bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictability of the Chile Niño/Niña
Authors: Xue Jiaqing , Doi Takeshi , Luo Jing‐Jia , Yuan Chaoxia , Yamagata Toshio 
Published: October 2021

AbstractThe recently discovered Chile Niño/Niña is an intrinsic coupled climate mode in the southeast Pacific, which influences both regional climate and marine ecosystem. Using Scale Interaction Experiment‐Frontier version 2 seasonal prediction system, it is shown that the Chile Niño/Niña can be skillfully predicted up to 3‐month lead. Although the occurrences and related climate impacts of the Chile Niño/Niña are captured by the prediction system, the predicted magnitudes are weaker than observations in the ensemble mean. Further analyses of the inter‐member relationships indicate that the Chile Niño/Niña predictability depends on how well the coastal ocean‐atmosphere‐land positive feedback among alongshore surface winds, coastal upwelling and the sea surface temperature anomalies is captured. The insufficient reproduction of this essential feedback is responsible for the underestimated magnitude. Therefore, accurately predicting the Chile Niño/Niña remains a challenge. Improving model resolution and ensemble size may be a key to enhancing prediction skills of the coastal climate modes along the eastern boundary upwelling systems.
Lunar Tidal Effect on Equatorial Ionization Anomaly Region in China Low Latitude
Authors: Mo Xiaohua , Zhang Donghe , Liu Jing , Hao Yongqiang , Xiao Zuo , Shi Jiankui , Wang Guojun 
Published: October 2021

AbstractThe equatorial ionization anomaly (EIA) crest derived from GPS observations, F2‐layer peak height (hmF2), critical frequency (foF2), and equatorial electrojet (EEJ) in China low latitude are used to study the lunar tidal effect on EIA region for the years from 2006 to 2015. A predominant 14.76‐day periodic component in EIA crest, hmF2, and EEJ concurrently appears in some seasonal intervals, which coincides with the half of the lunar revolution period (29.53 days) and the lunar phase, indicating that the 14.76‐day periodic oscillation in EIA region is modulated by the lunar tide. This 14.76‐day periodic oscillation occurs in all Northern Hemisphere (NH) winter and corresponds to their respective sudden stratospheric warming (SSW) period from 2006 to 2015. In addition, this 14.76‐day periodic oscillation also occurs in other seasons for some years, for example, May and August, in which wave power is sometimes comparable to that in SSW period. The occurrence of the 14.76‐day periodic oscillation and its wave power during non‐SSW seasons in the solar maximum years (2012–2015) is more frequent and higher than that in the solar minimum years (2008–2010). Our results suggest that, besides the NH SSW condition, the solar activity and some other unclear factors are also responsible for the lunar tide enhancement in EIA region.
Multi-omic approach identifies a transcriptional network coupling innate immune response to proliferation in the blood of COVID-19 cancer patients
Authors: Sacconi Andrea , De Vitis Claudia , de Latouliere Luisa , di Martino Simona , De Nicola Francesca , Goeman Frauke , Mottini Carla , Paolini Francesca , D’Ascanio Michela , Ricci Alberto , Tafuri Agostino , Marchetti Paolo , Di Napoli Arianna , De Biase Luciano , Negro Andrea , Napoli Christian , Anibaldi Paolo , Salvati Valentina , Duffy Darragh , Terrier Benjamin , Fanciulli Maurizio , Capalbo Carlo , Sciacchitano Salvatore , Blandino Giovanni , Piaggio Giulia , Mancini Rita , Ciliberto Gennaro 
Published: October 2021

AbstractClinical outcomes of COVID-19 patients are worsened by the presence of co-morbidities, especially cancer leading to elevated mortality rates. SARS-CoV-2 infection is known to alter immune system homeostasis. Whether cancer patients developing COVID-19 present alterations of immune functions which might contribute to worse outcomes have so far been poorly investigated. We conducted a multi-omic analysis of immunological parameters in peripheral blood mononuclear cells (PBMCs) of COVID-19 patients with and without cancer. Healthy donors and SARS-CoV-2-negative cancer patients were also included as controls. At the infection peak, cytokine multiplex analysis of blood samples, cytometry by time of flight (CyTOF) cell population analyses, and Nanostring gene expression using Pancancer array on PBMCs were performed. We found that eight pro-inflammatory factors (IL-6, IL-8, IL-13, IL-1ra, MIP-1a, IP-10) out of 27 analyzed serum cytokines were modulated in COVID-19 patients irrespective of cancer status. Diverse subpopulations of T lymphocytes such as CD8+T, CD4+T central memory, Mucosal-associated invariant T (MAIT), natural killer (NK), and γδ T cells were reduced, while B plasmablasts were expanded in COVID-19 cancer patients. Our findings illustrate a repertoire of aberrant alterations of gene expression in circulating immune cells of COVID-19 cancer patients. A 19-gene expression signature of PBMCs is able to discriminate COVID-19 patients with and without solid cancers. Gene set enrichment analysis highlights an increased gene expression linked to Interferon α, γ, α/β response and signaling which paired with aberrant cell cycle regulation in cancer patients. Ten out of the 19 genes, validated in a real-world consecutive cohort, were specific of COVID-19 cancer patients independently from different cancer types and stages of the diseases, and useful to stratify patients in a COVID-19 disease severity-manner. We also unveil a transcriptional network involving gene regulators of both inflammation response and proliferation in PBMCs of COVID-19 cancer patients.
A missense mutation in Pitx2 leads to early-onset glaucoma via NRF2-YAP1 axis
Authors: Yang Yeming , Li Xiao , Wang Jieping , Tan Junkai , Fitzmaurice Bernie , Nishina Patsy M. , Sun Kuanxiang , Tian Wanli , Liu Wenjing , Liu Xuyang , Chang Bo , Zhu Xianjun 
Published: October 2021

AbstractGlaucoma is a leading cause of blindness, affecting 70 million people worldwide. Owing to the similarity in anatomy and physiology between human and mouse eyes and the ability to genetically manipulate mice, mouse models are an invaluable resource for studying mechanisms underlying disease phenotypes and for developing therapeutic strategies. Here, we report the discovery of a new mouse model of early-onset glaucoma that bears a transversion substitution c. G344T, which results in a missense mutation, p. R115L in PITX2. The mutation causes an elevation in intraocular pressure (IOP) and progressive death of retinal ganglion cells (RGC). These ocular phenotypes recapitulate features of pathologies observed in human glaucoma. Increased oxidative stress was evident in the inner retina. We demonstrate that the mutant PITX2 protein was not capable of binding to Nuclear factor-like 2 (NRF2), which regulates Pitx2 expression and nuclear localization, and to YAP1, which is necessary for co-initiation of transcription of downstream targets. PITX2-mediated transcription of several antioxidant genes were also impaired. Treatment with N-Acetyl-L-cysteine exerted a profound neuroprotective effect on glaucoma-associated neuropathies, presumably through inhibition of oxidative stress. Our study demonstrates that a disruption of PITX2 leads to glaucoma optic pathogenesis and provides a novel early-onset glaucoma model that will enable elucidation of mechanisms underlying the disease as well as to serve as a resource to test new therapeutic strategies.
NLRP3 associated with chronic kidney disease progression after ischemia/reperfusion-induced acute kidney injury
Authors: Zheng Zhihuang , Xu Kexin , Li Chuanlei , Qi Chenyang , Fang Yili , Zhu Nan , Bao Jinfang , Zhao Zhonghua , Yu Qing , Wu Huijuan , Liu Jun 
Published: October 2021

AbstractNod-like receptor protein 3 (NLRP3), as an inflammatory regulator, has been implicated in acute kidney injury (AKI). Failed recovery after AKI can lead to chronic kidney disease (CKD). However, the role of NLRP3 in the AKI-CKD transition is still unknown. A mild or severe AKI mouse model was performed by using ischemia-reperfusion injury (IRI). We evaluated the renal NLRP3 expression in acute and chronic phases of ischemic AKI, respectively. Although serum creatinine (Cr) and blood urea nitrogen (BUN) levels in AKI chronic phase were equivalent to normal baseline, histological analysis and fibrotic markers revealed that severe AKI-induced maladaptive tubular repair with immune cell infiltration and fibrosis. Tubular damage was restored completely in mild AKI rather than in severe AKI. Of note, persistent overexpression of NLRP3 was also found in severe AKI but not in mild AKI. In the severe AKI-induced chronic phase, there was a long-term high level of NLRP3 in serum or urine. Overt NLRP3 was mainly distributed in the abnormal tubules surrounded by inflammatory infiltrates and fibrosis, which indicated the maladaptive repair. Renal Nlrp3 overexpression was correlated with infiltrating macrophages and fibrosis. Renal NLRP3 signaling-associated genes were upregulated after severe AKI by RNA-sequencing. Furthermore, NLRP3 was found increased in renal tubular epitheliums from CKD biopsies. Together, persistent NLRP3 overexpression was associated with chronic pathological changes following AKI, which might be a new biomarker for evaluating the possibility of AKI-CKD transition.
A novel TAB2 mutation detected in a putative case of frontometaphyseal dysplasia
Authors: Hori Asuka , Migita Ohsuke , Kawaguchi-Kawata Rika , Narumi-Kishimoto Yoko , Takada Fumio , Hata Kenichiro 
Published: October 2021

AbstractFrontometaphyseal dysplasia (FMD) type 2 is an autosomal dominant disorder characterized by skeletal abnormalities and caused by MAP3K7 mutation. We identified a novel missense mutation in TAB2 associated with FMD in a child with multiple congenital malformations. This case was diagnosed as FMD due to joint contractures and bone deformities. This is the third report of FMD caused by a TAB2 mutation located in the TAK1-binding region.
The hereditary mutation G51D unlocks a distinct fibril strain transmissible to wild-type α-synuclein
Authors: Sun Yunpeng , Long Houfang , Xia Wencheng , Wang Kun , Zhang Xia , Sun Bo , Cao Qin , Zhang Yaoyang , Dai Bin , Li Dan , Liu Cong 
Published: October 2021

Abstractα-Synuclein (α-Syn) can form different fibril strains with distinct polymorphs and neuropathologies, which is associated with the clinicopathological variability in synucleinopathies. How different α-syn fibril strains are produced and selected under disease conditions remains poorly understood. In this study, we show that the hereditary mutation G51D induces α-syn to form a distinct fibril strain in vitro. The cryogenic electron microscopy (cryo-EM) structure of the G51D fibril strain was determined at 2.96 Å resolution. The G51D fibril displays a relatively small and extended serpentine fold distinct from other α-syn fibril structures. Moreover, we show by cryo-EM that wild-type (WT) α-syn can assembly into the G51D fibril strain via cross-seeding with G51D fibrils. Our study reveals a distinct structure of G51D fibril strain triggered by G51D mutation but feasibly adopted by both WT and G51D α-syn, which suggests the cross-seeding and strain selection of WT and mutant α-syn in familial Parkinson’s disease (fPD).
Robust recognition and exploratory analysis of crystal structures via Bayesian deep learning
Authors: Leitherer Andreas , Ziletti Angelo , Ghiringhelli Luca M. 
Published: October 2021

AbstractDue to their ability to recognize complex patterns, neural networks can drive a paradigm shift in the analysis of materials science data. Here, we introduce ARISE, a crystal-structure identification method based on Bayesian deep learning. As a major step forward, ARISE is robust to structural noise and can treat more than 100 crystal structures, a number that can be extended on demand. While being trained on ideal structures only, ARISE correctly characterizes strongly perturbed single- and polycrystalline systems, from both synthetic and experimental resources. The probabilistic nature of the Bayesian-deep-learning model allows to obtain principled uncertainty estimates, which are found to be correlated with crystalline order of metallic nanoparticles in electron tomography experiments. Applying unsupervised learning to the internal neural-network representations reveals grain boundaries and (unapparent) structural regions sharing easily interpretable geometrical properties. This work enables the hitherto hindered analysis of noisy atomic structural data from computations or experiments.
Clinical outcomes and cost-effectiveness of COVID-19 vaccination in South Africa
Authors: Reddy Krishna P. , Fitzmaurice Kieran P. , Scott Justine A. , Harling Guy , Lessells Richard J. , Panella Christopher , Shebl Fatma M. , Freedberg Kenneth A. , Siedner Mark J. 
Published: October 2021

AbstractLow- and middle-income countries are implementing COVID-19 vaccination strategies in light of varying vaccine efficacies and costs, supply shortages, and resource constraints. Here, we use a microsimulation model to evaluate clinical outcomes and cost-effectiveness of a COVID-19 vaccination program in South Africa. We varied vaccination coverage, pace, acceptance, effectiveness, and cost as well as epidemic dynamics. Providing vaccines to at least 40% of the population and prioritizing vaccine rollout prevented >9 million infections and >73,000 deaths and reduced costs due to fewer hospitalizations. Model results were most sensitive to assumptions about epidemic growth and prevalence of prior immunity to SARS-CoV-2, though the vaccination program still provided high value and decreased both deaths and health care costs across a wide range of assumptions. Vaccination program implementation factors, including prompt procurement, distribution, and rollout, are likely more influential than characteristics of the vaccine itself in maximizing public health benefits and economic efficiency.
Effects of surface treatments on flux tunable transmon qubits
Authors: Mergenthaler M. , Müller C. , Ganzhorn M. , Paredes S. , Müller P. , Salis G. , Adiga V. P. , Brink M. , Sandberg M. , Hertzberg J. B. , Filipp S. , Fuhrer A. 
Published: October 2021

AbstractOne of the main limitations in state-of-the art solid-state quantum processors is qubit decoherence and relaxation due to noise from adsorbates on surfaces, impurities at interfaces, and material defects. For the field to advance towards full fault-tolerant quantum computing, a better understanding of these microscopic noise sources is therefore needed. Here, we use an ultra-high vacuum package to study the impact of vacuum loading, UV-light exposure, and ion irradiation treatments on relaxation and coherence times, as well as slow parameter fluctuations of flux tunable superconducting transmon qubits. The treatments studied do not significantly impact the relaxation rate Γ1 and the echo decay rate $${{{\Gamma }}}_{2,{{{\rm{SS}}}}}^{{{{\rm{e}}}}}$$

Γ

2
,
SS

e

at the sweet spot, except for Ne ion bombardment which reduces Γ1. In contrast, flux noise parameters are improved by removing magnetic adsorbates from the chip surfaces with UV-light and NH3 treatments. Additionally, we demonstrate that SF6 ion bombardment can be used to adjust qubit frequencies in situ and post-fabrication without affecting qubit relaxation and coherence times at the sweet spot.
Systematic review and meta-analysis of preclinical studies testing mesenchymal stromal cells for traumatic brain injury
Authors: Pischiutta Francesca , Caruso Enrico , Lugo Alessandra , Cavaleiro Helena , Stocchetti Nino , Citerio Giuseppe , Salgado António , Gallus Silvano , Zanier Elisa R. 
Published: October 2021

AbstractMesenchymal stromal cells (MSCs) are widely used in preclinical models of traumatic brain injury (TBI). Results are promising in terms of neurological improvement but are hampered by wide variability in treatment responses. We made a systematic review and meta-analysis: (1) to assess the quality of evidence for MSC treatment in TBI rodent models; (2) to determine the effect size of MSCs on sensorimotor function, cognitive function, and anatomical damage; (3) to identify MSC-related and protocol-related variables associated with greater efficacy; (4) to understand whether MSC manipulations boost therapeutic efficacy. The meta-analysis included 80 studies. After TBI, MSCs improved sensorimotor and cognitive deficits and reduced anatomical damage. Stratified meta-analysis on sensorimotor outcome showed similar efficacy for different MSC sources and for syngeneic or xenogenic transplants. Efficacy was greater when MSCs were delivered in the first-week post-injury, and when implanted directly into the lesion cavity. The greatest effect size was for cells embedded in matrices or for MSC-derivatives. MSC therapy is effective in preclinical TBI models, improving sensorimotor, cognitive, and anatomical outcomes, with large effect sizes. These findings support clinical studies in TBI.
Low-dose in vivo protection and neutralization across SARS-CoV-2 variants by monoclonal antibody combinations
Authors: Dussupt Vincent , Sankhala Rajeshwer S. , Mendez-Rivera Letzibeth , Townsley Samantha M. , Schmidt Fabian , Wieczorek Lindsay , Lal Kerri G. , Donofrio Gina C. , Tran Ursula , Jackson Nathaniel D. , Zaky Weam I. , Zemil Michelle , Tritsch Sarah R. , Chen Wei-Hung , Martinez Elizabeth J. , Ahmed Aslaa , Choe Misook , Chang William C. , Hajduczki Agnes , Jian Ningbo , Peterson Caroline E. , Rees Phyllis A. , Rutkowska Magdalena , Slike Bonnie M. , Selverian Christopher N. , Swafford Isabella , Teng I-Ting , Thomas Paul V. , Zhou Tongqing , Smith Clayton J. , Currier Jeffrey R. , Kwong Peter D. , Rolland Morgane , Davidson Edgar , Doranz Benjamin J. , Mores Christopher N. , Hatziioannou Theodora , Reiley William W. , Bieniasz Paul D. , Paquin-Proulx Dominic , Gromowski Gregory D. , Polonis Victoria R. , Michael Nelson L. , Modjarrad Kayvon , Joyce M. Gordon , Krebs Shelly J. 
Published: October 2021

AbstractPrevention of viral escape and increased coverage against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern require therapeutic monoclonal antibodies (mAbs) targeting multiple sites of vulnerability on the coronavirus spike glycoprotein. Here we identify several potent neutralizing antibodies directed against either the N-terminal domain (NTD) or the receptor-binding domain (RBD) of the spike protein. Administered in combinations, these mAbs provided low-dose protection against SARS-CoV-2 infection in the K18-human angiotensin-converting enzyme 2 mouse model, using both neutralization and Fc effector antibody functions. The RBD mAb WRAIR-2125, which targets residue F486 through a unique heavy-chain and light-chain pairing, demonstrated potent neutralizing activity against all major SARS-CoV-2 variants of concern. In combination with NTD and other RBD mAbs, WRAIR-2125 also prevented viral escape. These data demonstrate that NTD/RBD mAb combinations confer potent protection, likely leveraging complementary mechanisms of viral inactivation and clearance.
Cell spinpods are a simple inexpensive suspension culture device to deliver fluid shear stress to renal proximal tubular cells
Authors: Hammond Timothy G. , Nislow Corey , Christov Ivan C. , Batuman Vecihi , Nagrani Pranay P. , Barazandeh Marjan , Upadhyay Rohit , Giaever Guri , Allen Patricia L. , Armbruster Michael , Raymond Allen , Birdsall Holly H. 
Published: October 2021

AbstractRotating forms of suspension culture allow cells to aggregate into spheroids, prevent the de-differentiating influence of 2D culture, and, perhaps most importantly of all, provide physiologically relevant, in vivo levels of shear stress. Rotating suspension culture technology has not been widely implemented, in large part because the vessels are prohibitively expensive, labor-intensive to use, and are difficult to scale for industrial applications. Our solution addresses each of these challenges in a new vessel called a cell spinpod. These small 3.5 mL capacity vessels are constructed from injection-molded thermoplastic polymer components. They contain self-sealing axial silicone rubber ports, and fluoropolymer, breathable membranes. Here we report the two-fluid modeling of the flow and stresses in cell spinpods. Cell spinpods were used to demonstrate the effect of fluid shear stress on renal cell gene expression and cellular functions, particularly membrane and xenobiotic transporters, mitochondrial function, and myeloma light chain, cisplatin and doxorubicin, toxicity. During exposure to myeloma immunoglobulin light chains, rotation increased release of clinically validated nephrotoxicity cytokine markers in a toxin-specific pattern. Addition of cisplatin or doxorubicin nephrotoxins reversed the enhanced glucose and albumin uptake induced by fluid shear stress in rotating cell spinpod cultures. Cell spinpods are a simple, inexpensive, easily automated culture device that enhances cellular functions for in vitro studies of nephrotoxicity.
The interaction between daylight and fifteenth and sixteenth century glass windows from the Low Countries
Authors: Meulebroeck Wendy , Nys Karin , Patin Mathilde , Thienpont Hugo 
Published: October 2021

AbstractThe positive impact of daylight on various forms of life is well understood. The daylight conditions a person experiences inside a building strongly depend on the character of the glazing. Contemporary windows maximize the transmission of visible daylight. In post-medieval times glassmakers were confronted with less pure materials. Driven by the Reformation and Counter-Reformation they were at the same time challenged by the demand for increased daylight. Luckily, technological evolutions allowed the production of thinner windows. It is currently an open question if glassmakers in the (Southern) Low Countries during the booming economic period from the fifteenth to seventeenth century made use of the interplay between material and fabrication properties to bring light into the darkness. Therefore, this paper links the impact of glass purity and production technique to light transmission for a well-diagnosed group of excavated glass window pieces from the castle of Middelburg-in-Flanders and a set of roundels, all dating back to between the fifteenth and seventeenth centuries and explores what factors have influenced this technological improvement. A non-destructive approach making use of UV–vis–NIR absorption spectroscopy unveiled that the more recent material is less pure compared to the older dated material but that light transmission was maximized due to the applied production technique.