bluuebunny/crossref_metadata_2025_split huggingface dataset:
The hinge region of the scaffolding protein of cell contacts, zonula occludens protein 1, regulates interacting with various signaling proteins
Authors: Bal Manjot Singh , Castro Victor , Piontek Jörg , Rueckert Christine , Walter Juliane K. , Shymanets Aliaksei , Kurig Barbara , Haase Hannelore , Nürnberg Bernd , Blasig Ingolf E. 
Published: December 2011

AbstractZonula occludens protein 1 (ZO‐1) is a ubiquitous scaffolding protein, but it is unknown why it functions in very different cellular contacts. We hypothesized that a specific segment, the unique hinge region, can be bound by very different regulatory proteins. Using surface plasmon resonance spectroscopy and binding assays to peptide libraries, we show, for the first time, that the hinge region directly interacts with disparate signal elements such as G‐proteins alpha 12 and alpha i2, the regulator of G‐protein signaling 5, multifunctional signaling protein ahnak1, and L‐type Ca2+‐channel beta‐2‐subunit. The novel binding proteins specifically bound to a coiled coil‐helix predicted in the hinge region of ZO‐1. The interactions were modulated by phosphorylation in the hinge helix. Activation of the G‐proteins influenced their association to ZO‐1. In colon cells, G alpha i2 and ZO‐1 were associated, as shown by coimmunoprecipitation. After cotransfection in kidney cells, G alpha i2 barely colocalized with ZO‐1; the colocalization coefficient was significantly increased when epinephrine activated G‐protein signaling. In conclusion, proteins with different regulatory potential adhere to and influence cellular functions of ZO‐proteins, and the interactions can be modulated via its hinge region and/or the binding proteins. J. Cell. Biochem. 113: 934–945, 2012. © 2011 Wiley Periodicals, Inc.
Oxidative‐mechanical stress signals stem cell niche mediated Lrp5 osteogenesis in eNOS−/− null mice
Authors: Rajamannan Nalini M. 
Published: December 2011

AbstractCalcific aortic valve disease (CAVD) is the most common indication for valve surgery in the USA. This study hypothesizes that CAVD develops secondary to Wnt3a/Lrp5 activation via oxidative‐mechanical stress in eNOS null mice. eNOS−/− mice were tested with experimental diets including a control (n = 20), cholesterol (n = 20), cholesterol + Atorvastatin (n = 20). After 23 weeks the mice were tested for the development of aortic stenosis by Echo, Histology, MicroCT, and RTPCR for bone markers. In vitro studies measured Wnt3a secretion from aortic valve endothelial cells and confirmed oxidative stress via eNOS activity. Anion exchange chromatography was performed to isolate the mitogenic protein. Myofibroblast cells were tested to induce bone formation. Cholesterol treated eNOS mice develop severe stenosis with an increase in Wnt3a, Lrp5, Runx2 (threefold increase (P < 0.0001) in the bicuspid versus tricuspid aortic valves. Secretion of Wnt3a from aortic valve endothelium in the presence of abnormal oxidative stress was correlated with diminished eNOS enzymatic activity and tissue nitrite levels. Initial characterization of the architecture for a stem cell nice was determined by protein isolation using anion‐exchange chromatography and cell proliferation via thymidine incorporation. Osteoblastogenesis in the myofibroblast cell occurred via Lrp5 receptor upregulation in the presence of osteogenic media. Targeting the Wnt3a/Lrp5 pathway in valve calcification and activation of osteogenesis is via an oxidative‐mechanical stress in CAVD. These findings provide a foundation for treating this disease process by targeting the cross talk mechanism in a resident stem cell niche. J. Cell. Biochem. 113: 1623–1634, 2012. © 2011 Wiley Periodicals, Inc.
Investigating the Impact of SERVQUAL Dimensions on Customer Satisfaction: The Lessons Learnt from Serbian Travel Agencies
Authors: Marinković Veljko , Senić Vladimir , Kocić Milan , Šapić Srđan 
Published: December 2011

ABSTRACTDespite the rise of online travel booking services, it seems that traditional travel agencies remain an intractable part in the process of making travel arrangements for most travelers. Nevertheless, the question remains as to what triggers travelers' satisfaction with travel agencies. In order to explore this, we focused on Serbian travel agencies and researched the impact of the five individual SERVQUAL dimensions on travelers' satisfaction. Results revealed that four SERVQUAL dimensions (reliability, responsiveness, empathy and tangibility) had a significant influence on customer satisfaction. Copyright © 2011 John Wiley & Sons, Ltd.
THE LOGICAL LIMITS OF BEST PRACTICE ADMINISTRATIVE SOLUTIONS IN DEVELOPING COUNTRIES
Authors: Andrews Matt 
Published: December 2011

SUMMARYDeveloping countries are pressured to adopt administrative solutions that the international community considers best practice. Some claim that these practices do not fit such contexts. How could one assess the fit or relevance of a best practice? This article suggests a basic answer: Look at the degree of difference between the proposed adoption context and the context in which such practice emerged as ‘best’. This answer emerges from a discussion on the basis of the new institutional ideas about change and diffusion. An empirical analysis of public financial management reform in African countries suggests support for this answer: Good practices are most evident in countries least different to the developed nations where practices originated and least evident in countries most different to these developed nations. The article contributes to a literature on best practice and yields fundamental messages for development, including the point that best practices are limited as administrative solutions in many developing countries. Copyright © 2011 John Wiley & Sons, Ltd.
Fast and accurate modeling of protein–protein interactions by combining template‐interface‐based docking with flexible refinement
Authors: Tuncbag Nurcan , Keskin Ozlem , Nussinov Ruth , Gursoy Attila 
Published: December 2011

AbstractThe similarity between folding and binding led us to posit the concept that the number of protein–protein interface motifs in nature is limited, and interacting protein pairs can use similar interface architectures repeatedly, even if their global folds completely vary. Thus, known protein–protein interface architectures can be used to model the complexes between two target proteins on the proteome scale, even if their global structures differ. This powerful concept is combined with a flexible refinement and global energy assessment tool. The accuracy of the method is highly dependent on the structural diversity of the interface architectures in the template dataset. Here, we validate this knowledge‐based combinatorial method on the Docking Benchmark and show that it efficiently finds high‐quality models for benchmark complexes and their binding regions even in the absence of template interfaces having sequence similarity to the targets. Compared to “classical” docking, it is computationally faster; as the number of target proteins increases, the difference becomes more dramatic. Further, it is able to distinguish binders from nonbinders. These features allow performing large‐scale network modeling. The results on an independent target set (proteins in the p53 molecular interaction map) show that current method can be used to predict whether a given protein pair interacts. Overall, while constrained by the diversity of the template set, this approach efficiently produces high‐quality models of protein–protein complexes. We expect that with the growing number of known interface architectures, this type of knowledge‐based methods will be increasingly used by the broad proteomics community. Proteins 2012; © 2011 Wiley Periodicals, Inc.
A simple and efficient authentication scheme for mobile satellite communication systems
Authors: Lee Cheng‐Chi , Li Chun‐Ta , Chang Rui‐Xiang 
Published: December 2011

SUMMARYIn this article, the authors shall propose a simple and efficient authentication scheme for mobile satellite communication systems. The proposed scheme can achieve the following security requirements: (S1) withstand impersonation attacks; (S2) withstand denial server attacks; (S3) withstand smart card loss attacks; (S4) withstand replay attacks; and (S5) withstand stolen‐verifier attacks, and achieve the following functionality requirements: (F1) freely choose identity; (F2) provide mutual authentication; (F3) provide session key agreement; (F4) provide user anonymity; and (F5) provide perfect forward secrecy. In additional, the proposed scheme does not use the high complex computation, such as public key cryptosystem or secret key cryptosystem, for the mobile users' side. The proposed scheme is only based on hash functions and exclusive‐OR operations. Compared with other schemes, the proposed scheme has a lower computation cost. It is more simple and efficient scheme. Copyright © 2011 John Wiley & Sons, Ltd.
Non-stringent tissue-source requirements for BMP ligand expression in regulation of body size inCaenorhabditis elegans
Authors: SAVAGE-DUNN CATHY , YU LING , GILL KWESI , AWAN MUHAMMAD , FERNANDO THILINI 
Published: December 2011

SummaryInCaenorhabditis elegans, the Bone Morphogenetic Protein (BMP)-related ligand Dpp- and BMP-like-1 (DBL-1) regulates body size by promoting the larval and adult growth of the large epidermal syncytium hyp7 without affecting cell division. This system provides an excellent model for dissecting the growth-promoting activities of BMP ligands, since in this context the growth and differentiation functions of DBL-1 are naturally uncoupled.dbl-1is expressed primarily in neurons and the DBL-1 ligand signals to its receptors and Smad signal transducers in the target tissue of the epidermis. The requirements constraining the source(s) of DBL-1, however, have not previously been investigated. We show here thatdbl-1expression requirements are strikingly relaxed. Expression in non-overlapping subsets of the endogenous expression pattern, as well as ectopic expression, can provide sufficient levels of activity for rescue of the small body size ofdbl-1mutants. By analysingdbl-1expression levels in transgenic strains with different degrees of rescue, we corroborate the model that DBL-1 is a dose-dependent regulator of growth. We conclude that, for body size regulation, the site of expression ofdbl-1is less important than the level of expression.
msechBari, a new MITE-like element inDrosophila sechelliarelated to theBaritransposon
Authors: DIAS ELAINE SILVA , CARARETO CLAUDIA MARCIA APARECIDA 
Published: December 2011

SummaryA few occurrences ofminiatureinverted-repeattransposableelements (MITEs) have been reported in species of the genusDrosophila. Here, we describemsechBari, a MITE-like element inDrosophila sechellia. The element is short, approximately 90 bp in length, AT-rich and occurs in association with, or close to, genes, characteristics that are typical for MITEs. The identification was performedin silicousing the sequenced genome ofD. sechelliaand confirmed in a laboratory strain. This short element is related to theBari_DMtransposon ofDrosophila melanogaster, havingterminalinvertedrepeats (TIRs) of a similar length and a high identity with the full-lengthBari_DMelement. The estimated recent origin of the element and the homogeneity observed between copies found in the genome suggests thatmsechBaricould be active inD. sechellia.
The dynamic architecture of photoreceptor ribbon synapses: Cytoskeletal, extracellular matrix, and intramembrane proteins
Authors: MERCER AARON J. , THORESON WALLACE B. 
Published: December 2011

AbstractRod and cone photoreceptors possess ribbon synapses that assist in the transmission of graded light responses to second-order bipolar and horizontal cells of the vertebrate retina. Proper functioning of the synapse requires the juxtaposition of presynaptic release sites immediately adjacent to postsynaptic receptors. In this review, we focus on the synaptic, cytoskeletal, and extracellular matrix proteins that help to organize photoreceptor ribbon synapses in the outer plexiform layer. We examine the proteins that foster the clustering of release proteins, calcium channels, and synaptic vesicles in the presynaptic terminals of photoreceptors adjacent to their postsynaptic contacts. Although many proteins interact with one another in the presynaptic terminal and synaptic cleft, these protein–protein interactions do not create a static and immutable structure. Instead, photoreceptor ribbon synapses are remarkably dynamic, exhibiting structural changes on both rapid and slow time scales.
The Shannon information content of hyperspectral shortwave cloud albedo measurements: Quantification and practical applications
Authors: Coddington Odele , Pilewskie Peter , Vukicevic Tomislava 
Published: December 2011

The Shannon information content provides an objective measure of the information in a data set. In this paper, we quantify the information content of hyperspectral liquid water cloud measurements over a spectral range (300–2500 nm) representing approximately 95% of the total energy in the solar spectrum. We also use the Shannon information content to analyze the cloud retrieval wavelengths and weightings used by the Solar Spectral Flux Radiometer (SSFR) and to determine the cumulative information in the SSFR retrieval. These applications illustrate the utility of the Shannon information content in guiding the effective processing of hyperspectral data. Such efficiency is of growing importance considering the push toward spectrally resolved satellite measurements of reflected solar irradiance used to study climate.
High-resolution Fourier-transform extreme ultraviolet photoabsorption spectroscopy of 14N15N
Authors: Heays A. N. , Dickenson G. D. , Salumbides E. J. , de Oliveira N. , Joyeux D. , Nahon L. , Lewis B. R. , Ubachs W. 
Published: December 2011

The first comprehensive high-resolution photoabsorption spectrum of 14N15N has been recorded using the Fourier-transform spectrometer attached to the Desirs beamline at the Soleil synchrotron. Observations are made in the extreme ultraviolet and span 100 000–109 000 cm−1 (100–91.7 nm). The observed absorption lines have been assigned to 25 bands and reduced to a set of transition energies, f values, and linewidths. This analysis has verified the predictions of a theoretical model of N2 that simulates its photoabsorption and photodissociation cross section by solution of an isotopomer independent formulation of the coupled-channel Schrödinger equation. The mass dependence of predissociation linewidths and oscillator strengths is clearly evident and many local perturbations of transition energies, strengths, and widths within individual rotational series have been observed.
Inferring convective responses to El Niño with atmospheric electricity
measurements at Shetland
Authors: Harrison R G , Joshi M , Pascoe K 
Published: December 2011

Abstract
Pacific ocean temperature anomalies associated with the El Niño–Southern Oscillation
(ENSO) modulate atmospheric convection and hence thunderstorm electrification. The
generated current flows globally via the atmospheric electric circuit, which can be
monitored anywhere on Earth. Atmospheric electricity measurements made at Shetland
(in Scotland) display a mean global circuit response to ENSO that is characterized by
strengthening during ‘El Niño’ conditions, and weakening during ‘La Niña’ conditions.
Examining the hourly varying response indicates that a potential gradient (PG)
increase around noon UT is likely to be associated with a change in atmospheric
convection and resultant lightning activity over equatorial Africa and Eastern Asia.
A secondary increase in PG just after midnight UT can be attributed to more shower
clouds in the central Pacific ocean during an ‘El Niño’.
ESpritz: accurate and fast prediction of protein disorder
Authors: Walsh Ian , Martin Alberto J. M. , Di Domenico Tomàs , Tosatto Silvio C. E. 
Published: December 2011

Abstract
Motivation: Intrinsically disordered regions are key for the function of numerous proteins, and the scant available experimental annotations suggest the existence of different disorder flavors. While efficient predictions are required to annotate entire genomes, most existing methods require sequence profiles for disorder prediction, making them cumbersome for high-throughput applications.
Results: In this work, we present an ensemble of protein disorder predictors called ESpritz. These are based on bidirectional recursive neural networks and trained on three different flavors of disorder, including a novel NMR flexibility predictor. ESpritz can produce fast and accurate sequence-only predictions, annotating entire genomes in the order of hours on a single processor core. Alternatively, a slower but slightly more accurate ESpritz variant using sequence profiles can be used for applications requiring maximum performance. Two levels of prediction confidence allow either to maximize reasonable disorder detection or to limit expected false positives to 5%. ESpritz performs consistently well on the recent CASP9 data, reaching a Sw measure of 54.82 and area under the receiver operator curve of 0.856. The fast predictor is four orders of magnitude faster and remains better than most publicly available CASP9 methods, making it ideal for genomic scale predictions.
Conclusions: ESpritz predicts three flavors of disorder at two distinct false positive rates, either with a fast or slower and slightly more accurate approach. Given its state-of-the-art performance, it can be especially useful for high-throughput applications.
Availability: Both a web server for high-throughput analysis and a Linux executable version of ESpritz are available from: http://protein.bio.unipd.it/espritz/
Contact: silvio.tosatto@unipd.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Wnt Blockade With Dickkopf Reduces Intestinal Crypt Fission and Intestinal Growth in Infant Rats
Authors: Fauser Jane K. , Donato Rino P. , Woenig Joshua A. , Proctor Simon J. , Trotta Andrew P. , Grover Phulwinder K. , Howarth Gordon S. , Penttila Irmeli A. , Cummins Adrian G. 
Published: December 2011

ABSTRACTObjectives:Intestinal crypt fission peaks during infancy. In human and experimental familial polyposis coli, increased crypt fission is due to activation of Wnt/β‐catenin signalling, but the molecular basis of crypt fission during intestinal growth has not been examined. The aim of this project was to investigate whether crypt fission and intestinal growth are affected by experimental blockade of the Wnt/β‐catenin signalling pathway.Methods:Hooded Wistar rats were given either the Wnt inhibitor, dickkopf (30 and 100 ng), daily or vehicle control intraperitoneally from days 11 to 15 and were killed at day 16. Intestinal morphometry was used to measure villous area, crypt area, percentage of crypt fission, and crypt mitotic count. Intestinal stem cells were assessed by expression of real time‐polymerase chain reaction for Lgr5 (a stem cell marker), and the number of β‐catenin–expressing crypts by immunostaining was determined after 100‐ng dickkopf treatment.Results:Dickkopf at 30 and 100 ng/day reduced villous area to 71% (P = 0.013) and 29% (P < 0.0001), crypt area to 42% (P = 0.0026) and 30% (P = 0.0067), and crypt fission to 51% (P = 0.006) and 29% (P < 0.0001), respectively, of control values. Mitotic count per crypt did not change. Lgr5 RNA expression and the number of β‐catenin–expressing crypts decreased in dickkopf‐treated animals.Conclusions:We conclude that intestinal crypt fission during infancy is mediated by Wnt signalling. It is possible that local treatment with Wnt agonists could be used to increase intestinal growth.
Overexpression of T‐LAK cell‐originated protein kinase predicts poor prognosis in patients with stage I lung adenocarcinoma
Authors: Wei Di‐Cing , Yeh Yi‐Chen , Hung Jung‐Jyh , Chou Teh‐Ying , Wu Yu‐Chung , Lu Pei‐Jung , Cheng Hui‐Chuan , Hsu Yu‐Lin , Kuo Yu‐Lun , Chen Kuan‐Yu , Lai Jin‐Mei 
Published: December 2011

Tumor recurrence is the most common cause of disease failure after surgical resection in early‐stage lung adenocarcinoma. Identification of clinically relevant prognostic markers could help to predict patients with high risk of disease recurrence. A meta‐analysis of available lung adenocarcinoma microarray datasets revealed that T‐LAK cell‐originated protein kinase (TOPK), a serine/threonine protein kinase, is overexpressed in lung cancer. Using stable cell lines with overexpression or knockdown of TOPK, we have shown that TOPK can promote cell migration, invasion, and clonogenic activity in lung cancer cells, suggesting its crucial role in lung tumorigenesis. To evaluate the prognostic value of TOPK expression in resected stage I lung adenocarcinoma, a retrospective analysis of 203 patients diagnosed with pathological stage I lung adenocarcinoma was carried out to examine the expression of TOPK by immunohistochemistry (IHC). The prognostic significance of TOPK overexpression was examined. Overexpression of TOPK (IHC score >3) was detected in 67.0% of patients, and these patients were more frequently characterized with disease recurrence and angiolymphatic invasion. Using multivariate analysis, patient age (>65 years old; P = 0.002) and TOPK overexpression (IHC score >3; P < 0.001) significantly predicted a shortened overall survival. Moreover, TOPK overexpression (IHC score >3; P = 0.005) also significantly predicted a reduced time to recurrence in the patients. Our results indicate that overexpression of TOPK could predetermine the metastatic capability of tumors and could serve as a significant prognostic predictor of shortened overall survival and time to recurrence. (Cancer Sci 2012; 103: 731–738)
Rapid genetic diversification within dog breeds as evidenced by a case study on Schnauzers
Authors: Streitberger K. , Schweizer M. , Kropatsch R. , Dekomien G. , Distl O. , Fischer M. S. , Epplen J. T. , Hertwig S. T. 
Published: December 2011

SummaryAs a result of strong artificial selection, the domesticated dog has arguably become one of the most morphologically diverse vertebrate species, which is mirrored in the classification of around 400 different breeds. To test the influence of breeding history on the genetic structure and variability of today's dog breeds, we investigated 12 dog breeds using a set of 19 microsatellite markers from a total of 597 individuals with about 50 individuals analysed per breed. High genetic diversity was noted over all breeds, with the ancient Asian breeds (Akita, Chow Chow, Shar Pei) exhibiting the highest variability, as was indicated chiefly by an extraordinarily high number of rare and private alleles. Using a Bayesian clustering method, we detected significant genetic stratification within the closely related Schnauzer breeds. The individuals of these three recently differentiated breeds (Miniature, Standard and Giant Schnauzer) could not be assigned to a single cluster each. This hidden genetic structure was probably caused by assortative mating owing to breeders’ preferences regarding coat colour types and the underlying practice of breeding in separate lineages. Such processes of strong artificial disruptive selection for different morphological traits in isolated and relatively small lineages can result in the rapid creation of new dog types and potentially new breeds and represent a unique opportunity to study the evolution of genetic and morphological differences in recently diverged populations.