bluuebunny/crossref_metadata_2025 huggingface dataset:
Epidemiology, Diagnosis, and Prevention of Sparganosis in Asia
Authors: Liu Wei , Gong Tengfang , Chen Shuyu , Liu Quan , Zhou Haoying , He Junlin , Wu Yong , Li Fen , Liu Yisong
Published: June 2022

Sparganosis is a zoonotic parasitic disease caused by the larvae (spargana) of the genus Spirometra, which is widely distributed globally and threatens human health. More than 60 species of Spirometra have already been identified, and over 2000 cases have been reported. This review summarizes the prevalence of humans, frogs, snakes, and other animals with spargana. Furthermore, the infection mode, distribution, and site are summarized and analyzed. We also describe the epidemiology, molecular diagnosis, and other aspects which are of considerable significance to preventing sparganum.
Antivirulence Agent as an Adjuvant of β-Lactam Antibiotics in Treating Staphylococcal Infections
Authors: Gao Peng , Wei Yuanxin , Tai Sherlock Shing Chiu , Halebeedu Prakash Pradeep , Iu Ho Ting Venice , Li Yongli , Yam Hin Cheung Bill , Chen Jonathan Hon Kwan , Ho Pak Leung , Davies Julian , Kao Richard Yi Tsun
Published: June 2022

Staphylococcus aureus can cause a plethora of life-threatening infections. Antibiotics have been extensively used to treat S. aureus infections. However, when antibiotics are used at sub-inhibitory concentrations, especially for β-lactam antibiotics, they may enhance staphylococcal pathogenicity and exacerbate the infection. The combination of antivirulence agents and antibiotics may be a novel approach to controlling antibiotic-induced S. aureus pathogenicity. We have illustrated that under in vitro conditions, antivirulence agent M21, when administered concurrently with ampicillin, suppressed the expression and production of virulence factors induced by ampicillin. In a mouse peritonitis model, M21 reduced bacterial load irrespective of administration of ampicillin. In a bacteremia model, combinatorial treatment consisting of ampicillin or ceftazidime and M21 increased the survival rate of mice and reduced cytokine abundance, suggesting the suppression of antibiotic-induced virulence by M21. Different from traditional antibiotic adjuvants, an antivirulence agent may not synergistically inhibit bacterial growth in vitro, but effectively benefit the host in vivo. Collectively, our findings from this study demonstrated the benefits of antivirulence–antibiotic combinatorial treatment against S. aureus infections and provide a new perspective on the development of antibiotic adjuvants.
Antimicrobial Resistance Development Pathways in Surface Waters and Public Health Implications
Authors: Kusi Joseph , Ojewole Catherine Oluwalopeye , Ojewole Akinloye Emmanuel , Nwi-Mozu Isaac
Published: June 2022

Human health is threatened by antibiotic-resistant bacteria and their related infections, which cause thousands of human deaths every year worldwide. Surface waters are vulnerable to human activities and natural processes that facilitate the emergence and spread of antibiotic-resistant bacteria in the environment. This study evaluated the pathways and drivers of antimicrobial resistance (AR) in surface waters. We analyzed antibiotic resistance healthcare-associated infection (HAI) data reported to the CDC’s National Healthcare Safety Network to determine the number of antimicrobial-resistant pathogens and their isolates detected in healthcare facilities. Ten pathogens and their isolates associated with HAIs tested resistant to the selected antibiotics, indicating the role of healthcare facilities in antimicrobial resistance in the environment. The analyzed data and literature research revealed that healthcare facilities, wastewater, agricultural settings, food, and wildlife populations serve as the major vehicles for AR in surface waters. Antibiotic residues, heavy metals, natural processes, and climate change were identified as the drivers of antimicrobial resistance in the aquatic environment. Food and animal handlers have a higher risk of exposure to resistant pathogens through ingestion and direct contact compared with the general population. The AR threat to public health may grow as pathogens in aquatic systems adjust to antibiotic residues, contaminants, and climate change effects. The unnecessary use of antibiotics increases the risk of AR, and the public should be encouraged to practice antibiotic stewardship to decrease the risk.
Effect of Fluoroquinolone Use in Primary Care on the Development and Gradual Decay of Escherichia coli Resistance to Fluoroquinolones: A Matched Case-Control Study
Authors: Kurotschka Peter Konstantin , Fulgenzio Chiara , Da Cas Roberto , Traversa Giuseppe , Ferrante Gianluigi , Massidda Orietta , Gágyor Ildikó , Aschbacher Richard , Moser Verena , Pagani Elisabetta , Spila Alegiani Stefania , Massari Marco
Published: June 2022

The reversibility of bacterial resistance to antibiotics is poorly understood. Therefore, the aim of this study was to determine, over a period of five years, the effect of fluoroquinolone (FQ) use in primary care on the development and gradual decay of Escherichia coli resistance to FQ. In this matched case–control study, we linked three sources of secondary data of the Health Service of the Autonomous Province of Bolzano, Italy. Cases were all those with an FQ-resistant E. coli (QREC)-positive culture from any site during a 2016 hospital stay. Data were analyzed using conditional logistic regression. A total of 409 cases were matched to 993 controls (FQ-sensitive E. coli) by the date of the first isolate. Patients taking one or more courses of FQ were at higher risk of QREC colonization/infection. The risk was highest during the first year after FQ was taken (OR 2.67, 95%CI 1.92–3.70, p < 0.0001), decreased during the second year (OR 1.54, 95%CI 1.09–2.17, p = 0.015) and became undetectable afterwards (OR 1.09, 95%CI 0.80–1.48, p = 0.997). In the first year, the risk of resistance was highest after greater cumulative exposure to FQs. Moreover, older age, male sex, longer hospital stays, chronic obstructive pulmonary disease (COPD) and diabetes mellitus were independent risk factors for QREC colonization/infection. A single FQ course significantly increases the risk of QREC colonization/infection for no less than two years. This risk is higher in cases of multiple courses, longer hospital stays, COPD and diabetes; in males; and in older patients. These findings may inform public campaigns and courses directed to prescribers to promote rational antibiotic use.
Patterns and Determinants of Antibiotic Use Behaviors among Rural Community Residents in Eastern China
Authors: Wang Yanhuan , Zhao Xinping , Li Yurong , Wang Na , Jiang Feng , Lambert Helen , Yan Fei , Fu Chaowei , Jiang Qingwu
Published: June 2022

Inappropriate antibiotic use may lead to antibiotic resistance, which has become a serious global crisis. Addressing suboptimal antibiotic use in the general population can play a significant role in the fight against antimicrobial resistance. This study aims to describe antibiotic use and sources of acquisition, and to identify factors influencing antibiotic access among rural community residents in Eastern China. A cross-sectional survey was conducted from July to August 2020, and 1494 participants from two villages in Eastern China were enrolled. Information was obtained using face-to-face interviews with a structured electronic questionnaire. Chi-squared and multinominal logistic regression analysis were used to explore possible determinants. In total, 1379 participants were eligible for the analysis. In the past 12 months, nearly half the respondents had taken any antibiotic (48.4%), and this proportion varied across marital status and age group. Two thirds of them (59.9%) obtained antibiotics from medical facilities with a prescription when they last took antibiotics, while 17.7% and 22.4% chose retail pharmacies and other sources, respectively. Multinominal analysis found that a higher proportion obtained antibiotics outside medical facilities among those aged 15 to 44 years, unmarried, non-white collar workers, with more years of education, lower annual household income per capita and lower levels of antibiotic knowledge. The antibiotic use behavior of rural community residents in Eastern China remains suboptimal. Antibiotic use and access behaviors need to be further addressed. Effective antibiotic stewardship in non-medical facility sources and training programs targeted for rural Chinese is warranted in future.
Genotoxic Assessment of Nutraceuticals Obtained from Agricultural Biowaste: Where Do We “AMES”?
Authors: Musto Giorgia , Laurenzi Valentina , Annunziata Giuseppe , Novellino Ettore , Stornaiuolo Mariano
Published: June 2022

Several pharmaceutical companies are nowadays considering the use of agri-food waste as alternative raw material for the extraction of bioactive compounds to include in nutraceuticals and food supplements. This recycling activity is encountering the support of authorities, which are alarmed by air, soil and water pollution generated by agricultural waste disposal. Waste reuse has several economic advantages: (i) its low cost; (ii) its abundance; (iii) the high content of bioactive molecule (antioxidants, minerals, fibers, fatty acids); as well as (iv) the financial support received by governments eager to promote eco-compatible and pollution-reducing practices. While nutraceuticals produced from biowaste are becoming popular, products that have been risk-assessed in terms of safety are quite rare. This despite waste biomass, in virtue of its chemical complexity, could, in many cases, mine the overall safety of the final nutraceutical product. In this review, we summarize the scientific results published on genotoxicity risk-assessment of bioactive compounds extracted from agricultural waste. The review depicts a scenario where the risk-assessment of biowaste derived products is still scarcely diffuse, but when available, it confirms the safety of these products, and lets us envisage their future inclusion in the list of botanicals allowed for formulation intended for human consumption.
SOD3 and IL-18 Predict the First Kidney Disease-Related Hospitalization or Death during the One-Year Follow-Up Period in Patients with End-Stage Renal Disease
Authors: Liu Yu-Hsien , Chen Yu-Hsuan , Ko Chi-Hua , Kuo Chia-Wen , Yen Chih-Ching , Chen Wei , Chong Kowit-Yu , Chen Chuan-Mu
Published: June 2022

End-stage renal disease (ESRD) patients experience oxidative stress due to excess exogenous or endogenous oxidants and insufficient antioxidants. Hence, oxidative stress and inflammation cause endothelial damage, contributing to vascular dysfunction and atherosclerosis. Therefore, ESRD patients suffer more cardiovascular and hospitalization events than healthy people. This study aims to test the correlations between ROS, SOD3, IL-2, IL-6, and IL-18 and the first kidney disease-related hospitalization or death events in ESRD patients undergoing regular hemodialysis. A total of 212 participants was enrolled, including 45 normal healthy adults and 167 ESRD patients on regular dialysis. Blood samples from all participants were collected for ROS, SOD3, IL-2, IL-6, and IL-18 measurement at the beginning of the study, and every kidney disease-related admission or death was recorded for the next year. Multivariate analysis was conducted by fitting a linear regression model, logistic regression model, and Cox proportional hazards model to estimate the adjusted effects of risk factors, prognostic factors, or predictors on continuous, binary, and survival outcome data. The results showed that plasma SOD3 and serum IL-18 were two strong predictors of the first kidney disease-related hospitalization or death. In the Cox proportional hazards models (run in R), higher IL-18 concentration (>69.054 pg/mL) was associated with a hazard ratio of 3.376 for the first kidney disease-related hospitalization or death (95% CI: 1.2644 to 9.012), while log(SOD3) < 4.723 and dialysis clearance (Kt/V; 1.11 < value < 1.869) had a hazard ratio = 0.2730 (95% CI: 0.1133 to 0.6576) for reducing future kidney disease-related hospitalization or death. Other markers, including body mass index (BMI), transferrin saturation, total iron binding capacity, and sodium and alkaline phosphate, were also found to be significant in our study. These results reveal the new predictors SOD3 and IL-18 for the medical care of end-stage renal disease patients.
Antioxidant and Antimicrobial Biofoil Based on Chitosan and Japanese Knotweed (Fallopia japonica, Houtt.) Rhizome Bark Extract
Authors: Naumoska Katerina , Jug Urška , Kõrge Kristi , Oberlintner Ana , Golob Majda , Novak Uroš , Vovk Irena , Likozar Blaž
Published: June 2022

A 70% ethanol(aq) extract of the rhizome bark of the invasive alien plant species Japanese knotweed (JKRB) with potent (in the range of vitamin C) and stable antioxidant activity was incorporated in 1% w/v into a chitosan biofoil, which was then characterized on a lab-scale. The 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay confirmed the antioxidant activity of the JKRB biofoil upon contact with the food simulants A, B, C, and D1 (measured half-maximal inhibitory concentrations—IC50) and supported the Folin–Ciocalteu assay result. The migration of the antioxidant marker, (−)-epicatechin, into all food simulants (A, B, C, D1, D2, and E) was quantified using liquid chromatography hyphenated to mass spectrometry (LC-MS). Calculations showed that 1 cm2 of JKRB biofoil provided antioxidant activity to ~0.5 L of liquid food upon 1 h of contact. The JKRB biofoil demonstrated antimicrobial activity against Gram-positive bacteria. The incorporation of JKRB into the chitosan biofoil resulted in improved tensile strength from 0.75 MPa to 1.81 MPa, while elongation decreased to 28%. JKRB biofoil’s lower moisture content compared to chitosan biofoil was attributed to the formation of hydrogen bonds between chitosan biofoil and JKRB compounds, further confirmed with attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). The JKRB biofoil completely degraded in compost in 11 days. The future upscaled production of JKRB biofoil from biowastes for active packaging may support the fights against plastic waste, food waste, and the invasiveness of Japanese knotweed, while greatly contributing to the so-called ‘zero-waste’ strategy and the reduction in greenhouse gas emissions.
Simulation of Electromagnetic Generator as Biomechanical Energy Harvester
Authors: Gurusamy Nedunchelien , Elamvazuthi Irraivan , Yahya Norashikin , Su Steven , Truong Bao-Huy
Published: June 2022

Portable electronic devices are dependent on batteries as the ultimate source of power. Irrefutably, batteries only have a limited operating period as they need to be regularly replaced or recharged. In many situations, the power grid infrastructure is not easily accessible to recharge the batteries and the recharging duration is also not convenient for the user to wait. Enhancement of a reliable electronic system by preventing power interruptions in remote areas is essential. Similarly, modern medical instruments and implant devices need reliable, almost maintenance-free power to ensure they are able to operate in all situations without any power interruptions. In this paper, the small-sized electromagnetic generator was designed to produce higher power by utilizing the knee angle transition involved during the walking phase as the input rotary force. The proposed generator design was investigated through COMSOL Multiphysics simulation. The achieved output RMS power was in the range of 3.31 W to 14.95 W based on the RPM range between 360 RPM to 800 RPM.
Complete Genome Report of a Hydrocarbon-Degrading Sphingobium yanoikuyae S72
Authors: Lopez Eric Sanchez , Elufisan Temidayo Oluyomi , Bustos Patricia , Charles Claudia Paola Mendoza , Mendoza-Herrera Alberto , Guo Xianwu
Published: June 2022

Sphingobium yanoikuyae S72 was isolated from the rhizosphere of sorghum plant in Mexico and we evaluated its survival and role in the degradation of some selected monoaromatic hydrocarbons and polycyclic aromatic hydrocarbons (PAHs) using minimal medium (Bushnell Hass medium (BH)) in which each of the hydrocarbons (naphthalene, phenanthrene, xylene, toluene, and biphenyl) served as sole carbon source. Gas column chromatography–mass spectrometry analysis was used to evaluate the effect of S72’s growth in the medium with the hydrocarbons. The genome of the S72 was sequenced to determine the genetic basis for the degradation of the selected hydrocarbon in S72. The genome was assembled de novo with Spades assembler and Velvet assembler and the obtained contigs were reduced to 1 manually using Consed software. Genome annotation was carried out Prokka version 1.12, and gene calling and further annotation was carried out with NCBI PGAAP. Pangenome analysis and COG annotation were done with bacteria pangenome analysis tool (BPGA) and with PATRIC online server, respectively. S72 grew effectively in the culture medium with the hydrocarbon with concentration ranging from 20–100 mg/mL for each hydrocarbon tested. S72 degraded biphenyl by 85%, phenanthrene by 93%, naphthalene by 81%, xylene by 19%, and toluene by 30%. The sequenced S72 genome was reduced to 1 contig and genome analysis revealed the presence of genes essential for the degradation of hydrocarbons in S72. A total of 126 unique genes in S72 are associated with the degradation of hydrocarbons and xenobiotics. S72 grew effectively in the tested hydrocarbon and shows good degradation efficiency. S72 will therefore be a good candidate for bioremediation of hydrocarbon contaminated soil.
Application of Continuous Non-Gaussian Mortality Models with Markov Switchings to Forecast Mortality Rates
Authors: Sliwka Piotr , Socha Leslaw
Published: June 2022

The ongoing pandemic has resulted in the development of models dealing with the rate of virus spread and the modelling of mortality rates μx,t. A new method of modelling the mortality rates μx,t with different time intervals of higher and lower dispersion has been proposed. The modelling was based on the Milevski–Promislov class of stochastic mortality models with Markov switches, in which excitations are modelled by second-order polynomials of results from a linear non-Gaussian filter. In contrast to literature models where switches are deterministic, the Markov switches are proposed in this approach, which seems to be a new idea. The obtained results confirm that in the time intervals with a higher dispersion of μx,t, the proposed method approximates the empirical data more accurately than the commonly used the Lee–Carter model.
Performance of Numerically Optimized Tuned Mass Damper with Inerter (TMDI)
Authors: Weber Felix , Borchsenius Fredrik , Distl Johann , Braun Christian
Published: June 2022

In recent years, the Tuned Mass Damper with inerter (TMDI) has received significant attention. The inerter is defined to exert a force that is in proportion to the relative acceleration of the two inerter terminals. Here, two TMDI topologies are investigated. The conventional topology is given by the inerter being in parallel to the spring and viscous damper of the TMDI. The other topology is the serial arrangement of spring, inerter and viscous damper being in parallel to the stiffness of the mass spring oscillator of the TMDI. While the first topology intends to increase the inertial force of the TMDI, the second topology aims at producing an additional degree of freedom. The considered TMDI concepts are simulated for harmonic and random excitations, with parameters set according to those described in the literature and with numerically optimized parameters which minimize the primary structure displacement response. The classical TMD is used as a benchmark. The findings are twofold. The conventional TMDI with typical inertance ratio of 1% and the very small value of 0.02% performs significantly worse than the classical TMD with the same mass ratio. In contrast, the TMDI with an additional degree of freedom can improve the mitigation of the primary structure if the inertance ratio is set very small and if the TMDI parameters are numerically optimized.
Case Study on the Deformation Coupling Effect of a Deep Foundation Pit Group in a Coastal Soft Soil Area
Authors: Chen Shangrong , Cui Jifei , Liang Fayun
Published: June 2022

Simultaneous construction of adjacent projects may lead to emergencies in a foundation pit group, which significantly affects the deformation and safety of foundation pits. In this study, the deformation characteristics of a deep foundation pit group and the mutual interactions among the adjacent foundation pits were observed by a monitoring system during excavation. Field data of the foundation pit group, including the lateral deflections of the enclosure pile, the ground subsidence, as well as the vertical column movements, were analyzed and compared with individual excavations in Shanghai. The field data showed that the excavation of the adjacent foundation pit reduced the lateral deformation of the enclosure structure, caused by the reduction of active earth pressure acting on the retaining pile. Furthermore, the foundation pit excavated later caused upward movements of the soil between them. However, the foundation pit excavated earlier had a negligible influence on the vertical column movements of the foundation pit excavated later. Due to the optimized excavation sequence of the deep foundation pit group, the deformation of this special excavation was well controlled.
Estimating the Potential Differential Settlement of a Tailings Deposit Based on Consolidation Properties Heterogeneity
Authors: Badiozamani Mohammad Mahdi , Beier Nicholas
Published: June 2022

Processing of extracted oil sands generates substantial volumes of tailings slurries. Due to the scale and inherent variability of the tailings properties, consolidation settlement is expected to occur at different rates and magnitudes across the tailings deposit. Estimating potential differential settlement of the consolidated deposit surface is an essential input for closure design. This paper presents a three-step methodology that generates multiple realizations of quasi-three-dimensional (3D) surfaces of the consolidated deposit based on the adjacent points. Each point is based on a stochastic one-dimensional (1D) large strain consolidation model developed with Monte Carlo techniques in GoldSim. The simulated surfaces provide early estimates of differential settlement based on the variability of consolidation properties expected in the tailings deposit. Comprehensive sensitivity analyses are performed for differently treated tailings material through 28 distinct scenarios to evaluate the sensitivity of the developed 1D and 3D models to consolidation input parameters over a 40-year time period. The analysis demonstrated that differential settlement is highly sensitive to tailings compressibility and hydraulic conductivity governed by the constitutive relationship parameters, and less sensitive to the solids content, specific gravity or thickness of a surcharge load. Tailings that underwent steady continuous settlement exhibited the largest degree of differential settlement.
Co-Culture of THP-1 Cells and Normal Human Epidermal Keratinocytes (NHEK) for Modified Human Cell Line Activation Test (h-CLAT)
Authors: Sawada Yuka , Tsukumo Hanae , Fukuda Junji , Iijima Kazutoshi , Itagaki Hiroshi
Published: June 2022

To improve the accuracy of skin sensitization prediction of chemicals by conventional alternative methods using cells, it is important to reproduce the environment of skin in vitro, such as the crosstalk between keratinocytes and dendritic cells (DCs). We developed a skin sensitization test system based on the markers and criteria of the human cell line activation test (h-CLAT), which combines THP-1 cells as a surrogate for DCs and keratinized normal human epidermal keratinocytes (NHEK). After exposure to chemicals via keratinized NHEK, the cell surface expression of CD54 and CD86 on THP-1 was measured by flow cytometry. This co-culture system evaluated 2,4-dinitrochlorobenzene (DNCB), a typical sensitizer, as positive, lactic acid (LA), a non-sensitizer, as negative, and isoeugenol (IE), a prohapten that requires biological activation to acquire skin sensitization, as positive. However, the expression levels of CD54 and CD86 in DNCB-treated THP-1 were lower than those in normal h-CLAT. Therefore, we investigated the effects of the medium and secretion by NHEK cells on THP-1 cells. CD54 and CD86 expression was enhanced in monocultured THP-1 in the medium for keratinized NHEK and in the conditioned medium of keratinized NHEK. The increase in CD54 and CD86 by changes in the medium type was higher than that by the NHEK secretion; therefore, it was found that the medium composition has a large effect on the evaluation index among the experimental parameters in the co-culture system. It is necessary to find the optimal medium for immunotoxicity assessment in the co-culture system.
Analysis of Shield Tunnel Ground Deformation Characteristics and Affecting Factors in Water-Rich Soft Stratum: A Case Study on the Section Tunnel of Tianjin Metro Line 6
Authors: Li Xinyu , Zhang Dingli , Hou Yanjuan
Published: June 2022

With the increasing intensity of underground development, the planned metro lines will inevitably pass through water-rich soft stratum. The existing research results show that shield tunneling in water-rich stratum is prone to ground settlement and segment cracking due to the large moisture content and the low soil strength, which will pose risks to the safety of construction. The prediction of ground deformation characteristics and influencing ranges caused by shield tunneling in water-rich soft stratum has been a topical issue among the tunnel research community. Based on the shield tunnel project of Tianjin Metro Line 6, supported by the monitoring data, this paper analyses the ground deformation characteristics caused by shield tunneling in water-rich soft stratum. The results suggest that the surface settlement ranges from −14.20 mm to −28.00 mm in Tianjin’s water-rich soft stratum, which is at an acceptable level of engineering. A refined 3D model addressing fluid–structure interactions is developed to consider the construction process in water-rich soft stratum. Based on this technique, this article focuses on the effect of the support pressure at the excavation surface, the friction between the shield skin and the soil, and synchronous grouting quantity on the ground settlement and structural deformation. The results show that the friction between the shield skin and the soil is the most detrimental to deformation control, whereas the synchronous grouting quantity is the most advantageous to ground and segment deformation control. In practice, timely injection of bentonite slurry reduces friction between the shield skin and the soil, and effective synchronous grouting reduces shield tunneling disruption. This technique can provide calculation support in the optimization of shield tunneling schemes in water-rich soft stratum.
CleanSeq: A Pipeline for Contamination Detection, Cleanup, and Mutation Verifications from Microbial Genome Sequencing Data
Authors: Wang Caiyan , Xia Yang , Liu Yunfei , Kang Chen , Lu Nan , Tian Di , Lu Hui , Han Fuhai , Xu Jian , Yomo Tetsuya
Published: June 2022

Contaminations frequently occur in bacterial cultures, which significantly affect the reproducibility and reliability of the results from whole-genome sequencing (WGS). Decontaminated WGS data with clean reads is the only desirable source for detecting possible variants correctly. Improvements in bioinformatics are essential to analyze the contaminated WGS dataset. Existing pipelines usually contain contamination detection, decontamination, and variant calling separately. The efficiency and results from existing pipelines fluctuate since distinctive computational models and parameters are applied. It is then promising to develop a bioinformatical tool containing functions to discriminate and remove contaminated reads and improve variant calling from clean reads. In this study, we established a Python-based pipeline named CleanSeq for automatic detection and removal of contaminating reads, analyzing possible genome variants with proper verifications via local re-alignments. The application and reproducibility are proven in either simulated, publicly available datasets or actual genome sequencing reads from our experimental evolution study in Escherichia coli. We successfully obtained decontaminated reads, called out all seven consistent mutations from the contaminated bacterial sample, and derived five colonies. Collectively, the results demonstrated that CleanSeq could effectively process the contaminated samples to achieve decontaminated reads, based on which reliable results (i.e., variant calling) could be obtained.
An fMRI Sequence Representation Learning Framework for Attention Deficit Hyperactivity Disorder Classification
Authors: Xie Jin , Huo Zhiyong , Liu Xianru , Wang Zhishun
Published: June 2022

For attention deficit hyperactivity disorder (ADHD), a common neurological disease, accurate identification is the basis for treatment. In this paper, a novel end-to-end representation learning framework for ADHD classification of functional magnetic resonance imaging (fMRI) sequences is proposed. With such a framework, the complexity of the sequence representation learning neural network decreases, the overfitting problem of deep learning for small samples cases is solved effectively, and superior classification performance is achieved. Specifically, a data conversion module was designed to convert a two-dimensional sequence into a three-dimensional image, which expands the modeling area and greatly reduces the computational complexity. The transfer learning method was utilized to freeze or fine-tune the parameters of the pre-trained neural network to reduce the risk of overfitting in the cases with small samples. Hierarchical feature extraction can be performed automatically by combining the sequence representation learning modules with a weighted cross-entropy loss. Experiments were conducted both with individual imaging sites and combining them, and the results showed that the classification average accuracies with the proposed framework were 73.73% and 72.02%, respectively, which are much higher than those of the existing methods.
Numerical Analysis of the Factors Influencing the Erosion of the Valve Port of a High-Speed On/Off Valve
Authors: Li Yuzheng , Du Jintao , Lan Yijun , Du Heng , Huang Hui
Published: June 2022

Aiming at the problem of valve port erosion caused by contaminated particles, a three-dimensional prediction model of valve orifice erosion was established based on computational fluid dynamics (CFD) and erosion theory, considering the influence of the valve port eddy current on the oil flow. The discrete phase model (DPM) of fluent is used to obtain the orifice erosion location and erosion rate, and the causes of erosion of the high-speed on/off valve are analyzed. On this basis, several factors influencing valve port erosion are simulated to investigate the relationship between particle collision behavior and valve port erosion morphology under different factors, and the change rule of valve port erosion under different factors is analyzed. The results show that the high-speed on/off valve service life decreases with a larger cone angle of the spool, a larger pressure difference at the valve port, a larger proportion of large particle contaminants in the oil, a higher oil contamination level, and a larger filter aperture. In addition, the grey relational analysis method is used to clarify the pressure difference at the valve port, the particle size, and the filter aperture as the three most important factors affecting the erosion of the valve port of a high-speed on/off valve.
Torsional Fracture Resistance of Niti Rotary Glide Path Files under Flexural Stress
Authors: Oh Soram , Park Ju-Hyo , Kim Hyun-Jung , Kim Hye-Jeong , Shim Eurok , Woo Jee-Yeon , Perinpanayagam Hiran , Choi Kyung-Kyu , Chang Seok Woo
Published: June 2022

This study aimed to evaluate the effects of flexural stress on the torsional fracture resistance of NiTi glide path files. PathFile #16/02, RaCe #15/04, RaCe Evo #15/04, HyFlex EDM #15/03, TruNatomy Glider #17/02, and V Taper 2H #17/04 were examined by scanning electron microscopy (SEM) (n = 3/brand) and subjected to differential scanning calorimetry (n = 2/brand). Torsional fracture resistance testing was performed in straight (ISO 3630-1) and flexural modes (n = 15/brand/mode). Flexural mode testing involved instruments rotating within a stainless-steel artificial double-curved canal. Ultimate strength and distortion angle until failure were recorded, and fractured instruments were examined by SEM. Statistical analyses involved independent sample t-test and one-way analysis of variance with Games–Howell pots hoc test. Austenitic transformation- finishing temperatures of heat-treated files were above body temperature. For RaCe Evo, HyFlex EDM, TruNatomy Glider, and V Taper 2H, the flexural mode resulted in a significantly higher distortion angle compared to the straight mode (p < 0.05). The maximum torque of RaCe Evo, HyFlex EDM increased with the flexural stress (p < 0.05). V taper 2H showed the highest distortion angle and ultimate strength. SEM showed typical patterns of torsional fracture for all tested files. The flexural stress positively affected distortion angle of heat-treated NiTi glide path files.
Subjective Distance Estimates and Sense of Agency in Robotic Wheelchair Control
Authors: Yashin Artem S. , Zhao Darisy G. , Stolyarova Anastasiya N. , Moscowsky Anton D. , Yakovlev Dmitry S. , Nazhestkin Ivan A. , Shishkin Sergei L. , Dubynin Ignat A.
Published: June 2022

Sense of agency (SoA) refers to an individual’s awareness of their own actions. SoA studies seek to find objective indicators for the feeling of agency. These indicators, being related to the feeling of control, have practical application in vehicle design. However, they have not been investigated for actions related to the agent’s body movement inherent to steering a vehicle. In our study, participants operated a robotic wheelchair under three conditions: active control by a participant, direct control by the experimenter and remote control by the experimenter. In each trial, a participant drove the wheelchair until a sound signal occurred, after which they stopped the wheelchair and estimated the travelled distance. The subjective estimates were significantly greater when participants operated the wheelchair by themselves. This result contrasts with observations under static settings in previous studies. In an additional study on the electroencephalographic response to a sound presented at a random time after movement onset, the observed latencies in the N1 component implied that participants might have a higher sense of control when they drove the wheelchair. The proposed methodology might become useful to indirectly assess the degree of operator control of a vehicle, primarily in the field of rehabilitation technologies.
A Graph-Cut-Based Approach to Community Detection in Networks
Authors: Shin Hyungsik , Park Jeryang , Kang Dongwoo
Published: June 2022

Networks can be used to model various aspects of our lives as well as relations among many real-world entities and objects. To detect a community structure in a network can enhance our understanding of the characteristics, properties, and inner workings of the network. Therefore, there has been significant research on detecting and evaluating community structures in networks. Many fields, including social sciences, biology, engineering, computer science, and applied mathematics, have developed various methods for analyzing and detecting community structures in networks. In this paper, a new community detection algorithm, which repeats the process of dividing a community into two smaller communities by finding a minimum cut, is proposed. The proposed algorithm is applied to some example network data and shows fairly good community detection results with comparable modularity Q values.
Use of Integrated Core Proteomics, Immuno-Informatics, and In Silico Approaches to Design a Multiepitope Vaccine against Zoonotic Pathogen Edwardsiella tarda
Authors: Islam Sk Injamamul , Mahfuj Sarower , Islam Md Jakiul , Mou Moslema Jahan , Sanjida Saloa
Published: June 2022

Multidrug-resistant Edwardsiella tarda has been reported as the main causative agent for massive fish mortality. The pathogen is well-known for causing hemorrhagic septicemia in fish and has been linked to gastrointestinal infections in humans. Formalin-inactivated Edwardsiella vaccination has previously been found to be ineffective in aquaculture species. Therefore, based on E. tarda’s integrated core complete sequenced genomes, the study aimed to design a subunit vaccine based on T and B cell epitopes employing immunoinformatics approach. Initially, the top immunodominant and antigenic epitopes were predicted from the core complete sequenced genomes of the E. tarda genome and designed the vaccine by using linkers and adjuvant. In addition, vaccine 3D structure was predicted followed by refinement, and molecular docking was performed for the analysis of interacting residues between vaccines with TLR5, MHC-I, and MHC-II, respectively. The final vaccine constructs demonstrated strong hydrogen bond interactions. Molecular dynamic simulation of vaccine-TLR5 receptor complex showed a stable structural binding and compactness. Furthermore, E. coli used as a model organism for codon optimization proved optimal GC content and CAI value, which were subsequently cloned in vector pET2+ (a). Overall, the findings of the study imply that the designed epitope vaccine might be a good option for prophylaxis for E. tarda.
Landfill Emissions of Methane Inferred from Unmanned Aerial Vehicle and Mobile Ground Measurements
Authors: Olaguer Eduardo , Jeltema Shelley , Gauthier Thomas , Jermalowicz Dustin , Ostaszewski Arthur , Batterman Stuart , Xia Tian , Raneses Julia , Kovalchick Michael , Miller Scott , Acevedo Jorge , Lamb Jonathan , Benya Jeff , Wendling April , Zhu Joyce
Published: June 2022

Municipal solid waste landfills are significant sources of atmospheric methane, the second most important greenhouse gas after carbon dioxide. Large emissions of methane from landfills contribute not only to global climate change, but also to local ozone formation due to the enhancement of radical chain lengths in atmospheric reactions of volatile organic compounds and nitrogen oxides. Several advanced techniques were deployed to measure methane emissions from two landfills in the Southeast Michigan ozone nonattainment area during the Michigan–Ontario Ozone Source Experiment (MOOSE). These techniques included mobile infrared cavity ringdown spectrometry, drone-mounted meteorological sensors and tunable diode laser spectrometry, estimation of total landfill emissions of methane based on flux plane measurements, and Gaussian plume inverse modeling of distributed methane emissions in the presence of complex landfill terrain. The total methane emissions measured at the two landfills were of the order of 500 kg/h, with an uncertainty of around 50%. The results indicate that both landfill active faces and leaking gas collection systems are important sources of methane emissions.
Ambient Size-Segregated Particulate Matter Characterization from a Port in Upstate New York
Authors: Moyebi Omosehin D. , Frank Brian P. , Tang Shida , LaDuke Gil , Carpenter David O. , Khwaja Haider A.
Published: June 2022

Air pollution impacts human health and the environment, especially in urban cities with substantial industrial activities and vehicular traffic emissions. Despite increasingly strict regulations put in place by regulatory agencies, air pollution is still a significant environmental problem in cities across the world. The objective of this study was to evaluate the environmental pollution from stationary and mobile sources using real-time monitoring and sampling techniques to characterize size-segregated particulate matter (PM), black carbon (BC), and ozone (O3) at the Port of Albany, NY. Air pollution monitoring was carried out for 3 consecutive weeks under a 24-hour cycle in 2018 at the New York State Department of Environmental Conservation (NYSDEC) site within the Port. Sampling was done with an AEROCET 531, optical particle sizer (OPS), ozone monitor, and MicroAeth AE51. Higher mass and number concentrations of size-segregated particles were observed during the daytime. PM2.5 and PM10 concentrations ranged from 1 to 271 micrograms per cubic meter (µg/m3) and 1 to 344 µg/m3, respectively. While these values do not exceed the level of the USEPA 24-hour standards, frequent sharp peaks were observed at higher concentrations. Size-segregated PM at sizes 0.3 µm and 0.374 µm recorded maximum concentrations of 101,631 particle number per cubic centimeter (#/cm3) and 43,432 #/cm3, respectively. Wide variations were observed in the particle number concentrations for 0.3 µm, 0.374 µm, and 0.465 µm sizes, which ranged from 1521 to 101,631 #/cm3; 656 to 43,432 #/cm3; and 311 to 29,271 #/cm3, respectively. BC concentration increased during morning and evening rush hours with the maximum concentration of 11,971 ng/m3 recorded at 8:00 AM. This suggests that mobile sources are the primary contributor to anthropogenic sources of BC within the Port. Episodic elevations in the concentrations of size-segregated PM and BC confirmed the contribution of industrial and vehicular activities around the Port of Albany. This study underscores the importance of measuring particles on a size-segregated basis in order to more fully understand the contributions of the multiple sources present within and surrounding a port environment.
Data Assimilation of Doppler Wind Lidar for the Extreme Rainfall Event Prediction over Northern Taiwan: A Case Study
Authors: Chen Chih-Ying , Yeh Nan-Ching , Lin Chuan-Yao
Published: June 2022

On 4 June 2021, short-duration extreme precipitation occurred in Taipei. Within 2 h, over 200 mm of rainfall accumulated in the Xinyi district. In this study, advanced data assimilation technology (e.g., hybrid data and 3D variations) was incorporated to develop a high-resolution, small-scale (e.g., northern Taiwan) data assimilation forecast system, namely the weather research and forecast-grid statistical interpolation (WRF-GSI) model. The 3D wind field data recorded by the Doppler wind lidar system of Taipei Songshan Airport were assimilated for effective simulation of the extreme precipitation. The results revealed that the extreme rainfall was caused by the interaction between the northeast wind incurred by a front to the north of Taiwan, a humid southerly wind generated by Typhoon Choi-wan, and the regional sea–land breeze circulation. For the Xinyi district, the WRF-GSI_lidar model reported accumulated rainfall 30 mm higher than that in the non-assimilated experiment (WRF-GSI_noDA), indicating that the WRF-GSI model with lidar observation was improved 15% more than the nonassimilated run.
Identification of a Unique Cytotoxic Thieno[2,3-c]Pyrazole Derivative with Potent and Selective Anticancer Effects In Vitro
Authors: Hess Jessica D. , Macias Luca H. , Gutierrez Denisse A. , Moran-Santibanez Karla , Contreras Lisett , Medina Stephanie , Villanueva Paulina J. , Kirken Robert A. , Varela-Ramirez Armando , Penichet Manuel L. , Aguilera Renato J.
Published: June 2022

In recent years, the thienopyrazole moiety has emerged as a pharmacologically active scaffold with antitumoral and kinase inhibitory activity. In this study, high-throughput screening of 2000 small molecules obtained from the ChemBridge DIVERset library revealed a unique thieno[2,3-c]pyrazole derivative (Tpz-1) with potent and selective cytotoxic effects on cancer cells. Compound Tpz-1 consistently induced cell death at low micromolar concentrations (0.19 μM to 2.99 μM) against a panel of 17 human cancer cell lines after 24 h, 48 h, or 72 h of exposure. Furthermore, an in vitro investigation of Tpz-1’s mechanism of action revealed that Tpz-1 interfered with cell cycle progression, reduced phosphorylation of p38, CREB, Akt, and STAT3 kinases, induced hyperphosphorylation of Fgr, Hck, and ERK 1/2 kinases, and disrupted microtubules and mitotic spindle formation. These findings support the continued exploration of Tpz-1 and other thieno[2,3-c]pyrazole-based compounds as potential small-molecule anticancer agents.
Embolization for Type Ia Endoleak after EVAR for Abdominal Aortic Aneurysms: A Systematic Review of the Literature
Authors: Marchiori Elena , Ibrahim Abdulhakim , Schäfers Johannes Frederik , Oberhuber Alexander
Published: June 2022

(1) Successful endovascular repair for abdominal aortic aneurysms is based on the complete exclusion of the aneurysm sac from the systemic circulation. Type Ia endoleak (ELIA) is defined as the persistent perfusion of the aneurysm sac due to incomplete proximal sealing between aorta and endograft, with a consequent risk of rupture and death. Endoleak embolization has been sporadically reported as a viable treatment for ELIA. (2) A systematic literature search in PubMed of all publications in English about ELIA embolization was performed until February 2022. Research methods and reporting were performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Data regarding patient numbers, technical success (endoleak absence at control angiography), reinterventions, clinical and imaging follow-up, and outcomes were collected and examined by two independent authors. (3) Twenty-one papers (12 original articles, 9 case reports) reported on 126 patients (age range 58–96 years) undergoing ELIA embolization 0–139 months after the index procedure. Indication for embolization was most often founded on unfavorable anatomy and patient comorbidities. Embolic agents used include liquid embolic agents, coils, plugs and combinations thereof. Technical success in this highly selected cohort ranged from 67–100%; the postprocedural complication rate within 30 days was 0–24%. ELIA recurrence was reported as 0–42.8%, with a secondary ELIA-embolization-intervention success rate of 50–100%. At a follow-up at 0–68 months, freedom from sac enlargement amounted to 76–100%, freedom from ELIA to 66.7–100%. (4) Specific literature about ELIA embolization is scant. ELIA embolization is a valuable bailout strategy for no-option patients; the immediate technical success rate is high and midterm and long-term outcomes are acceptable.
Antidepressant-like Effects of Polygonum minus Aqueous Extract in Chronic Ultra-Mild Stress-Induced Depressive Mice Model
Authors: Bashir Muhammad Irfan , Abdul Aziz Nur Hidayah Kaz , Noor Dzul Azri Mohamed
Published: June 2022

Depression is the most common behavior disorder that leads to many disabilities. The main aim of this study was to evaluate the effects of a Polygonum minus (P. minus) aqueous extract on chronic ultra-mild stress (CUMS)-induced depressive mice model. Chronic ultra-mild stress can disturb the neurotransmitters levels and plasticity of the hippocampus. Balb/c male mice were used in this study, which consisted of six groups (n = 14). Treatment was given for eight weeks, and chronic ultra-mild stress was applied for six weeks. Commercially available P. minus extract (BioKesum®) was used in this study. The behavior and neurochemical parameters were investigated through behavioral Tests and ELISA assays. P. minus administration significantly (p < 0.05) restored CUMS-induced behavior abnormalities, decreased the immobility time, and increased the sucrose preference and increased the spatial memory. P. minus treatment also showed the decreased level of serum corticosterone and increased the level of hippocampal neurotransmitters (Serotonin and Norepinephrine) significantly (p < 0.05). The brain-derived neurotrophic factor (BDNF) level also increased significantly in both the prefrontal cortex and hippocampus (p < 0.05). P. minus treatment exhibited significant (p < 0.05) reduction of Monoamine Oxidase-A (MAO-A) in the hippocampus. These findings indicate that P. minus aqueous extract exhibits antidepressant effects, including decreased immobility time, increased spatial memory, reduced corticosterone, increased BDNF level, and reduced MAO-A enzyme level with increasing the monoamines (serotonin and norepinephrine) in the hippocampus.