bluuebunny/crossref_metadata_2025_split huggingface dataset:
The In-Flight Realtime Trigger and Localization Software of GECAM
Authors: Zhao Xiao-Yun , Xiong Shao-Lin , Wen Xiang-Yang , Li Xin-Qiao , Cai Ce , Xiao Shuo , Luo Qi , Peng Wen-Xi , Guo Dong-Ya , An Zheng-Hua , Gong Ke , Liao Jin-Yuan , Zhang Yan-Qiu , Huang Yue , Li Lu , Wen Xing , Zhang Fei , Duan Jing , Wang Chen-Wei , Shi Dong-Li , Zhang Peng , Yi Qi-Bin , Li Chao-Yang , Xu Yan-Bing , Liang Xiao-Hua , Liu Ya-Qing , Zhang Da-Li , Sun Xi-Lei , Zhang Fan , Chen Gang , Wang Huan-Yu , Yang Sheng , Liu Xiao-Jing , Gao Min , Li Mao-Shun , Wang Jin-Zhou , Zhou Xing , Zhao Yi , Xue Wang-Chen , Zheng Chao , Liu Jia-Cong , Han Xing-Bo , Qi Jin-Ling , Huang Jia , Zhang Ke-Ke , Chen Can , Yang Xiong-Tao , Hou Dong-Jie , Wang Yu-Sa , Qiao Rui , Ma Xiang , Li Xiao-Bo , Wang Ping , Song Xin-Ying , Song Li-Ming , Zheng Shi-Jie , Li Bing , Zhang Hong-Mei , Zhu Yue , Chen Wei , He Jian-Jian , Zhang Zhen , Hou Jin , Wang Hong-Jun , Hao Yan-Chao , Wang Xiang-Yu , Yang Zong-Yuan , Wen Zhi-Long , Chang Zhi , Du Yuan-Yuan , Gao Rui , Lan Xiao-Fei , Li Yan-Guo , Li Gang , Li Xu-Fang , Lu Fang-Jun , Lu Hong , Meng Bin , Shi Feng , Wang Hui , Wang Hui-Zhen , Xu Yu-Peng , Yang Jia-Wei , Yang Xue-Juan , Zhang Shuang-Nan , Zhang Chao-Yue , Zhang Cheng-Mo , Tang Zhi-Cheng , Cheng Cheng 
Published: July 2024

Abstract
Realtime trigger and localization of bursts are the key functions of GECAM, an all-sky gamma-ray monitor launched on 2020 December 10. We developed a multifunctional trigger and localization software operating in the CPU of the GECAM Electronic Box. This onboard software has the following features: high trigger efficiency for real celestial bursts with a suppression of false triggers caused by charged particle bursts and background fluctuation, dedicated localization algorithm optimized for both short and long bursts, and low time latency of the trigger information which is downlinked through the Global Short Message Communication service of the global BeiDou navigation system. This paper provides a detailed description of the design and development of the trigger and localization software system for GECAM. It covers the general design, workflow, the main functions, and the algorithms used in the system. The paper also includes on-ground trigger tests using simulated gamma-ray bursts generated by a dedicated X-ray tube, as well as an overview of the performance for real celestial bursts during its in-orbit operation.
Nanofabrication of nanostructure lattices: from high-quality large patterns to precise hybrid units
Authors: Ma Rui , Zhang Xiaodan , Sutherland Duncan , Bochenkov Vladimir , Deng Shikai 
Published: July 2024

Abstract
Sub-wavelength nanostructure lattices provide versatile platforms for light control and the basis for various novel phenomena and applications in physics, material science, chemistry, biology, and energy. The thriving study of nanostructure lattices is building on the remarkable progress of nanofabrication techniques, especially for the possibility of fabricating larger-area patterns while achieving higher-quality lattices, complex shapes, and hybrid materials units. In this review, we present a comprehensive review of techniques for large-area fabrication of optical nanostructure arrays, encompassing direct writing, self-assembly, controllable deposition, and nanoimprint/print methods. Furthermore, a particular focus is made on the recent improvement of unit accuracy and diversity, leading to integrated and multifunctional structures for devices and applications.
Electrically driven cavity plasmons in Au nanowire over Au film
Authors: Zhang Junhao , Wu Yu , Zhou Wenna , Tang Jibo , Zhang Shunping , Xu Hongxing 
Published: July 2024

Abstract
Light emission via inelastic tunneling electrons is appealing for integrated optoelectronic devices due to its femtosecond time scale that can in principle allow terahertz modulation bandwidth. It has gained renewed interest since 2015 due to the improved quantum efficiency, highly tunable emission wavelength, linewidth, or directionality once the electrodes are designed as a plasmonic nanocavity. However, efficient construction of stable tunnel junctions with desired plasmonic resonances is still technically challenging because of the subnanometer precision required in the electrical and optical design. Here, we demonstrate an easily accessible electrically driven cavity plasmon in metal-insulator-metal (MIM) tunnel junctions, comprised by a Au nanowire (NW) across two separate ultrasmooth Au electrodes. Two layers of self-assembled thiol molecule defines a reliable tunneling barrier. The contribution from the localized cavity plasmons to the total light emission is found to be dominant over that from the propagating surface plasmon polariton in the MIM waveguide, different from the traditional explanations. This work introduces a simplified method for constructing electrically driven cavity plasmons using crystalline metals, which holds promise for applications in in situ chemical or biosensing and the development of flexible light-emitting metasurfaces.
Bidirectional Relationships Between Loneliness, Social Isolation, and Physical Inactivity in the Household, Income and Labour Dynamics in Australia Cohort Study
Authors: Smith Ben J , Lim Michelle H , Manera Karine E , Phongsavan Philayrath , Owen Katherine B 
Published: July 2024

Abstract

Background
Cross-sectional studies show associations between loneliness, social isolation and physical inactivity. Cohort studies are shedding light on these relationships and further longitudinal investigations are needed.

Purpose
This study aimed to assess the longitudinal and bidirectional associations between loneliness, social isolation, and physical inactivity.

Methods
Data were drawn from five annual waves of the Household and Labour Dynamics of Australia Survey (2015–2019), providing a sample of 17,303 persons (mean age = 46.3 years [SD = 18.0], 49.4% female). Relationships between loneliness, social isolation, and physical inactivity were examined using cross-lagged panel modeling, with estimation of simultaneous cross-lagged effects across each wave. Models adjusted for sociodemographic factors, chronic disease status, psychological distress, and mutually for social isolation or loneliness. Moderation of associations by sex was explored.

Results
There were modest lagged effects of physical inactivity on loneliness across the survey waves (odds ratio 1.16 [95% confidence interval 1.04–1.29] to 1.20 [1.07, 1.33]). A lagged effect of physical inactivity upon social isolation was only present across three of the waves (odds ratio 1.20 [1.02–1.41] to 1.23 [1.05–1.42]). While loneliness and social isolation showed lagged effects upon physical inactivity, these did not persist with adjustment for psychological distress.

Conclusions
Longitudinal analysis found that physical inactivity consistently predicted loneliness, but not social isolation. After adjustment for confounding, loneliness and social isolation were not predictive of physical inactivity. While the strength of the associations was modest, further investigation is warranted of the type and dose of physical activity that is most beneficial for reducing loneliness.
Generality and Exception in Islamic Legal Theory: Intent, Language, and the Jurist’s Role
Authors: Farahat Omar 
Published: July 2024

Abstract
Whenever discussions arise about the generality or specificity of law and legal provisions, they occur on at least two different levels. On the external level, there is an expectation that law should be general insofar as similar cases and factual situations are concerned, and specific with regards to different and exceptional cases. This is often invoked as a requirement for what constitutes good law or proper governance. On the internal level, generality refers to the expectation that law must offer coherent rules, principles, or standards of action in some form. General and specific language (al-ʿām wal-khāṣṣ) in Islamic legal theory (uṣūl al-fiqh) enjoyed a noteworthy degree of attention in modern scholarship. This attention largely centers on those concepts’ external potential for driving reform in specific areas of law. This Article, by contrast, focuses on the generality–specificity binary as a tool for ensuring the law’s internal cohesiveness, including its claims to legitimacy and its enforceability. To this end, the Article offers an overview of the examination of general and specific expressions in the thought of two influential twelfth-century C.E. (sixth-centuryA.H.)jurist-theologians of different juristic and theological affiliation: the Shāfiʿī-Ashʿarī Abū Ḥāmid al-Ghazālī (d. 1111C.E./505 A.H.) and the Central Asian Ḥanafī-Māturīdī ʿAlāʾ al-Dīn al-Samarqandī (d. 1145C.E./539A.H.). The Article then goes on to argue that ensuring a coherent relation between intent, language, and norms was a central guiding purpose of these studies. We can see this with particular clarity in the fact that, despite reaching comparable practical positions concerning how norms ought to follow from general language, each jurist attained his conclusion through a different path, reflecting different understandings of the relation of norms to divine intent.
Imagining others
Authors: Spaulding Shannon 
Published: July 2024

Abstract
How good are we at imagining what it is like to be someone else? Clearly we sometimes get it right. Proponents of empathy suggest that it is an important and useful tool in our interactions with other people. But, also clearly, there are many inauspicious instances where we badly misimagine what it is like to be someone else. In this paper, I consider the epistemic utility of empathic imagination. I argue that most views fail to explain the distinctive patterns of success and failure of empathic imagination, and I put forward a view that seems to offer the best explanation of those patterns.
Background selection for camouflage shifts in accordance with color change in an intertidal prawn
Authors: Green Samuel D , Wilson Alastair , Stevens Martin 
Published: July 2024

Abstract
To maximize camouflage across visually heterogeneous habitats, animals have evolved a variety of strategies, including polyphenism, color change, and behavioral background matching. Despite the expected importance of behavioral processes for mediating camouflage, such as selection for matching substrates, behavior has received less attention than color traits themselves, and interactions between color change and behavior are largely unexplored. Here, we investigated behavioral background matching in green and red chameleon prawns (Hippolyte varians) over the course of a color change experiment. Prawns were housed on mismatching green and red seaweeds for 30 days and periodically given a choice test between the same seaweeds in y-choice trials over the experiment. We found that, as prawns change color and improve camouflage (to the perspective of a fish predator), there is a reinforcing shift in behavior. That is, as prawns shift from red to green color, or vice versa, their seaweed color preference follows this. We provide key empirical evidence that plasticity of appearance (color) is accompanied by a plastic shift in behavior (color preference) that reinforces camouflage in a color changing species on its natural substrate. Overall, our research highlights how short-term plasticity of behavior and longer-term color change act in tandem to maintain crypsis over time.
scLEGA: an attention-based deep clustering method with a tendency for low expression of genes on single-cell RNA-seq data
Authors: Liu Zhenze , Liang Yingjian , Wang Guohua , Zhang Tianjiao 
Published: July 2024

Abstract
Single-cell RNA sequencing (scRNA-seq) enables the exploration of biological heterogeneity among different cell types within tissues at a resolution. Inferring cell types within tissues is foundational for downstream research. Most existing methods for cell type inference based on scRNA-seq data primarily utilize highly variable genes (HVGs) with higher expression levels as clustering features, overlooking the contribution of HVGs with lower expression levels. To address this, we have designed a novel cell type inference method for scRNA-seq data, termed scLEGA. scLEGA employs a novel zero-inflated negative binomial (ZINB) loss function that fully considers the contribution of genes with lower expression levels and combines two distinct scRNA-seq clustering strategies through a multi-head attention mechanism. It utilizes a low-expression optimized denoising autoencoder, based on the novel ZINB model, to extract low-dimensional features and handle dropout events, and a GCN-based graph autoencoder (GAE) that leverages neighbor information to guide dimensionality reduction. The iterative fusion of denoising and topological embedding in scLEGA facilitates the acquisition of cluster-friendly cell representations in the hidden embedding, where similar cells are brought closer together. Compared to 12 state-of-the-art cell type inference methods on 15 scRNA-seq datasets, scLEGA demonstrates superior performance in clustering accuracy, scalability, and stability. Our scLEGA model codes are freely available at https://github.com/Masonze/scLEGA-main.
SCCNAInfer: a robust and accurate tool to infer the absolute copy number on scDNA-seq data
Authors: Zhang Liting , Zhou Xin Maizie , Mallory Xian 
Published: July 2024

Abstract

Motivation
Copy number alterations (CNAs) play an important role in disease progression, especially in cancer. Single-cell DNA sequencing (scDNA-seq) facilitates the detection of CNAs of each cell that is sequenced at a shallow and uneven coverage. However, the state-of-the-art CNA detection tools based on scDNA-seq are still subject to genome-wide errors due to the wrong estimation of the ploidy.

Results
We developed SCCNAInfer, a computational tool that utilizes the subclonal signal inside the tumor cells to more accurately infer each cell’s ploidy and CNAs. Given the segmentation result of an existing CNA detection method, SCCNAInfer clusters the cells, infers the ploidy of each subclone, refines the read count by bin clustering, and accurately infers the CNAs for each cell. Both simulated and real datasets show that SCCNAInfer consistently improves upon the state-of-the-art CNA detection tools such as Aneufinder, Ginkgo, SCOPE, and SeCNV.

Availability and implementation
SCCNAInfer is freely available at https://github.com/compbio-mallory/SCCNAInfer.
Decoding molecular features of bovine oocyte fate during antral follicle growth via single-cell multi-omics analysis
Authors: Zhang Qiang , Zhang Jingyao , Chang Gang , Zhao Kun , Yao Yujun , Liu Li , Du Zihuan , Wang Yanping , Guo Xingrong , Zhao Zongsheng , Zeng Weibin , Gao Shuai 
Published: July 2024

Abstract
Antral follicle size is a useful predictive marker of the competency of enclosed oocytes for yielding an embryo following in vitro maturation and fertilization. However, the molecular mechanisms underpinning oocyte developmental potential during bovine antral follicle growth are still unclear. Here, we used a modified single-cell multi-omics approach to analyze the transcriptome, DNA methylome, and chromatin accessibility in parallel for oocytes and cumulus cells collected from bovine antral follicles of different sizes. Transcriptome profiling identified three types of oocytes (small, medium, and large) that underwent different developmental trajectories, with large oocytes exhibiting the largest average follicle size and characteristics resembling metaphase-II oocytes. Differential expression analysis and real-time polymerase chain reaction assay showed that most replication-dependent histone genes were highly expressed in large oocytes. The joint analysis of multi-omics data revealed that the transcription of 20 differentially expressed genes in large oocytes was associated with both DNA methylation and chromatin accessibility. In addition, oocyte–cumulus interaction analysis showed that inflammation, DNA damage, and p53 signaling pathways were active in small oocytes, which had the smallest average follicle sizes. We further confirmed that p53 pathway inhibition in the in vitro maturation experiments using oocytes obtained from small antral follicles could improve the quality of oocytes and increased the blastocyte rate after in vitro fertilization and culture. Our work provides new insights into the intricate orchestration of bovine oocyte fate determination during antral folliculogenesis, which is instrumental for optimizing in vitro maturation techniques to optimize oocyte quality.
Pulling Back the Curtain on the California Gang Database: Evidence of Racial, Ethnic and Gender Disparities Among 222 Law Enforcement Agencies
Authors: Pyrooz David C , Densley James A 
Published: July 2024

Abstract
The California Gang Database (CalGang) is the first, largest and arguably most controversial shared gang database in the United States. This study examined its demographic composition and disparities in 103,840 records input by 222 unique law enforcement agencies between 2017 and 2022; the database was 94 per cent male, 66 per cent Hispanic, 23 per cent Black, 51 per cent 18 to 30 years old and 38 per cent 31–45 years old. About one-quarter of 1 per cent of Californians are listed in CalGang. Age-standardized estimates indicated that males were overrepresented relative to females by a factor of 17 and that Black and Hispanic males were overrepresented relative to White males by factors of 33 and 11, respectively, while Asian males were underrepresented. These demographic disparities generalized across nearly all law enforcement agencies. Gang databases will remain highly controversial owing to significant racial/ethnic disparities, but also concerns about civil liberties, due process, privacy rights and collateral consequences. The generative questions that remain are whether the observed disparities can be explained by legal factors and whether any public safety value can be achieved while protecting individual rights.
Margin clearance greater than 1 mm in nodal-positive pancreatic adenocarcinoma patients: multicentre retrospective analysis
Authors: Ahola Reea P , Zwart Eline S , Kurlinkus Benediktas , Halimi Asif , Yilmaz Bengi S , Belfiori Giulio , Roberts Keith , Pande Rupaly , Al-Saffar Hasan A , Maisonneuve Patrick , Ceyhan Güralp O , Laukkarinen Johanna 
Published: July 2024

Abstract

Background
The introduction of the 1 mm cut-off for resection margin according to the Leeds Pathology Protocol has transformed the concept of surgical radicality. Its impact on nodal-positive resected pancreatic ductal adenocarcinoma patients is unclear. The aim of this study was to analyse the effect of margin clearance on survival among resected, nodal-positive pancreatic ductal adenocarcinoma patients whose specimens were analysed according to the Leeds Pathology Protocol.

Methods
Data were collected retrospectively from multicentre clinical databases. Resected patients with nodal involvement were included. Overall survival and disease-free survival were analysed according to minimum reported margin clearances of 0, 0.5, 1, and 2 mm. The results are reported separately for patients who had not undergone venous resection and for patients for whom data were available regarding the superior mesenteric vein-facing margin or the vein specimen. The eighth edition of TNM classification by the AJCC was used.

Results
The study comprised 290 stage IIB patients and 215 stage III patients without venous resection. The superior mesenteric vein margin analysis comprised 127 stage IIB patients and 198 stage III patients. The different resection margin distances were not associated with overall survival and disease-free survival among patients without venous resection (P &gt; 0.050). Receiving adjuvant therapy was associated with longer overall survival among stage IIB patients (P = 0.034) and stage III patients (P = 0.003) and with longer disease-free survival among stage III patients (P &lt; 0.001).

Conclusions
In this study, a margin clearance greater than 1 mm showed no clear effect on overall survival in pancreatic ductal adenocarcinoma patients with nodal involvement, whereas adjuvant therapy was confirmed to be essential to ensure longer overall survival.
High socioeconomic status is significantly associated with psoriasis: results from a cross-sectional, population-based study of 129,855 patients
Authors: Dagan Or , Schonmann Yochai , Shavit Eran , Cohen Arnon D , Valdman-Grinshpoun Yuliya , Czarnowicki Tali 
Published: July 2024

Abstract

Background
While the contribution of environmental factors including smoking, overweight and stress has been validated, data mining for the association between socioeconomic status (SES) and psoriasis prevalence has yielded contradicting observations.

Objective
To evaluate the association between psoriasis prevalence and SES.

Methods
This was a nationwide population-based cross-sectional retrospective study that included all patients insured by the “Clalit” Health Services (N=4,604,994). Univariable and multivariable logistic regression analyses were conducted to explore the association between psoriasis and SES while controlling for potential sociodemographic and clinical confounders.

Results
The study population included 129,855 patients with psoriasis and 4,475,139 individuals without psoriasis. Higher SES was associated with an increased prevalence of psoriasis; in a fully adjusted model, Clalit members within the highest SES were 1.43-fold more likely to have psoriasis (95% CI, 1.39-1.48; P&lt; 0.001), and those at medium SES were 1.2-fold more likely to have psoriasis, compared to those at the lowest SES group (95% CI, 1.18-1.26; P&lt; 0.001; P for linear trend &lt;0.001).

Conclusions
Positive correlation was found between SES and psoriasis prevalence. Further investigation is warranted to elucidate the factors accounting for this observation.
Revisiting serum storage protocols: assessing the impact of temperature variations on indirect immunofluorescence testing for pemphigus and bullous pemphigoid
Authors: Pinkaew Sumruay , Kulthanan Kanokvalai , Tuchinda Papapit , Chularojanamontri Leena , Pongkittilar Bawonpak , Buranaporn Panyapat , Nuttawong Sasipha , Rujitharanawong Chuda 
Published: July 2024

Abstract

Background
Indirect immunofluorescence (IIF) plays a crucial role in the diagnosis of pemphigus and bullous pemphigoid (BP) by detecting the presence of circulating autoantibodies in the serum of patients. The standard serum transportation method requires delivery to laboratories at 2–8 °C within a day and storage at –20 to –80 °C. However, this protocol poses logistical challenges.

Objectives
To carry out a study assessing how temperature variations affect the accuracy of IIF tests.

Methods
This case–control study analysed 203 serum specimens: 102 from patients with pemphigus and 101 from patients with BP. Specimens were stored at –80 °C (control), 24 °C and 40 °C for 7 days before analysis to investigate variations in IIF titres between test and control conditions.

Results
In pemphigus serum, 95% of specimens at 24 °C and 76% at 40 °C showed no titre difference compared with controls. Similarly, 89% of BP serum specimens at 24 °C and 82% at 40 °C matched the control titres. While 57 specimens across both groups experienced reduced titres, the decrease was primarily marginal (a 1-step reduction in 54 cases, 2-step in 3), with no transition from positive to negative results.

Conclusions
Storing serum at 24–40 °C for up to 7 days before testing only slightly influences IIF outcomes for pemphigus and BP. These findings could prompt a significant revision in the existing strict transport guidelines, ensuring efficient use of resources without sacrificing the accuracy of diagnostic tests.