bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trustworthy AI: a plea for modest anthropocentrism
Authors: Nyrup Rune 
Published: July 2023

AbstractSimion and Kelp defend a non-anthropocentric account of trustworthy AI, based on the idea that the obligations of AI systems should be sourced in purely functional norms. In this commentary, I highlight some pressing counterexamples to their account, involving AI systems that reliably fulfil their functions but are untrustworthy because those functions are antagonistic to the interests of the trustor. Instead, I outline an alternative account, based on the idea that AI systems should not be considered primarily as tools but as technological participants in social practices. Specifically, I propose to source the obligations of an AI system in the norms that should govern the role it plays within the social practices it participates in, taking into account any changes to the social practices that its participation may bring about. This proposal is anthropocentric insofar as it ascribes obligations to AI systems that are similar to those of human participants in social practices, but only modestly so, as it does not require trustworthy AI to have contentious anthropomorphic capacities (e.g. for consciousness or moral responsibility).
What counts as a multimodal metaphor and metonymy? Evolution of inter-rater reliability across rounds of annotation
Authors: Pérez Sobrino Paula , Ford Samantha 
Published: July 2023

AbstractAn open question in research on multimodal figuration is how to mitigate the analyst’s bias in identifying and interpreting metaphor and metonymy; an issue that determines the generalizability of the findings. Little is known about the causes that motivate different annotations. Inter-rater reliability tests are useful to investigate the sources of variation in annotations by independent researchers that can help inform and refine protocols.Inspired by existing procedures for verbal, visual, and filmic metaphor identification, we formulated instructions to identify multimodal metaphor and metonymy and tested it against a corpus of 21 generic advertisements and 21 genre-specific advertisements (mobile phones). Two independent researchers annotated the advertisements in six rounds. A joint discussion followed each round to consider conflicting annotations and refine the protocol for the ensuing round.By examining the evolution of inter-rater reliability results, we found that (1) we reached similar levels of agreement for the identification of metaphor and metonymy, although converging on the interpretation of metonymy was more difficult; (2) some genre specificities made it easier to agree on the annotations for mobile advertisements than for the general advertisements; and (3) there was a consistent increase in the kappa scores reaching substantial agreement by the sixth round.
Impact of implementing a free varicella vaccination policy on incidence in Wuxi City, China: an interrupted time series analysis
Authors: Xiu Shixin , Wang Xuwen , Wang Qiang , Jin Hui , Shen Yuan 
Published: July 2023

Abstract
Varicella vaccination is optional and requires self-payment. On 1 December 2018, Wuxi City launched a free varicella vaccination program for children. This study aimed to evaluate the changes in varicella incidence before and after the implementation of the policy. The data were obtained from official information systems and statistical yearbooks. We divided the period into chargeable (January 2017 to November 2018) and free (December 2018 to December 2021) periods. Interrupt time series analysis was used to conduct a generalised least-squares regression analysis for the two periods. A total of 51,071 varicella cases were reported between January 2017 and December 2021. After the implementation of the policy, there was a statistically significant decrease in the incidence of varicella (β2 = −0.140, P = 0.017), and the slope of the incidence also decreased by 0.012 (P = 0.015). Following policy implementation, the incidence decreased in all age groups, with the largest decline observed among children aged 8–14 years (β2 = −1.109, P = 0.009), followed by children aged ≤7 years (β2 = −0.894, P = 0.013). Our study found a significant reduction in the incidence of varicella in the total population after the introduction of free varicella vaccination in Wuxi City.
Hydrogeomorphology of Asymmetric Meandering Channels: Experiments and Field Evidence
Authors: Abad J. D. , Motta D. , Guerrero L. , Paredes M. , Kuroiwa J. M. , Garcia M. H. 
Published: July 2023

AbstractMeandering channels display complex planform configurations with upstream (US)‐ and downstream (DS)‐skewed bends. Bend orientation is linked to hydrodynamics, bed morphodynamic regime, bank characteristics, riparian vegetation, and geological environment, which are the modulating factors that act specially in high‐amplitude and high‐sinuosity conditions. Based on the interaction between hydrodynamics and morphodynamics, previous studies have suggested that sub‐ (β < βR) and super‐resonant (β > βR) morphodynamic regimes (where β is the half width‐to‐depth ratio of the channel, and βR is the resonance condition) may trigger a particular bend orientation (upstream‐ and downstream‐skewed, respectively). However, natural rivers exhibit both US‐skewed and DS‐skewed bend patterns along the same reach, independently of the morphodynamic regime. Little is known about the hydrogeomorphology (forced and free morphodynamic patterns) under these bend orientations. Herein, using the asymmetric Kinoshita laboratory channel, experiments under sub‐ and super‐resonant conditions (with presence or absence of free bars) for upstream‐and downstream‐skewed conditions are performed. The experiments with migrating bars (β = 10, 15) are compared with previous experiments where only migrating dunes (β = 2) under sub‐resonant condition were observed. Additional, detailed field measurements at US‐ and DS‐skewed bends of different skewness along the Tigre River in Peru are also presented. Conditions at field scale filter out the influence of the morphodynamic regime in high‐sinuosity and high amplitude bends, where nonlinear processes (width variation, bedform dynamics) can directly affect the development of the three‐dimensional flow structure, and consequently the erosional and depositional patterns, and the lateral migration patterns.
Causal associations of brain structure with bone mineral density: a large-scale genetic correlation study
Authors: Guo Bin , Wang Chao , Zhu Yong , Liu Zhi , Long Haitao , Ruan Zhe , Lin Zhangyuan , Fan Zhihua , Li Yusheng , Zhao Shushan 
Published: July 2023

AbstractIn this study, we aimed to investigate the causal associations of brain structure with bone mineral density (BMD). Based on the genome-wide association study (GWAS) summary statistics of 1 325 brain imaging-derived phenotypes (BIDPs) of brain structure from the UK Biobank and GWAS summary datasets of 5 BMD locations, including the total body, femoral neck, lumbar spine, forearm, and heel from the GEFOS Consortium, linkage disequilibrium score regression (LDSC) was conducted to determine the genetic correlations, and Mendelian randomization (MR) was then performed to explore the causal relationship between the BIDPs and BMD. Several sensitivity analyses were performed to verify the strength and stability of the present MR outcomes. To increase confidence in our findings, we also performed confirmatory MR between BIDPs and osteoporosis. LDSC revealed that 1.93% of BIDPs, with a false discovery rate (FDR) < 0.01, were genetically correlated with BMD. Additionally, we observed that 1.31% of BIDPs exhibited a significant causal relationship with BMD (FDR < 0.01) through MR. Both the LDSC and MR results demonstrated that the BIDPs “Volume of normalized brain,” “Volume of gray matter in Left Inferior Frontal Gyrus, pars opercularis,” “Volume of Estimated Total Intra Cranial” and “Volume-ratio of brain segmentation/estimated total intracranial” had strong associations with BMD. Interestingly, our results showed that more left BIDPs were causally associated with BMD, especially within and around the left frontal region. In conclusion, a part of the brain structure causally influences BMD, which may provide important perspectives for the prevention of osteoporosis and offer valuable insights for further research on the brain-bone axis.
Antiviral HIV-1 SERINC restriction factors disrupt virus membrane asymmetry
Authors: Leonhardt Susan A. , Purdy Michael D. , Grover Jonathan R. , Yang Ziwei , Poulos Sandra , McIntire William E. , Tatham Elizabeth A. , Erramilli Satchal K. , Nosol Kamil , Lai Kin Kui , Ding Shilei , Lu Maolin , Uchil Pradeep D. , Finzi Andrés , Rein Alan , Kossiakoff Anthony A. , Mothes Walther , Yeager Mark 
Published: July 2023

AbstractThe host proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce infectivity when incorporated into the viral envelope. The HIV-1 accessory protein Nef abrogates incorporation of SERINCs via binding to intracellular loop 4 (ICL4). Here, we determine cryoEM maps of full-length human SERINC3 and an ICL4 deletion construct, which reveal that hSERINC3 is comprised of two α-helical bundles connected by a ~ 40-residue, highly tilted, “crossmember” helix. The design resembles non-ATP-dependent lipid transporters. Consistently, purified hSERINCs reconstituted into proteoliposomes induce flipping of phosphatidylserine (PS), phosphatidylethanolamine and phosphatidylcholine. Furthermore, SERINC3, SERINC5 and the scramblase TMEM16F expose PS on the surface of HIV-1 and reduce infectivity, with similar results in MLV. SERINC effects in HIV-1 and MLV are counteracted by Nef and GlycoGag, respectively. Our results demonstrate that SERINCs are membrane transporters that flip lipids, resulting in a loss of membrane asymmetry that is strongly correlated with changes in Env conformation and loss of infectivity.
Oncolytic viruses engineered to enforce cholesterol efflux restore tumor-associated macrophage phagocytosis and anti-tumor immunity in glioblastoma
Authors: Wang Shiqun , Yan Wei , Kong Lingkai , Zuo Shuguang , Wu Jingyi , Zhu Chunxiao , Huang Huaping , He Bohao , Dong Jie , Wei Jiwu 
Published: July 2023

AbstractThe codependency of cholesterol metabolism sustains the malignant progression of glioblastoma (GBM) and effective therapeutics remain scarce. In orthotopic GBM models in male mice, we identify that codependent cholesterol metabolism in tumors induces phagocytic dysfunction in monocyte-derived tumor-associated macrophages (TAMs), resulting in disease progression. Manipulating cholesterol efflux with apolipoprotein A1 (ApoA1), a cholesterol reverse transporter, restores TAM phagocytosis and reactivates TAM-T cell antitumor immunity. Cholesterol metabolomics analysis of in vivo-sorted TAMs further reveals that ApoA1 mediates lipid-related metabolic remodeling and lowers 7-ketocholesterol levels, which directly inhibits tumor necrosis factor signaling in TAMs through mitochondrial translation inhibition. An ApoA1-armed oncolytic adenovirus is also developed, which restores antitumor immunity and elicits long-term tumor-specific immune surveillance. Our findings provide insight into the mechanisms by which cholesterol metabolism impairs antitumor immunity in GBM and offer an immunometabolic approach to target cholesterol disturbances in GBM.
Arbitrary aperture synthesis with nonlocal leaky-wave metasurface antennas
Authors: Xu Gengyu , Overvig Adam , Kasahara Yoshiaki , Martini Enrica , Maci Stefano , Alù Andrea 
Published: July 2023

AbstractThe emergence of new technological needs in 5 G/6 G networking and broadband satellite internet access amplifies the demand for innovative wireless communication hardware, including high-performance low-profile transceivers. In this context, antennas based on metasurfaces – artificial surfaces engineered to manipulate electromagnetic waves at will – represent highly promising solutions. In this article, we introduce leaky-wave metasurface antennas operating at micro/millimeter-wave frequencies that are designed using the principles of quasi-bound states in the continuum, exploiting judiciously tailored spatial symmetries that enable fully customized radiation. Specifically, we unveil additional degrees of control over leaky-wave radiation by demonstrating pointwise control of the amplitude, phase and polarization state of the metasurface aperture fields by carefully breaking relevant symmetries with tailored perturbations. We design and experimentally demonstrate metasurface antenna prototypes showcasing a variety of functionalities advancing capabilities in wireless communications, including single-input multi-output and multi-input multi-output near-field focusing, as well as far-field beam shaping.
Insertion sequence transposition inactivates CRISPR-Cas immunity
Authors: Sheng Yong , Wang Hengyu , Ou Yixin , Wu Yingying , Ding Wei , Tao Meifeng , Lin Shuangjun , Deng Zixin , Bai Linquan , Kang Qianjin 
Published: July 2023

AbstractCRISPR-Cas immunity systems safeguard prokaryotic genomes by inhibiting the invasion of mobile genetic elements. Here, we screened prokaryotic genomic sequences and identified multiple natural transpositions of insertion sequences (ISs) into cas genes, thus inactivating CRISPR-Cas defenses. We then generated an IS-trapping system, using Escherichia coli strains with various ISs and an inducible cas nuclease, to monitor IS insertions into cas genes following the induction of double-strand DNA breakage as a physiological host stress. We identified multiple events mediated by different ISs, especially IS1 and IS10, displaying substantial relaxed target specificity. IS transposition into cas was maintained in the presence of DNA repair machinery, and transposition into other host defense systems was also detected. Our findings highlight the potential of ISs to counter CRISPR activity, thus increasing bacterial susceptibility to foreign DNA invasion.
Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome
Authors: Mirhakkak Mohammad H. , Chen Xiuqiang , Ni Yueqiong , Heinekamp Thorsten , Sae-Ong Tongta , Xu Lin-Lin , Kurzai Oliver , Barber Amelia E. , Brakhage Axel A. , Boutin Sebastien , Schäuble Sascha , Panagiotou Gianni 
Published: July 2023

AbstractAspergillus fumigatus, an opportunistic human pathogen, frequently infects the lungs of people with cystic fibrosis and is one of the most common causes of infectious-disease death in immunocompromised patients. Here, we construct 252 strain-specific, genome-scale metabolic models of this important fungal pathogen to study and better understand the metabolic component of its pathogenic versatility. The models show that 23.1% of A. fumigatus metabolic reactions are not conserved across strains and are mainly associated with amino acid, nucleotide, and nitrogen metabolism. Profiles of non-conserved reactions and growth-supporting reaction fluxes are sufficient to differentiate strains, for example by environmental or clinical origin. In addition, shotgun metagenomics analysis of sputum from 40 cystic fibrosis patients (15 females, 25 males) before and after diagnosis with an A. fumigatus colonization suggests that the fungus shapes the lung microbiome towards a more beneficial fungal growth environment associated with aromatic amino acid availability and the shikimate pathway. Our findings are starting points for the development of drugs or microbiome intervention strategies targeting fungal metabolic needs for survival and colonization in the non-native environment of the human lung.
Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector
Authors: Ceglia Nicholas , Sethna Zachary , Freeman Samuel S. , Uhlitz Florian , Bojilova Viktoria , Rusk Nicole , Burman Bharat , Chow Andrew , Salehi Sohrab , Kabeer Farhia , Aparicio Samuel , Greenbaum Benjamin D. , Shah Sohrab P. , McPherson Andrew 
Published: July 2023

AbstractDeciphering individual cell phenotypes from cell-specific transcriptional processes requires high dimensional single cell RNA sequencing. However, current dimensionality reduction methods aggregate sparse gene information across cells, without directly measuring the relationships that exist between genes. By performing dimensionality reduction with respect to gene co-expression, low-dimensional features can model these gene-specific relationships and leverage shared signal to overcome sparsity. We describe GeneVector, a scalable framework for dimensionality reduction implemented as a vector space model using mutual information between gene expression. Unlike other methods, including principal component analysis and variational autoencoders, GeneVector uses latent space arithmetic in a lower dimensional gene embedding to identify transcriptional programs and classify cell types. In this work, we show in four single cell RNA-seq datasets that GeneVector was able to capture phenotype-specific pathways, perform batch effect correction, interactively annotate cell types, and identify pathway variation with treatment over time.
Comparative genomics reveals a unique nitrogen-carbon balance system in Asteraceae
Authors: Shen Fei , Qin Yajuan , Wang Rui , Huang Xin , Wang Ying , Gao Tiangang , He Junna , Zhou Yue , Jiao Yuannian , Wei Jianhua , Li Lei , Yang Xiaozeng 
Published: July 2023

AbstractThe Asteraceae (daisy family) is one of the largest families of plants. The genetic basis for its high biodiversity and excellent adaptability has not been elucidated. Here, we compare the genomes of 29 terrestrial plant species, including two de novo chromosome-scale genome assemblies for stem lettuce, a member of Asteraceae, and Scaevola taccada, a member of Goodeniaceae that is one of the closest outgroups of Asteraceae. We show that Asteraceae originated ~80 million years ago and experienced repeated paleopolyploidization. PII, the universal regulator of nitrogen-carbon (N-C) assimilation present in almost all domains of life, has conspicuously lost across Asteraceae. Meanwhile, Asteraceae has stepwise upgraded the N-C balance system via paleopolyploidization and tandem duplications of key metabolic genes, resulting in enhanced nitrogen uptake and fatty acid biosynthesis. In addition to suggesting a molecular basis for their ecological success, the unique N-C balance system reported for Asteraceae offers a potential crop improvement strategy.
Fungal small RNAs ride in extracellular vesicles to enter plant cells through clathrin-mediated endocytosis
Authors: He Baoye , Wang Huan , Liu Guosheng , Chen Angela , Calvo Alejandra , Cai Qiang , Jin Hailing 
Published: July 2023

AbstractSmall RNAs (sRNAs) of the fungal pathogen Botrytis cinerea can enter plant cells and hijack host Argonaute protein 1 (AGO1) to silence host immunity genes. However, the mechanism by which these fungal sRNAs are secreted and enter host cells remains unclear. Here, we demonstrate that B. cinerea utilizes extracellular vesicles (EVs) to secrete Bc-sRNAs, which are then internalized by plant cells through clathrin-mediated endocytosis (CME). The B. cinerea tetraspanin protein, Punchless 1 (BcPLS1), serves as an EV biomarker and plays an essential role in fungal pathogenicity. We observe numerous Arabidopsis clathrin-coated vesicles (CCVs) around B. cinerea infection sites and the colocalization of B. cinerea EV marker BcPLS1 and Arabidopsis CLATHRIN LIGHT CHAIN 1, one of the core components of CCV. Meanwhile, BcPLS1 and the B. cinerea-secreted sRNAs are detected in purified CCVs after infection. Arabidopsis knockout mutants and inducible dominant-negative mutants of key components of the CME pathway exhibit increased resistance to B. cinerea infection. Furthermore, Bc-sRNA loading into Arabidopsis AGO1 and host target gene suppression are attenuated in those CME mutants. Together, our results demonstrate that fungi secrete sRNAs via EVs, which then enter host plant cells mainly through CME.
Multi-campaign ship and aircraft observations of marine cloud condensation nuclei and droplet concentrations
Authors: Sanchez Kevin J. , Painemal David , Brown Matthew D. , Crosbie Ewan C. , Gallo Francesca , Hair Johnathan W. , Hostetler Chris A. , Jordan Carolyn E. , Robinson Claire E. , Scarino Amy Jo , Shingler Taylor J. , Shook Michael A. , Thornhill Kenneth L. , Wiggins Elizabeth B. , Winstead Edward L. , Ziemba Luke D. , Chambers Scott , Williams Alastair , Humphries Ruhi S , Keywood Melita D. , Ward Jason P. , Cravigan Luke , McRobert Ian M. , Flynn Connor , Kulkarni Gourihar R. , Russell Lynn M. , Roberts Gregory C. , McFarquhar Greg M. , Nenes Athanasios , Woods Sarah F. , Reid Jeffery S. , Small-Griswold Jennifer , Brooks Sarah , Kirschler Simon , Voigt Christianne , Wang Jian , Delene David J. , Quinn Patricia K. , Moore Richard H. 
Published: July 2023

AbstractIn-situmarine cloud droplet number concentrations (CDNCs), cloud condensation nuclei (CCN), and CCN proxies, based on particle sizes and optical properties, are accumulated from seven field campaigns: ACTIVATE; NAAMES; CAMP2EX; ORACLES; SOCRATES; MARCUS; and CAPRICORN2. Each campaign involves aircraft measurements, ship-based measurements, or both. Measurements collected over the North and Central Atlantic, Indo-Pacific, and Southern Oceans, represent a range of clean to polluted conditions in various climate regimes. With the extensive range of environmental conditions sampled, this data collection is ideal for testing satellite remote detection methods of CDNC and CCN in marine environments. Remote measurement methods are vital to expanding the available data in these difficult-to-reach regions of the Earth and improving our understanding of aerosol-cloud interactions. The data collection includes particle composition and continental tracers to identify potential contributing CCN sources. Several of these campaigns include High Spectral Resolution Lidar (HSRL) and polarimetric imaging measurements and retrievals that will be the basis for the next generation of space-based remote sensors and, thus, can be utilized as satellite surrogates.
Citizens’ Perceptions of Research and Innovation Dilemmas: Insights from a Large-Scale Survey in Four European Regions
Authors: Fellnhofer Katharina , Angelidou Margarita , Bakratsas Thomas , Buongiovanni Chiara , Eiser Toni , Hörndler Elena , Panori Anastasia , Wintjes Rene , Quaranta Gabriella 
Published: July 2023

AbstractThis study presents a valuable dataset supporting regional research and innovation systems in four European regions: Vestland (Norway), Kriti (Greece), Galicia (Spain), and Overijssel (Netherlands). It focuses on understanding citizens’ perceptions of research and innovation dilemmas within these regions. The dataset comprises 14 questions aligned with the Responsible Research and Innovation framework, evaluating stakeholders’ techno-moral attitudes towards technological change and socio-economic outcomes. A survey conducted between April and July 2020 gathered responses from 7,729 individuals, ensuring broad age and gender representation. This dataset is highly valuable for regional policymaking and policymakers’ engagement strategies, enhancing equity and effectiveness in addressing grand societal challenges. Research outcomes reveal citizens’ aspirations for developmental trajectories prioritizing quality-of-life, renewable energy, and support for innovative SMEs in their regions. The study contributes to existing research by highlighting limited citizen trust and expectations of effective government actions in addressing societal challenges at the regional level.