bluuebunny/crossref_metadata_2025_split huggingface dataset:
Title: Basal constriction during midbrain-hindbrain boundary morphogenesis is mediated by Wnt5b and Focal Adhesion Kinase
Authors: Gutzman Jennifer H. , Graeden Ellie , Brachmann Isabel , Yamazoe Sayumi , Chen James K. , Sive Hazel 
Published: January 2018

ABSTRACTBasal constriction occurs at the zebrafish midbrain-hindbrain boundary constriction (MHBC) and is likely a widespread morphogenetic mechanism. 3D reconstruction demonstrates that MHBC cells are wedge-shaped, and initially constrict basally, with subsequent apical expansion.wnt5bis expressed in the MHB and is required for basal constriction. Consistent with a requirement for this pathway, expression of dominant negative Gsk3β overcomeswnt5bknockdown. Immunostaining identifies focal adhesion kinase (Fak) as active in the MHB region, and knockdown demonstrates Fak is a regulator of basal constriction. Tissue specific knockdown further indicates that Fak functions cell autonomously within the MHBC. Fak is epistatic townt5b, suggesting that Wnt5b signals locally as an early step in basal constriction and acts together with more widespread Fak activation. This study delineates signaling pathways that regulate basal constriction during brain morphogenesis.
Insights into the effect of the J-domain on the substrate binding domain (SBD) of the 70 kDa heat shock protein, Hsp70, from a chimeric human J-SBD polypeptide
Authors: Tiroli-Cepeda Ana O. , Seraphim Thiago V. , Borges Júlio C. , Ramos Carlos H. I. 
Published: January 2018

AbstractDnaJ/Hsp40 chaperones deliver unfolded proteins and stimulate the ATPase activity of DnaK/Hsp70 via their J-domain, a crucial event for the function that this system has in assisting protein folding. The interaction between Hsp40 and Hsp70 is transient and thus difficult to study, since mixing the binding partners can lead to quick dissociation due to their low affinity, creating a challenge for detailed analysis. As a consequence, knowledge of many important aspects of the mechanism of interaction is still lacking, for instance, the effect that J-domain binding has on Hsp70. In this study, we investigated whether it would be possible to gain understanding of this interaction by engineering a chimeric polypeptide where the J-domain of Hsp40 was covalently attached to the substrate binding domain (SBD) of Hsp70 by a flexible linker. The rationale for this is that an increase in the proximity between the interacting partners in this engineered chimera will promote the natural interaction and facilitate the characterization of the protein– protein interaction, which is a requirement to gain further understanding of many biological processes. The resulting chimera, termed J-SBD, was properly folded and had properties not present in the SBD alone. J-SBD behaved primarily as a monomer in all conditions tested and exhibited chaperone activity, as shown by aggregation protection and substrate binding assays, which revealed decreased binding to bis-ANS, a probe for hydrophobic patches. Collectively, our results suggest that Hsp40 binding to Hsp70 via the J-domain shifts the Hsp70 equilibrium towards the monomer state to expose hydrophobic sites prone to substrate accommodation.AbbreviationsBis-ANS (4,4’-Dianilino-1,1’-Binaphthyl-5,5’-Disulfonic Acid; CD, circular dichroism; Hsp, heat shock protein; J-SBD, chimeric polypeptide in which the J-domain of Hsp40 (at the N-terminus) is covalently attached to the substrate binding domain of Hsp70 (at the C-terminus) by a flexible linker; SBD: substrate binding domain of Hsp70.
Enhancing resolution of natural methylome reprogramming behavior in plants
Authors: Sanchez Robersy , Yang Xiaodong , Barreras Jose R , Kundariya Hardik , Mackenzie Sally A. 
Published: January 2018

AbstractBackgroundNatural methylome reprogramming within chromatin involves changes in local energy landscapes that are subject to thermodynamic principles. Signal detection permits the discrimination of methylation signal from dynamic background noise that is induced by thermal fluctuation. Current genome-wide methylation analysis methods do not incorporate biophysical properties of DNA, and focus largely on DNA methylation density changes, which limits resolution of natural, more subtle methylome behavior in relation to gene activity.ResultsWe present here a novel methylome analysis procedure, Methyl-IT, based on information thermodynamics and signal detection. Methylation analysis involves a signal detection step, and the method was designed to discriminate methylation regulatory signal from background variation. Comparisons with commonly used programs and two publicly available methylome datasets, involving stages of seed development and drought stress effects, were implemented. Information divergence between methylation levels from different groups, measured in terms of Hellinger divergence, provides discrimination power between control and treatment samples. Differentially informative methylation positions (DIMPs) achieved higher sensitivity and accuracy than standard differentially methylated positions (DMPs) identified by other methods. Differentially methylated genes (DMG) that are based on DIMPs were significantly enriched in biologically meaningful networks.ConclusionsMethyl-IT analysis enhanced resolution of natural methylome reprogramming behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods.
Selection-free, high frequency genome editing by homologous recombination of human pluripotent stem cells using Cas9 RNP and AAV6
Authors: Martin Renata M. , Ikeda Kazuya , Uchida Nobuko , Cromer Kyle , Nishimura Toshi , Dever Daniel P. , Camarena Joab , Bak Rasmus , Laustsen Anders , Jakobsen Martin R. , Wiebking Volker , Sebastiano Vittorio , Nakauchi Hiromitsu , Porteus Matthew 
Published: January 2018

AbstractCombination of genome editing and human pluripotent stem cells (hPSCs) offers a platform for in vitro disease modeling, drug discovery and personalized stem cell therapeutics. However, incorporation of large modifications using CRISPR/Cas9-based genome editing in hPSCs typically requires the use of selection markers due to low editing efficiencies. Here we report a novel editing technology in hPSCs using Cas9 protein complexed with chemically modified single guide RNA (sgRNA) and recombinant AAV6 (rAAV6) vectors for donor delivery without marker selection. With these components, we demonstrate targeted integration of a 2.2 kb DNA expression cassette in hPSCs at frequencies up to 94% and 67% at the HBB and MYD88 loci, respectively. We used this protocol to correct the homozygous sickle cell disease (SCD) mutation in an iPSC line derived from a SCD patient with a frequency of 63%. This Cas9/AAV6 system allows for both the integration of large gene cassettes and the creation of single nucleotide changes in hPSCs at high frequencies, eliminating the need for multiple editing steps and marker selection, thus increasing the potential of editing human pluripotent cells for both research and translational applications.
Spatiotemporal mosaic patterning of pluripotent stem cells using CRISPR interference
Authors: Libby Ashley R.G. , Joy David A. , So Po-Lin , Mandegar Mohammad A. , Muncie Jonathon M. , Weaver Valerie M. , Conklin Bruce R. , McDevitt Todd C. 
Published: January 2018

ABSTRACTMorphogenesis results from the interactions of asymmetric cell populations to form complex multicellular patterns and structures comprised of distinct cell types. However, current methods to model morphogenic events offer little control over parallel cell type co-emergence and do not offer the capability to selectively perturb gene expression in specific subpopulations of cells. We have developed anin vitrosystem that can spatiotemporally interrogate cell-cell interactions and multicellular organization within human induced pluripotent stem cell (hiPSC) colonies. We examined the effects of independently knocking down molecular regulators of cortical tension and cell-cell adhesion using inducible CRISPRi: Rho-associated kinase-1 (ROCK1) and E-cadherin (CDH1), respectively. Induced mosaic knockdown of ROCK1 or CDH1 in hiPSC populations resulted in differential patterning events within hiPSC colonies indicative of cell-driven population organization. Patterned colonies retained an epithelial phenotype and nuclear expression of pluripotency markers. Gene expression within each of the mixed populations displayed a transient wave of differential expression with induction of knockdown that stabilized in coordination with intrinsic pattern formation. Mosaic patterning of hiPSCs enables the genetic interrogation of emergent multicellular properties of pluripotent cells, leading to a greater mechanistic understanding of the specific molecular pathways regulating the dynamics of symmetry breaking events that transpire during developmental morphogenesis.SIGNIFICANCEHuman embryonic development entails a series of multicellular morphogenic events that lead to primitive tissue formation. Attempts to study human morphogenic processes experimentally have been limited due to divergence from model organisms and the inability of current humanin vitromodels to accurately control the coincident emergence of heterogeneous cell populations in the spatially controlled manner necessary for proper tissue structure. We developed a human induced pluripotent stem cell (iPSC)in vitromodel that enables temporal control over the emergence of heterotypic subpopulations of cells. We examined mosaic knockdown of two target molecules to create predictable and robust cell-patterning events within hiPSC colonies. This method allows for dynamic interrogation of intrinsic cell mechanisms that initiate symmetry breaking events and provides direct insight(s) into tissue developmental principles.
High precision automated detection of labeled nuclei in Gigapixel resolution image data of Mouse Brain
Authors: Das Sukhendu , Jayakumar Jaikishan , Banerjee Samik , Ramaswamy Janani , Vangala Venu , Ram Keerthi , Mitra Partha 
Published: January 2018

AbstractThere is a need in modern neuroscience for accurate and automated image processing techniques for analyzing the large volume of neuroanatomical imaging data. Even at light microscopic levels, imaging mouse brains produces individual data volumes in the TerraByte range. A fundamental task involves the detection and quantification of objects of a given type, e.g. neuronal nuclei or somata, in brain scan dataset. Traditionally this quantification has been performed by human visual inspection with high accuracy, that is not scalable. When modern automated CNN and SVM-based methods are used to solve this classification problem, they achieve accuracy levels that range between 85 – 92%. However, higher rates of precision and recall that are close to that of human performance are necessary. In this paper, we describe an unsupervised, iterative algorithm, which provides a high performance for a specific problem of detecting Green Fluorescent Protein labeled nuclei in 2D scans of mouse brains. The algorithm judiciously combines classical computer vision techniques and is focused on the complex problem of decomposing strong overlapped objects of interest. Our proposed technique uses feature detection methods on ridge lines over distance transformation of the image and an arc based iterative spatial-filling method to solve the problem. We demonstrate our results on mouse brain dataset of Gigabyte resolution and compare it with manual annotation of the brains. Our results show that an aptly designed CV algorithm with classical feature extractors when tailored to this problem of interest achieves near-ideal human-like performance. Quantitative comparative analysis, using manually annotated ground truth, reveals that our approach performs better on mouse brain scans than general purpose machine learning (including deep CNN) methods.
Altered Developmental Trajectories in Intrinsic Function between Default, Salience, and Executive Networks in High-Functioning Autism
Authors: Yang Liu , Chen Xiao , Li Xue , Shen Yang-Qian , Wang Hui , Liu Jing-Ran , Mei Ting , Ji Zhao-Zheng , Guo Yan-Qing , Wang Fei-Fei , Xu Ling-Zi , Tang Xin-Zhou , Ma Zeng-Hui , Wang Li-Qi , Liu Jing , Cao Qing-Jiu , Yan Chao-Gan 
Published: January 2018

AbstractAlthough many studies have focused on abnormal patterns of brain functional connectivity in Autism spectrum disorder (ASD), one important factor, the developmental effect of brain networks was largely overlooked. To clarify the abnormal developmental trajectory of brain functional connectivity in ASD, we focused on the age-related changes in three “core” neurocognitive networks: default mode network (DMN), salience network (SN) and central executive network (CEN, also divided into left and right CEN, i.e., lCEN and rCEN). The development of intrinsic functional connectivity (iFC) within and between these networks were analyzed in 107 Chinese participants, including children, adolescents, and adults (54 patients with ASD and 53 typically developed (TD) participants; ages 6-30 years). We found that diagnosis-related distinctions in age-related changes suggest three maturation patterns in networks’ or nodes’ iFC: delayed (iFC between SN and rCEN), ectopic (iFC between SN and DMN, and iFC between posterior cingulate cortex (PCC) and right anterior insula/dorsal anterior cingulate cortex (dACC)), and failure maturation (iFC between dACC and ventral medial prefrontal cortex). Compared with age-matched TD participants, ASD patients in children and adolescents exhibited hypo-connectivity, while that in adults showed hyper-connectivity. In addition, an independent verification based on Autism Brain Imaging Data Exchange (ABIDE) datasets confirmed our findings of developmental trajectories in ASD group, which also showed unchanged functional connectivity with age between DMN and SN and increasing iFC between rCEN and SN. The conspicuous differences in the development of three “core” networks in ASD were demonstrated, which may lead a nuanced understanding towards the abnormal brain network maturation trajectory of autism.
Brain network segregation and integration during an epoch-related working memory fMRI experiment
Authors: Fransson Peter , Schiffler Björn C. , Hedley Thompson William 
Published: January 2018

AbstractThe characterization of brain subnetwork segregation and integration has previously focused on changes that are detectable at the level of entire sessions or epochs of imaging data. In this study, we applied time-varying functional connectivity analysis together with temporal network theory to calculate point-by-point estimates in subnetwork segregation and integration during an epoch-based (2-back, 0-back, baseline) working memory fMRI experiment as well as during resting-state. This approach allowed us to follow task-related changes in subnetwork segregation and integration at a high temporal resolution. At a global level, the cognitively more taxing 2-back epochs elicited an overall stronger response of integration between subnetworks compared to the 0-back epochs. Moreover, the visual and fronto-parietal subnetworks displayed characteristic and distinct temporal profiles of segregation and integration during the 0- and 2-back epochs. During the interspersed epochs of baseline, many subnetworks, including the default mode, visual, fronto-parietal, cingulo-opercular and dorsal attention subnetworks showed pronounced increases in segregation. Using a drift diffusion model we show that the response time for the 2-back trials are correlated with integration for the fronto-parietal subnetwork and correlated with segregation for the visual subnetwork. Our results elucidate the fast-evolving events with regard to subnetwork integration and segregation that occur in an epoch-related task fMRI experiment. Our findings suggest that minute changes in subnetwork integration are of importance for task performance.
EssC is a specificity determinant for Staphylococcus aureus type VII secretion
Authors: Jäger Franziska , Kneuper Holger , Palmer Tracy 
Published: January 2018

ABSTRACTThe Type VII protein secretion system (T7SS) is found in actinobacteria and firmicutes, and plays important roles in virulence and interbacterial competition. A membrane-bound ATPase protein, EssC in Staphylococcus aureus, lies at the heart of the secretion machinery. The EssC protein from S. aureus strains can be grouped into four variants (EssC1-EssC4) that display sequence variability in the C-terminal region. Here we show that the EssC2, EssC3 and EssC4 variants can be produced in a strain deleted for essC1 and that they are able to mediate secretion of EsxA, an essential component of the secretion apparatus. They are, however, unable to support secretion of the substrate protein EsxC, which is encoded only in essC1-specific strains. This finding indicates that EssC is a specificity determinant for T7 protein secretion. Our results support a model where the C-terminal domain of EssC interacts with substrate proteins whereas EsxA interacts elsewhere.
An NAD+–dependent sirtuin depropionylase and deacetylase (Sir2La) from the probiotic bacteriumLactobacillus acidophilusNCFM
Authors: Olesen Sita V. , Rajabi Nima , Svensson Birte , Olsen Christian A. , Madsen Andreas S. 
Published: January 2018

ABSTRACTSirtuins—a group of NAD+-dependent deacylases—have emerged as key in the connection between NAD+metabolism and aging. This class of enzymes hydrolyze a range ofε-N-acyllysine PTMs and determining the repertoire of catalyzed deacylation reactions is of high importance to fully elucidate the roles of a given sirtuin. Here we have identified and produced two potential sirtuins from the probiotic bacteriumLactobacillus acidophilusNCFM and screening more than 80 different substrates, covering 26 acyl groups on five peptide scaffolds, showed that one of the investigated proteins—Sir2La—is abona fideNAD+-dependent sirtuin, catalyzing hydrolysis of acetyl‐, propionyl‐, and butyryllysine. Further substantiating the identity as a sirtuin, known sirtuin inhibitors nicotinamide and suramin as well as a thioacetyllysine compound inhibit the deacylase activity in a concentration-dependent manner. Based on steady-state kinetics Sir2La showed a slight preference for propionyllysine over acetyllysine and butyryllysine, driven both byKM(14 μMvs21 μM and 15 μM) andkcat(4.4·10−3s−1vs2.5·10−3s−1and 1.21·10−3s−1). Moreover, while NAD+is a prerequisite for Sir2La-mediated deacylation, Sir2La has very highKMfor NAD+compared to the expected levels of the dinucleotide inL. acidophilus. Sir2La is the first sirtuin from Lactobacillales and of the Gram-positive bacterial subclass of sirtuins to be functionally characterized. The ability to hydrolyze propionyl‐ and butyryllysine emphasizes the relevance of further exploring the role of other short-chain acyl moieties as PTMs.
Direct vs indirect e-government adoption: an exploratory study
Authors: Kumar Rajiv , Sachan Amit , Mukherjee Arindam 
Published: January 2018

Purpose
The purpose of this study is to investigate the factors that influence direct and indirect adoption of e-government services in India.

Design/methodology/approach
A conceptual model has been proposed by integrating the factors influencing adoption of e-government services from extant literature. A quantitative technique is used for the purpose of the study.

Findings
The study classifies e-government adoption in two types: direct adoption and indirect adoption. The study has found that there is some difference between the factors influencing direct and indirect e-government adoption. Perceived awareness, perceived usefulness, trust in internet, trust in government and social influence are found to be positively correlated to direct and indirect e-government adoption. Availability of resources, computer self-efficacy, perceived ease-of-use, perceived compatibility, multilingual option and voluntariness are positively correlated to direct e-government adoption and negatively correlated to indirect e-government adoption. Perceived image is found to be significant for direct e-government adoption but non-significant for indirect adoption. Trust in intermediary is found to be significant only for indirect e-government adoption.

Research limitations/implications
The sample size of 382 may not be a proper representation of a country like India, which has huge diversity and is densely populated. The study has been conducted in India, which is a developing country. The result might not be significant for developed countries.

Practical implications
The findings of this study provide useful insights into the decision-making process of e-government users in India and similar emerging economies. These findings can be important for government officials tasked with providing e-governance services.

Originality/value
Despite the digital divide, how the government is expecting its citizens to access e-government services and derive benefits and how the needy will be able to cope with the mandatory e-government services is an interesting topic to study. This leads to a new concept of indirect adoption.
Users’ reactions captured by means of an EEG headset on viewing the presentation of sustainable designs using verbal narrative
Authors: Royo Marta , Chulvi Vicente , Mulet Elena , Galán Julia 
Published: January 2018

Purpose
The aim of this paper is to determine whether consumers accept new arguments for choosing a product that adapts to future needs. It is also seeking to investigate whether the design of products and their ensuing advertising and promotion through a sustainable approach by means of verbal narrative ads can generate a more positive emotional response in the future users of the product than with the application of visual narrative ads.

Design/methodology/approach
To this end, an experiment was conducted consisting of consumers, with and without experience with the product, watching a promotional video based on verbal narrative, created using the new usage scenarios approach, in which the advantages of a sustainable product are shown. The neuronal response of the possible users was then measured by means of the electroencephalogram (EEG) headset. To be able to establish a comparison, the same response was also measured in the same consumers when they viewed a commercial video based on visual narrative about a product with similar characteristics.

Findings
The results show, among other conclusions, that viewing the verbal narrative ad first triggers higher emotional values of excitement, both in the short and the long term, as well as frustration. It is also observed that having no experience with the product causes higher meditation values.

Practical implications
This research pretends to discern the emotional effect of watching a green advertisement in the consumers. This can be useful to enterprises both to design their products to orientate them to consumer concerns, and to design the advertisements to emotionally link consumers with the product.

Originality/value
This can be useful to enterprises both to design their products in such a way as to orientate them towards consumer concerns, and to design advertisements in such a way as to link consumers emotionally with the product.