bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of Shear Stress for Enhanced Osteogenic Differentiation of Mouse Induced Pluripotent Stem Cells
Authors: Limraksasin Phoonsuk , Nattasit Praphawi , Manokawinchoke Jeeranan , Tiskratok Watcharaphol , Vinaikosol Naruephorn , Okawa Hiroko , Limjeerajarus Chalida Nakalekha , Limjeerajarus Nuttapol , Pavasant Prasit , Osathanon Thanaphum , Egusa Hiroshi 
Published: July 2022

Abstract
The self-organizing potential of induced pluripotent stem cells (iPSCs) represents a promising tool for bone tissue engineering. Shear stress promotes the osteogenic differentiation of mesenchymal stem cells, leading us to hypothesize that specific shear stress could enhance the osteogenic differentiation of iPSCs. For osteogenesis, embryoid bodies were formed for two days and then maintained in medium supplemented with retinoic acid for three days, followed by adherent culture in osteogenic induction medium for one day. The cells were then subjected to shear loading (0.15, 0.5, or 1.5 Pa) for two days. Among different magnitudes tested, 0.5 Pa induced the highest levels of osteogenic gene expression and greatest mineral deposition, corresponding to upregulated connexin 43 (Cx43) and phosphorylated Erk1/2 expression. Erk1/2 inhibition during shear loading resulted in decreased osteogenic gene expression and the suppression of mineral deposition. These results suggest that shear stress (0.5 Pa) enhances the osteogenic differentiation of iPSCs, partly through Cx43 and Erk1/2 signaling. Our findings shed light on the application of shear-stress technology to improve iPSC-based tissue-engineered bone for regenerative bone therapy.
Trichloromethane concentration pretreatment of inoculum for enhancing biohydrogen yield by food waste via two-stage batch fermentation
Authors: Xue Shengrong , WANG Fei 
Published: July 2022

Abstract
Trichloromethane is often used as a chemical inhibitor to pretreat the inoculum to improve hydrogen yield in dark fermentation. In this study, five different doses of trichloromethane were used for methanogenic inhibition of methanogenic microbial community operating in stable (inoculum A) and anaerobic microbial community in natural environment (inoculum B). High concentrations of trichloromethane inhibited the activity of microbial community in the system and hindered the production of hydrogen and methane. At the same time, it would greatly reduce the pH, causing it to fall below the threshold of suitable hydrogen yield. In turn, ethanol-type fermentation was triggered, and the ethanol content of the system increased with increasing concentration of trichloromethane addition. The comprehensive assessment concluded that a 0.10% (v/v) trichloromethane concentration gave the best hydrogen yield performance in both inoculums. However, anaerobic microbial community in natural environment was able to produce hydrogen more efficiently than the operationally stable methanogenic microbial community. The highest cumulative hydrogen yield was 111.16, 34.36, and 72.76 mL/g VS in phase Ⅰ, phase Ⅱ, and the whole stage, respectively. In addition, the butyrate production in the reactor at this concentration was considerable, with an average yield of 21.3 g/L.
Nicotine consumption rate through wastewater-based epidemiology: A systematic review, meta-analysis and probabilistic risk assessment
Authors: Asadi Anvar , Fakhri Yadolah , Salimi Yahya , Daglioglu Nebile , fard mina tahmasebi , Aghajarinezhad Maryam 
Published: July 2022

Abstract
Wastewater-based epidemiology (WBE) with advantages like complementary, cost-effective, comprehensive, and rapid tool is used for measuring and monitoring of illicit drugs in the population. Smoking cigarettes and tobacco use are common habits in nowadays community. This systematic review and meta-analysis are the first study to calculate the consumption amount of nicotine (NIC) by searching in WBE studies on a global scale. The related studies were retrieved within the international databases including Scopus and web of science up to February 2021 and 21 articles containing 87 measurements covering 275.3 million people with a total wastewater samples of 2250 were included. ​Results show that the maximum and minimum nicotine consumption rate (mg/1000 inh./day) was in Portugal (5860) and Viet Nam (1201), respectively. The global pooled amount of nicotine consumption rate was 2476 mg/1000 inh./day (95% CI (2289–2663). Risk assessment of nicotine consumption rate through WBE was calculated by the margin of exposure (MOE) approach. The MOE amounts were obtained by probabilistic Monte Carlo simulations for daily nicotine consumption. In total, 82% of nicotine consumption measurements located in the "risk" level (MOE < 100) and 18% of the MOE values were between 100–1000. The results imply that the risk of nicotine consumption need an immediate action and also these findings are useful for healthcare agencies and policy-makers to take action against the tobacco use prevalence.
Sustainable management and environmental protection for basin water allocation: a differential game based multi-objective programming
Authors: Di Danyang , Wu Zening , Wang Huiliang 
Published: July 2022

Abstract
It is important to manage water resources under emergy theory and its implementation mechanism for water dispatching considering both economic development and environmental needs. To balance compromise resources consumption, economic development and environment protection, a multi-objective dynamic differential game is proposed in this study to determine the optimal tax rate (OTR), optimal trading quantity of water (OTQW) in each province, and the optimal bargain price (OBP). Considering the sustainability of ecological environment, the quantification of negative sewage value and net carbon emission constraints are introduced into the water allocation. To maximize the target revenue functions, minimize the net carbon emission constraints and obtain the sustainable equilibrium solutions in the triple-level game, the costate function, Hamiltonian, and Lagrangian multiplier method are introduced. Then, a water dispatching structure is constructed for error correction between the predicted and actual runoff of the YRB. Taking Yellow River Basin as an example, the validity of the proposed framework and solution method were verified under different hydrological years, 6.5%~9.1% economic benefits higher than other schemes and 4.3%~5.9% net carbon emission lower than other schemes. Compared to previous studies, the standard deviation of economic value, social value, negative ecological environment value in this paper are the least, which indicates that this scheme can better meet the requirements of sustainable development and environmental protection.
Vitamin D binding protein gene polymorphism and its association with free serum bioavailability among tuberculosis patients and household contacts
Authors: Acen Ester Lilian , Joloba Moses L. , Akintola Ashraf , Nabi Rizwana Begum Syed , Biraro Irene Andia , Worodria William , Okeng Alfred , Bbuye Mudarshiru , Kateete David Patrick 
Published: July 2022

Abstract
Genetic variants influence the distribution of vitamin D in circulation leading to vitamin D deficiency. This study aimed to determine the association between the DBP gene polymorphism with vitamin D bioavailability among active tuberculosis patients, latent Tuberculosis and with no Tuberculosis infection individuals. This was a cross-sectional study of 52 active tuberculosis patients, 23 latent tuberculosis individuals, and 27 with no tuberculosis infection. Sanger sequencing was performed and single nucleotide polymorphisms were identified using the BioEdit tool. Logistic regression was used to determine associations. Frequencies of 97% Gc1F, 2% Gc2 and 1% Gc1S genotypes were reported. The median (IQR) vitamin D levels of the predominant genotype, Gc1F were 3.8 (1.1-10.5) ng/ml, Gc1S individual, 2.2 ng/ml, and Gc2 individuals were 1.9 ng/ml. No significant association was found between vitamin D binding protein gene and free and bioavailable vitamin D levels, p=value 0.05. Spearman’s correlation revealed a negative association (r-0.0404) between the two. The Gc1F genotype was predominantly found in the study population with the minor alleles associated with active and latent TB states. However, the non-significant association observed between the vitamin D Binding Protein gene and the free and bioavailable vitamin D levels may be a consequence of the homogenous population.
Fractionation of yellow thatching grass (Hyparrhenia filipendula) for sugar production using combined Alkaline and Deep eutectic solvent pretreatment
Authors: Masuku F , Ayaa F. , Onyelucheya C.M. , Iwarere S.A. , Daramola Michael , Kirabira John 
Published: July 2022

Abstract
Purpose Biomass pretreatment followed by enzymatic hydrolysis is one of the most viable ways to obtain sugars from biomass. In this work, the effect combined alkaline pretreatment and Deep Eutectic Solvent (DES) on enzyme hydrolysis of Hyparrhenia filipendula by cellulase is investigated. There is no previously reported literature on this substrate and the authors aim to establish baseline values for further research in the utilization of Hyparrhenia filipendula. Methods The yellow thatching grass (Hyparrhenia filipendula) was fractionated with a combination of alkaline and Deep Eutectic Solvent (DES) to increase sugar recovery. An alkaline solution of 10 wt % (w/v) of Sodium Hydroxide (NaOH) was used for the first stage of pretreatment at 100 °C for 4 h. Three DES, namely, Choline chloride (ChCl): urea; ChCl: glycerol; and Ethylene glycol: Citric acid at 1:2 molar ratio each, were heated to 80 °C until a clear solution was formed. The DESs were used for the second stage of pretreatment at 110 °C for 6 h in a Parr reactor. During the pretreatment, a solid: solvent ratio of 1:10 was used for the first and second stages of pre-treatment. Enzymatic hydrolysis was accomplished with a cellulase enzyme blend, Cellic CTec2, in a 50 mM sodium citrate buffer (pH 4.8) at 50 °C using a shaking incubator at a speed of 150 rpm. A solid loading of 2 % and enzyme dosage of 50 g/100 g cellulose in the sample was used for all the experiments. Furthermore, samples were withdrawn every 24 hours for 7 days and analyzed for glucose and xylose using High-Performance Liquid Chromatography (HPLC). Results A high delignification of 90 % and hemicellulose removal of 70 % was achieved with a combination of Alkali and ChCl: Urea pretreatment. Subsequently, the highest glucose and xylose conversion of 90 % and 92 % were observed, respectively, with the same sample. Additionally, the highest glucose yield achieved was 25 gL-1 from the combined alkaline/ChCl: Glycerol treated sample after 120 h. Moreover, the highest xylose yield was 3 gL-1 from the raw sample, the NaOH- pulped sample, and the ChCl: Glycerol-treated sample. Conclusion The results from this study demonstrated that the solvents used for fractionating biomass have a significant effect on the sugar recovery during enzymatic hydrolysis. Also, the pretreatment with a combination of NaOH and DES of ChCl: Glycerol was the most effective for the recovery of glucose and total sugar. In conclusion, yellow thatching grass is a promising substrate for bio-refineries. However, the ideal conditions for enzyme hydrolysis should be investigated further to promote its utilization for value-added products.
In‑silico analysis predicting effects of some Protein conding SNPs of human tumor suppressor protein53 (TP53 gene) by using different Bioinformatic tools
Authors: Waheed Zainab Abdullah , Sarhan Nadia Habeeb , Hamzah Ahmed Ibrahim , Shaker Mustafa Mohammed 
Published: July 2022

Abstract
BackgroundTp53 gene encodes a tumor suppressor protein containing transcriptional activation, DNA binding, and oligomerization domains. The encoded protein responds to diverse cellular stresses to regulate expression of target genes, thereby inducing cell cycle arrest, apoptosis, senescence, DNA repair, or changes in metabolism. Mutations in this gene are associated with a variety of human cancers, including hereditary cancers such as Li-Fraumeni syndrome. Alternative splicing of this gene and the use of alternate promoters result in multiple transcript variants and isoformsAim of studyThe study is aimed to study the effect of some protein coding SNPs on human health and if it benign or neutral by using different bioinformatics tools (I-MUTANT 3. 0,PROVEAN,and SNPS&GO; PhD-snp)ResultsThe result shows that the protein sequence identification was as the following:MAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQMLLDLRWCYFLINSSanalysis of (10) SNPs shows that 5 SNPs(50%) having a nuclic acid change which result in a new amino acid formation and this change was considerd large increase stability according to I-Mutant while just 1SNP (1%)have neutral stability in the same tool but only 4(40%)SNPs showed large decrease stability in the analysis at the same tool which can be considered having effect on human health .While as in PhD-SNP,SNP&GO,PROVEAN showed 0(0%) increase stability but prdected that (50%,50%,40%)have neutral affect in the protein modification while(40%,40%,50%) had Large decrease stability according to PhD-SNP,SNP&GO,PROVEAN respectively which may lead to human disease.
Characteristic analysis of BpbZIP family genes and BpbZIP26 significantly enhanced triterpenoid production in Betula platyphylla under S-nitrosothiol treatment
Authors: Wang Bo , Yang Haixin , Gao Xinglei , Liu Huimin , Fan Guizhi 
Published: July 2022

Abstract
Background: Basic leucine zipper (bZIP) transcription factors are crucial in plant development, and response to environmental stress, etc. With the development of sequencing technology and bioinformatics analysis, the bZIP family genes has been screened and identified in many plant species, but bZIP family genes has not been systematically characterized and identified their function in B. platyphylla.Methods: B. platyphylla reference genome was used to characterize bZIP family genes. The physicochemical properties, chromosome distribution, gene structure, and syntenic relationships were analyzed by bioinformatics methods. The effect of BpbZIP26 on triterpenoid production was investigated using Agrobacterium-mediated transient transformation under N6022 treatment.Results: 51 bZIP family genes were identified in B. platyphylla, and named BpbZIP1~BpbZIP51 sequentially according to their positions on chromosomes. All BpbZIP genes were unevenly distributed on 14 chromosomes, and divided into 13 subgroups according to the classification of A. thaliana bZIP proteins. 12 duplication events were detected in the B. platyphylla genome, and 28 orthologs existed between B. platyphylla and A. thaliana, 83 orthologs existed between B. platyphylla and G. max, and 73 orthologs existed between B. platyphylla and P. trichocarpa. N6022 treatment changed gene expression levels of most BpbZIPs in seedlings of Betula platyphylla. Among of them, N6022 treatment significantly enhanced gene expression levels BpbZIP26 in leaves, stems and roots of B. platyphylla. BpbZIP26 mediated triterpenoid production, and N6022 treatment further enhanced triterpenoid production in BpbZIP26 overexpression calli of B. platyphylla using Agrobacterium-mediated transient transformation. Conclusion: This work highlights potential BpbZIP family genes responding to S-nitrosothiol and their roles in triterpenoid production.
Binding and dynamics demonstrate the destabilisation of ligand binding for the S688Y mutation in the NMDA receptor GluN1 subunit
Authors: Chen Zheng , Church W. Bret , Bastard Karine , Duff Anthony P. , Balle Thomas 
Published: July 2022

Abstract
Encephalopathies are brain dysfunctions which leads to cognitive, sensory, and motor development impairments. Recently, the identification of several mutations within the N-methyl-D-aspartate receptor (NMDAR) have been identified as significant in the aetiology of this group of conditions. However, a complete understanding of the underlying molecular mechanism and changes to the receptor due to these mutations has been elusive. We studied the molecular mechanisms by which one of the first mutation within the NMDAR GluN1 ligand binding domain, Ser688Tyr, cause the encephalopathies. We performed molecular docking, randomly seeded molecular dynamics simulations, and binding free energy calculations to determine the behaviour of the 2 major co-agonists: glycine and D-serine in both the wild-type and S688Y receptor. We observed that the Ser688Tyr mutation leads to instability of both ligands within the ligand binding site due to structural changes associated with the mutation. The binding free energy for both ligands was significantly more unfavourable in the mutated receptor. These results explain previously observed in vitro electrophysiological data and provide detailed aspects of ligand association, and its effects on receptor activity. Our study provides valuable insight into the consequences of mutations within the NMDAR GluN1 ligand binding domain.
The mechanism of action of carbon nanostructures in tribochemical reactions
Authors: Ozimina Dariusz , Kulczycki Andrzej , Janas Dawid , Desaniuk Tomasz , Dzięgielewski Wojciech 
Published: July 2022

Abstract
The aim of this article is to experimentally verify the modified Arrhenius equation for catalytic reactions. The theoretical mathematical reactivity model proposed in the authors’ previous articles assumes that: a) the catalytic reaction rate constant depends not only on the temperature at which the reaction occurs but also on the additional energy supplied to the reactants as a result of the flow of electrons emitted by the catalyst, b) the catalytic reaction rate constant changes in a periodic manner. The research focused on two areas of catalyst applications: controlling tribological processes and converting methanol to hydrogen under visible light irradiation. The article proposes a new interpretation of the earlier findings in tribology and photocatalytic decomposition of methanol. The experimental data show that graphene and nanotubes (CNTs) act as catalysts in tribochemical reactions and that catalytic reactions are initiated by light energy. The key feature of the mechanism by which the nanostructures behave is that they absorb various forms of energy from the surroundings, which are to be stored, transported, or released as pulses back to the surroundings when a catalyzed reaction takes place.
Clinical outcome of drug-coated balloons in patients with femoropopliteal chronic total occlusive lesions: results from the multicenter EAGLE study
Authors: Hayakawa Naoki , Takahara Mitsuyoshi , Nakama Tatsuya , Horie Kazunori , Takanashi Keisuke , Kanagami Teruaki , Ichihara Shinya , Arakawa Masataka , Tobita Kazuki , Mori Shinsuke , Iwata Yo , Suzuki Kenji , Kanda Junji 
Published: July 2022

Abstract
Background: Several studies have reported the efficacy of drug-coated balloons (DCB) for simple femoropopliteal (FP) lesions. However, the effectiveness of DCB for FP chronic total occlusive lesions (CTO) is controversial. The present study investigated the clinical outcomes of DCB for FP-CTO.Materials and methods: We retrospectively analyzed 359 limbs of 318 patients who underwent EVT with DCB for FP-CTO between July 2017 and February 2021 at seven cardiovascular centers. The primary endpoint was 12-month primary patency. The secondary endpoints were the 12-month rates of freedom from: (1) clinically-driven target lesion revascularization (CD-TLR), and (2) re-occlusion. The association of baseline characteristics with the 12-month restenosis risk was investigated using the Cox proportional hazards regression model.Results: The 12-month rate of primary patency was 79.8% (95% confidence interval [95%CI], 75.1% to 84.8%), whereas the corresponding rates of freedom from CD-TLR and re-occlusion were 86.4% (95%CI: 82.6% to 90.4%) and 88.5% (95%CI: 84.7% to 92.4%), respectively. The bailout stent rate was 8.9%. Independent risk factors for restenosis were hemodialysis (adjusted hazard ratio, 2.18 [1.39 to 3.45]; P=0.001), chronic limb-threatening ischemia (CLTI) (2.02 [1.33 to 3.07]; P=0.001), and restenosis lesion (2.02 [1.32 to 3.08]; P=0.001). Use of dual antiplatelet therapy (DAPT) was identified as a protective factor for restenosis (0.54 [0.35 to 0.82]; P=0.003).Conclusion: Despite the low rate of bailout stent, DCB treatment for FP-CTO was effective in real-world clinical practice. Hemodialysis, CLTI, and restenosis lesion were independent risk factors for 12-month restenosis, and the use of DAPT significantly attenuated the risk of 12-month restenosis.
Automatic Segmentation of Hepatic Metastases on DWI images Based on a Deep Learning Method: Assessment of Tumor Treatment Response According to the RECIST 1.1 Criteria
Authors: Liu Xiang , Wang Rui , Zhu Zemin , Wang Kexin , Gao Yue , Li Jialun , Zhang Yaofeng , Wang Xiangpeng , Zhang Xiaodong , Wang Xiaoying 
Published: July 2022

Abstract
Background
Evaluation of treated tumors according to Response Evaluation Criteria in Solid Tumors (RECIST) criteria is an important but time-consuming task in medical imaging. Deep learning methods are expected to automate the evaluation process and improve the efficiency of imaging interpretation.
Objective
To develop an automated algorithm for segmentation of liver metastases based on a deep learning method and assess its efficacy for treatment response assessment according to the RECIST 1.1 criteria.
Methods
One hundred and sixteen treated patients with clinically confirmed liver metastases were enrolled. All patients had baseline and post-treatment MR images. They were divided into an initial (n = 86) and validation cohort (n = 30) according to the examined time. The metastatic foci on DWI images were annotated by two researchers in consensus. Then the treatment responses were assessed by the two researchers according to RECIST 1.1 criteria. A 3D U-Net algorithm was trained for automated liver metastases segmentation using the initial cohort. Based on the segmentation of liver metastases, the treatment response was assessed automatically with a rule-based program according to the RECIST 1.1 criteria. The segmentation performance was evaluated using the Dice similarity coefficient (DSC), volumetric similarity (VS), and Hausdorff distance (HD). The area under the curve (AUC) and Kappa statistics were used to assess the accuracy and consistency of the treatment response assessment by the deep learning model and compared with two radiologists [attending radiologist (R1) and fellow radiologist (R2)] in the validation cohort.
Results
In the validation cohort, the mean DSC, VS, and HD were 0.85 ± 0.08, 0.89 ± 0.09, and 25.53 ± 12.11 mm for the liver metastases segmentation. The accuracies of R1, R2 and automated segmentation-based assessment were 0.77, 0.65, and 0.74, respectively, and the AUC values were 0.81, 0.73, and 0.83, respectively. The consistency of treatment response assessment based on automated segmentation and manual annotation was moderate [K value: 0.60 (0.34–0.84)].
Conclusion
The deep learning-based liver metastases segmentation was capable of evaluating treatment response according to RECIST 1.1 criteria, with comparable results to the junior radiologist and superior to that of the fellow radiologist.