bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice
Authors: Tang Xing , Liu Huayang , Srivastava Arunima , Pécot Thierry , Chen Zhong , Wang Qianben , Huang Kun , Sáenz-Robles Maria Teresa , Cantalupo Paul , Pipas James , Leone Gustavo
Published: February 2016

E2F3 and MYC are transcription factors that control cellular proliferation. To study their mechanism of action in the context of a regenerating tissue, we isolated both proliferating (crypts) and non-dividing (villi) cells from wild-type and Rb depleted small intestines of mice and performed ChIP-exo-seq (chromatin immunoprecipitation combined with lambda exonuclease digestion followed by high-throughput sequencing). The genome-wide chromatin occupancy of E2F3 and MYC was determined by mapping sequence reads to the genome and predicting preferred binding sites (peaks). Binding sites could be accurately identified within small regions of only 24 bp-28 bp long, highlighting the precision to which binding peaks can be identified by ChIP-exo-seq. Forty randomly selected E2F3- and MYC-specific binding sites were validated by ChIP-PCR. In addition, we also presented gene expression data sets from wild type, Rb-, E2f3- and Myc-depleted crypts and villi within this manuscript. These represent comprehensive and validated datasets that can be integrated to identify putative direct targets of E2F3 and MYC involved in the control of cellular proliferation in normal and Rb-deficient small intestines.
Associations of Plasma FGF2 Levels and Polymorphisms in the FGF2 Gene with Obesity Phenotypes in Han Chinese Population
Authors: Hao Ruo-Han , Guo Yan , Dong Shan-Shan , Weng Gai-Zhi , Yan Han , Zhu Dong-Li , Chen Xiao-Feng , Chen Jia-Bin , Yang Tie-Lin
Published: February 2016

Obesity is highly heritable, but the specific genes influencing obesity related traits are largely unknown. Fibroblast growth factor 2 (FGF2) could influence adipocyte differentiation. However, the association of FGF2 polymorphisms and obesity remains unclear. This study aimed to investigate the associations of both the plasma FGF2 levels and SNPs in FGF2 gene with obesity phenotypes in Han Chinese populations. Plasma FGF2 levels were measured and subjected to association analyses in 62 subjects. Eleven SNPs in FGF2 were genotyped and tested for associations in a discovery sample of 1,300 subjects. SNPs significantly associated with obesity were subjected to replication in another independent sample of 1,035 subjects. We found that plasma FGF2 levels were positively correlated with fat mass (P = 0.010). Association analyses in the discovery sample identified three SNPs (rs1449683, rs167428, rs308442) significantly associated with fat mass after multiple testing adjustments (P < 0.0045). Subsequent replication study successfully validated one SNP (rs167428) associated with fat mass (Pcombine = 3.46 × 10−5). eQTL analyses revealed that SNPs associated with obesity also affected FGF2 expression. Our findings suggested that high plasma FGF2 level correlated with increased risk of obesity and FGF2 gene polymorphisms could affect individual variances of obesity in Han Chinese population.
Phenotypic and functional alterations of pDCs in lupus-prone mice
Authors: Zhou Zhenyuan , Ma Jianyang , Xiao Chunyuan , Han Xiao , Qiu Rong , Wang Yan , Zhou Yingying , Wu Li , Huang Xinfang , Shen Nan
Published: February 2016

Plasmacytoid dendritic cells (pDCs) were considered to be the major IFNα source in systemic lupus erythematosus (SLE) but their phenotype and function in different disease status have not been well studied. To study the function and phenotype of pDCs in lupus-prone mice we used 7 strains of lupus-prone mice including NZB/W F1, NZB, NZW, NZM2410, B6.NZMSle1/2/3, MRL/lpr and BXSB/Mp mice and C57BL/6 as control mice. Increased spleen pDC numbers were found in most lupus mice compared to C57BL/6 mice. The IFNα-producing ability of BM pDCs was similar between lupus and C57BL/6 mice, whereas pDCs from the spleens of NZB/W F1 and NZB mice produced more IFNα than pDCs from the spleens of C57BL/6 mice. Furthermore, spleen pDCs from MRL-lpr and NZM2410 mice showed increased responses to Tlr7 and Tlr9, respectively. As the disease progressed, IFN signature were evaluated in both BM and spleen pDC from lupus prone mice and the number of BM pDCs and their ability to produce IFNα gradually decreased in lupus-prone mice. In conclusion, pDC are activated alone with disease development and its phenotype and function differ among lupus-prone strains and these differences may contribute to the development of lupus in these mice.
The heterogeneous energy landscape expression of KWW relaxation
Authors: Wu J. H. , Jia Q.
Published: February 2016

Here we show a heterogeneous energy landscape approach to describing the Kohlrausch-Williams-Watts (KWW) relaxation function. For a homogeneous dynamic process, the distribution of free energy landscape is first proposed, revealing the significance of rugged fluctuations. In view of the heterogeneous relaxation given in two dynamic phases and the transmission coefficient in a rate process, we obtain a general characteristic relaxation time distribution equation for the KWW function in a closed, analytic form. Analyses of numerical computation show excellent accuracy, both in time and frequency domains, in the convergent performance of the heterogeneous energy landscape expression and shunning the catastrophic truncations reported in the previous work. The stretched exponential β, closely associated to temperature and apparent correlation with one dynamic phase, reveals a threshold value of 1/2 defining different behavior of the probability density functions. Our work may contribute, for example, to in-depth comprehension of the dynamic mechanism of glass transition, which cannot be provided by existing approaches.
Ab initio molecular dynamics simulation of the effects of stacking faults on the radiation response of 3C-SiC
Authors: Jiang M. , Peng S. M. , Zhang H. B. , Xu C. H. , Xiao H. Y. , Zhao F. A. , Liu Z. J. , Zu X. T.
Published: February 2016

In this study, an ab initio molecular dynamics method is employed to investigate how the existence of stacking faults (SFs) influences the response of SiC to low energy irradiation. It reveals that the C and Si atoms around the SFs are generally more difficult to be displaced than those in unfaulted SiC, and the corresponding threshold displacement energies for them are generally larger, indicative of enhanced radiation tolerance caused by the introduction of SFs, which agrees well with the recent experiment. As compared with the unfaulted state, more localized point defects are generated in faulted SiC. Also, the efficiency of damage production for Si recoils is generally higher than that of C recoils. The calculated potential energy increases for defect generation in SiC with intrinsic and extrinsic SFs are found to be higher than those in unfaulted SiC, due to the stronger screen-Coulomb interaction between the PKA and its neighbors. The presented results provide a fundamental insight into the underlying mechanism of displacement events in faulted SiC and will help to advance the understanding of the radiation response of SiC with and without SFs.
Albuminuria, Cerebrovascular Disease and Cortical Atrophy: among Cognitively Normal Elderly Individuals
Authors: Cho Eun Bin , Shin Hee-Young , Park Sang Eon , Chun Phillip , Jang Hye Ryoun , Yang Jin-ju , Kim Hee Jin , Kim Yeo Jin , Jung Na-Yeon , Lee Jin San , Lee Juyoun , Jang Young Kyoung , Jang Eun Young , Kang Mira , Lee Jong-Min , Kim Changsoo , Min Ju-Hong , Ryu Seungho , Na Duk L. , Seo Sang Won
Published: February 2016

We tested the hypothesis that decreased glomerular filtration rate and albuminuria have different roles in brain structure alterations. We enrolled 1,215 cognitively normal individuals, all of whom underwent high-resolution T1-weighted volumetric magnetic resonance imaging scans. The cerebral small vessel disease burdens were assessed with white matter hyperintensities (WMH), lacunes, and microbleeds. Subjects were considered to have an abnormally elevated urine albumin creatinine ratio if the value was ≥17 mg/g for men and ≥25 mg/g for women. Albuminuria, but not estimated glomerular filtration rate (eGFR), was associated with increased WMH burdens (p = 0.002). The data was analyzed after adjusting for age, sex, education, history of hypertension, diabetes mellitus, hyperlipidemia, ischemic heart disease, stroke, total cholesterol level, body mass index, status of smoking and alcohol drinking, and intracranial volume. Albuminuria was also associated with cortical thinning, predominantly in the frontal and occipital regions (both p < 0.01) in multiple linear regression analysis. However, eGFR was not associated with cortical thickness. Furthermore, path analysis for cortical thickness showed that albuminuria was associated with frontal thinning partially mediated by WMH burdens. The assessment of albuminuria is needed to improve our ability to identify individuals with high risk for cognitive impairments, and further institute appropriate preventive measures.
Nanoscale optical interferometry with incoherent light
Authors: Li Dongfang , Feng Jing , Pacifici Domenico
Published: February 2016

Optical interferometry has empowered an impressive variety of biosensing and medical imaging techniques. A widely held assumption is that devices based on optical interferometry require coherent light to generate a precise optical signature in response to an analyte. Here we disprove that assumption. By directly embedding light emitters into subwavelength cavities of plasmonic interferometers, we demonstrate coherent generation of surface plasmons even when light with extremely low degrees of spatial and temporal coherence is employed. This surprising finding enables novel sensor designs with cheaper and smaller light sources and consequently increases accessibility to a variety of analytes, such as biomarkers in physiological fluids, or even airborne nanoparticles. Furthermore, these nanosensors can now be arranged along open detection surfaces and in dense arrays, accelerating the rate of parallel target screening used in drug discovery, among other high volume and high sensitivity applications.
Diagnostic Accuracy of Transcranial Sonography of the Substantia Nigra in Parkinson’s disease: A Systematic Review and Meta-analysis
Authors: Li Dun-Hui , He Ya-Chao , Liu Jun , Chen Sheng-Di
Published: February 2016

A large number of articles have reported substantia nigra hyperechogenicity in Parkinson’s disease (PD) and have assessed the diagnostic accuracy of transcranial sonography (TCS); however, the conclusions are discrepant. Consequently, this systematic review and meta-analysis aims to consolidate the available observational studies and provide a comprehensive evaluation of the clinical utility of TCS in PD. Totally, 31 studies containing 4,386 participants from 13 countries were included. A random effects model was utilized to pool the effect sizes. Meta-regression and sensitivity analysis were performed to explore potential heterogeneity. Overall diagnostic accuracy of TCS in differentiating PD from normal controls was quite high, with a pooled sensitivity of 0.83 (95% CI: 0.81–0.85) and a pooled specificity of 0.87 (95% CI: 0.85–0.88). The positive likelihood ratio, the negative likelihood ratio and diagnostic odds ratio were calculated 6.94 (95% CI: 5.09–9.48), 0.19 (95% CI: 0.16–0.23) and 42.89 (95% CI: 30.03–61.25) respectively. Our systematic review of the literature and meta-analysis suggest that TCS has high diagnostic accuracy in the diagnosis of PD when compared to healthy control.
Post-illumination activity of SnO2 nanoparticle-decorated Cu2O nanocubes by H2O2 production in dark from photocatalytic “memory”
Authors: Liu Lingmei , Sun Wuzhu , Yang Weiyi , Li Qi , Shang Jian Ku
Published: February 2016

Most photocatalysts only function under illumination, while many potential applications require continuous activities in dark. Thus, novel photocatalysts should be developed, which could store part of their photoactivity in “memory” under illumination and then be active from this “memory” after the illumination is turned off for an extended period of time. Here a novel composite photocatalyst of SnO2 nanoparticle-decorated Cu2O nanocubes is developed. Their large conduction band potential difference and the inner electrostatic field formed in the p-n heterojunction provide a strong driving force for photogenerated electrons to move from Cu2O to SnO2 under visible light illumination, which could then be released to react with O2 in dark to produce H2O2 for its post-illumination activity. This work demonstrates that the selection of decoration components for photocatalysts with the post-illumination photocatalytic “memory” could be largely expanded to semiconductors with conduction band potentials less positive than the two-electron reduction potential of O2.
Local electron-electron interaction strength in ferromagnetic nickel determined by spin-polarized positron annihilation
Authors: Ceeh Hubert , Weber Josef Andreas , Böni Peter , Leitner Michael , Benea Diana , Chioncel Liviu , Ebert Hubert , Minár Jan , Vollhardt Dieter , Hugenschmidt Christoph
Published: February 2016

We employ a positron annihilation technique, the spin-polarized two-dimensional angular correlation of annihilation radiation (2D-ACAR), to measure the spin-difference spectra of ferromagnetic nickel. The experimental data are compared with the theoretical results obtained within a combination of the local spin density approximation (LSDA) and the many-body dynamical mean-field theory (DMFT). We find that the self-energy defining the electronic correlations in Ni leads to anisotropic contributions to the momentum distribution. By direct comparison of the theoretical and experimental results we determine the strength of the local electronic interaction U in ferromagnetic Ni as 2.0 ± 0.1 eV.
Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection
Authors: Crellen Thomas , Allan Fiona , David Sophia , Durrant Caroline , Huckvale Thomas , Holroyd Nancy , Emery Aidan M. , Rollinson David , Aanensen David M. , Berriman Matthew , Webster Joanne P. , Cotton James A.
Published: February 2016

Schistosoma mansoniis a parasitic fluke that infects millions of people in the developing world. This study presents the first application of population genomics toS. mansonibased on high-coverage resequencing data from 10 global isolates and an isolate of the closely-relatedSchistosoma rodhaini, which infects rodents. Using population genetic tests, we document genes under directional and balancing selection inS. mansonithat may facilitate adaptation to the human host. Coalescence modeling reveals the speciation ofS. mansoniandS. rodhainias 107.5–147.6KYA, a period which overlaps with the earliest archaeological evidence for fishing in Africa. Our results indicate thatS. mansonioriginated in East Africa and experienced a decline in effective population size 20–90KYA, before dispersing across the continent during the Holocene. In addition, we find strong evidence thatS. mansonimigrated to the New World with the 16–19thCentury Atlantic Slave Trade.
HIV-1 Vaccine-elicited Antibodies Reverted to Their Inferred Naive Germline Reveal Associations between Binding Affinity and in vivo Activation
Authors: Dai Kaifan , Khan Salar N , Wang Yimeng , He Linling , Guenaga Javier , Ingale Jidnyasa , Sundling Christopher , O’Dell Sijy , McKee Krisha , Phad Ganesh , Corcoran Martin , Wilson Richard , Mascola John R , Zhu Jiang , Li Yuxing , Hedestam Gunilla B Karlsson , Wyatt Richard T
Published: February 2016

The elicitation of HIV-1 broadly neutralizing antibodies following envelope glycoprotein (Env) vaccination is exceedingly difficult. Suboptimal engagement of naïve B cells is suggested to limit these low frequency events, especially at the conserved CD4bs. Here, we analyzed CD4bs-directed monoclonal antibodies (mAbs) elicited by YU2 gp140-foldon trimers in a non-human primate by selective sorting using CD4bs “knock out” trimers. Following two inoculations, the CD4bs-directed mAbs efficiently recognized the eliciting immunogen in their affinity-maturing state but did not recognize CD4bs-defective probes. We reverted these mAbs to their most likely inferred germline (igL) state, leaving the HCDR3 unaltered, to establish correlates of in vitro affinity to in vivo activation. Most igL-reverted mAbs bound the eliciting gp140 immunogen, indicating that CD4bs-directed B cells possessing reasonable affinity existed in the naïve repertoire. We detected relatively high affinities for the majority of the igL mAbs to gp120 and of Fabs to gp140, which, as expected, increased when the antibodies ‘matured’ following vaccination. Affinity increases were associated with slower off-rates as well as with acquisition of neutralizing capacity. These data reveal in vitro binding properties associated with in vivo activation that result in functional archiving of antigen-specific B cells elicited by a complex glycoprotein antigen following immunization.
Amyloidβ Peptides in interaction with raft-mime model membranes: a neutron reflectivity insight
Authors: Rondelli Valeria , Brocca Paola , Motta Simona , Messa Massimo , Colombo Laura , Salmona Mario , Fragneto Giovanna , Cantù Laura , Del Favero Elena
Published: February 2016

The role of first-stage β–amyloid aggregation in the development of the Alzheimer disease, is widely accepted but still unclear. Intimate interaction with the cell membrane is invoked. We designed Neutron Reflectometry experiments to reveal the existence and extent of the interaction between β–amyloid (Aβ) peptides and a lone customized biomimetic membrane and their dependence on the aggregation state of the peptide. The membrane, asymmetrically containing phospholipids, GM1 and cholesterol in biosimilar proportion, is a model for a raft, a putative site for amyloid-cell membrane interaction. We found that the structured-oligomer of Aβ(1-42), its most acknowledged membrane-active state, is embedded as such into the external leaflet of the membrane. Conversely, the Aβ(1-42) unstructured early-oligomers deeply penetrate the membrane, likely mimicking the interaction at neuronal cell surfaces, when the Aβ(1-42) is cleaved from APP protein and the membrane constitutes a template for its further structural evolution. Moreover, the smaller Aβ(1-6) fragment, the N-terminal portion of Aβ, was also used. Aβ N-terminal is usually considered as involved in oligomer stabilization but not in the peptide-membrane interaction. Instead, it was seen to remove lipids from the bilayer, thus suggesting its role, once in the whole peptide, in membrane leakage, favouring peptide recruitment.
The establishment of species-specific primers for the molecular identification of ten stored-product psocids based on ITS2 rDNA
Authors: Zhao Zi-Hua , Cui Bing-Yi , Li Zhi-Hong , Jiang Fan , Yang Qian-Qian , Kučerová Zuzana , Stejskal Václav , Opit George , Cao Yang , Li Fu-Jun
Published: February 2016

Psocids are important stored product pests found worldwide that can be spread through grain trade. Most stored-product psocids, including eggs, nymphs, and adults, are very small (~1 mm) and difficult to identify morphologically. Here, we collected 10 economically important stored-productLiposcelisspp. psocids (L. bostrychophila,L. entomophila,L. decolor,L. paeta,L. brunnea,L. corrodens,L. mendax,L. rufa,L. pearmani, andL. tricolor) from 35 geographical locations in 5 countries (China, Czech Republic, Denmark, Germany, and the United States). The ITS2 rDNA gene was extracted and sequenced. The interspecific genetic distance of the stored-product psocids was significantly higher than the intraspecific genetic distance according to the barcoding gap analysis. Ten pairs of species-specific primers based on the ITS2 rDNA were developed for psocid identification. The sensitivity estimation indicated that the species-specific primers could correctly amplify the target ITS2 gene and successfully identify psocids at 1.0 ng/mL. Additionally, these species-specific primers could quantify specificity and identify 10 stored-product psocids; this approach could also be used to accurately identify other stored-product psocids. This work provides a practical approach for the precise examination of 10 stored-product psocid species and also contributes to the development of an identification method using ITS2 rDNA.
A first-principles study on the phonon transport in layered BiCuOSe
Authors: Shao Hezhu , Tan Xiaojian , Liu Guo-Qiang , Jiang Jun , Jiang Haochuan
Published: February 2016

First-principles calculations are employed to investigate the phonon transport of BiCuOSe. Our calculations reproduce the lattice thermal conductivity of BiCuOSe. The calculated grüneisen parameter is 2.4 ~ 2.6 at room temperature, a fairly large value indicating a strong anharmonicity in BiCuOSe, which leads to its ultralow lattice thermal conductivity. The contribution to total thermal conductivity from high-frequency optical phonons, which are mostly contributed by the vibrations of O atoms, is larger than 1/3, remarkably different from the usual picture with very little contribution from high-frequency optical phonons. Our calculations show that both the high group velocities and low scattering processes involved make the high-frequency optical modes contribute considerably to the total lattice thermal conductivity. In addition, we show that the sound velocity and bulk modulus along a and c axes exhibit strong anisotropy, which results in the anisotropic thermal conductivity in BiCuOSe.
Serum microRNA microarray analysis identifies miR-4429 and miR-4689 are potential diagnostic biomarkers for biliary atresia
Authors: Dong Rui , Shen Zhen , Zheng Chao , Chen Gong , Zheng Shan
Published: February 2016

This study aimed to investigate pathogenesis and novel diagnostic biomarkers of biliary atresia (BA). Serum samples from infants with BA and non-BA neonatal cholestasis (NC) were collected for miRNA microarray analysis and then differentially expressed miRNAs were screened. Differentially expressed miRNAs were validated by qRT-PCR using an independent serum samples from infants with BA and NC. Diagnostic utility of validated miRNAs was further analyzed using serum samples by receiver-operating characteristic curve analysis. Totally, 13 differentially expressed miRNAs were identified including 11 down-regulated and 2 up-regulated ones. Target genes of hsa-miR-4429 and hsa-miR-4689 were significantly involved in FoxO signaling pathway. Eight differentially expressed miRNAs were chosen for validation by qRT-PCR analysis and four miRNAs (hsa-miR-150-3p, hsa-miR-4429, hsa-miR-4689 and hsa-miR-92a-3p) were differentially expressed. The area under the curve of hsa-miR-4429 and hsa-miR-4689 was 0.789 (sensitivity = 83.33%, specificity = 80.00%) and 0.722 (sensitivity = 66.67%, specificity = 80.00%), respectively. Differentially expressed miRNAs including hsa-miR-4429 and hsa-miR-4689 might play critical roles in BA by regulating their target genes and these two miRNAs may have the potential to become diagnostic biomarkers.
Interface Structure of MoO3 on Organic Semiconductors
Authors: White Robin T. , Thibau Emmanuel S. , Lu Zheng-Hong
Published: February 2016

We have systematically studied interface structure formed by vapor-phase deposition of typical transition metal oxide MoO3on organic semiconductors. Eight organic hole transport materials have been used in this study. Ultraviolet photoelectron spectroscopy and X-ray photoelectron spectroscopy are used to measure the evolution of the physical, chemical and electronic structure of the interfaces at various stages of MoO3deposition on these organic semiconductor surfaces. For the interface physical structure, it is found that MoO3diffuses into the underlying organic layer, exhibiting a trend of increasing diffusion with decreasing molecular molar mass. For the interface chemical structure, new carbon and molybdenum core-level states are observed, as a result of interfacial electron transfer from organic semiconductor to MoO3. For the interface electronic structure, energy level alignment is observed in agreement with the universal energy level alignment rule of molecules on metal oxides, despite deposition order inversion.
Iron mitigates DMT1-mediated manganese cytotoxicity via the ASK1-JNK signaling axis: Implications of iron supplementation for manganese toxicity
Authors: Tai Yee Kit , Chew Katherine C. M. , Tan Bryce W. Q. , Lim Kah-Leong , Soong Tuck Wah
Published: February 2016

Manganese (Mn2+) neurotoxicity from occupational exposure is well documented to result in a Parkinson-like syndrome. Although the understanding of Mn2+ cytotoxicity is still incomplete, both Mn2+ and Fe2+ can be transported via the divalent metal transporter 1 (DMT1), suggesting that competitive uptake might disrupt Fe2+ homeostasis. Here, we found that DMT1 overexpression significantly enhanced Mn2+ cytoplasmic accumulation and JNK phosphorylation, leading to a reduction in cell viability. Although a robust activation of autophagy was observed alongside these changes, it did not trigger autophagic cell death, but was instead shown to be essential for the degradation of ferritin, which normally sequesters labile Fe2+. Inhibition of ferritin degradation through the neutralization of lysosomal pH resulted in increased ferritin and enhanced cytoplasmic Fe2+ depletion. Similarly, direct Fe2+ chelation also resulted in aggravated Mn2+-mediated JNK phosphorylation, while Fe2+ repletion protected cells and this occurs via the ASK1-thioredoxin pathway. Taken together, our study presents the novel findings that Mn2+ cytotoxicity involves the depletion of the cytoplasmic Fe2+ pool and the increase in autophagy-lysosome activity is important to maintain Fe2+ homeostasis. Thus, Fe2+ supplementation could have potential applications in the prevention and treatment of Mn2+-mediated toxicity.
Competition in the presence of aging: dominance, coexistence, and alternation between states
Authors: Pérez Toni , Klemm Konstantin , Eguíluz Víctor M.
Published: February 2016

We study the stochastic dynamics of coupled states with transition probabilities depending on local persistence, this is, the time since a state has changed. When the system has a preference to adopt older states the system orders quickly due to the dominance of old states. When preference for new states prevails, the system can show coexistence of states or synchronized collective behavior resulting in long ordering times. In this case, the magnetization of the system oscillates around zero. Finally we discuss a potential application in social systems.
Spectroscopic Study of Terahertz Generation in Mid-Infrared Quantum Cascade Lasers
Authors: Jiang Yifan , Vijayraghavan Karun , Jung Seungyong , Jiang Aiting , Kim Jae Hyun , Demmerle Frederic , Boehm Gerhard , Amann Markus C. , Belkin Mikhail A.
Published: February 2016

Terahertz quantum cascade laser sources based on intra-cavity difference-frequency generation are currently the only room-temperature mass-producible diode-laser-like emitters of coherent 1–6 THz radiation. Device performance has improved dramatically over the past few years to reach milliwatt-level power output and broad tuning from 1.2 to 5.9 THz, all at room-temperature. Terahertz output in these sources originates from intersubband optical nonlinearity in the laser active region. Here we report the first comprehensive spectroscopic study of the optical nonlinearity and investigate its dependence on the mid-infrared pump frequencies. Our work shows that the terahertz generation efficiency can vary by a factor of 2 or greater depending on the spectral position of the mid-infrared pumps for a fixed THz difference-frequency. We have also measured for the first time the linewidth for transitions between the lower quantum cascade laser states, which is critical for determining terahertz nonlinearity and predicting optical loss in quantum cascade laser waveguides.
Hierarchically structured activated carbon for ultracapacitors
Authors: Kim Mok-Hwa , Kim Kwang-Bum , Park Sun-Min , Roh Kwang Chul
Published: February 2016

To resolve the pore-associated bottleneck problem observed in the electrode materials used for ultracapacitors, which inhibits the transport of the electrolyte ions, we designed hierarchically structured activated carbon (HAC) by synthesizing a mesoporous silica template/carbon composite and chemically activating it to simultaneously remove the silica template and increase the pore volume. The resulting HAC had a well-designed, unique porous structure, which allowed for large interfaces for efficient electric double-layer formation. Given the unique characteristics of the HAC, we believe that the developed synthesis strategy provides important insights into the design and fabrication of hierarchical carbon nanostructures. The HAC, which had a specific surface area of 1,957 m2 g−1, exhibited an extremely high specific capacitance of 157 F g−1 (95 F cc−1), as well as a high rate capability. This indicated that it had superior energy storage capability and was thus suitable for use in advanced ultracapacitors.
Detecting signatures of positive selection associated with musical aptitude in the human genome
Authors: Liu Xuanyao , Kanduri Chakravarthi , Oikkonen Jaana , Karma Kai , Raijas Pirre , Ukkola-Vuoti Liisa , Teo Yik-Ying , Järvelä Irma
Published: February 2016

Abilities related to musical aptitude appear to have a long history in human evolution. To elucidate the molecular and evolutionary background of musical aptitude, we compared genome-wide genotyping data (641 K SNPs) of 148 Finnish individuals characterized for musical aptitude. We assigned signatures of positive selection in a case-control setting using three selection methods: haploPS, XP-EHH and FST. Gene ontology classification revealed that the positive selection regions contained genes affecting inner-ear development. Additionally, literature survey has shown that several of the identified genes were known to be involved in auditory perception (e.g. GPR98, USH2A), cognition and memory (e.g. GRIN2B, IL1A, IL1B, RAPGEF5), reward mechanisms (RGS9), and song perception and production of songbirds (e.g. FOXP1, RGS9, GPR98, GRIN2B). Interestingly, genes related to inner-ear development and cognition were also detected in a previous genome-wide association study of musical aptitude. However, the candidate genes detected in this study were not reported earlier in studies of musical abilities. Identification of genes related to language development (FOXP1 and VLDLR) support the popular hypothesis that music and language share a common genetic and evolutionary background. The findings are consistent with the evolutionary conservation of genes related to auditory processes in other species and provide first empirical evidence for signatures of positive selection for abilities that contribute to musical aptitude.
Niclosamide inhibits leaf blight caused by Xanthomonas oryzae in rice
Authors: Kim Sung-Il , Song Jong Tae , Jeong Jin-Yong , Seo Hak Soo
Published: February 2016

Rice leaf blight, which is caused by the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo), results in huge losses in grain yield. Here, we show that Xoo-induced rice leaf blight is effectively controlled by niclosamide, an oral antihelminthic drug and molluscicide, which also functions as an anti-tumor agent. Niclosamide directly inhibited the growth of the three Xoo strains PXO99, 10208 and K3a. Niclosamide moved long distances from the site of local application to distant rice tissues. Niclosamide also increased the levels of salicylate and induced the expression of defense-related genes such as OsPR1 and OsWRKY45, which suppressed Xoo-induced leaf wilting. Niclosamide had no detrimental effects on vegetative/reproductive growth and yield. These combined results indicate that niclosamide can be used to block bacterial leaf blight in rice with no negative side effects.
Mitigation of Coral Reef Warming Across the Central Pacific by the Equatorial Undercurrent: A Past and Future Divide
Authors: Karnauskas Kristopher B. , Cohen Anne L. , Gove Jamison M.
Published: February 2016

Global climate models (GCMs) predict enhanced warming and nutrient decline across the central tropical Pacific as trade winds weaken with global warming. Concurrent changes in circulation, however, have potential to mitigate these effects for equatorial islands. The implications for densely populated island nations, whose livelihoods depend on ecosystem services, are significant. A unique suite of in situ measurements coupled with state-of-the-art GCM simulations enables us to quantify the mitigation potential of the projected circulation change for three coral reef ecosystems under two future scenarios. Estimated historical trends indicate that over 100% of the large-scale warming to date has been offset locally by changes in circulation, while future simulations predict a warming mitigation effect of only 5–10% depending on the island. The pace and extent to which GCM projections overwhelm historical trends will play a key role in defining the fate of marine ecosystems and island communities across the tropical Pacific.
Correction: Corrigendum: Overexpression of miRNA-497 inhibits tumor angiogenesis by targeting VEGFR2
Authors: Tu Yingfeng , Liu Li , Zhao Dongliang , Liu Youbin , Ma Xiaowei , Fan Yuhua , Wan Lin , Huang Tao , Cheng Zhen , Shen Baozhong
Published: February 2016

Scientific Reports 5: Article number: 13827; published online: 08 September 2015; updated: 16 February 2016. In this Article, Figure 4 is incorrect. The correct Figure 4 appears below as Figure 1.
Quantitative molecular phenotyping with topically applied SERS nanoparticles for intraoperative guidance of breast cancer lumpectomy
Authors: Wang Yu , Kang Soyoung , Khan Altaz , Ruttner Gabriel , Leigh Steven Y. , Murray Melissa , Abeytunge Sanjee , Peterson Gary , Rajadhyaksha Milind , Dintzis Suzanne , Javid Sara , Liu Jonathan T.C.
Published: February 2016

There is a need to image excised tissues during tumor-resection procedures in order to identify residual tumors at the margins and to guide their complete removal. The imaging of dysregulated cell-surface receptors is a potential means of identifying the presence of diseases with high sensitivity and specificity. However, due to heterogeneities in the expression of protein biomarkers in tumors, molecular-imaging technologies should ideally be capable of visualizing a multiplexed panel of cancer biomarkers. Here, we demonstrate that the topical application and quantification of a multiplexed cocktail of receptor-targeted surface-enhanced Raman scattering (SERS) nanoparticles (NPs) enables rapid quantitative molecular phenotyping (QMP) of the surface of freshly excised tissues to determine the presence of disease. In order to mitigate the ambiguity due to nonspecific sources of contrast such as off-target binding or uneven delivery, a ratiometric method is employed to quantify the specific vs. nonspecific binding of the multiplexed NPs. Validation experiments with human tumor cell lines, fresh human tumor xenografts in mice and fresh human breast specimens demonstrate that QMP imaging of excised tissues agrees with flow cytometry and immunohistochemistry and that this technique may be achieved in less than 15 minutes for potential intraoperative use in guiding breast-conserving surgeries.
Nocturnally migrating songbirds drift when they can and compensate when they must
Authors: Horton Kyle G. , Van Doren Benjamin M. , Stepanian Phillip M. , Hochachka Wesley M. , Farnsworth Andrew , Kelly Jeffrey F.
Published: February 2016

The shortest possible migratory route for birds is not always the best route to travel. Substantial research effort has established that birds in captivity are capable of orienting toward the direction of an intended goal, but efforts to examine how free-living birds use navigational information under conditions that potentially make direct flight toward that goal inefficient have been limited in spatiotemporal scales and in the number of individuals observed because of logistical and technological limitations. Using novel and recently developed techniques for analysis of Doppler polarimetric weather surveillance radar data, we examined two impediments for nocturnally migrating songbirds in eastern North America following shortest-distance routes: crosswinds and oceans. We found that migrants in flight often drifted sideways on crosswinds, but most strongly compensated for drift when near the Atlantic coast. Coastal migrants’ tendency to compensate for wind drift also increased through the night, while no strong temporal differences were observed at inland sites. Such behaviors suggest that birds migrate in an adaptive way to conserve energy by assessing while airborne the degree to which they must compensate for wind drift.
Enhancing performance and uniformity of CH3NH3PbI3−xClx perovskite solar cells by air-heated-oven assisted annealing under various humidities
Authors: Zhou Qing , Jin Zhiwen , Li Hui , Wang Jizheng
Published: February 2016

To fabricate high-performance metal-halide perovskite solar cells, a thermal annealing process is indispensable in preparing high quality perovskite film. And usually such annealing is performed on hot plate. However hot-plate annealing could cause problems such as inhomogeneous heating (induced by non-tight contact between the sample and the plate), it is also not fit for large scale manufactory. In this paper, we conduct the annealing process in air-heated oven under various humidity environments, and compared the resulted films (CH3NH3PbI3−xClx) and devices (Al/PC61BM/CH3NH3PbI3−xClx/PEDOT:PSS/ITO/glass) with that obtained via hot-plate annealing. It is found that the air-heated-oven annealing is superior to the hot-plate annealing: the annealing time is shorter, the films are more uniform, and the devices exhibit higher power conversion efficiency and better uniformity. The highest efficiencies achieved for the oven and hot-plate annealing processes are 14.9% and 13.5%, and the corresponding standard deviations are 0.5% and 0.8%, respectively. Our work here indicates that air-heated-oven annealing could be a more reliable and more efficient way for both lab research and large-scale production.
Facile synthesis of flexible macroporous polypropylene sponges for separation of oil and water
Authors: Wang Guowei , Uyama Hiroshi
Published: February 2016

Oil spill disasters always occur accidentally, accompanied by the release of plenty of crude oil that could spread quickly over a wide area, creating enormous damage to the fragile marine ecological system. Therefore, the facile large-scale synthesis of hydrophobic three-dimensional (3-D) porous sorbents from low cost raw materials is in urgent demand. In this study, we report the facile template-free synthesis of polypropylene (PP) sponge by using a thermally-induced phase separation (TIPS) technique. The obtained sponge showed macroporous structure, excellent mechanical property, high hydrophobicity and superoleophilicity. Oil could be separated from an oil/water mixture by simple immersing the sponge into the mixture and subsequent squeezing the sponge. All of these features make this sponge the most promising oil sorbent that will replace commercial non-woven PP fabrics.
Demonstration of Synaptic Behaviors and Resistive Switching Characterizations by Proton Exchange Reactions in Silicon Oxide
Authors: Chang Yao-Feng , Fowler Burt , Chen Ying-Chen , Zhou Fei , Pan Chih-Hung , Chang Ting-Chang , Lee Jack C.
Published: February 2016

We realize a device with biological synaptic behaviors by integrating silicon oxide (SiOx) resistive switching memory with Si diodes. Minimal synaptic power consumption due to sneak-path current is achieved and the capability for spike-induced synaptic behaviors is demonstrated, representing critical milestones for the use of SiO2–based materials in future neuromorphic computing applications. Biological synaptic behaviors such as long-term potentiation (LTP), long-term depression (LTD) and spike-timing dependent plasticity (STDP) are demonstrated systematically using a comprehensive analysis of spike-induced waveforms and represent interesting potential applications for SiOx-based resistive switching materials. The resistive switching SET transition is modeled as hydrogen (proton) release from (SiH)2 to generate the hydrogen bridge defect and the RESET transition is modeled as an electrochemical reaction (proton capture) that re-forms (SiH)2. The experimental results suggest a simple, robust approach to realize programmable neuromorphic chips compatible with large-scale CMOS manufacturing technology.
Genetic analysis of arsenic accumulation in maize using QTL mapping
Authors: Fu Zhongjun , Li Weihua , Xing Xiaolong , Xu Mengmeng , Liu Xiaoyang , Li Haochuan , Xue Yadong , Liu Zonghua , Tang Jihua
Published: February 2016

Arsenic (As) is a toxic heavy metal that can accumulate in crops and poses a threat to human health. The genetic mechanism of As accumulation is unclear. Herein, we used quantitative trait locus (QTL) mapping to unravel the genetic basis of As accumulation in a maize recombinant inbred line population derived from the Chinese crossbred variety Yuyu22. The kernels had the lowest As content among the different maize tissues, followed by the axes, stems, bracts and leaves. Fourteen QTLs were identified at each location. Some of these QTLs were identified in different environments and were also detected by joint analysis. Compared with the B73 RefGen v2 reference genome, the distributions and effects of some QTLs were closely linked to those of QTLs detected in a previous study; the QTLs were likely in strong linkage disequilibrium. Our findings could be used to help maintain maize production to satisfy the demand for edible corn and to decrease the As content in As-contaminated soil through the selection and breeding of As pollution-safe cultivars.
Chemical control of xylem differentiation by thermospermine, xylemin and auxin
Authors: Yoshimoto Kaori , Takamura Hiroyoshi , Kadota Isao , Motose Hiroyasu , Takahashi Taku
Published: February 2016

The xylem conducts water and minerals from the root to the shoot and provides mechanical strength to the plant body. The vascular precursor cells of the procambium differentiate to form continuous vascular strands, from which xylem and phloem cells are generated in the proper spatiotemporal pattern. Procambium formation and xylem differentiation are directed by auxin. In angiosperms, thermospermine, a structural isomer of spermine, suppresses xylem differentiation by limiting auxin signalling. However, the process of auxin-inducible xylem differentiation has not been fully elucidated and remains difficult to manipulate. Here, we found that an antagonist of spermidine can act as an inhibitor of thermospermine biosynthesis and results in excessive xylem differentiation, which is a phenocopy of a thermospermine-deficient mutant acaulis5 in Arabidopsis thaliana. We named this compound xylemin owing to its xylem-inducing effect. Application of a combination of xylemin and thermospermine to wild-type seedlings negates the effect of xylemin, whereas co-treatment with xylemin and a synthetic proauxin, which undergoes hydrolysis to release active auxin, has a synergistic inductive effect on xylem differentiation. Thus, xylemin may serve as a useful transformative chemical tool not only for the study of thermospermine function in various plant species but also for the control of xylem induction and woody biomass production.
Diagnosis of adults Xp11.2 translocation renal cell carcinoma by immunohistochemistry and FISH assays: clinicopathological data from ethnic Chinese population
Authors: Qu Yuanyuan , Gu Chengyuan , Wang Hongkai , Chang Kun , Yang Xiaoqun , Zhou Xiaoyan , Dai Bo , Zhu Yao , Shi Guohai , Zhang Hailiang , Ye Dingwei
Published: February 2016

This study aimed to assess the utility of transcription factor E3 (TFE3) break-apart fluorescence in situ hybridization (FISH) assay in diagnosis of Xp11.2 translocation renal cell carcinoma (Xp11.2 RCC) and to compare the clinicopathological features between adult Xp11.2 RCC and non-Xp11.2 RCC. 76 pathologically suspected Xp11.2 RCCs were recruited from our institution. Both TFE3 immunohistochemistry (IHC) and TFE3 FISH assay were performed for the entire cohort. The progression-free survival (PFS) and overall survival (OS) curves were estimated using the Kaplan-Meier method. FISH analysis confirmed 30 Xp11.2 RCCs, including 28 cases with positive TFE3 immunostaining and 2 cases with negative immunostaining. The false-positive and false-negative rates were 6.7% (2/30) and 4.3% (2/46), respectively, for TFE3 IHC compared with FISH assay. Xp11.2 RCC was significantly associated with higher pathological stage and Fuhrman nuclear grade compared with non-Xp11.2 RCC (P < 0.05). The median PFS and OS for TFE3 FISH-positive group were 13.0 months (95% CI, 8.4–17.6 months) and 50.0 months (95% CI, 27.6–72.4 months), respectively, while the median PFS and OS had not been reached for TFE3 FISH-negative group. In conclusion, TFE3 break-apart FISH assay is a highly useful and standard diagnostic method for Xp11.2 RCC. Adult Xp11.2 RCC is clinically aggressive and often presents at advanced stage with poor prognosis.
Non-Radiative Carrier Recombination Enhanced by Two-Level Process: A First-Principles Study
Authors: Yang Ji-Hui , Shi Lin , Wang Lin-Wang , Wei Su-Huai
Published: February 2016

Non-radiative recombination plays an important role in the performance of optoelectronic semiconductor devices such as solar cells and light-emitting diodes. Most textbook examples assume that the recombination process occurs through a single defect level, where one electron and one hole are captured and recombined. Based on this simple picture, conventional wisdom is that only defect levels near the center of the bandgap can be effective recombination centers. Here, we present a new two-level recombination mechanism: first, one type of carrier is captured through a defect level forming a metastable state; then the local defect configuration rapidly changes to a stable state, where the other type of carrier is captured and recombined through another defect level. This novel mechanism is applied to the recombination center "Equation missing" in CdTe. We show that this two-level process can significantly increase the recombination rate (by three orders of magnitude) in agreement with experiments. We expect that this two-level recombination process can exist in a wide range of semiconductors, so its effect should be carefully examined in characterizing optoelectronic materials.
Knockout of BRD7 results in impaired spermatogenesis and male infertility
Authors: Wang Heran , Zhao Ran , Guo Chi , Jiang Shihe , Yang Jing , Xu Yang , Liu Yukun , Fan Liqing , Xiong Wei , Ma Jian , Peng Shuping , Zeng Zhaoyang , Zhou Yanhong , Li Xiayu , Li Zheng , Li Xiaoling , Schmitt David C. , Tan Ming , Li Guiyuan , Zhou Ming
Published: February 2016

BRD7 was originally identified as a novel bromodomain gene and a potential transcriptional factor. BRD7 was found to be extensively expressed in multiple mouse tissues but was highly expressed in the testis. Furthermore, BRD7 was located in germ cells during multiple stages of spermatogenesis, ranging from the pachytene to the round spermatid stage. Homozygous knockout of BRD7 (BRD7−/−) resulted in complete male infertility and spermatogenesis defects, including deformed acrosomal formation, degenerative elongating spermatids and irregular head morphology in postmeiotic germ cells in the seminiferous epithelium, which led to the complete arrest of spermatogenesis at step 13. Moreover, a high ratio of apoptosis was determined by TUNEL analysis, which was supported by high levels of the apoptosis markers annexin V and p53 in knockout testes. Increased expression of the DNA damage maker λH2AX was also found in BRD7−/− mice, whereas DNA damage repair genes were down−regulated. Furthermore, no or lower expression of BRD7 was detected in the testes of azoospermia patients exhibiting spermatogenesis arrest than that in control group. These data demonstrate that BRD7 is involved in male infertility and spermatogenesis in mice, and BRD7 defect might be associated with the occurrence and development of human azoospermia.