bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying the Importance of Soil‐Forming Factors Using Multivariate Soil Data at Landscape Scale
Authors: Eger A. , Koele N. , Caspari T. , Poggio M. , Kumar K. , Burge O. R. 
Published: July 2021

AbstractThe role of soil‐forming factors (time, parent material, climate, biota, and topography) on soil processes has commonly been studied using soil sequences where only one factor varies between sites. However, when multiple factors change, it becomes difficult to partition the importance of different soil‐forming factors for soil formation. We show for an altitudinal gradient how proximal sensing (portable XRF, Fourier‐Transform Infrared [FTIR]), multivariate statistics, and Bayesian mixing modeling can help to quantify the importance of two soil‐forming factors. First, we confirmed the existing qualitative soil‐landscape model of concomitant shifts in parent material (greywacke loess to mafic volcanics) and climate (higher precipitation) with altitude, leading to increases in pedogenic oxides, soil carbon, and soil Fe, while Si concentrations and pH declined. Second, we applied a mixing model using immobile elements as parent material tracers to quantify the parent material contribution in soils across our gradient. Third, we conducted a variation analysis to determine how much variation in the soil FTIR spectra could be explained by parent material and climate. We found that parent material explained a larger proportion of the variation than climate. However, because of the strong spatial correlation between climate and parent material, a large proportion of the variation in the FTIR data could be explained by either parent material or climate, potentially concealing the leading role of parent material. Given that parent material is often omitted in modern digital soil mapping, our results emphasize the importance of parent material as a predictor of spatial soil distribution.
Inverse Analysis of Experimental Scale Turbidity Currents Using Deep Learning Neural Networks
Authors: Cai Zhirong , Naruse Hajime 
Published: July 2021

AbstractDespite the importance of turbidity currents in environmental and resource geology, their flow conditions and mechanisms are not well understood. This study proposes and verifies a novel method for the inverse analysis of turbidity currents using a deep learning neural network (DNN) with numerical and flume experiment data sets. Numerical data sets of turbidites were generated with a forward model. Then, the DNN model was trained to find the functional relationship between flow conditions and turbidites by processing the numerical data sets. The performance of the trained DNN model was evaluated with 2,000 numerical test data sets and five experiment data sets. Inverse analysis results on numerical test data sets indicated that flow conditions can be reconstructed from depositional characteristics of turbidites. For experimental turbidites, spatial distributions of grain size and thickness were consistent with the sample values. Concerning hydraulic conditions, flow depth, layer‐averaged velocity, and flow duration were reconstructed with a certain level of deviation. The reconstructed flow depth and duration had percent errors less than 36.0% except for one experiment, which had an error of 193% in flow duration. The flow velocity was reconstructed with percent errors 2.38%–73.7%. Greater discrepancies between the measured and reconstructed values of flow concentration (1.79%–300%) were observed relative to the former three parameters, which may be attributed to difficulties in measuring the flow concentration during experiments. Although the DNN model did not provide perfect reconstruction, it proved to be a significant advance for the inverse analysis of turbidity currents.
Storm‐Scale and Seasonal Dynamics of Carbon Export From a Nested Subarctic Watershed Underlain by Permafrost
Authors: Koch Joshua C. , Dornblaser Mark M. , Striegl Robert G. 
Published: July 2021

AbstractSubarctic catchments underlain by permafrost sequester a major stock of frozen organic carbon (C), which may be mobilized as the Arctic warms. Warming can impact C export from thawing soils by altering the depth and timing of runoff related to changing storm and fire regimes and altered soil thaw depths. We investigated C export in a first order headwater stream (West Twin Creek) and its receiving third order river (Beaver Creek) in interior Alaska using discrete sampling of dissolved organic and inorganic C (DOC and DIC) and 15‐min collection of specific conductance (SC), fluorescent dissolved organic matter (fDOM) and water discharge (Q). Storm SC‐Q relationships displayed negative slopes, indicating solute limitation and limited influence of seasonal soil thaw on storm runoff chemistry. Concurrently, fDOM‐Q displayed positive slopes that decreased over the summer, indicating flushing of a limited fDOM pool. Baseflow DIC increased over the season concurrent with soil thaw, with higher DIC at the larger scale indicating greater influence of deeper, mineral‐rich flow paths. Storm and seasonal trends were generally similar at both scales. The biggest difference was in fDOM, which displayed higher concentrations and slower depletion in the first order stream. Improved process understanding from this study can be used to better predict carbon export and cycling by stream networks as northern forests and arctic regions continue to warm.
Region-specific elevations of glutamate + glutamine correlate with the sensory symptoms of autism spectrum disorders
Authors: He Jason L. , Oeltzschner Georg , Mikkelsen Mark , Deronda Alyssa , Harris Ashley D. , Crocetti Deana , Wodka Ericka L. , Mostofsky Stewart H. , Edden Richard A. E. , Puts Nicolaas A. J. 
Published: July 2021

AbstractIndividuals on the autism spectrum are often reported as being hyper- and/or hyporeactive to sensory input. These sensory symptoms were one of the key observations that led to the development of the altered excitation-inhibition (E-I) model of autism, which posits that an increase ratio of excitatory to inhibitory signaling may explain certain phenotypical expressions of autism spectrum disorders (ASD). While there has been strong support for the altered E-I model of autism, much of the evidence has come from animal models. With regard to in-vivo human studies, evidence for altered E-I balance in ASD come from studies adopting magnetic resonance spectroscopy (MRS). Spectral-edited MRS can be used to provide measures of the levels of GABA + (GABA + macromolecules) and Glx (glutamate + glutamine) in specific brain regions as proxy markers of inhibition and excitation respectively. In the current study, we found region-specific elevations of Glx in the primary sensorimotor cortex (SM1) in ASD. There were no group differences of GABA+ in either the SM1 or thalamus. Higher levels of Glx were associated with more parent reported difficulties of sensory hyper- and hyporeactivity, as well as reduced feed-forward inhibition during tactile perception in children with ASD. Critically, the finding of elevated Glx provides strong empirical support for increased excitation in ASD. Our results also provide a clear link between Glx and the sensory symptoms of ASD at both behavioral and perceptual levels.
EGR2-mediated regulation of m6A reader IGF2BP proteins drive RCC tumorigenesis and metastasis via enhancing S1PR3 mRNA stabilization
Authors: Ying Yufan , Ma Xueyou , Fang Jiajie , Chen Shiming , Wang Weiyu , Li Jiangfeng , Xie Haiyun , Wu Jian , Xie Bo , Liu Ben , Wang Xiao , Zheng Xiangyi , Xie Liping 
Published: July 2021

AbstractEmerging discoveries of dynamic and reversible N6-methyladenosine (m6A) modification on RNA in mammals have revealed the key roles of the modification in human tumorigenesis. As known m6A readers, insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) are upregulated in most cancers and mediates the enhancement of m6A-modified mRNAs stability. However, the mechanisms of IGF2BPs in renal cell cancer (RCC) still remain unclear. Bioinformatic analysis and RT-qPCR were performed to evaluate the expression of IGF2BPs and m6A writer Wilms tumor 1-associating protein (WTAP) in RCC samples and its correlation with patient prognosis. In vitro, in vivo biological assays were performed to investigate the functions of IGF2BPs and WTAP in RCC. Chromatin immunoprecipitation-qPCR (ChIP-qPCR) combined with bioinformatics analysis and following western blot assay, dual-luciferase reporter assays were performed to validate the regulatory relationships between transcription factor (TF) early growth response 2 (EGR2) and potential target genes IGF2BPs. RNA sequencing (RNA-seq), methylated RNA immunoprecipitation-qPCR (MERIP-qPCR), RIP-qPCR, m6A dot blot, and dual-luciferase reporter assays combined with bioinformatics analysis were employed to screen and validate the direct targets of IGF2BPs and WTAP. Here, we showed that early growth response 2 (EGR2) transcription factor could increase IGF2BPs expression in RCC. IGF2BPs in turn regulated sphingosine-1-phosphate receptor 3 (S1PR3) expression in an m6A-dependent manner by enhancing the stability of S1PR3 mRNA. They also promoted kidney tumorigenesis via PI3K/AKT pathway. Furthermore, IGF2BPs and WTAP upregulation predicted poor overall survival in RCC. Our studies showed that the EGR2/IGF2BPs regulatory axis and m6A-dependent regulation of S1PR3-driven RCC tumorigenesis, which enrich the m6A-modulated regulatory network in renal cell cancer. Together, our findings provide new evidence for the role of N6-methyladenosine modification in RCC.
Patient reported psychosocial functioning following successful ptosis surgery
Authors: Richards H. S. , Jenkinson E. , White P. , Harrad R. A. 
Published: July 2021

Abstract
Background
Ptosis may result in increased anxiety, appearance-related distress and social avoidance, and impacts visual function. Previous work demonstrates the benefits of ptosis surgery for health-related quality of life, but there is a paucity of research comparing such outcomes before and after surgery. The aim of this study was to determine potential patient benefits in health-related quality of life, social dysfunction and anxiety following successful ptosis surgery using validated measures.

Methods
Adult ptosis correction surgery patients completed validated measures of appearance-related social anxiety and avoidance, anxiety and depression, and fear of negative evaluation pre-surgery. Following successful surgery, these measures were repeated post-discharge in addition to another health-related quality of life measure.

Results
Of 61 patients recruited, follow-up measures were sent to 33 and completed by 23. Paired samples t-tests demonstrated positive significant changes in appearance-related social distress pre-op m = 30.94, post-op m = 23.67 (t(17) = 3.46, 95% CI 2.84–11.72, p = 0.003), anxiety pre-op m = 7.6, post-op m = 4.9 (t(19) = 4.27, 95% CI 1.38–4.02, p < 0.001) and fear of negative evaluation pre-op m = 34.79, post-op m = 31.26 (t(18) = 2.47, 95% CI 0.52–6.53, p = 0.024). There was no significant difference in depression scores pre-op m = 3.6; post-op m = 3.2 (t(19) = 0.672, 65% CL −0.85 to 1.65, p = 0.510). In total, 85% of patients reported positive benefit to well-being following surgery.

Conclusion
Increasingly, evidence suggests ptosis surgery may benefit patient’s well-being, appearance-related social anxiety and avoidance, as well as improving visual function. These psychosocial benefits should be considered alongside functional benefits in the provision of ptosis surgery.
Pseudomonas aeruginosa PA14 produces R-bodies, extendable protein polymers with roles in host colonization and virulence
Authors: Wang Bryan , Lin Yu-Cheng , Vasquez-Rifo Alejandro , Jo Jeanyoung , Price-Whelan Alexa , McDonald Shujuan Tao , Brown Lewis M. , Sieben Christian , Dietrich Lars E. P. 
Published: July 2021

AbstractR-bodies are long, extendable protein polymers formed in the cytoplasm of some bacteria; they are best known for their role in killing of paramecia by bacterial endosymbionts. Pseudomonas aeruginosa PA14, an opportunistic pathogen of diverse hosts, contains genes (referred to as the reb cluster) with potential to confer production of R-bodies and that have been implicated in virulence. Here, we show that products of the PA14 reb cluster associate with R-bodies and control stochastic expression of R-body structural genes. PA14 expresses reb genes during colonization of plant and nematode hosts, and R-body production is required for full virulence in nematodes. Analyses of nematode ribosome content and immune response indicate that P. aeruginosa R-bodies act via a mechanism involving ribosome cleavage and translational inhibition. Our observations provide insight into the biology of R-body production and its consequences during P. aeruginosa infection.
SLITRK5 is a negative regulator of hedgehog signaling in osteoblasts
Authors: Sun Jun , Shin Dong Yeon , Eiseman Mark , Yallowitz Alisha R. , Li Na , Lalani Sarfaraz , Li Zan , Cung Michelle , Bok Seoyeon , Debnath Shawon , Marquez Sofia Jenia , White Tommy E. , Khan Abdul G. , Lorenz Ivo C. , Shim Jae-Hyuck , Lee Francis S. , Xu Ren , Greenblatt Matthew B. 
Published: July 2021

AbstractHedgehog signaling is essential for bone formation, including functioning as a means for the growth plate to drive skeletal mineralization. However, the mechanisms regulating hedgehog signaling specifically in bone-forming osteoblasts are largely unknown. Here, we identified SLIT and NTRK-like protein-5(Slitrk5), a transmembrane protein with few identified functions, as a negative regulator of hedgehog signaling in osteoblasts. Slitrk5 is selectively expressed in osteoblasts and loss of Slitrk5 enhanced osteoblast differentiation in vitro and in vivo. Loss of SLITRK5 in vitro leads to increased hedgehog signaling and overexpression of SLITRK5 in osteoblasts inhibits the induction of targets downstream of hedgehog signaling. Mechanistically, SLITRK5 binds to hedgehog ligands via its extracellular domain and interacts with PTCH1 via its intracellular domain. SLITRK5 is present in the primary cilium, and loss of SLITRK5 enhances SMO ciliary enrichment upon SHH stimulation. Thus, SLITRK5 is a negative regulator of hedgehog signaling in osteoblasts that may be attractive as a therapeutic target to enhance bone formation.
The origin of the boundary strengthening in polycrystal-inspired architected materials
Authors: Liu Chen , Lertthanasarn Jedsada , Pham Minh-Son 
Published: July 2021

AbstractCrystal-inspired approach is found to be highly successful in designing extraordinarily damage-tolerant architected materials. i.e. meta-crystals, necessitating in-depth fundamental studies to reveal the underlying mechanisms responsible for the strengthening in meta-crystals. Such understanding will enable greater confidence to control not only strength, but also spatial local deformation. In this study, the mechanisms underlying shear band activities were investigated and discussed to provide a solid basis for predicting and controlling the local deformation behaviour in meta-crystals. The boundary strengthening in polycrystal-like meta-crystals was found to relate to the interaction between shear bands and polygrain-like boundaries. More importantly, the boundary type and coherency were found to be influential as they govern the transmission of shear bands across meta-grains boundaries. The obtained insights in this study provide crucial knowledge in developing high strength architected materials with great capacity in controlling and programming the mechanical strength and damage path.
An integrated functional and clinical genomics approach reveals genes driving aggressive metastatic prostate cancer
Authors: Das Rajdeep , Sjöström Martin , Shrestha Raunak , Yogodzinski Christopher , Egusa Emily A. , Chesner Lisa N. , Chen William S. , Chou Jonathan , Dang Donna K. , Swinderman Jason T. , Ge Alex , Hua Junjie T. , Kabir Shaheen , Quigley David A. , Small Eric J. , Ashworth Alan , Feng Felix Y. , Gilbert Luke A. 
Published: July 2021

AbstractGenomic sequencing of thousands of tumors has revealed many genes associated with specific types of cancer. Similarly, large scale CRISPR functional genomics efforts have mapped genes required for cancer cell proliferation or survival in hundreds of cell lines. Despite this, for specific disease subtypes, such as metastatic prostate cancer, there are likely a number of undiscovered tumor specific driver genes that may represent potential drug targets. To identify such genetic dependencies, we performed genome-scale CRISPRi screens in metastatic prostate cancer models. We then created a pipeline in which we integrated pan-cancer functional genomics data with our metastatic prostate cancer functional and clinical genomics data to identify genes that can drive aggressive prostate cancer phenotypes. Our integrative analysis of these data reveals known prostate cancer specific driver genes, such as AR and HOXB13, as well as a number of top hits that are poorly characterized. In this study we highlight the strength of an integrated clinical and functional genomics pipeline and focus on two top hit genes, KIF4A and WDR62. We demonstrate that both KIF4A and WDR62 drive aggressive prostate cancer phenotypes in vitro and in vivo in multiple models, irrespective of AR-status, and are also associated with poor patient outcome.
Large-area patterning of full-color quantum dot arrays beyond 1000 pixels per inch by selective electrophoretic deposition
Authors: Zhao Jinyang , Chen Lixuan , Li Dongze , Shi Zhiqing , Liu Pai , Yao Zhenlei , Yang Hongcheng , Zou Taoyu , Zhao Bin , Zhang Xin , Zhou Hang , Yang Yixing , Cao Weiran , Yan Xiaolin , Zhang Shengdong , Sun Xiao Wei 
Published: July 2021

AbstractColloidal quantum dot (QD) emitters show great promise in the development of next-generation displays. Although various solution-processed techniques have been developed for nanomaterials, high-resolution and uniform patterning technology amicable to manufacturing is still missing. Here, we present large-area, high-resolution, full-color QD patterning utilizing a selective electrophoretic deposition (SEPD) technique. This technique utilizes photolithography combined with SEPD to achieve uniform and fast fabrication, low-cost QD patterning in large-area beyond 1,000 pixels-per-inch. The QD patterns only deposited on selective electrodes with precisely controlled thickness in a large range, which could cater for various optoelectronic devices. The adjustable surface morphology, packing density and refractive index of QD films enable higher efficiency compared to conventional solution-processed methods. We further demonstrate the versatility of our approach to integrate various QDs into large-area arrays of full-color emitting pixels and QLEDs with good performance. The results suggest a manufacture-viable technology for commercialization of QD-based displays.
Endogenous control of inflammation characterizes pregnant women with asymptomatic or paucisymptomatic SARS-CoV-2 infection
Authors: De Biasi Sara , Tartaro Domenico Lo , Gibellini Lara , Paolini Annamaria , Quong Andrew , Petes Carlene , Awong Geneve , Douglas Samuel , Lin Dongxia , Nieto Jordan , Galassi Francesco Maria , Borella Rebecca , Fidanza Lucia , Mattioli Marco , Leone Chiara , Neri Isabella , Meschiari Marianna , Cicchetti Luca , Iannone Anna , Trenti Tommaso , Sarti Mario , Girardis Massimo , Guaraldi Giovanni , Mussini Cristina , Facchinetti Fabio , Cossarizza Andrea 
Published: July 2021

AbstractSARS-CoV-2 infection can affect all human beings, including pregnant women. Thus, understanding the immunological changes induced by the virus during pregnancy is nowadays of pivotal importance. Here, using peripheral blood from 14 pregnant women with asymptomatic or mild SARS-CoV-2 infection, we investigate cell proliferation and cytokine production, measure plasma levels of 62 cytokines, and perform a 38-parameter mass cytometry analysis. Our results show an increase in low density neutrophils but no lymphopenia or gross alterations of white blood cells, which display normal levels of differentiation, activation or exhaustion markers and show well preserved functionality. Meanwhile, the plasma levels of anti-inflammatory cytokines such as interleukin (IL)-1RA, IL-10 and IL-19 are increased, those of IL-17, PD-L1 and D-dimer are decreased, but IL-6 and other inflammatory molecules remain unchanged. Our profiling of antiviral immune responses may thus help develop therapeutic strategies to avoid virus-induced damages during pregnancy.
Spin–spin interactions in defects in solids from mixed all-electron and pseudopotential first-principles calculations
Authors: Ghosh Krishnendu , Ma He , Onizhuk Mykyta , Gavini Vikram , Galli Giulia 
Published: July 2021

AbstractUnderstanding the quantum dynamics of spin defects and their coherence properties requires an accurate modeling of spin-spin interaction in solids and molecules, for example by using spin Hamiltonians with parameters obtained from first principles calculations. We present a real-space approach based on density functional theory for the calculation of spin-Hamiltonian parameters, where only selected atoms are treated at the all-electron level, while the rest of the system is described with the pseudopotential approximation. Our approach permits calculations for systems containing more than 1000 atoms, as demonstrated for defects in diamond and silicon carbide. We show that only a small number of atoms surrounding the defect needs to be treated at the all-electron level, in order to obtain an overall all-electron accuracy for hyperfine and zero-field splitting tensors. We also present results for coherence times, computed with the cluster correlation expansion method, highlighting the importance of accurate spin-Hamiltonian parameters for quantitative predictions of spin dynamics.
Modelling charge transport and electro-optical characteristics of quantum dot light-emitting diodes
Authors: Jung Sung-Min , Lee Tae Hoon , Bang Sang Yun , Han Soo Deok , Shin Dong-Wook , Lee Sanghyo , Choi Hyung Woo , Suh Yo-Han , Fan Xiang-Bing , Jo Jeong-Wan , Zhan Shijie , Yang Jiajie , Samarakoon Chatura , Kim Yoonwoo , Occhipinti Luigi G. , Amaratunga Gehan , Kim Jong Min 
Published: July 2021

AbstractsQuantum dot light-emitting diodes (QD-LEDs) are considered as competitive candidate for next-generation displays or lightings. Recent advances in the synthesis of core/shell quantum dots (QDs) and tailoring procedures for achieving their high quantum yield have facilitated the emergence of high-performance QD-LEDs. Meanwhile, the charge-carrier dynamics in QD-LED devices, which constitutes the remaining core research area for further improvement of QD-LEDs, is, however, poorly understood yet. Here, we propose a charge transport model in which the charge-carrier dynamics in QD-LEDs are comprehensively described by computer simulations. The charge-carrier injection is modelled by the carrier-capturing process, while the effect of electric fields at their interfaces is considered. The simulated electro-optical characteristics of QD-LEDs, such as the luminance, current density and external quantum efficiency (EQE) curves with varying voltages, show excellent agreement with experiments. Therefore, our computational method proposed here provides a useful means for designing and optimising high-performance QD-LED devices.