bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete assembly ofEscherichia coliST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts
Authors: Decano Arun , Ludden Catherine , Feltwell Theresa , Judge Kim , Parkhill Julian , Downing Tim 
Published: February 2019

AbstractThe incidence of infections caused by extraintestinalEscherichia coli(ExPEC) is rising globally, which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been associated with excess mortality, prolonged hospital stays and higher healthcare costs.E. coliST131 is a major ExPEC clonal group worldwide with variable plasmid composition, and has an array of genes enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genesblaCTX-M-14/15/27, which are often rearranged, amplified and translocated by mobile genetic elements (MGEs). Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow MGE structures encodingblaCTX-Mgenes to be fully determined. Here, we performed long read sequencing to decipher the genome structures of sixE. coliST131 isolated from six patients. Most long read assemblies generated entire chromosomes and plasmids as single contigs, contrasting with more fragmented assemblies created with short reads alone. The long read assemblies highlighted diverse accessory genomes withblaCTX-M-15,blaCTX-M-14andblaCTX-M-27genes identified in three, one and one isolates, respectively. One sample had noblaCTX-Mgene. Two samples had chromosomalblaCTX-M-14andblaCTX-M-15genes, and the latter was at three distinct locations, likely transposed by the adjacent MGEs: ISEcp1, IS903Band Tn2. This study showed that AMR genes exist in multiple different chromosomal and plasmid contexts even between closely-related isolates within a clonal group such asE. coliST131.ImportanceDrug-resistant bacteria are a major cause of illness worldwide and a specific subtype calledEscherichia coliST131 cause a significant amount of these infections. ST131 become resistant to treatment by modifying their DNA and by transferring genes among one another via large packages of genes called plasmids, like a game of pass-the-parcel. Tackling infections more effectively requires a better understanding of what plasmids are being exchanged and their exact contents. To achieve this, we applied new high-resolution DNA sequencing technology to six ST131 samples from infected patients and compared the output to an existing approach. A combination of methods shows that drug-resistance genes on plasmids are highly mobile because they can jump into ST131’s chromosomes. We found that the plasmids are very elastic and undergo extensive rearrangements even in closely related samples. This application of DNA sequencing technologies illustrates at a new level the highly dynamic nature of ST131 genomes.
Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria that may stimulate TLR4 receptors
Authors: Olm Matthew R. , Bhattacharya Nicholas , Crits-Christoph Alexander , Firek Brian A. , Baker Robyn , Song Yun S. , Morowitz Michael J. , Banfield Jillian F. 
Published: February 2019

AbstractNecrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in premature infants. We performed genome-resolved metagenomic analysis of 1,163 fecal samples from premature infants to identify microbial features predictive of NEC. Features considered include genes, bacterial strain types, eukaryotes, bacteriophages, plasmids and growth rates. A machine learning classifier found that samples collected prior to NEC diagnosis harbored significantly more Klebsiella, bacteria encoding fimbriae, and bacteria encoding secondary metabolite gene clusters related to quorum sensing and bacteriocin production. Notably, replication rates of all bacteria, especially Enterobacteriaceae, were significantly higher two days before NEC diagnosis. The findings uncover biomarkers that could lead to early detection of NEC and targets for microbiome-based therapeutics.
Programmable DNA cleavage by Ago nucleases from mesophilic bacteria Clostridium butyricum and Limnothrix rosea
Authors: Kuzmenko Anton , Yudin Denis , Ryazansky Sergei , Kulbachinskiy Andrey , Aravin Alexei A. 
Published: February 2019

ABSTRACTArgonaute (Ago) proteins are the key players in RNA interference in eukaryotes, where they function as RNA-guided RNA endonucleases. Prokaryotic Argonautes (pAgos) are much more diverse than their eukaryotic counterparts but their cellular functions and mechanisms of action remain largely unknown. Some pAgos were shown to use small DNA guides for endonucleolytic cleave of complementary DNA in vitro. However, previously studied pAgos from thermophilic prokaryotes function at elevated temperatures which limits their potential use as a tool in genomic applications. Here, we describe two pAgos from mesophilic bacteria, Clostridium butyricum (CbAgo) and Limnothrix rosea (LrAgo), that act as DNA-guided DNA nucleases at physiological temperatures. In contrast to previously studied pAgos, CbAgo and LrAgo can use not only 5’-phosphorylated but also 5’-hydroxyl DNA guides, with diminished precision of target cleavage. Both LrAgo and CbAgo can tolerate guide/target mismatches in the seed region, but are sensitive to mismatches in the 3’-guide region. CbAgo is highly active under a wide range of conditions and can be used for programmable endonucleolytic cleavage of both single-stranded and double-stranded DNA substrates at moderate temperatures. The biochemical characterization of mesophilic pAgo proteins paths the way for their use for DNA manipulations both in vitro and in vivo.
YAP is involved in replenishment of granule cell progenitors following injury to the neonatal cerebellum
Authors: Yang Zhaohui , Joyner Alexandra L. 
Published: February 2019

ABSTRACTThe cerebellum (CB) undergoes major rapid growth during the third trimester and early neonatal stage in humans, making it vulnerable to injuries in pre-term babies. Experiments in mice have revealed a remarkable ability of the neonatal CB to recover from injuries around birth. In particular, recovery following irradiation-induced ablation of granule cell precursors (GCPs) involves adaptive reprogramming of Nestin-expressing glial progenitors (NEPs). Sonic hedgehog signaling is required for the initial step in NEP reprogramming; however, the full spectrum of developmental signaling pathways that promote NEP-driven regeneration is not known. Since the growth regulatory Hippo pathway has been implicated in the repair of several tissue types, we tested whether Hippo signaling is involved in regeneration of the CB. Using mouse models, we found that the Hippo pathway transcriptional co-activator YAP (Yes-associated protein) but not TAZ (transcriptional coactivator with PDZ binding motif) is required in NEPs for full recovery of the CB following irradiation one day after birth. The size of the adult CB, and in particular the internal granule cell layer produced by GCPs, is significantly reduced in mutants, and the organization of Purkinje cells and Bergmann glial fibers is disrupted. Surprisingly, the initial proliferative response ofYapmutant NEPs to irradiation is normal and the cells migrate to the GCP niche, but then undergo increased cell death. Loss ofYapin NEPs or GCPs during normal development leads to only mild defects in differentiation. Moreover, loss ofTazdoes not abrogate regeneration of GCPs byYapmutant NEPs or alter development of the cerebellum. Our study provides new insights into the molecular signaling underlying postnatal cerebellar development and regeneration.
Analysis of synapse-level neuronal morphology in human post-mortem brain tissue
Authors: Das Sujan C. , Chen Danli , Callor W. Brandon , Christensen Eric , Coon Hilary , Williams Megan E. 
Published: February 2019

ABSTRACTMany cognitive and psychiatric disorders are thought to be disorders of the synapse, yet the precise synapse defects underlying these disorders remain unknown. Because synapses are highly specialized anatomical structures, defects in synapse formation and function can often be observed as changes in micro-scale neuroanatomy. Unfortunately, few methods are available for accurate analysis of synapses in human post-mortem tissues. Here, we present a new methodological pipeline for assessing synapse-level neuron morphology in human post-mortem tissue that is accurate, rapid, and relatively inexpensive. Our method uses small tissue blocks from postmortem human brains, immersion fixation, single cell resolution by dye labeling, and confocal microscopy. As proof of principle, we analyzed pre-and postsynaptic structures from hippocampi of 13 individuals aged 4 months to 71 years. Our results suggest that postsynaptic CA1 dendritic spine shape and density are stable across ages, while presynaptic DG mossy fiber boutons undergo significant structural rearrangements with normal aging. This suggests that mossy fiber synapses, which play a major role in learning and memory, remain dynamic throughout life. Importantly, we find no effect of postmortem intervals up to 28 hours on neuron morphology. Thus, the ease of our new protocol should facilitate higher powered studies of human synapse structure in healthy and diseased states.
Differential functional roles of fibroblasts and pericytes in the formation of tissue-engineered microvascular networks in vitro
Authors: Kosyakova Natalia , Kao Derek D. , López-Giráldez Francesc , Spindler Susann , Graham Morven , James Kevin J. , Shin Jee Won , Liu Xinran , Tietjen Gregory T. , Pober Jordan S. , Chang William G. 
Published: February 2019

AbstractAimsFormation of a perfusable microvascular network (μVN) is critical for tissue engineering of solid organs. Stromal cells can support endothelial cell (EC) self-assembly into a μVN, but distinct stromal cell populations may play different roles in this process. Here we investigated the effects that two widely used stromal cells populations, fibroblasts (FBs) and pericytes (PCs), have on μVN formation.Methods and resultsWe examined the effects of adding defined stromal cell populations on the self-assembly of ECs derived from human endothelial colony forming cells (ECFCs) into perfusable μVNs in fibrin gels cast within a microfluidics chamber. ECs alone fail to fully assemble a perfusable μVN. Human lung FBs stimulate the formation of EC lined μVNs within microfluidic devices. RNA-seq analysis suggested that FBs produce high levels of hepatocyte growth factor (HGF), and addition of recombinant HGF improved μVN formation within devices. Human placental PCs could not substitute for FBs, but in the presence of FBs, PCs closely associated with ECs, formed a common basement membrane, extended microfilaments intercellularly, and reduced microvessel diameters.ConclusionsDifferent stromal cell types provide different functions in microvessel assembly by ECs. FBs support μVN formation by providing paracrine growth factors whereas PCs directly interact with ECs to modify microvascular morphology.Statement of ContributionNatalia Kosyakova, Derek Kao, William G. Chang were primarily responsible for the conception, design, interpretation of experiments, and drafting of the manuscript. Francesc López-Giráldez carried out analysis of RNA-seq data. Susann Spindler and Gregory Tietjen assisted with microvessel analysis software. Morven Graham and Xinran Liu assisted with the electron microscopy. Kevin J. James and Jee Won Shin assisted with data collection. Jordan Pober assisted with a critical review of manuscript and experimental design.
CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing
Authors: de Kanter Jurrian K. , Lijnzaad Philip , Candelli Tito , Margaritis Thanasis , Holstege Frank C.P. 
Published: February 2019

ABSTRACTCell type identification is essential for single-cell RNA sequencing (scRNA-seq) studies that are currently transforming the life sciences. CHETAH (CHaracterization of cEll Types Aided by Hierarchical clustering) is an accurate cell type identification algorithm that is rapid and selective, including the possibility of intermediate or unassigned categories. Evidence for assignment is based on a classification tree of previously available scRNA-seq reference data and includes a confidence score based on the variance in gene expression per cell type. For cell types represented in the reference data, CHETAH’s accuracy is as good as existing methods. Its specificity is superior when cells of an unknown type are encountered, such as malignant cells in tumor samples which it pinpoints as intermediate or unassigned. Although designed for tumor samples in particular, the use of unassigned and intermediate types is also valuable in other exploratory studies. This is exemplified in pancreas datasets where CHETAH highlights cell populations not well represented in the reference dataset, including cells with profiles that lie on a continuum between that of acinar and ductal cell types. Having the possibility of unassigned and intermediate cell types is pivotal for preventing misclassification and can yield important biological information for previously unexplored tissues.
Human genetic disease is greatly influenced by the underlying fragility of evolutionarily ancient genes
Authors: Martin-Geary Alexandra , Reardon Mark , Keith Benjamin , Tassabehji May , Robertson David L. 
Published: February 2019

AbstractThe ability to predict disease association in human genes is enhanced by an evolutionary understanding. Importantly genes linked with heritable disease, particularly dominant disorders, tend to have undergone duplication in our early vertebrate ancestors, with a strong asymmetric relationship between disease-association within duplicate/paralog pairs. Using a novel phylogenetic approach, alongside a whole-genome comparative analysis, we show that contrary to the accepted compensatory model of disease evolution, the majority of disease-associations reside with the more evolutionary constrained gene, inferred to most closely resemble the progenitor. This indicates that the strong association between paralogs, specifically ohnologs, and dominant disorders is often a consequence of a mechanism through which pre-existing dosage sensitive/haploinsufficient genes are successfully duplicated and retained. Heritable disease is thus as much a consequence of the fragility of evolutionarily more ancient genes as compensatory mechanisms. From these findings, we demonstrate the utility of a new model with which to predict disease associated genes in the human genome.
Transient developmental increase of prefrontal activity alters network maturation and causes cognitive dysfunction in adult mice
Authors: Bitzenhofer Sebastian H. , Pöpplau Jastyn A. , Chini Mattia , Marquardt Annette , Hanganu-Opatz Ileana L. 
Published: February 2019

AbstractDisturbed neuronal activity in neuropsychiatric pathologies emerges during development and might cause multifold neuronal dysfunction by interfering with apoptosis, dendritic growth and synapse formation. However, how altered electrical activity early in life impacts neuronal function and behavior of adults is unknown. Here, we address this question by transiently increasing the coordinated activity of layer 2/3 pyramidal neurons in the medial prefrontal cortex of neonatal mice and monitoring long-term functional and behavioral consequences. We show that increased activity during early development causes premature maturation of pyramidal neurons and alters interneuron density. Consequently, reduced inhibitory feedback by fast-spiking interneurons and excitation/inhibition imbalance in prefrontal circuits of young adults result in weaker evoked synchronization in gamma frequency. These structural and functional changes ultimately lead to poorer mnemonic and social abilities. Thus, prefrontal activity during early development actively controls the cognitive performance of adults and might be critical for cognitive symptoms of neuropsychiatric diseases.
Temporal dynamics of inhalation-linked activity across defined subpopulations of mouse olfactory bulb neurons imaged in vivo
Authors: Short Shaina M. , Wachowiak Matt 
Published: February 2019

ABSTRACTIn mammalian olfaction, inhalation drives the temporal patterning of neural activity that underlies early olfactory processing, and a single inhalation of odorant is sufficient for odor perception. However, how the neural circuits that process incoming olfactory information are activated in the context of inhalation-linked dynamics remains poorly understood. To better understand early olfactory processing in vivo, we used an artificial inhalation paradigm combined with two-photon calcium imaging to compare the dynamics of activity evoked by odorant inhalation across major cell types of the mouse olfactory bulb. Transgenic models and cell-type specific genetic tools were used to express GCaMP6f or jRGECO1a in mitral and tufted cell subpopulations, olfactory sensory neurons and two major juxtaglomerular interneuron classes, and responses to a single inhalation of odorant were compared. Activity in all cell types was strongly linked to inhalation, and all cell types showed some variance in the latency, rise-times and durations of their inhalation-linked response patterns. The dynamics of juxtaglomerular interneuron activity closely matched that of sensory neuron inputs, while mitral and tufted cells showed the highest diversity in dynamics, with a range of latencies and durations that could not be accounted for by heterogeneity in the dynamics of sensory input. Surprisingly, temporal response patterns of mitral and superficial tufted cells were highly overlapping such that these two subpopulations could not be distinguished on the basis of their inhalation-linked dynamics, with the exception of a subpopulation of superficial tufted cells expressing the peptide transmitter cholecystokinin. Overall, these results support a model in which diversity in inhalation-linked patterning of OB output arises first at the level of OSN inputs to the OB and is enhanced by feedforward inhibition from juxtaglomerular interneurons which differentially impacts different subpopulations of OB output neurons.
Individual alpha frequency increases during a task but is unchanged by alpha-band flicker
Authors: Gray Michael J. , Emmanouil Tatiana A. 
Published: February 2019

AbstractVisual perception fluctuates in-synch with ongoing neural oscillations in the delta, theta, and alpha frequency bands of the human EEG. Supporting the relationship between alpha and perceptual sampling, recent work has demonstrated that variations in individual alpha frequency (IAF) correlate with the ability to discriminate one from two stimuli presented briefly in the same location. Other studies have found that after being presented with a flickering stimulus at alpha frequencies, perception of near-threshold stimuli fluctuates for a short time at the same frequency. Motivated by previous work, we were interested in whether this alpha entrainment involves shifts in IAF. While recording EEG, we tested whether two-flash discrimination (a behavioral correlate of IAF) can be influenced by ∼1s of rhythmic visual stimulation at two different alpha frequencies (8.3hz and 12.5hz). Speaking against the bottom-up malleability of IAF, we found no change in IAF during stimulation and no change in two-flash discrimination immediately afterwards. We also found synchronous activity that persisted after 12.5hz stimulation, which suggests that a separate source of alpha was entrained. Importantly, we replicated the correlation between IAF and two-flash discrimination in a no-stimulation condition, demonstrating the sensitivity of our behavioral measure. We additionally found that IAF increased during the task compared to rest, which demonstrates that IAF is influenced by top-down factors but is not involved in entrainment. In the framework of existing findings, we suggest that visual entrainment may involve ongoing perceptually-relevant oscillations from the delta to alpha frequency bands, serving to maintain rhythmic temporal expectations.
Combining Pole Placement and Online Empirical Mode Decomposition Methods to Adaptive Active Control of Structural Vibration
Authors: Massouleh S. H. Momeni , Kordkheili S. A. Hosseini , Navazi H. Mohammad , Bahai H. 
Published: February 2019

Abstract
Using a combination of the pole placement and online empirical mode decomposition (EMD) methods, a new algorithm is proposed for adaptive active control of structural vibration. The EMD method is a time-frequency domain analysis method that can be used for nonstationary and nonlinear problems. Combining the EMD method and Hilbert transform, which is called Hilbert–Huang transform, achieves a method that can be implemented to extract instantaneous properties of signals such as structural response dominant instantaneous frequencies. In the proposed algorithm, these estimated instantaneous properties are utilized to improve the pole-placement method as an adaptive active control technique. The required active control gains are obtained using a genetic algorithm scheme, and optimal gains are calculated corresponding to preselected excitation frequencies. An algorithm is also introduced to choose excitation frequencies based on online EMD method resolution. In order to investigate the efficiency of the proposed method, some case studies that include a discrete model, continuous samples of beam and plate structures, and experimental cantilevered beam are carried out, and the results of the proposed method are compared with the preset (nonadaptive) optimal gains conditions.
Effect of Surface Wave on Development of Turbulent Boundary Layer Over a Train of Rib Roughness
Authors: Singh Santosh Kumar , Raushan Pankaj Kumar , Debnath Koustuv , Mazumder B. S. 
Published: February 2019

Abstract
In this paper, detailed experimental results are reported to study the effect of the surface wave of different frequencies on unidirectional current over the bed-mounted train of rib roughness. The model roughness used in this study is transverse square ribs that lengthened across the entire width of the recirculating wave channel. The center-to-center rib pitch (P) was constant during the experiments, thus generating a broad range of near-bed flow patterns for each of the three different surface wave frequencies studied here. The relative submergence associated with the roughness height (k) was 8, which fall in the category of large roughness. Velocity measurements were conducted using acoustic Doppler velocimeter (ADV), and a surface wave of different frequencies was generated using the plunger-type wavemaker. The measured velocity data were analyzed to determine the relative importance of mean flow over the train of rib roughness. Mean velocity profiles illustrate the well-known downward shift from the flat surface data of the semi-logarithmic portion of the law of the wall. The width of the turbulent boundary layer increases with the superposition of surface wave compared to that of the current-only flow. The results also show that the mean reattachment length decreases due to the superposition of surface wave on unidirectional current.