bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetic CRAC uncovers a role for Nab3 in determining gene expression profiles during stress
Authors: van Nues Rob , Schweikert Gabriele , de Leau Erica , Selega Alina , Langford Andrew , Franklin Ryan , Iosub Ira , Wadsworth Peter , Sanguinetti Guido , Granneman Sander 
Published: April 2017

AbstractRNA-binding proteins play a key role in shaping gene expression profiles during stress, however, little is known about the dynamic nature of these interactions and how this influences the kinetics of gene expression. To address this, we developed kinetic cross-linking and analysis of cDNAs (χCRAC), an ultraviolet cross-linking method that enabled us to quantitatively measure the dynamics of protein–RNA interactions in vivo on a minute time-scale. Here, using χCRAC we measure the global RNA-binding dynamics of the yeast transcription termination factor Nab3 in response to glucose starvation. These measurements reveal rapid changes in protein–RNA interactions within 1 min following stress imposition. Changes in Nab3 binding are largely independent of alterations in transcription rate during the early stages of stress response, indicating orthogonal transcriptional control mechanisms. We also uncover a function for Nab3 in dampening expression of stress-responsive genes. χCRAC has the potential to greatly enhance our understanding of in vivo dynamics of protein–RNA interactions.
Precise treatment of aortic aneurysm by three-dimensional printing and simulation before endovascular intervention
Authors: Yuan Ding , Luo Han , Yang Hongliu , Huang Bin , Zhu Jingqiang , Zhao Jichun 
Published: April 2017

AbstractIn this study, three-dimensional printing (3Dp) models and simulation surgeries (SSs) were applied in two challenging aortic cases. The first was an abdominal aortic aneurysm with a complex neck, and the second was a thoracic aortic dissection aneurysm (TADA) with an angled arch. In order to avoid unpredictable obstacles and difficulties, we made optimal surgical plans by using 3D models and virtual simulations. Based on preoperative evaluation system, the surgical plans seemed more reasonable and time-saving.
Maternal plasma miRNAs as biomarkers during mid-pregnancy to predict later spontaneous preterm birth: a pilot study
Authors: Gray Clint , McCowan Lesley M. , Patel Rachna , Taylor Rennae S. , Vickers Mark H. 
Published: April 2017

AbstractMore than 10% of babies are born too early resulting in over 15 million preterm births and more than one million new-born deaths globally. Although women with a previous spontaneous preterm birth (SPTB) are considered at high risk for recurrence, the majority occur in women without prior history. Prediction of SPTB risk allows for improved care and potential for targeting novel and existing therapeutics to prevent SPTB, which may result in improved outcomes for infant and mother. In this pilot study, a miRNA array was used to analyse plasma from healthy women in their first pregnancy at 20 weeks of gestation who then went on to deliver either at term or experience SPTB at 28–32 weeks. We identified specific miRNA expression profiles that differentiated between those mothers who delivered at term or delivered following SPTB. miR302b, miR1253 and a clustering of miR548 miRNAs were underexpressed in SPTB cases compared to term controls. Conversely, miR223 was elevated in mothers that later experienced a SPTB. The circulating miRNAs identified in the present study may therefore be attractive candidates as non-invasive biomarkers for the early prediction of SPTB. Further larger studies are now warranted to investigate the potential clinical utility of these markers.
Prediction of Bacterial Contamination Outbursts in Water Wells through Sparse Coding
Authors: Frolich Levi , Vaizel-Ohayon Dalit , Fishbain Barak 
Published: April 2017

AbstractMaintaining water quality is critical for any water distribution company. One of the major concerns in water quality assurance, is bacterial contamination in water sources. To date, bacteria growth models cannot predict with sufficient accuracy when a bacteria outburst will occur in a water well. This is partly due to the natural sparsity of the bacteria count time series, which hinders the observation of deviations from normal behavior. This precludes the application of mathematical models nor statistical quality control methods for the detection of high bacteria counts before contamination occurs. As a result, currently a future outbreak prediction is a subjective process. This research developed a new cost-effective method that capitalizes on the sparsity of the bacteria count time series. The presented method first transforms the data into its spectral representation, where it is no longer sparse. Capitalizing on the spectral representation the dimensions of the problem are reduced. Machine learning methods are then applied on the reduced representations for predicting bacteria outbursts from the bacterial counts history of a well. The results show that these tools can be implemented by the water quality engineering community to create objective, more robust, quality control techniques to ensure safer water distribution.
Effect of surface state hybridization on current-induced spin-orbit torque in thin topological insulator films
Authors: Ho Cong Son , Wang Yi , Siu Zhou Bin , Tan Seng Ghee , Jalil Mansoor B. A. , Yang Hyunsoo 
Published: April 2017

AbstractWe investigate the thickness optimization for maximum current-induced spin-orbit torque (SOT) generated by topological surface states (TSS’s) in a bilayer system comprising of a ferromagnetic layer coupled to a thin topological insulator (TI) film. We show that by reducing the TI thickness, two competing effects on the SOT are induced: (i) the torque strength is stronger as the bulk contribution is decreased; (ii) on the other hand, the torque strength becomes suppressed due to increasing hybridization of the surface states. The latter is attributed to the opposite helicities of the coupled TSS’s. We theoretically model the interplay of these two effects and derive the optimal TI thickness to maximize the spin torque, which is estimated to be about 3–5 nm for typical Bi2Se3 films.
Rational development of Stafib-2: a selective, nanomolar inhibitor of the transcription factor STAT5b
Authors: Elumalai Nagarajan , Berg Angela , Rubner Stefan , Blechschmidt Linda , Song Chen , Natarajan Kalaiselvi , Matysik Jörg , Berg Thorsten 
Published: April 2017

AbstractThe transcription factor STAT5b is a target for tumour therapy. We recently reported catechol bisphosphate and derivatives such as Stafib-1 as the first selective inhibitors of the STAT5b SH2 domain. Here, we demonstrate STAT5b binding of catechol bisphosphate by solid-state nuclear magnetic resonance, and report on rational optimization of Stafib-1 (Ki = 44 nM) to Stafib-2 (Ki = 9 nM). The binding site of Stafib-2 was validated using combined isothermal titration calorimetry (ITC) and protein point mutant analysis, representing the first time that functional comparison of wild-type versus mutant protein by ITC has been used to characterize the binding site of a small-molecule ligand of a STAT protein with amino acid resolution. The prodrug Pomstafib-2 selectively inhibits tyrosine phosphorylation of STAT5b in human leukaemia cells and induces apoptosis in a STAT5-dependent manner. We propose Pomstafib-2, which currently represents the most active, selective inhibitor of STAT5b activation available, as a chemical tool for addressing the fundamental question of which roles the different STAT5 proteins play in various cell processes.
Nano silica diaphragm in-fiber cavity for gas pressure measurement
Authors: Liu Shen , Wang Yiping , Liao Changrui , Wang Ying , He Jun , Fu Cailing , Yang Kaiming , Bai Zhiyong , Zhang Feng 
Published: April 2017

AbstractWe demonstrate an ultrahigh-sensitivity gas pressure sensor based on the Fabry-Perot interferometer employing a fiber-tip diaphragm-sealed cavity. The cavity is comprised of a silica capillary and ultrathin silica diaphragm with a thickness of 170 nm, with represents the thinnest silica diaphragm fabricated thus far by an electrical arc discharge technique. The resulting Fabry-Perot interferometer-based gas pressure sensor demonstrates a gas pressure sensitivity of about 12.22 nm/kPa, which is more than two orders of magnitude greater than that of a similarly configured fiber-tip air bubble sensor. Moreover, our gas pressure sensor has a low temperature cross-sensitivity of about 106 Pa/°C, and the sensor functions well up to a temperature of about 1000 °C. As such, the sensor can potentially be employed in high-temperature environments.
Maternal lipids and leptin concentrations are associated with large-for-gestational-age births: a prospective cohort study
Authors: Farias Dayana Rodrigues , Poston Lucilla , Franco-Sena Ana Beatriz , Moura da Silva Antônio Augusto , Pinto Thatiana , de Oliveira Lívia Costa , Kac Gilberto 
Published: April 2017

AbstractThe change in maternal lipid, leptin and adiponectin concentrations during pregnancy and infant birth weight (BW) is still poorly characterized. Thus, the aim of the study was to evaluate the association of maternal lipids, leptin and adiponectin throughout pregnancy with large-for-gestational-age (LGA) births and BW z-score. A prospective cohort of 199 mothers was followed during pregnancy in Rio de Janeiro, Brazil. The statistical analyses comprised multiple logistic and linear regression. Women delivered 36 LGA and 11 small-for-gestational-age newborns. HDL-c rate of change throughout pregnancy was negatively associated with BW z-score (β = −1.99; p = 0.003) and the delivery of a LGA newborn (OR = 0.02; p = 0.043). Pregnancy baseline concentration of log leptin was positively associated (OR = 3.92; p = 0.025) with LGA births. LDL-c rate of change throughout pregnancy was positively associated with BW z-score (β = 0.31; p = 0.004). Log triglycerides and log adiponectin were not significantly associated with BW z-score or LGA birth. In conclusion, a higher log leptin pregnancy baseline concentration and a lower HDL-c rate of change during pregnancy were associated with higher odds of having a LGA newborn. These maternal biomarkers are important to foetal growth and could be used in prenatal care as an additional strategy to screen women at risk of inadequate BW.
Investigation of spin-orbit torque using current-induced magnetization curve
Authors: Koyama Tomohiro , Guan Yicheng , Chiba Daichi 
Published: April 2017

AbstractManipulation of magnetization using current-induced torque is crucial for magnetic recording devices. Recently, the spin-orbit torque (SOT) that emerges in a ferromagnetic thin film on a heavy metal is focused as a new scheme for magnetization switching in perpendicularly magnetized systems. Since the SOT provides a perpendicular effective field to the system, the formation of a magnetic multiple domain state because of Joule heating is supressed in the magnetization reversal process. This means that high reliable switching is possible using the SOT. Here, by utilizing the SOT induced domain stability, we show that an electrical current directly injected to a perpendicularly magnetized Pt/Co/Pd system can magnetize itself, that is, current-induced magnetization process from multi to single domain state. A quantitative determination of the SOT is performed using the current-induced magnetization curve. The present results are of great importance as another approach to evaluate the SOT effect, as well as a demonstration of domain state switching caused by the SOT.
Tropicalization strengthens consumer pressure on habitat-forming seaweeds
Authors: Zarco-Perello Salvador , Wernberg Thomas , Langlois Tim J. , Vanderklift Mathew A. 
Published: April 2017

AbstractOcean warming is driving species poleward, causing a ‘tropicalization’ of temperate ecosystems around the world. Increasing abundances of tropical herbivores on temperate reefs could accelerate declines in habitat-forming seaweeds with devastating consequences for these important marine ecosystems. Here we document an expansion of rabbitfish (Siganus fuscescens), a tropical herbivore, on temperate reefs in Western Australia following a marine heatwave and demonstrate their impact on local kelp forests (Ecklonia radiata). Before the heatwave there were no rabbitfish and low rates of kelp herbivory but after the heatwave rabbitfish were common at most reefs and consumption of kelp was high. Herbivory increased 30-fold and kelp abundance decreased by 70% at reefs where rabbitfish had established. In contrast, where rabbitfish were absent, kelp abundance and herbivory did not change. Video-analysis confirmed that rabbitfish were the main consumers of kelp, followed by silver drummers (Kyphosus sydneyanus), a temperate herbivore. These results represent a likely indirect effect of the heatwave beyond its acute impacts, and they provide evidence that range-shifting tropical herbivores can contribute to declines in habitat-forming seaweeds within a few years of their establishment.
Global evolutionary history and spatio-temporal dynamics of dengue virus type 2
Authors: Wei Kaifa , Li Yuhan 
Published: April 2017

AbstractDENV-2 spread throughout the tropical and subtropical regions globally, which is implicated in deadly outbreaks of DHF and DSS. Since dengue cases have grown dramatically in recent years, about half of the world’s population is now at risk. Our timescale analysis indicated that the most recent common ancestor existed about 100 years ago. The rate of nucleotide substitution was estimated to be 8.94 × 10−4subs/site/year. Selection pressure analysis showed that two sites 160 and 403 were under positive selection, while E gene is mainly shaped by stronger purifying selection. BSP analysis showed that estimating effective population size from samples of sequences has undergone three obvious increases, additionally, Caribbean and Puerto Rico maintained higher levels of genetic diversity relative to other 6 representative geographical populations using GMRF method. The phylogeographic analysis indicated that two major transmission routes are from South America to Caribbean and East&SouthAsia to Puerto Rico. The trunk reconstruction confirmed that the viral evolution spanned 50 years occurred primarily in Southeast Asia and East&South Asia. In addition, phylogeographic association-trait analysis indicated that the viral phenotypes are highly correlated with phylogeny in Nicaragua and Puerto Rico (P < 0.05).
Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling
Authors: Boers Stefan A. , Hays John P. , Jansen Ruud 
Published: April 2017

AbstractIn the last decade, many researchers have embraced 16S rRNA gene sequencing techniques, which has led to a wealth of publications and documented differences in the composition of microbial communities derived from many different ecosystems. However, comparison between different microbiota studies is currently very difficult due to the lack of a standardized 16S rRNA gene sequencing protocol. Here we report on a novel approach employing micelle PCR (micPCR) in combination with an internal calibrator that allows for standardization of microbiota profiles via their absolute abundances. The addition of an internal calibrator allows the researcher to express the resulting operational taxonomic units (OTUs) as a measure of 16S rRNA gene copies by correcting the number of sequences of each individual OTU in a sample for efficiency differences in the NGS process. Additionally, accurate quantification of OTUs obtained from negative extraction control samples allows for the subtraction of contaminating bacterial DNA derived from the laboratory environment or chemicals/reagents used. Using equimolar synthetic microbial community samples and low biomass clinical samples, we demonstrate that the calibrated micPCR/NGS methodology possess a much higher precision and a lower limit of detection compared with traditional PCR/NGS, resulting in more accurate microbiota profiles suitable for multi-study comparison.
Silk-fibronectin protein alloy fibres support cell adhesion and viability as a high strength, matrix fibre analogue
Authors: Jacobsen Matthew M. , Li David , Gyune Rim Nae , Backman Daniel , Smith Michael L. , Wong Joyce Y. 
Published: April 2017

AbstractSilk is a natural polymer with broad utility in biomedical applications because it exhibits general biocompatibility and high tensile material properties. While mechanical integrity is important for most biomaterial applications, proper function and integration also requires biomaterial incorporation into complex surrounding tissues for many physiologically relevant processes such as wound healing. In this study, we spin silk fibroin into a protein alloy fibre with whole fibronectin using wet spinning approaches in order to synergize their respective strength and cell interaction capabilities. Results demonstrate that silk fibroin alone is a poor adhesive surface for fibroblasts, endothelial cells, and vascular smooth muscle cells in the absence of serum. However, significantly improved cell attachment is observed to silk-fibronectin alloy fibres without serum present while not compromising the fibres’ mechanical integrity. Additionally, cell viability is improved up to six fold on alloy fibres when serum is present while migration and spreading generally increase as well. These findings demonstrate the utility of composite protein alloys as inexpensive and effective means to create durable, biologically active biomaterials.
Off-target effects and clinical outcome in metastatic colorectal cancer patients receiving regorafenib: The TRIBUTE analysis
Authors: Giampieri Riccardo , Prete Michela del , Prochilo Tiziana , Puzzoni Marco , Pusceddu Valeria , Pani Fabiana , Maccaroni Elena , Mascia Roberta , Baleani Maria Giuditta , Meletani Tania , Berardi Rossana , Lanzillo Anna Maria , Mariotti Stefano , Zaniboni Alberto , Cascinu Stefano , Scartozzi Mario 
Published: April 2017

AbstractRegorafenib is an orally administered multikinase inhibitor indicated for the treatment of heavily pretreated metastatic colorectal cancer patients with good performance status, albeit less than 50% treated patients achieve disease stabilisation or better at the first radiological evaluation. In addition to that a particularly broad spectrum of toxicities (experienced as G3 or more NCI CTCAE graded by 50% of patients treated) have led to reconsider its widespread use in the majority of patients. We retrospectively collected data about the magnitude of off-target effects experienced during the first 8-weeks of regorafenib monotherapy and analysed their correlation with overall survival, progression free survival and disease control rate. Our findings suggest that skin rash (Exp (B): 0.52, p = 0.0133) or hypothyroidism (Exp (B): 0.11, p = 0.0349) were significantly correlated with improved overall survival at multivariate regression analysis. It was also demonstrated a statistically significant role of diarrhea as predictor of improved survival but its independent prognostic role was lost at multivariate analysis (Exp (B): 0.63, p = 0.162). This is the first analysis showing a potential correlation between the onset of these forms of side effects and regorafenib efficacy, however sample size limitations and the retrospective nature of our analysis prevent us from drawing definitive conclusions.
Spin-resolved band structure of heterojunction Bi-bilayer/3D topological insulator in the quantum dimension regime in annealed Bi2Te2.4Se0.6
Authors: Klimovskikh I. I. , Sostina D. , Petukhov A. , Rybkin A. G. , Eremeev S. V. , Chulkov E. V. , Tereshchenko O. E. , Kokh K. A. , Shikin A. M. 
Published: April 2017

AbstractTwo- and three-dimensional topological insulators are the key materials for the future nanoelectronic and spintronic devices and quantum computers. By means of angle- and spin-resolved photoemission spectroscopy we study the electronic and spin structure of the Bi-bilayer/3D topological insulator in quantum tunneling regime formed under the short annealing of Bi2Te2.4Se0.6. Owing to the temperature-induced restructuring of the topological insulator’s surface quintuple layers, the hole-like spin-split Bi-bilayer bands and the parabolic electronic-like state are observed instead of the Dirac cone. Scanning Tunneling Microscopy and X-ray Photoemission Spectroscopy measurements reveal the appearance of the Bi2 terraces at the surface under the annealing. The experimental results are supported by density functional theory calculations, predicting the spin-polarized Bi-bilayer bands interacting with the quintuple-layers-derived states. Such an easily formed heterostructure promises exciting applications in spin transport devices and low-energy electronics.
Degradation potentials of dissolved organic carbon (DOC) from thawed permafrost peat
Authors: Panneer Selvam Balathandayuthabani , Lapierre Jean-François , Guillemette Francois , Voigt Carolina , Lamprecht Richard E. , Biasi Christina , Christensen Torben R. , Martikainen Pertti J. , Berggren Martin 
Published: April 2017

AbstractGlobal warming can substantially affect the export of dissolved organic carbon (DOC) from peat-permafrost to aquatic systems. The direct degradability of such peat-derived DOC, however, is poorly constrained because previous permafrost thaw studies have mainly addressed mineral soil catchments or DOC pools that have already been processed in surface waters. We incubated peat cores from a palsa mire to compare an active layer and an experimentally thawed permafrost layer with regard to DOC composition and degradation potentials of pore water DOC. Our results show that DOC from the thawed permafrost layer had high initial degradation potentials compared with DOC from the active layer. In fact, the DOC that showed the highest bio- and photo-degradability, respectively, originated in the thawed permafrost layer. Our study sheds new light on the DOC composition of peat-permafrost directly upon thaw and suggests that past estimates of carbon-dioxide emissions from thawed peat permafrost may be biased as they have overlooked the initial mineralization potential of the exported DOC.
Failure criterion of silver nanowire electrodes on a polymer substrate for highly flexible devices
Authors: Kim Donggyun , Kim Sung-Hoon , Kim Jong Hak , Lee Jae-Chul , Ahn Jae-Pyoung , Kim Sang Woo 
Published: April 2017

AbstractNanomechanical characteristics of standalone silver nanowires (Ag NWs) are a key issue for providing a failure criterion of advanced flexible electrodes that are trending towards smaller radius of curvatures (ROCs). Through in-situ tensile and buckling tests of pentagonal Ag NWs, we demonstrated that the intrinsic fracture strain provides a significant criterion to predict the mechanical and electrical failure of Ag NW electrodes under various strain modes, because the decrease in fracture strain limits figure of merit of flexible devices. The Ag NW electrodes on a polymer substrate exhibited a strain-dependent electrical failure owing to the unique deformation characteristics with a size-dependent brittle-to-ductile transition of the five-fold twinned Ag NWs. All the Ag NWs greater than approximately 40 nm in diameter exhibited brittle fracture with a size-independent stress-strain response under tensile and buckling modes, which leads to the electrical failure of flexible electrodes at the almost same threshold ROC. Meanwhile, the higher ductility of Ag NWs less than 40 nm in diameter resulted in much smaller threshold ROCs of the electrodes due to the highly extended fracture strains, which can afford a high degree of freedom for highly flexible devices.