bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors affecting drug retention of Janus kinase inhibitors in patients with rheumatoid arthritis: the ANSWER cohort study
Authors: Ebina Kosuke , Hirano Toru , Maeda Yuichi , Yamamoto Wataru , Hashimoto Motomu , Murata Koichi , Onishi Akira , Jinno Sadao , Hara Ryota , Son Yonsu , Amuro Hideki , Takeuchi Tohru , Yoshikawa Ayaka , Katayama Masaki , Yamamoto Keiichi , Okita Yasutaka , Hirao Makoto , Etani Yuki , Kumanogoh Atsushi , Okada Seiji , Nakata Ken 
Published: January 2022

AbstractThis multi-center, retrospective study aimed to clarify the factors affecting drug retention of the Janus kinase inhibitors (JAKi) including baricitinib (BAR) and tofacitinib (TOF) in patients with RA. Patients were as follows; females, 80.6%; age, 60.5 years; DAS28-ESR, 4.3; treated with either BAR (n = 166) or TOF (n = 185); bDMARDs- or JAKi-switched cases (76.6%). The reasons for drug discontinuation were classified into four major categories. The drug retention was evaluated at 24 months using the Kaplan–Meier method and multivariate Cox proportional hazards modelling adjusted by confounders. Discontinuation rates for the corresponding reasons were as follows; ineffectiveness (22.3%), toxic adverse events (13.3%), non-toxic reasons (7.2%) and remission (0.0%). Prior history of anti-interleukin-6 receptor antibody (aIL-6R) ineffectiveness significantly increased the risk of treatment discontinuation due to ineffectiveness (p = 0.020). Aging (≥ 75 years) (p = 0.028), usage of PSL ≥ 5 mg/day (p = 0.017) and female sex (p = 0.041) significantly increased the risk of treatment discontinuation due to toxic adverse events. Factors not associated with treatment discontinuation were: number of prior bDMARDs or JAKi, concomitant MTX usage, difference of JAKi, and prior use of TNF inhibitor, CTLA4-Ig or other JAKi.
Influence of brain atrophy using semiquantitative analysis in [123I]FP-CIT single-photon emission computed tomography by a Monte Carlo simulation study
Authors: Nosaka Hiroki , Onoguchi Masahisa , Tsushima Hiroyuki , Suda Masaya , Kurata Satoshi , Onoma Ayano , Murakawa Ryosuke 
Published: January 2022

AbstractThe specific binding ratio (SBR) is an objective indicator of N-ω-fluoropropyl-2β-carbomethoxy-3β-(4-[123I] iodophenyl) nortropane ([123I]FP-CIT) single-photon emission computed tomography (SPECT) that could be used for the diagnosis of Parkinson’s disease and Lewy body dementia. One of the issues of the SBR analysis is that the setting position of the volume of interest (VOI) may contain cerebral ventricles and cerebral grooves. These areas may become prominent during the brain atrophy analysis; however, this phenomenon has not been evaluated enough. This study thus used Monte Carlo simulations to examine the effect of brain atrophy on the SBR analysis. The brain atrophy model (BAM) used to simulate the three stages of brain atrophy was made using a morphological operation. Brain atrophy levels were defined in the descending order from 1 to 3, with Level 3 indicating to the most severe damage. Projection data were created based on BAM, and the SPECT reconstruction was performed. The ratio of the striatal to background region accumulation was set to a rate of 8:1, 6:1, and 4:1. The striatal and the reference VOI mean value were decreased as brain atrophy progressed. Additionally, the Bolt’s analysis methods revealed that the reference VOI value was more affected by brain atrophy than the striatal VOI value. Finally, the calculated SBR value was overestimated as brain atrophy progressed, and a similar trend was observed when the ratios of the striatal to background region accumulation were changed. This study thus suggests that the SBR can be overestimated in cases of advanced brain atrophy.
O-ring-induced transverse aortic constriction (OTAC) is a new simple method to develop cardiac hypertrophy and heart failure in mice
Authors: Nakao Yasuhisa , Aono Jun , Hamaguchi Mika , Takahashi Kayo , Sakaue Tomohisa , Inoue Katsuji , Ikeda Shuntaro , Yamaguchi Osamu 
Published: January 2022

AbstractSuture-based transverse aortic constriction (TAC) in mice is one of the most frequently used experimental models for cardiac pressure overload-induced heart failure. However, the incidence of heart failure in the conventional TAC depends on the operator’s skill. To optimize and simplify this method, we proposed O-ring-induced transverse aortic constriction (OTAC) in mice. C57BL/6J mice were subjected to OTAC, in which an o-ring was applied to the transverse aorta (between the brachiocephalic artery and the left common carotid artery) and tied with a triple knot. We used different inner diameters of o-rings were 0.50 and 0.45 mm. Pressure overload by OTAC promoted left ventricular (LV) hypertrophy. OTAC also increased lung weight, indicating severe pulmonary congestion. Echocardiographic findings revealed that both OTAC groups developed LV hypertrophy within one week after the procedure and gradually reduced LV fractional shortening. In addition, significant elevations in gene expression related to heart failure, LV hypertrophy, and LV fibrosis were observed in the LV of OTAC mice. We demonstrated the OTAC method, which is a simple and effective cardiac pressure overload method in mice. This method will efficiently help us understand heart failure (HF) mechanisms with reduced LV ejection fraction (HFrEF) and cardiac hypertrophy.
Cultivated and wild pearl millet display contrasting patterns of abundance and co-occurrence in their root mycobiome
Authors: Mofini Marie-Thérèse , Diedhiou Abdala G. , Simonin Marie , Dondjou Donald Tchouomo , Pignoly Sarah , Ndiaye Cheikh , Min Doohong , Vigouroux Yves , Laplaze Laurent , Kane Aboubacry 
Published: January 2022

AbstractFungal communities associated with roots play a key role in nutrient uptake and in mitigating the abiotic and biotic stress of their host. In this study, we characterized the roots mycobiome of wild and cultivated pearl millet [Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] in three agro-ecological areas of Senegal following a rainfall gradient. We hypothesized that wild pearl millet could serve as a reservoir of endophytes for cultivated pearl millet. We therefore analyzed the soil factors influencing fungal community structure and whether cultivated and wild millet shared the same fungal communities. The fungal communities associated with pearl millet were significantly structured according to sites and plant type (wild vs cultivated). Besides, soil pH and phosphorus were the main factors influencing the fungal community structure. We observed a higher fungal diversity in cultivated compared to wild pearl millet. Interestingly, we detected higher relative abundance of putative pathotrophs, especially plant pathogen, in cultivated than in wild millet in semi-arid and semi-humid zones, and higher relative abundance of saprotrophs in wild millet in arid and semi-humid zones. A network analysis based on taxa co-occurrence patterns in the core mycobiome revealed that cultivated millet and wild relatives had dissimilar groups of hub taxa. The identification of the core mycobiome and hub taxa of cultivated and wild pearl millet could be an important step in developing microbiome engineering approaches for more sustainable management practices in pearl millet agroecosystems.
Assessment of factors associated with PSA level in prostate cancer cases and controls from three geographical regions
Authors: Karunasinghe Nishi , Minas Tsion Zewdu , Bao Bo-Ying , Lee Arier , Wang Alice , Zhu Shuotun , Masters Jonathan , Goudie Megan , Huang Shu-Pin , Jenkins Frank J. , Ferguson Lynnette R. 
Published: January 2022

AbstractIt is being debated whether prostate-specific antigen (PSA)-based screening effectively reduces prostate cancer mortality. Some of the uncertainty could be related to deficiencies in the age-based PSA cut-off thresholds used in screening. Current study considered 2779 men with prostate cancer and 1606 men without a cancer diagnosis, recruited for various studies in New Zealand, US, and Taiwan. Association of PSA with demographic, lifestyle, clinical characteristics (for cases), and the aldo–keto reductase 1C3 (AKR1C3) rs12529 genetic polymorphisms were analysed using multiple linear regression and univariate modelling. Pooled multivariable analysis of cases showed that PSA was significantly associated with demographic, lifestyle, and clinical data with an interaction between ethnicity and age further modifying the association. Pooled multivariable analysis of controls data also showed that demographic and lifestyle are significantly associated with PSA level. Independent case and control analyses indicated that factors associated with PSA were specific for each cohort. Univariate analyses showed a significant age and PSA correlation among all cases and controls except for the US-European cases while genetic stratification in cases showed variability of correlation. Data suggests that unique PSA cut-off thresholds factorized with demographics, lifestyle and genetics may be more appropriate for prostate cancer screening.
Degenerative joint disease induced by repeated intra-articular injections of monosodium urate crystals in rats as investigated by translational imaging
Authors: Accart Nathalie , Dawson Janet , Obrecht Michael , Lambert Christian , Flueckiger Manuela , Kreider Julie , Hatakeyama Shinji , Richards Peter J. , Beckmann Nicolau 
Published: January 2022

AbstractThe objective of this work was to assess the consequences of repeated intra-articular injection of monosodium urate (MSU) crystals with inflammasome priming by lipopolysaccharide (LPS) in order to simulate recurrent bouts of gout in rats. Translational imaging was applied to simultaneously detect and quantify injury in different areas of the knee joint. MSU/LPS induced joint swelling, synovial membrane thickening, fibrosis of the infrapatellar fat pad, tidemark breaching, and cartilage invasion by inflammatory cells. A higher sensitivity to mechanical stimulus was detected in paws of limbs receiving MSU/LPS compared to saline-injected limbs. In MSU/LPS-challenged joints, magnetic resonance imaging (MRI) revealed increased synovial fluid volume in the posterior region of the joint, alterations in the infrapatellar fat pad reflecting a progressive decrease of fat volume and fibrosis formation, and a significant increase in the relaxation time T2 in femoral cartilage, consistent with a reduction of proteoglycan content. MRI also showed cyst formation in the tibia, femur remodeling, and T2 reductions in extensor muscles consistent with fibrosis development. Repeated intra-articular MSU/LPS injections in the rat knee joint induced pathology in multiple tissues and may be a useful means to investigate the relationship between urate crystal deposition and the development of degenerative joint disease.
Slope stability calculation method for highwall mining with open-cut mines
Authors: Jiang Juyu , Lu Ye , Wang Dong , Han Xinping 
Published: January 2022

AbstractSlope stability is a prominent problem for the efficient application and promotion of highwall mining technology, especially when mining residual coal under high and steep end-slope conditions. This study proposes the concept of target time pillar strength based on the required coal pillar service time. Creep tests were performed to measure the time-varying properties of coal shear strength parameters under different loads, and a time-varying function was established by regression. The highwall mining length is divided into three categories based on discontinuous structural plane theory, including goaf, yielding, and elastic zones, all of which are considered to have resistances against shear stress. The basal coal seam is prone to weakening owing to the weight of overlying strata, which may shift the slope failure mode from circular to sliding along the weak layer. Numerical modeling was used to study the influence of the bearing stress and target time strength on the development of the yielding zone at the coal pillar ribs. The coefficients of the three zones were determined, and the temporal and spatial evolution patterns of the shear strength parameters of the weak layer were acquired. A slope stability calculation method is proposed based on rigid body-limit equilibrium theory that can quantify the influence of highwall mining operations on slope stability, which is significant for popularizing highwall mining technology.
Real-world effectiveness of liraglutide versus dulaglutide in Japanese patients with type 2 diabetes: a retrospective study
Authors: Tanaka Kenichi , Okada Yosuke , Tokutsu Akemi , Tanaka Yoshiya 
Published: January 2022

AbstractReal-world data comparing the effectiveness of various glucagon-like peptide 1 receptor agonists (GLP-1 RAs) in type 2 diabetes mellitus (T2DM) are limited. We investigated the clinical effectiveness of liraglutide and dulaglutide in Japanese T2DM in a real-world setting. This retrospective study included 179 patients with T2DM who were treated with GLP-1 RA for at least 12 months (liraglutide, n = 97; dulaglutide, n = 82). We used stabilized propensity score-based inverse probability of treatment weighting (IPTW) to reduce selection bias and confounding by observed covariates. Changes in glycated hemoglobin (HbA1c) at the end of the 12-month treatment were evaluated. After adjustment by stabilized propensity score-based IPTW, no significant differences were observed in patient characteristics between the liraglutide and dulaglutide groups. HbA1c was significantly lower at 12 months in both groups (liraglutide, 8.9 to 7.4%; dulaglutide, 8.7 to 7.5%). Multivariate linear regression analysis showed no differences in the extent of changes in HbA1c at 12 months between the two agents. High baseline HbA1c, the addition of GLP-1 RA treatment modality, and in-hospital initiation of GLP-1 RA treatment were identified as significant contributing factors to HbA1c reduction. The effects of liraglutide and dulaglutide on lowering HbA1c levels at 12 months were comparable in a real-world setting.
Validation of satellite-based sea surface temperature products against in situ observations off the western coast of Sumatra
Authors: Moteki Qoosaku 
Published: January 2022

AbstractThis study validated the sea surface temperature (SST) datasets from the Group for High-Resolution SST Multi Product Ensemble (GMPE), National Oceanic and Atmospheric Administration (NOAA) Optimal Interpolation (OI) SST version 2 and 2.1 (OIv2 and OIv2.1), and Estimating the Circulation and Climate of the Ocean, Phase II (ECCO2) in the area off the western coast of Sumatra against in situ observations. Furthermore, the root mean square differences (RMSDs) of OIv2, OIv2.1, and ECCO2 were investigated with respect to GMPE, whose small RMSD < 0.2 K against in situ observations confirmed its suitability as a reference. Although OIv2 showed a large RMSD (1–1.5 K) with a significant negative bias, OIv2.1 (RMSD < 0.4 K) improved remarkably. In the average SST distributions for December 2017, the differences among the 4 datasets were significant in the areas off the western coast of Sumatra, along the southern coast of Java, and in the Indonesian inland sea. These results were consistent with the ensemble spread distribution obtained with GMPE. The large RMSDs of OIv2 corresponded to high clouds, and it was suggested that the change in the satellites used for SST estimation contributed to the improvement in OIv2.1.
Confocal microscopy analysis reveals that only a small proportion of extracellular vesicles are successfully labelled with commonly utilised staining methods
Authors: Melling Genevieve E. , Conlon Ross , Pantazi Paschalia , Dellar Elizabeth R. , Samuel Priya , Baena-Lopez Luis Alberto , Simpson Jeremy C. , Carter David R. F. 
Published: January 2022

AbstractAssessing genuine extracellular vesicle (EV) uptake is crucial for understanding the functional roles of EVs. This study measured the bona fide labelling of EVs utilising two commonly used fluorescent dyes, PKH26 and C5-maleimide-Alexa633. MCF7 EVs tagged with mEmerald-CD81 were isolated from conditioned media by size exclusion chromatography (SEC) and characterised using Nanoparticle Tracking Analysis (NTA), Transmission Electron Microscopy (TEM), MACsPlex immunocapture assay and immunoblots. These fluorescently tagged EVs were subsequently stained with C5-maleimide-Alexa633 or PKH26, according to published protocols. Colocalisation of dual-labelled EVs was assessed by confocal microscopy and quantified using the Rank-Weighted Colocalisation (RWC) algorithm. We observed strikingly poor colocalisation between mEmerald-CD81-tagged EVs and C5-Maleimide-Alexa633 (5.4% ± 1.8) or PKH26 (4.6% ± 1.6), that remained low even when serum was removed from preparations. Our data confirms previous work showing that some dyes form contaminating aggregates. Furthermore, uptake studies showed that maleimide and mEmerald-CD81-tagged EVs can be often located into non-overlapping subcellular locations. By using common methods to isolate and stain EVs we observed that most EVs remained unstained and most dye signal does not appear to be EV associated. Our work shows that there is an urgent need for optimisation and standardisation in how EV researchers use these tools to assess genuine EV signals.
Research on quantum cognition in autonomous driving
Authors: Song Qingyuan , Wang Wen , Fu Weiping , Sun Yuan , Wang Denggui , Gao Zhiqiang 
Published: January 2022

AbstractAutonomous vehicles for the intention of human behavior of the estimated traffic participants and their interaction is the main problem in automatic driving system. Classical cognitive theory assumes that the behavior of human traffic participants is completely reasonable when studying estimation of intention and interaction. However, according to the quantum cognition and decision theory as well as practical traffic cases, human behavior including traffic behavior is often unreasonable, which violates classical cognition and decision theory. Based on the quantum cognitive theory, this paper studies the cognitive problem of pedestrian crossing. Through the case analysis, it is proved that the Quantum-like Bayesian (QLB) model can consider the reasonability of pedestrians when crossing the street compared with the classical probability model, being more consistent with the actual situation. The experiment of trajectory prediction proves that the QLB model can cover the edge events in interactive scenes compared with the data-driven Social-LSTM model, being more consistent with the real trajectory. This paper provides a new reference for the research on the cognitive problem of intention on bounded rational behavior of human traffic participants in autonomous driving.
Transcriptomics and network analysis highlight potential pathways in the pathogenesis of pterygium
Authors: de Guimarães Juliana Albano , Hounpke Bidossessi Wilfried , Duarte Bruna , Boso Ana Luiza Mylla , Viturino Marina Gonçalves Monteiro , de Carvalho Baptista Letícia , de Melo Mônica Barbosa , Alves Monica 
Published: January 2022

AbstractPterygium is a common ocular surface condition frequently associated with irritative symptoms. The precise identity of its critical triggers as well as the hierarchical relationship between all the elements involved in the pathogenesis of this disease are not yet elucidated. Meta-analysis of gene expression studies represents a novel strategy capable of identifying key pathogenic mediators and therapeutic targets in complex diseases. Samples from nine patients were collected during surgery after photo documentation and clinical characterization of pterygia. Gene expression experiments were performed using Human Clariom D Assay gene chip. Differential gene expression analysis between active and atrophic pterygia was performed using limma package after adjusting variables by age. In addition, a meta-analysis was performed including recent gene expression studies available at the Gene Expression Omnibus public repository. Two databases including samples from adults with pterygium and controls fulfilled our inclusion criteria. Meta-analysis was performed using the Rank Production algorithm of the RankProd package. Gene set analysis was performed using ClueGO and the transcription factor regulatory network prediction was performed using appropriate bioinformatics tools. Finally, miRNA-mRNA regulatory network was reconstructed using up-regulated genes identified in the gene set analysis from the meta-analysis and their interacting miRNAs from the Brazilian cohort expression data. The meta-analysis identified 154 up-regulated and 58 down-regulated genes. A gene set analysis with the top up-regulated genes evidenced an overrepresentation of pathways associated with remodeling of extracellular matrix. Other pathways represented in the network included formation of cornified envelopes and unsaturated fatty acid metabolic processes. The miRNA-mRNA target prediction network, also reconstructed based on the set of up-regulated genes presented in the gene ontology and biological pathways network, showed that 17 target genes were negatively correlated with their interacting miRNAs from the Brazilian cohort expression data. Once again, the main identified cluster involved extracellular matrix remodeling mechanisms, while the second cluster involved formation of cornified envelope, establishment of skin barrier and unsaturated fatty acid metabolic process. Differential expression comparing active pterygium with atrophic pterygium using data generated from the Brazilian cohort identified differentially expressed genes between the two forms of presentation of this condition. Our results reveal differentially expressed genes not only in pterygium, but also in active pterygium when compared to the atrophic ones. New insights in relation to pterygium’s pathophysiology are suggested.
Automating microsatellite screening and primer design from multi-individual libraries using Micro-Primers
Authors: Alves Filipe , Martins Filipa M. S. , Areias Miguel , Muñoz-Mérida Antonio 
Published: January 2022

AbstractAnalysis of intra- and inter-population diversity has become important for defining the genetic status and distribution patterns of a species and a powerful tool for conservation programs, as high levels of inbreeding could lead into whole population extinction in few generations. Microsatellites (SSR) are commonly used in population studies but discovering highly variable regions across species’ genomes requires demanding computation and laboratorial optimization. In this work, we combine next generation sequencing (NGS) with automatic computing to develop a genomic-oriented tool for characterizing SSRs at the population level. Herein, we describe a new Python pipeline, named Micro-Primers, designed to identify, and design PCR primers for amplification of SSR loci from a multi-individual microsatellite library. By combining commonly used programs for data cleaning and microsatellite mining, this pipeline easily generates, from a fastq file produced by high-throughput sequencing, standard information about the selected microsatellite loci, including the number of alleles in the population subset, and the melting temperature and respective PCR product of each primer set. Additionally, potential polymorphic loci can be identified based on the allele ranges observed in the population, to easily guide the selection of optimal markers for the species. Experimental results show that Micro-Primers significantly reduces processing time in comparison to manual analysis while keeping the same quality of the results. The elapsed times at each step can be longer depending on the number of sequences to analyze and, if not assisted, the selection of polymorphic loci from multiple individuals can represent a major bottleneck in population studies.