bluuebunny/crossref_metadata_2025 huggingface dataset:
Compromised trabecular microarchitecture and lower finite element estimates of radius and tibia bone strength in adults with turner syndrome: A cross-sectional study using high-resolution–pQCT
Authors: Hansen Stinus , Brixen Kim , Gravholt Claus H
Published: April 2012

Although bone mass appear ample for bone size in Turner syndrome (TS), epidemiological studies have reported an increased risk of fracture in TS. We used high-resolution peripheral quantitative computed tomography (HR-pQCT) to measure standard morphological parameters of bone geometry and microarchitecture, as well as estimated bone strength by finite element analysis (FEA) to assess bone characteristics beyond bone mineral density (BMD) that possibly contribute to the increased risk of fracture. Thirty-two TS patients (median age 35, range 20–61 years) and 32 healthy control subjects (median age 36, range 19–58 years) matched with the TS participants with respect to age and body-mass index were studied. A full region of interest (ROI) image analysis and a height-matched ROI analysis adjusting for differences in body height between groups were performed. Mean bone cross-sectional area was lower in TS patients in radius (−15%) and tibia (−13%) (both p < 0.01) whereas cortical thickness was higher in TS patients in radius (18%, p < 0.01) but not in tibia compared to controls. Cortical porosity was lower in TS patients at both sites (−32% in radius, −36% in tibia, both p < 0.0001). Trabecular integrity was compromised in TS patients with lower bone volume per tissue volume (BV/TV) (−27% in radius, −22% in tibia, both p < 0.0001), trabecular number (−27% in radius, −12% in tibia, both p < 0.05), and higher trabecular spacing (54% in radius, 23% in tibia, both p < 0.01). In the height-matched ROI analysis, differences remained significant apart from total area at both sites, cortical thickness in radius, and trabecular number in tibia. FEA estimated failure load was lower in TS patients in both radius (−11%) and tibia (−16%) (both p < 0.01) and remained significantly lower in the height-matched ROI analysis. Conclusively, TS patients had compromised trabecular microarchitecture and lower bone strength at both skeletal sites, which may partly account for the increased risk of fracture observed in these patients. © 2012 American Society for Bone and Mineral Research.
Osteoblast maturation and new bone formation in response to titanium implant surface features are reduced with age
Authors: Olivares-Navarrete Rene , Raines Andrew L , Hyzy Sharon L , Park Jung Hwa , Hutton Daphne L , Cochran David L , Boyan Barbara D , Schwartz Zvi
Published: April 2012

The surface properties of materials contribute to host cellular response and play a significant role in determining the overall success or failure of an implanted biomaterial. Rough titanium (Ti) surface microtopography and high surface free energy have been shown to enhance osteoblast maturation in vitro and increase bone formation in vivo. Whereas the surface properties of Ti are known to affect osteoblast response, host bone quality also plays a significant role in determining successful osseointegration. One factor affecting host bone quality is patient age. We examined both in vitro and in vivo whether response to Ti surface features was affected by animal age. Calvarial osteoblasts isolated from 1-, 3-, and 11-month-old rats all displayed a reduction in cell number and increases in alkaline phosphatase–specific activity and osteocalcin in response to increasing Ti surface microtopography and surface energy. Further, osteoblasts from the three ages examined displayed increased production of osteocalcin and local factors osteoprotegerin, vascular endothelial growth factor (VEGF)-A, and active transforming growth factor (TGF)-β1 in response to increasing Ti surface roughness and surface energy. Latent TGF-β1 only increased in cultures of osteoblasts from 1- and 3-month-old rats. Treatment with the systemic osteotropic hormone 1α,25(OH)2D3 further enhanced the response of osteoblasts to Ti surface features for all three age groups. However, osteoblasts derived from 11-month-old animals had a reduced response to 1α,25(OH)2D3 compared to osteoblasts derived from 1-or 3-month-old animals. These results were confirmed in vivo. Ti implants placed in the femoral intramedullary canal of old (9-month-old) mice yielded lower bone-to-implant contact and neovascularization in response to Ti surface roughness and energy compared to younger (2-month-old) mice. These results show that rodent osteoblast maturation in vitro as well as new bone formation in vivo is reduced with age. Whether comparable age differences exist in humans needs to be determined. © 2012 American Society for Bone and Mineral Research.
Calcium/calmodulin-signaling supports TRPV4 activation in osteoclasts and regulates bone mass
Authors: Masuyama Ritsuko , Mizuno Atsuko , Komori Hisato , Kajiya Hiroshi , Uekawa Atsushi , Kitaura Hideki , Okabe Koji , Ohyama Kaname , Komori Toshihisa
Published: April 2012

Osteoclast differentiation is critically dependent on calcium (Ca2+) signaling. Transient receptor potential vanilloid 4 (TRPV4), mediates Ca2+ influx in the late stage of osteoclast differentiation and thereby regulates Ca2+ signaling. However, the system-modifying effect of TRPV4 activity remains to be determined. To elucidate the mechanisms underlying TRPV4 activation based on osteoclast differentiation, TRPV4 gain-of-function mutants were generated by the amino acid substitutions R616Q and V620I in TRPV4 and were introduced into osteoclast lineage in Trpv4 null mice to generate Trpv4R616Q/V620I transgenic mice. As expected, TRPV4 activation in osteoclasts increased the number of osteoclasts and their resorption activity, thereby resulting in bone loss. During in vitro analysis, Trpv4R616Q/V620I osteoclasts showed activated Ca2+/calmodulin signaling compared with osteoclasts lacking Trpv4. In addition, studies of Trpv4R616Q/V620I mice that lacked the calmodulin-binding domain indicated that bone loss due to TRPV4 activation was abrogated by loss of interactions between Ca2+/calmodulin signaling and TRPV4. Finally, modulators of TRPV4 interactions with the calmodulin-binding domain were investigated by proteomic analysis. Interestingly, nonmuscle myosin IIa was identified by liquid chromatography–tandem mass spectroscopy (LC-MS/MS) analysis, which was confirmed by immunoblotting following coimmunoprecipitation with TRPV4. Furthermore, myosin IIa gene silencing significantly reduced TRPV4 activation concomitant with impaired osteoclast maturation. These results indicate that TRPV4 activation reciprocally regulates Ca2+/calmodulin signaling, which involves an association of TRPV4 with myosin IIa, and promotes sufficient osteoclast function. © 2012 American Society for Bone and Mineral Research.
Habitual levels of high, but not moderate or low, impact activity are positively related to hip BMD and geometry: Results from a population-based study of adolescents
Authors: Deere Kevin , Sayers Adrian , Rittweger Jörn , Tobias Jon H
Published: April 2012

Whether a certain level of impact needs to be exceeded for physical activity (PA) to benefit bone accrual is currently unclear. To examine this question, we performed a cross-sectional analysis between PA and hip BMD in 724 adolescents (292 boys, mean 17.7 years) from the Avon Longitudinal Study of Parents and Children (ALSPAC), partitioning outputs from a Newtest accelerometer into six different impact bands. Counts within 2.1 to 3.1g, 3.1 to 4.2g, 4.2 to 5.1g, and >5.1g bands were positively related to femoral neck (FN) BMD, in boys and girls combined, in our minimally adjusted model including age, height, and sex (0.5–1.1g: beta = −0.007, p = 0.8; 1.1–2.1g: beta = 0.003, p = 0.9; 2.1–3.1g: beta = 0.042, p = 0.08; 3.1–4.2g: beta = 0.058, p = 0.009; 4.2–5.1g: beta = 0.070, p = 0.001; >5.1g: beta = 0.080, p < 0.001) (beta = SD change per doubling in activity). Similar positive relationships were observed between high-impact bands and BMD at other hip sites (ward's triangle, total hip), hip structure indices derived by hip structural analysis of dual-energy X-ray absorptiometry (DXA) scans (FN width, cross-sectional area, cortical thickness), and predicted strength (cross-sectional moment of inertia). In analyses where adjacent bands were combined and then adjusted for other impacts, high impacts (>4.2g) were positively related to FN BMD, whereas, if anything, moderate (2.1–4.2g) and low impacts (0.5–2.1g) were inversely related (low: beta = −0.052, p = 0.2; medium: beta = −0.058, p = 0.2; high: beta = 0.137, p < 0.001). Though slightly attenuated, the positive association between PA and FN BMD, confined to high impacts, was still observed after adjustment for fat mass, lean mass, and socioeconomic position (high: beta = 0.096, p = 0.016). These results suggest that PA associated with impacts >4.2g, such as jumping and running (which further studies suggested requires speeds >10 km/h) is positively related to hip BMD and structure in adolescents, whereas moderate impact activity (eg, jogging) is of little benefit. Hence, PA may only strengthen lower limb bones in adolescents, and possibly adults, if this comprises high-impact activity. © 2012 American Society for Bone and Mineral Research.
Microtomographic evaluation of the bone–cell interactions with a silorane‐based composite
Authors: Wu Xiaohong , Deng Feng , Wang Lu , Watts David C.
Published: April 2012

The low‐shrink Silorane‐based composite could bond effectively to bone and showed the potential be used as a bone cement. Bone organ culture maintains the anatomical order, natural cell‐to‐cell and cell‐to‐matrix relationship. The purpose of this study was to evaluate the responses of bone cells to a Silorane‐based composite which was compared with a representative polymethyl methacrylate (PMMA) bone cement. The critical size defects were created through the parietal bones from one litter of mice. The paired bones were divided into two groups: Silorane‐based composite group and PMMA group. The prepared two groups of disks were put into the defects. The cultures were grown in vitro for 38 days and analyzed with microcomputed‐tomography, dissecting‐microscope, phase‐ contrast‐microscope, scanning‐electron‐microscopy, and energy‐ dispersive‐X‐ray. At the 10th day, the Silorane disk was almost fully covered by a sheet of cells but the cells hardly attached to the disk surface. The edge of the PMMA disk was covered by a sheet of cells and the migrated individual cells attached to the whole surface of the disk. At the 38th day, some cells attached to the exposed disk area of the Silorane disk while the formed tissues covered the whole surface of the PMMA disk. The collagen fibers, globular deposits and bone formation were visible in both groups. The Silorane‐based composite showed promise as a potential bone cement when compared with PMMA which is used in clinical orthopedics. However, the cell attachment to PMMA was evidently better than to Silorane‐based composite. Microsc. Res. Tech. 75:1176–1184, 2012. © 2012 Wiley Periodicals, Inc.
Duck nest success adjacent to predator‐reduced sites
Authors: Pieron Matthew R. , Darr Margaret J. K. , Rohwer Frank C.
Published: April 2012

Predator reduction regularly improves waterfowl nest success within management units, but the impact of predator reduction on nest success adjacent to trapped areas is not known. Trapping could reduce predator activity and increase nest success adjacent to trapped sites, as individual mammalian predators with home ranges largely outside the trapped area may still be killed when using portions of their home range that overlap the trapped area. We monitored 1,952 nests adjacent to (within 0–4.8 km) 7 trapped sites (each 93.2 km2) in eastern North Dakota, USA during 2005–2006 and found that nest success adjacent to trapped sites, regardless of distance from trapping, was similar to nest success in nontrapped areas and less than nest success inside trapped areas. Managers should not assume any benefits to nest success beyond the borders of trapped sites. © 2012 The Wildlife Society.
Steryl ferulates, bioactive compounds in cereal grains
Authors: Mandak Eszter , Nyström Laura
Published: April 2012

Steryl ferulates are minor bioactive phytochemicals present in various cereal grains and other seeds. They possess well‐established health promoting properties, such as antioxidant and cholesterol lowering activities. However, the health promoting potential of steryl ferulates extracted from different sources can vary depending on their characteristic sterol composition.
Extraction of phospholipids from structured dry chicken egg
Authors: Wang Hui , Yao Linxing , Wang Tong
Published: April 2012

Chicken egg contains a high level of phospholipids (PL) in the yolk. Recovering yolk total lipids and extracting egg PL with efficiency are important to the availability and utilization of these health‐promoting lipid products. In this study, we prepared two structured dry egg yolk materials and used two common solvents to extract and concentrate the PL. We found that drum‐dried flake‐like yolk is an ideal starting material for lipid extraction. Anhydrous ethanol can extract almost all the neutral lipids and PL. PL with purity over 90% can be prepared by cold acetone precipitation from the total lipids.
Effect of pH on the Micellar Morphology of Semicrystalline PCL‐b‐PEO Block Copolymers in Aqueous Solution
Authors: He Wei‐Na , Xu Jun‐Ting , Du Bin‐Yang , Fan Zhi‐Qiang , Sun Fang‐Li
Published: April 2012

The effect of pH on the micellar morphology of a semicrystalline poly(ϵ‐caprolactone)‐block‐poly(ethylene oxide) block copolymer (PCL66‐b‐PEO44) in aqueous solution is investigated. Spherical micelles are formed in neutral and acidic solutions. However, addition of alkali to the neutral micellar solution triggers a sphere‐to‐cylinder transformation of the micellar morphology. The micelles are stable in both neutral and acidic solutions, but the size of the micelles becomes gradually larger in the alkali solution. This phenomenon is interpreted in terms of the effect of pH value on the reduced tethering density of the corona in the semicrystalline micelles.
Separation of High‐Impact Polypropylene Using Interactive Liquid Chromatography
Authors: Macko Tibor , Ginzburg Anton , Remerie Klaas , Bruell Robert
Published: April 2012

Fractionation techniques such as temperature rising elution fractionation or crystallization analysis fractionation fail to fractionate the ethylene–propylene (EP) copolymers, which are a component of high‐impact polypropylene (hiPP), according to their chemical composition. High‐temperature high‐performance liquid chromatography separates blends of EP‐copolymers and polypropylene. The elution volume of the EP‐copolymers depends linearly on the average content of ethylene. The separation according to the chemical composition was hyphenated with size exclusion chromatography. In this way, the relationship between the distribution with regard to chemical composition and molar mass, that is, the full chemical heterogeneity of hiPP, was revealed for the first time.
Direct Insertion Mass Spectrometric Analysis of Thermal Degradation of Poly(2‐alkyl‐2‐oxazoline)
Authors: Atılkan Nurcan , Nur Yusuf , Hacaloglu Jale , Schlaad Helmut
Published: April 2012

Direct pyrolysis mass spectrometry is applied to investigate the thermal behavior of poly(2‐isopropyl‐2‐oxazoline) (PIPOX, a thermoresponsive polymer) and poly[2‐(3‐butenyl)‐2‐oxazoline] (PBOX, a “clickable” polymer). It is found that the thermal degradation of PIPOX is started by a loss of side chains. At slightly higher temperatures the degradation of the polymer backbone occurs by random chain scission processes. In the case of PBOX, vinyl polymerization of the side chains produces chains with variable thermal stabilities. The number of repeating units of the polymer has almost no effect on the thermal behavior of PIPOX, but significantly affects both thermal stability and degradation product distribution of PBOX.
Identification of a putative glycosyltransferase responsible for the transfer of pseudaminic acid onto the polar flagellin of Aeromonas caviae Sch3N
Authors: Parker Jennifer L. , Day‐Williams Michaela J. , Tomas Juan M. , Stafford Graham P. , Shaw Jonathan G.
Published: April 2012

Motility in Aeromonas caviae, in a liquid environment (in broth culture), is mediated by a single polar flagellum encoded by the fla genes. The polar flagellum filament of A. caviae is composed of two flagellin subunits, FlaA and FlaB, which undergo O‐linked glycosylation with six to eight pseudaminic acid glycans linked to serine and threonine residues in their central region. The flm genetic locus in A. caviae is required for flagellin glycosylation and the addition of pseudaminic acid (Pse) onto the lipopolysaccharide (LPS) O‐antigen. However, none of the flm genes appear to encode a candidate glycotransferase that might add the Pse moiety to FlaA/B. The motility‐associated factors (Maf proteins) are considered as candidate transferase enzymes, largely due to their conserved proximity to flagellar biosynthesis loci in a number of pathogens. Bioinformatic analysis performed in this study indicated that the genome of A. caviae encodes a single maf gene homologue (maf1). A maf mutant was generated and phenotypic analysis showed it is both nonmotile and lacks polar flagella. In contrast to flm mutants, it had no effect on the LPS O‐antigen pattern and has the ability to swarm. Analysis of flaA transcription by reverse transcriptase PCR (RT‐PCR) showed that its transcription was unaltered in the maf mutant while a His‐tagged version of the FlaA flagellin protein produced from a plasmid was detected in an unglycosylated intracellular form in the maf strain. Complementation of the maf strain in trans partially restored motility, but increased levels of glycosylated flagellin to above wild‐type levels. Overexpression of maf inhibited motility, indicating a dominant negative effect, possibly caused by high amounts of glycosylated flagellin inhibiting assembly of the flagellum. These data provide evidence that maf1, a pseudaminyl transferase, is responsible for glycosylation of flagellin and suggest that this event occurs prior to secretion through the flagellar Type III secretion system.
Nurses' treatment of tobacco dependence in hospitalized smokers in three states
Authors: Sarna Linda , Bialous Stella , Ong Michael , Wells Marjorie , Kotlerman Jenny
Published: April 2012

Hospital‐based nurses (N = 1,790) from three states reported their interventions to help patients quit smoking. Frequency of nurses' interventions in one low tobacco use state, California (n = 651), were compared to nurses' interventions in two high tobacco use states, Indiana (n = 720) and West Virginia (n = 419). Nurses in California were significantly more likely to Advise smokers to quit (OR 1.34, 95% CI [1.06, 1.69]) and Refer smokers to a Quitline (OR 2.82, 95% CI [1.36, 5.88]) compared with nurses in the high tobacco prevalence states. Other aspects of their interventions did not differ by state. Quitline referral was infrequent (16%) but was quadrupled if nurses arranged for smokers to quit (OR 4.07, 95% CI [3.11, 5.32]). © 2012 Wiley Periodicals, Inc. Res Nurs Health 35:250–264, 2012
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

Background

Malnutrition 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.

Procedures

Medical 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.

Results

PEG 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.

Conclusions

Early 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

We 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

A 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

Although 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

Teaching 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

Objective

We 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.

Methods

Participants 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.

Results

Binary 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).

Conclusions

These 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

Background

Patients 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.

Methods

A 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.

Results

Eighty‐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]).

Conclusions

Pre‐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

Essential 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

We 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

The 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

Contemporary 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

Triterpene 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

RNA 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

SWI1 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

Ultrapure 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.

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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

Background

Magnetic 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.

Methods

As 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.

Results

The 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.

Conclusions

The 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.
From black and white to full color: extending redescription mining outside the Boolean world
Authors: Galbrun Esther , Miettinen Pauli
Published: April 2012

Redescription mining is a powerful data analysis tool that is used to find multiple descriptions of the same entities. Consider geographical regions as an example. They can be characterized by the fauna that inhabits them on one hand and by their meteorological conditions on the other hand. Finding such redescriptors, a task known as niche‐finding, is of much importance in biology. Current redescription mining methods cannot handle other than Boolean data. This restricts the range of possible applications or makes discretization a pre‐requisite, entailing a possibly harmful loss of information. In niche‐finding, while the fauna can be naturally represented using a Boolean presence/absence data, the weather cannot. In this paper, we extend redescription mining to categorical and real‐valued data with possibly missing values using a surprisingly simple and efficient approach. We provide extensive experimental evaluation to study the behavior of the proposed algorithm. Furthermore, we show the statistical significance of our results using recent innovations on randomization methods. © 2012 Wiley Periodicals, Inc. Statistical Analysis and Data Mining, 2012
Miniaturized Lab‐on‐a‐Disc (miniLOAD)
Authors: Glass Nick R. , Shilton Richie J. , Chan Peggy P. Y. , Friend James R. , Yeo Leslie Y.
Published: April 2012

A miniaturized centrifugal microfluidic platform for lab‐on‐a‐chip applications is presented. Unlike its macroscopic Lab‐on‐a‐CD counterpart, the miniature Lab‐on‐a‐Disc (miniLOAD) device does not require moving parts to drive rotation of the disc, is inexpensive, disposable, and significantly smaller, comprising a 10‐mm‐diameter SU‐8 disc fabricated through two‐step photolithography. The disc is driven to rotate using surface acoustic wave irradiation incident upon a fluid coupling layer from a pair of offset, opposing single‐phase unidirectional transducers patterned on a lithium niobate substrate. The irradiation causes azimuthally oriented acoustic streaming with sufficient intensity to rotate the disc at several thousand revolutions per minute. In this first proof‐of‐concept, the capability of the miniLOAD platform to drive capillary‐based valving and mixing in microfluidic structures on a disc similar to much larger Lab‐on‐a‐CD devices is shown. In addition, the ability to concentrate aqueous particle suspensions at radial positions in a channel in the disc dependent on the particles’ size is demonstrated. To the best of our knowledge, the miniLOAD concept is the first centrifugal microfluidic platform small enough to be self‐contained in a handheld device.
Size‐Dependent Nonlinear Weak‐Field Magnetic Behavior of Maghemite Nanoparticles
Authors: de Montferrand Caroline , Lalatonne Yoann , Bonnin Dominique , Lièvre Nicole , Lecouvey Marc , Monod Philippe , Russier Vincent , Motte Laurence
Published: April 2012

The magnetic behavior at room temperature of maghemite nanoparticles of variable sizes (from 7 to 20 nm) is compared using a conventional super quantum interference device (SQUID) and a recently patented technology, called MIAplex. The SQUID usually measures the magnetic response versus an applied magnetic field in a quasi‐static mode until high field values (from –4000 to 4000 kA m−1) to determine the field‐dependence and saturation magnetization of the sample. The MIAplex is a handheld portable device that measures a signal corresponding to the second derivative of the magnetization around zero field (between –15 and 15 kA m−1). In this paper, the magnetic response of the size series is correlated, both in diluted and powder form, between the SQUID and MIAplex. The SQUID curves are measured at room temperature in two magnetic field ranges from –4000 to 4000 kA m−1 (–5T to 5T) and from –15 to 15 kA m−1. Nonlinear behavior at weak fields is highlighted and the magnetic curves for diluted solutions evolve from quasi‐paramagnetic to superparamagnetic behavior when the size of the nanoparticles increases. For the 7‐nm sample, the fit of the magnetization with the Langevin model weighted with log‐normal distribution corresponds closely to the magnetic size. This confirms the accuracy of the model of non‐interacting superparamagnetic particles with a magnetically frustrated surface layer of about 0.5 nm thickness. For the other samples (10‐nm to 21‐nm), the experimental weak‐field magnetization curves are modeled by more than one population of magnetically responding species. This behavior is consistent with a chemically uniform but magnetically distinct structure composed of a core and a magnetically active nanoparticle canted shell. Accordingly the weak‐field signature corresponds to the total assembly of the nanoparticles. The impact of size polydispersity is also discussed.
Incremental testing of finite state machines
Authors: Chaves Pedrosa Lehilton Lelis , Vieira Moura Arnaldo
Published: April 2012

The automatic generation of test suites for systems modelled as finite state machines (FSMs) is an important problem that impacts several critical applications. Known methods that automatically generate tests for FSMs, specially the W‐method and some derivations, strongly assume that the number of system states is small. If the overall number of states in the FSM specification is relatively large, such methods become difficult to use. However, often in practice, a system is defined as a combination of several subsystems, with the latter already independently designed, developed and tested. In this paper, we define the concept of combined FSMs and introduce a new method to test modular compositions of FSMs. This method allows for a new incremental testing strategy that turns the testing of new systems into a much more scalable process. As an example, we present an infinite family of naturally occurring FSM models for which our method produces exponentially more compact test suites than the W‐method. Copyright © 2012 John Wiley & Sons, Ltd.