bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-invasive assessment of coronary artery bypass graft patency using 16-slice computed tomography angiography
Authors: Houslay Emma S , Lawton Tristan , Sengupta Anshuman , Uren Neal G , McKillop Graham , Newby David E 
Published: June 2007

Abstract

Background
Invasive coronary angiography is the gold standard means of imaging bypass vessels and carries a small but potentially serious risk of local vascular complications, including myocardial infarction, stroke and death. We evaluated computed tomography as a non-invasive means of assessing graft patency.

Methods
Fifty patients with previous coronary artery bypass surgery who were listed for diagnostic coronary angiography underwent contrast enhanced computed tomography angiography using a 16-slice computed tomography scanner. Images were retrospectively gated to the electrocardiogram and two dimensional axial, multiplanar and three dimensional reconstructions acquired. Sensitivity, specificity, positive and negative predictive value, accuracy and level of agreement for detection of graft patency by multidetector computed tomography.

Results
A total of 116 grafts were suitable for analysis. The specificity of CT for the detection of graft patency was 100%, with a sensitivity of 92.8%, positive predictive value 100%, negative predictive value 85.8% and an accuracy of 94.8%. The kappa value of agreement between the two means of measuring graft patency was 0.9. Mean radiation dose was 9.0 ± 7.2 mSv for coronary angiography and 18.5 ± 4 mSv for computed tomography. Pooled analysis of eight studies, incorporating 932 grafts, confirmed a 97% accuracy for the detection of graft patency by multidetector computed tomography.

Conclusion
Computed tomography is an accurate, rapid and non-invasive method of assessing coronary artery bypass graft patency. However, this was achieved at the expense of an increase in radiation dose.
Genetic flux over time in the Salmonella lineage
Authors: Vernikos Georgios S , Thomson Nicholas R , Parkhill Julian 
Published: June 2007

Abstract
Background
DNA sequences that are shared between closely related organisms while being absent from their common ancestor and from sister lineages of that ancestor are likely to have been acquired by horizontal gene transfer. Over time, the composition of those sequences tends to become more similar to the compositional signature of their host (amelioration).

Results
From a whole-genome comparative analysis of eleven Salmonella, three Escherichia coli and one Shigella strain, we inferred the relative time of insertion of putative horizontally acquired (PHA) genes in three Salmonella strains on different branches of the S. enterica phylogenetic tree. Compositional analysis suggests that most of the PHA genes are still undergoing an amelioration process and shows a clear correlation between time of insertion and the level of amelioration.

Conclusion
The results show that older insertions include almost all functional classes. However, very recent horizontal transfer events in the Salmonella lineage involve primarily prophage elements that are shared only between very recently diverged lineages; despite this, the prophage sequence composition is close to that of the host, indicating that host adaptation, rather than amelioration, is likely to be the source of the compositional similarity. Almost half of the PHA genes were acquired at the base of the Salmonella lineage, whereas nearly three-quarters are shared between most S. enterica subspecies. The numerical distribution of PHA genes in the Salmonella tree topology correlates well with the divergence of the major Salmonella species, highlighting the major impact of horizontal transfer on the evolution of the salmonellae.
Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
Authors: Li Long , Zhu Qianqian , He Xin , Sinha Saurabh , Halfon Marc S 
Published: June 2007

Abstract
Background
Transcriptional cis-regulatory modules (for example, enhancers) play a critical role in regulating gene expression. While many individual regulatory elements have been characterized, they have never been analyzed as a class.

Results
We have performed the first such large-scale study of cis-regulatory modules in order to determine whether they have common properties that might aid in their identification and contribute to our understanding of the mechanisms by which they function. A total of 280 individual, experimentally verified cis-regulatory modules from Drosophila were analyzed for a range of sequence-level and functional properties. We report here that regulatory modules do indeed share common properties, among them an elevated GC content, an increased level of interspecific sequence conservation, and a tendency to be transcribed into RNA. However, we find that dense clustering of transcription factor binding sites, especially homotypic clustering, which is commonly believed to be a general characteristic of regulatory modules, is rather a feature that belongs chiefly to a specific subclass. This has important implications for current computational approaches, many of which are biased toward this subset. We explore two new strategies to assess binding site clustering and gauge their performances with respect to their ability to detect all 280 modules and various functionally coherent subsets.

Conclusion
Our findings demonstrate that cis-regulatory modules share common features that help to define them as a class and that may lead to new insights into mechanisms of gene regulation. However, these properties alone may not be sufficient to reliably distinguish regulatory from non-regulatory sequences. We also demonstrate that there are distinct subclasses of cis-regulatory modules that are more amenable to in silico detection than others and that these differences must be taken into account when attempting genome-wide regulatory element discovery.
Comparison of Francisella tularensis genomes reveals evolutionary events associated with the emergence of human pathogenic strains
Authors: Rohmer Laurence , Fong Christine , Abmayr Simone , Wasnick Michael , Larson Freeman Theodore J , Radey Matthew , Guina Tina , Svensson Kerstin , Hayden Hillary S , Jacobs Michael , Gallagher Larry A , Manoil Colin , Ernst Robert K , Drees Becky , Buckley Danielle , Haugen Eric , Bovee Donald , Zhou Yang , Chang Jean , Levy Ruth , Lim Regina , Gillett Will , Guenthener Don , Kang Allison , Shaffer Scott A , Taylor Greg , Chen Jinzhi , Gallis Byron , D'Argenio David A , Forsman Mats , Olson Maynard V , Goodlett David R , Kaul Rajinder , Miller Samuel I , Brittnacher Mitchell J 
Published: June 2007

Abstract
Background
Francisella tularensis subspecies tularensis and holarctica are pathogenic to humans, whereas the two other subspecies, novicida and mediasiatica, rarely cause disease. To uncover the factors that allow subspecies tularensis and holarctica to be pathogenic to humans, we compared their genome sequences with the genome sequence of Francisella tularensis subspecies novicida U112, which is nonpathogenic to humans.

Results
Comparison of the genomes of human pathogenic Francisella strains with the genome of U112 identifies genes specific to the human pathogenic strains and reveals pseudogenes that previously were unidentified. In addition, this analysis provides a coarse chronology of the evolutionary events that took place during the emergence of the human pathogenic strains. Genomic rearrangements at the level of insertion sequences (IS elements), point mutations, and small indels took place in the human pathogenic strains during and after differentiation from the nonpathogenic strain, resulting in gene inactivation.

Conclusion
The chronology of events suggests a substantial role for genetic drift in the formation of pseudogenes in Francisella genomes. Mutations that occurred early in the evolution, however, might have been fixed in the population either because of evolutionary bottlenecks or because they were pathoadaptive (beneficial in the context of infection). Because the structure of Francisella genomes is similar to that of the genomes of other emerging or highly pathogenic bacteria, this evolutionary scenario may be shared by pathogens from other species.
Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains
Authors: Hogg Justin S , Hu Fen Z , Janto Benjamin , Boissy Robert , Hayes Jay , Keefe Randy , Post J Christopher , Ehrlich Garth D 
Published: June 2007

Abstract
Background
The distributed genome hypothesis (DGH) posits that chronic bacterial pathogens utilize polyclonal infection and reassortment of genic characters to ensure persistence in the face of adaptive host defenses. Studies based on random sequencing of multiple strain libraries suggested that free-living bacterial species possess a supragenome that is much larger than the genome of any single bacterium.

Results
We derived high depth genomic coverage of nine nontypeable Haemophilus influenzae (NTHi) clinical isolates, bringing to 13 the number of sequenced NTHi genomes. Clustering identified 2,786 genes, of which 1,461 were common to all strains, with each of the remaining 1,328 found in a subset of strains; the number of clusters ranged from 1,686 to 1,878 per strain. Genic differences of between 96 and 585 were identified per strain pair. Comparisons of each of the NTHi strains with the Rd strain revealed between 107 and 158 insertions and 100 and 213 deletions per genome. The mean insertion and deletion sizes were 1,356 and 1,020 base-pairs, respectively, with mean maximum insertions and deletions of 26,977 and 37,299 base-pairs. This relatively large number of small rearrangements among strains is in keeping with what is known about the transformation mechanisms in this naturally competent pathogen.

Conclusion
A finite supragenome model was developed to explain the distribution of genes among strains. The model predicts that the NTHi supragenome contains between 4,425 and 6,052 genes with most uncertainty regarding the number of rare genes, those that have a frequency of <0.1 among strains; collectively, these results support the DGH.
Mammography Surveillance and Mortality in Older Breast Cancer Survivors
Authors: Lash Timothy L. , Fox Matthew P. , Buist Diana S.M. , Wei Feifei , Field Terry S. , Frost Floyd J. , Geiger Ann M. , Quinn Virginia P. , Yood Marianne Ulcickas , Silliman Rebecca A. 
Published: June 2007

Purpose There are more than 2,000,000 breast cancer survivors in the United States today. While surveillance for asymptomatic recurrence and second primary is included in consensus recommendations, the effectiveness of this surveillance has not been well characterized. Our purpose is to estimate the effectiveness of surveillance mammography in a cohort of breast cancer survivors with complete ascertainment of surveillance mammograms and negligible losses to follow-up. Patients and Methods We enrolled 1,846 stage I and II breast cancer patients who were at least 65 years old at six integrated health care delivery systems. We used medical record review and existing databases to ascertain patient, tumor, and therapy characteristics, as well as receipt of surveillance mammograms. We linked personal identifiers to the National Death Index to ascertain date and cause of death. We matched four controls to each breast cancer decedent to estimate the association between receipt of surveillance mammogram and breast cancer mortality. Results One hundred seventy-eight women died of breast cancer during 5 years of follow-up. Each additional surveillance mammogram was associated with a 0.69-fold decrease in the odds of breast cancer mortality (95% CI, 0.52 to 0.92). The protective association was strongest among women with stage I disease, those who received mastectomy, and those in the oldest age group. Conclusion Given existing recommendations for post-therapy surveillance, trials to compare surveillance with no surveillance are unlikely. This large observational study provides support for the recommendations, suggesting that receipt of surveillance mammograms reduces the rate of breast cancer mortality in older patients diagnosed with early-stage disease.
Study of Np speciation in citrate medium
Authors: Bonin L. , Den Auwer Christophe , Ansoborlo Eric , Cote Gérard , Moisy Philippe 
Published: June 2007

In the framework of the French Environmental Nuclear Toxicology program, additional experiments related to the decorporation of actinides are planned. Decorporation is the removal or release from target organs (bones, liver, kidney …), tissues or cells of radioactive material previously incorporated in them, using chelating agents or other administrated pharmaceutical agents. The contradictory data on the neptunium complexation behaviour within blood and its transfer to target organs, as well as the inefficiency of therapeutic treatments, led us to study the complexation of this element with biological constituents. Within this purpose, the in vitro behaviour of Np(IV) and Np(V) in simple media simulating biological fluids was studied.
This study was more specifically focused on the behaviour of neptunium with citrate ion, which is an essential component in a number of metalloenzyme active sites. In order to determine the speciation of this system, spectrophotometry was more particularly used. Concerning the complexation phenomenon, the existence of several complexes of Np(V) with various acido-basic forms of the citrate anion was observed; regarding Np(IV), complexes with Cit3- have been observed. From the quantitative study of these equilibria, the values of the absolute constants for the complexation of Np(IV) and Np(V) with citrate were determined.
Concerning the stability of neptunium towards oxydo-reduction, it was confirmed that Np(VI) was very quickly reduced to Np(V) by the citrate anions, whereas Np(IV) was stable. In the case of Np(V), it was observed that, depending on the pH and the citrate concentration, Np(V) was unstable and was reduced to Np(IV). The E–pH diagrams, constructed using the stability constants determined in this study, showed that this instability was due to the Np(V) disproportionation.
Detection and Significance of Serum Protein Marker of Hirschsprung Disease
Authors: Wang Jia-xiang , Qin Pan , Liu Qiu-liang , Yang He-ying , Fan Ying-zhong , Yu Jie-kai , Zheng Shu 
Published: June 2007

OBJECTIVE. The objective of this study was to identify a specific fingerprint chromatogram model of serum proteins for early screening and diagnosis of Hirschsprung disease.
METHODS. To detect the protein mass spectrograms of 78 serum specimens (42 specimens of Hirschsprung disease, 16 specimens of adhesive ileus including appendicitis and Meckel diverticulum after operation and inflammatory bowel disease, and 20 specimens of normal control subjects), we used surface-enhanced laser desorption/ionization time of flight mass spectrometry technology, combined with bioinformatics methods (support vector machine) to develop and compare protein mass spectrograms from serum samples.
RESULTS. We identified 3 protein markers, the mass-to-charge ratio of which is positioned at 3221.7, 5639.2, and 6884.2 from the fingerprint chromatogram model of serum protein for early screening and diagnosis of Hirschsprung disease. The markers had 100% sensitivity and specificity.
CONCLUSION. The fingerprint chromatogram model of serum protein using surface-enhanced laser desorption/ionization time of flight mass spectrometry technology combining support vector machine is a new method of early screening and diagnosis of Hirschsprung disease that is worthy of additional research and application.
Króm(III)-pikolinát vizsgálata a talaj-növény rendszerben
Authors: Szegvári Ildikó , Simon László , Prokisch József 
Published: June 2007

A Cr(III)-pikolinát hatását vizsgáltuk a
takarmányretek
(Raphanus sativus
L. convar.
oleiformis
Pers., cv.
Leveles olajretek) krómfelvételére tenyészedényes kísérletekben. Az első
kísérletben öt (0-0,1-1-10-100 mg·kg
-1
koncentráció), a második
kísérletben két kezelést (1´, ill. 4´10 mg·kg
-1
koncentráció) állítottunk be három
ismétlésben, összesen 21 edényt használva a kísérletekhez. A humuszos
homoktalajban [pH(KCl): 7,48; leiszapolható rész: 13,2 m/m%; humusz: 0,97 m/
m%; szénsavas mész: 2,2 m/m%; T-érték: 6,2 cmol
c
·kg
-1
;
„összes” króm: 10,6 mg·kg
-1
]
nevelt növények kis mennyiségű krómot akkumuláltak gyökerükben (5,98 mg·kg
-1
)
és hajtásukban (1,38 mg·kg
-1
). A talajba közvetlenül kijuttatott
Cr(III)-pikolinát hatására jelentősen megnőtt a takarmányretek hajtásának,
illetve gyökerének krómtartalma. A kisdózisú kezelés hatására (10 mg·kg
-1
)
a gyökérben tízszer, a hajtásban kétszer több króm jelent meg; a nagydózisú
kezelés (100 mg·kg
-1
) egy
nagyságrenddel nagyobb mértékű növekedést mutatott, a gyökérben százötvenszer,
a hajtásban ötvenszer több krómot mértünk. A nagy dózisban (100 mg·kg
-1
)
és a többször kis koncentrációban (4×10 mg·kg
-1
) kijuttatott
Cr(III)-pikolinát közel azonos mértékben növelte meg a króm transzlokációját a
takarmányretek növényben, mindkét kezelésnél a hajtás krómtartalma a teljes
növény krómtartalmához viszonyítva azonos értékűnek adódott (TI = 7). A
többször kijuttatott Cr(III)-pikolinát hatására az egyes növényi szervek
krómtartalma a többszörösére növekedett; a gyökérben háromszor, a hajtásban
hatszor nagyobb krómkoncentráció jelent meg az azonos koncentrációjú, egyszeri
kezeléshez képest. A Cr(III)-pikolinát jelentős mértékben megnövelte a króm
felvételét a talaj-növény rendszerben. Ennek a jelenségnek gyakorlati
jelentősége lehet a krómmal szennyezett talajok növényekkel történő tisztítása
(fitoremediációja), illetve a krómmal dúsított növények előállítása során.
Transport of As in the Soil-Plant System in a Long-term Field Experiment
Authors: Kádár Imre 
Published: June 2007

The first grown deep-rooting crop, maize in 1991 and
sunflower in 1998 did not reveal any yield loss on the contaminated soil. The
crops responding most sensitively to As were peas, winter wheat and winter
barley. In the 4
th
year of the trial the peas practically died out
on the highest As level. The “total” As
(digested with cc. HNO
3
+ cc. H
2
O
2
) amounted
to 70-80% of the As added to the ploughed layer 4 years earlier. The NH
4
-acetate
+ EDTA soluble As fractions revealed great fluctuations during the sampling
time. In the first 4 years the ratio of As detectable in the ploughed layer in
this form ranged between 12 and 30%, while in 2000 between 10 and 13%. On the
basis of deep profile sampling, it was established that As displayed no
significant vertical movement after 10 years, using
the HN
4
-acetate + EDTA method (Lakenen
& Erviö, 1974). The concentration
of As, as a rule of thumb, declined in the direction
from root-shoot-leaves-straw-grain in grain crops. The mobility of As is
limited within the soil-plant system at this site. Even on the heavily loaded
soil, the amount of As in the whole above-ground biomass remained negligible,
usually below 5-10 mg As/kg dry matter. Under such conditions, the remediation
of soil contaminated with higher loads would theoretically take thousands of
years in the case of As via plant uptake. The transfer coefficient,
expressing the total straw/soil As concentration by barley, had a value of 0.02.
As does not seem to be a very dangerous contaminant either to soil, plants or
groundwater. Extreme loads, however, caused phytotoxicity in some crops and
resulted in products unfit for animal or human consumption. Soil life was also
damaged. Higher As loads decreased nodule formation by green peas, and the
endomycorrhizal symbiosis was hindered as well.
Normalization Method for the Detection of Low Level Chromium Contamination in the Soil of the Tisza River Floodplain (Hungary)
Authors: Prokisch József , Kovács B. , Győri Z. , Németh T. , West L. , Harper S. , Adriano D. 
Published: June 2007

A normalization method was tested for the detection
of low level chromium contamination in the soil of the Tisza River Floodplain
in Hungary. The soils' so-called “total” metal concentration (strong acid
extractable fraction) is the basis of many environmental evaluation methods,
soil tests. In the floodplain soils
cadmium, lead, zinc and copper occur in elevated concentrations, but their
chromium concentration is not significantly higher than that of the control
soils. The normalization method makes it
possible to calculate the anthropogenic and geogenic chromium concentration in
soil. Anthropogenic chromium was not detectable on the control sites, but a
significant amount (4-14 mg/kg) was found in the floodplain soil samples. The
applied normalization method proved the low level chromium contamination in the
floodplain.
Synthesis and Patterning of Luminescent CaCO3–Poly(p‐phenylene) Hybrid Materials and Thin Films
Authors: Sindhu S. , Jegadesan S. , Hairong L. , Ajikumar P. K. , Vetrichelvan M. , Valiyaveettil S. 
Published: June 2007

AbstractNature employs specialized macromolecules to produce highly complex structures and understanding the role of these macromolecules allows us to develop novel materials with interesting properties. Herein, we report the role of modified conjugated polymers in the nucleation, growth, and morphology of calcium carbonate (CaCO3) crystals. In situ incorporation of sulfonated poly(p‐phenylene) (s(PPP)) into a highly oriented calcium carbonate matrix is investigated along with the synthesis and patterning of luminescent CaCO3–PPP hybrid materials. Functionalized PPP with polar and nonpolar groups are used as additives in the mineralization medium. The polymer (P1) with polar groups give iso‐oriented calcite crystals, whereas PPP with an additional alkyl chain (P2) results in vaterite crystals. The crystallization mechanism can be explained based on self‐assembly and aggregation of polymers in an aqueous environment. Such light‐emitting hybrid composites with tunable optical properties are excellent candidates for optoelectronics and biological applications.
Isothermal crystallization kinetics and melting behavior of multiwalled carbon nanotubes/polyamide‐6 composites
Authors: Li Juan , Fang Zhengping , Zhu Yan , Tong Lifang , Gu Aijuan , Liu Fu 
Published: June 2007

AbstractPristine and functionalized multiwalled carbon nanotubes (MWNTs) were used to fabricate polyamide 6 (PA6) composites through melt blending. The functionalized MWNTs were obtained by grafting 1,6‐hexamethylenediamine (HMD) onto the pristine MWNTs to improve their compatibility with PA6 matrix. The effect of MWNTs on the isothermal crystallization and melting behavior of PA6 was investigated by differential scanning calorimetry (DSC) and X‐ray diffraction (XRD). The Avrami and Lauritzen–Hoffmann equations are used to describe the isothermal crystallization kinetics. The values of the Avrami exponent found for neat PA6, the pristine MWNTs/PA6 and functionalized MWNTs/PA6 composite samples are about 4.0, 1.7, and 2.3, respectively. The activation energies are determined by the Arrhenius method, which is lower for the composites, −320.52 KJ/mol for pristine MWNTs/PA6 and −293.83 KJ/mol for functionalized MWNTs/PA6, than that for the neat PA6 (−284.71 KJ/mol). The following melting behavior reveals that all the isothermally crystallized samples exhibit triple melting endotherms at lower crystallization temperature and double melting endotherms at higher crystallization temperature. The multiple melting endotherms are mainly caused by the recrystallization of PA6 during heating. The resulting equilibrium melting temperature is lower for the composites than for neat PA6. In addition, polarizing microscopy (PLM) and small angle light scanning (SALS) were used to study the spherulite morphology. The results show that the MWNTs reduce the spherulite radius of PA6. This reduction is more significant for pristine MWNTs. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 2007