bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complications of endoscopic sinus surgery in a residency training program
Authors: Kinsella John B. , Calhoun Karen H. , Bradfield Joseph J. , Hokanson John A. , Bailey Byron J. 
Published: October 2006

AbstractEndoscopic sinus surgery (ESS) is now taught in most otolaryngology residency programs in the United States. However, this is techically challenging surgery and concerns exist regarding patient safety early in the surgeon's learning curve. The authors reviewed 193 cases of ESS performed by residents, under faculty supervision at our program, between 1987 and 1992. Sixty‐seven percent of patients underwent bilateral anterior ethmoidectomy, 40% had bilateral total ethmoidectomy, and 44% had bilateral middle turbinate reduction. The overall complication rate was 22% and included one major complication. Synechiae accounted for 50% of minor complications. There was no correlation between middle or inferior turbinate reduction and the formation of synechiae. Posterior ethmoidectomy was not associated with a significant increase in complications. We conclude that ESS can be safely performed by otolaryngology residents in carefully structured and supervised training programs.
Snare uvulopalatoplasty
Authors: Weingarten Charles 
Published: October 2006

AbstractSingle‐stage outpatient treatment of snoring with snare dissection uvulopalatoplasty (UPP) has been developed and found to be safe and effective. Single‐stage snare dissection UPP (SUPP) was performed on 25 habitual loud snorers with readily available instrumentation in an ambulatory setting. Fourteen had associated septoplasty. When only SUPP was performed, local and topical anesthesia and minimal oral premedication were used in most cases. No significant immediate or delayed bleeding occurred. Postoperative discomfort persisted for 3 to 12 days and required only oral analgesics. No postoperative complications occurred. Ninety‐one percent of patients reported satisfactory reduction or elimination of snoring after surgery. Preoperative and postoperative acoustic analysis of sleeping respiration (SNAP testing) was used to document the effects of SUPP in eight patients. SUPP is a safe, cost‐effective method of treating patients with habitual snoring.
Gunshot injuries of the temporal bone
Authors: Haberkamp Thomas J. , Mcfadden Edith , Harvey Steven A. , Khafagy Yasser 
Published: October 2006

AbstractDespite an increasing incidence of gunshot wounds to the temporal bone, there is little in the literature regarding management of survivors of these serious injuries. Twelve patients were treated for such wounds between 1986 and 1994. The most frequent presentations were cranial nerve injury, especially facial paralysis (9 patients), hearing loss (7), vascular injury (4), and vestibular dysfunction (3). Persistent cerebrospinal fluid otorrhea was uncommon (1 patient) in this series. Computed tomography and audiovestibular testing were helpful in evaluating the severity of injury and guiding the surgical approach when necessary. Electroneurography was helpful in evaluating facial nerve function; however, documented disruption of the facial nerve canal in itself was considered an indication for surgical exploration. Other indications for surgical intervention included evidence of dural tear, vascular injury, and severe disruption of the external auditory canal.
Severe laryngomalacia: Surgical indications and results in 115 patients
Authors: Roger G. , Garabedian E.N. , Denoyelle F. , Triglia J.M. 
Published: October 2006

AbstractBetween 1987 and 1993, 115 children were operated on for severe forms of laryngomalacia in two pediatric ear, nose, and throat (ENT) departments. The criteria used to determine the severity of the illness were selected following short hospitalization periods during which the children received both pediatric and ENT checkups. Based on clinical manifestations and/or the results of pH monitoring gastroesophageal reflux was found to be present in 68% of the children in the study. Detailed analysis and endoscopy were used to differentiate the symptoms that were related to laryngomalacia from those that were caused by other conditions, including mixed‐breathing, swallowing, and sucking difficulties.Endoscopic resection of the aryepiglottic folds, with or without the use of a carbon dioxide laser, resulted in rapid improvement of both ventilation and swallowing. The success rate of this simple and effective procedure, which has no inherent morbidity, was 98% in an average follow‐up period of 30 months. Only seven children required an additional similar procedure. The procedure failed in only two children, who needed to be tracheotomized. Given these excellent results, endoscopic resection can be considered an effective technique for the management of severe laryngomalacia.
The X Chromosome in Quantitative Trait Locus Mapping
Authors: Broman Karl W , Sen Śaunak , Owens Sarah E , Manichaikul Ani , Southard-Smith E Michelle , Churchill Gary A 
Published: October 2006

AbstractThe X chromosome requires special treatment in the mapping of quantitative trait loci (QTL). However, most QTL mapping methods, and most computer programs for QTL mapping, have focused exclusively on autosomal loci. We describe a method for appropriate treatment of the X chromosome for QTL mapping in experimental crosses. We address the important issue of formulating the null hypothesis of no linkage appropriately. If the X chromosome is treated like an autosome, a sex difference in the phenotype can lead to spurious linkage on the X chromosome. Further, the number of degrees of freedom for the linkage test may be different for the X chromosome than for autosomes, and so an X chromosome-specific significance threshold is required. To address this issue, we propose a general procedure to obtain chromosome-specific significance thresholds that controls the genomewide false positive rate at the desired level. We apply our methods to data on gut length in a large intercross of mice carrying the Sox10Dom mutation, a model of Hirschsprung disease. We identified QTL contributing to variation in gut length on chromosomes 5 and 18. We found suggestive evidence of linkage to the X chromosome, which would be viewed as strong evidence of linkage if the X chromosome was treated as an autosome. Our methods have been implemented in the package R/qtl.
Association Mapping of Complex Trait Loci With Context-Dependent Effects and Unknown Context Variable
Authors: Sillanpää Mikko J , Bhattacharjee Madhuchhanda 
Published: October 2006

AbstractA novel method for Bayesian analysis of genetic heterogeneity and multilocus association in random population samples is presented. The method is valid for quantitative and binary traits as well as for multiallelic markers. In the method, individuals are stochastically assigned into two etiological groups that can have both their own, and possibly different, subsets of trait-associated (disease-predisposing) loci or alleles. The method is favorable especially in situations when etiological models are stratified by the factors that are unknown or went unmeasured, that is, if genetic heterogeneity is due to, for example, unknown genes × environment or genes × gene interactions. Additionally, a heterogeneity structure for the phenotype does not need to follow the structure of the general population; it can have a distinct selection history. The performance of the method is illustrated with simulated example of genes × environment interaction (quantitative trait with loosely linked markers) and compared to the results of single-group analysis in the presence of missing data. Additionally, example analyses with previously analyzed cystic fibrosis and type 2 diabetes data sets (binary traits with closely linked markers) are presented. The implementation (written in WinBUGS) is freely available for research purposes from http://www.rni.helsinki.fi/∼mjs/.
On the Generalized Poisson Regression Mixture Model for Mapping Quantitative Trait Loci With Count Data
Authors: Cui Yuehua , Kim Dong-Yun , Zhu Jun 
Published: October 2006

AbstractStatistical methods for mapping quantitative trait loci (QTL) have been extensively studied. While most existing methods assume normal distribution of the phenotype, the normality assumption could be easily violated when phenotypes are measured in counts. One natural choice to deal with count traits is to apply the classical Poisson regression model. However, conditional on covariates, the Poisson assumption of mean–variance equality may not be valid when data are potentially under- or overdispersed. In this article, we propose an interval-mapping approach for phenotypes measured in counts. We model the effects of QTL through a generalized Poisson regression model and develop efficient likelihood-based inference procedures. This approach, implemented with the EM algorithm, allows for a genomewide scan for the existence of QTL throughout the entire genome. The performance of the proposed method is evaluated through extensive simulation studies along with comparisons with existing approaches such as the Poisson regression and the generalized estimating equation approach. An application to a rice tiller number data set is given. Our approach provides a standard procedure for mapping QTL involved in the genetic control of complex traits measured in counts.
Selection, Recombination and Demographic History in Drosophila miranda
Authors: Bachtrog Doris , Andolfatto Peter 
Published: October 2006

Abstract
Selection, recombination, and the demographic history of a species can all have profound effects on genomewide patterns of variability. To assess the impact of these forces in the genome of Drosophila miranda, we examine polymorphism and divergence patterns at 62 loci scattered across the genome. In accordance with recent findings in D. melanogaster, we find that noncoding DNA generally evolves more slowly than synonymous sites, that the distribution of polymorphism frequencies in noncoding DNA is significantly skewed toward rare variants relative to synonymous sites, and that long introns evolve significantly slower than short introns or synonymous sites. These observations suggest that most noncoding DNA is functionally constrained and evolving under purifying selection. However, in contrast to findings in the D. melanogaster species group, we find little evidence of adaptive evolution acting on either coding or noncoding sequences in D. miranda. Levels of linkage disequilibrium (LD) in D. miranda are comparable to those observed in D. melanogaster, but vary considerably among chromosomes. These patterns suggest a significantly lower rate of recombination on autosomes, possibly due to the presence of polymorphic autosomal inversions and/or differences in chromosome sizes. All chromosomes show significant departures from the standard neutral model, including too much heterogeneity in synonymous site polymorphism relative to divergence among loci and a general excess of rare synonymous polymorphisms. These departures from neutral equilibrium expectations are discussed in the context of nonequilibrium models of demography and selection.
The Maintenance of Sex in Bacteria Is Ensured by Its Potential to Reload Genes
Authors: Szöllősi Gergely J , Derényi Imre , Vellai Tibor 
Published: October 2006

Abstract
Why sex is maintained in nature is a fundamental question in biology. Natural genetic transformation (NGT) is a sexual process by which bacteria actively take up exogenous DNA and use it to replace homologous chromosomal sequences. As it has been demonstrated, the role of NGT in repairing deleterious mutations under constant selection is insufficient for its survival, and the lack of other viable explanations have left no alternative except that DNA uptake provides nucleotides for food. Here we develop a novel simulation approach for the long-term dynamics of genome organization (involving the loss and acquisition of genes) in a bacterial species consisting of a large number of spatially distinct populations subject to independently fluctuating ecological conditions. Our results show that in the presence of weak interpopulation migration NGT is able to subsist as a mechanism to reload locally lost, intermittently selected genes from the collective gene pool of the species through DNA uptake from migrants. Reloading genes and combining them with those in locally adapted genomes allow individual cells to readapt faster to environmental changes. The machinery of transformation survives under a wide range of model parameters readily encompassing real-world biological conditions. These findings imply that the primary role of NGT is not to serve the cell with food, but to provide homologous sequences for restoring genes that have disappeared from or become degraded in the local population.
Duplication of Centromeric Histone H3 (HTR12) Gene in Arabidopsis halleri and A. lyrata, Plant Species With Multiple Centromeric Satellite Sequences
Authors: Kawabe Akira , Nasuda Shuhei , Charlesworth Deborah 
Published: October 2006

Abstract
Arabidopsis halleri and lyrata have three different major centromeric satellite sequences, a unique finding for a diploid Arabidopsis species. Since centromeric histones coevolve with centromeric satellites, these proteins would be predicted to show signs of selection when new centromere satellites have recently arisen. We isolated centromeric protein genes from A. halleri and lyrata and found that one of them, HTR12 (CENP-A), is duplicated, while CENP-C is not. Phylogenetic analysis indicates that the HTR12 duplication occurred after these species diverged from A. thaliana. Genetic mapping shows that HTR12 copy B has the same genomic location as the A. thaliana gene; the other copy (A, at the other end of the same chromosome) is probably the new copy. To test for selection since the duplication, we surveyed diversity at both HTR12 loci within A. lyrata. Overall, there is no strong evidence for an “evolutionary arms race” causing multiple replacement substitutions. The A. lyrata HTR12B sequences fall into three classes of haplotypes, apparently maintained for a long time, but they all encode the same amino acid sequence. In contrast, HTR12A has low diversity, but many variants are amino acid replacements, possibly due to independent selective sweeps within populations of the species.
roXRNAs Are Required for Increased Expression of X-Linked Genes inDrosophila melanogasterMales
Authors: Deng Xinxian , Meller Victoria H 
Published: October 2006

AbstractThe male-specific lethal (MSL) ribonucleoprotein complex is necessary for equalization of X:A expression levels in Drosophila males, which have a single X chromosome. It binds selectively to the male X chromosome and directs acetylation of histone H4 at lysine 16 (H4Ac16), a modification linked to elevated transcription. roX1 and roX2 noncoding RNAs are essential but redundant components of this complex. Simultaneous removal of both roX RNAs reduces X localization of the MSL proteins and permits their ectopic binding to autosomal sites and the chromocenter. However, the MSL proteins still colocalize, and low levels of H4Ac16 are detected at ectopic sites of MSL binding and residual sites on the X chromosome of roX1− roX2− males. Microarray analysis was performed to reveal the effect of roX1 and roX2 elimination on X-linked and autosomal gene expression. Expression of the X chromosome is decreased by 26% in roX1− roX2−male larvae. Enhanced expression could not be detected at autosomal sites of MSL binding in roX1− roX2− males. These results implicate failure to compensate X-linked genes, rather than inappropriate upregulation of autosomal genes at ectopic sites of MSL binding, as the primary cause of male lethality upon loss of roX RNAs.
An Integrated in Silico Gene Mapping Strategy in Inbred Mice
Authors: Cervino Alessandra C L , Darvasi Ariel , Fallahi Mohammad , Mader Christopher C , Tsinoremas Nicholas F 
Published: October 2006

Abstract
In recent years in silico analysis of common laboratory mice has been introduced and subsequently applied, in slightly different ways, as a methodology for gene mapping. Previously we have demonstrated some limitation of the methodology due to sporadic genetic correlations across the genome. Here, we revisit the three main aspects that affect in silico analysis. First, we report on the use of marker maps: we compared our existing 20,000 SNP map to the newly released 140,000 SNP map. Second, we investigated the effect of varying strain numbers on power to map QTL. Third, we introduced a novel statistical approach: a cladistic analysis, which is well suited for mouse genetics and has increased flexibility over existing in silico approaches. We have found that in our examples of complex traits, in silico analysis by itself does fail to uniquely identify quantitative trait gene (QTG)-containing regions. However, when combined with additional information, it may significantly help to prioritize candidate genes. We therefore recommend using an integrated work flow that uses other genomic information such as linkage regions, regions of shared ancestry, and gene expression information to obtain a list of candidate genes from the genome.
Correlation of mRNA Expression and Protein Abundance Affected by Multiple Sequence Features Related to Translational Efficiency in Desulfovibrio vulgaris: A Quantitative Analysis
Authors: Nie Lei , Wu Gang , Zhang Weiwen 
Published: October 2006

Abstract
The modest correlation between mRNA expression and protein abundance in large-scale data sets is explained in part by experimental challenges, such as technological limitations, and in part by fundamental biological factors in the transcription and translation processes. Among various factors affecting the mRNA–protein correlation, the roles of biological factors related to translation are poorly understood. In this study, using experimental mRNA expression and protein abundance data collected from Desulfovibrio vulgaris by DNA microarray and liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) proteomic analysis, we quantitatively examined the effects of several translational-efficiency-related sequence features on mRNA–protein correlation. Three classes of sequence features were investigated according to different translational stages: (i) initiation, Shine–Dalgarno sequences, start codon identity, and start codon context; (ii) elongation, codon usage and amino acid usage; and (iii) termination, stop codon identity and stop codon context. Surprisingly, although it is widely accepted that translation initiation is the rate-limiting step for translation, our results showed that the mRNA–protein correlation was affected the most by the features at elongation stages, i.e., codon usage and amino acid composition (5.3–15.7% and 5.8–11.9% of the total variation of mRNA–protein correlation, respectively), followed by stop codon context and the Shine–Dalgarno sequence (3.7–5.1% and 1.9–3.8%, respectively). Taken together, all sequence features contributed to 15.2–26.2% of the total variation of mRNA–protein correlation. This study provides the first comprehensive quantitative analysis of the mRNA–protein correlation in bacterial D. vulgaris and adds new insights into the relative importance of various sequence features in prokaryotic protein translation.
Diet and Digestion in Chinese Mud Carp Cirrhinus molitorella Compared with Other Ilyophagous Fishes
Authors: Bowen S. H. , Gu B. , Huang Zhanghan 
Published: October 2006

AbstractIlyophagous fishes, that is, those that feed on soft sediments, are widely distributed throughout temperate and tropical freshwater and estuarine environments. Despite their abundance (they constituted over half of the ichthyomass in some systems), the role of these fishes in ecosystem structure and function has received little attention. In particular, data on diet and digestion in Cirrhinus, a genus abundant through much of Southeast Asia, are yet to be reported. In this study we examined gut contents of Chinese mud carp Cirrhinus molitorella; fish ranged from 16 to 29 cm total length and were collected from five ponds each in Wuchuan and Shunde Counties, Guangdong Province, China. Their diets were made up of sand, mud, and amorphous organic matter. Foregut samples averaged 0.226‐mg ash‐free dry weight (AFDW)/mg dry weight and 0.155 mg total amino acids (AA)/mg AFDW. Assimilation efficiency averaged 0.113 for AFDW and 0.153 for total AA. Compared with that in other ilyophagous fishes, digestion in Chinese mud carp is inefficient. Nonetheless, the ratio of AA (mg) assimilated to total organic matter (mg) assimilated—0.209—is in the range expected to support moderate growth, as has been reported for this species. Review of the literature on ilyophagous fishes reveals four groups characterized by different gut morphologies that each appear to be adapted to the use of relatively indigestible diets. The extremely long, undifferentiated alimentary canal in Chinese mud carp and related species is the simplest of these, and its relative inefficiency may be related to this simple morphology.
New Approaches to the Adjuvant Therapy of Colon Cancer
Authors: Benson Al B. 
Published: October 2006

Learning Objectives
After completing this course, the reader will be able to: Discuss clinical trial and SEER data for patients with stage II colon cancer and describe the impact of adjuvant therapy.Discuss clinical trial data supporting the use of adjuvant therapy for stage III colon cancer, including recent trial results with oxaliplatin and irinotecan.Discuss whether stage II colon cancer patients should receive adjuvant chemotherapy and describe the new clinical trial design that integrates molecular marker data.
Access and take the CME test online and receive 1 AMA PRA Category 1 Credit™ at CME.TheOncologist.com
Growth and Growth Factor Production by Human Nasal Septal Chondrocytes in Serum-Free Media
Authors: Kita Magdalena , Hanasono Matthew M. , Mikulec Anthony A. , Pollard Jeffrey D. , Kadleck James M. , Koch R. James 
Published: October 2006

BackgroundTissue-engineered human cartilage offers vast possibilities as a source of graft implant material for reconstructive surgery. Serum-supplemented growth media is successful in supporting chondrocyte proliferation in vitro. Serum, however, contains exogenous growth factors that hamper the identification and quantification of growth factors autogenously produced by chondrocytes. We explore the possibility of using a commercially available serum-free medium UltraCULTURE as an alternative to modified Webber's medium (MWM), the standard media used in chondrocyte cell culture.MethodsHuman nasal septal chondrocytes were grown in UltraCULTURE containing various concentrations of basic fibroblast growth factor (bFGF; 0, 1, 10, and 100 ng/mL) with or without insulin-like growth factor and compared with chondrocytes grown in MWM. Growth curves and transforming growth factor (TGF) β1 production were analyzed.ResultsWe found no differences in the ability to sustain cell viability in culture between the two base media types. We also found no statistically significant differences in TGF-β1 production by chondrocytes grown in either system. Finally, there were no statistically significant differences in chondrocyte proliferation between cultures supplemented with bFGF at 10 and 100 ng/mL.ConclusionUltraCULTURE media is a cost-effective, serum-free alternative to standard media with compatible growth characteristics. It offers specific advantages over standard serum-containing media for the precise measurement of autogenous growth factor production by cultured chondrocytes. Furthermore, UltraCULTURE's serum-free environment would be ideal for safely producing tissue-engineered cartilage grafts.