bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of understaging on local recurrence of rectal cancer
Authors: Giesen Louis J. X. , Borstlap Wernard A. A. , Bemelman Willem A. , Tanis Pieter J. , Verhoef Cornelis , Olthof Pim B. ,   DUTCH SNAPSHOT RESEARCH GROUP
Published: July 2020

AbstractBackground and ObjectivesMagnetic resonance imaging of the pelvis has a limited accuracy to detect positive lymph nodes but does dictate neoadjuvant treatment in rectal cancer. This study aimed to investigate preoperative lymph node understaging and its effects on postoperative local recurrence rate.MethodsPatients were selected from a retrospective cross‐sectional snapshot study. Patients with emergency surgery, cM1 disease, or unknown cN‐ or (y)pN category were excluded. Clinical and pathologic N‐categories were compared and the impact on local recurrence was determined by multivariable analysis.ResultsOut of 1548 included patients, 233 had preoperatively underestimated lymph node staging based on (y)pN category. Out of the 695 patients staged cN0, 168 (24%) had positive lymph nodes at pathology, and out of the 594 patients staged cN1, 65 (11%) were (y)pN2. Overall 3‐year local recurrence rate was 5%. Clinical N‐category was not associated with local recurrence when corrected for pT‐category, neoadjuvant therapy, and resection margin, neither in patients with (y)pN1 (hazard ratio [HR]: 1.67 (95% confidence interval [CI]: 0.68‐4.12) P = .263) nor (y)pN2‐category (HR: 1.91 95% CI: [0.75‐4.84], P = .175).ConclusionPreoperative understaging of nodal status in rectal cancer is not uncommon. No significant effect on local recurrence or overall survival rates were found in the present study.
Statistical characterization of the linear attenuation coefficient in polychromatic CT scans
Authors: Vegas‐Sánchez‐Ferrero Gonzalo , San José Estépar Raúl 
Published: July 2020

PurposeTo provide a unifying statistical model that characterizes the integrated x‐ray intensity at the detector after logarithmic transformation and can be extended to the characterization of computed tomography (CT) numbers in the reconstructed image.MethodsWe study the statistical characteristics of polyenergetic x‐ray beams in the detector. Firstly, we consider the characterization of the integrated x‐ray intensity at the detector through a probabilistic model (compound Poisson) that describes its statistics. We analyze its properties and derive the probabilistic distribution after the logarithmic transformation analytically. Finally, we propose a more tractable probabilistic distribution with the same features observed in the characterization, the noncentral Gamma (nc‐Gamma). This distribution exhibits desirable properties for the statistical characterization across the reconstruction process. We assess the assumptions adopted in the derivation of the statistical models throughout Monte Carlo simulations and validate them with a water phantom and a lung phantom acquired in a Siemens clinical CT scan. We evaluate the statistical similarities between the theoretical distribution and the nc‐Gamma using a power analysis with a Kolmogorov–Smirnov test for a 95% confidence level.ResultsThe Kolmogorov–Smirnov goodness‐of‐fit test obtained for the Monte Carlo simulation shows an extremely high agreement between the empirical distribution of the post‐logarithmic‐integrated x‐ray intensity and the nc‐Gamma. The experimental validation performed with both phantoms confirmed the excellent match between the theoretical distribution, the proposed nc‐Gamma, and sample distributions in all situations.ConclusionWe derive an analytical model describing the post‐log distribution of the linear attenuation coefficient in the sensor for polychromatic CT scans. We also demonstrate that the nc‐Gamma distribution approximates well the theoretical distribution. This distribution also approximates well the CT numbers after reconstruction since it naturally extends across linear operations involved in filtered back projection reconstructions. This probabilistic model may provide the analytical foundation to define new likelihood‐based reconstruction methodologies for polychromatic scans.
CT‐based multi‐organ segmentation using a 3D self‐attention U‐net network for pancreatic radiotherapy
Authors: Liu Yingzi , Lei Yang , Fu Yabo , Wang Tonghe , Tang Xiangyang , Jiang Xiaojun , Curran Walter J. , Liu Tian , Patel Pretesh , Yang Xiaofeng 
Published: July 2020

PurposeSegmentation of organs‐at‐risk (OARs) is a weak link in radiotherapeutic treatment planning process because the manual contouring action is labor‐intensive and time‐consuming. This work aimed to develop a deep learning‐based method for rapid and accurate pancreatic multi‐organ segmentation that can expedite the treatment planning process.MethodsWe retrospectively investigated one hundred patients with computed tomography (CT) simulation scanned and contours delineated. Eight OARs including large bowel, small bowel, duodenum, left kidney, right kidney, liver, spinal cord and stomach were the target organs to be segmented. The proposed three‐dimensional (3D) deep attention U‐Net is featured with a deep attention strategy to effectively differentiate multiple organs. Performance of the proposed method was evaluated using six metrics, including Dice similarity coefficient (DSC), sensitivity, specificity, Hausdorff distance 95% (HD95), mean surface distance (MSD) and residual mean square distance (RMSD).ResultsThe contours generated by the proposed method closely resemble the ground‐truth manual contours, as evidenced by encouraging quantitative results in terms of DSC, sensitivity, specificity, HD95, MSD and RMSD. For DSC, mean values of 0.91 ± 0.03, 0.89 ± 0.06, 0.86 ± 0.06, 0.95 ± 0.02, 0.95 ± 0.02, 0.96 ± 0.01, 0.87 ± 0.05 and 0.93 ± 0.03 were achieved for large bowel, small bowel, duodenum, left kidney, right kidney, liver, spinal cord and stomach, respectively.ConclusionsThe proposed method could significantly expedite the treatment planning process by rapidly segmenting multiple OARs. The method could potentially be used in pancreatic adaptive radiotherapy to increase dose delivery accuracy and minimize gastrointestinal toxicity.
Comparison of CBCT‐based dose calculation methods in head and neck cancer radiotherapy: from Hounsfield unit to density calibration curve to deep learning
Authors: Barateau Anaïs , De Crevoisier Renaud , Largent Axel , Mylona Eugenia , Perichon Nicolas , Castelli Joël , Chajon Enrique , Acosta Oscar , Simon Antoine , Nunes Jean‐Claude , Lafond Caroline 
Published: July 2020

PurposeAnatomical variations occur during head and neck (H&N) radiotherapy treatment. kV cone‐beam computed tomography (CBCT) images can be used for daily dose monitoring to assess dose variations owing to anatomic changes. Deep learning methods (DLMs) have recently been proposed to generate pseudo‐CT (pCT) from CBCT to perform dose calculation. This study aims to evaluate the accuracy of a DLM and to compare this method with three existing methods of dose calculation from CBCT in H&N cancer radiotherapy.MethodsForty‐four patients received VMAT for H&N cancer (70‐63‐56 Gy). For each patient, reference CT (Bigbore, Philips) and CBCT images (XVI, Elekta) were acquired. The DLM was based on a generative adversarial network. The three compared methods were: (a) a method using a density to Hounsfield Unit (HU) relation from phantom CBCT image (HU‐D curve method), (b) a water–air‐bone density assignment method (DAM), and iii) a method using deformable image registration (DIR). The imaging endpoints were the mean absolute error (MAE) and mean error (ME) of HU from pCT and reference CT (CTref). The dosimetric endpoints were dose discrepancies and 3D gamma analyses (local, 2%/2 mm, 30% dose threshold). Dose discrepancies were defined as the mean absolute differences between DVHs calculated from the CTref and pCT of each method.ResultsIn the entire body, the MAEs and MEs of the DLM, HU‐D curve method, DAM, and DIR method were 82.4 and 17.1 HU, 266.6 and 208.9 HU, 113.2 and 14.2 HU, and 95.5 and −36.6 HU, respectively. The MAE obtained using the DLM differed significantly from those of other methods (Wilcoxon, P ≤ 0.05). The DLM dose discrepancies were 7 ± 8 cGy (maximum = 44 cGy) for the ipsilateral parotid gland Dmean and 5 ± 6 cGy (max = 26 cGy) for the contralateral parotid gland mean dose (Dmean). For the parotid gland Dmean, no significant dose difference was observed between the DLM and other methods.The mean 3D gamma pass rate ± standard deviation was 98.1 ± 1.2%, 91.0 ± 5.3%, 97.9 ± 1.6%, and 98.8 ± 0.7% for the DLM, HU‐D method, DAM, and DIR method, respectively. The gamma pass rates and mean gamma results of the HU‐D curve method, DAM, and DIR method differed significantly from those of the DLM.ConclusionsFor H&N radiotherapy, DIR method and DLM appears as the most appealing CBCT‐based dose calculation methods among the four methods in terms of dose accuracy as well as calculation time. Using the DIR method or DLM with CBCT images enables dose monitoring in the parotid glands during the treatment course and may be used to trigger replanning.
Diffusion tensor imaging reveals changes in non‐fat infiltrated muscles in late onset Pompe disease
Authors: Rehmann Robert , Froeling Martijn , Rohm Marlena , Forsting Johannes , Kley Rudolf André , Schmidt‐Wilcke Tobias , Karabul Nesrin , Meyer‐Frießem Christine H. , Vollert Jan , Tegenthoff Martin , Vorgerd Matthias , Schlaffke Lara 
Published: July 2020

AbstractMRI is a helpful tool for monitoring disease progression in late‐onset Pompe disease (LOPD). Our study aimed to evaluate if muscle diffusion tensor imaging (mDTI) shows alterations in muscles of LOPD patients with <10% fat‐fraction. We evaluated 6 thigh and 7 calf muscles (both legs) of 18 LOPD and 29 healthy controls (HC) with muscle diffusion tensor imaging (mDTI), T1w, and mDixonquant sequences in a 3T MRI scanner. The quantitative mDTI‐values axial diffusivity (λ1), mean diffusivity (MD), radial diffusivity (RD), and fractional anisotropy (FA) as well as fat‐fraction were analyzed. 6‐Minute Walk Test (6‐MWT) data were correlated to diffusion metrics. We found that mDTI showed significant differences between LOPD and HC in diffusion parameters (P < .05). Thigh muscles with <10% fat‐fraction showed significant differences in MD, RD, and λ1‐3. MD positively correlated with 6‐MWT (P = .06). To conclude, mDTI reveals diffusion restrictions in muscles of LOPD with and without fat‐infiltration and reflects structural changes prior to fatty degeneration.
Neuropathy symptom and change: Inotersen treatment of hereditary transthyretin amyloidosis
Authors: Dyck P. James B. , Coelho Teresa , Waddington Cruz Marcia , Brannagan Thomas H. , Khella Sami , Karam Chafic , Berk John L. , Polydefkis Michael J. , Kincaid John C. , Wiesman Janice F. , Litchy William J. , Mauermann Michelle L. , Ackermann Elizabeth J. , Baker Brenda F. , Jung Shiangtung W. , Guthrie Spencer , Pollock Michael , Dyck Peter J. 
Published: July 2020

AbstractIntroductionHereditary transthyretin‐mediated amyloidosis (hATTR) manifests as multisystem dysfunction, including progressive polyneuropathy. Inotersen, an antisense oligonucleotide, improved the course of neuropathic impairment in patients with hATTR in the pivotal NEURO‐TTR study (NCT01737398). To determine inotersen's impact on symptoms and patients’ neuropathy experience, we performed a post hoc analysis of the Neuropathy Symptoms and Change (NSC) score.MethodsStage 1 or 2 hATTR patients were randomized to receive weekly subcutaneous inotersen or placebo for 65 weeks. NSC score was assessed at baseline and 35 and 66 weeks.ResultsAt 66 weeks, inotersen‐treated patients had symptom stabilization as compared with worsening in patients receiving placebo, based on total NSC score. There were also improvements in the subdomains of muscle weakness, sensory, pain, and autonomic symptoms, and for various individual items.DiscussionInotersen treatment stabilized neuropathy symptoms, including autonomic symptoms, in patients with hATTR according to NSC score. Thus, the NSC may be an effective measure to assess neuropathy progression and patients’ neuropathy experience in clinical practice.
Material parameter optimization for interior and exterior fluid‐structure acoustic problems
Authors: Ramaswamy Harisankar , Dey Saikat , Oberai Assad A. 
Published: July 2020

SummaryWe present an efficient adjoint‐based framework for computing sensitivities of quantities of interest with respect to material parameters for coupled fluid‐structural acoustic systems with explicit interface coupling. The fluid is modeled using the Helmholtz equation and the structure is modeled using the Navier‐Cauchy equations. Sensitivities are used to drive a gradient based optimization algorithm to solve important problems in structural acoustics, viz noise minimization and vibration isolation. For each problem, we consider two different priors: one where the optimal solution has a smooth variation and another with a bimaterial distribution. These priors are imposed with the help of suitable regularization terms. The effectiveness of this approach is demonstrated on both interior and exterior structural acoustic problems.
Architecture and self‐assembly of the SARS‐CoV‐2 nucleocapsid protein
Authors: Ye Qiaozhen , West Alan M. V. , Silletti Steve , Corbett Kevin D. 
Published: July 2020

AbstractThe COVID‐2019 pandemic is the most severe acute public health threat of the twenty‐first century. To properly address this crisis with both robust testing and novel treatments, we require a deep understanding of the life cycle of the causative agent, the SARS‐CoV‐2 coronavirus. Here, we examine the architecture and self‐assembly properties of the SARS‐CoV‐2 nucleocapsid protein, which packages viral RNA into new virions. We determined a 1.4 Å resolution crystal structure of this protein's N2b domain, revealing a compact, intertwined dimer similar to that of related coronaviruses including SARS‐CoV. While the N2b domain forms a dimer in solution, addition of the C‐terminal spacer B/N3 domain mediates formation of a homotetramer. Using hydrogen‐deuterium exchange mass spectrometry, we find evidence that at least part of this putatively disordered domain is structured, potentially forming an α‐helix that self‐associates and cooperates with the N2b domain to mediate tetramer formation. Finally, we map the locations of amino acid substitutions in the N protein from over 38,000 SARS‐CoV‐2 genome sequences. We find that these substitutions are strongly clustered in the protein's N2a linker domain, and that substitutions within the N1b and N2b domains cluster away from their functional RNA binding and dimerization interfaces. Overall, this work reveals the architecture and self‐assembly properties of a key protein in the SARS‐CoV‐2 life cycle, with implications for both drug design and antibody‐based testing.
Testicular volume in non‐obstructive azoospermia with a history of bilateral cryptorchidism may predict successful sperm retrieval by testicular sperm extraction
Authors: Osaka Akiyoshi , Iwahata Toshiyuki , Kobori Yoshitomo , Shimomura Yukihito , Yoshikawa Naoki , Onota Shin , Yamamoto Atsushi , Ide Hisamitsu , Sugimoto Kouhei , Okada Hiroshi 
Published: July 2020

AbstractPurposeCryptorchidism is one of the most common causes of non‐obstructive azoospermia (NOA) in adulthood. Even if early orchidopexy is performed to preserve fertility potential, some patients still suffer from azoospermia. Fertility potential is significantly lower in bilateral than unilateral cryptorchidism. The aims of this study were to identify clinical parameters that predict the likely success of sperm recovery by microscopic testicular sperm extraction (micro‐TESE) and also the likely outcome of intracytoplasmic sperm injection using sperm from NOA patients who submitted to bilateral orchidopexy.MethodsFifty‐two NOA patients with a history of bilateral cryptorchidism underwent micro‐TESE. The following clinical parameters were evaluated as predictive factors for successful sperm recovery: age at micro‐TESE; age at orchidopexy; period from orchidopexy to micro‐TESE; luteinizing hormone (LH); follicle‐stimulating hormone (FSH); testosterone; average testicular volume; and body mass index.ResultsIn the successful sperm retrieval group, average testicular volume was significantly greater, while serum LH and FSH, and body mass index were significantly lower. In a multivariate analysis, average testicular volume was positively correlated with successful sperm recovery.ConclusionOur results indicate that testicular volume in NOA patients with bilateral cryptorchidism is a predictor for successful sperm recovery.
Oxycodone injections not paired with conditioned place preference have little effect on the hippocampal opioid system in female and male rats
Authors: Ashirova Elina , Contoreggi Natalina H. , Johnson Megan A. , Al‐Khayat Fatima J. , Calcano Gabriela A. , Rubin Batsheva R. , O’Cinneide Emma M. , Zhang Yong , Zhou Yan , Gregoire Lennox , McEwen Bruce S. , Kreek Mary Jeanne , Milner Teresa A. 
Published: July 2020

AbstractOxycodone (Oxy) conditioned place preference (CPP) in Sprague Dawley rats results in sex‐specific alterations in hippocampal opioid circuits in a manner that facilitates opioid‐associative learning processes, particularly in females. Here, we examined if Oxy (3 mg/kg, I.P.) or saline (Sal) injections not paired with behavioral testing similarly affect the hippocampal opioid system. Sal‐injected females compared to Sal‐injected males had: (1) higher densities of cytoplasmic delta opioid receptors (DOR) in GABAergic hilar dendrites suggesting higher baseline reserve DOR pools and (2) elevated phosphorylated DOR levels, but lower phosphorylated mu opioid receptor (MOR) levels in CA3a suggesting that the baseline pools of activated opioid receptors vary in females and males. In contrast to CPP studies, Oxy‐injections in the absence of behavioral tests resulted in few changes in the hippocampal opioid system in either females or males. Specifically, Oxy‐injected males compared to Sal‐injected males had fewer DORs near the plasma membrane of CA3 pyramidal cell dendrites and in CA3 dendritic spines contacted by mossy fibers, and lower pMOR levels in CA3a. Oxy‐injected females compared to Sal‐injected females had higher total DORs in GABAergic dendrites and lower total MORs in parvalbumin‐containing dendrites. Thus, unlike Oxy CPP, Oxy‐injections redistributed opioid receptors in hippocampal neurons in a manner that would either decrease (males) or not alter (females) excitability and plasticity processes. These results indicate that the majority of changes within hippocampal opioid circuits that would promote opioid‐associative learning processes in both females and males do not occur with Oxy administration alone, and instead must be paired with CPP.
Activated carbon column adsorption of compounds that mimic urban stormwater dissolved organic nitrogen
Authors: Mohtadi Mehrdad , James Bruce R. , Davis Allen P. 
Published: July 2020

AbstractNutrients mobilized by stormwater can exacerbate eutrophication in receiving waters. While bioretention systems are increasingly employed to improve stormwater quality, they do not normally incorporate design attributes for removal of dissolved organic nitrogen (DON). Thus, the current study concentrated on continuous column adsorption of stormwater DON using a media mixture of coal activated carbon and quartz sand. Adsorption of eight model organic nitrogenous compounds was studied and only pyrrole showed an appreciable adsorption performance; other organic nitrogen compounds were weakly adsorbed. The breakthrough depth for pyrrole was 88 m (equivalent to 4.4 m simulated rainfall depth), at a superficial velocity of 61 cm/hr and influent DON concentration of 1 mg N/L. Subsequent experiments revealed that adsorption of pyrrole was minimally affected by superficial velocity, such that its DON removal efficiency was greater than 91% for all tested superficial velocities (7–489 cm/hr). Accordingly, adsorption processes may be employed for removing stormwater DON fractions behaving similarly to pyrrole; data suggest DON removal initially at greater than 95%, gradually falling to 30% through 25 years of service.Practitioner points

Adsorption of eight different organic nitrogenous compounds onto coal‐based activated carbon was investigated.

Amino acids and an amino sugar were weakly adsorbed onto the activated carbon.

Pyrrole, a moderately hydrophobic heterocyclic organic nitrogen compound was effectively adsorbed.

A 30‐cm depth was considered as adequate for removal of pyrrole and compounds that would similarly adsorb.

Evidence of biological ammonification was present in all studies except for pyrrole.
A comparison of thyroidal protection by stable iodine or perchlorate in the case of acute or prolonged radioiodine exposure
Authors: Eder Stefan , Hermann Cornelius , Lamkowski Andreas , Kinoshita Manabu , Yamamoto Tetsuo , Abend Michael , Shinomiya Nariyoshi , Port Matthias , Rump Alexis 
Published: July 2020

AbstractIn the case of a nuclear power plant accident, repetitive/prolonged radioiodine release may occur. Radioiodine accumulates in the thyroid and by irradiation enhances the risk of cancer. Large doses of non-radioactive iodine may protect the thyroid by inhibiting radioiodine uptake into the gland (iodine blockade). Protection is based on a competition at the active carrier site in the cellular membrane and the Wolff–Chaikoff effect, the latter being, however, only transient (24–48 h). Perchlorate may alternatively provide protection by a carrier competition mechanism only. Perchlorate has, however, a stronger affinity to the carrier than iodide. Based on an established biokinetic–dosimetric model developed to study iodine blockade, and after its extension to describe perchlorate pharmacokinetics and the inhibition of iodine transport through the carrier, we computed the protective efficacies that can be achieved by stable iodine or perchlorate in the case of an acute or prolonged radioiodine exposure. In the case of acute radioiodine exposure, perchlorate is less potent than stable iodine considering its ED50. A dose of 100 mg stable iodine has roughly the same protective efficacy as 1000 mg perchlorate. For prolonged exposures, single doses of protective agents, whether stable iodine or perchlorate, offer substantially lower protection than after acute radioiodine exposure, and thus repetitive administrations seem necessary. In case of prolonged exposure, the higher affinity of perchlorate for the carrier in combination with the fading Wolff–Chaikoff effect of iodine confers perchlorate a higher protective efficacy compared to stable iodine. Taking into account the frequency and seriousness of adverse effects, iodine and perchlorate at equieffective dosages seem to be alternatives in case of short-term acute radioiodine exposure, whereas preference should be given to perchlorate in view of its higher protective efficacy in the case of longer lasting radioiodine exposures.