bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanoscale patterning of collagens in C. elegans apical extracellular matrix
Authors: Adams Jennifer R. G. , Pooranachithra Murugesan , Jyo Erin M. , Zheng Sherry Li , Goncharov Alexandr , Crew Jennifer R. , Kramer James M. , Jin Yishi , Ernst Andreas M. , Chisholm Andrew D. 
Published: November 2023

AbstractApical extracellular matrices (aECMs) are complex extracellular compartments that form important interfaces between animals and their environment. In the adult C. elegans cuticle, layers are connected by regularly spaced columnar structures known as struts. Defects in struts result in swelling of the fluid-filled medial cuticle layer (‘blistering’, Bli). Here we show that three cuticle collagens BLI-1, BLI-2, and BLI-6, play key roles in struts. BLI-1 and BLI-2 are essential for strut formation whereas activating mutations in BLI-6 disrupt strut formation. BLI-1, BLI-2, and BLI-6 precisely colocalize to arrays of puncta in the adult cuticle, corresponding to struts, initially deposited in diffuse stripes adjacent to cuticle furrows. They eventually exhibit tube-like morphology, with the basal ends of BLI-containing struts contact regularly spaced holes in the cuticle. Genetic interaction studies indicate that BLI strut patterning involves interactions with other cuticle components. Our results reveal strut formation as a tractable example of precise aECM patterning at the nanoscale.
Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks
Authors: Ming Luchang , Fu Debao , Wu Zhaona , Zhao Hu , Xu Xingbing , Xu Tingting , Xiong Xiaohu , Li Mu , Zheng Yi , Li Ge , Yang Ling , Xia Chunjiao , Zhou Rongfang , Liao Keyan , Yu Qian , Chai Wenqi , Li Sijia , Liu Yinmeng , Wu Xiaokun , Mao Jianquan , Wei Julong , Li Xu , Wang Lei , Wu Changyin , Xie Weibo 
Published: November 2023

AbstractPanicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the transcriptome of the 1-2 mm young panicles from 275 rice varieties and identified thousands of genes whose expression levels were associated with panicle traits. Multimodel association studies suggested that many small-effect genetic loci determine spikelet per panicle (SPP) by regulating the expression of genes associated with panicle traits. We found that alleles atcis-expression quantitative trait loci of SPP-associated genes underwent positive selection, with a strong preference for alleles increasing SPP. We further developed a method that integrates the associations ofcis- andtrans-expression components of genes with traits to identify causal genes at even small-effect loci and construct regulatory networks. We identified 36 putative causal genes of SPP, includingSDT (MIR156j)andOsMADS17, and inferred thatOsMADS17regulatesSDTexpression, which was experimentally validated. Our study reveals the impact of regulatory variants on rice panicle architecture and provides new insights into the gene regulatory networks of panicle traits.
Flood insurance is a driver of population growth in European floodplains
Authors: Tesselaar Max , Botzen W. J. Wouter , Tiggeloven Timothy , Aerts Jeroen C. J. H. 
Published: November 2023

AbstractFuture flood risk assessments typically focus on changing hazard conditions as a result of climate change, where flood exposure is assumed to remain static or develop according to exogenous scenarios. However, this study presents a method to project future riverine flood risk in Europe by simulating population growth in floodplains, where households’ settlement location decisions endogenously depend on environmental and institutional factors, including amenities associated with river proximity, riverine flood risk, and insurance against this risk. Our results show that population growth in European floodplains and, consequently, rising riverine flood risk are considerably higher when the dis-amenity caused by flood risk is offset by insurance. This outcome is particularly evident in countries where flood risk is covered collectively and notably less where premiums reflect the risk of individual households.
Comprehensive analysis reveals potential therapeutic targets and an integrated risk stratification model for solitary fibrous tumors
Authors: Zhang Renjing , Yang Yang , Hu Chunfang , Huang Mayan , Cen Wenjian , Ling Dongyi , Long Yakang , Yang Xin-Hua , Xu Boheng , Peng Junling , Wang Sujie , Zhu Weijie , Wei Mingbiao , Yang Jiaojiao , Xu Yuxia , Zhang Xu , Ma Jiangjun , Wang Fang , Zhang Hongtu , Ma Peiqing , Zhu Xiaojun , Song Guohui , Sun Li-Yue , Wang De-Shen , Wang Feng-Hua , Li Yu-Hong , Santagata Sandro , Li Qin , Feng Yan-Fen , Du Ziming 
Published: November 2023

AbstractSolitary fibrous tumors (SFTs) are rare mesenchymal tumors with unpredictable evolution and with a recurrence or metastasis rate of 10-40%. Current medical treatments for relapsed SFTs remain ineffective. Here, we identify potential therapeutic targets and risk factors, including IDH1 p.R132S, high PD-L1 expression, and predominant macrophage infiltration, suggesting the potential benefits of combinational immune therapy and targeted therapy for SFTs. An integrated risk model incorporating mitotic count, density of Ki-67+ cells and CD163+ cells, MTOR mutation is developed, applying a discovery cohort of 101 primary non-CNS patients with negative tumor margins (NTM) and validated in three independent cohorts of 210 SFTs with the same criteria, and in 36 primary CNS SFTs with NTM. Compared with the existing models, our model shows significantly improved efficacy in identifying high-risk primary non-CNS and CNS SFTs with NTM for tumor progression.Our findings hold promise for advancing therapeutic strategies and refining risk prediction in SFTs.
On-tissue dataset-dependent MALDI-TIMS-MS2 bioimaging
Authors: Heuckeroth Steffen , Behrens Arne , Wolf Carina , Fütterer Arne , Nordhorn Ilona D. , Kronenberg Katharina , Brungs Corinna , Korf Ansgar , Richter Henning , Jeibmann Astrid , Karst Uwe , Schmid Robin 
Published: November 2023

AbstractTrapped ion mobility spectrometry (TIMS) adds an additional separation dimension to mass spectrometry (MS) imaging, however, the lack of fragmentation spectra (MS2) impedes confident compound annotation in spatial metabolomics. Here, we describe spatial ion mobility-scheduled exhaustive fragmentation (SIMSEF), a dataset-dependent acquisition strategy that augments TIMS-MS imaging datasets with MS2 spectra. The fragmentation experiments are systematically distributed across the sample and scheduled for multiple collision energies per precursor ion. Extendable data processing and evaluation workflows are implemented into the open source software MZmine. The workflow and annotation capabilities are demonstrated on rat brain tissue thin sections, measured by matrix-assisted laser desorption/ionisation (MALDI)-TIMS-MS, where SIMSEF enables on-tissue compound annotation through spectral library matching and rule-based lipid annotation within MZmine and maps the (un)known chemical space by molecular networking. The SIMSEF algorithm and data analysis pipelines are open source and modular to provide a community resource.
Lattice-mismatch-free construction of III-V/chalcogenide core-shell heterostructure nanowires
Authors: Liu Fengjing , Zhuang Xinming , Wang Mingxu , Qi Dongqing , Dong Shengpan , Yip SenPo , Yin Yanxue , Zhang Jie , Sa Zixu , Song Kepeng , He Longbing , Tan Yang , Meng You , Ho Johnny C. , Liao Lei , Chen Feng , Yang Zai-xing 
Published: November 2023

AbstractGrowing high-quality core-shell heterostructure nanowires is still challenging due to the lattice mismatch issue at the radial interface. Herein, a versatile strategy is exploited for the lattice-mismatch-free construction of III-V/chalcogenide core-shell heterostructure nanowires by simply utilizing the surfactant and amorphous natures of chalcogenide semiconductors. Specifically, a variety of III-V/chalcogenide core-shell heterostructure nanowires are successfully constructed with controlled shell thicknesses, compositions, and smooth surfaces. Due to the conformal properties of obtained heterostructure nanowires, the wavelength-dependent bi-directional photoresponse and visible light-assisted infrared photodetection are realized in the type-I GaSb/GeS core-shell heterostructure nanowires. Also, the enhanced infrared photodetection is found in the type-II InGaAs/GeS core-shell heterostructure nanowires compared with the pristine InGaAs nanowires, in which both responsivity and detectivity are improved by more than 2 orders of magnitude. Evidently, this work paves the way for the lattice-mismatch-free construction of core-shell heterostructure nanowires by chemical vapor deposition for next-generation high-performance nanowire optoelectronics.
Single PbS colloidal quantum dot transistors
Authors: Shibata Kenji , Yoshida Masaki , Hirakawa Kazuhiko , Otsuka Tomohiro , Bisri Satria Zulkarnaen , Iwasa Yoshihiro 
Published: November 2023

AbstractColloidal quantum dots are sub-10 nm semiconductors treated with liquid processes, rendering them attractive candidates for single-electron transistors operating at high temperatures. However, there have been few reports on single-electron transistors using colloidal quantum dots due to the difficulty in fabrication. In this work, we fabricated single-electron transistors using single oleic acid-capped PbS quantum dot coupled to nanogap metal electrodes and measured single-electron tunneling. We observed dot size-dependent carrier transport, orbital-dependent electron charging energy and conductance, electric field modulation of the electron confinement potential, and the Kondo effect, which provide nanoscopic insights into carrier transport through single colloidal quantum dots. Moreover, the large charging energy in small quantum dots enables single-electron transistor operation even at room temperature. These findings, as well as the commercial availability and high stability, make PbS quantum dots promising for the development of quantum information and optoelectronic devices, particularly room-temperature single-electron transistors with excellent optical properties.
Amphibious epidermal area networks for uninterrupted wireless data and power transfer
Authors: Hajiaghajani Amirhossein , Rwei Patrick , Afandizadeh Zargari Amir Hosein , Escobar Alberto Ranier , Kurdahi Fadi , Khine Michelle , Tseng Peter 
Published: November 2023

AbstractThe human body exhibits complex, spatially distributed chemo-electro-mechanical processes that must be properly captured for emerging applications in virtual/augmented reality, precision health, activity monitoring, bionics, and more. A key factor in enabling such applications involves the seamless integration of multipurpose wearable sensors across the human body in different environments, spanning from indoor settings to outdoor landscapes. Here, we report a versatile epidermal body area network ecosystem that enables wireless power and data transmission to and from battery-free wearable sensors with continuous functionality from dry to underwater settings. This is achieved through an artificial near field propagation across the chain of biocompatible, magneto-inductive metamaterials in the form of stretchable waterborne skin patches—these are fully compatible with pre-existing consumer electronics. Our approach offers uninterrupted, self-powered communication for human status monitoring in harsh environments where traditional wireless solutions (such as Bluetooth, Wi-Fi or cellular) are unable to communicate reliably.
Mid-cell migration of the chromosomal terminus is coupled to origin segregation in Escherichia coli
Authors: Sadhir Ismath , Murray Seán M. 
Published: November 2023

AbstractBacterial chromosomes are dynamically and spatially organised within cells. In slow-growing Escherichia coli, the chromosomal terminus is initially located at the new pole and must therefore migrate to midcell during replication to reproduce the same pattern in the daughter cells. Here, we use high-throughput time-lapse microscopy to quantify this transition, its timing and its relationship to chromosome segregation. We find that terminus centralisation is a rapid discrete event that occurs ~25 min after initial separation of duplicated origins and ~50 min before the onset of bulk nucleoid segregation but with substantial variation between cells. Despite this variation, its movement is tightly coincident with the completion of origin segregation, even in the absence of its linkage to the divisome, suggesting a coupling between these two events. Indeed, we find that terminus centralisation does not occur if origin segregation away from mid-cell is disrupted, which results in daughter cells having an inverted chromosome organisation. Overall, our study quantifies the choreography of origin-terminus positioning and identifies an unexplored connection between these loci, furthering our understanding of chromosome segregation in this bacterium.
Serine peptidase Vpr forms enzymatically active fibrils outside Bacillus bacteria revealed by cryo-EM
Authors: Cheng Yijia , Han Jianting , Song Meinai , Zhang Shuqin , Cao Qin 
Published: November 2023

AbstractBacteria develop a variety of extracellular fibrous structures crucial for their survival, such as flagella and pili. In this study, we use cryo-EM to identify protein fibrils surrounding lab-cultured Bacillus amyloiquefaciens and discover an unreported fibril species in addition to the flagellar fibrils. These previously unknown fibrils are composed of Vpr, an extracellular serine peptidase. We find that Vpr assembles into fibrils in an enzymatically active form, potentially representing a strategy of enriching Vpr activities around bacterial cells. Vpr fibrils are also observed under other culture conditions and around other Bacillus bacteria, such as Bacillus subtilis, which may suggest a general mechanism across all Bacillus bacterial groups. Taken together, our study reveals fibrils outside the bacterial cell and sheds light on the physiological role of these extracellular fibrils.
Anomalous excitonic phase diagram in band-gap-tuned Ta2Ni(Se,S)5
Authors: Chen Cheng , Tang Weichen , Chen Xiang , Kang Zhibo , Ding Shuhan , Scott Kirsty , Wang Siqi , Li Zhenglu , Ruff Jacob P. C. , Hashimoto Makoto , Lu Dong-Hui , Jozwiak Chris , Bostwick Aaron , Rotenberg Eli , da Silva Neto Eduardo H. , Birgeneau Robert J. , Chen Yulin , Louie Steven G. , Wang Yao , He Yu 
Published: November 2023

AbstractDuring a band-gap-tuned semimetal-to-semiconductor transition, Coulomb attraction between electrons and holes can cause spontaneously formed excitons near the zero-band-gap point, or the Lifshitz transition point. This has become an important route to realize bulk excitonic insulators – an insulating ground state distinct from single-particle band insulators. How this route manifests from weak to strong coupling is not clear. In this work, using angle-resolved photoemission spectroscopy (ARPES) and high-resolution synchrotron x-ray diffraction (XRD), we investigate the broken symmetry state across the semimetal-to-semiconductor transition in a leading bulk excitonic insulator candidate system Ta2Ni(Se,S)5. A broken symmetry phase is found to be continuously suppressed from the semimetal side to the semiconductor side, contradicting the anticipated maximal excitonic instability around the Lifshitz transition. Bolstered by first-principles and model calculations, we find strong interband electron-phonon coupling to play a crucial role in the enhanced symmetry breaking on the semimetal side of the phase diagram. Our results not only provide insight into the longstanding debate of the nature of intertwined orders in Ta2NiSe5, but also establish a basis for exploring band-gap-tuned structural and electronic instabilities in strongly coupled systems.
Direct methane protonic ceramic fuel cells with self-assembled Ni-Rh bimetallic catalyst
Authors: Hong Kyungpyo , Choi Mingi , Bae Yonggyun , Min Jihong , Lee Jaeyeob , Kim Donguk , Bang Sehee , Lee Han-Koo , Lee Wonyoung , Hong Jongsup 
Published: November 2023

AbstractDirect methane protonic ceramic fuel cells are promising electrochemical devices that address the technical and economic challenges of conventional ceramic fuel cells. However, Ni, a catalyst of protonic ceramic fuel cells exhibits sluggish reaction kinetics for CH4 conversion and a low tolerance against carbon-coking, limiting its wider applications. Herein, we introduce a self-assembled Ni-Rh bimetallic catalyst that exhibits a significantly high CH4 conversion and carbon-coking tolerance. It enables direct methane protonic ceramic fuel cells to operate with a high maximum power density of ~0.50 W·cm−2 at 500 °C, surpassing all other previously reported values from direct methane protonic ceramic fuel cells and even solid oxide fuel cells. Moreover, it allows stable operation with a degradation rate of 0.02%·h−1 at 500 °C over 500 h, which is ~20-fold lower than that of conventional protonic ceramic fuel cells (0.4%·h−1). High-resolution in-situ surface characterization techniques reveal that high-water interaction on the Ni-Rh surface facilitates the carbon cleaning process, enabling sustainable long-term operation.
Integrative genome-wide analyses identify novel loci associated with kidney stones and provide insights into its genetic architecture
Authors: Hao Xingjie , Shao Zhonghe , Zhang Ning , Jiang Minghui , Cao Xi , Li Si , Guan Yunlong , Wang Chaolong 
Published: November 2023

AbstractKidney stone disease (KSD) is a complex disorder with high heritability and prevalence. We performed a large genome-wide association study (GWAS) meta-analysis for KSD to date, including 720,199 individuals with 17,969 cases in European population. We identified 44 susceptibility loci, including 28 novel loci. Cell type-specific analysis pinpointed the proximal tubule as the most relevant cells where susceptibility variants might act through a tissue-specific fashion. By integrating kidney-specific omics data, we prioritized 223 genes which strengthened the importance of ion homeostasis, including calcium and magnesium in stone formation, and suggested potential target drugs for the treatment. The genitourinary and digestive diseases showed stronger genetic correlations with KSD. In this study, we generate an atlas of candidate genes, tissue and cell types involved in the formation of KSD. In addition, we provide potential drug targets for KSD treatment and insights into shared regulation with other diseases.
Anti-TACI single and dual-targeting CAR T cells overcome BCMA antigen loss in multiple myeloma
Authors: Larson Rebecca C. , Kann Michael C. , Graham Charlotte , Mount Christopher W. , Castano Ana P. , Lee Won-Ho , Bouffard Amanda A. , Takei Hana N. , Almazan Antonio J. , Scarfó Irene , Berger Trisha R. , Schmidts Andrea , Frigault Matthew J. , Gallagher Kathleen M. E. , Maus Marcela V. 
Published: November 2023

AbstractChimeric Antigen Receptor (CAR) T cells directed to B cell maturation antigen (BCMA) mediate profound responses in patients with multiple myeloma, but most patients do not achieve long-term complete remissions. In addition, recent evidence suggests that high-affinity binding to BCMA can result in on-target, off-tumor activity in the basal ganglia and can lead to fatal Parkinsonian-like disease. Here we develop CAR T cells against multiple myeloma using a binder to targeting transmembrane activator and CAML interactor (TACI) in mono and dual-specific formats with anti-BCMA. These CARs have robust, antigen-specific activity in vitro and in vivo. We also show that TACI RNA expression is limited in the basal ganglia, which may circumvent some of the toxicities recently reported with BCMA CARs. Thus, single-targeting TACI CARs may have a safer toxicity profile, whereas dual-specific BCMA-TACI CAR T cells have potential to avoid the antigen escape that can occur with single-antigen targeting.
Explainable deep learning for tumor dynamic modeling and overall survival prediction using Neural-ODE
Authors: Laurie Mark , Lu James 
Published: November 2023

AbstractWhile tumor dynamic modeling has been widely applied to support the development of oncology drugs, there remains a need to increase predictivity, enable personalized therapy, and improve decision-making. We propose the use of Tumor Dynamic Neural-ODE (TDNODE) as a pharmacology-informed neural network to enable model discovery from longitudinal tumor size data. We show that TDNODE overcomes a key limitation of existing models in its ability to make unbiased predictions from truncated data. The encoder-decoder architecture is designed to express an underlying dynamical law that possesses the fundamental property of generalized homogeneity with respect to time. Thus, the modeling formalism enables the encoder output to be interpreted as kinetic rate metrics, with inverse time as the physical unit. We show that the generated metrics can be used to predict patients’ overall survival (OS) with high accuracy. The proposed modeling formalism provides a principled way to integrate multimodal dynamical datasets in oncology disease modeling.
New acoustic monitoring system quantifying aspiration risk during monitored anaesthesia care
Authors: Shimizu Yoshitaka , Ohshimo Shinichiro , Saeki Noboru , Oue Kana , Sasaki Utaka , Imamura Serika , Kamio Hisanobu , Imado Eiji , Sadamori Takuma , Tsutsumi Yasuo M. , Shime Nobuaki 
Published: November 2023

AbstractRespiratory monitoring is crucial during monitored anaesthesia care (MAC) to ensure patient safety. Patients undergoing procedures like gastrointestinal endoscopy and dental interventions under MAC have a heightened risk of aspiration. Despite the risks, no current system or device can evaluate aspiration risk. This study presents a novel acoustic monitoring system designed to detect fluid retention in the upper airway during MAC. We conducted a prospective observational study with 60 participants undergoing dental treatment under MAC. We utilized a prototype acoustic monitoring system to assess fluid retention in the upper airway by analysing inspiratory sounds. Water was introduced intraorally in participants to simulate fluid retention; artificial intelligence (AI) analysed respiratory sounds pre and post-injection. We also compared respiratory sounds pre-treatment and during coughing events. Coughing was observed in 14 patients during MAC, and 31 instances of apnoea were detected by capnography. However, 27 of these cases had breath sounds. Notably, with intraoral water injection, the Stridor Quantitative Value (STQV) significantly increased; furthermore, the STQV was substantially higher immediately post-coughing in patients who coughed during MAC. In summary, the innovative acoustic monitoring system using AI provides accurate evaluations of fluid retention in the upper airway, offering potential to mitigate aspiration risks during MAC.Clinical trial number: jRCTs 062220054.