bluuebunny/crossref_metadata_2025_split huggingface dataset:
An objective comparison of detection and segmentation algorithms for artefacts in clinical endoscopy
Authors: Ali Sharib , Zhou Felix , Braden Barbara , Bailey Adam , Yang Suhui , Cheng Guanju , Zhang Pengyi , Li Xiaoqiong , Kayser Maxime , Soberanis-Mukul Roger D. , Albarqouni Shadi , Wang Xiaokang , Wang Chunqing , Watanabe Seiryo , Oksuz Ilkay , Ning Qingtian , Yang Shufan , Khan Mohammad Azam , Gao Xiaohong W. , Realdon Stefano , Loshchenov Maxim , Schnabel Julia A. , East James E. , Wagnieres Georges , Loschenov Victor B. , Grisan Enrico , Daul Christian , Blondel Walter , Rittscher Jens 
Published: February 2020

AbstractWe present a comprehensive analysis of the submissions to the first edition of the Endoscopy Artefact Detection challenge (EAD). Using crowd-sourcing, this initiative is a step towards understanding the limitations of existing state-of-the-art computer vision methods applied to endoscopy and promoting the development of new approaches suitable for clinical translation. Endoscopy is a routine imaging technique for the detection, diagnosis and treatment of diseases in hollow-organs; the esophagus, stomach, colon, uterus and the bladder. However the nature of these organs prevent imaged tissues to be free of imaging artefacts such as bubbles, pixel saturation, organ specularity and debris, all of which pose substantial challenges for any quantitative analysis. Consequently, the potential for improved clinical outcomes through quantitative assessment of abnormal mucosal surface observed in endoscopy videos is presently not realized accurately. The EAD challenge promotes awareness of and addresses this key bottleneck problem by investigating methods that can accurately classify, localize and segment artefacts in endoscopy frames as critical prerequisite tasks. Using a diverse curated multi-institutional, multi-modality, multi-organ dataset of video frames, the accuracy and performance of 23 algorithms were objectively ranked for artefact detection and segmentation. The ability of methods to generalize to unseen datasets was also evaluated. The best performing methods (top 15%) propose deep learning strategies to reconcile variabilities in artefact appearance with respect to size, modality, occurrence and organ type. However, no single method outperformed across all tasks. Detailed analyses reveal the shortcomings of current training strategies and highlight the need for developing new optimal metrics to accurately quantify the clinical applicability of methods.
Coherent control of Optical limiting in atomic systems
Authors: Ghaderi Goran Abad Mohsen , Mahdieh Mahsa , Veisi Mohadeseh , Nadjari Hamid , Mahmoudi Mohammad 
Published: February 2020

AbstractGeneration and control of the reverse saturable absorption (RSA) and optical limiting (OL) are investigated in a four-level Y-type quantum system. It is demonstrated that the applied laser fields induce the RSA and it can be coherently controlled by either intensity or frequency of the applied laser fields. The effect of the static magnetic field on the induced RSA is studied and we obtain that it has a constructive role in determining the intensity range in which the OL is established in the system. In addition, we find that the transmission of the suggested optical limiter can be decreased either by increasing the length of the medium or by getting the atomic system denser. Finally, the Z-scan technique is presented to confirm our theoretical results. The proposed scheme can be used in designing the coherent optical limiters with controllable threshold and intensity range of the OL.
Nitrogen Incorporated Photoactive Brownmillerite Ca2Fe2O5 for Energy and Environmental Applications
Authors: Vavilapalli Durga Sankar , Banik Soma , Peri Raja Gopal , B. Muthuraaman , Miryala Muralidhar , Murakami Masato , Alicja Klimkowicz , K. Asokan , M. S. Ramachandra Rao , Singh Shubra 
Published: February 2020

AbstractCa2Fe2O5 (CFO) is a potentially viable material for alternate energy applications. Incorporation of nitrogen in Ca2Fe2O5 (CFO-N) lattice modifies the optical and electronic properties to its advantage. Here, the electronic band structures of CFO and CFO-N were probed using Ultraviolet photoelectron spectroscopy (UPS) and UV-Visible spectroscopy. The optical bandgap of CFO reduces from 2.21 eV to 2.07 eV on post N incorporation along with a clear shift in the valence band of CFO indicating the occupation of N 2p levels over O 2p in the valence band. Similar effect is also observed in the bandgap of CFO, which is tailored upto 1.43 eV by N+ ion implantation. The theoretical bandgaps of CFO and CFO-N were also determined by using the Density functional theory (DFT) calculations. The photoactivity of these CFO and CFO-N was explored by organic effluent degradation under sunlight. The feasibility of utilizing CFO and CFO-N samples for energy storage applications were also investigated through specific capacitance measurements. The specific capacitance of CFO is found to increase to 224.67 Fg−1 upon N incorporation. CFO-N is thus found to exhibit superior optical, catalytic as well as supercapacitor properties over CFO expanding the scope of brownmillerites in energy and environmental applications.
Bioevaluation of superparamagnetic iron oxide nanoparticles (SPIONs) functionalized with dihexadecyl phosphate (DHP)
Authors: Mieloch Adam Aron , Żurawek Magdalena , Giersig Michael , Rozwadowska Natalia , Rybka Jakub Dalibor 
Published: February 2020

AbstractSuperparamagnetic iron oxide nanoparticles (SPIONs) have been investigated for wide variety of applications. Their unique properties render them highly applicable as MRI contrast agents, in magnetic hyperthermia or targeted drug delivery. SPIONs surface properties affect a whole array of parameters such as: solubility, toxicity, stability, biodistribution etc. Therefore, progress in the field of SPIONs surface functionalization is crucial for further development of therapeutic or diagnostic agents. In this study, SPIONs were synthesized by thermal decomposition of iron (III) acetylacetonate Fe(acac)3 and functionalized with dihexadecyl phosphate (DHP) via phase transfer. Bioactivity of the SPION-DHP was assessed on SW1353 and TCam-2 cancer derived cell lines. The following test were conducted: cytotoxicity and proliferation assay, reactive oxygen species (ROS) assay, SPIONs uptake (via Iron Staining and ICP-MS), expression analysis of the following genes: alkaline phosphatase (ALPL); ferritin light chain (FTL); serine/threonine protein phosphatase 2A (PP2A); protein tyrosine phosphatase non-receptor type 11 (PTPN11); transferrin receptor 1 (TFRC) via RT-qPCR. SPION-DHP nanoparticles were successfully obtained and did not reveal significant cytotoxicity in the range of tested concentrations. ROS generation was elevated, however not correlated with the concentrations. Gene expression profile was slightly altered only in SW1353 cells.
Alteration in the potential of sediment phosphorus release along series of rubber dams in a typical urban landscape river
Authors: Bao Linlin , Li Xuyong , Su Jingjun 
Published: February 2020

AbstractRubber dams are widely used for landscaping in urban rivers and they retain large amounts of sediments. The sediments are rich in phosphorus (P) which can cause river eutrophication. Little is known about P release in rubber dams. We investigated the potential of sediment P release by isotherm experiment in an urban river with 30 rubber dams of northern China. We found that the potential of sediment P release (percentage saturation of zero equilibrium P concentration, EPCsat) was 76% at natural river part above dams, and then decreased to 67% at the 4th dam because of high deposition of fine sediments within the upper 4 dams. Between the 5th and the 30th dams, EPCsat increased to 90% because of the decrease of fine sediments and water soluble reactive P. EPCsat was also significantly higher (p < 0.05) in April and August than in November. The results suggest that the potential of sediment P release in this dammed river was mainly controlled by sediment grain size and biological effects. Therefore, management strategies for dammed rivers should focus on reducing P inputs and improving the hydraulic conditions.
Variability in estimated gene expression among commonly used RNA-seq pipelines
Authors: Arora Sonali , Pattwell Siobhan S. , Holland Eric C. , Bolouri Hamid 
Published: February 2020

AbstractRNA-sequencing data is widely used to identify disease biomarkers and therapeutic targets using numerical methods such as clustering, classification, regression, and differential expression analysis. Such approaches rely on the assumption that mRNA abundance estimates from RNA-seq are reliable estimates of true expression levels. Here, using data from five RNA-seq processing pipelines applied to 6,690 human tumor and normal tissues, we show that nearly 88% of protein-coding genes have similar gene expression profiles across all pipelines. However, for >12% of protein-coding genes, current best-in-class RNA-seq processing pipelines differ in their abundance estimates by more than four-fold when applied to exactlythe same samplesandthe same setof RNA-seq reads. Expression fold changes are similarly affected. Many of the impacted genes are widely studied disease-associated genes. We show that impacted genes exhibit diverse patterns of discordance among pipelines, suggesting that many inter-pipeline differences contribute to overall uncertainty in mRNA abundance estimates. A concerted, community-wide effort will be needed to develop gold-standards for estimating the mRNA abundance of the discordant genes reported here. In the meantime, our list of discordantly evaluated genes provides an important resource for robust marker discovery and target selection.
A Microbial Signature Identifies Advanced Fibrosis in Patients with Chronic Liver Disease Mainly Due to NAFLD
Authors: Dong Tien S. , Katzka William , Lagishetty Venu , Luu Kayti , Hauer Meg , Pisegna Joseph , Jacobs Jonathan P. 
Published: February 2020

AbstractThe presence of advanced fibrosis is an important measure of the severity of chronic liver disease. Prior works that have examined the gut microbiome as a novel biomarker for advanced fibrosis have only examined patients with nonalcoholic fatty liver disease. Therefore, our goal was to examine the gut microbiome across varying etiologies of liver disease to create a predictive model for liver fibrosis based upon a microbial signature. Stool samples were obtained from patients with chronic liver disease (n = 50) undergoing FibroScan (ultrasound elastography) at the VA Greater Los Angeles Healthcare System. Healthy control patients (n = 25) were also recruited as a reference population. Fecal samples underwent 16S ribosomal RNA sequencing. Using differentially abundant microbes, a random forest classifier model was created to distinguish advanced fibrosis from mild/moderate fibrosis. The findings were then validated in a separate cohort of chronic liver disease patients (n = 37). Etiologies for liver disease included non-alcoholic liver disease (58.0%), hepatitis C (26.0%), hepatitis B (10.0%), and alcohol (6.0%). Microbiome composition was distinct in liver patients with advanced fibrosis compared to those with minimal fibrosis and healthy controls (p = 0.003). In multivariate negative binomial modeling, 26 bacterial taxa were differentially abundant in patients with advanced fibrosis as compared to those with minimal/moderate fibrosis (q-value < 0.05). A random forests classifier based on these taxa had an AUROC of 0.90 to predict advanced fibrosis. Prevotella copri, which was enriched in patients with advanced fibrosis, was the most strongly predictive microbe in the classifier. The classifier had an AUROC of 0.82 for advanced fibrosis in the validation cohort and Prevotella copri remained the strongest predictive microbe for advanced fibrosis. There is a distinct microbial signature for patients with advanced fibrosis independent of liver disease etiology and other comorbidities. These results suggest that microbial profiles can be used as a non-invasive marker for advanced fibrosis and support the hypothesis that microbes and their metabolites contribute to hepatic fibrosis.
Characteristics of Atrial Fibrillation Patients Suffering Esophageal Injury Caused by Ablation for Atrial Fibrillation
Authors: Zhang Pei , Zhang Yue-Yue , Ye Qian , Jiang Ru-Hong , Liu Qiang , Ye Yang , Wu Jia-Guo , Sheng Xia , Fu Guo-Sheng , Cha Yong-Mei , Jiang Chen-Yang 
Published: February 2020

AbstractThe close proximity of esophagus to the left atrial posterior wall predisposes esophagus to thermal injury during catheter ablation for atrial fibrillation (AF). In this retrospective study, we aimed to investigate risk factors of esophageal injury (EI) caused by catheter ablation for AF. Patients who underwent first-time AF ablation from July 2013 to June 2018 were included. The esophagus was visualized by oral soluble contrast during ablation for all patients and a subset of patients were selected to undergo endoscopic ultrasonography (EUS) to estimate EI post ablation. Degree of EI was categorized as Kansas City classification: type 1: erythema; type 2: ulcers (2a: superficial ulcers; 2b: deep ulcers); type 3: perforation (3a: perforation without communication with the atria; 3b: atrioesophageal fistula [AEF]). Of 3,852 patients, 236 patients (61.5 ± 9.7 years; male, 69%) received EUS (EUS group) and 3616 (63.2 ± 10.9 years; male, 61.1%) without EUS (No-EUS group). In EUS group, EI occurred in 63 patients (type 1 EI in 35 and type 2 EI in 28), and no type 3 EI was observed during follow up. In a multivariable logistic regression analysis, an overlap between the ablation lesion and esophagus was an independent predictor of EI (odds ratio, 21.2; 95% CI: 6.23–72.0; P < 0.001). In No-EUS group, esophagopericardial fistula (EPF; n = 3,0.08%) or AEF (n = 2,0.06%) was diagnosed 4–37 days after ablation. In 3 EPF patients, 2 completely recovered with conservative management and 1 died. Two AEF patients died. Ablation at the vicinity of the esophagus predicts risk of EI. EUS post ablation may prevent the progression of EI and should be considered in management of EI. It remains challenging to identify patients with high risk of EI.
Fabrication of triboelectric nanogenerators based on electrospun polyimide nanofibers membrane
Authors: Kim Yeongjun , Wu Xinwei , Oh Je Hoon 
Published: February 2020

AbstractSurface modification of polyimides (PIs) using electrospinning would significantly improve the performance of TENGs because of the larger surface area of the electrospun friction layer. However, PIs generally have high solvent resistance, so it is complicated to convert them into nanofibers using electrospinning process. This study aims to fabricate PI nanofibers via simple, one-step electrospinning and utilize them as a friction layer of TENGs for better performance. PI nanofibers were directly electrospun from PI ink made of polyimide powder without any additional process. The effect of PI concentration on spinnability was investigated. Uniform and continuous nanofibrous structures were successfully produced at concentrations of 15 wt% and 20 wt%. Electrospun PI nanofibers were then utilized as a friction layer for TENGs. A TENG with 20 wt% produced an open circuit voltage of 753 V and a short circuit current of 10.79 μA and showed a power density of 2.61 W m−2 at a 100 MΩ load resistance. During tapping experiment of 10,000 cycles, the TENG could stably harvest electrical energy. The harvested energy from the proposed TENG is sufficient to illuminate more than 55 LEDs and drive small electronic devices, and the TENGs exhibit excellent performance as a wearable energy harvester.
Recurrent gene duplication in the angiosperm tribe Delphinieae (Ranunculaceae) inferred from intracellular gene transfer events and heteroplasmic mutations in the plastid matK gene
Authors: Park Seongjun , An Boram , Park SeonJoo 
Published: February 2020

AbstractThe study of intracellular gene transfer may allow for the detection of interesting evolutionary processes such as ancient polyploidization. We compared 24 plastid genomes (plastomes) from tribe Delphinieae, one from tribe Nigelleae and one from tribe Ranunculeae, including five newly sequenced genomes. The functional transfers of the plastids rpl32 and rps16 to the nucleus in tribe Delphinieae were identified. Unexpectedly, we discovered multiple divergent copies of the nuclear-encoded plastid rpl32 in the genus Aconitum. Phylogenetic and synonymous substitution rate analyses revealed that the nuclear-encoded plastid rpl32 underwent two major duplication events. These ancient gene duplication events probably occurred via multiple polyploidization events in Aconitum between 11.9 and 24.7 Mya. Furthermore, our sequence rate analysis indicated that the eight plastid-encoded rpl subunits in Aconitum had a significantly accelerated evolutionary rate compared to those in other genera, suggesting that highly divergent paralogs targeted to the plastid may contribute to an elevated rate of evolution in plastid rpl genes. In addition, heteroplasmy of the plastid matK from two Aconitum species suggested the existence of potentially functional plastid maturases in its plastome. Our results provide insight into the evolutionary history of the tribe Delphinieae.
Study of electric conduction mechanisms in bismuth silicate nanofibers
Authors: Batool S. S. , Imran Z. , Rasool Kamran , Ambreen Jaweria , Hassan Safia , Arif Saira , Ahmad Mushtaq , Rafiq M. A. 
Published: February 2020

AbstractThis work represents the nature of conduction mechanism in bismuth silicate (BiSiO) nanofibers as a function of temperature and frequency. Scanning electron micrographs and X-rays diffraction patterns exhibited the formation of cubic phases of Bi4(SiO4)3 and Bi12SiO20 nanofibers respectively with an average diameter of ~200 nm. Temperature dependent (300 K–400 K) electrical characterization of fibers was carried out in frequency range of ~20 Hz–2 MHz. The complex impedance analysis showed contribution from bulk and intergranular parts of nanofibers in conduction. Moreover, analysis of the Cole-Cole plot confirmed the space charge dependent behavior of BiSiO nanofibers. Two types of relaxation phenomena were observed through Modulus analysis. In ac conductivity curve, step like feature of plateau and dispersive regions were described by Maxwell-Wagner effect while the dc part obeyed the Arrhenius law. However, frequency dependent ac conductivity revealed the presence of conduction mechanism in diverse regions that was ascribed to large polaron tunneling model. Detailed analysis of complex Impedance and ac conductivity measurement showed negative temperature coefficient of resistance for the BiSiO nanofibers. Current-voltage (IV) characteristics represented ohmic conduction; followed by space charge limited current conduction at intermediate voltages. Results from both ac and dc measurements were in good agreement with each other.
Identification and validation of reference genes for RT-qPCR normalization in wheat meiosis
Authors: Garrido José , Aguilar Miguel , Prieto Pilar 
Published: February 2020

AbstractMeiosis is a specialized type of cell division occurring in sexually reproducing organisms to generate haploid cells known as gametes. In flowering plants, male gametes are produced in anthers, being encased in pollen grains. Understanding the genetic regulation of meiosis key events such as chromosome recognition and pairing, synapsis and recombination, is needed to manipulate chromosome associations for breeding purposes, particularly in important cereal crops like wheat. Reverse transcription-quantitative PCR (RT-qPCR) is widely used to analyse gene expression and to validate the results obtained by other transcriptomic analyses, like RNA-seq. Selection and validation of appropriate reference genes for RT-qPCR normalization is essential to obtain reproducible and accurate expression data. In this work, twelve candidate reference genes were evaluated using the mainstream algorithms geNorm, Normfinder, BestKeeper and ΔCt, then ranked from most to least suitable for normalization with RefFinder. Different sets of reference genes were recommended to normalize gene expression data in anther meiosis of bread and durum wheat, their corresponding genotypes in the absence of the Ph1 locus and for comparative studies among wheat genotypes. Comparisons between meiotic (anthers) and somatic (leaves and roots) wheat tissues were also carried out. To the best of our knowledge, our study provides the first comprehensive list of reference genes for robust RT-qPCR normalization to study differentially expressed genes during male meiosis in wheat in a breeding framework.
Temporal-Spatial Analysis of the Warming Effect of Different Cultivated Land Urbanization of Metropolitan Area in China
Authors: Li Jiayang , Zhang Chunxiao , Zheng Xinqi , Chen Youmin 
Published: February 2020

AbstractThe regional warming effect is different when different cultivated land types are converted into urban construction land, while its temporal and spatial changes are unclear. We studied the temporal and spatial changes in the warming effect when dry land was converted to urban land (DL2UBL), and irrigated land to urban land (IL2UBL) in Yangtze River Delta (CSJ), Beijing-Tianjin- Hebei (JJJ) and Chengdu-Chongqing (CY) metropolitan areas from 2000 to 2015. The average warming effect of the three metropolitan areas was more intensive in DL2UBL than in IL2UBL in winter, and opposite occurred in summer. The diurnal warming changes between them were small during the day, but obvious at night, which corresponds to the diurnal change of the latent heat of evaporation. Due to the difference in the spatial distribution of humidity, to the north of 34°N, the warming effect of DL2UBL was stronger than that of IL2UBL, and to the south of 34°N, it was stronger for IL2UBL, while from west to east, the warming trend of DL2UBL and IL2UBL keep pace and decline slightly. The influence in planetary boundary layer was also analyzed. We hope that our findings provide scientific support for future metropolitan land use decisions associated with tradeoffs.
Dietary AGEs involvement in colonic inflammation and cancer: insights from an in vitro enterocyte model
Authors: Geicu Ovidiu I. , Stanca Loredana , Voicu Sorina N. , Dinischiotu Anca , Bilteanu Liviu , Serban Andreea I. , Calu Valentin 
Published: February 2020

AbstractThe number of colon cancer cases is increasing worldwide, and type II diabetes patients have an increased risk of developing colon cancer. Diet-borne advanced glycation end-products (AGEs) may promote neoplastic transformation; however, the mechanisms involved remain elusive. The present study helped to define the relationship between dietary AGEs and cancer progression. C2BBe1 adenocarcinoma enterocytes were exposed to 200 µg/mL glycated casein (AGEs-Csn) for up to 24 h. AGEs-Csn exposure resulted in increased cell proliferation, maladaptative changes in SOD and CAT activity and moderate levels of hydrogen peroxide (H2O2) intracellular accumulation. AGEs-Csn activated pro-survival and proliferation signalling, such as the phosphorylation of mTOR (Ser2448) and Akt (Ser473). GSK-3β phosphorylation also increased, potentially inducing extracellular matrix remodelling and thus enabling metastasis. Moreover, AGEs-Csn induced MMP-1, -3, -7, -9 and -10 expression and activated MMP-2 and MMP-9, which are regulators of the extracellular matrix and cytokine functions. AGEs-Csn induced inflammatory responses that included extracellular IL-1β at 6 h; time-dependent increases in IL-8; RAGE and NF-κB p65 upregulation; and IκB inhibition. Co-treatment with anti-RAGE or anti-TNF-α blocking antibodies and AGEs-Csn partially counteracted these changes; however, IL-8, MMP-1 and -10 expression and MMP-9 activation were difficult to prevent. AGEs-Csn perpetuated signalling that led to cell proliferation and matrix remodelling, strengthening the link between AGEs and colorectal cancer aggressiveness.