bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing OCHROdb, a comprehensive quality checked database of open chromatin regions from sequencing data
Authors: Shooshtari Parisa , Feng Samantha , Nelakuditi Viswateja , Asakereh Reza , Hosseini Naghavi Nader , Foong Justin , Brudno Michael , Cotsapas Chris 
Published: May 2023

AbstractInternational consortia, including ENCODE, Roadmap Epigenomics, Genomics of Gene Regulation and Blueprint Epigenome have made large-scale datasets of open chromatin regions publicly available. While these datasets are extremely useful for studying mechanisms of gene regulation in disease and cell development, they only identify open chromatin regions in individual samples. A uniform comparison of accessibility of the same regulatory sites across multiple samples is necessary to correlate open chromatin accessibility and expression of target genes across matched cell types. Additionally, although replicate samples are available for majority of cell types, a comprehensive replication-based quality checking of individual regulatory sites is still lacking. We have integrated 828 DNase-I hypersensitive sequencing samples, which we have uniformly processed and then clustered their regulatory regions across all samples. We checked the quality of open-chromatin regions using our replication test. This has resulted in a comprehensive, quality-checked database of Open CHROmatin (OCHROdb) regions for 194 unique human cell types and cell lines which can serve as a reference for gene regulatory studies involving open chromatin. We have made this resource publicly available: users can download the whole database, or query it for their genomic regions of interest and visualize the results in an interactive genome browser.
Application of non-degradable waste as building material for low-cost housing
Authors: Zuraida Siswanti , Dewancker Bart , Margono Romi Bramantyo 
Published: May 2023

AbstractBuilding material is one of the essential aspects in accommodating the supply and demand of low-cost housing in Indonesia. Recently, several researchers have devoted much time and effort to developing waste recycling for building materials since it is more ecologically benign, particularly for non-degradable waste. This article focuses on recycling disposable diaper waste as composite material for a structural and architectural component of the building based on Indonesian building standards. In addition to offering a broad perspective on the implementation of experimental findings, the design scenario comprised the construction of low-cost housing with a floorplan area of 36 m2. The experimental results indicate that disposable diapers waste to use as composite materials of the building has a maximum capacity of 10% for structural components and 40% for nonstructural and architectural components. The prototype housing also reveals that 1.73 m3 of disposable diaper waste can be decreased and utilised for a housing area of 36 m2.
A new spinosaurid dinosaur species from the Early Cretaceous of Cinctorres (Spain)
Authors: Santos-Cubedo Andrés , de Santisteban Carlos , Poza Begoña , Meseguer Sergi 
Published: May 2023

AbstractA new spinosaurid genus and species is described based on the right maxilla and five caudal vertebrae of a single specimen from the Arcillas de Morella Formation (Early Cretaceous) at the locality of Cinctorres (Castellón, Spain). Protathlitis cinctorrensis gen. et sp. nov. is diagnosed by one autapomorphic feature as well as by a unique combination of characters. The autapomorphy includes a subcircular depression in the anterior corner of the antorbital fossa in the maxilla. The new Iberian species is recovered as a basal baryonychine. The recognition of Protathlitis cinctorrensis gen. et sp. nov. as the first baryonychine dinosaur species identified from the Arcillas de Morella Formation (late Barremian) from the same time as Vallibonavenatrix cani, the first spinosaurine dinosaur from the same formation in the Morella subbasin (Maestrat Basin, eastern Spain), indicates that the Iberian Peninsula was home to a highly diverse assemblage of medium-to-large bodied spinosaurid dinosaurs. It seems that spinosaurids appeared during the Early Cretaceous in Laurasia, with the two subfamilies occupying the western part of Europe during this period. Later, during the Barremian–Aptian, they migrated to Africa and Asia, where they would diversify. In Europe, baryonychines were dominant, while in Africa, spinosaurines were most abundant.
Embedding responsibility in intelligent systems: from AI ethics to responsible AI ecosystems
Authors: Stahl Bernd Carsten 
Published: May 2023

AbstractIntelligent systems that are capable of making autonomous decisions based on input from their environment have great potential to do good, but they also raise significant social and ethical concerns. The discourse on ethics and artificial intelligence (AI) has covered these concerns in depth and developed an array of possible ways of addressing them. This article argues that a shortcoming of this discourse is that it concentrates on specific issues and their mitigation but neglects the nature of intelligent systems as socio-technical systems of systems that are often described as ecosystems. Building on the discussion of ethics and AI, the article suggests that it would be beneficial to come to an understanding of what would constitute responsible AI ecosystems. By introducing the concept of meta-responsibility or higher-level responsibility, the article proposes characteristics that an ecosystem would have to fulfil, in order to be considered a responsible ecosystem. This perspective is theoretically interesting because it extends the current AI ethics discourse. It furthermore offers a novel perspective for researchers and developers of intelligent system and helps them reflect on the way they relate to ethical issues.
A global conservation basic income to safeguard biodiversity
Authors: de Lange Emiel , Sze Jocelyne S. , Allan James , Atkinson Scott , Booth Hollie , Fletcher Robert , Khanyari Munib , Saif Omar 
Published: May 2023

AbstractBiodiversity conservation supporting a global sustainability transformation must be inclusive, equitable, just and embrace plural values. The conservation basic income (CBI), a proposed unconditional cash transfer to individuals residing in important conservation areas, is a potentially powerful mechanism for facilitating this radical shift in conservation. This analysis provides comprehensive projections for potential gross costs of global CBI using spatial analyses of three plausible future conservation scenarios. Gross costs vary widely, depending on the areas and populations included, from US$351 billion to US$6.73 trillion annually. A US$5.50 per day CBI in existing protected areas in low- and middle-income countries would cost US$478 billion annually. These costs are large compared with current government conservation spending (~US$133 billion in 2020) but represent a potentially sensible investment in safeguarding incalculable social and natural values and the estimated US$44 trillion in global economic production dependent on nature.
Gut microbial communities of hybridising pygmy angelfishes reflect species boundaries
Authors: Huggett Megan J. , Hobbs Jean-Paul A. , Vitelli Federico , Stat Michael , Sinclair-Taylor Tane H. , Bunce Michael , DiBattista Joseph D. 
Published: May 2023

AbstractHybridisation and introgression of eukaryotic genomes can generate new species or subsume existing ones, with direct and indirect consequences for biodiversity. An understudied component of these evolutionary forces is their potentially rapid effect on host gut microbiomes, and whether these pliable microcosms may serve as early biological indicators of speciation. We address this hypothesis in a field study of angelfishes (genusCentropyge), which have one of the highest prevalence of hybridisation within coral reef fish. In our study region of the Eastern Indian Ocean, the parent fish species and their hybrids cohabit and display no differences in their diet, behaviour, and reproduction, often interbreeding in mixed harems. Despite this ecological overlap, we show that microbiomes of the parent species are significantly different from each other in form and function based on total community composition, supporting the division of parents into distinct species, despite the confounding effects of introgression acting to homogenize parent species identity at other molecular markers. The microbiome of hybrid individuals, on the other hand, are not significantly different to each of the parents, instead harbouring an intermediate community composition. These findings suggest that shifts in gut microbiomes may be an early indicator of speciation in hybridising species.
Cumulative effects of weakly repressive regulatory regions in the 3’ UTR maintain PD-1 expression homeostasis in mammals
Authors: Lai Xiaoqian , Li Rong , Wang Panpan , Li Meng , Xiao Chenxi , Cao Qiang , Li Xin , Zhao Wenxue 
Published: May 2023

AbstractPD-1 has become a common target for cancer treatment. However, the molecular regulation of PD-1 expression homeostasis remains unclear. Here we report the PD-1 3’ UTR can dramatically repress gene expression via promoting mRNA decay. Deletion of the PD-1 3’ UTR inhibits T cell activity and promotes T-ALL cell proliferation. Interestingly, the robust repression is attributable to cumulative effects of many weak regulatory regions, which we show together are better able to maintain PD-1 expression homeostasis. We further identify several RNA binding proteins (RBPs) that modulate PD-1 expression via the 3’ UTR, including IGF2BP2, RBM38, SRSF7, and SRSF4. Moreover, despite rapid evolution, PD-1 3’ UTRs are functionally conserved and strongly repress gene expression through many common RBP binding sites. These findings reveal a previously unrecognized mechanism of maintaining PD-1 expression homeostasis and might represent a general model for how small regulatory effects play big roles in regulation of gene expression and biology.
Ultrastrong magnetic light-matter interaction with cavity mode engineering
Authors: Choi Hyeongrak , Englund Dirk 
Published: May 2023

AbstractMagnetic interaction between photons and dipoles is essential in electronics, sensing, spectroscopy, and quantum computing. However, its weak strength often requires resonators to confine and store the photons. Here, we present mode engineering techniques to create resonators with ultrasmall mode volume and ultrahigh quality factor. In particular, we show that it is possible to achieve an arbitrarily small mode volume only limited by materials or fabrication with minimal quality-factor degradation. We compare mode-engineered cavities in a trade-off space and show that the magnetic interaction can be strengthened more than 1016 times compared to free space. Proof-of-principles experiments using an ensemble of diamond nitrogen-vacancy spins show good agreement with our theoretical predictions. These methods enable new applications from high-cooperativity microwave-spin coupling in quantum computing or compact electron paramagnetic resonance sensors to fundamental science such as dark matter searches.
Risk‐return optimised energy asset allocation in transmission‐distribution system using tangency portfolio and Black–Litterman model
Authors: M Jisma , Mohan Vivek , Thomas Mini Shaji 
Published: May 2023

AbstractThe application of Markowitz and tangency portfolio and Black–Litterman models is extended by the authors to energy portfolio selection in transmission‐distribution environments with high penetration of renewable energy. As Transmission System Operator (TSO) and Distribution System Operator (DSO) contextually take mutualistic or conflicting positions in their portfolio selection process, their risk‐return interactions and behaviours depend on their subjective views on generation and operation. Here, the financial portfolio allocation tool Black–Litterman Model is adapted to incorporate subjective views of the operators to arrive at more intuitive portfolios. The best portfolios are searched within the acceptable risk‐return search space of each operator defined by their Markowitz efficient frontiers (EF), for Pareto‐optimising their profits. The tangency portfolio approach, which is generally used to determine the portfolio of risky and risk‐free assets in finance, is used here to determine the portfolio of renewable (energy‐risky) and fuel‐based sources (energy‐risk‐free). The proposed methodology is adopted in an HV–MV interconnected test system operated by one TSO and two DSOs, having wind, solar, coal, gas and nuclear generation technologies. It is observed that completely customisable portfolios can be constructed for TSO and DSO based on their inherent financial and energy risk‐return behaviours and posterior views.
Object detection network based on dense dilated encoder net
Authors: Liu Shaohua , Yang Ao , She Chundong , Du Kang 
Published: May 2023

AbstractIn this paper, the authors apply the feature pyramid network (FPN) to the single‐stage anchor‐free object detection algorithm CenterNet, and the effectiveness of the multi‐level feature fusion of FPN for the object detection algorithm is proved by experiments. However, multi‐level feature fusion leads to an increase in computational cost. In this regard, this paper proposes an object detection algorithm, called DDE‐Net, that does not use multi‐level feature fusion and only uses single‐level feature for optimization. The key component in it: the dense dilated encoder, which encourages dense information exchange of features between different spatial scales. This paper presents extensive experiments, and DDE‐Net shows strong performance compared to that of other popular models on the PASCAL VOC and on the COCO2017 dataset. On the COCO2017 dataset, the authors’ DDE‐Net achieves comparable results with its feature pyramids counterpart RetinaNet, while applying the same backbone with smaller params and GFLOPs than RetinaNet. With an image size of 512 × 512, DDE‐Net achieves 37.3 AP running at 81 fps on 2080 Ti.
Reconstruction of asteroid spin states from Gaia DR3 photometry
Authors: Ďurech J. , Hanuš J. 
Published: May 2023

Aims. Gaia Data Release 3 contains accurate photometric observations of more than 150 000 asteroids covering a time interval of 34 months. With a total of about 3 000 000 measurements, a typical number of observations per asteroid ranges from a few to several tens. We aimed to reconstruct the spin states and shapes of asteroids from this dataset.
Methods. We computed the viewing and illumination geometry for each individual observation and used the light curve inversion method to find the best-fit asteroid model, which was parameterized by the sidereal rotation period, the spin axis direction, and a low-resolution convex shape. To find the best-fit model, we ran the inversion for tens of thousands of trial periods on interval 2–10 000 h, with tens of initial pole directions. To find the correct rotation period, we also used a triaxial ellipsoid model for the shape approximation.
Results. In most cases the number of data points was insufficient to uniquely determine the rotation period. However, for about 8600 asteroids we were able to determine the spin state uniquely together with a low-resolution convex shape model. This large sample of new asteroid models enables us to study the spin distribution in the asteroid population. The distribution of spins confirms previous findings that (i) small asteroids have poles clustered toward ecliptic poles, likely because of the YORP-induced spin evolution, (ii) asteroid migration due to the Yarkovsky effect depends on the spin orientation, and (iii) members of asteroid families have the sense of rotation correlated with their proper semimajor axis: over the age of the family, orbits of prograde rotators evolved, due to the Yarkovsky effect, to larger semimajor axes, while those of retrograde rotators drifted in the opposite direction.
Burnout en especialistas de Ortopedia y Traumatología
Authors: Olate Catalina Vidal , Vial Pablo Besa , Salas María Jesús Lira , Daziano Mauricio Campos , Illanes Pamela Mery , Rosenberg Ianiv Klaber , Domíngez Sebastián Irarrázaval , Trivelli Luis Irribarra 
Published: May 2023

ResumenIntroducción El síndrome de burnout fue descrito como un conjunto de síntomas relacionados a cansancio emocional, despersonalización y falta de realización personal. En especialistas de Ortopedia y Traumatología, se ha descrito una prevalencia entre 4% y 59,4%. El objetivo de este estudio es evaluar, en especialistas de Ortopedia y Traumatología en Chile, la prevalencia de burnout en sus dimensiones y sus factores asociados.Materiales y Métodos Se invitó a participar a los especialistas inscritos al Congreso Chileno el año 2016. Se evaluó el síndrome de burnout con el cuestionario Maslach Burnout Inventory. Se describieron las variables numéricas y categóricas, y se analizó el burnout según sus dimensiones y variables asociadas. Se consideró la significancia estadística con valores de p < 0,05. Este proyecto fue aprobado por el Comité de Ética Científica Institucional.Resultados Se obtuvo la respuesta de la encuesta completa de 99 traumatólogos. La mediana de edad fue de 45 (rango: 29–76) años, y el 92% (n = 85) era del sexo masculino. Un 21% presentó un alto puntaje en la dimensión cansancio emocional, 20%, en despersonalización, y un 6% tenía alteración en la dimensión de realización personal. En la muestra total, un 35% presentó burnout. Las variables que se asociaron significativamente con la presencia de burnout fueron dormir menos de 5 horas y el consumo de modafinilo.Conclusión En este estudio se encontró una prevalencia de 35% de burnout, definido como la alteración de al menos una de las dimensiones. Futuros estudios deberán indagar en la prevención a partir de los factores de riesgo modificables.
Newton’s cradle and Astro-Blaster: toy hybridization for studying chain collisions
Authors: Sapia P , Bonanno A , Bozzo G 
Published: May 2023

Abstract
We present a multiple-collision apparatus, based on low-cost and easy-to-find materials, which offers the opportunity to plan and conduct a sequence of experimental activities aimed at studying, in a very simple way, the energy transfer in multiple collisions. Our apparatus is based on the use of everyday objects such as toys, which stimulate students’ interest by creating a familiar learning context. Two significant experiments on multiple collisions are described and the analyses of the corresponding experimental results are discussed. The first experiment makes it possible to analyze the kinetic energy transfer along a chain of adjacent balls. The second experiment offers the opportunity to give an analogical conceptual illustration of the bounce of a supernova core after gravitational collapse. Each experiment is pedagogically introduced by asking students to answer an appropriate stimulus questions, which were identified by instructors in a preliminary brainstorm session with students. Last, a theoretical model is given for kinetic energy transfer along a chain of balls and the experimental results are compared with the model predictions.
Category-aware dual adversarial domain adaptation model for rolling bearings fault diagnosis under variable conditions
Authors: Lu Xingchi , Xu Weiyang , Jiang Quansheng , Shen Yehu , Xu Fengyu , Zhu Qixin 
Published: May 2023

Abstract
The domain adaptation methods have good performance in solving the distribution discrepancy of vibration signals of rolling bearings under variable conditions, but without considering the alignment of different categories. To this end, a new dual adversarial domain adaptation (2ADA) mechanism for feature intra-category is proposed and a fault diagnosis model based on 2ADA is built in this paper. The method effectively uses category information to achieve category awareness, and avoids misclassification at the fuzzy decision boundary. In the training process, the multiple-kernel maximum mean discrepancy is used to reduce the discrepancy and perform a global alignment. The category-level alignment is performed when 2ADA is activated, which due to obtain more comprehensive domain adaptation performance and improve the accuracy of fault classification. The results of fault diagnosis experiments on the Case Western Reserve University (CWRU) bearing dataset and the rotating machinery fault platform dataset demonstrate that, the diagnosis accuracy of the proposed method is improved by up to 15.46% and 5.75% on tasks with high domain shift when compared with convolutional neural network method, which verifies the effectiveness of the method.
A subregion-based survival prediction framework for GBM via multi-sequence MRI space optimization and clustering-based feature bundling and construction
Authors: Chen Hao , Liu Yang , Pan Xiaoying , Yang Qing , Qiang Yongqian , Qi X Sharon 
Published: May 2023

Abstract
Aiming at accurate survival prediction of Glioblastoma (GBM) patients following radiation therapy, we developed a subregion-based survival prediction framework via a novel feature construction method on multi-sequence MRIs. The proposed method consists of two main steps: (1) a feature space optimization algorithm to determine the most appropriate matching relation derived between multi-sequence MRIs and tumor subregions, for using multimodal image data more reasonable; (2) a clustering-based feature bundling and construction algorithm to compress the high-dimensional extracted radiomic features and construct a smaller but effective set of features, for accurate prediction model construction. For each tumor subregion, a total of 680 radiomic features were extracted from one MRI sequence using Pyradiomics. Additional 71 geometric features and clinical information were collected resulting in an extreme high-dimensional feature space of 8231 to train and evaluate the survival prediction at 1 year, and the more challenging overall survival prediction. The framework was developed based on 98 GBM patients from the BraTS 2020 dataset under five-fold cross-validation, and tested on an external cohort of 19 GBM patients randomly selected from the same dataset. Finally, we identified the best matching relationship between each subregion and its corresponding MRI sequence, a subset of 235 features (out of 8231 features) were generated by the proposed feature bundling and construction framework. The subregion-based survival prediction framework achieved AUCs of 0.998 and 0.983 on the training and independent test cohort respectively for 1 year survival prediction, compared to AUCs of 0.940 and 0.923 for survival prediction using the 8231 initial extracted features for training and validation cohorts respectively. Finally, we further constructed an effective stacking structure ensemble regressor to predict the overall survival with the C-index of 0.872. The proposed subregion-based survival prediction framework allow us to better stratified patients towards personalized treatment of GBM.