bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear reaction cross sections for hadron therapy
Authors: Simpson E C 
Published: October 2020

Abstract
Treatment planning in hadron therapy uses Monte Carlo techniques that require total nuclear reaction cross sections for a variety of interacting systems and over a wide range of energies. Current empirical models are tuned to reproduce cross sections for stable isotopes, but in some cases, overestimate measured cross sections by 20%. Here we discuss an alternative approach: the optical limit of Glauber theory, which describes existing measurements better and offers more reliable predictions for the many systems where there is no experimental information. We also suggest how existing implementations of empirical models within GEANT4 could be improved. Ultimately, these calculations should contribute to improvements in planning of hadron therapy treatments.
Imaging and radiation isocentre determination for inline MR-guided radiotherapy systems – proof of principle using MR-phantom with embedded monolithic silicon detector
Authors: Causer T J , Alnaghy S J , Alnaghy S , Roberts N , Petasecca M , Rosenfeld A B , Metcalfe P , Oborn B M 
Published: October 2020

Abstract
Multiple vendors are now offering real-time MRI-guided radiotherapy systems. Quality assurance of the imaging and radiation isocentre alignment is an essential component of the QA programme for any linear accelerator used for delivering image-guided radiotherapy. In this work, the authors describe the design and feasibility testing of a device that combines a high resolution monolithic silicon strip detector with an MRI visible phantom for characterisation of optical, MR imaging and radiation isocentre for inline MR-guided radiotherapy systems.
Advancement of microdosimetric kinetic model in heavy-ion radiotherapy
Authors: Inaniwa T 
Published: October 2020

Abstract
To date, more than 11,000 cancer patients have been treated with therapeutic carbon-ion beams at the National Institute of Radiological Sciences (NIRS). In the treatment planning system, the biological effectiveness of the therapeutic carbon-ion beams has been predicted based on the microdosimetric kinetic (MK) model. The MK model has a variety of applications. For instance, it can be used to predict the biological effectiveness of therapeutic carbon-ion beams under protracted irradiations as well as under hypoxic conditions. Recently, we have updated the MK model to a stochastic microdosimetric kinetic (SMK) model for a new research project about hypo-fractionated multi-ion radiotherapy, referred to as a “Quantum Scalpel”. This report overviews advancement of the MK model in heavy-ion radiotherapy.
Microdosimetric study for helium-ion beam using fully 3D silicon microdosimeters
Authors: Lee S H , Mizushima K , Sakata D , Kohno R , Sakama M , Iwata Y , Shirai T , Pan V A , Tran L T , Rosenfeld A B , Suzuki M , Inaniwa T 
Published: October 2020

Abstract
In this study, the survival fraction of pancreatic cancer cells exposed to a spread-out Bragg peak (SOBP) helium-ion beam are estimated using the microdosimetric method with the microdosimetric kinetic (MK) model, by measuring the specific energy with a microdosimeter. To measure the microdosimetric spectra, a 3D mushroom microdosimeter was used by mounting it on silicon-on-insulator (SOI) substrates. At different positions of the Bragg curve of a pristine helium-ion beam of 166 MeV/u, microdosimetric spectra were measured via a scanning beam port in the National Institute of Radiological Sciences. The MK parameters were determined such that the survival fraction (SF) calculated by the MK model predicts the previously reported in vitro data. For a cuboid target of 10×10×6 cm3, a treatment plan that utilised helium-ion beam was designed from the in-house treatment planning software (TPS) to achieve a 10% SF of pancreatic cancer cells throughout the target. The physical doses and microdosimetric spectra were measured for different depths by irradiating the scanning-SOBP helium-ion beam; consequently, the SF at each position of the SOBP was predicted. The predicted SFs from measured physical dose and microdosimetric spectra were in good agreement with the planned SF from TPS.
Real-time, upstream, radiotherapy verification using a Monolithic Active Pixel Sensor System
Authors: Velthuis J J , Beck L , Hugtenburg R , Pritchard J , de Sio C 
Published: October 2020

Abstract
Intensity modulated radiotherapy is a widely used technique for accurately targeting cancerous tumours in difficult locations. As treatments are becoming more complex, new methods need to be developed to monitor them. Monolithic active pixel sensors are a viable candidate for providing upstream beam monitoring during treatment. A MAPS based system can be made thin enough to have less than 1% attenuation. We have already demonstrated leaf position resolutions below 130µm at the iso-centre for 5mm wide leaves sampled 34 times per second. We have shown that the signal due to therapeutic photons can be determined and thus the dose in patient. Furthermore, the sensor works well inside an MR-linac, allowing leaf position verification even in that challenging environment.
Thin low-gain avalanche detectors for particle therapy applications
Authors: Vignati A , Donetti M , Fausti F , Ferrero M , Giordanengo S , Hammad Ali O , Martì Villarreal O A , Mas Milian F , Mazza G , Monaco V , Sacchi R , Shakarami Z , Sola V , Staiano A , Tommasino F , Verroi E , Wheadon R , Cirio R 
Published: October 2020

Abstract
The University of Torino (UniTO) and the National Institute for Nuclear Physics (INFN-TO) are investigating the use of Ultra Fast Silicon Detectors (UFSD) for beam monitoring in radiobiological experiments with therapeutic proton beams. The single particle identification approach of solid state detectors aims at increasing the sensitivity and reducing the response time of the conventional monitoring devices, based on gas detectors. Two prototype systems are being developed to count the number of beam particles and to measure the beam energy with time-of-flight (ToF) techniques. The clinically driven precision (< 1%) in the number of particles delivered and the uncertainty < 1 mm in the depth of penetration (range) in radiobiological experiments (up to 108 protons/s fluxes) are the goals to be pursued. The future translation into clinics would allow the implementation of faster and more accurate treatment modalities, nowadays prevented by the limits of state-of-the-art beam monitors. The experimental results performed with clinical proton beams at CNAO (Centro Nazionale di Adroterapia Oncologica, Pavia) and CPT (Centro di Protonterapia, Trento) showed a counting inefficiency <2% up to 100 MHz/cm2, and a deviation of few hundreds of keV of measured beam energies with respect to nominal ones. The progresses of the project are reported.
Research on microstructure and mechanical properties of HIP Ti-6Al-4V treated by surface rolling at low-heating temperatures
Authors: Li Gang , Zhang Wenkang , Liu Yu , Xue Chuan , Ma Yan , Yuan Hengyi 
Published: October 2020

Abstract
This paper was to research the effects of surface rolling at low-heating temperatures (SRLT) on microstructure and mechanical properties of HIP Ti–6Al–4V alloy. An obviously plastic deformation emerged in surface modification layer and accompanied with the grain refinement and dense dislocations. The values of compressive residual stress and surface microhardness were also increased. The fretting friction tests were further compared without lubrication. The sample treated by surface rolling (SR) at 160 °C had the smaller steady-state CoF and less material loss relative to the untreated sample. But it still had the higher steady-state Coefficient of friction (CoF) and more material loss than surface-rolled sample at room temperature. On the one hand, the comparatively low microhardness and residual stress would damage the mechanical properties. On the other hand, the material’s friction would be increased by the high surface roughness and the absence of cold work strengthening would decrease the wear resistance. In addition, the low-heating temperature would also increase material deformation mechanism and decline the friction properties.
Durable slippery lubricant-infused multiscale-textured surfaces for repelling highly adhesive liquids
Authors: Hajeesaeh Sulaiman , Muensit Nantakan , van Dommelen Paphavee , Daengngam Chalongrat 
Published: October 2020

Abstract
Surfaces that can repel various types of liquid and retain surface properties over acceptably long periods of time are in great demand. Here, we presented a simple but effective technique to fabricate slippery, lubricant-infused surfaces with excellent liquid-repellent properties and resistance to hydrodynamic damage, evaporation, and high static pressure. Chemically-functionalized multiscale-textured surfaces were impregnated by highly-viscous and vacuum-grade lubricants that fully wetted the nanoscale roughness while conformed to the microscale textures. This generated slippery rough surfaces with improved liquid-resistant properties evaluated by water and highly-adhesive latex. The respective contact angles of water and latex droplets were above 130.1 ± 0.8° and 105.7 ± 1.1°, while water and latex sliding angles were less than 5.8 ± 0.7° and 8.7 ± 0.7°, respectively. More importantly, the slippery roughness reduced liquid-lubricant contact areas, and protected the lubricating layer from flow-induced erosion. The particular lubricant-infused surfaces can withstand an impact of a water jet speed up to 2.6 ms−1 for at least 10 min. Furthermore, the viscous lubricant layer was unaffected by evaporation at 65 °C for at least 11 weeks, and stable under hydrostatic pressure of 150 kPa for 20 min.
Recent progresses and challenges of metal sulfides as advanced anode materials in rechargeable sodium-ion batteries
Authors: Yang Xu , Liang Hao-Jie , Yu Hai-Yue , Wang Mei-Yi , Zhao Xin-Xin , Wang Xiao-Tong , Wu Xing-Long 
Published: October 2020

Abstract
Currently, rechargeable sodium-ion batteries (SIBs) with high voltage and high energy density have attracted considerable attention. However, compared with lithium-ion batteries (LIBs), there are many urgent challenges that need to be solved to achieve the practical application of SIBs. Due to the similar physicochemical properties of sodium and lithium, the study of SIBs is based on LIBs. However, the radius of Na+ is larger than that of Li+, a limited number of LIBs electrode materials can be used in SIBs, especially anode materials. Graphite can store sodium ions if an ether-based electrolyte is being used. The storage capacity of graphite for sodium is low (∼35 mAh g−1) when traditional carbonate-based electrolyte is used. Therefore, it is vital that anode materials with splendid rate capability, outstanding cycling performance and low cost are developed rapidly. Among all types of anode materials, metal sulfides (MSx) with higher theoretical specific capacity and lower cost are an ideal practical anode material. Here, a summaryof the recent research advances on MSx of SIBs is provided. The crystal structures, sodium storage mechanism and optimization strategies for high performance batteries are summarized. this paper hopes to provide inspiration for the development of MSx to assist the development of the next generation of rechargeable battery applications.
Molecular dynamics simulation of the material removal in the scratching of 4H-SiC and 6H-SiC substrates
Authors: Tian Zige , Chen Xun , Xu Xipeng 
Published: October 2020

Abstract
Single crystal silicon carbide (SiC) is widely used for optoelectronics applications. Due to the anisotropic characteristics of single crystal materials, the C face and Si face of single crystal SiC have different physical properties, which may fit for particular application purposes. This paper presents an investigation of the material removal and associated subsurface defects in a set of scratching tests on the C face and Si face of 4H-SiC and 6H-SiC materials using molecular dynamics simulations. The investigation reveals that the sample material deformation consists of plastic, amorphous transformations and dislocation slips that may be prone to brittle split. The results showed that the material removal at the C face is more effective with less amorphous deformation than that at the Si face. Such a phenomenon in scratching relates to the dislocations on the basal plane (0001) of the SiC crystal. Subsurface defects were reduced by applying scratching cut depths equal to integer multiples of a half molecular lattice thickness, which formed a foundation for selecting machining control parameters for the best surface quality.
Underrecognized Patterns of High-Grade Squamous Intraepithelial Lesion on ThinPrep Preparations
Authors: Goyal Abha , Heymann Jonas J , Alperstein Susan A , Siddiqui Momin T 
Published: October 2020

Abstract

Objectives
To identify less readily identifiable patterns of high-grade squamous intraepithelial lesions (HSIL) in negative human papillomavirus (HPV)–positive Papanicolaou (Pap) tests on ThinPrep preparations.

Methods
Of all HPV-positive Pap tests that were negative for intraepithelial lesion or malignancy (NILM) from July 2013 to June 2018, those with HSIL on subsequent histology within 6 months were identified. ThinPrep slides from the latter group (group 1) and from NILM HPV-negative Pap tests with negative follow-up (group 2) were reviewed independently by 4 participants. Group 1 cases were then reviewed together for consensus and with the ThinPrep Imaging System (TIS). Any discrepancies from the original interpretation were recorded.

Results
The study cohort included 57 cases each in groups 1 and 2. On final review of group 1 cases, 17 (29.8%) were classified as NILM or unsatisfactory. Of the remaining, 4 cases revealed rare abnormal cells not flagged by the TIS in the fields of view. In the 36 cases (63.1%) with screening or interpretative errors, the key cytologic findings accounting for major discrepancies included atypical metaplastic cells, atypical repair, rare syncytial groups, and atypical immature metaplastic cells.

Conclusions
There are 3 main underrecognized patterns of HSIL in cervical cytology: atypical metaplastic cells, atypical repair, and rare syncytial groups.
BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences
Authors: Khan Aziz , Riudavets Puig Rafael , Boddie Paul , Mathelier Anthony 
Published: October 2020

AbstractMotivationAccurate motif enrichment analyses depend on the choice of background DNA sequences used, which should ideally match the sequence composition of the foreground sequences. It is important to avoid false positive enrichment due to sequence biases in the genome, such as GC-bias. Therefore, relying on an appropriate set of background sequences is crucial for enrichment analysis.ResultsWe developed BiasAway, a command line tool and its dedicated easy-to-use web server to generate synthetic sequences matching any k-mer nucleotide composition or select genomic DNA sequences matching the mononucleotide composition of the foreground sequences through four different models. For genomic sequences, we provide precomputed partitions of genomes from nine species with five different bin sizes to generate appropriate genomic background sequences.Availability and implementationBiasAway source code is freely available from Bitbucket (https://bitbucket.org/CBGR/biasaway) and can be easily installed using bioconda or pip. The web server is available at https://biasaway.uio.no and a detailed documentation is available at https://biasaway.readthedocs.io.Supplementary informationSupplementary data are available at Bioinformatics online.
keras_dna: a wrapper for fast implementation of deep learning models in genomics
Authors: Routhier Etienne , Bin Kamruddin Ayman , Mozziconacci Julien 
Published: October 2020

Abstract

Summary
Prediction of genomic annotations from DNA sequences using deep learning is today becoming a flourishing field with many applications. Nevertheless, there are still difficulties in handling data in order to conveniently build and train models dedicated for specific end-user’s tasks. keras_dna is designed for an easy implementation of Keras models (TensorFlow high level API) for genomics. It can handle standard bioinformatic files formats as inputs such as bigwig, gff, bed, wig, bedGraph or fasta and returns standardized inputs for model training. keras_dna is designed to implement existing models but also to facilitate the development of news models that can have single or multiple targets or inputs.

Availability and implementation
Freely available with a MIT License using pip install keras_dna or cloning the github repo at https://github.com/etirouthier/keras_dna.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
Longitudinal expression changes are weak correlates of disease progression in Huntington’s disease
Authors: Mitchell Christopher T , Krier Irina , Arjomand Jamshid , Borowsky Beth , Tabrizi Sarah J , Leavitt Blair R ,   TRACK-HD Investigators, Arran N , Axelson E , Bardinet E , Bechtel N , Callaghan J , Campbell J C , Campbell M , Cash D M , Coleman A , Craufurd D , Dar Santos R , Decolongon J , Dumas E M , Durr A , Fox N C , Frajman E , Frost C , Hicks S L , Hobbs N , Hoffman A , Jauffret C , Johnson H , Jones R , Jurgens C , Justo D , Keenan S , Kennard C , Kraus P , Lahiri N , Landwehrmeier B , Langbehn D R , Lee S , Lehericy S , Marelli C , Milchman C , Monaco W , Nigaud K , Ordidge R , O’Regan A , Owen G , Pepple T , Queller S , Read J , Reilmann R , Roos R A C , Rosas H D , Say M , Scahill R I , Stout J C , Sturrock A , 't Hart E P , Tobin A J , Valabrègue R , van den Bogaard S J A , van der Grond J , Wang C , Whitlock K , Wild E , Witjes-Ane M-N , Luthi-Carter Ruth 
Published: October 2020

AbstractHuntington’s disease is a severe but slowly progressive hereditary illness for which only symptomatic treatments are presently available. Clinical measures of disease progression are somewhat subjective and may require years to detect significant change. There is a clear need to identify more sensitive, objective and consistent measures to detect disease progression in Huntington’s disease clinical trials. Whereas Huntington’s disease demonstrates a robust and consistent gene expression signature in the brain, previous studies of blood cell RNAs have lacked concordance with clinical disease stage. Here we utilized longitudinally collected samples from a well-characterized cohort of control, Huntington’s disease-at-risk and Huntington’s disease subjects to evaluate the possible correlation of gene expression and disease status within individuals. We interrogated these data in both cross-sectional and longitudinal analyses. A number of changes in gene expression showed consistency within this study and as compared to previous reports in the literature. The magnitude of the mean disease effect over 2 years’ time was small, however, and did not track closely with motor symptom progression over the same time period. We therefore conclude that while blood-derived gene expression indicators can be of value in understanding Huntington’s disease pathogenesis, they are insufficiently sensitive to be of use as state biomarkers.
Elections in Non-Democracies
Authors: Egorov Georgy , Sonin Konstantin 
Published: October 2020

AbstractFree and fair elections are the cornerstone of a democratic system, but elections are common in other regimes as well. Such an election might be a pure farce, with the incumbents getting close to 100% of the vote. In other instances, incumbents allow opposition candidates to be on the ballot and run campaigns, limit electoral fraud, e.g., by inviting international observers, all to make elections appear fair. In our model, the incumbent is informed about his popularity, and having a fair election allows him to signal his popularity to the people. After casting their vote, heterogeneous citizens decide whether or not to participate in a protest, and they are more willing to do so if they expect others to protest as well. We demonstrate theoretically that regimes that have a high level of elite repression are less likely to have fair elections, but regimes with a high cost of protesting for ordinary citizens make fair elections more likely.
An agenda for well-being in ELT: an ecological perspective
Authors: Mercer Sarah 
Published: October 2020

Abstract
Well-being is a basic human right according to the World Health Organization. It is the foundation of a life well lived and ought to be the basis of all educational endeavours and encounters. In this article, I urge ELT to make well-being a priority for research and practice. I make three main points. Firstly, we need to be serious in defining and understanding well-being for research and teaching and get beyond superficial conceptualizations, which inhibit growth in this area and meaningful debate. Secondly, we need to consider well-being for the whole ELT ecology, understanding that well-being does not reside solely within the individual but is socially situated too. Finally, I discuss learner and teacher well-being, which lie at the heart of ELT, and argue that we have a collective responsibility in the community to work towards better conditions for well-being for all members of the ELT ecology.
Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes
Authors: James Jennifer , Eyre-Walker Adam 
Published: October 2020

AbstractWhat determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here, we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest data set to date, using 639 mammalian species. In a multiple regression, we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of nonsynonymous to synonymous diversity, is also significantly negatively correlated to both range size and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12–20%, providing one of the first quantifications of the relationship between diversity and the census population size.