bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic regions with distinct genomic distance conservation in vertebrate genomes
Authors: Sun Hong , Skogerbø Geir , Zheng Xiaohui , Liu Wei , Li Yixue 
Published: March 2009

Abstract

Background
A number of vertebrate highly conserved elements (HCEs) have been detected and their genomic interval distances have been reported to be more conserved than protein coding genes among mammalian genomes. A characteristic of the human – non-mammalian comparisons is a bimodal distribution of relative distance difference of conserved consecutive HCE pairs; and it is difficult to attribute such profile to a random assortment. We therefore undertook an analysis of the human genomic regions confined by consecutive HCE pairs common to eight genomes (human, mouse, rat, chicken, frog, zebrafish, tetradon and fugu).

Results
Among HCE pairs, we found that some consistently preserve highly conserved interval distance among genomes while others have relatively low distance conservation. Using a partition method, we detected two groups of inter-HCE regions (IHRs) with distinct distance conservation pattern in vertebrate genomes: IHR1s that are bordered by HCE pairs with relative small distance variation, and IHR2s with larger distance difference values. Compared to random background, annotated repeat sequences are significantly less frequent in IHR1s than IHR2s, which reflects a correlation between repeat sequences and the length expansion of IHRs. Both groups of IHRs are unexpectedly enriched in human indel (i.e. insertion and deletion) polymorphism-variations than random background. The correlation between the percentage of conserved sequence and human IHR length was stronger for IHR1 than IHR2. Both groups of IHRs are significantly enriched for CpG islands.

Conclusion
The data suggest that subsets of HCE pairs may undergo different evolutionary paths in light of their genomic distance conservation, and that sets of genomic regions pertain to HCEs, as well as the region in which HCEs reside, should be treated as integrated domains.
Combined finite element-boundary element method modelling of elastic multi-asperity contacts
Authors: Ilincic S , Vorlaufer G , Fotiu P A , Vernes A , Franek F 
Published: March 2009

A novel formulation of elastic multi-asperity contacts based on the boundary element method (BEM) is presented for the first time, in which the influence coefficients are numerically calculated using a finite element method (FEM). The main advantage of computing the influence coefficients in this manner is that it makes it also possible to consider an arbitrary load direction and multilayer systems of different mechanical properties in each layer. Furthermore, any form of anisotropy can be modelled too, where Green's functions either become very complicated or are not available at all. The rest of the contact analysis is then performed applying a custom-developed boundary element algorithm. The scheme was tested by considering the frictionless contact between a flat surface and a sphere. The obtained results are in good agreement with the analytical solution known for a Hertzian contact. Applied to either a frictionless or a frictional contact between real surfaces of different samples, our FEM-BEM method has shown that the composite roughness of surfaces in contact uniquely determines the contact pressure distribution.
Steroid Hormone Analysis by Tandem Mass Spectrometry
Authors: Soldin Steven J , Soldin Offie P 
Published: March 2009

AbstractBackground: New high-performance liquid chromatography/tandem mass spectrometry (LC-MS/MS) methods are among the most successful approaches to improve specificity problems inherent in many immunoassays.Content: We emphasize problems with immunoassays for the measurement of steroids and review the emerging role of LC-MS/MS in the measurement of clinically relevant steroids. The latest generation of tandem mass spectrometers has superior limits of quantification, permitting omission of previously employed derivatization steps. The measurement of steroid profiles in the diagnosis and treatment of congenital adrenal hyperplasia, adrenal insufficiency, chronic pelvic pain and prostatitis, oncology (breast cancer), and athletes has important new applications.Conclusions: LC-MS/MS now affords the specificity, imprecision, and limits of quantification necessary for the reliable measurement of steroids in human fluids, enhancing diagnostic capabilities, particularly when steroid profiles are available.
Toward Standardization of Insulin Immunoassays
Authors: Miller W Greg , Thienpont Linda M , Van Uytfanghe Katleen , Clark Penelope M , Lindstedt Patrik , Nilsson Göran , Steffes Michael W ,   for the Insulin Standardization Work Group
Published: March 2009

AbstractBackground: Measurement of circulating insulin may improve the classification and management of diabetes mellitus and assist in treating people with insulin resistance.Methods: A work group convened by the American Diabetes Association evaluated results for a panel of 39 single donor sera measured by 10 commercial insulin methods from 9 manufacturers against an isotope dilution–liquid chromatography/tandem mass spectrometry (IDMS) measurement procedure calibrated using purified recombinant insulin. We used a candidate primary (pure substance) reference material, pooled serum, and single donor sera to evaluate approaches to achieve improved agreement of results between the routine and reference measurement procedures.Results: Four of 10 methods had ≥95% of individual serum results within 32% of the IDMS concentrations. However, the bias vs IDMS was more than 15.5% for 7 of 10 methods in 36%–100% of individual samples. A purified recombinant insulin preparation used as a common calibrator did not improve harmonization of results among routine methods but was not used as instructed by all participants. Calibration using serum pools achieved bias &lt;15.5% for nearly all results in the concentration range covered by the pools (&gt;60 pmol/L). Calibration using a panel of individual sera was the most effective to improve harmonization of results over the full measuring range.Conclusions: Agreement among methods can be improved by establishing traceability to the IDMS procedure using a panel of native sera. Pooled sera may be useful as trueness control materials. The usefulness of the pure insulin primary reference material [candidate reference material for insulin (cRMI)] requires clarification of protocols used by manufacturers.
Genetic Polymorphisms of the Natriuretic Peptide System in the Pathogenesis of Cardiovascular Disease: What Lies on the Horizon?
Authors: Vassalle Cristina , Andreassi Maria Grazia 
Published: March 2009

AbstractBackground: The natriuretic peptide hormone family includes various proteins characterized by similar chemical structure and shared biological functions, with important effects on the cardiovascular system. Accordingly, these molecules are widely recognized as key clinical biomarkers in the diagnosis and monitoring of heart failure, hypertension, and coronary heart disease.Content: Several single-nucleotide polymorphisms have been recently identified in genes associated with the natriuretic system. This review provides an overview of new insights into the functional role of these genetic variants, as well as their impact on cardiovascular physiopathology and drug response.Conclusions: Noteworthy relationships between some specific polymorphisms and clinical correlates of cardiovascular disease have emerged. Nevertheless, future confirming studies are needed to substantiate the clinical relevance of such variants.
Overview of Gene Silencing by RNA Interference
Authors: Kim Daniel H. , Rossi John J. 
Published: March 2009

AbstractThe potential of harnessing RNA interference (RNAi) for sequence‐specific gene silencing has generated much excitement and progress in the field. Recent advances in RNAi technology suggest that RNAi‐based approaches may soon become an effective therapeutic strategy against a myriad of diseases. This overview provides a brief description of important considerations when designing an RNAi‐based method for gene silencing and therapeutic development: (a) mechanistic aspects of RNAi‐mediated gene silencing in mammalian cells; (b) structural requirements for potent siRNA duplexes; (c) off‐target effects and interferon responses; and (d) effective delivery of RNAi‐inducing agents. Promising therapeutic applications of RNAi that are currently in the developmental pipeline are also described. Curr. Protoc. Nucleic Acid Chem. 36:16.1.1‐16.1.10. © 2009 by John Wiley & Sons, Inc.
Unusual Deactivation in the Asymmetric Hydrogenation of Itaconic Acid
Authors: Schmidt Thomas , Drexler Hans‐Joachim , Sun Jiangtao , Dai Zhenya , Baumann Wolfgang , Preetz Angelika , Heller Detlef 
Published: March 2009

Abstractmagnified imageDuring the asymmetric hydrogenation of itaconic acid with rhodium solvate complexes of the type [Rh(PP)(MeOH)2] BF4 (PP=DIPAMP, Me‐DuPHOS) a deactivation with increasing substrate concentration is observed. It is shown that this inhibition phenomenon is due to the in situ formation of an inactive rhodium(III)‐alkyl complex. Two crystal structures of single crystals of the responsible complexes (1) and (2) support the deactivation pathway.
A narrow and highly significant linkage signal for severe bipolar disorder in the chromosome 5q33 region in Latin American pedigrees
Authors: Jasinska A.J. , Service S. , Jawaheer D. , DeYoung J. , Levinson M. , Zhang Z. , Kremeyer B. , Muller H. , Aldana I. , Garcia J. , Restrepo G. , Lopez C. , Palacio C. , Duque C. , Parra M. , Vega J. , Ortiz D. , Bedoya G. , Mathews C. , Davanzo P. , Fournier E. , Bejarano J. , Ramirez M. , Araya Ortiz C. , Araya X. , Molina J. , Sabatti C. , Reus V. , Ospina J. , Macaya G. , Ruiz‐Linares A. , Freimer N.B. 
Published: March 2009

AbstractWe previously reported linkage of bipolar disorder to 5q33‐q34 in families from two closely related population isolates, the Central Valley of Costa Rica (CVCR) and Antioquia, Colombia (CO). Here we present follow up results from fine‐scale mapping in large CVCR and CO families segregating severe bipolar disorder, BP‐I, and in 343 population trios/duos from CVCR and CO. Employing densely spaced SNPs to fine map the prior linkage peak region increases linkage evidence and clarifies the position of the putative BP‐I locus. We performed two‐point linkage analysis with 1134 SNPs in an approximately 9 Mb region between markers D5S410 and D5S422. Combining pedigrees from CVCR and CO yields a LOD score of 4.9 at SNP rs10035961. Two other SNPs (rs7721142 and rs1422795) within the same 94 kb region also displayed LOD scores greater than 4. This linkage peak coincides with our prior microsatellite results and suggests a narrowed BP‐I susceptibility regions in these families. To investigate if the locus implicated in the familial form of BP‐I also contributes to disease risk in the population, we followed up the family results with association analysis in duo and trio samples, obtaining signals within 2 Mb of the peak linkage signal in the pedigrees; rs12523547 and rs267015 (P = 0.00004 and 0.00016, respectively) in the CO sample and rs244960 in the CVCR sample and the combined sample, with P = 0.00032 and 0.00016, respectively. It remains unclear whether these association results reflect the same locus contributing to BP susceptibility within the extended pedigrees. © 2009 Wiley‐Liss, Inc.
Die chemische Biologie von Aptameren
Authors: Mayer Günter 
Published: March 2009

AbstractAn einem Strang: Aptamere, kurze einzelsträngige Oligonucleotide mit klar definierter 3D‐Faltung, sind hoch affin und spezifisch für ihre Zielstrukturen und hemmen deren biologische Funktionen. Aptamere können chemisch und/oder enzymatisch hergestellt werden und lassen sich daher als chemische wie auch als biologische Substanzen einordnen. Der aktuelle Stand und neue Entwicklungen auf diesem Gebiet werden vorgestellt.magnified imageAptamere sind kurze einzelsträngige Nucleinsäuren mit einer klar definierten dreidimensionalen Faltung. Sie zeigen eine hohe Affinität und Spezifität für ihre Zielstrukturen und inhibieren deren biologische Funktionen. Aptamere gehören zur Stoffklasse der Nucleinsäuren und können entweder chemisch, enzymatisch oder durch Kombination beider Methoden hergestellt werden. Daher können Aptamere sowohl als chemische wie auch als biologische Substanzen eingeordnet werden. Etablierte Methoden ebenso wie neue Entwicklungen auf dem Gebiet der Aptamere sollen in diesem Aufsatz zusammengefasst werden. Die Verwendung von Aptameren in der chemischen Biologie wird diskutiert.
Cover Picture: Compartmentalization of Chemically Separated Components into Droplets (Angew. Chem. Int. Ed. 15/2009)
Authors: Edgar J. Scott , Milne Graham , Zhao Yiqiong , Pabbati Chaitanya P. , Lim David S. W. , Chiu Daniel T. 
Published: March 2009

AbstractElectroosmotic‐flow‐driven droplet generation integrated with capillary electrophoresis (CE) allows the molecular components separated by CE to be compartmentalized into a stream of droplets, as reported by D. T. Chiu and co‐workers in their Communication on page 2719 ff. and illustrated on the cover picture. After separation and droplet compartmentalization, the droplet‐confined bands either can be docked and studied on‐chip or removed off‐chip for a second‐dimension separation and further analysis.magnified image
Inside Cover: Artificial Ribozyme Switches Containing Natural Riboswitch Aptamer Domains (Angew. Chem. Int. Ed. 15/2009)
Authors: Wieland Markus , Benz Armin , Klauser Benedikt , Hartig Jörg S. 
Published: March 2009

AbstractFusions of a ribozyme and an aptamer of a natural riboswitch (thiamine pyrophosphate, TPP) are used to construct artificial thiamine‐dependent switches of gene expression. As J. S. Hartig et al. describe in their Communication on page 2715 ff., insertion of these RNA elements into bacterial mRNAs allows translation of the message to be switched on or off. TPP triggers changes to the ribozyme‐mediated mRNA cleavage, resulting in liberation of the message for translational initiation.magnified image
Comparative study of the mechanical properties of fiber‐reinforced denture base resin
Authors: Köroğlu Ayşegül , Özdemir Tonguç , Usanmaz Ali 
Published: March 2009

AbstractPoly(methyl methacrylate) (PMMA) is used for removable prostheses. However, PMMA denture base resin does not meet all the mechanical requirements of prostheses. The aim of this in vitro study was to compare the transverse strength, modulus of elasticity, and impact strength values of nonreinforced heat‐polymerized and microwave‐polymerized denture base resin with those of denture base resin reinforced with continuous unidirectional E‐glass, woven E‐glass, and ultrahigh‐molecular‐weight polyethylene fibers. The mechanical properties of polymer reinforced with polyethylene fibers showed no significant increase in flexural properties. However, reinforcement with Stick fiber improved the mechanical properties. The test specimens that expressed low fracture strength values showed void spaces inside the test specimens. © 2009 Wiley Periodicals, Inc. J Appl Polym, 2009
Bulk free‐radical polymerization of styrene on a spinning disc reactor
Authors: Moghbeli M. R. , Mohammadi S. , Alavi S. M. 
Published: March 2009

AbstractThe bulk free‐radical polymerization of styrene was carried out on a spinning disc reactor (SDR) with prepolymer feeds previously prepared in a stirred batch reactor at 70°C. The SDR significantly enhanced the reaction rate when the conversion of the prepolymer feed was about 50%. There was an optimal disc rotation speed, that is, 1500 rpm, at which the conversion enhancement was maximized. Increasing the disc rotation speed up to 1500 rpm increased the conversion, but a further increase beyond this speed caused the conversion enhancement to decrease. This behavior could be attributed to the dual effect of the disc speed (controlling both the residence time and the effective radial mixing of the reaction media) on the disc. On the other hand, the multipass disc feeding mode was used as an approach to increase the residence time and evolution of the conversion of the reacting mixture in the SDR. Surprisingly, a maximum conversion change of about 40% was achieved for a prepolymer feed of 50% after three passes across the rotating disc. Furthermore, the effect of multipass disc feeding on the molecular characteristics of the SDR products was investigated. In comparison with the results obtained at a feed conversion of 30%, the weight‐average molecular weight, the z‐average molecular weight, and the polydispersity index of the three‐pass SDR products prepared with a 50% feed conversion at a rotation speed of 1500 rpm were lower than those of the one‐pass products. This behavior could be attributed to probable chain scission of long polymer chains as a result of the high shear and elongation forces that arose on the disc surface. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009
Quantifying allowable harm in species at risk: application to the Laurentian black redhorse (Moxostoma duquesnei)
Authors: Vélez‐Espino Luis A. , Koops Marten A. 
Published: March 2009

Abstract
When a species is identified for conservation, often the only way to effect recovery is to reduce the harm imposed by stressors threatening the survival of the species. Ideally all threats would be removed; however, this is often not feasible or practical. Within this context, a demographic approach is presented to assess how much human‐induced harm could be allowed without impairing the persistence of the species. Harm is defined as a negative perturbation that can target one or more vital rates and life stages simultaneously.
Allowable harm, defined as a level of harm that will not jeopardize survival or recovery, will be a function of the vital rates affected by human actions, the sensitivity of population growth to changes in these vital rates (their elasticities), the population growth rate prevailing before harm occurs, and the set of demographic parameters considered safe for long‐term persistence. This life‐history based approach requires minimal data, can link demography with habitat‐explicit information, is flexible enough to encompass complex life histories, and follows a precautionary approach.
Quantification of allowable harm could be applied to any species at risk. This approach is introduced by applying it to a Canadian population of a freshwater fish, the black redhorse (Moxostoma duquesnei), demonstrating that in the absence of habitat constraints population dynamics of this species are most sensitive to the survival of young adults, but population fitness is particularly sensitive to the loss of habitat used by young‐of‐the‐year fish under current levels of habitat supply.
Copyright © 2009 John Wiley & Sons, Ltd.
Detection of resistive features using towed slingram electromagnetic induction instruments
Authors: Thiesson Julien , Dabas Michel , Flageul Sébastien 
Published: March 2009

AbstractSlingram frequency domain electromagnetic (FDEM) instruments allow simultaneous measurement of both magnetic susceptibility and electrical conductivity, which should justify their widespread use in archaeological surveying. However, this is not the case and their application remains quite limited due to: (i) a lack of knowledge about the role of coil orientation and spacing in terms of the detection abilities for archaeological features (especially for resistive bodies); and (ii) a lack of instrumentation specifically designed for shallow targets. We present here a test of a new version of the CS60 instrument (VCP coil configuration and 0.6 m intercoil spacing) for shallow depth resistive feature detection. This experiment was undertaken on the Roman site of Vieil‐Evreux where a complete series of control resistivity and radar data was obtained. Detection of buried Roman walls was successful, in accordance with what can be expected from three‐dimensional modelling. This confirms that the application of this type of instrument in archaeological surveys merits to be extended significantly. Copyright © 2009 John Wiley & Sons, Ltd.
A highly sensitive method for the determination of 7‐aminonitrazepam, a metabolite of nitrazepam, in human urine using high‐performance electrospray liquid chromatography tandem mass spectrometry
Authors: Kuang Hua , Li Qiusheng , Shen Chongyu , Xu Jinzhong , Yuan Yuan , Xu Chuanlai , Wang Wuyang 
Published: March 2009

AbstractA highly sensitive method has been developed for the determination of urinary 7‐aminonitrazepam (7‐ANZP), the major metabolite of nitrazepam, using high‐performance electrospray liquid chromatography tandem mass spectrometry. The samples were prepared for analysis by adding 7‐aminoclonazepam (7‐ACZP, internal standard), hydrolysis with β‐glucuronidase and liquid–liquid extraction. Mass spectral acquisition was achieved by selectively monitoring the reaction between the two diagnostic transition reactions. Qualitative analysis was based on the retention time, and the quantitation was carried out by comparison with the internal standard. The recoveries of different concentrations of 7‐ANZP from spiked blank samples was 89.0–95.2%, and the relative standard deviation was below 6.4%. The limit of determination in urine was 0.07 ng/mL, and the limit of quantitation was 0.5 ng/mL in the linear range of 1–50 ng/mL. This method possesses the merits of convenient operation, high sensitivity and good repeatability, making it a practical method for analysis of 7‐ANZP in urine. Copyright © 2009 John Wiley & Sons, Ltd.
Simultaneous determination of six herbal components in intestinal perfusate by high‐performance liquid chromatography
Authors: Wang Zhanguo , Du Qingqing , Qiu Xuelan , Liu Fang , Tan Fei , Lan Ke , Jiang Xuehua , Jiang Qian 
Published: March 2009

AbstractAn effective, accurate and reliable HPLC with UV detection method was developed and validated for quantitation of six components: baicalin, berberine hydrochloride, quercetin, kaempferol, isorhamnetin and baicalein in intestinal perfusate using rotundin as an internal standard. The chromatographic separation was performed on a Welchrom‐C18 column (250 × 4.6 mm i.d. with 5.0 µm particle size) with a mobile phase consisting of acetonitrile, water, phosphoric acid and triethylamine (30:70:0.2:0.1,v/v) at a flow rate of 1.0 mL/min and a UV detection at 270 nm. The method had a chromatographic run time of 30 min and excellent linear behavior over the investigated concentration ranges observed with the values of r higher than 0.99 for all the analytes. The lower limit of quantification of the analytical method was 0.09 µg/mL for berberine hydrochloride, quercetin, kaempferol and baicalein and 0.18 µg/mL for baicalin and isorhamnetin. The intra‐ and inter‐day precisions measured at three concentration levels were all less than 10% for all analytes. The bias ranged from −6.91 to 4.33%. The validated method has been successfully applied to investigate the rat intestine absorption profiles of baicalin, berberine hydrochloride, quercetin, kaempferol, isorhamnetin and baicalein. Copyright © 2009 John Wiley & Sons, Ltd.