bluuebunny/crossref_metadata_2025 huggingface dataset:
Grey and white matter volumes either in treatment-naïve or hormone-treated transgender women: a voxel-based morphometry study
Authors: Spizzirri Giancarlo , Duran Fábio Luis Souza , Chaim-Avancini Tiffany Moukbel , Serpa Mauricio Henriques , Cavallet Mikael , Pereira Carla Maria Abreu , Santos Pedro Paim , Squarzoni Paula , da Costa Naomi Antunes , Busatto Geraldo F. , Abdo Carmita Helena Najjar
Published: January 2018

Many previous magnetic resonance imaging (MRI) studies have documented sex differences in brain morphology, but the patterns of sexual brain differences in transgender women – male sex assigned at birth – with a diagnosis of gender dysphoria (TW) have been rarely investigated to date. We acquired T1-weighted MRI data for the following four (n = 80) groups: treatment-naïve TW (TNTW), TW treated with cross-sex hormones for at least one year (TTW), cisgender men, and cisgender women (cisgender individuals as controls). Differences in whole-brain and regional white matter volume and grey matter volume (GMV) were assessed using voxel-based morphometry. We found lower global brain volumes and regional GMVs in a large portion of the posterior-superior frontal cortex in the cisgender women group than in the TTW and cisgender men groups. Additionally, both transgender groups exhibited lower bilateral insular GMVs than the cisgender women group. Our results highlight differences in the insula in both transgender groups; such differences may be characteristic of TW. Furthermore, these alterations in the insula could be related to the neural network of body perception and reflect the distress that accompanies gender dysphoria.
Lamina Cribrosa Morphology Predicts Progressive Retinal Nerve Fiber Layer Loss In Eyes with Suspected Glaucoma
Authors: Kim Jeong-Ah , Kim Tae-Woo , Weinreb Robert N. , Lee Eun Ji , Girard Michaël J. A. , Mari Jean Martial
Published: January 2018

Although early diagnosis and treatment reduce the risk of blindness from glaucoma, the decision on whether or not to begin treatment in patients with suspected glaucoma is often a dilemma because the majority of patients never develop definite glaucoma. A growing body of evidences suggests that posterior bowing of the lamina cribrosa (LC) is the earliest structural change preceding the retinal nerve fiber layer (RNFL) loss in glaucomatous optic neuropathy. Based on this notion, we conducted a prospective study enrolling 87 eyes suspected of having glaucoma to investigate whether the future rate of RNFL loss is associated with the baseline LC curve evaluated by measuring the LC curve index (LCCI) using enhanced depth imaging optical coherence tomography. A faster rate of RNFL loss was significantly associated with greater LCCI (P < 0.001;standardized coefficient beta = −0.392), older age (P = 0.008;beta = −0.314), and greater vertical cup-to-disc ratio (P = 0.040;beta = −0.233). Assessment of LC morphology may help predict the disease outcome in eyes with suspected glaucoma.
A Global View of Transcriptome Dynamics During Male Floral Bud Development in Populus tomentosa
Authors: Chen Zhong , Rao Pian , Yang Xiaoyu , Su Xiaoxing , Zhao Tianyun , Gao Kai , Yang Xiong , An Xinmin
Published: January 2018

To obtain a comprehensive overview of the dynamic transcriptome during male floral bud development in Populus tomentosa, high-throughput RNA-seq was conducted during eight flowering-related stages. Among the 109,212 de novo assembled unigenes, 6,959 were differentially expressed during the eight stages. The overrepresented classed of genes identified by Gene Ontology (GO) enrichment included ‘response to environmental stimuli’ and ‘plant-type spore development’. One-third of the differentially expressed genes were transcription factors (TFs). Several genes and gene families were analyzed in depth, including MADS-box TFs, Squamosa promoter binding protein-like family, receptor-like kinases, FLOWERING LOCUS T/TERMINAL-FLOWER-LIKE 1 family, key genes involved in anther and tapetum development, as well as LEAFY, WUSCHEL and CONSTANS. The results provided new insights into the roles of these and other well known gene families during the annual flowering cycle. To explore the mechanisms regulating poplar flowering, a weighted gene co-expression network was constructed using 98 floral-related genes involved in flower meristem identity and flower development. Many modules of co-expressed genes and hub genes were identified, such as APETALA1 and HUA1. This work provides many new insights on the annual flowering cycle in a perennial plant, and a major new resource for plant biology and biotechnology.
Lifetime-preserving reference models for characterizing spreading dynamics on temporal networks
Authors: Li Mingwu , Rao Vikyath D. , Gernat Tim , Dankowicz Harry
Published: January 2018

To study how a certain network feature affects processes occurring on a temporal network, one often compares properties of the original network against those of a randomized reference model that lacks the feature in question. The randomly permuted times (PT) reference model is widely used to probe how temporal features affect spreading dynamics on temporal networks. However, PT implicitly assumes that edges and nodes are continuously active during the network sampling period – an assumption that does not always hold in real networks. We systematically analyze a recently-proposed restriction of PT that preserves node lifetimes (PTN), and a similar restriction (PTE) that also preserves edge lifetimes. We use PT, PTN, and PTE to characterize spreading dynamics on (i) synthetic networks with heterogeneous edge lifespans and tunable burstiness, and (ii) four real-world networks, including two in which nodes enter and leave the network dynamically. We find that predictions of spreading speed can change considerably with the choice of reference model. Moreover, the degree of disparity in the predictions reflects the extent of node/edge turnover, highlighting the importance of using lifetime-preserving reference models when nodes or edges are not continuously present in the network.
Evaluation of the effects of space allowance on measures of animal welfare in laboratory mice
Authors: Bailoo Jeremy D. , Murphy Eimear , Varholick Justin A. , Novak Janja , Palme Rupert , Würbel Hanno
Published: January 2018

We studied how space allowance affects measures of animal welfare in mice by systematically varying group size and cage type across three levels each in both males and females of two strains of mice (C57BL/6ByJ and BALB/cByJ; n = 216 cages, a total of 1152 mice). This allowed us to disentangle the effects of total floor area, group size, stocking density, and individual space allocation on a broad range of measures of welfare, including growth (food and water intake, body mass); stress physiology (glucocorticoid metabolites in faecal boli); emotionality (open field behaviour); brain function (recurrent perseveration in a two-choice guessing task); and home-cage behaviour (activity, stereotypic behaviour). While increasing group size was associated with a decrease in food and water intake in general, and more specifically with increased attrition due to escalated aggression in male BALB mice, no other consistent effects of any aspect of space allowance were found with respect to the measures studied here. Our results indicate that within the range of conditions commonly found in laboratory mouse housing, space allowance as such has little impact on measures of welfare, except for group size which may be a risk factor for escalating aggression in males of some strains.
Functionalisation of Detonation Nanodiamond for Monodispersed, Soluble DNA-Nanodiamond Conjugates Using Mixed Silane Bead-Assisted Sonication Disintegration
Authors: Edgington Robert , Spillane Katelyn M. , Papageorgiou George , Wray William , Ishiwata Hitoshi , Labarca Mariana , Leal-Ortiz Sergio , Reid Gordon , Webb Martin , Foord John , Melosh Nicholas , Schaefer Andreas T.
Published: January 2018

Nanodiamonds have many attractive properties that make them suitable for a range of biological applications, but their practical use has been limited because nanodiamond conjugates tend to aggregate in solution during or after functionalisation. Here we demonstrate the production of DNA-detonation nanodiamond (DNA-DND) conjugates with high dispersion and solubility using an ultrasonic, mixed-silanization chemistry protocol based on the in situ Bead-Assisted Sonication Disintegration (BASD) silanization method. We use two silanes to achieve these properties: (1) 3-(trihydroxysilyl)propyl methylphosphonate (THPMP); a negatively charged silane that imparts high zeta potential and solubility in solution; and (2) (3-aminopropyl)triethoxysilane (APTES); a commonly used functional silane that contributes an amino group for subsequent bioconjugation. We target these amino groups for covalent conjugation to thiolated, single-stranded DNA oligomers using the heterobifunctional crosslinker sulfosuccinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (Sulfo-SMCC). The resulting DNA-DND conjugates are the smallest reported to date, as determined by Dynamic Light Scattering (DLS) and Atomic Force Microscopy (AFM). The functionalisation method we describe is versatile and can be used to produce a wide variety of soluble DND-biomolecule conjugates.
The high concentration of progesterone is harmful for endometrial receptivity and decidualization
Authors: Liang Yu-Xiang , Liu Li , Jin Zhi-Yong , Liang Xiao-Huan , Fu Yong-Sheng , Gu Xiao-Wei , Yang Zeng-Ming
Published: January 2018

Progesterone is required for the establishment and maintenance of mammalian pregnancy and widely used for conservative treatment of luteal phase deficiency in clinics. However, there are limited solid evidences available for the optimal timing and dose of progesterone therapy, especially for the possible adverse effects on implantation and decidualization when progesterone is administrated empirically. In our study, mouse models were used to examine effects of excess progesterone on embryo implantation and decidualization. Our data indicate that excess progesterone is not only harmful for mouse implantation, but also impairs mouse decidualization. In excess progesterone-treated mice, the impaired LIF/STAT3 pathway and dysregulated endoplasmic reticulum stress may lead to the inhibition of embryo implantation and decidualization. It is possible that the decrease in birth weight of excess progesterone-treated mice is due to a compromised embryo implantation and decidualization. Furthermore, excess progesterone compromises in vitro decidualization of human endometrial stromal cells.
The effect of differentiation and TGFβ on mitochondrial respiration and mitochondrial enzyme abundance in cultured primary human skeletal muscle cells
Authors: Hoffmann Christoph , Höckele Selina , Kappler Lisa , Hrabĕ de Angelis Martin , Häring Hans-Ulrich , Weigert Cora
Published: January 2018

Measuring mitochondrial respiration in cultured cells is a valuable tool to investigate the influence of physiological and disease-related factors on cellular metabolism; however, the details of the experimental workflow greatly influence the informative value of the results. Working with primary cells and cell types capable of differentiation can be particularly challenging. We present a streamlined workflow optimised for investigation of primary human skeletal muscle cells. We applied the workflow to differentiated and undifferentiated cells and we investigated the effect of TGFβ1 treatment. Differentiation of myoblasts to myotubes increased mitochondrial respiration and abundance of mitochondrial enzymes and mitochondrial marker proteins. Differentiation also induced qualitative changes in mitochondrial protein composition and respiration. TGFβ1 reduced complex IV protein MTCO1 abundance in both myoblasts and myotubes. In myoblasts, spare electron transport system (ETS) capacity was reduced due to a reduction in maximal oxygen consumption. In TGFβ1-treated myotubes, the reduction in spare ETS capacity is mainly a consequence of increased oxidative phosphorylation capacity and complex III protein UQCRC2. Taken together, our data shows that it is important to monitor muscle cell differentiation when mitochondrial function is studied. Our workflow is not only sensitive enough to detect physiological-sized differences, but also adequate to form mechanistic hypotheses.
Chaotic universe model
Authors: Aydiner Ekrem
Published: January 2018

In this study, we consider nonlinear interactions between components such as dark energy, dark matter, matter and radiation in the framework of the Friedman-Robertson-Walker space-time and propose a simple interaction model based on the time evolution of the densities of these components. By using this model we show that these interactions can be given by Lotka-Volterra type equations. We numerically solve these coupling equations and show that interaction dynamics between dark energy-dark matter-matter or dark energy-dark matter-matter-radiation has a strange attractor for 0 > w
de
 >−1, w
dm
 ≥ 0, w
m
 ≥ 0 and w
r
 ≥ 0 values. These strange attractors with the positive Lyapunov exponent clearly show that chaotic dynamics appears in the time evolution of the densities. These results provide that the time evolution of the universe is chaotic. The present model may have potential to solve some of the cosmological problems such as the singularity, cosmic coincidence, big crunch, big rip, horizon, oscillation, the emergence of the galaxies, matter distribution and large-scale organization of the universe. The model also connects between dynamics of the competing species in biological systems and dynamics of the time evolution of the universe and offers a new perspective and a new different scenario for the universe evolution.
Functionalized Sugarcane Bagasse for U(VI) Adsorption from Acid and Alkaline Conditions
Authors: Su Shouzheng , Liu Qi , Liu Jingyuan , Zhang Hongsen , Li Rumin , Jing Xiaoyan , Wang Jun
Published: January 2018

The highly efficient removal of uranium from mine tailings effluent, radioactive wastewater and enrichment from seawater is of great significance for the development of nuclear industry. In this work, we prepared an efficient U(VI) adsorbent by EDTA modified sugarcane bagasse (MESB) with a simple process. The prepared adsorbent preserves high adsorptive capacity for UO22+ (pH 3.0) and uranyl complexes, such as UO2(OH)+, (UO2)2(OH)22+ and (UO2)3(OH)5+ (pH 4.0 and pH 5.0) and good repeatability in acidic environment. The maximum adsorption capacity for U(VI) at pH 3.0, 4.0 and 5.0 is 578.0, 925.9 and 1394.1 mg/g and the adsorption capacity loss is only 7% after five cycles. With the pH from 3.0 to 5.0, the inhibitive effects of Na+ and K+ decreased but increased of Mg2+ and Ca2+. MESB also exhibits good adsorption for [UO2(CO3)3]4− at pH 8.3 from 10 mg/L to 3.3 μg/L. Moreover, MESB could effectively extract U(VI) from simulated seawater in the presence of other metals ions. This work provided a general and efficient uranyl enriched material for nuclear industry.
Label-Free, High Resolution, Multi-Modal Light Microscopy for Discrimination of Live Stem Cell Differentiation Status
Authors: Zhang Jing , Moradi Emilia , Somekh Michael G. , Mather Melissa L.
Published: January 2018

A label-free microscopy method for assessing the differentiation status of stem cells is presented with potential application for characterization of therapeutic stem cell populations. The microscopy system is capable of characterizing live cells based on the use of evanescent wave microscopy and quantitative phase contrast (QPC) microscopy. The capability of the microscopy system is demonstrated by studying the differentiation of live immortalised neonatal mouse neural stem cells over a 15 day time course. Metrics extracted from microscope images are assessed and images compared with results from endpoint immuno-staining studies to illustrate the system’s performance. Results demonstrate the potential of the microscopy system as a valuable tool for cell biologists to readily identify the differentiation status of unlabelled live cells.
Robust fabrication of thin film polyamide-TiO2 nanocomposite membranes with enhanced thermal stability and anti-biofouling propensity
Authors: Khorshidi Behnam , Biswas Ishita , Ghosh Tanushree , Thundat Thomas , Sadrzadeh Mohtada
Published: January 2018

The development of nano-enabled composite materials has led to a paradigm shift in the manufacture of high-performance nanocomposite membranes with enhanced permeation, thermo-mechanical, and antibacterial properties. The major challenges to the successful incorporation of nanoparticles (NPs) to polymer films are the severe aggregation of the NPs and the weak compatibility of NPs with polymers. These two phenomena lead to the formation of non-selective voids at the interface of the polymer and NPs, which adversely affect the separation performance of the membrane. To overcome these challenges, we have developed a new method for the fabrication of robust TFN reverse osmosis membranes. This approach relies on the simultaneous synthesis and surface functionalization of TiO2 NPs in an organic solvent (heptane) via biphasic solvothermal reaction. The resulting stable suspension of the TiO2 NPs in heptane was then utilized in the interfacial (in-situ) polymerization reaction where the NPs were entrapped within the matrix of the polyamide (PA) membrane. TiO2 NPs of 10 nm were effectively incorporated into the thin PA layer and improved the thermal stability and anti-biofouling properties of the resulting TFN membranes. These features make our synthesized membranes potential candidates for applications where the treatment of high-temperature streams containing biomaterials is desirable.
Validation and optimization of the Systemic Inflammation-Based modified Glasgow Prognostic Score in predicting postoperative outcome of inflammatory bowel disease: preliminary data
Authors: Zhao Chenyan , Ding Chao , Xie Tingbin , Zhang Tenghui , Dai Xujie , Wei Yao , Li Yi , Gong Jianfeng , Zhu Weiming
Published: January 2018

Systemic Inflammation-Based modified Glasgow Prognostic Score (mGPS) was developed as an objective tool to grade state of inflammation. However, the association between mGPS and postoperative complications for inflammatory bowel disease (IBD) patients was still unknown. In our study, 270 IBD patients [Crohn’s disease (CD), n = 186; Ulcerative colitis (UC), n = 84] from January 2013 and January 2016 who underwent elective bowel resection were retrospectively analyzed, and, the levels of preoperative C-reactive protein (CRP) and albumin were included as parameters of mGPS. The incidence of overall postoperative complications was 44.81% (121/270), including 46.77% (87/186) of CD and 40.48% (34/84) of UC. According to multivariate analysis, mGPS (CD: OR = 3.47, p = 0.003; UC: OR = 3.28, p = 0.019) was independently associated with an increased risk of postoperative complications. Patients with a higher mGPS also suffered longer postoperative stay and increased SSIs (both p < 0.05). Combining mGPS with neutrophil ratio improved its prognostic value with a better area under the curve (AUC), using receiver operating characteristic (ROC) method. Then we confirmed that mGPS was associated with postoperative complications in IBD patients undergoing elective bowel resection and the addition of neutrophil ratio enhanced its prognostic value.
The PEG-responding desiccome of the alder microsymbiont Frankia alni
Authors: Ghedira Kais , Harigua-Souiai Emna , Ben Hamda Cherif , Fournier Pascale , Pujic Petar , Guesmi Sihem , Guizani Ikram , Miotello Guylaine , Armengaud Jean , Normand Philippe , Sghaier Haïtham
Published: January 2018

Actinorhizal plants are ecologically and economically important. Symbiosis with nitrogen-fixing bacteria allows these woody dicotyledonous plants to colonise soils under nitrogen deficiency, water-stress or other extreme conditions. However, proteins involved in xerotolerance of symbiotic microorganisms have yet to be identified. Here we characterise the polyethylene glycol (PEG)-responding desiccome from the most geographically widespread Gram-positive nitrogen-fixing plant symbiont, Frankia alni, by next-generation proteomics, taking advantage of a Q-Exactive HF tandem mass spectrometer equipped with an ultra-high-field Orbitrap analyser. A total of 2,052 proteins were detected and quantified. Under osmotic stress, PEG-grown F. alni cells increased the abundance of envelope-associated proteins like ABC transporters, mechano-sensitive ion channels and Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated (cas) components. Conjointly, dispensable pathways, like nitrogen fixation, aerobic respiration and homologous recombination, were markedly down-regulated. Molecular modelling and docking simulations suggested that the PEG is acting on Frankia partly by filling the inner part of an up-regulated osmotic-stress large conductance mechanosensitive channel.
Analysis of the HIV-2 protease’s adaptation to various ligands: characterization of backbone asymmetry using a structural alphabet
Authors: Triki Dhoha , Cano Contreras Mario Enrique , Flatters Delphine , Visseaux Benoit , Descamps Diane , Camproux Anne-Claude , Regad Leslie
Published: January 2018

The HIV-2 protease (PR2) is a homodimer of 99 residues with asymmetric assembly and binding various ligands. We propose an exhaustive study of the local structural asymmetry between the two monomers of all available PR2 structures complexed with various inhibitors using a structural alphabet approach. On average, PR2 exhibits asymmetry in 31% of its positions—i.e., exhibiting different backbone local conformations in the two monomers. This asymmetry was observed all along its structure, particularly in the elbow and flap regions. We first differentiated structural asymmetry conserved in most PR2 structures from the one specific to some PR2. Then, we explored the origin of the detected asymmetry in PR2. We localized asymmetry that could be induced by PR2’s flexibility, allowing transition from the semi-open to closed conformations and the asymmetry potentially induced by ligand binding. This latter could be important for the PR2’s adaptation to diverse ligands. Our results highlighted some differences between asymmetry of PR2 bound to darunavir and amprenavir that could explain their differences of affinity. This knowledge is critical for a better description of PR2’s recognition and adaptation to various ligands and for a better understanding of the resistance of PR2 to most PR2 inhibitors, a major antiretroviral class.
Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma
Authors: Tomasini Michael D. , Wang Yingjie , Karamafrooz Adak , Li Geoffrey , Beuming Thijs , Gao Jiali , Taylor Susan S. , Veglia Gianluigi , Simon Sanford M.
Published: January 2018

In fibrolamellar hepatocellular carcinoma a single genetic deletion results in the fusion of the first exon of the heat shock protein 40, DNAJB1, which encodes the J domain, with exons 2–10 of the catalytic subunit of protein kinase A, PRKACA. This produces an enzymatically active chimeric protein J-PKAcα. We used molecular dynamics simulations and NMR to analyze the conformational landscape of native and chimeric kinase, and found an ensemble of conformations. These ranged from having the J-domain tucked under the large lobe of the kinase, similar to what was reported in the crystal structure, to others where the J-domain was dislodged from the core of the kinase and swinging free in solution. These simulated dislodged states were experimentally captured by NMR. Modeling of the different conformations revealed no obvious steric interactions of the J-domain with the rest of the RIIβ holoenzyme.
Competitive influence maximization and enhancement of synchronization in populations of non-identical Kuramoto oscillators
Authors: Brede Markus , Stella Massimo , Kalloniatis Alexander C.
Published: January 2018

Many networked systems have evolved to optimize performance of function. Much literature has considered optimization of networks by central planning, but investigations of network formation amongst agents connecting to achieve non-aligned goals are comparatively rare. Here we consider the dynamics of synchronization in populations of coupled non-identical oscillators and analyze adaptations in which individual nodes attempt to rewire network topology to optimize node-specific aims. We demonstrate that, even though individual nodes’ goals differ very widely, rewiring rules in which each node attempts to connect to the rest of the network in such a way as to maximize its influence on the system can enhance synchronization of the collective. The observed speed-up of consensus finding in this competitive dynamics might explain enhanced synchronization in real world systems and shed light on mechanisms for improved consensus finding in society.
SPARC expression is associated with hepatic injury in rodents and humans with non-alcoholic fatty liver disease
Authors: Mazzolini Guillermo , Atorrasagasti Catalina , Onorato Agostina , Peixoto Estanislao , Schlattjan Martin , Sowa Jan-Peter , Sydor Svenja , Gerken Guido , Canbay Ali
Published: January 2018

Mechanisms that control progression from simple steatosis to steato-hepatitis and fibrosis in patients with non-alcoholic fatty liver disease (NAFLD) are unknown. SPARC, a secreted matricellular protein, is over-expressed in the liver under chronic injury. Contribution of SPARC accumulation to disease severity is largely unknown in NAFLD. We assessed the hypothesis that SPARC is increased in livers with more necrosis and inflammation and could be associated with more fibrosis. qrt-PCR, immunohistochemistry, and ELISA were employed to localize and quantify changes in SPARC in 62 morbidly obese patients with NAFLD/NASH and in a mouse model of diet-induced-NASH. Results were correlated with the severity of NAFLD/NASH. In obese patients 2 subgroups were identified with either high SPARC expression (n = 16) or low SPARC expression (n = 46) in the liver, with a cutoff of 1.2 fold expression. High expression of SPARC paralleled hepatocellular damage and increased mRNA expression of pro-fibrogenic factors in the liver. In line with these findings, in the NASH animal model SPARC knockout mice were protected from inflammatory injury, and showed less inflammation and fibrosis. Hepatic SPARC expression is associated with liver injury and fibrogenic processes in NAFLD. SPARC has potential as preventive or therapeutic target in NAFLD patients.
Gene and MicroRNA Perturbations of Cellular Response to Pemetrexed Implicate Biological Networks and Enable Imputation of Response in Lung Adenocarcinoma
Authors: Gamazon Eric R. , Trendowski Matthew R. , Wen Yujia , Wing Claudia , Delaney Shannon M. , Huh Won , Wong Shan , Cox Nancy J. , Dolan M. Eileen
Published: January 2018

Pemetrexed is indicated for non-small cell lung carcinoma and mesothelioma, but often has limited efficacy due to drug resistance. To probe the molecular mechanisms underlying chemotherapeutic response, we performed mRNA and microRNA (miRNA) expression profiling of pemetrexed treated and untreated lymphoblastoid cell lines (LCLs) and applied a hierarchical Bayesian method. We identified genetic variation associated with gene expression in human lung tissue for the most significant differentially expressed genes (Benjamini-Hochberg [BH] adjusted p < 0.05) using the Genotype-Tissue Expression data and found evidence for their clinical relevance using integrated molecular profiling and lung adenocarcinoma survival data from The Cancer Genome Atlas project. We identified 39 miRNAs with significant differential expression (BH adjusted p < 0.05) in LCLs. We developed a gene expression based imputation model of drug sensitivity, quantified its prediction performance, and found a significant correlation of the imputed phenotype generated from expression data with survival time in lung adenocarcinoma patients. Differentially expressed genes (MTHFD2 and SUFU) that are putative targets of differentially expressed miRNAs also showed differential perturbation in A549 fusion lung tumor cells with further replication in A549 cells. Our study suggests pemetrexed may be used in combination with agents that target miRNAs to increase its cytotoxicity.
Apparent shift in long-range motion trajectory by local pattern orientation
Authors: Nakayama Ryohei , Harada Daisuke , Kamachi Miyuki G. , Motoyoshi Isamu
Published: January 2018

The present study shows that the apparent direction of a moving pattern is systematically affected by its orientation. We found that the perceived direction of motion of a single Gabor grating changing position in discrete steps interleaved by blank inter-stimulus interval (ISI) is biased toward the orientation of the grating. This orientation-induced motion shift peaks for grating orientations ~±15 deg away from the physical motion trajectory and was profound for relatively short distances. Orientation adaptation revealed that the directional shift is determined by the apparent –not the physical –orientation of the grating, and a subsequent experiment demonstrated that directional shift is also influenced by the orientation of the contrast-defined stimulus envelope. Results provide further evidence that the apparent trajectory of a motion stimulus is determined by interactions between motion and pattern information at relatively high levels of visual processing.
Distinct ERP profiles for auditory processing in infants at-risk for autism and language impairment
Authors: Riva Valentina , Cantiani Chiara , Mornati Giulia , Gallo Martina , Villa Laura , Mani Elisa , Saviozzi Irene , Marino Cecilia , Molteni Massimo
Published: January 2018

Early identification of autism spectrum disorder (ASD) is crucial for the formulation of effective intervention programs. Language deficits may be a hallmark feature of ASD and language delay observed in ASD shows striking similarities to that observed in children with language impairment (LI). Auditory processing deficits are seen in both LI and ASD, however, they have not previously been compared directly using Event-Related Potentials (ERPs) in the two at-risk populations. This study aims to characterize infants at-risk for ASD (HR-ASD) at the electrophysiological level and to compare them with infants at-risk for LI (HR-LI) and controls, to find specific markers with predictive value. At 12-month-old, auditory processing in HR-ASD, HR-LI and controls was characterized via ERP oddball paradigm. All infants were then evaluated at 20 months, to investigate the associations between auditory processing and language/ASD-related outcomes. In both HR-ASD and HR-LI, mismatch response latency was delayed compared to controls, whereas only HR-ASD showed overall larger P3 amplitude compared to controls. Interestingly, these ERP measures correlated with later expressive vocabulary and M-CHAT critical items in the whole sample. These results may support the use of objective measurement of auditory processing to delineate pathophysiological mechanisms in ASD, as compared to LI.
Bacterial iron reduction and biogenic mineral formation for the stabilisation of corroded iron objects
Authors: Kooli Wafa M. , Comensoli Lucrezia , Maillard Julien , Albini Monica , Gelb Arnaud , Junier Pilar , Joseph Edith
Published: January 2018

Exploiting bacterial metabolism for the stabilisation of corroded iron artefacts is a promising alternative to conventional conservation-restoration methods. Bacterial iron reduction coupled to biogenic mineral formation has been shown to promote the conversion of reactive into stable corrosion products that are integrated into the natural corrosion layer of the object. However, in order to stabilise iron corrosion, the formation of specific biogenic minerals is essential. In this study, we used the facultative anaerobeShewanella loihicafor the production of stable biogenic iron minerals under controlled chemical conditions. The biogenic formation of crystalline iron phosphates was observed after iron reduction in a solution containing Fe(III) citrate. When the same biological treatment was applied on corroded iron plates, a layer composed of iron phosphates and iron carbonates was formed. Surface and cross-section analyses demonstrated that these two stable corrosion products replaced 81% of the reactive corrosion layer after two weeks of treatment. Such results demonstrate the potential of a biological treatment in the development of a stabilisation method to preserve corroded iron objects.
A framework for quantifying the relationship between intensity and severity of impact of disturbance across types of events and species
Authors: Iwasaki Aiko , Noda Takashi
Published: January 2018

Understanding the impacts of natural disturbances on wildlife populations is a central task for ecologists; in general, the severity of impact of a disturbance (e.g., the resulting degree of population decline) is likely to depend primarily on the disturbance intensity (i.e., strength of forcing), type of disturbance, and species vulnerability. However, differences among disturbance events in the physical units of forcing and interspecific differences in the temporal variability of population size under normal (non-disturbance) conditions hinder comprehensive analysis of disturbance severity. Here, we propose new measures of disturbance intensity and severity, both represented by the return periods. We use a meta-analysis to describe the severity–intensity relationship across various disturbance types and species. The severity and the range of its 95% confidential interval increased exponentially with increasing intensity. This nonlinear relationship suggests that physically intense events may have a catastrophic impact, but their severity cannot be extrapolated from the severity–intensity relationship for weak, frequent disturbance events. The framework we propose may help to clarify the influence of event types and species traits on the severity–intensity relationship, as well as to improve our ability to predict the ecological consequences of various disturbance events of unexperienced intensity.
Dipeptidyl peptidase-4 inhibitors, pancreatic cancer and acute pancreatitis: A meta-analysis with trial sequential analysis
Authors: Pinto Lana C. , Rados Dimitris V. , Barkan Sabrina S. , Leitão Cristiane B. , Gross Jorge L.
Published: January 2018

The use of dipeptidyl peptidase-4 (DPP-4) inhibitors may be associated with pancreatic cancer and acute pancreatitis. Recent meta-analyses have reported conflicting findings. Therefore, we performed a meta-analysis to assess the risk of both pancreatic cancer and acute pancreatitis associated with the use of DPP-4 inhibitors. We also used trial sequential analysis to evaluate whether the number of patients included was enough to reach conclusions. We included randomised controlled trials lasting 24 weeks or more that compared DPP-4 inhibitors with placebo or other antihyperglycaemic agents. A total of 59,404 patients were included. There was no relationship between the use of DPP-4 inhibitors and pancreatic cancer (Peto odds ratio 0.65; 95% CI 0.35–1.21), and the optimal sample size was reached to determine a number needed to harm (NNH) of 1000 patients. DPP-4 inhibitors were associated with increased risk for acute pancreatitis (Peto odds ratio 1.72; 95% CI 1.18–2.53), with an NNH of 1066 patients, but the optimal sample size for this outcome was not reached. In conclusion, there is no association between DPP-4 inhibitors and pancreatic cancer, and a small risk for acute pancreatitis was observed with DPP-4 inhibitor use, although the latter finding is not definitive.
Testing for the Presence of Correlation Changes in a Multivariate Time Series: A Permutation Based Approach
Authors: Cabrieto Jedelyn , Tuerlinckx Francis , Kuppens Peter , Hunyadi Borbála , Ceulemans Eva
Published: January 2018

Detecting abrupt correlation changes in multivariate time series is crucial in many application fields such as signal processing, functional neuroimaging, climate studies, and financial analysis. To detect such changes, several promising correlation change tests exist, but they may suffer from severe loss of power when there is actually more than one change point underlying the data. To deal with this drawback, we propose a permutation based significance test for Kernel Change Point (KCP) detection on the running correlations. Given a requested number of change points K, KCP divides the time series into K + 1 phases by minimizing the within-phase variance. The new permutation test looks at how the average within-phase variance decreases when K increases and compares this to the results for permuted data. The results of an extensive simulation study and applications to several real data sets show that, depending on the setting, the new test performs either at par or better than the state-of-the art significance tests for detecting the presence of correlation changes, implying that its use can be generally recommended.
Stretchable Electrospun PVDF-HFP/Co-ZnO Nanofibers as Piezoelectric Nanogenerators
Authors: Parangusan Hemalatha , Ponnamma Deepalekshmi , Al-Maadeed Mariam Al Ali
Published: January 2018

Herein, we investigate the morphology, structure and piezoelectric performances of neat polyvinylidene fluoride hexafluoropropylene (PVDF-HFP) and PVDF-HFP/Co-ZnO nanofibers, fabricated by electrospinning. An increase in the amount of crystalline β-phase of PVDF-HFP has been observed with the increase in Co-doped ZnO nanofiller concentration in the PVDF-HFP matrix. The dielectric constants of the neat PVDF-HFP and PVDF-HFP/2 wt.% Co-ZnO nanofibers are derived as 8 and 38 respectively. The flexible nanogenerator manipulated from the polymer nanocomposite (PVDF-HFP/Co-ZnO) exhibits an output voltage as high as 2.8 V compared with the neat PVDF-HFP sample (~120 mV). These results indicate that the investigated nanocomposite is appropriate for fabricating various flexible and wearable self-powered electrical devices and systems.
Co-action equilibrium fails to predict choices in mixed-strategy settings
Authors: Berger Ulrich
Published: January 2018

Social projection is the tendency to project one’s own characteristics onto others. This phenomenon can potentially explain cooperation in prisoner’s dilemma experiments and other social dilemmas. The social projection hypothesis has recently been formalized for symmetric games as co-action equilibrium and for general games as consistent evidential equilibrium. These concepts have been proposed to predict choice behavior in experimental one-shot games. We test the predictions of the co-action equilibrium concept in a simple binary minimizer game experiment. We find no evidence of social projection.
A Geodetic Strain Rate Model for the East African Rift System
Authors: Stamps D. S. , Saria E. , Kreemer C.
Published: January 2018

Here we describe the new Sub-Saharan Africa Geodetic Strain Rate Model v.1.0 (SSA-GSRM v.1.0), which provides fundamental constraints on long-term tectonic deformation in the region and an improved seismic hazards assessment in Sub-Saharan Africa. Sub-Saharan Africa encompasses the East African Rift System, the active divergent plate boundary between the Nubian and Somalian plates, where strain is largely accommodated along the boundaries of three subplates. We develop an improved geodetic strain rate field for sub-Saharan Africa that incorporates 1) an expanded geodetic velocity field, 2) redefined regions of deforming zones guided by seismicity distribution, and 3) updated constraints on block rotations. SSA-GSRM v.1.0 spans longitudes 22° to 55.5° and latitudes −52° to 20° with 0.25° (longitude) by 0.2° (latitude) spacing. For plates/sub-plates, we assign rigid block rotations as constraints on the strain rate calculation that is determined by fitting bicubic Bessel splines to a new geodetic velocity solution for an interpolated velocity gradient tensor field. We derive strain rates, velocities, and vorticity rates from the velocity gradient tensor field. A comparison with the Global Geodetic Strain Rate model v2.1 reveals regions of previously unresolved spatial heterogeneities in geodetic strain rate distribution, which indicates zones of elevated seismic risk.
Nanostructural Differentiation and Toxicity of Amyloid-β25-35 Aggregates Ensue from Distinct Secondary Conformation
Authors: Song Yongxiu , Li Ping , Liu Lei , Bortolini Christian , Dong Mingdong
Published: January 2018

Amyloid nanostructures are originated from protein misfolding and aberrant aggregation, which is associated with the pathogenesis of many types of degenerative diseases, such as Alzheimer’s disease (AD), Parkinson’s disease (PD) and Huntington’s disease. The secondary conformation of peptides is of a fundamental importance for aggregation and toxicity of amyloid peptides. In this work, Aβ25-35, a fragment of amyloid β(1-42) (Aβ42), was selected to investigate the correlation between secondary structures and toxicity of amyloid fibrils. Furthermore, each aggregation assemblies show different cell membrane disruption and cytotoxicity. The structural analysis of amyloid aggregates originated from different secondary structure motifs is helpful to understand the mechanism of peptides/cell interactions in the pathogenesis of amyloid diseases.
Trophic ecology of glass sponge reefs in the Strait of Georgia, British Columbia
Authors: Kahn Amanda S. , Chu Jackson W. F. , Leys Sally P.
Published: January 2018

Sponges link the microbial loop with benthic communities by feeding on bacteria. Glass sponge reefs on the continental shelf of western Canada have extremely high grazing rates, consuming seven times more particulate carbon than can be supplied by vertical flux alone. Unlike many sponges, the reef building species Aphrocallistes vastus has no microbial symbionts and removes little dissolved organic carbon. To determine how reef sponges therefore get enough food to sustain such substantial grazing we measured stable carbon and nitrogen isotope signatures of water, sediment and sponge tissues. To ensure samples were temporally associated, we also studied the duration particles were retained in tissues in controlled feeding studies using microscopic beads and 13C-labeled bacteria. Although fecal pellets were expelled from sponges within 24 hours of feeding, intact bacteria were still found in tissues and sponge tissues retained elevated 13C levels for at least 14 days. These independent lines of evidence suggest that carbon in reef sponge tissues may reflect food consumed from days to weeks earlier. Stable isotope analysis suggests that heterotrophic bacteria ingested by the sponges comes from a confluence of trophic subsidies: from terrestrial and oceanic sources, and also potentially on sediment-borne bacteria resuspended by tidal currents.
Net global warming potential and greenhouse gas intensity as affected by different water management strategies in Chinese double rice-cropping systems
Authors: Wu Xiaohong , Wang Wei , Xie Xiaoli , Yin Chunmei , Hou Haijun , Yan Wende , Wang Guangjun
Published: January 2018

This study provides a complete account of global warming potential (GWP) and greenhouse gas intensity (GHGI) in relation to a long-term water management experiment in Chinese double-rice cropping systems. The three strategies of water management comprised continuous (year-round) flooding (CF), flooding during the rice season but with drainage during the midseason and harvest time (F-D-F), and irrigation only for flooding during transplanting and the tillering stage (F-RF). The CH4 and N2O fluxes were measured with the static chamber method. Soil organic carbon (SOC) sequestration rates were estimated based on the changes in the carbon stocks during 1998–2014. Longer periods of soil flooding led to increased CH4 emissions, reduced N2O emissions, and enhanced SOC sequestration. The net GWPs were 22,497, 8,895, and 1,646 kg CO2-equivalent ha−1 yr−1 for the CF, F-D-F, and F-RF, respectively. The annual rice grain yields were comparable between the F-D-F and CF, but were reduced significantly (by 13%) in the F-RF. The GHGIs were 2.07, 0.87, and 0.18 kg CO2-equivalent kg−1 grain yr−1 for the CF, F-D-F, and F-RF, respectively. These results suggest that F-D-F could be used to maintain the grain yields and simultaneously mitigate the climatic impact of double rice-cropping systems.
A Collective Route to Head and Neck Cancer Metastasis
Authors: Kulasinghe Arutha , Schmidt Henri , Perry Chris , Whitfield Bernard , Kenny Liz , Nelson Colleen , Warkiani Majid E. , Punyadeera Chamindie
Published: January 2018

Distant metastasis (DM) from head and neck cancers (HNC) portends a poor patient prognosis. Despite its important biological role, little is known about the cells which seed these DM. Circulating tumour cells (CTCs) represent a transient cancer cell population, which circulate in HNC patients’ peripheral blood and seed at distant sites. Capture and analysis of CTCs offers insights into tumour metastasis and can facilitate treatment strategies. Whilst the data on singular CTCs have shown clinical significance, the role of CTC clusters in metastasis remains limited. In this pilot study, we assessed 60 treatment naïve HNC patients for CTCs with disease ranging from early to advanced stages, for CTC clusters utilizing spiral CTC enrichment technology. Single CTCs were isolated in 18/60–30% (Ranging from Stage I-IV), CTC clusters in 15/60–25% (exclusively Stage IV) with 3/15–20% of CTC clusters also containing leukocytes. The presence of CTC clusters associated with the development of distant metastatic disease(P = 0.0313). This study demonstrates that CTC clusters are found in locally advanced patients, and this may be an important prognostic marker. In vivo and in vitro studies are warranted to determine the role of these CTC clusters, in particular, whether leukocyte involvement in CTC clusters has clinical relevance.
Placental Morphology Is Associated with Maternal Depressive Symptoms during Pregnancy and Toddler Psychiatric Problems
Authors: Lahti-Pulkkinen Marius , Cudmore Melissa Jane , Haeussner Eva , Schmitz Christoph , Pesonen Anu-Katriina , Hämäläinen Esa , Villa Pia M. , Mehtälä Susanna , Kajantie Eero , Laivuori Hannele , Reynolds Rebecca M. , Frank Hans-Georg , Räikkönen Katri
Published: January 2018

Maternal depressive symptoms during pregnancy predict increased psychiatric problems in children. The underlying biological mechanisms remain unclear. Hence, we examined whether alterations in the morphology of 88 term placentas were associated with maternal depressive symptoms during pregnancy and psychiatric problems in 1.9–3.1-years old (Mean = 2.1 years) toddlers. Maternal depressive symptoms were rated biweekly during pregnancy with the Center of Epidemiological Studies Depression Scale (n = 86). Toddler psychiatric problems were mother-rated with the Child Behavior Checklist (n = 60). We found that higher maternal depressive symptoms throughout pregnancy [B = −0.24 Standard Deviation (SD) units: 95% Confidence Interval (CI) = −0.46; −0.03: P = 0.03; Mean difference = −0.66 SDs; 95% CI = −0.08; −1.23: P = 0.03; between those with and without clinically relevant depressive symptoms] were associated with lower variability in the placental villous barrier thickness of γ-smooth muscle actin-negative villi. This placental morphological change predicted higher total (B = −0.34 SDs: 95% CI = −0.60; −0.07: P = 0.01) and internalizing (B = −0.32 SDs: 95% CI = −0.56; −0.08: P = 0.01) psychiatric problems in toddlers. To conclude, our findings suggest that both maternal depressive symptoms during pregnancy and toddler psychiatric problems may be associated with lower variability in the villous membrane thickness of peripheral villi in term placentas. This lower heterogeneity may compromise materno-fetal exchange, suggesting a possible role for altered placental morphology in the fetal programming of mental disorders.