bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding dynamic implicit and explicit representations of facial expressions of emotion from EEG
Authors: Smith Fraser W. , Smith Marie L 
Published: October 2018

AbstractFaces transmit a wealth of important social signals. While previous studies have elucidated the network of cortical regions important for perception of facial expression, and the associated temporal components such as the P100, N170 and EPN, it is still unclear how task constraints may shape the representation of facial expression (or other face categories) in these networks. In the present experiment, we investigate the neural information available across time about two important face categories (expression and identity) when those categories are either perceived under explicit (e.g. decoding emotion when task is on emotion) or implicit task contexts (e.g. decoding emotion when task is on identity). Decoding of both face categories, across both task contexts, peaked in a 100-200ms time-window post-stimulus (across posterior electrodes). Peak decoding of expression, however, was not affected by task context whereas peak decoding of identity was significantly reduced under implicit processing conditions. In addition, errors in EEG decoding correlated with errors in behavioral categorization under explicit processing for both expression and identity, but only with implicit decoding of expression. Despite these differences, decoding time-courses and the spatial pattern of informative electrodes differed consistently for both tasks across explicit Vs implicit face processing. Finally our results show that information about both face identity and facial expression is available around the N170 time-window on lateral occipito-temporal sites. Taken together, these results reveal differences and commonalities in the processing of face categories under explicit Vs implicit task contexts and suggest that facial expressions are processed to a richer degree even under implicit processing conditions, consistent with prior work indicating the relative automaticity by which emotion is processed. Our work further demonstrates the utility in applying multivariate decoding analyses to EEG for revealing the dynamics of face perception.
Tethered homing gene drives: a new design for spatially restricted population replacement and suppression
Authors: Dhole Sumit , Lloyd Alun L. , Gould Fred 
Published: October 2018

ABSTRACTOptimism regarding potential epidemiological and conservation applications of modern gene drives is tempered by concern about the potential unintended spread of engineered organisms beyond the target population. In response, several novel gene drive approaches have been proposed that can, under certain conditions, locally alter characteristics of a population. One challenge for these gene drives is the difficulty of achieving high levels of localized population suppression without very large releases in face of gene flow. We present a new gene drive system, Tethered Homing (TH), with improved capacity for localized population alteration, especially for population suppression. The TH drive is based on driving a payload gene using a homing construct that is anchored to a spatially restricted gene drive. We use a proof of principle mathematical model to show the dynamics of a TH drive that uses engineered underdominance as an anchor. This system is composed of a split homing drive and a two-locus engineered underdominance drive linked to one part of the split drive (the Cas endonuclease). In addition to improved localization, the TH system offers the ability to gradually adjust the genetic load in a population after the initial alteration, with minimal additional release effort.
Feasibility of Topological Data Analysis for event-related fMRI
Authors: Ellis Cameron T. , Lesnick Michael , Henselman-Petrusek Gregory , Keller Bryn , Cohen Jonathan D. 
Published: October 2018

AbstractRecent fMRI research shows that perceptual and cognitive representations are instantiated in high-dimensional multi-voxel patterns in the brain. However, the methods for detecting these representations are limited. Topological Data Analysis (TDA) is a new approach, based on the mathematical field of topology, that can detect unique types of geometric features in patterns of data. Several recent studies have successfully applied TDA to study various forms of neural data; however, to our knowledge, TDA has not been successfully applied to data from event-related fMRI designs. Event-related fMRI is very common but limited in terms of the number of events that can be run within a practical time frame and the effect size that can be expected. Here, we investigate whether persistent homology — a popular TDA tool that identifies topological features in data and quantifies their robustness — can identify known signals given these constraints. We use fmrisim, a Python-based simulator of realistic fMRI data, to assess the plausibility of recovering a simple topological representation under a variety of conditions. Our results suggest that persistent homology can be used under certain circumstances to recover topological structure embedded in realistic fMRI data simulations.
Intraflagellar transport protein 74 is essential for mouse spermatogenesis and male fertility by regulating axonemal microtubule assembly in mice
Authors: Lin Shi , Ting Zhou , Qian Huang , Shiyang Zhang , Wei Li , Ling Zhang , Rex A Hess , Gregory J Pazour , Zhibing Zhang 
Published: October 2018

AbstractIFT74 is a component of the core intraflagellar transport (IFT) complex, a bidirectional movement of large particles along the axoneme microtubules for cilia formation. In this study, we investigated its role in sperm flagella formation and discovered that mice deficiency in IFT74 in male germ cells were infertile associated with low sperm counts and immotile sperm. The few developed spermatozoa displayed misshaped heads and short tails. Transmission electron microscopy revealed abnormal flagellar axoneme in the seminiferous tubules where sperm are made. Clusters of unassembled microtubules were present in the spermatids. Testicular expression levels of IFT27, IFT57, IFT81, IFT88 and IFT140 were significantly reduced in the mutant mice, with the exception of IFT20 and IFT25. The levels of ODF2 and SPAG16L proteins were also not changed. However, the processed AKAP4 protein, a major component of the fibrous sheath, a unique structure of sperm tail, was significantly reduced. Our study demonstrates that IFT74 is essential for mouse sperm formation, probably through assembly of the core axoneme and fibrous sheath, and highlights a potential genetic factor (IFT74) that contributes to human infertility in men.
Global lysine acetylation in Escherichia coli results from growth conditions that favor acetate fermentation
Authors: Schilling Birgit , Basisty Nathan , Christensen David G. , Sorensen Dylan , Orr James S. , Wolfe Alan J. , Rao Christopher V. 
Published: October 2018

ABSTRACTLysine acetylation is thought to provide a mechanism for regulating metabolism in diverse bacteria. Indeed, many studies have shown that the majority of enzymes involved in central metabolism are acetylated and that acetylation can alter enzyme activity. However, the details regarding this regulatory mechanism are still unclear, specifically with regards to the signals that induce lysine acetylation. To better understand this global regulatory mechanism, we profiled changes in lysine acetylation during growth of Escherichia coli on the hexose glucose or the pentose xylose at both high and low sugar concentrations using label-free mass spectrometry. The goal was to see whether lysine acetylation differed during growth on these two different sugars. No significant differences, however, were observed. Rather, the initial sugar concentration was the principal factor governing changes in lysine acetylation, with higher sugar concentrations causing more acetylation. These results suggest that acetylation does not target specific metabolic pathways but rather simply targets accessible lysines, which may or may not alter enzyme activity. They further suggest that lysine acetylation principally results from conditions that favor accumulation of acetyl phosphate, the principal acetate donor in E. coli.IMPORTANCEBacteria alter their metabolism in response to nutrient availability, growth conditions, and environmental stresses. This process is best understood at the level of transcriptional regulation, where many metabolic genes are conditionally expressed in response to diverse cues. However, additional modes of regulations are known to exist. One is lysine acetylation, a post-translational modification known to target many metabolic enzymes. However, unlike transcriptional regulation, little is known about this regulatory mode. We investigated the factors inducing changes in lysine acetylation by comparing growth on glucose and xylose. We found that the specific sugar used for growth did not alter the pattern of acetylation; rather, the principal factor was the amount of sugar, with more sugar yielding more acetylation. These results imply lysine acetylation is a global regulatory mechanism that is not responsive to the specific carbon source per se but rather the accumulation of downstream metabolites.
Human APOBEC3G prevents emergence of infectious endogenous retrovirus in mice
Authors: Treger Rebecca S. , Tokuyama Maria , Dong Huiping , Ross Susan R. , Kong Yong , Iwasaki Akiko 
Published: October 2018

AbstractEndogenous retroviruses (ERV) are found throughout vertebrate genomes and failure to silence their activation can have deleterious consequences on the host. Introduction of mutations that subsequently prevent transcription of ERV loci is therefore an indispensable cell-intrinsic defense mechanism that maintains the integrity of the host genome. Abundant in vitro and in silico evidence have revealed that APOBEC3 cytidine-deaminases, including human APOBEC3G (hA3G) can potently restrict retrotransposition; yet in vivo data demonstrating such activity is lacking, particularly since no replication competent human ERV has been identified. In mice deficient for Toll-like receptor 7 (TLR7), transcribed ERV loci can recombine and generate infectious ERV. In this study, we show that mice deficient in the only copy of Apobec3 in the genome did not have spontaneous reactivation of ERVs, nor elevated ERV reactivation when crossed to Tlr7-/- mice. In contrast, expression of a human APOBEC3G transgene abrogated emergence of infectious ERV in the Tlr7-/- background. No ERV RNA was detected in the plasma of hA3G+Apobec3-/-Tlr7-/- mice, and infectious ERV virions could not be amplified through co-culture with permissive cells. These data reveal that hA3G can potently restrict active ERV in vivo, and suggest that the expansion of the APOBEC3 locus in primates has helped restrict ERV reactivation in the human genome.ImportanceAlthough APOBEC3 proteins are known to be important antiviral restriction factors in both mice and humans, their roles in the restriction of endogenous retroviruses (ERV) have been limited to in vitro studies. Here, we report that human APOBEC3G expressed as a transgene in mice prevents the emergence of infectious ERV from endogenous loci. This study reveals that APOBEC3G can powerfully restrict active retrotransposons in vivo and demonstrates how ectopic expression of human factors in transgenic mouse models can be used to investigate host mechanisms that inhibit retrotransposons and reinforce genomic integrity.
SPRTN Protease and Checkpoint Kinase 1 Cross-Activation Loop Safeguards DNA Replication
Authors: Halder Swagata , Torrecilla Ignacio , Burkhalter Martin D. , Popovic Marta , Fielden John , Vaz Bruno , Oehler Judith , Pilger Domenic , Lessel Davor , Wiseman Katherine , Narayan Singh Abhay , Vendrell Iolanda , Fischer Roman , Philipp Melanie , Ramadan Kristijan 
Published: October 2018

AbstractThe SPRTN metalloprotease is essential for DNA-protein crosslink (DPC) repair and DNA replication in vertebrate cells. Cells deficient in SPRTN protease activity exhibit severe DPC-induced replication stress and genome instability, manifesting as premature ageing and liver cancer in humans and mice. Strikingly, SPRTN-deficient cells also show a severe G2/M checkpoint defect and fail to activate a robust checkpoint kinase 1 (CHK1) signalling cascade normally triggered in response to replication stress. Here, we show that SPRTN activates the CHK1 signalling cascade during physiological (steady-state) DNA replication by proteolysis-dependent eviction of CHK1 from chromatin. The N-terminal CHK1 fragments cleaved by SPRTN protease still possess kinase activity and phosphorylate SPRTN. This CHK1-dependent phosphorylation stimulates SPRTN recruitment to chromatin to further promote CHK1 eviction from chromatin, DPC removal and unperturbed DNA replication. Our data suggest that a SPRTN-CHK1 cross-activation loop is essential for steady-state DNA replication and protection from DNA replication stress, a major source of genome instability in diseases that cause premature ageing and cancer. In addition, we disclose a mechanism of CHK1 activation during physiological DNA replication, when long stretches of single stranded (ss) DNA that are induced by genotoxic stress and activate canonical and robust CHK1 signalling are not present.
Bacterial Zombies and Ghosts: Production of Inactivated Gram-Positive and Gram-Negative Species with Preserved Cellular Morphology and Cytoplasmic Content
Authors: Taddese Rahwa , Belzer Clara , Aalvink Steven , de Jonge Marien I. , Nagtegaal Iris D. , Dutilh Bas E. , Boleij Annemarie 
Published: October 2018

ABSTRACTThere are many approaches available to inactivate bacteria, each with a different efficacy, impact on cell integrity, and potential for application in high-throughput. The aim of this study was to compare these approaches and develop a standardized protocol for generation of intact Gram-positive as well as on Gram-negative “bacterial zombies”, i.e. cells that are metabolically dead with retained cellular integrity. Here, we introduce the term “bacterial zombies” in addition to “bacterial ghosts” to differentiate inactivated bacteria with preserved cellular integrity from those with perforated membranes, where DNA and cytoplasmic contents have been released. This differentiation of inactivated bacteria is important if the cell content is the subject of study, or if cell contents in the media may cause unwanted effects in downstream applications. We inactivated eight different bacterial species by treatment with beta-propiolactone, ethanol, formalin, sodium hydroxide, and pasteurization. Inactivation efficacy was determined by culturing, and cell wall integrity assessed by quantifying released DNA and visualization by scanning electron microscopy. Based on these results, we discuss the choice of bacterial inactivation methods, and conclude that beta-propiolactone and ethanol are the most promising approaches for standardized generation of bacterial zombies.IMPORTANCEFor applications such as vaccination or analyses that are sensitive to bacterial growth, inactivated bacteria are preferred because they simplify the analyses and the interpretation of results. This study compared various bacterial inactivation treatments that maintain cell integrity and may be used in high-throughput. Our results demonstrated that beta-propiolactone and 70% ethanol were the best techniques to achieve these goals.
Excessive ENaC-mediated sodium influx drives NLRP3 inflammasome-dependent autoinflammation in cystic fibrosis
Authors: Scambler Thomas , Jarosz-Griffiths Heledd H. , Lara-Reyna Samuel , Pathak Shelly , Wong Chi , Holbrook Jonathan , Martinon Fabio , Savic Sinisa , Peckham Daniel , McDermott Michael F. 
Published: October 2018

AbstractCystic Fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and results in defective CFTR-mediated chloride transport, dysregulation of epithelial sodium channels (ENaC) and exaggerated innate immune responses. We tested the hypothesis that upregulation of ENaC drives autoinflammation in this complex monogenic disease.We show that monocytes from patients with CF exhibit a systemic proinflammatory cytokine signature, with associated anti-inflammatory M2-type macrophage deficiency. Cells harboring CF mutations are hyperresponsive to NLRP3 stimulation, as evidenced by increased IL-18, IL-1β, ASC-specks levels in serum and caspase-1 activity in monocytes, and by increased IL-18 production and caspase-1 activity in human bronchial epithelial cells (HBECs). In both cell types there is an associated shift to glycolytic metabolism with succinate release, in response to increased energy requirements. Inhibition of amiloride-sensitive sodium channels partially reverses the NLRP3-dependent inflammation and metabolic shift in these cells. Overexpression of β-ENaC, in the absence of CFTR dysfunction, increases NLRP3-dependent inflammation, indicating a CFTR-independent ENaC axis in CF pathophysiology. Sodium channel modulation provides an important therapeutic strategy to combat lung inflammation in CF.
Temporal evolution of beta bursts in the parkinsonian cortico-basal ganglia network
Authors: Cagnan Hayriye , Nicolas Mallet , Moll Christian K.E. , Gulberti Alessandro , Westphal Manfred , Gerloff Christian , Engel Andreas K. , Hamel Wolfgang , Magill Peter J. , Brown Peter , Sharott Andrew 
Published: October 2018

AbstractPrevalence and temporal dynamics of transient oscillations in the beta frequency band (15-35 Hz), referred to as beta bursts, are correlated with motor performance and tactile perception. Disturbance of these activities is a candidate mechanism for motor impairment in Parkinson’s disease (PD), where the excessively long bursts correlate with symptom severity and are reduced by pharmacological and surgical treatments. To date, characterization of beta bursts in PD has been limited to the local field potentials in the subthalamic nucleus (STN) and cortical EEG. Here, we describe the changes that take place in spiking activity across the cortico-basal ganglia circuit, providing a unique insight into the network dynamics of these transient oscillations. Firstly, we demonstrate that rhythmic subthalamic spiking activity emerges at a fixed phase relationship with respect to cortical beta bursts in PD patients. Using multichannel recordings of ensembles of neurons in the 6-OHDA rat model of PD, we then dissect the beta burst dynamics across the sensorimotor cortex and several basal ganglia structures: striatum (Str), globus pallidus externus (GPe) and STN. Each subcortical structure exhibits enhanced rhythmic activity in the beta band locked to the onset of cortical beta bursts and longer cortical bursts lead to stronger subcortical rhythmicity. Crucially, enhanced subcortical rhythmic activity emerges at a fixed phase relationship with respect to the motor cortex, comparable to the relationship observed in PD patients. Striatal beta bursts terminate prior to the recruitment of those in the STN and GPe, suggesting that while they could play an important role in establishing synchrony in the beta band, they do not extensively contribute to its maintenance in other basal ganglia structures. Critically, changes in cortico-subcortical phase coupling precede the onset of a cortical beta burst, supporting the hypothesis that phase alignment across the cortico-basal ganglia network could recruit these structures into synchronous network oscillations. We provide a powerful approach that not only examines pathophysiology of PD across the motor circuit, but also offer insights that could aid in the design of novel neuromodulation strategies to manipulate the state of the motor system before pathological activities emerge.
Rediscovery and redescription of the endangered Hypostomus subcarinatus Castelnau, 1855 (Siluriformes: Loricariidae) from the rio São Francisco basin in Brazil, with comments on the urban water conservation
Authors: Zawadzki Cláudio Henrique , Penido Iago de Souza , Pessali Tiago Casarim 
Published: October 2018

AbstractHypostomus subcarinatus Castelnau, 1855 is rediscovered in the Pampulha lake, an urban lake pertaining to the rio das Velhas basin in the rio São Francisco system in the state of Minas Gerais, southeastern Brazil. Herein, H. subcarinatus is redescribed and its diagnosis from the congeners is established due to characters such as blue tan dorsal fin in live specimens, slender bicuspid teeth, dentaries angled more than 90 degrees, moderate keels along lateral series of plates, small roundish dark spots, one plate bordering supraoccipital, by having nuptial odontodes mainly on pectoral, dorsal and caudal-fin rays, and longer anal-fin unbranched ray. The rediscovery of H. subcarinatus after more than 160 years after its original description was one unexpected event, because the Pampulha lake is an artificial, shallow and polluted urban lake. The lake is located in the downtown of municipality of Belo Horizonte, the third largest urban agglomeration in Brazil with a population exceeding 5.9 million inhabitants. In the light of this finding we address the importance of urban body waters to maintenance of fish biodiversity in the neotropics.
Revealing an extended critical window of recovery post-stroke
Authors: Rubio Ballester Belen , Duff Armin , Maier Martina , Cameirao Monica , Bermudez Sergi , Duarte Esther , Cuxart Ampar , Rodríguez Susana , Verschure Paul F.M.J. 
Published: October 2018

ABSTRACTThe impact of rehabilitation on post-stroke motor recovery and its dependency on the patient’s chronicity remain unclear. The existence and regularity of a, so called, proportional recovery rule across a range of functional deficits and therapies supports the notion that functional interventions have little or no impact beyond spontaneous recovery rates in a ‘critical window of recovery’ which lasts from 3 to 6 months post-stroke. In this meta-analysis, we apply a bootstrap analysis method to assess the overall impact of a specific VR-based rehabilitation protocol for the upper extremities on a homogeneous sample of 219 individuals with hemiparesis at various stages post stroke. Our analysis uncovers a precise gradient of sensitivity to treatment that expands more than one year beyond the limits of the so-called ‘critical window of recovery’. These findings redefine the limits of the so-called ‘critical window of recovery’ and suggest that stroke-derived plasticity mechanisms do facilitate functional recovery even at the chronic and late chronic stage.