bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brain tumor segmentation using holistically nested neural networks in MRI images
Authors: Zhuge Ying , Krauze Andra V. , Ning Holly , Cheng Jason Y. , Arora Barbara C. , Camphausen Kevin , Miller Robert W. 
Published: July 2017

PurposeGliomas are rapidly progressive, neurologically devastating, largely fatal brain tumors. Magnetic resonance imaging (MRI) is a widely used technique employed in the diagnosis and management of gliomas in clinical practice. MRI is also the standard imaging modality used to delineate the brain tumor target as part of treatment planning for the administration of radiation therapy. Despite more than 20 yr of research and development, computational brain tumor segmentation in MRI images remains a challenging task. We are presenting a novel method of automatic image segmentation based on holistically nested neural networks that could be employed for brain tumor segmentation of MRI images.MethodsTwo preprocessing techniques were applied to MRI images. The N4ITK method was employed for correction of bias field distortion. A novel landmark‐based intensity normalization method was developed so that tissue types have a similar intensity scale in images of different subjects for the same MRI protocol. The holistically nested neural networks (HNN), which extend from the convolutional neural networks (CNN) with a deep supervision through an additional weighted‐fusion output layer, was trained to learn the multiscale and multilevel hierarchical appearance representation of the brain tumor in MRI images and was subsequently applied to produce a prediction map of the brain tumor on test images. Finally, the brain tumor was obtained through an optimum thresholding on the prediction map.ResultsThe proposed method was evaluated on both the Multimodal Brain Tumor Image Segmentation (BRATS) Benchmark 2013 training datasets, and clinical data from our institute. A dice similarity coefficient (DSC) and sensitivity of 0.78 and 0.81 were achieved on 20 BRATS 2013 training datasets with high‐grade gliomas (HGG), based on a two‐fold cross‐validation. The HNN model built on the BRATS 2013 training data was applied to ten clinical datasets with HGG from a locally developed database. DSC and sensitivity of 0.83 and 0.85 were achieved. A quantitative comparison indicated that the proposed method outperforms the popular fully convolutional network (FCN) method. In terms of efficiency, the proposed method took around 10 h for training with 50,000 iterations, and approximately 30 s for testing of a typical MRI image in the BRATS 2013 dataset with a size of 160 × 216 × 176, using a DELL PRECISION workstation T7400, with an NVIDIA Tesla K20c GPU.ConclusionsAn effective brain tumor segmentation method for MRI images based on a HNN has been developed. The high level of accuracy and efficiency make this method practical in brain tumor segmentation. It may play a crucial role in both brain tumor diagnostic analysis and in the treatment planning of radiation therapy.
Impact of respiratory motion and acquisition settings on SPECT liver dosimetry for radioembolization
Authors: Bastiaannet Remco , Viergever Max A. , de Jong Hugo W. A. M. 
Published: July 2017

PurposeRespiratory motion may impose significant inaccuracies on emission activity estimation in quantitative SPECT. This effect may be a major issue in dosimetry as used in the management of liver radioembolization. The purpose of this study was to investigate the impact of respiratory motion on radioembolization liver dosimetry for different SPECT acquisition settings.MethodsIn a series of SPECT/CT Monte Carlo simulations using several digital XCAT phantoms, the following parameters were varied: breathing/nonbreathing, liver tumor size (0.3–35 ml) and location, patient properties (body mass index ranging from underweight to obese; male and female), acquisition time (10–30 s/view), collimator setup (High Sensitivity, High Resolution, Ultra High Resolution) and tumor VOI. The effect of applying a respiratory gating scheme was examined as well.ResultsBreathing decreased activity recovery and tumor/non‐tumor (T/N) ratios on average from 90% to 66%. VOIs based on SPECT images instead of breath‐hold CT improved T/N values significantly. The most accurate results were obtained using a gating scheme combined with SPECT‐based VOIs. Scan duration, body mass index, sex, and location all had a minor effect. Lung shunt fraction estimations were relatively unaffected by any of the varied parameters.ConclusionsRespiratory motion has a large effect on SPECT activity quantitation of liver tumors as used in radioembolization treatment planning and assessment. As compared with the other parameters that were varied in this study, respiration is the predominant degrading effect on image quantitation. Gating alleviates much of this detrimental effect.
True constructive interference in the steady state (trueCISS)
Authors: Hilbert Tom , Nguyen Damien , Thiran Jean‐Philippe , Krueger Gunnar , Kober Tobias , Bieri Oliver 
Published: July 2017

PurposeTo introduce a novel time‐efficient method, termed true constructive interference in the steady state (trueCISS), that not only solves the problem of banding artifacts for balanced steady‐state free precession (bSSFP) but also provides its genuine, that is, true, on‐resonant signal.MethodsAfter a compressed sensing reconstruction from a set of highly undersampled phase‐cycled bSSFP scans, the local off‐resonance, relaxation time ratio, and equilibrium magnetization are voxel‐wise estimated using a dictionary‐based fitting routine. Subsequently, on‐resonant bSSFP images are generated using the previously estimated parameters. Due to the high undersampling factors used, the acquisition time is not prolonged with respect to a standard CISS acquisition.ResultsFrom a set of 16 phase‐cycled SSFP scans in combination with an eightfold undersampling, both phantom and in vivo whole‐brain experiments demonstrate that banding successfully can be removed. Additionally, trueCISS allows the derivation of synthetic bSSFP images with arbitrary flip angles, which enables image contrasts that may not be possible to acquire in practice due to safety constraints.ConclusionTrueCISS offers banding‐free bSSFP images with on‐resonant signal intensity and without requiring additional acquisition time compared to conventional methods. Magn Reson Med 79:1901–1910, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
An algorithmically consistent macroscopic tangent operator for FFT‐based computational homogenization
Authors: Göküzüm Felix Selim , Keip Marc‐André 
Published: July 2017

SummaryThe present work addresses a multiscale framework for fast‐Fourier‐transform–based computational homogenization. The framework considers the scale bridging between microscopic and macroscopic scales. While the macroscopic problem is discretized with finite elements, the microscopic problems are solved by means of fast‐Fourier‐transforms (FFTs) on periodic representative volume elements (RVEs). In such multiscale scenario, the computation of theeffective propertiesof the microstructure is crucial. While effective quantities in terms of stresses and deformations can be computed from surface integrals along the boundary of the RVE, the computation of the associated moduli is not straightforward. The key contribution of the present paper is the derivation and implementation of analgorithmically consistent macroscopic tangent operatorwhich directly resembles the effective moduli of the microstructure. The macroscopic tangent is derived by means of the classical Lippmann‐Schwinger equation and can be computed from a simple system of linear equations. This is performed through an efficient FFT‐based approach along with a conjugate gradient solver. The viability and efficiency of the method is demonstrated for a number of two‐ and three‐dimensional boundary value problems incorporating linear and nonlinear elasticity as well as viscoelastic material response.
Exercise capacity is not decreased in children who have undergone lung resection early in life for congenital thoracic malformations compared to healthy age‐matched children
Authors: Dunn Ashlee , Pearce Kasey , Callister Robin , Collison Adam , Morten Matthew , Mandaliya Payal , Platt Lauren , Dascombe Ben , Kumar Rajendra , Selvadurai Hiran , Robinson Paul D. , Mattes Joerg 
Published: July 2017

AbstractPurposeThe purpose of this study was to compare (i) the exercise capacity and (ii) lung function prior to and immediately post cardiopulmonary exercise tests (CPET) of children who underwent early life lung resection for Congenital Pulmonary Airway Malformations (CPAM) to healthy control children.MethodEight children with CPAM (four males, age 9.6 ± 1.8 years) and eight control children without respiratory disease (three males, age 9.4 ± 1.4 years) performed a CPET on a cycle ergometer, during which maximal oxygen consumption (V̇O2max) and heart rate were measured. Prior to and immediately post CPET, lung function measures including Nitrogen Multiple Breath Washout (MBW) and spirometry were performed.ResultsThere were no significant between group differences in pre CPET lung function (P > 0.05) or maximal exercise capacity (V̇O2max CPAM: 39.4 mL.kg−1.min−1, Control: 40.5 mL.kg−1.min−1). Post CPET, FEV1 was significantly lower in the CPAM group, with two participants diagnosed subsequently with exercise induced bronchospasm based on post‐CPET spirometry and follow‐up clinical investigations.ConclusionEarly life lung resection for CPAM does not appear to have negative implications for exercise capacity later in childhood. Clinicians should be aware that dyspnoea following exercise may be due to asthma rather than residual effects of CPAM in these children.
Non‐additive stabilization by halogenated amino acids reveals protein plasticity on a sub‐angstrom scale
Authors: Hosseini Azade S. , Pace Christopher J. , Esposito Adam A. , Gao Jianmin 
Published: July 2017

AbstractIt has been a long‐standing goal to understand the structure‐stability relationship of proteins, as optimal stability is essential for protein function and highly desirable for protein therapeutics. Halogenation has emerged as a minimally invasive strategy to probe the physical characteristics of proteins in solution, as well as enhance the structural stabilities of proteins for therapeutic applications. Although advances in synthetic chemistry and genetic code expansion have allowed for the rapid synthesis of proteins with diverse chemical sequences, much remains to be learned regarding the impact of these mutations on their structural integrity. In this contribution, we present a systematic study of three well‐folded model protein systems, in which their structural stabilities are assessed in response to various hydrogen‐to‐halogen atom mutations. Halogenation allows for the perturbation of proteins on a sub‐angstrom scale, offering unprecedented precision of protein engineering. The thermodynamic results from these model systems reveal that in certain cases, proteins can display modest steric tolerance to halogenation, yielding non‐additive consequences to protein stability. The observed sub‐angstrom sensitivity of protein stability highlights the delicate arrangement of a folded protein core structure. The stability data of various halogenated proteins presented herein should also provide guidelines for using halogenation as a strategy to improve the stability of protein therapeutics.
Evaluation of lumazine synthase from Bacillus anthracis as a presentation platform for polyvalent antigen display
Authors: Wei Yangjie , Wahome Newton , VanSlyke Greta , Whitaker Neal , Kumar Prashant , Barta Michael L. , Picking Wendy L. , Volkin David B. , Mantis Nicholas J. , Middaugh C. Russell 
Published: July 2017

AbstractPolyvalent antigen display is an effective strategy to enhance the immunogenicity of subunit vaccines by clustering them in an array‐like manner on a scaffold system. This strategy results in a higher local density of antigens, increased high avidity interactions with B cells and other antigen presenting cells, and therefore a more effective presentation of vaccine antigens. In this study, we used lumazine synthase (LS), an icosahedral symmetry capsid derived from Bacillus anthracis, as a scaffold to present 60 copies of a linear B cell epitope (PB10) from the ricin toxin fused to the C terminus of LS via four different linkers. We then investigated the effects of linker length, linker rigidity and formaldehyde crosslinking on the protein assembly, conformational integrity, thermal stability, in vitro antibody binding, and immunogenicity in mice. Fusion of the PB10 peptide onto LS, with varying linker lengths, did not affect protein assembly, thermal stability or exposure of the epitope, but had a minor impact on protein conformation. Formaldehyde crosslinking considerably improved protein thermal stability with only minor impact on protein conformation. All LS_PB10 constructs, when administered to mice by injection without adjuvant, elicited measurable anti‐ricin serum IgG titers, although the titers were not sufficient to confer protection against a 10× lethal dose ricin challenge. This work sheds light on the biophysical properties, immunogenicity and potential feasibility of LS from B. anthracis as a scaffold system for polyvalent antigen display.
Quantized sliding mode control in delta operator framework
Authors: Zheng Bo‐Chao , Yu Xinghuo , Xue Yanmei 
Published: July 2017

SummaryThis paper is concerned with quantized sliding mode control in the unified delta operator system framework. To solve the quantization measurement saturating problem, a dynamic quantization strategy including discrete on‐line open‐loop zooming‐out and closed‐loop zooming‐in policies is presented. By analyzing the sign relation between the traditional linear switching function and the quantized linear switching function, a novel quantized sliding mode control method is proposed, and both the amplitude of the control gain and the value of the quantization measurement saturating parameter are reduced compared with previous results. Some simulation results are presented to verify the effectiveness of the proposed method.
Chiral Copper(0) Nanoparticles: Direct Synthesis and Interfacial Chiral Induction via Phase Transfer of Copper Nanoparticles
Authors: Imanaka Yu , Nakahodo Tsukasa , Fujihara Hisashi 
Published: July 2017

AbstractNo clear‐cut example has been hitherto known for the phase transfer involving the ligand exchange of copper nanoparticles (NPs) from an aqueous phase into an organic phase, and chiral copper NPs. We present the first isolation of chiral copper(0) NPs prepared by either the reduction of copper ions with hydrazine in the presence of a new chiral binaphthyl carboxylic acid 1 as a protective ligand in an organic solvent or the two‐phase transfer involving the chiral ligand exchange of the polyvinyl pyrrolidone‐protected copper NPs from the water phase to organic phase in the presence of the chiral protective ligand 1. This is the first example for the asymmetric (chiral) induction on the surface of the copper NPs by two‐phase transfer of the achiral copper NPs.
Projector representation of isotropic linear elastic material laws for directed surfaces
Authors: Aßmus Marcus , Eisenträger Johanna , Altenbach Holm 
Published: July 2017

AbstractIn the framework of linear elasticity, it is possible to use eigenspace projectors to describe the elasticity tensor, at least for special cases of material symmetries. A similar procedure is also advantageous in the context of directed surfaces. It is thus possible to introduce this representation to stiffness measures of thin‐walled members. Hereby, we reduce our considerations to an elastic mid‐surface, where the in‐plane, out‐of‐plane, and transverse shear states are uncoupled, but superposed eventually. Thereby, we introduce a unique decomposition of the stiffness measures for the considered deformation states, while we limit our considerations to homogeneous materials without pronounced orientation dependency. For each of these three states, eigenvalues of the stiffness tensors are evaluated based on engineering material parameters. Finally, the whole procedure allows for the clear distinction of dilatoric and deviatoric portions in the constitutive equations.After all, a compact and mathematically easy‐to‐handle representation for the stiffness tensors with respect to in‐plane, out‐of‐plane, and transverse shear state has been found. Thereby, we show correlations to classical representations as well as advantages due to the clarity of present scheme.
Short‐ and Long‐Term Outcomes in Malnourished Patients After Laparoscopic or Open Radical Gastrectomy
Authors: Zheng Hua‐Long , Lu Jun , Zheng Chao‐Hui , Li Ping , Xie Jian‐Wei , Wang Jia‐Bin , Lin Jian‐Xian , Chen Qi‐Yue , Lin Mi , Tu Ru‐Hong , Huang Chang‐Ming 
Published: July 2017

AbstractObjectiveThe aim of this study was to compare the short‐ and long‐term outcomes of malnourished gastric cancer patients who underwent laparoscopic or open radical gastrectomy.BackgroundPreoperative malnutrition is an independent risk factor for postoperative mortality and morbidity in major gastrointestinal surgery. However, whether laparoscopic surgery can improve the short‐ and long‐term outcomes of malnourished gastric cancer patients has not been determined.MethodsWe reviewed prospectively collected data from 2441 patients with gastric cancer between January 2009 and December 2014 and compared the short‐ and long‐term outcomes in malnourished gastric cancer patients who underwent laparoscopic or open radical gastrectomy. Nutritional risk factors included weight loss >10% within 6 months, body mass index <18.5 kg/m2, Subjective Global Assessment Grade C, and serum albumin <3.0 g/dL.ResultsOverall, 501 patients (20.52%) were classified as malnourished. Patients with gastric stump carcinoma, neoadjuvant chemotherapy, distant metastases, palliative operation, or the presence of other malignancies were excluded. Finally, a total of 412 patients were analyzed; 304 in the laparoscopic group and 108 in the open group. There were no significant differences between the two groups regarding the clinicopathological characteristics. However, the operation time (181 ± 53 vs. 253 ± 81 min), intraoperative blood loss (80 ± 116 vs. 322 ± 502 mL), time to first ambulation (2.21 ± 1.04 vs. 2.55 ± 1.50 days), liquid diet (4.91 ± 1.61 vs. 5.72 ± 2.09 days) and semiliquid diet (7.67 ± 1.56 vs. 9.53 ± 2.09 days) as well as the postoperative hospital stay duration (13.00 ± 6.56 vs. 15.22 ± 6.87 days) were significantly lower in the laparoscopic group than those in the open group (p < 0.05). The instances of overall complications (laparoscopic vs. open: 18.4 vs. 30.6%, p = 0.008) and pneumonia (laparoscopic vs. open: 10.9 vs. 19.4%, p = 0.023) were significantly lower in the laparoscopic group. With a median follow‐up of 31.0 months (range 1.0–88.0), the 3‐year overall survival (OS), recurrence‐free survival (RFS), and cancer‐specific survival (CSS) rates for the entire cohort were 58.9, 54.0 and 63.0%, respectively. Further analysis showed that the OS (57.5 vs. 59.4%, p = 0.560), RFS (51.8 vs. 54.8%, p = 0.441) and CSS (62.8 vs. 63.0%, p = 0.789) between the laparoscopic and open groups, respectively, were no significantly different. Further analysis showed no significant differences in the OS rates of the two groups of patients stratified by tumor stage (p > 0.05).ConclusionCompared with open radical gastrectomy, laparoscopy would reduce the postoperative complications especially pneumonia and shorten the postoperative hospital stay for patients with preoperative malnutrition without affecting their long‐term survival.
Influence of Heat Treatment on the Surface Structure of 6082 Al Alloys
Authors: Bayat N. , Carlberg T. 
Published: July 2017

Abstract
The β-Al5FeSi intermetallic phase and coarse Mg2Si particles have negative effects on extrudability and workability of 6xxx Al alloys billets. To achieve extruded products with a high surface quality, the as-cast billets are heat-treated before extrusion. During heat treatment, the undesired intermetallic particles, i.e., β-AlFeSi platelets are transformed to rounded α-Al(FeMn)Si intermetallic phases. Although the heat treatment of the bulk areas of the 6xxx Al alloys has been the focus of many previous studies, the process of phase transformation at the very surface has not been paid the same attention. In this study, microstructures of a homogenized billet of a 6082 alloy at the area very close to the surface were investigated. By comparing the X-ray diffraction patterns (XRD) of heat-treated samples as a function of different holding times, the gradual phase transformations could be followed, and using GDOES and map analysis by EDX, the alloying elemental redistribution was analyzed. Partial remelting and porosity growth was detected, and transformation rates were faster than in bulk material and from what is known from industrial processes.
The Functional Barometer — An analysis of a self-assessment questionnaire with ICF-coding regarding functional/activity limitations and quality of life due to pain — Differences in age gender and origin of pain
Authors: Norrefalk Jan-Rickard , Borg Kristian 
Published: July 2017

Abstract
Long standing non-malignant pain leads to a variety of limitations which can be assessed by means of the self-assessment questionnaire Functional Barometer. It is designed to assess the extent and limitations in function, activity and decreased quality-of-life and is adapted to the International Classification of Functioning and Health.

Aim
To investigate the outcome and differences in age, gender and origin of pain in patients with longstanding non-malignant pain regarding the subjective experience of functional-, activity- and quality-of-life limitations.

Method
300 patients with a median duration of pain of 49 months referred to a Pain Management Centre filled out the Functional Barometer questionnaire, adapted to the International Classification of Functioning and Health.

Results
66% patients were women and 34% were men. Seventy-five percent were in working age, 18-64 years. The duration before being referred to a pain specialist was over 4 years and 65% reported pain from more than three origins. Significant differences in functioning, activity and quality-of-life were found in comparing gender, age and origin of pain. Men more often reported physiological limitations while women more often reported psychological limitations of functioning, activity and quality-of-life. The most important were that men more often had difficulties in walking and climbing stairs, while women reported problems with concentration, stress and psychological demands, family relations and contact with friends.

Conclusion
The significant differences regarding functioning, activity and quality-of-life between women and men as age and origin of pain must be taken into account when tailoring individual treatment and rehabilitation programmes.
An Economic Efficiency Approach to Reforming Corporate Governance: The Case of Multiple Stakeholder Boards
Authors: GOO Say H. 
Published: July 2017

AbstractThis paper points out the problems of the current law on directors’ duties that forces directors to ignore stakeholder interests, with the unintended consequences of misallocation of resources and the weaknesses of a traditional legal approach to law reform, and uses multiple stakeholder boards as an example to demonstrate how an economic efficiency approach to law reform, adopting economic principles, could avoid some of the unintended consequences of a legal approach to law reform and help design better rules that promote allocative efficiency for the benefit of society as a whole. It argues that international organizations should take the lead in promoting the use of stakeholder directors in the board of directors of multinational corporations that have a history of corporate abuses for corporate decisions that have an impact on all stakeholders.