bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic multiatlas selection‐based consensus segmentation of head and neck structures from CT images
Authors: Haq Rabia , Berry Sean L. , Deasy Joseph O. , Hunt Margie , Veeraraghavan Harini 
Published: October 2019

PurposeManual delineation of head and neck (H&N) organ‐at‐risk (OAR) structures for radiation therapy planning is time consuming and highly variable. Therefore, we developed a dynamic multiatlas selection‐based approach for fast and reproducible segmentation.MethodsOur approach dynamically selects and weights the appropriate number of atlases for weighted label fusion and generates segmentations and consensus maps indicating voxel‐wise agreement between different atlases. Atlases were selected for a target as those exceeding an alignment weight called dynamic atlas attention index. Alignment weights were computed at the image level and called global weighted voting (GWV) or at the structure level and called structure weighted voting (SWV) by using a normalized metric computed as the sum of squared distances of computed tomography (CT)‐radiodensity and modality‐independent neighborhood descriptors (extracting edge information). Performance comparisons were performed using 77 H&N CT images from an internal Memorial Sloan‐Kettering Cancer Center dataset (N = 45) and an external dataset (N = 32) using Dice similarity coefficient (DSC), Hausdorff distance (HD), 95th percentile of HD, median of maximum surface distance, and volume ratio error against expert delineation. Pairwise DSC accuracy comparisons of proposed (GWV, SWV) vs single best atlas (BA) or majority voting (MV) methods were performed using Wilcoxon rank‐sum tests.ResultsBoth SWV and GWV methods produced significantly better segmentation accuracy than BA (P < 0.001) and MV (P < 0.001) for all OARs within both datasets. SWV generated the most accurate segmentations with DSC of: 0.88 for oral cavity, 0.85 for mandible, 0.84 for cord, 0.76 for brainstem and parotids, 0.71 for larynx, and 0.60 for submandibular glands. SWV’s accuracy exceeded GWV's for submandibular glands (DSC = 0.60 vs 0.52, P = 0.019).ConclusionsThe contributed SWV and GWV methods generated more accurate automated segmentations than the other two multiatlas‐based segmentation techniques. The consensus maps could be combined with segmentations to visualize voxel‐wise consensus between atlases within OARs during manual review.
Effects of iso‐α‐acids, the hop‐derived bitter components in beer, on the MRI‐based Brain Healthcare Quotient in healthy middle‐aged to older adults
Authors: Kita Masahiro , Yoshida Satoshi , Kondo Keiji , Yamakawa Yoshinori , Ano Yasuhisa 
Published: October 2019

AbstractAimNeurological disorders are a major public health issue worldwide and are often associated with structural changes in the brain. We have previously demonstrated that iso‐α‐acids (IAAs), the hop‐derived bitter components in beer, improve memory impairment in aged and Alzheimer's disease mouse models. In this study, we evaluated the effects of IAA intake on the brain structure in healthy middle‐aged to older adults. This study was conducted under the Impulsing Paradigm Change through Disruptive Technologies Program (ImPACT) study launched by the Cabinet office of Japan.MethodThis study employed an open‐labeled, single‐arm, before and after design. Healthy middle‐aged to older adults consumed a beverage containing IAAs (3 mg/190 mL) for 4 weeks.Recently developed magnetic resonance imaging‐based brain health indicators were used to evaluate the following brain conditions: the Brain Healthcare Quotient (BHQ) based on gray matter volume (GM‐BHQ) and white matter fractional anisotropy (FA‐BHQ).ResultsIn total, 25 subjects were recruited, and GM‐BHQ and FA‐BHQ were measured before and after intervention. In all subjects, no significant differences in GM‐BHQ and FA‐BHQ were observed. In subjects aged ≥ 60 years (mean 54.5; standard deviation 3.9) (n = 8), GM‐BHQ was significantly increased 4 weeks after intervention compared with that before intervention.ConclusionIntake of beverages containing IAAs might affect brain aging, particularly in healthy older adults, which may prevent the development of neurological disorders. Future studies employing more robust designs can elucidate the effects of IAAs on GM‐BHQ and cognitive functions.
Mapping bedrock topography and moraine deposits by transient electromagnetic sounding: Oslo graben, Norway
Authors: Barsukov Pavel O. , Fainberg Edward B. 
Published: October 2019

ABSTRACTIn this research, we have studied the capabilities and limitations of the transient electromagnetic sounding applied to investigate the structure and composition of the moraine deposits covering a crystalline basement. It has been experimentally demonstrated that using the ungrounded antennas one can not only determine the electrical resistivity of different layers in the alluvium deposits and map the surface topography of the crystalline basement down to a depth of 70–100 m, but can also minimize the costs and the damage done to the environment. Additionally, transient electromagnetics helps to reveal the layers within the moraine strata that often have different resistivities and depths. The use of single antennas of size 12 m × 12 m–25 m × 25 m for field excitation and registration of transient responses allows for maximum localization of the targets and provides a high horizontal resolution in strongly heterogeneous media. The limitations of the method due to the induced polarization effect have also been investigated. Overall, despite some limitations, the transient electromagnetic method appears to be effective in the mapping, assessment and analysis of hazards in landslide‐prone areas, prior to geotechnical soundings in wells.
Risk Factors and Outcomes Associated with Prolonged Subtherapeutic Anticoagulation with Bivalirudin: A Retrospective Cohort Study
Authors: Orzel Libby A. , Abel Erik E. , Blais Danielle M. , Wang Tzu‐Fei , Porter Kyle A. , Burcham Pamela K. 
Published: October 2019

BackgroundBivalirudin, a direct thrombin inhibitor, is a treatment option for the management of heparin‐induced thrombocytopenia (HIT) and other coagulation disorders. To date, no published studies have identified patients at risk for or the consequence of subtherapeutic bivalirudin therapy.ObjectivesThe primary objective was to identify factors associated with failure to achieve early therapeutic anticoagulation (ETA) with bivalirudin, defined as achievement of two consecutive therapeutic activated partial thromboplastin times (aPTTs) within 24 hours. Secondary objectives included evaluating whether failure to achieve ETA was a risk factor for clinical outcomes of interest including thromboembolism, hemorrhage, and mortality.Patients/MethodsThis was a retrospective cohort study. Patients between the ages of 18 and 89 years treated with bivalirudin for 24 hours or longer were identified and classified as either achieving or failing to achieve ETA.ResultsNonadherence to the dosing protocol (odds ratio [OR] 1.7, 95% confidence interval [CI] 1.07‐2.71) and creatinine clearance (CrCl) of 60 ml/min or greater (OR 2.99, 95% CI 1.12‐7.97) were significantly associated with failure to achieve ETA in univariate analyses. Conversely, increasing age (OR 0.98, 95% CI 0.97‐0.99) was significantly associated with achievement of ETA. Failure to achieve ETA was associated with a 4‐fold increase in the odds of thromboembolism.ConclusionsYounger age, normal renal function, and nonadherence to the dosing protocol when targeting therapeutic anticoagulation is associated with increased risk of failure to achieve ETA. This confers an elevated risk of thromboembolism when using bivalirudin for the management of HIT or other coagulation disorders.
Paramagnetic relaxation enhancement‐assisted structural characterization of a partially disordered conformation of ubiquitin
Authors: Wakamoto Takuro , Ikeya Teppei , Kitazawa Soichiro , Baxter Nicola J. , Williamson Mike P. , Kitahara Ryo 
Published: October 2019

AbstractNuclear magnetic resonance (NMR) is a powerful tool to study three‐dimensional structures as well as protein conformational fluctuations in solution, but it is compromised by increases in peak widths and missing signals. We previously reported that ubiquitin has two folded conformations, N1 and N2 and plus another folded conformation, I, in which some amide group signals of residues 33–41 almost disappeared above 3 kbar at pH 4.5 and 273 K. Thus, well‐converged structural models could not be obtained for this region owing to the absence of distance restraints. Here, we reexamine the problem using the ubiquitin Q41N variant as a model for this locally disordered conformation, I. We demonstrate that the variant shows pressure‐induced loss of backbone amide group signals at residues 28, 33, 36, and 39–41 like the wild‐type, with a similar but smaller effect on CαH and CβH signals. In order to characterize this I structure, we measured paramagnetic relaxation enhancement (PRE) under high pressure to obtain distance restraints, and calculated the structure assisted by Bayesian inference. We conclude that the more disordered I conformation observed at pH 4.0, 278 K, and 2.5 kbar largely retained the N2 conformation, although the amide groups at residues 33–41 have more heterogeneous conformations and more contact with water, which differ from the N1 and N2 states. The PRE‐assisted strategy has the potential to improve structural characterization of proteins that lack NMR signals, especially for relatively more open and hydrated protein conformations.
Pre‐planting weed detection based on ground field spectral data
Authors: Pott Luan P , Amado Telmo JC , Schwalbert Raí A , Sebem Elodio , Jugulam Mithila , Ciampitti Ignacio A 
Published: October 2019

AbstractBACKGROUNDSite‐specific weed management (SSWM) demands higher resolution data for mapping weeds in fields, but the success of this tool relies on the efficiency of optical sensors to discriminate weeds relative to other targets (soils and residues) before cash crop establishment. The objectives of this study were to (i) evaluate the accuracy of spectral bands to differentiate weeds (target) and other non‐targets, (ii) access vegetation indices (VIs) to assist in the discrimination process, and (iii) evaluate the accuracy of the thresholds to distinguish weeds relative to non‐targets for each VI using training and validation data sets.RESULTSThe main outcomes of this study for effectively distinguishing weeds from other non‐targets are (i) training and validation data exhibited similar spectral curves, (ii) red and near‐infrared spectral bands presented greater accuracy relative to the other bands, and (iii) the tested VIs increased the discrimination accuracy related to single bands, with an overall accuracy above 95% and a kappa above 0.93.CONCLUSIONThis study provided a novel approach to distinguish weeds from other non‐targets utilizing a ground‐level sensor before cash crop planting based on field spectral data. However, the limitations of this study are related to the spatial resolution to distinguish weeds that might be closer to the one this study presented, and also related to the soil and crop residues conditions at the time of collecting the readings. Overall the results presented contribute to an improved understanding of spectral signatures from different targets (weeds, soils, and residues) before planting time supporting SSWM. © 2019 Society of Chemical Industry
A note on non‐negativity correction for a multimoment finite‐volume transport model with WENO limiter
Authors: Li Xingliang , Shen Xueshun , Chen Chungang , Tang Jie , Xiao Feng 
Published: October 2019

AbstractAn oscillation‐less multimoment global transport model was proposed by Tang et al. in 2018 by introducing a slope limiter based on the weighted essentially non‐oscillatory (WENO) concept. The spurious oscillations around the discontinuities and strong gradients can be effectively removed and the model preserves the fourth‐order accuracy in spherical geometry for smooth solutions. However, the WENO limiter does not strictly guarantee the non‐negativity of numerical solution and the resulting model will violate the physical principle due to the existence of the nonphysical negative undershoots. As the numerical fluxes, which determine the time tendency of the volume‐integrated average, are evaluated by the point values (PVs) defined along the cell boundaries in the multimoment finite‐volume schemes, the non‐negativity preserving model can be accomplished by modifying those PVs to implement the corrections on the numerical fluxes proposed in the positive definite flux‐corrected transport (FCT) method by Smolarkiewicz in 1989. In this study, a non‐negativity correction algorithm is proposed for a global transport model using the MM‐FVM_WENO scheme and verified by simulating the widely used benchmark tests.
Benzyl isothiocyanate promotes miR‐99a expression through ERK/AP‐1‐dependent pathway in bladder cancer cells
Authors: Tsai Te‐Fu , Chen Po‐Chun , Lin Yi‐Chia , Chou Kuang‐Yu , Chen Hung‐En , Ho Chao‐Yen , Lin Ji‐Fan , Hwang Thomas I‐S. 
Published: October 2019

AbstractBenzyl isothiocyanate (BITC), a bioactive natural product present in cruciferous vegetables, has been proved to prevent cancer progression through various mechanisms. In our previous report, we proved that BITC exhibits antitumor effects in bladder cancer by suppressing IGF1R, FGFR3, and mTOR, which is mediated by miR‐99a expression. In this study, we identified the signal pathway involved in regulating miR‐99a expression after BITC exposure in bladder cancer. Treatment with different BITC concentrations resulted in induction of miR‐99a expression in bladder cancer cell lines. Activation of extracellular signal‐regulated protein kinase (ERK) and c‐jun N‐terminal kinase was observed in bladder cancer after BITC treatment for 24 hours. Interestingly, by using a chemical inhibitor of candidate pathways, we found that only the ERK signal pathway is required for miR‐99a expression. Furthermore, we evaluated the transcription factor that may contribute to miR‐99a expression in response to BITC treatment. The results indicated that c‐Jun/AP‐1 was activated after BITC treatment. Moreover, we confirmed c‐Jun/AP‐1 activation through immunofluorescence and the luciferase reporter assay. The results showed that BITC treatment markedly improved nuclear translocation of c‐Jun/AP‐1 and luciferase activity dose dependently. Finally, pretreatment with the ERK inhibitor U0126 diminished c‐Jun phosphorylation and transcriptional activation, suggesting that BITC elicits ERK/c‐Jun signal transduction, which is responsible for miR‐99a expression in bladder cancer. The present work identifies the mechanism involved in upregulation miR‐99a after BITC treatment, which provides an explanation for BITC biological function in our previous work.
Prevalence of Antiphospholipid Antibodies Negativisation in Patients with Antiphospholipid Syndrome: A Long-Term Follow-Up Multicentre Study
Authors: Radin Massimo , Schreiber Karen , Sciascia Savino , Roccatello Dario , Cecchi Irene , Aguirre Zamorano María Ángeles , Cuadrado Maria Jose 
Published: October 2019

Abstract
Objective This article aims to analyse the rate of antiphospholipid antibodies (aPL) negativisation in patients with antiphospholipid syndrome (APS), and to evaluate potential new clinical manifestations after negativisation and/or aPL fluctuations in a long-term follow-up.
Methods Inclusion criteria are (1) any patients with an APS diagnosis according to the current Sydney criteria and (2) patients in whom aPL negativisation occurred. aPL negativisation was defined as repeated aPL measurements on at least two consecutive occasions at least 12 weeks apart, with a follow-up of at least 1 year since aPL first turned negative.
Results Out of 259 APS patients, a total of 23 patients (8.9%) met the inclusion criteria for persistent aPL negativisation. Patients were followed-up for 14.4 ± 8.1 years, experienced aPL negativisation after a mean of 5.3 ± 3.5 years and were followed-up after experiencing the aPL negativisation for a mean of 7.6 ± 5.8 years. Seventeen patients (73.9%) presented with thrombotic APS, 2 with pregnancy morbidity (8.7%) and 4 (17.4%) with both. Most of the patients (18; 78.3%) had a single aPL positivity, 5 (21.7%) double, while no triple aPL positivity was observed. At the time of data collection, after aPL negativisation, anticoagulation was stopped in 8 patients with previous thrombotic venous event (8/21, 38%) according to the treating physicians' judgements. None of the patients experienced any recurrent thrombotic event during the follow-up period after their aPL negativisation.
Conclusion In our patient cohort consisting of 259 patients with definitive APS, we observed over a mean observation period of > 5 years, that aPL negativisation occurred in approximately 9% of patients. Negativisation occurred most often in patients who were previously found to be positive for only one aPL.
Evaluation of a New, Rapid, Fully Automated Assay for the Measurement of ADAMTS13 Activity
Authors: Valsecchi Carla , Mirabet Maribel , Mancini Ilaria , Biganzoli Marina , Schiavone Lucia , Faraudo Susanna , Mane-Padros Daniel , Giles David , Serra-Domenech Josep , Blanch Silvia , Trisolini Silvia Maria , Facchini Luca , Rinaldi Erminia , Peyvandi Flora 
Published: October 2019

AbstractThrombotic thrombocytopenic purpura (TTP) is a rare thrombotic microangiopathy (TMA) characterized by the severe deficiency of a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13 (ADAMTS13) activity (< 10%). Rapid ADAMTS13 testing is crucial for an early diagnosis and optimal management of acute TTP. We evaluated the performance of the HemosIL AcuStar ADAMTS13 activity assay (Instrumentation Laboratory, Bedford, Massachusetts, United States), a fully automated chemiluminescent immunoassay with an analytical time of 33 minutes. A method comparison study was performed on 176 samples from 49 healthy donors and 127 TMA patients (109 TTP, 7 atypical hemolytic uremic syndrome, 11 other TMAs), comparing this new assay with an in-house FRETS-VWF73 assay and a commercial enzyme-linked immunosorbent assay (ELISA) (TECHNOZYM ADAMTS-13 Activity, Technoclone GmbH, Vienna, Austria). Agreement between methods was assessed with focus on ADAMTS13 activity less than 10%, the medical decision level relevant for TTP diagnosis. The HemosIL AcuStar ADAMTS13 Activity showed good correlation with both the FRETS-VWF73 (r = 0.96) and ELISA (r = 0.96) methods. Slope of the Passing–Bablok regression was 1.05 for FRETS-VWF73 and 1.02 for ELISA, and absolute bias at the medical decision level was +0.1 and +0.3%, respectively. The study also revealed high agreement with FRETS-VWF73 (kappa 0.97) and ELISA (kappa 0.98) methods in classifying TTP patients with a severe deficiency of ADAMTS13 activity. Because of its short turnaround time and full automation, the HemosIL AcuStar ADAMTS13 activity assay might become the assay of choice to rapidly test ADAMTS13 activity in plasma and thus establish the diagnosis of acute TTP in emergency settings.
Parental Education May Differentially Impact Pediatric Inflammatory Bowel Disease Phenotype Risk
Authors: Krishna Mahesh , Salako Aziza , Fofanova Tatiana , Kellermayer Richard 
Published: October 2019

Abstract

Background
The incidence of pediatric inflammatory bowel diseases (PIBDs: Crohn’s disease [CD], ulcerative colitis [UC]) is on the rise around the world. Yet, the critical risk factors for this rising incidence are not well understood. Demographic characteristics of PIBD may improve our understanding of their developmental origins and aid in prevention.

Methods
Four hundred eighty-eight consecutive PIBD patients diagnosed at Texas Children’s Hospital from 13 counties around Houston were studied. An annual incidence map was created by ZIP code of residence at diagnosis by using ArcGIS and the American Community Survey from the US Census Bureau. Correlation between demographic variables and PIBD incidence was examined. A model to explain incidence from different health factors was created in R.

Results
Hispanic children were more likely to be diagnosed with UC (P &lt; 0.01) and unclassified IBD (IBD-U) (P &lt; 0.03) compared with other races/ethnicities. A significant positive correlation (r = 0.35, P &lt; 0.0001) between median household income and PIBD incidence was observed (UC: r = 0.23, P &lt; 0.0001; CD: r = 0.22, P = 0.0004). ZIP codes with majority college-educated adults had a higher incidence of PIBD than ZIP codes with majority high school–educated adults (P &lt; 0.0001). Pediatric cases with CD were more common in ZIP codes where the majority of adults were college educated (P &lt; 0.0001). Pediatric cases with UC, however, were more common in ZIP codes where the majority of adults were high school educated (P = 0.0036).

Conclusions
Hispanic children more commonly present with UC and IBD-U in southern USA. Household income and/or adult education–related environmental/dietary differences may be important in the developmental origins of PIBD in large metro areas, such as Houston.
Detection of Fluorescent Powders and Their Effect on Survival and Recapture of Aedes aegypti (Diptera: Culicidae)
Authors: Rojas-Araya Diana , Alto Barry W , Burkett-Cadena Nathan , Cummings Derek At 
Published: October 2019

Abstract
The use of insect markers, such as fluorescent powders, is a useful tool for studying ecological and epidemiological questions. Evaluating their effect on vectors of human disease agents, such as the invasive mosquito vector Aedes aegypti (Linnaeus), is crucial for their practical and reliable use, especially in parameters linked to the risk of disease transmission such as adult survival, dispersal, and host-seeking. Seven fluorescent powders (Hercules Radiant, DayGlo (DG), Risk Reactor (RR), and Angstrom Technologies), applied externally on cohorts of Ae. aegypti female mosquitoes, were tested to determine their impact on survival and recapture by baited mosquito traps, and their detectability after being exposed to controlled laboratory and semifield environments. There were no significant differences in survival among marked and unmarked females across all powders. Marked females were significantly less likely to be captured in baited traps relative to unmarked females, except for one of the DG powders. All females remained visibly marked on five parts of their body for 30 d (under both environments), except for one of the RR powders. The tested powders and application method are suitable for tracking mosquitoes throughout most of their lives under different environments, without significantly affecting their survival, but with potential impact on recapture by baited traps, possibly due to effects on senses or other physiological traits.