bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preponderance of generalized chain functions in reconstructed Boolean models of biological networks
Authors: Mitra Suchetana , Sil Priyotosh , Subbaroyan Ajay , Martin Olivier C. , Samal Areejit 
Published: March 2024

AbstractBoolean networks (BNs) have been extensively used to model gene regulatory networks (GRNs). The dynamics of BNs depend on the network architecture and regulatory logic rules (Boolean functions (BFs)) associated with nodes. Nested canalyzing functions (NCFs) have been shown to be enriched among the BFs in the large-scale studies of reconstructed Boolean models. The central question we address here is whether that enrichment is due to certain sub-types of NCFs. We build on one sub-type of NCFs, the chain functions (or chain-0 functions) proposed by Gat-Viks and Shamir. First, we propose two other sub-types of NCFs, namely, the class of chain-1 functions and generalized chain functions, the union of the chain-0 and chain-1 types. Next, we find that the fraction of NCFs that are chain-0 (also holds for chain-1) functions decreases exponentially with the number of inputs. We provide analytical treatment for this and other observations on BFs. Then, by analyzing three different datasets of reconstructed Boolean models we find that generalized chain functions are significantly enriched within the NCFs. Lastly we illustrate that upon imposing the constraints of generalized chain functions on three different GRNs we are able to obtain biologically viable Boolean models.
Oxygen-dependent biofilm dynamics in leaf decay: an in vitro analysis
Authors: Karačić Sabina , Palmer Brianne , Gee Carole T. , Bierbaum Gabriele 
Published: March 2024

AbstractBiofilms are important in the natural process of plant tissue degradation. However, fundamental knowledge of biofilm community structure and succession on decaying leaves under different oxygen conditions is limited. Here, we used 16S rRNA and ITS gene amplicon sequencing to investigate the composition, temporal dynamics, and community assembly processes of bacterial and fungal biofilms on decaying leaves in vitro. Leaves harvested from three plant species were immersed in lake water under aerobic and anaerobic conditions in vitro for three weeks. Biofilm-covered leaf samples were collected weekly and investigated by scanning electron microscopy. The results showed that community composition differed significantly between biofilm samples under aerobic and anaerobic conditions, though not among plant species. Over three weeks, a clear compositional shift of the bacterial and fungal biofilm communities was observed. The alpha diversity of prokaryotes increased over time in aerobic assays and decreased under anaerobic conditions. Oxygen availability and incubation time were found to be primary factors influencing the microbial diversity of biofilms on different decaying plant species in vitro. Null models suggest that stochastic processes governed the assembly of biofilm communities of decaying leaves in vitro in the early stages of biofilm formation and were further shaped by niche-associated factors.
Estimating actual SARS-CoV-2 infections from secondary data
Authors: Rauch Wolfgang , Schenk Hannes , Rauch Nikolaus , Harders Matthias , Oberacher Herbert , Insam Heribert , Markt Rudolf , Kreuzinger Norbert 
Published: March 2024

AbstractEminent in pandemic management is accurate information on infection dynamics to plan for timely installation of control measures and vaccination campaigns. Despite huge efforts in diagnostic testing of individuals, the underestimation of the actual number of SARS-CoV-2 infections remains significant due to the large number of undocumented cases. In this paper we demonstrate and compare three methods to estimate the dynamics of true infections based on secondary data i.e., (a) test positivity, (b) infection fatality and (c) wastewater monitoring. The concept is tested with Austrian data on a national basis for the period of April 2020 to December 2022. Further, we use the results of prevalence studies from the same period to generate (upper and lower bounds of) credible intervals for true infections for four data points. Model parameters are subsequently estimated by applying Approximate Bayesian Computation—rejection sampling and Genetic Algorithms. The method is then validated for the case study Vienna. We find that all three methods yield fairly similar results for estimating the true number of infections, which supports the idea that all three datasets contain similar baseline information. None of them is considered superior, as their advantages and shortcomings depend on the specific case study at hand.
A microbially produced AhR ligand promotes a Tph1-driven tolerogenic program in multiple sclerosis
Authors: Zelante Teresa , Paolicelli Giuseppe , Fallarino Francesca , Gargaro Marco , Vascelli Gianluca , De Zuani Marco , Fric Jan , Laznickova Petra , Kohoutkova Marcela Hortova , Macchiarulo Antonio , Dolciami Daniela , Pieraccini Giuseppe , Gaetani Lorenzo , Scalisi Giulia , Trevisan Caterina , Frossi Barbara , Pucillo Carlo , De Luca Antonella , Nunzi Emilia , Spaccapelo Roberta , Pariano Marilena , Borghi Monica , Boscaro Francesca , Romoli Riccardo , Mancini Andrea , Gentili Lucia , Renga Giorgia , Costantini Claudio , Puccetti Matteo , Giovagnoli Stefano , Ricci Maurizio , Antonini Martina , Calabresi Paolo , Puccetti Paolo , Di Filippo Massimiliano , Romani Luigina 
Published: March 2024

AbstractMultiple sclerosis is a debilitating autoimmune disease, characterized by chronic inflammation of the central nervous system. While the significance of the gut microbiome on multiple sclerosis pathogenesis is established, the underlining mechanisms are unknown. We found that serum levels of the microbial postbiotic tryptophan metabolite indole-3-carboxaldehyde (3-IAld) inversely correlated with disease duration in multiple sclerosis patients. Much like the host-derived tryptophan derivative l-Kynurenine, 3-IAld would bind and activate the Aryl hydrocarbon Receptor (AhR), which, in turn, controls endogenous tryptophan catabolic pathways. As a result, in peripheral lymph nodes, microbial 3-IAld, affected mast-cell tryptophan metabolism, forcing mast cells to produce serotonin via Tph1. We thus propose a protective role for AhR–mast-cell activation driven by the microbiome, whereby natural metabolites or postbiotics will have a physiological role in immune homeostasis and may act as therapeutic targets in autoimmune diseases.
Plasma neutrophil gelatinase-associated lipocalin independently predicts dialysis need and mortality in critical COVID-19
Authors: Engström Jonas , Koozi Hazem , Didriksson Ingrid , Larsson Anders , Friberg Hans , Frigyesi Attila , Spångfors Martin 
Published: March 2024

AbstractNeutrophil gelatinase-associated lipocalin (NGAL) is a novel kidney injury and inflammation biomarker. We investigated whether NGAL could be used to predict continuous renal replacement therapy (CRRT) and mortality in critical coronavirus disease 2019 (COVID-19). This prospective multicenter cohort study included adult COVID-19 patients in six intensive care units (ICUs) in Sweden between May 11, 2020 and May 10, 2021. Blood was sampled at admission, days two and seven in the ICU. The samples were batch analyzed for NGAL, creatinine, and cystatin c after the end of the study period. Initiation of CRRT and 90-day survival were used as dependent variables in regression models. Of 498 included patients, 494 were analyzed regarding CRRT and 399 were analyzed regarding survival. Seventy patients received CRRT and 154 patients did not survive past 90 days. NGAL, in combination with creatinine and cystatin c, predicted the subsequent initiation of CRRT with an area under the curve (AUC) of 0.95. For mortality, NGAL, in combination with age and sex, had an AUC of 0.83. In conclusion, NGAL is a valuable biomarker for predicting subsequent initiation of CRRT and 90-day mortality in critical COVID-19. NGAL should be considered when developing future clinical scoring systems.
Modulation of the northward penetration of Antarctica intermediate waters into the eastern equatorial Indian Ocean under glacial and interglacial conditions
Authors: Le Houedec Sandrine , Tremblin Maxime , Champion Amaury , Samankassou Elias 
Published: March 2024

AbstractThe Indo-Pacific warm pool is the warmest and most dynamic ocean–atmosphere-climate system on Earth and was subject to significant climate changes during the Pleistocene glacial-interglacial transitions. This has been shown to significantly affected the strength of surface waters that redistribute heat from the tropics to the southern part of the Indian Ocean. Here we investigate the response of the oceanic circulation at intermediate depth (1200 m) of the eastern equatorial Indian Ocean (EEIO) with neodymium (Nd) isotopes in the context of the climatic oscillation of the last 500 ka. The most striking feature of our new dataset is the seesaw Nd record that mimics glacial-interglacial cycles. While the interglacial periods are characterized by a higher contribution of the less radiogenic neodymium (~ − 7εNd) Antarctic Intermediate Water (AAIW), the glacial periods are characterized by more radiogenic water mass of Pacific origin (~ − 5εNd). To explain the increase in the εNd signature toward a more radiogenic signature as the Indo-Pacific connection is reduced under the low sea level of the glacial periods, we show that under global cooling, the AAIW advances northward into the tropics, which is a consequence of the general slowdown of the thermohaline circulation. Therefore, oceanic mixing at intermediate depth in the eastern tropical Indian intermediate water is modulated by the production rate of the AAIW in the Southern Ocean. Our study provides new evidence for the role that changes in the deep oceanic conditions play in amplifying externally forced climate changes that ultimately lead to drier/moister atmospheric conditions and weaker/stronger monsoons during glacial/interglacial periods over eastern tropical Indian Ocean.
In situ electrochemically activated V2O3@MXene cathode for a super high-rate and long-life Zn-ion battery
Authors: Duan Yunlong , Geng Zhi , Zhang Daohong , Wang Qiufan 
Published: March 2024

An in situ electrochemically oxidized cathode is fabricated based on a V2O3@MXene cathode for Zn-ion storage, which delivered a high capacity of 450 mA h g−1 at 0.2 A g−1 as well as ultra-high-rate performance and cycling stability.
Cardiotoxic effects of common and emerging drugs: role of cannabinoid receptors
Authors: Bo Yiming , Zhao Xin , Li Liliang 
Published: March 2024

Abstract
Drug-induced cardiotoxicity has become one of the most common and detrimental health concerns, which causes significant loss to public health and drug resources. Cannabinoid receptors (CBRs) have recently achieved great attention for their vital roles in the regulation of heart health and disease, with mounting evidence linking CBRs with the pathogenesis and progression of drug-induced cardiotoxicity. This review aims to summarize fundamental characteristics of two well-documented CBRs (CB1R and CB2R) from aspects of molecular structure, signaling and their functions in cardiovascular physiology and pathophysiology. Moreover, we describe the roles of CB1R and CB2R in the occurrence of cardiotoxicity induced by common drugs such as antipsychotics, anti-cancer drugs, marijuana, and some emerging synthetic cannabinoids. We highlight the ‘yin-yang’ relationship between CB1R and CB2R in drug-induced cardiotoxicity and propose future perspectives for CBR-based translational medicine toward cardiotoxicity curation and clinical monitoring.
Automatic measurement of slug flow processes from in‐line videos
Authors: Qian Yanjun , Hulsizer Joel , Mou Mingyao , Vega Zambrano Consuelo , Smith Ema , Jiang Mo 
Published: March 2024

AbstractSlug flow processes draw much attention in chemical and pharmaceutical manufacturing thanks to their ability to eliminate downtime costs and batch‐to‐batch variation. Using in‐line video can monitor the current process status and improve the stability of the slug flow. However, there are no effective image processing methods aiming at such videos from chemical experiments due to limited training sample size and the variety of experimental settings. The paper proposes a training‐free method to automatically detect and measure the slugs from in‐line videos. Multiple image features are fused to identify the slug shapes under various lighting conditions, a six‐point model is fitted to achieve better volume estimation, and a consistency score is estimated to quantify the detection uncertainty. The proposed algorithm achieves similar results to manual labeling for various types of slug flow processes, improving the accuracy of slug column estimation by a large margin compared to the existing automatic methods. Finally, using it to monitor the slug flow process's stability and the change of the slug volume in an injection point are demonstrated. The method not only shows that handcrafted image features have the capability for detection and segmentation from chemical experiment images but also paves the road for a training‐based algorithm for the task.
CO outflows from young stars in the NGC2023 cluster
Authors: Sandell G. , Mookerjea B. , Güsten R. 
Published: March 2024

Context. Young early-type HAeBe stars are still embedded in the molecular clouds in which they formed. They illuminate reflection nebulae, which shape the surrounding molecular cloud and may trigger star formation. They are therefore ideal places to search for ongoing star formation activity.
Aims. NGC 2023 is illuminated by the Herbig Be star HD 37903. It is the most massive member of a small young cluster with about 30 PMS stars, several of which are Class I objects that still heavily accrete. It might therefore be expected that they might drive molecular outflows. We examined the whole region for outflows.
Methods. We analyzed previously published APEX data to search for and characterize the outflows in the NGC 2023 region. This is the first systematic search for molecular outflows in this region. Since the outflows were mapped in several CO transitions, we can determine their properties quite well.
Results. We have discovered four molecular outflows in the vicinity of NGC 2023, three of which are associated with Class I objects. MIR-63, a bright mid-infrared and submillimeter Class I source, is a binary with a separation of 2″.4 and drives two bipolar outflows orthogonal to each other. The large southeast–northwest outflow excites the Herbig-Haro flow HH 247. MIR-73, a Class I object, which is also a far-infrared source, drives a pole-on outflow. MIR-62 is a Class II object with strong infrared excess and a luminosity of 7 L⊙. It is not detected in the far-infrared. The Class I sources have bolometric luminosities of about 20 L⊙ or lower, that is, they are all low-mass stars. One other far-infrared source, MIR-75, may have powered an outflow in the past because it now illuminates an egg-shaped cavity.
Conclusions. The four outflows are all powered by young stars and are located in the immediate vicinity of NGC 2023. They are at a similar evolutionary stage, which suggests that their formation may have been triggered by the expanding C II region.
Advancements in solar spectral irradiance measurements by the TSIS-1 spectral irradiance monitor and its role for long-term data continuity
Authors: Richard Erik , Coddington Odele , Harber Dave , Chambliss Michael , Penton Steven , Brooks Keira , Charbonneau Luke , Peck Courtney , Béland Stéphane , Pilewskie Peter , Woods Tom 
Published: March 2024

The first implementation of NASA’s Total and Spectral Solar Irradiance Sensor (TSIS-1) launched on December 15th, 2017, and was integrated into the International Space Station (ISS) to measure both the total solar irradiance (TSI) and the solar spectral irradiance (SSI). The direct measurement of the SSI is made by the LASP Spectral Irradiance Monitor (SIM) and provides data essential to interpreting how the Earth system responds to solar spectral variability. Extensive advances in TSIS-1 SIM instrument design and new SI-traceable spectral irradiance calibration techniques have resulted in improved absolute accuracy with uncertainties of less than 0.5% over the continuous 200–2400 nm spectral range. Furthermore, improvements in the long-term spectral stability corrections provide lower trend uncertainties in SSI variability measurements. Here we present the early results of the TSIS-1 SIM measurements covering the first 5 years of operations. This time period includes the descending phase of solar cycle 24, the last solar minimum, and the ascending phase of solar cycle 25. The TSIS-1 SIM SSI results are compared to previous measurements both in the absolute scale of the solar spectrum and the time dependence of the SSI variability. The TSIS-1 SIM SSI spectrum shows lower IR irradiance (up to 6% at 2400 nm) and small visible increases (~0.5%) from some previous reference solar spectra. Finally, initial comparisons are made to current NRLSSI2 and SATIRE-S SSI model results and offer opportunities to validate model details both for short-term (solar rotation) spectral variability and, for the first time, the longer-term (near half solar cycle) spectral variability across the solar spectrum from the UV to the IR.
Fiber end integrated surface plasma lens for circular airy beam shaping
Authors: Xu Jiankang , Wang Jiejun , Yuan Libo , Guan Chunying , Liu Houquan 
Published: March 2024

Abstract
This paper presents a circular Airy beam generator based on a fiber end integrated surface plasma lens. The surface plasma lens consists of a nano-annular slot and an array of series concentric circular grooves etched on the gold film coated on the fiber end. When the fiber light field illuminates the nano-annular slot, surface plasmon polaritons (SPPs) will be excited, then the SPPs propagates along the surface of the gold film, and will finally be decoupled into free space to generate circular Airy beam by the array of concentric circular grooves. The effect of the parameters of the plasma lens on the properties of the output circular Airy beam, such as self-focusing, focal spot size, is studied in detail via FDTD simulations. In addition, we found that the proposed plasma lens has a high tolerance to manufacturing errors. The case that instead of the nano-annular slit with a circular wheat-spike shaped structure is also investigated. In this case, due to the different photon spin response of the circular wheat-spike shaped structure, the device can generate circular Airy beam when the input fiber light field is right-handed circularly polarized (RHCP) light, and subwavelength Bessel-like nondiffracting beam when the input fiber light field is left-handed circularly polarized (LHCP) light. These results provide a highly integrated all-fiber circular Airy beam and subwavelength Bessel-like nondiffracting beam generation scheme, which may be useful in the areas of fiber end structured light beam shaping and fiber-integrated photonic devices.
Recycled dark matter
Authors: Gehrman Thomas C. , Haghi Barmak Shams Es , Sinha Kuver , Xu Tao 
Published: March 2024

Abstract
We outline a new production mechanism for dark matter that we dub “recycling”: dark sector particles are kinematically trapped in the false vacuum during a dark phase transition; the false pockets collapse into primordial black holes (PBHs), which ultimately evaporate before Big Bang Nucleosynthesis (BBN) to reproduce the dark sector particles. The requirement that all PBHs evaporate prior to BBN necessitates high scale phase transitions and hence high scale masses for the dark sector particles in the true vacuum. Our mechanism is therefore particularly suited for the production of ultra heavy dark matter (UHDM) with masses above ∼ 1012 GeV. The correct relic density of UHDM is obtained because of the exponential suppression of the false pocket number density. Recycled UHDM has several novel features: the dark sector today consists of multiple decoupled species that were once in thermal equilibrium and the PBH formation stage has extended mass functions whose shape can be controlled by IR operators coupling the dark and visible sectors.
S-shaped rolling gait designed using curve transformations of a snake robot for climbing on a bifurcated pipe
Authors: Lu Jingwen , Tang Chaoquan , Hu Eryi , Li Zhipeng 
Published: March 2024

Abstract
In this work, we focus on overcoming the challenge of a snake robot climbing on the outside of a bifurcated pipe. Inspired by the climbing postures of biological snakes, we propose an S-shaped rolling gait designed using curve transformations. For this gait, the snake robot’s body presenting an S-shaped curve is wrapped mainly around one side of the pipe, which leaves space for the fork of the pipe. To overcome the difficulty in constructing and clarifying the S-shaped curve, we present a method for establishing the transformation between a plane curve and a 3D curve on a cylindrical surface. Therefore, we can intuitively design the curve in 3D space, while analytically calculating the geometric properties of the curve in simple planar coordinate systems. The effectiveness of the proposed gait is verified by actual experiments. In successful configuration scenarios, the snake robot could stably climb on the pipe and efficiently cross or climb to the bifurcation while maintaining its target shape.
Application of additively manufactured bone scaffold: a systematic review
Authors: Shi Qianyu , Chen Jibing , Chen Junsheng , Liu Yanfeng , Wang Hongze 
Published: March 2024

Abstract
The application of additive manufacturing (AM) technology plays a significant role in various fields, incorporating a wide range of cutting-edge technologies such as aerospace, medical treatment, electronic information, and materials. It is currently widely adopted for medical services, national defense, and industrial manufacturing. In recent years, AM has also been extensively employed to produce bone scaffolds and implant materials. Through AM, products can be manufactured without being constrained by complex internal structures. AM is particularly advantageous in the production of macroscopically irregular and microscopically porous biomimetic bone scaffolds, with short production cycles required. In this paper, AM commonly used to produce bone scaffolds and orthopedic implants is overviewed to analyze the different materials and structures adopted for AM. The applications of antibacterial bone scaffolds and bone scaffolds in biologically relevant animal models are discussed. Also, the influence on the comprehensive performance of product mechanics, mass transfer, and biology is explored. By identifying the reasons for the limited application of existing AM in the biomedical field, the solutions are proposed. This study provides an important reference for the future development of AM in the field of orthopedic healthcare. In conclusion, various AM technologies, the requirements of bone scaffolds and the important role of AM in building bridges between biomaterials, additives, and bone tissue engineering scaffolds are described and highlighted. Nevertheless, more caution should be exercised when designing bone scaffolds and conducting in vivo trials, due to the lack of standardized processes, which prevents the accuracy of results and reduces the reliability of information.