bluuebunny/crossref_metadata_2025_split huggingface dataset:
A protein kinase coordinates cycles of autophagy and glutaminolysis in invasive hyphae of the fungus Magnaporthe oryzae within rice cells
Authors: Li Gang , Gong Ziwen , Dulal Nawaraj , Marroquin-Guzman Margarita , Rocha Raquel O. , Richter Michael , Wilson Richard A. 
Published: July 2023

AbstractThe blast fungus Magnaporthe oryzae produces invasive hyphae in living rice cells during early infection, separated from the host cytoplasm by plant-derived interfacial membranes. However, the mechanisms underpinning this intracellular biotrophic growth phase are poorly understood. Here, we show that the M. oryzae serine/threonine protein kinase Rim15 promotes biotrophic growth by coordinating cycles of autophagy and glutaminolysis in invasive hyphae. Alongside inducing autophagy, Rim15 phosphorylates NAD-dependent glutamate dehydrogenase, resulting in increased levels of α-ketoglutarate that reactivate target-of-rapamycin (TOR) kinase signaling, which inhibits autophagy. Deleting RIM15 attenuates invasive hyphal growth and triggers plant immunity; exogenous addition of α-ketoglutarate prevents these effects, while glucose addition only suppresses host defenses. Our results indicate that Rim15-dependent cycles of autophagic flux liberate α-ketoglutarate – via glutaminolysis – to reactivate TOR signaling and fuel biotrophic growth while conserving glucose for antioxidation-mediated host innate immunity suppression.
Controlled alignment of supermoiré lattice in double-aligned graphene heterostructures
Authors: Hu Junxiong , Tan Junyou , Al Ezzi Mohammed M. , Chattopadhyay Udvas , Gou Jian , Zheng Yuntian , Wang Zihao , Chen Jiayu , Thottathil Reshmi , Luo Jiangbo , Watanabe Kenji , Taniguchi Takashi , Wee Andrew Thye Shen , Adam Shaffique , Ariando A. 
Published: July 2023

AbstractThe supermoiré lattice, built by stacking two moiré patterns, provides a platform for creating flat mini-bands and studying electron correlations. An ultimate challenge in assembling a graphene supermoiré lattice is in the deterministic control of its rotational alignment, which is made highly aleatory due to the random nature of the edge chirality and crystal symmetry. Employing the so-called “golden rule of three”, here we present an experimental strategy to overcome this challenge and realize the controlled alignment of double-aligned hBN/graphene/hBN supermoiré lattice, where the twist angles between graphene and top/bottom hBN are both close to zero. Remarkably, we find that the crystallographic edge of neighboring graphite can be used to better guide the stacking alignment, as demonstrated by the controlled production of 20 moiré samples with an accuracy better than ~ 0.2°. Finally, we extend our technique to low-angle twisted bilayer graphene and ABC-stacked trilayer graphene, providing a strategy for flat-band engineering in these moiré materials.
Infinite-layer nickelates as Ni-eg Hund’s metals
Authors: Kang Byungkyun , Melnick Corey , Semon Patrick , Ryee Siheon , Han Myung Joon , Kotliar Gabriel , Choi Sangkook 
Published: July 2023

AbstractThe recent and exciting discovery of superconductivity in the hole-doped infinite-layer nickelate Nd1−δSrδNiO2draws strong attention to correlated quantum materials. From a theoretical view point, this class of unconventional superconducting materials provides an opportunity to unveil a physics hidden in correlated quantum materials. Here we study the temperature and doping dependence of the local spectrum as well as the charge, spin and orbital susceptibilities from first principles. By using ab initio LQSGW+DMFT methodology, we show that onsite Hund’s coupling in Ni-dorbitals gives rise to multiple signatures of Hund’s metallic phase in Ni-egorbitals. The proposed picture of the nickelates as aneg(two orbital) Hund’s metal differs from the picture of the Fe-based superconductors as a five orbital Hund’s metal as well as the picture of the cuprates as doped charge transfer insulators. Our finding uncover a new class of the Hund’s metals and has potential implications for the broad range of correlated two orbital systems away from half-filling.
Regeneration of tracheal neotissue in partially decellularized scaffolds
Authors: Tan Zheng Hong , Dharmadhikari Sayali , Liu Lumei , Yu Jane , Shontz Kimberly M. , Stack Jacob T. , Breuer Christopher K. , Reynolds Susan D. , Chiang Tendy 
Published: July 2023

AbstractExtensive tracheal injury or disease can be life-threatening but there is currently no standard of care. Regenerative medicine offers a potential solution to long-segment tracheal defects through the creation of scaffolds that support the generation of healthy neotissue. We developed decellularized tracheal grafts (PDTG) by removing the cells of the epithelium and lamina propria while preserving donor cartilage. We previously demonstrated that PDTG support regeneration of host-derived neotissue. Here, we use a combination of microsurgical, immunofluorescent, and transcriptomic approaches to compare PDTG neotissue with the native airway and surgical controls. We report that PDTG neotissue is composed of native tracheal cell types and that the neoepithelium and microvasculature persisted for at least 6 months. Vascular perfusion of PDTG was established within 2 weeks and the graft recruited multipotential airway stem cells that exhibit normal proliferation and differentiation. Hence, PDTG neotissue recapitulates the structure and function of the host trachea and has the potential to regenerate.
From mobile crowdsourcing to crowd-trusted food price in Nigeria: statistical pre-processing and post-sampling
Authors: Arbia Giuseppe , Solano-Hermosilla Gloria , Nardelli Vincenzo , Micale Fabio , Genovese Giampiero , Amerise Ilaria Lucrezia , Adewopo Julius 
Published: July 2023

AbstractTimely and reliable monitoring of food market prices at high spatial and temporal resolution is essential to understanding market and food security developments and supporting timely policy and decision-making. Mostly, decisions rely on price expectations, which are updated with new information releases. Therefore, increasing the availability and timeliness of price information has become a national and international priority. We present two new datasets in which mobile app-based crowdsourced daily price observations, voluntarily submitted by self-selected participants, are validated in real-time within spatio-temporal markets (pre-processed data). Then, they are reweighted weekly using their geo-location to resemble a formal sample design and allow for more reliable statistical inference (post-sampled data). Using real-time data collected in Nigeria, we assess the accuracy and propose that our reweighted estimates are more accurate with respect to the unweighted version. Results have important implications for governments, food chain actors, researchers and other organisations.
Magnetic resonance imaging datasets with anatomical fiducials for quality control and registration
Authors: Taha Alaa , Gilmore Greydon , Abbass Mohamad , Kai Jason , Kuehn Tristan , Demarco John , Gupta Geetika , Zajner Chris , Cao Daniel , Chevalier Ryan , Ahmed Abrar , Hadi Ali , Karat Bradley G. , Stanley Olivia W. , Park Patrick J. , Ferko Kayla M. , Hemachandra Dimuthu , Vassallo Reid , Jach Magdalena , Thurairajah Arun , Wong Sandy , Tenorio Mauricio C. , Ogunsanya Feyi , Khan Ali R. , Lau Jonathan C. 
Published: July 2023

AbstractTools available for reproducible, quantitative assessment of brain correspondence have been limited. We previously validated the anatomical fiducial (AFID) placement protocol for point-based assessment of image registration with millimetric (mm) accuracy. In this data descriptor, we release curated AFID placements for some of the most commonly used structural magnetic resonance imaging datasets and templates. The release of our accurate placements allows for rapid quality control of image registration, teaching neuroanatomy, and clinical applications such as disease diagnosis and surgical targeting. We release placements on individual subjects from four datasets (N = 132 subjects for a total of 15,232 fiducials) and 14 brain templates (4,288 fiducials), totalling more than 300 human rater hours of annotation. We also validate human rater accuracy of released placements to be within 1 – 2 mm (using more than 45,000 Euclidean distances), consistent with prior studies. Our data is compliant with the Brain Imaging Data Structure allowing for facile incorporation into neuroimaging analysis pipelines.
A haplotype-resolved genome assembly of Rhododendron vialii based on PacBio HiFi reads and Hi-C data
Authors: Chang Yuhang , Zhang Rengang , Ma Yongpeng , Sun Weibang 
Published: July 2023

AbstractRhododendron vialii(subgen.Azaleastrum) is an evergreen shrub with high ornamental value. This species has been listed as a plant species with extremely small populations (PSESP) for urgent protection by China’s Yunnan provincial government in 2021, due to anthropogenic habitat fragmentation. However, limited genomic resources hinder scientifically understanding of genetic threats that the species is currently facing. In this study, we assembled a high-quality haplotype-resolved genome ofR.vialiibased on PacBio HiFi long reads and Hi-C reads. The assembly contains two haploid genomes with sizes 532.73 Mb and 521.98 Mb, with contig N50 length of 35.67 Mb and 34.70 Mb, respectively. About 99.92% of the assembled sequences could be anchored to 26 pseudochromosomes, and 14 gapless assembled chromosomes were included in this assembly. Additionally, 60,926 protein-coding genes were identified, of which 93.82% were functionally annotated. This is the first reported genome ofR.vialii, and hopefully it will lay the foundations for further research into the conservation genomics and horticultural domestication of this ornamentally important species.
Molecular system for an exponentially fast growing programmable synthetic polymer
Authors: Dabby Nadine , Barr Alan , Chen Ho-Lin 
Published: July 2023

AbstractIn this paper, we demonstrate a molecular system for the first active self-assembly linear DNA polymer that exhibits programmable molecular exponential growth in real time, also the first to implement “internal” parallel insertion that does not rely on adding successive layers to “external” edges for growth. Approaches like this can produce enhanced exponential growth behavior that is less limited by volume and external surface interference, for an early step toward efficiently building two and three dimensional shapes in logarithmic time. We experimentally demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism and results in the exponential growth of a population of polymers per unit time. In the supplementary material, we note that an “extension” beyond conventional Turing machine theory is needed to theoretically analyze exponential growth itself in programmable physical systems. Sequential physical Turing Machines that run a roughly constant number of Turing steps per unit time cannot achieve an exponential growth of structure per time. In contrast, the “active” self-assembly model in this paper, computationally equivalent to a Push-Down Automaton, is exponentially fast when implemented in molecules, but is taxonomically less powerful than a Turing machine. In this sense, a physical Push-Down Automaton can be more powerful than a sequential physical Turing Machine, even though the Turing Machine can compute any computable function. A need for an “extended” computational/physical theory arises, described in the supplementary material section S1.
Excess manganese increases photosynthetic activity via enhanced reducing center and antenna plasticity in Chlorella vulgaris
Authors: Smythers Amanda L. , Crislip Jessica R. , Slone Danielle R. , Flinn Brendin B. , Chaffins Jeffrey E. , Camp Kristen A. , McFeeley Eli W. , Kolling Derrick R. J. 
Published: July 2023

AbstractPhotosynthesis relies on many easily oxidizable/reducible transition metals found in the metalloenzymes that make up much of the photosynthetic electron transport chain (ETC). One of these is manganese, an essential cofactor of photosystem II (PSII) and a component of the oxygen-evolving complex, the only biological entity capable of oxidizing water. Additionally, manganese is a cofactor in enzymatic antioxidants, notably the superoxide dismutases—which are localized to the chloroplastic membrane. However, unlike other metals found in the photosynthetic ETC, previous research has shown exposure to excess manganese enhances photosynthetic activity rather than diminishing it. In this study, the impact of PSII heterogeneity on overall performance was investigated using chlorophyll fluorescence, a rapid, non-invasive technique that probed for overall photosynthetic efficiency, reducing site activity, and antenna size and distribution. These measurements unveiled an enhanced plasticity of PSII following excess manganese exposure, in which overall performance and reducing center activity increased while antenna size and proportion of PSIIβ centers decreased. This enhanced activity suggests manganese may hold the key to improving photosynthetic efficiency beyond that which is observed in nature.
Mitochondrial impairment but not peripheral inflammation predicts greater Gulf War illness severity
Authors: Golomb Beatrice A. , Sanchez Baez Roel , Schilling Jan M. , Dhanani Mehul , Fannon McKenzie J. , Berg Brinton K. , Miller Bruce J. , Taub Pam R. , Patel Hemal H. 
Published: July 2023

AbstractGulf War illness (GWI) is an important exemplar of environmentally-triggered chronic multisymptom illness, and a potential model for accelerated aging. Inflammation is the main hypothesized mechanism for GWI, with mitochondrial impairment also proposed. No study has directly assessed mitochondrial respiratory chain function (MRCF) on muscle biopsy in veterans with GWI (VGWI). We recruited 42 participants, half VGWI, with biopsy material successfully secured in 36. Impaired MRCF indexed by complex I and II oxidative phosphorylation with glucose as a fuel source (CI&CIIOXPHOS) related significantly or borderline significantly in the predicted direction to 17 of 20 symptoms in the combined sample. Lower CI&CIIOXPHOS significantly predicted GWI severity in the combined sample and in VGWI separately, with or without adjustment for hsCRP. Higher-hsCRP (peripheral inflammation) related strongly to lower-MRCF (particularly fatty acid oxidation (FAO) indices) in VGWI, but not in controls. Despite this, whereas greater MRCF-impairment predicted greater GWI symptoms and severity, greater inflammation did not. Surprisingly, adjusted for MRCF, higher hsCRP significantly predicted lesser symptom severity in VGWI selectively. Findings comport with a hypothesis in which the increased inflammation observed in GWI is driven by FAO-defect-induced mitochondrial apoptosis. In conclusion, impaired mitochondrial function—but not peripheral inflammation—predicts greater GWI symptoms and severity.
Development of a nomogram prediction model for gait speed trajectories in persons with knee osteoarthritis
Authors: Liu Peiyuan , Wang Cui , Chen Hongbo , Shang Shaomei 
Published: July 2023

AbstractTo examine heterogeneous trajectories of 8-year gait speed among patients with symptomatic knee osteoarthritis (KOA) and to develop a nomogram prediction model. We analyzed data from the Osteoarthritis Initiative (OAI) assessed at baseline and follow-up over 8 years (n = 1289). Gait speed was measured by the 20-m walk test. The gait speed trajectories among patients with KOA were explored by latent class growth analysis. A nomogram prediction model was created based on multivariable logistic regression. Three gait speed trajectories were identified: the fast gait speed group (30.4%), moderate gait speed group (50.5%) and slow gait speed group (19.1%). Age ≥ 60 years, female, non-white, nonmarried, annual income < $50,000, obesity, depressive symptoms, comorbidity and WOMAC pain score ≥ 5 were risk factors for the slow gait trajectory. The area under the ROC curve of the prediction model was 0.775 (95% CI 0.742–0.808). In the external validation cohort, the AUC was 0.773 (95% CI 0.697–0.848). Heterogeneous trajectories existed in the gait speed of patients with KOA and could be predicted by multiple factors. Risk factors should be earlier identified, and targeted intervention should be carried out to improve physical function of KOA patients.
Introduction and behavioral validation of the climate change distress and impairment scale
Authors: Hepp Johanna , Klein Sina A. , Horsten Luisa K. , Urbild Jana , Lane Sean P. 
Published: July 2023

AbstractGovernmental agencies and the medical and psychological professions are calling for a greater focus on the negative mental health effects of climate change (CC). As a first step, the field needs measures to distinguish affective/emotional distress due to CC from impairment that requires further scientific and diagnostic attention and that may require treatment in the future. To this end, we constructed the climate change distress and impairment scale, which distinguishes CC distress (spanning anger, anxiety, and sadness) from impairment. In four studies (N = 1699), we developed and validated English and German versions of the scale. Across samples, spanning 2021–2022, CC distress was at least moderate, while we observed general moderate to high levels of distress and low to moderate levels of impairment. In three English-speaking samples, younger individuals and women were most affected by CC distress, whereas this was not the case in a German-speaking sample, suggesting sociopolitical influencing factors. We demonstrate convergent validity with previous measures and discriminant validity for general negative affectivity and depressive and generalized anxiety disorder symptoms, which underlines that CC distress is not in itself pathological. Employing a fully incentivized social dilemma paradigm, we demonstrate that CC distress and (to a lesser degree) CC impairment predict pro-environmental behavior, underscoring them as possible drivers, and targets, of climate-change mitigation efforts.
Antigen test swabs are comparable to nasopharyngeal swabs for sequencing of SARS-CoV-2
Authors: Hassouneh Sayf Al-Deen , Trujillo Alexa , Ali Sobur , Cella Eleonora , Johnston Catherine , DeRuff Katherine C. , Sabeti Pardis C. , Azarian Taj 
Published: July 2023

AbstractViral genomic surveillance has been integral in the global response to the SARS-CoV-2 pandemic. Surveillance efforts rely on the availability of representative clinical specimens from ongoing testing activities. However, testing practices have recently shifted due to the widespread availability and use of rapid antigen tests, which could lead to gaps in future monitoring efforts. As such, genomic surveillance strategies must adapt to include laboratory workflows that are robust to sample type. To that end, we compare the results of RT-qPCR and viral genome sequencing using samples from positive BinaxNOW COVID-19 Antigen Card swabs (N = 555) to those obtained from nasopharyngeal (NP) swabs used for nucleic acid amplification testing (N = 135). We show that swabs obtained from antigen cards are comparable in performance to samples from NP swabs, providing a viable alternative and allowing for the potential expansion of viral genomic surveillance to outpatient clinic as well as other settings where rapid antigen tests are often used.
Hydrogen peroxide from l-amino acid oxidase of king cobra (Ophiophagus hannah) venom attenuates Pseudomonas biofilms
Authors: Singkham-In Uthaibhorn , Thaveekarn Wichit , Noiphrom Jureeporn , Khow Orawan , Ponwaranon Surada , Issara-Amphorn Jiraphorn , Sitprija Visith , Leelahavanichkul Asada 
Published: July 2023

AbstractBecause of the high incidence of Pseudomonas aeruginosa biofilms-related nosocomial infections, venoms from common Thai snakes were tested. Although venoms from king cobra (Ophiophagus hannah; OH) and green pit viper (Trimeresurus albolabris) showed the broadest antibacterial spectrum, OH venom demonstrated more profound anti-biofilm activities against P. aeruginosa. Additionally, purified l-amino acid oxidase from OH venom (OH-LAAO), using a three-step chromatography and protein identification, reduced biofilm mass as indicated by the downregulation of several genes, including the genes for biofilm synthesis (algD and pslB) and biofilm regulators (algU, gacA, and siaD). Moreover, OH-LAAO disrupted Pseudomonas-preformed biofilms via upregulation of several genes for biofilm dispersion (nbdA, bdlA, and dipA) and biofilm degradation (endA and pslG), resulting in a reduction of the biofilm biomass. Due to the antimicrobial effects and anti-biofilm activities (reduced production plus increased dispersion) neutralized by catalase, a hydrogen peroxide (H2O2)-degrading enzyme, the enhanced H2O2 by OH venom might be one of the anti-biofilm mechanisms. Hence, OH-LAAO was proposed as a novel agent against Pseudomonas biofilms for either treatment or prevention. More studies are interesting.
Recruitment and migration patterns reveal a key role for seed banks in the meta-population dynamics of an aquatic plant
Authors: Tomowski Maxi , Lozada-Gobilard Sissi , Jeltsch Florian , Tiedemann Ralph 
Published: July 2023

AbstractProgressive habitat fragmentation threatens plant species with narrow habitat requirements. While local environmental conditions define population growth rates and recruitment success at the patch level, dispersal is critical for population viability at the landscape scale. Identifying the dynamics of plant meta-populations is often confounded by the uncertainty about soil-stored population compartments. We combined a landscape-scale assessment of an amphibious plant’s population structure with measurements of dispersal complexity in time to track dispersal and putative shifts in functional connectivity. Using 13 microsatellite markers, we analyzed the genetic structure of extant Oenanthe aquatica populations and their soil seed banks in a kettle hole system to uncover hidden connectivity among populations in time and space. Considerable spatial genetic structure and isolation-by-distance suggest limited gene flow between sites. Spatial isolation and patch size showed minor effects on genetic diversity. Genetic similarity found among extant populations and their seed banks suggests increased local recruitment, despite some evidence of migration and recent colonization. Results indicate stepping-stone dispersal across adjacent populations. Among permanent and ephemeral demes the resulting meta-population demography could be determined by source-sink dynamics. Overall, these spatiotemporal connectivity patterns support mainland-island dynamics in our system, highlighting the importance of persistent seed banks as enduring sources of genetic diversity.