bluuebunny/crossref_metadata_2025 huggingface dataset:
Meta‐analysis methodology for combining treatment effects from Cox proportional hazard models with different covariate adjustments
Authors: Yuan Xing , Anderson Stewart J.
Published: July 2010

In Cox proportional hazard models with censored survival data, estimates of treatment effects with some important covariates omitted will be biased toward zero (Gailet al.,Biometrika71: 431–444). This can be especially problematic in meta‐analyses that combine estimates of parameters from studies where different covariate adjustments are made. Presently, few constructive solutions have been provided to address this issue. In this paper, we review the existing meta‐analysis methodologies for aggregated patient data (APD) and propose two meta‐regression models (meta‐ANOVA model and meta‐polynomial model) with indicators of different covariates in Cox proportional hazard models to adjust the heterogeneity of treatment effects due to omitted covariates across studies. Both parametric and nonparametric estimators for the pooled treatment effect and the heterogeneity variance are presented and compared. We illustrate the advantages of our proposed analytic procedures over the existing methodologies by simulation studies and real data analysis. The existing methodologies yield large estimation bias in the presence of an “incomparability” issue, whereas our proposed models can adjust the bias and thus provide an accurate estimation.
Substrate screening of protein kinases: Detection methods and combinatorial peptide libraries
Authors: Kim Mira , Shin Dong‐Sik , Kim Jaehi , Lee Yoon‐Sik
Published: July 2010

The study of protein kinases has become a matter of great importance in the development of new drugs for the treatment of diseases, including cancer and inflammation. Substrate screening is the first step in the fundamental investigation of protein kinases and the development of inhibitors for use in drug discovery. Towards this goal, various studies have been reported regarding the development of phospho‐peptide detection methods and the screening of phosphorylated peptide sites by protein kinases. This review introduces the detection methods for phosphorylation events using the reagents with (γ32P)ATP, ligand‐linked ATP, phospho‐peptide‐specific antibodies and metal chelating compounds. Chemical modification methods using β‐elimination for the detection of phospho‐Ser/Thr peptides are introduced as well. In addition, the implementations of combinatorial peptide libraries for screening peptide substrates of protein kinases are discussed. The phage display approach has been suggested as an alternative method of using synthetic peptides for screening the substrate specificities of protein kinase. However, a solid phase assay using a peptide library‐bound polymer resin or a peptide‐arrayed glass chip is preferred for high throughput screening (HTS). © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94: 753–762, 2010.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Overexpression of taurine transporter in Chinese hamster ovary cells can enhance cell viability and product yield, while promoting glutamine consumption
Authors: Tabuchi Hisahiro , Sugiyama Tomoya , Tanaka Saeko , Tainaka Satoshi
Published: July 2010

Transporters mediate the uptake of nutrients such as amino acids and the excretion of metabolites. The fact that transporters play crucial roles in regulating cell metabolism suggests that they might be useful targets for cell engineering to enhance the yield and/or quality of monoclonal antibody (MAb) produced by CHO cells. The taurine transporter (TAUT) is stably expressed in CHO‐DXB11 cells and is upregulated late in the culture period. We found that forcing the overexpression of TAUT delayed apoptotic cell death, extending the culture period. Thus, under fed‐batch small‐culture conditions, CHO cells that expressed pHyg‐TAUT plasmid (TAUT/CHO cells), but not those that contained the null plasmid pHyg (HYG/CHO cells), produced more MAb (P < 0.01) and less lactate (P < 0.05). In a 1‐L bioreactor, a representative high‐yield TAUT/CHO cell line (T10) showed >80% viability for more than 1 month and a 47% increase in medium MAb concentration. In T10 cells, the upregulation of TNF‐α mRNA (an apoptosis marker) and the accumulation of ammonia late in the culture period were suppressed. Moreover, if an excess of taurine was added, T10 cells efficiently consumed glutamine but not other amino acids, so T10 cells may have gained a glutamine transporter‐like function. Because a considerable amount of metabolic energy is derived from glutamine, this active glutamine consumption in T10 cells might be a reason for the improved cell viability and MAb concentration. These results demonstrate that forcing the overexpression of TAUT in CHO cells can enhance cell culture performance and increase MAb titer. Biotechnol. Bioeng. 2010;107: 998–1003. © 2010 Wiley Periodicals, Inc.
Generating stable chinese hamster ovary cell clones to produce a truncated SARS‐CoV spike protein for vaccine development
Authors: Lin Shih‐Chang , Leng Chih‐Hsiang , Wu Suh‐Chin
Published: July 2010

The spike (S) protein of the severe acute respiratory syndrome coronavirus (SARS‐CoV) is important for vaccine development. STR2 (an 88 kDa truncated SARS‐CoV TW1 S protein carrying the S fragments S‐74‐253, S‐294‐739, and S‐1129‐1255) is capable of expressing a major form of glycoprotein as endo H‐sensitive (∼115 kDa) in CHO cells. To establish stable expressing cell clones, we transfected CHO/dhFr‐cells with the amplifiable vectors ISID (IRES‐driven dhfr) and ISIZ (SV40‐driven dhfr) to select stepwise MTX, and observed enhanced ∼115 kDa glycoform generation through gene amplification. Following stepwise MTX selection, we compared gene amplification levels between two vectors in engineered CHO cell chromosomes. These results confirm that the IRES‐driven dhfr promoter generates greater gene amplification, which in turn enhances STR2 expression. Our results indicate that the ∼115 kDa glycoform of STR2 protein was capable of increasing after gene amplification. The STR2 glycoform did not change between suspension and serum‐free cultures, suggesting that the stable and amplified cell clones analyzed in this study have potential for producing homologous STR2 on a large scale. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010
Structure‐Guided Minimalist Redesign of the L‐Fuculose‐1‐Phosphate Aldolase Active Site: Expedient Synthesis of Novel Polyhydroxylated Pyrrolizidines and their Inhibitory Properties Against Glycosidases and Intestinal Disaccharidases
Authors: Garrabou Xavier , Gómez Livia , Joglar Jesús , Gil Sergi , Parella Teodor , Bujons Jordi , Clapés Pere
Published: July 2010

A minimalist active site redesign of the L‐fuculose‐1‐phosphate aldolase from E. coli FucA was envisaged, to extend its tolerance towards bulky and conformationally restricted N‐Cbz‐amino aldehyde acceptor substrates (Cbz=benzyloxycarbonyl). Various mutants at the active site of the FucA wild type were obtained and screened with seven sterically demanding N‐Cbz‐amino aldehydes including N‐Cbz‐prolinal derivatives. FucA F131A showed an aldol activity of 62 μmol h−1 mg−1 with (R)‐N‐Cbz‐prolinal, whereas no detectable activity was observed with the FucA wild type. For the other substrates, the F131A mutant gave aldol activities from 4 to about 25 times higher than those observed with the FucA wild type. With regard to the stereochemistry of the reactions, the (R)‐amino aldehydes gave exclusively the anti configured aldol adducts whereas their S counterparts gave variable ratios of anti/syn diastereoisomers. Interestingly, the F131A mutant was highly stereoselective both with (R)‐ and with (S)‐N‐Cbz‐prolinal, exclusively producing the anti and syn aldol adducts, respectively. Molecular models suggest that this improved activity towards bulky and more rigid substrates, such as N‐Cbz‐prolinal, could arise from a better fit of the substrate into the hydrophobic pocket created by the F131A mutation, due to an additional π–cation interaction with the residue K205′ and to efficient contact between the substrate and the mechanistically important Y113′ and Y209′ residues. An expedient synthesis of novel polyhydroxylated pyrrolizidines related to the hyacinthacine and alexine types was accomplished through aldol additions of dihydroxyacetone phosphate (DHAP) to hydroxyprolinal derivatives with the hyperactive FucA F131A as catalyst. The iminocyclitols obtained were fully characterised and found to be moderate to weak inhibitors (relative to 1,4‐dideoxy‐1,4‐imino‐L‐arabinitol (LAB) and 1,4‐dideoxy‐1,4‐imino‐D‐arabinitol (DAB)) against glycosidases and rat intestinal saccharidases.
Olfactory ensheathing glia express aquaporin 1
Authors: Shields Shannon D. , Moore Katherine D. , Phelps Patricia E. , Basbaum Allan I.
Published: July 2010

Olfactory ensheathing glia (OEG) are distinct from other glia in their developmental origin, presence in both the peripheral and central nervous systems, and highly restricted location. OEG are present only in the olfactory lamina propria, olfactory nerve, and the outer two layers of the olfactory bulb, where they envelop bundles of olfactory sensory neuron axons in a manner distinct from myelination. Because of their unique properties and their association with the continually generated olfactory sensory neurons, OEG have attracted interest for their potential capacity to support axonal regeneration, for example, after spinal cord injury. However, study of the properties and function of OEG has been hampered by a paucity of neurochemical markers with which to identify and distinguish them definitively from other types of glia. Here we provide evidence through anatomical colocalization studies that OEG express the water channel aquaporin 1 (AQP1), both in vivo and in vitro. We propose that AQP1 expression represents an important distinguishing characteristic of OEG, which may impart unique function to these glia. J. Comp. Neurol. 518:4329–4341, 2010. © 2010 Wiley‐Liss, Inc.
Expression of Pax6 and Sox2 in adult olfactory epithelium
Authors: Guo Zhen , Packard Adam , Krolewski Richard C. , Harris Margaret T. , Manglapus Glen L. , Schwob James E.
Published: July 2010

The olfactory epithelium maintains stem and progenitor cells that support the neuroepithelium's life‐long capacity to reconstitute after injury. However, the identity of the stem cells and their regulation remain poorly defined. The transcription factors Pax6 and Sox2 are characteristic of stem cells in many tissues, including the brain. Therefore, we assessed the expression of Pax6 and Sox2 in normal olfactory epithelium and during epithelial regeneration after methyl bromide lesion or olfactory bulbectomy. Sox2 is found in multiple kinds of cells in normal epithelium, including sustentacular cells, horizontal basal cells, and some globose basal cells. Pax6 is coexpressed with Sox2 in all these but is also found in duct/gland cells as well as olfactory neurons that innervate necklace glomeruli. Most of the Sox2/Pax6‐positive globose basal cells are actively cycling, but some express the cyclin‐dependent kinase inhibitor p27Kip1 and are presumably mitotically quiescent. Among globose basal cells, Sox2 and Pax6 are coexpressed by putatively multipotent progenitors (labeled by neither anti‐Mash1 nor anti‐Neurog1) and neuron‐committed transit amplifying cells (which express Mash1). However, Sox2 and Pax6 are expressed by only a minority of immediate neuronal precursors (Neurog1 and NeuroD1 expressing). The assignment of Sox2 and Pax6 to these categories of globose basal cells is confirmed by a temporal analysis of transcription factor expression during the recovery of the epithelium from methyl bromide‐induced injury. Each of the Sox2/Pax6‐colabeled cell types is at a remove from the birth of neurons; thus, suppressing neuronal differentiation may be among the roles of Sox2/Pax6 in the olfactory epithelium. J. Comp. Neurol. 518:4395–4418, 2010. © 2010 Wiley‐Liss, Inc.
Immunohistochemical parcellation of the ferret (Mustela putorius) visual cortex reveals substantial homology with the cat (Felis catus)
Authors: Homman‐Ludiye Jihane , Manger Paul R. , Bourne James A.
Published: July 2010

Electrophysiological mapping of the adult ferret visual cortex has until now determined the existence of 12 retinotopically distinct areas; however, in the cat, another member of the Carnivora, 20 distinct visual areas have been identified by using retinotopic mapping and immunolabeling. In the present study, the immunohistochemical approach to demarcate the areal boundaries of the adult ferret visual cortex was applied in order to overcome the difficulties in accessing the sulcal surfaces of a small, gyrencephalic brain. Nonphosphorylated neurofilament (NNF) expression profiles were compared with another classical immunostain of cortical nuclei, Cat‐301 chondroitin sulfate proteoglycan (CSPG). Together, these two markers reliably demarcated the borders of the 12 previously defined areas and revealed further arealization beyond those borders to a total of 19 areas: 21a and 21b; the anterolateral, posterolateral, dorsal, and ventral lateral suprasylvian areas (ALLS, PLLS, DLS, and VLS, respectively); and the splenial and cingulate visual areas (SVA and CVA). NNF expression profile and location of the newly defined areas correlate with previously defined areas in the cat. Moreover, NNF and Cat‐301 together revealed discrete expression domains in the posteroparietal (PP) cortex, demarcating four subdivisions in the caudal lateral and medial domains (PPcL and PPcM) and rostral lateral and medial domains (PPrL and PPrM), where only two retinotopic maps have been previously identified (PPc and PPr). Taken together, these studies suggest that NNF and Cat‐301 can illustrate the homology between cortical areas in different species and draw out the principles that have driven evolution of the visual cortex. J. Comp. Neurol. 518:4439–4462, 2010. © 2010 Wiley‐Liss, Inc.
Implementation of pigment‐dispersing factor‐immunoreactive neurons in a standardized atlas of the brain of the cockroachLeucophaea maderae
Authors: Wei Hongying , el Jundi Basil , Homberg Uwe , Stengl Monika
Published: July 2010

The cockroachLeucophaea maderaeis an established model in circadian rhythm research. Its circadian clock is located in the accessory medulla of the brain. Pigment‐dispersing factor‐immunoreactive (PDF‐ir) neurons of the accessory medulla act as circadian pacemakers controlling locomotor activity rhythms. To characterize the neuronal network of the circadian system inL. maderae, the PDF‐ir neurons were implemented into a standardized three‐dimensional atlas of the cockroach brain. Serial confocal images from 20 wholemount brains were used for the construction of the atlas comprising 21 neuropils. Two different standardization protocols were employed: the iterative shape averaging (ISA) procedure using an affine transformation followed by iterative non‐rigid registrations, and the virtual insect brain (VIB) protocol employing local non‐rigid transformations after global and local rigid transformations. Quantitative analysis of the 20 brains revealed that volumes of the accessory medulla are directly correlated with the volumes of the medulla, the protocerebral bridge, and the upper division of the central body, suggesting functional connections among these neuropils. For a standardized reconstruction of the circadian pacemaker network, the ISA protocol was used to register PDF‐ir neurons in the standard cockroach brain. The registration revealed that two PDF‐ir arborization areas in the brain are highly interconnected with other PDF‐ir projection sites and appear to be contacted both by fibers in the posterior and the anterior optic commissures. The distances between PDF‐ir branching areas show specific numerical relationships that might be physiologically relevant for temporal encoding. J. Comp. Neurol. 518:4113–4133, 2010. © 2010 Wiley‐Liss, Inc.
Endogenous GluR1‐containing AMPA receptors translocate to asymmetric synapses in the lateral amygdala during the early phase of fear memory formation: An electron microscopic immunocytochemical study
Authors: Nedelescu Hermina , Kelso Catherine M. , Lázaro‐Muñoz Gabriel , Purpura Mari , Cain Christopher K. , Ledoux Joseph E. , Aoki Chiye
Published: July 2010

Although glutamate receptor 1 (GluR1)‐containing α‐amino‐3‐hydroxyl‐5‐methyl‐4‐isoxazole‐propionate receptors (GluR1‐AMPARs) are implicated in synaptic plasticity, it has yet to be demonstrated whether endogenous GluR1‐AMPARs undergo activity‐dependent trafficking in vivo to synapses to support short‐term memory (STM) formation. The paradigm of pavlovian fear conditioning (FC) can be used to address this question, because a discrete region—the lateral amygdala (LA)—has been shown unambiguously to be necessary for the formation of the associative memory between a neutral stimulus (tone [CS]) and a noxious stimulus (foot shock [US]). Acquisition of STM for FC can occur even in the presence of protein synthesis inhibitors, indicating that redistribution of pre‐existing molecules to synaptic junctions underlies STM. We employed electron microscopic immunocytochemistry to evaluate alterations in the distribution of endogenous AMPAR subunits at LA synapses during the STM phase of FC. Rats were sacrificed 40 minutes following three CS‐US pairings. In the LA of paired animals, relative to naïve animals, the proportion of GluR1‐AMPAR‐labeled synapses increased 99% at spines and 167% in shafts. In the LA of unpaired rats, for which the CS was never associated with the US, GluR1 immunoreactivity decreased 84% at excitatory shaft synapses. GluR2/3 immunoreactivity at excitatory synapses did not change detectably following paired or unpaired conditioning. Thus, the early phase of FC involves rapid redistribution specifically of the GluR1‐AMPARs to the postsynaptic membranes in the LA, together with the rapid translocation of GluR1‐AMPARs from remote sites into the spine head cytoplasm, yielding behavior changes that are specific to stimulus contingencies. J. Comp. Neurol. 518:4723–4739, 2010. © 2010 Wiley‐Liss, Inc.
Energy‐efficient single‐clock‐cycle binary comparator
Authors: Frustaci Fabio , Perri Stefania , Lanuzza Marco , Corsonello Pasquale
Published: July 2010

A new fast low‐power single‐clock‐cycle binary comparator is presented. High speed is assured by using parallel‐prefix architecture, whereas low power is guaranteed by reducing the switching activities of the internal nodes. When implemented with the ST 90 nm 1 V CMOS technology, the proposed circuit exhibits a 4.5 GHz maximum running frequency and 0.77µW/ MHz energy dissipation. Copyright © 2010 John Wiley & Sons, Ltd.
Optimizing the setup of a flow cytometric cell sorter for efficient quantitative sorting of long filamentous cyanobacteria
Authors: van Dijk Mark A. , Gregori Gerald , Hoogveld Hans L. , Rijkeboer Machteld , Denis Michel , Malkassian Anthony , Gons Herman J.
Published: July 2010

Heterogeneity within natural phytoplankton communities makes it very difficult to analyze parameters at the single‐cell level. Flow cytometric sorting is therefore a useful tool in aquatic sciences, as it provides material for post‐sort analysis and culturing. Sorting subpopulations from natural communities, however, often requires handling morphologically diverse and complex particles with various abundances. Long particles, such as filament‐forming cyanobacteria (>100‐μm long), prove very difficult to handle. These potentially toxic organisms are widespread in eutrophic systems and have important ecological consequences. Being able to sort filamentous cyanobacteria efficiently and as viable cells is therefore highly desirable when studying factors associated with their toxicity and occurrence. This unconventional sorting requires extensive user experience and special instrument setup. We have investigated the effect of hydrodynamic and electromechanical components of a flow cytometer, and sorting protocol on the quantitative sorting efficiency of these long particles using two filamentous cyanobacterial strains with average lengths of ∼100 and ∼300 μm. Sorting efficiency ranged from 9.4 to 96.0% and was significantly affected by filament length, sorting envelope, drop delay (dd), and for the long species also by tip size, but not by cycle time. Filaments survived sorting and were not damaged. The optimal settings found for the modular MoFlo® cell‐sorter to sort the filaments were a 100‐μm flow tip at 30 psi (207 kPa) with a three‐droplet envelope in Enrich mode while using an extended analysis time of 17.6 μs and an intermediate plate charge and deflection percentage combination of 3,000 V/60%, combined with a dd 0 for the cultures with 100‐μm filaments and dd +1 for the culture with 300‐μm filaments. To the best of our knowledge, the filaments up to 1063.5 μm sorted in this study are the longest ever sorted. © 2010 International Society for Advancement of Cytometry
Screening and prevalence of peripheral neuropathy in type 2 diabetic outpatients: a randomized multicentre survey in 12 city hospitals of China
Authors: Liu Fang , Bao Yuqian , Hu Renming , Zhang Xiuzhen , Li Hong , Zhu Dalong , Li Yanbing , Yan Li , Li Yuxiu , Lu Juming , Li Qiang , Zhao Zhigang , Ji Qiuhe , Jia Weiping
Published: July 2010

Background

The 10‐g Semmes–Weinstein monofilament and 128‐Hz tuning fork examinations are considered simple and effective screening instruments for diabetic peripheral neuropathy. This study investigated the prevalence of diabetic peripheral neuropathy of combining both methods in type 2 diabetic outpatients in Chinese urban hospitals.

Methods

Pressure sensation and vibration perception were randomly screened using 10‐g Semmes–Weinstein monofilament and 128‐Hz tuning fork in type 2 diabetic outpatients from 12 centres in 8 Chinese cities in a randomized, multicentre epidemiological study. The prevalence and treatment status of neuropathy were assessed, and relevant risk factors were analysed.

Results

A total of 1197 outpatients were screened and 1193 were enrolled in this study, including 1067 known cases of diabetes (KDM group) and 126 newly diagnosed cases of diabetes (NDM group). Screening results showed that the prevalence of perception defects was 17.02% in the total population, 18.28% in the known DM group and 6.35% in the new DM group, respectively. The frequency of previous diabetic peripheral neuropathy examination was only 32% in the known DM group and 31.75% in the new DM group. Thirty‐two percent of known DM patients with diabetic peripheral neuropathy did not receive any treatment formerly. It also revealed that there was a region‐wise difference in prevalence of diabetic peripheral neuropathy, and it increased with age and diabetic duration. Retinopathy, HbA1c, diabetes duration and age were independent risk factors for diabetic peripheral neuropathy.

Conclusions

The screening and treatment rate of diabetic peripheral neuropathy is low in China. The prevalence of diabetic peripheral neuropathy in type 2 diabetic outpatients in Chinese city hospitals is 17.2%. Diabetic retinopathy is an independent risk factor for diabetic peripheral neuropathy. Copyright © 2010 John Wiley & Sons, Ltd.
Combined deficiency of MSH2 and Sμ region abolishes class switch recombination
Authors: Leduc Claire , Haddad Dania , Laviolette‐Malirat Nathalie , Nguyen Huu Ngoc‐Sa , Khamlichi Ahmed Amine
Published: July 2010

Class switch recombination (CSR) is mediated by G‐rich tandem repeated sequences termed switch regions. Transcription of switch regions generates single‐stranded R loops that provide substrates for activation‐induced cytidine deaminase. Mice deficient in MSH2 have a mild defect in CSR and analysis of their switch junctions has led to a model in which MSH2 is more critical for switch recombination events outside than within the tandem repeats. It is also known that deletion of the whole Sμ region severely impairs but does not abrogate CSR despite the lack of detectable R loops. Here, we demonstrate that deficiency of both MSH2 and the Sμ region completely abolishes CSR and that the abrogation occurs at the genomic level. This finding further supports the crucial role of MSH2 outside the tandem repeats. It also indicates that during CSR, MSH2 has access to activation‐induced cytidine deaminase targets in R‐loop‐deficient Iμ‐Cμ sequences rarely used in CSR, suggesting an MSH2‐dependent DNA processing activity at the Iμ exon that may decrease with transcription elongation across the Sμ region.
Systematic Hydrothermal Investigation of Metal Phosphonatobenzenesulfonates by High‐Throughput Methods
Authors: Maniam Palanikumar , Näther Christian , Stock Norbert
Published: July 2010

A high‐throughput (HT) investigation using the rigid bifunctional ligand 4‐phosphonobenzenesulfonic acid, H2O3P‐C6H4‐SO3H (H3L), generated five new phosphonatobenzenesulfonates with copper(II) or lead(II) ions. A comprehensive HT study comprising the screenings of different metal ions, metal salt types and the synthesis optimization were conducted whereby the influence of pH and molar ratios M2+/H3L were investigated. The HT‐study led to five new compounds Pb2[(O3P‐C6H4‐SO3)(OH)] (1), Cu1.5[(O3P‐C6H4‐SO3)(H2O)] (2), NaCu(O3P‐C6H4‐SO3)(H2O)3 (3), Cu2[(O3P‐C6H4‐SO3)(OH)(H2O)] (4) and Cu3[(O3P‐C6H4‐SO3)2(H2O)2] (5). Metal ion screening showed lead(II) and copper(II) to be suitable metal ions. The utilization of discovery and focused arrays allowed to determine the optimal formation fields of the respective compounds. The crystal structures were determined from single‐crystal X‐ray diffraction and revealed the presence of various MOx polyhedra that form clusters, chains or layers which are connected through the organic linker. IR spectra, thermogravimetric studies, magnetic susceptibility measurements and elemental analyses were conducted to further characterize the compounds 1, 3, 4 and 5.
Porous Porphyrin Nanoarchitectures on Surfaces
Authors: Makiura Rie , Kitagawa Hiroshi
Published: July 2010

Controlling the size and the growth direction of porous hybrid objects – metal–organic frameworks (MOFs) or porous coordination polymers (PCPs) – at the nanoscale is a critical issue for enabling their use in a number of potential applications that have arisen from the current remarkable activity in studying such porous materials. This microreview describes the recent progress in the design, growth, and characterization of multidimensional nanoarchitectures by employing porphyrin‐based components. The versatility of the sequential bottom‐up fabrication process, which uses multitopic molecular building units assembled by appropriately chosen linkers, is suitable to be extended to the formation of a rich variety of nanostructures endowed with pores on surfaces.
Effect of carnitine on serum cholesterol of alcoholic cardiomyopathy dogs
Authors: Yuan Lin , Li Wei‐Min , Jing Ling , Zhou Li‐Jun
Published: July 2010

Carnitine is known to be essential for metabolism regulation in some heart diseases such as coronary heart disease. We evaluated the effect of carnitine and valsartan on alcoholic cardiomyopathy (ACM); surprisingly, it was found that carnitine leads to variations in serum lipids. The results of our study, supported by cardiac function assessment, LVW/BW ratio, hematoxylin and eosin staining, and electron microscopic morphology, not only demonstrated the validity of our ACM model but also addressed the therapeutic benefits of carnitine and valsartan in antagonizing ACM development. The alcohol group displayed a high LVEDd and low EF and FS, indicating both heart failure and cardiac remodeling. Compared with the alcohol and alcohol/valsartan groups, the concentration of serum cholesterol in the alcohol/carnitine group was significantly increased between baseline and 6 months. The body weights of dogs from the alcohol group slowly increased between baseline and 6 months, although the LV weight increased quickly. The results suggest that both carnitine and valsartan have a favorable effect on ACM. However, the fact that carnitine could increase the serum cholesterol level should lead to caution in the treatment of ACM patients who are suffering from coronary disease in the meantime.
Analysis of triacylglycerols in refined edible oils by isocratic HPLC‐ESI‐MS
Authors: Zeb Alam , Murkovic Michael
Published: July 2010

A simple, fast and reproducible reversed‐phase high performance liquid chromatography (HPLC) method coupled to electrospray ionization mass spectrometry (ESI‐MS) for the analysis of triacylglycerols (TAGs) species in the commercial edible oils has been developed. The TAGs species were separated using isocratic 18% isopropanol in methanol and a Phenomenex C18 column. The ESI‐MS conditions were optimized using flow injection analysis of standard TAG. Fifteen, fourteen, and sixteen TAGs were separated and identified in corn oil, rapeseed oil, and sunflower oil, respectively. The presence of intense protonated molecular (M + H+), ammonium (M + ${\rm NH}_{4}^{ + } $), and sodium (M + Na+) adducts ions and their respective diacylglycerols ions in the ESI‐MS spectra showed correct identification of TAGs. Some minor potassium adducts (M + K+) were also found. In addition, the identity of the fatty acid, position of each fatty acid, and the location of the double bond in the fatty acid moiety were explained. It was found that this isocratic method is useful for fast screening and identification of triacylglycerols in lipids.
Self‐Assembling Depsipeptide Dendrimers and Dendritic Fullerenes with New cis‐ and trans‐Symmetric Hamilton Receptor Functionalized Zn–Porphyrins: Synthesis, Photophysical Properties and Cooperativity Phenomena
Authors: Maurer Katja , Grimm Bruno , Wessendorf Florian , Hartnagel Kristine , Guldi Dirk M. , Hirsch Andreas
Published: July 2010

Two novel supramolecular building blocks, namely cis‐ and trans‐symmetric zinc–porphyrins bearing Hamilton receptors as their focal points (10 and 15), were self‐assembled with (i) first‐, second‐ and third‐generation depsipeptide cyanurates (21–23); (ii) second‐generation dendrofullerene (24), and (iii) cyanuric acid substituted fullerene (20), and probed in a series of photophysical investigations. Importantly, an overall 1:2 stoichiometry was confirmed with binding constants Kn, and Hill coefficients nH that indicate remarkable cooperativities. As a general feature, stronger binding evolves from the trans‐symmetric porphyrin isomer, although the increased steric demand of the depsipeptide ligandsmeans that the binding constants decrease with each generation. The self‐assembly of 10 or 15 with 20 affords novel electron donor–acceptor hybrids that reveal, upon excitation,intra‐hybrid charge‐transfer events.
Stereochemical Analysis of the Enzymic Reduction of the Double Bond of α‐ and β‐Substituted Nitrostyrenes and α‐Ethoxycinnamaldehyde through Deuterium Labelling Experiments
Authors: Brenna Elisabetta , Fronza Giovanni , Fuganti Claudio , Gatti Francesco G.
Published: July 2010

2H NMR studies and comparison with authentic labelled reference compounds prepared from the (Z)‐acetamido‐cinnamic acid 10 and from (Z)‐2‐ethoxy‐3‐(4‐methoxyphenyl)prop‐2‐en‐1‐ol (14), respectively, by catalytic syn reduction with deuterium gas show that the baker's yeast‐mediated saturation in the presence of deuterated water of the double bond of (E)‐α‐(hydroxymethyl)nitrostyrene (2) and of the (Z)‐α‐ethoxycinnamaldehyde (3) leads to (2R,3R)‐[2,3‐2H2]‐3‐(4‐methoxyphenyl)‐2‐nitropropan‐1‐ol (5) and to(1R,2S,3R)‐[1,2,3‐3H2]‐2‐ethoxy‐3‐(4‐methoxyphenyl)propan‐1‐ol (6), respectively, thus supporting an anti mode of hydrogen addition across the activated double bond, with hydride delivery in β‐position respect to the activating group from the upper side of the molecule.
Quantitative assessment of multi‐laboratory reproducibility of SDS‐PAGE assays: Digestion pattern of β‐casein and β‐lactoglobulin under simulated conditions
Authors: Defernez Marianne , Mandalari Giuseppina , Mills Elizabeth Noami Clare
Published: July 2010

A digestion protocol was applied in triplicate by ten laboratories, simulating in vivo gastric and duodenal conditions. The intra‐ and inter‐laboratory variability in the kinetics of protein degradation was quantified, focussing on the digestion of β‐casein under gastric conditions, and of β‐lactoglobulin (β‐Lg) under duodenal conditions. The addition of surfactants such as phosphatidylcholine (PC) in the digestion mix was also evaluated. Identification and quantification of peptide bands on SDS‐PAGE gels formed the basis for analysis. An average intensity loss of 69% (SD=13.5) at 5 min (89% at 10 min, with SD=5.5) was observed for β‐casein, whereas the β‐Lg duodenal digestion showed an 82% loss at 30 min (SD=14.2). Constant rates of first‐order reactions showed that for fast reactions, inaccuracies in the time of first sampling contributed to the variability, which were also affected by image quality, saturation, and the splitting of time courses across gels. Breakdown products for β‐casein included ten other polypeptides, with four detected in all and two in most gels, and for β‐Lg ten polypeptides, with five detected in most, and two in two‐third of the cases. Addition of PC in the gastric phase led to β‐Lg intensity loss only a quarter as large as without PC and altered β‐Lg proteolysis in the duodenal compartment.
Epigenetic regulation of miR‐196b expression in gastric cancer
Authors: Tsai Kuo‐Wang , Hu Ling‐Yueh , Wu Chew‐Wun , Li Sung‐Chou , Lai Chun‐Hung , Kao Hsiao‐Wei , Fang Wen‐Liang , Lin Wen‐chang
Published: July 2010

MicroRNAs (miRNAs) are short noncoding RNAs that play important roles in cellular processes and disease pathogenesis via the control of specific targeted gene expression. The miR‐196s miRNA is encoded at three paralogous loci in three HOX clusters and acts as an oncogenic miRNA in cancer progression. Recent studies have demonstrated that the expression of miR‐196b increases cell proliferation and survival in leukemic cells. Here, we used a sequential methylation analysis to reveal that the methylation status correlated well with miR‐196b expression in different cell lines. Treatment with the demethylating drug 5‐Aza‐dC reactivated miR‐196b transcription in methylation‐silenced cells. Using in vitro methylation approach, we further provide evidences that promoter hypermethylation represses miR‐196b transcriptional activation tightly in human cancer cell lines. We also demonstrate that the expression of miR‐196b is significantly elevated in gastric cancer and that hypomethylation status of miR‐196b CpG islands frequently is observed in primary gastric tumors. Our results provide important information on miR‐196s regulation and demonstrate that abnormal DNA hypomethylation induces overexpression of miR‐196b in gastric cancer. © 2010 Wiley‐Liss, Inc.
Interphase fluorescence in situ hybridization on selected plasma cells is superior in the detection of cytogenetic aberrations in plasma cell dyscrasia
Authors: Put Natalie , Lemmens Heidi , Wlodarska Iwona , Konings Peter , Moreau Yves , Hagemeijer Anne , Vandenberghe Peter , Michaux Lucienne
Published: July 2010

Interphase fluorescence in situ hybridization (FISH) detects nonrandom cytogenetic abnormalities in plasma cell (PC) dyscrasia according to PC burden. However, when performed on cultured whole bone marrow (BM), it often fails to detect these aberrations. We have compared this interphase FISH technique with FISH after PC purification or identification to detect recurrent aberrations. In this study, 235 BM samples were collected from patients with multiple myeloma (MM) or related PC disorders regardless of disease status. All samples were analyzed in parallel. Clonal abnormalities were detected in 34.9% of cultured samples compared with 71.0% PC selected samples (P < 0.001). Moreover, FISH on PCs allowed to detect more abnormalities per case (P < 0.001) and identified higher percentages of abnormal nuclei (P < 0.001). This study indicates that FISH on PCs is the preferred technique for routine cytogenetic investigation of MM. © 2010 Wiley‐Liss, Inc.
The alcohol use disorders identification test (AUDIT) and its derivatives in screening for heavy drinking among the elderly
Authors: Aalto Mauri , Alho Hannu , Halme Jukka T. , Seppä Kaija
Published: July 2010

Objective

The performance of the Alcohol Use Disorders Identification Test (AUDIT) in screening for heavy drinking among the elderly has been unsatisfactory. The aim of the present study was to determine whether tailoring the cut point improves the performance of the AUDIT and its derivatives in this age group.

Methods

From a stratified random sample of 804 Finns aged 65–74 years, 517 subjects (64.3%) completed the AUDIT and the Timeline Follow‐back (TLFB) interview regarding alcohol consumption. A subject was defined as a heavy drinker if consumption of ≥8 drinks (approx. 12 g) on average in a week or ≥4 drinks at least in 1 day during the prior 28 days was reported. Combinations in which both sensitivity and specificity are ≥0.8 were defined as optimal. The elderly specific AUDIT‐3 is a modification in which the binge drinking threshold is ≥4 drinks.

Results

Based on the TLFB, 118 subjects (22.8%) were heavy drinkers. The areas under receiving operating characteristics curves (AUROCs) were equivalent (≥0.898) for all questionnaires. When using the standard cut point of ≥8 for the AUDIT, the sensitivity was 0.48. Lowering the cut point to ≥5 led to both a sensitivity and specificity over 0.85. The optimal cut point of the AUDIT‐C was ≥4. The AUDIT‐QF, AUDIT‐3 and elderly specific AUDIT‐3 did not provide optimal combinations of sensitivity and specificity with any cut point.

Conclusions

The AUDIT and AUDIT‐C are accurate in screening for heavy drinking among the elderly if the cut points are tailored to this age group. Copyright © 2010 John Wiley & Sons, Ltd.
The flexible alignment of molecular structures using simulated annealing with weighted Lagrangian multipliers
Authors: Raymond John W. , Holsworth Daniel D. , Jalaie Mehran
Published: July 2010

A framework for superimposing small molecules is presented. The proposed method consists of a simple atom‐based, flexible alignment. The optimization procedure used in the alignment is based on a recently published variant of the simulated annealing whereby nonlinear constraints are accommodated using Lagrangian multipliers. It differs from other published superposition algorithms in that any number of nonlinear constraints can be readily imposed on the structural alignment directly through the objective function without assuming an a priori trade‐off between competing conditions. These can include equality and equality constraints on distances, angles, and energy states. Examples illustrating the use of the proposed approach are also provided. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Understanding of bonding and mechanical characteristics of cementitious mineral tobermorite from first principles
Authors: Tunega Daniel , Zaoui Ali
Published: July 2010

This paper reports density functional theory study of the structural and mechanical properties of tobermorite mineral (9 Å phase) as one of the main component of cementitious materials in a concrete chemistry. Calculated bulk modulus and elastic constants reflect a relatively high resistance of the tobermorite structure with respect to external isostatic compression. Moreover, the elastic constants proved the anisotropic character of the tobermorite structure. The directions parallel to the axb plane are more resistant to the compression than the perpendicular direction. The largest contribution to this resistance comes from the “dreierketten” silicate chains. The bonding analysis linked macroscopic mechanical properties and the atomic structure of the tobermorite. It was found that polar covalent SiO bonds are stiffer than iono‐covalent CaO bonds. The SiO4 tetrahedra are resistant with respect to the compression and the effect of external pressure is reflected by the large mutual tilting of these tetrahedra as it is shown by changes of the SiOSi bridging angles. Polyhedra with the seven‐fold coordinated Ca2+ cations undergo large structural changes. Especially, axial CaO bonds perpendicular to the axb plane are significantly shortened. Besides, it was shown that structural parameters, more or less in parallel orientation to the axb plane, are mainly responsible for the high resistance of the tobermorite structure to external pressure. The main mechanism of a dissipation of energy entered to the structure through the compression is proceeded by the tilting of the tetrahedra of the silicate chains and by large shortening of the axial CaO distances. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
An estimation method of binding free energy in terms of ABEEMσπ/MM and continuum electrostatics fused into LIE method
Authors: Chen Shu‐Ling , Zhao Dong‐Xia , Yang Zhong‐Zhi
Published: July 2010

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. The linear interaction energy method is combined with atom‐bond electronegativity equalization method at σπ level Force field (fused into molecular mechanics) and generalized Born continuum model calculation of electrostatic solvation for the estimation of the absolute free energy of binding. The parameters of this method are calibrated by using a training set of 24 HIV‐1 protease–inhibitor complexes (PDB entry 1AAQ). A correlation coefficient of 0.93 was obtained with a root mean square deviation of 0.70 kcal mol−1. This approach is further tested on seven inhibitor and protease complexes, and it provides small root mean square deviation between the calculated binding free energy and experimental binding free energy without reparametrization. By comparing the radii of gyration and the hydrogen bond distances between ligand and protein of three training model molecules, the consistent comparison result of binding free energy is obtained. It proves that this method of calculating the binding free energy with appropriate structural analysis can be applied to quickly assess new inhibitors of HIV‐1 proteases. To test whether the parameters of this method can apply to other drug targets, we have validated this method for the drug target cyclooxygenase‐2. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Density functional theory study of a molecular allosteric switch for 2,2′‐bipyridyl‐3,3′‐15‐crown‐5
Authors: Miao Yuan , Wang Xueye , Jin Xin , Yi Ling , Ren Cuihuan
Published: July 2010

A classical model of “molecular machine,” which acts as an ON–OFF switch for 2,2′‐bipyridyl‐3,3′‐15‐crown‐5 (L), has been theoretically studied. It is highly important to understand the mechanism of this switch. The alkali‐metal cations (Na+ and K+) and W(CO)4 fragment are introduced to coordinate with the different active sites of L, respectively. The density functional theory (DFT) method is used for understanding the stereochemical structural natures and thermodynamic properties of all the target molecules at B3LYP/6‐31G(d) and SDD (Stuttgart–Dresden) level, together with the corresponding effective core potential (ECP) for tungsten (W). The fully optimized geometries have been performed with real frequencies, which indicate the minima states. The nucleophilicity of L has been investigated by the Fukui functions. The natural bond orbital analysis is used to study the intermolecular charge‐transfer interactions and explore the origin of the internal forces of the molecular switch. In addition, the binding energies, enthalpies, Gibbs free energies, and the cation exchange energies have been studied for L, W(CO)4L, and their corresponding complexes. The properties of the complexes displayed by in presence or absence of the W(CO)4 fragment are also analyzed. The calculated results of allosterism displayed by L are in a good agreement with the experimental results. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011
Promising antimicrobial agents: Synthetic approaches to novel tricyclic and tetracyclic pyrimidinones with antimicrobial properties
Authors: Gaber Hatem M. , Bagley Mark C. , Sherif Sherif M. , Abdul‐Raouf Usama M.
Published: July 2010

magnified image

New tricyclic pyrimidinone derivatives were obtained from the corresponding thiazolopyrimidinone or hydrazino systems. The annelation of tricyclic hydrazino compound with 1,2,4‐triazole and tetrazole moieties gave novel tetracyclic condensed pyrimidinones. The investigation of the antimicrobial properties of tricyclic and tetracyclic pyrimidinones, by agar‐well diffusion assay, was carried out against six pathogenic bacteria (Bacillus cereus, Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Klebsiella spp, and Salmonella typhyrium) and four pathogenic fungi (Aspergillus flavus, Aspergillus niger, Aspergillus fumigatus, and Trichderma horozianum). Most of the compounds tested exhibited some degree of antimicrobial activity against microorganisms. Among these compounds, 4‐benzylidenhydrazino‐8‐cyano‐7‐(furan‐2‐yl)thiazolo[3,2‐a:4,5‐d′]dipyrimidin‐9‐one (12) showed the most favorable antibacterial activity, while compound 17 showed the highest effect on fungi. Interestingly, tetrazole derivative 19 displayed a remarkable effect on fungi much more than the corresponding 3‐substituted triazole derivatives on the one hand, whereas the lowest effect on bacteria on the other. J. Heterocyclic Chem., (2010).
Ester‐ and ketone‐substituted (±)‐1‐alkyl‐6‐nitro‐1,2,3,4‐tetrahydroquinolines by a tandem SNAr‐Michael reaction
Authors: Bunce Richard A. , Lee Eric J.
Published: July 2010

magnified image

A synthesis of ester‐ and ketone‐substituted (±)‐1‐alkyl‐6‐nitro‐1,2,3,4‐tetrahydroquinolines has been developed from 2‐pentenoates and 2‐penten‐1‐ones substituted at C5 by a 2‐fluoro‐5‐nitrophenyl group. The cyclization involves an SNAr reaction followed by a Michael addition that occurs exo to the final ring. A previously reported version of this annulation proceeded by an initial endo Michael addition (acceptor became part of the final ring) followed by an SNAr ring closure. The current reactions proceed in 82–97% yields in DMSO using primary amines that are unbranched at the α carbon. The synthesis of the reaction substrates as well as process optimization, mechanistic studies to elucidate the reaction chronology and comparisons with the endo Michael variant are presented. J. Heterocyclic Chem., (2010).
Synthesis of new sulfur‐linked 1,2,4‐triazolothienopyrimidine and 1,2,4‐triazolopyrazolopyrimidine derivatives containing fused heterocyclic pyrimidines
Authors: Song Yang‐Heon , Son Hoon Young
Published: July 2010

magnified image

A series of novel bis‐heterocyclic compounds 12, 13, 14, 15, 16, 17, 18, 19, 20 were synthesized by integrating fused heterocyclic pyrimidines, such as thienopyrimidine and pyrazolopyrimidine into the scaffold of thienotriazolo‐ pyrimidines, and pyrazolotriazolopyrimidines through a sulfur‐linkage. J. Heterocyclic Chem., (2010).
Substance abuse and the impaired provider
Authors: Watkins Derek
Published: July 2010

Physicians have a similar rate of substance abuse as the general population, though their choice of substance may tend to be different. The impact on the physician and his or her patients seriously compromises the delivery of safe and effective medical care. This article reviews our knowledge base regarding the physician with substance abuse issues and presents a methodology to assist in mitigating the risks presented to the provider and patients.