bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of metal oxides toward organic dyes decolourisation and environmental remediation
Authors: Tan ThianKhoon , Khiew PoiSim , Chiu WeeSiong , Chia ChinHua
Published: July 2019

Enormous interest has been focused on metal oxides in its photocatalytic capabilities toward oxidizing organic dyes and environmental remediation. Zinc oxide (ZnO), titanium dioxide (TiO2) and iron oxide (Fe3O4) have been used as the heterogeneous photocatalysts to photodegrade three organic dyes, which are methylene blue (MB), phenol red (PR) and methyl orange (MO). Series of 3.0 ml dyes samples in aqueous solutions were placed into a UV chamber under UV-C (254 nm) light irradiation. The oxides powder was characterised by XRD, FESEM and TEM analysis, where ZnO nanoparticles was in hexagonal wurtzite crystal structure (SG: P63mc) with average crystalline size of (91 ± 12) nm and TiO2 nanoparticles was pure anatase of tetragonal crystal structure (SG: I4/
a

md) with average crystalline size of (117 ± 16) nm. Fe3O4 nanoparticles was in cubic spinel crystal structure with average crystalline size of (62.1 ± 5.7) nm. The photocatalyst loading (0.5 – 3.5wt%), initial dye concentration (MB: 2 – 12 ppm, PR: 8 – 48 ppm, MO: 12 – 32 ppm) and irradiation duration on the decolourisation of dye samples were examined. Based on time requirement, the photocatalytic decolourisation rate increased with increasing metal oxide loading and decreased with the increasing of the initial dye concentration. The superior photocatalyst was ZnO with a loading of 2.5 wt% followed by TiO2 (3.0 wt%) and least photocatalytic capability was Fe3O4 (3.0 wt%). On the other hand, the most photostable dye is MO followed by PR and MB.
Effects of electrochemical chloride extraction on the bonding properties of corroded reinforced concrete by the anode of magnesium phosphate cement bonding carbon fiber-reinforced plastics (CFRP)
Authors: Hao T Y , Lin H , Li Y , Zhao C
Published: July 2019

This paper studied the effects of electrochemical chloride extraction (ECE) on the bonding properties of corroded reinforced concrete with the anode of Magnesium phosphate cement (MPC) bond CFRP. The results indicated that ECE can efficiently remove the chloride ions in the concrete. The interfacial bonding properties of steel-concrete decreased with the increase of chloride removal current density. Proper corrosion ratio of steel bars can reduce the bonding strength loss caused by ECE treatment.
Research on Measurement of Loss Factor based on Transient State Decay Method
Authors: Peng Dewei , Wang Na , Li Guonan , Huo Ruidong
Published: July 2019

As an important parameter in application of the Statistical Energy Analysis (SEA), loss factor can measure damping characteristics of a system and determine the ability of vibration energy dissipation. First, the experimental models of steel plate structures are established. And then, the loss factor test is carried out based on transient state decay method. Finally, the variation characteristics of loss factor with medium, thickness and size of structures are explored. The results show that: (1) The loss factor of steel plates has the characteristics that larger at low frequency and small at high frequency, it decreases gradually with the increase of frequency. (2) For the same structure, the loss factor tested in water is greater than the loss factor tested in air. (3) The loss factor increases with the raise of thickness of plates when its cross-sectional dimension is constant.
Numerical Study of Hydrodynamic Noise of a Cone-column Combined Structure
Authors: Yu Chen , Shen Zhihua , Huang Guobing , Liu Jiangtao
Published: July 2019

Hydrodynamic noise is one of the main sound source of underwater vehicle. Flow noise and flow-excited noise are important part of hydrodynamic noise. In this paper, large eddy simulation is applied to simulate the flow field around a cone-column combined structure to obtain dipole sound source and turbulence fluctuating pressure. The surface pressure distribution is validated by experiment measured data. Structure dynamic response can be obtained by solving fluid-structure coupling equation. The flow noise and flow-excited noise of the structure are calculated according to acoustic analogy theory. From the numerical result, it can be seen the spectra characteristic of flow-excited noise is different from flow noise. The flow-excited noise obviously increases when system resonance occurs.
Large eddy simulation study on flow characteristics of ultrasonic heat meter at low Reynolds number
Authors: Liu Yonghui , Yi Fengyan , Zhou Changfeng , Tao Lili
Published: July 2019

Ultrasonic heat meter is widely used in heat metering, and its measurement accuracy depends on the flow characteristics of the reflected channel. In this paper, LES (Large Eddy Simulation) method is used to calculate the flow field of the ultrasonic heat meter at low Reynolds number. Through the analysis of the flow field, it is shown that the velocity gradient near the cylindrical reflector is larger, especially at the tail of the first cylindrical reflector; the eddy formed by the flow can scour the reflecting surface and prevent scaling; the average linear velocity over time of the reflecting channel is obtained by the calculation results. The range of velocity variation is 0.609%.
Innervated Dorsalis Pedis Advancement Flap for Burn Foot Contractures
Authors: Eubanks Ryan D , Bowker Harold Dean , Al-Mufarrej Faisal
Published: July 2019

Dorsal foot burns in children often result in contractures with hyperextension of the toes and secondary gait disturbances. Skin grafting a wound bed after contracture release can result in early recurrence. Adequate contracture release often requires tenolysis and/or joint releases that may be prohibitive of skin grafting and require flap coverage. Local flaps are often dismissed as inadequate. Free flaps and distraction techniques have both been described as difficult in the pediatric foot. We describe a single-stage V-Y advancement dorsalis pedis (DP) based fasciocutaneous flap technique that releases dorsal foot contractures in children without donor sites by recruiting tissue from the anterior ankle to the dorsal forefoot. DP-based flaps have not been described before in forefoot burn contracture release. The flap is performed on three children (ages 4–9 years) with unilateral dorsal feet contractures. Each child suffered from gait disturbance due to toe hyperextension. Three to four centimeters of advancement was obtained with each child. Contractures involved all toes but were worst in the second toe for all patients. Extensor tenolysis and/or metatarsal joint releases were performed in each case. Surgeries were performed as an outpatient with minimal postoperative pain. Postoperative leg splinting was not performed. All patients’ surgical sites healed without complication and with complete correction of contractures. Improved gait was noted postoperatively. The V-Y DP perforator advancement is a safe, effective, and reliable technique for dorsal foot burn contracture release in children without need for donor site or prolonged recovery.
Bactericidal Activity of Chrysomya rufifacies and Cochliomyia macellaria (Diptera: Calliphoridae) Larval Excretions–Secretions Against Staphylococcus aureus (Bacillales: Staphylococcaceae)
Authors: Fonseca-Muñoz Alicia , Pérez-Pacheco Rafael , Ortega-Morales Benjamín Otto , Reyes-Estebanez Manuela , Vásquez-López Alfonso , Chan-Bacab Manuel , Ruiz-Vega Jaime , Granados-Echegoyen Carlos A
Published: July 2019

The inhibitory effect of Chrysomya rufifacies (Macquart) and Cochliomyia macellaria (Fabricius) larval excretions–secretions (ES) on Staphylococcus aureus was determined using a portable colorimetric method without the need for any dedicated spectral instrument. Polystyrene 96 well microplates were used and 100 μl of the bacterial inoculum (5 × 105 CFU/ml) plus 100 μl of the dipteran exosecretions at different concentrations were added to each well. Subsequently, 50 μl of a 1% solution of the triphenyl tetrazolium chloride stain was added to each well to determine the bacterial viability. The color development in each well was measured with the ImageJ software S. aureus was exposed to different concentrations of the ES of both species individually. At a concentration of 800 ppm ES of C. rufifacies or Co. macellaria, bacterial growth was inhibited 97.45 ± 1.70% and 82.21 ± 1.88%, respectively. As expected, exposure to a lower concentration (i.e., 50 ppm) was less inhibitory (C. rufifacies ES, 77.65 ± 4.25% and Co. macellaria ES, 43.54 ± 4.63%). This study demonstrates for the first time the bactericidal activity of C. rufifacies and Co. macellaria ES against S. aureus. This finding is promising as it could result in the identification and synthesis of proteins capable of suppressing pathogen development in wounds. Additionally, the proposed method can simplify the use of expensive laboratory instruments for antimicrobial activity determination.
Identification of Host Blood Meals of Mosquitoes (Diptera: Culicidae) Collected at the Aripo Savannas Scientific Reserve in Trinidad, West Indies
Authors: Kang David S , Martinez Ray , Hosein Aliya , Shui Feng Rachel , James Lester , Lovin Diane D , Cunningham Joanne M , Miller Cally S T , Eng Matthew W , Chadee Dave D , Severson David W
Published: July 2019

Surveillance for blood-fed female mosquitoes was performed between August 2015 and February 2016 at sites along the periphery of the Aripo Savannas Environmentally Reserve (ASSR) located in northeastern Trinidad, West Indies. We collected engorged female mosquitoes representing 13 species. DNA extractions from dissected abdomens were subjected to PCR amplification with three primer pairs targeting the mitochondrial cytochrome oxidase I and cytochrome b gene sequences. High-quality sequence information and host identification were obtained for 42 specimens representing eight mosquito species with at least one primer combination. A broad range of vertebrates including humans were identified, but the majority were nonhuman mammals, both domestic and wild. Domestic dogs were the most common host and may represent potential sentinel species for monitoring local enzootic arbovirus activity in Trinidad. Culex declarator Dyer and Knab and Culex nigripalpus Theobald were the most common blood-fed mosquito species comprising 79.1% of the total number identified. These species obtained blood meals from birds, nonhuman mammals, and human hosts, and therefore pose significant risks as potential bridge vectors for epizootic arbovirus transmission in the ASSR area as well as other sylvan areas in Trinidad. These data represent the first such results for Trinidad.
Evaluating Screening Participation, Follow-up, and Outcomes for Breast, Cervical, and Colorectal Cancer in the PROSPR Consortium
Authors: Barlow William E , Beaber Elisabeth F , Geller Berta M , Kamineni Aruna , Zheng Yingye , Haas Jennifer S , Chao Chun R , Rutter Carolyn M , Zauber Ann G , Sprague Brian L , Halm Ethan A , Weaver Donald L , Chubak Jessica , Doria-Rose V Paul , Kobrin Sarah , Onega Tracy , Quinn Virginia P , Schapira Marilyn M , Tosteson Anna N A , Corley Douglas A , Skinner Celette Sugg , Schnall Mitchell D , Armstrong Katrina , Wheeler Cosette M , Silverberg Michael J , Balasubramanian Bijal A , Doubeni Chyke A , McLerran Dale , Tiro Jasmin A
Published: July 2019

Background

Cancer screening is a complex process encompassing risk assessment, the initial screening examination, diagnostic evaluation, and treatment of cancer precursors or early cancers. Metrics that enable comparisons across different screening targets are needed. We present population-based screening metrics for breast, cervical, and colorectal cancers for nine sites participating in the Population-based Research Optimizing Screening through Personalized Regimens consortium.

Methods

We describe how selected metrics map to a trans-organ conceptual model of the screening process. For each cancer type, we calculated calendar year 2013 metrics for the screen-eligible target population (breast: ages 40–74 years; cervical: ages 21–64 years; colorectal: ages 50–75 years). Metrics for screening participation, timely diagnostic evaluation, and diagnosed cancers in the screened and total populations are presented for the total eligible population and stratified by age group and cancer type.

Results

The overall screening-eligible populations in 2013 were 305 568 participants for breast, 3 160 128 for cervical, and 2 363 922 for colorectal cancer screening. Being up-to-date for testing was common for all three cancer types: breast (63.5%), cervical (84.6%), and colorectal (77.5%). The percentage of abnormal screens ranged from 10.7% for breast, 4.4% for cervical, and 4.5% for colorectal cancer screening. Abnormal breast screens were followed up diagnostically in almost all (96.8%) cases, and cervical and colorectal were similar (76.2% and 76.3%, respectively). Cancer rates per 1000 screens were 5.66, 0.17, and 1.46 for breast, cervical, and colorectal cancer, respectively.

Conclusions

Comprehensive assessment of metrics by the Population-based Research Optimizing Screening through Personalized Regimens consortium enabled systematic identification of screening process steps in need of improvement. We encourage widespread use of common metrics to allow interventions to be tested across cancer types and health-care settings.
Over-the-scope-clip treatment of gastrobronchial fistula following minimally invasive oesophagectomy: a novel approach
Authors: Kordzadeh Ali , Syllaios Athanasios , Davakis Spyridon , Lorenzi Bruno , Jayanthi Naga V , Tang Cheuk-Bong , Charalabopoulos Alexandros
Published: July 2019

Gastrobronchial fistulae (GBF) following minimally invasive oesophagectomy (MIO) is a rare entity, with an estimated incidence of 0.3–1.5% according to the published literature. It could present with persistent cough (Ohno’s sign), chest pain, haemoptysis and recurrent pneumonia. Barium swallow examination remains the most sensitive investigation in 78% of the cases; the main stay of management is surgical and in some cases endoscopic (stent insertion). We report a rare case of a GBF 1 month after two-stage MIO for cancer of the gastro-oesophageal junction, which was successfully treated for the first time with an over-the-scope-clip.
Closing the yield gap: can metabolomics be of help?
Authors: Sulpice Ronan
Published: July 2019

This article comments on:

Melandri G, AbdElgawad H, Riewe D, Hageman JA, Asard H, Beemster GTS, Kadam N, Jagadish K, Altmann T, Ruyter-Spira1 C, Bouwmeester H. 2019. Biomarkers for grain yield stability in rice under drought stress. Journal of Experimental Botany 71, 669–683.
On the ridges, undulations & streams in Gaia DR2: Linking the topography of phase-space to the orbital structure of an N-body bar
Authors: Fragkoudi F , Katz D , Trick W , White S D M , Di Matteo P , Sormani M C , Khoperskov S , Haywood M , Hallé A , Gómez A
Published: July 2019

We explore the origin of phase-space substructures revealed by the second Gaia data release in the disc of the Milky Way, such as the ridges in the Vφ-r plane, the undulations in the Vφ-r-Vr space and the streams in the Vφ-Vr plane. We use a collisionless N-body simulation with co-spatial thin and thick discs, along with orbit integration, to study the orbital structure close to the Outer Lindblad Resonance (OLR) of the bar. We find that a prominent, long-lived ridge is formed in the Vφ-r plane due to the OLR which translates to streams in the Vφ-Vr plane and examine which closed periodic and trapped librating orbits are responsible for these features. We find that orbits which carry out small librations around the x1(1) family are preferentially found at negative Vr, giving rise to a ‘horn’-like feature, while orbits with larger libration amplitudes, trapped around the x1(2) and x1(1) families, constitute the positive Vr substructure, i.e. the Hercules-like feature. This changing libration amplitude of orbits will translate to a changing ratio of thin/thick disc stars, which could have implications on the metallicity distribution in this plane. We find that a scenario in which the Sun is placed close to the OLR gives rise to a strong asymmetry in Vr in the Vφ-Vr plane (i.e. Hercules vs. ‘the horn’) and subsequently to undulations in the Vφ-r-Vr space. We also explore a scenario in which the Sun is placed closer to the bar corotation and find that the bar perturbation alone cannot give rise to the these features.
Dark matter and H i in ultra-diffuse galaxy UGC 2162
Authors: Sengupta Chandreyee , Scott T C , Chung Aeree , Wong O Ivy
Published: July 2019

Our GMRT (Giant Metrewave Radio Telescope) H i observations of the ultra-diffuse galaxy (UDG) UGC 2162, projected ∼ 300 kpc from the centre of the M 77 group, reveal it to a have an extended H i disc ($R_{\rm H\,{\small I}}/R_{25}$ ∼ 3.3) with a moderate rotational velocity (Vrot ∼ 31 km s−1). This Vrotis in line with that of dwarf galaxies with similar H i mass. We estimate an Mdyn of ∼1.14 × 109 M⊙ within the galaxy’s $R_ \rm {H\,{\small I}}$ ∼ 5.2 kpc. Additionally, our estimates of M200 for the galaxy from NFW models are in the range of 5.0–8.8 × 1010 M⊙. Comparing UGC 2162 to samples of UDGs with H i detections show it to have amongst the smallest Re with its MH i/M* being distinctly higher and g – icolour slightly bluer than typical values in those samples. We also compared H i and dark matter (DM) halo properties of UGC 2162 with dwarf galaxies in the LITTLE THINGS sample and find its DM halo mass and profile are within the range expected for a dwarf galaxy. While we were unable to determine the origin of the galaxy’s present-day optical form from our study, its normal H i rotation velocity in relation to its H i mass, H i morphology, environment, and dwarf mass DM halo ruled out some of the proposed ultra-diffuse galaxy formation scenarios for this galaxy.
SDSS-IV MaNGA: effects of morphology in the global and local star formation main sequences
Authors: Cano-Díaz M , Ávila-Reese V , Sánchez S F , Hernández-Toledo H M , Rodríguez-Puebla A , Boquien M , Ibarra-Medel H
Published: July 2019

We study the global star formation rate (SFR) versus stellar mass (M*) correlation, and the spatially resolved SFR surface density (ΣSFR) versus stellar mass surface density (Σ*) correlation, in a sample of ∼2000 galaxies from the MaNGA MPL-5 survey. We classify galaxies and spatially resolved areas into star forming and retired according to their ionization processes. We confirm the existence of a star-forming main sequence (SFMS) for galaxies and spatially resolved areas, and show that they have the same nature, with the global as a consequence of the local one. The latter presents a bend below a limit Σ* value, ≈3 × 107 M$\odot$ kpc−2, which is not physical. Using only star-forming areas (SFAs) above this limit, a slope and a scatter of ≈1 and ≈0.27 dex are determined. The retired galaxies/areas strongly segregate from their respective SFMSs, by ∼−1.5 dex on average. We explore how the global/local SFMSs depend on galaxy morphology, finding that for star-forming galaxies and SFAs, there is a trend to lower values of star formation activity with earlier morphological types, which is more pronounced for the local SFMS. The morphology not only affects the global SFR due to the diminish of SFAs with earlier types, but also affects the local SF process. Our results suggest that the local SF at all radii is established by some universal mechanism partially modulated by morphology. Morphology seems to be connected to the slow aging and sharp decline of the SF process, and on its own it may depend on other properties as the environment.
Detectability of neutron star merger afterglows
Authors: Gottlieb Ore , Nakar Ehud , Piran Tsvi
Published: July 2019

VLBI and JVLA observations revealed that GW170817 involved a narrow jet (θj ≈ 4°) that dominated the afterglow peak at our viewing angle, θobs ≈ 20°. This implies that at the time of the afterglow peak, the observed signal behaved like an afterglow of a top-hat jet seen at θobs ≫ θj, and it can be modelled by analytic expressions that describe such jets. We use a set of numerical simulations to calibrate these analytic relations and obtain generic equations for the peak time and flux of such an afterglow as seen from various observing angles. Using the calibrated equations and the estimated parameters of GW170817, we estimate the detectability of afterglows from future double neutron star mergers during the Advanced LIGO/Virgo observation run O3. GW170817 took place at a relatively low-density environment. Afterglows of similar events will be detectable only at small viewing angles, θobs ≲ 20°, and only 20 per cent of the GW detections of these events will be accompanied by a detectable afterglow. At higher densities, more typical to sGRB sites, up to $70\,\rm{per\,cent}$ of the GW detections are expected to be followed by a detectable afterglow, typically at θobs ∼ 30°. We also provide the latest time one should expect an afterglow detection. We find that for typical parameters, if the jet emission had not been detected within about a year after the merger, it is unlikely to be ever detected.
A Nationwide Survey of Cytomegalovirus Prevention Strategies in Kidney Transplant Recipients in a Resource-Limited Setting
Authors: Bruminhent Jackrapong , Bushyakanist Asalaysa , Kantachuvesiri Surasak , Kiertiburanakul Sasisopin
Published: July 2019

Objective

Strategies to prevent cytomegalovirus (CMV) infection in resource-limited settings have been under-explored. We investigated CMV prevention strategies utilized among transplant centers in Thailand.

Method

A questionnaire on CMV prevention strategies for kidney transplant (KT) recipients was developed using a web-based electronic survey website (www.surveymonkey.com). The survey was delivered to 31 transplant centers in Thailand. One infectious disease physician (ID) and 1 nephrologist (NP) from each center were included.

Results

There were 43 respondents from 26 of the 31 transplant centers (84%), including 26 (60%) IDs and 17 (40%) NPs. Forty-one 95% (41/43) physicians agreed on the necessity of CMV prevention. Of these, 77% (33/43) physicians implemented prevention strategies for their patients. Interventions included preemptive approaches (48%), prophylaxis (45%), hybrid approaches; surveillance after prophylaxis (3%), and CMV-specific immunity-guided approaches (3%). For CMV-seropositive KT recipients, use of preemptive approaches (84%) exceeded prophylaxis (12%). However, 81% of the former preferred targeted prophylaxis in patients receiving antithymocyte globulin therapy. Sixty-five percent and 93% of physicians started preemptive therapy when plasma CMV DNA loads reached 2000 and 3000 copies/mL (1820 and 2730 IU/mL), respectively. A significantly greater percentage of NPs initiated preemptive therapy at a plasma CMV DNA load of 1820 IU/mL compared with IDs (88% vs 50%; P = .02). The most common barrier to prevention strategy implementation was financial inaccessibility of oral valganciclovir (67%) and quantitative CMV DNA testing (12%).

Conclusions

Most physicians agreed on a need for preemptive approaches, although prophylaxis was targeted in those receiving intense immunosuppression. The financial implication is the main barrier for CMV prevention in Thailand.
Current practice in plankton metabarcoding: optimization and error management
Authors: Santoferrara Luciana F
Published: July 2019

High-throughput sequencing of a targeted genetic marker is being widely used to analyze biodiversity across taxa and environments. Amid a multitude of exciting findings, scientists have also identified and addressed technical and biological limitations. Improved study designs and alternative sampling, lab and bioinformatic procedures have progressively enhanced data quality, but some problems persist. This article provides a framework to recognize and bypass the main types of errors that can affect metabarcoding data: false negatives, false positives, artifactual variants, disproportions and incomplete or incorrect taxonomic identifications. It is crucial to discern potential error impacts on different ecological parameters (e.g. taxon distribution, community structure, alpha and beta-diversity), as error management implies compromises and is thus directed by the research question. Synthesis of multiple plankton metabarcoding evaluations (mock sample sequencing or microscope comparisons) shows that high-quality data for qualitative and some semiquantitative goals can be achieved by implementing three checkpoints: first, rigorous protocol optimization; second, error minimization; and third, downstream analysis that considers potentially remaining biases. Conclusions inform us about the reliability of metabarcoding for plankton studies and, because plankton provides unique chances to compare genotypes and phenotypes, the robustness of this method in general.
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies
Authors: Whidden Chris , Claywell Brian C , Fisher Thayer , Magee Andrew F , Fourment Mathieu , Matsen Frederick A
Published: July 2019

Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree space systematically, and never return to the same topology. In this article, we present an efficient parallelized method to map out the high likelihood set of phylogenetic tree topologies via systematic search, which we show to be a good approximation of the high posterior set of tree topologies on the data sets analyzed. Here, “likelihood” of a topology refers to the tree likelihood for the corresponding tree with optimized branch lengths. We call this method “phylogenetic topographer” (PT). The PT strategy is very simple: starting in a number of local topology maxima (obtained by hill-climbing from random starting points), explore out using local topology rearrangements, only continuing through topologies that are better than some likelihood threshold below the best observed topology. We show that the normalized topology likelihoods are a useful proxy for the Bayesian posterior probability of those topologies. By using a nonblocking hash table keyed on unique representations of tree topologies, we avoid visiting topologies more than once across all concurrent threads exploring tree space. We demonstrate that PT can be used directly to approximate a Bayesian consensus tree topology. When combined with an accurate means of evaluating per-topology marginal likelihoods, PT gives an alternative procedure for obtaining Bayesian posterior distributions on phylogenetic tree topologies.
Inactivation of the Phosphatase CheZ Alters Cell-Surface Properties of Azorhizobium caulinodans ORS571 and Symbiotic Association with Sesbania rostrata
Authors: Liu Xiaolin , Xie Zhihong
Published: July 2019

Azorhizobium caulinodans can form root and stem nodules with the host plant Sesbania rostrata. The role of the CheZ phosphatase in the A. caulinodans chemotaxis pathway was previously explored using the nonchemotactic cheZ mutant strain (AC601). This mutant displayed stronger attachment to the root surface, enhancing early colonization; however, this did not result in increased nodulation efficiency. In this study, we further investigated the role of CheZ in the interaction between strain ORS571 and the roots of its host plant. By tracking long-term colonization dynamic of cheZ mutant marked with LacZ, we found a decrease of colonization of the cheZ mutant during this process. Furthermore, the cheZ mutant could not spread on the root surface freely and was gradually outcompeted by the wild type in original colonization sites. Quantitative reverse-transcription PCR analyses showed that exp genes encoding exopolysaccharides synthesis, including oac3, were highly expressed in the cheZ mutant. Construction of a strain carrying a deletion of both cheZ and oac3 resulted in a mutant strain defective in the colonization process to the same extent as found with the oac3 single-mutant strain. This result suggested that the enhanced colonization of the cheZ mutant may be achieved through regulating the formation of exopolysaccharides. This shows the importance of the chemotactic proteins in the interaction between rhizobia and host plants, and expands our understanding of the symbiosis interaction between rhizobium and host plant.
QTL Mapping of Adult-Plant Resistance to Leaf and Stripe Rust in Wheat Cross SW 8588/Thatcher using the Wheat 55K SNP Array
Authors: Zhang Peipei , Li Xing , Gebrewahid Takele-Weldu , Liu Hexing , Xia Xianchun , He Zhonghu , Li Zaifeng , Liu Daqun
Published: July 2019

Wheat leaf rust (caused by Puccinia triticina) and stripe rust (caused by Puccinia striiformis f. sp. tritici) cause large production losses in many regions of the world. The objective of this study was to identify quantitative trait loci (QTL) for resistance to leaf rust and stripe rust in a recombinant inbred line population derived from a cross between wheat cultivars SW 8588 and Thatcher. The population and parents were genotyped with the Wheat 55K SNP Array and SSR markers and phenotyped for leaf rust severity at Zhoukou in Henan Province and Baoding in Hebei Province. Stripe rust responses were also evaluated at Chengdu in Sichuan Province, and at Baoding. Seven and six QTL were detected for resistance to leaf rust and stripe rust, respectively. Four QTL on chromosomes 1BL, 2AS, 5AL, and 7BL conferred resistance to both rusts. The QTL on 1BL and 2AS were identified as Lr46/Yr29 and Lr37/Yr17, respectively. QLr.hebau-2DS from Thatcher, identified as Lr22b that was previously thought to be ineffective in China, contributed a large effect for leaf rust resistance. QLr.hebau-5AL/QYr.hebau-5AL, QLr.hebau-3BL, QLr.hebau-6DS, QYr.hebau-4BS, and QYr.hebau-6DS are likely to be new QTL, but require further validation. Kompetitive allele-specific PCR (KASP) markers for QLr.hebau-2DS and QLr.hebau-5AL/QYr.hebau-5AL were successfully developed and validated in a diverse wheat panel from Sichuan Province, indicating their usefulness under different genetic backgrounds. These QTL and their closely linked SNP and SSR markers will be useful for fine mapping, candidate gene discovery, and marker-assisted selection in breeding for durable resistance to both leaf and stripe rusts.
Pathogenicity and a TaqMan Real-Time PCR for Specific Detection of Pantoea allii, a Bacterial Pathogen of Onions
Authors: Rahimi-Khameneh Shabnam , Hsieh Sanni , Xu Renlin , Avis Tyler J. , Li Sean , Smith Donna , Dutta Bhabesh , Gitaitis Ronald D. , Tambong James T.
Published: July 2019

Bacterial diseases of onion are reported to cause significant economic losses. Pantoea allii Brady, one of the pathogens causing the center rot on onions, has not yet been reported in Canada. We report the pathogenicity of P. allii on commercially available Canadian green onions (scallions). All P. allii-inoculated plants, irrespective of the inoculum concentration, exhibited typical leaf chlorotic discoloration on green onion leaves, which can reduce their marketability. Reisolation of P. allii from infected scallion tissues and reidentification by sequencing and phylogenetic analyses of the leuS gene suggest that the pathogen can survive in infected tissues 21 days after inoculation. This is the first report of P. allii as a potential pathogen of green onions. This study also reports the development and validation of a TaqMan real-time PCR assay targeting the leuS gene for reliable detection of P. allii in pure cultures and in planta. A 642-bp leuS gene fragment was targeted because it showed high nucleotide diversity and positively correlated with genome-based average nucleotide identity with respect to percent similarity index and identity of Pantoea species. The assay specificity was validated using 61 bacterial and fungal strains. Under optimal conditions, the selected primers and FAM-labeled TaqMan probe were specific for the detection of nine reference P. allii strains by real-time PCR. The 52 strains of other Pantoea spp. (n = 25), non-Pantoea spp. (n = 20), and fungi/oomycetes (n = 7) tested negative (no detectable fluorescence). Onion tissues spiked with P. allii, naturally infested onion bulbs, greenhouse infected green onion leaf samples, as well as an interlaboratory blind test were used to validate the assay specificity. The sensitivities of a 1-pg DNA concentration and 30 CFU are comparable to previously reported real-time PCR assays of other bacterial pathogens. The TaqMan real-time PCR assay developed in this study will facilitate reliable detection of P. allii and could be a useful tool for screening onion imports or exports for the presence of this pathogen.
Phytophthora abietivora, A New Species Isolated from Diseased Christmas Trees in Connecticut, U.S.A.
Authors: Li De-Wei , Schultes Neil P. , LaMondia James A. , Cowles Richard S.
Published: July 2019

A number of fir species (Abies) are produced as Christmas trees around the world. In particular, Fraser fir (Abies fraseri (Pursh) Poir.) is popular as it yields high-quality Christmas trees in temperate North America and Europe. A Phytophthora sp. causing root rot on Fraser fir was isolated from a Christmas tree farm in Connecticut, U.S.A., and found to be new to science according to morphological and molecular phylogenetic analysis using multilocus DNA sequences from ITS, Cox1, β-Tub, Nadh1, and Hsp90 loci. Thus, it was described and illustrated as Phytophthora abietivora. An informative Koch’s postulates test revealed that P. abietivora was the pathogen causing root rot of Fraser fir.
Pathogenicities of Rice Blast (Pyricularia oryzae Cavara) Isolates From Kenya
Authors: Fukuta Yoshimichi , Telebanco-Yanoria Mary Jeanie , Hayashi Nagao , Yanagihara Seiji , Machungo Catherine Wanjiku , Makihara Daigo
Published: July 2019

A total of 99 isolates of rice blast (Pyricularia oryzae Cavara) were collected from 2010 to 2015 from four regions in Kenya: Kirinyaga County and Embu County, Kisumu County, Tana River County, and Mombasa County. The pathogenicities of these isolates were clarified based on the reaction patterns of Lijiangxintuanheigu and differential varieties (DVs) targeting 23 resistance genes. The frequency of virulent isolates was high for DVs for Pib, Pia, Pii, Pi3, Pi5(t), Pik-s, Pik-m, Pi1, Pik-h, Pik, Pik-p, Pi7(t), Pi19(t), and Pi20(t); low for DVs for Pish, Pi9(t), Piz-5, and Piz-t; and intermediate for the remaining DVs for Pit, Piz, Pita-2, Pita, and Pi12(t). These blast isolates were classified into three cluster groups: Ia, Ib, and II. The frequencies of virulent isolates to DVs for Pit, Pii, Pik-m, Pi1, Pik-h, Pik, Pik-p, Pi7(t), Piz, and Pi12(t) differed markedly between clusters I and II, and those of DVs for Pib, Pit, Pia, Pi3, Pita-2, Pita, and Pi20(t) differed between Ia and Ib. The frequencies of cluster groups in the four geographical regions were different. A total of 62 races were found, with 19 blast isolates categorized into one race (U63-i7-k177-z00-ta003), whereas the other races included only some isolates in each.
First Report of Ectomycorrhizal Fungus, Laccaria ochropurpurea, Associated with Castanea dentata (American Chestnut) Roots in a Mixed-Species Plantation
Authors: Ritzi Morgan V. , Russell Stephen D. , Aime M. Catherine , McNickle Gordon G.
Published: July 2019

American chestnut (Castanea dentata) is critically endangered by chestnut blight caused by Cryphonectria parasitica. Beneficial interactions with mutualistic ectomycorrhizae sometimes confer resistance to pathogens; however, little is known about the mycorrhizal partners of American chestnut. Basidiocarps of Laccaria ochropurpurea were observed in a 10-year-old American chestnut plantation. The identity of the species was confirmed utilizing the nuclear ribosomal internal transcribed spacer. In spring 2018, root fragments were excised from beneath three American chestnut trees in three separate plots where basidiocarps were observed. Root tips with evidence of mycorrhizal fungal colonization were pooled, extracted, and sequenced to confirm both the plant host and mycorrhizal associates. To our knowledge, this is the first direct confirmation of American chestnut roots associated with L. ochropurpurea. We suggest further studies to investigate whether this association is common, whether it confers any disease resistance, and if this mutualistic association could be employed in restoration efforts of the American chestnut.
A Comparison of Costs: How California Teaching Hospitals Achieved Slower Growth Than Nonteaching Hospitals in Operating Room Costs From 2005 to 2014
Authors: Childers Christopher P. , Maggard-Gibbons Melinda , Nuckols Teryl
Published: July 2019

Purpose

Historically, teaching hospitals have had higher costs than nonteaching hospitals, introducing potential financial risk in value-based payment models. This study compared risk-adjusted operating room (OR) costs between California teaching and nonteaching hospitals.

Method

Using 2,992 financial statements from fiscal years (FYs) 2005–2014, the authors extracted data for OR total costs, components of direct costs, and indirect costs. Cross-sectional and longitudinal models estimated OR costs per minute of surgery by teaching status, ownership, case mix index, and geographic area.

Results

Risk-adjusted cost was $9.44 per minute less in teaching than nonteaching hospitals in FY 2014 (95% CI, 3.03–15.85, P = .004). Between FY 2005 and FY 2014, OR costs grew more slowly at teaching hospitals because of slower wage growth and indirect costs per minute (−$0.13 and −$0.77 per minute per year, respectively, P = .005 and P < .001). Hourly pay rose more at teaching hospitals ($0.26 per hour per year, P = .008) but was offset by slower full-time equivalents growth (−0.002 per 10,000 OR minutes per year, P = .001). Between FY 2005 and FY 2014, operative volume increased at teaching hospitals and decreased at nonteaching hospitals.

Conclusions

By 2014, California teaching hospitals had lower OR costs per minute than nonteaching hospitals because of relative labor productivity gains and slower indirect cost growth. The latter likely resulted from a volume shift from nonteaching to teaching facilities. These trends will help teaching hospitals compete under value-based models. Implications for patients and nonteaching hospitals warrant evaluation.
“Getting Out of That Siloed Mentality Early”: Interprofessional Learning in a Longitudinal Placement for Early Medical Students
Authors: Rivera Josette , O’Brien Bridget , Wamsley Maria
Published: July 2019

Purpose

Although descriptions of interprofessional education often focus on interactions among students from multiple professions, embedding students from 1 profession in clinical settings may also provide rich opportunities for interprofessional learning (IPL). This study examines affordances and barriers to medical students’ interactions with and opportunities to learn from health care professionals while learning health systems science in clinical workplaces.

Method

In May 2017, 14 first-year medical students at the University of California, San Francisco participated in a semistructured interview about IPL experiences during a 17-month, weekly half-day clinical microsystem placement focused on systems improvement (SI) projects and clinical skills. Communities of practice and workplace learning frameworks informed the interview guide. The authors analyzed interview transcripts using conventional qualitative content analysis.

Results

The authors found much variation among the 14 students’ interprofessional interactions and experiences in 12 placement sites (7 outpatient, 4 inpatient, 1 emergency department). Factors influencing the depth of interprofessional interactions included the nature of the SI project, clinical workflow, student and staff schedules, workplace culture, and faculty coach facilitation of interprofessional interactions. Although all students endorsed the value of learning about and from diverse health care professionals, they were reluctant to engage with, or “burden,” them.

Conclusions

There are significant IPL opportunities for early medical students in longitudinal placements focused on SI and clinical skills. Formal curricular activities, SI projects conducive to interprofessional interactions, and faculty development can enhance the quality of workplace-based IPL.
Interleukin-10 Does Not Augment Osseous Regeneration in the Scarred Calvarial Defect Achieved with Low-Dose Biopatterned BMP2
Authors: Brooker Jack E. , Bykowski Michael R. , Camison Liliana , Yerneni Saigopalakrishna , Campbell Phil G. , Weiss Lee , Mooney Mark P. , Cray James J. , Cooper Gregory M. , Losee Joseph E.
Published: July 2019

Background:

Large calvarial defects represent a major reconstructive challenge, as they do not heal spontaneously. Infection causes inflammation and scarring, further reducing the healing capacity of the calvaria. Bone morphogenetic protein-2 (BMP2) has been shown to stimulate osteogenesis but has significant side effects in high doses. BMP2 has not been tested in combination with antiinflammatory cytokines such as interleukin-10.

Methods:

Sixteen New Zealand White rabbits underwent 15 × 15-mm flap calvarectomies. The flap was incubated in Staphylococcus aureus and replaced, and infection and scarring were allowed to develop. The flap was subsequently removed and the wound débrided. A 15 × 15-mm square of acellular dermal matrix biopatterned with low-dose BMP2, interleukin-10, or a combination was implanted. Computed tomographic scans were taken over 42 days. Rabbits were then killed and histology was performed.

Results:

Defects treated with BMP2 showed significantly (p < 0.05) greater osseous regeneration than untreated controls. Interleukin-10 did not significantly augment the healing achieved with BMP2, and interleukin-10 alone did not significantly increase healing compared with controls. Histology showed evidence of bone formation in defects treated with BMP2. Untreated controls and defects treated with interleukin-10 alone showed only fibrous tissue in the defect site.

Conclusions:

Low-dose BMP2 delivered directly to the scarred calvarial defect augments bony healing. Interleukin-10 at the dose applied did not significantly augment healing alone or in combination with BMP2. Healing had not finished at 42 days and analysis at later time points or the use of higher doses of BMP2 may yield greater healing.
Three-Dimensional Outcome Assessments of Cleft Lip and Palate Patients Undergoing Maxillary Advancement
Authors: Wu Te-Ju , Lee Yi-Hao , Chang Yu-Jen , Lin Shiu-Shiung , Lin Feng-Chang , Kim Yong-Il , Ko Ching-Chang , Lai Jui-Pin
Published: July 2019

Background:

The aim of this retrospective case series study was to compare three-dimensional postsurgical outcomes of patients with cleft lip and palate following maxillary advancement.

Methods:

Fifty consecutive cleft lip and palate patients who underwent whole-pieced Le Fort I advancements were assigned to the major (advancement ≥ 5 mm) or minor (advancement < 5 mm) groups. Three-dimensional surgical simulation was used for presurgical evaluation and planning. Virtual triangles of the presurgical, simulated, and 6-month postoperative stages were used for comparison. Translational and angular changes of each endpoint (A-point, MxR, and MxL) on the virtual triangles and reference planes were recorded and analyzed. Relationships between possible related variables and outcome discrepancies from simulations among all subgroups were also investigated.

Results:

Analysis of covariance and the least significant difference test revealed that the outcome discrepancy measurements were affected by different combinations of independent variables. The reliability test showed high consistency of the authors’ method for three-dimensional measurements.

Conclusions:

The actual surgical outcomes of cleft lip and palate patients differed from the virtual simulations. The outcome discrepancies are impacted by multiple factors. The outcome discrepancies of all rotational surgical corrections (roll, yaw, and pitch) were positively correlated to the degree of planned surgical movement. Meanwhile, bilateral cleft lip and palate patients are more likely to incur outcome discrepancies in yaw correction with major maxillary advancement. However, a maxillary advancement cutoff value of 5 mm would not necessarily lead to significant translational outcome discrepancies among cleft lip and palate patients.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data
Authors: Danesh Gonché , Virlogeux Victor , Ramière Christophe , Charre Caroline , Cotte Laurent , Alizon Samuel
Published: July 2019

Opioid substitution and syringes exchange programs have drastically reduced hepatitis C virus (HCV) spread in France but HCV sexual transmission in men having sex with men (MSM) has recently arisen as a significant public health concern. The fact that the virus is transmitting in a heterogeneous population, with ‘new’ and ‘classical’ hosts, makes prevalence and incidence rates poorly informative. However, additional insights can be gained by analyzing virus phylogenies inferred from dated genetic sequence data. By combining a phylodynamics approach based on Approximate Bayesian Computation (ABC) and an original transmission model, we estimate key epidemiological parameters of an ongoing HCV epidemic among MSMs in Lyon (France). We show that this new epidemic is largely independent of the ‘classical’ HCV epidemics and that its doubling time is ten times lower (0.44 yearsversus4.37 years). These results have practical implications for HCV control and illustrate the additional information provided by virus genomics in public health.
CD44 regulates epigenetic plasticity by mediating iron endocytosis
Authors: Müller Sebastian , Sindikubwabo Fabien , Cañeque Tatiana , Lafon Anne , Versini Antoine , Lombard Bérangère , Loew Damarys , Durand Adeline , Vallot Céline , Baulande Sylvain , Servant Nicolas , Rodriguez Raphaël
Published: July 2019

CD44 is a transmembrane glycoprotein that is linked to various biological processes reliant on the epigenetic plasticity of cells, including development, inflammation, immune responses, wound healing and cancer progression. While thoroughly studied, functional regulatory roles of this so-called ‘cell surface marker’ remain elusive. Here, we report the discovery that CD44 mediates endocytosis of iron interacting with hyaluronates in tumorigenic cell lines and primary cancer cells. We found that this glycan-mediated iron endocytosis mechanism is enhanced during epithelial-mesenchymal transition, unlike the canonical transferrin-dependent pathway. This transition is further characterized by molecular changes required for iron-catalyzed oxidative demethylation of the repressive histone mark H3K9me2 that governs the expression of mesenchymal genes.CD44itself is transcriptionally regulated by nuclear iron, demonstrating a positive feedback loop, which is in contrast to the negative regulation of transferrin receptor by excess iron. Finally, we show that epigenetic plasticity can be altered by interfering with iron homeostasis using small molecules. This comprehensive study reveals an alternative iron uptake mechanism that prevails in the mesenchymal state of mammalian cells, illuminating a central role of iron as a rate-limiting regulator of epigenetic plasticity.