bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ordovician–Silurian true polar wander as a mechanism for severe glaciation and mass extinction
Authors: Jing Xianqing , Yang Zhenyu , Mitchell Ross N. , Tong Yabo , Zhu Min , Wan Bo 
Published: December 2022

AbstractThe Ordovician–Silurian transition experienced severe, but enigmatic, glaciation, as well as a paradoxical combination of mass extinction and species origination. Here we report a large and fast true polar wander (TPW) event that occurred 450–440 million years ago based on palaeomagnetic data from South China and compiled reliable palaeopoles from all major continents. Collectively, a ~50˚ wholesale rotation with maximum continental speeds of ~55 cm yr−1 is demonstrated. Multiple isolated continents moving rapidly, synchronously, and unidirectionally is less consistent with and plausible for relative plate motions than TPW. Palaeogeographic reconstructions constrained by TPW controlling for palaeolongitude explain the timing and migration of glacial centers across Gondwana, as well as the protracted end-Ordovician mass extinction. The global quadrature pattern of latitude change during TPW further explains why the extinction was accompanied by elevated levels of origination as some continents migrated into or remained in the amenable tropics.
Transcriptional reprogramming from innate immune functions to a pro-thrombotic signature by monocytes in COVID-19
Authors: Maher Allison K. , Burnham Katie L. , Jones Emma M. , Tan Michelle M. H. , Saputil Rocel C. , Baillon Laury , Selck Claudia , Giang Nicolas , Argüello Rafael , Pillay Clio , Thorley Emma , Short Charlotte-Eve , Quinlan Rachael , Barclay Wendy S. , Cooper Nichola , Taylor Graham P. , Davenport Emma E. , Dominguez-Villar Margarita 
Published: December 2022

AbstractAlthough alterations in myeloid cells have been observed in COVID-19, the specific underlying mechanisms are not completely understood. Here, we examine the function of classical CD14+monocytes in patients with mild and moderate COVID-19 during the acute phase of infection and in healthy individuals. Monocytes from COVID-19 patients display altered expression of cell surface receptors and a dysfunctional metabolic profile that distinguish them from healthy monocytes. Secondary pathogen sensing ex vivo leads to defects in pro-inflammatory cytokine and type-I IFN production in moderate COVID-19 cases, together with defects in glycolysis. COVID-19 monocytes switch their gene expression profile from canonical innate immune to pro-thrombotic signatures and are functionally pro-thrombotic, both at baseline and following ex vivo stimulation with SARS-CoV-2. Transcriptionally, COVID-19 monocytes are characterized by enrichment of pathways involved in hemostasis, immunothrombosis, platelet aggregation and other accessory pathways to platelet activation and clot formation. These results identify a potential mechanism by which monocyte dysfunction may contribute to COVID-19 pathology.
Deformation characteristics of solid-state benzene as a step towards understanding planetary geology
Authors: Zhang Wenxin , Zhang Xuan , Edwards Bryce W. , Zhong Lei , Gao Huajian , Malaska Michael J. , Hodyss Robert , Greer Julia R. 
Published: December 2022

AbstractSmall organic molecules, like ethane and benzene, are ubiquitous in the atmosphere and surface of Saturn’s largest moon Titan, forming plains, dunes, canyons, and other surface features. Understanding Titan’s dynamic geology and designing future landing missions requires sufficient knowledge of the mechanical characteristics of these solid-state organic minerals, which is currently lacking. To understand the deformation and mechanical properties of a representative solid organic material at space-relevant temperatures, we freeze liquid micro-droplets of benzene to form ~10 μm-tall single-crystalline pyramids and uniaxially compress them in situ. These micromechanical experiments reveal contact pressures decaying from ~2 to ~0.5 GPa after ~1 μm-reduction in pyramid height. The deformation occurs via a series of stochastic (~5-30 nm) displacement bursts, corresponding to densification and stiffening of the compressed material during cyclic loading to progressively higher loads. Molecular dynamics simulations reveal predominantly plastic deformation and densified region formation by the re-orientation and interplanar shear of benzene rings, providing a two-step stiffening mechanism. This work demonstrates the feasibility of in-situ cryogenic nanomechanical characterization of solid organics as a pathway to gain insights into the geophysics of planetary bodies.
A pH-responsive T1-T2 dual-modal MRI contrast agent for cancer imaging
Authors: Lu Hongwei , Chen An , Zhang Xindan , Wei Zixiang , Cao Rong , Zhu Yi , Lu Jingxiong , Wang Zhongling , Tian Leilei 
Published: December 2022

AbstractMagnetic resonance imaging (MRI) is a non-invasive imaging technology to diagnose health conditions, showing the weakness of low sensitivity. Herein, we synthesize a contrast agent, SPIO@SiO2@MnO2, which shows decreased T1 and T2 contrast intensity in normal physiological conditions. In the acid environment of tumor or inflamed tissue, the manganese dioxide (MnO2) layer decomposes into magnetically active Mn2+ (T1-weighted), and the T1 and T2 signals are sequentially recovered. In addition, both constrast quenching-activation degrees of T1 and T2 images can be accurately regulated by the silicon dioxide (SiO2) intermediate layer between superparamagnetic iron oxide (SPIO) and MnO2. Through the “dual-contrast enhanced subtraction” imaging processing technique, the contrast sensitivity of this MRI contrast agent is enhanced to a 12.3-time difference between diseased and normal tissue. Consequently, SPIO@SiO2@MnO2 is successfully applied to trace the tiny liver metastases of approximately 0.5 mm and monitor tissue inflammation.
Diverse monogenic subforms of human spermatogenic failure
Authors: Nagirnaja Liina , Lopes Alexandra M. , Charng Wu-Lin , Miller Brian , Stakaitis Rytis , Golubickaite Ieva , Stendahl Alexandra , Luan Tianpengcheng , Friedrich Corinna , Mahyari Eisa , Fadial Eloise , Kasak Laura , Vigh-Conrad Katinka , Oud Manon S. , Xavier Miguel J. , Cheers Samuel R. , James Emma R. , Guo Jingtao , Jenkins Timothy G. , Riera-Escamilla Antoni , Barros Alberto , Carvalho Filipa , Fernandes Susana , Gonçalves João , Gurnett Christina A. , Jørgensen Niels , Jezek Davor , Jungheim Emily S. , Kliesch Sabine , McLachlan Robert I. , Omurtag Kenan R. , Pilatz Adrian , Sandlow Jay I. , Smith James , Eisenberg Michael L. , Hotaling James M. , Jarvi Keith A. , Punab Margus , Rajpert-De Meyts Ewa , Carrell Douglas T. , Krausz Csilla , Laan Maris , O’Bryan Moira K. , Schlegel Peter N. , Tüttelmann Frank , Veltman Joris A. , Almstrup Kristian , Aston Kenneth I. , Conrad Donald F. 
Published: December 2022

AbstractNon-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable. Defining the genetic basis of NOA has proven challenging, and the most advanced classification of NOA subforms is not based on genetics, but simple description of testis histology. In this study, we exome-sequenced over 1000 clinically diagnosed NOA cases and identified a plausible recessive Mendelian cause in 20%. We find further support for 21 genes in a 2-stage burden test with 2072 cases and 11,587 fertile controls. The disrupted genes are primarily on the autosomes, enriched for undescribed human “knockouts”, and, for the most part, have yet to be linked to a Mendelian trait. Integration with single-cell RNA sequencing data shows that azoospermia genes can be grouped into molecular subforms with synchronized expression patterns, and analogs of these subforms exist in mice. This analysis framework identifies groups of genes with known roles in spermatogenesis but also reveals unrecognized subforms, such as a set of genes expressed across mitotic divisions of differentiating spermatogonia. Our findings highlight NOA as an understudied Mendelian disorder and provide a conceptual structure for organizing the complex genetics of male infertility, which may provide a rational basis for disease classification.
Constraints on the martian crust away from the InSight landing site
Authors: Li Jiaqi , Beghein Caroline , McLennan Scott M. , Horleston Anna C. , Charalambous Constantinos , Huang Quancheng , Zenhäusern Géraldine , Bozdağ Ebru , Pike W. T. , Golombek Matthew , Lekić Vedran , Lognonné Philippe , Bruce Banerdt W. 
Published: December 2022

AbstractThe most distant marsquake recorded so far by the InSight seismometer occurred at an epicentral distance of 146.3 ± 6.9o, close to the western end of Valles Marineris. On the seismogram of this event, we have identified seismic wave precursors, i.e., underside reflections off a subsurface discontinuity halfway between the marsquake and the instrument, which directly constrain the crustal structure away (about 4100−4500 km) from the InSight landing site. Here we show that the Martian crust at the bounce point between the lander and the marsquake is characterized by a discontinuity at about 20 km depth, similar to the second (deeper) intra-crustal interface seen beneath the InSight landing site. We propose that this 20-km interface, first discovered beneath the lander, is not a local geological structure but likely a regional or global feature, and is consistent with a transition from porous to non-porous Martian crustal materials.
Permafrost in the Cretaceous supergreenhouse
Authors: Rodríguez-López Juan Pedro , Wu Chihua , Vishnivetskaya Tatiana A. , Murton Julian B. , Tang Wenqiang , Ma Chao 
Published: December 2022

AbstractEarth’s climate during the last 4.6 billion years has changed repeatedly between cold (icehouse) and warm (greenhouse) conditions. The hottest conditions (supergreenhouse) are widely assumed to have lacked an active cryosphere. Here we show that during the archetypal supergreenhouse Cretaceous Earth, an active cryosphere with permafrost existed in Chinese plateau deserts (astrochonological age ca. 132.49–132.17 Ma), and that a modern analogue for these plateau cryospheric conditions is the aeolian–permafrost system we report from the Qiongkuai Lebashi Lake area, Xinjiang Uygur Autonomous Region, China. Significantly, Cretaceous plateau permafrost was coeval with largely marine cryospheric indicators in the Arctic and Australia, indicating a strong coupling of the ocean–atmosphere system. The Cretaceous permafrost contained a rich microbiome at subtropical palaeolatitude and 3–4 km palaeoaltitude, analogous to recent permafrost in the western Himalayas. A mindset of persistent ice-free greenhouse conditions during the Cretaceous has stifled consideration of permafrost thaw as a contributor of C and nutrients to the palaeo-oceans and palaeo-atmosphere.
Altered sulfation status of FAM20C-dependent chondroitin sulfate is associated with osteosclerotic bone dysplasia
Authors: Koike Toshiyasu , Mikami Tadahisa , Tamura Jun-Ichi , Kitagawa Hiroshi 
Published: December 2022

AbstractRaine syndrome, a lethal osteosclerotic bone dysplasia in humans, is caused by loss-of-function mutations in FAM20C; however, Fam20c deficiency in mice does not recapitulate the human disorder, so the underlying pathoetiological mechanisms remain poorly understood. Here we show that FAM20C, in addition to the reported casein kinase activity, also fine-tunes the biosynthesis of chondroitin sulfate (CS) chains to impact bone homeostasis. Specifically, FAM20C with Raine-originated mutations loses the ability to interact with chondroitin 4-O-sulfotransferase-1, and is associated with reduced 4-sulfation/6-sulfation (4S/6S) ratio of CS chains and upregulated biomineralization in human osteosarcoma cells. By contrast, overexpressing chondroitin 6-O-sulfotransferase-1 reduces CS 4S/6S ratio, and induces osteoblast differentiation in vitro and higher bone mineral density in transgenic mice. Meanwhile, a potential xylose kinase activity of FAM20C does not impact CS 4S/6S ratio, and is not associated with Raine syndrome mutations. Our results thus implicate CS 4S/6S ratio imbalances caused by FAM20C mutations as a contributor of Raine syndrome etiology.
Observation of enhanced nanoscale creep flow of crystalline metals enabled by controlling surface wettability
Authors: Xiang Jun-Xiang , Liu Ze 
Published: December 2022

AbstractUnderstanding and controlling interface friction are central to many science and engineering applications. However, frictional sliding is closely related to adhesion, surface roughness, surface chemistry, mechanical deformation of contact solids, which poses the major challenge to experimental studying and theoretical modeling of friction. Here, by exploiting the recent developed thermomechanical nanomolding technique, we present a simple strategy to decouple the interplay between surface chemistry, plastic deformation, and interface friction by monitoring the nanoscale creep flow of metals in nanochannels. We show that superhydrophobic nanochannels outperforming hydrophilic nanochannels can be up to orders of magnitude in terms of creep flow rate. The comparative experimental study on pressure and temperature dependent nanomolding efficiency uncovers that the enhanced creep flow rate originates from diffusion-based deformation mechanism as well as the superhydrophobic surface induced boundary slip. Moreover, our results reveal that there exists a temperature-dependent critical pressure below which the traditional lubrication methods to reduce friction will break down. Our findings not only provide insights into the understanding of mechanical deformation and nanotribology, but also show a general and practical technique for studying the fundamental processes of frictional motion. Finally, we anticipate that the increased molding efficiency could facilitate the application of nanoimprinting/nanomolding.
Arabidopsis γ-H2A.X-INTERACTING PROTEIN participates in DNA damage response and safeguards chromatin stability
Authors: Fan Tianyi , Kang Huijia , Wu Di , Zhu Xinyu , Huang Lin , Wu Jiabing , Zhu Yan 
Published: December 2022

AbstractUpon the occurrence of DNA double strand breaks (DSB), the proximal histone variant H2A.X is phosphorylated as γ-H2A.X, a critical signal for consequent DSB signaling and repair pathways. Although γ-H2A.X-triggered DNA damage response (DDR) has been well-characterized in yeast and animals, the corresponding pathways in plant DDR are less well understood. Here, we show that an Arabidopsis protein γ-H2A.X-INTERACTING PROTEIN (XIP) can interact with γ-H2A.X. Its C-terminal dual-BRCT-like domain contributes to its specific interaction with γ-H2A.X. XIP-deficient seedlings display smaller meristems, inhibited growth, and higher sensitivity to DSB-inducing treatment. Loss-of-function in XIP causes transcriptome changes mimicking wild-type plants subject to replicative or genotoxic stresses. After genotoxic bleomycin treatment, more proteins with upregulated phosphorylation modifications, more DNA fragments and cell death were found in xip mutants. Moreover, XIP physically interacts with RAD51, the key recombinase in homologous recombination (HR), and somatic HR frequency is significantly reduced in xip mutants. Collectively, XIP participates in plant response to DSB and contributes to chromatin stability.
Large-scale genotyping and phenotyping of a worldwide winter wheat genebank for its use in pre-breeding
Authors: Schulthess Albert W. , Kale Sandip M. , Zhao Yusheng , Gogna Abhishek , Rembe Maximilian , Philipp Norman , Liu Fang , Beukert Ulrike , Serfling Albrecht , Himmelbach Axel , Oppermann Markus , Weise Stephan , Boeven Philipp H. G. , Schacht Johannes , Longin C. Friedrich H. , Kollers Sonja , Pfeiffer Nina , Korzun Viktor , Fiebig Anne , Schüler Danuta , Lange Matthias , Scholz Uwe , Stein Nils , Mascher Martin , Reif Jochen C. 
Published: December 2022

AbstractPlant genetic resources (PGR) stored at genebanks are humanity’s crop diversity savings for the future. Information on PGR contrasted with modern cultivars is key to select PGR parents for pre-breeding. Genotyping-by-sequencing was performed for 7,745 winter wheat PGR samples from the German Federal ex situ genebank at IPK Gatersleben and for 325 modern cultivars. Whole-genome shotgun sequencing was carried out for 446 diverse PGR samples and 322 modern cultivars and lines. In 19 field trials, 7,683 PGR and 232 elite cultivars were characterized for resistance to yellow rust - one of the major threats to wheat worldwide. Yield breeding values of 707 PGR were estimated using hybrid crosses with 36 cultivars - an approach that reduces the lack of agronomic adaptation of PGR and provides better estimates of their contribution to yield breeding. Cross-validations support the interoperability between genomic and phenotypic data. The here presented data are a stepping stone to unlock the functional variation of PGR for European pre-breeding and are the basis for future breeding and research activities.
Trends of kidney cancer burden from 1990 to 2019 in European Union 15 + countries and World Health Organization regions
Authors: Jani Chinmay , Abdallah Nour , Mouchati Christian , Jani Ruchi , Sharma Rajesh , Bhatt Padmanabh , Hanbury Georgina , Salciccioli Justin , Singh Harpreet , Shalhoub Joseph , McKay Rana R. , Marshall Dominic C. 
Published: December 2022

AbstractIn recent decades, variability in the incidence and mortality of kidney cancer (KC) has been reported. This study aimed to compare trends in incidence, mortality, and disability-adjusted life years (DALY) of KC between the European Union (EU) 15 + countries and 6 World Health Organization (WHO) regions. The data of KC Age-standardized incidence rates (ASIRs), age-standardized mortality rates (ASMRs), and age-standardized DALYs were extracted from the Global Burden of Disease database. Joinpoint regression was employed to examine trends. From 1990 to 2019, the ASIR increased in most countries except for Luxembourg (males), the USA (females) and Austria and Sweden (both sexes). ASIR increased across all 6 WHO regions for both sexes except for females in Americas. The ASMR increased in 10/19 countries for males and 9/19 for females as well across most WHO regions. The mortality-to-incidence ratio (MIR) decreased in all countries and WHO regions. Trends in DALYs were variable across countries and WHO regions. While the incidence and mortality from KC rose in most EU15 + countries and WHO regions from 1990 to 2019, the universal drop in MIR suggests an overall improvement in KC outcomes. This is likely multifactorial, including earlier detection of KC and improved treatments.
Longitudinal change of reticular pseudodrusen area in ultrawide-field imaging
Authors: Yoon Je Moon , Choi Young Joo , Ham Don-Il 
Published: December 2022

AbstractThis study aimed to investigate the longitudinal change in the reticular pseudodrusen (RPD) area in the fundus and its association with late age-related macular degeneration (AMD). 91 RPD eyes (55 patients; age 67.9 ± 7.3 years) with > 5 years’ follow-up (6.8 ± 0.9 years) from a single medical center were enrolled. Ultrawide-field photography images were analyzed using the concentric rings method, and the RPD area was semi-quantitatively classified according to the affected segment number into central, intermediate, and extensive types. Correlations of longitudinal changes in the RPD area and late AMD risk were investigated. RPD area increased significantly during the follow-up (p < 0.001). The increase rate correlated with age (r = 0.207; p = 0.048), RPD area at first visit (r = − 0.222; p = 0.035), and the decrease rate of subfoveal choroidal thickness (SFCT) (r = 0.217; p = 0.039). Many central (18/49, 36.7%) and intermediate (15/23, 65.2%) types switched to the more advanced type during the follow-up. Macular neovascularization and geographic atrophy developed in 12.3% and 18.7% of patients by 7 years. Late AMD incidence was significantly higher in eyes with large than in those with small RPD areas (p = 0.002). Larger RPD area at baseline, faster increase in RPD area, thinner SFCT, rapid decrease in SFCT, and the presence of late AMD on fellow eye were associated with late AMD. All RPD areas progressively increase over time. The regular assessment of RPD area may help to predict late AMD risk in RPD eyes.
Brain parenchymal and leptomeningeal metastasis in non-small cell lung cancer
Authors: Li Qing , Lin Zhen , Hong Ye , Fu Yang , Chen Yueyun , Liu Ting , Zheng Yue , Tian Jiangfang , Liu Chunhua , Pu Wei , Ding Zhenyu , Wang Chun 
Published: December 2022

AbstractPatients with advanced non-small cell lung cancer (NSCLC) are prone to brain metastases (BM), which essentially include brain parenchymal metastases (PM) and leptomeningeal metastases (LM). We conducted a retrospective study to comprehensively assess the clinical characteristics and risk factors of patients with advanced NSCLC who develop PM and LM. Patients with advanced NSCLC were enrolled. These patients were then divided into three groups for analysis: patients without BM (No-BM), patients with PM and patients with LM. Data on clinical characteristics of each patient at the time of diagnosis advanced NSCLC were extracted and analyzed. In addition, prediction models were developed and evaluated for PM and LM. A total of 592 patients were enrolled in the study. BM was present in 287 patients (48.5%). Among them, 185 and 102 patients had PM or LM. Patients with LM had a higher proportion of EGFR exon 21point mutations (L858R) compared to patients with No-BM and PM (p < 0.0001). The median time to the onset of PM and LM from the diagnosis of advanced NSCLC was 0 months and 8.3 months, respectively. Patients with LM had a statistically shorter over survival (OS) compared to either No-BM or PM patients (p < 0.0001). Based on independent predictive variables, two nomogram models were constructed to predict the development of PM and LM in advanced NSCLC patients, and the C-indexes were 0.656 and 0.767, respectively. Although both considered as BM, PM and LM had different clinical characteristics. And the nomogram showed good performance in predicting LM development, but not PM.
Spatially structured multi-wave-mixing induced nonlinear absorption and gain in a semiconductor quantum well
Authors: Panchadhyayee Pradipta , Dutta Bibhas Kumar 
Published: December 2022

AbstractWe have studied two-dimensional absorption and gain spectrum in an asymmetric semiconductor triple-coupled-quantum-well (TCQW) nanostructure. Four subband transitions are coupled by using four coherent fields in a close-loop configuration to introduce cross-Kerr effect and four-wave-mixing (FWM) induced nonlinearity in achieving nonlinear absorption and gain profiles. Position-dependent absorption and gain are obtained by applying one, or two coherent fields in a variety of standing wave configurations including superposed field configuration in the standing-wave regime. In addition to the control parameters like Rabi frequency and detuning, the specialty of the model is to employ double-controlled spatial phase-coherence guided by the FWM-induced phase and the phases introduced by the standing wave formation. Our results highlight the high-precision electron localization in spatial domain. The evolution of spatially modulated gain without inversion may be a substitute for obtaining gain from a traditional quantum cascade laser. The importance of the present work is to find its application in designing electro-optic modulators in semiconductor nanostructures in near future.