bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping 20 years of irrigated croplands in China using MODIS and statistics and existing irrigation products
Authors: Zhang Chao , Dong Jinwei , Ge Quansheng 
Published: July 2022

AbstractAs a routine agricultural practice, irrigation is fundamental to protect crops from water scarcity and ensure food security in China. However, consistent and reliable maps about the spatial distribution and extent of irrigated croplands are still unavailable, impeding water resource management and agricultural planning. Here, we produced annual 500-m irrigated cropland maps across China for 2000–2019, using a two-step strategy that integrated statistics, remote sensing, and existing irrigation products into a hybrid irrigation dataset. First, we generated intermediate irrigation maps (MIrAD-GI) by fusing the MODIS-derived greenness index and statistical data. Second, we collected all existing available irrigation maps over China and integrated them with MIrAD-GI into an improved series of annual irrigation maps, using constrained statistics and a synergy mapping method. The resultant maps had moderate overall accuracies (0.732~0.819) based on nationwide reference ground samples and outperformed existing irrigation products by inter-comparison. As the first of this kind in China, the annual maps delineated the spatiotemporal pattern of irrigated croplands and could contribute to sustainable water use and agricultural development.
Reconstructed SPECT images of 177Lu homogeneous cylindrical phantom used for calibration and texture analysis
Authors: Mezzenga Emilio , Piccinini Filippo , Loi Emiliano , Belli Maria Luisa , Sarnelli Anna 
Published: July 2022

AbstractIn a clinical contest, it is common to use dedicated phantoms to perform quality assurance test to check the performance of a SPECT system. Some of these phantoms are also used to calibrate the system for dosimetric evaluation of patients undergoing radiometabolic cancer therapy. In this work, a 3D-OSEM reconstructed 177Lu SPECT dataset of a homogeneous cylindrical phantom is described. This dataset was acquired to investigate the variation of the SPECT calibration factor, counts convergence, noise and uniformity by varying the number of subsets and iterations. In particular, the dataset is composed of images reconstructed using five different numbers of subsets and sixteen different numbers of iterations, for a total of 80 different configurations. The dataset is suitable for comparison with other reconstruction algorithms (e.g. FBP, MLEM, etc.) and radionuclides (e.g. technetium, yttrium). In regards to the uniformity issue, the same dataset allows the user to perform radiomic investigations on the influence of the border effect on the reconstructed images.
Infant birth weight estimation and low birth weight classification in United Arab Emirates using machine learning algorithms
Authors: Khan Wasif , Zaki Nazar , Masud Mohammad M. , Ahmad Amir , Ali Luqman , Ali Nasloon , Ahmed Luai A. 
Published: July 2022

AbstractAccurate prediction of a newborn’s birth weight (BW) is a crucial determinant to evaluate the newborn’s health and safety. Infants with low BW (LBW) are at a higher risk of serious short- and long-term health outcomes. Over the past decade, machine learning (ML) techniques have shown a successful breakthrough in the field of medical diagnostics. Various automated systems have been proposed that use maternal features for LBW prediction. However, each proposed system uses different maternal features for LBW classification and estimation. Therefore, this paper provides a detailed setup for BW estimation and LBW classification. Multiple subsets of features were combined to perform predictions with and without feature selection techniques. Furthermore, the synthetic minority oversampling technique was employed to oversample the minority class. The performance of 30 ML algorithms was evaluated for both infant BW estimation and LBW classification. Experiments were performed on a self-created dataset with 88 features. The dataset was obtained from 821 women from three hospitals in the United Arab Emirates. Different performance metrics, such as mean absolute error and mean absolute percent error, were used for BW estimation. Accuracy, precision, recall, F-scores, and confusion matrices were used for LBW classification. Extensive experiments performed using five-folds cross validation show that the best weight estimation was obtained using Random Forest algorithm with mean absolute error of 294.53 g while the best classification performance was obtained using Logistic Regression with SMOTE oversampling techniques that achieved accuracy, precision, recall and F1 score of 90.24%, 87.6%, 90.2% and 0.89, respectively. The results also suggest that features such as diabetes, hypertension, and gestational age, play a vital role in LBW classification.
Association between serum albumin and mortality in Japan older people with dysphagia
Authors: Li Gaigai , Zhou Xun , Hou Xunrui , Luo Yuheng , Li Danmao , Fan Tongtao 
Published: July 2022

AbstractTo determine whether there is a link between serum albumin and mortality among participants in the elderly in Japan. This is a single-center,retrospective cohort study analysis of 253 old patients with dysphagia from Japan, conducted from January 2014 to January 2017. The primary outcome was mortality. We performed Cox regression analysis to compare the mortality between the two groups (divided by serum albumin = 3 g/dl). 253 patients were included in the analysis, of whom the number of serum albumin under 3 g/dl was 93. The log-rank test showed a significant longer mortality in the high group (serum albumin >  = 3 g/dl) compared with the low group (median, 382 vs. 176 days, P < 0.0001). Cox regression analysis showed that unadjusted HR for the high group relative to the low group was 0.40 (95% CI: 0.29–0.57; P < 0.001). After adjusting 3 models in multivariable analysis, serum albumin was significantly associated with mortality. The adjusted HRs (95% CI) for total mortality rates were 0.46 (0.33–0.65), 0.66 (0.44–0.99) and 0.64 (0.42–0.97), from model 2 to model 4. There is negative association between serum albumin and mortality in Japanese old people with dysphagia.
Avoiding sharp accelerations can mitigate the impacts of a Ferry’s radiated noise on the St. Lawrence whales
Authors: Lagrois Dominic , Chion Clément , Sénécal Jean-François , Kowalski Camille , Michaud Robert , Vergara Valeria 
Published: July 2022

AbstractExposure to anthropogenic noise from the commercial fleet is one of the primary constituents of the acoustic pollution perturbing the environment of aquatic life. Merchant ships (e.g. bulkers, tankers) have been the focus of numerous studies for underwater noise source level determination and modeling. This work extends pre-existing studies to the ferry ship class. Hydrophone-based measurements of the N.M. Trans-Saint-Laurent ferry near the Rivière-du-Loup harbor (Rivière-du-Loup, QC CANADA) were obtained for 186 transits between 2020 July 22th and 2020 September 5th. For each transit, monopole source levels are estimated for two (2) different modes of operation i.e., the low-speed phases of acceleration/deceleration when the ferry launches/docks at Rivière-du-Loup and the passages at quasi-operational speed at the hydrophone’s closest-point-of-approach. Relative differences between the two (2) modes of operation are presented here in the low-frequency domain between 141 and 707 Hz. An average excess of 8 to 11.5 dB indicates that the ferry is likely one order of magnitude noisier, within this frequency band, during acceleration/deceleration when compared to passages at operational speed. This highlights that, in terms of marine mammal conservation, a significant reduction of the noise pollution could be achieved, for instance, by avoiding sudden speed changes in the vicinity of whales.
Transmission history of SARS-CoV-2 in humans and white-tailed deer
Authors: Willgert Katriina , Didelot Xavier , Surendran-Nair Meera , Kuchipudi Suresh V. , Ruden Rachel M. , Yon Michele , Nissly Ruth H. , Vandegrift Kurt J. , Nelli Rahul K. , Li Lingling , Jayarao Bhushan M. , Levine Nicole , Olsen Randall J. , Davis James J. , Musser James M. , Hudson Peter J. , Kapur Vivek , Conlan Andrew J. K. 
Published: July 2022

AbstractThe emergence of a novel pathogen in a susceptible population can cause rapid spread of infection. High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission. Knowledge of the risk and direction of SARS-CoV-2 transmission between humans and potential reservoir hosts is essential for effective disease control and prioritisation of interventions. Using genomic data, we reconstruct the transmission history of SARS-CoV-2 in humans and deer, estimate the case finding rate and attempt to infer relative rates of transmission between species. We found no evidence of direct or indirect transmission from deer to human. However, with an estimated case finding rate of only 4.2%, spillback to humans cannot be ruled out. The extensive transmission of SARS-CoV-2 within deer populations and the large number of unsampled cases highlights the need for active surveillance at the human–animal interface.
Influence of source directivity and site effects of 2003 Tokachi-oki earthquake on the generation of high PGA in the near-fault zones
Authors: Pavlenko Olga V. 
Published: July 2022

AbstractWe study source directivity and site effects of 2003 Tokachi-oki earthquake (Japan, Mw ~ 8.3) and their influence on the distribution of peak ground accelerations (PGA) in the near-fault zones are studied. Based on records of KiK-net vertical arrays, models of soil behavior are constructed, i.e. vertical distributions of stresses and strains induced in soil layers by strong motion. We use the method of Pavlenko and Irikura (2003), previously applied for studying soil behavior during 1995 Kobe, 2000 Tottori, and 2011 Tohoku earthquakes. During the Tokachi-oki earthquake, we did not find a widespread nonlinearity of soft soil behavior. Manifestations of soil nonlinearity were observed at sites closest to the source; at remote sites where high PGA were recorded, soil behavior was virtually linear, and shear moduli in soils increased till the moments of the highest intensity of motion, then decreased. The shapes of acceleration time histories at remote sites indicate directivity effects: seismic waves radiated by the crack tip during its propagation along a section of the fault plane came to the stations simultaneously. Soil hardening occurred at these sites that increased amplification and PGA on the surface. Similar effects were observed during 2011 Tohoku earthquake; evidently, they can occur during future strong earthquakes.
Fast nonlinear model predictive planner and control for an unmanned ground vehicle in the presence of disturbances and dynamic obstacles
Authors: Khan Subhan , Guivant Jose 
Published: July 2022

AbstractThis paper presents a solution for the tracking control problem, for an unmanned ground vehicle (UGV), under the presence of skid-slip and external disturbances in an environment with static and moving obstacles. To achieve the proposed task, we have used a path-planner which is based on fast nonlinear model predictive control (NMPC); the planner generates feasible trajectories for the kinematic and dynamic controllers to drive the vehicle safely to the goal location. Additionally, the NMPC deals with dynamic and static obstacles in the environment. A kinematic controller (KC) is designed using evolutionary programming (EP), which tunes the gains of the KC. The velocity commands, generated by KC, are then fed to a dynamic controller, which jointly operates with a nonlinear disturbance observer (NDO) to prevent the effects of perturbations. Furthermore, pseudo priority queues (PPQ) based Dijkstra algorithm is combined with NMPC to propose optimal path to perform map-based practical simulation. Finally, simulation based experiments are performed to verify the technique. Results suggest that the proposed method can accurately work, in real-time under limited processing resources.
A dielectrophoresis-based microfluidic system having double-sided optimized 3D electrodes for label-free cancer cell separation with preserving cell viability
Authors: Varmazyari V. , Habibiyan H. , Ghafoorifard H. , Ebrahimi M. , Ghafouri-Fard S. 
Published: July 2022

AbstractEarly detection of circulating tumor cells (CTCs) in a patient's blood is essential to accurate prognosis and effective cancer treatment monitoring. The methods used to detect and separate CTCs should have a high recovery rate and ensure cells viability for post-processing operations, such as cell culture and genetic analysis. In this paper, a novel dielectrophoresis (DEP)-based microfluidic system is presented for separating MDA-MB-231 cancer cells from various subtypes of WBCs with the practical cell viability approach. Three configurations for the sidewall electrodes are investigated to evaluate the separation performance. The simulation results based on the finite-element method show that semi-circular electrodes have the best performance with a recovery rate of nearly 95% under the same operational and geometric conditions. In this configuration, the maximum applied electric field (1.11 × 105 V/m) to separate MDA-MB-231 is lower than the threshold value for cell electroporation. Also, the Joule heating study in this configuration shows that the cells are not damaged in the fluid temperature gradient (equal to 1 K). We hope that such a complete and step-by-step design is suitable to achieve DEP-based applicable cell separation biochips.
Spatial organization of hydrophobic and charged residues affects protein thermal stability and binding affinity
Authors: Desantis Fausta , Miotto Mattia , Di Rienzo Lorenzo , Milanetti Edoardo , Ruocco Giancarlo 
Published: July 2022

AbstractWhat are the molecular determinants of protein–protein binding affinity and whether they are similar to those regulating fold stability are two major questions of molecular biology, whose answers bring important implications both from a theoretical and applicative point of view. Here, we analyze chemical and physical features on a large dataset of protein–protein complexes with reliable experimental binding affinity data and compare them with a set of monomeric proteins for which melting temperature data was available. In particular, we probed the spatial organization of protein (1) intramolecular and intermolecular interaction energies among residues, (2) amino acidic composition, and (3) their hydropathy features. Analyzing the interaction energies, we found that strong Coulombic interactions are preferentially associated with a high protein thermal stability, while strong intermolecular van der Waals energies correlate with stronger protein–protein binding affinity. Statistical analysis of amino acids abundances, exposed to the molecular surface and/or in interaction with the molecular partner, confirmed that hydrophobic residues present on the protein surfaces are preferentially located in the binding regions, while charged residues behave oppositely. Leveraging on the important role of van der Waals interface interactions in binding affinity, we focused on the molecular surfaces in the binding regions and evaluated their shape complementarity, decomposing the molecular patches in the 2D Zernike basis. For the first time, we quantified the correlation between local shape complementarity and binding affinity via the Zernike formalism. In addition, considering the solvent interactions via the residue hydropathy, we found that the hydrophobicity of the binding regions dictates their shape complementary as much as the correlation between van der Waals energy and binding affinity. In turn, these relationships pave the way to the fast and accurate prediction and design of optimal binding regions as the 2D Zernike formalism allows a rapid and superposition-free comparison between possible binding surfaces.
Identification of multi-omics biomarkers and construction of the novel prognostic model for hepatocellular carcinoma
Authors: Liu Xiao , Xiao Chiying , Yue Kunyan , Chen Min , Zhou Hang , Yan Xiaokai 
Published: July 2022

AbstractGenome changes play a crucial role in carcinogenesis, and many biomarkers can be used as effective prognostic indicators in various tumors. Although previous studies have constructed many predictive models for hepatocellular carcinoma (HCC) based on molecular signatures, the performance is unsatisfactory. Because multi-omics data can more comprehensively reflect the biological phenomenon of disease, we hope to build a more accurate predictive model by multi-omics analysis. We use the TCGA to identify crucial biomarkers and construct prognostic models through difference analysis, univariate Cox, and LASSO/stepwise Cox analysis. The performances of predictive models were evaluated and validated through survival analysis, Harrell’s concordance index (C-index), receiver operating characteristic (ROC) curve, and decision curve analysis (DCA). Multiple mRNAs, lncRNAs, miRNAs, CNV genes, and SNPs were significantly associated with the prognosis of HCC. We constructed five single-omic models, and the mRNA and lncRNA models showed good performance with c-indexes over 0.70. The multi-omics model presented a robust predictive ability with a c-index over 0.77. This study identified many biomarkers that may help study underlying carcinogenesis mechanisms in HCC. In addition, we constructed multiple single-omic models and an integrated multi-omics model that may provide practical and reliable guides for prognosis assessment.
Discovery of a novel class of benzimidazoles as highly effective agonists of bone morphogenetic protein (BMP) receptor signaling
Authors: Najafi Sheyda , Barasa Leonard , Huang Sammy Y. , Yoganathan Sabesan , Perron Jeanette C. 
Published: July 2022

AbstractIncreasing or restoring Bone Morphogenetic Protein receptor signaling is an effective therapy for conditions such as bone fracture and pulmonary arterial hypertension. However, direct use of recombinant BMPs has encountered significant obstacles. Moreover, synthetic, full agonists of BMP receptor signaling have yet to be identified. Here, we report the discovery of a novel class of indolyl-benzimidazoles, synthesized using a one-pot synthetic methodology, which appear to mimic the biochemical and functional activity of BMPs. The first-in-series compounds, SY-LB-35 and SY-LB-57, stimulated significant increases in cell number and cell viability in the C2C12 myoblast cell line. Cell cycle analysis revealed that these compounds induced a shift toward proliferative phases. SY-LB-35 and SY-LB-57 stimulated canonical Smad and non-canonical PI3K/Akt, ERK, p38 and JNK intracellular signaling pathways, similar to BMP2-stimulated responses. Importantly, increases in Smad phosphorylation and cell viability were dependent on type I BMP receptor activity. Thus, these compounds robustly activate intracellular signaling in a BMP receptor-dependent manner and may signify the first known, full agonists of BMP receptor signaling. Moreover, discovery of small molecule activators of BMP pathways, which can be efficiently formulated and targeted to diseased or damaged areas, could potentially substitute recombinant BMPs for treatment of BMP-related pathologies.
Fatty acid tryptamide from cacao elongates Drosophila melanogaster lifespan with sirtuin-dependent heat shock protein expression
Authors: Kanno Kiko , Kayashima Yasunari , Tamura Kazuji , Miyara Takako , Baba Kento , Koganei Megumi , Natsume Midori , Imai Shinjiro 
Published: July 2022

AbstractLife span is increasing in developed countries as Japan, and an aging society is becoming a problem. In fact, healthy lifespan is not extended, and it is desired to extend it by functional food. Cacao (Theobroma cacao) contains various active components and is considered a preventative agent against metabolic disease. In addition, it has long been thought that regular cacao intake extends a healthy lifespan. However, there is no direct evidence for this belief. The purpose of this study is to identify the cacao component that elongate the lifespan of D. melanogaster as a model organism and to elucidate its functional mechanism. The activation of sirtuins, a family of NAD+-dependent deacetylases, has been reported to extend the lifespans of various organisms. Heat shock factor 1 is known to be deacetylated by reaction with sirtuins, thereby inducing gene expression of various heat shock proteins by heat stress and effectively extending the lifespan of organisms. Therefore, we evaluated whether components in cacao activate sirtuins and extend the lifespan of D. melanogaster. In the process, we discovered the fatty acid tryptamide as a lifespan-elongating component of cacao. Therefore, we investigated whether the fatty acid tryptamide from cacao upregulates the genes of heat shock proteins. As a result, it was confirmed that the gene expression of multiple heat shock proteins was significantly increased. This suggests that fatty acid tryptamide may activate sirtuins, increase gene expression of heat shock proteins, and elongate the lifespan of D. melanogaster.
Structure-based rational design of an enhanced fluorogen-activating protein for fluorogens based on GFP chromophore
Authors: Goncharuk Marina V. , Baleeva Nadezhda S. , Nolde Dmitry E. , Gavrikov Alexey S. , Mishin Alexey V. , Mishin Alexander S. , Sosorev Andrey Y. , Arseniev Alexander S. , Goncharuk Sergey A. , Borshchevskiy Valentin I. , Efremov Roman G. , Mineev Konstantin S. , Baranov Mikhail S. 
Published: July 2022

Abstract“Fluorescence-Activating and absorption-Shifting Tag” (FAST) is a well-studied fluorogen-activating protein with high brightness and low size, able to activate a wide range of fluorogens. This makes FAST a promising target for both protein and fluorogen optimization. Here, we describe the structure-based rational design of the enhanced FAST mutants, optimized for the N871b fluorogen. Using the spatial structure of the FAST/N871b complex, NMR relaxation analysis, and computer simulations, we identify the mobile regions in the complex and suggest mutations that could stabilize both the protein and the ligand. Two of our mutants appear brighter than the wild-type FAST, and these mutants provide up to 35% enhancement for several other fluorogens of similar structure, both in vitro and in vivo. Analysis of the mutants by NMR reveals that brighter mutants demonstrate the highest stability and lowest length of intermolecular H-bonds. Computer simulations provide the structural basis for such stabilization.
Structural insight into the activation mechanism of MrgD with heterotrimeric Gi-protein revealed by cryo-EM
Authors: Suzuki Shota , Iida Momoko , Hiroaki Yoko , Tanaka Kotaro , Kawamoto Akihiro , Kato Takayuki , Oshima Atsunori 
Published: July 2022

AbstractMrgD, a member of the Mas-related G protein-coupled receptor (MRGPR) family, has high basal activity for Gi activation. It recognizes endogenous ligands, such as β-alanine, and is involved in pain and itch signaling. The lack of a high-resolution structure for MrgD hinders our understanding of whether its activation is ligand-dependent or constitutive. Here, we report two cryo-EM structures of the MrgD-Gi complex in the β-alanine-bound and apo states at 3.1 Å and 2.8 Å resolution, respectively. These structures show that β-alanine is bound to a shallow pocket at the extracellular domains. The extracellular half of the sixth transmembrane helix undergoes a significant movement and is tightly packed into the third transmembrane helix through hydrophobic residues, creating the active form. Our structures demonstrate a structural basis for the characteristic ligand recognition of MrgD. These findings provide a framework to guide drug designs targeting the MrgD receptor.