bluuebunny/crossref_metadata_2025_split huggingface dataset:
Altered beta-band oscillations and connectivity underlie detail-oriented visual processing in autism
Authors: Ronconi Luca , Vitale Andrea , Federici Alessandra , Pini Elisa , Molteni Massimo , Casartelli Luca 
Published: February 2020

AbstractSensory and perceptual anomalies have been increasingly recognized as core phenotypic markers for autism spectrum disorders (ASD). A neurophysiological characterization of these anomalies is of utmost importance to understand more complex behavioural manifestations within the spectrum. The present study employed electroencephalography (EEG) to test whether detail-oriented visual perception, a recognized hallmark of ASD, is associated with altered neural oscillations and functional connectivity in beta (and alpha) frequency bands, considering their role in feedback and top-down reentrant signalling in the typical population. A sample of children with diagnosis of ASD (N=18) and typically developing peers (TD; N=20) performed a visual crowding task, where they had to discriminate a peripheral target letter surrounded by flankers at different distances, together with a control condition with no flankers. In TD participants the amplitude of the target-locked N1 component and its cortical sources was significantly modulated as a function of visual crowding, whereas such modulation was absent in the ASD group, suggesting that their visual scene analysis takes place without a flexible neural computation. The comparison between groups showed a decreased activity in the ASD group in occipital, infero-temporal and inferior/middle frontal regions in conditions requiring detail-oriented perception as opposed to conditions requiring the discrimination of target in isolation. Moreover, in TD participants detail-oriented perception was associated with an event-related beta power reduction (15-30 Hz), which was not evident in the ASD group. A data-driven functional connectivity analysis highlighted in the ASD sample an increased connectivity in the beta frequency range between occipital and infero-temporal regions. Notably, individual hyperconnectivity indexes correlated to less severe ASD symptomatology and to a diminished detail-oriented perception, suggesting a potential compensatory mechanism. Overall, these results show that altered communication in the beta frequency band may explain atypical perception in ASD, reflecting aberrant feedback connectivity within the visual system with potential cascade effects in visual scene parsing and higher-order functions.
Temporal expectation hastens decision onset but does not affect evidence quality
Authors: van den Brink Ruud L. , Murphy Peter R. , Desender Kobe , de Ru Nicole , Nieuwenhuis Sander 
Published: February 2020

ABSTRACTThe ability to predict the timing of forthcoming events, known as temporal expectation, has a strong impact on human information processing. Although there is growing consensus that temporal expectations enhance the speed and accuracy of perceptual decisions, it remains unclear whether they affect the decision process itself, or non-decisional (sensory / motor) processes. Here, healthy human participants (N = 21; 18 female) used predictive auditory cues to anticipate the timing of low-contrast visual stimuli they were required to detect. Modelling of the behavioral data using a prominent sequential sampling model indicated that temporal expectations speeded up non-decisional processes but had no effect on decision formation.Electrophysiological recordings confirmed and extended this result: temporal expectations hastened the onset of a neural signature of decision formation, but had no effect on its build-up rate. Anticipatory alpha-band power was modulated by temporal expectation, and co-varied with intrinsic trial-by-trial variability in behavioral and neural signatures of the onset latency of the decision process. These findings highlight how temporal predictions optimize our interaction with unfolding sensory events.SIGNIFICANCE STATEMENTTemporal expectation enhances performance, but the locus of this effect remains debated. Here, we contrasted the two dominant accounts: enhancement through (1) expedited decision onset, or (2) an increase in the quality of sensory evidence. We manipulated expectations about the onset of a dim visual target using a temporal cueing paradigm, and probed the locus of the expectation effect with two complementary approaches: drift diffusion modeling of behavior, and estimation of the onset and progression of the decision process from a supramodal accumulation-to-bound signal in simultaneously measured EEG signals. Behavioral modeling and neural data provided strong, converging evidence for an account in which temporal expectations enhance perception by speeding up decision onset, without affecting evidence quality.
Synchronous nonmonotonic changes in functional connectivity and white matter integrity in a rat model of sporadic Alzheimer’s disease
Authors: Pereira Catarina Tristão , Diao Yujian , Yin Ting , da Silva Analina R , Lanz Bernard , Pierzchala Katarzyna , Poitry-Yamate Carole , Jelescu Ileana O 
Published: February 2020

AbstractBrain glucose hypometabolism has been singled out as an important contributor and possibly main trigger to Alzheimer’s disease (AD). Intracerebroventricular injections of streptozotocin (icv-STZ) cause brain glucose hypometabolism without systemic diabetes. Here, a first-time longitudinal study of brain glucose metabolism, functional connectivity and white matter microstructure was performed in icv-STZ rats using PET and MRI. Histological markers of pathology were tested at an advanced stage of disease. STZ rats exhibited altered functional connectivity and intra-axonal damage and demyelination in brain regions typical of AD, in a temporal pattern of acute injury, transient recovery/compensation and chronic degeneration. In the context of sustained glucose hypometabolism, these nonmonotonic trends – also reported in behavioral studies of this animal model as well as in human AD – suggest a compensatory mechanism, possibly recruiting ketone bodies, that allows a partial and temporary repair of brain structure and function. The early acute phase could thus become a valuable therapeutic window to strengthen the recovery phase and prevent or delay chronic degeneration, to be considered both in preclinical and clinical studies of AD. In conclusion, this work reveals the consequences of brain insulin resistance on structure and function, highlights signature nonmonotonic trajectories in their evolution and proposes potent MRI-derived biomarkers translatable to human AD and diabetic populations.
Perfluorooctanoic acid activates multiple nuclear receptor pathways and skews expression of genes regulating cholesterol homeostasis in liver of humanized PPARα mice fed an American diet
Authors: Schlezinger JJ , Puckett H , Oliver J , Nielsen G , Heiger-Bernays W , Webster TF 
Published: February 2020

AbstractHumans are exposed to per- and polyfluoroalkyl substances (PFAS) in their drinking water, food, air, dust in their homes, and by direct use of consumer products. Increased concentrations of serum total cholesterol and low density lipoprotein cholesterol are among the endpoints best supported by epidemiology. The objectives of this study were to generate a new model for examining PFAS-induced dyslipidemia and to conduct molecular studies to better define mechanism(s) of action. We tested the hypothesis that PFOA exposure at a human-relevant level dysregulates expression of genes controlling cholesterol homeostasis in livers of mice expressing human PPARα (hPPARα). Female and male hPPARα and PPARα null mice were fed a diet based on the “What we eat in America” analysis and exposed to perfluorooctanoic acid (PFOA) in drinking water (8 µM) for 6 weeks. This resulted in a serum PFOA concentration of 48 μg/ml. PFOA increased liver mass, which was associated with histologically-evident lipid accumulation. PFOA induced PPARα and constitutive androstane receptor target gene expression in liver. Expression of genes in four pathways regulating cholesterol homeostasis were also measured. PFOA decreased expression ofHmgcrin a PPARα-dependent manner. PFOA decreased expression ofLdlrandCyp7a1in a PPARα-independent manner.Apobexpression was not changed. Gene expression in females appeared to be more sensitive to PFOA exposure than in males. This novel study design (hPPARα mice, American diet, long term exposure) generated new insight on the effects of PFOA on cholesterol regulation in the liver and the role of hPPARα.
Selection and subsequent physiological characterisation of industrialSaccharomyces cerevisiaestrains during continuous growth at sub- and- supra optimal temperatures
Authors: Lip Ka Ying Florence , García-Ríos Estéfani , Costa Carlos E. , Guillamón José Manuel , Domingues Lucília , Teixeira José , van Gulik Walter M. 
Published: February 2020

AbstractA phenotypic screening of 12 industrial yeast strains and the well-studied laboratory strain CEN.PK113-7D at cultivation temperatures between 12 °C and 40 °C revealed significant differences in maximum growth rates and temperature tolerance. TwoSaccharomyces cerevisiaestrains, one performing best at sub-, and the other at supra-optimal temperatures, plus the laboratory strain, were selected for further physiological characterization in well-controlled bioreactors. The strains were grown in anaerobic chemostats, at a fixed specific growth rate of 0.03 h-1and sequential batch cultures at 12, 30, and 39 °C. We observed significant differences in biomass and ethanol yields on glucose, biomass protein and storage carbohydrate contents, and biomass yields on ATP between strains and cultivation temperatures. Increased temperature tolerance coincided with higher energetic efficiency of cell growth, indicating that temperature intolerance is a result of energy wasting processes, such as increased turnover of cellular components (e.g. proteins) due to temperature induced damage.
Redox-active cysteines in TGACG-BINDING FACTOR 1 (TGA1) do not play a role in salicylic acid- or pathogen-induced expression of TGA1-regulated target genes inArabidopsis thaliana
Authors: Budimir Jelena , Treffon Katrin , Nair Aswin , Thurow Corinna , Gatz Christiane 
Published: February 2020

SummarySalicylic acid (SA) is an important signaling molecule of the plant immune system.SA biosynthesis is indirectly modulated by the closely related transcription factors TGA1 (TGACG-BINDING FACTOR 1) and TGA4. They activate expression ofSARD1(SYSTEMIC ACQUIRED RESISTANCE DEFICIENT1), the gene product of which regulates the key SA biosynthesis geneICS1(ISOCHORISMATE SYNTHASE 1).Since TGA1 interacts with the SA receptor NPR1 (NON EXPRESSOR OF PATHOGENESIS-RELATED GENES 1) in a redox-dependent manner and since the redox state of TGA1 is altered in SA-treated plants, TGA1 was assumed to play a role in the NPR1-dependent signaling cascade. Here we identified 193 out of 2090 SA-induced genes that require TGA1/TGA4 for maximal expression after SA treatment. One robustly TGA1/TGA4-dependent gene encodes for the SA hydroxylase DLO1 (DOWNY MILDEW RESISTANT 6-LIKE OXYGENASE 1) suggesting an additional regulatory role of TGA1/TGA4 in SA catabolism.Expression of TGA1/TGA4-dependent genes in mock/SA-treated or Pseudomonas-infected plants was rescued in thetga1 tga4double mutant after introduction of a mutant genomicTGA1fragment encoding a TGA1 protein without any cysteines. Thus, the functional significance of the observed redox modification of TGA1 in SA-treated tissues has remained enigmatic.SIGNIFICANCE STATEMENTPrevious findings demonstrating a redox-dependent interaction between transcription factor TGA1 and NPR1 attracted considerable attention. Here we show that TGA1 can act in the NPR1- and SA-dependent signaling cascade, but that its SA-regulated redox-active cysteines do not affect its function in this process.
Microbial trend analysis for common dynamic trend, group comparison and classification in longitudinal microbiome study
Authors: Wang Chan , Hu Jiyuan , Blaser Martin J. , Li Huilin 
Published: February 2020

AbstractMotivationThe human microbiome is inherently dynamic and its dynamic nature plays a critical role in maintaining health and driving disease. With an increasing number of longitudinal microbiome studies, scientists are eager to learn the comprehensive characterization of microbial dynamics and their implications to the health and disease-related phenotypes. However, due to the challenging structure of longitudinal microbiome data, few analytic methods are available to characterize the microbial dynamics over time.ResultsWe propose a microbial trend analysis (MTA) framework for the high-dimensional and phylogenetically-based longitudinal microbiome data. In particular, MTA can perform three tasks: 1) capture the common microbial dynamic trends for a group of subjects on the community level and identify the dominant taxa; 2) examine whether or not the microbial overall dynamic trends are significantly different in groups; 3) classify an individual subject based on its longitudinal microbial profiling. Our extensive simulations demonstrate that the proposed MTA framework is robust and powerful in hypothesis testing, taxon identification, and subject classification. Our real data analyses further illustrate the utility of MTA through a longitudinal study in mice.ConclusionsThe proposed MTA framework is an attractive and effective tool in investigating dynamic microbial pattern from longitudinal microbiome studies.
Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications
Authors: Parey Elise , Louis Alexandra , Cabau Cédric , Guiguen Yann , Crollius Hugues Roest , Berthelot Camille 
Published: February 2020

AbstractWhole genome duplications (WGD) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-descended species, which hinders the exploration of functional consequences of WGDs. Here we present SCORPiOs, a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-million-year-old WGD at the origin of teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,391) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art methods. Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade.
An injectable meta-biomaterial
Authors: Béduer A. , Bonini F. , Verheyen C. , Burch P. , Braschler T. 
Published: February 2020

AbstractWe present a novel type of injectable biomaterial with an elastic softening transition. The material enablesin-vivoshaping, followed by induction of 3D stable vascularized tissue adopting the desired shape. We establish the necessary geometrical and physical parameters by extensive numerical simulation. Irregular particle shape dramatically enhances yield strain forin-vivostability against deformation, while friction and porosity provide the elastic softening transition as an emergent meta-material property. Accordingly, we synthesize our injectable meta-biomaterial as a suspension of irregularly fragmented, highly porous sponge-like microgels. The meta-biomaterial exhibits both high yield strain, and the desired novel elastic softening transition forin-situshaping and unprecedented dynamic matching of adipose tissue mechanics.In vivo, predetermined shapes can be sculpted manually after subcutaneous injection in mice. The 3D shape is maintained during excellent host tissue integration into the particle pore space. The meta-biomaterial sustains vascularized connective tissue to the end of one-year follow-up.
A litmus test for harmonized mosquito monitoring across Europe and Africa
Authors: Graziosi Ignazio , Aranda Carles , Balestrino Fabrizio , Bellini Romeo , Busquets Núria , Coulibaly Mammadou , Crisanti Andrea , Diallo Diawo , Diallo Mawlouth , Gaye Alioune , Guelbeogo Moussa , Ignjatović-Ćupina Aleksandra , Napp Sebastián , N’Falé Sagnon , Petrić Dušan , Pollegioni Paola , Simoni Alekos , Zgomba Marija , Müller Ruth 
Published: February 2020

AbstractThe accelerating rate of outbreaks from mosquito borne diseases are urging the development of updated and effective tools for the surveillance of insect populations and their larval habitats. Harmonized field protocols help to build a comprehensive picture on species-specific vector ecology and generate important knowledge for implementing coordinated mosquito surveillance programs at regional scales and across continents. In this study, we test the efficiency and potential barriers of available harmonized protocols from earlier EU project VectorNet. As a kind of litmus test for such protocols, we specifically aim to capture the ecoregional variation of breeding site characteristics and population density of five mosquito vectors in Europe and Africa. As expected, the five species considered show different aquatic habitat preferences.Culex pipiens, Aedes albopictusin Europe andAe. aegyptiin Africa select breeding habitats within specific volume classes, whileAnopheles gambiaeandAn. coluzziimay select breeding habitats based on seasonal availability. Population densities in aquatic habitats greatly varied across species and countries, but larval production sites ofAe. albopictusgenerate populations with higher ratio of pupae compared to the other species. This result underlines the fundamental ecological difference between the selected vector species disregarding of the ecoregion. Mean water temperatures had limited variation across species and higher among countries. Understanding the ecology of native and non-native mosquito vectors is key in evaluating transmission risks for diseases such as West Nile, chikungunya and dengue fevers, zika and malaria. The available harmonized field protocols are a valuable tool for achieving homogeneous mosquito surveillance in Europe and Africa.
Proteomics Using Protease Alternatives to Trypsin Benefits from Sequential Digestion with Trypsin
Authors: Dau Therese , Bartolomucci Giulia , Rappsilber Juri 
Published: February 2020

ABSTRACTTrypsin is the most used enzyme in proteomics. Nevertheless, proteases with complementary cleavage specificity have been applied in special circumstances. In this work, we analyzed the characteristics of five protease alternatives to trypsin for protein identification and sequence coverage when applied toS. pombewhole cell lysates. The specificity of the protease heavily impacted on the number of proteins identified. Proteases with higher specificity let to the identification of more proteins than proteases with lower specificity. However, AspN, GluC, chymotrypsin and proteinase K largely benefited from being paired with trypsin in sequential digestion, as had been shown by us for elastase before. In the most extreme case, pre-digesting with trypsin improves the number of identified proteins for proteinase K by 731 %. Trypsin pre-digestion also improved the protein identifications of other proteases, AspN (+62 %), GluC (+80 %) and chymotrypsin (+21 %). Interestingly, the sequential digest with trypsin and AspN yielded even higher number of protein identifications than digesting with trypsin alone.
Plasticity of the glutamate transporter EAAT2 on striatal astrocytes regulates flexibility in behavior
Authors: Boender Arjen J. , Tonini Raffaella 
Published: February 2020

AbstractModulation of striatal circuits is necessary for behavioral flexibility and confers the ability to adapt to environmental changes. Striatal astrocytes contribute to circuit neuromodulation by controlling the activity of ambient neurotransmitters. In particular, extracellular glutamate levels are tightly controlled by the astrocytic glutamate transporter EAAT2, thereby influencing synaptic functioning and neural network activity. While disturbances in EAAT2 have been related to neurological dysfunctions, it remains unclear if environmental cues influence this protein’s function to specifically shape action control.In this study, we investigate the relationship between experience-dependent plasticity of EAAT2 expression and action inflexibility that follows overtraining for an instrumental task. We find that task overtraining is associated with the upregulation of EAAT2 in the lateral part of the dorsal striatum (DLS). Interfering with EAAT2 upregulation by chemogenetic activation of astrocytic Gq signaling or by transientin vivoknockdown of EAAT2 in the DLS restores behavioral flexibility. Astrocytes are emerging as critical regulators of striatal functions, and by demonstrating that plasticity of EAAT2 expression in the DLS shapes behavior, this work provides novel mechanistic insights into how flexibility in action control is regulated.
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data
Authors: Markowski Julia , Kempfer Rieke , Kukalev Alexander , Irastorza-Azcarate Ibai , Loof Gesa , Kehr Birte , Pombo Ana , Rahmann Sven , Schwarz Roland F 
Published: February 2020

AbstractMotivationGenome Architecture Mapping (GAM) was recently introduced as a digestion- and ligation-free method to detect chromatin conformation. Orthogonal to existing approaches based on chromatin conformation capture (3C), GAM’s ability to capture both inter- and intra-chromosomal contacts from low amounts of input data makes it particularly well suited for allele-specific analyses in a clinical setting. Allele-specific analyses are powerful tools to investigate the effects of genetic variants on many cellular phenotypes including chromatin conformation, but require the haplotypes of the individuals under study to be known a-priori. So far however, no algorithm exists for haplotype reconstruction and phasing of genetic variants from GAM data, hindering the allele-specific analysis of chromatin contact points in non-model organisms or individuals with unknown haplotypes.ResultsWe present GAMIBHEAR, a tool for accurate haplotype reconstruction from GAM data. GAMIBHEAR aggregates allelic co-observation frequencies from GAM data and employs a GAM-specific probabilistic model of haplotype capture to optimise phasing accuracy. Using a hybrid mouse embryonic stem cell line with known haplotype structure as a benchmark dataset, we assess correctness and completeness of the reconstructed haplotypes, and demonstrate the power of GAMIBHEAR to infer accurate genome-wide haplotypes from GAM data.AvailabilityGAMIBHEAR is available as an R package under the open source GPL-2 license athttps://bitbucket.org/schwarzlab/gamibhearMaintainer:julia.markowski@mdc-berlin.de