bluuebunny/crossref_metadata_2025 huggingface dataset:
The importance of illumination in nest site choice and nest characteristics of cavity nesting birds
Authors: Podkowa Paweł , Surmacki Adrian
Published: April 2017

Light has a significant impact on many aspects of avian biology, physiology and behaviour. An increasing number of studies show that illumination may positively influences birds’ offspring fitness by e.g. acceleration of embryo development, stimulation of skeleton growth or regulation of circadian rhythm. Because nest cavities have especially low illumination, suitable light levels may be especially important for species which nest there. We may therefore expect that birds breeding in relatively dim conditions should prefer brighter nest sites and/or evolve behavioral mechanisms to secure sufficient light levels in the nest. Using nest boxes with modified internal illumination, we experimentally tested whether light regime is a cue for nest site selection of secondary cavity-nesting species. Additionally, we investigated whether nest building strategies are tuned to internal illumination. Our results demonstrate that, nest boxes with elevated illumination were chosen twice as often as dark nest boxes. Moreover, birds built higher nests in dark nest boxes than birds in boxes with elevated illumination, which suggests a mechanism of compensating for low light conditions. Our results provide the first experimental support for the idea that nest site choice and nest building behaviour in cavity-nesting birds are influenced by ambient illumination.
Pulse Rate Measurement During Sleep Using Wearable Sensors, and its Correlation with the Menstrual Cycle Phases, A Prospective Observational Study
Authors: Shilaih Mohaned , Clerck Valérie de , Falco Lisa , Kübler Florian , Leeners Brigitte
Published: April 2017

An affordable, user-friendly fertility-monitoring tool remains an unmet need. We examine in this study the correlation between pulse rate (PR) and the menstrual phases using wrist-worn PR sensors. 91 healthy, non-pregnant women, between 22–42 years old, were recruited for a prospective-observational clinical trial. Participants measured PR during sleep using wrist-worn bracelets with photoplethysmographic sensors. Ovulation day was estimated with “Clearblue Digital-Ovulation-urine test”. Potential behavioral and nutritional confounders were collected daily. 274 ovulatory cycles were recorded from 91 eligible women, with a mean cycle length of 27.3 days (±2.7). We observed a significant increase in PR during the fertile window compared to the menstrual phase (2.1 beat-per-minute, p < 0.01). Moreover, PR during the mid-luteal phase was also significantly elevated compared to the fertile window (1.8 beat-per-minute, p < 0.01), and the menstrual phase (3.8 beat-per-minute, p < 0.01). PR increase in the ovulatory and mid-luteal phase was robust to adjustment for the collected confounders. There is a significant increase of the fertile-window PR (collected during sleep) compared to the menstrual phase. The aforementioned association was robust to the inter- and intra-person variability of menstrual-cycle length, behavioral, and nutritional profiles. Hence, PR monitoring using wearable sensors could be used as one parameter within a multi-parameter fertility awareness-based method.
Invisible body illusion modulates interpersonal space
Authors: D’Angelo Mariano , di Pellegrino Giuseppe , Frassinetti Francesca
Published: April 2017

Interpersonal space (e.g., IPS) refers to the physical distance individuals maintain from others during social interactions, and into which intrusion by others can cause discomfort. Here, we asked whether the size of IPS is affected by manipulation of one’s own body representation. To address this issue, in Experiment 1, IPS was measured through a comfort-distance task, before and after eliciting the illusion of owning an invisible body. To rule out a general, nonspecific change in space perception consequent the illusion, we also assessed peripersonal space, e.g., PPS, the area around the body used to act on nearby objects, through a reaching-distance task. Results showed that the experience of invisibility induces a selective contraction of IPS, without affecting the perceived reaching space around the body. In Experiment 2, a tool-use manipulation produced the opposite dissociation, modifying the boundaries of PPS, but leaving IPS distance unaltered. Collectively, these findings support a close relationship between IPS and the conscious representation of the body external appearance, i.e. the body image, and suggest the existence of two functionally separate representations of the space immediately surrounding the body in humans, which may form the basis of distinct processes engaged for different behavioural contexts.
High throughput single cell counting in droplet-based microfluidics
Authors: Lu Heng , Caen Ouriel , Vrignon Jeremy , Zonta Eleonora , El Harrak Zakaria , Nizard Philippe , Baret Jean-Christophe , Taly Valérie
Published: April 2017

Droplet-based microfluidics is extensively and increasingly used for high-throughput single-cell studies. However, the accuracy of the cell counting method directly impacts the robustness of such studies. We describe here a simple and precise method to accurately count a large number of adherent and non-adherent human cells as well as bacteria. Our microfluidic hemocytometer provides statistically relevant data on large populations of cells at a high-throughput, used to characterize cell encapsulation and cell viability during incubation in droplets.
Nanostructured laminar tungsten alloy with improved ductility by surface mechanical attrition treatment
Authors: Guo Hong-Yan , Xia Min , Chan Lap-Chung , Wang Kun , Zhang Xiao-Xin , Yan Qing-Zhi , He Man-Chao , Lu Jian , Ge Chang-Chun
Published: April 2017

A nanostructured laminar W-La2O3 alloy (WL10) with improved ductility was prepared using a surface mechanical attrition treatment (SMAT). φ1.5 mm ZrO2 WL10 balls subjected to SMAT (called φ1.5 mm ZrO2 ball SMATed WL10) samples possess the best surface profile and excellent integrated mechanical properties (the ductile-brittle transition temperature (DBTT) value decreases by approximately 200 °C, and the bending strength decreases by 100 Mpa). A highly dense group of laminates was detected near the surface of the φ1.5 mm ZrO2 ball SMATed WL10 sample. The SMATed WL10 laminates were composed of a micro-grain layer, an ultrafine-grain layer and a nanosized-grain layer. The nanostructured laminar surface layer of the φ1.5 mm ZrO2 ball SMATed WL10 sample is approximately 1–2 μm. The top surface of the WL10 plates with and without the SMAT process possesses residual compressive stress of approximately −883 MPa and −241 MPa, respectively, in the y direction and −859 MPa and −854 MPa, respectively, in the x direction. The SMAT process could be a complementary method to further improve the toughness of tungsten-based materials.
Multi-frequency sound production and mixing in graphene
Authors: Heath M. S. , Horsell D. W.
Published: April 2017

The ability to generate, amplify, mix and modulate sound in one simple electronic device would open up a new world in acoustics. Here we show how to build such a device. It generates sound thermoacoustically by Joule heating in graphene. A rich sonic palette is created by controlling the composition and flow of the electric current through the graphene. This includes frequency mixing (heterodyning), which results exclusively from the Joule mechanism. It also includes shaping of the sound spectrum by a dc current and modulating its amplitude with a transistor gate. We show that particular sounds are indicators of nonlinearity and can be used to quantify nonlinear contributions to the conduction. From our work, we expect to see novel uses of acoustics in metrology, sensing and signal processing. Together with the optical qualities of graphene, its acoustic capabilities should inspire the development of the first combined audio-visual nanotechnologies.
Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin
Authors: Ahn Richard S. , Taravati Keyon , Lai Kevin , Lee Kristina M. , Nititham Joanne , Gupta Rashmi , Chang David S. , Arron Sarah T. , Rosenblum Michael , Liao Wilson
Published: April 2017

Human skin consists of multiple cell types, including epithelial, immune, and stromal cells. Transcriptomic analyses have previously been performed from bulk skin samples or from epithelial and immune cells expanded in cell culture. However, transcriptomic analysis of bulk skin tends to drown out expression signals from relatively rare cells while cell culture methods may significantly alter cellular phenotypes and gene expression profiles. To identify distinct transcriptomic profiles of multiple cell populations without substantially altering cell phenotypes, we employed a fluorescence activated cell sorting method to isolate keratinocytes, dendritic cells, CD4+ T effector cells, and CD8+ T effector cells from healthy skin samples, followed by RNA-seq of each cell population. Principal components analysis revealed distinct clustering of cell types across samples, while differential expression and coexpression network analyses revealed transcriptional profiles of individual cell populations distinct from bulk skin, most strikingly in the least abundant CD8+ T effector population. Our work provides a high resolution view of cutaneous cellular gene expression and suggests that transcriptomic profiling of bulk skin may inadequately capture the contribution of less abundant cell types.
How doctors diagnose diseases and prescribe treatments: an fMRI study of diagnostic salience
Authors: Melo Marcio , Gusso Gustavo D. F. , Levites Marcelo , Amaro Edson , Massad Eduardo , Lotufo Paulo A. , Zeidman Peter , Price Cathy J. , Friston Karl J.
Published: April 2017

Understanding the brain mechanisms involved in diagnostic reasoning may contribute to the development of methods that reduce errors in medical practice. In this study we identified similar brain systems for diagnosing diseases, prescribing treatments, and naming animals and objects using written information as stimuli. Employing time resolved modeling of blood oxygen level dependent (BOLD) responses enabled time resolved (400 milliseconds epochs) analyses. With this approach it was possible to study neural processes during successive stages of decision making. Our results showed that highly diagnostic information, reducing uncertainty about the diagnosis, decreased monitoring activity in the frontoparietal attentional network and may contribute to premature diagnostic closure, an important cause of diagnostic errors. We observed an unexpected and remarkable switch of BOLD activity within a right lateralized set of brain regions related to awareness and auditory monitoring at the point of responding. We propose that this neurophysiological response is the neural substrate of awareness of one’s own (verbal) response. Our results highlight the intimate relation between attentional mechanisms, uncertainty, and decision making and may assist the advance of approaches to prevent premature diagnostic closure.
Development of structural colour in leaf beetles
Authors: Onelli Olimpia D. , Kamp Thomas van de , Skepper Jeremy N. , Powell Janet , Rolo Tomy dos Santos , Baumbach Tilo , Vignolini Silvia
Published: April 2017

Structural colours in living organisms have been observed and analysed in a large number of species, however the study of how the micro- and nano-scopic natural structures responsible of such colourations develop has been largely ignored. Understanding the interplay between chemical composition, structural morphology on multiple length scales, and mechanical constraints requires a range of investigation tools able to capture the different aspects of natural hierarchical architectures. Here, we report a developmental study of the most widespread strategy for structural colouration in nature: the cuticular multilayer. In particular, we focus on the exoskeletal growth of the dock leaf beetle Gastrophysa viridula, capturing all aspects of its formation: the macroscopic growth is tracked via synchrotron microtomography, while the submicron features are revealed by electron microscopy and light spectroscopy combined with numerical modelling. In particular, we observe that the two main factors driving the formation of the colour-producing multilayers are the polymerization of melanin during the ecdysis and the change in the layer spacing during the sclerotisation of the cuticle. Our understanding of the exoskeleton formation provides a unique insight into the different processes involved during metamorphosis.
Glassy nature of hierarchical organizations
Authors: Zamani Maryam , Vicsek Tamas
Published: April 2017

The 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

We 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

Commercial 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

Chaotic 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

Avian 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

Biological 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

To 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

Malaria, 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

Due 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

Excessive 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

An 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

Reduced 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

Small 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

The 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

Human 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

Long-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.
A Variation Code Accounts for the Perceived Roughness of Coarsely Textured Surfaces
Authors: Goodman James M. , Bensmaia Sliman J.
Published: April 2017

For decades, the dominant theory of roughness coding in the somatosensory nerves posited that perceived roughness was determined by the spatial pattern of activation in one population of tactile nerve fibers, namely slowly adapting type 1 (SA1) afferents. Indeed, the perceived roughness of coarsely textured surfaces tracks the spatial variation in SA1 responses – the degree to which response strength varies across SA1 afferents. However, in a later study, the roughness of a different set of dot patterns was found to be a monotonic function of dot spacing, a result interpreted as evidence that roughness was determined by the strength of SA1 responses – the population firing rate – rather than their spatial layout. Then again, the spatial variation hypothesis was not tested directly as afferent responses to the conflicting patterns were not measured. To fill this gap, we simulated afferent responses to the dot patterns used in these roughness coding experiments using a model of skin mechanics. We then implemented the spatial variation and firing rate models of roughness based on these simulated responses to generate predictions of perceived roughness. We found that the spatial variation model accounts for perceived roughness under all tested conditions whereas the firing rate model does not.
Ionizing radiation abrogates the pro-tumorigenic capacity of cancer-associated fibroblasts co-implanted in xenografts
Authors: Grinde Maria Tunset , Vik Jørg , Camilio Ketil André , Martinez-Zubiaurre Inigo , Hellevik Turid
Published: April 2017

Cancer-associated fibroblasts (CAFs) are abundantly present in solid tumors and affect tumorigenesis and therapeutic responses. In the context of clinical radiotherapy, the impact of irradiated CAFs to treatment outcomes is largely unexplored. Aiming at improving radiotherapy efficacy, we have here explored the effect of radiation on the inherent pro-tumorigenic capacity of CAFs in animals. Ionizing radiation was delivered to cultured CAFs as single-high or fractionated doses. Tumor development was compared in mice receiving A549 lung tumor cells admixed with irradiated or control CAFs. Biological mechanisms behind tumor growth regulation were investigated by quantitative histology and immunohistochemistry. Viability assessments confirmed that irradiated CAFs are fully functional prior to implantation. However, the enhanced tumorigenic effect observed in tumors co-implanted with control CAFs was abrogated in tumors established with irradiated CAFs. Experiments to ascertain fate of implanted fibroblasts showed that exogenously administered CAFs reside at the implantation site for few days, suggesting that tumor growth regulation from admixed CAFs take place during initial tumor formation. Our work demonstrate that irradiated CAFs lose their pro-tumorigenic potential in vivo, affecting angiogenesis and tumor engraftment. This finding propose a previously unknown advantageous effect induced by radiotherapy, adding to the direct cytotoxic effects on transformed epithelial cells.
Size and shape variations of the bony components of sperm whale cochleae
Authors: Schnitzler Joseph G. , Frédérich Bruno , Früchtnicht Sven , Schaffeld Tobias , Baltzer Johannes , Ruser Andreas , Siebert Ursula
Published: April 2017

Several mass strandings of sperm whales occurred in the North Sea during January and February 2016. Twelve animals were necropsied and sampled around 48 h after their discovery on German coasts of Schleswig Holstein. The present study aims to explore the morphological variation of the primary sensory organ of sperm whales, the left and right auditory system, using high-resolution computerised tomography imaging. We performed a quantitative analysis of size and shape of cochleae using landmark-based geometric morphometrics to reveal inter-individual anatomical variations. A hierarchical cluster analysis based on thirty-one external morphometric characters classified these 12 individuals in two stranding clusters. A relative amount of shape variation could be attributable to geographical differences among stranding locations and clusters. Our geometric data allowed the discrimination of distinct bachelor schools among sperm whales that stranded on German coasts. We argue that the cochleae are individually shaped, varying greatly in dimensions and that the intra-specific variation observed in the morphology of the cochleae may partially reflect their affiliation to their bachelor school. There are increasing concerns about the impact of noise on cetaceans and describing the auditory periphery of odontocetes is a key conservation issue to further assess the effect of noise pollution.
Toward surface orbitronics: giant orbital magnetism from the orbital Rashba effect at the surface of sp-metals
Authors: Go Dongwook , Hanke Jan-Philipp , Buhl Patrick M. , Freimuth Frank , Bihlmayer Gustav , Lee Hyun-Woo , Mokrousov Yuriy , Blügel Stefan
Published: April 2017

As the inversion symmetry is broken at a surface, spin-orbit interaction gives rise to spin-dependent energy shifts – a phenomenon which is known as the spin Rashba effect. Recently, it has been recognized that an orbital counterpart of the spin Rashba effect – the orbital Rashba effect – can be realized at surfaces even without spin-orbit coupling. Here, we propose a mechanism for the orbital Rashba effect based on sp orbital hybridization, which ultimately leads to the electric polarization of surface states. For the experimentally well-studied system of a BiAg2 monolayer, as a proof of principle, we show from first principles that this effect leads to chiral orbital textures in k-space. In predicting the magnitude of the orbital moment arising from the orbital Rashba effect, we demonstrate the crucial role played by the Berry phase theory for the magnitude and variation of the orbital textures. As a result, we predict a pronounced manifestation of various orbital effects at surfaces, and proclaim the orbital Rashba effect to be a key platform for surface orbitronics.
Sorption of Nickel(II) on a Calcareous Aridisol Soil, China: Batch, XPS, and EXAFS Spectroscopic Investigations
Authors: Qiang Shirong , Han Bin , Zhao Xiaolan , Yang Yunbo , Shao Dadong , Li Ping , Liang Jianjun , Fan Qiaohui
Published: April 2017

The sorption of Ni(II) on a calcareous aridisol (CA) soil, one of the major soil types in northwestern China, was investigated using batch and extended X-ray absorption fine structure (EXAFS) approaches in a 0.01 mol/L NaClO4 solution at different pH values (6.0–10.0), temperatures (25–60 °C) and contact times (2–15 days). Under alkaline conditions, EXAFS analysis showed that the interatomic distances between Ni and O atoms (RNi-O) were approximately 2.04 Å with a typical coordination number (CN) of ~6.0 O atoms in the contact time range from 2 to 15 days. The RNi-Ni (~3.07 Å) suggested that the structure of the Ni(II) adsorbed on the CA soil was basically the same as that of Ni(OH)2(s), while the Ni-Al shell (RNi-Al ~3.16 Å) gradually formed and grew with the increasing contact time. Under weakly acidic conditions, the sorption mechanism of Ni(II) on the CA soil possibly included at least two processes: (i) a fast accumulation dominated by ion exchange and surface complexation and (ii) the formation of a Ni-Al LDH phase over the long term. A high temperature is beneficial to the fixation of Ni(II) on the CA soil and the formation of a Ni-Al LDH.
Identifying N6-methyladenosine sites using multi-interval nucleotide pair position specificity and support vector machine
Authors: Xing Pengwei , Su Ran , Guo Fei , Wei Leyi
Published: April 2017

N6-methyladenosine (m6A) refers to methylation of the adenosine nucleotide acid at the nitrogen-6 position. It plays an important role in a series of biological processes, such as splicing events, mRNA exporting, nascent mRNA synthesis, nuclear translocation and translation process. Numerous experiments have been done to successfully characterize m6A sites within sequences since high-resolution mapping of m6A sites was established. However, as the explosive growth of genomic sequences, using experimental methods to identify m6A sites are time-consuming and expensive. Thus, it is highly desirable to develop fast and accurate computational identification methods. In this study, we propose a sequence-based predictor called RAM-NPPS for identifying m6A sites within RNA sequences, in which we present a novel feature representation algorithm based on multi-interval nucleotide pair position specificity, and use support vector machine classifier to construct the prediction model. Comparison results show that our proposed method outperforms the state-of-the-art predictors on three benchmark datasets across the three species, indicating the effectiveness and robustness of our method. Moreover, an online webserver implementing the proposed predictor has been established at http://server.malab.cn/RAM-NPPS/. It is anticipated to be a useful prediction tool to assist biologists to reveal the mechanisms of m6A site functions.
Polyamorphism in Yb-based metallic glass induced by pressure
Authors: Li Liangliang , Luo Qiang , Li Renfeng , Zhao Haiyan , Chapman Karena W. , Chupas Peter J. , Wang Luhong , Liu Haozhe
Published: April 2017

The Yb62.5Zn15Mg17.5Cu5 metallic glass is investigated using synchrotron x-ray total scattering method up to 38.4 GPa. The polyamorphic transformation from low density to high density with a transition region between 14.1 and 25.2 GPa is observed, accompanying with a volume collapse reflected by a discontinuousness of isothermal bulk modulus. This collapse is caused by that distortional icosahedron short range order precedes to perfect icosahedron, which might link to Yb 4f electron delocalization upon compression, and match the result of in situ electrical resistance measurement under high pressure conditions. This discovery in Yb-based metallic glass, combined with the previous reports on other metallic glass systems, demonstrates that pressure induced polyamorphism is the general behavior for typical lanthanide based metallic glasses.
The environmental yeast Cryptococcus liquefaciens produces capsular and secreted polysaccharides with similar pathogenic properties to those of C. neoformans
Authors: Araújo Glauber R. de S. , Freitas Gustavo J. C. , Fonseca Fernanda L. , Leite Paulo Emilio C. , Rocha Gustavo Miranda , de Souza Wanderley , Santos Daniel A. , Frases Susana
Published: April 2017

Invasive fungal infections, including cryptococcosis, are a growing threat to immunocompromised patients. AlthoughCryptococcus neoformansandCryptococcus gattiiare the main agents of human cryptococcosis, opportunistic infections by environmental species, such asC. liquefaciens, have been observed recently. The mainCryptococcusvirulence factor is the production and secretion of polysaccharides (PS). Previously, we showed that both species produce PS of similar composition. Here, we examined the ultrastructure and biological activity of capsular and secreted PS fromC. liquefaciens, and yeast pathogenicity to an invertebrate host, in comparison withC. neoformans. Ultrastructural analysis by high-resolution microscopy showed that both species produce large and complex capsules. PS from both species had indistinguishable effects on phagocytosis levels, NO production and the secretion of a variety of immune mediators. Challenge withC. liquefaciensorC. neoformansled to complete lethality ofG. mellonellalarvae. Treatment withC. liquefaciensPS could not protect mice against infection withC. neoformans. We conclude that polysaccharides of the environmental yeastC. liquefacienshave strikingly similar ultrastructural and biological properties to those ofC. neoformans, highlighting the importance of monitoring the emergence of new fungal pathogens for which thermotolerance may be an important transitional step towards pathogenesis in humans.
Correction: Corrigendum: KIF3A binds to β-arrestin for suppressing Wnt/β-catenin signalling independently of primary cilia in lung cancer
Authors: Kim Minsuh , Suh Young-Ah , Oh Ju-Hee , Lee Bo Ra , Kim Joon , Jang Se Jin
Published: April 2017

Scientific Reports 6: Article number: 32770; published online: 06 September 2016; updated: 25 April 2017 The Acknowledgments section of this Article contains a typographical error, where: “Ministry of Science, ICT & Future Planning (MSIP) (#NRF-2011-0013927)” should read “Ministry of Science, ICT & Future Planning (MSIP) (#NRF-2011-0030105)”.