bluuebunny/crossref_metadata_2025_split huggingface dataset:
The complete mitochondrial genomes of two skipper genera (Lepidoptera: Hesperiidae) and their associated phylogenetic analysis
Authors: Han Yuke , Huang Zhenfu , Tang Jing , Chiba Hideyuki , Fan Xiaoling 
Published: October 2018

AbstractThe systematic positions of two hesperiid genera, Apostictopterus and Barca (Lepidoptera: Hesperiidae), remain ambiguous. We sequenced and annotated the two mitogenomes of Apostictopterus fuliginosus and Barca bicolor and inferred the phylogenetic positions of the two genera within the Hesperiidae based on the available mitogenomes. The lengths of the two circular mitogenomes of A. fuliginosus and B. bicolor are 15,417 and 15,574 base pairs (bp), respectively. These two mitogenomes show similar AT skew, GC skew, codon usage and nucleotide bias of AT: the GC skew of the two species is negative, and the AT skew of A. fuliginosus is negative, while the AT skew of B. bicolor is slightly positive. The largest intergenic spacer is located at the same position between trnQ and ND2 in A. fuliginosus (73 bp) and B. bicolor (72 bp). Thirteen protein-coding genes (PCGs) start with ATN codons except for COI, which starts with CGA. The control regions of both mitogenomes possess a long tandem repeat, which is 30 bp long in A. fuliginosus, and 18 bp in B. bicolor. Bayesian inference and maximum likelihood methods were employed to infer the phylogenetic relationships, which suggested that A. fuliginosus and B. bicolor belong in the subfamily Hesperiinae.
Adipose tissue dysfunction is associated with low levels of the novel Palmitic Acid Hydroxystearic Acids
Authors: Hammarstedt Ann , Syed Ismail , Vijayakumar Archana , Eliasson Björn , Gogg Silvia , Kahn Barbara B. , Smith Ulf 
Published: October 2018

AbstractAdipose tissue dysfunction is considered an important contributor to systemic insulin resistance and Type 2 diabetes (T2D). Recently, a novel family of endogenous lipids, palmitic acid hydroxy stearic acids (PAHSAs), was discovered. These have anti-diabetic and anti-inflammatory effects in mice and are reduced in serum and adipose tissue of insulin resistant humans. In the present study, we investigate if adipose tissue dysfunction is associated with reduced PAHSA levels in human subjects and if PAHSAs influence adipocyte differentiation. Our results show that low expression of adipocyte GLUT4 and adipocyte hypertrophy, markers of adipose tissue dysfunction, are associated with reduced expression of key enzymes for de novo lipogenesis and adipose tissue levels of PAHSAs in human subjects. We also show that GLUT4 is not only a marker of adipose tissue dysfunction, but may be causally related to the observed impairments. PAHSAs may also act locally in the adipose tissue to improve adipogenesis through a mechanism bypassing direct activation of peroxisome proliferator-activated receptor (PPARγ). The discovery of PAHSAs and our current results provide novel insights into positive effects of lipid species in adipose tissue and mechanisms by which dysfunctional adipose tissue is associated with insulin resistance and risk of developing T2D.
Hierarchical decision-making produces persistent differences in learning performance
Authors: Knudsen Thorbjørn , Marchiori Davide , Warglien Massimo 
Published: October 2018

AbstractHuman organizations are commonly characterized by a hierarchical chain of command that facilitates division of labor and integration of effort. Higher-level employees set the strategic frame that constrains lower-level employees who carry out the detailed operations serving to implement the strategy. Typically, strategy and operational decisions are carried out by different individuals that act over different timescales and rely on different kinds of information. We hypothesize that when such decision processes are hierarchically distributed among different individuals, they produce highly heterogeneous and strongly path-dependent joint learning dynamics. To investigate this, we design laboratory experiments of human dyads facing repeated joint tasks, in which one individual is assigned the role of carrying out strategy decisions and the other operational ones. The experimental behavior generates a puzzling bimodal performance distribution–some pairs learn, some fail to learn after a few periods. We also develop a computational model that mirrors the experimental settings and predicts the heterogeneity of performance by human dyads. Comparison of experimental and simulation data suggests that self-reinforcing dynamics arising from initial choices are sufficient to explain the performance heterogeneity observed experimentally.
$${\mathscr{P}}{\mathscr{T}}$$-symmetric interference transistor
Authors: Gorbatsevich Alexander A. , Krasnikov Gennadiy Ya. , Shubin Nikolay M. 
Published: October 2018

AbstractWe present a model of the molecular transistor, operation of which is based on the interplay between two physical mechanisms, peculiar to open quantum systems that act in concert: $${\mathscr{P}}{\mathscr{T}}$$
P
T
-symmetry breaking corresponding to coalescence of resonances at the exceptional point of the molecule, connected to the leads, and Fano-Feshbach antiresonance. This switching mechanism can be realised in particular in a special class of molecules with degenerate energy levels, e.g. diradicals, which possess mirror symmetry. At zero gate voltage infinitesimally small interaction of the molecule with the leads breaks the $${\mathscr{P}}{\mathscr{T}}$$
P
T
-symmetry of the system that, however, can be restored by application of the gate voltage preserving the mirror symmetry. $${\mathscr{P}}{\mathscr{T}}$$
P
T
-symmetry broken state at zero gate voltage with minimal transmission corresponds to the “off” state while the $${\mathscr{P}}{\mathscr{T}}$$
P
T
-symmetric state at non-zero gate voltage with maximum transmission – to the “on” state. At zero gate voltage energy of the antiresonance coincides with exceptional point. We construct a model of an all-electrical molecular switch based on such transistors acting as a conventional CMOS inverter and show that essentially lower power consumption and switching energy can be achieved, compared to the CMOS analogues.
The common origin of symmetry and structure in genetic sequences
Authors: Cristadoro Giampaolo , Degli Esposti Mirko , Altmann Eduardo G. 
Published: October 2018

AbstractBiologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On the other hand, single-strand symmetry has been scrutinised using neutral models in which correlations are not considered or irrelevant, contrary to empirical evidence. Different studies investigated these two statistical features separately, reaching minimal consensus despite sustained efforts. Here we unravel previously unknown symmetries in genetic sequences, which are organized hierarchically through scales in which non-random structures are known to be present. These observations are confirmed through the statistical analysis of the human genome and explained through a simple domain model. These results suggest that domain models which account for the cumulative action of mobile elements can explain simultaneously non-random structures and symmetries in genetic sequences.
Binocular disparity can augment the capacity of vision without affecting subjective experience of depth
Authors: Railo Henry , Saastamoinen Joni , Kylmälä Sipi , Peltola Aapo 
Published: October 2018

AbstractBinocular disparity results in a tangible subjective experience of three-dimensional world, but whether disparity also augments objective perceptual performance remains debated. We hypothesized that the improved coding of depth enabled by binocular disparity allows participants to individuate more objects at a glance as the objects can be more efficiently differentiated from each other and the background. We asked participants to enumerate objects in briefly presented naturalistic (Experiment 1) and artificial (Experiment 2) scenes in immersive virtual reality. This type of enumeration task yields well-documented capacity limits where up to 3–4 items can be enumerated rapidly and accurately, known as subitizing. Our results show that although binocular disparity did not yield a large general improvement in enumeration accuracy or reaction times, it improved participants’ ability to process the items right after the limit of perceptual capacity. Binocular disparity also sped-up response times by 27 ms on average when artificial stimuli (cubes) were used. Interestingly, the influence of disparity on subjectively experienced depth revealed a clearly different pattern than the influence of disparity on objective performance. This suggests that the functional and subjective sides of stereopsis can be dissociated. Altogether our results suggest that binocular disparity may increase the number of items the visual system can simultaneously process. This may help animals to better resolve and track objects in complex, cluttered visual environments.
Effect of Deepwater Horizon Crude Oil Water Accommodated Fraction on Olfactory Function in the Atlantic Stingray, Hypanus sabinus
Authors: Cave Eloise J. , Kajiura Stephen M. 
Published: October 2018

AbstractThe Deepwater Horizon oil spill was the largest accidental marine oil spill in history, releasing nearly 5 million barrels of crude oil. Crude oil causes both lethal and sublethal effects on marine organisms, and sensory systems have the potential to be strongly affected. Marine fishes rely upon the effective functioning of their sensory systems for detection of prey, mates, and predators. However, despite the obvious importance of sensory systems, the impact of crude oil exposure upon sensory function remains largely unexplored. Here we show that olfactory organ responses to amino acids are significantly depressed in oil exposed stingrays. We found that the response magnitude of the electro-olfactogram (EOG) to 1 mM amino acids decreased by an average of 45.8% after 48 h of exposure to an oil concentration replicating that measured in coastal areas. Additionally, in oil exposed individuals, the EOG response onset was significantly slower, and the clearing time was protracted. This study is the first to employ an electrophysiological assay to demonstrate crude oil impairment of the olfactory system in a marine fish. We show that stingrays inhabiting an area impacted by an oil spill experience reduced olfactory function, which would detrimentally impact fitness, could lead to premature death, and could cause additional cascading effects through lower trophic levels.
Probing of G-Quadruplex Structures via Ligand-Sensitized Photochemical Reactions in BrU-Substituted DNA
Authors: Saha Abhijit , Bombard Sophie , Granzhan Anton , Teulade-Fichou Marie-Paule 
Published: October 2018

AbstractWe studied photochemical reactions of BrU-substituted G-quadruplex (G4) DNA substrates with two pyrene-substituted polyazamacrocyclic ligands, M-1PY and M-2PY. Both ligands bind to and stabilize G4-DNA structures without altering their folding topology, as demonstrated by FRET-melting experiments, fluorimetric titrations and CD spectroscopy. Notably, the bis-pyrene derivative (M-2PY) behaves as a significantly more affine and selective G4 ligand, compared with its mono-pyrene counterpart (M-1PY) and control compounds. Upon short UVA irradiation (365 nm) both ligands, in particular M-2PY, efficiently sensitize photoreactions at BrU residues incorporated in G4 structures and give rise to two kinds of photoproducts, namely DNA strand cleavage and covalent ligand–DNA photoadducts. Remarkably, the photoinduced strand cleavage is observed exclusively with G4 structures presenting BrU residues in lateral or diagonal loops, but not with parallel G4-DNA structures presenting only propeller loops. In contrast, the formation of fluorescent photoadducts is observed with all BrU-substituted G4-DNA substrates, with M-2PY giving significantly higher yields (up to 27%) than M-1PY. Both ligand-sensitized photoreactions are specific to BrU-modified G4-DNA structures with respect to double-stranded or stem-loop substrates. Thus, ligand-sensitized photoreactions with BrU-substituted G4-DNA may be exploited (i) as a photochemical probe, allowing “photofootprinting” of G4 folding topologies in vitro and (ii) for covalent trapping of G4 structures as photoadducts with pyrene-substituted ligands.
Transcriptome Dynamics During Turbot Spermatogenesis Predicting the Potential Key Genes Regulating Male Germ Cell Proliferation and Maturation
Authors: Wang Xueying , Liu Qinghua , Xu Shihong , Xiao Yongshuang , Wang Yanfeng , Feng Chengcheng , Xue Rui , Zhao Haixia , Song Zongcheng , Li Jun 
Published: October 2018

AbstractSpermatogenesis is a dynamic developmental process in which spermatogonial stem cells proliferate, differentiate and mature into functional spermatozoa. These processes require an accurate gene regulation network. Here, we investigated the dynamic changes that occur during spermatogenesis through a combination of histological and transcriptome analyses of different developmental stages of the testis. We constructed 18 testis transcriptome libraries, and the average length, N50, and GC content of the unigenes were 1,795 bp; 3,240 bp and 49.25%, respectively. Differentially expressed genes (DEGs) that were related to germ cell proliferation and maturation, such as NANOS3, RARs, KIFs, steroid hormone synthesis-related genes and receptor genes, were identified between pairs of testis at different developmental stages. Gene ontology annotation and pathway analyses were conducted on DEGs with specific expression patterns involved in the regulation of spermatogenesis. Nine important pathways such as steroid hormone biosynthesis related to spermatogenesis were identified. A total of 21 modules that ranged from 49 to 7,448 genes were designed by a weighted gene co-expression network analysis. Furthermore, a total of 83 candidate miRNA were identified by computational methods. Our study provides the first transcriptomic evidence for differences in gene expression between different developmental stages of spermatogenesis in turbot (Scophthalmus maximus).
Lower protein expression levels of MHC class I chain-related gene A in hepatocellular carcinoma are at high risk of recurrence after surgical resection
Authors: Huang Chung-Feng , Wang Shu-Chi , Chang Wen-Tsan , Yeh Ming-Lun , Huang Ching-I , Lin Zu-Yau , Chen Shinn-Cherng , Chuang Wan-Long , Huang Jee-Fu , Dai Chia-Yen , Chen Yao-Li , Yu Ming-Lung 
Published: October 2018

AbstractMHC class I chain-related gene A (MICA) variants have been associated with hepatocellular carcinoma (HCC). Their association with MICA expression in cancer cells and cancer recurrence is unknown. SNP rs2596542 of MICA was tested in 193 HCC patients with surgical resection. The corresponding MICA expression in the cancer tissue was measured by immunochemistry microarray. Patients with the SNP rs2596542 A allele had significantly lower MICA expression in tumor tissue than did those with the GG genotype (24.7 ± 15.1% vs. 41.5 ± 23.4%, P < 0.001). Patients who had HCC recurrence had significantly lower MICA expression in tumor tissue (34.2 ± 21.8% vs. 24.0 ± 19.8%, P = 0.03). Cox regression analysis revealed that the factors independently predictive of HCC recurrence included low MICA expression (hazard ratio [HR]/95%confidence intervals [CI]: 2.77/1.07–7.14, P = 0.035) and tumor size (HR/CI: 5.22/2.11–12.96, P < 0.001). Compared to patients with tumors <5 cm and MICA expression >30%, patients with either one and both two risk factors had HCC HRs of 9.76 (C.I. 1.27–75.03, P = 0.03) and 27.30 (C.I. 3.46–215.6, P = 0.002), respectively. We concluded that low cellular MICA expressions were at a greater risk of HCC recurrence after curative treatment.
Neighbors help neighbors control urban mosquitoes
Authors: Johnson Brian J. , Brosch David , Christiansen Arlene , Wells Ed , Wells Martha , Bhandoola Andre F. , Milne Amy , Garrison Sharon , Fonseca Dina M. 
Published: October 2018

AbstractThe worldwide spread of invasive Aedes mosquitoes and arboviral disease, have renewed the pressure for effective and sustainable urban mosquito control. We report on the success of a model we are confident will usher in a new era of urban mosquito control. The key innovation is the mobilization of neighbors guided by scientific advisors, an approach we termed Citizen Action through Science (Citizen AcTS). This approach was tested in a NE US town of approximately 1,000 residential yards infested with the invasive Asian tiger mosquito, Aedes albopictus, a major nuisance arboviral vector. We report a highly significant reduction in biting pressure that was maintained over time, and establish the thresholds needed for success. The Citizen AcTS model rejects the top-down approach consistently associated with intervention failures. Instead, it works through respectful exchanges among scientists and residents that lead to trust and individual ‘buy-in’ and transferring program ownership to the community.
IL-6, IL-17 and Stat3 are required for auto-inflammatory syndrome development in mouse
Authors: Oike Takatsugu , Kanagawa Hiroya , Sato Yuiko , Kobayashi Tami , Nakatsukasa Hiroko , Miyamoto Kana , Nakamura Satoshi , Kaneko Yosuke , Kobayashi Shu , Harato Kengo , Yoshimura Akihiko , Iwakura Yoichiro , Takeuchi Tsutomu , Matsumoto Morio , Nakamura Masaya , Niki Yasuo , Miyamoto Takeshi 
Published: October 2018

AbstractAuto-inflammatory syndrome, a condition clinically distinct from rheumatoid arthritis, is characterized by systemic inflammation in tissues such as major joints, skin, and internal organs. Autonomous innate-immune activation is thought to promote this inflammation, but underlying pathological mechanisms have not been clarified nor are treatment strategies established. Here, we newly established a mouse model in which IL-1 signaling is conditionally activated in adult mice (hIL-1 cTg) and observed phenotypes similar to those seen in auto-inflammatory syndrome patients. In serum of hIL-1 cTg mice, IL-6 and IL-17 levels significantly increased, and signal transducer and activator of transcription 3 (Stat3) was activated in joints. When we crossed hIL-1 cTg with either IL-6- or IL-17-deficient mice or with Stat3 conditional knockout mice, phenotypes seen in hIL-1 cTg mice were significantly ameliorated. Thus, IL-6, IL-17 and Stat3 all represent potential therapeutic targets for this syndrome.
Deciphering the bacterial composition in the rhizosphere of Baphicacanthus cusia (NeeS) Bremek
Authors: Zeng Meijuan , Zhong Yongjia , Cai Shijie , Diao Yong 
Published: October 2018

AbstractRhizobacteria is an important ingredient for growth and health of medicinal herbs, and synthesis of pharmacological effective substances from it. In this study, we investigated the community structure and composition of rhizobacteria inBaphicacanthus cusia(NeeS) Bremek via 16S rRNA amplicon sequencing. We obtained an average of 3,371 and 3,730 OTUs for bulk soil and rhizosphere soil samples respectively. Beta diversity analysis suggested that the bacterial community in the rhizosphere was distinctive from that in the bulk soil, which indicates thatB.cusiacan specifically recruit microbes from bulk soil and host in the rhizosphere.Burkholderiawas significantly enriched in the rhizosphere.Burkholderiais a potentially beneficial bacteria that has been reported to play a major role in the synthesis of indigo, which was a major effective substances inB. cusia. In addition, we found thatBacilliwere depleted in the rhizosphere, which are useful for biocontrol of soil-borne diseases, and this may explain the continuous cropping obstacles inB. cusia. Our results revealed the structure and composition of bacterial diversity inB. cusiarhizosphere, and provided clues for improving the medicinal value ofB. cusiain the future.
Enhanced excitonic emission efficiency in porous GaN
Authors: Ngo Thi Huong , Gil Bernard , Shubina Tatiana V. , Damilano Benjamin , Vezian Stéphane , Valvin Pierre , Massies Jean 
Published: October 2018

AbstractWe investigate the optical properties of porous GaN films of different porosities, focusing on the behaviors of the excitonic features in time-integrated and time-resolved photoluminescence. A substantial enhancement of both excitonic emission intensity and recombination rate, along with insignificant intensity weakening under temperature rise, is observed in the porous GaN films. These observations are in line with (i) the local concentration of electric field at GaN nanoparticles and pores due to the depolarization effect, (ii) the efficient light extraction from the nanoparticles. Besides, the porosification enlarges the surface of the air/semiconductor interface, which further promotes the extraction efficiency and suppresses non-radiative recombination channels. Our findings open a way to increasing the emission efficiency of nanophotonic devices based on porous GaN.
A novel approach to create an antibacterial surface using titanium dioxide and a combination of dip-pen nanolithography and soft lithography
Authors: Arango-Santander Santiago , Pelaez-Vargas Alejandro , Freitas Sidónio C. , García Claudia 
Published: October 2018

AbstractSoft lithography and Dip-Pen Nanolithography (DPN) are techniques that have been used to modify the surface of biomaterials. Modified surfaces play a role in reducing bacterial adhesion and biofilm formation. Also, titanium dioxide has been reported as an antibacterial substance due to its photocatalytic effect. This work aimed at creating patterns on model surfaces using DPN and soft lithography combined with titanium dioxide to create functional antibacterial micropatterned surfaces, which were tested against Streptococcus mutans. DPN was used to create a master pattern onto a model surface and microstamping was performed to duplicate and transfer such patterns to medical-grade stainless steel 316L using a suspension of TiO2. Modified SS316L plates were subjected to UVA black light as photocatalytic activator. Patterns were characterized by atomic force microscopy and biologically evaluated using S. mutans. A significant reduction of up to 60% in bacterial adhesion to TiO2 -coated and -micropatterned surfaces was observed. Moreover, both TiO2 surfaces reduced the viability of adhered bacteria after UV exposure. TiO2 micropatterned demonstrated a synergic effect between physical and chemical modification against S. mutans. This dual effect was enhanced by increasing TiO2 concentration. This novel approach may be a promising alternative to reduce bacterial adhesion to surfaces.
Rerouting of NADPH synthetic pathways for increased protopanaxadiol production in Saccharomyces cerevisiae
Authors: Kim Jae-Eung , Jang In-Seung , Sung Bong Hyun , Kim Sun Chang , Lee Ju Young 
Published: October 2018

AbstractGinseng (Panax ginseng) and its bioactive components, ginsenosides, are popular medicinal herbal products, exhibiting various pharmacological effects. Despite their advocated use for medication, the long cultivation periods of ginseng roots and their low ginsenoside content prevent mass production of this compound. Yeast Saccharomyces cerevisiae was engineered for production of protopanaxadiol (PPD), a type of aglycone characterizing ginsenoside. PPD-producing yeast cell factory was further engineered by obtaining a balance between enzyme expressions and altering cofactor availability. Different combinations of promoters (PGPD, PCCW12, and PADH2) were utilized to construct the PPD biosynthetic pathway. Rerouting the redox metabolism to improve NADPH availability in the engineered S. cerevisiae also increased PPD production. Combining these approaches resulted in more than an 11-fold increase in PPD titer over the initially constructed strain. The series of metabolic engineering strategies of this study provides a feasible approach for the microbial production of PPD and development of microbial platforms producing other industrially-relevant terpenoids.