bluuebunny/crossref_metadata_2025 huggingface dataset:
Tracing Acetylene Dissolved in Transformer Oil by Tunable Diode Laser Absorption Spectrum
Authors: Ma Guo-ming , Zhao Shu-jing , Jiang Jun , Song Hong-tu , Li Cheng-rong , Luo Ying-ting , Wu Hao
Published: October 2017

Dissolved gas analysis (DGA) is widely used in monitoring and diagnosing of power transformer, since the insulation material in the power transformer decomposes gases under abnormal operation condition. Among the gases, acetylene, as a symbol of low energy spark discharge and high energy electrical faults (arc discharge) of power transformer, is an important monitoring parameter. The current gas detection method used by the online DGA equipment suffers from problems such as cross sensitivity, electromagnetic compatibility and reliability. In this paper, an optical gas detection system based on TDLAS technology is proposed to detect acetylene dissolved in transformer oil. We selected a 1530.370 nm laser in the near infrared wavelength range to correspond to the absorption peak of acetylene, while using the wavelength modulation strategy and Herriott cell to improve the detection precision. Results show that the limit of detection reaches 0.49 ppm. The detection system responds quickly to changes of gas concentration and is easily to maintenance while has no electromagnetic interference, cross-sensitivity, or carrier gas. In addition, a complete detection process of the system takes only 8 minutes, implying a practical prospect of online monitoring technology.
Translation efficiency is a determinant of the magnitude of miRNA-mediated repression
Authors: Cottrell Kyle A. , Szczesny Pawel , Djuranovic Sergej
Published: October 2017

MicroRNAs are well known regulators of mRNA stability and translation. However, the magnitude of both translational repression and mRNA decay induced by miRNA binding varies greatly between miRNA targets. This can be the result of cis and trans factors that affect miRNA binding or action. We set out to address this issue by studying how various mRNA characteristics affect miRNA-mediated repression. Using a dual luciferase reporter system, we systematically analyzed the ability of selected mRNA elements to modulate miRNA-mediated repression. We found that changing the 3′UTR of a miRNA-targeted reporter modulates translational repression by affecting the translation efficiency. This 3′UTR dependent modulation can be further altered by changing the codon-optimality or 5′UTR of the luciferase reporter. We observed maximal repression with intermediate codon optimality and weak repression with very high or low codon optimality. Analysis of ribosome profiling and RNA-seq data for endogenous miRNA targets revealed translation efficiency as a key determinant of the magnitude of miRNA-mediated translational repression. Messages with high translation efficiency were more robustly repressed. Together our results reveal modulation of miRNA-mediated repression by characteristics and features of the 5′UTR, CDS and 3′UTR.
Alleviative effects of fluoxetine on depressive-like behaviors by epigenetic regulation of BDNF gene transcription in mouse model of post-stroke depression
Authors: Jin Hui-Juan , Pei Lei , Li Ya-Nan , Zheng Hui , Yang Shuai , Wan Yan , Mao Ling , Xia Yuan-Peng , He Quan-Wei , Li Man , Yue Zhen-Yu , Hu Bo
Published: October 2017

Fluoxetine, one of the selective serotonin reuptake inhibitor (SSRI) antidepressants, has been thought to be effective for treating post-stroke depression (PSD). Recent work has shown that fluoxetine may exert an antidepressive effect through increasing the level of brain-derived neurotrophic factor (BDNF), but the underlying mechanism still remains unclear. In the present study, we successfully established the PSD model using male C57BL/6 J mice by photothrombosis of the left anterior cortex combined with isolatied-housing conditions. In the process, we confirmed that fluoxetine could improve the depression-like behaviors of PSD mice and upregulate the expression of BDNF in the hippocampus. However, depletion of BDNF by transfecting lentivirus-derived shBDNF in hippocampus suppressed the effect of fluoxetine. Furthermore, we demonstrated the epigenetic mechanisms involved in regulation of BDNF expression induced by fluoxetine. We found a statistically significant increase in DNA methylation at specific CpG sites (loci 2) of Bdnf promoter IV in the hippocampus of PSD mice. We also found that fluoxetine treatment could disassociate the MeCP2-CREB-Bdnf promoter IV complex via phosphorylation of MeCP2 at Ser421 by Protein Kinase A (PKA). Our research highlighted the importance of fluoxetine in regulating BDNF expression which could represent a potential strategy for preventing PSD.
The MAPKKK gene family in cassava: Genome-wide identification and expression analysis against drought stress
Authors: Ye Jianqiu , Yang Hai , Shi Haitao , Wei Yunxie , Tie Weiwei , Ding Zehong , Yan Yan , Luo Ying , Xia Zhiqiang , Wang Wenquan , Peng Ming , Li Kaimian , Zhang He , Hu Wei
Published: October 2017

Mitogen-activated protein kinase kinase kinases (MAPKKKs), an important unit of MAPK cascade, play crucial roles in plant development and response to various stresses. However, little is known concerning the MAPKKK family in the important subtropical and tropical crop cassava. In this study, 62 MAPKKK genes were identified in the cassava genome, and were classified into 3 subfamilies based on phylogenetic analysis. Most of MAPKKKs in the same subfamily shared similar gene structures and conserved motifs. The comprehensive transcriptome analysis showed that MAPKKK genes participated in tissue development and response to drought stress. Comparative expression profiles revealed that many MAPKKK genes were activated in cultivated varieties SC124 and Arg7 and the function of MeMAPKKKs in drought resistance may be different between SC124/Arg7 and W14. Expression analyses of the 7 selected MeMAPKKK genes showed that most of them were significantly upregulated by osmotic, salt and ABA treatments, whereas slightly induced by H2O2 and cold stresses. Taken together, this study identified candidate MeMAPKKK genes for genetic improvement of abiotic stress resistance and provided new insights into MAPKKK -mediated cassava resistance to drought stress.
Clinical evaluation of final impressions from three-dimensional printed custom trays
Authors: Sun Yuchun , Chen Hu , Li Hong , Deng Kehui , Zhao Tian , Wang Yong , Zhou Yongsheng
Published: October 2017

This study aimed to evaluate the quality of the final impressions taken by three-dimensional printed custom trays for edentulous patients. Custom trays were designed with or without saddle-shaped tissue stops and fabricated by three-dimensional printing techniques. Manually made trays with photocurable materials were produced as controls. Both 3D printed custom trays and manually made ones were used to take impressions from edentulous patients. After 3D scanning of the final impression, the impression materials were removed, thus the underneath tray surfaces were able to be scanned, allowing the thickness of the impression materials to be measured. Final impressions obtained by pre-border-molded 3D printed trays were scanned as references, to which the flange extension deviations and morphology deviations of the impressions taken by both 3D printed trays and manually made ones were calculated. The results showed that (1) impressions from 3D printed custom trays had better thickness distribution than that of manually made ones; (2) impression morphology deviations in non-marginal area were neither statistic different between 3D printed trays and manually made trays, nor between trays with and without tissue stops; and (3) final impressions taken by custom trays without pre-border-molding were tended to have insufficient flange extensions.
On-Chip Glass Microspherical Shell Whispering Gallery Mode Resonators
Authors: Zhang Chenchen , Cocking Alexander , Freeman Eugene , Liu Zhiwen , Tadigadapa Srinivas
Published: October 2017

Arrays of on-chip spherical glass shells of hundreds of micrometers in diameter with ultra-smooth surfaces and sub-micrometer wall thicknesses have been fabricated and have been shown to sustain optical resonance modes with high Q-factors of greater than 50 million. The resonators exhibit temperature sensitivity of −1.8 GHz K−1 and can be configured as ultra-high sensitivity thermal sensors for a broad range of applications. By virtue of the geometry’s strong light-matter interaction, the inner surface provides an excellent on-chip sensing platform that truly opens up the possibility for reproducible, chip scale, ultra-high sensitivity microfluidic sensor arrays. As a proof of concept we demonstrate the sensitivity of the resonance frequency as water is filled inside the microspherical shell and is allowed to evaporate. By COMSOL modeling, the dependence of this interaction on glass shell thickness is elucidated and the experimentally measured sensitivities for two different shell thicknesses are explained.
Tuning the motility and directionality of self-propelled colloids
Authors: Gomez-Solano Juan Ruben , Samin Sela , Lozano Celia , Ruedas-Batuecas Pablo , van Roij René , Bechinger Clemens
Published: October 2017

Microorganisms are able to overcome the thermal randomness of their surroundings by harvesting energy to navigate in viscous fluid environments. In a similar manner, synthetic colloidal microswimmers are capable of mimicking complex biolocomotion by means of simple self-propulsion mechanisms. Although experimentally the speed of active particles can be controlled by e.g. self-generated chemical and thermal gradients, an in-situ change of swimming direction remains a challenge. In this work, we study self-propulsion of half-coated spherical colloids in critical binary mixtures and show that the coupling of local body forces, induced by laser illumination, and the wetting properties of the colloid, can be used to finely tune both the colloid’s swimming speed and its directionality. We experimentally and numerically demonstrate that the direction of motion can be reversibly switched by means of the size and shape of the droplet(s) nucleated around the colloid, depending on the particle radius and the fluid’s ambient temperature. Moreover, the aforementioned features enable the possibility to realize both negative and positive phototaxis in light intensity gradients. Our results can be extended to other types of half-coated microswimmers, provided that both of their hemispheres are selectively made active but with distinct physical properties.
Impact of blood urea nitrogen to creatinine ratio on mortality and morbidity in hemodialysis patients: The Q-Cohort Study
Authors: Tanaka Shigeru , Ninomiya Toshiharu , Taniguchi Masatomo , Tokumoto Masanori , Masutani Kosuke , Ooboshi Hiroaki , Kitazono Takanari , Tsuruya Kazuhiko
Published: October 2017

The association between blood urea nitrogen to creatinine ratio (UCR) and survival is uncertain in hemodialysis patients. We examined the influence of UCR on mortality and morbidity in hemodialysis patients. A total of 3,401 hemodialysis patients were prospectively followed for 4 years. The association between UCR with overall survival was analyzed using a Cox regression model. During a 4-year follow-up period, 545 patients died from any cause and 582 experienced MACE, 392 with coronary heart disease (CHD), 114 with infection-related death, 77 with hemorrhagic stroke, 141 with ischemic stroke, and 107 with cancer death. Every 1 increase in UCR level was significantly associated with an increased risk for all-cause mortality (hazard ratio [HR] 1.07; 95% confidence interval [CI] 1.03–1.12), CHD (HR 1.08; 95% CI 1.02–1.14), and infection-related death (HR 1.11; 95% CI 1.02–1.21). There was no evidence of a significant association between UCR and death from cancer, and incidence of stroke. A high UCR was significantly associated with an increased risk for all-cause mortality, infection-related death and incidence of CHD in hemodialysis patients.
Dinuclear Metal-Mediated Homo Base Pairs with Metallophilic Interactions: Theoretical Studies of G2M2
2+ (M = Cu, Ag, and Au) Ions
Authors: Cao Guo-Jin
Published: October 2017

Dinuclear metal-mediated homo base pairs are interesting clusters with highly symmetric structures and significant stabilities. The geometric and electronic structures of G2M22+ (G = Guanine, M = Cu, Ag or Au) cluster ions were studied with quantum chemical calculations. The lowest-energy isomers of G2M22+ cluster ions have C2h symmetries with an approximately antiparallel alignment of two sets of N-M∙∙∙O groups being formed in the planar structures. The M-M distances are shorter than the sum of van der Waals radii of corresponding two homo coinage metal atoms, showing that metallophilic interactions significantly exist in these complexes. They have the large HOMO−LUMO gaps of about 5.80 eV at the DFT level and the bond dissociation energies of more than 5.60 eV at the DFT/B3LYP level, indicating that these cluster dications are highly stable. The second lowest-energy isomers stabilized by an approximately parallel alignment of one set of O-M-O group and one set of N-M-N group are found to be close to the lowest-energy isomers in energy. The barrier between the two isomers of G2M22+ cluster ions is significantly large, also showing that these lowest-energy isomers are very stable.
Anion-conducting channelrhodopsins with tuned spectra and modified kinetics engineered for optogenetic manipulation of behavior
Authors: Wietek Jonas , Rodriguez-Rozada Silvia , Tutas Janine , Tenedini Federico , Grimm Christiane , Oertner Thomas G. , Soba Peter , Hegemann Peter , Wiegert J. Simon
Published: October 2017

Genetic engineering of natural light-gated ion channels has proven a powerful way to generate optogenetic tools for a wide variety of applications. In recent years, blue-light activated engineered anion-conducting channelrhodopsins (eACRs) have been developed, improved, and were successfully applied in vivo. We asked whether the approaches used to create eACRs can be transferred to other well-characterized cation-conducting channelrhodopsins (CCRs) to obtain eACRs with a broad spectrum of biophysical properties. We generated 22 variants using two conversion strategies applied to 11 CCRs and screened them for membrane expression, photocurrents and anion selectivity. We obtained two novel eACRs, Phobos and Aurora, with blue- and red-shifted action spectra and photocurrents similar to existing eACRs. Furthermore, step-function mutations greatly enhanced the cellular operational light sensitivity due to a slowed-down photocycle. These bi-stable eACRs can be reversibly toggled between open and closed states with brief light pulses of different wavelengths. All new eACRs reliably inhibited action potential firing in pyramidal CA1 neurons. In Drosophila larvae, eACRs conveyed robust and specific light-dependent inhibition of locomotion and nociception.
GRAFENE: Graphlet-based alignment-free network approach integrates 3D structural and sequence (residue order) data to improve protein structural comparison
Authors: Faisal Fazle E. , Newaz Khalique , Chaney Julie L. , Li Jun , Emrich Scott J. , Clark Patricia L. , Milenković Tijana
Published: October 2017

Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D contact approaches study 3D structures directly and are alignment-based. Instead, 3D structures can be modeled as protein structure networks (PSNs). Then, network approaches can compare proteins by comparing their PSNs. These can be alignment-based or alignment-free. We focus on the latter. Existing network alignment-free approaches have drawbacks: 1) They rely on naive measures of network topology. 2) They are not robust to PSN size. They cannot integrate 3) multiple PSN measures or 4) PSN data with sequence data, although this could improve comparison because the different data types capture complementary aspects of the protein structure. We address this by: 1) exploiting well-established graphlet measures via a new network alignment-free approach, 2) introducing normalized graphlet measures to remove the bias of PSN size, 3) allowing for integrating multiple PSN measures, and 4) using ordered graphlets to combine the complementary PSN data and sequence (specifically, residue order) data. We compare synthetic networks and real-world PSNs more accurately and faster than existing network (alignment-free and alignment-based), 3D contact, or sequence approaches.
Potential for social involvement modulates activity within the mirror and the mentalizing systems
Authors: Begliomini Chiara , Cavallo Andrea , Manera Valeria , Becchio Cristina , Stramare Roberto , Miotto Diego , Castiello Umberto
Published: October 2017

Processing biological motion is fundamental for everyday life activities, such as social interaction, motor learning and nonverbal communication. The ability to detect the nature of a motor pattern has been investigated by means of point-light displays (PLD), sets of moving light points reproducing human kinematics, easily recognizable as meaningful once in motion. Although PLD are rudimentary, the human brain can decipher their content including social intentions. Neuroimaging studies suggest that inferring the social meaning conveyed by PLD could rely on both the Mirror Neuron System (MNS) and the Mentalizing System (MS), but their specific role to this endeavor remains uncertain. We describe a functional magnetic resonance imaging experiment in which participants had to judge whether visually presented PLD and videoclips of human-like walkers (HL) were facing towards or away from them. Results show that coding for stimulus direction specifically engages the MNS when considering PLD moving away from the observer, while the nature of the stimulus reveals a dissociation between MNS -mainly involved in coding for PLD- and MS, recruited by HL moving away. These results suggest that the contribution of the two systems can be modulated by the nature of the observed stimulus and its potential for social involvement.
Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi
Authors: Meiser Anjuli , Otte Jürgen , Schmitt Imke , Grande Francesco Dal
Published: October 2017

The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes, is increasingly used for in-depth genomic characterization of ecological communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes ofEvernia prunastriandPseudevernia furfuraceabased on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using genome assemblies as reference which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space (86–90%). Metagenome skimming will facilitate genome mining, comparative (phylo)genomics, and population genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.
KIXBASE: A comprehensive web resource for identification and exploration of KIX domains
Authors: Yadav Archana , Thakur Jitendra K. , Yadav Gitanjali
Published: October 2017

The KIX domain has emerged in the last two decades as a critical site of interaction for transcriptional assembly, regulation and gene expression. Discovered in 1994, this conserved, triple helical globular domain has been characterised in various coactivator proteins of yeast, mammals and plants, including the p300/CBP (a histone acetyl transferase), MED15 (a subunit of the mediator complex of RNA polymerase II), and RECQL5 helicases. In this work, we describe the first rigorous meta analysis of KIX domains across all forms of life, leading to the development of KIXBASE, a predictive web server and global repository for detection and analysis of KIX domains. To our knowledge, KIXBASE comprises the largest online collection of KIX sequences, enabling assessments at the level of both sequence and structure, incorporating PSIPRED and MUSTER at the backend for further annotation and quality assessment. In addition, KIXBASE provides useful information about critical aspects of KIX domains such as their intrinsic disorder, hydrophobicity profiles, functional classification and annotation based on domain architectures. KIXBASE represents a significant enrichment of the currently annotated KIX dataset, especially in the plant kingdom, thus highlighting potential targets for biochemical characterization. The KIX webserver and database are both freely available to the scientific community, athttp://www.nipgr.res.in/kixbase/home.php.
Optical Assets of In situ Electro-assembled Platinum Black Nanolayers
Authors: Stanca S. E. , Hänschke F. , Zieger G. , Dellith J. , Ihring A. , Undisz A. , Meyer H.-G.
Published: October 2017

Optoelectronic technology has been increasingly driven towards miniaturization. In this regard, maintaining the optical properties of the bulk materials while reducing their size is a critical need. How thin must the film be to preserve the bulk material´s optical absorbance and reflectance characteristics? This is the central question for our study of the in situ electro-assembly broad band optical absorber films of platinum in non-aqueous solution of PtCl4. By reducing the in situ constructed film to sub-visible-wavelength thicknesses, the measured reflectance in the region from the ultraviolet to the infrared remained close to that exhibited by the micrometre-width films. These platinum black films broadly absorb electromagnetic waves at a sub-incident-wavelength thickness owing to their plasmonically increased absorbance cross-section. Simulation of various incident energy electron trajectories gives insights into the electron depth through the porous platinum black of ρ = 1.6 g/cm3 and previews the optical behaviour close to the atomic thickness.
Hodgkin Lymphoma has a seasonal pattern of incidence and mortality that depends on latitude
Authors: Borchmann Sven , Müller Horst , Engert Andreas
Published: October 2017

Seasonal variations in incidence and mortality after a Hodgkin lymphoma (HL) diagnosis have been previously described with partly conflicting results. The goal of this analysis is to provide a comprehensive analysis of these seasonal variations. In total, 41,405 HL cases diagnosed between 1973 and 2012 in the 18 Surveillance, Epidemiology, and End Results registries were included. Cosinor analysis and Cox proportional-hazards models were employed to analyze seasonality of incidence and mortality, respectively. HL shows a sinusoid seasonal incidence pattern (p < 0.001). Estimated incidence in March is 15.4% [95%-CI: 10.8-20.0] higher than in September. This sinusoid pattern is more pronounced at higher latitudes (p = 0.023). The risk of dying within the first three years after a HL diagnosis in winter is significantly increased compared to a HL diagnosis in summer at higher latitudes (HR = 1.082 [95%-CI: 1.009-1.161], p = 0.027). Furthermore, increasing northern latitude increases the additional mortality risk conferred by a diagnosis in winter (pinteraction0.033). The seasonality patterns presented here provide epidemiological evidence that Vitamin D might play a protective role in HL. Further evidence on the direct association between Vitamin D levels and the clinical course of HL needs to be collected to advance the understanding of the role of Vitamin D in HL.
Turbulent transport reduction induced by transition on radial electric field shear and curvature through amplitude and cross-phase in torus plasma
Authors: Kobayashi T. , Itoh K. , Ido T. , Kamiya K. , Itoh S.-I. , Miura Y. , Nagashima Y. , Fujisawa A. , Inagaki S. , Ida K.
Published: October 2017

Spatiotemporal evolutions of radial electric field and turbulence are measured simultaneously in the H-mode transition, which is a prototypical example of turbulence structure formation in high-temperature plasmas. In the dynamical phase where transport barrier is established abruptly, the time-space-frequency-resolved turbulent particle flux is obtained. Here we report the validation of the mechanism of transport barrier formation quantitatively. It is found that the particle flux is suppressed predominantly by reducing density fluctuation amplitude and cross phase between density fluctuation and potential fluctuation. Both radial electric field shear and curvature are responsible for the amplitude suppression as was predicted by theory. Turbulence amplitude reduction immediately responds to the growth of the radial electric field non-uniformity and saturates, while cross phase continuously approaches zero.
Functionalized vertical GaN micro pillar arrays with high signal-to-background ratio for detection and analysis of proteins secreted from breast tumor cells
Authors: Choi Mun-Ki , Kim Gil-Sung , Jeong Jin-Tak , Lim Jung-Taek , Lee Won-Yong , Umar Ahmad , Lee Sang-Kwon
Published: October 2017

The detection of cancer biomarkers has recently attracted significant attention as a means of determining the correct course of treatment with targeted therapeutics. However, because the concentration of these biomarkers in blood is usually relatively low, highly sensitive biosensors for fluorescence imaging and precise detection are needed. In this study, we have successfully developed vertical GaN micropillar (MP) based biosensors for fluorescence sensing and quantitative measurement of CA15-3 antigens. The highly ordered vertical GaN MP arrays result in the successful immobilization of CA15-3 antigens on each feature of the arrays, thereby allowing the detection of an individual fluorescence signal from the top surface of the arrays owing to the high regularity of fluorophore-tagged MP spots and relatively low background signal. Therefore, our fluorescence-labeled and CA15-3 functionalized vertical GaN-MP-based biosensor is suitable for the selective quantitative analysis of secreted CA15-3 antigens from MCF-7 cell lines, and helps in the early diagnosis and prognosis of serious diseases as well as the monitoring of the therapeutic response of breast cancer patients.
Character-based DNA barcoding for authentication and conservation of IUCN Red listed threatened species of genus Decalepis (Apocynaceae)
Authors: Mishra Priyanka , Kumar Amit , Sivaraman Gokul , Shukla Ashutosh K. , Kaliamoorthy Ravikumar , Slater Adrian , Velusamy Sundaresan
Published: October 2017

The steno-endemic species of genusDecalepisare highly threatened by destructive wild harvesting. The medicinally important fleshy tuberous roots ofDecalepis hamiltoniiare traded as substitute, to meet the international market demand ofHemidesmus indicus. In addition, the tuberous roots of all three species ofDecalepispossess similar exudates and texture, which challenges the ability of conventional techniques alone to perform accurate species authentication. This study was undertaken to generate DNA barcodes that could be utilized in monitoring and curtailing the illegal trade of these endangered species. The DNA barcode reference library was developed in BOLD database platform for candidate barcodesrbcL,matK,psbA-trnH,ITSandITS2. The average intra-specific variations (0–0.27%) were less than the distance to nearest neighbour (0.4–11.67%) withmatKandITS. Anchoring the coding regionrbcLin multigene tiered approach, the combinationrbcL + matK + ITSyielded 100% species resolution, using the least number of loci combinations either with PAUP or BLOG methods to support a character-based approach. Species-specific SNP position (230 bp) in thematKregion that is characteristic ofD.hamiltoniicould be used to design specific assays, enhancing its applicability for direct use in CITES enforcement for distinguishing it fromH.indicus.
Clinical symptoms and related risk factors in pulmonary embolism patients and cluster analysis based on these symptoms
Authors: Ji Qiao-ying , Wang Mao-feng , Su Cai-min , Yang Qiong-fang , Feng Lan-fang , Zhao Lan-yan , Fang Shuang-yan , Zhao Fen-hua , Li Wei-min
Published: October 2017

Pulmonary embolism (PE) remains largely underdiagnosed due to nonspecific symptoms. This study aims to evaluate typical symptoms of PE patients, their related predictors, and to differentiate typical clusters of patients and principal components of PE symptoms. Clinical data from a total of 551 PE patients between January 2012 and April 2016 were retrospectively reviewed. PE was diagnosed according to the European Society of Cardiology Guidelines. Logistic regression models, system clustering method, and principal component analysis were used to identify potential risk factors, different clusters of the patients, and principal components of PE symptoms. The most common symptoms of PE were dyspnea, cough, and tachypnea in more than 60% of patients. Some combined chronic conditions, laboratory and clinical indicators were found to be related to these clinical symptoms. Our study also suggested that PE is associated with a broad list of symptoms and some PE patients might share similar symptoms, and some PE symptoms were usually cooccurrence. Based on ten symptoms generated from our sample, we classified the patients into five clusters which represent five groups of PE patients during clinical practice, and identified four principal components of PE symptoms. These findings will improve our understanding of clinical symptoms and their potential combinations which are helpful for clinical diagnosis of PE.
Structural Insight into Inhibition of CsrA-RNA Interaction Revealed by Docking, Molecular Dynamics and Free Energy Calculations
Authors: Ren Xiaodong , Zeng Rui , Tortorella Micky , Wang Jinming , Wang Changwei
Published: October 2017

The carbon storage regulator A (CsrA) and its homologs play an important role in coordinating the expression of bacterial virulence factors required for successful host infection. In addition, bacterial pathogens with deficiency of CsrA are typically attenuated for virulence. In 2016, the first series of small-molecule inhibitors of CsrA-RNA interaction were identified, which were found to achieve the CsrA-RNA inhibition by binding to the CsrA, without interfering with the RNA. However, the binding mechanism of these inhibitors of CsrA is not known. Herein, we applied molecular docking, molecular dynamics and binding free energy calculations to investigate the binding mode of inhibitors to CsrA. We found that the G11(RNA)-binding site is the most important binding site for CsrA inhibitors. An inhibitor with the proper size range can bind to that site and form a stable complex. We also found that inhibitors with larger size ranges bind to the entire CsrA-RNA interface, but have loose binding. However, this loose binding still resulted in inhibitory activity. The calculated binding free energy from MM/GBSA has a good correlation with the derived experimental binding energy, which might be used as a tool to further select CsrA inhibitors after a first-round of high-throughput virtual screening.
Dynamics of coral-associated bacterial communities acclimated to temperature stress based on recent thermal history
Authors: Shiu Jia-Ho , Keshavmurthy Shashank , Chiang Pei-Wen , Chen Hsing-Ju , Lou Shueh-Ping , Tseng Ching-Hung , Justin Hsieh Hernyi , Allen Chen Chaolun , Tang Sen-Lin
Published: October 2017

Seasonal variation in temperature fluctuations may provide corals and their algal symbionts varying abilities to acclimate to changing temperatures. We hypothesized that different temperature ranges between seasons may promote temperature-tolerance of corals, which would increase stability of a bacterial community following thermal stress. Acropora muricata coral colonies were collected in summer and winter (water temperatures were 23.4–30.2 and 12.1–23.1 °C, respectively) from the Penghu Archipelago in Taiwan, then exposed to 6 temperature treatments (10–33 °C). Changes in coral-associated bacteria were determined after 12, 24, and 48 h. Based on 16S rRNA gene amplicons and Illumina sequencing, bacterial communities differed between seasons and treatments altered the dominant bacteria. Cold stress caused slower shifts in the bacterial community in winter than in summer, whereas a more rapid shift occurred under heat stress in both seasons. Results supported our hypothesis that bacterial community composition of corals in winter are more stable in cold temperatures but changed rapidly in hot temperatures, with opposite results for the bacterial communities in summer. We infer that the thermal tolerance ranges of coral-associated bacteria, with a stable community composition, are associated with their short-term (3 mo) seawater thermal history. Therefore, seasonal acclimation may increase tolerance of coral-associated bacteria to temperature fluctuations.
High-Mobility and High-Optical Quality Atomically Thin WS
2
Authors: Reale Francesco , Palczynski Pawel , Amit Iddo , Jones Gareth F. , Mehew Jake D. , Bacon Agnes , Ni Na , Sherrell Peter C. , Agnoli Stefano , Craciun Monica F. , Russo Saverio , Mattevi Cecilia
Published: October 2017

The rise of atomically thin materials has the potential to enable a paradigm shift in modern technologies by introducing multi-functional materials in the semiconductor industry. To date the growth of high quality atomically thin semiconductors (e.g. WS2) is one of the most pressing challenges to unleash the potential of these materials and the growth of mono- or bi-layers with high crystal quality is yet to see its full realization. Here, we show that the novel use of molecular precursors in the controlled synthesis of mono- and bi-layer WS2 leads to superior material quality compared to the widely used direct sulfidization of WO3-based precursors. Record high room temperature charge carrier mobility up to 52 cm2/Vs and ultra-sharp photoluminescence linewidth of just 36 meV over submillimeter areas demonstrate that the quality of this material supersedes also that of naturally occurring materials. By exploiting surface diffusion kinetics of W and S species adsorbed onto a substrate, a deterministic layer thickness control has also been achieved promoting the design of scalable synthesis routes.
Fragment-based screening identifies novel targets for inhibitors of conjugative transfer of antimicrobial resistance by plasmid pKM101
Authors: Casu Bastien , Arya Tarun , Bessette Benoit , Baron Christian
Published: October 2017

The increasing frequency of antimicrobial resistance is a problem of global importance. Novel strategies are urgently needed to understand and inhibit antimicrobial resistance gene transmission that is mechanistically related to bacterial virulence functions. The conjugative transfer of plasmids by type IV secretion systems is a major contributor to antimicrobial resistance gene transfer. Here, we present a structure-based strategy to identify inhibitors of type IV secretion system-mediated bacterial conjugation. Using differential scanning fluorimetry we screened a fragment library and identified molecules that bind the essential TraE protein of the plasmid pKM101 conjugation machinery. Co-crystallization revealed that fragments bind two alternative sites of the protein and one of them is a novel inhibitor binding site. Based on the structural information on fragment binding we designed novel small molecules that have improved binding affinity. These molecules inhibit the dimerization of TraE, bind to both inhibitor binding sites on TraE and inhibit the conjugative transfer of plasmid pKM101. The strategy presented here is generally applicable for the structure-based design of inhibitors of antimicrobial resistance gene transfer and of bacterial virulence.
TDP-43 accelerates age-dependent degeneration of interneurons
Authors: Tsuiji Hitomi , Inoue Ikuyo , Takeuchi Mari , Furuya Asako , Yamakage Yuko , Watanabe Seiji , Koike Masato , Hattori Mitsuharu , Yamanaka Koji
Published: October 2017

TDP-43 is an RNA-binding protein important for many aspects of RNA metabolism. Abnormal accumulation of TDP-43 in the cytoplasm of affected neurons is a pathological hallmark of the neurodegenerative diseases frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Several transgenic mouse models have been generated that recapitulate defects in TDP-43 accumulation, thus causing neurodegeneration and behavioural impairments. While aging is the key risk factor for neurodegenerative diseases, the specific effect of aging on phenotypes in TDP-43 transgenic mice has not been investigated. Here, we analyse age-dependent changes in TDP-43 transgenic mice that displayed impaired memory. We found the accumulation of abundant poly-ubiquitinated protein aggregates in the hippocampus of aged TDP-43 transgenic mice. Intriguingly, the aggregates contained some interneuron-specific proteins such as parvalbumin and calretinin, suggesting that GABAergic interneurons were degenerated in these mice. The abundance of aggregates significantly increased with age and with the overexpression of TDP-43. Gene array analyses in the hippocampus and other brain areas revealed dysregulation in genes linked to oxidative stress and neuronal function in TDP-43 transgenic mice. Our results indicate that the interneuron degeneration occurs upon aging, and TDP-43 accelerates age-dependent neuronal degeneration, which may be related to the impaired memory of TDP-43 transgenic mice.
Marked bias towards spontaneous synaptic inhibition distinguishes non-adapting from adapting layer 5 pyramidal neurons in the barrel cortex
Authors: Popescu Ion R. , Le Kathy Q. , Palenzuela Rocío , Voglewede Rebecca , Mostany Ricardo
Published: October 2017

Pyramidal neuron subtypes differ in intrinsic electrophysiology properties and dendritic morphology. However, do different pyramidal neuron subtypes also receive synaptic inputs that are dissimilar in frequency and in excitation/inhibition balance? Unsupervised clustering of three intrinsic parameters that vary by cell subtype – the slow afterhyperpolarization, the sag, and the spike frequency adaptation – split layer 5 barrel cortex pyramidal neurons into two clusters: one of adapting cells and one of non-adapting cells, corresponding to previously described thin- and thick-tufted pyramidal neurons, respectively. Non-adapting neurons presented frequencies of spontaneous inhibitory postsynaptic currents (sIPSCs) and spontaneous excitatory postsynaptic currents (sEPSCs) three- and two-fold higher, respectively, than those of adapting neurons. The IPSC difference between pyramidal subtypes was activity independent. A subset of neurons were thy1-GFP positive, presented characteristics of non-adapting pyramidal neurons, and also had higher IPSC and EPSC frequencies than adapting neurons. The sEPSC/sIPSC frequency ratio was higher in adapting than in non-adapting cells, suggesting a higher excitatory drive in adapting neurons. Therefore, our study on spontaneous synaptic inputs suggests a different extent of synaptic information processing in adapting and non-adapting barrel cortex neurons, and that eventual deficits in inhibition may have differential effects on the excitation/inhibition balance in adapting and non-adapting neurons.
MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation
Authors: Iquebal M. A. , Jaiswal Sarika , Mahato Ajay Kumar , Jayaswal Pawan K. , Angadi U. B. , Kumar Neeraj , Sharma Nimisha , Singh Anand K. , Srivastav Manish , Prakash Jai , Singh S. K. , Khan Kasim , Mishra Rupesh K. , Rajan Shailendra , Bajpai Anju , Sandhya B. S. , Nischita Puttaraju , Ravishankar K. V. , Dinesh M. R. , Rai Anil , Kumar Dinesh , Sharma Tilak R. , Singh Nagendra K.
Published: October 2017

Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world’s first web-based genomic resources for genetic improvement and germplasm management of mango.
Quality of medical therapy in heart failure patients undergoing elective revascularisation: A protective effect of disease modifying therapy at discharge
Authors: Wurm Raphael , Huelsmann Martin , Hienert Marius , Seidl Veronika , Wiedemann Dominik , Laufer Guenther , Kocher Alfred , Adlbrecht Christopher , Andreas Martin
Published: October 2017

The STICH(-ES) trial showed that coronary artery bypass grafting was superior to medical therapy alone in treating ischemic heart failure. However, dosages of disease modifying drugs were not reported. We included 128 (84% male, mean age 66 ± 11 years) consecutive patients with ischemic heart failure and an ejection fraction ≤35% undergoing isolated elective coronary artery bypass grafting. We defined optimal medical therapy (OMT) as prescription of ≥50% dosages of guideline recommended medications (i.e. beta-blocker (BB) and renin angiotensin system (RAS) antagonist) plus prescription of a mineralocorticoid receptor antagonist (MRA). The mean logistic EuroSCORE was 12.3 ± 13.8%. The five year survival was 74%. At discharge, 111 patients (87%) were on a BB and 106 (83%) were on a RAS antagonist. Forty-nine patients (38%) received an MRA. Only 8 patients (6%) received OMT. A Cox regression analysis revealed EuroSCORE (p < 0.001) and the use of MRA (p = 0.003) and BB (p = 0.037) at discharge as significant predictors of 5 year survival. Prescription rates of heart failure medication are comparable to those reported in the STICH trial, but rates of OMT are very low at admission and discharge. Prescription of BB and MRA was associated with improved survival, highlighting the need for disease management programs and rigorous discharge management.
A damping circadian clock drives weak oscillations in metabolism and locomotor activity of aphids (Acyrthosiphon pisum)
Authors: Beer Katharina , Joschinski Jens , Arrazola Sastre Alazne , Krauss Jochen , Helfrich-Förster Charlotte
Published: October 2017

Timing seasonal events, like reproduction or diapause, is crucial for the survival of many species. Global change causes phenologies worldwide to shift, which requires a mechanistic explanation of seasonal time measurement. Day length (photoperiod) is a reliable indicator of winter arrival, but it remains unclear how exactly species measure day length. A reference for time of day could be provided by a circadian clock, by an hourglass clock, or, as some newer models suggest, by a damped circadian clock. However, damping of clock outputs has so far been rarely observed. To study putative clock outputs ofAcyrthosiphon pisumaphids, we raised individual nymphs on coloured artificial diet, and measured rhythms in metabolic activity in light-dark illumination cycles of 16:08 hours (LD) and constant conditions (DD). In addition, we kept individuals in a novel monitoring setup and measured locomotor activity. We found thatA.pisumis day-active in LD, potentially with a bimodal distribution. In constant darkness rhythmicity of locomotor behaviour persisted in some individuals, but patterns were mostly complex with several predominant periods. Metabolic activity, on the other hand, damped quickly. A damped circadian clock, potentially driven by multiple oscillator populations, is the most likely explanation of our results.
Evaluating the contribution of gut microbiome to the variance of porcine serum glucose and lipid concentration
Authors: Huang Xiaochang , Fang Shaoming , Yang Hui , Gao Jun , He Maozhang , Ke Shanlin , Zhao Yuanzhang , Chen Congying , Huang Lusheng
Published: October 2017

Serum glucose and lipids are important indicators for host metabolic condition. Interaction of host and gut microbes regulates the metabolism process. However, how much the gut microbiome contributes to the variance of serum glucose and lipids is largely unknown. Here we carried out a 16S rRNA gene based association study between cecum microbiome and the concentration of serum glucose and lipids in 240 Chinese Erhualian pigs. We identified tens of bacterial taxa associated with serum glucose and lipids. The butyrate-producing bacteria were significantly associated with serum glucose level. The pathogenic bacteria belonging to Proteobacteria and Fusobacteria showed significant associations with increased serum lipid levels, while the bacteria Lactobacillus and Bacilli had negative correlations with serum lipids. Cross-validation analysis revealed that 23.8% variation of serum glucose and 1.6%~6.0% variations of serum lipids were explained by gut microbiome. Furthermore, predicted function capacities related to nutrition intake, transport and carbohydrate metabolism were significantly associated with serum glucose level, while the pathways related to antioxidant metabolism and bile synthesis tended to be associated with serum lipid level. The results provide meaningful information to get insight into the effect of gut microbiome on serum glucose and lipid levels in pigs.