bluuebunny/crossref_metadata_2025_split huggingface dataset:
Graph Signal Processing of Low and High-Order Dynamic Functional Connectivity Networks Using EEG Resting-State for Schizophrenia: A Whole Brain Breakdown
Authors: Dimitriadis Stavros I. 
Published: February 2019

AbstractConventional static or dynamic functional connectivity graph (FCG/DFCG) referred to as low-order FCG focusing on temporal correlation estimates of the resting-state electroencephalography (rs-EEG) time series between any potential pair of brain areas. A DFCG is first constructed from multichannel recordings by adopting the methodology of sliding-window and a proper functional connectivity estimator. However, low-order FC ignores the high-level inter-relationship of brain areas. Recently, a high-order version of FCG has emerged by estimating the correlations of the time series that describe the fluctuations of the functional strength of every pair of ROIs across experimental time.In the present study, a dynamic functional connectivity graph (DFCG) has been estimated using the imaginary part of phase lag value (iPLV). We analyzed DFCG profiles of electroencephalographic resting state (eyes-closed) recordings of healthy controls subjects (n=39) and subjects with symptoms of schizophrenia (n=45) in basic frequency bands {δ,θ,α1,α2,β1,β2,γ}. In our analysis, we incorporated both intra and cross-frequency coupling modes. Adopting our recent Dominant Intrinsic Coupling Mode (DICM) model leads to the construction of an integrated DFCG (iDFCG) that encapsulates both the functional strength but also the DICM of every pair of brain areas. Based on the LO - IDFCG, we constructed the HO- IDFCG by adopting the cosine similarity between the time-series derived from the LO-DIFCG. At a second level, we estimated the laplacian transformations of both LO and HO-IDFCG and by calculating the temporal evolution of Synchronizability (Syn), four network metric time series (NMTSSyn) were produced. Following, a machine learning approach based on multi-kernel SVM with the four NMTSSynused as potential features and appropriate kernels, we succeeded a superior classification accuracy (∼98%). DICM and flexibility index (FI) achieved a classification with absolute performance (100 %)Schizophrenic subjects demonstrated a hypo-synchronization compared to healthy control group which can be interpreted as a low global synchronization of co-fluctuate functional patterns. Our analytic pathway could be helpful both for the design of reliable biomarkers and also for evaluating non-intervention treatments tailored to schizophrenia. EEG offers a low-cost environment for applied neuroscience and the transfer of research knowledge from neuroimaging labs to daily clinical practice.
Changes in Anterior and Posterior Hippocampus Differentially Predict Item-Space, Item-Time, and Item-Item Memory Improvement
Authors: Lee Joshua K. , Fandakova Yana , Johnson Elliott G. , Cohen Neal J. , Bunge Silvia A. , Ghetti Simona 
Published: February 2019

AbstractRelational memory requires the hippocampus, but whether distinct hippocampal mechanisms along the anterior-posterior axis are required for different types of relations is debated. We investigated the contribution of structural changes in hippocampal head, body, and tail subregions to the capacity to remember item-space, item-time, and item-item relations. Memory for each relation and volumes of hippocampal subregions were assessed longitudinally in 171 participants across 3 time points (Mage at T1= 9.45 years; Mage at T2= 10.86 years, Mage at T3=12.12 years; comprising 393 behavioral assessments and 362 structural scans). Among older children, volumetric growth in: (a) head and body predicted improvements in item-time memory, (b) head predicted improvements in item-item memory; and (c) right tail predicted improvements in item-space memory. The present research establishes that volumetric changes in hippocampal subregions differentially predict changes in different aspects of relational memory, underscoring a division of labor along the hippocampal anterior-posterior axis.
Electrophysiology and transcriptomics reveal two photoreceptor classes and complex visual integration inHirudo verbana
Authors: Stowasser Annette , Stahl Aaron , Benoit Joshua B. , Wagenaar Daniel A. 
Published: February 2019

AbstractAmong animals with complex visual processing mechanisms, the leechHirudo verbanais a rare example in which all neurons can be identified. However, little is known about its visual system, which is composed of several pigmented head eyes and photosensitive non-pigmented sensilla that are distributed across its entire body. Although several interneurons are known to respond to visual stimuli, their response properties are poorly understood. Among these, the S cell system is especially intriguing: It is multimodal, spans the entire body of the leech, and is thought to be involved in complex sensory integration. To improve our understanding of the role of this system, we tested its spectral sensitivity, spatial integration, and adaptation properties. The response of the S cell system to visual stimuli was found to be strongly dependent on the size of the area stimulated, and adaptation was local. Furthermore, a “bleaching experiment” demonstrated that at least two color channels contributed to the response, and that their contribution was dependent on the adaptation to the background. The existence of at least two color channels was further supported by transcriptomic evidence, which indicated the existence of at least two distinct groups of putative opsins for leeches. Taken together, our results show that the S cell system has highly sophisticated response properties, and could be involved in the processing of complex visual stimuli. We propose the leech as a novel system to understand visual processing mechanisms with many practical advantages.Summary statementDetailed quantitative analysis of light responses in the medicinal leechHirudo verbanaunequivocally demonstrates the existence of parallel visual pathways processing visual and UV stimuli. Responses to spatially complex stimuli indicate relatively sophisticated information processing.
Retinoic acid promotes in vitro development of haploid germ cells from pre-pubertal porcine spermatogenic cells
Authors: Yu Kun , Zhang Yi , Zhang Bao-Lu , Wu Han-Yu , Wang Su-Tian , Han De-Ping , Lian Zheng-Xing , Liu Yi-Xun , Deng Shou-Long 
Published: February 2019

AbstractSpermatogonial stem cells (SSCs) self-renew and contribute genetic information to the next generation. Inducing directional differentiation of porcine SSCs may be an important strategy in exploring the mechanisms of spermatogenesis and developing better treatment methods for male sterility. Here, we established an in vitro culture model for porcine small seminiferous tubule segments, to induce SSCs to differentiate into single-tail haploid spermatozoa. The culture model subsequently enabled spermatozoa to express the sperm-specific protein acrosin, and oocytes to develop to blastocyst stage after round spermatid injection. The addition of retinoic acid (RA) to the differentiation media promoted the efficiency of haploid differentiation. RT-PCR analysis indicated that RA stimulated the expression of Stra8 but reduced the expression of NANOS2 in spermatogonia. Genes involved in post-meiotic development, Prm1 and Tnp1, were up-regulated in the presence of RA. The addition of RAR inhibitor, BMS439, showed that RA enhanced the expression of cAMP responsive-element binding protein through RAR, and promoted the formation of round spermatids.
Modelling the Perception of Colour Patterns in Vertebrates with HMAX
Authors: Renoult Julien P. , Guyl Bastien , Mendelson Tamra C. , Percher Alice , Dorignac Jérôme , Geniet Fredéric , François Molino 
Published: February 2019

AbstractIn order to study colour signals as animals perceive them, visual ecologists usually rely on models of colour vision that do not consider patterns–the spatial arrangement of features within a signal.HMAX describes a family of models that are used to study pattern perception in human vision research, and which have inspired many artificial intelligence algorithms. In this article, we highlight that the sensory and brain mechanisms modelled in HMAX are widespread, occurring in most if not all vertebrates, thus offering HMAX models a wide range of applications in visual ecology.We begin with a short description of the neural mechanisms of pattern perception in vertebrates, emphasizing similarities in processes across species. Then, we provide a detailed description of HMAX, highlighting how the model is linked to biological vision. We further present sparse-HMAX, an extension of HMAX that includes a sparse coding scheme, in order to make the model even more biologically realistic and to provide a tool for estimating efficiency in information processing. In an illustrative analysis, we then show that HMAX performs better than two other reference methods (manually-positioned landmarks and the SURF algorithm) for estimating similarities between faces in a nonhuman primate species.This manuscript is accompanied with MATLAB codes of an efficient implementation of HMAX and sparse-HMAX that can be further flexibly parameterized to model non-human colour vision, with the goal to encourage visual ecologists to adopt tools from computer vision and computational neuroscience.
Fastq-pair: efficient synchronization of paired-end fastq files
Authors: Edwards John A. , Edwards Robert A. 
Published: February 2019

AbstractPaired end DNA sequencing provides additional information about the sequence data that is used in sequence assembly, mapping, and other downstream bioinformatics analysis. Paired end reads are usually provided as two fastq-format files, with each file representing one end of the read. Many commonly used downstream tools require that the sequence reads appear in each file in the same order, and reads that do not have a pair in the corresponding file are placed in a separate file of singletons. Although most sequencing instruments capable of generating paired end reads produce files where each read has a corresponding mate, many downstream bioinformatics manipulations break the one-to-one correspondence between reads, and paired-end sequence files loose synchronicity, and contain either unordered sequences or sequences in one or other file without a mate. Trivial solutions to this problem require reading one or both of the DNA sequence files into memory but quickly become limited by computational resources for moderate to large sized sequence files that are common nowadays. Here, we introduce a fast and memory efficient solution, written in C for portability, that synchronizes paired-end fastq files for subsequent analysis and places unmatched reads into singleton files.Fastq-pair is freely available from https://github.com/linsalrob/fastq-pair and is released under the MIT license.
Robust archaeal and bacterial communities inhabit shallow subsurface sediments of the Bonneville Salt Flats
Authors: McGonigle Julia M. , Bernau Jeremiah A. , Bowen Brenda B. , Brazelton William J. 
Published: February 2019

ABSTRACTWe report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah–Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse Halobacteriaceae andSalinibacterspecies. Desulfuromonadales from GR-WP33-58 are also abundant in all samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. We found an increased presence of Thermoplasmatales, Nanohaloarchaeota, Woesearchaeota, Acetothermia, Halanaerobium, Parcubacteria, Planctomycetes, Clostridia, Gemmatimonadetes, Marinilabiaceae and other Bacteroidetes in this upper gypsum layer. This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically-sterile landscape.IMPORTANCEOver the last ∼13,000 years the Pleistocene Lake Bonneville, which covered a large portion of Utah, drained and desiccated leaving behind the Bonneville Salt Flats (BSF). Today BSF is famous for its use as a speedway, which has hosted many land-speed records and a community that greatly values this salty landscape. Additionally, the salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the roles of microbes in the formation and maintenance of the salt crust are generally unknown. This study is the first geospatial analysis of microbial diversity at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.
Cancer gene therapy by NF-κB-activated cancer cell-specific expression of CRISPR/Cas9 targeting to telomere
Authors: Dai Wei , Wu Jian , Wang Danyang , Wang Jinke 
Published: February 2019

AbstractNF-κB has been a luring target for cancer therapy due to its over activation in all tumors. In this study, we showed that a gene therapy named as NF-κB-activated gene expression (Nage) could be used to induce cancer cell deathin vitroandin vivoby utilizing the NF-κB activity in cancer cells; however, it had no effect on normal cells. In this gene therapy, we constructed a NF-κB-specific promoter by fusing a NF-κB decoy sequence to a minimal promoter, which could be bound by the intracellular over activated NF-κB and thus activate the expression of downstream effector gene in a NF-κB-specific manner. In this study, we firstly demonstrated the cancer cell-specific activation of NF-κB. We then demonstrated the cancer cell specificity of Nage vector expression by introducing a Nage vector that could express a reporter gene ZsGreen in various cell lines. We next demonstrated that a Nage vector that could express CRISPR/Cas9 protein and a telomere-targeting sgRNA could be used to specifically induce death of cancer cells. We finally showed that the Cas9/sgRNA Nage vector packaged into the adeno-associated virus (AAV) could be used to inhibit the growth of xenografted tumors in mouse by intravenously injecting recombinant AAV.
Adaptive introgression during environmental change can weaken reproductive isolation
Authors: Owens Gregory L. , Samuk Kieran 
Published: February 2019

AbstractAnthropogenic climate change is an urgent threat to species diversity. One aspect of this threat is the collapse of species reproductive barriers through increased hybridization. The primary mechanism for this collapse is thought to be the weakening of ecologically-mediated reproductive barriers, as demonstrated in many cases of “reverse speciation” . Here, we expand on this idea and show that adaptive introgression between species adapting to a shared, moving climatic optimum can readily weakenanyreproductive barrier, including those that are completely independent of the climatic variable. Using genetically explicit forward-time simulations, we show that genetic linkage between alleles conferring adaptation to a changing climate and alleles conferring reproductive isolation can lead to adaptive introgression facilitating the homogenization of reproductive isolation alleles. This effect causes the decay of species boundaries across a broad and biologically-realistic parameter space. We explore how the magnitude of this effect depends upon the rate of climate change, the genetic architecture of adaptation, the initial degree of reproductive isolation and the mutation rate. These results highlight a previously unexplored effect of rapid climate change on species diversity.
In situstructures of periplasmic flagella inBorreliareveals conformational changes essential for flagellar rotation
Authors: Chang Yunjie , Moon Kihwan , Zhao Xiaowei , Steven J. Norris , Motaleb Md A. , Liu Jun 
Published: February 2019

SUMMARYThe bacterial flagellar motor is a molecular machine that rotates the flagellar filament at high speed. Torque is generated by the stator-rotor interaction coupled to an ion flux through the torque-generating stator. Here, we employed cryo-electron tomography to visualize the intact flagellar motor in the Lyme disease spirocheteBorrelia burgdorferi. By analysis of the motor structures of wild-type and stator mutants, we localize the torque-generating units precisely and determine three-dimensional structure of the stator and its interactions with the rotor. Our study shows that the cytoplasmic domains of the stator are packed regularly around the circumference of the flagellar C-ring. The stator-rotor interaction induces a profound conformational change in the C-ring. Analysis of the motors of a less motilemotB-D24E mutant and a non-motilemotB-D24N mutant, in which the proton translocation is reduced and blocked, respectively, provides evidence that the conformational change of the C-ring is essential for flagellar rotation.
Auto-inhibition of myoblast fusion by cyclic receptor signalling
Authors: Sieiro Daniel , Melendez Julie , Morin Valérie , Salgado David , Marcelle Christophe 
Published: February 2019

AbstractFusion of nascent myoblasts to pre-existing myofibres is critical for skeletal muscle growth and repair. The vast majority of molecules known to regulate myoblast fusion are necessary in this process. Here we uncover, through high-throughputin vitroassays andin vivostudies in the chicken embryo, that TGFβ (SMAD2/3-dependent) signalling acts as a molecular brake on muscle fusion. While constitutive activation of the pathway arrests fusion, its inhibition leads to a striking over-fusion phenotype. This dynamic control of TGFβ signalling in the embryonic muscle relies on a unique receptor complementation mechanism, prompted by the merging of myoblasts with myofibres, each carrying one component of the heterodimer receptor complex. The competence of myofibres to fuse is restored through endocytic degradation of activated receptors. Altogether, this study shows that muscle fusion is a self-regulated process that relies on cyclic TGFβ signalling to regulate its pace.
Perturbation of the gut microbiota by antibiotics results in accelerated breast tumour growth and metabolic dysregulation
Authors: Kirkup Benjamin M , McKee Alastair , Makin Kate A , Paveley Jack , Caim Shabhonam , Alcon-Giner Cristina , Leclaire Charlotte , Dalby Matthew , Le Gall Gwenaelle , Andrusaite Anna , Kreuzaler Peter , Ghanate Avinash , Driscoll Paul , MacRae James , Calvani Enrica , Milling Simon WF , Yuneva Mariia , Weilbaecher Katherine N , Korcsmáros Tamas , Hall Lindsay J , Robinson Stephen D 
Published: February 2019

AbstractBackgroundBreast cancer is the second most prevalent cancer worldwide with around 1.7 million new cases diagnosed every year. Whilst prognosis is generally favourable in early stages, this worsens significantly in advanced disease. Therefore, it is pertinent to focus on mitigating factors that may slow growth or progression. Recently, the gut microbiome has been implicated in a wide-range of roles in tumour biology. Through modulation of immunity, the gut microbiota can improve the efficacy of several immunotherapies. However, despite the prevalence of breast cancer, there is still a lack of microbiota studies in this field, including exploring the influence of external microbiome-modulating factors such as antibiotics. We describe herein how disruption of the gut microbiota via antibiotics may be detrimental to patient outcomes through acceleration of tumour growth.ResultsSupplementing animals with a cocktail of antibiotics leads to gut microbiota alterations and is accompanied by significant acceleration of tumour growth. Surprisingly, and distinct from previous microbiome-tumour studies, the mechanism driving these effects do not appear to be due to gross immunological changes. Analysis of intratumoural immune cell populations and cytokine production are not affected by antibiotic administration. Through global tumour transcriptomics, we have uncovered dysregulated gene expression networks relating to protein and lipid metabolism that are correlated with accelerated tumour growth. Fecal metabolomics revealed a reduction of the microbial-derived short-chain fatty acid butyrate that may contribute to accelerated tumour growth. Finally, through use of a routinely administered antibiotic in breast cancer patients, Cephalexin, we have shown that tumour growth is also significantly affected. Metataxanomic sequencing and analysis highlighted significant antibiotic-associated reductions in the butyrate producing generaOdoribacterandAnaeotruncus, and increased abundance ofBacteroides.ConclusionsOur data indicate that perturbation of the microbiota by antibiotics may have negative impacts on breast cancer patient outcomes. This is of importance as antibiotics are regularly prescribed to breast cancer patients undergoing mastectomy or breast reconstruction. We have also shown that the metabolic impact of disruption to the microbiome should be considered alongside the potent immunological effects. We believe our work lays the foundation for improving the use of antibiotics in patients, and with further investigation could potentially inform clinical practice.
A quantitative tri-fluorescent yeast two-hybrid system: from flow cytometry to in-cellula affinities
Authors: Cluet David , Amri Ikram , Vergier Blandine , Léault Jérémie , Grosjean Clémence , Calabresi Dylan , Spichty Martin 
Published: February 2019

AbstractWe present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on PPIs with different affinities. After only two hours of reaction, expression of the reporter can easily be detected even for the weakest PPI. Through a simple gating analysis, it is possible to select only cells with identical expression levels of the reaction partners. As a result of this standardization of expression levels, the mean reporter levels directly reflects the affinities of the studied PPIs. With a set of PPIs with known affinities, it is straightforward to construct an affinity ladder that permits rapid classification of PPIs with thus far unknown affinities. Conventional software can be used for this analysis. To permit automated high-throughput analysis, we provide a graphical user interface for the Python-based FlowCytometryTools package.