bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing Individual Differences in Genome-Wide Gene Expression in Human Whole Blood: Reliability Over Four Hours and Stability Over 10 Months
Authors: Meaburn Emma L. , Fernandes Cathy , Craig Ian W. , Plomin Robert , Schalkwyk Leonard C. 
Published: August 2009

AbstractStudying the causes and correlates of natural variation in gene expression in healthy populations assumes that individual differences in gene expression can be reliably and stably assessed across time. However, this is yet to be established. We examined 4-hour test–retest reliability and 10 month test–retest stability of individual differences in gene expression in ten 12-year-old children. Blood was collected on four occasions: 10 a.m. and 2 p.m. on Day 1 and 10 months later at 10 a.m. and 2 p.m. Total RNA was hybridized to Affymetrix-U133 plus 2.0 arrays. For each probeset, the correlation across individuals between 10 a.m. and 2 p.m. on Day 1 estimates test–retest reliability. We identified 3,414 variable and abundantly expressed probesets whose 4-hour test–retest reliability exceeded .70, a conventionally accepted level of reliability, which we had 80% power to detect. Of the 3,414 reliable probesets, 1,752 were also significantly reliable 10 months later. We assessed the long-term stability of individual differences in gene expression by correlating the average expression level for each probe-set across the two 4-hour assessments on Day 1 with the average level of each probe-set across the two 4-hour assessments 10 months later. 1,291 (73.7%) of the 1,752 probe-sets that reliably detected individual differences across 4 hours on two occasions, 10 months apart, also stably detected individual differences across 10 months. Heritability, as estimated from the MZ twin intraclass correlations, is twice as high for the 1,752 reliable probesets versus all present probesets on the array (0.68 vs 0.34), and is even higher (0.76) for the 1,291 reliable probesets that are also stable across 10 months. The 1,291 probesets that reliably detect individual differences from a single peripheral blood collection and stably detect individual differences over 10 months are promising targets for research on the causes (e.g., eQTLs) and correlates (e.g., psychopathology) of individual differences in gene expression.
A Comparative Evaluation of Various Additives Used in the Stabilization of Sulfate Bearing Lean Clay
Authors: Solanki Pranshoo , Khoury Naji , Zaman Musharraf M. 
Published: August 2009

Abstract
A laboratory study was conducted on both raw and stabilized clay specimens to evaluate short- and long-term performance of three different additives, namely, hydrated lime, class C fly ash (CFA), and cement kiln dust (CKD), for providing better treatment of sulfate rich lean clay. Short-term performance evaluation experiments included Atterberg limits, resilient modulus (Mr), modulus of elasticity (ME), and unconfined compressive strength (UCS), after 28 days of curing. Long-term performance was evaluated in terms of moisture susceptibility (tube suction test) and three-dimensional swell during 120 days of capillary soaking. At the end of 120 days, specimens were also tested for Mr, ME, and UCS, as additional indicators to long-term pavement performance. Short-term performance evaluation projected 15 % CKD with highest improvement, while long-term performance evaluation showed 15 % CFA providing maximum enhancements after 120 days of capillary soaking. The study further indicated swelling of specimens stabilized with lime and CKD; however, CFA helped in reducing the swelling. All the percentages of additives used in the study helped in reducing the moisture susceptibility of clay. Mineralogical studies such as scanning electron microscopy, energy-dispersive spectroscopy, and X-ray diffraction were also used to verify research findings observed from the macro test results.
Cis-regulatory Changes atFLOWERING LOCUS TMediate Natural Variation in Flowering Responses ofArabidopsis thaliana
Authors: Schwartz Christopher , Balasubramanian Sureshkumar , Warthmann Norman , Michael Todd P , Lempe Janne , Sureshkumar Sridevi , Kobayashi Yasushi , Maloof Julin N , Borevitz Justin O , Chory Joanne , Weigel Detlef 
Published: August 2009

AbstractFlowering time, a critical adaptive trait, is modulated by several environmental cues. These external signals converge on a small set of genes that in turn mediate the flowering response. Mutant analysis and subsequent molecular studies have revealed that one of these integrator genes, FLOWERING LOCUS T (FT), responds to photoperiod and temperature cues, two environmental parameters that greatly influence flowering time. As the central player in the transition to flowering, the protein coding sequence of FT and its function are highly conserved across species. Using QTL mapping with a new advanced intercross-recombinant inbred line (AI-RIL) population, we show that a QTL tightly linked to FT contributes to natural variation in the flowering response to the combined effects of photoperiod and ambient temperature. Using heterogeneous inbred families (HIF) and introgression lines, we fine map the QTL to a 6.7 kb fragment in the FT promoter. We confirm by quantitative complementation that FT has differential activity in the two parental strains. Further support for FT underlying the QTL comes from a new approach, quantitative knockdown with artificial microRNAs (amiRNAs). Consistent with the causal sequence polymorphism being in the promoter, we find that the QTL affects FT expression. Taken together, these results indicate that allelic variation at pathway integrator genes such as FT can underlie phenotypic variability and that this may be achieved through cis-regulatory changes.
Worms With a Single Functional Sensory Cilium Generate Proper Neuron-Specific Behavioral Output
Authors: Senti Gabriele , Ezcurra Marina , Löbner Jana , Schafer William R , Swoboda Peter 
Published: August 2009

Abstract
Studying the development and mechanisms of sensory perception is challenging in organisms with complex neuronal networks. The worm Caenorhabditis elegans possesses a simple neuronal network of 302 neurons that includes 60 ciliated sensory neurons (CSNs) for detecting external sensory input. C. elegans is thus an excellent model in which to study sensory neuron development, function, and behavior. We have generated a genetic rescue system that allows in vivo analyses of isolated CSNs at both cellular and systemic levels. We used the RFX transcription factor DAF-19, a key regulator of ciliogenesis. Mutations in daf-19 result in the complete absence of all sensory cilia and thus of external sensory input. In daf-19 mutants, we used cell-specific rescue of DAF-19 function in selected neurons, thereby generating animals with single, fully functional CSNs. Otherwise and elsewhere these animals are completely devoid of any environmental input through cilia. We demonstrated the rescue of fully functional, single cilia using fluorescent markers, sensory behavioral assays, and calcium imaging. Our technique, functional rescue in single sensory cilia (FRISSC), can thus cell-autonomously and cell-specifically restore the function of single sensory neurons and their ability to respond to sensory input. FRISSC can be adapted to many different CSNs and thus constitutes an excellent tool for studying sensory behaviors, both in single animals and in populations of worms. FRISSC will be very useful for the molecular dissection of sensory perception in CSNs and for the analysis of the developmental aspects of ciliogenesis.
mec-15 Encodes an F-Box Protein Required for Touch Receptor Neuron Mechanosensation, Synapse Formation and Development
Authors: Bounoutas Alexander , Zheng Qun , Nonet Michael L , Chalfie Martin 
Published: August 2009

Abstract
Selective protein degradation is a key regulator of neuronal development and synaptogenesis. Complexes that target proteins for degradation often contain F-box proteins. Here we characterize MEC-15, an F-box protein with WD repeats, which is required for the development and function of Caenorhabditis elegans touch receptor neurons (TRNs). Mutations in mec-15 produce defects in TRN touch sensitivity, chemical synapse formation, and cell-body morphology. All mec-15 mutant phenotypes are enhanced by mutations in a MAP kinase pathway composed of the MAPKKK DLK-1, the MAPKK MKK-4, and the p38 MAPK PMK-3. A mutation of the rpm-1 gene, which encodes an E3 ubiquitin ligase that negatively regulates this pathway to promote synaptogenesis, suppresses only the mec-15 cell-body defect. Thus, MEC-15 acts in parallel with RPM-1, implicating a second protein degradation pathway in TRN development. In addition, all mec-15 phenotypes can be dominantly suppressed by mutations in mec-7, which encodes a β-tubulin, and dominantly enhanced by mutations in mec-12, which encodes an α-tubulin. Since mec-15 phenotypes depend on the relative levels of these tubulins, MEC-15 may target proteins whose function is affected by these levels.
Point Mutation Rate of Bacteriophage ΦX174
Authors: Cuevas José M , Duffy Siobain , Sanjuán Rafael 
Published: August 2009

Abstract
The point mutation rate of phage ΦX174 was determined using the fluctuation test. After identifying the genetic changes associated with the selected phenotype, we obtained an estimate of 1.0 × 10−6 substitutions per base per round of copying, which is consistent with Drake's rule (0.003 mutations per genome per round of copying in DNA-based microorganisms).
Alcohol Sensitivity in Drosophila: Translational Potential of Systems Genetics
Authors: Morozova Tatiana V , Ayroles Julien F , Jordan Katherine W , Duncan Laura H , Carbone Mary Anna , Lyman Richard F , Stone Eric A , Govindaraju Diddahally R , Ellison R Curtis , Mackay Trudy F C , Anholt Robert R H 
Published: August 2009

AbstractIdentification of risk alleles for human behavioral disorders through genomewide association studies (GWAS) has been hampered by a daunting multiple testing problem. This problem can be circumvented for some phenotypes by combining genomewide studies in model organisms with subsequent candidate gene association analyses in human populations. Here, we characterized genetic networks that underlie the response to ethanol exposure in Drosophila melanogaster by measuring ethanol knockdown time in 40 wild-derived inbred Drosophila lines. We associated phenotypic variation in ethanol responses with genomewide variation in gene expression and identified modules of correlated transcripts associated with a first and second exposure to ethanol vapors as well as the induction of tolerance. We validated the computational networks and assessed their robustness by transposon-mediated disruption of focal genes within modules in a laboratory inbred strain, followed by measurements of transcript abundance of connected genes within the module. Many genes within the modules have human orthologs, which provides a stepping stone for the identification of candidate genes associated with alcohol drinking behavior in human populations. We demonstrated the potential of this translational approach by identifying seven intronic single nucleotide polymorphisms of the Malic Enzyme 1 (ME1) gene that are associated with cocktail drinking in 1687 individuals of the Framingham Offspring cohort, implicating that variation in levels of cytoplasmic malic enzyme may contribute to variation in alcohol consumption.
Fine Mapping and Marker Development for the Crossability Gene SKr on Chromosome 5BS of Hexaploid Wheat (Triticum aestivum L.)
Authors: Alfares Walid , Bouguennec Annaig , Balfourier François , Gay Georges , Bergès Hélène , Vautrin Sonia , Sourdille Pierre , Bernard Michel , Feuillet Catherine 
Published: August 2009

Abstract
Most elite wheat varieties cannot be crossed with related species thereby restricting greatly the germplasm that can be used for alien introgression in breeding programs. Inhibition to crossability is controlled genetically and a number of QTL have been identified to date, including the major gene Kr1 on 5BL and SKr, a strong QTL affecting crossability between wheat and rye on chromosome 5BS. In this study, we used a recombinant SSD population originating from a cross between the poorly crossable cultivar Courtot (Ct) and the crossable line MP98 to characterize the major dominant effect of SKr and map the gene at the distal end of the chromosome near the 5B homeologous GSP locus. Colinearity with barley and rice was used to saturate the SKr region with new markers and establish orthologous relationships with a 54-kb region on rice chromosome 12. In total, five markers were mapped within a genetic interval of 0.3 cM and 400 kb of BAC contigs were established on both sides of the gene to lay the foundation for map-based cloning of SKr. Two SSR markers completely linked to SKr were used to evaluate a collection of crossable wheat progenies originating from primary triticale breeding programs. The results confirm the major effect of SKr on crossability and the usefulness of the two markers for the efficient introgression of crossability in elite wheat varieties.
Implications of 99mTc-DMSA Scintigraphy Performed During Urinary Tract Infection in Neonates
Authors: Siomou Ekaterini , Giapros Vasileios , Fotopoulos Andreas , Âasioti Maria , Papadopoulou Frederica , Serbis Anastasios , Siamopoulou Antigoni , Andronikou Styliani 
Published: August 2009

OBJECTIVE: To evaluate prospectively whether normal scintigraphic results during urinary tract infections (UTIs) in neonates were predictive of the absence of dilating vesicoureteral reflux (VUR) (grade ≥III) and permanent renal damage (PRD).
METHODS: Term neonates with a first symptomatic, community-acquired UTI participated in the study. Urinary tract ultrasonography and technetium-99m-labeled dimercaptosuccinic acid (99mTc-DMSA) scintigraphy were performed within 72 hours after diagnosis and voiding cystourethrography within 1 to 2 months. DMSA scintigraphy, to determine the development of PRD, was repeated 6 months after UTI.
RESULTS: Seventy-two neonates (144 renal units) were enrolled. Acute pyelonephritis was diagnosed through early DMSA scintigraphy in 19% of renal units, VUR in 22%, and grade ≥III VUR in 13%. The majority (71%) of renal units with grade ≥III VUR had normal early DMSA scintigraphic results. The sensitivity and specificity of abnormal early DMSA scintigraphic results to predict grade ≥III VUR were 29% (95% confidence interval: 11%–55%) and 82% (95% confidence interval: 74%–88%), respectively. PRD was found in 7% of renal units, all of which had abnormal early DMSA scintigraphic results. PRD was significantly more frequent among renal units with grade ≥III VUR than among nonrefluxing renal units (P &lt; .05).
CONCLUSIONS: Normal early DMSA scintigraphic results for neonates with symptomatic UTIs were helpful in ruling out later development of PRD but were not predictive of the absence of dilating VUR. To rule out dilating VUR, voiding cystourethrography may be required.
Reports of Repetitive Penile-Genital Penetration Often Have No Definitive Evidence of Penetration
Authors: Anderst Jim , Kellogg Nancy , Jung Inkyung 
Published: August 2009

OBJECTIVES: The goals were to evaluate the association of definitive hymenal findings with the number of reported episodes of penile-genital penetration, pain, bleeding, dysuria, and time since assault for girls presenting for nonacute, sexual assault examinations.METHODS: Charts of all girls 5 to 17 of age who provided a history of nonacute, penile-genital, penetrative abuse were reviewed. Interviews and examinations occurred over a 4-year period at a children's advocacy center. Characteristics of the histories provided by the subjects were examined for associations with definitive findings of penetrative trauma.RESULTS: Five hundred six patients were included in the study. Of the 56 children with definitive examination results, 52 had no history of consensual penile-vaginal intercourse and all were ≥10 years of age. Analysis was unable to detect an association between the number of reported penile-genital penetrative events and definitive genital findings. Eighty-seven percent of victims who provided a history of &gt;10 penetrative events had no definitive evidence of penetration. A history of bleeding with abuse was more than twice as likely for subjects with definitive findings. Children &lt;10 years of age were twice as likely to report &gt;10 penetrative events, although none had definitive findings on examination.CONCLUSIONS: Most victims who reported repetitive penile-genital contact that involved some degree of perceived penetration had no definitive evidence of penetration on examination of the hymen. Similar results were seen for victims of repetitive assaults involving perceived penetration over long periods of time, as well as victims with a history of consensual sex.
Physical Education Class Injuries Treated in Emergency Departments in the US in 1997–2007
Authors: Nelson Nicolas G. , Alhajj Maya , Yard Ellen , Comstock Dawn , McKenzie Lara B. 
Published: August 2009

OBJECTIVE: The goal was to describe the epidemiological features of physical education (PE)-related injuries treated in US emergency departments.
METHODS: A retrospective analysis was conducted with data for children and adolescents (5–18 years of age) from the National Electronic Injury Surveillance Study of the US Consumer Product Safety Commission, from 1997 through 2007. Sample weights provided by the National Electronic Injury Surveillance System were used to calculate national estimates of PE-related injuries. Trend significance of the number of PE-related injuries over time was analyzed by using linear regression analysis.
RESULTS: An estimated 405305 children and adolescents were treated in emergency departments for PE-related injuries. The annual number of cases increased 150% during the study period (P = .001). Nearly 70% of PE-related injuries occurred during 6 activities, that is, running, basketball, football, volleyball, soccer, and gymnastics. Boys' injuries were more likely to involve the head, to be diagnosed as a laceration or fracture, to be attributable to contact with a person or structure, and to occur during group activities. Girls' injuries were more likely to involve the lower extremities, to be strains and sprains, to be acute noncontact injuries, and to occur during individual activities.
CONCLUSION: More research is needed to identify the cause of the increase in PE-related injuries, to examine the gender difference in PE-related injuries, and to determine appropriate injury prevention solutions and policies.
Prevalence and Associations of 25-Hydroxyvitamin D Deficiency in US Children: NHANES 2001–2004
Authors: Kumar Juhi , Muntner Paul , Kaskel Frederick J. , Hailpern Susan M. , Melamed Michal L. 
Published: August 2009

OBJECTIVES: To determine the prevalence of 25-hydroxyvitamin D (25[OH]D) deficiency and associations between 25(OH)D deficiency and cardiovascular risk factors in children and adolescents.
METHODS: With a nationally representative sample of children aged 1 to 21 years in the National Health and Nutrition Examination Survey 2001–2004 (n = 6275), we measured serum 25(OH)D deficiency and insufficiency (25[OH]D &lt;15 ng/mL and 15–29 ng/mL, respectively) and cardiovascular risk factors.
RESULTS: Overall, 9% of the pediatric population, representing 7.6 million US children and adolescents, were 25(OH)D deficient and 61%, representing 50.8 million US children and adolescents, were 25(OH)D insufficient. Only 4% had taken 400 IU of vitamin D per day for the past 30 days. After multivariable adjustment, those who were older (odds ratio [OR]: 1.16 [95% confidence interval (CI): 1.12 to 1.20] per year of age), girls (OR: 1.9 [1.6 to 2.4]), non-Hispanic black (OR: 21.9 [13.4 to 35.7]) or Mexican-American (OR: 3.5 [1.9 to 6.4]) compared with non-Hispanic white, obese (OR: 1.9 [1.5 to 2.5]), and those who drank milk less than once a week (OR: 2.9 [2.1 to 3.9]) or used &gt;4 hours of television, video, or computers per day (OR: 1.6 [1.1 to 2.3]) were more likely to be 25(OH)D deficient. Those who used vitamin D supplementation were less likely (OR: 0.4 [0.2 to 0.8]) to be 25(OH)D deficient. Also, after multivariable adjustment, 25(OH)D deficiency was associated with elevated parathyroid hormone levels (OR: 3.6; [1.8 to 7.1]), higher systolic blood pressure (OR: 2.24 mmHg [0.98 to 3.50 mmHg]), and lower serum calcium (OR: −0.10 mg/dL [−0.15 to −0.04 mg/dL]) and high-density lipoprotein cholesterol (OR: −3.03 mg/dL [−5.02 to −1.04]) levels compared with those with 25(OH)D levels ≥30 ng/mL.
CONCLUSIONS: 25(OH)D deficiency is common in the general US pediatric population and is associated with adverse cardiovascular risks.
Vitamin D Status and Cardiometabolic Risk Factors in the United States Adolescent Population
Authors: Reis Jared P. , von Mühlen Denise , Miller Edgar R. , Michos Erin D. , Appel Lawrence J. 
Published: August 2009

OBJECTIVE: Evidence on the association of vitamin D with cardiovascular risk factors in youth is very limited. We examined whether low serum vitamin D levels (25-hydroxyvitamin D [25(OH)D]) are associated with cardiovascular risk factors in US adolescents aged 12 to 19 years.
METHODS: We conducted a cross-sectional analysis of 3577 fasting, nonpregnant adolescents without diagnosed diabetes who participated in the 2001–2004 National Health and Nutrition Examination Survey. Cardiovascular risk factors were measured using standard methods and defined according to age-modified Adult Treatment Panel III definitions.
RESULTS: Mean 25(OH)D was 24.8 ng/mL; it was lowest in black (15.5 ng/mL), intermediate in Mexican American (21.5 ng/mL), and highest in white (28.0 ng/mL) adolescents (P &lt; .001 for each pairwise comparison). Low 25(OH)D levels were strongly associated with overweight status and abdominal obesity (P for trend &lt; .001 for both). After adjustment for age, gender, race/ethnicity, BMI, socioeconomic status, and physical activity, 25(OH)D levels were inversely associated with systolic blood pressure (P = .02) and plasma glucose concentrations (P = .01). The adjusted odds ratio (95% confidence interval) for those in the lowest (&lt;15 ng/mL) compared with the highest quartile (&gt;26 ng/mL) of 25(OH)D for hypertension was 2.36 (1.33–4.19); for fasting hyperglycemia it was 2.54 (1.01–6.40); for low high-density lipoprotein cholesterol it was 1.54 (0.99–2.39); for hypertriglyceridemia it was 1.00 (0.49–2.04); and for metabolic syndrome it was 3.88 (1.57–9.58).
CONCLUSIONS: Low serum vitamin D in US adolescents is strongly associated with hypertension, hyperglycemia, and metabolic syndrome, independent of adiposity.