bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of imputation accuracy using the combination of two high-density panels in Nelore beef cattle
Authors: Bernardes Priscila Arrigucci , Nascimento Guilherme Batista do , Savegnago Rodrigo Pelicioni , Buzanskas Marcos Eli , Watanabe Rafael Nakamura , de Almeida Regitano Luciana Correia , Coutinho Luiz Lehmann , Gondro Cedric , Munari Danísio Prado 
Published: November 2019

AbstractThis study compared imputation from lower-density commercial and customized panels to high-density panels and a combined panel (Illumina and Affymetrix) in Nelore beef cattle. Additionally, linkage disequilibrium and haplotype block conformation were estimated in individual high-density panels and compared with corresponding values in the combined panel after imputation. Overall, 814 animals were genotyped using BovineHD BeadChip (IllumHD), and 93 of these animals were also genotyped using the Axion Genome-Wide BOS 1 Array Plate (AffyHD). In general, customization considering linkage disequilibrium and minor allele frequency had the highest accuracies. The IllumHD panel had higher values of linkage disequilibrium for short distances between SNPs than AffyHD and the combined panel. The combined panel had an increased number of small haplotype blocks. The use of a combined panel is recommended due to its increased density and number of haplotype blocks, which in turn increase the probability of a marker being close to a quantitative trait locus of interest. Considering common SNPs between IllumHD and AffyHD for the customization of a low-density panel increases the imputation accuracy for IllumHD, AffyHD and the combined panel.
Detection of colonic neoplasia in vivo using near-infrared-labeled peptide targeting cMet
Authors: Wu Xiaoli , Zhou Juan , Wang Fa , Meng Xiaoqing , Chen Jing , Chang Tse-Shao , Lee Miki , Li Gaoming , Li Xue , Appelman Henry D. , Kuick Rork , Wang Thomas D. 
Published: November 2019

AbstractWhite light colonoscopy is widely used to detect colorectal polyps, but flat and depressed lesions are often missed. Here, we report a molecular imaging strategy to potentially improve diagnostic performance by developing a fluorescently-labeled peptide specific for cMet. This 7mer is conjugated to Cy5.5, a near-infrared (NIR) cyanine dye. Specific binding to cMet was confirmed by cell staining, knockdown, and competition assays. The probe showed high binding affinity (kd = 57 nM) and fast onset (k = 1.6 min) to support topical administration in vivo. A mouse model (CPC;Apc) that develops spontaneous adenomas that overexpress cMet was used to demonstrate feasibility for real time in vivo imaging. This targeting ligand showed significantly higher target-to-background (T/B) ratio for polypoid and non-polypoid lesions by comparison with a scrambled control peptide. Immunofluorescence staining on human colon specimens show significantly greater binding to tubular and sessile serrated adenomas versus hyperplastic polyps and normal mucosa. These results demonstrate a peptide specific for cMet that is promising for endoscopic detection of pre-malignant lesions and guiding of tissue biopsy.
Differential DNA methylation in high-grade serous ovarian cancer (HGSOC) is associated with tumor behavior
Authors: Reyes Henry D. , Devor Eric J. , Warrier Akshaya , Newtson Andreea M. , Mattson Jordan , Wagner Vincent , Duncan Gabrielle N. , Leslie Kimberly K. , Gonzalez-Bosquet Jesus 
Published: November 2019

AbstractThe epigenome offers an additional facet of cancer that can help categorize patients into those at risk of disease, recurrence, or treatment failure. We conducted a retrospective, nested, case-control study of advanced and recurrent high-grade serous ovarian cancer (HGSOC) patients in which we assessed epigenome-wide association using Illumina methylationEPIC arrays to characterize DNA methylation status and RNAseq to evaluate gene expression. Comparing HGSOC tumors with normal fallopian tube tissues we observe global hypomethylation but with skewing towards hypermethylation when interrogating gene promoters. In total, 5,852 gene interrogating probes revealed significantly different methylation. Within HGSOC, 57 probes highlighting 17 genes displayed significant differential DNA methylation between primary and recurrent disease. Between optimal vs suboptimal surgical outcomes 99 probes displayed significantly different methylation but only 29 genes showed an inverse correlation between methylation status and gene expression. Overall, differentially methylated genes point to several pathways including RAS as well as hippo signaling in normal vs primary HGSOC; valine, leucine, and isoleucine degradation and endocytosis in primary vs recurrent HGSOC; and pathways containing immune driver genes in optimal vs suboptimal surgical outcomes. Thus, differential DNA methylation identified numerous genes that could serve as potential biomarkers and/or therapeutic targets in HGSOC.
The role of magnetic resonance imaging in the preoperative evaluation of anal fistulas
Authors: Vo Duc , Phan Chien , Nguyen Linh , Le Huyen , Nguyen Tin , Pham Hung 
Published: November 2019

AbstractThis study aimed to determine the role of magnetic resonance imaging (MRI) in diagnosing and describing the characteristics of fistula-in-ano, and the agreement between MRI and operative findings. We conducted a retrospective study in 367 patients with fistula-in-ano who were diagnosed and had an operation at the University Medical Center between January 2016 and January 2018. MRI findings were evaluated and compared with surgical findings using the kappa coefficient (k) method. 367 patients (327 male and 40 female, mean age 39.3 ± 12.4 years). A total of 411 primary fistulas were found during surgery. There was a strong agreement between MRI and surgery for classifying primary tracts (k = 0.89) and detecting secondary tracts (k = 0.94). While the sensitivity and specificity of MRI for detecting internal openings were 99% and 85.2% respectively; these rates were 100% for abscesses. Both T2-weighted turbo spin-echo (T2W TSE) and postcontrast fat-saturated T1-weighted turbo spin-echo (FS T1W TSE) sequences showed high sensitivity (96.6% and 98.4% respectively) and specificity (92.6% and 81.5% respectively) for depicting internal openings and secondary tracts. Post-contrast FS T1W TSE sequence was very effective in detecting abscesses with an accuracy of 100%. In conclusion, MRI can be considered an accurate tool for the preoperative evaluation of fistula-in-ano, which is a major determinant of the surgical outcome. Both T2W TSE and post-contrast FS T1W TSE sequences are highly accurate in depicting the features of fistula-in-ano. If there are no contraindications, contrast administration is recommended to differentiate abscesses from active inflammation.
Flow cytometric identification and cell-line establishment of macrophages in naked mole-rats
Authors: Wada Haruka , Shibata Yuhei , Abe Yurika , Otsuka Ryo , Eguchi Nanami , Kawamura Yoshimi , Oka Kaori , Baghdadi Muhammad , Atsumi Tatsuya , Miura Kyoko , Seino Ken-ichiro 
Published: November 2019

AbstractNaked mole rats (NMRs) have extraordinarily long lifespans and anti-tumorigenic capability. Recent studies of humans and mice have shown that many age-related diseases, including cancer, are strongly correlated with immunity, and macrophages play particularly important roles in immune regulation. Therefore, NMR macrophages may contribute to their unique phenotypes. However, studies of the roles of macrophages are limited by material restrictions and the lack of an established experimental strategy. In this study, we developed a flow cytometric strategy to identify NMR macrophages. The NMR macrophages were extractable using an off-the-shelf anti-CD11b antibody, M1/70, and forward/side scatter data obtained by flow cytometry. NMR macrophages proliferated in response to human/mouse recombinant M-CSF and engulfedEscherichia coliparticles. Interestingly, the majority of NMR macrophages exhibited co-staining with an anti-NK1.1 antibody, PK136. NK1.1 antigen crosslinking with PK136 results in mouse NK cell stimulation; similarly, NMR macrophages proliferated in response to NK1.1 antibody treatment. Furthermore, we successfully established an NMR macrophage cell line, NPM1, by transduction of Simian virus 40 early region that proliferated indefinitely without cytokines and retained its phagocytotic capacity. The NPM1 would contribute to further studies on the immunity of NMRs.
The intensification of metallic layered phenomena above thunderstorms through the modulation of atmospheric tides
Authors: Yu Bingkun , Xue Xianghui , Kuo Chengling , Lu Gaopeng , Scott Christopher J. , Wu Jianfei , Ma Ju , Dou Xiankang , Gao Qi , Ning Baiqi , Hu Lianhuan , Wang Guojun , Jia Mingjiao , Yu Chao , Qie Xiushu 
Published: November 2019

AbstractWe present a multi-instrument experiment to study the effects of tropospheric thunderstorms on the mesopause region and the lower ionosphere. Sodium (Na) lidar and ionospheric observations by two digital ionospheric sounders are used to study the variation in the neutral metal atoms and metallic ions above thunderstorms. An enhanced ionospheric sporadic E layer with a downward tidal phase is observed followed by a subsequent intensification of neutral Na number density with an increase of 600 cm−3 in the mesosphere. In addition, the Na neutral chemistry and ion-molecule chemistry are considered in a Na chemistry model to simulate the dynamical and chemical coupling processes in the mesosphere and ionosphere above thunderstorms. The enhanced Na layer in the simulation obtained by using the ionospheric observation as input is in agreement with the Na lidar observation. We find that the intensification of metallic layered phenomena above thunderstorms is associated with the atmospheric tides, as a result of the troposphere-mesosphere-ionosphere coupling.
On the emergence of conductivity at SrTiO3-based oxide interfaces – an in-situ study
Authors: von Soosten Merlin , Christensen Dennis. V. , Eom Chang-Beom , Jespersen Thomas. S. , Chen Yunzhong , Pryds Nini 
Published: November 2019

AbstractHeterostructures and crystal interfaces play a major role in state-of-the-art semiconductor devices and play a central role in the field of oxide electronics. In oxides the link between the microscopic properties of the interfaces and bulk properties of the resulting heterostructures challenge our fundamental understanding. Insights on the early growth stage of interfaces and its influence on resulting physical properties are scarce - typically the information is inferred from post growth characterization. Here, we report on real time measurements of the transport properties of SrTiO3-based heterostructures at room temperature, while the heterostructure is forming. Surprisingly, we detect a conducting interface already at the initial growth stage, much earlier than the well-established critical thickness limit for observing conductivity ex-situ after sample growth. We investigate how the conductivity depends on various physical processes occurring during pulsed laser depositions, including light illumination, particle bombardment by the plasma plume, interactions with the atmosphere and oxygen migration from SrTiO3 to the thin films of varying compositions. We conclude that the conductivity in these room-temperature grown interfaces stem from oxygen vacancies with a concentration determined primarily by a balance between vacancy formation through particle bombardment and interfacial redox reaction and vacancy annihilation through oxidation. Using this approach, we propose a new design tool to control the electrical properties of interfaces in real time during their formation.
Identification of Acinetobacter baumannii and its carbapenem-resistant gene blaOXA-23-like by multiple cross displacement amplification combined with lateral flow biosensor
Authors: Hu Shoukui , Niu Lina , Zhao Fan , Yan Linlin , Nong Jinqing , Wang Chunmei , Gao Naishu , Zhu Xiaoxue , Wu Lei , Bo Tianhui , Wang Hongyu , Gu Jin 
Published: November 2019

AbstractAcinetobacter baumannii is a frequent cause of the nosocomial infections. Herein, a novel isothermal amplification technique, multiple cross displacement amplification (MCDA) is employed for detecting all A. baumannii strains and identifying the strains harboring blaOXA-23-like gene. The duplex MCDA assay, which targets the pgaD and blaOXA-23-like genes, could identify the A. baumannii isolates and differentiate these isolates harboring blaOXA-23-like gene. The disposable lateral flow biosensors (LFB) were used for analyzing the MCDA products. A total of sixty-eight isolates, include fifty-three A. baumannii strains and fifteen non-A. baumannii strains, were employed to optimize MCDA methods and determine the sensitivity, specificity and feasibility. The optimal reaction condition is found to be 63 °C within 1 h, with limit of detection at 100 fg templates per tube for pgaD and blaOXA-23-like genes in pure cultures. The specificity of this assay is 100%. Moreover, the practical application of the duplex MCDA-LFB assay was evaluated using clinical samples, and the results obtained from duplex MCDA-LFB method were consistent with conventional culture-based technique. In sum, the duplex MCDA-LFB assay appears to be a reliable, rapid and specific technique to detect all A. baumannii strains and identify these strains harboring blaOXA-23-like gene for appropriate antibiotic therapy.
Dengue infection in mice inoculated by the intracerebral route: neuropathological effects and identification of target cells for virus replication
Authors: Amorim J. F. S. , Azevedo A. S. , Costa S. M. , Trindade G. F. , Basílio-de-Oliveira C. A. , Gonçalves A. J. S. , Salomão N. G. , Rabelo K. , Amaral R. , Geraldo L. H. M. , Lima F. R. S. , Mohana-Borges R. , Paes M. V. , Alves A. M. B. 
Published: November 2019

AbstractDengue is an important arboviral infection, causing a broad range symptom that varies from life-threatening mild illness to severe clinical manifestations. Recent studies reported the impairment of the central nervous system (CNS) after dengue infection, a characteristic previously considered as atypical and underreported. However, little is known about the neuropathology associated to dengue. Since animal models are important tools for helping to understand the dengue pathogenesis, including neurological damages, the aim of this work was to investigate the effects of intracerebral inoculation of a neuroadapted dengue serotype 2 virus (DENV2) in immunocompetent BALB/c mice, mimicking some aspects of the viral encephalitis. Mice presented neurological morbidity after the 7thday post infection. At the same time, histopathological analysis revealed that DENV2 led to damages in the CNS, such as hemorrhage, reactive gliosis, hyperplastic and hypertrophied microglia, astrocyte proliferation, Purkinje neurons retraction and cellular infiltration around vessels in the pia mater and in neuropil. Viral tropism and replication were detected in resident cells of the brain and cerebellum, such as neurons, astrocyte, microglia and oligodendrocytes. Results suggest that this classical mice model might be useful for analyzing the neurotropic effect of DENV with similarities to what occurs in human.
Phosphoproteomic analysis sheds light on intracellular signaling cascades triggered by Formyl-Peptide Receptor 2
Authors: Cattaneo Fabio , Russo Rosita , Castaldo Martina , Chambery Angela , Zollo Cristiana , Esposito Gabriella , Pedone Paolo Vincenzo , Ammendola Rosario 
Published: November 2019

AbstractFormyl peptide receptors (FPRs) belong to the family of seven transmembrane Gi-protein coupled receptors (GPCR). FPR2 is considered the most promiscuous member of this family since it recognizes a wide variety of ligands. It plays a crucial role in several physio-pathological processes and different studies highlighted the correlation between its expression and the higher propensity to invasion and metastasis of some cancers. FPR2 stimulation by its synthetic agonist WKYMVm triggers multiple phosphorylations of intracellular signaling molecules, such as ERKs, PKC, PKB, p38MAPK, PI3K, PLC, and of non-signaling proteins, such as p47phox and p67phox which are involved in NADPH oxidase-dependent ROS generation. Biological effects of FPR2 stimulation include intracellular Ca2+ mobilization, cellular proliferation and migration, and wound healing. A systematic analysis of the phosphoproteome in FPR2-stimulated cells has not been yet reported. Herein, we describe a large-scale phosphoproteomic study in WKYMVm-stimulated CaLu-6 cells. By using high resolution MS/MS we identified 290 differentially phosphorylated proteins and 53 unique phosphopeptides mapping on 40 proteins. Phosphorylations on five selected phospho-proteins were further validated by western blotting, confirming their dependence on FPR2 stimulation. Interconnection between some of the signalling readout identified was also evaluated. Furthermore, we show that FPR2 stimulation with two anti-inflammatory agonists induces the phosphorylation of selected differentially phosphorylated proteins, suggesting their role in the resolution of inflammation. These data provide a promising resource for further studies on new signaling networks triggered by FPR2 and on novel molecular drug targets for human diseases.
Local magnetic flux density measurements for temperature control of transient and non-homogeneous processing of steels
Authors: Sorger Gonçalo , Vilaça Pedro , Santos Telmo G. 
Published: November 2019

AbstractMeasuring temperatures during high-temperature processing of steels is usually limited to surface measurements that cannot directly assess the internal temperature distribution. Here, we demonstrate the feasibility of using a magnetic flux density measurement system to assess transient and non-homogeneous temperature fields in a modern high-strength steel, within the intercritical temperature range where microstructural evolution defines their key mechanical properties. The system accurately detects the Curie temperature and distinguishes temperature change rates within the processed volume. The magnetic measurements are also sensitive to the volume above Curie temperature and its shape, as revealed when integrated with thermal computational simulations. The electromagnetic signal provides real-time qualitative and quantitative information relevant to the metallurgical conditions enabling future intelligent control systems for the production and processing of steels. Contactless measurements of temperature-dependent electromagnetic properties can enable through-thickness temperature monitoring solutions, opening up opportunities for non-destructive full-field imaging of steels during thermal and thermomechanical processing.
Isolation distance between municipal solid waste landfills and drinking water wells for bacteria attenuation and safe drinking
Authors: Xiang Rui , Xu Ya , Liu Yu-Qiang , Lei Guo-Yuan , Liu Jing-Cai , Huang Qi-Fei 
Published: November 2019

AbstractGroundwater pollution and human health risks caused by leachate leakage have become a worldwide environmental problem, and the harm and influence of bacteria in leachate have received increased attention. Setting the isolation distance between landfill sites and groundwater isolation targets is particularly important. Firstly, the intensity model of pollutant leakage source and solute transport model were established for the isolation of pathogenic Escherichia coli. Then, the migration, removal and reduction of bacteria in the aerated zone and ground were simulated. Finally, the isolation distance was calculated based on the acceptable water quality limits, and the influence of hydrogeological arameters was analyzed based on the parameter uncertainty. The results of this study suggest that the isolation distances vary widely ranging from 106 m–5.46 km in sand aquifers, 292 m–13.5 km in gravel aquifers and 2.4–58.7 km in coarse gravel aquifers. The gradient change of groundwater from 0.001 to 0.05 resulted in the isolation distance at the highest gradient position being 2–30 times greater than that at the lowest gradient position. There was a difference in the influence of the thickness of the vadose zone. For example, under the same conditions, with the increase of the thickness of the aeration zone, the isolation distance will be reduced by 1.5–5 times, or under the same thickness of the aeration zone, the isolation distance will be significantly shortened. Accordingly, this needs to be determined based on specific safety isolation requirements. In conclusion, this research has important guiding significance for the environmental safety assessment technology of municipal solid waste landfill.
Predicting novel genomic regions linked to genetic disorders using GWAS and chromosome conformation data – a case study of schizophrenia
Authors: Buxton Daniel S. , Batten Declan J. , Crofts Jonathan J. , Chuzhanova Nadia 
Published: November 2019

AbstractGenome-wide association studies identified numerous loci harbouring single nucleotide polymorphisms (SNPs) associated with various human diseases, although the causal role of many of them remains unknown. In this paper, we postulate that co-location and shared biological function of novel genes with genes known to associate with a specific phenotype make them potential candidates linked to the same phenotype (“guilt-by-proxy”). We propose a novel network-based approach for predicting candidate genes/genomic regions utilising the knowledge of the 3D architecture of the human genome and GWAS data. As a case study we used a well-studied polygenic disorder ‒ schizophrenia ‒ for which we compiled a comprehensive dataset of SNPs. Our approach revealed 634 novel regions covering ~398 Mb of the human genome and harbouring ~9000 genes. Using various network measures and enrichment analysis, we identified subsets of genes and investigated the plausibility of these genes/regions having an association with schizophrenia using literature search and bioinformatics resources. We identified several genes/regions with previously reported associations with schizophrenia, thus providing proof-of-concept, as well as novel candidates with no prior known associations. This approach has the potential to identify novel genes/genomic regions linked to other polygenic disorders and provide means of aggregating genes/SNPs for further investigation.
Label fusion method combining pixel greyscale probability for brain MR segmentation
Authors: Wang Monan , Li Pengcheng 
Published: November 2019

AbstractMulti-atlas-based segmentation (MAS) methods have demonstrated superior performance in the field of automatic image segmentation, and label fusion is an important part of MAS methods. In this paper, we propose a label fusion method that incorporates pixel greyscale probability information. The proposed method combines the advantages of label fusion methods based on sparse representation (SRLF) and weighted voting methods using patch similarity weights (PSWV) and introduces pixel greyscale probability information to improve the segmentation accuracy. We apply the proposed method to the segmentation of deep brain tissues in challenging 3D brain MR images from publicly available IBSR datasets, including images of the thalamus, hippocampus, caudate, putamen, pallidum and amygdala. The experimental results show that the proposed method has higher segmentation accuracy and robustness than the related methods. Compared with the state-of-the-art methods, the proposed method obtains the best putamen, pallidum and amygdala segmentation results and hippocampus and caudate segmentation results that are similar to those of the comparison methods.