bluuebunny/crossref_metadata_2025_split huggingface dataset:
Consistent Patterns of Rate Asymmetry and Gene Loss Indicate Widespread Neofunctionalization of Yeast Genes After Whole-Genome Duplication
Authors: Byrne Kevin P , Wolfe Kenneth H 
Published: December 2006

AbstractWe investigated patterns of rate asymmetry in sequence evolution among the gene pairs (ohnologs) formed by whole-genome duplication (WGD) in yeast species. By comparing three species (Saccharomyces cerevisiae, Candida glabrata, and S. castellii) that underwent WGD to a nonduplicated outgroup (Kluyveromyces lactis), and by using a synteny framework to establish orthology and paralogy relationships at each duplicated locus, we show that 56% of ohnolog pairs show significantly asymmetric protein sequence evolution. For ohnolog pairs that remain duplicated in two species there is a strong tendency for the faster-evolving copy in one species to be orthologous to the faster copy in the other species, which indicates that the evolutionary rate differences were established before speciation and hence soon after the WGD. We also present evidence that in cases where one ohnolog has been lost from the genome of a post-WGD species, the lost copy was likely to have been the faster-evolving member of the pair prior to its loss. These results suggest that a significant fraction of the retained ohnologs in yeast species underwent neofunctionalization soon after duplication.
Power to Detect Higher-Order Epistatic Interactions in a Metabolic Pathway Using a New Mapping Strategy
Authors: Stich Benjamin , Yu Jianming , Melchinger Albrecht E , Piepho Hans-Peter , Utz H Friedrich , Maurer Hans P , Buckler Edward S 
Published: December 2006

Abstract
Epistatic interactions among quantitative trait loci (QTL) contribute substantially to the variation in complex traits. The main objectives of this study were to (i) compare three- vs. four-step genome scans to identify three-way epistatic interactions among QTL belonging to a metabolic pathway, (ii) investigate by computer simulations the power and proportion of false positives (PFP) for detecting three-way interactions among QTL in recombinant inbred line (RIL) populations derived from a nested mating design, and (iii) compare these estimates to those obtained for detecting three-way interactions among QTL in RIL populations derived from diallel and different partial diallel mating designs. The single-nucleotide polymorphism haplotype data of B73 and 25 diverse maize inbreds were used to simulate the production of various RIL populations. Compared to the three-step genome scan, the power to detect three-way interactions was higher with the four-step genome scan. Higher power to detect three-way interactions was observed for RILs derived from optimally allocated distance-based designs than from nested designs or diallel designs. The power and PFP to detect three-way interactions using a nested design with 5000 RILs were for both the 4-QTL and the 12-QTL scenario of a magnitude that seems promising for their identification.
Drosophila ATR in Double-Strand Break Repair
Authors: LaRocque Jeannine R , Jaklevic Burnley , Su Tin Tin , Sekelsky Jeff 
Published: December 2006

Abstract
The ability of a cell to sense and respond to DNA damage is essential for genome stability. An important aspect of the response is arrest of the cell cycle, presumably to allow time for repair. Ataxia telangiectasia mutated (ATM) and ATR are essential for such cell-cycle control, but some observations suggest that they also play a direct role in DNA repair. The Drosophila ortholog of ATR, MEI-41, mediates the DNA damage-dependent G2-M checkpoint. We examined the role of MEI-41 in repair of double-strand breaks (DSBs) induced by P-element excision. We found that mei-41 mutants are defective in completing the later steps of homologous recombination repair, but have no defects in end-joining repair. We hypothesized that these repair defects are the result of loss of checkpoint control. To test this, we genetically reduced mitotic cyclin levels and also examined repair in grp (DmChk1) and lok (DmChk2) mutants. Our results suggest that a significant component of the repair defects is due to loss of MEI-41-dependent cell cycle regulation. However, this does not account for all of the defects we observed. We propose a novel role for MEI-41 in DSB repair, independent of the Chk1/Chk2-mediated checkpoint response.
Cyclin and Cyclin-Dependent Kinase Substrate Requirements for Preventing Rereplication Reveal the Need for Concomitant Activation and Inhibition
Authors: Ikui Amy E , Archambault Vincent , Drapkin Benjamin J , Campbell Veronica , Cross Frederick R 
Published: December 2006

Abstract
DNA replication initiation in S. cerevisiae is promoted by B-type cyclin-dependent kinase (Cdk) activity. In addition, once-per-cell-cycle replication is enforced by cyclin-Cdk-dependent phosphorylation of the prereplicative complex (pre-RC) components Mcm2-7, Cdc6, and Orc1-6. Several of these controls must be simultaneously blocked by mutation to obtain rereplication. We looked for but did not obtain strong evidence for cyclin specificity in the use of different mechanisms to control rereplication: both the S-phase cyclin Clb5 and the mitotic cyclins Clb1–4 were inferred to be capable of imposing ORC-based and MCM-based controls. We found evidence that the S-phase cyclin Clb6 could promote initiation of replication without blocking reinitiation, and this activity was highly toxic when the ability of other cyclins to block reinitiation was prevented by mutation. The failure of Clb6 to regulate reinitiation was due to rapid Clb6 proteolysis, since this toxic activity of Clb6 was lost when Clb6 was stabilized by mutation. Clb6-dependent toxicity is also relieved when early accumulation of mitotic cyclins is allowed to impose rereplication controls. Cell-cycle timing of rereplication control is crucial: sufficient rereplication block activity must be available as soon as firing begins. DNA rereplication induces DNA damage, and when rereplication controls are compromised, the DNA damage checkpoint factors Mre11 and Rad17 provide additional mechanisms that maintain viability and also prevent further rereplication, and this probably contributes to genome stability.
Evolution of Different Y Chromosomes in Two Medaka Species,Oryzias dancenaandO. latipes
Authors: Takehana Yusuke , Demiyah Diana , Naruse Kiyoshi , Hamaguchi Satoshi , Sakaizumi Mitsuru 
Published: December 2006

AbstractAlthough the sex-determining gene DMY has been identified on the Y chromosome in the medaka (Oryzias latipes), this gene is absent in most Oryzias species, suggesting that closely related species have different sex-determining genes. Here, we investigated the sex-determination mechanism in O. dancena, which does not possess the DMY gene. Since heteromorphic sex chromosomes have not been reported in this species, a progeny test of sex-reversed individuals produced by hormone treatment was performed. Sex-reversed males yielded all-female progeny, indicating that O. dancena has an XX/XY sex-determination system. To uncover the cryptic sex chromosomes, sex-linked DNA markers were screened using expressed sequence tags (ESTs) established in O. latipes. Linkage analysis of isolated sex-linked ESTs showed a conserved synteny between the sex chromosomes in O. dancena and an autosome in O. latipes. Fluorescence in situ hybridization (FISH) analysis of these markers confirmed that sex chromosomes of these species are not homologous. These findings strongly suggest an independent origin of sex chromosomes in O. dancena and O. latipes. Further analysis of the sex-determining region in O. dancena should provide crucial insights into the evolution of sex-determination mechanisms in vertebrates.
Five Ovine Mitochondrial Lineages Identified From Sheep Breeds of the Near East
Authors: Meadows Jennifer R S , Cemal Ibrahim , Karaca Orhan , Gootwine Elisha , Kijas James W 
Published: December 2006

AbstractArchaeozoological evidence indicates that sheep were first domesticated in the Fertile Crescent. To search for DNA sequence diversity arising from previously undetected domestication events, this survey examined nine breeds of sheep from modern-day Turkey and Israel. A total of 2027 bp of mitochondrial DNA (mtDNA) sequence from 197 sheep revealed a total of 85 haplotypes and a high level of genetic diversity. Six individuals carried three haplotypes, which clustered separately from the known ovine mtDNA lineages A, B, and C. Analysis of genetic distance, mismatch distribution, and comparisons with wild sheep confirmed that these represent two additional mtDNA lineages denoted D and E. The two haplogroup E sequences were found to link the previously identified groups A and C. The single haplogroup D sequence branched with the eastern mouflon (Ovis orientalis), urial (O. vignei), and argali (O. ammon) sheep. High sequence diversity (K = 1.86%, haplogroup D and O. orientalis) indicates that the wild progenitor of this domestic lineage remains unresolved. The identification in this study of evidence for additional domestication events adds to the emerging view that sheep were recruited from wild populations multiple times in the same way as for other livestock species such as goat, cattle, and pig.
Substitution of Critical Isoleucines in the KH Domains of Drosophila Fragile X Protein Results in Partial Loss-of-Function Phenotypes
Authors: Banerjee Paromita , Nayar Shweta , Hebbar Sarita , Fox Catherine F , Jacobs Michele C , Park Jae H , Fernandes Joyce J , Dockendorff Thomas C 
Published: December 2006

Abstract
Fragile X mental retardation proteins (FMRP) are RNA-binding proteins that interact with a subset of cellular RNAs. Several RNA-binding domains have been identified in FMRP, but the contribution of these individual domains to FMRP function in an animal model is not well understood. In this study, we have generated flies with point mutations in the KH domains of the Drosophila melanogaster fragile X gene (dfmr1) in the context of a genomic rescue fragment. The substitutions of conserved isoleucine residues within the KH domains with asparagine are thought to impair binding of RNA substrates and perhaps the ability of FMRP to assemble into mRNP complexes. The mutants were analyzed for defects in development and behavior that are associated with deletion null alleles of dfmr1. We find that these KH domain mutations result in partial loss of function or no significant loss of function for the phenotypes assayed. The phenotypes resulting from these KH domain mutants imply that the capacities of the mutant proteins to bind RNA and form functional mRNP complexes are not wholly disrupted and are consistent with biochemical models suggesting that RNA-binding domains of FMRP can function independently.
An Unusual Pattern of Spontaneous Mutations Recovered in the Halophilic Archaeon Haloferax volcanii
Authors: Mackwan Reena R , Carver Geraldine T , Drake John W , Grogan Dennis W 
Published: December 2006

Abstract
Spontaneous mutations in the orotate:phosphoribosyl transferase (pyrE2) gene of the halophilic archaeon Haloferax volcanii were selected by 5-fluoroorotic acid plus uracil at a rate of ∼2 × 10−8/cell division in fluctuation and null-fraction tests but ∼6 × 10−8/cell division in mutation-accumulation tests. The corresponding genomic mutation rates were substantially lower than those observed for other mesophilic microbial DNA genomes on the basis of similar target genes. The mutational spectrum was dominated by indels adding or deleting multiples of 3 bp. Properties of the organism contributing to this unusual mutational pattern may include phenotypic lag caused by a high chromosomal copy number and efficient promotion of strand misalignments by short direct repeats.
Assistive Technology Use Among Adolescents and Young Adults With Spina Bifida
Authors: Johnson Kurt L. , Dudgeon Brian , Kuehn Carrie , Walker William 
Published: December 2006

Objectives. We sought to determine the use of assistive technology among a population of individuals with spina bifida. Methods. We performed a descriptive analysis of individuals aged 13 to 27 years diagnosed with myelomeningocele (n=348) using data obtained from an existing database at Children’s Hospital and Regional Medical Center, Seattle, Washington. We summarized disease characteristics, utilization of assistive technology, community and self-care independence, and other variables. Results. Eighty-four percent of the respondents lived with at least 1 of their natural parents. Fifty-seven percent used wheelchairs, 35% used braces, and 23% used walking aids. Independent self-care was a common skill, but 72% reported limited participation in structured activities. Half were aged 18 years or older; of those, only 50% had completed high school and 71% were unemployed. Those aged younger than 18 years were all still in school (100%). Conclusions. Adolescents and young adults with spina bifida rely on assistive technology and specialized care routines to maintain their health. Assistive technology use for mobility is common; little is known about secondary complications associated with use of these technologies or the use of assistive technology to address learning disabilities and other societal barriers. Underutilization of assistive technology could delay successful transitions to independent living and community participation.
Early Otitis Media Among Minnesota American Indians: The Little Ears Study
Authors: Daly Kathleen A. , Pirie Phyllis L. , Rhodes Kristine L. , Hunter Lisa L. , Davey Cynthia S. 
Published: December 2006

Objectives. We examined relationships between otitis media risk factors, sociodemographic characteristics, and maternal knowledge and attitudes and early onset of otitis media. Methods. Pregnant women from Minnesota American Indian reservations and an urban clinic were enrolled in our study between 1998 and 2001. Follow-up was performed on enrollees’ infants until the children were 2 years old. Research nurses collected data by ear examination, from interviews and questionnaires given to enrolled mothers, and otitis media episodes that were abstracted from medical records. Results. Sixty-three percent of infants had experienced an otitis media episode by 6 months of age. Logistic regression analyses showed that maternal otitis media history, infant history of upper respiratory infection, and compliance with study visits were significantly related to early otitis media onset. Although high percentages of infants were exposed to cigarette smoke and other children and were formula fed, these factors were not related to otitis media. Mothers’ prenatal awareness of otitis media risks associated with environmental tobacco smoke exposure and formula feeding did not predict their postpartum behaviors. Conclusions. We found that infant history of upper respiratory infection and maternal otitis media history are risk factors for early otitis media in American Indian infants. Mothers’ prepartum knowledge and attitudes regarding otitis media did not predict their postpartum avoidance of risk behaviors.
The Effect of Poverty and Caregiver Education on Perceived Need and Access to Health Services Among Children With Special Health Care Needs
Authors: Porterfield Shirley L. , McBride Timothy D. 
Published: December 2006

Objectives. We examined the association between several variables and the use of specialist physician services, developmental therapies, and prescription medications among children with special health care needs (N=38866). Methods. We used a bivariate probit model to estimate whether a given child needed specialized services and whether that child accessed those services; we controlled for activity limitations and severity of special needs. Variables included family income, mother’s (or other caregiver’s) educational level, health insurance coverage, and perceived need for specialized services. We used data from the 2001 National Survey of Children with Special Health Care Needs. Results. Lower-income and less-educated parents were less likely than higher-income and more-educated parents to say their special needs children needed specialized health services. The probability of accessing specialized health services—when needed—increased with both higher family income and insurance coverage. Conclusions. Children with special health care needs have less access to health services because their parents do not recognize the need for those services. An intervention in the form of information at the family level may be an appropriate policy response.
Framing the Public Health of Caregiving
Authors: Talley Ronda C. , Crews John E. 
Published: December 2006

Caregiving has only recently been acknowledged by the nation as an important topic for millions of Americans. A psychological or sociological approach to care-giving services has been most often applied, with little attention to the population-based public health outcomes of caregivers. We conceptualize caregiving as an emerging public health issue involving complex and fluctuating roles. We contend that caregiving must be considered in the context of life span needs that vary according to the ages, developmental levels, mental health needs, and physical health demands of both caregivers and care recipients.
Exposure to Lead and Length of Time Needed to Make Homes Lead-Safe for Young Children
Authors: Zierold Kristina M. , Havlena Jeff , Anderson Henry 
Published: December 2006

Objectives. We determined the length of time needed to make homes lead-safe in a population of children aged 0 to 6 years with blood lead levels (BLLs) of 20 micrograms per deciliter (μg/dL) or greater. Reducing this time would reduce children’s exposure to lead. Methods. Data came from the Wisconsin Childhood Lead Poisoning Prevention Program’s comprehensive blood lead surveillance system. Analysis was restricted to children whose first BLL test value during 1996–1999 was between 20 and 40 μg/dL and for whom housing intervention data were available (n=382). Results. The median length of time required to make a home lead-safe was 465 days. Only 18% of children lived in homes that were made lead-safe within 6 months; 45% lived in homes requiring more than 18 months to be lead-safe. Conclusions. Efforts are needed to reduce the time it takes to make a home lead-safe. Although abatement orders always include time limits, improved compliance with the orders must be enforced. Greater emphasis should be placed on securing lead-safe or lead-free housing for families, thus reducing lead exposure.
Malnutrition Among Children Younger Than 5 Years-Old in Conflict Zones of Chiapas, Mexico
Authors: Sánchez-Pérez Héctor Javier , Hernán Miguel A. , Ríos-González Adriana , Arana-Cedeño Marcos , Navarro Albert , Ford Douglas , Micek Mark A. , Brentlinger Paula 
Published: December 2006

We performed a cross-sectional, community-based survey, supplemented by interviews with community leaders in Chiapas, Mexico, to examine the prevalence and predictors of child malnutrition in regions affected by the Zapatista conflict. The prevalence rates of stunting, wasting, and underweight were 54.1%, 2.9%, and 20.3%, respectively, in 2666 children aged younger than 5 years. Stunting was associated with indigenous ethnicity, poverty, region of residence, and intracommunity division. The results indicate that malnutrition is a serious public health problem in the studied regions.
The Black–White Disparity in Pregnancy-Related Mortality From 5 Conditions: Differences in Prevalence and Case-Fatality Rates
Authors: Tucker Myra J. , Berg Cynthia J. , Callaghan William M. , Hsia Jason 
Published: December 2006

Objectives. We sought to determine whether differences in the prevalences of 5 specific pregnancy complications or differences in case fatality rates for those complications explained the disproportionate risk of pregnancy-related mortality for Black women compared with White women in the United States. Methods. We used national data sets to calculate prevalence and case-fatality rates among Black and White women for preeclampsia, eclampsia, abruptio placentae, placenta previa, and postpartum hemorrhage for the years 1988 to 1999. Results. Black women did not have significantly greater prevalence rates than White women. However, Black women with these conditions were 2 to 3 times more likely to die from them than were White women. Conclusions. Higher pregnancy-related mortality among Black women from preeclampsia, eclampsia, abruptio placentae, placenta previa, and postpartum hemorrhage is largely attributable to higher case-fatality rates. Reductions in case-fatality rates may be made by defining more precisely the mechanisms that affect complication severity and risk of death, including complex interactions of biology and health services, and then applying this knowledge in designing interventions that improve pregnancy-related outcomes.
Effects of Maternal and Provider Characteristics on Up-to-Date Immunization Status of Children Aged 19 to 35 Months
Authors: Kim Sam S. , Frimpong Jemima A. , Rivers Patrick A. , Kronenfeld Jennie J. 
Published: December 2006

Objectives. We examined the effects of maternal and provider characteristics on the up-to-date immunization status of children. Methods. We used data from the 2003 National Immunization Survey to determine variations in children’s up-to-date status in the 4:3:1:3 immunization series. Results. Low maternal educational levels and low socioeconomic status were associated with high 4:3:1:3 series completion rates. Also, completion rates were high in Hispanic and non-Hispanic Black families with low income-to-poverty ratios. Conclusions. We found that children of less educated mothers and children in Hispanic and non-Hispanic Black families with low income-to-poverty ratios were more likely to have completed the 4:3:1:3 series. Although the reasons for these results need further exploration in other data sets, possible factors are Hispanics’ positive cultural attitudes regarding the needs and importance of young children and provision of information on immunizations to low-income minority mothers who access government-subsidized health care programs.
Using Participant Event Monitoring in a Cohort Study of Unintentional Injuries Among Children and Adolescents
Authors: Wilkins J.R. , Crawford J. Mac , Stallones Lorann , Koechlin Kathleen M. , Shen Lei , Hayes John , Bean Thomas L. 
Published: December 2006

Objectives. We conducted a 3-year cohort study of 407 youths aged 9 to 18 years to develop multivariable risk prediction models of agriculture-related injuries. Methods. Data were obtained via participant event monitoring, with youths self-reporting injuries and exposures in daily diaries over a 13-week period. We evaluated data quality by comparing injury self-reports with other injury data. Results. Semilogarithmic plots of rates of all unintentional injuries combined (US data from 2000) as well as of agriculture-related injuries (US and Canadian data from 19 previous studies) graphed as a function of injury severity exhibited linearity, as did plots based on the present results. Severity-specific unintentional injury rates were 1.4- to 4.3-times higher than national rates, suggesting that our methodology can significantly reduce injury underreporting. In addition, at each severity level, estimated agriculture-related injury rates were 5.8- to 9.3-times higher than rates from previous national, regional, and state-based studies. Conclusions. Our approach to participant event monitoring can be implemented with youths aged 9 to 18 years and will yield reliable daily data on unintentional injuries.