bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vitro and in planta antagonistic effects of plant growth-promoting rhizobacteria consortium against soilborne plant pathogens of Solanum tuberosum and Solanum lycopersicum
Authors: Pellegrini Marika , Ercole Claudia , Di Zio Chiara , Matteucci Federica , Pace Loretta , Del Gallo Maddalena 
Published: June 2020

ABSTRACT
Potatoes (Solanum tuberosum L.) and tomatoes (Solanum lycopersicum L.), among the main crops belonging to the Solanaceae family, are attacked by several pathogens. Among them Fusarium oxysporum f. sp. radicis-lycopersici and Rhizoctonia solani are very common and cause significant losses. Four plant growth-promoting rhizobacteria, Azospirillum brasilense, Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae and Burkholderia ambifaria were tested against these pathogens. In vitro antagonistic activities of single strains were assessed through dual culture plates. Strains showing antagonistic activity (G. diazotrophicus, H. seropedicae and B. ambifaria) were combined and, after an in vitro confirmation, the consortium was applied on S. lycopersicum and S. tuberosum in a greenhouse pot experiment. The bioprotection was assessed in pre-emergence (infection before germination) and post-emergence (infection after germination). The consortium was able to successfully counteract the infection of both F. oxysporum and R. solani, allowing a regular development of plants. The biocontrol of the fungal pathogens was highlighted both in pre-emergence and post-emergence conditions. This selected consortium could be a valid alternative to agrochemicals and could be exploited as biocontrol agent to counteract losses due to these pathogenic fungi.
A novel model for predicting fatty liver disease by means of an artificial neural network
Authors: Chen Yi-Shu , Chen Dan , Shen Chao , Chen Ming , Jin Chao-Hui , Xu Cheng-Fu , Yu Chao-Hui , Li You-Ming 
Published: June 2020

Abstract

Background
The artificial neural network (ANN) emerged recently as a potent diagnostic tool, especially for complicated systemic diseases. This study aimed to establish a diagnostic model for the recognition of fatty liver disease (FLD) by virtue of the ANN.

Methods
A total of 7,396 pairs of gender- and age-matched subjects who underwent health check-ups at the First Affiliated Hospital, College of Medicine, Zhejiang University (Hangzhou, China) were enrolled to establish the ANN model. Indices available in health check-up reports were utilized as potential input variables. The performance of our model was evaluated through a receiver-operating characteristic (ROC) curve analysis. Other outcome measures included diagnostic accuracy, sensitivity, specificity, Cohen’s k coefficient, Brier score, and Hosmer-Lemeshow test. The Fatty Liver Index (FLI) and the Hepatic Steatosis Index (HSI), retrained using our training-group data with its original designated input variables, were used as comparisons in the capability of FLD diagnosis.

Results
Eight variables (age, gender, body mass index, alanine aminotransferase, aspartate aminotransferase, uric acid, total triglyceride, and fasting plasma glucose) were eventually adopted as input nodes of the ANN model. By applying a cut-off point of 0.51, the area under ROC curves of our ANN model in predicting FLD in the testing group was 0.908 [95% confidence interval (CI), 0.901–0.915]—significantly higher (P &lt; 0.05) than that of the FLI model (0.881, 95% CI, 0.872–0.891) and that of the HSI model (0.885; 95% CI, 0.877–0.893). Our ANN model exhibited higher diagnostic accuracy, better concordance with ultrasonography results, and superior capability of calibration than the FLI model and the HSI model.

Conclusions
Our ANN system showed good capability in the diagnosis of FLD. It is anticipated that our ANN model will be of both clinical and epidemiological use in the future.
Only a Single Taxonomically Restricted Gene Family in the Drosophila melanogaster Subgroup Can Be Identified with High Confidence
Authors: Zile Karina , Dessimoz Christophe , Wurm Yannick , Masel Joanna 
Published: June 2020

Abstract
Taxonomically restricted genes (TRGs) are genes that are present only in one clade. Protein-coding TRGs may evolve de novo from previously noncoding sequences: functional ncRNA, introns, or alternative reading frames of older protein-coding genes, or intergenic sequences. A major challenge in studying de novo genes is the need to avoid both false-positives (nonfunctional open reading frames and/or functional genes that did not arise de novo) and false-negatives. Here, we search conservatively for high-confidence TRGs as the most promising candidates for experimental studies, ensuring functionality through conservation across at least two species, and ensuring de novo status through examination of homologous noncoding sequences. Our pipeline also avoids ascertainment biases associated with preconceptions of how de novo genes are born. We identify one TRG family that evolved de novo in the Drosophila melanogaster subgroup. This TRG family contains single-copy genes in Drosophila simulans and Drosophila sechellia. It originated in an intron of a well-established gene, sharing that intron with another well-established gene upstream. These TRGs contain an intron that predates their open reading frame. These genes have not been previously reported as de novo originated, and to our knowledge, they are the best Drosophila candidates identified so far for experimental studies aimed at elucidating the properties of de novo genes.
Multiscale resistivity inversion based on convolutional wavelet transform
Authors: Pang Yonghao , Nie Lichao , Liu Bin , Liu Zhengyu , Wang Ning 
Published: June 2020

SUMMARY
The resistivity imaging method, an effective geophysical technique, has been widely used in environmental, engineering and hydrological fields. The inversion method based on smooth constraint is one of the most commonly used methods. However, this method causes the resistivity to change smoothly and makes it difficult to describe geological boundaries accurately. An accurate description of the target's boundaries often requires a priori information gained with other methods (such as other geophysical methods or geological drilling). To address this issue, a multiscale inversion method is proposed for extracting boundary features and inverting feature parameters from different scales. In this method, a convolution kernel is used to extract the boundary information from the resistivity model. The model parameters are transformed from the spatial domain to the feature domain via a convolutional wavelet transform. The feature parameters of different scales can then be obtained by solving the inversion equation in the feature domain. After that, the resistivity model of the spatial domain is reconverted from the feature domain by deconvolution transform of the inversion result. Numerical simulations and experiments show that the new multiscale resistivity inversion method has the ability to locate and depict boundaries of geological targets with high accuracy.
Curvature, a mechanical link between the geometrical complexities of a fault: application to bends, kinks and rough faults
Authors: Romanet Pierre , Sato Dye SK , Ando Ryosuke 
Published: June 2020

SUMMARY
Many recent studies have tried to determine the influence of geometry of faults in earthquake mechanics. However, it still remains largely unknown, and it is explored mainly with numerical models. In this paper, we will try to understand how exactly does the geometry come into play in the mechanics of an earthquake from analytical perspective. We suggest a new interpretation of the effect of geometry on the stress on a fault, where the curvatures of the fault that multiply the slip play a major role. Starting from the representation theorem, which links the displacement in a medium to the slip distribution on its boundary, and assuming a 3-D, homogeneous, infinite medium, a regularized boundary-element equation can be obtained. Using this equation, it is possible to separate the influence of geometry, as expressed by the curvatures and torsions of the field lines of slip on the fault surface, which multiply the slip, from the effect of the gradient of slip. This allows us to shed new light on the mechanical effects of geometrical complexities on the fault surface, with the key parameters being the curvatures and torsions of the slip field lines. We have used this new approach to show that, in 2-D static in-plane problems, the shear traction along the fault is mainly controlled by the gradient of slip along the fault, while the normal traction is mainly controlled by the slip that multiplies the curvature along the fault. Finally, we applied this new approach to re-interpret the effect of roughness (why there is a need for a minimum lengthscale in linear elasticity, how to study mechanically the difference of roughness measurements with the direction of slip, scaling of slip distribution versus geometry), bends and kinks (what is the difference between the two, are they sometimes equivalent), as well as to explain further the false paradox between smooth-and-abrupt-bends. This unified framework allows us to improve greatly our understanding of the effect of fault geometry on the mechanics of earthquakes.
Effects of fluid saturations on undrained poroelastic constants in layered media
Authors: Li Shengjie 
Published: June 2020

SUMMARYUnderstanding the fluid dependence of the poroelastic stiffness constants of a layered porous package is of great importance in subsurface exploration and development. While the effects of the pore-fluid distribution caused by coarse-scale heterogeneities within an isotropic medium have been studied for several decades, the role of these heterogeneities on the poroelastic constants of a finely layered package is still largely unexplored. In this study, we apply the poroelastic upscaling methods to estimate the fluid-dependent poroelastic stiffness constants of a layered package at the coarse scale. The numerical results show that the refined Gassmann's fluid substitution formulae presented in this paper is applicable if a single fluid phase is uniformly saturated within a layered package. The stiffness constants (${c_{11}}$ and ${c_{33}}$) of the layered package with patchy saturations are always higher than or equal to those obtained for the medium with homogeneous saturations, the stiffness constants predicted by the refined fluid substitution formulae for the package simultaneously saturated with different fluids fall between them. Experimental results confirm the relationship between the undrained vertical stiffness constant and the effective pore-fluid bulk modulus for the patch saturated package, indicating that a reasonable result can be achieved by properly choosing an effective poroelastic model that accounts both for the fluid hydraulic communication and the anisotropy of the medium. The results improve the understanding of the coarse-scale fluid dependence of the poroelastic stiffness constants of a layered package, and therefore, it can be used to interpret the seismically inverted elastic parameter for the petrophysical properties in heterogeneous reservoirs.
Colonoids From Patients With Pediatric Inflammatory Bowel Disease Exhibit Decreased Growth Associated With Inflammation Severity and Durable Upregulation of Antigen Presentation Genes
Authors: Kelsen Judith R , Dawany Noor , Conrad Maire A , Karakasheva Tatiana A , Maurer Kelly , Wei Jane M , Uman Selen , Dent Maiah H , Behera Rithika , Bryant Laura M , Ma Xianghui , Moreira Leticia , Chatterji Priya , Shraim Rawan , Merz Audrey , Mizuno Rei , Simon Lauren A , Muir Amanda B , Giraudo Claudio , Behrens Edward M , Whelan Kelly A , Devoto Marcella , Russo Pierre A , Andres Sarah F , Sullivan Kathleen E , Hamilton Kathryn E 
Published: June 2020

Abstract

Background
Defining epithelial cell contributions to inflammatory bowel disease (IBD) is essential for the development of much needed therapies for barrier repair. Children with very early onset (VEO)-IBD have more extensive, severe, and refractory disease than older children and adults with IBD and, in some cases, have defective barrier function. We therefore evaluated functional and transcriptomic differences between pediatric IBD (VEO and older onset) and non-IBD epithelium using 3-dimensional, biopsy-derived organoids.

Methods
We measured growth efficiency relative to histopathological and clinical parameters in patient enteroid (ileum) and colonoid (colon) lines. We performed RNA-sequencing on patient colonoids and subsequent flow cytometry after multiple passages to evaluate changes that persisted in culture.

Results
Enteroids and colonoids from pediatric patients with IBD exhibited decreased growth associated with histological inflammation compared with non-IBD controls. We observed increased LYZ expression in colonoids from pediatric IBD patients, which has been reported previously in adult patients with IBD. We also observed upregulation of antigen presentation genes HLA-DRB1 and HLA-DRA, which persisted after prolonged passaging in patients with pediatric IBD.

Conclusions
We present the first functional evaluation of enteroids and colonoids from patients with VEO-IBD and older onset pediatric IBD, a subset of which exhibits poor growth. Enhanced, persistent epithelial antigen presentation gene expression in patient colonoids supports the notion that epithelial cell-intrinsic differences may contribute to IBD pathogenesis.
From DNA to biomass: opportunities and challenges in species quantification of bulk fisheries products
Authors: Hansen Brian Klitgaard , Farrant Gregory Kevin , Ogden Rob , Humble Emily , Ólafsdóttir Guðbjörg , Bekkevold Dorte , Knudsen Steen Wilhelm , Møller Peter Rask , Nielsen Einar Eg 
Published: June 2020

Abstract
Fisheries enforcement relies on visual catch identification and quantification at sea or when landed. Silage (fish dissolved in acid) and fish blocks (block frozen fish) are promising methods for on-board processing and storage of low-value catches. We examined the use of non-destructive sampling and two DNA-based methods, quantitative PCR (qPCR) and metabarcoding, to assess species composition and relative abundance in industrial grade experimental silage and fish blocks. We demonstrate the ability to identify and quantify DNA from fish species in both products. qPCR analysis of small silage samples collected over 21 days detected all target control species. DNA from one species (Atlantic wolffish) was consistently overrepresented while, for three species of gadoids (Atlantic cod, haddock and whiting), the DNA content matched input tissue proportions with high accuracy. qPCR and metabarcoding of fish blocks, sampled as run-off water and exterior swabs, provided consistent species detection, with the highest variance observed in quantification from swab samples. Our analysis shows that DNA-based methods have significant potential as a tool for species identification and quantification of complex on-board-processed seafood products and are readily applicable to taxonomically and morphologically similar fish. There is, however, a need for establishing DNA/weight calibration factors for primary fisheries species.
Respiratory Syncytial Virus-Associated Hospital Admissions in Children Younger Than 5 Years in 7 European Countries Using Routinely Collected Datasets
Authors: Reeves Rachel M , van Wijhe Maarten , Tong Sabine , Lehtonen Toni , Stona Luca , Teirlinck Anne C , Fernandez Liliana Vazquez , Li You , Giaquinto Carlo , Fischer Thea Kølsen , Demont Clarisse , Heikkinen Terho , Speltra Irene , van Boven Michiel , Bøås Håkon , Campbell Harry ,   RESCEU Investigators, Reeves Rachel M , Li You , Campbell Harry , Nair Harish , van Wijhe Maarten , Fischer Thea Kølsen , Simonsen Lone , Trebbien Ramona , Tong Sabine , Bangert Mathieu , Demont Clarisse , Lehtonen Toni , Heikkinen Terho , Teirlinck Anne , van Boven Michiel , van der Hoek Wim , van der Maas Nicoline , Meijer Adam , Fernandez Liliana Vazquez , Bøas Håkon , Bekkevold Terese , Flem Elmira , Stona Luca , Speltra Irene , Giaquinto Carlo , Cheret Arnaud , Leach Amanda , Stoszek Sonia , Beutels Philippe , Bont Louis , Pollard Andrew , Openshaw Peter , Abram Michael , Swanson Kena , Rosen Brian , Molero Eva , Reeves Rachel M , Li You , Campbell Harry , Nair Harish , van Wijhe Maarten , Fischer Thea Kølsen , Simonsen Lone , Trebbien Ramona , Tong Sabine , Bangert Mathieu , Demont Clarisse , Lehtonen Toni , Heikkinen Terho , Teirlinck Anne , van Boven Michiel , van der Hoek Wim , van der Maas Nicoline , Meijer Adam , Fernandez Liliana Vazquez , Bøas Håkon , Bekkevold Terese , Flem Elmira , Stona Luca , Speltra Irene , Giaquinto Carlo , Cheret Arnaud , Leach Amanda , Stoszek Sonia , Beutels Philippe , Bont Louis , Pollard Andrew , Openshaw Peter , Abram Michael , Swanson Kena , Rosen Brian , Molero Eva 
Published: June 2020

Abstract

Background
Respiratory syncytial virus (RSV) is a leading cause of respiratory tract infection (RTI) in young children. Registries provide opportunities to explore RSV epidemiology and burden.

Methods
We explored routinely collected hospital data on RSV in children aged &lt; 5 years in 7 European countries. We compare RSV-associated admission rates, age, seasonality, and time trends between countries.

Results
We found similar age distributions of RSV-associated hospital admissions in each country, with the highest burden in children &lt; 1 years old and peak at age 1 month. Average annual rates of RTI admission were 41.3–112.0 per 1000 children aged &lt; 1 year and 8.6–22.3 per 1000 children aged &lt; 1 year. In children aged &lt; 5 years, 57%–72% of RTI admissions with specified causal pathogen were coded as RSV, with 62%–87% of pathogen-coded admissions in children &lt; 1 year coded as RSV.

Conclusions
Our results demonstrate the benefits and limitations of using linked routinely collected data to explore epidemiology and burden of RSV. Our future work will use these data to generate estimates of RSV burden using time-series modelling methodology, to inform policymaking and regulatory decisions regarding RSV immunization strategy and monitor the impact of future vaccines.
Current Status of Vancomycin Analytical Methods
Authors: Do Nascimento Patrícia Aleixa , Kogawa Ana Carolina , Salgado Hérida Regina Nunes 
Published: June 2020

Abstract

Background
The glycopeptide antibiotics are a class of antimicrobial drugs that are an important alternative for cases of bacterial infections resistant to penicillins, besides being able to be used to treat infections in people allergic to pencilin. They have great activity against Gram-positive microorganisms, including methicillin-resistant Staphylococcus aureus (MRSA), by inhibiting the cell wall synthesis.

Objective
There are many analytical methods in the literature for determination of antimicrobial glycopeptide vancomycin in different matrixes that are very effective; however, all of them use toxic solvents, contributing to the generation of waste, causing damage to the environment and to the operator, as well as increased costs of analysis.

Results
The most prevailing method found was high performance liquid chromatography (HPLC), followed by microbiological assays and, in less quantity, spectrometric methods. The chromatographic methods use organic solvents that are toxic, such as acetonitrile and methanol, and buffer solutions, that can damage the equipment and the column. In the microbiological assays the disc diffusion methods are still in the majority. The spectrophotometric methods were based in the UV-Vis region using buffer solutions as a diluent.

Conclusions
All these methods can become greener, following green analytical chemistry principles, which could bring benefits both to the environment and the operator, and reduce costs.

Highlights
In this paper, a literature review regarding analytical methods for determination of vancomycin was carried out with a suggestion of greener alternatives.
Egg Maturation and Daily Progeny Production in the Parasitoid, Gronotoma micromorpha (Hymenoptera: Figitidae: Eucoilinae)
Authors: Wu Yajiao , Abe Yoshihisa 
Published: June 2020

AbstractAn ovigeny index, which is the initial egg load divided by the potential lifetime fecundity, was developed for the parasitoid, Gronotoma micromorpha (Perkins), on the host Liriomyza trifolii (Burgess) (Diptera: Agromyzidae). The value obtained for the index was estimated to be 0.54, based on the initial egg load (mean ± SD: 41.0 ± 13.5) observed in the present study and the lifetime fecundity (75.6 ± 32.6) estimated in a previous study. Gronotoma micromorpha was previously regarded as being strictly pro-ovigenic based on daily progeny production data; however, the findings of the present study showed that this parasitoid is prosynovigenic. A 3-d cycle in daily progeny production was previously reported to occur during the lifetime of adult females (6.6 d) in this species. The present study showed that the initial egg load is nearly equal to the total number of eggs deposited in 3 d following adult emergence. Therefore, it is considered that the mature eggs stored during the pupal stage are deposited during the first 3 d after adult emergence and that egg maturation in the adult stage starts on day 1 and requires 3 d to complete in G. micromorpha. To clarify the relationship between the daily progeny production and the initial egg load, a reproductive cycle consisting of maturation, deposition, and depletion of eggs is proposed. In G. micromorpha, the reproductive cycle is considered to occur twice during the female lifetime. Furthermore, it is proposed that other prosynovigenic parasitoid species have a similar reproductive cycle.
Documenting the Establishment, Spread, and Severity of Phyllachora maydis on Corn, in the United States
Authors: Kleczewski Nathan M , Plewa Diane E , Bissonnette Kaitlyn M , Bowman Norman D , Byrne Jan M , LaForest Joseph , Dalla-Lana Felipe , Malvick Dean K , Mueller Daren S , Chilvers Martin I , Paul Pierce A , Raid Richard N , Robertson Alison E , Ruhl Gail E , Smith Damon L , Telenko Darcy E P 
Published: June 2020

AbstractTar spot on corn, caused by the fungus (Phyllachora maydis Maubl. [Phyllachorales: Phyllachoraceae]), is an emerging disease in the United States. In 2018 and 2019, significant but localized epidemics of tar spot occurred across the major corn producing region of the Midwest. After being first detected in 2015, tar spot was detected in 135 and 139 counties where the disease was not previously detected in 2018 and 2019, respectively, and is now established across 310 counties across the United Sates. Foliage with signs (stromata) of P. maydis and symptoms of tar spot were collected from 128 fields in 2018 and 191 fields in 2019, across seven states. Samples were assessed for severity of fungal stromata (percent leaf area covered with stromata) on foliage and the incidence of fisheye lesions (proportion of lesions with fisheye symptoms) associated with fungal stromata. Stromatal severity on samples in 2018 ranged from 0.5 to 67% and incidence of fisheye lesions ranged from 0 to 12%, whereas in 2019, stromatal severity ranged from 0.1 to 35% and incidence of fisheye lesions ranged from 0 to 80%, with 95% of samples presenting less than 6% incidence of fisheye lesions. Tar spot has spread substantially from where it was first reported in the United States. Collaborative efforts to monitor the spread and educate clientele on management are essential as this disease spreads into new areas.