bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biogeography and eye size evolution of the ogre-faced spiders
Authors: Chamberland Lisa , Agnarsson Ingi , Quayle Iris L. , Ruddy Tess , Starrett James , Bond Jason E. 
Published: October 2022

AbstractNet-casting spiders (Deinopidae) comprise a charismatic family with an enigmatic evolutionary history. There are 67 described species of deinopids, placed among three genera,Deinopis, Menneus,andAsianopis,that are distributed globally throughout the tropics and subtropics.DeinopisandAsianopis, the ogre-faced spiders, are best known for their giant light-capturing posterior median eyes (PME), whereasMenneusdoes not have enlarged PMEs. Molecular phylogenetic studies have revealed discordance between morphology and molecular data. We employed a character-rich ultra-conserved element (UCE) dataset and a taxon-rich cytochrome-oxidase I (COI) dataset to reconstruct a genus-level phylogeny of Deinopidae, aiming to investigate the group’s historical biogeography, and examine PME size evolution. Although the phylogenetic results support the monophyly ofMenneusand the single reduction of PME size in deinopids, these data also show thatDeinopisis not monophyletic. Consequently, we formally transfer 24Deinopisspecies toAsianopis; the transfers comprise all of the African, Australian, South Pacific, and a subset of Central American and Mexican species. Following the divergence of Eastern and Western deinopids in the Cretaceous,Deinopis/Asianopisdispersed from Africa, through Asia and into Australia with its biogeographic history reflecting separation of Western Gondwana as well as long-distance dispersal events.
Heating influence on hierarchical structures fabricated by direct laser interference patterning
Authors: Schröder Nikolai , Nyenhuis Fabian , Baumann Robert , Mulko Lucinda , Kiedrowski Thomas , L’huillier Johannes Albert , Lasagni Andrés Fabián 
Published: October 2022

AbstractThe combination of direct laser interference patterning (DLIP) with laser-induced periodic surface structures (LIPSS) enables the fabrication of functional surfaces reported for a wide spectrum of materials. The process throughput is usually increased by applying higher average laser powers. However, this causes heat accumulation impacting the roughness and shape of produced surface patterns. Consequently, the effect of substrate temperature on the topography of fabricated features requires detailed investigations. In this study, steel surfaces were structured with line-like patterns by ps-DLIP at 532 nm. To investigate the influence of substrate temperature on the resulting topography, a heating plate was used to adjust the temperature. Heating to 250$$^{\circ }$$∘C led to a significant reduction of the produced structure depths, from 2.33 to 1.06 µm. The reduction is associated with the appearance of a different LIPSS type, depending on the grain orientation of the substrates and laser-induced superficial oxidation. This study revealed a strong effect of substrate temperature, which is also to be expected when heat accumulation effects arise from processing surfaces at high average laser power.
Fabrication, characterization and optical properties of Au-decorated Bi2Se3 nanoplatelets
Authors: Wang Chih-Chiang , Chang Yu-Sung , Lin Pao-Tai , Shieu Fuh-Sheng , Shih Han-Chang 
Published: October 2022

AbstractAu-decorated Bi2Se3 nanoplatelet heterostructures are fabricated by a two-step process of thermal CVD at 600 °C and magnetron sputtering at room-temperature. The crystal structures and binding energies of rhombohedral Bi2Se3 and FCC Au are determined by XRD, HRTEM, XPS, and Raman spectroscopy. XPS and Raman spectroscopy reveal the interaction between Au and Bi2Se3 by shifting in the binding energies of Au–Au, Au–Se and Bi–Se bonds and the wavenumber of A1g2 and Eg2 modes. Au-decorated Bi2Se3 nanoplatelet heterostructures are observed using FESEM, and confirmed by XPS, Raman spectroscopy, and HRTEM imaging. Their optical band gap of the Au-decorated Bi2Se3 nanoplatelet heterostructures increases with Au thickness about 1.92-fold as much as that of pristine Bi2Se3 (0.39 eV), owing to the Burstein-Moss effect. The optical absorptance of the Au-decorated Bi2Se3 nanoplatelet heterostructures revealed increment with wavelength from 200 to 500 nm and decrement with increasing wavelength from 500 to 800 nm.
Hydrogel-based microfluidic device with multiplexed 3D in vitro cell culture
Authors: Clancy Allison , Chen Dayi , Bruns Joseph , Nadella Jahnavi , Stealey Samuel , Zhang Yanjia , Timperman Aaron , Zustiak Silviya P. 
Published: October 2022

AbstractMicrofluidic devices that combine an extracellular matrix environment, cells, and physiologically relevant perfusion, are advantageous as cell culture platforms. We developed a hydrogel-based, microfluidic cell culture platform by loading polyethylene glycol (PEG) hydrogel-encapsulated U87 glioblastoma cells into membrane-capped wells in polydimethyl siloxane (PDMS). The multilayer microfluidic cell culture system combines previously reported design features in a configuration that loads and biomimetically perfuses a 2D array of cell culture chambers. One dimension of the array is fed by a microfluidic concentration gradient generator (MCGG) while the orthogonal dimension provides loading channels that fill rows of cell culture chambers in a separate layer. In contrast to typical tree-like MCGG mixers, a fractional serial dilution of 1, ½, ¼, and 0 of the initial solute concentration is achieved by tailoring the input microchannel widths. Hydrogels are efficiently and reproducibly loaded in all wells and cells are evenly distributed throughout the hydrogel, maintaining > 90% viability for up to 4 days. In a drug screening assay, diffusion of temozolomide and carmustine to hydrogel-encapsulated U87 cells from the perfusion solution is measured, and dose–response curves are generated, demonstrating utility as an in vitro mimic of the glioblastoma microenvironment.
Oral expressions and functional analyses of the extracellular calcium-sensing receptor (CaSR) in chicken
Authors: Omori Hikaru , Kawabata Yuko , Yoshida Yuta , Nagamoto Yutaro , Kawabata Fuminori , Nishimura Shotaro , Tabata Shoji 
Published: October 2022

AbstractIn vertebrates, the extracellular calcium-sensing receptor (CaSR) plays a key role in calcium homeostasis by sensing slight changes in extracellular Ca2+. CaSR is also expressed in mammals including rodent taste cells and is involved in sensing kokumi, a rich, savory quality that enhances the intensities of salty, sweet, and umami tastes. In this study, we focused on chicken CaSR (cCaSR) since calcium is an essential nutrient that is necessary for making eggshell and for the extremely rapid initial growth of bones. First we confirmed that cCaSR is expressed in taste cells. Next we cloned the cCaSR gene from kidney and transiently transfected human embryonic kidney 293 T (HEK293T) cells with the recombinant cCaSR, or empty vector and looked for the agonists and allosteric modulators (including kokumi substances) of cCaSR by Ca2+ imaging. We found that cCaSR was activated by extracellular Ca2+ and Mg2+ in a dose dependent manner. Several L-amino acids and kokumi substances such as glutathione enhanced the response of cCaSR. In addition, NPS2143 as a negative allosteric modulator of human CaSR negatively modulated the response of cCaSR. These results suggest that cCaSR can sense extracellular Ca2+ and Mg2+ as well as positive and negative allosteric modulators. Taken together, the results imply that CaSR might be a multifunctional receptor for calcium, amino acids, and kokumi substances in chicken. The present finding that functional CaSR is expressed in the chicken oral tissues will allow us to further elucidate the physiological role of CaSR in the chickens' taste sense, and to create new feeds that will contribute to the poultry industry.
A semi-supervised adaptive Markov Gaussian embedding process (SAMGEP) for prediction of phenotype event times using the electronic health record
Authors: Ahuja Yuri , Wen Jun , Hong Chuan , Xia Zongqi , Huang Sicong , Cai Tianxi 
Published: October 2022

AbstractWhile there exist numerous methods to identify binary phenotypes (i.e. COPD) using electronic health record (EHR) data, few exist to ascertain the timings of phenotype events (i.e. COPD onset or exacerbations). Estimating event times could enable more powerful use of EHR data for longitudinal risk modeling, including survival analysis. Here we introduce Semi-supervised Adaptive Markov Gaussian Embedding Process (SAMGEP), a semi-supervised machine learning algorithm to estimate phenotype event times using EHR data with limited observed labels, which require resource-intensive chart review to obtain. SAMGEP models latent phenotype states as a binary Markov process, and it employs an adaptive weighting strategy to map timestamped EHR features to an embedding function that it models as a state-dependent Gaussian process. SAMGEP’s feature weighting achieves meaningful feature selection, and its predictions significantly improve AUCs and F1 scores over existing approaches in diverse simulations and real-world settings. It is particularly adept at predicting cumulative risk and event counting process functions, and is robust to diverse generative model parameters. Moreover, it achieves high accuracy with few (50–100) labels, efficiently leveraging unlabeled EHR data to maximize information gain from costly-to-obtain event time labels. SAMGEP can be used to estimate accurate phenotype state functions for risk modeling research.
Effects of mine water on growth characteristics of ryegrass and soil matrix properties
Authors: Xu Lianman , Du Linlin , Li Yajing , Li Weizhe , Wu Hasa 
Published: October 2022

AbstractIrrigation with mine water not only improves water resource utilization rates and alleviates water shortages but can also promote crop growth and yields. However, long-term irrigation with mine water can significantly change the physicochemical properties of soil due to its unique mineral content. In this study, two groups of experiments were conducted (pot experiments and soilless cultivation) using mine water from the Fushun mining area to explore its effects on the physiological and photosynthetic characteristics of ryegrass, as well as soil properties. Mine water irrigation inhibited all of the indicators evaluated in this study, whereas a mixture of clean water and mine water had a stimulatory effect. Interestingly, this stimulatory effect was weakened as the proportion of mine water increased but reached its maximum when the ratio was 2:1. Moreover, the inhibitory effect of the irrigation water was weakened as the proportion of clean water increased. The contents of K+, Na+, Ca2+ and Mg2+ in soil were higher than those in the soil matrix, and the content of the nutrient elements N, P and K, and metal cations increased gradually as the mine water ratio increased, and the electrical conductivity increased significantly. Moreover, the pH of the soil decreased steadily (i.e. acidity increased) with increased soil salinity. Our findings indicated that a mixture of mine water from Fushun mining area and clean water at a 1:2 ratio could improve the physiological, growth, and photosynthetic characteristics of ryegrass by enhancing soil quality. Our study thus provides an experimental precedent for the utilization of mine water in ecological restoration and agricultural irrigation, and could therefore serve as a basis for the development of novel strategies for environmental restoration and the utilization of water resources.
Single molecule microscopy to profile the effect of zinc status on transcription factor dynamics
Authors: Damon Leah J. , Aaron Jesse , Palmer Amy E. 
Published: October 2022

AbstractThe regulation of transcription is a complex process that involves binding of transcription factors (TFs) to specific sequences, recruitment of cofactors and chromatin remodelers, assembly of the pre-initiation complex and recruitment of RNA polymerase II. Increasing evidence suggests that TFs are highly dynamic and interact only transiently with DNA. Single molecule microscopy techniques are powerful approaches for tracking individual TF molecules as they diffuse in the nucleus and interact with DNA. Here we employ multifocus microscopy and highly inclined laminated optical sheet microscopy to track TF dynamics in response to perturbations in labile zinc inside cells. We sought to define whether zinc-dependent TFs sense changes in the labile zinc pool by determining whether their dynamics and DNA binding can be modulated by zinc. We used fluorescently tagged versions of the glucocorticoid receptor (GR), with two C4 zinc finger domains, and CCCTC-binding factor (CTCF), with eleven C2H2 zinc finger domains. We found that GR was largely insensitive to perturbations of zinc, whereas CTCF was significantly affected by zinc depletion and its dwell time was affected by zinc elevation. These results indicate that at least some transcription factors are sensitive to zinc dynamics, revealing a potential new layer of transcriptional regulation.
Characterization of the binding of MRTX1133 as an avenue for the discovery of potential KRASG12D inhibitors for cancer therapy
Authors: Issahaku Abdul Rashid , Mukelabai Namutula , Agoni Clement , Rudrapal Mithun , Aldosari Sahar M. , Almalki Sami G. , Khan Johra 
Published: October 2022

AbstractThe Kirsten rat sarcoma (KRAS) oncoprotein has been on drug hunters list for decades now. Initially considered undruggable, recent advances have successfully broken the jinx through covalent inhibition that exploits the mutated cys12 in the switch II binding pocket (KRASG12C). Though this approach has achieved some level of success, patients with mutations other than cys12 are still uncatered for. KRASG12D is the most frequent KRAS mutated oncoprotein. It is only until recently, MRTX1133 has been discovered as a potential inhibitor of KRASG12D. This study seeks to unravel the structural binding mechanism of MRTX1133 as well as identify potential drug leads of KRASG12D based on structural binding characteristics of MRTX1133. It was revealed that MRTX1133 binding stabilizes the binding site by increasing the hydrophobicity which resultantly induced positive correlated movements of switches I and II which could disrupt their interaction with effector and regulatory proteins. Furthermore, MRTX1133 interacted with critical residues; Asp69 (− 4.54 kcal/mol), His95 (− 3.65 kcal/mol), Met72 (− 2.27 kcal/mol), Thr58 (− 2.23 kcal/mol), Gln99 (− 2.03 kcal/mol), Arg68 (− 1.67 kcal/mol), Tyr96 (− 1.59 kcal/mol), Tyr64 (− 1.34 kcal/mol), Gly60 (− 1.25 kcal/mol), Asp12 (− 1.04 kcal/mol), and Val9 (− 1.03 kcal/mol) that contributed significantly to the total free binding energy of − 73.23 kcal/mol. Pharmacophore-based virtual screening based on the structural binding mechanisms of MRTX1133 identified ZINC78453217, ZINC70875226 and ZINC64890902 as potential KRASG12D inhibitors. Further, structural optimisations and biochemical testing of these compounds would assist in the discovery of effective KRASG12D inhibitors.
An improved sliding mode approach for trajectory following control of nonholonomic mobile AGV
Authors: Jiang Benchi , Li Jiankang , Yang Siyang 
Published: October 2022

AbstractThis paper attempts to address the trajectory following control problem of nonholonomic mobile AGV by proposing an improved sliding mode control approach in which, based on the kinematics and attitude deviations established for AGV, the motion characteristics are analyzed and a backstepping sliding mode control with a novel reaching law is designed. This reaching law integrates the merits of the power and exponential reaching laws and promotes the convergence rates of tracking errors. Moreover, with the improved sliding mode controller, the asymptotic stability of tracking deviations can be strictly guaranteed. The simulations have demonstrated the effectiveness and superiority of the proposed approach for mobile AGV.
Travel time optimization on multi-AGV routing by reverse annealing
Authors: Haba Renichiro , Ohzeki Masayuki , Tanaka Kazuyuki 
Published: October 2022

AbstractQuantum annealing has been actively researched since D-Wave Systems produced the first commercial machine in 2011. Controlling a large fleet of automated guided vehicles is one of the real-world applications utilizing quantum annealing. In this study, we propose a formulation to control the traveling routes to minimize the travel time. We validate our formulation through simulation in a virtual plant and authenticate the effectiveness for faster distribution compared to a greedy algorithm that does not consider the overall detour distance. Furthermore, we utilize reverse annealing to maximize the advantage of the D-Wave’s quantum annealer. Starting from relatively good solutions obtained by a fast greedy algorithm, reverse annealing searches for better solutions around them. Our reverse annealing method improves the performance compared to standard quantum annealing alone and performs up to 10 times faster than a commercial classical solver, Gurobi. This study extends a use of optimization with general problem solvers in the application of multi-AGV systems and reveals the potential of reverse annealing as an optimizer.
Stochastic learning and extremal-field map based autonomous guidance of low-thrust spacecraft
Authors: Singh Sandeep K. , Junkins John L. 
Published: October 2022

AbstractA supervised stochastic learning method called the Gaussian Process Regression (GPR) is used to design an autonomous guidance law for low-thrust spacecraft. The problems considered are both of the time- and fuel-optimal regimes and a methodology based on “perturbed back-propagation” approach is presented to generate optimal control along neighboring optimal trajectories which form the extremal bundle constituting the training data-set. The use of this methodology coupled with a GPR approximation of the spacecraft control via prediction of the costate n-tuple or the primer vector respectively for time- and fuel-optimal trajectories at discrete time-steps is demonstrated to be effective in designing an autonomous guidance law using the open-loop bundle of trajectories to-go. The methodology is applied to the Earth-3671 Dionysus time-optimal interplanetary transfer of a low-thrust spacecraft with off-nominal thruster performance and the resulting guidance law is evaluated under different design parameters using case-studies. The results highlight the utility and applicability of the proposed framework with scope for further improvements.
RELA is required for CD271 expression and stem-like characteristics in hypopharyngeal cancer
Authors: Nakazato Akira , Mochizuki Mai , Shibuya-Takahashi Rie , Fujimori Haruna , Fujii Keitaro , Saijoh Satoshi , Morita Shinkichi , Yamazaki Tomoko , Imai Takayuki , Sato Ikuro , Satoh Kennichi , Yamaguchi Kazunori , Sugamura Kazuo , Yasuda Jun , Matsuura Kazuto , Shojaku Hideo , Asada Yukinori , Tamai Keiichi 
Published: October 2022

AbstractCD271 (also referred to as nerve growth factor receptor or p75NTR) is expressed on cancer stem cells in hypopharyngeal cancer (HPC) and regulates cell proliferation. Because elevated expression of CD271 increases cancer malignancy and correlates with poor prognosis, CD271 could be a promising therapeutic target; however, little is known about the induction of CD271 expression and especially its promoter activity. In this study, we screened transcription factors and found that RELA (p65), a subunit of nuclear factor kappaB (NF-κB), is critical for CD271 transcription in cancer cells. Specifically, we found that RELA promoted CD271 transcription in squamous cell carcinoma cell lines but not in normal epithelium and neuroblastoma cell lines. Within the CD271 promoter sequence, region + 957 to + 1138 was important for RELA binding, and cells harboring deletions in proximity to the + 1045 region decreased CD271 expression and sphere-formation activity. Additionally, we found that clinical tissue samples showing elevated CD271 expression were enriched in RELA-binding sites and that HPC tissues showed elevated levels of both CD271 and phosphorylated RELA. These data suggested that RELA increases CD271 expression and that inhibition of RELA binding to the CD271 promoter could be an effective therapeutic target.
(Pre)diabetes, glycemia, and daily glucose variability are associated with retinal nerve fiber layer thickness in The Maastricht Study
Authors: van der Heide Frank C. T. , Foreman Yuri D. , Franken Iris W. M. , Henry Ronald M. A. , Kroon Abraham A. , Dagnelie Pieter C. , Eussen Simone J. P. M. , Berendschot Tos T. J. M. , Schouten Jan S. A. G. , Webers Carroll A. B. , Schram Miranda T. , van der Kallen Carla J. H. , van Greevenbroek Marleen M. J. , Wesselius Anke , Schalkwijk Casper G. , Schaper Nicolaas C. , Brouwers Martijn C. G. J. , Stehouwer Coen D. A. 
Published: October 2022

AbstractRetinopathy and neuropathy in type 2 diabetes are preceded by retinal nerve fibre layer (RNFL) thinning, an index of neurodegeneration. We investigated whether glucose metabolism status (GMS), measures of glycaemia, and daily glucose variability (GV) are associated with RNFL thickness over the entire range of glucose tolerance. We used cross-sectional data from The Maastricht Study (up to 5455 participants, 48.9% men, mean age 59.5 years and 22.7% with type 2 diabetes) to investigate the associations of GMS, measures of glycaemia (fasting plasma glucose [FPG], 2-h post-load glucose [2-h PG], HbA1c, advanced glycation endproducts [AGEs] assessed as skin autofluorescence [SAF]) and indices of daily GV (incremental glucose peak [IGP] and continuous glucose monitoring [CGM]-assessed standard deviation [SD]) with mean RNFL thickness. We used linear regression analyses and, for GMS, P for trend analyses. We adjusted associations for demographic, cardiovascular risk and lifestyle factors, and, only for measures of GV, for indices of mean glycaemia. After full adjustment, type 2 diabetes and prediabetes (versus normal glucose metabolism) were associated with lower RNFL thickness (standardized beta [95% CI], respectively − 0.16 [− 0.25; − 0.08]; − 0.05 [− 0.13;  0.03]; Ptrend = 0.001). Greater FPG, 2-h PG, HbA1c, SAF, IGP, but not CGM-assessed SD, were also associated with lower RNFL thickness (per SD, respectively − 0.05 [− 0.08; − 0.01]; − 0.06 [− 0.09; − 0.02]; − 0.05 [− 0.08; − 0.02]; − 0.04 [− 0.07; − 0.01]; − 0.06 [− 0.12; − 0.01]; and − 0.07 [− 0.21; 0.07]). In this population-based study, a more adverse GMS and, over the entire range of glucose tolerance, greater glycaemia and daily GV were associated with lower RNFL thickness. Hence, early identification of individuals with hyperglycaemia, early glucose-lowering treatment, and early monitoring of daily GV may contribute to the prevention of RNFL thinning, an index of neurodegeneration and precursor of retinopathy and neuropathy.