bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of a new open-source method for automatic delineation and dose assessment of the heart and LADCA in breast radiotherapy with simultaneous uncertainty estimation
Authors: Finnegan Robert , Laugaard Lorenzen Ebbe , Dowling Jason , Thwaites David , Delaney Geoff , Brink Carsten , Holloway Lois 
Published: November 2020

Abstract
Radiotherapy has been shown to increase risks of cardiotoxicities for breast cancer patients. Automated delineation approaches are necessary for consistent and efficient assessment of cardiac doses in large, retrospective datasets, while patient-specific estimation of the uncertainty in these doses provides valuable additional data for modelling and understanding risks. In this work, we aim to validate the consistency of our previously described open-source software model for automatic cardiac delineation in the context of dose assessment, relative to manual contouring. We also extend our software to introduce a novel method to automatically quantify the uncertainty in cardiac doses based on expected inter-observer variability (IOV) in contouring. This method was applied to a cohort of 15 left-sided breast cancer patients treated in Denmark using modern tangential radiotherapy techniques. On each image set, the whole heart and left anterior descending coronary artery (LADCA) were contoured by nine independent experts; the range of doses to these nine volumes provided a reference for the dose uncertainties generated from the automatic method. Local and external atlas sets were used to test the method. Results give confidence in the consistency of automatic segmentations, with mean whole heart dose differences for local and external atlas sets of −0.20 ± 0.17 and −0.10 ± 0.14 Gy, respectively. Automatic estimates of uncertainties in doses are similar to those from IOV for both the whole heart and LADCA. Overall, this study confirms that our automated approach can be used to accurately assess cardiac doses, and the proposed method can provide a useful tool in estimating dose uncertainties.
Characterizing blood clots using acoustic radiation force optical coherence elastography and ultrasound shear wave elastography
Authors: Liu Hsiao-Chuan , Abbasi Mehdi , Ding Yong Hong , Roy Tuhin , Capriotti Margherita , Liu Yang , Fitzgerald Seán , Doyle Karen M , Guddati Murthy , Urban Matthew W , Brinjikji Waleed 
Published: November 2020

Abstract
Thromboembolism in a cerebral blood vessel is associated with high morbidity and mortality. Mechanical thrombectomy (MT) is one of the emergenc proceduresperformed to remove emboli. However, the interventional approaches such as aspiration catheters or stent retriever are empirically selected. An inappropriate selection of surgical devices can influence the success rate during embolectomy, which can lead to an increase in brain damage. There has been growing interest in the study of clot composition and using a priori knowledge of clot composition to provide guidance for an appropriate treatment strategy for interventional physicians. Developing imaging tools which can allow interventionalists to understand clot composition could affect management and device strategy. In this study, we investigated how clots of different compositions can be characterized by using acoustic radiation force optical coherence elastography (ARF–OCE) and compared with ultrasound shear wave elastography (SWE). Five different clots compositions using human blood were fabricated into cylindrical forms from fibrin-rich (21% red blood cells, RBCs) to RBC-rich (95% RBCs). Using the ARF–OCE and SWE, we characterized the wave velocities measured in the time-domain. In addition, the semi-analytical finite element model was used to explore the relationship between the phase velocities with various frequency ranges and diameters of the clots. The study demonstrated that the wave group velocities generally decrease as RBC content increases in ARF–OCE and SWE. The correlation of the group velocities from the OCE and SWE methods represented a good agreement as RBC composition is larger than 39%. Using the phase velocity dispersion analysis applied to ARF–OCE data, we estimated the shear wave velocities decoupling the effects of the geometry and material properties of the clots. The study demonstrated that the composition of the clots can be characterized by elastographic methods using ARF–OCE and SWE, and OCE demonstrated better ability to discriminate between clots of different RBC compositions, compared to the ultrasound-based approach, especially in clots with low RBC compositions.
Generation of a noise-like pulse from an erbium-doped fiber laser based on nonlinear multimode interference
Authors: Zhao Fengyan , Li Ning , Wang Hushan 
Published: November 2020

Abstract
A noise-like pulse (NLP) is generated in an anomalous-dispersion passively mode-locked erbium-doped fiber laser using graded-index multimode fiber (GIMF) as the all-fiber saturable absorber (SA) for the first time. By splicing two sections of bending GIMF at both ends of a single mode fiber and optimizing the birefringence and nonlinear parameters, stable NLP mode-locking operation can be achieved within a wide pump power range. Meanwhile, the performances of NLP mode-locking have been analyzed experimentally by changing the length of the GIMF.
Evaluation of Strength Deterioration Factor on Blended Concrete Exposed to Magnesium Sulphate Solution
Authors: Jena Trilochan , Chandra Panda Kishor , Panda Chittaranjan 
Published: November 2020

Abstract
This paper reports the combined effects of industrial waste as fly ash (FA) and agro-waste such as silpozz on the compressive strength and strength deterioration factor (SDF) of blended cement concrete exposed to 5% and 10% MgSO4 solution and normal water. Silpozzis manufactured by burning of agro-waste rice husk in designed furnace in between 600° to 700°C which is one of the main agriculture.al residues obtained from the outer covering of rice grains during the milling process. There are four mix series taken with control mix. The control mix made 0% replacement of FA and silpozz with Ordinary Portland Cement (OPC). The first mix series made 0% FA and 10-30% replacement of silpozz with OPC. The second mix series made with 10% FA and 10-40% replacement of silpozz with OPC. The third mix series made 20% FA and 10-30% replacement of silpozz with OPC and the fourth mix series made 30% FA and 10-20% silpozz replaced with OPC. The samples (cubes) are prepared and cured in normal water and 5% and 10% MgSO4 solution for 7, 28 and 90 days. The studied parameters are compressive strength and strength deterioration factor (SDF) for 7, 28 and 90 days. The regression equations and value of correlation coefficient R2 between compressive strength and partial replacement of silpozz is obtained and revealed from these results that value of correlation coefficient is varied from 0.9602 to 1.
Advances in Seismic Strengthening Materials and Techniques
Authors: Mahadik Sanjivan , Mahajan Lomesh , Bhagat S. R. 
Published: November 2020

Abstract
Seismic strengthening of reinforced concrete (RC) members is a method of improving their existing capacity to withstand seismic forces. The process typically includes strengthening of RC structural members such beams, columns, slabs, footings, beam-column junctions, etc. to improve the axial, flexure, and shear capacity. Experiences during the recent earthquakes and changes in Indian Standards made it essential to carry out structural audit of buildings. The buildings, which do not comply with the recent Code provisions have to be reconstructed or to be strengthened to achieve the desired capacity level. Reconstruction of such buildings will consume time and money. In addition, evacuation of such buildings for reconstruction is a difficult task. In this paper an attempt has been made to focus on the seismic strengthening of structural members of RC buildings which are designed to only gravity loads or the structures designed prior to release of new building Codes. This paper covers a brief introduction of conventional methods of strengthening followed by an introduction of advanced FRP composite materials and techniques of retrofitting for existing RC buildings. Finally, it is concluded that the advanced FRP composite materials and recent innovative methods can more advantageously used for seismic strengthening of RC buildings.
Characterization of Alkali Activated Bentonite - Fly Ash as Brick Material
Authors: Rout P P , Garanayak L 
Published: November 2020

Abstract
Brick, one of the most common binding materials which need excess energy during manufacture. Gathering of excess industrial waste creates the environmental pollution as well as a health issue. To developing green environment, industrial waste can be used as an alternation of binder material as a brick. In this present study combination of sodium bentonite and fly ash get activated by sodium hydroxide (NaOH) and calcium oxide (CaO) whose Na2O/CaO proportion varied as 1 with mole content. Mixing proportion of both solid particles were varied as 40/60 and 60/40 as weight percentages. Casted samples were conducted for the curing period of 0 days, 3 days, 7 days, and 28 days. Mineralogy, morphology, and compressive strength tests are conducted and found that 1.5 moles are the best for developing compressive strength that obtained as 135.8 kPa at 60°C oven curing temperature.
Impact of Ultrafine Ground Granulated Blast Furnace Slag on the Properties of High Strength Durable Concrete
Authors: Sethy Kaliprasanna , Rojalin Nanda S 
Published: November 2020

Abstract
Ultrafine ground granulated blast furnace slag (UFGGBFS), because of its pozzolanic nature, could be an extraordinary resource for the advanced development needs, since slag cements concrete can be of elite, if properly planned. Improvement of the durability properties of concrete to support a more extended life expectancy and creating a climate amicable greener concrete are turning out to be significant standards in getting high quality concrete. Fusing Ultrafine Ground Granulated Blast Furnace Slag (UFGGBFS) as a mineral admixture enhances the workability of fresh concrete and decreased the link between pores; in this way, decreasing the permeability and improving the obstruction of the solid against chloride infiltration. The measure of ozone depleting substance delivered in making the concrete and the energy needed to create the concrete are significantly decreased with the utilization of UFGGBFS. Ultrafine GGBFS (UFGGBFS) with a normal molecule size less than 10m and a Blaine surface area more than 600m2/kg can significantly improve the properties of the concrete as far as diffusion and chemical reactivity impacts. Compared with GGBFS, the UFGGBFS increases the rate of hydration and pozzolanic responses and has a superior filling impact. In this study, the early development of mechanical strength and permeability properties of high strength concrete with UFGGBFS is examined. Total five mixes with 180kg/m3 each of both Ordinary Portland Cement (OPC) concrete and Ultrafine Ground Granulated Blast furnace Slag (UFGGBFS) concrete were designed. The mixes starts from 0% replacement and gradually increases up to 20% (i.e 0, 5, 10, 15 and 20%) of identical all total cementitious materials with UFGGBFS substitution were planned and a sum of 145 samples from the five blends were projected. Compressive strength parameters, flexural strength parameter, modulus of elasticity parameter and water permeability test outcomes are introduced.
Stress-Strain Behaviour of Compacted Pond Ash Reinforced with Stone Column
Authors: Naik J K 
Published: November 2020

Abstract
Ash pond deposits are characterized by its high compressibility and low bearing capacity which is unappropriated for the construction of engineering structures over it. There are several techniques to improve the bearing capacity of ash deposits. Stone column is one of the effective techniques employed to increase the bearing capacity for construction of engineering structures over soft soil deposits. Stone columns are extensively used to improve the bearing capacity of poor ground, time rate of settlements, stiffness, reduce the settlement of structure, and liquefaction potential of soft ground. This paper reports the load settlement behaviour of compacted pond ash beds reinforced with stone columns. Both end bearing and floating stone columns of different length ratios and area ratios were introduced in compacted pond ash beds having different densities. The load-settlement behaviour of footings supported on different configurations of stone columns was studied.
Sensitive detection of water/oxygen molecule adsorption and reaction on a titanium oxide nanosheet with a graphene field effect transistor
Authors: Yoshida Yuhsuke , Imafuku Tatsuya , Inoue Daiki , Uechi Seita , Shite Daiki , Katsuki Yuhto , Funatsu Asami , Shimojo Fuyuki , Hara Masahiro 
Published: November 2020

Abstract
We have investigated molecule adsorption phenomena on a chemically active surface of titanium oxide nanosheet by coupling with an electrically sensitive graphene field effect transistor (FET). Super-hydrophilic surface of the titanium oxide nanosheet forms a water-layer in ambient air which exhibits a large hysteresis of drain current in the hybrid FET for sweeping gate-voltage. The large hysteresis disappears in vacuum, which indicates physically adsorbed water molecules on the surface of the titanium oxide nanosheet dominantly contribute to the hysteresis. UV light irradiation in vacuum significantly changes the drain current due to desorption of the adsorbed molecules. Sufficient UV irradiation results in symmetric gate-voltage dependence similar to those of conventional graphene FETs. Exposure to an oxygen gas atmosphere leads to a heavy hole doping in the FET, where the binding of the oxygen molecules is stronger than that of water molecules. In a humidified nitrogen atmosphere, a large shift of charge neutrality point is observed in transfer characteristics crossing between electron doping and hole doping. By contrast, a clear square-shaped hysteresis loop is observed in a humidified oxygen atmosphere, where the hole density in the graphene drastically changed with O2/H2O redox couple reaction on the titanium oxide nanosheet.
How to Optimize Aesthetics for the Partial Mastectomy Patient
Authors: Losken Albert , Brown Ciara A 
Published: November 2020

Abstract
Aesthetic concern is one of the main driving forces behind the popularity of the oncoplastic approach to breast conservation therapy. Oncoplastic options at the time of lumpectomy include volume replacement techniques such as flaps and volume displacement techniques such as the oncoplastic reduction. These techniques can be employed to ensure preservation of breast shape and contour, size and symmetry, inframammary fold position, and position of the nipple-areola complex. The importance of aesthetic outcomes is not only to improve overall patient satisfaction but also to minimize the need for revisional surgeries for shape and symmetry. The purpose of this review is to discuss ways to optimize the aesthetic result and to review the evidence behind aesthetic outcomes.
IMIX: a multivariate mixture model approach to association analysis through multi-omics data integration
Authors: Wang Ziqiao , Wei Peng 
Published: November 2020

Abstract

Motivation
Integrative genomic analysis is a powerful tool used to study the biological mechanisms underlying a complex disease or trait across multiplatform high-dimensional data, such as DNA methylation, copy number variation and gene expression. It is common to perform large-scale genome-wide association analysis of an outcome for each data type separately and combine the results ad hoc, leading to loss of statistical power and uncontrolled overall false discovery rate (FDR).

Results
We propose a multivariate mixture model (IMIX) framework that integrates multiple types of genomic data and allows modeling of inter-data-type correlations. We investigated the across-data-type FDR control in IMIX and demonstrated lower misclassification rates at controlled overall FDR than established individual data type analysis strategies, such as the Benjamini–Hochberg FDR control, the q-value and the local FDR control by extensive simulations. IMIX features statistically principled model selection, FDR control and computational efficiency. Applications to The Cancer Genome Atlas data provided novel multi-omics insights into the genes and mechanisms associated with the luminal and basal subtypes of bladder cancer and the prognosis of pancreatic cancer.

Availabilityand implementation
We have implemented our method in R package ‘IMIX’ available at https://github.com/ziqiaow/IMIX, as well as CRAN soon.

Supplementary information
Supplementary data are available at Bioinformatics online.
MAGUS: Multiple sequence Alignment using Graph clUStering
Authors: Smirnov Vladimir , Warnow Tandy 
Published: November 2020

AbstractMotivationThe estimation of large multiple sequence alignments (MSAs) is a basic bioinformatics challenge. Divide-and-conquer is a useful approach that has been shown to improve the scalability and accuracy of MSA estimation in established methods such as SATé and PASTA. In these divide-and-conquer strategies, a sequence dataset is divided into disjoint subsets, alignments are computed on the subsets using base MSA methods (e.g. MAFFT), and then merged together into an alignment on the full dataset.ResultsWe present MAGUS, Multiple sequence Alignment using Graph clUStering, a new technique for computing large-scale alignments. MAGUS is similar to PASTA in that it uses nearly the same initial steps (starting tree, similar decomposition strategy, and MAFFT to compute subset alignments), but then merges the subset alignments using the Graph Clustering Merger, a new method for combining disjoint alignments that we present in this study. Our study, on a heterogeneous collection of biological and simulated datasets, shows that MAGUS produces improved accuracy and is faster than PASTA on large datasets, and matches it on smaller datasets.Availability and implementationMAGUS: https://github.com/vlasmirnov/MAGUSSupplementary informationSupplementary data are available at Bioinformatics online.
A span-graph neural model for overlapping entity relation extraction in biomedical texts
Authors: Fei Hao , Zhang Yue , Ren Yafeng , Ji Donghong 
Published: November 2020

Abstract

Motivation
Entity relation extraction is one of the fundamental tasks in biomedical text mining, which is usually solved by the models from natural language processing. Compared with traditional pipeline methods, joint methods can avoid the error propagation from entity to relation, giving better performances. However, the existing joint models are built upon sequential scheme, and fail to detect overlapping entity and relation, which are ubiquitous in biomedical texts. The main reason is that sequential models have relatively weaker power in capturing long-range dependencies, which results in lower performance in encoding longer sentences. In this article, we propose a novel span-graph neural model for jointly extracting overlapping entity relation in biomedical texts. Our model treats the task as relation triplets prediction, and builds the entity-graph by enumerating possible candidate entity spans. The proposed model captures the relationship between the correlated entities via a span scorer and a relation scorer, respectively, and finally outputs all valid relational triplets.

Results
Experimental results on two biomedical entity relation extraction tasks, including drug–drug interaction detection and protein–protein interaction detection, show that the proposed method outperforms previous models by a substantial margin, demonstrating the effectiveness of span-graph-based method for overlapping relation extraction in biomedical texts. Further in-depth analysis proves that our model is more effective in capturing the long-range dependencies for relation extraction compared with the sequential models.

Availability and implementation
Related codes are made publicly available at http://github.com/Baxelyne/SpanBioER.
movAPA: modeling and visualization of dynamics of alternative polyadenylation across biological samples
Authors: Ye Wenbin , Liu Tao , Fu Hongjuan , Ye Congting , Ji Guoli , Wu Xiaohui 
Published: November 2020

Abstract

Motivation
Alternative polyadenylation (APA) has been widely recognized as a widespread mechanism modulated dynamically. Studies based on 3′ end sequencing and/or RNA-seq have profiled poly(A) sites in various species with diverse pipelines, yet no unified and easy-to-use toolkit is available for comprehensive APA analyses.

Results
We developed an R package called movAPA for modeling and visualization of dynamics of alternative polyadenylation across biological samples. movAPA incorporates rich functions for preprocessing, annotation and statistical analyses of poly(A) sites, identification of poly(A) signals, profiling of APA dynamics and visualization. Particularly, seven metrics are provided for measuring the tissue-specificity or usages of APA sites across samples. Three methods are used for identifying 3′ UTR shortening/lengthening events between conditions. APA site switching involving non-3′ UTR polyadenylation can also be explored. Using poly(A) site data from rice and mouse sperm cells, we demonstrated the high scalability and flexibility of movAPA in profiling APA dynamics across tissues and single cells.

Availability and implementation
https://github.com/BMILAB/movAPA.

Supplementary information
Supplementary data are available at Bioinformatics online.
FinaleDB: a browser and database of cell-free DNA fragmentation patterns
Authors: Zheng Haizi , Zhu Michelle S , Liu Yaping 
Published: November 2020

Abstract

Summary
Circulating cell-free DNA (cfDNA) is a promising biomarker for the diagnosis and prognosis of many diseases, including cancer. The genome-wide non-random fragmentation patterns of cfDNA are associated with the nucleosomal protection, epigenetic environment and gene expression in the cell types that contributed to cfDNA. However, current progress on the development of computational methods and understanding of molecular mechanisms behind cfDNA fragmentation patterns is significantly limited by the controlled-access of cfDNA whole-genome sequencing (WGS) dataset. Here, we present FinaleDB (FragmentatIoN AnaLysis of cEll-free DNA DataBase), a comprehensive database to host thousands of uniformly processed and curated de-identified cfDNA WGS datasets across different pathological conditions. Furthermore, FinaleDB comes with a fragmentation genome browser, from which users can seamlessly integrate thousands of other omics data in different cell types to experience a comprehensive view of both gene-regulatory landscape and cfDNA fragmentation patterns.

Availability and implementation
FinaleDB service: http://finaledb.research.cchmc.org/. FinaleDB source code: https://github.com/epifluidlab/finaledb_portal, https://github.com/epifluidlab/finaledb_workflow.

Supplementary information
Supplementary data are available at Bioinformatics online.