bluuebunny/crossref_metadata_2025_split huggingface dataset:
Age-related differences in prestimulus subsequent memory effects assessed with event-related potentials
Authors: Koen Joshua D. , Horne Erin D. , Hauck Nedra , Rugg Michael D. 
Published: September 2017

AbstractPrestimulus subsequent memory effects (preSMEs) – differences in neural activity elicited by a task cue at encoding that are predictive of later memory performance – are thought to reflect differential engagement of preparatory processes that benefit episodic memory encoding. We investigated age differences in preSMEs indexed by differences in ERP amplitude just prior to the onset of a study item. Young and older adults incidentally encoded words for a subsequent memory test. Each study word was preceded by a task cue that signaled the judgment to perform on the word. Words were presented for either a short (300 ms) or a long (1000 ms) duration with the aim of placing differential benefits on engaging preparatory processes initiated by the task cue. ERPs associated with subsequent successful and unsuccessful recollection, operationalized here by source memory accuracy, were estimated time-locked to the onset of the task cue. In a late time-window (1000-2000 ms following onset of the cue), young adults demonstrated frontally distributed preSMEs for both the short and the long study durations, albeit with opposite polarities in the two conditions. This finding suggests that preSMEs in young adults are sensitive to perceived task demands. Although older adults showed no evidence of preSMEs in the same late time window, significant preSMEs were observed in an earlier time window (500-1000 ms) that were invariant with study duration. These results are broadly consistent with the proposal that older adults differ from their younger counterparts in how they engage preparatory processes during memory encoding.
Allosteric effector ppGpp potentiates the inhibition of transcript initiation by DksA
Authors: Molodtsov Vadim , Sineva Elena , Zhang Lu , Huang Xuhui , Cashel Michael , Ades Sarah E. , Murakami Katsuhiko S. 
Published: September 2017

SUMMARYDksA and ppGpp are the central players in theEscherichia colistringent response and mediate a complete reprogramming of the transcriptome from one optimized for rapid growth to one adapted for survival during nutrient limitation. A major component of the response is a reduction in ribosome synthesis, which is accomplished by the synergistic action of DksA and ppGpp bound to RNA polymerase (RNAP) inhibiting transcription of rRNAs. Here, we report the X-ray crystal structures ofE. coliRNAP holoenzyme in complex with DksA alone and with ppGpp. The structures show that DksA accesses the template strand at the active site and the downstream DNA binding site of RNAP simultaneously and reveal that binding of the allosteric effector ppGpp reshapes the RNAP–DksA complex. The structural data support a model for transcriptional inhibition in which ppGpp potentiates the destabilization of open complexes on rRNA promoters by DksA. We also determined the structure of RNAP–TraR complex, which reveals the mechanism of ppGpp-independent transcription inhibition by TraR. This work establishes new ground for understanding the pleiotropic effects of DksA and ppGpp on transcriptional regulation in proteobacteria.HighlightsDksA has two modes of binding to RNA polymeraseDksA is capable of inhibiting the catalysis and influences the DNA binding of RNAPppGpp acts as an allosteric effector of DksA functionppGpp stabilizes DksA in a more functionally important binding mode
Cell size and growth rate are modulated by TORC2-dependent signals
Authors: Lucena Rafael , Alcaide-Gavilán Maria , Schubert Katherine , He Maybo , Domnauer Matthew , Marquer Catherine , Kellogg Douglas R. 
Published: September 2017

SummaryThe size of all cells, from bacteria to vertebrates, is proportional to the growth rate set by nutrient availability, but the underlying mechanisms are unknown. Here, we show that nutrients modulate TORC2 signaling, and that cell size is proportional to TORC2 signaling in budding yeast. The TORC2 network controls production of ceramide lipids, which play roles in signaling. We discovered that ceramide-dependent signals control both growth rate and cell size. Thus, cells that can not make ceramides fail to modulate their growth rate or size in response to changes in nutrients. PP2A associated with the Rts1 regulatory subunit (PP2ARts1) is embedded in a feedback loop that controls TORC2 signaling and plays an important role in mechanisms that modulate TORC2 signaling in response to nutrients. Together, the data suggest a model in which growth rate and cell size are mechanistically linked by ceramide-dependent signals arising from the TORC2 network.
Cholecystokinin release triggered by presynaptic NMDA receptors produces LTP and sound-sound associative memory formation
Authors: Li Xiao , Chen Xi , Wong Yin Ting , Wang Haitao , Feng Hemin , Zheng Xuejiao , Feng Jingyu , Baibado Joewel T. , Jesky Robert , Peng Yujie , Wang Zhedi , Xie Hui , Sun Wenjian , Zhang Zicong , Zhang Xu , He Ling , Zhang Nan , Zhang Zhijian , Tang Peng , Su Jun-Feng , Hu Ling-Li , Liu Qing , He Xiao-Bin , Tan Ailian , Sun Xia , Li Min , Wong Kelvin , Wang Xiaoyu , Guo Yi Ping , Xu Fuqiang , He Jufang 
Published: September 2017

AbstractMemory is stored in neural networks via changes in synaptic strength mediated in part by NMDA-dependent long-term potentiation (LTP). There is evidence that entorhinal cortex enables neocortical neuroplasticity through cholecystokinin (CCK)-containing neocortical projections. Here we show that a CCKBantagonist blocks high-frequency stimulation (HFS)-induced LTP in the auditory cortex, whereas local infusion of CCK induces LTP. CCK-/-mice lacked neocortical LTP and showed deficits in a cue-cue associative learning paradigm; administration of CCK rescued associative learning. HFS of CCK-containing entorhino-neocortical projection neurons in anesthetized mice enabled cue-cue associative learning. Furthermore, when one cue was pre-conditioned to footshock, the mouse showed a freezing response to the other cue, indicating that the mice had formed an association. HFS-induced neocortical LTP was completely blocked by either NMDA antagonist or CCK-BR antagonist, while application of either NMDA or CCK induced LTP after low-frequency stimulation (LFS). Moreover, in the presence of CCK LTP was still induced, even after blockade of NMDA receptors. Local application of NMDA induced CCK release in the neocortex. To identify how NMDA receptor switches LTP, a stimulation protocol of 25 pulse-pairs was adopted to replace HFS; NMDA-dependent LTP was induced with the inter-pulse intervals between 10 and 100 ms, but not with those of 5 and 200 ms. LTP-mediated plasticity was linked to localization of the NMDA receptor subunit NR2a on cortical CCK terminals originating in the entorhinal cortex. These novel findings suggest that presynaptic NMDA receptors on CCK terminals control the release of CCK, which enables neocortical LTP and formation of cue-cue associative memory.One Sentence SummaryPresynaptic NMDA receptors switches the release of CCK from entorhinal neurons, which enables neocortical LTP and formation of sound-sound associative memory.
Global determinants of navigation ability
Authors: Coutrot A. , Silva R. , Manley E. , de Cothi W. , Sami S. , Bohbot V. D. , Wiener J. M. , Hölscher C. , Dalton R.C. , Hornberger M. , Spiers H. J. 
Published: September 2017

SummaryCountries vary in their geographical and cultural properties. Only a few studies have explored how such variations influence how humans navigate or reason about space [1–7]. We predicted that these variations impact human cognition, resulting in an organized spatial distribution of cognition at a planetary-wide scale. To test this hypothesis we developed a mobile-app-based cognitive task, measuring non-verbal spatial navigation ability in more than 2.5 million people, sampling populations in every nation state. We focused on spatial navigation due to its universal requirement across cultures. Using a clustering approach, we find that navigation ability is clustered into five distinct, yet geographically related, groups of countries. Specifically, the economic wealth of a nation was predictive of the average navigation ability of its inhabitants, and gender inequality was predictive of the size of performance difference between males and females. Thus, cognitive abilities, at least for spatial navigation, are clustered according to economic wealth and gender inequalities globally, which has significant implications for cross-cultural studies and multi-centre clinical trials using cognitive testing.
STDP forms associations between memory traces in networks of spiking neurons
Authors: Pokorny Christoph , Ison Matias J. , Rao Arjun , Legenstein Robert , Papadimitriou Christos , Maass Wolfgang 
Published: September 2017

AbstractMemory traces and associations between them are fundamental for cognitive brain function. Neuron recordings suggest that distributed assemblies of neurons in the brain serve as memory traces for spatial information, real-world items, and concepts. How-ever, there is conflicting evidence regarding neural codes for associated memory traces. Some studies suggest the emergence of overlaps between assemblies during an association, while others suggest that the assemblies themselves remain largely unchanged and new assemblies emerge as neural codes for associated memory items. Here we study the emergence of neural codes for associated memory items in a generic computational model of recurrent networks of spiking neurons with a data-constrained rule for spike-timing-dependent plasticity (STDP). The model depends critically on two parameters, which control the excitability of neurons and the scale of initial synaptic weights. By modifying these two parameters, the model can reproduce both experimental data from the human brain on the fast formation of associations through emergent overlaps between assemblies, and rodent data where new neurons are recruited to encode the associated memories. Hence our findings suggest that the brain can use both of these two neural codes for associations, and dynamically switch between them during consolidation.
Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation ofERAP2transcripts under balancing selection
Authors: Ye Chun Jimmie , Chen Jenny , Villani Alexandra-Chloé , Gate Rachel E. , Subramaniam Meena , Bhangale Tushar , Lee Mark N. , Raj Towfique , Raychowdhury Raktima , Li Weibo , Rogel Noga , Simmons Sean , Imboywa Selina H. , Chipendo Portia I. , McCabe Cristin , Lee Michelle H. , Frohlich Irene Y. , Stranger Barbara E. , De Jager Philip L. , Regev Aviv , Behrens Tim , Hacohen Nir 
Published: September 2017

AbstractWhile the impact of common genetic variants on gene expression response to cellular stimuli has been analyzed in depth, less is known about how stimulation modulates the genetic control of isoform usage. Analyzing RNA-seq profiles of monocyte-derived dendritic cells from 243 individuals, we uncovered thousands of unannotated isoforms synthesized in response to viral infection and stimulation with type I interferon. We identified more than a thousand single nucleotide polymorphisms associated with isoform usage (isoQTLs), > 40% of which are independent of expression QTLs for the same gene. Compared to eQTLs, isoQTLs are enriched for splice sites and untranslated regions, and depleted of sequences upstream of annotated transcription start sites. Both eQTLs and isoQTLs in stimulated cells explain a significant proportion of the disease heritability attributed to common genetic variants. At theIRF7locus, we found alternative promoter usage in response to influenza as a possible mechanism by which DNA variants previously associated with immune-related disorders mediate disease risk. At theERAP2locus, we shed light on the function of the major haplotype that has been maintained under long-term balancing selection. At baseline and following type 1 interferon stimulation, the major haplotype is associated with absence ofERAP2expression while the minor haplotype, known to increase Crohn’s disease risk, is associated with highERAP2expression. Surprisingly, in response to influenza infection, the major haplotype results in the expression of two uncharacterized, alternatively transcribed, spliced and translated short isoforms. Thus, genetic variants at a single locus could modulate independent gene regulatory processes in the innate immune response, and in the case ofERAP2, may confer a historical fitness advantage in response to virus.
FlashFry: a fast and flexible tool for large-scale CRISPR target design
Authors: McKenna Aaron , Shendure Jay 
Published: September 2017

AbstractFlashFry is a fast and flexible command-line tool for characterizing large numbers of CRISPR target sequences. While several CRISPR web application exist, genome-wide knockout studies, noncoding deletion scans, and other large-scale studies or methods development projects require a simple and lightweight framework that can quickly discover and score thousands of candidates guides targeting an arbitrary DNA sequence. With FlashFry, users can specify an unconstrained number of mismatches to putative off-targets, richly annotate discovered sites, and tag potential guides with commonly used on target and off-target scoring metrics. FlashFry runs at speeds comparable to widely used genome-wide sequence aligners, and output is provided as an easy-to-manipulate text file.AvailabilityFlashFry is written in Scala and bundled as a stand-alone Jar file, easily run on any system with an installed Java virtual machine (JVM). The tool is freely licensed under version 3 of the GPL, and code, documentation, and tutorials are available on the GitHub page:http://aaronmck.github.io/FlashFry/
Massive Mining of Publicly Available RNA-seq Data from Human and Mouse
Authors: Lachmann Alexander , Torre Denis , Keenan Alexandra B. , Jagodnik Kathleen M. , Lee Hyojin J. , Wang Lily , Silverstein Moshe C. , Ma’ayan Avi 
Published: September 2017

RNA-sequencing (RNA-seq) is currently the leading technology for genome-wide transcript quantification. While the volume of RNA-seq data is rapidly increasing, the currently publicly available RNA-seq data is provided mostly in raw form, with small portions processed non- uniformly. This is mainly because the computational demand, particularly for the alignment step, is a significant barrier for global and integrative retrospective analyses. To address this challenge, we developed all RNA-seq and ChIP-seq sample and signature search (ARCHS4), a web resource that makes the majority of previously published RNA-seq data from human and mouse freely available at the gene count level. Such uniformly processed data enables easy integration for downstream analyses. For developing the ARCHS4 resource, all available FASTQ files from RNA-seq experiments were retrieved from the Gene Expression Omnibus (GEO) and aligned using a cloud-based infrastructure. In total 137,792 samples are accessible through ARCHS4 with 72,363 mouse and 65,429 human samples. Through efficient use of cloud resources and dockerized deployment of the sequencing pipeline, the alignment cost per sample is reduced to less than one cent. ARCHS4 is updated automatically by adding newly published samples to the database as they become available. Additionally, the ARCHS4 web interface provides intuitive exploration of the processed data through querying tools, interactive visualization, and gene landing pages that provide average expression across cell lines and tissues, top co-expressed genes, and predicted biological functions and protein-protein interactions for each gene based on prior knowledge combined with co-expression. Benchmarking the quality of these predictions, co-expression correlation data created from ARCHS4 outperforms co-expression data created from other major gene expression data repositories such as GTEx and CCLE.ARCHS4 is freely accessible at:http://amp.pharm.mssm.edu/archs4
An efficient and novel technique for solving continuously variable fractional order mass-spring-damping system
Authors: Sahoo S. , Saha Ray S. , Das S. 
Published: September 2017

Purpose
In this paper, the formulation and analytic solutions for fractional continuously variable order dynamic models, namely, fractional continuously mass-spring damper (continuously variable fractional order) systems, have been presented. The authors will demonstrate via two cases where the frictional damping given by fractional derivative, the order of which varies continuously – while the mass moves in a guide. Here, the continuously changing nature of the fractional-order derivative for dynamic systems has been studied for the first time. The solutions of the fractional continuously variable order mass-spring damper systems have been presented here by using a successive recursive method, and the closed form of the solutions has been obtained. By using graphical plots, the nature of the solutions has been discussed for the different cases of continuously variable fractional order of damping force for oscillator. The purpose of the paper is to formulate the continuously variable order mass-spring damper systems and find their analytical solutions by successive recursion method.

Design/methodology/approach
The authors have used the viscoelastic and viscous – viscoelastic dampers for describing the damping nature of the oscillating systems, where the order of the fractional derivative varies continuously.

Findings
By using the successive recursive method, here, the authors find the solution of the fractional continuously variable order mass-spring damper systems, and then obtain close-form solutions. The authors then present and discuss the solutions obtained in the cases with the continuously variable order of damping for an oscillator through graphical plots.

Originality/value
Formulation of fractional continuously variable order dynamic models has been described. Fractional continuous variable order mass-spring damper systems have been analysed. A new approach to find solutions of the aforementioned dynamic models has been established. Viscoelastic and viscous – viscoelastic dampers are described. The discussed damping nature of the oscillating systems has not been studied yet.
Haar wavelets operational matrix based algorithm for computational modelling of hyperbolic type wave equations
Authors: Pandit Sapna , Jiwari Ram , Bedi Karan , Koksal Mehmet Emir 
Published: September 2017

Purpose
The purpose of this study is to develop an algorithm for approximate solutions of nonlinear hyperbolic partial differential equations.

Design/methodology/approach
In this paper, an algorithm based on the Haar wavelets operational matrix for computational modelling of nonlinear hyperbolic type wave equations has been developed. These types of equations describe a variety of physical models in nonlinear optics, relativistic quantum mechanics, solitons and condensed matter physics, interaction of solitons in collision-less plasma and solid-state physics, etc. The algorithm reduces the equations into a system of algebraic equations and then the system is solved by the Gauss-elimination procedure. Some well-known hyperbolic-type wave problems are considered as numerical problems to check the accuracy and efficiency of the proposed algorithm. The numerical results are shown in figures and Linf, RMS and L2 error forms.

Findings
The developed algorithm is used to find the computational modelling of nonlinear hyperbolic-type wave equations. The algorithm is well suited for some well-known wave equations.

Originality/value
This paper extends the idea of one dimensional Haar wavelets algorithms (Jiwari, 2015, 2012; Pandit et al., 2015; Kumar and Pandit, 2014, 2015) for two-dimensional hyperbolic problems and the idea of this algorithm is quite different from the idea for elliptic problems (Lepik, 2011; Shi et al., 2012). Second, the algorithm and error analysis are new for two-dimensional hyperbolic-type problems.
An algorithm inspired by social spiders for truss optimisation problems
Authors: Duarte Grasiele Regina , Lemonge Afonso Celso de Castro , da Fonseca Leonardo Goliatt 
Published: September 2017

PurposeThe purpose of this paper is to evaluate the performance of social spider algorithm (SSA) to solve constrained structural optimisation problems and to compare its results with others algorithms such as genetic algorithm, particle swarm optimisation, differential evolution and artificial bee colony.Design/methodology/approachTo handle the constraints of the problems, this paper couples to the SSA an efficient selection criteria proposed in the literature that promotes a tournament between two solutions in which the feasible or less infeasible solution wins. The discussion is conducted on the competitiveness of the SSA with other algorithms as well as its performance in constrained problems.FindingsSSA is a population algorithm proposed for global optimisation inspired by the foraging of social spiders. A spider moves on the web towards the position of the prey, guided by vibrations that occur around it in different frequencies. The SSA was proposed to solve problems without constraints, but these are present in most of practical problems. This paper evaluates the performance of SSA to solve constrained structural optimisation problems and compares its results with other algorithms such as genetic algorithm, particle swarm optimisation, differential evolution and artificial bee colony.Research limitations/implicationsThe proposed algorithm has no limitations, and it can be applied in other classes of constrained optimisation problems.Practical implicationsThis paper evaluated the proposed algorithm with a benchmark of constrained structural optimisation problems intensely used in the literature, but it can be applied to solve real constrained optimisation problems in engineering and others areas.Originality/valueThis is the first paper to evaluate the performance of SSA in constrained problems and to compare its results with other algorithms traditional in the literature.