bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do microsatellite instability profiles really differ between colorectal and endometrial tumors?
Authors: Ferreira Ana M. , Westers Helga , Wu Ying , Niessen Renée C. , Olderode‐Berends Maran , van der Sluis Tineke , van der Zee Ate G. , Hollema Harry , Kleibeuker Jan H. , Sijmons Rolf H. , Hofstra Robert M. W. 
Published: April 2009

AbstractMicrosatellite instability (MSI) occurs in more than 90% of the tumors of Lynch syndrome patients, and in 15–25% of sporadic colorectal (CRC) and endometrial carcinomas (EC). Previous studies comparing EC and CRC using BAT markers showed that the frequency of unstable markers is lower in EC, and that the size of the mutations is smaller in EC. In the present study, we analyzed the type (insertions/deletions), size, and frequency of mutations occurring at three BAT and three dinucleotide markers in CRC and EC, to elucidate whether it is possible to establish different MSI profiles in carcinomas of different tissue origin. We show that mononucleotide markers nearly always become shorter whereas dinucleotide markers can become shorter or longer, in both CRC and EC. We therefore conclude that the type of mutation is a marker‐dependent feature rather than tissue‐dependent. However, we observed that the size of the deletions/insertions differs between CRC and EC, with EC having shorter alterations. The frequency of mono‐ and dinucleotide instability found in both tissues is comparable, with mononucleotide and dinucleotide markers being affected at similar rates. We conclude that it is not possible to define clearly different MSI profiles that could distinguish MSI‐high in CRC and EC. We propose that the differences observed might indicate different durations of tumor development and/or differences in tissue turnover between colorectal and endometrial epithelium, rather than reflecting truly different MSI profiles. We therefore suggest that the same MSI tests can be used for both tumor types. © 2009 Wiley‐Liss, Inc.
Spontaneous regression of Merkel cell carcinoma of the nose
Authors: Karkos Petros D. , Sastry Anand , Hampal Sucha , Al‐Jafari Mohammad 
Published: April 2009

AbstractBackground.Merkel Cell Carcinoma (MCC) is a rare neurendocrine tumor of cutaneous origin.Methods and Results.A 79‐year‐old woman was seen with a neck lump and a lesion in the left nasal vestibule. Biopsy of the lesion revealed a primary neurendocrine MCC of the skin of the nasal vestibule with metastases to the cervical lymph nodes. The patient decided against any further active treatment. Follow‐up of patient for 30 months showed spontaneous regression of the lesions without any active treatment.Conclusions.Although spontaneous resolution of MCC has been described for other head neck sites, there has not been any published case of nasal MCC regression. We present this rare case of nasal MCC with neck metastases and its regression. © 2009 Wiley Periodicals, Inc. Head Neck, 2010
Significance of stromal desmoplasia and myofibroblast appearance at the invasive front in squamous cell carcinoma of the oral cavity
Authors: Kawashiri Shuichi , Tanaka Akira , Noguchi Natsuyo , Hase Takashi , Nakaya Hiromitsu , Ohara Teruhisa , Kato Koroku , Yamamoto Etsuhide 
Published: April 2009

AbstractBackground.Tumor invasion involves complex interactions between tumor and stromal cells. We examined the extent of connective tissue in the tumor stroma and whether myofibroblasts play a role in assisting cancer invasion and metastasis.Methods.Biopsy materials from 84 patients with oral squamous cell carcinoma (SCC) were used. We compared data from intrastromal collagen fibers using Azan staining, immunohistochemical identification of myofibroblasts by cytoskeletal markers, α‐smooth muscle actin, vimentin, desmin, and clinicopathological parameters. Clinical outcome was compared by 5‐year survival rate.Results.There were high levels of stromal collagen fibers in invasive tumors. Myofibroblast appearance increased with increasing tumor invasiveness. Lymph node metastasis occurred more frequently in the myofibroblast‐positive group, and the survival rate was significantly poorer in this group.Conclusions.Fibrous stroma in SCC appeared to have a desmoplastic response. However, an independent invasive mechanism may regulate the stroma, with tumor desmoplasia occurring in highly developed, invasive tumors. © 2009 Wiley Periodicals, Inc. Head Neck, 2009
Early oral feeding after salvage laryngectomy
Authors: Eustaquio Marcia , Medina Jesus E. , Krempl Greg A. , Hales Nathan 
Published: April 2009

AbstractBackground.Our aim was to determine the feasibility and safety of initiating early oral feeding in patients who underwent salvage laryngectomy on postoperative day 5 and to review the rate of pharyngocutaneous fistula formation.Methods.A retrospective review of 29 patients who underwent salvage laryngectomy was completed. Patients included in the study had radiation therapy ± chemotherapy for laryngeal squamous cell carcinoma with subsequent total laryngectomy. Patients were excluded from analysis if they were reliant on a gastrostomy tube preoperatively, had a concurrent complete glossectomy, or developed a fistula before beginning oral feedings. Early oral feeding was initiated on postoperative day 5.Results.Twenty patients met complete inclusion criteria. Pharyngocutaneous fistula occurred in 10% (2/20) of the patients. Patients without postoperative complications on an average remained in the hospital for 7 days.Conclusions.The risk of fistula formation is not increased and the duration of hospital stay may be shortened in patients who were given early postoperative feeds. © 2009 Wiley Periodicals, Inc. Head Neck, 2009
Trigeminal nerve palsy in nasopharyngeal carcinoma: Correlation between clinical findings and magnetic resonance imaging
Authors: Cui Chunyan , Liu Lizhi , Ma Jun , Liang Shaobo , Tian Li , Tang Linglong , Li Li 
Published: April 2009

AbstractBackground.Our aim was to document the relationship between clinical and MRI evidence of trigeminal nerve involvement.Methods.The MRI and medical records of 924 consecutive patients with newly diagnosed nasopharyngeal carcinoma (NPC) were reviewed retrospectively.Results.A total of 92 divisions of palsied trigeminal nerves were found clinically in 46 patients (5.0%). The involved trigeminal nerve was ophthalmic nerve (V1; n = 21), the maxillary division (V2; n = 41), and the mandibular division (V3; n = 30). Of the 316 patients with MRI‐demonstrated trigeminal nerve involvements, the symptoms were lacking in 270 patients (85.4%). Of the 92 clinical palsied trigeminal nerve divisions, 91 nerves (98.9%) showed MRI evidence of 1 or more trigeminal nerve involvements. Of the 91 palsied trigeminal nerve with MRI evidence, 85 divisions (93.4%) were found with intracranial or orbital segment involvement, 6 (6.6%) divisions were found only basicranial evidence, and 83 (91.2%) divisions were found with cavernous sinus invasion.Conclusion.The incidence of MRI‐evidenced trigeminal nerve involvement is high and often asymptomatic in NPC. Almost all patients with clinical trigeminal nerve palsies had MRI evidence of trigeminal nerve involvement in intracranial or orbital segment, especially in cavernous sinus. © 2009 Wiley Periodicals, Inc. Head Neck, 2009
Streamflow response to Pinus plantation harvesting: Canobolas State forest, southeastern Australia
Authors: Webb Ashley A. 
Published: April 2009

AbstractStreamflows were measured in two Pinus radiata plantation catchments and one native eucalypt forest catchment in Canobolas State forest from 1999 to 2007. In 2002/2003, clearfall harvesting of 43·2 and 40·3% of two plantation catchments occurred, respectively. Water yields increased by 54 mm (52%), 71 mm (35%) and 50 mm (19%) in the first three years post‐harvest in treated catchment A and by 103 mm (118%), 157 mm (82%) and 119 mm (48%) in treated catchment B relative to the native forest control catchment. In the fourth post‐harvest water year annual rainfall was only 488 mm, which resulted in negligible run‐off in all catchments, regardless of forest cover. In both plantation catchments, monthly streamflows increased significantly (p = 0·01, p < 0·001) due to a significant increase in baseflows (p < 0·001) after harvesting. Monthly stormflows were not significantly affected by harvesting. Flow duration curve analyses indicated a variable response between the two plantation catchments. Treated catchment A was converted from an ephemeral stream flowing 42% of the time pre‐harvest to a temporary stream flowing 82% of the time post‐harvest. These changes occurred throughout all seasons of the year but were most pronounced during summer and autumn when baseflows were maintained post‐harvest but were not observed under native forest or mature pine plantations. By contrast, flow duration increased in treated catchment B from 12% of the time pre‐harvest to 38% of the time post‐harvest with the greatest changes measured during the winter and spring months when streamflow would normally occur under native forest conditions. These observations have important implications for the development of models of plantation water use to be utilized in water resource planning in Australia. Copyright © 2009 John Wiley & Sons, Ltd.
Low and high flow analyses and wavelet application for characterization of the Blue Nile River system
Authors: Melesse Assefa , Abtew Wossenu , Dessalegne Tibebe , Wang Xixi 
Published: April 2009

AbstractThe low and high flow characteristic of the Blue Nile River (BNR) basin is presented. The study discusses low and high flow, flow duration curve (FDC) and trend analysis of the BNR and its major tributaries. Different probability density functions were fitted to better describe the low and high flows of the BNR and major tributaries in the basin. Wavelet analysis was used in understanding the variance and frequency‐time localization and detection of dominant oscillations in rainfall and flow. FDCs were developed, and low flow (below 50% exceedance) and high flow (over 75% exceedance) of the curves were analysed and compared. The Gravity Recovery and Climate Experiment (GRACE) satellite‐based maps of monthly changes in gravity converted to water equivalents from 2003 to 2006 for February, May and September showed an increase in the moisture influx in the BNR basin for the month of September, and loss of moisture in February and May. It was also shown that 2004 and 2005 were drier with less moisture influx compared to 2003 and 2006. On the basis of the Kolmogorov‐Smirnov, Anderson‐Darling and Chi‐square tests, Gen. Pareto, Frechet 3P, Log‐normal, Log‐logistics, Fatigue Life and Phased Bi‐Weibull distributions best describe the low and high flows within the BNR basin. This will be beneficial in developing flow hydrographs for similar ungauged watersheds within the BNR basin. The below 50% and above 75% exceedance on the FDC for five major rivers in addition to the BNR showed different characteristics depending on size, land cover, topography and other factors. The low flow frequency analysis of the BNR at Bahir Dar showed 0·55 m3/s as the monthly low flow with recurrence interval of 10 years. The wavelet analysis of the rainfall (at Bahir Dar and basin‐wide) and flows at three selected stations shows inter‐ and intra‐annual variability of rainfall and flows at various scales. Copyright © 2009 John Wiley & Sons, Ltd.
Forecasting US output growth using leading indicators: an appraisal using MIDAS models
Authors: Clements Michael P. , Galvão Ana Beatriz 
Published: April 2009

AbstractWe evaluate the predictive power of leading indicators for output growth at horizons up to 1 year. We use the MIDAS regression approach as this allows us to combine multiple individual leading indicators in a parsimonious way and to directly exploit the information content of the monthly series to predict quarterly output growth. When we use real‐time vintage data, the indicators are found to have significant predictive ability, and this is further enhanced by the use of monthly data on the quarter at the time the forecast is made. Copyright © 2009 John Wiley & Sons, Ltd.
Raman spectroscopy of DNA packaging in individual human sperm cells distinguishes normal from abnormal cells
Authors: Huser Thomas , Orme Christine A. , Hollars Christopher W. , Corzett Michele H. , Balhorn Rod 
Published: April 2009

AbstractHealthy human males produce sperm cells of which about 25–40% have abnormal head shapes. Increases in the percentage of sperm exhibiting aberrant sperm head morphologies have been correlated with male infertility, and biochemical studies of pooled sperm have suggested that sperm with abnormal shape may contain DNA that has not been properly repackaged by protamine during spermatid development. We have used micro‐Raman spectroscopy to obtain Raman spectra from individual human sperm cells and examined how differences in the Raman spectra of sperm chromatin correlate with cell shape. We show that Raman spectra of individual sperm cells contain vibrational marker modes that can be used to assess the efficiency of DNA‐packaging for each cell. Raman spectra obtained from sperm cells with normal shape provide evidence that DNA in these sperm is very efficiently packaged. We find, however, that the relative protein content per cell and DNA packaging efficiencies are distributed over a relatively wide range for sperm cells with both normal and abnormal shape. These findings indicate that single cell Raman spectroscopy should be a valuable tool in assessing the quality of sperm cells for in‐vitro fertilization. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
New therapeutic targets for the treatment of high‐risk neuroblastoma
Authors: Wagner Lars M. , Danks Mary K. 
Published: April 2009

AbstractHigh‐risk neuroblastoma remains a major problem in pediatric oncology, accounting for 15% of childhood cancer deaths. Although incremental improvements in outcome have been achieved with the intensification of conventional chemotherapy agents and the addition of 13‐cis‐retinoic acid, only one‐third of children with high‐risk disease are expected to be long‐term survivors when treated with current regimens. In addition, the cost of cure can be quite high, as surviving children remain at risk for additional health problems related to long‐term toxicities of treatment. Further advances in therapy will require the targeting of tumor cells in a more selective and efficient way so that survival can be improved without substantially increasing toxicity. In this review we summarize ongoing clinical trials and highlight new developments in our understanding of the molecular biology of neuroblastoma, emphasizing potential targets or pathways that may be exploitable therapeutically. J. Cell. Biochem. 107: 46–57, 2009. © 2009 Wiley‐Liss, Inc.
Insulin receptor kinase‐independent signaling via tyrosine phosphorylation of phosphatase PHLPP1
Authors: Zhang Manchao , Riedel Heimo 
Published: April 2009

AbstractMost insulin responses correlate well with insulin receptor (IR) Tyr kinase activation; however, critical exceptions to this concept have been presented. Specific IR mutants and stimulatory IR antibodies demonstrate a lack of correlation between IR kinase activity and specific insulin responses in numerous independent studies. IR conformation changes in response to insulin observed with various IR antibodies define an IR kinase‐independent signal that alters the C‐terminus. IR‐related receptors in lower eukaryotes that lack a Tyr kinase point to an alternative mechanism of IR signaling earlier in evolution. However, the implied IR kinase‐independent signaling mechanism remained obscure at the molecular level. Here we begin to define the molecular basis of an IR‐dependent but IR kinase‐independent insulin signal that is equally transmitted by a kinase‐inactive mutant IR. This insulin signal results in Tyr phosphorylation and catalytic activation of phosphatase PHLPP1 via a PI 3‐kinase‐independent, wortmannin‐insensitive signaling pathway. Dimerized SH2B1/PSM is a critical activator of the IR kinase and the resulting established insulin signal. In contrast it is an inhibitor of the IR kinase‐independent insulin signal and disruption of SH2B1/PSM dimer binding to IR potentiates this signal. Dephosphorylation of Akt2 by PHLPP1 provides an alternative, SH2B1/PSM‐regulated insulin‐signaling pathway from IR to Akt2 of opposite polarity and distinct from the established PI 3‐kinase‐dependent signaling pathway via IRS proteins. In combination, both pathways should allow the opposing regulation of Akt2 activity at two phosphorylation sites to specifically define the insulin signal in the background of interfering Akt‐regulating signals, such as those controlling cell proliferation and survival. J. Cell. Biochem. 107: 65–75, 2009. © 2009 Wiley‐Liss, Inc.
Down‐regulating cold shock protein genes impairs cancer cell survival and enhances chemosensitivity
Authors: Zeng Yu , Kulkarni Prakash , Inoue Takahiro , Getzenberg Robert H. 
Published: April 2009

AbstractThe microenvironment of the cancer cell is pivotal to its phenotypic regulation. One of the central components of the microenvironment is temperature. An elevation in environmental temperature has been shown to increase the cancer cell's susceptibility to chemo‐ and radiation therapy. The goal of the studies described here was to identify some of the pathways that are modified by a mild increase in temperature in cancer cells. Using prostate cancer cells as a model system we found that in addition to the well described and anticipated up‐regulation of the heat shock family of proteins, there is a significant down‐regulation of certain members of the “cold shock” family of proteins such as, RNA binding motif protein 3 (RBM3) and cold inducible RNA binding protein (CIRBP). siRNA‐mediated down‐regulation of the cold shock protein (CSP) encoding mRNAs dramatically attenuates cell survival in the absence of any heat application. Furthermore, we also demonstrate that knocking down the CSPs can enhance the therapeutic response of prostate cancer cells to chemotherapy. Our findings suggest that down‐regulating CSPs in cancer cells may “mimic” the stress response the cells experience when exposed to heat treatment rendering them more susceptible to therapy. Thus, the pharmacological modulation of RBM3 and CIRBP may represent novel therapeutic approaches for prostate cancer. J. Cell. Biochem. 107: 179–188, 2009. © 2009 Wiley‐Liss, Inc.
First‐principles study of molecular hydrogen dissociation on doped Al12X (X = B, Al, C, Si, P, Mg, and Ca) clusters
Authors: Wang Lu , Zhao Jijun , Zhou Zhen , Zhang S. B. , Chen Zhongfang 
Published: April 2009

AbstractInspired by the concept of superatom via substitutionally doping an Al13 magic cluster, we investigated the H2 molecule dissociation on the doped icosahedral Al12X (X = B, Al, C, Si, P, Mg, and Ca) clusters by means of density functional theory. The computed reaction energies and activation barriers show that the concept of superatom is still valid for the catalysis behavior of doped metal clusters. The hydrogen dissociation behavior on metal clusters characterized by the activation barrier and reaction energy can be tuned by controllable doping. Thus, doped Al12X clusters might serve as highly efficient and low‐cost catalysts for hydrogen dissociation. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Unorthodox uses of Bennett's acceptance ratio method
Authors: König Gerhard , Bruckner Stefan , Boresch Stefan 
Published: April 2009

AbstractWe illustrate the application of Bennett's acceptance ratio method (BAR) to problems in which standard methods to compute free energy differences (thermodynamic integration, exponential formula) are not practical. Our starting point is the observation that BAR can often compute the free energy difference between two states without the need for intermediate states usually employed (and necessary) in alchemical free energy simulations. This is demonstrated first for the free energy difference between ethane and methanol in aqueous solution. We then show how BAR can be used to compute directly rather unusual free energy differences, such as the free energy difference resulting from changing the treatment of electrostatic interactions, from switching the force field, or from using an implicit solvent model. Calculations of this kind should prove useful for force field development and the validation of implicit solvent methods. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
QSPR modeling of enthalpies of formation for organometallic compounds by SMART‐based optimal descriptors
Authors: Toropov Andrey A. , Toropova Alla P. , Benfenati Emilio , Manganaro Alberto 
Published: April 2009

AbstractA quantitative structure‐property relationship (QSPR) model for the prediction of gas‐phase enthalpy of formation has been developed, using as chemical information descriptors based on the SMART notation, which is an alternative to SMILES. The model is one‐variable equation. The SMART‐based descriptors are calculated with correlation weights of SMART attributes which are obtained by the Monte Carlo method. The model addressed organometallic compounds. Statistical characteristics of the model are the following: n = 104, r2 = 0.9944, s = 19.6 (kJ/mol), F = 18,269 (training set) and n = 28, r2 = 0.9909, s = 28.8 (kJ/mol), F = 2832 (test set). © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Linear response theory in dihedral angle space for protein structural change upon ligand binding
Authors: Omori Satoshi , Fuchigami Sotaro , Ikeguchi Mitsunori , Kidera Akinori 
Published: April 2009

AbstractCoupling between proteins motion and ligand binding can be well explained by the linear response theory (Ikeguchi, M.; Ueno, J.; Sato, M.; Kidera, A. Phys Rev Lett 2005, 94, 078102.), in which the structural change is treated as a response to ligand binding. The prediction accuracy of structural change upon ligand binding has been improved by replacing the variables in the linear response theory from Cartesian coordinates to dihedral angles. The dihedral angle theory can more accurately describe the rotational motions of protein domains compared with the Cartesian theory, which tends to shift the coordinate to the tangential direction of the domain rotation. In this study, the ligand‐bound form of Ferric‐binding protein was predicted from its ligand‐free form using the dihedral linear response theory. When the variance–covariance matrix, the key component in the linear response theory, was derived by linear conversion from Cartesian coordinates to dihedral angles, the dihedral linear response theory gave an improvement in the prediction. Therefore, the description of the rotational motion by dihedral angles is crucial for accurate prediction of protein structural change. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
Extension of QM/MM docking and its applications to metalloproteins
Authors: Cho Art E. , Rinaldo David 
Published: April 2009

AbstractTo overcome the limitation of conventional docking methods which assume fixed charge model from force field parameters, combined quantum mechanics/molecular mechanics (QM/MM) method has been applied to docking as a variable charge model and shown to exhibit improvement on the docking accuracy over fixed charge based methods. However, it has also been shown that there are a number of examples for which adoption of variable‐charge model fails to reproduce the native binding modes. In particular, for metalloproteins, previously implemented method of QM/MM docking failed most often. This class of proteins has highly polarized binding sites at which high‐coordinate‐numbered metal ions reside. We extend the QM/MM docking method so that protein atoms surrounding the binding site along with metal ions are included as quantum region, as opposed to only ligand atoms. This extension facilitates the required scaling of partial charges on metal ions leading to prediction of correct binding modes in metalloproteins. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009