bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of cell lineages in tumors from spatial transcriptomics data
Authors: Ru Beibei , Huang Jinlin , Zhang Yu , Aldape Kenneth , Jiang Peng 
Published: February 2023

AbstractSpatial transcriptomics (ST) technology through in situ capturing has enabled topographical gene expression profiling of tumor tissues. However, each capturing spot may contain diverse immune and malignant cells, with different cell densities across tissue regions. Cell type deconvolution in tumor ST data remains challenging for existing methods designed to decompose general ST or bulk tumor data. We develop the Spatial Cellular Estimator for Tumors (SpaCET) to infer cell identities from tumor ST data. SpaCET first estimates cancer cell abundance by integrating a gene pattern dictionary of copy number alterations and expression changes in common malignancies. A constrained regression model then calibrates local cell densities and determines immune and stromal cell lineage fractions. SpaCET provides higher accuracy than existing methods based on simulation and real ST data with matched double-blind histopathology annotations as ground truth. Further, coupling cell fractions with ligand-receptor coexpression analysis, SpaCET reveals how intercellular interactions at the tumor-immune interface promote cancer progression.
Cell surface-bound La protein regulates the cell fusion stage of osteoclastogenesis
Authors: Whitlock Jarred M. , Leikina Evgenia , Melikov Kamran , De Castro Luis Fernandez , Mattijssen Sandy , Maraia Richard J. , Collins Michael T. , Chernomordik Leonid V. 
Published: February 2023

AbstractMultinucleated osteoclasts, essential for skeletal remodeling in health and disease, are formed by the fusion of osteoclast precursors, where each fusion event raises their bone-resorbing activity. Here we show that the nuclear RNA chaperone, La protein has an additional function as an osteoclast fusion regulator. Monocyte-to-osteoclast differentiation starts with a drastic decrease in La levels. As fusion begins, La reappears as a low molecular weight species at the osteoclast surface, where it promotes fusion. La’s role in promoting osteoclast fusion is independent of canonical La-RNA interactions and involves direct interactions between La and Annexin A5, which anchors La to transiently exposed phosphatidylserine at the surface of fusing osteoclasts. Disappearance of cell-surface La, and the return of full length La to the nuclei of mature, multinucleated osteoclasts, acts as an off switch of their fusion activity. Targeting surface La in a novel explant model of fibrous dysplasia inhibits excessive osteoclast formation characteristic of this disease, highlighting La’s potential as a therapeutic target.
Antiferromagnetism-driven two-dimensional topological nodal-point superconductivity
Authors: Bazarnik Maciej , Lo Conte Roberto , Mascot Eric , von Bergmann Kirsten , Morr Dirk K. , Wiesendanger Roland 
Published: February 2023

AbstractMagnet/superconductor hybrids (MSHs) hold the promise to host emergent topological superconducting phases. Both one-dimensional (1D) and two-dimensional (2D) magnetic systems in proximity to s-wave superconductors have shown evidence of gapped topological superconductivity with zero-energy end states and chiral edge modes. Recently, it was proposed that the bulk transition-metal dichalcogenide 4Hb-TaS2 is a gapless topological nodal-point superconductor (TNPSC). However, there has been no experimental realization of a TNPSC in a MSH system yet. Here we present the discovery of TNPSC in antiferromagnetic (AFM) monolayers on top of an s-wave superconductor. Our calculations show that the topological phase is driven by the AFM order, resulting in the emergence of a gapless time-reversal invariant topological superconducting state. Using low-temperature scanning tunneling microscopy we observe a low-energy edge mode, which separates the topological phase from the trivial one, at the boundaries of antiferromagnetic islands. As predicted by the calculations, we find that the relative spectral weight of the edge mode depends on the edge’s atomic configuration. Our results establish the combination of antiferromagnetism and superconductivity as a novel route to design 2D topological quantum phases.
Mystery of fatal ‘staggering disease’ unravelled: novel rustrela virus causes severe meningoencephalomyelitis in domestic cats
Authors: Matiasek Kaspar , Pfaff Florian , Weissenböck Herbert , Wylezich Claudia , Kolodziejek Jolanta , Tengstrand Sofia , Ecke Frauke , Nippert Sina , Starcky Philip , Litz Benedikt , Nessler Jasmin , Wohlsein Peter , Baumbach Christina , Mundhenk Lars , Aebischer Andrea , Reiche Sven , Weidinger Pia , Olofsson Karin M. , Rohdin Cecilia , Weissenbacher-Lang Christiane , Matt Julia , Rosati Marco , Flegel Thomas , Hörnfeldt Birger , Höper Dirk , Ulrich Rainer G. , Nowotny Norbert , Beer Martin , Ley Cecilia , Rubbenstroth Dennis 
Published: February 2023

Abstract‘Staggering disease’ is a neurological disease entity considered a threat to European domestic cats (Felis catus) for almost five decades. However, its aetiology has remained obscure. Rustrela virus (RusV), a relative of rubella virus, has recently been shown to be associated with encephalitis in a broad range of mammalian hosts. Here, we report the detection of RusV RNA and antigen by metagenomic sequencing, RT-qPCR, in-situ hybridization and immunohistochemistry in brain tissues of 27 out of 29 cats with non-suppurative meningoencephalomyelitis and clinical signs compatible with’staggering disease’ from Sweden, Austria, and Germany, but not in non-affected control cats. Screening of possible reservoir hosts in Sweden revealed RusV infection in wood mice (Apodemus sylvaticus). Our work indicates that RusV is the long-sought cause of feline ‘staggering disease’. Given its reported broad host spectrum and considerable geographic range, RusV may be the aetiological agent of neuropathologies in further mammals, possibly even including humans.
Orientated crystallization of FA-based perovskite via hydrogen-bonded polymer network for efficient and stable solar cells
Authors: Li Mubai , Sun Riming , Chang Jingxi , Dong Jingjin , Tian Qiushuang , Wang Hongze , Li Zihao , Yang Pinghui , Shi Haokun , Yang Chao , Wu Zichao , Li Renzhi , Yang Yingguo , Wang Aifei , Zhang Shitong , Wang Fangfang , Huang Wei , Qin Tianshi 
Published: February 2023

AbstractIncorporating mixed ion is a frequently used strategy to stabilize black-phase formamidinum lead iodide perovskite for high-efficiency solar cells. However, these devices commonly suffer from photoinduced phase segregation and humidity instability. Herein, we find that the underlying reason is that the mixed halide perovskites generally fail to grow into homogenous and high-crystalline film, due to the multiple pathways of crystal nucleation originating from various intermediate phases in the film-forming process. Therefore, we design a multifunctional fluorinated additive, which restrains the complicated intermediate phases and promotes orientated crystallization of α-phase of perovskite. Furthermore, the additives in-situ polymerize during the perovskite film formation and form a hydrogen-bonded network to stabilize α-phase. Remarkably, the polymerized additives endow a strongly hydrophobic effect to the bare perovskite film against liquid water for 5 min. The unencapsulated devices achieve 24.10% efficiency and maintain >95% of the initial efficiency for 1000 h under continuous sunlight soaking and for 2000 h at air ambient of ~50% humid, respectively.
Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes
Authors: Ding Ya-Mei , Pang Xiao-Xu , Cao Yu , Zhang Wei-Ping , Renner Susanne S. , Zhang Da-Yong , Bai Wei-Ning 
Published: February 2023

AbstractIn lineages of allopolyploid origin, sets of homoeologous chromosomes may coexist that differ in gene content and syntenic structure. Presence or absence of genes and microsynteny along chromosomal blocks can serve to differentiate subgenomes and to infer phylogenies. We here apply genome-structural data to infer relationships in an ancient allopolyploid lineage, the walnut family (Juglandaceae), by using seven chromosome-level genomes, two of them newly assembled. Microsynteny and gene-content analyses yield identical topologies that placePlatycaryawithEngelhardiaas did a 1980s morphological-cladistic study. DNA-alignment-based topologies here and in numerous earlier studies instead groupPlatycaryawithCaryaandJuglans, perhaps misled by past hybridization. All available data support a hybrid origin of Juglandaceae from extinct or unsampled progenitors nested within, or sister to, Myricaceae.Rhoiptelea chiliantha, sister to all other Juglandaceae, contains proportionally more DNA repair genes and appears to evolve at a rate 2.6- to 3.5-times slower than the remaining species.
Comparison of fecal and blood metabolome reveals inconsistent associations of the gut microbiota with cardiometabolic diseases
Authors: Deng Kui , Xu Jin-jian , Shen Luqi , Zhao Hui , Gou Wanglong , Xu Fengzhe , Fu Yuanqing , Jiang Zengliang , Shuai Menglei , Li Bang-yan , Hu Wei , Zheng Ju-Sheng , Chen Yu-ming 
Published: February 2023

AbstractBlood metabolome is commonly used in human studies to explore the associations of gut microbiota-derived metabolites with cardiometabolic diseases. Here, in a cohort of 1007 middle-aged and elderly adults with matched fecal metagenomic (149 species and 214 pathways) and paired fecal and blood targeted metabolomics data (132 metabolites), we find disparate associations with taxonomic composition and microbial pathways when using fecal or blood metabolites. For example, we observe that fecal, but not blood butyric acid significantly associates with both gut microbiota and prevalent type 2 diabetes. These findings are replicated in an independent validation cohort involving 103 adults. Our results suggest that caution should be taken when inferring microbiome-cardiometabolic disease associations from either blood or fecal metabolome data.
Direct Cryo-ET observation of platelet deformation induced by SARS-CoV-2 spike protein
Authors: Kuhn Christopher Cyrus , Basnet Nirakar , Bodakuntla Satish , Alvarez-Brecht Pelayo , Nichols Scott , Martinez-Sanchez Antonio , Agostini Lorenzo , Soh Young-Min , Takagi Junichi , Biertümpfel Christian , Mizuno Naoko 
Published: February 2023

AbstractSARS-CoV-2 is a novel coronavirus responsible for the COVID-19 pandemic. Its high pathogenicity is due to SARS-CoV-2 spike protein (S protein) contacting host-cell receptors. A critical hallmark of COVID-19 is the occurrence of coagulopathies. Here, we report the direct observation of the interactions between S protein and platelets. Live imaging shows that the S protein triggers platelets to deform dynamically, in some cases, leading to their irreversible activation. Cellular cryo-electron tomography reveals dense decorations of S protein on the platelet surface, inducing filopodia formation. Hypothesizing that S protein binds to filopodia-inducing integrin receptors, we tested the binding to RGD motif-recognizing platelet integrins and find that S protein recognizes integrin αvβ3. Our results infer that the stochastic activation of platelets is due to weak interactions of S protein with integrin, which can attribute to the pathogenesis of COVID-19 and the occurrence of rare but severe coagulopathies.
Disentangling kinetics from thermodynamics in heterogeneous colloidal systems
Authors: Almohammadi Hamed , Martinek Sandra , Yuan Ye , Fischer Peter , Mezzenga Raffaele 
Published: February 2023

AbstractIn Nucleation and Growth, the process by which most heterogeneous systems form, thermodynamics sets the asymptotic boundaries toward which the system must evolve, while kinetics tries to cope with it by imposing the transport rates. In all heterogeneous colloidal systems observed in nature, composition, shape, structure and physical properties result from the trade-off between thermodynamics and kinetics. Here we show, by carefully selecting colloidal systems and controlling phase separation in microfluidic devices, that it becomes possible to disentangle kinetics effects from thermodynamics. Using amyloids and nanocellulose filamentous colloids, we demonstrate that decoupling kinetics from thermodynamics in the phase separation process unveils new physical phenomena, such as orders of magnitude shorter timescales, a wider phase diagram, and structures that are not observable via conventional liquid-liquid phase separation. Our approach enables on-demand fabrication of multicomponent heterogeneous liquid crystals, enhancing their potential, and introducing original fundamental and technological directions in multicomponent structured fluids.
Evidence for a rosiaite-structured high-pressure silica phase and its relation to lamellar amorphization in quartz
Authors: Otzen Christoph , Liermann Hanns-Peter , Langenhorst Falko 
Published: February 2023

AbstractWhen affected by impact, quartz (SiO2) undergoes an abrupt transformation to glass lamellae, the planar deformation features (PDFs). This shock effect is the most reliable indicator of impacts and is decisive in identifying catastrophic collisions in the Earth´s record such as the Chicxulub impact. Despite the significance of PDFs, there is still no consensus how they form. Here, we present time-resolved in-situ synchroton X-ray diffraction data of single-crystal quartz rapidly compressed in a dynamic diamond anvil cell. These experiments provide evidence for the transformation of quartz at pressures above 15 GPa to lamellae of a metastable rosiaite (PbSb2O6)-type high-pressure phase with octahedrally coordinated silicon. This phase collapses during decompression to amorphous lamellae, which closely resemble PDFs in naturally shocked quartz. The identification of rosiaite-structured silica provides thus an explanation for lamellar amorphization of quartz. Furthermore, it suggests that the mixed phase region of the Hugoniot curve may be related to the progressive formation of rosiaite-structured silica.
An updated suite of viral vectors for in vivo calcium imaging using intracerebral and retro-orbital injections in male mice
Authors: Grødem Sverre , Nymoen Ingeborg , Vatne Guro Helén , Rogge Frederik Sebastian , Björnsdóttir Valgerður , Lensjø Kristian Kinden , Fyhn Marianne 
Published: February 2023

AbstractGenetically encoded Ca2+ indicators (GECIs) are widely used to measure neural activity. Here, we explore the use of systemically administered PHP.eB AAVs for brain-wide expression of GECIs and compare the expression properties to intracerebrally injected AAVs in male mice. We show that systemic administration is a promising strategy for imaging neural activity. Next, we establish the use of EE-RR- (soma) and RPL10a (Ribo) soma-targeting peptides with the latest jGCaMP and show that EE-RR-tagged jGCaMP8 gives rise to strong expression but limited soma-targeting. In contrast, Ribo-tagged jGCaMP8 lacks neuropil signal, but the expression rate is reduced. To combat this, we modified the linker region of the Ribo-tag (RiboL1-). RiboL1-jGCaMP8 expresses faster than Ribo-jGCaMP8 but remains too dim for reliable use with systemic virus administration. However, intracerebral injections of the RiboL1-tagged jGCaMP8 constructs provide strong Ca2+ signals devoid of neuropil contamination, with remarkable labeling density.
Atomically dispersed iridium catalysts on silicon photoanode for efficient photoelectrochemical water splitting
Authors: Jun Sang Eon , Kim Youn-Hye , Kim Jaehyun , Cheon Woo Seok , Choi Sungkyun , Yang Jinwook , Park Hoonkee , Lee Hyungsoo , Park Sun Hwa , Kwon Ki Chang , Moon Jooho , Kim Soo-Hyun , Jang Ho Won 
Published: February 2023

AbstractStabilizing atomically dispersed single atoms (SAs) on silicon photoanodes for photoelectrochemical-oxygen evolution reaction is still challenging due to the scarcity of anchoring sites. Here, we elaborately demonstrate the decoration of iridium SAs on silicon photoanodes and assess the role of SAs on the separation and transfer of photogenerated charge carriers. NiO/Ni thin film, an active and highly stable catalyst, is capable of embedding the iridium SAs in its lattices by locally modifying the electronic structure. The isolated iridium SAs enable the effective photogenerated charge transport by suppressing the charge recombination and lower the thermodynamic energy barrier in the potential-determining step. The Ir SAs/NiO/Ni/ZrO2/n-Si photoanode exhibits a benchmarking photoelectrochemical performance with a high photocurrent density of 27.7 mA cm−2 at 1.23 V vs. reversible hydrogen electrode and 130 h stability. This study proposes the rational design of SAs on silicon photoelectrodes and reveals the potential of the iridium SAs to boost photogenerated charge carrier kinetics.
Hyperbolic matter in electrical circuits with tunable complex phases
Authors: Chen Anffany , Brand Hauke , Helbig Tobias , Hofmann Tobias , Imhof Stefan , Fritzsche Alexander , Kießling Tobias , Stegmaier Alexander , Upreti Lavi K. , Neupert Titus , Bzdušek Tomáš , Greiter Martin , Thomale Ronny , Boettcher Igor 
Published: February 2023

AbstractCurved spaces play a fundamental role in many areas of modern physics, from cosmological length scales to subatomic structures related to quantum information and quantum gravity. In tabletop experiments, negatively curved spaces can be simulated with hyperbolic lattices. Here we introduce and experimentally realize hyperbolic matter as a paradigm for topological states through topolectrical circuit networks relying on a complex-phase circuit element. The experiment is based on hyperbolic band theory that we confirm here in an unprecedented numerical survey of finite hyperbolic lattices. We implement hyperbolic graphene as an example of topologically nontrivial hyperbolic matter. Our work sets the stage to realize more complex forms of hyperbolic matter to challenge our established theories of physics in curved space, while the tunable complex-phase element developed here can be a key ingredient for future experimental simulation of various Hamiltonians with topological ground states.
Strong quartic anharmonicity, ultralow thermal conductivity, high band degeneracy and good thermoelectric performance in Na2TlSb
Authors: Yue Tongcai , Zhao Yinchang , Ni Jun , Meng Sheng , Dai Zhenhong 
Published: February 2023

AbstractWe employ first-principles calculations combined with self-consistent phonon theory and Boltzmann transport equations to investigate the thermal transport and thermoelectric properties of full-Heusler compound Na2TlSb. Our findings exhibit that the strong quartic anharmonicity and temperature dependence of the Tl atom with rattling behavior plays an important role in the lattice stability of Na2TlSb. We find that soft Tl-Sb bonding and resonant bonding in the pseudocage composed of the Na and Sb atoms interaction is responsible for ultralow κL. Meanwhile, the multi-valley band structure increases the band degeneracy, results in a high power factor in p-type Na2TlSb. The coexistence of ultralow κL and high power factor presents that Na2TlSb is a potential candidate for thermoelectric applications. Moreover, these findings help to understand the origin of ultralow κL of full-Heusler compounds with strong quartic anharmonicity, leading to the rational design of full-Heusler compounds with high thermoelectric performance.
A systematic review and meta-analysis of inflammatory biomarkers in Parkinson’s disease
Authors: Qu Yi , Li Jiangting , Qin Qixiong , Wang Danlei , Zhao Jingwei , An Ke , Mao Zhijuan , Min Zhe , Xiong Yongjie , Li Jingyi , Xue Zheng 
Published: February 2023

AbstractNeuroinflammation plays a crucial role in the pathogenesis of Parkinson’s disease (PD), but controversies persist. Studies reporting concentrations of blood or cerebrospinal fluid (CSF) markers for patients with PD and controls were included and extracted. Pooled Hedges’g was adopted to illustrate comparisons, and covariates were used to explore sources of heterogeneity. Finally, 152 studies were included. Increased IL-6, TNF-α, IL-1β, STNFR1, CRP, CCL2, CX3CL1, and CXCL12 levels and decreased INF-γ and IL-4 levels were noted in the PD group. In addition, increased CSF levels of IL-6, TNF-α, IL-1β, CRP and CCL2 were revealed in patients with PD compared to controls. Consequently, significantly altered levels of inflammatory markers were verified between PD group and control, suggesting that PD is accompanied by inflammatory responses in both the peripheral blood and CSF. This study was registered with PROSPERO, CRD42022349182.
Parkinsonism mutations in DNAJC6 cause lipid defects and neurodegeneration that are rescued by Synj1
Authors: Jacquemyn Julie , Kuenen Sabine , Swerts Jef , Pavie Benjamin , Vijayan Vinoy , Kilic Ayse , Chabot Dries , Wang Yu-Chun , Schoovaerts Nils , Corthout Nikky , Verstreken Patrik 
Published: February 2023

AbstractRecent evidence links dysfunctional lipid metabolism to the pathogenesis of Parkinson’s disease, but the mechanisms are not resolved. Here, we generated a new Drosophila knock-in model of DNAJC6/Auxilin and find that the pathogenic mutation causes synaptic dysfunction, neurological defects and neurodegeneration, as well as specific lipid metabolism alterations. In these mutants, membrane lipids containing long-chain polyunsaturated fatty acids, including phosphatidylinositol lipid species that are key for synaptic vesicle recycling and organelle function, are reduced. Overexpression of another protein mutated in Parkinson’s disease, Synaptojanin-1, known to bind and metabolize specific phosphoinositides, rescues the DNAJC6/Auxilin lipid alterations, the neuronal function defects and neurodegeneration. Our work reveals a functional relation between two proteins mutated in Parkinsonism and implicates deregulated phosphoinositide metabolism in the maintenance of neuronal integrity and neuronal survival.
Digital 3D Brain MRI Arterial Territories Atlas
Authors: Liu Chin-Fu , Hsu Johnny , Xu Xin , Kim Ganghyun , Sheppard Shannon M. , Meier Erin L. , Miller Michael I. , Hillis Argye E. , Faria Andreia V. 
Published: February 2023

AbstractThe locus and extent of brain damage in the event of vascular insult can be quantitatively established quickly and easily with vascular atlases. Although highly anticipated by clinicians and clinical researchers, no digital MRI arterial atlas is readily available for automated data analyses. We created a digital arterial territory atlas based on lesion distributions in 1,298 patients with acute stroke. The lesions were manually traced in the diffusion-weighted MRIs, binary stroke masks were mapped to a common space, probability maps of lesions were generated and the boundaries for each arterial territory was defined based on the ratio between probabilistic maps. The atlas contains the definition of four major supra- and infra-tentorial arterial territories: Anterior, Middle, Posterior Cerebral Arteries and Vertebro-Basilar, and sub-territories (thalamoperforating, lenticulostriate, basilar and cerebellar arterial territories), in two hierarchical levels. This study provides the first publicly-available, digital, 3D deformable atlas of arterial brain territories, which may serve as a valuable resource for large-scale, reproducible processing and analysis of brain MRIs of patients with stroke and other conditions.