bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance assessment of long-legged tightly-baffled divertor geometries in the ARC reactor concept
Authors: Wigram M.R.K. , LaBombard B. , Umansky M.V. , Kuang A.Q. , Golfinopoulos T. , Terry J.L. , Brunner D. , Rensink M.E. , Ridgers C.P. , Whyte D.G.
Published: August 2019

Extremely intense power exhaust channels are projected for tokamak-based fusion power reactors; a means to handle them remains to be demonstrated. Advanced divertor configurations have been proposed as potential solutions. Recent modelling of tightly baffled, long-legged divertor geometries for the divertor test tokamak concept, ADX, has shown that these concepts may access passively stable, fully detached regimes over a broad range of parameters. The question remains as to how such divertors may perform in a reactor setting. To explore this, numerical simulations are performed with UEDGE for the long-legged divertor geometry proposed for the ARC pilot plant conceptual design—a device with projected heat flux power width (

) of 0.4 mm and power exhaust of 93 MW—first for a simplified Super-X divertor configuration (SXD) and then for the actual X-point target divertor (XPTD) being proposed. It is found that the SXD, combined with 0.5% fixed-fraction neon impurity concentration, can produce passively stable, detached divertor regimes for power exhausts in the range of 80–108 MW—fully accommodating ARC’s power exhaust. The XPTD configuration is found to reduce the strike-point temperature by a factor of  ∼10 compared to the SXD for small separations (∼1.4

) between main and divertor X-point magnetic flux surfaces. Even greater potential reductions are identified for reducing separations to  ∼1

or less. The power handling response is found to be insensitive to the level of cross-field convective or diffusive transport assumed in the divertor leg. By raising the separatrix density by a factor of 1.5, stable fully detached divertor solutions are obtained that fully accommodate the ARC exhaust power without impurity seeding. To our knowledge, this is the first time an impurity-free divertor power handling scenario has been obtained in edge modelling for a tokamak fusion power reactor with

of 0.4 mm.
Estimating the contribution of crop residues to soil organic carbon conservation
Authors: Stella Tommaso , Mouratiadou Ioanna , Gaiser Thomas , Berg-Mohnicke Michael , Wallor Evelyn , Ewert Frank , Nendel Claas
Published: August 2019

Crop residues contribute to the maintenance of soil organic carbon (SOC) stores, a key component of soil fertility and soil-based climate change mitigation strategies, such as the ‘4 per 1000’ initiative. Residues are also in demand in sectors coupled to crop production, such as the supply chain of livestock and bioenergy production. Ongoing debate revolves around balancing these competing uses, but science-based assessments of the long-term sustainability of residue exploitation are rare. This work uses biophysical simulation modelling to explore the likely response of SOC to different management strategies, using the land area of North Rhine-Westphalia (Germany) as a case study. Four strategies are tested: zero, one third and 100% removal of cereal residues, plus an approach proposed by the State farm advisory service. Simulations are carried out for the period 1971–2050 and 19 crop rotations coincident with land use throughout the study area. Uncertainty associated with the modelled SOC changes is explored by sampling values of relevant parameters for SOC turnover and running an ensemble of model configurations. Simulated SOC is used to trace time-dependent response functions following a change in residue management under different soil textures, initial SOC levels and crop rotations. Results highlight a general exponential decrease in SOC, with relative changes in 2050 distributed between +10% and −40% with respect to a reference period. SOC loss can be buffered or offset by returning all crop residues to the soil. Under such management, an SOC increase can be achieved on clayey soils characterized by a low initial SOC. Under moderate crop residue removal, positive SOC trends are limited to a few crop rotations. In this context, 4 per 1000 increase rate in SOC appears largely out of reach through residue management, calling for additional measures to meet the targets of land-based mitigation of anthropogenic emissions.
Finite element analysis of hot roll-forming process of local thickened U-rib for bridge
Authors: Peng Xue-Feng , Han Jing-Tao , Liu Jia-Sheng
Published: August 2019

To solve the problems of small welding area and poor welding quality between traditional U-rib and bridge decks, a new type local thickened U-rib (LTU-rib) proposed by bridge experts. In this paper, the simulation software ABAQUS is used to simulate a hot roll-forming process of LTU-rib. Finite element model of hot roll-forming process was established. The influence of the pass design schemes and temperature parameters on the hot roll-forming process was analyzed and discussed. The simulation results show that first scheme is more suitable for hot roll-forming process. Although forming temperature can reduce the roll-forming force and improve the metal fluidity, excessive temperature will lead to redundant deformation. The simulation results provide a reference for the parameters design of actual hot roll-forming process.
Fiber Metal Laminate Structure, a good replacement for monolithic and composite materials
Authors: Sherkatghanad Ehsan , Lang Lihui , Blala Hamza , Li Lei , Alexandrov Sergei
Published: August 2019

Lightweight materials such as aluminium alloys, magnesium alloys, and composite material present a significant possibility for applications in automobile and aerospace structures. In order to consider the feasibility of selecting and replacing such materials in the form of hybrid laminated materials, calculations and simulations are investigated with different lightweight materials such as single layer aluminium, fiber-reinforced composite materials, and the aluminium composite laminates, the carbon and glass cloth as the middle layer, under the constant force condition. The stiffness and deflections of these materials are discussed and compared in details. According to calculations, FE and experimental results validate that the deflections and the stiffness of different materials can be predicted well. In order to finalize the material selection, especially for aerospace-based components, the weight ratios are very determinative. Actually, a material with the superior specific stiffness and strength will be the best one considering some other limitations such as corrosion. Calculating the mass ratio of the suggested lightweight materials were done to find an appropriate one. In fact, these kinds of materials have the advantages of both metallic alloys and composites. In addition, in cases where corrosion resistance, environmental protection, fatigue resistance, and impact resistance are needed, FMLs can be the best choice.
A novel way of avoiding stylus drop down from model while scanning
Authors: Lei Wu
Published: August 2019

Based on analysing the basic feature of scanning process, this paper proposes a new architecture to regulate autonomous scanning speed with the nominal vector DN
. In addition, explains and demonstrates how to introduce the nominal vector DN
into the tracer scanning for successive and self-adjusting scanning speed and autonomy contact level between stylus of trace and model according to the curved surface. The technical activities and experimental results shown that the parameter of nominal vector DN
play a proper role in the case of retaining tracer contact on curved surface especially when stylus scanning from horizontal plane to the vertical plane.
On the Inclusion Model of Localized Heating in an Elastic Plane
Authors: Li P , Jin X , Zhang X , Luo D , An Y
Published: August 2019

Failure localization in a variety of mechanical structures may be ascribed to elevated temperature, which may be effectively analyzed by employing the inclusion model. This work presents an explicit solution to the plane thermal inclusion problem, based on the customized Green’s function. A contour integral representation is further developed so as to provide an effective and straightforward approach for treating an arbitrarily shaped inclusion. Several benchmark examples are examined to validate the present solution.
Enhancement of critical heat flux under subcooled boiling of deionized water in a curved flow channel
Authors: Urfa Rasool , Lu Daogang , Asran Noor Farooq , Munib Ansari , Aazim Rasool
Published: August 2019

The numerical calculations are performed to predict critical heat flux (CHF) during subcooled boiling of deionized water through 90° curved flow channel with square cross-section. Two types of flow regimes have been observed at low and high flow velocities. In case of low flow velocities, the continuous accumulation of vapors formed a vapor blanket on heating surface which consequently reduced heat dissipation out of the surface and triggered CHF due to drying out of liquid between vapor blanket and heating wall. On the other hand, coolant circulation at higher velocities hindered the formation of vapor blanket and allowed subcooled liquid for rewetting. The consistent rewetting led the formation of small and separate vapor blankets. The enhancement in CHF has been observed with increased degree of subcooling and by increasing flow velocity in present study.
Extreme precipitation over East Asia under 1.5 °C and 2 °C global warming targets: a comparison of stabilized and overshoot projections
Authors: Li Donghuan , Zhou Tianjun , Zhang Wenxia
Published: August 2019

Highly populated East Asia is vulnerable to extreme precipitation. Here, we use Community Earth System Model low-warming simulations to examine how extreme precipitation events may change in East Asia under the Paris Agreement global warming targets. The frequency and intensity of extreme precipitation will increase markedly over East Asia in the warmer climates. Limiting end-of-century warming to 1.5 °C, in comparison with 2 °C, will reduce the risks of extreme precipitation frequency and intensity in East Asia by 26%–31%, with the greatest reductions (38%–54%) in Japan. A brief overshoot of the 1.5 °C target would affect Mongolia, the Korean Peninsula and Japan from the aspects of regional average. More than 25% of the increase in the frequency and intensity of extreme precipitation in these regions can be avoided during the end of the 21st century (2081–2100) if there is no temperature overshoot, according to the best estimate. Vertical moisture advection is the main contributor to changes in precipitation-minus-evaporation in East Asia in the warmer climates. The increased low-level specific humidity and cyclonic circulation changes are the dominant thermodynamic and dynamical processes that contribute to the increase of precipitation over South China and Japan. Our work suggests that limiting warming to 1.5 °C without overshoot is beneficial to minimizing the impacts associated with precipitation extremes across East Asia.
Microstructural and compositional optimization of La0.5Ba0.5CoO3−δ—BaZr1−zYzO3−δ (z = 0, 0.05 and 0.1) nanocomposite cathodes for protonic ceramic fuel cells
Authors: Rioja-Monllor Laura , Bernuy-Lopez Carlos , Fontaine Marie-Laure , Grande Tor , Einarsrud Mari-Ann
Published: August 2019

Cathodes are one of the key components of protonic ceramic fuel cells (PCFCs) requiring further development to enhance the performance of PCFCs. This encompasses the optimization of material compositions and microstructures, as well as a further understanding of the electrode processes. Here, a compositional optimization of a La0.5Ba0.5CoO3−δ
—BaZrO3-based nano-composite cathode prepared by exsolution of a single-phase material was performed by substituting 5 and 10 mol% Y at the B-site in the BaZrO3 phase. Electrodes with different microstructures were prepared by two different deposition methods, spray coating and screen printing, and by varying the firing temperature from 600°C to 1100 °C. Further, composite electrodes were prepared by directly coating and firing the single-phase materials on the dense electrolyte to prepare symmetric cells. A good adhesion of the cathode to the electrolyte was observed in all cases. In general, a more homogeneous microstructure was observed for the cathodes prepared by screen printing. The single step method encompassing exsolution of the single phase and firing of the symmetric cells yielded significant improvement in the cathode performance compared to the other routes. The best electrochemical performance was observed for La0.5Ba0.5CoO3−δ
—BaZr0.9Y0.1O2.95 cathode with an area specific resistance of 4.02 Ω · cm2 at 400 °C and 0.21 Ω · cm2 at 600 °C in 3% moist synthetic air. These results are among the best reported for cathodes of PCFCs as will be discussed.
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

We 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

Motivation

Gram-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.

Results

In 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 implementation

http://pengaroo.erc.monash.edu/.

Supplementary information

Supplementary 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

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

In 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.
Handedness, language areas and neuropsychiatric diseases: insights from brain imaging and genetics
Authors: Wiberg Akira , Ng Michael , Al Omran Yasser , Alfaro-Almagro Fidel , McCarthy Paul , Marchini Jonathan , Bennett David L , Smith Stephen , Douaud Gwenaëlle , Furniss Dominic
Published: August 2019

The brain signature and genetic basis of handedness are unclear. Wiberg et al. show that left-handers have higher functional connectivity between language networks, and identify four genomic regions associated with handedness. Variants within these regions appear, by influencing brain architecture, to predispose both to left-handedness and to certain neuropsychiatric diseases.
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

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

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 > 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

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

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

Thirty-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

Domestication 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

Pantoea 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

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

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

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.
How does performance-based financing affect the availability of essential medicines in Cameroon? A qualitative study
Authors: Sieleunou Isidore , Turcotte-Tremblay Anne-Marie , De Allegri Manuela , Taptué Fotso Jean-Claude , Azinyui Yumo Habakkuk , Magne Tamga Denise , Ridde Valéry
Published: August 2019

Performance-based financing (PBF) is being implemented across low- and middle-income countries to improve the availability and quality of health services, including medicines. Although a few studies have examined the effects of PBF on the availability of essential medicines (EMs) in low- and middle-income countries, there is limited knowledge of the mechanisms underlying these effects. Our research aimed to explore how PBF in Cameroon influenced the availability of EMs, and to understand the pathways leading to the experiential dimension related with the observed changes. The design was an exploratory qualitative study. Data were collected through in-depth interviews, using semi-structured questionnaires. Key informants were selected using purposive sampling. The respondents (n = 55) included health services managers, healthcare providers, health authorities, regional drugs store managers and community members. All interviews were recorded, transcribed and analysed using qualitative data analysis software. Thematic analysis was performed. Our findings suggest that the PBF programme improved the perceived availability of EMs in three regions in Cameroon. The change in availability of EMs experienced by stakeholders resulted from several pathways, including the greater autonomy of facilities, the enforced regulation from the district medical team, the greater accountability of the pharmacy attendant and supply system liberalization. However, a sequence of challenges, including delays in PBF payments, limited autonomy, lack of leadership and contextual factors such as remoteness or difficulty in access, was perceived to hinder the capacity to yield optimal changes, resulting in heterogeneity in performance between health facilities. The participants raised concerns regarding the quality control of drugs, the inequalities between facilities and the fragmentation of the drug management system. The study highlights that some specific dimensions of PBF, such as pharmacy autonomy and the liberalization of drugs supply systems, need to be supported by equity interventions, reinforced regulation and measures to ensure the quality of drugs at all levels.
Racial Disparities in Breast Cancer Outcomes in the Metropolitan Atlanta Area: New Insights and Approaches for Health Equity
Authors: Collin Lindsay J , Jiang Renjian , Ward Kevin C , Gogineni Keerthi , Subhedar Preeti D , Sherman Mark E , Gaudet Mia M , Breitkopf Carmen Radecki , D’Angelo Olivia , Gabram-Mendola Sheryl , Aneja Ritu , Gaglioti Anne H , McCullough Lauren E
Published: August 2019

Background

Racial disparities in breast cancer (BC) outcomes persist where non-Hispanic black (NHB) women are more likely to die from BC than non-Hispanic white (NHW) women, and the extent of this disparity varies geographically. We evaluated tumor, treatment, and patient characteristics that contribute to racial differences in BC mortality in Atlanta, Georgia, where the disparity was previously characterized as especially large.

Methods

We identified 4943 NHW and 3580 NHB women in the Georgia Cancer Registry with stage I–IV BC diagnoses in Atlanta (2010–2014). We used Cox proportional hazard regression to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) comparing NHB vs NHW BC mortality by tumor, treatment, and patient characteristics on the additive and multiplicative scales. We additionally estimated the mediating effects of these characteristics on the association between race and BC mortality.

Results

At diagnosis, NHB women were younger—with higher stage, node-positive, and triple-negative tumors relative to NHW women. In age-adjusted models, NHB women with luminal A disease had a 2.43 times higher rate of BC mortality compared to their NHW counterparts (95% CI = 1.99 to 2.97). High socioeconomic status (SES) NHB women had more than twice the mortality rates than their white counterparts (HR = 2.67, 95% CI = 1.65 to 4.33). Racial disparities among women without insurance, in the lowest SES index, or diagnosed with triple-negative BC were less pronounced.

Conclusions

In Atlanta, the largest racial disparities are observed in luminal tumors and most pronounced among women of high SES. More research is needed to understand drivers of disparities within these treatable features.
Integrating the dynamics of yield traits in rice in response to environmental changes
Authors: Nutan Kamlesh Kant , Rathore Ray Singh , Tripathi Amit Kumar , Mishra Manjari , Pareek Ashwani , Singla-Pareek Sneh Lata
Published: August 2019

Reductions in crop yields as a consequence of global climate change threaten worldwide food security. It is therefore imperative to develop high-yielding crop plants that show sustainable production under stress conditions. In order to achieve this aim through breeding or genetic engineering, it is crucial to have a complete and comprehensive understanding of the molecular basis of plant architecture and the regulation of its sub-components that contribute to yield under stress. Rice is one of the most widely consumed crops and is adversely affected by abiotic stresses such as drought and salinity. Using it as a model system, in this review we present a summary of our current knowledge of the physiological and molecular mechanisms that determine yield traits in rice under optimal growth conditions and under conditions of environmental stress. Based on physiological functioning, we also consider the best possible combination of genes that may improve grain yield under optimal as well as environmentally stressed conditions. The principles that we present here for rice will also be useful for similar studies in other grain crops.
AtNSE1 and AtNSE3 are required for embryo pattern formation and maintenance of cell viability during Arabidopsis embryogenesis
Authors: Li Gang , Zou Wenxuan , Jian Liufang , Qian Jie , Zhao Jie
Published: August 2019

Embryogenesis is an essential process during seed development in higher plants. It has previously been shown that mutation of the Arabidopsis non-SMC element genes AtNSE1 or AtNSE3 leads to early embryo abortion, and their proteins can interact with each other directly. However, the crucial regions of these proteins in this interaction and how the proteins are cytologically involved in Arabidopsis embryo development are unknown. In this study, we found that the C-terminal including the Ring-like motif of AtNSE1 can interact with the N-terminal of AtNSE3, and only the Ring-like motif is essential for binding with three α motifs of AtNSE2 (homologous to AtMMS21). Using genetic assays and by analysing molecular markers of cell fate decisions (STM, WOX5, and WOX8) in mutant nse1 and nse3 embryos, we found that AtNSE1 and AtNSE3 work non-redundantly in early embryo development, and that differentiation of the apical meristem and the hypophysis fails in the mutants, which have disrupted auxin transportation and responses. However, the upper cells of the suspensor in the mutants seem to have proper embryo cell identity. Cytological examination showed that cell death occurred from the early embryo stage, and that vacuolar programmed cell death and necrosis in the nse1 and nse3 mutant embryos led to ovule abortion. Thus, AtNSE1 and AtNSE3 are essential for maintaining cell viability and growth during early embryogenesis. Our results improve our understanding of the functions of SMC5/6 complex in early embryogenesis in Arabidopsis.
Examination of the Comatose Patient
Authors: Posner Jerome B. , Saper Clifford B. , Schiff Nicholas D. , Claassen Jan
Published: August 2019

Chapter 2 defines a brief but informative neurologic examination that is necessary to determine if reduced consciousness has a structural cause (and therefore may require immediate imaging and perhaps surgical treatment) or a metabolic cause (in which case the diagnostic approach can be more lengthy and extensive). The authors stress that a coma or any alteration of consciousness is a medical emergency, and, as such, the physician must begin examination and treatment simultaneously. The examination must be thorough, but brief. The chapter also describes some of the physical findings that distinguish structural from nonstructural causes of stupor and coma.
Specific Causes of Structural Coma
Authors: Posner Jerome B. , Saper Clifford B. , Schiff Nicholas D. , Claassen Jan
Published: August 2019

This chapter is the second of two chapters to discuss the pathophysiology and specific causes of structural injury to the brain that result in defects of consciousness. This chapter examines, in turn, the specific causes of supratentorial and infratentorial compressive and destructive lesions that cause coma. It also gives brief descriptions of the approach to treatment. Among the insults and injuries described are various hematomas, abscesses, empyema, tumors, infections, and, as well as infarctions, distal basilar occlusion, venous sinus thrombosis, vasculitis. Concussion and other traumatic brain injuries are described and discussed, as are vascular destructive and inflammatory disorders like basilar migraine, leukoencephalopathy syndrome, and myelinolysis.
Psychogenic Unresponsiveness
Authors: Posner Jerome B. , Saper Clifford B. , Schiff Nicholas D. , Claassen Jan
Published: August 2019

Chapter 6 explores psychiatric causes of unresponsiveness, which must be differentiated from organic causes of stupor and coma. The chapter notes that several psychiatric disorders can result in psychogenic unresponsiveness. These include conversion reaction, catatonic stupor, a dissociative or “fugue” state, and factitious disorder or malingering. The chapter looks at these in turn. Various diagnostic tests are described in detail, including the electroencephalogram, magnetic resonance imaging, computed tomographic imaging, caloric testing, and the “Amytal interview.” Sections describes the diagnosis and treatment of catatonia, psychogenic seizures (which must be differentiated from epileptic seizures), and cerebellar mutism. The authors emphasize the importance of treating patients with psychiatric causes of unresponsiveness with compassion and understanding.
Respiratory drugs
Authors: Waldmann Carl , Rhodes Andrew , Soni Neil , Handy Jonathan
Published: August 2019

This chapter discusses respiratory drugs and includes discussion on bronchodilators (describing β‎2-agonists, anticholinergic agents, and xanthine derivatives), nitric oxide (history, biochemistry, clinical use of inhaled nitric oxide, administration of inhaled nitric oxide, adverse effects of inhaled nitric oxide, and adjunctive therapies), mucolytics (properties of mucus, types of mucolytics, clinical applications, and side-effects), and helium–oxygen gas mixtures (including nomenclature, rationale, indications, expected effects, presentation, face mask administration, nebulization, patient monitoring during therapy, stopping helium–oxygen therapy, indications for helium–oxygen mask ventilation, indications for helium–oxygen intermittent positive pressure ventilation (IPPV) via endotracheal or tracheostomy tube, patient monitoring during IPPV therapy, stopping helium–oxygen therapy, and published trials).
Haematological drugs
Authors: Waldmann Carl , Rhodes Andrew , Soni Neil , Handy Jonathan
Published: August 2019

This chapter discusses haematological drugs and includes discussion on anticoagulants and heparin-induced thrombocytopenia (including unfractionated heparin, low-molecular weight heparins, danaparoid, coumarins, synthetic pentasaccharides, the direct oral anticoagulants, and thromboprophylaxis in critical care patients), thrombolysis (definition of thrombolysis, physiology of fibrinolysis, contraindications to thrombolysis, factors influencing a successful outcome, myocardial infarction, acute limb ischaemia, and pulmonary embolism), and antifibrinolytics (describing the efficacy of tranexamic acid in reducing traumatic bleeding, the efficacy of tranexamic acid in reducing surgical bleeding, and the efficacy of tranexamic acid in postpartum haemorrhage).
Renal disorders
Authors: Waldmann Carl , Rhodes Andrew , Soni Neil , Handy Jonathan
Published: August 2019

This chapter discusses renal disorders and includes discussion on prevention of acute kidney injury, including optimizing renal perfusion with the use of volume expansion, inotropic, vasopressor, and vasodilator medications; modulation of renal physiology, including renal metabolism, tubular obstruction, oxygen radical damage, and renal regeneration and repair. This chapter also discusses the diagnosis of acute kidney injury, including parameters of glomerular function, urine analyses, biomarkers, ultrasound, autoimmune profiling, and renal biopsy.