bluuebunny/crossref_metadata_2025_split huggingface dataset:
Screening for major driver oncogene alterations in adenosquamous lung carcinoma using PCR coupled with next-generation and Sanger sequencing methods
Authors: Shi Xiaohua , Wu Huanwen , Lu Junliang , Duan Huanli , Liu Xuguang , Liang Zhiyong 
Published: February 2016

AbstractWe investigated the frequency of major driver oncogenes in lung adenosquamous cell carcinoma (ASC) cases. Frequency of EGFR, K-Ras, B-Raf, PIK3CA, DDR2, ALK, and PDGFRA gene mutations was examined in 56 patients using next-generation sequencing, polymerase chain reaction, and Sanger sequencing. Macrodissection or microdissection was performed in 37 cases to separate the adenomatous and squamous components of ASC. The overall mutation rate was 64.29%, including 55.36%, 7.14%, and 1.79% for EGFR, K-Ras, and B-Raf mutations, respectively. PIK3CA mutation was detected in three cases; all involved coexisting EGFR mutations. Of the 37 cases, 34 were convergent in two components, while three showed EGFR mutations in the glandular components and three showed PIK3CA mutations in the squamous components. With respect to EGFR mutations, the number of young female patients, nonsmokers, and those with positive pleural invasion was higher in the mutation-positive group than that in the mutation-negative. K-Ras mutation was significantly associated with smoking. Overall survival in the different EGFR mutation groups differed significantly. The frequency and clinicopathological characteristics of EGFR- and K-Ras-mutated adenosquamous lung carcinoma were similar to that noted in Asian adenocarcinomas patients. The high convergence mutation rate in both adenomatous and squamous components suggests monoclonality in ASC.
Ultra sub-wavelength surface plasmon confinement using air-gap, sub-wavelength ring resonator arrays
Authors: Lee Jaehak , Sung Sangkeun , Choi Jun-Hyuk , Eom Seok Chan , Mortensen N. Asger , Shin Jung H. 
Published: February 2016

AbstractArrays of sub-wavelength, sub-10 nm air-gap plasmonic ring resonators are fabricated using nanoimprinting. In near infra-red (NIR) range, the resonator supports a single dipole mode which is excited and identified via simple normal illumination and explored through transmission measurements. By controlling both lateral and vertical confinement via a metal edge, the mode volume is successfully reduced down to 1.3 × 10−5 λ03. The advantage of such mode confinement is demonstrated by applying the resonators biosensing. Using bovine serum albumin (BSA) molecules, a dramatic enhancement of surface sensitivity up to 69 nm/nm is achieved as the modal height approaches the thickness of the adsorbed molecule layers.
Composition of the outgrowth medium modulates wake-up kinetics and ampicillin sensitivity of stringent and relaxed Escherichia coli
Authors: Varik Vallo , Oliveira Sofia Raquel Alves , Hauryliuk Vasili , Tenson Tanel 
Published: February 2016

AbstractThe transition of Escherichia coli from the exponential into the stationary phase of growth induces the stringent response, which is mediated by the rapid accumulation of the alarmone nucleotide (p)ppGpp produced by the enzyme RelA. The significance of RelA’s functionality during the transition in the opposite direction, i.e. from the stationary phase into new exponential growth, is less well understood. Here we show that the relaxed strain, i.e. lacking the relA gene, displays a relative delay in regrowth during the new exponential growth phase in comparison with the isogenic wild type strain. The severity of the effect is a function of both the carbon source and amino acid composition of the outgrowth media. As a result, the loss of RelA functionality increases E. coli tolerance to the bactericidal antibiotic ampicillin during growth resumption in fresh media in a medium-specific way. Taken together, our data underscore the crucial role of medium composition and growth conditions for studies of the role of individual genes and regulatory networks in bacterial phenotypic tolerance to antibiotics.
Efficient Second Harmonic Generation in 3D Nonlinear Optical-Lattice-Like Cladding Waveguide Splitters by Femtosecond Laser Inscription
Authors: Nie Weijie , Jia Yuechen , Vázquez de Aldana Javier R. , Chen Feng 
Published: February 2016

AbstractIntegrated photonic devices with beam splitting function are intriguing for a broad range of photonic applications. Through optical-lattice-like cladding waveguide structures fabricated by direct femtosecond laser writing, the light propagation can be engineered via the track-confined refractive index profiles, achieving tailored output beam distributions. In this work, we report on the fabrication of 3D laser-written optical-lattice-like structures in a nonlinear KTP crystal to implement 1 × 4 beam splitting. Second harmonic generation (SHG) of green light through these nonlinear waveguide beam splitter structures provides the capability for the compact visible laser emitting devices. With Type II phase matching of the fundamental wavelength (@ 1064 nm) to second harmonic waves (@ 532 nm), the frequency doubling has been achieved through this three-dimensional beam splitter. Under 1064-nm continuous-wave fundamental-wavelength pump beam, guided-wave SHG at 532 nm are measured with the maximum power of 0.65 mW and 0.48 mW for waveguide splitters (0.67 mW and 0.51 mW for corresponding straight channel waveguides), corresponding to a SH conversion efficiency of approximately ~14.3%/W and 13.9%/W (11.2%/W, 11.3%/W for corresponding straight channel waveguides), respectively. This work paves a way to fabricate compact integrated nonlinear photonic devices in a single chip with beam dividing functions.
Atom Probe Tomographic Mapping Directly Reveals the Atomic Distribution of Phosphorus in Resin Embedded Ferritin
Authors: Perea Daniel E. , Liu Jia , Bartrand Jonah , Dicken Quinten , Thevuthasan S. Theva , Browning Nigel D. , Evans James E. 
Published: February 2016

AbstractHere we report the atomic-scale analysis of biological interfaces within the ferritin protein using atom probe tomography that is facilitated by an advanced specimen preparation approach. Embedding ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualise atomic distributions and distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell, as well as the organic-organic interface between the ferritin protein shell and embedding resin. In addition, we definitively show the atomic-scale distribution of phosphorus as being at the surface of the ferrihydrite mineral with the distribution of sodium mapped within the protein shell environment with an enhanced distribution at the mineral/protein interface. The sample preparation method is robust and can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.
An Inactivated Antibiotic-Exposed Whole-Cell Vaccine Enhances Bactericidal Activities Against Multidrug-Resistant Acinetobacter baumannii
Authors: Shu Meng-Hooi , MatRahim NorAziyah , NorAmdan NurAsyura , Pang Sui-Ping , Hashim Sharina H. , Phoon Wai-Hong , AbuBakar Sazaly 
Published: February 2016

AbstractVaccination may be an alternative treatment for infection with multidrug-resistance (MDR) Acinetobacter baumannii. The study reported here evaluated the bactericidal antibody responses following immunization of mice using an inactivated whole-cell vaccine derived from antibiotic-exposed MDR A. baumannii (I-M28-47-114). Mice inoculated with I-M28-47 (non-antibiotic-exposed control) and I-M28-47-114 showed a high IgG antibody response by day 5 post-inoculation. Sera from mice inoculated with I-M28-47-114 collected on day 30 resulted in 80.7 ± 12.0% complement-mediated bacteriolysis in vitro of the test MDR A. baumannii treated with imipenem, which was a higher level of bacteriolysis over sera from mice inoculated with I-M28-47. Macrophage-like U937 cells eliminated 49.3 ± 11.6% of the test MDR A. baumannii treated with imipenem when opsonized with sera from mice inoculated with I-M28-47-114, which was a higher level of elimination than observed for test MDR A. baumannii opsonized with sera from mice inoculated with I-M28-47. These results suggest that vaccination with I-M28-47-114 stimulated antibody responses capable of mounting high bactericidal killing of MDR A. baumannii. Therefore, the inactivated antibiotic-exposed whole-cell vaccine (I-M28-47-114) has potential for development as a candidate vaccine for broad clearance and protection against MDR A. baumannii infections.
Autonomous Graphene Vessel for Suctioning and Storing Liquid Body of Spilled Oil
Authors: Kim Taewoo , Lee Jeong Seok , Lee Geonhui , Seo Dong Kyun , Baek Youngbin , Yoon Jeyong , Oh Seung M. , Kang Tae June , Lee Hong H. , Kim Yong Hyup 
Published: February 2016

AbstractDespite remarkable strides in science and technology, the strategy for spilled oil collection has remained almost the same since the 1969 Santa Barbara oil spill. The graphene vessel devised here can bring about an important yet basic change in the strategy for spilled oil collection. When it is placed on the oil-covered seawater, the graphene vessel selectively separates the oil, then collects and stores the collected oil in the vessel all by itself without any external power inputs. Capillarity and gravity work together to fill this proto-type graphene vessel with the spilled oil at a rate that is higher than 20,000 liters per square meter per hour (LMH) with oil purity better than 99.9% and allow the vessel to withstand a water head of 0.5 m. The vessel also has a superb chemical stability and recyclability. An expanded oil contact area, considerably greater than the thickness of the oil layer, forms at the reduced graphene oxide (rGO) foam interface upon contact with the spilled oil. This expanded contact area does not change much even when the oil layer thins out. As a result, the high oil collection rate is maintained throughout the recovery of spilled oil.
Proton-conducting Micro-solid Oxide Fuel Cells with Improved Cathode Reactions by a Nanoscale Thin Film Gadolinium-doped Ceria Interlayer
Authors: Li Yong , Wang Shijie , Su Pei-Chen 
Published: February 2016

AbstractAn 8 nm-thick gadolinium-doped ceria (GDC) layer was inserted as a cathodic interlayer between the nanoscale proton-conducting yttrium-doped barium zirconate (BZY) electrolyte and the porous platinum cathode of a micro-solid oxide fuel cell (μ-SOFC), which has effectively improved the cathode reaction kinetics and rendered high cell power density. The addition of the GDC interlayer significantly reduced the cathodic activation loss and increased the peak power density of the μ-SOFC by 33% at 400 °C. The peak power density reached 445 mW/cm2 at 425 °C, which is the highest among the reported μ-SOFCs using proton-conducting electrolytes. The impressive performance was attributed to the mixed protonic and oxygen ionic conducting properties of the nano-granular GDC, and also to the high densities of grain boundaries and lattice defects in GDC interlayer that favored the oxygen incorporation and transportation during the oxygen reduction reaction (ORR) and the water evolution reaction at cathode.
A PTH-responsive circadian clock operates in ex vivo mouse femur fracture healing site
Authors: Kunimoto Tatsuya , Okubo Naoki , Minami Yoichi , Fujiwara Hiroyoshi , Hosokawa Toshihiro , Asada Maki , Oda Ryo , Kubo Toshikazu , Yagita Kazuhiro 
Published: February 2016

AbstractThe circadian clock contains clock genes including Bmal1 and Period2 and it maintains an interval rhythm of approximately 24 hours (the circadian rhythm) in various organs including growth plate and articular cartilage. As endochondral ossification is involved not only in growth plate but also in fracture healing, we investigated the circadian clock functions in fracture sites undergoing healing. Our fracture models using external fixation involved femurs of Period2::Luciferase knock-in mice which enables the monitoring of endogenous circadian clock state via bioluminescence. Organ culture was performed by collecting femurs and fracture sites were observed using bioluminescence imaging systems. Clear bioluminescence rhythms of 24-hour intervals were revealed in fracture healing sites. When parathyroid hormone (PTH) was administered to fractured femurs in organ culture, peak time of Period2::Luciferase activity in fracture sites and growth plates changed, indicating that PTH-responsive circadian clock functions in the mouse femur fracture healing site. While PTH is widely used in treating osteoporosis, many studies have reported that it contributes to improvement of fracture healing. Future studies of the role of this local clock in wound healing may reveal a novel function of the circadian timing mechanism in skeletal cells.
The influence of conversational context and the developing lexicon on the calculation of scalar implicatures
Authors: Syrett Kristen , Austin Jennifer , Sanchez Liliana , Germak Christina , Lingwall Anne , Perez-Cortes Silvia , Arias-Amaya Anthony , Baker Hannah 
Published: February 2016

AbstractAlthough monolingual children do not generally calculate the upper-bounded scalar implicature (SI) associated with ‘some’ without additional support, monolingual Spanish-speaking children have been reported to do so withalgunos(‘some’), and further distinguishalgunosfromunos. Given documented cross-linguistic influence in interface phenomena in bilinguals, we asked whether young Spanish-English bilinguals calculate SIs withalgunos, or if there is an effect of acquiring languages with overlapping but diverging lexical entries. Two experiments reveal that not only do bilinguals inconsistently calculate SIs, Spanish monolinguals do not always either. InExperiment 1, bilinguals did not calculate the SI associated withalgunos. However, inExperiment 2, which calls upon their awareness of speaker-hearer dynamics, they did. This research highlights the challenges arising from interpreting linguistic phenomena where lexical, semantic, and pragmatic information intersect, and is a call for further investigation with bilinguals in a rapidly growing area where bilingual research is lacking.
Direct visualization of replication dynamics in early zebrafish embryos
Authors: Kuriya Kenji , Higashiyama Eriko , Avşar-Ban Eriko , Okochi Nanami , Hattori Kaede , Ogata Shin , Takebayashi Shin-ichiro , Ogata Masato , Tamaru Yutaka , Okumura Katsuzumi 
Published: February 2016

AbstractWe analyzed DNA replication in early zebrafish embryos. The replicating DNA of whole embryos was labeled with the thymidine analog 5-ethynyl-2ʹ-deoxyuridine (EdU), and spatial regulation of replication sites was visualized in single embryo-derived cells. The results unveiled uncharacterized replication dynamics during zebrafish early embryogenesis.
Trails to the gibberellin receptor, GIBBERELLIN INSENSITIVE DWARF1
Authors: Yamaguchi Isomaro , Nakajima Masatoshi , Park Seung-Hyun 
Published: February 2016

Abstract
The researches on the identification of gibberellin receptor are reviewed from the early attempts in 1960s to the identification of GIBBERELLIN INSENSITIVE DWARF1 (GID1) as the receptor in 2005. Unpublished data of the gibberellin-binding protein in the seedlings of adzuki bean (Vigna angularis) are also included, suggesting that the active principle of the gibberellin-binding protein was a GID1 homolog.
Effect of Taurine Supplementation on Growth Response and Body Composition of Largemouth Bass
Authors: Frederick Catherine A , Coyle Shawn D , Durborow Robert M , Bright Leigh Anne , Tidwell James H 
Published: February 2016

Abstract
Taurine is “conditionally essential” for some fish species, particularly when fish meal levels in their diets are reduced. Taurine supplementation has not yet been evaluated in the Largemouth Bass Micropterus salmoides. A 12-week feeding trial was conducted using a 2 × 2 factorial design with the main effects being fish meal inclusion (0% or 30%) or taurine supplementation (0% or 2%). The fish meal diets contained sardine fish meal while the nonfish meal diets used pork meal, which has a very low taurine content, as the animal source protein. The four experimental diets were formulated to contain 40% crude protein and 12% lipid. The feeding trial was conducted using juvenile Largemouth Bass (19.3 ± 3.9 g; mean ± SD) stocked at 25 fish/tank into twelve 230-L aquaria within a recirculating system. Fish were fed to apparent satiation twice daily. Dissolved oxygen, pH, and temperature were monitored daily, while alkalinity, total ammonia nitrogen, and nitrite-nitrogen were monitored three times weekly. Analysis of harvest data indicated a significant statistical interaction between fish meal inclusion and taurine supplementation only for feed conversion ratio (FCR). In diets containing no fish meal, the addition of taurine significantly increased the FCR (from 2.2 to 2.6). However, in fish fed diets containing fish meal, supplemental taurine significantly decreased the FCR (from 2.2 to 1.9). In terms of main effects, taurine supplementation did not significantly affect any of the measured growth or survival variables. Survival and growth in Largemouth Bass fed 0% fish meal were not significantly different from survival and growth in those fed 30% fish meal. Body composition variables were not significantly affected by either fish meal inclusion or taurine supplementation. These data support previous studies that found that by-products from terrestrial animal sources can successfully replace fish meal in diets for Largemouth Bass. These data also indicate that Largemouth Bass do not have a significant dietary requirement for taurine.
Modelling the relationship between biomechanics and performance of young sprinting swimmers
Authors: Morais Jorge E , Silva António J , Marinho Daniel A , Marques Mário C , Batalha Nuno , Barbosa Tiago M 
Published: February 2016

AbstractThe aim of this study was to compute a swimming performance confirmatory model based on biomechanical parameters. The sample included 100 young swimmers (overall: 12.3 ± 0.74 years; 49 boys: 12.5 ± 0.76 years; 51 girls: 12.2 ± 0.71 years; both genders in Tanner stages 1–2 by self‐report) participating on a regular basis in regional and national‐level events. The 100 m freestyle event was chosen as the performance indicator. Anthropometric (arm span), strength (throwing velocity), power output (power to overcome drag), kinematic (swimming velocity) and efficiency (propelling efficiency) parameters were measured and included in the model. The path‐flow analysis procedure was used to design and compute the model. The anthropometric parameter (arm span) was excluded in the final model, increasing its goodness‐of‐fit. The final model included the throw velocity, power output, swimming velocity and propelling efficiency. All links were significant between the parameters included, but the throw velocity–power output. The final model was explained by 69% presenting a reasonable adjustment (model's goodness‐of‐fit; x2/df = 3.89). This model shows that strength and power output parameters do play a mediator and meaningful role in the young swimmers’ performance.
Species Identification by Bayesian Fingerprinting: A Powerful Alternative to DNA Barcoding
Authors: Yang Ziheng , Rannala Bruce 
Published: February 2016

AbstractA number of methods have been developed to use genetic sequence data to identify and delineate species. Some methods are based on heuristics, such as DNA barcoding which is based on a sequence-distance threshold, while others use Bayesian model comparison under the multispecies coalescent model. Here we use mathematical analysis and computer simulation to demonstrate large differences in statistical performance of species identification between DNA barcoding and Bayesian inference under the multispecies coalescent model as implemented in the BPP program. We show that a fixed genetic-distance threshold as used in DNA barcoding is problematic for delimiting species, even if the threshold is “optimized”, because different species have different population sizes and different divergence times, and therefore display different amounts of intra-species versus inter-species variation. In contrast, BPP can reliably delimit species in such situations with only one locus and rarely supports a wrong assignment with high posterior probability. While under-sampling or rare specimens may pose problems for heuristic methods, BPP can delimit species with high power when multi-locus data are used, even if the species is represented by a single specimen. Finally we demonstrate that BPP may be powerful for delimiting cryptic species using specimens that are misidentified as a single species in the barcoding library.
Neighbourhood satisfaction: responses from residents of green townships in Malaysia
Authors: Tan Teck Hong 
Published: February 2016

Purpose– The purpose of this study is to examine the residents’ satisfaction level with their neighbourhood and which dominant attributes can predict the neighbourhood satisfaction levels of the residents in the green-accredited township.Design/methodology/approach– In this survey, 300 self-administered questionnaires were distributed to respondents who have resided in the green-accredited township. Only 190 survey forms were returned and used in generating the analysis.Findings– Integrated connectivity and accessibility and environmental quality have been shown to exert a significant influence on neighbourhood satisfaction. However, residents were not satisfied with the security level and community participation in the green-accredited neighbourhood.Research limitations/implications– Neighbourhood attributes are noteworthy determinants in assessing the significance of the green-accredited township in Malaysia.Practical implications– The results of this study would assist policymaking in proposing actual improvements in a sustainable neighbourhood and help in prediction of satisfaction with the planned housing development project.Originality/value– Going green has become trendy amongst communities. With the government’s move to promote green living, stakeholders, such as residents, local government or housing developers, have urged to contribute towards ensuring a more sustainable and green neighbourhood.
Robust hedonic price indexes
Authors: Bourassa Steven C , Cantoni Eva , Hoesli Martin 
Published: February 2016

Purpose– The purpose of this paper is to demonstrate the application of robust techniques to the estimation of hedonic house price indexes.Design/methodology/approach– The authors use simulation analysis to compare an index estimated using ordinary least squares (OLS) with several indexes estimated using robust techniques. The analysis uses sales transactions data from a US city. The authors then explore how robust methods can correct for omitted variables under some circumstances and how they affect the revision problem that occurs when longitudinal hedonic indexes are updated.Findings– Robust methods can resolve missing variable problems in some circumstances and also can substantially reduce the revision problem in longitudinal hedonic indexes.Practical implications– Robust techniques may be preferable to OLS when constructing longitudinal hedonic indexes.Originality/value– This is the first paper to undertake a systematic analysis of the applicability of robust techniques in constructing hedonic house price indexes.