bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole genome methylation and transcriptome analyses to identify risk for cerebral palsy (CP) in extremely low gestational age neonates (ELGAN)
Authors: Massaro An N. , Bammler Theo K. , MacDonald James W. , Perez Krystle M. , Comstock Bryan , Juul Sandra E. 
Published: March 2021

AbstractPreterm birth remains the leading identifiable risk factor for cerebral palsy (CP), a devastating form of motor impairment due to developmental brain injury occurring around the time of birth. We performed genome wide methylation and whole transcriptome analyses to elucidate the early pathogenesis of CP in extremely low gestational age neonates (ELGANs). We evaluated peripheral blood cell specimens collected during a randomized trial of erythropoietin for neuroprotection in the ELGAN (PENUT Trial, NCT# 01378273). DNA methylation data were generated from 94 PENUT subjects (n = 47 CP vs. n = 47 Control) on day 1 and 14 of life. Gene expression data were generated from a subset of 56 subjects. Only one differentially methylated region was identified for the day 1 to 14 change between CP versus no CP, without evidence for differential gene expression of the associated gene RNA Pseudouridine Synthase Domain Containing 2. iPathwayGuide meta-analyses identified a relevant upregulation of JAK1 expression in the setting of decreased methylation that was observed in control subjects but not CP subjects. Evaluation of whole transcriptome data identified several top pathways of potential clinical relevance including thermogenesis, ferroptossis, ribosomal activity and other neurodegenerative conditions that differentiated CP from controls.
Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birds
Authors: Voukali Eleni , Veetil Nithya Kuttiyarthu , Němec Pavel , Stopka Pavel , Vinkler Michal 
Published: March 2021

AbstractCerebrospinal fluid (CSF) proteins regulate neurogenesis, brain homeostasis and participate in signalling during neuroinflammation. Even though birds represent valuable models for constitutive adult neurogenesis, current proteomic studies of the avian CSF are limited to chicken embryos. Here we use liquid chromatography–tandem mass spectrometry (nLC-MS/MS) to explore the proteomic composition of CSF and plasma in adult chickens (Gallus gallus) and evolutionarily derived parrots: budgerigar (Melopsittacus undulatus) and cockatiel (Nymphicus hollandicus). Because cockatiel lacks a complete genome information, we compared the cross-species protein identifications using the reference proteomes of three model avian species: chicken, budgerigar and zebra finch (Taeniopygia guttata) and found the highest identification rates when mapping against the phylogenetically closest species, the budgerigar. In total, we identified 483, 641 and 458 unique proteins consistently represented in the CSF and plasma of all chicken, budgerigar and cockatiel conspecifics, respectively. Comparative pathways analyses of CSF and blood plasma then indicated clusters of proteins involved in neurogenesis, neural development and neural differentiation overrepresented in CSF in each species. This study provides the first insight into the proteomics of adult avian CSF and plasma and brings novel evidence supporting the adult neurogenesis in birds.
Prediction of the histology of colorectal neoplasm in white light colonoscopic images using deep learning algorithms
Authors: Choi Seong Ji , Kim Eun Sun , Choi Kihwan 
Published: March 2021

AbstractThe treatment plan of colorectal neoplasm differs based on histology. Although new endoscopic imaging systems have been developed, there are clear diagnostic thresholds and requirements in using them. To overcome these limitations, we trained convolutional neural networks (CNNs) with endoscopic images and developed a computer-aided diagnostic (CAD) system which predicts the pathologic histology of colorectal adenoma. We retrospectively collected colonoscopic images from two tertiary hospitals and labeled 3400 images into one of 4 classes according to the final histology: normal, low-grade dysplasia, high-grade dysplasia, and adenocarcinoma. We implemented a CAD system based on ensemble learning with three CNN models which transfer the knowledge learned from common digital photography images to the colonoscopic image domain. The deep learning models were trained to classify the colorectal adenoma into these 4 classes. We compared the outcomes of the CNN models to those of two endoscopist groups having different years of experience, and visualized the model predictions using Class Activation Mapping. In our multi-center study, our CNN-CAD system identified the histology of colorectal adenoma with as sensitivity 77.25%, specificity of 92.42%, positive predictive value of 77.16%, negative predictive value of 92.58% averaged over the 4 classes, and mean diagnostic time of 0.12 s per image. Our experiments demonstrate that the CNN-CAD showed a similar performance to that of endoscopic experts and outperformed that of trainees. The model visualization results also showed reasonable regions of interest to explain the classification decisions of CAD systems. We suggest that CNN-CAD system can predict the histology of colorectal adenoma.
Design of micromagnetic arrays for on-chip separation of superparamagnetic bead aggregates and detection of a model protein and double-stranded DNA analytes
Authors: Rampini Stefano , Li Peng , Gandhi Dhruv , Mutas Marina , Ran Ying Fen , Carr Michael , Lee Gil U. 
Published: March 2021

AbstractMagnetically actuated lab-on-a-chip (LOC) technologies have enabled rapid, highly efficient separation of specific biomarkers and cells from complex biological samples. Nonlinear magnetophoresis (NLM) is a technique that uses a microfabricated magnet array (MMA) and a time varying external magnetic field to precisely control the transport of superparamagnetic (SPM) beads on the surface of a chip based on their size and magnetization. We analyze the transport and separation behavior of SPM monomers and dimers on four MMA geometries, i.e., circular, triangular, square and rectangular shaped micromagnets, across a range of external magnetic field rotation frequencies. The measured critical frequency of the SPM beads on an MMA, i.e., the velocity for which the hydrodynamic drag on a bead exceeds the magnetic force, is closely related to the local magnetic flux density landscape on a micromagnet in the presence of an external magnetic field. A set of design criteria has been established for the optimization of MMAs for NLM separation, with particular focus on the shape of the micromagnets forming the array. The square MMA was used to detect a model protein biomarker and gene fragment based on a magnetic bead assembly (MBA) assay. This assay uses ligand functionalized SPM beads to capture and directly detect an analyte through the formation of SPM bead aggregates. These beads aggregates were detected through NLM separation and microscopic analysis resulting in a highly sensitive assay that did not use carrier fluid.
Tear film break-up patterns in thyroid eye disease
Authors: Takahashi Yasuhiro , Lee Patricia Ann L. , Vaidya Aric , Kono Shinjiro , Kakizaki Hirohiko 
Published: March 2021

AbstractEvaluation of tear film break-up pattern (TFBUP) is the main diagnostic method for tear film-oriented therapy (TFOT) of dry eye. This prospective, observational study examined TFBUPs in 154 eyes/sides from 78 patients with thyroid eye disease (TED) who met the diagnostic criteria for dry eye in Japan. TFBUPs were classified as area, line, spot, dimple, and random breaks. Results for the status of TED and dry eye were compared between the TFBUPs. Consequently, line, spot, dimple, and random breaks were observed in 80 (51.9%), 29 (18.8%), 10 (6.5%), and 35 eyes (22.7%) while no eyes showed area breaks. The random break group had the highest incidence of lid lag/Graefe sign and superior limbic keratoconjunctivitis (SLK) (P < 0.050). Although the incidence of each TFBUP is almost equal in patients with simple dry eye without TED, line breaks were more frequently observed in TED. In addition, while random breaks in simple dry eye are usually only associated with minor ocular surface damages, those in TED were associated with a higher incidence of concomitant SLK. These results will be helpful for understanding the etiology of dry eye in TED and for TFOT in TED.
Single-cell differential splicing analysis reveals high heterogeneity of liver tumor-infiltrating T cells
Authors: Liu Shang , Zhou Biaofeng , Wu Liang , Sun Yan , Chen Jie , Liu Shiping 
Published: March 2021

AbstractRecent advances in single-cell RNA sequencing (scRNA-seq) have improved our understanding of the association between tumor-infiltrating lymphocyte (TILs) heterogeneity and cancer initiation and progression. However, studies investigating alternative splicing (AS) as an important regulatory factor of heterogeneity remain limited. Here, we developed a new computational tool, DESJ-detection, which accurately detects differentially expressed splicing junctions (DESJs) between cell groups at the single-cell level. We analyzed 5063 T cells of hepatocellular carcinoma (HCC) and identified 1176 DESJs across 11 T cell subtypes. Interestingly, DESJs were enriched in UTRs, and have putative effects on heterogeneity. Cell subtypes with a similar function closely clustered together at the AS level. Meanwhile, we identified a novel cell state, pre-activation with the isoform markers ARHGAP15-205. In summary, we present a comprehensive investigation of alternative splicing differences, which provided novel insights into T cell heterogeneity and can be applied to other full-length scRNA-seq datasets.
Consistent image processing based on co‐saliency
Authors: Ren Xiangnan , Li Jinjiang , Hua Zhen , Jiang Xinbo 
Published: March 2021

AbstractIn a group of images, the recurrent foreground objects are considered as the key objects in the group of images. In co‐saliency detection, these are described as common saliency objects. The aim is to be able to naturally guide the user's gaze to these common salient objects. By guiding the user's gaze, users can easily find these common saliency objects without interference from other information. Therefore, a method is proposed for reducing user visual attention based on co‐saliency detection. Through the co‐saliency detection algorithm and matting algorithm for image preprocessing, the exact position of non‐common saliency objects (called Region of Interest here, i.e. ROI) in the image group can be obtained. In the attention retargeting algorithm, the internal features of the image to adjust the saliency of the ROI areas are considered. In the HSI colour space, the three components H, S, and I are adjusted separately. First, the hue distribution is constructed by the Dirac kernel function, and then the most similar hue distribution to the surrounding environment is selected as the best hue distribution of ROI areas. The S and I components can be set as the contrast difference between ROI areas and surrounding background areas according to the user's demands. Experimental results show that this method effectively reduces the ROI areas' attraction to the user's visual attention. Moreover, comparing this method with other methods, the saliency adjustment effect achieved is much better, and the processed image is more natural.
Drone assisted device to device cooperative communication for critical environments
Authors: Kumar Pankaj , Darshi Sam , Shailendra Samar 
Published: March 2021

AbstractThis paper proposes drone assisted device‐to‐device cooperative communication (DA‐DDCC) for critical situations during post‐disaster management. The proposed network utilizes the autonomous mode of D2D communication for setting up the link in the absence of a central node. This network incorporates cooperative communication using drone in D2D session for improving reliability of the overall system. A probability‐based statistical channel model for such networks is proposed by taking the statistical independence of links into consideration. Unlike the existing air‐to‐ground (A2G) channel models that use either Rayleigh or Rician distribution for uplink (UL) and downlink (DL) channel modelling, our approach takes the probability of occurrence of line of sight (LoS) into account while predicting the appropriate channel distribution for UL and DL separately. For performance evaluation of the proposed network, average outage probability and average capacity are derived using the proposed channel model. Monte Carlo simulations are conducted to verify our analysis. Moreover, a multi‐cluster DA‐DDCC scenario is also being analyzed through simulations from an interference perspective to justify the usefulness of the proposed channel model. Results obtained through this investigation can be utilized in selecting various crucial system parameters judiciously for enhanced performance during post‐disaster scenario.
Influence of extended grading capacitor for suppressing secondary arc on the transient recovery voltage of multi‐break circuit breaker
Authors: Sun Qiuqin , Xiao Zhibin , Jiang Rong , Zhong Lipeng , Chen She 
Published: March 2021

AbstractThe extended grading capacitor (EGC) is a cost‐effective technique to suppress secondary arc. However, whether the use of EGC would weaken the interrupting capability of circuit breakers (CB) or not is still undetermined. In this work, an equivalent circuit model for ultra‐high voltage transmission line was established. The expressions of transient recovery voltage (TRV) across the contact gap of CB are derived, and hence the rate of rise of recovery voltage (RRRV). Then, a series of simulations have been performed, including the long‐line fault, the short‐line fault (SLF) and the terminal fault. It is found that the RRRV had approximately linear downward trend with the increase of the capacitance of EGC under long‐line fault but had approximately index downward trend under SLF. The SLF poses the strictest requirements to the CB. In addition to suppressing secondary arc current, the use of EGC would mitigate the interrupting severity and enhancing the interrupting performance of CB.
Empirical determination of atomic line parameters of the 1.5 μm spectral region
Authors: Trelles Arjona J. C. , Ruiz Cobo B. , Martínez González M. J. 
Published: March 2021

Context. Both the quality and amount of astrophysical data are steadily increasing over time owing to the improvement of telescopes and their instruments. This requires corresponding evolution of the techniques used for obtaining and analyzing the resulting data. The infrared spectral range at 1.56 μm usually observed by the GRegor Infrared Spectrograph (GRIS) at the GREGOR solar telescope has a width of around 30 Å and includes at least 15 spectral lines. Normally, only a handful of spectral lines (five at most) are used in studies using GRIS because of the lack of atomic parameters for the others. Including more spectral lines may alleviate some of the known ambiguities between solar atmospheric parameters.
Aims. We used high-precision spectropolarimetric data for the quiet Sun at 1.56 μm observed with GRIS on the GREGOR along with the SIR inversion code in order to obtain accurate atomic parameters for 15 spectral lines in this spectral range.
Methods. We used inversion techniques to infer both solar atmospheric models and the atomic parameters of spectral lines which, under the local thermodynamic equilibrium approximation, reproduce spectropolarimetric observations.
Results. We present accurate atomic parameters for 15 spectral lines within the spectral range from 15 644 to 15 674 Å. This spectral range is commonly used in solar studies because it enables the study of the low photosphere. Moreover, the infrared spectral lines are better tracers of the magnetic fields than the optical ones.
Development Cooperation as a Knowledge Creation Process: Rhythmanalytical Approach to a Capacity-Building Project in Zanzibar
Authors: Ojala Minna-Liina , Hooli Lauri 
Published: March 2021

AbstractIn development cooperation, the ideas of material support and instructive teaching have increasingly given way to those of reciprocal collaboration and non-material support. In this research, we explore the potential of rhythmanalysis as an approach to studying complex knowledge creation processes in an international development cooperation project. The Zan-SDI project aimed to enhance the geospatial infrastructure in Zanzibar through cooperation between Finnish and Zanzibarian experts. Our rhythmanalysis shows that knowledge creation in the everyday practices of development cooperation is extremely vulnerable to various distractions on multiple spatio-temporal scales. Continuous learning and efforts are required to sustain the project ensemble and knowledge creation. Although new partnerships and inter-organisational collaboration are a source of novelty and innovation, much of their potential remains unrealised without intensive long-term engagement, possibilities to quickly reform the project scheme, and a sufficient combination of financial, material and non-material support.
Double-layer metasurface for enhanced photon up-conversion
Authors: Manley Phillip , Segantini Michele , Ahiboz Doguscan , Hammerschmidt Martin , Arnaoutakis Georgios , MacQueen Rowan W. , Burger Sven , Becker Christiane 
Published: March 2021

We present a double-layer dielectric metasurface obtained by stacking a silicon nanodisk array and a silicon photonic crystal slab with equal periodicity on top of each other. We focus on the investigation of electric near-field enhancement effects occurring at resonant excitation of the metasurface and study its optical properties numerically and experimentally. We find that the major difference in multi-layer metasurfaces when compared to conventional single-layer structures appears to be in Rayleigh–Wood anomalies: they are split into multiple different modes, which are themselves spectrally broadened. As a proof of concept, we cover a double-layer metasurface with a lanthanide-doped up-conversion particle layer and study its interaction with a 1550 nm photoexcitation. We observe a 2.7-fold enhanced up-conversion photoluminescence by using the stacked metasurface instead of a planar substrate, although only around 1% of the up-conversion material is exposed to enhanced near fields. Two mechanisms are identified explaining this behavior: First, enhanced near fields when exciting the metasurface resonantly, and second, light trapping by total internal reflection in the particle layer when the metasurface redirects light into high angle diffraction orders. These results pave the way for low-threshold and, in particular, broadband photon up-conversion in future solar energy and biosensing applications.
Secondary recrystallization behavior in magnetostrictive Fe-Ga thin sheets induced by nano-sized composite precipitates
Authors: He Zhenghua , Du Hongji , Sha Yuhui , Chen Sihao , Zhang Fang , Chen Lijia , Zuo Liang 
Published: March 2021

Strengthening η texture (⟨001⟩//rolling direction) through secondary recrystallization can significantly improve the magnetostriction coefficient of Fe-Ga thin sheets and expand the use of Fe-Ga alloys in high-frequency applications. However, the secondary recrystallization of Goss texture in Fe-Ga thin sheets deteriorates significantly with the thinning of the sheet thickness under the current inhibitors of micron-sized NbC particles or precipitates. In this paper, a new composite inhibitor system, composed of nano-sized MnS and Nb(C,N) precipitates, is proposed to induce the secondary recrystallization Goss texture in Fe-Ga thin sheets with thicknesses less than 0.3 mm. The density and size of MnS and Nb(C,N) is designed based on the effect of alloy composition and hot rolling parameters on the precipitation kinetics of MnS and Nb(C,N), including the relative nucleation rate-temperature (NrT) and precipitation-time-temperature (PTT) curves. It is found that the stored deformation energy increases the maximum nucleation rate and the fastest precipitation temperature. A large number of lamellar and rectangular precipitates (MnS and Nb(C,N)) with a size of 5∼20 nm were precipitated after hot-rolling at a temperature of 800∼1,050 °C and a total thickness reduction of 80%. These nano-sized inhibitors provide a strong pinning effect for the primary recrystallized grains, and induce abnormal grain growth of Goss grains at an annealing temperature of 950∼1,050 °C. Resultingly, centimeter-sized Goss grains with a small deviation angle and maximum magnetostriction coefficient of 264 ppm are successfully achieved in Fe-Ga alloy thin sheets with a thickness of 0.25 mm.
Corellation of water quality to the prevalence of ectoparasite in milkfish (Chanos chanos) in Sedati District, Sidoarjo
Authors: Irawan H , Kismiyati  , Mahasri G 
Published: March 2021

Abstract
The management of fish aquaculture need to be considered. The poor quality of water can cause fish being easily stressed, so that can lead a disease in fish. This study aims to determine the prevalence of ectoparasites and knows the correlation between ectoparasites prevalence in milkfish, with the quality of the water contained in Sedati District, like Segoro Tambak Village, Banjar Kemuning, and Tambak Cemandi. The method is descriptive method which determined by specific criteria (purposive sampling). The sampling method was random sampling on each farm. The main parameter is water quality, such as temperature, salinity, pH, brightness, dissolved oxygen, and ammonia. Supporting parameters was the clinical symptoms of milkfish. The results showed that one ectoparasite species infested milkfish, namely Chilodonella with 0.2% total prevalence value of the three villages in Sedati District, the highest prevalence was in Tambak Cemandi, the lowest was in Segoro Tambak 0%, the measurement of water quality in the three villages ranged from temperature 26-27°C, salinity 12-22 ppt, pH 8-8.5, brightness 23-28 cm, dissolved oxygen 2-5 mg / L, ammonia 0.03-0.15 mg / L. There is a positive correlation between temperature, salinity, pH, dissolved oxygen, ammonia, and brightness with the prevalence of Chilodonella.
Addition of crude fish oil (CFO) in feed toward fat and energy retention of mud crab (Scylla serrata)
Authors: Hadijah S , Agustono  , Lokapirnasari W P 
Published: March 2021

Abstract
Mud crab (Scylla serrata) is a brackish water organism that has quite big market potential because it has tasty flavour and high nutrition. Natural feed of mud crab is trash fish, one of the example is kuniran fish that has 15.43% of protein, 0.46% of fat, 84.29% of water, and 0.77% of ash. Crab needed 4.8-10.8% fat in feed, but kuniran fish has 0.46% fat, so it needs the additional of fat. Fat is very important to support fish growth rate. Fat is needed as an energy source to maintenace the body and tissue function. Therefore it is needed the addition of fish oil as one of fatty acids source that have 55.8791% ether extract, 10.7173% omega-3 fatty acids EPA, and 7.0108% DHA. The aims is to know the addition of Crude Fish Oil (CFO) in feed affects fat and energy retention of mud crab. The methods was experimental methods with randomly complete design which consists of five treatments and four repetitions. The treatments used 0%, 2%, 4%, 6% and 8% as the addition of CFO in feed. Data analyzed by statistic and descriptive. Result showed that fat and energy retention for each treatments has no significantly different (p>0.05).