bluuebunny/crossref_metadata_2025 huggingface dataset:
CDC6, a key replication licensing factor, is overexpressed and confers poor prognosis in diffuse large B-cell lymphoma
Authors: Shen Mingfang , Zhang Yunfeng , Tang Lun , Fu Qinyan , Zhang Jiawei , Xu Yang , Zeng Hui , Li Yuan
Published: September 2022

Background: Cell division cycle 6 (CDC6) is a key licensing factor in the assembly of pre-replicative complexes at origins of replication. The role of CDC6 in the pathogenesis of in diffuse larger B-cell lymphoma (DLBCL) remains unknown. We aim to investigate the effects of CDC6 on the proliferation, apoptosis and cell cycle regulation in DLBCL cells, delineate its underlying mechanism, and to correlate CDC6 expression with clinical characteristics and prognosis of patients with DLBCL.
Methods: Initial bioinformatic analysis was performed to screen the potential role of CDC6 in DLBCL. Lentiviral constructs harboring CDC6 or shCDC6 was transfected to overexpress or knockdown CDC6 in SUDHL4 cells. The cell proliferation was evaluated by CCK-8 assay, cell apoptosis was detected by Annexin-V APC/7-AAD double staining, and cell cycle was measured by flow cytometry. Real time quantitative PCR and western blot was used to characterize CDC6 expression and its downstream signaling pathways. The clinical data of DLBCL patients were retrospectively reviewed, the CDC6 expression in DLBCL or lymph node reactive hyperplasia tissues was evaluated by immunohistochemistry.
Results: In silico data suggest that CDC6 overexpression is associated with inferior prognosis of DLBCL. We found that CDC6 overexpression increased SUDHL4 cell proliferation, while knockdown of CDC6 inhibited cell proliferation in a time-dependent manner. Upon overexpression, CDC6 reduced cells in G1 phase and did not affect cell apoptosis; CDC6 knockdown led to significant cell cycle arrest in G1 phase and increase in cell apoptosis. Western blot showed that CDC6 inhibited the expression of INK4, E-Cadherin and ATR, accompanied by increased Bcl-2 and deceased Bax expression. The CDC6 protein was overexpressed DLBCL compared with lymph node reactive hyperplasia, and CDC6 overexpression was associated with non-GCB subtype, and conferred poor PFS and OS in patients with DLBCL.
Conclusion: CDC6 promotes cell proliferation and survival of DLBCL cells through regulation of G1/S cell cycle checkpoint and apoptosis. CDC6 is overexpressed and serves as a novel prognostic marker in DLBCL.
Microscale vortexes in cellular media
Authors: Yan Peng , Li Hong , Zhang Yang , Hao Zhiqiang , Li Xingang , Ou Xiaoxia , Fan Xiaolei , Gao Xin
Published: September 2022

Vortex formation is one of the key phenomena of fluid transport within porous foam media, being responsible for improving mass transfer in relevant engineering applications such as separation and catalysis. Here, water flows through SiC open-cell foam media were investigated using the combined experimental and simulation method. Direct observation of pore-scale vortexes in the foam media was achieved experimentally, showing the formation of forced vortexes in foam cells with the constant exchange of fluid elements between vortexes and bulk fluid, which was confirmed by the CFD simulation using the virtual 3D replica of the foam media. Upon the validation of the simulation results by the experimental ones, further investigation of the vortex formation mechanism in the porous foam media was performed. Based on the Galileo invariance, a dimensionless vortex formation number (Vop) with the physical significance of vorticity was proposed, as the criteria to determine vortex formation in the porous channel of open-cell foams.
A deep learning solution to predict tumor mutational status : an evaluation as a first-line diagnostic tool
Authors: Vinçon Nathan , Morel Louis-Oscar , Derangère Valentin , Arnould Laurent , Ladoire Sylvain
Published: September 2022

The presence of genomic mutations in cancer can be associated with a response to a targeted therapy. Therefore, it has become a crucial information for giving more efficient treatments to every patient. Detection of mutation is routinely made by DNA-sequencing diagnostic tests. Recent developments showed promising results for tumoral mutational status prediction using new deep learning based methods on histopathological images. However, it is still unknown whether these methods can be useful aside from sequencing methods for efficient population diagnosis. Here, we use a standard prediction pipeline for the detection of clinically relevant genomic alterations in breast, lung and colon cancer. We propose 3 diagnostic strategies using deep learning methods as first-line diagnostic tools. We show that these methods help reduce DNA sequencing by up to 34.6% with a high sensitivity (95%). In a context of limited resources, these methods increase sensitivity up to 75% at a 30% capacity of DNA sequencing tests, up to 85.7% at a 50% capacity, and up to 92.3% at a 70% capacity. These methods can also be used to prioritize patients with a positive predictive value up to 86.7% in the 10% patient most at risk of being mutated.
An unexpected case of wind-pollination: ambophily in an ornithophilous tropical mountaintop Orobanchaceae
Authors: Pacheco Amanda , Bergamo Pedro Joaquim , Freitas Leandro
Published: September 2022

Some plant species have a kind of mixed pollination system – ambophily – which rely both on biotic and abiotic (most commonly wind) as pollen vectors. Ambophily remains poorly addressed in the pollination literature and may have been overlooked because existing studies do not quantify the wind contribution in animal-pollinated species. Moreover, it is expected in species pollinated by different insect groups and generalist floral phenotype. Esterhazya eitenorum is a (sub-)shrub endemic to a high-altitude grassland (campos de altitude) area in southeastern Brazil. Pollinated mainly by hummingbirds and secondarily by large bees, it presents features generally associated with ornithophily. Bird-pollinated species are not expected to be ambophilous, due to their high resource investment in floral construction and maintenance. However, here we detect ambophily in E. eitenorum by testing the potential for pollen export by wind as well as seed set after floral visitor exclusion and spontaneous self-pollination treatments, and comparing these with natural conditions. Esterhazya eitenorum has an ambophilous pollination system, with effect size analyses between floral visitor exclusion treatments and natural conditions revealing significant contributions from both abiotic and biotic components. Although its floral phenotype corresponds to the main pollinator, the occurrence of ambophily in E. eitenorum underscores the need for an independent approach to the association of floral phenotypes with pollination vectors, in particular for the detection and better understanding of the evolution of mixed pollination systems.
Optimization of continuous casting for preventing the surface peeling defects of Ti-containing ferrite stainless steel
Authors: Feng Chien-Cheng , Lin Ming-Hong , Chen Yi-Cheng , Ou Shih-Fu , Huang Ching-Chien
Published: September 2022

Owing to the durability of stainless steel, stainless steel components can be effectively reused, remanufactured, and indefinitely recycled. The production of stainless steel from scrap is expected to be a trend in the future to achieve a circular economy. However, the surface of cold-rolled Ti-containing ferrite stainless steel strips produced from scrap is prone to severe peeling. In this study, it was found that peeling defects were caused by cracking near slab inclusions during hot rolling. These inclusions mainly comprised Ti oxides, Ti nitrides, and Al oxides generated from clogged and submerged entrance nozzles. To prevent peeling defects and the clogging of the submerged entrance nozzle, the Taguchi method was used and the optimal casting parameters, such as casting overheating, casting speed, stirring time, and inclination, were determined. Increasing casting overheating and decreasing the casting speed inhibited clogging and effectively mitigated peeling defects. When casting overheat was fixed at 60°C with a casting speed in the range of 0.8–0.9 m/min, no peeling defects on the surface of the steel strip were observed. The steel strip produced using the optimized parameters fulfilled the required mechanical properties (tensile strength ≥ 415 MPa, yield strength ≥ 205 MPa, elongation ≥ 22%, and hardness ≤ 89 HRB) and design criteria.
The Risk of Ischemic Stroke Significantly Increases in Individuals with Blepharitis: A Population-based Study Involving 424,161 Patients
Authors: Li Jing-Xing , Tsai Yi-Yu , Shih Ying-Hsiu , Wu Ying-Hsuen , Li You-Ling , Chiang Chun-Chi
Published: September 2022

Introduction:
To investigate the association of blepharitis and ischemic stroke (IS).
Methods
This retrospective cohort study used population-based data in Taiwan. We identified 424,161 patients with blepharitis between 2008 and 2018.
Results
424,161 pairs of blepharitis cohort and non-blepharitis cohort were 1:1 propensity score matched for statistical analysis. Patients with blepharitis had significantly increased risks of IS compared with the individuals without blepharitis (adjusted hazard ratio 1.32, 95% CI 1.29–1.34, P < 0.001). A significantly higher risk of IS was observed in blepharitis cohort with a previous diagnosis of cancer than in those without cancer (P for interaction < 0.0001). Kaplan–Meier survival analysis revealed the cumulative incidence of IS increased in the blepharitis cohort compared with that in the non-blepharitis cohort in 10 years (log-rank P < 0.001). The follow-up period analysis further indicated 1.41-fold adjusted hazard (95% CI 1.35 − 1.46, P < 0.001) of IS within a year after blepharitis diagnosis.
Conclusions
Patients with blepharitis had an elevated risk of developing IS. Further research is required to determine the causal relationship between blepharitis and IS, as well as the underlying mechanism.
Unveiling Sex-based Differences in Parkinson's Disease: A Comprehensive Meta-analysis of Transcriptomic Studies
Authors: López-Cerdán Adolfo , Andreu Zoraida , Hidalgo Marta R. , Grillo-Risco Rubén , Català-Senent José Francisco , Soler-Saez Irene , Neva-Alejo Almudena , Gordillo Fernando , Iglesia-Vayá María de la , Garcia-Garcia Francisco
Published: September 2022

Background:In recent decades, increasing longevity (among other factors) has fostered a rise in Parkinson's disease incidence. Although not exhaustively studied in this devastating disease, the impact of sex represents a critical variable in Parkinson’s Disease as epidemiological and clinical features differ between males and females.Methods:To study sex bias in Parkinson’s Disease, we conducted a systematic review to select sex-labeled transcriptomic data from three relevant brain tissues: the frontal cortex, the striatum, and the substantia nigra. We performed differential expression analysis on each study chosen. Then we summarized the individual differential expression results with three tissue-specific meta-analyses and a global all-tissues meta-analysis. Finally, results from the meta-analysis were functionally characterized using different functional profiling approaches.Results:The tissue-specific meta-analyses linked Parkinson’s Disease to the enhanced expression ofMED31in the female frontal cortex and the dysregulation of 237 genes in the substantia nigra. The global meta-analysis detected 15 genes with sex-differential patterns in Parkinson’s disease, which participate in mitochondrial function, oxidative stress, neuronal degeneration, and cell death. Furthermore, functional analyses identified pathways, protein-protein interaction networks, and transcription factors that differed by sex. While male patients exhibited changes in oxidative stress based on metal ions, inflammation, and angiogenesis, female patients exhibited dysfunctions in mitochondrial and lysosomal activity, antigen processing and presentation functions, and glutamic and purine metabolism. All results generated during this study are readily available by accessing an open web resource (http://bioinfo.cipf.es/metafun-pd/) for consultation and reuse in further studies.Conclusions:Our in-silico approach has highlighted sex-based differential mechanisms in typical Parkinson Disease hallmarks (inflammation, mitochondrial dysfunction, and oxidative stress). Additionally, we have identified specific genes and transcription factors for male and female Parkinson Disease patients that represent potential candidates as biomarkers to diagnosis.
A Simulation of the Migration of a Cassava Contaminant Plume from a Processing Mill into Aquifers, Eku, Delta State, Nigeria
Authors: Atiti Prince , Ohwoghere-Asuma Oghenero , Ophori Duke
Published: September 2022

The migration of a cassava contaminant plume from a cassava mill into aquifers in Eku and its environs, Delta State, Nigeria, has been modeled using the Groundwater Modeling System (GMS). The cassava plume was modeled using Cyanide. It was found that the Cyanide transport generally follows the groundwater flow direction. Cyanide is attenuated as it infiltrates into the soil, but, with continuous introduction of the contaminant for 20 years, the mass of the contaminant at the aquifer increases with time. In 1460 days (4 years) the concentration of the contaminant that may be pumped from a well at the source is 0.246 mg/l which is above the U.S. Environmental Protection Agency (EPA) drinking water standard of 0.2 mg/l. The transport of the Cyanide is influenced by the groundwater recharge rate, the pumping rate of water from the aquifer, and by the dispersion rate of the contaminant. Variation in recharge rate was simulated to represent possible climate change at the study area, while variation in pumping rate was used to cover the range of possible demand for water. The dispersion rate was varied to account for the degree of uncertainty to which the rock dispersivity is known at the site. In a well at the contaminant source in the aquifer, a contaminant mass of 355000 mg was observed under increased recharge conditions in 7300 days. With reduced recharge, the mass observed was 76000 mg. With increased pumping rate in 7300 days, a contaminant mass of 88000 mg was detected in the aquifer. Under reduced pumping rate, a contaminant mass of 260000 mg was detected. Increased dispersion results in 230000 mg of contaminant in the well, while reduced dispersion results in a contaminant mass of 308000 mg. Of these parameters that control the fate of the Cyanide, recharge has the greatest impact on the spread, followed by the dispersion rate and pumping rate in that order.
Autoantibody to VASP is associated with neuropsychiatric systemic lupus erythematosus and elevated platelet level
Authors: Zhu Chenxi , Yang Hang , Zhao Yi , Xu Jiayi , Liu Yi
Published: September 2022

Background: Biomarkers for diagnosis in neuropsychiatric systemic lupus erythematosus (NPSLE) are still lacking, we implemented this study to identify potential antigenic targets that are associated with the pathogenic mechanism in this disease, combining transcriptomic and proteomics approach with chemiluminescence immune assay.
Methods: Transcriptomic analysis of 70 SLE patients with or without neuropsychiatric involvement was carried out to obtain NPSLE-related genes. Epitope mapping and sequence analysis were used to predict autoantigens. Then enzyme-linked immunosorbent assay (ELISA), immunoprecipitation (IP), and blotting were conducted to detect the autoantibodies.
Results: Analysis of transcriptomic data indicated a set of hub genes with a close correlation to NPSLE phenotype and higher platelet (PLT) levels. Epitope prediction for corresponding protein revealed that vasodilator-stimulated phosphoprotein (VASP) was a potential autoantigen in NPSLE, as it had sequences with optimal antigen index mapped to small nuclear ribonucleoprotein (snRNP). By ELISA and IP, we confirmed that the anti-VASP antibody (Ab) was positively related to both NPSLE phenotype and PLT levels.
Conclusions: Anti-VASP Ab was a novel candidate biomarker for NPSLE and might involve in its pathogenesis via coagulation and autoimmunity.
Downregulation of peroxidase activity of platinum cube enables minute-time scale colorimetric signaling of hypoxanthine for fish freshness monitoring
Authors: Ma Xiaoming , Feng Tingting , Zhang Peng , Zhang Hui , Hu Xuan , Yang Yuying , Wang Zhen , Zhang Huifang , Peng Dong , Lai Xiaoqi , Li Xun , Xu Jianguo
Published: September 2022

Due to the unique biological composition of aquatic products especially fish, it is extremely perishable than other muscle products. Herein, we proposed a polyvinylpyrrolidone-modified platinum cubic nanomaterials (PVP-PtNC) with peroxidase activity for colorimetric detection of hypoxanthine (Hx), the indicator of fish freshness, in a minute-time scale. The principle is based on the interaction of Hx with PVP-PtNC to occupy catalytic active sites on PVP-PtNC’s surface. This causes the downregulation of PVP-PtNC’s catalytic ability and weakened its ability to catalyze the oxidization of H2O2by TMB. Accordingly, the decrease of the UV-Vis absorption and the weakening of the colorimetric reaction color is proportional to the Hx concentration. On this basis, a target-triggered colorimetric method for detecting Hx is developed for fish freshness monitoring with a fast detection speed, low cost, high accuracy, and simplified operation. Experiments reveal that the correlation response of Hx is from 0.5 μM to 10 mM with a limit of detection of 0.16 μM. Especially, the Hx detected from real fish indicates the method possesses promising potentials for practical application. All these features are expected to promote the development of online detection tools for food safety monitoring.
Spatial distribution characteristics and ecological assembly process of bacteria and aerobic anoxygenic photosynthesis bacteria in Three Gorges Reservoir
Authors: Huo Lixin , Ma Anran , Liu Hong , Wang Xingzu , Song Cheng
Published: September 2022

Aerobic anoxygenic phototrophic bacteria (AAPB) is significant for productivity of freshwater ecosystems. However, it remains unclear that the distribution characteristics and ecological assembly process of AAPB in low illumination freshwater basins at present. Here, we track the diversity, abundance, spatial variations, ecological process and community interaction of bacteria and AAPB in sediment of the Three Gorges Reservoir (TGR), which is a typical low radiation freshwater reservoir, based on high-throughput sequencing of 16S rRNA and pufM gene and the qPCR of pufM gene. In TGR, the qPCR of AAPB ranged between (2.21±0.44) × 10 4 and (9.98±0.30) × 10 7 pufM gene copies/g, and Rhodobacteraceae-like pufM sequences were determined, and the sequences of Methylobacteriaceae-liked and Sphingomonadaceae-liked also existed here. The qPCR of AAPB was increasing while the Chao1 and Shannon indices decreased from the upstream to the downstream. However, the contribution of geographical and environmental factor is little to the spatial difference of community. The stochastic process played a dominant role in the aggregation and replacement of bacterial and AAPB communities, among which the most contribution was dispersal limitation. The network analysis showed that most of the keystone species were not the most abundant, which could not to be ignored in this unique environment. For pufM gene microbial network, Tabrizicola spp. and Gemmobacter spp. were the hubs for modules. In addition, these unclassified taxa based on pufM gene, also known as “microbial dark matter”, has important implications for ecosystem processes . The results obtained here provide help for further understanding distribution characteristics and ecological processes of bacteria and AAPB in TGR, a typical low illumination area.
Improvised Dynamic Round-Robin Scheduling for Optimum Resource Utilization in Cloud Systems
Authors: Aradhya Suvarna N , Priya Rashmi
Published: September 2022

Task Scheduling is the process of assigning the incoming tasks to the available systems for optimum utilization of resources (CPU, Memory, Bandwidth, etc.). Optimum, in the present context implies executing maximum number of tasks using minimum of resources. In large scale Cloud Computing, resource optimization plays a critical role as it determines the quality of service (QoS) offered to customers. Therefore, task scheduling algorithm for parallel processing directly relates to QoS and is fundamental to understanding Resource Utilization, Inter-Process Communication, Network Latency, Load Balancing, Job Migration and Fault Tolerance. In this paper, an effort is made to explore and understand some of the basic scheduling algorithms through an experimental study. Algorithms are implemented in a cloud scenario. The results are construed with respect to several performance indicators that affect the QoS.
Fossil-fuel consumption and CO2eq emissions of cut-to-length industrial roundwood logging operations in Finland
Authors: Kärhä Kalle , Haavikko Hanna , Kääriäinen Heikki , Palander Teijo , Eliasson Lars , Roininen Kimmo
Published: September 2022

The aim of this study was to measure and model the fuel consumption of cut-to-length (CTL) logging machinery in cutting and forwarding under Nordic harvesting conditions, and to clarify which factors had the greatest effect on the fuel consumption. In addition, the total annual fuel consumption and CO2eq emissions were calculated for CTL logging operations in Finland in 2020. The data were collected during a long-term follow-up study on the fuel consumption of harvesters and forwarders conducted between March 2018 and April 2019. The fuel consumption data was obtained from a total of 16 harvesters and 13 forwarders equipped with digital flow meters featuring an accuracy of ± 1%. The engine power of the forest machines explained most of the hour-based fuel consumption. Correspondingly, the harvesting conditions of the forest stand best explained the cubic-metre-based fuel consumption. The fuel consumption of CTL logging operations (cutting and forwarding) averaged 1.4 L m− 3 in final felling, and 3.1 and 2.2 L m− 3 in first and later thinning, respectively. There was a large variation in the cubic-metre-based fuel consumption between individual machines, both for harvesters and forwarders. The total calculated fuel consumption in Finnish CTL operations in 2020 was 126.6 million L, with the calculated CO2eq emissions totalling 334,209 t (i.e. 5.7 kg m− 3). Several measures to accelerate fuel and energy efficiency and reduce CO2eq emissions in CTL logging operations are discussed in the paper.
Implementation of HSE culture using CRM techniques in the construction industry
Authors: sadeghi Soheil , Sadeghi Saman
Published: September 2022

The project's objective is to make HSE more accessible and tangible in acquiring competencies and transferring HSE training content to practice by showing its relevance concerning a novel operation protocol. Although individually CRM has a high potential to improve the safety, health, and environmental (HSE) culture of individuals and reduce errors in various areas, its implementation in the construction industry and an integrated manner has not been investigated. The authors investigated the effect of the implementation of HSE-CRM in a project for a housing complex in Karaj, with 230 staff. Despite the assessment that said this training is slightly more difficult, staff reacted more positively to this training than to standard training. Across all responses, there was statistically considerable growth in scores on the HSE culture survey items. Also, this process improved teamwork, performance, efficiency, and staff morale. Most participants said this training format was seen as livelier, more interesting, and more practically relevant. After one year, participants claimed this approach protected the HSE Chief and other managers from distractions and wasted time at the beginning of each shift. The result of the project shows that this technique can be used in the environment of construction.
Clinical significance of serum levels of 14-3-3β protein in patients with stable chronic obstructive pulmonary disease
Authors: Wang Decai , Rao Lizong , Lei Huiren , Li Wencui , Yu Qiufang , Li Wei , Wei Jianghong , Xu Shuyun , Mo Biwen
Published: September 2022

We aimed to evaluate the clinical relevance of serum tyrosine3-monooxygenase/tryptophan5-monooxygenase activation protein β (14-3-3β) in stable COPD patients. The expression of serum 14-3-3β protein was evaluated by an enzyme-linked immunosorbent assay. The association between its concentrations and clinical parameters of stable COPD patients were analyzed by correlation analysis and ROC curve. The results before propensity score matching (PSM) showed that serum 14-3-3β protein concentrations (ng/ml) in stable COPD patients were significantly higher than in healthy controls (P<0.001). Furthermore, serum 14-3-3β protein concentrations were higher in GOLD 3&4 COPD patients compared with healthy participants, GOLD 1 and GOLD 2 COPD patients (P<0.05). After 1:1 PSM, there was also a statistically significant rise in 14-3-3 protein levels in stable COPD patients compared to healthy controls (P<0.01). Serum 14-3-3β protein levels were positively correlated with blood neutrophil levels (P<0.05), and negatively related to lung function parameters in stable COPD patients (P<0.01). When the cutoff value was set at 29.53ng/ml, the ROC curve yielded a sensitivity of 84.9% and a specificity of 68.3% for diagnosing stable COPD. The 14-3-3β protein may be a potential serum biomarker that was associated with disease severity, systemic inflammation, and small airway obstruction in stable COPD patients.
Flavin-enabled Oxidative C-C Bond Cleavage and Rearrangement Reactions in the Biosynthesis of Novel Oxaspiro Angucycline Derivatives
Authors: Zhang Guojian , Xu Xiao , Chang Yimin , Chen Yinghan , Zhou Luning , Zhang Falei , Ma Chuanteng , Che Qian , Pfeifer Blaine , Zhu Tianjiao , Li Dehai
Published: September 2022

Flavin-enabled oxidative C-C Bond cleavages lead to fantastic structural alternations and are crucial
for biological activity of many natural products. Here we report the discovery of novel atypical agucycline derivatives including spirocyclione A (1) which contains an unusual oxaspiro[5.5]undecane architecture and spirocyclione B (2) possessing an intriguing di-carboxylic substituted benzochromene scaffold by heterologous expression of a type II polyketide biosynthetic gene cluster. Biosynthesis studies demonstrated 1 and 2 are generated by sequential flavin-enabled C-C bond cleavage and rearrangement reactions where SpiH3 is responsible for the cleavage of C12a-C12b bond of early typical tetracyclic intermediate to form the oxaspiro structure of 1 and SpiH1, a new member of Baeyer-Villiger monooxygenases catalyzes the crucial cleavage of C12-C12a bond in 1 to give the ring-A opened product of 2. Our work reveals an unprecedented pattern of post-PKS modification on angucycline skeletons that contribute structural diversity and complexity to aromatic polyketides.
EFN-SMOTE — An improved unbalanced data set oversampling based on fuzzy C-means for Credit Cards Fraud detection
Authors: Kasasbeh Bassam , Ahmad Hadeel , Aldabaybah Balqees , Maitah Wasen , Rawashdeh Enas , Tang Zhenzhou
Published: September 2022

Recent developments in e-payment systems have led to increased financial fraud, such as credit card fraud. It is therefore essential to implement detection mechanisms for credit card fraud. However, due to the unbalanced class distribution in the credit card dataset, the machine learning techniques are used to train the model based on the majority class, resulting in inaccurate fraud predictions. Therefore, this paper mainly focuses on processing unbalanced data using the oversampling technique called Elbow Fuzzy Noice filtering SMOTE (EFN-SMOTE). This method divides the dataset into multiple clusters. The number of clusters is determined by an algorithm known as the Elbow method, after which noise filtering is applied to each cluster, after that, we use the SMOTE in each cluster to synthesize a new minority instance based on the nearest majority instance of each minority instance to effectively perceive the decision boundary which leads to a balanced database by oversam-pling technique. On the other hand, the result show that EFN-SMOTE achieved better classification performance using Artificial Neural Network (ANN) with four hidden layers with 0.999 accuracy, 0.998 precision, 0.999 sensitivity, 0.998 specificity, 0.999 F-measure, and 0.999 G-Mean.
Multi-attribute quality score computation for Internet of Things (IoT) based applications
Authors: Temkar Rohini , Chakrabarti Prasun , Jena Om Prakash , Elngar Ahmed A. , Margala Martin , Ravi Vinayakumar
Published: September 2022

In the world of technological advancement and emergence, the Internet of Things (IoT) has opened doors of opportunity and connectivity. Massive and heterogeneous devices generate enormous data. Assessing the quality of data is an important aspect of today’s IoT world. Conventional quality models were basically designed to assess the quality of the software applications. These cannot be as it is applied to IoT applications as they include wireless and mobile devices. Due to the inclusion of smart devices IoT applications show additional characteristics like intelligent hardware devices, software hardware collaboration model, networked, wireless and mobile connectivity, and remote monitoring of devices. This necessitates the enhancement of existing quality models. The quality evaluation approach presented in this work is based on the ISO/IEC 25010 quality model. Analytic Hierarchy Process (AHP) is used for pairwise comparison of the quality attribute. In comparison to existing models, the multi-attribute AHP-based quality analysis approach aids in determining the best suitable weights on various quality attributes mentioned in ISO/IEC 25010 model.
Clinical XLNet-based End-to-End Knowledge Discovery on Clinical Text Data using Natural Language Processing
Authors: Pagad Naveen S , N Pradeep , Chakrabarti Tulika , Chakrabarti Prasun , Elngar Ahmed A. , Margala Martin , Nami Mohammad , Sharma Neha , Frimpong Samuel
Published: September 2022

A modern framework for assessing patient histories and conducting clinical research has been developed as the number of clinical narratives evolves. To discover the knowledge from such clinical narratives, clinical entity recognition and relation extraction tasks were performed subsequently in existing approaches, which resulted in error propagation. Therefore, a novel end-to-end clinical knowledge discovery strategy has been proposed in this paper. The clinical XLNet was used as a base model for handling the discrepancy issue. To predict the dependent clinical relation association, the multinomial Naïve Bayes probability function has been incorporated. In order to improve the performance of the proposed strategy, it takes into account entity pairs presented consecutively through the multi-head attention layer. Tests have been conducted using the N2C2 corpus, and the proposed methodology achieves a greater than 20% improvement in accuracy over existing neural network-based and transformer-based methods.
Blood-brain barrier disruption in Long COVID-associated cognitive impairment
Authors: Campbell Matthew , Greene Chris , Connolly Ruairi , Brennan Declan , Laffan Aoife , O'Keeffe Eoin , Zaporojan Lilia , Connolly Emma , Cheallaigh Cliona Ni , Conlon Niall , Doherty Colin
Published: September 2022

Vascular disruption has been heavily implicated in COVID-19 pathogenesis and may predispose the neurological sequelae associated with the condition now known as long COVID. To date, no studies have objectively assessed blood-brain barrier (BBB) function in individuals with neurological complications stemming from prior SARS-CoV-2 infection. Here, we explored the neurobiological effects of SARS-CoV-2 infection in humans with acute infection (n = 76) and those with persistent long COVID with and without neurological impairment. Following acute infection, patients with neurological impairment had increased serum S100β, indicative of BBB disruption. Furthermore, using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in long COVID patients (n = 32), we observed elevated BBB permeability in distinct neuroanatomical regions including the frontal cortex, occipital lobe and temporal lobes which correlated with global brain volume and white matter volume deficits in patients with neurological impairment. Patients with neurological impairment had increased levels of blood-based biomarkers including GFAP, TGFβ and IL8 with levels of TGFβ that correlated with BBB permeability and structural brain changes. Peripheral blood mononuclear cells isolated from unaffected and long COVID patients had persistent upregulation of inflammatory markers including IFNA/G and showed increased adhesion to human brain endothelial cells in vitro. Finally, exposure of endothelial cells to serum from long COVID patients induced increases in ICAM-1, VCAM-1 and TNF irrespective of neurological sequelae. Together, these data suggest that sustained systemic inflammation and persistent localised BBB dysfunction is a feature of long COVID-associated neurological impairment. Importantly, this may also be therapeutically relevant in the treatment and clinical management of this patient group.
Novel 3D Flipwell system that models gut mucosal microenvironment for studying interactions between gut microbiota, epithelia and immunity
Authors: Beamer Maria A. , Zamora Cassandra , Nestor-Kalinoski Andrea L. , Furuta Saori
Published: September 2022

Gut mucosa consists of stratified layers of microbes, semi-permeable mucus, epithelium and stroma abundant in immune cells. Although tightly regulated, interactions between gut commensals and immune cells play indispensable roles in homeostasis and cancer pathogenesis in the body. Thus, there is a critical need to develop a robust model for the gut mucosal microenvironment. Here, we report our novel co-culture utilizing 3D Flipwell system for establishing the stratified layers of discrete mucosal components. This method allows for analyzing synchronous effects of test stimuli on gut bacteria, mucus, epithelium and immune cells, as well as their crosstalks. In the present report, we tested the immuno-stimulatory effects of sepiapterin (SEP, the precursor of the cofactor of nitric oxide synthase —BH4) on the gut mucosal community. We previously reported that SEP effectively reprogrammed tumor-associated macrophages and inhibited breast tumor cell growth. In our co-cultures, SEP largely promoted mucus integrity, bacterial entrapment, and M1-type polarization of macrophages. Conversely, these phenomena were absent in control-treated cultures. Our results demonstrate that this novel co-culture may serve as a robust in vitro system to recapitulate the effects of pharmacological agents on the gut mucosal microenvironment, and could potentially be expanded to test the effects outside the gut.
DEDTI vs IEDTI: Efficient and Predictive Models of Drug-Target Interactions
Authors: Zabihian Arash , Sayyad Faeze Zakaryapour , Hashemi Seyyed Morteza , Hooshmand Mohsen , Gharaghani Sajjad
Published: September 2022

Drug repurposing is an active area of research and effort due to decreasing the cost and time of drug development. Most of those efforts are primarily concerned with the prediction of drug-target interactions. Many evaluation models, from matrix factorization to more cutting-edge deep neural networks, have come to the scene to predict drug-target interactions. Most of the available information on drugs and targets is gathered and used as the features to feed the prediction models. Some predictive models are devoted to the prediction's quality, and others are devoted to the efficiency of the predictive models, e.g., embedding generation. In this work, we propose two predictive models of drug-target. To do this, we use the relations of drugs and targets and propose a method of similarity computations. Using these similarities, we generate an accumulative feature representation of these two objects. We propose two inductive, deep network models of IEDTI and DEDTI for drug-target interaction prediction. The former uses triplet and maps the input feature vectors into meaningful embedding vectors. Then, it applies a deep predictive model to each drug-target pair to evaluate their interaction. The DEDTI directly uses the feature vectors of drugs and targets and applies a predictive model to each pair to predict their interactions. The results show that both models outperform the state-of-the-art models.
Comparison of the efficacy and safety of rivaroxaban and low-molecular-weight heparin in Chinese lung cancer patients with nonhigh-risk pulmonary embolism
Authors: Song Yijun , Yang Dawei , Hou Dongni , She Jun , Song Yuanlin
Published: September 2022

Background
Data that guide selection of differing anticoagulant regimens for specific cancer-associated venous thromboembolism (VTE) are lacking. We aimed to compare the efficacy and safety of rivaroxaban and low-molecular-weight heparin (LMWH) against nonhigh-risk pulmonary embolism (PE) in Chinese lung cancer patients.
Methods
446 Chinese lung cancer patients with nonhigh-risk PE who initiated treatment with rivaroxaban or LMWH were identified from Zhongshan Hospital database from 2016 to 2020. The primary outcomes were the composite event of VTE recurrence or major bleeding, and all-cause mortality. The secondary outcomes were VTE recurrence, major bleeding and clinically relevant non-major bleeding (CRNMB). Propensity score matching was used to balance baseline covariates. We conducted sensitivity analysis by stabilized inverse probability of treatment weighting and competing risk analysis by a Fine and Gray subdistribution hazard model.
Results
In propensity score-matched cohorts, a trend for lower rate of the composite outcome was found in rivaroxaban group compared to LMWH group (hazard ratio (HR), 0.73; 95% confidence interval (CI), 0.45–1.21; P = 0.22). All-cause mortality was significantly lower in rivaroxaban group than LMWH group (HR, 0.52; 95% CI, 0.36–0.75; P < 0.001), while rivaroxaban was similar to LMWH in the risks of VTE recurrence (HR, 0.69; 95% CI, 0.36–1.34; P = 0.28), major bleeding (HR, 0.79; 95% CI, 0.37–1.68; P = 0.54) and CRNMB (HR, 1.13; 95% CI, 0.62–2.09; P = 0.69). The primary and secondary outcomes favored rivaroxaban over LMWH in all the subgroups expect for central PE and intermediate-risk PE. The sensitivity analysis yielded similar results, and competing risk analysis was in accordance with the primary findings.
Conclusions
Rivaroxaban might be a promising alternative to LMWH as initial treatment for nonhigh-risk PE in lung cancer patients.
Hydrogen diffusion and its electrical properties variation as a function of the IGZO stacking structure
Authors: Noh Hee Yeon , Lee Woo-Geun , R. Haripriya G. , Cha Jung-Hwa , Kim June-Seo , Yun Won Seok , Lee Myoung-Jae , Lee Hyeon-Jun
Published: September 2022

The oxygen vacancies and hydrogen in oxide semiconductors are regarded as the primary sources of charge carriers and various studies have investigated the effect of hydrogen on the properties of oxide semiconductors. However, the carrier generation mechanism between hydrogen and oxygen vacancies in an a-IGZO semiconductor has not yet been clearly examined. In this study we investigated the effect of hydrogen and the variation mechanisms of electrical properties of a thin film supplied with hydrogen from the passivation layer. SiOx and SiNx, which are used as passivation or gate insulator layers in the semiconductor process, respectively, were placed on the top or bottom of an a-IGZO semiconductor to determine the amount of hydrogen penetrating the a-IGZO active layer. The hydrogen diffusion depth was sufficiently deep to affect the entire thin semiconductor layer. A large amount of hydrogen in SiNx directly affects the electrical resistivity of a-IGZO semiconductor, whereas in SiOx, it induces a different behavior from that in SiNx, such as inducing an oxygen reaction and O-H bond behavior change at the interface of an a-IGZO semiconductor. Moreover, the change in electrical resistivity owing to the contribution of free electrons could be varied based on the bonding method of hydrogen and oxygen.
Definition and grading of anastomotic stricture/stenosis following low anastomosis after total mesorectal excision: A single-center study
Authors: Cong Jinchun , Zhang Hong , Chen Chunsheng
Published: September 2022

BACKGROUND: Anastomotic stricture/stenosis is an alarming complication after colorectal surgery, and there is still no recognized definition for anastomotic stricture/stenosis. This study aimed to determine the status and change of anastomotic stricture/stenosis after rectal surgery using a special anastomotic stricture/stenosis definition and grading system, discuss various risk factors for anastomotic stricture/stenosis, and explore the effect of different degrees of anastomotic stricture/stenosis on bowel function.
METHODS: This study included patients with confirmed rectal cancer who underwent total mesorectal excision between May 2014 and May 2021. A five-degree special anastomotic stricture/stenosis definition and grading system was used to determine anastomotic stricture/stenosis status, and clinical outcomes and risk factors for anastomotic stricture/stenosis were investigated. Furthermore, the low anterior resection syndrome score was used to assess bowel function.
RESULTS: A total of 473 patients were enrolled in this study. The low anterior resection syndrome assessment showed that the more severe the anastomotic stricture/stenosis, the more severe the low anterior resection syndrome (all p<0.001). Univariate and multivariate analyses of patient-related and technical risk factors for anastomotic stricture/stenosis were performed 3 months postoperatively. For univariate analysis, female sex was a lower risk factor for anastomotic stricture/stenosis. Defunctioning stoma, neoadjuvant chemoradiotherapy, chemotherapy, and anastomotic leakage were higher risk factors for anastomotic stricture/stenosis (all p<0.05). For multivariate analysis, only neoadjuvant chemoradiotherapy, chemotherapy, and anastomotic leakage were still higher risk factors for anastomotic stricture/stenosis (all p<0.05).
CONCLUSIONS: Through a special anastomotic stricture/stenosis definition and grading system’s evaluation, we noted the anastomotic stricture/stenosis severity significantly affected bowel function, and multivariate analysis showed that neoadjuvant chemoradiotherapy, chemotherapy, and anastomotic leakage were the higher risk factors for anastomotic stricture/stenosis.
Dynamics of White Shrimp Population (Penaeus merguiensis) in Karang Gading Deli Serdang Regency, as a Basis in Its Management Efforts
Authors: Mulya Miswar Budi , Yeanny Mayang Sari
Published: September 2022

This study can be used as a basis for its management in the future. The purpose of the study was "Analyze the dynamics of white shrimp populations such as growth patterns, long frequency distribution, growth parameters, mortality rates, and recruitment patterns. The study was conducted for 12 months, from January-December 2021. The method used in sampling is purposive sampling, using a mini sine purse fishing gear measuring 8 m x 2 m. White shrimp growth patterns were analyzed using FISAT 2 software, shell length frequency distribution and growth parameters using von Bertalanffy growth models, asymptotic length and growth coefficient using the ELEFAN method, total mortality rate, natural and capture using Pauly's empirical equations, and recruitment patterns using the FAO-ICLARM program. The results of the study found the highest density of white shrimp at station 3 (257 ind / m2) and the lowest at station 2 (213 ind / m2). The distribution pattern of white shrimp at each station is in groups. The growth pattern of white shrimp is allometric negative. The theoretical lifespan at the length of zero carapace is 0.02 years or 0.2 months. The natural mortality rate of white shrimp is 0.75/year, the total mortality rate is 0.91/year and the catch mortality rate is 0.16/year. The capture of white shrimp in the waters of Karang Gading Deli Serdang Regency, North Sumatra is still under exploitation. Peak recruitment was in May and June (18.92% and 18.33%) after four months of white shrimp spawning.
Histamine and Gamma-aminobutyric acid in the nervous system of Pygospio elegans (Annelida: Spionidae). Structure and recovery during reparative regeneration
Authors: Starunova Zinaida I. , Shunkina Ksenia V. , Novikova Elena L. , Starunov Viktor V.
Published: September 2022

Background
In recent two decades, studies of the annelid nervous systems were revolutionized by modern cell labeling techniques and state-of-the-art microscopy techniques. However, there are still huge white fields in our knowledge on nervous system organization and functioning. Though most recent studies were focused on the distribution of now routine serotonin and FMRFamide, data about many basic neurotransmitters such as histamine (HA) and gamma-aminobutyric acid (GABA) are scarce.
Results
Using immunohistochemistry and confocal microscopy we studied distribution of histamine and gamma-aminobutyric acid in nervous system of a spionid annelid Pygospio elegans and followed their redevelopment during reparative regeneration. Both neurotransmitters show specific patterns in central and peripheral nervous systems. HA-positive cells are concentrated mostly in the brain, while GABA-positive cell somata contribute equally to brain and segmental ganglia. Some immunoreactive elements were found in peripheral nerves. Both substances revealed high number of bipolar sensory cells in the palps. The first signs of regenerating HA- and GABA-ergic systems were detected only by 3 days after the amputation. Further redevelopment of GABA-ergic system proceeds faster than HA-ergic.
Conclusions
Comparisons with other studied annelids and mollusks reveal both similar and unique features in HA- and GABA-ergic systems organizations. Overall, difference between the full redevelopment of various neurotransmitters correlates with neuronal development during embryogenesis. All these results state the high importance of investigating different neurotransmitter distribution in comparative morphological and developmental studies.
Steady states of a diffusive predator-prey model with prey-taxis and fear effect
Authors: Cao Jianzhi , Li Fang , Hao Pengmiao
Published: September 2022

In this paper, a diffusive predator-prey system with prey-taxis response subject to Neumann boundary conditions is considered. First, the stability of the positive equilibrium and the conditions for the occurrence of Hopf bifurcation are provided. Second, the existence of nonconstant steady states is proved by applying the the bifurcation theory of Crandall and Rabinowitz, bifurcation types and stability of the bifurcation solutions are analyzed. Finally, numerical simulation results are carried out to verify the theoretical results.