bluuebunny/crossref_metadata_2025_split huggingface dataset:
A downsampling strategy to assess the predictive value of radiomic features
Authors: Dirand Anne-Sophie , Frouin Frédérique , Buvat Irène 
Published: November 2019

AbstractMany studies are devoted to the design of radiomic models for a prediction task. When no effective model is found, it is often difficult to know whether the radiomic features do not include information relevant to the task or because of insufficient data. We propose a downsampling method to answer that question when considering a classification task into two groups. Using two large patient cohorts, several experimental configurations involving different numbers of patients were created. Univariate or multivariate radiomic models were designed from each configuration. Their performance as reflected by the Youden index (YI) and Area Under the receiver operating characteristic Curve (AUC) was compared to the stable performance obtained with the highest number of patients. A downsampling method is described to predict the YI and AUC achievable with a large number of patients. Using the multivariate models involving machine learning, YI and AUC increased with the number of patients while they decreased for univariate models. The downsampling method better estimated YI and AUC obtained with the largest number of patients than the YI and AUC obtained using the number of available patients and identifies the lack of information relevant to the classification task when no such information exists.
Transcriptional control of central carbon metabolic flux in Bifidobacteria by two functionally similar, yet distinct LacI-type regulators
Authors: Lanigan Noreen , Kelly Emer , Arzamasov Aleksandr A. , Stanton Catherine , Rodionov Dmitry A. , van Sinderen Douwe 
Published: November 2019

AbstractBifidobacteria resident in the gastrointestinal tract (GIT) are subject to constantly changing environmental conditions, which require rapid adjustments in gene expression. Here, we show that two predicted LacI-type transcription factors (TFs), designated AraQ and MalR1, are involved in regulating the central, carbohydrate-associated metabolic pathway (the so-called phosphoketolase pathway or bifid shunt) of the gut commensal Bifidobacterium breve UCC2003. These TFs appear to not only control transcription of genes involved in the bifid shunt and each other, but also seem to commonly and directly affect transcription of other TF-encoding genes, as well as genes related to uptake and metabolism of various carbohydrates. This complex and interactive network of AraQ/MalR1-mediated gene regulation provides previously unknown insights into the governance of carbon metabolism in bifidobacteria.
Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor
Authors: Liu Jingxian , Wang Guiqun , Liu Liu , Wu Runjie , Wu Yi , Fang Cheng , Zhou Xinhong , Jiao Jing , Gu Ying , Zhou He , Xie Zhenhui , Sun Zhiwu , Chen Dakai , Dai Ken , Wang Dongxu , Tang Wei , Yang Teddy Tat Chi 
Published: November 2019

AbstractProgrammed cell death 1 (PD-1) monoclonal antibodies have been approved by regulatory agencies for the treatment of various types of cancer, and the mechanism involves the restoration of T cell functions. We report herein the X-ray crystal structure of a fully human monoclonal antibody mAb059c fragment antigen-binding (Fab) in complex with the PD-1 extracellular domain (ECD) at a resolution of 1.70 Å. Structural analysis indicates 1) an epitope, comprising fragments from the C’D, BC and FG loops of PD-1, contributes to mAb059c interaction, 2) an unique conformation of the C’D loop and a different orientation of R86 enabling the capture of PD-1 by the antibody complementarity determining region (CDR) and the formation of one salt-bridge contact – ASP101(HCDR3):ARG86(PD-1), and 3) the contact of FG with light chain (LC) CDR3 is maintained by a second salt-bridge and two backbone hydrogen bonds. Interface analysis reveals that N-glycosylation sites 49, 74 and 116 on PD-1 do not contact mAb059c; while N58 in the BC loop is recognized by mAb059c heavy chain CDR1 and CDR2. Mutation of N58 attenuated mAb059c binding to PD-1. These findings and the novel anti-PD-1 antibody will facilitate better understanding of the mechanisms of the molecular recognition of PD-1 receptor by anti-PD-1 mAb and, thereby, enable the development of new therapeutics with an expanded spectrum of efficacy for unmet medical needs.
Improving the Real-time Marine Forecasting of the Northern South China Sea by Assimilation of Glider-observed T/S Profiles
Authors: Peng Shiqiu , Zhu Yuhang , Li Zhijin , Li Yineng , Xie Qiang , Liu Shijie , Luo Yeteng , Tian Yu , Yu Jiancheng 
Published: November 2019

AbstractPrediction of marine conditions is notoriously challenging in the northern South China Sea (NSCS) due to inadequate observations in the region. The underwater gliders that were developed during the past decade may provide observing platforms that could produce required observations. During a field experiment, temperature/salinity (T/S) profiles from a set of underwater gliders were assimilated into a real-time marine forecasting system, along with the assimilation of climatological monthly mean Argo data to constrain the basin-wide model biases. The results show that, in addition to the reduction of the basin-wide model biases by the assimilation of the climatological monthly mean Argo data, the assimilation of glider-observed T/S profiles is efficient to reduce the local biases of the NSCS marine forecasting by as much as 28–31% (19–36%) in 24 h to 120 h forecasts for temperature (salinity) from sea surface to a depth of 1000 m. Our results imply that the real-time marine forecasting for the NSCS can largely benefit from a sustainable glider observing network of the NSCS in the future.
Inducing oculomotor plasticity to disclose the functional link between voluntary saccades and endogenous attention deployed perifoveally
Authors: Nicolas Judith , Bidet-Caulet Aurélie , Pélisson Denis 
Published: November 2019

AbstractTo what extent oculomotor and attention systems are linked remains strongly debated. Previous studies suggested that saccadic adaptation, a well-studied model of oculomotor plasticity, and orienting of attention rely on overlapping networks in the parietal cortex and can functionally interact. Using a Posner-like paradigm in healthy human subjects, we demonstrate for the first time that saccadic adaptation boosts endogenous attention orienting. Indeed, the discrimination of perifoveal targets benefits more from central cues after backward adaptation of leftward voluntary saccades than after a control saccade task. We propose that the overlap of underlying neural networks actually consists of neuronal populations co-activated by oculomotor plasticity and endogenous attention deployed perifoveally. The functional coupling demonstrated here plaids for conceptual models not belonging to the framework of the premotor theory of attention as the latter has been rejected precisely for this voluntary/endogenous modality. These results also open new perspective for rehabilitation of visuo-attentional deficits.
A stroma-corrected ZEB1 transcriptional signature is inversely associated with antitumor immune activity in breast cancer
Authors: Block C. James , Dyson Gregory , Campeanu Ion John , Watza Donovan , Ratnam Manohar , Wu Guojun 
Published: November 2019

AbstractThe epithelial-to-mesenchymal transition (EMT) is an essential developmental process which can be hijacked by cancer cells, leading to enhanced metastasis and chemoresistance in experimental models. Recent studies have linked gene expression of EMT-associated gene signatures to increased inflammatory immune response in multiple cancer types. However, these studies did not account for the potential confounding effects of gene expression by tumor-infiltrating mesenchymal stromal cells. In this study, we comprehensively dissect the associations between multiple EMT transcription factors and EMT markers with stromal and immune tumor infiltration. We find that EMT-related genes are highly correlated with intratumoral stromal cell abundance and identify a specific relationship between stroma-corrected ZEB1 expression and decreased immune activity in multiple cancer types. We derive a stroma-corrected ZEB1-activated transcriptional signature and demonstrate that this signature includes several known inhibitors of inflammation, including BMPR2. Finally, multivariate survival analysis reveals that ZEB1 and its expression signature are significantly associated with reduced overall survival in breast cancer patients. In conclusion, this study identifies a novel association between stroma-adjusted ZEB1 expression and tumor immune activity and addresses the critical issue of confounding between EMT-associated genes and tumor stromal content.
Characterization and assessment of barnacle larval settlement-inducing activity of extracellular polymeric substances isolated from marine biofilm bacteria
Authors: Siddik Aboobucker , Satheesh Sathianeson 
Published: November 2019

AbstractExtracellular polymeric substances (EPSs) are the hydrated gelatinous matrix produced by microorganisms for attachment in a biofilm environment. In this study, the compositional variation between EPSs of three marine biofilm bacteria (Pseudoalteromonas shioyasakiensis, Vibrio harveyi and Planomicrobium sp.) were analysed by GC-MS, 1H NMR, FT-IR and XRD and SEM. The ecological significance of exopolymers was assessed in vivo using marine model organism barnacle larvae for their settlement-inducing activity. Chemical analysis revealed the presence of glycan fucosylated oligosaccharides, tetraose, trisaccharides, iso-B-Pentasaccharides, sialyllactose, oligomannose, galacto-N-biose, difucosyl-para-lacto-N-neohexaose, 3′-sialyl N-acetyllactosamine and isoglobotriaose-β-N(Acetyl)-Propargyl in all extracted EPSs. Bioassay results indicated that treatment of the barnacle larvae with EPSs from three bacterial strains enhanced settlement on substrates. In conclusion, this study highlighted the role of water-soluble EPSs in the invertebrate larval settlement on artificial materials.
Navigated transcranial magnetic stimulation of the supplementary motor cortex disrupts fine motor skills in healthy adults
Authors: Schramm Severin , Albers Lucia , Ille Sebastian , Schröder Axel , Meyer Bernhard , Sollmann Nico , Krieg Sandro M. 
Published: November 2019

AbstractNavigated transcranial magnetic stimulation (nTMS) over the supplementary motor area (SMA) may impact fine motor skills. This study evaluates different nTMS parameters in their capacity to affect fine motor performance on the way to develop an SMA mapping protocol. Twenty healthy volunteers performed a variety of fine motor tests during baseline and nTMS to the SMA using 5 Hz, 10 Hz, and theta-burst stimulation (TBS). Effects on performance were measured by test completion times (TCTs), standard deviation of inter-tap interval (SDIT), and visible coordination problems (VCPs). The predominant stimulation effect was slowing of TCTs, i.e. a slowdown of test performances during stimulation. Furthermore, participants exhibited VCPs like accidental use of contralateral limbs or inability to coordinate movements. More instances of significant differences between baseline and stimulation occurred during stimulation of the right hemisphere compared to left-hemispheric stimulation. In conclusion, nTMS to the SMA could enable new approaches in neuroscience and enable structured mapping approaches. Specifically, this study supports interhemispheric differences in motor control as right-hemispheric stimulation resulted in clearer impairments. The application of our nTMS-based setup to assess the function of the SMA should be applied in patients with changed anatomo-functional representations as the next step, e.g. among patients with eloquent brain tumors.
Barley-ß-glucans reduce systemic inflammation, renal injury and aortic calcification through ADAM17 and neutral-sphingomyelinase2 inhibition
Authors: Arcidiacono Maria Vittoria , Carrillo-López Natalia , Panizo Sara , Castro-Grattoni Anabel L. , Valcheva Petya , Ulloa Catalina , Rodríguez-Carrio Javier , Cardús Anna , Quirós-Caso Covadonga , Martínez-Arias Laura , Martínez-Salgado Carlos , Motilva María José , Rodriguez-Suarez Carmen , Cannata-Andía Jorge B. , Dusso Adriana S. 
Published: November 2019

AbstractIn chronic kidney disease (CKD), hyperphosphatemia-induced inflammation aggravates vascular calcification (VC) by increasing vascular smooth muscle cell (VSMC) osteogenic differentiation, ADAM17-induced renal and vascular injury, and TNFα-induction of neutral-sphingomyelinase2 (nSMase2) to release pro-calcifying exosomes. This study examined anti-inflammatory β-glucans efficacy at attenuating systemic inflammation in health, and renal and vascular injury favoring VC in hyperphosphatemic CKD. In healthy adults, dietary barley β-glucans (Bβglucans) reduced leukocyte superoxide production, inflammatory ADAM17, TNFα, nSMase2, and pro-aging/pro-inflammatory STING (Stimulator of interferon genes) gene expression without decreasing circulating inflammatory cytokines, except for γ-interferon. In hyperphosphatemic rat CKD, dietary Bβglucans reduced renal and aortic ADAM17-driven inflammation attenuating CKD-progression (higher GFR and lower serum creatinine, proteinuria, kidney inflammatory infiltration and nSMase2), and TNFα-driven increases in aortic nSMase2 and calcium deposition without improving mineral homeostasis. In VSMC, Bβglucans prevented LPS- or uremic serum-induced rapid increases in ADAM17, TNFα and nSMase2, and reduced the 13-fold higher calcium deposition induced by prolonged calcifying conditions by inhibiting osteogenic differentiation and increases in nSMase2 through Dectin1-independent actions involving Bβglucans internalization. Thus, dietary Bβglucans inhibit leukocyte superoxide production and leukocyte, renal and aortic ADAM17- and nSMase2 gene expression attenuating systemic inflammation in health, and renal injury and aortic calcification despite hyperphosphatemia in CKD.
Partitioning of amino acids and proteins into decanol using phase transfer agents towards understanding life in non-polar liquids
Authors: Thompson Brooke , Burt Kayla , Lee Andrew , Lingard Kyle , Maurer Sarah E. 
Published: November 2019

AbstractWater has many roles in the context of life on Earth, however throughout the universe, other liquids may be able to support the emergence of life. We looked at the ability of amino acids, peptides, a depsipeptide, and proteins to partition into a non-polar decanol phase, with and without the addition of a phase transfer agent. Partitioning evaluated using UV detection, or with HPLC coupled to either charged aerosol detection or ESI-MS. For amino acids and short peptides, phase transfer agents were used to move the biomolecules to the decanol phase, and this transfer was pH dependent. For larger molecules, phase transfer agents did not seem to affect the transfer. Both the depsipetide, valinomycin, and the protein Taq DNA polymerase had solubility in the decanol phase. Additionally, valinomycin appeared to retain its biological ability to bind to potassium ions. These results show that most terrestrial biological molecules are not compatible with non-polar solvents, but it is possible to find and perhaps evolve polymers that are functional in such phases.
Violence reduces attention to faces and draws attention to points of contact
Authors: Scrivner Coltan , Choe Kyoung Whan , Henry Joseph , Lyu Muxuan , Maestripieri Dario , Berman Marc G. 
Published: November 2019

AbstractAlthough violence is a frequently researched topic, little is known about how different social features influence information gathering from violent interactions. Regions of an interaction that provide contextual information should receive more attention. We predicted the most informative features of a violent social interaction would be faces, points of contact, and objects being held. To test this, we tracked the eyes of 90 participants as they viewed images of social interactions that varied with respect to violence. When viewing violent interactions, participants attended significantly less to faces and significantly more to points of contact. Moreover, first-fixation analysis suggests that some of these biases are present from the beginning of scene-viewing. These findings are the first to demonstrate the visual relevance of faces and contact points in gathering information from violent social interactions. These results also question the attentional dominance of faces in active social scenes, highlighting the importance of using a variety of stimuli and contexts in social cognition research.
Performance of Cutting Tool with Cross-Chevron Surface Texture Filled with Green Synthesized Aluminium Oxide Nanoparticles
Authors: N. Sathiya Narayanan , N. Baskar , B. N. Vedha Hari , Sankaran Rohith , D. Ramya Devi 
Published: November 2019

AbstractThe newer methodology to improve the performance of cutting tool is by the constructive method of micro-texturing and green synthesized nanoparticles into the texture gaps for self-lubrication. Cross-chevron textures were made on the rake face of the cemented carbide tool using Neodymium Doped Yttrium Aluminium Garne (Nd-YAG) laser texturing machine. The environmentally friendly, non-hazardous and rapid method of producing nanoparticles was followed to produce Al2O3 nanoparticles. Various techniques used for characterizing the synthesized Al2O3 nanoparticles are Potential of Hydrogen (pH), Fourier Transform Infra-Red Spectroscopy Analysis (FTIR), Dynamic light scattering (DLS) and X-Ray Diffraction (XRD). The XRD shows the presence of required functional groups and the size of nanoparticles in the range of 500–550 nm. This article discusses the effect of textures, with and without nanoparticles filled on the texture gaps of the cemented carbide tool on the main cutting force, thrust force and co-efficient of friction while machining austenitic stainless steel 304. The combined effect of surface texturing and lubrication of Al2O3 nanoparticles enhanced the performance of the cutting tool compared with the conventional and textured tool.
The mitochondrial genomes of palaeopteran insects and insights into the early insect relationships
Authors: Song Nan , Li Xinxin , Yin Xinming , Li Xinghao , Yin Jian , Pan Pengliang 
Published: November 2019

AbstractPhylogenetic relationships of basal insects remain a matter of discussion. In particular, the relationships among Ephemeroptera, Odonata and Neoptera are the focus of debate. In this study, we used a next-generation sequencing approach to reconstruct new mitochondrial genomes (mitogenomes) from 18 species of basal insects, including six representatives of Ephemeroptera and 11 of Odonata, plus one species belonging to Zygentoma. We then compared the structures of the newly sequenced mitogenomes. A tRNA gene cluster of IMQM was found in three ephemeropteran species, which may serve as a potential synapomorphy for the family Heptageniidae. Combined with published insect mitogenome sequences, we constructed a data matrix with all 37 mitochondrial genes of 85 taxa, which had a sampling concentrating on the palaeopteran lineages. Phylogenetic analyses were performed based on various data coding schemes, using maximum likelihood and Bayesian inferences under different models of sequence evolution. Our results generally recovered Zygentoma as a monophyletic group, which formed a sister group to Pterygota. This confirmed the relatively primitive position of Zygentoma to Ephemeroptera, Odonata and Neoptera. Analyses using site-heterogeneous CAT-GTR model strongly supported the Palaeoptera clade, with the monophyletic Ephemeroptera being sister to the monophyletic Odonata. In addition, a sister group relationship between Palaeoptera and Neoptera was supported by the current mitogenomic data.
Screw-Dislocation-Driven Growth Mode in Two Dimensional GaSe on GaAs(001) Substrates Grown by Molecular Beam Epitaxy
Authors: Diep Nhu Quynh , Liu Cheng-Wei , Wu Ssu-Kuan , Chou Wu-Ching , Huynh Sa Hoang , Chang Edward Yi 
Published: November 2019

AbstractRegardless of the dissimilarity in the crystal symmetry, the two-dimensional GaSe materials grown on GaAs(001) substrates by molecular beam epitaxy reveal a screw-dislocation-driven growth mechanism. The spiral-pyramidal structure of GaSe multi-layers was typically observed with the majority in ε-phase. Comprehensive investigations on temperature-dependent photoluminescence, Raman scattering, and X-ray diffraction indicated that the structure has been suffered an amount of strain, resulted from the screw-dislocation-driven growth mechanism as well as the stacking disorders between monolayer at the boundaries of the GaSe nanoflakes. In addition, Raman spectra under various wavelength laser excitations explored that the common ε-phase of 2D GaSe grown directly on GaAs can be transformed into the β-phase by introducing a Se-pretreatment period at the initial growth process. This work provides an understanding of molecular beam epitaxy growth of 2D materials on three-dimensional substrates and paves the way to realize future electronic and optoelectronic heterogeneous integrated technology as well as second harmonic generation applications.
Cytokine/chemokine profiles in squamous cell carcinoma correlate with precancerous and cancerous disease stage
Authors: Tuong Zewen K. , Lewandowski Andrew , Bridge Jennifer A. , Cruz Jazmina L. G. , Yamada Miko , Lambie Duncan , Lewandowski Richard , Steptoe Raymond J. , Leggatt Graham R. , Simpson Fiona , Frazer Ian H. , Soyer H. Peter , Wells James W. 
Published: November 2019

AbstractActinic Keratosis (AK), Intraepidermal Carcinoma (IEC), and Squamous Cell Carcinoma (SCC) are generally considered to be advancing stages of the same disease spectrum. However, while AK often regress spontaneously, and IEC often regress in response to immune-activating treatments, SCC typically do not regress. Therefore, it is vital to define whether fundamental immunological changes occur during progression to SCC. Here we show that proinflammatory cytokine expression, chemokine expression, and immune cell infiltration density change during progression to SCC. Our findings suggest a switch from predominantly proinflammatory cytokine production to chemokine production is a key feature of progression from precancer to cancer. Together, these observations propose a model that can underpin current research and open new avenues of exploration into the clinical significance of these profiles with respect to immunotherapeutic or other treatment outcomes.