bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrostatic origin of the genome packing in viruses
Authors: Belyi Vladimir A. , Muthukumar M.
Published: November 2006

Many ssRNA/ssDNA viruses bind their genome by highly basic semiflexible peptide arms of capsid proteins. Here, we show that nonspecific electrostatic interactions control both the length of the genome and genome conformations. Analysis of available experimental data shows that the genome length is linear in the net charge on the capsid peptide arms, irrespective of the actual amino acid sequence, with a proportionality coefficient of 1.61 ± 0.03. This ratio is conserved across all ssRNA/ssDNA viruses with highly basic peptide arms, and is different from the one-to-one charge balance expected of specific binding. Genomic nucleotides are predicted to occupy a radially symmetric spherical shell detached from the viral capsid, in agreement with experimental data.
Analysis of oncogenic signaling networks in glioblastoma identifies
ASPM
as a molecular target
Authors: Horvath S. , Zhang B. , Carlson M. , Lu K. V. , Zhu S. , Felciano R. M. , Laurance M. F. , Zhao W. , Qi S. , Chen Z. , Lee Y. , Scheck A. C. , Liau L. M. , Wu H. , Geschwind D. H. , Febbo P. G. , Kornblum H. I. , Cloughesy T. F. , Nelson S. F. , Mischel P. S.
Published: November 2006

Glioblastoma is the most common primary malignant brain tumor of adults and one of the most lethal of all cancers. Patients with this disease have a median survival of 15 months from the time of diagnosis despite surgery, radiation, and chemotherapy. New treatment approaches are needed. Recent works suggest that glioblastoma patients may benefit from molecularly targeted therapies. Here, we address the compelling need for identification of new molecular targets. Leveraging global gene expression data from two independent sets of clinical tumor samples (
n
= 55 and
n
= 65), we identify a gene coexpression module in glioblastoma that is also present in breast cancer and significantly overlaps with the “metasignature” for undifferentiated cancer. Studies in an isogenic model system demonstrate that this module is downstream of the mutant epidermal growth factor receptor, EGFRvIII, and that it can be inhibited by the epidermal growth factor receptor tyrosine kinase inhibitor Erlotinib. We identify
ASPM
(abnormal spindle-like microcephaly associated) as a key gene within this module and demonstrate its overexpression in glioblastoma relative to normal brain (or body tissues). Finally, we show that
ASPM
inhibition by siRNA-mediated knockdown inhibits tumor cell proliferation and neural stem cell proliferation, supporting
ASPM
as a potential molecular target in glioblastoma. Our weighted gene coexpression network analysis provides a blueprint for leveraging genomic data to identify key control networks and molecular targets for glioblastoma, and the principle eluted from our work can be applied to other cancers.
Life-history evolution under a production constraint
Authors: Brown James H. , Sibly Richard M.
Published: November 2006

The recently formulated metabolic theory of ecology has profound implications for the evolution of life histories. Metabolic rate constrains the scaling of production with body mass, so that larger organisms have lower rates of production on a mass-specific basis than smaller ones. Here, we explore the implications of this constraint for life-history evolution. We show that for a range of very simple life histories, Darwinian fitness is equal to birth rate minus death rate. So, natural selection maximizes birth and production rates and minimizes death rates. This implies that decreased body size will generally be favored because it increases production, so long as mortality is unaffected. Alternatively, increased body size will be favored only if it decreases mortality or enhances reproductive success sufficiently to override the preexisting production constraint. Adaptations that may favor evolution of larger size include niche shifts that decrease mortality by escaping predation or that increase fecundity by exploiting new abundant food sources. These principles can be generalized to better understand the intimate relationship between the genetic currency of evolution and the metabolic currency of ecology.
Combinatorial biosynthesis of novel antibiotics related to daptomycin
Authors: Nguyen Kien T. , Ritz Daniel , Gu Jian-Qiao , Alexander Dylan , Chu Min , Miao Vivian , Brian Paul , Baltz Richard H.
Published: November 2006

Daptomycin, a cyclic lipopeptide produced by
Streptomyces roseosporus
, is the active ingredient of Cubicin (daptomycin-for-injection), a first-in-class antibiotic approved for treatment of skin and skin-structure infections caused by Gram-positive pathogens and bacteremia and endocarditis caused by
Staphylococcus aureus
, including methicillin-resistant strains. Genetic engineering of the nonribosomal peptide synthetase (NRPS) in the daptomycin biosynthetic pathway was exploited for the biosynthesis of novel active antibiotics. λ-Red-mediated recombination was used to exchange single or multiple modules in the DptBC subunit of the NRPS to modify the daptomycin cyclic peptide core. We combined module exchanges, NRPS subunit exchanges, inactivation of the tailoring enzyme glutamic acid 3-methyltransferase, and natural variations of the lipid tail to generate a library of novel lipopeptides, some of which were as active as daptomycin against Gram-positive bacteria. One compound was more potent against an
Escherichia coli imp
mutant that has increased outer membrane permeability. This study established a robust combinatorial biosynthesis platform to produce novel peptide antibiotics in sufficient quantities for antimicrobial screening and drug development.
Application of a simple likelihood ratio approximant to protein sequence classification
Authors: Kaján László , Kertész-Farkas Attila , Franklin Dino , Ivanova Neli , Kocsor András , Pongor Sándor
Published: November 2006

Motivation: Likelihood ratio approximants (LRA) have been widely used for model comparison in statistics. The present study was undertaken in order to explore their utility as a scoring (ranking) function in the classification of protein sequences.

Results: We used a simple LRA-based on the maximal similarity (or minimal distance) scores of the two top ranking sequence classes. The scoring methods (Smith–Waterman, BLAST, local alignment kernel and compression based distances) were compared on datasets designed to test sequence similarities between proteins distantly related in terms of structure or evolution. It was found that LRA-based scoring can significantly outperform simple scoring methods.

Contact:  pongor@icgeb.org.

Supplementary information:  .
ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes
Authors: Loots Gabriela , Ovcharenko Ivan
Published: November 2006

Motivation: Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes, entitled ECRbase, which is constructed from a collection of whole-genome alignments produced by the ECR Browser. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish and fugu genomes. It is freely accessible at .

Contact:  ovcharenko1@llnl.gov

Supplementary information: Supplementary Data are available at Bioinformatics online.
Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes
Authors: Barker Daniel , Meade Andrew , Pagel Mark
Published: November 2006

Motivation: We compare phylogenetic approaches for inferring functional gene links. The approaches detect independent instances of the correlated gain and loss of pairs of genes from species' genomes. We investigate the effect on results of basing evidence of correlations on two phylogenetic approaches, Dollo parsminony and maximum likelihood (ML). We further examine the effect of constraining the ML model by fixing the rate of gene gain at a low value, rather than estimating it from the data.

Results: We detect correlated evolution among a test set of pairs of yeast (Saccharomyces cerevisiae) genes, with a case study of 21 eukaryotic genomes and test data derived from known yeast protein complexes. If the rate at which genes are gained is constrained to be low, ML achieves by far the best results at detecting known functional links. The model then has fewer parameters but it is more realistic by preventing genes from being gained more than once.

Availability: BayesTraits by M. Pagel and A. Meade, and a script to configure and repeatedly launch it by D. Barker and M. Pagel, are available at

Contact:  m.pagel@rdg.ac.uk

Supplementary information: Supplementary Data are available at Bioinformatics online.
An RNA conformational shift in recent H5N1 influenza A viruses
Authors: Gultyaev Alexander P. , Heus Hans A. , Olsthoorn René C. L.
Published: November 2006

Recent outbreaks of avian influenza are being caused by unusually virulent H5N1 strains. It is unknown what makes these recent H5N1 strains more aggressive than previously circulating strains. Here, we have compared more than 3000 RNA sequences of segment 8 of type A influenza viruses and found a unique single nucleotide substitution typically associated with recent H5N1 strains. By phylogenetic analysis, biochemical and biophysical experiments, we demonstrate that this substitution dramatically affects the equilibrium between a hairpin and a pseudoknot conformation near the 3′ splice-site of the NS gene. This conformational shift may have consequences for splicing regulation of segment 8 mRNA. Our data suggest that besides changes at the protein level, changes in RNA secondary structure should be seriously considered when attempting to explain influenza virus evolution.

Contact:  olsthoor@chem.leidenuniv.nl

Supplementary information: Supplementary data is available here.
Computing the maximum similarity bi-clusters of gene expression data
Authors: Liu Xiaowen , Wang Lusheng
Published: November 2006

Motivations: Bi-clustering is an important approach in microarray data analysis. The underlying bases for using bi-clustering in the analysis of gene expression data are (1) similar genes may exhibit similar behaviors only under a subset of conditions, not all conditions, (2) genes may participate in more than one function, resulting in one regulation pattern in one context and a different pattern in another. Using bi-clustering algorithms, one can obtain sets of genes that are co-regulated under subsets of conditions.

Results: We develop a polynomial time algorithm to find an optimal bi-cluster with the maximum similarity score. To our knowledge, this is the first formulation for bi-cluster problems that admits a polynomial time algorithm for optimal solutions. The algorithm works for a special case, where the bi-clusters are approximately squares. We then extend the algorithm to handle various kinds of other cases. Experiments on simulation data and real data show that the new algorithms outperform most of the existing methods in many cases. Our new algorithms have the following advantages: (1) no discretization procedure is required, (2) performs well for overlapping bi-clusters and (3) works well for additive bi-clusters.

Availability: The software is available at .

Contact:  lwang@cs.cityu.edu.hk

Supplementary information: The Supplementary Data is available at .
New technology for transfusion safety
Authors: Dzik Walter H.
Published: November 2006

Hemovigilance programs from around the world document that the greatest risk to recipients of blood transfusion is human error, resulting in transfusion of the incorrect blood component. Errors in transfusion care have strong parallels with errors in medication administration. Errors often result from ‘lapse’ or ‘slip’ mistakes in which details of patient identification are overlooked. Three areas of transfusion are focal points for improved care: the labelling of the patient's pre‐transfusion sample, the decision to transfuse and the final bedside check designed to prevent mis‐transfusion. Both barcodes and radio‐frequency identification technology, each ideally suited to matching alpha‐numeric identifiers, are being implemented in order to improve performance sample labelling and the bedside check. The decision to transfuse should ultimately be enhanced through the use of nanotechnology sensors, computerised order entry and decision support systems. Obstacles to the deployment of new technology include resistance to change, confusion regarding the best technology, and uncertainty regarding the return‐on‐investment. By focusing on overall transfusion safety, deploying validated systems appropriate for both medication and blood administration, thoughtful integration of technology into bedside practice and demonstration of improved performance, the application of new technologies will improve care for patients in need of transfusion therapy.
Quantitative misorientation characteristics of interphase boundaries in composites
Authors: SZTWIERTNIA K. , FARYNA M. , SAWINA G.
Published: November 2006

Specific crystallographic correlations between neighbouring grains in composites were established by the use of selected area electron diffraction in the transmission electron microscope. However, it was the development of orientation mapping techniques that made it possible to obtain a quantitative description of the distribution of boundaries between the grains of both the same phase and different phases. This study shows that orientation topography measurements made by electron backscatter diffraction in the scanning electron microscope allowed determination of the crystallographic relationships between grains of different phases. An alumina‐based composite with a content of 10 vol% tungsten carbide was chosen for investigations. Misorientation distribution functions were calculated to describe the distribution density of misorientations with respect to the nearest neighbouring measured point located in the grain of the second phase. The analysis of misorientation distribution functions permitted the evaluation of preferences for some special crystallographic correlations between the grains of composite matrix and inclusions as well as shares of interphase boundaries characterized by those correlations.
Microstructural changes of CM186LC single‐crystal superalloy during creep deformation at 750 °C
Authors: DUBIEL B. , CZYRSKA‐FILEMONOWICZ A.
Published: November 2006

The microstructure of creep‐tested CM186LC Ni‐base single‐crystal alloy was studied to assess its suitability for use in the gas turbine environment. Creep tests were conducted at 750 °C and at stresses of 560 and 675 MPa up to 11 440 h. The microstructure of fractured and terminated specimens was investigated by light microscopy, scanning electron microscopy and analytical transmission electron microscopy. Microstructural analysis revealed the differences in the microstructure of creep‐tested CM186LC depending on the stress applied during creep at 750 °C.
Transmission electron microscopy investigations of AZ91 alloy deformed by equal‐channel angular pressing
Authors: BRASZCZYŃSKA‐MALIK K. N. , LITYŃSKA L. , BALIGA W.
Published: November 2006

The microstructure of transverse and longitudinal sections of a commercial AZ91 alloy processed by equal‐channel angular pressing was examined by transmission electron microscopy. A high dislocation density and large number of deformation twins were observed in the investigated material. The {102}matrix ‖ {012}twin twinning system was determined by selection area diffraction patterns obtained from the twin and matrix. Transmission electron microscopy analyses also revealed that the twins interacted with each other and pile‐ups of dislocations occurred near the twin boundary.
Structural analysis and intergranular corrosion tests of AISI 316L steel
Authors: STONAWSKÁ Z. , SVOBODA M. , SOZAŃSKA M. , KŘÍSTKOVÁ M. , SOJKA J. , DAGBERT C. , HYSPECKÁ L.
Published: November 2006

Pure AISI 316L steel is investigated after solution heat treatment (1050 °C/H2O) and structural sensitization (650 °C). Two quite different intergranular corrosion tests are used to determine the degree of structural sensitization due to the precipitation of secondary phases along the grain boundaries (mainly the M23C6 and σ‐phase): the oxalic acid etch test and the electrochemical potentio‐kinetic reactivation test. Generally, the dissolution of chromium‐rich carbides (M23C6) is provoked by oxalic acid etch tests, whereas the chromium‐depleted zones, in the vicinity of chromium‐rich carbides (M23C6), are attacked by electrochemical potentio‐kinetic reactivation tests. Both intergranular corrosion tests are used to determine the maximum degree of structural sensitization. Thus structural analysis by carbon replicas reveals the Laves phase, and both the M23C6 and (Cr,Mo)x(Fe,Ni)y phases. The results of intergranular corrosion tests are related to the findings of the structural analysis.
The effect of an Ni–Cr protective layer on cyclic oxidation of Ti3Al
Authors: CVIJOVIĆ I. , JOVANOVIĆ M. T. , VASILJEVIĆ‐RADOVIĆ D. , PERUŠKO D.
Published: November 2006

The effect of an 80Ni−20Cr (at.%) metallic coating on the cyclic oxidation behaviour of a Ti3Al‐based alloy with the composition Ti−25Al−11Nb (at.%) was investigated in this study. Cyclic oxidation tests were carried out in air at 600 °C and 900 °C for 120 h. For one cycle test, the specimens were held for 24 h at test temperature and then furnace‐cooled to room temperature. The oxidation rate was determined by plotting the mass gain per unit surface area of the specimen vs. exposure time. The morphology and composition of the oxidation products were characterized on the cross‐section of the specimens by scanning electron microscopy, energy‐dispersive X‐ray spectroscopy and atomic force microscopy. The oxidation scale forms during exposure at both 600 °C and 900 °C. TiO2 is the main oxide component, whereas the Al2O3 layer appears only discontinuously. The remarkable improvement in oxidation resistance at 900 °C was attributed to the chemical composition and structure of the scale formed on the 80Ni−20Cr coating.
Pretreatment plasma fibrinogen level correlates with tumor progression and metastasis in patients with squamous cell carcinoma of the esophagus
Authors: Takeuchi Hiroya , Ikeuchi Shunji , Kitagawa Yuko , Shimada Atsushi , Oishi Takashi , Isobe Yoh , Kubochi Kiyoshi , Kitajima Masaki , Matsumoto Sumio
Published: November 2006

Background:  Hypercoagulation has been reported to be associated with tumor progression and a poor prognosis in various carcinomas. In this study, we examined fibrinogen levels in pretreated patients with esophageal squamous cell carcinoma (ESCC) and assessed its correlation with clinicopathological factors and prognosis in patients with ESCC.

Methods:  Pretreatment fibrinogen levels were examined prior to surgery or other treatments (e.g. endoscopic mucosal resection and chemoradiotherapy [CRT]) in 105 patients with primary ESCC. We investigated the association of fibrinogen levels with clinicopathological background factors and the survival of ESCC patients.

Results:  The plasma fibrinogen concentration (PFC) ranged from 209.4 to 781.6 mg/dL. Pretreatment PFC correlated significantly with the depth of invasion (T factor). There also existed a significant correlation between higher fibrinogen levels and lymph node metastasis (N factor) and distant organ metastasis. Patients with a higher fibrinogen level experienced a significantly worse overall survival (P = 0.006). Fibrinogen levels strongly correlated with platelet counts, white blood cell counts and tumor length. Pretreatment PFC were observed to have a significant correlation with CRT responsiveness in ESCC patients in stages II and III (P = 0.005).

Conclusion:  This study revealed that higher levels of fibrinogen correlated with tumor progression, metastasis and poor responsiveness to CRT in ESCC patients.
Hepatocyte dynamics in a three‐dimensional rotating bioreactor
Authors: Miyazawa Mitsuo , Torii Takahiro , Toshimitsu Yasuko , Okada Katsuya , Koyama Isamu
Published: November 2006

Background and Aims:  The use of an artificial liver system with extracorporeal circulation or a three‐dimensional bioreactor perfused with liquid culture medium inevitably exposes hepatocytes to fluid mechanical stress (MS). The expression of liver‐specific hepatocyte functions seems to be modulated by the magnitude of MS. Nonetheless, few studies have focused on the direct effects of MS on hepatocytes. We subjected hepatocytes to MS using an MS loading device and investigated the effects on the cytoskeleton and hepatocyte dynamics inside three‐dimensional scaffolds by monitoring the changes in actin fiber, one of the components of the cytoskeleton. We also assessed the influence of MS on specific hepatocyte functions.

Methods:  We subjected hepatocytes to MS by a rotating radial flow bioreactor (RRFB) and examined the effects by comparing the MS‐loaded culture cells with cells cultured under stationary conditions without MS loading. The hepatocytes (1 × 106/cm3) were seeded on gauze without collagen coating and examined to determine morphological changes after 60 h incubation. Actin filaments in samples from the MS‐loaded hepatocyte culture were stained by fluorescein isothiocyanate‐labeled phalloidin.

Results:  Hepatocyte aggregation was observed in the MS‐loaded culture, but not in the unloaded stationary culture. Better albumin products were observed in the MS‐loaded group than in the stationary culture group at all measurement points. Actin filaments extended toward the scaffold after the start of MS loading incubation and polymerized around the hepatocytes. The hepatocyte aggregation eventually advanced to the formation of spheroids.

Conclusion:  These results suggest that MS‐induced polymerization of actin filaments stimulate hepatocyte aggregation and thereby improve hepatocyte‐specific function.
Predictors reflecting the pathological severity of non‐alcoholic fatty liver disease: Comprehensive study of clinical and immunohistochemical findings in younger Asian patients
Authors: Park Joong‐Won , Jeong Gyu , Kim Sang Jin , Kim Mi Kyung , Park Sill Moo
Published: November 2006

Background and Aims:  The spectrum of non‐alcoholic fatty liver disease (NAFLD) ranges from simple steatosis to severe steatohepatitis (NASH). The aim of our study was to identify clinical predictors distinguishing NASH from steatosis and to study the pathogenesis of NASH in a young Korean population.

Methods:  Clinical and biochemical variables from 39 biopsied NAFLD patients were retrospectively analyzed. All liver biopsy specimens were immunohistochemically examined for Kupffer cells (CD68, CD14), as well as expression of tumor necrosis factor‐alpha (TNF‐α) and mitochondrial uncoupling protein 2 (UCP‐2).

Results:  There were no significant differences in serum biochemistry between the two groups (15 steatosis vs 24 NASH). There was a significant difference between the body mass index (BMI) values (kg/m2) of the NASH (28.4 ± 3.4 kg/m2) and steatosis (25.8 ± 2.8 kg/m2) patients (P < 0.025), with a BMI of 28.9 kg/m2 representing the best threshold for distinguishing NASH from steatosis patients. BMI was significantly related to the degree of fibrosis (P < 0.01). CD68+ Kupffer cells were more common in the livers of NASH patients (P < 0.05), and TNF‐α and UCP‐2 were expressed in all NASH specimens and were related with the severity of inflammation and fibrosis (P < 0.05).

Conclusions:  BMI could be used to distinguish NASH from steatosis in younger Korean patients. A high BMI with a low alanine aminotransferase (ALT) value tended to suggest the presence of severe fibrosis in NASH, while the number of CD68+ Kupffer cells and the staining intensity of TNF‐α and UCP‐2 were correlated with general pathologic severity in patients with NAFLD.
Hepatic iron accumulation is associated with disease progression and resistance to interferon/ribavirin combination therapy in chronic hepatitis C
Authors: Fujita Naoki , Sugimoto Ryosuke , Urawa Naohito , Araki Jun , Mifuji Rumi , Yamamoto Mika , Horiike Shinichiro , Tanaka Hideaki , Iwasa Motoh , Kobayashi Yoshinao , Adachi Yukihiko , Kaito Masahiko
Published: November 2006

Background and Aims: Liver iron accumulation in patients with chronic hepatitis C (CHC) has received increasing attention in recent years. The aim of this study was to determine the prevalence and severity of liver iron deposition in CHC, to assess its relationship with clinical, biochemical and histological characteristics, and to study its influence on the response to interferon (IFN) plus ribavirin combination therapy.

Methods: We studied liver biopsy specimens from 103 hepatitis C virus (HCV) and 34 hepatitis B virus (HBV) infected patients and total iron score (TIS) was measured. Seventy patients infected with HCV genotype 1b were treated with IFN/ribavirin for 24 weeks.

Results: CHC patients had a significantly higher TIS than chronic hepatitis B (CHB) patients (7.03 ± 5.34vs4.41 ± 4.49,P = 0.0056). TIS was significantly correlated with alcohol intake (P = 0.0213,r = 0.290), transaminase level (P = 0.0126,r = 0.247), platelet count (P = 0.0002,r = −0.369), histological grading (P = 0.0121,r = 0.248) and staging (P = 0.0003,r = 0.356) in CHC patients. Pretreatment TIS was significantly higher in non‐sustained virological responders (SVR) than in SVR to IFN/ribavirin treatment (TIS = 7.69 ± 5.76vs4.39 ± 3.27,P = 0.0310). Multiple regression analysis showed that TIS was the only independent variable associated with resistance to IFN/ribavirin (P = 0.0277).

Conclusions: Liver iron deposition was common in CHC compared to CHB and was associated with liver disease progression. Increased hepatic iron stores in CHC were related to resistance to IFN/ribavirin treatment.
Perioperative infection control and its effectiveness in hepatectomy patients
Authors: Togo Shinji , Matsuo Kenichi , Tanaka Kuniya , Matsumoto Chizuru , Shimizu Tetsuya , Ueda Michio , Morioka Daisuke , Nagano Yasuhiko , Endo Itaru , Shimada Hiroshi
Published: November 2006

Background and Aim:  Post‐hepatectomy infections require careful attention, because they may deteriorate into liver failure. We retrospectively reviewed such infections in cases without biliary or intestinal reconstruction.

Methods:  This retrospective study involved 535 patients with liver tumors who underwent hepatectomy at the Department of Gastroenterological Surgery of Yokohama City University Hospital between April 1992 and March 2005. After classification into four groups depending on changes in infection countermeasures used during different periods, the treatment outcomes were examined. No such anti‐infection measures were taken during the first period; a closed suction drainage system and early enteral nutrition after surgery were introduced between the first and second periods; thorough management of bile leakage and prevention of nosocomial infection were added between the second and third periods; and surgical site infection (SSI) surveillance together with absorbable sutures instead of silk sutures between the third and fourth periods.

Results:  The incidence of postoperative infection decreased significantly with additional countermeasures: first period 44.7%; second period 24.1%; third period 15.0%; and fourth period 9.2%. The incidence of both SSI and remote infection were similarly reduced. Postoperative infection risk factors were age, presence of diabetes mellitus, the use of silk sutures and bile leakage, while those for SSI were the use of silk sutures and bile leakage.

Conclusion:  The incidence of postoperative infection and SSI were significantly reduced by our infection countermeasures, especially by bile leakage management and the use of absorbable sutures.
Insights into the historical construction of species‐rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure
Authors: Pennington R. Toby , Richardson James E. , Lavin Matt
Published: November 2006

Analytical methods are now available that can date all nodes in a molecular phylogenetic tree with one calibration, and which correct for variable rates of DNA substitution in different lineages. Although these techniques are approximate, they offer a new tool to investigate the historical construction of species‐rich biomes. Dated phylogenies of globally distributed plant families often indicate that dispersal, even across oceans, rather than plate tectonics, has generated their wide distributions. By contrast, there are indications that animal lineages have undergone less long distance dispersal. Dating the origin of biome‐specific plant groups offers a means of estimating the age of the biomes they characterize. However, rather than a simple emphasis on biome age, we stress the importance of studies that seek to unravel the processes that have led to the accumulation of large numbers of species in some biomes. The synthesis of biological inventory, systematics and evolutionary biology offered by the frameworks of neutral ecological theory and phylogenetic community structure offers a promising route for future work.

ContentsSummary605I.Introduction606II.Methodological issues606III.Insights into processes that give rise to species rich biomes608IV.Future directions: neutral ecological theory, community phylogenetic structure, and processes leading to species accumulation612V.Conclusions613Acknowledgements614References614
Amino Acid Alanine Reactivity with the Fingerprint Reagent Ninhydrin. A Detailed Ab Initio Computational Study
Authors: Petraco Nicholas D.K. , Proni Gloria , Jackiw Jennifer J. , Sapse Anne‐Marie
Published: November 2006

ABSTRACT: Ninhydrin is one of the most widely used reagents for chemical development of fingerprints on porous surfaces. The detection is based on the reaction of ninhydrin with a monoacidic component of the fingerprint to form an intensively colored compound named Ruhemann's Purple. A computational study of the mechanisms and reaction energetics of the formation of Ruhemann's Purple from ninhydrin and alanine is presented. Such a study is significant from a forensic science point of view because of the strong interest in the forensic chemistry and law enforcement communities in developing alternatives to the current generation of ninhydrin like chemicals for the detection and development of latent fingerprints. Information about the mechanism of reaction between ninhydrin and amino acids can ultimately help to design compounds with stronger chromo‐fluorogenic properties in aid of detecting fingerprints at crime scenes. The three most accepted mechanisms of formation have been considered using ab initio quantum mechanical calculations. At relatively high temperature (∼100°C) all three mechanisms are energetically feasible. However since it is recommended that forensic analyses be performed at room temperature, a revised mechanism is proposed for the formation of Ruhemann's Purple under this condition.
Bank Security Dye Packs: Synthesis, Isolation, and Characterization of Chlorinated Products of Bleached 1‐(methylamino)anthraquinone
Authors: Egan James M. , Rickenbach Michael , Mooney Kim E. , Palenik Chris S. , Golombeck Rebecca , Mueller Karl T.
Published: November 2006

ABSTRACT: Banknote evidence is often submitted after a suspect has attempted to disguise or remove red dye stain that has been released because of an anti‐theft device that activates after banknotes have been unlawfully removed from bank premises. Three chlorinated compounds have been synthesized as forensic chemical standards to indicate bank security dye bleaching as a suspect's intentional method for masking a robbery involving dye pack release on banknotes. A novel, facile synthetic method to provide three chlorinated derivatives of 1‐(methylamino)anthraquinone (MAAQ) is presented. The synthetic route involved Ultra Clorox™ bleach as the chlorine source, iron chloride as the catalyst, and MAAQ as the starting material and resulted in a three‐component product mixture. Two mono‐chlorinated isomers (2‐chloro‐1‐(methylamino)anthraquinone and 4‐chloro‐1‐(methylamino)anthraquinone) and one di‐chlorinated compound (2,4‐dichloro‐1‐(methylamino)anthraquinone) of the MAAQ parent molecule were detected by gas chromatography mass spectrometry (GC‐MS), and subsequently isolated by liquid chromatography (LC) with postcolumn fraction collection. Although GC‐MS is sensitive enough to detect all of the chlorinated products, it is not definitive enough to identify the structural isomers. Liquid‐state nuclear magnetic resonance (NMR) spectroscopy was utilized to elucidate structurally the ortho‐ and para‐mono‐chlorinated isomers once enough material was properly isolated. A reaction mechanism involving iron is proposed to explain the presence of chlorinated MAAQ species on stolen banknotes after attempted bleaching.
Relationship between smoking and folic acid, vitamin B12 and some haematological variables in patients with chronic periodontal disease
Authors: Erdemir Ebru Olgun , Bergstrom Jan
Published: November 2006

Aim: The purpose of this study was to investigate the relationship between cigarette smoking and the serum levels of folic acid, vitamin B12 and some haematological variables in patients with periodontal disease.

Patients and methods: The study base consisted of 88 volunteer patients with periodontal disease, including 45 current smokers in the age range 31–68 years and 43 non‐smokers in the range 32–66 years. The clinical parameters included plaque index (PI), gingival index (GI), bleeding on probing (BOP), probing depth (PD) and clinical attachment loss (CAL). Folic acid, vitamin B12 and haematological variables were determined from peripheral blood samples.

Results: PI, PD and CAL means were significantly higher in smokers than non‐smokers (p<0.05). The serum folic acid concentration of smokers was lower than that of non‐smokers (p<0.05), whereas the white blood cell count was higher in smokers than in non‐smokers (p<0.05).

Conclusion: The results of this study suggest that among patients with periodontal disease the serum folic acid concentration is lower in smokers compared with non‐smokers.
Periodontal conditions in male adolescents using smokeless tobacco (moist snuff)
Authors: Montén Ulrika , Wennström Jan L. , Ramberg Per
Published: November 2006

Aim: The aim of this study was to evaluate the potential association of the use of smokeless tobacco (moist snuff) on the periodontal conditions of adolescents.

Material and methods: A subject sample of one hundred and three 19‐year‐old male individuals (33 snuff users, 70 controls) living in Göteborg, Sweden, were clinically examined with regard to oral hygiene, gingivitis, probing pocket depth (PPD), clinical attachment loss (CAL) and gingival recession. Bitewing radiographs were obtained for assessments of alveolar bone level. Information about tobacco and oral hygiene habits was obtained by a structured questionnaire. Student 's t‐test, χ2‐test and logistic regression analysis were used for statistical analysis.

Results: The mean plaque and gingivitis scores in snuff‐users were 59% (SD 21.0) and 47% (18.6), respectively, and in controls 64% (22.4) and 50% (18.3), respectively. The average PPD and CAL in snuff‐users amounted to 2.3 mm (0.3) and 0.2 mm (0.1), respectively, and in controls 2.4 mm (0.3) and 0.1 mm (0.1) (p>0.05), respectively. The mean bone level was 1.3 mm (0.2) in both groups. The prevalence of subjects showing recession was 42% among snuff‐users and 17% among controls (p=0.006). In snuff users, an average of 4% (0.9) of the teeth showed recession, compared with 1% (0.3) in controls (p<0.001). Limiting the analysis to the maxillary anterior tooth region, 33% of the snuff‐users and 10% of the controls presented recessions (p=0.002). The use of snuff entailed an OR=5.1 to have gingival recessions.

Conclusion: In the present population sample of adolescents, the use of smokeless tobacco (moist snuff) was not associated with the presence of periodontal disease except for a significantly high prevalence of gingival recessions.
Immediately Loaded Titanium Implants with a Porous Anodized Surface with at Least 36 Months of Follow‐Up
Authors: Degidi Marco , Perrotti Vittoria , Piattelli Adriano
Published: November 2006

Background:  Results from some studies clearly suggest that immediate loading can achieve equal success rates as those found in delayed or unloaded implants. There is still a lack of knowledge about the role of surface oxide properties during the peri‐implant bone healing processes.

Purpose:  The aim of this study was a clinical follow‐up study of immediately loaded implants with a porous anodized surface.

Materials and Methods:  A total of 142 TiUniteTM (Nobel Biocare, Göteborg, Sweden) implants were inserted from January to September 2001. All implants have been used in fixed restorations. Fifty implants were inserted in completely edentulous mandibles, and 69 implants were inserted in completely edentulous maxillae. All 119 implants were subjected to immediate functional loading (IFL) (immediate restoration with full occlusal contact). The other 23 implants, inserted in 12 patients, underwent immediate nonfunctional loading (INFL) (immediate restoration without occlusal contact) in different anatomical configurations (single tooth, small bridges in the anterior mandible, anterior maxilla, and posterior maxilla). All 142 implants have been followed for at least 3 years.

Results:  All implants appeared to be osseointegrated from a clinical and radiographic point of view. No failures were observed in the IFL and INFL groups. The implant success was 100%. The mean marginal bone loss was 0.8 and 1.0 mm at 12 and 36 months, respectively.

Conclusion:  Implants with a porous anodized surface appear to work well under an immediate loading state in the long term.
Outcome of Oral Implant Treatment in Partially Edentulous Jaws Followed 20 Years in Clinical Function
Authors: Lekholm Ulf , Gröndahl Kerstin , Jemt Torsten
Published: November 2006

Background:  Most long‐term follow‐up studies of implants in partially edentulous jaws present their outcomes as mean values of implant survival and follow‐up time, and few address the fate of the remaining teeth.

Purpose:  The aim of this study was to investigate the results of oral implant treatment in partially edentulous jaws after 20 years, and simultaneously to assess what happens to teeth present at the time of implant placement.

Materials and Methods:  Seventeen partially edentulous patients, of 27 originally treated individuals, were retrospectively reviewed after receiving implants from 1983 to 1985. The parameters studied were implant survival, prosthesis stability, marginal bone loss at teeth and implants, treatment complications, need for dental treatment, and patient’s satisfaction with the outcome.

Results:  The cumulative survival rate was 91%, when all 27 patients were assessed, that is, including the 10 dropouts. Of the 69 inserted and followed implants (Brånemark system®; Nobel Biocare AB, Göteborg, Sweden), six failed (8.7%) during the 20‐year period, four during the first decade, and the remaining two during the second. A majority (n=4) of the losses were due to implant fractures, two after 8 years, and two after 17 years. In all, 10 of the original fixed bridges being followed (n=24) remained in function during the entire investigation period, whereas 12 were exchanged for new constructions after an average of 7 years. The mean marginal bone loss at teeth was 0.7 mm, and at implants it was 1.0 mm. The major complication observed during the second decade was veneer material fractures, which occurred 14 times in six patients. Component loosening and abutment‐ and bridge‐locking screw fractures were the second most common problems seen, indicating material/component fatigue. Most patients were satisfied with their treatment and many mentioned that they did not think of the constructions as anything but a part of their own body.

Conclusion:  Over the decades, treatment of partially edentulous jaws with turned titanium implants seems to function well and to provide patients with good support for fixed short‐span bridge constructions.
Correlation Between Implant Stability Quotient and Bone‐Implant Contact: A Retrospective Histological and Histomorphometrical Study of Seven Titanium Implants Retrieved from Humans
Authors: Scarano Antonio , Degidi Marco , Iezzi Giovanna , Petrone Giovanna , Piattelli Adriano
Published: November 2006

Background:  Primary stability has a relevant role in the long‐term success of dental implants. A quantitative method for the measurement of implant stability has been introduced (resonance frequency analysis RFA]). Information about the significance of RFA measurements and about the relationship between RFA values and their association with implant osseointegration, success, or failure is important from a clinical point of view.

Purpose:  The aim of the present histological and histomorphometric study was to see if a correlation existed between the bone‐implant contact (BIC) percentage of retrieved human implants and RFA values.

Materials and Methods:  Seven implants inserted in the posterior mandible, with a sandblasted and acid‐etched surface and retrieved after a 6‐month period, were evaluated in the present study. These seven implants had been retrieved for different causes. All these implants were submerged and were retrieved with a 5‐mm trephine bur and immersed in 10% buffered formalin to be processed for histology.

Results:  A statistically significant correlation could be detected between implant stability quotient and BIC (p=.016).

Conclusions:  Even if the relationship between bone structure and RFA is still not fully understood, in our study, a statistically significant correlation was found between RFA and BIC values. Further studies are needed to evaluate a correlation of RFA and BIC in human implants retrieved after a range of healing periods.
Tooth movement in the elderly: a case report
Authors: Ryan William , Hegarty David
Published: November 2006

Orthodontic appliances can take advantage of favourable growth in adolescents to achieve treatment goals. However in the elderly where growth potential is modest, tooth movement is still highly feasible and is a useful adjunct to multidisciplinary treatment. Orthodontic treatment of the elderly normally involves limited objectives with goals customised to the patients concerns and functional needs. This case report demonstrates that orthodontic treatment of the elderly is possible and can improve the function and aesthetics of the dentition and thus increase their quality of life.
The Yad Sarah geriatric dental clinic, a different model
Authors: Pietrokovski Jaime , Zini Avi
Published: November 2006

Introduction:  There are not sufficient dental services for elderly people around the world. Yad Sarah is an Israel‐wide network of volunteers aiding sick, elderly, isolated and housebound people with an array of services aimed at making home care possible. It provides medical and social services to more than 380 000 elderly persons per year and in addition, lends medical equipment free of charge, has day rehabilitation centres, legal aid council for seniors, provides transportation for the disabled, meal deliveries and geriatric dental services.

Materials and methods:  The latter are equipped with five dental units (one mobile unit) and a dental laboratory. During the 5 years from 2000 to 2004 the dental services provided dental care for 3890 elderly patients with the main clinic located in Jerusalem. Patients pay an average of 70% of the cost price of their dental care, with the difference being subsidised by Yad Sarah. Of the 515 patients who applied for treatment in 2004, 54% possessed natural teeth in both jaws, 28% were fully edentulous, 12% were edentulous in the maxilla and 6% were edentulous in the mandible. Females applied for dental treatment more often than the male population. Older patients (75–101 years old) required oral care at their homes or at old age residences, more frequently than the younger age groups (60–74 years old).

Conclusion:  Dental treatment was administered by 70 volunteer dental surgeons, two certified dental hygienists and dental hygienist students. The clinical staff was provided with a comprehensive in‐service training in geriatric dentistry during the 3‐year service learning period. A survey in 2004 showed that 83% of the selected patients were satisfied, compared with 14% who were not. The reasons for satisfaction were, mainly, the personal relationship with the attending staff (41%) and the professional ability of the dental team (46%).
Relationship between survival rates and numbers of natural teeth in an elderly Japanese population
Authors: Morita Ichizo , Nakagaki Haruo , Kato Kazuo , Murakami Taeko , Tsuboi Shinji , Hayashizaki Junko , Toyama Atsushi , Hashimoto Masanori , Simozato Tsukasa , Morishita Norikazu , Kawanaga Tetsuhiro , Igo Junko , Sheiham Aubrey
Published: November 2006

Objectives: The objective of this study was to assess whether elderly people with 20 or more natural teeth were more likely to live longer than a cohort with less than 20 teeth.

Materials and methods: Groups of elderly people over 80 years of age (24 males and 35 females) with 20 or more teeth (≥20 group) were compared with elderly people (24 males and 35 females) with less than 20 teeth (<20 group). Follow‐up studies were conducted at regular intervals for 10 years from July 1992 to July 2002. The cumulative survival rate of the ≥20 group (average ± SE tooth number of teeth – males, 23.9 ± 0.6; females, 23.8 ± 0.4) was compared with the <20 group (average number of teeth – males, 3.8 ± 1.1; females, 2.6 ± 0.8). The multivariate Cox proportional hazard models with the number of teeth in a group (≥20 group or <20 group). Smoking status and alcohol intake as covariates were used to adjust the cumulative survival rate.

Results: The male participants in the ≥20 group had a significantly higher cumulative survival rates (p < 0.05) than the <20 group at 18 and 21 months from baseline. There were no significant differences in survival rates between the female groups. Adjusted cumulative survival rate was significantly different at 72, 75 and 78 months between the ≥20 group and <20 group for males but not for females.

Conclusion: Having 20 or more natural teeth was associated with increased survival rate in elderly males, but not among the elderly females.
PHASE EQUILIBRIUM FOR SUPERCRITICAL CO2 AND THE METHYL ESTERIFIED PRODUCT FROM SOYBEAN OIL DEODORIZER DISTILLATE
Authors: LIU YUN , FANG TAO , DING XIAOLIN
Published: November 2006

In order to study the feasibility of using supercritical CO2 (SC‐CO2) to concentrate natural tocopherols from soybean oil deodorizer distillate (DOD), the vapor–liquid phase equilibrium data were determined for SC‐CO2 and methyl esterified DOD (ME‐DOD) at 40C and in the pressure range of 9.7–16.2 MPa. A vapor and liquid phase circulation apparatus was employed. The samples from the liquid and vapor phases were analyzed by gas chromatography and high‐performance liquid chromatography
methods. According to the determined data, the distribution coefficient and separation factor were calculated and discussed. The results showed that the separation factor between tocopherols and fatty acid methyl esters was from 2.5 to 3.8 at 40C and 9.7–16.2 MPa, which is fundamental and necessary for future process designs.