bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Views of People Living with Chronic Stroke and Aphasia on Their Potential Involvement as Research Partners: A Thematic Analysis
Authors: Charalambous Marina , Kountouris Alexia , Phylactou Phivos , Triantafyllidou Ioanna , Annoni Jean-Marie , Kambanaros Maria 
Published: January 2022

Abstract
Background Patient and Public Involvement (PPI) is the active partnership between researchers and patients. PPI in stroke aphasia research aims to ensure equal opportunities for informed decision-making and guarantee democratic representation in citizen control of PPI projects. Yet, little is known about the factors that hinder and/or promote the autonomous involvement of people with aphasia in stroke and aphasia PPI projects. This study aimed to explore the views and perspectives of people who live with chronic stroke, with and without aphasia, with experience in research prior to stroke, on their potential involvement as research partners.Methods The research team included a PPI partner with chronic stroke-induced aphasia. Semi-structured interviews were conducted online with people with chronic stroke (n=8), four with aphasia and four without. Interviews were subject to thematic analysis. Results Inductive thematic analysis generated four themes: (1) the kinds of Restrictions that make involvement in research difficult, (2) the preferred levels and ways of Involvement during the research process, (3) the Support required for active and collaborative involvement, and (4) the Impact of their involvement and how it benefits the study’s outcomes. Furthermore, people with aphasia stressed the importance of constant contextual and third-party support to sustain their active engagement within the research team. Conclusion People experiencing chronic stroke and aphasia are willing to be involved as PPI partners if the research team provides the necessary support. Recommendations for researchers to consider before commencing co-produced research with people with stroke and aphasia are provided.
Analysis of Extreme Precipitation under the New Low Radiative Forcing Scenario in the Inland River Basin of Northwest China
Authors: Xue Lianqing , Yang Mingjie , Liu Yuanhong , Chi Yixia , Wu Yunbiao , Wang Jing 
Published: January 2022

Abstract
With global warming, extreme weather events in various regions have become more abnormal. To study the variation characteristics of extreme precipitation in the inland river basin (IRB) of Northwest China, this paper selected four global climate models (GCMs) under a low radiative forcing scenario to analyze eight-core extreme precipitation indices in the basin. According to the changes of each index in the near future (NF) and the far future (FF), the changes of extreme precipitation have been determined under a low radiative forcing scenario in the basin. Our study shows that all four models can capture seasonality and all have uncertainty. The PRCPTOT showed a trend of decreasing from the center to the southeast and northwest. The SDII showed opposite trends in mountainous and central desert regions. The number of CDD will decrease, while the CWD will change significantly. The P1025 and PG25 will increase by more than 50%. The Rx1day and Rx5day are mainly distributed in some areas such as the desert and Gobi. Although we have predicted the future trend of extreme precipitation in the IRB, the precise prediction of extreme precipitation remains to be further studied.
Exploring Classification Tools for the Prediction of in-Vitro Microbial Pyruvate Yield From Organic Carbon Sources
Authors: Pant Manish , Joshi Tanuja , Omre Pramod Kumar , Singh Triveni Prasad , Kumar Anil , Pundir Hemlata , Chandra Subhash 
Published: January 2022

Abstract
The in-vitro microbial production is based on screening of parameters and statistical validation of parameters using regression analysis. The recent trends have shifted from full factorial design towards more complex response surface methodology designs such as Box-Behnken design, Central Composite design. The problem with these designs is apart from optimisation, the designs are not flexible enough in deducing properties of parameters in terms of class variables. Machine learning algorithms have unique visualisations for the dataset presented with appropriate learning algorithms. The classification algorithms cannot be applied on all datasets and selection of classifier is essential in this regard. The aim of the current study was to investigate the data-mining accuracy on the dataset developed using in-vitro pyruvate production using organic sources for the first time. The attributes were subjected to comparative classification on various classifiers and based on accuracy, multilayer perceptron was selected as classifier. As per the results, the model showed significant results for prediction of classes and a good fit. The learning curve developed also showed the datasets converging and were linearly separable.
Changes in diaphragm contractility in cigarette smoking–exposed and smoking cessation rats are associated with alterations in mitochondrial morphology and homeostasis
Authors: Zhang Yijie , Sheng Haiyan , Shi Xiaoqian , Hu Yuhan , Pang Baosen , Ma Yingmin , Jin Jiawei 
Published: January 2022

Abstract
Background: Cigarette smoking (CS) is one of the greatest risk factors for the pathogenesis and progression of chronic obstructive pulmonary disease (COPD). Although CS cessation is beneficial in preventing COPD progression, the effects of cessation on the diaphragm are unknown, as are the CS-induced mitochondrial changes in the diaphragm during COPD and CS-cessation. In this study, we examined the alterations in mitochondrial morphology and homeostasis, as well as changes in diaphragm contractility during CS exposure and after cessation.Methods: Rats were randomly divided into control, CS-exposure, and CS-cessation groups, including 3-month CS (S3), 6-month CS (S6), 6-month CS followed by 3 months cessation (S6N3), and age-matched control groups. The histological and functional changes in the lungs were examined to evaluate the CS-induced COPD model. The alterations in the diaphragm were further investigated, including contractile properties, the ultrastructure, and the expression of markers of mitochondrial homeostasis.Results: CS exposure caused histological disruption and functional depression in the lungs, and CS cessation failed to result in a significant recovery. CS induced a significant decline in diaphragmatic muscle contractility, accompanied with sever contractile dysfunction in extensor digitorum longus muscles, which was recovered after 3-month CS cessation. CS exposure in parallel disrupted the mitochondrial morphology in diaphragmatic muscle, including decreases in volume density and number density in the S6 group, which was significantly alleviated in the S6N3 group. The mitochondrial quality control was likely depressed in the S6 group, as indicated by the downregulation of Pink1 and Mfn1, markers for mitophagy and mitochondrial fusion/fission. Interestingly, the Mfn1 protein level was recovered after smoking cessation in the S6N3 group.Conclusions: Smoking cessation eased CS-induced diaphragmatic dysfunction and mitochondrial deregulation, but not the adverse changes in pulmonary structure. These diaphragmatic muscle changes are likely associated with deregulated mitochondrial homeostasis, including mitophagy and mitochondrial fusion/fission.
Nilpotent Bi-centers in Continuous Piecewise ℤ2-equivariant Cubic Polynomial Hamiltonian Systems
Authors: chen ting , li shi min , Llibre JAUME 
Published: January 2022

Abstract
One of the classical and difficult problems in the theory of planar differential systems is to classify their centers. Here we classify the global phase portraits in the Poincare disc of the class continuous piecewise differential systems separated by one straight line and formed by two ℤ2 -equivariant cubic Hamiltonian systems with nilpotent bi-centers at (±1,0). The main tools for proving our results are the Poincare compactification, the index theory, and the theory of sign lists for determining the exact number of real roots or negative real roots of a real polynomial in one variable.
A Deep Learning and Genetic Algorithm Based Feature Selection Processes on Leukemia Data
Authors: Frasca Maria , Francese Rita , Risi Michele , Tortora Genoveffa 
Published: January 2022

Abstract
Background: One of the challenges in the bioinformatics field is the characterization of genetic diseases, more precisely of the anomalies of the genetic code that lead to the onset of various pathologies. Concerning leukemia, there exist different types, such as acute and chronic leukemia. The acute ones are Acute Lymphoblastic Leukemia (ALL) and Acute Myeloid Leukemia (AML). This paper considers a dataset of patients belonging to two distinct classes: ALL and AML. The aim is to define a feature selection analysis process mainly based on Deep Learning for both classifying the leukemia of patients as ALL or AML and identifying the list of differential expressed genes. Method: The analyzed data are extracted from dual-channel microarray experiments from the Gene Express Omnibus (GEO) platform, a public database available on the NCBI website containing genomic data, which represent the methylation values for each gene of each sample. The analysis exploits feature selection techniques aimed at reducing the consistent number of variables (genes). To this aim, we use linear models for differential expression for microarray data, and an autoencoder based unsupervised deep learning model to simplify and speed up the classification. Results: Following the reduction in the number of variables, classification models have been implemented with the use of a deep neural network (DNN), obtaining a classification accuracy of approximately 92%. Then, the results have been compared with the ones provided by an approach based on support vector machines (SVM) giving an accuracy of 87,39%. Moreover, another feature selection approach based on genetic algorithms has been experimented obtaining 60,36% (DNN) and 30,63% (SVM) of accuracy. Conclusions: For further verification of the relevance of the selected set of genes, we conducted a gene enrichment analysis based on the functional annotation of the differentially expressed genes. As a result, a differentially expressed pathway between the two pathologies has been detected.
Cyclic guanosine monophosphate inhibits the palmitoylation of LETM1 and downregulates the activity of AKT in human pulmonary artery smooth muscle cells
Authors: Li Wenqing , Huang Wei , Miao Ran , Zou Lihui , Xiao Fei 
Published: January 2022

Abstract
Cyclic guanosine monophosphate (cGMP) is a drug target for the treatment of pulmonary arterial hypertension (PAH). However, the molecular mechanism of cGMP in the pathogenesis of PAH remains unclear, and long-term use of cGMP target drugs leads to drug resistance. We tried to explore the new targets downstream of cGMP signaling and develop novel therapies for PAH. We combined mass spectrometry (MS)-based quantitative proteomics with click-chemistry-probes to identified palmitoylated candidate proteins. S-palmitoylation assay was ultilized to test whether the palmitoylation level of the candidates were regulated by cGMP. We identified palmitoylated proteins in human pulmonary artery smooth muscle cells (HPASMCs). Functional enrichment of the palmitoylated proteins showed that 52 proteins were involved in transmembrane transport, of which 7 were engaged in mitochondrial transport. S-palmitoylation assay in vitro demonstrated that the inner mitochondrial membrane protein, LETM1, was palmitoylated in the cytoplasmic domain at C-terminus. More importantly, cGMP could inhibit the palmitoylation level of LETM1, which in turn suppressed the activity of AKT regulated by LETM1. Our study found that the palmitoylation of LETM1 was the new target downstream of cGMP signaling. The palmitoylated site of LETM1 may provide a new direction for the development of novel therapies for PAH. Moreover, the palmitoylation level of LEMT1 may be a new biomarker for the analysis of prognosis.
Ecotoxicity stress and bioaccumulation in Eisenia fetida earthworms exposed to vanadium pentoxide in soil
Authors: Zhao Shiqing , Ni Hong , Li Ji , Ai Shunhao , Wang Xiaonan , Gao Xiangyun , Xu Qianyun , Liu Zhengtao 
Published: January 2022

Abstract
As an important commercial form of vanadium, vanadium pentoxide (V2O5) is widely used in various modern industries, and its environmental impacts and ecotoxicity have been extensively studied. In this research, the ecotoxicity of V2O5 to earthworms (Eisenia fetida) in soil was tested by exposure to V2O5 at a series of doses, and biochemical response indices, such as the superoxide dismutase (SOD) and catalase (CAT) enzyme activity and malondialdehyde (MDA) content, were analysed to determine the mechanism by which antioxidant enzymes respond to V2O5 exposure. The bioaccumulation factor (BAF) of vanadium pentoxide in the earthworms and soil was also measured to explore the bioaccumulation process of V2O5 in the test period. The results showed that the acute and chronic lethal toxicity values of V2O5 towards E. fetida were 21.96 mg/kg (LC50, 14 days) and 6.28 mg/kg (LC10, 28 days), respectively. For the antioxidant enzymes, SOD and CAT were synchronously induced or inhibited within the time period, and the enzyme activity had a dose-effect relationship with the V2O5 concentration. MDA analysis indicated that lipid peroxidation in earthworms mainly occurred at the early stage and was eliminated slowly in the later stage during the test time. In addition, the BAFs were much less than 1, which indicated that V2O5 did not easily accumulate in earthworms, and the BAF was positively correlated with the exposure time and negatively linearly correlated with the V2O5 concentration in the soil. These results indicated that the bioconcentration and metabolic mechanism of V2O5 in earthworms differed with the different exposure concentrations, and bioaccumulation became balanced after 14-28 days in earthworms exposed to a relatively lower dose of V2O5. The analysis of the integrated biomarker response (IBR) index indicated that the trends of IBR values were positively related to the changing V2O5 concentration, and the IBR index could reflect the organism’s sensitivity to the external stimulus of V2O5. The toxicity of V2O5 is mainly caused by V5+, which is also an important factor in formulating guidelines regarding vanadium levels in soil, and the test earthworm species (Eisenia fetida) is a sensitive biological indicator for risk assessments of vanadium oxidation in the soil.
BM-MSCs ameliorate experimental autoimmune encephalomyelitis via modifying the expression of miR-193, miR-146a, miR-155, miR-21 and miR-326
Authors: Haghmorad Dariush , Khaleghian Ali , Eslami Majid , Farrokhi Amir Salek , Moghadam Bijan Sedighi , Sadeghnejad Abdolvahid , Hemati Maral , Yousefi Bahman 
Published: January 2022

Abstract
Background: Experimental Autoimmune Encephalomyelitis (EAE) is a demyelinating neurological illness having immunological, histological, and clinical parallels to MS (EAE). Cell-to-cell communication and exosomes are two mechanisms through which MSCs exert their effects. The purpose of this study was to see how effective BM-MSCs were at treating EAE patients.Materials and Procedures: Myelin Oligodendrocyte Glycoprotein (MOG35-55) was used to induce EAE in C57BL/6 mice (n=32), and then BM-MSCs 1×106 cells were administered. Every day, clinical and weight examinations were performed. Histology will be used to assess inflammation and demyelination in mouse CNS parts. Using Real-time PCR, we investigated the expression of pro and anti-inflammatory genes, as well as miRNAs intricate in the differentiation and function of Th cells in the control and progression of EAE.Results: In the EAE, BM.MSCs significantly reduced clinical symptoms, inflammation, and demyelination of the brain. Our findings suggest that improved expression of miR-193 miR-146a and decreased expression of miR-155 and miR-21 miR-326 was followed by an increase in cytokine expression levels of IL-10, TGF-β, and IL-4; however, IFN-γ and IL-27 levels were reduced in treatment groups. Treatment groups were also associated with suppressing effects on Th1 and Th17 immune responses, induction of Treg cells, and immunoregulatory responses.Conclusions: These findings provide compelling evidence that MSC-derived exosomes modulate immune suppression and highlight the significance of BM.MSCs and miRNAs in affecting T cell differentiation and reducing CNS inflammation, demyelination, and local neurodegeneration.
Efficient Management of the Nitritation-Anammox Microbiome Through Intermittent Aeration: Absence of the NOB Guild and Expansion and Diversity of the NOx Reducing Guild Suggests A Highly Reticulated Nitrogen Cycle
Authors: Palomo Alejandro , Silva Bruna Daniela Azevedo , Touceda-Suárez María , Félez Carlos Domingo , Mutlu A. Gizem , Dechesne Arnaud , Wang Yulin , Zhang Tong , Smets Barth 
Published: January 2022

Abstract
Obtaining efficient autotrophic ammonia removal (aka partial nitritation-anammox, or PNA) requires a balanced microbiome with abundant aerobic and anaerobic ammonia oxidizing prokaryotes and scarce nitrite oxidizing bacteria. Here, we analyzed the microbiome of an efficient PNA process that was obtained by sequential feeding and periodic aeration. The genomes of the dominant community members were inferred from metagenomes obtained over a 6 month period. Three Brocadia spp. genomes and three Nitrosomonas spp. genomes dominated the autotrophic community; no NOB genomes were retrieved. Two of the Brocadia spp. genomes lacked the genomic potential for nitrite reduction. A diverse set of heterotrophic genomes was retrieved – each containing genomic potential for only a fraction of the denitrification pathway. A mutual dependency in amino acid and vitamin synthesis was noted between autotrophic and heterotrophic community members. Our analysis suggests a highly-reticulated nitrogen cycle in the examined PNA microbiome with nitric oxide (NO) exchange between the heterotrophs and the anammox guild.
Association of Kaiso and Partner Proteins in Oral Squamous Cell Carcinoma
Authors: Salam Hira , Ahmed Shaheen , Bari Furqan , Bukhari Uzma , Haider Ghulam , Mughal Nouman 
Published: January 2022

Abstract
BackgroundE-cadherin loss liberates associated catenins, including p120 catenin, from adherens junctions. Liberated p120 binds a transcription factor, Kaiso, resulting in aberrant expression of the latter’s target genes, several of which are known oncogenes and tumor suppressor genes; therefore, Kaiso plays a dynamic role in various malignancies; however, its role in oral cancer remains to be investigated.Objectives1. To identify the protein expression and intracellular localization of E-cadherin, p120 catenin, and Kaiso, in oral cancer tissues using Immunohistochemistry2. To study the protein expression of selected Kaiso targets (Cyclin D1 and c-Myc) and to correlate their expression with the expression and localization of Kaiso3. To correlate the expression of the aforementioned proteins with clinicopathological parametersMaterials and Methods:Histological grading was performed using Broder’s criteria. IHC staining was used to study the expression and localization of E-cadherin, p120-catenin, Kaiso, Cyclin D1, and c-Myc. Data was analysed using SPSS version 21. The chi-square test was used to measure the statistical significance of associations, keeping a p-value <0.05 as significant.Results:Out of 47 oral cancer cases, E-cad expression was low in 36%, p120-ctn expression was low in 34%, and Kaiso expression was low in 78% tumor specimens. P120ctn was delocalized from membrane in 80.8% cases. Kaiso was expressed in the cytoplasm of 87% of tumor tissues, whereas 29.7% of cases had negative nuclear Kaiso expression. Kaiso expression was significantly associated with the expression of Cyclin D1 but not with c-Myc.Conclusion:The present study identified a change in the subcellular localization of Kaiso in oral cancer tissues. The important implications of this aberrant localization on oral carcinogenesis and tumour prognosis need to be investigated with further studies using larger sample sizes and more sensitive molecular tools.
Multi-omics analysis reveals a non-canonical regulatory pattern of UPL3 on carbon metabolism related cell senescence
Authors: Lan Ying Miao Yu Zhang Chenxing Huang Haisen Lu Yuhao Qiu Shuai 
Published: January 2022

Abstract
The HECT domain-containing UPL3 ligase plays critical roles in plant development and stress protection, but its mechanism of action remains limited. To globally identify its targets in Arabidopsis thaliana, we conducted proteomic analyses of ubiquitinated proteins in upl3 mutants via label-free mass spectrometry. In 6-week-old plants, a landscape of UPL3-dependent ubiquitinated proteins is constructed based on correlated datasets of ubiquitome, proteome, and transcriptome. Preferential ubiquitination of proteins related to carbon fixation represented the largest set of proteins with increased ubiquitination in the upl3 plant, while a small set of proteins with reduced ubiquitination caused by the upl3 mutation were linked to cysteine/methionine synthesis and protein translation processes. Furthermore, the upl3 mutation led to an increase in ubiquitination of some of proteins including chromatin remodeling ATPase (BRM), histone proteins, and most of carbon metabolic enzymes, but decreased the ubiquitination of hexokinase 1 (HXK1), phosphoenolpyruvate carboxylase 2 (PPC2), ribosomal protein S5, and H1/H5 domain proteins. Notably, ubiquitin hydrolase 12 (UBP12), BRM, and PPC2 were identified as the UPL3-interacting partners by both GFP-nanotrap-Mass-Spectrometry analyses and yeast two-hybrid assay. Characterization of upl3, brm, and ubp12 mutant plants and transcriptome analysis suggested that UPL3 fine-tunes carbon metabolism mediating cellular senescence by interacting with UBP12, BRM, and PPC2 in the nucleus. Our results highlight an important function of UPL3 as a hub of regulator on proteolysis-independent regulation and proteolysis-dependent degradation.
Development of a Real-time Framework between MATLAB and PLC through OPC-UA: A case study of a microgrid energy management system
Authors: ZERK Abdallah EL , OUASSAID Mohammed , ZIDANI Youssef 
Published: January 2022

Abstract
Many research laboratories, which develop advanced algorithms for controlling Renewable Energy Systems (RES), lack specialized equipment to carry out research activities and perform experiments. Real-time simulation platforms are suitable for designing specific applications such as fast or real-time computation models. In addition, these platforms provide fast, accurate and reliable studies for RES control implementation. However, Real-time platforms are too expensive and not affordable for most laboratories. In this context, a cost-effective platform is designed to assist researchers in their activities. The hardware solution consists of using a Programmable Logic Control (PLC) to acquire data from the various sensors and control the system through actuators and PID controllers. From a software standpoint, a communication framework between MATLAB and the PLC is developed using the OPC-UA (Open Platform Communications Unified Architecture) technology. In this paper, the operation and efficiency of the platform have been tested using the Software in the Loop (SIL) technique. Hence, the operating model is designed using MATLAB/Simulink to simulate and analyze the appropriate control technique suitable for PLC implementation, whereas the control is executed through Siemens S7-1200 PLC using TIA PORTAL. A visualization interface is set up using WinCC-RT. Furthermore, this paper describes the design of the platform and discusses its utilization, providing examples of its usage through a case study. Indeed, a complex algorithm developed in MATLAB/Simulink can be automatically executed by any PLC using the designed framework.