bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Screening of Genes Essential for Growth in High-Pressure and Cold Environments: Searching for Basic Adaptive Strategies Using a Yeast Deletion Library
Authors: Abe Fumiyoshi , Minegishi Hiroaki 
Published: February 2008

Abstract
Microorganisms display an optimal temperature and hydrostatic pressure for growth. To establish the molecular basis of piezo- and psychroadaptation, we elucidated global genetic defects that give rise to susceptibility to high pressure and low temperature in Saccharomyces cerevisiae. Here we present 80 genes including 71 genes responsible for high-pressure growth and 56 responsible for low-temperature growth with a significant overlap of 47 genes. Numerous previously known cold-sensitive mutants exhibit marked high-pressure sensitivity. We identified critically important cellular functions: (i) amino acid biosynthesis, (ii) microautophagy and sorting of amino acid permease established by the exit from rapamycin-induced growth arrest/Gap1 sorting in the endosome (EGO/GSE) complex, (iii) mitochondrial functions, (iv) membrane trafficking, (v) actin organization mediated by Drs2-Cdc50, and (vi) transcription regulated by the Ccr4-Not complex. The loss of EGO/GSE complex resulted in a marked defect in amino acid uptake following high-pressure and low-temperature incubation, suggesting its role in surface delivery of amino acid permeases. Microautophagy and mitochondrial functions converge on glutamine homeostasis in the target of rapamycin (TOR) signaling pathway. The localization of actin requires numerous associated proteins to be properly delivered by membrane trafficking. In this study, we offer a novel route to gaining insights into cellular functions and the genetic network from growth properties of deletion mutants under high pressure and low temperature.
Templated Mutagenesis in Bacteriophage T4 Involving Imperfect Direct or Indirect Sequence Repeats
Authors: Schultz Gary E , Drake John W 
Published: February 2008

AbstractSome mutations arise in association with a potential sequence donor that consists of an imperfect direct or reverse repeat. Many such mutations are complex; that is, they consist of multiple close sequence changes. Current models posit that the primer terminus of a replicating DNA molecule dissociates, reanneals with an ectopic template, extends briefly, and then returns to the cognate template, bringing with it a locally different sequence; alternatively, a hairpin structure may form the mutational intermediate when processed by mismatch repair. This process resembles replication repair, in which primer extension is blocked by a lesion in the template; in this case, the ectopic template is the other daughter strand, and the result is error-free bypass of the lesion. We previously showed that mutations that impair replication repair can enhance templated mutagenesis. We show here that the intensity of templated mutation can be exquisitely sensitive to its local sequence, that the donor and recipient arms of an imperfect inverse repeat can exchange roles, and that double mutants carrying two alleles, each affecting both templated mutagenesis and replication repair, can have unexpected phenotypes. We also record an instance in which the mutation rates at two particular sites change concordantly with a distant sequence change, but in a manner that appears unrelated to templated mutagenesis.
Targeted Gene Deletion and Phenotypic Analysis of theDrosophila melanogasterSeminal Fluid Protease Inhibitor Acp62F
Authors: Mueller Jacob L , Linklater Jon R , Ravi Ram Kristipati , Chapman Tracey , Wolfner Mariana F 
Published: February 2008

AbstractInternally fertilizing organisms transfer a complex assortment of seminal fluid proteins, a substantial fraction of which are proteolysis regulators. In mammals, some seminal protease inhibitors have been implicated in male infertility and these same molecular classes of protease inhibitors are also found in Drosophila seminal fluid. Here, we tested the reproductive functions of the Drosophila melanogaster seminal fluid protease inhibitor Acp62F by generating a precise deletion of the Acp62F gene. We did not detect a nonredundant function for Acp62F in modulating the egg laying, fertility, remating frequency, or life span of mated females. However, loss of Acp62F did alter a male's defensive sperm competitive ability, consistent with the localization of Acp62F to sperm storage organs. In addition, the processing of at least one seminal protein, the ovulation hormone ovulin, is slower in the absence of Acp62F.
Identification of Drosophila Mutants Altering Defense of and Endurance to Listeria monocytogenes Infection
Authors: Ayres Janelle S , Freitag Nancy , Schneider David S 
Published: February 2008

Abstract
We extended the use of Drosophila beyond being a model for signaling pathways required for pattern recognition immune signaling and show that the fly can be used to identify genes required for pathogenesis and host–pathogen interactions. We performed a forward genetic screen to identify Drosophila mutations altering sensitivity to the intracellular pathogen Listeria monocytogenes. We recovered 18 mutants with increased susceptibility to infection, none of which were previously shown to function in a Drosophila immune response. Using secondary screens, we divided these mutants into two groups: In the first group, mutants have reduced endurance to infections but show no change in bacterial growth. This is a new fly immunity phenotype that is not commonly studied. In the second group, mutants have a typical defense defect in which bacterial growth is increased and survival is decreased. By further challenging mutant flies with L. monocytogenes mutants, we identified subgroups of fly mutants that affect specific stages of the L. monocytogenes life cycle, exit from the vacuole, or actin-based movement. There is no overlap between our genes and the hundreds of genes identified in Drosophila S2 cells fighting L. monocytogenes infection, using genomewide RNAi screens in vitro. By using a whole-animal model and screening for host survival, we revealed genes involved in physiologies different from those that were found in previous screens, which all had defects in defensive immune signaling.
A Role for Chd1 and Set2 in Negatively Regulating DNA Replication in Saccharomyces cerevisiae
Authors: Biswas Debabrata , Takahata Shinya , Xin Hua , Dutta-Biswas Rinku , Yu Yaxin , Formosa Tim , Stillman David J 
Published: February 2008

Abstract
Chromatin-modifying factors regulate both transcription and DNA replication. The yFACT chromatin-reorganizing complex is involved in both processes, and the sensitivity of some yFACT mutants to the replication inhibitor hydroxyurea (HU) is one indication of a replication role. This HU sensitivity can be suppressed by disruptions of the SET2 or CHD1 genes, encoding a histone H3(K36) methyltransferase and a chromatin remodeling factor, respectively. The additive effect of set2 and chd1 mutations in suppressing the HU sensitivity of yFACT mutants suggests that these two factors function in separate pathways. The HU suppression is not an indirect effect of altered regulation of ribonucleotide reductase induced by HU. set2 and chd1 mutations also suppress the HU sensitivity of mutations in other genes involved in DNA replication, including CDC2, CTF4, ORC2, and MEC1. Additionally, a chd1 mutation can suppress the lethality normally caused by disruption of either MEC1 or RAD53 DNA damage checkpoint genes, as well as the lethality seen when a mec1 sml1 mutant is exposed to low levels of HU. The pob3 defect in S-phase progression is suppressed by set2 or chd1 mutations, suggesting that Set2 and Chd1 have specific roles in negatively regulating DNA replication.
The Contribution of Social Effects to Heritable Variation in Finishing Traits of Domestic Pigs (Sus scrofa)
Authors: Bergsma R , Kanis E , Knol E F , Bijma P 
Published: February 2008

AbstractSocial interactions among individuals are ubiquitous both in animals and in plants, and in natural as well as domestic populations. These interactions affect both the direction and the magnitude of responses to selection and are a key factor in evolutionary success of species and in the design of breeding schemes in agriculture. At present, however, very little is known of the contribution of social effects to heritable variance in trait values. Here we present estimates of the direct and social genetic variance in growth rate, feed intake, back fat thickness, and muscle depth in a population of 14,032 domestic pigs with known pedigree. Results show that social effects contribute the vast majority of heritable variance in growth rate and feed intake in this population. Total heritable variance expressed relative to phenotypic variance was 71% for growth rate and 70% for feed intake. These values clearly exceed the usual range of heritability for those traits. Back fat thickness and muscle depth showed no heritable variance due to social effects. Our results suggest that genetic improvement in agriculture can be substantially advanced by redirecting breeding schemes, so as to capture heritable variance due to social effects.
Adaptive Evolution of the Insulin Two-Gene System in Mouse
Authors: Shiao Meng-Shin , Liao Ben-Yang , Long Manyuan , Yu Hon-Tsen 
Published: February 2008

Abstract
Insulin genes in mouse and rat compose a two-gene system in which Ins1 was retroposed from the partially processed mRNA of Ins2. When Ins1 originated and how it was retained in genomes still remain interesting problems. In this study, we used genomic approaches to detect insulin gene copy number variation in rodent species and investigated evolutionary forces acting on both Ins1 and Ins2. We characterized the phylogenetic distribution of the new insulin gene (Ins1) by Southern analyses and confirmed by sequencing insulin genes in the rodent genomes. The results demonstrate that Ins1 originated right before the mouse–rat split (∼20 MYA), and both Ins1 and Ins2 are under strong functional constraints in these murine species. Interestingly, by examining a range of nucleotide polymorphisms, we detected positive selection acting on both Ins2 and Ins1 gene regions in the Mus musculus domesticus populations. Furthermore, three amino acid sites were also identified as having evolved under positive selection in two insulin peptides: two are in the signal peptide and one is in the C-peptide. Our data suggest an adaptive divergence in the mouse insulin two-gene system, which may result from the response to environmental change caused by the rise of agricultural civilization, as proposed by the thrifty-genotype hypothesis.
Mercury Levels in Newborns and Infants After Receipt of Thimerosal-Containing Vaccines
Authors: Pichichero Michael E. , Gentile Angela , Giglio Norberto , Umido Veronica , Clarkson Thomas , Cernichiari Elsa , Zareba Grazyna , Gotelli Carlos , Gotelli Mariano , Yan Lihan , Treanor John 
Published: February 2008

OBJECTIVES. Thimerosal is a mercurial preservative that was widely used in multidose vaccine vials in the United States and Europe until 2001 and continues to be used in many countries throughout the world. We conducted a pharmacokinetic study to assess blood levels and elimination of ethyl mercury after vaccination of infants with thimerosal-containing vaccines.
METHODS. Blood, stool, and urine samples were obtained before vaccination and 12 hours to 30 days after vaccination from 216 healthy children: 72 newborns (group 1), 72 infants aged 2 months (group 2), and 72 infants aged 6 months (group 3). Total mercury levels were measured by atomic absorption. Blood mercury pharmacokinetics were calculated by pooling the data on the group and were based on a 1-compartment first-order pharmacokinetics model.
RESULTS. For groups 1, 2, and 3, respectively, (1) mean ± SD weights were 3.4 ± 0.4, 5.1 ± 0.6, and 7.7 ± 1.1 kg; (2) maximal mean ± SD blood mercury levels were 5.0 ± 1.3, 3.6 ± 1.5, and 2.8 ± 0.9 ng/mL occurring at 0.5 to 1 day after vaccination; (3) maximal mean ± SD stool mercury levels were 19.1 ± 11.8, 37.0 ± 27.4, and 44.3 ± 23.9 ng/g occurring on day 5 after vaccination for all groups; and (4) urine mercury levels were mostly nondetectable. The blood mercury half-life was calculated to be 3.7 days and returned to prevaccination levels by day 30.
CONCLUSIONS. The blood half-life of intramuscular ethyl mercury from thimerosal in vaccines in infants is substantially shorter than that of oral methyl mercury in adults. Increased mercury levels were detected in stools after vaccination, suggesting that the gastrointestinal tract is involved in ethyl mercury elimination. Because of the differing pharmacokinetics of ethyl and methyl mercury, exposure guidelines based on oral methyl mercury in adults may not be accurate for risk assessments in children who receive thimerosal-containing vaccines.
Effect of a Short Course of Prednisolone in Infants With Oxygen-Dependent Bronchopulmonary Dysplasia
Authors: Bhandari Anita , Schramm Craig M. , Kimble Claudia , Pappagallo Mariann , Hussain Naveed 
Published: February 2008

OBJECTIVE. The purpose of this work was to determine whether oral prednisolone is effective in weaning infants with bronchopulmonary dysplasia, after 36 weeks' postmenstrual age, off supplemental oxygen and to identify factors associated with successful weaning.METHODS. Data were abstracted from a standardized prospectively collected database at the John Dempsey Hospital NICU. Logistic regression and receiver operating curve analyses were used.RESULTS. Of 385 infants, 131 (34%) received oral prednisolone and 254 (66%) did not. There was no significant difference in race, gender, birth weight, or gestational age between the groups receiving and not receiving oral prednisolone. Infants in the oral prednisolone group were more likely to have received previous dexamethasone therapy, had longer duration of mechanical ventilation, had longer length of hospital stay, and were more likely to be discharged from the hospital on oxygen. Of those in the oral prednisolone group, 63% responded to treatment. Pulmonary acuity score and Pco2 were the only parameters that remained significant on multiple logistic regression analyses. The oral prednisolone-responsive group had a lower pulmonary acuity score compared with the oral prednisolone-nonresponsive group. A pulmonary acuity score value of ≤0.5 had a sensitivity of 20% and specificity of 97.4%, with positive and negative predictive values of 94.1% and 42.1%, respectively. Capillary Pco2 values were significantly lower in the oral prednisolone-responsive group compared with the oral prednisolone-nonresponsive group. In predicting a successful response to oral prednisolone, a capillary Pco2 value of &lt;48.5 mmHg had a sensitivity of 50% and specificity of 89.7%, with positive and negative predictive values of 89.1% and 51.8%, respectively.CONCLUSIONS. Oral prednisolone therapy is effective in weaning off supplemental oxygen in a postterm infant with oxygen-dependent bronchopulmonary dysplasia who has a pulmonary acuity score of &lt;0.5 and Pco2 of &lt;48.5 mmHg. In addition, if a single course of prednisolone fails, there is no clear benefit of using multiple courses.
Burden and Economic Cost of Group A Streptococcal Pharyngitis
Authors: Pfoh Elizabeth , Wessels Michael R. , Goldmann Donald , Lee Grace M. 
Published: February 2008

OBJECTIVE. Our aim was to describe the morbidity, medical costs, and nonmedical costs associated with group A streptococcal pharyngitis in school-aged children.METHODS. Our study population included parents of children diagnosed as having group A streptococcal pharyngitis at 2 pediatric practice sites in the Boston, Massachusetts, metropolitan area. Telephone interviews were conducted with parents of eligible children, who were asked questions about health care utilization, medications, and time missed from work or school, for calculation of medical and nonmedical costs associated with illness.RESULTS. One hundred thirty-five parents completed interviews between October 2005 and January 2006. Older children were significantly more likely to present with headache, compared with those ≤5 years of age. No significant differences between older and younger children were found for rates of sore throat, fever, abdominal pain/nausea/vomiting, or rash. Children missed a mean of 1.9 days (range: 0–7 days) of school/day care, and 42% of parents missed a mean of 1.8 days of work. A second parent or caregiver also missed a mean of 1.5 days in 14% of families. The total societal cost per case of group A streptococcal pharyngitis was $205 (medical: $118; nonmedical: $87).CONCLUSIONS. The societal cost of group A streptococcal pharyngitis is substantial, with almost one half being attributable to nonmedical costs. Through extrapolation from this experience, the total cost of group A streptococcal pharyngitis among children in the United States ranges from $224 to $539 million per year.
Why Do Adolescents Say They Are Less Healthy Than Their Parents Think They Are? The Importance of Mental Health Varies by Social Class in a Nationally Representative Sample
Authors: Johnson Sara B. , Wang Constance 
Published: February 2008

OBJECTIVE. We sought to (1) confirm the discrepancy between parent-reported and youth-reported adolescent health in a nationally representative sample, (2) compare the predictors of parent-reported and adolescent self-reported health, and (3) determine whether the discrepancy between the 2 ratings differed by sociodemographic characteristics, particularly income.
METHODS. Data were from the 2001–2002 National Health and Nutrition Examination Survey. A total of 1157 adolescents aged 12 to 15 years, representative of 16227827 US youth, were included. Youth and their parents reported on the youth's health status along with other indicators of health and illness and sociodemographic characteristics. To examine predictors of self-rated and parent-rated adolescent health (excellent to poor), bivariate analyses were conducted, followed by multiple linear regression adjusted for relevant covariates. All of the analyses were stratified by income (standardized poverty income index: ≤1 vs &gt;1).
RESULTS. Parents and youth differed in subjective judgments regarding the child's health, even when these differences were not supported by other health indicators (days of school missed because of illness or injury or days of poor mental or physical health). Poor adolescents reported worse self-rated health than higher-income youth, and their parents did also. In income-stratified multiple regression models, higher-income adolescents' and their parents' ratings were predicted by indicators of physical health. In contrast, poor youth and parent ratings were better predicted by mental health care use. Poor youth with a mental health visit in the last year reported better health, but their parents saw these mental health visits as an indication of poor health.
CONCLUSIONS. The findings suggest that social class differences in subjective ratings of adolescents' health are related to the differential ways that youth and parents determine what constitutes health and are not simply a reflection of objective health status.
A Meta-analysis of the Effects of Oral Zinc in the Treatment of Acute and Persistent Diarrhea
Authors: Lukacik Marek , Thomas Ronald L. , Aranda Jacob V. 
Published: February 2008

OBJECTIVE. Children in developing countries are at a high risk for zinc deficiency. Supplemental zinc has previously been shown to provide therapeutic benefits in diarrhea. The objective of this study was to examine the efficacy and safety of supplemental oral zinc therapy during recovery from acute or persistent diarrhea.
METHODS. We conducted a meta-analysis of randomized, controlled trials to compare the efficacy and safety of supplementary oral zinc with placebo in children with acute and persistent diarrhea. Results were reported using a pooled relative risk or a weighted mean difference. A total of 22 studies were identified for inclusion: 16 examined acute diarrhea (n = 15231), and 6 examined persistent diarrhea (n = 2968).
RESULTS. Mean duration of acute diarrhea and persistent diarrhea was significantly lower for zinc compared with placebo. Presence of diarrhea between zinc and placebo at day 1 was not significantly different in acute diarrhea or persistent diarrhea trials. At day 3, presence was significantly lower for zinc in persistent diarrhea trials (n = 221) but not in acute diarrhea trials. Vomiting after therapy was significantly higher for zinc in 11 acute diarrhea trials (n = 4438) and 4 persistent diarrhea trials (n = 2969). Those who received zinc gluconate in comparison with zinc sulfate/acetate vomited more frequently. Overall, children who received zinc reported an 18.8% and 12.5% reduction in average stool frequency, 15.0% and 15.5% shortening of diarrhea duration, and a 17.9% and 18.0% probability of reducing diarrhea over placebo in acute and persistent trials, respectively.
CONCLUSIONS. Zinc supplementation reduces the duration and severity of acute and persistent diarrhea; however, the mechanisms by which zinc exerts its antidiarrheal effect have not been fully elucidated.
Comparison of canine capillary and jugular venous blood lactate concentrations determined by use of an enzymatic-amperometric bedside system
Authors: Ferasin Luca , Nguyenba Thaibinh P. 
Published: February 2008

Abstract
Objective—To evaluate the analytical agreement between blood lactate concentrations determined by use of an enzymatic-amperometric bedside system in capillary blood samples from the pinna and in jugular venous blood samples from dogs.
Animals—53 dogs.
Procedures—For each dog, venous and capillary blood samples were obtained from a jugular vein and from the ear pinna (by use of a lancing device), respectively, following a randomized sequence of collection. Lactate concentrations in both types of samples were analyzed by use of an enzymatic-amperometric bedside system intended for lactate detection in capillary blood samples from humans that was previously validated in dogs. The Passing-Bablock regression analysis was used to compare venous and capillary blood lactate concentrations; the level of agreement was calculated by use of the Bland-Altman method.
Results—Jugular venous blood samples were collected without difficulty from all 53 dogs. A capillary blood sample was obtained from only 47 dogs. The correlation coefficient between lactate concentrations measured in venous and capillary blood samples was 0.58 (slope, 2.0 [95% confidence interval, 1.5 to 3.0]; intercept, −1.2 [95% confidence interval, −3.1 to 0.4]). The mean difference between methods was 0.72 mmol/L (95% confidence interval, 0.38 to 1.06) with limits of agreement of −1.55 to 2.99 mmol/L.
Conclusions and Clinical Relevance—Because of the lack of agreement between lactate concentrations determined in capillary and jugular venous blood samples, measurement of capillary blood lactate concentration in dogs performed with the technique used in the study does not appear to be a reliable alternative to jugular venous blood measurements.