bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-assembled Cubic Boron Nitride Nanodots
Authors: Khanaki Alireza , Xu Zhongguang , Tian Hao , Zheng Renjing , Zuo Zheng , Zheng Jian-Guo , Liu Jianlin 
Published: June 2017

AbstractOne of the low-dimensional Boron Nitride (BN) forms, namely, cubic-BN (c-BN) nanodots (NDs), offers a variety of novel opportunities in battery, biology, deep ultraviolet light emitting diodes, sensors, filters, and other optoelectronic applications. To date, the attempts towards producing c-BN NDs were mainly performed under extreme high-temperature/high-pressure conditions and resulted in c-BN NDs with micrometer sizes, mixture of different BN phases, and containing process-related impurities/contaminants. To enhance device performance for those applications by taking advantage of size effect, pure, sub-100 nm c-BN NDs are necessary. In this paper, we report self-assembled growth of c-BN NDs on cobalt and nickel substrates by plasma-assisted molecular beam epitaxy. It is found that the nucleation, formation, and morphological properties of c-BN NDs can be closely correlated with the nature of substrate including catalysis effect, lattice-mismatch-induced strain, and roughness, and growth conditions, in particular, growth time and growth temperature. The mean lateral size of c-BN NDs on cobalt scales from 175 nm to 77 nm with the growth time. The growth mechanism of c-BN NDs on metal substrates is concluded to be Volmer-Weber (VW) mode. A simplified two-dimensional numerical modeling shows that the elastic strain energy plays a key role in determining the total formation energy of c-BN NDs on metals.
SOX2 is required for inner ear neurogenesis
Authors: Steevens Aleta R. , Sookiasian Danielle L. , Glatzer Jenna C. , Kiernan Amy E. 
Published: June 2017

AbstractNeurons of the cochleovestibular ganglion (CVG) transmit hearing and balance information to the brain. During development, a select population of early otic progenitors express NEUROG1, delaminate from the otocyst, and coalesce to form the neurons that innervate all inner ear sensory regions. At present, the selection process that determines which otic progenitors activate NEUROG1 and adopt a neuroblast fate is incompletely understood. The transcription factor SOX2 has been implicated in otic neurogenesis, but its requirement in the specification of the CVG neurons has not been established. Here we tested SOX2’s requirement during inner ear neuronal specification using a conditional deletion paradigm in the mouse. SOX2 deficiency at otocyst stages caused a near-absence of NEUROG1-expressing neuroblasts, increased cell death in the neurosensory epithelium, and significantly reduced the CVG volume. Interestingly, a milder decrease in neurogenesis was observed in heterozygotes, indicating SOX2 levels are important. Moreover, fate-mapping experiments revealed that the timing of SOX2 expression did not parallel the established vestibular-then-auditory sequence. These results demonstrate that SOX2 is required for the initial events in otic neuronal specification including expression of NEUROG1, although fate-mapping results suggest SOX2 may be required as a competence factor rather than a direct initiator of the neural fate.
Molecular switching system using glycosylphosphatidylinositol to select cells highly expressing recombinant proteins
Authors: Matabaro Emmanuel , He Zeng’an , Liu Yi-Shi , Zhang Hui-Jie , Gao Xiao-Dong , Fujita Morihisa 
Published: June 2017

AbstractAlthough many pharmaceutical proteins are produced in mammalian cells, there remains a challenge to select cell lines that express recombinant proteins with high productivity. Since most biopharmaceutical proteins are secreted by cells into the medium, it is difficult to select cell lines that produce large amounts of the target protein. To address this issue, a new protein expression system using the glycosylphosphatidylinositol (GPI)-anchor was developed. PGAP2 is involved in processing GPI-anchored proteins (GPI-APs) during transport. In PGAP2 mutant cells, most GPI-APs are secreted into the medium. Here, we established a HEK293 cell line where endogenous PGAP2 was knocked out and exogenous PGAP2 was inserted with a piggyBac transposon in the genome. Using these cells, human lysosomal acid lipase (LIPA) and α-galactosidase A (GLA) were expressed as GPI-anchored forms (LIPA-GPI and GLA-GPI) and cells expressing high levels of LIPA-GPI or GLA-GPI on the cell surface were enriched. Removal of the PGAP2 gene by piggyBac transposase or FLP recombinase converted LIPA-GPI and GLA-GPI from membrane-bound to the secreted forms. Thus, cells expressing LIPA or GLA in large amounts could be enriched using this approach. The GPI-based molecular switching system is an efficient approach to isolate cells expressing recombinant proteins with high productivity.
Structural basis for biologically relevant mechanical stiffening of a virus capsid by cavity-creating or spacefilling mutations
Authors: Guerra Pablo , Valbuena Alejandro , Querol-Audí Jordi , Silva Cristina , Castellanos Milagros , Rodríguez-Huete Alicia , Garriga Damià , Mateu Mauricio G. , Verdaguer Nuria 
Published: June 2017

AbstractRecent studies reveal that the mechanical properties of virus particles may have been shaped by evolution to facilitate virus survival. Manipulation of the mechanical behavior of virus capsids is leading to a better understanding of viral infection, and to the development of virus-based nanoparticles with improved mechanical properties for nanotechnological applications. In the minute virus of mice (MVM), deleterious mutations around capsid pores involved in infection-related translocation events invariably increased local mechanical stiffness and interfered with pore-associated dynamics. To provide atomic-resolution insights into biologically relevant changes in virus capsid mechanics, we have determined by X-ray crystallography the structural effects of deleterious, mechanically stiffening mutations around the capsid pores. Data show that the cavity-creating N170A mutation at the pore wall does not induce any dramatic structural change around the pores, but instead generates subtle rearrangements that propagate throughout the capsid, resulting in a more compact, less flexible structure. Analysis of the spacefilling L172W mutation revealed the same relationship between increased stiffness and compacted capsid structure. Implications for understanding connections between virus mechanics, structure, dynamics and infectivity, and for engineering modified virus-based nanoparticles, are discussed.
Disrupted pursuit compensation during self-motion perception in early Alzheimer’s disease
Authors: Wang Jingru , Guo Xiaojun , Zhuang Xianbo , Chen Tuanzhi , Yan Wei 
Published: June 2017

AbstractOur perception of the world is remarkably stable despite of distorted retinal input due to frequent eye movements. It is considered that the brain uses corollary discharge, efference copies of signals sent from motor to visual regions, to compensate for distortions and stabilize visual perception. In this study, we tested whether patients with Alzheimer’s disease (AD) have impaired corollary discharge functions as evidenced by reduced compensation during the perception of optic flow that mimics self-motion in the environment. We asked a group of early-stage AD patients and age-matched healthy controls to indicate the perceived direction of self-motion based on optic flow while tracking a moving target with smooth pursuit eye movement, or keeping eye fixation at a stationary target. We first replicated the previous findings that healthy participants were able to compensate for distorted optic flow in the presence of eye movements, as indicated by similar performance of self-motion perception between pursuit and fixation conditions. In stark contrast, AD patients showed impaired self-motion perception when the optic flow was distorted by eye movements. Our results suggest that early-stage AD pathology is associated with disrupted eye movement compensation during self-motion perception.
Comparing DNA enrichment of proliferating cells following administration of different stable isotopes of heavy water
Authors: Farthing Don E. , Buxbaum Nataliya P. , Lucas Philip J. , Maglakelidze Natella , Oliver Brittany , Wang Jiun , Hu Kevin , Castro Ehydel , Bare Catherine V. , Gress Ronald E. 
Published: June 2017

AbstractDeuterated water (2H2O) is a label commonly used for safe quantitative measurement of deuterium enrichment into DNA of proliferating cells. More recently, it has been used for labeling proteins and other biomolecules. Our in vitro - in vivo research reports important stable isotopic labeling enrichment differences into the DNA nucleosides and their isotopologues (e.g. deoxyadenosine (dA) M + 1, dA M + 2, dA M + 3), as well as tumor cell proliferation effects for various forms of commercially available stable heavy water (2H2O, H218O, and 2H218O). Using an in vitro mouse thymus tumor cell line, we determined that H218O provides superior DNA labeling enrichment quantitation, as measured by GC-positive chemical ionization (PCI)-MS/MS. In addition, at higher but physiologically relevant doses, both 2H218O and 2H2O down modulated mouse thymus tumor cell proliferation, whereas H218O water had no observable effects on cell proliferation. The in vivo labeling studies, where normal mouse bone marrow cells (i.e. high turnover) were evaluated post labeling, demonstrated DNA enrichments concordant with measurements from the in vitro studies. Our research also reports a headspace-GC-NCI-MS method, which rapidly and quantitatively measures stable heavy water levels in total body water.
Epigenetic targeting drugs potentiate chemotherapeutic effects in solid tumor therapy
Authors: Li Jingjing , Hao Dapeng , Wang Li , Wang Haitao , Wang Yuan , Zhao Zhiqiang , Li Peipei , Deng Chuxia , Di Li-jun 
Published: June 2017

AbstractEpigenetic therapy is a novel tumor therapeutic method and refers to the targeting of the aberrant epigenetic modifications presumably at cancer-related genes by chemicals which are epigenetic targeting drugs (ETDs). Not like in treating hematopoietic cancer, the clinical trials investigating the potential use of ETDs in the solid tumor is not encouraging. Instead, the curative effects of ETD delivered together with DNA targeting chemo drugs (DTDs) are quite promising according to our meta-analysis. To investigate the synergistic mechanism of ETD and DTD drug combination, the therapeutic effect was studied using both cell lines and mouse engrafted tumors. Mechanically we show that HDAC inhibitors and DNMT inhibitors are capable of increasing the chromatin accessibility to cisplatin (CP) and doxorubicin (Dox) through chromatin decompaction globally. Consequently, the combination of ETD and DTD enhances the DTD induced DNA damage and cell death. Engrafted tumors in SCID mice also show increased sensitivity to irradiation (IR) or CP when the tumors were pretreated by ETDs. Given the limited therapeutic effect of ETD alone, these results strongly suggest that the combination of DTD, including irradiation, and ETD treatment is a very promising choice in clinical solid tumor therapy.
Modulational instability of coupled ring waveguides with linear gain and nonlinear loss
Authors: Hung Nguyen Viet , Zegadlo Krzysztof , Ramaniuk Aliaksandr , Konotop Vladimir V. , Trippenbach Marek 
Published: June 2017

AbstractWe consider a nanostructure of two coupled ring waveguides with constant linear gain and nonlinear absorption - the system that can be implemented in various settings including polariton condensates, optical waveguides or atomic Bose-Einstein condensates. It is found that, depending on the parameters, this simple configuration allows for observing several complex nonlinear phenomena, which include spontaneous symmetry breaking, modulational instability leading to generation of stable circular flows with various vorticities, stable inhomogeneous states with interesting structure of currents flowing between rings, as well as dynamical regimes having signatures of chaotic behavior.
Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues
Authors: Mendez Pedro , Fang Li Tai , Jablons David M. , Kim Il-Jin 
Published: June 2017

AbstractSequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS). We therefore tested the two most commonly used WGA methods, multiple displacement amplification (MDA-Qiagen REPLI-g kit) and the hybrid or modified PCR-based method (Sigma/Rubicon Genomics Inc. GenomePlex kit) in FFPE normal and tumor tissue specimens. For the normalized copy number analysis, the FFPE process caused none or very minimal bias. Variations in copy number were minimal in samples amplified using the GenomePlex kit, but they were statistically significantly higher in samples amplified using the REPLI-g kit. The pattern was similar for variant allele frequencies across the samples, which was minimal for the GenomePlex kit but highly variable for the REPLI-g kit. These findings suggest that each WGA method should be tested thoroughly before using it for clinical cancer samples.
Metabolic changes in Medaka fish induced by cyanobacterial exposures in mesocosms: an integrative approach combining proteomic and metabolomic analyses
Authors: Sotton Benoît , Paris Alain , Le Manach Séverine , Blond Alain , Lacroix Gérard , Millot Alexis , Duval Charlotte , Huet Hélène , Qiao Qin , Labrut Sophie , Chiappetta Giovanni , Vinh Joelle , Catherine Arnaud , Marie Benjamin 
Published: June 2017

AbstractCyanobacterial blooms pose serious threats to aquatic organisms and strongly impact the functioning of aquatic ecosystems. Due to their ability to produce a wide range of potentially bioactive secondary metabolites, so called cyanotoxins, cyanobacteria have been extensively studied in the past decades. Proteomic and metabolomic analyses provide a unique opportunity to evaluate the global response of hundreds of proteins and metabolites at a glance. In this study, we provide the first combined utilization of these methods targeted to identify the response of fish to bloom-forming cyanobacteria. Medaka fish (Oryzias latipes) were exposed for 96 hours either to a MC-producing or to a non-MC-producing strain of Microcystis aeruginosa and cellular, proteome and metabolome changes following exposure to cyanobacteria were characterized in the fish livers. The results suggest that a short-term exposure to cyanobacteria, producing or not MCs, induces sex-dependent molecular changes in medaka fish, without causing any cellular alterations. Globally, molecular entities involved in stress response, lipid metabolism and developmental processes exhibit the most contrasted changes following a cyanobacterial exposure. Moreover, it appears that proteomic and metabolomic analyses are useful tools to verify previous information and to additionally bring new horizons concerning molecular effects of cyanobacteria on fish.
A genetically enhanced sterile insect technique against the fruit fly, Bactrocera dorsalis (Hendel) by feeding adult double-stranded RNAs
Authors: Ali Muhammad Waqar , Zheng Wenping , Sohail Summar , Li Qingmei , Zheng Weiwei , Zhang Hongyu 
Published: June 2017

AbstractRNAi based sterile insect technique (SIT) is an authentic insect management approach but requires proper target genes. During this study, spermless males were developed by interfering with germ cell differentiation and azoospermia related genes. Data demonstrates significant reductions in the target genes expressions (boul, zpg, dsx
M
, fzo and gas8) after oral dsRNAs administration. Knock down of target genes significantly affected the reproductive ability of males and reduced egg-hatching as compared to the control group. Furthermore, different combinations of selected gene dsRNAs (boul + zpg, boul + dsx
M
and zpg + dsx
M
) were made, which resulted up to 85.40% of male sterility. The most effective combination was selected to prepare different concentrations of dsRNA, 250, 500, 750 and 1000 ng/μl, that caused 18.97%, 38.68%, 58.02% and 85.40% male sterility, respectively. Subsequently, 1000 ng/μl of the same combination of ds-RNAs was used against differently aged adult flies (1, 5, 7, 10 days) which lead to 85.40%, 31.42%, 21.76% and 9.90% male sterility, respectively. SIT developed in this study showed that, boul + zpg combination of dsRNA feeding for 6 hours significantly reduced the number of spermatozoa and viability of sperm in 1-day-old B. dorsalis flies. In short, this study provides an effective SIT technique for long-term B. dorsalis management.
Nitrogen enrichment impacts on boreal litter decomposition are driven by changes in soil microbiota rather than litter quality
Authors: Maaroufi Nadia I. , Nordin Annika , Palmqvist Kristin , Gundale Michael J. 
Published: June 2017

AbstractIn nitrogen (N) limited boreal forests, N enrichment can impact litter decomposition by affecting litter quality and by changing the soil environment where litter decomposes. We investigated the importance of litter quality and soil factors on litter decomposition using a 2-year reciprocal transplant experiment for Picea abies needle litter, derived from plots subjected to 17 years of N addition, including control, low and high N treatments (ambient, 12.5 and 50 kg N ha−1 yr−1, respectively). Our data show that changes in soil factors were the main pathway through which N impacted litter decomposition, with rates reduced by ~15% when placed in high N relative to control plots, regardless of litter origin. Litter decomposition was correlated to soil microbiota, with Picea abies litter decomposition positively correlated with gram negative and fungal functional groups. Our results suggest that previous findings of increase soil C accumulation in response to N deposition is likely to occur as a result of changes in soil microbiota rather than altered litter quality.
Multi-layered NiOy/NbOx/NiOy fast drift-free threshold switch with high Ion/Ioff ratio for selector application
Authors: Park Jaehyuk , Hadamek Tobias , Posadas Agham B. , Cha Euijun , Demkov Alexander A. , Hwang Hyunsang 
Published: June 2017

AbstractNbO2 has the potential for a variety of electronic applications due to its electrically induced insulator-to-metal transition (IMT) characteristic. In this study, we find that the IMT behavior of NbO2 follows the field-induced nucleation by investigating the delay time dependency at various voltages and temperatures. Based on the investigation, we reveal that the origin of leakage current in NbOx is partly due to insufficient Schottky barrier height originating from interface defects between the electrodes and NbOx layer. The leakage current problem can be addressed by inserting thin NiOy barrier layers. The NiOy inserted NbOx device is drift-free and exhibits high Ion/Ioff ratio (>5400), fast switching speed (<2 ns), and high operating temperature (>453 K) characteristics which are highly suitable to selector application for x-point memory arrays. We show that NbOx device with NiOx interlayers in series with resistive random access memory (ReRAM) device demonstrates improved readout margin (>29 word lines) suitable for x-point memory array application.
Inhalation toxicity of indoor air pollutants in Drosophila melanogaster using integrated transcriptomics and computational behavior analyses
Authors: Eom Hyun-Jeong , Liu Yuedan , Kwak Gyu-Suk , Heo Muyoung , Song Kyung Seuk , Chung Yun Doo , Chon Tae-Soo , Choi Jinhee 
Published: June 2017

AbstractWe conducted an inhalation toxicity test on the alternative animal model, Drosophila melanogaster, to investigate potential hazards of indoor air pollution. The inhalation toxicity of toluene and formaldehyde was investigated using comprehensive transcriptomics and computational behavior analyses. The ingenuity pathway analysis (IPA) based on microarray data suggests the involvement of pathways related to immune response, stress response, and metabolism in formaldehyde and toluene exposure based on hub molecules. We conducted a toxicity test using mutants of the representative genes in these pathways to explore the toxicological consequences of alterations of these pathways. Furthermore, extensive computational behavior analysis showed that exposure to either toluene or formaldehyde reduced most of the behavioral parameters of both wild-type and mutants. Interestingly, behavioral alteration caused by toluene or formaldehyde exposure was most severe in the p38b mutant, suggesting that the defects in the p38 pathway underlie behavioral alteration. Overall, the results indicate that exposure to toluene and formaldehyde via inhalation causes severe toxicity in Drosophila, by inducing significant alterations in gene expression and behavior, suggesting that Drosophila can be used as a potential alternative model in inhalation toxicity screening.
Metabolic disturbances of non-alcoholic fatty liver resemble the alterations typical for type 2 diabetes
Authors: Brouwers Bram , Schrauwen-Hinderling Vera B. , Jelenik Tomas , Gemmink Anne , Havekes Bas , Bruls Yvonne , Dahlmans Dennis , Roden Michael , Hesselink Matthijs K.C. , Schrauwen Patrick 
Published: June 2017

Non-alcoholic fatty liver (NAFL) is an independent risk factor for the development of type 2 diabetes (T2DM). We examined metabolic perturbations in patients with NAFL, patients with T2DM, and control (CON) subjects with normal intrahepatic lipid (IHL) content.
A two-step (10 mU/m2 /min; 40 mU/m2/min) hyperinsulinemic–euglycemic clamp was performed in 11 NAFL, 13 T2DM, and 11 CON subjects, all matched for BMI, and aerobic fitness. IHL content was measured using proton magnetic resonance spectroscopy. Because of high IHL content variability in T2DM patients, this group was separated into a high IHL content group (IHL ≥ 5.0%, T2DM+NAFL) and a normal IHL content group (IHL &lt; 5.0%, T2DM-non-NAFL) for further analysis.
IHL content was increased in NAFL and T2DM+NAFL subjects (P&lt;0.050 versus CON and T2DM-non-NAFL subjects). Adipose tissue insulin sensitivity index (Adipo-IRi) was higher in NAFL (P&lt;0.050 versus CON and T2DM-non-NAFL subjects) and in T2DM+NAFL subjects (P=0.055 versus CON subjects, P&lt;0.050 versus T2DM-non-NAFL subjects). Suppression of plasma-free fatty acids (P=0.046) was lower in NAFL compared with CON subjects, with intermediate values for T2DM-non-NAFL, and T2DM+NAFL subjects. Suppression of endogenous glucose production (EGP) and insulin-stimulated glucose disposal (ΔRd) was comparable between NAFL, T2DM-non-NAFL, and T2DM+NAFL subjects (all P&gt;0.05), and was lower in comparison with CON subjects (all P&lt;0.01). Metabolic flexibility was lower in T2DM-non-NAFL subjects (P=0.047) and NAFL subjects (P=0.059) compared with CON subjects. Adipo-IRi (r=0.652, P&lt;0.001), hepatic insulin resistance index (HIRi) (r=0.576, P=0.001), and ΔRd (r=−0.653, P&lt;0.001) correlated with IHL content.
Individuals with NAFL suffer from metabolic perturbations to a similar degree as T2DM patients. NAFL is an important feature leading to severe insulin resistance and should be viewed as a serious health threat for the development of T2DM. ClinicalTrials.gov: NCT01317576