bluuebunny/crossref_metadata_2025 huggingface dataset:
Defining diurnal fluctuations in mouse choroid plexus and CSF at high molecular, spatial, and temporal resolution
Authors: Fame Ryann M. , Kalugin Peter N. , Petrova Boryana , Xu Huixin , Soden Paul A. , Shipley Frederick B. , Dani Neil , Grant Bradford , Pragana Aja , Head Joshua P. , Gupta Suhasini , Shannon Morgan L. , Chifamba Fortunate F. , Hawks-Mayer Hannah , Vernon Amanda , Gao Fan , Zhang Yong , Holtzman Michael J. , Heiman Myriam , Andermann Mark L. , Kanarek Naama , Lipton Jonathan O. , Lehtinen Maria K.
Published: June 2023

Transmission and secretion of signals via the choroid plexus (ChP) brain barrier can modulate brain states via regulation of cerebrospinal fluid (CSF) composition. Here, we developed a platform to analyze diurnal variations in male mouse ChP and CSF. Ribosome profiling of ChP epithelial cells revealed diurnal translatome differences in metabolic machinery, secreted proteins, and barrier components. Using ChP and CSF metabolomics and blood-CSF barrier analyses, we observed diurnal changes in metabolites and cellular junctions. We then focused on transthyretin (TTR), a diurnally regulated thyroid hormone chaperone secreted by the ChP. Diurnal variation in ChP TTR depended on Bmal1 clock gene expression. We achieved real-time tracking of CSF-TTR in awake TtrmNeonGreen mice via multi-day intracerebroventricular fiber photometry. Diurnal changes in ChP and CSF TTR levels correlated with CSF thyroid hormone levels. These datasets highlight an integrated platform for investigating diurnal control of brain states by the ChP and CSF.
Specific post-translational modifications of soluble tau protein distinguishes Alzheimer’s disease and primary tauopathies
Authors: Kyalu Ngoie Zola Nathalie , Balty Clémence , Pyr dit Ruys Sébastien , Vanparys Axelle A. T. , Huyghe Nicolas D. G. , Herinckx Gaëtan , Johanns Manuel , Boyer Emilien , Kienlen-Campard Pascal , Rider Mark H. , Vertommen Didier , Hanseeuw Bernard J.
Published: June 2023

Tau protein aggregates in several neurodegenerative disorders, referred to as tauopathies. The tau isoforms observed in post mortem human brain aggregates is used to classify tauopathies. However, distinguishing tauopathies ante mortem remains challenging, potentially due to differences between insoluble tau in aggregates and soluble tau in body fluids. Here, we demonstrated that tau isoforms differ between tauopathies in insoluble aggregates, but not in soluble brain extracts. We therefore characterized post-translational modifications of both the aggregated and the soluble tau protein obtained from post mortem human brain tissue of patients with Alzheimer’s disease, cortico-basal degeneration, Pick’s disease, and frontotemporal lobe degeneration. We found specific soluble signatures for each tauopathy and its specific aggregated tau isoforms: including ubiquitination on Lysine 369 for cortico-basal degeneration and acetylation on Lysine 311 for Pick’s disease. These findings provide potential targets for future development of fluid-based biomarker assays able to distinguish tauopathies in vivo.
A global meta-analysis of soil organic carbon in the Anthropocene
Authors: Beillouin Damien , Corbeels Marc , Demenois Julien , Berre David , Boyer Annie , Fallot Abigail , Feder Frédéric , Cardinael Rémi
Published: June 2023

Anthropogenic activities profoundly impact soil organic carbon (SOC), affecting its contribution to ecosystem services such as climate regulation. Here, we conducted a thorough review of the impacts of land-use change, land management, and climate change on SOC. Using second-order meta-analysis, we synthesized findings from 230 first-order meta-analyses comprising over 25,000 primary studies. We show that (i) land conversion for crop production leads to high SOC loss, that can be partially restored through land management practices, particularly by introducing trees and incorporating exogenous carbon in the form of biochar or organic amendments, (ii) land management practices that are implemented in forests generally result in depletion of SOC, and (iii) indirect effects of climate change, such as through wildfires, have a greater impact on SOC than direct climate change effects (e.g., from rising temperatures). The findings of our study provide strong evidence to assist decision-makers in safeguarding SOC stocks and promoting land management practices for SOC restoration. Furthermore, they serve as a crucial research roadmap, identifying areas that require attention to fill the knowledge gaps concerning the factors driving changes in SOC.
Interaction-driven transport of dark excitons in 2D semiconductors with phonon-mediated optical readout
Authors: Chand Saroj B. , Woods John M. , Quan Jiamin , Mejia Enrique , Taniguchi Takashi , Watanabe Kenji , Alù Andrea , Grosso Gabriele
Published: June 2023

The growing field of quantum information technology requires propagation of information over long distances with efficient readout mechanisms. Excitonic quantum fluids have emerged as a powerful platform for this task due to their straightforward electro-optical conversion. In two-dimensional transition metal dichalcogenides, the coupling between spin and valley provides exciting opportunities for harnessing, manipulating, and storing bits of information. However, the large inhomogeneity of single layers cannot be overcome by the properties of bright excitons, hindering spin-valley transport. Nonetheless, the rich band structure supports dark excitonic states with strong binding energy and longer lifetime, ideally suited for long-range transport. Here we show that dark excitons can diffuse over several micrometers and prove that this repulsion-driven propagation is robust across non-uniform samples. The long-range propagation of dark states with an optical readout mediated by chiral phonons provides a new concept of excitonic devices for applications in both classical and quantum information technology.
Occurrence and backtracking of microplastic mass loads including tire wear particles in northern Atlantic air
Authors: Goßmann Isabel , Herzke Dorte , Held Andreas , Schulz Janina , Nikiforov Vladimir , Georgi Christoph , Evangeliou Nikolaos , Eckhardt Sabine , Gerdts Gunnar , Wurl Oliver , Scholz-Böttcher Barbara M.
Published: June 2023

Few studies report the occurrence of microplastics (MP), including tire wear particles (TWP) in the marine atmosphere, and little data is available regarding their size or sources. Here we present active air sampling devices (low- and high-volume samplers) for the evaluation of composition and MP mass loads in the marine atmosphere. Air was sampled during a research cruise along the Norwegian coast up to Bear Island. Samples were analyzed with pyrolysis-gas chromatography-mass spectrometry, generating a mass-based data set for MP in the marine atmosphere. Here we show the ubiquity of MP, even in remote Arctic areas with concentrations up to 37.5 ng m−3. Cluster of polyethylene terephthalate (max. 1.5 ng m−3) were universally present. TWP (max. 35 ng m−3) and cluster of polystyrene, polypropylene, and polyurethane (max. 1.1 ng m−3) were also detected. Atmospheric transport and dispersion models, suggested the introduction of MP into the marine atmosphere equally from sea- and land-based emissions, transforming the ocean from a sink into a source for MP.
Striated muscle-specific base editing enables correction of mutations causing dilated cardiomyopathy
Authors: Grosch Markus , Schraft Laura , Chan Adrian , Küchenhoff Leonie , Rapti Kleopatra , Ferreira Anne-Maud , Kornienko Julia , Li Shengdi , Radke Michael H. , Krämer Chiara , Clauder-Münster Sandra , Perlas Emerald , Backs Johannes , Gotthardt Michael , Dieterich Christoph , van den Hoogenhof Maarten M. G. , Grimm Dirk , Steinmetz Lars M.
Published: June 2023

Dilated cardiomyopathy is the second most common cause for heart failure with no cure except a high-risk heart transplantation. Approximately 30% of patients harbor heritable mutations which are amenable to CRISPR-based gene therapy. However, challenges related to delivery of the editing complex and off-target concerns hamper the broad applicability of CRISPR agents in the heart. We employ a combination of the viral vector AAVMYO with superior targeting specificity of heart muscle tissue and CRISPR base editors to repair patient mutations in the cardiac splice factor Rbm20, which cause aggressive dilated cardiomyopathy. Using optimized conditions, we repair >70% of cardiomyocytes in two Rbm20 knock-in mouse models that we have generated to serve as an in vivo platform of our editing strategy. Treatment of juvenile mice restores the localization defect of RBM20 in 75% of cells and splicing of RBM20 targets including TTN. Three months after injection, cardiac dilation and ejection fraction reach wild-type levels. Single-nuclei RNA sequencing uncovers restoration of the transcriptional profile across all major cardiac cell types and whole-genome sequencing reveals no evidence for aberrant off-target editing. Our study highlights the potential of base editors combined with AAVMYO to achieve gene repair for treatment of hereditary cardiac diseases.
Tracing metal footprints via global renewable power value chains
Authors: Fu Rao , Peng Kun , Wang Peng , Zhong Honglin , Chen Bin , Zhang Pengfei , Zhang Yiyi , Chen Dongyang , Liu Xi , Feng Kuishuang , Li Jiashuo
Published: June 2023

The globally booming renewable power industry has stimulated an unprecedented interest in metals as key infrastructure components. Many economies with different endowments and levels of technology participate in various production stages and cultivate value in global renewable power industry production networks, known as global renewable power value chains (RPVCs), complicating the identification of metal supply for the subsequent low-carbon power generation and demand. Here, we use a multi-regional input-output model (MRIO) combined with a value chain decomposition model to trace the metal footprints (MFs) and value-added of major global economies’ renewable power sectors. We find that the MFs of the global renewable power demand increased by 97% during 2005—2015. Developed economies occupy the high-end segments of RPVCs while allocating metal-intensive (but low value-added) production activities to developing economies. The fast-growing demand for renewable power in developed economies or developing economies with upper middle income, particularly China, is a major contributor to the embodied metal transfer increment within RPVCs, which is partly offset by the declining metal intensities in developing economies. Therefore, it is urgent to establish a metal-efficient and green supply chain for upstream suppliers as well as downstream renewable power installers for just transition in the power sector across the globe.
A 13-million turnover-number anionic Ir-catalyst for a selective industrial route to chiral nicotine
Authors: Yin Congcong , Jiang Ya-Fei , Huang Fanping , Xu Cong-Qiao , Pan Yingmin , Gao Shuang , Chen Gen-Qiang , Ding Xiaobing , Bai Shao-Tao , Lang Qiwei , Li Jun , Zhang Xumu
Published: June 2023

Developing catalysts with both useful enantioselectivities and million turnover numbers (TONs) for asymmetric hydrogenation of ketones is attractive for industrial production of high-value bioactive chiral entities but remains a challenging. Herein, we report an ultra-efficient anionic Ir-catalyst integrated with the concept of multidentate ligation for asymmetric hydrogenation of ketones. Biocatalysis-like efficacy of up to 99% ee (enantiomeric excess), 13,425,000 TON (turnover number) and 224 s−1 TOF (turnover frequency) were documented for benchmark acetophenone. Up to 1,000,000 TON and 99% ee were achieved for challenging pyridyl alkyl ketone where at most 10,000 TONs are previously reported. The anionic Ir-catalyst showed a novel preferred ONa/MH instead of NNa/MH bifunctional mechanism. A selective industrial route to enantiopure nicotine has been established using this anionic Ir-catalyst for the key asymmetric hydrogenation step at 500 kg batch scale, providing 40 tons scale of product.
Accounting for forest condition in Europe based on an international statistical standard
Authors: Maes Joachim , Bruzón Adrián G. , Barredo José I. , Vallecillo Sara , Vogt Peter , Rivero Inés Marí , Santos-Martín Fernando
Published: June 2023

Covering 35% of Europe’s land area, forest ecosystems play a crucial role in safeguarding biodiversity and mitigating climate change. Yet, forest degradation continues to undermine key ecosystem services that forests deliver to society. Here we provide a spatially explicit assessment of the condition of forest ecosystems in Europe following a United Nations global statistical standard on ecosystem accounting, adopted in March 2021. We measure forest condition on a scale from 0 to 1, where 0 represents a degraded ecosystem and 1 represents a reference condition based on primary or protected forests. We show that the condition across 44 forest types averaged 0.566 in 2000 and increased to 0.585 in 2018. Forest productivity and connectivity are comparable to levels observed in undisturbed or least disturbed forests. One third of the forest area was subject to declining condition, signalled by a reduction in soil organic carbon, tree cover density and species richness of threatened birds. Our findings suggest that forest ecosystems will need further restoration, improvements in management and an extended period of recovery to approach natural conditions.
Structural basis of the interaction between BCL9-Pygo and LDB-SSBP complexes in assembling the Wnt enhanceosome
Authors: Wang Hongyang , Bienz Mariann , Yan Xiao-Xue , Xu Wenqing
Published: June 2023

The Wnt enhanceosome is responsible for transactivation of Wnt-responsive genes and a promising therapeutic target for treatment of numerous cancers with Adenomatous Polyposis Coli (APC) or β-catenin mutations. How the Wnt enhanceosome is assembled remains poorly understood. Here we show that B-cell lymphoma 9 protein (BCL9), Pygopus (Pygo), LIM domain-binding protein 1 (LDB1) and single-stranded DNA-binding protein (SSBP) form a stable core complex within the Wnt enhanceosome. Their mutual interactions rely on a highly conserved N-terminal asparagine proline phenylalanine (NPF) motif of Pygo, through which the BCL9-Pygo complex binds to the LDB-SSBP core complex. Our crystal structure of a ternary complex comprising the N-terminus of human Pygo2, LDB1 and SSBP2 reveals a single LDB1-SSBP2 complex binding simultaneously to two Pygo2 molecules via their NPF motifs. These interactions critically depend on the NPF motifs which bind to a deep groove formed between LDB1 and SSBP2, potentially constituting a binding site for drugs blocking Wnt/β-catenin signaling. Analysis of human cell lines lacking LDB or Pygo supports the functional relevance of the Pygo-LDB1-SSBP2 interaction for Wnt/β-catenin-dependent transcription.
Asymmetric transformation of achiral gold nanoclusters with negative nonlinear dependence between chiroptical activity and enantiomeric excess
Authors: Liu Chang , Zhao Yan , Zhang Tai-Song , Tao Cheng-Bo , Fei Wenwen , Zhang Sheng , Li Man-Bo
Published: June 2023

The investigation of chirality at the nanoscale is important to bridge the gap between molecular and macroscopic chirality. Atomically precise metal nanoclusters provide an ideal platform for this research, while their enantiopure preparation poses a challenge. Here, we describe an efficient approach to enantiopure metal nanoclusters via asymmetric transformation, that is, achiral Au23(SC6H11)16 nanoclusters are converted into chiral and enantiopure Au24(L)2(SC6H11)16 nanoclusters by a chiral inducer phosphoramidite (L). Two enantiomers of Au24(L)2(SC6H11)16 are obtained and the crystal structures reveal their hierarchical chirality, which originates from the two introduced chiral L molecules, the transformation-triggered asymmetric rearrangement of the staple motifs on the surface of the gold core, and the helical arrangement of nanocluster molecules. The construction of this type of enantiomerically pure nanoclusters is achieved based on the easy-to-synthesize and modular L. Lastly, the chirality-related chiroptical performance was investigated, revealing a negative nonlinear CD-ee dependence.
The ER calcium channel Csg2 integrates sphingolipid metabolism with autophagy
Authors: Liu Shiyan , Chen Mutian , Wang Yichang , Lei Yuqing , Huang Ting , Zhang Yabin , Lam Sin Man , Li Huihui , Qi Shiqian , Geng Jia , Lu Kefeng
Published: June 2023

Sphingolipids are ubiquitous components of membranes and function as bioactive lipid signaling molecules. Here, through genetic screening and lipidomics analyses, we find that the endoplasmic reticulum (ER) calcium channel Csg2 integrates sphingolipid metabolism with autophagy by regulating ER calcium homeostasis in the yeastSaccharomyces cerevisiae. Csg2 functions as a calcium release channel and maintains calcium homeostasis in the ER, which enables normal functioning of the essential sphingolipid synthase Aur1. Under starvation conditions, deletion of Csg2 causes increases in calcium levels in the ER and then disturbs Aur1 stability, leading to accumulation of the bioactive sphingolipid phytosphingosine, which specifically and completely blocks autophagy and induces loss of starvation resistance in cells. Our findings indicate that calcium homeostasis in the ER mediated by the channel Csg2 translates sphingolipid metabolism into autophagy regulation, further supporting the role of the ER as a signaling hub for calcium homeostasis, sphingolipid metabolism and autophagy.
Anxiety in synucleinopathies: neuronal circuitry, underlying pathomechanisms and current therapeutic strategies
Authors: Lai Thuy Thi , Gericke Birthe , Feja Malte , Conoscenti Michael , Zelikowsky Moriel , Richter Franziska
Published: June 2023

Synucleinopathies are neurodegenerative disorders characterized by alpha-synuclein (αSyn) accumulation in neurons or glial cells, including Parkinson’s disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA). αSyn-related pathology plays a critical role in the pathogenesis of synucleinopathies leading to the progressive loss of neuronal populations in specific brain regions and the development of motor and non-motor symptoms. Anxiety is among the most frequent non-motor symptoms in patients with PD, but it remains underrecognized and undertreated, which significantly reduces the quality of life for patients. Anxiety is defined as a neuropsychiatric complication with characteristics such as nervousness, loss of concentration, and sweating due to the anticipation of impending danger. In patients with PD, neuropathology in the amygdala, a central region in the anxiety and fear circuitry, may contribute to the high prevalence of anxiety. Studies in animal models reported αSyn pathology in the amygdala together with alteration of anxiety or fear learning response. Therefore, understanding the progression, extent, and specifics of pathology in the anxiety and fear circuitry in synucleinopathies will suggest novel approaches to the diagnosis and treatment of neuropsychiatric symptoms. Here, we provide an overview of studies that address neuropsychiatric symptoms in synucleinopathies. We offer insights into anxiety and fear circuitry in animal models and the current implications for therapeutic intervention. In summary, it is apparent that anxiety is not a bystander symptom in these disorders but reflects early pathogenic mechanisms in the cortico-limbic system which may even contribute as a driver to disease progression.
Genomes of fungi and relatives reveal delayed loss of ancestral gene families and evolution of key fungal traits
Authors: Merényi Zsolt , Krizsán Krisztina , Sahu Neha , Liu Xiao-Bin , Bálint Balázs , Stajich Jason E. , Spatafora Joseph W. , Nagy László G.
Published: June 2023

Fungi are ecologically important heterotrophs that have radiated into most niches on Earth and fulfil key ecological services. Despite intense interest in their origins, major genomic trends of their evolutionary route from a unicellular opisthokont ancestor to derived multicellular fungi remain poorly known. Here we provide a highly resolved genome-wide catalogue of gene family changes across fungal evolution inferred from the genomes of 123 fungi and relatives. We show that a dominant trend in early fungal evolution has been the gradual shedding of protist genes and the punctuated emergence of innovation by two main gene duplication events. We find that the gene content of non-Dikarya fungi resembles that of unicellular opisthokonts in many respects, owing to the conservation of protist genes in their genomes. The most rapidly duplicating gene groups included extracellular proteins and transcription factors, as well as ones linked to the coordination of nutrient uptake with growth, highlighting the transition to a sessile osmotrophic feeding strategy and subsequent lifestyle evolution as important elements of early fungal history. These results suggest that the genomes of pre-fungal ancestors evolved into the typical filamentous fungal genome by a combination of gradual gene loss, turnover and several large duplication events rather than by abrupt changes. Consequently, the taxonomically defined Fungi represents a genomically non-uniform assemblage of species.
Intrinsic strong light-matter coupling with self-hybridized bound states in the continuum in van der Waals metasurfaces
Authors: Weber Thomas , Kühner Lucca , Sortino Luca , Ben Mhenni Amine , Wilson Nathan P. , Kühne Julius , Finley Jonathan J. , Maier Stefan A. , Tittl Andreas
Published: June 2023

Photonic bound states in the continuum (BICs) provide a standout platform for strong light-matter coupling with transition metal dichalcogenides (TMDCs) but have so far mostly been implemented as traditional all-dielectric metasurfaces with adjacent TMDC layers, incurring limitations related to strain, mode overlap and material integration. Here, we demonstrate intrinsic strong coupling in BIC-driven metasurfaces composed of nanostructured bulk tungsten disulfide (WS2) and exhibiting resonances with sharp, tailored linewidths and selective enhancement of light-matter interactions. Tuning of the BIC resonances across the exciton resonance in bulk WS2 is achieved by varying the metasurface unit cells, enabling strong coupling with an anticrossing pattern and a Rabi splitting of 116 meV. Crucially, the coupling strength itself can be controlled and is shown to be independent of material-intrinsic losses. Our self-hybridized metasurface platform can readily incorporate other TMDCs or excitonic materials to deliver fundamental insights and practical device concepts for polaritonic applications.
Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids
Authors: Rybak-Wolf Agnieszka , Wyler Emanuel , Pentimalli Tancredi Massimo , Legnini Ivano , Oliveras Martinez Anna , Glažar Petar , Loewa Anna , Kim Seung Joon , Kaufer Benedikt B. , Woehler Andrew , Landthaler Markus , Rajewsky Nikolaus
Published: June 2023

Herpes simplex encephalitis is a life-threatening disease of the central nervous system caused by herpes simplex viruses (HSVs). Following standard of care with antiviral acyclovir treatment, most patients still experience various neurological sequelae. Here we characterize HSV-1 infection of human brain organoids by combining single-cell RNA sequencing, electrophysiology and immunostaining. We observed strong perturbations of tissue integrity, neuronal function and cellular transcriptomes. Under acyclovir treatment viral replication was stopped, but did not prevent HSV-1-driven defects such as damage of neuronal processes and neuroepithelium. Unbiased analysis of pathways deregulated upon infection revealed tumour necrosis factor activation as a potential causal factor. Combination of anti-inflammatory drugs such as necrostatin-1 or bardoxolone methyl with antiviral treatment prevented the damages caused by infection, indicating that tuning the inflammatory response in acute infection may improve current therapeutic strategies.
An Observation-Based Dataset of Global Sub-Daily Precipitation Indices (GSDR-I)
Authors: Pritchard David , Lewis Elizabeth , Blenkinsop Stephen , Patino Velasquez Luis , Whitford Anna , Fowler Hayley J.
Published: June 2023

Precipitation indices based on daily gauge observations are well established, openly available and widely used to detect and understand climate change. However, in many areas of climate science and risk management, it has become increasingly important to understand precipitation characteristics, variability and extremes at shorter (sub-daily) durations. Yet, no unified dataset of sub-daily indices has previously been available, due in large part to the lesser availability of suitable observations. Following extensive efforts in data collection and quality control, this study presents a new global dataset of sub-daily precipitation indices calculated from a unique database of 18,591 gauge time series. Developed together with prospective users, the indices describe sub-daily precipitation variability and extremes in terms of intensity, duration and frequency properties. The indices are published for each gauge where possible, alongside a gridded data product based on all gauges. The dataset will be useful in many fields concerned with variability and extremes in the climate system, as well as in climate model evaluation and management of floods and other risks.
A Database of Snow on Sea Ice in the Central Arctic Collected during the MOSAiC expedition
Authors: Macfarlane Amy R. , Schneebeli Martin , Dadic Ruzica , Tavri Aikaterini , Immerz Antonia , Polashenski Chris , Krampe Daniela , Clemens-Sewall David , Wagner David N. , Perovich Donald K. , Henna-Reetta Hannula , Raphael Ian , Matero Ilkka , Regnery Julia , Smith Madison M. , Nicolaus Marcel , Jaggi Matthias , Oggier Marc , Webster Melinda A. , Lehning Michael , Kolabutin Nikolai , Itkin Polona , Naderpour Reza , Pirazzini Roberta , Hämmerle Stefan , Arndt Stefanie , Fons Steven
Published: June 2023

Snow plays an essential role in the Arctic as the interface between the sea ice and the atmosphere. Optical properties, thermal conductivity and mass distribution are critical to understanding the complex Arctic sea ice system’s energy balance and mass distribution. By conducting measurements from October 2019 to September 2020 on the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition, we have produced a dataset capturing the year-long evolution of the physical properties of the snow and surface scattering layer, a highly porous surface layer on Arctic sea ice that evolves due to preferential melt at the ice grain boundaries. The dataset includes measurements of snow during MOSAiC. Measurements included profiles of depth, density, temperature, snow water equivalent, penetration resistance, stable water isotope, salinity and microcomputer tomography samples. Most snowpit sites were visited and measured weekly to capture the temporal evolution of the physical properties of snow. The compiled dataset includes 576 snowpits and describes snow conditions during the MOSAiC expedition.
A large expert-curated cryo-EM image dataset for machine learning protein particle picking
Authors: Dhakal Ashwin , Gyawali Rajan , Wang Liguo , Cheng Jianlin
Published: June 2023

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.
A ten-year numerical hindcast of hydrodynamics and sediment dynamics in the Loire Estuary
Authors: Grasso Florent , Caillaud Matthieu
Published: June 2023

A numerical hindcast of the macrotidal Loire Estuary (France) has been generated to provide a long-term dataset (2008–2018) of estuarine hydrodynamics, temperature, salinity, and sediment dynamics. This hindcast is based on simulations coupling water motion, wave and mixed sediment models, forced with realistic conditions and extensively validated in the salinity gradient and turbidity maximum areas. These data represent extremely valuable information for diverse scientific communities, providing (i) environmental parameters for ecosystemic studies along the Loire River–sea continuum, (ii) a singular estuarine configuration for inter-comparison of estuarine functioning, and (iii) a ten-year synoptical view of a major estuarine environment of the North Atlantic Ocean.
Long non-coding RNA and circular RNA and coding RNA profiling of plasma exosomes of osteosarcoma by RNA seq
Authors: Liu Yun , Tang Haijun , Li Chong , Huang Nenggan , Miao Jifeng , Chen Lin , Luo Kai , Li Feicui , Liu Shangyu , Liao Shijie , Feng Wenyu , Zhan Xinli , Xie Tianyu , Tang Wei , Wei Qingjun , Lu Jili
Published: June 2023

Osteosarcoma (OS) is a primary bone tumor with high malignancy and the mechanism of hematogenous metastasis in OS is still not clear. The plasma exosomes derived from osteosarcoma play a key role in the process of tumor metastasis. Here, we established RNA-seq dataset for lncRNAs, circRNAs and mRNAs in plasma exosomes from 10 OS patients and 5 healthy donors. A total of 329.52 Gb of clean data was obtained. Besides, 1754 lincRNAs, 7096 known and 1935 new circRNA was identified. Finally, gene expression profiles and differentially expressed genes (DEGs) were analyzed among these 15 samples. There were 331 DEGs of mRNA, 132 of lincRNA and 489 of circRNA was obtained, respectively. This data set provides a significant resource for relevant researchers to excavate potential dysregulated lncRNAs, circRNAs and mRNAs of plasma exosomes in OS versus normal conditions.
A phylotranscriptomic dataset of angiosperm species under cold stress
Authors: Wang Shuo , Zhang Yixian , Ye Xiaoxue , Shen Yirong , Liu Hua , Zhao Xijuan , Guo Liangyu , Cao Lu , Du Yunfei , Wu Wenwu
Published: June 2023

Angiosperms are one of the most diverse and abundant plant groups that are widely distributed on Earth, from tropical to temperate and polar zones. The wide distribution of angiosperms may be attributed to the evolution of sophisticated mechanisms of environmental adaptability, including cold tolerance. Since the development of high-throughput sequencing, transcriptome has been widely utilized to gain insights into the molecular mechanisms of plants in response to cold stress. However, previous studies generally focused on single or two species, and comparative transcriptome analyses for multispecies responding to cold stress were limited. In this study, we selected 11 representative angiosperm species, performed phylotranscriptome experiments at four time points before and after cold stress, and presented a profile of cold-induced transcriptome changes in angiosperms. Our multispecies cold-responsive RNA-seq datasets provide valuable references for exploring conserved and evolutionary mechanisms of angiosperms in adaptation to cold stress.
A convolutional recurrent neural network with attention for response prediction to repetitive transcranial magnetic stimulation in major depressive disorder
Authors: Shahabi Mohsen Sadat , Shalbaf Ahmad , Rostami Reza , Kazemi Reza
Published: June 2023

Prediction of response to Repetitive Transcranial Magnetic Stimulation (rTMS) can build a very effective treatment platform that helps Major Depressive Disorder (MDD) patients to receive timely treatment. We proposed a deep learning model powered up by state-of-the-art methods to classify responders (R) and non-responders (NR) to rTMS treatment. Pre-treatment Electro-Encephalogram (EEG) signal of public TDBRAIN dataset and 46 proprietary MDD subjects were utilized to create time–frequency representations using Continuous Wavelet Transform (CWT) to be fed into the two powerful pre-trained Convolutional Neural Networks (CNN) named VGG16 and EfficientNetB0. Equipping these Transfer Learning (TL) models with Bidirectional Long Short-Term Memory (BLSTM) and attention mechanism for the extraction of most discriminative spatiotemporal features from input images, can lead to superior performance in the prediction of rTMS treatment outcome. Five brain regions named Frontal, Central, Parietal, Temporal, and occipital were assessed and the highest evaluated performance in 46 proprietary MDD subjects was acquired for the Frontal region using the TL-LSTM-Attention model based on EfficientNetB0 with accuracy, sensitivity, specificity, and Area Under the Curve (AUC) of 97.1%, 97.3%, 97.0%, and 0.96 respectively. Additionally, to test the generalizability of the proposed models, these TL-BLSTM-Attention models were evaluated on a public dataset called TDBRAIN and the highest accuracy of 82.3%, the sensitivity of 80.2%, the specificity of 81.9% and the AUC of 0.83 were obtained. Therefore, advanced deep learning methods using a time–frequency representation of EEG signals from the frontal brain region and the convolutional recurrent neural networks equipped with the attention mechanism can construct an accurate platform for the prediction of response to the rTMS treatment.
Enteral administration of the protease inhibitor gabexate mesilate preserves vascular function in experimental trauma/hemorrhagic shock
Authors: J. D. Moreira Nathalia , dos Santos Fernando , Li Joyce B. , Aletti Federico , Irigoyen Maria Claudia C. , Kistler Erik B.
Published: June 2023

Preserving vascular function is crucial for preventing multiorgan failure and death in ischemic and low-pressure states such as trauma/hemorrhagic shock (T/HS). It has recently been reported that inhibiting circulating proteases released from the bowel to the circulation during T/HS may preserve vascular function and improve outcomes following T/HS. This study aimed to evaluate the role of the serine protease inhibitor gabexate mesilate (GM) in preserving vascular function during T/HS when given enterally. We studied the vascular reactivity of mesenteric arteries from male Wistar rats treated with enteral GM (10 mg/kg) (GM-treated, n = 6) or control (Shock-control, n = 6) following (T/HS) using pressure myography. Concentration–response curves of endothelial-dependent and endothelial-independent agonists (e.g., acetylcholine, sodium nitroprusside) ranging from 10−10 to 10−5 M were performed. In a second set of experiments, ex-vivo arteries from healthy rats were perfused with plasma from shocked animals from both groups and vascular performance was similarly measured. Arteries from the GM-treated group demonstrated a preserved concentration–response curve to the α1 adrenergic agonist phenylephrine compared to arteries from Shock-control animals (− logEC50: − 5.73 ± 0.25 vs. − 6.48 ± 0.2, Shock-control vs. GM-treated, p = 0.04). When perfused with plasma from GM-treated rats, healthy arteries exhibited an even greater constriction and sensitivity to phenylephrine (− logEC50: − 6.62 ± 0.21 vs. − 7.13 ± 0.21, Shock-control vs. GM-treated, p = 0.02). Enteral GM also preserved the endothelium-dependent vascular response to agonists following T/HS and limited syndecan-1 shedding as a marker of glycocalyx compromise (41.84 ± 9 vs. 17.63 ± 3.97 ng/mL, Shock-control vs. GM-treated, p = 0.02). Syndecan-1 cleavage was correlated with plasma trypsin-like activity (r2 = 0.9611). Enteral gabexate mesilate was able to maintain vascular function in experimental T/HS, which was reflected by improved hemodynamics (mean arterial pressure 50.39 ± 7.91 vs. 64.95 ± 3.43 mmHg, Shock-control vs. GM treated, p = 0.0001). Enteral serine protease inhibition may be a potential therapeutic intervention in the treatment of T/HS.
Physics-informed neural ODE (PINODE): embedding physics into models using collocation points
Authors: Sholokhov Aleksei , Liu Yuying , Mansour Hassan , Nabi Saleh
Published: June 2023

Building reduced-order models (ROMs) is essential for efficient forecasting and control of complex dynamical systems. Recently, autoencoder-based methods for building such models have gained significant traction, but their demand for data limits their use when the data is scarce and expensive. We propose aiding a model’s training with the knowledge of physics using a collocation-based physics-informed loss term. Our innovation builds on ideas from classical collocation methods of numerical analysis to embed knowledge from a known equation into the latent-space dynamics of a ROM. We show that the addition of our physics-informed loss allows for exceptional data supply strategies that improves the performance of ROMs in data-scarce settings, where training high-quality data-driven models is impossible. Namely, for a problem of modeling a high-dimensional nonlinear PDE, our experiments show$$\times$$×5 performance gains, measured by prediction error, in a low-data regime,$$\times$$×10 performance gains in tasks of high-noise learning,$$\times$$×100 gains in the efficiency of utilizing the latent-space dimension, and$$\times$$×200 gains in tasks of far-out out-of-distribution forecasting relative to purely data-driven models. These improvements pave the way for broader adoption of network-based physics-informed ROMs in compressive sensing and control applications.
The electrical properties of isolated microtubules
Authors: Gutierrez Brenda C. , Cantiello Horacio F. , Cantero María del Rocío
Published: June 2023

This study examines the electrical properties of isolated brain microtubules (MTs), which are long hollow cylinders assembled from αβ-tubulin dimers that form cytoskeletal structures engaged in several functions. MTs are implicated in sensory functions in cilia and flagella and cellular activities that range from cell motility, vesicular traffic, and neuronal processes to cell division in the centrosomes and centrioles. We determined the electrical properties of the MTs with the loose patch clamp technique in either the presence or absence of the MT stabilizer Paclitaxel. We observed electrical oscillations at different holding potentials that responded accordingly in amplitude and polarity. At zero mV in symmetrical ionic conditions, a single MT radiated an electrical power of 10–17 W. The spectral analysis of the time records disclosed a single fundamental peak at 39 Hz in the Paclitaxel-stabilized MTs. However, a richer oscillatory response and two mean conductances were observed in the non-Paclitaxel MTs. The findings evidence that the brain MTs are electrical oscillators that behave as "ionic-based" transistors to generate, propagate, and amplify electrical signals.
A method for selecting reference beam model of VMAT plans with three 6MV beam-matched linear accelerators during radiation oncology
Authors: Li Yi , Wu Wenjing , Yuan Wei , Chai Linyan , Tang Fengwen , He Ruixin , Lu Yongkai , Zhang Yuemei , Lu Yongkai , Wang Long , Wang Mengfei , Zhang Xiaozhi , Zhang Long
Published: June 2023

Our objective was to provide a method for selecting reference beam model and evaluating the dosimetric accuracy of volumetric modulated arc therapy (VMAT) plans delivered on three Elekta beam-matched linacs during radiation oncology. Beam data was measured on three beam-matched linacs including Synergy1, Synergy2 and VersaHD. For eighteen lung and esophagus cases, fifty-four plans were generated using VMAT technique with three linac beam models respectively for point dose measurement and three-dimensional dose measurement. Each VMAT plan was executed sequentially on three linacs respectively. Measurement results were compared with treatment planning system (TPS) calculation results for all VMAT plans. Among three beam-matched linacs, discrepancy in beam output factor, percentage depth dose at 5 cm, 10 cm, 20 cm depth and MLC leaf offset are all within 1% except 20 × 20 cm2and 30 × 30 cm2field sizes, and discrepancy in beam profile is all within 2%. With comparison between measurement result and TPS calculation result, the absolute dose deviations are within the range of ± 3%, and the gamma passing rates are all over 95% for all VMAT plans, which are within the tolerance of clinical acceptability. Compared with all plans delivered on Synegy1 and VersaHD, the point dose discrepancy between measured results and TPS calculated results for plans delivered on Synergy2 is smallest, and the gamma passing rate between measured results and TPS calculated results for plans delivered on Synergy2 is highest. The beam-matched linacs demonstrate good agreement between measurement result and TPS calculation result for VMAT plans. The method can be used for selecting reference beam model for VMAT plans.
Effect of synbiotics on growth performance, gut health, and immunity status in pre-ruminant buffalo calves
Authors: Sharma Amit N. , Chaudhary Parul , Kumar Sachin , Grover Chand Ram , Mondal Goutam
Published: June 2023

Synbiotics are employed as feed additives in animal production as an alternate to antibiotics for sustaining the gut microbiota and providing protection against infections. Dairy calves require a healthy diet and management to ensure a better future for the herd of dairy animals. Therefore, the present study was carried out to investigate the effect of synbiotics formulation on growth performance, nutrient digestibility, fecal bacterial count, metabolites, immunoglobulins, blood parameters, antioxidant enzymes and immune response of pre-ruminant Murrah buffalo calves. Twenty-four apparently healthy calves (5 days old) were allotted into four groups of six calves each. Group I (control) calves were fed a basal diet of milk, calf starter and berseem with no supplements. Group II (SYN1) calves were fed with 3 g fructooligosaccharide (FOS) + Lactobacillus plantarum CRD-7 (150 ml). Group III (SYN2) calves were fed with 6 g FOS + L. plantarum CRD-7 (100 ml), whereas calves in group IV (SYN3) received 9 g FOS + L. plantarum CRD-7 (50 ml). The results showed that SYN2 had the highest (P < 0.05) crude protein digestibility and average daily gain compared to the control. Fecal counts of Lactobacilli and Bifidobacterium were also increased (P < 0.05) in supplemented groups as compared to control. Fecal ammonia, diarrhea incidence and fecal scores were reduced in treated groups while lactate, volatile fatty acids and antioxidant enzymes were improved compared to the control. Synbiotic supplementation also improved both cell-mediated and humoral immune responses in buffalo calves. These findings indicated that synbiotics formulation of 6 g FOS + L. plantarum CRD-7 in dairy calves improved digestibility, antioxidant enzymes, and immune status, as well as modulated the fecal microbiota and decreased diarrhea incidence. Therefore, synbiotics formulation can be recommended for commercial use in order to achieve sustainable animal production.
Improving recycling sorting behaviour with human eye nudges
Authors: Lotti Lorenzo , Barile Lory , Manfredi Giovanni
Published: June 2023

This paper tests whether visual nudges help direct attention towards existing instructions designed to increase waste sorting accuracy. The study was conducted in a quasi-experimental setting over a period of 9 weeks in two buildings of a large UK university campus. Two treatments on recycling behaviour were tested against a control group: one considered the impact of visual nudges in the form of human eyes; the other one combined human eye with pre-existing sorting instructions. Results show that for mixed recycling the combination of visual and information nudges decreased sorting errors by 7 percentage points. In contrast, visual nudges alone increased sorting errors by 4.5 percentage points. These findings indicate that, when combined, information and a visual nudge are cost-effective tools to significantly improve waste sorting behaviour. This paper adds to existing experimental evidence based on neuroscientific theories.
A statistical modeling approach based on the small-scale field trial and meteorological data for preliminary prediction of the impact of low temperature on Eucalyptus globulus trees
Authors: Chubachi Tomoaki , Oguchi Taichi , Morita Kazuki , Hayashi Nanami , Kikuchi Akira , Watanabe Kazuo N.
Published: June 2023

Eucalyptus trees are important for industrial forestry plantations because of their high potential for biomass production, but their susceptibility to damage at low temperatures restricts their plantation areas. In this study, a 6-year field trial of Eucalyptus globulus was conducted in Tsukuba, Japan, which is the northernmost reach of Eucalyptus plantations, and leaf damage was quantitatively monitored over four of six winters. Leaf photosynthetic quantum yield (QY) levels, an indicator of cold stress-induced damage, fluctuated synchronously with temperature in the winters. We performed a maximum likelihood estimation of the regression model explaining leaf QY using training data subsets for the first 3 years. The resulting model explained QY by the number of days when the daily maximum temperature was below 9.5 °C over approximately the last 7 weeks as an explanatory variable. The correlation coefficient and coefficient of determination of prediction by the model between the predicted and observed values were 0.84 and 0.70, respectively. The model was then used to perform two kinds of simulations. Geographical simulations of potential Eucalyptus plantation areas using global meteorological data from more than 5,000 locations around the world successfully predicted an area that generally agreed with the global Eucalyptus plantation distribution reported previously. Another simulation based on meteorological data of the past 70 years suggested that global warming will increase the potential E. globulus plantation area in Japan approximately 1.5-fold over the next 70 years. These results suggest that the model developed herein would be applicable to preliminary predictions of E. globulus cold damage in the field.