bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climate-controlled submarine landslides on the Antarctic continental margin
Authors: Gales Jenny A. , McKay Robert M. , De Santis Laura , Rebesco Michele , Laberg Jan Sverre , Shevenell Amelia E , Harwood David , Leckie R. Mark , Kulhanek Denise K. , King Maxine , Patterson Molly , Lucchi Renata G. , Kim Sookwan , Kim Sunghan , Dodd Justin , Seidenstein Julia , Prunella Catherine , Ferrante Giulia M. ,   IODP Expedition 374 Scientists, Ash Jeanine , Beny François , Browne Imogen M. , Cortese Giuseppe , De Santis Laura , Dodd Justin P. , Esper Oliver M. , Gales Jenny A. , Harwood David M. , Ishino Saki , Keisling Benjamin A. , Kim Sookwan , Kim Sunghan , Kulhanek Denise K. , Laberg Jan Sverre , Leckie R. Mark , McKay Robert M. , Müller Juliane , Patterson Molly O. , Romans Brian W. , Romero Oscar E. , Sangiorgi Francesca , Seki Osamu , Shevenell Amelia E. , Singh Shiv M. , Cordeiro de Sousa Isabela M. , Sugisaki Saiko T. , van de Flierdt Tina , van Peer Tim E. , Xiao Whenshen , Xiong Zhifang 
Published: May 2023

AbstractAntarctica’s continental margins pose an unknown submarine landslide-generated tsunami risk to Southern Hemisphere populations and infrastructure. Understanding the factors driving slope failure is essential to assessing future geohazards. Here, we present a multidisciplinary study of a major submarine landslide complex along the eastern Ross Sea continental slope (Antarctica) that identifies preconditioning factors and failure mechanisms. Weak layers, identified beneath three submarine landslides, consist of distinct packages of interbedded Miocene- to Pliocene-age diatom oozes and glaciomarine diamicts. The observed lithological differences, which arise from glacial to interglacial variations in biological productivity, ice proximity, and ocean circulation, caused changes in sediment deposition that inherently preconditioned slope failure. These recurrent Antarctic submarine landslides were likely triggered by seismicity associated with glacioisostatic readjustment, leading to failure within the preconditioned weak layers. Ongoing climate warming and ice retreat may increase regional glacioisostatic seismicity, triggering Antarctic submarine landslides.
Demonstrating multi-round subsystem quantum error correction using matching and maximum likelihood decoders
Authors: Sundaresan Neereja , Yoder Theodore J. , Kim Youngseok , Li Muyuan , Chen Edward H. , Harper Grace , Thorbeck Ted , Cross Andrew W. , Córcoles Antonio D. , Takita Maika 
Published: May 2023

AbstractQuantum error correction offers a promising path for performing high fidelity quantum computations. Although fully fault-tolerant executions of algorithms remain unrealized, recent improvements in control electronics and quantum hardware enable increasingly advanced demonstrations of the necessary operations for error correction. Here, we perform quantum error correction on superconducting qubits connected in a heavy-hexagon lattice. We encode a logical qubit with distance three and perform several rounds of fault-tolerant syndrome measurements that allow for the correction of any single fault in the circuitry. Using real-time feedback, we reset syndrome and flag qubits conditionally after each syndrome extraction cycle. We report decoder dependent logical error, with average logical error per syndrome measurement in Z(X)-basis of ~0.040 (~0.088) and ~0.037 (~0.087) for matching and maximum likelihood decoders, respectively, on leakage post-selected data.
Mechanism of glycoform specificity and in vivo protection by an anti-afucosylated IgG nanobody
Authors: Gupta Aaron , Kao Kevin S. , Yamin Rachel , Oren Deena A. , Goldgur Yehuda , Du Jonathan , Lollar Pete , Sundberg Eric J. , Ravetch Jeffrey V. 
Published: May 2023

AbstractImmunoglobulin G (IgG) antibodies contain a complex N-glycan embedded in the hydrophobic pocket between its heavy chain protomers. This glycan contributes to the structural organization of the Fc domain and determines its specificity for Fcγ receptors, thereby dictating distinct cellular responses. The variable construction of this glycan structure leads to highly-related, but non-equivalent glycoproteins known as glycoforms. We previously reported synthetic nanobodies that distinguish IgG glycoforms. Here, we present the structure of one such nanobody, X0, in complex with the Fc fragment of afucosylated IgG1. Upon binding, the elongated CDR3 loop of X0 undergoes a conformational shift to access the buried N-glycan and acts as a ‘glycan sensor’, forming hydrogen bonds with the afucosylated IgG N-glycan that would otherwise be sterically hindered by the presence of a core fucose residue. Based on this structure, we designed X0 fusion constructs that disrupt pathogenic afucosylated IgG1-FcγRIIIa interactions and rescue mice in a model of dengue virus infection.
Autophagy receptor NDP52 alters DNA conformation to modulate RNA polymerase II transcription
Authors: dos Santos Ália , Rollins Daniel E. , Hari-Gupta Yukti , McArthur Hannah , Du Mingxue , Ru Sabrina Yong Zi , Pidlisna Kseniia , Stranger Ane , Lorgat Faeeza , Lambert Danielle , Brown Ian , Howland Kevin , Aaron Jesse , Wang Lin , Ellis Peter J. I. , Chew Teng-Leong , Martin-Fernandez Marisa , Pyne Alice L. B. , Toseland Christopher P. 
Published: May 2023

AbstractNDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear functions for NDP52. Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We find that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters. We also show that depletion of NDP52 impacts overall gene expression levels in two model mammalian cells, and that transcription inhibition affects the spatial organisation and molecular dynamics of NDP52 in the nucleus. This directly links NDP52 to a role in RNAPII-dependent transcription. Furthermore, we also show that NDP52 binds specifically and with high affinity to double-stranded DNA (dsDNA) and that this interaction leads to changes in DNA structure in vitro. This, together with our proteomics data indicating enrichment for interactions with nucleosome remodelling proteins and DNA structure regulators, suggests a possible function for NDP52 in chromatin regulation. Overall, here we uncover nuclear roles for NDP52 in gene expression and DNA structure regulation.
Assortative mixing in micro-architecturally annotated brain connectomes
Authors: Bazinet Vincent , Hansen Justine Y. , Vos de Wael Reinder , Bernhardt Boris C. , van den Heuvel Martijn P. , Misic Bratislav 
Published: May 2023

AbstractThe wiring of the brain connects micro-architecturally diverse neuronal populations, but the conventional graph model, which encodes macroscale brain connectivity as a network of nodes and edges, abstracts away the rich biological detail of each regional node. Here, we annotate connectomes with multiple biological attributes and formally study assortative mixing in annotated connectomes. Namely, we quantify the tendency for regions to be connected based on the similarity of their micro-architectural attributes. We perform all experiments using four cortico-cortical connectome datasets from three different species, and consider a range of molecular, cellular, and laminar annotations. We show that mixing between micro-architecturally diverse neuronal populations is supported by long-distance connections and find that the arrangement of connections with respect to biological annotations is associated to patterns of regional functional specialization. By bridging scales of cortical organization, from microscale attributes to macroscale connectivity, this work lays the foundation for next-generation annotated connectomics.
Association of gout with brain reserve and vulnerability to neurodegenerative disease
Authors: Topiwala Anya , Mankia Kulveer , Bell Steven , Webb Alastair , Ebmeier Klaus P. , Howard Isobel , Wang Chaoyue , Alfaro-Almagro Fidel , Miller Karla , Burgess Stephen , Smith Stephen , Nichols Thomas E. 
Published: May 2023

AbstractStudies of neurodegenerative disease risk in gout are contradictory. Relationships with neuroimaging markers of brain structure, which may offer insights, are uncertain. Here we investigated associations between gout, brain structure, and neurodegenerative disease incidence. Gout patients had smaller global and regional brain volumes and markers of higher brain iron, using both observational and genetic approaches. Participants with gout also had higher incidence of all-cause dementia, Parkinson’s disease, and probable essential tremor. Risks were strongly time dependent, whereby associations with incident dementia were highest in the first 3 years after gout diagnosis. These findings suggest gout is causally related to several measures of brain structure. Lower brain reserve amongst gout patients may explain their higher vulnerability to multiple neurodegenerative diseases. Motor and cognitive impairments may affect gout patients, particularly in early years after diagnosis.
The Cell Tracking Challenge: 10 years of objective benchmarking
Authors: Maška Martin , Ulman Vladimír , Delgado-Rodriguez Pablo , Gómez-de-Mariscal Estibaliz , Nečasová Tereza , Guerrero Peña Fidel A. , Ren Tsang Ing , Meyerowitz Elliot M. , Scherr Tim , Löffler Katharina , Mikut Ralf , Guo Tianqi , Wang Yin , Allebach Jan P. , Bao Rina , Al-Shakarji Noor M. , Rahmon Gani , Toubal Imad Eddine , Palaniappan Kannappan , Lux Filip , Matula Petr , Sugawara Ko , Magnusson Klas E. G. , Aho Layton , Cohen Andrew R. , Arbelle Assaf , Ben-Haim Tal , Raviv Tammy Riklin , Isensee Fabian , Jäger Paul F. , Maier-Hein Klaus H. , Zhu Yanming , Ederra Cristina , Urbiola Ainhoa , Meijering Erik , Cunha Alexandre , Muñoz-Barrutia Arrate , Kozubek Michal , Ortiz-de-Solórzano Carlos 
Published: May 2023

AbstractThe Cell Tracking Challenge is an ongoing benchmarking initiative that has become a reference in cell segmentation and tracking algorithm development. Here, we present a significant number of improvements introduced in the challenge since our 2017 report. These include the creation of a new segmentation-only benchmark, the enrichment of the dataset repository with new datasets that increase its diversity and complexity, and the creation of a silver standard reference corpus based on the most competitive results, which will be of particular interest for data-hungry deep learning-based strategies. Furthermore, we present the up-to-date cell segmentation and tracking leaderboards, an in-depth analysis of the relationship between the performance of the state-of-the-art methods and the properties of the datasets and annotations, and two novel, insightful studies about the generalizability and the reusability of top-performing methods. These studies provide critical practical conclusions for both developers and users of traditional and machine learning-based cell segmentation and tracking algorithms.
RNA stability controlled by m6A methylation contributes to X-to-autosome dosage compensation in mammals
Authors: Rücklé Cornelia , Körtel Nadine , Basilicata M. Felicia , Busch Anke , Zhou You , Hoch-Kraft Peter , Tretow Kerstin , Kielisch Fridolin , Bertin Marco , Pradhan Mihika , Musheev Michael , Schweiger Susann , Niehrs Christof , Rausch Oliver , Zarnack Kathi , Keller Valsecchi Claudia Isabelle , König Julian 
Published: May 2023

AbstractIn mammals, X-chromosomal genes are expressed from a single copy since males (XY) possess a single X chromosome, while females (XX) undergo X inactivation. To compensate for this reduction in dosage compared with two active copies of autosomes, it has been proposed that genes from the active X chromosome exhibit dosage compensation. However, the existence and mechanisms of X-to-autosome dosage compensation are still under debate. Here we show that X-chromosomal transcripts have fewer m6A modifications and are more stable than their autosomal counterparts. Acute depletion of m6A selectively stabilizes autosomal transcripts, resulting in perturbed dosage compensation in mouse embryonic stem cells. We propose that higher stability of X-chromosomal transcripts is directed by lower levels of m6A, indicating that mammalian dosage compensation is partly regulated by epitranscriptomic RNA modifications.
Swept-source multimode fiber imaging
Authors: Lochocki Benjamin , Ivanina Aleksandra , Bandhoe Akje , de Boer Johannes F. , Amitonova Lyubov V. 
Published: May 2023

AbstractHigh-resolution compressive imaging via a flexible multimode fiber is demonstrated using a swept-laser source and wavelength dependent speckle illumination. An in-house built swept-source allowing for independent control of bandwidth and scanning range is used to explore and demonstrate a mechanically scan-free approach for high-resolution imaging through an ultrathin and flexible fiber probe. The computational image reconstruction is shown by utilizing a narrow sweeping bandwidth of $$< 10$$

<
10

nm while acquisition time is decreased by 95% compared to conventional raster scanning endoscopy. Demonstrated narrow-band illumination in the visible spectrum is vital for the detection of fluorescence biomarkers in neuroimaging applications. The proposed approach yields device simplicity and flexibility for minimally invasive endoscopy.
Diagnosis of autism spectrum disorder based on functional brain networks and machine learning
Authors: Alves Caroline L. , Toutain Thaise G. L. de O. , de Carvalho Aguiar Patricia , Pineda Aruane M. , Roster Kirstin , Thielemann Christiane , Porto Joel Augusto Moura , Rodrigues Francisco A. 
Published: May 2023

AbstractAutism is a multifaceted neurodevelopmental condition whose accurate diagnosis may be challenging because the associated symptoms and severity vary considerably. The wrong diagnosis can affect families and the educational system, raising the risk of depression, eating disorders, and self-harm. Recently, many works have proposed new methods for the diagnosis of autism based on machine learning and brain data. However, these works focus on only one pairwise statistical metric, ignoring the brain network organization. In this paper, we propose a method for the automatic diagnosis of autism based on functional brain imaging data recorded from 500 subjects, where 242 present autism spectrum disorder considering the regions of interest throughout Bootstrap Analysis of Stable Cluster map. Our method can distinguish the control group from autism spectrum disorder patients with high accuracy. Indeed the best performance provides an AUC near 1.0, which is higher than that found in the literature. We verify that the left ventral posterior cingulate cortex region is less connected to an area in the cerebellum of patients with this neurodevelopment disorder, which agrees with previous studies. The functional brain networks of autism spectrum disorder patients show more segregation, less distribution of information across the network, and less connectivity compared to the control cases. Our workflow provides medical interpretability and can be used on other fMRI and EEG data, including small data sets.
Usefulness of health checkup for screening metabolic dysfunction-associated fatty liver disease and alcohol-related liver disease in Japanese male young adults
Authors: Tajirika Satoko , Miwa Takao , Francisque Cathelencia , Hanai Tatsunori , Imamura Nanako , Adachi Miho , Horita Ryo , Menezes Lynette J. , Shimizu Masahito , Yamamoto Mayumi 
Published: May 2023

AbstractWe aimed to assess metabolic dysfunction-associated fatty liver disease (MAFLD) and alcohol-related liver disease (ALD) prevalence in young male adults and the role of health checkups in disease screening. We recruited 313 male graduate students at Gifu University in April 2022. With hepatic steatosis diagnosed by ultrasonography, MAFLD and nonalcoholic fatty liver disease (NAFLD) were diagnosed based on health checkup data, and ALD was diagnosed with alcohol consumption > 30 g/day. The ability of each variable to identify MAFLD, NAFLD, and ALD was assessed using logistic regression and receiver-operating characteristic curve analyses. Participants’ mean age was 23 (± 4) years, and MAFLD, NAFLD, and ALD prevalence was 11%, 17%, and 1%, respectively. Among Japanese male young adults, alanine aminotransferase (ALT) (odds ratio [OR] 1.04; 95% confidence interval [CI] 1.01–1.07; P = 0.008) and body mass index (BMI) (OR 2.02; 95% CI 1.58–2.58; P < 0.001) were independently associated with MAFLD. Furthermore, only the alcohol use disorders identification test (AUDIT) was able to identify ALD (OR 1.49; 95% CI, 1.28–1.74; P = 0.001). Our study revealed that health checkups, including measurement of ALT, BMI, and AUDIT, are important for screening MAFLD and ALD in younger generations.
Phytochemical screening and allelopathic potential of phytoextracts of three invasive grass species
Authors: Jabeen Shaista , Ali Muhammad Fraz , Mohi ud Din Atta , Javed Talha , Mohammed Nouriya Salah , Chaudhari Sunbal Khalil , Javed Muhammad Ammar , Ali Baber , Zhang Lixin , Rahimi Mehdi 
Published: May 2023

AbstractUndoubtedly, it is important to remain vigilant and manage invasive grasses to prevent their spread and mitigate their negative impact on the environment. However, these aggressive plants can also play a beneficial role in certain contexts. For example, several invasive grasses provide valuable forage for livestock and have disease control potential. Therefore, a research experiment was conducted to explore the pros and cons of this approach, not only for surrounding vegetation but also for human and animal disease control. The study is primarily focused on developing livestock feed, plant-derived herbicides, and an understanding of the phytotoxic effects of invasive species. All plant parts of Cenchrus ciliaris L., Polypogon monspeliansis L., and Dicanthium annulatum (Forssk.) Stapf, were tested for their phyto-chemical screening, proximate, and toxicity analysis which was caused by the methanolic extract of these grass species. Qualitative phytochemical screening tests were performed for proximate composition analysis and toxicity assessment essays. The phytochemical analysis revealed the positive results for alkaloids, flavonoids, coumarins, phenols, saponins, and glycosides, while negative for tannins. Comparison of proximate analysis intimated maximum moisture (10.8%) and crude fat (4.1%) in P. monspeliensis, whereas maximum dry matter (84.1%), crude protein (13.95%), crude fiber (11%), and ash (7.2%) in D. annulatum. Five (10, 100, 500, 100, 10,000 ppm) and three (10, 1000, 10,000 ppm) different concentrations of methanolic extract prepared from C. ciliaris, P. monspeliansis, and D. annulatum were used respectively for root inhibition and seed germination essay. Furthermore, three different concentrations (10, 30, 50 mg) of plant fine powder were used for sandwich method test. There was a significant decline in the growth rate of experimental model radish seeds (P > 0.005), and results from sandwich method tests showed suppressed growth of root hairs, inhibiting the anchoring of the radish seed. In comparison, results manifest that; P. monspeliansis indicated an upsurge of inhibition (66.58% at 10,000 ppm), D. annulatum revealed soar germination (75.86% in controlled conditions), and C. ciliaris exhibited dramatic shoot up of inhibition because of sandwich method test (14.02% at 50 mg). In conclusion, although grasses are toxic, it is important to consider the beneficiary account.
SVSBI: sequence-based virtual screening of biomolecular interactions
Authors: Shen Li , Feng Hongsong , Qiu Yuchi , Wei Guo-Wei 
Published: May 2023

AbstractVirtual screening (VS) is a critical technique in understanding biomolecular interactions, particularly in drug design and discovery. However, the accuracy of current VS models heavily relies on three-dimensional (3D) structures obtained through molecular docking, which is often unreliable due to the low accuracy. To address this issue, we introduce a sequence-based virtual screening (SVS) as another generation of VS models that utilize advanced natural language processing (NLP) algorithms and optimized deep K-embedding strategies to encode biomolecular interactions without relying on 3D structure-based docking. We demonstrate that SVS outperforms state-of-the-art performance for four regression datasets involving protein-ligand binding, protein-protein, protein-nucleic acid binding, and ligand inhibition of protein-protein interactions and five classification datasets for protein-protein interactions in five biological species. SVS has the potential to transform current practices in drug discovery and protein engineering.
Near-infrared magnetic core-shell nanoparticles based on lanthanide metal-organic frameworks as a ratiometric felodipine sensing platform
Authors: Jiang Yu-Peng , Fang Xin-Hui , Wang Qian , Huo Jian-Zhong , Liu Yuan-Yuan , Wang Xin-Rui , Ding Bin 
Published: May 2023

AbstractFelodipine is an effective drug to treat hypertension, but its abuse can cause bardycardia. It is significant to develop highly sensitive detection platform for felodipine to enable the efficient treatment of hypertension diseases. In this work, to highly efficiently detect felodipine, multi-emission near-infrared (NIR) hierarchical magnetic core-shell lanthanide-MOF nanoparticles, namely Nd-MOF@Yb-MOF@SiO2@Fe3O4 (NIR-1), has been synthesized by layer-by-layer (LBL) method. LBL method can adjust the optical properties of NIR-1 and expose more active sites to improve sensitivity in detection process. NIR-1 has near-infrared luminescence emission, which can efficiently avoid the interference of autofluorescence in biological tissues. Photo-luminescent (PL) experiments also reveal that NIR-1 could be used as a near-infrared ratiometric luminescent sensor for felodipine detection with high selectivity and sensitivity, the low of detection limit (LOD) is 6.39 nM in felodipine detection, which is also performed using real biological samples. In addition, NIR-1 can be used as a ratiometric thermometer could also be applied in the temperature sensing from 293 K to 343 K. Finally, detection mechanisms for felodipine and temperature sensing performance based on near-infrared (NIR) emission were also investigated and discussed in detail.
FP‐BFT: A fast pipeline Byzantine consensus algorithm
Authors: Liu Xinlei , Liu Yang , Li Xiangyang , Cao Haohao , Wang Yaoqi 
Published: May 2023

AbstractThe Byzantine Fault Tolerant (BFT) consensus algorithms have been widely applied in the blockchain systems because of their fault tolerance capability to determine system consistency in the presence of malicious nodes. However, the BFT consensus algorithms are confronted with low efficiency and scalability problems caused by multiple rounds of handshake communication. In this paper, a pipeline‐based Fast Pipeline Byzantine Fault Tolerance consensus algorithm (FP‐BFT) is proposed, which adopts a non‐leader pipeline framework to process different rounds of transactions in parallel. By means of randomly selecting 2f+1 nodes to form a committee for one round of transactions, consensus agreement can be reached within the committee via nodes broadcasting and voting. Committee nodes participating in the consensus are chosen by chance to avoid the monopoly of which becomes the block producer. Consensus efficiency and the system throughput can be significantly improved with the pipeline framework. Comparison experiments are conducted to verify the superiority of the FP‐BFT algorithm, and the theoretical proof is given to guarantee the Byzantine fault‐tolerant security. Experimental results show that FP‐BFT has improved the consensus efficiency by decreasing communication overhead to make it better applied both in public blockchain and consortium blockchain systems.