bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross‐modality (CT‐MRI) prior augmented deep learning for robust lung tumor segmentation from small MR datasets
Authors: Jiang Jue , Hu Yu‐Chi , Tyagi Neelam , Zhang Pengpeng , Rimner Andreas , Deasy Joseph O. , Veeraraghavan Harini 
Published: July 2019

PurposeAccurate tumor segmentation is a requirement for magnetic resonance (MR)‐based radiotherapy. Lack of large expert annotated MR datasets makes training deep learning models difficult. Therefore, a cross‐modality (MR‐CT) deep learning segmentation approach that augments training data using pseudo MR images produced by transforming expert‐segmented CT images was developed.MethodsEighty‐one T2‐weighted MRI scans from 28 patients with non‐small cell lung cancers (nine with pretreatment and weekly MRI and the remainder with pre‐treatment MRI scans) were analyzed. Cross‐modality model encoding the transformation of CT to pseudo MR images resembling T2w MRI was learned as a generative adversarial deep learning network. This model was used to translate 377 expert segmented non‐small cell lung cancer CT scans from the Cancer Imaging Archive into pseudo MRI that served as additional training set. This method was benchmarked against shallow learning using random forest, standard data augmentation, and three state‐of‐the art adversarial learning‐based cross‐modality data (pseudo MR) augmentation methods. Segmentation accuracy was computed using Dice similarity coefficient (DSC), Hausdorff distance metrics, and volume ratio.ResultsThe proposed approach produced the lowest statistical variability in the intensity distribution between pseudo and T2w MR images measured as Kullback–Leibler divergence of 0.069. This method produced the highest segmentation accuracy with a DSC of (0.75 ± 0.12) and the lowest Hausdorff distance of (9.36 mm ± 6.00 mm) on the test dataset using a U‐Net structure. This approach produced highly similar estimations of tumor growth as an expert (P = 0.37).ConclusionsA novel deep learning MR segmentation was developed that overcomes the limitation of learning robust models from small datasets by leveraging learned cross‐modality information using a model that explicitly incorporates knowledge of tumors in modality translation to augment segmentation training. The results show the feasibility of the approach and the corresponding improvement over the state‐of‐the‐art methods.
DNA methylation regulated by ascorbic acids in yak preimplantation embryo helps to improve blastocyst quality
Authors: Li Qin , Pan Yangyang , He Honghong , Hu Xuequan , Zhao Tian , Jiang Jiaying , Cui Yan , Xu Gengquan , Wang Libin , He Junfeng , Fan Jiangfeng , Yu Sijiu 
Published: July 2019

AbstractDNA methylation as an important, essential epigenetic modification is critical for the successful development of mammalian embryos. In recent years, the important role of ascorbic acid (AA) as an irreplaceable cofactor for epigenetic regulation has been confirmed. However, the effect of AA on DNA methylation in preimplantation embryo development of plateau yak remains unknown. In this study, we explored whether AA can help regulates DNA methylation in yak preimplantation embryos to improve the blastocyst quality. First, our results indicate that the preimplantation of the yak still follows the classical pattern of DNA demethylation and remethylation, however, remethylation occurs in the blastocyst stage. Second, the unique expression pattern of the ten‐eleven translocation enzyme (TET3) in the cytoplasm plays a key role in the demethylation mechanism. Third, in the blastocyst stage, the pluripotency gene CDX2 promoter region was in a hypomethylated state, and the POU5F1, SOX2, and NANOG promoter regions were in moderate methylation states. In addition, treatment with 50 μg/ml AA mainly improved the expression levels of DNMT1, DNMT3a, and TET3, ensured the establishment, maintenance and transition of 5‐methylcytosine. After AA treatment, the methylation level of the pluripotency genes NANOG promoter regions was significantly reduced, and the mRNA transcript abundance of the pluripotency genes NANOG, POU5F1, and CDX2 was upregulated. In conclusion, our findings suggest that AA could increase blastocyst cell numbers by regulating DNA methylation of yak preimplantation embryos
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β‐Amyloid aggregation and heterogeneous nucleation
Authors: Srivastava Atul K. , Pittman Jay M. , Zerweck Jonathan , Venkata Bharat S. , Moore Patrick C. , Sachleben Joseph R. , Meredith Stephen C. 
Published: July 2019

AbstractIn this article, we consider the role of heterogeneous nucleation in β‐amyloid aggregation. Heterogeneous nucleation is more common and occurs at lower levels of supersaturation than homogeneous nucleation. The nucleation period is also the stage at which most of the polymorphism of amyloids arises, this being one of the defining features of amyloids. We focus on several well‐known heterogeneous nucleators of β‐amyloid, including lipid surfaces, especially those enriched in gangliosides and cholesterol, and divalent metal ions. These two broad classes of nucleators affect β‐amyloid particularly in light of the amphiphilicity of these peptides: the N‐terminal region, which is largely polar and charged, contains the metal binding site, whereas the C‐terminal region is aliphatic and is important in lipid binding. Notably, these two classes of nucleators can interact cooperatively, aggregation begetting greater aggregation.
Ultrafast Carrier Dynamics and Bandgap Renormalization in Layered PtSe2
Authors: Wang Gaozhong , Wang Kangpeng , McEvoy Niall , Bai Zhengyuan , Cullen Conor P. , Murphy Conor N. , McManus John B. , Magan John J. , Smith Christopher M. , Duesberg Georg S. , Kaminer Ido , Wang Jun , Blau Werner J. 
Published: July 2019

AbstractCarrier interactions in 2D nanostructures are of central importance not only in condensed‐matter physics but also for a wide range of optoelectronic and photonic applications. Here, new insights into the behavior of photoinduced carriers in layered platinum diselenide (PtSe2) through ultrafast time‐resolved pump–probe and nonlinear optical measurements are presented. The measurements reveal the temporal evolution of carrier relaxation, chemical potential and bandgap renormalization in PtSe2. These results imply that few‐layer PtSe2 has a semiconductor‐like carrier relaxation instead of a metal‐like one. The relaxation follows a triple‐exponential decay process and exhibits thickness‐dependent relaxation times. This occurs along with a band‐filling effect, which can be controlled based on the number of layers and may be applied in saturable absorption for generating ultrafast laser pulses. The findings may provide means to study many‐body physics in 2D materials as well as potentially leading to applications in the field of optoelectronics and ultrafast photonics.
Influence of shear‐axial force interaction on the seismic performance of a piloti building subjected to the 2017 earthquake in Pohang Korea
Authors: Dang‐Vu Hoang , Lee Do H. , Shin Jiuk , Lee Kihak 
Published: July 2019

AbstractThis study aims to investigate the influence of shear‐axial force interaction on the seismic performance of a piloti‐type building subjected to the Pohang earthquake. For this purpose, a four‐story piloti‐type building in Pohang, Korea whose columns were brutally damaged by the 2017 Pohang earthquake, one of this country's strongest earthquakes in modern history, was chosen as the object of the study. Columns of this piloti‐type building were designed with insufficient transverse reinforcement, resulting in an increased potential for shear‐axial failure. The piloti‐type building was simulated using Zeus‐NL, an efficient analysis and simulation platform developed for earthquake engineering applications to perform nonlinear time history analysis. A hysteretic shear model in Zeus‐NL capable of accounting for the variation in column axial force was adopted to capture the effect of the shear‐axial force interaction, caused by a combination of horizontal and vertical ground motions. The shear model was validated by comparing the simulated and experimental results. The seismic performance of the piloti‐type building under the effect of the shear‐axial force interaction was compared with that under the shear effect only. Results have indicated that shear effect and shear‐axial force interaction effect significantly reduce column maximum shear force and increase column drift demand. The influence is more intense considering shear‐axial interaction. The seismic response in terms of hysteretic behavior, energy dissipation, and stiffness degradation is presented and discussed.
Changes in design driving load cases: Operating an upwind turbine with a downwind rotor configuration
Authors: Wanke Gesine , Bergami Leonardo , Larsen Torben J. , Hansen Morten H. 
Published: July 2019

AbstractThis work considers the design driving load cases from a full design load basis analysis on an upwind turbine changed into a downwind configuration. The upwind turbine is a commercial class IIIA 2.1‐MW turbine, manufactured by Suzlon. The downwind turbine shows an increase in the normalized tower clearance by 6%, compared with the upwind concept. Removing the blade prebend increases the normalized minimum tower clearance by 17% in the downwind configuration compared with the upwind configuration. The extreme loads on the longitudinal tower bottom bending moment are seen to generally increase by 17% because of the overhanging gravity moment of the rotor‐nacelle assembly. The extreme blade root bending moments are reduced by 10% flapwise, because of the coning of the rotor in downwind direction. The fatigue loads suffer from the tower shadow, leading to an overall increase of the fatigue loads in the blades with up to 5% in flapwise direction in the downwind configuration. Because of blade deflection and coning direction, the downwind configuration shows a 0.75% lower annual energy production. Removing the prebend increases the annual energy production loss to 1.66%.
Approximation Schemes for Mixed Optimal Stopping and Control Problems with Nonlinear Expectations and Jumps
Authors: Dumitrescu Roxana , Reisinger Christoph , Zhang Yufei 
Published: July 2019

AbstractWe propose a class of numerical schemes for mixed optimal stopping and control of processes with infinite activity jumps and where the objective is evaluated by a nonlinear expectation. Exploiting an approximation by switching systems, piecewise constant policy timestepping reduces the problem to nonlocal semi-linear equations with different control parameters, uncoupled over individual time steps, which we solve by fully implicit monotone approximations to the controlled diffusion and the nonlocal term, and specifically the Lax–Friedrichs scheme for the nonlinearity in the gradient. We establish a comparison principle for the switching system and demonstrate the convergence of the schemes, which subsequently gives a constructive proof for the existence of a solution to the switching system. Numerical experiments are presented for a recursive utility maximization problem to demonstrate the effectiveness of the new schemes.
Long-term Paleolithic diet is associated with lower resistant starch intake, different gut microbiota composition and increased serum TMAO concentrations
Authors: Genoni Angela , Christophersen Claus T. , Lo Johnny , Coghlan Megan , Boyce Mary C. , Bird Anthony R. , Lyons-Wall Philippa , Devine Amanda 
Published: July 2019

Abstract
Background
The Paleolithic diet is promoted worldwide for improved gut health. However, there is little evidence available to support these claims, with existing literature examining anthropometric and cardiometabolic outcomes.

Objective
To determine the association between dietary intake, markers of colonic health, microbiota, and serum trimethylamine-N-oxide (TMAO), a gut-derived metabolite associated with cardiovascular disease.

Design
In a cross-sectional design, long-term (n = 44, > 1 year) self-reported followers of a Paleolithic diet (PD) and controls (n = 47) consuming a diet typical of national recommendations were recruited. Diets were assessed via 3-day weighed diet records; 48-h stool for short chain fatty acids using GC/MS, microbial composition via 16S rRNA sequencing of the V4 region using Illumina MiSeq. TMAO was quantified using LC–MS/MS.

Results
Participants were grouped according to PD adherence; namely excluding grains and dairy products. Strict Paleolithic (SP) (n = 22) and Pseudo-Paleolithic (PP) (n = 22) groups were formed. General linear modelling with age, gender, energy intake and body fat percentage as covariates assessed differences between groups. Intake of resistant starch was lower in both Paleolithic groups, compared to controls [2.62, 1.26 vs 4.48 g/day (P < 0.05)]; PERMANOVA analysis showed differences in microbiota composition (P < 0.05), with higher abundance of TMA-producer Hungatella in both Paleolithic groups (P < 0.001). TMAO was higher in SP compared to PP and control (P < 0.01), and inversely associated with whole grain intake (r = − 0.34, P < 0.01).

Conclusions
Although the PD is promoted for improved gut health, results indicate long-term adherence is associated with different gut microbiota and increased TMAO. A variety of fiber components, including whole grain sources may be required to maintain gut and cardiovascular health.

Clinical trial registrations
Australian and New Zealand Clinical Trial Registry (ANZCTRN12616001703493).
Steam balloon concept for lifting rockets to launch altitude
Authors: Janhunen P. , Toivanen P. , Ruosteenoja K. 
Published: July 2019

ABSTRACTLaunching orbital and suborbital rockets from a high altitude is beneficial because of e.g. nozzle optimisation and reduced drag. Aircraft and gas balloons have been used for the purpose. Here we present a concept where a balloon is filled with pure water vapour on ground so that it rises to the launch altitude. The system resembles a gas balloon because no onboard energy source is carried, and no hard objects fall down. We simulate the ascent behaviour of the balloon. In the baseline simulation, we consider a 10 tonne rocket lifted to an altitude of 18 km.We model the trajectory of the balloon by taking into account steam adiabatic cooling, surface cooling, water condensation and balloon aerodynamic drag. The required steam mass proves to be only 1.4 times the mass of the rocket stage, and the ascent time is around 10 minutes. For small payloads, surface cooling increases the relative amount of steam needed, unless insulation is applied to the balloon skin. The ground-filled steam balloon seems to be an attractive and sustainable method of lifting payloads such as rockets into high altitude.
Numerical study of the rotational direction effect on aerodynamic loading characteristics of shipborne helicopter rotor
Authors: Su D.C. , Shi Y.J. , Xu G.H. 
Published: July 2019

ABSTRACTNumerical simulations of ship/rotor-coupled flowfield have been performed to investigate the rotational direction effects on a shipborne single-rotor helicopter in different deck landing trajectories (i.e., lateral and longitudinal translation) based on Reynolds-averaged Navier-Stokes (RANS) solver. Both the momentum source model and moving overset mesh model are employed to simulate the effect of the rotor on the ship airwake for different levels of fidelity requirement. The aerodynamic loading characteristics in terms of time-averaged and root-mean-square (RMS) thrust and pitch and roll moments are compared for two helicopter rotors with opposite rotation directions in a starboard 30 degrees wind condition. The time-averaged results show that the mean thrust of a counterclockwise rotor is greater than that of a clockwise rotor, particularly in the lateral translation phase. This suggests that a helicopter with a counterclockwise rotor could provide more collective control margin under this condition. Furthermore, a more significant reduction in pitch moment is experienced by the counterclockwise rotor during the two landing trajectories, and thus the effect of the aircraft being pulled towards the hangar tends to be more severe on the helicopter with the counterclockwise rotor. RMS loading results indicate that the unsteady loading levels on the clockwise rotor are much higher than that of the counterclockwise rotor in all three axes for most of the lateral and longitudinal translation phases. As a result, the pilot is likely to experience a higher workload when operating a helicopter with a clockwise rotor in the case of a deck landing in this wind condition.
The relative importance of CEOS and non-CEOS over firm performance
Authors: Bolinger Alex , Brookman Jeff , Thistle Paul 
Published: July 2019

AbstractThe purpose of this study is to examine the relative contributions of the CEO and other (non-CEO) top management team members to firm performance. Using data from ExecuComp, we analyze 2,687 CEOs and 11,501 other top management team (TMT) members, by industry, during the period 2004–2017 using variance decomposition methods. We find that other TMT member effects are important but are smaller than CEO effects. We also find that the effect of new TMT members appointed by the CEO on firm performance is larger than the effect of continuing TMT members and that this differential effect on performance increases with CEO tenure.
Characterization and phylogenomics of the complete mitochondrial genome of the polyzoic cestode Gangesia oligonchis (Platyhelminthes: Onchoproteocephalidea)
Authors: Li W.X. , Zhang D. , Fu P.P. , Song R. , Zou H. , Li M. , Wu S.G. , Wang G.T. 
Published: July 2019

Abstract
The order Onchoproteocephalidea (Eucestoda) was recently erected to accommodate the hook-bearing tetraphyllideans and the proteocephalideans, which are characterized by internal proglottization and a tetra-acetabulate scolex. The recognized subfamilies in the Proteocephalidae appeared to be non-monophyletic based on 28S recombinant DNA (rDNA) sequence data. Other molecular markers with higher phylogenetic resolution, such as large mitochondrial DNA fragments and multiple genes, are obviously needed. Thus the mitochondrial genome of Gangesia oligonchis, belonging to the putative earliest diverging group of the Proteocephalidae, was sequenced. The circular mitogenome of G. oligonchis was 13,958 bp in size, and contained the standard 36 genes: 22 transfer RNA genes, two rRNA genes and 12 protein-coding genes, as well as two major non-coding regions. A short NCR and a large NCR (lNCR) region were 216 bp and 419 bp in size, respectively. Highly repetitive regions in the lNCR region were detected with that of 11 repeat units. The mitogenome of G. oligonchis shared 71.1% nucleotide identity with Testudotaenia sp. WL-2016. Phylogenetic analyses of the complete mitochondrial genomes with Bayesian inference and maximum likelihood methods indicated that G. oligonchis formed a sister clade with Testudotaenia sp. WL-2016 with maximum support. The ordinal topology is (Caryophyllidea, (Diphyllobothriidea, (Bothriocephalidea, (Onchoproteocephalidea, Cyclophyllidea)))). The mitogenomic gene arrangement of G. oligonchis was identical to that of Testudotaenia sp. WL-2016. Both mitogenomic and nuclear sequence data for many more taxa are required to effectively explore the inter-relationships among the Onchoproteocephalidea.
Impairment in the goal-directed corticostriatal learning system as a biomarker for obsessive–compulsive disorder
Authors: Dong Chenjie , Yang Qiong , Liang Jingjing , Seger Carol A. , Han Hongying , Ning Yuping , Chen Qi , Peng ZiWen 
Published: July 2019

AbstractBackgroundCompulsive behaviors in obsessive-compulsive disorder (OCD) have been related to impairment within the associative cortical-striatal system connecting the caudate and prefrontal cortex that underlies consciously-controlled goal-directed learning and behavior. However, little is known whether this impairment may serve as a biomarker for vulnerability to OCD.MethodsUsing resting-state functional magnetic resonance imaging (fMRI), we employed Granger causality analysis (GCA) to measure effective connectivity (EC) in previously validated striatal sub-regions, including the caudate, putamen, and the nucleus accumbens, in 35 OCD patients, 35 unaffected first-degree relatives and 35 matched healthy controls.ResultsBoth OCD patients and their first-degree relatives showed greater EC than controls between the left caudate and the orbital frontal cortex (OFC). Both OCD patients and their first-degree relatives showed lower EC than controls between the left caudate and lateral prefrontal cortex. These results are consistent with findings from task-related fMRI studies which found impairment in the goal-directed system in OCD patients.ConclusionsThe same changes in EC were present in both OCD patients and their unaffected first-degree relatives suggest that impairment in the goal-directed learning system may be a biomarker for OCD.
Labor Laid Waste: An Introduction to the Special Issue on Waste Work
Authors: Doherty Jacob , Brown Kate 
Published: July 2019

AbstractWaste studies brings to labor history a suite of conceptual tools to think about precarious labor, human capital, migration, the material quality of labor in urban and rural infrastructures, and the porosity and interchangeability of workers’ bodies in the toxic environments in which they labor. In this introduction, we explore the conceptual insights that the study of waste offers for the field of labor history, and what, in turn, a focus on labor history affords to social science research on waste. We examine the relationship between surplus populations and surplus materials, the location of waste work at the ambiguous fulcrum of trash and value, and the significance of labor for the understanding of infrastructure.
Do infants with transposition of the great arteries born outside a specialist centre have different outcomes?
Authors: Veal Colin , Hunt Richard , Tume Lyvonne N. 
Published: July 2019

AbstractBackground:Infants born with undiagnosed transposition of the great arteries continue to be born in district general hospitals despite the improvements made in antenatal scanning. Evidence indicates improved outcomes with early definitive treatment after birth, hence the recommendation of delivery in a tertiary centre. The role of specialist paediatric and neonatal transport teams, to advise, stabilise, and transport the infants to a tertiary centre in a timely manner, is critical for those infants born in a district general hospital. This pilot study aims to compare outcomes between infants born in district general hospitals and those who were born in a tertiary maternity unit in South West England and South Wales.Methods:This was a secondary data analysis of data collected from the local Paediatric Intensive Care Audit Network and the local transport database. Infants born with a confirmed diagnosis of transposition of the great arteries, that required an arterial switch operation as the definitive procedure between April, 2012 and March 2018 were included.Results:Forty-five infants with a confirmed diagnosis of transposition of the great arteries were included. Statistical analysis demonstrated there were no significant differences in the time to balloon atrial septostomy (p = 0.095), time to arterial switch operation (p = 0.461), length of paediatric ICU stay (p = 0.353), and hospital stay (p = 0.095) or mortality between the two groups.Conclusions:We found no significant differences in outcomes between infants delivered outside the specialist centre, who were transferred in by a specialist team.