bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regional Rainfall Warning System for Landslides with Creep Deformation in Three Gorges using a Statistical Black Box Model
Authors: Guo Zizheng , Yin Kunlong , Gui Lei , Liu Qingli , Huang Faming , Wang Tengfei 
Published: June 2019

AbstractEstablishing an efficient regional landslide rainfall warning system plays an important role in landslide prevention. To forecast the performance of landslides with creep deformation at a regional scale, a black box model based on statistical analysis was proposed and was applied to Yunyang County in the Three Gorges Reservoir area (TGRA), China. The data samples were selected according to the characteristics of the landslide displacement monitoring data. Then, the rainfall criteria applied to different time periods were determined by correlation analysis between rainfall events and landslides and by numerical simulation on landslide movement under certain rainfall conditions. The cumulative rainfall thresholds that were determined relied on the displacement ratio model, which considered landslide scale characteristics and the statistical relationship between daily rainfall data and monthly displacement data. These thresholds were then applied to a warning system to determine a five-level warning partition of landslides with creep deformation in Yunyang County. Finally, landslide cases and displacement monitoring data were used to validate the accuracy of the model. The validation procedure showed that the warning results of the model fit well with actual conditions and that this model could provide the basis for early warning of landslides with creep deformation.
QR code micro-certified gemstones: femtosecond writing and Raman characterization in Diamond, Ruby and Sapphire
Authors: Batista Andre Jaques , Vianna Pilar Gregory , Ribeiro Henrique Bucker , Matos Christiano Jose Santiago de , Gomes Anderson Stevens Leonidas 
Published: June 2019

AbstractThis paper reports on a micro-certification procedure using femtosecond laser irradiation to microscopically mark a single-crystalline gemological and natural diamond, synthetic ruby and synthetic sapphire, inscribing a QR Code on them. The QR-code was composed of a set of 25 × 25 micropoints, and the irradiation energy was optimized at 1kHz repetition rate. The code was made at a 20 µm relative depth into the gemstone surfaces by controlling the incident laser energy, that was set to 3 μJ for all the samples. Characterization by optical and electron microscopy, as well as micro-Raman hyperspectral imaging showed that the microdots have a diameter of about 14 µm perpendicular to the irradiation direction, being laterally spaced by 14 µm-18 µm applied for each sample. This work corroborates the feasibility of using ultrafast laser inscription technology to fabricate microdots with great quality on gemstone surfaces, which offers a great potential for the jewelry industry to safely micro-encrypt gemological certifications. The compositional and morphological characterization of the modified surface was carried by micro-Raman spectroscopy and scanning electron microscopy.
Machine-assisted cultivation and analysis of biofilms
Authors: Hansen Silla H. , Kabbeck Tobias , Radtke Carsten P. , Krause Susanne , Krolitzki Eva , Peschke Theo , Gasmi Jannis , Rabe Kersten S. , Wagner Michael , Horn Harald , Hubbuch Jürgen , Gescher Johannes , Niemeyer Christof M. 
Published: June 2019

AbstractBiofilms are the natural form of life of the majority of microorganisms. These multispecies consortia are intensively studied not only for their effects on health and environment but also because they have an enormous potential as tools for biotechnological processes. Further exploration and exploitation of these complex systems will benefit from technical solutions that enable integrated, machine-assisted cultivation and analysis. We here introduce a microfluidic platform, where readily available microfluidic chips are connected by automated liquid handling with analysis instrumentation, such as fluorescence detection, microscopy, chromatography and optical coherence tomography. The system is operable under oxic and anoxic conditions, allowing for different gases and nutrients as feeding sources and it offers high spatiotemporal resolution in the analysis of metabolites and biofilm composition. We demonstrate the platform’s performance by monitoring the productivity of biofilms as well as the spatial organization of two bacterial species in a co-culture, which is driven by chemical gradients along the microfluidic channel.
Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota)
Authors: Widhelm Todd J. , Grewe Felix , Huang Jen-Pan , Mercado-Díaz Joel A. , Goffinet Bernard , Lücking Robert , Moncada Bibiana , Mason-Gamer Roberta , Lumbsch H. Thorsten 
Published: June 2019

AbstractIn the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.
Antibiotic-induced decreases in the levels of microbial-derived short-chain fatty acids correlate with increased gastrointestinal colonization of Candida albicans
Authors: Guinan Jack , Wang Shaohua , Hazbun Tony R. , Yadav Hariom , Thangamani Shankar 
Published: June 2019

AbstractCandida albicans is the fourth most common cause of systemic nosocomial infections, posing a significant risk in immunocompromised individuals. As the majority of systemic C. albicans infections stem from endogenous gastrointestinal (GI) colonization, understanding the mechanisms associated with GI colonization is essential in the development of novel methods to prevent C. albicans-related mortality. In this study, we investigated the role of microbial-derived short-chain fatty acids (SCFAs) including acetate, butyrate, and propionate on growth, morphogenesis, and GI colonization of C. albicans. Our results indicate that cefoperazone-treated mice susceptible to C. albicans infection had significantly decreased levels of SCFAs in the cecal contents that correlate with a higher fungal load in the feces. Further, using in vivo concentration of SCFAs, we demonstrated that SCFAs inhibit the growth, germ tube, hyphae and biofilm development of C. albicans in vitro. Collectively, results from this study suggest that antibiotic-induced decreases in the levels of SCFAs in the cecum enhances the growth and GI colonization of C. albicans.
Diphtheria Toxin A-Resistant Cell Lines Enable Robust Production and Evaluation of DTA-Encoding Lentiviruses
Authors: Lange Margaret J. , Lyddon Terri D. , Johnson Marc C. 
Published: June 2019

AbstractSuicide genes have been widely investigated for their utility as therapeutic agents and as tools for in vitro negative selection strategies. Several methods for delivery of suicide genes have been explored. Two important considerations for delivery are the quantity of delivered cargo and the ability to target the cargo to specific cells. Delivery using a lentiviral vector is particularly attractive due to the ability to encode the gene within the viral genome, as well as the ability to limit off-target effects by using cell type-specific glycoproteins. Here, we present the design and validation of a diphtheria toxin A (DTA)-encoding lentiviral vector expressing DTA under the control of a constituitive promoter to allow for expression of DTA in a variety of cell types, with specificity provided via selection of glycoproteins for pseudotyping of the lentiviral particles. DTA exerts its toxic activity through inhibition of eukaryotic translation elongation factor 2 (eEF2) via adenosine diphosphate (ADP)-ribosylation of a modified histidine residue, diphthamide, at His715, which blocks protein translation and leads to cell death. Thus, we also detail development of DTA-resistant cell lines, engineered through CRISPR/Cas9-mediated knockout of the diphthamide 1 (DPH1) gene, which enable both robust virus production by transfection and evaluation of DTA-expressing virus infectivity.
Artificial skin through super-sensing method and electrical impedance data from conductive fabric with aid of deep learning
Authors: Duan Xi , Taurand Sebastien , Soleimani Manuchehr 
Published: June 2019

AbstractSense of touch is a major part of man’s communication with their environment. Artificial skins can help robots to have the same sense of touch, especially for their social interactions. This paper presents a pressure mapping sensing using piezo-resistive fabric to represent aspects of the sense of touch. In past few years’ electrical impedance tomography (EIT) is considered to be able offer a good alternative for artificial skin in particular for its ease of adaptation for large area skin compared to individual matrix based sensors. The EIT has also very good temporal performance in data collection allowing for monitoring of fast responses to touch stimulation, enabling a truly real time touch sensing. Electromechanical responses of a conductive fabric can be exploited using EIT to create a low cost and large area touch sensing. Such electromechanical properties are often very complex, so to improve the imaging resolution and touch visibility an artificial intelligent (AI) was used in addition to the state of the art spatio-temporal imaging algorithm. This work demonstrates a step towards an integrated seamless skin with large area sensing in dynamical settings, closer to natural human skin’s behaviour. For the first time a dynamical touch sensing are studies by means of a spatio-temporal based electrical impedance tomography (EIT) imaging on a conductive fabric. The experimental results demonstrated the successful results by a combined AI with dynamical EIT imaging results in single and multiple points of touch.
HSPD1 repressed E-cadherin expression to promote cell invasion and migration for poor prognosis in oral squamous cell carcinoma
Authors: Kang Bor-Hwang , Shu Chih-Wen , Chao Jian-Kang , Lee Cheng-Hsin , Fu Ting-Ying , Liou Huei-Han , Ger Luo-Ping , Liu Pei-Feng 
Published: June 2019

AbstractBuccal mucosa squamous cell carcinoma (BMSCC) is one of major subsites of oral cancer and is associated with a high rate of metastasis and poor prognosis. Heat shock proteins (HSPs) act as potential prognostic biomarkers in many cancer types. However, the role of HSPD1 in oral cancer, especially in BMSCC, is still unknown. Through data analysis with The Cancer Genome Atlas (TCGA), we found the association of HSPD1 gene expression with tumorigenesis and poor prognosis in oral cancer patients. Our cohort study showed that higher HSPD1 protein level was associated with tumorigenesis and poor prognosis in BMSCC patients with lymph node invasion, suggesting that HSPD1 may be involved in tumor metastasis. Moreover, knockdown of HSPD1 induced E-cadherin expression and decreased the migration and invasion of BMSCC cells. In contrast, ectopic expression of HSPD1 diminished E-cadherin expression and promoted the migration/invasion of BMSCC cells. Further, HSPD1 regulated RelA activation to repress E-cadherin expression, enhancing the migration and invasion of BMSCC cells. Furthermore, HSPD1 protein level was inversely correlated with E-cadherin protein level in tumor tissues and co-expression of high HSPD1/low E-cadherin showed a significant association with poor prognosis in BMSCC patients. Taken together, HSPD1 might repress E-cadherin expression and promote metastatic characters of BMSCC cells for poor prognosis of BMSCC patients.
Exploring the EEG mu rhythm associated with observation and execution of a goal-directed action in 14-month-old preterm infants
Authors: Montirosso Rosario , Piazza Caterina , Giusti Lorenzo , Provenzi Livio , Ferrari Pier Francesco , Reni Gianluigi , Borgatti Renato 
Published: June 2019

AbstractElectroencephalographic mu rhythm desynchronization is thought to reflect Mirror Neuron System (MNS) activity and represents an important neural correlate of the coupling between action execution and perception. It is still unclear if the MNS in human ontogeny is already available at the beginning of postnatal life and how early experience impacts its development. Premature birth provides a “natural condition” for investigating the effects of early, atypical extra-uterine experience on MNS. The main aim of the present study was to investigate whether the MNS activity is associated with prematurity. We compared the mu rhythm activity in preterm (PT) and full-term (FT) 14-month old infants during an action observation/execution (AO/AE) task. Mu rhythm desynchronization was computed over frontal, central, parietal and occipital regions. Both groups showed mu rhythm suppression in all the scalp regions during action execution. Different desynchronization patterns emerged during action observation. Specifically, FT infants showed mu suppression in the right frontal, bilateral parietal and occipital regions; whereas PT infants exhibited mu suppression only in the right parietal region. Overall, these preliminary findings indicate that an atypical extra uterine experience might have an impact on the MNS activity.
Creep in Primary Consolidation with Rate of Loading Approach
Authors: Bi Gang , Ni Shuna , Wang Dong , Chen Yeqiang , Wei Jianfei , Gong Wenzong 
Published: June 2019

AbstractThe debate on creep in primary consolidation is analysed with a power law model following an approach in which creep is considered as rate of loading. According to this approach, primary consolidation is one type of rate of loading. To verify this approach, two types of tests, standard oedometer test and oedometer test with drainage prevented, are conducted on three types of soils (two from NGES and the other from Port of Guangzhou). The result: creep exponents obtained from two kinds of tests agree well with each other. Moreover, the approach is further validated by tracking, for over 80 years, the data from settlement of the case history San Jacinto Monument, which is inconsistent with data calculated from the classical method. In the end, procedure of this approach, with which long term settlement is predicted, is illustrated, and this approach is compared with the classical method.
Spin-locking metasurface for surface plasmon routing
Authors: Revah Matan , Yaroshevsky Andre , Gorodetski Yuri 
Published: June 2019

AbstractNanophotonic circuitry requires an ability to externally control and analyze optical signals tightly confined in subwavelength volumes. Various schemes of surface plasmon (SP) routing have been presented using active and passive metasurfaces. One of the most appealing approaches is the use of plasmonic spin-orbit interaction where the incident light spin state is efficiently coupled to an orbital degree of freedom of the surface wave. Recently, a major attention has been drawn to an additional plasmonic degree of freedom - the transverse spin and some application for near-field plasmonic manipulations have been presented. Here we propose a spin-locking metasurface incorporating a transverse spin of the SP wave to selectively route the near-field beams. Owing to the combination of the oblique incidence of circularly polarized light with the accurately designed momentum matching of the grating we achieve a precise directional control over the plasmonic distributions. The experimental verification of the directional launching is performed by a time-resolved leakage radiation measurements allowing one to visualize the shape and the dynamics of the excited beam.
On the molecular and cellular effects of omeprazole to further support its effectiveness as an antigiardial drug
Authors: López-Velázquez Gabriel , Fernández-Lainez Cynthia , de la Mora-de la Mora José Ignacio , Caudillo de la Portilla Daniela , Reynoso-Robles Rafael , González-Maciel Angélica , Ridaura Cecilia , García-Torres Itzhel , Gutiérrez-Castrellón Pedro , Olivos-García Alfonso , Flores-López Luis Antonio , Enríquez-Flores Sergio 
Published: June 2019

AbstractResearch onGiardia lambliahas accumulated large information about its molecular cell biology and infection biology. However, giardiasis is still one of the commonest parasitic diarrheal diseases affecting humans. Additionally, an alarming increase in cases refractory to conventional treatment has been reported in low prevalence settings. Consequently, efforts directed toward supporting the efficient use of alternative drugs, and the study of their molecular targets appears promising. Repurposing of proton pump inhibitors is effectivein vitroagainst the parasite and the toxic activity is associated with the inhibition of theG. lambliatriosephosphate isomerase (GlTIM) via the formation of covalent adducts with cysteine residue at position 222. Herein, we evaluate the effectiveness of omeprazolein vitroandin situonGlTIM mutants lacking the most superficial cysteines. We studied the influence on the glycolysis ofGiardiatrophozoites treated with omeprazole and characterized, for the first time, the morphological effect caused by this drug on the parasite. Our results support the effectiveness of omeprazole againstGlTIM despite of the possibility to mutate the druggable amino acid targets as an adaptive response. Also, we further characterized the effect of omeprazole on trophozoites and discuss the possible mechanism involved in its antigiardial effect.
High throughput proteomics identifies a high-accuracy 11 plasma protein biomarker signature for ovarian cancer
Authors: Enroth Stefan , Berggrund Malin , Lycke Maria , Broberg John , Lundberg Martin , Assarsson Erika , Olovsson Matts , Stålberg Karin , Sundfeldt Karin , Gyllensten Ulf 
Published: June 2019

AbstractOvarian cancer is usually detected at a late stage and the overall 5-year survival is only 30–40%. Additional means for early detection and improved diagnosis are acutely needed. To search for novel biomarkers, we compared circulating plasma levels of 593 proteins in three cohorts of patients with ovarian cancer and benign tumors, using the proximity extension assay (PEA). A combinatorial strategy was developed for identification of different multivariate biomarker signatures. A final model consisting of 11 biomarkers plus age was developed into a multiplex PEA test reporting in absolute concentrations. The final model was evaluated in a fourth independent cohort and has an AUC = 0.94, PPV = 0.92, sensitivity = 0.85 and specificity = 0.93 for detection of ovarian cancer stages I–IV. The novel plasma protein signature could be used to improve the diagnosis of women with adnexal ovarian mass or in screening to identify women that should be referred to specialized examination.
Automated subset identification and characterization pipeline for multidimensional flow and mass cytometry data clustering and visualization
Authors: Meehan Stephen , Kolyagin Gleb A. , Parks David , Youngyunpipatkul Justin , Herzenberg Leonore A. , Walther Guenther , Ghosn Eliver E. B. , Orlova Darya Y. 
Published: June 2019

AbstractWhen examining datasets of any dimensionality, researchers frequently aim to identify individual subsets (clusters) of objects within the dataset. The ubiquity of multidimensional data has motivated the replacement of user-guided clustering with fully automated clustering. The fully automated methods are designed to make clustering more accurate, standardized and faster. However, the adoption of these methods is still limited by the lack of intuitive visualization and cluster matching methods that would allow users to readily interpret fully automatically generated clusters. To address these issues, we developed a fully automated subset identification and characterization (SIC) pipeline providing robust cluster matching and data visualization tools for high-dimensional flow/mass cytometry (and other) data. This pipeline automatically (and intuitively) generates two-dimensional representations of high-dimensional datasets that are safe from the curse of dimensionality. This new approach allows more robust and reproducible data analysis,+ facilitating the development of new gold standard practices across laboratories and institutions.
MicroRNA-221 promotes cisplatin resistance in osteosarcoma cells by targeting PPP2R2A
Authors: Yu Wen-chao , Chen Hui-hao , Qu Yan-yan , Xu Chun-wei , Yang Chen , Liu Yan 
Published: June 2019

Abstract
Osteosarcoma (OS), the most common malignant bone tumor, is the main cause of cancer-related deaths in children and young adults. Despite the combination of surgery and multi-agent chemotherapy, patients with OS who develop resistance to chemotherapy or experience recurrence have a dismal prognosis. MicroRNAs (miRNAs) are a class of small noncoding RNAs that repress their targets by binding to the 3′-UTR and/or coding sequences, leading to the inhibition of gene expression. miR-221 is found to be up-regulated in tumors when compared with their matched normal osteoblast tissues. We also observed significant miR-221 up-regulation in the OS cell lines, MG-63, SaoS-2, and U2OS, when compared with the normal osteoblast cell line, HOb. Overexpression of miR-221 promoted OS cell invasion, migration, proliferation, and cisplatin resistance. MG-63 and SaoS-2 cells transfected with miR-221 mimics were more resistant to cisplatin. The IC50 of MG-63 cells transfected with control mimics was 1.24 μM. However, the IC50 of MG-63 cells overexpressing miR-221 increased to 7.65 μM. Similar results were found in SaoS-2 cells, where the IC50 for cisplatin increased from 3.65 to 8.73 μM. Thus, we report that miR-221 directly targets PP2A subunit B (PPP2R2A) in OS by binding to the 3′-UTR of the PPP2R2A mRNA. Restoration of PPP2R2A in miR-221-overexpressing OS cells recovers the cisplatin sensitivity of OS cells. Therefore, the present study suggests a new therapeutic approach by inhibiting miR-221 for anti-chemoresistance in OS.