bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying image distortion of orthopedic materials in magnetic resonance imaging
Authors: Koff Matthew F. , Shah Parina , Koch Kevin M. , Potter Hollis G. 
Published: January 2013

Purpose:To determine the magnitude of image distortion between two‐dimensional (2D) fast‐spin‐echo (FSE) images and 3D‐MAVRIC by using a phantom with samples of common materials used in total joint arthroplasty.Materials and Methods:A phantom was constructed to hold samples of 316 stainless steel, cobalt chrome, titanium, and ultra‐high molecular weight polyethylene (UHMWPE), and to permit tracking of points between 2D‐FSE and 3D‐MAVRIC sequences. Imaging was performed with a 1.5 Tesla scanner. The displacement of points between the two acquisitions in regions of varying distance from the material sample was calculated. Measured displacements were compared with theoretical displacements calculated from MAVRIC frequency field maps, and to the known phantom dimensions.Results:Bulk in‐plane artifacts increased from the control scan (0.20 ± 0.07 mm), to UHMWPE (0.23 ± 0.04 mm), titanium (0.40 ± 0.34 mm), cobalt chrome (1.35 ± 0.57 mm), and to stainless steel (2.56 ± 0.62 mm). A similar pattern was found for bulk through‐plane measurements: control scan (0.36 ± 0.08 mm), UHMWPE (0.38 ± 0.05 mm), titanium (1.11 ± 0.51 mm), and cobalt chrome (2.08 ± 1.83 mm). Large distortions were observed near the metal samples, and reduced with distance from the samples. The differences between the measured displacement and theoretical displacement was typically less than one pixel or one slice dimension for in‐plane and through‐plane measurements, respectively. The difference between the 3D‐MAVRIC and known dimensions of the phantom was less than two pixels, whereas the results for the 2D‐FSE were less consistent.Conclusion:Distortion was reduced in 3D‐MAVRIC scans. Measured distortions corresponded well to theoretical calculations from frequency field map data. J. Magn. Reson. Imaging 2013;38:610–618. © 2013 Wiley Periodicals, Inc.
Comparison of dixon and T1‐weighted MR methods to assess the degree of fat infiltration in duchenne muscular dystrophy patients
Authors: Wokke Beatrijs H. , Bos Clemens , Reijnierse Monique , van Rijswijk Carla S. , Eggers Holger , Webb Andrew , Verschuuren Jan J. , Kan Hermien E. 
Published: January 2013

Purpose:To compare different lipid multipeak spectral models to the single‐peak model in Dixon‐based fat‐water separation and to evaluate differences between visually scored magnetic resonance (MR) images and quantitatively assessed fat fractions in muscle of Duchenne muscular dystrophy patients.Materials and Methods:T1‐weighted and 3‐point Dixon imaging of the upper and lower leg was performed in 13 Duchenne patients and six healthy controls. Three‐, four‐, and five‐peak lipid spectrum models were compared to a single‐peak model and to each other. T1‐weighted images were visually scored by two radiologists and quantitative fat fractions were obtained from Dixon images.Results:Differences between the multipeak spectral models were minimal. The three‐peak model was used for subsequent comparisons. Although there was high correlation between quantitative and visual scores, visual scores were consistently higher than quantitative values of the same muscles.Conclusion:There are minor differences between the various lipid spectral models in terms of quantifying fat fraction in a large number of skeletal muscles in the legs of Duchenne patients and healthy controls. Quantitative 3‐point Dixon MRI is more precise and reliable than visual radiological methods for evaluation of fat fractions for potential longitudinal follow‐up or therapy evaluation of Duchenne patients. J. Magn. Reson. Imaging 2013;38:619–624. © 2013 Wiley Periodicals, Inc.
Estimating abundance and population trends when detection is low and highly variable: A comparison of three methods for the Hermann's tortoise
Authors: Couturier Thibaut , Cheylan Marc , Bertolero Albert , Astruc Guillelme , Besnard Aurelien 
Published: January 2013

AbstractAssessing population trends is a basic prerequisite to carrying out adequate conservation strategies. Selecting an appropriate method to monitor animal populations can be challenging, particularly for low‐detection species such as reptiles. This study compares 3 detection‐corrected abundance methods (capture–recapture, distance sampling, and N‐mixture) used to assess population size of the threatened Hermann's tortoise. We used a single dataset of 432 adult tortoise observations collected at 118 sampling sites in the Plaine des Maures, southeastern France. We also used a dataset of 520 tortoise observations based on radiotelemetry data collected from 10 adult females to estimate and model the availability (g0) needed for distance sampling. We evaluated bias for N‐mixture and capture–recapture, by using simulations based on different values of detection probabilities. Finally, we conducted a power analysis to estimate the ability of the 3 methods to detect changes in Hermann's tortoise abundances. The abundance estimations we obtained using distance sampling and N‐mixture models were respectively 1.75 and 2.19 times less than those obtained using the capture–recapture method. Our results indicated thatg0was influenced by temperature variations and can differ for the same temperature on different days. Simulations showed that the N‐mixture models provide unstable estimations for species with detection probabilities <0.5, whereas capture–recapture estimations were unbiased. Power analysis showed that none of the 3 methods were precise enough to detect slow population changes. We recommend that great care should be taken when implementing monitoring designs for species with large variation in activity rates and low detection probabilities. Although N‐mixture models are easy to implement, we would not recommend using them in situations where the detection probability is very low at the risk of providing biased estimates. Among the 3 methods allowing estimation of tortoise abundances, capture–recapture should be preferred to assess population trends. © 2013 The Wildlife Society.
False negatives in thyroid cytology: Impact of large nodule size and follicular variant of papillary carcinoma
Authors: Mehanna Rania , Murphy Michael , McCarthy Julie , O'Leary Gerard , Tuthill Antoinette , Murphy Matthew S. , Sheahan Patrick 
Published: January 2013

Objectives/HypothesisFine‐needle aspiration (FNA) cytology is well established in the diagnosis of thyroid nodules. However, false‐negative rates for malignancy of 3% to 10% are reported. The purpose of the present study was to investigate the impact of nodule size and follicular variant of papillary carcinoma (FVPTC) on false‐negative FNA rates in thyroid nodules and on malignancy rates in nodules with indeterminate cytology.Study DesignRetrospective study.MethodsA total of 765 consecutive ultrasound‐guided FNAs were reviewed. Histological correlation was available in 262 cases.ResultsThe overall sensitivity of FNA for malignancy was 84%, and the false‐negative rate 9.1%. Nodules ≥3 cm were significantly more likely to ultimately be diagnosed as cancer by histology than nodules <3 cm (14% vs. 6.8%, P = .006); however, they were also significantly more likely to undergo surgery than smaller nodules (P < .0001). Among the surgical series, the false‐negative rate was 10.9% in nodules ≥3 cm and 6.1% in nodules <3 cm (P = .71). Most false negatives were due to FVPTC. FVPTC was significantly more likely to be missed by preoperative cytology than conventional or other variants of papillary carcinoma (P < .001). Among cases with indeterminate cytology, nodule size and Thy‐3f versus Thy‐3a subclassification did not have any significant impact on likelihood of malignancy.ConclusionsThe sensitivity of FNA for detection of FVPTC is reduced compared to conventional papillary carcinoma. The impact of nodule size is not significant.Level of Evidence4.
A test method to study the change in surface topography due to running‐in of a rolling contact
Authors: Jamari J. , Schipper D.J. 
Published: January 2013

ABSTRACTA method is proposed to determine the change in surface topography during running‐in of rolling contacts. Two types of experiments have been conducted in the present work to study the running‐in of the pure rolling contact situation: repeated moving and general free rolling using a high accuracy measurement setup. The results show that the surfaces run‐in with the proposed repeated moving contact method gives a fast running‐in when compared with the general free rolling contact method. The proposed repeated moving contact method appears to be a good method to study the ideal or pure rolling contact situation because wear, as present in the general free rolling contact method, is avoided. Copyright © 2013 John Wiley & Sons, Ltd.
Unusual evolution of the magnetism on oxygen in La1−χSrχCoO3
Authors: Medling Scott , Lee Y. , Zheng H. , Mitchell J. F. , Freeland J. W. , Harmon B. N. , Bridges F. 
Published: January 2013

AbstractWe present X‐ray absorption spectroscopy (XAS) and X‐ray magnetic circular dichroism (XMCD) data of La1−χSrχCoO3, for χ= 0.10‐0.30, at the O K edge and then compare the results to local density approximation (LDA) and generalized gradient approximation (GGA) calculations using a 2x2x2 supercell. Increases in the XAS and XMCD are nonlinear with χ, instead appearing correlated with the overall system magnetism, which changes from glass‐like to metallic ferromagnetism around χ=0.18. The magnetic states observed in XMCD only occur at the beginning of the pre‐edge; higher energy states show no orbital moment, suggesting two distinct types of holes exist. This is consistent with the formation of ferromagnetic clusters growing with χ and eventually overlapping for χ>0.18.Subsequent LDA and GGA calculations find a significant spin magnetic moment on O atoms (which are spinpolarized) and indicate that the doping‐induced holes are nearly equally distributed over the Co and O atoms. Calculations of the magnetization for individual O sites indicate that they are not all equivalent, but actually have different moments, depending on the proximity to Sr. This variation in the small fraction of oxygen state with angular momentum may explain in part the unusual magnetic behavior of these materials. Further, the orbitally decomposed density of states reveals that the bands from the traditional picture (localized eg and t2g states) overlap considerably and extend from ‐6 to 4 eV around E F, suggesting that the local picture is not the best for La1−χSrχCoO3 (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Assessing students' understanding of inquiry: What do prospective science teachers notice?
Authors: Talanquer Vicente , Tomanek Debra , Novodvorsky Ingrid 
Published: January 2013

AbstractThe theoretical construct of teacher noticing has allowed mathematics teacher educators to examine teacher thinking and practice by looking at the range of activities that teachers notice in the classroom. Guided by this approach to the study of teacher thinking, the central goal of this exploratory study was to identify what prospective science teachers notice when evaluating evidence of student understanding in another teacher's inquiry‐based unit. Our results are based on the qualitative analysis of 43 prospective teachers' evaluations of assessment evidence presented to them in the form of a video case and associated written artifacts. Analysis of our data revealed two major categories of elements, Task‐General and Task‐Specific, noticed by our study participants. Task‐General elements included attention to learning objectives, independent student work, and presentation issues and they often served to guide or qualify the specific inquiry skills that were evaluated. Task‐Specific elements included the noticing of students' abilities to perform different components of an investigation. In general, study participants paid attention to important general and specific aspects of student work in the context of inquiry. However, they showed preferential attention to those process skills associated with designing an investigation versus those practices related to the analysis of data and generation of conclusions. Additionally, their interpretations of assessment outcomes were largely focused on the demonstration of general science process skills; much less attention was paid to the analysis of the epistemological validity or scientific plausibility of students' ideas. Our results provide insights into the design of meaningful learning experiences for prospective teachers that elicit, challenge, and enrich their conceptions of student understanding in the context of inquiry. © 2013 Wiley Periodicals, Inc. J Res Sci Teach 50:189–208, 2013
First language attrition
Authors: Schmid Monika S. 
Published: January 2013

AbstractSpeakers who live in an L2 environment for an extended period of time often experience change in the way in which they use their L1, a process referred to as L1 attrition. This article provides an overview of language attrition phenomena at various linguistic levels. However, attrition cannot be trivially or linearly related to factors such as the frequency of use of the L1. It is argued here that attrition phenomena are not the outcome of a change to the underlying linguistic system nor of access problems due to an increase in activation thresholds, but of cross‐linguistic influence in online speech production. WIREs Cogn Sci 2013, 4:117–123. doi: 10.1002/wcs.1218This article is categorized under:

Linguistics > Language in Mind and Brain
Model‐based design of experiments for cellular processes
Authors: Chakrabarty Ankush , Buzzard Gregery T. , Rundell Ann E. 
Published: January 2013

AbstractModel‐based design of experiments (MBDOE) assists in the planning of highly effective and efficient experiments. Although the foundations of this field are well‐established, the application of these techniques to understand cellular processes is a fertile and rapidly advancing area as the community seeks to understand ever more complex cellular processes and systems. This review discusses the MBDOE paradigm along with applications and challenges within the context of cellular processes and systems. It also provides a brief tutorial on Fisher information matrix (FIM)‐based and Bayesian experiment design methods along with an overview of existing software packages and computational advances that support MBDOE application and adoption within the Systems Biology community. As cell‐based products and biologics progress into the commercial sector, it is anticipated that MBDOE will become an essential practice for design, quality control, and production. WIREs Syst Biol Med 2013, 5:181–203. doi: 10.1002/wsbm.1204This article is categorized under:

Models of Systems Properties and Processes > Cellular Models
Biological Mechanisms > Cell Signaling
Analytical and Computational Methods > Computational Methods
Effect of Preoperative Exercise on Cardiorespiratory Function and Recovery After Surgery: a Systematic Review
Authors: Lemanu Daniel P. , Singh Primal P. , MacCormick Andrew D. , Arroll Bruce , Hill Andrew G. 
Published: January 2013

AbstractBackgroundThis systematic review aims to investigate the extent to which preoperative conditioning (PREHAB) improves physiologic function and whether it correlates with improved recovery after major surgery.MethodsAn electronic database search identified randomized controlled trials (RCTs) investigating the safety and efficacy of PREHAB. The outcomes studied were changes in cardiorespiratory physiologic function, clinical outcomes (including length of hospital stay and rates of postoperative complications), and measures of changes in functional capacity (physical and psychological).ResultsEight low‐ to medium‐quality RCTs were included in the final analysis. The patients were elderly (mean age >60 years), and the exercise programs were significantly varied. Adherence to PREHAB was low. Only one study found that PREHAB led to significant improvement in physiologic function correlating with improved clinical outcomes.ConclusionThere are only limited data to suggest that PREHAB confers any measured physiologic improvement with subsequent clinical benefit. Further data are required to investigate the efficacy and safety of PREHAB in younger patients and to identify interventions that may help improve adherence to PREHAB.
Use of carbon‐13 and carbon‐14 natural abundances for stream food web studies
Authors: Ishikawa Naoto F. , Hyodo Fujio , Tayasu Ichiro 
Published: January 2013

AbstractWe review the use of stable carbon isotope ratios (δ13C) and radiocarbon natural abundances (Δ14C) for stream food web studies. The δ13C value of primary producers (e.g., periphytic algae, hereafter periphyton) in streams is controlled by isotopic fractionation during photosynthesis and variable δ13C of dissolved CO2. When periphyton δ13C differs from that of terrestrial primary producers, the relative contribution of autochthony and allochthony to stream food webs can be calculated. Moreover, the variation in periphyton δ13C can reveal how much stream consumers rely on local resources because each stream habitat (e.g., riffle vs. pool, open vs. shaded) usually has a distinctive δ13C. However, periphyton δ13C often overlaps with that of terrestrial organic matter. On the other hand, periphyton Δ14C is less variable than δ13C among habitats, and reflects the Δ14C of dissolved CO2, which could be a mixture of “aged” (Δ14C < 0 ‰) and “modern” (Δ14C > 0 ‰) carbon. This is because the Δ14C is corrected by its δ13C value for the isotopic fractionation during photosynthesis. Recent studies and our data indicate that many stream food webs are supported by “aged” carbon derived from the watershed via autochthonous production. The combined use of δ13C and Δ14C allows robust estimation of the carbon transfer pathway in a stream food web at multiple spatial scales ranging from the stream habitat level (e.g., riffle and pool) to watershed level (autochthony and allochthony). Furthermore, the Δ14C of stream food webs will expand our understanding about the time frame of carbon cycles in the watersheds.
Regulation of Toll-Like Receptors in the Choroid Plexus in the Immature Brain After Systemic Inflammatory Stimuli
Authors: Stridh Linnea , Ek C. Joakim , Wang Xiaoyang , Nilsson Holger , Mallard Carina 
Published: January 2013

Abstract
The choroid plexus is the site of the blood–cerebrospinal fluid (CSF) barrier (BCSFB) and has also been considered as a possible route for peripheral immune signals and cells to transfer to the central nervous system. Infection/inflammation stimulates innate and subsequent adaptive immune responses via Toll-like receptors (TLRs). In this study, we have investigated the mRNA expression of TLRs, cytokines, and tight junction proteins in the choroid plexus in the immature brain after systemic inflammation, as well as accumulation of immune cells into the CSF. Specific ligands for TLR-1/2, TLR-3, and TLR-4 were administered to postnatal day 8 mice and mRNA expression for the targeted genes was examined in the choroid plexus. We found that mRNA for all four TLRs was detected in the choroid plexus under control conditions. Following immune stimulation, expression of all the TLRs was upregulated by their respective ligands, except for TLR-4 mRNA, which was downregulated by Pam3CSK4 (PAM; a TLR-1/2 ligand). In addition, we investigated BCSFB regulation after TLR stimulation and found that TLR-1/2 and TLR-4 activation was associated with changes in mRNA expression of the tight junction protein occludin in the choroid plexus. PAM induced choroid plexus transcription of TNF-α and resulted in the most dramatic increase in numbers of white blood cells in the CSF. The data suggest a possible mechanism whereby systemic inflammation stimulates TLRs in the choroid plexus, which may lead to disturbances in choroid plexus barrier function, as well as infiltration of immune cells through the plexus.
iBIG: An Integrative Network Tool for Supporting Human Disease Mechanism Studies
Authors: Sun Jiya , Pan Yuyun , Feng Xuemei , Zhang Huijuan , Duan Yong , Lei Hongxing 
Published: January 2013

Abstract
Understanding the mechanism of complex human diseases is a major scientific challenge. Towards this end, we developed a web-based network tool named iBIG (stands for integrative BIoloGy), which incorporates a variety of information on gene interaction and regulation. The generated network can be annotated with various types of information and visualized directly online. In addition to the gene networks based on physical and pathway interactions, networks at a functional level can also be constructed. Furthermore, a supplementary R package is provided to process microarray data and generate a list of important genes to be used as input for iBIG. To demonstrate its usefulness, we collected 54 microarrays on common human diseases including cancer, neurological disorders, infectious diseases and other common diseases. We processed the microarray data with our R package and constructed a network of functional modules perturbed in common human diseases. Networks at the functional level in combination with gene networks may provide new insight into the mechanism of human diseases. iBIG is freely available at http://lei.big.ac.cn/ibig.
Anti-Colonialism and Social Science: Georges Balandier, Madeira Keita, and “the Colonial Situation” in French Africa
Authors: Mann Gregory 
Published: January 2013

AbstractTwo young men met on a quay at the port in Conakry, Guinea in 1946. One, waiting dockside, was Mamadou Madeira Keita, a low-level civil servant and archivist. Years later, when he was a political prisoner in the Malian Sahara, some would argue that he was “the first francophone African ethnographer.” The other, descending the gangplank, was the Frenchman Keita had come to meet. Georges Balandier was unknown then, but would soon become a leading figure in the fields of sociology and anthropology. The encounter between Keita and Balandier was foundational for both men. Conakry incubated a canonical intervention—Balandier's 1951 article “La Situation Coloniale”—that some attribute an ancestral role in a particular francophone tradition of postcolonial thought. Conakry, and Guinea at large, was also the crucible in which a powerful anti-colonial politics were forged by Madeira Keita and his allies. In this particular corner of West Africa, anti-colonial politics and an emergent, politically engaged social science conditioned each other, like the two strands of a double helix, each a necessary yet ultimately contingent element of the other's structure. Though these links did not last long, they had important effects. This article, by emphasizing the contingencies of the two men's intertwined biographies, seeks to carry out Balandier's dictate to emphasize the “concrete” nature of this particular situation in order to understand how and why anti-colonial politics and an innovative sociology converged and ultimately diverged.