bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-ethnic reference values for spirometry for the 3–95-yr age range: the global lung function 2012 equations
Authors: Quanjer Philip H. , Stanojevic Sanja , Cole Tim J. , Baur Xaver , Hall Graham L. , Culver Bruce H. , Enright Paul L. , Hankinson John L. , Ip Mary S.M. , Zheng Jinping , Stocks Janet ,   the ERS Global Lung Function Initiative
Published: June 2012

The aim of the Task Force was to derive continuous prediction equations and their lower limits of normal for spirometric indices, which are applicable globally. Over 160,000 data points from 72 centres in 33 countries were shared with the European Respiratory Society Global Lung Function Initiative. Eliminating data that could not be used (mostly missing ethnic group, some outliers) left 97,759 records of healthy nonsmokers (55.3% females) aged 2.5–95 yrs.Lung function data were collated and prediction equations derived using the LMS method, which allows simultaneous modelling of the mean (mu), the coefficient of variation (sigma) and skewness (lambda) of a distribution family.After discarding 23,572 records, mostly because they could not be combined with other ethnic or geographic groups, reference equations were derived for healthy individuals aged 3–95 yrs for Caucasians (n=57,395), African–Americans (n=3,545), and North (n=4,992) and South East Asians (n=8,255). Forced expiratory value in 1 s (FEV1) and forced vital capacity (FVC) between ethnic groups differed proportionally from that in Caucasians, such that FEV1/FVC remained virtually independent of ethnic group. For individuals not represented by these four groups, or of mixed ethnic origins, a composite equation taken as the average of the above equations is provided to facilitate interpretation until a more appropriate solution is developed.Spirometric prediction equations for the 3–95-age range are now available that include appropriate age-dependent lower limits of normal. They can be applied globally to different ethnic groups. Additional data from the Indian subcontinent and Arabic, Polynesian and Latin American countries, as well as Africa will further improve these equations in the future.
Impact of climate change on ozone-related mortality and morbidity in Europe
Authors: Orru Hans , Andersson Camilla , Ebi Kristie L. , Langner Joakim , Åström Christofer , Forsberg Bertil 
Published: June 2012

Ozone is a highly oxidative pollutant formed from precursors in the presence of sunlight, associated with respiratory morbidity and mortality. All else being equal, concentrations of ground-level ozone are expected to increase due to climate change.Ozone-related health impacts under a changing climate are projected using emission scenarios, models and epidemiological data. European ozone concentrations are modelled with the model of atmospheric transport and chemistry (MATCH)-RCA3 (50×50 km). Projections from two climate models, ECHAM4 and HadCM3, are applied under greenhouse gas emission scenarios A2 and A1B, respectively. We applied a European-wide exposure–response function to gridded population data and country-specific baseline mortality and morbidity.Comparing the current situation (1990–2009) with the baseline period (1961–1990), the largest increase in ozone-associated mortality and morbidity due to climate change (4–5%) have occurred in Belgium, Ireland, the Netherlands and the UK. Comparing the baseline period and the future periods (2021–2050 and 2041–2060), much larger increases in ozone-related mortality and morbidity are projected for Belgium, France, Spain and Portugal, with the impact being stronger using the climate projection from ECHAM4 (A2). However, in Nordic and Baltic countries the same magnitude of decrease is projected.The current study suggests that projected effects of climate change on ozone concentrations could differentially influence mortality and morbidity across Europe.
Global burden of chronic pulmonary aspergillosis complicating sarcoidosis
Authors: Denning David W. , Pleuvry Alex , Cole Donald C. 
Published: June 2012

Chronic pulmonary aspergillosis (CPA) may complicate pulmonary sarcoidosis. We re-estimated the global burden of sarcoidosis and the burden of CPA complicating sarcoidosis.We searched the literature and reference lists of retrieved papers to identify all published sarcoidosis incidence and prevalence data. We estimated the frequency of CPA from 11 papers relating to >3,000 patients with sarcoidosis to derive CPA patient numbers. We applied an annual attrition rate of 15% (range 10–25%) to estimate the global burden of CPA.We estimate that the annual incidence of sarcoidosis is 344,000 patients worldwide and the prevalence is ∼1,238,000 cases, distributed as follows: 165,979 in Europe, 224,000 in the Americas, 492,892 in Africa, 80,023 in the Eastern Mediterranean, 41,660 in the West Pacific and 234,010 in Southeast Asia. CPA complicates sarcoidosis in 3–12% of cases. Using a 6% frequency, we estimate a global burden of 71,907 (range 35,954–143,815 (3–12%)) CPA cases complicating sarcoidosis, with 24% and 37% of cases estimated to be present in the Americas and Africa, because of the higher incidence of sarcoidosis in black people.As CPA responds to long-term antifungal therapy, which may prevent life-threatening haemoptysis, screening periodically for CPA in those with pulmonary sarcoidosis may be important, especially in patients requiring corticosteroid therapy.
Generalized set-valued variational-like inclusions involving "Equation missing" -η-cocoercive operator in Banach spaces
Authors: Ahmad Rais , Dilshad Mohd , Wong Mu-Ming , Yao Jen-Chin 
Published: June 2012

Abstract
The aim of this paper is to introduce a new

H
(
⋅
,
⋅
)

-η-cocoercive operator and its resolvent operator. We study some of the properties of

H
(
⋅
,
⋅
)

-η-cocoercive operator and prove the Lipschitz continuity of resolvent operator associated with

H
(
⋅
,
⋅
)

-η-cocoercive operator. Finally, we apply the techniques of resolvent operator to solve a generalized set-valued variational-like inclusion problem in Banach spaces. Our results are new and generalize many known results existing in the literature. Some examples are given in support of definition of

H
(
⋅
,
⋅
)

-η-cocoercive operator.

MSC:47H19, 49J40.
Non-typeable Haemophilus influenzae decreases cilia beating via protein kinase C epsilon
Authors: Bailey Kristina L , LeVan Tricia D , Yanov Daniel A , Pavlik Jaqueline A , DeVasure Jane M , Sisson Joseph H , Wyatt Todd A 
Published: June 2012

Abstract

Background

Haemophilus influenzae infection of the nasal epithelium has long been associated with observations of decreased nasal ciliary beat frequency (CBF) and injury to the ciliated epithelium. Previously, we have reported that several agents that slow CBF also have the effect of activating protein kinase C epsilon (PKCϵ) activity in bronchial epithelial cells. The subsequent auto-downregulation of PKCϵ or the direct inhibition of PKCϵ leads to the specific detachment of the ciliated cells. METHODS: Primary cultures of ciliated bovine bronchial epithelial cells were exposed to filtered conditioned media supernatants from non-typeable H. influenzae (NTHi) cultures. CBF and motile points were measured and PKCϵ activity assayed.

Results
NTHi supernatant exposure significantly and rapidly decreased CBF in a dose-dependent manner within 10 minutes of exposure. After 3 hours of exposure, the number of motile ciliated cells significantly decreased. Direct measurement of PKCϵ activity revealed a dose-dependent activation of PKCϵ in response to NTHi supernatant exposure. Both CBF and PKCϵ activity changes were only observed in fresh NTHi culture supernatant and not observed in exposures to heat-inactivated or frozen supernatants.

Conclusions
Our results suggest that CBF slowing observed in response to NTHi is consistent with the stimulated activation of PKCϵ. Ciliated cell detachment is associated with PKCϵ autodownregulation.
RUNX2 tandem repeats and the evolution of facial length in placental mammals
Authors: Pointer Marie A , Kamilar Jason M , Warmuth Vera , Chester Stephen G B , Delsuc Frédéric , Mundy Nicholas I , Asher Robert J , Bradley Brenda J 
Published: June 2012

AbstractBackgroundWhen simple sequence repeats are integrated into functional genes, they can potentially act as evolutionary ‘tuning knobs’, supplying abundant genetic variation with minimal risk of pleiotropic deleterious effects. The genetic basis of variation in facial shape and length represents a possible example of this phenomenon. Runt-related transcription factor 2 (RUNX2), which is involved in osteoblast differentiation, contains a functionally-important tandem repeat of glutamine and alanine amino acids. The ratio of glutamines to alanines (the QA ratio) in this protein seemingly influences the regulation of bone development. Notably, in domestic breeds of dog, and in carnivorans in general, the ratio of glutamines to alanines is strongly correlated with facial length.ResultsIn this study we examine whether this correlation holds true across placental mammals, particularly those mammals for which facial length is highly variable and related to adaptive behavior and lifestyle (e.g., primates, afrotherians, xenarthrans). We obtained relative facial length measurements and RUNX2 sequences for 41 mammalian species representing 12 orders. Using both a phylogenetic generalized least squares model and a recently-developed Bayesian comparative method, we tested for a correlation between genetic and morphometric data while controlling for phylogeny, evolutionary rates, and divergence times. Non-carnivoran taxa generally had substantially lower glutamine-alanine ratios than carnivorans (primates and xenarthrans with means of 1.34 and 1.25, respectively, compared to a mean of 3.1 for carnivorans), and we found no correlation betweenRUNX2sequence and face length across placental mammals.ConclusionsResults of our diverse comparative phylogenetic analyses indicate that QA ratio does not consistently correlate with face length across the 41 mammalian taxa considered. Thus, although RUNX2 might function as a ‘tuning knob’ modifying face length in carnivorans, this relationship is not conserved across mammals in general.
Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation
Authors: Liu Yang , Yang Shi-xiong , Ji Peng-zhang , Gao Li-zhi 
Published: June 2012

AbstractBackgroundAs one of the most important but seriously endangered wild relatives of the cultivated tea,Camellia taliensisharbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species.ResultsHere, we sampled 21 natural populations from the species' range in China and performed the phylogeography ofC. taliensisby using the nuclearPALgene fragment and chloroplastrpl32-trnLintergenic spacer. Levels of haplotype diversity and nucleotide diversity detected atrpl32-trnL(h = 0.841;π = 0.00314) were almost as high as atPAL(h = 0.836;π = 0.00417). Significant chloroplast DNA population subdivision was detected (GST = 0.988;NST = 0.989), suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure inC. taliensishas been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222;NST = 0.301) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST;P < 0.01). The analysis ofPALhaplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel’s test of nrDNA haplotypes (r = 0.234,P < 0.001). We found that chlorotype C1 was fixed in seven populations of Lancang River Region, implying that the Lancang River might have provided a corridor for the long-distance dispersal of the species.ConclusionsWe found thatC. taliensisshowed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developingin situconservation of natural populations.
Whole-genome in-silico subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of Schistosoma mansoni
Authors: Portela Julien , Grunau Christoph , Cosseau Céline , Beltran Sophie , Dantec Christelle , Parrinello Hugues , Boissier Jérôme 
Published: June 2012

Abstract

Background
Emerging methods of massive sequencing that allow for rapid re-sequencing of entire genomes at comparably low cost are changing the way biological questions are addressed in many domains. Here we propose a novel method to compare two genomes (genome-to-genome comparison). We used this method to identify sex-specific sequences of the human blood fluke Schistosoma mansoni.

Results
Genomic DNA was extracted from male and female (heterogametic) S. mansoni adults and sequenced with a Genome Analyzer (Illumina). Sequences are available at the NCBI sequence read archive http://www.ncbi.nlm.nih.gov/Traces/sra/ under study accession number SRA012151.6. Sequencing reads were aligned to the genome, and a pseudogenome composed of known repeats. Straightforward comparative bioinformatics analysis was performed to compare male and female schistosome genomes and identify female-specific sequences. We found that the S. mansoni female W chromosome contains only few specific unique sequences (950 Kb i.e. about 0.2% of the genome). The majority of W-specific sequences are repeats (10.5 Mb i.e. about 2.5% of the genome). Arbitrarily selected W-specific sequences were confirmed by PCR. Primers designed for unique and repetitive sequences allowed to reliably identify the sex of both larval and adult stages of the parasite.

Conclusion
Our genome-to-genome comparison method that we call "whole-genome in-silico subtractive hybridization" (WISH) allows for rapid identification of sequences that are specific for a certain genotype (e.g. the heterogametic sex). It can in principle be used for the detection of any sequence differences between isolates (e.g. strains, pathovars) or even closely related species.
Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct
Authors: Hu Hao , Bandyopadhyay Pradip K , Olivera Baldomero M , Yandell Mark 
Published: June 2012

Abstract

Background
The fish-hunting cone snail, Conus geographus, is the deadliest snail on earth. In the absence of medical intervention, 70% of human stinging cases are fatal. Although, its venom is known to consist of a cocktail of small peptides targeting different ion-channels and receptors, the bulk of its venom constituents, their sites of manufacture, relative abundances and how they function collectively in envenomation has remained unknown.

Results
We have used transcriptome sequencing to systematically elucidate the contents the C. geographus venom duct, dividing it into four segments in order to investigate each segment’s mRNA contents. Three different types of calcium channel (each targeted by unrelated, entirely distinct venom peptides) and at least two different nicotinic receptors appear to be targeted by the venom. Moreover, the most highly expressed venom component is not paralytic, but causes sensory disorientation and is expressed in a different segment of the venom duct from venoms believed to cause sensory disruption. We have also identified several new toxins of interest for pharmaceutical and neuroscience research.

Conclusions

Conus geographus is believed to prey on fish hiding in reef crevices at night. Our data suggest that disorientation of prey is central to its envenomation strategy. Furthermore, venom expression profiles also suggest a sophisticated layering of venom-expression patterns within the venom duct, with disorientating and paralytic venoms expressed in different regions. Thus, our transcriptome analysis provides a new physiological framework for understanding the molecular envenomation strategy of this deadly snail.
Characterization of Mycobacterium tuberculosis Beijing isolates from the Mediterranean area
Authors: Alonso M , Alonso Rodriguez N , Garzelli C , Martínez Lirola M , Herranz M , Samper S , Ruiz Serrano MJ , Bouza E , García de Viedma D 
Published: June 2012

AbstractBackgroundThe Beijing lineage ofMycobacterium tuberculosisis causing concern due to its global distribution and its involvement in severe outbreaks. Studies focused on this lineage are mainly restricted to geographical settings where its prevalence is high, whereas those in other areas are scarce. In this study, we analyze Beijing isolates in the Mediterranean area, where this lineage is not prevalent and is mainly associated with immigrant cases.ResultsOnly 1% (N = 26) of the isolates from two population-based studies in Spain corresponded to Beijing strains, most of which were pan-susceptible and from Peruvian and Ecuadorian patients. Restriction fragment length polymorphism typing with the insertion sequence IS6110identified three small clusters (2-3 cases). Mycobacterial interspersed repetitive unit-variable number tandem repeat typing (MIRU-15) offered low discriminatory power, requiring the introduction of five additional loci. A selection of the Beijing isolates identified in the Spanish sample, together with a sample of Beijing strains from Italy, to broaden the analysis context in the Mediterranean area, were assayed in an infection model with THP-1 cells. A wide range of intracellular growth rates was observed with only two isolates showing an increased intracellular replication, in both cases associated with contained production of TNF-α. No correlation was observed between virulence and the Beijing phylogenetic group, clustered/orphan status, or resistance. The Beijing strain responsible for extensive spread on Gran Canaria Island was also identified in Madrid, but did not lead to secondary cases and did not show high infectivity in the infection model.ConclusionsThe Beijing lineage in our area is a non-homogeneous family, with only certain highly virulent representatives. The specific characterization of Beijing isolates in different settings could help us to accurately identify the virulent representatives before making general assumptions about this lineage.
Cloning, expression and characterization of an aryl-alcohol dehydrogenase from the white-rot fungus Phanerochaete chrysosporium strain BKM-F-1767
Authors: Yang Dong-Dong , François Jean Marie , de Billerbeck Gustavo M 
Published: June 2012

Abstract

Background
The white-rot fungus Phanerochaete chrysosporium is among the small group of fungi that can degrade lignin to carbon dioxide while leaving the crystalline cellulose untouched. The efficient lignin oxidation system of this fungus requires cyclic redox reactions involving the reduction of aryl-aldehydes to the corresponding alcohols by aryl-alcohol dehydrogenase. However, the biochemical properties of this enzyme have not been extensively studied. These are of most interest for the design of metabolic engineering/synthetic biology strategies in the field of biotechnological applications of this enzyme.

Results
We report here the cloning of an aryl-alcohol dehydrogenase cDNA from the white-rot fungus Phanerochaete chrysosporium, its expression in Escherichia coli and the biochemical characterization of the encoded GST and His6 tagged protein. The purified recombinant enzyme showed optimal activity at 37°C and at pH 6.4 for the reduction of aryl- and linear aldehydes with NADPH as coenzyme. NADH could also be the electron donor, while having a higher Km (220 μM) compared to that of NADPH (39 μM). The purified recombinant enzyme was found to be active in the reduction of more than 20 different aryl- and linear aldehydes showing highest specificity for mono- and dimethoxylated Benzaldehyde at positions 3, 4, 3,4 and 3,5. The enzyme was also capable of oxidizing aryl-alcohols with NADP + at 30°C and an optimum pH of 10.3 but with 15 to 100-fold lower catalytic efficiency than for the reduction reaction.

Conclusions
In this work, we have characterized the biochemical properties of an aryl-alcohol dehydrogenase from the white-rot fungus Phanerochaete chrysosporium. We show that this enzyme functions in the reductive sense under physiological conditions and that it displays relatively large substrate specificity with highest activity towards the natural compound Veratraldehyde.
Characterization of non-host resistance in broad bean to the wheat stripe rust pathogen
Authors: Cheng Yulin , Zhang Hongchang , Yao Juanni , Wang Xiaojie , Xu Jinrong , Han Qingmei , Wei Guorong , Huang Lili , Kang Zhensheng 
Published: June 2012

Abstract

Background
Non-host resistance (NHR) confers plant species immunity against the majority of microbial pathogens and represents the most robust and durable form of plant resistance in nature. As one of the main genera of rust fungi with economic and biological importance, Puccinia infects almost all cereals but is unable to cause diseases on legumes. Little is known about the mechanism of this kind of effective defense in legumes to these non-host pathogens.

Results
In this study, the basis of NHR in broad bean (Vicia faba L.) against the wheat stripe rust pathogen, Puccinia striiformis f. sp. tritici (Pst), was characterized. No visible symptoms were observed on broad bean leaves inoculated with Pst. Microscopic observations showed that successful location of stomata and haustoria formation were significantly reduced in Pst infection of broad bean. Attempted infection induced the formation of papillae, cell wall thickening, production of reactive oxygen species, callose deposition and accumulation of phenolic compounds in plant cell walls. The few Pst haustoria that did form in broad bean cells were encased in reactive oxygen and callose materials and those cells elicited cell death. Furthermore, a total of seven defense-related genes were identified and found to be up-regulated during the Pst infection.

Conclusions
The results indicate that NHR in broad bean against Pst results from a continuum of layered defenses, including basic incompatibility, structural and chemical strengthening of cell wall, posthaustorial hypersensitive response and induction of several defense-related genes, demonstrating the multi-layered feature of NHR. This work also provides useful information for further determination of resistance mechanisms in broad bean to rust fungi, especially the adapted important broad bean rust pathogen, Uromyces viciae-fabae, because of strong similarity and association between NHR of plants to unadapted pathogens and basal resistance of plants to adapted pathogens.