bluuebunny/crossref_metadata_2025_split huggingface dataset:
A minimal physiologically based pharmacokinetic model to study the combined effect of antibody size, charge, and binding affinity to FcRn/antigen on antibody pharmacokinetics
Authors: Patidar Krutika , Pillai Nikhil , Dhakal Saroj , Avery Lindsay B. , Mavroudis Panteleimon D. 
Published: February 2024

AbstractProtein therapeutics have revolutionized the treatment of a wide range of diseases. While they have distinct physicochemical characteristics that influence their absorption, distribution, metabolism, and excretion (ADME) properties, the relationship between the physicochemical properties and PK is still largely unknown. In this work we present a minimal physiologically-based pharmacokinetic (mPBPK) model that incorporates a multivariate quantitative relation between a therapeutic’s physicochemical parameters and its corresponding ADME properties. The model’s compound-specific input includes molecular weight, molecular size (Stoke’s radius), molecular charge, binding affinity to FcRn, and specific antigen affinity. Through derived and fitted empirical relationships, the model demonstrates the effect of these compound-specific properties on antibody disposition in both plasma and peripheral tissues using observed PK data in mice and humans. The mPBPK model applies the two-pore hypothesis to predict size-based clearance and exposure of full-length antibodies (150 kDa) and antibody fragments (50–100 kDa) within a onefold error. We quantitatively relate antibody charge and PK parameters like uptake rate, non-specific binding affinity, and volume of distribution to capture the relatively faster clearance of positively charged mAb as compared to negatively charged mAb. The model predicts the terminal plasma clearance of slightly positively and negatively charged antibody in humans within a onefold error. The mPBPK model presented in this work can be used to predict the target-mediated disposition of a drug when compound-specific and target-specific properties are known. To our knowledge, a combined effect of antibody weight, size, charge, FcRn, and antigen has not been incorporated and studied in a single mPBPK model previously. By conclusively incorporating and relating a multitude of protein’s physicochemical properties to observed PK, our mPBPK model aims to contribute as a platform approach in the early stages of drug development where many of these properties can be optimized to improve a molecule’s PK and ultimately its efficacy.
Forest fire, thinning, and flood in wildland-urban interface: UAV and lidar-based estimate of natural disaster impacts
Authors: Sankey Temuulen Ts. , Tango Lauren , Tatum Julia , Sankey Joel B. 
Published: February 2024

Abstract
Context
Wildland-urban interface (WUI) areas are facing increased forest fire risks and extreme precipitation events due to climate change, which can lead to post-fire flood events. The city of Flagstaff in northern Arizona, USA experienced WUI forest thinning, fire, and record rainfall events, which collectively contributed to large floods and damages to the urban neighborhoods and city infrastructure.

Objectives
We demonstrate multi-temporal, high resolution image applications from an unoccupied aerial vehicle (UAV) and terrestrial lidar in estimating landscape disturbance impacts within the WUI. Changes in forest vegetation and bare ground cover in WUIs are particularly challenging to estimate with coarse-resolution satellite images due to fine-scale landscape processes and changes that often result in mixed pixels.

Methods
Using Sentinel-2 satellite images, we document forest fire impacts and burn severity. Using 2016 and 2021 UAV multispectral images and Structure-from-Motion data, we estimate post-thinning changes in forest canopy cover, patch sizes, canopy height distribution, and bare ground cover. Using repeat lidar data within a smaller area of the watershed, we quantify geomorphic effects in the WUI associated with the fire and subsequent flooding.

Results
We document that thinning significantly reduced forest canopy cover, patch size, tree density, and mean canopy height resulting in substantially reduced active crown fire risks in the future. However, the thinning equipment ignited a forest fire, which burned the WUI at varying severity at the top of the watershed that drains into the city. Moderate-high severity burns occurred within 3 km of downtown Flagstaff threatening the WUI neighborhoods and the city. The upstream burned area then experienced 100-year and 200–500-year rainfall events, which resulted in large runoff-driven floods and sedimentation in the city.

Conclusion
We demonstrate that UAV high resolution images and photogrammetry combined with terrestrial lidar data provide detailed and accurate estimates of forest thinning and post-fire flood impacts, which could not be estimated from coarser-resolution satellite images. Communities around the world may need to prepare their WUIs for catastrophic fires and increase capacity to manage sediment-laden stormwater since both fires and extreme weather events are projected to increase.
Epigenetic modulation of myeloid cell functions in HIV and SARS-CoV-2 infection
Authors: Krause Carolyn , Bergmann Eva , Schmidt Susanne Viktoria 
Published: February 2024

Abstract
Myeloid cells play a vital role in innate immune responses as they recognize and phagocytose pathogens like viruses, present antigens, produce cytokines, recruit other immune cells to combat infections, and contribute to the attenuation of immune responses to restore homeostasis. Signal integration by pathogen recognition receptors enables myeloid cells to adapt their functions by a network of transcription factors and chromatin remodelers. This review provides a brief overview of the subtypes of myeloid cells and the main epigenetic regulation mechanisms. Special focus is placed on the epigenomic alterations in viral nucleic acids of HIV and SARS-CoV-2 along with the epigenetic changes in the host’s myeloid cell compartment. These changes are important as they lead to immune suppression and promote the progression of the disease. Finally, we highlight some promising examples of ‘epidrugs’ that modulate the epigenome of immune cells and could be used as therapeutics for viral infections.
Differential impact of high-salt levels in vitro and in vivo on macrophage core functions
Authors: Müller Linda , Nasr Aya Rafea , Jux Bettina , Makdissi Nikola , Trowbridge Justin Wayne , Schmidt Susanne V. , Schultze Joachim L. , Quast Thomas , Schulte-Schrepping Jonas , Kolanus Waldemar , Mass Elvira 
Published: February 2024

Abstract
The consumption of processed food is on the rise leading to huge intake of excess dietary salt, which strongly correlates with development of hypertension, often leading to cardiovascular diseases such as stroke and heart attack, as well as activation of the immune system. The effect of salt on macrophages is especially interesting as they are able to sense high sodium levels in tissues leading to transcriptional changes. In the skin, macrophages were shown to influence lymphatic vessel growth which, in turn, enables the transport of excess salt and thereby prevents the development of high blood pressure. Furthermore, salt storage in the skin has been linked to the onset of pro-inflammatory effector functions of macrophages in pathogen defence. However, there is only little known about the mechanisms which are involved in changing macrophage function to salt exposure. Here, we characterize the response of macrophages to excess salt both in vitro and in vivo. Our results validate and strengthen the notion that macrophages exhibit chemotactic migration in response to salt gradients in vitro. Furthermore, we demonstrate a reduction in phagocytosis and efferocytosis following acute salt challenge in vitro. While acute exposure to a high-salt diet in vivo has a less pronounced impact on macrophage core functions such as phagocytosis, our data indicate that prolonged salt challenge may exert a distinct effect on the function of macrophages. These findings suggest a potential role for excessive salt sensing by macrophages in the manifestation of diseases related to high-salt diets and explicitly highlight the need for in vivo work to decipher the physiologically relevant impact of excess salt on tissue and cell function.
LIGHT regulated gene expression in rheumatoid synovial fibroblasts
Authors: Fukuda Koji , Miura Yasushi , Maeda Toshihisa , Hayashi Shinya , Kikuchi Kenichi , Takashima Yoshinori , Matsumoto Tomoyuki , Kuroda Ryosuke 
Published: February 2024

Abstract

Background
Synovial hyperplasia caused by rheumatoid arthritis (RA), an autoimmune inflammatory disease, leads to the destruction of the articular cartilage and bone. A member of the tumor necrosis factor superfamily, Lymphotoxin-related inducible ligand that competes for glycoprotein D binding to herpes virus entry mediator on T cells (LIGHT) has been shown to correlate with the pathogenesis of RA.

Methods
We used cDNA microarray analysis to compare the expression of genes in rheumatoid fibroblast-like synoviocytes with and without LIGHT stimulation.

Results
Significant changes in gene expression (P-values < 0.05 and fold change ≥ 2.0) were associated mainly with biological function categories of glycoprotein, glycosylation site as N-linked, plasma membrane part, integral to plasma membrane, intrinsic to plasma membrane, signal, plasma membrane, signal peptide, alternative splicing, and topological domain as extracellular.

Conclusions
Our results indicate that LIGHT may regulate the expression in RA-FLS of genes which are important in the differentiation of several cell types and in cellular functions.
Conv-Attention: A Low Computation Attention Calculation Method for Swin Transformer
Authors: Lou Zhehang , Luo Suyun , Huang Xiaoci , Wei Dan 
Published: February 2024

AbstractTransformer networks have excellent performance in various different vision tasks, especially object detection. However, in practical applications, Transformer is difficult to use on-board due to its large computational complexity. In this paper, we propose a new approach for reducing the computation of self-attention, which is called conv-attention. Different from the work of self-attention, conv-attention is inspired by NetVLAD and adopts the probability obtained by soft classification to replace the similarity calculation between query and key. Moreover, we combine the three convolution operations for computing the attention matrix in order to reduce the computational effort. Using the Swin Transformer as a comparison, experiments show that the parameters and FLOPs are reduced by 15% and 16%. Meanwhile, MAP is improved in vehicle object detection, including both FILR and Nuscenses datasets.
Mycorrhizal fungi respiration dynamics in relation to gross primary production in a Hungarian dry grassland
Authors: De Luca Giulia , Papp Marianna , Fóti Szilvia , Posta Katalin , Mészáros Ádám , Pintér Krisztina , Nagy Zoltán , Péli Evelin Ramóna , Fekete Sándor , Balogh János 
Published: February 2024

Abstract
Aims
Soil respiration (Rs) is a complex process including a wide range of soil biota and pathways of carbon cycling, all being under the control of various drivers. The most important biotic driver is the photosynthetic activity of the vegetation providing supply mainly for the autotrophic component of Rs: roots and their symbiotic partners. The objective of this study was to describe the time-lagged relationship between gross primary production (GPP) and the mycorrhizal Rs component in order to determine the amount of carbon derived from GPP appearing as mycorrhizal respiration (Rmyc).

Methods
Measurements of Rs were conducted in three treatments - (i) undisturbed, root and arbuscular mycorrhizal fungi (AMF)-included (Rs), (ii) root-excluded (Rhet+myc) and (iii) root- and AMF-excluded (Rhet) plots - for three consecutive years in a Central-Hungarian dry sandy grassland. GPP data were derived from eddy-covariance measurements, while an automated system was used for continuous measurements of Rs. We analysed the relationship between Rmyc and GPP by using cross-correlation and by fitting sine wave models on the diel datasets.

Results
GPP was found to be the main driver of Rmyc, responding with an average time lag of 18 h. The greatest lags were detected during periods characterized by minimal photosynthetic activity, while lags were the smallest during active periods.

Conclusion
Based on the seasonal changes in the delay, we concluded that GPP and soil temperature had simultaneous effects on the diel pattern of CO2 emission of the different autotrophic components depending on the vegetation activity and environmental conditions.
The car-free journey to, and through, parenthood
Authors: Kent Jennifer L. 
Published: February 2024

AbstractIn the context of increasing urgency and interest in the need to reduce private car dependence, it is surprising that we know very little about people who choose to live without cars. This is particularly so for those living through life-stages, and in structural and cultural contexts, generally associated with private car use. Parenting children is one such life-stage. The common understanding is that the vulnerabilities and complexities associated with parenting are best attenuated by the autonomy, security and seclusion of the private car. Others, by choice or circumstance, parent by ‘altermobility’ – without the private car. Using data from in-depth interviews with car-free parents of young children in Sydney, Australia, this paper records how parents come to live without private cars in a city that is dominated by structures, cultures and expectations of private car use. It proposes travel trajectories based on past and present events, experiences and inclinations. In doing so, the paper exposes the sheer complexity of influences of the past on present and future mobility practices, calling into question linear understandings of travel socialisation and mobility biography research. Automobile childhoods, for example, do not necessarily produce car-dependent adults. And the onset of parenthood is not necessarily a time of increased private car attachment. In conclusion, the findings query assumptions about the impact of the early years of parenting on private car dependence, proposing that it is the child, not the infant, that cements the seemingly intractable bond between parenting and private car use.
How transformative are transformative agreements? Evidence from Germany across disciplines
Authors: Schmal W. Benedikt 
Published: February 2024

AbstractResearch institutions across the globe attempt to change the academic publishing system as digitization opens up new opportunities, and subscriptions to the large journal bundles of the leading publishers put library budgets under pressure. One approach is the negotiation of so-called transformative agreements. I study the ‘DEAL’ contracts between nearly all German research institutions and Springer Nature and Wiley. I investigate 6.1 million publications in 5,862 journals covering eight fields in the years 2016–2022 and apply a causal difference-in-differences design to identify whether the likelihood of a paper appearing in an eligible journal increases. The effect strongly depends on the discipline. While material science, chemistry, and economics s tend to hift towards these journals, all other disciplines in my sample do not react. Suggestive evidence hints at the market position of the encompassed publishers before the ‘DEAL’ was established: Springer Nature and Wiley appear to benefit more from the contracts in disciplines in which they possessed a higher market share ex ante. The transformative vigor of these agreements in terms of publication behavior seems to be limited. It and highlights that the developments in this intertwined market require further examination.
Positive Semiotics Construction: The Intersectionality of Fat Black Women, from fatphobia, Through Fat Appraisal to fat praise
Authors: Letouze Patrick , Mendes Dorkas Brandão 
Published: February 2024

AbstractThe intersectionality of fat black women has been in the cultural spotlight in recent years and a significant amount of them might feel invisible or even ask themselves why to exist. When one feels self-inexistence, an imagined reality reinforced by the world, sadness, depression, and anger install within a person. The imaginary inexistence is induced by the unaware shamelessness that others project in the ignored person, who feels being invisible, and being invisible in a digital world is to not exist. In this paper, we answer why they should exist. We approach the issue with Positive Semiotics on desirability based on Positive Psychology, which focuses on understanding and facilitating well-being. We propose a semiotic framework for the construction of positive meaning paving the way from fatphobia to fat praise, passing by fat appraisal, to promote the well-being of fat black women. The proposed framework is the Positive Semiotics Construction, which is simultaneously an individual and collective construction of meaning for well-being, with a Sign-System Functional Model applicable to the digital world. Furthermore, a semiotic approach to Law and Social Norms may understand norms as the ability to send and receive signals for cooperation, which derives from moral appraisals of and reactions to the behavior of others and ourselves, consequently forming the normative underpinning of Law. Hence, the Positive Semiotics Construction might impact normative values and influence Law affecting the language of a society.
Coordinated and uncoordinated punishment in a team investment game
Authors: Calabuig Vicente , Jiménez-Jiménez Natalia , Olcina Gonzalo , Rodriguez-Lara Ismael 
Published: February 2024

AbstractCoordinated punishment occurs when punishment requires a specific number of punishers to be effective, otherwise, no damage will be inflicted on the target. While societies often rely on this punishment device, its benefits are unclear compared to uncoordinated punishment, where punishment decisions are substitutes. In this paper, we compare the efficacy of coordinated and uncoordinated punishment in a team investment game with two investors and one allocator. Our findings indicate that coordinated punishment results in higher levels of cooperation and reciprocity, as measured by the levels of joint investment and the return by allocators. Importantly, this does not translate into higher payoffs: investors use punishment more frequently when this is coordinated, which destroys the efficiency gains generated by the highest investment. In fact, our results suggest that the highest level of efficiency would be achieved if investors were not allowed to punish.
How Public Statues Wrong: Affective Artifacts and Affective Injustice
Authors: Archer Alfred 
Published: February 2024

AbstractIn what way might public statues wrong people? In recent years, philosophers have drawn on speech act theory to answer this question by arguing that statues constitute harmful or disrespectful forms of speech. My aim in this paper will be add a different theoretical perspective to this discussion. I will argue that while the speech act approach provides a useful starting point for thinking about what is wrong with public statues, we can get a fuller understanding of these wrongs by drawing on resources from recent work in situated affectivity. I will argue that public statues can be understood as affective artifacts and that this can both help us understand both the deep affective wrongs caused by public statues and offer a possible explanation as to why some people are so strongly opposed to their removal.
Evidencing the importance of the functional unit in comparative life cycle assessment of organic berry crops
Authors: Pérez Reina , Argüelles Fernando , Laca Amanda , Laca Adriana 
Published: February 2024

AbstractLCA methodology provides the best framework to evaluate environmental impacts in agriculture systems. However, the interpretation of LCA results, in particular when the objective was to compare different production systems, could be affected by the selection of the functional unit (FU). That is why an accurate definition of the FU, in agreement with the function considered for the systems analysed, is essential. In this work, the organic production at small scale of blueberry, raspberry, blackberry and cape gooseberry in North Spain has been analysed following LCA methodology. Although a different distribution of environmental loads was obtained for each crop, in all cases, the main contributions to most of the considered environmental categories were electric and fertiliser consumptions. The different production systems have been compared on the basis of the environmental impacts associated considering different FUs, i.e. based on fruit mass, cultivated area, farm-gate price and nutritional quality of fruits. Carbon footprints (CF) have been also calculated. It was observed that the order of the crops with respect to their environmental performances was the same for the blueberry and raspberry crops (with the lowest and the highest CF, respectively), independently of the selected FU, whereas the order of the blackberry and cape gooseberry crops was interchanged, depending on the FU used. This work supports the need of being aware of the final objective of the orchards when choosing the FU (i.e. producing fruits, cultivating an area, economic benefits or nourishing people), so that valid conclusions can be achieved from the environmental comparison, even for different agricultural products.
Current trends and future directions of global research on wastewater to energy: a bibliometric analysis and review
Authors: Shi Zhining , Xing Ke , Rameezdeen Rameez , Chow Christopher W. K. 
Published: February 2024

AbstractThis paper presents a structured bibliometric analysis and review of the research publications recorded in the Web of Science database from 2000 to 2023 to methodically examine the landscape and development of the ‘wastewater to energy’ research field in relation to global trends, potential hotspots, and future research directions. The study highlights three main research themes in ‘wastewater to energy’, which are biogas production through anaerobic digestion of sewage sludge, methane generation from microbial wastewater treatment, and hydrogen production from biomass. The analysis reveals activated sludge, biochar, biomethane, biogas upgrading, hydrogen, and circular economy as key topics increasingly gaining momentum in recent research publications as well as representing potential future research directions. The findings also signify transformation to SDGs and circular economy practices, through the integration of on-site renewables and biogas upgrading for energy self-sufficiency, optimising energy recovery from wastewater treatment systems, and fostering research and innovation in ‘wastewater to energy’ supported by policy incentives. By shedding light on emerging trends, cross-cutting themes, and potential policy implications, this study contributes to informing both knowledge and practices of the ‘wastewater to energy’ research community.