bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ice Concentration Scaling Laws for Freshwater Lakes in Numerical Weather and Climate Prediction
Authors: MacKay Murray D. 
Published: June 2023

AbstractIf lake ice is assumed to deform and fail as a linear viscoelastic material under the action of wind stress, then a simple ice concentration scaling law can be constructed suitable for one‐dimensional lake models embedded within environmental prediction systems. Most 1‐D lake models assume no ice mechanics at all, while others adapt the viscous‐plastic rheology common in ice‐ocean models for the purpose of estimating ice fraction. Elastic buckling is generally disregarded as a significant failure mechanism in ice under low stress conditions at geophysical scales. However, by adding viscosity to the constitutive equation, the conditions for viscoelastic buckling seem quite plausible over a wide range of lake size and ice thickness. An ice concentration scaling law based on this process is evaluated here in multiannual simulations over North America and found to produce superior ice phenology statistics compared with simulations based on plastic failure or no ice mechanics.
Unlocking the monolithic integration scenario: optical coupling between GaSb diode lasers epitaxially grown on patterned Si substrates and passive SiN waveguides
Authors: Remis Andres , Monge-Bartolome Laura , Paparella Michele , Gilbert Audrey , Boissier Guilhem , Grande Marco , Blake Alan , O’Faolain Liam , Cerutti Laurent , Rodriguez Jean-Baptiste , Tournié Eric 
Published: June 2023

AbstractSilicon (Si) photonics has recently emerged as a key enabling technology in many application fields thanks to the mature Si process technology, the large silicon wafer size, and promising Si optical properties. The monolithic integration by direct epitaxy of III–V lasers and Si photonic devices on the same Si substrate has been considered for decades as the main obstacle to the realization of dense photonics chips. Despite considerable progress in the last decade, only discrete III–V lasers grown on bare Si wafers have been reported, whatever the wavelength and laser technology. Here we demonstrate the first semiconductor laser grown on a patterned Si photonics platform with light coupled into a waveguide. A mid-IR GaSb-based diode laser was directly grown on a pre-patterned Si photonics wafer equipped with SiN waveguides clad by SiO2. Growth and device fabrication challenges, arising from the template architecture, were overcome to demonstrate more than 10 mW outpower of emitted light in continuous wave operation at room temperature. In addition, around 10% of the light was coupled into the SiN waveguides, in good agreement with theoretical calculations for this butt-coupling configuration. This work lift an important building block and it paves the way for future low-cost, large-scale, fully integrated photonic chips.
Estimated exposure to perfluoroalkyl substances during infancy and serum-adipokine concentrations in later childhood
Authors: Grandjean Philippe , Shih Yu-Hsuan , Jørgensen Louise Helskov , Nielsen Flemming , Weihe Pál , Budtz-Jørgensen Esben 
Published: June 2023

Abstract
Background
Perfluoroalkyl substances (PFASs) are transferred through human milk and may cause elevated exposure during infancy. Given the lack of early postnatal blood samples, PFAS concentrations can be estimated to serve as predictors of subsequent metabolic toxicity.

Methods
A total of 298 children from a prospective birth cohort were followed up through to age 9 years. Serum-PFAS was measured at birth and 18 months of age, while exposures during infancy were estimated by structural equations. Adiponectin, resistin, leptin, and the leptin receptor were measured in serum at age 9. Adjusted regression coefficients for estimated serum-PFAS concentrations were calculated, with additional consideration of the duration of breastfeeding and potential effect modification by sex.

Results
A doubling in estimated serum-PFAS concentrations, particularly at ages 6 and 12 months, was associated with a loss of about 10–15% in age 9 resistin concentrations, while other associations were much weaker. Sex dependence of the associations was not observed, and neither did the duration of breastfeeding affect outcomes at age 9.

Conclusion
Lowered serum-resistin concentrations at age 9 years were most strongly associated with early postnatal PFAS exposures. These findings suggest that infancy may represent a vulnerable time window for some aspects of metabolic programming that may be affected by PFAS exposure.

Impact

Serum-PFAS concentrations during infancy can be estimated in the absence of blood samples.

Adipokine concentrations were measured at age 9 years as metabolic biomarkers.

Resistin was significantly lower in children with elevated PFAS exposures in infancy.

The findings suggest that early postnatal PFAS exposures may affect subsequent metabolic health.

Assessment of infancy vulnerability to PFAS can be explored using estimated serum-PFAS concentrations.
Out with AI, in with the psychiatrist: a preference for human-derived clinical decision support in depression care
Authors: Maslej Marta M. , Kloiber Stefan , Ghassemi Marzyeh , Yu Joanna , Hill Sean L. 
Published: June 2023

AbstractAdvancements in artificial intelligence (AI) are enabling the development of clinical support tools (CSTs) in psychiatry to facilitate the review of patient data and inform clinical care. To promote their successful integration and prevent over-reliance, it is important to understand how psychiatrists will respond to information provided by AI-based CSTs, particularly if it is incorrect. We conducted an experiment to examine psychiatrists’ perceptions of AI-based CSTs for treating major depressive disorder (MDD) and to determine whether perceptions interacted with the quality of CST information. Eighty-three psychiatrists read clinical notes about a hypothetical patient with MDD and reviewed two CSTs embedded within a single dashboard: the note’s summary and a treatment recommendation. Psychiatrists were randomised to believe the source of CSTs was either AI or another psychiatrist, and across four notes, CSTs provided either correct or incorrect information. Psychiatrists rated the CSTs on various attributes. Ratings for note summaries were less favourable when psychiatrists believed the notes were generated with AI as compared to another psychiatrist, regardless of whether the notes provided correct or incorrect information. A smaller preference for psychiatrist-generated information emerged in ratings of attributes that reflected the summary’s accuracy or its inclusion of important information from the full clinical note. Ratings for treatment recommendations were also less favourable when their perceived source was AI, but only when recommendations were correct. There was little evidence that clinical expertise or familiarity with AI impacted results. These findings suggest that psychiatrists prefer human-derived CSTs. This preference was less pronounced for ratings that may have prompted a deeper review of CST information (i.e. a comparison with the full clinical note to evaluate the summary’s accuracy or completeness, assessing an incorrect treatment recommendation), suggesting a role of heuristics. Future work should explore other contributing factors and downstream implications for integrating AI into psychiatric care.
SMURF1 attenuates endoplasmic reticulum stress by promoting the degradation of KEAP1 to activate NRF2 antioxidant pathway
Authors: Dong Lei , Xu Mengchuan , Li Yang , Xu Wanting , Wu Chengwei , Zheng Hanfei , Xiao Zhenyu , Sun Guochen , Ding Lei , Li Xiaobo , Li Wenming , Zhou Liying , Xia Qin 
Published: June 2023

AbstractCancer cells consistently utilize the unfolded protein response (UPR) to encounter the abnormal endoplasmic reticulum (ER) stress induced by the accumulation of misfolded proteins. Extreme activation of the UPR could also provoke maladaptive cell death. Previous reports have shown that NRF2 antioxidant signaling is activated by UPR and serves as noncanonical pathway to defense and reduce excessive ROS levels during ER stress. However, the mechanisms of regulating NRF2 signaling upon ER stress in glioblastoma have not been fully elucidated. Here we identify that SMURF1 protects against ER stress and facilitates glioblastoma cell survival by rewiring KEAP1-NRF2 pathway. We show that ER stress induces SMURF1 degradation. Knockdown of SMURF1 upregulates IRE1 and PERK signaling in the UPR pathway and prevents ER-associated protein degradation (ERAD) activity, leading to cell apoptosis. Importantly, SMURF1 overexpression activates NRF2 signaling to reduce ROS levels and alleviate UPR-mediated cell death. Mechanistically, SMURF1 interacts with and ubiquitinates KEAP1 for its degradation (NRF2 negative regulator), resulting in NRF2 nuclear import. Moreover, SMURF1 loss reduces glioblastoma cell proliferation and growth in subcutaneously implanted nude mice xenografts. Taken together, SMURF1 rewires KEAP1-NRF2 pathway to confer resistance to ER stress inducers and protect glioblastoma cell survival. ER stress and SMURF1 modulation may provide promising therapeutic targets for the treatment of glioblastoma.
Quantum bath suppression in a superconducting circuit by immersion cooling
Authors: Lucas M. , Danilov A. V. , Levitin L. V. , Jayaraman A. , Casey A. J. , Faoro L. , Tzalenchuk A. Ya. , Kubatkin S. E. , Saunders J. , de Graaf S. E. 
Published: June 2023

AbstractQuantum circuits interact with the environment via several temperature-dependent degrees of freedom. Multiple experiments to-date have shown that most properties of superconducting devices appear to plateau out at T ≈ 50 mK – far above the refrigerator base temperature. This is for example reflected in the thermal state population of qubits, in excess numbers of quasiparticles, and polarisation of surface spins – factors contributing to reduced coherence. We demonstrate how to remove this thermal constraint by operating a circuit immersed in liquid 3He. This allows to efficiently cool the decohering environment of a superconducting resonator, and we see a continuous change in measured physical quantities down to previously unexplored sub-mK temperatures. The 3He acts as a heat sink which increases the energy relaxation rate of the quantum bath coupled to the circuit a thousand times, yet the suppressed bath does not introduce additional circuit losses or noise. Such quantum bath suppression can reduce decoherence in quantum circuits and opens a route for both thermal and coherence management in quantum processors.
Genome expansion by a CRISPR trimmer-integrase
Authors: Wang Joy Y. , Tuck Owen T. , Skopintsev Petr , Soczek Katarzyna M. , Li Gary , Al-Shayeb Basem , Zhou Julia , Doudna Jennifer A. 
Published: June 2023

AbstractCRISPR–Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity1. CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR/Cas1–Cas2 integrase is necessary but not sufficient2–5. In some microorganisms, the Cas4 endonuclease assists CRISPR adaptation6,7, but many CRISPR–Cas systems lack Cas48. Here we show here that an elegant alternative pathway in a type I-E system uses an internal DnaQ-like exonuclease (DEDDh) to select and process DNA for integration using the protospacer adjacent motif (PAM). The natural Cas1–Cas2/exonuclease fusion (trimmer-integrase) catalyses coordinated DNA capture, trimming and integration. Five cryo-electron microscopy structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited9,10 exonucleases for faithful acquisition of new CRISPR immune sequences.
A tripartite rheostat controls self-regulated host plant resistance to insects
Authors: Guo Jianping , Wang Huiying , Guan Wei , Guo Qin , Wang Jing , Yang Jing , Peng Yaxin , Shan Junhan , Gao Mingyang , Shi Shaojie , Shangguan Xinxin , Liu Bingfang , Jing Shengli , Zhang Jing , Xu Chunxue , Huang Jin , Rao Weiwei , Zheng Xiaohong , Wu Di , Zhou Cong , Du Bo , Chen Rongzhi , Zhu Lili , Zhu Yuxian , Walling Linda L. , Zhang Qifa , He Guangcun 
Published: June 2023

AbstractPlants deploy receptor-like kinases and nucleotide-binding leucine-rich repeat receptors to confer host plant resistance (HPR) to herbivores1. These gene-for-gene interactions between insects and their hosts have been proposed for more than 50 years2. However, the molecular and cellular mechanisms that underlie HPR have been elusive, as the identity and sensing mechanisms of insect avirulence effectors have remained unknown. Here we identify an insect salivary protein perceived by a plant immune receptor. The BPH14-interacting salivary protein (BISP) from the brown planthopper (Nilaparvata lugens Stål) is secreted into rice (Oryza sativa) during feeding. In susceptible plants, BISP targets O. satvia RLCK185 (OsRLCK185; hereafter Os is used to denote O. satvia-related proteins or genes) to suppress basal defences. In resistant plants, the nucleotide-binding leucine-rich repeat receptor BPH14 directly binds BISP to activate HPR. Constitutive activation of Bph14-mediated immunity is detrimental to plant growth and productivity. The fine-tuning of Bph14-mediated HPR is achieved through direct binding of BISP and BPH14 to the selective autophagy cargo receptor OsNBR1, which delivers BISP to OsATG8 for degradation. Autophagy therefore controls BISP levels. In Bph14 plants, autophagy restores cellular homeostasis by downregulating HPR when feeding by brown planthoppers ceases. We identify an insect saliva protein sensed by a plant immune receptor and discover a three-way interaction system that offers opportunities for developing high-yield, insect-resistant crops.
A proposed FAIR approach for disseminating geospatial information system maps
Authors: Thompson P. Travis , Ojha Sweta , Powell Christian D. , Pennell Kelly G. , Moseley Hunter N. B. 
Published: June 2023

AbstractWe present a draft Minimum Information About Geospatial Information System (MIAGIS) standard for facilitating public deposition of geospatial information system (GIS) datasets that follows the FAIR (Findable, Accessible, Interoperable and Reusable) principles. The draft MIAGIS standard includes a deposition directory structure and a minimum javascript object notation (JSON) metadata formatted file that is designed to capture critical metadata describing GIS layers and maps as well as their sources of data and methods of generation. The associated miagis Python package facilitates the creation of this MIAGIS metadata file and directly supports metadata extraction from both Esri JSON and GEOJSON GIS data formats plus options for extraction from user-specified JSON formats. We also demonstrate their use in crafting two example depositions of ArcGIS generated maps. We hope this draft MIAGIS standard along with the supporting miagis Python package will assist in establishing a GIS standards group that will develop the draft into a full standard for the wider GIS community as well as a future public repository for GIS datasets.
Host nasopharyngeal transcriptome dataset of a SARS-CoV-2 positive Italian cohort
Authors: Salvati Annamaria , Ferravante Carlo , Lamberti Jessica , Rocco Teresa , Alexandrova Elena , D’Agostino Ylenia , Sorokin Maksim , Efimov Victor , Buzdin Anton , Strianese Oriana , Nassa Giovanni , Tarallo Roberta , Weisz Alessandro , Rizzo Francesca , Giurato Giorgio 
Published: June 2023

AbstractThe ongoing COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people worldwide and has significant implications for public health. Host transcriptomics profiling provides comprehensive understanding of how the virus interacts with host cells and how the host responds to the virus. COVID-19 disease alters the host transcriptome, affecting cellular pathways and key molecular functions. To contribute to the global effort to understand the virus’s effect on host cell transcriptome, we have generated a dataset from nasopharyngeal swabs of 35 individuals infected with SARS-CoV-2 from the Campania region in Italy during the three outbreaks, with different clinical conditions. This dataset will help to elucidate the complex interactions among genes and can be useful in the development of effective therapeutic pathways.
A draft genome assembly of reef-building octocoral Heliopora coerulea
Authors: Ip Jack Chi-Ho , Ho Ming-Hay , Chan Benny K. K. , Qiu Jian-Wen 
Published: June 2023

AbstractCoral reefs are under existential threat from climate change and anthropogenic impacts. Genomic studies have enhanced our knowledge of resilience and responses of some coral species to environmental stress, but reference genomes are lacking for many coral species. The blue coral Heliopora is the only reef-building octocoral genus and exhibits optimal growth at a temperature close to the bleaching threshold of scleractinian corals. Local and high-latitude expansions of Heliopora coerulea were reported in the last decade, but little is known about the molecular mechanisms underlying its thermal resistance. We generated a draft genome of H. coerulea with an assembled size of 429.9 Mb, scaffold N50 of 1.42 Mb and BUSCO completeness of 94.9%. The genome contains 239.1 Mb repetitive sequences, 27,108 protein coding genes, 6,225 lncRNAs, and 79 miRNAs. This reference genome provides a valuable resource for in-depth studies on the adaptive mechanisms of corals under climate change and the evolution of skeleton in cnidarian.
CD44 is a potential immunotherapeutic target and affects macrophage infiltration leading to poor prognosis
Authors: Liu Shuangqing , Liu Zehan , Shang Aichen , Xun Jing , Lv Zongjing , Zhou Siying , Liu Cui , Zhang Qi , Yang Yuming 
Published: June 2023

AbstractCD44 plays a key role in the communication of CSCs with the microenvironment and the regulation of stem cell properties. UALCAN was used to analyze the expression of CD44 in bladder cancer (BLCA) and normal tissue. The UALCAN was utilized to analyze the prognostic value of CD44 in BLCA. The TIMER database was used to explore the relationship between CD44 and PD-L1; CD44 and tumor-infiltrating immune cells. The regulatory effect of CD44 on PD-L1 was verified by cell experiments in vitro. IHC confirmed the results of the bioinformatics analysis. GeneMania and Metascape were used to analyze protein–protein interaction (PPI) investigations and functional enrichment analysis. We found that BLCA patients with high CD44 expression had worse survival than those with low CD44 expression (P < 0.05). IHC and the TIMER database results showed that CD44 expression was positively correlated with PD-L1 expression (P < 0.05). At the cellular level, the expression of PD-L1 was significantly inhibited after CD44 expression was inhibited by siRNA. Immune infiltration analysis showed that CD44 expression levels in BLCA were significantly correlated with immune infiltration levels of different immune cells. IHC staining results further confirmed that the expression of CD44 in tumor cells was positively associated with the number of CD68+ macrophages and CD163+ macrophages (P < 0.05). Our results suggest that CD44 is a positive regulator of PD-L1 in BLCA and may be a key regulator of tumor macrophages infiltration and may be involved in M2 macrophage polarization. Our study provided new insights into the prognosis and immunotherapy of BLCA patients through macrophage infiltration and immune checkpoints.
ABCA1 deficiency contributes to podocyte pyroptosis priming via the APE1/IRF1 axis in diabetic kidney disease
Authors: Ito Marie , Ducasa Gloria Michelle , Molina Judith David , Santos Javier Varona , Mallela Shamroop Kumar , Kim Jin Ju , Ge Mengyuan , Mitrofanova Alla , Sloan Alexis , Merscher Sandra , Mimura Imari , Fornoni Alessia 
Published: June 2023

AbstractDecreased ATP Binding Cassette Transporter A1 (ABCA1) expression and caspase-4-mediated noncanonical inflammasome contribution have been described in podocytes in diabetic kidney disease (DKD). To investigate a link between these pathways, we evaluated pyroptosis-related mediators in human podocytes with stable knockdown of ABCA1 (siABCA1) and found that mRNA levels of IRF1, caspase-4, GSDMD, caspase-1 and IL1β were significantly increased in siABCA1 compared to control podocytes and that protein levels of caspase-4, GSDMD and IL1β were equally increased. IRF1 knockdown in siABCA1 podocytes prevented increases in caspase-4, GSDMD and IL1β. Whereas TLR4 inhibition did not decrease mRNA levels of IRF1 and caspase-4, APE1 protein expression increased in siABCA1 podocytes and an APE1 redox inhibitor abrogated siABCA1-induced expression of IRF1 and caspase-4. RELA knockdown also offset the pyroptosis priming, but ChIP did not demonstrate increased binding of NFκB to IRF1 promoter in siABCA1 podocytes. Finally, the APE1/IRF1/Casp1 axis was investigated in vivo. APE1 IF staining and mRNA levels of IRF1 and caspase 11 were increased in glomeruli of BTBR ob/ob compared to wildtype. In conclusion, ABCA1 deficiency in podocytes caused APE1 accumulation, which reduces transcription factors to increase the expression of IRF1 and IRF1 target inflammasome-related genes, leading to pyroptosispriming.
Egg-mediated maternal effects in a cooperatively breeding cichlid fish
Authors: Reyes-Contreras Maria , de Vries Bonnie , van der Molen J. C. , Groothuis T. G. G. , Taborsky Barbara 
Published: June 2023

AbstractMothers can influence offspring phenotype through egg-mediated maternal effects, which can be influenced by cues mothers obtain from their environment during offspring production. Developing embryos use these components but have mechanisms to alter maternal signals. Here we aimed to understand the role of mothers and embryos in how maternal effects might shape offspring social phenotype. In the cooperatively breeding fish Neolamprologus pulcher different social phenotypes develop in large and small social groups differing in predation risk and social complexity. We manipulated the maternal social environment of N. pulcher females during egg laying by allocating them either to a small or a large social group. We compared egg mass and clutch size and the concentration of corticosteroid metabolites between social environments, and between fertilized and unfertilized eggs to investigate how embryos deal with maternal signalling. Mothers in small groups produced larger clutches but neither laid smaller eggs nor bestowed eggs differently with corticosteroids. Fertilized eggs scored lower on a principal component representing three corticosteroid metabolites, namely 11-deoxycortisol, cortisone, and 11-deoxycorticosterone. We did not detect egg-mediated maternal effects induced by the maternal social environment. We discuss that divergent social phenotypes induced by different group sizes may be triggered by own offspring experience.