bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Window into Domain Amplification Through Piccolo in Teleost Fish
Authors: Nonet Michael L 
Published: November 2012

AbstractI describe and characterize the extensive amplification of the zinc finger domain of Piccolo selectively in teleost fish. Piccolo and Bassoon are partially functionally redundant and play roles in regulating the pool of neurotransmitter-filled synaptic vesicles present at synapses. In mice, each protein contains two N-terminal zinc finger domains that have been implicated in interacting with synaptic vesicles. In all teleosts examined, both the Bassoon and Piccolo genes are duplicated. Both teleost bassoon genes and one piccolo gene show very similar domain structure and intron-exon organization to their mouse homologs. In contrast, in piccolo b a single exon that encodes a zinc finger domain is amplified 8 to 16 times in different teleost species. Analysis of the amplified exons suggests they were added and/or deleted from the gene as individual exons in rare events that are likely the result of unequal crossovers between homologous sequences. Surprisingly, the structure of the repeats from cod and zebrafish suggest that amplification of this exon has occurred independently multiple times in the teleost lineage. Based on the structure of the exons, I propose a model in which selection for high sequence similarity at the 5′ and 3′ ends of the exon drives amplification of the repeats and diversity in repeat length likely promotes the stability of the repeated exons by minimizing the likelihood of mispairing of adjacent repeat sequences. Further analysis of piccolo b in teleosts should provide a window through which to examine the process of domain amplification.
Effectiveness of Genomic Prediction of Maize Hybrid Performance in Different Breeding Populations and Environments
Authors: Windhausen Vanessa S , Atlin Gary N , Hickey John M , Crossa Jose , Jannink Jean-Luc , Sorrells Mark E , Raman Babu , Cairns Jill E , Tarekegne Amsal , Semagn Kassa , Beyene Yoseph , Grudloyma Pichet , Technow Frank , Riedelsheimer Christian , Melchinger Albrecht E 
Published: November 2012

Abstract
Genomic prediction is expected to considerably increase genetic gains by increasing selection intensity and accelerating the breeding cycle. In this study, marker effects estimated in 255 diverse maize (Zea mays L.) hybrids were used to predict grain yield, anthesis date, and anthesis-silking interval within the diversity panel and testcross progenies of 30 F2-derived lines from each of five populations. Although up to 25% of the genetic variance could be explained by cross validation within the diversity panel, the prediction of testcross performance of F2-derived lines using marker effects estimated in the diversity panel was on average zero. Hybrids in the diversity panel could be grouped into eight breeding populations differing in mean performance. When performance was predicted separately for each breeding population on the basis of marker effects estimated in the other populations, predictive ability was low (i.e., 0.12 for grain yield). These results suggest that prediction resulted mostly from differences in mean performance of the breeding populations and less from the relationship between the training and validation sets or linkage disequilibrium with causal variants underlying the predicted traits. Potential uses for genomic prediction in maize hybrid breeding are discussed emphasizing the need of (1) a clear definition of the breeding scenario in which genomic prediction should be applied (i.e., prediction among or within populations), (2) a detailed analysis of the population structure before performing cross validation, and (3) larger training sets with strong genetic relationship to the validation set.
Escherichia coli Lacking RpoS Are Rare in Natural Populations of Non-Pathogens
Authors: Snyder Emily , Gordon David M , Stoebel Daniel M 
Published: November 2012

Abstract
The alternative sigma factor RpoS controls a large regulon that allows E. coli to respond to a variety of stresses. Mutations in rpoS can increase rates of nutrient acquisition at the cost of a decrease in stress resistance. These kinds of mutations evolve rapidly under certain laboratory conditions where nutrient acquisition is especially challenging. The frequency of strains lacking RpoS in natural populations of E. coli is less clear. Such strains have been found at frequencies over 20% in some collections of wild isolates. However, laboratory handling can select for RpoS-null strains and may have affected some of these strain collections. Other studies have included an unknown diversity of strains or only used a phenotypic proxy as a measure of RpoS levels. We directly measured RpoS levels in a collection of E. coli that includes the full diversity of the species and that was handled in a manner to minimize the potential for laboratory evolution. We found that only 2% of strains produce no functional RpoS. Comparison of these strains in multiple labs shows that these rpoS mutations occurred in the laboratory. Earlier studies reporting much higher levels of RpoS polymorphism may reflect the storage history of the strains in laboratories rather than true frequency of such strains in natural populations.
On the Role of PDZ Domain-Encoding Genes in Drosophila Border Cell Migration
Authors: Aranjuez George , Kudlaty Elizabeth , Longworth Michelle S , McDonald Jocelyn A 
Published: November 2012

AbstractCells often move as collective groups during normal embryonic development and wound healing, although the mechanisms governing this type of migration are poorly understood. The Drosophila melanogaster border cells migrate as a cluster during late oogenesis and serve as a powerful in vivo genetic model for collective cell migration. To discover new genes that participate in border cell migration, 64 out of 66 genes that encode PDZ domain-containing proteins were systematically targeted by in vivo RNAi knockdown. The PDZ domain is one of the largest families of protein-protein interaction domains found in eukaryotes. Proteins that contain PDZ domains participate in a variety of biological processes, including signal transduction and establishment of epithelial apical-basal polarity. Targeting PDZ proteins effectively assesses a larger number of genes via the protein complexes and pathways through which these proteins function. par-6, a known regulator of border cell migration, was a positive hit and thus validated the approach. Knockdown of 14 PDZ domain genes disrupted migration with multiple RNAi lines. The candidate genes have diverse predicted cellular functions and are anticipated to provide new insights into the mechanisms that control border cell movement. As a test of this concept, two genes that disrupted migration were characterized in more detail: big bang and the Dlg5 homolog CG6509. We present evidence that Big bang regulates JAK/STAT signaling, whereas Dlg5/CG6509 maintains cluster cohesion. Moreover, these results demonstrate that targeting a selected class of genes by RNAi can uncover novel regulators of collective cell migration.
Identification of Gene Expression Changes Associated With Long-Term Memory of Courtship Rejection in Drosophila Males
Authors: Winbush Ari , Reed Danielle , Chang Peter L , Nuzhdin Sergey V , Lyons Lisa C , Arbeitman Michelle N 
Published: November 2012

AbstractLong-term memory formation in Drosophila melanogaster is an important neuronal function shaping the insect’s behavioral repertoire by allowing an individual to modify behaviors on the basis of previous experiences. In conditioned courtship or courtship suppression, male flies that have been repeatedly rejected by mated females during courtship advances are less likely than naïve males to subsequently court another mated female. This long-term courtship suppression can last for several days after the initial rejection period. Although genes with known functions in many associative learning paradigms, including those that function in cyclic AMP signaling and RNA translocation, have been identified as playing critical roles in long-term conditioned courtship, it is clear that additional mechanisms also contribute. We have used RNA sequencing to identify differentially expressed genes and transcript isoforms between naïve males and males subjected to courtship-conditioning regimens that are sufficient for inducing long-term courtship suppression. Transcriptome analyses 24 hours after the training regimens revealed differentially expressed genes and transcript isoforms with predicted and known functions in nervous system development, chromatin biology, translation, cytoskeletal dynamics, and transcriptional regulation. A much larger number of differentially expressed transcript isoforms were identified, including genes previously implicated in associative memory and neuronal development, including fruitless, that may play functional roles in learning during courtship conditioning. Our results shed light on the complexity of the genetics that underlies this behavioral plasticity and reveal several new potential areas of inquiry for future studies.
Identification of Genes Required for Alternative Oxidase Production in the Neurospora crassa Gene Knockout Library
Authors: Nargang Frank E , Adames Kelly , Rüb Cornelia , Cheung Serena , Easton Nancy , Nargang Cheryl E , Chae Michael S 
Published: November 2012

Abstract
The alternative oxidase (AOX) of Neurospora crassa transfers electrons from ubiquinol to oxygen. The enzyme is not expressed under normal conditions. However, when the function of the standard electron transport chain is compromised, AOX is induced, providing cells with a means to continue respiration and growth. Induction of the enzyme represents a form of retrograde regulation because AOX is encoded by a nuclear gene that responds to signals produced from inefficiently functioning mitochondria. To identify genes required for AOX expression, we have screened the N. crassa gene knockout library for strains that are unable to grow in the presence of antimycin A, an inhibitor of complex III of the standard electron transport chain. From the 7800 strains containing knockouts of different genes, we identified 62 strains that have reduced levels of AOX when grown under conditions known to induce the enzyme. Some strains have virtually no AOX, whereas others have only a slight reduction of the protein. A broad range of seemingly unrelated functions are represented in the knockouts. For example, we identified transcription factors, kinases, the mitochondrial import receptor Tom70, three subunits of the COP9 signalosome, a monothiol glutaredoxin, and several hypothetical proteins as being required for wild-type levels of AOX production. Our results suggest that defects in many signaling or metabolic pathways have a negative effect on AOX expression and imply that complex systems control production of the enzyme.
A Randomized Placebo-Controlled Trial of Massage Therapy on the Immune System of Preterm Infants
Authors: Ang Jocelyn Y. , Lua Jorge L. , Mathur Ambika , Thomas Ronald , Asmar Basim I. , Savasan Sureyya , Buck Steven , Long Michael , Shankaran Seetha 
Published: November 2012

OBJECTIVES:The aim of this study was to investigate the effects of massage therapy (MT) on the immune system of preterm infants. The primary hypothesis was that MT compared with sham therapy (control) will enhance the immune system of stable premature infants by increasing the proportion of their natural killer (NK) cell numbers.METHODS:A randomized placebo-controlled trial of MT versus sham therapy (control) was conducted among stable premature infants in the NICU. Study intervention was provided 5 days per week until hospital discharge for a maximum of 4 weeks. Immunologic evaluations (absolute NK cells, T and B cells, T cell subsets, and NK cytotoxicity), weight, number of infections, and length of hospital stay were also evaluated.RESULTS:The study enrolled 120 infants (58 massage; 62 control). At the end of the study, absolute NK cells were not different between the 2 groups; however, NK cytotoxicity was higher in the massage group, particularly among those who received ≥5 consecutive days of study intervention compared with control (13.79 vs 10 lytic units, respectively; P = .04). Infants in the massage group were heavier at end of study and had greater daily weight gain compared with those in the control group; other immunologic parameters, number of infections, and length of stay were not different between the 2 groups.CONCLUSIONS:In this study, MT administered to stable preterm infants was associated with higher NK cytotoxicity and more daily weight gain. MT may improve the overall outcome of these infants. Larger studies are needed.
Cost-Effectiveness of an Injury and Drowning Prevention Program in Bangladesh
Authors: Rahman Fazlur , Bose Saideep , Linnan Michael , Rahman Aminur , Mashreky Saidur , Haaland Benjamin , Finkelstein Eric 
Published: November 2012

OBJECTIVE:
Interventions that mitigate drowning risk in developing countries are needed. This study presents the cost-effectiveness of a low-cost, scalable injury and drowning prevention program called Prevention of Child Injuries through Social-Intervention and Education (PRECISE) in Bangladesh.

METHODS:
Between 2006 and 2010, the 2 components of PRECISE (Anchal, which sequestered children in crèches [n = 18 596 participants], and SwimSafe, which taught children how to swim [n = 79421 participants]) were implemented in rural Bangladesh. Mortality rates for participants were compared against a matched sample of nonparticipants in a retrospective cohort analysis. Effectiveness was calculated via Cox proportional hazard analysis. Cost-effectiveness was estimated according to World Health Organization–CHOosing Interventions that are Cost Effective guidelines.

RESULTS:
Anchal costs between $50.74 and $60.50 per child per year. SwimSafe costs $13.46 per child. For Anchal participants, the relative risk of a drowning death was 0.181 (P = .004). The relative risk of all-cause mortality was 0.56 (P = .001). For SwimSafe, the relative risk of a drowning death was 0.072 (P &lt; .0001). The relative risk of all-cause mortality was 0.750 (P = .024). For Anchal, the cost per disability-adjusted life-year (DALY) averted is $812 (95% confidence interval: $589\x{2013}$1777). For SwimSafe, the cost per DALY averted is $85 ($51\x{2013}$561). Combined, the cost per DALY averted is $362 ($232\x{2013}$1364).

CONCLUSIONS:
Based on World Health Organization criteria, PRECISE is very cost-effective and should be considered for implementation in other areas where drowning is a significant problem.
Fish Consumption in Infancy and Asthma-like Symptoms at Preschool Age
Authors: Kiefte-de Jong Jessica C. , de Vries Jeanne H. , Franco Oscar H. , Jaddoe Vincent W.V. , Hofman Albert , Raat Hein , de Jongste Johan C. , Moll Henriette A. 
Published: November 2012

OBJECTIVE:To assess whether timing of introduction of fish and the amount of fish consumption in infancy were associated with asthmalike symptoms at preschool age.METHODS:This study was embedded in the Generation R study (a population-based birth cohort in Rotterdam, Netherlands). At the age of 12 and 14 months, timing of introduction of fish into the infant’s diet was assessed. The amount of fish consumption at 14 months was assessed by a semiquantitative food frequency questionnaire. Presence of asthmalike symptoms in the past year was assessed at the child’s age of 36 and 48 months.RESULTS:Relative to no introduction in the first year of life, introduction between age 6 and 12 months was significantly associated with a lower risk of wheezing at 48 months (odds ratio [OR]: 0.64; 95% CI: 0.43–0.94). When compared with introduction between 6 and 12 months, no introduction in the first year and introduction between 0 and 6 months were associated with an increased risk of wheezing at 48 months (OR: 1.57; 95% CI: 1.07–2.31 and OR: 1.53; 95% CI: 1.07–2.19, respectively). The amount of fish at age 14 months was not associated with asthmalike symptoms (P &gt; .15).CONCLUSIONS:Introduction of fish between 6 and 12 months but not fish consumption afterward is associated with a lower prevalence of wheezing. A window of exposure between the age of 6 and 12 months might exist in which fish might be associated with a reduced risk of asthma.
Management of Neonates With Hyperbilirubinemia: Improving Timeliness of Care Using a Clinical Pathway
Authors: Wolff Margaret , Schinasi Dana Aronson , Lavelle Jane , Boorstein Naomi , Zorc Joseph John 
Published: November 2012

BACKGROUND:
Neonatal hyperbilirubinemia is a common reason for neonates to present to the emergency department (ED). Although clinical practice guidelines provide recommendations for evaluation and therapy, few studies have evaluated ways to apply them effectively in the ED setting. The primary objective of this study was to compare time to phototherapy in neonates presenting to the ED with jaundice before and after implementation of a nursing-initiated clinical pathway. Secondary outcomes included time to bilirubin result and ED length of stay in neonates.

METHODS:
We performed a retrospective historical control study comparing neonates presenting to the ED with jaundice during 9-month periods before and after initiation of the pathway. Charts were abstracted for times of assessment and treatment and final disposition.

RESULTS:
Three hundred neonates were included in this study: 149 before and 151 after pathway implementation. Median time to phototherapy (historical control: 128 minutes vs postintervention group: 52 minutes; P &lt; .001), median time to bilirubin result (157 vs 99; P &lt; .001), and median ED length of stay (268 minutes vs 195 minutes; P &lt; .001) were shorter for neonates treated after the implementation of the clinical pathway. No complications were reported during the study period.

CONCLUSIONS:
After implementation of a clinical pathway for the management of neonates with jaundice in the ED, we observed a reduction in time to phototherapy, time to bilirubin measurement, and overall length of stay.
Self-Report of Child Care Directors Regarding Return-to-Care
Authors: Hashikawa Andrew N. , Stevens Martha W. , Juhn Young J. , Nimmer Mark , Copeland Kristen , Simpson Pippa , Brousseau David C. 
Published: November 2012

BACKGROUND:The American Academy of Pediatrics (AAP) introduced revised return-to-care recommendations for mildly ill children in 2009 that were added to national standards in 2011. Child care directors' practices in a state without clear emphasis on return-to-care guidelines are unknown. We investigated director return-to-care practices just before the release of recently revised AAP guidelines.METHODS:A telephone survey with 5 vignettes of mild illness (cold symptoms, conjunctivitis, vomiting/diarrhea, fever, and ringworm) was administered to randomly sampled directors in metropolitan Milwaukee, Wisconsin. Directors were asked about return-to-care criteria for each illness. Questions for return-to-care criteria were open-ended; multiple responses were allowed. Answers were compared with AAP return-to-care recommendations.RESULTS:A total of 305 directors participated. Based on director responses to vignettes, the percentage of correct responses regarding return-to-child care management compared with AAP return-to-care recommendations was low: fever (0%); conjunctivitis (0%); diarrhea (1.6%); cold symptoms (12%); ringworm (21%); and vomiting (80%). Two illnesses (conjunctivitis and cold symptoms) would require the child to have an urgent medical evaluation or treatment not recommended by the AAP, as follows: Conjunctivitis—antibiotics for 24 hours (62%), physician visit (49%), any antibiotic treatment (6%), and symptom resolution (4%); and Cold Symptoms—physician visit (45.6%), antibiotics (10%), and symptom resolution (25%).CONCLUSIONS:Directors’ self-reported return-to-child care practices differed substantially before the release of revised AAP return-to-care recommendations. Active adoption of AAP return-to-child care guidelines would decrease the need for unnecessary urgent medical evaluation and treatment as well as unnecessary exclusion of a child from child care.
Pediatric Providers’ Self-Reported Knowledge, Practices, and Attitudes About Concussion
Authors: Zonfrillo Mark R. , Master Christina L. , Grady Matthew F. , Winston Flaura K. , Callahan James M. , Arbogast Kristy B. 
Published: November 2012

OBJECTIVE:
To determine the self-reported practices and attitudes surrounding concussion diagnosis and management in a single, large pediatric care network.

METHODS:
A cross-sectional survey was distributed to pediatric primary care and emergency medicine providers in a single, large pediatric care network. For all survey participants, practices and attitudes about concussion diagnosis and treatment were queried.

RESULTS:
There were 145 responses from 276 eligible providers, resulting in a 53% response rate, of which 91% (95% confidence interval [CI]: 86%–95%) had cared for at least 1 concussion patient in the previous 3 months. A Likert scale from 1 “not a barrier” to 5 “significant barrier” was used to assess providers’ barriers to educating families about the diagnosis of concussion. Providers selected 4 or 5 on the scale for the following barriers and frequencies: inadequate training to educate 16% (95% CI: 11%–23%), inadequate time to educate 15% (95% CI: 12%–24%), and not my role to educate 1% (95% CI: 0.4%–5%). Ninety-six percent (95% CI: 91%–98%) of providers without a provider decision support tool (such as a clinical pathway or protocol) specific to concussion, and 100% (95% CI: 94%–100%) of providers without discharge instructions specific to concussion believed these resources would be helpful.

CONCLUSIONS:
Although pediatric primary care and emergency medicine providers regularly care for concussion patients, they may not have adequate training or infrastructure to systematically diagnose and manage these patients. Specific provider education, decision support tools, and patient information could help enhance and standardize concussion management.