bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved high quality sand fly assemblies enabled by ultra low input long read sequencing
Authors: Huang Michelle , Kingan Sarah , Shoue Douglas , Nguyen Oanh , Froenicke Lutz , Galvin Brendan , Lambert Christine , Khan Ruqayya , Maheshwari Chirag , Weisz David , Maslen Gareth , Davison Helen , Aiden Erez Lieberman , Korlach Jonas , Dudchenko Olga , McDowell Mary Ann , Richards Stephen 
Published: August 2024

AbstractPhlebotomine sand flies are the vectors of leishmaniasis, a neglected tropical disease. High-quality reference genomes are an important tool for understanding the biology and eco-evolutionary dynamics underpinning disease epidemiology. Previous leishmaniasis vector reference sequences were limited by sequencing technologies available at the time and inadequate for high-resolution genomic inquiry. Here, we present updated reference assemblies of two sand flies, Phlebotomus papatasi and Lutzomyia longipalpis. These chromosome-level assemblies were generated using an ultra-low input library protocol, PacBio HiFi long reads, and Hi-C technology. The new P. papatasi reference has a final assembly span of 351.6 Mb and contig and scaffold N50s of 926 kb and 111.8 Mb, respectively. The new Lu. longipalpis reference has a final assembly span of 147.8 Mb and contig and scaffold N50s of 1.09 Mb and 40.6 Mb, respectively. Benchmarking Universal Single-Copy Orthologue (BUSCO) assessments indicated 94.5% and 95.6% complete single copy insecta orthologs for P. papatasi and Lu. longipalpis. These improved assemblies will serve as an invaluable resource for future genomic work on phlebotomine sandflies.
Microconfined High-Pressure Transcritical Channel Flow Database: Laminar, Transitional & Turbulent Regimes
Authors: Abdellatif Ahmed , Monteiro Carlos , Bernades Marc , Jofre Lluís 
Published: August 2024

AbstractThe potential of comprehending and managing microscale flows to enhance energy processes, especially in heat transfer and propulsion applications, remains largely untapped particularly for supercritical fluids, which have gained increased interest over the past years due to the higher power and thermodynamic efficiencies they provide. This work, therefore, presents the first comprehensive, open-source dataset carefully curated and structured for studying microconfined high-pressure transcritical fluid channel flows under various regimes. Particularly, the dataset contains 18 direct numerical simulations of carbon dioxide at different bulk pressures and velocities confined between differentially-heated walls. For all cases, the thermodynamic conditions selected impose the fluid to undergo a transcritical trajectory across the pseudo-boiling region. The data collection comprises an array of physical quantities that enable comprehensive parametric analyses spanning laminar, transitional, and turbulent flow regimes. This data repository is poised to provide access to the detailed study and modeling of the complex flow physics observed in high-pressure transcritical fluids, especially those closely linked to improving microfluidics performance.
A Dataset for Detection and Segmentation of Underwater Marine Debris in Shallow Waters
Authors: Đuraš Antun , Wolf Ben J. , Ilioudi Athina , Palunko Ivana , De Schutter Bart 
Published: August 2024

AbstractRobust object detection is crucial for automating underwater marine debris collection. While supervised deep learning achieves state-of-the-art performance in discriminative tasks, replicating this success on underwater data is challenging. The generalization of these methods suffers due to a lack of available annotated data considering different sources of variation in the unstructured underwater environment and imaging conditions. In this paper, we present the Seaclear Marine Debris Dataset, the first publicly available shallow-water marine debris dataset annotated for instance segmentation/object detection. The dataset contains 8610 images collected using ROVs at multiple locations and with different cameras, annotated for 40 object categories, encompassing not only litter but also observed animals, plants, and robot parts. As part of the technical validation, we provide baseline results for object detection using Faster RCNN and YOLOv6 models. Furthermore, we demonstrate the non-triviality of generalizing the trained model performance to unseen sites and cameras due to domain shift. This underscores the value of the presented dataset in further developing robust models for underwater debris detection.
Evaluating the role of amino acids and isothermal dry particle coating in modulating buccal permeation of large molecule drug vancomycin
Authors: Rajabi Anthony , Idrees Muhammed , Rahman Ayesha , Iyire Affiong , Wyatt David , Koner Jasdip , Mohammed Afzal R. 
Published: August 2024

AbstractThe formulation and delivery of macromolecules through the oral route pose considerable challenges due to factors such as large molecular weight, pH sensitivity, and limited formulation approaches. This challenge is compounded if the drug is poorly permeable, necessitating innovative drug delivery strategies. Vancomycin, a widely prescribed glycopeptide antibiotic, has an oral bioavailability of less than 10%, leading to predominantly intravenous administration and potential patient discomfort. This study explores the potential of the buccal route as a non-invasive, highly vascularised alternative route of administration, offering a rapid onset of action while bypassing the first-pass metabolism. In this study, vancomycin was coated with L-glutamic acid using an isothermal dry particle coater to modulate permeation through the buccal cell line, TR146. Results confirm significant impact of both amino acid concentration and dry particle coating on the rate and extent of drug permeability. With the introduction of L-glutamic acid and utilisation of the isothermal dry particle coater, vancomycin’s permeation profile increased six-fold compared to the control due to the formation of drug ion-pair complex. Imaging studies showed the presence of layered micronized glutamic acid particles on the surface of dry coated vancomycin particles which confirms the role of dry coating and amino acid concentration in modulating drug permeation. Microbiology experiments in Staphylococcus aureus, minimum inhibitory concentration and biofilm disruption studies, provided confirmatory evidence of antimicrobial activity of dry coated glutamic acid-vancomycin ion pair particulate structure. This study demonstrates, for the first-time, buccal delivery of dry coated large molecule drug, vancomycin, through controlled deposition of amino acid using innovative particle coating strategy.
Detailed analysis of Mdivi-1 effects on complex I and respiratory supercomplex assembly
Authors: Marx Nico , Ritter Nadine , Disse Paul , Seebohm Guiscard , Busch Karin B. 
Published: August 2024

AbstractSeveral human diseases, including cancer and neurodegeneration, are associated with excessive mitochondrial fragmentation. In this context, mitochondrial division inhibitor (Mdivi-1) has been tested as a therapeutic to block the fission-related protein dynamin-like protein-1 (Drp1). Recent studies suggest that Mdivi-1 interferes with mitochondrial bioenergetics and complex I function. Here we show that the molecular mechanism of Mdivi-1 is based on inhibition of complex I at the IQ site. This leads to the destabilization of complex I, impairs the assembly of N- and Q-respirasomes, and is associated with increased ROS production and reduced efficiency of ATP generation. Second, the calcium homeostasis of cells is impaired, which for example affects the electrical activity of neurons. Given the results presented here, a potential therapeutic application of Mdivi-1 is challenging because of its potential impact on synaptic activity. Similar to the Complex I inhibitor rotenone, Mdivi-1 may lead to neurodegenerative effects in the long term.
Statistical analysis of the effect of socio-political factors on individual life satisfaction
Authors: Itani Alaa , Hasan Isra , Younes Lolya , Alzaatreh Ayman 
Published: August 2024

AbstractLife satisfaction refers to an individual’s cognitive evaluation of the quality of their life. The aim of the present study is to develop the current understanding of how perceived corruption, attitudes toward migration, perceived security, and strength of national identity influence life satisfaction. Additionally, the study examines how demographic variables of relationship status, social class, sex, religious affiliation, and country impact life satisfaction in the provided cultural context. Ordinal logistic regression analysis, Confirmatory Factor Analysis, and Structural Equation Modeling are used to analyze data from the World Values Survey. Findings from the analyses indicate that perceived corruption, perceived security, and strength of national identity have a significant impact on life satisfaction, whereas migration has an indirect effect on life satisfaction through perceived security. The present research can develop our current understanding of life satisfaction from a socio-political perspective.
Self-interest overrides rank-reversal aversion in resource distribution
Authors: Kim Minyoung , Kim Kun Il , Kim Hackjin 
Published: August 2024

AbstractThe equitable allocation of resources has long been a central concern for humanity, prompting extensive research into various motivations that drive the pursuit of distributive justice. In contrast to one of the most fundamental motives, inequality aversion, a conflicting motive has been proposed: rank-reversal aversion. However, it remains unclear whether this rank-reversal aversion persists in the presence of self-rank. Here we provide evidence of rank-reversal aversion in the first-party context and explore diverse moral strategies for distribution. In a modified version of the redistribution game involving 55 online-recruited participants, we observed rank-reversal aversion only when one’s rank was maintained. When participants’ self-rank was altered, they tended to base their behavior on their new ranks. This behavioral tendency varied among individuals, revealing three distinct moral strategies, all incorporating considerations of rank-reversal. Our findings suggest that rank-reversal aversion can indeed influence one’s distribution behavior, although the extent of its impact may vary among individuals, especially when self-rank is a factor. These insights can be extended to political and economic domains, contributing to a deeper understanding of the underlying mechanisms of distributive justice.
Performance of different CT enhancement quantification methods as predictors of pancreatic cancer recurrence after upfront surgery
Authors: Mohamed Sherif A. , Barlemann Alina , Steinle Verena , Nonnenmacher Tobias , Güttlein Michelle , Hackert Thilo , Loos Martin , Gaida Matthias M. , Kauczor Hans-Ulrich , Klauss Miriam , Mayer Philipp 
Published: August 2024

AbstractThe prognosis of pancreatic cancer (PDAC) after tumor resection remains poor, mostly due to a high but variable risk of recurrence. A promising tool for improved prognostication is the quantification of CT tumor enhancement. For this, various enhancement formulas have been used in previous studies. However, a systematic comparison of these formulas is lacking. In the present study, we applied twenty-three previously published CT enhancement formulas to our cohort of 92 PDAC patients who underwent upfront surgery. We identified seven formulas that could reliably predict tumor recurrence. Using these formulas, weak tumor enhancement was associated with tumor recurrence at one and two years after surgery (p ≤ 0.030). Enhancement was inversely associated with adverse clinicopathological features. Low enhancement values were predictive of a high recurrence risk (Hazard Ratio ≥ 1.659, p ≤ 0.028, Cox regression) and a short time to recurrence (TTR) (p ≤ 0.027, log-rank test). Some formulas were independent predictors of TTR in multivariate models. Strikingly, almost all of the best-performing formulas measure solely tumor tissue, suggesting that normalization to non-tumor structures might be unnecessary. Among the top performers were also the absolute arterial/portal venous tumor attenuation values. These can be easily implemented in clinical practice for better recurrence prediction, thus potentially improving patient management.
Numerical model of the locomotion of oscillating ‘robots’ with frictional anisotropy on differently-structured surfaces
Authors: Filippov Alexander , Gorb Stanislav 
Published: August 2024

AbstractIn engineering materials, surface anisotropy is known in certain textured patterns that appear during the manufacturing process. In biology, there are numerous examples of mechanical systems which combine anisotropic surfaces with the motion, elicited due to some actuation using muscles or stimuli-responsive materials, such as highly ordered cellulose fiber arrays of plant seeds. The systems supplemented by the muscles are rather fast actuators, because of the relatively high speed of muscle contraction, whereas the latter ones are very slow, because they generate actuation depending on the daily changes in the environmental air humidity. If the substrate has ordered surface profile, one can expect certain statistical order of potential trajectories (depending on the order of the spatial distribution of the surface asperities). If not, the expected trajectories can be statistically rather random. The same presumably holds true for the artificial miniature robots that use actuation in combination with frictional anisotropy. In order to prove this hypothesis, we developed numerical model helping us to study abovementioned cases of locomotion in 2D space on an uneven terrain. We show that at extremely long times, these systems tends to behave according to the rules of ballistic diffusion. Physically, it means that their motion tends to be associated with the “channels” of the patterned substrate. Such a motion is more or less the same as it should be in the uniform space. Such asymptotic behavior is specific for the motion in model regular potential and would be impossible on more realistic (and complex) fractal reliefs. However, one can expect that in any kind of the potential with certain symmetry (hexagonal or rhombic, for example), where it is still possible to find the ways, the motion along fixed direction during long (or even almost infinite) time intervals is possible.
Rotation insensitive implantable wireless power transfer system for medical devices using metamaterial-polarization converter
Authors: Shaw Tarakeswar , Mandal Bappaditya , Samanta Gopinath , Voigt Thiemo , Mitra Debasis , Augustine Robin 
Published: August 2024

AbstractThis article introduces an innovative approach for creating a circular polarization (CP) antenna-based rotation-insensitive implantable wireless power transfer (WPT) system for medical devices. The system is constructed to work in the industrial, scientific, and medical (ISM) frequency band of 902–928 MHz. Initially, a flexible, wide-band, and bio-compatible open-ended CP slot antenna is designed within a single-layer human skin tissue model to serve as the receiving (Rx) element. To form the implantable WPT link, a circular patch antenna is also constructed in the free-space to use as a transmitting (Tx) source. Further, a new metamaterial-polarization converter (MTM-PC) structure is developed and incorporated into the proposed system to enhance the power transfer efficiency (PTE). Furthermore, the rotational phenomenon of the Rx implant has been studied to show how the rotation affects the system’s performance. Moreover, a numerical analysis of the specific absorption rate (SAR) is conducted to confirm compliance with safety regulations and prioritize human safety from electromagnetic exposure. Finally, to validate the introduced concept, prototypes of the different elements of the proposed WPT system were fabricated and tested using skin-mimicking gel and porcine tissue. The measured results confirm the feasibility of the introduced approach, exhibiting improved efficiency due to use of the MTM-PC. The amplitude of the transmission coefficient ($$|S_{21}|$$

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S
21

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) has improved by 6.94 dB in the simulation, whereas the enhancement of 7.04 dB and 6.76 dB is obtained from the experimental study due to the integration of MTM-PC. As a result, the PTE of the proposed MTM-PC integrated implantable WPT system is increased significantly compared to the system without MTM-PC.
Translation speed slowdown and poleward migration of western North Pacific tropical cyclones
Authors: Feng Xiangbo 
Published: August 2024

AbstractDetecting and interpreting long-term changes in typhoon translation speed in observations remains challenging, contrasting with increased confidence in the poleward migration of typhoons. Here, I show a significant relationship between the basin-wide translation speed and the latitudinal position of tropical cyclones in the western North Pacific over 1980–2023. First, because tropical cyclones move faster at higher latitudes, the significant poleward migration (80 km/decade) increases the yearly basin-wide translation speed by 5% over the period. This effect reduces the detectability of a slowing trend. Second, the basin-wide translation speed solely contributed by regional translation speed has slowed by 18%, mostly in the late stage of the cyclone lifecycle. The translation speed slowdown and the poleward migration are likely caused by the same climate drivers through the interconnected large-scale atmospheric circulation between the tropics and subtropics. My findings suggest exacerbated tropical cyclone-related risk in the subtropical regions in a changing climate.
Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity
Authors: Puente-Sánchez Fernando , Pascual-García Alberto , Bastolla Ugo , Pedrós-Alió Carlos , Tamames Javier 
Published: August 2024

AbstractThe structure of microbial communities arises from a multitude of factors, including the interactions of microorganisms with each other and with the environment. In this work, we sought to disentangle those drivers by performing a cross-study, cross-biome meta-analysis of microbial occurrence data in more than 5000 samples, applying a novel network clustering algorithm aimed to capture conditional taxa co-occurrences. We then examined the phylogenetic and functional composition of the resulting clusters, and searched for global patterns of assembly both at the community level and in the presence/absence of individual metabolic pathways.Our analysis highlighted the prevalence of functional redundancy in microbial communities, particularly between taxa that co-occur in more than one environment, pointing to a relationship between functional redundancy and environmental adaptation. In spite of this, certain pathways were observed in fewer taxa than expected by chance, suggesting the presence of auxotrophy, and presumably cooperation among community members. This hypothetical cooperation may play a role in genome reduction, since we observed a negative relationship between the size of bacterial genomes and the size of the community they belong to.Overall, our results suggest the microbial community assembly is driven by universal principles that operate consistently across different biomes and taxonomic groups.
The malonyl/acetyl-transferase from murine fatty acid synthase is a promiscuous engineering tool for editing polyketide scaffolds
Authors: Buyachuihan Lynn , Reiners Simon , Zhao Yue , Grininger Martin 
Published: August 2024

AbstractModular polyketide synthases (PKSs) play a vital role in the biosynthesis of complex natural products with pharmaceutically relevant properties. Their modular architecture makes them an attractive target for engineering to produce platform chemicals and drugs. In this study, we demonstrate that the promiscuous malonyl/acetyl-transferase domain (MAT) from murine fatty acid synthase serves as a highly versatile tool for the production of polyketide analogs. We evaluate the relevance of the MAT domain using three modular PKSs; the short trimodular venemycin synthase (VEMS), as well as modules of the PKSs deoxyerythronolide B synthase (DEBS) and pikromycin synthase (PIKS) responsible for the production of the antibiotic precursors erythromycin and pikromycin. To assess the performance of the MAT-swapped PKSs, we analyze the protein quality and run engineered polyketide syntheses in vitro. Our experiments include the chemoenzymatic synthesis of fluorinated macrolactones. Our study showcases MAT-based reprogramming of polyketide biosynthesis as a facile option for the regioselective editing of substituents decorating the polyketide scaffold.
Suzuki–Miyaura coupling of arylthianthrenium tetrafluoroborate salts under acidic conditions
Authors: Zhang Li , Xie Yuanhao , Bai Zibo , Ritter Tobias 
Published: August 2024

AbstractThe palladium-catalysed Suzuki–Miyaura cross-coupling (SMC) is currently the most commonly used reaction to construct carbon–carbon bonds in the pharmaceutical industry. Typical methods require the use of a base, which limits the substrate scope. To mitigate this shortcoming, substantial effort has been made to develop base-tolerant organoboron reagents, efficient catalysts and reaction conditions that do not require external bases. Still, many boronic acids cannot be used or must be independently protected, and many Lewis-basic functional groups poison the catalyst. Here we report a conceptually different SMC reaction that can proceed even under acidic conditions, with a broad substrate scope. Key to this advance is the formation of an acid-stable, palladium-based ion pair between the reaction partners that does not require base for subsequent productive transmetallation. Boronic acids that cannot be used directly in other SMC reactions, such as 2-pyridylboronic acid and boronic acids with strong Lewis bases, can now be used successfully.
A generalised dynamic energy flow model in multi‐energy network
Authors: Cai Qinqin , Yi Zhongkai , Xu Ying , Zhu Yongqiang , Ding Zhaohao , Xi Mengfei , Zhu Xuecheng , Rong Shuang , Sun Yong , Kuang Honghui 
Published: August 2024

AbstractThe analysis and calculation of dynamic energy flow for different energy forms are the basic work for the coordinated dispatching and operation of multi‐energy networks (MENs). A universal mathematical description of energy transfer is proposed based on the concept of intensity quantity and extensive quantity in thermodynamics. This paper derives the unified energy dynamic transfer equations of the electrical energy, incompressible viscous fluid, compressible gas, and heat transfer, that is, a generalised wave equation is established with the distributed parameters that characterise energy dissipation, storage and conductivity. Furthermore, the finite difference method is adopted to calculate the dynamic energy flow that varies with time and space. In the case analysis, the independent solution is firstly performed under four designed cases, and then the MEN composed of heat and gas is jointly solved. The calculation example verifies the feasibility and effectiveness of the proposed method.