bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian Inversion of Finite‐Fault Earthquake Slip Model Using Geodetic Data, Solving for Non‐Planar Fault Geometry, Variable Slip, and Data Weighting
Authors: Wei Guoguang , Chen Kejie , Meng Haoran 
Published: January 2023

AbstractA precise finite‐fault model including the fault geometry and slip distribution is essential to understand the physics of an earthquake. However, the conventional linear inversion of geodetic data for a finite‐fault model cannot fully resolve the fault geometry. In this study, we developed a Bayesian inversion framework that can comprehensively solve a non‐planar fault geometry, the corresponding fault slip distribution with spatially variable directions, and objective weighting for multiple data types. In the proposed framework, the probability distributions of all the model parameters are sampled using the Monte Carlo method. The developed methodology removes the requirement for manual intervention for the fault geometry and data weighting and can provide an ensemble of plausible model parameters. The performance of the developed method is tested and demonstrated through inversions for synthetic oblique‐slip faulting models. The results show that the constant rake assumption can significantly bias the estimates of fault geometry and data weighting, whereas additional consideration of the variability of slip orientations can allow plausible estimates of a non‐planar fault geometry with objective data weighting. We applied the method to the 2013 Mw 6.5 Lushan earthquake in Sichuan province, China. The result reveals dominant thrust slips with left‐lateral components and a curved fault geometry, with the confidence interval of the dip angles being between 20°–25° and 56°–58°. The proposed method provides useful insights into the scope of imaging a non‐planar fault geometry, and could help to interpret more complex earthquake sources in the future.
Toward an Integrated Probabilistic Coastal Vulnerability Assessment: A Novel Copula‐Based Vulnerability Index
Authors: Tanim Ahad Hasan , Goharian Erfan 
Published: January 2023

AbstractEstimating the exposure of the coastal systems to natural hazards using coastal vulnerability models, which benefits from index‐based approaches and utilize information about the characteristics of the system, has become extensively adopted in the past few decades in coastal management and planning. However, the explanatory power of index‐based approaches and subjective selection of vulnerability factors are still in dispute. This study aims to introduce a stochastic coastal vulnerability model and assess its skill in characterizing and preserving simultaneous information about various comprising factors. Two common coastal vulnerability indices, Additive Coastal Vulnerability Index and Multiplicative Coastal Vulnerability Index are formed, and then their performances are compared to the proposed Probabilistic Coastal Vulnerability Index (PCVI) for the coastal counties of South Carolina. PCVI is developed based on the joint‐probability analysis of vulnerability factors using copula functions, which makes it capable of preserving the importance of multivariate information, and in turn, forms a more informative index. The performance of indices is benchmarked against post‐hazard flood maps and the cost of fatalities from Hurricane Florence (2018) and Hurricane Matthew (2016). The PCVI revealed more accurate results in terms of explaining the importance of vulnerability associated with biophysical and socio‐economic factors. The capability of PCVI to preserve multivariate vulnerability information offers a more pragmatic approach to reflect the exposure and adaptive capacity of coastal communities facing coastal hazards.
Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea
Authors: Yu Yang , Wang Peng , Cao Hai-Yan , Teng Zhao-Jie , Zhu Yanping , Wang Min , McMinn Andrew , Chen Yin , Xiang Hua , Zhang Yu-Zhong , Chen Xiu-Lan , Zhang Yu-Qiang 
Published: January 2023

Abstract
D-glutamate (D-Glu) is an essential component of bacterial peptidoglycans, representing an important, yet overlooked, pool of organic matter in global oceans. However, little is known on D-Glu catabolism by marine microorganisms. Here, a novel catabolic pathway for D-Glu was identified using the marine bacterium Pseudoalteromonas sp. CF6-2 as the model. Two novel enzymes (DgcN, DgcA), together with a transcriptional regulator DgcR, are crucial for D-Glu catabolism in strain CF6-2. Genetic and biochemical data confirm that DgcN is a N-acetyltransferase which catalyzes the formation of N-acetyl-D-Glu from D-Glu. DgcA is a racemase that converts N-acetyl-D-Glu to N-acetyl-L-Glu, which is further hydrolyzed to L-Glu. DgcR positively regulates the transcription of dgcN and dgcA. Structural and biochemical analyses suggested that DgcN and its homologs, which use D-Glu as the acyl receptor, represent a new group of the general control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) superfamily. DgcA and DgcN occur widely in marine bacteria (particularly Rhodobacterales) and halophilic archaea (Halobacteria) and are abundant in marine and hypersaline metagenome datasets. Thus, this study reveals a novel D-Glu catabolic pathway in ecologically important marine bacteria and halophilic archaea and helps better understand the catabolism and recycling of D-Glu in these ecosystems.
Approximating defense mechanisms in a national study of adults: prevalence and correlates with functioning
Authors: Blanco Carlos , Kampe Leonie , Wall Melanie M. , Liu Shang-Min , Wang Shuai , Caligor Eve , Olfson Mark 
Published: January 2023

AbstractDespite the clinical relevance of defense mechanisms, there are no published studies in nationally representative samples of their prevalence, correlates, and association with psychosocial functioning. We sought to estimate the prevalence and correlates of 12 defense mechanisms in the general adult population by approximating from items used to assess personality traits in the National Epidemiological Survey on Alcohol and Related Conditions (NESARC), a representative sample of US adults (N = 36,653). We examined the associations between sociodemographic characteristics and prevalence of 3 types of defenses mechanisms (pathological, immature, and neurotic). For each defense mechanism, we used the Short-Form 12 to compare psychosocial functioning among 3 groups: those who (1) endorsed the mechanism with self-recognized impairment, (2) endorsed the mechanism without self-recognized impairment, and (3) did not endorse the defense mechanism. The prevalence of defense mechanisms ranged from 13.2% (splitting) to 44.5% (obsessive/controlling behavior). Pathological defenses were more strongly associated with immature defenses (OR = 5.4, 95% CI = 5.2–5.6) than with neurotic defenses (OR = 2.0, 95% CI = 1.9–2.0), whereas the association between immature and neurotic defenses had an intermediate value between the other two (OR = 2.2, 95% CI = 2.1–2.2). Pathological and immature defenses were associated with younger age, having been never married, lower educational attainment, and lower income. After adjusting the crude results for age and sex, individuals who did not endorse a given defense generally had higher scores on the mental health component of the SF-12 than those who endorsed the defense without self-recognized impairment who, in turn, had on average higher scores than those with self-recognized impairment. These results suggest that neurotic, immature, and pathological defense mechanisms are prevalent in the general population and associated with psychosocial impairment. Recognizing defense mechanisms may be important in clinical practice regardless of treatment modality.
Prognostic refinement of NSMP high-risk endometrial cancers using oestrogen receptor immunohistochemistry
Authors: Vermij Lisa , Jobsen Jan J. , León-Castillo Alicia , Brinkhuis Mariel , Roothaan Suzan , Powell Melanie E. , de Boer Stephanie M. , Khaw Pearly , Mileshkin Linda R. , Fyles Anthony , Leary Alexandra , Genestie Catherine , Jürgenliemk-Schulz Ina M. , Crosbie Emma J. , Mackay Helen J. , Nijman Hans. W. , Nout Remi A. , Smit Vincent T. H. B. M. , Creutzberg Carien L. , Horeweg Nanda , Bosse Tjalling ,   TransPORTEC Consortium, de Boer Stephanie M. 
Published: January 2023

Abstract
Background
Risk-assessment of endometrial cancer (EC) is based on clinicopathological factors and molecular subgroup. It is unclear whether adding hormone receptor expression, L1CAM expression or CTNNB1 status yields prognostic refinement.

Methods
Paraffin-embedded tumour samples of women with high-risk EC (HR-EC) from the PORTEC-3 trial (n = 424), and a Dutch prospective clinical cohort called MST (n = 256), were used. All cases were molecularly classified. Expression of L1CAM, ER and PR were analysed by whole-slide immunohistochemistry and CTNNB1 mutations were assessed with a next-generation sequencing. Kaplan–Meier method, log-rank tests and Cox’s proportional hazard models were used for survival analysis.

Results
In total, 648 HR-EC were included. No independent prognostic value of ER, PR, L1CAM, and CTNNB1 was found, while age, stage, and adjuvant chemotherapy had an independent impact on risk of recurrence. Subgroup-analysis showed that only in NSMP HR-EC, ER-positivity was independently associated with a reduced risk of recurrence (HR 0.33, 95%CI 0.15–0.75).

Conclusions
We confirmed the prognostic impact of the molecular classification, age, stage, and adjuvant CTRT in a large cohort of high-risk EC. ER-positivity is a strong favourable prognostic factor in NSMP HR-EC and identifies a homogeneous subgroup of NSMP tumours. Assessment of ER status in high-risk NSMP EC is feasible in clinical practice and could improve risk stratification and treatment.
The mitochondrial inhibitor IF1 binds to the ATP synthase OSCP subunit and protects cancer cells from apoptosis
Authors: Galber Chiara , Fabbian Simone , Gatto Cristina , Grandi Martina , Carissimi Stefania , Acosta Manuel Jesus , Sgarbi Gianluca , Tiso Natascia , Argenton Francesco , Solaini Giancarlo , Baracca Alessandra , Bellanda Massimo , Giorgio Valentina 
Published: January 2023

AbstractThe mitochondrial protein IF1 binds to the catalytic domain of the ATP synthase and inhibits ATP hydrolysis in ischemic tissues. Moreover, IF1 is overexpressed in many tumors and has been shown to act as a pro-oncogenic protein, although its mechanism of action is still debated. Here, we show that ATP5IF1 gene disruption in HeLa cells decreases colony formation in soft agar and tumor mass development in xenografts, underlining the role of IF1 in cancer. Notably, the lack of IF1 does not affect proliferation or oligomycin-sensitive mitochondrial respiration, but it sensitizes the cells to the opening of the permeability transition pore (PTP). Immunoprecipitation and proximity ligation analysis show that IF1 binds to the ATP synthase OSCP subunit in HeLa cells under oxidative phosphorylation conditions. The IF1–OSCP interaction is confirmed by NMR spectroscopy analysis of the recombinant soluble proteins. Overall, our results suggest that the IF1-OSCP interaction protects cancer cells from PTP-dependent apoptosis under normoxic conditions.
Development of a versatile nuclease prime editor with upgraded precision
Authors: Li Xiangyang , Zhang Guiquan , Huang Shisheng , Liu Yao , Tang Jin , Zhong Mingtian , Wang Xin , Sun Wenjun , Yao Yuan , Ji Quanjiang , Wang Xiaolong , Liu Jianghuai , Zhu Shiqiang , Huang Xingxu 
Published: January 2023

AbstractThe applicability of nuclease-based form of prime editor (PEn) has been hindered by its complexed editing outcomes. A chemical inhibitor against DNA-PK, which mediates the nonhomologous end joining (NHEJ) pathway, was recently shown to promote precise insertions by PEn. Nevertheless, the intrinsic issues of specificity and toxicity for such a chemical approach necessitate development of alternative strategies. Here, we find that co-introduction of PEn and a NHEJ-restraining, 53BP1-inhibitory ubiquitin variant potently drives precise edits via mitigation of unintended edits, framing a high-activity editing platform (uPEn) apparently complementing the canonical PE. Further developments involve exploring the effective configuration of a homologous region-containing pegRNA (HR-pegRNA). Overall, uPEn can empower high-efficiency installation of insertions (38%), deletions (43%) and replacements (52%) in HEK293T cells. When compared with PE3/5max, uPEn demonstrates superior activities for typically refractory base substitutions, and for small-block edits. Collectively, this work establishes a highly efficient PE platform with broad application potential.
Master mitotic kinases regulate viral genome delivery during papillomavirus cell entry
Authors: Rizzato Matteo , Mao Fuxiang , Chardon Florian , Lai Kun-Yi , Villalonga-Planells Ruth , Drexler Hannes C. A. , Pesenti Marion E. , Fiskin Mert , Roos Nora , King Kelly M. , Li Shuaizhi , Gamez Eduardo R. , Greune Lilo , Dersch Petra , Simon Claudia , Masson Murielle , Van Doorslaer Koenraad , Campos Samuel K. , Schelhaas Mario 
Published: January 2023

AbstractMitosis induces cellular rearrangements like spindle formation, Golgi fragmentation, and nuclear envelope breakdown. Similar to certain retroviruses, nuclear delivery during entry of human papillomavirus (HPV) genomes is facilitated by mitosis, during which minor capsid protein L2 tethers viral DNA to mitotic chromosomes. However, the mechanism of viral genome delivery and tethering to condensed chromosomes is barely understood. It is unclear, which cellular proteins facilitate this process or how this process is regulated. This work identifies crucial phosphorylations on HPV minor capsid protein L2 occurring at mitosis onset. L2’s chromosome binding region (CBR) is sequentially phosphorylated by the master mitotic kinases CDK1 and PLK1. L2 phosphorylation, thus, regulates timely delivery of HPV vDNA to mitotic chromatin during mitosis. In summary, our work demonstrates a crucial role of mitotic kinases for nuclear delivery of viral DNA and provides important insights into the molecular mechanism of pathogen import into the nucleus during mitosis.
Strong room-temperature bulk nonlinear Hall effect in a spin-valley locked Dirac material
Authors: Min Lujin , Tan Hengxin , Xie Zhijian , Miao Leixin , Zhang Ruoxi , Lee Seng Huat , Gopalan Venkatraman , Liu Chao-Xing , Alem Nasim , Yan Binghai , Mao Zhiqiang 
Published: January 2023

AbstractNonlinear Hall effect (NLHE) is a new type of Hall effect with wide application prospects. Practical device applications require strong NLHE at room temperature (RT). However, previously reported NLHEs are all low-temperature phenomena except for the surface NLHE of TaIrTe4. Bulk RT NLHE is highly desired due to its ability to generate large photocurrent. Here, we show the spin-valley locked Dirac state in BaMnSb2 can generate a strong bulk NLHE at RT. In the microscale devices, we observe the typical signature of an intrinsic NLHE, i.e. the transverse Hall voltage quadratically scales with the longitudinal current as the current is applied to the Berry curvature dipole direction. Furthermore, we also demonstrate our nonlinear Hall device’s functionality in wireless microwave detection and frequency doubling. These findings broaden the coupled spin and valley physics from 2D systems into a 3D system and lay a foundation for exploring bulk NLHE’s applications.
Mechanisms and function of de novo DNA methylation in placental development reveals an essential role for DNMT3B
Authors: Andrews Simon , Krueger Christel , Mellado-Lopez Maravillas , Hemberger Myriam , Dean Wendy , Perez-Garcia Vicente , Hanna Courtney W. 
Published: January 2023

AbstractDNA methylation is a repressive epigenetic modification that is essential for development, exemplified by the embryonic and perinatal lethality observed in mice lacking de novo DNA methyltransferases (DNMTs). Here we characterise the role for DNMT3A, 3B and 3L in gene regulation and development of the mouse placenta. We find that each DNMT establishes unique aspects of the placental methylome through targeting to distinct chromatin features. Loss of Dnmt3b results in de-repression of germline genes in trophoblast lineages and impaired formation of the maternal-foetal interface in the placental labyrinth. Using Sox2-Cre to delete Dnmt3b in the embryo, leaving expression intact in placental cells, the placental phenotype was rescued and, consequently, the embryonic lethality, as Dnmt3b null embryos could now survive to birth. We conclude that de novo DNA methylation by DNMT3B during embryogenesis is principally required to regulate placental development and function, which in turn is critical for embryo survival.
RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells
Authors: Durand Sébastien , Bruelle Marion , Bourdelais Fleur , Bennychen Bigitha , Blin-Gonthier Juliana , Isaac Caroline , Huyghe Aurélia , Martel Sylvie , Seyve Antoine , Vanbelle Christophe , Adrait Annie , Couté Yohann , Meyronet David , Catez Frédéric , Diaz Jean-Jacques , Lavial Fabrice , Ricci Emiliano P. , Ducray François , Gabut Mathieu 
Published: January 2023

AbstractEmbryonic stem cell (ESC) fate decisions are regulated by a complex circuitry that coordinates gene expression at multiple levels from chromatin to mRNA processing. Recently, ribosome biogenesis and translation have emerged as key pathways that efficiently control stem cell homeostasis, yet the underlying molecular mechanisms remain largely unknown. Here, we identified RSL24D1 as highly expressed in both mouse and human pluripotent stem cells. RSL24D1 is associated with nuclear pre-ribosomes and is required for the biogenesis of 60S subunits in mouse ESCs. Interestingly, RSL24D1 depletion significantly impairs global translation, particularly of key pluripotency factors and of components from the Polycomb Repressive Complex 2 (PRC2). While having a moderate impact on differentiation, RSL24D1 depletion significantly alters ESC self-renewal and lineage commitment choices. Altogether, these results demonstrate that RSL24D1-dependant ribosome biogenesis is both required to sustain the expression of pluripotent transcriptional programs and to silence PRC2-regulated developmental programs, which concertedly dictate ESC homeostasis.
Video-rate hyperspectral camera based on a CMOS-compatible random array of Fabry–Pérot filters
Authors: Yako Motoki , Yamaoka Yoshikazu , Kiyohara Takayuki , Hosokawa Chikai , Noda Akihiro , Tack Klaas , Spooren Nick , Hirasawa Taku , Ishikawa Atsushi 
Published: January 2023

AbstractHyperspectral (HS) imaging provides rich spatial and spectral information and extends image inspection beyond human perception. Existing approaches, however, suffer from several drawbacks such as low sensitivity, resolution and/or frame rate, which confines HS cameras to scientific laboratories. Here we develop a video-rate HS camera capable of collecting spectral information on real-world scenes with sensitivities and spatial resolutions comparable with those of a typical RGB camera. Our camera uses compressive sensing, whereby spatial–spectral encoding is achieved with an array of 64 complementary metal–oxide–semiconductor (CMOS)-compatible Fabry–Pérot filters placed onto a monochromatic image sensor. The array affords high optical transmission while minimizing the reconstruction error in subsequent iterative image reconstruction. The experimentally measured sensitivity of 45% for visible light, the spatial resolution of 3 px for 3 dB contrast, and the frame rate of 32.3 fps at VGA resolution meet the requirements for practical use. For further acceleration, we show that AI-based image reconstruction affords operation at 34.4 fps and full high-definition resolution. By enabling practical sensitivity, resolution and frame rate together with compact size and data compression, our HS camera holds great promise for the adoption of HS technology in real-world scenarios, including consumer applications such as smartphones and drones.
Comprehensive liquid biopsy analysis as a tool for the early detection of minimal residual disease in breast cancer
Authors: Stergiopoulou Dimitra , Markou Athina , Strati Areti , Zavridou Martha , Tzanikou Eleni , Mastoraki Sophia , Kallergi Galatea , Georgoulias Vassilis , Lianidou Evi 
Published: January 2023

AbstractLiquid biopsy (LB) provides a unique minimally invasive tool to follow-up cancer patients over time, to detect minimal residual disease (MRD), to study metastasis-biology and mechanisms of therapy-resistance. Molecular characterization of CTCs offers additionally the potential to understand resistance to therapy and implement individualized targeted treatments which can be modified during the disease evolution and follow-up period of a patient. In this study, we present a long-term follow-up of operable breast cancer patients based on a comprehensive liquid biopsy analysis. We performed a comprehensive liquid biopsy analysis in peripheral blood of 13 patients with early-stage operable breast cancer at several time points for a period of ten years, consisting of: (a) CTC enumeration using the CellSearch system, (b) phenotypic analysis of CTCs using Immunofluorescence, (c) gene expression analysis, in EpCAM(+) CTCs for CK-19, CD24,CD44, ALDH1, and TWIST1, (d) analysis of PIK3CA and ESR1 mutations in EpCAM(+) CTCs and corresponding plasma ctDNA and (e) DNA methylation of ESR1 in CTCs. 10/13 (77%) patients were found negative for LB markers in PB during the whole follow-up period, and these patients did not relapse during the follow-up. However, 3/13(18%) patients that were positive for at least one LB marker relapsed within the follow-up period. The molecular characteristics of CTCs were highly different even for the same patient at different time points, and always increased before the clinical relapse. Our results indicate that liquid biopsy can reveal the presence of MRD at least 4 years before the appearance of clinically detectable metastatic disease demonstrating that a comprehensive liquid biopsy analysis provides highly important information for the therapeutic management of breast cancer patients.
Out-of-reach rewards elicit human-oriented referential communicative behaviours in family dogs but not in family pigs
Authors: Pérez Fraga Paula , Morvai Boglárka , Gerencsér Linda , Lehoczki Fanni , Andics Attila 
Published: January 2023

AbstractHuman-oriented referential communication has been evidenced not only in domestic but also in some wild species, however, the importance of domestication-unrelated species’ characteristics in the emergence of this capacity remains largely unexplored. One shared property of all species reported to exhibit referential communication is the efficient use of visual social signals. To assess the potential role of species-specific characteristics in the emergence of human-oriented referential communication, we compared similarly socialised companion animals from two domestic species: dogs, which rely heavily on conspecific visual social signals; and pigs, which do not. We used an out-of-reach reward paradigm with three conditions: both human and reward present, only human present, only reward present. Both species exhibited certain behaviours (e.g. orientation towards the human, orientation alternation between the human and the reward) more often in the human’s presence. However, only dogs exhibited those behaviours more often in the simultaneous presence of the human and the reward. These results suggest similar readiness in dogs and pigs to attend to humans but also that pigs, unlike dogs, do not initiate referential communication with humans. The ability to referentially communicate with humans may not emerge in mammals, even if domesticated companion animals, that lack certain species characteristics, such as efficient intraspecific visual communication.