bluuebunny/crossref_metadata_2025_split huggingface dataset:
Grain density and its impact on grain filling characteristic of rice: mechanistic testing of the concept in genetically related cultivars
Authors: Das Kaushik , Panda Binay B. , Shaw Birendra P. , Das Satya R. , Dash Sushanta K. , Kariali Ekamber , Mohapatra Pravat K. 
Published: March 2018

AbstractPhysiological factors controlling assimilate partitioning was compared in relation to panicle architecture of lax- (Upahar) and compact-panicle (Mahalaxmi) rice cultivars. Grain number and ethylene production at anthesis are low, but filling rate is high in the former compared to high grain number and ethylene production and poor filling trait of the latter. Similar to Mahalaxmi, its progenitors Pankaj and Mahshuri, had attributes of high grain number and grain density, but grain filling was higher and ethylene evolution was lower. Disturbed genetic coherence owing to imbalance of gene groups brought in the cross combinations of Mahshuri and Pankaj could be responsible for high ethylene production leading to semi sterility of Mahalaxmi as the hormone slackened endosperm starch bio-synthesis enzyme activities. Mahalaxmi inherited grain compactness trait of its progenitors, but not the physiological attribute for reduced ethylene production, which impacted grain filling. Upahar, the progeny genotype of Mahalaxmi and IR62 cross, inherited the dominant allele for low ethylene production and good grain filling traits from the high yielding IR62. In conclusion grain filling in compact-panicle rice becomes poor subject to expression of recessive allele for high ethylene production, but the allele is amenable for suppression by corresponding dominant allele in a genetic breeding.
Low incubation temperature during early development negatively affects survival and related innate immune processes in zebrafish larvae exposed to lipopolysaccharide
Authors: Zhang Qirui , Kopp Martina , Babiak Igor , Fernandes Jorge M. O. 
Published: March 2018

AbstractIn many fish species, the immune system is significantly constrained by water temperature. In spite of its critical importance in protecting the host against pathogens, little is known about the influence of embryonic incubation temperature on the innate immunity of fish larvae. Zebrafish (Danio rerio) embryos were incubated at 24, 28 or 32 °C until first feeding. Larvae originating from each of these three temperature regimes were further distributed into three challenge temperatures and exposed to lipopolysaccharide (LPS) in a full factorial design (3 incubation × 3 challenge temperatures). At 24 h post LPS challenge, mortality of larvae incubated at 24 °C was 1.2 to 2.6-fold higher than those kept at 28 or 32 °C, regardless of the challenge temperature. LPS challenge at 24 °C stimulated similar immune-related processes but at different levels in larvae incubated at 24 or 32 °C, concomitantly with the down-regulation of some chemokine and lysozyme transcripts in the former group. Larvae incubated at 24 °C and LPS-challenged at 32 °C exhibited a limited immune response with up-regulation of hypoxia and oxidative stress processes. Annexin A2a, S100 calcium binding protein A10b and lymphocyte antigen-6, epidermis were identified as promising candidates for LPS recognition and signal transduction.
Celecoxib alleviates nonalcoholic fatty liver disease by restoring autophagic flux
Authors: Liu Cong , Liu Lian , Zhu Hai-Dan , Sheng Jia-Qi , Wu Xiao-Li , He Xing-Xing , Tian De-An , Liao Jia-Zhi , Li Pei-Yuan 
Published: March 2018

AbstractNonalcoholic fatty liver disease (NAFLD) is a kind of liver lipid synthesis and degradation imbalance related with metabolic syndrome. Celecoxib shows the function of ameliorating NAFLD, but the underlying mechanisms remain unknown. Here, we discuss the possible mechanisms of celecoxib alleviating NAFLD by restoring autophagic flux. Lipids were accumulated in L02 cells treated with palmitate as well as SD rats fed with high-fat diet. Western blot showed that LC3 II/I was higher and p62 was lower on the early stage of steatosis while on the late stage both of them were higher, indicating that autophagic flux was activated on the early stage of steatosis, but blocked on the late stage. Rapamycin alleviated steatosis with activating autophagic flux while chloroquine aggravated steatosis with inhibiting autophagic flux. COX-2 siRNA and celecoxib were used to inhibit COX-2. Western blot and RFP-GFP-LC3 double fluorescence system indicated that celecoxib could ameliorate steatosis and restore autophagic flux in L02 cells treated with palmitate as well as SD rats fed with high-fat diet. In conclusion, celecoxib partially restores autophagic flux via downregulation of COX-2 and alleviates steatosis in vitro and in vivo.
Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid
Authors: Kirstahler Philipp , Bjerrum Søren Solborg , Friis-Møller Alice , la Cour Morten , Aarestrup Frank M. , Westh Henrik , Pamp Sünje Johanna 
Published: March 2018

AbstractAdvances in genomics have the potential to revolutionize clinical diagnostics. Here, we examine the microbiome of vitreous (intraocular body fluid) from patients who developed endophthalmitis following cataract surgery or intravitreal injection. Endophthalmitis is an inflammation of the intraocular cavity and can lead to a permanent loss of vision. As controls, we included vitreous from endophthalmitis-negative patients, balanced salt solution used during vitrectomy and DNA extraction blanks. We compared two DNA isolation procedures and found that an ultraclean production of reagents appeared to reduce background DNA in these low microbial biomass samples. We created a curated microbial genome database (>5700 genomes) and designed a metagenomics workflow with filtering steps to reduce DNA sequences originating from: (i) human hosts, (ii) ambiguousness/contaminants in public microbial reference genomes and (iii) the environment. Our metagenomic read classification revealed in nearly all cases the same microorganism that was determined in cultivation- and mass spectrometry-based analyses. For some patients, we identified the sequence type of the microorganism and antibiotic resistance genes through analyses of whole genome sequence (WGS) assemblies of isolates and metagenomic assemblies. Together, we conclude that genomics-based analyses of human ocular body fluid specimens can provide actionable information relevant to infectious disease management.
Angular dependence of vortex instability in a layered superconductor: the case study of Fe(Se,Te) material
Authors: Grimaldi Gaia , Leo Antonio , Nigro Angela , Pace Sandro , Braccini Valeria , Bellingeri Emilio , Ferdeghini Carlo 
Published: March 2018

AbstractAnisotropy effects on flux pinning and flux flow are strongly effective in cuprate as well as iron-based superconductors due to their intrinsically layered crystallographic structure. However Fe(Se,Te) thin films grown on CaF2 substrate result less anisotropic with respect to all the other iron based superconductors. We present the first study on the angular dependence of the flux flow instability, which occurs in the flux flow regime as a current driven transition to the normal state at the instability point (I*, V*) in the current-voltage characteristics. The voltage jumps are systematically investigated as a function of the temperature, the external magnetic field, and the angle between the field and the Fe(Se,Te) film. The scaling procedure based on the anisotropic Ginzburg-Landau approach is successfully applied to the observed angular dependence of the critical voltage V*. Anyway, we find out that Fe(Se,Te) represents the case study of a layered material characterized by a weak anisotropy of its static superconducting properties, but with an increased anisotropy in its vortex dynamics due to the predominant perpendicular component of the external applied magnetic field. Indeed, I* shows less sensitivity to angle variations, thus being promising for high field applications.
Mycobacterium ahvazicum sp. nov., the nineteenth species of the Mycobacterium simiae complex
Authors: Bouam Amar , Heidarieh Parvin , Shahraki Abodolrazagh Hashemi , Pourahmad Fazel , Mirsaeidi Mehdi , Hashemzadeh Mohamad , Baptiste Emeline , Armstrong Nicholas , Levasseur Anthony , Robert Catherine , Drancourt Michel 
Published: March 2018

AbstractFour slowly growing mycobacteria isolates were isolated from the respiratory tract and soft tissue biopsies collected in four unrelated patients in Iran. Conventional phenotypic tests indicated that these four isolates were identical to Mycobacterium lentiflavum while 16S rRNA gene sequencing yielded a unique sequence separated from that of M. lentiflavum. One representative strain AFP-003T was characterized as comprising a 6,121,237-bp chromosome (66.24% guanosine-cytosine content) encoding for 5,758 protein-coding genes, 50 tRNA and one complete rRNA operon. A total of 2,876 proteins were found to be associated with the mobilome, including 195 phage proteins. A total of 1,235 proteins were found to be associated with virulence and 96 with toxin/antitoxin systems. The genome of AFP-003T has the genetic potential to produce secondary metabolites, with 39 genes found to be associated with polyketide synthases and non-ribosomal peptide syntases and 11 genes encoding for bacteriocins. Two regions encoding putative prophages and three OriC regions separated by the dnaA gene were predicted. Strain AFP-003T genome exhibits 86% average nucleotide identity with Mycobacterium genavense genome. Genetic and genomic data indicate that strain AFP-003T is representative of a novel Mycobacterium species that we named Mycobacterium ahvazicum, the nineteenth species of the expanding Mycobacterium simiae complex.
Electroconvulsive therapy (ECT) during pregnancy: quantifying and assessing the electric field strength inside the foetal brain
Authors: Kibret Behailu , Premaratne Malin , Sullivan Caley , Thomson Richard H. , Fitzgerald Paul B. 
Published: March 2018

AbstractElectroconvulsive therapy (ECT) is an effective treatment option for severe mental illness during pregnancy. However, there is little knowledge about the amount of electric field produced inside the foetus, which is important to understand the effects of ECT on the foetal excitable tissues. Thus, in this paper, the electric field strength inside the foetus was computed and compared to the basic restriction of the International Commission for Non-Ionizing Radiation Protection (ICNIRP). A computational human phantom representing a 30-weeks pregnant female, four types of electrode placements and a range of stimulus pulse width (0.25 ms–2 ms) and frequency (10 Hz–140 Hz) were used to compute the electric field inside the foetus. A linear relationship between the maximum electric field inside the foetal brain and the electrode current was derived. The results suggest that, considering the maximum current output, pulse width, and frequency range of constant-current ECT devices, the electric field produced inside the foetal brain is most likely below the ICNIRP basic restriction. This is based on the practical scenario of a 30-weeks foetus with a bottom-up and head-down foetal position and the mother taller than 1.62 m.
Conduit stability effects on intensity and steadiness of explosive eruptions
Authors: Aravena Álvaro , Cioni Raffaello , de’Michieli Vitturi Mattia , Neri Augusto 
Published: March 2018

AbstractConduit geometry affects magma ascent dynamics and, consequently, the style and evolution of volcanic eruptions. However, despite geological evidences support the occurrence of conduit widening during most volcanic eruptions, the factors controlling conduit enlargement are still unclear, and the effects of syn-eruptive variations of conduit geometry have not been investigated in depth yet. Based on numerical modeling and the application of appropriate stability criteria, we found out a strong relationship between magma rheology and conduit stability, with significant effects on eruptive dynamics. Indeed, in order to be stable, conduits feeding dacitic/rhyolitic eruptions need larger diameters respect to their phonolitic/trachytic counterparts, resulting in the higher eruption rates commonly observed in dacitic/rhyolitic explosive events. Thus, in addition to magma source conditions and viscosity-dependent efficiency for outgassing, we suggest that typical eruption rates for different magma types are also controlled by conduit stability. Results are consistent with a compilation of volcanological data and selected case studies. As stability conditions are not uniform along the conduit, widening is expected to vary in depth, and three axisymmetric geometries with depth-dependent radii were investigated. They are able to produce major modifications in eruptive parameters, suggesting that eruptive dynamics is influenced by syn-eruptive changes in conduit geometry.
Probing the Phylogenomics and Putative Pathogenicity Genes of Pythium insidiosum by Oomycete Genome Analyses
Authors: Rujirawat Thidarat , Patumcharoenpol Preecha , Lohnoo Tassanee , Yingyong Wanta , Kumsang Yothin , Payattikul Penpan , Tangphatsornruang Sithichoke , Suriyaphol Prapat , Reamtong Onrapak , Garg Gagan , Kittichotirat Weerayuth , Krajaejun Theerapong 
Published: March 2018

AbstractPythium insidiosum is a human-pathogenic oomycete. Many patients infected with it lose organs or die. Toward the goal of developing improved treatment options, we want to understand how Py. insidiosum has evolved to become a successful human pathogen. Our approach here involved the use of comparative genomic and other analyses to identify genes with possible functions in the pathogenicity of Py. insidiosum. We generated an Oomycete Gene Table and used it to explore the genome contents and phylogenomic relationships of Py. insidiosum and 19 other oomycetes. Initial sequence analyses showed that Py. insidiosum is closely related to Pythium species that are not pathogenic to humans. Our analyses also indicated that the organism harbours secreted and adhesin-like proteins, which are absent from related species. Putative virulence proteins were identified by comparison to a set of known virulence genes. Among them is the urease Ure1, which is absent from humans and thus a potential diagnostic and therapeutic target. We used mass spectrometric data to successfully validate the expression of 30% of 14,962 predicted proteins and identify 15 body temperature (37 °C)-dependent proteins of Py. insidiosum. This work begins to unravel the determinants of pathogenicity of Py. insidiosum.
Brettanomyces bruxellensis population survey reveals a diploid-triploid complex structured according to substrate of isolation and geographical distribution
Authors: Avramova Marta , Cibrario Alice , Peltier Emilien , Coton Monika , Coton Emmanuel , Schacherer Joseph , Spano Giuseppe , Capozzi Vittorio , Blaiotta Giuseppe , Salin Franck , Dols-Lafargue Marguerite , Grbin Paul , Curtin Chris , Albertin Warren , Masneuf-Pomarede Isabelle 
Published: March 2018

AbstractBrettanomyces bruxellensisis a unicellular fungus of increasing industrial and scientific interest over the past 15 years. Previous studies revealed high genotypic diversity amongstB. bruxellensisstrains as well as strain-dependent phenotypic characteristics. Genomic assemblies revealed that some strains harbour triploid genomes and based upon prior genotyping it was inferred that a triploid population was widely dispersed across Australian wine regions. We performed an intraspecific diversity genotypic survey of 1488B. bruxellensisisolates from 29 countries, 5 continents and 9 different fermentation niches. Using microsatellite analysis in combination with different statistical approaches, we demonstrate that the studied population is structured according to ploidy level, substrate of isolation and geographical origin of the strains, underlying the relative importance of each factor. We found that geographical origin has a different contribution to the population structure according to the substrate of origin, suggesting an anthropic influence on the spatial biodiversity of this microorganism of industrial interest. The observed clustering was correlated to variable stress response, as strains from different groups displayed variation in tolerance to the wine preservative sulfur dioxide (SO2). The potential contribution of the triploid state for adaptation to industrial fermentations and dissemination of the speciesB. bruxellensisis discussed.
Effect of antibiotics and NSAIDs on cyclooxygenase-2 in the enamel mineralization
Authors: Serna Muñoz Clara , Pérez Silva Amparo , Solano Francisco , Castells María Teresa , Vicente Ascensión , Ortiz Ruiz Antonio José 
Published: March 2018

AbstractThe objective of this study was to determine whether the use of the most commonly prescribed antibiotics and non-steroidal anti-inflammatory drugs in childhood could disturb enamel mineralization. Forty-two Swiss mice were divided into seven groups: controls; amoxicillin; amoxicillin/clavulanate; erythromycin; acetaminophen; ibuprofen and celecoxib, to inhibit cyclooxygenase 2 (COX2). SEM-EDX analysis was conducted on all cusps of the third molars. Calcium (Ca), phosphorus (P), aluminum, potassium, sodium, magnesium and chlorine were quantified. The stoichiometric Ca/P molar ratios were calculated. Immunohistochemical quantification of COX2 in incisors was carried out by image analysis using COX2-specific immunostaining. Groups treated with antibiotics showed no significant differences in the content of the chemical elements. Only acetaminophen and celecoxib showed a significant decrease in Ca and P compared with the control samples. Ca/P ratios showed no difference. Groups treated with amoxicillin, amoxicillin/clavulanate, erythromycin and acetaminophen showed significantly lower amounts of immunoreactive COX2 at the enamel organ maturation stage of the mouse incisors. Our results suggest that COX2 is involved in the maturation stage of the enamel organ and that its inhibition would appear to alter amelogenesis, producing hypomineralization.
Effects of Treatment Intensity on Outcomes in Acquired Apraxia of Speech
Authors: Wambaugh Julie L. , Wright Sandra , Boss Emily , Mauszycki Shannon C. , DeLong Catharine , Hula William , Doyle Patrick J. 
Published: March 2018

Purpose
This investigation was designed to examine the effects of treatment intensity (i.e., dose frequency) on the outcomes of Sound Production Treatment (SPT) for acquired apraxia of speech.

Method
Five men with chronic apraxia of speech and aphasia received both intense SPT (3 hr per day/3 days per week) and nonintense/traditional SPT (SPT-T; 1 hr per day/3 days per week) in the context of single-case experimental designs. Each treatment was applied separately to a designated set of experimental words with 1 treatment applied at a time. Twenty-seven treatment sessions were conducted with each phase of treatment. Accuracy of articulation of target sounds within treated and untreated experimental words was measured during the course of the investigation.

Results
All participants demonstrated improved articulation with both treatment intensities. Better maintenance of gains for treated items was found with SPT-T for 2 participants as measured at an 8-week posttreatment retention probe. Superior maintenance of increased accuracy of production of untreated items was also observed with SPT-T for all participants.

Conclusion
A less intense (distributed) application of SPT facilitated better maintenance of improved articulatory accuracy for untreated items, and in some cases treated items, than intense SPT.

Supplemental Materials

https://doi.org/10.23641/asha.5734053
What Matters in Semantic Feature Analysis: Practice-Related Predictors of Treatment Response in Aphasia
Authors: Gravier Michelle L. , Dickey Michael W. , Hula William D. , Evans William S. , Owens Rebecca L. , Winans-Mitrik Ronda L. , Doyle Patrick J. 
Published: March 2018

Purpose
This study investigated the predictive value of practice-related variables—number of treatment trials delivered, total treatment time, average number of trials per hour, and average number of participant-generated features per trial—in response to semantic feature analysis (SFA) treatment.

Method
SFA was administered to 17 participants with chronic aphasia daily for 4 weeks. Individualized treatment and semantically related probe lists were generated from items that participants were unable to name consistently during baseline testing. Treatment was administered to each list sequentially in a multiple-baseline design. Naming accuracy for treated and untreated items was obtained at study entry, exit, and 1-month follow-up.

Results
Item-level naming accuracy was analyzed using logistic mixed-effect regression models. The average number of features generated per trial positively predicted naming accuracy for both treated and untreated items, at exit and follow-up. In contrast, total treatment time and average trials per hour did not significantly predict treatment response. The predictive effect of number of treatment trials on naming accuracy trended toward significance at exit, although this relationship held for treated items only.

Conclusions
These results suggest that the number of patient-generated features may be more strongly associated with SFA-related naming outcomes, particularly generalization and maintenance, than other practice-related variables.

Supplemental Materials

https://doi.org/10.23641/asha.5734113
Tau-U: A Quantitative Approach for Analysis of Single-Case Experimental Data in Aphasia
Authors: Lee Jaime B. , Cherney Leora R. 
Published: March 2018

Purpose
Tau-U is a quantitative approach for analyzing single-case experimental design (SCED) data. It combines nonoverlap between phases with intervention phase trend and can correct for a baseline trend (Parker, Vannest, & Davis, 2011). We demonstrate the utility of Tau-U by comparing it with the standardized mean difference approach (Busk & Serlin, 1992) that is widely reported within the aphasia SCED literature.

Method
Repeated writing measures from 3 participants with chronic aphasia who received computer-based writing treatment are analyzed visually and quantitatively using both Tau-U and the standardized mean difference approach.

Results

Visual analysis alone was insufficient for determining an effect between the intervention and writing improvement. The standardized mean difference yielded effect sizes ranging from 4.18 to 26.72 for trained items and 1.25 to 3.20 for untrained items. Tau-U yielded significant (
p
< .05) effect sizes for 2 of 3 participants for trained probes and 1 of 3 participants for untrained probes. A baseline trend correction was applied to data from 2 of 3 participants.

Conclusions
Tau-U has the unique advantage of allowing for the correction of an undesirable baseline trend. Although further study is needed, Tau-U shows promise as a quantitative approach to augment visual analysis of SCED data in aphasia.