bluuebunny/crossref_metadata_2025 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

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

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

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

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

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

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

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

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

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

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

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

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 > 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 < 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

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< 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< 0.001; P for linear trend <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

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.
[Ti]-YNU-5: a large-pore titanosilicate as an efficient catalyst for selective oxidations
Authors: Zhang Shengxiang , Asanuma Kai , Inagaki Satoshi , Kubota Yoshihiro
Published: July 2024

A novel large-pore titanosilicate with YFI topology, [Ti]-YNU-5, was prepared via post-synthetic isomorphous substitution of Ti for Al in the YFI framework. It exhibited the enhanced catalytic performances in the liquid-phase epoxidation of bulky alkenes and the oxidation of phenol with hydrogen peroxide. Hydrophobicity was found to be an important factor.
Electrochemical synthesis of heterocyclic compounds via carbon–heteroatom bond formation: direct and indirect electrolysis
Authors: Okumura Yasuyuki , Sato Eisuke , Mitsudo Koichi , Suga Seiji
Published: July 2024

Electrochemical organic synthesis has attracted attention as an environmentally friendly method for constructing heterocyclic compounds via carbon–heteroatom bond formation. Herein, we describe the representative examples of electrochemical reactions to produce heterocycles and discuss them according to whether they involve direct or indirect electrolysis.
Geopolitical Kingmakers: South Korea and the Philippines as Linchpins amid the China–US Competition
Authors: Cook Richard J , Ohle Maximilian , Han Zhaoying
Published: July 2024

South Korea and the Philippines hold pivotal geopolitical positions amidst escalating tensions between the USA and China. Both Seoul and Manila find themselves ensnared in the expanding rivalry between these great powers, subjecting them to numerous strategic challenges amid the prevailing regional status quo of instability. Despite their efforts to maintain a delicate balance, often characterized as hedging behavior, the space available for such maneuvering is diminishing, compelling them toward perilous geopolitical alignments. Therefore, this paper seeks to address the following questions: How does the shrinking space to hedge influence the alignment strategies of South Korea and the Philippines? How do their alignment choices impact the geopolitical dynamics of the China–US strategic competition? It argues that as this space contracts, they possess the capability to significantly influence the regional balance of power through their alignment, which we frame as the kingmaker’s role and the power of the weak paradox. Seoul, navigating the complex dynamics of the Korean Peninsula, must carefully weigh its commitments to both Washington and Beijing, particularly in light of ongoing developments with North Korea. Meanwhile, Manila, in the aftermath of the Duterte administration’s alignment oscillations, has sought to establish a clearer strategic direction largely influenced by tensions in the South China Sea. Both are now increasingly tacking hard toward Washington for security assurances and have acknowledged economic security anxieties concerning their links with Beijing. Furthermore, they are placing greater emphasis on upholding the rules-based international order amid growing global uncertainties.
Tensions and duality in developing a circular fashion economy in Kenya
Authors: England Lauren , Ikpe Eka , Comunian Roberta
Published: July 2024

This paper critically considers the circular economy in the Kenyan fashion industry context, addressing structural and geographical hierarchies and inequalities in the conceptualisation of the circular economy and its associated practices in fashion. From the perspective of fashion designers, it highlights specific geopolitical and geo-economic tensions between local cultural foundations of ‘circular’ fashion and the impact of global market forces. Focusing on dynamics relating to second-hand clothing imports and Export Processing Zones (EPZs) for garment manufacturing, we present findings from qualitative research with Kenyan fashion designers (2019–2023) demonstrating how they both inhibit circular economy development in fashion and provide opportunities for innovations through creative adaptation practices.
Time and place affect the acoustic structure of frog advertisement calls
Authors: James Logan S , Ryan Michael J
Published: July 2024

Acoustic communication signals are important for species recognition and mate attraction across numerous taxa. For instance, most of the thousands of species of frogs have a species-specific advertisement call that females use to localize and discriminate among potential mates. Thus, the acoustic structure of the advertisement call is critical for reproductive success. The acoustic structure of calls will generally diverge over evolutionary time and can be influenced by the calls of sympatric species. While many studies have shown the influence of geography on contemporary call variation in populations of frogs, no study has compared the acoustic structure of frog calls across many species to ask whether we can detect an influence of divergence time and overall geographic overlap on the differences in acoustic structure of species-typical calls that we observe now. To this end, we compared acoustic features of the calls of 225 species of frogs within 4 families. Furthermore, we used a behavioral assay from 1 species of frog to determine which acoustic features to prioritize in our large-scale analyses. We found evidence that both phylogeny (time) and geography (place) relate to advertisement call acoustics albeit with large variation in these relationships across the 4 families in the analysis. Overall, these results suggest that, despite the many ecological and evolutionary forces that influence call structure, the broad forces of time and place can shape aspects of advertisement call acoustics.
Improving biomedical entity linking for complex entity mentions with LLM-based text simplification
Authors: Borchert Florian , Llorca Ignacio , Schapranow Matthieu-P
Published: July 2024

Large amounts of important medical information are captured in free-text documents in biomedical research and within healthcare systems, which can be made accessible through natural language processing (NLP). A key component in most biomedical NLP pipelines is entity linking, i.e. grounding textual mentions of named entities to a reference of medical concepts, usually derived from a terminology system, such as the Systematized Nomenclature of Medicine Clinical Terms. However, complex entity mentions, spanning multiple tokens, are notoriously hard to normalize due to the difficulty of finding appropriate candidate concepts. In this work, we propose an approach to preprocess such mentions for candidate generation, building upon recent advances in text simplification with generative large language models. We evaluate the feasibility of our method in the context of the entity linking track of the BioCreative VIII SympTEMIST shared task. We find that instructing the latest Generative Pre-trained Transformer model with a few-shot prompt for text simplification results in mention spans that are easier to normalize. Thus, we can improve recall during candidate generation by 2.9 percentage points compared to our baseline system, which achieved the best score in the original shared task evaluation. Furthermore, we show that this improvement in recall can be fully translated into top-1 accuracy through careful initialization of a subsequent reranking model. Our best system achieves an accuracy of 63.6% on the SympTEMIST test set. The proposed approach has been integrated into the open-source xMEN toolkit, which is available online via https://github.com/hpi-dhc/xmen.
Can temporomandibular joint osteoarthritis be diagnosed on MRI proton density-weighted images with diagnostic support from the latest deep learning classification models?
Authors: Nozawa Michihito , Fukuda Motoki , Kotaki Shinya , Araragi Marino , Akiyama Hironori , Ariji Yoshiko
Published: July 2024

Objectives

This study aimed to clarify the performance of MRI-based deep learning classification models in diagnosing temporomandibular joint osteoarthritis (TMJ-OA) and to compare the developed diagnostic assistance with human observers.

Methods

The subjects were 118 patients who underwent MRI for examination of TMJ disorders. One hundred condyles with TMJ-OA and 100 condyles without TMJ-OA were enrolled. Deep learning was performed with 4 networks (ResNet18, EfficientNet b4, Inception v3, and GoogLeNet) using 5-fold cross validation. Receiver operating characteristics (ROC) curves were drawn for each model and diagnostic metrics were determined. The performances of the 4 network models were compared using Kruskal-Wallis tests and post hoc Scheffe tests, and ROCs between the best model and human were compared using chi-square tests, with P < .05 considered significant.

Results

ResNet18 had areas under the curves (AUCs) of 0.91-0.93 and accuracy of 0.85-0.88, which were the highest among the 4 networks. There were significant differences in AUC and accuracy between ResNet and GoogLeNet (P = .0264 and.0418, respectively). The kappa values of the models were large, 0.95 for ResNet and 0.93 for EfficientNet. The experts achieved similar AUC and accuracy values to the ResNet metrics, 0.94 and 0.85, and 0.84 and 0.84, respectively, but with a lower kappa of 0.67. Those of the dental residents showed lower values. There were significant differences in AUCs between ResNet and residents (P < .0001) and between experts and residents (P < .0001).

Conclusions

Using a deep learning model, high performance was confirmed for MRI diagnosis of TMJ-OA.
Close relationship with the glandular capsule: a highly sensitive diagnostic indicator of major salivary gland metastatic malignancies in ultrasound
Authors: Su Huan-Zhong , Lin Yan-Ting , Huang Shu-Jing , Su Yu-Qing , Liu Qi-Xia , Bai Dong-Yu , Hong Long-Cheng , Zhang Xiao-Dong , Su Yi-Ming
Published: July 2024

Objectives

To investigate the ultrasound (US) characteristics of metastatic malignancies (MM) in the major salivary glands and to assess the diagnostic value of the close relationship with the glandular capsule in identifying MM.

Methods

From January 2016 and April 2022, 122 patients with major salivary gland malignancies, including 20 patients with MM and 102 patients with primary malignancies (PM) confirmed by histopathological examination, were enrolled in this study. Their clinicopathologic and US data were recorded and analysed. The diagnostic performance of the close relationship with the glandular capsule for differentiating MM from PM was analysed.

Results

The mean age of MM were older than that of PM (59.50 ± 14.57 vs. 49.96 ± 15.73, P = .013). Compared with PM patients, MM were associated with a higher prevalence of local pain symptoms (P = .007) and abnormal facial nerve function (P < .001). MM were also more frequently characterized by unclear borders, rough margins, irregular shapes, heterogeneous internal echos, absence of cystic areas, presence of calcifications, close relationship with the glandular capsule, and US-reported positive cervical lymph nodes (all P < .05). The close relationship with the glandular capsule showed to be a good indicator in distinguishing between MM and PM, with an area under the receiver operating characteristic curve of 0.863, a sensitivity of 100%, a specificity of 72.5%, and an accuracy of 92.2%. Positive and negative predictive were calculated at 41.7% and 100%, respectively.

Conclusions

The US finding of a close relationship with the glandular capsule is a highly sensitive diagnostic indicator for MM. Following this finding, US-guided needle biopsy should be recommended to further confirm the diagnosis.
Late dysfunction of a mechanical aortic valve after long-term low molecular weight heparin therapy: a case report
Authors: Mon Aye , Shanmuganathan Selvaraj , Uddin Akhlaque
Published: July 2024

Background

To date, vitamin K anticoagulants are the only recommended long-term therapy for mechanical heart valves. Bleeding episodes, thromboembolic events, and international normalized ratio monitoring are difficult and prevalent complications for these patients. This report reflects the late mechanical aortic valve dysfunction after long-term low molecular weight heparin therapy.

Case summary

A 66-year-old male patient underwent mechanical aortic valve replacement in 2007. He was administered therapeutic doses of enoxaparin for nearly 12 years due to warfarin-related bleeding complications and labile international normalized ratios. However, he experienced multiple cardiovascular and cerebrovascular thromboembolic events, including an anterolateral ST-elevation myocardial infarction with left anterior descending artery thrombus, treated with thrombus aspiration and stenting. The patient was eventually admitted with symptoms and signs of acute heart failure, and echocardiography, fluoroscopy, and a cardiac computed tomography detected mechanical aortic valve prosthesis dysfunction, with an immobile leaflet and pannus. The patient demonstrated no improvement despite switching to unfractionated heparin, and he ultimately underwent redo aortic bioprosthetic valve surgery with a favourable outcome.

Discussion

Low molecular weight heparin is prescribed for patients with aortic mechanical valves who are intolerant to vitamin K antagonists or as bridging in certain situations. Anti-Xa factor monitoring should be considered for long-term prescriptions.
Stroke outcomes in patients with new onset perioperative atrial fibrillation complicating major abdominal surgery compared with patients with new onset non-perioperative atrial fibrillation
Authors: Tas Amine , Fosbøl Emil Loldrup , Vester-Andersen Morten , Burcharth Jakob , Butt Jawad Haider , Køber Lars , Gundlund Anna
Published: July 2024

Background

Major emergency abdominal surgery is associated with postoperative complications and high mortality. Long-term outcomes in patients with perioperative atrial fibrillation (POAF) have recently received increased attention, especially POAF in non-thoracic surgery.

Purpose

This study aimed to compare long-term AF related hospitalization and stroke in patients with POAF in relation to major emergency abdominal surgery and in patients with non-perioperative AF.

Methods and results

We crosslinked data from Danish nationwide registries and identified all patients who underwent major emergency abdominal surgery (2000–2018) and were diagnosed with POAF, and patients who developed AF in a non-perioperative setting. Patients with POAF were matched in a 1:5 ratio on age, sex, year of AF diagnosis, and oral anticoagulation (OAC) status at the beginning of follow-up with patients with non-perioperative AF. From discharge, we examined adjusted hazard ratios (HRs) of stroke using multivariable Cox regression analysis. The study population comprised 1041 (out of 42 021 who underwent major emergency abdominal surgery) patients with POAF and 5205 patients with non-perioperative AF. The median age was 78 years [interquartile range: 71–84] for those initiated on OAC therapy and 78 years [interquartile range: 71–85] for those not initiated on OAC therapy. During the first year of follow up, POAF was associated with similar rates of stroke as non-perioperative AF {patients initiated on OAC: HR 0.96 [95% confidence interval (CI) 0.52–1.77] and patients not initiated on OAC: HR 0.69 (95% CI 0.41–1.15)}.

Conclusion

POAF in relation to major emergency abdominal surgery was associated with similar rates of stroke as non-perioperative AF. These results suggest that POAF not only carry an acute burden but also a long-term burden in patients undergoing major emergency abdominal surgery.
Endogenous Cushing's syndrome and cancer risk
Authors: Rudman Yaron , Fleseriu Maria , Dery Laura , Masri-Iraqi Hiba , Sasson Liat , Shochat Tzipora , Kushnir Shiri , Shimon Ilan , Akirov Amit
Published: July 2024

Objective

Cancer incidence in patients with endogenous Cushing's syndrome (CS) has never been established. Here, we aimed to assess the cancer risk in patients with CS as compared with individually matched controls.

Design

A nationwide retrospective matched cohort study of patients with endogenous CS diagnosed between 2000 and 2023 using the database of Clalit Health Services in Israel.

Methods

Patients with adrenal carcinoma or ectopic CS were excluded. Patients with CS were matched in a 1:5 ratio, with controls individually matched for age, sex, socioeconomic status, and body mass index. The primary outcome was defined as the first diagnosis of any malignancy following a CS diagnosis. Risk of malignancy was calculated using the Cox proportional hazard model, with death as a competing event.

Results

A total of 609 patients with CS and 3018 controls were included [mean age at diagnosis, 48.0 ± 17.2 years; 2371 (65.4%) women]. The median follow-up was 14.7 years (IQR, 9.9–20.2 years). Patients with CS had an increased cancer risk, with a hazard ratio (HR) of 1.78 (95% CI 1.44–2.20) compared with their matched controls. The risk of malignancy was elevated in patients with Cushing's disease (251 cases and 1246 controls; HR 1.65, 95% CI 1.15–2.36) and in patients with adrenal CS (200 cases and 991 controls; HR 2.36, 95% CI 1.70–3.29). The increased cancer risk in patients with CS persists after exclusion of thyroid malignancies.

Conclusion

Endogenous CS is associated with increased malignancy risk. These findings underscore the need for further research to establish recommendations for cancer screening in this population.
Birc5 and Nudc are screened as candidate reference genes for RT-qPCR studies in mouse cementoblast mineralization using time-series RNA-seq data
Authors: Sun Qiao , Li Biao , Li Yicun , Cao Zhengguo , He Hong
Published: July 2024

Background

The robustness and credibility of RT-qPCR results are critically dependent on the selection of suitable reference genes. However, the mineralization of the extracellular matrix can alter the intracellular tension and energy metabolism within cells, potentially impacting the expression of traditional reference genes, namely Actb and Gapdh.

Objective

To methodically identify appropriate reference genes for research focused on mouse cementoblast mineralization.

Materials and methods

Time-series transcriptomic data of mouse cementoblast mineralization were used. To ensure expression stability and medium to high expression levels, three specific criteria were applied to select potential reference genes. The expression stability of these genes was ranked based on the DI index (1/coefficient of variation) to identify the top six potential reference genes. RT-qPCR validation was performed on these top six candidates, comparing their performance against six previously used reference genes (Rpl22, Ppib, Gusb, Rplp0, Actb, and Gapdh). Cq values of these 12 genes were analyzed by RefFinder to get a stability ranking.

Results

A total of 4418 (12.27%) genes met the selection criteria. Among them, Rab5if, Chmp4b, Birc5, Pea15a, Nudc, Supt4a were identified as candidate reference genes. RefFinder analyses revealed that two candidates (Birc5 and Nudc) exhibited superior performance compared to previously used reference genes.

Limitations

RefFinder’s stability ranking does not consider the influence of primer efficiency.

Conclusions and implications

We propose Birc5 and Nudc as candidate reference genes for RT-qPCR studies investigating mouse cementoblast mineralization and cementum repair.
Chromosome-scale genome assembly and annotation of the tetraploid potato cultivar Diacol Capiro adapted to the Andean region
Authors: Reyes-Herrera Paula H , Delgadillo-Duran Diego A , Flores-Gonzalez Mirella , Mueller Lukas A , Cristancho Marco A , Barrero Luz Stella
Published: July 2024

Potato (Solanum tuberosum) is an essential crop for food security and is ranked as the third most important crop worldwide for human consumption. The Diacol Capiro cultivar holds the dominant position in Colombian cultivation, primarily catering to the food processing industry. This highly heterozygous, autotetraploid cultivar belongs to the Andigenum group and it stands out for its adaptation to a wide variety of environments spanning altitudes from 1,800 to 3,200 meters above sea level. Here, a chromosome-scale assembly, referred to as DC, is presented for this cultivar. The assembly was generated by combining circular consensus sequencing with proximity ligation Hi-C for the scaffolding and represents 2.369 Gb with 48 pseudochromosomes covering 2,091 Gb and an anchor rate of 88.26%. The reference genome metrics, including an N50 of 50.5 Mb, a BUSCO (Benchmarking Universal Single-Copy Orthologue) score of 99.38%, and an Long Terminal Repeat Assembly Index score of 13.53, collectively signal the achieved high assembly quality. A comprehensive annotation yielded a total of 154,114 genes, and the associated BUSCO score of 95.78% for the annotated sequences attests to their completeness. The number of predicted NLR (Nucleotide-Binding and Leucine-Rich-Repeat genes) was 2107 with a large representation of NBARC (for nucleotide binding domain shared by Apaf-1, certain R gene products, and CED-4) containing domains (99.85%). Further comparative analysis of the proposed annotation-based assembly with high-quality known potato genomes, showed a similar genome metrics with differences in total gene numbers related to the ploidy status. The genome assembly and annotation of DC presented in this study represent a valuable asset for comprehending potato genetics. This resource aids in targeted breeding initiatives and contributes to the creation of enhanced, resilient, and more productive potato varieties, particularly beneficial for countries in Latin America.
Genomic and Transcriptomic Insights into the Evolution of C4 Photosynthesis in Grasses
Authors: Lyu Haomin , Yim Won Cheol , Yu Qingyi
Published: July 2024

C4 photosynthesis has independently evolved over 62 times within 19 angiosperm families. The recurrent evolution of C4 photosynthesis appears to contradict the complex anatomical and biochemical modifications required for the transition from C3 to C4 photosynthesis. In this study, we conducted an integrated analysis of genomics and transcriptomics to elucidate the molecular underpinnings of convergent C4 evolution in the grass family. Our genome-wide exploration of C4-related gene families suggests that the expansion of these gene families may have played an important role in facilitating C4 evolution in the grass family. A phylogenomic synteny network analysis uncovered the emergence of C4 genes in various C4 grass lineages from a common ancestral gene pool. Moreover, through a comparison between non-C4 and C4  PEPCs, we pinpointed 14 amino acid sites exhibiting parallel adaptations. These adaptations, occurring post the BEP–PACMAD divergence, shed light on why all C4 origins in grasses are confined to the PACMAD clade. Furthermore, our study revealed that the ancestor of Chloridoideae grasses possessed a more favorable molecular preadaptation for C4 functions compared to the ancestor of Panicoideae grasses. This molecular preadaptation potentially explains why C4 photosynthesis evolved earlier in Chloridoideae than in Panicoideae and why the C3-to-C4 transition occurred once in Chloridoideae but multiple times in Panicoideae. Additionally, we found that C4 genes share similar cis-elements across independent C4 lineages. Notably, NAD-ME subtype grasses may have retained the ancestral regulatory machinery of the C4  NADP-ME gene, while NADP-ME subtype grasses might have undergone unique cis-element modifications.