bluuebunny/crossref_metadata_2025 huggingface dataset:
A Decision Support Tool for Long-Term Planning of Marine Operations in Ocean Energy Projects
Authors: Correia da Fonseca Francisco X. , Amaral Luís , Chainho Paulo
Published: July 2021

Ocean energy is a relevant source of clean renewable energy, and as it is still facing challenges related to its above grid-parity costs, tariffs intended to support in a structured and coherent way are of great relevance and potential impact. The logistics and marine operations required for installing and maintaining these systems are major cost drivers of marine renewable energy projects. Planning the logistics of marine energy projects is a highly complex and intertwined process, and to date, limited advances have been made in the development of decision support tools suitable for ocean energy farm design. The present paper describes the methodology of a novel, opensource, logistic and marine operation planning tool, integrated within DTOceanPlus suite of design tools, and responsible for producing logistic solutions comprised of optimal selections of vessels, port terminals, equipment, as well as operation plans, for ocean energy projects. Infrastructure selection logistic functions were developed to select vessels, ports, and equipment for specific projects. A statistical weather window model was developed to estimate operation delays due to weather. A vessel charter rate modeling approach, based on an in-house vessel database and industry experience, is described in detail. The overall operation assumptions and underlying operating principles of the statistical weather window model, maritime infrastructure selection algorithms, and cost modeling strategies are presented. Tests performed for a case study based a theoretical floating wave energy converter produced results in good agreement with reality.
Controlling Factors of Phytoplankton Productivity in Marshes in a Hot Climate with High Seasonal Variation
Authors: Ameen Fuad , Albueajee Alaa I. , Hassan Fikrat M. , Stephenson Steven L. , Douabul Ali A. Z.
Published: July 2021

In this work the Auda marsh, which is part of a system of Iraqi marshes, was sampled to assess the seasonal dynamics and controlling factors of microalgae productivity. The marshes are situated in a hot climate with high seasonal variation near the Arabian Gulf. Physicochemical and biological measurements were taken for water in three areas. Bio-optical models were constructed to describe the primary productivity and chlorophyll-a concentrations in the wet and dry seasons separately and also for the entire area of the Iraqi marshes. The models, as well as almost all measurements, showed high seasonal variation. The mean water temperature was 16 °C in the wet season and 28 °C in the dry season. An almost twofold difference was measured for turbidity and the concentrations of dissolved oxygen and chlorophyll-a for the two seasons. Chlorophyll-a appeared to be a better indicator of ecosystem conditions than primary productivity or biological oxygen demand, according to the results obtained from canonical correlation analysis. Nitrogen or phosphorous did not explain primary productivity or chlorophyll-a to an appreciable extent. Biological variables were related most strongly to water temperature and turbidity, which were the factors most important for controlling phytoplankton productivity in the marshes.
An Overview of Underwater Connectors
Authors: Song Wentao , Cui Weicheng
Published: July 2021

Underwater connectors are very essential and complex components of deep-sea engineering equipment and their design and manufacture have apparent multidisciplinary characteristics. Wet-mateable connectors (WMCs) represent the highest level of technology in this field, and only a very few countries in the world can produce WMCs. So, WMCs are likely to be a constraining factor to some maritime powers that might try to achieve breakthroughs in this field, constraining the innovation-driven development of deep-sea equipment. This paper gives a detailed overview of underwater connectors, both electrical and optical. First, the background of underwater connectors is introduced, and then the main available commercial off-the-shelf (COTS) products are described. Next, the new concept of functional units is proposed by the authors to help readers to have a better understanding of underwater connectors. Then, the basic theories of design are introduced according to different functional units, covering the aspects of electrical/optical connection, pressure-balanced oil-filled (PBOF) technology, penetrable self-sealing, aligning and locking structures. Finally, some discussions and conclusions are presented. This paper aims to reveal the secrets of key technologies used in underwater connectors, especially in WMCs.
Antifungal Combination Therapy in Children with Cancer—A 4-Year Analysis of Real-Life Data of Two Major Pediatric Cancer Centers
Authors: Schöning Stefan , Bochennek Konrad , Gordon Kathrin , Groll Andreas H. , Lehrnbecher Thomas
Published: July 2021

Clinical data on antifungal combination therapy are limited, in particular in the pediatric setting. We analyzed real-life data collected in two major pediatric cancer centers over a period of 4 years. Patients were identified in an observational study on children with acute leukemia and lymphoma or undergoing hematopoietic cell transplantation. Out of 438 patients, 19 patients received 21 episodes of antifungal combination therapy. Therapy was mostly started for sepsis (n = 5) or clinical deterioration with pulmonary infiltrates (n = 10), and less often for periorbital swelling with suspected mold infection (n = 2), clinical deterioration and new skin lesions, secondary antifungal prophylaxis, a persistently elevated galactomannan index, or as pre-emptive treatment (n = 1 each). Diagnostics revealed proven, probable, and possible invasive fungal disease in two, seven and four episodes, respectively. Most regimens included caspofungin (n = 19), and treatment was initiated as first line therapy in 10 episodes. The median duration was 13 days (4–46 days). Nine of the 13 patients with proven, probable, or possible invasive fungal disease survived, which was comparable to patients receiving antifungal monotherapy. Our analysis demonstrates that combination therapy has mainly been prescribed in selected immunocompromised patients with clinical deterioration due to suspected invasive fungal disease or those with sepsis, and is well tolerated. Future studies need to better characterize clinical settings in which patients may benefit from antifungal combination therapy.
Aflatoxin Biosynthesis, Genetic Regulation, Toxicity, and Control Strategies: A Review
Authors: Khan Rahim , Ghazali Farinazleen Mohamad , Mahyudin Nor Ainy , Samsudin Nik Iskandar Putra
Published: July 2021

Aflatoxins (AFs) are highly toxic and cancer-causing compounds, predominantly synthesized by the Aspergillus species. AFs biosynthesis is a lengthy process that requires as minimum as 30 genes grouped inside 75 kilobytes (kB) of gene clusters, which are regulated by specific transcription factors, including aflR, aflS, and some general transcription factors. This paper summarizes the status of research on characterizing structural and regulatory genes associated with AF production and their roles in aflatoxigenic fungi, particularly Aspergillus flavus and A. parasiticus, and enhances the current understanding of AFs that adversely affect humans and animals with a great emphasis on toxicity and preventive methods.
Feasibly of CD24/CD11b as a Screening Test for Hematological Malignancies
Authors: Shapira Shiran , Kazanov Dina , Mdah Fatin , Yaakobi Hadas , Herishanu Yair , Perry Chava , Avivi Irit , Itchaki Gilad , Shacham-Abulafia Adi , Raanani Pia , Hay-Levy Mori , Aiger Gal , Mashiah Jacob , Lev-Ari Shahar , Arber Nadir
Published: July 2021

An estimated 1.24 million blood cancer cases occur annually worldwide, accounting for approximately 6% of all cancer cases. Currently, there are no standardized hematology cancer screening tests that are recommended for the general population. CD24 is a mucin-like cell surface molecule and P-selectin ligand, which plays a significant role in the maturation of B-lymphocytes and was found to be overexpressed in a number of hematological malignancies. Our primary aim was to assess the sensitivity and specificity of the CD24/CD11b-based blood test for the detection of hematological malignancies. Our cohort included 488 subjects with positive hematological cancer diagnosis (n = 122) and healthy subjects (n = 366). CD24/CD11b expression in peripheral blood leukocytes (PBLs) obtained from blood samples of participants was analyzed by flow cytometry. Our results demonstrated that the average levels of CD24/CD11b in healthy patients (21.7 ± 9.0) were statistically significantly lower compared to levels of CD24/CD11b in cancer patients (29.5 ± 18.7, p < 0.001). The highest levels of CD24/CD11b were found in multiple myeloma (39.1 ± 23.6), followed by chronic myeloid leukemia (33.0 ± 13.7) and non-Hodgkin lymphoma (32.3 ± 13.3). The test had an overall sensitivity for hematologic cancers of 78.5% (95% CI, 70.7–86.3%) and specificity of 80.2% (95% CI, 76.1–84.3%). In conclusion, our findings indicate the feasibility of a CD24/CD11b-based blood test as a screening test of hematological malignancies.
Evaluating, Filtering and Clustering Genetic Disease Cohorts Based on Human Phenotype Ontology Data with Cohort Analyzer
Authors: Rojano Elena , Córdoba-Caballero José , Jabato Fernando M. , Gallego Diana , Serrano Mercedes , Pérez Belén , Parés-Aguilar Álvaro , Perkins James R. , Ranea Juan A. G. , Seoane-Zonjic Pedro
Published: July 2021

Exhaustive and comprehensive analysis of pathological traits is essential to understanding genetic diseases, performing precise diagnosis and prescribing personalized treatments. It is particularly important for disease cohorts, as thoroughly detailed phenotypic profiles allow patients to be compared and contrasted. However, many disease cohorts contain patients that have been ascribed low numbers of very general and relatively uninformative phenotypes. We present Cohort Analyzer, a tool that measures the phenotyping quality of patient cohorts. It calculates multiple statistics to give a general overview of the cohort status in terms of the depth and breadth of phenotyping, allowing us to detect less well-phenotyped patients for re-examining or excluding from further analyses. In addition, it performs clustering analysis to find subgroups of patients that share similar phenotypic profiles. We used it to analyse three cohorts of genetic diseases patients with very different properties. We found that cohorts with the most specific and complete phenotypic characterization give more potential insights into the disease than those that were less deeply characterised by forming more informative clusters. For two of the cohorts, we also analysed genomic data related to the patients, and linked the genomic data to the patient-subgroups by mapping shared variants to genes and functions. The work highlights the need for improved phenotyping in this era of personalized medicine. The tool itself is freely available alongside a workflow to allow the analyses shown in this work to be applied to other datasets.
Estimating Air Pollution Removal and Monetary Value for Urban Green Infrastructure Strategies Using Web-Based Applications
Authors: Russo Alessio , Chan Wing Tung , Cirella Giuseppe T.
Published: July 2021

More communities around the world are recognizing the benefits of green infrastructure (GI) and are planting millions of trees to improve air quality and overall well-being in cities. However, there is a need for accurate tools that can measure and value these benefits whilst also informing the community and city managers. In recent years, several online tools have been developed to assess ecosystem services. However, the reliability of such tools depends on the incorporation of local or regional data and site-specific inputs. In this communication, we have reviewed two of the freely available tools (i.e., i-Tree Canopy and the United Kingdom Office for National Statistics) using Bristol City Centre as an example. We have also discussed strengths and weaknesses for their use and, as tree planting strategy tools, explored further developments of such tools in a European context. Results show that both tools can easily calculate ecosystem services such as air pollutant removal and monetary values and at the same time be used to support GI strategies in compact cities. These tools, however, can only be partially utilized for tree planting design as they do not consider soil and root space, nor do they include drawing and painting futures. Our evaluation also highlights major gaps in the current tools, suggesting areas where more research is needed.
Adaptive Direct Teaching Control with Variable Load of the Lower Limb Rehabilitation Robot (LLR-II)
Authors: Wang Xincheng , Wang Hongbo , Hu Xinyu , Tian Yu , Lin Musong , Yan Hao , Niu Jianye , Sun Li
Published: July 2021

Most lower limb rehabilitation robots use fixed training trajectories and lack participation of physiotherapists. In addition, there is a lack of attention on combining direct teaching function with rehabilitation robots, which enables physiotherapists to plan trajectories directly. In this paper, an adaptive direct teaching function with variable load that can be applied to the sitting/lying lower limb rehabilitation robot-II (LLR-II) is proposed. First, the structural design and electrical system of LLR-II are introduced. The dynamic equation of LLR-II considering joint flexibility is derived and analyzed. Then, the impact of joint flexibility on LLR-II is reduced by introducing the intermediate input variables. Based on this, the control law of the dragging teaching stage and the replay stage in the direct teaching function with variable load is designed and the adaptive control strategy eliminates the influence of different patients. In addition, the control law is simulated and verified. Finally, some preliminary experiments of the adaptive direct teaching function with variable load on LLR-II are carried out, and the results showed that the control law has good performance, which lays the foundation for future work.
YOLOMask, an Instance Segmentation Algorithm Based on Complementary Fusion Network
Authors: Hua Jiang , Hao Tonglin , Zeng Liangcai , Yu Gui
Published: July 2021

Object detection and segmentation can improve the accuracy of image recognition, but traditional methods can only extract the shallow information of the target, so the performance of algorithms is subject to many limitations. With the development of neural network technology, semantic segmentation algorithms based on deep learning can obtain the category information of each pixel. However, the algorithm cannot effectively distinguish each object of the same category, so YOLOMask, an instance segmentation algorithm based on complementary fusion network, is proposed in this paper. Experimental results on public data sets COCO2017 show that the proposed fusion network can accurately obtain the category and location information of each instance and has good real-time performance.
The Machine-Part Cell Formation Problem with Non-Binary Values: A MILP Model and a Case of Study in the Accounting Profession
Authors: del Pozo-Antúnez Jose Joaquin , Fernández-Navarro Francisco , Molina-Sánchez Horacio , Ariza-Montes Antonio , Carbonero-Ruz Mariano
Published: July 2021

The traditional machine-part cell formation problem simultaneously clusters machines and parts in different production cells from a zero–one incidence matrix that describes the existing interactions between the elements. This manuscript explores a novel alternative for the well-known machine-part cell formation problem in which the incidence matrix is composed of non-binary values. The model is presented as multiple-ratio fractional programming with binary variables in quadratic terms. A simple reformulation is also implemented in the manuscript to express the model as a mixed-integer linear programming optimization problem. The performance of the proposed model is shown through two types of empirical experiments. In the first group of experiments, the model is tested with a set of randomized matrices, and its performance is compared to the one obtained with a standard greedy algorithm. These experiments showed that the proposed model achieves higher fitness values in all matrices considered than the greedy algorithm. In the second type of experiment, the optimization model is evaluated with a real-world problem belonging to Human Resource Management. The results obtained were in line with previous findings described in the literature about the case study.
Fixed-Time Third-Order Super-Twisting-like Sliding Mode Motion Control for Piezoelectric Nanopositioning Stage
Authors: Wang Guangwei , Wang Bo , Zhang Chengxi
Published: July 2021

This paper presents a novel third-order super-twisting-like integral sliding mode controller (3-ISMC) for trajectory tracking of nanopositioning applications. Different from traditional sliding mode control methods presenting with chattering problems, the proposed approach provides continuous control inputs, which brings much convenience for practical applications. Moreover, the fixed-time convergence of the proposed 3-ISMC is guaranteed independently of initial conditions. The estimation of the fixed convergence time and stability are derived based on the Lyapunov method. Simulation results demonstrate that the proposed controller exhibits chattering free and quick transient response performance for a piezoelectric nanopositioning system under model uncertainties and external disturbances.
Acoustics of Fractal Porous Material and Fractional Calculus
Authors: Fellah Zine El Abiddine , Fellah Mohamed , Ongwen Nicholas O. , Ogam Erick , Depollier Claude
Published: July 2021

In this paper, we present a fractal (self-similar) model of acoustic propagation in a porous material with a rigid structure. The fractal medium is modeled as a continuous medium of non-integer spatial dimension. The basic equations of acoustics in a fractal porous material are written. In this model, the fluid space is considered as fractal while the solid matrix is non-fractal. The fluid–structure interactions are described by fractional operators in the time domain. The resulting propagation equation contains fractional derivative terms and space-dependent coefficients. The fractional wave equation is solved analytically in the time domain, and the reflection and transmission operators are calculated for a slab of fractal porous material. Expressions for the responses of the fractal porous medium (reflection and transmission) to an acoustic excitation show that it is possible to deduce these responses from those obtained for a non-fractal porous medium, only by replacing the thickness of the non-fractal material by an effective thickness depending on the fractal dimension of the material. This result shows us that, thanks to the fractal dimension, we can increase (sometimes by a ratio of 50) and decrease the equivalent thickness of the fractal material. The wavefront speed of the fractal porous material depends on the fractal dimension and admits several supersonic values. These results open a scientific challenge for the creation of new acoustic fractal materials, such as metamaterials with very specific acoustic properties.
Performance of Enhanced Multiple-Searching Genetic Algorithm for Test Case Generation in Software Testing
Authors: Khamprapai Wanida , Tsai Cheng-Fa , Wang Paohsi , Tsai Chi-En
Published: July 2021

Test case generation is an important process in software testing. However, manual generation of test cases is a time-consuming process. Automation can considerably reduce the time required to create adequate test cases for software testing. Genetic algorithms (GAs) are considered to be effective in this regard. The multiple-searching genetic algorithm (MSGA) uses a modified version of the GA to solve the multicast routing problem in network systems. MSGA can be improved to make it suitable for generating test cases. In this paper, a new algorithm called the enhanced multiple-searching genetic algorithm (EMSGA), which involves a few additional processes for selecting the best chromosomes in the GA process, is proposed. The performance of EMSGA was evaluated through comparison with seven different search-based techniques, including random search. All algorithms were implemented in EvoSuite, which is a tool for automatic generation of test cases. The experimental results showed that EMSGA increased the efficiency of testing when compared with conventional algorithms and could detect more faults. Because of its superior performance compared with that of existing algorithms, EMSGA can enable seamless automation of software testing, thereby facilitating the development of different software packages.
Polar Lipids Composition, Antioxidant and Anti-Inflammatory Activities of the Atlantic Red Seaweed Grateloupia turuturu
Authors: da Costa Elisabete , Melo Tânia , Reis Mariana , Domingues Pedro , Calado Ricardo , Abreu Maria Helena , Domingues Maria Rosário
Published: July 2021

Grateloupia turuturu Yamada, 1941, is a red seaweed widely used for food in Japan and Korea which was recorded on the Atlantic Coast of Europe about twenty years ago. This seaweed presents eicosapentaenoic acid (EPA) and other polyunsaturated fatty acids (PUFAs) in its lipid fraction, a feature that sparked the interest on its potential applications. In seaweeds, PUFAs are mostly esterified to polar lipids, emerging as healthy phytochemicals. However, to date, these biomolecules are still unknown for G. turuturu. The present work aimed to identify the polar lipid profile of G. turuturu, using modern lipidomics approaches based on high performance liquid chromatography coupled to high resolution mass spectrometry (LC–MS) and gas chromatography coupled to mass spectrometry (GC–MS). The health benefits of polar lipids were identified by health lipid indices and the assessment of antioxidant and anti-inflammatory activities. The polar lipids profile identified from G. turuturu included 205 lipid species distributed over glycolipids, phospholipids, betaine lipids and phosphosphingolipids, which featured a high number of lipid species with EPA and PUFAs. The nutritional value of G. turuturu has been shown by its protein content, fatty acyl composition and health lipid indices, thus confirming G. turuturu as an alternative source of protein and lipids. Some of the lipid species assigned were associated to biological activity, as polar lipid extracts showed antioxidant activity evidenced by free radical scavenging potential for the 2,2′-azino-bis-3-ethyl benzothiazoline-6-sulfonic acid (ABTS●+) radical (IC50 ca. 130.4 μg mL−1) and for the 2,2-diphenyl-1-picrylhydrazyl (DPPH●) radical (IC25 ca. 129.1 μg mL−1) and anti-inflammatory activity by inhibition of the COX-2 enzyme (IC50 ca. 33 µg mL−1). Both antioxidant and anti-inflammatory activities were detected using a low concentration of extracts. This integrative approach contributes to increase the knowledge of G. turuturu as a species capable of providing nutrients and bioactive molecules with potential applications in the nutraceutical, pharmaceutical and cosmeceutical industries.
Pharmacological Activities of Sulfated Fucose-Rich Polysaccharides after Oral Administration: Perspectives for the Development of New Carbohydrate-Based Drugs
Authors: Fonseca Roberto J. C. , Mourão Paulo A. S.
Published: July 2021

Marine organisms are a source of active biomolecules with immense therapeutic and nutraceutical potential. Sulfated fucose-rich polysaccharides are present in large quantities in these organisms with important pharmacological effects in several biological systems. These polysaccharides include sulfated fucan (as fucoidan) and fucosylated chondroitin sulfate. The development of these polysaccharides as new drugs involves several important steps, among them, demonstration of the effectiveness of these compounds after oral administration. The oral route is the more practical, comfortable and preferred by patients for long-term treatments. In the past 20 years, reports of various pharmacological effects of these polysaccharides orally administered in several animal experimental models and some trials in humans have sparked the possibility for the development of drugs based on sulfated polysaccharides and/or the use of these marine organisms as functional food. This review focuses on the main pharmacological effects of sulfated fucose-rich polysaccharides, with an emphasis on the antidislipidemic, immunomodulatory, antitumor, hypoglycemic and hemostatic effects.
Transcriptomics and Metabolomics Analyses Provide Novel Insights into Glucose-Induced Trophic Transition of the Marine Diatom Nitzschia laevis
Authors: Mao Xuemei , Ge Mengdie , Wang Xia , Yu Jianfeng , Li Xiaojie , Liu Bin , Chen Feng
Published: July 2021

Diatoms have important ecological roles and are natural sources of bioactive compounds. Nitzschia laevis is a member of marine diatoms that accumulates high-value products including fucoxanthin and eicosapentaenoic acid (EPA). In this study, physiological data showed that comparing to autotrophic growth, mixotrophic cultivation with glucose supplementation led to a decrease of chlorophyll and fucoxanthin content in N. laevis, and an increase of biomass density and EPA yield. To further examine the metabolic barriers for fucoxanthin and EPA biosynthesis, comparative transcriptomic and metabolome analyses were conducted, with a focus on the genes related to carotenoids biosynthesis and fatty acid metabolism. The results indicated that phytoene desaturase (PDS) and zeta-carotene isomerase (ZISO) could be the rate-limiting enzymes in carotenoid biosynthesis. The transcription regulation of 3-ketoacyl-CoA synthase (KCS) and elongation of very long chain fatty acids protein (EVOVL) are important contributors associated with polyunsaturated fatty acids (PUFAs) accumulation. Furthermore, we also investigated the glucose-associated regulatory genes using weighted gene co-expression network analysis, and identified potential hub genes linked with cell cycle, carbohydrate metabolism, purine biosynthesis, and lipid metabolism. This study offers a high-quality transcriptome resource for N. laevis and provides a molecular framework for further metabolic engineering studies on fucoxanthin and EPA production.
Serum Osteoprotegerin Level Is Negatively Associated with Bone Mineral Density in Patients Undergoing Maintenance Hemodialysis
Authors: Lu Chia-Wen , Wang Chih-Hsien , Hsu Bang-Gee , Tsai Jen-Pi
Published: July 2021

Background and Objectives: Osteoprotegerin (OPG), a potent osteoclast activation inhibitor, decreases bone resorption and plays a role in mediating bone mineral density (BMD). Our aim was to evaluate the relationship between BMD and serum OPG in maintenance hemodialysis (MHD) patients. Materials and Methods: Fasting blood samples were obtained from 75 MHD patients. BMD was measured by dual-energy X-ray absorptiometry in lumbar vertebrae (L2–L4). The WHO classification criteria were applied to define osteopenia and osteoporosis. A commercial enzyme-linked immunosorbent assay was used to measure serum OPG values. Results: Among all MHD patients, seven (9.3%) and 20 patients (26.7%) were defined as osteoporosis and osteopenia, respectively. Female patients had lower lumbar BMD than males (p = 0.002). Older age (p = 0.023), increased serum OPG (p < 0.001) urea reduction rate (p = 0.021), Kt/V (p = 0.027), and decreased body mass index (p = 0.006) and triglycerides (p = 0.020) were significantly different between the normal, osteopenia, and osteoporosis groups. Lumbar spine BMD was positively correlated with body mass index (BMI) (p < 0.001) but negatively correlated with OPG (p < 0.001) and age (p = 0.003). After grouping patients into T scores < −1 and < −2.5, female sex and OPG (adjusted odds ratio [aOR] 1.022, 95% confidence interval [C.I.] 1.011–1.034, p < 0.001) were predictors of T scores < −1, whereas only OPG was predictive of T scores < −2.5 (aOR 1.015, 95% C.I. 1.005–1.026, p = 0.004) by multivariate stepwise logistic regression analysis. The areas under the curve for predicting T scores < −1 or < −2.5 were 0.920 (95% C.I. 0.834–0.970, p < 0.001) and 0.958 (95% C.I. 0.885–0.991, p < 0.001), respectively. Conclusions: Increased serum OPG negatively correlated with lumbar BMD and could be a potential biomarker predictive of osteoporosis in MHD patients.
Multi-Trait Wheat Rhizobacteria from Calcareous Soil with Biocontrol Activity Promote Plant Growth and Mitigate Salinity Stress
Authors: Venieraki Anastasia , Chorianopoulou Styliani N. , Katinakis Panagiotis , Bouranis Dimitris L.
Published: July 2021

Plant growth promoting rhizobacteria (PGPR) can be functional microbial fertilizers and/or biological control agents, contributing to an eco-spirit and safe solution for chemical replacement. Therefore, we have isolated rhizospheric arylsulfatase (ARS)-producing bacteria, belonging to Pseudomonas and Bacillus genus, from durum wheat crop grown on calcareous soil. These isolates harbouring plant growth promoting (PGP) traits were further evaluated in vitro for additional PGP traits, including indole compounds production and biocontrol activity against phytopathogens, limiting the group of multi-trait strains to eight. The selected bacterial strains were further evaluated for PGP attributes associated with biofilm formation, compatibility, salt tolerance ability and effect on plant growth. In vitro studies demonstrated that the multi-trait isolates, Bacillus (1.SG.7, 5.SG.3) and Pseudomonas (2.SG.20, 2.C.19) strains, enhanced the lateral roots abundance and shoots biomass, mitigated salinity stress, suggesting the utility of beneficial ARS-producing bacteria as potential microbial fertilizers. Furthermore, in vitro studies demonstrated that compatible combinations of multi-trait isolates, Bacillus sp. 1.SG.7 in a mixture coupled with 5.SG.3, and 2.C.19 with 5.SG.3 belonging to Bacillus and Pseudomonas, respectively, may enhance plant growth as compared to single inoculants.
Oligosaccharide Metabolism and Lipoteichoic Acid Production in Lactobacillus gasseri and Lactobacillus paragasseri
Authors: Shiraishi Tsukasa , Maeno Shintaro , Kishi Sayoko , Fujii Tadashi , Tanno Hiroki , Hirano Katsuaki , Tochio Takumi , Tanizawa Yasuhiro , Arita Masanori , Yokota Shin-ichi , Endo Akihito
Published: July 2021

Lactobacillus gasseri and Lactobacillus paragasseri are human commensal lactobacilli that are candidates for probiotic application. Knowledge of their oligosaccharide metabolic properties is valuable for synbiotic application. The present study characterized oligosaccharide metabolic systems and their impact on lipoteichoic acid (LTA) production in the two organisms, i.e., L. gasseri JCM 1131T and L. paragasseri JCM 11657. The two strains grew well in medium with glucose but poorly in medium with raffinose, and growth rates in medium with kestose differed between the strains. Oligosaccharide metabolism markedly influenced their LTA production, and apparent molecular size of LTA in electrophoresis recovered from cells cultured with glucose and kestose differed from that from cells cultured with raffinose in the strains. On the other hand, more than 15-fold more LTA was observed in the L. gasseri cells cultured with raffinose when compared with glucose or kestose after incubation for 15 h. Transcriptome analysis identified glycoside hydrolase family 32 enzyme as a potential kestose hydrolysis enzyme in the two strains. Transcriptomic levels of multiple genes in the dlt operon, involved in D-alanine substitution of LTA, were lower in cells cultured with raffinose than in those cultured with kestose or glucose. This suggested that the different sizes of LTA observed among the carbohydrates tested were partly due to different levels of alanylation of LTA. The present study indicates that available oligosaccharide has the impact on the LTA production of the industrially important lactobacilli, which might influence their probiotic properties.
Preservation of Underground Microbial Diversity in Ancient Subsurface Deposits (>6 Ma) of the Rio Tinto Basement
Authors: Fernández-Remolar David C. , Gómez-Ortiz David , Malmberg Per , Huang Ting , Shen Yan , Anglés Angélica , Amils Ricardo
Published: July 2021

The drilling of the Rio Tinto basement has provided evidence of an underground microbial community primarily sustained by the Fe and S metabolism through the biooxidation of pyrite orebodies. Although the gossan is the microbial activity product, which dates back to the Oligocene (25 Ma), no molecular evidence of such activity in the past has been reported yet. A Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS) molecular analysis of a subsurface sample in the Peña de Hierro basement has provided novel data of the ancient underground microbial community. It shows that the microbial remains are preserved in a mineral matrix composed of laminated Fe-oxysulfates and K- and Na-bearing sulfates alternating with secondary silica. In such a mineral substrate, the biomolecule traces are found in five different microstructure associations, (1) <15 micron-sized nodular microstructures composed of POn(2≤n≤4)−, (2) <30 micron-size micronodules containing fatty acids, acylglycerides, and alkanol chains, (3) <20 micro-sized nodules containing NOn−(2≤n≤3) ions, (4) 40-micron size nodules with NH4+ and traces of peptides, and (5) >200-micron thick layer with N-bearing adducts, and sphingolipid and/or peptide traces. It suggests the mineralization of at least five microbial preserved entities with different metabolic capabilities, including: (1) Acidiphilium/Tessaracoccus-like phosphate mineralizers, (2) microbial patches preserving phosphate-free acylglycerides bacteria, (3) nitrogen oxidizing bacteria (e.g., Acidovorax sp.), (4) traces of heterotrophic ammonifying bacteria, and (5) sphingolipid bearing bacteria (e.g., Sphingomonadales, and δ-Proteobacteria) and/or mineralized biofilms. The primary biooxidation process acted as a preservation mechanism to release the inorganic ions that ultimately mineralized the microbial structures.
Habitats Are More Important Than Seasons in Shaping Soil Bacterial Communities on the Qinghai-Tibetan Plateau
Authors: Wang Rui , Wang Miao , Wang Jing , Lin Yinghua
Published: July 2021

Both habitats and seasons can determine the dynamics of microbial communities, but the relative importance of different habitats and seasonal changes in shaping the soil bacterial community structures on a small spatial scale in permafrost areas remains controversial. In this study, we explored the relative effect of four typical alpine meadow habitats (swamp wetland, swamp meadow, meadow and mature meadow) versus seasons on soil bacterial communities based on samples from the Qinghai-Tibetan Plateau in four months (March, May, July and September). The results showed that habitats, rather than seasons explained more variation of soil bacterial composition and structure. Environmental cofactors explained the greatest proportion of bacterial variation observed and can help elucidate the driving force of seasonal changes and habitats on bacterial communities. Soil temperature played the most important role in shaping bacterial beta diversities, followed by soil total nitrogen and pH. A group of microbial biomarkers, used as indicators of different months, were identified using random forest modeling, and for which relative abundance was shaped by different environmental factors. Furthermore, seasonality in bacterial co-occurrence patterns was observed. The data showed that co-occurrence relationships changed over months. The inter-taxa connections in May and July were more pronounced than that in March and September. Bryobacter, a genus of subgroup_22 affiliated to Acidobacteria, and Pseudonocardia belonging to Actinobacteria were observed as the keystone taxa in different months in the network. These results demonstrate that the bacterial community was clustered according to the seasonal mechanism, whereas the co-occurrence relationships changed over months, which indicated complex bacterial dynamics in a permafrost grassland on the eastern edge of Qinghai-Tibetan.
Decontamination Strategies Used for AFB Culture Significantly Reduce the Viability of Mycobacterium abscessus Complex in Sputum Samples from Patients with Cystic Fibrosis
Authors: Stephenson Dominic , Perry Audrey , Nelson Andrew , Robb Ali E. , Thomas Matthew F. , Bourke Stephen J. , Perry John D. , Jones Amanda L.
Published: July 2021

Nontuberculous mycobacteria are important respiratory pathogens in patients with cystic fibrosis (CF). For diagnosis, international guidelines recommend culture of sputum that has been decontaminated via chemical treatment. Fifty-six sputum samples from 32 patients known to be previously colonized or infected with NTM were subdivided, and the aliquots were subjected to six different decontamination strategies, followed by quantitative culture for NTM. Thirty sputum samples contained Mycobacterium abscessus complex (MABSC) and 11 contained Mycobacterium avium complex (MAC). Decontamination strategies included treatment with N-acetyl L-cysteine with 2% sodium hydroxide (NALC-NaOH), 4% NaOH, 1% chlorhexidine, 0.5 N sulfuric acid, 5% oxalic acid, double decontamination with NALC-NaOH, followed by 5% oxalic acid, and saline (0.85%) as a control. The samples were also cultured directly with no treatment. Treatment with NALC-NaOH resulted in an average reduction in colony count of 87% for MABSC when compared with direct culture. NaOH at 4% caused a 98.3% average reduction in colony count. All treatments that included NaOH resulted in colony counts that were statistically lower than those obtained from direct culture or the saline-treated control (p < 0.05). Standard treatments using sulfuric or oxalic acids were less deleterious, but still resulted in an average reduction in colony count of at least 30%. The viability of MAC was much less affected by most decontamination treatments. In conclusion, the viability of MABSC was severely compromised by standard decontamination regimens. This supports recent evidence showing that optimal recovery of MABSC is achieved by culture on an appropriate selective agar without decontamination of sputum samples.
Increasing Phosphorus Uptake Efficiency by Phosphorus-Starved Microalgae for Municipal Wastewater Post-Treatment
Authors: Lavrinovičs Aigars , Murby Fredrika , Zīverte Elīna , Mežule Linda , Juhna Tālis
Published: July 2021

Four microalgal species, Chlorella vulgaris, Botryococcus braunii, Ankistrodesmus falcatus, and Tetradesmus obliquus were studied for enhanced phosphorus removal from municipal wastewater after their exposure to phosphorus starvation. Microalgae were exposed to phosphorus starvation conditions for three and five days and then used in a batch experiment to purify an effluent from a small WWTP. After 3-day P-starvation, C. vulgaris biomass growth rate increased by 50% and its PO4 removal rate reached > 99% within 7 days. B. braunii maintained good biomass growth rate and nutrient removal regardless of the P-starvation. All species showed 2–5 times higher alkaline phosphatase activity increase for P-starved biomass than at the reference conditions, responding to the decline of PO4 concentration in wastewater and biomass poly-P content. The overall efficiency of biomass P-starvation on enhanced phosphorus uptake was found to be dependent on the species, N/P molar ratio in the wastewater, as well as the biomass P content.
Current and Future Antiviral Strategies to Tackle Gastrointestinal Viral Infections
Authors: Santos-Ferreira Nanci , Van Dycke Jana , Neyts Johan , Rocha-Pereira Joana
Published: July 2021

Acute gastroenteritis caused by virus has a major impact on public health worldwide in terms of morbidity, mortality, and economic burden. The main culprits are rotaviruses, noroviruses, sapoviruses, astroviruses, and enteric adenoviruses. Currently, there are no antiviral drugs available for the prevention or treatment of viral gastroenteritis. Here, we describe the antivirals that were identified as having in vitro and/or in vivo activity against these viruses, originating from in silico design or library screening, natural sources or being repurposed drugs. We also highlight recent advances in model systems available for this (hard to cultivate) group of viruses, such as organoid technologies, and that will facilitate antiviral studies as well as fill some of current knowledge gaps that hamper the development of highly efficient therapies against gastroenteric viruses.
Colonization with Altered Schaedler Flora Impacts Leukocyte Adhesion in Mesenteric Ischemia-Reperfusion Injury
Authors: Bayer Franziska , Ascher Stefanie , Kiouptsi Klytaimnistra , Kittner Jens M. , Stauber Roland H. , Reinhardt Christoph
Published: July 2021

The microbiota impacts mesenteric ischemia-reperfusion injury, aggravating the interaction of leukocytes with endothelial cells in mesenteric venules. The role of defined gut microbiomes in this life-threatening pathology is unknown. To investigate how a defined model microbiome affects the adhesion of leukocytes in mesenteric ischemia-reperfusion, we took advantage of gnotobiotic isolator technology and transferred altered Schaedler flora (ASF) from C3H/HeNTac to germ-free C57BL/6J mice. We were able to detect all eight bacterial taxa of ASF in fecal samples of colonized C57BL/6J mice by PCR. Applying qRT-PCR for quantification of species-specific 16S rDNA sequences of ASF bacteria, we found a major shift in the abundance of ASF 500, which was greater in C57BL/6J mice relative to the C3H/HeNTac founder breeding pair. Using high-speed epifluorescence intravital microscopy to visualize the venules of the small bowel mesentery, we found that gnotobiotic ASF-colonized mice showed reduced leukocyte adherence, both pre- and post-ischemia. Relative to germ-free mice, the counts of adhering leukocytes were increased pre-ischemia but did not significantly increase in ASF-colonized mice in the post-ischemic state. Collectively, our results suggest a protective role of the minimal microbial consortium ASF in mesenteric ischemia-reperfusion injury.
Surface Properties of Parabacteroides distasonis and Impacts of Stress-Induced Molecules on Its Surface Adhesion and Biofilm Formation Capacities
Authors: Chamarande Jordan , Cunat Lisiane , Caillet Céline , Mathieu Laurence , Duval Jérôme F. L. , Lozniewski Alain , Frippiat Jean-Pol , Alauzet Corentine , Cailliez-Grimal Catherine
Published: July 2021

The gut microbiota is a complex and dynamic ecosystem whose balance and homeostasis are essential to the host’s well-being and whose composition can be critically affected by various factors, including host stress. Parabacteroides distasonis causes well-known beneficial roles for its host, but is negatively impacted by stress. However, the mechanisms explaining its maintenance in the gut have not yet been explored, in particular its capacities to adhere onto (bio)surfaces, form biofilms and the way its physicochemical surface properties are affected by stressing conditions. In this paper, we reported adhesion and biofilm formation capacities of 14 unrelated strains of P. distasonis using a steam-based washing procedure, and the electrokinetic features of its surface. Results evidenced an important inter-strain variability for all experiments including the response to stress hormones. In fact, stress-induced molecules significantly impact P. distasonis adhesion and biofilm formation capacities in 35% and 23% of assays, respectively. This study not only provides basic data on the adhesion and biofilm formation capacities of P. distasonis to abiotic substrates but also paves the way for further research on how stress-molecules could be implicated in P. distasonis maintenance within the gut microbiota, which is a prerequisite for designing efficient solutions to optimize its survival within gut environment.
Association of Skin Microbiome with the Onset and Recurrence of Pressure Injury in Bedridden Elderly People
Authors: Okamoto Shigefumi , Ogai Kazuhiro , Mukai Kanae , Sugama Junko
Published: July 2021

Pressure injuries have been identified as one of the main health hazards among bedridden elderly people. Bedridden elderly people often stay in the same position for a long time, because they cannot switch positions; thus, the blood flow in the part of the body that is being compressed between the bed and their own weight is continuously blocked. As a result, redness and ulcers occur due to lacking oxygen and nutrients in the skin tissues, and these sites are often infected with microorganisms and, thus, become suppurative wounds, a condition commonly determined as pressure injuries. If left untreated, the pressure injury will recur with microbial infections, often resulting in cellulitis, osteomyelitis, and sepsis. The skin microbiome, in which many types of bacteria coexist, is formed on the skin surface. However, it remains unclear what characteristic of the skin microbiome among the bedridden elderly constitutes the development and severity of pressure injuries and the development of post-pressure injury infections. Thus, in this review article, we outlined the changes in the skin microbiome among the bedridden elderly people and their potential involvement in the onset and recurrence of pressure injuries.
Lipemia in the Plasma Sample Affects Fentanyl Measurements by Means of HPLC-MS2 after Liquid-Liquid Extraction
Authors: Tikhomirov Marta , Śniegocki Tomasz , Poźniak Błażej
Published: July 2021

Examination of fentanyl levels is frequently performed in certain scientific evaluations and forensic toxicology. It often involves the collection of very variable blood samples, including lipemic plasma or serum. To date, many works have reported the methods for fentanyl detection, but none of them have provided information about the impact on the assay performance caused by an excessive amount of lipids. This aspect may be, however, very important for highly lipophilic drugs like fentanyl. To address this issue, we developed the liquid chromatography method with mass spectrometry detection and utilized it to investigate the impact of lipids presence in rabbit plasma on the analytical method performance and validation. The validation procedure, conducted for normal plasma and lipemic plasma separately, resulted in good selectivity, sensitivity and linearity. The limits of detection and quantification were comparable between the two matrices, being slightly lower in normal plasma (0.005 and 0.015 µg/L) than in lipemic plasma (0.008 and 0.020 µg/L). Liquid–liquid extraction provided a low matrix effect regardless of the lipid levels in the samples (<10%), but pronounced differences were found in the recovery and accuracy. In the normal plasma, this parameter was stable and high (around 100%), but in the lipemic matrix, much more variable and less efficient results were obtained. Nevertheless, this difference had no impact on repeatability and reproducibility. In the present work, we provided reliable, convenient and sensitive method for fentanyl detection in the normal and lipemic rabbit plasma. However, construction of two separate validation curves was necessary to provide adequate results since the liquid-liquid extraction was utilized. Therefore, special attention should be paid during fentanyl quantification that involves lipemic plasma samples purified by this technique.