bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracts from cultures of Pseudomonas fluorescens induce defensive patterns of gene expression and enzyme activity while depressing visible injury and reactive oxygen species in Arabidopsis thaliana challenged with pathogenic Pseudomonas syringae
Authors: Martin-Rivilla H , Garcia-Villaraco A , Ramos-Solano B , Gutierrez-Mañero F J , Lucas J A 
Published: August 2019

AbstractWe evaluated the ability of metabolic elicitors extracted from Pseudomonas fluorescens N21.4 to induce systemic resistance (ISR) in Arabidopsis thaliana against the pathogen Pseudomonas syringae DC3000. Metabolic elicitors were obtained from bacteria-free culture medium with n-hexane, ethyl acetate and n-butanol in three consecutive extractions. Each extract showed plant protection activity. The n-hexane fraction was the most effective and was used to study the signal transduction pathways involved by evaluating expression of marker genes of the salicylic acid (SA) signalling pathway (NPR1, PR1, ICS and PR2) and the jasmonic acid/ethylene (JA/ET) signalling pathway (PDF1, MYC2, LOX2 and PR3). In addition, the level of oxidative stress was tested by determining the activity of enzymes related to the ascorbate-glutathione cycle. N-hexane extracts stimulated both pathways based on overexpression of ICS, PR1, PR2, PDF1 and LOX2 genes. In addition, activity of the pathogenesis-related proteins glucanase (PR2) and chitinase (PR3), lipoxygenase and polyphenol oxidase was enhanced together with an increased capacity to remove reactive oxygen species (ROS). This was associated with less oxidative stress as indicated by a decrease in malondialdehyde (MDA), suggesting a causative link between defensive metabolism against P. syringae and ROS scavenging.
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins
Authors: Zhang Yanju , Yu Sha , Xie Ruopeng , Li Jiahui , Leier André , Marquez-Lago Tatiana T , Akutsu Tatsuya , Smith A Ian , Ge Zongyuan , Wang Jiawei , Lithgow Trevor , Song Jiangning 
Published: August 2019

AbstractMotivationGram-positive bacteria have developed secretion systems to transport proteins across their cell wall, a process that plays an important role during host infection. These secretion mechanisms have also been harnessed for therapeutic purposes in many biotechnology applications. Accordingly, the identification of features that select a protein for efficient secretion from these microorganisms has become an important task. Among all the secreted proteins, ‘non-classical’ secreted proteins are difficult to identify as they lack discernable signal peptide sequences and can make use of diverse secretion pathways. Currently, several computational methods have been developed to facilitate the discovery of such non-classical secreted proteins; however, the existing methods are based on either simulated or limited experimental datasets. In addition, they often employ basic features to train the models in a simple and coarse-grained manner. The availability of more experimentally validated datasets, advanced feature engineering techniques and novel machine learning approaches creates new opportunities for the development of improved predictors of ‘non-classical’ secreted proteins from sequence data.ResultsIn this work, we first constructed a high-quality dataset of experimentally verified ‘non-classical’ secreted proteins, which we then used to create benchmark datasets. Using these benchmark datasets, we comprehensively analyzed a wide range of features and assessed their individual performance. Subsequently, we developed a two-layer Light Gradient Boosting Machine (LightGBM) ensemble model that integrates several single feature-based models into an overall prediction framework. At this stage, LightGBM, a gradient boosting machine, was used as a machine learning approach and the necessary parameter optimization was performed by a particle swarm optimization strategy. All single feature-based LightGBM models were then integrated into a unified ensemble model to further improve the predictive performance. Consequently, the final ensemble model achieved a superior performance with an accuracy of 0.900, an F-value of 0.903, Matthew’s correlation coefficient of 0.803 and an area under the curve value of 0.963, and outperforming previous state-of-the-art predictors on the independent test. Based on our proposed optimal ensemble model, we further developed an accessible online predictor, PeNGaRoo, to serve users’ demands. We believe this online web server, together with our proposed methodology, will expedite the discovery of non-classically secreted effector proteins in Gram-positive bacteria and further inspire the development of next-generation predictors.Availability and implementationhttp://pengaroo.erc.monash.edu/.Supplementary informationSupplementary data are available at Bioinformatics online.
Where’s The Crime? Exploring Divergences Between Call Data and Perceptions of Local Crime
Authors: Porter Lauren C , Curtis Andrew , Jefferis Eric , Mitchell Susanne 
Published: August 2019

Abstract
Scholars typically use calls to the police to study crime patterning; however, crime reporting may be systematic across space. Using spatial video and geonarrative methodology, we investigate the overlap between perceived crime hot spots among 35 neighbourhood insiders (police officers, ex-offenders and residents) and hot spots gleaned from call data. In general, perceptual hot spots diverge from call data, but in particular, a corner store emerges as a perceptual hot spot across all groups, but not in call data. We use our data to explore the microgeographic dynamics of this ‘hidden hot spot’. We find that the corner store is relatively isolated, with few occupied residences around it and participants avoiding it. In addition, our geonarratives suggest that the store lacks adequate guardianship. We argue that mixed methodological approaches such as these are useful for understanding discrepancies between measures as well as the situational and environmental dynamics of problem places.
Plastome phylogenomics of Poaceae: alternate topologies depend on alignment gaps
Authors: Duvall Melvin R , Burke Sean V , Clark Dylan C 
Published: August 2019

AbstractIn Poaceae there is an evolutionary radiation of c. 5000 species called the ‘PACMAD’ grasses. Two hypotheses explain deep PACMAD relationships: the ‘aristidoid sister’ and the ‘panicoid sister’ hypotheses. In each case, the named subfamily is sister to all other taxa. These hypotheses were investigated with data partitions from plastid genomes (plastomes) of 169 grasses including five newly sequenced aristidoids. Plastomes were analysed 40 times with successive addition of more gapped positions introduced by sequence alignment, until all such positions were included. Alignment gaps include low complexity, AT-rich regions. Without gaps, the panicoid sister hypothesis (P(ACMAD)) was moderately supported, but as gaps were gradually added into the input matrix, the topology and support values fluctuated through a transition zone with stripping thresholds from 2–11% until a weakly supported aristidoid sister topology was retrieved. Support values for the aristidoid sister topology then rose and plateaued for remaining analyses until all gaps were allowed. The fact that the aristidoid sister hypothesis was retrieved largely when gapped positions were included suggests that this result might be artefactual. Knowledge of the deep PACMAD topology explicitly impacts our understanding of the radiation of PACMAD grasses into open habitats.
Population-Based Assessment of Clinical Risk Factors for Legionnaires’ Disease
Authors: Cooley Laura A , Pondo Tracy , Francois Watkins Louise K , Shah Priti , Schrag Stephanie ,   Active Bacterial Core Surveillance Program of the Emerging Infections Program Network, Vugia Duc , Alden Nisha , Cartter Matthew , Thomas Stephanie (Stepy) , Ryan Patricia A , Laine Ellen , Pradhan Eva , Dunn John 
Published: August 2019

Abstract
We used US population-based surveillance data to characterize clinical risk factors for Legionnaires’ disease (LD). The LD incidence increased by age and the risk was elevated for 12 clinical conditions, when compared to healthy adults. This information can be used to guide testing, treatment, and public health prevention efforts.
Crohn Disease and Fracture Risk Assessment With FRAX
Authors: Jonasson Grethe B , Hilon Jack , Hasseus Bengt , Alstad Torgny , Kashani Hossein 
Published: August 2019

Abstract

Background
Studies are inconsistent whether people with Crohn disease (CD) have an increased fracture risk.
This study showed that patients with Crohn’s disease (CD) had a higher ten year probability of fracture, assessed by the fracture assessment tool FRAX, and more fractures, but the proportion of CD patients with a fracture was not significantly higher than that of controls.

Methods
Forty-nine CD and 49 controls participated. All 98 completed a health questionnaire. A score with the fracture assessment tool FRAX &gt; 15% was considered risk factor for fracture.

Results
Mean FRAX score for 49 CD was 10.1 ± 10.3% and for 49 controls 5.0 ± 3.9% (P = 0.002). The variables correlated with fracture were being female (P = 0.04) and having a fractured mother (P = 0.002).

Conclusion
The CD group had significantly higher FRAX scores and more fractures, but the proportion of CD subjects with a fracture was not significantly higher than that of controls.
Trauma-Informed Elementary Schools: Evaluation of School-Based Early Intervention for Young Children
Authors: Rishel Carrie W , Tabone Jiyoung K , Hartnett Helen P , Szafran Kathy F 
Published: August 2019

Abstract
Trauma-Informed Elementary Schools (TIES) is a program designed to bring trauma-informed services to early elementary classrooms. Built on a foundation of adverse childhood experiences research and the Attachment, Self-Regulation, and Competency framework, TIES provides early intervention to children who exhibit symptoms of chronic stress or trauma in the classroom. Designed as an innovative school-based approach, TIES provides classrooms with a resource liaison to support teachers in recognizing and responding to trauma indicators. This article describes a study that examined the effectiveness of the TIES intervention across multiple domains, measuring the quality of classroom interaction by comparing TIES classrooms with comparison classrooms in 11 schools in a rural Appalachian state. CLASS (Classroom Assessment Scoring System) was used to measure classroom outcomes at the beginning (baseline) and end (follow-up) of the school year. Results indicate that TIES classrooms demonstrated significant improvement from baseline to follow-up in multiple domains, whereas comparison classrooms showed decline. The article concludes with a discussion of the study’s implications.
Invasive left ventricle pressure–volume analysis: overview and practical clinical implications
Authors: Bastos Marcelo B , Burkhoff Daniel , Maly Jiri , Daemen Joost , den Uil Corstiaan A , Ameloot Koen , Lenzen Mattie , Mahfoud Felix , Zijlstra Felix , Schreuder Jan J , Van Mieghem Nicolas M 
Published: August 2019

Abstract
Ventricular pressure–volume (PV) analysis is the reference method for the study of cardiac mechanics. Advances in calibration algorithms and measuring techniques brought new perspectives for its application in different research and clinical settings. Simultaneous PV measurement in the heart chambers offers unique insights into mechanical cardiac efficiency. Beat to beat invasive PV monitoring can be instrumental in the understanding and management of heart failure, valvular heart disease, and mechanical cardiac support. This review focuses on intra cardiac left ventricular PV analysis principles, interpretation of signals, and potential clinical applications.
New chromosomal lineages within Microvirga and Bradyrhizobium genera nodulate Lupinus angustifolius growing on different Tunisian soils
Authors: Rejili M , Msaddak A , Filali I , Benabderrahim M A , Mars M , Marín M 
Published: August 2019

ABSTRACTThirty-one rhizobial isolates nodulating native Lupinus angustifolius (blue lupine) plants growing in Northern Tunisian soils were isolated and analysed using different chromosomal and symbiotic gene markers. Phylogenetic analyses based on recA partial sequences grouped them into at least five groups: four of them within the genus Bradyrhizobium (26 isolates) and one into the genus Microvirga (5 isolates). Representative strains were analysed by multilocus sequence analysis of three housekeeping genes rrs-recA-glnII and rrs-gyrB-dnaK for Bradyrhizobium and Microvirga isolates, respectively. Based on this analysis, eight isolates clustered with the previously described strains Bradyrhizobium lupini USDA3051 and Bradyrhizobium canariense BTA-1. However, five of the isolates clustered separately and may constitute a new species within the Bradyrhizobium genus. The remaining five isolates were closely related to the strain Microvirga sp. LmiM8 and may constitute a new Microvirga species. The analysis of the nodC gene showed that all Bradyrhizobium strains nodulating blue lupine belong to the symbiovar genistearum, whereas the Microvirga isolates are associated with the symbiovar mediterranense. The results of this study support that the L. angustifolius root nodule symbionts isolated in Northern Tunisia belong mostly to the B. canariense/B. lupini lineages. However, new clades of Bradyrhizobium and Microvirga have been identified as L. angustifolius endosymbionts.
The impact of human-facilitated selection on the gut microbiota of domesticated mammals
Authors: Alessandri Giulia , Milani Christian , Mancabelli Leonardo , Mangifesta Marta , Lugli Gabriele Andrea , Viappiani Alice , Duranti Sabrina , Turroni Francesca , Ossiprandi Maria Cristina , van Sinderen Douwe , Ventura Marco 
Published: August 2019

ABSTRACTDomestication is the process by which anthropogenic forces shape lifestyle and behavior of wild species to accommodate human needs. The impact of domestication on animal physiology and behavior has been extensively studied, whereas its effect on the gut microbiota is still largely unexplored. For this reason, 16S rRNA gene-based and internal transcribed spacer-mediated bifidobacterial profiling, together with shotgun metagenomics, was employed to investigate the taxonomic composition and metabolic repertoire of 146 mammalian fecal samples, corresponding to 12 domesticated–feral dyads. Our results revealed that changes induced by domestication have extensively shaped the taxonomic composition of the mammalian gut microbiota. In this context, the selection of microbial taxa linked to a more efficient feed conversion into body mass and putative horizontal transmission of certain bacterial genera from humans were observed in the fecal microbiota of domesticated animals when compared to their feral relatives and to humans. In addition, profiling of the metabolic arsenal through metagenomics highlighted extensive functional adaptation of the fecal microbial community of domesticated mammals to changes induced by domestication. Remarkably, domesticated animals showed, when compared to their feral relatives, increased abundance of specific glycosyl hydrolases, possibly due to the higher intake of complex plant carbohydrates typical of commercial animal feeds.
Pantoea agglomeransYS19 poly(A) polymerase I gene possesses the indole-sensing sequence in the promoter region
Authors: Zheng Jing , Liu Qi , Xia Yifan , Bai Lijuan , Feng Yongjun 
Published: August 2019

ABSTRACTPantoea agglomerans YS19 is a predominant diazotrophic endophyte with multiple growth-promoting effects on its host plant that was isolated from rice. Indole is confirmed to induce many changes of physiological and biochemical characteristics in bacteria. Although YS19 cannot produce indole, it can sense indole in the environment and be regulated by indole. Here, using gfp as a reporter gene, we constructed a series of recombinant plasmids containing the promoter region of the poly(A) polymerase I gene (pcnB) fused with gfp, and compared the green fluorescence intensity at different concentrations of exogenous indole by a flow cytometer. In this research, we confirmed that exogenous indole significantly inhibited the expression of pcnB by its promoter; the regulation sequence sensitive to indole in the promoter region of the pcnB gene (In-pcnB) was between −129 and −88 bp. In-pcnB is widely distributed and strictly conserved in the same genus. These results suggest novel roles of In-pcnB in P. agglomerans YS19, showing its special relation to the indole regulatory pathway.
Gloeosporiocide, a new antifungal cyclic peptide from Streptomyces morookaense AM25 isolated from the Amazon bulk soil
Authors: Vicente dos Reis Gislâine , Abraham Wolf-Rainer , Grigoletto Diana Fortkamp , de Campos Jessica Bueno , Marcon Joelma , da Silva Jose Antonio , Quecine Maria Carolina , de Azevedo João Lúcio , Ferreira Antonio Gilberto , de Lira Simone Possedente 
Published: August 2019

ABSTRACT
Actinobacteria are known by their ability to produce several antimicrobial compounds of biotechnological interest. Thus, in this study, we isolated and identified by partial 16S RNA sequencing ∼100 actinobacteria isolates from guarana (Paullinia cupana) bulk soil. Besides, we isolated from the actinobacteria Streptomyces morookaense AM25 a novel cyclic peptide, named gloeosporiocide, molecular formula C44H48N11O7S3 (calculated 938.2901), and characterized by the presence of cyclized cysteins to form three thiazols. The novel compound had activity against the plant pathogen Colletotrichum gloeosporioides, assayed by the paper disk diffusion method (42.7% inhibition, 0.1 mg disk−1) and by the microdilution assay (1.25 g L−1). Our results reveal the potential of the actinobacteria from the Amazon rhizospheric soils as biocontrol agents as well as producers of new compounds with antifungal activity. Thus, this work constitutes a step forward in the development of the biotechnology of actinobacteria in the production of compounds of agronomic interest.
Novel high resolution melt curve assay for the analysis of predominance of Helicobacter pylori clarithromycin resistance
Authors: Boltin Doron , Ashorov Olga , Benejat Lucie , Hamouda Dalal , Belfer Rachel Gingold , Niv Yaron , Dickman Ram , Perets Tsachi Tsadok 
Published: August 2019

ABSTRACT
Clarithromycin resistance is the most common cause of Helicobacter pylori treatment failure and it is attributed to three point mutations, A2142G, A2142C and A2143G, within the 23S rRNA gene. We aimed to determine the prevalence of H. pylori clarithromycin resistance using a novel high resolution melt assay. A total of 151 stool samples were collected from treatment-naïve patients with general gastric discomfort who also performed 13CO2 breath tests. Stool antigen tests were also performed on 126 of the 151 stool samples collected. Bacterial DNA was extracted from the stool and analyzed by comparing it with four reference plasmids incorporating the three mutations and the wild type (WT) sequences. The melt assay detected 106 H. pylori positive samples, of which 54 had a WT sequence, and 52 had a point mutation associated with clarithromycin resistance, including A2142G in 10, A2142C in 13, A2143G in 18 and heterozygosity (multiple peaks) in 11. Compared with the gold standards (13CO2 breath and stool antigen tests), the melt assay had a sensitivity of 100% and 99% and a specificity of 82% and 78%, respectively. Therefore, our stool-based molecular assay is able to identify H. pylori infection and clarithromycin resistance. It could be used for screening prior to administration of clarithromycin eradication therapy.
Thirteen New Plastid Genomes from Mixotrophic and Autotrophic Species Provide Insights into Heterotrophy Evolution in Neottieae Orchids
Authors: Lallemand Félix , Logacheva Maria , Le Clainche Isabelle , Bérard Aurélie , Zheleznaia Ekaterina , May Michał , Jakalski Marcin , Delannoy Étienne , Le Paslier Marie-Christine , Selosse Marc-André 
Published: August 2019

Abstract
Mixotrophic species use both organic and mineral carbon sources. Some mixotrophic plants combine photosynthesis and a nutrition called mycoheterotrophy, where carbon is obtained from fungi forming mycorrhizal symbiosis with their roots. These species can lose photosynthetic abilities and evolve full mycoheterotrophy. Besides morphological changes, the latter transition is associated with a deep alteration of the plastid genome. Photosynthesis-related genes are lost first, followed by housekeeping genes, eventually resulting in a highly reduced genome. Whether relaxation of selective constraints already occurs for the plastid genome of mixotrophic species, which remain photosynthetic, is unclear. This is partly due to the difficulty of comparing plastid genomes of autotrophic, mixotrophic, and mycoheterotrophic species in a narrow phylogenetic framework. We address this question in the orchid tribe Neottieae, where this large assortment of nutrition types occurs. We sequenced 13 new plastid genomes, including 9 mixotrophic species and covering all 6 Neottieae genera. We investigated selective pressure on plastid genes in each nutrition type and conducted a phylogenetic inference of the group. Surprisingly, photosynthesis-related genes did not experience selection relaxation in mixotrophic species compared with autotrophic relatives. Conversely, we observed evidence for selection intensification for some plastid genes. Photosynthesis is thus still under purifying selection, maybe because of its role in fruit formation and thus reproductive success. Phylogenetic analysis resolved most relationships, but short branches at the base of the tree suggest an evolutionary radiation at the beginning of Neottieae history, which, we hypothesize, may be linked to mixotrophy emergence.