bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved inertial projection and contraction method for solving pseudomonotone variational inequality problems
Authors: Tian Ming , Xu Gang 
Published: June 2021

AbstractThe objective of this article is to solve pseudomonotone variational inequality problems in a real Hilbert space. We introduce an inertial algorithm with a new self-adaptive step size rule, which is based on the projection and contraction method. Only one step projection is used to design the proposed algorithm, and the strong convergence of the iterative sequence is obtained under some appropriate conditions. The main advantage of the algorithm is that the proof of convergence of the algorithm is implemented without the prior knowledge of the Lipschitz constant of cost operator. Numerical experiments are also put forward to support the analysis of the theorem and provide comparisons with related algorithms.
An uncertain SIR rumor spreading model
Authors: Sun Hang , Sheng Yuhong , Cui Qing 
Published: June 2021

AbstractIn this paper, an uncertain SIR (spreader, ignorant, stifler) rumor spreading model driven by one Liu process is formulated to investigate the influence of perturbation in the transmission mechanism of rumor spreading. The deduced process of the uncertain SIR rumor spreading model is presented. Then an existence and uniqueness theorem concerning the solution is proved. Moreover, the stability of uncertain SIR rumor spreading differential equation is proved. In addition, the influence of different parameters on rumor spreading is analyzed through numerical simulation. This paper also presents a paradox of stochastic SIR rumor spreading model.
Modeling bacterial resistance to antibiotics: bacterial conjugation and drug effects
Authors: Techitnutsarut Pirommas , Chamchod Farida 
Published: June 2021

AbstractAntibiotic resistance is a major burden in many hospital settings as it drastically reduces the successful probability of treating bacterial infections. Generally, resistance is associated with bacterial fitness reduction and selection pressure from antibiotic usage. Here, we investigate the effects of bacterial conjugation, plasmid loss, and drug responses on the population dynamics of sensitive and resistant bacteria by using a mathematical model. Two types of drugs are considered here: antibiotic M that kills only sensitive bacteria and antibiotic N that kills both bacteria. Our results highlight that larger dose and longer dosing interval of antibiotic M may result in the higher prevalence of resistant bacteria while they do the opposite for antibiotic N. When delays in administering initial and second doses are incorporated, the results demonstrate that the delays may lead to the higher prevalence of resistant bacteria when antibiotic M or N is administered with the longer time of bacteria remaining at the lower prevalence of the latter. Our results highlight that switching antibiotic agents during a treatment course and different bacterial strain characteristics result in a significant impact on the prevalence of resistant bacteria.
Double auction and profit maximization mechanism for jobs with heterogeneous durations in cloud federations
Authors: Lu Runhao , Liang Yuning , Ling Qing , Li Changle , Wu Weigang 
Published: June 2021

AbstractBy sharing resources with each other, different cloud providers in a cloud federation can exploit their diversity in resource configuration and operational cost so as to improve service performance. They should consider the strategy of resource pricing, job scheduling and server provisioning altogether to maximize their own interests. On the other hand, they need to efficiently trade the resources with a suitable mechanism, typically auction, so as to guarantee the participants’ profits. Nevertheless, in consideration of the heterogeneous execution times of jobs, both the pricing strategy and trading mechanism should be delicately designed, which is obviously a challenging task. In this paper, we firstly propose a truthful, individual-rational and ex-post budget-balanced auction mechanism for selecting pairs of buyer and seller winners to trade virtual machines for different durations. Then, to maximize the individual profits, we propose a dynamic resource bidding scheme and a job scheduling strategy based on our importance model of jobs with heterogeneous execution times and resource requirements. The simulation results show that, compared with existing ones, our design can better handle varieties of both execution time and resource requirement and make the participants obtain more individual profits.
Selenogenome and AMPK signal insight into the protective effect of dietary selenium on chronic heat stress-induced hepatic metabolic disorder in growing pigs
Authors: Liu Yan , Tang Jiayong , He Ying , Jia Gang , Liu Guangmang , Tian Gang , Chen Xiaoling , Cai Jingyi , Kang Bo , Zhao Hua 
Published: June 2021

Abstract
Background
Chronic heat stress (CHS) disrupts hepatic metabolic homeostasis and jeopardizes product quality of pigs. Selenium (Se) may regulate the metabolic state through affect selenoprotein. Thus, we investigate the protective effect of dietary hydroxy-4-methylselenobutanoic acid (HMSeBA) on CHS induced hepatic metabolic disorder in growing pigs, and the corresponding response of selenoprotein.

Methods
Forty crossbreed growing pigs were randomly assigned to five groups: control group raised in the thermoneutral environment (22 ± 2 °C) with basal diet; four CHS groups raised in hyperthermal condition (33 ± 2 °C) with basal diet and supplied with 0.0, 0.2, 0.4, and 0.6 mg Se/kg HMSeBA, respectively. The trial lasted 28 d. The serum biochemical, hepatic metabolism related enzyme, protein and gene expression and 25 selenoproteins in liver tissue were determined by real-time PCR, ELISA and western blot.

Results
CHS significantly increased the rectal temperature, respiration rate, serum aspartate aminotransferase (AST) and low-density lipoprotein cholesterol (LDL-C) of pigs, up-regulated hepatic heat shock protein 70 (HSP70) and induced lower liver weight, glycogen content, hepatic glucokinase and glutathione peroxidase (GSH-Px). The CHS-induced liver metabolic disorder was associated with the aberrant expression of 6 metabolism-related gene and 11 selenoprotein encoding genes, and decreased the protein abundance of GCK, GPX4 and SELENOS. HMSeBA improved anti-oxidative capacity of liver. 0.4 or 0.6 mg Se/kg HMSeBA supplementation recovered the liver weight, glycogen content and rescue of mRNA abundance of genes related to metabolism and protein levels of GCK. HMSeBA supplementation changed expressions of 15 selenoprotein encoding genes, and enhanced protein expression of GPX1, GPX4 and SELENOS in the liver affected by CHS. CHS alone showed no impact while HMSeBA supplementation increased protein levels of p-AMPKα in the liver.

Conclusions
In summary, HMSeBA supplementation beyond nutrient requirement mitigates CHS-induced hepatic metabolic disorder, recovered the liver glycogen content and the processes that are associated with the activation of AMPK signal and regulation of selenoproteins in the liver of growing pigs.
Recent advances in Lynch syndrome
Authors: Li Xi , Liu Guodong , Wu Wei 
Published: June 2021

AbstractLynch syndrome is one of the most common hereditary cancer syndromes and is characterized by the development of many cancers, such as colorectal cancer (CRC), endometrial cancer, ovarian cancer, stomach cancer and many other cancers. Lynch syndrome is caused by pathogenic germline variants in one of four DNA mismatch repair genes (MLH1, MSH2, MSH6, or PMS2) or by an EPCAM deletion. The MLH1 variant is correlated with the highest risk of CRC, while the MSH2 variant is correlated with the highest risk of other cancers. CRC is the most common cancer type that develops in individuals with Lynch syndrome, followed by endometrial cancer. Recent advances have been made to help us further understand the molecular pathogenesis of this disease and help improve diagnostic testing efficiency and surveillance strategies. Moreover, recent advances in immunotherapy provided by clinical trials also provide clinicians with more chances to better treat Lynch syndrome. This study aims to review many advances in the molecular genetics, clinical features, diagnosis, surveillance and treatment of Lynch syndrome.
An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants
Authors: Xie Fei , Jin Wei , Si Huazhe , Yuan Yuan , Tao Ye , Liu Junhua , Wang Xiaoxu , Yang Chengjian , Li Qiushuang , Yan Xiaoting , Lin Limei , Jiang Qian , Zhang Lei , Guo Changzheng , Greening Chris , Heller Rasmus , Guan Le Luo , Pope Phillip B. , Tan Zhiliang , Zhu Weiyun , Wang Min , Qiu Qiang , Li Zhipeng , Mao Shengyong 
Published: June 2021

Abstract
Background
Gastrointestinal tract (GIT) microbiomes in ruminants play major roles in host health and thus animal production. However, we lack an integrated understanding of microbial community structure and function as prior studies are predominantly biased towards the rumen. In this study, we used shotgun metagenomics to profile the microbiota of 370 samples that represent 10 GIT regions of seven ruminant species.

Results
Our analyses reconstructed a GIT microbial reference catalog with > 154 million nonredundant genes and identified 8745 uncultured candidate species from over 10,000 metagenome-assembled genomes. The integrated gene catalog across the GIT regions demonstrates spatial associations between the microbiome and physiological adaptations, and 8745 newly characterized genomes substantially expand the genomic landscape of ruminant microbiota, particularly those from the lower gut. This substantially expands the previously known set of endogenous microbial diversity and the taxonomic classification rate of the GIT microbiome. These candidate species encode hundreds of enzymes and novel biosynthetic gene clusters that improve our understanding concerning methane production and feed efficiency in ruminants. Overall, this study expands the characterization of the ruminant GIT microbiota at unprecedented spatial resolution and offers clues for improving ruminant livestock production in the future.

Conclusions
Having access to a comprehensive gene catalog and collections of microbial genomes provides the ability to perform efficiently genome-based analysis to achieve a detailed classification of GIT microbial composition and function. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production.
Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution
Authors: Shen Liang , Liu Yongqin , Allen Michelle A. , Xu Baiqing , Wang Ninglian , Williams Timothy J. , Wang Feng , Zhou Yuguang , Liu Qing , Cavicchioli Ricardo 
Published: June 2021

AbstractBackgroundMicroorganisms drive critical global biogeochemical cycles and dominate the biomass in Earth’s expansive cold biosphere. Determining the genomic traits that enable psychrophiles to grow in cold environments informs about their physiology and adaptive responses. However, defining important genomic traits of psychrophiles has proven difficult, with the ability to extrapolate genomic knowledge to environmental relevance proving even more difficult.ResultsHere we examined the bacterial genusArthrobacterand, assisted by genome sequences of new Tibetan Plateau isolates, defined a new clade, Group C, that represents isolates from polar and alpine environments. Group C had a superior ability to grow at −1°C and possessed genome G+C content, amino acid composition, predicted protein stability, and functional capacities (e.g., sulfur metabolism and mycothiol biosynthesis) that distinguished it from non-polar or alpine Group AArthrobacter. Interrogation of nearly 1000 metagenomes identified an over-representation of Group C in Canadian permafrost communities from a simulated spring-thaw experiment, indicative of niche adaptation, and an under-representation of Group A in all polar and alpine samples, indicative of a general response to environmental temperature.ConclusionThe findings illustrate a capacity to define genomic markers of specific taxa that potentially have value for environmental monitoring of cold environments, including environmental change arising from anthropogenic impact. More broadly, the study illustrates the challenges involved in extrapolating from genomic and physiological data to an environmental setting.
Indoor bacterial, fungal and viral species and functional genes in urban and rural schools in Shanxi Province, China–association with asthma, rhinitis and rhinoconjunctivitis in high school students
Authors: Fu Xi , Ou Zheyuan , Zhang Mei , Meng Yi , Li Yanling , Wen Jikai , Hu Qiansheng , Zhang Xin , Norbäck Dan , Deng Yiqun , Zhao Zhuohui , Sun Yu 
Published: June 2021

Abstract
Background
Studies in developed countries have reported that the prevalence of asthma and rhinitis is higher in urban areas than in rural areas, and this phenomenon is associated with urbanization and changing indoor microbiome exposure. Developing countries such as China have experienced rapid urbanization in past years, but no study has investigated microbiome exposure and urban-rural health effects in these countries.

Methods
Nine high schools from urban and rural areas were randomly selected in Shanxi Province, China, and classroom vacuum dust was collected for shotgun metagenomic sequencing. A self-administered questionnaire was collected from 1332 students for personal information and health data. Three-level logistic regression was performed between microbial richness/abundance/functional pathways and the occurrence of asthma and rhinitis symptoms.

Results
Consistent with developed countries, the prevalence of wheeze and rhinitis was higher in urban areas than in rural areas (p < 0.05). Metagenomic profiling revealed 8302 bacterial, 395 archaeal, 744 fungal, 524 protist and 1103 viral species in classroom dust. Actinobacteria (mean relative abundance 49.7%), Gammaproteobacteria (18.4%) and Alphaproteobacteria (10.0%) were the most abundant bacterial classes. The overall microbiome composition was significantly different between urban and rural schools (p = 0.001, Adonis). Species from Betaproteobactera, Gammaproteobacteria and Bacilli were enriched in urban schools, and species from Actinobacteria and Cyanobacteria were enriched in rural schools. Potential pathogens were present in higher abundance in urban schools than in rural schools (p < 0.05). Pseudoalteromonas, Neospora caninum and Microbacterium foliorum were positively associated with the occurrence of wheeze, rhinitis and rhinoconjunctivitis, and Brachybacterium was protectively (negatively) associated with rhinitis (p < 0.01). The abundance of human endocrine and metabolic disease pathways was positively associated with rhinitis (p = 0.008), and butyrate and propionate metabolic genes and pathways were significantly enriched in rural schools (p < 0.005), in line with previous findings that these short-chain fatty acids protect against inflammatory diseases in the human gut.

Conclusions
We conducted the first indoor microbiome survey in urban/rural environments with shotgun metagenomics, and the results revealed high-resolution microbial taxonomic and functional profiling and potential health effects.
Microbial production of butyl butyrate: from single strain to cognate consortium
Authors: Sinumvayo Jean Paul , Li Yin , Zhang Yanping 
Published: June 2021

AbstractButyl butyrate (BB) is an important chemical with versatile applications in beverage, food and cosmetics industries. Since chemical synthesis of BB may cause adverse impacts on the environment, biotechnology is an emerging alternative approach for microbial esters biosynthesis. BB can be synthesized by using a single Clostridium strain natively producing butanol or butyrate, with exogenously supplemented butyrate or butanol, in the presence of lipase. Recently, E. coli strains have been engineered to produce BB, but the titer and yield remained very low. This review highlighted a new trend of developing cognate microbial consortium for BB production and associated challenges, and end up with new prospects for further improvement for microbial BB biosynthesis.
Experimental phantom evaluation to identify robust positron emission tomography (PET) radiomic features
Authors: Carles Montserrat , Fechter Tobias , Martí-Bonmatí Luis , Baltas Dimos , Mix Michael 
Published: June 2021

Abstract
Background
Radiomics analysis usually involves, especially in multicenter and large hospital studies, different imaging protocols for acquisition, reconstruction, and processing of data. Differences in protocols can lead to differences in the quantification of the biomarker distribution, leading to radiomic feature variability. The aim of our study was to identify those radiomic features robust to the different degrading factors in positron emission tomography (PET) studies. We proposed the use of the standardized measurements of the European Association Research Ltd. (EARL) accreditation to retrospectively identify the radiomic features having low variability to the different systems and reconstruction protocols. In addition, we presented a reproducible procedure to identify PET radiomic features robust to PET/CT imaging metal artifacts. In 27 heterogeneous homemade phantoms for which ground truth was accurately defined by CT segmentation, we evaluated the segmentation accuracy and radiomic feature reliability given by the contrast-oriented algorithm (COA) and the 40% threshold PET segmentation. In the comparison of two data sets, robustness was defined by Wilcoxon rank tests, bias was quantified by Bland–Altman (BA) plot analysis, and strong correlations were identified by Spearman correlation test (r > 0.8 and p satisfied multiple test Bonferroni correction).

Results
Forty-eight radiomic features were robust to system, 22 to resolution, 102 to metal artifacts, and 42 to different PET segmentation tools. Overall, only 4 radiomic features were simultaneously robust to all degrading factors. Although both segmentation approaches significantly underestimated the volume with respect to the ground truth, with relative deviations of −62 ± 36% for COA and −50 ± 44% for 40%, radiomic features derived from the ground truth were strongly correlated and/or robust to 98 radiomic features derived from COA and to 102 from 40%.

Conclusion
In multicenter studies, we recommend the analysis of EARL accreditation measurements in order to retrospectively identify the robust PET radiomic features. Furthermore, 4 radiomic features (area under the curve of the cumulative SUV volume histogram, skewness, kurtosis, and gray-level variance derived from GLRLM after application of an equal probability quantization algorithm on the voxels within lesion) were robust to all degrading factors. In addition, the feasibility of 40% and COA segmentations for their use in radiomics analysis has been demonstrated.
Design and system evaluation of a dual-panel portable PET (DP-PET)
Authors: Zeng Tianyi , Zheng Jiaxu , Xia Xinyuan , Chen Xin , Wang Beien , Zhang Shuangyue , Chandler Adam , Cao Tuoyu , Hu Lingzhi , Chen Qun , Chu Xu 
Published: June 2021

Abstract
Background
Integrated whole-body PET/MR technology continues to mature and is now extensively used in clinical settings. However, due to the special design architecture, integrated whole-body PET/MR comes with a few inherent limitations. Firstly, whole-body PET/MR lacks sensitivity and resolution for focused organs. Secondly, broader clinical access of integrated PET/MR has been significantly restricted due to its prohibitively high cost. The MR-compatible PET insert is an independent and removable PET scanner which can be placed within an MRI bore. However, the mobility and configurability of all existing MR-compatible PET insert prototypes remain limited.

Methods
An MR-compatible portable PET insert prototype, dual-panel portable PET (DP-PET), has been developed for simultaneous PET/MR imaging. Using SiPM, digital readout electronics, novel carbon fiber shielding, phase-change cooling, and MRI compatible battery power, DP-PET was designed to achieve high-sensitivity and high-resolution with compatibility with a clinical 3-T MRI scanner. A GPU-based reconstruction method with resolution modeling (RM) has been developed for the DP-PET reconstruction. We evaluated the system performance on PET resolution, sensitivity, image quality, and the PET/MR interference.

Results
The initial results reveal that the DP-PET prototype worked as expected in the MRI bore and caused minimal compromise to the MRI image quality. The PET performance was measured to show a spatial resolution ≤ 2.5 mm (parallel to the detector panels), maximum sensitivity = 3.6% at the center of FOV, and energy resolution = 12.43%. MR pulsing introduces less than 2% variation to the PET performance measurement results.

Conclusions
We developed a MR-compatible PET insert prototype and performed several studies to begin to characterize the performance of the proposed DP-PET. The results showed that the proposed DP-PET performed well in the MRI bore and would cause little influence on the MRI images. The Derenzo phantom test showed that the proposed reconstruction method could obtain high-quality images using DP-PET.
Increased pulmonary embolism in patients with COVID-19: a case series and literature review
Authors: Hesam-Shariati Sonia , Fatehi Poya , Abouzaripour Morteza , Fathi Fardin , Hesam-Shariati Negin , Hesam Shariati Mohammad Bakhtiar 
Published: June 2021

AbstractThere is some recent evidence that the coronavirus disease 2019 (COVID-19) increases the risk of venous thromboembolism by creating a prothrombotic state. COVID-19 and pulmonary embolism (PE) are both associated with tachypnoea, hypoxemia, dyspnoea, and increased D-dimer. Diagnosis of pulmonary embolism in a patient with COVID-19 compared to an individual without it, using the conventional clinical and biochemical evidence is challenging and somehow impossible. In this study, we reported four male cases affected by COVID-19 and admitted to hospitals in Sanandaj, Iran. The patients were all older adults (ranging between 56 and 95 years of age). Fever, chills, muscle pain, and cough were evident in all the cases. Red blood cell levels were low, and pulmonary embolism was clearly detected on spiral computed tomographic (CT) angiography of the pulmonary circulation of all patients. These cases demonstrated that COVID-19 may lead to pulmonary embolism by causing blood coagulation problems. As COVID-19 continues to cause considerable mortality, more information is emerging which reveals its complicated pathogenicity. In the meantime, venous thromboembolism remains an uncommon finding in patients with COVID-19. It is essential that health care providers perform the necessary diagnostic evaluations and provide appropriate treatment for patients.