bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anatomical Relationship of the Inferior Bundle of the Incisivus Labii Inferioris With the Depressor Labii Inferioris and the Platysma
Authors: Hur Mi-Sun 
Published: August 2017

Abstract
The current study examined the inferior bundle of the incisivus labii inferioris muscle (ILI) and its morphologic and spatial relationships with regard to the depressor labii inferioris muscle (DLI) and the platysma. Incisivus labii inferioris muscles and their inferior bundles were investigated in 50 specimens from embalmed Korean adult cadavers. The inferior bundle of the ILI was divided from the originating fibers of the ILI, and it was present in all specimens (100%). The inferior bundle of the ILI could be distinguished into the transverse and inferolateral slips according to their courses and locations. The inferior bundle of the ILI was classified into 3 types according to the presence of the transverse and inferolateral slips. In Type I (44%), the inferior bundle of the ILI had both the transverse and inferolateral slips. In Type II (48%), the inferior bundle of the ILI had only the transverse slip. In Type III (8%), the inferior bundle of the ILI had only the inferolateral slip. The transverse and inferolateral slips were usually attached to the deep fibers of both the platysma lateral to the DLI and the lateral portion of the DLI via aponeurosis, just below the ILI and above the inferior margin of the mandible, respectively. The new anatomical findings of the present study might contribute to the understanding of the detailed movements required to raise the lower lip. This knowledge will be useful for botulinum toxin type A therapies, various facial surgeries, orthodontic treatment, and electromyographic analyses in this area.
From slow to fast faulting: recent challenges in earthquake fault mechanics
Authors: Nielsen S. 
Published: August 2017

Faults—thin zones of highly localized shear deformation in the Earth—accommodate strain on a momentous range of dimensions (millimetres to hundreds of kilometres for major plate boundaries) and of time intervals (from fractions of seconds during earthquake slip, to years of slow, aseismic slip and millions of years of intermittent activity). Traditionally, brittle faults have been distinguished from shear zones which deform by crystal plasticity (e.g. mylonites). However such brittle/plastic distinction becomes blurred when considering (i) deep earthquakes that happen under conditions of pressure and temperature where minerals are clearly in the plastic deformation regime (a clue for seismologists over several decades) and (ii) the extreme dynamic stress drop occurring during seismic slip acceleration on faults, requiring efficient weakening mechanisms. High strain rates (more than 104 s−1) are accommodated within paper-thin layers (principal slip zone), where co-seismic frictional heating triggers non-brittle weakening mechanisms. In addition, (iii) pervasive off-fault damage is observed, introducing energy sinks which are not accounted for by traditional frictional models. These observations challenge our traditional understanding of friction (rate-and-state laws), anelastic deformation (creep and flow of crystalline materials) and the scientific consensus on fault operation.This article is part of the themed issue ‘Faulting, friction and weakening: from slow to fast motion’.
Control of lineage-specific gene expression by functionalized gRNA barcodes
Authors: Al’Khafaji Aziz , Brock Amy 
Published: August 2017

AbstractLineage tracking delivers essential quantitative insight into dynamic, probabilistic cellular processes, such as somatic tumor evolution and differentiation. Methods for high diversity lineage quantitation rely on sequencing the population of DNA barcodes. However, molecular analysis of specific individual lineages is not possible with this approach. To address this challenge, we developed a functionalized lineage tracing tool that enables high diversity lineage tracing and lineage-specific manipulation of gene expression. This modular platform utilizes expressed barcode gRNAs to both track cell lineages and direct lineage specific gene expression.
A subset of UPR-induced transmembrane proteins are prematurely degraded during lipid perturbation
Authors: Ng Benjamin S.H. , Shyu Peter , Ho Nurulain , Chaw Ruijie , Ling Seah Yi , Thibault Guillaume 
Published: August 2017

ABSTRACTBackgroundPhospholipid homeostasis in biological membranes is essential to maintain functions of organelles such as the endoplasmic reticulum. Phospholipid perturbation has been associated to non-alcoholic fatty liver disease, obesity and other metabolic disorders. However, in most cases, the biological significance of lipid disequilibrium remains unclear. Previously, we reported thatSaccharomyces cerevisiaeadapts to lipid disequilibrium by upregulating several protein quality control pathways such as the endoplasmic reticulum-associated degradation (ERAD) pathway and the unfolded protein response (UPR).ResultsSurprisingly, we observed certain ER-resident transmembrane proteins (TPs), which form part of the UPR programme, to be destabilised under lipid perturbation (LP). Among these, Sbh1 was prematurely degraded by fatty acid remodelling and membrane stiffening of the ER. Moreover, the protein translocon subunit Sbh1 is targeted for degradation through its transmembrane domain in an unconventional Doa10-dependent manner.ConclusionPremature removal of key ER-resident TPs might be an underlying cause of chronic ER stress in metabolic disorders.
Exploring the role of stimulus similarity on the summation effect in causal learning
Authors: Pérez Omar D. , Martín Rene San , Soto Fabián A. 
Published: August 2017

AbstractSeveral contemporary models of associative learning anticipate that the higher responding to a compound of two cues separately trained with a common outcome than to each of the cues alone -a summation effect-is modulated by the similarity between the cues forming the compound. Here, we explored this hypothesis in a series of causal learning experiments with humans. Participants were presented with two visual cues that separately predicted a common outcome and later asked for the outcome predicted by the compound of the two cues. Importantly, the cues’ similarity was varied between groups through changes in shape, spatial position, color, configuration and rotation. In variance with the predictions of these models, we observed similar and strong levels of summation in both groups across all manipulations of similarity (Experiments 1-5). The summation effect was significantly reduced by manipulations intended to impact assumptions about the causal independence of the cues forming the compound, but this reduction was independent of stimulus similarity (Experiment 6). These results are problematic for similarity-based models and can be more readily explained by rational approaches to causal learning.
Detection of whole-field luminance changes by superficial interneurons in the zebrafish tectum
Authors: Barker Alison J. , Helmbrecht Thomas O. , Grob Aurélien A. , Baier Herwig 
Published: August 2017

AbstractThe superficial interneurons, SINs, of the zebrafish tectum, also known as tectal horizontal cells, have been implicated in a range of behavioral responses to visual cues, including prey capture and looming-evoked escape. However, there is limited information on their tuning properties, synaptic connectivity and molecular diversity. We have begun to close this gap in our knowledge by performing functional GCaMP6 imaging and electrophysiological recordings of SIN responses to simplified stimuli. We found that a large subset of the SINs strongly responded to luminance changes, with a preference for OFF steps. Although SINs were generally tuned to any dark-light, or light-dark, transition, they were often most sensitive to a narrow range of luminance steps. Tuning properties did not vary with the position of the SIN cell body along the depth of the tectal neuropil or with the orientation of the cell’s neurites within the neuropil. Receptive field (RF) mapping revealed that SINs sample over large areas of the visual field (>20°, typically 50°). RFs of individual SINs were sometimes spatially incoherent, indicating that SINs may receive sparse inputs from multiple RGCs scattered widely over the retina. Lastly, we found that, while most SINs express GABAergic markers, as reported before, a substantial minority express a vesicular glutamate transporter. We propose that the role of the SINs is more complex than previously reported, and provide evidence that at least one SIN subtype could function as a multi-purpose circuit element for signaling changes in ambient luminance for subsequent processing in the tectum.
Cryo-ET reveals nucleosome reorganisation in condensed mitotic chromosomesin vivo
Authors: Cai Shujun , Chen Chen , Tan Zhi Yang , Huang Yinyi , Shi Jian , Gan Lu 
Published: August 2017

SUMMARYChromosomes condense during mitosis in most eukaryotes. This transformation involves rearrangements at the nucleosome level and has consequences for transcription, but the details remain unclear. Here, we use cryo-electron tomography to determine the 3-D arrangement of nucleosomes and other large nuclear features in frozen-hydrated fission-yeast cells. Nucleosomes can form irregular clusters in both interphase and mitotic cells, but they are smaller than expected for Hi-C domains. The nucleosomes are co-mingled with two features: nucleosome-free pockets and megadalton-sized “megacomplexes”. Compared to interphase, the nucleosomes in mitotic chromosomes pack into slightly larger clusters. However, nearest-neighbor distance analysis reveals that mitotic nucleosome clusters have the same internal packing density as in interphase. Furthermore, mitotic chromosomes contain fewer megacomplexes. This uneven chromosome condensation helps explain a longstanding enigma of mitosis: most genes are repressed but a subset is upregulated.
Genomic imprinting mediates dosage compensation in a young plant XY system
Authors: Muyle Aline , Zemp Niklaus , Fruchard Cécile , Cegan Radim , Vrana Jan , Deschamps Clothilde , Tavares Raquel , Hobza Roman , Picard Franck , Widmer Alex , Marais Gabriel AB 
Published: August 2017

This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100044).Sex chromosomes have repeatedly evolved from a pair of autosomes1. Consequently, X and Y chromosomes initially have similar gene content, but ongoing Y degeneration leads to reduced Y gene expression and eventual Y gene loss. The resulting imbalance in gene expression between Y genes and the rest of the genome is expected to reduce male fitness, especially when protein networks have components from both autosomes and sex chromosomes. A diverse set of dosage compensating mechanisms that alleviates these negative effects has been described in animals2–4. However, the early steps in the evolution of dosage compensation remain unknown and dosage compensation is poorly understood in plants5. Here we show a novel dosage compensation mechanism in the evolutionarily young XY sex determination system of the plantSilene latifolia. Genomic imprinting results in higher expression from the maternal X chromosome in both males and females. This compensates for reduced Y expression in males but results in X overexpression in females and may be detrimental. It could represent a transient early stage in the evolution of dosage compensation. Our finding has striking resemblance to the first stage proposed by Ohno for the evolution of X inactivation in mammals.
Sex-related differences in behavioral and amygdalar responses to compound facial threat cues
Authors: Im Hee Yeon , Adams Reginald B. , Cushing Cody A. , Boshyan Jasmine , Ward Noreen , Kveraga Kestutis 
Published: August 2017

AbstractDuring face perception, we integrate facial expression and eye gaze to take advantage of their shared signals. For example, fear with averted gaze provides a congruent avoidance cue, signaling both threat presence and its location, whereas fear with direct gaze sends an incongruent cue, leaving threat location ambiguous. It has been proposed that the processing of different combinations of threat cues is mediated by dual processing routes: reflexive processing via magnocellular (M) pathway and reflective processing via parvocellular (P) pathway. Because growing evidence has identified a variety of sex differences in emotional perception, here we also investigated how M and P processing of fear and eye gaze might be modulated by observer’s sex, focusing on the amygdala, a structure important to threat perception and affective appraisal. We adjusted luminance and color of face stimuli to selectively engage M or P processing and asked observers to identify emotion of the face. Female observers showed more accurate behavioral responses to faces with averted gaze and greater left amygdala reactivity both to fearful and neutral faces. Conversely, males showed greater right amygdala activation only for M-biased averted-gaze fear faces. In addition to functional reactivity differences, females had greater bilateral amygdala volumes, which positively correlated with behavioral accuracy for M-biased fear. Conversely, in males only the right amygdala volume was positively correlated with accuracy for M-biased fear faces. Our findings suggest that M and P processing of facial threat cues is modulated by functional and structural differences in the amygdalae associated with observer’s sex.
Fast and Powerful Genome Wide Association Analysis of Dense Genetic Data with High Dimensional Imaging Phenotypes
Authors: Ganjgahi Habib , Winkler Anderson M. , Glahn David C. , Blangero John , Donohue Brian , Kochunov Peter , Nichols Thomas E. 
Published: August 2017

ABSTRACTGenome wide association (GWA) analysis of brain imaging phenotypes can advance our understanding of the genetic basis of normal and disorder-related variation in the brain. GWA approaches typically use linear mixed effect models to account for non-independence amongst subjects due to factors such as family relatedness and population structure. The use of these models with high-dimensional imaging phenotypes presents enormous challenges in terms of computational intensity and the need to account multiple testing in both the imaging and genetic domain. Here we present method that makes mixed models practical with high-dimensional traits by a combination of a transformation applied to the data and model, and the use of a non-iterative variance component estimator. With such speed enhancements permutation tests are feasible, which allows inference on powerful spatial tests like the cluster size statistic.
R2DGC: Threshold-free peak alignment and identification for 2D gas chromatography mass spectrometry in R
Authors: Ramaker Ryne C. , Gordon Emily , Cooper Sara J. 
Published: August 2017

AbstractSummaryComprehensive two dimensional gas chromatography-mass spectrometry is a powerful method for analyzing complex mixtures of volatile compounds. This method produces a large amount of raw data that requires downstream processing to align signals of interest (peaks) across multiple samples and match peak characteristics to reference standard libraries prior to downstream statistical analysis. To address the paucity of applications addressing this need, we have developed an R package that implements retention time and mass spectra similarity threshold-free alignments, seamlessly integrates retention time standards for universally reproducible alignments, performs common ion filtering, and provides compatibility with multiple peak quantification methods. We demonstrate the packages utility on a controlled mix of metabolite standards separated under variable chromatography conditions and data generated from cell lines.Availability and documentationR2DGC can be downloaded athttps://github.com/rramaker/R2DGCor installed via the Comprehensive R Archive Network (CRAN).Contactsjcooper@hudsonalpha.orgSupplementary informationSupplementary data are available at Bioinformatics online.
Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse
Authors: Buckley Reuben M , Kortschak R Daniel , Adelson David L 
Published: August 2017

AbstractThe forces driving the accumulation and removal of non-coding DNA and ultimately the evolution of genome size in complex organisms are intimately linked to genome structure and organisation. Our analysis provides a novel method for capturing the regional variation of lineage-specific DNA gain and loss events in their respective genomic contexts. To further understand this connection we used comparative genomics to identify genome-wide individual DNA gain and loss events in the human and mouse genomes. Focusing on the distribution of DNA gains and losses, relationships to important structural features and potential impact on biological processes, we found that in autosomes, DNA gains and losses both followed separate lineage-specific accumulation patterns. However, in both species chromosome X was particularly enriched for DNA gain, consistent with its high L1 retrotransposon content required for X inactivation. We found that DNA loss was associated with gene-rich open chromatin regions and DNA gain events with gene-poor closed chromatin regions. Additionally, we found that DNA loss events tended to be smaller than DNA gain events suggesting that they were more tolerated in open chromatin regions. GO term enrichment in human gain hotspots showed terms related to cell cycle/metabolism, human loss hotspots were enriched for terms related to gene silencing, and mouse gain hotspots were enriched for terms related to transcription regulation. Interestingly, mouse loss hotspots were strongly enriched for terms related to developmental processes, suggesting that DNA loss in mouse is associated with phenotypic changes in mouse morphology. This is consistent with a model in which DNA gain and loss results in turnover or “churning” of regulatory regions that are then subjected to selection, resulting in the differences we now observe, both genomic and phenotypic/morphological.
Progressive reconfiguration of resting-state brain networks as psychosis develops: Preliminary results from the North American Prodrome Longitudinal Study (NAPLS) consortium
Authors: Cao Hengyi , Chung Yoonho , McEwen Sarah C. , Bearden Carrie E. , Addington Jean , Goodyear Bradley , Cadenhead Kristin S. , Mirzakhanian Heline , Cornblatt Barbara A. , Olvet Doreen M. , Mathalon Daniel H. , McGlashan Thomas H. , Perkins Diana O. , Belger Aysenil , Seidman Larry J. , Thermenos Heidi , Tsuang Ming T. , van Erp Theo G.M. , Walker Elaine F. , Hamann Stephan , Anticevic Alan , Woods Scott W. , Cannon Tyrone D. 
Published: August 2017

AbstractMounting evidence has shown disrupted brain network architecture across the psychosis spectrum. However, whether these changes relate to the development of psychosis is unclear. Here, we used graph theoretical analysis to investigate longitudinal changes in resting-state brain networks in samples of 72 subjects at clinical high risk (including 8 cases who converted to full psychosis) and 48 healthy controls drawn from the North American Prodrome Longitudinal Study (NAPLS) consortium. We observed progressive reduction in global efficiency (P= 0.006) and increase in network diversity (P= 0.001) in converters compared with non-converters and controls. More refined analysis separating nodes into nine key brain networks demonstrated that these alterations were primarily driven by progressively diminished local efficiency in the default-mode network (P= 0.004) and progressively enhanced node diversity across all networks (P< 0.05). The change rates of network efficiency and network diversity were significantly correlated (P= 0.003), suggesting these changes may reflect shared underlying neural mechanisms. In addition, change rates of global efficiency and node diversity were significantly correlated with change rate of cortical thinning in the prefrontal cortex in converters (P< 0.03) and could be predicted by visuospatial memory scores at baseline (P< 0.04). These results provide preliminary evidence for longitudinal reconfiguration of resting-state brain networks during psychosis development and suggest that decreased network efficiency, reflecting an increase in path length between nodes, and increased network diversity, reflecting a decrease in the consistency of functional network organization, are implicated in the progression to full psychosis.
Supplement comprising of laccase and citric acid as an alternative for antibiotics –in vitrotriggers of melanin production
Authors: Chaali M. , Lecka J. , Suresh G. , Salem M. , Brar S. K. , Hernandez-Galan L. , Sévigny J. , Avalos Ramirez A. 
Published: August 2017

ABSTRACTAn indiscriminate use of antibiotics in humans and animals has led to a widespread selection of antibiotic-resistant bacterial strains. A possible solution to counter this problem could be to develop alternatives that may boost the host immunity, thus reducing in the quantity and frequency of antibiotic use. In this work, for the first time, citric acid and laccase were used as extracellular inducers of melanin production in yeast cells and human cell lines. It is proposed that the formulation of laccase and citric acid together could further promote melatonin stimulated melanocyte derived melanin production. Melanization test as a probe of immunity, described in this study, is an easy and a quicker test than the other immunity tests and is statistically significant. The results showed the synergistic effect of citric acid and laccase on melanin production by the yeast cells, with significant statistical differences compared to all other tested conditions (P: 0.0005- 0.005). Laccase and citric acid together boosted melanin production after 8 days of incubation. An increase in melanin production by two colon human cells lines (Cacao-2/15 and HT-29) was observed when both laccase and citric acid were present in cell growth medium. A formulation with citric acid and laccase may prove to be an excellent alternative to reduce the antibiotic load in human and animal subjects.Summary statementThis study shows, for the first time, that production of melanin in yeast and human intestinal cells is induced by extracellular addition of laccase and citric acid.
PI3K regulates intraepithelial cell positioning through Rho GTP-ases in the developing neural tube
Authors: Torroba Blanca , Herrera Antonio , Menendez Anghara , Pons Sebastian 
Published: August 2017

SUMMARY STATEMENTDuring neural tube development, PI3K pathway promotes cell survival and provides the apical-basal navigation clues that define the final location of neurons in the epithelium.SUMMARYPhosphatidylinositol 3-kinases (PI3Ks) are signal transducers of many biological processes. Class 1A PI3Ks are hetero dimers formed by a regulatory and a catalytic subunit. We have used the developing chicken neural tube (NT) to study the roles played by PI3K during the process of cell proliferation and differentiation. Notably, we have observed that in addition to its well characterized anti apoptotic activity, PI3K also plays a crucial role in intra epithelial cell positioning, and unlike its role in survival that mainly depends on AKT, the activity in cell positioning is mediated by Rho GTPase family members. Additionally, we have observed that activating mutations of PI3K that are remarkably frequent in many human cancers, cause an unrestrained basal migration of the neuroepithelial cells that end up breaking through the basal membrane invading the surrounding mesenchymal tissue. The mechanism described in this work contribute not only to acquire a greater knowledge of the intraepithelial cell positioning process, but also give new clues on how activating mutations of PI3K contribute to cell invasion during the first stages of tumour dissemination.