bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vitamin C epigenetically controls osteogenesis and bone mineralization
Authors: Thaler Roman , Khani Farzaneh , Sturmlechner Ines , Dehghani Sharareh S. , Denbeigh Janet M. , Zhou Xianhu , Pichurin Oksana , Dudakovic Amel , Jerez Sofia S. , Zhong Jian , Lee Jeong-Heon , Natarajan Ramesh , Kalajzic Ivo , Jiang Yong-hui , Deyle David R. , Paschalis Eleftherios P. , Misof Barbara M. , Ordog Tamas , van Wijnen Andre J. 
Published: October 2022

AbstractVitamin C deficiency disrupts the integrity of connective tissues including bone. For decades this function has been primarily attributed to Vitamin C as a cofactor for collagen maturation. Here, we demonstrate that Vitamin C epigenetically orchestrates osteogenic differentiation and function by modulating chromatin accessibility and priming transcriptional activity. Vitamin C regulates histone demethylation (H3K9me3 and H3K27me3) and promotes TET-mediated 5hmC DNA hydroxymethylation at promoters, enhancers and super-enhancers near bone-specific genes. This epigenetic circuit licenses osteoblastogenesis by permitting the expression of all major pro-osteogenic genes. Osteogenic cell differentiation is strictly and continuously dependent on Vitamin C, whereas Vitamin C is dispensable for adipogenesis. Importantly, deletion of 5hmC-writers, Tet1 and Tet2, in Vitamin C-sufficient murine bone causes severe skeletal defects which mimic bone phenotypes of Vitamin C-insufficient Gulo knockout mice, a model of Vitamin C deficiency and scurvy. Thus, Vitamin C’s epigenetic functions are central to osteoblastogenesis and bone formation and may be leveraged to prevent common bone-degenerating conditions.
DNA-delivered antibody cocktail exhibits improved pharmacokinetics and confers prophylactic protection against SARS-CoV-2
Authors: Parzych Elizabeth M. , Du Jianqiu , Ali Ali R. , Schultheis Katherine , Frase Drew , Smith Trevor R. F. , Cui Jiayan , Chokkalingam Neethu , Tursi Nicholas J. , Andrade Viviane M. , Warner Bryce M. , Gary Ebony N. , Li Yue , Choi Jihae , Eisenhauer Jillian , Maricic Igor , Kulkarni Abhijeet , Chu Jacqueline D. , Villafana Gabrielle , Rosenthal Kim , Ren Kuishu , Francica Joseph R. , Wootton Sarah K. , Tebas Pablo , Kobasa Darwyn , Broderick Kate E. , Boyer Jean D. , Esser Mark T. , Pallesen Jesper , Kulp Dan W. , Patel Ami , Weiner David B. 
Published: October 2022

AbstractMonoclonal antibody therapy has played an important role against SARS-CoV-2. Strategies to deliver functional, antibody-based therapeutics with improved in vivo durability are needed to supplement current efforts and reach underserved populations. Here, we compare recombinant mAbs COV2-2196 and COV2-2130, which compromise clinical cocktail Tixagevimab/Cilgavimab, with optimized nucleic acid-launched forms. Functional profiling of in vivo-expressed, DNA-encoded monoclonal antibodies (DMAbs) demonstrated similar specificity, broad antiviral potency and equivalent protective efficacy in multiple animal challenge models of SARS-CoV-2 prophylaxis compared to protein delivery. In PK studies, DNA-delivery drove significant serum antibody titers that were better maintained compared to protein administration. Furthermore, cryo-EM studies performed on serum-derived DMAbs provide the first high-resolution visualization of in vivo-launched antibodies, revealing new interactions that may promote cooperative binding to trimeric antigen and broad activity against VoC including Omicron lineages. These data support the further study of DMAb technology in the development and delivery of valuable biologics.
Mode coupling bi-stability and spectral broadening in buckled carbon nanotube mechanical resonators
Authors: Rechnitz Sharon , Tabachnik Tal , Shlafman Michael , Shlafman Shlomo , Yaish Yuval E. 
Published: October 2022

AbstractBi-stable mechanical resonators play a significant role in various applications, such as sensors, memory elements, quantum computing and mechanical parametric amplification. While carbon nanotube based resonators have been widely investigated as promising NEMS devices, a bi-stable carbon nanotube resonator has never been demonstrated. Here, we report a class of carbon nanotube resonators in which the nanotube is buckled upward. We show that a small upward buckling yields record electrical frequency tunability, whereas larger buckling can achieve Euler-Bernoulli bi-stability, the smallest mechanical resonator with two stable configurations to date. We believe that these recently-discovered carbon nanotube devices will open new avenues for realizing nano-sensors, mechanical memory elements and mechanical parametric amplifiers. Furthermore, we present a three-dimensional theoretical analysis revealing significant nonlinear coupling between the in-plane and out-of-plane static and dynamic modes of motion, and a unique three-dimensional Euler-Bernoulli snap-through transition. We utilize this coupling to provide a conclusive explanation for the low quality factor in carbon nanotube resonators at room temperature, key in understanding dissipation mechanisms at the nano scale.
A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome
Authors: Keraite Ieva , Becker Philipp , Canevazzi Davide , Frias-López Cristina , Dabad Marc , Tonda-Hernandez Raúl , Paramonov Ida , Ingham Matthew John , Brun-Heath Isabelle , Leno Jordi , Abulí Anna , Garcia-Arumí Elena , Heath Simon Charles , Gut Marta , Gut Ivo Glynne 
Published: October 2022

AbstractMethods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple deletions and to cover the mitochondrial genome evenly. Here we describe a method to target, multiplex and sequence at high coverage full-length human mitochondrial genomes as native single-molecules, utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks, that define the mtDNA beginning and end of the sequencing reads, as barcodes, we achieve high demultiplexing specificity and delineation of the full-length of the mtDNA, regardless of the structural variant pattern. The long-read sequencing data is analysed with a pipeline where our custom-developed software, baldur, efficiently detects single nucleotide heteroplasmy to below 1%, physically determines phase and can accurately disentangle complex deletions. Our workflow is a tool for studying mtDNA variation and will accelerate mitochondrial research.
The solution structure of Dead End bound to AU-rich RNA reveals an unusual mode of tandem RRM-RNA recognition required for mRNA regulation
Authors: Duszczyk Malgorzata M. , Wischnewski Harry , Kazeeva Tamara , Arora Rajika , Loughlin Fionna E. , von Schroetter Christine , Pradère Ugo , Hall Jonathan , Ciaudo Constance , Allain Frédéric H.-T. 
Published: October 2022

AbstractDead End (DND1) is an RNA-binding protein essential for germline development through its role in post-transcriptional gene regulation. The molecular mechanisms behind selection and regulation of its targets are unknown. Here, we present the solution structure of DND1’s tandem RNA Recognition Motifs (RRMs) bound to AU-rich RNA. The structure reveals how an NYAYUNN element is specifically recognized, reconciling seemingly contradictory sequence motifs discovered in recent genome-wide studies. RRM1 acts as a main binding platform, including atypical extensions to the canonical RRM fold. RRM2 acts cooperatively with RRM1, capping the RNA using an unusual binding pocket, leading to an unusual mode of tandem RRM-RNA recognition. We show that the consensus motif is sufficient to mediate upregulation of a reporter gene in human cells and that this process depends not only on RNA binding by the RRMs, but also on DND1’s double-stranded RNA binding domain (dsRBD), which is dispensable for binding of a subset of targets in cellulo. Our results point to a model where DND1 target selection is mediated by a non-canonical mode of AU-rich RNA recognition by the tandem RRMs and a role for the dsRBD in the recruitment of effector complexes responsible for target regulation.
Atomically dispersed chromium coordinated with hydroxyl clusters enabling efficient hydrogen oxidation on ruthenium
Authors: Zhang Bingxing , Zhang Baohua , Zhao Guoqiang , Wang Jianmei , Liu Danqing , Chen Yaping , Xia Lixue , Gao Mingxia , Liu Yongfeng , Sun Wenping , Pan Hongge 
Published: October 2022

AbstractOvercoming the sluggish kinetics of alkaline hydrogen oxidation reaction (HOR) is challenging but is of critical importance for practical anion exchange membrane fuel cells. Herein, abundant and efficient interfacial active sites are created on ruthenium (Ru) nanoparticles by anchoring atomically isolated chromium coordinated with hydroxyl clusters (Cr1(OH)x) for accelerated alkaline HOR. This catalyst system delivers 50-fold enhanced HOR activity with excellent durability and CO anti-poisoning ability via switching the active sites from Ru surface to Cr1(OH)x-Ru interface. Fundamentally different from the conventional mechanism merely focusing on surface metal sites, the isolated Cr1(OH)x could provide unique oxygen species for accelerating hydrogen or CO spillover from Ru to Cr1(OH)x. Furthermore, the original oxygen species from Cr1(OH)x are confirmed to participate in hydrogen oxidation and H2O formation. The incorporation of such atomically isolated metal hydroxide clusters in heterostructured catalysts opens up new opportunities for rationally designing advanced electrocatalysts for HOR and other complex electrochemical reactions. This work also highlights the importance of size effect of co-catalysts, which should also be paid substantial attention to in the catalysis field.
Optic nerve sheath diameter and spaceflight: defining shortcomings and future directions
Authors: Fall Dylan A. , Lee Andrew G. , Bershad Eric M. , Kramer Larry A. , Mader Thomas H. , Clark Jonathan B. , Hirzallah Mohammad I. 
Published: October 2022

AbstractNeuro-ocular changes during long-duration space flight are known as spaceflight-associated neuro-ocular syndrome (SANS). The ability to detect, monitor, and prevent SANS is a priority of current space medicine research efforts. Optic nerve sheath diameter (ONSD) measurement has been used both terrestrially and in microgravity as a proxy for measurements of elevated intracranial pressure. ONSD shows promise as a potential method of identifying and quantitating neuro-ocular changes during space flight. This review examines 13 studies measuring ONSD and its relationship to microgravity exposure or ground-based analogs, including head-down tilt, dry immersion, or animal models. The goal of this correspondence is to describe heterogeneity in the use of ONSD in the current SANS literature and make recommendations to reduce heterogeneity in future studies through standardization of imaging modalities, measurement techniques, and other aspects of study design.
Lysosomal lipid alterations caused by glucocerebrosidase deficiency promote lysosomal dysfunction, chaperone-mediated-autophagy deficiency, and alpha-synuclein pathology
Authors: Navarro-Romero Alba , Fernandez-Gonzalez Irene , Riera Jordi , Montpeyo Marta , Albert-Bayo Merce , Lopez-Royo Tresa , Castillo-Sanchez Pablo , Carnicer-Caceres Clara , Arranz-Amo Jose Antonio , Castillo-Ribelles Laura , Pradas Eddie , Casas Josefina , Vila Miquel , Martinez-Vicente Marta 
Published: October 2022

AbstractMutations in the GBA gene that encodes the lysosomal enzyme β-glucocerebrosidase (GCase) are a major genetic risk factor for Parkinson’s disease (PD). In this study, we generated a set of differentiated and stable human dopaminergic cell lines that express the two most prevalent GBA mutations as well as GBA knockout cell lines as a in vitro disease modeling system to study the relationship between mutant GBA and the abnormal accumulation of α-synuclein. We performed a deep analysis of the consequences triggered by the presence of mutant GBA protein and the loss of GCase activity in different cellular compartments, focusing primarily on the lysosomal compartment, and analyzed in detail the lysosomal activity, composition, and integrity. The loss of GCase activity generates extensive lysosomal dysfunction, promoting the loss of activity of other lysosomal enzymes, affecting lysosomal membrane stability, promoting intralysosomal pH changes, and favoring the intralysosomal accumulation of sphingolipids and cholesterol. These local events, occurring only at a subcellular level, lead to an impairment of autophagy pathways, particularly chaperone-mediated autophagy, the main α-synuclein degradative pathway. The findings of this study highlighted the role of lysosomal function and lipid metabolism in PD and allowed us to describe a molecular mechanism to understand how mutations in GBA can contribute to an abnormal accumulation of different α-synuclein neurotoxic species in PD pathology.
Dissipation of reactive inhibition is sufficient to explain post-rest improvements in motor sequence learning
Authors: Gupta Mohan W. , Rickard Timothy C. 
Published: October 2022

AbstractThe prevailing hypothesis for observed post-rest motor reaction time improvements is offline consolidation. In the present study, we present evidence for an alternate account involving the accrual and dissipation of reactive inhibition. Four groups of participants (N = 159) performed a finger-tapping task involving either massed (30 s per trial) or spaced (10 s per trial) training, and with one of two break intervals between each trial: 10 s or 30 s. After 360 s of training in each group, there was a 300 s rest period followed by a final test on the same task. The results show that the smaller the ratio of break time to on-task trial time during training, the larger the improvement in reaction time after the rest period. Those results are fully consistent with a model that assumes no facilitating offline consolidation, but rather learning that is concurrent with performance and reactive inhibition that builds during performance and dissipates during breaks.
Elucidation of the role of nucleolin as a cell surface receptor for nucleic acid-based adjuvants
Authors: Kitagawa Satoki , Matsuda Teppei , Washizaki Ayaka , Murakami Hirotomo , Yamamoto Takuya , Yoshioka Yasuo 
Published: October 2022

AbstractNucleic acid-based adjuvants such as CpG oligonucleotides (CpG ODNs) and poly(I:C) are potential vaccine adjuvants for infectious diseases and cancers. However, the mechanism by which their cell surface receptors promote their uptake into dendritic cells (DCs) and shuttle them to intracellular Toll-like receptors remains to be further investigated. Here, we demonstrated a role for nucleolin, a multifunctional DNA- and RNA-binding protein and a major constituent of the nucleolus, as one of the cell-surface receptors for nucleic acid-based adjuvants. Nucleolin on mouse DC surface bound directly to A-type CpG ODN, B-type CpG ODN, and poly(I:C) and promoted their internalization into cells following DC maturation in vitro. In human DCs, nucleolin also contributed to the binding and internalization of both types of CpG ODNs and subsequent cytokine production. Furthermore, nucleolin played a crucial role in cytokine production and activating antigen-specific antibodies and T cell responses induced by B-type CpG ODN in vivo in mice. Our findings provide valuable information that can help improve the efficacy and safety of these adjuvants.
Observation of the quantum Gouy phase
Authors: Hiekkamäki Markus , Barros Rafael F. , Ornigotti Marco , Fickler Robert 
Published: October 2022

AbstractControlling the evolution of photonic quantum states is crucial for most quantum information processing and metrology tasks. Due to its importance, many mechanisms of quantum state evolution have been tested in detail and are well understood; however, the fundamental phase anomaly of evolving waves, called the Gouy phase, has had a limited number of studies in the context of elementary quantum states of light, especially in the case of photon number states. Here we outline a simple method for calculating the quantum state evolution upon propagation and demonstrate experimentally how this quantum Gouy phase affects two-photon quantum states. Our results show that the increased phase sensitivity of multi-photon states also extends to this fundamental phase anomaly and has to be taken into account to fully understand the state evolution. We further demonstrate how the Gouy phase can be used as a tool for manipulating quantum states of any bosonic system in future quantum technologies, outline a possible application in quantum-enhanced sensing, and dispel a common misconception attributing the increased phase sensitivity of multi-photon quantum states solely to an effective de Broglie wavelength.
Electrons with Planckian scattering obey standard orbital motion in a magnetic field
Authors: Ataei Amirreza , Gourgout A. , Grissonnanche G. , Chen L. , Baglo J. , Boulanger M.-E. , Laliberté F. , Badoux S. , Doiron-Leyraud N. , Oliviero V. , Benhabib S. , Vignolles D. , Zhou J.-S. , Ono S. , Takagi H. , Proust C. , Taillefer Louis 
Published: October 2022

AbstractIn various so-called strange metals, electrons undergo Planckian dissipation1,2, a strong and anomalous scattering that grows linearly with temperature3, in contrast to the quadratic temperature dependence expected from the standard theory of metals. In some cuprates4,5 and pnictides6, a linear dependence of resistivity on a magnetic field has also been considered anomalous—possibly an additional facet of Planckian dissipation. Here we show that the resistivity of the cuprate strange metals Nd0.4La1.6−xSrxCuO4 (ref. 7) and La2−xSrxCuO4 (ref. 8) is quantitatively consistent with the standard Boltzmann theory of electron motion in a magnetic field, in all aspects—field strength, field direction, temperature and disorder level. The linear field dependence is found to be simply the consequence of scattering rate anisotropy. We conclude that Planckian dissipation is anomalous in its temperature dependence, but not in its field dependence. The scattering rate in these cuprates does not depend on field, which means that their Planckian dissipation is robust against fields up to at least 85 T.
neuromaps: structural and functional interpretation of brain maps
Authors: Markello Ross D. , Hansen Justine Y. , Liu Zhen-Qi , Bazinet Vincent , Shafiei Golia , Suárez Laura E. , Blostein Nadia , Seidlitz Jakob , Baillet Sylvain , Satterthwaite Theodore D. , Chakravarty M. Mallar , Raznahan Armin , Misic Bratislav 
Published: October 2022

AbstractImaging technologies are increasingly used to generate high-resolution reference maps of brain structure and function. Comparing experimentally generated maps to these reference maps facilitates cross-disciplinary scientific discovery. Although recent data sharing initiatives increase the accessibility of brain maps, data are often shared in disparate coordinate systems, precluding systematic and accurate comparisons. Here we introduce neuromaps, a toolbox for accessing, transforming and analyzing structural and functional brain annotations. We implement functionalities for generating high-quality transformations between four standard coordinate systems. The toolbox includes curated reference maps and biological ontologies of the human brain, such as molecular, microstructural, electrophysiological, developmental and functional ontologies. Robust quantitative assessment of map-to-map similarity is enabled via a suite of spatial autocorrelation-preserving null models. neuromaps combines open-access data with transparent functionality for standardizing and comparing brain maps, providing a systematic workflow for comprehensive structural and functional annotation enrichment analysis of the human brain.
Rhode Island gastroenterology video capsule endoscopy data set
Authors: Charoen Amber , Guo Averill , Fangsaard Panisara , Taweechainaruemitr Supakorn , Wiwatwattana Nuwee , Charoenpong Theekapun , Rich Harlan G. 
Published: October 2022

AbstractComplete endoscopic evaluation of the small bowel is challenging due to its length and anatomy. Although several advances have been made to achieve diagnostic and therapeutic goals, including double-balloon enteroscopy, single-balloon enteroscopy, and spiral enteroscopy, video capsule endoscopy (VCE) remains the least invasive tool for complete visualization of the small bowel and is the preferred method for initial diagnostic evaluation. At present, interpretation of VCE data requires manual annotation of landmarks and abnormalities in recorded videos, which can be time consuming. Computer-assisted diagnostic systems using artificial intelligence may help to optimize VCE reading efficiency by reducing the need for manual annotation. Here we present a large VCE data set compiled from studies performed at two United States hospitals in Providence, Rhode Island, including 424 VCE studies and 5,247,588 total labeled images. In conjunction with existing published data sets, these files may aid in the development of algorithms to further improve VCE.
Dynamic gill and mucus microbiomes during a gill disease episode in farmed Atlantic salmon
Authors: Birlanga Victor B. , McCormack Grace , Ijaz Umer Z. , MacCarthy Eugene , Smith Cindy , Collins Gavin 
Published: October 2022

AbstractAmoebic gill disease (AGD) and complex gill disease (CGD) are recurrent gill disorders in Atlantic salmon, resulting in significant aquaculture losses. The role of gill microbiomes in gill disease development is unclear. We undertook a longitudinal study to characterise the gill tissue and gill mucus microbiomes of farmed Atlantic salmon before, and during, a gill disease episode. Using a newly optimised DNA extraction protocol, we sequenced rRNA genes from microbiomes of gill samples taken from 105 individual salmon on a farm, over a summer season. The AGD aetiological agent, Neoparamoeba perurans, was PCR-quantified targeting 18S rRNA genes. Similar analyses were carried out on mucus samples. Mucus scrapings were suitable, non-lethal substitutes for characterisation of the gill prokaryotic community in this study. Gill tissue and gill mucus microbiomes changed during the campaign, correlating with N. perurans concentrations. Time explained 35% of the gill tissue and gill mucus microbiome variance, while N. perurans concentrations explained 5%. Genera including Dyadobacter, Shewanella and Pedobacter were maximally abundant in gill and mucus samples at the timepoint prior to the the detection of gill disorder signs, at T3. Shewanella was significantly more abundant before than during the gill disease episode, and we suggest this genus could be considered in future studies addressing relationships between gill disease and the gill microbiome.
Atmospheric muography for imaging and monitoring tropic cyclones
Authors: Tanaka Hiroyuki K. M. , Gluyas Jon , Holma Marko , Joutsenvaara Jari , Kuusiniemi Pasi , Leone Giovanni , Lo Presti Domenico , Matsushima Jun , Oláh László , Steigerwald Sara , Thompson Lee F. , Usoskin Ilya , Poluianov Stepan , Varga Dezső , Yokota Yusuke 
Published: October 2022

AbstractLarge-scale solid bodies on Earth such as volcanoes and man-made pyramids have been visualized with solid earth muography, and the recently invented technique, acqueous muography, has already demonstrated its capability to visualize ocean tides and tsunami. In this work, atmospheric muography, a technique to visualize and monitor the vertical profile of tropic cyclones (TCs) is presented for the first time. The density distribution and time-dependent behavior of several TCs which had approached Kagoshima, Japan, has been investigated with muography. The resultant time-sequential images captured their warm cores, and their movements were consistent with the TC trails and barometric pressure variations observed at meteorological stations. By combining multidirectional muographic images with barometric data, we anticipate that muography will become a useful tool to monitor the three-dimensional density distribution of a targeted mesoscale convective system.