bluuebunny/crossref_metadata_2025_split 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

AbstractIn 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

AbstractThe 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

AbstractTransporters 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

AbstractThe 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

AbstractA 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

AbstractOlfactory 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

AbstractThe 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

AbstractElectrophysiological 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

AbstractThe 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

AbstractAlthough 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

SUMMARYA 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

AbstractHeterogeneity 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

AbstractBackgroundThe 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.MethodsPressure 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.ResultsA 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.ConclusionsThe 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.