bluuebunny/crossref_metadata_2025 huggingface dataset:
A Platform for Co-Culture of Primary Human Colonic Epithelium With Anaerobic Probiotic Bacteria
Authors: Kim Raehyun , Wang Yuli , Sims Christopher E. , Allbritton Nancy L.
Published: June 2022

An in vitro platform was designed and optimized for the co-culture of probiotic anaerobic bacteria with a primary human colonic epithelium having a goal of assessing the anti-inflammatory impact of the probiotic bacteria. The device maintained a luminal O2 concentration at <1% while also supporting an oxygenated basal compartment at 10% for at least 72 h. Measurement of the transepithelial resistance of a confluent colonic epithelium showed high monolayer integrity while fluorescence assays demonstrated that the monolayer was comprised primarily of goblet cells and colonocytes, the two major differentiated cell subtypes of the colonic epithelium. High monolayer barrier function and viability were maintained during co-culture of the epithelium with the probiotic obligate anaerobe Anaerobutyricum hallii (A. hallii). Importantly the device supported a static co-culture of microbes and colonic epithelium mimicking the largely static or low flow conditions within the colonic lumen. A model inflamed colonic epithelium was generated by the addition of tumor necrosis factor-α (TNF-α) and lipopolysaccharide (LPS) to the basal and luminal epithelium sides, respectively. Co-culture of A. hallii with the LPS/TNF-α treated intestine diminished IL-8 secretion by ≥40% which could be mimicked by co-culture with the A. hallii metabolite butyrate. In contrast, co-culture of the inflamed epithelium with two strains of lactic acid-producing bacteria, Lactobacillus rhamnosus GG (LGG) and Bifidobacterium adolescentis (B. adolescentis), did not diminish epithelial IL-8 secretion. Co-culture with colonic epithelial cells from different donors demonstrated a consistent anti-inflammatory effect by A. hallii, but distinct responses to co-culture with LGG and B. adolescentis. The demonstrated system offers a simple and easily adopted platform for examining the physiologic impact of alterations in the intestinal epithelium that occur in the presence of probiotic bacteria and their metabolites.
Hyaluronic Acid-Based Nanomaterials as a New Approach to the Treatment and Prevention of Bacterial Infections
Authors: Alipoor Reza , Ayan Mohammad , Hamblin Michael R , Ranjbar Reza , Rashki Somaye
Published: June 2022

Bacterial contamination of medical devices is a great concern for public health and an increasing risk for hospital-acquired infections. The ongoing increase in antibiotic-resistant bacterial strains highlights the urgent need to find new effective alternatives to antibiotics. Hyaluronic acid (HA) is a valuable polymer in biomedical applications, partly due to its bactericidal effects on different platforms such as contact lenses, cleaning solutions, wound dressings, cosmetic formulations, etc. Because the pure form of HA is rapidly hydrolyzed, nanotechnology-based approaches have been investigated to improve its clinical utility. Moreover, a combination of HA with other bactericidal molecules could improve the antibacterial effects on drug-resistant bacterial strains, and improve the management of hard-to-heal wound infections. This review summarizes the structure, production, and properties of HA, and its various platforms as a carrier in drug delivery. Herein, we discuss recent works on numerous types of HA-based nanoparticles to overcome the limitations of traditional antibiotics in the treatment of bacterial infections. Advances in the fabrication of controlled release of antimicrobial agents from HA-based nanosystems can allow the complete eradication of pathogenic microorganisms.
Regulation of 3D Organization and Its Role in Cancer Biology
Authors: Peng Anghui , Peng Wang , Wang Ruiqi , Zhao Hao , Yu Xinyang , Sun Yihao
Published: June 2022

Three-dimensional (3D) genomics is the frontier field in the post-genomics era, its foremost content is the relationship between chromatin spatial conformation and regulation of gene transcription. Cancer biology is a complex system resulting from genetic alterations in key tumor oncogenes and suppressor genes for cell proliferation, DNA replication, cell differentiation, and homeostatic functions. Although scientific research in recent decades has revealed how the genome sequence is mutated in many cancers, high-order chromosomal structures involved in the development and fate of cancer cells represent a crucial but rarely explored aspect of cancer genomics. Hence, dissection of the 3D genome conformation of cancer helps understand the unique epigenetic patterns and gene regulation processes that distinguish cancer biology from normal physiological states. In recent years, research in tumor 3D genomics has grown quickly. With the rapid progress of 3D genomics technology, we can now better determine the relationship between cancer pathogenesis and the chromatin structure of cancer cells. It is becoming increasingly explicit that changes in 3D chromatin structure play a vital role in controlling oncogene transcription. This review focuses on the relationships between tumor gene expression regulation, tumor 3D chromatin structure, and cancer phenotypic plasticity. Furthermore, based on the functional consequences of spatial disorganization in the cancer genome, we look forward to the clinical application prospects of 3D genomic biomarkers.
Comparison of Descriptor- and Fingerprint Sets in Machine Learning Models for ADME-Tox Targets
Authors: Orosz Álmos , Héberger Károly , Rácz Anita
Published: June 2022

The screening of compounds for ADME-Tox targets plays an important role in drug design. QSPR models can increase the speed of these specific tasks, although the performance of the models highly depends on several factors, such as the applied molecular descriptors. In this study, a detailed comparison of the most popular descriptor groups has been carried out for six main ADME-Tox classification targets: Ames mutagenicity, P-glycoprotein inhibition, hERG inhibition, hepatotoxicity, blood–brain-barrier permeability, and cytochrome P450 2C9 inhibition. The literature-based, medium-sized binary classification datasets (all above 1,000 molecules) were used for the model building by two common algorithms, XGBoost and the RPropMLP neural network. Five molecular representation sets were compared along with their joint applications: Morgan, Atompairs, and MACCS fingerprints, and the traditional 1D and 2D molecular descriptors, as well as 3D molecular descriptors, separately. The statistical evaluation of the model performances was based on 18 different performance parameters. Although all the developed models were close to the usual performance of QSPR models for each specific ADME-Tox target, the results clearly showed the superiority of the traditional 1D, 2D, and 3D descriptors in the case of the XGBoost algorithm. It is worth trying the classical tools in single model building because the use of 2D descriptors can produce even better models for almost every dataset than the combination of all the examined descriptor sets.
Deciphering the Impact of Mutations on the Binding Efficacy of SARS-CoV-2 Omicron and Delta Variants With Human ACE2 Receptor
Authors: Khan Alamgir , Khan Salman Ali , Zia Komal , Altowyan Mezna Saleh , Barakat Assem , Ul-Haq Zaheer
Published: June 2022

The pandemic of COVID-19, caused by SARS-CoV-2, has globally affected the human health and economy. Since the emergence of the novel coronavirus SARS-CoV-2, the life-threatening virus continues to mutate and evolve. Irrespective of acquired natural immunity and vaccine-induced immunity, the emerging multiple variants are growing exponentially, crossing the territorial barriers of the modern world. The rapid emergence of SARS-CoV-2 multiple variants challenges global researchers regarding the efficacy of available vaccines and variant transmissibility. SARS-CoV-2 surface-anchored S-protein recognizes and interacts with the host-cell ACE2, facilitating viral adherence and entrance into the cell. Understanding the interfacial interactions between the spike protein of SARS-CoV-2 variants and human ACE2 receptor is important for the design and development of antiviral therapeutics against SARS-CoV-2 emerging variants. Despite extensive research, the crucial determinants related to the molecular interactions between the spike protein of SARS-CoV-2 variants and host receptors are poorly understood. Thus, in this study, we explore the comparative interfacial binding pattern of SARS-CoV-2 spike RBD of wild type, Delta, and Omicron with the human ACE2 receptor to determine the crucial determinants at the atomistic level, using MD simulation and MM/GBSA energy calculations. Based on our findings, the substitution of Q493R, G496S, Q498R, and Y505H induced internal conformational changes in Omicron spike RBD, which leads to higher binding affinity than Delta spike RBD with the human ACE2 receptor, eventually contributing to higher transmission and infectivity. Taken together, these results could be used for the structure-based design of effective antiviral therapeutics against SARS-CoV-2 variants.
Synthesis of Melatonin Derivatives and the Neuroprotective Effects on Parkinson’s Disease Models of Caenorhabditis elegans
Authors: He Li , Du Jing-Jing , Zhou Jun-Jie , Chen Meng-Ting , Luo Lu , Li Bao-Qiong , Zhang Xiang-Zhi , Ma Wen-Zhe , Ma Ai-Jun , Feng Na
Published: June 2022

Melatonin (MT) is a hormone with antioxidant activity secreted by the pineal gland in the human brain, which is highly efficient in scavenging free radicals and plays an important role in the neuro-immuno-endocrine system. Emerging evidence showed that MT supplementation was a potential therapeutic strategy for Parkinson’s disease (PD), which inhibits pathways associated with oxidative stress in PD. In this study, we reported a C7-selective olefination of melatonin under rhodium catalysis with the aid of PIII-directing groups and synthesized 10 new melatonin-C7-cinnamic acid derivatives (6a–6j). The antioxidant potential of the compounds was evaluated both by ABTS and ORAC methods. Among these newly synthesized melatonin derivatives, 6a showed significantly higher activity than MT at 10−5 M. In the transgenic Caenorhabditis elegans model of PD, 6a significantly reduces alpha-synuclein aggregation and dopaminergic neuronal damage in nematodes while reducing intracellular ROS levels and recovers behavioral dysfunction induced by dopaminergic neurodegeneration. Further study of the mechanism of action of this compound can provide new therapeutic ideas and treatment strategies for PD.
Lithospheric Thermal Structure in Jinggangshan City: Implications for High Geothermal Background
Authors: Liao Yuzhong , Liu Yanguang , Liu Feng , Wei Shuaichao , Duan Hexiao
Published: June 2022

Jinggangshan City, which is located in the southwestern part of Jiangxi Province, is rich in hot springs. However, lack of geothermal studies has limited the exploration and utilization of the geothermal resources in this city. This study estimated the terrestrial heat flow in Jinggangshan City through well logging and analyses of rock thermal conductivity and heat production. Based on this and the surrounding geoscience transect and the Crust 1.0 model, this study constructed a one-dimensional lithospheric thermal structure by solving the steady-state heat conduction equation. Furthermore, the deep temperature distribution in Jinggangshan City was obtained to better understand the geodynamic condition of the geothermal resources in this city. The results show that the heat flow in this city is around 83.52 mW/m2, indicating the high heat background for the formation of geothermal resources. According to the lithospheric thermal structure of Jinggangshan City, the mantle contributes more to the terrestrial heat flow (qm/qc > 1) than the crust. The temperature of the Mohorovicic discontinuity (the Moho) is 671.7°C, which is consistent with that below the Tanlu deep fault (620–690°C). Moreover, the calculated depth of the Curie surface (585°C) is 27 km, which is consistent with the Curie isotherm depth estimated from aeromagnetic data. This consistency verifies the validity of the lithospheric thermal structure of Jinggangshan City constructed in this study. In summary, the high heat background plays an important role in the formation of geothermal resources in Jinggangshan City.
Geochemical Characteristics of Catalytic Hydrogenation of Low-Mature Kerogen Under Deep Fluids
Authors: Huang Xiaowei , Jin Zhijun , Liu Quanyou , Meng Qingqiang , Zhu Dongya , Wang Lu , Liu Jiayi , Zhang Panpan , Wang Jingbin
Published: June 2022

There is increasingly valued attention on whether the matter and energy carried in the deep fluids can significantly change the hydrocarbon (HC) generation of low-mature source rocks. Previous studies suggest that the upward movement of deep fluids to sedimentary basins will change the HC generation evolution mode of low-mature source rocks, and the matter and energy carried by the fluid will transform the evolution process as transient events. However, there is a lack of quantitative evaluation of the specific changes of gaseous HC generation in the process of modification. In this study, the effect of deep fluids on HC generation and evolution of low maturity source rocks were quantitatively studied through simulation experiments of the gold tube closed system. We quantitatively selected hydrogen and catalysts (ZnCl2 and MoS2) to conduct catalytic hydrogenation of kerogen and explore the quantitative effects of deep fluids on HC generation in low-mature source rocks. Through the experimental results, it is found that catalytic hydrogenation has significant changes in a HC generation transformation of organic matter (OM). With the increase of catalytic hydrogenation reaction intensity, the maximum gaseous HC generation yield is 3.16–3.24 times that of the control groups without hydrogenation. In the relatively low-temperature stage (<400°C), the competitive hydrogenation effect occurs and the drying coefficient is high. After the high-temperature stage, a large amount of hydrogen participates in the reaction, which significantly promotes the increase of gaseous HCs and decreases the drying coefficient. ZnCl2 or MoS2 can change the relative content ratio of isomerism and isomorphism of butane and pentane, suggesting that cationic catalysis plays a greater role. In the reaction process, OM plays the most important role in the contribution to HC generation, exogenous hydrogen is more likely to participate in HC generation reaction than water and has the potential contribution to HC generation in Fischer-Tropsch synthesis (FFT) under catalytic conditions. The results of this study effectively verify that exogenous hydrogen and metal elements in deep fluids significantly modify the thermal evolution of low-mature source rocks, and enhance the HC generation potential in the high-temperature stage.
Characteristics of Karst Formations and Their Significance for Shale Gas Exploration
Authors: Hu Xiuquan , Liu Hong , Tan Xiucheng , Dan Yong , He Heng , Xiao Chenjing , Li Ruixue
Published: June 2022

The classification method of karst formations is widely used in engineering and environmental geology but is seldom used in petroleum geology. In this study, the classification method of karst formations is applied to the sealing study of shale gas roof and floor carbonate rocks, and the influence on shale gas accumulation and drilling is discussed. The Paleozoic black shale in southern China is primarily formed by marine and transitional faces, and the intergrowth between shale and carbonate rocks is a basic geological feature of the Paleozoic strata in southern China. Carbonate karst is an unavoidable problem in shale gas exploration in southern China. Around the black shale target layer, in the Upper Paleozoic trait region, the study starts from the development strength of karst strata, through geological profile survey, spring flow statistics, test, and other methods and means; the shale and the carbonate rock contacted with it are taken as a whole to explore the impact of karst strata on shale gas drilling. The Upper Paleozoic karst strata in the study area were divided into two kinds, four types, and six subtypes. It was determined that the limestone continuous karst strata of the Sidazhai Formation and the second member of the Nandan Formation are the sensitive layers of shale gas drilling, whereas the first number of Nandan and Wuzhishan formations are shale reservoir-forming packers. In addition, a method for evaluating the karst sensitivity of shale gas exploration is summarized. The karst avoidance, karst-sensitive, and karst-insensitive areas for shale gas exploration were divided. Combined with the surface and underground conditions and the basic geological conditions of shale gas not being significantly different, shale gas drilling should avoid the fold core and fault zones.
Preparation and Thermophysical Properties of Sodium Nitrate/Nanoparticle/Expanded Graphite Composite Heat Storage Material
Authors: Song Wenbing , Lu Yuanwei , Fan Zhansheng , Wu Yuting
Published: June 2022

As a medium and high temperature heat storage medium, the thermal performance of molten salt plays an important role in the thermal energy storage system. In order to improve the specific heat capacity and thermal conductivity of molten salt, a mechanical dispersion method is used to prepare a shape-stable composite phase change material for thermal energy storage. Nitrate (NaNO3) has a higher phase change latent heat, which was chosen to combined with different nanoparticles (SiO2, SiO2+TiO2) to improve its specific heat capacity, and with expanded graphite (EG) as a carrier matrix to improve thermal conductivity. Through the characterization of its chemical compatibility and thermophysical properties, the results show that the nanoparticles, EG and NaNO3 have good chemical compatibility. Compared to NaNO3, the thermophysical properties of composite (NaNO3:(SiO2+TiO2):EG = 84%:0.1% + 0.9%:15%, mass ratio) was improved obviously. The average specific heat capacity before the phase change increased from 1.45 J/(g·K) to 1.81 J/(g·K), and the average specific heat capacity after the phase change increased from 1.69 J/(g·K) to 2.47 J/(g·K); The thermal conductivity is about 13.9 times higher than that of NaNO3; in the range of 100–380°C, the heat storage density of the composites is about 679.2 kJ/kg 300 thermal stability tests showed that the latent heat of the composites is reduced by 7.4%, and the specific heat capacity before and after the phase change is reduced by 6.1 and 6.0%, respectively. The research can provide a broad application prospects in the field of medium temperature energy storage.
Edge Computing Based Electricity-Theft Detection of Low-Voltage Users
Authors: Zheng Yingjun , Chen Feng , Yang Hongming , Su Sheng
Published: June 2022

Electricity theft of low voltage (LV) users could result not only in the escalation of power loss but also in dangerous electric shock. Since LV users are served by distribution transformers, electricity theft of an LV user will cause line loss escalation of the associated distribution serving zone (DTSZ). Therefore, it seems promising to identify anomaly users of electricity theft with a Granger causality test to find out the user causing an escalation of line loss in DTSZ with time series of users’ usage and line loss. However, meters of LV users in severe environments occasionally suffer from communication failure to upload metering data to the head end of advanced metering infrastructure (AMI), which could distort the daily electricity usage of the associate user. Consequently, it could cause false alarms unavoidably once we detect electricity theft with these distorted data. Since the distribution transformer unit (DTU) collects metering data of LV users within associate DTSZ without distortion, an edge computing–based electricity theft detection approach is proposed in this article. The correlation between line loss of a DTSZ and electricity usage of anomaly users of electricity theft is first analyzed. Thereafter, the Granger causality test is used to identify anomaly users with authentic usage data with edge computing in DTU. Finally, the abnormal data and the data repaired by different missing data filling algorithms are used on the main station to detect electricity theft. Numerical simulation suggests that although missing data completion could recover information in missing data partially, it could result in notable false positive alarms in electricity theft, while the proposed method based on edge computing can completely eliminate the data distortion caused by communication failure.
Influence of Supercritical CO2 on the Formation Sensitivity of Tight Sandstone
Authors: Peng Huan , Zhou Lang , Yang Jian , Peng Junliang , Han Huifen , Gou Xinghao , Wang Zhouyang
Published: June 2022

It is challenging to get water-based fracture fluid to flow back into low-pressure gas reservoirs. In order to solve the problem, supercritical CO2 is a novel type of non-aqueous fracturing technique with a wide range of applications prospect in low-pressure tight sandstone. In order to determine whether supercritical CO2 fracturing with low-pressure tight sandstone is feasible tight sandstone cores from the Jinqiu Gas field in the Sichuan Basin were used to evaluate the influence of supercritical CO2 on the formation sensitivity of sandstone reservoirs. Supercritical CO2 was used to interact with tight sandstone samples under formation conditions, and then the changes in velocity sensitivity, water sensitivity, salinity sensitivity, alkaline sensitivity, acid sensitivity, and stress sensitivity of tight sandstone were observed. Velocity sensitivity damage decreased by 5.4%, water sensitivity damage decreased by 13.3%, salinity sensitivity damage decreased by 16.6%, alkaline sensitivity damage decreased by 2%, acid sensitivity damage decreased by 14.4%, and stress sensitivity damage increased by 8% after the interaction between tight sandstone and supercritical CO2. This finding provides a quantitative assessment of the impact of supercritical CO2 on formation sensitivity, and it can be used to build a supercritical CO2 fracturing scheme for low-pressure water-sensitive tight sandstone.
Hygroscopicity and Ice Nucleation Properties of Dust/Salt Mixtures Originating from the Source of East Asian Dust Storms
Authors: Li Jun , Liu Wanyu , Castarède Dimitri , Gu Wenjun , Li Linjie , Ohigashi Takuji , Zhang Guiqian , Tang Mingjin , Thomson Erik S. , Hallquist Mattias , Wang Sen , Kong Xiangrui
Published: June 2022

Dust storms are common meteorological events that occur frequently in the late spring and early summer in arid and semi-arid areas. The resulting lofted dust and salt mixtures can impact atmospheric chemistry and climate systems through the many pathways represented by aerosol-cloud-climate interactions. In this study, dust/salt samples were collected from important sources of the East Asian dust storm, including the Badain Jaran Desert, the Tengger Desert and the Ulan Buh Desert in northwestern China. Ion chromatography (IC) measurements were performed to determine the concentrations of cations and anions. The ionic concentrations, pH and dissolvable fractions of sand samples show a positive correlation, indicating that the dissolved content is rich in alkaline ions. A positive matrix factorization (PMF) receptor model was employed to analyze the IC results, and from the PMF solutions non-obvious connections to local geography emerge. The results of hygroscopic experiments of sand samples which were measured by a vapor sorption analyzer indicate that the hygroscopicity may be related to the soluble content of samples, and the observed hygroscopic behavior can be well described by a thermodynamic model. The morphology of individual particles was chemically mapped by the synchrotron-based scanning transmission X-ray microscopy, and needle-shaped CaCO3 particles were observed to adhere to more irregular high K-containing particles. Moreover, a continuous flow diffusion chamber was used to investigate the ice nucleation abilities of typical salts, with both homogeneous freezing and deposition nucleation being observed. The results indicate that the salts primarily act as cloud condensation nuclei but can also act as ice nucleating particles at low temperatures.
Genome-Wide Characterization and Comprehensive Analysis of NAC Transcription Factor Family in Nelumbo nucifera
Authors: Song Heyun , Liu Yanling , Dong Gangqiang , Zhang Minghua , Wang Yuxin , Xin Jia , Su Yanyan , Sun Heng , Yang Mei
Published: June 2022

NAC (NAM, ATAF, and CUC) is a ubiquitously expressed plant-specific transcription factor (TF) family which is involved in the regulation of various biological processes. However, a systematic characterization of NAC gene family is yet to be reported in lotus. Here, 82 NnNAC genes which included five predicted membrane-bound NAC proteins were identified in the lotus genome. Phylogenetic analysis revealed seven-subfamily clusters (I–VII) of NnNAC proteins, with homologous gene pairs displaying similar conserved motifs and gene structure characteristics. Transactivation assay of NnNAC proteins revealed an extensive transcriptional activation capacity which is mediated by the highly divergent C-terminal activation domain (AD). Expression analysis of NnNAC genes in lotus tissues showed high transcript levels in root, stamen, petal and seed coat. In addition, 30 and 29 differentially expressed NnNAC candidate genes putatively involved in lotus seed development and response to complete submergence stress, respectively, were identified. Overall, our study provides potentially useful candidate gene resources for future molecular breeding of lotus varieties with novel agronomic traits.
Characterization of Necroptosis-Related Molecular Subtypes and Therapeutic Response in Lung Adenocarcinoma
Authors: Zhang Jingchen , He Xujian , Hu Jia , Li Tong
Published: June 2022

Lung adenocarcinoma (LUAD) is one of the most common malignant tumors with high morbidity and mortality and is usually associated with therapeutic resistance and poor prognosis because of individual biological heterogeneity. There is an unmet need to screen for reliable parameters, especially immunotherapy-related biomarkers to predict the patient’s outcomes. Necroptosis is a special caspase-independent form of necrotic cell death associated with the pathogenesis, progression, and prognosis of multiple tumors but the potential connection between necroptosis-related genes (NRGs) and LUAD still remains unclear. In this study, we expounded mutational and transcriptional alterations of 67 NRGs in 522 LUAD samples and proposed a consensus-clustering subtype of these patients into two cohorts with distinct immunological and clinical prognosis characteristics. Cluster B patients were associated with a better prognosis and characterized by relatively lower expression of NRGs, higher immune scores in the tumor microenvironment (TME), more mild clinical stages, and downregulated expression of immunotherapy checkpoints. Subsequently, the NRG score was further established to predict the overall survival (OS) of LUAD patients using univariate Cox, LASSO, and multivariate Cox regression analyses. The immunological characteristics and potential predictive capability of NRG scores were further validated by 583 LUAD patients in external datasets. In addition to better survival and immune-activated conditions, low-NRG-score cohorts exhibited a significant positive correlation with the mRNA stem index (mRNAsi) and tumor mutation burden (TMB) levels. Combined with classical clinical characteristics and NRG scores, we successfully defined a novel necroptosis-related nomogram to accurately predict the 1/3/5-year survival rate of individual LUAD patients, and the potential predictive capability was further estimated and validated in multiple test datasets with high AUC values. Integrated transcriptomic analysis helps us seek vital NRGs and supplements a novel clinical application of NRG scores in predicting the overall survival and therapeutic benefits for LUAD patients.
Novel Gene Rearrangement in the Mitochondrial Genome of Three Garra and Insights Into the Phylogenetic Relationships of Labeoninae
Authors: Zhang Chi , Zhang Kun , Peng Ying , Zhou Jianshe , Liu Yifan , Liu Bingjian
Published: June 2022

Complete mitochondrial genomes (mitogenomes) can provide valuable information for phylogenetic relationships, gene rearrangement, and molecular evolution. Here, we report the mitochondrial whole genomes of three Garra species and explore the mechanisms of rearrangements that occur in their mitochondrial genomes. The lengths of the mitogenomes’ sequences of Garra dengba, Garra tibetana, and Garra yajiangensis were 16,876, 16,861, and 16,835, respectively. They contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genomes of three Garra species were rearranged compared to other fish mitochondrial genomes. The tRNA-Thr, tRNA-Pro and CR (T-P-CR) genes undergo replication followed by random loss of the tRNA-Thr and tRNA-Pro genes to form tRNA-Thr, CR1, tRNA-Pro and CR2 (T-CR-P-CR). Tandem duplication and random loss best explain this mitochondrial gene rearrangement. These results provide a foundation for future characterization of the mitochondrial gene arrangement of Labeoninae and further phylogenetic studies.
Investigation of the Effect of Roof Color on the Energy Use of a Selected House in Amman, Jordan
Authors: Alrwashdeh Saad S. , Qadourah Jenan Abu , Al-Falahat Ala’a M.
Published: June 2022

Energy consumption in the buildings sector is considered one of the most important sources of energy consumption in Jordan, as the reason for this is due to the traditional building pattern and the buildings’ lack of various energy saving and rationalization systems. The development of the buildings sector in terms of the capacity of buildings to save and produce energy is one of the most important reasons that lead to saving energy consumption at the national level in Jordan. In this study, the effect of paint colors on the roofs of buildings was studied by studying three different colors, which are blue, white, and black, where it was confirmed that the best colors in energy conservation is black, and white is the opposite of it, which is considered the worst in energy conservation.
Comparative Analysis of Gut Microbial Composition and Functions in Przewalski’s Gazelle (Procapra przewalskii) From Various Habitats
Authors: Zhang Jingjie , Gao Hongmei , Jiang Feng , Liu Daoxin , Hou Yuansheng , Chi Xiangwen , Qin Wen , Song Pengfei , Cai Zhenyuan , Zhang Tongzuo
Published: June 2022

Gut microbiota of mammals participates in host nutrient metabolism and plays an important role in host adaptation to the environment. Herein, to understand the relationship between environment differences and the composition and abundance of the gut microbiota of Przewalski’s gazelle (Procapra przewalskii) in almost all its habitats, high throughput sequencing of the 16S rRNA gene was used to compared the characteristics of the gut microbiota based on total 120 fecal samples. The results showed that Przewalski’s gazelle exhibited different characteristics of microbiota diversity in different habitats. The Jiangxigou Rescue Station (JX), Nongchang (NC), and Ganzihe and Haergai townships (GH) groups had a relatively high microbiota diversity, while the Niaodao scenic area (ND) group had the lowest diversity. This finding seemed to follow a similar pattern of change in the population of Przewalski’s gazelle. Bacteroidetes and Actinobacteria were the phyla with significant differences, especially between the Wayu township (WY) and the other groups. The difference in the microbiota mainly included the Ruminococcaceae UCG-005, Christensenellaceae R-7 group, and Bacteroidaceae and was enriched in the ND, WY, and other regions. We speculated that the difference in the gut microbiota was due to a difference in environmental characteristics, particularly the food resources that the host can obtain. We speculated that a similar microbiome has important functions for species survival and represents the evolutionary commonality of Przewalski’s gazelle, while a different microbiome plays an important role in the adaptation of Przewalski’s gazelle to a different environment. The results of this study illustrate how the same species adapts to different environments from the perspective of gut microbiota plasticity and therefore are of great significance for the protection and restoration of the population of this species.
Combination of Acupoints for Alzheimer’s Disease: An Association Rule Analysis
Authors: Wang Yao-Chin , Wu Chieh-Chen , Huang Abel Po-Hao , Hsieh Po-Chun , Kung Woon-Man
Published: June 2022

Background

Alzheimer’s disease (AD) is an ongoing neurological degeneration characterized by amnesia and a decline in cognitive abilities. Hippocampal neurogenesis is the leading cause of AD. Mild cognitive impairment (MCI), a prodromal state of AD, is mainly due to the degradation of neuropsychiatric manifestations. Previous systematic reviews demonstrated that treatment with acupuncture with Chinese herbs is tolerable and effective in improving cognitive function in patients with AD. Our investigation aimed to discover the main acupoint combination for AD management based on a preceding systematic review and meta-analysis of randomized control trials (RCTs).

Materials and Methods

Our investigation was executed using association rule analysis, which is a common data mining technique accessible within R. Our study elucidated acupoint locations as binary data from 15 of the included studies using the Apriori algorithm.

Results

Thirty-two acupoints were selected from 15 RCTs. The 10 most frequent acupoints were selected. We inspected 503 association rules using the interpreted acupuncture data. The obtained results showed that {SP6, BI10} ≥ {HT7} and {HT7, BI10} ≥ {SP6} were the most associated rules in 15 RCTs.

Conclusion

The combination of acupoints ({SP6, BI10} ≥ {HT7} and {HT7, BI10} ≥ {SP6}) can be acknowledged as a core combination for future acupuncture regimens of AD.
Differential Expression and Correlation Analysis of Global Transcriptome for Hemorrhagic Transformation After Acute Ischemic Stroke
Authors: Han Rongrong , Zhang Peng , Li Hongfang , Chen Yun , Hao Yongnan , Guo Qiang , Zhang Aimei , Li Daojing
Published: June 2022

In order to explore the epigenetic characteristics of hemorrhagic transformation (HT) after acute ischemic stroke, we used transcriptome sequencing technology to analyze the global transcriptome expression profile of patients with and without HT after acute ischemic stroke and to study the differential expression of messenger RNA (mRNA), long noncoding RNA (lncRNA), circular RNA (circRNA) and mircoRNA (miRNA) between the two groups. To further explore the role of differentially expressed genes in HT, we annotated the function of differentially expressed genes by using gene ontology (GO) and pathway analysis on the results and showed that there were 1,051 differential expressions of lncRNAs, 2,575 differential expressions of mRNAs, 447 differential expressions of circRNAs and 47 miRNAs in patients with HT compared with non-HT patients. Pathway analysis showed that ubiquitin-mediated proteolysis, MAPK signal pathway, axon guidance, HIF-1 signal pathway, NOD-like receptor signal pathway, beta-alanine metabolism, Wnt signal pathway, sphingolipid signal pathway, neuroactive ligand-receptor interaction, and intestinal immune network used in IgA production play an important role in HT. Terms such as iron homeostasis, defense response, immune system process, DNA conformational change, production of transforming growth factor beta-2, and oxidoreductase activity were enriched in the gene list, suggesting a potential correlation with HT. A total of 261 lncRNA-miRNA relationship pairs and 21 circRNA-miRNA relationship pairs were obtained; additionally, 5 circRNAs and 13 lncRNAs were screened, which can be used as competing endogenous RNA (ceRNA) to compete with miRNA in the co-expression network. Co-expression network analysis shows that these differentially expressed circRNA and lncRNA may play a vital role in HT and provide valuable information for new biomarkers or therapeutic targets.
LncRNA OIP5-AS1 Knockdown Targets miR-183-5p/GLUL Axis and Inhibits Cell Proliferation, Migration and Metastasis in Nasopharyngeal Carcinoma
Authors: Li Shuo , Tang Mingxing , Zen Nan , Liang Junyi , Xing Xiao , Huang Danglin , Liu Fei , Zhang Xiaomeng
Published: June 2022

Nasopharyngeal carcinoma (NPC) is often associated with the infection of Epstein-Barr virus in nasopharynx and is mainly happened in South China and Southeast Asia. Recently, noncoding RNAs have been reported to regulate NPC carcinogenesis. LncRNA OIP5-AS1 participates in tumorigenesis and progression; however, the inherent mechanism of OIP5-AS1-mediated progression of NPC is unclear. In the current study, we aimed to explore the role of OIP5-AS1 in NPC progression. We measured the cell viability, apoptosis, migration, and invasion in NPC cells after OIP5-AS1 modulation. Moreover, we determined whether OIP5-AS1 exerts its oncogenic functions via sponging miR-183-5p in NPC. Furthermore, we determined whether glutamate ammonia ligase (GLUL) was a downstream target of miR-183-5p. We found that OIP5-AS1 downregulation inhibited the viability, migration and invasion of NPC via targeting miR-183-5p. We also identified that GLUL might be a potential downstream target of miR-183-5p in NPC cells. Mechanistically, OIP5-AS1 promotes cell motility via regulating miR-183-5p and GLUL in NPC cells. We concluded that OIP5-AS1 performed its biological functions via targeting miR-183-5p and GLUL in NPC cells.
Relief Effects of Icariin on Inflammation-Induced Decrease of Tight Junctions in Intestinal Epithelial Cells
Authors: Li Yanli , Liu Jie , Pongkorpsakol Pawin , Xiong Zhengguo , Li Li , Jiang Xuemei , Zhao Haixia , Yuan Ding , Zhang Changcheng , Guo Yuhui , Dun Yaoyan
Published: June 2022

Inflammatory cytokines including TNF-α and IL-1β impair intestinal barrier function in aging by disrupting intestinal tight junction integrity. Icariin (ICA) has a variety of pharmacological effects. Indeed, ICA produces anti-inflammatory, anti-oxidative stress, and inhibitory effects on microRNA (miRNA) expression. This study was to explore whether ICA could alleviate inflammation-associated intestinal barrier function impairment in aging and its underlying mechanism. Of particular interest, network pharmacology prediction indicated the potential therapeutic impacts of ICA for the treatment of colitis. Then, rats were used to study whether ICA has a protective effect on the reduction of tight junctions caused by inflammatory cytokines. Next, Caco-2 cell monolayers were used to explore the mechanism by which ICA alleviates the down-regulation of tight junctions. Network pharmacology prediction revealed that ICA alleviated colitis via suppressing oxidative stress. After ICA intervention, expressions of inflammatory cytokines were reduced, but tight junctions, antioxidant enzymes in aging rats were up-regulated. ICA reversed the TNF-α-induced decrease in abundance of Occludin protein in Caco-2 cell monolayers. Meanwhile, ICA alleviated the increase in permeability and expression of miR-122a. However, the protective effect of ICA was markedly attenuated after transfection with miR-122a mimics. In conclusion, ICA reduced the expressions of Occludin, Claudin1, and Claudin5 in colon, which were related to the reduction of TNF-α and IL-1β and alleviation of colonic in vivore. And ICA attenuated TNF-α-induced Occludin disruption and epithelial barrier impairment by decreasing miR-122a expression in Caco-2 cell monolayers.
New Structural and Mechanistic Insights Into Functional Roles of Cytochrome b559 in Photosystem II
Authors: Chiu Yi-Fang , Chu Hsiu-An
Published: June 2022

Cytochrome (Cyt) b559 is a key component of the photosystem II (PSII) complex for its assembly and proper function. Previous studies have suggested that Cytb559 has functional roles in early assembly of PSII and in secondary electron transfer pathways that protect PSII against photoinhibition. In addition, the Cytb559 in various PSII preparations exhibited multiple different redox potential forms. However, the precise functional roles of Cytb559 in PSII remain unclear. Recent site-directed mutagenesis studies combined with functional genomics and biochemical analysis, as well as high-resolution x-ray crystallography and cryo-electron microscopy studies on native, inactive, and assembly intermediates of PSII have provided important new structural and mechanistic insights into the functional roles of Cytb559. This mini-review gives an overview of new exciting results and their significance for understanding the structural and functional roles of Cytb559 in PSII.
Holitouch: Conveying Holistic Touch Illusions by Combining Pseudo-Haptics With Tactile and Proprioceptive Feedback During Virtual Interaction With 3DUIs
Authors: Ariza Nunez Oscar Javier , Zenner André , Steinicke Frank , Daiber Florian , Krüger Antonio
Published: June 2022

Virtual reality technology and immersive virtual environments often support realistic hand representations via hand-posture-sensing controllers or hand tracking for natural hand-based interaction. However, one limiting factor remains as the lack of realistic haptic feedback including tactile and proprioceptive cues; even for simple haptic interactions like touching a virtual object. This paper introduces the Holitouch technique to improve the haptic realism of essential 3D user interface elements such as buttons. Holitouch is a feedback technique based on a wearable device that combines different types of haptic feedback (i.e., 1) pseudo-haptic, 2) tactile, and 3) proprioceptive) to convey the holistic sensation of stiffness, contact, and activation while interacting with 3D buttons. Our approach provides these sensations by utilizing redundant multisensory cues, i.e., congruent feedback, to create plausible illusions of touch. The results of two experiments show that the proposed feedback combination contributes to delivering a holistic sensation when interacting with buttons in VR while having high user acceptance.
Nomograms for Predicting Overall Survival and Cancer-Specific Survival of Patients With Renal Cell Carcinoma and Venous Tumor Thrombus: A Population-Based Study
Authors: Yang Lin , Fu Bin
Published: June 2022

Background

To provide better prognostic information for patients with renal cell carcinoma (RCC) combined with venous tumor thrombus (VTT). In turn, guide patients’ families and doctors to formulate plans for follow-up treatment and follow-up. We developed nomograms to predict cancer-specific survival (CSS) and overall survival (OS).

Methods

A total of 2961 cases were included in this study. Through univariate and multivariate Cox proportional hazard regression analysis, independent risk factors affecting CSS and OS were screened out, and then a nomogram was drawn based on the screened variables.

Results

Independent risk factors affecting CSS include: tumor size (HR = 1.05), histology (HR = 1.75), grade (HR = 1.94), N staging (HR = 2.06), and M staging (HR = 2.87). The median survival time for CSS was 106 months. Independent risk factors for OS include age (HR = 1.60), tumor size (HR = 1.04), histology (HR = 1.60), grade (HR = 1.68), N staging (HR-1.99), M staging (HR = 2.45). The median survival time for OS is 67 months.

Conclusions

The nomogram based on independent risk factors affecting CSS and OS can well predict the prognosis of renal cell carcinoma with venous tumor thrombus.
Does Change in Physical Activity During the Initial Phase of the COVID-19 Pandemic Predict Psychological Symptoms in Physically Active Adults? A Six-Month Longitudinal Study
Authors: Havnen Audun , Ernstsen Linda
Published: June 2022

Objectives: The current study aimed to investigate if change in physical activity during the initial phase of the COVID-19 pandemic predicted severity of anxiety and depression symptoms 6 months later in physically active adults.

Methods: A total of 855 respondents (32.6% women) completed the Hospital Anxiety and Depression Scale (HADS) at two time points and reported change in physical activity habits in the first 3 months of the COVID-19 lockdown in Norway.

Results: Women had higher prevalence rates than men for both anxiety and depression symptoms in the Unchanged, Increased and Decreased physical activity (PA) subgroups. Women and men who reported Increased PA at baseline were associated with increased risk for anxiety symptoms at time 2. Increased PA was associated with higher risk for depression at time 2 for women, but not for men.

Conclusion: The results indicate that the COVID-19 pandemic is associated with deterioration in mental health also for physically active adults.
Use of Diagnostic Imaging Modalities in Modern Screening, Diagnostics and Management of Breast Tumours 1st Central-Eastern European Professional Consensus Statement on Breast Cancer
Authors: Forrai Gábor , Kovács Eszter , Ambrózay Éva , Barta Miklós , Borbély Katalin , Lengyel Zsolt , Ormándi Katalin , Péntek Zoltán , Tünde Tasnádi , Sebő Éva
Published: June 2022

Breast radiologists and nuclear medicine specialists updated their previous recommendation/guidance at the 4th Hungarian Breast Cancer Consensus Conference in Kecskemét. A recommendation is hereby made that breast tumours should be screened, diagnosed and treated according to these guidelines. These professional guidelines include the latest technical developments and research findings, including the role of imaging methods in therapy and follow-up. It includes details on domestic development proposals and also addresses related areas (forensic medicine, media, regulations, reimbursement). The entire material has been agreed with the related medical disciplines.
Surgical or conservative treatment of an adult patient with a natural course of Chiari I malformation, what should we choose? (brief literature review, clinical case)
Authors:   Bashkir State Medical University, Ufa, Russia, Derevyanko Khristina P. , Safin Shamil M. ,   Bashkir State Medical University, Ufa, Russia, Novikov Yurii O. ,   Bashkir State Medical University
Published: June 2022

Special attention in medicine is paid to a personalized approach to treating patients. Pathology of the craniovertebral junction — Chiari type I malformation has a natural and asymptomatic course. The article provides a literature review of clinical symptoms in non-operated adult patients with a natural course of Chiari type I malformation. A frequent complaint among patients with an asymptomatic course of Chiari type I malformation was headache (77 %). In the structure of cephalgia, the most common forms were: headache associated with cough — 34 %, with migraine — 21.4 % and headache associated with cough and migraine — 21.8 %. Comparative data of surgical and conservative treatment of patients with cephalgic syndrome with Chiari type I malformation. So, cough-related headaches decreased by 95 % after surgery and by 40 % after conservative treatment. In other headaches, pain intensity decreased by 93 % and 61.5 % after conservative and surgical treatment, respectively. A more balanced approach is needed when choosing the tactics of treating these patients. Clinical follow-up of patient K., 58 years old, who has been seen by neurologists, neurosurgeons, chiropractors for Chiari I malformation for 26 years. The patient is a professional ballerina, but the course of her disease did not affect her career and did not lead to surgical intervention. Tactics of management type, there are still no clear criteria for the treatment of asymptomatic and asymptomatic patients with Chiari I malformation. It is necessary to carefully evaluate the nature of structural changes in the brain, the clinical course of the disease, and individually determine the tactics and personalized treatment approach.