bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combined functions of two RRMs in Dead‐end1 mimic helicase activity to promote nanos1 translation in the germline
Authors: Aguero Tristan , Jin Zhigang , Owens Dawn , Malhotra Arun , Newman Karen , Yang Jing , King Mary Lou 
Published: September 2018

Dead‐end1 (Dnd1) expression is restricted to the vertebrate germline where it is believed to activate translation of messenger RNAs (mRNAs) required to protect and promote that unique lineage. Nanos1 is one such germline mRNA whose translation is blocked by a secondary mRNA structure within the open reading frame (ORF). Dnd1 contains a canonical RNA recognition motif (RRM1) in its N‐terminus but also contains a less conserved RRM2. Here we provide a mechanistic picture of the
nanos1 mRNA–Dnd1 interaction in the
Xenopus germline. We show that RRM1, but not RRM2, is required for binding
nanos1. Similar to the zebrafish homolog,
Xenopus Dnd1 possesses ATPase activity. Surprisingly, this activity appears to be within the RRM2, different from the C‐terminal region where it is found in zebrafish. More importantly, we show that RRM2 is required for
nanos1 translation and germline survival. Further, Dnd1 functions as a homodimer and binds
nanos1 mRNA just downstream of the secondary structure required for
nanos1 repression. We propose a model in which the RRM1 is required to bind
nanos1 mRNA while the RRM2 is required to promote translation through the action of ATPase. Dnd1 appears to use RRMs to mimic the function of helicases.
Dual‐step iterative temperature estimation method for accurate and precise fat‐referenced PRFS temperature imaging
Authors: Cheng Chuanli , Zou Chao , Wan Qian , Qiao Yangzi , Pan Min , Tie Changjun , Liang Dong , Zheng Hairong , Liu Xin 
Published: September 2018

PurposeThe aim of this study was to propose dual‐step iterative temperature estimation (DITE) of a fat‐referenced proton resonance frequency shift (PRFS) method to improve both the accuracy and precision of temperature estimations in fat‐containing tissues.MethodsA fat‐water signal model with multiple fat peaks was used to simultaneously estimate the temperature, fat/water intensity and , and field offset. In DITE, model fitting was implemented with alternating 2‐step minimizations. The estimated temperature map was smoothed between the 2‐step minimizations, which is considered to be the most important step for improving the temperature precision. The performance of DITE was evaluated with a Monte Carlo simulation, fat/water phantoms, and ex vivo brown adipose tissue experiments and then compared with the performance of previous fat‐referenced proton resonance frequency shift methods.ResultsIn fat/water phantom experiment with a smooth temperature profile, the temperatures estimated by DITE are consistent with the thermometer results and present a better accuracy and precision than those of previous fat‐referenced proton resonance frequency shift methods. In the brown adipose tissue heating experiment, the average mean error, SD, and RMS error were −0.08ºC, 0.46ºC, and 0.56ºC, respectively, over all of the measurements within the region of interest.ConclusionOur proposed DITE method improves both the accuracy and precision of temperature measurements in tissues with fat fractions between 20% and 80% under smooth distribution of the temperature profile and represents a simple fat‐referenced thermometry method.
Mapping electrical properties heterogeneity of tumor using boundary informed electrical properties tomography (BIEPT) at 7T
Authors: Wang Yicun , Shao Qi , Van de Moortele Pierre‐Francois , Racila Emilian , Liu Jiaen , Bischof John , He Bin 
Published: September 2018

PurposesTo develop and evaluate a boundary informed electrical properties tomography (BIEPT) technique for high‐resolution imaging of tumor electrical properties (EPs) heterogeneity on a rodent tumor xenograft model.MethodsTumor EP distributions were inferred from a reference area external to the tumor, as well as internal EP spatial variations derived from a plurality of relative transmit B1 measurements at 7T. Edge sparsity constraint was enforced to enhance numerical stability. Phantom experiments were performed to determine the imaging accuracy and sensitivity for structures of various EP values, as well as geometrical sizes down to 1.5 mm. Numerical simulation of a realistic rodent model was used to quantify the algorithm performance in the presence of noise. Eleven athymic rats with human breast cancer xenograft were imaged in vivo, and representative pathological samples were acquired for comparison.ResultsReconstructed EPs of the phantoms correspond well to the ground truth acquired from dielectric probe measurements, with the smallest structure reliably detectable being 3 mm. EPs heterogeneity inside a tumor is successfully retrieved in both simulated and experimental cases. In vivo tumor imaging results demonstrate similar local features and spatial patterns to anatomical MRI and pathological slides. The imaged conductivity of necrotic tissue is higher than that of viable tissues, which agrees with our expectation.ConclusionBIEPT enables robust detection of tumor EPs heterogeneity with high accuracy and sensitivity to small structures. The retrieved quantitative EPs reflect tumor pathological features (e.g., necrosis). These results provide strong rationale to further expand BIEPT studies toward pathological conditions where EPs may yield valuable, non‐invasive biomarkers.
Optimization of the spatial modulation function of vessel‐encoded pseudo‐continuous arterial spin labeling and its application to dynamic angiography
Authors: Suzuki Yuriko , van Osch Matthias J. P. , Fujima Noriyuki , Okell Thomas W. 
Published: September 2018

Purpose:In vessel‐encoded pseudo‐continuous arterial spin labeling (ve‐pCASL), vessel‐selective labeling is achieved by modulation of the inversion efficiency across space. However, the spatial transition between the labeling and control conditions is rather gradual, which can cause partial labeling of vessels, reducing SNR‐efficiency and necessitating complex postprocessing to decode the vessel‐selective signals. The purpose of this study is to optimize the pCASL labeling parameters to obtain a sharper spatial inversion profile of the labeling and thereby minimizing the risk of partial labeling of untargeted arteries.Methods: Bloch simulations were performed to investigate how the inversion profile was influenced by the pCASL labeling parameters: the maximum (Gmax) and mean (Gmean) labeling gradient were varied for ve‐pCASL with unipolar and bipolar gradients. The findings in the simulation study were subsequently confirmed in an in vivo volunteer study. Moreover, conventional and optimized settings were compared for 4D‐MRA using four‐cycle Hadamard ve‐pCASL; the visualization of arteries and the presence of the partial labeling were assessed by an expert observer.Results: When using unipolar gradient, lower Gmean resulted in a steeper spatial transition, whereas the width of the control region was broader for higher Gmax. The in vivo study confirmed these findings. When using bipolar gradients, the control region was always very narrow. Qualitative comparison of the 4D‐MRA demonstrated lower occurrence of partial labeling when using the optimized gradient parameters.Conclusion: The shape of the ve‐pCASL inversion profile can be optimized by changing Gmean and Gmax to reduce partial labeling of untargeted arteries.
Shutter‐speed dynamic contrast‐enhanced MRI: Is it fit for purpose?
Authors: Buckley David L. 
Published: September 2018

PurposeTo test the ability of shutter‐speed dynamic contrast‐enhanced (DCE) MRI to estimate water exchange (WX) using simulations and assess its performance in clinical case studies of malignant and benign breast tumors.MethodsData were simulated using a 1‐compartment tracer kinetic (TK) model combined with a 2‐pool WX model (2PX) and with a 2‐compartment TK model. Typical DCE‐MRI acquisition parameters were used with both WX‐sensitive (8°) and ‐insensitive (25°) flip angles. Clinical data were obtained from patients with malignant and benign breast tumors. Data were fitted using a 2‐compartment TK model and a 1‐compartment TK model combined with 4 WX models: fast exchange limit (FXL), no exchange, 2PX, and shutter‐speed.ResultsFits to the 1‐compartment simulated data were excellent, but estimates of WX obtained using the 2PX and shutter‐speed models were poor. One‐compartment TK model fits to the clinical malignant tumor data were bad, except for the shutter‐speed model. However, that overestimated TK parameters compared to the best‐fit 2‐compartment TK model, which predicted a significant blood volume and leaky capillaries (1 tracer compartment is insufficient, 2 are necessary). All models produced excellent fits to the clinical benign tumor data with little variation between parameter estimates (1 tracer compartment is sufficient).ConclusionThe 2PX and shutter‐speed models were unable to estimate WX from the DCE‐MRI data. A good fit to malignant tumor data using the shutter‐speed model was not explained by WX, but the choice of an inappropriate TK model leading to distorted parameter estimates.
T2 relaxation time bias in gagCEST at 3T and 7T: comparison of saturation schemes
Authors: Peterson Pernilla , Olsson Emma , Svensson Jonas 
Published: September 2018

PurposeTo characterize the effects of water T2 relaxation time in the glycosaminoglycan chemical exchange saturation transfer method (gagCEST) and compare them between 3T and 7T as well as between various saturation schemes.MethodsSimulations and a phantom experiment were conducted at 3T and 7T in a range of water T2 values and GAG concentrations using various saturation schemes. For both simulations and MRI measurements, unsaturated signal as well as the saturated Z‐spectrum were generated, and the magnetization transfer ratio asymmetry at 1 parts per million was used as a measure of the gagCEST effect size.ResultsThe simulations and phantom experiment results showed a clear GAG concentration and T2 dependence of the gagCEST effect size. Whereas the gagCEST effect size was much larger at 7T, the impact of the T2 bias was more pronounced at 3T. The saturation train length, duty cycle, and average B1 all had clear impact on both the gagCEST effect size and T2 bias.ConclusionThe water T2 relaxation is important to consider in gagCEST, especially at 3T. The T2 differences can introduce a pronounced bias, which may obscure the gagCEST effect when using low duty cycles and long saturation trains.
Targeted partial reconstruction for real‐time fMRI with arbitrary trajectories
Authors: Riemenschneider Bruno , LeVan Pierre , Hennig Jürgen 
Published: September 2018

AbstractPurposeA partial image reconstruction formalism is introduced for the targeted extraction of real‐time feedback from arbitrary trajectories when full image reconstruction in real time is computationally too demanding.MethodsExplicit calculation and storage of linear combinations of lines of the reconstruction matrix by an incomplete basis change in spatial coordinates lead to translation of the expensive full reconstruction from a frame‐wise application to a region of interest (ROI)‐wise application. This step is independent from signal data and can be executed before the experiment. Subsequently, the results of the sum over fully reconstructed voxels can be evaluated directly. Data from a high‐speed fMRI acquisition was used to investigate the targeted partial reconstruction of a functional ROI atlas, incorporating an intravolume dephasing correction. The same data and ROIs were used for a comparison of the time series obtained with those obtained from already existing methods for compartment‐wise reconstruction. To examine real‐time feasibility, the reconstruction was implemented and tested for online reconstruction performance.ResultsThe reconstruction yields results that are virtually identical to the standard reconstruction (i.e., the magnitude sums over the ROIs), with negligible discrepancies even after termination of the conjugate gradient algorithm at a feasible number of iterations. Notably, more discrepancies arise with existing compartment‐wise reconstructions. The online real‐time implementation evaluated 1 ROI within 2.8 ms in the case of a highly parallel 3D whole brain acquisition.ConclusionThe high reconstruction fidelity and speed are satisfying for the exemplary application of real‐time functional feedback using a highly parallel 3D whole brain acquisition.
Functional exercise capacity evaluated by timed walk tests in myasthenia gravis
Authors: Salci Yeliz , Karanfil Ecem , Balkan Ayla Fil , Kütükçü Ebru Çalik , Ceren Ali Naim , Ayvat Fatma , Bekircan‐Kurt Can Ebru , Armutlu Kadriye 
Published: September 2018

ABSTRACTIntroduction: We sought to evaluate the test–retest reliability and construct validity of the 6‐ and 2‐minute walk tests (6mWT and 2mWT, respectively) in patients with myasthenia gravis (MG). Methods: Thirty‐one patients with generalized MG were enrolled in this study. The 6mWT, 2mWT, MG‐specific quality of life questionnaire Turkish version (MG‐QoL15T), quantitative myasthenia gravis test (QMG), and pulmonary function tests were administered. Results: The intraclass correlation coefficients of 2mWT and 6mWT were 0.894 and 0.932, respectively. The 6mWT and 2mWT had moderate correlations with forced vital capacity, maximal inspiratory pressure, QMG score, and MG‐QoL15T score (ρ for 6mWT: 0.579, 0.539, −0.572, and −0.474; ρ for 2mWT: 0.460, 0.446, −0.532, −0.457). Both tests had similar performances for predicting disease severity (area under the curve = 0.761 for 6mWT and 0.759 for 2mWT). Discussion: The 6mWT and 2mWT have excellent test–retest reliability as well as moderate construct validity for the evaluation of functional exercise capacity patients with MG. Muscle Nerve 59:208–212, 2019
Clustering‐based quality selection heuristics for HTTP adaptive streaming over cache networks
Authors: van der Hooft Jeroen , Bouten Niels , De Vleeschauwer Danny , Van Leekwijck Werner , Wauters Tim , Latré Steven , De Turck Filip 
Published: September 2018

SummaryHyperText Transfer Protocol (HTTP) Adaptive Streaming (HAS) has become the de facto standard video‐streaming technology. The benefits of HAS are manifold: reliable transmission of video data avoiding artifacts caused by packet loss, easy fire wall, and Network Address Translation (NAT) traversal and the seamless reuse of existing HTTP caching infrastructure. However, introducing transparent, intermediary caching nodes on the delivery path can impact the Quality of Experience (QoE) perceived by the end user. In cache‐assisted HAS, segments can be served from different origins based on the content of the caches, causing highly fluctuating throughput and Round‐Trip Time (RTT) measurements, negatively impacting the stability and optimality of the quality decisions due to incorrect throughput estimations. In this paper, we propose heuristics that are able to use information on the streaming origin and intermediary cache contents to optimize the quality selection process. Using more accurate per origin throughput measurements, buffer starvations can be avoided. Moreover, including the cache state information in the decision process can positively impact the streaming quality. Furthermore, approximation techniques based on unsupervised incremental clustering are proposed to detect the streaming origin in absence of an external information channel. Similarly, a cache probability‐based heuristic is proposed to predict the content of the expected delivery location when this information is not transferred. With perfect information, the proposed heuristics improve the QoE with 0.52 on a scale between 1 and 5, while the approximation techniques result in a performance gain between 0.04 and 0.36 for a dynamic scenario and a reduction of buffer starvations with a factor 3 to 7.
An engineering method for complex structural optimization involving both size and topology design variables
Authors: Huang Hai , An Haichao , Ma Haibo , Chen Shenyan 
Published: September 2018

SummaryThis work presents an engineering method for optimizing structures made of bars, beams, plates, or a combination of those components. Corresponding problems involve both continuous (size) and discrete (topology) variables. Using a branched multipoint approximate function, which involves such mixed variables, a series of sequential approximate problems are constructed to make the primal problem explicit. To solve the approximate problems, genetic algorithm (GA) is utilized to optimize discrete variables, and when calculating individual fitness values in GA, a second‐level approximate problem only involving retained continuous variables is built to optimize continuous variables. The solution to the second‐level approximate problem can be easily obtained with dual methods. Structural analyses are only needed before improving the branched approximate functions in the iteration cycles. The method aims at optimal design of discrete structures consisting of bars, beams, plates, or other components. Numerical examples are given to illustrate its effectiveness, including frame topology optimization, layout optimization of stiffeners modeled with beams or shells, concurrent layout optimization of beam and shell components, and an application in a microsatellite structure. Optimization results show that the number of structural analyses is dramatically decreased when compared with pure GA while even comparable to pure sizing optimization.
Strengthening nursing role and functions in stroke rehabilitation 24/7: A mixed‐methods study assessing the feasibility and acceptability of an educational intervention programme
Authors: Loft Mia Ingerslev , Poulsen Ingrid , Martinsen Bente , Mathiesen Lone Lunbak , Iversen Helle Klingenberg , Esbensen Bente Appel 
Published: September 2018

AbstractAimTo assess the feasibility of a nursing educational intervention for inpatient stroke rehabilitation and its acceptability from the nursing staff’s perspective.BackgroundThere is currently a lack of interventions that integrate the diversity of nurses’ role and functions in stroke rehabilitation and explore their effect on patient outcomes.DesignWe used a convergent, parallel, mixed‐method design with data interviews and questionnaires.MethodsData collection was undertaken between February ‐ July 2016. Data from questionnaires (N = 31) were analysed using descriptive statistics. The interviews (N = 10) were analysed using deductive content analysis.ResultsThere was a high level of satisfaction with the educational programme in terms of its acceptability and feasibility. The qualitative findings disclosed the nursing staff's experiences with the educational programme. Mixed‐methods analysis showed confirmatory results that were convergent and expanded. Only minor adjustments are required before an effect study can be conducted.
Metacarpal cortical bone loss and osteoporotic fractures in the Coimbra Identified Skeletal Collection
Authors: Curate Francisco , Perinha Andreia , Silva Ana Maria , Cunha Eugénia , Umbelino Cláudia , Nogueira Catarina 
Published: September 2018

AbstractThere has been considerable progress in recent years in our understanding of the patterns of cortical bone loss in the second metacarpal in archeological skeletal samples. Nevertheless, cortical data from reference skeletal collections are insufficient, and the possible connection of metacarpal cortical parameters with osteoporotic fractures has not been thoroughly addressed. As such, this article aims to identify and explain sex‐specific and age‐associated metacarpal cortical bone loss in a large sample (N = 302; females: 154/males: 148) from the Coimbra Identified Skeletal Collection. Another objective is to evaluate the association of cortical and demographic features with osteoporotic fractures. Age‐related endocortical bone loss is significant in women but not evident in men. Periosteal accretion of the bone is absent in both sexes. Overall, there is a net loss of the cortical bone in women, whereas cortical bone strength seems to be preserved in men. The prevalence of osteoporotic fractures is similar in both sexes, with age at death significantly influencing the probability of exhibiting a fracture. Metacarpal cortical index does not seem to be an independent risk factor for osteoporotic fractures in this sample.
Ferns as healing plants in medieval Mallorca, Spain? Evidence from human dental calculus
Authors: Fiorin Elena , Sáez Llorenç , Malgosa Assumpció 
Published: September 2018

AbstractDental calculus, or calcified plaque, is a potential source of archaeological information relating to the lives of past societies. The recovery and identification of organic microremains entrapped within dental calculus provide new data regarding diet, health, and lifestyle. This paper presents, for the first time, microscopic evidence of the sporangium annulus of a fern within the dental calculus of an adult male from the medieval necropolis of Can Reiners (Balearic Islands, Spain). The sporangium evidence was compared with modern sporangia collected in northern Mallorca and the Iberian Peninsula. The results revealed that the features of the Can Reiners sporangium sample were compatible with the speciesAsplenium trichomanes. Through a historical and modern botanical literature review, it is known that this species has been widely regarded as a cure for kidney stones and alopecia. Moreover, this species was used as an expectorant, diuretic, and emmenagogue (herb that provokes menstruation or abortion). Considering that sporangia are attached to leaves and when they are mature only spores are released in the air, the presence of the annulus within dental calculus provides direct evidence of the consumption of ferns by the population living in the Balearic Islands during the Middle Ages. Although the use of these plants as constituents of diet is not attested, we may suggest that they could be employed as medicinal plants.
“Whare ye ennemy used to bury there dead”: A New Englander burial at the 18th century Fortress of Louisbourg in Atlantic Canada
Authors: Scott Amy B. , Morgan Jennifer A. , MacInnes Sarah , Fonzo Mattia , Hinton Jessica 
Published: September 2018

AbstractKnown as one of the largest and most expansive French fortress sites in North America, Louisbourg had a short yet rich history of prosperity, warfare, and abandonment during the 18th century. Throughout its tumultuous 45‐year history, the community at Louisbourg was a mosaic of individuals including civilians, soldiers, fishermen, merchants, and privateers, originating from both North America and Europe. This diverse population no doubt contributed to Louisbourg's large and multifaceted cemetery composition. During recent excavations at Louisbourg's Rochefort Point, variable burial patterns have begun to emerge that contribute to our understanding of who these individuals were and how they fit within this 18th century community. This paper presents a case study analysis of Burial 21/2017, an adult male aged between 27 and 33 years who was buried in a coffin that bore biographical information that is consistent with previously documented English burials. When comparing this unique coffin adornment with temporally similar examples from Britain and other British colonies, it is clear that despite burial on French soil, this individual's identity as a New Englander was maintained through mortuary treatment. Evidence of healed fracture trauma to multiple skeletal elements, infection, and likely gout speaks to their lived experience as a soldier. This case study highlights the significance of burial context when extrapolating elements of identity from skeletal remains and the challenges of bioarchaeological research when working in regions with highly transient and mobile individuals.