bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology
Authors: Leung Szi Kay , Bamford Rosemary A. , Jeffries Aaron R. , Castanho Isabel , Chioza Barry , Flaxman Christine S. , Moore Karen , Dempster Emma L. , Harvey Joshua , Brown Jonathan T. , Ahmed Zeshan , O’Neill Paul , Richardson Sarah J. , Hannon Eilis , Mill Jonathan 
Published: August 2024

AbstractIncreasing evidence suggests that alternative splicing plays an important role in Alzheimer’s disease (AD) pathology. We used long-read sequencing in combination with a novel bioinformatics tool (FICLE) to profile transcript diversity in the entorhinal cortex of female transgenic (TG) mice harboring a mutant form of human tau. Our analyses revealed hundreds of novel isoforms and identified differentially expressed transcripts – including specific isoforms of Apoe, App, Cd33, Clu, Fyn and Trem2 – associated with the development of tau pathology in TG mice. Subsequent profiling of the human cortex from AD individuals and controls revealed similar patterns of transcript diversity, including the upregulation of the dominant TREM2 isoform in AD paralleling the increased expression of the homologous transcript in TG mice. Our results highlight the importance of differential transcript usage, even in the absence of gene-level expression alterations, as a mechanism underpinning gene regulation in the development of AD neuropathology.
Holimap: an accurate and efficient method for solving stochastic gene network dynamics
Authors: Jia Chen , Grima Ramon 
Published: August 2024

AbstractGene-gene interactions are crucial to the control of sub-cellular processes but our understanding of their stochastic dynamics is hindered by the lack of simulation methods that can accurately and efficiently predict how the distributions of gene product numbers vary across parameter space. To overcome these difficulties, here we present Holimap (high-order linear-mapping approximation), an approach that approximates the protein or mRNA number distributions of a complex gene regulatory network by the distributions of a much simpler reaction system. We demonstrate Holimap’s computational advantages over conventional methods by applying it to predict the stochastic time-dependent dynamics of various gene networks, including transcriptional networks ranging from simple autoregulatory loops to complex randomly connected networks, post-transcriptional networks, and post-translational networks. Holimap is ideally suited to study how the intricate network of gene-gene interactions results in precise coordination and control of gene expression.
Olfactory sampling volume for pheromone capture by wing fanning of silkworm moth: a simulation-based study
Authors: Nakata Toshiyuki , Terutsuki Daigo , Fukui Chihiro , Uchida Tomoya , Kanzaki Kohei , Koeda Taito , Koizumi Sakito , Murayama Yuta , Kanzaki Ryohei , Liu Hao 
Published: August 2024

AbstractOdours used by insects for foraging and mating are carried by the air. Insects induce airflows around them by flapping their wings, and the distribution of these airflows may strongly influence odour source localisation. The flightless silkworm moth, Bombyx mori, has been a prominent insect model for olfactory research. However, although there have been numerous studies on antenna morphology and its fluid dynamics, neurophysiology, and localisation algorithms, the airflow manipulation of the B. mori by fanning has not been thoroughly investigated. In this study, we performed computational fluid dynamics (CFD) analyses of flapping B. mori to analyse this mechanism in depth. A three-dimensional simulation using reconstructed wing kinematics was used to investigate the effects of B. mori fanning on locomotion and pheromone capture. The fanning of the B. mori was found to generate an aerodynamic force on the scale of its weight through an aerodynamic mechanism similar to that of flying insects. Our simulations further indicate that the B. mori guides particles from its anterior direction within the ~ 60° horizontally by wing fanning. Hence, if it detects pheromones during fanning, the pheromone can be concluded to originate from the direction the head is pointing. The anisotropy in the sampling volume enables the B. mori to orient to the pheromone plume direction. These results provide new insights into insect behaviour and offer design guidelines for robots for odour source localisation.
Pathways and timescales of Southern Ocean hydrothermal iron and manganese transport
Authors: Birchill Antony J. , Baker Chelsey A. , Wyatt Neil J. , Pabortsava Katsiaryna , Venables Hugh J. , Moore C. Mark , Turnbull Isobel , Milne Angela , Ussher Simon J. , Oliver Sophy , Martin Adrian P. 
Published: August 2024

AbstractScarcity of iron and manganese limits the efficiency of the biological carbon pump over large areas of the Southern Ocean. The importance of hydrothermal vents as a source of these micronutrients to the euphotic zone of the Southern Ocean is debated. Here we present full depth profiles of dissolved and total dissolvable trace metals in the remote eastern Pacific sector of the Southern Ocean (55–60° S, 89.1° W), providing evidence of enrichment of iron and manganese at depths of 2000–4000 m. These enhanced micronutrient concentrations were co-located with 3He enrichment, an indicator of hydrothermal fluid originating from ocean ridges. Modelled water trajectories revealed the understudied South East Pacific Rise and the Pacific Antarctic Ridge as likely source regions. Additionally, the trajectories demonstrate pathways for these Southern Ocean hydrothermal ridge-derived trace metals to reach the Southern Ocean surface mixed layer within two decades, potentially supporting a regular supply of micronutrients to fuel Southern Ocean primary production.
The re-emergence of sexually transmissible multidrug resistant Shigella flexneri 3a, England, United Kingdom
Authors: Mason Lewis C. E. , Charles Hannah , Thorley Katie , Chong Charlotte E. , De Silva P. Malaka , Jenkins Claire , Baker Kate S. 
Published: August 2024

AbstractShigellosis is an enteric infection that transmits through the faecal-oral route, which can occur during sex between men who have sex with men (MSM). Between 2009 and 2014, an epidemic of sexually transmissible Shigella flexneri 3a occurred in England that subsequently declined. However, from 2019 to 2021, despite SARS-CoV-2 restrictions, S. flexneri 3a continued to re-emerge. We explored possible drivers of re-emergence by comparing host demography and pathogen genomics. Cases were primarily among 35–64 year old men in London. Genomic analyses of 502 bacterial isolates showed that the majority (58%) of re-emerging MSM strains were a clonal replacement of the original, with reduced antimicrobial resistance, conservation of plasmid col156_1, and two SNPs with 19 predicted effects. The absence of major changes in the pathogen or host demographics suggest that other factors may have driven the re-emergence of S. flexneri 3a and highlight the need for further work in the area.
Inferring enterovirus D68 transmission dynamics from the genomic data of two 2022 North American outbreaks
Authors: Grunnill Martin , Eshaghi Alireza , Damodaran Lambodhar , Nagra Sandeep , Gharouni Ali , Braukmann Thomas , Clark Shawn , Peci Adriana , Isabel Sandra , Banh Philip , Plessis Louis du , Murall Carmen Lia , Colijn Caroline , Mubareka Samira , Hasso Maan , Bahl Justin , Mostafa Heba H. , Gubbay Jonathan B. , Patel Samir N. , Wu Jianhong , Duvvuri Venkata R. 
Published: August 2024

AbstractEnterovirus D68 (EV-D68) has emerged as a significant cause of acute respiratory illness in children globally, notably following its extensive outbreak in North America in 2014. A recent outbreak of EV-D68 was observed in Ontario, Canada, from August to October 2022. Our phylogenetic analysis revealed a notable genetic similarity between the Ontario outbreak and a concurrent outbreak in Maryland, USA. Utilizing Bayesian phylodynamic modeling on whole genome sequences (WGS) from both outbreaks, we determined the median peak time-varying reproduction number (Rt) to be 2.70, 95% HPD (1.76, 4.08) in Ontario and 2.10, 95% HPD (1.41, 3.17) in Maryland. The Rt trends in Ontario closely matched those derived via EpiEstim using reported case numbers. Our study also provides new insights into the median infection duration of EV-D68, estimated at 7.94 days, 95% HPD (4.55, 12.8) in Ontario and 10.8 days, 95% HPD (5.85, 18.6) in Maryland, addressing the gap in the existing literature surrounding EV-D68’s infection period. We observed that the estimated Time since the Most Recent Common Ancestor (TMRCA) and the epidemic’s origin coincided with the easing of COVID-19 related social contact restrictions in both areas. This suggests that the relaxation of non-pharmaceutical interventions, initially implemented to control COVID-19, may have inadvertently facilitated the spread of EV-D68. These findings underscore the effectiveness of phylodynamic methods in public health, demonstrating their broad application from local to global scales and underscoring the critical role of pathogen genomic data in enhancing public health surveillance and outbreak characterization.
Some paradoxes and unresolved aspects of hepatic de novo lipogenesis
Authors: Jones John G. 
Published: August 2024

AbstractHepatic de novo lipogenesis (DNL) is a critical pathway in both liver intermediary metabolism and whole-body nutrient management. In the setting of excessive caloric intake, increased DNL fluxes are implicated in the pathogenesis of metabolic-associated steatotic liver disease (MASLD). As a result, there is intense interest both in the measurement of DNL activity and in gaining a better understanding on how this drives MASLD development. While much progress has been made towards these objectives, a number of intriguing uncertainties and paradoxes remain. This short perspective will focus on some of these aspects, namely a), how DNL contributes to triglyceride overload, b), the timing of DNL pathway activation with nutrient availability, c) the sources of acetyl-CoA for DNL and d), the sources of NADPH reducing equivalents for DNL. The implications of these uncertainties on pharmacological targeting of hepatic DNL activity will also be discussed.
Quantum illumination radars: Target detection
Authors: Wang Jingxin , Wong Kon Max 
Published: August 2024

AbstractThe authors consider a quantum radar which operates on the quantum illumination principle. The authors’ attention is focused on its function of target detection in a noisy environment. The role of the optical parametric amplifier (OPA) in detection is first examined by the authors, and a dual‐OPA design for more flexible combination of optimised gains is proposed, resulting in a detector substantially improved in its performance from the normally used 1‐OPA design. Then, the use of the entanglement information in the covariance matrix (CM) between the returned signal and idler beams for detection is considered, and a technique to extract such information is proposed. By employing some statistical relationships between positive definite matrices, the authors come up with a new target detection method. Numerical experiments confirm the superior detection performance of the CM detectors compared to that of the OPA detectors.
Critical review on resource scheduling in IaaS clouds: Taxonomy, issues, challenges, and future directions
Authors: Madni Syed Hamid Hussain , Faheem Muhammad , Younas Muhammad , Masum Maidul Hasan , Shah Sajid 
Published: August 2024

AbstractIn a cloud computing environment, the primary goal of resource scheduling is to reduce the economic expenditures for cloud users and grow fiscal achievement for cloud providers. In this article, the study of numerous forms of resource scheduling algorithms is presented that has been applied in IaaS clouds. The selected research articles are classified into six categories, according to the nature of the algorithm used. Further, the authors pointed out several issues and challenges with the help of the resource scheduling algorithms, the comparative performance metrics, and the simulation tools used to validate the several algorithms. The enhancement illustrates better performance concerns decreasing the cost and time while improving the competence and utilization of resources for IaaS clouds. These algorithms are executed in numerous simulation tools and real environments similar to CloudSim, SimGrid, MATLAB, and test‐bed environments (practical implementation). This critical review and classification will serve as a foundation for further research in IaaS clouds in the Internet of Things (IoT) environments.
Immuntherapie von Schilddrüsenkarzinomen
Authors: Essler Markus 
Published: August 2024

ZusammenfassungIn den letzten Jahren hat die Immuntherapie mit „checkpoint-inhibitoren“ (CI) wie Pebrolizumab, Ipilimumab und Nivulomab die
Behandlung von metastasierten malignen Melanomen, dem „non-small-cell-lung-cancer“ (NSCLC) und anderen bis dahin unzureichend
therapierbaren Tumorentitäten erheblich verbessert, wenn nicht gar revolutioniert. Zahlreiche
prospektive und randomisierte Studien belegen dies mit hoher Evidenz. Bei der Therapie mancher
Tumorentitäten spielen CI allerdings keine zentrale Rolle. Hierzu gehören die
Schilddrüsenkarzinome. Ein Grund hierfür ist die Effektivität der Behandlung mit primärer
Operation und ablativer Radioiodtherapie. Die Prognose der meisten Schilddrüsenkarzinome ist
durch diese Therapieoptionen mit 5-Jahres-Überlebensraten von mehr als 95% sehr günstig.
Klinische Studien mit CIs sind daher in diesem Bereich wohl wenig relevant, da sie auch bei
positivem Ergebnis das Überleben nur unwesentlich verbessern könnten. Die Prognose der
schlecht differenzierten-, iodnegativen, anaplastischen und medullären Schilddrüsenkarzinome
ist hingegen weit ungünstiger. Es wurden zwar Multikinaseinhibitoren wie Lenvatinib, Sorafenib
und Cabozantinib mit einer Verbesserung des „progressionsfreien Überlebens“ (PFS) zur
Behandlung zugelassen, keines dieser Medikamente hatte jedoch Einfluss auf das Gesamtüberleben
(OS). Zudem sind die MKIs für viele Patienten wenig verträglich und anfällig für die
Entwicklung von Resistenzen. Es ist naheliegend, dass die Immuntherapie am ehesten für
Patientengruppen getestet werden sollte, die nicht (mehr) für eine Operation oder
Radioiodtherapie infrage kommen und für die keine Option einer Therapie mit MKIs mehr besteht.
In diesem Zusammenhang wurden global zahlreiche Studien gestartet, von denen allerdings nur
wenige bereits publiziert wurden. In Zukunft sind jedoch evidenzbasierte immuntherapeutische
Optionen für die Schilddrüsenmalignome zu erwarten. Es ist erfreulich, dass die erste
erfolgreiche klinische Studie zur Immuntherapie des anaplastischen Schilddrüsenkarzinoms
(ATLEB-Studie) von einer deutschen Arbeitsgruppe durchgeführt wurde.
Fontan Completion in Adult Patients with Functionally Univentricular Hearts
Authors: Alpat Safak , Aydin Ahmet , Aykan Hakan , Yilmaz Mustafa 
Published: August 2024

Abstract
Background Although there are considerable amounts of data on the outcomes of pediatric patients who have undergone Fontan repair, little is known about having Fontan completed in adulthood. The study presented the midterm results of our unit's experience with the Fontan completion procedure in adult patients with functionally univentricular hearts.
Methods Between 2014 and 2023, 16 adult patients underwent total cavopulmonary connection (TCPC) completion. Relevant information was retrospectively collected.
Results Sixteen patients with a median age of 19 years (18–21 years) were included. Median arterial oxygen saturation was 76% (70–80.75%), and 62.5% of the patients were New York Heart Association (NYHA) Class III. The median mean pulmonary artery pressure was 14 mm Hg (9.5–14.5 mm Hg). Nine patients (56%) had heterotaxy syndrome, and the median time between the last operation and TCPC was 15.5 years (6.75–17.5 years). The median durations for bypass and cross-clamp were 160 minutes (130–201 minutes) and 120 minutes (84.5–137.5 minutes), consecutively. The postoperative course was straightforward in all. The median arterial oxygen saturation before discharge was 89.5% (85–90%), and 68.75% of the patients were NYHA Class II. Follow-up was complete for all patients with a median of 24 months. There was no early or late mortality or significant morbidity during the study period.
Conclusion We concluded that the intra-extracardiac Fontan technique was feasible for meticulously selected adults undergoing TCPC completion, as evidenced by an acceptable mortality rate and a satisfactory midterm outcome, including improvements in their NYHA functional class. However, the long-term consequences must be monitored.
Reference-frame-independent quantum key distribution with two-way classical communication
Authors: Zhou 周 Chun 淳 , Wang 汪 Hai-Tao 海涛 , Lu 陆 Yi-Fei 宜飞 , Jiang 姜 Xiao-Lei 晓磊 , Zhao 赵 Yan-Mei 燕美 , Zhou 周 Yu 雨 , Wang 汪 Yang 洋 , Li 李 Jia-Ji 家骥 , Zhou 周 Yan-Yang 砚扬 , Wang 汪 Xiang 翔 , Li 李 Hong-Wei 宏伟 , Bao 鲍 Wan-Su 皖苏 
Published: August 2024

Abstract
The data post-processing scheme based on two-way classical communication (TWCC) can improve the tolerable bit error rate and extend the maximal transmission distance when used in a quantum key distribution (QKD) system. In this study, we apply the TWCC method to improve the performance of reference-frame-independent quantum key distribution (RFI-QKD), and analyze the influence of the TWCC method on the performance of decoy-state RFI-QKD in both asymptotic and non-asymptotic cases. Our numerical simulation results show that the TWCC method is able to extend the maximal transmission distance from 175 km to 198 km and improve the tolerable bit error rate from 10.48% to 16.75%. At the same time, the performance of RFI-QKD in terms of the secret key rate and maximum transmission distance are still greatly improved when statistical fluctuations are considered. We conclude that RFI-QKD with the TWCC method is of practical interest.
Mapping aerotropolis planning: A Bibliometric Analysis
Authors: Iswati T Y , Setyono P , Trinugroho I , Purwani O 
Published: August 2024

Abstract
This study intends to reveal a better mapping of knowledge about aerotropolis referring to global literature reviews in 2007-2023. This study uses a bibliometric approach to find out the trend of publication of articles on aerotropolis using vosviewer for visual analysis, covering several categories of research, namely journal analysis, time analysis, subject area analysis, co-authorship analysis, and keyword analysis. The literature survey used the direction of aerotropolis causality taken from Scopus. The level of research contribution globally has been on a downward trend since 2019. This study suggests that researchers can study more on the aerotropolis topic because there has been a decline in article publications in 2019-2022.
The advance of El Niño phase locking from period 1982–2000 to 2001–2022
Authors: Li Panpan , Zheng Fei , Fang Xiagnhui , Yu Jin-Yi 
Published: August 2024

Abstract
The mature phases of El Niño-Southern Oscillation (ENSO) events exhibit a distinct tendency to peak towards the end of the calendar year, a phenomenon commonly referred to as ENSO phase locking. This phase locking is a fundamental property of the ENSO. The observed characteristics of phase locking are intricately tied to the seasonality of ENSO-related Sea Surface Temperature (SST) growth rate. In this study, notable observational evidence is presented: the strength of phase locking of El Niño weakened, and the phase locking advanced to peak at an earlier time during the period 2001 to 2022 compared to 1982 to 2000. The advancement of El Niño Phase Locking is explored by analyzing the contributions of different oceanic feedbacks to the El Niño phenomenon. Specifically, our findings highlight the significant role of nonlinear advective dynamic heating (NDH), which is influenced by the decrease in equatorial pacific surface zonal current anomaly and the equatorial pacific surface zonal gradient of sea SST anomaly. This investigation enhances our understanding of the evolving dynamics of El Niño phase locking, shedding light on the intricate interplay of oceanic feedbacks in influencing this fundamental aspect of ENSO behavior.
Biomedical prospects and challenges of metal dichalcogenides nanomaterials
Authors: Goswami Preeti , Kumar Videsh , Gupta Govind 
Published: August 2024

Abstract
The biomedical applications of metal dichalcogenides (MDCs) nanomaterials (NMs) are an emerging discipline because of their unique attributes like high surface-to-volume ratio, defect sites, superb catalytic performance, and excitation-dependent emission, which is helpful in bio-imaging and cancer cell killing. Due to the compatibility of sensing material with cells and tissues, MoS2, WS2, and SnS2 NMs have piqued the interest of researchers in various biomedical applications like photothermal therapy used in killing cancer cells, drug delivery, photoacoustic tomography (PAT) used in bio-imaging, nucleic acid or gene delivery, tissue engineering, wound healing, etc. Furthermore, these NMs’ functionalization and defect engineering can enhance therapeutic efficacy, biocompatibility, high drug transport efficiency, adjustable drug release, dispersibility, and biodegradability. Among the aforementioned materials, MoS2 NMs have extensively been explored via functionalization and defects engineering to improve biosensing properties. However, further enhancement is still available. Aside from MoS2, the distinct chemo-physical and optical features of WS2 and SnS2 NMs promise considerable potential in biosensing, nanomedicine, and pharmaceuticals. This article mainly focuses on the challenges and future aspects of two-dimensional MDCs NMs in biomedical applications, along with their advancements in various medical diagnosis processes.
Fuzzy decision-making for cost-effective production planning in manufacturing systems
Authors: Vadivel Kuppulakshmi , Chandrasekar Sugapriya , Deivanayagampillai Nagarajan , Jacob Kavikumar 
Published: August 2024

Abstract
This research addresses the critical issue of production planning through innovative methodologies. By introducing a fresh perspective to the classical Economic Production Quantity (EPQ) model, the study incorporates hexagonal fuzzy numbers to accommodate a single-stage system with rework. In today’s manufacturing landscape, the presence of imperfect items significantly impacts industry operations. The proposed model offers a promising solution by effectively reducing system costs. Central to the study is the enhancement of single-machine maintenance and lifespan, ensuring optimal production costs across both regular production periods and revamp periods. Through meticulous analysis, the research aims to minimize the anticipated annual total cost by evaluating reworkable item costs, disposal costs, and penalty lost sale costs within the realms of fuzzy and Neutrosophic arenas. Furthermore, the consideration of service level constraints is integral, with the research demonstrating the convexity of the proposed model under such constraints. To illustrate the efficacy of the approach, a numerical example based on a uniform distribution is presented. Crucially, the study compares results between traditional crisp cases and uncertain fuzzy environments to validate optimal policies. Additionally, the research proposes novel algorithms to define the total cost function of the production process. By leveraging triangular fuzzy numbers, hexagonal fuzzy numbers, and hexagonal interval-valued Neutrosophic numbers, unexpected cost functions are effectively addressed. An illustrative example further elucidates the application of these algorithms. Simulation analysis is employed to validate its accuracy to ensure the robustness and reliability of the proposed approach. Through these comprehensive methodologies and findings, the research contributes significantly to advancing production planning strategies and optimization techniques in modern manufacturing environments.