bluuebunny/crossref_metadata_2025_split huggingface dataset:
A survey of 165 sporotrichosis cases examined in Nagasaki prefecture from 1951 to 2012
Authors: Takenaka Motoi , Yoshizaki Asako , Utani Atushi , Nishimoto Katsutaro 
Published: November 2013

SummaryA total of 165 sporotrichosis cases occurring in Nagasaki prefecture, and examined at Nagasaki University Hospital, were evaluated. Both males and females were equally affected, with no significant differences in the affected body regions. Lesions were frequently seen on the face (49 cases, 29.5%) and upper limbs (101 cases, 60.9%). The localised cutaneous type of sporotrichosis (105 cases, 62.9%) was much more frequent than the lymphocutaneous type (62 cases, 37.1%). The infection rate in patients over 50 years of age was 73.1%. The most frequent occupation among the patients was farming (52 cases, 37.4%), and 34 patients had a history of injury. Regarding the geographical distribution of sporotrichosis, 48 cases occurred in the Shimabara peninsula (31.2%) and this is much higher than expected for the population size. Before 1994, almost all sporotrichosis cases (112 cases, 96.5%) were treated with potassium iodide (KI). After 1995, the number of patients treated with KI decreased (nine cases, 23.1%), and itraconazole (ITZ) was used in 21 cases (59.0%) and terbinafine in six cases (15.3%). The time between ITZ and KI treatment and cure was 13.8 weeks and 12.5 weeks, respectively. All 116 cases, for which the outcome was known, were cured or improved.
High‐density genome‐wide association mapping implicates an F‐box encoding gene in Medicago truncatula resistance to Aphanomyces euteiches
Authors: Bonhomme Maxime , André Olivier , Badis Yacine , Ronfort Joëlle , Burgarella Concetta , Chantret Nathalie , Prosperi Jean‐Marie , Briskine Roman , Mudge Joann , Debéllé Frédéric , Navier Hélène , Miteul Henri , Hajri Ahmed , Baranger Alain , Tiffin Peter , Dumas Bernard , Pilet‐Nayel Marie‐Laure , Young Nevin D. , Jacquet Christophe 
Published: November 2013

Summary

The use of quantitative disease resistance (QDR) is a promising strategy for promoting durable resistance to plant pathogens, but genes involved in QDR are largely unknown. To identify genetic components and accelerate improvement of QDR in legumes to the root pathogen Aphanomyces euteiches, we took advantage of both the recently generated massive genomic data for Medicago truncatula and natural variation of this model legume.

A high‐density (≈5.1 million single nucleotide polymorphisms (SNPs)) genome‐wide association study (GWAS) was performed with both in vitro and glasshouse phenotyping data collected for 179 lines.

GWAS identified several candidate genes and pinpointed two independent major loci on the top of chromosome 3 that were detected in both phenotyping methods. Candidate SNPs in the most significant locus ( = 23%) were in the promoter and coding regions of an F‐box protein coding gene. Subsequent qRT‐PCR and bioinformatic analyses performed on 20 lines demonstrated that resistance is associated with mutations directly affecting the interaction domain of the F‐box protein rather than gene expression.

These results refine the position of previously identified QTL to specific candidate genes, suggest potential molecular mechanisms, and identify new loci explaining QDR against A. euteiches.
A dual gene‐silencing vector system for monocot and dicot plants
Authors: Liou Ming‐Ru , Huang Ying‐Wen , Hu Chung‐Chi , Lin Na‐Sheng , Hsu Yau‐Heiu 
Published: November 2013

SummaryPlant virus‐based gene‐silencing vectors have been extensively and successfully used to elucidate functional genomics in plants. However, only limited virus‐induced gene‐silencing (VIGS) vectors can be used in both monocot and dicot plants. Here, we established a dual gene‐silencing vector system based on Bamboo mosaic virus (BaMV) and its satellite RNA (satBaMV). Both BaMV and satBaMV vectors could effectively silence endogenous genes in Nicotiana benthamiana and Brachypodium distachyon. The satBaMV vector could also silence the green fluorescent protein (GFP) transgene in GFP transgenic N. benthamiana. GFP transgenic plants co‐agro‐inoculated with BaMV and satBaMV vectors carrying sulphur and GFP genes, respectively, could simultaneously silence both genes. Moreover, the silenced plants could still survive with the silencing of genes essential for plant development such as heat‐shock protein 90 (Hsp90) and Hsp70. In addition, the satBaMV‐ but not BaMV‐based vector could enhance gene‐silencing efficiency in newly emerging leaves of N. benthamiana deficient in RNA‐dependant RNA polymerase 6. The dual gene‐silencing vector system of BaMV and satBaMV provides a novel tool for comparative functional studies in monocot and dicot plants.
Long‐Term Treatment with Oral Propranolol Reduces Relapses of Infantile Hemangiomas
Authors: Giachetti Ana , Garcia‐Monaco Ricardo , Sojo Magdalena , Scacchi María F. , Cernadas Carolina , Guerchicoff Lemcke Marianna , Dovasio Fernanda 
Published: November 2013

AbstractOral propranolol (OP) has been shown to be effective in the treatment of complicated infantile hemangiomas (IHs), but optimal treatment duration to avoid relapses after stopping OP treatment has not been established. The objective of this study was to compare the frequency of relapses in long‐term OP treatment with that of short‐term OP treatment. This was a retrospective cohort study of 30 patients with complicated IHs who received treatment with OP. Patients were divided into two groups: OP treatment of 8 months or less and OP treatment of longer than 8 months. OP was started at 1 mg/kg/day in three doses every 8 hours for 1 week and increased to 1.5 to 4 mg/kg/day afterward. Ultrasound was used to objectively measure the response to treatment. Clinical and ultrasound assessment showed a decrease in IH size and resolution of complications in all patients (n = 30). In the short‐term group (n = 10), nine patients (90%) relapsed after stopping treatment. In the long‐term group (n = 20), the duration of treatment was 12 months in all patients, and only 1 patient out of the 20 treated (5%) showed relapse 2 months after finishing the full treatment (odds ratio = 18, 95% confidence interval 2.6, 123, p < 0.001. Twelve months of treatment of IH with OP is associated with a significantly lower rate of relapse than with shorter treatment.
Impact of palifermin on incidence of oral mucositis and healthcare utilization in children undergoing autologous hematopoietic stem cell transplantation for malignant diseases
Authors: Vitale Kelly M. , Violago Leah , Cofnas Paige , Bishop Jacquelyn , Jin Zhezhen , Bhatia Monica , Kung Andrew L. , George Diane , Garvin James , Satwani Prakash 
Published: November 2013

AbstractPalifermin has been demonstrated to decrease the incidence of severe oral mucositis in adults following TBI containing conditioning regimens prior to AHSCT. The impact of palifermin on the incidence of oral mucositis in children undergoing AHSCT has never been studied. We compared the effect of palifermin on the incidence of oral mucositis and supportive care in 58 children undergoing myeloablative AHSCT; 25 children received palifermin and 33 children did not receive palifermin (control arm). Oral mucositis was graded as per WHO criteria. The demographic characteristics were comparable between the two arms. Results comparing the palifermin vs. control arm showed that the incidence of grade III–IV oral mucositis was 20% vs. 42.4% (p = 0.072). The number of days patients received patient‐controlled analgesia and total parenteral nutrition in the palifermin vs. control arm were 8.80 ± 8.39 vs. 8.30 ± 8.54 (p = 0.826) and 13.52 ± 11.32 vs. 11.55 ± 9.63 (p = 0.484), respectively. The average length of hospitalization in the palifermin vs. control arm was 31.44 ± 7.42 vs. 28.61 ± 10.38 (p = 0.252), respectively. In this study, we were unable to demonstrate a statistical difference in the incidence of oral mucositis and other supportive care needs or a decrease in hospital stay between the two arms.
Philosophy and Phylogenetics
Authors: Velasco Joel D. 
Published: November 2013

AbstractPhylogenetics is the study and reconstruction of evolutionary history and is filled with numerous foundational issues of interest to philosophers. This paper briefly introduces some central concepts in the field, describes some of the main methods for inferring phylogenies, and provides some arguments for the superiority of model‐based methods such as Likelihood and Bayesian methods over nonparametric methods such as parsimony. It also raises some underdeveloped issues in the field of interest to philosophers.
Nutritional abrogation of photoimmunosuppression: in vivo investigations
Authors: Pilkington Suzanne M. , Gibbs Neil K. , Friedmann Peter S. , Rhodes Lesley E. 
Published: November 2013

SummarySkin cancer is a major public health concern, and the primary aetiological factor in the majority of skin cancers is ultraviolet radiation (UVR) exposure. UVR not only induces potentially mutagenic DNA damage but also suppresses cell‐mediated immunity (CMI), allowing cancerous cells to escape destruction and progress to tumours. A considerable proportion of an individual's annual sun exposure is obtained outside the vacation period when topical and physical measures for photoprotection are irregularly used. Certain nutrients could provide an adjunctive protective role, and evidence is accruing from experimental studies to support their use in abrogation of photoimmunosuppression. Moreover, developments in clinical research methods to evaluate impact of solar‐simulated radiation on cutaneous CMI allow the immune protective potential of nutritional agents to be examined in humans in vivo. This article summarises the mediation of CMI and its suppression by UVR, evaluates the methodology for quantitative assessment in vivo, reviews the human studies reported on nutritional abrogation of photoimmunosuppression including recent randomized controlled trials and discusses the mechanisms of photoprotection by the nutrients. This includes, in addition to antioxidants, novel studies of omega‐3 polyunsaturated fatty acids and nicotinamide.
Genotypic variation and population structure of Sclerotinia trifoliorum infecting chickpea in California
Authors: Njambere E. N. , Peever T. L. , Vandemark G. , Chen W. 
Published: November 2013

Sclerotinia trifoliorum, an important pathogen of cool season legumes, displays both homothallism and heterothallism in its life cycle, unique among members of the genus Sclerotinia. Very little is known about its genetic diversity and population structure. A sample of 129 isolates of S. trifoliorum from diseased chickpea in California was investigated for genetic diversity, population differentiation and reproductive mode. Genetic diversity was estimated using mycelial compatibility (MCG) phenotypes, rDNA intron variation, and allelic diversity at seven microsatellite loci. Genetic analysis revealed high levels of genotypic diversity demonstrated by high genotypic richness (0·88). Similarly, high levels of gene diversity (mean expected heterozygosity HE = 0·68) were observed at the microsatellite loci. Geographic populations of S. trifoliorum were highly admixed as evident from low FST values (0–0·11), suggesting high contemporary or historical gene flow. Hierarchical analysis of molecular variance showed that more than 92% of the genetic variation occurred among isolates within populations. Bayesian clustering analysis identified four cryptic genetic populations that were not correlated to geographic location, and index of multilocus association was non‐significant in each of the four genetic populations. However, the presence of identical haplotypes within and among populations indicates clonal reproduction. The high levels of haplotype diversity and population heterogeneity, a lack of correspondence between MCG and microsatellite haplotype, and low levels of population differentiation suggest that populations of S. trifoliorum in chickpea have been undergoing extensive outcrossing and migration events probably shaped by human‐mediated dissemination, the underlying diverse cropping systems, and chickpea disease management practices.
The Sputum Colour Chart as a predictor of lung inflammation, proteolysis and damage in non‐cystic fibrosis bronchiectasis: A case–control analysis
Authors: Goeminne Pieter C. , Vandooren Jennifer , Moelants Eva A. , Decraene Ann , Rabaey Evelyn , Pauwels Ans , Seys Sven , Opdenakker Ghislain , Proost Paul , Dupont Lieven J. 
Published: November 2013

AbstractBackground and objectiveNon‐cystic fibrosis bronchiectasis (NCFB) is characterized by a vicious cycle of airway infection, inflammation and structural damage with inappropriate mucus clearance. Our aim was to relate the value of proteolytic enzymes, proteolytic enzyme activity and inflammatory markers to disease severity and symptoms in patients with NCFB.MethodsSputum induction in NCFB patients and healthy controls was performed. Sputum was analysed for total and differential cell count, markers of inflammation (CXCL8 (also known as interleukin‐8) and tumour necrosis factor‐α (TNF‐α)) and proteolytic enzymes (neutrophil elastase (NE), gelatin zymography and total gelatinolytic activity (TGA)). Each patient was evaluated by spirometry, Leicester Cough Questionnaire (LCQ) and Sputum Colour Chart (SCC). Patient files were analysed to determine Pseudomonas aeruginosa colonization status. The computed tomography (CT) closest to the date sputum induction was scored by a radiologist.ResultsNCFB patients showed significantly higher neutrophils, CXCL8, TNF‐α, NE and TGA than healthy controls. TGA subanalysis showed that the majority of the activity was NE (82 ± 6.4%). Residual activity was mainly zinc ion‐dependent matrix metalloproteinase (MMP) activity (18 ± 6.4%). Subanalysis showed that patients with chronic Pseudomonas aeruginosa colonization had more activated MMP‐9. Correlations were seen between proteolytic enzymes and inflammation and disease severity (spirometry and CT score), but not with the LCQ. SCC was associated with increased markers of inflammation, proteolytic enzymes and worse CT score.ConclusionsWe show that sputum purulence assessment in daily clinical practice using the SCC is a quick and easy tool that reflects severity of inflammation, destruction and proteolytic enzymatic activity/presence.
Farmers' Contribution to Agricultural Social Capital: Evidence from Southern Spain
Authors: Gómez‐Limón José A. , Vera‐Toscano Esperanza , Garrido‐Fernández Fernando E. 
Published: November 2013

AbstractSocial capital is the whole set of shared norms, values, attitudes, and beliefs that promote cooperation among individuals within the community and that has proved to be a key factor in explaining development processes. This article aims to provide an analytically reliable notion of social capital within the farming sector and a methodological tool for empirically measuring how social capital is accumulated at the farmer level. The theoretical framework proposed is based on the multidimensionality of the complex concept of social capital. Thus, to develop a comprehensive index for social capital, we identify three dimensions of the concept, structural, relational, and cognitive social capital, each one also comprising several subdimensions. This integrative approach permits creation of a composite indicator of the agricultural social capital accumulated at the farmer level, further identifying socioeconomic factors that influence its accumulation at that level. We empirically apply this methodological approach to farmers in Andalusia in southern Spain as a case study. This research provides an interesting starting point for informing policymakers about social capital and helping them implement the necessary programs to facilitate sustainable development in the agricultural sector.
Expansion of the dengue transmission area in Brazil: the role of climate and cities
Authors: Barcellos Christovam , Lowe Rachel 
Published: November 2013

AbstractObjectivesTo examine the spatial and temporal patterns of the recent expansion of dengue transmission area in Brazil (2001–2012) with the aim to identify pathways and constraints to dengue diffusion.MethodsSynthetic indicators were calculated to characterise timing (year of first dengue outbreak), permanence (number of years with dengue outbreaks) and intensity (outbreak occurrence). The indicators were used to map dengue diffusion and compare cities within different climatic zones, with varying population densities.ResultsCurrently, a large portion of the country comprises a dengue transmission area, but cities situated in the mesothermal zone, in the south, and remote areas, in the north, are relatively exempt. Diffusion waves are spread from metropolitan areas towards medium and small cities generating outbreaks in their influence region. However, long‐term permanence of transmission depends on the existence of a favourable climate, abundant population and connectivity.ConclusionsLarge and warm cities sustain and spread dengue viruses, for which specific dengue control measures must be developed. The concentration of outbreaks along climate transition fringes indicates a boundary between two transmission regimes and raises awareness to the effects of ongoing climatic and socio‐economic changes.
Comparative performance of modern digital mammography systems in a large breast screening program
Authors: Yaffe Martin J. , Bloomquist Aili K. , Hunter David M. , Mawdsley Gordon E. , Chiarelli Anna M. , Muradali Derek , Mainprize James G. 
Published: November 2013

Purpose:To compare physical measures pertaining to image quality among digital mammography systems utilized in a large breast screening program. To examine qualitatively differences in these measures and differences in clinical cancer detection rates between CR and DR among sites within that program.Methods:As part of the routine quality assurance program for screening, field measurements are made of several variables considered to correlate with the diagnostic quality of medical images including: modulation transfer function, noise equivalent quanta, d′ (an index of lesion detectability) and air kerma to allow estimation of mean glandular dose. In addition, images of the mammography accreditation phantom are evaluated.Results:It was found that overall there were marked differences between the performance measures of DR and CR mammography systems. In particular, the modulation transfer functions obtained with the DR systems were found to be higher, even for larger detector element sizes. Similarly, the noise equivalent quanta, d′, and the phantom scores were higher, while the failure rates associated with low signal‐to‐noise ratio and high dose were lower with DR. These results were consistent with previous findings in the authors’ program that the breast cancer detection rates at sites employing CR technology were, on average, 30.6% lower than those that used DR mammography.Conclusions:While the clinical study was not large enough to allow a statistically powered system‐by‐system assessment of cancer detection accuracy, the physical measures expressing spatial resolution, and signal‐to‐noise ratio are consistent with the published finding that sites employing CR systems had lower cancer detection rates than those using DR systems for screening mammography.
Absence of an Important Vaccine and Diagnostic Target in Carriage- and Disease-Related Nontypeable Haemophilus influenzae
Authors: Smith-Vaughan Heidi C. , Chang Anne B. , Sarovich Derek S. , Marsh Robyn L. , Grimwood Keith , Leach Amanda J. , Morris Peter S. , Price Erin P. 
Published: November 2013

ABSTRACTNontypeableHaemophilus influenzae(NTHi)-associated disease is a major health problem globally. Whole-genome sequence analysis identified the absence ofhpdgenes encodingHaemophilusprotein D in 3 of 16 phylogenetically distinct NTHi isolates. This novel finding is of potential clinical significance, as protein D andhpdrepresent important NTHi vaccine antigen and diagnostic targets, respectively.
Characterization of the Complete Genome Sequence of a Beak and Feather Disease Virus from a Moluccan Red Lory (
Eos bornea
)
Authors: Sarker Subir , Ghorashi Seyed A. , Forwood Jade K. , Metz Stewart , Raidal Shane R. 
Published: November 2013

ABSTRACT

The complete genome sequence of a beak and feather disease virus (BFDV) encoding two major open reading frames (ORFs) was characterized in a wild Moluccan red lory (
Eos bornea
). This is the first report of a BFDV genome from Indonesia and the first reported BFDV infection for this host species.
Changuinola Virus Serogroup, New Genomes within the Genus
Orbivirus
(Family
Reoviridae
) Isolated in the Brazilian Amazon Region
Authors: Silva Sandro P. , Dilcher Meik , Weidmann Manfred , Carvalho Valéria L. , Casseb Alexandre R. , Silva Eliana V. P. , Nunes Keley N. B. , Chiang Jannifer O. , Martins Lívia C. , Vasconcelos Pedro F. C. , Nunes Márcio R. T. 
Published: November 2013

ABSTRACT

We report here the first complete genome sequence of a
Changuinola virus
(CGLV) serotype
Irituia virus
(BE AN 28873) isolated from a wild rodent (
Oryzomys goeldi
) in the municipality of Ipixuna, State of Pará, northern Brazil. All genome segments showed similarity with those belonging to members of the genus
Orbivirus
, family
Reoviridae
.
Draft Genome Sequence of Marine Cyanobacterium
Synechococcus
sp. Strain NKBG15041c
Authors: Yoshino Tomoko , Honda Toru , Tanaka Masayoshi , Tanaka Tsuyoshi 
Published: November 2013

ABSTRACT

Synechococcus
sp. strain NKBG15041c was isolated as a fast-growing marine cyanobacterium. Genetic transformation techniques using this strain have been well established for metabolic engineering. Here we report the draft genome sequence for this strain, consisting of 44 contigs containing a total of 3,180,043 bp and 3,224 putative protein-coding genes.
Genome Sequence of the Extreme Obligate Alkaliphile Bacillus marmarensis Strain DSM 21297
Authors: Wernick David G. , Choi Kwon-Young , Tat Christine A. , Lafontaine Rivera Jimmy G. , Liao James C. 
Published: November 2013

ABSTRACT

Bacillus marmarensis
strain DSM 21297 is an extreme obligate alkaliphile able to grow in medium up to pH 12.5. A whole-shotgun strategy and
de novo
assembly led to the generation of a 4-Mbp genome of this strain. The genome features alkaliphilic adaptations and pathways for
n
-butanol and poly(3-hydroxybutyrate) synthesis.
Draft Genome Sequence of Serratia fonticola UTAD54, a Carbapenem-Resistant Strain Isolated from Drinking Water
Authors: Henriques Isabel , Jucá Ramos Rommel Thiago , Baraúna Rafael Azevedo , de Sá Pablo Henrique , Marinho Almeida Diogo , Carneiro Adriana Ribeiro , Barbosa Silvanira , Pereira Anabela , Alves Artur , Saavedra Maria José , Egas Conceição , Silva Artur , Correia António 
Published: November 2013

ABSTRACT

Serratia fonticola
UTAD54 is an environmental isolate that is resistant to carbapenems due to the presence of a class A carbapenemase and a metallo-β-lactamase that are unique to this strain. Its draft genome sequence was obtained to clarify the molecular basis of its carbapenem resistance and identify the genomic context of its carbapenem resistance determinants.
Genome Sequence of Rickettsia gravesii, Isolated from Western Australian Ticks
Authors: Sentausa Erwin , Abdad Mohammad Yazid , Robert Catherine , Stenos John , Raoult Didier , Fournier Pierre-Edouard 
Published: November 2013

ABSTRACT

Rickettsia gravesii
is a new
Rickettsia
species closely related to the human pathogen
Rickettsia massiliae
. Here, we describe the genome sequence of
R. gravesii
strain BWI-1, isolated from
Amblyomma triguttatum triguttatum
ticks collected from humans on Barrow Island, Western Australia.