bluuebunny/crossref_metadata_2025_split huggingface dataset:
The formation mechanism of Li4Ti5O12−y solid solutions prepared by carbothermal reduction and the effect of Ti3+ on electrochemical performance
Authors: Yang Guijun , Park Soo-Jin 
Published: March 2019

AbstractSamples of Li4Ti5O12−y solid solutions are synthesized by one-step solid-state carbothermal reduction reaction using Li2CO3, anatase, and carbon black under a nitrogen atmosphere. The underlying formation mechanism that leads to Li4Ti5O12−y solid solutions is proposed. The formation mechanism of the Li4Ti5O12−y solid solution is investigated by in situ variable temperature X-Ray diffraction (VT-XRD) and thermogravimetric analysis/differential scanning calorimetry (TGA-DSC). First, some Ti4+ centers are converted to Ti3+ (TiO2-TiO2−x) because of the presence of carbon black. Secondly, Li2CO3 reacts with TiO2−x (anatase) to form Li2TiO3. Thirdly, Li2TiO3 reacts with TiO2−x to form the Li4Ti5O12−y solid solution, while anatase starts to transform into rutile at the same time. Rutile reacts with Li2TiO3 to form Li4Ti5O12−y at higher temperatures. The presence of Ti3+ not only improves the electrical conductivity but also improves the ionic conductivity. As a result, the as-prepared material exhibits good rate capability and cycling stability with 99.3% capacity retention after 200 cycles.
Targeted Single Primer Enrichment Sequencing with Single End Duplex-UMI
Authors: Peng Quan , Xu Chang , Kim Daniel , Lewis Marcus , DiCarlo John , Wang Yexun 
Published: March 2019

AbstractFor specific detection of somatic variants at very low levels, artifacts from the NGS workflow have to be eliminated. Various approaches using unique molecular identifiers (UMI) to analytically remove NGS artifacts have been described. Among them, Duplex-seq was shown to be highly effective, by leveraging the sequence complementarity of two DNA strands. However, all of the published Duplex-seq implementations so far required pair-end sequencing and in the case of combining duplex sequencing with target enrichment, lengthy hybridization enrichment was required. We developed a simple protocol, which enabled the retrieval of duplex UMI in multiplex PCR based enrichment and sequencing. Using this protocol and reference materials, we demonstrated the accurate detection of known SNVs at 0.1–0.2% allele fractions, aided by duplex UMI. We also observed that low level base substitution artifacts could be introduced when preparing in vitro DNA reference materials, which could limit their utility as a benchmarking tool for variant detection at very low levels. Our new targeted sequencing method offers the benefit of using duplex UMI to remove NGS artifacts in a much more simplified workflow than existing targeted duplex sequencing methods.
Urine-NMR metabolomics for screening of advanced colorectal adenoma and early stage colorectal cancer
Authors: Kim Eun Ran , Kwon Hyuk Nam , Nam Hoonsik , Kim Jae J. , Park Sunghyouk , Kim Young-Ho 
Published: March 2019

AbstractAlthough colorectal cancer (CRC) is considered one of the most preventable cancers, no non-invasive, accurate diagnostic tool to screen CRC exists. We explored the potential of urine nuclear magnetic resonance (NMR) metabolomics as a diagnostic tool for early detection of CRC, focusing on advanced adenoma and stage 0 CRC. Urine metabolomics profiles from patients with colorectal neoplasia (CRN; 36 advanced adenomas and 56 CRCs at various stages, n = 92) and healthy controls (normal, n = 156) were analyzed by NMR spectroscopy. Healthy and CRN groups were statistically discriminated using orthogonal projections to latent structure discriminant analysis (OPLS-DA). The class prediction model was validated by three-fold cross-validation. The advanced adenoma and stage 0 CRC were grouped together as pre-invasive CRN. The OPLS-DA score plot showed statistically significant discrimination between pre-invasive CRN as well as advanced CRC and healthy controls with a Q2 value of 0.746. In the prediction validation study, the sensitivity and specificity for diagnosing pre-invasive CRN were 96.2% and 95%, respectively. The grades predicted by the OPLS-DA model showed that the areas under the curve were 0.823 for taurine, 0.783 for alanine, and 0.842 for 3-aminoisobutyrate. In multiple receiver operating characteristics curve analyses, taurine, alanine, and 3-aminoisobutyrate were good discriminators for CRC patients. NMR-based urine metabolomics profiles significantly and accurately discriminate patients with pre-invasive CRN as well as advanced CRC from healthy individuals. Urine-NMR metabolomics has potential as a screening tool for accurate diagnosis of pre-invasive CRN.
Near real-time enumeration of live and dead bacteria using a fibre-based spectroscopic device
Authors: Ou Fang , McGoverin Cushla , Swift Simon , Vanholsbeeck Frédérique 
Published: March 2019

AbstractA rapid, cost-effective and easy method that allows on-site determination of the concentration of live and dead bacterial cells using a fibre-based spectroscopic device (the optrode system) is proposed and demonstrated. Identification of live and dead bacteria was achieved by using the commercially available dyes SYTO 9 and propidium iodide, and fluorescence spectra were measured by the optrode. Three spectral processing methods were evaluated for their effectiveness in predicting the original bacterial concentration in the samples: principal components regression (PCR), partial least squares regression (PLSR) and support vector regression (SVR). Without any sample pre-concentration, PCR achieved the most reliable results. It was able to quantify live bacteria from 108 down to 106.2 bacteria/mL and showed the potential to detect as low as 105.7 bacteria/mL. Meanwhile, enumeration of dead bacteria using PCR was achieved between 108 and 107 bacteria/mL. The general procedures described in this article can be applied or modified for the enumeration of bacteria within populations stained with fluorescent dyes. The optrode is a promising device for the enumeration of live and dead bacterial populations particularly where rapid, on-site measurement and analysis is required.
Diversity of incubation rhythms in a facultatively uniparental shorebird – the Northern Lapwing
Authors: Sládeček Martin , Vozabulová Eva , Šálek Miroslav E. , Bulla Martin 
Published: March 2019

AbstractIn birds, incubation by both parents is a common form of care for eggs. Although the involvement of the two parents may vary dramatically between and within pairs, as well as over the course of the day and breeding season, detailed descriptions of this variation are rare, especially in species with variable male contributions to care. Here, we continuously video-monitored 113 nests of Northern LapwingsVanellus vanellusto reveal the diversity of incubation rhythms and parental involvement, as well as their daily and seasonal variation. We found great between-nest variation in the overall nest attendance (68–94%; median = 87%) and in how much males attended their nests (0–37%; median = 13%). Notably, the less the males attended their nests, the lower was the overall nest attendance, even though females partially compensated for the males’ decrease. Also, despite seasonal environmental trends (e.g. increasing temperature), incubation rhythms changed little over the season and 27-day incubation period. However, as nights shortened with the progressing breeding season, the longest night incubation bout of females shortened too. Importantly, within the 24h-day, nest attendance was highest, incubation bouts longest, exchange gaps shortest and male involvement lowest during the night. Moreover, just after sunrise and before sunset males attended the nest the most. To conclude, we confirm substantial between nest differences in Lapwing male nest attendance, reveal how such differences relates to variation in incubation rhythms, and describe strong circadian incubation rhythms modulated by sunrise and sunset.
Mechanical Response of He-Implanted Amorphous SiOC/Crystalline Fe Nanolaminates
Authors: Zare A. , Su Q. , Gigax J. , Harriman T. A. , Nastasi M. , Shao L. , Lucca D. A. 
Published: March 2019

AbstractThis study investigates the microstructural evolution and mechanical response of sputter-deposited amorphous silicon oxycarbide (SiOC)/crystalline Fe nanolaminates, a single layer SiOC film, and a single layer Fe film subjected to ion implantation at room temperature to obtain a maximum He concentration of 5 at. %. X-ray diffraction and transmission electron microscopy indicated no evidence of implantation-induced phase transformation or layer breakdown in the nanolaminates. Implantation resulted in the formation of He bubbles and an increase in the average size of the Fe grains in the individual Fe layers of the nanolaminates and the single layer Fe film, but the bubble density and grain size were found to be smaller in the former. By reducing the thicknesses of individual layers in the nanolaminates, bubble density and grain size were further decreased. No He bubbles were observed in the SiOC layers of the nanolaminates and the single layer SiOC film. Nanoindentation and scanning probe microscopy revealed an increase in the hardness of both single layer SiOC and Fe films after implantation. For the nanolaminates, changes in hardness were found to depend on the thicknesses of the individual layers, where reducing the layer thickness to 14 nm resulted in mitigation of implantation-induced hardening.
Temporal evolution of quantitative EEG within 3 days of birth in early preterm infants
Authors: O’Toole John M. , Pavlidis Elena , Korotchikova Irina , Boylan Geraldine B. , Stevenson Nathan J. 
Published: March 2019

AbstractFor the premature newborn, little is known about changes in brain activity during transition to extra-uterine life. We aim to quantify these changes in relation to the longer-term maturation of the developing brain. We analysed EEG for up to 72 hours after birth from 28 infants born <32 weeks of gestation. These infants had favourable neurodevelopment at 2 years of age and were without significant neurological compromise at time of EEG monitoring. Quantitative EEG was generated using features representing EEG power, discontinuity, spectral distribution, and inter-hemispheric connectivity. We found rapid changes in cortical activity over the 3 days distinct from slower changes associated with gestational age: for many features, evolution over 1 day after birth is equivalent to approximately 1 to 2.5 weeks of maturation. Considerable changes in the EEG immediately after birth implies that postnatal adaption significantly influences cerebral activity for early preterm infants. Postnatal age, in addition to gestational age, should be considered when analysing preterm EEG within the first few days after birth.
Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis
Authors: Blair Emily J. , Bonnot Titouan , Hummel Maureen , Hay Erika , Marzolino Jill M. , Quijada Ivan A. , Nagel Dawn H. 
Published: March 2019

AbstractInArabidopsis, a large subset of heat responsive genes exhibits diurnal or circadian oscillations. However, to what extent the dimension of time and/or the circadian clock contribute to heat stress responses remains largely unknown. To determine the direct contribution of time of day and/or the clock to differential heat stress responses, we probed wild-type and mutants of the circadian clock genesCCA1,LHY,PRR7, andPRR9following exposure to heat (37 °C) and moderate cold (10 °C) in the early morning (ZT1) and afternoon (ZT6). Thousands of genes were differentially expressed in response to temperature, time of day, and/or the clock mutation. Approximately 30% more genes were differentially expressed in the afternoon compared to the morning, and heat stress significantly perturbed the transcriptome. Of the DEGs (~3000) specifically responsive to heat stress, ~70% showed time of day (ZT1 or ZT6) occurrence of the transcriptional response. For the DEGs (~1400) that are shared between ZT1 and ZT6, we observed changes to the magnitude of the transcriptional response. In addition, ~2% of all DEGs showed differential responses to temperature stress in the clock mutants. The findings in this study highlight a significant role for time of day in the heat stress responsive transcriptome, and the clock throughCCA1andLHY, appears to have a more profound role thanPRR7andPRR9in modulating heat stress responses during the day. Our results emphasize the importance of considering the dimension of time in studies on abiotic stress responses inArabidopsis.
Complex regulatory network allows Myriophyllum aquaticum to thrive under high-concentration ammonia toxicity
Authors: Wang Rui , Xu Shengjun , Sun Haishu , Feng Shugeng , Jiang Cancan , Zhou Sining , Wu Shimin , Zhuang Guoqiang , Chen Baodong , Bai Zhihui , Zhuang Xuliang 
Published: March 2019

AbstractPlants easily experience ammonia (NH4+) toxicity, especially aquatic plants. However, a unique wetland plant species,Myriophyllum aquaticum, can survive in livestock wastewater with more than 26 mM NH4+. In this study, the mechanisms of theM. aquaticumresponse to NH4+toxicity were analysed with RNA-seq. Preliminary analysis of enzyme activities indicated that key enzymes involved in nitrogen metabolism were activated to assimilate toxic NH4+into amino acids and proteins. In response to photosystem damage,M. aquaticumseemed to remobilize starch and cellulose for greater carbon and energy supplies to resist NH4+toxicity. Antioxidative enzyme activity and the secondary metabolite content were significantly elevated for reactive oxygen species removal. Transcriptomic analyses also revealed that genes involved in diverse functions (e.g., nitrogen, carbon and secondary metabolisms) were highly responsive to NH4+stress. These results suggested that a complex physiological and genetic regulatory network inM. aquaticumcontributes to its NH4+tolerance.
Comprehensive analysis of resistance-nodulation-cell division superfamily (RND) efflux pumps from Serratia marcescens, Db10
Authors: Toba Shinsuke , Minato Yusuke , Kondo Yuma , Hoshikawa Kanami , Minagawa Shu , Komaki Shiho , Kumagai Takanori , Matoba Yasuyuki , Morita Daichi , Ogawa Wakano , Gotoh Naomasa , Tsuchiya Tomofusa , Kuroda Teruo 
Published: March 2019

AbstractWe investigated the role of the resistance-nodulation-cell division superfamily (RND) efflux system on intrinsic multidrug resistance in Serratia marcescens. We identified eight putative RND efflux system genes in the S. marcescens Db10 genome that included the previously characterized systems, sdeXY, sdeAB, and sdeCDE. Six out of the eight genes conferred multidrug resistance on KAM32, a drug hypersensitive strain of Escherichia coli. Five out of the eight genes conferred resistance to benzalkonium, suggesting the importance of RND efflux systems in biocide resistance in S. marcescens. The energy-dependent efflux activities of five of the pumps were examined using a rhodamine 6 G efflux assay. When expressed in the tolC-deficient strain of E. coli, KAM43, none of the genes conferred resistance on E. coli. When hasF, encoding the S. marcescens TolC ortholog, was expressed in KAM43, all of the genes conferred resistance on E. coli, suggesting that HasF is a major outer membrane protein that is used by all RND efflux systems in this organism. We constructed a sdeXY deletion mutant from a derivative strain of the clinically isolated multidrug-resistant S. marcescens strain and found that the sdeXY deletion mutant was sensitive to a broad spectrum of antimicrobial agents.
Revealing transient events of molecular recognition via super-localization imaging of single-particle motion
Authors: Kong Qing-Ying , Yang Fan , Song Juan , Ruan Yi-Fan , Li Shan-Shan , Gao Zhao-Shuai , Kang Bin , Chen Hong-Yuan , Xu Jing-Juan 
Published: March 2019

AbstractMolecular recognition plays an important role in biological systems and relates to a wide range of applications in disease diagnostics and therapeutics. Studies based on steady state or ensemble analysis may mask critical dynamic information of single recognition events. Here we report a study of monitoring the transient molecular recognition via single particle motion. We utilized a super-localization imaging methodology, to comprehensively evaluate the rotational Brownian motion of a single nanoparticle in spatial-temporal-frequential domain, with a spatial accuracy ~20 nm and a temporal resolution of ~10 ms. The transient moment of molecular encountering was captured and different binding modes were discriminated. We observed that the transient recognition events were not static states of on or off, but stochastically undergoes dynamical transformation between different binding modes. This study improves our understanding about the dynamic nature of molecular recognition events beyond the ensemble characterization via binding constant.
Design principles of biologically fabricated avian nests
Authors: Jessel Hadass R. , Chen Sagi , Osovski Shmuel , Efroni Sol , Rittel Daniel , Bachelet Ido 
Published: March 2019

AbstractMaterials and construction methods of nests vary between bird species and at present, very little is known about the relationships between architecture and function in these structures. This study combines computational and experimental techniques to study the structural biology of nests fabricated by the edible nest swiftlet Aerodramus fuciphagus on vertical rock walls using threaded saliva. Utilizing its own saliva as a construction material allows the swiftlets full control over the structural features at a very high resolution in a process similar to additive manufacturing. It was hypothesized that the mechanical properties would vary between the structural regions of the nest (i.e. anchoring to the wall, center of the cup, and rim) mainly by means of architecture to offer structural support and bear the natural loads of birds and eggs. We generated numerical models of swiftlet nests from μCT scans based on collected swiftlet nests, which we loaded with a force of birds and eggs. This was done in order to study and assess the stress distribution that characterizes the specific nest’s architecture, evaluate its strength and weak points if any, as well as to understand the rationale and benefits that underlie this natural structure. We show that macro- and micro-scale structural patterns are identical in all nests, suggesting that their construction is governed by specific design principles. The nests’ response to applied loads of birds and eggs in finite element simulations suggests a mechanical overdesign strategy, which ensures the stresses experienced by its components in any loading scenario are actively minimized to be significantly smaller than the tensile fracture strength of the nests’ material. These findings highlight mechanical overdesign as a biological strategy for resilient, single-material constructions designed to protect eggs and hatchlings.
A critical regulator of Bcl2 revealed by systematic transcript discovery of lncRNAs associated with T-cell differentiation
Authors: Saadi Wiam , Kermezli Yasmina , Dao Lan T. M. , Mathieu Evelyne , Santiago-Algarra David , Manosalva Iris , Torres Magali , Belhocine Mohamed , Pradel Lydie , Loriod Beatrice , Aribi Mourad , Puthier Denis , Spicuglia Salvatore 
Published: March 2019

AbstractNormal T-cell differentiation requires a complex regulatory network which supports a series of maturation steps, including lineage commitment, T-cell receptor (TCR) gene rearrangement, and thymic positive and negative selection. However, the underlying molecular mechanisms are difficult to assess due to limited T-cell models. Here we explore the use of the pro-T-cell line P5424 to study early T-cell differentiation. Stimulation of P5424 cells by the calcium ionophore ionomycin together with PMA resulted in gene regulation of T-cell differentiation and activation markers, partially mimicking the CD4-CD8-double negative (DN) to double positive (DP) transition and some aspects of subsequent T-cell maturation and activation. Global analysis of gene expression, along with kinetic experiments, revealed a significant association between the dynamic expression of coding genes and neighbor lncRNAs including many newly-discovered transcripts, thus suggesting potential co-regulation. CRISPR/Cas9-mediated genetic deletion ofRobnr, an inducible lncRNA located downstream of the anti-apoptotic geneBcl2, demonstrated a critical role of theRobnrlocus in the induction ofBcl2. Thus, the pro-T-cell line P5424 is a powerful model system to characterize regulatory networks involved in early T-cell differentiation and maturation.
RNAi-Mediated PD-L1 Inhibition for Pancreatic Cancer Immunotherapy
Authors: Yoo Byunghee , Jordan Veronica Clavijo , Sheedy Patrick , Billig Ann-Marie , Ross Alana , Pantazopoulos Pamela , Medarova Zdravka 
Published: March 2019

AbstractThe recent past has seen impressive progress in the treatment of various malignancies using immunotherapy. One of the most promising approaches involves immune checkpoint inhibitors. However, the clinical results with these agents have demonstrated variability in the response. Pancreatic cancer, in particular, has proven resistant to initial immunotherapy approaches. Here, we describe an alternative strategy that relies on combining gemcitabine and a novel programmed death-ligand 1 (PD-L1) inhibitor, termed MN-siPDL1. MN-siPDL1 incorporates small interfering RNA against PD-L1 (siPDL1) conjugated to a magnetic nanocarrier (MN). We show that noninvasive magnetic resonance imaging (MRI) could be used to monitor therapeutic response. Combination therapy consisting of gemcitabine and MN-siPDL1 in a syngeneic murine pancreatic cancer model resulted in a significant reduction in tumor growth and an increase in survival. Following optimization, a 90% reduction in tumor volume was achieved 2 weeks after the beginning of treatment. Whereas 100% of the control animals had succumbed to their tumors by week 6 after the beginning of treatment, there was no mortality in the experimental group by week 5, and 67% of the experimental animals survived for 12 weeks. This method could provide therapeutic benefit against an intractable disease for which there are no effective treatments and which is characterized by a mere 1% 5-year survival.
Mathematical modelling of the impact of treating latent tuberculosis infection in the elderly in a city with intermediate tuberculosis burden
Authors: Chong Ka Chun , Leung Chi Chiu , Yew Wing Wai , Zee Benny Chung Ying , Tam Greta Chun Huen , Wang Maggie Haitian , Jia Katherine Min , Chung Pui Hong , Lau Steven Yuk Fai , Han Xiaoran , Yeoh Eng Kiong 
Published: March 2019

AbstractHong Kong is a high-income city with intermediate tuberculosis (TB) burden primarily driven by endogenous reactivations. A high proportion of remote latently infected people, particularly elderly, hinders the effectiveness of current strategies focusing on passive TB detection. In this study, we developed a mathematical model to evaluate the impact of treating latent TB infection (LTBI) in the elderly in addition to current TB control strategies. The model was calibrated using the annual age-stratified TB notifications from 1965–2013 in Hong Kong. Our results showed that at present, approximately 75% of annual new notifications were from reactivations. Given the present treatment completion rate, even if only a low to moderate proportion (approximately 20% to 40%) of elderly people were screened and treated for LTBI, the overall TB incidence could be reduced by almost 50%, to reach the 2025 milestone of the global End TB Strategy. Nevertheless, due to a high risk of hepatotoxicity in elderly population, benefit-risk ratios were mostly below unity; thus, intervention programs should be carefully formulated, including prioritising LTBI treatment for high-risk elderly groups who are closely monitored for possible adverse side effects.