bluuebunny/crossref_metadata_2025 huggingface dataset:
Sensitivity of unsteady collapsible channel flows to modelling assumptions
Authors: Liu H. F. , Luo X. Y. , Cai Z. X. , Pedley T. J.
Published: January 2009

We investigate the influences of modelling assumptions on the dynamic behaviour of collapsible channel flows. The elastic wall is modelled in various different ways: as a large strain Bernoulli–Euler beam, as a small strain Timoshenko beam, and as a 2D‐solid model derived from a general virtual work approach, using small strain or large strain assumptions. Different inlet boundary conditions are also considered. The in‐house finite element codes and the commercial finite element package ADINA 8.4 are used. The steady results agree very well when using the different models/approaches. The unsteady results, on the other hand, can be quite different. The dynamic behaviour of the system is analysed for a set of chosen parameters, using the full numerical solvers, the linear stability analysis, and the Fourier transform. It is found that the system stability is highly sensitive to the solid modelling assumptions used, numerical solvers adopted, or the boundary conditions imposed. Accuracy of the numerical schemes also has an impact on the system's unsteady behaviour. However, despite the high sensitivity of the unsteady solutions to the modelling assumptions, a cascade stability structure previously revealed by the authors seems to exist when different numerical approaches are used. Copyright © 2009 John Wiley & Sons, Ltd.
Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin
Authors: Berka Karel , Hobza Pavel , Vondrášek Jiří
Published: January 2009

Dispersion interactions are mainly responsible for holding together the structural arrangement of amino‐acid residues forming the hydrophobic core of the protein rubredoxin (see picture), according to symmetry‐adapted perturbation theory calculations.

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The hydrophobic core of globular proteins is responsible for major stabilization of the protein tertiary structure. The prevailing amino‐acid residues in the core are of aliphatic or aromatic character, and therefore, the core in a folded protein structure is mostly stabilized by noncovalent interactions of van der Waals origin between the amino‐acid side chains. Herein, we present a theoretical analysis of the interaction energy between the amino acids of the hydrophobic core of the small globular protein rubredoxin (Rd) based on the symmetry‐adapted perturbation theory (SAPT) method. The results show uniform proportions between the second‐order dispersion and first‐order electrostatic energy terms in favor of dispersion interaction, which plays a major role in the stabilization of this important structural element. To demonstrate the contrast between systems stabilized by different mechanisms, we perform a SAPT analysis of the typical hydrogen bonds involved in the formation of protein secondary structure elements in Rd, where dispersion still plays a non‐negligible role but electrostatic energy is the major stabilizing factor.
Applying the Inductive Effect for Synthesizing Low‐Melting and Low‐Viscosity Imidazolium‐Based Ionic Liquids
Authors: Ludwig Ralf , Paschek Dietmar
Published: January 2009

Fluidizing ionic liquids: By applying the inductive effect, a synthesis strategy to introduce strong, directional and localized H‐bonds into imidazolium‐based ionic liquids is proposed. In opposite to H‐bonded molecular liquids these strong H‐bonds could reduce the melting points and decrease the viscosities of the ILs (see figure).

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Value of P63 and CK5/6 in distinguishing squamous cell carcinoma from adenocarcinoma in lung fine‐needle aspiration specimens
Authors: Khayyata Said , Yun Shine , Pasha Theresa , Jian Bo , McGrath Cindy , Yu Gordon , Gupta Prabodh , Baloch Zubair
Published: January 2009

The current FDA‐approved standard of care for nonsmall cell lung cancer is Carboplastin/Taxol/Avastin based upon an impressive survival benefit; however, patients with squamous carcinoma (SQCC) cannot receive Avastin because of a 30% mortality rate due to fatal hemoptysis.

In this study we evaluated the role of cytomorphology and immunohistochemistry in differentiating SQCC from adenocarcinoma (ADC) in lung FNA specimens.

The case cohort included 53 FNA cases of nonsmall cell lung carcinoma with surgical pathology follow‐up. All FNA specimens were reviewed independently by a panel of cytopathologists to differentiate between SQCC and ADC. The cell block material was available in 23 cases (11 ADC and 12 SQCC) to perform immunohistochemical stains for TTF‐1, CK7, CK20, P63, and CK5/6.

On surgical resection, 35/53 (66%) cases were diagnosed as ADC and 18/53 (34%) as SQCC. The number of cases classified correctly on the basis of cytomorphology was 66% for ADC and 53% for SQCC (combined accuracy 60%). By immunohistochemical staining, 14/23 (61%) cases expressed TTF‐1. Nine cases were TTF‐1 negative; eight of the TTF‐1 negative cases (89%) were SQCC.

Twenty‐three cases expressed CK7 (87%); one ADC case (4%) showed focal CK20 positivity. Both P63 and CK5/6 expression was seen in 9/12 (75%) SQCC cases; none of the ADC cases showed this dual expression.

Cytomorphology alone may not be able to stratify all cases of nonsmall cell lung carcinoma into ADC and SQCC in FNA specimens. The immune‐panel of TTF‐1, CK7, CK20, P63, and CK5/6 is useful in differentiating SQCC from ADC. Diagn. Cytopathol. 2009. © 2009 Wiley‐Liss, Inc.
Koilocytosis: Correlations with high‐risk HPV and its comparison on tissue sections and cytology, urothelial carcinoma
Authors: Aggarwal Seema , Arora Vinod K. , Gupta Sanjay , Singh Navjeevan , Bhatia Arati
Published: January 2009

The aim of this study were (1) To correlate koilocytosis with high risk HPV(HrHPV) DNA in urinary bladder carcinoma and (2) To compare detection of koilocytosis on tissue sections and urine cytology. Biopsy and cytologic specimens from 33 patients of urinary bladder carcinoma were analyzed. HPV DNA was detected by PCR on biopsy specimens using consensus primers MY09 and MY11. Koilocytosis was assessed both on tissue sections and urine cytology. HrHPV DNA was found in 14 of 33 bladder carcinoma. Koilocytosis was seen in tissue sections from 13 patients. Eleven of these were HrHPV DNA positive (positive predictive value 84.6%). Koilocytosis was seen in urine cytology in three patients. All three were positive for HrHPV DNA. To conclude koilocytosis is a good morphological marker for HrHPV DNA in the urothelium. Tissue sections are better than cytologic smears for detection of koilocytes. Diagn. Cytopathol. 2009. © 2009 Wiley‐Liss, Inc.
Primary small cell carcinoma of the lung initially presenting as a breast mass: A fine‐needle aspiration diagnosis
Authors: Liu Wei , Palma‐Diaz Fernando , Alasio Teresa M.
Published: January 2009

The incidence of metastases to the breast from extramammary sites is relatively low compared with the incidence of primary breast carcinoma. Primary sites which have a predilection for metastases to the breast include, in the order of decreasing frequency, malignant melanoma, lymphoma, lung carcinoma, ovarian carcinoma, and soft tissue sarcoma, followed by gastrointestinal and genitourinary primaries. Most lung primaries metastasizing to breast represent adenocarcinoma. Other types of lung carcinoma, including small cell carcinoma, are relatively rare. We report a case of lung small cell carcinoma metastasizing to the breast and initially presenting with a breast mass in a 50‐year‐old female. The tumor was first diagnosed on a fine‐needle aspiration biopsy specimen (FNAB) from the breast lesion and subsequently supported by core biopsy. A discussion of the differential diagnoses to consider on FNAB follows. Because of the difference in treatment for primary small cell carcinoma of breast versus primary small cell carcinoma of the lung, as well as the difference in prognosis for both malignancies, determining the site of primary malignancy is crucial to adequate patient care. Diagn. Cytopathol. 2009. © 2009 Wiley‐Liss, Inc.
gfap and nestin reporter lines reveal characteristics of neural progenitors in the adult zebrafish brain
Authors: Lam Chen Sok , März Martin , Strähle Uwe
Published: January 2009

Adult neurogenesis arises from niches that harbor neural stem cells (NSC). Although holding great promise for regenerative medicine, the identity of NSC remains elusive. In mammals, a key attribute of NSC is the expression of the filamentous proteins glial fibrillary acidic protein (GFAP) and NESTIN. To assess whether these two markers are relevant in the fish model, two transgenic zebrafish lines for gfap and nestin were generated. Analysis of adult brains showed that the fusion GFAP–green fluorescent protein closely mimics endogenous GFAP, while the nestin transgene recapitulates nestin at the ventricular zones. Cells expressing the two reporters display radial glial morphology, colocalize with the NSC marker Sox2, undergo proliferation, and are capable of self‐renewal within the matrix of distinct thickness in the telencephalon. Together, these two transgenic lines reveal a conserved feature of putative NSC in the adult zebrafish brain and provide a means for the identification and manipulation of these cells in vivo. Developmental Dynamics 238:475–486, 2009. © 2009 Wiley‐Liss, Inc.
Governing forests of the European Union: institutional framework for interest representation at the European Community level
Authors: Lazdinis Marius , Angelstam Per , Lazdinis Imantas
Published: January 2009

We analyse whether the European Community provides for articulating a common set of priorities for society and supports openness and participation in the area of forest policy at the Community level. In doing so, we review the institutional framework and, using the results of the internet‐based stakeholder consultation, assess the presence of interested parties at the level of the European Community. In addition, from the same consultation we learn about the opinions of the interest groups concerning possible areas for enhancing coherence in forest governance in the European Union.

The results of the study demonstrate that there is a range of possibilities for participation of different interest groups and flow of information between the European Commission and the stakeholders. However, the number of interest groups prepared to actively participate in Community‐level forest and forestry‐related policy‐ and decision‐making is relatively low.

We conclude that the present institutional arrangements should be sufficient for open and participatory priority setting in forest governance at the European Community level. However, based on the ‘stakeholder consultation’ we also conclude that co‐ordination and co‐operation, and hence coherence, in forest and forestry‐related policy‐ and decision‐making at the Community level should be improved. Copyright © 2009 John Wiley & Sons, Ltd and ERP Environment.
Low cost, portable detection of gold nanoparticle‐labeled microfluidic immunoassay with camera cell phone
Authors: Lu Yao , Shi Weiwei , Qin Jianhua , Lin Bingcheng
Published: January 2009

This paper describes the use of camera cell phone to detect the gold nanoparticle‐labeled immunoassay results on microfluidic chip. On‐chip heterogeneous immunoassay between anti‐human IgG and human IgG (hIgG) was performed and the results were amplified by gold nanoparticle‐enhanced silver staining to transform the nano‐scale probe into detectable silver precipitation film. The detection results obtained by camera phone showed good correlation with the concentration of hIgG. This detection scheme is simple, low cost and easy to use and has significant promise for portable diagnosis and point of care testing on microfluidic platform.
Digital mapping of riverine waterway hydrodynamic and geomorphic features
Authors: Hauet A. , Muste M. , Ho H‐C.
Published: January 2009

This paper proposes an innovative, non‐intrusive method for mapping waterway characteristics in riverine areas. The technique uses photogrammetry to provide quantitative information about the dry area in the vicinity of the waterways (banks and floodplain) and image processing algorithms to characterize the flow. Riverside images of a riverine area are decomposed into quasi‐planar areas and ortho‐rectified and re‐assembled to obtain a panoramic ortho‐view of the area of interest. Morphological features of interest (such as river bank positions, flood plain edges, mud deposits, vegetation and erosion patterns) are then identified on the ortho‐view and mapped digitally. Image sequences of the river flow are recorded, allowing a surface velocity analysis to be obtained through Large Scale Particle Image Velocimetry (LSPIV). Finally, the mapped elements and the surface velocities are displayed together in a GIS‐like visualization. Through the presentation of a case study of a flood event at a culvert site, this paper demonstrates the capability of the technique to monitor characteristics of waterways over time. The method is inexpen‐sive (a conventional video or digital camera can be used), fast and requires minimum preparation. It can be applied in such important river‐related research areas as morphodynamic and sediment transport studies. It also fosters an improved understand‐ing of the coupling between the river and its banks, which is essential for river restoration and eco‐habitat studies. The present methodology is readily available for implementation in routine bridge inspections, fitted with an easy‐to‐use graphical interface. Copyright © 2009 John Wiley & Sons, Ltd.
Joint network‐channel coding for the multiple‐access relay channel based on turbo codes
Authors: Hausl Christoph
Published: January 2009

We consider the time‐division multiple‐access relay channel (MARC) with block‐fading channels and Gaussian noise, where two sources communicate with one destination with the help of one relay. Such a system can be used for the cooperative uplink of two mobile stations to a base station with the help of a relay. We propose a joint network‐channel code design based on turbo codes for the MARC. We compare the proposed system with a distributed turbo code for the time‐division relay channel and with a system which uses separate network‐channel coding for the MARC. Our results show that the proposed code can gain diversity compared to the system for the time‐division relay channel and allows to more efficiently exploit the redundancy in the transmission of the relay than separate network‐channel coding. Copyright © 2009 John Wiley & Sons, Ltd.
A new information share measure
Authors: Lien Donald , Shrestha Keshab
Published: January 2009

In this study, we modify the information share (IS) originally proposed by Hasbrouck, J. (1995). The proposed modified information share (MIS) leads to a unique measure of price discovery instead of the upper and lower IS bounds. Performance of MIS is compared with the Hasbrouck IS measure and the Gonzalo–Granger permanent–transitory decomposition (PT/GG)‐based measure using simulations with 1,000 replications applied to the same three examples considered by Hasbrouck, J. (2002). The MIS is found to outperform both Hasbrouck IS measure and PT/GG measure. The empirical application of the MIS to three major stock indices indicates that price discovery takes place mostly in the futures market. Hence, the evidence supports the transaction cost hypothesis as well as the model proposed by Garbade, K. D., and Silber, W. L. (1983). © 2009 Wiley Periodicals, Inc. Jrl Fut Mark 29:377–395, 2009
Risk management with options and futures under liquidity risk
Authors: Adam‐Müller Axel F. A. , Panaretou Argyro
Published: January 2009

Futures hedging creates liquidity risk through marking to market. Liquidity risk matters if interim losses on a futures position have to be financed at a markup over the risk‐free rate. This study analyzes the optimal risk management and production decisions of a firm facing joint price and liquidity risk. It provides a rationale for the use of options on futures in imperfect capital markets. If liquidity risk materializes, the firm sells options on futures in order to partly cover this liquidity need. It is shown that liquidity risk reduces the optimal hedge ratio and that options are not normally used before a liquidity need actually arises. © 2009 Wiley Periodicals, Inc. Jrl Fut Mark 29:297–318, 2009
Asymptotic tests of association with multiple SNPs in linkage disequilibrium
Authors: Pan Wei
Published: January 2009

We consider detecting associations between a trait and multiple single nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD). To maximize the use of information contained in multiple SNPs while minimizing the cost of large degrees of freedom (DF) in testing multiple parameters, we first theoretically explore the sum test derived under a working assumption of a common association strength between the trait and each SNP, testing on the corresponding parameter with only one DF. Under the scenarios that the association strengths between the trait and the SNPs are close to each other (and in the same direction), as considered by Wang and Elston [Am. J. Hum. Genet. [2007] 80:353–360], we show with simulated data that the sum test was powerful as compared to several existing tests; otherwise, the sum test might have much reduced power. To overcome the limitation of the sum test, based on our theoretical analysis of the sum test, we propose five new tests that are closely related to each other and are shown to consistently perform similarly well across a wide range of scenarios. We point out the close connection of the proposed tests to the Goeman test. Furthermore, we derive the asymptotic distributions of the proposed tests so that P‐values can be easily calculated, in contrast to the use of computationally demanding permutations or simulations for the Goeman test. A distinguishing feature of the five new tests is their use of a diagonal working covariance matrix, rather than a full covariance matrix as used in the usual Wald or score test. We recommend the routine use of two of the new tests, along with several other tests, to detect disease associations with multiple linked SNPs. Genet. Epidemiol. 33:497–507, 2009. © 2009 Wiley‐Liss, Inc.
Endothelial NOS‐deficient mice reveal dual roles for nitric oxide during experimental autoimmune encephalomyelitis
Authors: Wu Muzhou , Tsirka Stella E.
Published: January 2009

Multiple sclerosis (MS) is a demyelinating autoimmune disease characterized by infiltration of T cells into the central nervous system (CNS) after compromise of the blood‐brain barrier. A model used to mimic the disease in mice is experimental autoimmune encephalomyelitis (EAE). In this report, we examine the clinical and histopathological course of EAE in eNOS‐deficient (eNOS−/−) mice to determine the role of nitric oxide (NO) derived from this enzyme in the disease progression. We find that eNOS−/− mice exhibit a delayed onset of EAE that correlates with delayed BBB breakdown, thus suggesting that NO production by eNOS underlies the T cell infiltration into the CNS. However, the eNOS−/− mice also eventually exhibit more severe EAE and delayed recovery, indicating that NO undertakes dual roles in MS/EAE, one proinflammatory that triggers disease onset, and the other neuroprotective that promotes recovery from disease exacerbation events. © 2009 Wiley‐Liss, Inc.
Mechanical control of cAMP signaling through integrins is mediated by the heterotrimeric Gαs protein
Authors: Alenghat Francis J. , Tytell Jessica D. , Thodeti Charles K. , Derrien Alexandrine , Ingber Donald E.
Published: January 2009

Mechanical stresses that are preferentially transmitted across the cell surface via transmembrane integrin receptors activate gene transcription by triggering production of intracellular chemical second messengers, such as cAMP. Here we show that the sensitivity of the cAMP signaling pathway to mechanical stresses transferred across β1 integrins is mediated by force‐dependent activation of the heterotrimeric G protein subunit Gαs within focal adhesions at the site of stress application. Gαs is recruited to focal adhesions that form within minutes following clustering of β1 integrins induced by cell binding to magnetic microbeads coated with activating integrin ligands, and β1 integrin and Gαs co‐precipitate when analyzed biochemically. Stress application to activated β1 integrins using magnetic twisting cytometry increases Gαs recruitment and activates these large G proteins within focal adhesions, as measured by binding of biotinylated azido‐anilido‐GTP, whereas application of similar stresses to inactivated integrins or control histocompatibility antigens has little effect. This response is relevant physiologically as application of mechanical strain to cells bound to flexible extracellular matrix‐coated substrates induce translocation of phospho‐CREB to the nucleus, which can be attenuated by inhibiting Gαs activity, either using the inhibitor melittin or suppressing its expression using siRNA. Although integrins are not typical G protein‐coupled receptors, these results show that integrins focus mechanical stresses locally on heterotrimeric G proteins within focal adhesions at the site of force application, and transduce mechanical stimuli into an intracellular cAMP signaling response by activating Gαs at these membrane signaling sites. J. Cell. Biochem. 106: 529–538, 2009. © 2009 Wiley‐Liss, Inc.
FGF8 regulates myogenesis and induces Runx2 expression and osteoblast differentiation in cultured cells
Authors: Omoteyama Kazuki , Takagi Minoru
Published: January 2009

In the current study, treatment of the rat osteogenic cell line ROB‐C26 cells with fibroblast growth factor 8 (FGF8) stimulated alkaline phosphatase (ALP) activity, and also induced the expression of the Runx2 transcription factor, and increased the activity of a luciferase reporter gene containing the osteocalcin (OCN) promoter and six copies of the osteoblast specific cis‐acting element 2 (OSE2) response element. In contrast, FGF8 treatment of the mouse myoblast cell line C2C12 inhibited the expression of desmin and the synthesis of myotubes. The expression of MyoD, Myogenin, Foxc2, and Hand1 was also decreased by FGF8. Transient expression of Foxc2 in C2C12 cells induced the expression of Hand1, and chromatin immunoprecipitation (ChIP) analysis indicated that Foxc2 binds to the promoter region of the Hand1 gene. These results indicated that Foxc2 is directly involved in the regulation of Hand1 expression. The results of the current study indicate that FGF8 regulates myoblast differentiation through the regulation of MyoD expression, and that this regulation is independent of Hand1 in cultured cells. Conversely, FGF8 supports bone development and cell differentiation though the induction of Runx2 expression. J. Cell. Biochem. 106: 546–552, 2009. © 2009 Wiley‐Liss, Inc.
IFI16 and NM23 bind to a common DNA fragment both in the P53 and the cMYC gene promoters
Authors: Egistelli Lorenza , Chichiarelli Silvia , Gaucci Elisa , Eufemi Margherita , Schininà M. Eugenia , Giorgi Alessandra , Lascu Ioan , Turano Carlo , Giartosio Anna , Cervoni Laura
Published: January 2009

In the melanoma M14 cell line, we found that the antimetastatic protein NM23/nucleoside diphosphate kinase binds to the promoters of the oncogene cMYC and of P53, a gene often mutated in human cancer (Cervoni et al. [2006] J. Cell. Biochem. 98:421–428). In a further study, we find now that IFI16, a transcriptional repressor, in both promoters binds to the G‐rich fragment that also binds NM23/NDPK. These fragments possess non‐B DNA structures. Moreover, by sequential chromatin immunoprecipitation (re‐ChIP) we show that the two proteins (IFI16 and NM23/NDPK) are simultaneously bound in vivo to the same DNA fragments. Since P53 stimulates apoptosis and inhibits cellular growth, and cMYC promotes cell growth and, in several instances, also apoptosis, the presence of NM23 and IFI16 on the same DNA fragments suggests their common involvement in the reduced development of some tumors. J. Cell. Biochem. 106: 666–672, 2009. © 2009 Wiley‐Liss, Inc.
SHARPEN—Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network
Authors: Loksha Ilya V. , Maiolo James R. , Hong Cheng W. , Ng Albert , Snow Christopher D.
Published: January 2009

Algorithms for discrete optimization of proteins play a central role in recent advances in protein structure prediction and design. We wish to improve the resources available for computational biologists to rapidly prototype such algorithms and to easily scale these algorithms to many processors. To that end, we describe the implementation and use of two new open source resources, citing potential benefits over existing software. We discuss CHOMP, a new object‐oriented library for macromolecular optimization, and SHARPEN, a framework for scaling CHOMP scripts to many computers. These tools allow users to develop new algorithms for a variety of applications including protein repacking, protein–protein docking, loop rebuilding, or homology model remediation. Particular care was taken to allow modular energy function design; protein conformations may currently be scored using either the OPLSaa molecular mechanical energy function or an all‐atom semiempirical energy function employed by Rosetta. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Perfusion affects the tissue developmental patterns of human mesenchymal stem cells in 3D scaffolds
Authors: Zhao Feng , Grayson Warren L. , Ma Teng , Irsigler Andre
Published: January 2009

Human mesenchymal stem cells (hMSCs) developed in three‐dimensional (3D) scaffolds are significantly affected by culture conditions. We hypothesized that the hydrodynamic forces generated in perfusion bioreactors significantly affected hMSC functionality in 3D scaffolds by shaping the extracellular matrix (ECM) proteins. In this study, hMSCs were grown in 3D poly(ethylene terephthalate) (PET) scaffolds in static and a parallel perfusion system under similar initial conditions for up to 35 days. Results demonstrated that even at very low media velocities (O [10−4 cm/sec]), perfusion cultures affected the ability of hMSCs to form an organized ECM network as illustrated by the immunostaining of collagen I and laminin fibrous structure. The change in the ECM microenvironment consequently influenced the nuclear shape. The hMSCs grown at the lower surface of static culture displayed a 15.2 times higher nuclear elongation than those at the upper surface, whereas cells grown in the perfusion bioreactor displayed uniform spherical nuclei on both surfaces. The difference in ECM organization and nuclear morphology associated with gene expression and differentiation characteristics of hMSCs. The cells exhibited lower CFU‐F colony forming ability and decreased expressions of stem‐cell genes of Rex‐1 and Oct‐4, implying a less primitive stem‐cell phenotype was maintained in the perfusion culture relative to the static culture conditions. The significantly higher expression level of osteonectin gene in the perfusion culture at day 28 indicated an upregulation of osteogenic ability of hMSCs. The study highlights the critical role of dynamic culture conditions on 3D hMSC construct development and properties. J. Cell. Physiol. 219: 421–429, 2009. © 2009 Wiley‐Liss, Inc.
CCCTC‐binding factor meets poly(ADP‐ribose) polymerase‐1
Authors: Caiafa Paola , Zlatanova Jordanka
Published: January 2009

CCCTC‐binding factor (CTCF) is a ubiquitous Zn‐finger‐containing protein with numerous recognized functions, including, but not limited to, gene activation and repression, enhancer‐blocking, X‐chromosome inactivation, and gene imprinting. It is believed that the protein performs such a variety of functions by interacting with an array of very diverse proteins. In addition, CTCF undergoes several post‐translational modifications, including poly(ADP‐ribosyl)ation. The PARylated form of CTCF has recently been implicated in two important functions: gene imprinting and control of ribosomal gene transcription. Here, we summarize and critically discuss the available data on the interplay between CTCF and poly(ADP‐ribosyl)ation in these two processes. We consider the newly described phenomena in the broader context of PARP's activities, including the crucial role of protein PARylation in the regulation of the genome methylation pattern. J. Cell. Physiol. 219: 265–270, 2009. © 2009 Wiley‐Liss, Inc.
Sonographic measurement of cross‐sectional area of the median nerve in the diagnosis of carpal tunnel syndrome: Correlation with nerve conduction studies
Authors: Moran Luz , Perez Maria , Esteban Angel , Bellon Jose , Arranz Beatriz , del Cerro Miguel
Published: January 2009

Purpose.

To assess the usefulness of sonographic measurement of the median nerve cross‐sectional area (CSA) in the diagnosis of carpal tunnel syndrome (CTS) and grading of its severity using nerve conduction (NC) studies as the standard.

Method.

The CSA of the median nerve was measured at the tunnel inlet and outlet using the ellipse formula and automatic tracing in 72 hands with suspicion of CTS.

Result.

The lack of inter‐reader reliability led to excluding CSA measurements obtained at the tunnel outlet. Based on the receiver operating characteristic curves, the following cut‐off points for the CSA of the median nerve at the tunnel inlet was selected: 9.8 mm and 12.3 mm2 for the ellipse formula and 11 and 13 mm2 for automatic tracing. For the ellipse formula, a CSA less than or equal to 9.8 mm2 excluded CTS whereas a CSA greater than or equal to 12.3 mm2 was diagnostic of CTS with measurements between 9.8 and 12.3 mm2 being indeterminate and requiring NC studies. For automatic tracing, the cutoff value of 11 mm2 was excluded because of the high percentage of false negatives, whereas CSAs greater than or equal to 13 mm2 were diagnostic of CTS. There were no statistically significant differences in CSA measurements between the various degrees of CTS severity determined by NC studies.

Conclusion.

Sonographic measurement of median nerve CSA at the tunnel inlet is a good alternative to NC studies as the initial diagnostic test for CTS, but it cannot grade the severity of CTS as well as NC studies. © 2009 Wiley Periodicals, Inc. J Clin Ultrasound 2009
LEEM investigations of surfaces using a beam of energetic self‐ions
Authors: Ondrejcek Michal , Swiech Wacek , Petrov Ivan , Rajappan Mahesh , Flynn C. Peter
Published: January 2009

This article reviews recent research using a low‐energy electron microscope, built by Tromp at IBM, and equipped with an accelerator that permits in situ irradiation with a beam of self‐ions. The available ion energies of 20 eV to 5 keV span the range from epitaxial growth by a hyperthermal beam to sputtering at the level of ∼10 atoms per incident ion. The design criteria and instrument calibration are described. The research described is surface science that requires a vacuum maintained below 10−10 Torr, with all components contained in the same vacuum. Two general categories of applications are sketched. Experiments that accurately measure important physical quantities include surface mass diffusion over an extended temperature range; determining the critical chemical potential at which island nucleation occurs; observation and explanation of the universal evolution by which adatom and advacancy islands both grow and shrink by beam‐driven processes; and the study of sublimation (regarded as negative ion beam intensity). Experiments described here with other goals include beam‐assisted synthesis first of large pans and mesas for isolating surface experiments (e.g., nucleation) from the surrounding crystal, and second of Fourier waves on steps, for studies of diffusive relaxation. Operation of exotic structures including Bardeen‐Herring sources and Frank growth spirals deformed by crystal anisotropy are also described. Microsc. Res. Tech., 2009. © 2009 Wiley‐Liss, Inc.
Catastrophic payments for health care among households in urban Tamil Nadu, India
Authors: Vaishnavi Salem Deenadayalan , Dash Umakant
Published: January 2009

Urban residents in India face important health problems due to unhygienic conditions, excessive crowding and lack of proper sanitation. The private sector has started occupying the centre stage of the health system and households are burdened with increasing levels of health expenditure. This paper aims to study out‐of‐pocket expenditure (OOPE) and the extent of catastrophic payments for health care among households in a highly urbanised state, Tamil Nadu. The study used data on morbidity and health care for the year 2004 collected by the National Sample Survey Organization, India. Care was sought for 84 per cent of illness episodes in urban areas, and the majority used private sector providers (67 per cent for inpatients and 78 per cent for outpatients). Mean OOPE for inpatients and outpatients was higher for households with higher income. The average cost burden per visit was higher among those who sought care from private providers for inpatient services (29 per cent of household consumption expenditure) and outpatient services (20% of household consumption expenditure) compared with the burden associated with public health service use (3–4 per cent of consumption expenditure). About 60 per cent of households which used private health services faced catastrophic payments at the 10 per cent threshold level. To avoid catastrophic expenditure, greater use of the public sector which is providing services at an affordable cost is needed. Improving access to public health services, better gate‐keeping systems, stronger controls on drug prices and increasing the quality of services are required to reduce the incidence of catastrophic expenditure both on inpatients and outpatients. Greater use of risk pooling mechanisms would encourage the poor to seek health care and also to protect households from all socio‐economic groups from catastrophic expenditure. Copyright © 2009 John Wiley & Sons, Ltd.
A two‐step one‐pot radiosynthesis of the potent dopamine D2/D3 agonist PET radioligand [11C]MNPA
Authors: Steiger C. , Finnema S. J. , Raus L. , Schou M. , Nakao R. , Suzuki K. , Pike V. W. , Wikström H. V. , Halldin C.
Published: January 2009

(R)‐(−)‐2‐[11C]Methoxy‐N‐n‐propylnorapomorphine ([11C]MNPA ([11C]2)) is an agonist radioligand of interest for imaging D2/D3 receptors in vivo. Here we sought to develop an improved radiosynthesis of this radioligand. Reference 2 was synthesized in nine steps with an overall yield of about 5%, starting from codeine. Trimethylsilyldiazomethane proved to be a practical improvement in comparison to diazomethane in the penultimate methylation step. A protected precursor for radiolabeling ((R)‐(−)‐2‐hydroxy‐10,11‐acetonide‐N‐n‐propylnoraporphine, 4) was prepared from (R)‐(−)‐2‐hydroxy‐N‐n‐propylnorapomorphine (1) in 30% yield. [11C]2 was prepared from 4 via a two‐step one‐pot radiosynthesis. The first step, methylation of 4 with [11C]methyl triflate, occurred in quantitative radiochemical yield. The second step, deprotection of the catechol moiety with HCl and heat, yielded 60–90% of [11C]2 giving an overall incorporation yield from [11C]methyl triflate of 60–90%. In a typical run more than 1 GBq of [11C]2, was produced from carbon‐11 generated from a 10‐min proton irradiation (16 MeV; 35 µA) of nitrogen–hydrogen target gas. The radiochemical purity of [11C]2 was > 99% and specific radioactivity at the time of injection was 901±342 GBq/µmol (n=10). The total synthesis time was 35–38 min from the end of radionuclide production. The identity of [11C]2 was confirmed by comparing its LC‐MS/MS spectrum with those of reference 2 and (R)‐(−)‐10‐methoxy‐2,11‐dihydroxy‐N‐n‐propylnoraporphine. Copyright © 2009 John Wiley & Sons, Ltd.
Glucose‐dependent insulinotropic polypeptide (GIP) and its receptor (GIPR): Cellular localization, lesion‐affected expression, and impaired regenerative axonal growth
Authors: Buhren Bettina A. , Gasis Marcia , Thorens Bernard , Müller Hans Werner , Bosse Frank
Published: January 2009

Glucose‐dependent insulinotropic polypeptide (GIP) was initially described to be rapidly regulated by endocrine cells in response to nutrient ingestion, with stimulatory effects on insulin synthesis and release. Previously, we demonstrated a significant up‐regulation of GIP mRNA in the rat subiculum after fornix injury. To gain more insight into the lesion‐induced expression of GIP and its receptor (GIPR), expression profiles of the mRNAs were studied after rat sciatic nerve crush injury in 1) affected lumbar dorsal root ganglia (DRG), 2) spinal cord segments, and 3) proximal and distal nerve fragments by means of quantitative RT‐PCR. Our results clearly identified lesion‐induced as well as tissue type‐specific mRNA regulation of GIP and its receptor. Furthermore, comprehensive immunohistochemical stainings not only confirmed and exceeded the previous observation of neuronal GIP expression but also revealed corresponding GIPR expression, implying putative modulatory functions of GIP/GIPR signaling in adult neurons. In complement, we also observed expression of GIP and its receptor in myelinating Schwann cells and oligodendrocytes. Polarized localization of GIPR in the abaxonal Schwann cell membranes, plasma membrane‐associated GIPR expression of satellite cells, and ependymal GIPR expression strongly suggests complex cell type‐specific functions of GIP and GIPR in the adult nervous system that are presumably mediated by autocrine and paracrine interactions, respectively. Notably, in vivo analyses with GIPR‐deficient mice suggest a critical role of GIP/GIPR signal transduction in promoting spontaneous recovery after nerve crush, insofar as traumatic injury of GIPR‐deficient mouse sciatic nerve revealed impaired axonal regeneration compared with wild‐type mice. © 2009 Wiley‐Liss, Inc.
Neuropathy‐induced apoptosis: Protective effect of physostigmine
Authors: Di Cesare Mannelli L. , Bartolini A. , Ghelardini C.
Published: January 2009

Traumatic, infectious, metabolic, and chemical noxa to the nervous system are the etiology of a crippling disease generally termed neuropathy. Motor disorders, altered sensibility, and pain are the pathognomonic traits. Cellular alterations induced by this chronic pathology include mitochondrial dysfunctions that lead to the activation of the apoptotic cascade. Energy imbalance can compromise the maintenance of mitochondrial membrane potential, furthering the release of cytochrome C and the subsequent cleavage and activation of caspases. Chronic constriction injury (CCI) of the rat sciatic nerve is a neuropathy model able to induce a strong mitochondrial impairment with a consequent apoptotic induction. In this model, the acetylcholinesterase inhibitor physostigmine is administered at 0.125 mg/kg i.p. (twice per day) starting from the operation and for 15 days after. The cholinergic activation reduces cytosolic levels of cytochrome C, suggesting an improved stability of the mitochondrial membrane, and the expression level of the active caspase 3 fragments (19, 16 kDa) is reduced significantly with respect to saline treatment. Accordingly, physostigmine impairs caspase 3 protease activity. In fact, the target of the activated caspase 3, the 89‐kDa PARP fragment, is significantly less expressed in the ligated nerve of physostigmine‐treated rats, reaching levels that are comparable to those in the contralateral unligated nerve. Finally, this natural acetylcholinesterase inhibitor reduces DNA fragmentation both in the proximal and in the distal parts of the nerve. This protection correlates with the induction of XIAP. Therefore, apoptosis, central to tissue degeneration, is prevented by repeated physostigmine treatment of CCI animals. © 2009 Wiley‐Liss, Inc.
Recombinant human platelet‐derived growth factor BB (rhPDGF‐BB) and beta‐tricalcium phosphate/collagen matrix enhance fracture healing in a diabetic rat model
Authors: Al‐Zube Loay , Breitbart Eric A. , O'Connor J. Patrick , Parsons J. Russell , Bradica Gino , Hart Charles E. , Lin Sheldon S.
Published: January 2009

Diabetes mellitus is a common systemic disease that has been associated with poor fracture healing outcomes. The mechanism through which diabetes impairs bone regeneration is unknown. One possible mechanism may be related to either decreased or uncoordinated release of local growth factors at the fracture site. Indeed, previous studies have found reduced platelet‐derived growth factor (PDGF) levels in the fracture callus of diabetic rats, suggesting that local application of PDGF may overcome the negative effects of diabetes and promote fracture healing. To test this hypothesis, low (22 µg) and high (75 ug) doses of recombinant human PDGF‐BB (rhPDGF‐BB) were applied directly to femur fracture sites in BB Wistar diabetic rats that were then compared to untreated or vehicle‐treated animals. rhPDGF‐BB treatment significantly increased early callus cell proliferation compared to that in control specimens. Low dose rhPDGF‐BB treatment significantly increased callus peak torque values (p < 0.05) at 8 weeks after fracture as compared to controls. High dose rhPDGF‐BB treatment increased callus bone area at 12 weeks postfracture. These data indicate that rhPDGF‐BB treatment ameliorates the effects of diabetes on fracture healing by promoting early cellular proliferation that ultimately leads to more bone formation. Local application of rhPDGF‐BB may be a new therapeutic approach to treat diabetes‐impaired fracture healing. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 27: 1074–1081, 2009
Lymph node assessment and lymphadenectomy in prostate cancer
Authors: Ordon Michael , Nam Robert K.
Published: January 2009

The role of lymph node assessment for patients with clinically localized prostate cancer has significantly evolved over the last 20 years. The status of pelvic lymph nodes primarily served as a prognostic marker for prostate cancer. Improved methods in assessing the risk for cancer progression and metastasis have enhanced our ability to identify patients who require pelvic lymphadenectomy during radical prostatectomy. The status of pelvic lymph nodes is also being used to guide further treatments after surgery. Also, recent data has shown possible therapeutic benefit of lymphadenectomy in improving cancer specific survival. J. Surg. Oncol. 2009;99:215–224. © 2009 Wiley‐Liss, Inc.
Electrodynamic constraints on homogeneity and radiofrequency power deposition in multiple coil excitations
Authors: Lattanzi Riccardo , Sodickson Daniel K. , Grant Aaron K. , Zhu Yudong
Published: January 2009

The promise of increased signal‐to‐noise ratio and spatial/spectral resolution continues to drive MR technology toward higher magnetic field strengths. SAR management and B1 inhomogeneity correction become critical issues at the high frequencies associated with high field MR. In recent years, multiple coil excitation techniques have been recognized as potentially powerful tools for controlling specific absorption rate (SAR) while simultaneously compensating for B1 inhomogeneities. This work explores electrodynamic constraints on transmit homogeneity and SAR, for both fully parallel transmission and its time‐independent special case known as radiofrequency shimming. Ultimate intrinsic SAR—the lowest possible SAR consistent with electrodynamics for a particular excitation profile but independent of transmit coil design—is studied for different field strengths, object sizes, and pulse acceleration factors. The approach to the ultimate intrinsic limit with increasing numbers of finite transmit coils is also studied, and the tradeoff between homogeneity and SAR is explored for various excitation strategies. In the case of fully parallel transmission, ultimate intrinsic SAR shows flattening or slight reduction with increasing field strength, in contradiction to the traditionally cited quadratic dependency, but consistent with established electrodynamic principles. Magn Reson Med 61:315–334, 2009. © 2009 Wiley‐Liss, Inc.
Comparison of gradient encoding directions for higher order tensor diffusion data
Authors: Mang Sarah C. , Gembris Daniel , Grodd Wolfgang , Klose Uwe
Published: January 2009

Recently, higher order tensors were proposed for a more advanced representation of non‐Gaussian diffusion. These advanced diffusion models have new requirements for the gradient encoding schemes used in the diffusion weighted image acquisition. The influence of the gradient encoding schemes on the estimated standard second order diffusion tensor was previously investigated. Here, we focus on the suitability of different encoding scheme types for higher order tensor models. Two quality measures for the gradient encoding schemes, the condition number of the estimation matrix and a new measure that evaluates the signal deviation on simulated data, are used to determine which gradient encoding is suited best for higher order tensor estimations. Six different gradient encoding scheme types were investigated. A certain force‐minimizing scheme type gave the best results in the evaluations presented here. Magn Reson Med 61:335–343, 2009. © 2009 Wiley‐Liss, Inc.
Effect of inflow of fresh blood on vascular‐space‐occupancy (VASO) contrast
Authors: Donahue Manus J. , Hua Jun , Pekar James J. , van Zijl Peter C.M.
Published: January 2009

In vascular‐space‐occupancy (VASO)‐MRI, cerebral blood volume (CBV)‐weighted contrast is generated by applying a nonselective inversion pulse followed by imaging when blood water magnetization is zero. An uncertainty in VASO relates to the completeness of blood water nulling. Specifically, radio frequency (RF) coils produce a finite inversion volume, rendering the possibility of fresh, non‐nulled blood. Here, VASO‐functional MRI (fMRI) was performed for varying inversion volume and TR using body coil RF transmission. For thin inversion volume thickness (δtot < 10 mm), VASO signal changes were positive (ΔS/S = 2.1–2.6%). Signal changes were negative and varied in magnitude for intermediate inversion volumes (δtot = 100–300 mm), yet did not differ significantly (P > 0.05) for δtot > 300 mm. These data suggest that blood water is in steady state for δtot > 300 mm. In this appropriate range, long‐TR VASO data converged to a less negative value (ΔS/S = –1.4% ± 0.2%) than short‐TR data (ΔS/S = –2.2% ± 0.2%), implying that cerebral blood flow or transit‐state effects may influence VASO contrast at short TR. Magn Reson Med 61:473–480, 2009. © 2009 Wiley‐Liss, Inc.
Intra‐thoracic blood volume measurement by contrast magnetic resonance imaging
Authors: Mischi M. , van den Bosch H.C.M. , den Boer J.A. , Verwoerd J. , Grouls R.J.E. , Peels C.H. , Korsten H.H.M.
Published: January 2009

The intra‐thoracic blood volume (ITBV) is a cardiovascular parameter related to the cardiac preload and left ventricular function. Its assessment is, therefore, important for diagnosis and follow‐up of several cardiovascular dysfunctions. Nowadays, the ITBV can be accurately measured only by invasive indicator dilution techniques, which require a double catheterization of the patient. In this study, a novel technique is presented for ITBV assessment by dynamic magnetic resonance imaging after intravenous injection of a small bolus of gadolinium chelate. The dose was chosen on the basis of in vitro calibration. The bolus first pass is detected from a simultaneous dynamic image series of the right and left ventricles. Two indicator dilution curves are derived and used to inspect the transpulmonary dilution system. Various mathematical models for the interpretation of the measured indicator dilution curves are compared. The ITBV is assessed as the product of the transpulmonary mean transit time of the indicator and the cardiac output, obtained by phase contrast magnetic resonance angiography. In vitro measurements showed a correlation coefficient larger than 0.99 and preliminary tests with volunteers proved the feasibility of the method, opening new possibilities for noninvasive quantitative cardiovascular diagnostics. Magn Reson Med 61:344–353, 2009. © 2009 Wiley‐Liss, Inc.