bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of RNA‐dependent liquid‐liquid phase separation proteins using an artificial intelligence strategy
Authors: Ahmed Zahoor , Shahzadi Kiran , Jin Yanting , Li Rui , Momanyi Biffon Manyura , Zulfiqar Hasan , Ning Lin , Lin Hao 
Published: June 2024

AbstractRNA‐dependent liquid‐liquid phase separation (LLPS) proteins play critical roles in cellular processes such as stress granule formation, DNA repair, RNA metabolism, germ cell development, and protein translation regulation. The abnormal behavior of these proteins is associated with various diseases, particularly neurodegenerative disorders like amyotrophic lateral sclerosis and frontotemporal dementia, making their identification crucial. However, conventional biochemistry‐based methods for identifying these proteins are time‐consuming and costly. Addressing this challenge, our study developed a robust computational model for their identification. We constructed a comprehensive dataset containing 137 RNA‐dependent and 606 non‐RNA‐dependent LLPS protein sequences, which were then encoded using amino acid composition, composition of K‐spaced amino acid pairs, Geary autocorrelation, and conjoined triad methods. Through a combination of correlation analysis, mutual information scoring, and incremental feature selection, we identified an optimal feature subset. This subset was used to train a random forest model, which achieved an accuracy of 90% when tested against an independent dataset. This study demonstrates the potential of computational methods as efficient alternatives for the identification of RNA‐dependent LLPS proteins. To enhance the accessibility of the model, a user‐centric web server has been established and can be accessed via the link: http://rpp.lin‐group.cn.
A complementary metaproteomic approach to interrogate microbiome cultivated from clinical colon biopsies
Authors: Duong Van‐An , Enkhbayar Altai , Bhasin Nobel , Senavirathna Lakmini , Preisner Eva C. , Hoffman Kristi L. , Shukla Richa , Jenq Robert R. , Cheng Kai , Bronner Mary P. , Figeys Daniel , Britton Robert A. , Pan Sheng , Chen Ru 
Published: June 2024

AbstractThe human gut microbiome plays a vital role in preserving individual health and is intricately involved in essential functions. Imbalances or dysbiosis within the microbiome can significantly impact human health and are associated with many diseases. Several metaproteomics platforms are currently available to study microbial proteins within complex microbial communities. In this study, we attempted to develop an integrated pipeline to provide deeper insights into both the taxonomic and functional aspects of the cultivated human gut microbiomes derived from clinical colon biopsies. We combined a rapid peptide search by MSFragger against the Unified Human Gastrointestinal Protein database and the taxonomic and functional analyses with Unipept Desktop and MetaLab‐MAG. Across seven samples, we identified and matched nearly 36,000 unique peptides to approximately 300 species and 11 phyla. Unipept Desktop provided gene ontology, InterPro entries, and enzyme commission number annotations, facilitating the identification of relevant metabolic pathways. MetaLab‐MAG contributed functional annotations through Clusters of Orthologous Genes and Non‐supervised Orthologous Groups categories. These results unveiled functional similarities and differences among the samples. This integrated pipeline holds the potential to provide deeper insights into the taxonomy and functions of the human gut microbiome for interrogating the intricate connections between microbiome balance and diseases.
LGALS3 cfDNA methylation in seminal fluid as a novel prostate cancer biomarker outperforming PSA
Authors: Abramovic Irena , Pezelj Ivan , Dumbovic Leo , Skara Abramovic Lucija , Vodopic Tonci , Bulimbasic Stela , Stimac Goran , Bulic‐Jakus Floriana , Kulis Tomislav , Katusic Bojanac Ana , Tomas Davor , Ulamec Monika , Sincic Nino 
Published: June 2024

AbstractBackgroundThe unmet challenge in prostate cancer (PCa) management is to discriminate it from benign prostate hyperplasia (BPH) due to the lack of specific diagnostic biomarkers. Contemporary research on potential PCa biomarkers is directed toward methylated cell‐free DNA (cfDNA) from liquid biopsies since epigenetic mechanisms are strongly involved in PCa development.MethodsIn the present research, cfDNA methylation of the LGALS3 gene in blood and seminal plasma of PCa and BPH patients was assessed using pyrosequencing, as well as LGALS3 DNA methylation in tissue biopsies. Liquid biopsy samples were taken from patients with clinical suspicion of PCa, who were subsequently divided into two groups, that is, 42 with PCa and 55 with BPH, according to the histopathological analysis.ResultsStatistically significant higher cfDNA methylation of LGALS3 in seminal plasma of BPH than in PCa patients was detected by pyrosequencing. ROC curve analysis showed that it could distinguish PCa and BPH patients with 56.4% sensitivity and 70.4% specificity, while PSA did not differ between the two patient groups. In contrast, there was no statistically significant difference in LGALS3 cfDNA methylation in blood plasma between the two patient groups. In prostate tumor tissue, there was a statistically significant DNA hypermethylation of LGALS3 compared to surrounding nontumor tissue and BPH tissue.ConclusionsThe DNA hypermethylation of the LGALS3 gene represents an event specific to PCa development. In conclusion, LGALS3 cfDNA methylation in seminal fluid discriminates early PCa and BPH presenting itself as a powerful novel PCa biomarker highly outperforming PSA.
Retrospective analysis of the learning curve in perineal robot‐assisted prostate biopsy
Authors: Himmelsbach Ruth , Hackländer Alexander , Weishaar Moritz , Morlock Jonathan , Schoeb Dominik , Jilg Cordula , Gratzke Christian , Grabbert Markus , Sigle August 
Published: June 2024

AbstractIntroductionMagnetic resonance imaging‐transrectal ultrasound (MRI‐TRUS)‐fusion biopsy (FBx) of the prostate allows targeted sampling of suspicious lesions within the prostate, identified by multiparametric MRI. Due to its reliable results and feasibility, perineal MRI/TRUS FBx is now the gold standard for prostate cancer (PC) diagnosis. There are various systems for performing FBx on the market, for example, software‐based, semirobotic, or robot‐assisted platform solutions. Their semiautomated workflow promises high process quality independent of the surgeon's experience. The aim of this study was to analyze how the surgeon's experience influences the cancer detection rate (CDR) via targeted biopsy (TB) and the procedure's duration in robot‐assisted FBx.Patients and MethodsA total of 1716 men who underwent robot‐assisted FBx involving a combination of targeted and systematic sampling between October 2015 and April 2022 were analyzed. We extracted data from the patients' electronic medical records retrospectively. Primary endpoints were the CDR by TB and the procedure's duration. For our analysis, surgeons were divided into three levels of experience: ≤20 procedures (little), 21–100 procedures (intermediate), and >100 procedures (high). Statistical analysis was performed via regression analyses and group comparisons.ResultsMedian age, prostate‐specific antigen level, and prostate volume of the cohort were 67 (±7.7) years, 8.13 (±9.4) ng/mL, and 53 (±34.2) mL, respectively. Median duration of the procedure was 26 (±10.9) min. The duration decreased significantly with the surgeon's increasing experience from 35.1 (little experience) to 28.4 (intermediate experience) to 24.0 min (high experience) (p < 0.001). Using TB only, significant PC (sPC) was diagnosed in 872/1758 (49.6%) of the men. The CDR revealed no significant correlation with the surgeon's experience in either group comparison (p = 0.907) or in regression analysis (p = 0.65).ConclusionWhile the duration of this procedure decreases with increasing experience, the detection rate of sPC in TB is not significantly associated with the experience of the surgeon performing robot‐assisted FBx. This robot‐assisted biopsy system's diagnostic accuracy therefore appears to be independent of experience.
Assessing quality of life in pulmonary arterial hypertension: An independent prognostic marker
Authors: Reeves Glenn Edward Malcolm , Shepherd Julie , Collins Nicholas John , Twaddell Scott , Harjit Singh Rajinder 
Published: June 2024

AbstractPulmonary arterial hypertension (PAH, or PH Group 1), a disease of aberrant pulmonary vascular remodeling, causing progressive right heart failure (RHF) due to elevation of pulmonary vascular resistance (PVR). Patient mortality risk stratification guides choice and intensity of pharmacological intervention and is assessed by haemodynamics (especially PVR) as well as noninvasive tools including WHO functional class (FC), 6‐min walk distance (6MWD), and NT‐proBNP levels. Quality of life (QOL) assessment is acknowledged as a central aspect of patient‐centered care, but our study sought to extend QOL's role as an additional noninvasive risk marker that could further refine risk stratification and hence therapeutic choices within a “treatment to target” paradigm (aiming to achieve low‐risk status). This study found that QOL assessment using the PAH‐SYMPACT© physical activity tool provided enhanced, independent mortality risk information, with one unit rise in this score associated with a 41% increase in likelihood risk (odds ratio 1.41, 95% confidence interval: 1.01–1.98 (p < 0.05)) of falling within intermediate versus low‐group category. We therefore found further support for additional prognostic value being conferred by measurement of QOL as part of routine PAH evaluation, reinforcing its critical role.
Radical prostatectomy using the Hinotori robot‐assisted surgical system: Docking‐free design may contribute to reduction in postoperative pain
Authors: Sasaki Yutaro , Kusuhara Yoshito , Oyama Takuro , Nishiyama Mitsuki , Kobayashi Saki , Daizumoto Kei , Tomida Ryotaro , Ueno Yoshiteru , Fukawa Tomoya , Yamaguchi Kunihisa , Yamamoto Yasuyo , Takahashi Masayuki , Kanayama Hiroomi , Furukawa Junya 
Published: June 2024

AbstractBackgroundThe docking‐free design of the Japanese Hinotori surgical robotic system allows the robotic arm to avoid trocar grasping, thereby minimising excessive abdominal wall stress. The aim of this study was to evaluate the safety and efficacy of robotic‐assisted radical prostatectomy (RARP) using the Hinotori system and to explore the potential contribution of its docking‐free design to postoperative pain reduction.MethodsThis study reviewed the clinical records of 94 patients who underwent RARP: 48 patients in the Hinotori group and 46 in the da Vinci Xi group.ResultsHinotori group had significantly longer operative and console times (p = 0.030 and p = 0.029, respectively). Perioperative complications and oncologic outcomes did not differ between the two groups. On postoperative day 4, the rate of decline from the maximum visual analogue scale score was marginally significant in the Hinotori group (p = 0.062).ConclusionsThe docking‐free design may contribute to reducing postoperative pain.
“Sometimes it looks fake”:Hiyaland contrivances as tools for exploring aspirations for radical social change
Authors: Pitluck Aaron Z. 
Published: June 2024

AbstractOn one hand, Islamic banking and finance is an aspiration to radically transform banks and the financial system to conform with interpretations of Islamic ethics and morals. On the other hand, such high aspirations patently conflict with the existing global, US$3.6 trillion market dominated by profit‐oriented private banks. These aspirations also potentially conflict with the technical details of how financial products are constructed to be “Shariah compliant.” How do Islamic financial practitioners reconcile their vision of the Islamic good society with the products and processes observed at work? One such theological tool and cultural concept is to interpret Islamic financial products as relying onhiyal, a legal stratagem used to provide remedies and alleviate predicaments, to provide an escape from the unlawful to the lawful. This essay summarizes how thinkers in Malaysia are developing the concept ofhiyaleither to critique or to promote Islamic finance. As a contribution to anthropological and postcolonial theorizing, the essay concludes by exploring how the concept ofhiyalcan help us understand contrivances, conspiracies, cons, and stratagems. This theoretical tool kit can assist social scientists in exploring the gap between people's economic behaviors and their aspirations for what a good economy should look like.
Energy Transfer Between i‐Motif DNA Encapsulated Silver Nanoclusters and Fluorescein Amidite Efficiently Visualizes the Redox State of Live Cells
Authors: Yadavalli Hari Chandana , Kim Yeolhoe , Jung Il Lae , Park Sooyeon , Kim Tae‐Hwan , Shin Jin Young , Nagda Riddhi , Thulstrup Peter Waaben , Bjerrum Morten Jannik , Bhang Yong Joo , Lee Phil Hyu , Yang Won Ho , Shah Pratik , Yang Seong Wook 
Published: June 2024

AbstractThe redox regulation, maintaining a balance between oxidation and reduction in living cells, is vital for cellular homeostasis, intricate signaling networks, and appropriate responses to physiological and environmental cues. Here, a novel redox sensor, based on DNA‐encapsulated silver nanoclusters (DNA/AgNCs) and well‐defined chemical fluorophores, effectively illustrating cellular redox states in live cells is introduced. Among various i‐motif DNAs, the photophysical property of poly‐cytosines (C20)‐encapsulated AgNCs that sense reactive oxygen species (ROS) is adopted. However, the sensitivity of C20/AgNCs is insufficient for evaluating ROS levels in live cells. To overcome this drawback, the ROS sensing mechanism of C20/AgNCs through gel electrophoresis, mass spectrometry, and small‐angle X‐ray scattering is primarily defined. Then, by tethering fluorescein amidite (FAM) and Cyanine 5 (Cy5) dyes to each end of the C20/AgNCs sensor, an Energy Transfer (ET) between AgNCs and FAM is achieved, resulting in intensified green fluorescence upon ROS detection. Taken together, the FAM‐C20/AgNCs‐Cy5 redox sensor enables dynamic visualization of intracellular redox states, yielding insights into oxidative stress‐related processes in live cells.
Deep learning or classical machine learning? An empirical study on line‐level software defect prediction
Authors: Zhou Yufei , Liu Xutong , Guo Zhaoqiang , Zhou Yuming , Zhang Corey , Qian Junyan 
Published: June 2024

AbstractBackgroundLine‐level software defect prediction (LL‐SDP) serves as a valuable tool for developers to detect defective lines with minimal human effort. Recently, GLANCE was proposed as a readily implementable baseline for assessing the efficacy of newly proposed LL‐SDP models.ProblemWhile DeepLineDP, a cutting‐edge LL‐SDP model rooted in deep learning, has demonstrated state‐of‐the‐art performance, it has not yet been compared against GLANCE.ObjectiveWe aim to empirically compare DeepLineDP with GLANCE to obtain a comprehensive understanding of how deep learning contributes to solving the LL‐SDP challenge.MethodWe compare GLANCE against DeepLineDP to assess the extent to which DeepLineDP surpasses GLANCE in predicting defective files and identifying problematic lines. In order to obtain a reliable conclusion, we use the same dataset and performance metrics utilized by DeepLineDP.ResultOur experimental findings indicate that DeepLineDP does not outperform GLANCE in LL‐SDP. This suggests that the application of deep learning, in this context, does not yield the anticipated significant improvements.ConclusionThis finding underscores the need for further research in deep learning‐based LL‐SDP to attain the state‐of‐the‐art performance that remains elusive for less advanced techniques.
Self‐Regenerating Photothermal Agents for Tandem Photothermal and Thermodynamic Tumor Therapy
Authors: Li Xiangli , Jiang Yao‐Wen , Tang Wen‐Jing , Yue Shuzhen , Wang Wei , Yao Huiqin , Xu Junpeng , Chen Zixuan , Zhu Jun‐Jie 
Published: June 2024

AbstractSmall molecule‐based photothermal agents (PTAs) hold promising future for photothermal therapy; however, unexpected inactivation exerts negative impacts on their application clinically. Herein, a self‐regenerating PTA strategy is proposed by integrating 2,2′‐azino‐bis(3‐ethylbenzothiazoline‐6‐sulfonic acid) radical cation (ABTS•+) with a thermodynamic agent (TDA) 2,2′‐azobis[2‐(2‐imidazolin‐2‐yl) propane] dihydrochloride (AIPH). Under NIR laser, the photothermal effect of ABTS•+ accelerates the production of alkyl radicals by AIPH, which activates the regeneration of ABTS•+, thus creating a continuous positive feedback loop between photothermal and thermodynamic effects. The combination of ABTS•+ regeneration and alkyl radical production leads to the tandem photothermal and thermodynamic tumor therapy. In vitro and in vivo experiments confirm that the synergistic action of thermal ablation, radical damage, and oxidative stress effectively realizes tumor suppression. This work offers a promising approach to address the unwanted inactivation of PTAs and provides valuable insights for optimizing combination therapy.
Female patients have higher in‐hospital mortality after type A aortic dissection repair: A population study from the national inpatient sample
Authors: Li Renxi , Prastein Deyanira 
Published: June 2024

AbstractBackgroundStanford Type A Aortic Dissection (TAAD) is an emergent condition with high in‐hospital mortality. Gender disparity in TAAD has been a topic of ongoing debate. This study aimed to conduct a population‐based examination of gender disparities in short‐term TAAD outcomes using the National/Nationwide Inpatient Sample (NIS) database, the largest all‐payer database in the US.MethodsPatients undergoing TAAD repair were identified in NIS from the last quarter of 2015–2020. Multivariable logistic regressions were used to compare in‐hospital outcomes between male and female patients, adjusted for demographics, comorbidities, hospital characteristics, primary payer status, and transfer status.ResultsThere were 1454 female and 2828 male patients identified who underwent TAAD repair. Female patients presented with TAAD were at a more advanced mean age (64.03 ± 13.81 vs. 58.28 ± 13.43 years, p < 0.01) and had greater comorbid burden. Compared to male patients, female patients had higher risks of in‐hospital mortality (17.88% vs. 13.68%, adjusted odds ratio (aOR) = 1.266, p = 0.01). In addition, female patients had higher pericardial complications (20.29% vs. 17.22%, aOR = 1.227, p = 0.02), but lower acute kidney injury (AKI; 39.96% vs. 53.47%, aOR = 0.476, p < 0.01) and venous thromboembolism (VTE; 1.38% vs. 2.65%, aOR = 0.517, p = 0.01). Female patients had comparable time from admission to operation and transfer‐in status, longer hospital stays, but fewer total hospital expenses.ConclusionFemale patients were 1.27 times as likely to die in‐hospital after TAAD repair but had less AKI and VTE. While there is no evidence suggesting delay in TAAD repair for female patients, the disparities might stem from other differences such as in care provided or intrinsic physiological variations.
The Power of Many: Securing Organisational Identity Through Distributed Key Management
Authors: Bakhtina Mariia , Kvapil Jan , Švenda Petr , Matulevičius Raimundas 
Published: June 2024

AbstractOrganisational Digital Identity (ODI) often relies on the credentials and keys being controlled by a single person-representative. Moreover, some Information Systems (IS) outsource the key management to a third-party controller. Both the centralisation and outsourcing of the keys threaten data integrity within the IS, allegedly provided by a trusted organisation. Also, outsourcing the control prevents an organisation from cryptographically enforcing custom policies, e.g. time-based, regarding the data originating from it. To address this, we propose a Distributed Key Management System (DKMS) that eliminates the risks associated with centralised control over an organisation’s identity and allows organisation-enforceable policies. The DKMS employs threshold signatures to directly involve multiple organisation’s representatives (e.g. employees, IS components, and external custodians) in data signing on its behalf. The threshold signature creation and, therefore, the custom signing policy inclusion, is fully backwards compatible with commonly used signing schemes, such as RSA or ECDSA. The feasibility of the proposed system is shown in an example data exchange system, X-Road. The implementation confirms the ability of the design to achieve distributed control over the ODI during the operational key phase. Excluding a network delay, the implementation introduces less than 200 ms overhead compared to the built-in signing solution.
General hydrodynamic features of elastoviscoplastic fluid flows through randomised porous media
Authors: Parvar Saeed , Chaparian Emad , Tammisola Outi 
Published: June 2024

Abstract
A numerical study of yield-stress fluids flowing in porous media is presented. The porous media is randomly constructed by non-overlapping mono-dispersed circular obstacles. Two class of rheological models are investigated: elastoviscoplastic fluids (i.e. Saramito model) and viscoplastic fluids (i.e. Bingham model). A wide range of practical Weissenberg and Bingham numbers is studied at three different levels of porosities of the media. The emphasis is on revealing some physical transport mechanisms of yield-stress fluids in porous media when the elastic behaviour of this kind of fluids is incorporated. Thus, computations of elastoviscoplastic fluids are performed and are compared with the viscoplastic fluid flow properties. At a constant Weissenberg number, the pressure drop increases both with the Bingham number and the solid volume fraction of obstacles. However, the effect of elasticity is less trivial. At low Bingham numbers, the pressure drop of an elastoviscoplastic fluid increases compared to a viscoplastic fluid, while at high Bingham numbers we observe drag reduction by elasticity. At the yield limit (i.e. infinitely large Bingham numbers), elasticity of the fluid systematically promotes yielding: elastic stresses help the fluid to overcome the yield stress resistance at smaller pressure gradients. We observe that elastic effects increase with both Weissenberg and Bingham numbers. In both cases, elastic effects finally make the elastoviscoplastic flow unsteady, which consequently can result in chaos and turbulence.

Graphical abstract
From bits to emissions: how FinTech benefits climate resilience?
Authors: Wu Qingyang 
Published: June 2024

AbstractWith financial technology (FinTech) emerging as a pivotal force driving business model innovation and reshaping market competitiveness, its potential contribution to sustainability has garnered widespread attention. Drawing on carbon emissions data at the county level from 2011 to 2017 in China, alongside information on the FinTech companies, this study reveals that FinTech significantly reduces regional carbon emissions intensity. This effect is particularly pronounced in developed regions and metropolitan cities. These findings withstand rigorous scrutiny, including the application of instrumental variable strategies, controlling for financial attributes, and robustness checks altering model specifications. Mechanism analysis indicates that FinTech fosters optimization and upgrading of industrial structure and promotes the development of the ICT industry, while simultaneously driving down the proportion of coal in electricity generation and per unit GDP energy consumption, and increasing the proportion of new energy generation, thereby enhancing overall energy efficiency. The evidence presented herein supports the role of FinTech in enhancing Nationally Determined Contributions and achieving the objectives of the Paris Agreement.