bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Tropical Atlantic's Asymmetric Impact on the El Niño‐Southern Oscillation
Authors: van Rensch Peter , McGregor Shayne , Dommenget Dietmar , Bi Daohua , Liguori Giovanni 
Published: February 2024

AbstractUsing observations and Atlantic forced coupled model simulations, we show evidence for an asymmetry in the link between beginning of year tropical Atlantic sea surface temperature anomalies (SSTAs) and end of the year El Niño‐Southern Oscillation events. We find a greater tendency for warm Atlantic SSTAs to lead to a La Niña than for cold anomalies to lead to El Niño. The model experiments showed that the Atlantic had a greater chance to force the tropical Pacific if the Pacific was initially in a neutral state. In the model, a warm Atlantic from March–May was able to produce an atmospheric response leading to easterly wind anomalies in the western Pacific. This in turn induces a subsurface oceanic response, leading to La Niña at the end of the year. The atmospheric response does not occur for a cold Atlantic, leading to no impacts in the Pacific.
Decadal Prediction of Location of Tropical Cyclone Maximum Intensity Over the Western North Pacific
Authors: Zhang Ruikang , Wang Chao , Wang Bin , Guan Zhaoyong , Wu Liguang , Luo Jingjia 
Published: February 2024

AbstractAttaining skillful decadal predictions for the western North Pacific tropical cyclone (TC) emerges as a formidable challenge, mainly stemming from the limited prediction skills of Pacific Decadal Variability (PDV) within the state‐of‐the‐art models. Assessing sixth Coupled Model Intercomparison Project models' retrospective predictions finds that the predictability of PDV transcends the expectations set by raw forecasts featured by constrained temporal skills and low signal‐to‐noise ratio. Employing a refined approach, we selectively identify the models that capture the diverse phases of PDV and subsequently adjust their variances. This tailored approach yields a compelling concordance between the predicted PDV and observation in phases and variances. Anchored in the heightened prediction skill of PDV, we establish a sophisticated statistical model adept at predicting the latitude of TC's lifetime maximum intensity (LMI). The near‐term prediction indicates a sustained poleward migration of LMI latitude by 1.53° during 2020–2027, increasing subtropical East Asia's TC‐related disaster vulnerability in the coming decade.
Seasonal Enhancement in Upper Atmospheric D/H at Mars Driven by Both Thermospheric Temperature and Mesospheric Water
Authors: Cangi E. M. , Chaffin M. S. , Yelle R. V. , Gregory B. S. , Deighan J. 
Published: February 2024

AbstractThe D/H ratio in water on Mars, Rwater, is 4–6× the Earth ratio, signifying past water loss to space. Recently, measurements have revealed high values of the D/H ratio in hydrogen, Ratomic, in the thermosphere during southern summer. Here, we use a photochemical model to explore the potential drivers of Ratomic, testing three: thermospheric temperatures, excess mesospheric water, and changing insolation. We find that Ratomic can achieve values between 15× the Earth ratio (due to water) and 23× the Earth ratio (due to temperature). The effects arise because H escape is diffusion‐limited, while D escape is energy‐limited. Our results underscore how Ratomic reflects mesospheric dynamics, and the need for concurrent measurements of mesospheric water, thermospheric temperatures, and Ratomic to understand seasonal changes in the martian water cycle and atmospheric loss.
Constraining the Influence of Callisto's Perturbed Electromagnetic Environment on Energetic Particle Observations
Authors: Liuzzo Lucas , Poppe Andrew R. , Nénon Quentin , Simon Sven , Addison Peter 
Published: February 2024

AbstractThis study focuses on constraining the role that Callisto's perturbed electromagnetic environment had on energetic charged particle signatures observed during the Galileo mission. To do so, we compare data from the Energetic Particle Detector (EPD) obtained during four close encounters of the moon with a model framework that combines hybrid simulations for low‐energy plasma and test‐particle tracing simulations for high‐energy particles. By comparing model results for energetic particle dynamics in both uniform and perturbed electromagnetic fields, we systematically disentangle the role that geometric effects (i.e., absorption of particles by Callisto's solid surface) have on observed energetic particle signatures compared to those associated with Callisto's perturbed electromagnetic environment (generated by the moon's induced magnetic field and plasma interaction currents). We show that observed flux drop‐outs in the energetic ion pitch angle distributions (PADs) are largely driven by their absorption by Callisto's surface: their large gyroradii exceed the size of the moon, facilitating their impact onto the icy surface and preventing their detection by EPD. However, features observed in the energetic electron PADs can only be explained with an accurate representation of the moon's perturbed environment, since electrons closely follow the orientation of the electromagnetic fields. Our findings therefore illustrate the key role that the moon's induced field and magnetospheric plasma interaction have on the dynamics of energetic electrons, emphasizing the importance of accurately modeling Callisto's locally perturbed electromagnetic environment when attempting to interpret data from past and future encounters, including those anticipated from the upcoming JUICE mission.
20th Century Warming in the Western Florida Keys Was Dominated by Increasing Winter Temperatures
Authors: Flannery Jennifer A. , Richey Julie N. , Toth Lauren T. , Mette Madelyn J. 
Published: February 2024

AbstractLong‐lived Atlantic coral species like Orbicella faveolata are important archives of oceanographic change in shallow, marine environments like the Florida Keys. Not only can coral‐based records extend for multiple centuries beyond the limits of the instrumental record, but they can also provide a more accurate representation of in situ conditions than gridded interpolated sea‐surface temperature (SST) products for nearshore reef environments. We use the coral Sr/Ca paleothermometer to produce a 150‐year (1830–1980 C.E.) monthly SST reconstruction from an O. faveolata colony collected in the Marquesas Keys, FL, USA. An important feature of our record is a significant 20th‐century warming trend in winter SSTs. We hypothesize that the winter warming trend was driven partially by a decrease in upwelling associated cyclonic eddies spinning off the Florida Current. A long‐term weakening of winter Florida Current transport over the 20th century could be responsible for decreased cyclonic eddy formation in the Florida Straits. Another feature of the record is pronounced multidecadal fluctuations of mean annual warming and cooling in the record, which correspond to Atlantic Multidecadal Variability (AMV), with the AMV lagging behind western Florida Keys temperatures by 5–11 years. Strong coherence between coral‐based SST reconstructions in the western Florida Keys with broader scale Atlantic oceanographic trends over the past century suggests a common driver of regional SST variability.
Assessing the Behavior of Microplastics in Fluvial Systems: Infiltration and Retention Dynamics in Streambed Sediments
Authors: Boos Jan‐Pascal , Dichgans Franz , Fleckenstein Jan H. , Gilfedder Benjamin Silas , Frei Sven 
Published: February 2024

AbstractMicroplastics (MPs) have been detected ubiquitously in fluvial systems and advective transfer has been proposed as a potential mechanism for the transport of (sub‐) pore‐scale MPs from surface waters into streambed sediments. However, the influence of particle and sediment properties, as well as the hydrodynamic flow regime, on the infiltration behavior and mobility of MPs in streambed sediments remains unclear. In this study, we conducted a series of flume experiments to investigate the effect of particle size (1–10 μm), sediment type (fine and coarse sand), and flow regime (high/low flow) on particle infiltration dynamics in a rippled streambed. Quantification of particles in the flume compartments (surface flow, streambed interface, and in the streambed) was achieved using continuous fluorescence techniques. Results indicated that the maximum infiltration depth into the streambed decreased with increasing particle size (11, 10, and 7 cm for 1, 3, and 10 μm). The highest particle retardation was observed in the fine sediment experiment, where 22% of the particles were still in the streambed at the end of the experiment. Particle residence times were shortest under high flow conditions, suggesting that periods of increased discharge can effectively flush MPs from streambed sediments. This study provides novel insights into the complex dynamics of MP infiltration and retention in streambed sediments and contributes to a better understanding of MPs fate in fluvial ecosystems. Quantitative data from this study can improve existing modeling frameworks for MPs transport and assist in assessing the exposure risk of MPs ingestion by benthic organisms.
Variation in communication of side effects in prostate cancer treatment consultations
Authors: Daskivich Timothy J. , Naser-Tavakolian Aurash , Gale Rebecca , Luu Michael , Friedrich Nadine , Venkataramana Abhi , Khodyakov Dmitry , Posadas Edwin , Sandler Howard , Spiegel Brennan , Freedland Stephen J. 
Published: February 2024

Abstract

Background
Effective communication of treatment side effects (SE) is critical for shared decision-making (SDM) in localized prostate cancer. We sought to qualitatively characterize how physicians communicate SE in consultations.

Methods
We transcribed 50 initial prostate cancer treatment consultations across nine multidisciplinary providers (Urologists, Radiation Oncologists, Medical Oncologists) at our tertiary referral, academic center. Coders identified quotes describing SE and used an inductive approach to establish a hierarchy for granularity of communication: (1) not mentioned, (2) name only, (3) generalization(“high”), (4) average incidence without timepoint, (5) average incidence with timepoint, and (6) precision estimate. We reported the most granular mode of communication for each SE throughout the consultation overall and across specialty and tumor risk.

Results
Among consultations discussing surgery (n = 40), erectile dysfunction (ED) and urinary incontinence (UI) were omitted in 15% and 12%, not quantified (name only or generalization) in 47% and 30%, and noted as average incidence without timeline in 8% and 8%, respectively. In only 30% and 49% were ED and UI quantified with timeline (average incidence with timeline or precision estimate), respectively. Among consultations discussing radiation (n = 36), irritative urinary symptoms, ED, and other post-radiotherapy SE were omitted in 22%, 42%, and 64–67%, not quantified in 61%, 33%, and 23–28%, and noted as average incidence without timeline in 8%, 22%, and 6–8%, respectively. In only 3–8% were post-radiotherapy SE quantified with timeline. Specialty concordance (but not tumor risk) was associated with higher granularity of communication, though physicians frequently failed to quantify specialty-concordant SE.

Conclusions
SE was often omitted, not quantified, and/or lacked a timeline in treatment consultations in our sample. Physicians should articulate, quantify, and assign a timeline for SE to optimize SDM.
Causal influences of neuropsychiatric disorders on Alzheimer’s disease
Authors: Baranova Ancha , Zhao Qian , Cao Hongbao , Chandhoke Vikas , Zhang Fuquan 
Published: February 2024

AbstractPrevious studies have observed a significant comorbidity between Alzheimer’s disease (AD) and some other neuropsychiatric disorders. However, the mechanistic connections between neuropsychiatric disorders and AD are not well understood. We conducted a Mendelian randomization analysis to appraise the potential influences of 18 neurodegenerative and neuropsychiatric disorders on AD. We found that four disorders are causally associated with increased risk for AD, including bipolar disorder (BD) (OR: 1.09), migraine (OR: 1.09), schizophrenia (OR: 1.05), and Parkinson’s disease (PD) (OR: 1.07), while attention-deficit/hyperactivity disorder (ADHD) was associated with a decreased risk for AD (OR: 0.80). In case of amyotrophic lateral sclerosis (OR: 1.04) and Tourette’s syndrome (OR: 1.05), there was suggestive evidence of their causal effects of on AD. Our study shows that genetic components predisposing to BD, migraine, schizophrenia, and PD may promote the development of AD, while ADHD may be associated with a reduced risk of AD. The treatments aimed at alleviating neuropsychiatric diseases with earlier onset may also influence the risk of AD-related cognitive decline, which is typically observed later in life.
A multi-cohort study of the hippocampal radiomics model and its associated biological changes in Alzheimer’s Disease
Authors: Xia Huwei , Luan Xiaoqian , Bao Zhengkai , Zhu Qinxin , Wen Caiyun , Wang Meihao , Song Weihong 
Published: February 2024

AbstractThere have been no previous reports of hippocampal radiomics features associated with biological functions in Alzheimer’s Disease (AD). This study aims to develop and validate a hippocampal radiomics model from structural magnetic resonance imaging (MRI) data for identifying patients with AD, and to explore the mechanism underlying the developed radiomics model using peripheral blood gene expression. In this retrospective multi-study, a radiomics model was developed based on the radiomics discovery group (n = 420) and validated in other cohorts. The biological functions underlying the model were identified in the radiogenomic analysis group using paired MRI and peripheral blood transcriptome analyses (n = 266). Mediation analysis and external validation were applied to further validate the key module and hub genes. A 12 radiomics features-based prediction model was constructed and this model showed highly robust predictive power for identifying AD patients in the validation and other three cohorts. Using radiogenomics mapping, myeloid leukocyte and neutrophil activation were enriched, and six hub genes were identified from the key module, which showed the highest correlation with the radiomics model. The correlation between hub genes and cognitive ability was confirmed using the external validation set of the AddneuroMed dataset. Mediation analysis revealed that the hippocampal radiomics model mediated the association between blood gene expression and cognitive ability. The hippocampal radiomics model can accurately identify patients with AD, while the predictive radiomics model may be driven by neutrophil-related biological pathways.
Targeting SIRT3 sensitizes glioblastoma to ferroptosis by promoting mitophagy and inhibiting SLC7A11
Authors: Li Xiaohe , Zhang Wenlong , Xing Zhengcao , Hu Shuming , Zhang Geqiang , Wang Tiange , Wang Tianshi , Fan Qiuju , Chen Guoqiang , Cheng Jinke , Jiang Xianguo , Cai Rong 
Published: February 2024

AbstractGlioblastoma (GBM) cells require large amounts of iron for tumor growth and progression, which makes these cells vulnerable to destruction via ferroptosis induction. Mitochondria are critical for iron metabolism and ferroptosis. Sirtuin-3 (SIRT3) is a deacetylase found in mitochondria that regulates mitochondrial quality and function. This study aimed to characterize SIRT3 expression and activity in GBM and investigate the potential therapeutic effects of targeting SIRT3 while also inducing ferroptosis in these cells. We first found that SIRT3 expression was higher in GBM tissues than in normal brain tissues and that SIRT3 protein expression was upregulated during RAS-selective lethal 3 (RSL3)-induced GBM cell ferroptosis. We then observed that inhibition of SIRT3 expression and activity in GBM cells sensitized GBM cells to RSL3-induced ferroptosis both in vitro and in vivo. Mechanistically, SIRT3 inhibition led to ferrous iron and ROS accumulation in the mitochondria, which triggered mitophagy. RNA-Sequencing analysis revealed that upon SIRT3 knockdown in GBM cells, the mitophagy pathway was upregulated and SLC7A11, a critical antagonist of ferroptosis via cellular import of cystine for glutathione (GSH) synthesis, was downregulated. Forced expression of SLC7A11 in GBM cells with SIRT3 knockdown restored cellular cystine uptake and consequently the cellular GSH level, thereby partially rescuing cell viability upon RSL3 treatment. Furthermore, in GBM cells, SIRT3 regulated SLC7A11 transcription through ATF4. Overall, our study results elucidated novel mechanisms underlying the ability of SIRT3 to protect GBM from ferroptosis and provided insight into a potential combinatorial approach of targeting SIRT3 and inducing ferroptosis for GBM treatment.
Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial
Authors: Alves Costa Silva Carolina , Piccinno Gianmarco , Suissa Déborah , Bourgin Mélanie , Schreibelt Gerty , Durand Sylvère , Birebent Roxanne , Fidelle Marine , Sow Cissé , Aprahamian Fanny , Manghi Paolo , Punčochář Michal , Asnicar Francesco , Pinto Federica , Armanini Federica , Terrisse Safae , Routy Bertrand , Drubay Damien , Eggermont Alexander M. M. , Kroemer Guido , Segata Nicola , Zitvogel Laurence , Derosa Lisa , Bol Kalijn F. , de Vries I. Jolanda M. 
Published: February 2024

AbstractTumor immunosurveillance plays a major role in melanoma, prompting the development of immunotherapy strategies. The gut microbiota composition, influencing peripheral and tumoral immune tonus, earned its credentials among predictors of survival in melanoma. The MIND-DC phase III trial (NCT02993315) randomized (2:1 ratio) 148 patients with stage IIIB/C melanoma to adjuvant treatment with autologous natural dendritic cell (nDC) or placebo (PL). Overall, 144 patients collected serum and stool samples before and after 2 bimonthly injections to perform metabolomics (MB) and metagenomics (MG) as prespecified exploratory analysis. Clinical outcomes are reported separately. Here we show that different microbes were associated with prognosis, with the health-related Faecalibacterium prausnitzii standing out as the main beneficial taxon for no recurrence at 2 years (p = 0.008 at baseline, nDC arm). Therapy coincided with major MB perturbations (acylcarnitines, carboxylic and fatty acids). Despite randomization, nDC arm exhibited MG and MB bias at baseline: relative under-representation of F. prausnitzii, and perturbations of primary biliary acids (BA). F. prausnitzii anticorrelated with BA, medium- and long-chain acylcarnitines. Combined, these MG and MB biomarkers markedly determined prognosis. Altogether, the host-microbial interaction may play a role in localized melanoma. We value systematic MG and MB profiling in randomized trials to avoid baseline differences attributed to host-microbe interactions.
Complex regulatory networks influence pluripotent cell state transitions in human iPSCs
Authors: Arthur Timothy D. , Nguyen Jennifer P. , D’Antonio-Chronowska Agnieszka , Matsui Hiroko , Silva Nayara S. , Joshua Isaac N. ,   iPSCORE Consortium, Aguiar Lana Ribeiro , Arias Angelo D. , Benaglio Paola , Berggren W. Travis , Belmonte Juan Carlos Izpisua , Borja Victor , Cook Megan , DeBoever Christopher , Diffenderfer Kenneth E. , Donovan Margaret K. R. , Farnam KathyJean , Fujita Kyohei , Garcia Melvin , Henson Benjamin A. , Harismendy Olivier , Jakubosky David , Jepsen Kristen , Li He , Nariai Naoki , O’Connor Daniel T. , Okubo Jonathan , Panopoulos Athanasia D. , Rao Fengwen , Reyna Joaquin , Salgado Bianca M. , Smith Erin N. , Sohmer Josh , Yost Shawn , Luchessi André D. , Greenwald William W. Young , D’Antonio Matteo , Pera Martin F. , Frazer Kelly A. 
Published: February 2024

AbstractStem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discover 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which are highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlie the coordinated expression of genes in the GNMs. Epigenetic analyses reveal that regulatory networks underlying self-renewal and pluripotency are more complex than previously realized. Genetic analyses identify thousands of regulatory variants that overlapped predicted transcription factor binding sites and are associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network are significantly enriched for regulatory variants with large effects, suggesting that they play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work bins tens of thousands of regulatory elements in hiPSCs into discrete regulatory networks, shows that pluripotency and self-renewal processes have a surprising level of regulatory complexity, and suggests that genetic factors may contribute to cell state transitions in human iPSC lines.
Autonomous error correction of a single logical qubit using two transmons
Authors: Li Ziqian , Roy Tanay , Rodríguez Pérez David , Lee Kan-Heng , Kapit Eliot , Schuster David I. 
Published: February 2024

AbstractLarge-scale quantum computers will inevitably need quantum error correction to protect information against decoherence. Traditional error correction typically requires many qubits, along with high-efficiency error syndrome measurement and real-time feedback. Autonomous quantum error correction instead uses steady-state bath engineering to perform the correction in a hardware-efficient manner. In this work, we develop a new autonomous quantum error correction scheme that actively corrects single-photon loss and passively suppresses low-frequency dephasing, and we demonstrate an important experimental step towards its full implementation with transmons. Compared to uncorrected encoding, improvements are experimentally witnessed for the logical zero, one, and superposition states. Our results show the potential of implementing hardware-efficient autonomous quantum error correction to enhance the reliability of a transmon-based quantum information processor.
Insights into structural defect formation in individual InP/ZnSe/ZnS quantum dots under UV oxidation
Authors: Baek Hayeon , Kang Sungsu , Heo Junyoung , Choi Soonmi , Kim Ran , Kim Kihyun , Ahn Nari , Yoon Yeo-Geon , Lee Taekjoon , Chang Jae Bok , Lee Kyung Sig , Park Young-Gil , Park Jungwon 
Published: February 2024

AbstractInP/ZnSe/ZnS quantum dots (QDs) stand as promising candidates for advancing QD-organic light-emitting diodes (QLED), but low emission efficiency due to their susceptibility to oxidation impedes applications. Structural defects play important roles in the emission efficiency degradation of QDs, but the formation mechanism of defects in oxidized QDs has been less investigated. Here, we investigated the impact of diverse structural defects formation on individual QDs and propagation during UV-facilitated oxidation using high-resolution (scanning) transmission electron microscopy. UV-facilitated oxidation of the QDs alters shell morphology by the formation of surface oxides, leaving ZnSe surfaces poorly passivated. Further oxidation leads to the formation of structural defects, such as dislocations, and induces strain at the oxide-QD interfaces, facilitating In diffusion from the QD core. These changes in the QD structures result in emission quenching. This study provides insight into the formation of structural defects through photo-oxidation, and their effects on emission properties of QDs.