bluuebunny/crossref_metadata_2025 huggingface dataset:
Toward Accurate and Robust Environmental Surveillance Using Metagenomics
Authors: Shen Jiaxian , McFarland Alexander G. , Young Vincent B. , Hayden Mary K. , Hartmann Erica M.
Published: March 2021

Environmental surveillance is a critical tool for combatting public health threats represented by the global COVID-19 pandemic and the continuous increase of antibiotic resistance in pathogens. With its power to detect entire microbial communities, metagenomics-based methods stand out in addressing the need. However, several hurdles remain to be overcome in order to generate actionable interpretations from metagenomic sequencing data for infection prevention. Conceptually and technically, we focus on viability assessment, taxonomic resolution, and quantitative metagenomics, and discuss their current advancements, necessary precautions and directions to further development. We highlight the importance of building solid conceptual frameworks and identifying rational limits to facilitate the application of techniques. We also propose the usage of internal standards as a promising approach to overcome analytical bottlenecks introduced by low biomass samples and the inherent lack of quantitation in metagenomics. Taken together, we hope this perspective will contribute to bringing accurate and consistent metagenomics-based environmental surveillance to the ground.
Needs and Gaps in Optical Underwater Technologies and Methods for the Investigation of Marine Animal Forest 3D-Structural Complexity
Authors: Rossi Paolo , Ponti Massimo , Righi Sara , Castagnetti Cristina , Simonini Roberto , Mancini Francesco , Agrafiotis Panagiotis , Bassani Leonardo , Bruno Fabio , Cerrano Carlo , Cignoni Paolo , Corsini Massimiliano , Drap Pierre , Dubbini Marco , Garrabou Joaquim , Gori Andrea , Gracias Nuno , Ledoux Jean-Baptiste , Linares Cristina , Mantas Torcuato Pulido , Menna Fabio , Nocerino Erica , Palma Marco , Pavoni Gaia , Ridolfi Alessandro , Rossi Sergio , Skarlatos Dimitrios , Treibitz Tali , Turicchia Eva , Yuval Matan , Capra Alessandro
Published: March 2021

Marine animal forests are benthic communities dominated by sessile suspension feeders (such as sponges, corals, and bivalves) able to generate three-dimensional (3D) frameworks with high structural complexity. The biodiversity and functioning of marine animal forests are strictly related to their 3D complexity. The present paper aims at providing new perspectives in underwater optical surveys. Starting from the current gaps in data collection and analysis that critically limit the study and conservation of marine animal forests, we discuss the main technological and methodological needs for the investigation of their 3D structural complexity at different spatial and temporal scales. Despite recent technological advances, it seems that several issues in data acquisition and processing need to be solved, to properly map the different benthic habitats in which marine animal forests are present, their health status and to measure structural complexity. Proper precision and accuracy should be chosen and assured in relation to the biological and ecological processes investigated. Besides, standardized methods and protocols are strictly necessary to meet the FAIR (findability, accessibility, interoperability, and reusability) data principles for the stewardship of habitat mapping and biodiversity, biomass, and growth data.
Sol-Gel Thin Film Processing for Integrated Waveguide Sensors
Authors: Alberti Sebastián , Jágerská Jana
Published: March 2021

Integrated opto-chemical sensors present great advantages in comparison to the current lab equipment. They bring portability, reduced costs, facilitate in-situ measurements, as well as largely reduced sample volumes. In this quest, standard processing protocols over established materials, such as silicon nitride, silicon, silicon dioxide, titanium oxide, and even a wide variety of polymers have so far been the key toward on-chip devices. However, if very specific materials in terms of composition and tailored properties are required, the deposition via a solution represents a viable alternative. In this review, we highlight the role of sol-gel chemistry and top-down processing of sol-gel thin film layers in the design of waveguide-based optical sensors. In particular, we stress the advantages of porous sol-gel based materials as a new approach to increase sensitivity and selectivity, first when used as claddings, and, more recently, as waveguides with enhanced light–analyte interaction. We finally discuss the future perspectives of such devices to increase specificity in complex matrices, which is of utmost importance for bio-sensing.
Management of Staphylococcus aureus Bloodstream Infections
Authors: Kimmig Aurelia , Hagel Stefan , Weis Sebastian , Bahrs Christina , Löffler Bettina , Pletz Mathias W.
Published: March 2021

Staphylococcus aureus bloodstream infections are associated with a high morbidity and mortality. Nevertheless, significance of a positive blood culture with this pathogen is often underestimated or findings are misinterpreted as contamination, which can result in inadequate diagnostic and therapeutic consequences. We here review and discuss current diagnostic and therapeutic key elements and open questions for the management of Staphylococcus aureus bloodstream infections.
The Added Value of Bloodpool SPECT/CT in Painful Non-Operated Foot and Ankle Undiagnosed With Standard Three-Phase Bone Scintigraphy
Authors: Cuvilliers Cécile , Palard-Novello Xavier , Pontoizeau Clémence , Meneret Pierre , Devillers Anne , Le Jeune Florence , Girard Antoine
Published: March 2021

Purpose: To evaluate the interest of adding a bloodpool SPECT/CT to standard three-phase bone scintigraphy (BS) for etiological diagnosis of subacute and chronic lower extremity pains.

Methods: We prospectively included patients addressed for pain of lower extremities lasting for at least 6 weeks, without previous surgery. They underwent a standard three-phase BS including late phase SPECT/CT, modified with an additional bloodpool SPECT/CT acquisition. Two independent physicians interpreted the images provided by both protocols. Diagnostic conclusion, diagnostic confidence, and interrater agreements were compared.

Results: One hundred and eighteen lower extremities from 113 patients were analyzed (71 men, median age of 53 years). Adding bloodpool SPECT/CT to standard three-phase BS changed diagnostic conclusions in 24.6% (29/118) of lower extremities. The modified protocol revealed at least one diagnostic conclusion explaining the pain in 89% of extremities, rather than 83.1% with the standard protocol (p = 0.02). Tendinopathies were diagnosed in 12.7% of lower extremities, rather than 4.2% with standard BS (p = 0.002). Adding bloodpool SPECT/CT substantially increased overall confidence of each reader (p < 0.001). Inter-reader agreement was not significantly impacted.

Conclusion: Adding bloodpool SPECT/CT to standard three-phase BS impacted diagnostic conclusion in a quarter of the patients with painful lower extremities, notably by revealing significantly more tendonitis.
Bio-Active Free Direct Optical Sensing of Aflatoxin B1 and Ochratoxin A Using a Manganese Oxide Nano-System
Authors: Singh Avinash Kumar , Lakshmi G. B. V. S. , Dhiman Tarun Kumar , Kaushik Ajeet , Solanki Pratima R.
Published: March 2021

Aflatoxins-B1 (AFB1) and Ochratoxin-A (OchA) are the two types of major mycotoxin produced by Aspergillus flavus, Aspergillus parasiticus fungi, Aspergillus carbonarius, Aspergillus niger, and Penicillium verrocusumv. These toxins are mainly found in metabolite cereals, corn, coffee beans, and other oil-containing food items. Excessive consumption of these toxins can be carcinogenic and lead to cancer. Thus, their rapid testing became essential for food quality control. Herein, manganese oxide nanoparticles (MnO2 nps) have been proposed to explore the interaction with AFB1 and OchA using UV-visible spectroscopy. MnO2 nps were synthesized using the co-precipitation method. They were pure and crystalline with an average crystallite size of 5–6 nm. In the UV-vis study, the maximum absorbance for MnO2 nps was observed around 260 nm. The maximum absorbance for AFB1 and OchA was observed at 365 and 380 nm, respectively, and its intensity enhanced with the addition of MnO2 nps. Sequential changes were observed with varying the concentration of AFB1 and OchA with a fixed concentration of MnO2 nps, resulting in proper interaction. The binding constant (kb) and Gibbs free energy for MnO2 nps-AFB1 and OchA were observed as 1.62 × 104 L g−1 and 2.67 × 104 L g−1, and −24.002 and −25.256 kJ/mol, respectively. The limit of detection for AFB1 and OchA was measured as 4.08 and 10.84 ng/ml, respectively. This bio‐active free direct sensing approach of AFB1 and OchA sensing can be promoted as a potential analytical tool to estimate food quality rapidly and affordable manner at the point of use.
Modeling of Astrocyte Networks: Toward Realistic Topology and Dynamics
Authors: Verisokin Andrey Yu. , Verveyko Darya V. , Postnov Dmitry E. , Brazhe Alexey R.
Published: March 2021

Neuronal firing and neuron-to-neuron synaptic wiring are currently widely described as orchestrated by astrocytes—elaborately ramified glial cells tiling the cortical and hippocampal space into non-overlapping domains, each covering hundreds of individual dendrites and hundreds thousands synapses. A key component to astrocytic signaling is the dynamics of cytosolic Ca2+ which displays multiscale spatiotemporal patterns from short confined elemental Ca2+ events (puffs) to Ca2+ waves expanding through many cells. Here, we synthesize the current understanding of astrocyte morphology, coupling local synaptic activity to astrocytic Ca2+ in perisynaptic astrocytic processes and morphology-defined mechanisms of Ca2+ regulation in a distributed model. To this end, we build simplified realistic data-driven spatial network templates and compile model equations as defined by local cell morphology. The input to the model is spatially uncorrelated stochastic synaptic activity. The proposed modeling approach is validated by statistics of simulated Ca2+ transients at a single cell level. In multicellular templates we observe regular sequences of cell entrainment in Ca2+ waves, as a result of interplay between stochastic input and morphology variability between individual astrocytes. Our approach adds spatial dimension to the existing astrocyte models by employment of realistic morphology while retaining enough flexibility and scalability to be embedded in multiscale heterocellular models of neural tissue. We conclude that the proposed approach provides a useful description of neuron-driven Ca2+-activity in the astrocyte syncytium.
Development of a Machine Learning Model for Optimal Applicator Selection in High-Dose-Rate Cervical Brachytherapy
Authors: Stenhouse Kailyn , Roumeliotis Michael , Ciunkiewicz Philip , Banerjee Robyn , Yanushkevich Svetlana , McGeachy Philip
Published: March 2021

Purpose

To develop and validate a preliminary machine learning (ML) model aiding in the selection of intracavitary (IC) versus hybrid interstitial (IS) applicators for high-dose-rate (HDR) cervical brachytherapy.

Methods

From a dataset of 233 treatments using IC or IS applicators, a set of geometric features of the structure set were extracted, including the volumes of OARs (bladder, rectum, sigmoid colon) and HR-CTV, proximity of OARs to the HR-CTV, mean and maximum lateral and vertical HR-CTV extent, and offset of the HR-CTV centre-of-mass from the applicator tandem axis. Feature selection using an ANOVA F-test and mutual information removed uninformative features from this set. Twelve classification algorithms were trained and tested over 100 iterations to determine the highest performing individual models through nested 5-fold cross-validation. Three models with the highest accuracy were combined using soft voting to form the final model. This model was trained and tested over 1,000 iterations, during which the relative importance of each feature in the applicator selection process was determined.

Results

Feature selection indicated that the mean and maximum lateral and vertical extent, volume, and axis offset of the HR-CTV were the most informative features and were thus provided to the ML models. Relative feature importances indicated that the HR-CTV volume and mean lateral extent were most important for applicator selection. From the comparison of the individual classification algorithms, it was found that the highest performing algorithms were tree-based ensemble methods – AdaBoost Classifier (ABC), Gradient Boosting Classifier (GBC), and Random Forest Classifier (RFC). The accuracy of the individual models was compared to the voting model for 100 iterations (ABC = 91.6 ± 3.1%, GBC = 90.4 ± 4.1%, RFC = 89.5 ± 4.0%, Voting Model = 92.2 ± 1.8%) and the voting model was found to have superior accuracy. Over the final 1,000 evaluation iterations, the final voting model demonstrated a high predictive accuracy (91.5 ± 0.9%) and F1 Score (90.6 ± 1.1%).

Conclusion

The presented model demonstrates high discriminative performance, highlighting the potential for utilization in informing applicator selection prospectively following further clinical validation.
The National Children's Study Archive Model: A 3-Tier Framework for Dissemination of Data and Specimens for General Use and Secondary Analysis
Authors: Gilbertson Peter K. , Forrester Susan , Andrews Linda , McCann Kathleen , Rogers Lydia , Park Christina , Moye Jack
Published: March 2021

The National Children's Study (NCS) Archive was created as a repository of samples, data, and information from the NCS Vanguard Study—a longitudinal pregnancy and birth cohort evaluating approaches to study influence of environmental exposures on child health and development—to provide qualified researchers with access to NCS materials for use in secondary research. The National Children's Study Archive (NCSA) model is a 3-tiered access model designed to make the wealth of information and materials gathered during the NCS Vanguard Study available at a user appropriate level. The NCSA model was developed as a 3-tier framework, for users of varying access levels, providing intuitive data exploration and visualization tools, an end-to-end data and sample request management system, and a restricted portal for participant-level data access with a team of experts available to assist users. This platform provides a model to accelerate transformation of information and materials from existing studies into new scientific discoveries.

Trial Registration:ClinicalTrials.gov Identifier: NCT00852904 (first posted February 27, 2009).
Perchloroethylene and Dry Cleaning: It's Time to Move the Industry to Safer Alternatives
Authors: Ceballos Diana M. , Fellows Katie M. , Evans Ashley E. , Janulewicz Patricia A. , Lee Eun Gyung , Whittaker Stephen G.
Published: March 2021

Perchloroethylene (PERC) is the most common solvent used for dry cleaning in the United States. PERC is a reproductive toxicant, neurotoxicant, potential human carcinogen, and a persistent environmental pollutant. The Environmental Protection Agency is evaluating PERC under the Frank R. Lautenberg Chemical Safety for the 21st Century Act, which amended the Toxic Substances Control Act (amended TSCA), and has mandated that PERC dry cleaning machines be removed from residential buildings. Some local and state programs are also requiring or facilitating transitions to alternative cleaning technologies. However, the potential for these alternatives to harm human health and the environment is not well-understood. This review describes the issues surrounding the use of PERC and alternative solvents for dry cleaning while highlighting the lessons learned from a local government program that transitioned PERC dry cleaners to the safest current alternative: professional wet cleaning. Implications for future public health research and policy are discussed: (1) we must move away from PERC, (2) any transition must account for the economic instability and cultural aspects of the people who work in the industry, (3) legacy contamination must be addressed even after safer alternatives are adopted, and (4) evaluations of PERC alternatives are needed to determine their implications for the long-term health and sustainability of the people who work in the industry.
Deployable Telescopic Tubular Mechanisms With a Steerable Tongue Depressor Towards Self-Administered Oral Swab
Authors: Kumar Kirthika Senthil , Nguyen Tuan Dung , Kalairaj Manivannan Sivaperuman , Hema Vishnu Mani , Cai Catherine Jiayi , Huang Hui , Lim Chwee Ming , Ren Hongliang
Published: March 2021

Swabbing tests have proved to be an effective method of diagnosis for a wide range of diseases. Potential occupational health hazards and reliance on healthcare workers during traditional swabbing procedures can be mitigated by self-administered swabs. Hence, we report possible methods to apply closed kinematic chain theory to develop a self-administered viral swab to collect respiratory specimens. The proposed sensorized swab models utilizing hollow polypropylene tubes possess mechanical compliance, simple construction, and inexpensive components. In detail, the adaptation of the slider-crank mechanism combined with concepts of a deployable telescopic tubular mechanical system is explored through four different oral swab designs. A closed kinematic chain on suitable material to create a developable surface allows the translation of simple two-dimensional motion into more complex multi-dimensional motion. These foldable telescopic straws with multiple kirigami cuts minimize components involved in the system as the characteristics are built directly into the material. Further, it offers a possibility to include soft stretchable sensors for realtime performance monitoring. A variety of features were constructed and tested using the concepts above, including 1) tongue depressor and cough/gag reflex deflector; 2) changing the position and orientation of the oral swab when sample collection is in the process; 3) protective cover for the swabbing bud; 4) a combination of the features mentioned above.
Severe Periodontitis and Biomarkers of Bacterial Burden. Results From a Case-Control and Intervention Clinical Trial
Authors: Leira Yago , Fragkiskos Dimitrios , Orlandi Marco , Suvan Jeanie , Nibali Luigi , Tonetti Maurizio S. , Belibasakis Georgios N. , Bostanci Nagihan , D'Aiuto Francesco
Published: March 2021

Background and aims: Periodontitis is an inflammatory-infectious disease. Identifying markers of systemic exposure of periodontitis might be of interest to study its interaction with other conditions. Soluble triggering receptor expressed on myeloid cells 1 (sTREM-1) is upregulated during bacterial infections. Our aim was therefore to investigate whether periodontitis and its treatment are associated with bacterial endotoxin and sTREM-1.

Methods: Fifty patients with severe periodontitis and 50 age-matched controls were included in a case-control study (all never smokers). A secondary analysis of a previously published intervention study was performed, in which included 69 patients with severe periodontitis were randomized to receive either intensive (IPT) or control periodontal therapy (CPT) and monitored over 6 months. Serum levels of bacterial endotoxin and sTREM-1 were determined at one time point (case-control study) and at baseline, 1 day, 1 and 6 months after periodontal treatment (intervention study).

Results: Severe periodontitis was associated with elevated circulating endotoxin levels when cases (22.9 ± 2.2 EU/ml) were compared to controls (3.6 ± 0.5 EU/ml, p < 0.001) and with sTREM-1 levels (1302.6 ± 47.8 vs. 870.6 ± 62.0 pg/ml, p < 0.001). A positive correlation was observed between sTREM-1 and endotoxin levels (r = 0.4, p < 0.001). At 6 months after treatment, IPT significantly decreased serum levels of sTREM-1 compared to CPT (adjusted mean difference of 500.2 pg/ml, 95% CI: 18.9–981.4; p = 0.042). No substantial differences were noted in endotoxin levels at any time point after treatment between groups.

Conclusions: Severe periodontitis is linked to increased circulating endotoxin and sTREM-1 levels and following IPT a reduction in sTREM-1 levels is observed.
The NASA High-Resolution Speckle Interferometric Imaging Program: Validation and Characterization of Exoplanets and Their Stellar Hosts
Authors: Howell Steve B. , Scott Nicholas J. , Matson Rachel A. , Everett Mark E. , Furlan Elise , Gnilka Crystal L. , Ciardi David R. , Lester Kathryn V.
Published: March 2021

Starting in 2008, NASA has provided the exoplanet community an observational program aimed at obtaining the highest resolution imaging available as part of its mission to validate and characterize exoplanets, as well as their stellar environments, in search of life in the Universe. Our current program uses speckle interferometry in the optical (320–1,000 nm) with new instruments on the 3.5-m WIYN and both 8-m Gemini telescopes. Starting with Kepler and K2 follow-up, we now support TESS and other space- and ground-based exoplanet related discovery and characterization projects. The importance of high-resolution imaging for exoplanet research comes via identification of nearby stellar companions that can dilute the transit signal and confound derived exoplanet and stellar parameters. Our observations therefore provide crucial information allowing accurate planet and stellar properties to be determined. Our community program obtains high-resolution imagery, reduces the data, and provides all final data products, without any exclusive use period, to the community via the Exoplanet Follow-Up Observation Program (ExoFOP) website maintained by the NASA Exoplanet Science Institute. This paper describes the need for high-resolution imaging and gives details of the speckle imaging program, highlighting some of the major scientific discoveries made along the way.
Native Grasslands at the Core: A New Paradigm of Intensification for the Campos of Southern South America to Increase Economic and Environmental Sustainability
Authors: Jaurena Martín , Durante Martín , Devincenzi Thais , Savian Jean V. , Bendersky Diego , Moojen Fernanda G. , Pereira Marcelo , Soca Pablo , Quadros Fernando L. F. , Pizzio Rafael , Nabinger Carlos , Carvalho Paulo C. F. , Lattanzi Fernando A.
Published: March 2021

Extensive livestock production in southern South America occupies ~0.5 M km2in central-eastern Argentina, Uruguay and southern Brazil. These systems have been sustained for more than 300 years by year-long grazing of the highly biodiverse native Campos ecosystems that provides many valuable additional ecosystem services. However, their low productivity (~70 kg liveweight/ha per year), at least relative to values recorded in experiments and by best farmers, has been driving continued land use conversion towards agriculture and forestry. Therefore, there is a pressing need for usable, cost effective technological options based on scientific knowledge that increase profitability while supporting the conservation of native grasslands. In the early 2000s, existing knowledge was synthesized in a path of six sequential steps of increasing intensification. Even though higher productivity underlined that path, it was recognized that trade-offs would occur, with increases in productivity being concomitant to reductions in diversity, resilience to droughts, and a higher exposure to financial risks. Here, we put forward a proposal to shift the current paradigm away from a linear sequence and toward a flexible dashboard of intensification options to be implemented in defined modules within a farm whose aims are (i) to maintain native grasslands as the main feed source, and (ii) ameliorate its two major productive drawbacks: marked seasonality and relatively rapid loss of low nutritive value-hence the title “native grasslands at the core.” At its center, the proposal highlights a key role for optimal grazing management of native grasslands to increase productivity and resilience while maintaining low system wide costs and financial risk, but acknowledges that achieving the required spatio-temporal control of grazing intensity requires using (a portfolio of) complementary, synergistic intensification options. We sum up experimental evidence and case studies supporting the hypothesis that integrating intensification options increases both profitability and environmental sustainability of livestock production in Campos ecosystems.
Soft Hybrid Suction Cup Capable of Sticking to Various Objects and Environments
Authors: Tsukagoshi Hideyuki , Osada Yuichi
Published: March 2021

A universal suction cup that can stick to various objects expands the areas in which robots can work. However, the size, shape, and surface roughness of objects to which conventional suction cups can stick are limited. To overcome this challenge, we propose a new hybrid suction cup structure that uses the adhesive force of sticky gel and the suction force of negative pressure. In addition, a flexible and thin pneumatic balloon actuator with a check valve function is installed in the interior, enabling the controllable detachment from objects. The prototype has an outer diameter of 55 mm, a weight of 18.8 g, and generates an adsorption force of 80 N in the vertical direction and 60 N in the shear direction on porous walls where conventional suction cups struggle to adsorb. We confirmed that parts smaller than the suction cup and fragile potato chips are adsorbed by the prototype. Finally, the effectiveness of the proposed method is verified through experiments in which a drone with the prototypes can be attached to and detached from concrete walls and ceilings while flying; the possibility of adsorption to dusty and wet plates is discussed.
Development of a Novel Deployable Solar Panel and Mechanism for 6U CubeSat of STEP Cube Lab-II
Authors: Bhattarai Shankar , Go Ji-Seong , Kim Hongrae , Oh Hyun-Ung
Published: March 2021

The structural safety of solar cells mounted on deployable solar panels in the launch vibration environment is a significant aspect of a successful CubeSat mission. This paper presents a novel highly damped deployable solar panel module that is effective in ensuring structural protection of solar cells under the launch environment by rapidly suppressing the vibrations transmitting through the solar panel by constrained layer damping achieved using printed circuit board (PCB)-based multilayered thin stiffeners with double-sided viscoelastic tapes. A high-damping solar panel demonstration model with a three-pogo pin-based burn wire release mechanism was fabricated and tested for application in the 6U CubeSat “STEP Cube Lab-II” developed by Chosun University, South Korea. The reliable release function and radiation hardness assurance of the mechanism in an in-orbit environment were confirmed by performing solar panel deployment tests and radiation tests, respectively. The design effectiveness and structural safety of the proposed solar panel module were validated by launch vibration and in-orbit environment tests at the qualification level.
Absorption and Elimination of the Allelochemical MBOA by Weeds during Seedling Growth
Authors: Oliveros-Bastidas Alberto , Molinillo José M. G. , Macias Francisco A. , Chinchilla Nuria
Published: March 2021

6-Methoxy-2-benzoxazolinone (MBOA) is an allelochemical that is found in Poaceae and is generally associated with monocotyledon species. This compound is formed from the glycosylated form of 2,4-dihydroxy-(2H)-1,4-benzoxazin-3(4H)-one (Gly-DIMBOA) by a two-stage degradation process. The MBOA detoxification capacity of two weed species, namely Echinochloa crus-galli and Lolium rigidum, and a resistant biotype of Lolium rigidum (SLR31) was studied both qualitatively and quantitatively. The product of metabolism is similar for both weed species. This finding indicates that these weeds probably metabolize xenobiotics by an identical route, since the product detected was the same in both cases. Kinetic studies on the absorption and translocation to the shoot showed differences in these processes depending on the species. The analysis of treated plants, which were subsequently transplanted to a growth medium without xenobiotic compound, showed that the weeds studied are capable of transmitting the previously absorbed compound to the medium by root exudation. The results show that this process is another defense mechanism of plants facing external threats.
Principles and Prospects of Prunus Cultivation in Greenhouse
Authors: Martínez-Gómez Pedro , Rahimi Devin Sama , Salazar Juan A. , López-Alcolea Jesús , Rubio Manuel , Martínez-García Pedro J.
Published: March 2021

Throughout history, new strategies and technologies have played a key role in promoting the development of agriculture. New strategies have led to substantial improvements in crop productivity and fruit quality. The cultivation of peach and apricot in controlled greenhouse conditions is one such strategy. The aim of the protected cultivation of these species in greenhouses is to grow fruit trees by modifying the natural environment of the tree, including the harvest duration, which can be extended. This protected cultivation should improve yield, thus increasing the benefit–cost ratio, especially in the case of organic production. Here we review the main factors involved in greenhouse fruit tree cultivation, including the planting systems and substrate, cultivar and rootstock selection, pollination management, orchard management, and environmental management. Greenhouse cultivation makes it possible to control environmental conditions like wind speed, moisture, temperature, mineral nutrients, light intensity, and the atmospheric composition, and thus gives us a better understanding of growth factor requirements, and the means to improve fruit productivity. A protected environment has been shown to be effective in maintaining a relatively high temperature and preventing leaf injury due to environmental factors, resulting in a longer period of photosynthetic activity, which increases the photosynthetic production, and is therefore a suitable alternative strategy for production in cold regions. The main benefits of apricot and peach cultivation in greenhouses are: (1) precocity; (2) high fruit quality, storage life, and market proximity; and (3) good plant health, suitable for organic cultivation. However, the main limiting factors for fruit tree production in greenhouse conditions to take into account are: (1) light scarcity at high latitudes; (2) a lack of cold for bud breaking, flowering, and fruit production; (3) potentially excessive temperatures in warm regions, which reduce the photosynthesis rate; and (4) a reduction of fruit quality, coloring, and aroma compounds in certain warm conditions with light day/night temperature variations.
Kaolin Application Modulates Grapevine Photochemistry and Defence Responses in Distinct Mediterranean-Type Climate Vineyards
Authors: Bernardo Sara , Luzio Ana , Machado Nelson , Ferreira Helena , Vives-Peris Vicente , Malheiro Aureliano C. , Correia Carlos , Gómez-Cadenas Aurelio , Moutinho-Pereira José , Dinis Lia-Tânia
Published: March 2021

At a local scale, kaolin particle-film technology is considered a short-term adaptation strategy to mitigate the adverse effects of global warming on viticulture. This study aims to evaluate kaolin application effects on photochemistry and related defence responses of Touriga Franca (TF) and Touriga Nacional (TN) grapevines planted at two Portuguese winegrowing regions (Douro and Alentejo) over two summer seasons (2017 and 2018). For this purpose, chlorophyll a fluorescence transient analysis, leaf temperature, foliar metabolites, and the expression of genes related to heat stress (VvHSP70) and stress tolerance (VvWRKY18) were analysed. Kaolin application had an inhibitory effect on VvHSP70 expression, reinforcing its protective role against heat stress. However, VvWRKY18 gene expression and foliar metabolites accumulation revealed lower gene expression in TN-treated leaves and higher in TF at Alentejo, while lipid peroxidation levels decreased in both treated varieties and regions. The positive kaolin effect on the performance index parameter (PIABS) increased at ripening, mainly in TN, suggesting that stress responses can differ among varieties, depending on the initial acclimation to kaolin treatment. Moreover, changes on chlorophyll fluorescence transient analysis were more pronounced at the Douro site in 2017, indicating higher stress severity and impacts at this site, which boosted kaolin efficiency in alleviating summer stress. Under applied contexts, kaolin application can be considered a promising practice to minimise summer stress impacts in grapevines grown in Mediterranean-like climate regions.
I-Solar, a Real-Time Photovoltaic Simulation Model for Accurate Estimation of Generated Power
Authors: Cervera-Gascó Jorge , Montero Jesús , Moreno Miguel
Published: March 2021

Global energy consumption and costs have increased exponentially in recent years, accelerating the search for viable, profitable, and sustainable alternatives. Renewable energy is currently one of the most suitable alternatives. The high variability of meteorological conditions (irradiance, ambient temperature, and wind speed) requires the development of complex and accurate management models for the optimal performance of photovoltaic systems. The simplification of photovoltaic models can be useful in the sizing of photovoltaic systems, but not for their management in real time. To solve this problem, we developed the I-Solar model, which considers all the elements that comprise the photovoltaic system, the meteorologic conditions, and the energy demand. We have validated it on a solar pumping system, but it can be applied to any other system. The I-Solar model was compared with a simplified model and a machine learning model calibrated in a high-power and complex photovoltaic pumping system located in Albacete, Spain. The results show that the I-Solar model estimates the generated power with a relative error of 7.5%, while the relative error of machine learning models was 5.8%. However, models based on machine learning are specific to the system evaluated, while the I-Solar model can be applied to any system.
Does Leaf Waxiness Confound the Use of NDVI in the Assessment of Chlorophyll When Evaluating Genetic Diversity Panels of Wheat?
Authors: Khadka Kamal , Burt Andrew J. , Earl Hugh J. , Raizada Manish N. , Navabi Alireza
Published: March 2021

Ground and aerial-based high throughput phenotyping platforms (HTPPs) to evaluate chlorophyll-related traits have been utilized to predict grain yield in crops including wheat (Triticum aestivum L.). This study evaluated chlorophyll-related and other physiological and yield traits in a panel of 318 Nepali spring wheat genotypes, termed the Nepali Wheat Diversity Panel (NWDP). Field experiments were conducted using an alpha-lattice design in Nepal and Canada. Chlorophyll-related traits were evaluated with a Soil Plant Analysis Development (SPAD) meter and the normalized difference vegetation index (NDVI) using a handheld GreenSeeker and an Unmanned Aerial Vehicle (UAV). Relative leaf epicuticular waxiness was recorded using visual assessments. There was a significant positive association (p < 0.001) between waxiness and SPAD-based chlorophyll estimates, and both of these traits displayed a significant positive relationship with grain yield. However, unexpectedly, NDVI derived from both GreenSeeker and UAV was negatively associated with waxiness and grain yield. The results obtained after segregating the trait means into groups based on waxiness scores and breeding history of genotypes indicated that waxiness along with precipitation could be affecting the multispectral reflectance. These results suggest that caution should be taken when evaluating a large and diverse wheat population for leaf chlorophyll using high-throughput NDVI methods.
FtsZ Interactions and Biomolecular Condensates as Potential Targets for New Antibiotics
Authors: Zorrilla Silvia , Monterroso Begoña , Robles-Ramos Miguel-Ángel , Margolin William , Rivas Germán
Published: March 2021

FtsZ is an essential and central protein for cell division in most bacteria. Because of its ability to organize into dynamic polymers at the cell membrane and recruit other protein partners to form a “divisome”, FtsZ is a leading target in the quest for new antibacterial compounds. Strategies to potentially arrest the essential and tightly regulated cell division process include perturbing FtsZ’s ability to interact with itself and other divisome proteins. Here, we discuss the available methodologies to screen for and characterize those interactions. In addition to assays that measure protein-ligand interactions in solution, we also discuss the use of minimal membrane systems and cell-like compartments to better approximate the native bacterial cell environment and hence provide a more accurate assessment of a candidate compound’s potential in vivo effect. We particularly focus on ways to measure and inhibit under-explored interactions between FtsZ and partner proteins. Finally, we discuss recent evidence that FtsZ forms biomolecular condensates in vitro, and the potential implications of these assemblies in bacterial resistance to antibiotic treatment.
Correlation between the Antibiotic Resistance Genes and Susceptibility to Antibiotics among the Carbapenem-Resistant Gram-Negative Pathogens
Authors: Abdelaziz Salma M. , Aboshanab Khaled M. , Yahia Ibrahim S. , Yassien Mahmoud A. , Hassouna Nadia A.
Published: March 2021

In this study, the correlation between the antibiotic resistance genes and antibiotic susceptibility among the carbapenem-resistant Gram-negative pathogens (CRGNPs) recovered from patients diagnosed with acute pneumonia in Egypt was found. A total of 194 isolates including Klebsiella pneumoniae (89; 46%), Escherichia coli (47; 24%) and Pseudomonas aeruginosa (58; 30%) were recovered. Of these, 34 (18%) isolates were multiple drug resistant (MDR) and carbapenem resistant. For the K. pneumoniae MDR isolates (n = 22), blaNDM (14; 64%) was the most prevalent carbapenemase, followed by blaOXA-48 (11; 50%) and blaVIM (4; 18%). A significant association (p value < 0.05) was observed between the multidrug efflux pump (AcrA) and resistance to β-lactams and the aminoglycoside acetyl transferase gene (aac-6’-Ib) gene and resistance to ciprofloxacin, azithromycin and β-lactams (except for aztreonam). For P. aeruginosa, a significant association was noticed between the presence of the blaSHV gene and the multidrug efflux pump (MexA) and resistance to fluoroquinolones, amikacin, tobramycin, co-trimoxazole and β-lactams and between the aac-6’-Ib gene and resistance to aminoglycosides. All P. aeruginosa isolates (100%) harbored the MexAB-OprM multidrug efflux pump while 86% of the K. pneumoniae isolates harbored the AcrAB-TolC pump. Our results are of great medical importance for the guidance of healthcare practitioners for effective antibiotic prescription.
Comparison of the Staphylococcal Chromosome Cassette (SCC) mec in Methicillin-Resistant Staphylococcus aureus (MRSA) and Non-aureus Staphylococci (MRNAS) from Animals and Humans
Authors: Ngassam Tchamba Cyrille , Duprez Jean-Noël , Lucas Pierrick , Blanchard Yannick , Boyen Filip , Haesebrouck Freddy , Argudín Maria A. , Mainil Jacques , Thiry Damien
Published: March 2021

Methicillin-resistant Staphylococcus aureus (MRSA) and non-aureus staphylococci (MRNAS) cause different infections in animals, including mastitis, in livestock and humans. This study aimed to identify and compare the staphylococcal chromosome cassette mec (SCCmec) types of MRSA or MRNAS isolated from several animal species and humans in different countries. Of 1462 S. aureus and non-aureus staphylococci, 68 grew on Chrom MRSA ID® agar, were phenotypically resistant to cefoxitin and tested positive with the PCR for the mecA gene. These 60 MRSA and 8 MRNAS were isolated in Belgium mainly from cows (livestock-associated (LA) MRS) and humans (community-acquired (CA) MRS) and in Japan from dogs and cats. The SCCmec cassettes were identified by multiplex PCR in 52 MRSA and 7 MRNAS and by whole genome sequencing (WGS) in 8 additional MRSA. The SCCmec types IV and V were the most frequent in Belgian LA-MRS and CA-MRS, while the SCCmec type II was identified in four of the five Japanese MRSA. The remaining isolate was a bovine S. haemolyticus in which no SCCmec was identified. These results confirm the high prevalence of the SCCmec types IV and V in LA-MRS and CA-MRS in Belgium, emphasizing the possible public health hazard of the former, and the absence of SCCmec in some MRNAS.
Migratory Wild Birds as a Potential Disseminator of Antimicrobial-Resistant Bacteria around Al-Asfar Lake, Eastern Saudi Arabia
Authors: Elsohaby Ibrahim , Samy Ahmed , Elmoslemany Ahmed , Alorabi Mohammed , Alkafafy Mohamed , Aldoweriej Ali , Al-Marri Theeb , Elbehiry Ayman , Fayez Mahmoud
Published: March 2021

Migratory wild birds acquire antimicrobial-resistant (AMR) bacteria from contaminated habitats and then act as reservoirs and potential spreaders of resistant elements through migration. However, the role of migratory wild birds as antimicrobial disseminators in the Arabian Peninsula desert, which represents a transit point for birds migrating all over Asia, Africa, and Europe not yet clear. Therefore, the present study objective was to determine antimicrobial-resistant bacteria in samples collected from migratory wild birds around Al-Asfar Lake, located in Al-Ahsa Oasis, Eastern Saudi Arabia, with a particular focus on Escherichia coli virulence and resistance genes. Cloacal swabs were collected from 210 migratory wild birds represent four species around Al-Asfar. E. coli, Staphylococcus, and Salmonella spp. have been recovered from 90 (42.9%), 37 (17.6%), and 5 (2.4%) birds, respectively. Out of them, 19 (14.4%) were a mixed infection. All samples were subjected to AMR phenotypic characterization, and results revealed (14–41%) and (16–54%) of E. coli and Staphylococcus spp. isolates were resistant to penicillins, sulfonamides, aminoglycoside, and tetracycline antibiotics. Multidrug-resistant (MDR) E. coli and Staphylococcus spp. were identified in 13 (14.4%) and 7 (18.9%) isolates, respectively. However, none of the Salmonella isolates were MDR. Of the 90 E. coli isolates, only 9 (10%) and 5 (5.6%) isolates showed the presence of eaeA and stx2 virulence-associated genes, respectively. However, both eaeA and stx2 genes were identified in four (4.4%) isolates. None of the E. coli isolates carried the hlyA and stx1 virulence-associated genes. The E. coli AMR associated genes blaCTX-M, blaTEM, blaSHV, aac(3)-IV, qnrA, and tet(A) were identified in 7 (7.8%), 5 (5.6%), 1 (1.1%), 8 (8.9%), 4 (4.4%), and 6 (6.7%) isolates, respectively. While the mecA gene was not detected in any of the Staphylococcus spp. isolates. Regarding migratory wild bird species, bacterial recovery, mixed infection, MDR, and AMR index were relatively higher in aquatic-associated species. Overall, the results showed that migratory wild birds around Al-Asfar Lake could act as a reservoir for AMR bacteria enabling them to have a potential role in maintaining, developing, and disseminating AMR bacteria. Furthermore, results highlight the importance of considering migratory wild birds when studying the ecology of AMR.
Whole-Genome Sequencing Reveals the Presence of the blaCTX-M-65 Gene in Extended-Spectrum β-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands
Authors: Burnett Elton , Ishida Maria , de Janon Sofia , Naushad Sohail , Duceppe Marc-Olivier , Gao Ruimin , Jardim Armando , Chen Jessica C. , Tagg Kaitlin A. , Ogunremi Dele , Vinueza-Burgos Christian
Published: March 2021

Salmonella Infantis, a common contaminant of poultry products, is known to harbor mobile genetic elements that confer multi-drug resistance (MDR) and have been detected in many continents. Here, we report four MDR S. Infantis strains recovered from poultry house environments in Santa Cruz Island of the Galapagos showing extended-spectrum β-lactamase (ESBL) resistance and reduced fluoroquinolone susceptibility. Whole-genome sequencing (WGS) revealed the presence of the ESBL-conferring blaCTX-M-65 gene in an IncFIB-like plasmid in three S. Infantis isolates. Multi-locus sequence typing (MLST) and single nucleotide variant/polymorphism (SNP) SNVPhyl analysis showed that the S. Infantis isolates belong to sequence type ST32, likely share a common ancestor, and are closely related (1–3 SNP difference) to blaCTX-M-65-containing clinical and veterinary S. Infantis isolates from the United States and Latin America. Furthermore, phylogenetic analysis of SNPs following core-genome alignment (i.e., ParSNP) inferred close relatedness between the S. Infantis isolates from Galapagos and the United States. Prophage typing confirmed the close relationship among the Galapagos S. Infantis and was useful in distinguishing them from the United States isolates. This is the first report of MDR blaCTX-M-65-containing S. Infantis in the Galapagos Islands and highlights the need for increased monitoring and surveillance programs to determine prevalence, sources, and reservoirs of MDR pathogens.
Exploiting the Freshwater Shrimp Neocaridina denticulata as Aquatic Invertebrate Model to Evaluate Nontargeted Pesticide Induced Toxicity by Investigating Physiologic and Biochemical Parameters
Authors: Siregar Petrus , Suryanto Michael Edbert , Chen Kelvin H.-C. , Huang Jong-Chin , Chen Hong-Ming , Kurnia Kevin Adi , Santoso Fiorency , Hussain Akhlaq , Ngoc Hieu Bui Thi , Saputra Ferry , Audira Gilbert , Roldan Marri Jmelou M. , Fernandez Rey Arturo , Macabeo Allan Patrick G. , Lai Hong-Thih , Hsiao Chung-Der
Published: March 2021

As a nicotinoid neurotoxic insecticide, imidacloprid (IMI) works by disrupting nerve transmission via nicotinic acetylcholine receptor (nAChR). Although IMI is specifically targeting insects, nontarget animals such as the freshwater shrimp, Neocaridina denticulata, could also be affected, thus causing adverse effects on the aquatic environment. To investigate IMI toxicity on nontarget organisms like N. denticulata, their physiology (locomotor activity, heartbeat, and gill ventilation) and biochemical factors (oxidative stress, energy metabolism) after IMI exposure were examined. IMI exposure at various concentrations (0.03125, 0.0625, 0.125, 0.25, 0.5, and 1 ppm) to shrimp after 24, 48, 72 h led to dramatic reduction of locomotor activity even at low concentrations. Meanwhile, IMI exposure after 92 h caused reduced heartbeat and gill ventilation at high concentrations. Biochemical assays were performed to investigate oxidative stress and energy metabolism. Interestingly, locomotion immobilization and cardiac activity were rescued after acetylcholine administration. Through molecular docking, IMI demonstrated high binding affinity to nAChR. Thus, locomotor activity and heartbeat in shrimp after IMI exposure may be caused by nAChR blockade and not alterations caused by oxidative stress and energy metabolism. To summarize, N. denticulata serves as an excellent and sensitive aquatic invertebrate model to conduct pesticide toxicity assays that encompass physiologic and biochemical examinations.