bluuebunny/crossref_metadata_2025_split huggingface dataset:
Self-righting potential and the evolution of shell shape in Galápagos tortoises
Authors: Chiari Ylenia , van der Meijden Arie , Caccone Adalgisa , Claude Julien , Gilles Benjamin 
Published: November 2017

AbstractSelf-righting, the capacity of an animal to self-turn after falling on its back, is a fitness-related trait. Delayed self-righting can result in loss of mating opportunities or death. Traits involved in self-righting may therefore be under selection. Galápagos giant tortoises have two main shell morphologies - saddleback and domed – that have been proposed to be adaptive. The more sloped shape on the sides of the shell and the longer extension of neck and legs of the saddlebacks could have evolved to optimize self-righting. The drier environments with more uneven surfaces where the saddleback tortoises occur increases their risk to fall on their back while walking. The ability to fast overturn could reduce the danger of dying. To test this hypothesis, we used 3D shell reconstructions of 89 Galápagos giant tortoises from three domed and two saddleback species to compare self-righting potential of the two shell morphotypes. Our results indicate that saddleback shells require higher energy input to self-right than domed ones. This suggests that several traits associated with the saddleback shell morphology could have evolved to facilitate self-righting. Studying the functional performances of fitness-related traits, as in this work, could provide important insight into the adaptive value of traits.
Disentangling physical and biological drivers of phytoplankton dynamics in a coastal system
Authors: Cianelli Daniela , D’Alelio Domenico , Uttieri Marco , Sarno Diana , Zingone Adriana , Zambianchi Enrico , d’Alcalà Maurizio Ribera 
Published: November 2017

AbstractThis proof-of-concept study integrates the surface currents measured by high-frequency coastal radars with plankton time-series data collected at a fixed sampling point from the Mediterranean Sea (MareChiara Long Term Ecological Research site in the Gulf of Naples) to characterize the spatial origin of phytoplankton assemblages and to scrutinize the processes ruling their dynamics. The phytoplankton community generally originated from the coastal waters whereby species succession was mainly regulated by biological factors (life-cycle processes, species-specific physiological performances and inter-specific interactions). Physical factors, e.g. the alternation between coastal and offshore waters and the horizontal mixing, were also important drivers of phytoplankton dynamics promoting diversity maintenance by i) advecting species from offshore and ii) diluting the resident coastal community so as to dampen resource stripping by dominant species and thereby increase the numerical importance of rarer species. Our observations highlight the resilience of coastal communities, which may favour their persistence over time and the prevalence of successional events over small time and space scales. Although coastal systems may act differently from one another, our findings provide a conceptual framework to address physical–biological interactions occurring in coastal basins, which can be generalised to other areas.
Hypoxia inducible factor-1α mediates the profibrotic effect of albumin in renal tubular cells
Authors: Hu Junping , Wang Weili , Zhang Fan , Li Pin-Lan , Boini Krishna M. , Yi Fan , Li Ningjun 
Published: November 2017

AbstractProteinuria is closely associated with the progression of chronic kidney diseases (CKD) by producing renal tubulointerstitial fibrosis. Over-activation of hypoxia inducible factor (HIF)-1α has been implicated in the progression of CKD. The present study tested the hypothesis that HIF-1α mediates albumin-induced profibrotic effect in cultured renal proximal tubular cells. Incubation of the cells with albumin (40 μg/ml) for 72 hrs significantly increased the protein levels of HIF-1α, tissue inhibitor of metalloproteinase (TIMP)-1 and collagen-I, which were blocked by HIF-1α shRNA. Albumin also stimulated an epithelial-mesenchymal transition (EMT) as indicated by the decrease in epithelial marker E-cadherin, and the increase in mesenchymal markers α-smooth muscle actin and fibroblast-specific protein 1. HIF-1α shRNA blocked albumin-induced changes in these EMT markers as well. Furthermore, albumin reduced the level of hydroxylated HIF-1α, indicating an inhibition of the activity of prolyl-hydroxylases, enzymes promoting the degradation of HIF-1α. An anti-oxidant ascorbate reversed albumin-induced inhibition of prolyl-hydroxylase activity. Overexpression of prolyl-hydroxylase 2 (PHD2) transgene, a predominant isoform of PHDs in renal tubules, to reduce HIF-1α level significantly attenuated albumin-induced increases in TIMP-1 and collagen-I levels. These results suggest that albumin-induced oxidative stress inhibits PHD activity to accumulate HIF-1α, which mediates albumin-induced profibrotic effects in renal tubular cells.
Re-evaluation of the origin of relaxor ferroelectricity in vinylidene fluoride terpolymers: An approach using switching current measurements
Authors: Tsutsumi Naoto , Okumachi Kyohei , Kinashi Kenji , Sakai Wataru 
Published: November 2017

AbstractRelaxor-ferroelectric vinylidene fluoride (VDF)-based terpolymers have attracted increased attention for industrial applications because of their large dielectric constants, low voltage operation for nonvolatile memory, and energy storage capabilities. However, the origin of the relaxor ferroelectricity of VDF-based terpolymers is still under investigation. Here, we investigate the ferroelectric behaviour of thin films of terpolymers of VDF, trifluoroethylene (TrFE), and chlorofluoroethylene (CFE) (P(VDF-TrFE-CFE)) and terpolymers of VDF, TrFE, and chlorotrifluoroethylene (CTFE) (P(VDF-TrFE-CTFE)) using switching current – electric field (I-E) loop measurements. I-E loop measurements have substantial advantages because they directly provide information regarding the independent switching behaviour of dipoles. We show that the I-E loops of P(VDF-TrFE-CFE) are the summation of three pairs of Gaussian peak functions. Moreover, we provide definite proof of the presence of double hysteresis loop-like antiferroelectric behaviour and relaxor-ferroelectricity in the nanodomains of the dipoles when applying positive or negative sinusoidal electric fields to the sample films.
Highly expressed genes evolve under strong epistasis from a proteome-wide scan in E. coli
Authors: Dasmeh Pouria , Girard Éric , Serohijos Adrian W. R. 
Published: November 2017

AbstractEpistasis or the non-additivity of mutational effects is a major force in protein evolution, but it has not been systematically quantified at the level of a proteome. Here, we estimated the extent of epistasis for 2,382 genes in E. coli using several hundreds of orthologs for each gene within the class Gammaproteobacteria. We found that the average epistasis is ~41% across genes in the proteome and that epistasis is stronger among highly expressed genes. This trend is quantitatively explained by the prevailing model of sequence evolution based on minimizing the fitness cost of protein unfolding and aggregation. The genes with the highest epistasis are also functionally involved in the maintenance of proteostasis, translation and central metabolism. In contrast, genes evolving with low epistasis mainly encode for membrane proteins and are involved in transport activity. Our results highlight the coupling between selection and epistasis in the long-term evolution of a proteome.
Efficient Cross-talk Reduction of Nanophotonic Circuits Enabled by Fabrication Friendly Periodic Silicon Strip Arrays
Authors: Bian Yusheng , Ren Qiang , Kang Lei , Qin Yifeng , Werner Pingjuan L. , Werner Douglas H. 
Published: November 2017

AbstractReduction of the crosstalk between adjacent photonic components has been regarded as one of the most effective, yet most challenging approaches for increasing the packing density of photonic integrated circuits. Recently, extensive efforts have been devoted to this field, leading to a number of elaborate designs, such as waveguide supperlattice and nanophotonic cloaking, among others. Here we develop a simple and efficient crosstalk reduction approach for silicon-based nanophotonic circuits by introducing a periodic array of silicon strips between adjacent waveguides. Studies indicate that the coupling lengths can be extended by more than two orders of magnitude for a waveguide pair with an edge-to-edge distance of ~λ/3 at the telecommunication wavelength. Further investigations reveal that our method is effective for both strongly and weakly confined silicon photonic modes, and works well over a broad band of operational wavelengths. In addition, the crosstalk reduction technique is shown to be capable of improving the coupling lengths of other elements as well, such as vertical silicon slot waveguides. Our approach offers a promising platform for creating ultra-compact functional components that is fabrication friendly, thereby providing a feasible route toward the realization of photonic integrated circuits with ultra-high packing densities.
The Triglycerides and Glucose Index rather than HOMA-IR is more associated with Hypogonadism in Chinese men
Authors: Zhang Kun , Chen Yi , Liu Lijie , Lu Meng , Cheng Jing , Gao Fengbin , Wang Ningjian , Shen Zhoujun , Lu Yingli 
Published: November 2017

AbstractPrevious studies have reported that insulin resistant and low testosterone are related. The triglyceride and glucose index (TyG) well mirrors insulin sensitivity. No study investigated the application of TyG in male hypogonadism. We aimed to explore whether TyG was associated with hypogonadism, and also evaluate the ability of TyG compared to HOMA-IR as a possible hypogonadism predictor. A total of 4299 male subjects were enrolled from 22 sites in East China. Hypogonadism was defined as total testosterone <11.3 nmol/L. 695 (16.2%) hypogonadal men had significantly higher TyG index. The prevalence of hypogonadism stepwise increased across increasing TyG quartiles (P < 0.01). TyG was negatively associated with sex hormones and hypogonadism after adjustment for age, current smoking status, hypertension and overweight/obesity (all P for trend <0.01). The full-adjusted odds ratio was 6.1 for the highest quartile compared with the lowest quartile of TyG (95% CI 4.51, 8.25, P < 0.001). On ROC curve analysis, a larger area under the curve was found for TyG (0.71, 95% CI 0.69,0.73) than for HOMA-IR (0.68, 95% CI 0.66,0.70). Thus, the TyG was significantly associated with a higher prevalence of hypogonadism in Chinese men. TyG had a better predictive power for hypogonadism than HOMA-IR.
Optogenetic silencing of nociceptive primary afferents reduces evoked and ongoing bladder pain
Authors: Samineni Vijay K. , Mickle Aaron D. , Yoon Jangyeol , Grajales-Reyes Jose G. , Pullen Melanie Y. , Crawford Kaitlyn E. , Noh Kyung Nim , Gereau Graydon B. , Vogt Sherri K. , Lai H. Henry , Rogers John A. , Gereau Robert W. 
Published: November 2017

AbstractPatients with interstitial cystitis/bladder pain syndrome (IC/BPS) suffer from chronic pain that severely affects quality of life. Although the underlying pathophysiology is not well understood, inhibition of bladder sensory afferents temporarily relieves pain. Here, we explored the possibility that optogenetic inhibition of nociceptive sensory afferents could be used to modulate bladder pain. The light-activated inhibitory proton pump Archaerhodopsin (Arch) was expressed under control of the sensory neuron-specific sodium channel (sns) gene to selectively silence these neurons. Optically silencing nociceptive sensory afferents significantly blunted the evoked visceromotor response to bladder distension and led to small but significant changes in bladder function. To study of the role of nociceptive sensory afferents in freely behaving mice, we developed a fully implantable, flexible, wirelessly powered optoelectronic system for the long-term manipulation of bladder afferent expressed opsins. We found that optogenetic inhibition of nociceptive sensory afferents reduced both ongoing pain and evoked cutaneous hypersensitivity in the context of cystitis, but had no effect in uninjured, naïve mice. These results suggest that selective optogenetic silencing of nociceptive bladder afferents may represent a potential future therapeutic strategy for the treatment of bladder pain.
Insights into gene expression profiles induced by Socs3 depletion in keratinocytes
Authors: Bajpai Archana , Ishii Takashi , Miyauchi Kosuke , Gupta Vipul , Nishio-Masaike Yuka , Shimizu-Yoshida Yuki , Kubo Masato , Kitano Hiroaki 
Published: November 2017

AbstractSpecific deletion of suppressor of cytokine signaling 3 (Socs3) in keratinocytes can cause severe skin inflammation with infiltration of immune cells. The molecular mechanisms and key regulatory pathways involved in these processes remain elusive. To investigate the role of Socs3 in keratinocytes, we generated and analyzed global RNA-Seq profiles from Socs3 conditional knockout (cKO) mice of two different ages (2 and 10 weeks). Over 400 genes were significantly regulated at both time points. Samples from 2-week-old mice exhibited down-regulation of genes involved in keratin-related functions and up-regulation of genes involved in lipid metabolism. At week 10, multiple chemokine and cytokine genes were up-regulated. Functional annotation revealed that the genes differentially expressed in the 2-week-old mice play roles in keratinization, keratinocyte differentiation, and epidermal cell differentiation. By contrast, differentially expressed genes in the 10-week-old animals are involved in acute immune-related functions. A group of activator protein-1–related genes were highly up-regulated in Socs3 cKO mice of both ages. This observation was validated using qRT-PCR by SOCS3-depleted human keratinocyte–derived HaCaT cells. Our results suggest that, in addition to participating in immune-mediated pathways, SOCS3 also plays important roles in skin barrier homeostasis.
Convergent evolution of plant and animal embryo defences by hyperstable non-digestible storage proteins
Authors: Pasquevich María Yanina , Dreon Marcos Sebastián , Qiu Jian-Wen , Mu Huawei , Heras Horacio 
Published: November 2017

AbstractPlants have evolved sophisticated embryo defences by kinetically-stable non-digestible storage proteins that lower the nutritional value of seeds, a strategy that have not been reported in animals. To further understand antinutritive defences in animals, we analysed PmPV1, massively accumulated in the eggs of the gastropod Pomacea maculata, focusing on how its structure and structural stability features affected its capacity to withstand passage through predator guts. The native protein withstands >50 min boiling and resists the denaturing detergent sodium dodecyl sulphate (SDS), indicating an unusually high structural stability (i.e., kinetic stability). PmPV1 is highly resistant to in vitro proteinase digestion and displays structural stability between pH 2.0–12.0 and 25–85 °C. Furthermore, PmPV1 withstands in vitro and mice digestion and is recovered unchanged in faeces, supporting an antinutritive defensive function. Subunit sequence similarities suggest a common origin and tolerance to mutations. This is the first known animal genus that, like plant seeds, lowers the nutritional value of eggs by kinetically-stable non-digestible storage proteins that survive the gut of predators unaffected. The selective pressure of the harsh gastrointestinal environment would have favoured their appearance, extending by convergent evolution the presence of plant-like hyperstable antinutritive proteins to unattended reproductive stages in animals.
Analysis of the gut microbiome and plasma short-chain fatty acid profiles in a spontaneous mouse model of metabolic syndrome
Authors: Nishitsuji Kazuchika , Xiao Jinzhong , Nagatomo Ryosuke , Umemoto Hitomi , Morimoto Yuki , Akatsu Hiroyasu , Inoue Koichi , Tsuneyama Koichi 
Published: November 2017

AbstractMale Tsumura Suzuki obese diabetes (TSOD) mice spontaneously develop obesity and obesity-related metabolic syndrome. Gut dysbiosis, an imbalance of gut microbiota, has been implicated in the pathogenesis of metabolic syndrome, but its mechanisms are unknown. Short-chain fatty acids (SCFAs) are the main fermentation products of gut microbiota and a link between the gut microbiota and the host’s physiology. Here, we investigated a correlation among gut dysbiosis, SCFAs, and metabolic syndrome in TSOD mice. We detected enriched levels of Gram-positive bacteria and corresponding decreases in Gram-negative bacteria in 24-wk-old metabolic syndrome-affected TSOD mice compared with age-matched controls. The abundance of Bacteroidetes species decreased, the abundance of Firmicutes species increased, and nine genera of bacteria were altered in 24-wk-old TSOD mice. The total plasma SCFA level was significantly lower in the TSOD mice than in controls. The major plasma SCFA—acetate—decreased in TSOD mice, whereas propionate and butyrate increased. TSOD mice had no minor SCFAs (valerate and hexanoate) but normal mice did. We thus concluded that gut dysbiosis and consequent disruptions in plasma SCFA profiles occurred in metabolic syndrome-affected TSOD mice. We also propose that the TSOD mouse is a useful model to study gut dysbiosis, SCFAs, and metabolic syndrome.
Influences of lone-pair electrons on directionality of hydrogen bonds formed by hydrophilic amino acid side chains in molecular dynamics simulation
Authors: Oroguchi Tomotaka , Nakasako Masayoshi 
Published: November 2017

AbstractThe influence of lone-pair electrons on the directionality of hydrogen bonds that are formed by oxygen and nitrogen atoms in the side chains of nine hydrophilic was investigated using molecular dynamics simulations. The simulations were conducted using two types of force fields; one incorporated lone-pair electrons placed at off-atom sites and the other did not. The density distributions of the hydration water molecules around the oxygen and nitrogen atoms were calculated from the simulation trajectories, and were compared with the empirical hydration distribution functions, which were constructed from a large number of hydration water molecules found in the crystal structures of proteins. Only simulations using the force field explicitly incorporating lone-pair electrons reproduced the directionality of hydrogen bonds that is observed in the empirical distribution functions for the deprotonated oxygen and nitrogen atoms in thesp2-hybridization. The amino acids that include such atoms are functionally important glutamate, aspartate, and histidine. Therefore, a set of force field that incorporates lone-pair electrons as off-atom charge sites would be effective for considering hydrogen bond formation by these amino acids in molecular dynamics simulation studies.
Section 1Tunable broadband terahertz absorbers based on multiple layers of graphene ribbons
Authors: Chen Dingbo , Yang Junbo , Zhang Jingjing , Huang Jie , Zhang Zhaojian 
Published: November 2017

AbstractA novel metamaterial structure consisting of multiple graphene/dielectric layers and metallic substrate is proposed to achieve the broadband absorption response at terahertz (THz) frequencies. Utilizing the phase modulation effect generated by graphene ribbons, the bright-dark field is formed to suppress the reflection based on interference theory in a wide period. By irregularly stacking four graphene ribbons of varying widths on four dielectric layers with unequal thickness in a period, we merge successive absorption peaks into a broadband absorption spectrum successfully. The absorption decreases with fluctuations as the incident angle increases. The position of the absorption spectrum can be dynamically tuned by a small change in the Fermi level of graphene instead of re-optimizing and re-fabricating the device. In addition, the bandwidth of the absorber can be further improved by means of increasing the graphene/dielectric layers. The structure proposed in this paper has potential applications in tunable terahertz photonic devices such as dynamic broadband filters, modulators and sensors.
Computational design of fully overlapping coding schemes for protein pairs and triplets
Authors: Opuu Vaitea , Silvert Martin , Simonson Thomas 
Published: November 2017

AbstractGene pairs that overlap in their coding regions are rare except in viruses. They may occur transiently in gene creation and are of biotechnological interest. We have examined the possibility to encode an arbitrary pair of protein domains as a dual gene, with the shorter coding sequence completely embedded in the longer one. For 500 × 500 domain pairs (X, Y), we computationally designed homologous pairs (X′, Y′) coded this way, using an algorithm that provably maximizes the sequence similarity between (X′, Y′) and (X, Y). Three schemes were considered, with X′ and Y′ coded on the same or complementary strands. For 16% of the pairs, an overlapping coding exists where the level of homology of X′, Y′ to the natural proteins represents an E-value of 10−10 or better. Thus, for an arbitrary domain pair, it is surprisingly easy to design homologous sequences that can be encoded as a fully-overlapping gene pair. The algorithm is general and was used to design 200 triple genes, with three proteins encoded by the same DNA segment. The ease of design suggests overlapping genes may have occurred frequently in evolution and could be readily used to compress or constrain artificial genomes.
Transcriptomic profiling of human breast and melanoma cells selected by migration through narrow constraints
Authors: Rudzka Dominika A. , Clark William , Hedley Ann , Kalna Gabriela , Olson Michael F. 
Published: November 2017

AbstractThe metastatic spread of cancer cells is a step-wise process that starts with dissociation from primary tumours and local invasion of adjacent tissues. The ability to invade local tissues is the product of several processes, including degradation of extracellular matrices (ECM) and movement of tumour cells through physically-restricting gaps. To identify properties contributing to tumour cells squeezing through narrow gaps, invasive MDA-MB-231 human breast cancer and MDA-MB-435 human melanoma cells were subjected to three successive rounds of selection using cell culture inserts with highly constraining 3 μm pores. For comparison purposes, flow cytometry was also employed to enrich for small diameter MDA-MB-231 cells. RNA-Sequencing (RNA-seq) using the Illumina NextSeq 500 platform was undertaken to characterize how gene expression differed between parental, invasive pore selected or small diameter cells. Gene expression results obtained by RNA-seq were validated by comparing with RT-qPCR. Transcriptomic data generated could be used to determine how alterations that enable cell passage through narrow spaces contribute to local invasion and metastasis.