bluuebunny/crossref_metadata_2025_split huggingface dataset:
FAP106 is an interaction hub for assembling microtubule inner proteins at the cilium inner junction
Authors: Shimogawa Michelle M. , Wijono Angeline S. , Wang Hui , Zhang Jiayan , Sha Jihui , Szombathy Natasha , Vadakkan Sabeeca , Pelayo Paula , Jonnalagadda Keya , Wohlschlegel James , Zhou Z. Hong , Hill Kent L. 
Published: August 2023

AbstractMotility of pathogenic protozoa depends on flagella (synonymous with cilia) with axonemes containing nine doublet microtubules (DMTs) and two singlet microtubules. Microtubule inner proteins (MIPs) within DMTs influence axoneme stability and motility and provide lineage-specific adaptations, but individual MIP functions and assembly mechanisms are mostly unknown. Here, we show in the sleeping sickness parasite Trypanosoma brucei, that FAP106, a conserved MIP at the DMT inner junction, is required for trypanosome motility and functions as a critical interaction hub, directing assembly of several conserved and lineage-specific MIPs. We use comparative cryogenic electron tomography (cryoET) and quantitative proteomics to identify MIP candidates. Using RNAi knockdown together with fitting of AlphaFold models into cryoET maps, we demonstrate that one of these candidates, MC8, is a trypanosome-specific MIP required for parasite motility. Our work advances understanding of MIP assembly mechanisms and identifies lineage-specific motility proteins that are attractive targets to consider for therapeutic intervention.
Practical diagnosis of cirrhosis in non-alcoholic fatty liver disease using currently available non-invasive fibrosis tests
Authors: Boursier Jérôme , Roux Marine , Costentin Charlotte , Chaigneau Julien , Fournier-Poizat Céline , Trylesinski Aldo , Canivet Clémence M. , Michalak Sophie , Le Bail Brigitte , Paradis Valérie , Bedossa Pierre , Sturm Nathalie , de Ledinghen Victor ,   AFEF group for the study of liver fibrosis, Barthelon Justine , Boursier Jerome , Cales Paul , Canivet Clémence , Decaens Thomas , Delamarre Adèle , Hermabessiere Paul , Irles-Depé Marie , de Ledinghen Victor , Hilleret Marie-Noelle , Fouchard-Hubert Isabelle , Lannes Adrien , Le Bail Brigitte , Moal Valérie , Oberti Fréderic ,   M118 study group, Allison Michael , Anstee Quentin M. , Cobbold Jeremy F. , Deeks Jonathan J. , Eddowes Peter J. , Guha Indra N. , Sheridan David , Tsochatzis Emmanuel , Newsome Philip N. 
Published: August 2023

AbstractUnlike for advanced liver fibrosis, the practical rules for the early non-invasive diagnosis of cirrhosis in NAFLD remain not well defined. Here, we report the derivation and validation of a stepwise diagnostic algorithm in 1568 patients with NAFLD and liver biopsy coming from four independent cohorts. The study algorithm, using first the elastography-based tests Agile3+ and Agile4 and then the specialized blood tests FibroMeterV3G and CirrhoMeterV3G, provides stratification in four groups, the last of which is enriched in cirrhosis (71% prevalence in the validation set). A risk prediction chart is also derived to allow estimation of the individual probability of cirrhosis. The predicted risk shows excellent calibration in the validation set, and mean difference with perfect prediction is only −2.9%. These tools improve the personalized non-invasive diagnosis of cirrhosis in NAFLD.
Two-photon nanoprobes based on bioorganic nanoarchitectonics with a photo-oxidation enhanced emission mechanism
Authors: Li Shukun , Chang Rui , Zhao Luyang , Xing Ruirui , van Hest Jan C. M. , Yan Xuehai 
Published: August 2023

AbstractTwo-photon absorption (TPA) fluorescence imaging holds great promise in diagnostics and biomedicine owing to its unparalleled spatiotemporal resolution. However, the adaptability and applicability of currently available TPA probes, which act as a critical element for determining the imaging contrast effect, is severely challenged by limited photo-luminescence in vivo. This is particularly a result of uncontrollable aggregation that causes fluorescence quenching, and inevitable photo-oxidation in harsh physiological milieu, which normally leads to bleaching of the dye. Herein, we describe the remarkably enhanced TPA fluorescence imaging capacity of self-assembling near-infrared (NIR) cyanine dye-based nanoprobes (NPs), which can be explained by a photo-oxidation enhanced emission mechanism. Singlet oxygen generated during photo-oxidation enables chromophore dimerization to form TPA intermediates responsible for enhanced TPA fluorescence emission. The resulting NPs possess uniform size distribution, excellent stability, more favorable TPA cross-section and anti-bleaching ability than a popular TPA probe rhodamine B (RhB). These properties of cyanine dye-based TPA NPs promote their applications in visualizing blood circulation and tumoral accumulation in real-time, even to cellular imaging in vivo. The photo-oxidation enhanced emission mechanism observed in these near-infrared cyanine dye-based nanoaggregates opens an avenue for design and development of more advanced TPA fluorescence probes.
Structural mechanism of R2D2 and Loqs-PD synergistic modulation on DmDcr-2 oligomers
Authors: Deng Ting , Su Shichen , Yuan Xun , He Jinqiu , Huang Ying , Ma Jinbiao , Wang Jia 
Published: August 2023

AbstractSmall interference RNAs are the key components of RNA interference, a conserved RNA silencing or viral defense mechanism in many eukaryotes. In Drosophila melanogaster, Dicer-2 (DmDcr-2)-mediated RNAi pathway plays important roles in defending against viral infections and protecting genome integrity. During the maturation of siRNAs, two cofactors can regulate DmDcr-2’s functions: Loqs-PD that is required for dsRNA processing, and R2D2 that is essential for the subsequent loading of siRNAs into effector Ago2 to form RISC complexes. However, due to the lack of structural information, it is still unclear whether R2D2 and Loqs-PD affect the functions of DmDcr-2 simultaneously. Here we present several cryo-EM structures of DmDcr-2/R2D2/Loqs-PD complex bound to dsRNAs with various lengths by the Helicase domain. These structures revealed that R2D2 and Loqs-PD can bind to different regions of DmDcr-2 without interfering with each other. Furthermore, the cryo-EM results demonstrate that these complexes can form large oligomers and assemble into fibers. The formation and depolymerization of these oligomers are associated with ATP hydrolysis. These findings provide insights into the structural mechanism of DmDcr-2 and its cofactors during siRNA processing.
Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling
Authors: Vierra Nicholas C. , Ribeiro-Silva Luisa , Kirmiz Michael , van der List Deborah , Bhandari Pradeep , Mack Olivia A. , Carroll James , Le Monnier Elodie , Aicher Sue A. , Shigemoto Ryuichi , Trimmer James S. 
Published: August 2023

AbstractJunctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration of intracellular signaling machinery near ER-PM junctions allows these domains to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular compartmentalization of protein kinase A (PKA) signaling also regulates essential cellular functions, however, no specific association between PKA and ER-PM junctional domains is known. Here, we show that in brain neurons type I PKA is directed to Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and ER-resident VAP proteins results in the concentration of type I PKA between stacked ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome enables reciprocal regulation between PKA and Ca2+ signaling machinery to support Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal ER-PM junctions support a receptor-independent form of PKA signaling driven by membrane depolarization and intracellular Ca2+, allowing conversion of information encoded in electrical signals into biochemical changes universally recognized throughout the cell.
Discovery and construction of surface kagome electronic states induced by p-d electronic hybridization in Co3Sn2S2
Authors: Huang Li , Kong Xianghua , Zheng Qi , Xing Yuqing , Chen Hui , Li Yan , Hu Zhixin , Zhu Shiyu , Qiao Jingsi , Zhang Yu-Yang , Cheng Haixia , Cheng Zhihai , Qiu Xianggang , Liu Enke , Lei Hechang , Lin Xiao , Wang Ziqiang , Yang Haitao , Ji Wei , Gao Hong-Jun 
Published: August 2023

AbstractKagome-lattice materials possess attractive properties for quantum computing applications, but their synthesis remains challenging. Herein, based on the compelling identification of the two cleavable surfaces of Co3Sn2S2, we show surface kagome electronic states (SKESs) on a Sn-terminated triangular Co3Sn2S2surface. Such SKESs are imprinted by verticalp-delectronic hybridization between the surface Sn (subsurface S) atoms and the buried Co kagome-lattice network in the Co3Sn layer under the surface. Owing to the subsequent lateral hybridization of the Sn and S atoms in a corner-sharing manner, the kagome symmetry and topological electronic properties of the Co3Sn layer is proximate to the Sn surface. The SKESs and both hybridizations were verified via qPlus non-contact atomic force microscopy (nc-AFM) and density functional theory calculations. The construction of SKESs with tunable properties can be achieved by the atomic substitution of surface Sn (subsurface S) with other group III-V elements (Se or Te), which was demonstrated theoretically. This work exhibits the powerful capacity of nc-AFM in characterizing localized topological states and reveals the strategy for synthesis of large-area transition-metal-based kagome-lattice materials using conventional surface deposition techniques.
A cage-on-MOF strategy to coordinatively functionalize mesoporous MOFs for manipulating selectivity in adsorption and catalysis
Authors: Liang Yu , Yang Xiaoxin , Wang Xiaoyu , Guan Zong-Jie , Xing Hang , Fang Yu 
Published: August 2023

AbstractFunctionalizing porous materials with capping agents generates hybrid materials with enhanced properties, while the challenge is how to improve the selectivity and maintain the porosity of the parent framework. Herein, we developed a “Cage-on-MOF” strategy to tune the recognition and catalytic properties of MOFs without impairing their porosity. Two types of porous coordination cages (PCCs) of opposite charges containing secondary binding groups were developed to coordinatively functionalize two distinct porous MOFs, namely MOF@PCC nanocomposites. We demonstrated that the surface-capped PCCs can act as “modulators” to effectively tune the surface charge, stability, and adsorption behavior of different host MOF particles. More importantly, the MOF@PCCs can serve as selective heterogeneous catalysts for condensation reactions to achieve reversed product selectivity and excellent recyclability. This work sets the foundation for using molecular cages as porous surface-capping agents to functionalize and manipulate another porous material, without affecting the intrinsic properties of the parent framework.
Behavioural individuality determines infection risk in clonal ant colonies
Authors: Li Zimai , Bhat Bhoomika , Frank Erik T. , Oliveira-Honorato Thalita , Azuma Fumika , Bachmann Valérie , Parker Darren J. , Schmitt Thomas , Economo Evan P. , Ulrich Yuko 
Published: August 2023

AbstractIn social groups, infection risk is not distributed evenly across individuals. Individual behaviour is a key source of variation in infection risk, yet its effects are difficult to separate from other factors (e.g., age). Here, we combine epidemiological experiments with chemical, transcriptomic, and automated behavioural analyses in clonal ant colonies, where behavioural individuality emerges among identical workers. We find that: (1) Caenorhabditis-related nematodes parasitise ant heads and affect their survival and physiology, (2) differences in infection emerge from behavioural variation alone, and reflect spatially-organised division of labour, (3) infections affect colony social organisation by causing infected workers to stay in the nest. By disproportionately infecting some workers and shifting their spatial distribution, infections reduce division of labour and increase spatial overlap between hosts, which should facilitate parasite transmission. Thus, division of labour, a defining feature of societies, not only shapes infection risk and distribution but is also modulated by parasites.
QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize
Authors: Wang Xi , Li Juan , Han Linqian , Liang Chengyong , Li Jiaxin , Shang Xiaoyang , Miao Xinxin , Luo Zi , Zhu Wanchao , Li Zhao , Li Tianhuan , Qi Yongwen , Li Huihui , Lu Xiaoduo , Li Lin 
Published: August 2023

AbstractGenetic dissection of agronomic traits is important for crop improvement and global food security. Phenotypic variation of tassel branch number (TBN), a major breeding target, is controlled by many quantitative trait loci (QTLs). The lack of large-scale QTL cloning methodology constrains the systematic dissection of TBN, which hinders modern maize breeding. Here, we devise QTG-Miner, a multi-omics data-based technique for large-scale and rapid cloning of quantitative trait genes (QTGs) in maize. Using QTG-Miner, we clone and verify seven genes underlying seven TBN QTLs. Compared to conventional methods, QTG-Miner performs well for both major- and minor-effect TBN QTLs. Selection analysis indicates that a substantial number of genes and network modules have been subjected to selection during maize improvement. Selection signatures are significantly enriched in multiple biological pathways between female heterotic groups and male heterotic groups. In summary, QTG-Miner provides a large-scale approach for rapid cloning of QTGs in crops and dissects the genetic base of TBN for further maize breeding.
Sea-ice decline could keep zooplankton deeper for longer
Authors: Flores Hauke , Veyssière Gaëlle , Castellani Giulia , Wilkinson Jeremy , Hoppmann Mario , Karcher Michael , Valcic Lovro , Cornils Astrid , Geoffroy Maxime , Nicolaus Marcel , Niehoff Barbara , Priou Pierre , Schmidt Katrin , Stroeve Julienne 
Published: August 2023

AbstractAs Arctic sea ice deteriorates, more light enters the ocean, causing largely unknown effects on the ecosystem. Using an autonomous biophysical observatory, we recorded zooplankton vertical distribution under Arctic sea ice from dusk to dawn of the polar night. Here we show that zooplankton ascend into the under-ice habitat during autumn twilight, following an isolume of 2.4 × 10−4 W m−2. We applied this trigger isolume to CMIP6 model outputs accounting for incoming radiation after sunset and before sunrise of the polar night. The models project that, in about three decades, the total time spent by zooplankton in the under-ice habitat could be reduced by up to one month, depending on geographic region. This will impact zooplankton winter survival, the Arctic foodweb, and carbon and nutrient fluxes. These findings highlight the importance of biological processes during the twilight periods for predicting change in high-latitude ecosystems.
Digitization of the Australian Parliamentary Debates, 1998–2022
Authors: Katz Lindsay , Alexander Rohan 
Published: August 2023

AbstractPublic knowledge of what is said in parliament is a tenet of democracy, and a critical resource for political science research. In Australia, following the British tradition, the written record of what is said in parliament is known as Hansard. While the Australian Hansard has always been publicly available, it has been difficult to use for the purpose of large-scale macro- and micro-level text analysis because it has only been available as PDFs or XMLs. Following the lead of the Linked Parliamentary Data project which achieved this for Canada, we provide a new, comprehensive, high-quality, rectangular database that captures proceedings of the Australian parliamentary debates from 1998 to 2022. The database is publicly available and can be linked to other datasets such as election results. The creation and accessibility of this database enables the exploration of new questions and serves as a valuable resource for both researchers and policymakers.
Development of global monthly dataset of CMIP6 climate variables for estimating evapotranspiration
Authors: Song Young Hoon , Chung Eun-Sung , Shahid Shamsuddin , Kim Yeonjoo , Kim Dongkyun 
Published: August 2023

AbstractReliable projection of evapotranspiration (ET) is important for planning sustainable water management for the agriculture field in the context of climate change. A global dataset of monthly climate variables was generated to estimate potential ET (PET) using 14 General Circulation Models (GCMs) for four main shared socioeconomic pathways (SSPs). The generated dataset has a spatial resolution of 0.5° × 0.5° and a period ranging from 1950 to 2100 and can estimate historical and future PET using the Penman-Monteith method. Furthermore, this dataset can be applied to various PET estimation methods based on climate variables. This paper presents that the dataset generated to estimate future PET could reflect the greenhouse gas concentration level of the SSP scenarios in latitude bands. Therefore, this dataset can provide vital information for users to select appropriate GCMs for estimating reasonable PETs and help determine bias correction methods to reduce between observation and model based on the scale of climate variables in each GCM.
Label-free tumor cells classification using deep learning and high-content imaging
Authors: Piansaddhayanon Chawan , Koracharkornradt Chonnuttida , Laosaengpha Napat , Tao Qingyi , Ingrungruanglert Praewphan , Israsena Nipan , Chuangsuwanich Ekapol , Sriswasdi Sira 
Published: August 2023

AbstractMany studies have shown that cellular morphology can be used to distinguish spiked-in tumor cells in blood sample background. However, most validation experiments included only homogeneous cell lines and inadequately captured the broad morphological heterogeneity of cancer cells. Furthermore, normal, non-blood cells could be erroneously classified as cancer because their morphology differ from blood cells. Here, we constructed a dataset of microscopic images of organoid-derived cancer and normal cell with diverse morphology and developed a proof-of-concept deep learning model that can distinguish cancer cells from normal cells within an unlabeled microscopy image. In total, more than 75,000 organoid-drived cells from 3 cholangiocarcinoma patients were collected. The model achieved an area under the receiver operating characteristics curve (AUROC) of 0.78 and can generalize to cell images from an unseen patient. These resources serve as a foundation for an automated, robust platform for circulating tumor cell detection.
Tamoxifen associated to the conservative CKD treatment promoted additional antifibrotic effects on experimental hypertensive nephrosclerosis
Authors: Fanelli Camilla , Francini Ana L. R. , Celestrino Giovanna A. , Teles Flávio , Barbosa Ana P. , Noda Paloma , Iannuzzi Leandro R. , Guzzo Cristiane R. , Ornellas Felipe M. , Noronha Irene L. 
Published: August 2023

AbstractCKD progression depends on the activation of an intricate set of hemodynamic and inflammatory mechanisms, promoting renal leukocyte infiltration, inflammation and fibrosis, leading to renal function loss. There are currently no specific drugs to detain renal fibrogenesis, which is a common end-point for different nephropathies. Clinical therapy for CKD is mostly based on the management of hypertension and proteinuria, partially achieved with renin–angiotensin–aldosterone system (RAAS) blockers, and the control of inflammation by immunosuppressive drugs. The aim of the present study was to verify if the administration of tamoxifen (TAM), an estrogen receptor modulator, clinically employed in the treatment of breast cancer and predicted to exert antifibrotic effects, would promote additional benefits when associated to a currently used therapeutic scheme for the conservative management of experimental CKD. Wistar rats underwent the NAME model of hypertensive nephrosclerosis, obtained by daily oral administration of a nitric oxide synthesis inhibitor, associated to dietary sodium overload. The therapeutic association of TAM to losartan (LOS), and mofetil mycophenolate (MMF) effectively reduced the severe hypertension, marked albuminuria and glomerular damage exhibited by NAME animals. Moreover, the association also succeeded in limiting renal inflammation in this model, and promoted further reduction of ECM interstitial accumulation and renal fibrosis, compared to the monotherapies. According to our results, the association of TAM to the currently used conservative treatment of CKD added significant antifibrotic effects both in vivo and in vitro, and may represent an alternative to slow the progression of chronic nephropathy.
Multiphoton microscopy is a nondestructive label-free approach to investigate the 3D structure of gas cell walls in bread dough
Authors: Castanha Nanci , Challois Sylvain , Grenier David , Le-Bail Patricia , Dubreil Laurence , Lucas Tiphaine 
Published: August 2023

AbstractDuring the different steps of bread-making, changes in the microstructure of the dough, particularly in the gas cell walls (GCW), have a major influence on the final bread crumb texture. Investigation of the spatial conformation of GCWs is still a challenge because it requires both high resolutions and 3D depth imaging. The originality of the present work lies in the use of label-free non-destructive multiphoton microscopy (NLOM) to image the 3D structure of GCWs, shedding light on their behavior and organization in wheat bread dough. We demonstrated that second and third harmonic generation (SHG, THG) allow imaging, respectively, of starch granules and interfaces in bread dough, while the gluten matrix was detected via two-photon excitation fluorescence (TPEF). Last, a distinction between the gluten network and starch granules was achieved using gluten endogenous fluorescence (EF) imaging, while the position, size, and 3D orientation of starch granules in GCWs were determined from harmonic imaging, made possible by the acquisition of backward and forward SHG with linear polarization. These innovative experiments highlight the strengths of NLOM for a label-free characterization of bread dough microstructure for the first time, in order to understand the role of starch granules in dough stabilization.
A new distinguishing attack on reduced round ChaCha permutation
Authors: Dey Chandan , Sarkar Santanu 
Published: August 2023

AbstractThis work concentrates on differential-linear distinguishing attacks on the prominent ARX-based permutation ChaCha. Here, we significantly improve the 7-round differential-linear distinguisher for ChaCha permutation by introducing a new path of linear approximation. We first introduce a new single-bit differential distinguisher for the 3.5th round of the permutation that assists us in inventing a new path for the differential-linear distinguisher. We show that one can distinguish a 7-round ChaCha permutation with time complexity of $$2^{207}$$

2
207

. This improves the recent work of Coutinho et al. (in: Advances in Cryptology—ASIACRYPT 2022—28nd International Conference on the Theory and Application of Cryptology and Information Security, Taipei, Taiwan, December 5–9, 2012, Springer, 2022), which achieved time complexity $$2^{214}$$

2
214

. We also propose a distinguisher for the 7.25-round of ChaCha permutation and this is the first distinguishing attack for more than 7-round of ChaCha permutation. We provide theoretical proofs and the corresponding experimental results for the linear approximations that we use for differential-linear distinguisher. We point out that the existing multibit distinguishing attacks on the cipher ChaCha are invalid. These attacks are worked only for the ChaCha permutation.