bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dosimetric evaluation of 4D‐CBCT reconstructed by Simultaneous Motion Estimation and Image Reconstruction (SMEIR) for carbon ion therapy of lung cancer
Authors: Shrestha Deepak , Tsai Min‐Yu , Qin Nan , Zhang You , Jia Xun , Wang Jing 
Published: July 2019

PurposeMotion management is critical for the efficacy of carbon ion therapy for moving targets such as lung tumors. We evaluated the feasibility of using four‐dimensional cone beam computed tomography (4D‐CBCT) reconstructed by Simultaneous Motion Estimation and Image Reconstruction (SMEIR) for dose calculation and accumulation in carbon ion treatment of lung cancer.MethodsMotion‐compensated 4D‐CBCT images were reconstructed with the SMEIR algorithm to capture the most updated anatomy and motion with an updated interphase motion model on the treatment day. Projections of all CBCT phases were simulated from the planning 4D‐CT by the ray tracing technique. Treatment planning and dose calculation were performed with a GPU‐based Monte Carlo dose calculation software for carbon ion therapy. The treatment plan was optimized on the average computed tomography (CT) to obtain optimal intensity of the carbon ions. From the optimized plan, dose distributions on individual phases of 4D‐CT and 4D‐CBCT were calculated by the Monte Carlo‐based dose engine. Dose accumulation was performed on 4D‐CBCT images using deformable vector fields (DVF) generated by SMEIR. The accumulated planning target volume (PTV) dose based on 4D‐CBCT was then compared to the accumulated dose calculated on 4D‐CT, where the DVFs between different phases were obtained by the demons deformable registration algorithm.ResultsDose value histograms (DVH) as well as absolute deviations of the maximum dose (), mean dose (), and dose coverage metrics ( and ) for PTV were quantitatively evaluated for the two sets of plans. Good agreement was found between the 4D‐CT and 4D‐CBCT‐based PTV‐DVH curves. The average values of , , and calculated between the 4D‐CT and SMEIR‐4D‐CBCT‐based plans were , , 2.12%, and , respectively, for the PTVs of ten patient case studies.ConclusionsBased on these results, SMEIR‐reconstructed 4D‐CBCTs can potentially be used for motion estimation, dose evaluation, and adaptive treatment planning in lung cancer carbon ion therapy.
Automatic detection of small bowel tumors in wireless capsule endoscopy images using ensemble learning
Authors: Vieira Pedro M. , Freitas Nuno R , Valente João , Vaz Ismael F. , Rolanda Carla , Lima Carlos S. 
Published: July 2019

PurposeWireless Capsule Endoscopy (WCE) is a minimally invasive diagnosis tool for lesion detection in the gastrointestinal tract, reaching places where conventional endoscopy is unable to. However, the significant amount of acquired data leads to difficulties in the diagnosis by the physicians; which can be eased with computer assistance. This paper addresses a method for the automatic detection of tumors in WCE by using a two‐step based procedure: region of interest selection and classification.MethodsThe first step aims to separate abnormal from normal tissue by using automatic segmentation based on a Gaussian Mixture Model (GMM). A modified version of the Anderson method for convergence acceleration of the expectation–maximization (EM) algorithm is proposed. The proposed features for both segmentation and classification are based on the CIELab color space, as a way of bypassing lightness variations, where theLcomponent is discarded. Tissue variability among subjects, light inhomogeneities and even intensity differences among different devices can be overcome by using simultaneously features from both regions. In the second step, an ensemble system with partition of the training data with a new training scheme is proposed. At this stage, the gating network is trained after the experts have been trained decoupling the joint maximization of both modules. The partition module is also used at the test step, leading the incoming data to the most likely expert allowing incremental adaptation by preserving data diversity.ResultsThis algorithm outperforms others based on texture features selected from Wavelets and Curvelets transforms, classified by a regular support vector machine (SVM) in more than 5%.ConclusionsThis work shows that simpler features can outperform more elaborate ones if appropriately designed. In the current case, luminance was discarded to cope with saturated tissue, facilitating the color perception. Ensemble systems remain an open research field. In the current case, changes in both topology and training strategy have led to significant performance improvements. A system with this level of performance can be used in current clinical practice.
Coil profile estimation strategies for parallel imaging with hyperpolarized 13C MRI
Authors: Hansen Rie B. , Sánchez‐Heredia Juan Diego , Bøgh Nikolaj , Hansen Esben Søvsø Szocska , Laustsen Christoffer , Hanson Lars G. , Ardenkjær‐Larsen Jan H. 
Published: July 2019

PurposeTo investigate auto‐ and pre‐calibration coil profile estimation for parallel imaging reconstruction of hyperpolarized 13C MRI volumetric data.MethodsParallel imaging reconstruction was studied with 3 different approaches for coil profile estimation: auto‐calibration, phantom calibration, and theoretic calibration. Acquisition was performed with a 3D stack‐of‐spirals sequence with spectral–spatial excitation and Cartesian undersampling. Parallel imaging reconstructions were done with conjugate gradient SENSE and 3D gridding with inhomogeneity correction. The approaches were compared in simulations with different SNR, through phantom experiments, and in an in vivo pig study focused on the kidneys. All imaging was done with a rigid home‐built 12‐channel 13C receive coil at 3T.ResultsThe phantom calibrated and theoretic approaches resulted in the best structural similarities in simulations and demonstrated higher image quality in the phantom experiments compared to the auto‐calibrated approach. In vivo mapping of pyruvate uptake and lactate conversion improved for accelerated acquisitions because of a better temporal resolution. From a practical and image quality point of view, use of theoretic coil profiles led to improved results compared to the other approaches.ConclusionThe success of the theoretic coil profile estimation demonstrates a negligible effect of load on sensitivity profiles at the carbon frequency at 3T. Through theoretic or phantom calibrated parallel imaging, accelerated 3D volumes could be reconstructed with sufficient sensitivity, temporal, and spatial resolution to map the metabolism of kidneys exemplifying abdominal organs. This approach overcomes a critical step in the clinical translation of parallel imaging in hyperpolarized 13C MR.
Nusinersen improves walking distance and reduces fatigue in later‐onset spinal muscular atrophy
Authors: Montes Jacqueline , Dunaway Young Sally , Mazzone Elena S. , Pasternak Amy , Glanzman Allan M. , Finkel Richard S. , Darras Basil T. , Muntoni Francesco , Mercuri Eugenio , De Vivo Darryl C. , Bishop Kathie M. , Schneider Eugene , Bennett C. Frank , Foster Richard , Farwell Wildon ,   on behalf of the CS2 and CS12 Study Groups
Published: July 2019

AbstractIntroductionAmbulatory individuals with spinal muscular atrophy (SMA) experience muscle weakness, gait impairments, and fatigue that affect their walking ability. Improvements have been observed in motor function in children treated with nusinersen, but its impact on fatigue has not been studied.MethodsPost hoc analyses were used to examine changes in 6‐minute walk test (6MWT) distance and fatigue in children and adolescents with SMA type II and III who received their first dose of nusinersen in the phase Ib/IIa, open‐label CS2 study and were ambulatory during CS2 or the extension study, CS12.ResultsFourteen children performed the 6MWT. Median (25th, 75th percentile) distance walked increased over time by 98.0 (62.0, 135.0) meters at day 1050, whereas median fatigue changed by −3.8% (−19.7%, 1.4%).DiscussionThese results support previous studies demonstrating clinically meaningful effects of nusinersen on motor function in children and adolescents with later‐onset SMA.
Outcomes of renal calculi in patients with spinal cord injury
Authors: Lane Giulia I. , Roberts William W. , Mann Rachel , O'Dell Diana , Stoffel John T. , Clemens J. Quentin , Cameron Anne P. 
Published: July 2019

AbstractAimsPatients with spinal cord injury (SCI) are at risk of developing renal calculi. This study describes the management of renal calculi among patients with SCI with attention to factors influencing surgical management vs observation.MethodsThis retrospective, cohort study identified patients with SCI and renal calculi between 2009 to 2016 from an institutional neurogenic bladder database and detailed the management of their stones. A stone episode was defined as radiographic evidence of new calculi.ResultsOf 205 patients with SCI, 34 had renal stones, for a prevalence of 17%. The mean age was 50 years (range 22,77) and most had cervical SCI (n = 22, 65%). There were 41 stone episodes with 98 individual stones identified with a mean stone size of 4.9 mm (range 1‐19).Of the 41 episodes, 10 (24%) underwent surgery after initial diagnosis. Pain was the most common primary indication for surgery (n = 9, 60%). The median time from diagnosis to intervention for all patients was 4 months (interquartile range 1,23). Of the 41 episodes, 31 (76%) were initially observed and among these, 5 ultimately required surgery (16%) while 26 (84%) did not. Of these 26, 12 (46%) stones passed spontaneously and 14 (53%) remained unchanged. The need for surgery correlated with more stone episodes (P = .049).ConclusionIn this cohort of patients with SCI and small, nonobstructing renal stones, 76% (n = 31) were offered observation. Of these observed patients, 84% (n = 26) did not require further intervention at a median of 4 years of follow‐up.
CD163 as a valuable diagnostic and prognostic biomarker of sepsis‐associated hemophagocytic lymphohistiocytosis in critically ill children
Authors: Cui Yun , Xiong Xi , Ren Yuqian , Wang Fei , Wang Chunxia , Zhang Yucai 
Published: July 2019

AbstractObjectiveTo investigate CD163 as an effective biomarker for identifying and predicting the outcomes of sepsis‐associated hemophagocytic lymphohistiocytosis (SAHS) in children.MethodsWe prospectively enrolled presumed sepsis patients who had developed prolonged fever (>7 days), hepatosplenomegaly, cytopenias, and hyperferritinemia (>500 ng/mL) despite antibiotic therapy. Blood samples were collected within 24 hours after enrolment. A nested case–control study was performed. The number of patients who fulfilled the HLH‐2004 criteria, 28‐day mortality outcomes, and 90‐day mortality outcomes were recorded.ResultsSixty‐nine patients were enrolled in the study. Significant increases in the levels of ferritin and soluble CD163 (sCD163) and the percentage of CD163‐positive peripheral blood mononuclear cells (mCD163) and decreases in fibrinogen levels and the percentage of natural killer cells (NK %) were observed in patients with SAHS (n = 23) compared with those of patients with sepsis (n = 46). The area under the ROC curve (AUC) for ferritin combined with sCD163 was superior to the AUC for either ferritin or sCD163 for distinguishing SAHS from sepsis. Moreover, sCD163 was a prognostic factor for 28‐day mortality (0.857 [0.659–1.000]).ConclusionssCD163 is a valuable biomarker for the differential diagnosis of SAHS from sepsis and effectively predicts 28‐day mortality in children with SAHS.
Inhibition of Anaplerotic Glutaminolysis Underlies Selenite Toxicity in Human Lung Cancer
Authors: Bruntz Ronald C. , Belshoff Alex C. , Zhang Yan , Macedo Jessica K. A. , Higashi Richard M. , Lane Andrew N. , Fan Teresa W.‐M. 
Published: July 2019

AbstractLarge clinical trials and model systems studies suggest that the chemical form of selenium dictates chemopreventive and chemotherapeutic efficacy. Selenite induces excess ROS production, which mediates autophagy and eventual cell death in non‐small cell lung cancer adenocarcinoma A549 cells. As the mechanisms underlying these phenotypic effects are unclear, the clinical relevance of selenite for cancer therapy remains to be determined. The authors' previous stable isotope‐resolved metabolomics and gene expression analysis showed that selenite disrupts glycolysis, the Krebs cycle, and polyamine metabolism in A549 cells, potentially through perturbed glutaminolysis, a vital anaplerotic process for proliferation of many cancer cells. Herein, the role of the glutaminolytic enzyme glutaminase 1 (GLS1) in selenite's toxicity in A549 cells and in patient‐derived lung cancer tissues is investigated. Using [13C6]‐glucose and [13C5,15N2]‐glutamine tracers, selenite's action on metabolic networks is determined. Selenite inhibits glutaminolysis and glutathione synthesis by suppressing GLS1 expression, and blocks the Krebs cycle, but transiently activates pyruvate carboxylase activity. Glutamate supplementation partially rescues these anti‐proliferative and oxidative stress activities. Similar metabolic perturbations and necrosis are observed in selenite‐treated human patients' cancerous lung tissues ex vivo. The results support the hypothesis that GLS1 suppression mediates part of the anti‐cancer activity of selenite both in vitro and ex vivo.
Electronic effects on diaminocarbenes: a theoretical quest
Authors: Khorshidvand Neda , Kassaee Mohammad Z. 
Published: July 2019

AbstractFollowing our recent steric studies on diaminocarbenes, here, electronic effects of symmetric acyclic, cyclic saturated, and cyclic unsaturated 2,4‐disubstituted structures (1X, 3X, and 5X, respectively) are compared with their asymmetric corresponding 2,5‐disubstituted isomers (2X, 4X, and 6X, respectively), at B3LYP/6‐311++G** level of theory (X = NH2, OH, OMe, SH, Ph, CN, CF3, NO2). Both symmetric and asymmetric species (1X‐6X) appear with singlet(s) ground states. These are suggested by the conductor‐like polarizable continuum model (CPCM) on both gas‐phase and solvent‐phase optimized structures. Regardless of X, singlet‐triplet energy gap (ΔES‐T) and band gap (ΔEH‐L) increase in going from acyclic to cyclic saturated and cyclic unsaturated structures (except 6X). More importantly, nucleophilicity (N) decreases (while electrophilicity, ω, increases) in going from acyclic to cyclic saturated and cyclic unsaturated structures for both symmetric and asymmetric carbenes. Acyclic 1X and 2X appear less stable than their corresponding cyclic 3X and 6X in the presence of either electron‐withdrawing or electron‐releasing substituents. The proton affinity (PA) increases in going from acyclic to cyclic saturated, while decreases in going to cyclic unsaturated structures for both symmetric and asymmetric carbenes. The calculated metal‐ligand isodesmic complexation energies, ΔEcom, indicate that 1X‐6X complexes have very strong M─(carbene) bonds. The trend of ΔEcom for symmetric series is 1X > 3X > 5X, while that for asymmetric appears as 6X > 2X > 4X. Atoms in molecules (AIM) wavefunction analysis shows internal hydrogen bondings for 1OH, 1OMe, 1CF3, 2Ph, and 4NO2. Hammett assessments are made on sensitivity of thermodynamic parameters of 1X to 6X toward electronic effects. Finally, basicity increases as a function of the carbenic bond angle for 1X to 6X. Hence, basicity increases in going from the unsaturated 5X and 6X (96°) to the saturated 3X and 4X (102°) and lastly to acyclic 1X and 2X (120°).
Assessment of rock glaciers and permafrost distribution in Uttarakhand, India
Authors: Baral Prashant , Haq Mohd Anul , Yaragal Shivaprakash 
Published: July 2019

AbstractWe have compiled an inventory of 1004 rock glaciers for Uttarakhand State, India, using high‐resolution satellite data freely available on Google Earth. The inventory is used to analyze the origin, spatial distribution, geometry and dynamics of rock glaciers using a combination of optical remote sensing techniques with a geographic information system (GIS). Results show that development of rock glaciers in this region depends strongly on high elevation (> 4000 m a.s.l.) and slope aspect. Rock glaciers are more dominant towards the southern quadrant (S, SE, SW) than the northern quadrant (N, NE, NW). A large number (n = 608) of small (<0.5 km2) rock glaciers originating from glacial moraine indicates glacial retreat in this region as one of the major causes for the formation of such a large number of rock glaciers. Median elevation of intact rock glaciers indicates that climatic conditions above 4600 m a.s.l. are suitable for the existence of permafrost in this region and that the lower limit of discontinuous permafrost gradually increases from west to east. Despite mean annual air temperatures below 0°C, increasing mean temperatures during warmest quarter of the year could be a strong controlling factor for permafrost thawing in the region. Logistic regression modeling using WorldClim version 2 climate data sets and Moderate Resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) data show that these models can produce fairly reliable estimates of permafrost probability in the studied area. MODIS LST climate data sets can be crucial for mapping and monitoring permafrost in the region.
Supervised classification of landforms in Arctic mountains
Authors: Mithan Huw Thomas , Hales Tristram Charles , Cleall Peter John 
Published: July 2019

AbstractErosional and sediment fluxes from Arctic mountains are lower than for temperate mountain ranges due to the influence of permafrost on geomorphic processes. As permafrost extent declines in Arctic mountains, the spatial distribution of geomorphic processes and rates will change. Improved access to high‐quality remotely sensed topographic data in the Arctic provides an opportunity to develop our understanding of the spatial distribution of Arctic geomorphological processes and landforms. Utilizing newly available Arctic digital topography data, we have developed a method for geomorphic mapping using a pixel‐based linear discriminant analysis method that could be applied across Arctic mountains. We trained our classifier using landforms within the Adventdalen catchment in Svalbard and applied it to two adjacent catchments and one in Alaska. Slope gradient, elevation–relief ratio and landscape roughness distinguish landforms to a first order with >80% accuracy. Our simple classification system has a similar overall accuracy when compared across our field sites. The simplicity and robustness of our classification suggest that it is possible to use it to understand the distribution of Arctic mountain landforms using extant digital topography data and without specialized classifications. Our preliminary assessments of the distribution of geomorphic processes within these catchments demonstrate the importance of post‐glacial hillslope processes in governing sediment movement in Arctic mountains.
Illegal wildlife trade and the persistence of “plant blindness”
Authors: Margulies Jared D. , Bullough Leigh‐Anne , Hinsley Amy , Ingram Daniel J. , Cowell Carly , Goettsch Bárbara , Klitgård Bente B. , Lavorgna Anita , Sinovas Pablo , Phelps Jacob 
Published: July 2019

Societal Impact StatementA wide variety of plant species are threatened by illegal wildlife trade (IWT), and yet plants receive scant attention in IWT policy and research, a matter of pressing global concern. This review examines how “plant blindness” manifests within policy and research on IWT, with serious and detrimental effects for biodiversity conservation. We suggest several key points: (a) perhaps with the exception of the illegal timber market, plants are overlooked in IWT policy and research; (b) there is insufficient attention from funding agencies to the presence and persistence of illegal trade in plants; and (c) these absences are at least in part resultant from plant blindness as codified in governmental laws defining the meaning of “wildlife.”SummaryThis review investigates the ways in which “plant blindness,” first described by Wandersee and Schussler (1999, p. 82) as “the misguided anthropocentric ranking of plants as inferior to animals,” intersects with the contemporary boom in research and policy on illegal wildlife trade (IWT). We argue that plants have been largely ignored within this emerging conservation arena, with serious and detrimental effects for biodiversity conservation. With the exception of the illegal trade in timber, we show that plants are absent from much emerging scholarship, and receive scant attention by US and UK funding agencies often driving global efforts to address illegal wildlife trade, despite the high levels of threat many plants face. Our article concludes by discussing current challenges posed by plant blindness in IWT policy and research, but also suggests reasons for cautious optimism in addressing this critical issue for plant conservation.
Being in the forest—A matter of cultural connections with a natural environment
Authors: Häggström Margaretha 
Published: July 2019

Societal Impact StatementForests have a positive impact on the health and well‐being of humans. In this study, examination of the human–forest relationship reveals that the experience of being in a forest produces a larger, more nuanced, response than the simple experience of being in a forest itself. This larger experience can encompass an individual's past experiences, childhood memories, history, and connections to cultural representations, which signify a sense of belonging to the ‘more‐than‐human’ world. Insight into the relationships that humans have with forest environments will be important to educators and those wishing to draw attention to the botanical world.SummaryIt is known that forests have a positive impact on human health and well‐being. The aim of this study was to examine human relationships with forest environments on a different level. Specifically, how people in western Sweden relate to a particular place in a forest.Data were collected using a questionnaire placed on a tree located in a specific forest setting over the course of a year. The results were examined from a phenomenological (the philosophical study of the structures of experience and consciousness) life‐world perspective that highlights the intersubjectivity and historicity of people's connections to a forest environment.The results reveal that the experience of ‘being’ or ‘doing’ in a forest produces a larger, more nuanced, response than the simple experience itself. This complex response includes an individual's previous experiences, childhood memories, history and connections to cultural representations.Examining and understanding more deeply the relationships that humans have with forests is important for those that aim to engage people with forests and the botanical world.