bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Cyclic-di-GMP signalling network regulates biofilm formation and surface associated motility of Acinetobacter baumannii 17978
Authors: Ahmad Irfan , Nygren Evelina , Khalid Fizza , Myint Si Lhyam , Uhlin Bernt Eric 
Published: February 2020

AbstractAcinetobacter baumannii has emerged as an increasing multidrug-resistant threat in hospitals and a common opportunistic nosocomial pathogen worldwide. However, molecular details of the pathogenesis and physiology of this bacterium largely remain to be elucidated. Here we identify and characterize the c-di-GMP signalling network and assess its role in biofilm formation and surface associated motility. Bioinformatic analysis revealed eleven candidate genes for c-di-GMP metabolizing proteins (GGDEF/EAL domain proteins) in the genome of A. baumannii strain 17978. Enzymatic activity of the encoded proteins was assessed by molecular cloning and expression in the model organisms Salmonella typhimurium and Vibrio cholerae. Ten of the eleven GGDEF/EAL proteins altered the rdar morphotype of S. typhimurium and the rugose morphotype of V. cholerae. The over expression of three GGDEF proteins exerted a pronounced effect on colony formation of A. baumannii on Congo Red agar plates. Distinct panels of GGDEF/EAL proteins were found to alter biofilm formation and surface associated motility of A. baumannii upon over expression. The GGDEF protein A1S_3296 appeared as a major diguanylate cyclase regulating macro-colony formation, biofilm formation and the surface associated motility. AIS_3296 promotes Csu pili mediated biofilm formation. We conclude that a functional c-di-GMP signalling network in A. baumannii regulates biofilm formation and surface associated motility of this increasingly important opportunistic bacterial pathogen.
A combined Far-FTIR, FTIR Spectromicroscopy, and DFT Study of the Effect of DNA Binding on the [4Fe4S] Cluster Site in EndoIII
Authors: Hassan Ayaz , Macedo Lucyano J. A. , Souza João C. P. de , Lima Filipe C. D. A. , Crespilho Frank N. 
Published: February 2020

AbstractEndonuclease III (EndoIII) is a DNA glycosylase that contains the [4Fe4S] cluster, which is essential for the protein to bind to damaged DNA in a process called base excision repair (BER). Here we propose that the change in the covalency of Fe–S bonds of the [4Fe4S] cluster caused by double-stranded (ds)-DNA binding is accompanied by a change in their strength, which is due to alterations of the electronic structure of the cluster. Micro-FTIR spectroscopy in the mid-IR region and FTIR spectroscopy in the far IR (450 and 300 cm−1) were used independently to study the structural changes in EndoIII and the behavior of the [4Fe4S] cluster it contains, in the native form and upon its binding to ds-DNA. Structural changes in the DNA itself were also examined. The characteristics vibrational modes, corresponding to Fe–S (sulfide) and Fe–S (thiolate) bonds were identified in the cluster through far IR spectroscopy as well through quantum chemistry calculations. Based on the experimental results, these vibrational modes shift in their spectral positions caused by negatively charged DNA in the vicinity of the cluster. Modifications of the Fe–S bond lengths upon DNA binding, both of the Fe–S (sulfide) and Fe–S (thiolate) bonds in the [4Fe4S] cluster of EndoIII are responsible for the stabilization of the cluster towards higher oxidation state (3+), and hence its redox communication along the ds-DNA helix.
Automated high-throughput heartbeat quantification in medaka and zebrafish embryos under physiological conditions
Authors: Gierten Jakob , Pylatiuk Christian , Hammouda Omar T. , Schock Christian , Stegmaier Johannes , Wittbrodt Joachim , Gehrig Jochen , Loosli Felix 
Published: February 2020

AbstractAccurate quantification of heartbeats in fish models is an important readout to study cardiovascular biology, disease states and pharmacology. However, dependence on anaesthesia, laborious sample orientation or requirement for fluorescent reporters have hampered the use of high-throughput heartbeat analysis. To overcome these limitations, we established an efficient screening assay employing automated label-free heart rate determination of randomly oriented, non-anesthetized medaka (Oryzias latipes) and zebrafish (Danio rerio) embryos in microtiter plates. Automatically acquired bright-field data feeds into an easy-to-useHeartBeatsoftware with graphical user interface for automated quantification of heart rate and rhythm. Sensitivity of the assay was demonstrated by profiling heart rates during entire embryonic development. Our analysis revealed rapid adaption of heart rates to temperature changes, which has implications for standardization of experimental layout. The assay allows scoring of multiple embryos per well enabling a throughput of >500 embryos per 96-well plate. In a proof of principle screen for compound testing, we captured concentration-dependent effects of nifedipine and terfenadine over time. Our novel assay permits large-scale applications ranging from phenotypic screening, interrogation of gene functions to cardiovascular drug development.
Developing a xenograft model of human vasculature in the mouse ear pinna
Authors: Meehan Gavin R. , Scales Hannah E. , Osii Rowland , De Niz Mariana , Lawton Jennifer C. , Marti Matthias , Garside Paul , Craig Alister , Brewer James M. 
Published: February 2020

AbstractHumanised xenograft models allow for the analysis of human tissue within a physiological environmentin vivo. However, current models often rely on the angiogenesis and ingrowth of recipient vasculature to perfuse tissues, preventing analysis of biological processes and diseases involving human blood vessels. This limits the effectiveness of xenografts in replicating human physiology and may lead to issues with translating findings into human research. We have designed a xenograft model of human vasculature to address this issue. Human subcutaneous fat was culturedin vitroto promote blood vessel outgrowth prior to implantation into immunocompromised mice. We demonstrate that implants survived, retained human vasculature and anastomosed with the circulatory system of the recipient mouse. Significantly, by performing transplants into the ear pinna, this system enabled intravital observation of xenografts by multiphoton microscopy, allowing us to visualise the steps leading to vascular cytoadherence of erythrocytes infected with the human parasitePlasmodium falciparum. This model represents a useful tool for imaging the interactions that occur within human tissuesin vivoand permits visualization of blood flow and cellular recruitment in a system which is amenable to intervention for various studies in basic biology together with drug evaluation and mechanism of action studies.
High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes
Authors: Vivien Régis , Apothéloz-Perret-Gentil Laure , Pawlowski Jan , Werner Inge , Lafont Michel , Ferrari Benoit J. D. 
Published: February 2020

AbstractAquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.
Coalescence dynamics of 3D islands on weakly-interacting substrates
Authors: Gervilla V. , Almyras G. A. , Lü B. , Sarakinos K. 
Published: February 2020

AbstractWe use kinetic Monte Carlo simulations and analytical modelling to study coalescence of three-dimensional (3D) nanoscale faceted silver island pairs on weakly-interacting fcc(111) substrates, with and without concurrent supply of mobile adatoms from the vapor phase. Our simulations show that for vapor flux arrival rates F < 1 monolayer/second (ML/s) coalescence manifests itself by one of the islands absorbing the other via sidewall facet migration. This process is mediated by nucleation and growth of two-dimensional (2D) layers on the island facets, while the supply of mobile atoms increases the nucleation probability and shortens the time required for coalescence completion. When F is increased above 1 ML/s, coalescence is predominantly governed by deposition from the vapor phase and the island pair reaches a compact shape via agglomeration. The crucial role of facets for the coalescence dynamics is further supported by a mean-field thermodynamic description of the nucleation energetics and kinetics. Our findings explain experimental results which show that two-dimensional film growth morphology on weakly-interacting substrates is promoted when the rate of island coalescence is suppressed. The present study also highlights that deviations of experimentally reported film morphological evolutions in weakly-interacting film/substrate systems from predictions based on the sintering and particle growth theories may be understood in light of the effect of deposition flux atoms on the energetics and kinetics of facet-layer nucleation during coalescence.
DeepBTS: Prediction of Recurrence-free Survival of Non-small Cell Lung Cancer Using a Time-binned Deep Neural Network
Authors: Lee Bora , Chun Sang Hoon , Hong Ji Hyung , Woo In Sook , Kim Seoree , Jeong Joon Won , Kim Jae Jun , Lee Hyun Woo , Na Sae Jung , Beck Kyongmin Sarah , Gil Bomi , Park Sungsoo , An Ho Jung , Ko Yoon Ho 
Published: February 2020

AbstractAccurate prediction of non-small cell lung cancer (NSCLC) prognosis after surgery remains challenging. The Cox proportional hazard (PH) model is widely used, however, there are some limitations associated with it. In this study, we developed novel neural network models called binned time survival analysis (DeepBTS) models using 30 clinico-pathological features of surgically resected NSCLC patients (training cohort, n = 1,022; external validation cohort, n = 298). We employed the root-mean-square error (in the supervised learning model, s- DeepBTS) or negative log-likelihood (in the semi-unsupervised learning model, su-DeepBTS) as the loss function. The su-DeepBTS algorithm achieved better performance (C-index = 0.7306; AUC = 0.7677) than the other models (Cox PH: C-index = 0.7048 and AUC = 0.7390; s-DeepBTS: C-index = 0.7126 and AUC = 0.7420). The top 14 features were selected using su-DeepBTS model as a selector and could distinguish the low- and high-risk groups in the training cohort (p = 1.86 × 10−11) and validation cohort (p = 1.04 × 10−10). When trained with the optimal feature set for each model, the su-DeepBTS model could predict the prognoses of NSCLC better than the traditional model, especially in stage I patients. Follow-up studies using combined radiological, pathological imaging, and genomic data to enhance the performance of our model are ongoing.
Upregulation of GPNCA is associated with poor prognosis through enhancement of tumor growth via regulating GSK3B
Authors: Liao Weijie , Liu Fuhai , Zhang Haowei , Liao Weifang , Xu Naihan , Xie Weidong , Zhang Yaou 
Published: February 2020

AbstractGPNCA is a long non-coding RNA with unknown functions. In this study, using data from 9 cancers obtained from The Cancer Genome Atlas (TCGA), GPNCA was identified as overexpressed in cancer vs. normal tissues. The upregulation of GPNCA was associated with poor overall prognosis in colon, liver, renal clear cell and breast cancers. The upregulation of GPNCA was partly due to enhanced H3K27ac occupancy on its promoter region via EP300 and KAT2A/GCN5. The overexpression of GPNCA was positively related to tumor metastasis in colon cancer and poor disease-free and recurrence-free survival in colon and liver cancer. Both gene ontology (GO) enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis indicated that GPNCA was closely linked to regulation of gene transcription and post-transcriptional modifications, which was further supported by in vitro cell cytoplasmic and nuclear RNA purification assessments. Furthermore, GPNCA was associated with cell growth. Our in vitro experiments demonstrated that GPNCA silencing inhibited tumor growth via inhibiting its nearby gene GSK3B. Taken together, these findings highlight GPNCA as a biomarker for cancer diagnosis and a potential target for future cancer drug development.
Leveraging Signatures of Plant Functional Strategies in Wood Density Profiles of African Trees to Correct Mass Estimations From Terrestrial Laser Data
Authors: Momo Stéphane Takoudjou , Ploton Pierre , Martin-Ducup Olivier , Lehnebach Romain , Fortunel Claire , Sagang Le Bienfaiteur Takougoum , Boyemba Faustin , Couteron Pierre , Fayolle Adeline , Libalah Moses , Loumeto Joel , Medjibe Vincent , Ngomanda Alfred , Obiang Diosdado , Pélissier Raphaël , Rossi Vivien , Yongo Olga ,   PREREDD Collaborators, Bocko Yannick , Fonton Noël , Kamdem Narcisse , Katembo John , Kondaoule Henriette Josiane , Maïdou Hervé Martial , Mankou Géraud , Mbasi Michel , Mengui Thomas , Mofack Gislain I. I. , Moundounga Cynel , Moundounga Quentin , Nguimbous Lydie , Ncham Norberto Nsue , Asue Francisco Ondo Meye , Senguela Yvon-Patrick , Viard Lionel , Zapfack Louis , Sonké Bonaventure , Barbier Nicolas 
Published: February 2020

AbstractWood density (WD) relates to important tree functions such as stem mechanics and resistance against pathogens. This functional trait can exhibit high intraindividual variability both radially and vertically. With the rise of LiDAR-based methodologies allowing nondestructive tree volume estimations, failing to account for WD variations related to tree function and biomass investment strategies may lead to large systematic bias in AGB estimations. Here, we use a unique destructive dataset from 822 trees belonging to 51 phylogenetically dispersed tree species harvested across forest types in Central Africa to determine vertical gradients in WD from the stump to the branch tips, how these gradients relate to regeneration guilds and their implications for AGB estimations. We find that decreasing WD from the tree base to the branch tips is characteristic of shade-tolerant species, while light-demanding and pioneer species exhibit stationary or increasing vertical trends. Across all species, the WD range is narrower in tree crowns than at the tree base, reflecting more similar physiological and mechanical constraints in the canopy. Vertical gradients in WD induce significant bias (10%) in AGB estimates when using database-derived species-average WD data. However, the correlation between the vertical gradients and basal WD allows the derivation of general correction models. With the ongoing development of remote sensing products providing 3D information for entire trees and forest stands, our findings indicate promising ways to improve greenhouse gas accounting in tropical countries and advance our understanding of adaptive strategies allowing trees to grow and survive in dense rainforests.
Crystallization Mechanism in Spark Plasma Sintered Bulk Metallic Glass Analyzed using Small Angle Neutron Scattering
Authors: Paul Tanaji , Singh Ashish , Littrell Kenneth C. , Ilavsky Jan , Harimkar Sandip P. 
Published: February 2020

AbstractUnderstanding the thermal stability of metallic glasses is critical to determining their safe temperatures of service. In this paper, the crystallization mechanism in spark plasma sintered Fe48Cr15Mo14Y2C15B6 metallic glass is established by analyzing the crystal size distribution using x-ray diffraction, transmission electron microscopy and in-situ small angle neutron scattering. Isothermal annealing at 700 °C and 725 °C for 100 min resulted in the formation of (Fe,Cr)23C6 crystals, measured from transmission electron micrographs, to be from 10 to 30 nm. The small angle neutron scattering intensity measured in-situ, over a Q-range of 0.02 to 0.3 Å−1, during isothermal annealing of the sintered samples, confirmed the presence of (Fe,Cr)23C6 crystals. The measured scattering intensity, fitted by the maximum entropy model, over the Q-range of 0.02 to 0.06 Å−1, revealed that the crystals had radii ranging from 3 to 18 nm. The total volume fraction of crystals were estimated to be 0.13 and 0.22 upon isothermal annealing at 700 °C and 725 °C for 100 min respectively. The mechanism of crystallization in this spark plasma sintered iron based metallic glass was established to be from pre-existing nuclei as confirmed by Avrami exponents of 0.25 ± 0.01 and 0.39 ± 0.01 at the aforesaid temperatures.
Hepatitis C Virus Clearance with Glucose Improvement and Factors Affecting the Glucose Control in Chronic Hepatitis C Patients
Authors: Yuan Man , Zhou Juan , Du Lingyao , Yan Libo , Tang Hong 
Published: February 2020

AbstractThe study aimed to investigate whether the glucose level improves and what factors affect the improvement in glucose control after the eradication of hepatitis C virus (HCV). A total of 1090 patients with HCV infections were enrolled, among which 278 (25.5%) patients were diagnosed with prediabetes, and 89 (8.16%) patients were diagnosed with diabetes. In the cohort, 990 patients belonged to sustained virological response (SVR) group and 100 belonged to non-SVR group. Decreases in the fasting plasma glucose (FPG) level were found in the SVR group but not in the non-SVR group (p < 0.001; p = 0.267). In the SVR group, subjects with baseline FPG ≥ 5.6 mmol/L were further stratified into glycometabolism-improved (N = 182) and unimproved (N = 150) groups according to their FPG after viral eradication. Multivariate analysis showed that older age, higher baseline HCV RNA, glucose, total bilirubin and alanine aminotransferase levels were independent risk factors for insufficient glucose improvement. In conclusion, patients with HCV infection had a higher prevalence of abnormal glycometabolism. It could be improved after viral eradication, indicating that HCV may influence glycometabolism. Moreover, Age, baseline HCV RNA, glucose, total bilirubin and alanine aminotransferase levels were impact factor for glycometabolism improvement after viral eradication.
Probing phase transition in VO2 with the novel observation of low-frequency collective spin excitation
Authors: Basu Raktima , Srihari V. , Sardar Manas , Srivastava Sachin Kumar , Bera Santanu , Dhara Sandip 
Published: February 2020

AbstractVO2 is well known for its first order, reversible, metal-to-insulator transition (MIT) along with a simultaneous structural phase transition (SPT) from a high-temperature metallic rutile tetragonal (R) to an insulating low-temperature monoclinic (M1) phase via two other insulating metastable phases of monoclinic M2 and triclinic T. At the same time, VO2 gains tremendous attention because of the half-a-century-old controversy over its origin, whether electron-electron correlation or electron-phonon coupling trigger the phase transition. In this regard, V1-xMgxO2 samples were grown in stable phases of VO2 (M1, M2, and T) by controlled doping of Mg. We have observed a new collective mode in the low-frequency Raman spectra of all three insulating M1, M2 and T phases. We identify this mode with the breather (singlet spin excitation) mode about a spin-Pierls dimerized one dimensional spin ½ Heisenberg chain. The measured frequencies of these collective modes are phenomenologically consistent with the superexchange coupling strength between V spin ½ moments in all three phases. The significant deviation of Stokes to anti-Stokes intensity ratio of this low-frequency Raman mode from the usual thermal factor exp(hʋ/KBT) for phonons, and the orthogonal dependency of the phonon and spinon vibration in the polarized Raman study confirm its origin as spin excitations. The shift in the frequency of spin-wave and simultaneous increase in the transition temperature in the absence of any structural change confirms that SPT does not prompt MIT in VO2. On the other hand, the presence of spin-wave confirms the perturbation due to spin-Peierls dimerization leading to SPT. Thus, the observation of spin-excitations resulting from 1-D Heisenberg spin-½ chain can finally resolve the years-long debate in VO2 and can be extended to oxide-based multiferroics, which are useful for various potential device applications.
Shoes with active insoles mitigate declines in balance after fatigue
Authors: Moon Jeongin , Pathak Prabhat , Kim Sudeok , Roh Se-gon , Roh Changhyun , Shim Youngbo , Ahn Jooeun 
Published: February 2020

AbstractFatigue can induce postural instability and even lead to falls. However, most current methods to delay or reduce fatigue require long preparatory time, or large and expensive equipment. We propose a convenient method to alleviate postural instability due to fatigue. We paid attention to that fatigue and aging share similar neurophysiological deterioration of sensory-motor function. Considering that stochastic resonance via sub-sensory mechanical vibration increases postural stability in the elderly, we propose that sub-sensory insole vibration reduces the negative effect of fatigue on postural control. We performed experiments with 21 young and healthy adult participants, and demonstrated that insole vibration compensates for the loss of balance ability due to fatigue. The sub-sensory insole vibration restored both the area of center of pressure and the complexity of the time series of the motor output after fatigue to the pre-fatigue levels. The insole units generating the vibration were completely concealed in shoes and controlled by a smart phone. This compact implementation contrasts with the cumbersome procedure of current solutions to fatigue-induced postural instability.