bluuebunny/crossref_metadata_2025 huggingface dataset:
Oblique Propagation and Refraction of Gravity Waves Over the Andes Observed by GLORIA and ALIMA During the SouthTRAC Campaign
Authors: Krasauskas L. , Kaifler B. , Rhode S. , Ungermann J. , Woiwode W. , Preusse P.
Published: April 2023

Gravity waves (GW) carry energy and momentum from the troposphere to the middle atmosphere and have a strong influence on the circulation there. Global atmospheric models cannot fully resolve GWs, and therefore rely on highly simplified GW parametrizations that, among other limitations, account for vertical wave propagation only and neglect refraction. This is a major source of uncertainty in models, and leads to well‐known problems, such as the late break‐up of polar vortex due to the “missing” GW drag around 60°S. To investigate these phenomena, GW observations over Southern Andes were performed during SouthTRAC aircraft campaign. This paper presents measurements from a SouthTRAC flight on 21 September 2019, including 3‐D tomographic temperature data of the infrared limb imager GLORIA (8–15 km altitude) and temperature profiles of the ALIMA lidar (20–80 km altitude). GLORIA observations revealed multiple overlapping waves of different wavelengths. 3‐D wave vectors were determined from the GLORIA data and used to initialize a GW ray‐tracer. The ray‐traced GW parameters were compared with ALIMA observations, showing good agreement between the instruments and direct evidence of oblique (partly meridional) GW propagation. ALIMA data analysis confirmed that most waves at 25–40 km altitudes were indeed orographic GWs, including waves seemingly upstream of the Andes. We directly observed horizontal GW refraction, which has not been achieved before SouthTRAC. Refraction and oblique propagation caused significant meridional transport of horizontal momentum as well as horizontal momentum exchange between waves and the background flow all along the wave paths, not just in wave excitation and breaking regions.
Hand Magnets and the Destruction of Ancient Meteorite Magnetism
Authors: Vervelidou Foteini , Weiss Benjamin P. , Lagroix France
Published: April 2023

Meteorites provide invaluable records of planetary formation and evolution. Studies of their paleomagnetism have constrained accretion in the protoplanetary disk, the thermal evolution and differentiation of planetesimals, and the history of planetary dynamos. Yet, the potential of these magnetic records in advancing the field of planetary science is severely hindered by a widely used technique: application of hand magnets to assist in meteorite classification. Touching a meteorite with a magnet results in near‐instantaneous destruction of its magnetic record. Here, we showcase the destructive effects of exposing meteorites to magnets through numerical modeling, a controlled remagnetization experiment on a terrestrial basalt, and a paleomagnetic study of the oldest known Martian meteorite, the Northwest Africa (NWA) 7034 pairing group. NWA 7034 is a polymict regolith breccia containing zircon crystals with crystallization ages older than 4.4 billion years. As such it contains materials that are sufficiently old to have formed during the time Mars is most likely to have had a core dynamo. Unfortunately, we found that all nine paired stones of NWA 7034 that we investigated were remagnetized by hand magnets, as has been observed for many other hot desert meteorites. We recommend that magnets not be applied to meteorites during collection and curation. Instead, a low‐field susceptibility meter is a far more sensitive and completely nondestructive tool for meteorite classification.
Effects of Forcing Uncertainties on the Thermospheric and Ionospheric States During Geomagnetic Storm and Quiet Periods
Authors: Hsu C.‐T. , Pedatella N. M.
Published: April 2023

Upper‐atmospheric weather prediction is subject to various types of forcing uncertainties. Understanding the sensitivity of the thermosphere and ionosphere to forcing uncertainties under different geomagnetic conditions is critical for space weather predictions. Ensemble simulations of a whole atmospheric model, the National Center for Atmospheric Research Whole Atmosphere Community Climate Model with thermosphere and ionosphere eXtension (WACCM‐X), with various kinds of forcing perturbation is used to evaluate the upper atmosphere's response to the uncertainties of different forcings. Two kinds of forcing uncertainties are addressed: the lower atmospheric wave and tide forcing uncertainties and high‐latitude electric potential uncertainty. These uncertainties are estimated in different ways and applied to generate forcing perturbations in the WACCM‐X. WACCM‐X can simulate the upper atmosphere's response to the uncertainties of the lower atmospheric wave and tide forcings related to different lower atmospheric conditions. High‐latitude electric potential uncertainty is estimated based on the SuperMag and SuperDARN data through the Assimilative Mapping of Geospace Observations, which is applied to generate the forcing perturbation of high‐latitude electric potential in the WACCM‐X. The results show that the impact of high‐latitude electric potential uncertainty is significant globally during the 2013 St. Patrick's Day storm. The lower atmospheric wave and tide forcing uncertainties result in a global impact on the upper atmosphere in the model. The sensitivity of the upper atmosphere to both uncertainties is approximately the combination of the two individually, though the combined effects are not a linear sum, indicating non‐linearities in the ionosphere and thermosphere response to forcing uncertainties.
Iron, glucose and fat metabolism and obesity: an intertwined relationship
Authors: Hilton Catriona , Sabaratnam Rugivan , Drakesmith Hal , Karpe Fredrik
Published: April 2023

A bidirectional relationship exists between adipose tissue metabolism and iron regulation. Total body fat, fat distribution and exercise influence iron status and components of the iron-regulatory pathway, including hepcidin and erythroferrone. Conversely, whole body and tissue iron stores associate with fat mass and distribution and glucose and lipid metabolism in adipose tissue, liver, and muscle. Manipulation of the iron-regulatory proteins erythroferrone and erythropoietin affects glucose and lipid metabolism. Several lines of evidence suggest that iron accumulation and metabolism may play a role in the development of metabolic diseases including obesity, type 2 diabetes, hyperlipidaemia and non-alcoholic fatty liver disease. In this review we summarise the current understanding of the relationship between iron homoeostasis and metabolic disease.
Sex-specific Mendelian randomisation to assess the causality of sex differences in the effects of risk factors and treatment: spotlight on hypertension
Authors: de Ruiter Sophie C. , Schmidt A. Floriaan , Grobbee Diederick E. , den Ruijter Hester M. , Peters Sanne A. E.
Published: April 2023

Hypertension is a key modifiable risk factor for cardiovascular disease. Several observational studies have found a stronger association of blood pressure and cardiovascular disease risk in women compared to men. Since observational studies can be affected by sex-specific residual confounding and reverse causation, it remains unclear whether these differences reflect actual differential effects. Other study designs are needed to uncover the causality of sex differences in the strength of risk factor and treatment effects. Mendelian randomisation (MR) uses genetic variants as instrumental variables to provide evidence about putative causal relations between risk factors and outcomes. By exploiting the random allocation of genes at gamete forming, MR is unaffected by confounding and results in more reliable causal effect estimates. In this review, we discuss why and how sex-specific MR and cis-MR could be used to study sex differences in risk factor and drug target effects. Sex-specific MR can be helpful to strengthen causal inferences in the field of sex differences, where it is often challenging to distinguish nature from nurture. The challenge of sex-specific (drug target) MR lays in leveraging robust genetic instruments from sex-specific GWAS studies which are not commonly available. Knowledge on sex-specific causal effects of hypertension, or other risk factors, could improve clinical practice and health policies by tailoring interventions based on personalised risk. Drug target MR can help to determine the anticipated on-target effects of a drug compound and to identify targets to pursue in drug development.
NICU sensory experiences associated with positive outcomes: an integrative review of evidence from 2015–2020
Authors: Pineda Roberta , Kellner Polly , Guth Rebecca , Gronemeyer Audrey , Smith Joan
Published: April 2023

To inform changes to the Supporting and Enhancing NICU Sensory Experiences (SENSE) program, studies investigating sensory-based interventions in the NICU with preterm infants born ≤32 weeks were identified. Studies published between October 2015 to December 2020, and with outcomes related to infant development or parent well-being, were included in this integrative review. The systematic search used databases including MEDLINE, Cumulative Index to Nursing and Allied Health Literature, the Cochrane Library, and Google Scholar. Fifty-seven articles (15 tactile, 9 auditory, 5 visual, 1 gustatory/olfactory, 5 kinesthetic, and 22 multimodal) were identified. The majority of the sensory interventions that were identified within the articles were reported in a previous integrative review (1995–2015) and already included in the SENSE program. New evidence has led to refinements of the SENSE program, notably the addition of position changes across postmenstrual age (PMA) and visual tracking starting at 34 weeks PMA.
Phase separation of DDX21 promotes colorectal cancer metastasis via MCM5-dependent EMT pathway
Authors: Gao Huabin , Wei Huiting , Yang Yang , Li Hui , Liang Jiangtao , Ye Jiecheng , Zhang Fenfen , Wang Liyuan , Shi Huijuan , Wang Jia , Han Anjia
Published: April 2023

RNA binding proteins (RBPs) contributes to cancer progression, but the underlying mechanism reminds unclear. Here, we find that DDX21, a representative RBP, is highly expressed in colorectal cancer (CRC), which leads to CRC cell migration and invasion in vitro, and CRC to liver metastasis and lung metastasis in vivo. This effect of DDX21 on CRC metastasis is correlated to the activation of Epithelial-mesenchymal transition (EMT) pathway. Moreover, we reveal that DDX21 protein is phase separated in vitro and in CRC cells, which controls CRC metastasis. Phase-separated DDX21 highly binds on MCM5 gene locus, which is markedly reduced when phase separation is disrupted by mutations on its intrinsically disordered region (IDR). The impaired metastatic ability of CRC upon DDX21 loss is restored by ectopic expression of MCM5, indicating MCM5 is a key downstream target of DDX21 for CRC metastasis. Furthermore, co-higher expressions of DDX21 and MCM5 is significantly correlated with poor survival outcomes of stage III and IV CRC patients, indicating the importance of this mechanism in CRC late and metastatic stage. Altogether, our results elucidate a new model of DDX21 in regulating CRC metastasis via phase separation.
Regulation of c-SMAC formation and AKT-mTOR signaling by the TSG101-IFT20 axis in CD4+ T cells
Authors: Jeong Jiung , Kang In , Kim Yumin , Ku Keun Bon , Park Jang Hyun , Kim Hyun-Jin , Kim Chae Won , La Jeongwoo , Jung Hi Eun , Kim Hyeon Cheol , Choi Young Joon , Kim Jaeho , Kim Joon , Lee Heung Kyu
Published: April 2023

CD4+ T cells play major roles in the adaptive immune system, which requires antigen recognition, costimulation, and cytokines for its elaborate orchestration. Recent studies have provided new insight into the importance of the supramolecular activation cluster (SMAC), which comprises concentric circles and is involved in the amplification of CD4+ T cell activation. However, the underlying mechanism of SMAC formation remains poorly understood. Here, we performed single-cell RNA sequencing of CD4+ T cells left unstimulated and stimulated with anti-CD3 and anti-CD28 antibodies to identify novel proteins involved in their regulation. We found that intraflagellar transport 20 (IFT20), previously known as cilia-forming protein, was upregulated in antibody-stimulated CD4+ T cells compared to unstimulated CD4+ T cells. We also found that IFT20 interacted with tumor susceptibility gene 101 (TSG101), a protein that endocytoses ubiquitinated T-cell receptors. The interaction between IFT20 and TSG101 promoted SMAC formation, which led to amplification of AKT-mTOR signaling. However, IFT20-deficient CD4+ T cells showed SMAC malformation, resulting in reduced CD4+ T cell proliferation, aerobic glycolysis, and cellular respiration. Finally, mice with T-cell-specific IFT20 deficiency exhibited reduced allergen-induced airway inflammation. Thus, our data suggest that the IFT20-TSG101 axis regulates AKT-mTOR signaling via SMAC formation.
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

Alveolar 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

Bright-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

Optical 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

Plant 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

Epoxides 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

Bombyx 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

Recent 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

Two-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

Epigenetics 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

In 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

Saccharomyces 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

The 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

Defining 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

Trends 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

Using 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

The 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.
Projecting the impact of an ebola virus outbreak on endangered mountain gorillas
Authors: Zimmerman Dawn M. , Hardgrove Emily , Sullivan Sara , Mitchell Stephanie , Kambale Eddy , Nziza Julius , Ssebide Benard , Shalukoma Chantal , Cranfield Mike , Pandit Pranav S. , Troth Sean P. , Callicrate Taylor , Miller Philip , Gilardi Kirsten , Lacy Robert C.
Published: April 2023

Ebola virus is highly lethal for great apes. Estimated mortality rates up to 98% have reduced the global gorilla population by approximately one-third. As mountain gorillas (Gorilla beringei beringei) are endangered, with just over 1000 individuals remaining in the world, an outbreak could decimate the population. Simulation modeling was used to evaluate the potential impact of an Ebola virus outbreak on the mountain gorilla population of the Virunga Massif. Findings indicate that estimated contact rates among gorilla groups are high enough to allow rapid spread of Ebola, with less than 20% of the population projected to survive at 100 days post-infection of just one gorilla. Despite increasing survival with vaccination, no modeled vaccination strategy prevented widespread infection. However, the model projected that survival rates greater than 50% could be achieved by vaccinating at least half the habituated gorillas within 3 weeks of the first infectious individual.
Using machine learning to predict student retention from socio-demographic characteristics and app-based engagement metrics
Authors: Matz Sandra C. , Bukow Christina S. , Peters Heinrich , Deacons Christine , Dinu Alice , Stachl Clemens
Published: April 2023

Student attrition poses a major challenge to academic institutions, funding bodies and students. With the rise of Big Data and predictive analytics, a growing body of work in higher education research has demonstrated the feasibility of predicting student dropout from readily available macro-level (e.g., socio-demographics or early performance metrics) and micro-level data (e.g., logins to learning management systems). Yet, the existing work has largely overlooked a critical meso-level element of student success known to drive retention: students’ experience at university and their social embeddedness within their cohort. In partnership with a mobile application that facilitates communication between students and universities, we collected both (1) institutional macro-level data and (2) behavioral micro and meso-level engagement data (e.g., the quantity and quality of interactions with university services and events as well as with other students) to predict dropout after the first semester. Analyzing the records of 50,095 students from four US universities and community colleges, we demonstrate that the combined macro and meso-level data can predict dropout with high levels of predictive performance (average AUC across linear and non-linear models = 78%; max AUC = 88%). Behavioral engagement variables representing students’ experience at university (e.g., network centrality, app engagement, event ratings) were found to add incremental predictive power beyond institutional variables (e.g., GPA or ethnicity). Finally, we highlight the generalizability of our results by showing that models trained on one university can predict retention at another university with reasonably high levels of predictive performance.
DUSP6 is a memory retention feedback regulator of ERK signaling for cellular resilience of human pluripotent stem cells in response to dissociation
Authors: Yoo Dae Hoon , Im Young Sam , Oh Ji Young , Gil Dayeon , Kim Yong-Ou
Published: April 2023

Cultured human pluripotent stem cells (hPSCs) grow as colonies that require breakdown into small clumps for further propagation. Although cell death mechanism by single-cell dissociation of hPSCs has been well defined, how hPSCs respond to the deadly stimulus and recover the original status remains unclear. Here we show that dissociation of hPSCs immediately activates ERK, which subsequently activates RSK and induces DUSP6, an ERK-specific phosphatase. Although the activation is transient, DUSP6 expression persists days after passaging. DUSP6 depletion using the CRISPR/Cas9 system reveals that DUSP6 suppresses the ERK activity over the long term. Elevated ERK activity by DUSP6 depletion increases both viability of hPSCs after single-cell dissociation and differentiation propensity towards mesoderm and endoderm lineages. These findings provide new insights into how hPSCs respond to dissociation in order to maintain pluripotency.
Disruptions of default mode network and precuneus connectivity associated with cognitive dysfunctions in tinnitus
Authors: Rosemann Stephanie , Rauschecker Josef P.
Published: April 2023

Tinnitus is the perception of a ringing, buzzing or hissing sound “in the ear” without external stimulation. Previous research has demonstrated changes in resting-state functional connectivity in tinnitus, but findings do not overlap and are even contradictory. Furthermore, how altered functional connectivity in tinnitus is related to cognitive abilities is currently unknown. Here we investigated resting-state functional connectivity differences between 20 patients with chronic tinnitus and 20 control participants matched in age, sex and hearing loss. All participants underwent functional magnetic resonance imaging, audiometric and cognitive assessments, and filled in questionnaires targeting anxiety and depression. Significant differences in functional connectivity between tinnitus patients and control participants were not obtained. However, we did find significant associations between cognitive scores and functional coupling of the default mode network and the precuneus with the superior parietal lobule, supramarginal gyrus, and orbitofrontal cortex. Further, tinnitus distress correlated with connectivity between the precuneus and the lateral occipital complex. This is the first study providing evidence for disruptions of default mode network and precuneus coupling that are related to cognitive dysfunctions in tinnitus. The constant attempt to decrease the tinnitus sensation might occupy certain brain resources otherwise available for concurrent cognitive operations.
Association between maternal postpartum depressive symptoms, socioeconomic factors, and birth outcomes with infant growth in South Africa
Authors: Ricci Hannah , Nakiranda Regina , Malan Linda , Kruger Herculina S. , Visser Marina , Ricci Cristian , Faber Mieke , Smuts Cornelius M.
Published: April 2023

This study aimed to investigate the association between maternal postpartum depressive symptoms, household demographic, socioeconomic, and infant characteristics with infant physical growth, and how these factors correlate to determine latent factors. This study was based on the baseline data of a 6-month randomised controlled trial aimed at providing an egg a day to infants aged 6 to 9-months from a low socioeconomic community in South Africa. Information collected on household demographic, socioeconomic, and infant characteristics was by face-to-face structured interviews, and trained assessors took anthropometric measurements. The Edinburgh Postnatal Depression Scale (EPDS) was used to assess maternal postpartum depressive symptoms. The analysis was based on 428 mother-infant pairs. Total EPDS score and its subscales score were not associated with stunting or underweight risk. However, a three- to four-fold increased risk of stunting and underweight, respectively was observed for premature birth. Low birthweight was associated with an estimated six-fold increased risk of underweight and stunting. Being female was associated with about 50% reduced risk of stunting and underweight. In conclusion, more robust studies are needed to substantiate these findings, with more awareness creation on the consequences of LBW and prematurity on the physical growth of infants from resource-limited settings.
The unraveling of balanced complexes in metabolic networks
Authors: Langary Damoun , Küken Anika , Nikoloski Zoran
Published: April 2023

Balanced complexes in biochemical networks are at core of several theoretical and computational approaches that make statements about the properties of the steady states supported by the network. Recent computational approaches have employed balanced complexes to reduce metabolic networks, while ensuring preservation of particular steady-state properties; however, the underlying factors leading to the formation of balanced complexes have not been studied, yet. Here, we present a number of factorizations providing insights in mechanisms that lead to the origins of the corresponding balanced complexes. The proposed factorizations enable us to categorize balanced complexes into four distinct classes, each with specific origins and characteristics. They also provide the means to efficiently determine if a balanced complex in large-scale networks belongs to a particular class from the categorization. The results are obtained under very general conditions and irrespective of the network kinetics, rendering them broadly applicable across variety of network models. Application of the categorization shows that all classes of balanced complexes are present in large-scale metabolic models across all kingdoms of life, therefore paving the way to study their relevance with respect to different properties of steady states supported by these networks.
Sensor-cable-probe and sampler for early detection and prediction of dry matter loss and real-time corn grain quality in transport and storage
Authors: Nunes Camila Fontoura , Coradi Paulo Carteri , Jaques Lanes Beatriz Acosta , Teodoro Larissa Pereira Ribeiro , Teodoro Paulo Eduardo
Published: April 2023

Taking into account that the transport of grains can be carried out over long distances and that the mass of grains during transport often has high moisture content, there may be risks of heat and moisture transfer and heating of the grains mass, proving quanti-qualitative losses. Thus, this study aimed to validate a method with probe system for real-time monitoring of temperature, relative humidity and carbon dioxide in the grain mass of corn during transport and storage to detect early dry matter losses and predict possible changes on the grain physical quality. The equipment consisted of a microcontroller, system's hardware, digital sensors to detect air temperature and relative humidity, a non-destructive infrared sensor to detect CO2 concentration. Real-time monitoring system determined early and satisfactorily in an indirect way the changes in the physical quality of the grains confirming by the physical analyses of electrical conductivity and germination. The equipment in real-time monitoring and the application of Machine Learning was effective to predict dry matter loss, due to the high equilibrium moisture content and respiration of the grain mass on the 2-h period. All machine learning models, except support vector machine, obtained satisfactory results, equaling the multiple linear regression analysis.