bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glassy nature of hierarchical organizations
Authors: Zamani Maryam , Vicsek Tamas 
Published: April 2017

AbstractThe question of why and how animal and human groups form temporarily stable hierarchical organizations has long been a great challenge from the point of quantitative interpretations. The prevailing observation/consensus is that a hierarchical social or technological structure is optimal considering a variety of aspects. Here we introduce a simple quantitative interpretation of this situation using a statistical mechanics-type approach. We look for the optimum of the efficiency function$${E}_{eff}=1/N{\sum }_{ij}{J}_{ij}{a}_{i}{a}_{j}$$Eeff=1/N∑ijJijaiajwithJijdenoting the nature of the interaction between the unitsiandjandaistanding for the ability of memberito contribute to the efficiency of the system. Notably, this expression forEeffhas a similar structure to that of the energy as defined for spin-glasses. Unconventionally, we assume thatJij-s can have the values 0 (no interaction), +1 and −1;furthermore, a direction is associated with each edge. The essential and novel feature of our approach is that instead of optimizing the state of the nodes of a pre-defined network, we search for extrema for givenai-s in the complex efficiency landscape by finding locally optimal network topologies for a given number of edges of the subgraphs considered.
Comparative indoor and outdoor stability measurements of polymer based solar cells
Authors: Zhang Yiwei , Yi Hunan , Iraqi Ahmed , Kingsley James , Buckley Alastair , Wang Tao , Lidzey David G. 
Published: April 2017

AbstractWe report comparative indoor and outdoor stability testing of organic solar cells based on a blend between a donor-acceptor polyfluorene copolymer and a fullerene derivative. The outdoor testing was conducted for a period over 12,000 hours in Sheffield, England, with a Ts80 lifetime determined in excess of 10,000 hours (420 days). Indoor lifetime testing was performed on solar cells using a solar simulator under a constant irradiance of 1000 W/m2 for more than 650 hours. We show that under the conditions explored here, device degradation under the two sets of conditions is approximately dependent on the absorbed optical energy dose.
Sequence variation in Plasmodium falciparum Histidine Rich Proteins 2 and 3 in Indian isolates: Implications for Malaria Rapid Diagnostic Test Performance
Authors: Kumar Bharti Praveen , Singh Chandel Himanshu , Krishna Sri , Nema Shrikant , Ahmad Amreen , Udhayakumar Venkatachalam , Singh Neeru 
Published: April 2017

AbstractCommercial malaria rapid diagnostic tests (RDTs) detect P. falciparum histidine rich protein 2 (PfHRP2) and cross react with PfHRP3, a structural homologue. Here, we analysed natural variations in PfHRP2 and PfHRP3 sequences from Indian isolates and correlated these variations with RDT reactivity. A total 1392 P. falciparum positive samples collected from eight endemic states were PCR amplified for Pfhrp2 and Pfhrp3 genes and were sequenced. The deduced protein sequences were analysed for repeat variations and correlated with RDT reactivity. Out of 1392 PCR amplified samples, a single sample was Pfhrp2 negative and two samples were Pfhrp3 negative. Complete Pfhrp2 and Pfhrp3 sequences were obtained for 769 samples and 750 samples, respectively. A total of 16 distinct repeat motifs were observed for Pfhrp2 and 11 for Pfhrp3, including some new repeat types. No correlation was found between variations in the size of Pfhrp2 repeat types 2 and 7, nor between any combinations of repeat motifs, and performance of a commercial RDT at low parasite densities. The findings suggest that sequence diversity in Pfhrp2 and Pfhrp3 genes in Indian isolates is not likely to negatively influence performance of currently used PfHRP2 RDTs.
Chaotic Resonance in Typical Routes to Chaos in the Izhikevich Neuron Model
Authors: Nobukawa Sou , Nishimura Haruhiko , Yamanishi Teruya 
Published: April 2017

AbstractChaotic resonance (CR), in which a system responds to a weak signal through the effects of chaotic activities, is a known function of chaos in neural systems. The current belief suggests that chaotic states are induced by different routes to chaos in spiking neural systems. However, few studies have compared the efficiency of signal responses in CR across the different chaotic states in spiking neural systems. We focused herein on the Izhikevich neuron model, comparing the characteristics of CR in the chaotic states arising through the period-doubling or tangent bifurcation routes. We found that the signal response in CR had a unimodal maximum with respect to the stability of chaotic orbits in the tested chaotic states. Furthermore, the efficiency of signal responses at the edge of chaos became especially high as a result of synchronization between the input signal and the periodic component in chaotic spiking activity.
A reassortant H9N2 influenza virus containing 2009 pandemic H1N1 internal-protein genes acquired enhanced pig-to-pig transmission after serial passages in swine
Authors: Mancera Gracia José Carlos , Van den Hoecke Silvie , Richt Juergen A. , Ma Wenjun , Saelens Xavier , Van Reeth Kristien 
Published: April 2017

AbstractAvian H9N2 and 2009 pandemic H1N1 (pH1N1) influenza viruses can infect pigs and humans, raising the concern that H9N2:pH1N1 reassortant viruses could emerge. Such reassortants demonstrated increased replication and transmissibility in pig, but were still inefficient when compared to pH1N1. Here, we evaluated if a reassortant virus containing the hemagglutinin and neuraminidase of A/quail/Hong Kong/G1/1997 (H9N2) in the A/California/04/2009 (pH1N1) backbone could become better adapted to pigs by serial passaging. The tropism of the original H9N2:pH1N1 (P0) virus was restricted to the nasal mucosa, with no virus detected in the trachea or lungs. Nevertheless, after seven passages the H9N2:pH1N1 (P7) virus replicated in the entire respiratory tract. We also compared the transmissibility of H9N2:pH1N1 (P0), H9N2:pH1N1 (P7) and pH1N1. While only 2/6 direct-contact pigs showed nasal virus excretion of H9N2:pH1N1 (P0) ≥five days, 4/6 direct-contact animals shed the H9N2:pH1N1 (P7). Interestingly, those four animals shed virus with titers similar to those of the pH1N1, which readily transmitted to all six contact animals. The broader tissue tropism and the increased post-transmission replication after seven passages were associated with the HA-D225G substitution. Our data demonstrate that the pH1N1 internal-protein genes together with the serial passages favour H9N2 virus adaptation to pigs.
Numerical analysis of wide-field optical imaging with a sub-20 nm resolution based on a meta-sandwich structure
Authors: Cao Shun , Wang Taisheng , Yang Jingzhong , Hu Bingliang , Levy Uriel , Yu Weixing 
Published: April 2017

AbstractBiological research requires wide-field optical imaging techniques with resolution down to the nanometer scale to study the biological process in a sub-cell or single molecular level. To meet this requirement, wide-field structured illumination method (WFSIM) has been extensively studied. The resolution of WFSIM is determined by the period of the optical interference pattern. However, in traditional WFSIM this period is diffraction limited so that pattern having periodicity smaller than 100 nm cannot be generated and as a result achieving an imaging resolution better than 50 nm is a great challenge. Here, we demonstrate a wide-field optical nanoimaging method based on a meta-sandwich structure (MSS) model. It is found that this structure can support standing wave surface plasmons interference pattern with a period of only 31 nm for 532 nm wavelength incident light. Furthermore, the potential application of the MSS for wide-field super-resolution imaging is discussed and the simulation results show an imaging resolution of sub-20 nm can be achieved. The demonstrated method paves a new route for the improvement of the wide field optical nanoimaging, which can be applied by biological researchers to study biological process conducted in cell membrane, such as mass transportation and others.
Prognostic value of impaired estimated glomerular filtration rate in intravesical BCG-treated non–muscle-invasive bladder cancer patients
Authors: Tae Bum Sik , Kim Jung Kwon , Kang Minyong , Jeong Chang Wook , Kwak Cheol , Kim Hyeon Hoe , Ku Ja Hyeon 
Published: April 2017

AbstractTo evaluate the influence of patient-associated parameters and comorbities, with a special focus on renal function after intravesical adjuvant bacillus Calmette-Gue´rin (BCG) immunotherapy in patients with non–muscle-invasive bladder cancer (NMIBC). We retrospectively reviewed the medical records of patients treated from October, 1991 to December, 2013 at Seoul National University who were diagnosed with NMIBC and treated with intravesical BCG. A total of 344 patients who were diagnosed with NMIBC and treated with intravesical BCG were enrolled in this study. Tumor recurrence was observed in 171 patients (49.3%); progression to higher pT category or grade was found in 68 patients (15.1%). Multivariate analysis demonstrated that recurrent tumors and the presence of multiple tumors increased the risk of recurrence. However, other factors also appeared to predict recurrence, such as impaired renal function (<60 ml/min), which was associated with recurrence in univariate and multivariate analyses (HR 1.879 p = 0.008). It is worthy of notice that impaired renal function was an independent predictor of tumor recurrence after BCG instillation in multivariate analysis. Therefore, we should consider not only the clinical or pathologic findings of a tumor but also renal function during decision-making for additional therapy.
Malaria was a weak selective force in ancient Europeans
Authors: Gelabert Pere , Olalde Iñigo , de-Dios Toni , Civit Sergi , Lalueza-Fox Carles 
Published: April 2017

AbstractMalaria, caused by Plasmodium parasites, is thought to be one of the strongest selective forces that has shaped the genome of modern humans and was endemic in Europe until recent times. Due to its eradication around mid-twentieth century, the potential selective history of malaria in European populations is largely unknown. Here, we screen 224 ancient European genomes from the Upper Palaeolithic to the post-Roman period for 22 malaria-resistant alleles in twelve genes described in the literature. None of the most specific mutations for malaria resistance, like those at G6PD, HBB or Duffy blood group, have been detected among the available samples, while many other malaria-resistant alleles existed well before the advent of agriculture. We detected statistically significant differences between ancient and modern populations for the ATP2B4, FCGR2B and ABO genes and we found evidence of selection at IL-10 and ATP2B4 genes. However it is unclear whether malaria is the causative agent, because these genes are also involved in other immunological challenges. These results suggest that the selective force represented by malaria was relatively weak in Europe, a fact that could be associated to a recent historical introduction of the severe malaria pathogen.
Identifying disease-associated pathways in one-phenotype data based on reversal gene expression orderings
Authors: Hong Guini , Li Hongdong , Zhang Jiahui , Guan Qingzhou , Chen Rou , Guo Zheng 
Published: April 2017

AbstractDue to the invasiveness nature of tissue biopsy, it is common that investigators cannot collect sufficient normal controls for comparison with diseased samples. We developed a pathway enrichment tool,DRFunc, to detect significantly disease-disrupted pathways by incorporating normal controls from other experiments. The method was validated using both microarray and RNA-seq expression data for different cancers. The high concordant differentially ranked (DR) gene pairs were identified between cases and controls from different independent datasets. The DR gene pairs were used in theDRFuncalgorithm to detect significantly disrupted pathways in one-phenotype expression data by combing controls from other studies. TheDRFuncalgorithm was exemplified by the detection of significant pathways in glioblastoma samples. The algorithm can also be used to detect altered pathways in the datasets with weak expression signals, as shown by the analysis on the expression data of chemotherapy-treated breast cancer samples.
Incidence, worsening and risk factors of daytime sleepiness in a population-based 5-year longitudinal study
Authors: Jaussent I. , Morin C. M. , Ivers H. , Dauvilliers Y. 
Published: April 2017

AbstractExcessive daytime sleepiness (EDS) is highly prevalent in the general population; however little is known about its evolution and predictors. Our objectives were to document its natural history, provide estimates of its prevalence, incidence and persistence rates, and to identify predictors of increased daytime sleepiness (DS) in a longitudinal community study of 2157 adults over 5 years. Participants completed postal assessment at baseline and at each yearly follow-up. DS was evaluated by the Epworth Sleepiness scale (ESS). At baseline, 33% reported EDS (ESS > 10) with 33% of them reported persistent EDS. Of those without EDS at baseline, 28% developed incident EDS (15% were persistent) and 31% increased DS (augmentation ≥4-points between two consecutive evaluations). Younger age and depression were independent predictors of incident EDS and DS increase while lower coffee consumption, smoking, insomnia, tiredness and chronic pain were associated with incident EDS, and living alone with DS increase only. Persistent vs transient EDS or DS showed association with poor general health including metabolic diseases. Thus, sleepiness fluctuated over time and it was predicted by common lifestyle and psychological factors potentially modifiable. However, persistent sleepiness was associated with chronic medical diseases thus highlighting a homogeneous group at risk requiring a dedicated management.
Mechanistic insights into manganese oxidation of a soil-borne Mn(II)-oxidizing Escherichia coli strain by global proteomic and genetic analyses
Authors: Wang Zhiyong , Wang Jieping , Liu Jin , Chen Hong , Li Mingshun , Li Lin 
Published: April 2017

AbstractAn iTRAQ-based comparative and quantitative proteomics analysis of a soil-borne Mn(II)-oxidizing bacterium, Escherichia coli MB266, was conducted during the exponential and stationary growth phases. A total of 1850 proteins were identified in 4 samples, of which 373 and 456 proteins were significantly up- or down-regulated in at least one pairwise comparison, respectively. The iTRAQ data indicated that several enzymes involved in fatty acid metabolism (i.e., FabA, FabD and FabZ) and pyruvate metabolism (particularly pyruvate oxidase PoxB) were significantly up-regulated, while those related to the tricarboxylic acid cycle (such as FrdB, FumB and AcnA) and methylcitrate cycle (i.e., PrpC) were inactivated in the presence of 1 mM Mn(II); the amounts of some stress response and signal transduction system-related proteins (i.e., Spy) were remarkably increased, and the cold shock protein CspD was significantly up-regulated during the exponential growth phase. However, all verified heat shock proteins remained unchanged. The reactive oxygen species response and some redox enzymes might also be involved in Mn oxidation processes. The involvement of several cellular proteins in Mn(II) oxidation, including PoxB, Spy and MCO266, was further confirmed by gene disruption and expression complementation experiments. Based on these results, a signal transduction mechanism coupled to Mn oxidation was proposed.
Participants with Normal Weight or with Obesity Show Different Relationships of 6-n-Propylthiouracil (PROP) Taster Status with BMI and Plasma Endocannabinoids
Authors: Carta Gianfranca , Melis Melania , Pintus Stefano , Pintus Paolo , Piras Carla A. , Muredda Laura , Demurtas Daniela , Di Marzo Vincenzo , Banni Sebastiano , Barbarossa Iole Tomassini 
Published: April 2017

AbstractReduced taste sensitivity to 6-n-propylthiouracil (PROP), a genetic trait regarded as a general index for oral chemosensory perception, has been associated with a calorie-rich food preference and lower circulating endocannabinoid levels in participants with normal weight (NW), which suggests an adaptive mechanism to maintain a lean phenotype. In this study, we assessed whether participants with obesity (OB) show different patterns of plasma endocannabinoids and lipid metabolism biomarkers from those of NW, with further categorization based on their PROP sensitivity. NW and OB were classified by their PROP taster status as non-tasters (NT), medium-tasters (MT) and supertasters (ST). The blood samples were analysed for plasma endocannabinoids, nonesterified fatty acids (NEFA) and retinol, which have been associated to metabolic syndrome. In OB, we found a higher BMI and lower circulating endocannabinoids in ST vs. OB NT. However, OB ST showed lower circulating NEFA and retinol levels, which suggested a more favourable lipid metabolism and body fat distribution than those of OB NT. We confirmed lower plasma endocannabinoid levels in NW NT than in NW ST. These data suggest that PROP taste sensitivity determines metabolic changes and ultimately body mass composition differently in OB and NW.
Survival changes in patients with small cell lung cancer and disparities between different sexes, socioeconomic statuses and ages
Authors: Wang Shuncong , Tang Jianjun , Sun Tiantian , Zheng Xiaobin , Li Jie , Sun Hongliu , Zhou Xiuling , Zhou Cuiling , Zhang Hongyu , Cheng Zhibin , Ma Haiqing , Sun Huanhuan 
Published: April 2017

AbstractSmall cell lung cancer (SCLC), as a proportion, makes up only 15–17% of lung cancer cases. The development of treatments for SCLC has remained stagnant for decades, and SCLC is expected to persist as a threat to human health. To date, no publications based on large populations have been reported. We calculated survival changes in patients with SCLC during each decade between 1983 and 2012 to determine the roles of race, sex, age, and socioeconomic status (SES) on survival rates based on the Surveillance, Epidemiology, and End Results (SEER) registries. In total, 106,296 patients with SCLC were identified, with the overall incidence per 100,000 decreasing each decade from 9.6 to 7.8 to 5.8. The median survival for SCLC remained 7 months, and the 12-month relative survival rates (RSRs) remained relatively stable at 32.9%, 33.2% and 33.2% during each decade. The 5-year RSRs significantly improved from 4.9% to 5.9% to 6.4% during each decade, but remained extremely low. In addition, a narrowing of the survival gaps among SES groups and stable survival gaps between sexes were observed. Although the incidence of SCLC decreased during each decade, the overall survival remained relatively stable, highlighting the urgency of developing novel treatments and the importance of prevention and early detection.
A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies
Authors: Ramos Vitor , Morais João , Vasconcelos Vitor M. 
Published: April 2017

AbstractThe dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies.
Automated and manual patch clamp data of human induced pluripotent stem cell-derived dopaminergic neurons
Authors: Franz Denise , Olsen Hervør Lykke , Klink Oliver , Gimsa Jan 
Published: April 2017

AbstractHuman induced pluripotent stem cells can be differentiated into dopaminergic neurons (Dopa.4U). Dopa.4U neurons expressed voltage-gated NaV and KV channels and showed neuron-like spontaneous electrical activity. In automated patch clamp measurements with suspended Dopa.4U neurons, delayed rectifier K+ current (delayed KV) and rapidly inactivating A-type K+ current (fast KV) were identified. Examination of the fast KV current with inhibitors yielded IC50 values of 0.4 mM (4-aminopyridine) and 0.1 mM (tetraethylammonium). In manual patch clamp measurements with adherent Dopa.4U neurons, fast KV current could not be detected, while the delayed KV current showed an IC50 of 2 mM for 4-aminopyridine. The NaV channels in adherent and suspended Dopa.4U neurons showed IC50 values for tetrodotoxin of 27 and 2.9 nM, respectively. GABA-induced currents that could be observed in adherent Dopa.4U neurons could not be detected in suspended cells. Application of current pulses induced action potentials in approx. 70 % of the cells. Our results proved the feasibility of automated electrophysiological characterization of neuronal cells.
Understanding the Rising Phase of the PM2.5 Concentration Evolution in Large China Cities
Authors: Lv Baolei , Cai Jun , Xu Bing , Bai Yuqi 
Published: April 2017

AbstractLong-term air quality observations are seldom analyzed from a dynamic view. This study analyzed fine particulate matter (PM2.5) pollution processes using long-term PM2.5 observations in three Chinese cities. Pollution processes were defined as linearly growing PM2.5 concentrations following the criteria of coefficient of determination R2 > 0.8 and duration time T ≥ 18 hrs. The linear slopes quantitatively measured pollution levels by PM2.5 concentrations rising rates (PMRR, μg/(m3·hr)). The 741, 210 and 193 pollution processes were filtered out, respectively, in Beijing (BJ), Shanghai (SH), and Guangzhou (GZ). Then the relationships between PMRR and wind speed, wind direction, 24-hr backward points, gaseous pollutants (CO, NO2 and SO2) concentrations, and regional PM2.5 levels were studied. Inverse relationships existed between PMRR and wind speed. The wind directions and 24-hr backward points converged in specific directions indicating long-range transport. Gaseous pollutants concentrations increased at variable rates in the three cities with growing PMRR values. PM2.5 levels at the upwind regions of BJ and SH increased at high PMRRs. Regional transport dominated the PM2.5 pollution processes of SH. In BJ, both local contributions and regional transport increased during high-PMRR pollution processes. In GZ, PM2.5 pollution processes were mainly caused by local emissions.