bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hallmarks of mycolic acid biosynthesis: A comparative genomics study
Authors: Raman Karthik , Rajagopalan Preethi , Chandra Nagasuma 
Published: June 2007

AbstractMycolic acids, which render unique qualities to mycobacteria, are known to be important for mycobacterial growth, survival, and pathogenicity. It is of interest to understand the evolutionary origins of the mycolic acid pathway (MAP), as well as the common minimum principles critical for generating the capability of mycolic acid biosynthesis. The recent curation of a comprehensive model of the MAP in Mycobacterium tuberculosis and the availability of a large number of genome sequences make it feasible to carry out detailed sequence and phylogenetic analyses, to address these questions. A comprehensive phylogenetic pathway profile analysis was carried out for 318 fully sequenced bacterial genomes, for each of the proteins present in the MAP. The organisms were clustered on the basis of co‐occurrence of the MAP proteins in their proteome, while the proteins were clustered on the basis of their phylogenetic profiles. The MAP proteins were also searched against the nonredundant sequence database, to identify similar proteins from other phyla. The pathway profiles indicate that four proteins and certain protein domains stand out as more characteristic to mycolate producing organisms. Further analysis leads to the identification of the desaturases DesA1 and DesA2 and certain domains of Fas and Pks13 as hallmarks of the pathway. The roles of these proteins in some other organisms, as well as the distribution of these proteins across all known genome sequences are also briefly discussed. The clustering of organisms, carried out to group organisms with similar profiles, provides a means of obtaining finer classification as compared to the standard taxonomic method. The results indicate that the MAP and hence the capacity of mycolic acid production in mycobacteria is an example of an emergent property that has come about by recruiting enzymes from unrelated pathways in plants, presumably through lateral gene transfer. The understanding of the hallmarks of mycolic acid biosynthesis will also find application in evaluating drug targets. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Hydrogen blistering of silicon: Progress in fundamental understanding
Authors: Terreault Bernard 
Published: June 2007

AbstractWhen silicon is implanted with a sufficient concentration of H ions, at low to moderate temperature, and subsequently annealed at high temperature, dome‐shaped gas‐filled blisters and/or craters of exploded blisters appear on the surface. Under particular conditions, blistering can be produced by plasma hydrogenation as well. The phenomenon is another facet of hydrogen behaviour in silicon, a question with both fundamental and applied implications. Blistering is at the origin of the “ion‐cutting” process for the fabrication of silicon‐on‐insulator and other heterostructures; this process is particularly useful whenever atomically sharp interfaces between layers are required. The novelty and vast potential of this process has spurred since the mid‐1990's a burst of experimental activity on blistering. The purposes of those works were either to improve or extend the ion‐cut process, or to clarify its underlying mechanisms. In “mechanisms”, the plural is used to convey the fact that it is a multi‐step phenomenon. Because of this complexity, the theoretical work, in comparison, is far less abundant. Hydrogen blistering of silicon is qualitatively understood in broad terms: H being insoluble in Si, it tends to segregate into cavities which grow and coalesce at high temperature, and the H2pressure in the cavities finally deforms the surface. In fact, our understanding of the microscopic mechanisms has progressed much beyond that level thanks to the sophisticated work that has been carried out using techniques such as transmission electron microscopy, Rutherford backscattering in the channelling mode, infrared spectroscopy of local vibrational modes, stress and strain measurements, and others. The effects of n‐ or p‐doping, He ion coimplantation, and isotope substitution have also greatly helped in discriminating between different hypotheses. After a review of the most relevant experimental facts, the blistering mechanisms that have been proposed in the literature will be discussed and their conformity with the data assessed. Finally an attempt will be made to identify the key questions and suggest a few avenues for future work. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The ensemble‐transform scheme adapted for the generation of stochastic forecast perturbations
Authors: McLay Justin G. , Bishop Craig H. , Reynolds Carolyn A. 
Published: June 2007

AbstractA method for generating stochastic perturbations is derived from the ensemble‐transform analysis‐error sampling scheme. The method produces stochastic perturbations that not only have multivariate spatial correlation, balance, and prescribed mean and variance statistics, but also conditioning for growth. The perturbations can serve as modification for numerical weather prediction (NWP) ensemble forecasts either during integration or post‐processing. A practical demonstration of the method is given, in which operational global NWP ensemble forecasts are modified with the stochastic perturbations as a post‐processing exercise. The results suggest that the method can produce stochastic perturbations whose spatially‐integrated statistics match target mean and variance statistics reasonably well, if a moderate number of archived NWP forecast perturbations are provided as input. They also suggest that the stochastic perturbations' correlation, balance, and conditioning for growth are functional, in the sense that the perturbations are not predisposed to marked decay at the outset of integration by an NWP model. Copyright © 2007 Royal Meteorological Society
Baroclinic development within zonally‐varying flows
Authors: Schultz David M. , Zhang Fuqing 
Published: June 2007

AbstractPrevious idealized‐modelling studies have shown the importance of across‐jet barotropic shear to the resulting evolution of cyclones, anticyclones, surface‐based fronts, and upper‐level fronts. Meanwhile, many observational studies of cyclones have shown the importance of along‐jet variations in the horizontal wind speed (i.e. confluence and diffluence). This study investigates the importance of these along‐jet (zonal, for zonally‐oriented jets) variations in the horizontal wind speed to the resulting structures and evolutions of baroclinic waves, using idealized models of growing baroclinic waves. An idealized primitive‐equation channel model is configured with growing baroclinic perturbations embedded within confluent and diffluent background flows. When the baroclinic perturbations are placed in background confluence, the lower‐tropospheric frontal structure and evolution initially resemble the Shapiro–Keyser cyclone model, with a zonally‐oriented cyclone, strong warm front, and bent‐back warm front. Later, as the baroclinic wave is amplified in the stronger downstream baroclinicity, the warm sector of the cyclone narrows, becoming more reminiscent of the Norwegian cyclone model. The upper‐level frontal structure develops with a southwest–northeast orientation, and becomes strongest at the base of the trough, where geostrophic cold advection is occurring. In contrast, when the baroclinic perturbations are placed in background diffluence, the lower‐tropospheric frontal structure and evolution resemble the Norwegian cyclone model, with a meridionally‐oriented cyclone, strong cold front, and occluded front. The upper‐level frontal structure is initially oriented northwest–southeast on the western side of the trough, before becoming zonally oriented. Weak geostrophic temperature advection occurs along its length. These results are compared to those from previous observational and idealized‐modelling studies. Copyright © 2007 Royal Meteorological Society
Effect of Electron Beam‐Induced Deposition and Etching Under Bias
Authors: Choi Young R. , Rack Philip D. , Frost Bernhard , Joy David C. 
Published: June 2007

AbstractElectron‐beam‐induced deposition (EBID) and etching (EBIE) provides a simple way to fabricate or etch submicron or nanoscale structures of various materials in a direct‐write (i.e.nonlithographic) fashion. The growth rate or the etch rate are influenced by many factors such as beam energy, beam current, temperature of the substrate material, pressure of the chamber, and geometry of the gas injector etc.The mechanism of EBID and EBIE involves the interaction of the incident electron beam or emitted electron from the target material. The role of these electrons is still not completely understood although the contribution of low energy secondary electrons (SE) has been assumed to be the dominant contributor of EBID and EBIE based on its overlap with the dissociation cross section. We have studied the growth and etching phenomenon under various biasing conditions to investigate how low voltage biasing of the substrate affects secondary electron trajectories and subsequently modifies electron‐beam‐induced deposition and etching.SCANNING 29: 000–000, 2007. © 2007 Wiley Periodicals, Inc.
FIB/SEM Characterization of Carbon‐based Fibers
Authors: Magni S. , Milani M. , Riccardi C. , Tatti F. 
Published: June 2007

AbstractThe aim of this paper is to show how a focused ion beam combined with a scanning electron microscope (FIB/SEM machine) can be adopted to characterize composite fibers with different electrical behavior and to gain information about their production and modification. This comparative morphology investigation is carried out on polyacrylonitrile (PAN) carbon fibers and their chemical precursor (the oxidized PAN or oxypan) which has different electrical properties. Fibers are imaged by electron and ion beams and sectioned by the focused ion beam (FIB). A sample of oxypan fibers processed by a radio frequency (RF) plasma is also investigated and the role of the conductive carbon layer around their unmodified, insulating bulk is discussed. A suitable developed edge detection technique (EDT) on electron, ion images, and after the FIB sectioning, provides quantitative information about the thickness of the created layer. SCANNING 29: 000–000, 2007. © 2007 Wiley Periodicals, Inc.
An analytical approach to sustainable development in Turkey
Authors: Kizilaslan Nuray , Gürler A. Zafer , Kizilaslan Halil 
Published: June 2007

AbstractSustainable development is meeting the expectations and necessities of the current era and future generations without making any sacrifices. The focus of the sustainable development concept is humankind. Humankind has the responsibility of protecting the environment it lives in, as much as it has the right to continue living a healthy productive life in harmony with nature. These responsibilities will be the main elements in determining continuity. With these aspects in mind, the research deals with the basic criteria predicted by Meadows on sustainable development. These criteria are divided into three: ‘sustainable’, ‘critical’ and ‘destructive’. The first element evaluated in these predicted criteria is the increase in population. From the pace of the population increase observed in Turkey, it can be said that Turkey affects the sustainable development in a ‘destructive’ way. Other criteria, such as economic development, deforestation rate, the area of the forests and the density of the population show an inclination towards the ‘critical area’. Turkey, in terms of its agricultural development, self‐sufficiency rate and urban population, is to be found in the sustainable development range. Copyright © 2006 John Wiley & Sons, Ltd and ERP Environment.
Detection of Unlabeled Oligonucleotide Targets Using Whispering Gallery Modes in Single, Fluorescent Microspheres
Authors: Nuhiji Edin , Mulvaney Paul 
Published: June 2007

AbstractThe development of an inexpensive, highly sensitive, whispering gallery mode (WGM) based biosensing system is demonstrated. The system comprises a silica microsphere functionalized with a fluorophore and a dense monolayer of single‐strand oligonucleotides. The adsorption of the complementary strand causes spectral shifts in the emission spectrum of the microsphere that can be registered using a conventional optical microscope and CCD detector. The system is capable of detecting low‐abundance, unlabeled‐oligonucleotide targets. The spectral shifts can be used to monitor both the hybridization kinetics and the denaturation of the double‐strand DNA at elevated temperatures. The hybridization appears to be completely reversible. Complementary oligonucleotide probes more than 30 bases in length are most readily detected while a complete assay takes only a few minutes.
Liquid Chromatography–Mass Spectrometric Analysis of Lipids Present in Human Meibomian Gland Secretions
Authors: Butovich Igor A. , Uchiyama Eduardo , di Pascuale Mario A. , McCulley James P. 
Published: June 2007

AbstractThe purpose of the study was to qualitatively characterize the major lipid species present in human meibomian gland secretions (MGS) by means of high‐performance liquid chromatography with atmospheric pressure ionization mass spectrometric detection of the analytes (NP HPLC‐MS). Two different NP HPLC‐MS methods have been developed to analyze lipid species that were expected to be present in MGS. The first method was optimized for the analysis of relatively nonpolar lipids [wax esters (WE), di‐ and triacyl glycerols (DAG and TAG), cholesterol (Chl) and its esters (Chl‐E), and ceramides (Cer)], while the second method was designed to separate and detect phospholipids. The major lipid species in MGS were found to be WE, Chl‐E, and TAG. A minor amount of free Chl (less then 0.5% of the Chl‐E fraction) was detected in MGS. No appreciable amounts of DAG and Cer were found in MGS. The second NP HPLC‐MS method, capable of analyzing model mixtures of authentic phospholipids (e.g. phosphatidylglycerol, phosphatidylethanolamine, phosphatidic acid, phosphatidylinositol, phosphatidylserine, phosphatidylcholine, and sphingomyelin) in submicrogram/mL concentrations, showed little or no presence of these species in the MGS samples. These observations suggest that MGS are a major source of the nonpolar lipids of the WE and Chl‐E families for the tear film lipid layer (TFLL), but not of the previously reported phospholipid components of the TFLL.
First use of cardiac contractility modulation (CCM) in a patient failing CRT therapy: Clinical and technical aspects of combined therapies
Authors: Butter Christian , Meyhöfer Jürgen , Seifert Martin , Neuss Michael , Minden Hans‐Heinrich 
Published: June 2007

AbstractCardiac contractility modulating (CCM) signals delivered by the OPTIMIZER System are being investigated as a treatment for medically refractory heart failure. Previous chronic studies of CCM have excluded patients with prolonged QRS and a cardiac resynchronization therapy (CRT) device. However, symptoms persist in more than 25% of these CRT patients. CCM may offer a therapeutic option for these non‐responders. Here we report the first use of CCM signals in a patient who did not respond to treatment with a CRT‐D device. We show that the implantation is technically feasible, that the OPTIMIZER and CRT‐D devices can coexist without interference and that acute haemodynamic and clinical improvements can be observed. The results suggest that systematic investigation of CCM treatment in CRT non‐responders is warranted.
Time‐dependent changes in distribution of basic fibroblast growth factor immunoreactive cells in hippocampus after kainic acid injection in rat pups
Authors: Erkanli Gozde , Ercan Feriha , Sirvanci Serap , Salik Emsal , Yananli Hasan Raci , Onat Filiz , San Tangul 
Published: June 2007

AbstractFive‐day‐old Wistar albino rats were injected with kainic acid (KA) or saline i.p. to investigate time‐dependent alterations in morphology and number of basic fibroblast growth factor (bFGF) immunoreactive (‐ir) astrocytes and neurons in hippocampus at 15, 30, and 90 days after the injections. Sections were stained with cresyl violet for morphological evaluation and bFGF immunohistochemistry was used for quantitative evaluation of bFGF‐ir cell density. Fifteen days after KA injection, there was gliosis but no neuronal loss although disorganization in CA1, CA3, CA4 pyramidal layers and neuronal loss were evident 30 and 90 days after the injection. KA injected rats demonstrated significantly increased number of bFGF‐ir astrocytes throughout the hippocampus and pyramidal neurons in CA2 after 15 days and decreased number of bFGF‐ir cells after 30 and 90 days. The decrease in the number of bFGF‐ir astroglia and neurons in long term after KA injection may indicate a decrease in the production of bFGF and/or number of bFGF‐ir cells suggesting that protective effects of bFGF may be altered during epileptogenesis in hippocampus.
Emergency obstetric care: Impact on emerging issues
Authors: Moyo N.T. , Liljestrand J. 
Published: June 2007

AbstractAccess to Emergency obstetric care (EmOC) remains a challenge for women. This paper presents a summary of issues and suggestions from one of the working groups at the FIGO precongress workshop on access of sexual and reproductive health care in November, 2006, in Kuala Lumpur.
New evidence for high discharge to the Chukchi shelf since the Last Glacial Maximum
Authors: Hill Jenna C. , Driscoll Neal W. , Brigham-Grette Julie , Donnelly Jeffrey P. , Gayes Paul T. , Keigwin Lloyd 
Published: June 2007

AbstractUsing CHIRP subbottom profiling across the Chukchi shelf, offshore NW Alaska, we observed a large incised valley that measures tens of kilometers in width. The valley appears to have been repeatedly excavated during sea level lowering; however, the two most recent incisions appear to have been downcut during the last sea level rise, suggesting an increase in the volume of discharge. Modern drainage from the northwestern Alaskan margin is dominated by small, low-discharge rivers that do not appear to be large enough to have carved the offshore drainage. The renewed downcutting and incision during the deglaciation and consequent base level rise implies there must have been an additional source of discharge. Paleoprecipitation during deglaciation is predicted to be at least 10% less than modern precipitation and thus cannot account for the higher discharge to the shelf. Glacial meltwater is the most likely source for the increased discharge.
Root and canal morphology of maxillary first and second permanent molar teeth in a Ugandan population
Authors: Rwenyonyi C. M. , Kutesa A. M. , Muwazi L. M. , Buwembo W. 
Published: June 2007

AbstractAim  To investigate the root and canal morphology of permanent maxillary molar teeth from a Ugandan population.Methodology  Maxillary first (n = 221) and second molar (n = 221) teeth were collected from patients attending dental clinics in Kampala. Teeth were prepared using a clearing technique: the pulp chambers were accessed and the teeth placed consecutively into 5% sodium hypochlorite, 10% nitric acid, then methyl salicylate. Indian ink was injected into the pulp chambers to demonstrate the canal system.Results  In the first molars, 95.9% of the teeth had separate roots. The mesiobuccal root was fused with the palatal root in 3% of specimens and with the distobuccal root in 0.5% of teeth. In the second molars, 86% of the teeth had separate roots. The mesiobuccal root was fused with the palatal root in 6.3% of specimens and with the distobuccal root in 6.8% of teeth. Apical deltas were more frequent in the mesiobuccal root when compared with distobuccal and palatal roots of both the first and second molars. A type I canal configuration (>75%) was the most frequent in all the roots of both the first and second molars. Canal intercommunications and lateral canals were more frequent in the mesiobuccal root when compared with other roots.Conclusions  The mesiobuccal root tended to have more variations in the canal system followed by the distobuccal root, whereas the palatal root had the least. The findings in root and canal morphology of this Ugandan population were different from previous studies, which may partly be attributed to racial differences.
Root canal treatment on a patient with zinc oxide allergy: a case report
Authors: Karabucak B. , Stoopler E. T. 
Published: June 2007

AbstractAim To describe successful root canal treatment of a patient with a true zinc oxide allergy and to discuss allergic reactions to dental materials.Summary Dental materials have been reported as aetiologic agents for both local and systemic allergic reactions. It is essential for the oral healthcare provider to recognize the clinical symptoms associated with allergic reactions and to modify dental treatment, if necessary, to prevent these reactions from occurring. This article describes an unusual case of a patient with an allergy to zinc oxide. To our knowledge, this is the first case of successful root canal treatment of a patient with confirmed zinc oxide allergy to be reported in the dental literature.Key learning points Medical and dental histories must be evaluated to prevent medical complications secondary to dental treatment.Any patient suspected of having an allergy to dental materials should be referred to a healthcare professional capable of performing and interpreting allergy tests prior to dental treatment.
One of two gbpC gene homologues is involved in dextran‐dependent aggregation of Streptococcus sobrinus
Authors: Kagami A. , Okamoto‐Shibayama K. , Yamamoto Y. , Sato Y. , Kizaki H. 
Published: June 2007

Introduction:  Streptococcus sobrinus exhibits marked dextran‐dependent aggregation mediated by glucan‐binding proteins (GBPs). In contrast to Streptococcus mutans, in which the gbpC gene responsible for dextran‐dependent aggregation of this organism has been characterized, genes encoding the S. sobrinus GBPs have not yet been identified.Methods:  Recently, we identified the gbpC gene homologue from Streptococcus macacae using polymerase chain reaction primers based on the conserved regions of the gbpC sequence exhibiting intraspecies variations. This method was applied to amplify a S. sobrinus homologue.Results:  Unexpectedly, two gbpC gene homologues were identified in S. sobrinus strain 100‐4. One homologue, named gbpC, was more similar to the S. mutans gbpC gene than the other and was approximately half the molecular size of its homologue with similar regions interrupted by several non‐similar stretches. However, the dextran‐binding activity of the protein expressed from gbpC in Escherichia coli was not detected in contrast to the other homologue, a protein designated as Dbl, expressing this activity. The gbpC gene was shown to be intact on the chromosome of strain OMZ176, which does not exhibit dextran‐dependent aggregation, while the dbl gene of this strain contained a single adenine nucleotide insertion at approximately one‐third the distance from the 5′‐end. The insertion mutation in the dbl gene resulted in translation of a premature protein missing its LPXTG sequence signature sequence of the wall‐anchored proteins.Conclusion:  These results suggest that the dbl gene is very likely responsible for S. sobrinus dextran‐dependent aggregation.