bluuebunny/crossref_metadata_2025 huggingface dataset:
Enforcing biphasic eye development in a directly developing insect by transient knockdown of single eye selector genes
Authors: Dong Ying , Friedrich Markus
Published: July 2009

The visual system of indirectly developing insects such as Drosophila passes through two phases of development. Larval eyes form in the embryo, whereas the adult compound eyes form during metamorphosis. Comparative evidence implies that this biphasic mode of visual system development evolved from the continuously developing eye of directly developing insects. We investigated the developmental basis of this evolutionary transformation in a directly developing insect taking advantage of the time‐limited nature of systemic RNAi in the grasshopper Schistocerca americana. Transient knockdown of the homologs of the early retinal genes eyes absent (eya) or sine oculis (so) both induced long‐term arrest of eye development in grasshopper nymphs. Eye development, however, resumed after knockdown expiry. This finding sheds first light on the molecular regulation of postembryonic eye development in directly developing insects and unravels an inherent capacity of the underlying gene regulatory network to accommodate for partitioning visual system development into discrete phases, as in indirectly developing insects. J. Exp. Zool. (Mol. Dev. Evol.) 314B:104–114, 2010. © 2009 Wiley‐Liss, Inc.
The impact of non‐performance information on ratings of job performance: A policy‐capturing approach
Authors: Spence Jeffrey R. , Keeping Lisa M.
Published: July 2009

Researchers have suggested that rater motives and the organizational context should be considered as sources of performance appraisal inaccuracies. A review of the performance appraisal literature revealed three primary non‐performance factors that managers consider when rating employee performance: (a) Potential negative consequences of ratings, (b) organizational norms, and (c) the opportunity to advance self‐interests. Using a policy‐capturing methodology, the current study investigated if these three non‐performance factors, as well as individual rater differences (e.g., conscientiousness, agreeableness, and performance appraisal experience), influence performance ratings. A sample of 303 experienced managers rated the performance of a fictitious employee, featured in a series of hypothetical scenarios, in which the above information was manipulated. Using hierarchical linear modeling, the results revealed that each of the three non‐performance related considerations accounted for variance incremental to objective employee performance. Managers' performance appraisal experience also predicted ratings, such that more experience was associated with lower ratings. These results provide support for the view that non‐performance factors can be a substantive component of performance ratings. Copyright © 2009 John Wiley & Sons, Ltd.
Influence of land use change on urban heat island derived from multi‐sensor data
Authors: Hu Yonghong , Jia Gensuo
Published: July 2009

Regional climate change was demonstrated to be likely influenced by anthropogenic dominated land surface processes. Urban heat island (UHI) is one of the important outcomes of such land surface processes induced by urbanization, and it is an urban climate phenomenon influenced by land use pattern and it represents the difference in albedo, roughness, and heat flux exchange of land surface. This study tries to examine the influence of land use change on UHI in greater Guangzhou from 1980–2007 by analysing Landsat MSS/TM/ETM+ and MODIS satellite data, meteorological records, and census data. An integrated and modified single‐channel method was used to retrieve land surface temperature (LST). Decadal changes in land use fraction and UHI pattern show that cropland decreased in parallel to the increase in built‐up area and the correlation coefficient reached 0.97. The UHI effect expanded from urban areas to surrounding suburban areas and countryside with an increase in land surface temperature (mean LST increased by 2.48 from 1990 to 2007) and a decrease in the green vegetation fraction (GVF) (mean GVF decreased by 0.16 from 1990 to 2007). The spatial heterogeneity of UHI expansion can be explained by spatial patterns of economic development, population increase, and abundance of vegetation cover. In addition, remarkable changes in air temperature due to relocation of meteorological stations are significant signals for detecting the influence of urbanization on urban heat island. Copyright © 2009 Royal Meteorological Society
Repairing large bone fractures with low frequency electromagnetic fields
Authors: Lin Hsin‐Yi , Lu Ko‐Hsien
Published: July 2009

The healing effects of low frequency pulse electromagnetic field (EMF) on bone fractures larger than 1 cm are unsatisfactory. Three‐ dimensional chitosan scaffolds are designed to fill in larger bone fractures and have been shown to be osteogenic. We hypothesized that EMF could accelerate the repair process of larger bone fractures with the use of chitosan scaffolds. Chitosan (96% deacetylation) films and lyophilized scaffolds, with and without osteoblast cells, were exposed to EMF (18–30 Gauss, 75 Hz) for 2 h a day for 3 weeks. Each week, the growth and phenotype expressions of osteoblasts and properties of chitosan were examined. The hydrophilicity, Young's modulus, and biodegradability of chitosan were not altered by EMF exposure. EMF osteoblasts showed 37% higher cell proliferation, 15% lower alkaline phosphatase activity, and 74% more calcium deposition than the controls. Based on SEM photomicrographs, EMF‐ treated cells appeared to produce more collagen fibrils, matrix vesicles, and calcium in the extracellular matrix than the controls. In conclusion, EMF was capable of enhancing the proliferation and mineralization of osteoblasts cultured on chitosan scaffolds. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 28:265–270, 2010
Enhanced effects of BMP‐binding peptide combined with recombinant human BMP‐2 on the healing of a rodent segmental femoral defect
Authors: Morishita Yuichiro , Naito Masatoshi , Miyazaki Masashi , He Wubing , Wu Guizhong , Wei Feng , Sintuu Chananit , Hymanson Henry , Brochmann Elsa J. , Murray Samuel S. , Wang Jeffrey C.
Published: July 2009

BMP‐binding peptide (BBP) enhances the osteogenic activity of recombinant human bone morphogenetic protein‐2 (rhBMP‐2), but the mechanism underlying the enhancement remains unclear. We aimed to elucidate the potential enhanced efficacy of BBP using critical‐sized segmental femoral bone defects in rats. Seventy defects in seven groups of rats were filled with various amounts (0, 2, 5, and 10 µg) of rhBMP‐2 with or without 1000 µg BBP. Radiographs were obtained after 4 and 8 weeks. The animals were euthanized at 8 weeks, and femoral specimens were assessed manually, evaluated for bone volume using microcomputed tomography, and subjected to histological or biomechanical analysis. Although 10 µg rhBMP‐2 yielded consistent results in terms of bone healing and quality of bone repair across the segmental defect, lower doses of rhBMP‐2 failed to induce satisfactory bone healing. However, the combined administration of lower doses of rhBMP‐2 and BBP induced the formation of significantly large amounts of bone. Our results suggest that the combined administration of rhBMP‐2 and BBP facilitates bone healing and has potential clinical applications. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 28:258–264, 2010
An artificial tendon with durable muscle interface
Authors: Melvin Alan , Litsky Alan , Mayerson Joel , Witte David , Melvin David , Juncosa‐Melvin Natalia
Published: July 2009

A coupling mechanism that can permanently fix a forcefully contracting muscle to a bone anchor or any totally inert prosthesis would meet a serious need in orthopaedics. Our group developed the OrthoCoupler™ device to satisfy these demands. The objective of this study was to test OrthoCoupler's performance in vitro and in vivo in the goat semitendinosus tendon model. For in vitro evaluation, 40 samples were fatigue‐tested, cycling at 10 load levels, n = 4 each. For in vivo evaluation, the semitendinosus tendon was removed bilaterally in eight goats. Left sides were reattached with an OrthoCoupler, and right sides were reattached using the Krackow stitch with #5 braided polyester sutures. Specimens were harvested 60 days postsurgery and assigned for biomechanics and histology. Fatigue strength of the devices in vitro was several times the contractile force of the semitendinosus muscle. The in vivo devices were built equivalent to two of the in vitro devices, providing an additional safety factor. In strength testing at necropsy, suture controls pulled out at 120.5 ± 68.3 N, whereas each OrthoCoupler was still holding after the muscle tore, remotely, at 298 ± 111.3 N (mean ± SD) (p < 0.0003). Muscle tear strength was reached with the fiber–muscle composite produced in healing still soundly intact. This technology may be of value for orthopaedic challenges in oncology, revision arthroplasty, tendon transfer, and sports‐injury reconstruction. © 2009 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 28:218–224, 2010
Abiotic soil properties and the occurrence of Rhizoctonia crown and root rot in sugar beet
Authors: Kühn Jürgen , Rippel Rudolf , Schmidhalter Urs
Published: July 2009

Since 1993, Rhizoctonia crown and root rot (Rhizoctonia solani AG 2–2 IIIB) has represented an increasing problem for sugar beet production in Germany. Up to now, the outbreak of the infection and the spread of the disease within a field cannot be predicted and effective countermeasures are not available. Although little is known about the living conditions of R. solani in soils, abiotic soil properties are likely to influence the disease occurrence. Investigations were carried out based on 60 pairwise comparisons, each consisting of a disease‐affected and an adjacent nonaffected patch on farmers' fields in 2002 and 2003. Soil samples from the top soil layer (0–30 cm) were collected before harvest, and eight of the most frequently mentioned soil properties potentially influencing Rhizoctonia crown and root rot infection were examined: bulk density, texture, carbonate carbon, potassium, phosphorus, organic carbon, total nitrogen, and pH. The occurrence of the disease was significantly related to the soil C : N ratio, indicating the influence of soil organic matter on the disease occurrence. Examinations of soil thin sections showed that organic‐matter particles in the soil serve as a substrate for R. solani. All other soil physical and chemical properties examined did not differ between the disease‐affected and nonaffected patches and seem to be of minor importance.
Cesium‐137‐based erosion‐rate determination of a steep mountainous region
Authors: Konz Nadine , Schaub Monika , Prasuhn Volker , Baenninger Dominik , Alewell Christine
Published: July 2009

Data on quantification of erosion rates in alpine grasslands remain scarce but are urgently needed to estimate soil degradation. We determined soil‐erosion rates based on 137Cs in situ measurements. The method integrates soil erosion over the last 22 y (time after the Chernobyl accident). Measured erosion rates were compared with erosion rates modeled with the Universal Soil Loss Equation (USLE). The comparison was done in order to find out if the USLE is a useful tool for erosion prediction in steep mountainous grassland systems. Three different land‐use types were investigated: hayfields, pasture with dwarf shrubs, and pasture without dwarf shrubs. Our test plots are situated in the Urseren Valley (Central Switzerland) with a mean slope steepness of 37°. Mean annual soil‐erosion rates determined with 137Cs of the investigated sites ranged between the minimum of 4.7 t ha–1 y–1 for pastures with dwarf shrubs to >30 t ha–1 y–1 at hayfields and pastures without dwarf shrubs. The determined erosion rates are 10 to 20 times higher compared to previous measurements in alpine regions. Our measurements integrated over the last 22 y, including extreme rainfall events as well as winter processes, whereas previous studies mostly reported erosion rates based on summer time and short‐term rainfall simulation experiments. These results lead to the assumption that heavy‐rainfall events as well as erosion processes during winter time and early spring do have a considerable influence on the high erosion amounts that were measured. The latter can be confirmed by photographs of damaged plots after snowmelt. Erosion rates based on the USLE are in the same order of magnitude compared to 137Cs‐based results for the land‐use type “pasture with dwarf shrubs”. However, erosion amounts on hayfields and pasture without dwarf shrubs are underestimated by the USLE compared to 137Cs‐based erosion rates. We assume that the underestimation is due to winter processes that cause soil erosion on sites without dwarf shrubs that is not considered by the USLE. Dwarf shrubs may possibly prevent from damage of soil erosion through winter processes. The USLE is not able to perform well on the affected sites. Thus, a first attempt was done to create an alpine factor for the USLE based on the measured data.
Comparison of Polish and German maps of agricultural soil quality using GIS
Authors: Dobers Eike Stefan , Ahl Christian , Stuczyński Tomasz
Published: July 2009

Soil maps serve different purposes in rural planning, environmental protection, and agricultural production. On the scale of the European Union, soil‐quality maps are used as main input‐data source in the process of “less favored area's” (LFA) delineation, which in course get special financial support. However, every EU member state uses its own national soil‐map resources to derive soil‐quality estimates, as no uniform mapping scheme or map resources exist for the whole territory. Information about the actual comparability of these map resources is missing. Because of historical reasons, for some parts of the Republic of Poland soil‐quality maps exist, which were edited using the German mapping scheme.

In this study, we used nine German map sheets at a generalized scale of 1:25,000 and compared the German soil‐map attributes (German: “Bodenschätzung”) with the respective Polish information (Polish: “mapa glebowo‐rolnicza”) at the same scale. Map analysis of 94,000 ha in a study area near Płock, Central Poland, was performed on vector data that was digitized from original raster maps in a Geographic Information System (GIS). An automatically produced, stratified‐random point‐sampling scheme was used to statistically compare the map attributes. The distance of each sampling point to the vector polygon borders of the two maps in the GIS served for continuously excluding data points from the analysis to acknowledge spatial uncertainties due to mapping accuracy and other factors. Qualitative soil‐texture information was translated into water‐storage‐capacity values.

Correlation coefficients between Polish and German arable‐soil‐quality assessments were between 0.57 for all data points and 0.72, when the data set was restricted to points with minimum distance of 60 m to any polygon border. Further increase of spatial restrictions did not improve correlation coefficients. Correlations between soil‐quality assessments and water‐storage capacities of the respective other national mapping scheme fell between 0.53 and 0.71. Higher amounts of variation of German soil quality could be explained using a factorial model with soil‐texture and soil‐type information, than by simple linear regression of quality assessments. Soil water‐storage capacities for German soil‐texture information resulted in average estimates, which were only 70%–88% of the respective Polish values, but only 41% in the case of sandy soil texture. Our analysis indicated that information of the Polish soil‐quality map with regard to soil texture in different depths could contribute to a more refined and differentiated quantitative assessment of agricultural soil quality.
Separation and determination of closely related lantibiotics by micellar electrokinetic chromatography
Authors: Stanley Bob , Mehr Kevin A. , Kellock Trent , Van Hamme Jonathan D. , Donkor Kingsley K.
Published: July 2009

A sensitive micellar electrokinetic chromatography (MEKC) method was developed for the separation and determination of four closely related lantibiotics: gallidermin, cinnamycin, duramycin and nisin. Factors affecting the separation of the lantibiotics such as pH, phosphate buffer concentration, SDS concentration and wavelength for UV detection were investigated. By optimizing these experimental conditions, successful separation was achieved between class 1A lantibiotics (nisin and gallidermin) and class 1B lantibiotics (duramycin and cinnamycin). The four lantibiotics were separated within 12 min in 50 mM phosphate buffer at pH 3.95 ± 0.1 containing 80 mM SDS with UV detection of 214 nm. The LOD (S/N = 3) were 61 ng/mL for gallidermin, 57 ng/mL for cinnamycin, 55 ng/mL for duramycin and 58 ng/mL for nisin. The method was successfully applied to real samples such as fermentation broth, bovine colostrum and predrop beer. This method yielded satisfactory results, with quantitative recoveries of spiked lantibiotics in the three samples ranging from 86.1 to 99.6%.
Acute stress disorder and posttraumatic stress disorder in parents of injured children
Authors: Kassam‐Adams Nancy , Fleisher Courtney Landau , Winston Flaura Koplin
Published: July 2009

Acute stress disorder (ASD) and posttraumatic stress disorder (PTSD) were examined in 334 parents of children with traffic‐related injuries. In the first month after their child's injury, 12% of parents had ASD and another 25% had partial ASD. Among 251 parents assessed again approximately 6 months postinjury, 8% had PTSD and another 7% had partial PTSD. The ASD and PTSD severity were associated (r = .54), but ASD status was not a sensitive predictor of later PTSD. Independent predictors of ASD severity included prior trauma exposure, peritrauma exposure and perceptions of the child's pain and life threat, and child ASD severity. Independent predictors of PTSD severity included prior trauma exposure, parent ASD severity, and parent‐rated child physical health at follow‐up.
Effects of low‐level laser therapy after Corticision on tooth movement and paradental remodeling
Authors: Kim Su‐Jung , Moon Sung‐Uk , Kang Seung‐Goo , Park Young‐Guk
Published: July 2009

Background and Objective

Both Corticision and low‐level laser therapy (LLLT) are known to affect the rate of tooth movement. Our objective was to investigate the combined effects of Corticision and LLLT on the tooth movement rate and paradental remodeling in beagles.

Study Design/Materials and Methods

The maxillary second premolars (n = 24) of 12 beagles were randomly divided into four groups (n = 6 per group) based on the treatment modality: group A, only orthodontic force (control); group B, orthodontic force plus Corticision; group C, orthodontic force plus LLLT; group D, orthodontic force plus Corticision and LLLT.

Results

Ratios of second premolar‐to‐canine movement were greater by 2.23‐fold in group B and 2.08‐fold in group C, but 0.52‐fold lesser in group D than in group A. The peak velocity was observed at an earlier stage of tooth movement in group B but at a later stage in group C during the 8‐week treatment period. At week 8, both tartrate‐resistant acid phosphatase (TRAP)‐positive osteoclasts on the compression side and proliferating cell nuclear antigen (PCNA)‐positive osteoblasts on the tension side increased significantly (P<.05) in group C but decreased in group D. Histomorphometric analysis revealed that the mean apposition length of newly formed mineralized bone during the 8 weeks of treatment significantly increased in both group B (2.8‐fold) and group C (2.2‐fold). In group D, the labeling lines on lamina dura were thin and discontinuous, but intratrabecular remodeling and lamellation were found to be active.

Conclusion

Periodic LLLT after Corticision around a moving tooth decreased the tooth movement rate and alveolar remodeling activity. Lasers Surg. Med. 41:524–533, 2009. © 2009 Wiley‐Liss, Inc.
Comparison of a 1,550 nm Erbium:Glass fractional laser and a chemical reconstruction of skin scars (CROSS) method in the treatment of acne scars: A simultaneous split‐face trial
Authors: Kim Hee Jung , Kim Tae Gyun , Kwon Yeon Sook , Park Jin Mo , Lee Ju Hee
Published: July 2009

Background and Objective

Acne scarring is a common complication of acne but no effective single treatment modality has been developed. To compare the efficacy of 1,550 nm Er:Glass fractional laser and chemical reconstruction of skin scar (CROSS) method in the treatment of acne scars.

Study Design/Materials and Methods

A split‐face trial was conducted in 20 patients (10 rolling, 10 icepick types) with acne scars. One side was treated with the 1,550 nm Er:Glass fractional laser three times with a 6‐week interval. And the other side was treated with CROSS method two times every 12 weeks.

Results

Significant improvement was observed in both sides of the face. In rolling type, the objective and subjective improvement rates were significantly higher in the sides treated with laser than CROSS method. However, in icepick type, there were no statistically significant differences between the two treatment sides. In the laser sides, grades of pain were significantly higher than that of treated with CROSS method. However, downtimes and lasting days of erythema were significantly longer in the sides treated with CROSS method.

Conclusion

A 1,550 nm Er:Glass fractional laser and CROSS method are both well‐tolerated and effective treatment options in the acne scars. However, there was a relatively small difference between the two treatment modalities. Therefore, dermatologists should consider the acne scar type to select the treatment options. Lasers Surg. Med. 41:545–549, 2009. © 2009 Wiley‐Liss, Inc.
Laser induced explosive vapor and cavitation resulting in effective irrigation of the root canal. Part 2: Evaluation of the efficacy
Authors: De Moor Roeland Jozef Gentil , Blanken Jan , Meire Maarten , Verdaasdonk Rudolf
Published: July 2009

Background and Objectives

Limited information exists regarding the efficacy of laser activated irrigation (LAI) on removal of root canal debris. This study compares the efficacy of LAI for removal of debris in root canals as compared to conventional irrigation (CI) and passive ultrasonic irrigation (PUI).

Materials and Methods

A splitted tooth model was constructed with straight roots prepared to a 0.06 taper and an apical diameter of ISO 40. A vertical groove was cut in the canal wall at 2–6 mm to the end of the canal in one halve of the root canal wall and filled with dentinal debris. In group 1 root canals were irrigated with 2.5% NaOCl by hand (20 seconds) with the needle 1 mm short from the apical stop, in group 2 NaOCl was ultrasonically activated (20 seconds) with an Irrisafe tip 1 mm short from the apical stop, and in group 3 NaOCl was activated with an Er,Cr:YSGG laser (Z2 Endolase tip −200 µm fiber, four times for 5 seconds, 75 mJ, 20 Hz, stationary at 5 mm from the apical stop). The remaining quantity of dentin debris in the groove was evaluated using a scoring system.

Results

LAI resulted in significantly less debris than PUI (P<0.005) and CI (P<0.0005). PUI also showed significantly less debris than CI (P<0.005).

Conclusion

Under the conditions of this study LAI is statistically significantly more effective in removing artificially placed dentin debris in a root canal as PUI and CI. Lasers Surg. Med. 41:520–523, 2009. © 2009 Wiley‐Liss, Inc.
Assessment of the optical radiation hazard from a home‐use intense pulsed light (IPL) source
Authors: Eadie Ewan , Miller Paul , Goodman Teresa , Moseley Harry
Published: July 2009

Background and Objectives

Intense pulsed light (IPL) systems have evolved and crossed over from the clinic to the home. Studies have shown home‐use IPLs to be clinically effective but there has been no published data on ocular safety. It was our aim to measure the spectral and temporal optical radiation output from a home‐use IPL and assess the ocular hazard.

Materials and Methods

The iPulse Personal is a new home‐use IPL hair reduction system. We measured its optical radiation spectral output using a calibrated diode array spectrometer that was traceable to national standards. Pulse duration was determined by measurement with a fast photodiode. The results from these measurements were used to assess the optical radiation hazard to the human eye. Retinal thermal hazard (RTH), blue light hazard (BLH), and infrared radiation hazard to the cornea and lens were assessed in accordance with IEC TR 60825‐9 and the International Committee on Non‐Ionizing Radiation Protection (ICNIRP) Guidelines on Limits of Exposure to Broad‐band Incoherent Optical Radiation, as there are no specific international IPL standards.

Results

Neither the BLH radiance dose nor the infrared radiation hazard to the cornea and lens irradiance exceeded the exposure limit values (ELVs) set by the ICNIRP. The RTH radiance, however, was exceeded at a fluence of 11 J cm−2 and pulse duration of 16 milliseconds. Following these results the settings on the IPL were adjusted and the RTH was no longer exceeded at a new fluence of 10 J cm−2 and pulse duration of 26 milliseconds.

Conclusions

The home‐use device that we assessed does not present an optical hazard according to currently available international standards. Lasers Surg. Med. 41:534–539, 2009. © 2009 Wiley‐Liss, Inc.
Metabonomic investigations into the global biochemical sequelae of exposure to the pancreatic toxin 1‐cyano‐2‐hydroxy‐3‐butene in the rat
Authors: Bohus Eszter , Rácz Ákos , Noszál Béla , Coen Muireann , Beckonert Olaf , Keun Hector C. , Ebbels Timothy M. D. , Cantor Glenn H. , Wijsman John A. , Holmes Elaine , Lindon John C. , Nicholson Jeremy K.
Published: July 2009

The time‐related metabolic effects of 1‐cyano‐2‐hydroxy‐3‐butene (CHB, crambene), a naturally occurring nitrile and experimental model toxin causing exocrine pancreatitis, have been investigated in rats using high‐resolution NMR spectroscopy of urine and serum in combination with pattern recognition analysis. Rats were administered CHB subcutaneously in two doses, 15 mg/kg dose (n = 10) and 150 mg/kg (n = 10), and conventional histopathology and clinical chemistry assessments were performed. Urine samples were collected at − 16 and 0, 8, 24, 48, 72, 96, 120, 144 and 168 h postdosing and serum samples were collected at 48 and 168 h postdosing; these were analyzed using a range of 1D and 2D NMR spectroscopic methods. The metabolic profile perturbations seen throughout the time‐course of the study are described, and the application of the spectral correlation technique Statistical TOtal Correlation SpectroscopY (STOCSY) to detect both structural and novel toxicological connectivities between xenobiotic and endogenous metabolite signals is illustrated for the first time. As a result, it is suggested that the STOCSY approach may be of wider application in the identification of toxic versus nontoxic metabolites in drug metabolism studies. Copyright © 2009 John Wiley & Sons, Ltd.
Eigenvalue bounds for some classes of P‐matrices
Authors: Peña J. M.
Published: July 2009

Eigenvalue bounds are provided. It is proved that the minimal eigenvalue of a Z‐matrix strictly diagonally dominant with positive diagonals lies between the minimal and the maximal row sums. A similar upper bound does not hold for the minimal eigenvalue of a matrix strictly diagonally dominant with positive diagonals but with off‐diagonal entries with arbitrary sign. Other new bounds for nonsingular M‐matrices and totally nonnegative matrices are obtained. Copyright © 2009 John Wiley & Sons, Ltd.
Rapid knowledge: ‘Bridging research and policy’ at the Overseas Development Institute
Authors: Stone Diane
Published: July 2009

Numerous organizations advocate the need to ‘bridge research and policy’. Philanthropic foundations, national social science funding regimes and international organizations have sought to improve knowledge utilization. Similarly, research consumers such as NGOs and government departments complain of research irrelevance for policy purposes. The concern of this article is with ‘evidence informed policy’ within the field of international development in which the Overseas Development Institute (ODI), a London‐based think tank, forms the case study. Most think tanks are driven by the need to influence immediate political agendas but ODI has also developed organizational strategies of policy entrepreneurship that extend to longer term influence through creating human capital, building networks and engaging policy communities. Copyright © 2009 John Wiley & Sons, Ltd.
Using action research to develop a model of patient‐centred day care
Authors: Bothe Janine , Donoghue Judith
Published: July 2009

The objective of this study was to develop a model of care that was patient centred, safe and effective for day surgery patients undergoing complex surgical procedures. The research team used Habermas' (1987) theory of communicative action to guide a process that enabled honest communication and equality within the group necessary to obtain sustained technical and emancipatory change. An action research method was used to make changes based on the best available evidence. Three criteria were used as a basis for change – the effectiveness of care, patient safety and patient‐centeredness. Prior to the study, no patient had had complex day surgery at this hospital. During the study, 55 patients underwent complex day surgery in an effective, safe and patient‐centred way. Improved communication and increased confidence enabled the research team to achieve significant technical outcomes. The group matured into autonomous, accountable and engaged clinicians that demonstrated emancipation. Copyright © 2009 John Wiley & Sons, Ltd.
Optimal analysis of complex protein mass spectra
Authors: Dijkstra Martijn , Jansen Ritsert C.
Published: July 2009

Due to physical and chemical phenomena, a simple sample can give rise to a complex mass spectrum with many more peaks than the number of molecular species present in the sample. We link peaks within and between different spectra, and come up with an advanced analysis approach to produce reliable estimates of the molecule masses and abundances. By linking peaks, we can locate multiple‐charge peaks at the correct position in the spectrum, we can deconvolute complex regions with many overlapping peaks by including information from related regions with lower complexity and higher resolution, and we reduce the total number of observed peaks in a spectrum to a much smaller number of underlying molecular species. In this paper we properly model 29 952 peaks in 64 spectra, using only 39 location parameters and one shape parameter. This major reduction from many different molecules to a limited set of molecular species reduces the statistical test multiplicity for biomarker discovery and therefore we imply that the reduction should eventually increase the biomarker discovery power significantly, too.
Proteomic analysis of β‐catenin activation in mouse liver by DIGE analysis identifies glucose metabolism as a new target of the Wnt pathway
Authors: Chafey Philippe , Finzi Laetitia , Boisgard Raphael , Caüzac Michèle , Clary Guillem , Broussard Cédric , Pégorier Jean‐Paul , Guillonneau François , Mayeux Patrick , Camoin Luc , Tavitian Bertrand , Colnot Sabine , Perret Christine
Published: July 2009

The Wnt/β‐catenin signaling pathway has been increasingly implicated in liver development and physiology. Aberrant activation of this pathway is one of the major genetic events observed during the process of human HCC development. To gain insight into the mechanism underlying β‐catenin action in the liver, we conducted a quantitative differential proteomic analysis using 2‐D DIGE combined with MS, in mice with liver‐specific deletion of Apc resulting in acute activation of β‐catenin signaling (ApcKOliv mice). We identified 94 protein spots showing differential expression between mutant ApcKOliv and control mice, corresponding to 56 individual proteins. Most of the proteins identified were associated with metabolic pathways, such as ammonia and glucose metabolism. Our analysis showed an increase in lactate dehydrogenase activity together with a downregulation of two mitochondrial ATPase subunits (ATP5a1 and ATP5b). These observations indicate that β‐catenin signaling may induce a shift in the glucose metabolism from oxidative phosphorylation to glycolysis, known as the “Warburg effect”. Imaging with 18F‐fluoro‐2‐deoxy‐D‐glucose‐positron emission tomography suggests that the specific metabolic reprogramming induced by β‐catenin in the liver does not imply the first step of glycolysis. This observation may explain why some HCCs are difficult to assess by fluoro‐2‐deoxy‐D‐glucose‐positron emission tomography imaging.
The plasma membrane proteome of germinating barley embryos
Authors: Hynek Radovan , Svensson Birte , Jensen Ole Nørregaard , Barkholt Vibeke , Finnie Christine
Published: July 2009

Cereal seed germination involves a complex coordination between different seed tissues. Plasma membranes must play crucial roles in coordination and execution of germination; however, very little is known about seed plasma membrane proteomes due to limited tissue amounts combined with amphiphilicity and low abundance of membrane proteins. A fraction enriched in plasma membranes was prepared from embryos dissected from 18 h germinated barley seeds using aqueous two‐phase partitioning. Reversed‐phase chromatography on C4 resin performed in micro‐spin columns with stepwise elution by 2‐propanol was used to reduce soluble protein contamination and enrich for hydrophobic proteins. Sixty‐one proteins in 14 SDS‐PAGE bands were identified by LC‐MS/MS and database searches. The identifications provide new insight into the plasma membrane functions in seed germination.
OMSSA Parser: An open‐source library to parse and extract data from OMSSA MS/MS search results
Authors: Barsnes Harald , Huber Steffen , Sickmann Albert , Eidhammer Ingvar , Martens Lennart
Published: July 2009

Protein identification by MS is an important technique in both gel‐based and gel‐free proteome studies. The Open Mass Spectrometry Search Algorithm (OMSSA) (http://pubchem.ncbi.nlm.nih.gov/omssa) is an open‐source search engine that can be used to identify MS/MS spectra acquired in these experiments. We here present a lightweight, open‐source Java software library, OMSSA Parser (http://code.google.com/p/omssa‐parser), which parses OMSSA omx result files into easy accessible and fully functional object models. In addition, we also provide examples illustrating the usage of our library.
iTRAQ‐coupled 2‐D LC‐MS/MS analysis of protein profile associated with HBV‐modulated DNA methylation
Authors: Niu Dandan , Sui Jianjun , Zhang Jianhua , Feng Huixing , Chen Wei Ning
Published: July 2009

The development of hepatocellular carcinoma (HCC) is believed to be associated with multiple risk factors, including the infection of hepatitis B virus (HBV). Based on the analysis of individual genes, evidence has indicated the association between HCC and HBV and has also been expanded to epigenetic regulation, with an involvement of HBV in the DNA methylation of the promoter of cellular target genes leading to changes in their expression. Proteomic study has been widely used to map a comprehensive protein profile, which in turn could provide a better understanding of underlying mechanisms of disease onset. In the present study, we performed a proteomic profiling by using iTRAQ‐coupled 2‐D LC/MS‐MS analysis to identify cellular genes down‐regulated in HBV‐producing HepG2.2.15 cells compared with HepG2 cells. A total of 15 proteins including S100A6 and Annexin A2 were identified by our approach. The significance of these cellular proteins as target of HBV‐mediated epigenetic regulation was supported by our validation assays, including their reactivation in cells treated with 5‐aza‐2′‐deoxycytidine (a DNA methyltransferase inhibitor) by real‐time RT‐PCR and Western blot analysis, as well as the DNA methylation status analysis by bisulfite genome sequencing. Our approach provides a comprehensive analysis of cellular target proteins to HBV‐mediated epigenetic regulation and further analysis should facilitate a better understanding of its involvement in HCC development.
Sol–gel transparent nano‐glass‐ceramics comprising rare‐earth‐doped NaYF4 nanocrystals
Authors: Santana‐Alonso A. , Yanes A. C. , Méndez‐Ramos J. , del‐Castillo J. , Rodríguez V. D.
Published: July 2009

Transparent nano‐glass‐ceramics containing rare‐earth‐doped NaYF4 nanocrystals (Eu3+ single‐doped and Yb3+–Er3+ co‐doped) have been successfully developed for the first time by thermal treatment of precursor bulk glasses obtained by sol–gel technique. X‐ray diffraction and high‐resolution transmission electron microscopy measurements reveal the precipitation of NaYF4 nanocrystals during the heat treatment and their corresponding sizes have been calculated. Luminescence measurements confirm the partition of rare‐earth ions in NaYF4 nanocrystals. In Eu3+‐doped samples, changes in the local environment of these rare‐earth ions have been investigated by site‐selective emission and excitation spectra. In Yb3+–Er3+ co‐doped samples, efficient visible up‐conversion luminescence has been obtained under infrared excitation at 980 nm. The red to green up‐conversion emission ratio can be varied as a function of temperature of heat treatment, resulting in colour tuneable up‐conversion phosphors with applications in optical integrated devices. Colour tuneability has been analysed and quantified in terms of Comission Internationale d'Eclairage standard chromaticity diagram.

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Infrared spectrum of potassium‐cationized triethylphosphate generated using tandem mass spectrometry and infrared multiple photon dissociation
Authors: Groenewold Gary S. , Leavitt Christopher M. , Dain Ryan P. , Oomens Jos , Steill Jeffrey D. , van Stipdonk Michael J.
Published: July 2009

Tandem mass spectrometry and wavelength‐selective infrared photodissociation were used to generate an infrared spectrum of gas‐phase triethylphosphate cationized by attachment of K+. Prominent absorptions were observed in the region of 900 to 1300 cm−1 that are characteristic of phosphate PO and POR stretches. The relative positions and intensities of the IR absorptions were reproduced well by density functional theory (DFT) calculations performed using the B3LYP functional and the 6‐31+G(d), 6‐311+G(d,p) and 6‐311++G(3df,2pd) basis sets. Because of good correspondence between experiment and theory for the cation, DFT was then used to generate a theoretical spectrum for neutral triethylphosphate, which in turn accurately reproduces the IR spectrum of the neat liquid when solvent effects are included in the calculations. Copyright © 2009 John Wiley & Sons, Ltd.
Can density functional theory (DFT) be used as an aid to a deeper understanding of tandem mass spectrometric fragmentation pathways?
Authors: Alex Alexander , Harvey Sophie , Parsons Teresa , Pullen Frank S. , Wright Patricia , Riley Jo‐Anne
Published: July 2009

Prediction of tandem mass spectrometric (MS/MS) fragmentation for non‐peptidic molecules based on structure is of immense interest to the mass spectrometrist. If a reliable approach to MS/MS prediction could be achieved its impact within the pharmaceutical industry could be immense. Many publications have stressed that the fragmentation of a molecular ion or protonated molecule is a complex process that depends on many parameters, making prediction difficult. Commercial prediction software relies on a collection of general heuristic rules of fragmentation, which involve cleaving every bond in the structure to produce a list of ‘expected’ masses which can be compared with the experimental data. These approaches do not take into account the thermodynamic or molecular orbital effects that impact on the molecule at the point of protonation which could influence the potential sites of bond cleavage based on the structural motif. A series of compounds have been studied by examining the experimentally derived high‐resolution MS/MS data and comparing it with the in silico modelling of the neutral and protonated structures. The effect that protonation at specific sites can have on the bond lengths has also been determined. We have calculated the thermodynamically most stable protonated species and have observed how that information can help predict the cleavage site for that ion. The data have shown that this use of in silico techniques could be a possible way to predict MS/MS spectra. Copyright © 2009 John Wiley & Sons, Ltd.
An integrated serum proteomic approach capable of monitoring the low molecular weight proteome with sequencing of intermediate to large peptides
Authors: Merrell Karen , Thulin Craig D. , Esplin M. Sean , Graves Steven W.
Published: July 2009

The low‐abundance, low molecular weight serum proteome has high potential for the discovery of new biomarkers using mass spectrometry (MS). Because the serum proteome is large and complex, defining relative quantitative differences for a molecular species between comparison groups requires an approach with robust separation capability, high sensitivity, as well as high mass resolution. Capillary liquid chromatography (cLC)/MS provides both the necessary separation technique and the sensitivity to observe many low‐abundance peptides. Subsequent identification of potential serum peptide biomarkers observed in the cLC/MS step can in principle be accomplished by in series cLC/MS/MS without further sample preparation or additional instrumentation. In this report a novel cLC/MS/MS method for peptide sequencing is described that surpasses previously reported size limits for amino acid sequencing accomplished by collisional fragmentation using a tandem time‐of‐flight MS instrument. As a demonstration of the approach, two low‐abundance peptides with masses of ∼4000–5000 Da were selected for MS/MS sequencing. The multi‐channel analyzer (MCA) was used in a novel way that allowed for summation of 120 fragmentation spectra for each of several customized collision energies, providing more thorough fragmentation coverage of each peptide with improved signal to noise. The peak list from this composite analysis was submitted to Mascot for identification. The two index peptides, 4279 Da and 5061 Da, were successfully identified. The peptides were a 39 amino acid immunoglobulin G heavy chain variable region fragment and a 47 amino acid fibrin alpha isoform C‐terminal fragment. The method described here provides the ability both to survey thousands of serum molecules and to couple that with markedly enhanced cLC/MS/MS peptide sequencing capabilities, providing a promising technique for serum biomarker discovery. Copyright © 2009 John Wiley & Sons, Ltd.
Identification of active compounds and their metabolites by high‐performance liquid chromatography/electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry from Xiao‐xu‐ming decoction (XXMD)
Authors: Wang Yilin , Ding Chunguang , Du Kehe , Xiao Yao , Wu Caisheng , Zhang Jinlan , Qin Hailin , Du Guanhua
Published: July 2009

Xiao‐xu‐ming decoction (XXMD) prescription is a traditional Chinese prescription that has been widely used to treat theoplegia and the sequela of theoplegia. Modern pharmacological research has also indicated that the active fraction from XXMD is able to treat cardiovascular diseases and Alzheimer's disease. In the study reported here, high‐performance liquid chromatography coupled with Fourier transform ion cyclotron resonance mass spectrometry (HPLC/FTICR‐MS) was developed to identify active compounds and their metabolites after oral administration of active fraction from Xiao‐xu‐ming decoction to rats, using parent mass list triggered data‐dependent multiple‐stage mass analysis at a resolving power of 100 000 in the external calibration mode. The mass accuracies obtained for full‐scan MS were within 2 ppm in most cases. Fifteen constituents were identified in the active fraction from XXMD and the biological samples of rats. The fragmentation behaviors of these constituents were summarized which would be helpful for structural characterization. The profiles of the constituents in the active fraction and biological samples of rats were obtained which provided us with much information for a better understanding of the chemical basis of the pharmacologic actions of XXMD. Copyright © 2009 John Wiley & Sons, Ltd.
Mass spectrometry study of PRL‐3 phosphatase inactivation by disulfide bond formation and cysteine into glycine conversion
Authors: Orsatti Laura , Innocenti Federica , Surdo Paola Lo , Talamo Fabio , Barbato Gaetano
Published: July 2009

The Phosphatase of Regenerating Liver‐3 (PRL‐3) is a cysteine‐based phosphatase (CBP) that is highly over‐expressed in liver metastasis in colorectal cancer and suspected to be involved in the progression from tumor to metastasis. During substrate‐specificity studies based on the screening of PRL‐3 phosphatase activity on several phosphorylated synthetic peptides, we observed a decrease in activity depending on sample aging and storage conditions. By liquid chromatography combined with selective alkylation and mass spectrometry, we found two main PRL‐3 inactivation pathways: a disulfide bond formation between the catalytic C104 and C49, blocking the enzyme in an inactive oxidized form, or the conversion of the catalytic C104 into glycine. We also found that the disulfide formation and the cysteine into glycine conversion are catalyzed by cations present in the sample after protein purification through a nickel column. By adding a cation chelator such as EDTA and de‐oxygenating the sample with argon, PRL‐3 phosphatase activity was preserved. These findings suggest that PRL‐3, like other CBPs, is sensitive to inactivation by catalytic cysteine oxidation and this has implications for future studies of its activity and specificity. Copyright © 2009 John Wiley & Sons, Ltd.
Mass spectrometric analysis of carbohydrates labeled with a biotinylated tag
Authors: Kapková Petra
Published: July 2009

A derivatization method for mass spectrometric analysis of oligosaccharides is presented. Small saccharides, complex, high‐mannose‐type oligosaccharides and oligosaccharides released from hen ovalbumin were converted into their biotin derivatives by incubating them with biotinamidocaproyl hydrazide (BACH). Improved sensitivity of mass spectrometric analysis of labeled glycans in comparison with their natural counterparts was achieved after derivatization. The labeling reagent contains a biotin handle at one end and a hydrazide group at the other. Hence, the key feature of biotinylated sugars is that in addition to their usefulness in functional studies (e.g. analysis of the interaction between lectins and biotin‐derivatized oligosaccharides) they might be utilized also for structural analysis of oligosaccharides. Mass spectrometric studies were performed by matrix‐assisted laser desorption/ionization time‐of‐flight and electrospray ionization mass spectrometry. Copyright © 2009 John Wiley & Sons, Ltd.
Structure and end‐group analysis of complex hexanediol‐neopentylglycol‐adipic acid copolyesters by matrix‐assisted laser desorption/ionization collision‐induced dissociation tandem mass spectrometry
Authors: Weidner Steffen M. , Falkenhagen Jana , Knop Karin , Thünemann Andreas
Published: July 2009

Sequences and end groups of complex copolyesters were determined by fragmentation analysis by means of matrix‐assisted laser desorption/ionization collision‐induced dissociation tandem mass spectrometry (MALDI CID MS/MS). The complexity of the crude copolyester mixture was reduced by a chromatographic separation followed by a MALDI time‐of‐flight (TOF) investigation of fractions. Due to overlapping compositional and end‐group information a clear assignment of end groups was very difficult. However, the fragmentation of suitable precursor ions resulted in typical fragment ion patterns and, therefore, enabled a fast and unambiguous determination of the end groups and composition of this important class of polymers. Copyright © 2009 John Wiley & Sons, Ltd.