bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interferon‐γ down‐regulates NKG2D ligand expression and impairs the NKG2D‐mediated cytolysis of MHC class I‐deficient melanoma by natural killer cells
Authors: Schwinn Nicole , Vokhminova Daria , Sucker Antje , Textor Sonja , Striegel Sandra , Moll Iris , Nausch Norman , Tuettenberg Jochen , Steinle Alexander , Cerwenka Adelheid , Schadendorf Dirk , Paschen Annette 
Published: October 2008

AbstractNKG2D operates as an activating receptor on natural killer (NK) cells and costimulates the effector function of αβ CD8+ T cells. Ligands of NKG2D, the MHC class I chain‐related (MIC) and UL16 binding protein (ULBP) molecules, are expressed on a variety of human tumors, including melanoma. Recent studies in mice demonstrated that NKG2D mediates tumor immune surveillance, suggesting that antitumor immunity in humans could be enhanced by therapeutic manipulation of NKG2D ligand (NKG2DL) expression. However, signals and mechanisms regulating NKG2DL expression still need to be elucidated. Here, we asked whether the proinflammatory cytokine Interferon‐γ (IFN‐γ) affects NKG2DL expression in melanoma. Cell lines, established from MHC class I‐negative and ‐positive melanoma metastases, predominantly expressed MICA and ULBP2 molecules on their surface. Upon IFN‐γ treatment, expression of MICA, in some cases, also of ULBP2 decreased. Besides melanoma, this observation was made also for glioma cells. Down‐regulation of NKG2DL surface expression was dependent on the cytokine dose and the duration of treatment, but was neither due to an intracellular retention of the molecules nor to an increased shedding of ligands from the tumor cell surface. Instead, quantitative RT‐PCR revealed a decrease of MICA‐specific mRNA levels upon IFN‐γ treatment and siRNA experiments pointed to an involvement of STAT‐1 in this process. Importantly, IFN‐γ‐treated MHC class I‐negative melanoma cells were less susceptible to NKG2D‐mediated NK cell cytotoxicity. Our study suggests that IFN‐γ, by down‐regulating ligand expression, might facilitate escape of MHC class I‐negative melanoma cells from NKG2D‐mediated killing by NK cells. © 2008 Wiley‐Liss, Inc.
Response of two legume crops to soil salinity in gypsiferous soils
Authors: Webber Heidi , Madramootoo Chandra , Bourgault Maryse , Horst Mikhail , Stulina Galina , Smith Donald 
Published: October 2008

AbstractCompetition for water resources, increasing land salinization and the need to feed a growing population are challenges facing irrigated agriculture in the Fergana Valley of Uzbekistan. Growing short‐season legumes with water‐saving irrigation technologies is one strategy for increasing food production and land productivity using relatively less water. However, little information is available to assess how these crops will respond when produced with deficit irrigation on the gypsiferous soils of the region. This greenhouse study evaluated various growth components of common bean and green gram irrigated with deficit irrigation in soils with and without gypsum and at three levels of soil salinity. Results showed that biomass and leaf area decreased by approximately 20% for both crops, as ECe increased from 2.8 to 7 dS m−1. Yields were higher at all salinities for green gram than in common bean. However, relative yield reductions with increasing salinity were greater for green gram (43%) compared to common bean (19–31%). The presence of gypsum enabled both crops to maintain reasonable yield at ECe values which would be lethal in soils dominated both other salts. The effect of increasing salinity was the same at all levels of deficit irrigation. Copyright © 2008 John Wiley & Sons, Ltd.
Water for food as food for thought: case study of applying the PODIUMSim model to Uzbekistan
Authors: Yakubov Murat , Manthrithilake Herath 
Published: October 2008

AbstractUzbekistan, being historically one of the most populated and agriculture‐based republics in the former Soviet Union, still features quite high annual population growth rates and great dependence on agriculture as a backbone for the rest of the economic reforms. With water playing an extremely important role in producing a sufficient food base for the country's growing population and earning much needed foreign exchange for the government to ensure overall economic development, the pressures on this scarce resource will obviously and inevitably grow, putting it much at risk over a long‐term perspective. So would available water be enough to meet ever‐increasing demands from major economic uses in the foreseeable future, and what can be the options for meeting such demands – these are the key questions raised and researched in this article. As such the research concentrates on the two major country‐specific scenarios with water and its multiple uses for Uzbekistan – the business as usual and the best case. Both scenarios discuss possible future implications for the next quarter‐century given certain assumptions. Finally when summarizing the findings, the paper provides conclusions and recommendations as to how the model and further scenarios can be better optimized given the trans‐boundary nature of most water resources in Central Asia where Uzbekistan geographically belongs. Copyright © 2008 John Wiley & Sons, Ltd.
Beware expense reimbursement schemes!
Authors: McGee Jo Ann , Byington J. Ralph 
Published: October 2008

AbstractYour employees may be stealing your cash with clever expense reimbursement schemes that are difficult to spot. Reports of this kind of cash fraud appear in the press on a daily basis. What kinds of schemes are out there, and what can you do to prevent and detect them? © 2008 Wiley Periodicals, Inc.
Prevent large cash losses from small business fraud
Authors: Johnson Leigh Redd , Rudolph Holly R. 
Published: October 2008

AbstractOver the past few years, the spotlight has been on large corporate frauds. These resulted from cash management systems devoid of adequate controls and governance.But about half of all frauds occur in small businesses—and the effect is often devastating. The average loss for any small business fraud scheme was found to be greater than in any other business‐size category.Since fraud generally starts small—even in large companies—everyone can benefit from sharpening their cash management fraud prevention. This article examines five cases of smaller frauds that could lead to large cash losses. And the authors give advice on how to better detect and prevent such frauds in the future. © 2008 Wiley Periodicals, Inc.
Treasury products for mid‐to‐small corporations
Authors: Sagner James S. 
Published: October 2008

AbstractThe treasury and noncredit services market for mid‐size and smaller corporations is significantly different from the one for Fortune 500 companies—although the banks have focused mostly on the latter. As a result, bankers and other financial service professionals usually approach a “mid‐to‐small” business project using the wrong assumptions and techniques.The author examines this situation and suggests other ways for mid‐to‐small companies and banks to establish relationships. © 2008 Wiley Periodicals, Inc.
Simple, effective performance management: A top‐down and bottom‐up approach
Authors: Muras Andrew , Smith Thomas , Meyers Deborah 
Published: October 2008

AbstractPerformance management systems sometimes confuse rather than enlighten managers and employees. The combination of complex processes, competing IT systems, and multiple dashboards often fails to provide the insight needed to bring change, so the metrics become irrelevant. Using a back‐to‐basics approach and employing two well‐known processes—activity analysis and balanced scorecards—overcomes this irrelevance. Employing a simple, straightforward, and linked approach provides the information necessary to measure and improve performance from both an operational and strategic perspective. This article provides an overview of the linked concept and two case studies of implementations. © 2008 Wiley Periodicals, Inc.
Automated exploration of stable isomers of H+(H2O)n (n = 5–7) via ab initio calculations: An application of the anharmonic downward distortion following algorithm
Authors: Luo Yi , Maeda Satoshi , Ohno Koichi 
Published: October 2008

AbstractIsomers of protonated water clusters H+(H2O)n (n = 5–7) have been explored on ab initio potential energy surfaces by means of the anharmonic downward distortion following algorithm. Totally, 9, 24, and 131 isomers for n = 5, 6, and 7, respectively, were located by the automatic exploration, and all of known important isomers previously reported by conventional geometry optimization approaches have been included in the present results. Moreover, structure transitions depending on n and temperature, which were observed by experimental studies, could be reproduced via thermodynamic simulation on the basis of the superposition approach and the present isomer sets. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
tCONCOORD‐GUI: Visually supported conformational sampling of bioactive molecules
Authors: Seeliger Daniel , De Groot Bert L. 
Published: October 2008

AbstractConformational flexibility of bioactive molecules poses a major challenge to computational biology. tCONCOORD generates structure ensembles based on geometrical considerations and has been successfully applied to predict protein conformational flexibility and essential degrees of freedom. We have now developed a graphical user interface (GUI) for tCONCOORD, which substantially facilitates the simulation setup and provides valuable insights into the structure analysis and constraint definition process in tCONCOORD. Moreover, users can influence the constraint definition process by interactively turning interactions on and off, defining completely rigid or flexible regions, or by applying artifical constraints that cause a biased sampling of the conformational space. This interface offers a versatile environment not only for the setup and analysis of tCONCOORD simulations, but also for molecular modeling and structure analysis in general. Both tCONCOORD* and the tCONCOORD‐GUI† are distributed freely. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Probing the free energy landscape of the FBP28WW domain using multiple techniques
Authors: Periole Xavier , Allen Lucy R. , Tamiola Kamil , Mark Alan E. , Paci Emanuele 
Published: October 2008

AbstractThe free‐energy landscape of a small protein, the FBP 28 WW domain, has been explored using molecular dynamics (MD) simulations with alternative descriptions of the molecule. The molecular models used range from coarse‐grained to all‐atom with either an implicit or explicit treatment of the solvent. Sampling of conformation space was performed using both conventional and temperature‐replica exchange MD simulations. Experimental chemical shifts and NOEs were used to validate the simulations, and experimental ϕ values both for validation and as restraints. This combination of different approaches has provided insight into the free energy landscape and barriers encountered by the protein during folding and enabled the characterization of native, denatured and transition states which are compatible with the available experimental data. All the molecular models used stabilize well defined native and denatured basins; however, the degree of agreement with the available experimental data varies. While the most detailed, explicit solvent model predicts the data reasonably accurately, it does not fold despite a simulation time 10 times that of the experimental folding time. The less detailed models performed poorly relative to the explicit solvent model: an implicit solvent model stabilizes a ground state which differs from the experimental native state, and a structure‐based model underestimates the size of the barrier between the two states. The use of experimental ϕ values both as restraints, and to extract structures from unfolding simulations, result in conformations which, although not necessarily true transition states, appear to share the geometrical characteristics of transition state structures. In addition to characterizing the native, transition and denatured states of this particular system in this work, the advantages and limitations of using varying levels of representation are discussed. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
WebMTA: A web‐interface for ab initio geometry optimization of large molecules using molecular tailoring approach
Authors: Kavathekar Ritwik , Khire Subodh , Ganesh V. , Rahalkar Anuja P. , Gadre Shridhar R. 
Published: October 2008

AbstractA web‐interface for geometry optimization of large molecules using a linear scaling method, i.e., cardinality guided molecular tailoring approach (CG‐MTA), is presented. CG‐MTA is a cut‐and‐stitch, fragmentation‐based method developed in our laboratory, for linear scaling of conventional ab initio techniques. This interface provides limited access to CG‐MTA‐enabled GAMESS. It can be used to obtain fragmentation schemes for a given spatially extended molecule depending on the maximum allowed fragment size and minimum cut radius values provided by the user. Currently, we support submission of single point or geometry optimization jobs at Hartree‐Fock and density functional theory levels of theory for systems containing between 80 to 200 first row atoms and comprising up to 1000 basis functions. The graphical user interface is built using HTML and Python at the back end. The back end farms out the jobs on an in‐house Linux‐based cluster running on Pentium‐4 Class or higher machines using an @Home‐based parallelization scheme (http://chem.unipune.ernet.in/∼tcg/mtaweb/). © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Novel bi‐transition metallic encapsulated naphthalene‐like Si20 prismatic cage: A DFT investigation
Authors: Wang Jin , Liu Jin Huai 
Published: October 2008

AbstractA theoretical investigation of stabilities and electronic properties of novel transition bimetallic atoms (BTMAs) encapsulated naphthalene‐like Si20 prismatic cage is being reported for the first time. The symmetry and electronic state of naphthalene‐like TMA2@Si20 is significantly affected by the type of encapsulated TMA from 3d, 4d to 5d series. Because of high binding energies, relative high HOMO‐LUMO gaps, large charge‐reverse transferring from naphthalene‐like Si20 cage to BTMAs at the centre of the 5d series, the most stable species of TMA2@Si20 cage is favorable to form new 1D‐TMAn@Sim nanotube, which is based on array of the novel naphthalene‐like structure. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
The importance of aromatic‐type interactions in serotonin synthesis: Protein–ligand interactions in tryptophan hydroxylase and aromatic amino acid decarboxylase
Authors: Hofto Laura R. , Lee Caroline E. , Cafiero Mauricio 
Published: October 2008

AbstractThe biosynthesis of serotonin requires aromatic substrates to be bound in the active sites of the enzymes tryptophan hydroxylase and aromatic amino acid decarboxylase. These aromatic substrates are held in place partially by dispersion and induction interactions with the enzymes' aromatic amino acid residues. Mutations that decrease substrate binding can result in a decrease in serotonin production and thus can lead to depression and related disorders. We use optimized crystal structures of these two enzymes to examine pair‐wise electronic interaction energies between aromatic residues in the active sites and the aromatic ligands. We also perform in silico mutations on the aromatic residues to determine the change in interaction energies as mutations occur. Our second‐order Moller‐Plessett perturbation theory calculations show that drastic changes in interaction energy can occur and, in light of our previous work, we are able to use these data to offer predictions on the loss of protein function and on the possibility of disease upon mutation. We also examine local and gradient corrected density functional theory methods to evaluate their ability to predict these induction/dispersion‐dominated interaction energies. We find that the hybrid B3LYP cannot model these interactions well, whereas the GGA HCTH407 offers largely qualitatively correct results, and the local functional SVWN quantitatively mimics the MP2 results rather well. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Skeletal morphogenesis of the vertebral column of the miniature hylid frog Acris crepitans, with comments on anomalies
Authors: Pugener L. Analía , Maglia Anne M. 
Published: October 2008

AbstractAlthough the vertebral columns of anurans have received much study in the last 150 years, few detailed descriptions exist of the skeletal morphogenesis of this anatomical unit. Herein, the ontogeny of the vertebral skeleton of the hylid frog Acris crepitans is described based on cleared and double‐stained specimens, radiographs, and 3D reconstructions generated from synchrotron microCT scans. The adult axial formula is 1‐7‐1‐1, and the vertebral centra are epichordal and procoelous. The neural arches are nonimbricate, and there is a medial articulation between the laminae of Presacrals I and II. Free ribs are absent. The sacral diapophyses are uniform in width or slightly expanded distally. The urostyle is slender, round in cross section, and about equal in length to the presacral region. Presacral vertebrae are the first to form, developing in a cephalic‐to‐caudal sequence. However, development and growth are decoupled and growth is fastest initially in the posterior presacrals and sacrum. In addition, there is a time lag between the formation of the presacral/sacral region and the postsacral region. More than 8.5% of the specimens examined have vertebral anomalies, and about 50% display small variants from the typical vertebral column morphology. However, these malformations do not seem to have been so severe as to have affected survival. J. Morphol., 2009. © 2008 Wiley‐Liss, Inc.
Ultrastructure of spermatozoa and spermatophores of old world freshwater crabs (Brachyura: Potamoidea: Gecarcinucidae, Potamidae, and Potamonautidae)
Authors: Klaus Sebastian , Schubart Christoph D. , Brandis Dirk 
Published: October 2008

AbstractWe investigated the ultrastructure of spermatozoa and spermatophores of 19 palaeotropical freshwater crab species [12 species of the Gecarcinucidae, 6 of the Potamidae (Potamiscinae), and 1 species of the Potamonautidae (Deckeniinae: Hydrothelphusini)]. The investigated Potamiscinae have densely packed coenospermic spermatophores with the exception of Thaiphusa sirikit and Johora singaporensis that exhibit cleistospermia. In contrast, in the Gecarcinucidae the spermatozoa are loosely embedded in a mucous matrix. The gecarcinucid and potamiscine sperm differ, furthermore, in acrosomal structure and size. The acrosome in the Gecarcinucidae is much smaller and spherical, while the larger acrosome in the Potamiscinae has the tendency to be depressed. In the Potamiscinae, an additional middle acrosomal zone evolved between the acrosome ray zone and the outer acrosomal zone. Within the Gecarcinucidae, a differentiation into two groups (Gecarcinucinae and Parathelphusinae) is not supported by the present spermatological data. The sperm morphology of Hydrothelphusa aff. madagascariensis (Potamonautidae: Deckeniinae) differs from Potamonautes sidneyi (Potamonautidae: Potamonautinae) in acrosomal size and shape, and in the absence of a periopercular rim. A closer relationship of Deckeniinae and Gecarcinucidae cannot be confirmed by spermatology. J. Morphol., 2009. © 2008 Wiley‐Liss, Inc.
Structure and evolution of the pharynx simplex in acoel flatworms (Acoela)
Authors: Todt Christiane 
Published: October 2008

AbstractThe homology of pharynges within the mostly pharynx‐less Acoela has been a matter of discussion for decades and even the basic question of whether a pharynx is a primitive trait within the Acoela and homologous to the pharynx of platyhelminth turbellarians is open. By using fluorescence staining of musculature, as well as conventional histological techniques and transmission electron microscopy, the present study sets focus on the mouth and pharynx (where present) of seven species of Acoela within Paratomellidae, Solenofilomorphidae, Hofsteniidae, Proporidae, and Convolutidae, as well as one species of Nemertodermatida and Catenulida, respectively. It is shown that among the investigated families of acoels there is a great variability in muscle systems associated with the mouth and pharynx and that pharynx histology and ultrastructural characters are widely diverse. There are no close similarities between the acoel pharynges and the catenulid pharynx but there is a general resemblance of the musculature associated with the mouth in the representatives of Paratomellidae and Nemertodermatida. On the basis of the profound differences in pharynx morphology, three major conclusions are drawn: 1) the pharynges as present in Recent acoels are not homologous to the pharynx simplex characteristic for Catenulida and Macrostomida within the Platyhelminthes; 2) the different muscular pharynx types of acoels are not homologous between higher taxa and thus a single acoel‐type pharynx simplex cannot be defined; 3) the presence of a muscular pharynx most likely does not represent the ancestral state. J. Morphol, 2009. © 2008 Wiley‐Liss, Inc.
Electrospray ionization from an adjustable gap between two silicon chips
Authors: Ek Patrik , Schönberg Tommy , Sjödahl Johan , Jacksén Johan , Vieider Christian , Emmer Åsa , Roeraade Johan 
Published: October 2008

AbstractIn this paper, a silicon chip–based electrospray emitter with a variable orifice size is presented. The device consists of two chips, with a thin beam elevating from the center of each of the chips. The chips are individually mounted to form an open gap of a narrow, uniform width between the top areas of the beams. The electrospray is generated at the endpoint of the gap, where the spray point is formed by the very sharp intersection between the crystal planes of the < 100 > silicon chips. Sample solution is applied to the rear end of the gap from a capillary via a liquid bridge, and capillary forces ensure a spontaneous imbibition of the gap. The sample solution is confined to the gap by means of a hydrophobic treatment of the surfaces surrounding the gap, as well as the geometrical boundaries formed by the edges of the gap walls. The gap width could be adjusted between 1 and 25 µm during electrospray experiments without suffering from any interruption of the electrospray process. Using a peptide sample solution, a shift toward higher charge states and increased signal‐to‐noise ratios was observed when the gap width was decreased. The limit of detection for the peptide insulin (chain B, oxidized) was approximately 4 nM. We also show a successful interfacing of the electrospray setup with capillary electrophoresis. Copyright © 2008 John Wiley & Sons, Ltd.