bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of non-uniform oxidation based on a mechanochemical phase field model with nonlinear reaction kinetics and large inelastic deformation
Authors: Lin Chen , Jiang Jishen , Ruan Haihui , Ma Xianfeng 
Published: July 2023

AbstractA mechanochemical model is proposed to investigate the non-uniform oxidation of thermal barrier coatings (TBCs) that involves large inelastic deformation and nonlinear reaction kinetics. The large-deformation theory incorporates the higher-order term of geometric nonlinearity for a more precise description of the deformation and stress evolution in an oxide layer. The effect of stresses on the reaction kinetics is considered, which is expressed as the Eshelby stress tensor to account for the conformational volume change and deformation energy. A nonlinear reaction kinetics is adopted for a more accurate description of the nonequilibrium thermodynamic processes. The 2D simulations reveal a non-uniform oxide growth, three modes of oxide-metal interfacial morphology evolution, and tensile stress concentrations in the oxide scale. These simulation results agree with the experimental observations that cannot be described by the previous models. With the model, it is further demonstrated that a stable interfacial morphology and a significantly reduced tensile stress can be achieved by increasing the creep rate of the oxide and the flatness of the oxide-metal interface. This model thus provides an approach to extend the service time of TBCs.
Accurate medium-range global weather forecasting with 3D neural networks
Authors: Bi Kaifeng , Xie Lingxi , Zhang Hengheng , Chen Xin , Gu Xiaotao , Tian Qi 
Published: July 2023

AbstractWeather forecasting is important for science and society. At present, the most accurate forecast system is the numerical weather prediction (NWP) method, which represents atmospheric states as discretized grids and numerically solves partial differential equations that describe the transition between those states1. However, this procedure is computationally expensive. Recently, artificial-intelligence-based methods2 have shown potential in accelerating weather forecasting by orders of magnitude, but the forecast accuracy is still significantly lower than that of NWP methods. Here we introduce an artificial-intelligence-based method for accurate, medium-range global weather forecasting. We show that three-dimensional deep networks equipped with Earth-specific priors are effective at dealing with complex patterns in weather data, and that a hierarchical temporal aggregation strategy reduces accumulation errors in medium-range forecasting. Trained on 39 years of global data, our program, Pangu-Weather, obtains stronger deterministic forecast results on reanalysis data in all tested variables when compared with the world’s best NWP system, the operational integrated forecasting system of the European Centre for Medium-Range Weather Forecasts (ECMWF)3. Our method also works well with extreme weather forecasts and ensemble forecasts. When initialized with reanalysis data, the accuracy of tracking tropical cyclones is also higher than that of ECMWF-HRES.
The carbon costs of global wood harvests
Authors: Peng Liqing , Searchinger Timothy D. , Zionts Jessica , Waite Richard 
Published: July 2023

AbstractAfter agriculture, wood harvest is the human activity that has most reduced the storage of carbon in vegetation and soils1,2. Although felled wood releases carbon to the atmosphere in various steps, the fact that growing trees absorb carbon has led to different carbon-accounting approaches for wood use, producing widely varying estimates of carbon costs. Many approaches give the impression of low, zero or even negative greenhouse gas emissions from wood harvests because, in different ways, they offset carbon losses from new harvests with carbon sequestration from growth of broad forest areas3,4. Attributing this sequestration to new harvests is inappropriate because this other forest growth would occur regardless of new harvests and typically results from agricultural abandonment, recovery from previous harvests and climate change itself. Nevertheless some papers count gross emissions annually, which assigns no value to the capacity of newly harvested forests to regrow and approach the carbon stocks of unharvested forests. Here we present results of a new model that uses time discounting to estimate the present and future carbon costs of global wood harvests under different scenarios. We find that forest harvests between 2010 and 2050 will probably have annualized carbon costs of 3.5–4.2 Gt CO2e yr−1, which approach common estimates of annual emissions from land-use change due to agricultural expansion. Our study suggests an underappreciated option to address climate change by reducing these costs.
Martian dunes indicative of wind regime shift in line with end of ice age
Authors: Liu Jianjun , Qin Xiaoguang , Ren Xin , Wang Xu , Sun Yong , Zeng Xingguo , Wu Haibin , Chen Zhaopeng , Chen Wangli , Chen Yuan , Wang Cheng , Sun Zezhou , Zhang Rongqiao , Ouyang Ziyuan , Guo Zhengtang , Head James W. , Li Chunlai 
Published: July 2023

AbstractOrbital observations suggest that Mars underwent a recent ‘ice age’ (roughly 0.4–2.1 million years ago), during which a latitude-dependent ice-dust mantle (LDM)1,2was emplaced. A subsequent decrease in obliquity amplitude resulted in the emergence of an ‘interglacial period’1,3during which the lowermost latitude LDM ice4–6was etched and removed, returning it to the polar cap. These observations are consistent with polar cap stratigraphy1,7, but lower- to mid-latitude in situ surface observations in support of a glacial–interglacial transition that can be reconciled with mesoscale and global atmospheric circulation models8is lacking. Here we present a suite of measurements obtained by the Zhurong rover during its traverse across the southern LDM region in Utopia Planitia, Mars. We find evidence for a stratigraphic sequence involving initial barchan dune formation, indicative of north-easterly winds, cementation of dune sediments, followed by their erosion by north-westerly winds, eroding the barchan dunes and producing distinctive longitudinal dunes, with the transition in wind regime consistent with the end of the ice age. The results are compatible with the Martian polar stratigraphic record and will help improve our understanding of the ancient climate history of Mars9.
Cooperation between bHLH transcription factors and histones for DNA access
Authors: Michael Alicia K. , Stoos Lisa , Crosby Priya , Eggers Nikolas , Nie Xinyu Y. , Makasheva Kristina , Minnich Martina , Healy Kelly L. , Weiss Joscha , Kempf Georg , Cavadini Simone , Kater Lukas , Seebacher Jan , Vecchia Luca , Chakraborty Deyasini , Isbel Luke , Grand Ralph S. , Andersch Florian , Fribourgh Jennifer L. , Schübeler Dirk , Zuber Johannes , Liu Andrew C. , Becker Peter B. , Fierz Beat , Partch Carrie L. , Menet Jerome S. , Thomä Nicolas H. 
Published: July 2023

AbstractThe basic helix–loop–helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members1. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. 2,3). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry–exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A–H2B acidic patch4, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes5–7 at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors.
A harmonized resource of integrated prostate cancer clinical, -omic, and signature features
Authors: Laajala Teemu D. , Sreekanth Varsha , Soupir Alex C. , Creed Jordan H. , Halkola Anni S. , Calboli Federico C. F. , Singaravelu Kalaimathy , Orman Michael V. , Colin-Leitzinger Christelle , Gerke Travis , Fridley Brooke L. , Tyekucheva Svitlana , Costello James C. 
Published: July 2023

AbstractGenomic and transcriptomic data have been generated across a wide range of prostate cancer (PCa) study cohorts. These data can be used to better characterize the molecular features associated with clinical outcomes and to test hypotheses across multiple, independent patient cohorts. In addition, derived features, such as estimates of cell composition, risk scores, and androgen receptor (AR) scores, can be used to develop novel hypotheses leveraging existing multi-omic datasets. The full potential of such data is yet to be realized as independent datasets exist in different repositories, have been processed using different pipelines, and derived and clinical features are often not provided or not standardized. Here, we present the curatedPCaData R package, a harmonized data resource representing >2900 primary tumor, >200 normal tissue, and >500 metastatic PCa samples across 19 datasets processed using standardized pipelines with updated gene annotations. We show that meta-analysis across harmonized studies has great potential for robust and clinically meaningful insights. curatedPCaData is an open and accessible community resource with code made available for reproducibility.
Influence of particle size in supercritical carbon dioxide extraction of roselle (Hibiscus sabdariffa) on bioactive compound recovery, extraction rate, diffusivity, and solubility
Authors: Putra Nicky Rahmana , Rizkiyah Dwila Nur , Aziz Ahmad Hazim Abdul , Mamat Hasmadi , Jusoh Wan Muhammad Syahir Wan , Idham Zuhaili , Yunus Mohd Azizi Che , Irianto Irianto 
Published: July 2023

AbstractThe purpose of this work was to establish the best particle size for recovering high yields of total phenolic compounds (TPC), total anthocyanin compounds(TAC) and total flavonoid compounds (TFC) from roselle (Hibiscus sabdariffa) by applying supercritical carbon dioxide (ScCO2). The extraction rate, diffusivity and solubility of yield in ScCO2 were also studied and calculated utilizing models. Pressure (10 and 30 MPa), temperature (40 and 60 °C), and particle size (250 µm < dp < 355 µm, 355 µm < dp < 425 µm and 425 µm < dp < 500 µm) were employed as variables in this experiment. The greatest recovery was 11.96% yield, 7.16 mg/100 g TAC, 42.93 mg/100 g TPC and 239.36 mg/100 g TFC under the conditions of 30 MPA, 40 °C and 250 µm < dp < 355 µm, respectively. The extraction rate of supercritical carbon dioxide in roselle extraction ranged from 5.19 E−03 to 1.35 E−03 mg/s fitted using the Esquivel model. The diffusivity coefficient of ScCO2 ranged from 2.17E−12 to 3.72E−11 mg/s2, as fitted by a single sphere model. The greatest solubility of global yield, TAC, TPC and TFC in ScCO2 was 1.50 g/L, 0.3 mg/L, 1.69 mg/L and 9.97 mg/L, respectively, with a particle size of 250 µm < dp < 355 µm. The smaller particle size of roselle provides the maximum bioactive compound recovery and solubility. Furthermore, the diffusivity and extraction of ScCO2 are increased by decreasing the particle size. Therefore, a smaller particle size is appropriate for roselle extraction by ScCO2 based on the experimental and modelling data.
Influence of microbial cell morphology and composition on radio frequency heating of simple media at different frequencies
Authors: Espitia Julian , Verheyen Davy , Kozak Dmytro S. , Van Impe Jan F. M. 
Published: July 2023

AbstractThe effect of Listeria monocytogenes, Salmonella Typhimurium, and Saccharomyces cerevisiae on RF heating was studied in sterilized Milli-Q water and saline solution during treatments at 27.0 ± 0.6 MHz and 3.0 ± 0.02 MHz for 30 min. The presence of microorganisms caused a significant increase in temperature (maximum to 54.9 °C), with no significant decrease in cell numbers being observed for any conditions. For both media and frequencies, heating rates followed the order S. Typhimurium ≤ L. monocytogenes ≤ S. cerevisiae, except for heating at 3.0 ± 0.02 MHz in saline solution, where heating rates for S. cerevisiae and S. Typhimurium were equal. Generally, heating rates for microorganisms were significantly higher at 27.0 ± 0.6 MHz than at 3.0 ± 0.02 MHz, except for the S. cerevisiae case. Observed phenomena were probably caused by differences in the cell lipid and peptidoglycan content, with interaction effects with salt being present. This study was the first to investigate the influence of the presence of microorganisms on heating behavior of simple media. On the long term, more research on this topic could lead to finding specific RF frequencies more suitable for the heating of specific media and products for various applications.
Remote sensing imagery detects hydromorphic soils hidden under agriculture system
Authors: Mello Fellipe A. O. , Demattê José A. M. , Bellinaso Henrique , Poppiel Raul R. , Rizzo Rodnei , de Mello Danilo C. , Rosin Nícolas Augusto , Rosas Jorge T. F. , Silvero Nélida E. Q. , Rodríguez-Albarracín Heidy S. 
Published: July 2023

AbstractThe pressure for food production has expanded agriculture frontiers worldwide, posing a threat to water resources. For instance, placing crop systems over hydromorphic soils (HS), have a direct impact on groundwater and influence the recharge of riverine ecosystems. Environmental regulations improved over the past decades, but it is difficult to detect and protect these soils. To overcome this issue, we applied a temporal remote sensing strategy to generate a synthetic soil image (SYSI) associated with random forest (RF) to map HS in an 735,953.8 km2 area in Brazil. HS presented different spectral patterns from other soils, allowing the detection by satellite sensors. Slope and SYSI contributed the most for the prediction model using RF with cross validation (accuracy of 0.92). The assessments showed that 14.5% of the study area represented HS, mostly located inside agricultural areas. Soybean and pasture areas had up to 14.9% while sugar cane had just 3%. Here we present an advanced remote sensing technique that may improve the identification of HS under agriculture and assist public policies for their conservation.
Monitoring and risk analysis of residual pesticides drifted by unmanned aerial spraying
Authors: Kim Chang Jo , Yuan Xiu , Kim Min , Kyung Kee Sung , Noh Hyun Ho 
Published: July 2023

AbstractThis study aimed to investigate the residual characteristics of pesticides drifted by unmanned aerial spray according to buffer strip, windbreak, and morphological characteristics of non-target crops, suggest prevention for drift reduction, and finally conduct a risk analysis on pesticides exceeding the maximum residue limit (MRL) or uniform level (0.01 mg/kg) of the positive list system (PLS). Non-target crops were collected around the aerial sprayed area (paddy rice) in Boryeong, Seocheon, and Pyeongtaek after UAV spray. When pesticides were detected in more than three samples, Duncan’s multiple range test was performed. In cases where pesticides were detected in only two samples, an independent sample t-test was conducted (p < 0.05). The drift rate of pesticides tends to decrease by up to 100% as the buffer distance from aerial sprayed area increases or when a windbreak, such as maize, is present between two locations. Thus, the reduction of drifted pesticides could be effective if both factors were applied near the UAV spray area. Moreover, the residue of drifted pesticides was found to be the highest in leafy vegetables such as perilla leaves or leaf and stem vegetables such as Welsh onion, followed by fruit vegetables and cucurbits, owing to the morphological characteristics of crops. Therefore, selecting pulse or cereal such as soybean or maize as a farm product near the UAV spray area can be considered to minimize the drift. For pesticides that exceed the MRL or PLS uniform level, %acceptable dietary intake is 0–0.81% with no risk. Additionally, employing pesticides approved for both paddy rice and farm products in UAV spraying can effectively minimize instances where MRL or PLS are exceeded. Therefore, this study aims to provide farmers with effective guidelines for mitigating drift. Furthermore, we strive to promote stable and uninterrupted food production while facilitating the utilization of agricultural technologies such as UAV spraying to address labor shortages and ensure sustainable food security.
Comparison of translucency, thickness, and gap width of thermoformed and 3D-printed clear aligners using micro-CT and spectrophotometer
Authors: Park So Yeon , Choi Sung-Hwan , Yu Hyung-Seog , Kim Su-Jung , Kim Hoon , Kim Ki Beom , Cha Jung-Yul 
Published: July 2023

AbstractThe present study compared the thickness and gap width of thermoformed and 3D-printed clear aligners (CAs) using micro-computed tomography (micro-CT) and evaluated their translucency using spectrophotometer. Four groups of CAs were tested: thermoformed with polyethylene terephthalate glycol (TS) or copolyester-elastomer combination (TM), and 3D-printed TC-85 cleaned with alcohol (PA) or with centrifuge (PC). CIELab coordinates were measured (n = 10) to evaluate translucency. CAs (n = 10) were fitted onto respective models and micro-CT was performed to evaluate the thickness and gap width. Thickness and gap width were measured for different tooth type and location in sagittal sections on all sides. The PC group showed significantly higher translucency than the PA group, which was similar to the TS and TM groups (p < 0.01). After the manufacturing process, thickness reduction was observed in the thermoformed groups, whereas thickness increase was observed in the 3D printed-groups. The TM group showed the least gap width amongst the groups (p < 0.01). Thermoformed and 3D-printed CAs had significantly varied thicknesses and regions of best fit depending on the tooth type and location. Differences in the translucency and thickness of the 3D-printed CAs were observed depending on the cleaning methods.
Transient regulatory-T-cell interruption promotes skin-resident memory T cells mediated tumor protection
Authors: Zhao Shushu , Wu Shuting , Jiang Sheng , Zhou Xiaoyu , Zhao Gan , Wang Bin 
Published: July 2023

AbstractMost cancer immunotherapy approaches aim to stimulate cytotoxic CD8+ T lymphocytes to reject tumor cells. Due to the tumor-mediated suppressive micro-environment, of which the major contributor is regulatory T cells (Tregs), promising preclinical approaches were disappointing in clinical settings. Our recent study demonstrated that transient interruption of Tregs could induce CD8+ T cell responses to reject tumors in an animal model. The long-term tumor protective effect has yet not to be investigated. In this study, mice with Treg depletion rejected tumors and were rechallenged to study anti-tumor memory immune responses. The effects of major immune cell subsets on tumor protection were explored. Finally, we demonstrate that transient depletion of Tregs during primary tumor challenge can result in long-lasting protection against the tumor rechallenge. Skin-resident memory T cells (sTRM) were major factors in rejecting rechallenged tumors even when peripheral T cells were deficient. These findings highlight a promising strategy for empowering tissue-resident memory T cells for cancer prevention and immunotherapy in humans by interrupting Tregs.
Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species
Authors: Singh Jagveer , Sharma Ankush , Sharma Vishal , Gaikwad Popat Nanaso , Sidhu Gurupkar Singh , Kaur Gurwinder , Kaur Nimarpreet , Jindal Taveena , Chhuneja Parveen , Rattanpal H. S. 
Published: July 2023

AbstractCitrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.
Multi-landmark alignment of genomic signals reveals conserved expression patterns across transcription start sites
Authors: Vilar Jose M. G. , Saiz Leonor 
Published: July 2023

AbstractThe prevalent one-dimensional alignment of genomic signals to a reference landmark is a cornerstone of current methods to study transcription and its DNA-dependent processes but it is prone to mask potential relations among multiple DNA elements. We developed a systematic approach to align genomic signals to multiple locations simultaneously by expanding the dimensionality of the genomic-coordinate space. We analyzed transcription in human and uncovered a complex dependence on the relative position of neighboring transcription start sites (TSSs) that is consistently conserved among cell types. The dependence ranges from enhancement to suppression of transcription depending on the relative distances to the TSSs, their intragenic position, and the transcriptional activity of the gene. Our results reveal a conserved hierarchy of alternative TSS usage within a previously unrecognized level of genomic organization and provide a general methodology to analyze complex functional relationships among multiple types of DNA elements.