bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novoassembly and phasing of dikaryotic genomes from two isolates ofPuccinia coronataf. sp.avenae, the causal agent of oat crown rust
Authors: Miller Marisa E. , Zhang Ying , Omidvar Vahid , Sperschneider Jana , Schwessinger Benjamin , Raley Castle , Palmer Jonathan M. , Garnica Diana , Upadhyaya Narayana , Rathjen John , Taylor Jennifer M. , Park Robert F. , Dodds Peter N. , Hirsch Cory D. , Kianian Shahryar F. , Figueroa Melania 
Published: August 2017

AbstractOat crown rust, caused by the fungusPuccinia coronataf. sp.avenae(Pca), is a devastating disease that impacts worldwide oat production. For much of its life cycle,Pcais dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguousde novogenome assemblies of twoPcaisolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for a total assembly length of 99.16 Mbp for 12SD80 and 777 primary contigs with a total length of 105.25 Mbp for 12NC29, and approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of co-expressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms inPca.ImportanceDisease management strategies for oat crown rust are challenged by the rapid evolution ofPuccinia coronataf. sp.avenae(Pca), which renders resistance genes in oat varieties ineffective. Despite the economic importance of understandingPca, resources to study the molecular mechanisms underpinning pathogenicity and emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle ofPcaas well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations ofPca.
Primary cilia mediate diverse kinase inhibitor resistance mechanisms in cancer
Authors: Jenks Andrew D. , Vyse Simon , Wong Jocelyn P. , Keller Deborah , Burgoyne Tom , Shoemark Amelia , de la Roche Maike , Tsalikis Athanasios , Michaelis Martin , Cinatl Jindrich , Huang Paul H. , Tanos Barbara E. 
Published: August 2017

AbstractPrimary cilia are microtubule-based organelles that detect mechanical and chemical stimuli. Although cilia house a number of oncogenic molecules (including Smoothened, KRAS, EGFR, and PDGFR), their precise role in cancer remains unclear. We have interrogated the role of cilia in acquired andde novoresistance to a variety of kinase inhibitors, and found that in several examples, resistant cells are distinctly characterized by an increase in the number and/or length of cilia with altered structural features. Changes in cilia length seem to be linked to the lack of recruitment of Kif7 and IFT81 to cilia tips, and result in enhanced hedgehog pathway activation. Notably, Kif7 knockdown is sufficient to confer drug resistance in drug sensitive cells. Conversely, targeting of cilia length or integrity through genetic and pharmacological approaches overcomes kinase inhibitor resistance. The identification of a broad mechanism of pathway-unbiased drug resistance, represents a major advancement in oncology, and helps define a specific and important role for cilia in human cancer.
Prevalence ofMycoplasma genitaliumin different population groups: systematic review and meta-analysis
Authors: Baumann Lukas , Cina Manuel , Egli-Gany Dianne , Goutaki Myrofora , Halbeisen Florian , Lohrer Gian-Reto , Ali Hammad , Scott Pippa , Low Nicola 
Published: August 2017

AbstractBackgroundMycoplasma genitaliumis a common cause of non-gonococcal non-chlamydial urethritis and cervicitis. Testing of asymptomatic populations has been proposed, but prevalence rates in asymptomatic populations are not well established. We aimed to estimate the prevalence ofM. genitaliumin adults in the general population, in clinic-based samples, pregnant women, men who have sex with men (MSM) and female sex workers (FSW).MethodsWe searched Embase, Medline, IndMED, AIM and LILACS from 1 January 1991 to 12 July 2016 without language restrictions. We included studies with 500 participants or more. We screened and selected studies and extracted data in duplicate. We examined eligible studies in forest plots and conducted random effects meta-analysis to estimate prevalence, if appropriate. Between study heterogeneity was examined using the I2statistic and meta-regression.ResultsOf 3,316 screened records, 63 were included. In randomly selected samples from the general population, the summary prevalence estimate was 1.3% (95% confidence intervals, CI 1.0 to 1.8%, I241.5%, 3 studies) in countries with higher levels of development and 3.9% (95% CI 2.2 to 6.7, I289.2%, 3 studies) in countries with lower levels. Prevalence estimates were similar in women and men (p=0.47). In clinic-based samples prevalence estimates were higher, except in asymptomatic patients (0.8%, 95% CI 0.4 to 1.4, I20.0%, 3 studies). Summary prevalence estimates were: pregnant women 0.9% (95% CI 0.6 to 1.4%, I20%, 4 studies); MSM in the community 3.2% (95% CI 2.1 to 5.1, I278.3%, 5 studies); FSW in the community 15.9% (95% CI 13.5 to 18.9, I2=79.9%, 4 studies).DiscussionThis systematic review can inform testing guidelines forM. genitaliuminfection. The low estimated prevalence ofM. genitaliumin the general population, pregnant women and asymptomatic attenders at clinics does not support expansion of testing to asymptomatic people in these groups.Registration NumbersPROSPERO: CRD42015020420
Notos - a Galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types
Authors: Bulla Ingo , Aliaga Benoît , Lacal Virginia , Bulla Jan , Grunau Christoph , Chaparro Cristian 
Published: August 2017

AbstractBackgroundDNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it remains challenging to infer kingdom-wide general rules about the functions and evolutionary conservation of DNA methylation. Methylated cytosine is often found in specific CpN dinucleotides, and the frequency distributions of, for instance, CpG observed/expected (CpG o/e) ratios have been used to infer DNA methylation types based on higher mutability of methylated CpG.ResultsPredominantly model-based approaches essentially founded on mixtures of Gaussian distributions are currently used to investigate questions related to the number and position of modes of CpG o/e ratios. These approaches require the selection of an appropriate criterion for determining the best model and will fail if empirical distributions are complex or even merely moderately skewed. We use a kernel density estimation (KDE) based technique for robust and precise characterization of complex CpN o/e distributions withouta prioriassumptions about the underlying distributions.ConclusionsWe show that KDE delivers robust descriptions of CpN o/e distributions. For straightforward processing, we have developed a Galaxy tool, called Notos and available at the ToolShed, that calculates these ratios of input FASTA files and fits a density to their empirical distribution. Based on the estimated density the number and shape of modes of the distribution is determined, providing a rational for the prediction of the number and the types of different methylation classes. Notos is written in R and Perl.
The 10,000 Immunomes Project: A resource for human immunology
Authors: Zalocusky Kelly A. , Kan Matthew J. , Hu Zicheng , Dunn Patrick , Thomson Elizabeth , Wiser Jeffrey , Bhattacharya Sanchita , Butte Atul J. 
Published: August 2017

AbstractNew immunological assays now enable rich measurements of human immune function, but difficulty attaining enough measurements across sufficiently large and diverse cohorts has hindered describing normal human immune physiology on a large scale. Here we present the 10,000 Immunomes Project (10KIP), a diverse human immunology reference derived from over 44,000 individuals across 242 studies from ImmPort, a publicly available resource of raw immunology study data and protocols. We carefully curated datasets, aggregating subjects from healthy/control arms and harmonizing data across studies. We demonstrate 10KIP’s utility by describing variations in serum cytokines and leukocytes by age, race, and sex; defining a baseline cell-cytokine network; and using 10KIP as a common control to describe immunologic changes in pregnancy. Subject-level data is available for interactive visualization and download athttp://10kImmunomes.org/. We believe 10KIP can serve as a common control cohort and will accelerate hypothesis generation by clinical and basic immunologists across diverse populations.One Sentence SummaryAn open online resource of human immunology data from more than 10,000 normal subjects including interactive data visualization and download enables a new look at immune system differences across age and sex, rapid hypothesis generation, and creation of custom control cohorts.
MicroRNAs from the parasitic plantCuscuta campestristarget host messenger RNAs
Authors: Shahid Saima , Kim Gunjune , Johnson Nathan R. , Wafula Eric , Wang Feng , Coruh Ceyda , Bernal-Galeano Vivian , Phifer Tamia , dePamphilis Claude W. , Westwood James H. , Axtell Michael J. 
Published: August 2017

First paragraphDodders (Cuscutaspp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bi-directional movement of viruses, proteins, and mRNAs between host and parasite1, but the functional effects of these movements are not clear. Here we show thatC. campestrishaustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizingArabidopsis thalianahosts. Many of these miRNAs are 22 nts long, a usually rare size of plant miRNA associated with amplification of target silencing through secondary small interfering RNA (siRNA) production2. SeveralA. thalianamRNAs are targeted byC. campestris22 nt miRNAs during parasitism, resulting in mRNA cleavage, secondary siRNA production, and decreased mRNA accumulation levels. Hosts with mutations in two of the targets supported significantly higher growth ofC. campestris.Homologs of target mRNAs from diverse plants also have predicted target sites to inducedC. campestrismiRNAs, and the same miRNAs are expressed and active against host targets whenC. campestrisparasitizes a different host,Nicotiana benthamiana. These data show thatC. campestrismiRNAs act astrans-species regulators of host gene expression, and suggest that they may act as virulence factors during parasitism.
Stable representation of sounds in the posterior striatum during flexible auditory decisions
Authors: Guo Lan , Walker William I. , Ponvert Nicholas D. , Penix Phoebe L. , Jaramillo Santiago 
Published: August 2017

AbstractThe neuronal pathways that link sounds to rewarded actions remain elusive. It is unclear whether neurons in the posterior tail of the dorsal striatum (which receive direct input from the auditory system) mediate action selection, as other striatal circuits do. Here, we examined the role of posterior striatal neurons in auditory decisions in mice. We found that, in contrast to the anterior dorsal striatum, activation of the posterior striatum did not elicit systematic movement. However, activation of posterior striatal neurons during sound presentation in an auditory discrimination task biased the animals’ choices, and transient inactivation of these neurons largely impaired sound discrimination. Moreover, the activity of these neurons reliably encoded stimulus features, but was only minimally influenced by the animals’ choices. Our results suggest that posterior striatal neurons play an essential role in auditory decisions, yet these neurons provide sensory information downstream rather than motor commands during well-learned sound-driven tasks.
Ventral hippocampal CA1 and CA3 differentially mediate learned approach-avoidance conflict processing
Authors: Schumacher Anett , Villaruel Franz R. , Riaz Sadia , Lee Andy C. H. , Ito Rutsuko 
Published: August 2017

AbstractThe ventral hippocampus is thought to play a key role in the resolution of approach-avoidance conflict, a scenario that arises when stimuli with opposing valences are present simultaneously. Little is known, however, about the contributions of specific hippocampal sub-regions in this process, a critical issue given the functional and anatomical heterogeneity of this structure. Using a non-spatial cue-based paradigm in rats, we found that transient pharmacological inactivation of ventral CA1 produced an avoidance of a conflict cue imbued with both learned positive and negative outcomes, whereas inactivation of the ventral CA3 resulted in the opposite pattern of behavior, with significant preference for the conflict cue. In contrast, dorsal CA1- and CA3- inactivated rats showed no change in conflict behavior. Our findings provide important insight into the functions and circuitry of the ventral hippocampus by demonstrating that the ventral CA1 and CA3 subserve distinct and opposing roles in approach-avoidance conflict processing.Grant sponsorNatural Science and Engineering Research Council (N.S.E.R.C) of Canada awarded to RI (402642) and ACHL (402651).
Low Perfusion Compartments in Glioblastoma Quantified by Advanced Magnetic Resonance Imaging and Correlated with Patient Survival
Authors: Li Chao , Yan Jiun-Lin , Torheim Turid , McLean Mary A. , Boonzaier Natalie R. , Huang Yuan , Yuan Jianmin , Van Dijken Bart RJ , Matys Tomasz , Markowetz Florian , Price Stephen J. 
Published: August 2017

AbstractBackgroundGlioblastoma exhibits profound intratumoral heterogeneity in blood perfusion, which may cause inconsistent therapy response. Particularly, low perfusion may create hypoxic microenvironment and induce resistant clones. Thus, developing validated imaging approaches that define low perfusion compartments is crucial for clinical management.MethodsA total of 112 newly-diagnosed supratentorial glioblastoma patients were prospectively recruited for maximal safe resection. Preoperative MRI included anatomical, dynamic susceptibility contrast (DSC), diffusion tensor imaging (DTI) and chemical shift imaging (CSI). The apparent diffusion coefficient (ADC) and relative cerebral blood volume (rCBV) were calculated from DTI and DSC respectively. Using thresholding methods, two low perfusion compartments (ADCH-rCBVLand ADCL-rCBVL) were identified. Volumetric analysis was performed. Lactate and macromolecule/lipid levels were determined from multivoxel spectroscopy. Progression-free survival (PFS) and overall survival (OS) were analysed using Kaplan-Meier and multivariate Cox regression analyses.ResultsTwo compartments displayed higher lactate and macromolecule/lipid levels than normal controls (eachP< 0.001), suggesting hypoxic and pro-inflammatory microenvironment. The proportional volume of ADCL-rCBVLcompartment was associated with a larger infiltration area (P< 0.001, rho = 0.42). Lower lactate in this compartment was associated with a less invasive phenotype visualized on DTI. Multivariate Cox regression showed higher lactate level in the ADCL-rCBVLcompartment was associated with a worse survival (PFS: HR 2.995,P= 0.047; OS: HR 4.974,P= 0.005).ConclusionsThe ADCL-rCBVLcompartment represent a treatment resistant sub-region associated with glioblastoma invasiveness. This approach was based on clinically available imaging modalities and could thus provide crucial pretreatment information for clinical decision making.
Predictive feedback to V1 dynamically updates with sensory input
Authors: Edwards Grace , Vetter Petra , McGruer Fiona , Petro Lucy S. , Muckli Lars 
Published: August 2017

AbstractPredictive coding theories propose that the brain creates internal models of the environment to predict upcoming sensory input. Hierarchical predictive coding models of vision postulate that higher visual areas generate predictions of sensory inputs and feed them back to early visual cortex. In V1, sensory inputs that do not match the predictions lead to amplified brain activation, but does this amplification process dynamically update to new retinotopic locations with eye-movements? We investigated the effect of eye-movements in predictive feedback using functional brain imaging and eye-tracking whilst presenting an apparent motion illusion. Apparent motion induces an internal model of motion, during which sensory predictions of the illusory motion feed back to V1. We observed attenuated BOLD responses to predicted stimuli at the new post-saccadic location in V1. Therefore, pre-saccadic predictions update their retinotopic location in time for post-saccadic input, validating dynamic predictive coding theories in V1.
Synthesis, secretion, and perception of abscisic acid regulates stress responses inChlorella sorokiniana
Authors: Khasin Maya , Cahoon Rebecca E. , Alvarez Sophie , Beckeris Richard , Eyun Seong-il , Jia Qidong , Riethoven Jean-Jack , Nickerson Kenneth W. , Riekhof Wayne R. 
Published: August 2017

AbstractAbscisic acid (ABA) is a phytohormone that has been extensively characterized in higher plants for its roles in seed and bud dormancy, leaf abscission, and stress responses. Genomic studies have identified orthologs for ABA-related genes throughout theViridiplantae, including in unicellular algae; however, the role of ABA in algal physiology has not been characterized, and the existence of such a role has been a matter of dispute. In this study, we demonstrate that ABA is involved in regulating algal stress responses.Chlorella sorokinianastrain UTEX 1230 contains genes orthologous to those of higher plants which are essential for ABA biosynthesis, sensing, and degradation. RNAseq-based transcriptomic studies reveal that treatment with ABA induces dramatic changes in gene expression profiles, including the induction of a subset of genes involved in DNA replication and repair, a phenomenon which has been demonstrated in higher plants. Pretreatment ofC. sorokinianacultures with ABA exerts a protective effect on cell viability in response to ultraviolet radiation. Additionally,C. sorokinianaproduces and secretes biologically relevant amounts of both ABA and the oxylipin 12-oxo-phytodienoic acid (OPDA) into the growth medium in response to abiotic stressors. Taken together, these phenomena suggest that ABA signaling evolved as an intercellular stress response signaling molecule in eukaryotic microalgae prior to the evolution of multicellularity and colonization of land.
The influence of startReact on long-latency reflexive muscle activation during the transition from posture to movement
Authors: Honeycutt Claire F. , Ravichandran Vengateswaran J. , Perreault Eric J. 
Published: August 2017

AbstractMany motor tasks involve transitions from posture to movement such as shifting from holding an object to setting it on a surface. Although many movements are voluntary processes, they are facilitated through motor pathways that span the continuum between reflexive and voluntary control. The mechanisms driving the long-latency stretch reflex (LLSR) have remained hotly contested. Recently, startReact has been shown to influence the fast muscular response to perturbations (Ravichandran et. al. 2013). The objective of this study was to evaluate how the LLSR and startReact impact the muscular response during the transition from posture to movement. We hypothesized that both the LLSR and startReact would be involved throughout the transition from posture to movement; however there would be a clear transition from LLSR dominance during posture to startReact dominance near/during movement. We tested this hypothesis using perturbations of elbow posture at various times before a fast ballistic extension movement. We found clear evidence that both the LLSR and startReact components were influenced changes in the late long-latency time window. The results provide insights on how the nervous system regulates involuntary responses to perturbations during the transition from maintenance of arm posture to movement.New and NoteworthyWe recently demonstrated that the startReact effect, the startled release of a planned movement, can influence the muscular response during the LLSR. Here we observe how the influence of startReact can change from the transition from posture (no/little influence) to movement (strong influence). While not all paradigms trigger a startReact effect, this work demonstrates that when present startRect can have a profound effect on the overall muscle activity - even obscuring the traditional LLSR response.
Quasi-Periodic Patterns of Intrinsic Brain Activity in Individuals and their Relationship to Global Signal
Authors: Yousefi Behnaz , Shin Jaemin , Schumacher Eric H. , Keilholz Shella D. 
Published: August 2017

AbstractQuasiperiodic patterns (QPPs) as reported by Majeed et al., 2011 are prominent features of the brain’s intrinsic activity that involve important large-scale networks (default mode, DMN; task positive, TPN) and are likely to be major contributors to widely used measures of functional connectivity. We examined the variability of these patterns in 470 individuals from the Human Connectome Project resting state functional MRI dataset. The QPPs from individuals can be coarsely categorized into two types: one where strong anti-correlation between the DMN and TPN is present, and another where most areas are strongly correlated. QPP type could be predicted by an individual’s global signal, with lower global signal corresponding to QPPs with strong anti-correlation. After regression of global signal, all QPPs showed strong anti-correlation between DMN and TPN. QPP occurrence and type was similar between a subgroup of individuals with extremely low motion (or even high motion) and the rest of the sample, which shows that motion is not a major contributor to the QPPs. After regression of estimates of slow respiratory and cardiac induced signal fluctuations, more QPPs showed strong anti-correlation between DMN and TPN, an indication that while physiological noise influences the QPP type, it is not the primary source of the QPP itself. QPPs were more similar for the same subjects scanned on different days than for different subjects. These results provide the first assessment of the variability in individual QPPs and their relationship to physiological parameters.