bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of gene expression changes in peach leaves in response to Plum pox virus infection using RNA‐Seq
Authors: Rubio Manuel , Rodríguez‐Moreno Luis , Ballester Ana Rosa , de Moura Manuel Castro , Bonghi Claudio , Candresse Thierry , Martínez‐Gómez Pedro 
Published: July 2014

SummaryDifferences in gene expression were studied after Plum pox virus (PPV, sharka disease) infection in peach GF305 leaves with and without sharka symptoms using RNA‐Seq. For each sample, more than 80% of 100‐nucleotide paired‐end (PE) Illumina reads were aligned on the peach reference genome. In the symptomatic sample, a significant proportion of reads were mapped to PPV reference genomes (1.04% compared with 0.00002% in non‐symptomatic leaves), allowing for the ultra‐deep assembly of the complete genome of the PPV isolate used (9775 nucleotides, missing only 11 nucleotides at the 5′ genome end). In addition, significant alternative splicing events were detected in 359 genes and 12 990 single nucleotide polymorphisms (SNPs) were identified, 425 of which could be annotated. Gene ontology annotation revealed that the high‐ranking mRNA target genes associated with the expression of sharka symptoms are mainly related to the response to biotic stimuli, to lipid and carbohydrate metabolism and to the negative regulation of catalytic activity. A greater number of differentially expressed genes were observed in the early asymptomatic phase of PPV infection in comparison with the symptomatic phase. These early infection events were associated with the induction of genes related to pathogen resistance, such as jasmonic acid, chitinases, cytokinin glucosyl transferases and Lys‐M proteins. Once the virus had accumulated, the overexpression of Dicer protein 2a genes suggested a gene silencing plant response that was suppressed by the virus HCPro and P1 proteins. These results illustrate the dynamic nature of the peach–PPV interaction at the transcriptome level and confirm that sharka symptom expression is a complex process that can be understood on the basis of changes in plant gene expression.
Association of chronic periodontitis and psoriasis: periodontal status with severity of psoriasis
Authors: Sharma A , Raman A , Pradeep AR 
Published: July 2014

ObjectivesThe chronic periodontitis (CP) and psoriasis share common risk factors and co‐morbidities. This study was designed to explore how frequently CP is associated with patients with psoriasis compared to systemic healthy subjects.Materials and MethodsThe periodontal clinical parameters probing depth (PD), periodontal attachment level (PAL), and presence or absence of radiographic bone loss (J Periodontol, 78, 2007, 1387) were recorded in 33 psoriasis subjects and 35 healthy subjects. The severity of psoriasis was assessed and recorded by Psoriasis Area and Severity Index as described earlier by Cohen et al (J Dermatolog Treat, 16, 2005, 308). The other oral health characteristics were also recorded.ResultsProbing depth and PAL showed significant higher values in psoriasis group compared with healthy group. It was also found that periodontal status was associated with severity of psoriasis.ConclusionsThe results showed a link between CP and psoriasis. This suggests the need for a multidisciplinary approach to manage psoriasis patients with chronic periodontitis, especially in relation to current and future treatment.
DNA methylation profiles in primary cutaneous melanomas are associated with clinically significant pathologic features
Authors: Thomas Nancy E. , Slater Nathaniel A. , Edmiston Sharon N. , Zhou Xin , Kuan Pei‐Fen , Groben Pamela A. , Carson Craig C. , Hao Honglin , Parrish Eloise , Moschos Stergios J. , Berwick Marianne , Ollila David W. , Conway Kathleen 
Published: July 2014

SummaryDNA methylation studies have elucidated a methylation signature distinguishing primary melanomas from benign nevi and provided new insights about genes that may be important in melanoma development. However, it is unclear whether methylation differences among primary melanomas are related to tumor pathologic features with known clinical significance. We utilized the Illumina GoldenGate Cancer Panel array to investigate the methylation profiles of 47 primary cutaneous melanomas. Arraywide methylation patterns revealed a positive association of methylation with Breslow thickness and mutated BRAF, a negative association with mitotic rate, and a weak association with ulceration. Hierarchical clustering on CpG sites exhibiting the most variable methylation (n = 235) divided the melanoma samples into three clusters, including a highly methylated cluster that was positively associated with Breslow thickness and an intermediately methylated cluster associated with Breslow thickness and mitotic rate. Our findings provide support for the existence of methylation‐defined subsets in melanomas with increased methylation associated with Breslow thickness.
Physical activity and movement skills proficiency of young Filipino children
Authors: Capio Catherine M , Sit Cindy HP , Eguia Kathlynne F , Abernethy Bruce 
Published: July 2014

AbstractRecent reports indicate an increasing prevalence of overweight among Filipino children. Considering the known association of physical activity (PA) with obesity, this study reports the findings of an objective monitoring of PA in a sample of Filipino children. The study also explores the relationship of PA with fundamental movement skills (FMS) proficiency. Thirty‐two children (6.54 ± 2.45 years old) wore an accelerometer for 7 days of PA monitoring and were assessed on five FMS (throw, catch, kick, run, jump). The children met the World Health Organization's recommendation of 60 min of PA per day, with more active time being accrued during weekdays than weekends. Children with greater FMS proficiency were found to spend more time in PA than those who were less skillful during weekends. Further research is recommended to examine PA and FMS proficiency associations, exploring the role of social interactions on weekends and weekdays.
Prevalence of Emanuel syndrome: Theoretical frequency and surveillance result
Authors: Ohye Tamae , Inagaki Hidehito , Kato Takema , Tsutsumi Makiko , Kurahashi Hiroki 
Published: July 2014

AbstractConstitutional t(11;22)(q23;q11) is the most frequent recurrent non‐Robertsonian translocation in humans. Balanced carriers of t(11;22) usually manifest no clinical symptoms, and are often identified after the birth of offspring with an unbalanced form of this translocation, known as Emanuel syndrome. To determine the prevalence of the disorder, we sent surveillance questionnaires to 735 core hospitals in Japan. The observed number of Emanuel syndrome cases was 36 and that of t(11;22) balanced translocation carriers, 40. On the basis of the de novo t(11;22) translocation frequency in sperm from healthy men, we calculated the frequency of the translocations in the general population. Accordingly, the prevalence of Emanuel syndrome was estimated at 1 in 110 000. Based on this calculation, the estimated number of Emanuel syndrome cases in Japan is 1063 and of t(11;22) balanced translocation carriers, 16 604, which are much higher than the numbers calculated from the questionnaire responses. It is possible that this discordance is partly attributable to a lack of disease identification. Further efforts should be made to increase the awareness of Emanuel syndrome to ensure a better quality of life for affected patients and their families.
Academic‐Practice Partnership in Public Health Nursing: Working with Families in a Village‐Based Collaboration
Authors: Davis Rebecca A. , Travers Gustafson Dianne 
Published: July 2014

AbstractObjectivesThe purpose of this program development and evaluation project was to promote healthy families and communities by creating academic‐practice partnerships, educating BSN students and building family‐nursing student partnerships that were supported by a “village” of interconnected resources.Design and SampleA mixed‐methods design was used for the project. Data were collected from a convenience sample of vulnerable families, BSN students engaged in PHN practica, and partner members.MeasuresNine tools were developed to capture data over two semesters including a GIS mapping strategy.ResultsOne hundred and seventy‐five home visits were completed with 20 families, 14 of whom needed interpreter assistance. Families reported satisfaction with the quality of home visits, education, and assistance toward health goals. Fifty‐three students provided 202 educational interventions, 39 community resource connections, and 46 care transitions. Students reported linking theory with practice and valued the PHN practicum experience. Academic‐practice partners identified opportunities for program development and sustainability. GIS mapping illustrated complex family linkages to community resources.ConclusionsResults suggest that young, vulnerable families benefit from public health nursing (PHN) home visits, but sustaining home visit programs is challenging. Academic‐practice partnerships can guide students and families partnered in a reciprocal relationship with “village” resources.
Extensive emphysematous pyelonephritis in a renal allograft: case report and review of literature
Authors: Ágreda Castañeda F. , Lorente D. , Trilla Herrera E. , Gasanz Serrano C. , Servian Vives P. , Iztueta Saavedra I. , Morote Robles J. 
Published: July 2014

AbstractEmphysematous pyelonephritis (EPN) is an acute, severe necrotizing infection of the renal parenchyma and perirenal tissue, which results in the presence of gas within the renal parenchyma, collecting system, or perinephric tissue. EPN of renal allograft is rare, with only 23 cases reported in Western literature. Here, we report a patient treated successfully with surgery. We also review the literature, focusing on old and new suggested classification systems for EPN.
Assessing filter robustness at drinking water treatment plants
Authors: Hartshorn Andrew J. , Prpich George , Upton Andrew , Macadam Jitka , Jefferson Bruce , Jarvis Peter 
Published: July 2014

AbstractThis investigation explores the use of five‐parameter logistic curve fitting in quantifying turbidity robustness and risk scoring in clarification and filtrations stages of several surface water treatment works in the Anglian Water region of the United Kingdom. The approach taken reviews different scoring systems and addresses issues of weighting, averages and variability in robustness performance using turbidity robustness indices (TRIs). It also proposes an area‐based risk scoring profile to assess performance [relative area profile for T90 (RAP90)]. The metrics produced are considered to be a logical and rational way to help prioritise where resources for water treatment operation should be deployed.
Psychometric Analysis of Two New Scales: The Evidence‐Based Practice Nursing Leadership and Work Environment Scales
Authors: Pryse Yvette , McDaniel Anna , Schafer John 
Published: July 2014

ABSTRACTBackgroundThose in nursing have been charged with practicing to the full extent of their education and training by the Institute of Medicine. Therefore, evidence‐based practice (EBP) has never been more important to nursing than in the current healthcare environment. Frequently the burden of EBP is the responsibility of the bedside practitioner, but has been found to be a process that requires leadership and organizational support. A key underlying component of a strong EBP environment includes effective communications and collaboration among staff and nursing leadership.AimsDeveloping measurement tools that examine the milieu and nursing leadership in which the staff nurse practices is an important component of understanding the factors that support or hinder EBP. The aim of this study is to report on the development and analysis of two new scales designed to explore leadership and organizational support for EBP. The EBP Nursing Leadership Scale (10 items) examines the staff nurses perception of support provided by the nurse manager for EBP, and the EBP Work Environment Scale (8 items) examines organizational support for EBP.MethodsStaff nurses who worked at least .5 FTE in direct patient care, from two inner city hospitals (n = 422) completed the scales. The scales were evaluated for internal consistency reliability with the Cronbach alpha technique, content validity using a panel of experts, and construct validity byResultsThe content validity index computed from expert rankings was .78 to 1.0 with an average of.96. Cronbach's alpha was .96 (n = 422) for the EBP Nursing Leadership Scale and .86 (n = 422) for the EBP Work Environment Scale. Factor analysis confirmed that each scale measured a unidimensional construct (p < .000).Linking Evidence to ActionThe EBP Nursing Leadership Scale and the EBP Work Environment Scale are psychometrically sound instruments to examine organizational influences on EBP.
Stoichiometry and Turnover of the Bacterial Flagellar Switch Protein FliN
Authors: Delalez Nicolas J. , Berry Richard M. , Armitage Judith P. 
Published: July 2014

ABSTRACT

Some proteins in biological complexes exchange with pools of free proteins while the complex is functioning. Evidence is emerging that protein exchange can be part of an adaptive mechanism. The bacterial flagellar motor is one of the most complex biological machines and is an ideal model system to study protein dynamics in large multimeric complexes. Recent studies showed that the copy number of FliM in the switch complex and the fraction of FliM that exchanges vary with the direction of flagellar rotation. Here, we investigated the stoichiometry and turnover of another switch complex component, FliN, labeled with the fluorescent protein CyPet, in
Escherichia coli
. Our results confirm that,
in vivo
, FliM and FliN form a complex with stoichiometry of 1:4 and function as a unit. We estimated that wild-type motors contained 120 ± 26 FliN molecules. Motors that rotated only clockwise (CW) or counterclockwise (CCW) contained 114 ± 17 and 144 ± 26 FliN molecules, respectively. The ratio of CCW-to-CW FliN copy numbers was 1.26, very close to that of 1.29 reported previously for FliM. We also measured the exchange of FliN molecules, which had a time scale and dependence upon rotation direction similar to those of FliM, consistent with an exchange of FliM-FliN as a unit. Our work confirms the highly dynamic nature of multimeric protein complexes and indicates that, under physiological conditions, these machines might not be the stable, complete structures suggested by averaged fixed methodologies but, rather, incomplete rings that can respond and adapt to changing environments.

IMPORTANCE
The flagellum is one of the most complex structures in a bacterial cell, with the core motor proteins conserved across species. Evidence is now emerging that turnover of some of these motor proteins depends on motor activity, suggesting that turnover is important for function. The switch complex transmits the chemosensory signal to the rotor, and we show, by using single-cell measurement, that both the copy number and the fraction of exchanging molecules vary with the rotational bias of the rotor. When the motor is locked in counterclockwise rotation, the copy number is similar to that determined by averaged, fixed methodologies, but when locked in a clockwise direction, the number is much lower, suggesting that that the switch complex ring is incomplete. Our results suggest that motor remodeling is an important component in tuning responses and adaptation at the motor.
Comparison of Phylogenetically DistinctHistoplasmaStrains Reveals Evolutionarily Divergent Virulence Strategies
Authors: Sepúlveda Victoria E. , Williams Corinne L. , Goldman William E. 
Published: July 2014

ABSTRACTInfection with the dimorphic fungusHistoplasma capsulatumresults from the inhalation of contaminated soil. Disease outcome is variable and depends on the immune status of the host, number of organisms inhaled, and theH. capsulatumstrain.H. capsulatumis divided into seven distinct clades based on phylogenetic analyses, and strains from two separate clades have been identified in North America (denoted as NAm strains). We characterized anH. capsulatumisolate (WU24) from the NAm 1 lineage in relation to two other well-characterizedHistoplasmaisolates, the Panamanian strain G186A and the NAm 2 strain G217B. We determined that WU24 is a chemotype II strain and requires cell wall α-(1,3)-glucan for successfulin vitroinfection of macrophages. In a mouse model of histoplasmosis, WU24 exhibited a disease profile that was very similar to that of strain G186A at a high sublethal dose; however, at this dose G217B had markedly different kinetics. Surprisingly, infection with a lower dose mitigated many of the differences during the course of infection. The observed differences in fungal burden, disease kinetics, symptomology, and cytokine responses all indicate that there is a sophisticated relationship between host and fungus that drives the development and progression of histoplasmosis.IMPORTANCEHistoplasmosis has a wide range of clinical manifestations, presenting as mild respiratory distress, acute respiratory infection, or a life-threatening disseminated disease most often seen in immunocompromised patients. Additionally, the outcome appears to be dependent on the amount and strain of fungus inhaled. In this study, we characterized a recent clinicalH. capsulatumisolate that was collected from an HIV+individual in North America. In contrast to other isolates from the same lineage, this strain, WU24, infected both macrophages and wild-type mice. We determined that in contrast to many other North American strains, WU24 infection of macrophages is dependent on the presence of cell wall α-(1,3)-glucan. Surprisingly, comparison of WU24 with two previously characterized isolates revealed that many conclusions regarding relative strain virulence and certain hallmarks of histoplasmosis are dependent on the inoculum size.
Feasibility of using an epigenetic marker of risk for lung cancer, methylation of p16, to promote smoking cessation among US veterans
Authors: Shofer Scott , Beyea Matthew , Li Sufeng , Bastian Lori A , Wahidi Momen M , Kelley Michael , Lipkus Isaac M 
Published: July 2014

IntroductionProviding smokers feedback using epigenetic markers of lung cancer risk has yet to be tested as a strategy to motivate smoking cessation. Epigenetic modification of Rb-p16 (p16) due to tobacco exposure is associated with increased risk of developing lung cancer. This study examined the acceptance of testing for methylatedp16and the understanding of test results in smokers at risk for development of lung cancer.MethodsThirty-five current smokers with airways obstruction viewed an educational presentation regardingp16function followed by testing for the presence of methylatedp16in sputum. Participants were offered smoking cessation assistance and asked to complete surveys at the time of enrolment regarding their understanding of the educational material, perception of risk associated with smoking and desire to quit. Participants were notified of their test result and follow-up surveys were administered 2 and 10 weeks after notification of their test result.ResultsTwenty per cent of participants had methylatedp16. Participants showed high degree of understanding of educational materials regarding the function and risk associated withp16methylation. Sixty-seven per cent and 57% of participants with low-risk and high-risk test results, respectively, reported that the information was more likely to motivate them to quit smoking. Smoking cessation rates were similar between methylated and non-methylated participants.ConclusionsTesting for an epigenetic marker of lung cancer risk is accepted and understood by active smokers. A low-risk test result does not decrease motivation to stop smoking.Trial registration numberNCT01038492.
Prehospital end-tidal carbon dioxide differentiates between cardiac and obstructive causes of dyspnoea
Authors: Hunter Christopher L , Silvestri Salvatore , Ralls George , Papa Linda 
Published: July 2014

BackgroundDifferentiating between cardiac and obstructive causes for dyspnoea is essential for proper management, but is difficult in the prehospital setting.ObjectiveTo assess if prehospital levels of end-tidal carbon dioxide (ETCO2) differed in obstructive compared to cardiac causes of dyspnoea, and could suggest one diagnosis over the other.MethodsWe conducted a retrospective cohort study among patients transported by emergency medical services during a 29-month period who were diagnosed with either obstructive pulmonary disease or congestive heart failure (CHF) by ICD-9 codes. Initial prehospital vital signs, including ETCO2, were recorded. Records were linked by manual archiving of emergency medical services and hospital data.ResultsThere were 106 patients with a diagnosis of obstructive or cardiac causes of dyspnoea that had prehospital ETCO2 levels measured during the study period. ETCO2 was significantly lower in patients diagnosed with CHF (31 mm Hg 95% CI 27 to 35) versus obstructive pulmonary disease (39 mm Hg 95% CI 35 to 42; p<0.001). Lower ETCO2 levels predicted CHF, with an area under the Receiver Operating Characteristics Curve of 0.70 (95% CI 0.60 to 0.81). Using ETCO2 <40 mm Hg as a cut-off, the sensitivity for predicting heart failure was 93% (95% CI 88% to 98%), the specificity was 43% (95% CI 33% to 52%), the positive predictive value was 38% (95% CI 29% to 48%), and the negative predictive value was 94% (95% CI 89% to 99%).ConclusionsLower levels of ETCO2 were associated with CHF, and may serve as an objective diagnostic adjunct to predict this cause of dyspnoea in the prehospital setting.
Big Bubble Deep Anterior Lamellar Keratoplasty for Management of Deep Fungal Keratitis
Authors: Gao Hua , Song Peng , Echegaray Jose J. , Jia Yanni , Li Suxia , Du Man , Perez Victor L. , Shi Weiyun 
Published: July 2014

Objective. To evaluate the therapeutic effect of big bubble deep anterior lamellar keratoplasty (DALK) in patients with deep fungal keratitis.Methods. Consecutive patients who had DALK for deep fungal keratitis at Shandong Eye Hospital between July 2011 and December 2012 were included. In all patients, the infiltration depth was more than 4/5ths of the corneal thickness. DALK surgery was performed with bare Descemet membrane (DM) using the big bubble technique. Corrected distance visual acuity (CDVA), graft status, and intraoperative and postoperative complications were monitored.Results. Big bubble DALK was performed in 23 patients (23 eyes). Intraoperative perforation of the DM occurred in two eyes (8.7%) during stromal dissection. The patients received lamellar keratoplasty with an air bubble injected into the anterior chamber. Double anterior chamber formed in 3 eyes (13.0%). Mean CDVA of the patients without cataract, amblyopia, and fungal recurrence was improved from preoperative HM/20 cm−1.0 (LogMAR) to0.23 ± 0.13(LogMAR) at the last followup (P<0.01). Fungal recurrence was found in two patients (8.7%). Corneal stromal graft rejection was noted in one patient (4.3%).Conclusions. DALK using the big bubble technique seems to be effective and safe in the treatment of deep fungal keratitis unresponsive to medication.
Integral Transforms of Functions to Be in a Class of Analytic Functions Using Duality Techniques
Authors: Devi Satwanti , Swaminathan A. 
Published: July 2014

Let Wβ(α,γ), β<1, denote the class of all normalized analytic functions f in the unit disc D={z∈C:|z|<1} such that Re(eiϕ((1-α+2γ)(f/z)+(α-2γ)f'+γzf″-β))>0, z∈D, for some ϕ∈R with α≥0, γ≥0, and β<1. Let M(ξ), 0≤ξ≤1, denote the Pascu class of ξ-convex functions given by the analytic condition Re((ξz(zf'(z))'+(1-ξ)zf'(z))/ (ξzf'(z)+(1-ξ)f(z)))>0 which unifies the classes of starlike and convex functions. The aim of this paper is to find conditions on λ(t) so that the integral transform of the form Vλ(f)(z)=∫01‍λ(t)(f(tz)/t)dt
carry functions from Wβ(α,γ) into M(ξ). As for the applications, for specific values of λ(t), it is found that several known integral operators carry functions from Wβ(α,γ) into M(ξ). The results for a more generalized operator related to Vλ(f)(z) are also given.