bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clonal expansion of mitochondrial DNA deletions is a private mechanism of ageing in long-lived animals
Authors: Lakshmanan Lakshmi Narayanan , Yee Zhuangli , Ng Li Fang , Gunawan Rudiyanto , Halliwell Barry , Gruber Jan 
Published: March 2018

SummaryDisruption of mitochondrial metabolism and loss of mitochondrial DNA (mtDNA) integrity are widely considered as evolutionarily conserved (public) mechanisms of ageing (López-Otín et al. 2013). Human ageing is associated with loss in skeletal muscle mass and function (Sarcopenia), contributing significantly to morbidity and mortality. Muscle ageing is associated with loss of mtDNA integrity. In humans, clonally expanded mtDNA deletions co-localize with sites of fiber-breakage and atrophy in skeletal muscle. mtDNA deletions may therefore play an important, possibly causal role in sarcopenia. The nematode Caenorhabditis elegans also exhibits age-dependent decline in mitochondrial function and a form of sarcopenia. However, it is unclear if mtDNA deletions play a role in C. elegans ageing. Here we report identification of 266 novel mtDNA deletions in ageing nematodes. Analysis of the mtDNA mutation spectrum and quantification of mutation burden indicates that (1) mtDNA deletions in nematode is extremely rare, (2) there is no significant age-dependent increase in mtDNA deletions and (3) there is little evidence for clonal expansion driving mtDNA deletion dynamics. Thus, mtDNA deletions are unlikely to drive the age-dependent functional decline commonly observed in C. elegans. Computational modelling of mtDNA dynamics in C. elegans indicates that the lifespan of short-lived animals such as C. elegans is likely too short to allow for significant clonal expansion of mtDNA deletions. Together, these findings suggest that clonal expansion of mtDNA deletions is likely a private mechanism of ageing predominantly relevant in long-lived animals such as humans and rhesus monkey and possibly in rodents.
The hippocampal film-editor: sensitivity and specificity to event boundaries in continuous experience
Authors: Ben-Yakov Aya , Henson Richard 
Published: March 2018

AbstractThe function of the human hippocampus is normally investigated by experimental manipulation of discrete events. Less is unknown about what triggers hippocampal activity during more naturalistic, continuous experience. We hypothesized that the hippocampus would be sensitive to the occurrence of event boundaries, i.e. moments in time identified by observers as a transition between events. To address this, we analysed functional MRI data from two groups: one (N=253, 131 female) who viewed an 8.5min film and another (N=15, 6 female) who viewed a 120min film. We observed a strong hippocampal response at boundaries defined by independent observers, which was modulated by boundary strength (the number of observers that identified each boundary). In the longer film, there were sufficient boundaries to show that this modulation remained after covarying out a large number of perceptual factors. The hippocampus was the only brain region whose response showed a significant monotonic increase with boundary strength in both films, suggesting that modulation by boundary strength is selective to the hippocampus. This hypothesis-driven approach was complemented by a data-driven approach, in which we identified hippocampal-events as moments in time with the strongest hippocampal activity: The correspondence between these hippocampalevents and event boundaries was highly-significant, revealing that the hippocampal response is not only sensitive, but also specific to event boundaries. We conclude that the hippocampus plays an important role in segmenting the continuous experience that is typical of naturalistic settings.Significance statementRecent years have seen the field of human neuroscience research transitioning from experiments with simple stimuli to the study of more complex and naturalistic experience. Nonetheless, our understanding of the function of many brain regions, such as the hippocampus, is based primarily on the study of brief, discrete events. As a result, we know little of what triggers hippocampal activity in real-life settings, when we are exposed to a continuous stream of information. When does the hippocampus “decide” to respond during the encoding of naturalistic experience? We reveal here that hippocampal activity measured by fMRI during film-watching is both sensitive and specific to event boundaries, identifying a potential mechanism whereby event boundaries shape experience by modulation of hippocampal activity.
GenBank 2 Sequin - a file converter preparing custom GenBank files for database submission
Authors: Lehwark Pascal , Greiner Stephan 
Published: March 2018

AbstractThe typical wet lab user often annotates smaller sequences in the GenBank format, but resulting files are not accepted for database submission by NCBI. This makes submission of such annotations a cumbersome task. Here we present “GenBank 2 Sequin” an easy-to-use web application that converts custom annotations in the GenBank format into the NCBI direct submission format Sequin. Additionally, the program generates a “five-column, tab-delimited feature table” and a FASTA file required for submission through BankIt or for the update an existing GenBank entry. We specifically developed “GenBank 2 Sequin” for the regular wet lab researcher with strong focus on user-friendliness and flexibility. It is equipped with an intuitive graphical interface and a comprehensive documentation. The application can be employed to prepare any GenBank file for database submission. It is freely available online at https://chlorobox.mpimp-golm.mpg.de/GenBank2Sequin.html.
Microbiome-TP53 Gene Interaction in Human Lung Cancer
Authors: Greathouse K. Leigh , White James R. , Vargas Ashely J. , Bliskovsky Valery V. , Beck Jessica A. , Muhlinen Natalia von , Polley Eric C. , Bowman Elise D. , Khan Mohammed A. , Robles Ana I. , Cooks Tomer , Ryan Bríd M. , Dzutsev Amiran H. , Trinchieri Giorgio , Pineda Marbin A. , Bilke Sven , Meltzer Paul S. , Hokenstad Alexis N. , Stickrod Tricia M. , Walther-Antonio Marina R. , Earl Joshua P. , Mell Joshua C. , Krol Jaroslaw E. , Balashov Sergey V. , Bhat Archana S. , Ehrlich Garth D. , Valm Alex , Deming Clayton , Conlan Sean , Oh Julia , Segre Julie A. , Harris Curtis C. 
Published: March 2018

AbstractBackgroundLung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. Herein, we hypothesized that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from controls (n=33) and cancer cases (n=143), we conducted 16S rRNA bacterial gene sequencing, with RNA-seq data from lung cancer cases in The Cancer Genome Atlas (n=1112) serving as the validation cohort.ResultsOverall, we demonstrate a lower alpha diversity in normal lung as compared to non-tumor adjacent or tumor tissue. In squamous cell carcinoma (SCC) specifically, a separate group of taxa were identified, in which Acidovorax was enriched in smokers (P =0.0013). Acidovorax temporans was identified by fluorescent in situ hybridization within tumor sections, and confirmed by two separate 16S rRNA strategies. Further, these taxa, including Acidovorax, exhibited higher abundance among the subset of SCC cases with TP53 mutations, an association not seen in adenocarcinomas (AD).ConclusionsThe results of this comprehensive study show both a microbiome-gene and microbiome-exposure interactions in SCC lung cancer tissue. Specifically, tumors harboring TP53 mutations, which can damage epithelial function, have a unique bacterial consortia which is higher in relative abundance in smoking-associated SCC. Given the significant need for clinical diagnostic tools in lung cancer, this study may provide novel biomarkers for early detection.
Genome-wide diversity in temporal and regional populations of the betabaculovirusErinnyis ello granulovirus(ErelGV)
Authors: Brito A. F. , Melo F. L. , Ardisson-Araújo D. M. P , Sihler W. , Souza M. L. , Ribeiro B.M. 
Published: March 2018

AbstractBackgroundErinnyis ello granulovirus(ErelGV) is a betabaculovirus infecting caterpillars of the sphingid mothE. ello ello(cassava hornworm), an important pest of cassava crops (Manihot esculenta). In this study, the genome of seven field isolates of the virus ErelGV were deep sequenced and their inter-and intrapopulational sequence diversity were analyzed.ResultsNo events of gene gain/loss or translocations were observed, and indels were mainly found within highly repetitive regions (direct repeats,drs). A naturally occurring isolate from Northern Brazil (Acre State, an Amazonian region) has shown to be the most diverse population, with a unique pattern of polymorphisms. Overall, non-synonymous substitutions were found all over the seven genomes, with no specific gathering of mutations on hotspot regions. Independently of their sizes, some ORFs have shown higher levels of non-synonymous changes than others. Non-core genes of known functions and structural genes were among the most diverse ones; and as expected, core genes were the least variable genes. We observed remarkable differences on diversity of paralogous genes, as in multiple copies ofp10, fgf, andpep. Another important contrast on sequence diversity was found on genes encoding complex subunits and/or involved in the same biological processes, aslate expression factors(lefs) andper os infectivity factors(pifs). Interestingly, several polymorphisms in coding regions lie on sequences encoding specific protein domains.ConclusionsBy comparing and integrating information about inter-and intrapopulational diversity of viral isolates, we provide a detailed description on how evolution operates on field isolates of a betabaculovirus. Our results revealed that 35-41% of the SNPs of ErelGV lead to amino acid changes (non-synonymous substitutions). Some genes, especially non-core genes of unknown functions, tend to accumulate more mutations, while core genes evolve slowly and are more conserved. Additional studies would be necessary to understand the actual effects of such gene variations on viral infection and fitness.
Modulation of input sensitivity and output gain by retinal amacrine cells
Authors: Nategh Neda , Manu Mihai , Baccus Stephen A. 
Published: March 2018

AbstractThe prevailing hierarchical view of the visual system consists of parallel circuits that begin in the retina, which then sum effects across sequential levels, increasing in complexity. Yet a separate type of interaction, whereby one visual pattern changes the influence of another, known as modulation, has received much less attention in terms of its circuit mechanisms. Retinal amacrine cells are a diverse class of inhibitory interneurons that are thought to have modulatory effects, but we lack a general understanding of their functional types. Using dynamic causal experiments in the salamander retina perturbing amacrine cells along with an unsupervised computational framework, we find that amacrine cell modulatory effects cluster into two distinct types. One type controls ganglion cell sensitivity to individual visual features, and a second type controls the ganglion cell’s output gain, acting to gate all features. These results establish three separate general roles of amacrine cells – to generate primary visual features, to use context to select specific visual features and to gate retinal output.
The ecology of the Drosophila-yeast mutualism in wineries
Authors: Quan Allison S. , Eisen Michael B. 
Published: March 2018

AbstractThe fruit fly, Drosophila melanogaster, is preferentially found on fermenting fruits. The yeasts that dominate the microbial communities of these substrates are the primary food source for developing D. melanogaster larvae, and adult flies manifest a strong olfactory system-mediated attraction for the volatile compounds produced by these yeasts during fermentation. Although most work on this interaction has focused on the standard laboratory yeast Saccharomyces cerevisiae, a wide variety of other yeasts naturally ferment fallen fruit. Here we address the open question of whether D. melanogaster preferentially associates with distinct yeasts in different, closely-related environments. We characterized the spatial and temporal dynamics of Drosophila-associated fungi in Northern California wineries that use organic grapes and natural fermentation using high-throughput, short-amplicon sequencing. We found that there is nonrandom structure in the fungal communities that are vectored by flies both between and within vineyards. Within wineries, the fungal communities associated with flies in cellars, fermentation tanks, and pomace piles are distinguished by varying abundances of a small number of yeast species. To investigate the origins of this structure, we assayed Drosophila attraction to, oviposition on, larval development in, and longevity when consuming the yeasts that distinguish vineyard microhabitats from each other. We found that wild fly lines did not respond differentially to the yeast species that distinguish winery habitats in habitat specific manner. Instead, this subset of yeast shares traits that make them attractive to and ensure their close association with Drosophila.
Influence of microstructure morphology on multi-scale modeling of low-alloyed TRIP-steels
Authors: Prüger Stefan , Gandhi Ashutosh , Balzani Daniel 
Published: March 2018

Purpose
The purpose of this study is to quantify the impact of the variation of microstructural features on macroscopic and microscopic fields. The application of multi-scale methods in the context of constitutive modeling of microheterogeneous materials requires the choice of a representative volume element (RVE) of the considered microstructure, which may be based on some idealized assumptions and/or on experimental observations. In any case, a realistic microstructure within the RVE is either computationally too expensive or not fully accessible by experimental measurement techniques, which introduces some uncertainty regarding the microstructural features.

Design/methodology/approach
In this paper, a systematical variation of microstructural parameters controlling the morphology of an RVE with an idealized microstructure is conducted and the impact on macroscopic quantities of interest as well as microstructural fields and their statistics is investigated. The study is carried out under macroscopically homogeneous deformation states using the direct micro-macro scale transition approach.

Findings
The variation of microstructural parameters, such as inclusion volume fraction, aspect ratio and orientation of the inclusion with respect to the overall loading, influences the macroscopic behavior, especially the micromechanical fields significantly.

Originality/value
The systematic assessment of the impact of microstructural parameters on both macroscopic quantities and statistics of the micromechanical fields allows for a quantitative comparison of different microstructure morphologies and a reliable identification of microstructural parameters that promote failure initialization in microheterogeneous materials.
Efficient hybrid algorithms to solve mixed discrete-continuous optimization problems
Authors: Liu Dianzi , Liu Chengyang , Zhang Chuanwei , Xu Chao , Du Ziliang , Wan Zhiqiang 
Published: March 2018

PurposeIn real-world cases, it is common to encounter mixed discrete-continuous problems where some or all of the variables may take only discrete values. To solve these non-linear optimization problems, the use of finite element methods is very time-consuming. The purpose of this study is to investigate the efficiency of the proposed hybrid algorithms for the mixed discrete-continuous optimization and compare it with the performance of genetic algorithms (GAs).Design/methodology/approachIn this paper, the enhanced multipoint approximation method (MAM) is used to reduce the original nonlinear optimization problem to a sequence of approximations. Then, the sequential quadratic programing technique is applied to find the continuous solution. Following that, the implementation of discrete capability into the MAM is developed to solve the mixed discrete-continuous optimization problems.FindingsThe efficiency and rate of convergence of the developed hybrid algorithms outperforming GA are examined by six detailed case studies in the ten-bar planar truss problem, and the superiority of the Hooke–Jeeves assisted MAM algorithm over the other two hybrid algorithms and GAs is concluded.Originality/valueThe authors propose three efficient hybrid algorithms, the rounding-off, the coordinate search and the Hooke–Jeeves search-assisted MAMs, to solve nonlinear mixed discrete-continuous optimization problems. Implementations include the development of new procedures for sampling discrete points, the modification of the trust region adaptation strategy and strategies for solving mix optimization problems. To improve the efficiency and effectiveness of metamodel construction, regressorsfdefined in this paper can have the form in common with the empirical formulation of the problems in many engineering subjects.
Statistical inference of empirical constituents in partitioned analysis from integral-effect experiments
Authors: Stevens Garrison N. , Atamturktur Sez , Brown D. Andrew , Williams Brian J. , Unal Cetin 
Published: March 2018

Purpose
Partitioned analysis is an increasingly popular approach for modeling complex systems with behaviors governed by multiple, interdependent physical phenomena. Yielding accurate representations of reality from partitioned models depends on the availability of all necessary constituent models representing relevant physical phenomena. However, there are many engineering problems where one or more of the constituents may be unavailable because of lack of knowledge regarding the underlying principles governing the behavior or the inability to experimentally observe the constituent behavior in an isolated manner through separate-effect experiments. This study aims to enable partitioned analysis in such situations with an incomplete representation of the full system by inferring the behavior of the missing constituent.

Design/methodology/approach
This paper presents a statistical method for inverse analysis infer missing constituent physics. The feasibility of the method is demonstrated using a physics-based visco-plastic self-consistent (VPSC) model that represents the mechanics of slip and twinning behavior in 5182 aluminum alloy. However, a constituent model to carry out thermal analysis representing the dependence of hardening parameters on temperature is unavailable. Using integral-effect experimental data, the proposed approach is used to infer an empirical constituent model, which is then coupled with VPSC to obtain an experimentally augmented partitioned model representing the thermo-mechanical properties of 5182 aluminum alloy.

Findings
Results demonstrate the capability of the method to enable model predictions dependent upon relevant operational conditions. The VPSC model is coupled with the empirical constituent, and the newly enabled thermal-dependent predictions are compared with experimental data.

Originality/value
The method developed in this paper enables the empirical inference of a functional representation of input parameter values in lieu of a missing constituent model. Through this approach, development of partitioned models in the presence of uncertainty regarding a constituent model is made possible.
Sparse representation of delay differential equation of Pantograph type using multi-wavelets Galerkin method
Authors: Nemati Saray Behzad , Manafian Jalil 
Published: March 2018

Purpose
The purpose of this study is an application of the multi-wavelets Galerkin method to delay differential equations with vanishing delay known as Pantograph equation.

Design/methodology/approach
The method consists of expanding the required approximate solution at the elements of the Alpert multi-wavelets. Using the operational matrices of integration and wavelet transform matrix, the authors reduce the problem to a set of algebraic equations.

Findings
Because of the large size of the system, thresholding is used to obtain a new sparse system, and then this new system is solved to reduce the computational effort and related computer run time. The authors demonstrate that the solutions may be efficiently represented in a multi-wavelets basis because of flexible vanishing moments property of this type of multi-wavelets.

Originality/value
The L2 convergence of the scheme for the proposed equation has been investigated. A series of numerical tests is provided to demonstrate the validity and applicability of the technique.
Statistical energy analysis for vibro-acoustic coupled system with fuzzy parameters
Authors: Wang Yue , Wu Di , Wang Lei , Wang Xiaojun 
Published: March 2018

Purpose
This paper aims to propose a novel statistic energy analysis method with fuzzy parameters to study the dynamic and acoustic responses of coupled system with fuzzy parameters, which can expand the applied range of statistic energy analysis method in engineering to some extent.

Design/methodology/approach
On the basis of the property of membership level, the uncertain fuzzy parameters are expressed as the interval forms. Interval mathematics and interval expansion principle are adopted to solve the problem with interval parameters. At last, two numerical examples, which include a two-plate coupled system and a single-partition sound-insulation system, are carried out to demonstrate the feasibility and validity of the presented method.

Findings
Interval mathematics and interval expansion principle are adopted to solve the problem with interval parameters.

Originality/value
By integrating the interval analysis, optimization technique and Taylor expansion method, two non-probabilistic, set-theoretical statistical energy analyses are proposed for predicting the dynamical and acoustical response of the complex coupled system with uncertain parameters in high-frequency domain.