bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Loss of Bmsei Causes Thermosensitive Epilepsy in Contractile Mutant Silkworm, Bombyx mori
Authors: Nie Hongyi , Cheng Tingcai , Huang Xiaofeng , Zhou Mengting , Zhang Yinxia , Dai Fangyin , Mita Kazuei , Xia Qingyou , Liu Chun 
Published: July 2015

AbstractThe thermoprotective mechanisms of insects remain largely unknown. We reported the Bombyx mori contractile (cot) behavioral mutant with thermo-sensitive seizures phenotype. At elevated temperatures, the cot mutant exhibit seizures associated with strong contractions, rolling, vomiting and a temporary lack of movement. We narrowed a region containing cot to ~268 kb by positional cloning and identified the mutant gene as Bmsei which encoded a potassium channel protein. Bmsei was present in both the cell membrane and cytoplasm in wild-type ganglia but faint in cot. Furthermore, Bmsei was markedly decreased upon high temperature treatment in cot mutant. With the RNAi method and injecting potassium channel blockers, the wild type silkworm was induced the cot phenotype. These results demonstrated that Bmsei was responsible for the cot mutant phenotype and played an important role in thermoprotection in silkworm. Meanwhile, comparative proteomic approach was used to investigate the proteomic differences. The results showed that the protein of Hsp-1 and Tn1 were significantly decreased and increased on protein level in cot mutant after thermo-stimulus, respectively. Our data provide insights into the mechanism of thermoprotection in insect. As cot phenotype closely resembles human epilepsy, cot might be a potential model for the mechanism of epilepsy in future.
A versatile class of prototype dynamical systems for complex bifurcation cascades of limit cycles
Authors: Sándor Bulcsú , Gros Claudius 
Published: July 2015

AbstractA general class of prototype dynamical systems is introduced, which allows to study the generation of complex bifurcation cascades of limit cycles, including bifurcations breaking spontaneously a symmetry of the system, period doubling and homoclinic bifurcations and transitions to chaos induced by sequences of limit cycle bifurcations. The prototype systems are adaptive, with friction forces f(V(x)) being functionally dependent exclusively on the mechanical potential V(x), characterized in turn by a finite number of local minima. We discuss several low-dimensional systems, with friction forces f(V) which are linear, quadratic or cubic polynomials in the potential V. We point out that the zeros of f(V) regulate both the relative importance of energy uptake and dissipation respectively, serving at the same time as bifurcation parameters, hence allowing for an intuitive interpretation of the overall dynamical behavior. Starting from simple Hopf- and homoclinic bifurcations, complex sequences of limit cycle bifurcations are observed when the energy uptake gains progressively in importance.
Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio
Authors: Clausson Carl-Magnus , Arngården Linda , Ishaq Omer , Klaesson Axel , Kühnemund Malte , Grannas Karin , Koos Björn , Qian Xiaoyan , Ranefall Petter , Krzywkowski Tomasz , Brismar Hjalmar , Nilsson Mats , Wählby Carolina , Söderberg Ola 
Published: July 2015

AbstractRolling circle amplification (RCA) for generation of distinct fluorescent signals in situ relies upon the self-collapsing properties of single-stranded DNA in commonly used RCA-based methods. By introducing a cross-hybridizing DNA oligonucleotide during rolling circle amplification, we demonstrate that the fluorophore-labeled RCA products (RCPs) become smaller. The reduced size of RCPs increases the local concentration of fluorophores and as a result, the signal intensity increases together with the signal-to-noise ratio. Furthermore, we have found that RCPs sometimes tend to disintegrate and may be recorded as several RCPs, a trait that is prevented with our cross-hybridizing DNA oligonucleotide. These effects generated by compaction of RCPs improve accuracy of visual as well as automated in situ analysis for RCA based methods, such as proximity ligation assays (PLA) and padlock probes.
A strategy for the identification of combinatorial bioactive compounds contributing to the holistic effect of herbal medicines
Authors: Long Fang , Yang Hua , Xu Yanmin , Hao Haiping , Li Ping 
Published: July 2015

AbstractIt has been well claimed that herbal medicines (HMs) elicit effects via a multi-compounds and multi-targets synergistic mode. However, it lacks appropriate strategies to uncover the combinatory compounds that take effect together and contribute to a certain pharmacological effect of an herb as a whole, which represents a major bottleneck in providing sound evidence in supporting the clinic benefits of HMs. Here, we proposed a strategy to the identification of combinatory compounds contributing to the anti-inflammatory activity of Cardiotonic Pill (CP). The strategy proposed herein contains four core steps, including the identification of bioequivalent combinatorial compounds, chemical family classification-based combinatorial screen, interactive mode evaluation and activity contribution index assay. Using this strategy, we have successfully identified six compounds in combination responsible for the anti-inflammatory effect of CP, whose anti-inflammatory activities were found comparable to that of the whole CP. Additionally, these six compounds take effect via an additive mode but little synergism. This study, together with our recent work in the identification of bioactive equivalent compounds combination, provides a widely applicable strategy to the identification of combinatory compounds responsible for a certain pharmacological activity of HMs.
Position-specific prediction of methylation sites from sequence conservation based on information theory
Authors: Shi Yinan , Guo Yanzhi , Hu Yayun , Li Menglong 
Published: July 2015

AbstractProtein methylation plays vital roles in many biological processes and has been implicated in various human diseases. To fully understand the mechanisms underlying methylation for use in drug design and work in methylation-related diseases, an initial but crucial step is to identify methylation sites. The use of high-throughput bioinformatics methods has become imperative to predict methylation sites. In this study, we developed a novel method that is based only on sequence conservation to predict protein methylation sites. Conservation difference profiles between methylated and non-methylated peptides were constructed by the information entropy (IE) in a wider neighbor interval around the methylation sites that fully incorporated all of the environmental information. Then, the distinctive neighbor residues were identified by the importance scores of information gain (IG). The most representative model was constructed by support vector machine (SVM) for Arginine and Lysine methylation, respectively. This model yielded a promising result on both the benchmark dataset and independent test set. The model was used to screen the entire human proteome and many unknown substrates were identified. These results indicate that our method can serve as a useful supplement to elucidate the mechanism of protein methylation and facilitate hypothesis-driven experimental design and validation.
New “haploid biofilm model” unravels IRA2 as a novel regulator of Candida albicans biofilm formation
Authors: Seneviratne Chaminda Jayampath , Zeng Guisheng , Truong Thuyen , Sze Sarah , Wong Wah , Samaranayake Lakshman , Chan Fong Yee , Wang Yan-Ming , Wang Haitao , Gao Jiaxin , Wang Yue 
Published: July 2015

AbstractClinical isolates of the fungal human pathogen Candida albicans are invariably diploid and heterozygous, impeding genetic study. Recent isolation of C. albicans haploids opens opportunities to apply technologies unfeasible in diploids. However, doubts remain on whether the haploids, derived from chromosome loss, can represent the diploids. Here, we use C. albicans haploids to investigate biofilm, a key virulence attribute. We conducted the first comprehensive characterization of biofilm formation of the haploids in comparison with the diploids. We demonstrate that the haploids form biofilms with essentially the same characteristics as the diploids. Screening a haploid mutant library has uncovered novel GTPase-related genes as biofilm regulators, including IRA2 that encodes an activator of the Ras GTPase. IRA2-deletion mutants develop poorly constructed biofilm in both haploid and diploid C. albicans. Our results demonstrate that the haploids are a valid model for C. albicans biofilm research and a powerful tool for uncovering novel regulators.
Clock gene polymorphism and scheduling of migration: a geolocator study of the barn swallow Hirundo rustica
Authors: Bazzi Gaia , Ambrosini Roberto , Caprioli Manuela , Costanzo Alessandra , Liechti Felix , Gatti Emanuele , Gianfranceschi Luca , Podofillini Stefano , Romano Andrea , Romano Maria , Scandolara Chiara , Saino Nicola , Rubolini Diego 
Published: July 2015

AbstractCircannual rhythms often rely on endogenous seasonal photoperiodic timers involving ‘clock’ genes andClockgene polymorphism has been associated to variation in phenology in some bird species. In the long-distance migratory barn swallowHirundo rustica, individuals bearing the rareClockallele with the largest number of C-terminal polyglutamine repeats found in this species (Q8) show a delayed reproduction and moult later. We explored the association betweenClockpolymorphism and migration scheduling, as gauged by light-level geolocators, in two barn swallow populations (Switzerland; Po Plain, Italy). Genetic polymorphism was low: 91% of the 64 individuals tracked year-round were Q7/Q7homozygotes. We compared the phenology of the rare genotypes with the phenotypic distribution of Q7/Q7homozygotes within each population. In Switzerland, compared to Q7/Q7, two Q6/Q7males departed earlier from the wintering grounds and arrived earlier to their colony in spring, while a single Q7/Q8female was delayed for both phenophases. On the other hand, in the Po Plain, three Q6/Q7individuals had a similar phenology compared to Q7/Q7. The Swiss data are suggestive for a role of genetic polymorphism at a candidate phenological gene in shaping migration traits and support the idea thatClockpolymorphism underlies phenological variation in birds.
Experimental demonstration of a quantum router
Authors: Yuan X. X. , Ma J.-J. , Hou P.-Y. , Chang X.-Y. , Zu C. , Duan L.-M. 
Published: July 2015

AbstractThe router is a key element for a network. We describe a scheme to realize genuine quantum routing of single-photon pulses based on cascading of conditional quantum gates in a Mach-Zehnder interferometer and report a proof-of-principle experiment for its demonstration using linear optics quantum gates. The polarization of the control photon routes in a coherent way the path of the signal photon while preserving the qubit state of the signal photon represented by its polarization. We demonstrate quantum nature of this router by showing entanglement generated between the initially unentangled control and signal photons and confirm that the qubit state of the signal photon is well preserved by the router through quantum process tomography.
Cultural differences in ant-dipping tool length between neighbouring chimpanzee communities at Kalinzu, Uganda
Authors: Koops Kathelijne , Schöning Caspar , Isaji Mina , Hashimoto Chie 
Published: July 2015

AbstractCultural variation has been identified in a growing number of animal species ranging from primates to cetaceans. The principal method used to establish the presence of culture in wild populations is the method of exclusion. This method is problematic, since it cannot rule out the influence of genetics and ecology in geographically distant populations. A new approach to the study of culture compares neighbouring groups belonging to the same population. We applied this new approach by comparing ant-dipping tool length between two neighbouring communities of chimpanzees (Pan troglodytes schweinfurthii) in the Kalinzu Forest, Uganda. Ant-dipping tool length varies across chimpanzee study sites in relation to army ant species (Dorylusspp.) and dipping location (nest vs. trail). We compared the availability of army ant species and dipping tool length between the two communities. M-group tools were significantly longer than S-group tools, despite identical army ant target species availabilities. Moreover, tool length in S-group was shorter than at all other sites where chimpanzees prey on epigaeic ants at nests. Considering the lack of ecological differences between the two communities, the tool length difference appears to be cultural. Our findings highlight how cultural knowledge can generate small-scale cultural diversification in neighbouring chimpanzee communities.
A Novel Serum 4-microRNA Signature for Lung Cancer Detection
Authors: Nadal Ernest , Truini Anna , Nakata Asuka , Lin Jules , Reddy Rishindra M. , Chang Andrew C. , Ramnath Nithya , Gotoh Noriko , Beer David G. , Chen Guoan 
Published: July 2015

AbstractThe aim of this study was to identify differentially-expressed miRNAs in the serum of non-small cell lung cancer (NSCLC) patients that might be a clinically-useful tool for lung cancer early detection. We performed miRNA expression profile analysis using TaqMan OpenArray Human panel in a discovery set of 70 serum samples obtained at lung tumor resection and 22 non-cancer subjects (NC). Selected serum miRNAs were then validated by quantitative PCR using an independent validation set of serum samples from LC patients (n = 84) and NC (n = 23). Sixty miRNAs were significantly up-regulated and 31 were down-regulated in the serum from NSCLC patients versus NC (adjusted p < 0.001). Four miRNAs (miR-193b, miR-301, miR-141 and miR-200b) were selected for validating their diagnostic value in an independent cohort. In the discovery set, the ROC plot derived from the combination of these miRNAs yielded an area under the curve (AUC) of 0.985 (95% CI 0.961–1.000, p < 0.001). In the test set, this miRNA signature exhibited an AUC of 0.993 (95% CI 0.979–1.000, p < 0.001). In conclusion, we identified a serum 4-miRNA signature that discriminated with high accuracy lung cancer patients from NC. Further prospective validation of this miRNA signature is warranted.
Characterization of the honeybee AmNaV1 channel and tools to assess the toxicity of insecticides
Authors: Gosselin-Badaroudine Pascal , Moreau Adrien , Delemotte Lucie , Cens Thierry , Collet Claude , Rousset Matthieu , Charnet Pierre , Klein Michael L. , Chahine Mohamed 
Published: July 2015

AbstractPollination is important for both agriculture and biodiversity. For a significant number of plants, this process is highly and sometimes exclusively, dependent on the pollination activity of honeybees. The large numbers of honeybee colony losses reported in recent years have been attributed to colony collapse disorder. Various hypotheses, including pesticide overuse, have been suggested to explain the disorder. Using the Xenopus oocytes expression system and two microelectrode voltage-clamp, we report the functional expression and the molecular, biophysical and pharmacological characterization of the western honeybee’s sodium channel (Apis Mellifera NaV1). The NaV1 channel is the primary target for pyrethroid insecticides in insect pests. We further report that the honeybee’s channel is also sensitive to permethrin and fenvalerate, respectively type I and type II pyrethroid insecticides. Molecular docking of these insecticides revealed a binding site that is similar to sites previously identified in other insects. We describe in vitro and in silico tools that can be used to test chemical compounds. Our findings could be used to assess the risks that current and next generation pesticides pose to honeybee populations.
Vacuum-free transparent quantum dot light-emitting diodes with silver nanowire cathode
Authors: Jing Pengtao , Ji Wenyu , Zeng Qinghui , Li Di , Qu Songnan , Wang Jia , Zhang Dandan 
Published: July 2015

AbstractEfficient transparent quantum-dot light emitting diodes (QD-LEDs) are demonstrated by using a silver nanowire (AgNW) cathode. The devices are fabricated through a solution technique, not any vacuum processes are involved. Almost identical performance is obtained for both sides of the transparent device, which is primary due to the high transmittance of AgNW cathode. The maximum luminance (efficiency) for ITO and AgNW side is 25,040 cd/m2 (5.6 cd/A) and 23,440 cd/m2 (5.2 cd/A), respectively. The average specular transmittance of the device (involving the glass substrate) is over 60% in the visible range. This study indicates that AgNW electrodes can serve as a cost-effective, flexible alternative to ITO and thereby improve the economic viability and mechanical stability of QD-LEDs. All the results suggest that this is an important progress toward producing transparent QD-LEDs based displays and lighting sources.
DDB2 is involved in ubiquitination and degradation of PAQR3 and regulates tumorigenesis of gastric cancer cells
Authors: Qiao Shanshan , Guo Weiwei , Liao Lujian , Wang Lin , Wang Zheng , Zhang Rui , Xu Daqian , Zhang Yuxue , Pan Yi , Wang Zhenzhen , Chen Yan 
Published: July 2015

DDB2 (damage-specific DNA-binding protein 2) is the product of the xeroderma pigmentosum group E gene which is involved in the initiation of nucleotide excision repair via an ubiquitin ligase complex together with DDB1 and CUL4A (cullin 4A). PAQR3 (progestin and adipoQ receptor family member III) is a newly discovered tumour suppressor that is implicated in the development of many types of human cancers. In the present paper, we report that DDB2 is involved in ubiquitination and degradation of PAQR3. DDB2 is able to interact with PAQR3 in vivo and in vitro. Both overexpression and knockdown experiments reveal that the protein expression level, protein stability and polyubiquitination of PAQR3 are changed by DDB2. Negative regulation of EGF (epidermal growth factor)- and insulin-induced signalling by PAQR3 is also altered by DDB2. At the molecular level, Lys61 of PAQR3 is targeted by DDB2 for ubiquitination. The cell proliferation rate and migration of gastric cancer cells are inhibited by DDB2 knockdown and such effects are abrogated by PAQR3 knockdown, indicating that the effect of DDB2 on the cancer cells is mediated by PAQR3. Collectively, our studies not only pinpoint that DDB2 is a post-translational regulator of PAQR3, but also indicate that DDB2 may play an active role in tumorigenesis via regulating PAQR3.
Interaction in endothelium of non-muscular myosin light-chain kinase and the NF-κB pathway is critical to lipopolysaccharide-induced vascular hyporeactivity
Authors: Recoquillon Sylvain , Carusio Nunzia , Lagrue-Lakhal Anne-Hélène , Tual-Chalot Simon , Filippelli Amelia , Andriantsitohaina Ramaroson , Martinez M. Carmen 
Published: July 2015

During sepsis, endothelial barrier dysfunction contributes to cardiovascular failure, mainly through the release of oxidative metabolites by penetrant leukocytes. We reported the non-muscular isoform of myosin light chain kinase (nmMLCK) playing a pivotal role in endotoxin shock injury associated with oxidative and nitrative stresses, and vascular hyporeactivity. The present study was aimed at understanding the molecular mechanism of lipopolysaccharide (LPS)-induced vascular alterations as well as studying a probable functional association of nmMLCK with nuclear factor κ-light-chain enhancer of activated B cells (NF-κB). Aortic rings from mice were exposed in vitro to LPS and, then, vascular reactivity was measured. Human aortic endothelial cells (HAoECs) were incubated with LPS, and interaction of nmMLCK with NF-κB was analysed. We provide evidence that nmMLCK deletion prevents vascular hyporeactivity induced by in vitro LPS treatment but not endothelial dysfunction in the aorta. Deletion of nmMLCK inhibits LPS-induced NF-κB activation and increases nitric oxide (NO) release via induction of inducible NO synthase (iNOS) within the vascular wall. Also, removal of endothelium prevented both NF-κB and iNOS expression in aortic rings. Among the proinflammatory factors released by LPS-treated endothelial cells, interleukin-6 accounts for the induction of iNOS on smooth muscle cells in response to LPS. Of particular interest is the demonstration that, in HAoECs, LPS-induced NF-κB activation occurs via increased MLCK activity sensitive to the MLCK inhibitor, ML-7, and physical interactions between nmMLCK and NF-κB. We report for the first time on NF-κB as a novel partner of nmMLCK within endothelial cells. The present study demonstrates a pivotal role of nmMLCK in vascular inflammatory pathologies.
Lower cutoff frequency improvement of planar EBG‐patterned PDN using edge termination
Authors: Sadr A. , Masoumi N. 
Published: July 2015

A designed, fabricated and tested electromagnetic bandgap (EBG) structure is proposed for resolving the problem of the lower cut‐off frequency of conventional planar‐type EBGs. Bandwidth enhancement is achieved by incorporating edge termination along the edges of the whole EBG‐patterned power plane. Measurement results show that the lower cutoff frequency is shifted downwards from 800 to 13 MHz. This structure also improves the upper cutoff frequency of 4.3 GHz for the conventional planar EBG to 5.2 GHz. Using this structure, simultaneous switching noise can be suppressed over the relative bandwidth of 63%, which is higher than the commonly used EBGs. The structure is easily fabricated with the current method of printed circuit board manufacturing processes and commonly used SMD resistors and capacitors.
Computational redesign of the lipid-facing surface of the outer membrane protein OmpA
Authors: Stapleton James A. , Whitehead Timothy A. , Nanda Vikas 
Published: July 2015

Significance
The ability to construct novel proteins from basic principles of molecular structure is the fundamental goal of protein design. This is particularly challenging in the case of the β-barrel outer membrane proteins, where our understanding of the rules governing structure and function lags behind that of other classes of proteins. Here, we took a step toward understanding β-barrel membrane protein architecture by focusing on the outward-facing amino acid positions that contact the cell membrane. We replaced the membrane-facing surface of OmpA with new surfaces designed to resemble natural β-barrel surfaces. We were able to design versions of OmpA with mutations at about two-thirds of all surface positions, indicating that β-barrel membrane protein surface design is achievable.
Investigations of initial particle stages during spark discharge
Authors: Ludvigsson Linus , Meuller Bengt O , Messing Maria E 
Published: July 2015

Abstract
The number of nanoparticle-based products on the market is expected to increase considerably during the coming decades. This forces the industry to have highly meticulous manufacturing of large amounts of nanoparticles using cheap and environmentally friendly methods. For the production of metal nanoparticles spark discharge generation is a promising route to fulfill these demands. The spark discharge generator can be easily scaled-up for mass production due to its simple design solely by placing several units in parallel. Before doing so, one first needs to optimize a single spark discharge generator unit. To optimize the spark discharge generator in a controlled way the first stage of nanoparticle formation needs to be understood. To improve this understanding we have constructed a customized nanoparticle sampler to enable sampling of the initial stages of particle formation for imaging in a TEM. In this article we present the design of the sampler and discuss optimal sampling parameters. We also present how the generation parameters can be tuned in order to affect the first stages of particle formation and hence the final nanoparticles.