bluuebunny/crossref_metadata_2025 huggingface dataset:
Article Commentary: Progress in Addiction Treatment: From One-Size-Fits-All to Medications and Treatment Matching
Authors: Woody George E.
Published: March 2014

This paper briefly reviews the development of treatment for substance use disorders over the last 100 years from the perspective of the author, who has participated in treatment outcome studies since the mid-1970s. It includes some personal events that contributed to the author's involvement in addiction treatment and research, and describes the gradual evolution of an approach that began with a focus on detoxification and psychosocial treatment to one that involves blending psychosocial treatments with use of Food and Drug Administration (FDA)-approved medications and adding treatments for psychiatric and medical disorders when necessary based on patient assessments. It ends with comments on the gap between what is known and the degree to which existing knowledge is applied, and how the Affordable Care Act holds promise for bridging that gap.
Potential effects of climate change on the distribution of the common frog Rana temporaria at its northern range margin
Authors: Blank Lior , Luoto Miska , Merilä Juha
Published: March 2014

Climate change is projected to be particularly strong in northern latitudes, and subarctic species are thus likely to be especially susceptible to the effects of climate warming. We forecast potential effects of climate change on the extent of the suitable habitat of the common frog,Rana temporaria,at the margin of its northern range. We investigated 179 potential breeding sites in subarctic Finland and subjected the data to detailed bioclimate envelope modelling using three state-of-the-art techniques: generalized additive models, maximum entropy and generalized boosting methods. Moreover, we included local environmental factors in the models to investigate whether they improve model performance. Under all tested climate change projections and irrespective of the modelling method, the suitable habitat forR. temporariaincreased in warming climate. The inclusion of local abiotic variables significantly improved the performance of the models. However, June temperature appeared to be the most informative variable in all modelling approaches: a major increase in the extent of suitable habitat occurred when it increased by 1°C. Overall, the modelling results indicate that the distribution of northernR. temporariais likely to be very sensitive to climate warming. The results also highlight the fact that overlooking local abiotic variation can significantly bias bioclimatic modelling results.
Wrangling Galaxy’s reference data
Authors: Blankenberg Daniel , Johnson James E. ,   The Galaxy Team, Taylor James , Nekrutenko Anton
Published: March 2014

Summary: The Galaxy platform has developed into a fully featured collaborative workbench, with goals of inherently capturing provenance to enable reproducible data analysis, and of making it straightforward to run one’s own server. However, many Galaxy platform tools rely on the presence of reference data, such as alignment indexes, to function efficiently. Until now, the building of this cache of data for Galaxy has been an error-prone manual process lacking reproducibility and provenance.

The Galaxy Data Manager framework is an enhancement that changes the management of Galaxy’s built-in data cache from a manual procedure to an automated graphical user interface (GUI) driven process, which contains the same openness, reproducibility and provenance that is afforded to Galaxy’s analysis tools. Data Manager tools allow the Galaxy administrator to download, create and install additional datasets for any type of reference data in real time.

Availability and implementation: The Galaxy Data Manager framework is implemented in Python and has been integrated as part of the core Galaxy platform. Individual Data Manager tools can be defined locally or installed from a ToolShed, allowing the Galaxy community to define additional Data Manager tools as needed, with full versioning and dependency support.

Contact:  dan@bx.psu.edu. or anton@bx.psu.edu

Supplementary information:  Supplementary data is available at Bioinformatics online.
Transcription factors controlling development and function of innate lymphoid cells
Authors: Tanriver Yakup , Diefenbach Andreas
Published: March 2014

Innate lymphoid cells (ILCs) are a heterogeneous group of lymphocytes, which play an important role in tissue homeostasis at epithelial surfaces. They are scarce in spleen and lymph nodes, but substantial numbers can be found in the intestinal mucosa even at steady state. There, they represent the first line of defence against invading pathogens and contribute to lymphorganogenesis, tissue repair and, when inappropriately activated, immune pathology. Lineage-specific development, function and maintenance of these cells depend on a restricted set of transcription factors that partially emerged as a result of diversification and selection during vertebrate evolution. The differential expression of transcription factors regulates unique developmental programs, which endow the different ILC subsets with specific effector functions. Despite this division of labour, ILCs are considered to share a common origin, as they all are progeny of the common lymphoid progenitor, rely on the common γ-chain (γc) used by various cytokine receptors and show a developmental requirement for the transcriptional regulator Id2 (inhibitor of DNA binding 2). Here, we review the transcriptional programs required for the development and function of ILCs and give an overview of the evolution of transcription factors and cytokines expressed by ILCs.
The Galactic Centre pulsar population
Authors: Chennamangalam Jayanth , Lorimer D. R.
Published: March 2014

The recent discovery of a magnetar in the Galactic Centre region has allowed Spitler et al. to characterize the interstellar scattering in that direction. They find that the temporal broadening of the pulse profile of the magnetar is substantially less than that predicted by models of the electron density of that region. This raises the question of what the plausible limits for the number of potentially observable pulsars – i.e. the number of pulsars beaming towards the Earth – in the Galactic Centre are. In this Letter, using reasonable assumptions – namely (i) the luminosity function of pulsars in the Galactic Centre region is the same as that in the field, (ii) the region has had a constant pulsar formation rate, (iii) the spin and luminosity evolution of magnetars and pulsars are similar and (iv) the scattering in the direction of the Galactic Centre magnetar is representative of the entire inner parsec – we show that the potentially observable population of pulsars in the inner parsec has a conservative upper limit of ∼200 and that it is premature to conclude that the number of pulsars in this region is small. We also show that the observational results so far are consistent with this number and make predictions for future radio pulsar surveys of the Galactic Centre.
Bradyrhizobium ganzhouense sp. nov., an effective symbiotic bacterium isolated from Acacia melanoxylon R. Br. nodules
Authors: Lu Jun Kun , Dou Ya Jing , Zhu Ya Jie , Wang Sheng Kun , Sui Xin Hua , Kang Li Hua
Published: March 2014

Three slow-growing rhizobial strains, designated RITF806T, RITF807 and RITF211, isolated from root nodules of Acacia melanoxylon grown in Ganzhou city, Jiangxi Province, China, had been previously defined, based on amplified 16S rRNA gene restriction analysis, as a novel group within the genus

Bradyrhizobium

. To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. According to 16S rRNA gene sequence analysis, the isolates formed a group that was closely related to ‘Bradyrhizobium rifense’ CTAW71, with a similarity value of 99.9 %. In phylogenetic analyses of the housekeeping and symbiotic gene sequences, the three strains formed a distinct lineage within the genus

Bradyrhizobium

, which was consistent with the results of DNA–DNA hybridization. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related species of the genus

Bradyrhizobium

, indicating that these three strains constituted a novel group distinct from any recognized species of the genus

Bradyrhizobium

. Based on the data obtained in this study, we conclude that our strains represent a novel species of the genus

Bradyrhizobium

, for which the name Bradyrhizobium ganzhouense sp. nov. is proposed, with RITF806T ( = CCBAU 101088T = JCM 19881T) as the type strain. The DNA G+C content of strain RITF806T is 64.6 mol% (T
m).
‘Candidatus Phytoplasma palmicola’, associated with a lethal yellowing-type disease of coconut (Cocos nucifera L.) in Mozambique
Authors: Harrison Nigel A. , Davis Robert E. , Oropeza Carlos , Helmick Ericka E. , Narváez María , Eden-Green Simon , Dollet Michel , Dickinson Matthew
Published: March 2014

In this study, the taxonomic position and group classification of the phytoplasma associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique were addressed. Pairwise similarity values based on alignment of nearly full-length 16S rRNA gene sequences (1530 bp) revealed that the Mozambique coconut phytoplasma (LYDM) shared 100 % identity with a comparable sequence derived from a phytoplasma strain (LDN) responsible for Awka wilt disease of coconut in Nigeria, and shared 99.0–99.6 % identity with 16S rRNA gene sequences from strains associated with Cape St Paul wilt (CSPW) disease of coconut in Ghana and Côte d’Ivoire. Similarity scores further determined that the 16S rRNA gene of the LYDM phytoplasma shared <97.5 % sequence identity with all previously described members of ‘Candidatus

Phytoplasma
’. The presence of unique regions in the 16S rRNA gene sequence distinguished the LYDM phytoplasma from all currently described members of ‘Candidatus

Phytoplasma
’, justifying its recognition as the reference strain of a novel taxon, ‘Candidatus Phytoplasma palmicola’. Virtual RFLP profiles of the F2n/R2 portion (1251 bp) of the 16S rRNA gene and pattern similarity coefficients delineated coconut LYDM phytoplasma strains from Mozambique as novel members of established group 16SrXXII, subgroup A (16SrXXII-A). Similarity coefficients of 0.97 were obtained for comparisons between subgroup 16SrXXII-A strains and CSPW phytoplasmas from Ghana and Côte d’Ivoire. On this basis, the CSPW phytoplasma strains were designated members of a novel subgroup, 16SrXXII-B.
Xenophilus arseniciresistens sp. nov., an arsenite-resistant bacterium isolated from soil
Authors: Li Qin-Fen , Sun Li-Na , Kwon Soon-Wo , Chen Qing , He Jian , Li Shun-Peng , Zhang Jun
Published: March 2014

A Gram-reaction-negative, aerobic, motile, rod-shaped, arsenite [As(III)]-resistant bacterium, designated strain YW8T, was isolated from agricultural soil. 16S rRNA gene sequence analysis showed over 97 % sequence similarity to strains of the environmental species

Xenophilus azovorans

,

Xenophilus aerolatus

,

Simplicispira metamorpha

,

Variovorax soli

, and

Xylophilus ampelinus

. However, the phylogenetic tree indicated that strain YW8T formed a separate clade from

Xenophilus azovorans

. DNA–DNA hybridization experiments showed that the DNA–DNA relatedness values between strain YW8T and its closest phylogenetic neighbours were below 24.2–35.5 %, which clearly separated the strain from these closely related species. The major cellular fatty acids of strain YW8T were C16 : 0, C 17 : 0 cyclo, C18 : 1ω7c, and summed feature 3(C16 : 1ω6c and/or C16 : 1ω7c). The genomic DNA G+C content was 69.3 mol%, and the major respiratory quinone was ubiquinone-8. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, an unknown polar lipid and phosphatidylserine. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of morphological, physiological and biochemical characteristics, phylogenetic position, DNA–DNA hybridization and chemotaxonomic data, strain YW8T is considered to represent a novel species of the genus

Xenophilus

, for which the name Xenophilus
arseniciresistens sp. nov. is proposed; the type strain is YW8T ( = CCTCC AB2012103T = KACC 16853T).
Sequential, concomitant and hybrid first-line therapies for Helicobacter pylori eradication: a prospective randomized study
Authors: De Francesco Vincenzo , Hassan Cesare , Ridola Lorenzo , Giorgio Floriana , Ierardi Enzo , Zullo Angelo
Published: March 2014

Helicobacter pylori eradication remains a challenge for physicians. Sequential, concomitant and the hybrid regimens have been proposed as novel, more effective therapies. We compare the efficacy of these therapies. Dyspeptic patients referred for upper endoscopy with H. pylori infection were enrolled. Patients were randomized to receive: (a) sequential therapy – 20 mg omeprazole and 1 g amoxicillin for 5 days, followed by 20 mg omeprazole, 500 mg clarithromycin and 500 mg tinidazole for the successive 5 days; (b) concomitant therapy – 20 mg omeprazole, 1 g amoxicillin, 500 mg clarithromycin and 500 mg tinidazole for either 5 days (5 day concomitant) or 14 days (14 day concomitant); or (c) hybrid therapy – 20 mg omeprazole and 1 g amoxicillin for 7 days, followed by 20 mg omeprazole, 1 g amoxicillin, 500 mg clarithromycin and 500 mg tinidazole for the successive 7 days. All drugs were given twice daily. Bacterial eradication was checked by using a [13C]urea breath test. In ‘intention-to-treat’ analysis, sequential therapy achieved the highest eradication rate, which was higher than that of 5 day concomitant therapy (90  vs 78.1 %; P = 0.02). The success rate did not statistically differ among the sequential and either 14 day concomitant (90  vs 86.3 %; P = not significant) or hybrid therapies (90  vs 82.7 %; P = not significant). The 10 day sequential, 14 day concomitant and 14 day hybrid therapies, but not the 5 day concomitant regimen, achieved similarly high eradication rates. The lower therapeutic cost coupled with the lower number of tablets needed would favour the sequential therapy as the first-line H. pylori treatment in clinical practice.
Detection of benzalkonium chloride resistance in community environmental isolates of staphylococci
Authors: He Gui-Xin , Landry Michael , Chen Huizhong , Thorpe Conner , Walsh Dennis , Varela Manuel F. , Pan Hongmiao
Published: March 2014

We isolated a total of 653 strains from 64 community environmental samples in Massachusetts, USA. Among these isolates, 9.65 % (63 strains) were benzalkonium chloride (BC)-resistant staphylococci. All BC-resistant strains were collected from surfaces upon which antibacterial wipes or antibacterial sprays containing 0.02–0.12 % BC had frequently been used in the fitness centres. However, isolates from surfaces upon which antibacterial wipes or antibacterial sprays had not been used were all sensitive to BC. All BC-resistant strains were also resistant to erythromycin, penicillin and ampicillin. In addition, 51 strains showed resistance to cetyltrimethylammonium bromide (CTAB), 15 strains showed resistance to chloramphenicol, 12 strains showed resistance to ciprofloxacin and four strains showed resistance to meticillin. Resistance gene analysis demonstrated that 41 strains containedqacA/B, 30 strains hadqacC, 25 strains containedqacG, 16 strains hadqacHand eight strains containedqacJ. These data indicate that application of BC is associated with environmental staphylococcal antimicrobial resistance.
Diversification of CRISPR within coexisting genotypes in a natural population of the bloom-forming cyanobacterium Microcystis aeruginosa
Authors: Kuno Sotaro , Sako Yoshihiko , Yoshida Takashi
Published: March 2014

The clustered regularly interspaced short palindromic repeat (CRISPR) confers adaptive immunity against phages via sequence fragments (spacers) derived from mobile genetic elements (MGEs), thus serving as a memory of past host–phage co-evolution. To understand co-evolutionary dynamics in natural settings, we examined CRISPR diversity in 94 isolates ofMicrocystis aeruginosafrom a small eutrophic pond. Fifty-two isolates possessed the CRISPR and were classified into 22 different CRISPR-related genotypes, suggesting stable coexistence of multiple genotypes with different phage susceptibility. Seven CRISPR-related genotypes showed variation of spacers at the leader-end of the CRISPR, indicating active spacer addition from MGEs. An abundant phylotype (based on the internal transcribed spacer of the rRNA gene) contained different CRISPR spacer genotypes with the same CRISPR-associatedcas2gene. These data suggest that selective phage infection and possibly plasmid transfer may contribute to maintenance of multiple genotypes ofM. aeruginosaand that rapid co-evolution within a host–phage combination may be driven by increased contact frequency. Forty-two isolates lacked detectable CRISPR loci. Relative abundance of the CRISPR-lacking genotypes in the population suggests that CRISPR loss may be selected for enhanced genetic exchange.
Resistance to oxidative stress via regulating siderophore-mediated iron acquisition by the citrus fungal pathogen Alternaria alternata
Authors: Chen Li-Hung , Yang Siwy Ling , Chung Kuang-Ren
Published: March 2014

The ability of the necrotrophic fungus Alternaria alternata to detoxify reactive oxygen species (ROS) is crucial for pathogenesis to citrus. We report regulation of siderophore-mediated iron acquisition and ROS resistance by the NADPH oxidase (NOX), the redox activating yes-associated protein 1 (YAP1) regulator, and the high-osmolarity glycerol 1 (HOG1) mitogen-activated protein kinase (MAPK). The A. alternata nonribosomal peptide synthetase (NPS6) is essential for the biosynthesis of siderophores, contributing to iron uptake under low-iron conditions. Fungal strains impaired for NOX, YAP1, HOG1 or NPS6 all display increased sensitivity to ROS. Exogenous addition of iron at least partially rescues ROS sensitivity seen for NPS6, YAP1, HOG1, and NOX mutants. Importantly, expression of the NPS6 gene and biosynthesis of siderophores are regulated by NOX, YAP1 and HOG1, supporting a functional link among these regulatory pathways. Although iron fully rescues H2O2 sensitivity seen in mutants impaired for the response regulator SKN7, neither expression of NPS6 nor biosynthesis of siderophores is controlled by SKN7. Our results indicate that the acquisition of environmental iron has profound effects on ROS detoxification.
Genome sequencing identifies genetic and antigenic divergence of porcine picobirnaviruses
Authors: Bányai Krisztián , Potgieter Christiaan , Gellért Ákos , Ganesh Balasubramanian , Tempesta Maria , Lorusso Eleonora , Buonavoglia Canio , Martella Vito
Published: March 2014

The full-length genome sequence of a porcine picobirnavirus (PBV) detected in Italy in 2004 was determined. The smaller (S) genome segment was 1730 nt, coding for a putative RNA-dependent RNA polymerase. Two distinct subpopulations of larger (L) genome segment (LA and LB) were identified in the sample, with the sizes ranging from 2351 to 2666 nt. The ORF1, coding for a protein of unknown function, contained a variable number of repetitions of the ExxRxNxxxE motif. The capsid protein-coding ORF2 spanned nt 810–2447 in the LB variants and started at nt 734 in the LA variants. However, a termination codon was present only in one of all the LA segment variants. Three-dimensional modelling of the porcine PBV capsids suggested structural differences in the protruding domain, tentatively involved as antigens in the humoral immune response. Altogether, these findings suggest the simultaneous presence of two different PBV strains sharing the same S segment but displaying genetically diverse L segments. In addition, the sample probably contained a mixture of PBVs with aberrant RNA replication products. Altered structure in the L segments could be tolerated and retained in the presence of functionally integer-cognate genes and represents a mechanism of virus diversification.
Novel antibody binding determinants on the capsid surface of serotype O foot-and-mouth disease virus
Authors: Asfor Amin S. , Upadhyaya Sasmita , Knowles Nick J. , King Donald P. , Paton David J. , Mahapatra Mana
Published: March 2014

Five neutralizing antigenic sites have been described for serotype O foot-and-mouth disease viruses (FMDV) based on monoclonal antibody (mAb) escape mutant studies. However, a mutant virus selected to escape neutralization of mAb binding at all five sites was previously shown to confer complete cross-protection with the parental virus in guinea pig challenge studies, suggesting that amino acid residues outside the mAb binding sites contribute to antibody-mediated in vivo neutralization of FMDV. Comparison of the ability of bovine antisera to neutralize a panel of serotype O FMDV identified three novel putative sites at VP2-74, VP2-191 and VP3-85, where amino acid substitutions correlated with changes in sero-reactivity. The impact of these positions was tested using site-directed mutagenesis to effect substitutions at critical amino acid residues within an infectious copy of FMDV O1 Kaufbeuren (O1K). Recovered viruses containing additional mutations at VP2-74 and VP2-191 exhibited greater resistance to neutralization with both O1K guinea pig and O BFS bovine antisera than a virus that was engineered to include only mutations at the five known antigenic sites. The changes at VP2-74 and VP3-85 are adjacent to critical amino acids that define antigenic sites 2 and 4, respectively. However VP2-191 (17 Å away from VP2-72), located at the threefold axis and more distant from previously identified antigenic sites, exhibited the most profound effect. These findings extend our knowledge of the surface features of the FMDV capsid known to elicit neutralizing antibodies, and will improve our strategies for vaccine strain selection and rational vaccine design.
Viral determinants of influenza A virus host range
Authors: Cauldwell Anna V. , Long Jason S. , Moncorgé Olivier , Barclay Wendy S.
Published: March 2014

Typical avian influenza A viruses are restricted from replicating efficiently and causing disease in humans. However, an avian virus can become adapted to humans by mutating or recombining with currently circulating human viruses. These viruses have the potential to cause pandemics in an immunologically naïve human population. It is critical that we understand the molecular basis of host-range restriction and how this can be overcome. Here, we review our current understanding of the mechanisms by which influenza viruses adapt to replicate efficiently in a new host. We predominantly focus on the influenza polymerase, which remains one of the least understood host-range barriers.
Effect of alternating red and blue light irradiation generated by light emitting diodes on the growth of leaf lettuce
Authors: Shimokawa Akihiro , Tonooka Yuki , Matsumoto Misato , Ara Hironori , Suzuki Hiroshi , Yamauchi Naoki , Shigyo Masayoshi
Published: March 2014

Because global climate change has made agricultural supply unstable, plant factories are expected to be a safe and stable means of food production. As the light source of a plant factory or controlled greenhouse, the light emitting diode (LED) is expected to solve cost problems and promote plant growth efficiently. In this study, we examined the light condition created by using monochromatic red and blue LEDs, to provide both simultaneous and alternating irradiation to leaf lettuce. The result was that simultaneous red and blue irradiation promoted plant growth more effectively than monochromatic and fluorescent light irradiation. Moreover, alternating red and blue light accelerated plant growth significantly even when the total light intensity per day was the same as with simultaneous irradiation. The fresh weight in altering irradiation was almost two times higher than with fluorescent light and about 1.6 times higher than with simultaneous irradiation. The growth-promoting effect of alternating irradiation of red and blue light was observed in different cultivars. From the results of experiments, we offer a novel plant growth method named "Shigyo Method", the core concept of which is the alternating irradiation of red and blue light.
Genomic Repeat Element Analyzer for Mammals (GREAM)
Authors: Chandrashekar Darshan S , Dey Poulami , Acharya Kshitish K
Published: March 2014

Background: Understanding the mechanism behind the transcriptional regulation of genes is still a challenge. Recent findings indicate that the genomic repeat elements (such as LINES, SINES and LTRs) could play an important role in the transcription control. Hence, it is important to further explore the role of genomic repeat elements in the gene expression regulation, and perhaps in other molecular processes. Although many computational tools exists for repeat element analysis, almost all of them simply identify and/or classifying the genomic repeat elements within query sequence(s); none of them facilitate identification of repeat elements that are likely to have a functional significance, particularly in the context of transcriptional regulation.

Result: We developed the ‘Genomic Repeat Element Analyzer for Mammals’ (GREAM) to allow gene-centric analysis of genomic repeat elements in 17 mammalian species, and validated it by comparing with some of the existing experimental data. The output provides a categorized list of the specific type of transposons, retro-transposons and other genome-wide repeat elements that are statistically over-represented across specific neighborhood regions of query genes. The position and frequency of these elements, within the specified regions, are displayed as well. The tool also offers queries for position-specific distribution of repeat elements within chromosomes. In addition, GREAM facilitates the analysis of repeat element distribution across the neighborhood of orthologous genes.

Conclusion: GREAM allows researchers to short-list the potentially important repeat elements, from the genomic neighborhood of genes, for further experimental analysis. GREAM is free and available for all athttp://resource.ibab.ac.in/GREAM/
A Genetic Screen Identifies Two Novel Rice Cysteine-rich Receptor-like Kinases That Are Required for the Rice NH1-mediated Immune Response
Authors: Chern Mawsheng , Bart Rebecca , Bai Wei , Ruan Deling , Sze-To Wing Hoi , Patrick Canlas , Jain Rashmi , Chen Xuewei , Ronald Pamela
Published: March 2014

Over-expression of rice NH1 (NH1ox), the ortholog of Arabidopsis NPR1, confers immunity to bacterial and fungal pathogens and induces the appearance of necrotic lesions due to activation of defense genes at the pre-flowering stage. This lesion-mimic phenotype can be enhanced by the application of benzothiadiazole (BTH). To identify genes regulating these responses, we screened a fast neutron-irradiated NH1ox rice population. We identified one mutant, called snl1 (suppressor of NH1-mediated lesion-mimic 1), which is impaired both in BTH-induced necrotic lesion formation and in the immune response. Using a comparative genome hybridization approach employing rice whole genome tiling array, we identified 11 genes associated with the snl1 phenotype. Transgenic analysis revealed that RNA interference of two of the genes, encoding previously uncharacterized cysteine-rich receptor-like kinases (CRK6 and CRK10), re-created the snl1 phenotype. Elevated expression of CRK10 using an inducible expression system resulted in enhanced immunity. Quantitative PCR revealed that BTH treatment and elevated levels of rice NH1 and its paralog NH3 induced expression of CRK10 and CRK6 RNA. These results indicate that CRK6 and CRK10 are required for the BTH-activated immune response mediated by NH1.
High Bacterial Load Predicts Poor Outcomes in Patients with Idiopathic Pulmonary Fibrosis
Authors: Molyneaux P L , Cox M J , Willis-Owen S A G , Russell K E , Mallia P , Russell A M , Johnston S L , Wells A U , Cookson W O C , Maher T M , Moffatt M F
Published: March 2014

Background

Repetitive alveolar damage and aberrant repair may be important in the development of the fatal condition Idiopathic Pulmonary Fibrosis (IPF). The role played by microorganisms in this cycle is unknown.

Methods

We consecutively enrolled patients diagnosed with IPF according to international criteria together with healthy smokers, non-smokers and subjects with moderate Chronic Obstructive Pulmonary Disease (COPD) as controls. Subjects underwent bronchoalveolar lavage (BAL) from which genomic DNA was isolated. The V3-V5 region of the bacterial 16S rRNA gene was amplified, allowing quantification of bacterial load and identification of communities by 16S rRNA qPCR and pyrosequencing.

Results

Our 65 IPF patients had 3.9×109copies of the 16S rRNA gene per ml of BAL, two-fold more than the 1.8×109copies in 44 sex- and smoking-matched controls (P<0.0001). Baseline BAL bacterial burden predicted Forced Vital Capacity (FVC) decline (P=0.02). Patients in the highest tertile of bacterial burden were at a higher risk of mortality compared to subjects in the lowest tertile (hazard ratio 4.59 (95% CI, 1.05-20);P=0.04).

Sequencing yielded 912,883 high quality reads from all subjects. Operational Taxonomic Units (OTUs) representingHaemophilus, Streptococcus, NeisseriaandVeillonellawere 1.5 to 3.5 fold more abundant in cases than controls (P<0.05). Regression analyses indicated that these specific OTUs as well as bacterial burden associated independently with IPF.

Conclusions

IPF is characterised by an increased bacterial burden in BAL that predicts decline in lung function and death. Clinical trials of antimicrobial therapy may determine if microbial burden is causal or not in IPF progression.
Ultraviolet-B-Induced Stomatal Closure in Arabidopsis Is Regulated by the UV RESISTANCE LOCUS8 Photoreceptor in a Nitric Oxide-Dependent Mechanism
Authors: Tossi Vanesa , Lamattina Lorenzo , Jenkins Gareth I. , Cassia Raúl O.
Published: March 2014

UV RESISTANCE LOCUS8 (UVR8) signaling involves CONSTITUTIVELY PHOTOMORPHOGENIC1, the ELONGATED HYPOCOTYL5 (HY5) transcription factor, and the closely related HY5 HOMOLOG. Some UV-B responses mediated by UVR8 are also regulated by nitric oxide (NO), a bioactive molecule that orchestrates a wide range of processes in plants. In this study, we investigated the participation of the UVR8 pathway and its interaction with NO in UV-B-induced stomatal movements in Arabidopsis (Arabidopsis thaliana). Stomata in abaxial epidermal strips of Arabidopsis ecotype Landsberg erecta closed in response to increasing UV-B fluence rates, with maximal closure after 3-h exposure to 5.46 μmol m–2 s–1 UV-B. Both hydrogen peroxide (H2O2) and NO increased in response to UV-B, and stomatal closure was maintained by NO up to 24 h after the beginning of exposure. Stomata of plants expressing bacterial NO dioxygenase, which prevents NO accumulation, did not close in response to UV-B, although H2O2 still increased. When the uvr8-1 null mutant was exposed to UV-B, stomata remained open, irrespective of the fluence rate. Neither NO nor H2O2 increased in stomata of the uvr8-1 mutant. However, the NO donor S-nitrosoglutathione induced closure of uvr8-1 stomata to the same extent as in the wild type. Experiments with mutants in UVR8 signaling components implicated CONSTITUTIVELY PHOTOMORPHOGENIC1, HY5, and HY5 HOMOLOG in UV-B-induced stomatal closure. This research provides evidence that the UVR8 pathway regulates stomatal closure by a mechanism involving both H2O2 and NO generation in response to UV-B exposure.
Arabidopsis WRKY45 Transcription Factor Activates PHOSPHATE TRANSPORTER1;1 Expression in Response to Phosphate Starvation
Authors: Wang Hui , Xu Qian , Kong You-Han , Chen Yun , Duan Jun-Ye , Wu Wei-Hua , Chen Yi-Fang
Published: March 2014

The WRKY transcription factor family has more than 70 members in the Arabidopsis (Arabidopsis thaliana) genome, and some of them are involved in plant responses to biotic and abiotic stresses. This study evaluated the role of WRKY45 in regulating phosphate (Pi) uptake in Arabidopsis. WRKY45 was localized in the nucleus and mainly expressed in roots. During Pi starvation, WRKY45 expression was markedly induced, typically in roots. WRKY45 overexpression in Arabidopsis increased Pi content and uptake, while RNA interference suppression of WRKY45 decreased Pi content and uptake. Furthermore, the WRKY45-overexpressing lines were more sensitive to arsenate, the analog of Pi, compared with wild-type seedlings. These results indicate that WRKY45 positively regulates Arabidopsis Pi uptake. Quantitative real-time polymerase chain reaction and β-glucuronidase staining assays showed that PHOSPHATE TRANSPORTER1;1 (PHT1;1) expression was enhanced in the WRKY45-overexpressing lines and slightly repressed in the WRKY45 RNA interference line. Chromatin immunoprecipitation and eclectrophoretic mobility shift assay results indicated that WRKY45 can bind to two W-boxes within the PHT1;1 promoter, confirming the role of WRKY45 in directly up-regulating PHT1;1 expression. The pht1;1 mutant showed decreased Pi content and uptake, and overexpression of PHT1;1 resulted in enhanced Pi content and uptake. Furthermore, the PHT1;1-overexpressing line was much more sensitive to arsenate than WRKY45-overexpressing and wild-type seedlings, indicating that PHT1;1 overexpression can enhance Arabidopsis Pi uptake. Moreover, the enhanced Pi uptake and the increased arsenate sensitivity of the WRKY45-overexpressing line was impaired by pht1;1 (35S:WRKY45-18::pht1;1), demonstrating an epistatic genetic regulation between WRKY45 and PHT1;1. Together, our results demonstrate that WRKY45 is involved in Arabidopsis response to Pi starvation by direct up-regulation of PHT1;1 expression.
Diagnostic challenges in patients with bleeding phenotype and von Willebrand exon 28 polymorphism p.D1472H
Authors: Francis J. C. , Hui S.‐K. , Mahoney D. , Dietrich J. E. , Friedman K. D. , Soundar E. , Srivaths L. V.
Published: March 2014

Exon 28 polymorphism p.D1472H is associated with significantly lower von Willebrand Ristocetin cofactor activity (VWF:RCoF) to von Willebrand antigen (VWF:Ag) ratio compared to normal, but has been reported as not conferring haemorrhagic risk. The impact of this polymorphism while assessing symptomatic patients for von Willebrand disease (VWD) has not been previously analysed. We retrospectively reviewed charts of children with clinically significant bleeding and abnormal VW panel who underwent VW exon 28 analysis. Twenty‐three of 63 patients studied had p.D1472H. Of these 23 patients, 6 with borderline low VWF:RCo were given provisional diagnosis of VWD type 1 by treating physicians, which could be alternatively explained as due to the effect of p.D1472H. None of the patients with low VWF:RCo, decreased VWF:RCo/VWF:Ag ratio and p.D1472H had VWD type 2M mutations identified. This study illustrates the challenge in diagnosing VWD using ristocetin‐based VW assay in symptomatic patients with p.D1472H.
An unusual presentation of probable dementia: Rhyming, associations, and verbal disinhibition
Authors: Robinson Gail , Ceslis Amelia
Published: March 2014

We report a case of probable Alzheimer's disease who presented with the unusual feature of disinhibited rhyming. Core language skills were largely intact but generative language was characterized by semantic‐based associations, evident in tangential and associative content, and phonology‐based associations, evident in rhyming, in the context of prominent executive dysfunction. We suggest this pattern is underpinned by a failure to terminate or inhibit verbal associations resulting in a ‘loosening’ of associations at the level of conceptual preparation for spoken language.
Tail-Enabled Spiraling Maneuver for Gliding Robotic Fish
Authors: Zhang Feitian , Zhang Fumin , Tan Xiaobo
Published: March 2014

Gliding robotic fish, a new type of underwater robot, combines both strengths of underwater gliders and robotic fish, featuring long operation duration and high maneuverability. In this paper, we present both analytical and experimental results on a novel gliding motion, tail-enabled three-dimensional (3D) spiraling, which is well suited for sampling a water column. A dynamic model of a gliding robotic fish with a deflected tail is first established. The equations for the relative equilibria corresponding to steady-state spiraling are derived and then solved recursively using Newton's method. The region of convergence for Newton's method is examined numerically. We then establish the local asymptotic stability of the computed equilibria through Jacobian analysis and further numerically explore the basins of attraction. Experiments have been conducted on a fish-shaped miniature underwater glider with a deflected tail, where a gliding-induced 3D spiraling maneuver is confirmed. Furthermore, consistent with model predictions, experimental results have shown that the achievable turning radius of the spiraling can be as small as less than 0.4 m, demonstrating the high maneuverability.
Simulated Microstructural Evolution and Design of Porous Sintered Wicks
Authors: Bodla Karthik K. , Garimella Suresh V.
Published: March 2014

Porous structures formed by sintering of powders, which involves material-bonding under the application of heat, are commonly employed as capillary wicks in two-phase heat transport devices such as heat pipes. These sintered wicks are often fabricated in an ad hoc manner, and their microstructure is not optimized for fluid and thermal performance. Understanding the role of sintering kinetics—and the resulting microstructural evolution—on wick transport properties is important for fabrication of structures with optimal performance. A cellular automaton model is developed in this work for predicting microstructural evolution during sintering. The model, which determines mass transport during sintering based on curvature gradients in digital images, is first verified against benchmark cases, such as the evolution of a square shape into an area-preserving circle. The model is then employed to predict the sintering dynamics of a side-by-side, two-particle configuration conventionally used for the study of sintering. Results from previously published studies on sintering of cylindrical wires are used for validation. Randomly packed multiparticle configurations are then considered in two and three dimensions. Sintering kinetics are described by the relative change in overall surface area of the compact compared to the initial random packing. The effect of sintering parameters, particle size, and porosity on fundamental transport properties, viz., effective thermal conductivity and permeability, is analyzed. The effective thermal conductivity increases monotonically as either the sintering time or temperature is increased. Permeability is observed to increase with particle size and porosity. As sintering progresses, the slight increase observed in the permeability of the microstructure is attributed to a reduction in the surface area.
Synthesis and Characterization of Solid-State Phase Change Material Microcapsules for Thermal Management Applications
Authors: Cao Fangyu , Ye Jing , Yang Bao
Published: March 2014

Polyalcohols such as neopentyl glycol (NPG) undergo solid-state crystal transformations that absorb/release significant latent heat. These solid–solid phase change materials (PCM) can be used in practical thermal management applications without concerns about liquid leakage and thermal expansion during phase transitions. In this paper, microcapsules of NPG encapsulated in silica shells were successfully synthesized with the use of emulsion techniques. The size of the microcapsules range from 0.2 to 4 μm, and the thickness of the silica shell is about 30 nm. It was found that the endothermic phase transition of these NPG-silica microcapsules was initiated at around 39 °C and the latent heat was about 96.0 J/g. A large supercooling of about 43.3 °C was observed in the pure NPG particles without shells, while the supercooling of the NPG microcapsules was reduced to about 14 °C due to the heterogeneous nucleation sites provided by the silica shell. These NPG microcapsules were added to the heat transfer fluid PAO to enhance its heat capacity and the effective heat capacity of the fluid was increased by 56% with the addition of 20 wt. % NPG-silica microcapsules.
The Biomimetic Shark Skin Optimization Design Method for Improving Lubrication Effect of Engineering Surface
Authors: Lu Yan , Hua Meng , Liu Zuomin
Published: March 2014

Nature has long been an important source of inspiration for mankind to develop artificial ways to mimic the remarkable properties of biological systems. In this work, a new method was explored to fabricate a biomimetic engineering surface comprising both the shark-skin, the shark body denticle, and rib morphology. It can help reduce water resistance and the friction contact area as well as accommodate lubricant. The lubrication theory model was established to predict the effect of geometric parameters of a biomimetic surface on tribological performance. The model has been proved to be feasible to predict tribological performance by the experimental results. The model was then used to investigate the effect of the grid textured surface on frictional performance of different geometries. The investigation was aimed at providing a rule for deriving the design parameters of a biomimetic surface with good lubrication characteristics. Results suggest that: (i) the increase in depression width ratio Λ decreases its corresponding coefficient of friction, and (ii) the small coefficient of friction is achievable when Λ is beyond 0.45. Superposition of depth ratio Γ and angle's couple under the condition of Λ < 0.45 affects the value of friction coefficient. It shows the decrease in angle decreases with the increase in dimension depth Γ.
Detecting Loosening of Bolted Connections in a Pipeline Using Changes in Natural Frequencies
Authors: He K. , Zhu W. D.
Published: March 2014

Loosening of bolted connections in a structure can significantly reduce its load-bearing capacity. Detecting loosening of bolted connections at an early stage can prevent failure of the structure. Due to the complex geometry of a bolted connection and material discontinuity between clamped components, it is difficult to detect loosening of a bolted connection using conventional nondestructive test methods. A vibration-based method that uses changes in natural frequencies of a structure to detect locations and extent of damage can be used to detect loosening of bolted connections since the method focuses on detecting a stiffness reduction, which can result from loosening of bolted connections. Experimental and numerical damage detection was conducted to detect loosening of bolted connections in a full-size steel pipeline with bolted flanges using the vibration-based method. With the recent development of a modeling technique for bolted connections in thin-walled structures, an accurate physics-based finite element model of the pipeline that is required by the vibration-based damage detection method is developed. A trust-region search strategy is employed to improve the damage detection method so that global convergence of the damage detection algorithm can be ensured for underdetermined systems, and robustness of the algorithm can be enhanced when relatively large modeling error and measurement noise are present. The location and extent of loosened bolted connections were successfully detected in experimental damage detection using changes in natural frequencies of the first several elastic modes of the pipeline; the exact location and extent of the loosened bolted connections can be detected in numerical simulation where there are no modeling error and measurement noise.
Experimental Studies of Cavity and Core Flow Interactions With Application to Ultra-Compact Combustors
Authors: Blunck David L. , Shouse Dale T. , Neuroth Craig , Lynch Amy , Erdmann Timothy J. , Burrus David L. , Zelina Joseph , Richardson Daniel , Caswell Andrew
Published: March 2014

Reducing the weight and decreasing pressure losses of aviation gas turbine engines improves the thrust-to-weight ratio and improves efficiency. In ultra-compact combustors (UCC), engine length is reduced and pressure losses are decreased by merging a combustor with adjacent components using a systems engineering approach. High-pressure turbine inlet vanes can be placed in a combustor to form a UCC. In this work, experiments were performed to understand the performance and associated physics within a UCC. Experiments were performed using a combustor operating at pressures in the range of 520–1030 kPa (75–150 psia) and inlet temperature equal to 480–620 K (865 R–1120 R). The primary reaction zone is in a single trapped-vortex cavity where the equivalence ratio was varied from 0.7 to 1.8. Combustion efficiencies and NOx emissions were measured and exit temperature profiles were obtained for various air loadings, cavity equivalence ratios, and configurations with and without representative turbine inlet vanes. A combined diffuser-flameholder (CDF) was used to study the interaction of cavity and core flows. Discrete jets of air immediately above the cavity result in the highest combustion efficiencies. The air jets reinforce the vortex structure within the cavity, as confirmed through coherent structure velocimetry of high-speed images. The combustor exit temperature profile is peaked away from the cavity when a CDF is used. Testing of a CDF with vanes showed that combustion efficiencies greater than 99.5% are possible for 0.8 ≤ Φcavity ≤ 1.8. Temperature profiles at the exit of the UCC with vanes agreed within 10% of the average value. Exit-averaged emission indices of NOx ranged from 3.5 to 6.5 g/kgfuel for all test conditions. Increasing the air loading enabled greater mass flow rates of fuel with equivalent combustion efficiencies. This corresponds to increased vortex strength within the cavity due to the greater momentum of the air driver jets.
Theoretical and Experimental Study of Bimetal-Pipe Hydroforming
Authors: Dezhi Zeng , Kuanhai Deng , Taihe Shi , Yuanhua Lin , Hongjun Zhu , Tianlei Li , Yongxing Sun
Published: March 2014

The corrosion of oil country tubular goods (OCTG) gets more and more serious especially in the acidic environment. So, it is very important to develop a perfect anticorrosion technology for exploring sour oil and gas fields economically and safely. Analysis indicates that the bimetal-pipe (BP) which consists of the base layer of low carbon steel and a corrosion resistant alloy (CRA) cladding layer is an economic and reliable anticorrosion technology and has broad application prospects in the transportation of acid medium. However, theoretical study of hydraulic expansion mechanism for BP is not enough. In this paper, the deformation compatibility condition of BP was obtained by studying the deformation rule of the (CRA) liner and the outer pipe of carbon steel in the forming process; the mechanical model which can compute the hydroforming pressure of BP has been established based on the nonlinear kinematic hardening characteristics of material; furthermore, based on the stress strain curve of inner pipe simultaneously, the calculation method of the plastic hardening stress has been proposed. Thus, the accurate method for computing the forming pressure was obtained. The experimental data show that results are consistent with results of the proposed model. It indicates that the model can be used to provide theoretical guidance for the design and production as well as use of BP.