bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanical performance of co-deposited immiscible Cu–Ta thin films
Authors: Raeker Evan , Powers Max , Misra Amit 
Published: October 2020

AbstractThe immiscible alloy Cu–Ta has the potential for enhanced mechanical performance in applications as a functional coating. To establish baseline mechanical properties, four Cu–Ta films were co-sputtered at the temperatures 23, 400, 600, and 800 °C and tested with nanoindentation at strain rates 5$$\times $$×10−3 s−1to 10 s−1. Each film had a unique microstructure morphology. The hardness and elastic modulus of the four films were insensitive to strain rate changes. Instead, the measured properties were spatially dependent, particularly in the 600 and 800 °C films. In those two films, there is a bimodal deformation behavior due to Cu-agglomeration under protruding grains and planar Ta-rich regions. Increasing the indentation depth revealed shear band suppression which is related to a homogenous distribution of flow stresses for all four microstructure morphologies. Finally, the Cu–Ta hardness appeared to follow a rule-of-mixtures when compared to extrapolated data of Cu and Ta monolithic films.
Image segmentation of plexiform neurofibromas from a deep neural network using multiple b-value diffusion data
Authors: Ho Chang Y. , Kindler John M. , Persohn Scott , Kralik Stephen F. , Robertson Kent A. , Territo Paul R. 
Published: October 2020

AbstractWe assessed the accuracy of semi-automated tumor volume maps of plexiform neurofibroma (PN) generated by a deep neural network, compared to manual segmentation using diffusion weighted imaging (DWI) data. NF1 Patients were recruited from a phase II clinical trial for the treatment of PN. Multiple b-value DWI was imaged over the largest PN. All DWI datasets were registered and intensity normalized prior to segmentation with a multi-spectral neural network classifier (MSNN). Manual volumes of PN were performed on 3D-T2 images registered to diffusion images and compared to MSNN volumes with the Sørensen-Dice coefficient. Intravoxel incoherent motion (IVIM) parameters were calculated from resulting volumes. 35 MRI scans were included from 14 subjects. Sørensen-Dice coefficient between the semi-automated and manual segmentation was 0.77 ± 0.016. Perfusion fraction (f) was significantly higher for tumor versus normal tissue (0.47 ± 0.42 vs. 0.30 ± 0.22, p = 0.02), similarly, true diffusion (D) was significantly higher for PN tumor versus normal (0.0018 ± 0.0003 vs. 0.0012 ± 0.0002, p < 0.0001). By contrast, the pseudodiffusion coefficient (D*) was significantly lower for PN tumor versus normal (0.024 ± 0.01 vs. 0.031 ± 0.005, p < 0.0001). Volumes generated by a neural network from multiple diffusion data on PNs demonstrated good correlation with manual volumes. IVIM analysis of multiple b-value diffusion data demonstrates significant differences between PN and normal tissue.
Alternative feed ingredients in the finisher diets for sustainable broiler production
Authors: El-Deek Ahmed A. , Abdel-Wareth Ahmed A. A. , Osman Mona , El-Shafey Mohammed , Khalifah Ayman M. , Elkomy Alaa E. , Lohakare Jayant 
Published: October 2020

AbstractThe main objective of this study was to evaluate the utilization of alternative protein feed ingredients including sunflower meal (SFM), corn gluten meal (CGM), and dried distillers’ grains with solubles (DDGS) as a mixture in a partial replacement of soybean meal (SBM) in broiler finisher diets with different protein levels and also to evaluate their effect on birds’ performance, environmental aspects of litter, cecal microbes, and economic prospects. A total of 576 (19 days old) Cobb 500 broiler chicks were fed eight finisher diets consisting of 4 control (CTL) diets based on SBM with different crude protein (CP) levels (CTL21, CTL20, CTL19, and CTL18, containing 21%, 20%, 19%, and 18% CP, respectively) and 4 test diets with alternative protein sources (APS21, APS20, APS19, and APS18, containing 21%, 20%, 19%, and 18% CP, respectively) using a 15% combination of alternative protein sources (2.5% CGM, 5% SFM, and 7.5% DDGS) until 35 days of age. The results indicated that birds fed test diets APS21 and APS20 recorded the highest (P < 0.05) body weight compared to other treatments, but it was not different than the CTL diets fed at these CP levels. The birds fed CTL18 or APS18 recorded the worst feed conversion ratio (FCR) compared to other treatments. Moreover, birds fed test diet containing APS21 recorded better (P < 0.05) European performance efficiency factor and better economic efficiency when compared to other treatments, but it was not different than CTL21. In addition, birds fed diets APS21 and CTL19 showed significantly increased litter Lactobacillus spp. (P < 0.05) compared to other treatments. Cecal Lactobacillus spp. and Escherichia coli (E. coli) were not affected by CTL or APS diets. The counts of cecal Salmonella spp. increased in the CTL21 group compared to other groups. In conclusion, alternative feed ingredients (protein sources) in broiler finisher diets have positive effects in a sustainable way on the productive performance, litter and cecal microbial counts, and improved economic efficiency when compared to CTL diets.
Satellite radar observation of large surface collapses induced by the 2017 North Korea nuclear test
Authors: Baek Won-Kyung , Jung Hyung-Sup , Kim Tae Sung 
Published: October 2020

AbstractThe artificial earthquake of mb 6.1 related to the North Korea’s sixth nuclear test occured at Mt. Mantap, North Korea on September 3, 2017. It was reported that a large and complex surface deformation was caused by the event. The surface deformation was composed of expansion of explosions, collapse, compaction and landslides. Since the precise vertical deformation measurement is very important to estimate the stability of the nuclear test facility, we retrieved a precise 3D surface deformation field and then decomposed the vertical deformation pattern from the 3D deformation. The measured maximum deformation was about − 491, − 343 and 166 cm with the measurement uncertainty of about 3.3, 4.1 and 2.7 cm in the east, north and up directions, respectively. The maximum horizontal deformation was approximately 515 cm. The horizontal deformation clearly showed a radial pattern because it was mainly caused by the explosions and landslides, while the vertical deformation displayed a rugged pattern because it was affected by the explosions, compaction and collapse. The collapse may seem to occur along the underground tunnels and at the test site’s epicenter as well. Moreover, the severe collapse was observed westside from the epicenter of the sixth nuclear test, and it has a depth of about 68.6 cm on the area of 0.3765 km2. On the basis of our results including the shapes, locations and volume changes of the large collapse, evidently a new vital piece of information was obtained so that it could be used to interprete the sixth nuclear test more accurately.
In vitro maturation in the presence of Leukemia Inhibitory Factor modulates gene and miRNA expression in bovine oocytes and embryos
Authors: Vendrell-Flotats Meritxell , García-Martínez Tania , Martínez-Rodero Iris , López-Béjar Manel , LaMarre Jonathan , Yeste Marc , Mogas Teresa 
Published: October 2020

AbstractMembers of the interleukin-6 (IL-6) family of cytokines are important for reproductive function that are mediated through changes in gene and miRNA expression. Herein, we characterized the expression of miR-21, miR-155, miR-34c and miR-146a in bovine oocytes and cumulus cells during in vitro maturation (IVM) with leukemia inhibitory factor (LIF), IL-6 and IL-11 or unsupplemented controls. LIF-exposed COCs showed higher expression of miR-21 and miR-155 in oocytes, whereas miR-146a expression was increased in oocytes matured with IL-6 and IL-11. In cumulus cells, miR-155 expression was elevated by all treatments while only LIF increased miR-21 expression. Based on these results, we next examined how LIF exposure during IVM affected oocyte competence, through IVF and the expression of specific genes in GV- and MII-oocytes, in 2- and 8-cell embryos, and in Day 8-blastocysts. LIF supplementation did not affect cleavage rate, blastocyst yield or several other developmental parameters, but did increase hatching rate. LIF suppressed DPPA3, ZAR1 and NPM2 expression in 2 cell- and/or 8-cell embryos. LIF increased the expression of KAT2A and HSPA1A in MII-oocytes, and that of HDAC1, KAT2A and HSP90AA1 and the BAX:BCL2L1 ratio in 2-cell embryos. In contrast, HDAC1, KAT2A and HSP90AA1 expression and BAX:BCL2L1 ratio was lower in 8-cell embryos derived from LIF oocytes. IVM with LIF also increased the expression of DNMT3A, HSPA1A and HSP90AA1 in blastocysts. In conclusion, supplementation with LIF during IVM was consistently associated with changes in the relative abundance of transcripts in mature bovine oocytes and in specific embryo developmental stages.
Diversity of voltage-gated potassium channels and cyclic nucleotide-binding domain-containing channels in eukaryotes
Authors: Pozdnyakov Ilya , Safonov Pavel , Skarlato Sergei 
Published: October 2020

AbstractVoltage-gated potassium channels (Kv) and cyclic nucleotide-binding domain-containing cation channels HCN, CNG, and KCNH are the evolutionarily related families of ion channels in animals. Their homologues were found in several lineages of eukaryotes and prokaryotes; however, the actual phylogenetic and structural diversity of these ion channels remains unclear. In this work, we present a taxonomically broad investigation of evolutionary relationships and structural diversity of Kv, HCN, CNG, and KCNH and their homologues in eukaryotes focusing on channels from different protistan groups. We demonstrate that both groups of channels consist of a more significant number of lineages than it was shown before, and these lineages can be grouped in two clusters termed Kv-like channels and CNBD-channels. Moreover, we, for the first time, report the unusual two-repeat tandem Kv-like channels and CNBD-channels in several eukaryotic groups, i.e. dinoflagellates, oomycetes, and chlorarachniophytes. Our findings reveal still underappreciated phylogenetic and structural diversity of eukaryotic ion channel lineages.
Gene expression profile of CD14+ blood monocytes following lifestyle-induced weight loss in individuals with metabolic syndrome
Authors: Biemann Ronald , Roomp Kirsten , Noor Fozia , Krishnan Shruthi , Li Zhen , Shahzad Khurrum , Borucki Katrin , Luley Claus , Schneider Jochen G. , Isermann Berend 
Published: October 2020

AbstractLifestyle-induced weight loss is regarded as an efficient therapy to reverse metabolic syndrome (MetS) and to prevent disease progression. The objective of this study was to investigate whether lifestyle-induced weight loss modulates gene expression in circulating monocytes. We analyzed and compared gene expression in monocytes (CD14+cells) and subcutaneous adipose tissue biopsies by unbiased mRNA profiling. Samples were obtained before and after diet-induced weight loss in well-defined male individuals in a prospective controlled clinical trial (ICTRP Trial Number: U1111-1158-3672). The BMI declined significantly (− 12.6%) in the treatment arm (N = 39) during the 6-month weight loss intervention. This was associated with a significant reduction in hsCRP (− 45.84%) and circulating CD14+cells (− 21.0%). Four genes were differentially expressed (DEG’s) in CD14+cells following weight loss (ZRANB1, RNF25, RB1CC1 and KMT2C). Comparative analyses of paired CD14+monocytes and subcutaneous adipose tissue samples before and after weight loss did not identify common genes differentially regulated in both sample types. Lifestyle-induced weight loss is associated with specific changes in gene expression in circulating CD14+monocytes, which may affect ubiquitination, histone methylation and autophagy.
A metasurface composed of 3-bit coding linear polarization conversion elements and its application to RCS reduction of patch antenna
Authors: Kong Xiangkun , Wang Qi , Jiang Shunliu , Kong Lingqi , Yuan Jing , Yan Xiangxi , Wang Xuemeng , Zhao Xing 
Published: October 2020

AbstractIn this paper, a metasurface composed of 3-bit coding linear polarization conversion elements and its application to RCS reduction of the patch antenna is intensively studied. At first, 3-bit coding metasurface are constructed by a sequence of eight coded unit cells, which have a similar cross-polarized reflected amplitude response and gradient reflected phase responses covering 0–2π, respectively. Equivalent circuit models of these unit cells are created to describe their electrical behavior for the two linear incident polarizations at the same time. Then, a patch antenna is integrated on the 3-bit metasurface, of which the elements are placed with a 2-dimensional linear coding sequence. The metal square ring is set around the patch antenna to protect it from the disturbance of metasurface. Both the simulation and experiment results demonstrate that the designed metasurface can primarily reduce the antenna RCS at a broadband, while the antenna performances are not degraded significantly.
Asynchronous multi-decadal time-scale series of biotic and abiotic responses to precipitation during the last 1300 years
Authors: Yi Sangheon , Jun Chang-Pyo , Jo Kyoung-nam , Lee Hoil , Kim Min-Seok , Lee Sang Deuk , Cao Xianyong , Lim Jaesoo 
Published: October 2020

AbstractEast Asian summer monsoon (EASM)-driven rapid hydroclimatic variation is a crucial factor with major socioeconomic impacts. Nevertheless, decadal- to centennial-scale EASM variability over the last two millennia is still poorly understood. Pollen-based quantitative annual precipitation (PqPann) and annual precipitation reconstructed by artificial neural networks (ANNs) for the period 650–1940 CE were reconstructed from a paleo-reservoir in South Korea. ANNs reconstruction was performed to compensate for a hiatus section. On a decadal timescale, 10 high-precipitation periods were identified, and PqPann and ANNs reconstructions were comparable to local instrumental rainfall and historic drought records. Biotic lags to rapid climatic changes ranging from 25 to 100 years were recognized by asynchronous pollen and speleothem responses to precipitation. We suggest that PqPann-based decadal- to centennial-scale climatic change reconstruction should take biotic lags into account, although the lags can be ignored on the millennial scale. The position of the EASM rainband influenced rainfall magnitude.
Fine-tuning of AMPK–ULK1–mTORC1 regulatory triangle is crucial for autophagy oscillation
Authors: Holczer Marianna , Hajdú Bence , Lőrincz Tamás , Szarka András , Bánhegyi Gábor , Kapuy Orsolya 
Published: October 2020

AbstractAutophagy is an intracellular digestive process, which has a crucial role in maintaining cellular homeostasis by self-eating the unnecessary and/or damaged components of the cell at various stress events. ULK1, one of the key elements of autophagy activator complex, together with the two sensors of nutrient and energy conditions, called mTORC1 and AMPK kinases, guarantee the precise function of cell response mechanism. We claim that the feedback loops of AMPK–mTORC1–ULK1 regulatory triangle determine an accurate dynamical characteristic of autophagic process upon cellular stress. By using both molecular and theoretical biological techniques, here we reveal that a delayed negative feedback loop between active AMPK and ULK1 is essential to manage a proper cellular answer after prolonged starvation or rapamycin addition. AMPK kinase quickly gets induced followed by AMPK-P-dependent ULK1 activation, whereas active ULK1 has a rapid negative effect on AMPK-P resulting in a delayed inhibition of ULK1. The AMPK-P → ULK1 ˧ AMPK-P negative feedback loop results in a periodic repeat of their activation and inactivation and an oscillatory activation of autophagy, as well. We demonstrate that the periodic induction of self-cannibalism is necessary for the proper dynamical behaviour of the control network when mTORC1 is inhibited with respect to various stress events. By computational simulations we also suggest various scenario to introduce “delay” on AMPK-P-dependent ULK1 activation (i.e. extra regulatory element in the wiring diagram or multi-phosphorylation of ULK1).
Antibodies exhibit multiple paratope states influencing VH–VL domain orientations
Authors: Fernández-Quintero Monica L. , Pomarici Nancy D. , Math Barbara A. , Kroell Katharina B. , Waibl Franz , Bujotzek Alexander , Georges Guy , Liedl Klaus R. 
Published: October 2020

AbstractIn the last decades, antibodies have emerged as one of the most important and successful classes of biopharmaceuticals. The highest variability and diversity of an antibody is concentrated on six hypervariable loops, also known as complementarity determining regions (CDRs) shaping the antigen-binding site, the paratope. Whereas it was assumed that certain sequences can only adopt a limited set of backbone conformations, in this study we present a kinetic classification of several paratope states in solution. Using molecular dynamics simulations in combination with experimental structural information we capture the involved conformational transitions between different canonical clusters and additional dominant solution structures occurring in the micro-to-millisecond timescale. Furthermore, we observe a strong correlation of CDR loop movements. Another important aspect when characterizing different paratope states is the relative VH/VLorientation and the influence of the distinct CDR loop states on the VH/VLinterface. Conformational rearrangements of the CDR loops do not only have an effect on the relative VH/VLorientations, but also influence in some cases the elbow-angle dynamics and shift the respective distributions. Thus, our results show that antibodies exist as several interconverting paratope states, each contributing to the antibody’s properties.
A substrate-trapping strategy to find E3 ubiquitin ligase substrates identifies Parkin and TRIM28 targets
Authors: Watanabe Masashi , Saeki Yasushi , Takahashi Hidehisa , Ohtake Fumiaki , Yoshida Yukiko , Kasuga Yusuke , Kondo Takeshi , Yaguchi Hiroaki , Suzuki Masanobu , Ishida Hiroki , Tanaka Keiji , Hatakeyama Shigetsugu 
Published: October 2020

AbstractThe identification of true substrates of an E3 ligase is biologically important but biochemically difficult. In recent years, several techniques for identifying substrates have been developed, but these approaches cannot exclude indirect ubiquitination or have other limitations. Here we develop an E3 ligase substrate-trapping strategy by fusing a tandem ubiquitin-binding entity (TUBE) with an anti-ubiquitin remnant antibody to effectively identify ubiquitinated substrates. We apply this method to one of the RBR-type ligases, Parkin, and to one of the RING-type ligases, TRIM28, and identify previously unknown substrates for TRIM28 including cyclin A2 and TFIIB. Furthermore, we find that TRIM28 promotes cyclin A2 ubiquitination and degradation at the G1/S phase and suppresses premature entry into S phase. Taken together, the results indicate that this method is a powerful tool for comprehensively identifying substrates of E3 ligases.
Dynamical decoupling of laser phase noise in compound atomic clocks
Authors: Dörscher Sören , Al-Masoudi Ali , Bober Marcin , Schwarz Roman , Hobson Richard , Sterr Uwe , Lisdat Christian 
Published: October 2020

AbstractThe frequency stability of many optical atomic clocks is limited by the coherence of their local oscillator. Here, we present a measurement protocol that overcomes the laser coherence limit. It relies on engineered dynamical decoupling of laser phase noise and near-synchronous interrogation of two clocks. One clock coarsely tracks the laser phase using dynamical decoupling; the other refines this estimate using a high-resolution phase measurement. While the former needs to have a high signal-to-noise ratio, the latter clock may operate with any number of particles. The protocol effectively enables minute-long Ramsey interrogation for coherence times of few seconds as provided by the current best ultrastable laser systems. We demonstrate implementation of the protocol in a realistic proof-of-principle experiment, where we interrogate for 0.5 s at a laser coherence time of 77 ms. Here, a single lattice clock is used to emulate synchronous interrogation of two separate clocks in the presence of artificial laser frequency noise. We discuss the frequency instability of a single-ion clock that would result from using the protocol for stabilisation, under these conditions and for minute-long interrogation, and find expected instabilities of σy(τ) = 8 × 10−16(τ/s)−1/2 and σy(τ) = 5 × 10−17(τ/s)−1/2, respectively.
MicroRNA-183-5p contributes to malignant progression through targeting PDCD4 in human hepatocellular carcinoma
Authors: Duan Xiaohui , Li Wei , Hu Peng , Jiang Bo , Yang Jianhui , Zhou Lixue , Mao Xianhai , Tian Bingzhang 
Published: October 2020

Abstract
Hepatocellular carcinoma (HCC) remains one of the most common malignant tumors worldwide. The present study aimed to investigate the biological role of microRNA-183-5p (miR-183-5p), a novel tumor-related microRNA (miRNA), in HCC and illuminate the possible molecular mechanisms. The expression patterns of miR-183-5p in clinical samples were characterized using qPCR analysis. Kaplan–Meier survival curve was applied to evaluate the correlation between miR-183-5p expression and overall survival of HCC patients. Effects of miR-183-5p knockdown on HCC cell proliferation, apoptosis, migration and invasion capabilities were determined via Cell Counting Kit-8 (CCK8) assays, flow cytometry, scratch wound healing assays and Transwell invasion assays, respectively. Mouse neoplasm transplantation models were established to assess the effects of miR-183-5p knockdown on tumor growth in vivo. Bioinformatics analysis, dual-luciferase reporter assays and rescue assays were performed for mechanistic researches. Results showed that miR-183-5p was highly expressed in tumorous tissues compared with adjacent normal tissues. Elevated miR-183-5p expression correlated with shorter overall survival of HCC patients. Moreover, miR-183-5p knockdown significantly suppressed proliferation, survival, migration and invasion of HCC cells compared with negative control treatment. Consistently, miR-183-5p knockdown restrained tumor growth in vivo. Furthermore, programmed cell death factor 4 (PDCD4) was identified as a direct target of miR-183-5p. Additionally, PDCD4 down-regulation was observed to abrogate the inhibitory effects of miR-183-5p knockdown on malignant phenotypes of HCC cells. Collectively, our data suggest that miR-183-5p may exert an oncogenic role in HCC through directly targeting PDCD4. The current study may offer some new insights into understanding the role of miR-183-5p in HCC.
Targeting RNA structures in diseases with small molecules
Authors: Shao Yanqiu , Zhang Qiangfeng Cliff 
Published: October 2020

Abstract
RNA is crucial for gene expression and regulation. Recent advances in understanding of RNA biochemistry, structure and molecular biology have revealed the importance of RNA structure in cellular processes and diseases. Various approaches to discovering drug-like small molecules that target RNA structure have been developed. This review provides a brief introduction to RNA structural biology and how RNA structures function as disease regulators. We summarize approaches to targeting RNA with small molecules and highlight their advantages, shortcomings and therapeutic potential.