bluuebunny/crossref_metadata_2025 huggingface dataset:
Greenup Variability Impact on Seasonal Streamflow and Soil Moisture Dynamics in Humid, Temperate Forests
Authors: Hwang Taehee , Band Lawrence E. , Oishi A. Christopher , Kang Hojeong
Published: December 2023

In this study, we investigate how seasonal streamflow and soil moisture patterns have responded to variability in vegetation phenology in humid, temperate forested watersheds without significant seasonal snowmelt over the last four decades. We characterize spring streamflow peaks using 50th percentiles of cumulative daily precipitation, streamflow, and soil moisture measurements, and investigate interactions with remotely sensed, greenup anomalies. After removing a dominant precipitation control, 1‐day earlier greenup is usually associated with about 1‐day early spring flow peak at four low‐elevation deciduous catchments using both sequential and multiple linear regressions. This indicates that the strong dependency of seasonal flow regimes on precipitation is mediated by vegetation seasonality, especially by greenup variability. In contrast, we find less significant correlations of the greenup anomalies on flow percentiles from two paired evergreen and two high‐elevation deciduous catchments. At a plot scale, similar correlations were found only at an upslope topographic position, where precipitation also showed tighter coupling with moisture seasonal patterns than downslope. Our study suggests that rainfall‐runoff and rainfall‐soil moisture relations have been closely mediated by vegetation seasonality in deciduous forests, especially by greenup anomalies, but patterned along topoclimate and hillslope gradients. This study emphasizes that it is important to understand phenological responses to ongoing climate change (in both long‐term and interannual variability) for prediction of seasonal flow regimes especially in deciduous forested catchments.
Remote Sensing of Ocean Dynamics Parameters by Wide‐Beam High‐Frequency Hybrid Sky‐Surface Wave Radar: Localization of Sea Surface Scattering Points and Decontamination of Semi‐Physical Ionosphere Phase
Authors: Feng Mengyan , Fang Hanxian , Wu Xiongbin , Ai Weihua , Yue Xianchang , Zhang Lan
Published: December 2023

This study addresses the issue of locating the scattering points on the sea surface and rectifying the interference caused by the ionosphere phase in the remote sensing of ocean dynamics parameters. Wide‐beam high‐frequency hybrid sky‐surface wave radar (WB‐HFSSWR) was used for this purpose. In order to mitigate the impact of ionosphere phase contamination on the electron density variation along the sky‐wave path of a radio wave, we present two algorithms: the WB‐HFSSWR Single‐Station sea surface scattering point localization algorithm (WB‐SPLA) and the semi‐physical ionosphere phase decontamination algorithm (SP‐IPDA). Compared with the currently employed ionosphere phase decontamination algorithm, the SP‐IPDA algorithm exhibited enhanced physical characteristics. To evaluate the efficacy of the proposed algorithms, we calculate the root‐mean‐square errors (RMSEs) of the elliptical current velocity (vE‐IRI and vE‐GST) of the WB‐HFSSWR, based on the SP‐IPDA and generalized S‐transform algorithm (GST). The results demonstrated that the RMSEs of vE‐IRI and vE‐GST were comparable to the precision of the bistatic surface‐wave radar elliptical current velocity. The data volume of vE‐IRI was 20.5% larger than that of vE‐GST, and vE‐IRI was more precise than vE‐GST, with RMSEs of 11.98 and 12.63 cm/s, respectively. Furthermore, on the common sea surface scattering points, the precision of vE‐IRI was approximately 18.4% higher than that of vE‐GST.
Future Amplification of Multivariate Risk of Compound Drought and Heatwave Events on South Asian Population
Authors: Ullah Irfan , Zeng Xin‐Min , Mukherjee Sourav , Aadhar Saran , Mishra Ashok Kumar , Syed Sidra , Ayugi Brian Odhiambo , Iyakaremye Vedaste , Lv Haishen
Published: December 2023

Over the past few decades, South Asia (SA) has experienced an upsurge in the frequency of severe monsoonal compound drought and heatwave (CDHW) occurrences. Climate models that identify land‐atmosphere coupling as a major contributing factor for this exacerbation and anticipate an increase in the intensity and frequency of CDHW occurrences in future also represent this. For the first time, this study investigated the future evolution of monsoonal CDHW events based on new generations of the CMIP6 and population products by applying a multivariate framework. Specifically, this study explored the impacts of natural climate variability and future land‐atmosphere coupling on the monsoonal CDHW event risks and their bivariate return periods for two future time‐periods and emission scenarios across SA and its subregions. The odds of CDHW occurrences were then examined using a logistic regression model and its association with the natural and anthropogenic drivers was determined. The results indicate that the monsoonal CDHWs occurrence is anticipated to increase substantially during the late twenty‐first century (2056–2090). The 50‐year CDHW events might increase by two‐fold across most of SA by the mid‐21st century under the high emission scenario. We find that the co‐occurring dry and warm conditions rapidly strengthens with soil moisture and temperature coupling and are further exacerbated by land‐atmospheric feedback loops. Our findings show that persistent dry spells contribute significantly to heatwave events, emphasizing regional exposure to changing climates.
An Electrifying Approach to Carbon Capture
Authors: Morris Bill
Published: December 2023

A new sodium-ion “battery” promises an environmentally friendly method of sequestering carbon in the ocean, but experts remain cautious.
JGR: Machine Learning and Computation is Open for Submissions
Authors: Giampoala Matt
Published: December 2023

The founding Editor-in-Chief discusses how AGU’s newest journal will capture critical advancements of the techniques moving scientific discovery forward.
A Spatially Resolved and Environmentally Informed Forecast Model of West Nile Virus in Coachella Valley, California
Authors: Ward Matthew J. , Sorek‐Hamer Meytar , Henke Jennifer A. , Little Eliza , Patel Aman , Shaman Jeffery , Vemuri Krishna , DeFelice Nicholas B.
Published: December 2023

West Nile virus (WNV) is the most significant arbovirus in the United States in terms of both morbidity and mortality. West Nile exists in a complex transmission cycle between avian hosts and the arthropod vector, Culex spp. mosquitoes. Human spillover events occur when humans are bitten by an infected mosquito and predicting these rates of infection and therefore the risk to humans may be associated with fluctuations in environmental conditions. In this study, we evaluate the hydrological and meteorological drivers associated with mosquito biology and viral development to determine if these associations can be used to forecast seasonal mosquito infection rates with WNV in the Coachella Valley of California. We developed and tested a spatially resolved ensemble forecast model of the WNV mosquito infection rate in the Coachella Valley using 17 years of mosquito surveillance data and North American Land Data Assimilation System‐2 environmental data. Our multi‐model inference system indicated that the combination of a cooler and dryer winter, followed by a wetter and warmer spring, and a cooler than normal summer was most predictive of the prevalence of West Nile positive mosquitoes in the Coachella Valley. The ability to make accurate early season predictions of West Nile risk has the potential to allow local abatement districts and public health entities to implement early season interventions such as targeted adulticiding and public health messaging before human transmission occurs. Such early and targeted interventions could better mitigate the risk of WNV to humans.
Accretion Cycles, Structural Evolution, and Thrust Activity in Accretionary Wedges With Various Décollement Configurations: Insights From Sandbox Analog Modeling
Authors: Noda Atsushi , Graveleau Fabien , Witt Cesar , Chanier Frank , Vendeville Bruno
Published: December 2023

The architecture (geometry, fault network, and stacking pattern of accreted thrust sheets) of accretionary wedges influences subduction zone processes. However, it remains challenging to constrain the architectural evolution in natural accretionary wedges over geological timescales. In this study, we undertook sandbox analog modeling, with quantitative analysis of the wedge geometry and digital image correlation‐based kinematics, to delineate the wedge growth history with four décollement settings (single or double and continuous or discontinuous). The results show that the wedge is formed by repeated episodic frontal accretion with a constant cycle (i.e., the accretion cycle), and the degree of coupling between the base of the wedge and subducting plate interface appears to depend on the relative strengths of the wedge and detachment. An interbedded décollement layer in the incoming sediment facilitated wedge segmentation and rearrangement of the internal fault network, which weakened the wedge strength. A combination of a detachable high‐friction patch in the basal décollement and a continuous interbedded weak layer enabled underplating of underthrusted sediment beneath the inner wedge, which involved a low‐angle, long‐lived forethrust and multiple cycles of frontal accretion on short‐lived forethrusts at the deformation front. Our findings suggest that décollement configuration is a key factor in controlling the accretion cycle, strain distribution, fault network, and wedge strength on timescales of ∼105 yr in natural accretionary systems. This result should be considered when investigating modern subduction zones.
Assessing Storm Surge Multiscenarios Based on Ensemble Tropical Cyclone Forecasting
Authors: Rezuanul Islam Md. , Duc Le , Sawada Yohei
Published: December 2023

Ensemble forecasting is a promising tool to aid in making informed decisions against risks of coastal storm surges. Although tropical cyclone (TC) ensemble forecasts are commonly used in operational numerical weather prediction systems, their potential for disaster prediction has not been maximized. Here we present a novel, efficient, and practical method to utilize a large ensemble forecast of 1,000 members to analyze storm surge scenarios toward effective decision making such as evacuation planning and issuing surge warnings. We perform the simulation of TC Hagibis (2019) using the Japan Meteorological Agency's (JMA) nonhydrostatic model. The simulated atmospheric predictions were utilized as inputs for a statistical surge model named the Storm Surge Hazard Potential Index to estimate peak surge heights along the central coast of Japan. We show that Pareto‐optimized solutions from an ensemble storm surge forecast can describe potential worst (maximum) and optimum (minimum) storm surge scenarios. These solutions exemplify a diversity of trade‐off surge outcomes across diverse coastal locations, reflecting variations in coastal geometry, including bathymetry. For example, some of the Pareto‐optimized solutions that illustrate worst surge scenarios for inner bay locations are not necessarily accountable for bringing severe surge cases in open coasts. We further emphasize that an in‐depth evaluation of Pareto‐optimal solutions can shed light on how meteorological variables such as track, intensity, and size of TCs influence the worst and optimum surge scenarios, which is not clearly quantified in current multiscenario assessment methods such as those used by JMA/National Hurricane Center in the United States.
Lunar Impact Craters: New Perspectives From Full‐Polarimetric Analysis of Chandrayaan‐2 Dual‐Frequency SAR Data
Authors: Putrevu Deepak , Chakraborty Tathagata , Mukhopadhyay Jayanta , Syed Tajdarul Hassan , Bhiravarasu Sriram S. , Das Anup , Pandey Dharmendra Kr. , Misra Arundhati
Published: December 2023

With the availability of the full‐polarimetry data from Chandrayaan‐2 Dual‐frequency Synthetic Aperture Radar (DFSAR) for the first time, the lunar impact craters are studied for comprehensive characterization, which was earlier limited due to hybrid‐polarimetry based observations. In conjunction with the conventional Circular Polarization Ratio (CPR), we explore the unique full‐polarimetric parameters such as Single‐bounce Eigenvalue Relative Difference and T‐Ratio which are sensitive to surface roughness and dielectric constant, respectively. We studied the polarimetric behavior of a total of 115 nos. of impact craters within a specific size range (∼1–25 km diameter) belonging to different categories viz. fresh, degraded, polar and non‐polar anomalous craters. Our results confirm that both kinds of non‐polar and polar anomalous craters overall hold centimeter‐decimeter scale surface roughness similar to the exterior of the fresh craters, which mainly leads to the anomalous nature of the craters. Our analysis indicates possible control of the crater degradation process on the change in the radar scattering behavior of the studied lunar craters. The crater degradation causes a reduction in the surface roughness and dielectric property (density) of the scatterers present in various craters leading to a change in the radar scattering behavior. Alongside, water ice, if at all present admixed into the regolith in the polar anomalous craters, is not in the form of dominant scatterers that can influence the radar signature. However, the occurrence of relatively higher CPR values in smooth low dielectric crater interiors supports the possibility of the presence of water ice in some of the studied polar anomalous craters belonging to Pre‐Imbrian to Imbrian lunar geological periods.
Performance Analysis of a Strong Constraint 4DVar and 4DEnVar on Regional Ionosphere Imaging
Authors: Ssessanga Nicholas , Miloch Wojciech Jacek , Clausen Lasse Boy Novock , Kotova Daria
Published: December 2023

Data assimilation (DA) techniques have recently gained traction in the ionospheric community, particularly at regional operational centers where more precise data are becoming prevalent. At center stage is the argument over which technique or scheme merits realization. At 4DSpace, we have in‐house developed and assessed the performance of two regional flavors of short‐term forecast strong constraint four‐dimensional (4D, space and time) variational (SC4DVar) DA schemes; the orthodox incremental (SC4DVar‐Inc) and ensemble‐based (SC4DEnVar) approach. SC4DVar‐Inc is bottled‐necked by expensive Tangent Linear Models (TLMs) and model Ad‐joints (MAs), while SC4DEnVar design mitigates these limitations. Both schemes initialize from the same background (IRI‐2016), and electron densities forward propagated (30‐min) by a Gauss Markov filter‐ the densities take on a log‐normal distribution to assert the mandatory ionosphere density positive definiteness. Preliminary assimilation is performed only with ubiquitous Global Navigation Satellite System observables from ground‐based receivers, with a focus on moderately stable mid‐latitudes, specifically the Japanese archipelago and neighboring areas. Using a simulation analysis, we find that under model space localization, 30 member Ensembles are sufficient for regional SC4DEnVar. Verification of reconstructions is with independent observations from ground‐based ionosonde and satellite radio occultations: the performance of both schemes is fairly adequate during the quiet period when the background has a better estimation of the hmF2. SC4DVar‐Inc is slightly better over areas densely populated with measurements, but SC4DEnVar estimates the overall 3D ionosphere picture better, particularly in remote areas and during severe conditions. These results warrant SC4DEnVar as a better candidate for precise short‐time regional forecasts.
Modeling the Streamflow Response to Heatwaves Across Glacierized Basins in Southwestern Canada
Authors: Anderson Sam , Radić Valentina
Published: December 2023

In addition to having far‐reaching impacts on human health, agriculture, wildfires, ecosystems, and infrastructure, heatwaves control streamflow through the melting of seasonal snow and glacier ice. Despite their importance, there is limited understanding of how heatwaves modify streamflow at regional scales, how these impacts vary by heatwave timing and duration, and how glaciers control the streamflow response. Here, we use a deep learning hydrological model, which has previously been trained, evaluated, and interpreted in southwestern Canada, to simulate the streamflow response to heatwaves at 111 basins in the region. The model, driven by gridded ERA5 reanalysis temperature and precipitation data from 1979 to 2015, is forced by synthetic heatwave conditions that vary in their duration and onset throughout the year. We consider how the streamflow response to heatwaves is sensitive to annual temperatures by adding spatially and temporally uniform warming of 2°C across the study region, under the assumption that the underlying hydrological system behavior remains unchanged. We find that heatwaves, particularly in spring and summer, induce an initial streamflow surplus followed by a streamflow deficit, relative to the non‐heatwave case. In summer, glacier contributions to streamflow partially compensate for streamflow deficits that arise from heatwaves earlier in the melt season. In the scenario with 2°C warmer annual temperatures, heatwaves induce a lesser streamflow response in spring when the seasonal streamflow is most increased due to the advancing freshet. Our findings demonstrate how glaciers buffer the impacts of heatwaves on streamflow, but this buffering effect is expected to diminish as glaciers retreat.
Looking for Theory‐Practice Synthesis for Actionable Outcomes: A Continuing Special Collection for Translational Water Research
Authors: Islam Shafiqul , Illangasekare Tissa H. , Selker John , Destouni Georgia
Published: December 2023

Translational research (TR) represents a promising systematic process for going from scientific discoveries to practical applications. Through conversations with academics, practitioners, decision‐makers and users, there has emerged a broad level of water science community support for including TR in Water Resources Research (WRR) publications. Based on this, we now open a continuing special collection of TR papers in WRR. The aim is to facilitate a community within hydrology and water science that seeks to provide actionable knowledge for societal benefit across disciplines, scales and contexts, with a focus on water as a key societal resource or a risk (e.g., of floods, droughts, or as pollutant carrier). This Editorial discusses what the multi‐faceted nature of TR may include in the context of WRR, why it is important to encourage TR papers in WRR, and how the opening of a continuing special collection of translational water research papers initiates a process to include such articles in the journal.
Azithromycin for acute bronchiolitis and wheezing episodes in children – a systematic review with meta-analysis
Authors: Ukkonen Rosa-Maria , Renko Marjo , Kuitunen Ilari
Published: December 2023

Background

The aim of this systematic review and meta-analysis was to analyse the efficacy of azithromycin in acute bronchiolitis and wheezing.

Methods

PubMed, Scopus, and Web of Science databases were searched for randomized controlled trials comparing azithromycin to placebo in children <2 years of age. Main outcomes were progress of acute wheezing episode and recurrence of wheezing. We used random-effects model to calculate mean difference (MD) with 95% confidence interval (CI) or risk ratios (RR) with CI.

Results

We screened 1604 abstracts and included 7 studies. Risk of bias was low in three and had some concerns in four studies. Need for intensive care unit treatment was assessed in four studies (446 children) and the risk difference was 0.0% (CI –2.0 to 2.0; low quality evidence). Hospitalization duration was –0.27 days shorter in the azithromycin group (MD-0.27, CI –0.47 to –0.07; three studies; moderate quality evidence). Azithromycin did not prevent recurrence of wheezing (RR 0.84, CI 0.45–1.56; three studies), hospital readmissions (RR 1.14, CI 0.82–1.60; four studies).

Conclusions

We found moderate quality evidence that azithromycin may reduce hospitalization duration. Low certainty evidence suggests that azithromycin does not reduce the need for intensive care unit treatment. Furthermore, azithromycin did not prevent wheezing recurrence.

Impact

Azithromycin may reduce hospitalization time in acute bronchiolitis and wheezing episodes among children aged less than two.

Azithromycin administrated during the acute wheezing period, does not have preventive effect on wheezing recurrence.

Azithromycin seemed to have similar adverse event profile than placebo.

Future studies with clinically relevant outcomes, and sufficient sample sizes are needed, before implementing azithromycin into clinical use.
m6A and m5C modification of GPX4 facilitates anticancer immunity via STING activation
Authors: Chen Baoxiang , Hong Yuntian , Zhai Xiang , Deng Yanrong , Hu Heng , Tian Shunhua , Zhang Yukang , Ren Xianghai , Zhao Jianhong , Jiang Congqing
Published: December 2023

Cancer immunotherapy is arguably the most rapidly advancing realm of cancer treatment. Glutathione peroxidase 4 (GPX4) has emerged as the vital enzyme to prevent lipid peroxidation and maintain cellular redox homeostasis. However, the mechanism of GPX4 in the regulation of cancer immunotherapy of colon adenocarcinoma (COAD) are incompletely understood. In pan-cancer analysis, we found that GPX4 showed remarkably upregulated expression and exhibited significant association with overall survival in multiple cancer types, especially COAD. Furthermore, upregulated GPX4 expression was positively correlated with increased immune cells infiltration and enhanced expression of immunomodulators. Mechanistically, RBM15B- and IGFBP2-mediated N6-methyladenosine (m6A) modification and NSUN5-mediated 5-methylcytosine (m5C) modification of GPX4 facilitated anticancer immunity via activation of cyclic GMP-AMP synthase (cGAS)-stimulator of interferon (STING) signaling by maintaining redox homeostasis in COAD. The risk model and nomogram model constructed based on the GPX4-derived genes further confirmed the prognostic and treatment-guiding value of GPX4. In all, our study demonstrated that m6A and m5C modification of GPX4 may be a promising target for cancer immunotherapy via activating the cGAS-STING signaling pathway in COAD.
Gp78 deficiency in hepatocytes alleviates hepatic ischemia-reperfusion injury via suppressing ACSL4-mediated ferroptosis
Authors: Li Changbiao , Wu Yichao , Chen Kangchen , Chen Ronggao , Xu Shengjun , Yang Beng , Lian Zhengxing , Wang Xiaodong , Wang Kai , Xie Haiyang , Zheng Shusen , Liu Zhikun , Wang Di , Xu Xiao
Published: December 2023

Ferroptosis, which is driven by iron-dependent lipid peroxidation, plays an essential role in liver ischemia-reperfusion injury (IRI) during liver transplantation (LT). Gp78, an E3 ligase, has been implicated in lipid metabolism and inflammation. However, its role in liver IRI and ferroptosis remains unknown. Here, hepatocyte-specific gp78 knockout (HKO) or overexpressed (OE) mice were generated to examine the effect of gp78 on liver IRI, and a multi-omics approach (transcriptomics, proteomics, and metabolomics) was performed to explore the potential mechanism. Gp78 expression decreased after reperfusion in LT patients and mice with IRI, and gp78 expression was positively correlated with liver damage. Gp78 absence from hepatocytes alleviated liver damage in mice with IRI, ameliorating inflammation. However, mice with hepatic gp78 overexpression showed the opposite phenotype. Mechanistically, gp78 overexpression disturbed lipid homeostasis, remodeling polyunsaturated fatty acid (PUFA) metabolism, causing oxidized lipids accumulation and ferroptosis, partly by promoting ACSL4 expression. Chemical inhibition of ferroptosis or ACSL4 abrogated the effects of gp78 on ferroptosis and liver IRI. Our findings reveal a role of gp78 in liver IRI pathogenesis and uncover a mechanism by which gp78 promotes hepatocyte ferroptosis by ACSL4, suggesting the gp78-ACSL4 axis as a feasible target for the treatment of IRI-associated liver damage.
Structural and thermodynamic insights into antibody light chain tetramer formation through 3D domain swapping
Authors: Sakai Takahiro , Mashima Tsuyoshi , Kobayashi Naoya , Ogata Hideaki , Duan Lian , Fujiki Ryo , Hengphasatporn Kowit , Uda Taizo , Shigeta Yasuteru , Hifumi Emi , Hirota Shun
Published: December 2023

Overexpression of antibody light chains in small plasma cell clones can lead to misfolding and aggregation. On the other hand, the formation of amyloid fibrils from antibody light chains is related to amyloidosis. Although aggregation of antibody light chain is an important issue, atomic-level structural examinations of antibody light chain aggregates are sparse. In this study, we present an antibody light chain that maintains an equilibrium between its monomeric and tetrameric states. According to data from X-ray crystallography, thermodynamic and kinetic measurements, as well as theoretical studies, this antibody light chain engages in 3D domain swapping within its variable region. Here, a pair of domain-swapped dimers creates a tetramer through hydrophobic interactions, facilitating the revelation of the domain-swapped structure. The negative cotton effect linked to the β-sheet structure, observed around 215 nm in the circular dichroism (CD) spectrum of the tetrameric variable region, is more pronounced than that of the monomer. This suggests that the monomer contains less β-sheet structures and exhibits greater flexibility than the tetramer in solution. These findings not only clarify the domain-swapped structure of the antibody light chain but also contribute to controlling antibody quality and advancing the development of future molecular recognition agents and drugs.
Quadrupole anomalous Hall effect in magnetically induced electron nematic state
Authors: Koizumi Hiroki , Yamasaki Yuichi , Yanagihara Hideto
Published: December 2023

Berry phases in both momentum and real space cause transverse motion in itinerant electrons, manifesting various off-diagonal transport effect such anomalous and topological Hall effects. Although these Hall effects are isotropic within the plane perpendicular to the fictitious magnetic field, here, we report the manifestation of the anisotropic linear anomalous Hall effect (AHE) in the spinel oxide NiCo2O4 epitaxial film. The unconventional Hall effect indicates a quadrupole dependence on the in-plane current direction being added to the uniform AHE. Moreover, its sign can be manipulated just by magnetic-field cooling. The anisotropic effect is attributed to an electron nematic state originating from a deformed electronic state owing to an extended magnetic toroidal quadrupole and ferrimagnetic order.
The anti-symmetric and anisotropic symmetric exchange interactions between electric dipoles in hafnia
Authors: Yu Longju , Zhao Hong Jian , Chen Peng , Bellaiche Laurent , Ma Yanming
Published: December 2023

The anti-symmetric and anisotropic symmetric exchange interactions between two magnetic dipole moments – responsible for intriguing magnetic textures (e.g., magnetic skyrmions) – have been discovered since last century, while their electric analogues were either hidden for a long time or still not known. It is only recently that the anti-symmetric exchange interactions between electric dipoles was proved to exist (with materials hosting such an interaction being still rare) and the existence of anisotropic symmetric exchange interaction between electric dipoles remains ambiguous. Here, by symmetry analysis and first-principles calculations, we identify hafnia as a candidate material hosting the non-collinear dipole alignments, the analysis of which reveals the anti-symmetric and anisotropic symmetric exchange interactions between electric dipoles in this material. Our findings can hopefully deepen the current knowledge of electromagnetism in condensed matter, and imply the possibility of discovering novel states of matter (e.g., electric skyrmions) in hafnia-related materials.
Mental search of concepts is supported by egocentric vector representations and restructured grid maps
Authors: Viganò Simone , Bayramova Rena , Doeller Christian F. , Bottini Roberto
Published: December 2023

The human hippocampal-entorhinal system is known to represent both spatial locations and abstract concepts in memory in the form of allocentric cognitive maps. Using fMRI, we show that the human parietal cortex evokes complementary egocentric representations in conceptual spaces during goal-directed mental search, akin to those observable during physical navigation to determine where a goal is located relative to oneself (e.g., to our left or to our right). Concurrently, the strength of the grid-like signal, a neural signature of allocentric cognitive maps in entorhinal, prefrontal, and parietal cortices, is modulated as a function of goal proximity in conceptual space. These brain mechanisms might support flexible and parallel readout of where target conceptual information is stored in memory, capitalizing on complementary reference frames.
Airway environment drives the selection of quorum sensing mutants and promote Staphylococcus aureus chronic lifestyle
Authors: Ding Xiongqi , Robbe-Masselot Catherine , Fu Xiali , Léonard Renaud , Marsac Benjamin , Dauriat Charlene J. G. , Lepissier Agathe , Rytter Héloïse , Ramond Elodie , Dupuis Marion , Euphrasie Daniel , Dubail Iharilalao , Schimmich Cécile , Qin Xiaoquan , Parraga Jessica , Leite-de-Moraes Maria , Ferroni Agnes , Chassaing Benoit , Sermet-Gaudelus Isabelle , Charbit Alain , Coureuil Mathieu , Jamet Anne
Published: December 2023

Staphylococcus aureus is a predominant cause of chronic lung infections. While the airway environment is rich in highly sialylated mucins, the interaction of S. aureus with sialic acid is poorly characterized. Using S. aureus USA300 as well as clinical isolates, we demonstrate that quorum-sensing dysfunction, a hallmark of S. aureus adaptation, correlates with a greater ability to consume free sialic acid, providing a growth advantage in an air-liquid interface model and in vivo. Furthermore, RNA-seq experiment reveals that free sialic acid triggers transcriptional reprogramming promoting S. aureus chronic lifestyle. To support the clinical relevance of our results, we show the co-occurrence of S. aureus, sialidase-producing microbiota and free sialic acid in the airway of patients with cystic fibrosis. Our findings suggest a dual role for sialic acid in S. aureus airway infection, triggering virulence reprogramming and driving S. aureus adaptive strategies through the selection of quorum-sensing dysfunctional strains.
Delineating the early dissemination mechanisms of acral melanoma by integrating single-cell and spatial transcriptomic analyses
Authors: Wei Chuanyuan , Sun Wei , Shen Kangjie , Zhong Jingqin , Liu Wanlin , Gao Zixu , Xu Yu , Wang Lu , Hu Tu , Ren Ming , Li Yinlam , Zhu Yu , Zheng Shaoluan , Zhu Ming , Luo Rongkui , Yang Yanwen , Hou Yingyong , Qi Fazhi , Zhou Yuhong , Chen Yong , Gu Jianying
Published: December 2023

Acral melanoma (AM) is a rare subtype of melanoma characterized by a high incidence of lymph node (LN) metastasis, a critical factor in tumor dissemination and therapeutic decision-making. Here, we employ single-cell and spatial transcriptomic analyses to investigate the dynamic evolution of early AM dissemination. Our findings reveal substantial inter- and intra-tumor heterogeneity in AM, alongside a highly immunosuppressive tumor microenvironment and complex intercellular communication networks, particularly in patients with LN metastasis. Notably, we identify a strong association between MYC+ Melanoma (MYC+MEL) and FGFBP2+NKT cells with LN metastasis. Furthermore, we demonstrate that LN metastasis requires a metabolic shift towards fatty acid oxidation (FAO) induced by MITF in MYC+MEL cells. Etomoxir, a clinically approved FAO inhibitor, can effectively suppress MITF-mediated LN metastasis. This comprehensive dataset enhances our understanding of LN metastasis in AM, and provides insights into the potential therapeutic targeting for the management of early AM dissemination.
Recent advances in single-cell engineered live biotherapeutic products research for skin repair and disease treatment
Authors: Roslan Muhamad Aidilfitri Mohamad , Omar Mohd Norfikri , Sharif Nur Azlina Mohd , Raston Nurul Hanun Ahmad , Arzmi Mohd Hafiz , Neoh Hui-Min , Ramzi Ahmad Bazli
Published: December 2023

The human microbiome has emerged as a key player in maintaining skin health, and dysbiosis has been linked to various skin disorders. Amidst growing concerns regarding the side effects of antibiotic treatments, the potential of live biotherapeutic products (LBPs) in restoring a healthy microbiome has garnered significant attention. This review aims to evaluate the current state of the art of the genetically or metabolically engineered LBPs, termed single-cell engineered LBPs (eLBPs), for skin repair and disease treatment. While some studies demonstrate promising outcomes, the translation of eLBPs into clinical applications remains a significant hurdle. Substantial concerns arise regarding the practical implementation and scalability of eLBPs, despite the evident potential they hold in targeting specific cells and delivering therapeutic agents. This review underscores the need for further research, robust clinical trials, and the exploration of current advances in eLBP-based bioengineered bacterial chassis and new outlooks to substantiate the viability and effectiveness of eLBPs as a transformative approach in skin repair and disease intervention.
Effects of independent versus dependent stressful life events on major symptom domains of schizophrenia
Authors: Ma Yizhou , Chiappelli Joshua , Kvarta Mark D. , Bruce Heather , van der Vaart Andrew , Goldwaser Eric L. , Du Xiaoming , Sampath Hemalatha , Lightner Samantha , Endres Jane , Yusuf Akram , Yuen Alexa , Narvaez Samantha , Campos-Saravia Danny , Kochunov Peter , Hong L. Elliot
Published: December 2023

We evaluated two models to link stressful life events (SLEs) with the psychopathology of schizophrenia spectrum disorders (SSD). We separated SLEs into independent (iSLEs, unlikely influenced by one’s behavior) and dependent (dSLEs, likely influenced by one’s behavior). Stress-diathesis and stress generation models were evaluated for the relationship between total, i- and d- SLEs and the severity of positive, negative, and depressive symptoms in participants with SSD. Participants with SSD (n = 286; 196 males; age = 37.5 ± 13.5 years) and community controls (n = 121; 83 males; 35.4 ± 13.9 years) completed self-report of lifetime negative total, i- and d- SLEs. Participants with SSD reported a significantly higher number of total SLEs compared to controls (B = 1.11, p = 6.4 × 10–6). Positive symptom severity was positively associated with the total number of SLEs (β = 0.20, p = 0.001). iSLEs (β = 0.11, p = 0.09) and dSLEs (β = 0.21, p = 0.0006) showed similar association with positive symptoms (p = 0.16) suggesting stress-diathesis effects. Negative symptom severity was negatively associated with the number of SLEs (β = –0.19, p = 0.003) and dSLEs (β = −0.20, p = 0.001) but not iSLEs (β = –0.04, p = 0.52), suggesting stress generation effects. Depressive symptom severity was positively associated with SLEs (β = 0.34, p = 1.0 × 10–8), and the association was not statistically stronger for dSLEs (β = 0.33, p = 2.7 × 10–8) than iSLEs (β = 0.21, p = 0.0006), p = 0.085, suggesting stress-diathesis effects. The SLE – symptom relationships in SSD may be attributed to stress generation or stress-diathesis, depending on symptom domain. Findings call for a domain-specific approach to clinical intervention for SLEs in SSD.
Chromosome-level genome assembly of chub mackerel (Scomber japonicus) from the Indo-Pacific Ocean
Authors: Lee Young Ho , Abueg Linelle , Kim Jin-Koo , Kim Young Wook , Fedrigo Olivier , Balacco Jennifer , Formenti Giulio , Howe Kerstin , Tracey Alan , Wood Jonathan , Thibaud-Nissen Françoise , Nam Bo Hye , No Eun Soo , Kim Hye Ran , Lee Chul , Jarvis Erich D. , Kim Heebal
Published: December 2023

Chub mackerels (Scomber japonicus) are a migratory marine fish widely distributed in the Indo-Pacific Ocean. They are globally consumed for their high Omega-3 content, but their population is declining due to global warming. Here, we generated the first chromosome-level genome assembly of chub mackerel (fScoJap1) using the Vertebrate Genomes Project assembly pipeline with PacBio HiFi genomic sequencing and Arima Hi-C chromosome contact data. The final assembly is 828.68 Mb with 24 chromosomes, nearly all containing telomeric repeats at their ends. We annotated 31,656 genes and discovered that approximately 2.19% of the genome contained DNA transposon elements repressed within duplicated genes. Analyzing 5-methylcytosine (5mC) modifications using HiFi reads, we observed open/close chromatin patterns at gene promoters, including the FADS2 gene involved in Omega-3 production. This chromosome-level reference genome provides unprecedented opportunities for advancing our knowledge of chub mackerels in biology, industry, and conservation.
Morpho-chemical characterization of individual ancient starches retrieved on ground stone tools from Palaeolithic sites in the Pontic steppe
Authors: Birarda G. , Badetti E. , Cagnato C. , Sorrentino G. , Pantyukhina I. , Stani C. , Dal Zilio S. , Khlopachev G. , Covalenco S. , Obada T. , Skakun N. , Sinitsyn A. , Terekhina V. , Marcomini A. , Lubritto C. , Cefarin N. , Vaccari L. , Longo L.
Published: December 2023

Despite the extensive literature on the retrieval of digestible starches from archaeological contexts, there are still significant concerns regarding their genuine origin and durability. Here, we propose a multi-analytical strategy to identify the authenticity of ancient starches retrieved from macrolithic tools excavated at Upper Paleolithic sites in the Pontic steppe. This strategy integrates the morphological discrimination of starches through optical microscopy and scanning electron microscopy with single starch chemo-profiling using Fourier transform infrared imaging and microscopy. We obtained evidence of aging and biomineralization in the use-related starches from Palaeolithic sites, providing a methodology to establish their ancient origin, assess their preservation status, and attempt their identification. The pivotal application of this multidisciplinar approach demonstrates that the macrolithic tools, from which starches were dislodged, were used for food-processing across the Pontic Steppe around 40,000 years ago during the earliest colonization of Eurasia by Homo sapiens.
Circadian rhythm and circulating cell-free DNA release on healthy subjects
Authors: Poulet Geoffroy , Hulot Jean-Sébastien , Blanchard Anne , Bergerot Damien , Xiao Wenjin , Ginot Frederic , Boutonnet-Rodat Audrey , Justine Abdelli , Beinse Guillaume , Geromel Vanna , Pellegrina Laurence , Azizi Michel , Laurent-Puig Pierre , Benhaim Leonor , Taly Valerie
Published: December 2023

In the last decade, clinical studies have investigated the clinical relevance of circulating cell-free-DNA (ccfDNA) as a diagnostic and prognosis tool in various diseases including cancers. However, limited knowledge on ccfDNA biology restrains its full development in the clinical practice. To improve our understanding, we evaluated the impact of the circadian rhythm on ccfDNA release in healthy subjects over a 24-h period. 10 healthy female subjects underwent blood sampling at 8am and 20 healthy male subjects underwent serial blood sampling (8:00 AM, 9:00 AM, 12:00 PM, 4:00 PM, 8:00 PM, 12:00 AM, 4 AM (+ 1 Day) and 8 AM (+ 1 Day)). We performed digital droplet-based PCR (ddPCR) assays to target 2 DNA fragments (69 & 243 bp) located in the KRAS gene to determine the ccfDNA concentration and fragmentation profile. As control, half of the samples were re-analyzed by capillary miniaturized electrophoresis (BIAbooster system). Overall, we did not detect any influence of the circadian rhythm on ccfDNA release. Instead, we observed a decrease in the ccfDNA concentration after meal ingestion, suggesting either a post-prandial effect or a technical detection bias due to a higher plasma load in lipids and triglycerides. We also noticed a potential effect of gender, weight and creatinine levels on ccfDNA concentration.
Prognostic factors of resected pathological stage I lung adenocarcinoma: evaluating subtypes and PD-L1/CD155 expression
Authors: Nishizawa Natsumasa , Shimajiri Shohei , Oyama Rintaro , Manabe Takehiko , Nemoto Yukiko , Matsumiya Hiroki , Honda Yohei , Taira Akihiro , Takenaka Masaru , Kuroda Koji , Tanaka Fumihiro
Published: December 2023

We aimed to compare the prognostic impacts of adenocarcinoma subtypes, programmed death-ligand I (PD-L1), and CD155 expression on patients with resected pathological stage (p-stage) I lung adenocarcinoma. In total, 353 patients with completely resected p-stage I lung adenocarcinomas were retrospectively reviewed. The expression levels of PD-L1 and CD155 in tumour cells from each adenocarcinoma subtype were evaluated using several clinicopathological and histological features, such as the presence of a micropapillary pattern. A total of 52 patients (14.7%) had PD-L1-positive tumours, whereas 128 patients (36.3%) had CD155-positive tumours, with a tumour proportion score of 5% for both PD-L1 and CD155 expression. Compared with patients with other adenocarcinoma subtypes, those with solid-predominant adenocarcinomas were significantly more positive for PD-L1 and CD155. Multivariate analysis showed that PD-L1 expression status was significantly associated with progression-free survival and overall survival, whereas CD155 expression and the presence of a micropapillary pattern were not significantly associated with either parameter. Patients with PD-L1-positive tumours had poorer prognoses than those with CD155-positive tumours. Moreover, PD-L1 and CD155 were significantly expressed in solid-predominant adenocarcinomas. The results of this study suggest that immune checkpoint inhibitors can be used as adjuvants in the treatment of patients with p-stage I adenocarcinoma.
Identification of CT-based non-invasive radiomic biomarkers for overall survival prediction in oral cavity squamous cell carcinoma
Authors: Ling Xiao , Alexander Gregory S. , Molitoris Jason , Choi Jinhyuk , Schumaker Lisa , Mehra Ranee , Gaykalova Daria A. , Ren Lei
Published: December 2023

This study addresses the limited non-invasive tools for Oral Cavity Squamous Cell Carcinoma (OSCC) survival prediction by identifying Computed Tomography (CT)-based biomarkers to improve prognosis prediction. A retrospective analysis was conducted on data from 149 OSCC patients, including CT radiomics and clinical information. An ensemble approach involving correlation analysis, score screening, and the Sparse-L1 algorithm was used to select functional features, which were then used to build Cox Proportional Hazards models (CPH). Our CPH achieved a 0.70 concordance index in testing. The model identified two CT-based radiomics features, Gradient-Neighboring-Gray-Tone-Difference-Matrix-Strength (GNS) and normalized-Wavelet-LLL-Gray-Level-Dependence-Matrix-Large-Dependence-High-Gray-Level-Emphasis (HLE), as well as stage and alcohol usage, as survival biomarkers. The GNS group with values above 14 showed a hazard ratio of 0.12 and a 3-year survival rate of about 90%. Conversely, the GNS group with values less than or equal to 14 had a 49% survival rate. For normalized HLE, the high-end group (HLE > − 0.415) had a hazard ratio of 2.41, resulting in a 3-year survival rate of 70%, while the low-end group (HLE ≤ − 0.415) had a 36% survival rate. These findings contribute to our knowledge of how radiomics can be used to predict the outcome so that treatment plans can be tailored for patients people with OSCC to improve their survival.
Testing a vaccine candidate against Hepatitis C virus designed by combinatorial optimization
Authors: Malaina Iker , Martinez Luis , Salcines-Cuevas David , Teran-Navarro Hector , Ocejo-Vinyals J. Gonzalo , Gonzalez-Lopez Elena , Soriano Vicente , Ubeda María , Perez Pinilla Martin-Blas , Martinez de la Fuente Ildefonso , Alvarez-Dominguez Carmen
Published: December 2023

This paper presents a new procedure for vaccine design against highly variable viruses such as Hepatitis C. The procedure uses an optimization algorithm to design vaccines that maximize the coverage of epitopes across different virus variants. Weighted epitopes based on the success ratio of immunological assays are used to prioritize the selection of epitopes for vaccine design. The procedure was successfully applied to design DC vaccines loaded with two HCV peptides, STG and DYP, which were shown to be safe, immunogenic, and able to induce significant levels of anti-viral cytokines, peptide-specific cellular immune responses and IgG antibodies. The procedure could potentially be applied to other highly variable viruses that currently lack effective vaccines.
Facile method for 3D printing conformally onto uneven surfaces and its application to face masks
Authors: Ji Zehao , Brion Douglas A. J. , Samson Kerr D. G. , Pattinson Sebastian W.
Published: December 2023

Conventional additive manufacturing processes, where parts are built through layer-wise deposition of material on a horizontal plane, can be limiting when a part must be printed or fit onto uneven surfaces. Such situations will arise with increasing frequency as additive manufacturing application areas such as construction and medical devices continue to grow. In this work, we develop a simple and practical approach to generate toolpaths to print 3D structures onto uneven surfaces conformally. The algorithm uses only conventional planar toolpaths of both the structure to be printed and the substrate to be printed on and converts these to non-planar toolpaths, allowing easy integration with existing additive manufacturing workflows. The technique is demonstrated by printing flexible seals onto bespoke rigid face mask frames conformally via a conventional single-material 3D printer using the generated conformal toolpath. A notable improvement in air seal performance was observed for customized face masks with conformal soft seals compared to conventionally 3D-printed fully rigid face masks. This also shows the potential of the developed toolpath generation method to aid in the prototyping and fabrication of conformal medical and other devices.