bluuebunny/crossref_metadata_2025 huggingface dataset:
Optoelectronic properties and applications of two-dimensional layered semiconductor van der Waals heterostructures: perspective from theory
Authors: Li Xueping , Yuan Peize , He Mengjie , Li Lin , Du Juan , Xiong Wenqi , Xia Congxin , Kou Liangzhi
Published: November 2022

Van der Waals heterostructures (vdWHs) which combine two different materials together have attracted extensive research attentions due to the promising applications in optoelectronic and electronic devices, the investigations from theoretical simulations can not only predict the novel properties and the interfacial coupling, but also provide essential guidance for experimental verification and fabrications. This review summarizes the recent theoretical studies on electronic and optical properties of two-dimensional semiconducting vdWHs. The characteristics of different band alignments are discussed, together with the optoelectronic modulations from external fields and the promising applications in solar cells, tunneling field-effect transistors and photodetectors. At the end of the review, the further perspective and possible research problems of the vdWHs are also presented.
Nonparametric estimation-based five-layer neural network RAIM with improved availability
Authors: Huang Guoxian , Xu Chengdong , Zheng Xueen
Published: November 2022

The monitoring performance of receiver autonomous integrity monitoring (RAIM) is restricted when visible satellites are limited in challenging environments. For that, artificial neural network-based RAIM methods have been investigated to improve the detection efficacy. Nevertheless, their corresponding fault exclusion and protection level algorithms are hardly provided for integrity assessments. In this regard, a nonparametric estimation-based RAIM method (NE-RAIM) is investigated to support fault detection, exclusion, and protection level calculation in this paper, boosting the declined monitoring capacity caused by the decrease of visible satellites. We propose a classification variable and a dynamic sampling method based on the variance inflation theory and then obtain the regression of the classification variable using nonparametric estimation. In this way, a five-layer NE-RAIM neural network is constructed to enhance the detection capability further. We also provide a NE-RAIM-based fault exclusion strategy by analyzing the detection result vector. Meanwhile, a protection level algorithm is proposed to enable direct integrity and availability evaluation based on searching the worst-case scenario where the missed detection risk is maximized. Results show that NE-RAIM requires a minimum pseudorange bias of 35 m to realize 100% detection rates under all single-faulty-satellite modes. Compared with least-square RAIM and advanced RAIM, NE-RAIM improves overall 24 h availability by 59.30% and 4.52%, respectively.
A fault diagnosis method for rotating machinery with variable speed based on multi-feature fusion and improved ShuffleNet V2
Authors: Luo Zhiyong , Tan Hongkai , Dong Xin , Zhu Guangming , Li Jialin
Published: November 2022

Using deep learning to classify the time-frequency images of bearing vibration signals has become a mainstream method in the field of fault diagnosis. Most studies, however, assume a constant rotational speed, and the accuracy and reliability of the diagnosis model diminishes once the rotational speed changes. Moreover, due to the large model size and high computational complexity, the convolutional neural networks are not suitable for industrial applications. This paper proposes a novel fault diagnosis method for rotating machinery with variable speed based on multi-feature fusion and improved ShuffleNet V2. First, complementary ensemble empirical mode decomposition is used to denoise the time-domain signal. Then the denoised time domain signal is converted into an angular domain signal using the resampling technique, while the envelope spectrums of the angular domain signals are obtained by the Hilbert transform, and the three signals are fused into an red-green-blue image form to enhance the sample features. Finally, to perform fast and accurate classification of the features, the squeeze and excitation blocks are placed after the branch splicing operation of ShuffleNet V2 to enhance the recognition accuracy, and the rectified linear unit activation function is replaced by the HardSwish activation function to avoid necrosis. The experimental results show that the fault recognition accuracy of the proposed method for rolling bearings under variable speed is 96.4%, and the size of the fault diagnosis model is 7.82 MB, indicating that the method can effectively improve the accuracy and ensures that the model size does not increase significantly.
Performance evaluation of peanut-shaped tubular auxetics with enhanced stiffness: a finite element study
Authors: Solak Kemal , ORHAN Suleyman Nazif
Published: November 2022

Auxetic materials or structures possess a negative Poisson’s ratio in contrast to conventional materials, and they shrink or expand transversely under uniaxial compression or tension, respectively. These unique deformation features leads to enhance the mechanical properties compared with the conventional materials. Auxetic tubular structures are of significant interest in the literature because of their superior mechanical qualities, applicability and extensive application. Various auxetic tubular structures with different geometries have been proposed and examined before including conventional peanut-shaped tubular structures. However, application of the peanut-shaped structures is limited due to their low stiffness. In this study, it is aimed to enhance the stiffness of the peanut-shaped tubular auxetic by either adding stiffener to the conventional structure or rotating the unit cell of the structure by a certain angle. Also, the effect of the above-mentioned modifications on the Poisson’s ratio of the structure is investigated. A total of 12 different peanut-shaped auxetics are modelled and the elastic behaviour of these structures under uniaxial compression is compared numerically using finite element simulation. As a result of this analysis, it is observed that both the Poisson’s ratio and stiffness values obtained from the models utilising stiffener were higher than the values obtained from their conventional counterparts. Besides, it is seen that the stiffness values increased while the Poisson’s ratios decreased with the rotation of the unit cell in all of the peanut-shaped tubular auxetics.
Humidity- tunable liquefaction of Cr thin-film and its application to patterning
Authors: Ghosh Swapnendu Narayan , Talukder Santanu
Published: November 2022

Electric field induced liquefaction of chromium (Cr) thin-films, being a surface-based process, is affected by the moisture content in the surroundings. The said process is an electrochemical reaction, which takes place on an electrically stressed Cr thin-film. The reaction results in a liquid region, which appears to flow out radially from the tip of the cathode. A proper understanding of the phenomenon is warranted as it is applied for performing a nanolithography process, electrolithography (ELG). In this study we have focused on the effect of relative humidity (RH) on the material formation and transport on electrically stressed Cr thin-film. Varying the RH over a wide range, the phenomenon is studied using different levels of DC stress. The effect of the applied DC stress coupled with varying levels of RH showed trends which are explained qualitatively and quantitatively. The results indicate that RH could be a pivotal parameter affecting the above-mentioned phenomenon on electrically stressed Cr thin-films and could significantly alter the minimum feature size attainable by ELG. To demonstrate the effect of RH on ELG, lines are drawn at various humidity levels resulting in greater than 100% increase in the attainable line width when RH is increased by about 40%.
Can a robot be a scientist? Developing students’ epistemic insight through a lesson exploring the role of human creativity in astronomy
Authors: Billingsley Berry , Heyes Joshua M , Lesworth Tim , Sarzi Marc
Published: November 2022

Artificial intelligence is transforming the practice of science worldwide. Breakthroughs in machine learning are enabling, for example, the discovery of potentially habitable exoplanets beyond our solar system. The growing role of artificial intelligence (AI) in science raises questions for scientists, philosophers, computer scientists … and educators. How will the scholarship and practice of science education respond to the growing role of artificial intelligence in science? Questions like ‘Can a robot be a scientist?’ can help stimulate students’ epistemic curiosity, about the nature of scientific knowledge, including the value and importance of apparently uniquely human attributes such as creativity. In this article we explain the development and delivery of a science lesson using the question ‘can a robot be a scientist?’ to explore the role of human creativity in scientific observation and classification, using resources and activities created for the citizen scientist project ‘Galaxy Zoo’.
Computational dosimetry in MRI in presence of hip, knee or shoulder implants: do we need accurate surgery models?
Authors: Arduino Alessandro , Baruffaldi Fabio , Bottauscio Oriano , Chiampi Mario , Martinez Jessica A , Zanovello Umberto , Zilberti Luca
Published: November 2022

Objective. To quantify the effects of different levels of realism in the description of the anatomy around hip, knee or shoulder implants when simulating, numerically, radiofrequency and gradient-induced heating in magnetic resonance imaging. This quantification is needed to define how precise the digital human model modified with the implant should be to get realistic dosimetric assessments. Approach. The analysis is based on a large number of numerical simulations where four ‘levels of realism’ have been adopted in modelling human bodies carrying orthopaedic implants. Main results. Results show that the quantification of the heating due to switched gradient fields does not strictly require a detailed local anatomical description when preparing the digital human model carrying an implant. In this case, a simple overlapping of the implant CAD with the body anatomy is sufficient to provide a quite good and conservative estimation of the heating. On the contrary, the evaluation of the electromagnetic field distribution and heating caused by the radiofrequency field requires an accurate description of the tissues around the prosthesis. Significance. The results of this paper provide hints for selecting the ‘level of realism’ in the definition of the anatomical models with embedded passive implants when performing simulations that should reproduce, as closely as possible, the in vivo scenarios of patients carrying orthopaedic implants.
Bi-criteria Pareto optimization to balance irradiation time and dosimetric objectives in proton arc therapy
Authors: Wuyckens Sophie , Zhao Lewei , Saint-Guillain Michael , Janssens Guillaume , Sterpin Edmond , Souris Kevin , Ding Xuanfeng , Lee John A
Published: November 2022

Objective. Proton arc therapy (PAT) is a new delivery technique that exploits the continuous rotation of the gantry to distribute the therapeutic dose over many angular windows instead of using a few static fields, as in conventional (intensity-modulated) proton therapy. Although coming along with many potential clinical and dosimetric benefits, PAT has also raised a new optimization challenge. In addition to the dosimetric goals, the beam delivery time (BDT) needs to be considered in the objective function. Considering this bi-objective formulation, the task of finding a good compromise with appropriate weighting factors can turn out to be cumbersome. Approach. We have computed Pareto-optimal plans for three disease sites: a brain, a lung, and a liver, following a method of iteratively choosing weight vectors to approximate the Pareto front with few points. Mixed-integer programming (MIP) was selected to state the bi-criteria PAT problem and to find Pareto optimal points with a suited solver. Main results. The trade-offs between plan quality and beam irradiation time (static BDT) are investigated by inspecting three plans from the Pareto front. The latter are carefully picked to demonstrate significant differences in dose distribution and delivery time depending on their location on the frontier. The results were benchmarked against IMPT and SPArc plans showing the strength of degrees of freedom coming along with MIP optimization. Significance. This paper presents for the first time the application of bi-criteria optimization to the PAT problem, which eventually permits the planners to select the best treatment strategy according to the patient conditions and clinical resources available.
In-situ deposition of tungsten oxide hole-contact by Hot-Wire CVD and its application in dopant-free heterojunction solar cells
Authors: Guo Cong , Li Junjun , Liu Run , Zhang Dongdong , Qiu Junyang , Zhuang Zihan , Chen Yang , Qiu Qingqing , Liu Wenzhu , Huang Yuelong , Yu Jian , Chen Tao
Published: November 2022

The tungsten oxide (WO
x
) thin films have been deposited by a novel hot filament oxidation-sublimation process and applied in the dopant-free heterojunction solar cells as the hole selective contacts. The oxygen flow ratio plays a significant role during the deposition process. With increasing the oxygen flow ratio from 1.7% to 6.7%, the morphology of WO
x
films changes from small cauliflower-like particles to large cluster accumulation, and the ratio of W6+ increases from 76.1% to 91.4% with the ratio of W5+ decreasing from 23.9% to 8.6%. The work function of WO
x
can be tailored in a range of 5.5–6.1 eV by increasing the oxygen flow ratio. Its optical band gap maintains above 3.2 eV with the conductivity of about 10−5 S·cm−1. We have applied the WO
x
films in dopant-free silicon heterojunction solar cells as the hole selective contact layer by replacing the p-type amorphous silicon layer. By taking advantage of the highly transparent WO
x
layer, a high photon-current density of 39.6 mA·cm−2 was achieved with the oxygen flow ratio of 1.7%. It is interesting to find that the optimum cell conversion efficiencies of 14.9% were obtained with the oxygen flow ratio of 1.7% and the thickness of 10–20 nm for the deposition of WO
x
layer. This work proves the feasibility and good potential of Hot-Wire CVD prepared WO
x
hole selective contact for efficient dopant-free silicon heterojunction solar cells.
Quantum security and theory of decoherence
Authors: Mironowicz P
Published: November 2022

We sketch a relation between two crucial, yet independent, fields in quantum information research, viz. quantum decoherence and quantum cryptography. We investigate here how the standard cryptographic assumption of shielded laboratory, stating that data generated by a secure quantum device remain private unless explicitly published, is disturbed by the einselection mechanism of quantum Darwinism explaining the measurement process by interaction with the external environment. We illustrate the idea with a paradigmatic example of a quantum random number generator compromised by a quantum analog of the Van Eck phreaking. In particular, we derive a trade-off relation between the eavesdropper’s guessing probability

P

g
u
e
s
s

and the collective decoherence factor Γ of the simple form

P

g
u
e
s
s

+
Γ
⩾
1

.
Molecular dynamics simulations of irradiated defect clusters evolution in different crystal structures
Authors: Guo Xinhui , Li Huan , Wang Junjie , Liu Chengze , Xu Jianping , Xi Yuntao , Wu Jinping
Published: November 2022

Irradiation damage is an important cause of material failure in in-service nuclear reactors. It is important to explore the resistance to irradiation of metals with different crystal structures. As the formation and evolution of point defects on the atomic scale caused by cascade collisions in the early stages of irradiation are currently difficult to observe experimentally, it is currently possible to simulate the dynamic process of irradiation damage on the atomic scale by means of molecular dynamics (MD) methods. In this paper, some atomic scale numerical simulations are performed to study the irradiation behaviour and displacement cascades in metals with different crystal structures of bcc-Fe, hcp-Ti, hcp-Zr and fcc-Ni by the MD methods. The effect of temperature and the magnitude of the primary knock-on atom (PKA) energy on the generation and evolution of point defects is mainly studied. Results show that an increase in cascade energies from 0.5 keV to 10 keV can significantly promote defect formation for different crystal structures, while ambient temperature (T) has a slight effect on the number of surviving defects. The simulations also illustrate that high-energy cascades can significantly promote the formation of defect clusters. Statistical results of the displacement cascades show that bcc-Fe produces a small number of stable defects, a small cluster size and number relative to fcc-Ni, hcp-Ti, and hcp-Zr structures, which indicates that the bcc-Fe structure has a good radiation resistance. These findings could provide an appropriate idea for obtaining potential radiation-resistant materials for nuclear reactors.
Curcumin nanoparticles combined with 3D printed bionic tumor models for breast cancer treatment
Authors: Su Ya , Hu Xueyan , Kang Yue , Zhang Cheng , Cheng Yuen Yee , Jiao Zeren , Nie Yi , Song Kedong
Published: November 2022

Compared with conventional therapeutic approaches, nanomedicines are attracting a growing interest due to their better targeting ability, higher delivery efficiency, and good water solubility. However, conventional drug efficacy assessment methods are based on a two-dimensional (2D) culture approach of single cells to obtain in vitro therapeutic effects, which may not be representative of actual tumors. Based on the above considerations, the three-dimensional (3D) cell culture models became a better choice since they can increase the complexity of in vitro systems and provide a biomimetic microenvironment that is closer to the in vivo native than 2D cultures. In our study, curcumin nanoparticle (CurNPs) with good water solubility and good tumor therapeutic effects were prepared by combining polymeric non-ionic surfactant (Pluronic F127) with curcumin. The hybrid scaffolds based on nano-clay, sodium alginate, and gelatin were also prepared, which showed good printability and excellent biocompatibility. We then studied the therapeutic effects of CurNPs on metastatic breast cancer using a 3D tumor model fabricated with scaffold-bound metastatic breast cancer (MDA-MB-231) cells. It was showed that the 3D cell model presented better cell proliferation effect while compared with 2D version. Additionally, there was good enhanced permeability and retention effect when CurNPs entered with better accumulate in 3D cell ‘tumor’ sites which represented more realistic response of a more real tumor treatment effect for breast cancer cells. Our study indicated that the combinational of nanomaterials with 3D cell ‘tumor’ models provided an alternative and better platform for drug screening and has great potential be used as safe and effective treatment screening for breast cancer.
Families of Abelian Varieties and Large Galois Images
Authors: Zywina David
Published: November 2022

Associated with an abelian variety $A$ of dimension $g$ over a number field $K$ is a Galois representation $\rho _A\colon \operatorname {Gal}({\overline {K}}/K)\to \operatorname {GL}_{2g}(\widehat {{\mathbb {Z}}})$. The representation $\rho _A$ encodes the Galois action on the torsion points of $A$ and its image is an interesting invariant of $A$ that contains a lot of arithmetic information. We consider abelian varieties over $K$ parametrized by the $K$-points of a non-empty open subvariety $U\subseteq {\mathbb {P}}^n_K$. We show that away from a set of density $0$, the image of $\rho _A$ will be very large; more precisely, it will have uniformly bounded index in a group obtained from the family of abelian varieties. This generalizes earlier results that assumed that the family of abelian varieties has “big monodromy”. We also give a version for families of abelian varieties with a more general base.
Technical requirements for cardiac CT scanning
Authors: Haberland Ulrike , Allmendinger Thomas
Published: November 2022

The clinical requirements for high-quality cardiac imaging can be directly translated into technical requirements for the CT scanner. The ability to freeze cardiac motion in each individual image yields the notion of temporal resolution (scanner rotation time, number of sources, multisegment reconstruction, and motion correction algorithms). The aim of minimizing the number of involved cardiac cycles is translated into detector coverage (physical collimation, number of slices, slice width). The structure size of interest in typical coronary lesions is on the sub-millimetre level resulting in the need for isotropic spatial resolution-enabled reconstruction (number of detector channels, detector element size). Finally, in the case of angiographic imaging, which is based on high iodine contrast imaging, requirements towards the X-ray tube and generator come into play (low kV, maximum tube current, tube power).
Patient selection and preparation
Authors: Rajani Ronak , Károlyi Mihály
Published: November 2022

Cardiovascular CT should only be performed when reasonable image quality is expected and the test results may affect patient management. Appropriate patient selection and preparation is fundamental to meet these criteria. Firstly, referral for cardiac CT should be evaluated for its appropriateness based on current recommendations of professional bodies. Secondly, it should only be performed by those personnel who have been appropriately trained and where the host institute has appropriate clinical governance measures in place. Finally, patient preparation should be optimized. This includes appropriate information being relayed to the patient, the completion of a pre-procedural CT safety checklist, and the active steps of cannulation and administration of medication.
Scanner setup, cardiac protocols, and contrast injection
Authors: Haberland Ulrike , Allmendinger Thomas , Pugliese Francesca
Published: November 2022

Coronary CT angiography uses two primary acquisition techniques: the prospective electrocardiogram (ECG)-triggered sequential mode (step-and-shoot or axial scanning), and the retrospectively ECG-gated spiral or helical mode. The term ‘mode’ refers to the axial/sequential or spiral/helical approaches for CT data acquisition. The term ‘protocol’ indicates the scan mode associated with the specific algorithm for data synchronization (i.e. prospectively ECG-triggered or retrospectively ECG-gated acquisition). Wide-detector CT systems can provide coverage of the entire heart in a single cardiac cycle without movement of the scanner table. Dual-source CT systems offer a prospectively ECG-triggered high-pitch spiral protocol with fast table movement. Motion-free imaging depends on the scanner’s temporal resolution, on the heart rate, and on the cardiac ‘phase(s)’ selected for image acquisition. Appropriate intracoronary contrast enhancement practically means achieving an intracoronary attenuation of at least 250 HU or (ideally) higher. This can be achieved by adjusting the contrast injection rate based on the iodine concentration of the contrast medium, in order to achieve a desired iodine delivery rate of 1.6–2.0 g/s (e.g. for an iodine delivery rate of 2.0 g/s, use a 5 ml/s injection rate of a 400 mg/ml concentration contrast material).
Tips and tricks to improve image quality
Authors: Marwan Mohamed , Károlyi Mihály
Published: November 2022

Obtaining a high-quality CT data set is crucial to deliver correct diagnostic information and provide the answer to the clinical question or to plan interventions (e.g. for structural heart disease). The spectrum of cardiac CT indications has increased over the last decade and now extends from assessment of the coronary arteries to the comprehensive analysis of different cardiac structures prior to or after structural heart disease interventions. In this chapter, several tips for obtaining high-quality cardiac and coronary CT data sets will be discussed, complemented by some specific considerations for data sets acquired for non-coronary assessment.
Coronary CT angiography interpretation and reporting
Authors: Szilveszter Bálint , Celeng Csilla , Takx Richard , Maurovich-Horvat Pál
Published: November 2022

CT imaging has demonstrated unparalleled technical advancements for the assessment of cardiac chambers and coronary arteries. Coronary CT angiography (CCTA) has emerged as a reliable, noninvasive tool for the qualitative and quantitative assessment of coronary artery disease. Owing to its high negative predictive value, CCTA has been established as the first-line test to rule out obstructive CAD in patients with chronic coronary syndrome. Developments in scanner technology including wide-detector panels, dose-saving strategies, dual-source imaging, faster gantry rotation, and novel iterative reconstruction algorithms enable high-quality image acquisition of the cardiac structures. The contemporary role of CT imaging not only rules out CAD, but also provides prognostic information and guides downstream patient management.
Atherosclerotic plaque imaging
Authors: Kolossváry Márton
Published: November 2022

Aside from coronary artery stenosis assessment, coronary CT angiography (CCTA) provides a large amount of data on plaque extent, distribution, morphology, and composition, which may facilitate a more refined risk stratification of the patient. Calcified plaque components can be easily distinguished from non-calcified parts based on CT density, while further differentiation of soft tissue components (lipid-rich necrotic vs. predominantly fibrous) may be more challenging. Morphological high-risk plaque features associated with increased risk of ischaemic coronary events include the ‘napkin ring sign’, low intraplaque attenuation, positive (outward) plaque remodelling, and spotty calcification. Ultrastructural information from CCTA may be combined with biological signals from other imaging modalities (e.g. radionuclide imaging tracers of inflammatory plaque activity) to provide a more comprehensive assessment of plaque vulnerability.
Ventricular volume and function
Authors: Takx Richard A.P. , Celeng Csilla
Published: November 2022

Precise measurement of left (LV) and right ventricular (RV) volume, mass, and function is relevant for patients with heart disease. Echocardiography and magnetic resonance imaging are considered the techniques of choice, although they are not always feasible due to contraindications. CT provides a good alternative with isotropic sub-millimetre spatial resolution and good temporal resolution. To lower radiation dose, functional information can be acquired by using retrospective gating with tube current modulation. In order to extract functional information, contours have to be traced in end systole and end diastole for both ventricles. In patients with acute coronary syndrome, heart failure, valvular disease, and cardiac devices, accurate assessment of LV function is important. RV function is important in patients with pulmonary hypertension, pulmonary embolism, right-sided heart failure, and other disease of the RV. Global and regional LV function can be scored according to standard myocardial segmentation models.
Thoracic great vessels
Authors: Messerli Michael
Published: November 2022

CT has evolved as the most important imaging tool for the assessment of the great thoracic vessels (i.e. the aortic and pulmonary arteries) owing to its fast acquisition time and high temporal/spatial resolution. Typical CT protocols of the aorta include a non-contrast phase, an arterial phase, as well as a venous phase in some circumstances. The non-contrast phase allows for the assessment of aortic calcifications, intramural haematoma, and surgical material; the arterial phase depicts the lumen of the aorta; and the venous phase may detect leakage of contrast media in the context of prior endovascular repair. Electrocardiogram gating improves image quality of the aortic root and ascending aorta, as artefacts from cardiac motion may mimic dissection flaps and generally degrade evaluation of these structures. Diseases of the pulmonary artery include pulmonary embolism, pulmonary hypertension with arterial enlargement, and the rare pulmonary artery sarcoma.
Pericardial disease
Authors: Moharem-Elgamal Sarah
Published: November 2022

Pericardial diseases are often assessed by echocardiography and/or cardiac magnetic resonance. Cardiac CT offers a useful alternative to both techniques, with isotropic spatial and good temporal resolution, which allows for comprehensive assessment of the pericardial anatomy and characterization of different pericardial lesions. Knowledge of the normal pericardial anatomy, anatomical variants, and the CT appearances of different pericardial conditions is crucial for proper diagnosis and treatment.
Implanted cardiac devices and how to recognize them on CT
Authors: Benz Dominik C.
Published: November 2022

Implanted cardiac devices are more commonly encountered in patients undergoing cardiac CT—either to assess the device itself or for various other cardiac or extracardiac indications (e.g. coronary CT angiography, left atrial anatomical map for radiofrequency ablations, and CT pulmonary angiography). Therefore, it is paramount for the cardiovascular imager to recognize the devices and be familiar with the normal findings. Meanwhile, patients with implanted devices may pose challenges to CT imaging, including beam hardening and partial volume effects, and motion artefacts from a rapid and irregular heart rate. Therefore, imaging protocols should be optimized for image quality. This chapter will present the most common implanted cardiac devices. They range from valvular devices to rhythm-management devices like pacemakers or implantable cardioverter defibrillators, occluders of the left atrial appendage, persistent foramen ovale, or septal defects to circulatory assist devices. Moreover, the chapter will address the most common complications associated with these devices one should be aware of.
Imaging for treatment planning
Authors: Lavender Frances , Whitelaw Gemma
Published: November 2022

This chapter, ‘Imaging for treatment planning’, describes, compares, and contrasts the key imaging modalities used to support the treatment planning processes. These are computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). The advantages and disadvantages of each modality in respect of their roles in treatment planning are presented. The basic principles of CT image acquisition are described, including four-dimensional CT imaging which accounts for organ movement during the scan. The most significant physical factors which affect the quality of CT images are stated. The use of registration/fusion, using rigid body and deformable methods, to combine datasets from different imaging sources is introduced.
Imaging for treatment delivery: Image-guided radiotherapy
Authors: Lavender Frances
Published: November 2022

This chapter, ‘Imaging for treatment delivery: Image-guided radiotherapy’, discusses the technology and workflows used to verify the geometric accuracy of treatment delivery. A review of the relevant photon interaction processes (photoelectric effect and Compton scattering) precedes a discussion on cone beam CT imaging (CBCT), how this differs from fan-beam CT imaging and how it is used in clinical practice. The importance of patient positioning is highlighted. Other techniques used to improve treatment accuracy, such as gating and tracking are described. The use of adaptive radiotherapy is outlined and the chapter closes with a brief introduction to the possibilities presented by MR-linac technology.
Radiation protection in radiotherapy
Authors: Thurston Jim
Published: November 2022

This chapter, ‘Radiation Protection’, discusses the reduction of the risk of harm from the use of radiation while retaining the required beneficial effects in the diagnosis and treatment of cancer. Mechanisms of cell damage are covered and comparisons are made between doses received due to natural and manmade radiations. The deterministic and stochastic effects of radiation on tissue are described. The current UK legislation (IRR, IR(ME)R) in place to protect staff, patients, and members of the public from unnecessary exposure to radiation is outlined. This chapter also covers the management of incidents involving radiation and the key factors essential to the design of a safe radiation treatment facility are considered.
Coronary plaque progression is greater in systemic lupus erythematosus than rheumatoid arthritis
Authors: Moore Jeff , Lakshmanan Suvasini , Manubolu Venkat Sanjay , Kinninger April , Stojan George , Goldman Daniel W. , Petri Michelle , Budoff Matthew , Karpouzas George A.
Published: November 2022

Background

Systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) are associated with a high incidence of cardiovascular disease. Coronary atherosclerosis, particularly total plaque and noncalcified plaque on coronary computed tomography angiography (CCTA) has been correlated with cardiovascular events. We compared baseline coronary plaque burden and progression by serial CCTA in SLE and RA patients.

Methods

We prospectively evaluated 44 patients who underwent serial CCTA examinations to quantify coronary plaque progression, 22 SLE patients, and 22 age- and sex-matched RA patients. Semiautomated plaque software was used for quantitative plaque assessment. Linear regression examined the effect of SLE diagnosis (versus RA) on annualized change in natural log-transformed total normalized atheroma volume (ln-TAVnorm) for low-attenuation, fibrofatty, fibrous, total noncalcified, densely calcified, and total plaque.

Results

No quantitative differences for any plaque types were observed at baseline between SLE and RA patients (P = 0.330–0.990). After adjustment for baseline plaque and cardiovascular risk factors, the increase in ln-TAVnorm was higher in SLE than RA patients for fibrous [Exp-β: 0.202 (0.398), P = 0.0003], total noncalcified [Exp-β: 0.179 (0.393), P = 0.0001], and total plaque volume [Exp-β: 0.154 (0.501), P = 0.0007], but not for low-attenuation, fibrofatty, or densely calcified plaque (P = 0.103–0.489). Patients with SLE had 80% more fibrous, 82% more noncalcified, and 85% more total plaque increase than those with RA.

Conclusion

Coronary plaque volume was similar in RA and SLE at baseline. Progression was greater in SLE, which may explain the greater cardiovascular risk in this disease. Further research to evaluate screening and management strategies for cardiovascular disease in these high-risk patients is warranted.
Immunotherapy approaches for rare pediatric solid tumors: advances and future directions
Authors: Fierro Pineda Juan C. , Wedekind Mary Frances , Glod John W.
Published: November 2022

Purpose of review

Immunotherapy for pediatric tumors is rapidly evolving. From major successes in pediatric hematologic malignancies, immunotherapy utility increased in the pediatric solid tumor landscape. Numerous pediatric solid tumors are defined as rare with limitations in diagnosis and treatment. This review will describe four major immunotherapies used in pediatrics and discuss results seen in rare pediatric tumors. We will also briefly review the challenges of immunotherapy in solid tumors and opportunities to drive this therapy forward.

Recent findings

Despite rare success employing immunotherapy for pediatric solid tumors, recently there have been several successes in pediatric rare solid tumors. After describing the evolving landscape of rare pediatric tumors, we will demonstrate the successes or disappointments of immunotherapy. We will describe the mechanism of four immunotherapies used in the pediatrics, followed by the published results. Finally, we will discuss the challenges and opportunities for immunotherapies in pediatric rare tumors.

Pediatric rare tumors are lacking in treatment options. Despite numerous disappointments utilizing immunotherapies in the more common pediatric solid tumors, there have been several successes within the pediatric rare tumor landscape. Much work is still needed to enhance our understanding and knowledge on utilizing these immunotherapies for pediatric rare solid tumors.
Exploring the association between Body Mass Index, Sex and Gene Expression in human colorectal epithelium
Authors: Lemler L. , Donnelly K. , Tomlinson I. P. M. , Timofeeva M. , Theodoratou E. , Rozadilla C. Fernández , Fernandez-Tajes J. , Grimes Graeme , Farrington Susan M. , Dunlop M. G.
Published: November 2022

Introduction

Colorectal cancer (CRC) is the second most common cause of cancer death globally. Genome-wide association studies have established that cancer risk mediated through common genetic variants can be linked to variation in gene expression. Since obesity and male sex impart substantially elevated CRC risk, we studied transcriptional profiles of normal colorectal mucosa using RNA sequencing to better understand the relationship of these risk factors with gene expression levels.

Methods

Normal colorectal mucosa was sampled from 365 participants (208 males, 157 females) either during surgery (n=103) or through endoscopic biopsy (n=262) from cancer patients and patients with other unrelated conditions. In total, 238 samples were used for our discovery dataset and 380 samples were obtained for the validation of our findings. The transcription analysis was done using paired-end total RNA sequencing. Data processing and gene filtering followed the Genotype-Tissue Expression (GTEx) Project pipeline v8. Differential Expression Analysis (DEA) was performed on normalised counts to evaluate effects of sex and body mass index on the total gene expression, as well as possible confounding effects of cancer presence on the gene expression in normal colorectal tissue.

Results

Following filtering, there were 15,465 genes available for analysis. DEA identified two genes that were significantly associated with sex and five associated with body mass index. However, whilst these nominal signals are of interest, none of the genes associated with sex remained significant in a replication dataset. Due to the missing BMI information, replication of DEA by BMI was not possible.

Conclusion

We found no systematic differences in gene expression in normal colorectal epithelium between males and females, nor did we find a strong association between gene expression and BMI. Although sample size may limit our analysis, the results suggest no or limited confounding effects of BMI and sex on gene expression in normal colorectal mucosa samples.
Feedback brings scene information to the representation of occluded image regions in area V1 of monkeys and humans
Authors: Papale Paolo , Wang Feng , Morgan A. Tyler , Chen Xing , Gilhuis Amparo , Petro Lucy S. , Muckli Lars , Roelfsema Pieter R. , Self Matthew W.
Published: November 2022

Neuronal activity in the primary visual cortex (V1) is driven by feedforward input from within the neurons’ receptive fields (RFs) and modulated by contextual information in regions surrounding the RF. The effect of contextual information on spiking activity occurs rapidly, and is therefore challenging to dissociate from feedforward input. To address this challenge, we recorded the spiking activity of V1 neurons in monkeys viewing either natural scenes or scenes where the information in the RF was occluded, effectively removing the feedforward input. We found that V1 neurons responded rapidly and selectively to occluded scenes. V1 responses elicited by occluded stimuli could be used to decode scene identity and could be predicted from those elicited by non-occluded images, indicating that there is overlap between visually-driven and contextual responses. We used representational similarity analysis to show that the structure of V1 representations of occluded scenes measured with electrophysiology in monkeys correlates strongly with the representations of the same scenes in humans measured with fMRI. Our results reveal that contextual influences alter the spiking activity of V1 in monkeys across large distances on a rapid time scale, carry information about scene identity and resemble those in human V1.
“The Free Association Sessions”. Perspectives on a Novel Teaching Platform by Final Year Medical Students and Basic Specialist Trainees in Psychiatry
Authors: McFarland John , Brar Gurjot , Hayes Peter , Abdalla De Mohamed Elhassan
Published: November 2022

Introduction

Notwithstanding the many advantages of outcomes-based education within Psychiatry placements in Medical School and Basic Specialist Training within the College of Psychiatry of Ireland, there is limited protected time for broad Reflective Practice that appreciates the complexity of working in the Mental Health setting. Furthermore, there are limitations to the current model of restricting Reflective Practice sessions to the Balint Group Format.

Methods

A novel programme of structured Reflective Practice was offered to students in the School of Medicine in The University of Limerick and trainees in the Mid-West Deanery. Six student and fourteen trainee participants were subsequently invited to provide perspectives on the programme via Focus Groups. The study employed an inductive latent phenomenological approach for analysis of qualitative data.

Results

Five major themes emerged: These related to the teaching environment, personal identity, complexity, awareness of cognitive dissonance and the structure of the sessions. There were a number of different perceptions, relating to the participants’ stage of training.

Conclusions

There was evidence that the structured reflective sessions created a comfortable environment, addressed hierarchy issues and facilitated wide-ranging opportunities for reflective practice, with an observed increased appreciation for complexity in Psychiatry. There was apparent tension between controllingcontentand facilitating theformof group process. Nonetheless, the structure appeared more approachable for medical students and those early in training.
The role of vertical and horizontal transmission in the assembly of seed fungal endophyte communities in wheat and wheat wild relatives
Authors: Sharon Or , Sun Xiang , Ezrati Smadar , Kagan-Trushina Naomi , Sharon Amir
Published: November 2022

Plants acquire fungal endophytes either from the environment or from their progenitors. These transmission modes are central in shaping the community as they affect species composition and balance. We studied fungal endophyte communities (FEC) and their seed-to-seed transmission in three Triticeae plant species: bread wheat (Triticum aestivum), wild emmer wheat (Triticum turgidum dicoccoides) and wild barley (Hordeum spontaneum). The FECs in the three plant species contained similar fungal taxa, however they were overall different. The most prevalent class of fungi was Dothideomycetes, which was dominated by the taxon Alternaria infectoria. In field collected plants, the number of taxa in the seeds was less than half the number in stems, with close to 90% of the taxa found in seeds also found in stems. Growing the same plant species in a controlled environment infection greatly affected their FEC composition; the FECs in the stems and seeds of these plants were richer and more diverse than in the original seeds, they were not dominated by a single taxon, and FECs in the new seeds had a similar richness and diversity to the stem FECs, with only 40% overlap. The controlled environment experiment confirmed vertical transmission of certain species, but also showed that external infection of the seeds is the main source for specific taxa, including A. infectoria. Collectively, our results show that many taxa can reach the seeds through the internal pathway, albeit in different abundance, and both internal and external sources significantly affect the composition of seed FECs.
Database of recurrent mutations (DORM), a web tool to browse recurrent mutations in cancers
Authors: Chakroborty Deepankar , Paatero Ilkka , Kurppa Kari J. , Elenius Klaus
Published: November 2022

Advances in sequencing technologies have facilitated the genetic characterization of large numbers of clinical cancer samples, leading to accumulation of extensive amounts of data. While potentially very useful for directing research and for clinical decision making, the increasing quantity of data generates challenges in its optimal management, and translation to informing clinical and research questions. Here, we presentDatabaseOfRecurrentMutations (DORM), a database listing recurrent mutations (tissue-agnostic population frequency > 1) identified from cancer samples analyzed with whole genome or whole exome sequencing. The DORM database is a fast and feature-rich database supporting searching for several proteins, amino acid substitutions as well as queries using regular expressions.
Node-degree aware edge sampling mitigates inflated classification performance in biomedical graph representation learning
Authors: Cappelletti Luca , Rekerle Lauren , Fontana Tommaso , Hansen Peter , Casiraghi Elena , Ravanmehr Vida , Mungall Christopher J , Yang Jeremy , Spranger Leonard , Karlebach Guy , Harry Caufield J. , Carmody Leigh , Coleman Ben , Oprea Tudor , Reese Justin , Valentini Giorgio , Robinson Peter N
Published: November 2022

Graph representation learning is a family of related approaches that learn low-dimensional vector representations of nodes and other graph elements called embeddings. Embeddings approximate characteristics of the graph and can be used for a variety of machine-learning tasks such as novel edge prediction. For many biomedical applications, partial knowledge exists about positive edges that represent relationships between pairs of entities, but little to no knowledge is available about negative edges that represent the explicit lack of a relationship between two nodes. For this reason, classification procedures are forced to assume that the vast majority of unlabeled edges are negative. Existing approaches to sampling negative edges for training and evaluating classifiers do so by uniformly sampling pairs of nodes. We show here that this sampling strategy typically leads to sets of positive and negative edges with imbalanced edge degree distributions. Using representative homogeneous and heterogeneous biomedical knowledge graphs, we show that this strategy artificially inflates measured classification performance. We present a degree-aware node sampling approach for sampling negative edge examples that mitigates this effect and is simple to implement.