bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling Study on the Impacts of Mineral Dust Photocatalytic Heterogeneous Chemistry on the Sulfur Removal Over East Asia
Authors: Li Xiao , Yu Zechen , Yue Man , Liu Yaman , Huang Kan , Chi Xuguang , Nie Wei , Ding Aijun , Dong Xinyi , Wang Minghuai
Published: December 2024

Dust heterogeneous chemistry substantially influences the atmosphere and has profound impacts on our environment and climate. Gas‐particle partitioning on dust not only modifies species' chemical evolutions but also influences their deposition velocity. However, how does dust heterogeneous chemistry impacts acid deposition remains unexplored. In this research, we integrated dust photocatalytic mechanism into GEOS‐Chem to assess its impact on sulfur removal across various regions and time spans in China. We find the photocatalytic mechanism enhances simulation performances of acid deposition. Observational validation demonstrates significant reductions in modeling bias for sulfur dioxide (SO2) dry deposition and sulfate (SO4) total deposition. Additionally, the improved model captures the declining trend of SO4 deposition over 2006–2020. We further identified two key impacts of photocatalytic chemistry: firstly, our findings indicate it enhances sulfur removal more efficiently in near‐desert areas like North China Plain (NCP) than in downwind areas like Yunnan‐Guizhou‐Chongqing region (YGY). Lifetimes of total sulfur reduced from 3.29 to 2.46 days in NCP, and from 2.46 to 1.95 days in YGY. This discrepancy results from faster conversion of SO2 to dust‐phase SO4 and larger proportions of coarse‐mode particles in NCP, resulting in accelerated SO4 deposition velocity. Secondly, our results indicate that because dust photocatalytic chemistry amplifies removal of sulfur through SO4 formation and deposition, decreased dust emission resulted in enhanced sulfur lifetimes over 2006–2014. Sensitivity experiments further show higher dust concentrations accelerate pollutants' removal. These findings underscore the importance of dust heterogeneous chemistry in influencing sulfur deposition, providing scientific insights for mitigating acid deposition in China.
Disorder-specific neurodynamic features in schizophrenia inferred by neurodynamic embedded contrastive variational autoencoder model
Authors: Ding Chaoyue , Sun Yuqing , Li Kunchi , Xie Sangma , Yan Hao , Li Peng , Yan Jun , Chen Jun , Wang Huiling , Wang Huaning , Chen Yunchun , Yang Yongfeng , Lv Luxian , Zhang Hongxing , Lu Lin , Zhang Dai , Chen Yaojing , Zhang Zhanjun , Jiang Tianzi , Liu Bing
Published: December 2024

Neurodynamic models that simulate how micro-level alterations propagate upward to impact macroscopic neural circuits and overall brain function may offer valuable insights into the pathological mechanisms of schizophrenia (SCZ). In this study, we integrated a neurodynamic model with the classical Contrastive Variational Autoencoder (CVAE) to extract and evaluate macro-scale SCZ-specific features, including subject-level, region-level parameters, and time-varying states. Firstly, we demonstrated the robust fitting of the model within our multi-site dataset. Subsequently, by employing representational similarity analysis and a deep learning classifier, we confirmed the specificity and disorder-related information capturing ability of SCZ-specific features. Moreover, analysis of the attractor characteristics of the neurodynamic system revealed significant differences in attractor space patterns between SCZ-specific states and shared states. Finally, we utilized Partial Least Squares (PLS) regression to examine the multivariate mapping relationship between SCZ-specific features and symptoms, identifying two sets of correlated modes implicating unique molecular mechanisms: one mode corresponding to negative and general symptoms, and another mode corresponding to positive symptoms. Our results provide valuable insights into disorder-specific neurodynamic features and states associated with SCZ, laying the foundation for understanding the intricate pathophysiology of this disorder.
Metabolic shifts in lipid utilization and reciprocal interactions within the lung metastatic niche of triple-negative breast cancer revealed by spatial multi-omics
Authors: Kan Jung-Yu , Lee Hsiao-Chen , Hou Ming-Feng , Tsai Hung-Pei , Jian Shu-Fang , Chang Chao-Yuan , Tsai Pei-Hsun , Lin Yi-Shiuan , Tsai Ying-Ming , Wu Kuan-Li , Huang Yung-Chi , Hsu Ya-Ling
Published: December 2024

The Triple-Negative Breast Cancer (TNBC) subtype constitutes 15-20% of breast cancer cases and is associated with the poorest clinical outcomes. Distant metastasis, particularly to the lungs, is a major contributor to the high mortality rates in breast cancer patients. Despite this, there has been a lack of comprehensive insights into the heterogeneity of metastatic tumors and their surrounding ecosystem in the lungs. In this study, we utilized spatial RNA sequencing technology to investigate the heterogeneity of lung metastatic tumors and their microenvironment in two spontaneous lung metastatic mouse models. Our findings revealed an increase in metabolic-related genes within the cancer cells, with the hub gene Dlat (Dihydrolipoamide S-Acetyltransferase) showing a significant association with the development of lung metastatic tumors. Upregulation of Dlat led to the reprogramming of fatty acid utilization, markedly enhancing the bioenergetic capacity of cancer cells. This finding was corroborated by the increased dependence on fatty acid utilization in lung metastatic cancer cells, and inhibition of Dlat in breast cancer cells exhibited a reduced oxygen consumption rate. Consequently, inhibition of Dlat resulted in decreased survival capacity of breast cancer by reducing cancer stem cell properties and cell adhesion in the lung in vivo. The three cell components within the lung metastatic niche, including CD163+ macrophages, neutrophils, and endothelial cells, expressed elevated levels of ApoE, leading to the secretion of various protumorigenic molecules that promote cancer cell growth in the lung. These molecules include galectin-1, S100A10, S100A4, and S100A6. Collectively, our findings highlight the lipid metabolism reprogramming of cancer and components of the tumor microenvironment that support lung metastasis of TNBC breast cancer.
Tumor- and host-derived heparanase-2 (Hpa2) attenuates tumorigenicity: role of Hpa2 in macrophage polarization and BRD7 nuclear localization
Authors: Soboh Soaad , Vorontsova Avital , Farhoud Malik , Barash Uri , Naroditsky Inna , Gross-Cohen Miriam , Weissmann Marina , Nishioka Yasuhiko , Woolf Adrian S. , Roberts Neil A. , Shaked Yuval , Ilan Neta , Vlodavsky Israel
Published: December 2024

Little attention was given to heparanase 2 (Hpa2) over the last two decades, possibly because it lacks a heparan sulfate (HS)-degrading activity typical of heparanase. Emerging results suggest, nonetheless, that Hpa2 plays a role in human pathologies, including cancer progression where it functions as a tumor suppressor. Here, we examined the role of Hpa2 in cervical carcinoma. We report that high levels of Hpa2 correlate with prolonged survival of cervical carcinoma patients. Strong staining intensity of Hpa2 also correlates with low tumor grade. Overexpression of Hpa2 in SiHa cervical carcinoma cells resulted in tumor xenografts that were two-fold smaller than control tumors. Interestingly, even smaller tumor xenografts were developed by SiHa cells overexpressing the Pro140Arg and Asn543Ile Hpa2 missense mutations that were identified in patients diagnosed with urofacial syndrome (UFS). Utilizing the Ras recruitment system, we identified bromodomain-containing protein 7 (BRD7) to interact with Hpa2 and found that both BRD7 and the Hpa2 mutants are translocated to the cell nucleus in tumors developed by the Pro140Arg and Asn543Ile Hpa2 mutants. Utilizing our newly developed conditional Hpa2-KO mice, we further show that Hpa2 plays a critical role in macrophage polarization; in the absence of Hpa2, macrophages are shifted towards pro-tumorigenic, M2 phenotype. Notably, implanting SiHa cervical carcinoma cells together with Hpa2-KO macrophages promoted tumor growth. These results support, and further expand, the notion that Hpa2 functions as a tumor suppressor, co-operating with another tumor suppressor, BRD7.
LOC730101 improves ovarian cancer drug sensitivity by inhibiting autophagy-mediated DNA damage repair via BECN1
Authors: Zhong Yancheng , Shuai Yang , Yang Juan , Zhang Mojian , He Tiantian , Zheng Leliang , Yang Sheng , Peng Shuping
Published: December 2024

Drug resistance and recurrence are still the bottlenecks in the clinical treatment of ovarian cancer (OC), seriously affecting patients’ prognosis. Therefore, it is an urgent challenge for OC to be overcome towards precision therapy by studying the mechanism of OC drug resistance, finding new drug resistance targets and developing new effective treatment strategies. In this study, we found that lncRNA LOC730101 played an essential role in attenuating drug resistance in OC. LOC730101 was significantly down-regulated in platinum-resistant ovarian cancer tissues, and ectopic overexpression of LOC730101 substantially increased chemotherapy-induced apoptosis. Mechanistically, LOC730101 specifically binds to BECN1 and inhibits the formation of autophagosome BECN1/VPS34 by reducing phosphorylation of BECN1, thereby inhibiting autophagy and promoting drug sensitivity in ovarian cancer cells following treatment with cisplatin and PARP inhibitors. Moreover, LOC730101 inhibits the expression and activity of RNF168 via p62, which in turn affects H2A ubiquitination-mediated DNA damage repair and promotes drug sensitivity in ovarian cancer cells. Our findings demonstrated that LOC730101 played an important role in regulating the formation of the autophagic complex and that inhibition of autophagy significantly enhances the drug sensitivity of OC. And LOC730101 may be used as a prognostic marker to predict the sensitivity of OC to platinum and PARP inhibitors.
miR-184, a downregulated ovary-elevated miRNA transcriptionally activated by SREBF2, exerts anti-apoptotic properties in ovarian granulosa cells through inducing SMAD3 expression
Authors: Shan Baosen , Huo Yangan , Guo Zhennan , Li Qiqi , Pan Zengxiang , Li Qifa , Du Xing
Published: December 2024

Follicular atresia is the primary threat to female fertility. miRNAs are dysregulated in granulosa cells (GCs) during follicular atresia, and have emerged as crucial regulators of the initiation and progression of follicular atresia. However, the downregulated ovary-elevated (OE) miRNAs and their biological functions in ovary remain elusive. Here, 13 downregulated OE miRNAs were systematically identified by integrating tissue expression high-throughput data and comparative transcriptome analyses, among which miR-184 was specifically highly expressed in ovary but dramatically downregulated during follicular atresia. Low miR-184 levels were also positively correlated with follicular atresia. Based on the in vitro GC and follicle culture system, we found that miR-184 suppressed GC apoptosis and follicular atresia. Mechanistically, miR-184 induced SMAD3 transcription by acting as a saRNA, and also stabilized SMAD3 mRNA by directly binding to its 5′-UTR, which promoted TGF-β pathway activity and its anti-apoptotic effect. In addition, miR-184 was transcribed independently of host gene, which was activated by SREBF2 in an H3K4me3-dependent manner. Comparative analysis revealed that SREBF2 expression and H3K4me3 enrichment on miR-184 promoter in GCs from atretic follicles were dramatically reduced, which leads to the downregulation of miR-184 during follicular atresia. Moreover, the expression pattern, function, target, and regulatory mechanism of miR-184 among mammals are highly conserved and universal. Taken together, our findings demonstrate that miR-184, transcriptionally activated by SREBF2 in an H3K4me3-dependent manner, exerts anti-atretic effects by inducing SMAD3 expression, highlighting that it is a promising regulator for improving follicular development, ovarian health and female fertility.
Downregulation of tRNA methyltransferase FTSJ1 by PM2.5 promotes glycolysis and malignancy of NSCLC via facilitating PGK1 expression and translation
Authors: Wang Yiling , Wen Yuxin , Chen Qianqian , Huang Yongyi , Zhou Duanyang , Yang Wenhan , Yang Lin , Xiong Juan , Gao Kaiping , Sun Liyuan , Zhai Rihong
Published: December 2024

Fine particulate matter (PM2.5) exposure has been associated with increased incidence and mortality of lung cancer. However, the molecular mechanisms underlying PM2.5 carcinogenicity remain incompletely understood. Here, we identified that PM2.5 suppressed the expression of tRNA methyltransferase FTSJ1 and Am modification level of tRNA in vitro and in vivo. FTSJ1 downregulation enhanced glycolytic metabolism of non-small cell lung cancer (NSCLC) cells, as indicated by increased levels of lactate, pyruvate, and extracellular acidification rate (ECAR). Whereas treatment with glycolytic inhibitor 2-DG reversed this effect. In contrast, upregulation of FTSJ1 significantly suppressed glycolysis of NSCLC cells. Mechanistically, the silencing of FTSJ1 increased NSCLC cell proliferation and glycolysis through enhancing the expression and translation of PGK1. In human NSCLC tumor samples, FTSJ1 expression was negatively correlated with PGK1 expression level and the SUVmax value of PET/CT scan. In summary, our work reveals a previously unrecognized function of PM2.5-downregulated FTSJ1 on PGK1-mediated glycolysis in NSCLC, suggesting that targeted upregulation of FTSJ1 may represent a potential therapeutic strategy for NSCLC.
A20 negatively regulates necroptosis-induced microglia/macrophages polarization and mediates cerebral ischemic tolerance via inhibiting the ubiquitination of RIP3
Authors: Qiu Meiqian , Zhang Wenhao , Dai Jiahua , Sun Weiwen , Lai Meijing , Tang Shiyi , Xu En , Ning Yuping , Zhan Lixuan
Published: December 2024

Neuronal necroptosis appears to be suppressed by the deubiquitinating enzyme A20 and is capable to regulate the polarization of microglia/macrophages after cerebral ischemia. We have demonstrated that hypoxic preconditioning (HPC) can alleviate receptor interacting protein 3 (RIP3)-induced necroptosis in CA1 after transient global cerebral ischemia (tGCI). However, it is still unclear whether HPC serves to regulate the phenotypic polarization of microglia/macrophages after cerebral ischemia by mitigating neuronal necroptosis. We hence aim to elucidate the underlying mechanism(s) by which the ubiquitination of RIP3-dependent necroptosis regulated by A20 affects microglia/macrophages phenotype after cerebral ischemic tolerance. We found that microglia/macrophages in CA1 of rats underwent M1 and M2 phenotypic polarization in response to tGCI. Notably, the treatment with HPC, as well as inhibitors of necroptosis, including Nec-1 and mixed lineage kinase domain-like (MLKL) siRNA, attenuated neuroinflammation associated with M1 polarization of microglia/macrophages induced by tGCI. Mechanistically, HPC was revealed to upregulate A20 and in turn enhance the interaction between A20 and RIP3, thereby reducing K63-linked polyubiquitination of RIP3 in CA1 after tGCI. Consequently, RIP3-dependent necroptosis and the M1 polarization of microglia/macrophages were blocked either by HPC or via overexpression of A20 in neurons, which ultimately mitigated cerebral injury in CA1 after tGCI. These data support that A20 serves as a crucial mediator of microglia/macrophages polarization by suppressing neuronal necroptosis in a RIP3 ubiquitination-dependent manner after tGCI. Also, a novel mechanism by which HPC functions in cerebral ischemic tolerance is elucidated.
CUL4B protects kidneys from acute injury by restraining p53/PAI-1 signaling
Authors: Liu Kaixuan , Hao Xiaoyu , Gao Yangfan , Cao Zhiyuan , Hou Min , Qin Lining , Song Yu , Wang Molin , Jiang Baichun , Liu Qiao , Zou Yongxin , Gong Yaoqin , Liu Guangyi , Sun Gongping
Published: December 2024

Acute kidney injury (AKI) caused by nephrotoxins, ischemia reperfusion (IR) or sepsis is associated with high morbidity and mortality. Unveiling new mechanisms underlying AKI can help develop new therapeutic strategy. Cullin 4B (CUL4B) is a scaffold protein in the CUL4B-RING E3 ubiquitin ligase (CRL4B) complex. Here, we demonstrate that CUL4B can protect kidneys from acute injury induced by cisplatin and IR. CUL4B is upregulated in mouse tubular epithelial cells (TECs) after cisplatin treatment or IR. Loss of CUL4B in kidneys exacerbates renal injury, inflammation, and apoptosis of TECs caused by cisplatin and IR. Transcriptome analysis reveals that Cul4b deficiency enhances injury-induced PAI-1 expression. CUL4B suppresses PAI-1 expression by promoting polyubiquitination and degradation of p53. Inhibition of either PAI-1 or p53 can prevent the aggravated renal injury and inflammation caused by loss of CUL4B. Our work has identified the kidney-protective role of CUL4B against acute injury.
DARPins as a novel tool to detect and degrade p73
Authors: Münick Philipp , Zielinski Jasmin , Strubel Alexander , Gutfreund Niklas , Dreier Birgit , Schaefer Jonas V. , Schäfer Birgit , Gebel Jakob , Osterburg Christian , Chaikuad Apirat , Knapp Stefan , Plückthun Andreas , Dötsch Volker
Published: December 2024

The concept of Targeted Protein Degradation (TPD) has been introduced as an attractive alternative to the development of classical inhibitors. TPD can extend the range of proteins that can be pharmacologically targeted beyond the classical targets for small molecule inhibitors, as a binding pocket is required but its occupancy does not need to lead to inhibition. The method is based on either small molecules that simultaneously bind to a protein of interest and to a cellular E3 ligase and bring them in close proximity (molecular glue) or a bi-functional molecule synthesized from the chemical linkage of a target protein-specific small molecule and one that binds to an E3 ligase (Proteolysis Targeting Chimeras (PROTAC)). The further extension of this approach to bioPROTACs, in which a small protein-based binding module is fused directly to an E3 ligase or an E3 ligase adaptor protein, makes virtually all proteins amenable to targeted degradation, as this method eliminates the requirement for binding pockets for small molecules. Designed Ankyrin Repeat Proteins (DARPins) represent a very attractive class of small protein-based binding modules that can be used for the development of bioPTOTACS. Here we describe the characterization of two DARPins generated against the oligomerization domain and the SAM domain of the transcription factor p73, a member of the p53 protein family. The DARPins can be used for (isoform-)selective pulldown experiments both in cell culture as well as primary tissue lysates. We also demonstrate that they can be used for staining in cell culture experiments. Fusing them to the speckle type POZ protein (SPOP), an adaptor protein for cullin-3 E3 ligase complexes, yields highly selective and effective degraders. We demonstrate that selective degradation of the ΔNp73α isoform reactivates p53.
SMURF1 and SMURF2 directly target GLI1 for ubiquitination and proteasome-dependent degradation
Authors: Bordin Fabio , Terriaca Gloria , Apostolico Adriano , Di Fiore Annamaria , Mir Faranak Taj , Bellardinelli Sara , Bufalieri Francesca , Bordone Rosa , Bellardinilli Francesca , Giannini Giuseppe , Canettieri Gianluca , Di Marcotullio Lucia , Ferretti Elisabetta , Moretti Marta , De Smaele Enrico
Published: December 2024

The transcription factor GLI1 is the main and final effector of the Hedgehog signaling pathway, which is involved in embryonic development, cell proliferation and stemness. Whether activated through canonical or non-canonical mechanisms, GLI1 aberrant activity is associated with Hedgehog-dependent cancers, including medulloblastoma, as well as other tumoral contexts. Notwithstanding a growing body of evidence, which have highlighted the potential role of post translational modifications of GLI1, the complex mechanisms modulating GLI1 stability and activity have not been fully elucidated. Here, we present a novel role played by SMURF1 and SMURF2 in the suppression of the Hedgehog/GLI signaling pathway through a direct targeting of GLI1. Indeed, the two SMURFs can interact with GLI1, exploiting the proline rich regions present on GLI1 protein, and trigger its polyubiquitination and proteasomal degradation, leading to a suppression of the Hedgehog pathway activity and a reduction of Hh-dependent tumor cell proliferation. Overall, this study adds new relevance to a tumor suppressive role of SMURFs on the Hedgehog pathway and confers upon them the status of potential therapeutic tools, either in canonical or non-canonical Hedgehog pathway aberrant activation.
Structural mechanism of CB1R binding to peripheral and biased inverse agonists
Authors: Kumari Punita , Dvorácskó Szabolcs , Enos Michael D. , Ramesh Karthik , Lim Darrix , Hassan Sergio A. , Kunos George , Cinar Resat , Iyer Malliga R. , Rosenbaum Daniel M.
Published: December 2024

The cannabinoid receptor 1 (CB1R) regulates synaptic transmission in the central nervous system, but also has important roles in the peripheral organs controlling cellular metabolism. While earlier generations of brain penetrant CB1R antagonists advanced to the clinic for their effective treatment of obesity, such molecules were ultimately shown to exhibit negative effects on central reward pathways that thwarted their further therapeutic development. The peripherally restricted CB1R inverse agonists MRI-1867 and MRI-1891 represent a new generation of compounds that retain the metabolic benefits of CB1R inhibitors while sparing the negative psychiatric effects. To understand the mechanism of binding and inhibition of CB1R by peripherally restricted antagonists, we developed a nanobody/fusion protein strategy for high-resolution cryo-EM structure determination of the GPCR inactive state, and used this method to determine structures of CB1R bound to either MRI-1867 or MRI-1891. These structures reveal how these compounds retain high affinity and specificity for CB1R’s hydrophobic orthosteric site despite incorporating polar functionalities that lead to peripheral restriction. Further, the structure of the MRI-1891 complex along with accompanying molecular dynamics simulations shows how differential engagement with transmembrane helices and the proximal N-terminus can propagate through the receptor to contribute to biased inhibition of β-arrestin signaling.
On the equilibrium limit of liquid stability in pressurized aqueous systems
Authors: Zarriz Arian , Journaux Baptiste , Powell-Palm Matthew J.
Published: December 2024

Phase stability, and the limits thereof, are a central concern of materials thermodynamics. However, the temperature limits of equilibrium liquid stability in chemical systems have only been widely characterized under constant (typically atmospheric) pressure conditions, whereunder these limits are represented by the eutectic. At higher pressures, the eutectic will shift in both temperature and chemical composition, opening a wide thermodynamic parameter space over which the absolute limit of liquid stability, i.e., the limit under arbitrary values of the thermodynamic forces at play (here pressure and concentration), might exist. In this work, we use isochoric freezing and melting to measure this absolute limit for the first time in several binary aqueous brines, and nodding to the etymology of “eutectic”, we name it the “cenotectic” (from Greek “κοινός-τῆξῐς”, meaning “universal-melt”). We discuss the implications of our findings on ocean worlds within our solar system and cold ocean exoplanets; estimate thermodynamic limits on ice crust thickness and final ocean depth (of the cenotectic or “endgame” ocean) using measured cenotectic pressures; and finally provide a generalized thermodynamic perspective on (and definition for) this fundamental thermodynamic invariant point.
Protein purification with light via a genetically encoded azobenzene side chain
Authors: Mayrhofer Peter , Anneser Markus R. , Schira Kristina , Sommer Carina A. , Theobald Ina , Schlapschy Martin , Achatz Stefan , Skerra Arne
Published: December 2024

Affinity chromatography is the method of choice for the rapid purification of proteins from cell extracts or culture supernatants. Here, we present the light-responsive Azo-tag, a short peptide comprising p-(phenylazo)-L-phenylalanine (Pap), whose side chain can be switched from its trans-ground state to the metastable cis-configuration by irradiation with mild UV light. Since only trans-Pap shows strong affinity to α-cyclodextrin (α-CD), a protein exhibiting the Azo-tag selectively binds to an α-CD chromatography matrix under daylight or in the dark but elutes quickly under physiological buffer flow when illuminating the column at 355 nm. We demonstrate the light-controlled single-step purification – termed Excitography – of diverse proteins, including enzymes and antibody fragments, without necessitating competing agents or harsh buffer conditions as normally applied. While affinity chromatography has so far been governed by chemical interactions, introducing control by electromagnetic radiation as a physical principle adds another dimension to this widely applied separation technique.
Enabling dynamic 3D coherent diffraction imaging via adaptive latent space tuning of generative autoencoders
Authors: Scheinker Alexander , Pokharel Reeju
Published: December 2024

Coherent diffraction imaging (CDI) is an advanced non-destructive 3D X-ray imaging technique for measuring a sample’s electron density. The main challenge of CDI is loss of phase information in diffraction intensity measurements, resulting in lengthy iterative reconstruction processes that can return non-unique solutions, which pose challenges for experiments attempting to track dynamic sample evolution through multiple states. As the increased brightness of fourth-generation light sources enables faster sample measurements and drives operando experiments with Bragg CDI, there is a growing need for faster reconstruction techniques that can keep pace. We have developed an adaptive generative autoencoder approach for uniquely tracking a sample’s electron density as it dynamically evolves. Our approach adaptively tunes the low-dimensional latent embedding of a generative autoencoder, enabling a computationally efficient manner to account for time-varying shifting distributions in real-time. Analytic proof of convergence is provided as well as numerical demonstration of sample tracking with noisy measurements.
Two decades of three-dimensional movement data from adult female northern elephant seals
Authors: Costa Daniel P. , Holser Rachel R. , Keates Theresa R. , Adachi Taiki , Beltran Roxanne S. , Champagne Cory D. , Crocker Daniel E. , Favilla Arina B. , Fowler Melinda A. , Gallo-Reynoso Juan Pablo , Goetsch Chandra , Hassrick Jason L. , Hückstädt Luis A. , Kendall-Bar Jessica M. , Kienle Sarah S. , Kuhn Carey E. , Maresh Jennifer L. , Maxwell Sara M. , McDonald Birgitte I. , McHuron Elizabeth A. , Morris Patricia A. , Naito Yasuhiko , Pallin Logan J. , Peterson Sarah H. , Robinson Patrick W. , Simmons Samantha E. , Takahashi Akinori , Teuschel Nicole M. , Tift Michael S. , Tremblay Yann , Villegas-Amtmann Stella , Yoda Ken
Published: December 2024

Northern elephant seals (Mirounga angustirostris) have been integral to the development and progress of biologging technology and movement data analysis, which continue to improve our understanding of this and other species. Adult female elephant seals at Año Nuevo Reserve and other colonies along the west coast of North America were tracked annually from 2004 to 2020, resulting in a total of 653 instrument deployments. This paper outlines the compilation and curation process of these high-resolution diving and location data, now accessible in two Dryad repositories. The code used for data processing alongside the corresponding workflow is available through GitHub and Zenodo. This data set represents 3,844,927 dives and 596,815 locations collected from 475 individual seals with 178 repeat samplings over 17 years. We anticipate that these data will stimulate further analysis and investigation into elephant seal biology and aid in developing new analytical approaches for large marine predators.
Active and passive organic carbon fluxes during a bloom in the Southern Ocean (South Georgia)
Authors: Major William , Giering Sarah L. C. , Ainsworth Joanna , Belcher Anna , Blackbird Sabena , Bridger Martin , Briggs Nathan , Carvalho Filipa , Clément Louis , Cook Kathryn , Dumousseaud Cynthia , Espinola Benoit , Evans Claire , Fielding Sophie , Hartmann Manuela , Henson Stephanie , Iversen Morten , Kiriakoulakis Konstadinos , Lampitt Richard , Lovecchio Elisa , Martin Adrian , Mayor Dan , Moore Mark , Pabortsava Katsiaryna , Pebody Corinne , Peel Kate , Preece Calum , Poulton Alex , Rayne Rachel , Saw Kevin , Stinchcombe Mark , Stowasser Gabriele , Tarling Geraint A. , Thomalla Sandy , Villa-Alfageme María , Wolff George A. , Sanders Richard
Published: December 2024

The Controls Over Mesopelagic Interior Carbon Storage (COMICS) cruise DY086 took place aboard the RRS Discovery in the South Atlantic during November and December, 2017. Physical, chemical, biogeochemical and biological data were collected during three visits to ocean observatory station P3, off the coast of South Georgia, during an austral spring bloom. A diverse range of equipment including CTD-rosette, Acoustic Doppler Current Profiler (ADCP), net deployments, marine snow catchers (MSCs), Stand Alone Pump System (SAPS) and PELAGRA Sediment Traps were used to produce a comprehensive, high-quality dataset. The data can provide excellent insight into regional biological carbon pump (BCP) processes; it is recommended for use by observational scientists and modellers to enhance understanding of ecosystem interactions relating to mesopelagic carbon storage.
Chromosome-scale assembly of the African yam bean genome
Authors: Waweru Bernice , Njaci Isaac , Paliwal Rajneesh , Maranga Mary , Muli Collins , Murungi Edwin , Kaimenyi Davies , Lyimo Beatus , Nigussie Helen , Ahadi Bwihangane Birindwa , Assefa Ermias , Ishag Hassan , Olomitutu Oluwaseyi , Abberton Michael , Darby Christopher , Uauy Cristobal , Yao Nasser , Adewale Daniel , Emmrich Peter , Entfellner Jean-Baka Domelevo , Shorinola Oluwaseyi
Published: December 2024

Genomics-informed breeding of locally adapted, nutritious, albeit underutilised African crops can help mitigate food and nutrition insecurity challenges in Africa, particularly against the backdrop of climate change. However, utilisation of modern genome-assisted crop improvement tools including genomic selection and genome editing for many African indigenous crops is hampered by the scarcity of genomic resources. Here we report on the assembly of the genome of African yam bean (Sphenostylis stenocarpa), a tuberous legume crop that is indigenous to Africa. By combining Nanopore-based assembly with Hi-C scaffolding, we produced a high-quality chromosome-scale assembly with an N50 of 69.5 Mbp. Using transcriptome evidence from Nanopore RNASeq and protein homology evidence from related crops, we predicted and annotated 31,614 putative protein coding genes. We also show how this genome substantially improves anchoring of genetic markers from African yam bean, confirming its significance as a resource for genetic research in African yam bean.
A dataset for 15N natural abundance of soil ammonia volatilization
Authors: Peng Lingyun , Ti Chaopu , Yin Bin , Bai Xiao , Li Miao , Tao Limin , Yan Xiaoyuan
Published: December 2024

Investigating the sources of ammonia (NH3) in the atmosphere and the contribution of each source is essential for environmental pollution control. The presented dataset aims to provide 15N natural abundance (δ15N) data collected from different controlled treatments to fill the knowledge gap between insufficient data of soil δ15N-NH3 and accurately identifying atmospheric NH3 source apportionments. Our results showed that the overall δ15N-NH3 values emitted from soil ranged from −46.09 to 10.22‰, with an average of −26.81 ± 11.17‰. The mean δ15N-NH3 values under different nitrogen (N) application rates, N fertilizer types, air temperatures, soil moisture, soil pH, soil types, and land use types were −29.41 ± 10.91, −32.43 ± 6.86, −29.10 ± 10.04, −30.31 ± 6.18, −24.84 ± 13.76, −23.53 ± 7.66, and −14.57 ± 12.54‰, respectively. Significant correlations were observed between δ15N-NH3 values and soil pH, soil NO3−-N concentration, and NH3 volatilization. This unique database provides basic data and evidence for the qualification of atmospheric NH3 source apportionments under different study area conditions.
Sardinian deer increase feeding diversity within sheltering vegetation in a fragmented Mediterranean landscape
Authors: Aboling Sabine , Ahmed Fahad , Kreisel Gunnar , Kamphues Josef , Cappai Maria Grazia
Published: December 2024

This study was carried out to investigate the feeding behavior of Sardinian deer roaming within a site of community interest (SCI, ITB042250), on Sardinian Island (39° 51’ N 8° 45’ E). Crop fields bordering the natural environment (wood forest and Mediterranean macchia, where the reserve of Sardinian deer partly overlaps) were monitored and turned into a living lab. The interest on wildlife-related crop damage poses a significant economic challenge, while anthropogenic pressures, such as urbanization and agricultural practices, increasingly impact wildlife by limiting habitat, feeding source diversity and access, and space distribution. In view of this, dietary habits of a group of 25 Sardinian deer (Cervus elaphus corsicanus Erxleben, 1777) were studied over an area of 45 hectares, in spring and autumn over two consecutive years. Within six representative sites (habitats) of investigation (SOI = 3 ha), two transects of 20 × 10 m per SOI, amounting to 240 m², served as parts of these sites, respectively, and were analyzed as to floristic composition and dominating plants. The number of freshly browsed/grazed plants by missing shoots was counted and assumed as signs of foraging activity of the Sardinian deer. The evenness of the dietary preference per habitat was calculated with the number of missing shoots and the number of plant species selected. The Mediterranean macchia accounted for the highest species (n = 76); crop field the fewest species (n = 19). Plants showing foraging signs by Sardinian deer ranged between n. 5 out of 46 species (10.9%) in the fallow and n. 6 out of 19 species (31.6%) in the crop field. Complementary feeding based on the availability of floristic diversity revealed to align to the typical foraging behavior of intermediate feeder in all SOIs: the higher the species, the higher the number of foraged species (ρ = 0.86). Sardinian deer foraged on n. 35 out of 129 plant species present (27.1%) within the whole transect area. Data highlight two feeding behavior: 1)high evenness-feeding (less foraging on high number of plant species, respectively: fallow, crop field, macchia border); 2) low evenness-feeding (large foraging on few species, Avena or Cytisus: field, bordering both macchia and fallow, macchia).The Sardinian deer fed on every SOI, with highest consumption in the macchia and least in oat open field. The feeding behavior of Sardinian deer confirms the ability to adapt to the varying vegetation in each habitat, respectively, by seeking energy and nutrients on the one hand and shelter on the other, by limiting the preference for crop field center.
Psychometric validation of the Vaccination Attitudes Examination (VAX) scale in German pre-pandemic and mid-pandemic samples
Authors: Wilhelm Marcel , Bender Friederike L. , Euteneuer Frank , Salzmann Stefan , Ewen Anne-Catherine I. , Rief Winfried
Published: December 2024

Despite the public health value of immunizations, vaccine hesitancy is a widespread phenomenon and received special attention during the global COVID-19 pandemic. The Vaccination Attitudes Examination (VAX) Scale aims to identify anti-vaccination attitudes for understanding vaccine hesitancy. The present study is the validation of the German version of the VAX scale in pre-/mid-pandemic samples. All individuals completed an online-survey assessing prior and expected future vaccination behaviors, further constructs associated with vaccine hesitancy, as well as anti-vaccination attitudes using the translated VAX scale among others. In a first study, 297 individuals were surveyed before the COVID-19 pandemic. A second study included 260 individuals recruited during the COVID-19 pandemic. For validation, two confirmatory factor analyses have been conducted. Reliability measures (internal consistency, test–retest-correlation) were determined. The four subscales were confirmed by Confirmation Factor Analysis with a very good to excellent fit. The subscales showed good to excellent reliability and convergent validity determinants. Average VAX values significantly distinguished between individuals who had previously received or refused immunization and predicted expected vaccination behavior. The German translation of the VAX scale is effective in identifying anti-vaccination attitudes and can be used for further research on anti-vaccination attitudes and vaccine hesitancy.
Implantable silicon neural probes with nanophotonic phased arrays for single-lobe beam steering
Authors: Chen Fu-Der , Sharma Ankita , Xue Tianyuan , Jung Youngho , Govdeli Alperen , Mak Jason C. C. , Chameh Homeira Moradi , Movahed Mandana , Brunk Michael G. K. , Luo Xianshu , Chua Hongyao , Lo Patrick Guo-Qiang , Valiante Taufik A. , Sacher Wesley D. , Poon Joyce K. S.
Published: December 2024

In brain activity mapping with optogenetics, patterned illumination is crucial for targeted neural stimulation. However, due to optical scattering in brain tissue, light-emitting implants are needed to bring patterned illumination to deep brain regions. A promising solution is silicon neural probes with integrated nanophotonic circuits that form tailored beam patterns without lenses. Here we propose neural probes with grating-based light emitters that generate a single steerable beam. The light emitters, optimized for blue or amber light, combine end-fire optical phased arrays with slab gratings to suppress higher-order sidelobes. In vivo experiments in mice demonstrated that the optical phased array provided sufficient power for optogenetic stimulation. While beam steering performance in tissue reveals challenges, including beam broadening from scattering and the need for a wider steering range, this proof-of-concept demonstration illustrates the design principles for realizing compact optical phased arrays capable of continuous single-beam scanning, laying the groundwork for advancing optical phased arrays toward targeted optogenetic stimulation.
Biased expectations about future choice options predict sequential economic decisions
Authors: van de Wouw Didrika S. , McKay Ryan T. , Furl Nicholas
Published: December 2024

Considerable research has shown that people make biased decisions in “optimal stopping problems”, where options are encountered sequentially, and there is no opportunity to recall rejected options or to know upcoming options in advance (e.g. when flat hunting or choosing a spouse). Here, we used computational modelling to identify the mechanisms that best explain decision bias in the context of an especially realistic version of this problem: the full-information problem. We eliminated a number of factors as potential instigators of bias. Then, we examined sequence length and payoff scheme: two manipulations where an optimality model recommends adjusting the sampling rate. Here, participants were more reluctant to increase their sampling rates when it was optimal to do so, leading to increased undersampling bias. Our comparison of several computational models of bias demonstrates that many participants maintain these relatively low sampling rates because of suboptimally pessimistic expectations about the quality of future options (i.e. a mis-specified prior distribution). These results support a new theory about how humans solve full information problems. Understanding the causes of decision error could enhance how we conduct real world sequential searches for options, for example how online shopping or dating applications present options to users.
Advances in 4-π-photocyclization reactions
Authors: Coote Susannah C.
Published: December 2024

A review of recent advances in 4-π-photocyclization reactions is presented, including an overview of the current substrate scope, innovations in scale-up, and applications of the strained cyclobutene products as versatile building blocks in drug discovery and total synthesis, as strained monomers for novel polymers suitable for post-polymerization derivatization, and as precursors to reactive intermediates such as cyclobutadienes.
Delayed fluorescence in anoxygenic photosynthesis
Authors: Trotta Massimo , Maróti Péter
Published: December 2024

A survey of the most recent advancements in the field of delayed fluorescence (DF) emission has been reported in the present chapter.
Photocycloadditions of aromatic compounds with alkenes: the role of spin multiplicity
Authors: Hoffmann Norbert , Desvals Arthur
Published: December 2024

Attractive for applications to organic synthesis, photocycloadditions of electronically excited benzene derivatives with alkenes represent an interesting example of photochemical reactions that cause complete changes in the reaction. Starting from simple compounds, in only one step, the photochemical reaction, a high degree of molecular complexity and diversity is generated without using a chemical reagent. Another important aspect is the use of benzene derivatives and alkenes to build up complex three dimensional structures by the transformation of sp2 into sp3 hybridized carbons. These reactions can find important applications in pharmaceutical chemistry and are the basis of this review.
NMR of Metal Centers and Doped Metals in MOFs and COFs
Authors: Chen Shoushun , Lucier Bryan E. G. , Du Xin , Peng Yun-lei , Huang Yining
Published: December 2024

There have been tremendous advances in the fields of metal–organic frameworks (MOFs) and covalent-organic frameworks (COFs) over the past two decades. The rapidly expanding number of MOFs and COFs, along with their various associated properties, has highlighted the need for effective structural characterization routes in order to elucidate structure–property relationships. Solid-state nuclear magnetic resonance (SSNMR) spectroscopy provides unique insights that are helpful for understanding and rationalizing the local structure of various materials. In this chapter, we summarize the significant number of studies from the last 15 years which have used SSNMR to examine incorporated metal centers and dopant metals in MOFs and COFs, with targets ranging from spin-1/2 nuclei such as 111Cd and 207Pb to challenging quadrupolar nuclei including 25Mg, 47/49Ti, 43Ca, 67Zn and 115In. Examples of the detailed information available from metal SSNMR are provided, illustrating how this technique can shed light on the local structure around the target metal, investigate host–guest interactions, and monitor changes in the MOF structure. General acquisition strategies for metal SSNMR spectra of MOFs and COFs are also discussed.
Dynamic Nuclear Polarization-enhanced NMR and Its Applications for the Structural Investigation of MOFs and COFs
Authors: Cao Wei , Lucier Bryan E. G. , Wang Wei
Published: December 2024

Dynamic nuclear polarization (DNP) is a cutting-edge technique designed to enhance NMR signal intensities and overcome the intrinsically low sensitivity of NMR spectroscopy. The DNP transfer of spin polarization from unpaired electrons to the surrounding nuclei results in signal enhancement by two to three orders of magnitude. In this chapter, we first provide an introduction to DNP, and then focus on the applications of DNP-enhanced NMR for structural characterization of metal–organic frameworks (MOFs) and covalent organic frameworks (COFs). The tremendous sensitivity improvements provided by DNP, along with the advent of high magnetic fields and NMR probes capable of fast and ultra-fast magic angle spinning (MAS) rates, now allow researchers to answer various questions regarding MOFs and COFs that cannot be addressed by conventional solid-state NMR spectroscopy or other characterization techniques. With the aid of DNP, very challenging NMR experiments have been proven to be feasible; DNP has been used to perform typically insensitive 27Al–13C 2D experiments, obtain ultra-wideline 195Pt NMR spectra over 10 000 ppm in breadth, and acquire high-resolution quadrupolar-broadened 17O NMR spectra, among other applications. Furthermore, MOFs and COFs can also act as a matrix for polarizing agents, permitting the homogeneous distribution of radicals and offering promise for further DNP enhancement of framework and guest NMR signals. The current body of published work regarding DNP of MOFs and COFs shows tremendous promise in this experimental avenue and clearly indicates that this will be an active field of research in the years to come.
Label-free miRNA fluorescent biosensors based on duplex-specific nucleases and silver nanoclusters
Authors: Zheng Yuxin , Wang Qian , Jin Zhiying , Zhang Tingting , Huang Jianshe , Ye Jianshan , Yang Xiurong
Published: December 2024

Herein, we constructed a novel fluorescent biosensor for the detection of miRNA-155 based on duplex specific nuclease assisted amplification and DNA-templated silver nanoclusters as fluorescence signal probes. This work provides a potential universal biosensing platform for miRNA detection.
A flexible 3D ordered SERS sensor for rapid and reliable detection of pesticide residues in fruits
Authors: Lu Han , Huang Guangfei , Wang Dan , Ma Qilin , Zhang Yuan , Jin Mingliang , Shui Lingling
Published: December 2024

Development of a flexible 3D ordered SiNW@AgNP SERS sensor for sensitive detection of pesticide residues on curved surfaces.
Speciating volatile organic compounds in indoor air: using in situ GC to interpret real-time PTR-MS signals
Authors: Ditto Jenna C. , Huynh Han N. , Yu Jie , Link Michael F. , Poppendieck Dustin , Claflin Megan S. , Vance Marina E. , Farmer Delphine K. , Chan Arthur W. H. , Abbatt Jonathan P. D.
Published: December 2024

Gas chromatography paired with proton transfer reaction mass spectrometry allows for a more accurate assessment of gas-phase chemicals in indoor air.
Efficiency and mechanisms of combined persulfate and nanofiltration for the removal of typical perfluorinated compounds
Authors: Sun Lihua , Zhang Yan , Xi Zixuan , Li Ruiying , Zhang Kaiquan
Published: December 2024

Perfluorinated compounds (PFCs) are a class of emerging pollutants that are commonly detected in surface water and pose significant risks to both the environment and public health.
Exfoliation of triazole-based C3N4.8, C3N6, and C3N7 nanosheets for efficient photocatalytic ammonia production
Authors: Yoon Ayoung , Kim Taehoon , Kim Dokyung , Lee Young Joo , Hwang Seong-Ju , Kim In Young
Published: December 2024

Triazole-based C3N7 nanosheets exhibit excellent photocatalytic ammonia production performance, attributed to their inherent properties of an optimised conduction band position and efficient charge separation.
Transformation of semicrystalline polymer mechanics by cyclic polymers
Authors: Bension Yishayah , Wijesekera Andrew , Collins Coby S. , Zhang Siteng , Zheng Juncheng , Zhao Hai , Cheng Shiwang , Stefik Morgan , Ge Ting , Tang Chuanbing
Published: December 2024

Cyclic polymers, lacking chain ends and featuring unique topological constraints, offer distinctive mechanical behaviors.
Simultaneous synthesis of oxygen doped carbon electrodes at the anode and cathode via potential cycling for promoted H2O2 electrosynthesis
Authors: Mao Suhua , Li Xin , Li Bingshuang , Li Jin , Huang Xiaoxi
Published: December 2024

Two carbon electrodes are oxidized simultaneously via the potential cycling method. This method can realize the oxidation of the microporous layer in a gas diffusion electrode to generate high current density in a flow cell.