bluuebunny/crossref_metadata_2025_split huggingface dataset:
ASPSCR1::TFE3 orchestrates the angiogenic program of alveolar soft part sarcoma
Authors: Tanaka Miwa , Chuaychob Surachada , Homme Mizuki , Yamazaki Yukari , Lyu Ruyin , Yamashita Kyoko , Ae Keisuke , Matsumoto Seiichi , Kumegawa Kohei , Maruyama Reo , Qu Wei , Miyagi Yohei , Yokokawa Ryuji , Nakamura Takuro 
Published: April 2023

AbstractAlveolar soft part sarcoma (ASPS) is a soft part malignancy affecting adolescents and young adults. ASPS is characterized by a highly integrated vascular network, and its high metastatic potential indicates the importance of ASPS’s prominent angiogenic activity. Here, we find that the expression of ASPSCR1::TFE3, the fusion transcription factor causatively associated with ASPS, is dispensable for in vitro tumor maintenance; however, it is required for in vivo tumor development via angiogenesis. ASPSCR1::TFE3 is frequently associated with super-enhancers (SEs) upon its DNA binding, and the loss of its expression induces SE-distribution dynamic modification related to genes belonging to the angiogenesis pathway. Using epigenomic CRISPR/dCas9 screening, we identify Pdgfb, Rab27a, Sytl2, and Vwf as critical targets associated with reduced enhancer activities due to the ASPSCR1::TFE3 loss. Upregulation of Rab27a and Sytl2 promotes angiogenic factor-trafficking to facilitate ASPS vascular network construction. ASPSCR1::TFE3 thus orchestrates higher ordered angiogenesis via modulating the SE activity.
Confocal interferometric scattering microscopy reveals 3D nanoscopic structure and dynamics in live cells
Authors: Küppers Michelle , Albrecht David , Kashkanova Anna D. , Lühr Jennifer , Sandoghdar Vahid 
Published: April 2023

AbstractBright-field light microscopy and related phase-sensitive techniques play an important role in life sciences because they provide facile and label-free insights into biological specimens. However, lack of three-dimensional imaging and low sensitivity to nanoscopic features hamper their application in many high-end quantitative studies. Here, we demonstrate that interferometric scattering (iSCAT) microscopy operated in the confocal mode provides unique label-free solutions for live-cell studies. We reveal the nanometric topography of the nuclear envelope, quantify the dynamics of the endoplasmic reticulum, detect single microtubules, and map nanoscopic diffusion of clathrin-coated pits undergoing endocytosis. Furthermore, we introduce the combination of confocal and wide-field iSCAT modalities for simultaneous imaging of cellular structures and high-speed tracking of nanoscopic entities such as single SARS-CoV-2 virions. We benchmark our findings against simultaneously acquired fluorescence images. Confocal iSCAT can be readily implemented as an additional contrast mechanism in existing laser scanning microscopes. The method is ideally suited for live studies on primary cells that face labeling challenges and for very long measurements beyond photobleaching times.
Meta-optics empowered vector visual cryptography for high security and rapid decryption
Authors: Zhang Fei , Guo Yinghui , Pu Mingbo , Chen Lianwei , Xu Mingfeng , Liao Minghao , Li Lanting , Li Xiong , Ma Xiaoliang , Luo Xiangang 
Published: April 2023

AbstractOptical encryption is a promising approach to protecting secret information owing to the advantages of low-power consumption, parallel, high-speed, and multi-dimensional processing capabilities. Nevertheless, conventional strategies generally suffer from bulky system volume, relatively low security level, redundant measurement, and/or requirement of digital decryption algorithms. Here, we propose a general optical security strategy dubbed meta-optics-empowered vector visual cryptography, which fully exploits the abundant degrees of freedom of light as well as the spatial dislocation as key parameters, significantly upgrading the security level. We also demonstrate a decryption meta-camera that can implement the reversal coding procedure for real-time imaging display of hidden information, avoiding redundant measurement and digital post-processing. Our strategy features the merits of a compact footprint, high security, and rapid decryption, which may open an avenue for optical information security and anti-counterfeiting.
No carbon storage in growth-limited trees in a semi-arid woodland
Authors: Thompson R. Alexander , Adams Henry D. , Breshears David D. , Collins Adam D. , Dickman L. Turin , Grossiord Charlotte , Manrique‐Alba Àngela , Peltier Drew M. , Ryan Michael G. , Trowbridge Amy M. , McDowell Nate G. 
Published: April 2023

AbstractPlant survival depends on a balance between carbon supply and demand. When carbon supply becomes limited, plants buffer demand by using stored carbohydrates (sugar and starch). During drought, NSCs (non-structural carbohydrates) may accumulate if growth stops before photosynthesis. This expectation is pervasive, yet few studies have combined simultaneous measurements of drought, photosynthesis, growth, and carbon storage to test this. Using a field experiment with mature trees in a semi-arid woodland, we show that growth and photosynthesis slow in parallel as $${\psi }_{{pd}}$$

ψ

p
d

declines, preventing carbon storage in two species of conifer (J. monosperma and P. edulis). During experimental drought, growth and photosynthesis were frequently co-limited. Our results point to an alternative perspective on how plants use carbon that views growth and photosynthesis as independent processes both regulated by water availability.
Br−/BrO−-mediated highly efficient photoelectrochemical epoxidation of alkenes on α-Fe2O3
Authors: Zhao Yukun , Duan Mengyu , Deng Chaoyuan , Yang Jie , Yang Sipeng , Zhang Yuchao , Sheng Hua , Li Youji , Chen Chuncheng , Zhao Jincai 
Published: April 2023

AbstractEpoxides are significant intermediates for the manufacture of pharmaceuticals and epoxy resins. In this study, we develop a Br−/BrO− mediated photoelectrochemical epoxidation system on α-Fe2O3. High selectivity (up to >99%) and faradaic efficiency (up to 82 ± 4%) for the epoxidation of a wide range of alkenes are achieved, with water as oxygen source, which are far beyond the most reported electrochemical and photoelectrochemical epoxidation performances. Further, we can verify that the epoxidation reaction is mediated by Br−/BrO− route, in which Br− is oxidized non-radically to BrO− by an oxygen atom transfer pathway on α-Fe2O3, and the formed BrO− in turn transfers its oxygen atom to the alkenes. The non-radical mediated characteristic and the favorable thermodynamics of the oxygen atom transfer process make the epoxidation reactions very efficient. We believe that this photoelectrochemical Br−/BrO−-mediated epoxidation provides a promising strategy for value-added production of epoxides and hydrogen.
Bombyx Vasa sequesters transposon mRNAs in nuage via phase separation requiring RNA binding and self-association
Authors: Yamazaki Hiroya , Namba Yurika , Kuriyama Shogo , Nishida Kazumichi M. , Kajiya Asako , Siomi Mikiko C. 
Published: April 2023

AbstractBombyx Vasa (BmVasa) assembles non-membranous organelle, nuage or Vasa bodies, in germ cells, known as the center for Siwi-dependent transposon silencing and concomitant Ago3-piRISC biogenesis. However, details of the body assembly remain unclear. Here, we show that the N-terminal intrinsically disordered region (N-IDR) and RNA helicase domain of BmVasa are responsible for self-association and RNA binding, respectively, but N-IDR is also required for full RNA-binding activity. Both domains are essential for Vasa body assembly in vivo and droplet formation in vitro via phase separation. FAST-iCLIP reveals that BmVasa preferentially binds transposon mRNAs. Loss of Siwi function derepresses transposons but has marginal effects on BmVasa-RNA binding. This study shows that BmVasa assembles nuage by phase separation via its ability to self-associate and bind newly exported transposon mRNAs. This unique property of BmVasa allows transposon mRNAs to be sequestered and enriched in nuage, resulting in effective Siwi-dependent transposon repression and Ago3-piRISC biogenesis.
Data-driven analysis to understand long COVID using electronic health records from the RECOVER initiative
Authors: Zang Chengxi , Zhang Yongkang , Xu Jie , Bian Jiang , Morozyuk Dmitry , Schenck Edward J. , Khullar Dhruv , Nordvig Anna S. , Shenkman Elizabeth A. , Rothman Russell L. , Block Jason P. , Lyman Kristin , Weiner Mark G. , Carton Thomas W. , Wang Fei , Kaushal Rainu 
Published: April 2023

AbstractRecent studies have investigated post-acute sequelae of SARS-CoV-2 infection (PASC, or long COVID) using real-world patient data such as electronic health records (EHR). Prior studies have typically been conducted on patient cohorts with specific patient populations which makes their generalizability unclear. This study aims to characterize PASC using the EHR data warehouses from two large Patient-Centered Clinical Research Networks (PCORnet), INSIGHT and OneFlorida+, which include 11 million patients in New York City (NYC) area and 16.8 million patients in Florida respectively. With a high-throughput screening pipeline based on propensity score and inverse probability of treatment weighting, we identified a broad list of diagnoses and medications which exhibited significantly higher incidence risk for patients 30–180 days after the laboratory-confirmed SARS-CoV-2 infection compared to non-infected patients. We identified more PASC diagnoses in NYC than in Florida regarding our screening criteria, and conditions including dementia, hair loss, pressure ulcers, pulmonary fibrosis, dyspnea, pulmonary embolism, chest pain, abnormal heartbeat, malaise, and fatigue, were replicated across both cohorts. Our analyses highlight potentially heterogeneous risks of PASC in different populations.
Two-dimensional infrared-Raman spectroscopy as a probe of water’s tetrahedrality
Authors: Begušić Tomislav , Blake Geoffrey A. 
Published: April 2023

AbstractTwo-dimensional spectroscopic techniques combining terahertz (THz), infrared (IR), and visible pulses offer a wealth of information about coupling among vibrational modes in molecular liquids, thus providing a promising probe of their local structure. However, the capabilities of these spectroscopies are still largely unexplored due to experimental limitations and inherently weak nonlinear signals. Here, through a combination of equilibrium-nonequilibrium molecular dynamics (MD) and a tailored spectrum decomposition scheme, we identify a relationship between the tetrahedral order of liquid water and its two-dimensional IR-IR-Raman (IIR) spectrum. The structure-spectrum relationship can explain the temperature dependence of the spectral features corresponding to the anharmonic coupling between low-frequency intermolecular and high-frequency intramolecular vibrational modes of water. In light of these results, we propose new experiments and discuss the implications for the study of tetrahedrality of liquid water.
The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine
Authors: Li Jiang , Han Fangxu , Yuan Tongqi , Li Wei , Li Yue , Wu Harry X. , Wei Hairong , Niu Shihui 
Published: April 2023

AbstractEpigenetics has been revealed to play a crucial role in the long-term memory in plants. However, little is known about whether the epigenetic modifications occur with age progressively in conifers. Here, we present the single-base resolution DNA methylation landscapes of the 25-gigabase Chinese pine (Pinus tabuliformis) genome at different ages. The result shows that DNA methylation is closely coupled with the regulation of gene transcription. The age-dependent methylation profile with a linearly increasing trend is the most significant pattern of DMRs between ages. Two segments at the five-prime end of the first ultra-long intron in DAL1, a conservative age biomarker in conifers, shows a gradual decline of CHG methylation as the age increased, which is highly correlated with its expression profile. Similar high correlation is also observed in nine other age marker genes. Our results suggest that DNA methylation serves as an important epigenetic signature of developmental age in conifers.
Aberrant somatic calcium channel function in cNurr1 and LRRK2-G2019S mice
Authors: Skiteva Olga , Yao Ning , Mantas Ioannis , Zhang Xiaoqun , Perlmann Thomas , Svenningsson Per , Chergui Karima 
Published: April 2023

AbstractIn Parkinson’s disease (PD), axons of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNc) degenerate before their cell bodies. Calcium influx during pacemaker firing might contribute to neuronal loss, but it is not known if dysfunctions of voltage-gated calcium channels (VGCCs) occur in DA neurons somata and axon terminals. We investigated T-type and L-type VGCCs in SNc-DA neurons of two mouse models of PD: mice with a deletion of theNurr1gene in DA neurons from an adult age (cNurr1 mice), and mice bearing the G2019S mutation in the gene coding for LRRK2 (G2019S mice). Adult cNurr1 mice displayed motor and DA deficits, while middle-aged G2019S mice did not. The number and morphology of SNc-DA neurons, most of their intrinsic membrane properties and pacemaker firing were unaltered in cNurr1 and G2019S mice compared to their control and wild-type littermates. L-type VGCCs contributed to the pacemaker firing of SNc-DA neurons in G2019S mice, but not in control, wild-type, and cNurr1 mice. In cNurr1 mice, but not G2019S mice, the contribution of T-type VGCCs to the pacemaker firing of SNc-DA neurons was reduced, and somatic dopamine-D2 autoreceptors desensitized more. Altered contribution of L-type and T-type VGCCs to the pacemaker firing was not observed in the presence of a LRRK2 kinase inhibitor in G2019S mice, and in the presence of a flavonoid with antioxidant activity in G2019S and cNurr1 mice. The role of L-type and T-type VGCCs in controlling dopamine release from axon terminals in the striatum was unaltered in cNurr1 and G2019S mice. Our findings uncover opposite changes, linked to oxidative stress, in the function of two VGCCs in DA neurons somata, but not axon terminals, in two different experimental PD models.
High-throughput metabolomics for the design and validation of a diauxic shift model
Authors: Brunnsåker Daniel , Reder Gabriel K. , Soni Nikul K. , Savolainen Otto I. , Gower Alexander H. , Tiukova Ievgeniia A. , King Ross D. 
Published: April 2023

AbstractSaccharomyces cerevisiae is a very well studied organism, yet ∼20% of its proteins remain poorly characterized. Moreover, recent studies seem to indicate that the pace of functional discovery is slow. Previous work has implied that the most probable path forward is via not only automation but fully autonomous systems in which active learning is applied to guide high-throughput experimentation. Development of tools and methods for these types of systems is of paramount importance. In this study we use constrained dynamical flux balance analysis (dFBA) to select ten regulatory deletant strains that are likely to have previously unexplored connections to the diauxic shift. We then analyzed these deletant strains using untargeted metabolomics, generating profiles which were then subsequently investigated to better understand the consequences of the gene deletions in the metabolic reconfiguration of the diauxic shift. We show that metabolic profiles can be utilised to not only gaining insight into cellular transformations such as the diauxic shift, but also on regulatory roles and biological consequences of regulatory gene deletion. We also conclude that untargeted metabolomics is a useful tool for guidance in high-throughput model improvement, and is a fast, sensitive and informative approach appropriate for future large-scale functional analyses of genes. Moreover, it is well-suited for automated approaches due to relative simplicity of processing and the potential to make massively high-throughput.
Late-season corn stalk nitrate measurements across the US Midwest from 2006 to 2018
Authors: Laurent Anabelle , Cleveringa Alex , Fey Suzanne , Kyveryga Peter , Wiese Nathan , Lefebvre Mark , Newville Darren , Quinn Daniel , McGuire John , Tao Haiying , Morris Thomas F. , Miguez Fernando E. 
Published: April 2023

AbstractThe late-season Corn Stalk Nitrate Test (CSNT) is a well-known tool to help evaluate the after-the-fact performance of nitrogen management. The CSNT has the unique ability to distinguish between optimal and excessive corn nitrogen status, which makes it helpful for identifying the over-application of N so that farmers can adjust their future nitrogen decisions. This paper presents a multi-year and multi-location dataset of late-season corn stalk nitrate test measurements across the US Midwest from 2006 to 2018. The dataset consists of 32,025 corn stalk nitrate measurements from 10,675 corn fields. The nitrogen form, total N rate applied, US state, year of harvest, and climatic conditions are included for each corn field. When available, previous crop, manure source, tillage, and timing of N application are also informed. We provide a detailed description of the dataset to make it usable by the scientific community. Data are published through an R package and also available at the USDA National Agricultural Library Ag Data Commons repository and through an interactive website.
Cross-platform dataset of multiplex fluorescent cellular object image annotations
Authors: Aleynick Nathaniel , Li Yanyun , Xie Yubin , Zhang Mianlei , Posner Andrew , Roshal Lev , Pe’er Dana , Vanguri Rami S. , Hollmann Travis J. 
Published: April 2023

AbstractDefining cellular and subcellular structures in images, referred to as cell segmentation, is an outstanding obstacle to scalable single-cell analysis of multiplex imaging data. While advances in machine learning-based segmentation have led to potentially robust solutions, such algorithms typically rely on large amounts of example annotations, known as training data. Datasets consisting of annotations which are thoroughly assessed for quality are rarely released to the public. As a result, there is a lack of widely available, annotated data suitable for benchmarking and algorithm development. To address this unmet need, we release 105,774 primarily oncological cellular annotations concentrating on tumor and immune cells using over 40 antibody markers spanning three fluorescent imaging platforms, over a dozen tissue types and across various cellular morphologies. We use readily available annotation techniques to provide a modifiable community data set with the goal of advancing cellular segmentation for the greater imaging community.
A novel dataset and efficient deep learning framework for automated grading of renal cell carcinoma from kidney histopathology images
Authors: Chanchal Amit Kumar , Lal Shyam , Kumar Ranjeet , Kwak Jin Tae , Kini Jyoti 
Published: April 2023

AbstractTrends of kidney cancer cases worldwide are expected to increase persistently and this inspires the modification of the traditional diagnosis system to respond to future challenges. Renal Cell Carcinoma (RCC) is the most common kidney cancer and responsible for 80–85% of all renal tumors. This study proposed a robust and computationally efficient fully automated Renal Cell Carcinoma Grading Network (RCCGNet) from kidney histopathology images. The proposed RCCGNet contains a shared channel residual (SCR) block which allows the network to learn feature maps associated with different versions of the input with two parallel paths. The SCR block shares the information between two different layers and operates the shared data separately by providing beneficial supplements to each other. As a part of this study, we also introduced a new dataset for the grading of RCC with five different grades. We obtained 722 Hematoxylin & Eosin (H &E) stained slides of different patients and associated grades from the Department of Pathology, Kasturba Medical College (KMC), Mangalore, India. We performed comparable experiments which include deep learning models trained from scratch as well as transfer learning techniques using pre-trained weights of the ImageNet. To show the proposed model is generalized and independent of the dataset, we experimented with one additional well-established data called BreakHis dataset for eight class-classification. The experimental result shows that proposed RCCGNet is superior in comparison with the eight most recent classification methods on the proposed dataset as well as BreakHis dataset in terms of prediction accuracy and computational complexity.
Soil phosphorus availability and fractionation in response to different phosphorus sources in alkaline and acid soils: a short-term incubation study
Authors: Wang Yuan , Zhang Wei , Müller Torsten , Lakshmanan Prakash , Liu Yu , Liang Tao , Wang Lin , Yang Huaiyu , Chen Xinping 
Published: April 2023

AbstractUsing agricultural wastes as an alternative phosphorus (P) source has great prospects to improve soil P status. A 70-day incubation experiment was carried out to investigate the effects of superphosphate (SSP), poultry manure (PM), cattle manure (CM), maize straw (MS), and cattle bone meal (CB) with the same total P input on soil P availability and fractions in typical acidic (red soil) and alkaline (fluvo-aquic soil) soils. The results showed that in both fluvo-aquic and red soils, CM out-performed other P sources in improving soil P availability. Changes in soil Olsen-P (ΔOlsen-P) were greater in fluvo-aquic soils with SSP, PM and CM additions than in red soils. Among the different P sources used, only CM has increased the labile soil P fractions to levels similar to that with SSP. Compared with SSP, more monoester P and inositol hexakisphosphate were detected in soils amended with PM and CM. A structural equation model (SEM) analysis suggested that soil pH had a direct positive effect on the labile P fractions in the acidic red soil amended with different P sources. In summary, CM is a superior P source for increasing plant available soil P, with considerable practical implications for P recycling.
Consequences of changing Canadian activity patterns since the COVID-19 pandemic include increased residential radon gas exposure for younger people
Authors: Cholowsky Natasha L. , Chen Myra J. , Selouani Ghozllane , Pett Sophie C. , Pearson Dustin D. , Danforth John M. , Fenton Shelby , Rydz Ela , Diteljan Matthew J. , Peters Cheryl E. , Goodarzi Aaron A. 
Published: April 2023

AbstractThe COVID-19 pandemic has produced widespread behaviour changes that shifted how people split their time between different environments, altering health risks. Here, we report an update of North American activity patterns before and after pandemic onset, and implications to radioactive radon gas exposure, a leading cause of lung cancer. We surveyed 4009 Canadian households home to people of varied age, gender, employment, community, and income. Whilst overall time spent indoors remained unchanged, time in primary residence increased from 66.4 to 77% of life (+ 1062 h/y) after pandemic onset, increasing annual radiation doses from residential radon by 19.2% (0.97 mSv/y). Disproportionately greater changes were experienced by younger people in newer urban or suburban properties with more occupants, and/or those employed in managerial, administrative, or professional roles excluding medicine. Microinfluencer-based public health messaging stimulated health-seeking behaviour amongst highly impacted, younger groups by > 50%. This work supports re-evaluating environmental health risks modified by still-changing activity patterns.