bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence-Based Mapping of the Polyploid Wheat Genome
Authors: Saintenac Cyrille , Jiang Dayou , Wang Shichen , Akhunov Eduard 
Published: May 2013

AbstractThe emergence of new sequencing technologies has provided fast and cost-efficient strategies for high-resolution mapping of complex genomes. Although these approaches hold great promise to accelerate genome analysis, their application in studying genetic variation in wheat has been hindered by the complexity of its polyploid genome. Here, we applied the next-generation sequencing of a wheat doubled-haploid mapping population for high-resolution gene mapping and tested its utility for ordering shotgun sequence contigs of a flow-sorted wheat chromosome. A bioinformatical pipeline was developed for reliable variant analysis of sequence data generated for polyploid wheat mapping populations. The results of variant mapping were consistent with the results obtained using the wheat 9000 SNP iSelect assay. A reference map of the wheat genome integrating 2740 gene-associated single-nucleotide polymorphisms from the wheat iSelect assay, 1351 diversity array technology, 118 simple sequence repeat/sequence-tagged sites, and 416,856 genotyping-by-sequencing markers was developed. By analyzing the sequenced megabase-size regions of the wheat genome we showed that mapped markers are located within 40−100 kb from genes providing a possibility for high-resolution mapping at the level of a single gene. In our population, gene loci controlling a seed color phenotype cosegregated with 2459 markers including one that was located within the red seed color gene. We demonstrate that the high-density reference map presented here is a useful resource for gene mapping and linking physical and genetic maps of the wheat genome.
The Rate and Effects of Spontaneous Mutation on Fitness Traits in the Social Amoeba,Dictyostelium discoideum
Authors: Hall David W , Fox Sara , Kuzdzal-Fick Jennie J , Strassmann Joan E , Queller David C 
Published: May 2013

AbstractWe performed a mutation accumulation (MA) experiment in the social amoeba Dictyostelium discoideum to estimate the rate and distribution of effects of spontaneous mutations affecting eight putative fitness traits. We found that the per-generation mutation rate for most fitness components is 0.0019 mutations per haploid genome per generation or larger. This rate is an order of magnitude higher than estimates for fitness components in the unicellular eukaryote Saccharomyces cerevisiae, even though the base-pair substitution rate is two orders of magnitude lower. The high rate of fitness-altering mutations observed in this species may be partially explained by a large mutational target relative to S. cerevisiae. Fitness-altering mutations also may occur primarily at simple sequence repeats, which are common throughout the genome, including in coding regions, and may represent a target that is particularly likely to give fitness effects upon mutation. The majority of mutations had deleterious effects on fitness, but there was evidence for a substantial fraction, up to 40%, being beneficial for some of the putative fitness traits. Competitive ability within the multicellular slug appears to be under weak directional selection, perhaps reflecting the fact that slugs are sometimes, but not often, comprised of multiple clones in nature. Evidence for pleiotropy among fitness components across MA lines was absent, suggesting that mutations tend to act on single fitness components.
Spatial Profiling of Nuclear Receptor Transcription Patterns over the Course ofDrosophilaDevelopment
Authors: Wilk Ronit , Hu Jack , Krause Henry M 
Published: May 2013

AbstractPrevious work has shown that many of the 18 family members of Drosophila nuclear receptor transcription factors function in a temporal hierarchy to coordinate developmental progression and growth with the rate limiting process of metabolism. To gain further insight into these interactions and processes, we have undertaken a whole-family analysis of nuclear receptor mRNA spatial expression patterns over the entire process of embryogenesis, as well as the 3rd instar wandering larva stage, by using high-resolution fluorescence in situ hybridization. Overall, the patterns of expression are remarkably consistent with previously mapped spatial activity profiles documented during the same time points, with similar hot spots and temporal profiles in endocrine and metabolically important tissues. Among the more remarkable of the findings is that the majority of mRNA expression patterns observed show striking subcellular distributions, indicating potentially critical roles in the control of protein synthesis and subsequent subcellular distributions. These patterns will serve as a useful reference for future studies on the tissue-specific roles and interactions of nuclear receptor proteins, partners, cofactors and ligands.
How Good Are Indirect Tests at Detecting Recombination in Human mtDNA?
Authors: White Daniel James , Bryant David , Gemmell Neil John 
Published: May 2013

AbstractEmpirical proof of human mitochondrial DNA (mtDNA) recombination in somatic tissues was obtained in 2004; however, a lack of irrefutable evidence exists for recombination in human mtDNA at the population level. Our inability to demonstrate convincingly a signal of recombination in population data sets of human mtDNA sequence may be due, in part, to the ineffectiveness of current indirect tests. Previously, we tested some well-established indirect tests of recombination (linkage disequilibrium vs. distance using D′ and r2, Homoplasy Test, Pairwise Homoplasy Index, Neighborhood Similarity Score, and Max χ2) on sequence data derived from the only empirically confirmed case of human mtDNA recombination thus far and demonstrated that some methods were unable to detect recombination. Here, we assess the performance of these six well-established tests and explore what characteristics specific to human mtDNA sequence may affect their efficacy by simulating sequence under various parameters with levels of recombination (ρ) that vary around an empirically derived estimate for human mtDNA (population parameter ρ = 5.492). No test performed infallibly under any of our scenarios, and error rates varied across tests, whereas detection rates increased substantially with ρ values &gt; 5.492. Under a model of evolution that incorporates parameters specific to human mtDNA, including rate heterogeneity, population expansion, and ρ = 5.492, successful detection rates are limited to a range of 7−70% across tests with an acceptable level of false-positive results: the neighborhood similarity score incompatibility test performed best overall under these parameters. Population growth seems to have the greatest impact on recombination detection probabilities across all models tested, likely due to its impact on sequence diversity. The implications of our findings on our current understanding of mtDNA recombination in humans are discussed.
Neonatal End-of-Life Care: A Single-Center NICU Experience in Israel Over a Decade
Authors: Eventov-Friedman Smadar , Kanevsky Hana , Bar-Oz Benjamin 
Published: May 2013

OBJECTIVES:
To follow changes in the causes of neonatal deaths in the NICU at Hadassah Medical Center, Jerusalem, Israel, over a decade; to examine trends regarding types of end-of-life-care provided (primary nonintervention, maximal intensive, and redirection of intensive care, including limitation of care and withdrawal of life-sustaining treatment); and to assess the parental role in the decision-making process given that the majority of the population is religious.

METHODS:
All neonates who died between 2000 and 2009 were identified. The causes and circumstances of death were abstracted from the medical records. Trends in end-of-life decisions were compared between 2 time periods: 2000–2004 versus 2005–2009.

RESULTS:
Overall, 239 neonates died. The leading cause of death in both study periods was prematurity and its complications (76%). Among term infants, the leading cause of death was congenital anomalies (48%). Fifty-six percent of the infants received maximal intensive care; 28% had redirection of intensive care, of whom 10% had withdrawal of life-sustaining treatment; and 16% had primary nonintervention care. Over the years, maximal intensive care decreased from 65% to 46% (P &lt; .02), whereas redirection of care increased from 19.2% to 37.5% (P &lt; .0005). An active parental role in the end-of-life decision process increased from 38% to 84%.

CONCLUSIONS:
Even among religious families of extremely sick neonates, redirection of care is a feasible treatment option, suggesting that apart from survival, quality-of-life considerations emerge as an important factor in the decision-making process for the infant, parents, and caregivers.
Internet-Based Therapy for Adolescents With Chronic Fatigue Syndrome: Long-term Follow-up
Authors: Nijhof Sanne L. , Priesterbach Loudy P. , Uiterwaal Cuno S. P. M. , Bleijenberg Gijs , Kimpen Jan L. L. , van de Putte Elise M. 
Published: May 2013

OBJECTIVE:Cognitive behavioral therapy (CBT) is known to be an effective treatment of adolescents with chronic fatigue syndrome (CFS), but its availability is limited. Fatigue in Teenagers on the Internet (FITNET), an Internet-based CBT program for adolescents with CFS, has been developed as an alternative to face-to-face CBT. Recently, its short-term effectiveness has been proven in a randomized clinical trial. Here we aimed to assess the long-term outcome of CFS in adolescents after FITNET treatment and after usual care. In addition, factors related to recovery at long-term follow-up (LTFU) for adolescents treated with the FITNET program were investigated.METHODS:The study was an LTFU of participants of the FITNET trial. Data were completed for 112 (88.2%) of 127 approached FITNET study participants. Primary outcomes were fatigue severity (Checklist Individual Strength–20), physical functioning (87-item Child Health Questionnaire), and school/work attendance.RESULTS:After a mean follow-up of 2.7 years, 66 (58.9%) adolescents had recovered from CFS. Most adolescents who recovered directly after treatment with FITNET were still recovered at LTFU. At LTFU there was no difference between the recovery rates for the different treatment strategies (original randomization: FITNET [64%] versus any form of usual care [52.8%]). Per additional month of “pretreatment disease duration,” the odds for recovery were 4% lower (odds ratio: 0.96; 95% confidence interval: 0.93–0.99; P = .016), and per added point on “focus on bodily symptoms” (Body Consciousness Scale) of the mother (0–20 points) the odds for recovery were 11% lower (odds ratio: 0.89; 95% confidence interval: 0.80–0.99; P = .029).CONCLUSIONS:The short-term effectiveness of Internet-based CBT on adolescent CFS is maintained at LTFU. At LTFU, usual care led to similar recovery rates, although these rates were achieved at a slower pace.
Bacteremia Risk and Outpatient Management of Febrile Patients With Sickle Cell Disease
Authors: Baskin Marc N. , Goh Xin Lyn , Heeney Matthew M. , Harper Marvin B. 
Published: May 2013

BACKGROUND AND OBJECTIVES:
Previous studies have indicated that febrile children with sickle cell disease (SCD) had a 3% to 5% risk of being bacteremic due to compromised immune function. The introduction of routine penicillin prophylaxis and conjugate vaccines may have lowered the risk of bacteremia. Our goals were to determine the rate of bacteremia among children with SCD per febrile episode and to estimate the safety of outpatient management among these febrile SCD patients.

METHODS:
This 18-year retrospective cohort study included febrile SCD patients who presented to Boston Children’s Hospital between 1993 and 2010.

RESULTS:
A total of 1118 febrile episodes were evaluated. Nine blood specimens had growth of a pathogen in culture (0.8%; 95% confidence interval: 0.3%–1.3%). Of the 466 febrile patients initially managed as outpatients, 3 were bacteremic (0.6%). All 3 received intravenous ceftriaxone at the initial outpatient visit and returned when contacted after growth of bacteria was detected in the blood culture. Upon return to the hospital, none were “ill appearing,” required supportive care, or were admitted to an ICU.

CONCLUSIONS:
Our rate of bacteremia among febrile children with SCD is much lower than previous estimates, and there was no associated morbidity or mortality among the patients managed as outpatients. A well-appearing febrile child with SCD may be managed as an outpatient after blood is obtained for bacterial culture and parenteral antibiotics are administered, provided there are no other reasons for admission and the patient is able to return promptly for worsening condition or for growth of a pathogen from their blood culture.
Elevated Blood Lead Levels and Reading Readiness at the Start of Kindergarten
Authors: McLaine Pat , Navas-Acien Ana , Lee Rebecca , Simon Peter , Diener-West Marie , Agnew Jacqueline 
Published: May 2013

OBJECTIVE:
To evaluate the relationship between blood lead levels (BLLs) and reading readiness at kindergarten entry, an early marker of school performance, in a diverse urban school population.

METHODS:
Kindergarten reading readiness test scores for children attending public kindergarten in Providence, Rhode Island, were linked to state health department records of blood lead testing by using individual identifiers. The study population (N = 3406) was 59% Hispanic. For each child, the geometric mean BLL was estimated by using all previously reported BLLs. Analyses were adjusted for gender, age, year enrolled, race, child language, and free/reduced lunch status as a measure of socioeconomic status.

RESULTS:
The median geometric mean BLL was 4.2 µg/dL; 20% of children had at least 1 venous BLL ≥10 µg/dL. Compared with children with BLLs &lt;5 µg/dL, the adjusted prevalence ratios (95% confidence interval [CI]) for failing to achieve the national benchmark for reading readiness were 1.21 (1.19 to 1.23) and 1.56 (1.51 to 1.60) for children with BLLs of 5 to 9 and ≥10 µg/dL, respectively. On average, reading readiness scores decreased by 4.5 (95% CI: −2.9 to −6.2) and 10.0 (95% CI: −7.0 to −13.3) points for children with BLLs of 5 to 9 and ≥10 µg/dL, respectively, compared with BLLs &lt;5 µg/dL.

CONCLUSIONS:
BLLs well below 10 µg/dL were associated with lower reading readiness at kindergarten entry. The high prevalence of elevated BLLs warrants additional investigation in other high-risk US populations. Results suggest benefits from additional collaboration between public health, public education, and community data providers.
Current Status of Transition Preparation Among Youth With Special Needs in the United States
Authors: McManus Margaret A. , Pollack Lauren R. , Cooley W. Carl , McAllister Jeanne W. , Lotstein Debra , Strickland Bonnie , Mann Marie Y. 
Published: May 2013

OBJECTIVE:
To examine current US performance on transition from pediatric to adult health care and discuss strategies for improvement.

METHODS:
The 2009–2010 National Survey of Children with Special Health Care Needs is a nationally representative sample with 17 114 parent respondents who have youth with special health care needs (YSHCN) ages 12 and 18. They are asked about transition to an adult provider, changing health care needs, increasing responsibility for health care needs, and maintaining insurance coverage. We analyzed the association of selected characteristics with successful transition preparation.

RESULTS:
Overall, 40% of YSHCN meet the national transition core outcome. Several factors are associated with transition preparation, including female gender; younger age; white race; non-Hispanic ethnicity; income ≥400% of poverty; little or no impact of condition on activities; having a condition other than an emotional, behavioral, or developmental condition; having a medical home; and being privately insured.

CONCLUSIONS:
Most YSHCN are not receiving needed transition preparation. Although most providers are encouraging YSHCN to assume responsibility for their own health, far fewer are discussing transfer to an adult provider and insurance continuity. Although changes in sample design limit trend analysis, there have been no discernible improvements since this transition outcome was measured in the 2005–2006 National Survey of Children with Special Health Care Needs. The 2011 release of the American Academy of Pediatrics/American Academy of Family Physicians/American College of Physicians clinical recommendations on transition, new transition tools, and the spread of medical home should stimulate future improvements in transition performance.
Dynamic Properties of Spectrally Selective Reactively Sputtered Metal Oxides
Authors: Adedeji A.V. , Worsley S.D. , Baker T.L. , Mundle R. , Pradhan A.K. , Ahyi A.C. , Isaacs-Smith T. 
Published: May 2013

ABSTRACTThin films of Transition Metal Oxides (TMOs) were deposited by reactive sputtering of pure transition metal targets in Argon-Oxygen gas mixture at elevated substrate temperature for efficient energy consumption. The atomic composition and thickness of the TMO films was determined by Rutherford Backscattering Spectroscopy (RBS). Optical transmittance and reflectance spectrum of the films on quartz substrate was measured with thin film measuring system at room temperature and slightly elevated temperature. The surface morphology and structure of the TMO films was determined with Atomic Force Microscope (AFM).
Defect Engineered Multi-Walled Carbon Nanotube arrays as Electrochemical Double Layer Capacitors
Authors: Narayanan Rajaram , Hoefer Mark , Bandaru Prabhakar R. 
Published: May 2013

ABSTRACTThe efficacy of vertically aligned defect engineered multi-walled carbon nanotube (MWCNT) arrays as electrochemical double layer capacitors (EDLCs) was investigated using standard electrochemical techniques such as cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). We report a ∼ 200% improvement in specific double layer capacitance of MWCNT arrays by extrinsically introducing defects using argon plasma irradiation. The capacitance-voltage characteristics of argon irradiated MWCNTs provide insights into the nature of the defects and their influence on the specific capacitance (capacitance/area).
Fabrication of 0.6(Bi0.85La0.15)FeO3-0.4PbTiO3 Multiferroic Ceramics by Tape Casting Method
Authors: Jin Guoxi , Chen Jianguo , Bu Shundong , Wang Dalei , Dai Rui , Cheng Jinrong 
Published: May 2013

ABSTRACTThe 0.6(Bi0.85La0.15)FeO3-0.4PbTiO3 (BLF-PT) ceramics were prepared by tape casting method. Effects of binder (polyvinylbutyl dibutyl PVB), plasticizer (phthalate-polyethylene glycol DBP-PEG) and dispersant (triethylolamine, TEA) concentration on the rheological properties of BLF-PT slurry were investigated. The optimized component ratio for ceramics powders, binder, plasticizer, dispersant and solvent (ethanol, EtOH) in the slurry was 50 wt.%, 4 wt.%, 6 wt.%, 1 wt.% and 39 wt.%. The dielectric constant εr, loss tanδ, and remnant polarization Pr of BLF-PT ceramics laminated from the tapes were 525 (1 kHz), 1.7% (1 kHz) and 30 μC/cm2 (45 kV/cm), respectively, which were comparable to those of BLF-PT ceramics prepared by traditional solid state reaction method.
Pathogenicity associated genes in Fusarium oxysporum f. sp. cubense race 4
Authors: Sutherland René , Viljoen Altus , Myburg Alexander A. , Van den Berg Noëlani 
Published: May 2013

Fusarium oxysporum f. sp. cubense (Foc) is a fungus that infects banana roots and causes a destructive plant disease called Fusarium wilt. Foc consists of three pathogenic races (Foc races 1, 2 and 4), classified according to their selective impairment of banana cultivars. Foc race 4 is economically important as it comprises strains that infect Cavendish bananas, which are the most widely planted variety of bananas in the world, in both the tropics (Foc TR4) and subtropics (Foc STR4). The aim of this study was to investigate which genes are potentially involved in fungal pathogenicity by comparing transcript-derived cDNA fragments (TDFs) from Foc STR4 and TR4 to those from non-pathogenic F. oxysporum using cDNA-AFLP analysis. This comparison resulted in the identification of 229 unique gene fragments which include the putative pathogenicity-related TDFs encoding chitinase class V (chsV), GTPase activating protein, Major Facilitator Superfamily (MFS) multidrug transporter and serine/threonine protein kinase (ste12) genes. Quantitative analysis of transcript abundance showed a significant increase in expression of chsV, MFS multidrug transporter and ste12 genes in Foc STR4 and TR4 compared with the non-pathogenic F. oxysporum. These genes play a role in escaping host defence responses and in cell wall degradation. In addition, pathogenicity-related genes from other formae speciales of F. oxysporum, such as the sucrose non-fermenting, cytochrome P450 and F-box protein required for pathogenicity genes, were significantly up-regulated in Foc STR4 and TR4 but not in F. oxysporum isolates non-pathogenic to banana. This study provides the first in vitro comparative analysis of TDFs expressed in pathogenic Foc race 4 isolates and non-pathogenic F. oxysporum isolates from banana.
Fractional-order TV-L2 model for image denoising
Authors: Chen Dali , Sun Shenshen , Zhang Congrong , Chen YangQuan , Xue Dingyu 
Published: May 2013

Abstract
This paper proposes a new fractional order total variation (TV) denoising method, which provides a much more elegant and effective way of treating problems of the algorithm implementation, ill-posed inverse, regularization parameter selection and blocky effect. Two fractional order TV-L2 models are constructed for image denoising. The majorization-minimization (MM) algorithm is used to decompose these two complex fractional TV optimization problems into a set of linear optimization problems which can be solved by the conjugate gradient algorithm. The final adaptive numerical procedure is given. Finally, we report experimental results which show that the proposed methodology avoids the blocky effect and achieves state-of-the-art performance. In addition, two medical image processing experiments are presented to demonstrate the validity of the proposed methodology.
Critical cardiac tamponade in newborn, life-saving emergency interventions and possibility of parvovirus B19 congenital infection
Authors: Jaworski Radoslaw , Haponiuk Ireneusz , Irga-Jaworska Ninela , Zablocka Jolanta , Chojnicki Maciej , Steffens Mariusz , Juscinski Jacek 
Published: May 2013

Abstract
The presence of pericardial effusion in neonates usually indicates a poor prognosis. Here, we report a case of isolation of cardiac tamponade in a newly born. This may be related to vertical human parvovirus B19, an infection with atypical clinical manifestation. Any neonate with unexplained fetal pericardial effusion should always be tested for parvovirus B19 infection, even in the absence of known and proved fetal exposure. Despite the etiology of a tamponade the only reasonable procedure is a surgical evacuation during diagnosis.