bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hidden geometries in networks arising from cooperative self-assembly
Authors: Šuvakov Milovan , Andjelković Miroslav , Tadić Bosiljka 
Published: January 2018

AbstractMultilevel self-assembly involving small structured groups of nano-particles provides new routes to development of functional materials with a sophisticated architecture. Apart from the inter-particle forces, the geometrical shapes and compatibility of the building blocks are decisive factors. Therefore, a comprehensive understanding of these processes is essential for the design of assemblies of desired properties. Here, we introduce a computational model for cooperative self-assembly with the simultaneous attachment of structured groups of particles, which can be described by simplexes (connected pairs, triangles, tetrahedrons and higher order cliques) to a growing network. The model incorporates geometric rules that provide suitable nesting spaces for the new group and the chemical affinity of the system to accept excess particles. For varying chemical affinity, we grow different classes of assemblies by binding the cliques of distributed sizes. Furthermore, we characterize the emergent structures by metrics of graph theory and algebraic topology of graphs, and 4-point test for the intrinsic hyperbolicity of the networks. Our results show that higher Q-connectedness of the appearing simplicial complexes can arise due to only geometric factors and that it can be efficiently modulated by changing the chemical potential and the polydispersity of the binding simplexes.
Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa)
Authors: Krawczyk Katarzyna , Nobis Marcin , Myszczyński Kamil , Klichowska Ewelina , Sawicki Jakub 
Published: January 2018

AbstractPresent study was designed to verify which or if any of plastome loci is a hotspot region for mutations and hence might be useful for molecular species identification in feather grasses. 21 newly sequenced complete plastid genomes representing 19 taxa from the genus of Stipa were analyzed in search of the most variable and the most discriminative loci within Stipa. The results showed that the problem with selecting a good barcode locus for feather grasses lies in the very low level of genetic diversity within its plastome. None of the single chloroplast loci is polymorphic enough to play a role of a barcode or a phylogenetic marker for Stipa. The biggest number of taxa was successfully identified by the analysis of 600 bp long DNA fragment comprising a part of rbcL gene, the complete rbcL-rpl23 spacer and a part of rpl23 gene. The effectiveness of multi-locus barcode composed of six best-performing loci for Stipa (ndhH, rpl23, ndhF-rpl32, rpl32-ccsA, psbK-psbI and petA-psbJ) didn’t reach 70% of analyzed taxa. The analysis of complete plastome sequences as a super-barcode for Stipa although much more effective, still didn’t allow for discrimination of all the analyzed taxa of feather grasses.
Femoral ontogeny in humans and great apes and its implications for their last common ancestor
Authors: Morimoto Naoki , Nakatsukasa Masato , Ponce de León Marcia S. , Zollikofer Christoph P. E. 
Published: January 2018

AbstractInferring the morphology of the last common ancestor of humans, chimpanzees and gorillas is a matter of ongoing debate. Recent findings and reassessment of fossil hominins leads to the hypothesis that the last common ancestor was not extant African ape-like. However, an African great-ape-like ancestor with knuckle walking features still remains plausible and the most parsimonious scenario. Here we address this question via an evolutionary developmental approach, comparing taxon-specific patterns of shape change of the femoral diaphysis from birth to adulthood in great apes, humans, and macaques. While chimpanzees and gorillas exhibit similar locomotor behaviors, our data provide evidence for distinct ontogenetic trajectories, indicating independent evolutionary histories of femoral ontogeny. Our data further indicate that anthropoid primates share a basic pattern of femoral diaphyseal ontogeny that reflects shared developmental constraints. Humans escaped from these constraints via differential elongation of femur.
Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies
Authors: Campanaro Stefano , Treu Laura , Kougias Panagiotis G. , Zhu Xinyu , Angelidaki Irini 
Published: January 2018

AbstractIn the past few years, many studies investigated the anaerobic digestion microbiome by means of 16S rRNA amplicon sequencing. Results obtained from these studies were compared to each other without taking into consideration the followed procedure for amplicons preparation and data analysis. This negligence was mainly due to the lack of knowledge regarding the biases influencing specific steps of the microbiome investigation process. In the present study, the main technical aspects of the 16S rRNA analysis were checked giving special attention to the approach used for high throughput sequencing. More specifically, the microbial compositions of three laboratory scale biogas reactors were analyzed before and after addition of sodium oleate by sequencing the microbiome with three different approaches: 16S rRNA amplicon sequencing, shotgun DNA and shotgun RNA. This comparative analysis revealed that, in amplicon sequencing, abundance of some taxa (Euryarchaeota and Spirochaetes) was biased by the inefficiency of universal primers to hybridize all the templates. Reliability of the results obtained was also influenced by the number of hypervariable regions under investigation. Finally, amplicon sequencing and shotgun DNA underestimated the Methanoculleus genus, probably due to the low 16S rRNA gene copy number encoded in this taxon.
Omega-3 docosahexaenoic acid induces pyroptosis cell death in triple-negative breast cancer cells
Authors: Pizato Nathalia , Luzete Beatriz Christina , Kiffer Larissa Fernanda Melo Vasconcelos , Corrêa Luís Henrique , de Oliveira Santos Igor , Assumpção José Antônio Fagundes , Ito Marina Kiyomi , Magalhães Kelly Grace 
Published: January 2018

AbstractThe implication of inflammation in pathophysiology of several type of cancers has been under intense investigation. Omega-3 fatty acids can modulate inflammation and present anticancer effects, promoting cancer cell death. Pyroptosis is an inflammation related cell death and so far, the function of docosahexaenoic acid (DHA) in pyroptosis cell death has not been described. This study investigated the role of DHA in triggering pyroptosis activation in breast cancer cells. MDA-MB-231 breast cancer cells were supplemented with DHA and inflammation cell death was analyzed. DHA-treated breast cancer cells triggered increased caspase-1and gasdermin D activation, enhanced IL-1β secretion, translocated HMGB1 towards the cytoplasm, and membrane pore formation when compared to untreated cells, suggesting DHA induces pyroptosis programmed cell death in breast cancer cells. Moreover, caspase-1 inhibitor (YVAD) could protect breast cancer cells from DHA-induced pyroptotic cell death. In addition, membrane pore formation showed to be a lysosomal damage and ROS formation-depended event in breast cancer cells. DHA triggered pyroptosis cell death in MDA-MB-231by activating several pyroptosis markers in these cells. This is the first study that shows the effect of DHA triggering pyroptosis programmed cell death in breast cancer cells and it could improve the understanding of the omega-3 supplementation during breast cancer treatment.
An optimal strategy to solve the Prisoner’s Dilemma
Authors: Bravetti Alessandro , Padilla Pablo 
Published: January 2018

AbstractCooperation is a central mechanism for evolution. It consists of an individual paying a cost in order to benefit another individual. However, natural selection describes individuals as being selfish and in competition among themselves. Therefore explaining the origin of cooperation within the context of natural selection is a problem that has been puzzling researchers for a long time. In the paradigmatic case of the Prisoner’s Dilemma (PD), several schemes for the evolution of cooperation have been proposed. Here we introduce an extension of the Replicator Equation (RE), called the Optimal Replicator Equation (ORE), motivated by the fact that evolution acts not only at the level of individuals of a population, but also among competing populations, and we show that this new model for natural selection directly leads to a simple and natural rule for the emergence of cooperation in the most basic version of the PD. Contrary to common belief, our results reveal that cooperation can emerge among selfish individuals because of selfishness itself: if the final reward for being part of a society is sufficiently appealing, players spontaneously decide to cooperate.
Methylation-based enrichment facilitates low-cost, noninvasive genomic scale sequencing of populations from feces
Authors: Chiou Kenneth L. , Bergey Christina M. 
Published: January 2018

AbstractObtaining high-quality samples from wild animals is a major obstacle for genomic studies of many taxa, particularly at the population level, as collection methods for such samples are typically invasive. DNA from feces is easy to obtain noninvasively, but is dominated by bacterial and other non-host DNA. The high proportion of non-host DNA drastically reduces the efficiency of high-throughput sequencing for host animal genomics. To address this issue, we developed an inexpensive capture method for enriching host DNA from noninvasive fecal samples. Our method exploits natural differences in CpG-methylation density between vertebrate and bacterial genomes to preferentially bind and isolate host DNA from majority-bacterial samples. We demonstrate that the enrichment is robust, efficient, and compatible with downstream library preparation methods useful for population studies (e.g., RADseq). Compared to other enrichment strategies, our method is quick and inexpensive, adding only a negligible cost to sample preparation. In combination with downstream methods such as RADseq, our approach allows for cost-effective and customizable genomic-scale genotyping that was previously feasible in practice only with invasive samples. Because feces are widely available and convenient to collect, our method empowers researchers to explore genomic-scale population-level questions in organisms for which invasive sampling is challenging or undesirable.
Spatial memory is as important as weapon and body size for territorial ownership in a lekking hummingbird
Authors: Araya-Salas Marcelo , Gonzalez-Gomez Paulina , Wojczulanis-Jakubas Katarzyna , López Virgilio , Wright Timothy F. 
Published: January 2018

AbstractAdvanced cognitive abilities have long been hypothesized to be important in mating. Yet, most work on sexual selection has focused on morphological traits and its relevance for cognitive evolution is poorly understood. We studied the spatial memory of lekking long-billed hermits (Phaethornis longirostris) and evaluated its role in lek territory ownership, the magnitude of its effect compared to phenotypic traits expected to influence sexual selection, and whether its variation is indicated in the structure of mating vocal signal. Spatial memory (the ability to recall the position of a rewarding feeder) was compared between “territorial” and “floater” males. Interestingly, although spatial memory and body size both positively affected the probability of lek territory ownership, our results suggest a stronger effect of spatial memory. Bill tip length (used as weapon in agonistic interactions) also showed a positive but smaller effect. Load lifting during vertical flight, a measure of physical performance relevant to agonistic interactions, had no effect on territory ownership. Finally, both body size and spatial memory were indicated in the structure of male song: body size negatively correlated with song lowest frequency, while spatial memory positively predicted song consistency. Together, our findings lend support for cognition as a sexual selection target.
Fracture and damage localization in volcanic edifice rocks from El Hierro, Stromboli and Tenerife
Authors: Harnett Claire E. , Benson Philip M. , Rowley Pete , Fazio Marco 
Published: January 2018

AbstractWe present elastic wave velocity and strength data from a suite of three volcanic rocks taken from the volcanic edifices of El Hierro and Tenerife (Canary Islands, Spain), and Stromboli (Aeolian Islands, Italy). These rocks span a range of porosity and are taken from volcanoes that suffer from edifice instability. We measure elastic wave velocities at known incident angles to the generated through-going fault as a function of imposed strain, and examine the effect of the damage zone on P-wave velocity. Such data are important as field measurements of elastic wave tomography are key tools for understanding volcanic regions, yet hidden fractures are likely to have a significant effect on elastic wave velocity. We then use elastic wave velocity evolution to calculate concomitant crack density evolution which ranges from 0 to 0.17: highest values were correlated to the damage zone in rocks with the highest initial porosity.
Nonlinear Absorption Response Correlated to Embedded Ag Nanoparticles in BGO Single Crystal: From Two-Photon to Three-Photon Absorption
Authors: Li Rang , Dong Ningning , Ren Feng , Amekura Hiro , Wang Jun , Chen Feng 
Published: January 2018

AbstractWe report on the embedded silver (Ag) nanoparticles fabricated by Ag+ ion implantation into the Bi4Ge3O12 (BGO) crystal. Localized surface plasmon resonance (LSPR) phenomenon has been observed by linear optical absorption spectrum, which is accordance with the expectation based on Mie theory calculation. Further proofs are given by SRIM, TEM and SAED analysis, which explain the slight difference between experiment and calculation. Based on the z-scan system, it is found that the nonlinear optical response is converted from two-photon absorption to three-photon absorption under the 515 nm femtosecond pulse excitation within the LSPR band. The nonlinear absorption coefficient is measured to be ~3.1 × 10−9 cm/W (two-photon absorption coefficient) and ~8.9 × 10−14cm3/W2 (three-photon absorption coefficient) for pure BGO crystal and the sample embedded with Ag nanoparticles (Ag:BGO), respectively. Finally, we have proposed a model to explain the asymmetric nonlinear transmittance, which is in good agreement with the experimental results.
Thyroid stimulating hormone stimulates the expression of glucose transporter 2 via its receptor in pancreatic β cell line, INS-1 cells
Authors: Lyu Jingya , Imachi Hitomi , Yoshimoto Takuo , Fukunaga Kensaku , Sato Seisuke , Ibata Tomohiro , Kobayashi Toshihiro , Dong Tao , Yonezaki Kazuko , Yamaji Nao , Kikuchi Fumi , Iwama Hisakazu , Ishikawa Ryou , Haba Reiji , Sugiyama Yasunori , Zhang Huanxiang , Murao Koji 
Published: January 2018

AbstractThyroid stimulating hormone (TSH) stimulates the secretion of thyroid hormones by binding the TSH receptor (TSHR). TSHR is well-known to be expressed in thyroid tissue, excepting it, TSHR has also been expressed in many other tissues. In this study, we have examined the expression of TSHR in rat pancreatic islets and evaluated the role of TSH in regulating pancreas-specific gene expression. TSHR was confirmed to be expressed in rodent pancreatic islets and its cell line, INS-1 cells. TSH directly affected the glucose uptake in INS cells by up-regulating the expression of GLUT2, and furthermore this process was blocked by SB203580, the specific inhibitor of the p38 MAPK signaling pathway. Similarly, TSH stimulated GLUT2 promoter activity, while both a dominant-negative p38MAPK α isoform (p38MAPK α-DN) and the specific inhibitor for p38MAPK α abolished the stimulatory effect of TSH on GLUT2 promoter activity. Finally, INS-1 cells treated with TSH showed increased protein level of glucokinase and enhanced glucose-stimulated insulin secretion. Together, these results confirm that TSHR is expressed in INS-1 cells and rat pancreatic islets, and suggest that activation of the p38MAPK α might be required for TSH-induced GLUT2 gene transcription in pancreatic β cells.
Interactive Holographic Display Based on Finger Gestures
Authors: Yamada Shota , Kakue Takashi , Shimobaba Tomoyoshi , Ito Tomoyoshi 
Published: January 2018

AbstractIn this paper, we demonstrate an interactive, finger-sensitive system which enables an observer to intuitively handle electro-holographic images in real time. In this system, a motion sensor detects finger gestures (swiping and pinching) and translates them into the rotation and enlargement/reduction of the holographic image, respectively. By parallelising the hologram calculation using a graphics processing unit, we realised the interactive handling of the holographic image in real time. In a demonstration of the system, we used a Leap Motion sensor and a phase modulation-type spatial light modulator with 1,920 × 1,080 pixels and a pixel pitch of 8.0 µm × 8.0 µm. The constructed interactive finger-sensitive system was able to rotate a holographic image composed of 4,096 point light sources using a swiping gesture and enlarge or reduce it using a pinching gesture in real time. The average calculation speed was 27.6 ms per hologram. Finally, we extended the constructed system to a full-colour reconstruction system that generates a more realistic three-dimensional image. The extended system successfully allowed the handling of a full-colour holographic image composed of 1,709 point light sources with a calculation speed of 22.6 ms per hologram.
The role of local-geometrical-orders on the growth of dynamic-length-scales in glass-forming liquids
Authors: Wong Kaikin , Krishnan Rithin P. , Chen Changjiu , Du Qing , Yu Dehong , Lu Zhaoping , Samwer K. , Chathoth Suresh M. 
Published: January 2018

AbstractThe precise nature of complex structural relaxation as well as an explanation for the precipitous growth of relaxation time in cooling glass-forming liquids are essential to the understanding of vitrification of liquids. The dramatic increase of relaxation time is believed to be caused by the growth of one or more correlation lengths, which has received much attention recently. Here, we report a direct link between the growth of a specific local-geometrical-order and an increase of dynamic-length-scale as the atomic dynamics in metallic glass-forming liquids slow down. Although several types of local geometrical-orders are present in these metallic liquids, the growth of icosahedral ordering is found to be directly related to the increase of the dynamic-length-scale. This finding suggests an intriguing scenario that the transient icosahedral connectivity could be the origin of the dynamic-length-scale in metallic glass-forming liquids.
Development of an Immune-Pathology Informed Radiomics Model for Non-Small Cell Lung Cancer
Authors: Tang Chad , Hobbs Brian , Amer Ahmed , Li Xiao , Behrens Carmen , Canales Jaime Rodriguez , Cuentas Edwin Parra , Villalobos Pamela , Fried David , Chang Joe Y. , Hong David S. , Welsh James W. , Sepesi Boris , Court Laurence , Wistuba Ignacio I. , Koay Eugene J. 
Published: January 2018

AbstractWith increasing use of immunotherapy agents, pretreatment strategies for identifying responders and non-responders is useful for appropriate treatment assignment. We hypothesize that the local immune micro-environment of NSCLC is associated with patient outcomes and that these local immune features exhibit distinct radiologic characteristics discernible by quantitative imaging metrics. We assembled two cohorts of NSCLC patients treated with definitive surgical resection and extracted quantitative parameters from pretreatment CT imaging. The excised primary tumors were then quantified for percent tumor PDL1 expression and density of tumor-infiltrating lymphocyte (via CD3 count) utilizing immunohistochemistry and automated cell counting. Associating these pretreatment radiomics parameters with tumor immune parameters, we developed an immune pathology-informed model (IPIM) that separated patients into 4 clusters (designated A-D) utilizing 4 radiomics features. The IPIM designation was significantly associated with overall survival in both training (5 year OS: 61%, 41%, 50%, and 91%, for clusters A-D, respectively, P = 0.04) and validation (5 year OS: 55%, 72%, 75%, and 86%, for clusters A-D, respectively, P = 0.002) cohorts and immune pathology (all P < 0.05). Specifically, we identified a favorable outcome group characterized by low CT intensity and high heterogeneity that exhibited low PDL1 and high CD3 infiltration, suggestive of a favorable immune activated state. We have developed a NSCLC radiomics signature based on the immune micro-environment and patient outcomes. This manuscript demonstrates model creation and validation in independent cohorts.
LLO-mediated Cell Resealing System for Analyzing Intracellular Activity of Membrane-impermeable Biopharmaceuticals of Mid-sized Molecular Weight
Authors: Murakami Masataka , Kano Fumi , Murata Masayuki 
Published: January 2018

AbstractCell-based assays have become increasingly important in the preclinical studies for biopharmaceutical products such as specialty peptides, which are of interest owing to their high substrate specificity. However, many of the latter are membrane impermeable and must be physically introduced into cells to evaluate their intracellular activities. We previously developed a “cell-resealing technique” that exploited the temperature-dependent pore-forming activity of the streptococcal toxin, streptolysin O (SLO), that enabled us to introduce various molecules into cells for evaluation of their intracellular activities. In this study, we report a new cell resealing method, the listeriolysin O (LLO)-mediated resealing method, to deliver mid-sized, membrane-impermeable biopharmaceuticals into cells. We found that LLO-type resealing required no exogenous cytosol to repair the injured cell membrane and allowed the specific entry of mid-sized molecules into cells. We use this method to introduce either a membrane-impermeable, small compound (8-OH-cAMP) or specialty peptide (Akt-in), and demonstrated PKA activation or Akt inhibition, respectively. Collectively, the LLO-type resealing method is a user-friendly and reproducible intracellular delivery system for mid-sized membrane-impermeable molecules into cells and for evaluating their intracellular activities.
Analogies of the classical Euler top with a rotor to spin squeezing and quantum phase transitions in a generalized Lipkin-Meshkov-Glick model
Authors: Opatrný Tomáš , Richterek Lukáš , Opatrný Martin 
Published: January 2018

AbstractWe show that the classical model of Euler top (freely rotating, generally asymmetric rigid body), possibly supplemented with a rotor, corresponds to a generalized Lipkin-Meshkov-Glick (LMG) model describing phenomena of various branches of quantum physics. Classical effects such as free precession of a symmetric top, Feynman’s wobbling plate, tennis-racket instability and the Dzhanibekov effect, attitude control of satellites by momentum wheels, or twisting somersault dynamics, have their counterparts in quantum effects that include spin squeezing by one-axis twisting and two-axis countertwisting, transitions between the Josephson and Rabi regimes of a Bose-Einstein condensate in a double-well potential, and other quantum critical phenomena. The parallels enable us to expand the range of explored quantum phase transitions in the generalized LMG model, as well as to present a classical analogy of the recently proposed LMG Floquet time crystal.