bluuebunny/crossref_metadata_2025_split huggingface dataset:
Embedding interactive, three‐dimensional content in portable document format to deliver gross anatomy information and knowledge
Authors: Azkue Jon Jatsu 
Published: May 2021

AbstractThe Portable Document Format (PDF) is likely the most widely used digital file format for scholarly and scientific electronic publishing. Since format specification version 1.6, three‐dimensional (3D) models in Universal 3D (U3D) format can be embedded into PDF files. The present study demonstrates a repertoire of graphic strategies and modes of presentation that exploit the potentials of 3D models embedded in PDF to deliver anatomical information and knowledge. Three‐dimensional models and scenes representing anatomical structures generated by 3D surface scanning or by segmentation from either clinical imaging data or cadaver sectional images were converted into U3D format and then embedded into PDF files using both freely and commercially available software. The relevant steps and required software tools are described. Built‐in tools in Adobe Acrobat and JavaScript scripting both were used to pre‐configure user interaction with 3D contents. Eight successive proof‐of‐concept examples of increasing complexity are presented and provided as supplementary material, including both unannotated and annotated 3D specimens, use of bitmap‐textures, guided navigation through predetermined 3D scenes, 3D animation, and interactive navigation through tri‐planar sectional human cadaver images. Three‐dimensional contents embedded in PDF files are generally comparable to multimedia and dedicated 3D software in terms of quality, flexibility, and convenience, and offer new unprecedented opportunities to deliver anatomical information and knowledge.
WGCNA identification of TLR7 as a novel diagnostic biomarker, progression and prognostic indicator, and immunotherapeutic target for stomach adenocarcinoma
Authors: Yuan Qihang , Zhou Qi , Ren Jie , Wang Guan , Yin Chunlai , Shang Dong , Xia Shilin 
Published: May 2021

AbstractStomach adenocarcinoma (STAD) is a malignant tumor with high histological heterogeneity. However, the potential mechanism of STAD tumorigenesis remains to be elucidated. The purpose of our research was to identify candidate genes associated with the diagnosis, progression, prognosis, and immunotherapeutic targets of STAD. Based on tumor samples from the GSE28541 dataset, weighted gene co‐expression network analysis revealed 16 modules related to STAD stage and grade. The salmon module emerged as the most relevant module (cor = 0.34), and functional enrichment analysis showed that the genes in the salmon were primarily related to major histocompatibility complex, immune response, and cell differentiation. Toll‐like receptor 7 (TLR7) was recognized as the real hub gene in the salmon module. Compared to normal stomach tissues, the transcriptional and translational levels of TLR7 were significantly elevated in STAD. Receiver operating characteristic curves verified that TLR7 displayed remarkable sensitivity and specificity for the diagnosis of STAD. The functions of TLR7 were primarily enriched in the regulation of Toll‐like receptor signaling pathway, pattern recognition receptor signaling pathway, and innate immune response. Overexpression of TLR7 tended to indicate more advanced STAD, higher degree of STAD, and poorer prognosis of STAD. In addition, TLR7 expression was positively correlated with immune cell infiltration and immune checkpoint expression. Somatic copy number alteration of TLR7 was also significantly related to immune cell infiltration. In conclusion, this study revealed the crucial role of TLR7 in STAD and provided new perspectives for the selection of biomarkers, progression and prognosis indicators, and immunotherapeutic targets for STAD.
Alkali‐induced Transformation of Ni‐MOF into Ni(OH)2 Nanostructured Flowers for Efficient Electrocatalytic Methanol Oxidation Reaction
Authors: Li Lanqing , Gao Wei , Lei Min , Wen Dan 
Published: May 2021

AbstractPost treatment of metal‐organic frameworks (MOFs) is widely employed to develop efficient electrocatalysts with better catalytic properties. But the complex processes of post treatment generally led to the collapse of the original structures of MOFs, making the preservation of their pristine hierarchical porous structure a great challenge. Herein, we propose the strategy of alkali treatment of Ni‐MOF to transform it into Ni(OH)2 with similar morphology and enhanced electrocatalytic properties for methanol oxidation reaction (MOR). The structure and electrocatalytic properties of as‐obtained Ni(OH)2 nanostructured flowers were seriously depended on the alkali concentrations. As the result, Ni(OH)2 obtained from Ni‐MOF treated by 0.25 M NaOH (noted as Ni(OH)2‐0.25) performs 1.5 and 2.5 times larger current density than those of Ni(OH)2‐0.025 and Ni(OH)2‐0.5 for MOR. Moreover, the electrocatalytic process and mechanism of MOR on the catalyst of Ni(OH)2‐0.25 are also revealed. Hence, this ex situ conversion strategy of alkali treatment for Ni‐MOF uncovered the transformation of MOFs in alkaline solution and develops robust electrocatalyst for practical application of methanol fuel cells.
New isolate from Salvinia molesta with antioxidant and urease inhibitory activity
Authors: Naheed Nadra , Maher Saima , Saleem Farooq , Khan Ajmal , Wadood Abdul , Rasheed Saima , Choudhary M. Iqbal , Froeyen Matheus , Abdullah Iskandar , Mirza Muhammad Usman , Trant John F. , Ahmad Sarfraz 
Published: May 2021

AbstractUrease plays a significant role in the pathogenesis of urolithiasis pyelonephritis, urinary catheter encrustation, hepatic coma, hepatic encephalopathy, and peptic acid duodenal ulcers. Salvinia molesta was explored to identify new bioactive compounds with particular emphasis on urease inhibitors. The aqueous methanol extract was fractionated using solvents of increasing polarity. A series of column chromatography and later HPLC were performed on butanol extract. The structures of the resulting pure compounds were resolved using NMR (1D and 2D), infrared, and mass spectroscopy. The novel isolate was evaluated for antioxidant activity (using DPPH, superoxide anion radical scavenging, oxidative burst, and Fe+2 chelation assays), anti‐glycation behavior, anticancer activity, carbonic anhydrase inhibition, phosphodiesterase inhibition, and urease inhibition. One new glucopyranose derivative 6′‐O‐(3,4‐dihydroxybenzoyl)‐4′‐O‐(4‐hydroxybenzoyl)‐α/β‐D‐glucopyranoside (1) and four known glycosides were identified. Glycoside 1 demonstrated promising antioxidant potential with IC50 values of 48.2 ± 0.3, 60.3 ± 0.6, and 42.1 ± 1.8 μM against DPPH, superoxide radical, and oxidative burst, respectively. Its IC50 in the Jack bean urease inhibition assay was 99.1 ± 0.8 μM. The mechanism‐based kinetic studies presented that compound 1 is a mixed‐type inhibitor of urease with a Ki value of 91.8 ± 0.1 μM. Finally, molecular dynamic simulations exploring the binding mode of compound 1 with urease provided quantitative agreement between estimated binding free energies and the experimental results. The studies corroborate the use of compound 1 as a lead for QSAR studies as an antioxidant and urease inhibitor. Moreover, it needs to be further evaluated through the animal model, that is, in vivo or tissue culture‐based ex‐vivo studies, to establish their therapeutic potential against oxidative stress phosphodiesterase‐II and urease‐induced pathologies.
Latitudinal embryonic thermal tolerance and plasticity shape the vulnerability of oviparous species to climate change
Authors: Sun Bao‐jun , Ma Liang , Wang Yang , Mi Chun‐rong , Buckley Lauren B. , Levy Ofir , Lu Hong‐liang , Du Wei‐Guo 
Published: May 2021

AbstractHeat tolerance at the immobile embryonic stage is expected to be critical in determining species vulnerability to climate change. However, how the mean and developmental plasticity of embryonic heat tolerance vary geographically, and how these geographic variations affect species' vulnerability under climate change remain unknown. We experimentally determined the mean and developmental plasticity of embryonic acute heat tolerance (EAHT, i.e., heat shock temperature at which embryonic heartbeats ceased) for three latitudinally distributed populations of an oviparous lacertid lizard. The experimental results suggested that the mean EAHT decreased with decreasing latitude and that the reaction norms of EAHT in relation to developmental temperatures showed “flat,” “bell‐shaped,” and “decreasing” patterns at high, medium, and low latitudes, respectively. Based on the means and plasticity of EAHT and weather data across China, we project that the heat stress frequency would increase from the present to the future and increase toward low latitudes. Furthermore, heat stress becomes more extensive with the incorporation of developmental plasticity. Incorporating the mean EAHT during the embryonic development season, heat stress frequency, and climate variables in a species distribution model projects that suitable habitats could move northward in response to ongoing climate change and shrink due to the loss of southern habitat. Moreover, even lizards within the areas that are predicted to remain highly suitable are expected to experience increases in heat stress over time, particularly at medium and low latitudes. Our study reveals geographic variation in the mean and developmental plasticity of EAHT and highlights its importance for predicting species vulnerability and range shifts in response to climate change.
Two heads are not always better than one: Craniofacial and axial bifurcation in cheloniid embryos and hatchlings (Chelonia mydas and Caretta caretta)
Authors: Ingle Danielle N. , Meredith Tricia L. , Perrault Justin R. , Wyneken Jeanette 
Published: May 2021

AbstractMorphological data on craniofacial and axial bifurcation in sea turtles is not well documented in the literature. Here, we use micro‐computed tomography (μ‐CT) imaging to describe the body, skull, and vertebral morphology in axially‐bifurcated cheloniid sea turtle embryos and hatchlings (Chelonia mydas and Caretta caretta) from south Florida beaches. We describe three types of craniofacial and axial bifurcations: bifacial, bicephalic, and bicephalic with biaxial duplication ranging from facial bones to the sacrum. We predicted smaller body dimensions in bifacial and bicephalic embryos and hatchlings compared with their normal counterparts. In addition, we hypothesized that bicephalic individuals would have greater rostral deviation angles than bifacial animals, and that vertebral dimensions would vary between the control and anomalous embryos and hatchlings. Among hatchlings (developmental Stage 31), we found that maximum curved carapace length and curved carapace width were greatest in the control specimens when compared with the anomalous specimens. Overall, we found that rostral deviations were smaller in bifacial animals compared with their bicephalic counterparts. Right and left rostral deviations were symmetrical or nearly symmetrical in all bifacial and bicephalic specimens. Among C. caretta, we found that bicephalic animals had greater standardized vertebral measurements than their bifacial conspecifics. In bifacial animals, bifurcation extended to either the frontal or parietal skull bones, while duplication extended to C5 vertebrae and T8 vertebrae in bicephalic animals. This study provides an in‐depth description of anatomical alterations associated with these abnormalities. Prognosis of these organisms is poor; however, understanding the prevalence of these malformations can allow for better assessments of population health, as numerous environmental factors are known to lead to these changes.
Interdecadal changes of summer precipitation dominant mode over East Asia‐Northwest Pacific around late 1990s
Authors: Li Shuai , Yang Jie , Gong Zhiqiang , Zhao Junhu , Qiao Shaobo , Feng Guolin 
Published: May 2021

AbstractIn this study, we investigate the interdecadal variation characteristics of the dominant mode of summer precipitation over East Asia‐Northwest Pacific (EA‐NWP) before and after late 1990s, reveal the physical mechanism, and address its possible connection with the regional ocean warming background. Study results show that the empirical orthogonal function mode 1 (EOF1) of summer precipitation anomalies over EA‐NWP during the global ocean warming acceleration period (1979–1998) present a more significant dipole pattern between Yangtze River Basin (YRB) and tropical NWP compared with that during the global ocean warming slowdown period (1999–2012). And then we find that the anomalous dipoles of low‐level winds, geopotential height, convection, and associated wave activity fluxes over NWP significantly shift westward (eastward) and enhance (weaken) in 1979–1998 (1999–2012), which are regarded as the direct cause of the adjustment of dipole pattern between YRB and tropical NWP. Further analysis reveals that the negative sea surface temperature (SST) anomalies in the tropical NWP are prominent (not prominent), resulting in the stronger (weaker) Pacific–Japan Teleconnection over Japan and Tropics in NWP during the period 1979–1998 (1999–2012), and ultimately lead to the change of summer precipitation EOF1 in EA‐NWP. By regressing vertical velocity, outgoing longwave radiation, relative vorticity, wave activity fluxes, and precipitation onto the NWP SST in the two periods, the impacts of the SST in the NWP on the interdecadal variation of summer precipitation EOF1 in EA‐NWP are verified. Finally, the mechanism diagram of interdecadal variation of summer precipitation is given, which can be useful for short‐term precipitation prediction of East Asia.
Gut microbiota and its diet‐related activity in children with intestinal failure receiving long‐term parenteral nutrition
Authors: Neelis Esther G. , de Koning Barbara A. E. , Hulst Jessie M. , Papadopoulou Rodanthi , Kerbiriou Caroline , Rings Edmond H. H. M. , Wijnen René M. H. , Nichols Ben , Gerasimidis Konstantinos 
Published: May 2021

AbstractBackgroundThis study characterized gut microbiota and its diet‐related activity in children with intestinal failure (IF) receiving parenteral nutrition (PN) compared with those of healthy controls (HC) and in relation to disease characteristics.MethodsThe fecal microbiota and short‐chain fatty acids (SCFAs) were measured in 15 IF patients (n = 68) and 25 HC (n = 25).ResultsPatients with IF had a lower bacterial load (P = .003), diversity (P < .001), evenness (P < .001) and richness (P = 0.006) than HC. Patients with surgical IF had lower diversity (P < .039) than those with functional IF. Propionic acid and butyric acid (p < .001) were lower and d‐lactate and l‐lactate were higher (p < 0.001) in IF patients than in HC. The energy supplied by PN (%PN) was negatively associated with microbiota diversity and SCFA profile. IF patients had more Escherichia‐Shigella (P = .006), Cronobacter (P = .001), and Staphylococcus (Operational Taxonomic Unit 14, P < .001) and less Faecalibacterium (P < 0.001) and Ruminococcus 1 and 2 (P < .001). Duration of PN (P = .005), %PN (P = .005), and fiber intake (P = .011) were predictive of microbiota structure. Higher intake of enteral nutrition was associated with microbiota structure and function closer to those of HC.ConclusionsMicrobiota composition and its diet‐related function are altered in IF, with depletion of beneficial SCFAs and species and supraphysiological increase of potentially harmful pathobionts. The influence of this compositional and functional microbial dysbiosis on patients’ outcomes and management warrants further exploration.
Label‐free detection of polysulfides and glycogen of Cyanidium caldarium using ultra‐multiplex coherent anti‐Stokes Raman scattering microspectroscopy
Authors: Oka Yuki , Yoshida Masaki , Minoda Ayumi , Leproux Philippe , Watanabe Makoto M. , Kano Hideaki 
Published: May 2021

AbstractLiving microalga Cyanidium caldarium was visualized using ultra‐multiplex coherent anti‐Stokes Raman scattering (CARS) microspectroscopy. The Raman band related to the SO42− ion at 982 cm−1 was detected at the peripheral part of the cells and showed a signal amplitude that was approximately threefold larger than that in the medium, indicating accumulation of SO42− ions. Depending on the incubation conditions, a broad and sharp Raman band at approximately 505 cm−1 was observed at the peripheral part and inside the cells, respectively. Based on comparison of the results with model substances, these broad and sharp bands were assigned to polysulfides and glycogen, respectively.
Sustainable management of paddy crop residues: effects on methanotrophs diversity and value for soil health restoration
Authors: Singh Chhatarpal , Tiwari Shashank , Rai Pradeep Kumar , Singh Jay Shankar 
Published: May 2021

AbstractIn recent years, improved paddy crop varieties, advanced tools and technologies have resulted in a huge quantity of crop residues (CRs) production. Hence, appropriate sustainable management of the paddy CRs produced annually is needed. In this study, a field experiment was conducted to evaluate the impact of rice husk biochar (RHB) amendments on soil physico‐chemical characteristics, methanotrophs diversity, and functionalpmoAgenes numbers in paddy soil. ThepmoAgene (27 kDa) encodes the β‐subunit of the particulate methane monooxygenase (pMMO), an enzyme responsible for methane oxidation found in most of the methanotrophs. A marked variation in methanotrophs diversity, functionalpmoAgenes abundance, and physico‐chemical parameters in paddy soil have been noted across the given amendments. The RHB significantly improves soil physico‐chemical status and enhances methanotrophs community structure and number ofpmoAgene numbers in paddy soils. The various soil physico‐chemical parameters were improved due to RHB + microbial inoculant treatments. Maximum rice grain yield (5.91 ± 0.07 t ha−1) and methanotrophic functionalpmoAgene numbers (57.25 ± 0.88 × 107 g−1paddy soil) were found in the RHB + microbial inoculant treated plot compared to untreated (control) plot. The predominant methanotrophic bacteria identified by the denaturing gradient gel electrophoresis (DGGE) in RHB treated paddy soils wereMethylovulumandMethylobactermembers of the Methylococcaceae family. Consequently, the methanotrophs community study based on DGGE analysis shows that RHB could be a beneficial amendment to increase the methanotrophic community composition in paddy soils. Overall, the results suggest that the RHB amendment could markedly enhance soil conditions and methanotrophs abundance via regulating soil physico‐chemical properties in nutrient‐deprived and degraded paddy agriculture soils.
Unique Property of Nontraditional Intrinsic Luminescence in the Transforming of Solution‐Hydrogel‐Solid and Its Applications
Authors: Wang Hongyang , Lan Shuai , Zhang Yu , Zhang Lu , Jia Dandan , Zhang Weiguo , Liu Chun , Cao Lei , Wang Dongjun 
Published: May 2021

AbstractFor the unusual phenomenon of nontraditional intrinsic luminescence, a systematic fluorescence study is conducted in the phase transformation from solution through hydrogel to solid states. In this process, significant differences are found in fluorescence intensity, peak position, lifetime, and excitation‐dependent emission. In particular, the samples in the hydrogel state show two fluorescent peaks at 480 and 516 nm, respectively, while only one fluorescent peak is detected in the cases of solution (at 516 nm) or solid (at around 450 nm). More interestingly, the longer wavelength peak presents excitation‐dependent fluorescence, and the shorter one is excitation‐independent. These unique fluorescent observations can be ascribed to the fact that the aggregates of amine groups act as the actual fluorescent centers, which are quite sensitive to their surrounding microenvironments. Based on these results, some simulation tests of sensors and intelligent hydrogels in response to water are also studied.
A broadband filtering quasi‐YAGI antenna with wide stopband
Authors: Lee Zongze , Li Hua , Ding Xiao 
Published: May 2021

AbstractThis article presents a novel filtering quasi‐Yagi antenna with ultra‐wide passband and ultra‐wide stopband. By employing an antipodal connection between the dipole arms and the feedline, the profitable modes of the dipole can be excited and controlled to produce a wide operating band. Without increasing the antenna size, the elaborately arranged parasitic elements and the band‐stop element can realize the filter‐like response with sharp roll‐off rates and high out‐of‐band suppression levels. Measured results show that passband and stopband can be improved to 2.65–6.05 GHz (78.2%) and 6.3–13.3 GHz (up to 3.1 f0, f0 is the center frequency of the antenna), respectively. Radiations keep stable across the passband. The measured in‐band average gain is ∼ 4.4 dBi, whereas the out‐of‐band radiation suppression is more than 20.2 dB.
A wavelet‐based sparse row‐action method for image reconstruction in magnetic particle imaging
Authors: Lieb Florian , Knopp Tobias 
Published: May 2021

PurposeMagnetic particle imaging (MPI) is a preclinical imaging technique capable of visualizing the spatio‐temporal distribution of magnetic nanoparticles. The image reconstruction of this fast and dynamic process relies on efficiently solving an ill‐posed inverse problem. Current approaches to reconstruct the tracer concentration from its measurements are either adapted to image characteristics of MPI but suffer from higher computational complexity and slower convergence or are fast but lack in the image quality of the reconstructed images.MethodsIn this work we propose a novel MPI reconstruction method to combine the advantages of both approaches into a single algorithm. The underlying sparsity prior is based on an undecimated wavelet transform and is integrated into a fast row‐action framework to solve the corresponding MPI minimization problem.ResultsIts performance is numerically evaluated against a classical FISTA (Fast Iterative Shrinkage‐Thresholding Algorithm) approach on simulated and real MPI data. The experimental results show that the proposed method increases image quality with significantly reduced computation times.ConclusionsIn comparison to state‐of‐the‐art MPI reconstruction methods, our approach shows better reconstruction results and at the same time accelerates the convergence rate of the underlying row‐action algorithm.
State-Space Model to Estimate Salmon Escapement Using Multiple Data Sources
Authors: See Kevin E. , Kinzer Ryan N. , Ackerman Michael W. 
Published: May 2021

Abstract
Accurate estimates of salmonids passing Lower Granite Dam on the Snake River, by species and origin, are a critical input to assessing the status and trends of various populations as well as successful management of fisheries in the Snake River basin. Here, we describe a state-space model that estimates such escapement past a dam by using window counts, PIT tag observations, and data from an adult fish trap, accounting for issues such as nighttime passage, fallback and reascension, potential observation error at the window, and uncertainty in the adult trap rate. We tested the approach using a simulation framework that mimicked several levels of observation error, differences between nighttime passage and reascension rates, and the possibility of the adult trap being closed for some period of time. Our results demonstrate that the model produced unbiased estimates across all tested scenarios. We also applied this model to empirical data from Lower Granite Dam to produce estimates of wild, clipped hatchery, and unclipped hatchery spring/summer-run Chinook Salmon Oncorhynchus tshawytscha and steelhead O. mykiss from spawn years 2010–2019.