bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal cultivation rules in multi‐crop irrigation areas
Authors: Haddad O. Bozorg , Moradi‐Jalal M. , Mirmomeni M. , Kholghi M. Kh. , Mariño M. A. 
Published: June 2008

AbstractA linear programming model is developed for annual cultivation rules of multi‐crop irrigation areas in a reservoir–irrigation system. The objective is to maximize the annual benefit of the system by assigning annual irrigation areas as well as monthly irrigation schedules over the planning horizon. The annual irrigation areas are considered to be a linear function of both total volume of storage at the end of the last operating year and the average inflow rate of the current year. The methodology is applied to a previously analyzed problem, without considering operational rules. Results are compared with those of a linearized modeling of the problem and the advantages of the proposed approach are discussed. Furthermore, results indicate that although there is a 40% decrease in the value of the objective function when using cultivation rules, the model is nonetheless a helpful tool for planners and/or stakeholders to decide at the beginning of each year how much and which type of product should be cultivated. This has been verified by applying the extracted rules with a generated five‐year inflow time series. Results show the robustness of the rules facing the uncertainty of model parameters. Copyright © 2008 John Wiley & Sons, Ltd.
Raman scattering and X‐ray diffraction on YBiTi2O7 prepared at low temperature
Authors: Garbout A. , Rubbens A. , Vannier R. N. , Bouattour S. , Kolsi A. W. 
Published: June 2008

AbstractThe conditions of preparation of a pure YBiTi2O7 phase by sol–gel were optimised. A single phase was obtained at temperature as low as 800 °C when triethanolamine/diethanolamine was used as additional ligands. The expected composition was confirmed by energy dispersive spectroscopy (EDS) and X‐ray diffraction (XRD). YBiTi2O7 exhibits the pyrochlore structure with a unit‐cell parameter of 10.2117(5) Å. This structure was confirmed by Raman spectroscopy, which revealed a shift of the main Eg mode towards lower wavenumbers when bismuth is introduced in the structure. Broad bands were observed for all the recorded spectra, which characterise rather a disorder due to bismuth III cations in the structure than an effect of particle size. This study confirmed the possibility to lower the temperature of preparation of pyrochlores containing bismuth, which could be of interest as photocatalyst for the decomposition of organic and toxic materials. Copyright © 2008 John Wiley & Sons, Ltd.
An efficient use of the WATERGATE W5 sequence for observing a ligand binding with a protein receptor
Authors: Furihata Kazuo , Shimotakahara Sakurako , Tashiro Mitsuru 
Published: June 2008

AbstractAn efficient pulse sequence for observing a ligand binding with a receptor has been developed by incorporating the WATERGATE W5 sequence. In the conventional water ligand observed via gradient spectroscopy (WaterLOGSY) techniques, the water resonance is selectively excited using,e.g. the double‐pulsed field gradient spin–echo (DPFGSE) sequence at the initial portion of pulse sequence. In the current version, the modified WATERGATE W5 sequence is incorporated at the initial portion of the pulse sequence, and the resonance at the water frequency can be selectively reserved by the modified WATERGATE W5 sequence. The efficiency of ligand‐observed NMR screening techniques has been demonstrated using the human serum albumin (HSA)–tryptophan complex. Copyright © 2008 John Wiley & Sons, Ltd.
A communication‐efficient framework for outlier‐free data reporting in data‐gathering sensor networks
Authors: Jayashree L. S. , Arumugam S. , Meenakshi A. R. 
Published: June 2008

AbstractIn this paper, we address the problem of reducing the communication cost and hence the energy costs incurred in data‐gathering applications of a sensor network. Environmental data depicts a huge amount of correlation in both the spatial and temporal domains. We exploit these temporal–spatial correlations to address the aforementioned problem. More specifically, we propose a framework that partitions the physical sensor network topology into a number of feature regions. Each sensor node builds a data model that represents the underlying structure of the data. A representative node in each feature region communicates only the model coefficients to the sink, which then uses them to answer queries. The temporal and spatial similarity has special meaning in outlier cleaning too. We use a modifiedz‐score technique to precisely label the outliers and use the spatial similarity to confirm whether the outliers are due to a true change in the phenomenon under study or due to faulty sensor nodes. Copyright © 2008 John Wiley & Sons, Ltd.
New insights into pig taxonomy, domestication and human dispersal in Island South East Asia: molar shape analysis ofSusremains from Niah Caves, Sarawak
Authors: Cucchi T. , Fujita M. , Dobney K. 
Published: June 2008

AbstractDespite the almost ubiquitous presence of HoloceneSusremains in Island South East Asia (ISEA), the domestication of pigs and their dispersal in this region remains somewhat confused. Using molar shape geometric morphometric analysis, archaeologicalSusdental series from the Sarawak caves of Niah (Aceramic, Neolithic) and Lobang Kudih (Ming period), are compared with extant ISEA wild pigs to establish their taxonomic status and to further explore the evidence for local domestication or introduction of allochthonous populations. Results on modern data‐sets show that outline analysis of the third lower molar achieves highly significant inter‐ and intra‐specific differentiation among ISEA wild pigs, with a phenotypic divergence structure displaying congruence with molecular phylogenies. Both tooth shape and mtDNA evidence strongly suggest the so‐called wild pigs of New Guinea to be the descendants of pigs domesticated in mainland South East Asia and introduced by early farmers to ISEA. None of our data provide clear evidence for a Neolithic introduction of domesticated pigs, or for the local domestication of indigenous bearded pigs, since all Aceramic and Neolithic pigs from Niah cave have been identified as indigenous bearded pig (Sus barbatus). Local domestication experiments by foragers have not been ruled out, since evidence of hypoplasia as a marker of domestication processes has been observed. Introduction of allochthonous domestic pigs between the Late Neolithic and the Metal Age is suggested, since this small domestic breed from Lobang Kudih cave displays strong phenetic relationships withS. scrofaof New Guinea, recognised by molecular phylogeography as part of the ‘Pacific Clade’ linked both with Lapita and Polynesian dispersals. Introduction ofcelebensis‐like species has also been suggested. Future studies should incorporate broader time‐scale and geographical framework data‐sets to strengthen these assumptions. Copyright © 2008 John Wiley & Sons, Ltd.
Effect of thermal expansion on shape memory behavior of polyurethane and its nanocomposites
Authors: Gunes I. Sedat , Cao Feina , Jana Sadhan C. 
Published: June 2008

AbstractThe effects of thermal expansion on shape memory performance of shape memory polyurethanes and their nanocomposites with organoclay, carbon nanofiber (CNF), silicon carbide (SiC), and carbon black (CB) were evaluated. The shape memory test cycle involved tensile deformation at above the trigger temperature to initiate shape memory function, cooling to room temperature to fix the shape, and shape recovery induced by heating to above the trigger temperature. Phenomenological models were used to interpret the experimental data on coefficient of thermal expansion (CTE). It was found that Kerner model showed good fit for composites of SiC and CB, and Halpin model gave better fit for composites of organoclay and CNF. It was observed that thermal expansion exerts negative effect on recovered strain, the extent of which depends on the magnitude of temperature gradient, CTE, and the level of tensile strain. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1437–1449, 2008
Structure–property studies and orientation effects of polythiophenes containing mesogenic side chains
Authors: Radhakrishnan S. , Somanathan N. , Narasimhaswamy T. 
Published: June 2008

AbstractLiquid crystalline materials display unique properties, which can be exploited in organic light emitting diodes. Polythiophene model compounds containing phenyl groups linked with azomethine, ester, and alkoxy groups [thiophene‐3‐alkyloxy benzoyloxy aniline series (N series) and thiophene‐3‐alkoxy phenoxy amino benzoate series (R Series)] were synthesized. Molecular orbital calculations were performed and the predicted band gaps compared to understand the effects of spacer length and linkage. The experimental photoabsorption characteristics are compared with the theoretically predicted band gap. Photoabsorption and emission studies on N series and R series polymers as the function of polarizer angle suggest that polymers of both series emit polarized light in all base color ranges. The electroemission characteristics of the above‐synthesized polymers were also recorded as the function of polarizer angle. The results show that the compounds also emit polarized electroemission, and the EL polarization ratio decreases with the increase of alkoxy chain length for N and R polymers. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1463–1477, 2008
Sequence variants of α‐methylacyl‐CoA racemase are associated with prostate cancer risk: A replication study in an ethnically homogeneous population
Authors: FitzGerald Liesel M. , Thomson Russell , Polanowski Andrea , Patterson Briony , McKay James D. , Stankovich James , Dickinson Joanne L. 
Published: June 2008

AbstractBACKGROUNDExamination of variants of the α‐methylacyl‐CoA racemase (AMACR) gene, as genetic contributors to prostate cancer risk, has been of considerable interest given the gene's recently established role as a diagnostic biomarker for prostate cancer.METHODSThe AMACR gene variants, M9V and D175G, were genotyped in a familial dataset comprising 127 cases and in a second sporadic prostate cancer dataset comprising 414 cases and 319 controls. Genotype‐disease associations were examined employing the MQLS test and unconditional logistic regression. Differences in allele frequencies were examined using the Fisher's exact test. Association between the AMACR haplotypes and prostate cancer risk was also investigated using haplo.score.RESULTSSignificant evidence for association with prostate cancer risk for both the M9V and D175G variants was observed in the Tasmanian prostate cancer dataset. Whilst this association remained significant, it was diminished when relatedness amongst the familial prostate cancer cases was considered.CONCLUSIONThis study, performed in a relatively genetically homogenous Tasmanian population, provides further evidence for a significant association between variants within the AMACR gene and prostate cancer risk. Risk was found to be more significantly associated with AMACR gene variants in sporadic compared to familial prostate cancer cases. These findings again highlight that genetic heterogeneity in the study population should be considered when examining genetic risk factors in prostate cancer. Prostate 68: 1373–1379, 2008. © 2008 Wiley‐Liss, Inc.
A secure business framework for file purchasing in vehicular networks
Authors: Yuan Shuang , Zhang Chenxi , Ho Pin‐Han 
Published: June 2008

AbstractVehicular ad hoc networks (VANETs) are gaining growing interest from both industry and academia. The primitive objective of VANETs is to enhance the road safety for public transportation systems through dedicated short range communications (DSRC) protocol. In addition to the powerful radios and abundant spectrums, DSRC also paves the way for VANETs to support numerous emerging Internet‐related applications. In this paper, we introduce a promising commercial application which allows each vehicle to purchase file/data through a roadside unit (RSU). Due to the high mobility of vehicles, the contact period between an RSU and a vehicle could be insufficient to download the complete file. Thus, in the proposed file purchasing systems, once a vehicle in the process of downloading a file leaves the transmission range of the RSU, its neighboring vehicles with a piece of the file can cooperatively help to complete the file transfer via vehicle‐to‐vehicle (V2V) communications. Such a commercial file purchasing system can obviously initiate a new application scenario; however, it cannot be put into practice unless the security issues, such as the user privacy, incentives for inter‐vehicle cooperation, and the copyright protection for∼the file content, are well addressed. In order to deal with these security issues, we develop a secure framework for the file purchasing system in VANETs. Performance evaluation will be conducted to verify the proposed scheme. Copyright © 2008 John Wiley & Sons, Ltd.
Enzymatic Cleavage of Nucleic Acids on Gold Nanoparticles: A Generic Platform for Facile Colorimetric Biosensors
Authors: Zhao Weian , Lam Jeffrey C. F. , Chiuman William , Brook Michael A. , Li Yingfu 
Published: June 2008

AbstractThe enzymatic cleavage of nucleic acids (DNA or DNA with a single RNA linkage) on well‐dispersed gold nanoparticles (AuNPs) is exploited in the design of facile colorimetric biosensors. The assays are performed at salt concentrations such that DNA‐modified AuNPs are barely stabilized by the electrostatic and steric stabilization. Enzymatic cleavage of DNA chains on the AuNP surface destabilizes the AuNPs, resulting in a rapid aggregation driven by van der Waals attraction, and a red‐to‐purple color change. Two different systems are chosen, DNase I (a DNA endonuclease) and 8‐17 (a Pb2+‐depedent RNA‐cleaving DNAzyme), to demonstrate the utility of our assay for the detection of metal ions and sensing enzyme activities. Compared with previous studies in which AuNP aggregates are converted into dispersed AuNPs by enzymatic cleavage of DNA crosslinkers, the present assay is technically simpler. Moreover, the accessibility of DNA to biomolecular recognition elements (e.g. enzymes) on well‐dispersed AuNPs in our assay appears to be higher than that embedded inside aggregates. This biosensing system should be readily adaptable to other enzymes or substrates for detection of analytes such as small molecules, proteases and their inhibitors.
Spatial distribution of lichens on twigs in remote Siberian silver fir forests indicates changing atmospheric conditions
Authors: OTNYUKOVA T. N. , SEKRETENKO O. P. 
Published: June 2008

Abstract:The distribution of different ecological groups of lichens (acidophytes, ‘nitrophytes’, indifferent species) was compared on 1–24 year-old twigs of Abies sibirica sampled in the ‘pristine’ West Sayan and the polluted East Sayan Mountains (Krasnoyarsk District, South Siberia, Russia) to test their value as indicators of current pollution effects. Bark pH of twigs and bark chemistry (N, S, Ca, Mg, Al, Fe) were measured, and a preliminary estimate of emissions in the Krasnoyarsk District from livestock animal populations was calculated. In both regions, an unusually high twig bark pH and an abnormal species composition for A. sibirica canopy were found (e.g. Physcia aipolia, P. dubia, P. tenella, Phaeophyscia sp., Melanelia exasperatula and Candelariella vitellina), with P. tenella (East Sayan) and M. exasperatula (West Sayan) as dominants. The results confirm that the distribution of lichen species on Abies sibirica twigs is a valuable indicator of current changes in atmospheric conditions.
Observations on lichenicolous fungi described by Spegazzini
Authors: ETAYO Javier , ROSATO Vilma G. 
Published: June 2008

Abstract:We have studied and tried to clarify the application of names of all the lichenicolous fungi described by Carlos Spegazzinii. Several of these names have not previously been treated by mycologists currently specializing in lichenicolous fungi. Verruculina gen. nov. is introduced with V. sigmatospora (Speg.) Etayo (syn. Metanectria sigmatospora) as type, and the new combination Scutula nephromatis (Speg.) Etayo (syn. Patellea nephromatis) is made. Material of several species, Diplosporium caudatum (on Punctelia), Pleurotus lichenicolus (on Usnea), Pyrenopeziza lichenicola (on Flavoparmelia), Selenosporium lichenicola (on Candelaria) and Vermiculariella lichenicolum (on Physcia and Peltigera), could not be located in Spegazzini’s collections in La Plata (LPS), therefore these names remain to be clarified.
Additions and corrections to the lichens of Heard Island
Authors: ØVSTEDAL D.O. , GREMMEN N. J. M. 
Published: June 2008

Abstract:Nineteen lichens new to sub-Antarctic Heard Island are recorded. Three species are described as new: Gyalideopsis heardense Øvstedal, Mycobilimbia subbyssoidea Øvstedal and Psoroma absconditum Øvstedal. Altogether the total number of lichen species recorded on the island is now 90.
Modeling promoter grammars with evolving hidden Markov models
Authors: Won Kyoung-Jae , Sandelin Albin , Marstrand Troels Torben , Krogh Anders 
Published: June 2008

Abstract
Motivation: Describing and modeling biological features of eukaryotic promoters remains an important and challenging problem within computational biology. The promoters of higher eukaryotes in particular display a wide variation in regulatory features, which are difficult to model. Often several factors are involved in the regulation of a set of co-regulated genes. If so, promoters can be modeled with connected regulatory features, where the network of connections is characteristic for a particular mode of regulation.
Results: With the goal of automatically deciphering such regulatory structures, we present a method that iteratively evolves an ensemble of regulatory grammars using a hidden Markov Model (HMM) architecture composed of interconnected blocks representing transcription factor binding sites (TFBSs) and background regions of promoter sequences. The ensemble approach reduces the risk of overfitting and generally improves performance. We apply this method to identify TFBSs and to classify promoters preferentially expressed in macrophages, where it outperforms other methods due to the increased predictive power given by the grammar.
Availability: The software and the datasets are available from http://modem.ucsd.edu/won/eHMM.tar.gz
Contact: krogh@binf.ku.dk
Supplementary information: Supplementary data are available at Bioinformatics online.
Optimal vaccination schedules using simulated annealing
Authors: Pennisi Marzio , Catanuto Roberto , Pappalardo Francesco , Motta Santo 
Published: June 2008

Abstract
Summary: Since few years the problem of finding optimal solutions for drug or vaccine protocols have been tackled using system biology modeling. These approaches are usually computationally expensive. Our previous experiences in optimizing vaccine or drug protocols using genetic algorithms required the use of a high performance computing infrastructure for a couple of days. In the present article we show that by an appropriate use of a different optimization algorithm, the simulated annealing, we have been able to downsize the computational effort by a factor102. The new algorithm requires computational effort that can be achieved by current generation personal computers.
Availability: Software and additional data can be found at http://www.immunomics.eu/SA/
Contact: francesco@dmi.unict.it
Emerging stem cell concepts for imatinib‐resistant chronic myeloid leukaemia: implications for the biology, management, and therapy of the disease
Authors: Valent Peter 
Published: June 2008

SummaryChronic myeloid leukaemia (CML) is a myeloid neoplasm defined by the BCR/ABL oncoprotein that is considered essential for leukaemogenesis and accumulation of neoplastic cells. The BCR/ABL kinase inhibitor imatinib is an effective agent in most patients and can now be regarded as front‐line therapy. Hence, intrinsic and acquired resistance to imatinib has been described and is an emerging challenge in clinical practice. While CML stem cells display primary resistance, stem cell subclones may, in addition, acquire imatinib‐resistant mutants of BCR/ABL. Other factors that are considered to contribute to stem cell resistance include the genetic background, clonal evolution, additional biological features of subclones, gene amplifications, silencing of tumour suppressor genes and specific pharmacological aspects. In this article, mechanisms of resistance of CML (stem) cells against imatinib and other BCR/ABL inhibitors are discussed, together with strategies to overcome and/or to prevent resistance with available drugs or novel anti‐leukaemic approaches.
Molecular pathways in myelodysplastic syndromes and acute myeloid leukemia: relationships and distinctions–a review
Authors: Bernasconi Paolo 
Published: June 2008

SummaryThe myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) are both hematopoietic stem cell disorders. However, while leukemic stem cells have been revealed by clonal tracking experiments, dysplastic stem cells have never been demonstrated by xeno‐transplantation assays because of poor engraftment problems. These engraftment difficulties may be due to the unique nature of MDS genetic lesions that are truly able to recapitulate the disease phenotype. MDS and AML of younger patients harbour clonal yet different chromosomal markers, whereas MDS and AML of the elderly present similar defects. Potential involvement of tumor suppressor genes in MDS has been hypothesized but never confirmed, while cooperation between class I and class II mutations has been identified in AML. The reciprocal interactions between stromal cells and neoplastic clones are disrupted in both MDS and AML. In early MDS, stromal and neoplastic cells produce high levels of inhibitory cytokines, whereas in advanced MDS and AML they produce high levels of anti‐apoptotic molecules.
Atypical cells in the urinary sediment: a protocol for cytological analysis of the urinary sediment
Authors: Fernández‐Aceñero M. J. , Lorence D. , Criado L. , Aguirregoicoa E. 
Published: June 2008

Introduction:  The Department of Clinical Chemistry of the General Hospital of Móstoles (Madrid, Spain) has for many years diagnosed the presence of atypical cells in the urinary sediment (ACUS), but this finding only led to a comment in the final report of the urinalysis, informing the clinician of this fact in case he/she decided to perform further studies in these patients.Methods:  Since 2004, the Clinical Chemistry Department has implemented a new protocol together with the Department of Surgical Pathology of the Hospital, according to which all the urinary sediment samples with ACUS are sent for cytological analysis. In this report, we comment on the results corresponding to 99 samples.Results:  With this new strategy, we can directly diagnose if the ACUS correspond to a carcinoma or to another process, and this has allowed us to reduce time until diagnosis in our patients and also to avoid unnecessary studies in negative cases. We comment on our results with this new management strategy.