bluuebunny/crossref_metadata_2025 huggingface dataset:
First Daytime Red‐Line Emission Measurements of the Stable Auroral Red (SAR) Arcs
Authors: Upadhyay Kshitiz , Pallamraju Duggirala
Published: January 2024

We present the first ground‐based measurements of daytime stable auroral red (SAR) arc using OI 630.0 nm emissions. SAR arc is a direct consequence of heat conduction from the inner‐magnetosphere to the ionospheric regions characterized by increased electron temperatures and low electron density in the region of mid‐latitude trough. So far, SAR arc emissions have only been reported for nighttime conditions. For the present study, daytime optical measurements were enabled using a high‐resolution imaging echelle spectrograph from Boston (42.36°N, 71.05°W, MLAT ≈ 53°). Simultaneous Millstone Hill Incoherent Scatter Radar and Defense Meteorological Satellite Program measurements of electron density and temperature confirm our findings. Forward modeling approach enabled estimation of daytime electron temperatures in 200–650 km altitude during this SAR arc event to be varying between 3,500 and 4,400 K. These observations open numerous possibilities of optical investigations of magnetospheric‐ionospheric interactions during daytime, when the upper atmosphere is dynamic with large gradients in ionospheric conductivities, temperatures, and winds.
Mechanisms of Added Value of a Coupled Global Ocean‐Regional Atmosphere Climate Model Over Central Equatorial Africa
Authors: Tamoffo Alain T. , Weber Torsten , Cabos William , Sein Dmitry V. , Dosio Alessandro , Rechid Diana , Remedio Armelle R. , Jacob Daniela
Published: January 2024

There is an urgent need to enhance climate projections for Central Equatorial Africa (CEA), given the region's high vulnerability to climatic hazards and its economy's heavy dependence on climate‐sensitive sectors. This study aims to evaluate the performance of the regional earth system model ROM, composed of the atmosphere‐only regional climate model (RCM) REMO coupled with the global Max Planck Institute for Meteorology Ocean Model (MPIOM), in reproducing the precipitation climatology over CEA. ROM results are compared to those of REMO in two sets of experiments, one driven by the ERA‐Interim reanalysis and the other by the MPI‐ESM‐LR earth system model (ESM), both at ∼25‐km horizontal resolution. Results show that ocean coupling improves rainfall climatology thanks to a better representation of the physical processes and mechanisms underlying the rainfall system. In particular, an improved sea surface temperature (SST) results in a more realistic simulation of land‐atmosphere‐ocean interactions, and subsequently the atmospheric baroclinicity. Specifically, the coupling reduces the positive SST bias inherited by the driving ESM across the entire Guinea Gulf and Benguela‐Angola coastal seas. This leads to better simulated land‐ocean thermal and pressure contrasts. Improvements in land‐ocean contrasts, in turn, enhance the representation of the regional atmospheric circulation, and thus precipitation. Interestingly, the coupling is more beneficial when ROM is driven by the ESM than the reanalysis. This study emphasizes the advantage of dynamically downscaling ESMs using regional earth system models rather than atmosphere‐only RCMs, with the potential to enhance confidence in future climate projections.
Biomarker Reconstruction of a High‐Latitude Late Paleocene to Early Eocene Coal Swamp Environment Across the PETM and ETM‐2 (Ellesmere Island, Arctic Canada)
Authors: Blumenberg Martin , Naafs B. David A. , Lückge Andreas , Lauretano Vittoria , Schefuß Enno , Galloway Jennifer M. , Scheeder Georg , Reinhardt Lutz
Published: January 2024

The Paleocene‐Eocene Thermal Maximum (PETM) and early Eocene hyperthermal events were characterized by a Hothouse climate state. Our understanding of the climatic impact of these hyperthermals is currently biased toward marine settings and the mid‐latitudes. Here we present organic geochemical data from Stenkul Fiord, Ellesmere Island, Arctic Canada. This organic rich formation was deposited in a high northern latitude wetland setting during the late Paleocene to early Eocene, spanning the PETM and subsequent ETM‐2 hyperthermals. Biomarker data (e.g., diterpenoids), combined with published palynological data from the site, indicate Cupressaceae‐dominated vegetation. Biomarkers suggest that land plant composition remained fairly unchanged across the two hyperthermal events. Increases in abundance and 13C‐depletion of hopanoid biomarkers (minima <−50‰ (VPDB)) highlight periods of enhanced bacterial methane consumption, particularly during the PETM. However, periods of low hopanoid δ13C values were also found outside the hyperthermal intervals. Relatively low δ2H values of higher plant n‐alkanes (average δ2H values of n‐C25, n‐C27, n‐C29 ∼ −230 to −270‰ (SMOW)) indicate that deposition formed during times with enhanced precipitation. The wettest intervals, as identified by the lowest δ2H n‐alkane values, contain high abundances of hopenes, indicating enhanced bacterial turnover. At Stenkul Fiord, high temperatures and CO2 concentrations likely fostered the growth of widespread wetland forests that became a CO2 sink and may have played an important role in carbon drawdown during the Early Paleogene.
Surface-emitting lasers meet metasurfaces
Authors: Shitrit Nir
Published: January 2024

The integration between vertical-cavity surface-emitting lasers and metasurfaces has been demonstrated to enable on-chip high-angle illumination for total internal reflection and dark-field microscopy. Such an ultracompact combined laser–beam shaper system provides a versatile illumination module for high-contrast imaging, thus leveraging biophotonics and lab-on-a-chip devices and facilitating life-science applications.
Hyperreflective photonic crystals created by shearing colloidal dispersions at ultrahigh volume fraction
Authors: Kim Minji , Kim Jong Bin , Kim Shin-Hyun
Published: January 2024

Colloidal crystallization serves as one of the most economic and scalable production methods for photonic crystals. However, insufficient optical performance, nonuniformity and low reproducibility remain challenges for advanced high-value applications. In this study, we optimally formulate a photocurable dispersion of silica particles and apply shear flow to unify the orientation of the colloidal crystals, ensuring high optical performance and uniformity. The silica particles experience strong repulsion at ultrahigh volume fractions of 50% but demonstrate low mobility, leading to polycrystalline structures. Applying shear flow to the dispersions allows the silica particles to rearrange into larger crystalline domains with a unidirectional orientation along the flow. This shear-induced structural change produces absolute reflectivity at the stopband as high as 90% and a high transparency of 90% at off-resonant wavelengths with minimal diffusive scattering. Furthermore, the strong interparticle repulsion ensures a uniform volume fraction of particles throughout the dispersion, reducing deviations in the optical properties. We intricately micropattern the photocurable dispersions using photolithography. Additionally, the photonic films and patterns can be stacked to form multiple layers, displaying mixed structural colors and multiple reflectance peaks without sacrificing reflectivity. These superior photonic materials hold promise for various optical applications, including optical components and anticounterfeiting patches.
Blood epigenome-wide association studies of suicide attempt in adults with bipolar disorder
Authors: Mirza Salahudeen , Lima Camila N. C. , Del Favero-Campbell Alexandra , Rubinstein Alexandre , Topolski Natasha , Cabrera-Mendoza Brenda , Kovács Emese H. C. , Blumberg Hilary P. , Richards Jenny Gringer , Williams Aislinn J. , Wemmie John A. , Magnotta Vincent A. , Fiedorowicz Jess G. , Gaine Marie E. , Walss-Bass Consuelo , Quevedo Joao , Soares Jair C. , Fries Gabriel R.
Published: January 2024

Suicide attempt (SA) risk is elevated in individuals with bipolar disorder (BD), and DNA methylation patterns may serve as possible biomarkers of SA. We conducted epigenome-wide association studies (EWAS) of blood DNA methylation associated with BD and SA. DNA methylation was measured at >700,000 positions in a discovery cohort ofn = 84 adults with BD with a history of SA (BD/SA),n = 79 adults with BD without history of SA (BD/non-SA), andn = 76 non-psychiatric controls (CON). EWAS revealed six differentially methylated positions (DMPs) and seven differentially methylated regions (DMRs) between BD/SA and BD/non-SA, with multiple immune-related genes implicated. There were no epigenome-wide significant differences when BD/SA and BD/non-SA were each compared to CON, and patterns suggested that epigenetics differentiating BD/SA from BD/non-SA do not differentiate BD/non-SA from CON. Weighted gene co-methylation network analysis and trait enrichment analysis of the BD/SA vs. BD/non-SA contrast further corroborated immune system involvement, while gene ontology analysis implicated calcium signalling. In an independent replication cohort ofn = 48 BD/SA andn = 47 BD/non-SA, fold changes at the discovery cohort’s significant sites showed moderate correlation across cohorts and agreement on direction. In both cohorts, classification accuracy for SA history among individuals with BD was highest when methylation at the significant CpG sites as well as information from clinical interviews were combined, with an AUC of 88.8% (CI = 83.8–93.8%) and 82.1% (CI = 73.6–90.5%) for the combined epigenetic-clinical classifier in the discovery and replication cohorts, respectively. Our results provide novel insight to the role of immune system functioning in SA and BD and also suggest that integrating information from multiple levels of analysis holds promise to improve risk assessment for SA in adults with BD.
Targeting FBXO22 enhances radiosensitivity in non-small cell lung cancer by inhibiting the FOXM1/Rad51 axis
Authors: Chen Yunshang , Zhou Yun , Feng Xue , Wu Zilong , Yang Yongqiang , Rao Xinrui , Zhou Rui , Meng Rui , Dong Xiaorong , Xu Shuangbing , Zhang Sheng , Wu Gang , Jie Xiaohua
Published: January 2024

Radioresistance is a major constraint on the efficacy of lung cancer radiotherapy, but its mechanism has not been fully elucidated. Here, we found that FBXO22 was aberrantly highly expressed in lung cancer and that FBXO22 knockdown increased the radiosensitivity of lung cancer cells. Mechanistically, FBXO22 promoted Rad51 gene transcription by increasing the level of FOXM1 at the Rad51 promoter, thereby inducing the formation of lung cancer radioresistance. Furthermore, we found that deguelin, a potential inhibitor of FBXO22, enhanced radiosensitivity in an FBXO22/Rad51-dependent manner and was safely tolerated in vivo. Collectively, our results illustrate that FBXO22 induces lung cancer radioresistance by activating the FOXM1/Rad51 axis and provide preclinical evidence for the clinical translation of this critical target.
DENND6A links Arl8b to a Rab34/RILP/dynein complex, regulating lysosomal positioning and autophagy
Authors: Kumar Rahul , Khan Maleeha , Francis Vincent , Aguila Adriana , Kulasekaran Gopinath , Banks Emily , McPherson Peter S.
Published: January 2024

Lysosomes help maintain cellular proteostasis, and defects in lysosomal positioning and function can cause disease, including neurodegenerative disorders. The spatiotemporal distribution of lysosomes is regulated by small GTPases including Rabs, which are activated by guanine nucleotide exchange factors (GEFs). DENN domain proteins are the largest family of Rab GEFs. Using a cell-based assay, we screened DENND6A, a member of the DENN domain protein family against all known Rabs and identified it as a potential GEF for 20 Rabs, including Rab34. Here, we demonstrate that DENND6A activates Rab34, which recruits a RILP/dynein complex to lysosomes, promoting lysosome retrograde transport. Further, we identify DENND6A as an effector of Arl8b, a major regulatory GTPase on lysosomes. We demonstrate that Arl8b recruits DENND6A to peripheral lysosomes to activate Rab34 and initiate retrograde transport, regulating nutrient-dependent lysosomal juxtanuclear repositioning. Loss of DENND6A impairs autophagic flux. Our findings support a model whereby Arl8b/DENND6A/Rab34-dependent lysosomal retrograde trafficking controls autophagy.
Skillful multiyear prediction of marine habitat shifts jointly constrained by ocean temperature and dissolved oxygen
Authors: Chen Zhuomin , Siedlecki Samantha , Long Matthew , Petrik Colleen M. , Stock Charles A. , Deutsch Curtis A.
Published: January 2024

The ability to anticipate marine habitat shifts responding to climate variability has high scientific and socioeconomic value. Here we quantify interannual-to-decadal predictability of habitat shifts by combining trait-based aerobic habitat constraints with a suite of initialized retrospective Earth System Model forecasts, for diverse marine ecotypes in the North American Large Marine Ecosystems. We find that aerobic habitat viability, defined by joint constraints of temperature and oxygen on organismal energy balance, is potentially predictable in the upper-600 m ocean, showing a substantial improvement over a simple persistence forecast. The skillful multiyear predictability is dominated by the oxygen component in most ecosystems, yielding higher predictability than previously estimated based on temperature alone. Notable predictability differences exist among ecotypes differing in temperature sensitivity of hypoxia vulnerability, especially along the northeast coast with predictability timescale ranging from 2 to 10 years. This tool will be critical in predicting marine habitat shifts in face of a changing climate.
Searching for ultralight dark matter conversion in solar corona using Low Frequency Array data
Authors: An Haipeng , Chen Xingyao , Ge Shuailiang , Liu Jia , Luo Yan
Published: January 2024

Ultralight dark photons and axions are well-motivated hypothetical dark matter candidates. Both dark photon dark matter and axion dark matter can resonantly convert into electromagnetic waves in the solar corona when their mass is equal to the solar plasma frequency. The resultant electromagnetic waves appear as monochromatic signals within the radio-frequency range with an energy equal to the dark matter mass, which can be detected via radio telescopes for solar observations. Here we show our search for converted monochromatic signals in the observational data collected by the high-sensitivity Low Frequency Array (LOFAR) telescope and establish an upper limit on the kinetic mixing coupling between dark photon dark matter and photon, which can reach values as low as 10−13within the frequency range of 30 − 80 MHz. This limit represents an improvement of approximately one order of magnitude better than the existing constraint from the cosmic microwave background observation. Additionally, we derive an upper limit on the axion-photon coupling within the same frequency range, which is better than the constraints from Light-Shining-through-a-Wall experiments while not exceeding the CERN Axion Solar Telescope (CAST) experiment or other astrophysical bounds.
Experimentally validated design principles of heteroatom-doped-graphene-supported calcium single-atom materials for non-dissociative chemisorption solid-state hydrogen storage
Authors: Gao Yong , Li Zhenglong , Wang Pan , Cui Wen-Gang , Wang Xiaowei , Yang Yaxiong , Gao Fan , Zhang Mingchang , Gan Jiantuo , Li Chenchen , Liu Yanxia , Wang Xinqiang , Qi Fulai , Zhang Jing , Han Xiao , Du Wubin , Chen Jian , Xia Zhenhai , Pan Hongge
Published: January 2024

Non-dissociative chemisorption solid-state storage of hydrogen molecules in host materials is promising to achieve both high hydrogen capacity and uptake rate, but there is the lack of non-dissociative hydrogen storage theories that can guide the rational design of the materials. Herein, we establish generalized design principle to design such materials via the first-principles calculations, theoretical analysis and focused experimental verifications of a series of heteroatom-doped-graphene-supported Ca single-atom carbon nanomaterials as efficient non-dissociative solid-state hydrogen storage materials. An intrinsic descriptor has been proposed to correlate the inherent properties of dopants with the hydrogen storage capability of the carbon-based host materials. The generalized design principle and the intrinsic descriptor have the predictive ability to screen out the best dual-doped-graphene-supported Ca single-atom hydrogen storage materials. The dual-doped materials have much higher hydrogen storage capability than the sole-doped ones, and exceed the current best carbon-based hydrogen storage materials.
Impact of palladium/palladium hydride conversion on electrochemical CO2 reduction via in-situ transmission electron microscopy and diffraction
Authors: Abdellah Ahmed M. , Ismail Fatma , Siig Oliver W. , Yang Jie , Andrei Carmen M. , DiCecco Liza-Anastasia , Rakhsha Amirhossein , Salem Kholoud E. , Grandfield Kathryn , Bassim Nabil , Black Robert , Kastlunger Georg , Soleymani Leyla , Higgins Drew
Published: January 2024

Electrochemical conversion of CO2 offers a sustainable route for producing fuels and chemicals. Pd-based catalysts are effective for converting CO2 into formate at low overpotentials and CO/H2 at high overpotentials, while undergoing poorly understood morphology and phase structure transformations under reaction conditions that impact performance. Herein, in-situ liquid-phase transmission electron microscopy and select area diffraction measurements are applied to track the morphology and Pd/PdHx phase interconversion under reaction conditions as a function of electrode potential. These studies identify the degradation mechanisms, including poisoning and physical structure changes, occurring in PdHx/Pd electrodes. Constant potential density functional theory calculations are used to probe the reaction mechanisms occurring on the PdHx structures observed under reaction conditions. Microkinetic modeling reveals that the intercalation of *H into Pd is essential for formate production. However, the change in electrochemical CO2 conversion selectivity away from formate and towards CO/H2 at increasing overpotentials is due to electrode potential dependent changes in the reaction energetics and not a consequence of morphology or phase structure changes.
Effect of aging on the human myometrium at single-cell resolution
Authors: Punzon-Jimenez Paula , Machado-Lopez Alba , Perez-Moraga Raul , Llera-Oyola Jaime , Grases Daniela , Galvez-Viedma Marta , Sibai Mustafa , Satorres-Perez Elena , Lopez-Agullo Susana , Badenes Rafael , Ferrer-Gomez Carolina , Porta-Pardo Eduard , Roson Beatriz , Simon Carlos , Mas Aymara
Published: January 2024

Age-associated myometrial dysfunction can prompt complications during pregnancy and labor, which is one of the factors contributing to the 7.8-fold increase in maternal mortality in women over 40. Using single-cell/single-nucleus RNA sequencing and spatial transcriptomics, we have constructed a cellular atlas of the aging myometrium from 186,120 cells across twenty perimenopausal and postmenopausal women. We identify 23 myometrial cell subpopulations, including contractile and venous capillary cells as well as immune-modulated fibroblasts. Myometrial aging leads to fewer contractile capillary cells, a reduced level of ion channel expression in smooth muscle cells, and impaired gene expression in endothelial, smooth muscle, fibroblast, perivascular, and immune cells. We observe altered myometrial cell-to-cell communication as an aging hallmark, which associated with the loss of 25 signaling pathways, including those related to angiogenesis, tissue repair, contractility, immunity, and nervous system regulation. These insights may contribute to a better understanding of the complications faced by older individuals during pregnancy and labor.
Fluorogenic CRISPR for genomic DNA imaging
Authors: Zhang Zhongxuan , Rong Xiaoxiao , Xie Tianjin , Li Zehao , Song Haozhi , Zhen Shujun , Wang Haifeng , Wu Jiahui , Jaffrey Samie R. , Li Xing
Published: January 2024

Genomic DNA exhibits high heterogeneity in terms of its dynamic within the nucleus, its structure and functional roles. CRISPR-based imaging approaches can image genomic loci in living cells. However, conventional CRISPR-based tools involve expressing constitutively fluorescent proteins, resulting in high background and nonspecific nucleolar signal. Here, we construct fluorogenic CRISPR (fCRISPR) to overcome these issues. fCRISPR is designed with dCas9, an engineered sgRNA, and a fluorogenic protein. Fluorogenic proteins are degraded unless they are bound to specific RNA hairpins. These hairpins are inserted into sgRNA, resulting in dCas9: sgRNA: fluorogenic protein ternary complexes that enable fluorogenic DNA imaging. With fCRISPR, we image various genomic DNA in different human cells with high signal-to-noise ratio and sensitivity. Furthermore, fCRISPR tracks chromosomes dynamics and length. fCRISPR also allows DNA double-strand breaks (DSBs) and repair to be tracked in real time. Taken together, fCRISPR offers a high-contrast and sensitive platform for imaging genomic loci.
Single nuclei transcriptomics in human and non-human primate striatum in opioid use disorder
Authors: Phan BaDoi N. , Ray Madelyn H. , Xue Xiangning , Fu Chen , Fenster Robert J. , Kohut Stephen J. , Bergman Jack , Haber Suzanne N. , McCullough Kenneth M. , Fish Madeline K. , Glausier Jill R. , Su Qiao , Tipton Allison E. , Lewis David A. , Freyberg Zachary , Tseng George C. , Russek Shelley J. , Alekseyev Yuriy , Ressler Kerry J. , Seney Marianne L. , Pfenning Andreas R. , Logan Ryan W.
Published: January 2024

In brain, the striatum is a heterogenous region involved in reward and goal-directed behaviors. Striatal dysfunction is linked to psychiatric disorders, including opioid use disorder (OUD). Striatal subregions are divided based on neuroanatomy, each with unique roles in OUD. In OUD, the dorsal striatum is involved in altered reward processing, formation of habits, and development of negative affect during withdrawal. Using single nuclei RNA-sequencing, we identified both canonical (e.g., dopamine receptor subtype) and less abundant cell populations (e.g., interneurons) in human dorsal striatum. Pathways related to neurodegeneration, interferon response, and DNA damage were significantly enriched in striatal neurons of individuals with OUD. DNA damage markers were also elevated in striatal neurons of opioid-exposed rhesus macaques. Sex-specific molecular differences in glial cell subtypes associated with chronic stress were found in OUD, particularly female individuals. Together, we describe different cell types in human dorsal striatum and identify cell type-specific alterations in OUD.
BCL7A and BCL7B potentiate SWI/SNF-complex-mediated chromatin accessibility to regulate gene expression and vegetative phase transition in plants
Authors: Lei Yawen , Yu Yaoguang , Fu Wei , Zhu Tao , Wu Caihong , Zhang Zhihao , Yu Zewang , Song Xin , Xu Jianqu , Liang Zhenwei , Lü Peitao , Li Chenlong
Published: January 2024

Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes are multi-subunit machineries that establish and maintain chromatin accessibility and gene expression by regulating chromatin structure. However, how the remodeling activities of SWI/SNF complexes are regulated in eukaryotes remains elusive. B-cell lymphoma/leukemia protein 7 A/B/C (BCL7A/B/C) have been reported as subunits of SWI/SNF complexes for decades in animals and recently in plants; however, the role of BCL7 subunits in SWI/SNF function remains undefined. Here, we identify a unique role for plant BCL7A and BCL7B homologous subunits in potentiating the genome-wide chromatin remodeling activities of SWI/SNF complexes in plants. BCL7A/B require the catalytic ATPase BRAHMA (BRM) to assemble with the signature subunits of the BRM-Associated SWI/SNF complexes (BAS) and for genomic binding at a subset of target genes. Loss of BCL7A and BCL7B diminishes BAS-mediated genome-wide chromatin accessibility without changing the stability and genomic targeting of the BAS complex, highlighting the specialized role of BCL7A/B in regulating remodeling activity. We further show that BCL7A/B fine-tune the remodeling activity of BAS complexes to generate accessible chromatin at the juvenility resetting region (JRR) of the microRNAs MIR156A/C for plant juvenile identity maintenance. In summary, our work uncovers the function of previously elusive SWI/SNF subunits in multicellular eukaryotes and provides insights into the mechanisms whereby plants memorize the juvenile identity through SWI/SNF-mediated control of chromatin accessibility.
A 5 × 200 Gbps microring modulator silicon chip empowered by two-segment Z-shape junctions
Authors: Yuan Yuan , Peng Yiwei , Sorin Wayne V. , Cheung Stanley , Huang Zhihong , Liang Di , Fiorentino Marco , Beausoleil Raymond G.
Published: January 2024

Optical interconnects have been recognized as the most promising solution to accelerate data transmission in the artificial intelligence era. Benefiting from their cost-effectiveness, compact dimensions, and wavelength multiplexing capability, silicon microring resonator modulators emerge as a compelling and scalable means for optical modulation. However, the inherent trade-off between bandwidth and modulation efficiency hinders the device performance. Here we demonstrate a dense wavelength division multiplexing microring modulator array on a silicon chip with a full data rate of 1 Tb/s. By harnessing the two individual p-n junctions with an optimized Z-shape doping profile, the inherent trade-off of silicon depletion-mode modulators is greatly mitigated, allowing for higher-speed modulation with energy consumption of sub-ten fJ/bit. This state-of-the-art demonstration shows that all-silicon modulators can practically enable future 200 Gb/s/lane optical interconnects.
Correlated order at the tipping point in the kagome metal CsV3Sb5
Authors: Guo Chunyu , Wagner Glenn , Putzke Carsten , Chen Dong , Wang Kaize , Zhang Ling , Gutierrez-Amigo Martin , Errea Ion , Vergniory Maia G. , Felser Claudia , Fischer Mark H. , Neupert Titus , Moll Philip J. W.
Published: January 2024

Spontaneously broken symmetries are at the heart of many phenomena of quantum matter and physics more generally. However, determining the exact symmetries that are broken can be challenging due to imperfections such as strain, in particular when multiple electronic orders are competing. This is exemplified by charge order in some kagome systems, where evidence of nematicity and flux order from orbital currents remains inconclusive due to contradictory measurements. Here we clarify this controversy by fabricating highly symmetric samples of a member of this family, CsV3Sb5, and measuring their transport properties. We find that a measurable anisotropy is absent at any temperature in the unperturbed material. However, a pronounced in-plane transport anisotropy appears when either weak magnetic fields or strains are present. A symmetry analysis indicates that a perpendicular magnetic field can indeed lead to in-plane anisotropy by inducing a flux order coexisting with more conventional bond order. Our results provide a unifying picture for the controversial charge order in kagome metals and highlight the need for materials control at the microscopic scale in the identification of broken symmetries.
The Swedish National Facility for Magnetoencephalography Parkinson’s disease dataset
Authors: Vinding Mikkel C. , Eriksson Allison , Comarovschii Igori , Waldthaler Josefine , Manting Cassia Low , Oostenveld Robert , Ingvar Martin , Svenningsson Per , Lundqvist Daniel
Published: January 2024

Parkinson’s disease (PD) is characterised by a loss of dopamine and dopaminergic cells. The consequences hereof are widespread network disturbances in brain function. It is an ongoing topic of investigation how the disease-related changes in brain function manifest in PD relate to clinical symptoms. We present The Swedish National Facility for Magnetoencephalography Parkinson’s Disease Dataset (NatMEG-PD) as an Open Science contribution to identify the functional neural signatures of Parkinson’s disease and contribute to diagnosis and treatment. The dataset contains whole-head magnetoencephalographic (MEG) recordings from 66 well-characterised PD patients on their regular dose of dopamine replacement therapy and 68 age- and sex-matched healthy controls. NatMEG-PD contains three-minute eyes-closed resting-state MEG, MEG during an active movement task, and MEG during passive movements. The data includes anonymised MRI for source analysis and clinical scores. MEG data is rich in nature and can be used to explore numerous functional features. By sharing these data, we hope other researchers will contribute to advancing our understanding of the relationship between brain activity and disease state or symptoms.
Molecular insights into the dynamic modulation of bacterial ClpP function and oligomerization by peptidomimetic boronate compounds
Authors: Alves França Bruno , Falke Sven , Rohde Holger , Betzel Christian
Published: January 2024

Bacterial caseinolytic protease P subunit (ClpP) is important and vital for cell survival and infectivity. Recent publications describe and discuss the complex structure–function relationship of ClpP and its processive activity mediated by 14 catalytic sites. Even so, there are several aspects yet to be further elucidated, such as the paradoxical allosteric modulation of ClpP by peptidomimetic boronates. These compounds bind to all catalytic sites, and in specific conditions, they stimulate a dysregulated degradation of peptides and globular proteins, instead of inhibiting the enzymatic activity, as expected for serine proteases in general. Aiming to explore and explain this paradoxical effect, we solved and refined the crystal structure of native ClpP from Staphylococcus epidermidis (Se), an opportunistic pathogen involved in nosocomial infections, as well as ClpP in complex with ixazomib at 1.90 Å and 2.33 Å resolution, respectively. The interpretation of the crystal structures, in combination with complementary biochemical and biophysical data, shed light on how ixazomib affects the ClpP conformational state and activity. Moreover, SEC-SAXS and DLS measurements show, for the first time, that a peptidomimetic boronate compound also induces the assembly of the tetradecameric structure from isolated homomeric heptameric rings of a gram-positive organism.
Mismatch between subjective and objective dysautonomia
Authors: Novak Peter , Systrom David M. , Marciano Sadie P. , Knief Alexandra , Felsenstein Donna , Giannetti Matthew P. , Hamilton Matthew J. , Nicoloro-SantaBarbara Jennifer , Saco Tara V. , Castells Mariana , Farhad Khosro , Pilgrim David M. , Mullally William J.
Published: January 2024

Autonomic symptom questionnaires are frequently used to assess dysautonomia. It is unknown whether subjective dysautonomia obtained from autonomic questionnaires correlates with objective dysautonomia measured by quantitative autonomic testing. The objective of our study was to determine correlations between subjective and objective measures of dysautonomia. This was a retrospective cross-sectional study conducted at Brigham and Women’s Faulkner Hospital Autonomic Laboratory between 2017 and 2023 evaluating the patients who completed autonomic testing. Analyses included validated autonomic questionnaires [Survey of Autonomic Symptoms (SAS), Composite Autonomic Symptom Score 31 (Compass-31)] and standardized autonomic tests (Valsalva maneuver, deep breathing, sudomotor, and tilt test). The autonomic testing results were graded by a Quantitative scale for grading of cardiovascular reflexes, sudomotor tests and skin biopsies (QASAT), and Composite Autonomic Severity Score (CASS). Autonomic testing, QASAT, CASS, and SAS were obtained in 2627 patients, and Compass-31 in 564 patients. The correlation was strong between subjective instruments (SAS vs. Compass-31, r = 0.74, p < 0.001) and between objective instruments (QASAT vs. CASS, r = 0.81, p < 0.001). There were no correlations between SAS and QASAT nor between Compass-31 and CASS. There continued to be no correlations between subjective and objective instruments for selected diagnoses (post-acute sequelae of COVID-19, n = 61; postural tachycardia syndrome, 211; peripheral autonomic neuropathy, 463; myalgic encephalomyelitis/chronic fatigue syndrome, 95; preload failure, 120; post-treatment Lyme disease syndrome, 163; hypermobile Ehlers-Danlos syndrome, 213; neurogenic orthostatic hypotension, 86; diabetes type II, 71, mast cell activation syndrome, 172; hereditary alpha tryptasemia, 45). The lack of correlation between subjective and objective instruments highlights the limitations of the commonly used questionnaires with some patients overestimating and some underestimating true autonomic deficit. The diagnosis-independent subjective–objective mismatch further signifies the unmet need for reliable screening surveys. Patients who overestimate the symptom burden may represent a population with idiosyncratic autonomic-like symptomatology, which needs further study. At this time, the use of autonomic questionnaires as a replacement of autonomic testing cannot be recommended.
Structural, dielectric, and antimicrobial evaluation of PMMA/CeO2 for optoelectronic devices
Authors: Bakr Ahmed M. , Darwish Abdelfattah , Azab A. A. , El Awady Mohamed E. , Hamed Ahmed A. , Elzwawy Amir
Published: January 2024

In the current report, we have successfully synthesized nanocomposites of PMMA incorporating different doping of CeO2 through a chemical approach. XRD results reflects decent matching for CeO2 nanoparticles with 29 nm crystallite size. FTIR spectroscopy demonstrates the characteristic functional groups validating the successful formation of the composite. The optical study of PMMA and the nanocomposites has proven that the optical properties such as band gap, refractive index, optical permittivity, and loss tangent factor are affected by adding CeO2 to the PMMA matrix.The peak residing around 420 nm by UV measurements is allocated to occurring electrons photoexcitation from the valence to conduction band inherent in CeO2. The dielectric measurements were achieved using broadband dielectric spectroscopy upon a wide span of frequencies (10–1–107 Hz) and within temperatures from − 10 to 80 °C with a step of 10 °C. The permittivity decreases by adding CeO2 and the dielectric parameters are thermally enhanced, however, the temperature influence is based on CeO2 content, the higher the CeO2 amount, the higher the influence of temperature. The results of the nanocomposites revealed antibacterial activity counter to gram-positive bacteria strain (S. aureus, and B. subtilis), and gram-negative bacteria (E. coli, and K. pneumoniae), yeast (C. albicans, as well as fungi (A. niger). Inherently, the change in CeO2 concentration from 0.01 to 0.1 wt% delivers maximum influence against gram-negative bacteria. These PMMA CeO2-doped composites are beneficial for optoelectronic areas and devices.
Methods for controlling heavy metals in environmental soils based on artificial neural networks
Authors: Luo Ninglin
Published: January 2024

The problem of heavy metal pollution in soil has become a global environmental problem, and it is very important to predict and manage the heavy metals in the environmental soil in a timely manner. The changes in heavy metal content in soil have characteristics such as nonlinearity and large delay, making it difficult to predict heavy metals in soil using traditional methods. Traditional prediction methods are complex and cumbersome, which can lead to longer treatment time and easy secondary pollution. This article analyzed the Back Propagation neural network (BPNN) in artificial neural networks (ANN) and applied it to the prediction of heavy metals in environmental soils. BPNN has good nonlinear function approximation ability, so it can be well applied to complex problems such as soil heavy metal prediction. The methods of treating soil heavy metals include physical repair method, chemical repair method, microbial repair method, plant repair method, plant microbial combined repair method and so on. The use of BPNN can predict heavy metals in environmental soils through adaptive dynamic learning. However, the training time of the BPNN is relatively long and the convergence speed is relatively slow. Therefore, additional momentum terms were added to adjust the weights and thresholds of the network to improve the BPNN. In the experiment, the prediction performance of the improved BPNN was compared before and after the improvement. This article took 50 monitoring data of heavy metals in the same soil in a certain region in 2021 as sample data and predicted the content of heavy metals in the soil using improved and improved BPNN. Due to time constraints, this article only conducted experimental analysis on heavy metals such as lead and cadmium. In the first experiment, when the soil sample data was 50, the prediction accuracy of the BPNN for cadmium before and after improvement was 75.95% and 89.56%, respectively. In the second experiment, when the soil sample data was 50, the prediction accuracy of the BPNN for cadmium before and after improvement was 77.99% and 89.85%, respectively. The improved BPNN has good prediction accuracy and can effectively predict the status of heavy metals in soil. The analysis in this article can provide scientific basis for the comprehensive prevention and control of heavy metals in regional soil, and also provide reference for the development of pollution-free agriculture and ensuring food safety.
Reference genes for Eucalyptus spp. under Beauveria bassiana inoculation and subsequently infestation by the galling wasp Leptocybe invasa
Authors: Daude Matheus Martins , Ságio Solange Aparecida , Rodrigues Jovielly Neves , Lima Nívea Maria Pereira , Lima André Almeida , Sarmento Maíra Ignacio , Sarmento Renato Almeida , Barreto Horllys Gomes
Published: January 2024

Relative gene expression analysis through RT-qPCR is an important molecular technique that helps understanding different molecular mechanisms, such as the plant defense response to insect pests. However, the use of RT-qPCR for gene expression analysis can be affected by factors that directly affect the reliability of the results. Among these factors, the appropriate choice of reference genes is crucial and can strongly impact RT-qPCR relative gene expression analyses, highlighting the importance in correctly choosing the most suitable genes for the success of the analysis. Thus, this study aimed to select and validate reference genes for relative gene expression studies through RT-qPCR in hybrids of Eucalyptus tereticornis × Eucalyptus camaldulensis (drought tolerant and susceptible to Leptocybe invasa) under conditions of inoculation by the Beauveria bassiana fungus and subsequent infestation by L. invasa. The expression level and stability of eleven candidate genes were evaluated. Stability was analyzed using the RefFinder tool, which integrates the geNorm, NormFinder, BestKeeper, and Delta-Ct algorithms. The selected reference genes were validated through the expression analysis of the transcriptional factor EcDREB2 (dehydration-responsive element-binding protein 2). For all treatments evaluated, EcPTB, EcPP2A-1, and EcEUC12 were the best reference genes. The triplets EcPTB/EcEUC12/EcUBP6, EcPP2A-1/EcEUC12/EcPTB, EcIDH/EcSAND/Ecα-TUB, EcPP2A-1/Ecα-TUB/EcPTB, and EcPP2A-1/EcUPL7/EcSAND were the best reference genes for the control plants, mother plants, plants inoculated with B. bassiana, plants infested with L. invasa, and plants inoculated with B. bassiana and subsequently infested with L. invasa, respectively. The best determined reference genes were used to normalize the RT-qPCR expression data for each experimental condition evaluated. The results emphasize the importance of this type of study to ensure the reliability of relative gene expression analyses. Furthermore, the findings of this study can be used as a basis for future research, comprising gene expression analysis of different eucalyptus metabolic pathways.
Influence of copper(I) nicotinate complex on the Notch1 signaling pathway in triple negative breast cancer cell lines
Authors: Abdel-Mohsen Mohamed A. , Badawy Asmaa M. , Abu-Youssef Morsy A. , Yehia Mona A. , Abou Shamaa Lobna D. , Mohamed Shymaa Abdullah
Published: January 2024

Triple negative breast cancer (TNBC) is a subtype of breast cancer which is characterized by its aggressiveness, poor and short overall survival. In this concept, there is a growing demand for metal-based compounds in TNBC therapy as copper complex that have a less toxic effect on normal cells and could stimulate apoptotic cell death. Additionally, Notch1 signaling pathway has received great attention as one of the most important potential targets for developing a novel therapeutic strategy. The present study is an attempt to assess the promising chemotherapeutic activities of copper(I) nicotinate (CNC) through its impact on the expression of downstream genes of Notch1 signaling pathway and the cell fate of TNBC. The co-treatment of TNBC cells with doxorubicin (Doxo) and CNC was also investigated. To approach the objective of the present study, TNBC cell lines; HCC1806 and MDAMB231, were utilized. MTT assay was used to determine the IC50 values of CNC and Doxo. After treatment, microtubule-associated protein light chain3 (LC3) were determined by flow cytometry. Additionally, qRT-PCR technique was used to detect the changes in genes levels that are involved Notch1 signaling pathway. Moreover, autophagosomes were monitored and imaged by Transmission electron microscopy. Treatment of TNBC cells with CNC modulated Notch1 signaling pathway in different manners with respect to the type of cells and the applied dose of CNC. The observed effects of CNC may reflect the possible anti-cancer activities of CNC in both types of TNBC. However, cell type and CNC dose should be considered.
Rat microbial biogeography and age-dependent lactic acid bacteria in healthy lungs
Authors: Zhao Lan , Cunningham Christine M. , Andruska Adam M. , Schimmel Katharina , Ali Md Khadem , Kim Dongeon , Gu Shenbiao , Chang Jason L. , Spiekerkoetter Edda , Nicolls Mark R.
Published: January 2024

The laboratory rat emerges as a useful tool for studying the interaction between the host and its microbiome. To advance principles relevant to the human microbiome, we systematically investigated and defined the multitissue microbial biogeography of healthy Fischer 344 rats across their lifespan. Microbial community profiling data were extracted and integrated with host transcriptomic data from the Sequencing Quality Control consortium. Unsupervised machine learning, correlation, taxonomic diversity and abundance analyses were performed to determine and characterize the rat microbial biogeography and identify four intertissue microbial heterogeneity patterns (P1–P4). We found that the 11 body habitats harbored a greater diversity of microbes than previously suspected. Lactic acid bacteria (LAB) abundance progressively declined in lungs from breastfed newborn to adolescence/adult, and was below detectable levels in elderly rats. Bioinformatics analyses indicate that the abundance of LAB may be modulated by the lung–immune axis. The presence and levels of LAB in lungs were further evaluated by PCR in two validation datasets. The lung, testes, thymus, kidney, adrenal and muscle niches were found to have age-dependent alterations in microbial abundance. The 357 microbial signatures were positively correlated with host genes in cell proliferation (P1), DNA damage repair (P2) and DNA transcription (P3). Our study established a link between the metabolic properties of LAB with lung microbiota maturation and development. Breastfeeding and environmental exposure influence microbiome composition and host health and longevity. The inferred rat microbial biogeography and pattern-specific microbial signatures could be useful for microbiome therapeutic approaches to human health and life quality enhancement.
PTEN pathogenic variants are associated with poor prognosis in patients with advanced soft tissue sarcoma
Authors: Pan Minggui , Zhou Maggie Y. , Jiang Chen , Zhang Zheyang , Bui Nam , Bien Jeffrey , Siy Amanda , Achacoso Ninah , Solorzano Aleyda V. , Tse Pam , Chung Elaine , Hu Wenwei , Thomas Sachdev , Ganjoo Kristen , Habel Laurel A.
Published: January 2024

Background

We aimed to examine whether PTEN pathogenic variants (mutPTEN) were associated with overall survival (OS) in patients with advanced soft tissue sarcoma (STS) with the presence of one or more of the most common genomic alterations including p53, CDKN2A, RB1, and ATRX pathogenic variants.

Methods

This study included patients from Kaiser Permanente Northern California and Stanford Cancer Center with grade 2 or higher locally advanced and metastatic STS.

Results

A total of 174 patients had leiomyosarcoma (LMS), 136 had undifferentiated pleomorphic sarcoma (UPS), 78 had Liposarcoma (LPS), and 214 had other histology subtypes (Others). Among all patients with STS, OS was worse for those with mutPTEN versus wild-type PTEN (wtPTEN, adjusted HR [aHR] = 1.58 [95% CI, 1.11–2.23]), mutCDKN2A vs wtCDKN2A (aHR = 1.33 [95% CI .99–1.80]), and mutRB1 vs wtRB1 (aHR = 1.26 [95% CI 0.93–1.70[), while OS was similar for mutp53 vs wtp53 and mutATRX vs wtATRX. MutPTEN versus wtPTEN was consistently associated with worse OS in histologic subtypes including LMS and UPS and molecular subgroups.

Conclusion

MutPTEN vs wtPTEN was associated with worse OS in advanced STS. If confirmed, our findings could be helpful for prognostic stratification in clinical practice and for further understanding the molecular mechanisms of STS.
Infected erythrocytes and plasma proteomics reveal a specific protein signature of severe malaria
Authors: Fraering Jeremy , Salnot Virginie , Gautier Emilie-Fleur , Ezinmegnon Sem , Argy Nicolas , Peoc’h Katell , Manceau Hana , Alao Jules , Guillonneau François , Migot-Nabias Florence , Bertin Gwladys I , Kamaliddin Claire ,   NeuroCM consortium, Aubouy Agnes , Affolabi Dissou , Biokou Bibiane , Cot Michel , Degbelo Jean-Eudes , Deloron Philippe , Dramane Latifou , Faucher Jean-François , Guillochon Emilie , Houze Ludivine , Jafari-Guemouri Sayeh , Houze Sandrine , Joste Valentin , Labrunie Anaïs , Ladipo Yélé , Lathiere Thomas , Massougbodji Achille , Mowendabeka Audrey , Papin Jade , Pipy Bernard , Preux Pierre-Marie , Raymondeau Marie , Royo Jade , Sossou Darius , Techer Brigitte , Vianou Bertin
Published: January 2024

Cerebral malaria (CM), the most lethal complication of Plasmodium falciparum severe malaria (SM), remains fatal for 15–25% of affected children despite the availability of treatment. P. falciparum infects and multiplies in erythrocytes, contributing to anemia, parasite sequestration, and inflammation. An unbiased proteomic assessment of infected erythrocytes and plasma samples from 24 Beninese children was performed to study the complex mechanisms underlying CM. A significant down-regulation of proteins from the ubiquitin–proteasome pathway and an up-regulation of the erythroid precursor marker transferrin receptor protein 1 (TFRC) were associated with infected erythrocytes from CM patients. At the plasma level, the samples clustered according to clinical presentation. Significantly, increased levels of the 20S proteasome components were associated with SM. Targeted quantification assays confirmed these findings on a larger cohort (n = 340). These findings suggest that parasites causing CM preferentially infect reticulocytes or erythroblasts and alter their maturation. Importantly, the host plasma proteome serves as a specific signature of SM and presents a remarkable opportunity for developing innovative diagnostic and prognostic biomarkers.
A three-stage deep learning-based training frame for spectra baseline correction
Authors: Jiao Qingliang , Cai Boyong , Liu Ming , Dong Liquan , Hei Mei , Kong Lingqin , Zhao Yuejin
Published: January 2024

For spectrometers, baseline drift seriously affects the measurement and quantitative analysis of spectral data.