bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining Bone Collagen Matrix with HUC-MSCs for Application to Alveolar Process Cleft in a Rabbit Model
Authors: Sun Xue-Cheng , Wang Hu , Zhang Dan , Li Jian-Hui , Yin Li-Qiang , Yan Yu-Fang , Ma Xu , Xia Hong-Fei 
Published: July 2021

Abstract
Background: Most materials used clinically for filling severe bone defects either cannot induce bone re-generation or exhibit low bone conversion, therefore, their therapeutic effects are limited. Human umbilical cord mesenchymal stem cells (hUC-MSCs) exhibit good osteoinduction. However, the mechanism by which combining a heterogeneous bone collagen matrix with hUC-MSCs to repair the bone defects of alveolar process clefts remains unclear.Methods: A rabbit alveolar process cleft model was established by removing the bone tissue from the left maxillary bone. 48 young Japanese white rabbits (JWRs) were divided into normal, control, material and MSCs groups. An equal volume of a bone collagen matrix alone or combined with hUC-MSCs was implanted in the defect. X-ray, micro-focus computed tomography (micro-CT), blood analysis, histochemical staining and TUNEL were used to detect the newly formed bone in the defect area at 3 and 6 months after the surgery. Results: The bone formation rate obtained from the skull tissue in MSCs group was significantly higher than that in control group at 3 months (P<0.01) and 6 months (P<0.05) after the surgery. The apoptosis rate in the MSCs group was significantly higher at 3 months after the surgery (P<0.05) and lower at 6 months after the surgery (P<0.01) than those in the normal group.Conclusions: Combining bone collagen matrix with hUC-MSCs promoted the new bone regeneration in the rabbit alveolar process cleft model through promoting osteoblasts formations and chondrocyte growth, and inducing type 1 collagen formation and BMP-2 generation.
Gaussian Processes Regression for Cyclodextrin Host-Guest Binding Prediction
Authors: Carvalho Ruan M , Rosa Iago G. L. , Gomes Diego E. B. , Goliatt Priscila V. Z. C. , Goliatt Leonardo 
Published: July 2021

Abstract
Machine Learning (ML) techniques are becoming an integral part of rational drug design and discovery. Data-driven modeling regularly outperforms physics-based models for predicting molecular binding affinities, placing ML as a promising tool. Cyclodextrins are nano-cages used to improve the delivery of insoluble or toxic drugs. Due to chemical similarity to proteins, ML approaches could vastly profit to improve affinity prediction and enhance their carriable drug portfolio. Here we evaluate the performance of the Gaussian Process Regression (GPR) to predict the binding affinity of cyclodextrin and known ligands. GPR performance is compared with two well-known ML methods - Support Vector Regression (SVR), and eXtreme Gradient Boosting (XGB). We perform hyperparameter tuning through a Random Search strategy. GPR was able to increase the prediction performance when compared to SVR and XGB, leading to better performance to adjust the data ($R^2$ = 0.803) with low prediction errors (RMSE = 1.811 kJ/mol and MAE = 1.201 kJ/mol).
Effects of forest cover pattern on water quality of low-order streams in an agricultural landscape in the Pirapora river basin, Brazil
Authors: de Mello Kaline , Valente Roberta Averna , Ribeiro Marina Pannunzio , Randhir Timothy 
Published: July 2021

Abstract
Low-order streams are important regions for river formation and are highly vulnerable to changes in terrestrial systems. Thus, the land-use/land-cover plays an important role in the maintenance of water quality. However, only its composition may not explain the spatial variation in water quality, because it does not consider landscape configurations. In this context, the study aimed to evaluate the forest cover pattern effects on water quality on low-order streams, which integrated an agricultural landscape. Applying a paired watershed method, we selected watersheds classified according to their morphometry and average slope to discard other physical factors that could influence the water quality. Land-use/land-cover pattern was analyzed for composition and forest cover configuration using landscape metrics, including the riparian zone composition. Water quality variables were obtained every two weeks during the hydrological year. This way, watersheds had similar morphometry, slope, and land-use/land-cover composition but differed in landscape configuration. Watershed with more aggregated forest cover had a better water quality than the other one. The results show that forest cover contributes to water quality maintenance, while forest fragmentation influences the water quality negatively, especially in sediment retention. Agricultural practices are sources of sediment and nutrients to the river, especially in steep relief. Thus, in addition to land-use/land-cover composition, landscape pattern must be considered in management of low-order streams in tropical agricultural watersheds.
Machine Learning Methods for Intrusive Detection of Wormhole Attack in Mobile Ad-Hoc Network (MANET)
Authors: Abdan Masoud , Seno Seyed Amin Hosseini 
Published: July 2021

Abstract
A wormhole attack is a type of attack on the network layer which reflects the issue of routing protocols. The classification is performed with several methods of machine learning consisting of K-Nearest Neighbor (KNN), Support Vector Machine (SVM), Decision Tree (DT), Linear Discrimination Analysis (LDA), Naive Bayes (NB), and Convolutional neural network (CNN). Moreover, for feature extraction, we used the properties of nodes, especially nodes speed in the MANET. We have collected 3997 distinct (normal 3781 and malicious 216) samples that comprise normal and malicious samples. Results of the classification show that the accuracy of KNN, SVM, DT, LDA, NB, and CNN methods are 97.1%, 98.2%, 98.9%, 95.2%, 94.7%, and 96.4%, respectively. Based on our findings, the DT method's accuracy is 98.9% and higher than other methods. In the next priority, SVM, KNN, CNN, LDA, and NB indicate high accuracy, respectively.
Big Data Palaeoecology reveals significant variation in Black Death mortality in Europe
Authors: Izdebski Adam , Guzowski Piotr , Poniat Radosław , Masci Lucrezia , Palli Jordan , Vignola Cristiano , Bauch Martin , Cocozza Carlo , Fernandes Ricardo , Ljungqvist Fredrik , Newfield Timothy , Seim Andrea , Abel-Schaad Daniel , Alba-Sánchez Francisca , Björkman Leif , Brauer Achim , Brown Alex , Czerwiński Sambor , Ejarque Ana , Fiłoc Magdalena , Florenzano Assunta , Fredh Erik , Fyfe Ralph , Jasiunas Nauris , Kołaczek Piotr , Kouli Katerina , Kozáková Radka , Kupryjanowicz Mirosława , Lagerås Per , Lamentowicz Mariusz , Lindbladh Matts , López-Sáez Jose Antonio , Luelmo-Lautenschlaeger Reyes , Marcisz Katarzyna , Mazier Florence , Mensing Scott , Mercuri Anna Maria , Milecka Krystyna , Miras Yannick , Noryśkiewicz Agnieszka , Novenko Elena , Obremska Milena , Pędziszewska Anna , Pérez-Díaz Sebastián , Piovesan Gianluca , Pluskowski Aleks , Pokorný Petr , Poska Anneli , Reitalu Triin , Rösch Manfred , Sadori Laura , Ferreira Carla Sá , Sebag David , Słowiński Michał , Stančikaitė Migle , Stivrins Normunds , Tunno Irene , Veski Siim , Wacnik Agnieszka , Masi Alessia 
Published: July 2021

Abstract
The Black Death is the most reknown pandemic in human history, believed by many to have killed half of Europe's population. However, despite the advances in ancient DNA research that allowed for the successful identification of the pandemic's causative agent (bacterium Yersinia pestis), our knowledge of the Black Death is still limited, based primarily on medieval texts available for single areas of Western Europe. In our study we remedy this situation and we focus in particular on the scale of the Black Death mortality. We collected data on landscape change from 261 coring sites (lakes and wetlands) located in 19 European countries. We used two independent methods of analysis to evaluate whether the changes we see in the landscape at the time of the Black Death agree with the hypothesis that half of the population died within a single year in each of the 21 regions we studied. We discovered that while the Black Death had devastating impact in some regions, it had negligible or no impact in others. The inter-regional differences in the Black Death mortality across Europe demonstrate the significance of cultural, ecological, economic and climatic factors that mediate the dissemination and impact of the disease. The complex interplay of these factors, along with the identification of the pathogen that caused disease outbreaks, should be the focus of future research on historical pandemics.
Achieving increased resolution and reconstructed image quality with gradient variance modified super-resolution radial fluctuations
Authors: Gong Xingyu , Zhou Li , Yao Longfang , Zhang Li , Chen Liwen , Fei Yiyan , Mi Lan , Wang Baoju , Ma Jiong 
Published: July 2021

Abstract
Based on the calculation of the degree of gradient convergence, the super-resolution radial fluctuations (SRRF) algorithm can achieve higher resolution by combining temporal fluctuation analysis with localization microscopy methods. The algorithm is also capable of processing high-density fluorescence images. However, there are considerable artifacts due to high density, which lead to a loss of image resolution and low fidelity of images. This study demonstrates the use of fluorescence gradient fluctuations in super-resolution analysis and proposes gradient variance modified SRRF (gmSRRF) algorithm. The gmSRRF algorithm resolves finer structures and compensates for the loss of resolution caused by artifacts in SRRF images using relatively high-density stochastic optical reconstruction microscopy (STORM) data and conventional widefield, confocal, or structured illumination microscopy (SIM) imaging sequences. The effectiveness of this algorithm is proven by means of relevant simulations and experiments, which allow the reconstructed SRRF image to improve resolution and reduce artifacts and background noise.
Weathering controls on the Phanerozoic phosphate cycle
Authors: Sharoni Shlomit , Halevy Itay 
Published: July 2021

Abstract
Although phosphate is an essential macronutrient for marine biota, critical to our understanding of marine productivity, biogeochemistry, and evolution, its long-timescale geologic history is poorly constrained. We constrain weathering-derived fluxes and seawater concentrations of phosphate throughout the Phanerozoic (541 Ma to present), by developing a model for the coupled, long-term biogeochemical cycles of phosphate, carbon, oxygen, and calcium. We find that the relative contribution of continental and seafloor weathering to the total weathering rate exerts a first-order control on ocean productivity, through a previously uninvestigated mechanism. Specifically, continental weathering is a source of the limiting nutrient phosphate, but seafloor weathering is not. As a result, times in Earth history in which seafloor weathering constitutes a large fraction of the total weathering rate (e.g., the early Paleozoic and Mesozoic), are also times in which phosphate delivery to the ocean is relatively low. A lower concentration of phosphate in seawater likely affected primary productivity, oceanic and atmospheric oxygen concentrations, with possible implications for the evolution of marine fauna over Earth history.
Associations Between Physical Activity and Cognitive Function, Daily Physical Function in Chinese With Heart Disease: A Cross-Sectional Study
Authors: Ding Meng , Jia Ningxin , Zhou Yanan , Dong Xiaosheng , Tian Caijun 
Published: July 2021

Abstract
Background: To investigate the associations between different dimensions (intensity, frequency, duration, volume, metabolic equivalent) of physical activity (PA) and cognitive function, daily physical function in Chinese with heart disease. Methods: This study included 2792 individuals from the China Health and Retirement Longitudinal Study (CHARLS) conducted in 2015. PA was divided into vigorous PA (VPA), moderate PA (MPA), and light PA (LPA). Linear regression models and binary logistic regression models were established to assess the associations be-tween indicators respectively. Results: Compared with taking no PA, MPA and VPA with a frequency of 6-7 d/w had lower risks of impaired daily physical function (OR=0.47, 95%CI: 0.25, 0.91; OR= 0.57, 95%CI: 0.37, 0.88) and higher cognitive function scores (β=1.22, 95%CI: 0.42, 2.03; β=1.08, 95%CI: 0.43, 1.73), while VPA of 3-5 d/w had lower cognitive function scores (β=-1.96, 95%CI: -3.51, -0.40). LPA with a duration of 30-119 min/d had lower risks of impaired daily physical function (OR=0.59, 95%CI: 0.36, 0.97). MPA and VPA of 30-119 min/d had higher cognitive function scores (β=1.43, 95%CI: 0.49, 2.37; β=1.30, 95%CI: -0.56, 2.06). Lower cognitive function scores in volume of ≥ 300 min/w. (β=-1.18, 95%CI: -2.14, -0.23). 1800-8999 METs had lower risks of impaired daily physical function and higher cognitive function scores. 1800-2999 METs had lowest risks of impaired daily physical function and highest cognitive function scores. (OR=0.18, 95%CI: 0.04, 0.75; β=2.94, 95%CI: 1.67, 4.21). Conclusions: This study found that VPA are associated with lower cognition, MPA and LPA are beneficial to cognition and daily physical function.Trial registration: IRB00001052-11015.
Onset location of periventricular white matter hyperintensities co-localizes with peak ependymal cell stretch
Authors: Visser Valery , Rusinek Henry , Weickenmeier Johannes 
Published: July 2021

Abstract
Deep and periventricular white matter hyperintensities (dWMH/pvWMH) are bright appearing white matter tissue lesions in T2-weighted fluid attenuated inversion recovery magnetic resonance images and are frequent observations in the aging human brain. While early stages of these white matter lesions are only weakly associated with cognitive impairment, their progressive growth is a strong indicator for long-term functional decline. DWMHs are typically associated with diffuse vascular degeneration; for pvWMHs, however, no unifying theory exists to explain their characteristic onset locations and progression patterns. We use structural and functional patient imaging data to create anatomically accurate finite element models of the lateral ventricles, white and gray matter, and cerebrospinal fluid. We simulated the mechanical loading of the ependymal cells forming the primary brain-fluid interface, the ventricular wall, and its surrounding tissues at peak ventricular pressure during the hemodynamic cycle. We observe that both the maximum principal tissue strain and the largest ependymal cell stretch consistently localize in the anterior and posterior horns. Strikingly, these locations coincide with the pvWMHs observed in FLAIR images. We submit that the tight junctions between ependymal cells experience significant loads that cause the ventricular wall to be stretched thin and ultimately begin to leak. Besides age-related vascular degeneration, progressive wall failure causes neurotoxic fluid to diffuse into surrounding white matter structures and appear as growing pvWMHs. The physics-based approach presented here provides a novel model system to systematically study the progressive tissue deterioration associated with pvWMHs.
NOS and SONOS redox switches in proteins
Authors: von Pappenheim Fabian Rabe , Wensien Marie , Ye Jin , Uranga Jon , Funk Lisa-Marie , Mata Ricardo , Tittmann Kai 
Published: July 2021

Abstract
We recently reported on the discovery of a lysine-cysteine redox switch in proteins with a covalent NOS bridge. Here, a systematic survey of the whole protein structure database discloses that NOS bridges are ubiquitous, hitherto overlooked redox switches in proteins of all domains of life and are found in diverse structural motifs and chemical variants. In several instances, lysines are observed in simultaneous linkage with two cysteines forming a SONOS bridge with a trivalent nitrogen, which constitutes the first native branching crosslink in proteins. In many proteins, the NOS switch contains a functionally essential lysine with direct roles in enzyme catalysis or binding of substrates, DNA or effectors linking lysine chemistry and redox biology as a novel regulatory principle. The NOS/SONOS switches are frequently found in proteins from human and plant pathogens including i.a. SARS-CoV-2 but also in many human proteins with established roles in gene expression, redox signaling and homeostasis in both physiological and pathophysiological conditions. Targeting, mimicking, controlling and engineering the NOS and SONOS redox switches appear to open novel avenues in drug, antiviral, antibiotic and herbicide development, in biocatalytic applications as well as in protein design and bioorganic chemistry.
Transcriptome change in Staphylococcus aureus in infecting mice
Authors: Hamamoto Hiroshi , Panthee Suresh , Paudel Atmika , Suguru Ohgi , Suzuki Yutaka , Sekimizu Kazuhisa 
Published: July 2021

Abstract
We performed in vivo RNA-sequencing analysis of Staphylococcus aureus in infected mouse liver using the 2-step cell-crush method. We compared the transcriptome of S. aureus at 6, 24, and 48 h post-infection (h.p.i) in mice and in culture medium. Genes related to anaerobic respiration were highly upregulated at 24 and 48 h.p.i. The gene expression patterns of virulence factors differed depending on the type of toxin. For example, hemolysins, but not leukotoxins and serine proteases, were highly upregulated at 6 h.p.i. Gene expression of metal transporters, such as iron transporters, gradually increased at 24 and 48 h.p.i. We also analyzed the transcriptome of mouse liver infected with S. aureus. Hypoxia response genes were upregulated at 24 and 48 h.p.i., and immune response genes were upregulated from 6 h.p.i. These findings suggest that gene expression of S. aureus in the host changes in response to changes in the host environment, such as oxygenation status or immune system attacks during infection.
Numerical investigations of micro bubble drag reduction effect for container ships
Authors: Gamal Mohammed , Kotb Mohammed , naguib ahmed , elsherbiny khaled 
Published: July 2021

Abstract
In the course of the most recent thirty years reduction of ship resistance and saving fuel consumption to accomplish higher speed with reduction of pollutants has been the significant subject for researchers. Micro bubble drag reduction technique is the one of the most interesting thoughts in this field owing to its great advantages, such as considerable potential drag reduction, easy operations, environmental friendliness and low costs. In this study a 3-D numerical investigation into frictional drag reduction by air micro bubbles is applied on KRISO container ship model. The objective is to understand the mechanism of resistance reduction through micro bubbles injection under model ship at different Froude numbers, injection rate and of course volume fractions. The numerical simulations are performed using a commercial CFD code solving Reynolds averaged Navier-Stokes (RANS) equations. For more than 36 simulations has performed to investigate the effect of injection of micro bubble under ship model hull and to estimate the local Coefficient of friction values along ship hull model. The results show that at all of the examined Froude number, frictional resistance reduction attained but at different rates and a maximum drag reduction of 27.6 % obtained at 0.282 Froude number with 4.8 % air volume fraction.
Realization of ZnCdO Coated Films: Under Laser Irradiation
Authors: Zargar Rayees 
Published: July 2021

Abstract
Promising Zinc Oxide (ZnO) and Cadmium Oxide (CdO) alloying (ZnCdO) films were fabricated on glass substrates by screen printing route for optoelectronic applications. The Nd:YAG green diode laser of wavelength 532 nm and laser fluence of 1.8 J/cm2 was used to irradiate the fabricated films at room temperature. The characterization of these films were systematically studied by means of X-ray diffraction (XRD), UV–vis, photoluminescence (PL), Raman spectroscopy and two probe method for conductivity measurement. The XRD pattern shows that all the films were well crystallized with maximum diffraction of (101) plane and mixed phases of ZnO and CdO were detected. The structure, space group and other crystal related parameters were confirmed from Rietveld refinement of XRD data.The basic optical parameters (band gap, refractive index and extinction coefficient) have estimated using absorbance spectra. The PL spectrum of ZnCdO composite films exhibits red shift and blue- green emissions shift upon laser irradiation were confirmed from CIE 1931 diagram.The Raman spectroscopy indicates that the quality of the ZnCdO films was increased while their structure defects were increased.DC conductivity measurement confirms semiconductor behaviour. All the parameters such as particle size, optical constants, colour emission and activation energy have been significantly improved upon laser irradiations dose of 1.8 J/cm2 for different durations of time. This study could be opting for optoelectronic applications.
In-Hospital Death Due to COVID-19 Disease in Iranian Patients: A Systematic Review and Meta-Analysis Study
Authors: Ghanei Mostafa , Saadat Seyed Hassan , Najimi-Varzaneh Alireza , Fesharaki Mohammad Gholami 
Published: July 2021

Abstract
Context: The prevalence of in-hospital death due to COVID-19 hospital is one of the qualitative indexes, which can be used to assess the quality of care, as well as the mortality patterns in COVID-19 pandemic.Objectives: Therefore, this systematic and meta-analysis study has been done with the aim of estimating overall prevalence in-hospital death due to COVID-19 disease in iranian patients Evidence Acquisition: Articles were identified through international searching databases including PubMed, Scopus, Elsevier, Google Scholar, and Web of Science and Iranian scientific information database (SID), Health.barakatkns, IranDoc, Civilica and MagIran. We reviewed systematically all studies reporting the prevalence of in-hospital death due to COVID-19 disease. In this study meta-analysis method with random effect model has been used to estimate the pooled prevalence. Results: 118 records were identified by the electronic search, of which 43 studies were identified as relevant papers that were meta-analyzed for the pooled in-hospital death due to COVID-19 prevalence. Overall, prevalence of death were 12.16% (95% CI: 10.72%-13.61%). The highest and lowest death prevalence has been reported in Northern Provinces (Gilan, 27.27% (95% CI: 8.66%-45.88%) and Mazandaran, 21.27% (95% CI: 18.14%-24.40%)) and Turkish-speaking provinces (Azerbaijan, East, 3.29% (95% CI: 2.11%-4.47%) and Zanjan, 3.42% (95% CI: 1.82%-5.02%)) respectively. Conclusions: Considering the death rate obtained in this study and its comparison with other countries, it can be said that the performance of the Iranian medical system in COVID-19 pandemic is acceptable.