bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial reduction in sealed caries lesions is strain- and material-specific
Authors: Marggraf Teresa , Ganas Petra , Paris Sebastian , Schwendicke Falk 
Published: February 2018

AbstractSealing can arrest caries lesions. We aimed to evaluate if sealing effects and kinetics are bacterial-strain and sealing-material specific. Human dentin discs were mounted in a dual-chamber device. Caries lesions were induced chemically and contaminated with either Lactobacillus rhamnosus (LR) or Streptococcus sobrinus (SS). For (1) kinetics assessment, the initial bacterial load and the sealing period were varied, and lesions sealed using a self-etch adhesive and composite. For (2) comparing materials, six sealing protocols (#1-#6) were evaluated: 1# Self-etch adhesive plus composite placed without a liner, or #2 calcium hydroxide, or #3 mineral trioxide aggregate, or #4 Biodentine liners; #5 antibacterial adhesive plus composite; #6 glass ionomer cement. Pulpal fluid flow was simulated during sealing. The outcome was the number of surviving bacteria (CFU) per g dentin. For LR, bacterial survival increased significantly with increasing initial bacterial load and decreased with longer sealing periods. The relative reduction followed a first-order kinetics. More LR survived under calcium hydroxide or MTA than other materials (p < 0.001). For SS, nearly no bacteria survived sealing regardless of sealing period, initial bacterial load or sealing material. In conclusion, sealing effects and kinetics were strain- and material-specific.
Acquired Enamel Pellicle Engineered Peptides: Effects on Hydroxyapatite Crystal Growth
Authors: Valente Maria Teresa , Moffa Eduardo Buozi , Crosara Karla Tonelli Bicalho , Xiao Yizhi , de Oliveira Thais Marchini , Machado Maria Aparecida de Andrade Moreira , Siqueira Walter Luiz 
Published: February 2018

AbstractThe aim of this study was to test the hypothesis that duplication/hybridization of functional domains of naturally occurring pellicle peptides amplified the inhibitory effect of hydroxyapatite crystal growth, which is related to enamel remineralization and dental calculus formation. Histatin 3, statherin, their functional domains (RR14 and DR9), and engineered peptides (DR9-DR9 and DR9-RR14) were tested at seven different concentrations to evaluate the effect on hydroxyapatite crystal growth inhibition. A microplate colorimetric assay was used to quantify hydroxyapatite crystal growth. The half-maximal inhibitory concentration (IC50) was determined for each group. ANOVA and Student-Newman-Keuls pairwise comparisons were used to compare the groups. DR9-DR9 increased the inhibitory effect of hydroxyapatite crystal growth compared to single DR9 (p < 0.05), indicating that functional domain multiplication represented a strong protein evolution pathway. Interestingly, the hybrid peptide DR9-RR14 had an intermediate inhibitory effect compared to DR9 and DR9-DR9. This study used an engineered peptide approach to investigate a potential evolution protein pathway related to duplication/hybridization of acquired enamel pellicle’s natural peptide constituents, contributing to the development of synthetic peptides for therapeutic use against dental caries and periodontal disease.
Adult mouse eIF2Bε Arg191His astrocytes display a normal integrated stress response in vitro
Authors: Wisse Lisanne E. , ter Braak Timo J. , van de Beek Malu-Clair , van Berkel Carola G. M. , Wortel Joke , Heine Vivi M. , Proud Chris G. , van der Knaap Marjo S. , Abbink Truus E. M. 
Published: February 2018

AbstractVanishing white matter (VWM) is a genetic childhood white matter disorder, characterized by chronic as well as episodic, stress provoked, neurological deterioration. Treatment is unavailable and patients often die within a few years after onset. VWM is caused by recessive mutations in the eukaryotic initiation factor 2B (eIF2B). eIF2B regulates protein synthesis rates in every cell of the body. In normal cells, various types of cellular stress inhibit eIF2B activity and induce the integrated stress response (ISR). We have developed a VWM mouse model homozygous for the pathogenic Arg191His mutation in eIF2Bε (2b5
ho
), representative of the human disease. Neuropathological examination of VWM patient and mouse brain tissue suggests that astrocytes are primarily affected. We hypothesized that VWM astrocytes are selectively hypersensitive to ISR induction, resulting in a heightened response. We cultured astrocytes from wildtype and VWM mice and investigated the ISR in assays that measure transcriptional induction of stress genes, protein synthesis rates and cell viability. We investigated the effects of short- and long-term stress as well as stress recovery. We detected congruent results amongst the various assays and did not detect a hyperactive ISR in VWM mouse astrocytes.
Multimorbidity patterns in relation to polypharmacy and dosage frequency: a nationwide, cross-sectional study in a Japanese population
Authors: Aoki Takuya , Yamamoto Yosuke , Ikenoue Tatsuyoshi , Onishi Yoshihiro , Fukuhara Shunichi 
Published: February 2018

AbstractIn the present study, we aimed to identify multimorbidity patterns in a Japanese population and investigate whether these patterns have differing effects on polypharmacy and dosage frequency. Data was collected on 17 chronic health conditions via nationwide cross-sectional survey of 3,256 adult Japanese residents. Factor analysis was performed to identify multimorbidity patterns, and associations were determined with excessive polypharmacy [concurrent use of ≥ 10 prescription or over-the-counter (OTC) medications] and higher dosage frequency ( ≥ 3 doses per day). Secondary outcomes were the number of concurrent prescription medications and the number of concurrent OTC medications. We used a generalized linear model to adjust for individual sociodemographic characteristics. Five multimorbidity patterns were identified: cardiovascular/renal/metabolic, neuropsychiatric, skeletal/articular/digestive, respiratory/dermal, and malignant/digestive/urologic. Among these patterns, malignant/digestive/urologic and cardiovascular/renal/metabolic patterns showed the strongest associations with excessive polypharmacy and the number of concurrent OTC medications. Malignant/digestive/urologic, respiratory/dermal, and skeletal/articular/digestive patterns were also associated with higher dosage frequency. Multimorbidity patterns have differing effects on excessive polypharmacy and dosage frequency. Malignant/digestive/urologic pattern may be at higher risk of impaired medication safety and increased treatment burden, than other patterns. Continued study is warranted to determine how to incorporate multimorbidity patterns into risk assessments of polypharmacy and overall treatment burden.
Development and Evaluation of Novel Statistical Methods in Urine Biomarker-Based Hepatocellular Carcinoma Screening
Authors: Wang Jeremy , Jain Surbhi , Chen Dion , Song Wei , Hu Chi-Tan , Su Ying-Hsiu 
Published: February 2018

AbstractHepatocellular carcinoma is one of the fastest growing cancers in the US and has a low survival rate, partly due to difficulties in early detection. Because of HCC’s high heterogeneity, it has been suggested that multiple biomarkers would be needed to develop a sensitive HCC screening test. This study applied random forest (RF), a machine learning technique, and proposed two novel models, fixed sequential (FS) and two-step (TS), for comparison with two commonly used statistical techniques, logistic regression (LR) and classification and regression trees (CART), in combining multiple urine DNA biomarkers for HCC screening using biomarker values obtained from 137 HCC and 431 non-HCC (224 hepatitis and 207 cirrhosis) subjects. The sensitivity, specificity, area under the receiver operating curve, and variability were estimated through repeated 10-fold cross-validation to compare the models’ performances in accuracy and robustness. We show that RF and TS have higher accuracy and stability; specifically, they reach 90% specificity and 86%/87% sensitivity respectively along with 15% higher sensitivity and 10% higher specificity than LR in cross-validation. The potential of RF and TS to develop a panel of multiple biomarkers and the possibility for self-training, cloud-based models for HCC screening are discussed.
Dietary n-3 and n-6 polyunsaturated fatty acids, the FADS gene, and the risk of gastric cancer in a Korean population
Authors: Lee Sunghee , Lee Jeonghee , Choi Il Ju , Kim Young-Woo , Ryu Keun Won , Kim Young-Il , Kim Jeongseon 
Published: February 2018

Abstractn-3 polyunsaturated fatty acids (PUFAs) and n-6 PUFAs are reported to have immunomodulatory effects, but few studies have examined these functions. Thus, we examined whether dietary n-3 and n-6 PUFAs are associated with the risk of gastric cancer and further investigated whether fatty acid desaturases 1 and 2 (FADS1 and FADS2) modify this association. In a case-control study, 1,464 participants (402 cases and 1,062 controls) were enrolled. A semi-quantitative food frequency questionnaire was utilized to measure dietary PUFA intake. Genotyping was performed using the Axiom® Exome 319 Array. Multivariable logistic models were established after adjusting for confounding variables. The risk of gastric cancer was significantly decreased among participants who had the highest tertile intake of docosahexaenoic acid (DHA), an n-3 PUFA, even after adjusting for covariates [odds ratios (OR) = 0.72, 95% confidence intervals (95% CIs) = 0.53–0.99]. However, no significant interaction according to FADS1 rs174546 or FADS2 rs174583 was observed. In conclusion, we observed a significant inverse association between dietary DHA and the risk of gastric cancer but found that FADS1 rs174546 and FADS2 rs174583 did not modify the association between dietary n-3 or n-6 PUFAs and gastric cancer risk.
Estimating apple tree canopy chlorophyll content based on Sentinel-2A remote sensing imaging
Authors: Li Cheng , Zhu Xicun , Wei Yu , Cao Shujing , Guo Xiaoyan , Yu Xinyang , Chang Chunyan 
Published: February 2018

AbstractThe remote sensing technology provides a new means for the determination of chlorophyll content in apple trees that includes a rapid analysis, low cost and large monitoring area. The Back-Propagation Neural Network (BPNN) and the Supported Vector Machine Regression (SVMR) methods were both frequently used method to construct estimation model based on remote sensing imaging. The aim of this study was to find out which estimation model of apple tree canopy chlorophyll content based on the vegetation indices constructed with visible, red edge and near-infrared bands of the sensor of Sentinel-2 was more accurate and stabler. The results were as follows: The calibration set coefficient of determination (R2) value of 0.729 and validation set R2 value of 0.667 of the model using the SVMR method based on the vegetation indices (NDVIgreen + NDVIred + NDVIre) were higher than those of the model using the BPNN method by 8.2% and 11.0%, respectively. The calibration set root mean square error (RMSE) of 0.159 and validation set RMSE of 0.178 of the model using the SVMR method based on the vegetation indices (NDVIgreen + NDVIred + NDVIre) were lower than those of the model using the BPNN method by 5.9% and 3.8%, respectively.
A symbolic network-based nonlinear theory for dynamical systems observability
Authors: Letellier Christophe , Sendiña-Nadal Irene , Bianco-Martinez Ezequiel , Baptista Murilo S. 
Published: February 2018

AbstractWhen the state of the whole reaction network can be inferred by just measuring the dynamics of a limited set of nodes the system is said to be fully observable. However, as the number of all possible combinations of measured variables and time derivatives spanning the reconstructed state of the system exponentially increases with its dimension, the observability becomes a computationally prohibitive task. Our approach consists in computing the observability coefficients from a symbolic Jacobian matrix whose elements encode the linear, nonlinear polynomial or rational nature of the interaction among the variables. The novelty we introduce in this paper, required for treating large-dimensional systems, is to identify from the symbolic Jacobian matrix the minimal set of variables (together with their time derivatives) candidate to be measured for completing the state space reconstruction. Then symbolic observability coefficients are computed from the symbolic observability matrix. Our results are in agreement with the analytical computations, evidencing the correctness of our approach. Its application to efficiently exploring the dynamics of real world complex systems such as power grids, socioeconomic networks or biological networks is quite promising.
Egr2-dependent microRNA-138 is dispensable for peripheral nerve myelination
Authors: Lin Hsin-Pin , Oksuz Idil , Svaren John , Awatramani Rajeshwar 
Published: February 2018

AbstractRecent studies have elucidated the crucial role for microRNAs in peripheral nerve myelination by ablating components of the microRNA synthesis machinery. Few studies have focused on the role of individual microRNAs. To fill this gap, we focused this study on miR-138, which was shown to be drastically reduced in Dicer1 and Dgcr8 knockout mice with hypomyelinating phenotypes and to potentially target the negative regulators of Schwann cell differentiation. Here, we show that of two miR-138 encoding loci, mir-138-1 is the predominant locus transcribed in Schwann cells. mir-138-1 is transcriptionally upregulated during myelination and downregulated upon nerve injury. EGR2 is required for mir-138-1 transcription during development, and both SOX10 and EGR2 bind to an active enhancer near the mir-138-1 locus. Based on expression analyses, we hypothesized that miR-138 facilitates the transition between undifferentiated Schwann cells and myelinating Schwann cells. However, in conditional knockouts, we could not detect significant changes in Schwann cell proliferation, cell cycle exit, or myelination. Overall, our results demonstrate that miR-138 is an Egr2-dependent microRNA but is dispensable for Schwann cell myelination.
Expanding biological space coverage enhances the prediction of drug adverse effects in human using in vitro activity profiles
Authors: Huang Ruili , Xia Menghang , Sakamuru Srilatha , Zhao Jinghua , Lynch Caitlin , Zhao Tongan , Zhu Hu , Austin Christopher P. , Simeonov Anton 
Published: February 2018

AbstractIn vitro assay data have recently emerged as a potential alternative to traditional animal toxicity studies to aid in the prediction of adverse effects of chemicals on humans. Here we evaluate the data generated from a battery of quantitative high-throughput screening (qHTS) assays applied to a large and diverse collection of chemicals, including approved drugs, for their capacity in predicting human toxicity. Models were built with animal in vivo toxicity data, in vitro human cell-based assay data, as well as in combination with chemical structure and/or drug-target information to predict adverse effects observed for drugs in humans. Interestingly, we found that the models built with the human cell-based assay data performed close to those of the models based on animal in vivo toxicity data. Furthermore, expanding the biological space coverage of assays by including additional drug-target annotations was shown to significantly improve model performance. We identified a small set of targets, which, when added to the current suite of in vitro human cell-based assay data, result in models that greatly outperform those built with the existing animal toxicity data. Assays can be developed for this set of targets to screen compounds for construction of robust models for human toxicity prediction.
Femtosecond Laser Mass Spectrometry and High Harmonic Spectroscopy of Xylene Isomers
Authors: Alharbi Abdullah , Boguslavskiy Andrey E. , Austin Dane , Thiré Nicolas , Wood D. , Hawkins P. , McGrath Felicity , Johnson A. S. , Lopez-Quintas I. , Schmidt Bruno , Légaré Francois , Marangos J. P. , Le Anh-Thu , Bhardwaj Ravi 
Published: February 2018

AbstractStructural isomers, molecules having the same chemical formula but with atoms bonded in different order, are hard to identify using conventional spectroscopy and mass spectrometry. They exhibit virtually indistinguishable mass spectra when ionized by electrons. Laser mass spectrometry based on photoionization of the isomers has emerged as a promising alternative but requires shaped ultrafast laser pulses. Here we use transform limited femtosecond pulses to distinguish the isomers using two methods. First, we probe doubly charged parent ions with circularly polarized light. We show that the yield of doubly charged ortho-xylene decreases while para-xylene increases over a range of laser intensities when the laser polarization is changed from linear to circular. Second, we probe high harmonic generation from randomly oriented isomer molecules subjected to an intense laser field. We show that the yield of high-order harmonics varies with the positioning of the methyl group in xylene isomers (ortho-, para- and meta-) and is due to differences in the strength of tunnel ionization and the overlap between the angular peaks of ionization and photo-recombination.
Dynamical Casimir Effect for Gaussian Boson Sampling
Authors: Peropadre Borja , Huh Joonsuk , Sabín Carlos 
Published: February 2018

AbstractWe show that the Dynamical Casimir Effect (DCE), realized on two multimode coplanar waveg-uide resonators, implements a gaussian boson sampler (GBS). The appropriate choice of the mirror acceleration that couples both resonators translates into the desired initial gaussian state and many-boson interference in a boson sampling network. In particular, we show that the proposed quantum simulator naturally performs a classically hard task, known as scattershot boson sampling. Our result unveils an unprecedented computational power of DCE, and paves the way for using DCE as a resource for quantum simulation.
I-AbACUS: a Reliable Software Tool for the Semi-Automatic Analysis of Invasion and Migration Transwell Assays
Authors: Cortesi Marilisa , Llamosas Estelle , Henry Claire E. , Kumaran Raani-Yogeeta A. , Ng Benedict , Youkhana Janet , Ford Caroline E. 
Published: February 2018

AbstractThe quantification of invasion and migration is an important aspect of cancer research, used both in the study of the molecular processes involved in this collection of diseases and the evaluation of the efficacy of new potential treatments. The transwell assay, while being one of the most widely used techniques for the evaluation of these characteristics, shows a high dependence on the operator’s ability to correctly identify the cells and a low protocol standardization. Here we present I-AbACUS, a software tool specifically designed to aid the analysis of transwell assays that automatically and specifically recognizes cells in images of stained membranes and provides the user with a suggested cell count. A complete description of this instrument, together with its validation against the standard analysis technique for this assay is presented. Furthermore, we show that I-AbACUS is versatile and able to elaborate images containing cells with different morphologies and that the obtained results are less dependent on the operator and their experience. We anticipate that this instrument, freely available (Gnu Public Licence GPL v2) at www.marilisacortesi.com as a standalone application, could significantly improve the quantification of invasion and migration of cancer cells.
Social content and emotional valence modulate gaze fixations in dynamic scenes
Authors: Rubo Marius , Gamer Matthias 
Published: February 2018

AbstractPrevious research has shown that low-level visual features (i.e., low-level visual saliency) as well as socially relevant information predict gaze allocation in free viewing conditions. However, these studies mainly used static and highly controlled stimulus material, thus revealing little about the robustness of attentional processes across diverging situations. Secondly, the influence of affective stimulus characteristics on visual exploration patterns remains poorly understood. Participants in the present study freely viewed a set of naturalistic, contextually rich video clips from a variety of settings that were capable of eliciting different moods. Using recordings of eye movements, we quantified to what degree social information, emotional valence and low-level visual features influenced gaze allocation using generalized linear mixed models. We found substantial and similarly large regression weights for low-level saliency and social information, affirming the importance of both predictor classes under ecologically more valid dynamic stimulation conditions. Differences in predictor strength between individuals were large and highly stable across videos. Additionally, low-level saliency was less important for fixation selection in videos containing persons than in videos not containing persons, and less important for videos perceived as negative. We discuss the generalizability of these findings and the feasibility of applying this research paradigm to patient groups.
Comprehensive detection of pathogens in immunocompromised children with bloodstream infections by next-generation sequencing
Authors: Horiba Kazuhiro , Kawada Jun-ichi , Okuno Yusuke , Tetsuka Nobuyuki , Suzuki Takako , Ando Shotaro , Kamiya Yasuko , Torii Yuka , Yagi Tetsuya , Takahashi Yoshiyuki , Ito Yoshinori 
Published: February 2018

AbstractBloodstream infection (BSI) is a severe complication in immunocompromised patients. Next-generation sequencing (NGS) allows us to analyze comprehensively and quantitatively all microorganisms present in a clinical sample. Thirty-five pediatric patients (12 with BSI and 23 with suspected BSI/negative blood culture) were enrolled. Plasma/serum samples were used for sequencing and the results were compared with those from blood culture. Sequencing reads of bacteria isolated in blood culture were identified by NGS in all plasma/serum samples at disease onset. Bacteria isolated in blood culture were identical to the dominant bacteria by NGS in 8 of 12 patients. Bacterial reads per million reads of the sequence depth (BR) > 200 and relative importance values of the dominant bacteria (P1) > 0.5 were employed to determine causative pathogens. Causative pathogens were detected using these criteria in 7 of 12 patients with BSI. Additionally, causative bacteria were detected in the plasma/serum at 7 days before disease onset in two patients with catheter-related BSI. Causative pathogens, including virus, were identified in three patients with suspected BSI. Lastly, a total of 62 resistance genes were detected by NGS. In conclusion, NGS is a new method to identify causative microorganisms in BSI and may predict BSI in some patients.