bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nondestructive cellular-level 3D observation of mouse kidney using laboratory-based X-ray microscopy with paraffin-mediated contrast enhancement
Authors: Kunishima Naoki , Hirose Raita , Takeda Yoshihiro , Ito Koichiro , Furuichi Kengo , Omote Kazuhiko 
Published: June 2022

AbstractFor three-dimensional observation of unstained bio-specimens using X-ray microscopy with computed tomography (CT), one main problem has been low contrast in X-ray absorption. Here we introduce paraffin-mediated contrast enhancement to visualize biopsy samples of mouse kidney using a laboratory-based X-tray microscope. Unlike conventional heavy-atom staining, paraffin-mediated contrast enhancement uses solid paraffin as a negative contrast medium to replace water in the sample. The medium replacement from water to paraffin effectively lowers the absorption of low-energy X-rays by the medium, which eventually enhances the absorption contrast between the medium and tissue. In this work, paraffin-mediated contrast enhancement with 8 keV laboratory X-rays was used to visualize cylindrical renal biopsies with diameters of about 0.5 mm. As a result, reconstructed CT images from 19.4 h of data collection achieved cellular-level resolutions in all directions, which provided 3D structures of renal corpuscles from a normal mouse and from a disease model mouse. These two structures with and without disease allowed a volumetric analysis showing substantial volume differences in glomerular subregions. Notably, this nondestructive method presents CT opacities reflecting elemental composition and density of unstained tissues, thereby allowing more unbiased interpretation on their biological structures.
Post-exposure persistence of nitric oxide upregulation in skin cells irradiated by UV-A
Authors: Hazell Gareth , Khazova Marina , Cohen Howard , Felton Sarah , Raj Ken 
Published: June 2022

AbstractEvidence suggests that exposure to UV-A radiation can liberate nitric oxide from skin cells eliciting vasodilation in-vivo. However, the duration of nitric oxide release in skin cells after UV exposure is not well studied, with emphasis on UV-B mediated iNOS upregulation. The current study demonstrated persistence of nitric oxide release in a dark reaction after moderate UV-A exposure, peaking around 48 h post exposure; this effect was shown in keratinocytes, fibroblasts and endothelial cells from neonatal donors and keratinocytes from aged donors and confirmed the hypothesis that UV-A exposure appeared to upregulate cNOS alongside iNOS. Release of nitric oxide in the skin cells induced by a moderate exposure to UV-A in sunlight may be especially beneficial for some demographic groups such as the elderly, hypertensive patients or those with impaired nitric oxide function, not only during exposure but many hours and days after that.
Development of a filter device for the prevention of aquatic bacterial disease using a single-chain variable fragment (scFv)-conjugated affinity silk
Authors: Prakash Harsha , Sato Mitsuru , Kojima Katsura , Sato Atsushi , Maruyama Shinpei , Nagasawa Takahiro , Nakao Miki , Somamoto Tomonori 
Published: June 2022

AbstractInfectious disease is one of the most serious problems in the aquaculture industry for ornamental or edible fish. This study attempted to develop a new device for preventing an aquatic bacterial disease, ulcer disease, caused by Aeromonas salmonicida (As), using “affinity silk”. Affinity silk is a silk protein-containing fibroin L-chain (FibL) fused to the single-chain variable fragment (scFv). It can be easily processed into different formats such as fibers, gels, sponges, or films. A transgenic silkworm that could express a cDNA construct containing FibL fused to an scFv derived from a monoclonal antibody (MAb) against As was successfully generated. An enzyme-linked immunosorbent assay was used to detect As by employing 96-well plates coated with scFv-conjugated affinity silk. As could be captured efficiently by glass wool coated with affinity silk in the column. Furthermore, the air-lift water filter equipped with the affinity silk-coated wool could considerably reduce the concentration of As in water and was estimated to have sufficient ability to trap a lethal dose of As. These findings show that the “affinity silk filter” is a potential device for the prophylaxis of aquatic animal diseases.
Peripapillary RNFL/vessel density ratio in patients with type2 diabetes without clinical diabetic retinopathy
Authors: Lee Min-Woo , Lee Jong-Wook , Lee Kook-Hyung , Lee Young-Hoon , Kim Jung-Yeul 
Published: June 2022

AbstractTo identify how diabetic retinal neurodegeneration (DRN) and microvascular impairment are affected differently by various factors in type 2 diabetes (T2DM) patients without diabetic retinopathy via the ratio of RNFL thickness/vessel density (RNFL/VD) ratio. In this retrospective cross-sectional study, subjects were divided into two groups: controls (control group) and patients with T2DM (DM group). The RNFL thickness, VD, and RNDL/VD ratio were compared between two groups, and correlation analyses were performed to identify the relationship between the RNFL/VD ratio and various factors. A total of 411 eyes were enrolled: 195 eyes in the control group and 216 eyes in the DM group. The mean RNFL thickness was 95.9 ± 8.6 and 93.7 ± 8.7 μm (P = 0.016), the VD was 18.2 ± 0.7 and 17.6 ± 1.1 mm−1(P < 0.001), and the RNFL/VD ratio was 5.11 ± 0.47 and 5.22 ± 0.53 (P = 0.033) in the control group and DM group, respectively. In the DM group, age (coefficient = − 0.139, P = 0.041), axial length (coefficient = 0.163, P = 0.017), and T2DM duration (coefficient = − 0.180, P = 0.008) were significantly correlated with the RNFL/VD ratio. The RNFL/VD ratio of T2DM patients was higher than that of normal control, which would indicate that the impairment of microvasculature precedes DRN. Additionally, age and T2DM duration were negatively correlated with the RNFL/VD ratio, which suggests that inner retinal damage by DRN becomes more prominent over time than microvascular impairment in T2DM.
The neuropeptide Y receptor gene repository, phylogeny and comparative expression in allotetraploid common carp
Authors: Zou Xiaoqing , Chen Lin , Li Bijun , Xiao Junzhu , Xu Peng 
Published: June 2022

AbstractNPY-family receptors belong to G protein-coupled receptors (GPCR), which lays a physiological foundation for the transmembrane transport of an endogenous appetite-stimulating factor neuropeptide Y and related peptides. In this study, we investigated the npyr genes in ten representative species, and twelve npyr genes were identified from allotetraploid C. carpio, the npyr gene number of C. carpio was twice the number of its subgenome B progenitor-like diploid Poropuntius huangchuchieni. Phylogenetic analysis showed that all npyr genes were divided into three subgroups, and they underwent strong purifying selection according to selection pressure analysis. Subsequently, synteny analysis showed that most npyr genes were evenly distributed on the homologous chromosomes of two subgenomes in allotetraploid C. carpio, in which npy1r and npy2r were tandem duplicated, respectively. In addition, the global expression of npyr genes during embryonic development in allotetraploid C. carpio suggested the potential function of npyr genes in immunity and reproduction. In adult tissues, npyr genes were mainly distributed in the brain, gonad, and skin, which displayed a similar expression pattern between the C. carpio B subgenome and P. huangchuchieni. In general, our research could provide reference information for future exploration of the NPY receptors and neuroendocrine system of allotetraploid C. carpio and vertebrates.
Analysis of the vulnerability estimation and neighbor value prediction in autonomous systems
Authors: Rahmatov Nematullo , Saeed Faisal , Paul Anand 
Published: June 2022

AbstractThe security within autonomous systems (AS)s is one of the important measures to keep network users safe and stable from the various type of Distributed Denial of Service (DDoS) attacks. Similar to the other existing attack types Internet control message protocol (ICMP) based attacks are remained open challenge on the Internet environment. In this study, we have proposed a method to estimate the vulnerability of 600 AS provider edge (PE) routers by sending ICMP packets and predicted AS neighbor values using least square regression (LSR) approach. The results of our study show that 265 AS PE routers are vulnerable due to ICMP flood attack from the 600 ASs which were analyzed. Additionally, we have predicted that about 60% of total AS neighbors will be reduced in the next 3 years. Our results indicate that some ASs still did not deploy the firewall system in the boundary of their networks. Similarly, we also observed that the majority of ASs which expected to have less neighbor values in the next 3 years is due to change their routing paths to find adjacent paths.
Seasonal and sex-dependent gene expression in emu (Dromaius novaehollandiae) fat tissues
Authors: Wright Kristina , Nip Ka Ming , Kim Ji Eun , Cheng Kimberly M. , Birol Inanc 
Published: June 2022

AbstractEmu (Dromaius novaehollandiae) farming has been gaining wide interest for fat production. Oil rendered from this large flightless bird’s fat is valued for its anti-inflammatory and antioxidant properties for uses in therapeutics and cosmetics. We analyzed the seasonal and sex-dependent differentially expressed (DE) genes involved in fat metabolism in emus. Samples were taken from back and abdominal fat tissues of a single set of four male and four female emus in April, June, and November for RNA-sequencing. We found 100 DE genes (47 seasonally in males; 34 seasonally in females; 19 between sexes). Seasonally DE genes with significant difference between the sexes in gene ontology terms suggested integrin beta chain-2 (ITGB2) influences fat changes, in concordance with earlier studies. Six seasonally DE genes functioned in more than two enriched pathways (two female: angiopoietin-like 4 (ANGPTL4) and lipoprotein lipase (LPL); four male: lumican (LUM), osteoglycin (OGN), aldolase B (ALDOB), and solute carrier family 37 member 2 (SLC37A2)). Two sexually DE genes, follicle stimulating hormone receptor (FSHR) and perilipin 2 (PLIN2), had functional investigations supporting their influence on fat gain and loss. The results suggested these nine genes influence fat metabolism and deposition in emus.
Optimization of echo-enabled harmonic generation toward coherent EUV and soft X-ray free-electron laser at NSLS-II
Authors: Yang X. , Penn G. , Yu L. H. , Smaluk V. , Shaftan T. 
Published: June 2022

AbstractPrebunching via echo-enabled harmonic generation (EEHG) is an efficient way to reduce the radiator length and improve the longitudinal coherence as well as output stability in storage-ring-based free-electron lasers. We propose a conceptual design, which uses two straight sections to seed coherent extreme-ultraviolet (EUV) and soft X-ray emission with nearly MHz repetition rate. To take the large energy spread (10−3) of a storage ring into account and utilize the existing bending magnets between the two straight sections as the first chicane, we implement a special modeling tool, named EEHG optimizer. This tool has been successfully applied to maximize the prebunching with a reasonably low energy modulation, thereby generating intense coherent X-ray pulses within a short undulator length (a few meters) limited by the available space of a storage ring. Numerical simulations confirm that the optimized EEHG parameters can be directly applied to generate a 10 MW scale peak power with fully coherent ultrafast EUV to soft X-ray pulses based on the NSLS-II parameters. This method can be easily extended to other types of diffraction-limited storage rings.
Anti-dermatophytic activity of cold atmospheric plasma against Trichophyton rubrum via affecting fungal growth, morphology, drug susceptibility and HSP90 gene expression
Authors: Safi-Samghabadi Asal , Atyabi Seyed-Mohammad , Razzaghi-Abyaneh Mehdi 
Published: June 2022

AbstractTrichophyton rubrum, a major human pathogenic dermatophyte, is responsible for the most recurrent dermatophytoses as globally important superficial fungal infections. Typical chemotherapy is used to handle such infections; however, emerging drug resistance and side effects necessitate the new remedial method development. Cold atmospheric plasma (CAP) is an emerging technology, consisted of neutral and charged particles and photons newly developed as a potent and safe antimicrobial technique to combat drug-resistant microbial pathogens. In the present study, the vast effects of CAP irradiation containing oxygen (2%) and helium (98%) on T. rubrum growth and pathogenicity were explored. After exposure of T. rubrum to CAP jet for 90, 120, 150, 180, and 210 s in 96-well microtiter plates, cell morphology and viability, ergosterol content of fungal hyphae, HSP90 gene expression, and the pattern of drug susceptibility were studied by using electron microscopy, RT-qPCR, spectrophotometry, disk diffusion and CLSI microbroth dilution methods. CAP irradiation significantly inhibited the fungal growth by 25.83 to 89.10%, reduced fungal cell viability by 11.68 to 87.71%, disrupted cellular membranous organelles and structures of the fungal hyphae, and suppressed efficiently the expression of HSP90 gene by 2 folds in 210 s exposure. Taken together, our results demonstrated that CAP is an efficient tool with potential in-vivo therapeutic applications against chronic dermatophytosis caused by T. rubrum due to its effectiveness, harmless, and ease of access.
Highlighting uncertainty in clinical risk prediction using a model of emergency laparotomy mortality risk
Authors: Mathiszig-Lee Jakob F. , Catling Finneas J. R. , Moonesinghe S. Ramani , Brett Stephen J. 
Published: June 2022

AbstractClinical prediction models typically make point estimates of risk. However, values of key variables are often missing during model development or at prediction time, meaning that the point estimates mask significant uncertainty and can lead to over-confident decision making. We present a model of mortality risk in emergency laparotomy which instead presents a distribution of predicted risks, highlighting the uncertainty over the risk of death with an intuitive visualisation. We developed and validated our model using data from 127134 emergency laparotomies from patients in England and Wales during 2013–2019. We captured the uncertainty arising from missing data using multiple imputation, allowing prospective, patient-specific imputation for variables that were frequently missing. Prospective imputation allows early prognostication in patients where these variables are not yet measured, accounting for the additional uncertainty this induces. Our model showed good discrimination and calibration (95% confidence intervals: Brier score 0.071–0.078, C statistic 0.859–0.873, calibration error 0.031–0.059) on unseen data from 37 hospitals, consistently improving upon the current gold-standard model. The dispersion of the predicted risks varied significantly between patients and increased where prospective imputation occurred. We present a case study that illustrates the potential impact of uncertainty quantification on clinical decision making. Our model improves mortality risk prediction in emergency laparotomy and has the potential to inform decision-makers and assist discussions with patients and their families. Our analysis code was robustly developed and is publicly available for easy replication of our study and adaptation to predicting other outcomes.
Predicting biochemical recurrence of prostate cancer with artificial intelligence
Authors: Pinckaers Hans , van Ipenburg Jolique , Melamed Jonathan , De Marzo Angelo , Platz Elizabeth A. , van Ginneken Bram , van der Laak Jeroen , Litjens Geert 
Published: June 2022

Abstract
Background
The first sign of metastatic prostate cancer after radical prostatectomy is rising PSA levels in the blood, termed biochemical recurrence. The prediction of recurrence relies mainly on the morphological assessment of prostate cancer using the Gleason grading system. However, in this system, within-grade morphological patterns and subtle histopathological features are currently omitted, leaving a significant amount of prognostic potential unexplored.

Methods
To discover additional prognostic information using artificial intelligence, we trained a deep learning system to predict biochemical recurrence from tissue in H&E-stained microarray cores directly. We developed a morphological biomarker using convolutional neural networks leveraging a nested case-control study of 685 patients and validated on an independent cohort of 204 patients. We use concept-based explainability methods to interpret the learned tissue patterns.

Results
The biomarker provides a strong correlation with biochemical recurrence in two sets (n = 182 and n = 204) from separate institutions. Concept-based explanations provided tissue patterns interpretable by pathologists.

Conclusions
These results show that the model finds predictive power in the tissue beyond the morphological ISUP grading.
Keeping synapses in shape: degradation pathways in the healthy and aging brain
Authors: Kuijpers Marijn 
Published: June 2022

AbstractSynapses maintain their molecular composition, plasticity and function through the concerted action of protein synthesis and removal. The complex and polarized neuronal architecture poses specific challenges to the logistics of protein and organelle turnover since protein synthesis and degradation mainly happen in the cell soma. In addition, post-mitotic neurons accumulate damage over a lifetime, challenging neuronal degradative pathways and making them particularly susceptible to the effects of aging. This review will summarize the current knowledge on neuronal protein turnover mechanisms with a particular focus on the presynapse, including the proteasome, autophagy and the endolysosomal route and their roles in regulating presynaptic proteostasis and function. In addition, the author will discuss how physiological brain aging, which entails a progressive decline in cognitive functions, affects synapses and the degradative machinery.
Natural polymer‐based adhesive hydrogel for biomedical applications
Authors: Long Siyu , Xie Chaoming , Lu Xiong 
Published: June 2022

AbstractHydrogel is a polymer network system that can form a hydrophilic three‐dimensional network structure through different cross‐linking methods. In recent years, hydrogels have received considerable attention due to their good biocompatibility and biodegradability by introducing different cross‐linking mechanisms and functional components. Compared with synthetic hydrogels, natural polymer‐based hydrogels have low biotoxicity, high cell affinity, and great potential for biomedical fields; however, their mechanical properties and tissue adhesion capabilities have been unable to meet clinical requirements. In recent years, many efforts have been made to solve these issues. In this review, the recent progress in the field of natural polymer‐based adhesive hydrogels is highlighted. The authors first introduce the general design principles for the natural polymer‐based adhesive hydrogels being used as excellent tissue adhesives and the challenges associated with their design. Next, their usages in biomedical applications are summarised, such as wound healing, haemostasis, nerve repair, bone tissue repair, cartilage tissue repair, electronic devices, and other tissue repairs. Finally, the potential challenges of natural polymer‐based adhesive hydrogels are presented.
Metal surface wettability modification by nanosecond laser surface texturing: A review
Authors: Liu Zhifang , Niu Tong , Lei Yaxi , Luo Yuanxin 
Published: June 2022

AbstractLaser surface texturing (LST) is a non‐contact manufacturing process for fabricating functional surfaces in a manner that improves the corresponding wettability, and is widely used in biomedicine and industry. Laser surface texturing is a facile approach that is compatible with various materials, can result in a hierarchical texture, and enables a high degree of surface wetting (i.e., extreme wetting). In addition to surface structures, surface chemical modification is a primary factor in producing extreme wetting surfaces. This review discusses the effects of various surface textures and surface chemistries on wettability. Optimal laser parameters for the desired surface texture are based on the fundamental wettability and laser mechanism. In particular, bumps in the morphology are conducive to obtaining extreme wetting. Diverse surface chemical strategies result in extreme wetting by different mechanisms. This paper makes a rigorous evaluation of the laser parameters and optimal surface chemical modifications by elucidating the relationships between the surface structure, surface chemical modification, and wettability, and in so doing, determines the final wettability. The unresolved problems of LST are presented in the conclusion. This review provides guidance, development directions, and an integrated framework for LST, which will be useful for fabricating extreme wetting surfaces on various metals.
Energy efficient short‐packet‐communication in UAV‐assisted cognitive network
Authors: Han Huizhu , Huang Yangchao , Hu Hang , Pan Yu , An Qi , Liu Shihao , Zhao Senhao 
Published: June 2022

AbstractThis paper studies unmanned aerial vehicle (UAV)‐assisted cognitive network, where the UAV can improve the communication quality of edge users. Short packet communication (SPC) is widely used due to its low delay transmission characteristic. Unlike long packet communication in conventional wireless networks, SPC has a non‐negligible packet error rate and its data transmission rate is less than Shannon capacity. Considering the fact that the UAV is usually powered by battery, the energy efficiency (EE) maximisation problem is investigated based on short packet transmission in the UAV‐assisted cognitive network. Firstly, the closed‐form expression of EE is analysed, and then the optimisation problem is formulated by jointly optimising the spectrum sensing time, packet error rate, the flight speed, and the coverage range of UAV. Secondly, the optimisation problem is solved by dividing it into four subproblems. Then, an efficient iterative algorithm is proposed to tackle this problem. Simulation results show that the proposed optimisation scheme can evidently improve the EE performance compared with other benchmark schemes. In addition, the proposed joint optimisation algorithm not only has better convergence than exhaustive method, but also has higher stability than PSO algorithm.
Adaptive neural control of non‐linear fractional order multi‐agent systems in the presence of error constraints and input saturation
Authors: Mohammadzamani Fatemeh , Hashemi Mahnaz , Shahgholian Ghazanfar 
Published: June 2022

AbstractThis paper presents a tracking control problem for fractional order multi‐agent systems in the presence of uncertainties. The study takes into account the problems of error constraints, saturated inputs and transient response suitability. Because of the existing challenges, a neural adaptive control approach is used in this study. Fractional order multi‐agent systems are investigated with uncertainty in the presence of error constraints. A controller is designed on the basis of adaptive control and dynamic surface control. As a result, the control objective of pursuing the desired output is achieved in the presence of required constraints. The effective performance of the proposed controller is demonstrated by simulation using MATLAB software.