bluuebunny/crossref_metadata_2025_split huggingface dataset:
NR3C1 hypermethylation in depressed and bullied adolescents
Authors: Efstathopoulos Paschalis , Andersson Filip , Melas Philippe A. , Yang Liu L. , Villaescusa J. Carlos , Rȕegg Joëlle , Ekström Tomas J. , Forsell Yvonne , Galanti Maria Rosaria , Lavebratt Catharina 
Published: June 2018

AbstractThe disruption of key epigenetic processes during critical periods of brain development can increase an individual’s vulnerability to psychopathology later in life. For instance, DNA methylation in the glucocorticoid receptor gene (NR3C1) in adulthood is known to be associated with early-life adversities and has been suggested to mediate the development of stress-related disorders. However, the association between NR3C1 methylation and the emergence of internalizing symptoms in childhood and adolescence has not been studied extensively. In the present report, we used saliva DNA from a cohort of Swedish adolescents (13–14 years old; N = 1149) to measure NR3C1 methylation in the exon 1F region. Internalizing psychopathological symptoms were assessed using the Center for Epidemiologic Studies Depression Scale for Children (CES-DC). We found that NR3C1 hypermethylation was cross-sectionally associated with high score for internalizing symptoms in the whole group as well as among the female participants. In addition, an analysis of social environmental stressors revealed that reports of bullied or lacking friends were significantly associated with NR3C1 hypermethylation. This cross-sectional association of NR3C1 exon 1F hypermethylation with internalizing psychopathology in adolescents, as well as with bullying and lack of friends are novel results in this field. Longitudinal studies are needed to address whether NR3C1 methylation mediates the link between social stressors and psychopathology in adolescence.
NEURAPRO: a multi-centre RCT of omega-3 polyunsaturated fatty acids versus placebo in young people at ultra-high risk of psychotic disorders—medium-term follow-up and clinical course
Authors: Nelson B. , Amminger G. P. , Yuen H. P. , Markulev C. , Lavoie S. , Schäfer M. R. , Hartmann J. A. , Mossaheb N. , Schlögelhofer M. , Smesny S. , Hickie I. B. , Berger G. , Chen E. Y. H. , de Haan L. , Nieman D. H. , Nordentoft M. , Riecher-Rössler A. , Verma S. , Thompson A. , Yung A. R. , McGorry P. D. 
Published: June 2018

AbstractThis study reports a medium-term follow-up of a randomised, double-blind, placebo-controlled trial of omega-3 polyunsaturated fatty acids (PUFA) in ultra-high risk for psychosis (UHR) patients. Primary outcomes of interest were transition to psychosis and symptomatic and functional outcome. A secondary aim was to investigate clinical predictors of medium-term outcome. Three hundred four UHR participants were recruited across 10 specialised early psychosis services in Australia, Asia, and Europe. The intervention consisted of 1.4 g/daily of omega-3 PUFA or placebo, plus up to 20 sessions of cognitive-behavioural case management (CBCM), over the 6-month study period, with participants receiving further CBCM sessions on basis of need between months 6–12. Mean time to follow-up was 3.4 (median = 3.3; SD = 0.9) years. There was a modest increase in transitions between 12-month and medium-term follow-up (11–13%) and substantial improvement in symptoms and functioning between baseline and follow-up, with no differences between the treatment groups. Most improvement had been achieved by end of the intervention. 55% of the sample received mental health treatment between end of intervention and follow-up. Omega-3 PUFA did not provide additional benefits to good quality psychosocial intervention over the medium term. Although most improvement had been achieved by end of intervention the substantial rates of post-intervention mental health service use indicate longer-term clinical need in UHR patients. The post-intervention phase treatment or the longer-term effect of CBCM, or a combination of the two, may have contributed to maintaining the gains achieved during the intervention phase and prevented significant deterioration after this time.
Ligand Binding Stabilizes Cellulosomal Cohesins as Revealed by AFM-based Single-Molecule Force Spectroscopy
Authors: Verdorfer Tobias , Gaub Hermann E. 
Published: June 2018

AbstractThe cohesin-dockerin receptor-ligand family is the key element in the formation of multi-enzyme lignocellulose-digesting extracellular complexes called cellulosomes. Changes in a receptor protein upon binding of a ligand - commonly referred to as allostery - are not just essential for signalling, but may also alter the overall mechanical stability of a protein receptor. Here, we measured the change in mechanical stability of a library of cohesin receptor domains upon binding of their dockerin ligands in a multiplexed atomic force microscopy-based single-molecule force spectroscopy experiment. A parallelized, cell-free protein expression and immobilization protocol enables rapid mechanical phenotyping of an entire library of constructs with a single cantilever and thus ensures high throughput and precision. Our results show that dockerin binding increases the mechanical stability of every probed cohesin independently of its original folding strength. Furthermore, our results indicate that certain cohesins undergo a transition from a multitude of different folds or unfolding pathways to a single stable fold upon binding their ligand.
Transparent anti-fogging and self-cleaning TiO2/SiO2 thin films on polymer substrates using atmospheric plasma
Authors: Chemin Jean-Baptiste , Bulou Simon , Baba Kamal , Fontaine Charly , Sindzingre Thierry , Boscher Nicolas D. , Choquet Patrick 
Published: June 2018

AbstractTransparent anti-fogging and self-cleaning coatings are of great interest for many applications, including solar panels, windshields and displays or lenses to be used in humid environments. In this paper, we report on the simultaneous synthesis, at atmospheric pressure, of anatase TiO2 nanoparticles and low-temperature, high-rate deposition of anatase TiO2/SiO2 nanocomposite coatings. These coatings exhibit durable super-hydrophilic and photocatalytic properties. The strategy followed relies on concomitant and separated injections of titania, i.e. titanium isopropoxide, and silica, i.e. hexamethyldisiloxane, precursors in the stream of a blown-arc discharge to form transparent anti-fogging and self-cleaning anatase TiO2/SiO2 nanocomposite coatings on polymer substrates.
Neck-specific exercise improves impaired interactions between ventral neck muscles in chronic whiplash: A randomized controlled ultrasound study
Authors: Peterson Gunnel , Nilsson David , Trygg Johan , Peolsson Anneli 
Published: June 2018

AbstractChronic pain and disability is common in whiplash-associated disorders (WAD), leading to personal suffering, sick leave, and social cost. The cervical spine is heavily dependent on muscular support and whiplash injury can cause damage to the neck muscles, but diagnostic tools to measure neck muscle impairment and evaluate exercise interventions are lacking. Therefore, the present study investigated ventral neck muscle interactions in 26 individuals with chronic WAD randomized to neck-specific exercise (NSE) or remaining on a waiting list (WL) in 3 months. We performed real-time, non-invasive ultrasound measurements with speckle tracking analysis and calculated the deformation area and deformation rate in three ventral neck muscles. Multivariate statistics were used to analyse interactions between the muscles. After 3 months of NSE, significant improvements were observed in neck muscle interactions and pain intensity in the NSE group compared to the WL group. Thus, this study demonstrates that non-invasive ultrasound can be a diagnostic tool for muscle impairment and used to evaluate exercise interventions in WAD and stands to make a breakthrough for better management in chronic WAD.
Maternal Trophic Status and Offpsring Phenotype in a Marine Invertebrate
Authors: González-Ortegón Enrique , Vay Lewis Le , Walton Mark Edward Mackay , Giménez Luis 
Published: June 2018

AbstractOffspring size variation in relation to maternal size and season is characteristic of a range of species living in seasonal environments. Little is known about the proximate mechanisms explaining the links between maternally driven variation in offspring phenotypes, for instance when mothers have different diets depending on their size or the season. Here, we use stable isotopes techniques to quantify size dependent and seasonal variations in diet in mothers of shrimp Palaemon serratus and explore possible links between maternal diet and phenotype of embryos and freshly hatched larvae. We found that larger females, which occur more frequently in winter, produce larvae with higher carbon and nitrogen content as well as higher percent carbon, than smaller mothers collected in winter. In addition, isotopic composition suggest that larger mothers collected in winter, were feeding at a higher trophic level, or on an enriched prey pool compared with smaller mothers collected in summer. Overall, there seems to be a strong association between offspring size and maternal diet, mediated by maternal size and/or season.
Imaging through scattering media with the auxiliary of a known reference object
Authors: Yang Wanqin , Li Guowei , Situ Guohai 
Published: June 2018

AbstractImaging through scattering media has been one of the main challenges in optics, and are encountered in many different disciplines of sciences, ranging from biology, mesoscopic physics to astronomy. Recently, various methods have been proposed. In this manuscript, we propose a robust method for imaging through scattering media in a reflective geometry, a scenario widely encountered in non-invasive and marker-free biological imaging. The proposed method relies on the a priori information of a known reference object in the neighborhood of the target, and uses it as an auxiliary to reconstruct the target image. We show that the target image can be analytically reconstructed from the autocorrelation of the recorded speckle if the reference is point-like, otherwise, deconvolution with the reference speckle should be performed. We experimentally demonstrate the proposed method in a proof-of-concept system with an LED illumination through a thick ground glass.
A genome-wide mutation analysis method enabling high-throughput identification of chemical mutagen signatures
Authors: Matsumura Shoji , Fujita Yurika , Yamane Masayuki , Morita Osamu , Honda Hiroshi 
Published: June 2018

AbstractTrinucleotide mutational signatures extracted from cancer genomes provide clues useful in understanding the roles of mutagens and mutagenic mechanisms in cancer development. The lack of a simple method for genome-wide analysis of alterations induced by mutagens hampers the identification of trinucleotide signatures of mutagen exposure and evaluation of their relationships with human cancers. Here, we describe a novel approach to facilitate analysis of chemically induced mutations in bacterial cells by detection of increased frequencies of base substitutions after mutagen exposure, using paired-end overlapping next-generation sequencing. DNA samples from Salmonella typhimurium strain TA100, exposed to three alkylating agents, ethylnitrosourea (ENU), methylnitrosourea (MNU), and ethyl methansulphonate (EMS), were analysed. The G:C > A:T mutation frequency was increased in all samples, whereas A:T base pair substitution frequencies were increased specifically in samples exposed to ENU, consistent with previous reports. Mutation patterns in the context of 96 possible trinucleotide formats in these samples exhibited a sharp peak corresponding to an NpCpY consensus sequence, which is similar to the mutational signature of alkylating agents in human cancer. These results indicate that our approach can be useful in facilitating the understanding of mechanisms underlying chemical mutagenicity and for identification of unknown causal mutagens in human cancer.
Pan4Draft: A Computational Tool to Improve the Accuracy of Pan-Genomic Analysis Using Draft Genomes
Authors: Veras Allan , Araujo Fabricio , Pinheiro Kenny , Guimarães Luis , Azevedo Vasco , Soares Siomar , da Costa da Silva Artur , Ramos Rommel 
Published: June 2018

AbstractHigh-throughput sequencing technologies are a milestone in molecular biology for facilitating great advances in genomics by enabling the deposit of large volumes of biological data to public databases. The availability of such data has made possible the comparative genomic analysis through pipelines, using the entire gene repertoire of genomes. However, a large number of unfinished genomes exist in public databases; their number is approximately 16-fold higher than the number of complete genomes, which creates bias during comparative analyses. Therefore, the present work proposes a new tool called Pan4Drafts, an automated pipeline for pan-genomic analysis of draft prokaryotic genomes to maximize the representation and accuracy of the gene repertoire of unfinished genomes by using reads from sequencing data. Pan4Draft allows to perform comparative analyses using different methodologies such as combining complete and draft genomes, using only draft genomes or only complete genomes. Pan4Draft is available at http://www.computationalbiology.ufpa.br/pan4drafts and the test dataset is available at https://sourceforge.net/projects/pan4drafts.
A novel adenovirus isolated from the Egyptian fruit bat in South Africa is closely related to recent isolates from China
Authors: Jansen van Vuren Petrus , Allam Mushal , Wiley Michael R. , Ismail Arshad , Storm Nadia , Birkhead Monica , Markotter Wanda , Palacios Gustavo , Paweska Janusz T. 
Published: June 2018

AbstractRecently a number of novel adenoviruses have been isolated from diverse bat species and from diverse geographical locations. We describe the isolation of a novel adenovirus (Family Adenoviridae, genus Mastadenovirus) from a pool of liver and spleen tissue of an apparently healthy wild-caught Egyptian fruit bat (Rousettus aegyptiacus) in South Africa. Genetically the virus is most closely related to four mastadenoviruses recently isolated in China, from Miniopterus schreibersi and Rousettus leschenaultii bats, which are highly divergent from previously identified bat adenoviruses. The length of the Rousettus aegyptiacus adenovirus-3085 (RaegAdV-3085) genome, at 29,342 bp is similar to its closest relatives, and contains 27 open reading frames. The RaegAdV-3085 genome has a low G + C content (36.4%) relative to other viruses in the genus (between 43.6 and 63.9%) but similar to its closest relatives. The inverted terminal repeat (ITR) of RaegAdV-3085 is only 40 bp compared to between 61 and 178 bp of its closest relatives. The discovery of RaegAdV-3085 expands the diversity of known adenoviruses in bats and might represent a member of a new mastadenovirus species in bats.
Fabrication of 3D Fingerprint Phantoms via Unconventional Polycarbonate Molding
Authors: Schultz Clayton W. , Wong Jessica X. H. , Yu Hua-Zhong 
Published: June 2018

AbstractFingerprint biometrics is a valuable and convenient security tool; every fingerprint is highly detailed and unique, we always have them on “hand”. Herein we describe a novel bench-top method of making 3D fingerprint replicas (namely, fingerprint phantoms) by exploring a unique microfabrication approach using conventional polymeric materials, to aid the development of reliable and accurate fingerprint biometrics. By pressing an impression of human fingerprints onto solvent-softened plastic plates (e.g., polycarbonate chips), followed by casting with polydimethylsiloxane (PDMS, a popular elastomer), we can produce a flexible, nanoscale detailed, 3D reproduction of the fingerprint (“phantom”). By testing with standard optical fingerprint scanners, we have shown that all three levels of fingerprint details can be precisely recorded and match well with the original fingerprint. Superior to artificial fingerprint patterns, these phantoms have the exact 3D features of fingerprints and introduce no variability compared to human sampling, which make them perfect targets for standardizing fingerprint scanners and for biometric applications. We envision that the microcontact replication protocol via unconventional PC molding promises a practical, bench-top, instrumentation-free method to mass reproduce many other micro/nanostructures with high fidelity.
Application of Whole Genome Resequencing in Mapping of a
Tomato Yellow Leaf Curl Virus Resistance Gene
Authors: Wang Yinlei , Jiang Jing , Zhao Liping , Zhou Rong , Yu Wengui , Zhao Tongmin 
Published: June 2018

AbstractTomato yellow leaf curl virus (TYLCV) has significantly impacted the
tomato industry around the world, and the use of insecticides and insect nets have
not effectively controlled the spread of this pathogen. The tomato line AVTO1227 is
highly resistant to TYLCV. In this study, F2 and
BC1 populations derived from AVTO1227 and the susceptible
line Money maker were used to assess the genetic mechanism underlying TYLCV
resistance. We have identified a recessive TYLCV resistance gene, hereby designated
as ty-5, which is linked to SlNACI. Genomic DNA pools from resistant and susceptible
groups were constructed, and their genomes were resequenced. The ty-5 gene was identified on an interval encompassing the
genomic positions 2.22 Mb to 3.19 Mb on tomato chromosome 4. Genotyping using
linkage markers further mapped ty-5 within the
interval between markers ty5–25 and ty5–29, where only the pelota gene is located. Consequently, pelota was considered as the candidate gene corresponding to ty-5. Two nucleotide transversions within the promoter
region and one transversion in exon region of the pelota gene were detected in the parental lines. However, the relative
transcript levels of pelota did not significantly
differ among the three tomato lines, regardless of TYLCV infection. This study will
facilitate marker-assisted breeding for resistance to TYLCV and lay a foundation for
the research of the resistance mechanism of ty-5
in tomato.
Genetic association and functional analysis of rs7903456 in FAM35A gene and hyperuricemia: a population based study
Authors: Yan Feng , Sun Peng , Zhao Huishou , Zhao Changhai , Zhang Nana , Dai Yujie 
Published: June 2018

AbstractRecent studies have identified SNP rs7903456 of FAM35A to be associated with gout. Because of the close connections between hyperuricemia and gout, we hypothesized that the effect of rs7903456 on gout might be mediated by hyperuricemia or its related quantitative trait, uric acid level. We investigated the association between 31 SNPs of FAM35A, including rs7903456, and hyperuricemia based on 2,773 hyperuricemia patients and controls. We fitted a simple model for each of these 31 SNPs to screen the candidate SNP for further analyses. Moreover, we selected potential confounders and fitted a multivariate model to investigate the adjusted effects of the targeted SNPs. Both disease status of hyperuricemia and blood uric acid level were considered as the main phenotype. We have identified rs7903456 to be associated with hyperuricemia and uric acid level. The significant signal was identified between rs7903456 and uric acid level after adjusted by several potential confounders. Our findings showed that the T allele of rs7903456 could increase the uric acid level by ~10 mmol/L on average after adjusting several biochemical and clinical variables. Our findings indicated that the previously identified effects of rs7903456 on gout might partly be mediated by its effect on uric acid levels.
Vibration and damping characteristics of 3D printed Kagome lattice with viscoelastic material filling
Authors: Wang Rong , Shang Jianzhong , Li Xin , Luo Zirong , Wu Wei 
Published: June 2018

AbstractConstrained layer dampers (CLD) are in widespread use for passive vibration damping, in applications including aerospace structures. However, the introducing of the damping layer can reduce the stiffness of the sandwich structures. A viscoelastic material filling (VMF) is chosen to balance structural and vibrational performance of lattice truss in this work. The recently brought forward 3D Kagome truss with face sheet was manufactured by selective laser sintering technology and the thermosetting polyurethane was chosen as the viscoelastic filling material. A novel complex modal analysis finite element method for Hybrid composite lattice truss sandwich is introduced in this paper. Dynamic analysis experiment results show that the VMF method is found to be effective in reducing the vibration amplitude and it has the potential for band-gap design. The VMF method can provide high stiffness at low mass and considerable vibrational performance at low cost and it can be considered as a general vibration design method in lattice truss manufacture.
Common variants in the GNL3 contribute to the increasing risk of knee osteoarthritis in Han Chinese population
Authors: Liu Bo , Cheng Huiguang , Ma Wenlong , Gong Futai , Wang Xiangyang , Duan Ning , Dang Xiaoqian 
Published: June 2018

AbstractOsteoarthritis (OA) is a complex degenerative joint disorder, which is caused by both environmental and genetic factors. Previous studies have indicated that the GNL3 gene is associated with knee osteoarthritis (KOA) susceptibility in Europeans; however, the exact molecular mechanism is still unclear. In the present study, we investigated the potential genetic association of GNL3 with KOA in a two-stage sample of 6,704 individuals from the Han Chinese population. Subjects containing 1,052 KOA patients and 2,117 controls were considered the discovery dataset, while subjects consisting of 1,173 KOA patients and 2,362 controls were utilized as the replication dataset. Single-SNP association, imputation, and haplotypic association analyses were performed. The SNP of rs11177 in GNL3 was identified to be significantly associated with KOA after accounting for age, gender and BMI in both stages. The imputed SNP of rs6617 in SPCS1 was found to be strongly associated with KOA risk, and the significant association signal was confirmed in the replication stage. Moreover, a haplotype-based analysis also indicated a positive genetic effect of GNL3 on KOA susceptibility. In summary, our results proved that GNL3 plays an important role in the etiology of KOA, suggesting that GNL3 is a potential genetic modifier for KOA development.
2-[2-(4-(trifluoromethyl)phenylamino)thiazol-4-yl]acetic acid (Activator-3) is a potent activator of AMPK
Authors: Bung Navneet , Surepalli Sobhitha , Seshadri Sriram , Patel Sweta , Peddasomayajula Saranya , Kummari Lalith Kumar , Kumar Sireesh T. , Babu Phanithi Prakash , Parsa Kishore V. L. , Poondra Rajamohan Reddy , Bulusu Gopalakrishnan , Misra Parimal 
Published: June 2018

AbstractAMPK is considered as a potential high value target for metabolic disorders. Here, we present the molecular modeling, in vitro and in vivo characterization of Activator-3, 2-[2-(4-(trifluoromethyl)phenylamino)thiazol-4-yl]acetic acid, an AMP mimetic and a potent pan-AMPK activator. Activator-3 and AMP likely share common activation mode for AMPK activation. Activator-3 enhanced AMPK phosphorylation by upstream kinase LKB1 and protected AMPK complex against dephosphorylation by PP2C. Molecular modeling analyses followed by in vitro mutant AMPK enzyme assays demonstrate that Activator-3 interacts with R70 and R152 of the CBS1 domain on AMPK γ subunit near AMP binding site. Activator-3 and C2, a recently described AMPK mimetic, bind differently in the γ subunit of AMPK. Activator-3 unlike C2 does not show cooperativity of AMPK activity in the presence of physiological concentration of ATP (2 mM). Activator-3 displays good pharmacokinetic profile in rat blood plasma with minimal brain penetration property. Oral treatment of High Sucrose Diet (HSD) fed diabetic rats with 10 mg/kg dose of Activator-3 once in a day for 30 days significantly enhanced glucose utilization, improved lipid profiles and reduced body weight, demonstrating that Activator-3 is a potent AMPK activator that can alleviate the negative metabolic impact of high sucrose diet in rat model.