bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractLysosomes 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

AbstractThe 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

AbstractUltralight 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

AbstractNon-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

AbstractElectrochemical 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

AbstractAge-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

AbstractGenomic 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

AbstractIn 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

AbstractSwitch 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

AbstractOptical 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

AbstractSpontaneously 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

AbstractParkinson’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

AbstractBacterial 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

AbstractAutonomic 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.