bluuebunny/crossref_metadata_2025_split huggingface dataset:
MRI‐only based synthetic CT generation using dense cycle consistent generative adversarial networks
Authors: Lei Yang , Harms Joseph , Wang Tonghe , Liu Yingzi , Shu Hui‐Kuo , Jani Ashesh B. , Curran Walter J. , Mao Hui , Liu Tian , Yang Xiaofeng 
Published: May 2019

PurposeAutomated synthetic computed tomography (sCT) generation based on magnetic resonance imaging (MRI) images would allow for MRI‐only based treatment planning in radiation therapy, eliminating the need for CT simulation and simplifying the patient treatment workflow. In this work, the authors propose a novel method for generation of sCT based on dense cycle‐consistent generative adversarial networks (cycle GAN), a deep‐learning based model that trains two transformation mappings (MRI to CT and CT to MRI) simultaneously.Methods and materialsThe cycle GAN‐based model was developed to generate sCT images in a patch‐based framework. Cycle GAN was applied to this problem because it includes an inverse transformation from CT to MRI, which helps constrain the model to learn a one‐to‐one mapping. Dense block‐based networks were used to construct generator of cycle GAN. The network weights and variables were optimized via a gradient difference (GD) loss and a novel distance loss metric between sCT and original CT.ResultsLeave‐one‐out cross‐validation was performed to validate the proposed model. The mean absolute error (MAE), peak signal‐to‐noise ratio (PSNR), and normalized cross correlation (NCC) indexes were used to quantify the differences between the sCT and original planning CT images. For the proposed method, the mean MAE between sCT and CT were 55.7 Hounsfield units (HU) for 24 brain cancer patients and 50.8 HU for 20 prostate cancer patients. The mean PSNR and NCC were 26.6 dB and 0.963 in the brain cases, and 24.5 dB and 0.929 in the pelvis.ConclusionWe developed and validated a novel learning‐based approach to generate CT images from routine MRIs based on dense cycle GAN model to effectively capture the relationship between the CT and MRIs. The proposed method can generate robust, high‐quality sCT in minutes. The proposed method offers strong potential for supporting near real‐time MRI‐only treatment planning in the brain and pelvis.
Dose distribution prediction in isodose feature‐preserving voxelization domain using deep convolutional neural network
Authors: Ma Ming , K. Buyyounouski Mark , Vasudevan Varun , Xing Lei , Yang Yong 
Published: May 2019

PurposeTo implement a framework for dose prediction using a deep convolutional neural network (CNN) based on the concept of isodose feature‐preserving voxelization (IFPV) in simplifying the representation of the dose distribution.MethodsThe concept of IFPV was introduced for concise representation of a treatment plan. IFPV is a sparse voxelization scheme that partitions the voxels into subgroups according to their geometric, anatomical, and dosimetric features. In this study a deep CNN was constructed to buildup a dose prediction model in IFPV domain based on 60 volumetric modulated arc therapy (VMAT) treatment plans from a database of previously treated 70 prostate cancer patients. The dose prediction model learns the contour to dose relationship and predicts the dose distribution in IFPV domain given the input contours. Additional ten independent prostate cases were selected as testing data.DVH comparison, dose difference maps, and residual analysis with the sum of absolute residual (SAR) were used to evaluate the performance of the proposed method.ResultsThe proposed IFPV‐based method achieved good prediction performance in terms of DVH comparison and dose difference maps. Statistical results of SARs showed that the IFPV‐based method is comparable with voxel‐based method even though the number of dose representation points used in the IFPV‐based method was substantially reduced. The proposed approach achieved mean SARs of 0.029 ± 0.020 and 0.077 ± 0.030 for bladder and rectum, respectively, compared with mean SARs of 0.039 ± 0.029 and 0.069 ± 0.028 in the conventional voxel‐based method.ConclusionsA novel deep CNN‐based dose prediction method in IFPV domain was proposed. The proposed approach has great potential to significantly improve the efficiency of dose prediction and facilitate the treatment planning workflow.
Nonuniform Fourier‐decomposition MRI for ventilation‐ and perfusion‐weighted imaging of the lung
Authors: Bondesson David , Schneider Moritz J. , Gaass Thomas , Kühn Bernd , Bauman Grzegorz , Dietrich Olaf , Dinkel Julien 
Published: May 2019

PurposeTo improve the robustness of pulmonary ventilation‐ and perfusion‐weighted imaging with Fourier decomposition (FD) MRI in the presence of respiratory and cardiac frequency variations by replacing the standard fast Fourier transform with the more general nonuniform Fourier transform.Theory and MethodsDynamic coronal single‐slice MRI of the thorax was performed in 11 patients and 5 healthy volunteers on a 1.5T whole‐body scanner using a 2D ultra‐fast balanced steady‐state free‐precession sequence with temporal resolutions of 4‐9 images/s. For the proposed nonuniform Fourier‐decomposition (NUFD) approach, the original signal with variable physiological frequencies that was acquired with constant sampling rate was retrospectively transformed into a signal with (ventilation or perfusion) frequency‐adapted sampling rate. For that purpose, frequency tracking was performed with the synchro‐squeezed wavelet transform. Ventilation‐ and perfusion‐weighted NUFD amplitude and signal delay maps were generated and quantitatively compared with regularly sampled FD maps based on their signal‐to‐noise ratio (SNR).ResultsVolunteers and patients showed statistically significant increases of SNR in frequency‐adapted NUFD results compared to regularly sampled FD results. For ventilation data, the mean SNR increased by and in volunteers and patients, respectively; for perfusion data, SNR increased by and . Two patients showed perfusion signal in pulmonary areas with NUFD that could not be imaged with FD.ConclusionThis study demonstrates that using nonuniform Fourier transform in combination with frequency tracking can significantly increase SNR and reduce frequency overlaps by collecting the signal intensity onto single frequency bins.
On-Site Capabilities of a Mobile Laboratory for Aquatic Germplasm Cryopreservation
Authors: Childress William M , Bosworth Brian , Chesney Edward , Walter Ronald B , Tiersch Terrence R 
Published: May 2019

Abstract
The cryopreservation of genetic material can be an important tool for researchers and others involved with imperiled fishes, wild fisheries, aquaculture, and biomedical research. The standardization and reliable collection of diverse, high-quality samples are persistent challenges to the successful cryopreservation of aquatic species. The overall goal of this study was to work with different user groups, cryopreserving sperm on-site at their facilities to evaluate the uses and challenges of a mobile laboratory with high-throughput and quality control capabilities comparable to those of a specialized central facility. The objectives were to demonstrate the collection and cryopreservation of sperm from (1) large-bodied freshwater Blue Catfish Ictalurus furcatus for aquaculture; (2) small-bodied freshwater swordtails and platyfishes Xiphophorus spp. for biomedical research and repository development for gametes from imperiled species; and (3) saltwater Red Snapper Lutjanus campechanus for wild fisheries research. Over the course of this project, the mobile laboratory traveled more than 4,000 km, collecting germplasm from more than 650 male fish. A total of 137 Blue Catfish were processed in 2015 and 2016, yielding 6,146 0.5-mL French straws. A total of 521 males from 11 different species in the genus Xiphophorus were processed over 4 d in 2015, yielding 488 0.25-mL French straws. Lastly, a total of 17 Red Snapper males were processed during 2015, yielding 316 0.5-mL French straws. This study documents the development of a mobile cryopreservation laboratory with high-throughput capability for aquatic species. If mobile laboratories prove to be effective, user groups will no longer be limited to germplasm resources that can be shipped as samples or transported as live animals to a central cryopreservation facility. Mobile laboratories would thus create opportunities to collect higher-quality germplasm and provide access to new species. Also, they would enable direct cooperation, including training, among a wide variety of user groups for numerous applications.
Adipose Tissue Protein Glycoxidation is Associated with Weight‐Loss Potential
Authors: Serrano José C. E. , Baena‐Fustegueras Juan Antonio , Martin‐Gari Meritxell , Rassendren Helene , Cassanye Anna , Naudí Alba , López‐Cano Carolina , Sánchez Enric , de la Fuente‐Juárez María Cruz , Herrerías González Fernando , Olsina Kissler Jorge J. , Lecube Albert , Portero‐Otín Manuel 
Published: May 2019

ObjectiveThis study aimed to characterize the differences in protein oxidation biomarkers in adipose tissue (AT) as an indicator of AT metabolism and bariatric surgery weight‐loss success.MethodsA human model, in which sixty‐five individuals with obesity underwent bariatric surgery, and a diet‐induced obesity animal model, in which animals were treated for 2 months with normocaloric diets, were analyzed to determine the associations between AT protein oxidation and body weight loss. Protein oxidative biomarkers were determined by gas chromatography/mass spectrometry in AT from human volunteers before the surgery, as well as 2 months after a diet treatment in the animal model.ResultsThe levels of carboxyethyl‐lysine (CEL) and 2‐succinocystein (2SC) in both visceral and subcutaneous AT before the surgery directly correlated with greater weight loss in both human and animal models. 2SC levels in subcutaneous AT greater than 4.7 × 106 μmol/mol lysine (95% CI: 3.4 × 106 to 6.0 × 106) may predict greater weight loss after bariatric surgery (receiver operating characteristic curve area = 0.8222; P = 0.0047). Additionally, it was observed that individuals with diabetes presented lower levels of CEL and 2SC in subcutaneous AT (P = 0.0266 and P = 0.0316, respectively) compared with individuals without diabetes.ConclusionsCEL and 2SC in AT are useful biomarkers of AT metabolism and predict the individual's ability to reduce body weight after bariatric surgery.
Inverse optimal neural control via passivity approach for nonlinear anaerobic bioprocesses with biofuels production
Authors: Gurubel Kelly J. , Sanchez Edgar N. , Coronado‐Mendoza Alberto , Zuniga‐Grajeda Virgilio , Sulbaran‐Rangel Belkis , Breton‐Deval Luz 
Published: May 2019

SummaryThis paper proposes an inverse optimal neural control method of a nonlinear anaerobic bioprocesses model for simultaneous hydrogen and methane production in presence of disturbances. Based on the fundamental properties of the system, a passivity approach is designed such that asymptotic stability is guaranteed. A recurrent high‐order neural network for unknown nonlinear systems in presence of unknown bounded disturbances and parameter uncertainties is proposed to identify nonmeasurable state variables of the system, which are directly related to biofuels production. Optimal control laws based on the neural model are proposed so that the passivation of the entire plant is preserved. The neural control strategy performance for trajectory tracking in presence of disturbances is proven. Results via simulation show the optimal control methodology efficiency to stabilize the H2 and CH4 productions along desired trajectories even in presence of disturbances.
Hematopoietic stem cell transplantation for children with acute myeloid leukemia in second remission: A report from the Australasian Bone Marrow Transplant Recipient Registry and the Australian and New Zealand Children's Haematology Oncology Group
Authors: Selim Adrian , Alvaro Frank , Cole Catherine H. , Fraser Chris J. , Mechinaud Francoise , O'Brien Tracey A. , Shaw Peter J. , Tapp Heather , Teague Lochie , Nivison‐Smith Ian , Moore Andrew S. 
Published: May 2019

AbstractBackgroundApproximately one‐third of children with acute myeloid leukemia (AML) relapse, requiring re‐treatment and allogeneic hematopoietic stem cell transplantation (HSCT). Although achieving second complete remission (CR2) prior to HSCT is desirable, once CR2 is attained, it is unclear if there is any benefit from further chemotherapy prior to HSCT. Moreover, although pre‐HSCT minimal residual disease (MRD) has prognostic value in acute lymphoblastic leukemia, the benefit of MRD reduction after achieving CR prior to HSCT is less clear for AML.ProcedureTo address these questions, we analyzed data from pediatric transplant centers in Australia and New Zealand concerning relapsed childhood AML cases occurring between 1998 and 2013. Given the retrospective nature of our analysis and assay data available, we analyzed patients on the basis of measurable residual disease (MeRD) by any methodology, rather than MRD in the conventional sense.ResultsWe observed improved overall survival (OS) in children receiving two chemotherapy cycles, compared to one cycle or three or more cycles pre‐HSCT. Improved OS with two cycles remained significant for patients without MeRD after cycle 1.ConclusionsThese data suggest that a second chemotherapy cycle pre‐HSCT may improve survival by lowering disease burden. Prospective trials assessing strategies to reduce pre‐HSCT MRD in relapsed childhood AML are warranted.
Short lookback periods causing exaggerated stroke risk estimates in atrial fibrillation may expose patients to unnecessary anticoagulant treatment
Authors: Friberg Leif 
Published: May 2019

AbstractPurposeThe purpose was to investigate how different lookback periods in observational registry studies affect estimates of stroke risk in patients with atrial fibrillation and stroke risk score CHA2DS2‐VASc 1, a level where the appreciated risk is likely to affect decisions about oral anticoagulation.MethodsAll 354 854 individuals in Sweden with a hospital diagnosis of atrial fibrillation during 2010‐2016 were included. At least 13 years of observational data prior to inclusion was available for all patients. The prevalence of hypertension, heart failure, diabetes, previous thromboembolism, and vascular disease was estimated from data with different lookback periods. The incident stroke rates at CHA2DS2‐VASc score 1 was then assessed using data with successively longer lookback periods.ResultsDepending on duration of lookback period, the proportion of patients with heart failure varied 2.7 times, thromboembolism 3.7 times, hypertension 4.0 times, and diabetes and vascular disease both approximately 4.5 times. During follow‐up, 22 237 patients suffered an ischaemic stroke. The estimated risk without anticoagulant treatment at CHA2DS2‐VASc score 1 was 51% higher if the scores had been calculated with the shortest lookback period than if all information had been used.ConclusionsShort lookback periods underestimate comorbidity, cause high‐risk patients to be misclassified as low risk, and overestimate stroke risk at CHA2DS2‐VASc 1. This may lead to unnecessary anticoagulant treatment of true low‐risk patients. Transparency regarding lookback periods is essential for interpretation and comparison of registry studies.
Microstructure and relaxation behavior of flexible dielectric PVDF and HNBR blends: An assessment through small‐angle x‐ray scattering and dielectric relaxation spectroscopy
Authors: Saha Subhabrata , Bhowmick Anil K. 
Published: May 2019

ABSTRACTThe work demonstrated the microstructure and the relaxation behavior of flexible electroactive blends of poly(vinylidene fluoride) (PVDF)/hydrogenated nitrile rubber (HNBR) by small‐angle X‐ray scattering and dielectric relaxation spectroscopy. Very few studies have been done so far on this topic for crystalline/rubbery blends. Lamellar morphology was observed for both the PVDF and its blends. HNBR suppressed the mobility of PVDF above its melting temperature, as evident from lowering of crystallization temperature, due to physical interaction. The interaction was increased with HNBR content. However, after complete crystallization, HNBR segments were expelled out from the lamella, and crystal long period remained intact in all the blends. Interestingly, some HNBR segments remained in the amorphous part of PVDF which reduced the electron density contrast of its crystalline and amorphous region. When HNBR was crosslinked, the interaction was reduced, and consequently, the crystallization became faster and electron density contrast increased. From the microscopic study, polydispersed particles were observed within the crystalline lamella. Interfacial polarization (IP) relaxation of PVDF was absent in the blends due to physical interaction, whereas IP relaxation of HNBR shifted to a higher frequency. The shift was higher at higher HNBR content and decreased when HNBR was crosslinked. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019, 57, 851–866
PTEN loss in prostatic adenocarcinoma correlates with specific adverse histologic features (intraductal carcinoma, cribriform Gleason pattern 4 and stromogenic carcinoma)
Authors: Shah Rajal B. , Shore Karen T. , Yoon Jiyoon , Mendrinos Savvas , McKenney Jesse K. , Tian Wei 
Published: May 2019

AbstractBackgroundThe loss of PTEN tumor suppressor gene is one of the most common somatic genetic aberrations in prostate cancer (PCa) and is frequently associated with high‐risk disease. Deletion or mutation of at least one PTEN allele has been reported to occur in 20% to 40% of localized PCa and up to 60% of metastases. The goal of this study was to determine if somatic alteration detected by PTEN immunohistochemical loss of expression is associated with specific histologic features.MethodsTwo hundred sixty prostate core needle biopsies with PCa were assessed for PTEN loss using an analytically validated immunohistochemical assay. Blinded to PTEN status, each tumor was assessed for the Grade Group (GG) and the presence or absence of nine epithelial features. Presence of stromogenic PCa was also assessed and defined as grade 3 reactive tumor stroma as previously described: the presence of carcinoma associated stromal response with epithelial to stroma ratio of greater than 50% reactive stroma.ResultsEight‐eight (34%) cases exhibited PTEN loss while 172 (66%) had intact PTEN. PTEN loss was significantly (P < 0.05) associated with increasing GG, poorly formed glands (74% of total cases with loss vs 49% of intact), and three well‐validated unfavorable pathological features: intraductal carcinoma of the prostate (IDC‐P) (69% of total cases with loss vs 12% of intact), cribriform Gleason pattern 4 (38% of total cases with loss vs 10% of intact) and stromogenic PCa (23% of total cases with loss vs 6% of intact). IDC‐P had the highest relative risk (4.993, 95% confidence interval, 3.451‐7.223, P < 0.001) for PTEN loss. At least one of these three unfavorable pathological features were present in 67% of PCa exhibiting PTEN loss, while only 11% of PCa exhibited PTEN loss when none of these three unfavorable pathological features were present.ConclusionsPCa with PTEN loss demonstrates a strong correlation with known unfavorable histologic features, particularly IDC‐P. This is the first study showing the association of PTEN loss with stromogenic PCa.
Comparative analysis of p16 expression among African American and European American prostate cancer patients
Authors: Wong Myra , Bierman Yaeli , Pettaway Curtis , Kittles Rick , Mims Martha , Jones Jeffrey , Ittmann Michael 
Published: May 2019

AbstractBackgroundExpression of p16 is increased in a number of malignancies, including prostate cancer (PCa). Recent studies in a European cohort showed that expression of p16 is correlated with expression of the TMPRSS2/ERG (T/E) fusion protein. The T/E fusion is significantly less common in PCas in African American (AA) men. Thus, it would be predicted that p16 expression should be less common in PCas in AA men. We, therefore, sought to compare the expression of p16 in benign prostate and PCas from AA and European American (EA) men.MethodsImmunohistochemistry for p16 and ERG was performed on tissue microarrays constructed from radical prostatectomies performed on AA and EA veterans. Staining was scored and the scores compared with demographic, clinical and pathological parameters. Percent of West African ancestry in the AA cohort was assessed using ancestry informative markers.ResultsContrary to our predictions, p16 expression was similar in the cancers in the AA and EA cohorts. Consistent with prior reports, expression of p16 was quite low in benign prostate tissues from EA patients but surprisingly was significantly higher in benign tissues from AA patients. Expression of p16 was significantly associated with a family history of PCa in AA men. In addition, p16 was associated with ERG expression in AA PCa.ConclusionsWhile overall expression of p16 is similar in PCas from the two racial groups, the expression of p16 in benign tissues from a subset of AA men and the stronger correlation with ERG expression implies that there are different mechanisms for p16 overexpression in PCas from the two racial groups.
A review on non‐relativistic, fully numerical electronic structure calculations on atoms and diatomic molecules
Authors: Lehtola Susi 
Published: May 2019

AbstractThe need for accurate calculations on atoms and diatomic molecules is motivated by the opportunities and challenges of such studies. The most commonly used approach for all‐electron electronic structure calculations in general—the linear combination of atomic orbitals (LCAO) method—is discussed in combination with Gaussian, Slater a.k.a. exponential, and numerical radial functions. Even though LCAO calculations have major benefits, their shortcomings motivate the need for fully numerical approaches based on, for example, finite differences, finite elements, or the discrete variable representation, which are also briefly introduced. Applications of fully numerical approaches for general molecules are briefly reviewed, and their challenges are discussed. It is pointed out that the high level of symmetry present in atoms and diatomic molecules can be exploited to fashion more efficient fully numerical approaches for these special cases, after which it is possible to routinely perform all‐electron Hartree‐Fock and density functional calculations directly at the basis set limit on such systems. Applications of fully numerical approaches to calculations on atoms as well as diatomic molecules are reviewed. Finally, a summary and outlook is given.
Synchronization and Estimation of Gravity‐Induced Time Difference for Quantum Clocks
Authors: Wang Jieci , Liu Tonghua , Jing Jiliang , Chen Songbai 
Published: May 2019

AbstractIt has recently been reported that, under an operational definition of time, quantum clocks would get entangled through gravitational effects. Here, an alternative scenario is studied: The clocks have different masses and energy gaps, which would produce time differences via gravitational interaction. The proposal of quantum clock synchronization (QCS) for the gravity‐induced time difference is discussed. It is illustrated how the stability of measurement probability in the QCS proposal is influenced by the gravitational interaction induced by the clocks themselves. It is found that the precision of clock synchronization depends on the energy gaps of the clocks and the improvement of precision in quantum metrology is in fact an indicator of entanglement generation. The quantum enhanced estimation of time difference is also presented and it is found that the quantum Fisher information is very sensitive to the distance between the clocks.