bluuebunny/crossref_metadata_2025 huggingface dataset:
A Collocated Finite Volume Scheme for High-Performance Simulation of Induced Seismicity in Geo-Energy Applications
Authors: Novikov A. , Voskov D. V. , Khait M. , Hajibeygi H. , Jansen J. D.
Published: October 2021

We develop a collocated Finite Volume Method (FVM) to study induced seismicity as a result of pore pressure fluctuations. A discrete system is obtained based on a fully-implicit coupled description of flow, elastic deformation, and contact mechanics at fault surfaces on a fully unstructured mesh. The cell-centered collocated scheme leads to convenient integration of the different physical equations, as the unknowns share the same discrete locations on the mesh. Additionally, a multi-point flux approximation is formulated in a general procedure to treat heterogeneity, anisotropy, and cross-derivative terms for both flow and mechanics equations. The resulting system, though flexible and accurate, can lead to excessive computational costs for field-relevant applications. To resolve this limitation, a scalable parallel solution algorithm is developed and presented. Several proof-of-concept numerical tests, including benchmark studies with analytical solutions, are investigated. It is found that the presented method is indeed accurate, stable and efficient; and as such promising for accurate and efficient simulation of induced seismicity.
Theoretical and Numerical Investigation of Supersonic Multiphase Gas Injection
Authors: Zhu Da , Sivagnanam Mohan , Gates Ian
Published: October 2021

Supersonic gas injection can help deliver gas uniformly to a reservoir, regardless of reservoir conditions. This technology has played a key role in enhanced oil recovery (EOR) and in particular, thermal enhanced oil recovery operations. Most previous studies have focused on single phase gas injection whereas in most field applications, multiphase and multicomponent situations occur.

In the research documented in this paper, we report on results of evaluations of compressible multiphase supersonic gas flows in which gas is the continuous phase is seeded with dispersed liquid droplets or solid particles. Theoretical derivation and numerical simulations with and without relative motions between continuous and disperse phases are examined first. The results illustrate that the shock wave structures and flow properties associated with the multiphase gas flows are different than that of single-phase isentropic flows. The existence and importance of relaxation zones after the normal shock wave in multiphase flow is described. Numerical computational fluid dynamics (CFD) simulations are conducted to show how the multiphase multicomponent flow affects gas phase injection under different conditions. The impact of solid/liquid mass loading on flow performance is discussed. Finally, the practical application of the findings is discussed.
TAS-Seq: A Robust and Sensitive Amplification Method for Beads-based ScRNA-seq
Authors: Shichino Shigeyuki , Ueha Satoshi , Hashimoto Shinichi , Ogawa Tatsuro , Aoki Hiroyasu , Wu Bin , Chen Chang-Yu , Kitabatake Masahiro , Ouji-Sageshima Noriko , Sawabata Noriyoshi , Kawaguchi Takeshi , Okayama Toshitugu , Sugihara Eiji , Hontsu Shigeto , Ito Toshihiro , Ikeo Kazuho , Sato Taka-aki , Matushima Kouji
Published: October 2021

Single-cell RNA-sequencing (scRNA-seq) is valuable for analyzing cellular heterogeneity. Cell composition accuracy is critical for analyzing cell–cell interaction networks from scRNA-seq data. We developed terminator-assisted solid-phase cDNA amplification and sequencing (TAS-Seq) for scRNA-seq based on a terminator, terminal transferase, and nanowell/bead-based scRNA-seq platform; TAS-Seq showed high tolerance to variations in the terminal transferase reaction, which complicate the handling of existing terminal transferase-based scRNA-seq methods. In murine and human lung samples, TAS-Seq yielded scRNA-seq data that were highly correlated with flow-cytometric data, showing higher gene-detection sensitivity and more robust detection of important cell–cell interactions and specific cell subsets that significantly contribute to specific gene expression than widely-used methods.
Investigating polystyrene nanoplastics-induced reproductive toxicity in vitro: Focus on Nrf2-PKM2-autophagy signaling pathway
Authors: Li Siwen , Ma Yu , Ye Shuzi , Su Ying , Hu Die , Xiao Fang
Published: October 2021

As an issue of widespread concern, microplastics pollution has emerged as a harmful environmental pollutant. Nanoplastics (NaPs) has reported to accumulate in the testes and cause degeneration in the seminiferous tubules. However, the current research involving NaPs-induced reproductive toxicity remains poorly understood. The current work aimed to investigate the mechanisms of NaPs-induced reproductive injury in vitro. At first, we found that 80 nm fluorescent NaPs could enter into GC-2spd(ts) cells by fluorescent inverted microscope. Our results also demonstrated that suppression of reactive oxygen species (ROS) inhibited NaPs-triggered mitochondrial apoptosis and autophagy in GC-2spd(ts) cells. We also found that NaPs treatment did not change the interaction between nuclear factor erythroid-derived 2-related factor (Nrf2) and Kelch-like ECH associated protein 1 (Keap1), while inhibiting nuclear accumulation of Nrf2 protein. Further in vitro experiments showed that NaPs-induced reproductive toxicity associated with reducing dimerize pyruvate kinase M2 (PKM2), which are ascribed to the loss of Nrf2. Meanwhile, improving nuclear accumulation of Nrf2 might interact with PKM2 to rescue mitochondrial apoptosis caused by NaPs. Together, this study highlight that disturbing Nrf2-PKM2 signaling is essential process of NaPs-induced reproductive toxicity and provide valuable insights into the mechanism of microplastics-induced reproductive toxicity.
Molecular Epidemiology of Community-Onset Clostridioides Difficile Infections At A Tertiary Hospital In Mainland China: A Ten-Year (2010-2019) Retrospective Study
Authors: Chen Yunbo , Bu Lihong , Lv Tao , Zheng Lisi , Gu Silan , He Jianqin
Published: October 2021

Background: Clostridioides difficile infection (CDI) is an increasingly common disease in healthcare facilities and community settings. However, there are limited reports of community-onset CDI (CO-CDI) in China. We retrospectively analyzed the molecular epidemiology of CO-CDI at a tertiary hospital over a period of 10 years. A total of 1307 stool samples from 1213 outpatients were tested by culturing. The presence of toxin genes (tcdA, tcdB, cdtA, and cdtB) were confirmed by PCR. Toxigenic strains were typed using multilocus sequence typing (MLST). Susceptibility to 9 antimicrobials was evaluated using the E-test.Results: Eighty-nine of 1213 outpatients (7.3%) had CO-CDI, 4 of these patients (4.5%) had one or more recurrence, and there were 95 strains of toxigenic C. difficile. Among these strains, 82 (86.3%) had the tcdA and tcdB genes (A+B+) and 5 of these 82 strains were positive for the binary toxin genes (cdtA and cdtB); the other 13 strains (13.7%) had the tcdB gene only (A−B+). There were 15 different STs, and the most prevalent were ST-54 (23.2%), ST-35 (16.8%), and ST-2 (13.7%). All strains were susceptible to metronidazole and vancomycin, and had low resistance to moxifloxacin and tetracycline, but had high resistance to ciprofloxacin, clindamycin, and erythromycin. Twenty-three isolates (24.2%) were multidrug-resistant.Conclusions: Outpatients with CDI were common during this period in our hospital. The C. difficile isolates had high genetic diversity. All isolates were susceptible to metronidazole and vancomycin, and nearly one quarter of all isolates had multidrug resistance.
Qualitative analysis of the response regimes and triggering mechanism of bistable NES
Authors: WU Zhenhang , Seguy Sébastien , Paredes Manuel
Published: October 2021

The main focus of this study is the development of an adapted complex variable method in the vicinity of equilibrium in bistable NES. A simplified chaos trigger model is established to describe the distance between the stable phase cycle and the pseudo-separatrix. An analytical expression can predict the excitation threshold for chaos occurrence. The relative positions between the chaos trigger threshold line and the Slow Invariant Manifold (SIM) structure can express the distribution of response regimes under growing harmonic excitation. This topological structure implies the alternation of the response regime and helps to classify the bistable NES. The experiment compares the analytical result of intra-well oscillation with the numerical result in the frequency domain. The experimental response regimes under different input energy levels and frequency domains have been observed and give ideas to guide the optimal design of a bistable NES. It is shown that the modest bistable NES possesses strong robustness to frequency perturbation.
Assessment of Groundwater Vulnerability and Pollution Risk using AVI Model, PSI and RGPI Indexes: Applied to Southern Gabes Aquifer System, Tunisia
Authors: Atoui Mounir , Agoubi Belgacem
Published: October 2021

Southern Gabes aquifer is part of coastal Jeffara plain located in southeastern Tunisia. It consists a semi-arid area in which groundwater is the main source to water supply for several socio-economic sectors. Southern Gabes aquifer suffers from excessive abstraction and heavy anthropogenic pressures that make local groundwater resources threatened by pollution risks. This study aims to assess groundwater vulnerability, evaluate and delineate groundwater risk regions. For this a 17 water samples were carried out in the study area and chemical composition were analyzed. A well-known AVI model has been used to assess aquifer vulnerability and new algorithms of sensitivity to pollution index (PSI) and risk groundwater to pollution index (RGPI) were implemented and used to assess, classify and mapping groundwater pollution risk. The method used in this study seems giving more precise results compared to conventional approaches. Moreover, this method allows assessing the pollution risk with flexible and reliable algorithm even with limited dataset. Results reveal that study area suffers from high risk. 41% of total surface of study area has a very high risk. Nonetheless only 30% of study area has a low to insignificant risk to pollution which necessitates taking severe precautions to protect the southern Gabes aquifer system. Hence, the poor natural protective capacity of study area needs a rapid intervention by local authorities in order to develop proactive solutions to protect and preserve groundwater resources from pollution risks and establish a long-term program for groundwater resources sustainable development.
Conceptualization of Pollution of Groundwater Resources in Ilaje Area, Nigeria, West Africa: Contribution From Hydrogeochemical and Numerical Index Techniques
Authors: Erukubami Omowumi Funmilola , Adelakun Adeboye Tolu , Asiwaju-Bello Yinusa Ayodele , Olabode Oluwaseun Franklin
Published: October 2021

Ilaje is a coastal settlement in Nigeria with a large number of its population depending on groundwater, through hand-dug wells, for domestic and irrigation use. Due to the vulnerability of coastal aquifers to contamination, for this study, 29 groundwater samples were analyzed for physicochemical parameters, major ions and trace elements to appraise the quality, pollution status and health risks of Ilaje water sources. Hydrogeochemical analysis revealed cationic, anionic and trace metals concentrations in these orders: Na+>K+>Mg2+>Ca2+, HCO3->Cl->SO42->NO3-, and Fe2+> Co2+>Pb2+> Ni2+> Mn2+ respectively and prevalence of Na-Cl facies suggesting imprints of saline-water intrusion. The results from the pollution evaluation and irrigation index methods revealed that the groundwater has significant trace metal pollution and has low to no suitability for irrigation. Furthermore, in this study, the carcinogenic and non-carcinogenic health risks posed by ingestion of the water to adults and children were determined using Probability of Cancer Risk, Chronic Daily Intake, Health hazard Quotient and Indices. It was discovered that upon exposure to the water for a long period of time, residents are prone to illnesses such as kidney disfunction, brain damage, diabetes and cancer. The pollution of the shallow groundwater resources hinges on the highly porous and permeable nature of the alluvial aquifer system of the area. This work recommends solutions like proper monitoring system and treatment plants installation to control the problem of groundwater pollution in the area.
Lessons Learned: Developing a Better Treatment for Patients With Chronic Pain and Opioid User Disorder
Authors: Wachholtz Amy , Robinson Dallas , Epstein Elizabeth
Published: October 2021

Introduction: It is critical to develop empirically based, community-treatment friendly, psychotherapy interventions to improve treatment for patients with comorbid chronic pain and Opioid Use Disorder (OUD). Understanding factors that increase patient adherence and attendance is important, along with strategies targeted to address those issues.Methods: Based on initial psychophysiology research on adults with OUD and chronic pain, we created an integrated cognitive-behavioral, 12-week outpatient group therapy called STOP (Self-regulation Therapy for Opioid addiction and Pain). In this study, we pilot tested STOP in a Stage 1a feasibility and acceptability study to identify unique treatment needs and factors that increased session attendance, adherence to treatment, and improved outcomes. Fourteen individuals on medication for OUD with co-occurring chronic pain participated.Results: STOP had high attendance rates (80%; and active patient engagement). Urine toxicology showed no illicit drug use after week 8. Data analysis from pre-intervention to a 3-month follow-up showed significant functional improvement (F(1,12)=45.82;p<0.001) and decreased pain severity levels (F(1,12)=37.62;p<0.01). Participants reported appreciation of the unique tools to counteract physiological activation during a pain flare or craving. Participants also reported benefit from in-session visual aids, applicable pain psychology information, take-home worksheets, tools for relaxation practice, learning to apply the therapy tools. Discussion: STOP is a 90-minute 12-week rolling-entry group therapy based on previous research identifying psychophysiological needs of pain and OUD patients that can be integrated into community addiction treatment clinics. Conclusion: Preliminary results of STOP are promising with high patient engagement and adherence and significant reductions in drug use and pain. Trial registration: ClinicalTrials.Gov NCT03363243, Registered Dec 6, 2017, https://clinicaltrials.gov/ct2/show/NCT03363243
Long-term Performance of Nanoparticle Incorporated Eco-friendly Concrete in Natural Seawater Environment
Authors: Philip John , Harilal Manu , Balakrishnan Anandkumar , George Rani Pongachira , Albert Shaju Kattukaran
Published: October 2021

The use of blended concrete has widely gained industrial importance owing to the CO2 gas emissions and carbon footprint resulting from the production of ordinary Portland cement (OPC). Despite the advancements, the deterioration of concrete structures raises a significant threat to their long term durability and service life in aggressive conditions. In this work, the long-term antifouling, strength and durability properties of a blended eco-friendly concrete with OPC, fly ash, nanoparticles, and corrosion inhibitor is evaluated in natural seawater for one year. The biofouling attachment, total viability count (TVC), mechanical strength, alkalinity and free chloride contents were measured and the results were compared with OPC concrete. A four-order reduction in the total biomass and total bacterial density is observed on the surface of the blended concrete. Further, a significantly lower chloride and water penetration depth, free chloride content, compact and smooth surface morphology devoid of cracks and high C-S-H content are observed in blended concrete, compared to the OPC concrete, after exposure in seawater for one year. From the results, it is seen that the blended concrete mix is promising for applications in seawater environments because of its superior biofouling resistance, mechanical properties and durability.
Long-term Outcomes of Endoscopic Resection Versus Open Surgery for Locally Advanced Sinonasal Malignancies in Combination With Radiotherapy
Authors: Liu Qian , Huang Xiaodong , Chen Xuesong , Zhang Jianghu , Wang Jingbo , Qu Yuan , Wang Kai , Wu Runye , Zhang Ye , Xiao Jianping , Yi Junlin , Xu Guozhen , Luo Jingwei
Published: October 2021

Objective:To compare the long-term oncological outcomes of endoscopic resection versus open surgery in combination with radiotherapy for locally advanced sinonasal malignancies.Methods:Data for continuous patients with sinonasal epithelial tumors treated in our center between Jan 1999 and Dec 2016 were retrospectively reviewed. Those who received surgery (endoscopic or open surgery) combined with radiotherapy were identified, and 1:1 matching with propensity scores was performed. The primary endpoints of overall survival (OS) and progression-free survival (PFS) were evaluated using the Kaplan-Meier method and Cox proportional hazards modeling. The local recurrence rate (LRR) was assessed by competing risk analysis.Results:We identified 267 eligible patients, 90 of whom were included after matching: 45 patients in the endoscopy group and 45 in the open group. The median follow-up time was 87 months. In the endoscopic group, 84.4% of patients received intensity-modulated radiotherapy (IMRT), with a mean gross tumor volume (GTV) dose of 68.28 Gy; in the open surgery group, 64.4% of patients received IMRT, with a mean GTV dose of 64 Gy. The 5-year OS, PFS and LRR were 69.9%, 58.6%, and 24.5% in the endoscopic group and 64.6%, 54.4%, and 31.8% in the open surgery group, respectively. Multivariable regression analysis revealed that surgical approach was not associated with lower OS, PFS or LRR. Age, histopathology and stage were independent risk factors for OS.Conclusion:For patients with locally advanced sinonasal carcinoma, minimally invasive endoscopic resection, in combination with a higher radiation dose and new radiation techniques such as IMRT, yields survival outcomes similar to those of open surgery in combination with radiotherapy.
Fizeau Interferometer to Measure Refractive Index of Air With Permanent Vacuum Prism Etalon
Authors: Kruger Oelof , Chetty Naven
Published: October 2021

Over the years much research has been done into the measurement of the speed of light. The speed of light has had many applications in measurements since it has been determined with the required accuracy. The refractive index of the medium in which the measurements are performed is critical in order to use the speed of light for accurate measurements. In dimensional metrology, most measurements are performed in air, and therefore, the refractive index of the air must be determined to a higher accuracy than the dimensional measurements performed. The most accurate way to determine the refractive index is to use a refractometer. Previous research by the authors looked at using a prism as the vacuum cell instead of a cylinder. The main advantage was that it eliminates the use of a vacuum pump. In this research, a new prism was designed to overcome difficulties with the previously used prism. A new method to use an optical flatness interferometer with a Fizeau interferometer layout to measure the air/vacuum ratio was researched and the results are presented here. The results achieved in the measurement method of the refractive index of air were accurate to 6 × 10-8, which compares well with other refractometers with the added described advantage.
Effects of ondansetron, metoclopramide and granisetron on perioperative nausea and vomiting in patients undergone bariatric surgery: a randomized clinical trial
Authors: Oshidari Bahador , Ebrahimian Manoochehr , Ghayebi Negin
Published: October 2021

IntroductionPost-operative nausea and vomiting (PONV) is a common problem after bariatric surgeries. In recent years, following the expansion of the number of this type of surgery, special attention has been paid to prevent this phenomenon. Also, several prophylaxis methods have been developed including Enhanced Recovery After Surgery (ERAS) and antiemetics. Nevertheless, PONV has not been completely eliminated and the clinicians are trying to reduce the incidence of PONV, yet.MethodsAfter successful ERAS implementation, patients divided into five groups including control and interventional groups. Metoclopramide (MA), Ondansetron (OA), Granisetron (GA) and combination of Metoclopramide and Ondansetron (MO) were used as antiemetics for each groups. The frequency of PONV during first and second days of admission has been recorded.Resultsone hundred thirty patients were enrolled in this study. The MO group showed lower incidence of PONV (46.1%) in comparison to control group (53.8%) as well as other groups. Also, the MO group didn’t require rescue antiemetic while one-third of control cases used antiemetics (0 vs 34%).ConclusionUsing a combination of metoclopramide and ondansetron is a cost-effective antiemetic regimen for reducing PONV after bariatric surgeries. This combination is more helpful when implemented alongside ERAS protocols.
Construction of an immune-related lncRNA signature pair for predicting oncologic outcomes and the sensitivity of drugs to treat adverse reactions to immunotherapy in lung adenocarcinoma
Authors: Zhuang Jinman , Chen Zhongwu , Chen Zishan , Chen Jin , Liu Maolin , Xu Xinying , Liu Yuhang , Yang Shuyan , Hu Zhijian , He Fei
Published: October 2021

Background

Although immunotherapy has shown clinical activity in lung adenocarcinoma (LUAD), LUAD prognosis has been a perplexing problem. We aimed to construct an immune-related lncRNA pair (IRLPs) score for LUAD and identify the best drugs to treat immune-related adverse events (ir AEs).
Methods

Based on The Cancer Genome Atlas (TCGA) LUAD dataset, IRLPs were identified to construct an IRLPs scoring system by Cox regression and were validated in the Gene Expression Omnibus (GEO) dataset. Next, immune and molecular characteristics were explored in different IRLP subgroups. The “pRRophetic” package was used to predict the sensitivity of drugs used to treat ir AEs.
Results

A total of 477 LUAD patients in TCGA with gene expression and mutation data with complete clinicopathological features were found in our study and used as a training set. The study also included 318 patients from three GEO datasets. The IRLPs score was constructed based on eight IRLPs, and patients with a high IRLP risk score had a better overall survival (OS). Immune score (Cor=-0.18893, P<0.001), stoma score (Cor=-0.24804, P<0.001), and microenvironment score (Cor=-0.22338, P<0.001) were significantly decreased in the patients with the highest IRLP risk score. The high-risk group was found enriched in molecular changes in DNA and chromosomes, and in this group the tumor mutation burden (TMB) was higher than in the low-risk group (P=0.0015). Immunosuppressor methotrexate sensitivity was higher in the high-risk group (P=0.0052), whereas parthenolide (P<0.001) and rapamycin (P=0.013) sensitivity were lower in the high-risk group.
Conclusions

Our study established an IRLPs scoring system as a biomarker to help in the prognosis, the identification of molecular and immune characteristics, and the patient-tailored selection of the most suitable drugs for ir AEs therapy.
Water and Nitrogen Coupling Effects on Grain Yield, Water and Nitrogen use Efficiency of Oilseed Flax in Semiarid Area of China
Authors: Cui Zhengjun , Gao Yuhong , Yan Bin , Wu Bing , Wang Yifan , Xu Peng , Wang Haidi , Zhao Bangqing , Cao Zhi , Xie Yaping , Niu Junyi , Ma Jun , Yang Kun
Published: October 2021

Irrigation and nitrogen management are essential for sustainable agricultural development in arid and semi-arid regions. Lower water availability and fertilizer utilization are two major factors of constrainting agricultural production in the semi-arid regions. Therefore, improving the utilization efficiency of water and fertilizer has become an important research goal. A two-year field experiment was laid out in a split-plot design with no irrigation (I0), 1200 m3 ha−1 (I1200) and 1800 m3 ha−1 (I1800) as the main factor and 0 (N0), 60 (N60) and 120 (N120) kg N ha−1 nitrogen rate as a sub-factor to investigate the effects of irrigation and nitrogen rates on precipitation storage efficiency (PSE), soil water storage, grain yield, and water and nitrogen use efficiency of oilseed flax in the Loess Plateau of China. The result showed that irrigation and nitrogen significantly increased PSE, soil water storage during the fallow period (ΔSWCf), dry matter accumulation and grain yeild of oilseed flax. However, the change of soil-water storage during the growing season (ΔSWCg) and the change of soil-water storage in the whole year (ΔSWCy) decreased. Soil water storage in irrigation supply treatment at after harvest in each growing season was higher than that in non-irrigation. PSE was highest under I1800N120 treatment. I1800 increased SWSs, SWSh and ETg at 2018 and improved above-ground biomass (anthesis and maturity stage), while decreased WUE and WUEI. Grain yield under 60 and 120 kg N ha−1 with 1800 m3 ha−1 increased by 69.12, 68.07 (2017) and 22.77, 15.23% (2018), respectively, when compared to the I0N0 treatment. Considering flax grain yield, water and nitrogen productivity, 60 or 120 kg/ha N and irrigation of 1800 m3/ha are recommended for water and nitrogen management of oilseed flax in Loess Plateau of China.
Immunoreactivity of Humanized Single-Chain Variable Fragment Against Its Functional Epitope On Domain 1 of CD147
Authors: Intasai Nutjeera , Rangnoi Kuntalee , Yamabhai Montarop , Pamonsupornwichit Thanathat , Soponpong Suthinee , Thongkum Weeraya , Yasamut Umpa , Chupradit Koollawat , Takheaw Nuchira , Nimmanpipug Piyarat , Tayapiwatana Chatchai
Published: October 2021

Domain 1 of CD147 participates in matrix metalloproteinase (MMP) production and is a candidate for targeted therapy to prevent cancer invasion and metastasis. A functional mouse anti-CD147 monoclonal antibody, M6-1B9, was found to recognize domain 1 of CD147, and its respective mouse single-chain variable fragment (ScFvM61B9) was subsequently generated. The EDLGS epitope candidate for M6-1B9 was identified using the phage display peptide technique in this study. For future clinical applications, humanized ScFv specific to domain 1 of CD147 (HuScFvM61B9) was partially adopted from the hypervariable sequences of parental mouse ScFvM61B9 and grafted onto suitable human immunoglobulin frameworks. Molecular modelling and simulation were performed in silico to generate the conformational structure of HuScFvM61B9. These results elucidated the amino acid residues that contributed to the interactions between CDRs and the epitope motif. The expressed HuScFvM61B9 specifically interacted with CD147 at the same epitope as the original mAb, M6-1B9, and retained immunoreactivity against CD147 in SupT1 cells. Binding affinity of HuScFvM61B9 by biolayer interferometry was higher than the predicted one. should be considered a potential therapeutic antibody. As domain 1 is responsible for cancer invasion and metastasis, HuScFvM61B9 would be a candidate for cancer targeted therapy in the future.
Development of nested PCR for identification of Entamoeba coli in stool samples
Authors: Rattaprasert Pongruj , Nitatsukprasert Chanyapat , Thima Kanthinich , Chavalitshewinkoon-Petmitr Porntip
Published: October 2021

Background

The accurate detection of Entamoeba species provides for a better understanding of the nature of these parasites in humans and helps to provide accurate epidemiological data. However, the microscopic method is not sensitive and specific to identify the precise identification of Entamoeba spp. in stool specimens especially if it was examined by inexperienced laboratory technicians. In this study, nested PCR was developed for detection of Entamoeba coli, and can be differentiated from the other human Entamoeba spp. especially Entamoeba histolytica, Entamoeba dispar, and Entamoeba moshkovskii.
Methods

Nested PCR assay was performed using Entamoeba genus-specific primers for the first round PCR reaction and newly designed E. coli-specific primers targeting small subunit ribosomal RNA (SSU rRNA) gene in the second round. Both sensitivity and specificity of nested PCR for detection of E. coli were determined. This assay was validated for detection of E. coli by using DNA obtained from 55 stool samples which previously examined by microscopy. Results obtained from developed nested PCR, genus-specific PCR, and microscopy were analyzed.
Results

Nested PCR was successfully developed to diagnose E. coli infection with a product size of 166 base pairs (bp). The nested PCR method could detect as little as 1 pg of E. coli DNA. The high specificity was confirmed by testing with DNA from the different intestinal pathogens, including bacteria and other protozoa. After testing with all stool samples, 50.9% of tested samples were positive for Entamoeba spp. by genus-specific PCR assay, 32.7% of E. coli positive samples detected by nested PCR, and 29.1% were positive by microscopic examination. Interestingly, four samples previously negative for E. coli by microscopy demonstrated E. coli by nested PCR. In addition, microscopy showed two false-positive compared with both nested PCR and genus-specific primers results.
Conclusions

The developed nested PCR assay based on genus Entamoeba-specific primers and newly designed E. coli-specific primers shows high sensitivity and specificity for the diagnosis of E. coli in stool samples. This nested PCR assay will be beneficial not only for diagnostic purposes but also for a better understanding of the epidemiology of E. coli in the human population worldwide.
Multiple Long-range Host Shifts of Major Wolbachia Supergroups Infecting Arthropods
Authors: Gomes Tiago M. F. F. , Wallau Gabriel L. , Loreto Elgion L. S.
Published: October 2021

Wolbachia is genus of intracellular bacterial endosymbionts found in 20–66% of all insect species and a range of other invertebrates. It is classified as a single species, Wolbachia pipiens, divided into supergroups A to U, with supergroups A and B infecting arthropods exclusively. Wolbachia is transmitted mainly via vertical transmission through female oocytes, but can also be transmitted across different taxa by host shift (HS)—the direct transmission of Wolbachia cells between organisms without involving vertically transmitted gametic cells. To assess the contribution of HS, we recovered 50 orthologous genes from over 1000 Wolbachia genomes, reconstructed their phylogeny and calculated gene similarity. Of 15 supergroup A Wolbachia lineages, 10 have similarities ranging from 95% to 100%, while their hosts’ similarities are around 60 to 80%. For supergroup B, four out of eight lineages, which infect diverse and distantly-related organisms such as Acari, Hemiptera and Diptera, showed similarities from 93 to 97%. These results show that Wolbachia genomes have a much higher similarity when compared to their hosts’ genes, which is a major indicator of HS. Our comparative genomic analysis suggests that, at least for supergroups A and B, HS is more frequent than expected, occurring even between distantly-related species.
Caregivers of people with dementia and mental health during COVID-19: findings from a cross-sectional study.
Authors: Messina Anna , Lattanzi Martina , Albanese Emiliano , Fiordelli Maddalena
Published: October 2021

Background
There is sparse evidence on the impact on vulnerable populations of the COVID-19 pandemic. The aim of our study was to explore burden and mental wellbeing (including depressive, anxiety, and stress symptoms) in caregivers of people with dementia during the first wave of the pandemic in Italy and southern Switzerland, two bordering regions severely hit by the COVID-19 pandemic.
Methods
We conducted an online cross-sectional survey with family carers of people with dementia between May and June 2020. We registered socio-demographic characteristics, and information about the relationship with the care recipient, dementia subtype, care inputs from others, and the need of care of the person with dementia. We measured caregiver burden with the Zarit Burden Interview (ZBI), psychological distress with the Depression, Anxiety and Stress Scale (DASS-21), and perceived isolation with the 3-item UCLA Loneliness Scale (UCLALS3).
Results
Caregivers (N=571) reported moderate to severe care-related burden (mean=54.30; SD=18.33), moderate anxiety symptoms (mean=10.04; SD=6.93), mild depressive symptoms (mean=11.79; SD=6.12) and mild stress (mean=12.95; SD=5.53), and 72.3% of participants reported to feel lonely. All scores were significantly more severe in Swiss compared to Italian caregivers (all p values<0.001).
Conclusions
We found that caregivers’ burden, anxiety symptoms, depression and perceived loneliness were marked during the first wave of the COVID-19 pandemic, in two severely hit bordering countries. Regional differences in the impact of the epidemic on caregivers could be due to contextual, societal, and cultural circumstances. As the pandemic endures, support to caregivers of people with dementia should be proportionate and tailored to needs and adapted to contextual factors.
Prediction of Anti-Icing Longevity of Asphalt Pavement With Salt-Storage Additive
Authors: Zhang Yan , Deng Yong , Shi Xianming
Published: October 2021

This study established a systematic simulation framework to predict the anti-icing longevity of a thin overlay of asphalt pavement with salt-storage additive (APSSA). The water and chloride transport in the overlay when subjected to varying precipitation, temperature, thermal cracking, and fatigue cracking over time were modeled using a Finite Element Method based software. The simulation included two parts: water transport followed by chloride transport. Water transport that obeys the law of conservation of mass was modeled using the phase transport in porous media (phtr) interface of COMSOL, while chloride transport based on Fick’s second law was modeled with the transport of diluted species (tds) interface. The simulation results show the anti-icing function of a 16-mm thick overlay was fully effective in 2 years and 5 years for the minimum pavement temperature above -3.4 °C and -2.4 °C, respectively. These two pavement temperatures are equivalent to 97.4-percentile and 96.3-percentile of historical hourly pavement temperature near Pullman, Washington.
Synthesis, Antioxidant activity and Structure-Activity Relationship of gallic hydrazones Analogues
Authors: Wu Zhengrong , Chen Peng , Liu Ying-Qian
Published: October 2021

A series of gallic acid hydrazones were designed and synthesized as new potential anti-oxidant agents. Most of these compounds are potent antioxidants. The strongest compounds are 11 and 15 (EC50: 6.42 μg·mL−1, 6.86 μg·mL−1, DPPH) and (EC50: 12.85μg·mL−1, 12.49μg·mL−1ABTS), more potent than the positive control Trolox. Furthermore, the promising compounds 11 and 15 exhibited very low cytotoxic activity against HEK293 cell (IC50 >56.4 µM). The SAR study revealed that the pattern of hydroxyl, methoxy and methyl substituents on the gallic hydrazones framework can increase the antioxidant properties of the prototype compounds. Moreover, the results also showed that the activity increased with the number of the groups and increased following hydroxyl > methoxy > methyl. Overall, the present study suggests that the designed compounds may serve as lead molecules for developing novel anti-oxidative agents in food industry.
Is Smaller Thyroid Gland Volume in COVID-19 Survivors Indicative of Chronic Thyroid Dysfunction?
Authors: Urhan Emre , Karaca Zuleyha , Kara Canan Sehit , Yuce Zeynep Ture , Unluhizarci Kursad
Published: October 2021

Purpose.Data about the effects of COVID-19 on the endocrine system are increasing, but COVID-19-associated thyroid dysfunctions are not known clearly. We investigated the effects of SARS-CoV-2 on the thyroid gland in COVID-19 survivors.Methods.64 adult COVID-19 survivors and 70 healthy adults were enrolled. The COVID-19 survivors were evaluated at median 5.7 months (IQR: 4-6.5) (range: 2-7 months) after acute infection. The blood tests were obtained for thyroid antibodies and function tests. Thyroid ultrasonography (USG) was done by the same physician. The ellipsoid formula was used for calculation of thyroid gland volume.Results. There was no significant difference between the groups for thyroid hormone levels. The mean thyroid gland volume was significantly lower in COVID-19 survivors (10.3 ± 3.4 ml) than in the controls (14 ± 5.3 ml) (p = 0.001). Mild TSH elevation was detected in 4 (6.2%) patients and all of the other patients (93.7%) were euthyroid. Thirty-one patients, who had pre-COVID thyroid hormone levels, were compared with their post-COVID thyroid hormone levels, and no significant difference was found. Twelve patients, who had acute-COVID infection were compared with their post-COVID thyroid function tests, and free triiodothyronine (FT3) values during acute-COVID infection were significantly lower than in their post-COVID period (p = 0.02).Conclusions.The effects of COVID-19 on the thyroid gland may have a variable course. Our results revealed that a significant decrease in thyroid gland volume in the early post-COVID compared to the healthy subjects and COVID-19 survivors may be candidates for thyroid gland disorders.
Computational Study of 16S rRNA of Microbe Cluster Implicated in Diarrhoeal: Phylogeny, Docking, and Dynamics
Authors: Ugboko Harriet U. , Fatoki Toluwase Hezekiah , Nwinyi Obinna C. , Ibraheem Omodele , Omonhinmin Conrad A. , Fatoki Jesupemi Mercy , Adetuyi Oluwafijimi Yomi
Published: October 2021

In this study, 16S rRNA of diarrhoea microbial cluster was investigated computationally. The phylogeny, two- and three-dimensional structures, molecular docking and dynamics simulations were carried out. The result showed that Escherichia coli, Campylobacter jejuni, Campylobacter upsaliensis, Streptococcus lutetiensis 033, Streptococcus infantarius, Enterococcus ratti, Helicobacter sp. 'feline isolate, Helicobacter canadensis, Anaerobiospirillum sp. B0101, Anaerobiospirillum sp. 3J102 as well as uncultured bacterium (Prevotella) and unidentified bacterium (Lactobacillus) were involved in diarrhoea infection. Optimal secondary structure alignment from ClustalO has a minimum free energy (MFE) of -764.31 kcal/mol while that Aligner has MFE of -592.43 kcal/mol. The free energies from molecular docking reveal possible efficacy in the order of doxycycline > metacycline > streptomycin > rolitetracycline > tetracycline > tigecycline. Out of 17 antibiotics used in this study, chlortetracycline and minocycline have high affinity for methyltransferase KsgA (PDB ID: 3TPZ), kanamycin has almost equal affinity for both enzymes, while the remaining 14 antibiotic compounds have high affinity for pseudouridine synthase RsuA (PDB ID: 1KSV). The modelled three-dimensional structure of 16S rRNA bind to 1KSV and 3TPZ with free energy of -367.52 kcal/mol and-371.55 kcal/mol respectively. Moreover, the active site nucleotide residues were found to have direct interaction with amino acid residues in the active site of the enzymes. This study provides insight on the mechanism of action of antibiotics that targeted 16S rRNA by inhibition of key enzymes that involve in protein synthesis.
Design Optimization of Conformal Cooling Channels For Injection Molds: 2D Transient Heat Transfer Analysis
Authors: Silva Hugo Miguel , Noversa Tiago , Fernandes Leandro , Rodrigues Hugo , Pontes António
Published: October 2021

The fabrication of Conformal Cooling Channels (CCC's) has become easier and more affordable with recent developments in additive manufacturing. The use of CCC's allows for better cooling performance than the conventional (straight drilled) channels, in injection molding. The main reason for this is that the CCC's are able to follow the trajectories of the molded geometry, while the conventional channels made by conventional machining techniques are not able to do so. Some of the parameters that can be significantly improved by using CCC are cooling time, total injection time, uniform temperature distribution, thermal stress and distortion thickness. This article focuses the design optimization of an injection mold, with the aim of optimizing the placement of cooling channels for the minimization of the ejection time and maximization of the uniformity of temperature distribution. In this work, an optimization methodology was developed, with the aim of optimizing the placement of cooling channels in the design stage of the mold, for obtaining pre-optimized molds from a geometric standpoint. It can be concluded that the developed methodology is efficient and useful for the aims of the work.
Karyotype and genome size determination of Jarilla chocola, an additional sister clade of Carica papaya
Authors: Zerpa-Catanho Dessireé Patricia , Jatt Tahira , Ming Ray
Published: October 2021

Jarilla chocola is an herbaceous plant species that belongs to the Jarilla genus and the Caricaceae family. No information on chromosome number or genome size has been reported for J. chocola that confirms the occurrence of dysploidy events and explore the existence of heteromorphic sex chromosomes. Therefore, the total number of chromosomes of this species was determined by karyotyping and counting the number of chromosomes observed, and the genome size of female and male plants was estimated separately by flow cytometry. Results showed that J. chocola has eight pairs of chromosomes (2n = 2x = 16), and its chromosomes are classified as metacentric for five pairs, submetacentric for two pairs and telocentric for one pair. The nuclear DNA content (1C-value) in picograms and diploid genome size was estimated separately from female and male plants using two species as the standards, Phaseolus vulgaris (1C = 0.60 pg) and Carica papaya (1C = 0.325 pg), to look for the possible existence of heteromorphic sex chromosomes. C. papaya proved to be a better standard for the determination of J. chocola DNA content and diploid genome size. No significant difference on the DNA content was observed between female (1C = 1.02 ± 0.003 pg) and male (1C = 1.02 ± 0.008 pg) plants. The estimated genome size of J. chocola per haploid genome in base pairs was calculated from the obtained C-values. Results showed an estimated genome size per haploid genome of 1018.44 ± 3.07 Mb and 1022.08 ± 7.76 Mb for female and male plants, respectively. Due to the observed chromosome number and genome size, only the occurrence of one of two previously reported dysploidy events in Jarilla could be confirmed for J. chocola and no evidence of heteromorphic sex chromosomes was found. These results provide fundamental information of the J. chocola genome and will expedite investigation of sex chromosomes and genome evolution in this species, the Jarilla genus and the Caricaceae family
Pre-emergence herbicidal activity and persistence of 2,4-di-tertbutylphenol in relation to soil types
Authors: Zain Norhafizah Md , Mat Mazira Che , Seng Chuah Tse
Published: October 2021

Although 2,4-di-tert-butylphenol (2,4-DTBP) has demonstrated strong phytotoxic effect on various weedy plants in previous findings, research on its pre-emergence herbicidal activity in the soil is still scanty. The aim of this study was to investigate the effects of two soil types on pre-emergence herbicidal activity and persistence of 2,4-DTBP. The bioassay was carried out in a growth chamber where goosegrass [Eleusine indica (L.) Gaertn.] seeds were sown in different rates of 2,4-DTBP in two soil series under sterilized and non-sterilized soil conditions. Bioassays of each treatment were conducted in four replicates and arranged in completely randomized design. 2,4-DTBP exhibited potent pre-emergence activity as a root inhibitor where it completely inhibited (100% inhibition) of the root growth of E. indica in sandy loam soil at an application rate of 6.14 kg ai/ha. 2,4-DTBP was rapidly detoxified in silt loam soil as a result of high microbial activity where it completely lost its phytotoxicity by giving 100% emergence within 10 weeks even it was applied at an application as high as 20.4 kg ai/ha. However, 2,4-DTBP remained highly phytotoxic in sandy loam soil where it reduced the root and shoot growth by 47 and 36%, respectively, throughout 10 weeks duration of the investigation. The presence of microbes in non-sterilized soil further suggest that soil microbes may modify the chemical structure of the 2,4-DTBP, which in turn decreased its toxicity. The high level of pre-emergence herbicidal activity in conjunction with its biodegradation in silt loam soil imply that 2,4-DTBP may have potential for development as a natural-soil applied herbicide
Rational pharmacotherapy in modern gastroenterology
Authors: Minushkin O. N.
Published: October 2021

Abstract Introduction. Modern gastroenterology is characterized by the combined (comorbid) nature of the diseases. In treatment, this promotes polypharmacy and increases complications (drug lesions, allergic reactions, exacerbation of diseases of other organs and systems), and, importantly, increases the cost of pharmacotherapy.

Aim. To compare two pharmacotherapy options for patients with gallstone disease at the stage of biliary sludge and patients with biliary sludge combined with irritable bowel syndrome.

Materials and methods. In the work, based on the experience of treating 170 patients, two options for pharmacotherapy are considered, which may well turn out to be rational in all respects. Option 1 - monotherapy aimed at one of the components that form a complex pathogenetic symptom complex. The basis for offering this treatment option is the biological concept of the “regulatory cascade”. Option 2  – “stepwise” (stepwise) therapy with the  choice of  the “base” drug for  the  first step. Evaluation of the effectiveness and rational correction for the second step of treatment and subsequent ones – if necessary.

 Results. The biliary sludge was eliminated or reduced in patients who received the UDCA monotherapy against the background of recovery of gastrointestinal motility. The overall treatment effect (for each nosology) in patients with biliary sludge and irritable bowel syndrome using the complex therapy (UDCA and mebeverin) was 84 and 87.8% respectively.

Conclusions. Both options are rational today: 1st requires further study; 2nd – active use. Both options exclude polypharmacy and other adverse effects.