bluuebunny/crossref_metadata_2025_split huggingface dataset:
454 sequencing put to the test using the complex genome of barley
Authors: Wicker Thomas , Schlagenhauf Edith , Graner Andreas , Close Timothy J , Keller Beat , Stein Nils 
Published: October 2006

Abstract

Background
During the past decade, Sanger sequencing has been used to completely sequence hundreds of microbial and a few higher eukaryote genomes. In recent years, a number of alternative technologies became available, among them adaptations of the pyrosequencing procedure (i.e. "454 sequencing"), promising a ~100-fold increase in throughput over Sanger technology – an advancement which is needed to make large and complex genomes more amenable to full genome sequencing at affordable costs. Although several studies have demonstrated its potential usefulness for sequencing small and compact microbial genomes, it was unclear how the new technology would perform in large and highly repetitive genomes such as those of wheat or barley.

Results
To study its performance in complex genomes, we used 454 technology to sequence four barley Bacterial Artificial Chromosome (BAC) clones and compared the results to those from ABI-Sanger sequencing. All gene containing regions were covered efficiently and at high quality with 454 sequencing whereas repetitive sequences were more problematic with 454 sequencing than with ABI-Sanger sequencing. 454 sequencing provided a much more even coverage of the BAC clones than ABI-Sanger sequencing, resulting in almost complete assembly of all genic sequences even at only 9 to 10-fold coverage. To obtain highly advanced working draft sequences for the BACs, we developed a strategy to assemble large parts of the BAC sequences by combining comparative genomics, detailed repeat analysis and use of low-quality reads from 454 sequencing. Additionally, we describe an approach of including small numbers of ABI-Sanger sequences to produce hybrid assemblies to partly compensate the short read length of 454 sequences.

Conclusion
Our data indicate that 454 pyrosequencing allows rapid and cost-effective sequencing of the gene-containing portions of large and complex genomes and that its combination with ABI-Sanger sequencing and targeted sequence analysis can result in large regions of high-quality finished genomic sequences.
P5L mutation in Ank results in an increase in extracellular inorganic pyrophosphate during proliferation and nonmineralizing hypertrophy in stably transduced ATDC5 cells
Authors: Zaka Raihana , Stokes David , Dion Arnold S , Kusnierz Anna , Han Fei , Williams Charlene J 
Published: October 2006

AbstractAnk is a multipass transmembrane protein that regulates the cellular transport of inorganic pyrophosphate. In the progressive ankylosis (ank) mouse, a premature termination mutation at glutamic acid 440 results in a phenotype characterized by inappropriate deposition of basic calcium phosphate crystals in skeletal tissues. Mutations in the amino terminus of ANKH, the human homolog of Ank, result in familial calcium pyrophosphate dihydrate deposition disease. It has been hypothesized that these mutations result in a gain-of-function with respect to the elaboration of extracellular inorganic pyrophosphate. To explore this issue in a mineralization-competent system, we stably transduced ATDC5 cells with wild-type Ank as well as with familial chondrocalcinosis-causing Ank mutations. We evaluated the elaboration of inorganic pyrophosphate, the activity of pyrophosphate-modulating enzymes, and the mineralization in the transduced cells. Expression of transduced protein was confirmed by quantitative real-time PCR and by ELISA. Levels of inorganic pyrophosphate were measured, as were the activities of nucleotide pyrophosphatase phosphodiesterase and alkaline phosphatase. We also evaluated the expression of markers of chondrocyte maturation and the nature of the mineralization phase elaborated by transduced cells. The cell line expressing the proline to leucine mutation at position 5 (P5L) consistently displayed higher levels of extracellular inorganic pyrophosphate and higher phosphodiesterase activity than the other transduced lines. During hypertrophy, however, extracellular inorganic pyrophosphate levels were modulated by alkaline phosphatase activity in this cell system, resulting in the deposition of basic calcium phosphate crystals only in all transduced cell lines. Cells overexpressing wild-type Ank displayed a higher level of expression of type X collagen than cells transduced with mutant Ank. Other markers of hypertrophy and terminal differentiation, such as alkaline phosphatase, osteopontin, and runx2, were not significantly different in cells expressing wild-type or mutant Ank in comparison with cells transduced with an empty vector or with untransduced cells. These results suggest that the P5L Ank mutant is capable of demonstrating a gain-of-function with respect to extracellular inorganic pyrophosphate elaboration, but this effect is modified by high levels of expression of alkaline phosphatase in ATDC5 cells during hypertrophy and terminal differentiation, resulting in the deposition of basic calcium phosphate crystals.
Global analysis of mRNA stability in the archaeon Sulfolobus
Authors: Andersson Anders F , Lundgren Magnus , Eriksson Stefan , Rosenlund Magnus , Bernander Rolf , Nilsson Peter 
Published: October 2006

Abstract
Background
Transcript half-lives differ between organisms, and between groups of genes within the same organism. The mechanisms underlying these differences are not clear, nor are the biochemical properties that determine the stability of a transcript. To address these issues, genome-wide mRNA decay studies have been conducted in eukaryotes and bacteria. In contrast, relatively little is known about RNA stability in the third domain of life, Archaea. Here, we present a microarray-based analysis of mRNA half-lives in the hyperthermophilic crenarchaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, constituting the first genome-wide study of RNA decay in archaea.

Results
The two transcriptomes displayed similar half-life distributions, with medians of about five minutes. Growth-related genes, such as those involved in transcription, translation and energy production, were over-represented among unstable transcripts, whereas uncharacterized genes were over-represented among the most stable. Half-life was negatively correlated with transcript abundance and, unlike the situation in other organisms, also negatively correlated with transcript length.

Conclusion
The mRNA half-life distribution of Sulfolobus species is similar to those of much faster growing bacteria, contrasting with the earlier observation that median mRNA half-life is proportional to the minimal length of the cell cycle. Instead, short half-lives may be a general feature of prokaryotic transcriptomes, possibly related to the absence of a nucleus and/or more limited post-transcriptional regulatory mechanisms. The pattern of growth-related transcripts being among the least stable in Sulfolobus may also indicate that the short half-lives reflect a necessity to rapidly reprogram gene expression upon sudden changes in environmental conditions.
Anatomical measurements of the cochlear aqueduct, round window membrane, round window niche, and facial recess.
Authors: Su Wen‐Yang , Marion Mitchell S. , Hinojosa Raul , Matz Gregory J. 
Published: October 2006

AbstractThe otologic surgeon must continue to familiarize himself with the anatomy of the temporal bone. For this purpose, we made precise histologic measurements of the cochlear aqueduct, round window membrane, round window niche, and facial recess. Measurements were taken from a large series of sectioned temporal bones and analyzed according to age. Our results demonstrated a high degree of individual variability in each area measured.
Homograft ossicles in tympanoplasty
Authors: Wehrs Roger E. 
Published: October 2006

AbstractHomograft ossicles have been utilized in reconstructive middle ear surgery since 1964. In the first few years, simple repositioning of the incus was the method used. Due to the shortcomings of this procedure, a sculptured ossicle, the notched incus, was introduced in 1970 and this has gradually evolved into two standardized and reliable prostheses.In 1973 hearing results were published on the first 122 cases. An expanded study in 1977 reported in detail on 361 ears. The current study reports the results of 326 patients operated upon during the 5 year period of 1976 through 1980 and compares them with the previous studies. The overall hearing results are very similar for both series with little change being noted in the failure rate. However, in the successful categories, progress seems to have been made in that a greater percentage of the fair to good results has been shifted to the excellent category.A new concept of ossicular reconstruction is demonstrated with the introduction of the notched incus with high and low profile, to compensate for differences in the stapedial mallear relationship.
Fiber orientation of the facial nerve: An experimental study in the cat
Authors: Gacek Richard R. , Radpour Shokri 
Published: October 2006

AbstractThe Marchi technique and an osmium stain were used to demonstrate the distribution of degenerated motor fibers in the facial nerve and 3 peripheral branches after complete and partial transection of the nerve at the internal auditory meatus. The results in 16 specimens from 10 cats revealed that fibers to all 3 peripheral branches were injured regardless of the section of the facial nerve that was cut. Therefore the motor axons to the peripheral branches are diffusely located throughout the temporal course of the facial nerve.
Malignant histiocytosis showing facial involvement
Authors: Aozasa Katsuyuki , Tokuno Nagao , Ikuno Hiromichi , Mishima Yasuhiko 
Published: October 2006

AbstractIn general, malignant histiocytosis (MH) presents with fever, lymphadenopathy, general fatigue and malaise. Although facial involvement with MH has been mentioned previously, the present report emphasizes the significance and frequency of facial involvement in MH. The patient was a 51‐year‐old woman who presented with fever, general fatigue, diplopia, and numbness on the right side of the face. A roentgenogram of the face showed parasinusitis. Histologic findings of the biopsy from the sinuses showed infiltration by atypical histiocytes. She died two months after onset of symptoms. Autopsy revealed a systemic neoplastic proliferation of atypical histiocytes diagnostic of MH. Facial involvement in MH is discussed with a review of reported cases and our own cases with MH.
Autoimmune hypothesis of acquired subglottic stenosis in premature infants
Authors: Stolovitzky J. Pablo , Todd N. Wendell 
Published: October 2006

AbstractAcquired subglottic stenosis is a devastating additional burden for nearly 4% of premature infants receiving neonatal intensive care. The duration of endotracheal intubation is considered the most important etiologic factor. Surprisingly, most premature infants do not acquire subglottic stenosis. Infants with similar clinical characteristics and care have varying laryngeal outcomes. We hypothesized an autoimmune mechanism to type‐II collagen to explain the varying laryngeal outcomes of these infants.A retrospective study of premature infants of comparable birth weight, gestational age, and duration of endotracheal intubation was conducted. The eight control children, who did not manifest symptoms of airway obstruction, had longer durations of intubation than did the infants who developed subglottic stenosis. Three of five affected infants had serum antibodies to type‐II collagen, in contrast to none of the control infants (P = .035). This finding warrants additional study, and might lead to new diagnostic and therapeutic measures for these patients.
Head and neck sequelae of cardiac transplantation
Authors: Teixido Michael , Kron Thomas K. , Plainse Michael 
Published: October 2006

AbstractCardiac transplantation has become the treatment of choice for end‐stage cardiomyopathies. In 1987, nearly 2000 cardiac transplants were performed in the United States. Otolaryngologists will be asked with increasing frequency to evaluate and treat these patients. The otolaryngology service at Loyola University Medical Center has been involved in the follow‐up and treatment of head and neck complications in 100 transplant patients. Sixty percent of these patients manifest head and neck sequelae. The results of this review are presented.The otolaryngologist should be aware of the special features of this patient population that require modification of the treatment approach, such as 1. the need to avoid the drugs erythromycin, trimethoprim/sulfamethoxazole, and ketoconazole, 2. the need to preserve the right internal jugular vein, and 3. the high risk of silent myocardial infarction. A discussion of these treatment modifications is provided. All patients should be treated in close communication with the medical transplant treatment team.
Asbestos and cancer of the larynx: Is there a relationship?
Authors: Parnes Steven M. 
Published: October 2006

AbstractA head and neck examination was conducted on 322 personnel in a plant that manufactures brake linings and disks where asbestos is a major component. The personnel were categorized according to occupational risk, duration of employment, and smoking and alcohol habits. Thirty‐nine percent had abnormalities, the most common being laryngitis (15%), deviated nasal septum (13%), and neck mass (5.3%). Six members required a biopsy, but no cancer was discovered. Of 47 personnel with laryngitis, 46 were smokers (P<.01). In regard to asbestos exposure, 20% of the high‐risk group had laryngitis, compared to 11% in the low‐risk group (P<.05). The data were compared to a previously prepared longitudinal study of plant personnel (2057 individuals and 37,361.5 person years), where three cases of laryngeal cancer had been observed (0.77 expected). As these cases involved smokers with limited asbestos exposure, neither the longitudinal or cross‐sectional data could support asbestos as an etiologic factor for laryngeal cancer, but it may act as an irritant.
Age‐related changes in the neuromuscular junctions in the human posterior cricoarytenoid muscles: A quantitative study
Authors: Gambino Dean R. , Malmgren Leslie T. , Gacek Richard R. 
Published: October 2006

AbstractThe posterior cricoarytenoid muscle is unique histo‐chemically, ultrastructurally, and functionally. It has been suggested that the posterior cricoarytenoid muscle undergoes early aging. Aging in peripheral nerves has been reported to resemble a “dying back” neuropathy in that the most severe and earliest age‐related changes occur at the most distal levels of the nerve fibers. The lengths and terminal axonal branching of neuromuscular junctions in 17 human posterior cricoarytenoid muscles aged 4 days to 95 years were determined. Both neuromuscular junction lengths and the numbers of axonal terminal branches in the very young group differed significantly from values in two older groups. In contrast to results reported for some other muscles, there was no significant age‐related change in these parameters in the posterior cricoarytenoid muscle during adult life. This difference may be related to the repetitive contraction of the posterior cricoarytenoid muscle.
Production rate and composition of cerumen: Influence of sex and season
Authors: Cipriani C. , Taborelli G. , Gaddia G. , Melagrana A. , Rebora A. 
Published: October 2006

AbstractThe production rate and composition of cerumen have been studied in 11 participants (5 men and 6 women), 25 to 42 years old. The cerumen was obtained in January, May, July, and November to investigate the possible influence of the season. Only the triglyceride content decreased from November to July. Sex was not a factor, which supported the hypothesis that sex hormones play a minor role in the production rate of the lipid component of cerumen.
Interface Direct Shear Testing of Unsaturated Soil
Authors: Miller GA , Hamid TB 
Published: October 2006

Abstract
A commercially available direct shear apparatus was modified for testing unsaturated soil and interfaces between unsaturated soil and stainless steel. Major modifications include the addition of apparatus for suction-controlled testing using the axis translation method, and construction of shear boxes for testing unsaturated soil and interfaces. The major features of the device are described and results of performance tests are presented in this paper. In addition, typical results of tests on unsaturated clayey silt and interfaces are presented for drained tests conducted under different matric suction and net normal stress conditions. The Extended Mohr-Coulomb Failure Envelope for the soil is compared to that obtained for the rough interface. The soil/interface test results demonstrate the successful implementation of the device.
Comparison of Glargine Insulin Versus Rosiglitazone Addition in Poorly Controlled Type 2 Diabetic Patients on Metformin Plus Sulfonylurea
Authors: Triplitt Curtis , Glass Leonard , Miyazaki Yoshiniro , Wajcberg Estela , Gastaldelli Amalia , De Filippis Elena , Cersosimo Eugenio , DeFronzo Ralph A. 
Published: October 2006

OBJECTIVE—We sought to examine the mechanisms by which the addition of glargine insulin or rosiglitazone improves glycemic control in type 2 diabetic subjects poorly controlled on maximally effective doses of metformin plus sulfonylurea.
RESEARCH DESIGN AND METHODS—Subjects (aged 47 ± 11 years, BMI 31 ± 5 kg/m2, HbA1c [A1C] 9.4 ± 1.3%) received bedtime glargine insulin (titrated based on the fasting plasma glucose [FPG], n = 10) or rosiglitazone (4 mg twice daily, n = 10). At baseline and after 4 months, A1C was measured and an oral glucose tolerance test and a 3-h euglycemic insulin (80 mU/m2 per min) clamp with [3-3H]glucose were performed.
RESULTS—A1C and FPG decreased similarly in the glargine insulin (9.1 ± 0.4 to 7.6 ± 0.3% and 212 ± 14 to 139 ± 5 mg/dl, respectively, both P &lt; 0.0001) and rosiglitazone (9.4 ± 0.3 to 7.6 ± 0.4% and 223 ± 14 to 160 ± 19 mg/dl, respectively, both P &lt; 0.005) groups. After 4 months, endogenous glucose production (EGP) declined similarly with glargine insulin (2.27 ± 0.10 to 1.73 ± 0.12 mg · kg−1 · min−1, P &lt; 0.0001) and rosiglitazone (2.21 ± 0.12 to 1.88 ± 0.12 mg · kg−1 · min−1, P = 0.01). The hepatic insulin resistance index declined in the rosiglitazone group (32 ± 3 to 21 ± 1 mg · kg−1 · min−1 × μU/ml, P = 0.03 vs. baseline and P &lt; 0.05 vs. glargine insulin) and did not change in the glargine group (22 ± 5 to 20 ± 3 mg · kg−1 · min−1 × μU/ml, P = NS). At 4 months, glargine insulin (3.6 ± 0.5 to 4.2 ± 0.4 mg · kg−1 · min−1, P &lt; 0.01) and rosiglitazone (2.7 ± 0.3 to 3.8 ± 0.3 mg · kg−1 · min−1, P &lt; 0.0005) increased Rd, but the increment was greater in the rosiglitazone group (P &lt; 0.05). Diastolic blood pressure was reduced only by rosiglitazone (P &lt; 0.01).
CONCLUSIONS—Triple therapy with glargine insulin or rosiglitazone similarly reduced A1C, primarily by suppressing basal EGP (hepatic). Glargine insulin reduced basal EGP by increasing plasma insulin levels, while rosiglitazone decreased basal hepatic glucose production by improving hepatic insulin sensitivity.
Long-Term Efficacy of Metformin Therapy in Nonobese Individuals With Type 2 Diabetes
Authors: Ong Cynthia R. , Molyneaux Lynda M. , Constantino Maria I. , Twigg Stephen M. , Yue Dennis K. 
Published: October 2006

OBJECTIVE—The U.K. Prospective Diabetes Study (UKPDS) has demonstrated that metformin is as effective as sulfonylureas in obese subjects and is associated with less weight gain, fewer hypoglycemic episodes, and better cardiovascular outcomes. It is hence the pharmacological therapy of choice in this subgroup. However, a gap in our present knowledge is the long-term response to metformin in nonobese individuals. In this study, we compared metformin therapy in normal, overweight, and obese individuals with type 2 diabetes.
RESEARCH DESIGN AND METHODS—A database of patients treated at a referral center in Sydney, Australia, were analyzed. Patients with type 2 diabetes and complete HbA1c (A1C) data and treated with metformin or sulfonylurea monotherapy for at least three visits before receiving dual oral therapy were included (n = 644). Analysis by BMI and the type of oral agent was performed. Individuals were categorized as normal, overweight, or obese (BMI &lt;25, 25–29.9, and ≥30 kg/m2, respectively).
RESULTS—There were no differences between the initial, follow-up, and last A1C between the three metformin-treated groups. The duration of successful glycemic control with metformin monotherapy in the normal and overweight individuals and their incidences of diabetes-related complications for the entire duration of follow-up were not inferior to those of the obese individuals. The nonobese patients performed better regardless of the type of oral hypoglycemic agent used.
CONCLUSIONS—We conclude that metformin is at least as efficacious in normal and overweight individuals as it is in those who are obese. Our study provides evidence-based data to support metformin use in nonobese individuals with type 2 diabetes.
Combination of Multiple Genetic Risk Factors Is Synergistically Associated With Carotid Atherosclerosis in Japanese Subjects With Type 2 Diabetes
Authors: Yamasaki Yoshimitsu , Katakami Naoto , Sakamoto Ken’ya , Kaneto Hideaki , Matsuhisa Munehide , Sato Hiroshi , Hori Masatsugu , Haneda Masakazu , Kashiwagi Atsunori , Tanaka Yasushi , Kawamori Ryuzo , Kuno Shin-ichi 
Published: October 2006

OBJECTIVE— Several genetic risk factors, such as single nucleotide polymorphisms (SNPs), in candidate genes have been reported to be responsible for intima-media thickness (IMT), which is one of the surrogate end points of cardiovascular events. However, the synergistic effects of SNPs have not been evaluated in detail.
RESEARCH DESIGN AND METHODS— We measured the average IMT of the common and internal carotid artery in Japanese type 2 diabetic patients (n = 690) (&gt;50 years old) using ultrasonography. We also determined their genotypes regarding 106 SNPs in candidate genes responsible for cardiovascular diseases. Among the 106 SNPs, we selected 40 common (frequency of minor allele ≥10%) SNPs. We compared the average IMT of subjects with and without any pairs of four genotypes selected from the 40 common SNPs.
RESULTS— The combination of methylen-tetrahydrofolate reductase 677 TT genotype and lymphotoxin-α (LTA) 252 GG genotype and that of ACE DD genotype and LTA 252 GG genotype were evaluated as responsible for a statistically significant (P = 2.7 × 10−9 and 3.5 × 10−6, respectively) increase in average IMT (mean [±SD] 1.54 ± 0.60 and 1.43 ± 0.58 mm, respectively) compared with those of the subjects without these combinations (1.04 ± 0.34 and 1.04 ± 0.34 mm, respectively). No single genotype was shown to be responsible for the statistically significant difference in average IMT after Bonferroni’s multiple comparison procedure.
CONCLUSIONS— The present analysis demonstrates an approach to evaluate combinations of multiple genetic risk factors that are synergistically associated with carotid atherosclerosis.