bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Essential Role of Local Context in Shaping Risk and Risk Reduction Strategies for Snowmelt‐Dependent Irrigated Agriculture
Authors: Gordon Beatrice L. , Boisrame Gabrielle F. S. , Carroll Rosemary W. H. , Ajami Newsha K. , Leonard Bryan , Albano Christine , Mizukami Naoki , Andrade Manuel A. , Koebele Elizabeth , Taylor Michael H. , Harpold Adrian A. 
Published: June 2024

AbstractClimate change‐induced shifts in snow storage and snowmelt patterns pose risks for adverse impacts to people, the environment, and irrigated agriculture. Existing research primarily focuses on evaluating these risks to irrigated agriculture at large scales, overlooking the role of local context in shaping risk dynamics. Consequently, many “at‐risk” areas lack insight into how adaptation strategies for managing risk through water supply augmentation or water conservation vary across contexts and over time. To address this gap, we develop a comprehensive index for evaluating irrigated agriculture's risk and adaptation potential to changes in snow at local scales and apply it throughout the western US. Results confirm trends toward escalating risk for changes in snow storage and snowmelt patterns over the century. However, substantial heterogeneity in the extent and drivers of risk exists due to variability in localized interactions between declines in water supply (approximately −9% ± 13% by 2100) and increased agricultural demand (approximately 7% ± 5% by 2100). Despite an existing focus on supply augmentation as a critical adaptation strategy to reduce risk, we show its effectiveness diminishes for many areas over time, declining to an average of −54% of historical augmentation potential by 2100. Conserving water through historical changes in crop acreage and type emerges as a more stable adaptation measure, reducing demand by 7%–8% regardless of time. While particularly relevant for higher elevation, less intensive agricultural settings in snowmelt‐dependent regions, findings underscore the need for strategies that support local‐scale, context‐appropriate adaptation to effectively manage escalating risk as snow changes.
Genetically programmable cell membrane-camouflaged nanoparticles for targeted combination therapy of colorectal cancer
Authors: Yang Yun , Liu Qingya , Wang Meng , Li Lang , Yu Yan , Pan Meng , Hu Danrong , Chu Bingyang , Qu Ying , Qian Zhiyong 
Published: June 2024

AbstractCell membrane-camouflaged nanoparticles possess inherent advantages derived from their membrane structure and surface antigens, including prolonged circulation in the bloodstream, specific cell recognition and targeting capabilities, and potential for immunotherapy. Herein, we introduce a cell membrane biomimetic nanodrug platform termed MPB-3BP@CM NPs. Comprising microporous Prussian blue nanoparticles (MPB NPs) serving as both a photothermal sensitizer and carrier for 3-bromopyruvate (3BP), these nanoparticles are cloaked in a genetically programmable cell membrane displaying variants of signal regulatory protein α (SIRPα) with enhanced affinity to CD47. As a result, MPB-3BP@CM NPs inherit the characteristics of the original cell membrane, exhibiting an extended circulation time in the bloodstream and effectively targeting CD47 on the cytomembrane of colorectal cancer (CRC) cells. Notably, blocking CD47 with MPB-3BP@CM NPs enhances the phagocytosis of CRC cells by macrophages. Additionally, 3BP, an inhibitor of hexokinase II (HK2), suppresses glycolysis, leading to a reduction in adenosine triphosphate (ATP) levels and lactate production. Besides, it promotes the polarization of tumor-associated macrophages (TAMs) towards an anti-tumor M1 phenotype. Furthermore, integration with MPB NPs-mediated photothermal therapy (PTT) enhances the therapeutic efficacy against tumors. These advantages make MPB-3BP@CM NPs an attractive platform for the future development of innovative therapeutic approaches for CRC. Concurrently, it introduces a universal approach for engineering disease-tailored cell membranes for tumor therapy.
Single-cell sequencing depicts tumor architecture and empowers clinical decision in metastatic conjunctival melanoma
Authors: Shi Hanhan , Tian Hao , Zhu Tianyu , Liao Qili , Liu Chang , Yuan Peng , Li Yongyun , Yang Jie , Zong Chunyan , Jia Shichong , Ruan Jing , Ge Shengfang , Jia Renbing , Chai Peiwei , Xu Shiqiong , Fan Xianqun 
Published: June 2024

AbstractConjunctival melanoma (CoM) is a potentially devastating tumor that can lead to distant metastasis. Despite various therapeutic strategies for distant metastatic CoM, the clinical outcomes remain unfavorable. Herein, we performed single-cell RNA sequencing (scRNA-seq) of 47,017 cells obtained from normal conjunctival samples (n = 3) and conjunctival melanomas (n = 7). Notably, we noticed a higher abundance of cancer-associated fibroblasts (CAFs) in tumor microenvironment (TME), correlated with enhanced angiogenic capacity and increased VEGFR expression in distal metastatic CoM. Additionally, we observed a significant decrease in the proportion of total CD8+ T cells and an increase in the proportion of naive CD8+ T cells, contributing to a relatively quiescent immunological environment in distal metastatic CoM. These findings were confirmed through the analyses of 70,303 single-cell transcriptomes of 7 individual CoM samples, as well as spatially resolved proteomes of an additional 10 samples of CoMs. Due to the increase of VEGFR-mediated angiogenesis and a less active T cell environment in distal metastatic CoMs, a clinical trial (ChiCTR2100045061) has been initiated to evaluate the efficacy of VEGFR blockade in combination with anti-PD1 therapy for patients with distant metastatic CoM, showing promising tumor-inhibitory effects. In conclusion, our study uncovered the landscape and heterogeneity of the TME during CoM tumorigenesis and progression, empowering clinical decisions in the management of distal metastatic CoM. To our knowledge, this is the initial exploration to translate scRNA-seq analysis to a clinical trial dealing with cancer, providing a novel concept by accommodating scRNA-seq data in cancer therapy.
DOT: a flexible multi-objective optimization framework for transferring features across single-cell and spatial omics
Authors: Rahimi Arezou , Vale-Silva Luis A. , Fälth Savitski Maria , Tanevski Jovan , Saez-Rodriguez Julio 
Published: June 2024

AbstractSingle-cell transcriptomics and spatially-resolved imaging/sequencing technologies have revolutionized biomedical research. However, they suffer from lack of spatial information and a trade-off of resolution and gene coverage, respectively. We propose DOT, a multi-objective optimization framework for transferring cellular features across these data modalities, thus integrating their complementary information. DOT uses genes beyond those common to the data modalities, exploits the local spatial context, transfers spatial features beyond cell-type information, and infers absolute/relative abundance of cell populations at tissue locations. Thus, DOT bridges single-cell transcriptomics data with both high- and low-resolution spatially-resolved data. Moreover, DOT combines practical aspects related to cell composition, heterogeneity, technical effects, and integration of prior knowledge. Our fast implementation based on the Frank-Wolfe algorithm achieves state-of-the-art or improved performance in localizing cell features in high- and low-resolution spatial data and estimating the expression of unmeasured genes in low-coverage spatial data.
Space radiation damage rescued by inhibition of key spaceflight associated miRNAs
Authors: McDonald J. Tyson , Kim JangKeun , Farmerie Lily , Johnson Meghan L. , Trovao Nidia S. , Arif Shehbeel , Siew Keith , Tsoy Sergey , Bram Yaron , Park Jiwoon , Overbey Eliah , Ryon Krista , Haltom Jeffrey , Singh Urminder , Enguita Francisco J. , Zaksas Victoria , Guarnieri Joseph W. , Topper Michael , Wallace Douglas C. , Meydan Cem , Baylin Stephen , Meller Robert , Muratani Masafumi , Porterfield D. Marshall , Kaufman Brett , Mori Marcelo A. , Walsh Stephen B. , Sigaudo-Roussel Dominique , Mebarek Saida , Bottini Massimo , Marquette Christophe A. , Wurtele Eve Syrkin , Schwartz Robert E. , Galeano Diego , Mason Christopher E. , Grabham Peter , Beheshti Afshin 
Published: June 2024

AbstractOur previous research revealed a key microRNA signature that is associated with spaceflight that can be used as a biomarker and to develop countermeasure treatments to mitigate the damage caused by space radiation. Here, we expand on this work to determine the biological factors rescued by the countermeasure treatment. We performed RNA-sequencing and transcriptomic analysis on 3D microvessel cell cultures exposed to simulated deep space radiation (0.5 Gy of Galactic Cosmic Radiation) with and without the antagonists to three microRNAs: miR-16-5p, miR-125b-5p, and let-7a-5p (i.e., antagomirs). Significant reduction of inflammation and DNA double strand breaks (DSBs) activity and rescue of mitochondria functions are observed after antagomir treatment. Using data from astronaut participants in the NASA Twin Study, Inspiration4, and JAXA missions, we reveal the genes and pathways implicated in the action of these antagomirs are altered in humans. Our findings indicate a countermeasure strategy that can potentially be utilized by astronauts in spaceflight missions to mitigate space radiation damage.
Dynamic label-free analysis of SARS-CoV-2 infection reveals virus-induced subcellular remodeling
Authors: Saunders Nell , Monel Blandine , Cayet Nadège , Archetti Lorenzo , Moreno Hugo , Jeanne Alexandre , Marguier Agathe , Buchrieser Julian , Wai Timothy , Schwartz Olivier , Fréchin Mathieu 
Published: June 2024

AbstractAssessing the impact of SARS-CoV-2 on organelle dynamics allows a better understanding of the mechanisms of viral replication. We combine label-free holotomographic microscopy with Artificial Intelligence to visualize and quantify the subcellular changes triggered by SARS-CoV-2 infection. We study the dynamics of shape, position and dry mass of nucleoli, nuclei, lipid droplets and mitochondria within hundreds of single cells from early infection to syncytia formation and death. SARS-CoV-2 infection enlarges nucleoli, perturbs lipid droplets, changes mitochondrial shape and dry mass, and separates lipid droplets from mitochondria. We then used Bayesian network modeling on organelle dry mass states to define organelle cross-regulation networks and report modifications of organelle cross-regulation that are triggered by infection and syncytia formation. Our work highlights the subcellular remodeling induced by SARS-CoV-2 infection and provides an Artificial Intelligence-enhanced, label-free methodology to study in real-time the dynamics of cell populations and their content.
Lanthanide-regulating Ru-O covalency optimizes acidic oxygen evolution electrocatalysis
Authors: Li Lu , Zhang Gengwei , Zhou Chenhui , Lv Fan , Tan Yingjun , Han Ying , Luo Heng , Wang Dawei , Liu Youxing , Shang Changshuai , Zeng Lingyou , Huang Qizheng , Zeng Ruijin , Ye Na , Luo Mingchuan , Guo Shaojun 
Published: June 2024

AbstractPrecisely modulating the Ru-O covalency in RuOx for enhanced stability in proton exchange membrane water electrolysis is highly desired. However, transition metals with d-valence electrons, which were doped into or alloyed with RuOx, are inherently susceptible to the influence of coordination environment, making it challenging to modulate the Ru-O covalency in a precise and continuous manner. Here, we first deduce that the introduction of lanthanide with gradually changing electronic configurations can continuously modulate the Ru-O covalency owing to the shielding effect of 5s/5p orbitals. Theoretical calculations confirm that the durability of Ln-RuOx following a volcanic trend as a function of Ru-O covalency. Among various Ln-RuOx, Er-RuOx is identified as the optimal catalyst and possesses a stability 35.5 times higher than that of RuO2. Particularly, the Er-RuOx-based device requires only 1.837 V to reach 3 A cm−2 and shows a long-term stability at 500 mA cm−2 for 100 h with a degradation rate of mere 37 μV h−1.
Supercooled erythritol for high-performance seasonal thermal energy storage
Authors: Yang Sheng , Shi Hong-Yi , Liu Jia , Lai Yang-Yan , Bayer Özgür , Fan Li-Wu 
Published: June 2024

AbstractSeasonal storage of solar thermal energy through supercooled phase change materials (PCM) offers a promising solution for decarbonizing space and water heating in winter. Despite the high energy density and adaptability, natural PCMs often lack the necessary supercooling for stable, long-term storage. Leveraging erythritol, a sustainable mid-temperature PCM with high latent heat, we introduce a straightforward method to stabilize its supercooling by incorporating carrageenan (CG), a bio-derived food thickener. By improving the solid-liquid interfacial energy with the addition of CG the latent heat of erythritol can be effectively locked at a very low temperature. We show that the composite PCM can sustain an ultrastable supercooled state below −30 °C, which guarantees no accidental loss of the latent heat in severe cold regions on Earth. We further demonstrate that the common ultrasonication method can be used as the key to unlocking the latent heat stored in the CG-thickened erythritol, showing its great potential to serve as a high-performance, eco-friendly PCM for long-term seasonal solar energy storage.
Electroreductive alkylations of (hetero)arenes with carboxylic acids
Authors: Wang Bing , Huang Xianshuai , Bi Huihua , Liu Jie 
Published: June 2024

AbstractCarboxylic acids are widely available and generally inexpensive from abundant biomass feedstocks, and they are suitable and generic coupling partners in synthetic chemistry. Reported herein is an electroreductive coupling of stable and versatile carboxylic acids with (hetero)arenes using protons as the hydrogen source. The application of an earth-abundant titanium catalyst has significantly improved the deoxygenative reduction process. Preliminary mechanistic studies provide insights into the deoxygenative reduction of in-situ generated ketone pathway, and the intermediacy generation of ketyl radical and alkylidene titanocene. Without the necessity of pressurized hydrogen or stoichiometric hydride as reductants, this protocol enables highly selective and straightforward synthesis of various functionalized and structurally diverse alkylbenzenes under mild conditions. The utility of this reaction is further demonstrated through practical and valuable isotope incorporation from readily available deuterium source.
Targeting mosquito X-chromosomes reveals complex transmission dynamics of sex ratio distorting gene drives
Authors: Haber Daniella An , Arien Yael , Lamdan Lee Benjamin , Alcalay Yehonathan , Zecharia Chen , Krsticevic Flavia , Yonah Elad Shmuel , Avraham Rotem Daniel , Krzywinska Elzbieta , Krzywinski Jaroslaw , Marois Eric , Windbichler Nikolai , Papathanos Philippos Aris 
Published: June 2024

AbstractEngineered sex ratio distorters (SRDs) have been proposed as a powerful component of genetic control strategies designed to suppress harmful insect pests. Two types of CRISPR-based SRD mechanisms have been proposed: X-shredding, which eliminates X-bearing sperm, and X-poisoning, which eliminates females inheriting disrupted X-chromosomes. These differences can have a profound impact on the population dynamics of SRDs when linked to the Y-chromosome: an X-shredder is invasive, constituting a classical meiotic Y-drive, whereas X-poisoning is self-limiting, unable to invade but also insulated from selection. Here, we establish X-poisoning strains in the malaria vector Anopheles gambiae targeting three X-linked genes during spermatogenesis, resulting in male bias. We find that sex distortion is primarily driven by a loss of X-bearing sperm, with limited evidence for postzygotic lethality of female progeny. By leveraging a Drosophila melanogaster model, we show unambiguously that engineered SRD traits can operate differently in these two insects. Unlike X-shredding, X-poisoning could theoretically operate at early stages of spermatogenesis. We therefore explore premeiotic Cas9 expression to target the mosquito X-chromosome. We find that, by pre-empting the onset of meiotic sex chromosome inactivation, this approach may enable the development of Y-linked SRDs if mutagenesis of spermatogenesis-essential genes is functionally balanced.
Characterizing dehydration in short-term spaceflight using evidence from Project Mercury
Authors: Reynolds Robert J. , Shelhamer Mark , Antonsen Erik L. , Carpentier William R. 
Published: June 2024

AbstractShort-term spaceflight is commonly perceived as posing minimal risk to human health and performance. However, despite their duration, short-term flights potentially induce acute physiological changes that create risk to crews. One such change is dehydration (primarily body water loss) due to a heat-stressed environment. Such loss, if severe and prolonged, can lead to decrements in performance as well as increase the risk of more serious medical conditions. Though the general mechanisms of dehydration are broadly understood, the rate and extent of dehydration in short-term spaceflight has not been characterized. Combining data from the six spaceflights of the US Mercury program with a causal diagram illustrating the mechanisms of dehydration, we fit a path model to estimate the causal effects for all pathways in the causal model. Results demonstrate that Mercury astronauts experienced some degree of dehydration across the range of suited time and that the relationship between suited time and dehydration appears to be logarithmic. We discuss causal interpretations of the results and how the results from this and similar analyses can inform countermeasure development for short-term spaceflight.
Deep-learning-enabled antibiotic discovery through molecular de-extinction
Authors: Wan Fangping , Torres Marcelo D. T. , Peng Jacqueline , de la Fuente-Nunez Cesar 
Published: June 2024

AbstractMolecular de-extinction aims at resurrecting molecules to solve antibiotic resistance and other present-day biological and biomedical problems. Here we show that deep learning can be used to mine the proteomes of all available extinct organisms for the discovery of antibiotic peptides. We trained ensembles of deep-learning models consisting of a peptide-sequence encoder coupled with neural networks for the prediction of antimicrobial activity and used it to mine 10,311,899 peptides. The models predicted 37,176 sequences with broad-spectrum antimicrobial activity, 11,035 of which were not found in extant organisms. We synthesized 69 peptides and experimentally confirmed their activity against bacterial pathogens. Most peptides killed bacteria by depolarizing their cytoplasmic membrane, contrary to known antimicrobial peptides, which tend to target the outer membrane. Notably, lead compounds (including mammuthusin-2 from the woolly mammoth, elephasin-2 from the straight-tusked elephant, hydrodamin-1 from the ancient sea cow, mylodonin-2 from the giant sloth and megalocerin-1 from the extinct giant elk) showed anti-infective activity in mice with skin abscess or thigh infections. Molecular de-extinction aided by deep learning may accelerate the discovery of therapeutic molecules.
Self-administered mindfulness interventions reduce stress in a large, randomized controlled multi-site study
Authors: Sparacio Alessandro , IJzerman Hans , Ropovik Ivan , Giorgini Filippo , Spiessens Christoph , Uchino Bert N. , Landvatter Joshua , Tacana Tracey , Diller Sandra J. , Derrick Jaye L. , Segundo Joahana , Pierce Jace D. , Ross Robert M. , Francis Zoë , LaBoucane Amanda , Ma-Kellams Christine , Ford Maire B. , Schmidt Kathleen , Wong Celia C. , Higgins Wendy C. , Stone Bryant M. , Stanley Samantha K. , Ribeiro Gianni , Fuglestad Paul T. , Jaklin Valerie , Kübler Andrea , Ziebell Philipp , Jewell Crystal L. , Kovas Yulia , Allahghadri Mahnoosh , Fransham Charlotte , Baranski Michael F. , Burgess Hannah , Benz Annika B. E. , DeSousa Maysa , Nylin Catherine E. , Brooks Janae C. , Goldsmith Caitlyn M. , Benson Jessica M. , Griffin Siobhán M. , Dunne Stephen , Davis William E. , Watermeyer Tam J. , Meese William B. , Howell Jennifer L. , Standiford Reyes Laurel , Strickland Megan G. , Dickerson Sally S. , Pescatore Samantha , Skakoon-Sparling Shayna , Wunder Zachary I. , Day Martin V. , Brenton Shawna , Linden Audrey H. , Hawk Christopher E. , O’Brien Léan V. , Urgyen Tenzin , McDonald Jennifer S. , van der Schans Kim Lien , Blocker Heidi , Ng Tseung-Wong Caroline , Jiga-Boy Gabriela M. 
Published: June 2024

AbstractMindfulness witnessed a substantial popularity surge in the past decade, especially as digitally self-administered interventions became available at relatively low costs. Yet, it is uncertain whether they effectively help reduce stress. In a preregistered (OSF https://doi.org/10.17605/OSF.IO/UF4JZ; retrospective registration at ClinicalTrials.gov NCT06308744) multi-site study (nsites = 37, nparticipants = 2,239, 70.4% women, Mage = 22.4, s.d.age = 10.1, all fluent English speakers), we experimentally tested whether four single, standalone mindfulness exercises effectively reduced stress, using Bayesian mixed-effects models. All exercises proved to be more efficacious than the active control. We observed a mean difference of 0.27 (d = −0.56; 95% confidence interval, −0.43 to −0.69) between the control condition (M = 1.95, s.d. = 0.50) and the condition with the largest stress reduction (body scan: M = 1.68, s.d. = 0.46). Our findings suggest that mindfulness may be beneficial for reducing self-reported short-term stress for English speakers from higher-income countries.
A Global Multi-Source Tropical Cyclone Precipitation (MSTCP) Dataset
Authors: Morin Gabriel , Boudreault Mathieu , García-Franco Jorge L. 
Published: June 2024

AbstractA global tropical cyclone precipitation dataset covering the period from January 1979 to February 2023 is presented. Global precipitation estimates were taken from the newly developed high-resolution Multi-Source Weighted-Ensemble Precipitation, version 2 (MSWEP V2) and TC tracks were obtained from the International Best Track Archive for Climate Stewardship (IBTrACS) dataset. This Global Multi-Source Tropical Cyclone Precipitation (MSTCP) dataset is comprised of two main products and files in the format of tables: the main and profile datasets. The main file provides various TCP statistics per TC track, including mean and maximum precipitation rates over a fixed and symmetrical radius of 500 km. The profile dataset comprises the azimuthally averaged precipitation every 10-km away from the center of each storm (until 500 km). The case study of Hurricane Harvey is used to show that MSWEP estimates agree well with another commonly used satellite product. The main statistics of the dataset are analyzed as well, including the differences in the dataset metrics for each of the six TC basins and for each Saffir-Simpson category for storm intensity.