bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network Catastrophe: Self-Organized Patterns Reveal both the Instability and the Structure of Complex Networks
Authors: Moon Hankyu , Lu Tsai-Ching 
Published: March 2015

AbstractCritical events in society or biological systems can be understood as large-scale self-emergent phenomena due to deteriorating stability. We often observe peculiar patterns preceding these events, posing a question of—how to interpret the self-organized patterns to know more about the imminent crisis. We start with a very general description — of interacting population giving rise to large-scale emergent behaviors that constitute critical events. Then we pose a key question: is there a quantifiable relation between the network of interactions and the emergent patterns? Our investigation leads to a fundamental understanding to: 1. Detect the system's transition based on the principal mode of the pattern dynamics; 2. Identify its evolving structure based on the observed patterns. The main finding of this study is that while the pattern is distorted by the network of interactions, its principal mode is invariant to the distortion even when the network constantly evolves. Our analysis on real-world markets show common self-organized behavior near the critical transitions, such as housing market collapse and stock market crashes, thus detection of critical events before they are in full effect is possible.
"Turn on" and label-free core−shell Ag@SiO2 nanoparticles-based metal-enhanced fluorescent (MEF) aptasensor for Hg2+
Authors: Pang Yuanfeng , Rong Zhen , Xiao Rui , Wang Shengqi 
Published: March 2015

AbstractA turn on and label-free fluorescent apasensor for Hg2+ with high sensitivity and selectivity has been demonstrated in this report. Firstly, core−shell Ag@SiO2 nanoparticles (NPs) were synthetized as a Metal-Enhanced Fluorescent (MEF) substrate, T-rich DNA aptamers were immobilized on the surface of Ag@SiO2 NPs and thiazole orange (TO) was selected as fluorescent reporter. After Hg2+ was added to the aptamer-Ag@SiO2 NPs and TO mixture buffer solution, the aptamer strand can bind Hg2+ to form T-Hg2+-T complex with a hairpin structure which TO can insert into. When clamped by the nucleic acid bases, the fluorescence quanta yield of TO will be increased under laser excitation and emitted a fluorescence emission. Furthermore, the fluorescence emission can be amplified largely by the MEF effect of the Ag@SiO2 NPs. The whole experiment can be finished within 30 min and the limit of detection is 0.33 nM even with interference by high concentrations of other metal ions. Finally, the sensor was applied for detecting Hg2+ in different real water samples with satisfying recoveries over 94%.
Re-annotation of presumed noncoding disease/trait-associated genetic variants by integrative analyses
Authors: Chen Geng , Yu Dianke , Chen Jiwei , Cao Ruifang , Yang Juan , Wang Huan , Ji Xiangjun , Ning Baitang , Shi Tieliu 
Published: March 2015

AbstractUsing RefSeq annotations, most disease/trait-associated genetic variants identified by genome-wide association studies (GWAS) appear to be located within intronic or intergenic regions, which makes it difficult to interpret their functions. We reassessed GWAS-Associated single-nucleotide polymorphisms (herein termed as GASs) for their potential functionalities using integrative approaches. 8834 of 9184 RefSeq “noncoding” GASs were reassessed to have potential regulatory functionalities. As examples, 3 variants (rs3130320, rs3806932 and rs6890853) were shown to have regulatory properties in HepG2, A549 and 293T cells. Except rs3130320 as a known expression quantitative trait loci (eQTL), rs3806932 and rs6890853 were not reported as eQTLs in previous reports. 1999 of 9184 “noncoding” GASs were re-annotated to the promoters or intragenic regions using Ensembl, UCSC and AceView gene annotations but they were not annotated into corresponding regions in RefSeq database. Moreover, these GAS-harboring genes were broadly expressed across different tissues and a portion of them was expressed in a tissue-specific manner, suggesting that they could be functional. Collectively, our study demonstrates the benefits of using integrative analyses to interpret genetic variants and may help to predict or explain disease susceptibility more accurately and comprehensively.
Fluorescence-Raman Dual Modal Endoscopic System for Multiplexed Molecular Diagnostics
Authors: Jeong Sinyoung , Kim Yong-il , Kang Homan , Kim Gunsung , Cha Myeong Geun , Chang Hyejin , Jung Kyung Oh , Kim Young-Hwa , Jun Bong-Hyun , Hwang Do Won , Lee Yun-Sang , Youn Hyewon , Lee Yoon-Sik , Kang Keon Wook , Lee Dong Soo , Jeong Dae Hong 
Published: March 2015

AbstractOptical endoscopic imaging, which was recently equipped with bioluminescence, fluorescence and Raman scattering, allows minimally invasive real-time detection of pathologies on the surface of hollow organs. To characterize pathologic lesions in a multiplexed way, we developed a dual modal fluorescence-Raman endomicroscopic system (FRES), which used fluorescence and surface-enhanced Raman scattering nanoprobes (F-SERS dots). Real-time, in vivo and multiple target detection of a specific cancer was successful, based on the fast imaging capability of fluorescence signals and the multiplex capability of simultaneously detected SERS signals using an optical fiber bundle for intraoperative endoscopic system. Human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR) on the breast cancer xenografts in a mouse orthotopic model were successfully detected in a multiplexed way, illustrating the potential of FRES as a molecular diagnostic instrument that enables real-time tumor characterization of receptors during routine endoscopic procedures.
Interactome of the negative regulator of nuclear import BRCA1-binding protein 2
Authors: Fatima Shadma , Wagstaff Kylie M. , Loveland Kate L. , Jans David A. 
Published: March 2015

AbstractAlthough the negative regulator of nuclear import (NRNI) BRCA1 binding protein 2 (BRAP2) is highly expressed in testis, its role is largely unknown. Here we address this question by documenting the BRAP2 interactome from human testis, using the yeast 2-hybrid system to identify BRAP2-interacting proteins with roles in diverse cellular processes, including regulation of the actin cytoskeleton, ubiquitinylation, cell cycle/apoptosis and transcription. Interaction with BRAP2 in adult mouse testis with three of these, PH domain and leucine rich repeat protein phosphatase 1 (PHLPP1), A-Kinase anchor protein (AKAP3) and DNA methyl transferase 1 (DNMT1), was confirmed by coimmunoprecipitation assays. BRAP2's ability to inhibit PHLPP1 and DNMT1 nuclear localisation was also confirmed by quantitative confocal microscopy. Importantly, the physiological relevance thereof was implied by the cytoplasmic localisation of PHLPP1, AKAP3 and DNMT1 in pachytene spermatocytes/round spermatids where BRAP2 is present at high levels and nuclear localisation of PHLPP1 and DNMT1 in spermatogonia concomitant with lower levels of BRAP2. Interestingly, BRAP2 was also present in murine spermatozoa, in part colocalised with AKAP3. Together the results indicate for the first time that BRAP2 may play an important NRNI role in germ cells of the testis, with an additional, scaffold/structural role in mature spermatozoa.
A novel PKD2L1 C-terminal domain critical for trimerization and channel function
Authors: Zheng Wang , Hussein Shaimaa , Yang JungWoo , Huang Jun , Zhang Fan , Hernandez-Anzaldo Samuel , Fernandez-Patron Carlos , Cao Ying , Zeng Hongbo , Tang Jingfeng , Chen Xing-Zhen 
Published: March 2015

AbstractAs a transient receptor potential (TRP) superfamily member, polycystic kidney disease 2-like-1 (PKD2L1) is also called TRPP3 and has similar membrane topology as voltage-gated cation channels. PKD2L1 is involved in hedgehog signaling, intestinal development and sour tasting. PKD2L1 and PKD1L3 form heterotetramers with 3:1 stoichiometry. C-terminal coiled-coil-2 (CC2) domain (G699-W743) of PKD2L1 was reported to be important for its trimerization but independent studies showed that CC2 does not affect PKD2L1 channel function. It thus remains unclear how PKD2L1 proteins oligomerize into a functional channel. By SDS-PAGE, blue native PAGE and mutagenesis we here identified a novel C-terminal domain called C1 (K575-T622) involved in stronger homotrimerization than the non-overlapping CC2 and found that the PKD2L1 N-terminus is critical for dimerization. By electrophysiology and Xenopus oocyte expression, we found that C1, but not CC2, is critical for PKD2L1 channel function. Our co-immunoprecipitation and dynamic light scattering experiments further supported involvement of C1 in trimerization. Further, C1 acted as a blocking peptide that inhibits PKD2L1 trimerization as well as PKD2L1 and PKD2L1/PKD1L3 channel function. Thus, our study identified C1 as the first PKD2L1 domain essential for both PKD2L1 trimerization and channel function and suggest that PKD2L1 and PKD2L1/PKD1L3 channels share the PKD2L1 trimerization process.
Pyrosequencing reveals a shift in symbiotic bacteria populations across life stages of Bactrocera dorsalis
Authors: Andongma Awawing A. , Wan Lun , Dong Yong-Cheng , li Ping , Desneux Nicolas , White Jennifer A. , Niu Chang-Ying 
Published: March 2015

AbstractBactrocera dorsalis is one of the most economically important fruit flies around the world. In this study, 454 pyrosequencing was used to identify the bacteria associated with different developmental stages of B. dorsalis. At ≥ 97% nucleotide similarity, total reads could be assigned to 172 Operational Taxonomic Units belonging to six phyla. Proteobacteria dominated in immature stages while Firmicutes dominated in adult stages. The most abundant families were Enterococcaceae and Comamondaceae. The genus Comamonas was most abundant in pupae whereas completely absent in adults. Some identified species had low sequence similarity to reported species indicating the possibility of novel taxa. However, a majority sequence reads were similar to sequences previously identified to be associated with Bactrocera correcta, suggesting a characteristic microbial fauna for this insect genus. The type and abundance of different bacterial groups varied across the life stages of B. dorsalis. Selection pressure exerted by the host insect as a result of its habitat and diet choices could be the reason for the observed shift in the bacteria groups. These findings increase our understanding of the intricate symbiotic relationships between bacteria and B. dorsalis and provide clues to develop potential biocontrol techniques against this fruit fly.
Opposite rheological properties of neuronal microcompartments predict axonal vulnerability in brain injury
Authors: Grevesse Thomas , Dabiri Borna E. , Parker Kevin Kit , Gabriele Sylvain 
Published: March 2015

AbstractAlthough pathological changes in axonal morphology have emerged as important features of traumatic brain injury (TBI), the mechanical vulnerability of the axonal microcompartment relative to the cell body is not well understood. We hypothesized that soma and neurite microcompartments exhibit distinct mechanical behaviors, rendering axons more sensitive to a mechanical injury. In order to test this assumption, we combined protein micropatterns with magnetic tweezer rheology to probe the viscoelastic properties of neuronal microcompartments. Creep experiments revealed two opposite rheological behaviors within cortical neurons: the cell body was soft and characterized by a solid-like response, whereas the neurite compartment was stiffer and viscous-like. By using pharmacological agents, we demonstrated that the nucleus is responsible for the solid-like behavior and the stress-stiffening response of the soma, whereas neurofilaments have a predominant contribution in the viscous behavior of the neurite. Furthermore, we found that the neurite is a mechanosensitive compartment that becomes softer and adopts a pronounced viscous state on soft matrices. Together, these findings highlight the importance of the regionalization of mechanical and rigidity-sensing properties within neuron microcompartments in the preferential damage of axons during traumatic brain injury and into potential mechanisms of axonal outgrowth after injury.
Contact Effects in thin 3D-Topological Insulators: How does the current flow?
Authors: Gupta Gaurav , Jalil Mansoor Bin Abdul , Liang Gengchiau 
Published: March 2015

AbstractThe effect of different contact configurations (semi-infinite extended-channel, normal metal and ferromagnetic metal) on quantum transport through thin Bi2Se3 three-dimensional (3D) topological insulator (TI) slab (channel) has been investigated through Non-Equilibrium Green Function. The issue of contact dependent current flow and distribution across quintuple layers of 3D-TI has been addressed in this work and applied to expound the explanation for recent experimental work on electrical detection of spin-momentum locking on topological surface for long channel device. A theoretical model is propounded to develop a microscopic understanding of transport in 3D-TI in which contact type and magnetization concur with helical surface states of the TI channel to manifest seemingly counter-intuitive current distribution across layers. The quantum transport calculations for short channel devices with magnetic source and drain contacts postulate negative surface current for anti-phase magnetization whose axis is transverse to both current and quintuple layers. For in-phase magnetization at the two terminals, it is shown that observations can change fundamentally to result in anomalous current distribution. Such results are explained to stem from the confinement of 3D-TI between ferromagnetic contacts along the transport direction. A simple mechanism to validate topological insulators via quantum transport experiments has also been suggested.
A novel high light-inducible carotenoid-binding protein complex in the thylakoid membranes of Synechocystis PCC 6803
Authors: Daddy Soumana , Zhan Jiao , Jantaro Saowarath , He Chenliu , He Qingfang , Wang Qiang 
Published: March 2015

AbstractSynechocystis sp. PCC 6803 is a model cyanobacterium extensively used to study photosynthesis. Here we reveal a novel high light-inducible carotenoid-binding protein complex (HLCC) in the thylakoid membranes of Synechocystis PCC 6803 cells exposed to high intensity light. Zeaxanthin and myxoxanthophyll accounted for 29.8% and 54.8%, respectively, of the carotenoids bound to the complex. Using Blue-Native PAGE followed by 2D SDS-PAGE and mass spectrometry, we showed that the HLCC consisted of Slr1128, IsiA, PsaD and HliA/B. We confirmed these findings by SEAD fluorescence cross-linking and anti-PsaD immuno-coprecipitation analyses. The expression of genes encoding the protein components of the HLCC was enhanced by high light illumination and artificial oxidative stress. Deletion of these proteins resulted in impaired state transition and increased sensitivity to oxidative and/or high light stress, as indicated by increased membrane peroxidation. Therefore, the HLCC protects thylakoid membranes from extensive photooxidative damage, likely via a mechanism involving state transition.
Quantum interference measurement of spin interactions in a bio-organic/semiconductor device structure
Authors: Deo Vincent , Zhang Yao , Soghomonian Victoria , Heremans Jean J. 
Published: March 2015

AbstractQuantum interference is used to measure the spin interactions between an InAs surface electron system and the iron center in the biomolecule hemin in nanometer proximity in a bio-organic/semiconductor device structure. The interference quantifies the influence of hemin on the spin decoherence properties of the surface electrons. The decoherence times of the electrons serve to characterize the biomolecule, in an electronic complement to the use of spin decoherence times in magnetic resonance. Hemin, prototypical for the heme group in hemoglobin, is used to demonstrate the method, as a representative biomolecule where the spin state of a metal ion affects biological functions. The electronic determination of spin decoherence properties relies on the quantum correction of antilocalization, a result of quantum interference in the electron system. Spin-flip scattering is found to increase with temperature due to hemin, signifying a spin exchange between the iron center and the electrons, thus implying interactions between a biomolecule and a solid-state system in the hemin/InAs hybrid structure. The results also indicate the feasibility of artificial bioinspired materials using tunable carrier systems to mediate interactions between biological entities.
Diagnostic Accuracy of Calretinin for Malignant Mesothelioma in Serous Effusions: a Meta-analysis
Authors: Li Diandian , Wang Bo , Long Hongyu , Wen Fuqiang 
Published: March 2015

AbstractNumerous studies have investigated the utility of calretinin in differentiating malignant mesothelioma (MM) from metastatic carcinoma (MC) in serous effusions. However, the results remain controversial. The aim of this study is to determine the overall accuracy of calretinin in serous effusions for MM through a meta-analysis of published studies. Publications addressing the accuracy of calretinin in the diagnosis of MM were selected from the Medline (Ovid), PubMed, the Cochrane Library Database and the Web of Science. Data from selected studies were pooled to yield summary sensitivity, specificity, positive and negative likelihood ratio (LR), diagnostic odds ratio (DOR) and receiver operating characteristic (SROC) curve. Statistical analysis was performed by Meta-Disc 1.4 and STATA 12.0 softwares. 18 studies met the inclusion criteria and the summary estimating for calretinin in the diagnosis of MM were: sensitivity 0.91 (95%CI: 0.87–0.94), specificity 0.96 (95%CI: 0.95–0.96), positive likelihood ratio (PLR) 14.42 (95%CI: 7.92–26.26), negative likelihood ratio (NLR) 0.1 (95%CI: 0.05–0.2) and diagnostic odds ratio 163.03 (95%CI: 54.62–486.63). The SROC curve indicated that the maximum joint sensitivity and specificity (Q-value) was 0.92; the area under the curve was 0.97. Our findings suggest that calretinin may be a useful diagnostic tool for confirming MM in serous effusions.
A clinical characteristic analysis of pregnancy-associated intracranial haemorrhage in China
Authors: Liang Zhu-Wei , Lin Li , Gao Wan-Li , Feng Li-Min 
Published: March 2015

AbstractIntracerebral haemorrhage (ICH) occurring during pregnancy and the puerperium is an infrequent but severe complication with a high mortality and poor prognosis. Until recently, previous studies have mainly focused on the effect of different treatments on prognosis. However, few studies have provided solid evidence to clarify the key predisposing factors affecting the prognosis of ICH. In the present study, based on a unique sample with a high ICH incidence and mortality rate, we described the main clinical characteristics of ICH patients and found that the prognosis of patients who underwent surgical intervention was not better than that of patients who received other treatment modalities. However, pre-eclampsia patients had higher maternal and neonatal mortality rates than other aetiology groups. Furthermore, univariate regression analysis identified onset to diagnosis time (O-D time) and pre-eclampsia as the only factors showing independent correlation with poor maternal outcomes (modified Rankin Scale, mRS ≥ 3) and only O-D time was identified as a predictor of maternal mortality. These results revealed that the aetiology of ICH and O-D time might be crucial predisposing factors to prognosis, especially for patients with pre-eclampsia. The study highlighted a novel direction to effectively improve the prognosis of pregnancy-associated ICH.
Enhanced Thermoelectric Efficiency of Porous Silicene Nanoribbons
Authors: Sadeghi Hatef , Sangtarash Sara , Lambert Colin J. 
Published: March 2015

AbstractThere is a critical need to attain new sustainable materials for direct upgrade of waste heat to electrical energy via the thermoelectric effect. Here we demonstrate that the thermoelectric performance of silicene nanoribbons can be improved dramatically by introducing nanopores and tuning the Fermi energy. We predict that values of electronic thermoelectric figure of merit ZTe up to 160 are achievable, provided the Fermi energy is located approximately 100 meV above the charge neutrality point. Including the effect of phonons yields a value for the full figure of merit of ZT = 3.5. Furthermore the sign of the thermopower S can be varied with achievable values as high as S = +/− 500 μV/K. As a method of tuning the Fermi energy, we analyse the effect of doping the silicene with either a strong electron donor (TTF) or a strong electron acceptor (TCNQ) and demonstrate that adsorbed layers of the former increases ZTe to a value of 3.1, which is insensitive to temperature over the range 100 K – 400 K. This combination of a high, temperature-insensitive ZTe and the ability to choose the sign of the thermopower identifies nanoporous silicene as an ideal thermoelectric material with the potential for unprecedented performance.
A large temperature fluctuation may trigger an epidemic erythromelalgia outbreak in China
Authors: Liu Tao , Zhang Yonghui , Lin Hualiang , Lv Xiaojuan , Xiao Jianpeng , Zeng Weilin , Gu Yuzhou , Rutherford Shannon , Tong Shilu , Ma Wenjun 
Published: March 2015

AbstractAlthough erythromelalgia (EM) has been documented in the literature for almost 150 years, it is still poorly understood. To overcome this limitation, we examined the spatial distribution of epidemic EM and explored the association between temperature fluctuation and epidemic EM outbreaks in China. We searched all peer-reviewed literature on primary epidemic EM outbreaks in China. A two-stage model was used to characterize the relationship between temperature fluctuation and epidemic EM outbreaks. We observed that epidemic EM outbreaks were reported from 13 provinces during 1960–2014 and they mainly occurred between February and March in southern China. The majority of EM cases were middle school students, with a higher incidence rate in female and resident students. The major clinical characteristics of EM cases included burning, sharp, tingling and/or stinging pain in toes, soles and/or dorsum of feet, fever, erythema and swelling. A large “V”-shaped fluctuation of daily average temperature (TM) observed during the epidemic EM outbreaks was significantly associated with the number of daily EM cases (β = 1.22, 95%CI: 0.66 ~ 1.79), which indicated that this “V”-shaped fluctuation of TM probably triggered the epidemic EM outbreaks.