bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mussel adhesion is dictated by time-regulated secretion and molecular conformation of mussel adhesive proteins
Authors: Petrone Luigi , Kumar Akshita , Sutanto Clarinda N. , Patil Navinkumar J. , Kannan Srinivasaraghavan , Palaniappan Alagappan , Amini Shahrouz , Zappone Bruno , Verma Chandra , Miserez Ali 
Published: October 2015

AbstractInterfacial water constitutes a formidable barrier to strong surface bonding, hampering the development of water-resistant synthetic adhesives. Notwithstanding this obstacle, the Asian green mussel Perna viridis attaches firmly to underwater surfaces via a proteinaceous secretion (byssus). Extending beyond the currently known design principles of mussel adhesion, here we elucidate the precise time-regulated secretion of P. viridis mussel adhesive proteins. The vanguard 3,4-dihydroxy-L-phenylalanine (Dopa)-rich protein Pvfp-5 acts as an adhesive primer, overcoming repulsive hydration forces by displacing surface-bound water and generating strong surface adhesion. Using homology modelling and molecular dynamics simulations, we find that all mussel adhesive proteins are largely unordered, with Pvfp-5 adopting a disordered structure and elongated conformation whereby all Dopa residues reside on the protein surface. Time-regulated secretion and structural disorder of mussel adhesive proteins appear essential for optimizing extended nonspecific surface interactions and byssus’ assembly. Our findings reveal molecular-scale principles to help the development of wet-resistant adhesives.
Human caspase-4 and caspase-5 regulate the one-step non-canonical inflammasome activation in monocytes
Authors: Viganò Elena , Diamond Catherine Emma , Spreafico Roberto , Balachander Akhila , Sobota Radoslaw M. , Mortellaro Alessandra 
Published: October 2015

AbstractMonocytes promote the early host response to infection releasing key pro-inflammatory cytokines, such as IL-1β. The biologically inactive IL-1β precursor is processed to active form by inflammasomes, multi-protein complexes activating caspase-1. Human monocytes exhibit an unconventional one-step pathway of inflammasome activation in response to lipopolysaccharide (LPS) alone. Although this lineage-restricted mechanism is likely to contribute to the pathology of endotoxin shock, signalling pathways regulating this mechanism are currently unknown. Here we report that caspase-4 and caspase-5 mediate IL-1α and IL-1β release from human monocytes after LPS stimulation. Although caspase-4 remains uncleaved, caspase-5 undergoes rapid processing upon LPS treatment. We also identify an additional caspase-5 cleavage product in LPS-stimulated monocytes, which correlates with IL-1 secretion. This one-step pathway requires Syk activity and Ca2+ flux instigated by CD14/TLR4-mediated LPS internalization. Identification of caspase-4/5 as the key determinants of one-step inflammasome activation in human monocytes provides potential targets for therapeutic intervention in endotoxin shock.
Alternative application of Tau protein in Creutzfeldt-Jakob disease diagnosis: Improvement for weakly positive 14-3-3 protein in the laboratory
Authors: Hyeon Jae Wook , Kim Su Yeon , Lee Jeongmin , Park Jun Sun , Hwang Kyu Jam , Lee Sol Moe , An SeongSoo A. , Lee Myung Koo , Ju Young Ran 
Published: October 2015

AbstractThe 14-3-3 protein has been used as a biomarker for the diagnosis of sporadic Creutzfeldt-Jakob disease (sCJD). However, weakly positive 14-3-3 leads to false positive results and an incorrect diagnosis. We attempted to use quantitative data for tau protein to provide an accurate diagnosis based on weak 14-3-3 protein. Sixty-two patients with sCJD, including pathologically confirmed, clinically definite and probable cases and 89 non-CJD patients were investigated based on a Korean population. Among them, 20 sCJD and 14 non-CJD showed weakly positive 14-3-3. The total tau (t-tau) and phosphorylated tau (p-tau) protein levels were measured by ELISA and the p-tau to t-tau ratio (p/t ratio) was calculated. The combined use of the 14-3-3 protein assay, t-tau levels and p/t ratio improved the specificity of diagnosis compared with the use of the 14-3-3 protein assay alone (47% for 14-3-3 alone; 85.94% for 14-3-3 combined with t-tau; 90.62% for 14-3-3 combined with the p/t ratio). In addition, 18 of 20 sCJD and 12 of 14 non-CJD who were weakly positive for 14-3-3 were positive for the p/t ratio and negative for the p/t ratio, respectively. When used in combination with the 14-3-3 protein, the tau protein is useful as a biomarker for the precise diagnosis of sCJD.
Sexual behavior, risk perception and HIV transmission can respond to HIV antiviral drugs and vaccines through multiple pathways
Authors: Tully Stephen , Cojocaru Monica , Bauch Chris T. 
Published: October 2015

AbstractThere has been growing use of highly active antiretroviral treatment (HAART) for HIV and significant progress in developing prophylactic HIV vaccines. The simplest theories of counterproductive behavioral responses to such interventions tend to focus on single feedback mechanisms: for instance, HAART optimism makes infection less scary and thus promotes risky sexual behavior. Here, we develop an agent based, age-structured model of HIV transmission, risk perception and partner selection in a core group to explore behavioral responses to interventions. We find that interventions can activate not one, but several feedback mechanisms that could potentially influence decision-making and HIV prevalence. In the model, HAART increases the attractiveness of unprotected sex, but it also increases perceived risk of infection and, on longer timescales, causes demographic impacts that partially counteract HAART optimism. Both HAART and vaccination usually lead to lower rates of unprotected sex on the whole, but intervention effectiveness depends strongly on whether individuals over- or under-estimate intervention coverage. Age-specific effects cause sexual behavior and HIV prevalence to change in opposite ways in old and young age groups. For complex infections like HIV—where interventions influence transmission, demography, sexual behavior and risk perception—we conclude that evaluations of behavioral responses should consider multiple feedback mechanisms.
Shortcuts to adiabatic passage for fast generation of Greenberger-Horne-Zeilinger states by transitionless quantum driving
Authors: Chen Ye-Hong , Xia Yan , Song Jie , Chen Qing-Qin 
Published: October 2015

AbstractBerry’s approach on “transitionless quantum driving” shows how to set a Hamiltonian which drives the dynamics of a system along instantaneous eigenstates of a reference Hamiltonian to reproduce the same final result of an adiabatic process in a shorter time. In this paper, motivated by transitionless quantum driving, we construct shortcuts to adiabatic passage in a three-atom system to create the Greenberger-Horne-Zeilinger states with the help of quantum Zeno dynamics and of non-resonant lasers. The influence of various decoherence processes is discussed by numerical simulation and the result proves that the scheme is fast and robust against decoherence and operational imperfection.
Biogeographical role of the Kuroshio Current in the amphibious mudskipper Periophthalmus modestus indicated by mitochondrial DNA data
Authors: He Lijun , Mukai Takahiko , Hou Chu Ka , Ma Qiang , Zhang Jing 
Published: October 2015

AbstractQuaternary climatic cycles have influenced marine organisms’ spatial distribution and population dynamics. This study aimed to elucidate the evolutionary influences of contemporary and glacial physical barriers on the population structure, demography and colonization history of the mudskipper (Periophthalmus modestus) based on a mitochondrial gene segment (ND5) from 131 individual fish sampled in the northwestern Pacific Ocean. The current Kuroshio Current and the glacial exposure of the Taiwan Strait appeared to have restricted migration among the South China Sea, coastal East China and Japan. However, genetic homogeneity (Nm>1) also suggested contemporary larval transportation by sea circulation between the East China Sea and the South China Sea or historical dispersal along the glacial exposed shoreline among China, Japan and the Ryukyu Islands. Evolutionary signals of the strengthened East Asian Summer Monsoon in the mid-Pleistocene and regional difference in intertidal primary productions were indicated by a late-Pleistocene population expansion ofP. modestuswith a higher effective population size in the South China Sea than in the East China Sea. Furthermore, a potential colonization origin from the South China Sea was consistently inferred by different clues, including the populations’ coalescence times, the ancestral haplotype distribution, the number of private haplotypes and species/genetic diversity.
Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species
Authors: Kim Kyunghee , Lee Sang-Choon , Lee Junki , Yu Yeisoo , Yang Kiwoung , Choi Beom-Soon , Koh Hee-Jong , Waminal Nomar Espinosa , Choi Hong-Il , Kim Nam-Hoon , Jang Woojong , Park Hyun-Seung , Lee Jonghoon , Lee Hyun Oh , Joh Ho Jun , Lee Hyeon Ju , Park Jee Young , Perumal Sampath , Jayakodi Murukarthick , Lee Yun Sun , Kim Backki , Copetti Dario , Kim Soonok , Kim Sunggil , Lim Ki-Byung , Kim Young-Dong , Lee Jungho , Cho Kwang-Su , Park Beom-Seok , Wing Rod A. , Yang Tae-Jin 
Published: October 2015

AbstractCytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis.
Development of High Resolution Melting Analysis for the Diagnosis of Human Malaria
Authors: Chua Kek Heng , Lim Siew Chee , Ng Ching Ching , Lee Ping Chin , Lim Yvonne Ai Lian , Lau Tze Pheng , Chai Hwa Chia 
Published: October 2015

AbstractMolecular detection has overcome limitations of microscopic examination by providing greater sensitivity and specificity in Plasmodium species detection. The objective of the present study was to develop a quantitative real-time polymerase chain reaction coupled with high-resolution melting (qRT-PCR-HRM) assay for rapid, accurate and simultaneous detection of all five human Plasmodium spp. A pair of primers targeted the 18S SSU rRNA gene of the Plasmodium spp. was designed for qRT-PCR-HRM assay development. Analytical sensitivity and specificity of the assay were evaluated. Samples collected from 229 malaria suspected patients recruited from Sabah, Malaysia were screened using the assay and results were compared with data obtained using PlasmoNexTM, a hexaplex PCR system. The qRT-PCR-HRM assay was able to detect and discriminate the five Plasmodium spp. with lowest detection limits of 1–100 copy numbers without nonspecific amplifications. The detection of Plasmodium spp. in clinical samples using this assay also achieved 100% concordance with that obtained using PlasmoNexTM. This indicated that the diagnostic sensitivity and specificity of this assay in Plasmodium spp. detection is comparable with those of PlasmoNexTM. The qRT-PCR-HRM assay is simple, produces results in two hours and enables high-throughput screening. Thus, it is an alternative method for rapid and accurate malaria diagnosis.
Effect of the thin-film limit on the measurable optical properties of graphene
Authors: Holovský Jakub , Nicolay Sylvain , De Wolf Stefaan , Ballif Christophe 
Published: October 2015

AbstractThe fundamental sheet conductance of graphene can be directly related to the product of its absorption coefficient, thickness and refractive index. The same can be done for graphene’s fundamental opacity if the so-called thin-film limit is considered. Here, we test mathematically and experimentally the validity of this limit on graphene, as well as on thin metal and semiconductor layers. Notably, within this limit, all measurable properties depend only on the product of the absorption coefficient, thickness and refractive index. As a direct consequence, the absorptance of graphene depends on the refractive indices of the surrounding media. This explains the difficulty in determining separately the optical constants of graphene and their widely varying values found in literature so far. Finally, our results allow an accurate estimation of the potential optical losses or gains when graphene is used for various optoelectronic applications.
Discovery of Small Molecules that Inhibit the Disordered Protein, p27Kip1
Authors: Iconaru Luigi I. , Ban David , Bharatham Kavitha , Ramanathan Arvind , Zhang Weixing , Shelat Anang A. , Zuo Jian , Kriwacki Richard W. 
Published: October 2015

AbstractDisordered proteins are highly prevalent in biological systems, they control myriad signaling and regulatory processes and their levels and/or cellular localization are often altered in human disease. In contrast to folded proteins, disordered proteins, due to conformational heterogeneity and dynamics, are not considered viable drug targets. We challenged this paradigm by identifying through NMR-based screening small molecules that bound specifically, albeit weakly, to the disordered cell cycle regulator, p27Kip1 (p27). Two groups of molecules bound to sites created by transient clusters of aromatic residues within p27. Conserved chemical features within these two groups of small molecules exhibited complementarity to their binding sites within p27, establishing structure-activity relationships for small molecule:disordered protein interactions. Finally, one compound counteracted the Cdk2/cyclin A inhibitory function of p27 in vitro, providing proof-of-principle that small molecules can inhibit the function of a disordered protein (p27) through sequestration in a conformation incapable of folding and binding to a natural regulatory target (Cdk2/cyclin A).
A competing risk analysis of sequential complication development in Asian type 2 diabetes mellitus patients
Authors: Cheng Li-Jen , Chen Jeng-Huei , Lin Ming-Yen , Chen Li-Chia , Lao Chun-Huan , Luh Hsing , Hwang Shang-Jyh 
Published: October 2015

AbstractThis retrospective cohort study investigated the progression risk of sequential complication in Asian type 2 diabetes (T2D) patients using the Taiwan Pay-for-Performance Diabetes Registry and claim data from November 2003 to February 2009. 226,310 adult T2D patients without complication were followed from diagnosis to complications, including myocardial infarction (MI), other ischemic heart disease (IHD), congestive heart failure (CHF), stroke, chronic kidney disease (CKD), retinopathy, amputation, death or to the end of study. Cumulative incidences (CIs) of first and second complications were analyzed in 30 and 4 years using the cumulative incidence competing risk method. IHD (29.8%), CKD (24.5%) and stroke (16.0%) are the most common first complications. The further development of T2D complications depends on a patient’s existing complication profiles. Patients who initially developed cardiovascular complications had a higher risk (9.2% to 24.4%) of developing IHD or CKD, respectively. All-cause mortality was the most likely consequence for patients with a prior MI (12.0%), so as stroke in patients with a prior MI (10.8%) or IHD (8.9%). Patients with CKD had higher risk of developing IHD (16.3%), stroke (8.9%) and all-cause mortality (8.7%) than end-stage renal disease (4.0%). Following an amputation, patients had a considerable risk of all-cause mortality (42.1%).
Choroidal neovascularization is inhibited via an intraocular decrease of inflammatory cells in mice lacking complement component C3
Authors: Tan Xue , Fujiu Katsuhito , Manabe Ichiro , Nishida Junko , Yamagishi Reiko , Nagai Ryozo , Yanagi Yasuo 
Published: October 2015

AbstractIn early age-related macular degeneration (AMD), complement component C3 can be observed in drusen, which is the accumulation of material beneath the retinal pigment epithelium. The complement pathways, via the activation of C3, can upregulate the expression of cytokines and their receptors and the recruitment of inflammatory leukocytes, both of which play an important role in the development of choroidal neovascularization (CNV) in exudative AMD. Laser-induced CNV lesions were found to be significantly smaller in C3−/− mice than in wild-type mice. By using flow cytometry, we demonstrated that the proportions of intraocular granulocytes, CD11b+F4/80+Ly6Chi and CD11b+F4/80+Ly6Clo cells, were lower in C3−/− mice than in wild-type mice as early as day 1 after laser injury and the proportions of granulocytes and three macrophage/monocyte subsets were significantly lower on day 3. In contrast, C3−/− mice had more granulocytes and CD11b+F4/80+Ly6Chi cells in peripheral blood than wild-type mice after injury. Further, the expression levels of Vegfa164 were upregulated in intraocular Ly6Chi macrophages/monocytes of C3−/− mice, but not as much as in wild-type mice. Collectively, our data demonstrate that despite a more pronounced induction of systemic inflammation, inhibition of complement factor C3 suppresses CNV by decreasing the recruitment of inflammatory cells to the lesion.
The effect of environmental heterogeneity on species richness depends on community position along the environmental gradient
Authors: Yang Zhiyong , Liu Xueqi , Zhou Mohua , Ai Dexiecuo , Wang Gang , Wang Youshi , Chu Chengjin , Lundholm Jeremy T. 
Published: October 2015

AbstractEnvironmental heterogeneity is among the most important factors governing community structure. Besides the widespread evidence supporting positive relationships between richness and environmental heterogeneity, negative and unimodal relationships have also been reported. However, few studies have attempted to test the role of the heterogeneity on species richness after removing the confounding effect of resource availability or environmental severity. Here we constructed an individual-based spatially explicit model incorporating a long-recognized tradeoff between competitive ability and stress-tolerance ability of species. We explored the impact of the level of resource availability (i.e. the position of the community along a gradient of environmental severity) on the heterogeneity-diversity relationship (HDR). The results indicate that the shape of HDR depends on the community position along the environmental gradient: at either end of the gradient of environmental severity, a positive HDR occurred, whereas at the intermediate levels of the gradient, a unimodal HDR emerged. Our exploration demonstrates that resource availability/environmental severity should be considered as a potential factor influencing the shape of the HDR. Our theoretical predictions represent hypotheses in need of further empirical study.
Nondestructive detection of lead chrome green in tea by Raman spectroscopy
Authors: Li Xiao-Li , Sun Chan-Jun , Luo Liu-Bin , He Yong 
Published: October 2015

AbstractRaman spectroscopy was first adopted for rapid detecting a hazardous substance of lead chrome green in tea, which was illegally added to tea to disguise as high-quality. 160 samples of tea infusion with different concentrations of lead chrome green were prepared for Raman spectra acquirement in the range of 2804 cm−1–230 cm−1 and the spectral intensities were calibrated with relative intensity standards. Then wavelet transformation (WT) was adopted to extract information in different time and frequency domains from Raman spectra and the low-frequency approximation signal (ca4) was proved as the most important information for establishment of lead chrome green measurement model and the corresponding partial least squares (PLS) regression model obtained good performance in prediction with Rp and RMSEP of 0.936 and 0.803, respectively. To further explore the important wavenumbers closely related to lead chrome green, successive projections algorithm (SPA) was proposed. Finally, 8 characteristic wavenumbers closely related to lead chrome green were obtained and a more convenient and fast model was also developed. These results proved the feasibility of Raman spectroscopy for nondestructive detection of lead chrome green in tea quality control.
Plasmon-Induced Transparency by Hybridizing Concentric-Twisted Double Split Ring Resonators
Authors: Parvinnezhad Hokmabadi Mohammad , Philip Elizabath , Rivera Elmer , Kung Patrick , Kim Seongsin M. 
Published: October 2015

AbstractAs a classical analogue of electromagnetically induced transparency, plasmon induced transparency (PIT) has attracted great attention by mitigating otherwise cumbersome experimental implementation constraints. Here, through theoretical design, simulation and experimental validation, we present a novel approach to achieve and control PIT by hybridizing two double split ring resonators (DSRRs) on flexible polyimide substrates. In the design, the large rings in the DSRRs are stationary and mirror images of each other, while the small SRRs rotate about their center axes. Counter-directional rotation (twisting) of the small SRRs is shown to lead to resonance shifts, while co-directional rotation results in splitting of the lower frequency resonance and emergence of a PIT window. We develop an equivalent circuit model and introduce a mutual inductance parameter M whose sign is shown to characterize the existence or absence of PIT response from the structure. This model attempts to provide a quantitative measure of the physical mechanisms underlying the observed PIT phenomenon. As such, our findings can support the design of several applications such as optical buffers, delay lines and ultra-sensitive sensors.
Time-averaged serum potassium levels and its fluctuation associate with 5-year survival of peritoneal dialysis patients: two-center based study
Authors: Li Shen-Heng , Xie Jian-Teng , Long Hai-Bo , Zhang Jun , Zhou Wei-Dong , Niu Hong-Xin , Tang Xun , Feng Zhong-Lin , Ye Zhi-Ming , Zuo Yang-Yang , Fu Lei , Wen Feng , Wang Li-Ping , Wang Wen-Jian , Shi Wei 
Published: October 2015

AbstractThe time-averaged serum potassium was more comprehensive to reflect the all-time changes of serum potassium levels during peritoneal dialysis (PD). However, the association of fluctuation of time-averaged serum potassium level with long-time survival of PD patients remains unknown. In this retrospective study, we included 357 incident PD patients in 2 centers from January 1, 2007 to October 31, 2012 with follow-up through October 31, 2014. Our data demonstrated that it was the lower time-averaged serum potassium level rather than baseline of serum potassium level that was associated with high risk of death. Patients with higher standard deviation (SD) had significantly poorer all-cause (p = 0.016) and cardiovascular mortality (p = 0.041). Among the patients with time-averaged serum potassium levels below 4.0 mEq/L, a lower mean value was more important than its SD to predict death risk. In contrast, the patients with time-averaged serum potassium levels above 4.0 mEq/L, those with serum potassium SD < 0.54 mEq/L, exhibited a higher 3-year and 5-year survival rate for both all-cause and cardiovascular mortality compared to the control groups. Our data clearly suggested both time-averaged serum potassium and its fluctuation contributed disproportionately to the high death risk in PD patients.