bluuebunny/crossref_metadata_2025_split huggingface dataset:
Encapsulated mononuclear stem cells: paracrine action for the treatment of acute myocardial infarction
Authors: Tobar Santiago A. , Andrades M. , Olsen V , Silvello D. , Phaelante A , Lopes A , Biolo A , Matte U , Rohde LE , Clausell NO 
Published: October 2018

AbstractCell therapy is considered as a treatment option for acute myocardial infarction (AMI). Released molecules by cells paracrine action may promote tissue regeneration. Therefore we used bone-marrow mononuclear cells (BMMNCs) from GFP+ Wistar rats encapsulated in sodium alginate for AMI treatment. Animals were randomly allocated into groups – empty (EC); BMMNC capsules; or sham. AMI was induced by occlusion of left anterior artery and capsules were delivered intrathoracically. Troponin I was measured 24h after AMI and echocardiography was performed at 48h and 7d after AMI. On day 7 animals were euthanized and their hearts were harvested. Tissue levels of TNF-α, IL-6, IL-10, cleaved caspase-3, and catalase were measured. Technical procedures were performed by blinded operators. There was no difference in either heart morphofunctional parameters or biochemical analysis between AMI groups. We conclude that the paracrine effects of BMMNCs lacks efficacy to modulate events associated with AMI in the rat.
Old fibroblasts secrete inflammatory cytokines that drive variability in reprogramming efficiency and may affect wound healing between old individuals
Authors: Mahmoudi Salah , Mancini Elena , Moore Alessandra , Xu Lucy , Jahanbani Fereshteh , Hebestreit Katja , Srinivasan Rajini , Li Xiyan , Devarajan Keerthana , Prélot Laurie , Ang Cheen Euong , Shibuya Yohei , Benayoun Bérénice A. , Chang Anne Lynn S. , Wernig Marius , Wysocka Joanna , Longaker Michael T. , Snyder Michael P. , Brunet Anne 
Published: October 2018

AbstractAge-associated chronic inflammation (inflammaging) has emerged as a central hallmark of aging1-3, but its impact on specific cells is still largely unknown. Fibroblasts are present in all tissues and contribute to wound healing4-6. They are also the cell type that is mostly used for induced pluripotent stem cell (iPSC) reprogramming7– a process that has implications for regenerative medicine and rejuvenation strategies8-17. Here we show that primary fibroblasts from old mice secrete inflammatory cytokines and that there is an increased variability in reprogramming efficiency between fibroblast cultures from old individuals. Individual-to-individual variability is emerging as a key feature of old age18-21, which could reflect distinct aging trajectories, but the underlying causes remain unknown. To identify drivers of this variability, we perform a multi-omic assessment of young and old fibroblast cultures with different reprogramming efficiency. This approach, coupled with single cell transcriptomics, reveals that old fibroblast cultures are heterogeneous and show a greater proportion of ‘activated fibroblasts’ that secrete inflammatory cytokines, which correlates with reprogramming efficiency. We experimentally validate that activated fibroblasts express inflammatory cytokinesin vivoand that their presence is linked to enhanced reprogramming efficiency in culture. Conditioned-media swapping experiments show that extrinsic factors secreted by activated fibroblasts are more critical than intrinsic factors for the individual-to-individual variability in reprogramming efficiency, and we identify TNFα as a key inflammatory cytokine underlying this variability. Interestingly, old mice also exhibit variability in wound healing efficiencyin vivoand old wounds show an increased subpopulation of activated fibroblasts with a unique TNFα signature. Our study shows that a switch in fibroblast composition, and the ratio of inflammatory cytokines they secrete, drives variability in reprogrammingin vitroand may influence wound healingin vivo. These findings could help identify personalized strategies to improve iPSC generation and wound healing in older individuals.
Transduction of the Geomagnetic Field as Evidenced from Alpha-band Activity in the Human Brain
Authors: Wang Connie X. , Hilburn Isaac A. , Wu Daw-An , Mizuhara Yuki , Cousté Christopher P. , Abrahams Jacob N. H. , Bernstein Sam E. , Matani Ayumu , Shimojo Shinsuke , Kirschvink Joseph L. 
Published: October 2018

AbstractMagnetoreception, the perception of the geomagnetic field, is a sensory modality well-established across all major groups of vertebrates and some invertebrates, but its presence in humans has been tested rarely, yielding inconclusive results. We report here a strong, specific human brain response to ecologically-relevant rotations of Earth-strength magnetic fields. Following geomagnetic stimulation, a drop in amplitude of EEG alpha oscillations (8-13 Hz) occurred in a repeatable manner. Termed alpha event-related desynchronization (alpha-ERD), such a response is associated with sensory and cognitive processing of external stimuli. Biophysical tests showed that the neural response was sensitive to the dynamic components and axial alignment of the field but also to the static components and polarity of the field. This pattern of results implicates ferromagnetism as the biophysical basis for the sensory transduction and provides a basis to start the behavioral exploration of human magnetoreception.
Visual control of landing maneuvers in houseflies on vertical and inverted surfaces
Authors: Balebail Sujay , Raja Satish K , Sane Sanjay P. 
Published: October 2018

AbstractLanding maneuvers in flies are complex behaviors that may be conceptually decomposed into a sequence of modular behaviors such as body deceleration, extension of legs, and body rotations which are coordinated to ensure controlled touchdown. The composite nature of these behaviors means that there is variability in the kinematics of landing maneuvers, making it difficult to identify the general rules that govern this behavior. Many previous studies have relied on tethered preparations to study landing behaviors, but tethering constrains some behavioral modules to operate in an open feedback control loop while others remain in closed-loop, thereby inducing experimental artefacts. On the other hand, freely flying insects are hard to precisely control, which may also increase behavioral variability. One approach towards understanding the general rules underlying landing behavior is to determine the common elements of landing kinematics on surfaces that are oriented in different ways. We conducted a series of experiments in which the houseflies,Musca Domestica, were lured to specific visual targets on either vertical or inverted horizontal substrates. These conditions elicited landing behaviors in the flies that could be captured accurately using multiple high-speed video cameras. We filmed the houseflies landing on surfaces oriented along two directions: vertical (vertical landings), and upside down (inverted landings). Our experiments reveal that flies that are able to land feet-first in a controlled manner must satisfy specific criteria, failing which their landing performance is compromised causing their heads to bump into the surface during landing. Flies landing smoothly on both surfaces initiate deceleration at approximately fixed distances from the substrate and in direct proportion to the component of flight velocity normal to the landing surface. The ratio of perpendicular distance to the substrate and velocity at the onset of deceleration was conserved, despite the large differences in the mechanics of the vertical vs. inverted landings. Flies extend their legs independently of distance from the landing surface or their approach velocity normal to the surface, regardless of the orientation of the landing substrate. Together, these results show that the visual initiation of deceleration is robust to orientation of the landing surface, whereas the initiation of leg-extension may be context-dependent and variable which allows flies to land on substrates of various orientations in a versatile manner. These findings may also be of interest to roboticists that are interested in developing flapping robots that can land on surfaces of different orientations.
Dynamics of gene expression in single root cells ofA. thaliana
Authors: Jean-Baptiste Ken , McFaline-Figueroa José L. , Alexandre Cristina M. , Dorrity Michael W. , Saunders Lauren , Bubb Kerry L. , Trapnell Cole , Fields Stanley , Queitsch Christine , Cuperus Josh T. 
Published: October 2018

ABSTRACTSingle-cell RNA-seq can yield high-resolution cell-type-specific expression signatures that reveal new cell types and the developmental trajectories of cell lineages. Here, we apply this approach toA. thalianaroot cells to capture gene expression in 3,121 root cells. We analyze these data with Monocle 3, which orders single cell transcriptomes in an unsupervised manner and uses machine learning to reconstruct single-cell developmental trajectories along pseudotime. We identify hundreds of genes with cell-type-specific expression, with pseudotime analysis of several cell lineages revealing both known and novel genes that are expressed along a developmental trajectory. We identify transcription factor motifs that are enriched in early and late cells, together with the corresponding candidate transcription factors that likely drive the observed expression patterns. We assess and interpret changes in total RNA expression along developmental trajectories and show that trajectory branch points mark developmental decisions. Finally, by applying heat stress to whole seedlings, we address the longstanding question of possible heterogeneity among cell types in the response to an abiotic stress. Although the response of canonical heat shock genes dominates expression across cell types, subtle but significant differences in other genes can be detected among cell types. Taken together, our results demonstrate that single-cell transcriptomics holds promise for studying plant development and plant physiology with unprecedented resolution.
IsoSense: Frequency enhanced sensorless adaptive optics through structured illumination
Authors: Žurauskas Mantas , Dobbie Ian M. , Parton Richard M. , Phillips Mick A. , Göhler Antonia , Davis Ilan , Booth Martin J. 
Published: October 2018

AbstractWe present IsoSense, a wavefront sensing method that mitigates sample dependency in image based sensorless adaptive optics applications in microscopy. Our method employs structured illumination to create additional, high spatial frequencies in the image through custom illumination patterns. This improves the reliability of image quality metric calculations and enables sensorless wavefront measurement even in samples with sparse spatial frequency content. We demonstrate the feasibility of IsoSense for aberration correction in a deformable mirror based structured illumination superresolution fluorescence microscope.
Antifungal effects of 3-(4-Phenyl-thiazol-2-yl)-2-thioxo-2, 3-dihydro-1H-quinazolin-4-one against Aspergillus Species
Authors: Singh Desh D. , Tiwari V. K. , Singh Rambir , Sharam G L , Dabur Rajesh 
Published: October 2018

AbstractAspergillus infections have become an important health problem with the increasing number of patients. Available antifungal drugs are lack with their spectrum, toxic or immunosuppressive in nature, so that need to develop new compound with high efficacy. To evaluate antifungal efficacy of synthesized compound and to identify the protein profile of Aspergillus fumigatus treated with antifungal. Clinical isolates of A. fumigatus, A. flavus and A. niger were cultured and efficacy of compound were conducted by Disc Diffusion Assay (DDA), Microbroth Dilution Assay (MDA). Percent of spore germination inhibition assay (PSGI), Time kill analysis and toxicity assay. The culture filtrate containing secretory proteins was collected after 24 h growth and expression of downregulated proteins were identified. We developed a new and useful quinazoline derivatives expected to antifungal activity. The result of anti-Aspergillus evolution revealed that one of the 3-(4-Phenyl-thiazol-2-yl)-2-thioxo-2, 3-dihydro-1H-quinazolin-4-one (DDVKT4Q) exhibited appreciable activity. The potency of compound was found concentration of 3.125 µg/disc by disc diffusion assay (DDA) and 15.625 µg/ml. by Microbroth Dilution Assay (MDA). The compound was nontoxic up to concentration 625 µg/ml and its lysed only 35.9% of human erythrocytes, at the highest dose tested. It’s observed that the treatment of pathogen with DDVKT-4Q targeted the expression of four proteins having molecular weights 18 kDa 37 KDa and 43 KDa proteins was completely inhibited or down regulated by the compound the extra cellular. The novel compound DDVKT-4Q, having antifungal activity Can be exploited further to develop new ideal antimycotic drugs.
Nanoscale robots exhibiting quorum sensing
Authors: Amir Yaniv , Abu-Horowitz Almogit , Werfel Justin , Bachelet Ido 
Published: October 2018

AbstractMulti-agent systems demonstrate the ability to collectively perform complex tasks—e.g., construction1–2, search3, and locomotion4,5—with greater speed, efficiency, or effectiveness than could a single agent alone. Direct and indirect coordination methods allow agents to collaborate to share information and adapt their activity to fit dynamic situations. A well-studied example is quorum sensing (QS), a mechanism allowing bacterial communities to coordinate and optimize various phenotypes in response to population density. Here we implement, for the first time, bio-inspired QS in robots fabricated from DNA origami, which communicate by transmitting and receiving diffusing signals. The mechanism we describe includes features such as programmable response thresholds and quorum quenching, and is capable of being triggered by proximity of a specific target cell. Nanoscale robots with swarm intelligence could carry out tasks that have been so far unachievable in diverse fields such as industry, manufacturing and medicine.
Identification and characterization of Aedes albopictus long noncoding RNAs provides insights into their roles in development and flavivirus infection
Authors: Azlan Azali , Yunus Muhammad Amir , Azzam Ghows 
Published: October 2018

AbstractAedes albopictus (Ae. albopictus) is an important vector of arboviruses such as Dengue virus (DENV), Chikungunya virus (CHIKV), and Zika virus (ZIKV). Long noncoding RNA (lncRNAs) have been identified in other vectors including Aedes aegypti and Anopheles mosquitoes, few of which have been implicated in immunity and viral replication. To identify lncRNAs with potential biological functions in Ae. albopictus, we performed RNA-seq on Ae. albopictus cells infected with DENV and ZIKV, and analyzed them together with public datasets. We identified a total of 23,899 transcripts, 16,089 were intergenic while 3,126 and 4,183 of them were antisense and intronic to annotated genes respectively. Ae. albopictus lncRNAs shared many of the characteristics with their invertebrate and vertebrate counterparts, such as low expression, low GC content, short in length, and low conservation even among closely related species. Compared to protein-coding genes, lncRNAs exhibited higher tendency to be expressed in a stage-specific manner. Besides, expression of lncRNAs and nearest protein-coding genes tended to be correlated, especially for the gene pairs within 1kb from each other. We also discovered that Ae. albopictus lncRNAs have the potential to act as precursors for miRNA and piRNAs, both of which have been implicated in antiviral defense in Aedes mosquito. Upon flavivirus infection, lncRNAs were observed to be differentially expressed, which possibly indicates the involvement of lncRNAs in the host-antiviral defense. Our study provides the first systematic identification of lncRNAs in Ae. albopictus, hence, offering a foundation for future studies of lncRNA functions.
A network of transcriptional repressors mediates auxin response specificity
Authors: Truskina Jekaterina , Han Jingyi , Galvan-Ampudia Carlos S. , Lainé Stéphanie , Brunoud Géraldine , Porco Silvana , Bågman Anne-Maarit , Smit Margot E. , Bennett Malcolm , Roudier Francois , Brady Siobhan M. , Bishopp Anthony , Vernoux Teva 
Published: October 2018

INTRODUCTORY PARAGRAPHThe regulation of signalling capacity plays a pivotal role in setting developmental patterns in both plants and animals (1). The hormone auxin is a key signal for plant growth and development that acts through the AUXIN RESPONSE FACTOR (ARF) transcription factors (2). A subset of these ARFs comprises transcriptional activators of target genes in response to auxin, and are essential for regulating auxin signalling throughout the plant lifecycle (3). While ARF activators show tissue-specific expression patterns, it is unknown how their expression patterns are established. Chromatin modifications and accessibility studies revealed the chromatin of loci encoding ARF activators is constitutively open for transcription. Using a high-throughput yeast one-hybrid (Y1H) approach, we discovered a network of transcriptional regulators ofARFactivator genes fromArabidopsis thaliana. Expression analyses demonstrated that the majority of these regulators act as repressors of ARF transcriptionin planta. Our observations support a scenario where the default configuration of open chromatin enables a network of transcriptional repressors to shape the expression pattern of ARF activators and provide specificity in auxin signalling output throughout development.
Comparison of Analytical Techniques for Thermal Stability Analysis of β-Cyclodextrin for an Ebola Virus Infection Treatment
Authors: Murillo Mayte , Lodder Robert A. 
Published: October 2018

ABSTRACTEach New Drug Application filed with the Food and Drug Administration (FDA) must include the analytical procedures to ensure the identity, strength, quality, purity, and potency of a drug substance and drug product. The BSN389 drug product (being developed to treat Ebola virus infections) includes beta cyclodextrin. Evidence must be provided that the analytical procedures used in testing BSN389 meet proper standards of accuracy, sensitivity, specificity, and reproducibility and are suitable for their intended purpose. The Bootstrap Error-adjusted Single-Sample Technique (BEST) software was used to compare the quantitative and qualitative power of IR and 1H NMR to differentiate new and partially decomposed samples of beta cyclodextrin, and the best assay will be incorporated into the thermal stability protocol for ВCD.
Lexical Access in Comprehension vs. Production: Spatiotemporal Localization of Semantic Facilitation and Interference
Authors: Dirani Julien , Pylkkänen Liina 
Published: October 2018

ABSTRACTHumans understand words faster when they are preceded by semantically related words. This facilitation is thought to result from spreading activation between words with similar meanings. Interestingly, in language production, semantic relatedness often has the opposite effect: in object naming for example, a related prior word delays the naming time of the current object. This could be due to competition during conceptual search or later interference at the motor preparation stage. However, no study has systematically compared the facilitory and inhibitory effects and thus their neurobiological relationship is unknown. We contrasted maximally parallel production and comprehension tasks during magnetoencephalography and found that in comprehension (specifically word reading), semantic relatedness modulated activity in the left middle STG at 180-335ms, consistent with prior findings on the spatiotemporal localization of lexical access. In contrast, a semantic interference pattern for the production task (object naming) occurred in a post-lexical time-window at 395-485ms in left posterior insular cortex, consistent with post-lexical motor preparation. Thus, our data show that semantic priming during comprehension and interference during production are not two sides of the same coin but rather they clearly dissociate in space and time, consistent with a lexical account for comprehension and a post-lexical one for production.Significance statementThe processing of semantically related words has been a central tool for understanding the organization of the mental lexicon. One striking observation is that semantic relatedness tends to be facilitory in comprehension but inhibitory in language production, perhaps because only production involves a conceptual search through semantically related candidates. The neurobiology of this contrast is not understood. Our magnetoencephalography results demonstrate that the facilitory pattern is first observed in classic left temporal lexical access regions at ~200ms, whereas the inhibitory pattern occurs later and in the insular cortex. These findings show that the two effects do not co-localize in space or time and suggest that the inhibitory effects in production stem from a late motor preparation stage.
Navigome: Navigating the Human Phenome
Authors: Gaspar Héléna A , Hübel Christopher , Coleman Jonathan R. I. , Hanscombe Ken , Breen Gerome 
Published: October 2018

AbstractWe now have access to a sufficient number of genome-wide association studies (GWAS) to cluster phenotypes into genetic-informed categories and to navigate the “phenome” space of human traits. Using a collection of 465 GWAS, we generated genetic correlations, pathways, gene-wise and tissue-wise associations using MAGMA and S-PrediXcan for 465 human traits. Testing 7267 biological pathways, we found that only 898 were significantly associated with any trait. Similarly, out of ~20,000 tested protein-coding genes, 12,311 genes exhibited an association. Based on the genetic correlations between all traits, we constructed a phenome map using t-distributed stochastic neighbor embedding (t-SNE), where each of the 465 traits can be visualized as an individual point. This map reveals well-defined clusters of traits such as education/high longevity, lower longevity, height, body composition, and depression/anxiety/neuroticism. These clusters are enriched in specific groups of pathways, such as lipid pathways in the lower longevity cluster, and neuronal pathways for body composition or education clusters. The map and all other analyses are available in the Navigome web interface (https://phenviz.navigome.com).
Finding the P3 in the P600: Decoding shared neural mechanisms of responses to syntactic violations and oddball target detection
Authors: Sassenhagen Jona , Fiebach Christian J. 
Published: October 2018

AbstractThe P600 Event-Related Brain Potential, elicited by syntactic violations in sentences, is generally interpreted as indicating language-specific structural/combinatorial processing, with far-reaching implications for models of language. P600 effects are also often taken as evidence for language-like grammars in non-linguistic domains like music or arithmetic. An alternative account, however, interprets the P600 as a P3, a domain-general brain response to salience. Using time-generalized multivariate pattern analysis, we demonstrate that P3 EEG patterns, elicited in a visual Oddball experiment, account for the P600 effect elicited in a syntactic violation experiment: P3 pattern-trained MVPA can classify P600 trials just as well as P600-trained ones. A second study replicates and generalizes this finding, and demonstrates its specificity by comparing it to face- and semantic mismatch-associated EEG responses. These results indicate that P3 and P600 share neural patterns to a substantial degree, calling into question the interpretation of P600 as a language-specific brain response and instead strengthening its association with the P3. More generally, our data indicate that observing P600-like brain responses provides no direct evidence for the presence of language-like grammars, in language or elsewhere.