bluuebunny/crossref_metadata_2025_split huggingface dataset:
Egg retrieval versus egg rejection in cuckoo hosts
Authors: Yang Canchao , Liang Wei , Møller Anders P. 
Published: February 2019

Before complex nests evolved, birds laid eggs on the ground, and egg retrieval evolved as an adaptation against accidental displacement of eggs outside the nest. Therefore, egg retrieval is an ancient, and likely ancestral, widespread behaviour in birds. However, it has received little attention in studies of avian brood parasitism, perhaps because most parasitism occurs in species with complex nests, a context in which egg retrieval seems irrelevant. However, for cavity-nesting hosts of avian brood parasites, egg retrieval may still play an important role in the coevolutionary interactions between obligate brood parasites and hosts, because egg retrieval can be considered to be antagonistic to egg rejection behaviour in hosts, yet both may involve cognition to recognize eggs. We hypothesized that (1) cavity-nesting hosts should retrieve misplaced eggs from outside the nest cup, (2) brood parasitism has modulated egg retrieval behaviour in cavity-nesting hosts and (3) hosts use the same visual cues for decision-making during egg recognition in both egg retrieval and egg rejection actions. To test these hypotheses, we performed a series of experiments in a cavity-nesting host, the green-backed tit (Parus monticolus). Foreign eggs with different levels of mimicry were placed within or outside nest cups of hosts to test their responses. We found that host decisions about whether to retrieve or reject an egg both depended on the degree of mimicry. However, hosts sometimes first retrieved poorly mimetic foreign eggs and then rejected them. Alternatively, hosts sometimes failed to retrieve highly mimetic conspecific eggs. We suggest that egg retrieval in hosts is likely to be a result of the interaction between ancient retrieval behaviour and subsequent adaptation against brood parasitism.This article is part of the theme issue ‘The coevolutionary biology of brood parasitism: from mechanism to pattern’.
Does data cleaning improve brain state classification?
Authors: Meisler Steven L. , Ezzyat Youssef , Kahana Michael J. 
Published: February 2019

AbstractBackgroundNeuroscientists routinely seek to identify and remove noisy or artifactual observations from their data. They do so guided by the belief that including such data would reduce power to detect effects of interest. Whereas standard methods can exclude certain well defined noise sources (e.g., line noise), most forms of noise do not easily separate from signals of interest. Here we ask how well methods routinely used to “clean” human electrophysiological recordings actually boost power to detect brain-behavior correlations.New MethodThis, to the authors’ knowledge, is the first large-scale study of the impact of intracranial EEG preprocessing on brain state classification.ResultsWe find that several commonly used data cleaning methods (automated methods based on statistical properties of the signal and manual methods based on expert review) reduce statistical power for both univariate and multivariate classification of successful memory encoding, a behavioral state with very well-characterized electrophysiological biomarkers.Comparison with Existing MethodsBy reallocating resources towards collecting more within-patient data instead of attempting to “clean” data, neuroscientists may see increases in the statistical power to detect physiological phenomena.ConclusionsThese findings highlight the challenge of partitioning signal and noise in the analysis of brain-behavior relations. They also prescribe increases in sample size and numbers of observations, rather than data cleaning, as the best approach to improving statistical power.
Multiplex immunofluorescence methods in neurodegenerative diseases
Authors: Ehrenberg Alexander J. , Morales Dulce Ovando , Tejedor Jorge Santos , Mulder Jan , Grinberg Lea T. 
Published: February 2019

AbstractThe application of multiplex immunofluorescence to human post-mortem tissue would drive observational studies of selective vulnerability in neurodegenerative proteinopathies. Efficient elution of antibodies is critical for flexibility of antibody combinations and the ability to utilize a sample in multiple rounds of immunostaining. Here, we test two elution strategies for antibodies relevant to the study of selective vulnerability in neurodegenerative diseases in post-mortem human samples from both long-fixed and short-fixed tissue. Both 2-Mercaptoethanol/SDS-based and Urea/SDS/Glycine-based elution strategies work well with the antibodies selected, confirming observations from previous studies with other antibody types.
Socioeconomic and Genomic Roots of Verbal Ability
Authors: Guo Guang , Lin Meng-Jung , Harris Kathleen M. 
Published: February 2019

ABSTRACTCognitive ability is one of the most potent and contentious human traits. Many issues surrounding cognitive ability especially those related to heredity is highly charged. Yet, all of the discussion on heredity has been based on non-DNA evidence. It is largely neglected that DNA and environmental data at individual level are indispensable for understanding the development of cognitive ability. In this article, we report findings from a study that uses both ability-related polygenic scores (PGSs) and a rich set of socioeconomic measures from Add Health. In an all-ethnicity sample excluding blacks, a social-science model predicts verbal ability well yielding an R2 of 17.5%. Adding two ability-related PGSs increases this R2 by 1.7%. Such models yield more accurate estimates of the effects of the PGSs and those of SES context, and provide an estimated degree to which SES context is influenced by parental genomes. Schooling and neighborhood remain important to verbal ability even after an early measure of verbal ability is adjusted in the model. Although the influence from the genome is evident, the influences of SES context are critical and cannot be dismissed.
When expectations are not met: unraveling the computational mechanisms underlying the effect of expectation on perceptual thresholds
Authors: Urgen Buse M. , Boyaci Huseyin 
Published: February 2019

AbstractExpectations and prior knowledge strongly affect and even shape our visual perception. Specifically, valid expectations speed up perceptual decisions, and determine what we see in a noisy stimulus. Bayesian models have been remarkably successful to capture the behavioral effects of expectation. On the other hand several more mechanistic neural models have also been put forward, which will be referred as “predictive computation models” here. Both Bayesian and predictive computation models treat perception as a probabilistic inference process, and combine prior information and sensory input. Despite the well-established effects of expectation on recognition or decision-making, its effects on low-level visual processing, and the computational mechanisms underlying those effects remain elusive. Here we investigate how expectations affect early visual processing at the threshold level. Specifically, we measured temporal thresholds (shortest duration of presentation to achieve a certain success level) for detecting the spatial location of an intact image, which could be either a house or a face image. Task-irrelevant cues provided prior information, thus forming an expectation, about the category of the upcoming intact image. The validity of the cue was set to 100, 75 and 50% in different experimental sessions. In a separate session the cue was neutral and provided no information about the category of the upcoming intact image. Our behavioral results showed that valid expectations do not reduce temporal thresholds, rather violation of expectation increases the thresholds specifically when the expectation validity is high. Next, we implemented a recursive Bayesian model, in which the prior is first set using the validity of the specific experimental condition, but in subsequent iterations it is updated using the posterior of the previous iteration. Simulations using the model showed that the observed increase of the temporal thresholds in the unexpected trials is not due to a change in the internal parameters of the system (e.g. decision threshold or internal uncertainty). Rather, further processing is required for a successful detection when the expectation and actual input disagree. These results reveal some surprising behavioral effects of expectation at the threshold level, and show that a simple parsimonious computational model can successfully predict those effects.
Metabolome-Wide Mendelian Randomization Analysis of Emotional and Behavioral Responses to Traumatic Stress
Authors: Carvalho Carolina Muniz , Wendt Frank R. , Stein Dan J. , Stein Murray B. , Gelernter Joel , Belangero Sintia I. , Polimanti Renato 
Published: February 2019

AbstractTrauma exposure is an important risk factor for several psychiatric disorders; however, the mechanisms that underlie emotional and behavioral responses to traumatic stress are unclear. To understand these mechanisms, this study investigated the genetic overlap and causal relationship between blood metabolites and traits related to trauma response using genome-wide data. Five traits related to trauma response “in the past month” ascertained in the UK Biobank (52 816<N<117 900 individuals) were considered: i) “Avoided activities or situations because of previous stressful experience” (Avoidance); ii) “Felt distant from other people” (Distant); iii) “Felt irritable or had angry outbursts” (Irritable); iv) “Felt very upset when reminded of stressful experience” (Upset); v) “Repeated disturbing thoughts of stressful experience” (Repeated Thoughts). These were investigated with respect to 52 metabolites assessed using nuclear magnetic resonance metabolomics in a previous genome-wide association study (up to 24,925 individuals of European descent). Applying linkage disequilibrium score regression (LDSC), polygenic risk scoring (PRS), and Mendelian randomization (MR), we observed that 14 metabolites were significantly correlated with trauma response traits (p<0.05); PRS of 4 metabolites (citrate (CIT); glycoprotein acetyls (GP); concentration of large very-low-density lipoproteins (VLDL) particles (LVLDLP); total cholesterol in medium particles of VLDL (MVLDLC)) were associated with traits related to trauma response (false discovery rate Q<10%). These associations were partially due to causal relationships (CIT→Upset β=-0.058, p=9.1×10−4; GP→Avoidance β=0.008, p=0.003; LVLDLP→Distant β=0.008, p=0.022; MVLDLC→Avoidance β=0.019, p=3×10−4). No reverse associations were observed. In conclusion, the genetics of certain blood-metabolites are potentially implicated in the response to traumatic experience.
Distinct cytoskeletal proteins define zones of enhanced cell wall synthesis inHelicobacter pylori
Authors: Taylor Jennifer A. , Bratton Benjamin P. , Sichel Sophie R. , Blair Kris M. , Jacobs Holly M. , DeMeester Kristen E. , Kuru Erkin , Gray Joe , Biboy Jacob , VanNieuwenhze Michael S. , Vollmer Waldemar , Grimes Catherine L. , Shaevitz Joshua W. , Salama Nina R. 
Published: February 2019

AbstractHelical cell shape is necessary for efficient stomach colonization byHelicobacter pylori, but the molecular mechanisms for generating helical shape remain unclear. We show that the helical centerline pitch and radius of wild-typeH. pyloricells dictate surface curvatures of considerably higher positive and negative Gaussian curvatures than those present in straight- or curved-rod bacteria. Quantitative 3D microscopy analysis of short pulses with eitherN-acetylmuramic acid or D-alanine metabolic probes showed that cell wall growth is enhanced at both sidewall curvature extremes. Immunofluorescence revealed MreB is most abundant at negative Gaussian curvature, while the bactofilin CcmA is most abundant at positive Gaussian curvature. Strains expressing CcmA variants with altered polymerization properties lose helical shape and associated positive Gaussian curvatures. We thus propose a model where CcmA and MreB promote PG synthesis at positive and negative Gaussian curvatures, respectively, and that this patterning is one mechanism necessary for maintaining helical shape.
Cryptochromes-mediated Inhibition of the CRL4Cop1-Complex Assembly Defines an Evolutionary Conserved Signaling Mechanism
Authors: Rizzini Luca , Levine Daniel C. , Perelis Mark , Bass Joseph , Peek Clara B. , Pagano Michele 
Published: February 2019

AbstractIn plants, Cryptochromes are photoreceptors that negatively regulate CRL4Cop1(Cul4-RING ubiquitin ligase and its substrate receptor Cop1). In mammals, Cryptochromes are core components of the circadian clock and repressors of the glucocorticoid receptor (GR). Moreover, mammalian Cryptochromes lost their ability to interact with Cop1, suggesting that they are unable to inhibit CRL4Cop1. Contrary to this assumption, we found that mammalian Cryptochromes are also negative regulators of CRL4Cop1and through this mechanism they repress the GR transcriptional network both in cultured cells and in mouse liver. Mechanistically, Cryptochromes inactivate Cop1 by interacting with Det1, a specific subunit of the mammalian CRL4Cop1complex. Through this interaction, the ability of Cop1 to join the CRL4 complex is inhibited; therefore, its substrates accumulate. Thus, the interaction between Cryptochromes and Det1 in mammals mirrors the interaction between Cryptochromes and Cop1in planta,pointing to a common ancestor in which the cryptochrome-Cop1 axis originated.
Habitat type and interannual variation shape unique fungal pathogen communities on a California native bunchgrass
Authors: Farner Johannah E. , Spear Erin R. , Mordecai Erin A. 
Published: February 2019

AbstractThe role of infectious disease in regulating host populations is increasingly recognized, but how environmental conditions affect pathogen communities and infection levels remains poorly understood. Over three years, we compared foliar disease burden, fungal pathogen community composition, and foliar chemistry in the perennial bunchgrassStipa pulchraoccurring in adjacent serpentine and nonserpentine grassland habitats with distinct soil types and plant communities. We found that serpentine and nonserpentineS. pulchraexperienced consistent, low disease pressure associated with distinct fungal pathogen communities with high interannual species turnover. Additionally, plant chemistry differed with habitat type. The results indicate that this species experiences minimal foliar disease associated with diverse fungal communities that are structured across landscapes by spatially and temporally variable conditions. Distinct fungal communities associated with different growing conditions may shieldS. pulchrafrom large disease outbreaks, contributing to the low disease burden observed on this and other Mediterranean grassland species.
Measuring phenotypic heterogeneity in isogenic bacterial populations using flow cytometry and Raman spectroscopy
Authors: García-Timermans Cristina , Rubbens Peter , Heyse Jasmine , Kerckhof Frederiek-Maarten , Props Ruben , Skirtach Andre G. , Waegeman Willem , Boon Nico 
Published: February 2019

AbstractInvestigating phenotypic heterogeneity can help to better understand and manage microbial communities. However, characterizing phenotypic heterogeneity remains a challenge, as there is no standardized analysis framework. Several optical tools are available, which often describe properties of the individual cell. In this work, we compare Raman spectroscopy and flow cytometry to study phenotypic heterogeneity in bacterial populations. The growth phase ofE. colipopulations was characterized using both technologies. Our findings show that flow cytometry detects and quantifies shifts in phenotypic heterogeneity at the population level due to its high-throughput nature. Raman spectroscopy, on the other hand, offers a much higher resolution at the single-cell level (i.e. more biochemical information is recorded). Therefore, it is capable of identifying distinct phenotypic populations when coupled with standardized data analysis. In addition, it provides information about biomolecules that are present, which can be linked to cell functionality. We propose an automated workflow to distinguish between bacterial phenotypic populations using Raman spectroscopy and validated this approach with an external dataset. We recommend to apply flow cytometry to characterize phenotypic heterogeneity at the population level, and Raman spectroscopy to perform a more in-depth analysis of heterogeneity at the single-cell level.ImportanceSingle-cell techniques are frequently applied tools to study phenotypic characteristics of bacterial populations. As flow cytometry and Raman spectroscopy gain popularity in the field, there is a need to understand their advantages and limitations, as well as to create a more standardized data analysis framework. Our work shows that flow cytometry allows to study and quantify shifts at the bacterial population level, but since its resolution is limited for microbial purposes, distinct phenotypic populations cannot be distinguished at the single-cell level. Raman spectroscopy, combined with appropriate data analysis, has sufficient resolving power at the single-cell level, enabling the identification of distinct phenotypic populations. As regions in a Raman spectrum are associated with specific (bio)molecules, it is possible to link these to the cell state and/or its function.
Characterization of Intellectual disability and Autism comorbidity through gene panel sequencing
Authors: Aspromonte Maria Cristina , Bellini Mariagrazia , Gasparini Alessandra , Carraro Marco , Bettella Elisa , Polli Roberta , Cesca Federica , Bigoni Stefania , Boni Stefania , Carlet Ombretta , Negrin Susanna , Mammi Isabella , Milani Donatella , Peron Angela , Sartori Stefano , Toldo Irene , Soli Fiorenza , Turolla Licia , Stanzial Franco , Benedicenti Francesco , Marino-Buslje Cristina , Tosatto Silvio C.E. , Murgia Alessandra , Leonardi Emanuela 
Published: February 2019

ABSTRACTIntellectual disability (ID) and autism spectrum disorder (ASD) are clinically and genetically heterogeneous diseases. Recent whole exome sequencing studies indicated that genes associated with different neurological diseases are shared across disorders and converge on common functional pathways. Using the Ion Torrent platform, we developed a low-cost next generation sequencing (NGS) gene panel that has been transferred into clinical practice, replacing single disease gene analyses for the early diagnosis of individuals with ID/ASD. The gene panel was designed using an innovativein silicoapproach based on disease networks and mining data from public resources to score disease-gene associations. We analyzed 150 unrelated individuals with ID and/or ASD and a confident diagnosis has been reached in 26 cases (17%). Likely pathogenic mutations have been identified in another 15 patients, reaching a total diagnostic yield of 27%. Our data also support the pathogenic role of genes recently proposed to be involved in ASD. Although many of the identified variants need further investigation to be considered disease-causing, our results indicate the efficiency of the targeted gene panel on the identification of novel and rare variants in patients with ID and ASD.
A large self-transmissible plasmid from Nigeria confers resistance to multiple antibacterials without a carrying cost
Authors: Monárrez Rubén , Braun Molly , Coburn-Flynn Olivia , Botelho João , Odeotyin Babatunde W. , Otero-Vera Jose I. , Quartey Naa Kwarley , Peixe Luísa , Aboderin A. Oladipo , Okeke Iruka N. 
Published: February 2019

AbstractAntimicrobial resistance is rapidly expanding, in a large part due to mobile genetic elements. We screened 94 fecal fluoroquinolone-resistantEscherichia coliisolates from Nigeria for six plasmid-mediated quinolone resistance (PMQR) genes. Sixteen isolates harbored at least one of the PMQR genes and four were positive foraac-6-Ib-cr. In one strain,aac-6-Ib-crwas mapped to a 125 Kb self-transmissible IncFII plasmid, pMB2, which also bearsblaCTX-M-15, seven other functional resistance genes and multiple resistance pseudogenes. We hypothesized that pMB2 had been selected by antimicrobials and that its large size would confer a growth disadvantage. However, laboratory strains carrying pMB2 grew at least as fast as isogenic strains lacking the plasmid in both rich and minimal media. We excised a 32 Kb fragment containing thesitABCDand another putative transporter,pefB, apapBhomolog, and several open-reading frames of unknown function. The resulting 93 Kb mini-plasmid conferred slower growth rates and lower fitness than wildtype pMB2. Trans-complementing the deletion with the clonedsitABCDgenes confirmed that they accounted for the growth advantage conferred by pMB2 in iron-depleted media. The mini-plasmid additionally conferred autoaggregation and was less transmissible and both phenotypes could be complemented with apefBclone. pMB2 is a large plasmid with a flexible resistance region that contains multiple loci that can account for evolutionary success in the absence of antimicrobials. Ancillary functions conferred by resistance plasmids can mediate their retention and transmissibility, worsening the trajectory for antimicrobial resistance and potentially circumventing efforts to contain resistance through restricted use.
Mutation of the ATPase domain of MutS homolog-5 (MSH5) reveals a requirement for a functional MutSγ complex for all crossovers in mammalian meiosis
Authors: Milano Carolyn R. , Holloway J. Kim , Zhang Yongwei , Jin Bo , Bergman Aviv , Edelmann Winfried , Cohen Paula E. 
Published: February 2019

ABSTRACTDuring meiosis, induction of DNA double strand breaks (DSB) leads to recombination between homologous chromosomes, resulting in crossovers (CO) and non-crossovers (NCO). Only 10% DSBs resolve as COs, mostly through a class I pathway dependent on MutSγ (MSH4/ MSH5). Class II CO events represent a minor proportion of the total CO count and also arise from DSBs, but are not thought to involve MutSγ. However, loading of MutSγ occurs very early in prophase I at a frequency that far exceeds the final number of class I COs found in late prophase I. Moreover, loss of MutSγ in mouse results in apoptosis before CO formation, preventing analysis of its CO function. We generated a mutation in the ATP binding domain ofMsh5(Msh5GA). While this mutation was not expected to affect MutSγ complex formation, MutSγ foci do not accumulate during prophase I. Nevertheless, while some spermatocytes fromMsh5-/-animals progress into pachynema, most spermatocytes fromMsh5GA/GAmice progress to late pachynema and beyond. Some spermatocytes fromMsh5GA/GAmice complete prophase I entirely, allowing for the first time an assessment of MSH5 function in CO formation. At pachynema,Msh5GA/GAspermatocytes show persistent DSBs, incomplete homolog pairing, and fail to accumulate MutLγ (MLH1/MLH3). Unexpectedly,Msh5GA/GAdiakinesis-staged spermatocytes have no chiasmata at all from any CO pathway, indicating that a functional MutSγ complex in early prophase I is a pre-requisite for all COs.ARTICLE SUMMARYMSH4/MSH5 are critical components of the class I crossover (CO) machinery, which is responsible for >90% of the COs that arise in mammalian meiosis. We generated a point mutation in the ATP binding motif ofMsh5, and found that mutant spermatocytes lose all COs, not just those arising from the class I pathway.