bluuebunny/crossref_metadata_2025_split huggingface dataset:
A hexa-species transcriptome atlas of mammalian embryogenesis delineates metabolic regulation across three different implantation modes
Authors: Malkowska Anna , Penfold Christopher , Bergmann Sophie , Boroviak Thorsten E. 
Published: June 2022

AbstractMammalian embryogenesis relies on glycolysis and oxidative phosphorylation to balance the generation of biomass with energy production. However, the dynamics of metabolic regulation in the postimplantation embryo in vivo have remained elusive due to the inaccessibility of the implanted conceptus for biochemical studies. To address this issue, we compiled single-cell embryo profiling data in six mammalian species and determined their metabolic dynamics through glycolysis and oxidative phosphorylation associated gene expression. Strikingly, we identify a conserved switch from bivalent respiration in the late blastocyst towards a glycolytic metabolism in early gastrulation stages across species, which is independent of embryo implantation. Extraembryonic lineages followed the dynamics of the embryonic lineage, except visceral endoderm. Finally, we demonstrate that in vitro primate embryo culture substantially impacts metabolic gene regulation by comparison to in vivo samples. Our work reveals a conserved metabolic programme despite different implantation modes and highlights the need to optimise postimplantation embryo culture protocols.
Coordination chemogenetics for activation of GPCR-type glutamate receptors in brain tissue
Authors: Ojima Kento , Kakegawa Wataru , Yamasaki Tokiwa , Miura Yuta , Itoh Masayuki , Michibata Yukiko , Kubota Ryou , Doura Tomohiro , Miura Eriko , Nonaka Hiroshi , Mizuno Seiya , Takahashi Satoru , Yuzaki Michisuke , Hamachi Itaru , Kiyonaka Shigeki 
Published: June 2022

AbstractDirect activation of cell-surface receptors is highly desirable for elucidating their physiological roles. A potential approach for cell-type-specific activation of a receptor subtype is chemogenetics, in which both point mutagenesis of the receptors and designed ligands are used. However, ligand-binding properties are affected in most cases. Here, we developed a chemogenetic method for direct activation of metabotropic glutamate receptor 1 (mGlu1), which plays essential roles in cerebellar functions in the brain. Our screening identified a mGlu1 mutant, mGlu1(N264H), that was activated directly by palladium complexes. A palladium complex showing low cytotoxicity successfully activated mGlu1 in mGlu1(N264H) knock-in mice, revealing that activation of endogenous mGlu1 is sufficient to evoke the critical cellular mechanism of synaptic plasticity, a basis of motor learning in the cerebellum. Moreover, cell-type-specific activation of mGlu1 was demonstrated successfully using adeno-associated viruses in mice, which shows the potential utility of this chemogenetics for clarifying the physiological roles of mGlu1 in a cell-type-specific manner.
Disentangling the genetic basis of rhizosphere microbiome assembly in tomato
Authors: Oyserman Ben O. , Flores Stalin Sarango , Griffioen Thom , Pan Xinya , van der Wijk Elmar , Pronk Lotte , Lokhorst Wouter , Nurfikari Azkia , Paulson Joseph N. , Movassagh Mercedeh , Stopnisek Nejc , Kupczok Anne , Cordovez Viviane , Carrión Víctor J. , Ligterink Wilco , Snoek Basten L. , Medema Marnix H. , Raaijmakers Jos M. 
Published: June 2022

AbstractMicrobiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating ‘microbiomics’ and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.
Ly6D+Siglec-H+ precursors contribute to conventional dendritic cells via a Zbtb46+Ly6D+ intermediary stage
Authors: Lutz Konstantin , Musumeci Andrea , Sie Christopher , Dursun Ezgi , Winheim Elena , Bagnoli Johannes , Ziegenhain Christoph , Rausch Lisa , Bergen Volker , Luecken Malte D. , Oostendorp Robert A. J. , Schraml Barbara U. , Theis Fabian J. , Enard Wolfgang , Korn Thomas , Krug Anne B. 
Published: June 2022

AbstractPlasmacytoid and conventional dendritic cells (pDC and cDC) are generated from progenitor cells in the bone marrow and commitment to pDCs or cDC subtypes may occur in earlier and later progenitor stages. Cells within the CD11c+MHCII−/loSiglec-H+CCR9lo DC precursor fraction of the mouse bone marrow generate both pDCs and cDCs. Here we investigate the heterogeneity and commitment of subsets in this compartment by single-cell transcriptomics and high-dimensional flow cytometry combined with cell fate analysis: Within the CD11c+MHCII−/loSiglec-H+CCR9lo DC precursor pool cells expressing high levels of Ly6D and lacking expression of transcription factor Zbtb46 contain CCR9loB220hi immediate pDC precursors and CCR9loB220lo (lo-lo) cells which still generate pDCs and cDCs in vitro and in vivo under steady state conditions. cDC-primed cells within the Ly6DhiZbtb46– lo-lo precursors rapidly upregulate Zbtb46 and pass through a Zbtb46+Ly6D+ intermediate stage before acquiring cDC phenotype after cell division. Type I IFN stimulation limits cDC and promotes pDC output from this precursor fraction by arresting cDC-primed cells in the Zbtb46+Ly6D+ stage preventing their expansion and differentiation into cDCs. Modulation of pDC versus cDC output from precursors by external factors may allow for adaptation of DC subset composition at later differentiation stages.
Statistical considerations of nonrandom treatment applications reveal region-wide benefits of widespread post-fire restoration action
Authors: Simler-Williamson Allison B. , Germino Matthew J. 
Published: June 2022

AbstractAccurate predictions of ecological restoration outcomes are needed across the increasingly large landscapes requiring treatment following disturbances. However, observational studies often fail to account for nonrandom treatment application, which can result in invalid inference. Examining a spatiotemporally extensive management treatment involving post-fire seeding of declining sagebrush shrubs across semiarid areas of the western USA over two decades, we quantify drivers and consequences of selection biases in restoration using remotely sensed data. From following more than 1,500 wildfires, we find treatments were disproportionately applied in more stressful, degraded ecological conditions. Failure to incorporate unmeasured drivers of treatment allocation led to the conclusion that costly, widespread seedings were unsuccessful; however, after considering sources of bias, restoration positively affected sagebrush recovery. Treatment effects varied with climate, indicating prioritization criteria for interventions. Our findings revise the perspective that post-fire sagebrush seedings have been broadly unsuccessful and demonstrate how selection biases can pose substantive inferential hazards in observational studies of restoration efficacy and the development of restoration theory.
Therapeutic efficacy of combined active and passive immunization in ART-suppressed, SHIV-infected rhesus macaques
Authors: Walker-Sperling Victoria E. K. , Mercado Noe B. , Chandrashekar Abishek , Borducchi Erica N. , Liu Jinyan , Nkolola Joseph P. , Lewis Mark , Murry Jeffrey P. , Yang Yunling , Geleziunas Romas , Robb Merlin L. , Michael Nelson L. , Pau Maria G. , Wegmann Frank , Schuitemaker Hanneke , Fray Emily J. , Kumar Mithra R. , Siliciano Janet D. , Siliciano Robert F. , Barouch Dan H. 
Published: June 2022

AbstractThe latent viral reservoir is the critical barrier for developing an HIV-1 cure. Previous studies have shown that therapeutic vaccination or broadly neutralizing antibody (bNAb) administration, together with a Toll-like receptor 7 (TLR7) agonist, enhanced virologic control or delayed viral rebound, respectively, following discontinuation of antiretroviral therapy (ART) in SIV- or SHIV-infected rhesus macaques. Here we show that the combination of active and passive immunization with vesatolimod may lead to higher rates of post-ART virologic control compared to either approach alone. Therapeutic Ad26/MVA vaccination and PGT121 administration together with TLR7 stimulation with vesatolimod resulted in 70% post-ART virologic control in SHIV-SF162P3-infected rhesus macaques. These data suggest the potential of combining active and passive immunization targeting different immunologic mechanisms as an HIV-1 cure strategy.
Unconventional excitonic states with phonon sidebands in layered silicon diphosphide
Authors: Zhou Ling , Huang Junwei , Windgaetter Lukas , Ong Chin Shen , Zhao Xiaoxu , Zhang Caorong , Tang Ming , Li Zeya , Qiu Caiyu , Latini Simone , Lu Yangfan , Wu Di , Gou Huiyang , Wee Andrew T. S. , Hosono Hideo , Louie Steven G. , Tang Peizhe , Rubio Angel , Yuan Hongtao 
Published: June 2022

AbstractComplex correlated states emerging from many-body interactions between quasiparticles (electrons, excitons and phonons) are at the core of condensed matter physics and material science. In low-dimensional materials, quantum confinement affects the electronic, and subsequently, optical properties for these correlated states. Here, by combining photoluminescence, optical reflection measurements and ab initio theoretical calculations, we demonstrate an unconventional excitonic state and its bound phonon sideband in layered silicon diphosphide (SiP2), where the bound electron–hole pair is composed of electrons confined within one-dimensional phosphorus–phosphorus chains and holes extended in two-dimensional SiP2 layers. The excitonic state and emergent phonon sideband show linear dichroism and large energy redshifts with increasing temperature. Our ab initio many-body calculations confirm that the observed phonon sideband results from the correlated interaction between excitons and optical phonons. With these results, we propose layered SiP2 as a platform for the study of excitonic physics and many-particle effects.
The cohesin acetylation cycle controls chromatin loop length through a PDS5A brake mechanism
Authors: van Ruiten Marjon S. , van Gent Démi , Sedeño Cacciatore Ángela , Fauster Astrid , Willems Laureen , Hekkelman Maarten L. , Hoekman Liesbeth , Altelaar Maarten , Haarhuis Judith H. I. , Brummelkamp Thijn R. , de Wit Elzo , Rowland Benjamin D. 
Published: June 2022

AbstractCohesin structures the genome through the formation of chromatin loops and by holding together the sister chromatids. The acetylation of cohesin’s SMC3 subunit is a dynamic process that involves the acetyltransferase ESCO1 and deacetylase HDAC8. Here we show that this cohesin acetylation cycle controls the three-dimensional genome in human cells. ESCO1 restricts the length of chromatin loops, and of architectural stripes emanating from CTCF sites. HDAC8 conversely promotes the extension of such loops and stripes. This role in controlling loop length turns out to be distinct from the canonical role of cohesin acetylation that protects against WAPL-mediated DNA release. We reveal that acetylation controls the interaction of cohesin with PDS5A to restrict chromatin loop length. Our data support a model in which this PDS5A-bound state acts as a brake that enables the pausing and restart of loop enlargement. The cohesin acetylation cycle hereby provides punctuation in the process of genome folding.
Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes
Authors: Rinzema Niels J. , Sofiadis Konstantinos , Tjalsma Sjoerd J. D. , Verstegen Marjon J. A. M. , Oz Yuva , Valdes-Quezada Christian , Felder Anna-Karina , Filipovska Teodora , van der Elst Stefan , de Andrade dos Ramos Zaria , Han Ruiqi , Krijger Peter H. L. , de Laat Wouter 
Published: June 2022

AbstractDevelopmental gene expression is often controlled by distal regulatory DNA elements called enhancers. Distant enhancer action is restricted to structural chromosomal domains that are flanked by CTCF-associated boundaries and formed through cohesin chromatin loop extrusion. To better understand how enhancers, genes and CTCF boundaries together form structural domains and control expression, we used a bottom-up approach, building series of active regulatory landscapes in inactive chromatin. We demonstrate here that gene transcription levels and activity over time reduce with increased enhancer distance. The enhancer recruits cohesin to stimulate domain formation and engage flanking CTCF sites in loop formation. It requires cohesin exclusively for the activation of distant genes, not of proximal genes, with nearby CTCF boundaries supporting efficient long-range enhancer action. Our work supports a dual activity model for enhancers: its classic role of stimulating transcription initiation and elongation from target gene promoters and a role of recruiting cohesin for the creation of chromosomal domains, the engagement of CTCF sites in chromatin looping and the activation of distal target genes.
Analysis of the fluid contents of simple bone cyst in the mandible
Authors: Choi So-Young , Boboeva Obida , Ham Ji Yeon , An Chang-Hyeon , Lee Sung-Tak , Kim Jin-Wook , An Seo-Young 
Published: June 2022

AbstractDescription of simple bone cyst (SBC) content has been controversial. This study aimed to assess and give a clearer picture of the SBC cavity contents. Between 2014 and 2016, 19 patients with SBC verified by histopathological examination were included in this study. SBC cavity content was investigated using clinical, radiographic, surgical, and laboratory findings. The difference in components among cavity fluid, blood, and serum was evaluated using a paired sample t-test for statistical analysis. All 19 SBC cases radiographically and surgically revealed a fluid-filled cavity. The patients’ average age was 21.3 ± 13.2 years, with no sex predominance found. SBCs were found mostly in the anterior mandible (n = 12, 63.2%). All lesions were filled with clear straw-colored or blood-colored floods with low concentration. Although the fluid components were similar to those in the blood and serum in the laboratory analysis, the statistical analysis revealed that the fluid components were not significantly different only for eosinophil (p = 0.43) and basophil (p = 0.06) counts as blood components and sodium (p = 0.76), potassium (p = 0.08), and chloride (p = 0.13) concentration as serum components. The results show that SBC is a fluid-filled cavity, with the cavity fluid being more likely similar to serum rather than blood regarding internal components.
Wireless muometric navigation system
Authors: Tanaka Hiroyuki K. M. 
Published: June 2022

AbstractWhile satellite-based global navigation systems have become essential tools in our daily lives, their effectiveness is often hampered by the fact that the signals cannot be accessed in underground, indoor, or underwater environments. Recently, a novel navigation system has been invented to address this issue by utilizing the characteristics of the ubiquitous and highly penetrative cosmic-ray muons. This technique, muometric navigation, does not require active signal generation and enables positioning in the aforementioned environments within a reference coordinate defined by the three-dimensional positions of multiple detectors. In its first phase of development, these reference detectors had to be connected to the receivers via a wired configuration to guarantee precise time synchronization. This work describes more versatile, wireless muometric navigation system (MuWNS), which was designed in conjunction with a cost-effective, crystal-oscillator-based grandmaster clock and a performance evaluation is reported for shallow underground/indoor, deep underground and undersea environments. It was confirmed that MuWNS offers a navigation quality almost equivalent to aboveground GPS-based handheld navigation by determining the distance between the reference frame and the receivers within a precision range between 1 and 10 m.
Topological transitions in ac/dc﻿-driven superconductor nanotubes
Authors: Fomin Vladimir M. , Rezaev Roman O. , Dobrovolskiy Oleksandr V. 
Published: June 2022

AbstractExtending of nanostructures into the third dimension has become a major research avenue in condensed-matter physics, because of geometry- and topology-induced phenomena. In this regard, superconductor 3D nanoarchitectures feature magnetic field inhomogeneity, non-trivial topology of Meissner currents and complex dynamics of topological defects. Here, we investigate theoretically topological transitions in the dynamics of vortices and slips of the phase of the order parameter in open superconductor nanotubes under a modulated transport current. Relying upon the time-dependent Ginzburg–Landau equation, we reveal two distinct voltage regimes when (i) a dominant part of the tube is in either the normal or superconducting state and (ii) a complex interplay between vortices, phase-slip regions and screening currents determines a rich FFT voltage spectrum. Our findings unveil novel dynamical states in superconductor open nanotubes, such as paraxial and azimuthal phase-slip regions, their branching and coexistence with vortices, and allow for control of these states by superimposed dc and ac current stimuli.
Amyloid-β impairs mitochondrial dynamics and autophagy in Alzheimer’s disease experimental models
Authors: de la Cueva Macarena , Antequera Desiree , Ordoñez-Gutierrez Lara , Wandosell Francisco , Camins Antonio , Carro Eva , Bartolome Fernando 
Published: June 2022

AbstractThe most accepted hypothesis in Alzheimer’s disease (AD) is the amyloid cascade which establishes that Aβ accumulation may induce the disease development. This accumulation may occur years before the clinical symptoms but it has not been elucidated if this accumulation is the cause or the consequence of AD. It is however, clear that Aβ accumulation exerts toxic effects in the cerebral cells. It is important then to investigate all possible associated events that may help to design new therapeutic strategies to defeat or ameliorate the symptoms in AD. Alterations in the mitochondrial physiology have been found in AD but it is not still clear if they could be an early event in the disease progression associated to amyloidosis or other conditions. Using APP/PS1 mice, our results support published evidence and show imbalances in the mitochondrial dynamics in the cerebral cortex and hippocampus of these mice representing very early events in the disease progression. We demonstrate in cellular models that these imbalances are consequence of Aβ accumulation that ultimately induce increased mitophagy, a mechanism which selectively removes damaged mitochondria by autophagy. Along with increased mitophagy, we also found that Aβ independently increases autophagy in APP/PS1 mice. Therefore, mitochondrial dysfunction could be an early feature in AD, associated with amyloid overload.
Digital haptics improve speed of visual search performance in a dual-task setting
Authors: Tivadar Ruxandra I. , Arnold Rebecca C. , Turoman Nora , Knebel Jean-François , Murray Micah M. 
Published: June 2022

AbstractDashboard-mounted touchscreen tablets are now common in vehicles. Screen/phone use in cars likely shifts drivers’ attention away from the road and contributes to risk of accidents. Nevertheless, vision is subject to multisensory influences from other senses. Haptics may help maintain or even increase visual attention to the road, while still allowing for reliable dashboard control. Here, we provide a proof-of-concept for the effectiveness of digital haptic technologies (hereafter digital haptics), which use ultrasonic vibrations on a tablet screen to render haptic perceptions. Healthy human participants (N = 25) completed a divided-attention paradigm. The primary task was a centrally-presented visual conjunction search task, and the secondary task entailed control of laterally-presented sliders on the tablet. Sliders were presented visually, haptically, or visuo-haptically and were vertical, horizontal or circular. We reasoned that the primary task would be performed best when the secondary task was haptic-only. Reaction times (RTs) on the visual search task were fastest when the tablet task was haptic-only. This was not due to a speed-accuracy trade-off; there was no evidence for modulation of VST accuracy according to modality of the tablet task. These results provide the first quantitative support for introducing digital haptics into vehicle and similar contexts.
Improved polar-code-based efficient post-processing algorithm for quantum key distribution
Authors: Fang Junbin , Yi Zhengzhong , Li Jin , Liang Zhipeng , Wu Yulin , Lei Wen , Jiang Zoe Lin , Wang Xuan 
Published: June 2022

AbstractCombined with one-time pad encryption scheme, quantum key distribution guarantees the unconditional security of communication in theory. However, error correction and privacy amplification in the post-processing phase of quantum key distribution result in high time delay, which limits the final secret key generation rate and the practicability of quantum key distribution systems. To alleviate this limitation, this paper proposes an efficient post-processing algorithm based on polar codes for quantum key distribution. In this algorithm, by analyzing the channel capacity of the main channel and the wiretap channel respectively under the Wyner’s wiretap channel model, we design a codeword structure of polar codes, so that the error correction and privacy amplification could be completed synchronously in a single step. Through combining error correction and privacy amplification into one single step, this efficient post-processing algorithm reduces complexity of the system and lower the post-processing delay. Besides, the reliable and secure communicaiton conditions for this algorithm has been given in this paper. Simulation results show that this post-processing algorithm satisfies the reliable and secure communication conditions well.