bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pharyngeal Entry through the Vallecula
Authors: Wei William I. , Ho W.K. , Ng Raymond W.M. 
Published: December 2003

AbstractThe authors describe a technique of entry into the vallecula with the guide of a small Deaver retractor inserted transorally, beyond the tongue base, into the vallecula. The tip of the Deaver directs the surgeon to the pharyngotomy site and allows pharyngeal entry and access without damaging structures in the region. This technique is particularly useful in total laryngectomy with or without pharyngectomy and is applicable whenever entry to the pharynx through the vallecula is indicated.
The
trp
RNA-Binding Attenuation Protein of
Bacillus subtilis
Regulates Translation of the Tryptophan Transport Gene
trpP
(
yhaG
) by Blocking Ribosome Binding
Authors: Yakhnin Helen , Zhang Hong , Yakhnin Alexander V. , Babitzke Paul 
Published: December 2003

ABSTRACT

Expression of the
Bacillus subtilis
tryptophan biosynthetic genes (
trpEDCFBA
and
pabA
[
trpG
]) is regulated in response to tryptophan by TRAP, the
trp
RNA-binding attenuation protein. TRAP-mediated regulation of the tryptophan biosynthetic genes includes a transcription attenuation and two distinct translation control mechanisms. TRAP also regulates translation of
trpP
(
yhaG
), a single-gene operon that encodes a putative tryptophan transporter. Its translation initiation region contains triplet repeats typical of TRAP-regulated mRNAs. We found that regulation of
trpP
and
pabA
is unaltered in a
rho
mutant strain. Results from filter binding and gel mobility shift assays demonstrated that TRAP binds specifically to a segment of the
trpP
transcript that includes the untranslated leader and translation initiation region. While the affinities of TRAP for the
trpP
and
pabA
transcripts are similar, TRAP-mediated translation control of
trpP
is much more extensive than for
pabA
. RNA footprinting revealed that the
trpP
TRAP binding site consists of nine triplet repeats (five GAG, three UAG, and one AAG) that surround and overlap the
trpP
Shine-Dalgarno (S-D) sequence and translation start codon. Results from toeprint and RNA-directed cell-free translation experiments indicated that tryptophan-activated TRAP inhibits TrpP synthesis by preventing binding of a 30S ribosomal subunit. Taken together, our results establish that TRAP regulates translation of
trpP
by blocking ribosome binding. Thus, TRAP coordinately regulates tryptophan synthesis and transport by three distinct mechanisms: attenuation transcription of the
trpEDCFBA
operon, promoting formation of the
trpE
S-D blocking hairpin, and blocking ribosome binding to the
pabA
and
trpP
transcripts.
Molecular and Functional Characterization of a Unique Sucrose Hydrolase from
Xanthomonas axonopodis
pv. glycines
Authors: Kim Hong-Suk , Park Hyoung-Joon , Heu Sunggi , Jung Jin 
Published: December 2003

ABSTRACT

A novel sucrose hydrolase (SUH) from
Xanthomonas axonopodis
pv. glycines, a causative agent of bacterial pustule disease on soybeans, was studied at the functional and molecular levels. SUH was shown to act rather specifically on sucrose (

K
m

= 2.5 mM) but not on sucrose-6-phosphate. Protein analysis of purified SUH revealed that, in this monomeric enzyme with an estimated molecular mass of 70,223 ± 12 Da, amino acid sequences determined for several segments have corresponding nucleotide sequences in
XAC3490
, a protein-coding gene found in the genome of
X. axonopodis
pv. citri. Based on this information, the SUH gene, consisting of an open reading frame of 1,935 bp, was cloned by screening a genomic library of
X. axonopodis
pv. glycines 8ra. Database searches and sequence comparison revealed that SUH has significant homology to some family 13 enzymes, with all of the crucial invariant residues involved in the catalytic mechanism conserved, but it shows no similarity to known invertases belonging to family 32.
suh
expression in
X. axonopodis
pv. glycines requires sucrose induction, and insertional mutagenesis resulted in an absence of sucrose-inducible sucrose hydrolase activity in crude protein extracts and a sucrose-negative phenotype. Recombinant SUH, overproduced in
Escherichia coli
and purified, was shown to have the same enzymatic characteristics in terms of kinetic parameters.
Comparative Genomics of
Rickettsia prowazekii
Madrid E and Breinl Strains
Authors: Ge Hong , Chuang Yao-Yu Eric , Zhao Shuping , Tong Min , Tsai Mong-Hsun , Temenak Joseph J. , Richards Allen L. , Ching Wei-Mei 
Published: December 2003

ABSTRACT

Rickettsia prowazekii
, the causative agent of epidemic typhus, has been responsible for millions of human deaths. Madrid E is an attenuated strain of
R. prowazekii
, while Breinl is a virulent strain. The genomic DNA sequence of Madrid E has recently been published. To study the genomic variations between Madrid E (reference) and Breinl (test) DNAs, cohybridization experiments were performed on a DNA microarray containing all 834 protein-coding genes of Madrid E. Of the 834 genes assessed, 24 genes showed 1.5- to 2.0-fold increases in hybridization signals in Breinl DNA compared to Madrid E DNA, indicating the presence of genomic variations in ∼3% of the total genes. Eighteen of these 24 genes are predicted to be involved in different functions. Southern blot analysis of five genes,
virB4
,
ftsK
,
rfbE
,
lpxA
, and
rpoH
, suggested the presence of an additional paralog(s) in Breinl, which might be related to the observed increase in hybridization signals. Studies by real-time reverse transcription-PCR revealed an increase in expression of the above-mentioned five genes and five other genes. In addition to the elevated hybridization signals of 24 genes observed in the Breinl strain, one gene (
rp084
) showed only 1/10 the hybridization signal of Madrid E. Further analysis of this gene by PCR and sequencing revealed a large deletion flanking the whole
rp084
gene and part of the
rp083
gene in the virulent Breinl strain. The results of this first rickettsial DNA microarray may provide some important information for the elucidation of pathogenic mechanisms of
R. prowazekii
.
Cloning and Characterization of Acetohydroxyacid Synthase from
Bacillus stearothermophilus
Authors: Porat Iris , Vinogradov Michael , Vyazmensky Maria , Lu Chung-Dar , Chipman David M. , Abdelal Ahmed T. , Barak Ze'ev 
Published: December 2003

ABSTRACT

Five genes from the
ilv-leu
operon from
Bacillus stearothermophilus
have been sequenced. Acetohydroxyacid synthase (AHAS) and its subunits were separately cloned, purified, and characterized. This thermophilic enzyme resembles AHAS III of
Escherichia coli
, and regulatory subunits of AHAS III complement the catalytic subunit of the AHAS of
B. stearothermophilus
, suggesting that AHAS III is functionally and evolutionally related to the single AHAS of gram-positive bacteria.
THE STABILIZING EFFECT OF POSTERIOR FIXATIONS IN A DESTABILIZED ATLANTOAXIAL COMPLEX MODEL IN CANINES
Authors: Chang Ching-Hong , Lee E-Jian , Chang Guan-Liang , Chang Jia-Hao , Hung Yu-Chang , Lee Ming-Yang 
Published: December 2003

Purpose: This study was conducted to evaluate the kinematic responses and the restorative effectiveness of three posterior fixations in a canine atlantoaxial ( C1-2) complex model.Methods: Nine canine ligamentous C1-2complexes were non-destructively tested in an intact condition, after ligamentous destabilization, and after bilateral stabilization with each of three posterior fixation methods: (1) Halifax inter-laminar clamps; (2) sub-laminar wiring; and (3) individual fixation of the C1lateral mass and the C2pedicle with screws and plates. Specimens were subjected to a relevantly applied loads through a loading frame rigidly attached to the C1. Two sets of three markers was separately attached to the mounting jigs of the C1and the C2to record the spatial locations after each loading step with a Vicron 370 system. The load-deformation data were analyzed.Results: Under a realistic loading paradigm, destabilized canine C1-2complex had 3-dimensional motion ranges highly consistent with the corresponding values observed in destabilized cadaveric human C1-2complex following a non-destructive loading paradigm. All the three posterior fixations significantly restricted the motion range of axial rotation loads (P<0.05). However, fixation either with posterior inter-articular screws and plates or inter-laminar clamps also effectively restricted the motion ranges of flexion/extension and lateral bending loads, whereas posterior wiring did not.Conclusion: We described a destabilized canine C1-2complex model. Under a realistic loading paradigm, the model had kinematic analogue of destabilized human C1-2complex. Our results indicated that posterior stabilization using inter-articular fixation techniques or inter-laminar clamps could effectively restrict hypermotility caused by C1-2ligamentous destabilization, and, therefore, appeared to be reliable fixation methods. In contrast, posterior wiring alone would preserve more residual motions, and, thus, might need other adjunctive fixations to offer an optimal condition for solid bony fusion.
Genomic regions linked to alcohol consumption in the Framingham Heart Study
Authors: Bergen Andrew W , Yang Xiaohong Rose , Bai Yan , Beerman Michael B , Goldstein Alisa M , Goldin Lynn R 
Published: December 2003

Abstract
Background
Pedigree, demographic, square-root transformed maximum alcohol (SRMAXAPD) and maximum cigarette (MAXCPD) consumption, and genome-wide scan data from the Framingham Heart Study (FHS) were used to investigate genetic factors that may affect alcohol and cigarette consumption in this population-based sample.

Results
A significant sister:sister correlation greater than spouse correlation was observed for MAXCPD only. Single-point sib-pair regression analysis provided nominal evidence for linkage of loci to both SRMAXAPD and MAXCPD consumption traits, with more significant evidence of linkage to SRMAXAPD than to MAXCPD. One genomic region, chr9q21.11, exhibits significant multi-point sib-pair regression to SRMAXAPD.

Conclusion
SRMAXAPD exhibits greater evidence for genetic linkage than does MAXCPD in the FHS sample. Four regions of the genome exhibiting nominal evidence for linkage to SRMAXAPD in the FHS sample correspond to regions of the genome previously identified as linked to alcoholism or related traits in the family data set ascertained on individuals affected with alcohol dependence known as COGA.
Multiple genome-wide analyses of smoking behavior in the Framingham Heart Study
Authors: Goode Ellen L , Badzioch Michael D , Kim Helen , Gagnon France , Rozek Laura S , Edwards Karen L , Jarvik Gail P 
Published: December 2003

Abstract
Background
Cigarette smoking behavior may have a genetic basis. We assessed evidence for quantitative trait loci (QTLs) affecting the maximum number of cigarettes smoked per day, a trait meant to quantify this behavior, using data collected over 40 years as part of the Framingham Heart Study's original and offspring cohorts.

Results
Heritability was estimated to be approximately 21% using variance components (VC) methods (SOLAR), while oligogenic linkage and segregation analysis based on Bayesian Markov chain Monte Carlo (MCMC) methods (LOKI) estimated a mean of two large QTLs contributing approximately 28% and 20%, respectively, to the trait's variance. Genome-wide parametric (FASTLINK) and VC linkage analyses (SOLAR) revealed several LOD scores greater than 1.0, with peak LOD scores using both methods on chromosomes 2, 17, and 20; multi-point MCMC methods followed up on these chromosomes. The most robust linkage results were for a QTL between 65 and 84 cM on chromosome 20 with signals from multiple sex- and age-adjusted analyses including two-point LOD scores of 1.30 (parametric) and 1.07 (heritability = 0.17, VC) at 70.51 cM, a multi-point LOD score of 1.50 (heritability = 0.20, VC) at 84 cM, and an intensity ratio of 12.0 (MCMC) at 65 cM.

Conclusion
Familial aggregation of the maximum number of cigarettes smoked per day was consistent with a genetic component to this behavior, and oligogenic segregation analyses using MCMC suggested two important QTLs. Linkage signals on chromosome 20 between 65 and 84 cM were seen using multiple analytical methods. No linkage result, however, met genome-wide statistical significance criteria, and the true relationship between these regions and smoking behavior remains unclear.
Mapping susceptibility loci for alcohol consumption using number of grams of alcohol consumed per day as a phenotype measure
Authors: Ma Jennie Z , Zhang Dong , Dupont Randolph T , Dockter Michael , Elston Robert C , Li Ming D 
Published: December 2003

Abstract
Background
There is substantial evidence for a significant genetic component to the risk for alcoholism. However, susceptibility loci or genes for alcohol dependence remain largely unknown. To identify susceptibility loci for alcohol dependence, we selected 329 extended families from the Framingham Heart Study population in which at least one family member reported alcohol consumption during the interview in 1970–1971, and performed genome-wide linkage analyses using various analytical methods.

Results
Multi-point sib-pair regression analysis using the SIBPAL program of S.A.G.E. provided strong evidence for linkage of alcohol dependence to chromosomes 9 (p-value < 0.0001) and weak evidence to chromosomes 15 and 16 (p-value < 0.005). To confirm these findings, we re-analyzed the same data set by various methods implemented in GENEHUNTER and found that only one region was significant with a LOD score > 2.0 by the variance-component method. This region is located on chromosome 9 between markers GATA21F05 and GATA81C04.

Conclusion
Analyses of the Framingham Heart Study population provided evidence of genetic susceptibility loci for alcohol dependence on chromosomes 9, 15, and 16. The genomic region identified on chromosome 9 was particularly interesting because the region has also been previously reported to be linked to alcohol dependence in the American Indian population by another group.
Are there mappable genes for family resemblance for the magnitude of intra-individual variation in systolic blood pressure?
Authors: Lin Jennifer , Hinrichs Anthony , Suarez Brian K 
Published: December 2003

Abstract
Background
The genetic regulation of variation in intra-individual fluctuations in systolic blood pressure over time is poorly understood. Analysis of the magnitude of the average fluctuation of a person's systolic blood pressure around his or her age-adjusted trend line, however, shows moderate, albeit significant, family resemblance in Cohort 1 of the Framingham Heart Study. To determine whether genomic regions affecting this phenotype could be identified, we pursued a "model-free" multipoint quantitative linkage analysis.

Results
Two different linkage methods revealed multiple nominally significant signals, two to four of which are "replicated" in Cohort 2. When both cohorts are assembled into extended pedigrees, three linkage signals remain nominally significant by one or both methods.

Conclusion
Any or all of the genomic regions in the vicinity of D5S1456, D11S2359, and D20S470 may contain elements that regulate systolic blood pressure homeostasis.
The genetics of cross-sectional and longitudinal body mass index
Authors: Strug Lisa , Sun Lei , Corey Mary 
Published: December 2003

AbstractThere has been a lack of consistency in detecting chromosomal loci that are linked to obesity-related traits. This may be due, in part, to the phenotype definition. Many studies use a one-time, single measurement as a phenotype while one's weight often fluctuates considerably throughout adulthood. Longitudinal data from the Framingham Heart Study were used to derive alternative phenotypes that may lead to more consistent findings. Body mass index (BMI), a measurement for obesity, is known to increase with age and then plateau or decline slightly; the decline phase may represent a threshold or survivor effect. We propose to use the weight gain phase of BMI to derive phenotypes useful for linkage analysis of obesity. Two phenotypes considered in the present study are the average of and the slope of the BMI measurements in the gain phase (gain mean and gain slope). For comparison, we also considered the average of all BMI measurements available (overall mean). Linkage analysis using the gain mean phenotype exhibited two markers with LOD scores greater than 3, with the largest score of 3.52 on chromosome 4 at ATA2A03. In contrast, no LOD scores greater than 3 were observed when overall mean was used. The gain slope produced weak evidence for linkage on chromosome 4 with a multipoint LOD score of 1.77 at GATA8A05. Our analysis shows how omitting the decline phase of BMI in the definition of obesity phenotypes can result in evidence for linkage which might have been otherwise overlooked.
Empirically derived phenotypic subgroups – qualitative and quantitative trait analyses
Authors: Wilcox Marsha A , Wyszynski Diego F , Panhuysen Carolien I , Ma Qianli , Yip Agustin , Farrell John , Farrer Lindsay A 
Published: December 2003

Abstract
Background
The Framingham Heart Study has contributed a great deal to advances in medicine. Most of the phenotypes investigated have been univariate traits (quantitative or qualitative). The aims of this study are to derive multivariate traits by identifying homogeneous groups of people and assigning both qualitative and quantitative trait scores; to assess the heritability of the derived traits; and to conduct both qualitative and quantitative linkage analysis on one of the heritable traits.

Methods
Multiple correspondence analysis, a nonparametric analogue of principal components analysis, was used for data reduction. Two-stage clustering, using both k-means and agglomerative hierarchical clustering, was used to cluster individuals based upon axes (factor) scores obtained from the data reduction. Probability of cluster membership was calculated using binary logistic regression. Heritability was calculated using SOLAR, which was also used for the quantitative trait analysis. GENEHUNTER-PLUS was used for the qualitative trait analysis.

Results
We found four phenotypically distinct groups. Membership in the smallest group was heritable (38%, p < 1 × 10-6) and had characteristics consistent with atherogenic dyslipidemia. We found both qualitative and quantitative LOD scores above 3 on chromosomes 11 and 14 (11q13, 14q23, 14q31). There were two Kong & Cox LOD scores above 1.0 on chromosome 6 (6p21) and chromosome 11 (11q23).

Conclusion
This approach may be useful for the identification of genetic heterogeneity in complex phenotypes by clarifying the phenotype definition prior to linkage analysis. Some of our findings are in regions linked to elements of atherogenic dyslipidemia and related diagnoses, some may be novel, or may be false positives.
Power of maximum HLOD tests to detect linkage to obesity genes
Authors: Yoo Yun Joo , Huo Yanling , Ning Yuming , Gordon Derek , Finch Stephen , Mendell Nancy R 
Published: December 2003

Abstract
Background
We investigate the power of heterogeneity LOD test to detect linkage when a trait is determined by several major genes using Genetic Analysis Workshop 13 simulated data. We consider three traits, two of which are disease-causing traits: 1) the rate of change in body mass index (BMI); and 2) the maximum BMI; and 3) the disease itself (hypertension). Of interest is the power of "HLOD2", the maximum heterogeneity LOD obtained upon maximizing over the two genetic models.

Results
Using a trait phenotype Obesity Slope, we observe that the power to detect the two markers closest to the two genes (S1, S2) at the 0.05 level using HLOD2 is 13% and 10%. The power of HLOD2 for Max BMI phenotype is 12% and 9%. The corresponding values for the Hypertension phenotype are 8% and 6%.

Conclusion
The power to detect linkage to the slope genes is quite low. But the power using disease-related traits as a phenotype is greater than the power using the disease (hypertension) phenotype.
Comparison of longitudinal variance components and regression-based approaches for linkage detection on chromosome 17 for systolic blood pressure
Authors: Andrade Mariza de , Olswold Curtis 
Published: December 2003

AbstractWe compare two methods to detect genetic linkage by using serial observations of systolic blood pressure in pedigree data from the Framingham Heart Study focusing on chromosome 17. The first method is a variance components (VC) approach that incorporates longitudinal pedigree data, and the second method is a regression-based approach that summarizes all longitudinal measures in one single measure. No evidence of linkage was found either using the VC longitudinal approach or the regression-based approach, except when all time points were used from Cohorts 1 and 2 and only subjects aged 25 and 75 years were included.
Multilevel modeling for the analysis of longitudinal blood pressure data in the Framingham Heart Study pedigrees
Authors: Briollais Laurent , Tzontcheva Anjela , Bull Shelley 
Published: December 2003

Abstract
Background
The data arising from a longitudinal familial study have a complex correlation structure that cannot be modeled using classical methods for the analysis of familial data at a single time point.

Methods
To fit the longitudinal systolic blood pressure (SBP) pedigree data arising from the Framingham Heart Study, we proposed to use multilevel modeling. That approach was used to distinguish multiple levels of information with individual repeated measurements (Level 1) being made within individuals (Level 2), and individuals clustered within pedigrees (Level 3). Residuals from the subject-specific and pedigree-specific regression models were summed both for the mean SBP and slope of SBP change over time, in order to define two new outcomes that were then used in a genome-wide linkage analysis.

Results
Evidence for linkage for the two outcomes (mean SBP and slope) was found in several chromosomal regions with a maximum LOD score of 3.6 on chromosome 8 and 3.5 on chromosome 17 for the mean SBP, and 2.5 on chromosome 1 for SBP slope. However, the linkage on chromosome 8 was only detected when the sample was restricted to subjects between age 25 and 75 and with at least four exams (Cohort 1) or 3 exams (Cohort 2).

Discussion
Multilevel modeling is a powerful approach to detect genes involved in complex traits when longitudinal data are available. It allows for complex hierarchical data structure to be taken into account and therefore, a better partitioning of random within-individual variation from other sources of variability (genetic or nongenetic).