bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis
Authors: Zhu Yan , Song Jiangning , Xu Zixiang , Sun Jibin , Zhang Yanping , Li Yin , Ma Yanhe 
Published: October 2012

AbstractFlux balance analysis (FBA) has been widely used in calculating steady‐state flux distributions that provide important information for metabolic engineering. Several thermodynamics‐based methods, for example, quantitative assignment of reaction directionality and energy balance analysis have been developed to improve the prediction accuracy of FBA. However, these methods can only generate a thermodynamically feasible range, rather than the most thermodynamically favorable solution. We therefore developed a novel optimization method termed as thermodynamic optimum searching (TOS) to calculate the thermodynamically optimal solution, based on the second law of thermodynamics, the minimum magnitude of the Gibbs free energy change and the maximum entropy production principle (MEPP). Then, TOS was applied to five physiological conditions of Escherichia coli to evaluate its effectiveness. The resulting prediction accuracy was found significantly improved (10.7–48.5%) by comparing with the 13C‐fluxome data, indicating that TOS can be considered an advanced calculation and prediction tool in metabolic engineering. Biotechnol. Bioeng. 2013; 110: 914–923. © 2012 Wiley Periodicals, Inc.
Identification and profiling of targeted oxidized linoleic acid metabolites in rat plasma by quadrupole time‐of‐flight mass spectrometry
Authors: Yuan Zhi‐Xin , Rapoport Stanley I. , Soldin Steven J. , Remaley Alan T. , Taha Ameer Y. , Kellom Matthew , Gu Jianghong , Sampson Maureen , Ramsden Christopher E. 
Published: October 2012

ABSTRACTLinoleic acid (LA) and LA‐esters are the precursors of LA hydroperoxides, which are readily converted to 9‐ and 13‐hydroxy‐​octadecadienoic acid (HODE) and 9‐ and 13‐oxo‐​octadecadienoic acid (oxo ODE) metabolites in vivo. These four oxidized LA metabolites (OXLAMs) have been implicated in a variety of pathological conditions. Therefore, their accurate measurement may provide mechanistic insights into disease pathogenesis. Here we present a novel quadrupole time‐of‐flight mass spectrometry (Q‐TOFMS) method for quantitation and identification of target OXLAMs in rat plasma. In this method, the esterified OXLAMs were base‐hydrolyzed and followed by liquid–liquid extraction. Quantitative analyses were based on one‐point standard addition with isotope dilution. The Q‐TOFMS data of target metabolites were acquired and multiple reaction monitoring extracted‐ion chromatograms were generated post‐acquisition with a 10 ppm extraction window. The limit of quantitation was 9.7–35.9 nmol/L depending on the metabolite. The method was reproducible with a coefficient of variation of <18.5%. Mean concentrations of target metabolites in rat plasma were 57.8, 123.2, 218.1 and 57.8 nmol/L for 9‐HODE, 13‐HODE, 9‐oxoODE and 13‐oxoODE, respectively. Plasma levels of total OXLAMs were 456.9 nmol/L, which correlated well with published concentrations obtained by gas chromatography/mass spectrometry (GC/MS). The concentrations were also obtained utilizing a standard addition curve approach. The calibration curves were linear with correlation coefficients of >0.991. Concentrations of 9‐HODE, 13‐HODE, 9‐oxoODE and 13‐oxoODE were 84.0, 138.6, 263.0 and 69.5 nmol/L, respectively, which were consistent with the results obtained from one‐point standard addition. Target metabolites were simultaneously characterized based on the accurate Q‐TOFMS data. This is the first study of secondary LA metabolites using Q‐TOFMS. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.
The Complexity of Community Engagement: Developing Staff–Community Relationships in a Participatory Child Education and Women's Rights Intervention in Kolkata Slums
Authors: Nic a Bháird Caoimhe 
Published: October 2012

ABSTRACTDissatisfaction with inflexible top‐down development interventions has led to a demand for more community‐led approaches and the proliferation of terms such as participation, empowerment, and community ownership. However, the practical implications of these terms remain unclear. This study examined how sociocultural factors influenced relationship building between NGO staff and community members, and how this mediated community participation in a child education and women's rights intervention in Kolkata. Twenty interviews and one focus group were conducted with NGO staff, pupils, and members of a women's group. A thematic analysis produced five global themes: Sociocultural Context, Staff–Community Divide, Power Dynamics, Building Relationships, and Unstable Progress. Differences in social status, lifestyle, and priorities marked clear divisions between staff and community members, leading to communication difficulties and resistance ranging from suspicious stares to open hostility. Establishing mutual respect was a slow and unpredictable process often fuelled by unanticipated events such as staff helping with medical emergencies. A campaign against domestic violence prompted some women to physically attack men and vandalise property, provoking violent retaliation and creating divides within the community. Overcoming these challenges required a responsive approach which often deviated from operational and funding plans. The more participatory and community‐led an intervention, the less predictable it becomes. The flexibility needed to gain community acceptance and manage unanticipated events relies on trusting relationships between both communities and staff, and staff and donors. Copyright © 2012 John Wiley & Sons, Ltd.
Hemin‐Functionalized Reduced Graphene Oxide Nanosheets Reveal Peroxynitrite Reduction and Isomerization Activity
Authors: Vernekar Amit A. , Mugesh Govindasamy 
Published: October 2012

AbstractFacile and efficient reduction of graphene oxide (GO) and novel applications of the reduced graphene oxide (RGO) based materials are of current interest. Herein, we report a novel and facile method for the reduction of GO by using a biocompatible reducing agent dithiothreitol (DTT). Stabilization of DTT by the formation of a six‐membered ring with internal disulfide linkage upon oxidation is responsible for the reduction of GO. The reduced graphene oxide is characterized by several spectroscopic and microscopic techniques. Dispersion of RGO in DMF remained stable for several weeks suggesting that the RGO obtained by DTT‐mediated reduction is hydrophobic in nature. This method can be considered for large scale production of good quality RGO. Treatment of RGO with hemin afforded a functional hemin‐reduced graphene oxide (H‐RGO) hybrid material that exhibited remarkable protective effects against the potentially harmful peroxynitrite (PN). A detailed inhibition study on PN‐mediated oxidation and nitration reactions indicate that the interaction between hemin and RGO results in a synergistic effect, which leads to an efficient reduction of PN to nitrate. The RGO also catalyzes the isomerization of PN to nitrate as the RGO layers facilitate the rapid recombination of .NO2 with FeIV=O species. In the presence of reducing agents such as ascorbic acid, the FeIV=O species can be reduced to FeIII, thus helping to maintain the PN reductase cycle.
Association of CD1a‐positive dendritic cells with papillary thyroid carcinoma in thyroid fine‐needle aspirations
Authors: Pusztaszeri Marc P. , Sadow Peter M. , Faquin William C. 
Published: October 2012

AbstractBACKGROUND:In contrast to other primary thyroid neoplasms and benign thyroid tissue, it has been demonstrated histologically that dendritic cells (DCs) are associated with papillary thyroid carcinoma (PTC). However, the presence and potential diagnostic value of DCs in thyroid fine‐needle aspirations (FNAs) have not been previously described.METHODS:The authors quantitatively assessed for the presence of DCs that were positive for cluster of differentiation 1a (CD1a) (a 43‐49 kD protein expressed on DCs and cortical thymocytes) in cytologic samples of histologically confirmed PTC (n = 31) and in a control group of benign thyroid nodules (BTNs) (n = 29) using immunocytochemical staining with antibodies against CD1a. A subset of the corresponding PTCs (n = 11) and BTNs (n = 10) from surgical resection specimens also were assessed immunohistochemically for both CD1a and Langerin (a type II transmembrane cell surface receptor produced by Langerhans cells).RESULTS:CD1a‐positive DCs were identified in 97% PTCs (n = 30 of 31 PTCs) in thyroid FNA specimens. DCs were largely present in 2 distinct patterns: either as isolated DCs in the background (n = 29 of 31) and/or associated with tumor cells (n = 30 of 31). Tumor‐associated DCs (mean ± standard deviation: 6.44 ± 6.13 DCs per tumor cluster) exhibited multiple dendritic cytoplasmic processes extending over and between malignant cells within groups. The 3 PTC cases with the least DCs corresponded to the follicular variant at excision. In contrast, only 31% of BTNs (n = 9 of 29 BTNs; P = .0048) contained CD1a‐positive DCs. When DCs were present in BTN, they were isolated primarily in the background (27%; n = 8 of 29), although 17% of BTNs (n = 5 of 29) contained rare DCs among thyrocytes, revealing both patterns in 4 cases. Both thyrocyte‐associated DCs and background DCs were more numerous in PTC FNAs than in BTN FNAs, but only the thyrocyte‐associated group of DCs was statistically significant (P < .0001 and P = .1173, respectively). Similar findings were reported in histologic samples in which all PTCs examined (n = 11 of 11) contained both CD1a‐positive and Langerin‐positive DCs; only 20% of BTNs (n = 2 of 10) contained rare DCs.CONCLUSIONS:CD1a‐positive DCs were present in FNA specimens of PTC, typically in close association with tumor cells, whereas they were rare in BTNs. The increased presence of CD1a‐positive DCs in PTC may be a useful diagnostic adjuvant. Cancer (Cancer Cytopathol) 2013;121:206–213. © 2012 American Cancer Society.
Answering the demands of digital genomics
Authors: Titmus Matthew A. , Gurtowski James , Schatz Michael C. 
Published: October 2012

SUMMARYThe continuing revolution in DNA sequencing and biological sensor technologies is driving a digital transformation to our approaches for observation, experimentation, and interpretation that form the foundation of modern biology and genomics. Whereas classical experiments were limited to thousands of hand‐collected observations, today's improved sensors allow billions of digital observations and are improving at an exponential rate that exceeds Moore's law. These improvements have made it possible to monitor the dynamics of biological processes on an unprecedented scale, but have proportionally greater quantitative and computational requirements.The exponentially growing digital demands have motivated extensive research into improved algorithms and parallel systems. Recently, a great deal of research has been focused on applying emerging scalable computing systems to genomic research. One of the most promising is the Hadoop open‐source implementation of MapReduce: it is specifically designed to scale to very large datasets, its intuitive design supports rich parallel algorithms, and is naturally applied to analysis of many biological assays. There has also been success accelerating numerically intensive genomics applications using heterogeneous processors such as GPUs and FPGAs. These are promising early results, but it is clear that continued computational research will become even more important in the years to come. Copyright © 2012 John Wiley & Sons, Ltd.
Synthesis of Mesoporous MoO3 Nanoribbons through a Multi‐molybdate Coordination‐Polymer‐Precursor Route
Authors: Wang Longqiang , Gao Peng , Zhang Guoli , Chen Guorui , Chen Yujin , Wang Ying , Bao Di 
Published: October 2012

AbstractA multi‐molybdate coordination‐polymer‐precursor route was developed to synthesize mesoporous MoO3 nanoribbons. In this reaction process, the coordination‐polymer‐precursor (i.e., {Mo36} ions) was firstly synthesized, as proven by FTIR spectroscopy. By controlling the experimental conditions, the {Mo36} ions underwent a directed assembly process and a dehydration process to form 1D mesoporous MoO3 nanoribbons. HRTEM examination and BJH measurements demonstrated that the mesopores had an average diameter of about 3 nm in the nanoribbons. As a result of their mesoporous nature and their 1D nanostructure, the nanoribbons exhibited better selectivity, higher sensor response, and lower working temperature to H2S gas compared with previously reported1D MoO3 nanostructures.
Synthesis of Tin‐Containing Cyclodextrins as Potential Enzyme Models
Authors: Zhou You , Marinescu Lavinia , Pedersen Christian Marcus , Bols Mikael 
Published: October 2012

AbstractThe synthesis and the characterization of two types of water‐soluble β‐cyclodextrin‐supported organotin derivatives is described. These new tin‐containing macromolecules were prepared through a free radical bishydrostannylation of the corresponding β‐cyclodextrin propargylic ethers using Me2SnClH prepared in situ with AIBN as initiator. The tin moieties were attached both on the primary and on the secondary rim of β‐cyclodextrin in excellent yield.
A Comparison of the Photosensitized Rearrangement and the Lewis‐Acid‐Catalyzed Rearrangement of Spirooxindole Epoxides
Authors: Wang Lihong , Su Yibing , Xu Xinmin , Zhang Wei 
Published: October 2012

AbstractSpirooxindole epoxides undergo smooth rearrangement either under photosensitization conditions or under Lewis acid catalysis to give different products. The photosensitized rearrangement of spirooxindole epoxides leads to 3‐acyl‐2‐indolones, such as spiro[cycloalkane‐1,3′‐indolin]‐2,2′‐diones, by cleavage of the Cα–O bond followed by alkyl migration. The SnCl4‐catalyzed rearrangement of spirooxindole epoxides gives 4,4‐dialkylquinolin‐2,3‐diones, such as spiro[cycloalkane‐1,4′‐quinolin]‐2′,3′‐diones, by cleavage of the Cβ–O bond followed by aryl migration.
Assessment of terrestrial laser scanning technology for obtaining high‐resolution DEMs of soils
Authors: Barneveld Robert Jan , Seeger Manuel , Maalen‐Johansen Ivar 
Published: October 2012

ABSTRACTTerrestrial Laser Scanners (TLS) provide a non‐contact method to measure soil microtopography of relatively large surface areas. The appropriateness of the technology in relatation to the derived Digital Elevation Models (DEM) however has not been reported. The suitability of TLS for soil microtopography measurements was tested on‐field for three large soil surface areas in agricultural fields. The acquired point clouds were filtered with a custom cloud import algorithm, and converted into digital elevation models (DEM) of different resolutions. To assess DEM quality, point clouds measured from different viewpoints were statistically compared. The statistical fit between point clouds from different viewpoints depends on spatial resolution of the DEM. The best results were obtained at the higher resolutions (0.02 to 0.04 cm), where less than 5 % of the grid cells showed significant differences between one viewpoint and the next (p < 0.01). Copyright © 2012 John Wiley & Sons, Ltd.
Reduced channel morphological response to urbanization in a flood‐dominated humid tropical environment
Authors: Phillips Colin B. , Scatena Frederick N. 
Published: October 2012

ABSTRACTUrbanization through the addition of impervious cover can alter catchment hydrology, often resulting in increased peak flows during floods. This phenomenon and the resulting impact on stream channel morphology is well documented in temperate climatic regions, but not well documented in the humid tropics where urbanization is rapidly occurring. This study investigates the long‐term effects of urbanization on channel morphology in the humid sub‐tropical region of Puerto Rico, an area characterized by frequent high‐magnitude flows, and steep coarse‐grained rivers. Grain size, low‐flow channel roughness, and the hydraulic geometry of streams across a land‐use gradient that ranges from pristine forest to high density urbanized catchments are compared. In areas that have been urbanized for several decades changes in channel features were measurable, but were smaller than those reported for comparable temperate streams. Decades of development has resulted in increased fine sediment and anthropogenic debris in urbanized catchments. Materials of anthropogenic origin comprise an average of 6% of the bed material in streams with catchments with 15% or greater impervious cover. At‐a‐station hydraulic geometry shows that velocity makes up a larger component of discharge for rural channels, while depth contributes a larger component of discharge in urban catchments. The average bank‐full cross‐sectional area of urbanized reaches was 1.5 times larger than comparable forested reaches, and less than the world average increase of 2.5. On average, stream width at bank‐full height did not change with urbanization while the world average increase is 1.5 times. Overall, this study indicates that the morphologic changes that occur in response to urban runoff are less in channels that are already subject to frequent large magnitude storms. Furthermore, this study suggests that developing regions in the humid tropics shouldn't rely on temperate analogues to determine the magnitude of impact of urbanization on stream morphology. Copyright © 2012 John Wiley & Sons, Ltd.
Interaction between odorants and proteins involved in the perception of smell: the case of odorant‐binding proteins probed by molecular modelling and biophysical data
Authors: Golebiowski Jérôme , Topin Jérémie , Charlier Landry , Briand Loïc 
Published: October 2012

ABSTRACTA joint approach that combines molecular modelling and fluorescence spectroscopy is used to study the affinity of an odorant binding protein towards various odorant molecules. We focus on the capability of molecular modelling to rank odorants according to their affinity with this protein, which is involved in the sense of smell. Although ligand‐based approaches are unable to propose an accurate model attending to the strength of the bond with the odorant‐binding protein, receptor‐based structures considering either static or dynamic structure of the protein perform equally to discriminate between good, medium and low affinity odorants. Such approaches will be useful for further rational design of either odorants or bio‐inspired sensors. Copyright © 2012 John Wiley & Sons, Ltd.
Pressure, Temperature, and Dew Point Broadband Electrical Spectroscopy (PTD‐BES) for the Investigation of Membranes for PEMFCs▴
Authors: Di Noto V. , Fontanella J. J. , Wintersgill M. C. , Giffin G. A. , Vezzù K. , Piga M. , Negro E. 
Published: October 2012

AbstractThis work describes the construction, testing, and implementation of an instrument to measure the complex impedance (Z*(ω)) spectra, from which the complex conductivity (σ*(ω)) and complex permittivity (ϵ*(ω)) spectra are derived, of conducting polymer membranes for fuel cells. The instrument consists of several interconnected components including a humidifier, a broadband electrical measurement cell with pressure, temperature, and humidity sensors, a heat circulator and a broadband electrical spectrometer. It is possible to control the cell (Tgas) and dew point (Tdp) temperatures with a precision greater than ±0.2 °C to obtain values of relative humidity (RH) with an error lower than ±1.4%. The experiments demonstrate that the values of Tdp and Tgas inside the cell are stable over time at the set point temperatures of Tgas = 0–140 °C and Tdp = ‐20–99.9 °C (for any desired value of Tgas within ±0.2 °C). The powerful capability of the broadband electrical spectroscopy (BES) method is demonstrated by studying the electrical response of Nafion117® at various temperatures and dew points. This technique allows the investigation of the electrical response of ionomeric materials, where the thermal effects are decoupled from the compositional modulation of the membranes in the presence of water vapor.
A dominant negative Cx43 mutant differentially affects tumorigenic and invasive properties in human metastatic melanoma cells
Authors: Zucker Shoshanna N. , Bancroft Tara A. , Place David E. , Des Soye Benjamin , Bagati Archis , Berezney Ronald 
Published: October 2012

AbstractPrevious reports have implicated connexin 43 (Cx43) as a tumor suppressor in early stages of tumorigenesis and in some cases as an enhancer of cell migration in later stages. To address the role of Cx43 in melanoma tumor progression, we utilized two melanoma cell lines derived from the same patient in pre‐metastasis (WM793B) and following isolation from a lung metastasis in nude mice (1205Lu). Our results demonstrate a strikingly increased expression of Cx43 in both the pre‐metastatic and metastatic melanoma cell lines that were actively migrating compared to non‐migrating cells. To further investigate the role of Cx43 in these melanoma cells, we overexpressed wild type (wt) Cx43 as well as a mutant dominant negative Cx43 mutant that causes closed channels (T154A). The metastatic 1205Lu cells expressing Cx43‐T154A showed a twofold decrease in colony formation on soft agar while the nonmetastatic WM793B cells showed no significant change. In invasion assays through a collagen matrix, the same Cx43‐T154A 1205Lu cells demonstrated a three‐ to fourfold increase in the invasion index compared to either wt Cx43 or vector control cells. The increase in invasiveness was eliminated by migration towards media with charcoal‐stripped serum, suggesting that migration may be directed towards a lipophilic compound(s). Our findings demonstrate that a dominant negative Cx43 mutant deficient in channel formation exhibits a dual pattern of regulation in metastatic melanoma cells with a decrease in anchorage‐independent growth and an increase in invasive potential. J. Cell. Physiol. 228: 853–859, 2013. © 2012 Wiley Periodicals, Inc.
Retinoic acid regulates gap junction intercellular communication in human endometrial stromal cells through modulation of the phosphorylation status of connexin 43
Authors: Wu Juanjuan , Taylor Robert N. , Sidell Neil 
Published: October 2012

AbstractPrevious studies revealed that gap junction intercellular communication (GJIC) among uterine stromal cells plays critical roles in modulating decidualization, neovasularization, and embryo implantation. Connexin (Cx) proteins are the major component of gap junctions and Cx43 is the most widely expressed connexin in endometrium. Phosphorylation of Cx43 was found to impair gap junction communication in this tissue. Using primary human endometrial stromal cells (ESCs) and a stable high telomerase‐expressing ESC transfectant (T‐HESC), we found that retinoic acid (RA) altered the phosphorylation status of Cx43 protein such that there was a decrease in the phosphorylated (P1 and P2) species accompanied by an increase in the non‐phosphorylated (P0) form. This process is dependent on protein phosphatase 2A (PP2A) activity since selective PP2A inhibitors prevented the ability of RA to dephosphorylate Cx43. Although RA had no effect on total PP2A expression or activity, it significantly increased the intracellular association of Cx43 and PP2A. Inhibition of transcription and protein synthesis by actinomycin D and cycloheximide, respectively, had no effect on the RA‐induced changes in the Cx43 phosphorylation pattern. Furthermore, BMS493, a potent antagonist of the classical RA‐mediated transcriptional pathway, did not inhibit RA‐induced Cx43 dephosphorylation. Our data indicate that RA stimulates physical association of PP2A with Cx43, resulting in the dephosphorylation of Cx43 and, as a consequence, up‐regulation of GJIC in ESCs. This process is independent of new mRNA and protein synthesis and suggests a novel mechanism by which aberrant retinoid metabolism can explain certain reproductive disorders manifested by dysfunctional endometrial cell GJIC. J. Cell. Physiol. 228: 903–910, 2013. © 2012 Wiley Periodicals, Inc.