bluuebunny/crossref_metadata_2025_split huggingface dataset:
Explaining the dosimetric impact of contouring errors in head and neck radiotherapy
Authors: González Patrick J , Simões Rita , Kiers Karen , Janssen Tomas M 
Published: June 2022

Abstract

Objective. Auto-contouring of organs at risk (OAR) is becoming more common in radiotherapy. An important issue in clinical decision making is judging the quality of the auto-contours. While recent studies considered contour quality by looking at geometric errors only, this does not capture the dosimetric impact of the errors. In this work, we studied the relationship between geometrical errors, the local dose and the dosimetric impact of the geometrical errors. Approach. For 94 head and neck patients, unmodified atlas-based auto-contours and clinically used delineations of the parotid glands and brainstem were retrieved. VMAT plans were automatically optimized on the auto-contours and evaluated on both contours. We defined the dosimetric impact on evaluation (DIE) as the difference in the dosimetric parameter of interest between the two contours. We developed three linear regression models to predict the DIE using: (1) global geometric metrics, (2) global dosimetric metrics, (3) combined local geometric and dosimetric metrics. For model (3), we next determined the minimal amount of editing information required to produce a reliable prediction. Performance was assessed by the root mean squared error (RMSE) of the predicted DIE using 5-fold cross-validation. Main results. In model (3), the median RMSE of the left parotid was 0.4 Gy using 5% of the largest editing vectors. For the right parotid and brainstem the results were 0.5 Gy using 10% and 0.4 Gy using 1% respectively. The median RMS of the DIE was 0.6 Gy, 0.7 Gy and 0.9 Gy for the left parotid, the right parotid and the brainstem, respectively. Model (3), combining local dosimetric and geometric quantities, outperformed the models that used only geometric or dosimetric information. Significance. We showed that the largest local errors plus the local dose suffice to accurately predict the dosimetric impact, opening the door to automated dosimetric QA of auto-contours.
A camera array based reconstruction method for limited observation windows projection in three-dimensional flame chemiluminescence tomography
Authors: Rong Shaohua , Song Yang , Wu Chunxia , Yuan Qun , Gao Zhishan , Guo Zhenyan 
Published: June 2022

Abstract
Three-dimensional(3D) flame chemiluminescence tomography (FCT) is realized in multi-direction and multi-angle using traditional iterative algorithms. However, 3D-FCT is often challenged by insufficient sampling data because of the limited observation windows provided in practical for flame measurement. To obtain flame multiple projections in limited observation windows, we develop a camera array arrangement in FCT. In addition, a residual network with a new loss function combing physical model of flame is proposed to achieve higher reconstruction accuracy, faster reconstruction speed and efficient image feature in residual network for 3D FCT measurement. Furthermore, the determination of the weight coefficient in the loss function is performed by numerical simulation experiments. The flame reconstruction results show that the proposed residual network method including the new loss function has more reliable structural similarity and noise immunity compared with the ART algorithm and the CNN algorithm. This work provides a faster and more accurate method for combustion diagnosis under limited observation windows with insufficient projections.
Electromechanical switching voltage converters with application to cold start for thermoelectric generators
Authors: Kozalakis Konstantinos , Siskos Stylianos 
Published: June 2022

Abstract
This work proposes a novel technique for the control of modern inductor-based switching voltage converters (SVC) (e.g., boost, or buck converter), which is inspired by an old self-oscillating mechanical converter topology. According to the proposed technique, a relay component replaces both the inductor and the semiconductor switch of the SVC. The magnetic coupling between the switch and the inductor eliminates the need for a separate oscillating control circuit, which is usually required for the operation of an SVC, leading to a very simple converter topology. The electromechanical SVC (EMSVC) is self-oscillating, operating automatically whenever sufficient power is applied at its input. In this work a boost converter EMSVC design, as well as a buck converter EMSVC design are presented. Additionally, a boost converter EMSVC implementation, optimized towards thermoelectric cold start applications, is presented with experimental results. The converter can operate with an input of only 25 mV and 6.5 mA, and if combined with a thermoelectric harvester, it can be used for heat energy harvesting from temperature difference as low as 1 °C.
Figbird: a probabilistic method for filling gaps in genome assemblies
Authors: Tarafder Sumit , Islam Mazharul , Shatabda Swakkhar , Rahman Atif 
Published: June 2022

AbstractMotivationAdvances in sequencing technologies have led to the sequencing of genomes of a multitude of organisms. However, draft genomes of many of these organisms contain a large number of gaps due to the repeats in genomes, low sequencing coverage and limitations in sequencing technologies. Although there exists several tools for filling gaps, many of these do not utilize all information relevant to gap filling.ResultsHere, we present a probabilistic method for filling gaps in draft genome assemblies using second-generation reads based on a generative model for sequencing that takes into account information on insert sizes and sequencing errors. Our method is based on the expectation-maximization algorithm unlike the graph-based methods adopted in the literature. Experiments on real biological datasets show that this novel approach can fill up large portions of gaps with small number of errors and misassemblies compared to other state-of-the-art gap-filling tools.Availability and implementationThe method is implemented using C++ in a software named ‘Filling Gaps by Iterative Read Distribution (Figbird)’, which is available at https://github.com/SumitTarafder/Figbird.Supplementary informationSupplementary data are available at Bioinformatics online.
Altered brain rhythms and behaviour in the accelerated ovarian failure mouse model of human menopause
Authors: Vrontou Sophia , Bédécarrats Alexis , Wei Xiaofei , Ayodeji Morikeoluwa , Brassai Attila , Molnár László , Mody Istvan 
Published: June 2022

Abstract
To date, potential mechanisms of menopause-related memory and cognitive deficits have not been elucidated. Therefore, we studied brain oscillations, their phase–amplitude coupling, sleep and vigilance state patterns, running wheel use and other behavioural measures in a translationally valid mouse model of menopause, the 4-vinylcyclohexene-diepoxide-induced accelerated ovarian failure. After accelerated ovarian failure, female mice show significant alterations in brain rhythms, including changes in the frequencies of θ (5–12 Hz) and γ (30–120 Hz) oscillations, a reversed phase–amplitude coupling, altered coupling of hippocampal sharp-wave ripples to medial prefrontal cortical sleep spindles and reduced δ oscillation (0.5–4 Hz) synchrony between the two regions during non-rapid eye movement sleep. In addition, we report on significant circadian variations in the frequencies of θ and γ oscillations, and massive synchronous δ oscillations during wheel running. Our results reveal novel and specific network alterations and feasible signs for diminished brain connectivity in the accelerated ovarian failure mouse model of menopause. Taken together, our results may have identified changes possibly responsible for some of the memory and cognitive deficits previously described in this model. Corresponding future studies in menopausal women could shed light on fundamental mechanisms underlying the neurological and psychiatric comorbidities present during this important transitional phase in women’s lives.
Diagnosis of coexistent neurodegenerative dementias in multiple sclerosis
Authors: Londoño Diana P , Arumaithurai Kogulavadanan , Constantopoulos Eleni , Basso Michael R , Reichard R Ross , Flanagan Eoin P , Keegan B Mark 
Published: June 2022

Abstract
Among people with multiple sclerosis, cognitive impairment occurs commonly and is a potent predictor of disability. Some multiple sclerosis patients present with severe cognitive impairment, and distinguishing multiple sclerosis-related cognitive impairment from co-existent progressive neurodegenerative diseases such as Alzheimer disease poses a diagnostic challenge. The use of biomarkers such as PET and CSF proteins may facilitate this distinction. The study was a retrospective, descriptive study on convenience samples of separate cohorts, one of cognitively impaired multiple sclerosis patients evaluated on autopsy to demonstrate coincidence of both multiple sclerosis and neurodegenerative cognitive diseases. The second cohort were cognitively impaired multiple sclerosis patients evaluated by biomarker to investigate possible additional neurodegenerative cognitive disorders contributing to the cognitive impairment. We investigated selected biomarkers among 31 severely impaired patients (biomarker cohort) and 12 severely impaired patients assessed at autopsy and selected 24 (23 biomarker cohort, 1 autopsy cohort) had comprehensive neurocognitive testing. Biomarker cohort investigations included 18F-Fluorodeoxyglucose PET and/or CSF amyloid Aβ1-42, phospho-tau and total tau levels. The autopsy cohort was evaluated with comprehensive neuropathological assessment for aetiology of cognitive impairment. The cohorts shared similar sex, age at multiple sclerosis onset and multiple sclerosis clinical course. The autopsy-cohort patients were older at diagnosis (69.5 versus 57 years, P = 0.006), had longer disease duration [median (range) 20 years (3–59) versus 9 (1–32), P = 0.001] and had more impaired bedside mental status scores at last follow-up [Kokmen median (range) 23 (1–38) versus 31 (9–34) P = 0.01]. Autopsy-cohort patients confirmed, or excluded, coexistent neurogenerative disease by neuropathology gold standard. Most biomarker-cohort patients had informative results evaluating coexistent neurogenerative disease. Biomarkers may be useful in indicating a coexistent neurodegenerative disease earlier, and in life, in patients with multiple sclerosis and significant cognitive impairment.
Anti-glutathione S-transferase omega 1-1 (GSTO1-1) antibodies are increased during acute and chronic inflammation in humans
Authors: Piaggi Simona , Lorenzini Evelina , Pratesi Federico , Migliorini Paola , Pompella Alfonso , Bruschi Fabrizio , Corti Alessandro 
Published: June 2022

Abstract
Glutathione S-transferase omega-1 (GSTO1-1) is a cytosolic enzyme involved in the modulation of critical inflammatory pathways as well as in cancer progression. Auto-antibodies against GSTO1-1 were detected in the serum of patients with esophageal squamous cell carcinoma and were proposed as potential biomarkers in the early detection of the disease. Our findings show that anti-GSTO1-1 antibodies can be found in a variety of inflammatory diseases, including autoimmune rheumatoid arthritis, infectious SARS-CoV-2, and trichinellosis. Our findings strongly suggest that anti-GSTO1-1 antibodies may be a marker of tissue damage/inflammation rather than a specific tumor-associated biomarker.
Beta-Lactam Antibiotic Therapeutic Drug Monitoring in Critically Ill Patients: A Systematic Review and Meta-Analysis
Authors: Pai Mangalore Rekha , Ashok Aadith , Lee Sue J , Romero Lorena , Peel Trisha N , Udy Andrew A , Peleg Anton Y 
Published: June 2022

Abstract
Therapeutic drug monitoring (TDM) of beta-lactam antibiotics is recommended to address the variability in exposure observed in critical illness. However, the impact of TDM-guided dosing on clinical outcomes remains unknown. We conducted a systematic review and meta-analysis on TDM-guided dosing and clinical outcomes (all-cause mortality, clinical cure, microbiological cure, treatment failure, hospital and intensive care unit length of stay, target attainment, antibiotic-related adverse events, and emergence of resistance) in critically ill patients with suspected or proven sepsis. Eleven studies (n = 1463 participants) were included. TDM-guided dosing was associated with improved clinical cure (relative risk, 1.17; 95% confidence interval [CI], 1.04 to 1.31), microbiological cure (RR, 1.14; 95% CI, 1.03 to 1.27), treatment failure (RR, 0.79; 95% CI, .66 to .94), and target attainment (RR, 1.85; 95% CI, 1.08 to 3.16). No associations with mortality and length of stay were found. TDM-guided dosing improved clinical and microbiological cure and treatment response. Larger, prospective, randomized trials are required to better assess the utility of beta-lactam TDM in critically ill patients.
Scaling laws for properties of random graphs that grow via successive combination
Authors: Grindrod Peter 
Published: June 2022

Abstract
We consider undirected graphs that grow through the successive combination of component sub-graphs. For any well-behaved functions defined for such graphs, taking values in a Banach space, we show that there must exist a scaling law applicable when successive copies of the same component graph are combined. Crucially, we extend the approach introduced in previous work to the successive combination of component random sub-graphs. We illustrate this by generalizing the preferential attachment operation for the combination of stochastic block models. We discuss a further wide range of random graph combination operators to which this theory now applies, indicating the ubiquity of growth scaling laws (and asymptotic decay scaling laws) within applications, where the modules are quite distinct, yet may be considered as instances drawn from the same random graph. This is a type of statistically self-similar growth process, as opposed to a deterministic growth process incorporating exact copies of the same motif, and it represents a natural, partially random, growth processes for graphs observed in the analysis of social and technology contexts.
Three-dimensional topographic effects on infrasound propagation across Ascension Island
Authors: Khodr Codor , Green David N , Azarpeyvand Mahdi 
Published: June 2022

SUMMARYNarrowband harmonic infrasound signals within the 1–8 Hz passband, generated by wind turbines on Ascension Island, have been recorded at four microbarometers located at distances of between 1.8 and 4.6 km from the source along different azimuths. Across one month of recordings in October 2010, amplitude ratios between the four recordings show temporal stability but deviate from the ratios expected for propagation across a flat plane. Using a recently developed 3-D parabolic equation method, that can incorporate realistic topography as a lower boundary, it is shown that these time-independent amplitude ratio deviations can be, in part, explained by acoustic interactions with topography that has scale lengths on the order of a few hundreds of metres. These interactions comprise both 2-D barrier effects that reduce sound levels behind high topography, and 3-D diffractive effects that increase sound levels behind topographic obstacles. For the Ascension Island case study, amplitudes along two of the four paths can be successfully modelled using a 2-D model, indicating that barrier effects dominate for these path geometries. Amplitude ratios along a third path, and the frequency-dependence of these ratios, are better simulated using a 3-D model that captures the out-of-plane diffractive effects around a prominent hill. The fourth path is poorly modelled using the 3-D model, which overpredicts acoustic amplitudes in this case. We hypothesize that this mismatch is likely to be due to a simplified description of the wind turbine source term. This study provides further observational confirmation that topographic interactions need to be considered when interpreting locally propagating infrasound, and shows that for harmonic narrowband sources a parabolic equation solver incorporating realistic boundary conditions provides an efficient method for simulating topographic interactions.
Measuring the phase of ambient noise cross correlations: anisotropic Rayleigh and Love wave tomography across the Oman Mountains
Authors: Wiesenberg L , Weidle C , El-Sharkawy A , Timkó M , Lebedev S , Meier T 
Published: June 2022

SUMMARYAmbient seismic noise tomography has, over the last two decades, developed into a well-established tool for imaging seismic properties of the Earth’s crust. Fundamental mode Rayleigh and Love wave phase velocity dispersion curves can be measured from ambient noise cross-correlation functions (CCF) either using a high-frequency approximation theory, or by fitting the spectrum of the CCF to a Bessel function. Here, we advance the latter approach and present an automated algorithm that fits the phase of the Hankel function to the phase of the causal symmetric part of the CCF in order to determine phase velocity curves as continuous functions of frequency. Synthetic tests verify the reliability of the proposed method in the presence of low signal-to-noise ratio (SNR). Moreover, usage of the phase allows for robust phase velocity measurements at longer periods than when using the zero crossings of the Bessel function only and is, therefore, particularly useful at short inter-station distances. In the frequency domain, acceptable bandwidths of smooth phase velocity curves are obtained in an automated procedure using a set of fine-tuned quality criteria. We apply the method to 2.5 yr of continuous waveform data recorded by 58 temporary and permanent broad-band seismic stations in northern Oman. We obtain 1072 and 670 phase velocity curves for Rayleigh and Love waves, respectively, in the period range of 2–40 s. The data are inverted for isotropic and azimuthally anisotropic period-dependent phase velocity maps. Synthetic reconstruction tests show that the phase velocity maps have a lateral resolution of ∼30 km. The results suggest distinctly different middle to lower crustal architecture between the northern and eastern Oman Mountains. Azimuthal anisotropy shows contrasting fast propagation orientations in the shallow and deep crust, which we attribute to stress-induced and structural anisotropy in the upper crust and to lattice-preferred orientation in the lower crust.
Surface-wave tomography using SeisLib: a Python package for multiscale seismic imaging
Authors: Magrini Fabrizio , Lauro Sebastian , Kästle Emanuel , Boschi Lapo 
Published: June 2022

Summary
To improve our understanding of the Earth’s interior, seismologists often have to deal with enormous amounts of data, requiring automatic tools for their analyses. It is the purpose of this study to present SeisLib, an open-source Python package for multiscale seismic imaging. At present, SeisLib includes routines for carrying out surface-wave tomography tasks based on seismic ambient noise and teleseismic earthquakes. We illustrate here these functionalities, both from the theoretical and algorithmic point of view and by application of our library to seismic data from North America. We first show how SeisLib retrieves surface-wave phase velocities from the ambient noise recorded at pairs of receivers, based on the zero crossings of their normalized cross-spectrum. We then present our implementation of the two-station method, to measure phase velocities from pairs of receivers approximately lying on the same great-circle path as the epicentre of distant earthquakes. We apply these methods to calculate dispersion curves across the conterminous United States, using continuous seismograms from the transportable component of USArray and earthquake recordings from the permanent networks. Overall, we measure 144 272 ambient-noise and 2055 earthquake-based dispersion curves, that we invert for Rayleigh-wave phase-velocity maps. To map the lateral variations in surface-wave velocity, SeisLib exploits a least-squares inversion algorithm based on ray theory. Our implementation supports both equal-area and adaptive parametrizations, with the latter allowing for a finer resolution in the areas characterized by high density of measurements. In the broad period range 4–100 s, the retrieved velocity maps of North America are highly correlated (on average, 96 per cent) and present very small average differences (0.14 ± 0.1 per cent) with those reported in the literature. This points to the robustness of our algorithms. We also produce a global phase-velocity map at the period of 40 s, combining our dispersion measurements with those collected at global scale in previous studies. This allows us to demonstrate the reliability and optimized computational speed of SeisLib, even in presence of very large seismic inverse problems and strong variability in the data coverage. The last part of the manuscript deals with the attenuation of Rayleigh waves, which can be estimated through SeisLib based on the seismic ambient noise recorded at dense arrays of receivers. We apply our algorithm to produce an attenuation map of the United States at the period of 4 s, which we find consistent with the relevant literature.
Repair of contained ventricular rupture with infected intrapericardial thrombus
Authors: Hasan Dania , DeBoard Zach M 
Published: June 2022

Abstract
Contained left ventricular rupture, or pseudoaneurysm, is a rare entity resulting from adhesions confining the defect to a localized portion of the pericardial space. Concomitant infection is even more infrequent. We present the first-known case of a patient with an infected intrapericardial thrombus from a left ventricular rupture.
Genetic architecture underlying variation in floral meristem termination in Aquilegia
Authors: Min Ya , Ballerini Evangeline S , Edwards Molly B , Hodges Scott A , Kramer Elena M 
Published: June 2022

Abstract
Floral organs are produced by floral meristems (FMs), which harbor stem cells in their centers. Since each flower only has a finite number of organs, the stem cell activity of an FM will always terminate at a specific time point, a process termed floral meristem termination (FMT). Variation in the timing of FMT can give rise to floral morphological diversity, but how this process is fine-tuned at a developmental and evolutionary level is poorly understood. Flowers from the genus Aquilegia share identical floral organ arrangement except for stamen whorl number (SWN), making Aquilegia a well-suited system for investigation of this process: differences in SWN between species represent differences in the timing of FMT. By crossing A. canadensis and A. brevistyla, quantitative trait locus (QTL) mapping has revealed a complex genetic architecture with seven QTL. We explored potential candidate genes under each QTL and characterized novel expression patterns of select loci of interest using in situ hybridization. To our knowledge, this is the first attempt to dissect the genetic basis of how natural variation in the timing of FMT is regulated, and our results provide insight into how floral morphological diversity can be generated at the meristematic level.