bluuebunny/crossref_metadata_2025_split huggingface dataset:
The superiority of the time-to-event continual reassessment method to the rolling six design in pediatric oncology Phase I trials
Authors: Zhao Lili , Lee Julia , Mody Rajen , Braun Thomas M 
Published: May 2011

Background The rolling six design (RSD) is currently being used by the Children’s Oncology Group (COG) as their standard design for Phase I trials. Because the COG has large multi-center trials with fast accrual, the motivation for adopting the RSD is to hasten accrual and shorten the duration of their trials. However, trial suspension due to completion of follow-up still cannot be entirely avoided by the RSD. Therefore, a design that allows continuous enrollment of patients throughout the entire trial is needed. Purpose To demonstrate the superior performance of the Time-to-Event Continual Reassessment Method (TITE-CRM) with continuous patient recruitment relative to the RSD, in terms of identifying the maximum tolerated dose (MTD) and reducing exposure of patients to toxic doses. Methods Using scenarios that were based on an actual pediatric Phase I trial at the University of Michigan, Monte Carlo simulations were used to investigate the operational characteristics of RSD and TITE-CRM. Results The TITE-CRM treated all available patients, identified the MTD more accurately than the RSD and did not increase the probability of exposing patients to toxic doses. Limitations Both the TITE-CRM and RSD assume that the probability of dose limiting toxicity increases with higher dose level. Conclusions The TITE-CRM, which allows for continual enrollment of patients, provides a safe design for pediatric oncology Phase I trials with better accuracy than the RSD.
MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries
Authors: Chen Wen Han , Sun Ping Ping , Lu Yang , Guo William W , Huang Yan Xin , Ma Zhi Qiang 
Published: May 2011

Abstract

Background
A B-cell epitope is a group of residues on the surface of an antigen which stimulates humoral responses. Locating these epitopes on antigens is important for the purpose of effective vaccine design. In recent years, mapping affinity-selected peptides screened from a random phage display library to the native epitope has become popular in epitope prediction. These peptides, also known as mimotopes, share the similar structure and function with the corresponding native epitopes. Great effort has been made in using this similarity between such mimotopes and native epitopes in prediction, which has resulted in better outcomes than statistics-based methods can. However, it cannot maintain a high degree of satisfaction in various circumstances.

Results
In this study, we propose a new method that maps a group of mimotopes back to a source antigen so as to locate the interacting epitope on the antigen. The core of this method is a searching algorithm that is incorporated with both dynamic programming (DP) and branch and bound (BB) optimization and operated on a series of overlapping patches on the surface of a protein. These patches are then transformed to a number of graphs using an adaptable distance threshold (ADT) regulated by an appropriate compactness factor (CF), a novel parameter proposed in this study. Compared with both Pep-3D-Search and PepSurf, two leading graph-based search tools, on average from the results of 18 test cases, MimoPro, the Web-based implementation of our proposed method, performed better in sensitivity, precision, and Matthews correlation coefficient (MCC) than both did in epitope prediction. In addition, MimoPro is significantly faster than both Pep-3D-Search and PepSurf in processing.

Conclusions
Our search algorithm designed for processing well constructed graphs using an ADT regulated by CF is more sensitive and significantly faster than other graph-based approaches in epitope prediction. MimoPro is a viable alternative to both PepSurf and Pep-3D-Search for epitope prediction in the same kind, and freely accessible through the MimoPro server located at http://informatics.nenu.edu.cn/MimoPro.
Adaptation to HIF-1 deficiency by upregulation of the AMP/ATP ratio and phosphofructokinase activation in hepatomas
Authors: Golinska Monika , Troy Helen , Chung Yuen-Li , McSheehy Paul M , Mayr Manuel , Yin Xiaoke , Ly Lucy , Williams Kaye J , Airley Rachel E , Harris Adrian L , Latigo John , Perumal Meg , Aboagye Eric O , Perrett David , Stubbs Marion , Griffiths John R 
Published: May 2011

Abstract

Background
HIF-1 deficiency has marked effects on tumour glycolysis and growth. We therefore investigated the consequences of HIF-1 deficiency in mice, using the well established Hepa-1 wild-type (WT) and HIF-1β-deficient (c4) model. These mechanisms could be clinically relevant, since HIF-1 is now a therapeutic target.

Methods
Hepa-1 WT and c4 tumours grown in vivo were analysed by 18FDG-PET and 19FDG Magnetic Resonance Spectroscopy for glucose uptake; by HPLC for adenine nucleotides; by immunohistochemistry for GLUTs; by immunoblotting and by DIGE followed by tandem mass spectrometry for protein expression; and by classical enzymatic methods for enzyme activity.

Results
HIF-1β deficient Hepa-1 c4 tumours grew significantly more slowly than WT tumours, and (as expected) showed significantly lower expression of many glycolytic enzymes. However, HIF-1β deficiency caused no significant change in the rate of glucose uptake in c4 tumours compared to WT when assessed in vivo by measuring fluoro-deoxyglucose (FDG) uptake. Immunohistochemistry demonstrated less GLUT-1 in c4 tumours, whereas GLUT-2 (liver type) was similar to WT. Factors that might upregulate glucose uptake independently of HIF-1 (phospho-Akt, c-Myc) were shown to have either lower or similar expression in c4 compared to WT tumours. However the AMP/ATP ratio was 4.5 fold higher (p < 0.01) in c4 tumours, and phosphofructokinase-1 (PFK-1) activity, measured at prevailing cellular ATP and AMP concentrations, was up to two-fold higher in homogenates of the deficient c4 cells and tumours compared to WT (p < 0.001), suggesting that allosteric PFK activation could explain their normal level of glycolysis. Phospho AMP-Kinase was also higher in the c4 tumours.

Conclusions
Despite their defective HIF-1 and consequent down-regulation of glycolytic enzyme expression, Hepa-1 c4 tumours maintain glucose uptake and glycolysis because the resulting low [ATP] high [AMP] allosterically activate PFK-1. This mechanism of resistance would keep glycolysis functioning and also result in activation of AMP-Kinase and growth inhibition; it may have major implications for the therapeutic activity of HIF inhibitors in vivo. Interestingly, this control mechanism does not involve transcriptional control or proteomics, but rather the classical activation and inhibition mechanisms of glycolytic enzymes.
Back and neck pain are related to mental health problems in adolescence
Authors: Rees Clare S , Smith Anne J , O'Sullivan Peter B , Kendall Garth E , Straker Leon M 
Published: May 2011

Abstract

Background
There is a high prevalence of mental health problems amongst adolescents. In addition there is a high prevalence of spinal pain in this population. Evidence suggests that these conditions are related. This study sought to extend earlier findings by examining the relationship between mental health problems as measured by the Child Behaviour Check List (CBCL) and the experience of back and neck pain in adolescents.

Methods
One thousand five hundred and eighty participants (mean age 14.1 years) from the Western Australian Pregnancy (Raine) Study provided cross-sectional spinal pain and CBCL data.

Results
As predicted, there was a high prevalence of back and neck pain in this cohort. On the whole, females reported more mental health difficulties than males. There were strong relationships between the majority of symptom scales of the CBCL and back and neck pain. Scores on the CBCL were associated with higher odds of comorbid back and neck pain.

Conclusions
These findings strongly support the need to consider both psychological and pain symptoms when providing assessments and treatment for adolescents. Further research is required to inform causal models.
The HPV-16 E7 oncoprotein induces centriole multiplication through deregulation of Polo-like kinase 4 expression
Authors: Korzeniewski Nina , Treat Benjamin , Duensing Stefan 
Published: May 2011

Abstract

Background
Infection with high-risk human papillomaviruses (HPVs) such as HPV-16 is intimately associated with squamous cell carcinomas (SCCs) of the anogenital tract and a subset of oropharyngeal carcinomas. Such lesions, including pre-invasive precursors, frequently show multipolar mitoses and aneuploidy. The high-risk HPV-16-encoded E7 oncoprotein has been shown to rapidly induce centrosome abnormalities thereby causing the formation of supernumerary mitotic spindle poles and increasing the risk for chromosome missegregation. HPV-16 E7 has been found to rapidly induce centriole overduplication, in part, through the simultaneous formation of more than one daughter centriole at single maternal centrioles (centriole multiplication). The precise molecular mechanism that underlies HPV-16 E7-induced centriole multiplication, however, remains poorly understood.

Findings
Here, we show that human keratinocytes engineered to stably express the HPV-16 E7 oncoprotein exhibit aberrant Polo-like kinase 4 (PLK4) protein expression at maternal centrioles. Real-time quantitative reverse transcriptase (qRT-PCR) analysis of these cells revealed an increase of PLK4 mRNA levels compared to control cells. Importantly, the ability of the HPV-16 E7 oncoprotein to induce centriole multiplication was found to correlate with its ability to activate the PLK4 promoter and to up-regulate PLK4 mRNA.

Conclusions
These results highlight the critical role of PLK4 transcriptional deregulation in centriole multiplication in HPV-16 E7-expressing cells. Our findings encourage further experiments to test transcriptional inhibitors or small molecules targeting PLK4 to prevent centriole abnormalities, mitotic infidelity and malignant progression in HPV-associated neoplasms and other tumors in which PLK4 regulation is disrupted.
Visual and Colorimetric Detection of Cyanide Anion Based on a “Turn-off” Daylight Fluorescent Molecule
Authors: Jiao Lijuan , Liu Mingming , Zhang Min , Yu Changjiang , Wang Zhaoyun , Hao Erhong 
Published: May 2011

Abstract
A strong daylight-fluorescent boron dipyrromethene (BODIPY) derivative 1 has been synthesized for the visual and colorimetric detection of cyanide anion in solution. BODIPY 1 shows a glow characteristic of daylight-fluorescent material since emitted fluorescent light has been added to the simple reflection light under daylight illumination. This green daylight fluorescence is diminished upon interaction with cyanide anion, resulting in a highly selective and sensitive naked-eye detection of cyanide anion over other common anions.
Polyoxomolybdate–Surfactant Hybrid Layered Crystal with Unusually Long Periodicity
Authors: Ito Takeru , Mikurube Keisuke , Hasegawa Kimiko , Kurasawa Mariko , Naruke Haruo , Ozeki Tomoji 
Published: May 2011

Abstract
An inoranic–organic hybrid crystal was synthesized by using polyoxomolybdate and hexadecylpyridinium surfactant. The unit cell was monoclinic having quite a long cell dimension (b = 75.0111(14) Å). The crystal structure was formed by alternative stacking of β-octamolybdate bilayers and interdigitated hexadecylpyridinium bilayers with layered periodicity of 3.75 nm, which is the largest value for polyoxometalate–surfactant hybrid crystals.
Ferrocene-appended Subporphyrins
Authors: Sugimoto Hisashi , Tanaka Takayuki , Osuka Atsuhiro 
Published: May 2011

Abstract
meso-Tris(4-ferrocenylphenyl)subporphyrin 1 and meso-triferrocenylsubporphyrin 2 were prepared. The structure of 2 was confirmed by X-ray analysis. Both molecules exhibit substantially red-shifted absorption spectra and almost complete fluorescence quenching, due to the influence of the electron-donating ferrocene substituents. Subporphyrin 1 exhibits a nonsplit oxidation wave for the oxidation of the ferrocene moieties, while subporphyrin 2 exhibits a split reversible oxidation wave with ΔE = 168 mV to indicate effective electronic communication.
Total Synthesis of Doubly Locked 5Za15Ea-Biliverdin Derivative: A Convergent Synthesis of the E-anti Dipyrrole Component Locked with a 7-Membered Ring
Authors: Chen Liyi , Iwamoto Ryoji , Ukaji Yutaka , Inomata Katsuhiko 
Published: May 2011

Abstract
Doubly locked 5Za15Ea-biliverdin (BV) derivative was synthesized toward the investigation of stereochemistry and function of the Pfr-form chromophore in bacteriophytochromes. A convergent synthetic method was established for the locked E-anti dipyrrole component with a 7-membered ring.
Effect of Inorganic Salt on Formation of Porous PLGA Microspheres
Authors: Takai Chika , Hotta Tadashi , Shiozaki Shuji , Matsumoto Shuhei , Fukui Takehisa 
Published: May 2011

Abstract
Porous microspheres were prepared by a solid-in-oil-in-water (S/O/W) emulsion. Effects of inorganic salt on pore formation were investigated. Sodium chloride (NaCl) is a proper pore inducing agent, and large uniform pores were obtained with addition of 0.5 M NaCl.
Synthesis and Photochromic Properties of [2.2]Thiophenophan-8-ene-1,2-diol
Authors: Takeshita Michinori , Yamaguchi Shouhei 
Published: May 2011

Abstract
A photochromic [2.2]thiophenophan-8-ene-1,2-diol, which is the first ethylene-bridged dithienylethene, has been synthesized by pinacol coupling and this compound indicates fairly good photochromic properties such as high quantum yield for photocyclization and high thermal stability.
Radiographer-acquired and radiologist-reviewed ultrasound examination – agreement with radiologist's bedside evaluation
Authors: Stenman Carina , Thorelius Lars , Knutsson Anders , Smedby Örjan 
Published: May 2011

BackgroundGrowing demand for ultrasound examinations and higher quality requirements motivate searching for routines combining the diagnostic accuracy of radiologist-performed examinations with the economical advantages of sonographer-performed examinations. One possible approach is to use strictly standardized acquisition and documentation schemes that give the radiologist access to all relevant information after the examination.PurposeTo compare a recently introduced routine, combining acquisition by a radiographer, documentation as standardized cine-loops, and review by a radiologist (‘standardized method’), with the formerly used routine where the diagnosis is made bedside by the radiologist (‘traditional method’).Material and MethodsIn 64 policlinic patients, the kidneys ( n = 27) or the gallbladder ( n = 37) were examined with both the standardized and the traditional method. The radiologists' findings of hydronephrosis, tumors, cysts, echogenicity changes, and cortical thickness (in the kidneys), and wall thickness, concrements, and polyps (in the gallbladder) were compared between the methods with respect to agreement (proportion of agreement and kappa coefficient) as well as systematic differences (McNemar's test).ResultsThe findings at the gallbladder examination showed a median agreement of 97% (86–100%; kappa = 0.64–1.00), and those at the kidney examination, an agreement of 90% (78–100%; kappa = 0.69–1.00). There were no significant systematic differences between the methods.ConclusionThe satisfactory agreement in this preliminary study indicates that the new workflow with ultrasound examinations performed by a radiographer and analyzed off-line by a radiologist is promising, and motivates further studies.
Effects of outsourcing magnetic resonance examinations from a public university hospital to a private agent
Authors: Tavakol Parvin , Labruto Fausto , Bergstrand Lott , Blomqvist Lennart 
Published: May 2011

Background Sometimes the measures taken to make a radiology department more effective, such as prioritizing the workload and keeping equipment running for as many hours as staffing permits, are not enough. In such cases, outsourcing radiological examinations is a potential solution for reducing waiting times. Purpose To investigate differences in waiting time, quality and costs between magnetic resonance (MR) examinations performed in a university hospital and examinations outsourced to private service. Material and Methods We retrospectively selected a group of consecutive, outsourced MR examinations ( n = 97) and a control group of in-house MR examinations, matched for type of examination. In each group there were referrals that had a specified preferred timeframe for completion. We measured the percentage of cases in which this timeframe was met and if it was not met, how many days exceeded the preferred time. In referrals without a specified preferred timeframe, we also calculated the waiting time. Quality standards were measured by the percentage of examinations that had to be re-done and re-assessed. Finally, we calculated the cumulative costs, taking into account the costs for re-doing and re-assessing examinations. Results There was no statistically significant difference between the groups, in either the number of examinations that were not performed within the preferred time or the number of days that exceeded the preferred timeframe. For referrals without a preferred timeframe, the waiting time was shorter for outsourced examinations than those not outsourced. There were no differences in the number of examinations that had to be re-done, but more examinations needed to be re-assessed in the outsourced group than in the in-house group. The calculated costs for outsourced examinations were lower than the costs for internally performed examinations. Conclusion Outsourcing magnetic resonance examinations may be an effective way of reducing a radiology department's workload. Ways in which to reduce the additional costs incurred for re-assessment of outsourced examinations must be investigated further.
Aliasing artifact depicted on ultrasound (US)-elastography for breast cystic lesions mimicking solid masses
Authors: Cho Nariya , Moon Woo Kyung , Chang Jung Min , Kim Seung Ja , Lyou Chae Yeon , Choi Hye Young 
Published: May 2011

BackgroundIt has been reported that ultrasound (US)-elastography is helpful in differentiation of benign and malignant solid masses and in reducing benign biopsy procedures for the supplemental breast US in addition to screening mammography. Furthermore, potential application of US-elastography in distinguishing cystic lesions which is known to be a major source of benign biopsy results has been suggested.PurposeTo describe the aliasing artifact on US-elastography for breast cystic lesions that mimic solid masses.Material and MethodsWe retrospectively reviewed 13 lesions which showed a blue-green-red pattern artifact on US-elastography in 13 women (mean age 50 years; age range 3–66 years). They disappeared immediately after a needle biopsy. Breast composition, mammography and US findings, histology and follow-up imaging findings were analyzed.ResultsAll 13 patients showed heterogeneously dense ( n = 5) or extremely dense breast parenchyma ( n = 8). The most common US findings were an irregular shape ( n = 7, 54%) and a circumscribed margin ( n = 7, 54%). All 13 lesions had internal echogenicity and were initially considered as solid masses; 62% ( n = 8) showed hypoechogenicity and 38% ( n = 5) had echogenic and anechoic components. Posterior shadowing was seen in 31% ( n = 4) of the lesions. All 13 lesions have been proven to be fibrocystic changes on biopsy histology. Follow-up US performed for 10 of 13 lesions showed no residual lesion ( n = 9) or decreased its size ( n = 1).ConclusionAn aliasing artifact that appears as a blue-green-red pattern in a breast mass as depicted on US-elastography is suggestive of a possible cystic breast lesion.
Texture-based quantification of lumbar intervertebral disc degeneration from conventional T2-weighted MRI
Authors: Michopoulou Sofia , Costaridou Lena , Vlychou Marianna , Speller Robert , Todd-Pokropek Andrew 
Published: May 2011

Background Disc degeneration quantification is important for monitoring the effects of new therapeutic methods, such as cell and growth factor therapy. Magnetic resonance (MR) image texture reflects biochemical and structural tissue properties and has been used for differentiating between normal and pathological status in a variety of medical applications. Purpose To investigate the suitability of textural descriptors for the quantification of intervertebral disc degeneration using conventional T2-weighted magnetic resonance images of the lumbar spine. Material and Methods A 3 Tesla scanner was used, and conventional T2- weighted MR images were obtained, and a total of 255 lumbar discs were analyzed. An atlas-based method was used for segmenting the disc regions from the images. A set of first and second order statistics describing texture of each region were calculated. The validity and reliability of these descriptors for disc degeneration severity quantification was tested through their correlation with patient age and qualitative clinical grading of degeneration severity. Texture quantification results were compared to a widely accepted method for disc degeneration quantification based on the measurement of disc's mean signal intensity. Results Out of the set of texture descriptors tested, two descriptors quantifying image intensity inhomogeneity, i.e. the grey level standard deviation and co-occurrence derived sum of squares displayed the strongest association to patient age and clinical grading of disc degeneration severity ( P < 0.001). This is attributed to these inhomogeneity descriptors' capability to capture the progressive loss of nucleus-annulus distinction in the degenerative progress. Statistical analysis indicates that these descriptors can effectively separate between early stages of degeneration. Quantitative measurements are highly repeatable (intraclass correlation >0.98). Conclusion Inhomogeneity descriptors could be a valuable tool for tracking the evolution of disc degeneration and monitoring the response to treatment in a simple, precise and repeatable manner.
Minimally invasive application of thrombin in the treatment of pseudoaneurysms following open aortic surgery
Authors: Schellhammer Frank , Cohnen Mathias , Fürst Günter , Mödder Ullrich 
Published: May 2011

Background Anastomotic leaks are uncommon complications following aortic surgery. To avoid the morbidity associated with a second surgical procedure, minimally invasive techniques have become increasingly popular. Purpose To evaluate the feasibility and safety of thrombin in interventional treatment of postoperative pseudoaneurysms. Material and Methods CT-guided percutaneous injection was chosen in four cases. Endovascular access using an occlusion balloon catheter placed in the orifice of the pseudoaneurysm was utilized in one case. Results The average volume of all pseudoaneurysms was 178 ± 190 mL with a volume of the patent lumen of 25 ± 28 mL. All aneurysms thrombosed after injection of 600 ± 237 IU of thrombin. During the follow-up period of an average of 10 months all pseudoaneurysms remained occluded. Conclusion Our series demonstrates the feasibility of thrombin in the treatment of aortic anastomotic pseudoaneurysms. In combination with occlusion balloon catheters, even wide-necked pseudoaneurysms may be treated successfully. However, further investigations are warranted.