bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling ICRP110 Adult Reference Voxel Phantoms for dosimetric applications: Development of a new Geant4 Advanced Example
Authors: Large M J , Malaroda A , Petasecca M , Rosenfeld A B , Guatelli S 
Published: October 2020

Abstract
The reference adult male and female voxel phantoms described in the International Commission on Radiological Protection (ICRP) publication 110 have been successfully implemented in a Geant4 application named ICRP110Phantoms. The application allows users to simulate either the whole or a partial phantom, including as little as a single cross-sectional slice. The Geant4 application allows users to estimate the absorbed dose in individual voxels and in entire organs. As example of application, the ICRP110Phantoms was used to estimate the dose deposited by a mono-energetic 125 MeV proton pencil beam, incident on the left breast and passing through the lungs and heart, modelled in partial chest phantoms of both male and female ICRP110 phantoms. The ICRP110Phantoms will be released in Geant4 as an Advanced Example to allow its use in the wider scientific community. This Geant4 Advanced Example application can be utilised for dosimetric studies in radiotherapy, nuclear medicine and radiation protection.
Assessing small-field output factors using a 2D monolithic diode array on a beam-matched Elekta linear accelerator
Authors: Muñoz L , Petasecca M , Metcalfe P , Bucci J , Jackson M , Rosenfeld A B , Biasi G 
Published: October 2020

Abstract
The goal of this work was to assess small-field output factors (OPF) on a newly commissioned linear accelerator (linac) using a ‘correction-less’ 2D monolithic array of diodes, the Duo, which has a spatial resolution of 0.2 mm. The results would validate a set of OPF extracted from the golden beam data (GBD) used to represent the dosimetric characteristics of that linac, an Elekta Versa HD (Elekta, Crawley), fit with an Agility multileaf collimator (MLC). The Duo acquired relative OPF in real time for square fields of nominal side 1, 2, 3 and 4 cm, for 6 MV with flattening filter (WFF) and 6 MV flattening filter free (FFF) photon energies. Results revealed at most a 1.0% difference in OPF when compared to baseline, and bolstered confidence in the acceptance and commissioning of the linac using local GBD as a baseline match.
Nanoscale calculation of the relative efficiency of 7LiF:Mg,Ti (MTS-7) and 7LiF:Mg,Cu,P (MCP-7) thermoluminescent detectors for measuring electrons and positrons
Authors: Parisi Alessio , Struelens Lara , Vanhavere Filip 
Published: October 2020

Abstract
Using the Microdosimetric d(z) Model in combination with PHITS-simulated specific energy probability density distributions, the relative efficiency of 7LiF:Mg,Ti (MTS) and 7LiF:Mg,Cu,P (MCP-7) thermoluminescent detectors was assessed as function of the incident energy for electrons and positrons spanning from 2 keV to 1 GeV. Additionally, the effect of the dopant concentration on the determined efficiency values was carefully investigated. Finally, the results are presented in combination with calculated specific energy frequency mean values and possible correlations were discussed.
Electron Paramagnetic Resonance Spectroscopy for Gamma Knife Dosimetry
Authors: Ramachandran P , Noble C , Jones C , Seshadri V , Foote M 
Published: October 2020

Abstract
Alanine chips exposed to high doses of radiation produces long lived free radicals that could be easily measured with electron paramagnetic resonance (EPR) spectrometers. In this study, the feasibility of using alanine dosimeters for performing rapid quality assurance of Leksell Gamma Knife (LGK) treatment plans was demonstrated. A 3D printed grid was placed inside the LGK spherical solid water phantom (SWP) for measurement of doses at isocentre and off-axis points. The EPR spectroscopy was performed on a Magnettech MS-5000 EPR/ESR spectrometer. A set of dose calibration curves were established prior to the use of alanine chips for LGK dosimetry. Absolute dose, transit dose and dose/timer linearity were performed with the alanine chips positioned at the centre of the LGK solid water phantom (SWP). Five patients of different sites were selected, and patient specific quality assurance (PSQA) was performed in the LGK SWP. The absolute dose measured with the EPR alanine dosimeter agreed well within 2% of the ion chamber results and PSQA results were within 2.1%. Alanine-based EPR dosimetry offers rapid dose measurement with high accuracy and can also be used as a dosimeter for Gamma Knife PSQA.
Evaluation of spot size using volumetric repainting technique on a ProteusPLUS PBS Proton Therapy System
Authors: Rana S , Bennouna J , Gutierrez A , Rosenfeld A 
Published: October 2020

Abstract
Volumetric repainting is considered as one of the techniques for motion mitigation in proton therapy. Faster layer switching time to deliver a volumetric repainting proton plan is very critical to reduce the overall treatment time. Recently, IBA (proton therapy vendor at the Miami Cancer Institute) has implemented a “field regulation” – a new feature to reduce the switching time between layers by applying a magnetic field setpoint to specific groups of magnets. In order to investigate the impact of field regulation and volumetric repainting technique on the spot size, several spot maps were generated. The spot sizes were measured at the isocenter and four off-axis points using the Lynx 2D scintillation detector. The average difference in spot size between two delivery sequences (“down” vs. “up” directions) for given energy at all five locations was 0.6±0.5%. The measurement results from the current study demonstrated that the impact of field regulation on the spot size was very minimal, and this was true for both the volumetric and non-volumetric techniques on a ProteusPLUS proton system with a PBS dedicated nozzle.
Challenges in dosimetry of particle beams with ultra-high pulse dose rates
Authors: Romano F. , Subiel A. , McManus M. , Lee N. D. , Palmans H. , Thomas R. , McCallum S. , Milluzzo G. , Borghesi M. , McIlvenny A. , Ahmed H. , Farabolini W. , Gilardi A. , Schüller A. 
Published: October 2020

Abstract
Recent results from pre-clinical studies investigating the so-called FLASH effect suggest that the ultrahigh pulse dose rates (UHPDR) of this modality reduces normal tissue damage whilst preserving tumour response, when compared with conventional radiotherapy (RT). FLASH-RT is characterized by average dose rates of dozens of Gy/s instead of only a few Gy/min. For some studies, dose rates exceeding hundreds of Gy/s have been used for investigating the tissue response. Moreover, depending on the source of radiation, pulsed beams can be used with low repetition rate and large doses per pulse. Accurate dosimetry of high dose-rate particle beams is challenging and requires the development of novel dosimetric approaches, complementary to the ones used for conventional radiotherapy. The European Joint Research Project “UHDpulse” will develop a measurement framework, encompassing reference standards traceable to SI units and validated reference methods for dose measurements with UHPDR beams. In this paper, the UHDpulse project will be presented, discussing the dosimetric challenges and showing some first results obtained in experimental campaigns with pulsed electron beams and laser-driven proton beams.
Evaluating the use of Silica and PMMA Optical Fibres as Proton Beam Monitors
Authors: Santos A M C , Depauw N 
Published: October 2020

Abstract
Recent reports have shown both poly (methyl methacrylate) (PMMA) and silica optical fibres to be ionization quenching free, making them possibly very useful dosimeters for proton beams. In this study, the response from PMMA and silica optical fibres to therapeutic proton beams are evaluated. The light output was recorded from both optical fibres, exposed to varying dose-rates of 0.5 Gy/min to 20 Gy/min from a 235 MeV isochronous cyclotron. The PMMA optical fibre was observed to have a linear dose-rate response, and a constant light emission for a constant dose-rate exposure. However, in the case of the silica optical fibres, the light output was observed to increase during a constant dose-rate exposure. If uncorrected, this accumulated dose sensitivity observed in the silica optical fibres can result in erroneous measurements.
Real-time in-vivo dosimetry for DaRT
Authors: Su Fang-Yi , Tran Linh T , Biasi Giordano , Petasecca Marco , Lerch Michael L F , Cutajar Dean L , Bucci Joseph , Jackson Michael , Rosenfeld Anatoly B 
Published: October 2020

Abstract
Diffusing alpha-emitters radiation therapy (DaRT) is a revolutionary brachytherapy technique used to treat solid tumours. Implant seeds are coated with 224Ra which, along its shortlived daughter atoms, emits alpha particles of high linear energy transfer (LET) and of high relative biological efficiency (RBE), creating a tumour-killing dose distribution a few mm wide. Those alpha particles are of energy between 5.67 and 8.78 MeV. DaRT is under investigation in clinical trials, but there currently is no obvious solution for dosimetry aimed at quality assurance of treatment. This study introduces alpha-RAD, a dosimeter based on a metal-oxide-semiconductor (MOS) sensor technology. Alpha-RAD was characterized with 241Am, which emits alpha particles of energy 5.49 MeV. The results showed that alpha-RAD had good linearity with dose, with the signal increasing linearly in the range from 0 to 6.84 Gy. Also, an external bias in the range between 15 and 60 V, applied on the gate of alpha-RAD during irradiation, would optimize sensitivity to alpha particles of energies typical of DaRT. Alpha-RAD, owing to its compactness, can fit into a brachytherapy needle, to be placed next to 224Ra seed implants in the tumour, for real-time in vivo dosimetry.
Biological washout effect in in-beam PET: animal studies
Authors: Toramatsu C , Mohammadi A , Wakizaka H , Seki C , Nishikido F , Sato S , Kanno I , Takahashi M , Karasawa K , Hirano Y , Yamaya T 
Published: October 2020

Abstract
Positron emission tomography (PET) is a practical tool for range verification of hadron therapy. As well, the quantitative washout of the positron emitters has a potential usefulness as a diagnostic index, but the modelling for this has not been established. In this study, we measured washout rates of rabbit brain and performed kinetic analysis to explore the washout mechanism. Six rabbit brains were irradiated by 11C and 15O ion beams, and dynamic PET scan was performed using our original depth of interest (DOI)-PET prototype. The washout rate was obtained based on the two-compartment model, where efflux from tissue to blood (k2), influx (k3) and efflux (k4) from the first to second compartments in tissue were evaluated. The observed k2, k3 and k4 of 11C were 0.086, 0.137 and 0.007 min−1, and those of 15O were 0.502, 0.360 and 0.007 min−1, respectively. It was suggested permeability of a molecule containing 11C atoms might be regulated by a transporter. The k2 of 15O was comparable with 15O-water. This study provides basic data for modelling of the washout effect.
Safety Evaluation of a Long-Lived Tumour-Specific Gadolinium (Gd)-Based Imaging Agent in Proton Therapy
Authors: Velten Christian , Tomé Wolfgang A. 
Published: October 2020

Abstract
We assessed the dosimetric safety of a potential diapeutic Gadolinium-based contrast agent for diagnostic MR imaging and MR-guided radiotherapy by calculating depth-dependent reactions rates in a spread-out Bragg peak (SOBP) in water. Energy-dependent cross-sections for inelastic proton reactions on Gadolinium were folded with proton energy spectra at depth. Particle transport, dose, and phase space scoring was performed using Geant4-based TOPAS Monte Carlo software. The isotopic Terbium yield at depth was calculated to be between 103 to 105 atoms/mmolnatGd per Gray SOBP dose in a 2.4 cm3 volume. At currently achievable Gadolinium concentrations of 0.2 μmol/cm3 this yields approximately 26 atoms/(cm3 GySOBP), corresponding to less than 1 Bq activity. Additional dose from evaporation neutrons and subsequent capture gammas is on the order of 1 μSv/GySOBP. Thus, use of this long-lived contrast agent is dosimetrically safe at current concentrations and induced radioactivity is negligible.
Assessing Heterogeneity of Treatment Effects in Observational Studies
Authors: Robertson Sarah E , Leith Andrew , Schmid Christopher H , Dahabreh Issa J 
Published: October 2020

AbstractHere we describe methods for assessing heterogeneity of treatment effects over prespecified subgroups in observational studies, using outcome-model–based (g-formula), inverse probability weighting, doubly robust, and matching estimators of subgroup-specific potential outcome means, conditional average treatment effects, and measures of heterogeneity of treatment effects. We compare the finite-sample performance of different estimators in simulation studies where we vary the total sample size, the relative frequency of each subgroup, the magnitude of treatment effect in each subgroup, and the distribution of baseline covariates, for both continuous and binary outcomes. We find that the estimators’ bias and variance vary substantially in finite samples, even when there is no unobserved confounding and no model misspecification. As an illustration, we apply the methods to data from the Coronary Artery Surgery Study (August 1975–December 1996) to compare the effect of surgery plus medical therapy with that of medical therapy alone for chronic coronary artery disease in subgroups defined by previous myocardial infarction or left ventricular ejection fraction.
Does Alcohol Hangover Affect Emotion Regulation Capacity? Evidence From a Naturalistic Cross-Over Study Design
Authors: Gunn Craig , Fairchild Graeme , Verster Joris C , Adams Sally 
Published: October 2020

Abstract

Aims
The aim of this study was to investigate the effects of alcohol hangover on emotion regulation.

Methods
Forty-five non-smoking, healthy participants aged between 18 and 30 years completed a lab-based emotion regulation task assessing cognitive reappraisal and an emotion regulation questionnaire (State-Difficulties in Emotion Regulation Scale [S-DERS]) when hungover (morning following a night of heavy drinking) and under a no-hangover condition in a naturalistic, within-subjects design study.

Results
Participants reported poorer emotion regulation overall (P &lt; 0.001, d = 0.75), and for the subscales ‘Non-Acceptance’, ‘Modulation’ and ‘Clarity’ (Ps ≤ 0.001, ds ≥ 0.62), but not ‘Awareness’ on the S-DERS, in the hangover versus the no-hangover condition. Hangover did not impair emotion regulation ability as assessed using the lab-based task (Ps ≥ 0.21, ds ≤ 0.40), but there was a general negative shift in valence ratings (i.e. all images were rated more negatively) in the hangover relative to the no-hangover condition (P &lt; 0.001, d = 1.16).

Conclusion
These results suggest that emotion regulation in everyday life and emotional reactivity may be adversely affected by alcohol hangover, but some emotion regulation strategies (e.g. deliberate cognitive reappraisal) may be unaffected.
Transforming pediatric neuropsychology through video-based teleneuropsychology: an innovative private practice model pre-COVID-19
Authors: Salinas Christine M , Bordes Edgar Veronica , Berrios Siervo Gretchen , Bender Heidi A 
Published: October 2020

Abstract

Objective
In pediatric neuropsychology multiple barriers such as long wait times until an appointment, insurance coverage, and limited providers who are bilingual/bicultural or who sub-specialize in pediatric neuropsychology, often slow families from receiving diagnoses and interventions in a timely and affordable manner. This paper focuses on increasing accessibility through the development of a video-based, pediatric teleneuropsychology (TeleNP) practice model that was developed in a private practice 2 years before the COVID-19 pandemic.

Method
‘Design thinking’ methodology to problem-solving was utilized to innovate the traditional neuropsychology practice model in under-served areas who may have limited financial and healthcare resources. The practice model approach to include a virtual diagnostic clinic with increased patient and provider efficiency was created to enhance accessibility for patients and sustainability for providers.

Results
Video-based TeleNP screenings were conducted for 67 children with developmental (i.e., attention deficit hyperactivity disorder, autism spectrum disorder) and language disorders, as well as concussion and psychiatric diagnoses. Additional comorbidities were identified in 65.6% of children. Follow-up data approximately 2 months later revealed 98.5% of children were receiving new interventions as a result of the video-based TeleNP assessment.

Conclusion
Video-based TeleNP benefits the consumer as it can reduce wait times, decrease family financial burden (i.e., travel and parent time off work), expedite referrals for interventions, and provide geographically under-served populations access to providers who are linguistically and culturally responsive. For providers, this model revealed improvements with direct implications for cost-saving, thereby facilitating long-term economic sustainability within a private practice healthcare marketplace.
DReSS: a method to quantitatively describe the influence of structural perturbations on state spaces of genetic regulatory networks
Authors: Yin Ziqiao , Guo Binghui , Ma Shuangge , Sun Yifan , Mi Zhilong , Zheng Zhiming 
Published: October 2020

Abstract
Structures of genetic regulatory networks are not fixed. These structural perturbations can cause changes to the reachability of systems’ state spaces. As system structures are related to genotypes and state spaces are related to phenotypes, it is important to study the relationship between structures and state spaces. However, there is still no method can quantitively describe the reachability differences of two state spaces caused by structural perturbations. Therefore, Difference in Reachability between State Spaces (DReSS) is proposed. DReSS index family can quantitively describe differences of reachability, attractor sets between two state spaces and can help find the key structure in a system, which may influence system’s state space significantly. First, basic properties of DReSS including non-negativity, symmetry and subadditivity are proved. Then, typical examples are shown to explain the meaning of DReSS and the differences between DReSS and traditional graph distance. Finally, differences of DReSS distribution between real biological regulatory networks and random networks are compared. Results show most structural perturbations in biological networks tend to affect reachability inside and between attractor basins rather than to affect attractor set itself when compared with random networks, which illustrates that most genotype differences tend to influence the proportion of different phenotypes and only a few ones can create new phenotypes. DReSS can provide researchers with a new insight to study the relation between genotypes and phenotypes.
DeepSELEX: inferring DNA-binding preferences from HT-SELEX data using multi-class CNNs
Authors: Asif Maor , Orenstein Yaron 
Published: October 2020

Abstract

Motivation
Transcription factor (TF) DNA-binding is a central mechanism in gene regulation. Biologists would like to know where and when these factors bind DNA. Hence, they require accurate DNA-binding models to enable binding prediction to any DNA sequence. Recent technological advancements measure the binding of a single TF to thousands of DNA sequences. One of the prevailing techniques, high-throughput SELEX, measures protein–DNA binding by high-throughput sequencing over several cycles of enrichment. Unfortunately, current computational methods to infer the binding preferences from high-throughput SELEX data do not exploit the richness of these data, and are under-using the most advanced computational technique, deep neural networks.

Results
To better characterize the binding preferences of TFs from these experimental data, we developed DeepSELEX, a new algorithm to infer intrinsic DNA-binding preferences using deep neural networks. DeepSELEX takes advantage of the richness of high-throughput sequencing data and learns the DNA-binding preferences by observing the changes in DNA sequences through the experimental cycles. DeepSELEX outperforms extant methods for the task of DNA-binding inference from high-throughput SELEX data in binding prediction in vitro and is on par with the state of the art in in vivo binding prediction. Analysis of model parameters reveals it learns biologically relevant features that shed light on TFs’ binding mechanism.

Availability and implementation
DeepSELEX is available through github.com/OrensteinLab/DeepSELEX/.

Supplementary information
Supplementary data are available at Bioinformatics online.
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data
Authors: Jain Dhawal , Chu Chong , Alver Burak Han , Lee Soohyun , Lee Eunjung Alice , Park Peter J 
Published: October 2020

ABSTRACT

Hi-C is a common technique for assessing 3D chromatin conformation. Recent studies have shown that long-range interaction information in Hi-C data can be used to generate chromosome-length genome assemblies and identify large-scale structural variations. Here, we demonstrate the use of Hi-C data in detecting mobile transposable element (TE) insertions genome-wide. Our pipeline Hi-C-based TE analyzer (HiTea) capitalizes on clipped Hi-C reads and is aided by a high proportion of discordant read pairs in Hi-C data to detect insertions of three major families of active human TEs. Despite the uneven genome coverage in Hi-C data, HiTea is competitive with the existing callers based on whole-genome sequencing (WGS) data and can supplement the WGS-based characterization of the TE-insertion landscape. We employ the pipeline to identify TE-insertions from human cell-line Hi-C samples.

Availability and implementation
HiTea is available at https://github.com/parklab/HiTea and as a Docker image.

Supplementary information
Supplementary data are available at Bioinformatics online.
Selectin-targeting glycosaminoglycan-peptide conjugate limits neutrophil-mediated cardiac reperfusion injury
Authors: Dehghani Tima , Thai Phung N , Sodhi Harkanwalpreet , Ren Lu , Sirish Padmini , Nader Carol E , Timofeyev Valeriy , Overton James L , Li Xiaocen , Lam Kit S , Chiamvimonvat Nipavan , Panitch Alyssa 
Published: October 2020

AbstractAimsOne of the hallmarks of myocardial infarction (MI) is excessive inflammation. During an inflammatory insult, damaged endothelial cells shed their glycocalyx, a carbohydrate-rich layer on the cell surface which provides a regulatory interface to immune cell adhesion. Selectin-mediated neutrophilia occurs as a result of endothelial injury and inflammation. We recently designed a novel selectin-targeting glycocalyx mimetic (termed DS-IkL) capable of binding inflamed endothelial cells. This study examines the capacity of DS-IkL to limit neutrophil binding and platelet activation on inflamed endothelial cells, as well as the cardioprotective effects of DS-IkL after acute myocardial infarction.Methods and resultsIn vitro, DS-IkL diminished neutrophil interactions with both recombinant selectin and inflamed endothelial cells, and limited platelet activation on inflamed endothelial cells. Our data demonstrated that DS-IkL localized to regions of vascular inflammation in vivo after 45 min of left anterior descending coronary artery ligation-induced MI. Further, findings from this study show DS-IkL treatment had short- and long-term cardioprotective effects after ischaemia/reperfusion of the left anterior descending coronary artery. Mice treated with DS-IkL immediately after ischaemia/reperfusion and 24 h later exhibited reduced neutrophil extravasation, macrophage accumulation, fibroblast and endothelial cell proliferation, and fibrosis compared to saline controls.ConclusionsOur findings suggest that DS-IkL has great therapeutic potential after MI by limiting reperfusion injury induced by the immune response.