric polarization (P) generates a trilinear term in the refractive index, δn ∝ k ⋅ (P × M), where k is the propagation vector of light. Its sharp magnetoelectric resonances in the terahertz regime, which are simultaneously electric and magnetic dipole active excitations, make Co2Mo3O8 an ideal compound to demonstrate this fundamental relation via independent variation of M, P, and k. Remarkably, the material shows almost perfect one-way transparency in moderate magnetic fields for one of these magnetoelectric resonances.
The clinical potential of articular cartilage-derived progenitor cells: a systematic review
Authors: Rikkers Margot , Korpershoek Jasmijn V. , Levato Riccardo , Malda Jos , Vonk Lucienne A. 
Published: January 2022

AbstractOver the past two decades, evidence has emerged for the existence of a distinct population of endogenous progenitor cells in adult articular cartilage, predominantly referred to as articular cartilage-derived progenitor cells (ACPCs). This progenitor population can be isolated from articular cartilage of a broad range of species, including human, equine, and bovine cartilage. In vitro, ACPCs possess mesenchymal stromal cell (MSC)-like characteristics, such as colony forming potential, extensive proliferation, and multilineage potential. Contrary to bone marrow-derived MSCs, ACPCs exhibit no signs of hypertrophic differentiation and therefore hold potential for cartilage repair. As no unique cell marker or marker set has been established to specifically identify ACPCs, isolation and characterization protocols vary greatly. This systematic review summarizes the state-of-the-art research on this promising cell type for use in cartilage repair therapies. It provides an overview of the available literature on endogenous progenitor cells in adult articular cartilage and specifically compares identification of these cell populations in healthy and osteoarthritic (OA) cartilage, isolation procedures, in vitro characterization, and advantages over other cell types used for cartilage repair. The methods for the systematic review were prospectively registered in PROSPERO (CRD42020184775).
Human EEG recordings for 1,854 concepts presented in rapid serial visual presentation streams
Authors: Grootswagers Tijl , Zhou Ivy , Robinson Amanda K. , Hebart Martin N. , Carlson Thomas A. 
Published: January 2022

AbstractThe neural basis of object recognition and semantic knowledge has been extensively studied but the high dimensionality of object space makes it challenging to develop overarching theories on how the brain organises object knowledge. To help understand how the brain allows us to recognise, categorise, and represent objects and object categories, there is a growing interest in using large-scale image databases for neuroimaging experiments. In the current paper, we present THINGS-EEG, a dataset containing human electroencephalography responses from 50 subjects to 1,854 object concepts and 22,248 images in the THINGS stimulus set, a manually curated and high-quality image database that was specifically designed for studying human vision. The THINGS-EEG dataset provides neuroimaging recordings to a systematic collection of objects and concepts and can therefore support a wide array of research to understand visual object processing in the human brain.
Response of atomic spin-based sensors to magnetic and nonmagnetic perturbations
Authors: Padniuk Mikhail , Kopciuch Marek , Cipolletti Riccardo , Wickenbrock Arne , Budker Dmitry , Pustelny Szymon 
Published: January 2022

AbstractSearches for pseudo-magnetic spin couplings require implementation of techniques capable of sensitive detection of such interactions. While Spin-Exchange Relaxation Free (SERF) magnetometry is one of the most powerful approaches enabling the searches, it suffers from a strong magnetic coupling, deteriorating the pseudo-magnetic coupling sensitivity. To address this problem, here, we compare, via numerical simulations, the performance of SERF magnetometer and noble-gas-alkali-metal co-magnetometer, operating in a so-called self-compensating regime. We demonstrate that the co-magnetometer allows reduction of the sensitivity to low-frequency magnetic fields without loss of the sensitivity to nonmagnetic couplings. Based on that we investigate the responses of both systems to the oscillating and transient spin perturbations. Our simulations reveal about five orders of magnitude stronger response to the neutron pseudo-magnetic coupling and about three orders of magnitude stronger response to the proton pseudo-magnetic coupling of the co-magnetometer than those of the SERF magnetometer. Different frequency responses of the co-magnetometer to magnetic and nonmagnetic perturbations enables differentiation between these two types of interactions. This outlines the ability to implement the co-magnetometer as an advanced sensor for the Global Network of Optical Magnetometer for Exotic Physics searches (GNOME), aiming at detection of ultra-light bosons (e.g., axion-like particles).
Prediction of steady flows passing fixed cylinders using deep learning
Authors: Ozaki Hiroto , Aoyagi Takeshi 
Published: January 2022

AbstractConsiderable attention has been given to deep-learning and machine-learning techniques in an effort to reduce the computational cost of computational fluid dynamics simulation. The present paper addresses the prediction of steady flows passing many fixed cylinders using a deep-learning model and investigates the accuracy of the predicted velocity field. The deep-learning model outputs the x- and y-components of the flow velocity field when the cylinder arrangement is input. The accuracy of the predicted velocity field is investigated, focusing on the velocity profile of the fluid flow and the fluid force acting on the cylinders. The present model accurately predicts the flow when the number of cylinders is equal to or close to that set in the training dataset. The extrapolation of the prediction to a smaller number of cylinders results in error, which can be interpreted as internal friction of the fluid. The results of the fluid force acting on the cylinders suggest that the present deep-learning model has good generalization performance for systems with a larger number of cylinders.
Machine learning for emerging infectious disease field responses
Authors: Chiu Han-Yi Robert , Hwang Chun-Kai , Chen Shey-Ying , Shih Fuh-Yuan , Han Hsieh-Cheng , King Chwan-Chuen , Gilbert John Reuben , Fang Cheng-Chung , Oyang Yen-Jen 
Published: January 2022

AbstractEmerging infectious diseases (EIDs), including the latest COVID-19 pandemic, have emerged and raised global public health crises in recent decades. Without existing protective immunity, an EID may spread rapidly and cause mass casualties in a very short time. Therefore, it is imperative to identify cases with risk of disease progression for the optimized allocation of medical resources in case medical facilities are overwhelmed with a flood of patients. This study has aimed to cope with this challenge from the aspect of preventive medicine by exploiting machine learning technologies. The study has been based on 83,227 hospital admissions with influenza-like illness and we analysed the risk effects of 19 comorbidities along with age and gender for severe illness or mortality risk. The experimental results revealed that the decision rules derived from the machine learning based prediction models can provide valuable guidelines for the healthcare policy makers to develop an effective vaccination strategy. Furthermore, in case the healthcare facilities are overwhelmed by patients with EID, which frequently occurred in the recent COVID-19 pandemic, the frontline physicians can incorporate the proposed prediction models to triage patients suffering minor symptoms without laboratory tests, which may become scarce during an EID disaster. In conclusion, our study has demonstrated an effective approach to exploit machine learning technologies to cope with the challenges faced during the outbreak of an EID.
Effects of azithromycin on bronchial remodeling in the natural model of severe neutrophilic asthma in horses
Authors: Mainguy-Seers Sophie , Boivin Roxane , Pourali Dogaheh Sheila , Beaudry Francis , Hélie Pierre , Bonilla Alvaro G. , Martin James G. , Lavoie Jean-Pierre 
Published: January 2022

AbstractSteroid resistance in asthma has been associated with neutrophilic inflammation and severe manifestations of the disease. Macrolide add-on therapy can improve the quality of life and the exacerbation rate in refractory cases, possibly with greater effectiveness in neutrophilic phenotypes. The mechanisms leading to these beneficial effects are incompletely understood and whether macrolides potentiate the modulation of bronchial remodeling induced by inhaled corticosteroids (ICS) is unknown. The objective of this study was to determine if adding azithromycin to ICS leads to further improvement of lung function, airway inflammation and bronchial remodeling in severe asthma. The combination of azithromycin (10 mg/kg q48h PO) and inhaled fluticasone (2500 µg q12h) was compared to the sole administration of fluticasone for five months in a randomized blind trial where the lung function, airway inflammation and bronchial remodeling (histomorphometry of central and peripheral airways and endobronchial ultrasound) of horses with severe neutrophilic asthma were assessed. Although the proportional reduction of airway neutrophilia was significantly larger in the group receiving azithromycin, the lung function and the peripheral and central airway smooth muscle mass decreased similarly in both groups. Despite a better control of airway neutrophilia, azithromycin did not potentiate the other clinical effects of fluticasone.
Susceptibility artifacts induced by crowns of different materials with prepared teeth and titanium implants in magnetic resonance imaging
Authors: Gao Xiaomeng , Wan Qianbing , Gao Qingping 
Published: January 2022

AbstractThis study aimed to investigate the artifacts induced by crowns composed of different materials with prepared teeth and titanium implants. Resin, metal-ceramic, ceramic and zirconia crowns were fabricated and placed onto the prepared teeth on a human cadaver head or titanium implants with prosthesis abutments on a dry human mandible. The samples were scanned on a 1.5 T MRI apparatus, and artifact areas were defined as the signal intensity and signal loss adjacent to the prosthesis and measured by a threshold tool with ImageJ2x. Data were analyzed using SPSS 22.0. Resin, ceramic, zirconia, and precious metal-ceramic crowns barely produced artifacts on the cadaver skull (p > 0.999). By contrast, pure Ti and nonprecious metal-ceramic crowns created significant artifacts (p < 0.001). The average artifacts reduction of double Au-Pt and Ag-Pd metal-ceramic crowns combined with titanium implants and abutments was 79.49 mm2 (p < 0.001) and 74.17 mm2 (p < 0.001) respectively, while artifact areas were increased in double Co-Cr and Ni–Cr metal-ceramic crowns by 150.10 mm2 (p < 0.001) and 175.50 mm2 (p < 0.001) respectively. Zirconia, ceramic and precious metal-ceramic crowns induce less MRI artifacts after tooth preparation while precious metal-ceramic crowns alleviate artifacts in combination with titanium implants.
The sphingosine 1-phosphate receptor 2/4 antagonist JTE-013 elicits off-target effects on sphingolipid metabolism
Authors: Pitman Melissa R. , Lewis Alexander C. , Davies Lorena T. , Moretti Paul A. B. , Anderson Dovile , Creek Darren J. , Powell Jason A. , Pitson Stuart M. 
Published: January 2022

AbstractSphingosine 1-phosphate (S1P) is a signaling lipid that has broad roles, working either intracellularly through various protein targets, or extracellularly via a family of five G-protein coupled receptors. Agents that selectively and specifically target each of the S1P receptors have been sought as both biological tools and potential therapeutics. JTE-013, a small molecule antagonist of S1P receptors 2 and 4 (S1P2 and S1P4) has been widely used in defining the roles of these receptors in various biological processes. Indeed, our previous studies showed that JTE-013 had anti-acute myeloid leukaemia (AML) activity, supporting a role for S1P2 in the biology and therapeutic targeting of AML. Here we examined this further and describe lipidomic analysis of AML cells that revealed JTE-013 caused alterations in sphingolipid metabolism, increasing cellular ceramides, dihydroceramides, sphingosine and dihydrosphingosine. Further examination of the mechanisms behind these observations showed that JTE-013, at concentrations frequently used in the literature to target S1P2/4, inhibits several sphingolipid metabolic enzymes, including dihydroceramide desaturase 1 and both sphingosine kinases. Collectively, these findings demonstrate that JTE-013 can have broad off-target effects on sphingolipid metabolism and highlight that caution must be employed in interpreting the use of this reagent in defining the roles of S1P2/4.
Two-step screening method to identify α-synuclein aggregation inhibitors for Parkinson’s disease
Authors: Hideshima Makoto , Kimura Yasuyoshi , Aguirre César , Kakuda Keita , Takeuchi Toshihide , Choong Chi-Jing , Doi Junko , Nabekura Kei , Yamaguchi Keiichi , Nakajima Kichitaro , Baba Kousuke , Nagano Seiichi , Goto Yuji , Nagai Yoshitaka , Mochizuki Hideki , Ikenaka Kensuke 
Published: January 2022

AbstractParkinson’s disease is a neurodegenerative disease characterized by the formation of neuronal inclusions of α-synuclein in patient brains. As the disease progresses, toxic α-synuclein aggregates transmit throughout the nervous system. No effective disease-modifying therapy has been established, and preventing α-synuclein aggregation is thought to be one of the most promising approaches to ameliorate the disease. In this study, we performed a two-step screening using the thioflavin T assay and a cell-based assay to identify α-synuclein aggregation inhibitors. The first screening, thioflavin T assay, allowed the identification of 30 molecules, among a total of 1262 FDA-approved small compounds, which showed inhibitory effects on α-synuclein fibrilization. In the second screening, a cell-based aggregation assay, seven out of these 30 candidates were found to prevent α-synuclein aggregation without causing substantial toxicity. Of the seven final candidates, tannic acid was the most promising compound. The robustness of our screening method was validated by a primary neuronal cell model and a Caenorhabditis elegans model, which demonstrated the effect of tannic acid against α-synuclein aggregation. In conclusion, our two-step screening system is a powerful method for the identification of α-synuclein aggregation inhibitors, and tannic acid is a promising candidate as a disease-modifying drug for Parkinson’s disease.
Fucoidan from Sargassum hemiphyllum inhibits infection and inflammation of Helicobacter pylori
Authors: Chen Bo-Rui , Li Wei-Ming , Li Tsung-Lin , Chan Yi-Lin , Wu Chang-Jer 
Published: January 2022

AbstractHaving infected byHelicobacter pylori, the infection often leads to gastritis, gastric ulcer, or even gastric cancer. The disease is typically treated with antibiotics as they used to effectively inhibit or killH. pylori, thus reducing the incidence of gastric adenoma and cancer to significant extent.H. pylori, however, has developed drug resistance to many clinically used antibiotics over the years, highlighting the crisis of antibiotic failure during theH. pyloritreatment. We report here that the fucoidan fromSargassum hemiphyllumcan significantly reduce the infection ofH. pyloriwithout developing to drug resistance. Fucoidan appears to be a strong anti-inflammation agent as manifested by the RAW264.7 cell model examination. Fucoidan can prohibitH. pyloriadhesion to host cells, thereby reducing the infection rate by 60%, especially in post treatment in the AGS cell model assay. Mechanistically, fucoidan intervenes the adhesion of BabA and AlpA ofH. pylorisignificantly lowering the total count ofH. pyloriand the level of IL-6 and TNF-α in vivo. These results all converge on the same fact that fucoidan is an effective agent in a position to protect the stomach from theH. pyloriinfection by reducing both the total count and induced inflammation.