bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tolerance and efficacy of preventive gastrostomy feeding in pediatric oncology
Authors: Schmitt Françoise , Caldari Dominique , Corradini Nadège , Gicquel Philippe , Lutz Patrick , Leclair Marc‐David , Podevin Guillaume 
Published: April 2012

AbstractBackgroundMalnutrition in pediatric oncology remains underestimated, although having a negative impact on outcome. Enteral nutrition (EN) using percutaneous endoscopic gastrostomy (PEG) may prevent or reverse malnutrition consequences. We aimed to evaluate both efficacy and safety of early EN during tumors treatment in children.ProceduresMedical records of pediatric patients having a PEG tube inserted between 1995 and 2009 were retrospectively reviewed. We compared type and incidence of complications in Group 1, including 74 patients suffering from cancer, and control Group 2, including 57 patients with neurological impairment. Efficacy of EN was evaluated through nutritional parameters [Z‐scores weight for height (W/H) and height for age (H/A)], post‐operative complications and relapse rates. Statistical significance was set for P < 0.05.ResultsPEG tolerance was similar in both groups, as shown by comparable complication rates (62% vs. 76%, NS). EN allowed improvement or stabilization of Z‐score W/H in 76% of oncologic patients. The final height loss was lower (−0.5 vs. −1.2 SD of Z‐scores H/A) when EN was started at the beginning of the oncologic treatment. In bone tumors, EN prevented weight loss during chemotherapy, and tended to lessen surgical complications, relapses and deaths.ConclusionsEarly gastrostomy feeding represents a relatively safe way to prevent malnutrition in children with cancer, and might play a role in bone tumors oncological outcome. Further prospective studies are needed to confirm these results and assess the impact of EN and PEG on quality of life. Pediatr Blood Cancer 2012; 59: 874–880. © 2012 Wiley Periodicals, Inc.
Sorafenib and bevacizumab for recurrent metastatic hepatoblastoma: Stable radiographic disease with decreased AFP
Authors: Marsh Anne M. , Lo Louise , Cohen Ronald A. , Feusner James H. 
Published: April 2012

AbstractWe report the use of sorafenib and bevacizumab in combination for a patient with recurrent metastatic hepatoblastoma (HB). This combination demonstrated activity against our patient's refractory HB that had been extensively treated with multiple prior chemotherapeutic regimens. The patient had stabilization of radiographic disease coupled with an 83% decrease in his alpha‐fetoprotein level. Given the response in this setting and the paucity of other available options, consideration could be given to using this combination as therapy in patients with recurrent HB who have failed more traditional agents. Pediatr Blood Cancer 2012; 59: 939–940. © 2012 Wiley Periodicals, Inc.
Collaborative models of instruction: The empirical foundations of inclusion and co‐teaching
Authors: Solis Michael , Vaughn Sharon , Swanson Elizabeth , Mcculley Lisa 
Published: April 2012

AbstractA summary of inclusion and co‐teaching syntheses was conducted to better understand the evidence base associated with collaborative models of instruction. Six syntheses were identified: four investigated inclusion, and two investigated co‐teaching. Collectively, the syntheses represented 146 studies. The syntheses investigated research on collaborative models; student outcomes; teachers' attitudes, beliefs, and perceptions; and students' perceptions. Common themes of collaborative models were identified across the six syntheses, which included collaborative models; student outcomes; teacher support issues; and attitudes, beliefs, and perceptions of collaborative models. Findings provide an empirical foundation to assist school psychologists in evidence‐based decision making. © 2012 Wiley Periodicals, Inc.
Collaboration between general and special educators and student outcomes: A need for more research
Authors: van Garderen Delinda , Stormont Melissa , Goel Nidhi 
Published: April 2012

AbstractAlthough collaboration between general and special educators is frequently recommended in the literature, how much is known and understood about actual collaboration practices remains unclear. Yet, current reforms and law are calling for increased collaboration. Therefore, the purpose of this review of the literature was to explore the research base on the impact that collaboration has on academic and/or social or behavioral outcomes for students with disabilities. A total of 19 studies were located for review. Although the studies generally support collaboration for improved student outcomes, this finding is tentative at best, given the small number of studies representing a variety of research designs and collaboration models. © 2012 Wiley Periodicals, Inc.
QUEST: A collaborative professional development model to meet the needs of diverse learners in K‐6 science
Authors: van Garderen Delinda , Hanuscin Deborah , Lee Eun , Kohn Pat 
Published: April 2012

AbstractTeaching science to diverse learners can be a demanding and challenging task. Teachers may be underprepared and thus unsure of how to best address the needs of their students in their classroom. One approach to helping teachers is through professional development. Yet, programs that focus mainly on science or special education can fail to fully meet teachers' needs for assisting all students in succeeding in the science classroom. We argue that a collaborative approach that combines the expertise of both fields is needed address this complex problem. The purpose of this article is to describe the collaborative efforts of teacher educators in both science education and special education who designed a professional development program to support teachers' implementation of inquiry‐based instruction, formative assessment, and Universal Design for Learning as a way to meet the needs of diverse learners in kindergarten through sixth‐grade classrooms. © 2012 Wiley Periodicals, Inc.
Correlates of continued smoking versus cessation among survivors of smoking‐related cancers
Authors: Berg Carla J. , Thomas Akilah N. , Mertens Ann C. , Schauer Gillian L. , Pinsker Erika A. , Ahluwalia Jasjit S. , Khuri Fadlo R. 
Published: April 2012

AbstractObjectiveWe examined correlates of continued smoking versus cessation among a sample of survivors of smoking‐related cancers who were actively smoking at the time of cancer diagnosis.MethodsParticipants with a history of smoking and a smoking‐related cancer diagnosis (lung, oral, pharynx, larynx, esophagus, bladder, stomach, cervix, kidney, pancreas, acute myeloid leukemia) within the past 4 years were identified in the electronic medical record. We recruited 613 individuals to complete a mail‐based survey and received 139 completed surveys (22.7% response rate). We focused on 105 participants who smoked at the time of diagnosis and dichotomized them to having either quit since diagnosis (48.6%;n = 51) or continued smoking (51.4%;n = 54). We assessed sociodemographics, type of cancer and treatment(s), and psychosocial factors (depressive symptoms, social support, hope, quality of life). We then conducted structured interviews with a subset of 21 survey respondents.ResultsBinary logistic regression indicated that, controlling for age, gender, ethnicity, marital status, and income, factors associated with continued smoking versus cessation included being diagnosed with other smoking‐related cancers versus lung or head and neck cancer (OR = 11.21, CI 2.85, 44.02) and having significant depressive symptoms (OR = 1.25, CI 1.08, 1.45). Qualitative findings highlighted motivators for cessation (impact of being diagnosed with cancer, doctor advice to quit, social influences) and barriers to cessation (hopelessness, stress, addiction).ConclusionsThese findings highlight the need to address depressive symptoms among cancer survivors, particularly those continuing to smoke and the importance of exploring messages cancer survivors are given regarding the need for cessation post cancer diagnosis. Copyright © 2012 John Wiley & Sons, Ltd.
Feasibility and Effectiveness of Pre‐operative Inspiratory Muscle Training in Patients Undergoing Oesophagectomy: A Pilot Study
Authors: Dettling Daniela S. , van der Schaaf Marike , Blom Rachel L.G.M. , Nollet Frans , Busch Olivier R.C. , van Berge Henegouwen Mark I. 
Published: April 2012

AbstractBackgroundPatients undergoing oesophageal surgery have a high risk for post‐operative complications including pulmonary infections. Recently, physical therapy has shifted from the post‐operative to the pre‐operative phase to diminish post‐operative complications and to shorten hospital stay. The purpose of this pilot study was to investigate the feasibility and initial effectiveness of pre‐operative inspiratory muscle training (IMT) on the incidence of pneumonia in patients undergoing oesophagectomy.MethodsA pragmatic non‐randomized controlled trial was conducted among all patients who underwent an oesophagectomy between January 2009 and February 2010. Patients in the intervention group received IMT prior to surgery. Feasibility was assessed on the basis of the occurrence of adverse effects during testing or training and patient satisfaction. Initial effectiveness on respiratory function was evaluated by maximal inspiratory pressure (MIP) and endurance, the incidence of post‐operative pneumonia and length of hospital stay.ResultsEighty‐three patients were included, of which 44 received pre‐operative IMT. No adverse effects were observed. IMT was well tolerated and appreciated. In the intervention group, the median MIP and endurance improved significantly after IMT by 32% and 41%, respectively (p < 0.001). The incidence of post‐operative pneumonia and the length of hospital stay were comparable for the intervention and the conventional care groups (pneumonia, 25% vs. 23% [p = 0.84]; hospitalization, 13.5 vs. 12 days [p = 0.08]).ConclusionsPre‐operative IMT is feasible in patients with oesophageal carcinoma and significantly improves respiratory muscle function. This, however, did not result in a reduction of post‐operative pneumonia in patients undergoing oesophagectomy. Copyright © 2012 John Wiley & Sons, Ltd.
Exploring the essential collective dynamics of interacting proteins: Application to prion protein dimers
Authors: Issack Bilkiss B. , Berjanskii Mark , Wishart David S. , Stepanova Maria 
Published: April 2012

AbstractEssential collective dynamics is a promising and robust approach for analysing the slow motions of macromolecules from short molecular dynamics trajectories. In this study, an extension of the method to treat a collection of interacting protein molecules is presented. The extension is applied to investigate the effects of dimerization on the collective dynamics of ovine prion protein molecules in two different arrangements. Examination of the structural plasticity shows that aggregation has a restricting effect on the local mobility of the prion protein molecules in the interfacial regions. Domain motions of the two dimeric ovine prion protein conformations are distinctly different and can be related to interatomic correlations at the interface. Correlated motions are among the slow collective modes extensively analysed by considering both main‐chain and side‐chain atoms. Correlation maps reveal the existence of a vast network of dynamically correlated side groups, which extends beyond individual subunits via interfacial interconnections. The network is formed by a core of hydrophobic side chains surrounded by hydrophilic groups at the periphery. The relevance of these findings are discussed in the context of mutations associated with prion diseases. The binding free energy of the dimeric conformations is evaluated to probe their thermodynamic stability. The descriptions afforded by the analysis of the essential collective dynamics of the prion dimers are consistent with their binding free energies. The agreement validates the extension of the methodology and provides a means of interpreting the collective dynamics in terms of the thermodynamic stability of ovine prion proteins. Proteins 2012. © 2012 Wiley Periodicals, Inc.
A protein–RNA docking benchmark (I): Nonredundant cases
Authors: Barik Amita , C. Nithin , P. Manasa , Bahadur Ranjit Prasad 
Published: April 2012

AbstractWe have developed a nonredundant protein–RNA docking benchmark dataset, which is derived from the available bound and unbound structures in the Protein Data Bank involving polypeptide and nucleic acid chains. It consists of nine unbound–unbound cases where both the protein and the RNA are available in the free form. The other 36 cases are of unbound–bound type where only the protein is available in the free form. The conformational change upon complex formation is calculated by a distance matrix alignment method, and based on that, complexes are classified into rigid, semi‐flexible, and full flexible. Although in the rigid body category, no significant conformational change accompanies complex formation, the fully flexible test cases show large domain movements, RNA base flips, etc. The benchmark covers four major groups of RNA, namely, t‐RNA, ribosomal RNA, duplex RNA, and single‐stranded RNA. We find that RNA is generally more flexible than the protein in the complexes, and the interface region is as flexible as the molecule as a whole. The structural diversity of the complexes in the benchmark set should provide a common ground for the development and comparison of the protein–RNA docking methods. The benchmark can be freely downloaded from the internet. Proteins 2012. © 2012 Wiley Periodicals, Inc.
Crystal structure of a supercharged variant of the human enteropeptidase light chain
Authors: Simeonov Peter , Zahn Michael , Sträter Norbert , Zuchner Thole 
Published: April 2012

AbstractThe highly specific serine protease human enteropeptidase light chain cleaves the Asp4Lys recognition sequence and represents an interesting enzyme for biotechnological applications. The human enzyme shows 10 times faster kinetics compared to other animal sources but low solubility under low salt conditions, which hampers protein production and crystallization. Therefore, a supercharged variant (N6D/G21D/G22D/N142D/K210E/C112S) with increased solubility was used for crystallization. The structure (resolution, 1.9 Å) displays a typical α/β trypsin‐like serine protease‐fold. The mutations introduced for protein supercharging generate larger clusters of negative potential on both sites of the active cleft but do not affect the structural integrity of the protein. Proteins 2012. © 2012 Wiley Periodicals, Inc.
Refinement of unreliable local regions in template‐based protein models
Authors: Park Hahnbeom , Seok Chaok 
Published: April 2012

AbstractContemporary template‐based modeling techniques allow applications of modeling methods to vast biological problems. However, they tend to fail to provide accurate structures for less‐conserved local regions in sequence even when the overall structure can be modeled reliably. We call these regions unreliable local regions (ULRs). Accurate modeling of ULRs is of enormous value because they are frequently involved in functional specificity. In this article, we introduce a new method for modeling ULRs in template‐based models by employing a sophisticated loop modeling technique. Combined with our previous study on protein termini, the method is applicable to refinement of both loop and terminus ULRs. A large‐scale test carried out in a blind fashion in CASP9 (the 9th Critical Assessment of techniques for protein structure prediction) shows that ULR structures are improved over initial template‐based models by refinement in more than 70% of the successfully detected ULRs. It is also notable that successful modeling of several long ULRs over 12 residues is achieved. Overall, the current results show that a careful application of loop and terminus modeling can be a promising tool for model refinement in template‐based modeling. Proteins 2012. © 2012 Wiley Periodicals, Inc.
The triterpene cyclase protein family: A systematic analysis
Authors: Racolta Silvia , Juhl P. Benjamin , Sirim Demet , Pleiss Jürgen 
Published: April 2012

AbstractTriterpene cyclases catalyze a broad range of cyclization reactions to form polycyclic triterpenes. Triterpene cyclases that convert squalene to hopene are named squalene‐hopene cyclases (SHC) and triterpene cyclases that convert oxidosqualene are named oxidosqualene cyclases (OSC). Many sequences have been published, but there is only one structure available for each of SHCs and OSCs. Although they catalyze a similar reaction, the sequence similarity between SHCs and OSCs is low. A family classification based on phylogenetic analysis revealed 20 homologous families which are grouped into two superfamilies, SHCs and OSCs. Based on this family assignment, the Triterpene Cyclase Engineering Database (TTCED) was established. It integrates available information on sequence and structure of 639 triterpene cyclases as well as on structurally and functionally relevant amino acids. Family specific multiple sequence alignments were generated to identify the functionally relevant residues. Based on sequence alignments, conserved residues in SHCs and OSCs were analyzed and compared to experimentally confirmed mutational data. Functional schematic models of the central cavities of OSCs and SHCs were derived from structure comparison and sequence conservation analysis. These models demonstrate the high similarity of the substrate binding cavity of SHCs and OSCs and the equivalences of the respective residues. The TTCED is a novel source for comprehensive information on the triterpene cyclase family, including a compilation of previously described mutational data. The schematic models present the conservation analysis in a readily available fashion and facilitate the correlation of residues to a specific function or substrate interaction. Proteins 2012; © 2012 Wiley Periodicals, Inc.
A dynamic model for processive transcription elongation and backtracking long pauses by multisubunit RNA polymerases
Authors: Xie Ping 
Published: April 2012

AbstractRNA polymerases are enzymes that transcribe genes from DNA onto strands of RNA. The transcription elongation by multisubunit RNA polymerases is processive but nonuniform: one enzyme can translocate along the DNA template for thousands of nucleotide addition steps but, sometimes, it can enter backtracking long pauses. Here, we present a Brownian ratchet model for the processive transcription elongation and the backtracking long pauses, which is developed based on the available structural and biochemical studies. Using the model, we analytically study the dynamics of the transcription elongation, such as the effects of external force and NTP concentration on the transcription velocity free of pauses, and the dynamics of backtracking long pauses, such as the probabilities of entering and returning from the backtracking pauses, with the analytical results in good agreement with the available single molecule experimental data. Values of several parameters for both Escherichia coli and Saccharomyces cerevisiae RNA polymerases such as their affinities for the DNA/RNA substrate during transcription elongation are determined. Moreover, some testable predictions are presented. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Solution structure of SWI1 AT‐rich interaction domain from Saccharomyces cerevisiae and its nonspecific binding to DNA
Authors: Wang Tao , Zhang Jiahai , Zhang Xuecheng , Tu Xiaoming 
Published: April 2012

AbstractSWI1 is a subunit of the SWI/SNF complex involved in chromatin remodeling. It contains an AT‐rich interaction domain (ARID) which has the potential DNA binding activity. In this study, we determined the solution structure of the SWI1 ARID domain from Saccharomyces cerevisiae by nuclear magnetic resonance spectroscopy. Yeast SWI1 ARID domain is composed of seven alpha helices, six of which are conserved among the ARID family. In addition, the DNA‐binding activity of the SWI1 ARID domain was confirmed by chemical shift perturbation assay. Similar to its human homolog, the yeast SWI1 ARID domain binds DNA nonspecifically. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Ultra‐thin anodic alumina capacitor films for plastic electronics
Authors: Mardare Andrei Ionut , Kaltenbrunner Martin , Sariciftci Niyazi Serdar , Bauer Siegfried , Hassel Achim Walter 
Published: April 2012

AbstractUltrapure aluminium was thermally evaporated onto various plastics (polyethylene 2.6‐naphthalate, PEN; polyethylene terephthalate, PET; polyimide, PI and glass for comparison) and potentiostatically anodized in a citric buffer. The anodisation procedure was monitored coulometrically and each alumina film formed was characterized by impedance spectroscopy. The resulting anodic alumina films were amorphous (proven by X‐ray diffraction, XRD) and acted as dielectric material in a solid state capacitor with Au top electrode. The capacitors characteristics were evaluated using IV curves and frequency domain measurements. The performance of the capacitors demonstrated low leakage currents and low dielectric losses. The contrary properties capacity and breakdown voltage could be chosen by selecting the anodisation voltage. For each substrate apparent oxide formation factors and capacities were determined coulometrically. The ratio between apparent formation factor and projected area allowed determining the surface roughness. This surface roughness together with the high purity aluminium films and the anodisation compression was responsible for the unexpected high mechanical stability of this composite material. magnified image
A workspace‐orientated needle‐guiding robot for 3T MRI‐guided transperineal prostate intervention: evaluation of in‐bore workspace and MRI compatibility
Authors: Song Sang‐Eun , Hata Nobuhiko , Iordachita Iulian , Fichtinger Gabor , Tempany Clare , Tokuda Junichi 
Published: April 2012

AbstractBackgroundMagnetic resonance imaging (MRI)‐guided prostate interventions have been introduced to enhance the cancer detection. For accurate needle positioning, in‐bore‐operated robotic systems have been developed and optimal use of the confined in‐bore space become a critical engineering challenge.MethodsAs preliminary evaluation of our prostate intervention robot, we conducted a workspace design analysis, using a new evaluation method that we developed for in‐bore‐operated robots for transperineal prostate interventions, and an MRI compatibility study.ResultsThe workspace analysis resulted in the effective workspace (VW) of 0.32, which is greater than that of our early prototype, despite the current robot being ca. 50% larger than the early prototype in sectional space. The MRI compatibility study resulted in < 15% signal:noise ratio (SNR) reduction.ConclusionsThe new workspace evaluation method quantifies the workspace utilization of the in‐bore‐operated robots for MRI‐guided transperineal prostate interventions, providing a useful tool for evaluation and new robot design. The robot creates insignificant electromagnetic noise during typical prostate imaging sequences. Copyright © 2012 John Wiley & Sons, Ltd.