bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adenosine as an endogenous regulating factor of hippocampal sharp waves
Authors: Wu Chiping , Wong Teser , Wu Xiadi , Sheppy Evan , Zhang Liang 
Published: September 2008

AbstractThe rodent hippocampus exhibits population activities called sharp waves (SPWs) during slow wave sleep and wake immobility. SPWs are important for hippocampal‐cortical communication and memory consolidation, and abnormal sharp wave‐ripple complexes are closely related to epileptic seizures. Although the SPWs are known to arise from the CA3 circuit, the local mechanisms underlying their generation are not fully understood. We hypothesize that endogenous adenosine is a local regulator of hippocampal SPWs. We tested this hypothesis in thick mouse hippocampal slices that encompass a relatively large hippocampal circuit and have a high propensity of generating spontaneous in vitro SPWs. We found that application of adenosine A1 receptor antagonists induced in vitro SPWs and that such induction was sensitive to blockade by NMDA receptor antagonists. By contrast, an increase in endogenous adenosine via pharmacological inhibition of adenosine transporters or adenosine degrading enzymes suppressed spontaneous in vitro SPWs. We thus suggest that the initiation and incidence of sharp wave‐like population events are under tight control by the activity of endogenously stimulated A1 receptors. © 2008 Wiley‐Liss, Inc.
River flow forecasting using wavelet and cross‐wavelet transform models
Authors: Adamowski Jan F. 
Published: September 2008

AbstractIn this study, short‐term river flood forecasting models based on wavelet and cross‐wavelet constituent components were developed and evaluated for forecasting daily stream flows with lead times equal to 1, 3, and 7 days. These wavelet and cross‐wavelet models were compared with artificial neural network models and simple perseverance models. This was done using data from the Skrwa Prawa River watershed in Poland. Numerical analysis was performed on daily maximum stream flow data from the Parzen station and on meteorological data from the Plock weather station in Poland. Data from 1951 to 1979 was used to train the models while data from 1980 to 1983 was used to test the models. The study showed that forecasting models based on wavelet and cross‐wavelet constituent components can be used with great accuracy as a stand‐alone forecasting method for 1 and 3 days lead time river flood forecasting, assuming that there are no significant trends in the amplitude for the same Julian day year‐to‐year, and that there is a relatively stable phase shift between the flow and meteorological time series. It was also shown that forecasting models based on wavelet and cross‐wavelet constituent components for forecasting river floods are not accurate for longer lead time forecasting such as 7 days, with the artificial neural network models providing more accurate results. Copyright © 2008 John Wiley & Sons, Ltd.
How nature uses overland flow regime to maximize equilibrium detention storage and flood attenuation
Authors: Wong Tommy S. W. 
Published: September 2008

AbstractEquilibrium detention storage is an important parameter as it has a proportional effect on flood attenuation. In this paper, based on the kinematic wave theory, a working formula for the equilibrium detention storage of an overland plane with upstream inflow has been derived. Since the flow regime over a concrete plane can vary throughout the entire range laminar to turbulent, this case has been selected to examine the effect of flow regime on the equilibrium detention storage. In the examination, the derived formula has been applied to four flow regimes: (a) laminar, (b) transitional, (c) near turbulent, and (d) turbulent. The examination shows that for planes with a small discharge, laminar flow gives the maximum detention storage. For planes with a medium discharge, transitional flow gives the maximum detention storage, and for planes with a large discharge, near turbulent flow gives the maximum detention storage. The flow regime can cause more than two‐fold increase in detention storage. All these results can be attributed to the respective flow resistance, and have been endorsed with analyses of the water surface profile and the rising limb of the hydrograph. Finally, relating the results to real‐life situations, it shows that the flow regime that gives the maximum detention storage is also the dominating flow regime in nature. Hence, extraordinarily, the flow regimes that exist in nature in fact provide maximum flood attenuation. Copyright © 2008 John Wiley & Sons, Ltd.
Shift trend and step changes for runoff time series in the Shiyang River basin, northwest China
Authors: Li Z. L. , Xu Z. X. , Li J. Y. , Li Z. J. 
Published: September 2008

AbstractShift trend and step changes were detected for runoff time series in the Shiyang River basin, one of the inland river basins in north‐west China. Annual runoff data from eight tributaries as well as both annual and monthly runoff from the mainstream from 1958 to 2003 were used. Seven statistical test methods were employed to identify the shift trends and step changes in the study. Mann–Kendall test, Spearman's Rho test, linear regression and Hurst exponent were used to detect past and future shift trends for runoff time series, while the distributed‐free CUSUM test, cumulative deviations and the Worsley likelihood ratio test were used to detect step changes for the same time series. Results showed that the annual runoff from Zamu, Huangyang and Gulang rivers, as well as both annual and monthly runoff from the mainstream, show statistically significant decreasing trends. Future tendency of runoff for both tributaries and mainstream were consistent with that from 1958 to 2003. Step changes probably occurred in 1961 for the runoff from Huangyang, Gulang and Dajing rivers according to the Worsley likelihood ratio test, but no similar results were found using the other two test methods. Three change points (1979, 1974 and 1973) were detected for the mainstream using different methods. These change points were close to the years that reservoirs started to be operated. Both climate change and human activities, especially the latter, contributed to the decreasing runoff in the study area. Between 21% and 79% of the reduction in runoff from the mainstream was due to the impact of human activities during the past few decades. Copyright © 2008 John Wiley & Sons, Ltd.
An ANN‐based model for spatiotemporal groundwater level forecasting
Authors: Nourani Vahid , Mogaddam Asghar Asghari , Nadiri Ata Ollah 
Published: September 2008

AbstractThis paper evaluates the feasibility of using an artificial neural network (ANN) methodology for estimating the groundwater levels in some piezometers placed in an aquifer in north‐western Iran. This aquifer is multilayer and has a high groundwater level in urban areas. Spatiotemporal groundwater level simulation in a multilayer aquifer is regarded as difficult in hydrogeology due to the complexity of the different aquifer materials. In the present research the performance of different neural networks for groundwater level forecasting is examined in order to identify an optimal ANN architecture that can simulate the piezometers water levels. Six different types of network architectures and training algorithms are investigated and compared in terms of model prediction efficiency and accuracy. The results of different experiments show that accurate predictions can be achieved with a standard feedforward neural network trained usung the Levenberg–Marquardt algorithm. The structure and spatial regressions of the ANN parameters (weights and biases) are then used for spatiotemporal model presentation. The efficiency of the spatio‐temporal ANN (STANN) model is compared with two hybrid neural‐geostatistics (NG) and multivariate time series‐geostatistics (TSG) models. It is found in this study that the ANNs provide the most accurate predictions in comparison with the other models. Based on the nonlinear intrinsic ANN approach, the developed STANN model gives acceptable results for the Tabriz multilayer aquifer. Copyright © 2008 John Wiley & Sons, Ltd.
Characterization of humoral immune responses against p16, p53, HPV16 E6 and HPV16 E7 in patients with HPV‐associated cancers
Authors: Reuschenbach Miriam , Waterboer Tim , Wallin Keng‐Ling , Einenkel Jens , Dillner Joakim , Hamsikova Eva , Eschenbach Denise , Zimmer Heike , Heilig Bernhard , Kopitz Jürgen , Pawlita Michael , Doeberitz Magnus von Knebel , Wentzensen Nicolas 
Published: September 2008

AbstractThe cellular tumor suppressor p16 is strongly overexpressed in cervical cancers and precancers. We have previously demonstrated that infiltrating T lymphocytes reactive against p16 can be found in cervical cancer patients. Here, we analyzed whether p16 induces humoral immune responses. Sera of patients with cervical cancer, oropharyngeal cancer, colorectal cancer and autoimmune disease were included. A total of 919 sera were analyzed, including 486 matched sera from a cervical cancer case control study. p16 antibodies were analyzed in Western blot and a newly developed peptide ELISA covering the complete p16 protein. In addition, a Luminex‐based multiplex assay was used for simultaneous detection of antibodies directed against p16, p53, HPV16 E6 and HPV16 E7. In all entities, only low p16 antibody reactivity was observed. Epitope mapping revealed 2 predominant epitope regions of the p16 protein. No significant difference in p16 antibody frequency (OR = 0.9; 95% CI = 0.6–1.3) and p53 antibody frequency (OR = 0.6; 95% CI = 0.3–1.2) was found between patients and healthy controls in the cervical cancer case control study. Antibodies against the HPV16 oncoproteins E6 and E7 were detected more frequently in cervical cancer patients when compared with healthy controls (E6 OR = 27.8; 95% CI = 11.1–69.7, E7 OR = 5.7; 95% CI = 2.9–11.1). In conclusion, despite the strong expression of p16 and the observed induction of cellular immune responses, antibody reactivity against p16 was observed only at very low levels independent of the disease background. © 2008 Wiley‐Liss, Inc.
Effectiveness of an organized cervical cancer screening program in Korea: Results from a cohort study
Authors: Jun Jae Kwan , Choi Kui Son , Jung Kyu Won , Lee Hoo‐Yeon , Gapstur Susan M. , Park Eun‐Cheol , Yoo Keun‐Young 
Published: September 2008

AbstractAlthough the value of cervical cancer screening is widely acknowledged, the effectiveness of an organized cervical cancer screening program in Korea has never been evaluated. We investigated the associations of the frequency of cervical cancer screening with cervical cancer incidence using data from a large prospective cohort study. In this analysis, 253,472 women without a hysterectomy or previous cancer diagnosis were included. Follow‐up was between 1995 and 2002. Frequency of Pap smear testing was determined by searching the National Health Examination Database. Using the Korean Central Cancer Registry, 248 cases of invasive cervical cancer and 346 cases of carcinoma in situ (CIS) of the cervix were identified. Subjects screened 2 or more times showed a 71% (corrected reduction 60%) and a 66% (corrected reduction 53%) reduced risk of invasive cervical cancer and CIS of the cervix, respectively, as compared with unscreened subjects [relative risk (RR) = 0.29; 95% confidence interval (CI) = 0.20–0.45; RR = 0.34; 95% CI = 0.25–0.46, respectively]. Women with a normal or benign pap smear had a statistically significantly lower risk of invasive cervical cancer and CIS of cervix compared with those never screened. In age‐stratified analyses, there was a significant reduction in cervical cancer incidence among women aged 30 and over who were screened 2 or more times compared with women never screened. The results of this prospective cohort study show that regular screening of cervical cancer reduces invasive cervical cancer incidence and CIS of the cervix among Korean women. © 2008 Wiley‐Liss, Inc.
Serpin polymerization and its role in disease—The molecular basis of α1‐antitrypsin deficiency
Authors: Knaupp Anja S. , Bottomley Stephen P. 
Published: September 2008

AbstractProtein aggregation is the cause of several human diseases. Understanding the molecular mechanisms involved in protein aggregation requires knowledge of the kinetics and structures populated during the reaction. Arguably, the best structurally characterized misfolding reaction is that of α1‐antitrypsin. α1‐Antitrypsin misfolding leads to both liver disease and emphysema and affect approximately 1 in 2000 of the population. This review will focus on the mechanism of α1‐antitrypsin misfolding and the development of potential therapeutic strategies. © 2008 IUBMB IUBMB Life, 61(1): 1–5, 2009
A novel method for protein‐ligand binding affinity prediction and the related descriptors exploration
Authors: Li Shuyan , Xi Lili , Wang Chengqi , Li Jiazhong , Lei Beilei , Liu Huanxiang , Yao Xiaojun 
Published: September 2008

AbstractIn this study, a novel method was developed to predict the binding affinity of protein‐ligand based on a comprehensive set of structurally diverse protein‐ligand complexes (PLCs). The 1300 PLCs with binding affinity (493 complexes with Kd and 807 complexes with Ki) from the refined dataset of PDBbind Database (release 2007) were studied in the predictive model development. In this method, each complex was described using calculated descriptors from three blocks: protein sequence, ligand structure, and binding pocket. Thereafter, the PLCs data were rationally split into representative training and test sets by full consideration of the validation of the models. The molecular descriptors relevant to the binding affinity were selected using the ReliefF method combined with least squares support vector machines (LS‐SVMs) modeling method based on the training data set. Two final optimized LS‐SVMs models were developed using the selected descriptors to predict the binding affinities of Kd and Ki. The correlation coefficients (R) of training set and test set for Kd model were 0.890 and 0.833. The corresponding correlation coefficients for the Ki model were 0.922 and 0.742, respectively. The prediction method proposed in this work can give better generalization ability than other recently published methods and can be used as an alternative fast filter in the virtual screening of large chemical database. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
A multipole‐based water potential with implicit polarization for biomolecular simulations
Authors: Walsh T. R. , Liang T. 
Published: September 2008

AbstractA new water potential, DMIP (distributed multipoles, implicit polarization), is constructed using distributed multipoles to describe the electrostatic interactions, while accounting for polarization implicitly. In this procedure, small clusters are randomly sampled from atomistic simulations of bulk water using the AMOEBA (Ren and Ponder, J Comput Chem 2002, 23, 1497) potential. The multipole moments of the central water in each cluster are obtained from ab initio densities for each cluster, and the moments are then averaged over all clusters. Properties of bulk water calculated using DMIP compare favorably with existing data from AMOEBA simulations and experiment, with a conservative estimate of reduction in compute time of roughly 40%. The implicit force‐field is also shown to work compatibly with existing polarizable multipole‐based force‐fields for biomolecules. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
A group center overlap based approach for “3D QSAR” studies on TIBO derivatives
Authors: Sapre Nitin S. , Gupta Swagata , Pancholi Nilanjana , Sapre Neelima 
Published: September 2008

AbstractCurrent challenges in drug designing and lead optimization has reached a bottle neck where the main onus lies on rigorous validation to afford robust and predictive models. In the present study, we have suggested that predictive structure‐activity relationship (SAR) models based on robust statistical analyses can serve as effective screening tools for large volume of compounds present either in chemical databases or in virtual libraries. 3D descriptors derived from the similarity‐based alignment of molecules with respect to group center overlap from each individual template point and other “alignment averaged,” but significant descriptors (ClogP, molar refractivity, connolly accessible area) were used to generate QSAR models. The results indicated that the artificial neural network method (r2 = 0.902) proved to be superior to the multiple linear regression method (r2 = 0.810). Cross validation of the models with an external set was reasonably satisfactory. Screening PubChem compound database based on the models obtained, yielded 14 newer modified compounds belonging to the TIBO class of inhibitors, as well as, two novel scaffolds, with enhanced binding efficacy as hits. These hits may be targeted toward potent lead‐optimization and help in designing and synthesizing new compounds with potential therapeutic utility. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
13C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models
Authors: Zheng Anmin , Liu Shang‐Bin , Deng Feng 
Published: September 2008

AbstractPrecise theoretical predictions of NMR parameters are helpful for the spectroscopic identification of complicated biological molecules, especially for the carbon shielding tensors in amino acids. The 13C shielding tensors of various crystalline amino acids and peptides have been calculated using the gauge‐including projector augmented wave (GIPAW) method based on two different periodic structure models, namely that deduced from available crystallographic data and that from theoretically optimized structures. The incorporation of surrounding lattice effects is found to be crucial in obtaining reliable predictions of 13C shielding tensors that are comparable to the experimental data. This is accomplished by refining the experimental crystallographic data of the amino acids and peptides at the GGA/PBE level by which more accurate intramolecular CH bond lengths and intermolecular hydrogen‐bonding interactions are obtained. Accordingly, more accurate predictions of 13C shielding tensors comparable to the experimental results (within a maximum deviation of ±10 ppm) were achieved, rendering more explicit 13C shielding tensors assignments for solid biological systems particularly for amino acids with multiple carboxyl carbons, such as asparagine, glutamine, and glutamic acid. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Embedding 3D models of biological specimens in PDF publications
Authors: Ruthensteiner Bernhard , Heß Martin 
Published: September 2008

AbstractBy providing two examples, the option for embedding 3D models in electronic versions of life science publications is presented. These examples, presumably representing the first such models published, are developmental stages of an evertebrate (Patella caerulea, Mollusca) and a vertebrate species (Psetta maxima, Teleostei) obtained from histological section series reconstruction processed with the software package Amira. These surface rendering models are particularly suitable for a PDF file because they can easily be transformed to a file format required and components may be conveniently combined and hierarchically arranged. All methodological steps starting from specimen preparation until embedding of resulting models in PDF files with emphasis on conversion of Amira data to the appropriate 3D file format are explained. Usability of 3D models in PDF documents is exemplified and advantages over 2D illustrations are discussed, including better explanation capabilities for spatial arrangements, higher information contents, and limiting options for disguising results by authors. Possibilities for additional applications reaching far beyond the examples presented are suggested. Problems such as long‐term compatibility of file format and hardware plus software, editing and embedding of files, file size and differences in information contents between printed and electronic version will likely be overcome by technical development and increasing tendency toward electronic at the cost of printed publications. Since 3D visualization plays an increasing role in manifold disciplines of science and appropriate tools for the popular PDF format are readily available, we propose routine application of this way of illustration in electronic life science papers. Microsc. Res. Tech., 2008. © 2008 Wiley‐Liss, Inc.
X‐ray microscopy of plant cells by using LiF crystal as a detector
Authors: Reale Lucia , Bonfigli Francesca , Lai Antonia , Flora Francesco , Poma Anna , Albertano Patrizia , Bellezza Simona , Montereali Rosa Maria , Faenov Anatoly , Pikuz Tania , Almaviva Salvatore , Vincenti Maria Aurora , Francucci Massimo , Gaudio Pasqualino , Martellucci Sergio , Richetta Maria 
Published: September 2008

AbstractA lithium fluoride (LiF) crystal has been utilized as a new soft X‐ray detector to image different biological samples at a high spatial resolution. This new type of image detector for X‐ray microscopy has many interesting properties: high resolution (nanometer scale), permanent storage of images, the ability to clear the image and reuse the LiF crystal, and high contrast with greater dynamic range. Cells of the unicellular green algae Chlamydomonas dysosmos and Chlorella sorokiniana, and pollen grains of Olea europea have been used as biological materials for imaging. The biological samples were imaged on LiF crystals by using the soft X‐ray contact microscopy and contact micro‐radiography techniques. The laser plasma soft X‐ray source was generated using a Nd:YAG/Glass laser focused on a solid target. The X‐ray energy range for image acquisition was in the water‐window spectral range for single shot contact microscopy of very thin biological samples (single cells) and around 1 keV for multishots microradiography. The main aim of this article is to highlight the possibility of using a LiF crystal as a detector for the biological imaging using soft X‐ray radiation and to demonstrate its ability to visualize the microstructure within living cells. Microsc. Res. Tech., 2008. © 2008 Wiley‐Liss, Inc.
Fluorescence resonance energy transfer and anisotropy reveals both hetero‐ and homo‐energy transfer in the pleckstrin homology‐domain and the parathyroid hormone‐receptor
Authors: Steinmeyer Ralf , Harms Gregory S. 
Published: September 2008

AbstractWe present a method and an apparatus of polarized fluorescence resonance energy transfer (FRET) and anisotropy imaging microscopy done in parallel for improved interpretation of the photophysical interactions. We demonstrate this apparatus to better determine the protein–protein interactions in the pleckstrin homology domain and the conformational changes in the Parathyroid Hormone Receptor, a G‐protein coupled receptor, both fused to the cyan and yellow fluorescent proteins for either inter‐ or intramolecular FRET. In both cases, the expression levels of proteins and also background autofluorescence played a significant role in the depolarization values measured in association with FRET. The system has the sensitivity and low‐noise capability of single‐fluorophore detection. Using counting procedures from single‐molecule methods, control experiments were performed to determine number densities of green fluorescence protein variants CFP and YFP where homo resonance energy transfer can occur. Depolarization values were also determined for flavins, a common molecule of cellular background autofluorescence. From the anisotropy measurements of donor and acceptor, the latter when directly excited or when excited by energy transfer, we find that our instrumentation and method also characterizes crucial effects from homotransfer, polarization specific photobleaching and background molecules. Microsc. Res. Tech., 2009. © 2008 Wiley‐Liss, Inc.