bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical study on the structure of the ground state and photo-induced metastable states of [M(CN)5NO]2− (M = Ru, Fe), and mechanism of the photo-rearrangement among them
Authors: Ishikawa Takeshi , Tanaka Kiyoshi 
Published: May 2008

Abstract
In this note, we reviewed theoretical investigations of the photo-induced metastable states and discussed possible photo-rearrangement paths in [M(CN)5NO]2− (M = Fe and Ru). Using calculated results of ab initio multi-reference single and double excitation configuration interaction calculations with Davidson type quadruple correction (MRSDCI + Q) and those of density fuctional theory (DFT), we showed that the two metastable states (MS1 and MS2) were local minima of the electronic ground state potential surface. The theoretical calculations supported the experimental observation of the structure of the three isomers (GS, MS1 and MS2), relative stability of MS1 and MS2. We discussed the character of the lower electronic excited states and excitation energies of the three isomers of both compounds. Based on these results and excited state adiabatic potential energy surfaces, possible mechanism of photo-rearrangement among GS, MS1, and MS2 were discussed with the aid of our results on [Mn(CN)5NO]3− of which no photo-rearrangement has been reported.
Recurrent Deletion and Gene Presence/Absence Polymorphism: Telomere Dynamics Dominate Evolution at the Tip of 3L inDrosophila melanogasterandD. simulans
Authors: Kern Andrew D , Begun David J 
Published: May 2008

AbstractAlthough Drosophila melanogaster has been the subject of intensive analysis of polymorphism and divergence, little is known about the distribution of variation at the most distal regions of chromosomes arms. Here we report a survey of genetic variation on the tip of 3L in D. melanogaster and D. simulans. Levels of single nucleotide polymorphism in the most distal euchromatic sequence are approximately one order of magnitude less than that typically observed in genomic regions of normal crossing over, consistent with what might be expected under models of linked selection in regions of low crossing over. However, despite this reduced level of nucleotide variation, we found abundant deletion polymorphism. These deletions create at least three gene presence/absence polymorphisms within D. melanogaster: the putative G-protein coupled receptor mthl-8 (which is the most distal known or predicted gene on 3L) and the unannotated mRNAs AY060886 and BT006009. Strikingly, D. simulans is also segregating deletions that cause mthl8 presence/absence polymorphism. Breakpoint sequencing and tests of correlations with segregating SNPs in D. melanogaster suggest that each deletion is unique. Cloned breakpoint sequences revealed the presence of Het-A elements just distal to unique, canonical euchromatic sequences. This pattern suggests a model in which repeated telomeric deficiencies cause deletions of euchromatic sequence followed by subsequent “healing” by retrotranposition of Het-A elements. These data reveal the dominance of telomeric dynamics on the evolution of closely linked sequences in Drosophila.
Breeding Designs for Recombinant Inbred Advanced Intercross Lines
Authors: Rockman Matthew V , Kruglyak Leonid 
Published: May 2008

Abstract
Recombinant inbred lines derived from an advanced intercross, in which multiple generations of mating have increased the density of recombination breakpoints, are powerful tools for mapping the loci underlying complex traits. We investigated the effects of intercross breeding designs on the utility of such lines for mapping. The simplest design, random pair mating with each pair contributing exactly two offspring to the next generation, performed as well as the most extreme inbreeding avoidance scheme at expanding the genetic map, increasing fine-mapping resolution, and controlling genetic drift. Circular mating designs offer negligible advantages for controlling drift and exhibit greatly reduced map expansion. Random-mating designs with variance in offspring number are also poor at increasing mapping resolution. Given equal contributions of each parent to the next generation, the constraint of monogamy has no impact on the qualities of the final population of inbred lines. We find that the easiest crosses to perform are well suited to the task of generating populations of highly recombinant inbred lines.
Inferring Causal Phenotype Networks From Segregating Populations
Authors: Chaibub Neto Elias , Ferrara Christine T , Attie Alan D , Yandell Brian S 
Published: May 2008

AbstractA major goal in the study of complex traits is to decipher the causal interrelationships among correlated phenotypes. Current methods mostly yield undirected networks that connect phenotypes without causal orientation. Some of these connections may be spurious due to partial correlation that is not causal. We show how to build causal direction into an undirected network of phenotypes by including causal QTL for each phenotype. We evaluate causal direction for each edge connecting two phenotypes, using a LOD score. This new approach can be applied to many different population structures, including inbred and outbred crosses as well as natural populations, and can accommodate feedback loops. We assess its performance in simulation studies and show that our method recovers network edges and infers causal direction correctly at a high rate. Finally, we illustrate our method with an example involving gene expression and metabolite traits from experimental crosses.
A Mutation in the Putative MLH3 Endonuclease Domain Confers a Defect in Both Mismatch Repair and Meiosis inSaccharomyces cerevisiae
Authors: Nishant K T , Plys Aaron J , Alani Eric 
Published: May 2008

AbstractInterference-dependent crossing over in yeast and mammalian meioses involves the mismatch repair protein homologs MSH4-MSH5 and MLH1-MLH3. The MLH3 protein contains a highly conserved metal-binding motif DQHA(X)2E(X)4E that is found in a subset of MLH proteins predicted to have endonuclease activities (Kadyrov et al. 2006). Mutations within this motif in human PMS2 and Saccharomyces cerevisiae PMS1 disrupted the endonuclease and mismatch repair activities of MLH1-PMS2 and MLH1-PMS1, respectively (Kadyrov et al. 2006, 2007; Erdeniz et al. 2007). As a first step in determining whether such an activity is required during meiosis, we made mutations in the MLH3 putative endonuclease domain motif (-D523N, -E529K) and found that single and double mutations conferred mlh3-null-like defects with respect to meiotic spore viability and crossing over. Yeast two-hybrid and chromatography analyses showed that the interaction between MLH1 and mlh3-D523N was maintained, suggesting that the mlh3-D523N mutation did not disrupt the stability of MLH3. The mlh3-D523N mutant also displayed a mutator phenotype in vegetative growth that was similar to mlh3Δ. Overexpression of this allele conferred a dominant-negative phenotype with respect to mismatch repair. These studies suggest that the putative endonuclease domain of MLH3 plays an important role in facilitating mismatch repair and meiotic crossing over.
Levels of Selection on Threshold Characters
Authors: Moorad Jacob A , Linksvayer Timothy A 
Published: May 2008

AbstractThreshold models are useful for understanding the evolution of dimorphic traits with polygenic bases. Selection for threshold characters on individuals is expected to be frequency dependent because of the peculiar way that selection views underlying genetic and environmental factors. Selection among individuals is inefficient because individual phenotypes fall into only two discrete categories that map imperfectly to the underlying genes. Incidence, however, can be continuously distributed among groups, making among-group selection relatively more efficient. Differently put, the group-mean phenotype can be a better predictor of an individual's genotype than that individual's own phenotype. Because evolution in group-structured populations is governed by the balance of selection within and between groups, we can expect threshold traits to evolve in fundamentally different ways when group mean fitness is a function of morph frequency. We extend the theory of selection on threshold traits to include group selection using contextual analysis. For the simple case of linear group-fitness functions, we show that the group-level component of selection, like the individual-level component, is frequency dependent. However, the conditions that determine which component dominates when levels of selection are in conflict (as described by Hamilton's rule) are not frequency dependent. Thus, enhanced group selection is not an inherent property of threshold characters. Nevertheless, we show that predicting the effects of multiple levels of selection on dimorphic traits requires special considerations of the threshold model.
Single-Nucleotide-Polymorphism-Based Association Mapping of Dog Stereotypes
Authors: Jones Paul , Chase Kevin , Martin Alan , Davern Pluis , Ostrander Elaine A , Lark Karl G 
Published: May 2008

Abstract
Phenotypic stereotypes are traits, often polygenic, that have been stringently selected to conform to specific criteria. In dogs, Canis familiaris, stereotypes result from breed standards set for conformation, performance (behaviors), etc. As a consequence, phenotypic values measured on a few individuals are representative of the breed stereotype. We used DNA samples isolated from 148 dog breeds to associate SNP markers with breed stereotypes. Using size as a trait to test the method, we identified six significant quantitative trait loci (QTL) on five chromosomes that include candidate genes appropriate to regulation of size (e.g., IGF1, IGF2BP2 SMAD2, etc.). Analysis of other morphological stereotypes, also under extreme selection, identified many additional significant loci. Less well-documented data for behavioral stereotypes tentatively identified loci for herding, pointing, boldness, and trainability. Four significant loci were identified for longevity, a breed characteristic not under direct selection, but inversely correlated with breed size. The strengths and limitations of the approach are discussed as well as its potential to identify loci regulating the within-breed incidence of specific polygenic diseases.
The Frequency of Fitness Peak Shifts Is Increased at Expanding Range Margins Due to Mutation Surfing
Authors: Burton Olivia J , Travis Justin M J 
Published: May 2008

Abstract
Dynamic species' ranges, those that are either invasive or shifting in response to environmental change, are the focus of much recent interest in ecology, evolution, and genetics. Understanding how range expansions can shape evolutionary trajectories requires the consideration of nonneutral variability and genetic architecture, yet the majority of empirical and theoretical work to date has explored patterns of neutral variability. Here we use forward computer simulations of population growth, dispersal, and mutation to explore how range-shifting dynamics can influence evolution on rugged fitness landscapes. We employ a two-locus model, incorporating sign epistasis, and find that there is an increased likelihood of fitness peak shifts during a period of range expansion. Maladapted valley genotypes can accumulate at an expanding range front through a phenomenon called mutation surfing, which increases the likelihood that a mutation leading to a higher peak will occur. Our results indicate that most peak shifts occur close to the expanding front. We also demonstrate that periods of range shifting are especially important for peak shifting in species with narrow geographic distributions. Our results imply that trajectories on rugged fitness landscapes can be modified substantially when ranges are dynamic.
Trial of Computerized Screening for Adolescent Behavioral Concerns
Authors: Stevens Jack , Kelleher Kelly J. , Gardner William , Chisolm Deena , McGeehan Jennifer , Pajer Kathleen , Buchanan Lindsay 
Published: June 2008

OBJECTIVE. Injury risk, depressive symptoms, and substance use are the leading causes of adolescent morbidity and death. The goal of this randomized, controlled trial was to determine whether computerized screening with real-time printing of results for pediatricians increased the identification of these adolescent behavioral concerns.METHODS. A total of 878 primary care patients 11 to 20 years of age participated in computerized behavioral screening (the Health eTouch system) in waiting rooms of 9 urban clinics. These clinics all served predominantly low-income patients. The clinics were randomly assigned to have pediatricians receive screening results either just before face-to-face encounters with patients (immediate-results condition) or 2 to 3 business days later (delayed-results condition).RESULTS. Fifty-nine percent of Health eTouch respondents had positive results for ≥1 of the following behavioral concerns: injury risk behaviors, significant depressive symptoms, or substance use. Sixty-eight percent of youths in the immediate-results condition who screened positive were identified as having a problem by their pediatrician. This was significantly higher than the recognition rate of 52% for youths in the delayed-results condition.CONCLUSION. Immediate provision of an adolescent's self-report of behavioral concerns to a pediatrician increased recognition of those problems, compared with the delayed provision of results.
Vaccine-Era Varicella Epidemiology and Vaccine Effectiveness in a Public Elementary School Population, 2002–2007
Authors: Lee Lore E. , Ho Hon , Lorber Eileen , Fratto Jeanne , Perkins Sara , Cieslak Paul R. 
Published: June 2008

OBJECTIVE. We conducted ongoing varicella surveillance of public elementary school students to track changes in incidence from 2002 to 2007. In school year 2002–2003, we also conducted a retrospective cohort study to measure varicella vaccine effectiveness, assess relationships between risk factors for varicella in vaccine recipients (breakthrough varicella) identified in earlier studies, and assess the ability of school nurse surveillance to detect varicella cases.
PATIENTS AND METHODS. Varicella was defined as acute illness with maculo-papulo-vesicular rash without another apparent cause persisting &gt;24 hours, regardless of previous episodes of the same or a similar illness. Using case data reported by school nurses, we described breakthrough varicella rates (percentage of vaccinated students with varicella), annual varicella-incidence rates (varicella cases per 100 public elementary school students), vaccine effectiveness, risk factors for breakthrough varicella, clinical characteristics of vaccinated and susceptible varicella patients, and sensitivity and positive predictive value of school nurse surveillance.
RESULTS. During school years 2002–2007, 502 elementary school students met the varicella case definition. Breakthrough varicella rates among exposed students ranged from 6% to 8% per school year; annual incidence rates ranged from 0.2% to 0.3% of public elementary school students; and varicella was more severe and lasted longer in susceptible than in vaccinated students. The positive predictive value of school nurse surveillance was 94%, and sensitivity was 90%. Vaccine effectiveness was 81%.
CONCLUSIONS. School nurse surveillance has both high positive predictive value and sensitivity and is a useful means of tracking varicella occurrence. Annual incidence rates of varicella are low. Vaccine effectiveness and breakthrough varicella rates are comparable to findings of other studies.
Prevalence of Vitamin D Deficiency and Insufficiency in Children With Osteopenia or Osteoporosis Referred to a Pediatric Metabolic Bone Clinic
Authors: Bowden Sasigarn A. , Robinson Renee F. , Carr Roxane , Mahan John D. 
Published: June 2008

OBJECTIVES. The purpose of this work was to determine the prevalence of vitamin D deficiency and insufficiency in children with osteopenia or osteoporosis and to evaluate the relationship between serum 25-hydroxyvitamin D levels and bone parameters, including bone mineral density.
MATERIALS AND METHODS. Serum 25-hydroxyvitamin D, 1,25 dihydroxyvitamin D, parathyroid hormone, and other bone markers, as well as bone mineral density, were obtained for 85 pediatric patients with primary osteoporosis (caused by osteogenesis imperfecta or juvenile idiopathic osteoporosis) and secondary osteopenia or osteoporosis caused by various underlying chronic illnesses. Pearson's correlation was used to assess the relationship between vitamin D levels and different bone parameters.
RESULTS. Vitamin D insufficiency (defined as serum 25-hydroxyvitamin D &lt;30 ng/mL) was observed in 80.0% of patients. Overt vitamin D deficiency (defined as serum 25-hydroxyvitamin D &lt;10 ng/mL) was present in 3.5% of patients. Using a more recent definition for vitamin D deficiency in adults (defined as serum 25-hydroxyvitamin D &lt;20 ng/mL), 21.1% of the patients had vitamin D deficiency. There was a significant inverse correlation between 25-hydroxyvitamin D and parathyroid hormone levels. There was a positive correlation between 1,25 dihydroxyvitamin D and parathyroid hormone, alkaline phosphatase, and urine markers for bone turnover.
CONCLUSIONS. Vitamin D insufficiency was remarkably common in pediatric patients with primary and secondary osteopenia or osteoporosis. The inverse relationship between 25-hydroxyvitamin D and parathyroid hormone levels suggests a physiologic impact of insufficient vitamin D levels that may contribute to low bone mass or worsen the primary bone disease. We suggest that monitoring and supplementation of vitamin D should be a priority in the management of pediatric patients with osteopenia or osteoporosis.
Serial Immune Markers Do Not Correlate With Clinical Exacerbations in Pediatric Autoimmune Neuropsychiatric Disorders Associated With Streptococcal Infections
Authors: Singer Harvey S. , Gause Colin , Morris Christina , Lopez Pablo ,   and the Tourette Syndrome Study Group
Published: June 2008

OBJECTIVE. Pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections is hypothesized to be a poststreptococcal autoimmune disorder. If clinical exacerbations are triggered by a streptococcal infection that activates cross-reacting antibodies against neuronal tissue or alters the production of cytokines, then a longitudinal analysis would be expected to identify a correlation between clinical symptoms and a change in autoimmune markers.PATIENTS AND METHODS. Serial serum samples were available on 12 children with pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections participating in a prospective blinded study: 2 samples before an exacerbation point, 1 during the clinical exacerbation, and 2 after the exacerbation. Six subjects had a well-defined clinical exacerbation in association with a documented streptococcal infection, and 6 had a clinical exacerbation without an associated streptococcal infection. All of the serum samples were assayed for antibodies against human postmortem caudate, putamen, and prefrontal cortex; commercially prepared antigens; and complex sugars. Cytokines were measured by 2 different methodologies.RESULTS. No correlation was identified between clinical exacerbations and autoimmune markers, including: enzyme-linked immunosorbent assay measures of antineuronal antibodies; Western immunoblotting with emphasis on brain region proteins located at 40, 45, and 60 kDa or their corresponding identified antigens; competitive inhibition enzyme-linked immunosorbent assay to evaluate lysoganglioside GM1 antibodies; and measures of inflammatory cytokines. No differences were identified between individuals with pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections with or without exacerbations triggered by streptococcal infections.CONCLUSIONS. The failure of immune markers to correlate with clinical exacerbations in children with pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections raises serious concerns about the viability of autoimmunity as a pathophysiological mechanism in this disorder.
Effects of functionalized and nonfunctionalized single-walled carbon nanotubes on root elongation of select crop species
Authors: Cañas Jaclyn E , Long Monique , Nations Shawna , Vadan Rodica , Dai Lenore , Luo Mingxiang , Ambikapathi Ramya , Lee E. Henry , Olszyk David 
Published: May 2008

Abstract
Single-walled carbon nanotubes have many potential beneficial uses, with additional applications constantly being investigated. Their unique properties, however, create a potential concern regarding toxicity, not only in humans and animals but also in plants. To help develop protocols to determine the effects of nanotubes on plants, we conducted a pilot study on the effects of functionalized and nonfunctionalized single-walled carbon nanotubes on root elongation of six crop species (cabbage, carrot, cucumber, lettuce, onion, and tomato) routinely used in phytotoxicity testing. Nanotubes were functionalized with poly-3-aminoben-zenesulfonic acid. Root growth was measured at 0, 24, and 48 h following exposure. Scanning-electron microscopy was used to evaluate potential uptake of carbon nanotubes and to observe the interaction of nanotubes with the root surface. In general, nonfunctionalized carbon nanotubes affected root length more than functionalized nanotubes. Nonfunctionalized nanotubes inhibited root elongation in tomato and enhanced root elongation in onion and cucumber. Functionalized nanotubes inhibited root elongation in lettuce. Cabbage and carrots were not affected by either form of nanotubes. Effects observed following exposure to carbon nanotubes tended to be more pronounced at 24 h than at 48 h. Microscopy images showed the presence of nanotube sheets on the root surfaces, but no visible uptake of nanotubes was observed.
Scale Inhibitor Solutions for High Temperature ESP Lifted Wells in California: A Case History Of Failure Followed By Success
Authors: Wylde J. J. , Fell D. A. 
Published: May 2008

Abstract
Calcium carbonate had been reported in many wells at this Californian asset. All these wells used electronic submersible pumps (ESP) to assist the lift of produced fluids from the reservoir. Scale deposition was causing malfunction of the ESP pumps due to deposition on the pump internals, especially the rotor tips, causing excessive friction and ultimate failure. The temperature around the motor has been measured as 10 – 24°C higher than the bulk produced water temperature of 107 – 121°C. Previously this has not been considered during the selection of scale inhibitors. The cause of scale failures on the ESP wells has been instead attributed to the adsorption of scale inhibitor onto the sometimes significant formation fines produced from the wells.
Several scale inhibitor chemicals had been used in an attempt to inhibit deposition. Whilst general scaling in the bulk fluids seems to be under control, as indicated by the lack of scale deposits elsewhere in the well, deposition still occurred on the ESP pumps themselves. This was likely to be due to a combination of a large pressure drop in the fluids resulting in localized degassing of the produced water (below the bubble point of CO2) and also localized high temperatures on the tips of the pump rotors. Incumbent chemistries used included several different type of phosphonate chemistry.
This paper details the best-in-class chemical reselection process study to determine that the root cause failure hypothesis was correct. This included compatibility testing and scale loop testing using real produced water. The paper then goes onto detail some of the incumbent chemical treatments as well as the step change in performance realized when deployment of a newly evaluated polymeric scale inhibitor.