bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toll-like receptor 9 deficiency induces osteoclastic bone loss via gut microbiota-associated systemic chronic inflammation
Authors: Ding Peng , Tan Qiyuan , Wei Zhanying , Chen Qiyu , Wang Chun , Qi Luyue , Wen Li , Zhang Changqing , Yao Chen 
Published: May 2022

AbstractToll-like receptors (TLRs) play pivotal roles in inflammation and provide important links between the immune and skeletal systems. Although the activation of TLRs may affect osteoclast differentiation and bone metabolism, whether and how TLRs are required for normal bone remodeling remains to be fully explored. In the current study, we show for the first time that TLR9−/−mice exhibit a low bone mass and low-grade systemic chronic inflammation, which is characterized by the expansion of CD4+T cells and increased levels of inflammatory cytokines, including TNFα, RANKL, and IL1β. The increased levels of these cytokines significantly promote osteoclastogenesis and induce bone loss. Importantly, TLR9 deletion alters the gut microbiota, and this dysbiosis is the basis of the systemic inflammation and bone loss observed in TLR9−/−mice. Furthermore, through single-cell RNA sequencing, we identified myeloid-biased hematopoiesis in the bone marrow of TLR9−/−mice and determined that the increase in myelopoiesis, likely caused by the adaptation of hematopoietic stem cells to systemic inflammation, also contributes to inflammation-induced osteoclastogenesis and subsequent bone loss in TLR9−/−mice. Thus, our study provides novel evidence that TLR9 signaling connects the gut microbiota, immune system, and bone and is critical in maintaining the homeostasis of inflammation, hematopoiesis, and bone metabolism under normal conditions.
The dental demolition derby: bruxism and its impact - part 2: early management of bruxism
Authors: Thayer Mark L. T. , Ali Rahat 
Published: May 2022

AbstractBruxism is a term that encompasses a range of presentations of rhythmic and repetitive muscular activity. For many, this is not a significant problem but for some, the behaviour leads to significant problems and extensive tissue damage. This is different to temporomandibular disorders. This paper will review methods of managing cases where bruxism is destructive, or potentially destructive, before needing to resort to full reconstruction.
Identifying a novel KLF2/lncRNA SNHG12/miR-494-3p/RAD23B axis in Spare Nerve Injury-induced neuropathic pain
Authors: Zhang Jinyuan , Zhao Hanping , Zhang Aimin , Zhao Chengyi , Mei Zhi , Yao Haiyan , Fan Zhidan , Liang Daochen 
Published: May 2022

AbstractSpinal cord injury (SCI) is a devastating condition for patients, affecting nearly 2.5 million people globally. Multiple side effects of SCI have resulted in a terrible life experience for SCI patients, of which neuropathic pain has attracted the most scientific interest. Even though many efforts have been made to attenuate or eliminate neuropathic pain induced by SCI, the outcomes for patients are still poor. Therefore, identifying novel diagnosis or therapeutic targets of SCI-induced neuropathic pain is urgently needed. Recently, multiple functions of long non-coding RNA (lncRNA) have been elucidated, including those in SCI-induced neuropathic pain. In this study, lncRNA small nucleolar RNA host gene 12 (SNHG12) was found to be upregulated in the dorsal root ganglion (DRGs) of rats with spare nerve injury (SNI). By constructing SCI rat models, we found that lncRNA SNHG12 expression was increased in the DRGs, and mainly distributed in the cytoplasm of PC12 cells. Paw withdrawal threshold (PWT), paw withdrawal latency (PWL), and enzyme linked immunosorbent assay (ELISA) results indicated that lncRNA SNHG12 knockdown attenuated SNI-induced neuropathic pain, and decreased the expression levels of interleukin (IL)−1β, IL-6, and tumour necrosis factor α (TNF-α) in the DRGs. Bioinformatics analysis, RNA pull-down, chromatin immunoprecipitation (ChIP), and luciferase reporter gene assays showed that lncRNA SNHG12 regulates the RAD23 homologue B, nucleotide excision repair protein (RAD23B) expression, through targeting micro RNA (miR)−494-3p. Furthermore, the study indicated that Kruppel-Like Factor 2 (KLF2) could regulate lncRNA SNHG12 expression in PC12 cells. This study identified a novel KLF2/lncRNA SNHG12/miR-494-3p/RAD23B axis in SNI-induced neuropathic pain, which might provide a new insight for developing novel diagnosis, or therapeutic targets of SCI-induced neuropathic pain in the future.
Host genetic basis of COVID-19: from methodologies to genes
Authors: Zguro Kristina , Fallerini Chiara , Fava Francesca , Furini Simone , Renieri Alessandra 
Published: May 2022

AbstractThe COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is having a massive impact on public health, societies, and economies worldwide. Despite the ongoing vaccination program, treating COVID-19 remains a high priority; thus, a better understanding of the disease is urgently needed. Initially, susceptibility was associated with age, sex, and other prior existing comorbidities. However, as these conditions alone could not explain the highly variable clinical manifestations of SARS-CoV-2 infection, the attention was shifted toward the identification of the genetic basis of COVID-19. Thanks to international collaborations like The COVID-19 Host Genetics Initiative, it became possible the elucidation of numerous genetic markers that are not only likely to help in explaining the varied clinical outcomes of COVID-19 patients but can also guide the development of novel diagnostics and therapeutics. Within this framework, this review delineates GWAS and Burden test as traditional methodologies employed so far for the discovery of the human genetic basis of COVID-19, with particular attention to recently emerged predictive models such as the post-Mendelian model. A summary table with the main genome-wide significant genomic loci is provided. Besides, various common and rare variants identified in genes like TLR7, CFTR, ACE2, TMPRSS2, TLR3, and SELP are further described in detail to illustrate their association with disease severity.
Periodic corner holes on the Si(111)-7×7 surface can trap silver atoms
Authors: Osiecki Jacek R. , Suto Shozo , Chutia Arunabhiram 
Published: May 2022

AbstractAdvancement in nanotechnology to a large extent depends on the ability to manipulate materials at the atomistic level, including positioning single atoms on the active sites of the surfaces of interest, promoting strong chemical bonding. Here, we report a long-time confinement of a single Ag atom inside a corner hole (CH) of the technologically relevant Si(111)-7×7 surface, which has comparable size as a fullerene C60 molecule with a single dangling bond at the bottom center. Experiments reveal that a set of 17 Ag atoms stays entrapped in the CH for the entire duration of experiment, 4 days and 7 h. Warming up the surface to about 150 °C degrees forces the Ag atoms out of the CH within a few minutes. The processes of entrapment and diffusion are temperature dependent. Theoretical calculations based on density functional theory support the experimental results confirming the highest adsorption energy at the CH for the Ag atom, and suggest that other elements such as Li, Na, Cu, Au, F and I may display similar behavior. The capability of atomic manipulation at room temperature makes this effect particularly attractive for building single atom devices and possibly developing new engineering and nano-manufacturing methods.
Solution-processable microporous polymer platform for heterogenization of diverse photoredox catalysts
Authors: Liu Richard Y. , Guo Sheng , Luo Shao-Xiong Lennon , Swager Timothy M. 
Published: May 2022

AbstractIn contemporary organic synthesis, substances that access strongly oxidizing and/or reducing states upon irradiation have been exploited to facilitate powerful and unprecedented transformations. However, the implementation of light-driven reactions in large-scale processes remains uncommon, limited by the lack of general technologies for the immobilization, separation, and reuse of these diverse catalysts. Here, we report a new class of photoactive organic polymers that combine the flexibility of small-molecule dyes with the operational advantages and recyclability of solid-phase catalysts. The solubility of these polymers in select non-polar organic solvents supports their facile processing into a wide range of heterogeneous modalities. The active sites, embedded within porous microstructures, display elevated reactivity, further enhanced by the mobility of excited states and charged species within the polymers. The independent tunability of the physical and photochemical properties of these materials affords a convenient, generalizable platform for the metamorphosis of modern photoredox catalysts into active heterogeneous equivalents.
Activation of Nkx2.5 transcriptional program is required for adult myocardial repair
Authors: de Sena-Tomás Carmen , Aleman Angelika G. , Ford Caitlin , Varshney Akriti , Yao Di , Harrington Jamie K. , Saúde Leonor , Ramialison Mirana , Targoff Kimara L. 
Published: May 2022

AbstractThe cardiac developmental network has been associated with myocardial regenerative potential. However, the embryonic signals triggered following injury have yet to be fully elucidated. Nkx2.5 is a key causative transcription factor associated with human congenital heart disease and one of the earliest markers of cardiac progenitors, thus it serves as a promising candidate. Here, we show that cardiac-specific RNA-sequencing studies reveal a disrupted embryonic transcriptional profile in the adult Nkx2.5 loss-of-function myocardium. nkx2.5−/− fish exhibit an impaired ability to recover following ventricular apex amputation with diminished dedifferentiation and proliferation. Complex network analyses illuminate that Nkx2.5 is required to provoke proteolytic pathways necessary for sarcomere disassembly and to mount a proliferative response for cardiomyocyte renewal. Moreover, Nkx2.5 targets embedded in these distinct gene regulatory modules coordinate appropriate, multi-faceted injury responses. Altogether, our findings support a previously unrecognized, Nkx2.5-dependent regenerative circuit that invokes myocardial cell cycle re-entry, proteolysis, and mitochondrial metabolism to ensure effective regeneration in the teleost heart.
Automated vitrification of cryo-EM samples with controllable sample thickness using suction and real-time optical inspection
Authors: Koning Roman I. , Vader Hildo , van Nugteren Martijn , Grocutt Peter A. , Yang Wen , Renault Ludovic L. R. , Koster Abraham J. , Kamp Arnold C. F. , Schwertner Michael 
Published: May 2022

AbstractThe speed and efficiency of data collection and image processing in cryo-electron microscopy have increased over the last decade. However, cryo specimen preparation techniques have lagged and faster, more reproducible specimen preparation devices are needed. Here, we present a vitrification device with highly automated sample handling, requiring only limited user interaction. Moreover, the device allows inspection of thin films using light microscopy, since the excess liquid is removed through suction by tubes, not blotting paper. In combination with dew-point control, this enables thin film preparation in a controlled and reproducible manner. The advantage is that the quality of the prepared cryo specimen is characterized before electron microscopy data acquisition. The practicality and performance of the device are illustrated with experimental results obtained by vitrification of protein suspensions, lipid vesicles, bacterial and human cells, followed by imaged using single particle analysis, cryo-electron tomography, and cryo correlated light and electron microscopy.
ZrTe2/CrTe2: an epitaxial van der Waals platform for spintronics
Authors: Ou Yongxi , Yanez Wilson , Xiao Run , Stanley Max , Ghosh Supriya , Zheng Boyang , Jiang Wei , Huang Yu-Sheng , Pillsbury Timothy , Richardella Anthony , Liu Chaoxing , Low Tony , Crespi Vincent H. , Mkhoyan K. Andre , Samarth Nitin 
Published: May 2022

AbstractThe rapid discovery of two-dimensional (2D) van der Waals (vdW) quantum materials has led to heterostructures that integrate diverse quantum functionalities such as topological phases, magnetism, and superconductivity. In this context, the epitaxial synthesis of vdW heterostructures with well-controlled interfaces is an attractive route towards wafer-scale platforms for systematically exploring fundamental properties and fashioning proof-of-concept devices. Here, we use molecular beam epitaxy to synthesize a vdW heterostructure that interfaces two material systems of contemporary interest: a 2D ferromagnet (1T-CrTe2) and a topological semimetal (ZrTe2). We find that one unit-cell (u.c.) thick 1T-CrTe2grown epitaxially on ZrTe2is a 2D ferromagnet with a clear anomalous Hall effect. In thicker samples (12 u.c. thick CrTe2), the anomalous Hall effect has characteristics that may arise from real-space Berry curvature. Finally, in ultrathin CrTe2(3 u.c. thickness), we demonstrate current-driven magnetization switching in a full vdW topological semimetal/2D ferromagnet heterostructure device.
Single-cell RNA sequencing reveals evolution of immune landscape during glioblastoma progression
Authors: Yeo Alan T. , Rawal Shruti , Delcuze Bethany , Christofides Anthos , Atayde Agata , Strauss Laura , Balaj Leonora , Rogers Vaughn A. , Uhlmann Erik J. , Varma Hemant , Carter Bob S. , Boussiotis Vassiliki A. , Charest Al 
Published: May 2022

AbstractGlioblastoma (GBM) is an incurable primary malignant brain cancer hallmarked with a substantial protumorigenic immune component. Knowledge of the GBM immune microenvironment during tumor evolution and standard of care treatments is limited. Using single-cell transcriptomics and flow cytometry, we unveiled large-scale comprehensive longitudinal changes in immune cell composition throughout tumor progression in an epidermal growth factor receptor-driven genetic mouse GBM model. We identified subsets of proinflammatory microglia in developing GBMs and anti-inflammatory macrophages and protumorigenic myeloid-derived suppressors cells in end-stage tumors, an evolution that parallels breakdown of the blood–brain barrier and extensive growth of epidermal growth factor receptor+ GBM cells. A similar relationship was found between microglia and macrophages in patient biopsies of low-grade glioma and GBM. Temozolomide decreased the accumulation of myeloid-derived suppressor cells, whereas concomitant temozolomide irradiation increased intratumoral GranzymeB+ CD8+T cells but also increased CD4+ regulatory T cells. These results provide a comprehensive and unbiased immune cellular landscape and its evolutionary changes during GBM progression.
Downburst-like experimental impinging jet measurements at the WindEEE Dome
Authors: Canepa Federico , Burlando Massimiliano , Romanic Djordje , Solari Giovanni , Hangan Horia 
Published: May 2022

AbstractThis paper describes the dataset of measurements collected and published in the context of the comprehensive experimental campaign on downburst-like outflows that was performed at the WindEEE Dome at Western University, Canada. Downbursts are strong downdrafts of air that originate from thunderstorm clouds and create vigorous radial outflows upon hitting the ground. Downbursts are here simulated as transient phenomena produced by large-scale impinging jet. Two jet velocities were adopted in the experiments. The three-component velocity measurements were recorded using 7 Cobra probes mounted on a vertical stiff mast and displaced at 10 radial positions in respect to the downdraft centerline. For every radial position, each experiment with the same initial condition was repeated 20 times to inspect the deterministic features of the signal. Overall, the total of 2800 tests (2 jet velocities × 20 repetitions × 10 radial positions × 7 heights) represent one of the largest experimental campaigns on downburst winds carried out in a wind tunnel facility thus far.
FAIR and Interactive Data Graphics from a Scientific Knowledge Graph
Authors: Deagen Michael E. , McCusker Jamie P. , Fateye Tolulomo , Stouffer Samuel , Brinson L. Cate , McGuinness Deborah L. , Schadler Linda S. 
Published: May 2022

AbstractGraph databases capture richly linked domain knowledge by integrating heterogeneous data and metadata into a unified representation. Here, we present the use of bespoke, interactive data graphics (bar charts, scatter plots, etc.) for visual exploration of a knowledge graph. By modeling a chart as a set of metadata that describes semantic context (SPARQL query) separately from visual context (Vega-Lite specification), we leverage the high-level, declarative nature of the SPARQL and Vega-Lite grammars to concisely specify web-based, interactive data graphics synchronized to a knowledge graph. Resources with dereferenceable URIs (uniform resource identifiers) can employ the hyperlink encoding channel or image marks in Vega-Lite to amplify the information content of a given data graphic, and published charts populate a browsable gallery of the database. We discuss design considerations that arise in relation to portability, persistence, and performance. Altogether, this pairing of SPARQL and Vega-Lite—demonstrated here in the domain of polymer nanocomposite materials science—offers an extensible approach to FAIR (findable, accessible, interoperable, reusable) scientific data visualization within a knowledge graph framework.
Whales from space dataset, an annotated satellite image dataset of whales for training machine learning models
Authors: Cubaynes Hannah C. , Fretwell Peter T. 
Published: May 2022

AbstractMonitoring whales in remote areas is important for their conservation; however, using traditional survey platforms (boat and plane) in such regions is logistically difficult. The use of very high-resolution satellite imagery to survey whales, particularly in remote locations, is gaining interest and momentum. However, the development of this emerging technology relies on accurate automated systems to detect whales, which are currently lacking. Such detection systems require access to an open source library containing examples of whales annotated in satellite images to train and test automatic detection systems. Here we present a dataset of 633 annotated whale objects, created by surveying 6,300 km2 of satellite imagery captured by various very high-resolution satellites (i.e. WorldView-3, WorldView-2, GeoEye-1 and Quickbird-2) in various regions across the globe (e.g. Argentina, New Zealand, South Africa, United States, Mexico). The dataset covers four different species: southern right whale (Eubalaena australis), humpback whale (Megaptera novaeangliae), fin whale (Balaenoptera physalus), and grey whale (Eschrichtius robustus).
Differences between diaphragmatic compound muscle action potentials recorded from over the sternum and lateral chest wall in healthy subjects
Authors: Younis Gihan , El Sawy Noha , Elnemr Rehab , Madkour Doaa 
Published: May 2022

AbstractTo report normative data for diaphragmatic compound muscle action potentials (DCMAPs) recorded from over the sternum and lateral chest wall (LCW) and highlight factors that may contribute to variations in DCMAP parameters at the two sites. The phrenic nerve of seventy-three healthy subjects was bilaterally stimulated at the posterior border of the sternocleidomastoid muscle. DCMAPs from over the sternum and LCW were recorded (inspiration/expiration). Normative values of sternal and LCW DCMAPs were presented. The mean values of latency of LCW DCMAPs, duration of sternal DCMAPs and area from both recording sites are close to values reported by other studies. The mean values of latency of sternal DCMAPs are higher than that reported by other studies. Significant differences were found between sternal and LCW potentials in the mean latency, amplitude, and area (p < 0.001). The duration did not differ between the two sites. Differences were found between inspiration and expiration, right and left sides, and men and women. Regression analysis showed a relation between latency of sternal and LCW potentials and age. Latency (LCW potentials) and amplitude and area (sternal/LCW potentials) were related to gender. Amplitude (LCW potentials/inspiration) and area (sternal potentials/inspiration) were related to chest circumference (p = 0.023 and 0.013 respectively). Area (sternal potentials/expiration) was related to the BMI (p = 0.019). Our normative values for sternal and LCW DCMAPs are provided. Notable differences in the DCMAPs parameters were detected between the two recording sites, inspiration and expiration, right and left, and men and women. The technique of phrenic nerve should be standardized.
Molecular signatures written in bone proteins of 79 AD victims from Herculaneum and Pompeii
Authors: Ntasi Georgia , Palomo Ismael Rodriguez , Marino Gennaro , Piaz Fabrizio Dal , Cappellini Enrico , Birolo Leila , Petrone Pierpaolo 
Published: May 2022

AbstractAn extensive proteomic analysis was performed on a set of 12 bones of human victims of the eruption that in AD 79 rapidly buried Pompeii and Herculaneum, allowing the detection of molecular signatures imprinted in the surviving protein components. Bone collagen survived the heat of the eruption, bearing a piece of individual biological history encoded in chemical modifications. Here we show that the human bone proteomes from Pompeii are more degraded than those from the inhabitants of Herculaneum, despite the latter were exposed to temperatures much higher than those experienced in Pompeii. The analysis of the specimens from Pompeii shows lower content of non-collagenous proteins, higher deamidation level and higher extent of collagen modification. In Pompeii, the slow decomposition of victims’ soft tissues in the natural dry–wet hydrogeological soil cycles damaged their bone proteome more than what was experienced at Herculaneum by the rapid vanishing of body tissues from intense heat, under the environmental condition of a permanent waterlogged burial context. Results herein presented are the first proteomic analyses of bones exposed to eruptive conditions, but also delivered encouraging results for potential biomarkers that might also impact future development of forensic bone proteomics.