bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fixation Probability for Lytic Viruses: The Attachment-Lysis Model
Authors: Patwa Z , Wahl L M 
Published: September 2008

Abstract
The fixation probability of a beneficial mutation is extremely sensitive to assumptions regarding the organism's life history. In this article we compute the fixation probability using a life-history model for lytic viruses, a key model organism in experimental studies of adaptation. The model assumes that attachment times are exponentially distributed, but that the lysis time, the time between attachment and host cell lysis, is constant. We assume that the growth of the wild-type viral population is controlled by periodic sampling (population bottlenecks) and also include the possibility that clearance may occur at a constant rate, for example, through washout in a chemostat. We then compute the fixation probability for mutations that increase the attachment rate, decrease the lysis time, increase the burst size, or reduce the probability of clearance. The fixation probability of these four types of beneficial mutations can be vastly different and depends critically on the time between population bottlenecks. We also explore mutations that affect lysis time, assuming that the burst size is constrained by the lysis time, for experimental protocols that sample either free phage or free phage and artificially lysed infected cells. In all cases we predict that the fixation probability of beneficial alleles is remarkably sensitive to the time between population bottlenecks.
Efficient Ends-Out Gene Targeting In Drosophila
Authors: Huang Juan , Zhou Wenke , Watson Annie M , Jan Yuh-Nung , Hong Yang 
Published: September 2008

Abstract
In this report, we describe several approaches to improve the scalability and throughput of major genetic crosses in ends-out gene targeting. We generated new sets of targeting vectors and fly stocks and introduced a novel negative selection marker that drastically reduced the frequency of false-positive targeting candidates.
Requirement of Rad5 for DNA Polymerase ζ-Dependent Translesion Synthesis in Saccharomyces cerevisiae
Authors: Pagès Vincent , Bresson Anne , Acharya Narottam , Prakash Satya , Fuchs Robert P , Prakash Louise 
Published: September 2008

Abstract
In yeast, Rad6–Rad18-dependent lesion bypass involves translesion synthesis (TLS) by DNA polymerases η or ζ or Rad5-dependent postreplication repair (PRR) in which error-free replication through the DNA lesion occurs by template switching. Rad5 functions in PRR via its two distinct activities—a ubiquitin ligase that promotes Mms2–Ubc13-mediated K63-linked polyubiquitination of PCNA at its lysine 164 residue and a DNA helicase that is specialized for replication fork regression. Both these activities are important for Rad5's ability to function in PRR. Here we provide evidence for the requirement of Rad5 in TLS mediated by Polζ. Using duplex plasmids carrying different site-specific DNA lesions—an abasic site, a cis–syn TT dimer, a (6-4) TT photoproduct, or a G-AAF adduct—we show that Rad5 is needed for Polζ-dependent TLS. Rad5 action in this role is likely to be structural, since neither the inactivation of its ubiquitin ligase activity nor the inactivation of its helicase activity impairs its role in TLS.
mei-38 Is Required for Chromosome Segregation During Meiosis in Drosophila Females
Authors: Wu Changjian , Singaram Vinod , McKim Kim S 
Published: September 2008

Abstract
Meiotic chromosome segregation occurs in Drosophila oocytes on an acentrosomal spindle, which raises interesting questions regarding spindle assembly and function. One is how to organize a bipolar spindle without microtubule organizing centers at the poles. Another question is how to orient the chromosomes without kinetochore capture of microtubules that grow from the poles. We have characterized the mei-38 gene in Drosophila and found it may be required for chromosome organization within the karyosome. Nondisjunction of homologous chromosomes occurs in mei-38 mutants primarily at the first meiotic division in females but not in males where centrosomes are present. Most meiotic spindles in mei-38 oocytes are bipolar but poorly organized, and the chromosomes appear disorganized at metaphase. mei-38 encodes a novel protein that is conserved in the Diptera and may be a member of a multigene family. Mei-38 was previously identified (as ssp1) due to a role in mitotic spindle assembly in a Drosophila cell line. MEI-38 protein localizes to a specific population of spindle microtubules, appearing to be excluded from the overlap of interpolar microtubules in the central spindle. We suggest MEI-38 is required for the stability of parallel microtubules, including the kinetochore microtubules.
Genetic Basis of Evolutionary Adaptation by Escherichia coli to Stressful Cycles of Freezing, Thawing and Growth
Authors: Sleight Sean C , Orlic Christian , Schneider Dominique , Lenski Richard E 
Published: September 2008

Abstract
Microbial evolution experiments offer a powerful approach for coupling changes in complex phenotypes, including fitness and its components, with specific mutations. Here we investigate mutations substituted in 15 lines of Escherichia coli that evolved for 1000 generations under freeze–thaw–growth (FTG) conditions. To investigate the genetic basis of their improvements, we screened many of the lines for mutations involving insertion sequence (IS) elements and identified two genes where multiple lines had similar mutations. Three lines had IS150 insertions in cls, which encodes cardiolipin synthase, and 8 lines had IS150 insertions in the uspA-uspB intergenic region, encoding two universal stress proteins. Another line had an 11-bp deletion mutation in the cls gene. Strain reconstructions and competitions demonstrated that this deletion is beneficial under the FTG regime in its evolved genetic background. Further experiments showed that this cls mutation helps maintain membrane fluidity after freezing and thawing and improves freeze–thaw (FT) survival. Reconstruction of isogenic strains also showed that the IS150 insertions in uspA/B are beneficial under the FTG regime. The evolved insertions reduce uspB transcription and increase both FT survival and recovery, but the physiological mechanism for this fitness improvement remains unknown.
Diploid/Polyploid Syntenic Shuttle Mapping and Haplotype-Specific Chromosome Walking Toward a Rust Resistance Gene (Bru1) in Highly Polyploid Sugarcane (2n ∼ 12x ∼ 115)
Authors: Le Cunff Loïc , Garsmeur Olivier , Raboin Louis Marie , Pauquet Jérome , Telismart Hugues , Selvi Athiappan , Grivet Laurent , Philippe Romain , Begum Dilara , Deu Monique , Costet Laurent , Wing Rod , Glaszmann Jean Christophe , D'Hont Angélique 
Published: September 2008

Abstract
The genome of modern sugarcane cultivars is highly polyploid (∼12x), aneuploid, of interspecific origin, and contains 10 Gb of DNA. Its size and complexity represent a major challenge for the isolation of agronomically important genes. Here we report on the first attempt to isolate a gene from sugarcane by map-based cloning, targeting a durable major rust resistance gene (Bru1). We describe the genomic strategies that we have developed to overcome constraints associated with high polyploidy in the successive steps of map-based cloning approaches, including diploid/polyploid syntenic shuttle mapping with two model diploid species (sorghum and rice) and haplotype-specific chromosome walking. Their applications allowed us (i) to develop a high-resolution map including markers at 0.28 and 0.14 cM on both sides and 13 markers cosegregating with Bru1 and (ii) to develop a physical map of the target haplotype that still includes two gaps at this stage due to the discovery of an insertion specific to this haplotype. These approaches will pave the way for the development of future map-based cloning approaches for sugarcane and other complex polyploid species.
Preservation of a Pseudogene by Gene Conversion and Diversifying Selection
Authors: Takuno Shohei , Nishio Takeshi , Satta Yoko , Innan Hideki 
Published: September 2008

AbstractInterlocus gene conversion is considered a crucial mechanism for generating novel combinations of polymorphisms in duplicated genes. The importance of gene conversion between duplicated genes has been recognized in the major histocompatibility complex and self-incompatibility genes, which are likely subject to diversifying selection. To theoretically understand the potential role of gene conversion in such situations, forward simulations are performed in various two-locus models. The results show that gene conversion could significantly increase the number of haplotypes when diversifying selection works on both loci. We find that the tract length of gene conversion is an important factor to determine the efficacy of gene conversion: shorter tract lengths can more effectively generate novel haplotypes given the gene conversion rate per site is the same. Similar results are also obtained when one of the duplicated genes is assumed to be a pseudogene. It is suggested that a duplicated gene, even after being silenced, will contribute to increasing the variability in the other locus through gene conversion. Consequently, the fixation probability and longevity of duplicated genes increase under the presence of gene conversion. On the basis of these findings, we propose a new scenario for the preservation of a duplicated gene: when the original donor gene is under diversifying selection, a duplicated copy can be preserved by gene conversion even after it is pseudogenized.
The Influence of Gene Conversion on Linkage Disequilibrium Around a Selective Sweep
Authors: Jones Danielle A , Wakeley John 
Published: September 2008

Abstract
In a 2007 article, McVean studied the effect of recombination on linkage disequilibrium (LD) between two neutral loci located near a third locus that has undergone a selective sweep. The results demonstrated that two loci on the same side of a selected locus might show substantial LD, whereas the expected LD for two loci on opposite sides of a selected locus is zero. In this article, we extend McVean's model to include gene conversion. We show that one of the conclusions is strongly affected by gene conversion: when gene conversion is present, there may be substantial LD between two loci on opposite sides of a selective sweep.
A Genetic Screen Identifies New Regulators of Steroid-Triggered Programmed Cell Death in Drosophila
Authors: Wang Lei , Evans Janelle , Andrews Hillary K , Beckstead Robert B , Thummel Carl S , Bashirullah Arash 
Published: September 2008

Abstract
The steroid hormone ecdysone triggers the rapid and massive destruction of larval tissues through transcriptional cascades that culminate in rpr and hid expression and caspase activation. Here we describe the use of genetic screens to further our understanding of this steroid-triggered programmed cell death response. Pupal lethal mutants were screened for specific defects in larval salivary gland destruction. A pilot screen using existing P-element collections resulted in the identification of mutations in known cell death regulators, E74 and hid, as well as multiple alleles in CBP (nejire) and dTrf2. A large-scale EMS mutagenesis screen on the third chromosome resulted in the recovery of 48 mutants. These include seven multiallelic complementation groups, at least five of which do not map to regions or genes previously associated with cell death. Five mutants display defects in the transcriptional induction of rpr and hid, and all display a penetrant block in caspase activation. Three were mapped to specific genes: CG5146, which encodes a protein of unknown function, Med24, which encodes a component of the RNA polymerase II mediator complex, and CG7998, which encodes a putative mitochondrial malate dehydrogenase. These genetic screens provide new directions for understanding the regulation of programmed cell death during development.
Evaluation of Community-Based Health Projects: The Healthy Tomorrows Experience
Authors: Ruch-Ross Holly , Keller David , Miller Nicole , Bassewitz Jane , Melinkovich Paul 
Published: September 2008

OBJECTIVES. To address the “millennial morbidities,” pediatricians must partner with community-based organizations to develop interventions. Little is known about the capacity of the resulting programs for program evaluation or the importance of evaluation in project success and sustainability. The objective of this study was to examine the capacity of community-based health programs to conduct project evaluations and determine the impact of project evaluation on project outcome.METHODS. Project directors from 149 community-based programs funded from 1989 to 2003 through the Healthy Tomorrows Partnership for Children Program were surveyed regarding their project experience with evaluation and documentation of project outcomes and the current status of their project.RESULTS. Program directors from 123 (83%) programs completed the survey. Despite barriers to the evaluation process, 83% of the respondents indicated that their evaluations produced useful information. Programs that were described by respondents as “well evaluated” were more likely to report that the evaluation was implemented as planned and that the evaluation included outcome measures. Projects were more likely to be sustained in their original form when at least 1 outcome was reported on the survey.CONCLUSIONS. Evaluation of community-based programs, although challenging, is beneficial to project success and sustainability. Policy makers and funding agencies should consider ways to encourage community partnerships to incorporate evaluation into their planning process.
Health-Related Quality of Life for Extremely Low Birth Weight Adolescents in Canada, Germany, and the Netherlands
Authors: Verrips Erik , Vogels Ton , Saigal Saroj , Wolke Dieter , Meyer Renate , Hoult Lorraine , Verloove-Vanhorick S. Pauline 
Published: September 2008

OBJECTIVE. The goal was to compare health-related quality of life of 12- to 16-year-old adolescents born at an extremely low birth weight in regional cohorts from Ontario (Canada), Bavaria (Germany), and the Netherlands.
METHODS. Patients were extremely low birth weight survivors from Canada, Germany, and the Netherlands. Health-related quality of life was assessed with Health Utilities Index 3. Missing data were substituted by proxy reports. Differences in mean Health Utilities Index 3 scores were tested by using analysis of variance. Differences in the numbers of children with affected attributes were tested by using logistic regression analyses.
RESULTS. Survival rates were similar; response rates varied between 71% and 90%. Significant differences in health-related quality of life were found between the cohorts, with Dutch children scoring highest on Health Utilities Index 3 and German children scoring lowest, independent of birth weight, gestational age, and cerebral palsy. Differences in mean utility scores were mainly attributable to differences in the cognition health attribute. Most of the results were corroborated by logistic regression analyses.
CONCLUSIONS. There were significant differences between the 3 cohorts in health-related quality of life, not related to differences in birth weight, gestational age, or cerebral palsy. Survival and response rates alone cannot explain these differences.
Elevated Temperature After Hypoxic-Ischemic Encephalopathy: Risk Factor for Adverse Outcomes
Authors: Laptook Abbot , Tyson Jon , Shankaran Seetha , McDonald Scott , Ehrenkranz Richard , Fanaroff Avroy , Donovan Edward , Goldberg Ronald , O'Shea T. Michael , Higgins Rosemary D. , Poole W. Kenneth ,   and the National Institute of Child Health and Human Development Neonatal Research Network
Published: September 2008

OBJECTIVE. The goal was to determine whether the risk of death or moderate/severe disability in term infants with hypoxic-ischemic encephalopathy increases with relatively high esophageal or skin temperature occurring between 6 and 78 hours after birth.METHODS. This was an observational secondary study within the National Institute of Child Health and Human Development Neonatal Research Network randomized trial comparing whole-body cooling and usual care (control) for term infants with hypoxic-ischemic encephalopathy. Esophageal and skin temperatures were recorded serially for 72 hours. Each infant's temperatures for each site were rank ordered. The high temperature was defined for each infant as the mean of all temperature measurements in the upper quartile. The low temperature was similarly defined as the mean of the lower quartile. Outcomes were related to temperatures in 3 logistic regression analyses for the high, median, and low temperatures at each temperature site for each group, with adjustment for the level of encephalopathy, gender, gestational age, and race.RESULTS. In control infants, the mean esophageal temperature was 37.2 ± 0.7°C over the 72-hour period, and 63%, 22%, and 8% of all temperatures were &gt;37°C, &gt;37.5°C, and &gt;38°C, respectively. The mean skin temperature was 36.5 ± 0.8°C, and 12%, 5%, and 2% of all temperatures were &gt;37°C, &gt;37.5°C, and &gt;38°C, respectively. The odds of death or disability were increased 3.6–4 fold for each 1°C increase in the highest quartile of skin or esophageal temperatures. There were no associations between temperatures and outcomes in the cooling-treated group.CONCLUSIONS. Relatively high temperatures during usual care after hypoxia-ischemia were associated with increased risk of adverse outcomes. The results may reflect underlying brain injury and/or adverse effects of temperature on outcomes.
Identifying Postpartum Depression: Are 3 Questions as Good as 10?
Authors: Kabir Karolyn , Sheeder Jeanelle , Kelly Lisa S. 
Published: September 2008

BACKGROUND. Postpartum depression is the most common medical problem that new mothers face. Anxiety is a more prominent feature of postpartum depression than of depression that occurs at other times in life. Routine, universal screening significantly improves detection in primary health care settings. Thus, an ultrabrief scale that could be incorporated into a general health survey or interview would be useful.
OBJECTIVE. We tested the hypothesis that, during the first 6 postpartum months, the 3-item anxiety subscale of the Edinburgh Postpartum Depression Scale is a better ultrabrief depression screener than 2 Edinburgh Postpartum Depression Scale questions that are almost identical to the widely used Patient Health Questionnaire.
METHODS. A cohort of 199 14- to 26-year-old participants in an adolescent-oriented maternity program completed the Edinburgh Postpartum Depression Scale at well-child visits during the first 6 postpartum months. Three subscales of the Edinburgh Postpartum Depression Scale were examined as ultrabrief alternatives: the anxiety subscale (3 items; Edinburgh Postpartum Depression Scale-3), the depressive symptoms subscale (7 items; Edinburgh Postpartum Depression Scale-7), and 2 questions that resemble the Patient Health Questionnaire (Edinburgh Postpartum Depression Scale-2). The reliability, stability, and construct validity of the Edinburgh Postpartum Depression Scale and 3 subscales were compared. Criterion validity was assessed by comparison with a score of ≥10 on the full, 10-item Edinburgh Postpartum Depression Scale.
RESULTS. A total of 41 mothers (20.6%) met study criteria for referral for evaluation of depression (Edinburgh Postpartum Depression Scale-10 score ≥ 10). The Edinburgh Postpartum Depression Scale-3 exhibited the best screening performance characteristics, with sensitivity at 95% and negative predictive value at 98%. It identified 16% more mothers as depressed than the Edinburgh Postpartum Depression Scale did. The performance of the Edinburgh Postpartum Depression Scale-2 was markedly inferior, with sensitivity at 48% to 80%. Moreover, the Edinburgh Postpartum Depression Scale-2 was unreliable for mothers who had not been depressed in the past.
CONCLUSION. The brevity, reliability, and operating characteristics of the Edinburgh Postpartum Depression Scale-3 make it an attractive postpartum depression screening tool for primary health care settings in which the goal is to detect depression, not to assess its severity. Validation by diagnostic psychiatric interview is needed.
Incidence of Fractures Attributable to Abuse in Young Hospitalized Children: Results From Analysis of a United States Database
Authors: Leventhal John M. , Martin Kimberly D. , Asnes Andrea G. 
Published: September 2008

OBJECTIVE. The goal was to assess the proportion of children with fractures attributable to abuse and the incidence of fractures caused by abuse among children &lt;36 months of age who were hospitalized in the United States.
METHODS. We used the Kids' Inpatient Database, which has discharge data on 80% of acute pediatric hospitalizations in the United States, for 3 time periods (1997, 2000, and 2003). Fractures attributable to abuse in children &lt;36 months of age were identified by both an International Classification of Diseases, Ninth Revision, Clinical Modification code for fracture and a diagnosis external-cause-of-injury code for abuse. Weighted estimates of the incidence were calculated.
RESULTS. Among children &lt;36 months of age who were hospitalized with fractures, the proportions of cases attributable to abuse were 11.9% in 1997, 11.9% in 2000, and 12.1% in 2003. The proportions of cases attributable to abuse decreased with increasing age; for example, in 2003, the proportions attributable to abuse were 24.9% for children &lt;12 months of age, 7.2% for children 12 to 23 months of age, and 2.9% for children 24 to 35 months of age. In 2003, the incidence of fractures caused by abuse was 15.3 cases per 100000 children &lt;36 months of age. The incidence was 36.1 cases per 100000 among children &lt;12 months of age; this decreased to 4.8 cases per 100000 among 12- to 23-month-old children and 4.8 cases per 100000 among 24- to 35-month-old children.
CONCLUSIONS. The Kids' Inpatient Database can be used to provide reasonable estimates of the incidence of hospitalization with fractures attributable to child abuse. For children &lt;12 months of age, the incidence was 36.1 cases per 100000, a rate similar to that of inflicted traumatic brain injury (25–32 cases per 100000).