bluuebunny/crossref_metadata_2025_split huggingface dataset:
Engineer design process assisted by explainable deep learning network
Authors: Hsu Chia-Wei , Yang An-Cheng , Kung Pei-Ching , Tsou Nien-Ti , Chen Nan-Yow 
Published: November 2021

AbstractEngineering simulation accelerates the development of reliable and repeatable design processes in various domains. However, the computing resource consumption is dramatically raised in the whole development processes. Making the most of these simulation data becomes more and more important in modern industrial product design. In the present study, we proposed a workflow comprised of a series of machine learning algorithms (mainly deep neuron networks) to be an alternative to the numerical simulation. We have applied the workflow to the field of dental implant design process. The process is based on a complex, time-dependent, multi-physical biomechanical theory, known as mechano-regulatory method. It has been used to evaluate the performance of dental implants and to assess the tissue recovery after the oral surgery procedures. We provided a deep learning network (DLN) with calibrated simulation data that came from different simulation conditions with experimental verification. The DLN achieves nearly exact result of simulated bone healing history around implants. The correlation of the predicted essential physical properties of surrounding bones (e.g. strain and fluid velocity) and performance indexes of implants (e.g. bone area and bone-implant contact) were greater than 0.980 and 0.947, respectively. The testing AUC values for the classification of each tissue phenotype were ranging from 0.90 to 0.99. The DLN reduced hours of simulation time to seconds. Moreover, our DLN is explainable via Deep Taylor decomposition, suggesting that the transverse fluid velocity, upper and lower parts of dental implants are the keys that influence bone healing and the distribution of tissue phenotypes the most. Many examples of commercial dental implants with designs which follow these design strategies can be found. This work demonstrates that DLN with proper network design is capable to replace complex, time-dependent, multi-physical models/theories, as well as to reveal the underlying features without prior professional knowledge.
Robust unsupervised deconvolution of linear motifs characterizes 68 protein modifications at proteome scale
Authors: Smith Theodore G. , Uzozie Anuli C. , Chen Siyuan , Lange Philipp F. 
Published: November 2021

AbstractThe local sequence context is the most fundamental feature determining the post-translational modification (PTM) of proteins. Recent technological improvements allow for the detection of new and less prevalent modifications. We found that established state-of-the-art algorithms for the detection of PTM motifs in complex datasets failed to keep up with this technological development and are no longer robust. To overcome this limitation, we developed RoLiM, a new linear motif deconvolution algorithm and webserver, that enables robust and unbiased identification of local amino acid sequence determinants in complex biological systems demonstrated here by the analysis of 68 modifications found across 30 tissues in the human draft proteome map. Furthermore, RoLiM analysis of a large-scale phosphorylation dataset comprising 30 kinase inhibitors of 10 protein kinases in the EGF signalling pathway identified prospective substrate motifs for PI3K and EGFR.
Ice-cream used as cryotherapy during high-dose melphalan conditioning reduces oral mucositis after autologous hematopoietic stem cell transplantation
Authors: Jasiński Marcin , Maciejewska Martyna , Brodziak Anna , Górka Michał , Skwierawska Kamila , Jędrzejczak Wiesław W. , Tomaszewska Agnieszka , Basak Grzegorz W. , Snarski Emilian 
Published: November 2021

AbstractOral mucositis (OM) is one of the most frequent adverse events of high-dose conditioning chemotherapy with melphalan prior to autologous hematopoietic stem cell transplantation (AHSCT). It significantly reduces the patients’ quality of life. One of the preventive strategies for OM is cryotherapy. We retrospectively analyzed whether commercially available ice-cream could prevent OM during the melphalan infusion. We retrospectively analyzed 74 patients after AHSCT to see whether there is any correlation between OM and cryotherapy (ice-cream), melphalan dose (140 mg/m2 or 200 mg/m2). The incidence of OM in our study inversely correlated with cryotherapy in the form of ice-cream. Out of 74 patients receiving conditioning chemotherapy with high-dose melphalan, 52 received cryotherapy. Fifteen patients in the cryotherapy group (28.84%) developed OM, whereas 13 patients (59.09%) developed it in the group without cryotherapy. In a multiple linear regression test cryotherapy remained a significant protective factor against OM (p = 0.02) We have also seen the relationship between melphalan dose with OM (p < 0.005). Cryotherapy in the form of ice-cream is associated with a lower rate of OM and, therefore, could potentially be used as a cost-effective, less burdensome, and easy to implement method in prevention of oral mucositis.
Factor H-related protein 1 (FHR-1) is associated with atherosclerotic cardiovascular disease
Authors: Irmscher Sarah , Zipfel Svante L. H. , Halder Luke D. , Ivanov Lia , Gonzalez-Delgado Andres , Waldeyer Christoph , Seiffert Moritz , Brunner Fabian J. , von der Heide Monika , Löschmann Ina , Wulf Sonia , Czamara Darina , Papac-Milicevic Nikolina , Strauß Olaf , Lorkowski Stefan , Reichenspurner Hermann , Holers Michael V. , Banda Nirmal K. , Zeller Tania , Binder Elisabeth B. , Binder Christoph J. , Wiech Thorsten , Zipfel Peter F. , Skerka Christine 
Published: November 2021

AbstractAtherosclerotic cardiovascular disease (ACVD) is a lipid-driven inflammatory disease and one of the leading causes of death worldwide. Lipid deposits in the arterial wall lead to the formation of plaques that involve lipid oxidation, cellular necrosis, and complement activation, resulting in inflammation and thrombosis. The present study found that homozygous deletion of theCFHR1gene, which encodes the plasma complement protein factor H-related protein 1 (FHR-1), was protective in two cohorts of patients with ACVD, suggesting that FHR-1 accelerates inflammation and exacerbates the disease. To test this hypothesis, FHR-1 was isolated from human plasma and was found to circulate on extracellular vesicles and to be deposited in atherosclerotic plaques. Surface-bound FHR-1 induced the expression of pro-inflammatory cytokines and tissue factor in both monocytes and neutrophils. Notably, plasma concentrations of FHR-1, but not of factor H, were significantly (p < 0.001) elevated in patients with ACVD, and correlated with the expression of the inflammation markers C-reactive protein, apolipoprotein serum amyloid protein A, and neopterin. FHR-1 expression also significantly correlated with plasma concentrations of low-density lipoprotein (LDL) (p < 0.0001) but not high-density lipoprotein (HDL). Taken together, these findings suggest that FHR-1 is associated with ACVD.
Right heart exercise-training-adaptation and remodelling in endurance athletes
Authors: Conti Valeria , Migliorini Filippo , Pilone Marco , Barriopedro María I. , Ramos-Álvarez Juan José , Montero Francisco Javer Calderon , Maffulli Nicola 
Published: November 2021

AbstractLong-term sports training leads to myocardial adaptations, with remodelling of the heart chambers. However, while myocardial adaptations of the left heart are well described, remodelling of the right heart and its impact on the development of arrhythmias is still debated. To conduct a systematic review on right ventricle (RV) and right atrium (RA) structural and functional changes in athletes who participate in long-term endurance training. Systematic review. A systematic literature search was conducted. All the articles reporting right heart echocardiographic (ECHO) and cardiac magnetic resonance (CMR) parameters evaluated in endurance athletes and sedentary subjects were considered eligible. A multivariate analysis was conducted to investigate whether age, sex, body surface area (BSA), intensity of training are associated with RV ECHO, CMR parameters and RA ECHO parameters. A positive association between age and right atrium area (RAA) (P = 0.01) was found. This is a negative association to RV E/A (P = 0.004), and RV end diastolic diameter (RVED) longitudinal (P = 0.01). A positive association between BSA and RVED middle (P = 0.001), as well between BSA and RAA (P = 0.05) was found, along with a negative association with RV E/A (P = 0.002). A positive association between intensity of training and RV end systolic area (RVESA) (P = 0.03), RV end diastolic volume indexed (RVEDVI) (P = 0.01), RV end systolic volume indexed (RVESVI) (P = 0.01) was found, along with a negative association with ejection fraction (EF %) (P = 0.01). Endurance athletes demonstrated an association between RV remodelling and age, BSA and intensity of training.
Evaluation of bone formation on orthopedic implant surfaces using an ex-vivo bone bioreactor system
Authors: Dua Rupak , Jones Hugh , Noble Philip C. 
Published: November 2021

AbstractRecent advances in materials and manufacturing processes have allowed the fabrication of intricate implant surfaces to facilitate bony attachment. However, refinement and evaluation of these new design strategies are hindered by the cost and complications of animal studies, particularly during early iterations in the development process. To address this problem, we have previously constructed and validated an ex-vivo bone bioreactor culture system that can maintain the viability of bone samples for an extended period ex-vivo. In this study, we investigated the mineralization of a titanium wire mesh scaffold under both static and dynamic culturing using our ex vivo bioreactor system. Thirty-six cancellous bone cores were harvested from bovine metatarsals at the time of slaughter and divided into five groups under the following conditions: Group 1) Isolated bone cores placed in static culture, Group 2) Unloaded bone cores placed in static culture in contact with a fiber-mesh metallic scaffold, Group 3) Bone cores placed in contact with a fiber-mesh metallic scaffold under the constant pressure of 150 kPa, Group 4) Bone core placed in contact with a fiber-mesh metallic scaffold and exposed to cyclic loading with continuous perfusion flow of media within the ex-vivo culture system and Group 5) Bone core evaluated on Day 0 to serve as a positive control for comparison with all other groups at weeks 4 and 7. Bone samples within Groups 1–4 were incubated for 4 and 7 weeks and then evaluated using histological examination (H&E) and the Live-Dead assay (Life Technologies). Matrix deposits on the metallic scaffolds were examined with scanning electron microscopy (SEM), while the chemical composition of the matrix was measured using energy-dispersive x-ray spectroscopy (EDX). We found that the viability of bone cores was maintained after seven weeks of loading in our ex vivo system. In addition, SEM images revealed crystallite-like structures on the dynamically loaded metal coupons (Group 4), corresponding to the initial stages of mineralization. EDX results further confirmed the presence of carbon at the interface and calcium phosphates in the matrix. We conclude that a bone bioreactor can be used as an alternate tool for in-vivo bone ingrowth studies of new implant surfaces or coatings.
Grindability of carbon fiber reinforced polymer using CNT biological lubricant
Authors: Gao Teng , Zhang Yanbin , Li Changhe , Wang Yiqi , An Qinglong , Liu Bo , Said Zafar , Sharma Shubham 
Published: November 2021

AbstractCarbon fiber-reinforced polymer (CFRP) easily realizes the integrated manufacturing of components with high specific strength and stiffness, and it has become the preferred material in the aerospace field. Grinding is the key approach to realize precision parts and matching the positioning surface for assembly and precision. Hygroscopicity limits the application of flood lubrication in CFRP grinding, and dry grinding leads to large force, surface deterioration, and wheel clogging. To solve the above technical bottleneck, this study explored the grindability and frictional behavior of CNT biological lubricant MQL through grinding experiments and friction-wear tests. Results showed that the CNT biological lubricant reduced the friction coefficient by 53.47% compared with dry condition, showing optimal and durable antifriction characteristics. The new lubrication was beneficial to suppressing the removal of multifiber block debris, tensile fracture, and tensile-shear fracture, with the advantages of tribological properties and material removal behavior, the tangential and normal grinding force, and the specific grinding energy were reduced by 40.41%, 31.46%, and 55.78%, respectively, compared with dry grinding. The proposed method reduced surface roughness and obtained the optimal surface morphology by preventing burrs, fiber pull-out, and resin smearing, and wheel clogging was prevented by temperature reduction and lubricating oil film formation. Sa and Sq of the CNT biological lubricant were reduced by 8.4% and 7.9%, respectively, compared with dry grinding. This study provides a practical basis for further application of CNT biological lubricant in CFRP grinding.
Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes
Authors: Feng Yuqing , Wang Yanan , Zhu Baoli , Gao George Fu , Guo Yuming , Hu Yongfei 
Published: November 2021

AbstractGut microbial reference genomes and gene catalogs are necessary for understanding the chicken gut microbiome. Here, we assembled 12,339 microbial genomes and constructed a gene catalog consisting of ~16.6 million genes by integrating 799 public chicken gut microbiome samples from ten countries. We found that 893 and 38 metagenome-assembled genomes (MAGs) in our dataset were putative novel species and genera, respectively. In the chicken gut,Lactobacillus aviariusandLactobacillus crispatuswere the most common lactic acid bacteria, and glycoside hydrolases were the most abundant carbohydrate-active enzymes (CAZymes). Antibiotic resistome profiling results indicated that Chinese chicken samples harbored a higher relative abundance but less diversity of antimicrobial resistance genes (ARGs) than European samples. We also proposed the effects of geography and host species on the gut resistome. Our study provides the largest integrated metagenomic dataset from the chicken gut to date and demonstrates its value in exploring chicken gut microbial genes.
Precancerous liver diseases do not cause increased mutagenesis in liver stem cells
Authors: Nguyen Luan , Jager Myrthe , Lieshout Ruby , de Ruiter Petra E. , Locati Mauro D. , Besselink Nicolle , van der Roest Bastiaan , Janssen Roel , Boymans Sander , de Jonge Jeroen , IJzermans Jan N. M. , Doukas Michail , Verstegen Monique M. A. , van Boxtel Ruben , van der Laan Luc J. W. , Cuppen Edwin , Kuijk Ewart 
Published: November 2021

AbstractInflammatory liver disease increases the risk of developing primary liver cancer. The mechanism through which liver disease induces tumorigenesis remains unclear, but is thought to occur via increased mutagenesis. Here, we performed whole-genome sequencing on clonally expanded single liver stem cells cultured as intrahepatic cholangiocyte organoids (ICOs) from patients with alcoholic cirrhosis, non-alcoholic steatohepatitis (NASH), and primary sclerosing cholangitis (PSC). Surprisingly, we find that these precancerous liver disease conditions do not result in a detectable increased accumulation of mutations, nor altered mutation types in individual liver stem cells. This finding contrasts with the mutational load and typical mutational signatures reported for liver tumors, and argues against the hypothesis that liver disease drives tumorigenesis via a direct mechanism of induced mutagenesis. Disease conditions in the liver may thus act through indirect mechanisms to drive the transition from healthy to cancerous cells, such as changes to the microenvironment that favor the outgrowth of precancerous cells.
Astrocytic ApoE underlies maturation of hippocampal neurons and cognitive recovery after traumatic brain injury in mice
Authors: Yu Tzong-Shiue , Tensaouti Yacine , Stephanz Elizabeth P. , Chintamen Sana , Rafikian Elizabeth E. , Yang Mu , Kernie Steven G. 
Published: November 2021

AbstractPolymorphisms in the apolipoprotein E (ApoE) gene confer a major genetic risk for the development of late-onset Alzheimer’s disease (AD) and are predictive of outcome following traumatic brain injury (TBI). Alterations in adult hippocampal neurogenesis have long been associated with both the development of AD and recovery following TBI and ApoE is known to play a role in this process. In order to determine how ApoE might influence hippocampal injury-induced neurogenesis, we generated a conditional knockout system whereby functional ApoE from astrocytes was ablated prior to injury. While successfully ablating ApoE just prior to TBI in mice, we observed an attenuation in the development of the spines in the newborn neurons. Intriguingly, animals with a double-hit, i.e. injury and ApoE conditionally inactivated in astrocytes, demonstrated the most pronounced impairments in the hippocampal-dependent Morris water maze test, failing to exhibit spatial memory after both acquisition and reversal training trials. In comparison, conditional knockout mice without injury displayed impairments but only in the reversal phase of the test, suggesting accumulative effects of astrocytic ApoE deficiency and traumatic brain injury on AD-like phenotypes. Together, these findings demonstrate that astrocytic ApoE is required for functional injury-induced neurogenesis following traumatic brain injury.
Pseudo-single domain colloidal superparamagnetic nanoparticles designed at a physiologically tolerable AC magnetic field for clinically safe hyperthermia
Authors: Kim Ji-wook , Heo Dan , Wang Jie , Kim Hyung-sub , Ota Satoshi , Takemura Yasushi , Huh Chulhaeng , Bae Seongtae 
Published: November 2021

Pseudo-single domain superparamagnetic nanoparticles demonstrate highly efficient magnetic hyperthermia performance at the biologically safe and physiologically tolerable range of AC magnetic field (fappl < 120 kHz and Happl < 190 Oe).
Real-time kinetic studies of Mycobacterium tuberculosis LexA–DNA interaction
Authors: Chatterjee Chitral , Majumdar Soneya , Deshpande Sachin , Pant Deepak , Matheshwaran Saravanan 
Published: November 2021

Abstract
Transcriptional repressor, LexA, regulates the ‘SOS’ response, an indispensable bacterial DNA damage repair machinery. Compared with its Escherichia coli ortholog, LexA from Mycobacterium tuberculosis (Mtb) possesses a unique N-terminal extension of additional 24 amino acids in its DNA-binding domain (DBD) and 18 amino acids insertion at its hinge region that connects the DBD to the C-terminal dimerization/autoproteolysis domain. Despite the importance of LexA in ‘SOS’ regulation, Mtb LexA remains poorly characterized and the functional importance of its additional amino acids remained elusive. In addition, the lack of data on kinetic parameters of Mtb LexA–DNA interaction prompted us to perform kinetic analyses of Mtb LexA and its deletion variants using Bio-layer Interferometry (BLI). Mtb LexA is seen to bind to different ‘SOS’ boxes, DNA sequences present in the operator regions of damage-inducible genes, with comparable nanomolar affinity. Deletion of 18 amino acids from the linker region is found to affect DNA binding unlike the deletion of the N-terminal stretch of extra 24 amino acids. The conserved RKG motif has been found to be critical for DNA binding. Overall, the present study provides insights into the kinetics of the interaction between Mtb LexA and its target ‘SOS’ boxes. The kinetic parameters obtained for DNA binding of Mtb LexA would be instrumental to clearly understand the mechanism of ‘SOS’ regulation and activation in Mtb.
ZNF76 predicts prognosis and response to platinum chemotherapy in human ovarian cancer
Authors: Hua Tian , Wang Rui-min , Zhang Xiao-chong , Zhao Bei-bei , Fan Shao-bei , Liu Deng-xiang , Wang Wei 
Published: November 2021

Abstract
Ovarian cancer (OV) is the most lethal gynecologic malignancy. One major reason of the high mortality of the disease is due to platinum-based chemotherapy resistance. Increasing evidence reveal the important biological functions and clinical significance of zinc finger proteins (ZNFs) in OV. In the present study, the relationship between the zinc finger protein 76 (ZNF76) and clinical outcome and platinum resistance in patients with OV was explored. We further analyzed ZNF76 expression via multiple gene expression databases and identified its functional networks using cBioPortal. RT-qPCR and IHC assay shown that the ZNF76 mRNA and protein expression were significantly lower in OV tumor than that in normal ovary tissues. A strong relationship between ZNF76 expression and platinum resistance was determined in patients with OV. The low expression of ZNF76 was associated with worse survival in OV. Multivariable analysis showed that the low expression of ZNF76 was an independent factor predicting poor outcome in OV. The prognosis value of ZNF76 in pan-cancer was validated from multiple cohorts using the PrognoScan database and GEPIA 2. A gene-clinical nomogram was constructed by multivariate cox regression analysis, combined with clinical characterization and ZNF76 expression in TCGA. Functional network analysis suggested that ZNF76 was involved in several biology progressions which associated with OV. Ten hub genes (CDC5L, DHX16, SNRPC, LSM2, CUL7, PFDN6, VARS, HSD17B8, PPIL1, and RGL2) were identified as positively associated with the expression of ZNF76 in OV. In conclusion, ZNF76 may serve as a promising prognostic-related biomarker and predict the response to platinum in OV patients.
Trajectory prediction of cyclist based on spatial‐temporal multi‐graph network in crowded scenarios
Authors: Li Meng , Chen Tao , Du Hao 
Published: November 2021

AbstractCyclist trajectory prediction is an essential task in autonomous driving and surveillance systems. This task is challenging due to that the bicycles go much faster than the pedestrians and a minor prediction error could lead to a severe deviation in the actual path. Existing cyclist trajectory prediction models usually employ the social pooling mechanism to depict the mutual interactions between targets. They ignore that the pooling operation is leaky in information. Moreover, they prefer to use the recurrent architecture to capture the time‐varying features, which is not efficient in computation and parameter learning. To address these issues, a spatial‐temporal multi‐graph module which employs the topology of graphs to represent social interactions and design multi‐kernel functions to depict the social attributes from various aspects is proposed. Instead of the recurrent architecture, a temporal convolution to forecast the future paths is introduced. Experimental results on real‐world datasets demonstrate its superior performance against state‐of‐the‐art baselines. It reduces 9% prediction error when compared to recurrent neural network based models and is more effective in crowded scenarios.