bluuebunny/crossref_metadata_2025 huggingface dataset:
Predictors of Plasma Fluoride Concentrations in Children and Adolescents
Authors: Carwile Jenny L. , Ahrens Katherine A. , Seshasayee Shravanthi M. , Lanphear Bruce , Fleisch Abby F.
Published: December 2020

Despite increasing concerns about neurotoxicity of fluoride in children, sources of fluoride exposure apart from municipal water fluoridation are poorly understood. We aimed to describe the associations of demographics, drinking water characteristics, diet, and oral health behaviors with plasma fluoride concentrations in U.S. children. We used data from 3928 6–19-year-olds from the 2013–2016 National Health and Nutrition Examination Survey. We used a 24-h dietary recall to estimate recent consumption of fluoridated tap water and select foods. We estimated the associations of fluoridated tap water, time of last dental visit, use of toothpaste, and frequency of daily tooth brushing with plasma fluoride concentrations. The participants who consumed fluoridated (≥0.7 mg/L) tap water (n = 560, 16%) versus those who did not had 36% (95% CI: 22, 51) higher plasma fluoride. Children who drank black or green tea (n = 503, 13%) had 42% higher plasma fluoride concentrations (95% CI: 27, 58) than non-tea drinkers. The intake of other foods and oral health behaviors were not associated with plasma fluoride concentrations. The consumption of fluoridated tap water and tea substantially increases plasma fluoride concentrations in children. Quantifying the contribution of diet and other sources of fluoride is critical to establishing safe target levels for municipal water fluoridation.
Thioredoxin-Interacting Protein (TXNIP) with Focus on Brain and Neurodegenerative Diseases
Authors: Tsubaki Haruka , Tooyama Ikuo , Walker Douglas Gordon
Published: December 2020

The development of new therapeutic approaches to diseases relies on the identification of key molecular targets involved in amplifying disease processes. One such molecule is thioredoxin-interacting protein (TXNIP), also designated thioredoxin-binding protein-2 (TBP-2), a member of the α-arrestin family of proteins and a central regulator of glucose and lipid metabolism, involved in diabetes-associated vascular endothelial dysfunction and inflammation. TXNIP sequesters reduced thioredoxin (TRX), inhibiting its function, resulting in increased oxidative stress. Many different cellular stress factors regulate TXNIP expression, including high glucose, endoplasmic reticulum stress, free radicals, hypoxia, nitric oxide, insulin, and adenosine-containing molecules. TXNIP is also directly involved in inflammatory activation through its interaction with the nucleotide-binding domain, leucine-rich-containing family, and pyrin domain-containing-3 (NLRP3) inflammasome complex. Neurodegenerative diseases such as Alzheimer’s disease have significant pathologies associated with increased oxidative stress, inflammation, and vascular dysfunctions. In addition, as dysfunctions in glucose and cellular metabolism have been associated with such brain diseases, a role for TXNIP in neurodegeneration has actively been investigated. In this review, we will focus on the current state of the understanding of possible normal and pathological functions of TXNIP in the central nervous system from studies of in vitro neural cells and the brains of humans and experimental animals with reference to other studies. As TXNIP can be expressed by neurons, microglia, astrocytes, and endothelial cells, a complex pattern of regulation and function in the brain is suggested. We will examine data suggesting TXNIP as a therapeutic target for neurodegenerative diseases where further research is needed.
Identification of the 3-lncRNA Signature as a Prognostic Biomarker for Colorectal Cancer
Authors: Liu Shuzhen , Cao Qing , An Guoyan , Yan Bianbian , Lei Lei
Published: December 2020

Colorectal cancer (CRC) is one of the most common malignant carcinomas in the world, and metastasis is the main cause of CRC-related death. However, the molecular network involved in CRC metastasis remains poorly understood. Long noncoding RNA (lncRNA) plays a vital role in tumorigenesis and may act as a competing endogenous RNA (ceRNA) to affect the expression of mRNA by suppressing miRNA function. In this study, we identified 628 mRNAs, 144 lncRNAs, and 25 miRNAs that are differentially expressed (DE) in metastatic CRC patients compared with nonmetastatic CRC patients from the Cancer Genome Atlas (TCGA) database. Functional enrichment analyses confirmed that the identified DE mRNAs are extensively involved in CRC tumorigenesis and migration. By bioinformatics analysis, we constructed a metastasis-associated ceRNA network for CRC that includes 28 mRNAs, 12 lncRNAs, and 15 miRNAs. We then performed multivariate Cox regression analysis on the ceRNA-related DE lncRNAs and identified a 3-lncRNA signature (LINC00114, LINC00261, and HOTAIR) with the greatest prognostic value for CRC. Clinical feature analysis and functional enrichment analysis further proved that these three lncRNAs are involved in CRC tumorigenesis. Finally, we used Transwell, Cell Counting Kit (CCK)-8, and colony formation assays to clarify that the inhibition of LINC00114 promotes the migratory, invasive, and proliferative abilities of CRC cells. The results of the luciferase assay suggest that LINC00114 is the direct target of miR-135a, which also verified the ceRNA network. In summary, this study provides a metastasis-associated ceRNA network for CRC and suggests that the 3-lncRNA signature may be a useful candidate for the diagnosis and prognosis of CRC.
Differential RNA Editing and Intron Splicing in Soybean Mitochondria during Nodulation
Authors: Sun Yuzhe , Xie Min , Xu Zhou , Chan Koon Chuen , Zhong Jia Yi , Fan Kejing , Wong-Bajracharya Johanna , Lam Hon-Ming , Lim Boon Leong
Published: December 2020

Nitrogen fixation in soybean consumes a tremendous amount of energy, leading to substantial differences in energy metabolism and mitochondrial activities between nodules and uninoculated roots. While C-to-U RNA editing and intron splicing of mitochondrial transcripts are common in plant species, their roles in relation to nodule functions are still elusive. In this study, we performed RNA-seq to compare transcript profiles and RNA editing of mitochondrial genes in soybean nodules and roots. A total of 631 RNA editing sites were identified on mitochondrial transcripts, with 12% or 74 sites differentially edited among the transcripts isolated from nodules, stripped roots, and uninoculated roots. Eight out of these 74 differentially edited sites are located on the matR transcript, of which the degrees of RNA editing were the highest in the nodule sample. The degree of mitochondrial intron splicing was also examined. The splicing efficiencies of several introns in nodules and stripped roots were higher than in uninoculated roots. These include nad1 introns 2/3/4, nad4 intron 3, nad5 introns 2/3, cox2 intron 1, and ccmFc intron 1. A greater splicing efficiency of nad4 intron 1, a higher NAD4 protein abundance, and a reduction in supercomplex I + III2 were also observed in nodules, although the causal relationship between these observations requires further investigation.
Hepatocyte-Derived Igκ Exerts a Protective Effect against ConA-Induced Acute Liver Injury
Authors: Yin Sha , Shi Qianwen , Shao Wenwei , Zhang Chi , Zhang Yixiao , Qiu Xiaoyan , Huang Jing
Published: December 2020

Immunoglobulin (Igκ) has been reported to be expressed in sorted liver epithelial cells of μMT mice, and the sequence characteristics of hepatocyte-derived Igκ were different from those of classical B-cell-derived Igκ. However, the physiological function of hepatocyte-derived Igκ is still unclear. The expression of Igκ was firstly identified in primary hepatocytes and normal liver cell line (NCTC1469), and hepatocyte-derived Igκ expression was elevated and displayed unique localization in hepatocytes of concanavalin A (ConA)-induced hepatitis model. Moreover, Igκ knockout mice were more sensitive to ConA-induced hepatitis and had higher serum aspartate aminotransferase (AST) levels, more severe histological injury and a greater number of terminal deoxynucleotide transferase-mediated deoxyuridine triphosphate nick end-labeling (TUNEL)-positive cells as compared with littermate controls. Furthermore, knockdown of Igκ in primary hepatocytes and NCTC1469 cells led to accelerated activation of the mitochondrial death pathway and caspase-3 cleavage in vitro, which might be related to inhibition of NF-κB signaling pathway and activation of JNK via the cytoskeleton dynamics. Taken together, these results indicate that hepatocyte-derived Igκ mediates cellular resistance to ConA-induced liver injury by inhibiting activation of caspase-3 and the mitochondrial death pathway, suggesting that Igκ plays an important role in hepatocyte survival and exerts a protective effect against ConA-induced liver injury in mice.
Employer Branding Applied to SMEs: A Pioneering Model Proposal for Attracting and Retaining Talent
Authors: Monteiro Beatriz , Santos Vasco , Reis Isabel , Sampaio Marta Correia , Sousa Bruno , Martinho Filipa , José Sousa Maria , Au-Yong-Oliveira Manuel
Published: December 2020

Most business enterprises are small and medium-sized enterprises (SMEs), and many of them are without a human resource and recruitment department. Thus, one of the challenges that organizations currently face is to find a strategy to retain and attract talent. To overcome this difficulty, enterprises must invest in employer branding policies and be aware of the factors that differentiate them from others when attracting employees. This study aims to develop an employer branding model applicable to SMEs, to increase and enhance the attraction and retention of talents. An exploratory approach based on a quantitative perspective was adopted to develop an employer branding model applied to SMEs, with two major reference employer branding models and frameworks used as the main support. The model of employer branding was applied to SMEs regarding four dimensions, whereby essential questions are asked, namely (1) organizational culture (e.g., do employees have a job description aligned with the corporate culture?), (2) company strategy (e.g., what is the strategy if business volume decreases?), (3) company reputation (e.g., how do you perceive and treat negative feedback?), and (4) reward systems (e.g., do you feel that your employees are motivated intrinsically or extrinsically or both?), ordered by layers based on a logical sequence. The new proposed model is expected to serve as a useful strategic tool and as a basis for attracting, retaining and managing talent, specifically in the SMEs context. This new model provides a set of strategic and competitiveness benefits for SMEs, while contributing to making enterprises more profitable. The model also contributes to SMEs having a better image and reputation, enabling them to stand out from others in the war for talent.
A New Species of Spongilla (Porifera, Demospongiae) from a Karst Lake in Ha Long Bay (Vietnam)
Authors: Calcinai Barbara , Cerrano Carlo , Núñez-Pons Laura , Pansini Maurizio , Thung Do Cong , Bertolino Marco
Published: December 2020

Cahong in Ha Long Bay (Vietnam) is a small lake with a reduced, invisible connection with the open sea. The water column conditions locally experience notable fluctuations across the year, mostly driven by biannual monsoon seasons. Salinity, temperature, and pH often reach extreme values, unsustainable for the majority of the marine fauna. Therefore, the biodiversity of the benthic macrofauna in this peculiar habitat is remarkably low. In particular, a single sponge species new to science was found solely populating this characteristic brackish lake during our last survey in August 2018. Spongilla manconiae sp. nov. is a new Porifera species described here. It belongs to an exclusively freshwater taxon and seems to have acquired adaptive traits to tolerate extreme peaks of temperature and salinity. The mitochondrial Cytochrome C Oxidase subunit 1 (COI) and the nuclear Internal Transcribed Spacers 1 and 2 (ITSs) gene markers were used for barcoding tagging and phylogenetic analyses. The new species revealed large genetic distances and separate clustering in the tree topology, with respect to other reference spongillid sequences from various geographic areas. The study provides evidence for an urgency to protect these unique marine lake systems because they represent rare, fluctuant, fragile habitats that may speed up speciation processes.
Toward Campus Mail Delivery Using BDI
Authors: Onyedinma Chidiebere , Gavigan Patrick , Esfandiari Babak
Published: December 2020

Autonomous systems developed with the Belief-Desire-Intention (BDI) architecture tend to be mostly implemented in simulated environments. In this project we sought to build a BDI agent for use in the real world for campus mail delivery in the tunnel system at Carleton University. Ideally, the robot should receive a delivery order via a mobile application, pick up the mail at a station, navigate the tunnels to the destination station, and notify the recipient. In this paper, we discuss how we linked the Robot Operating System (ROS) with a BDI reasoning system to achieve a subset of the required use casesand demonstrated the system performance in an analogue environment. ROS handles the connections to the low-level sensors and actuators, while the BDI reasoning system handles the high-level reasoning and decision making. Sensory data is sent to the reasoning system as perceptions using ROS. These perceptions are then deliberated upon, and an action string is sent back to ROS for interpretation and driving of the necessary actuator for the action to be performed. In this paper we present our current implementation, which closes the loop on the hardware-software integration and implements a subset of the use cases required for the full system. We demonstrated the performance of the system in an analogue environment.
Physical Crust Formation on Sandy Soils and Their Potential to Reduce Dust Emissions from Croplands
Authors: Vos Heleen , Fister Wolfgang , Eckardt Frank , Palmer Anthony , Kuhn Nikolaus
Published: December 2020

The sandy croplands in the Free State have been identified as one of the main dust sources in South Africa. The aim of this study was to investigate the occurrence and strength of physical soil crusts on cropland soils in the Free State, to identify the rainfall required to form a stable crust, and to test their impact on dust emissions. Crust strength was measured using a fall cone penetrometer and a torvane, while laboratory rainfall simulations were used to form experimental crusts. Dust emissions were measured with a Portable In-Situ Wind Erosion Laboratory (PI-SWERL). The laboratory rainfall simulations showed that stable crusts could be formed by 15 mm of rainfall. The PI-SWERL experiments illustrated that the PM10 emission flux of such crusts is between 0.14% and 0.26% of that of a non-crusted Luvisol and Arenosol, respectively. The presence of abraders on the crust can increase the emissions up to 4% and 8% of the non-crusted dust flux. Overall, our study shows that crusts in the field are potentially strong enough to protect the soil surfaces against wind erosion during a phase of the cropping cycle when the soil surface is not protected by plants.
A Bibliometric Analysis of Food–Energy–Water Nexus: Progress and Prospects
Authors: Zhu Jing , Kang Shenghong , Zhao Wenwu , Li Qiujie , Xie Xinyuan , Hu Xiangping
Published: December 2020

Food, energy and water are important basic resources that affect the sustainable development of a region. The influence of food–energy–water (FEW) nexus on sustainable development has quickly become a frontier topic since the Sustainable Development Goals (SDGs) were put forward. However, the overall context and core issues of the FEW nexus contributions to SDGs are still unclear. Using co-citation analysis, this paper aims to map the knowledge domains of FEW nexus research, disentangles its evolutionary context, and analyzes the core issues in its research, especially the progress of using quantitative simulation models to study the FEW nexus. We found that (1) studies within the FEW nexus focused on these following topics: correlation mechanisms, influencing factors, resource footprints, and sustainability management policies; (2) frontier of FEW studies have evolved from silo-oriented perspective on single resource system to nexus-oriented perspective on multiple systems; (3) quantitative research on the FEW nexus was primarily based on spatiotemporal evolution analysis, input–output analysis and scenario analysis; (4) the resource relationship among different sectors was synergies and tradeoffs within a region. In general, current research still focuses on empirical data, mostly qualitative and semiquantitative analyses, and there is a lack of research that can systematically reflect the temporal and spatial contribution of the FEW nexus to multiple SDGs. We believe that future research should focus more on how FEW nexus can provide mechanistic tools for achieving sustainable development.
Substituent Effect on Porphyrin Film-Gas Interaction by Optical Waveguide: Spectrum Analysis and Molecular Dynamic Simulation
Authors: Kari Nuerguli , Zannotti Marco , Mamtmin Gulgina , Giovannetti Rita , Minofar Babak , Řeha David , Maimaiti Patigu , Kutilike Buayishamu , Yimit Abliz
Published: December 2020

Substituent effect on optical gas sensing performance in porphyrin-based optical waveguide detection system was studied by molecular dynamics simulation (MDS), absorption/emission spectrum analysis, and optical waveguide (OWG) detection. The affinities of porphyrin with seven types of substituents (–H, –OH, –tBu, –COOH, –NH2, –OCH3, –SO3−) on para position of meso-phenyl porphyrin toward gas molecules in adsorption process were studied in different size of boxes with the same pressure and concentration. Analyte gases (CO2, H2S, HCl, NO2) were exposed to porphyrin film in absorption spectrophotometer, and in OWG with evanescent field excited by a guiding laser light with 670 nm wavelength. The extent of interaction between host molecule and the guest analytes was analyzed by the number of gas molecules in vicinity of 0.3 nm around substituents of porphyrin molecules. Optical waveguide results reveal that sulfonate porphyrin is mostly responsive to hydrochloride, hydrosulfide gas and nitrogen dioxide gases with strong response intensity. Molecular dynamics and spectral analysis provide objective information about the molecular state and sensing properties. Molecular rearrangements induced by gas exposure was studied by spectral analysis and surface morphology before and after gas exposure taking hydrosulfide gas as an example. Film-gas interaction mechanism was discussed in terms of each gas and substituent group characters.
Recent Advances in Marine-Based Nutraceuticals and Their Health Benefits
Authors: Šimat Vida , Elabed Nariman , Kulawik Piotr , Ceylan Zafer , Jamroz Ewelina , Yazgan Hatice , Čagalj Martina , Regenstein Joe M. , Özogul Fatih
Published: December 2020

The oceans have been the Earth’s most valuable source of food. They have now also become a valuable and versatile source of bioactive compounds. The significance of marine organisms as a natural source of new substances that may contribute to the food sector and the overall health of humans are expanding. This review is an update on the recent studies of functional seafood compounds (chitin and chitosan, pigments from algae, fish lipids and omega-3 fatty acids, essential amino acids and bioactive proteins/peptides, polysaccharides, phenolic compounds, and minerals) focusing on their potential use as nutraceuticals and health benefits.
Particulate Matter-Induced Inflammation/Oxidative Stress in Macrophages: Fucosterol from Padina boryana as a Potent Protector, Activated via NF-κB/MAPK Pathways and Nrf2/HO-1 Involvement
Authors: Jayawardena Thilina U. , Sanjeewa K. K. Asanka , Lee Hyo-Geun , Nagahawatta D. P. , Yang Hye-Won , Kang Min-Cheol , Jeon You-Jin
Published: December 2020

Fucosterol is a phytosterol that is abundant in marine brown algae and is a renowned secondary metabolite. However, its ability to protect macrophages against particulate matter (PM) has not been clarified with regard to inflammation; thus, this study aimed to illustrate the above. Padina boryana, a brown algae that is widespread in Indo–Pacific waters, was applied in the isolation of fucosterol. Isolation was conducted using silica open columns, while identification was assisted with gas chromatography-mass spectroscopy (GC-MS) and NMR. Elevated levels of PM led the research objectives toward the implementation of it as a stimulant. Both inflammation and oxidative stress were caused due the fact of its effect. RAW 264.7 macrophages were used as a model system to evaluate the process. It was apparent that the increased NO production levels, due to the PM, were mediated through the inflammatory mediators, such as inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2) and pro-inflammatory cytokines (i.e., interleukin-6 (IL-6), interleukin-1 (IL-1β) and tumor necrosis factor-α (TNF-α), including prostaglandin E2 (PGE2)). Further, investigations provided solid evidence regarding the involvement of NF-κB and mitogen-activated protein kinases (MAPKs) in the process. Oxidative stress/inflammation which are inseparable components of the cellular homeostasis were intersected through the Nrf2/HO-1 pathway. Conclusively, fucosterol is a potent protector against PM-induced inflammation in macrophages and hence be utilized as natural product secondary metabolite in a sustainable manner.
Discussion on Water Condensation in Membrane Pores during CO2 Absorption at High Temperature
Authors: Chan Zhe Phak , Li Lin , Kang Guodong , Ab Manan Norfaizah , Cao Yiming , Wang Tonghua
Published: December 2020

Water condensation is a possible cause of membrane wetting in the operation of membrane contactors, especially under high-temperature conditions. In this study, water condensation in pores of polytetrafluoroethylene (PTFE) hollow fiber membranes was investigated during high-pressure CO2 absorption around 70 °C. It was found that the liquid accumulation rate in the treated gas knock-out drum was constant during continuous operation for 24 h when all experimental conditions were fixed, indicating a stable degree of membrane wetting. However, as the operating parameters were changed, the equilibrium vapor pressure of water within membrane pores could change, which may result in a condensation-conducive environment. Water condensation in membrane pores was detected and proven indirectly through the increase in liquid accumulation rate in the treated gas knock-out drum. The Hagen–Poiseuille equation was used to correlate the liquid accumulation rate with the degree of membrane wetting. The degree of membrane wetting increased significantly from 1.8 × 10−15 m3 to 3.9 × 10−15 m3 when the feed gas flow rate was reduced from 1.45 kg/h to 0.40 kg/h in this study due to water condensation in membrane pores. The results of this study provide insights into potential operational limitations of membrane contactor for CO2 absorption under high-temperature conditions.
Inhibitory Activity of Essential Oils against Vibrio campbellii and Vibrio parahaemolyticus
Authors: Zheng Xiaoting , Feyaerts Adam F. , Van Dijck Patrick , Bossier Peter
Published: December 2020

Vibriosis, caused by Vibrio strains, is an important bacterial disease and capable of causing significant high mortality in aquatic animals. Essential oils (EOs) have been considered as an alternative approach for the treatment of aquatic bacterial diseases. In this study, we evaluated the antibacterial activity of essential oils (n = 22) or essential oil components (EOCs, n = 12) against Vibrio strains belonging to the harveyi clade. It was verified by three different approaches, e.g., (i) a bacterial growth assay, comparing Vibrio growth with or without EO(C)s at various concentrations; (ii) a vapor-phase-mediated susceptibility assay, comparing the effect of EO(C)s on bacterial growth through the vapor phase; and (iii) a quorum sensing-inhibitory assay, based on specific inhibition of quorum sensing-regulated bioluminescence. The results showed that, in the bacterial growth assay, EOs of Melaleuca alternifolia and Litsea citrata at 0.0001%, Eucalyptus citriodora at 0.01% can inhibit the growth of Vibrio campbellii BB120. These EOs can also prevent the growth of V. parahaemolyticus strains but need to be present at a higher concentration (0.1%). Moreover, in the vapor-phase-mediated susceptibility assay, EOs of M. alternifolia, L. citrata and E. citriodora can inhibit the growth of V. campbellii BB120 through their vapor phase. However, V. parahaemolyticus strains (CAIM170, LMG2850 and MO904) cannot be inhibited by these EOs. Additionally, in the quorum sensing-inhibitory assay, EOs of Mentha pulegium, Cuminum cyminum, Zingiber officinalis, and E. citriodora, all at 0.001%, have quorum sensing-inhibitory activity in V. campbellii BB120. Taken together, our study provides substantial evidence that usage of the major components, individually or in combination, of the tested commercial EOs (extracted from M. alternifolia, L. citrata, and E. citriodora) could be a promising approach to control V. campbellii BB120.
Establishment of a New PNA-FISH Method for Aspergillus fumigatus Identification: First Insights for Future Use in Pulmonary Samples
Authors: Cerqueira Laura , Moura Sara , Almeida Carina , Vieira Maria João , Azevedo Nuno Filipe
Published: December 2020

Aspergillus fumigatus is the main causative agent of Invasive Aspergillosis. This mold produces conidia that when inhaled by immunocompromized hosts can be deposited in the lungs and germinate, triggering disease. In this paper, the development of a method using peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) is described. The PNA-FISH probe was tested in several strains and a specificity and sensitivity of 100% was obtained. Detection of A. fumigatussensu stricto was then achieved in artificial sputum medium (ASM) pre-inoculated with 1 × 102 conidia·mL−1–1 × 103 conidia·mL−1, after a germination step of 24 h. The PNA-FISH method was evaluated in 24 clinical samples (10 sputum, 8 bronchoalveolar lavage (BAL), and 6 bronchial lavage (BL)) that were inoculated with 1 × 104 conidia·mL−1 in sputum; 1 × 103 conidia·mL−1 in BL and BAL, for 24 h. Despite a specificity of 100%, the sensitivity was 79%. This relatively low sensitivity can be explained by the fact that hyphae can yield “fungal ball“ clusters, hindering pipetting procedures and subsequent detection, leading to false negative results. Nonetheless, this study showed the potential of the PNA-FISH method for A. fumigatussensu stricto detection since it takes only 1 h 30 m to perform the procedure with a pre-enrichment step of 6 h (pure cultures) and 24 h (clinical samples), and might provide a suitable alternative to the existing methods for studies in pure cultures and in clinical settings.
The Limits and Avoidance of Biases in Metagenomic Analyses of Human Fecal Microbiota
Authors: Bergsten Emma , Mestivier Denis , Sobhani Iradj
Published: December 2020

An increasing body of evidence highlights the role of fecal microbiota in various human diseases. However, more than two-thirds of fecal bacteria cannot be cultivated by routine laboratory techniques. Thus, physicians and scientists use DNA sequencing and statistical tools to identify associations between bacterial subgroup abundances and disease. However, discrepancies between studies weaken these results. In the present study, we focus on biases that might account for these discrepancies. First, three different DNA extraction methods (G’NOME, QIAGEN, and PROMEGA) were compared with regard to their efficiency, i.e., the quality and quantity of DNA recovered from feces of 10 healthy volunteers. Then, the impact of the DNA extraction method on the bacteria identification and quantification was evaluated using our published cohort of sample subjected to both 16S rRNA sequencing and whole metagenome sequencing (WMS). WMS taxonomical assignation employed the universal marker genes profiler mOTU-v2, which is considered the gold standard. The three standard pipelines for 16S RNA analysis (MALT and MEGAN6, QIIME1, and DADA2) were applied for comparison. Taken together, our results indicate that the G’NOME-based method was optimal in terms of quantity and quality of DNA extracts. 16S rRNA sequence-based identification of abundant bacteria genera showed acceptable congruence with WMS sequencing, with the DADA2 pipeline yielding the highest congruent levels. However, for low abundance genera (<0.5% of the total abundance) two pipelines and/or validation by quantitative polymerase chain reaction (qPCR) or WMS are required. Hence, 16S rRNA sequencing for bacteria identification and quantification in clinical and translational studies should be limited to diagnostic purposes in well-characterized and abundant genera. Additional techniques are warranted for low abundant genera, such as WMS, qPCR, or the use of two bio-informatics pipelines.
Innovation and Application of the Type III Secretion System Inhibitors in Plant Pathogenic Bacteria
Authors: Yuan Xiaochen , Yu Manda , Yang Ching-Hong
Published: December 2020

Many Gram-negative pathogenic bacteria rely on a functional type III secretion system (T3SS), which injects multiple effector proteins into eukaryotic host cells, for their pathogenicity. Genetic studies conducted in different host-microbe pathosystems often revealed a sophisticated regulatory mechanism of their T3SSs, suggesting that the expression of T3SS is tightly controlled and constantly monitored by bacteria in response to the ever-changing host environment. Therefore, it is critical to understand the regulation of T3SS in pathogenic bacteria for successful disease management. This review focuses on a model plant pathogen, Dickeyadadantii, and summarizes the current knowledge of its T3SS regulation. We highlight the roles of several T3SS regulators that were recently discovered, including the transcriptional regulators: FlhDC, RpoS, and SlyA; the post-transcriptional regulators: PNPase, Hfq with its dependent sRNA ArcZ, and the RsmA/B system; and the bacterial second messenger cyclic-di-GMP (c-di-GMP). Homologs of these regulatory components have also been characterized in almost all major bacterial plant pathogens like Erwiniaamylovora, Pseudomonassyringae, Pectobacterium spp., Xanthomonas spp., and Ralstonia spp. The second half of this review shifts focus to an in-depth discussion of the innovation and development of T3SS inhibitors, small molecules that inhibit T3SSs, in the field of plant pathology. This includes T3SS inhibitors that are derived from plant phenolic compounds, plant coumarins, and salicylidene acylhydrazides. We also discuss their modes of action in bacteria and application for controlling plant diseases.
Production Allocation: Rosetta Stone or Red Herring? Best Practices for Understanding Produced Oils in Resource Plays
Authors: Barrie Craig , Donohue Catherine , Zumberge J. , Zumberge John
Published: December 2020

The production of crude oil from resource plays has increased enormously over the past decade. In the USA, around 63% of total output in 2019 was from unconventional production. The major unconventional plays in the USA (e.g., Permian Basin, Anadarko Basin, Eagle Ford, etc.) have become some of the world’s largest oil producers. However, unlike “conventional” exploitation, the target zones in unconventional systems are generally the source rocks themselves or adjacent strata and require numerous horizontal wells and stimulation via hydraulic fracturing to meet production targets. In order to maximize production, operators have developed various well stacking methods, all of which require some form of monitoring to ensure that well spacing is optimized and fluid production is not being “stolen” from adjacent formations, thereby reducing the production potential in associated wells. This necessity, amongst other geochemical considerations related to source rock characterization, has resulted in the expansion of “production allocation” and “time lapse geochemistry” methods. These methods were initially developed for conventional production decades ago, but have since been adapted to unconventional systems. However, the direct applicability of this method is not straightforward and numerous considerations need to be taken into account, foremost among which are: (1) “What defines your end-members?” (2) “Are these end-members valid across a meaningful development area?” and (3) “What is the most appropriate use of geochemistry data in these systems?”. Reservoir geochemistry studies, which include both “time lapse geochemistry/production monitoring” and “production allocation”, are valuable geochemical methods in unconventional plays but need to be used appropriately to provide the cost savings and business direction that operators expect. In this paper, we will discuss a number of case studies, both theoretical and natural, and outline the important factors which need to be considered when designing a reservoir geochemistry study and the common pitfalls which exist. The case studies and best practice approach discussed are designed to highlight the power and flexibility of geochemical data collection methods, integration with the operator’s knowledgebase, and other analytical methods to customize the program for individual development programs. Emphasis is placed upon developing robust and applicable fluid relationships from geochemical data and evidence for statistically significant changes through time.
Inflammatory Bowel Disease: The Emergence of New Trends in Lifestyle and Nanomedicine as the Modern Tool for Pharmacotherapy
Authors: Jacob Eden Mariam , Borah Ankita , Pillai Sindhu C , Kumar D. Sakthi
Published: December 2020

The human intestine, which harbors trillions of symbiotic microorganisms, may enter into dysbiosis when exposed to a genetic defect or environmental stress. The naissance of chronic inflammation due to the battle of the immune system with the trespassing gut bacteria leads to the rise of inflammatory bowel disease (IBD). Though the genes behind the scenes and their link to the disease are still unclear, the onset of IBD occurs in young adults and has expanded from the Western world into the newly industrialized countries. Conventional drug deliveries depend on a daily heavy dosage of immune suppressants or anti-inflammatory drugs targeted for the treatment of two types of IBD, ulcerative colitis (UC) and Crohn’s disease (CD), which are often associated with systemic side effects and adverse toxicities. Advances in oral delivery through nanotechnology seek remedies to overcome the drawbacks of these conventional drug delivery systems through improved drug encapsulation and targeted delivery. In this review, we discuss the association of genetic factors, the immune system, the gut microbiome, and environmental factors like diet in the pathogenesis of IBD. We also review the various physiological concerns required for oral delivery to the gastrointestinal tract (GIT) and new strategies in nanotechnology-derived, colon-targeting drug delivery systems.
Bioinstructive Micro-Nanotextured Zirconia Ceramic Interfaces for Guiding and Stimulating an Osteogenic Response In Vitro
Authors: Elena Sima Livia , Bonciu Anca , Baciu Madalina , Anghel Iulia , Dumitrescu Luminita Nicoleta , Rusen Laurentiu , Dinca Valentina
Published: December 2020

Osseous implantology’s material requirements include a lack of potential for inducing allergic disorders and providing both functional and esthetic features for the patient’s benefit. Despite being bioinert, Zirconia ceramics have become a candidate of interest to be used as an alternative to titanium dental and cochlear bone-anchored hearing aid (BAHA) implants, implying the need for endowing the surface with biologically instructive properties by changing basic parameters such as surface texture. Within this context, we propose anisotropic and isotropic patterns (linear microgroove arrays, and superimposed crossline microgroove arrays, respectively) textured in zirconia substrates, as bioinstructive interfaces to guide the cytoskeletal organization of human mesenchymal stem cells (hMSCs). The designed textured micro-nano interfaces with either steep ridges and microgratings or curved edges, and nanoroughened walls obtained by direct femtosecond laser texturing are used to evaluate the hMSC response parameters and osteogenic differentiation to each topography. Our results show parallel micro line anisotropic surfaces are able to guide cell growth only for the steep surfaces, while the curved ones reduce the initial response and show the lowest osteogenic response. An improved osteogenic phenotype of hMSCs is obtained when grown onto isotropic grid/pillar-like patterns, showing an improved cell coverage and Ca/P ratio, with direct implications for BAHA prosthetic development, or other future applications in regenerating bone defects.
Breakfast Habits of a Representative Sample of the Spanish Child and Adolescent Population (The ENALIA Study): Association with Diet Quality
Authors: Cuadrado-Soto Esther , López-Sobaler Ana M. , Jiménez-Ortega Ana Isabel , Bermejo Laura M. , Aparicio Aránzazu , Ortega Rosa M.
Published: December 2020

The association between breakfast quality and total diet quality of children and adolescents ((1–17.9 years (n = 1570)) from the National Dietary Survey on the Child and Adolescent Population in Spain (ENALIA) was analyzed. Dietary information was collected using two non–consecutive one–day food diaries (1–10 years old) or two 24 h dietary recalls (>10 years). Breakfast quality index (BQI) and a variant of Nutrient Rich Foods index (NRF9.3) were calculated to assess the total diet quality. Children and adolescents who had breakfast on at least one day (n = 1561) were divided into two groups according to BQI: Worse Quality Breakfast (WQB) (BQI < 4 points (P66), n = 781) and Good Quality Breakfast (GQB) (BQI ≥ 4, n = 780). Younger children and those whose parents have university education presented higher BQI. GQB group had significantly higher intakes of micronutrients (vitamins A, D, C, B1, B2, B6, niacin, folate, calcium, potassium, magnesium). Fewer GQB children exceeded the Acceptable Macronutrient Distribution Range for fat and had folate and calcium intakes below their estimated average requirement. Daily NRF9.3 was 496.2 ± 54.0, being higher in GQB (503.8 ± 50.6 vs. 488.6 ± 56.2, p < 0.001). Increasing the quality of breakfast increased the possibility of having a NRF9.3 higher than P50 (OR: 1.893, CI: 1.549–2.315, p < 0.0001). Breakfasts have room for quality improvement in a high percentage of children. A higher quality breakfast is associated with a benefit in the quality of the total diet.
Correlation of NHR-48 Transcriptional Modulator Expression with Selected CYP Genes’ Expression during Thiabendazole Treatment of Anisakis simplex (s.l.)?—An In Vitro Study
Authors: Łopieńska-Biernat Elżbieta , Stryiński Robert , Paukszto Łukasz , Jastrzębski Jan P.
Published: December 2020

Anisakis simplex (s.l.) is a complex of three sibling (biological) species of parasitic nematodes of marine mammals, including A. berlandi, A. pegreffii and A. simplex (s.s.). It is characterized by a complex life cycle in which humans can become accidental hosts by consuming dishes made of raw or undercooked fish containing L3 larvae, which in many regions of the world is related to the national or regional culinary tradition. This has spurred scientific efforts to develop new methods for treating the disease, called anisakiasis, and to neutralize invasive L3. Thiabendazole (TBZ) is a wide-spectrum anthelminthic with a higher efficacy than albendazole, a drug whose long-term use induces resistance in many parasitic species. Cytochromes P450 participate in TBZ metabolism, and the expression of their genes is controlled by nuclear hormone receptors (NHR). This study aimed to examine the effects of TBZ on the above-described pathway in invasive larvae of A. simplex (s.l.). The efficacy of TBZ against A. simplex (s.l.) larvae was observed for the first time. Larvae were cultured in vitro for 72 h in a medium containing TBZ at five concentrations from 0.5 to 1.5 mM. However, the survival curves did not significantly differ from each other. This means that all of the concentrations of TBZ had a similar effect on the A. simplex (s.l.) L3 larvae during in vitro culture. Nevertheless, TBZ modified the expression of nhr-48, cyp13a3 and cyp1a1 genes in the L3 of A. simplex (s.l.).
Genomic Analysis of Aeromonas veronii C198, a Novel Mcr-3.41-Harboring Isolate from a Patient with Septicemia in Thailand
Authors: Hatrongjit Rujirat , Kerdsin Anusak , Takeuchi Dan , Wongsurawat Thidathip , Jenjaroenpun Piroon , Chopjitt Peechanika , Boueroy Parichart , Akeda Yukihiro , Hamada Shigeyuki
Published: December 2020

The resistance of Gram-negative bacteria to colistin, mediated by plasmid-borne mcr genes, is an emerging public health concern. The complete genome sequence (4.55 Mb) of a clinical isolate of Aeromonas veronii biovar veronii obtained from a patient with septicemia was determined using short-read and long-read platforms. This isolate (C198) was found to harbor a novel mcr-3 gene, designated mcr-3.41. Isolate C198 revealed adjacent mcr-3.41 and mcr-3-like genes. It contained one chromosome and two plasmids, both of which encoded a RepB replication protein. Other antimicrobial resistance genes, including blacphA3, blaOXA-12, tetA, rsmA, and adeF, were also present. Isolate C198 was resistant to amoxicillin–clavulanate, ampicillin–sulbactam and tetracycline, and showed intermediate resistance to trimethoprim–sulfamethoxazole. The isolate was susceptible to piperacillin–tazobactam, carbapenem, third-generation cephalosporins, fluoroquinolones, chloramphenicol, and aminoglycosides. Putative virulence genes in the C198 genome encoded type II, III, and VI secretion systems; type IV Aeromonas pili; and type I fimbria, flagella, hemagglutinin, aerolysin, and hemolysins. Multilocus sequence typing revealed a novel sequence type (ST), ST720 for C198. Phylogenetic analysis of the single nucleotide polymorphisms in C198 demonstrated that the strain was closely related to A. veronii 17ISAe. The present study provides insights into the genomic characteristics of human A. veronii isolates.
Interactive Robot for Playing Russian Checkers
Authors: Kopets Ekaterina E. , Karimov Artur I. , Kolev Georgii Y. , Scalera Lorenzo , Butusov Denis N.
Published: December 2020

Human–robot interaction in board games is a rapidly developing field of robotics. This paper presents a robot capable of playing Russian checkers designed for entertaining, training, and research purposes. Its control program is based on a novel unsupervised self-learning algorithm inspired by AlphaZero and represents the first successful attempt of using this approach in the checkers game. The main engineering challenge in mechanics is to develop a board state acquisition system non-sensitive to lighting conditions, which is achieved by rejecting computer vision and utilizing magnetic sensors instead. An original robot face is designed to endow the robot an ability to express its attributed emotional state. Testing the robot at open-air multiday exhibitions shows the robustness of the design to difficult exploitation conditions and the high interest of visitors to the robot.
Evaluation of Precipitation Products by Using Multiple Hydrological Models over the Upper Yellow River Basin, China
Authors: Guan Xiaoxiang , Zhang Jianyun , Yang Qinli , Tang Xiongpeng , Liu Cuishan , Jin Junliang , Liu Yue , Bao Zhenxin , Wang Guoqing
Published: December 2020

In this study, 6 widely used precipitation products APHRODITE, CPC_UNI_PRCP, CN05.1, PERSIANN-CDR, Princeton Global Forcing (PGF), and TRMM 3B42 V7 (TMPA), were evaluated against gauge observations (CMA data) from 1998 to 2014, and applied to streamflow simulation over the Upper Yellow River basin (UYRB), using 4 hydrological models (DWBM, RCCC-WBM, GR4J, and VIC). The relative membership degree (u), as the comprehensive evaluation index in the hydrological evaluation, was calculated by the optimum fuzzy model. The results showed that the spatial pattern of precipitation from the CMA dataset and the other 6 precipitation products were very consistent with each other. The satellite-derived rainfall products (SDFE), like PSERSIANN-CDR and TMPA, depicted considerably finer and more detailed spatial heterogeneity. The SDFE and reanalysis (RA) products could estimate the monthly precipitation very well at both gauge and basin-average scales. The runoff simulation results indicated that the APHRODITE and TMPA were superior to the other 4 precipitation datasets, obtaining much higher scores, with average u values of 0.88 and 0.77. The precipitation estimation products tended to show better performance in streamflow simulation at the downstream hydrometric stations. In terms of performance of hydrological models, the RCCC–WBM model showed the best potential for monthly streamflow simulation, followed by the DWBM. It indicated that the monthly models were more flexible than daily conceptual or distributed models in hydrological evaluation of SDFE or RA products, and that the difference in precipitation estimates from various precipitation datasets were more influential in the GR4J and VIC models.
Numerical Simulation Study on the Influence of Branching Structure of Longmen Shan Thrust Belt on the Nucleation of Mw7.9 Wenchuan Earthquake
Authors: Yue Chong , Qu Chunyan , Shan Xinjian , Yan Wei , Zhao Jing , Yu Huaizhong , Ma Weiyu , Yao Qi
Published: December 2020

On the Longmen Shan thrust belt (LMS) on the eastern margin of Tibet Plateau, the Mw7.9 Wenchuan earthquake occurred in 2008. As for the dynamic cause of the Wenchuan earthquake, many scholars have studied the rheological difference and terrain elevation difference on both sides of the fault. However, previous studies have simplified the LMS as a single listric-reverse fault. In fact, the LMS is composed of four faults with different dip angles in the shallow part, and the faults are Wenchuan-Maoxian fault (WMF), Yingxiu-Beichuan fault (YBF), Guanxian-Jiangyou fault (GJF) and Range Front Thrust (RFT) from west to east. However, the control of the branching structure of these faults on the distribution and accumulation of stress and strain during the seismogenic of the Wenchuan earthquake has not been discussed. In this paper, four viscoelastic finite element models with different fault numbers and combination structures are built to analyze the effect of fault branching structures on the stress distribution and accumulation during the seismogenic of Wenchuan earthquake, and we use geodetic data such as GPS and precise leveling data to constrain our models. At the same time, we also study the influence of the existence of the detachment layer, which is formed by the low-resistivity and low-velocity layer, between the upper and lower crust of the Bayan Har block and the change of its frontal edge position on the stress accumulation and distribution. The results show that the combinations of YBF and GJF is most conducive to the concentration of equivalent stress below the intersection of the two faults, and the accumulated stress on GJF is shallower than that on YBF, which means that more stress is transferred to the surface along GJF; and the existence of a detachment layer can effectively promote the accumulation of stress at the bottom of YBF and GJF, and the closer the frontal edge position of the detachment layer is to the LMS fault, the more favorable the stress accumulation is. Based on the magnitude of stress accumulation at the bottom of the intersection of YBF and GJF, we speculate that the frontal edge position of the detachment layer may cross YBF and expand eastward.