bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of digital real-time PCR assay as a molecular diagnostic tool for single-cell analysis
Authors: Chang Chia-Hao , Mau-Hsu Daxen , Chen Ke-Cheng , Wei Cheng-Wey , Chiu Chiung-Ying , Young Tai-Horng 
Published: February 2018

AbstractIn a single-cell study, isolating and identifying single cells are essential, but these processes often require a large investment of time or money. The aim of this study was to isolate and analyse single cells using a novel platform, the PanelChip™ Analysis System, which includes 2500 microwells chip and a digital real-time polymerase chain reaction (dqPCR) assay, in comparison with a standard PCR (qPCR) assay. Through the serial dilution of a known concentration standard, namely pUC19, the accuracy and sensitivity levels of two methodologies were compared. The two systems were tested on the basis of expression levels of the genetic markers vimentin, E-cadherin, N-cadherin and GAPDH in A549 lung carcinoma cells at two known concentrations. Furthermore, the influence of a known PCR inhibitor commonly found in blood samples, heparin, was evaluated in both methodologies. Finally, mathematical models were proposed and separation method of single cells was verified; moreover, gene expression levels during epithelial–mesenchymal transition in single cells under TGFβ1 treatment were measured. The drawn conclusion is that dqPCR performed using PanelChip™ is superior to the standard qPCR in terms of sensitivity, precision, and heparin tolerance. The dqPCR assay is a potential tool for clinical diagnosis and single-cell applications.
Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources
Authors: Jaiswal Sarika , Antala Tushar J. , Mandavia M. K. , Chopra Meenu , Jasrotia Rahul Singh , Tomar Rukam S. , Kheni Jashminkumar , Angadi U. B. , Iquebal M. A. , Golakia B. A. , Rai Anil , Kumar Dinesh 
Published: February 2018

AbstractPearl millet, (Pennisetum glaucum L.), an efficient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortification combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but field-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet. We found 19983 differentially expressed genes, 7595 transcription factors, gene regulatory network having 45 hub genes controlling drought response. We report 34652 putative markers (4192 simple sequence repeats, 12111 SNPs and 6249 InDels). Study reveals role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought. Results were validated by qPCR of 13 randomly selected genes. We report the first web-based genomic resource (http://webtom.cabgrid.res.in/pmdtdb/) which can be used for candidate genes-based SNP discovery programs and trait-based association studies. Looking at climatic change, nutritional and pharmaceutical importance of this crop, present investigation has immense value in understanding drought response in field condition. This is important in germplasm management and improvement in endeavour of pearl millet productivity.
Removal of artificial sweeteners and their effects on microbial communities in sequencing batch reactors
Authors: Li Shaoli , Geng Jinju , Wu Gang , Gao Xingsheng , Fu Yingying , Ren Hongqiang 
Published: February 2018

AbstractConcern is growing over contamination of the environment with artificial sweeteners (ASWs) because of their widespread existence in wastewater treatment plants (WWTPs). To evaluate ASWs removal and the effect on activated sludge, acesulfame (ACE), sucralose (SUC), cyclamate (CYC) and saccharin (SAC) were introduced individually or in mixture to sequencing batch reactors (SBRs) in environmentally relevant concentrations (100 ppb) for 100 days. Comparisons between ACE removal in a full-scale WWTP and in lab-scale SBRs were conducted. Results showed that CYC and SAC were completely removed, whereas SUC was persistent. However, ACE removal in lab-scale SBRs was significantly greater than in the full-scale WWTP. In SBRs, chemical oxygen demand (COD), ammonia nitrogen (NH4+-N) and total nitrogen (TN) removal appeared unchanged after adding ASWs (p > 0.05). Adenosine triphosphate (ATP) concentrations and triphenyl tetrazolium chloride-dehydrogenase activity (TTC-DHA) declined significantly (p < 0.05). The mixed ASWs had more evident effects than the individual ASWs. Microbial community analyses revealed that Proteobacteria decreased obviously, while Bacteroidetes, Chloroflexi and Actinobacteria were enriched with the addition of ASWs. Redundancy Analysis (RDA) indicated ACE had a greater impact on activated sludge than the other ASWs.
Printed Receive Coils with High Acoustic Transparency for Magnetic Resonance Guided Focused Ultrasound
Authors: Corea Joseph , Ye Patrick , Seo Dongjin , Butts-Pauly Kim , Arias Ana Claudia , Lustig Michael 
Published: February 2018

AbstractIn magnetic resonance guided focused ultrasound (MRgFUS) therapy sound waves are focused through the body to selectively ablate difficult to access lesions and tissues. A magnetic resonance imaging (MRI) scanner non-invasively tracks the temperature increase throughout the tissue to guide the therapy. In clinical MRI, tightly fitted hardware comprised of multichannel coil arrays are required to capture high quality images at high spatiotemporal resolution. Ablating tissue requires a clear path for acoustic energy to travel but current array materials scatter and attenuate acoustic energy. As a result coil arrays are placed outside of the transducer, clear of the beam path, compromising imaging speed, resolution, and temperature accuracy of the scan. Here we show that when coil arrays are fabricated by additive manufacturing (i.e., printing), they exhibit acoustic transparency as high as 89.5%. This allows the coils to be placed in the beam path increasing the image signal to noise ratio (SNR) five-fold in phantoms and volunteers. We also characterize printed coil materials properties over time when submerged in the water required for acoustic coupling. These arrays offer high SNR and acceleration capabilities, which can address current challenges in treating head and abdominal tumors allowing MRgFUS to give patients better outcomes.
dynGENIE3: dynamical GENIE3 for the inference of gene networks from time series expression data
Authors: Huynh-Thu Vân Anh , Geurts Pierre 
Published: February 2018

AbstractThe elucidation of gene regulatory networks is one of the major challenges of systems biology. Measurements about genes that are exploited by network inference methods are typically available either in the form of steady-state expression vectors or time series expression data. In our previous work, we proposed the GENIE3 method that exploits variable importance scores derived from Random forests to identify the regulators of each target gene. This method provided state-of-the-art performance on several benchmark datasets, but it could however not specifically be applied to time series expression data. We propose here an adaptation of the GENIE3 method, called dynamical GENIE3 (dynGENIE3), for handling both time series and steady-state expression data. The proposed method is evaluated extensively on the artificial DREAM4 benchmarks and on three real time series expression datasets. Although dynGENIE3 does not systematically yield the best performance on each and every network, it is competitive with diverse methods from the literature, while preserving the main advantages of GENIE3 in terms of scalability.
Hypoxia-induced long non-coding RNA Malat1 is dispensable for renal ischemia/reperfusion-injury
Authors: Kölling Malte , Genschel Celina , Kaucsar Tamas , Hübner Anika , Rong Song , Schmitt Roland , Sörensen-Zender Inga , Haddad George , Kistler Andreas , Seeger Harald , Kielstein Jan T. , Fliser Danilo , Haller Hermann , Wüthrich Rudolf , Zörnig Martin , Thum Thomas , Lorenzen Johan 
Published: February 2018

AbstractRenal ischemia-reperfusion (I/R) injury is a major cause of acute kidney injury (AKI). Non-coding RNAs are crucially involved in its pathophysiology. We identified hypoxia-induced long non-coding RNA Malat1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) to be upregulated in renal I/R injury. We here elucidated the functional role of Malat1 in vitro and its potential contribution to kidney injury in vivo. Malat1 was upregulated in kidney biopsies and plasma of patients with AKI, in murine hypoxic kidney tissue as well as in cultured and ex vivo sorted hypoxic endothelial cells and tubular epithelial cells. Malat1 was transcriptionally activated by hypoxia-inducible factor 1-α. In vitro, Malat1 inhibition reduced proliferation and the number of endothelial cells in the S-phase of the cell cycle. In vivo, Malat1 knockout and wildtype mice showed similar degrees of outer medullary tubular epithelial injury, proliferation, capillary rarefaction, inflammation and fibrosis, survival and kidney function. Small-RNA sequencing and whole genome expression analysis revealed only minor changes between ischemic Malat1 knockout and wildtype mice. Contrary to previous studies, which suggested a prominent role of Malat1 in the induction of disease, we did not confirm an in vivo role of Malat1 concerning renal I/R-injury.
The novel dithiocarbamate, DpdtC suppresses HER2-overexpressed cancer cells by up-regulating NDRG1 via inactivation of HER2-ERK 1/2 signaling
Authors: Yang Yun , Liu Youxun , Guo Rui , Fu Yun , Zhang Ziheng , Zhang Pengfei , Zhou Pingxin , Wang Tingting , Huang Tengfei , Li Xiaotong , Li Changzheng 
Published: February 2018

AbstractDithiocarbamate has been tested for its effective anti-tumor activity, but the underlying mechanism remains unclear. We previously prepared a novel diththiocarbamate derivative, DpdtC with an ability of catalase inhibition. Here, we for the first time investigated the growth inhibition effects of DpdtC on HER2-amplified cancer cells and elucidated its mechanism of action. Results showed that DpdtC exerted the potent anti-tumor effects against HER2-overexpressed SK-OV-3 and SK-BR-3 cells, especially on SK-OV-3 cells with a higher NDRG1 level, which was also confirmed in the SK-OV-3 xenograft model. Interestingly, we observed that NDRG1 was up-regulated, while membrane expression of HER2 was regressed in SK-OV-3 cells upon DpdtC treatment. In agreement, silencing endogenous NDRG1 also increased the expression of HER2 in SK-OV-3 cells, while overexpressing NDRG1 decreased HER2 expression in SK-BR-3 cells. Furthermore, our results showed the formation of the EGFR/HER2 heterodimer was attenuated and phosphorylation of ERK1/2 was inhibited in SK-OV-3 cells when treated with DpdtC. Collectively, these observations demonstrated that NDRG1 plays an important role in mediating the inhibition effects of DpdtC in HER2-overexpressed cancer cells via selective targeting of the HER2-ERK1/2 pathway. Hence, our investigation suggests that up-regulation of NDRG1 by DpdtC is a promising therapeutic approach in HER2-overexpressed cancers.
Effect of the environment microbiota on the flavour of light-flavour Baijiu during spontaneous fermentation
Authors: Pang Xiao-Na , Han Bei-Zhong , Huang Xiao-Ning , Zhang Xin , Hou Lin-Feng , Cao Ming , Gao Li-Juan , Hu Guang-Hui , Chen Jing-Yu 
Published: February 2018

AbstractLight-flavour Baijiu is a type of Chinese liquor with a pure and mild flavour produced by traditional spontaneous solid-state fermentation. The flavour of this liquor has been found to vary in the different periods of annual production. To explore the factors affecting flavour, the microbiota of the surrounding environment, starter and fermentation process in different periods were investigated. Results showed that the ester content and acidity of light-flavour Baijiu were significantly lower when annual production was resumed after a summer break. HCA plot of volatile flavour profile and bacterial PCoA results indicated that the differences occurred at later stages, mainly due to different structures of Lactobacillus. Correlation analysis by O2PLS indicated that Lactobacillus positively correlated with esters. Species-level analysis showed that the lack of L. acetotolerans on the surface of the jar might cause a lag in fermentation and lower ester content. Thereafter, L. acetotolerans was revived during fermentation and enriched on the surface of the jar, which promoted ester formation. As important sources of L. acetotolerans, the air and fermentation jars played a critical role during fermentation. Therefore, this systematic study on environmental microbial ecology is valuable for quality control and to explore environmental microbiota functions during spontaneous fermentation.
Structural transformation of layered double hydroxides: an in situ TEM analysis
Authors: Hobbs Christopher , Jaskaniec Sonia , McCarthy Eoin K. , Downing Clive , Opelt Konrad , Güth Konrad , Shmeliov Aleksey , Mourad Maurice C. D. , Mandel Karl , Nicolosi Valeria 
Published: February 2018

AbstractA comprehensive nanoscale understanding of layered double hydroxide (LDH) thermal evolution is critical for their current and future applications as catalysts, flame retardants and oxygen evolution performers. In this report, we applied in situ transmission electron microscopy (TEM) to extensively characterise the thermal progressions of nickel-iron containing (Ni-Fe) LDH nanomaterials. The combinative approach of TEM and selected area electron diffraction (SAED) yielded both a morphological and crystallographic understanding of such processes. As the Ni-Fe LDH nanomaterials are heated in situ, an amorphization occurred at 250 °C, followed by a transition to a heterogeneous structure of NiO particles embedded throughout a NiFe2O4 matrix at 850 °C, confirmed by high-resolution TEM and scanning TEM. Further electron microscopy characterisation methodologies of energy-filtered TEM were utilised to directly observe these mechanistic behaviours in real time, showing an evolution and nucleation to an array of spherical NiO nanoparticles on the platelet surfaces. The versatility of this characterisation approach was verified by the analogous behaviours of Ni-Fe LDH materials heated ex situ as well as parallel in situ TEM and SAED comparisons to that of an akin magnesium-aluminium containing (Mg-Al) LDH structure. The in situ TEM work hereby discussed allows for a state-of-the-art understanding of the Ni-Fe material thermal evolution. This is an important first, which reveals pivotal information, especially when considering LDH applications as catalysts and flame retardants.
Large-amplitude late-time radio variability in GRB 151027B
Authors: Greiner J. , Bolmer J. , Wieringa M. , van der Horst A. J. , Petry D. , Schulze S. , Knust F. , de Bruyn G. , Krühler T. , Wiseman P. , Klose S. , Delvaux C. , Graham J. F. , Kann D. A. , Moin A. , Nicuesa-Guelbenzu A. , Schady P. , Schmidl S. , Schweyer T. , Tanga M. , Tingay S. , van Eerten H. , Varela K. 
Published: February 2018

Context. Deriving physical parameters from gamma-ray burst (GRB) afterglow observations remains a challenge, even 20 years after the discovery of afterglows. The main reason for the lack of progress is that the peak of the synchrotron emission is in the sub-mm range, thus requiring radio observations in conjunction with X-ray/optical/near-infrared data in order to measure the corresponding spectral slopes and consequently remove the ambiguity with respect to slow vs. fast cooling and the ordering of the characteristic frequencies.
Aims. We have embarked on a multifrequency, multi-epoch observing campaign to obtain sufficient data for a given GRB that allows us to test the simplest version of the fireball afterglow model.
Methods. We observed GRB 151027B, the 1000th Swift-detected GRB, with GROND in the optical–near-IR, ALMA in the sub-millimeter, ATCA in the radio band; we combined this with public Swift/XRT X-ray data.
Results. While some observations at crucial times only return upper limits or surprising features, the fireball model is narrowly constrained by our data set, and allows us to draw a consistent picture with a fully determined parameter set. Surprisingly, we find rapid, large-amplitude flux density variations in the radio band which are extreme not only for GRBs, but generally for any radio source. We interpret them as scintillation effects, though their extreme nature requires the scattering screen to be at a much smaller distance than usually assumed, multiple screens, or a combination of the two.
Conclusions. The data are consistent with the simplest fireball scenario for a blast wave moving into a constant-density medium, and slow-cooling electrons. All fireball parameters are constrained at or better than a factor of 2, except for the density and the fraction of the energy in the magnetic field which has a factor of 10 uncertainty in both directions.
Intriguing X-ray and optical variations of the γ Cassiopeiae analog HD 45314
Authors: Rauw G. , Nazé Y. , Smith M. A. , Miroshnichenko A. S. , Guarro Fló J. , Campos F. , Prendergast P. , Danford S. , González-Pérez J. N. , Hempelmann A. , Mittag M. , Schmitt J. H. M. M. , Schröder K.-P. , Zharikov S. V. 
Published: February 2018

Context. A growing number of Be and Oe stars, named the γ Cas stars, are known for their unusually hard and intense X-ray emission. This emission could either trace accretion by a compact companion or magnetic interaction between the star and its decretion disk.
Aims. To test these scenarios, we carried out a detailed optical monitoring of HD 45314, the hottest member of the class of γ Cas stars, along with dedicated X-ray observations on specific dates.
Methods. High-resolution optical spectra were taken to monitor the emission lines formed in the disk, while X-ray spectroscopy was obtained at epochs when the optical spectrum of the Oe star was displaying peculiar properties.
Results. Over the last four years, HD 45314 has entered a phase of spectacular variations. The optical emission lines have undergone important morphology and intensity changes including transitions between single- and multiple-peaked emission lines as well as shell events, and phases of (partial) disk dissipation. Photometric variations are found to be anti-correlated with the equivalent width of the Hα emission. Whilst the star preserved its hard and bright X-ray emission during the shell phase, the X-ray spectrum during the phase of (partial) disk dissipation was significantly softer and weaker.
Conclusions. The observed behaviour of HD 45314 suggests a direct association between the level of X-ray emission and the amount of material simultaneously present in the Oe disk as expected in the magnetic star-disk interaction scenario.
Validation and Verification of Semi-Empirical Methods for Evaluating Liquefaction Using Finite Element Method
Authors: Touijrate Soukaina , Baba Khadija , Ahatri Mohamed , Bahi Lahcen 
Published: February 2018

Liquefaction is a hazardous and temporary phenomenon by which a soil saturated with water loses some or all of its resistance. The undrained conditions and a cyclic load increase the pores water pressure inside the soil and therefore a reduction of the effective stress.Nowadays many semi-empirical methods are used to introduce a proposition to evaluate the liquefaction's potential using the in-situ test results. The objective of this paper is to study their ability to correctly predict the liquefaction potential by modelling our case using finite element methods.The study is based on the data of Cone Penetration Tests experimental results of the Casablanca-Tangier High-Speed Line exactly between PK 116 + 450 and PK 116 + 950 and near of Moulay-Bousselham city. It belongs to the Drader-Soueir basin region which is located in the North-West of Morocco.This region had a specific soil’s formation, the first 50 meters are characterised by the existence of sand layers alternating with layers of clay. These formations are very loose and saturated which suggests the possibility of soil liquefaction.We present and discuss the results of applying the Olsen method [1], the Juang method [2] and the Robertson method [3], in the evaluation of liquefaction susceptibility.Apart from the previous empirical analysis to evaluate the liquefaction potential, numerical modelling is performed in this study.
Anticoagulant Preferences and Concerns among Venous Thromboembolism Patients
Authors: Lutsey Pamela , Horvath Keith , Fullam Lisa , Moll Stephan , Rooney Mary , Cushman Mary , Zakai Neil 
Published: February 2018

Background Warfarin and direct oral anticoagulants (DOACs) are used for the initial treatment and secondary prevention of venous thromboembolism (VTE), and have similar efficacy. Patient concerns and preferences are important considerations when selecting an anticoagulant, yet these are not well studied.
Methods VTE patients (n = 519) were surveyed from online sources (clotconnect.org, stoptheclot.org and National Blood Clot Alliance Facebook followers [n = 495]) and a haematology clinic in Vermont (n = 24).
Results Patients were 83% females and on average (±standard deviation [SD]) 45.7 ± 13.1 years; 65% self-reported warfarin as their initial VTE treatment and 35% a DOAC. Proportions reporting being extremely concerned about the following outcomes were as follows: recurrent VTE 33%, major bleeding 21%, moderate bleeding 16% and all-cause death 29%. When asked about oral anticoagulant characteristics, patients strongly preferred anticoagulants that are reversible (53%), and for which blood drug levels can be monitored (30%). Lower proportions agreed with statements that regular blood testing is inconvenient (18%), that they are comfortable using the newest drug versus an established drug (15%) and that it is difficult to change their diet to accommodate their anticoagulant (17%). In multivariable-adjusted models, patients tended to have had as their initial treatment, and to currently be taking, the oral anticoagulant option they personally preferred.
Discussion Patients held the greatest concern for recurrent VTE and mortality, regardless of which treatment they were prescribed. Potential weaknesses of warfarin (e.g., dietary restrictions, regular monitoring) were generally not considered onerous, while warfarin's advantages (e.g., ability to monitor) were viewed favourably.