bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuous Prediction for Tumor Mutation Burden Based on Transcriptional Data in Gastrointestinal Cancers
Authors: Hu Beibei , Yin Guohui , Zhu Jialin , Yi Bai , Sun Xuren 
Published: July 2022

Abstract
Background: Tumor mutation burden (TMB) has been considered biomarker for using of immune checkpoint inhibitors(ICIs), but whole exome sequencing(WES) and cancer gene panel(CGP) based on next generation sequencing for TMB detection are costly. Here, we use transcriptome data of TCGA to construct a model for TMB prediction in gastrointestinal tumors.Methods: Transcriptome data, somatic mutation data and clinical data of four gastrointestinal tumors from TCGA, including esophageal cancer (ESCA), stomach adenocarcinoma (STAD), colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ). Using R, we performed visual analysis of somatic mutation data, differentially expressed genes (DEGs) function enrichment analysis, gene set enrichment analysis (GSEA), and estimated the value of TMB in clinic. Finally, a deep neural network (DNN) model was constructed for TMB prediction.Results: Visualization of somatic mutation data summarized the classification of mutation, frequency of each mutation type, and top-mutated genes. GSEA showed the enrichment of CD4+/CD8+ T cells in the high TMB group and the activation of tumor suppressing pathways. Single-sample GSEA (ssGSEA) found that the high-TMB group had higher level of multiple immune cells infiltration. In addition, distribution of TMB was related to age, M stage, N stage, AJCC stage, and overall survival. After model optimization with the genetic algorithm, in the training set, validation set, and testing set, the Pearson relevance coefficient r between predicted values and actual values reaches 0.98, 0.82, and 0.92, respectively; the coefficient of determination R2 is 0.95, 0.82, and 0.7, respectively. Conclusion: TMB correlates with clinicopathological parameters in gastrointestinal carcinoma, and patients with high TMB have higher levels of immune infiltration. In addition, the DNN model based on 31 genes predicts TMB of gastrointestinal tumors in a high accuracy.
Development of (p-phenylenediamine/glycerol) copolymers by carbon nanotube and eggshell to enhance its properties
Authors: Mohamed Manal G , Mansour Nahla A , Fathy Dalia S , Elmesallamy Salwa M , Mazrouaa Azza M 
Published: July 2022

Abstract
Eggshell is environmental waste that is used daily, inexpensively, and has no economic feasibility in recycling, so, it is regarded as one of the ecologically beneficial additions to improve the physical and mechanical characteristics of polymers. In this work copolymer of (p-phenylenediamine/glycerol) was created via chemically oxidative polymerization with potassium persulfate as an oxidant at different ratios of 1:1, 1:2, and 2:1. The prepared copolymers were treated with eggshell nano, carbon nanotube, and (eggshell nano + carbon nanotube) with altered concentrations of 0.02gm (1%) and 0.04 gm (2%). These prepared samples were described using FT-IR, Raman spectra, H1NMR, and XRD. The morphology has been deliberate by TEM. It is observed that the presence of (eggshell nano + carbon nanotube) enhanced the thermal stability of the copolymers. The conductivity with a ratio of 1:2 of (p-phenylenediamine/glycerol) was 8.46x 10− 6 which is the highest value of the other ratios. The copolymers in presence of 0.04gm (2%) of (eggshell nano + carbon nanotube) for ratio 1:1, 1:2 and 2:1, reaches to 5.46x 10− 4, 1.2x 10− 3 and 1.8x10− 5 respectively. The hardness value increases in the weight of 0.04 gm (2%) (eggshell nano + carbon nanotube) more than the weight of 0.02 gm (1%) for all ratios of the copolymers. The hardness value in presence of (eggshell nano + carbon nanotube) at load 1Kg was high and out of the scale.
The renew plans of urban thermal environment optimization for traditional districts in Xi'an, China
Authors: Ma Dixuan , Wang Yupeng , Zhou Dian , Zhu Zongzhou , Yang Yujun 
Published: July 2022

Abstract
During the process of the high-speed urbanization in Chinese cities, traditional districts renewal is attracting more and more attention. Up to now, the social, economic, political status, and the interaction between each factor have been seriously discussed on urban traditional districts. However, the effects on urban microclimate and the residential living conditions in traditional districts are not well discussed. However, it is strongly related to the living comfort and citizens’ well-being. In this research, two typical traditional districts in Xi’an are selected as case study. According to the original situation of building functions and the community characteristics, two renewal plans are proposed by adding vegetation in open spaces (V), and adding vegetation combined with building redevelopment (V&B), in order to balance the living convenience and thermal environment. Via ENVI-met simulation, the effects of the district renewal plans on thermal environment includes wind speed, air temperature, and mean radiant temperature are evaluated. This study provides method of environmental evaluation for traditional districts renewal, which contributes to sustainable urban planning in historical districts, and provides recommendations for related policy development.
Efficiency of micropollutant removal through artificial recharge and riverbank filtration - case studies Káraný, Czech Republic and Dresden-Hosterwitz, Germany
Authors: Hrkal Zbynek , Adomat Yasmin , Rozman David , Grischek Thomas 
Published: July 2022

Abstract
The aim of the study was to compare the efficiency of pharmaceuticals and personal care products (PPCP) removal in the waterworks Káraný (Czech Republic) and Dresden-Hosterwitz (Germany). Both waterworks use a similar technology of drinking water production (combination of bank filtration and artificial recharge) and have similar river water quality (Jizera and Elbe river). A comparison of two-years monitoring results shows a high efficiency of removing PPCP contained in river water. However, at both waterworks there are groups of substances for which natural treatment steps alone are not sufficient. In the case of Káraný it is Benzotriazole, Sulfamethoxazole and Methylparaben, in the Dresden waterworks it is Oxypurinol, Sulfamethoxazole, Carbamazepine and Lamotrigine.
Characterization and efficiency of chitosan zinc-oxide nano-adsorbent coated sand filter bed for milk processing industry wastewater treatment
Authors: Dinesha Bettathavarekere Lingamurthy , Hiregoudar Sharanagouda , Nidoni Udaykumar , Ramappa Kotrappa Thowdur , Dandekar Anilkumar Tukaram , Hiremath Vijayakumar 
Published: July 2022

Abstract
Sustainable wastewater management in an industry is required to avoid widespread water scarcity problems. In this study, chitosan zinc oxide nano-adsorbent was synthesised and obtained a particle size of 88.35 ± 2.89 d.nm. Chitosan zinc-oxide nano-adsorbent coated sand filter bed was developed by coating CZnO with sand, and characterised by considering its adsorption properties as well as its surface morphology, crystallinity, and functional groups. Batch adsorption experiments were conducted to optimise the process parameters such as CZnO coating dosage, contact time, pH, and initial concentration of biological oxygen demand and chemical oxygen demand. Adsorbent efficiency was studied in treating simulated and real milk processing industry wastewater. The percent reduction efficiency of organic pollutants was found to increase with the increase in contact time and coating dosage of chitosan-zinc oxide nano-adsorbent. Adsorption was rapid and occurred within 140 min with different coating dosages. The percent reduction of biological oxygen demand and chemical oxygen demand increased with an increase in pH. The optimum solution pH for adsorption of both the pollutants from synthetic solution was 6.0. The equilibrium concentration of synthetic solution reached 200 mg/L and 250 mg/L for both pollutants. Four regeneration cycles could be applied without compromising the adsorption efficiency of the filter bed. The performance of the filter bed was compared with previous studies, and it was found to have excellent adsorption efficiency. Hence, chitosan zinc-oxide nano-adsorbent coated sand could be used as a promising filter bed for the removal of organic load from milk processing industry wastewater.
Ligand exchange used as double-edged sword for the removal of ammonia and dyes from wastewater
Authors: El-Ghobashy Marwa , Khamis Mohamed , Elsherbiny Abeer , Salem Ibrahim 
Published: July 2022

Abstract
Cationic ligand exchange is one of the most predominant mechanisms for the removal of ammonia from wastewater through complex formation. The complexation technique occurs between the metal ions loaded on the surface of Amberlite IR-120 (R-H) and ammonia which is present in medium. Cu(II)-loaded Amberlite IR-120 (R-Cu2+) was prepared and described using FT-IR, TGA, XRD, SEM, EDX techniques. The prepared R-Cu2+ was applied for elimination of ammonia from aqueous solution. Different cations such as Co2+, Ni2+ were loaded onto Amberlite IR-120 to study the impact of counter cation on the removal efficiency of ammonia. The ammonia removal percentage followed the order; R-Cu2+ > R-Ni2+ > R-Co2+. The removal of ammonia using R-Cu2+ obeyed Freundlich isotherm model. Thermodynamic parameters characteristics of the adsorption of ammonia onto R-Cu2+ were determined. The time-adsorption data were followed the pseudo-second-order and intraparticle diffusion models. Moreover, the resulting product (R-Cu(II)-amine composite) from the adsorption process exhibited high catalytic activity and could be applicable as low cost catalyst for enhancement the elimination of dyes from wastewater.
Green bionanocomposites based on polyhydroxybutyrate and filled with cellulose nanocrystals: melting processing and characterization
Authors: Schmidt Anja , Bittmann-Hennes Birgit , Montero Belén , Wetzel Bernd , Barral Luis 
Published: July 2022

Abstract
This article contributes to the understanding of biobased and biodegradable polyhydroxybutyrate (PHB) bionanocomposites reinforced by weight contents of 1 wt.% and 3 wt.% of cellulose nanocrystals (CNC), which are derived from waste streams of the paper industry. Samples were melt processed by extrusion and injection molding. Subsequently, the CNC dispersion analysis was completed by transmission electron microscopy. Their thermal properties and their crystallization behavior were investigated by thermogravimetric analysis, differential scanning analysis, X-ray diffraction and polarized optical microscopy. Investigations on the bending properties were made in conjunction with the analysis of their dynamic mechanical behavior. The fracture surface characterization was made by scanning electron microscopy. All these analyses provide a deep insight into their structure-property relationship. The applicability of the processed bionanocomposites in the packaging industry was studied through the analysis of their moisture absorption measurements and their gas barrier properties, which have given an insight of their behavior under environmental conditions. It was found that PHB bionanocomposites with a low content of 1 wt.% CNC, which showed a better dispersion quality of CNC and higher crystallinity, revealed the best performance with an increase in nearly all investigated thermal and mechanical properties, a minor less tendency to moisture absorption and better barrier properties against oxygen and water vapor. All these findings demonstrated that these bionanocomposites could be used for applications in the packaging industry.
Comprehensive analysis of Distal-Less homeobox family gene expression in colon cancer
Authors: Chen Yongcheng , Li Dongbing , Wang Dongliang , Peng Hui 
Published: July 2022

Abstract
Background. The Distal-Less homeobox (DLX) gene family plays an important role in several tumors. However, the expression pattern, prognostic and diagnostic value, possible regulatory mechanisms, and the relationship between DLX family and immune infiltration in colon cancer (COAD) have not been systematically reported.Methods. We used Wilcoxon rank sum test and t-test to assess DLX gene family expression between COAD tissues and unpaired normal colon tissues, cBioPortal to analyze DLX gene family variants, R (version 3.6.3) to analyze DLX gene expression in COAD and the relationship between DLX gene family expression and clinical features and correlation heat map, the survival package [version 3.2-10] and the Cox regression module to assess the prognostic value of the DLX gene family, the pROC package [version 1.17.0.1] to analyze the diagnostic value of the DLX gene family, the R ( version 3.6.3) to analyze the possible regulatory mechanisms of DLX gene family members and related genes, the GSVA package [version 1.34.0] to analyze the relationship between the DLX gene family and immune infiltration, and the ggplot2 [version 3.3.3], and survminer package [version 0.4.9] and clusterProfiler package [version 3.14.3] for visualization.Results. DLX 2/3/4/5/6 were significantly upregulated in COAD patients. The expression of DLX family was associated with M stage, pathologic stage, primary therapy outcome, residual tumor, lymphatic invasion, T stage, N stage, age, perineural invasion, and history of colon polyps. DLX2/5 were independently correlated with the prognosis of COAD in multivariate analysis. DLX1/2/3/4/5/6 were involved in the development and progression of COAD by participating in immune infiltration and pathways, including breast cancer, gastric cancer, Hippo signaling pathway, Wnt signaling pathway, signaling pathways regulating pluripotency of stem cells, basal cell carcinoma, melanoma, and staphylococcus aureus infection. Conclusion. The DLX gene family can be used as potential diagnostic or prognostic biomarkers and therapeutic targets for COAD.
MYBPC3 deficiency in cardiac fibroblasts drives their activation and contributes to fibrosis
Authors: Zou Xiaodong , ouyang hongsheng , Lin Feng , Zhang Huanyu , Yang Yang , Pang Daxin , Han Renzhi , Tang xiaochun 
Published: July 2022

Abstract
Genetic mutations in the MYBPC3 gene encoding cardiac myosin binding protein C (cMyBP-C) are the most common cause of hypertrophic cardiomyopathy (HCM). Myocardial fibrosis (MF) plays a critical role in the development of HCM. However, the mechanism for mutant MYBPC3-induced MF is not well defined. In this study, we developed a R495Q mutant pig model using cytosine base editing and observed an early-onset MF in these mutant pigs shortly after birth. Unexpectedly, we found that the “cardiac-specific” MYBPC3 gene was actually expressed in cardiac fibroblasts from different species as well as NIH3T3 fibroblasts at the transcription and protein levels. CRISPR-mediated disruption of Mybpc3 in NIH3T3 fibroblasts activated nuclear factor κB (NF-κB) signaling pathway, which increased the expression of transforming growth factor beta (TGF-β1) and other pro-inflammatory genes. The up-regulation of TGF-β1 promoted the expression of hypoxia-inducible factor-1 subunit α (HIF-1α) and its downstream targets involved in glycolysis such as GLUT1, PFK and LDHA. Consequently, the enhanced aerobic glycolysis with higher rate of ATP biosynthesis accelerated the activation of cardiac fibroblasts, contributing to the development of HCM. This work reveals an intrinsic role of MYBPC3 in maintaining cardiac fibroblast homeostasis and disruption of MYBPC3 in these cells contributes to the disease pathogenesis of HCM.
Diagnostic approach to cerebellar disorders amongst Egyptian children
Authors: Megahed Hisham , Selim Ashraf , Galal Nadia , Hindawy Amina , Hamed Khaled 
Published: July 2022

Abstract
Our present study includes 72 Egyptian children diagnosed to suffer from cerebellar atrophy by brain MRI. All cases were subjected to detailed clinical examination, laboratory tests, neuro-physiological, neuro-radiological, and genetic studies using whole-exome sequencing (WES). Accordingly, we stratified our cases into initial groups. Neuronal ceroid lipofuscinosis (NCL) is the most commonly identified disorder in the cohort. This is followed by metachromatic leukodystrophy, mitochondrial encephalopathy, adreno-leukodystrophy, Aicardi syndrome, and Joubert syndrome. Integration of proper clinical examination, laboratory investigations, neurophysiological, and neuro-radiological investigations are essential to prioritize the optimal further potential genetic assessment.
Meaningful co-production with clinicians: Establishing a practice-based research network with physiotherapists in regional Australia.
Authors: Gleadhill Connor Patrick , Williams Christopher Michael , Kamper Steven , Bolsewicz Katarzyna , Delbridge Andrew , Mahon Benjamin , Donald Bruce , Delore Caitlin , Boettcher Craig , Renfrew David , Manvell Joshua , Dooley Katherine , Byrne Michael , Manvell Nicole , Watson Toby , Makaroff Andrew , Gibbs Benedicta , Barnett Christopher , Corrigan Michael , Leyland Murray , Mullen Nicholas , Gallagher Ryan , Zelinski Samuel , Lamond Steven , Maude Travis , Davidson Simon , Robson Emma , Silva Priscilla Viana Da 
Published: July 2022

Abstract
Background: The disconnect between research and clinical practice leads to research evidence that is often not useful for clinical practice. Practice-based research networks are collaborations between researchers and clinicians aimed at co-producing more useful research. Such networks are rare in the physiotherapy field. We aimed to describe i) clinician’s motivations behind, and enablers to, participating in a network; ii) the process of network establishment; and iii) research priorities for a practice-based network of physiotherapists in the Hunter Region of New South Wales (NSW), Australia that supports research co-production. MethodsWe describe the methods and outcomes of three steps we used to establish the network. Step one involved consultation with local opinion leaders and a formative evaluation to understand clinician’s motivations behind, and enablers to, participating in a network. Step two involved establishment activities to generate a founding membership group and co-design a governance model. Step three involved mapping clinical problems through a workshop guided by systems thinking theory with local stakeholders and prioritising research areas.ResultsThrough formative evaluation focus groups, we generated five key motivating themes and three key enablers for physiotherapists’ involvement in the network. Establishment activities led to a founding membership group (n=29, 67% from private practice clinics), a network vision and mission statement, and a joint governance group (9/13 (70%) are private practice clinicians). Our problem mapping and prioritisation process led to three clinically relevant priority research areas with the potential for significant change in practice and patient outcomes. ConclusionsClinicians are motivated to collaborate with researchers to not only improve research relevance, but to solve a wide array of issues with the delivery of care. Research that follows from this collaboration should, therefore, be maximally useful to clinical practice by addressing issues that may not be possible to address when working in silos. More work is needed to explore the proposed benefits of practice-based research networks.
QTL analysis of drought tolerance traits in rice during vegetative growth period
Authors: chen li 
Published: July 2022

Abstract
Drought affects the growth and development of rice from direct seeding or transplanting to maturity in north China. It is important to carry out QTL mapping for drought resistance to improve rice breeding. In this study, a rice RIL population consisting of 253 families was constructed by crossing Miyang 23 with Jileng 1, both of which exhibit strong drought resistance. The leaf rolling index (LRI), leaf withering degree (LWD) and leaf chlorophyll content (SPAD) were measured over three years, and QTLs for these traits were mapped. The results showed that LRI, LWD and SPAD were all quantitative traits controlled by multiple genes. A total of 28 QTLs related to three drought-resistant indices were detected; four loci controlling LRI and LWD were detected on Chromosome 1. qLRI1-1 and qLWD1-4 were located in the interval of AH01001843-RM302, explaining 10.30% and 4.90% of the phenotypic variation respectively; qLWD1-2B and qLRI-1JC were both located in RM315-S01167A, and qLWD1-2B was detected three times in different growth periods in 2018, and explained 4.04%-11.15% of the phenotypic variation. qLRI-1JC was detected four times in different growth periods in 2019, which explaining 4.45%-7.96% of the phenotypic variation. The three QTLs located on Chromosome 5, qLRI5-1, qLWD5-1B and qLRI5-2B, were all located in CMB0526.3486-RM87. qLWD5-1B and qLRI5-2B were detected three times in 2019 at different growth stages, and their contribution rates to phenotypic variation ranged from 6.81% to 6.93% and 5.46% to 9.13%, respectively. The four QTLs detected on Chromosome 12, qLWD12-1, qLWD12-3, qLRI12-1A and qLRI12-3A, were all located in the S12099-CMB1226.0 interval and were repeatedly detected in 2018-2019, explaining the 4.59%-7.25% of the phenotypic variation. The above QTLs, including qLWD1-2B, qLRI1-1JC, qLWD5-1B and qLRI5-2B, have been detected many times. In the future, it would be interesting to implement in-depth fine mapping of the QTLs and use the identified markers in the drought resistance molecular marker selection breeding of rice.
On resonances and transverse and longitudinal oscillations in a hoisting system due to boundary excitations
Authors: Wang Jing , Horssen Wim T. van 
Published: July 2022

Abstract
In this paper, we study transverse and longitudinal oscillations and resonances in a hoisting system induced by boundary disturbances. The dynamics can be described by an initial-boundary value problem for a coupled system of nonlinear wave-equations on a slowly time-varying spatial domain. It will be shown how the boundary excitations and the nonlinear terms influence transverse and longitudinal vibrations of the system. Firstly, due to the slow variation of the cable length, a singular perturbation problem arises. By using an interior layer analysis many resonance manifolds are detected. Secondly, it will be shown that resonances in the system are caused not only by boundary disturbances but also by nonlinear interactions. Based on these observations, a three time-scales perturbation method is used to approximate the solution of the initial-boundary value problem analytically. It turns out that for special frequencies in the boundary excitations and for certain parameter values of the longitudinal stiffness and the conveyance mass, many oscillation modes jump up from small to large amplitudes in the transverse and longitudinal directions. Finally, numerical simulations are presented to verify the obtained analytical results.