bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel DNA pyrosequencing unveils new zebrafish microRNAs
Authors: Soares Ana R , Pereira Patrícia M , Santos Bruno , Egas Conceição , Gomes Ana C , Arrais Joel , Oliveira José L , Moura Gabriela R , Santos Manuel AS 
Published: April 2009

Abstract

Background
MicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biology. Their small size, low abundance and high instability complicated early identification, however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes.

Results
We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish (Danio rerio). For this, a series of cDNA libraries were prepared from miRNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics. Twenty five novel miRNAs were predicted, 107 miRNA star sequences and also 41 candidate miRNA targets were identified. A miRNA expression profile built on the basis of pyrosequencing read numbers showed high expression of most miRNAs throughout zebrafish development and identified tissue specific miRNAs.

Conclusion
This study increases the number of zebrafish miRNAs from 192 to 217 and demonstrates that a single DNA mini-chip pyrosequencing run is effective in miRNA identification in zebrafish. This methodology also produced sufficient information to elucidate miRNA expression patterns during development and in differentiated organs. Moreover, some zebrafish miRNA star sequences were more abundant than their corresponding miRNAs, suggesting a functional role for the former in gene expression control in this vertebrate model organism.
Inhibitors of apoptosis proteins (IAPs) expression and their prognostic significance in hepatocellular carcinoma
Authors: Augello Claudia , Caruso Luca , Maggioni Marco , Donadon Matteo , Montorsi Marco , Santambrogio Roberto , Torzilli Guido , Vaira Valentina , Pellegrini Caterina , Roncalli Massimo , Coggi Guido , Bosari Silvano 
Published: April 2009

Abstract

Background
Similarly to other tumor types, an imbalance between unrestrained cell proliferation and impaired apoptosis appears to be a major unfavorable feature of hepatocellular carcinoma (HCC). The members of IAP family are key regulators of apoptosis, cytokinesis and signal transduction. IAP survival action is antagonized by specific binding of Smac/DIABLO and XAF1. This study aimed to investigate the gene and protein expression pattern of IAP family members and their antagonists in a series of human HCCs and to assess their clinical significance.

Methods
Relative quantification of IAPs and their antagonist genes was assessed by quantitative Real Time RT-PCR (qPCR) in 80 patients who underwent surgical resection for HCC. The expression ratios of XIAP/XAF1 and of XIAP/Smac were also evaluated. Survivin, XIAP and XAF1 protein expression were investigated by immunohistochemistry. Correlations between mRNA levels, protein expression and clinicopathological features were assessed. Follow-up data were available for 69 HCC patients. The overall survival analysis was estimated according to the Kaplan-Meier method.

Results
Survivin and Livin/ML-IAP mRNAs were significantly over-expressed in cancer tissues compared to non-neoplastic counterparts. Although Survivin immunoreactivity did not correlate with qPCR data, a significant relation was found between higher Survivin mRNA level and tumor stage, tumor grade and vascular invasion.
The mRNA ratio XIAP/XAF1 was significantly higher in HCCs than in cirrhotic tissues. Moreover, high XIAP/XAF1 ratio was an indicator of poor prognosis when overall survival was estimated and elevated XIAP immunoreactivity was significantly associated with shorter survival.

Conclusion
Our study demonstrates that alterations in the expression of IAP family members, including Survivin and Livin/ML-IAP, are frequent in HCCs. Of interest, we could determine that an imbalance in XIAP/XAF1 mRNA expression levels correlated to overall patient survival, and that high XIAP immunoreactivity was a poor prognostic factor.
Potentials of on-line repositioning based on implanted fiducial markers and electronic portal imaging in prostate cancer radiotherapy
Authors: Graf Reinhold , Wust Peter , Budach Volker , Boehmer Dirk 
Published: April 2009

Abstract

Background
To evaluate the benefit of an on-line correction protocol based on implanted markers and weekly portal imaging in external beam radiotherapy of prostate cancer. To compare the use of bony anatomy versus implanted markers for calculation of setup-error plus/minus prostate movement. To estimate the error reduction (and the corresponding margin reduction) by reducing the total error to 3 mm once a week, three times per week or every treatment day.

Methods
23 patients had three to five, 2.5 mm Ø spherical gold markers transrectally inserted into the prostate before radiotherapy. Verification and correction of treatment position by analysis of orthogonal portal images was performed on a weekly basis. We registered with respect to the bony contours (setup error) and to the marker position (prostate motion) and determined the total error. The systematic and random errors are specified. Positioning correction was applied with a threshold of 5 mm displacement.

Results
The systematic error (1 standard deviation [SD]) in left-right (LR), superior-inferior (SI) and anterior-posterior (AP) direction contributes for the setup 1.6 mm, 2.1 mm and 2.4 mm and for prostate motion 1.1 mm, 1.9 mm and 2.3 mm. The random error (1 SD) in LR, SI and AP direction amounts for the setup 2.3 mm, 2.7 mm and 2.7 mm and for motion 1.4 mm, 2.3 mm and 2.7 mm. The resulting total error suggests margins of 7.0 mm (LR), 9.5 mm (SI) and 9.5 mm (AP) between clinical target volume (CTV) and planning target volume (PTV). After correction once a week the margins were lowered to 6.7, 8.2 and 8.7 mm and furthermore down to 4.9, 5.1 and 4.8 mm after correcting every treatment day.

Conclusion
Prostate movement relative to adjacent bony anatomy is significant and contributes substantially to the target position variability. Performing on-line setup correction using implanted radioopaque markers and megavoltage radiography results in reduced treatment margins depending on the online imaging protocol (once a week or more frequently).
Comparing Adult and Pediatric Rhabdomyosarcoma in the Surveillance, Epidemiology and End Results Program, 1973 to 2005: An Analysis of 2,600 Patients
Authors: Sultan Iyad , Qaddoumi Ibrahim , Yaser Sameer , Rodriguez-Galindo Carlos , Ferrari Andrea 
Published: April 2009

Purpose To compare clinical features and outcomes of adults and children reported to have rhabdomyosarcoma. Patients and Methods We analyzed data from 1,071 adults (age > 19 years) and 1,529 children (age ≤ 19 years) reported in the public-access Surveillance, Epidemiology and End Results database as having rhabdomyosarcoma, diagnosed from 1973 to 2005. Survival estimates were determined using survival time with the end point being death from any cause. Results Adults with rhabdomyosarcoma had significantly worse outcome than children (5-year overall survival rates, 27% ± 1.4% and 61% ± 1.4%, respectively; P < .0001). Tumors in adults were more likely to be at an unfavorable site (65% v 55%; P < .0001) and to have histologies that are unusual during childhood, particularly the pleomorphic subtype (19%) and not otherwise specified (43%). Regional and distant spread was not more frequent in adults. Adults had significantly worse outcome than children with similar tumors. The most significant difference was in localized disease; 5-year survival estimates were 82% ± 2.0% for children and 47% ± 2.9% for adults (P < .0001). Multivariate analysis showed that age, histologic subtype, primary site location, stage, and local control with surgery and/or radiation were significant predictors of survival. However, alveolar subtype and unfavorable primary site lost significance when analysis was restricted to adults. Conclusion Adults reported to have rhabdomyosarcoma had worse survival than children with similar tumors. Predictors of poor outcome in children were valid in adults except for alveolar histology and unfavorable tumor site.
PTEN Expression and KRAS Mutations on Primary Tumors and Metastases in the Prediction of Benefit From Cetuximab Plus Irinotecan for Patients With Metastatic Colorectal Cancer
Authors: Loupakis Fotios , Pollina Luca , Stasi Irene , Ruzzo Annamaria , Scartozzi Mario , Santini Daniele , Masi Gianluca , Graziano Francesco , Cremolini Chiara , Rulli Eliana , Canestrari Emanuele , Funel Niccola , Schiavon Gaia , Petrini Iacopo , Magnani Mauro , Tonini Giuseppe , Campani Daniela , Floriani Irene , Cascinu Stefano , Falcone Alfredo 
Published: April 2009

Purpose PTEN, AKT, and KRAS are epidermal growth factor receptor (EGFR) downstream regulators. KRAS mutations confer resistance to cetuximab. This retrospective study investigated the role of PTEN loss, AKT phosphorylation, and KRAS mutations on the activity of cetuximab plus irinotecan in patients with metastatic colorectal cancer (mCRC). Patients and Methods A cohort of patients with irinotecan-refractory mCRC who were treated with cetuximab plus irinotecan was tested for PTEN immunoreactivity (ie, immunohistochemistry; IHC), pAKT IHC, and KRAS mutations. Analyses were performed both on primary tumors and on related metastases, and the association among IHC, mutational results, and treatment outcomes was investigated. Results One-hundred two patients were eligible. Ninety-six primary tumors, 59 metastases, and 53 paired samples were available. Forty-nine primary tumors (58% of assessable samples) had a preserved PTEN expression (PTEN-positive), whereas 35 (40% of assessable samples) were pAKT-positive. Levels of concordance between primary tumors and metastases were 60%, 68%, and 95% for PTEN, pAKT, and KRAS, respectively. PTEN status on primary tumors and pAKT status both on primary tumors and on metastases did not predict response or progression-free survival (PFS). On metastases, 12 (36%) of 33 patients with PTEN-positive tumors were responders compared with one (5%) of 22 who had PTEN-negative tumors (P = .007). The median PFS of patients with PTEN-positive metastases was 4.7 months compared with 3.3 months for those with PTEN-negative metastases (hazard ratio [HR], 0.49; P = .005). Patients with PTEN-positive metastases and KRAS wild type had longer PFS compared with other patients (5.5 months v 3.8 months; HR, 0.42; P = .001). Conclusion PTEN loss in metastases may be predictive of resistance to cetuximab plus irinotecan. The combination of PTEN IHC and KRAS mutational analyses could help to identify a subgroup of patients with mCRC who have higher chances of benefiting from EGFR inhibition.
Margin Clearance and Outcome in Resected Pancreatic Cancer
Authors: Chang David K. , Johns Amber L. , Merrett Neil D. , Gill Anthony J. , Colvin Emily K. , Scarlett Christopher J. , Nguyen Nam Q. , Leong Rupert W.L. , Cosman Peter H. , Kelly Mark I. , Sutherland Robert L. , Henshall Susan M. , Kench James G. , Biankin Andrew V. 
Published: April 2009

PurposeCurrent adjuvant therapies for pancreatic cancer (PC) are inconsistently used and only modestly effective. Because a high proportion of patients who undergo resection for PC likely harbor occult metastatic disease, any adjuvant trials assessing therapies such as radiotherapy directed at locoregional disease are significantly underpowered. Stratification based on the probability (and volume) of residual locoregional disease could play an important role in the design of future clinical trials assessing adjuvant radiotherapy.Patients and MethodsWe assessed the relationships between margin involvement, the proximity to operative resection margins and outcome in a cohort of 365 patients who underwent operative resection for PC.ResultsMicroscopic involvement of a resection margin by tumor was associated with a poor prognosis. Stratifying the minimum clearance of resection margins by 0.5-mm increments demonstrated that although median survival was no different to clear margins based on these definitions, it was not until the resection margin was clear by more than 1.5 mm that optimal long-term survival was achieved.ConclusionThese data demonstrate that a margin clearance of more than 1.5 mm is important for long-term survival in a subgroup of patients. More aggressive therapeutic approaches that target locoregional disease such as radiotherapy may be beneficial in patients with close surgical margins. Stratification of patients for entry onto future clinical trials based on this criterion may identify those patients who benefit from adjuvant radiotherapy.
Abū Ḳurra über die Verehrung christlicher Bilder
Authors: Pochoshajew Igor 
Published: April 2009

Zusammenfassung
Unter Berücksichtigung der erzielten Einsichten ist der geschichtliche Entstehungszusammenhang der Schrift Über die Verehrung christlicher Bilder wie folgt zu bestimmen: Mit der Verdrängung aus dem öffentlichen Raum verlor das Christentum immer mehr an sozialer Plausibilität. Trotz der politischen Einbußen verfügten die Christen über eine Fülle der eigenen kulturellen Überlegenheit. Die fehlende Einheitlichkeit bezüglich der theologischen Berechtigung der Bilderverehrung im christlichen Lager gefährdete ein zentrales Element der eigenen kulturellen Tradition. Da die muslimische und jüdische Bilderkritik zum Gewicht der bilderfeindlichen Position innerhalb des Christentums indirekt beitrug, war eine theologische Auseinandersetzung mit ihren Argumenten dringend erforderlich. Es war insofern wichtig, den Standpunkt der Muslime fundiert zu entkräften, als der Islam mit der fortschreitenden Festigung seiner politischen Herrschaft immer überzeugender wirkte. Das christliche Bild bekam in diesem Zusammenhang die Bedeutung eines Symbols der Plausibilität des Christentums, welches es zu erhalten galt. Die Bilderabhandlung Abū Ḳurras ist ein Zeugnis des Überlebenskampfes der Christen in der Situation einer fortschreitenden inneren Expansion des Islams. Der Text belegt gleichzeitig, dass dieser Kampf von den Muslimen mit dem Mittel der strukturell-politischen Maßnahmen und des theologischen Arguments geführt wurde.
Enhanced Hardenability through Application of Magnetic Fields
Authors: Machado Izabel Fernanda 
Published: April 2009

Abstract
Even with the great improvements in new materials, the substitution of steels in most applications is not yet economically justifiable. Steels are the most important alloys utilized as structural materials and will certainly continue to be so in the next decades. The effects of the conventional heat treatments in changing the mechanical properties of steels are well known by now. However, the effects of magnetic fields on phase transformations have recently been considered and new perspectives of study and of applications are now being opened for steels. Magnetic fields lower the Gibbs free energy, and the transformation temperature of steels increases for an applied magnetic field. As a result, different properties and microstructures could be achieved after heat treatments due to magnetic field effect. The main objective of this work is to show a process to enhance the hardenability of steels through modifications in heat treatment. The chemical composition of the material studied is similar to AISI 52100 steel. The procedure consists of applying a magnetic field in the sample throughout or in different steps of the heat treatment. All the samples were heat treated at the same temperature and cooled at the same cooling rate. The results of the magnetic field applied in steel samples were compared to conventional heat treatments. A significant improvement in microhardness of the samples was measured after applying a magnetic field. A considerable rise in the hardenability and a modification in the Fe-C equilibrium diagram were also verified, as shown in the literature.
The Influence of Tank Mix Additives While Making Low Volume Aerial Fungicide Applications
Authors: Wolf Robert , Gardisser Dennis , Bretthaurer Scott , Mauromoustakos Andy , Baxter Lynn 
Published: April 2009

Abstract
Multiple experiments using low volume aerial applications with nine different adjuvants in combination with fungicide were conducted to compare coverage, droplet spectra, yield, and disease control. Four locations were scattered over three states: Arkansas, Kansas, and Illinois. Four aircraft with different nozzle and boom setups were used to complete the studies. Volume median size (DV0.5) ranged from 232 μm to 364 μm. Kromekote® papers used as collectors were placed in the center 9 m of each aerial swath/treatment (20 m) at three different plant heights: top corn leaf, ear leaf, and the leaf three collars below ear leaf. In each treatment, sampling consisted of 30 papers; 10 corn plants at the three heights, with all papers at 30 cm from the main stalk. DropletScan™, utilizing a high resolution color scanner to digitize the images on the Kromekote® papers, was used to analyze each paper. Means for percent area coverage and DV0.5 were used to separate differences in treatments. Relative span was calculated as an indicator of the range in the droplet spectrum. Yields were taken from the center of each treatment. Three to five replications per treatment were completed and a SAS GLIMMIX analysis was performed. Significant differences were measured among adjuvant treatments for both droplet spectra and deposition/coverage. Mixed results are reported across all treatments and locations. A mixture of water, Headline, and Crop Oil Concentrate (Treatment 2) was consistently measured with the lowest amount of coverage, and in two of four locations had the largest DV0.5. Overall, droplet spectra were impacted by the addition of adjuvants to the tank mix. The largest droplets were not associated with the best coverage, and the trend was for the lowest coverage to be associated with the smallest droplets. Treatment 5 (NIS+Interlock) had the smallest DV0.5 in three of the test locations. A limited number of significant yield differences were found. This effect could be due to low disease pressure.
X-ray crystal structure and conformation of N-(tert-butyloxycarbonyl)-L-methionyl-(1-aminocyclopent-3-ene-1-carbonyl)-L-phenylalanine methyl ester (Boc0-Met1-Cpg2-Phe3-OMe)
Authors: Mura Pasquale , Camalli Mercedes , Campi Gaetano , Lucente Gino , Giordano Cesare , Mollica Adriano , Sansone Anna , Torino Domenica 
Published: April 2009

Abstract
Molecular structure and conformation in the crystal of N-Boc-Met-Cpg-Phe-OMe, a conformationally restricted tripeptide derivative, structurally related to the chemotactic antagonist agent N-Boc-Met-Leu-Phe-OMe is reported. In the title compound the native central Leu residue has been replaced with the unusual cyclic and achiral quaternary amino acid residue of the 1-aminocyclopent-3-ene-1-carboxylic acid (Cpg). The peptide backbone adopts a type II β-turn (C10) conformation at the –Met-Cpg- sequence with a distance, between the terminal pseudo-ring atoms O6 · · · C3, of 5.49(1)Å. The tripeptide crystallizes in the monoclinic crystal system, space group P21, cell parameter: a = 5.867(7) Å, b = 23.54(2) Å, c = 10.34(1) Å, β = 99.74(5)°, V = 1407(2) Å3; empirical formula C26H37N3O6S; needle crystals were obtained by slow evaporation of an ethyl acetate solution, after 4 days, at room temperature. The low diffraction power of the crystals, it was impossible to obtain crystal structure from normal diffractometer data, suggested to utilize X-ray synchrotron radiation.
Phase characterization of Sm–Lu mixed oxide powders prepared by sintering and radio frequency plasma spraying
Authors: Hübner Rene , Sun Xiaolong , Tok Alfred I. Y. , Boey Freddy Y. C. 
Published: April 2009

Abstract
Radio frequency plasma spraying is a promising technique to prepare rare earth oxide nano-particles. Applying this method after sintering of pellets at T = 1600 °C and subsequent grinding, Sm2O3—Lu2O3 mixed oxide powders of various compositions were synthesized. Analyzing the ground powders, the phase field can be divided into three regions: (1) Sm-rich monoclinic B-type solid solutions, (2) Lu-rich cubic C-type solid solutions, and (3) a diphasic region for Lu contents 0.33 ≤ x
Lu ≤ 0.54. In the single phase areas, the volume for one formula unit of the rare earth sesquioxide is found to depend linearly on the cubed average cation radius. Plasma spraying of the Lu-rich powders leads to a second monoclinic B-type phase. Excluding the solubility gap, the monoclinic lattice parameters show quadratic dependencies on the Lu content and the molecular volume is a function of third order on the cation radius.
Symmetry relationships of sodalite (SOD) – type crystal structures
Authors: Fischer Reinhard X. , Baur W.H. 
Published: April 2009

AbstractThe mineral sodalite with the ideal composition Na8[Al6Si6O24]Cl2is the prototype for numerous related crystal structures based on the same topology of the underlying net of strong bonds. This net has been assigned the code SOD by the Structure Commission of the International Zeolite Association. Minerals and synthetic compounds with a SOD-type framework represent the most comprehensive family of zeolite-type compounds with the highest number of published crystal structures. Among these are aluminosilicates (e.g., sodalite, haüyne, helvine, lazurite, nosean, tsaregorodtsevite), beryllosilicates (e.g., danalite, genthelvite, tugtupite), chlorides, sulfides (e.g., tetrahedrite, binnite, freibergite, galkhaite, goldfieldite, tennantite), borates (rhodizite), synthetic phosphates, aluminates, phosphides, nitrides and clathrate hydrates which have been shown by crystal structure analyses to adopt the SOD-type framework. More than 900 SOD-type crystal structures, which represent over 18% of the total number of published zeolite structures, are known. The complete symmetry relationships of SOD-type crystal structures comprising 27 space groups are listed in a Bärnighausen-tree together with the type and index of symmetry reduction. No other zeolite type displays such a rich harvest of symmetry as the sodalite-type. Seven additional space groups reported for SOD-types have not been considered here because they were not well supported by experimental evidence. Of the 26 low-symmetry derivatives six are due to an ordering of tetrahedrally coordinated framework cations. In two cases the lowering of symmetry is caused by some of the framework cations assuming 5- or 6-coordinations instead of the usual 4-coordination. This means that in 18 cases the lower space group symmetries are achieved by the influence of pore-filling matter.