bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pax3 cooperates with Ldb1 to direct local chromosome architecture during myogenic lineage specification
Authors: Magli Alessandro , Baik June , Pota Pruthvi , Cordero Carolina Ortiz , Kwak Il-Youp , Garry Daniel J. , Love Paul E. , Dynlacht Brian D. , Perlingeiro Rita C. R. 
Published: May 2019

AbstractChromatin looping allows enhancer-bound regulatory factors to influence transcription. Large domains, referred to as topologically associated domains, participate in genome organization. However, the mechanisms underlining interactions within these domains, which control gene expression, are not fully understood. Here we report that activation of embryonic myogenesis is associated with establishment of long-range chromatin interactions centered on Pax3-bound loci. Using mass spectrometry and genomic studies, we identify the ubiquitously expressed LIM-domain binding protein 1 (Ldb1) as the mediator of looping interactions at a subset of Pax3 binding sites. Ldb1 is recruited to Pax3-bound elements independently of CTCF-Cohesin, and is necessary for efficient deposition of H3K4me1 at these sites and chromatin looping. When Ldb1 is deleted in Pax3-expressing cells in vivo, specification of migratory myogenic progenitors is severely impaired. These results highlight Ldb1 requirement for Pax3 myogenic activity and demonstrate how transcription factors can promote formation of sub-topologically associated domain interactions involved in lineage specification.
Reversal of transmission and reflection based on acoustic metagratings with integer parity design
Authors: Fu Yangyang , Shen Chen , Cao Yanyan , Gao Lei , Chen Huanyang , Chan C. T. , Cummer Steven A. , Xu Yadong 
Published: May 2019

AbstractPhase gradient metagratings (PGMs) have provided unprecedented opportunities for wavefront manipulation. However, this approach suffers from fundamental limits on conversion efficiency; in some cases, higher order diffraction caused by the periodicity can be observed distinctly, while the working mechanism still is not fully understood, especially in refractive-type metagratings. Here we show, analytically and experimentally, a refractive-type metagrating which can enable anomalous reflection and refraction with almost unity efficiency over a wide incident range. A simple physical picture is presented to reveal the underlying diffraction mechanism. Interestingly, it is found that the anomalous transmission and reflection through higher order diffraction can be completely reversed by changing the integer parity of the PGM design, and such phenomenon is very robust. Two refractive acoustic metagratings are designed and fabricated based on this principle and the experimental results verify the theory.
Role of D3 dopamine receptors in modulating neuroanatomical changes in response to antipsychotic administration
Authors: Guma Elisa , Rocchetti Jill , Devenyi Gabriel A. , Tanti Arnaud , Mathieu Axel P. , Lerch Jason P. , Elgbeili Guillaume , Courcot Blandine , Mechawar Naguib , Chakravarty M. Mallar , Giros Bruno 
Published: May 2019

AbstractClinical research has shown that chronic antipsychotic drug (APD) treatment further decreases cortical gray matter and hippocampus volume, and increases striatal and ventricular volume in patients with schizophrenia. D2-like receptor blockade is necessary for clinical efficacy of the drugs, and may be responsible for inducing these volume changes. However, the role of other D2-like receptors, such as D3, remains unclear. Following our previous work, we undertook a longitudinal study to examine the effects of chronic (9-week) typical (haloperidol (HAL)) and atypical (clozapine (CLZ)) APDs on the neuroanatomy of wild-type (WT) and dopamine D3-knockout (D3KO) mice using magnetic resonance imaging (MRI) and histological assessments in a sub-region of the anterior cingulate cortex (the prelimbic [PL] area) and striatum. D3KO mice had larger striatal volume prior to APD administration, coupled with increased glial and neuronal cell density. Chronic HAL administration increased striatal volume in both WT and D3KO mice, and reduced PL area volume in D3KO mice both at trend level. CLZ increased volume of the PL area of WT mice at trend level, but decreased D3KO PL area glial cell density. Both typical and atypical APD administration induced neuroanatomical remodeling of regions rich in D3 receptor expression, and typically altered in schizophrenia. Our findings provide novel insights on the role of D3 receptors in structural changes observed following APD administration in clinical populations.
Rapamycin modulates tissue aging and lifespan independently of the gut microbiota in Drosophila
Authors: Schinaman Joseph M. , Rana Anil , Ja William W. , Clark Rebecca I. , Walker David W. 
Published: May 2019

AbstractThe FDA approved drug rapamycin can prolong lifespan in diverse species and delay the onset of age-related disease in mammals. However, a number of fundamental questions remain unanswered regarding the mechanisms by which rapamycin modulates age-related pathophysiology and lifespan. Alterations in the gut microbiota can impact host physiology, metabolism and lifespan. While recent studies have shown that rapamycin treatment alters the gut microbiota in aged animals, the causal relationships between rapamycin treatment, microbiota dynamics and aging are not known. Here, using Drosophila as a model organism, we show that rapamycin-mediated alterations in microbiota dynamics in aged flies are associated with improved markers of intestinal and muscle aging. Critically, however, we show that the beneficial effects of rapamycin treatment on tissue aging and lifespan are not dependent upon the microbiota. Indeed, germ-free flies show delayed onset of intestinal barrier dysfunction, improved proteostasis in aged muscles and a significant lifespan extension upon rapamycin treatment. In contrast, genetic inhibition of autophagy impairs the ability of rapamycin to mediate improved gut health and proteostasis during aging. Our results indicate that rapamycin-mediated modulation of the microbiota in aged animals is not causally required to slow tissue and organismal aging.
Human skin equivalents cultured under hypoxia display enhanced epidermal morphogenesis and lipid barrier formation
Authors: Mieremet Arnout , Vázquez García Adela , Boiten Walter , van Dijk Rianne , Gooris Gert , Bouwstra Joke A. , El Ghalbzouri Abdoelwaheb 
Published: May 2019

AbstractHuman skin equivalents (HSEs) are three-dimensional cell models mimicking characteristics of native human skin (NHS) in many aspects. However, a limitation of HSEs is the altered in vitro morphogenesis and barrier formation. Differences between in vitro and in vivo skin could have been induced by suboptimal cell culture conditions, of which the level of oxygen in vitro (20%) is much higher than in vivo (0.5–8%). Our aim is to study how external oxygen levels affect epidermal morphogenesis and barrier formation in HSEs. In the present study, fibroblast and keratinocyte monocultures, and HSEs were generated under 20% (normoxia) and 3% (hypoxia) oxygen level. In all cultures under hypoxia, expression of hypoxia-inducible factor target genes was increased. Characterization of HSEs generated under hypoxia using immunohistochemical analyses of morphogenesis biomarkers revealed a reduction in epidermal thickness, reduced proliferation, similar early differentiation, and an attenuated terminal differentiation program compared to normoxia, better mimicking NHS. The stratum corneum ceramide composition was studied with liquid chromatography coupled to mass spectrometry. Under hypoxia, HSEs exhibited a ceramide composition that more closely resembles that of NHS. Consequently, the lipid organization was improved. In conclusion, epidermal morphogenesis and barrier formation in HSEs reconstructed under hypoxia better mimics that of NHS.
Monodisperse droplet formation by spontaneous and interaction based mechanisms in partitioned EDGE microfluidic device
Authors: ten Klooster S. , Sahin S. , Schroën K. 
Published: May 2019

AbstractThe partitioned EDGE droplet generation device is known for its’ high monodisperse droplet formation frequencies in two distinct pressure ranges, and an interesting candidate for scale up of microfluidic emulsification devices. In the current study, we test various continuous and dispersed phase properties and device geometries to unravel how the device spontaneously forms small monodisperse droplets (6–18 μm) at low pressures, and larger monodisperse droplets (>28 μm) at elevated pressures. For the small droplets, we show that the continuous phase inflow in the droplet formation unit largely determines droplet formation behaviour and the resulting droplet size and blow-up pressure. This effect was not considered as a factor of significance for spontaneous droplet formation devices that are mostly characterised by capillary numbers in literature. We then show for the first time that the formation of larger droplets is caused by physical interaction between neighbouring droplets, and highly dependent on device geometry. The insights obtained here are an essential step toward industrial emulsification based on microfluidic devices.
Novel multimodel ensemble approach to evaluate the sole effect of elevated CO2 on winter wheat productivity
Authors: Ahmed Mukhtar , Stöckle Claudio O. , Nelson Roger , Higgins Stewart , Ahmad Shakeel , Raza Muhammad Ali 
Published: May 2019

AbstractElevated carbon-dioxide concentration [eCO2] is a key climate change factor affecting plant growth and yield. Conventionally, crop modeling work has evaluated the effect of climatic parameters on crop growth, without considering CO2. It is conjectured that a novel multimodal ensemble approach may improve the accuracy of modelled responses to eCO2. To demonstrate the applicability of a multimodel ensemble of crop models to simulation of eCO2, APSIM, CropSyst, DSSAT, EPIC and STICS were calibrated to observed data for crop phenology, biomass and yield. Significant variability in simulated biomass production was shown among the models particularly at dryland sites (44%) compared to the irrigated site (22%). Increased yield was observed for all models with the highest average yield at dryland site by EPIC (49%) and lowest under irrigated conditions (17%) by APSIM and CropSyst. For the ensemble, maximum yield was 45% for the dryland site and a minimum 22% at the irrigated site. We concluded from our study that process-based crop models have variability in the simulation of crop response to [eCO2] with greater difference under water-stressed conditions. We recommend the use of ensembles to improve accuracy in modeled responses to [eCO2].
First use of anatomical networks to study modularity and integration of heads, forelimbs and hindlimbs in abnormal anencephalic and cyclopic vs normal human development
Authors: Diogo Rui , Ziermann Janine M. , Smith Christopher , Alghamdi Malak , Fuentes Jose S. M. , Duerinckx Andre 
Published: May 2019

AbstractThe ill-named “logic of monsters” hypothesis of Pere Alberch - one of the founders of modern evo-devo - emphasized the importance of “internal rules” due to strong developmental constraints, linked teratologies to developmental processes and patterns, and contradicted hypotheses arguing that birth defects are related to a chaotic and random disarray of developmental mechanisms. We test these hypotheses using, for the first time, anatomical network analysis (AnNA) to study and compare the musculoskeletal modularity and integration of both the heads and the fore- and hindlimbs of abnormal cyclopic trisomy 18 and anencephalic human fetuses, and of normal fetal, newborn, and adult humans. Our previous works have shown that superficial gross anatomical analyses of these specimens strongly support the “logic of monsters” hypothesis, in the sense that there is an ‘order’ or ‘logic’ within the gross anatomical patterns observed in both the normal and abnormal individuals. Interestingly, the results of the AnNA done in the present work reveal a somewhat different pattern: at least concerning the musculoskeletal modules obtained in our AnNA, we observe a hybrid between the “logic of monsters” and the “lack of homeostasis” hypotheses. For instance, as predicted by the latter hypothesis, we found a high level of left-right asymmetry in the forelimbs and/or hindlimbs of the abnormal cyclopic trisomy 18 and anencephalic human fetuses. That is, a network analysis of the organization of/connection between the musculoskeletal structures of these fetuses reveals a more “chaotic” pattern than that detected by superficial gross anatomical comparisons. We discuss the broader developmental, evolutionary, and medical implications of these results.
Physiological and morphological differences of airways between COPD and asthma–COPD overlap
Authors: Karayama Masato , Inui Naoki , Yasui Hideki , Kono Masato , Hozumi Hironao , Suzuki Yuzo , Furuhashi Kazuki , Hashimoto Dai , Enomoto Noriyuki , Fujisawa Tomoyuki , Nakamura Yutaro , Watanabe Hiroshi , Suda Takafumi 
Published: May 2019

AbstractOverlap of asthma and COPD has attracted attention recently. We aimed to clarify physiological and morphological differences of the airways between COPD and asthma–COPD overlap (ACO). Respiratory resistance and reactance and three-dimensional computed tomography data were evaluated in 167 patients with COPD. Among them, 43 patients who fulfilled the diagnosis of asthma were defined as having ACO. Among 124 patients with COPD without ACO, 86 with a comparable smoking history and airflow limitation as those with ACO were selected using propensity score matching (matched COPD). The intraluminal area (Ai) and wall thickness (WT) of third- to sixth-generation bronchi were measured and adjusted by body surface area (BSA; Ai/BSA and WT/√BSA, respectively). Patients with ACO had higher respiratory resistance and reactance during tidal breathing, but a smaller gap between the inspiratory and expiratory phases, compared with matched patients with COPD. Patients with ACO had a greater WT/√BSA in third- to fourth-generation bronchi, smaller Ai/BSA in fifth- to sixth-generation bronchi, and less emphysematous changes than did matched patients with COPD. Even when patients with ACO and those with COPD have a comparable smoking history and fixed airflow limitation, they have different physiological and morphological features of the airways.
Star clusters in the dwarf irregular galaxy Leo A
Authors: Stonkutė R. , Naujalis R. , Čeponis M. , Leščinskaitė A. , Vansevičius V. 
Published: May 2019

Context. Leo A is an isolated gas-rich dwarf irregular galaxy of low stellar mass and metallicity residing at the outskirts of the Local Group. Ages of the stellar populations in Leo A range from ∼10 Myr to ∼10 Gyr. So far, only one star cluster has been discovered in this galaxy.
Aims. Our aim is to search for star cluster candidates in the Leo A galaxy.
Methods. We performed photometry of star-like objects on HST ACS archive observation frames in the F475W and F814W passbands and studied the spatial clustering of the Leo A stars down to the turn-off point of the old stellar populations.
Results. We report the discovery of four star clusters in the Leo A galaxy. This means that now a sample of five star clusters is known in Leo A. Two clusters are of a young age (∼20 Myr; overlapping with H II regions) and low in mass (≳400 M⊙ and ≳150 M⊙), the other three clusters are older (≳100 Myr) and also of low mass (≳300 M⊙). These rough estimates are made assuming the isochrones of a metallicity derived for H II regions (Z = 0.0007). Colour–magnitude diagrams of the stars residing in the circular areas of a 2.5″ radius around the clusters and integrated aperture photometry results of the clusters are presented.
In vivo microdialysis and in vitro HPLC analysis of the impact of paeoniflorin on the monoamine levels and their metabolites in the rodent brain
Authors: Lin Yuh-Tzy , Huang Wei-Shih , Tsai Huei-Yann , Lee Min-Min , Chen Yuh-Fung 
Published: May 2019

Background: Paeoniflorin (PF) possesses several effects such as analgesic, the anti-spasmodic effect on smooth muscle. It protects the cardiovascular system and reveals the neuroprotective effect on cerebral ischemia. Monoamine system has been identified to have complex regulatory effects in pain signaling. There are no reports regarding the impact of PF on monoamine levels in the rodent brain by microdialysis. In this study, the effects of PF on monoamines and their metabolites in the rodent brain using in vivo microdialysis and in vitro high performance liquid chromatography (HPLC) analysis.
Methods: Male S.D. rats were anesthetized, fixed onto the stereotaxic instrument to identify the positions of corpus striatum and cerebral cortex. Drilled a hole in the skull of anesthetic rats and proceeded microdialysis, and gave PF (100 μg, i.c.v.). Collected the dialysate and the concentration of monoamines and their metabolites in dialysate and analyzed with HPLC-ECD. Male ICR mice were administered with PF (96 μg, i.c.v.) and with Ringer solution as a control. After 20 mins of administration, the mice were cut off the brain immediately and separated into eight regions according to the method of Glowinski. Added extraction solution to each region, homogenized and extracted for further procedure. The extract was centrifuged, sucked the transparent layer and centrifuged once more. The transparent layer was filtered with a 0.22 μm nylon filter and analyzed with HPLC-ECD (electrochemical detection).
Results: PF increased the content of DOPAC and NE in the cortex, and increased the content of NE and decreased the content of 5-HT in the medulla of the homogenized mice brain tissue. By microdialysis, PF increased the content of DOPAC and 5-HIAA in anesthetic rat cortex and expanded the content of DOPAC, HVA, and 5-HIAA in anesthetic rat striatum.
Conclusions: It reveals that PF could activate the release of monoamines and increase their metabolites in the rodent brain.
Replisome activity slowdown after exposure to ultraviolet light in
Escherichia coli
Authors: Soubry Nicolas , Wang Andrea , Reyes-Lamothe Rodrigo 
Published: May 2019

Significance
A multicomponent molecular machine, called the replisome, mediates high fidelity genome duplication but requires error-free DNA as its template. The presence of lesions on DNA, like those generated after UV, halt replisome activity and can lead to replisome disassembly, a potentially life-threatening situation to the cell. Here, we show that, in cells exposed to UV, parts of the replisome independently localize at sites far from the place of DNA synthesis. In addition, we provide evidence that the replisome responds to UV by slowing down its rate of synthesis on the damaged DNA template. Modulation of the rate of DNA replication may be a general strategy used by other organisms to minimize the impact of DNA damage on the duplicating genome.
Using attribution to decode binding mechanism in neural network models for chemistry
Authors: McCloskey Kevin , Taly Ankur , Monti Federico , Brenner Michael P. , Colwell Lucy J. 
Published: May 2019

Significance
Advances in machine learning have led to neural network-based methods for virtual screening, making it possible to sift through trillions of small molecules to find those that are pharmacologically important. Such methods have the potential to make chemical discoveries, but only if it is possible to untangle why models make the predictions that they do. Here we use attribution methods to investigate neural network models for small-molecule binding, and show that, while it is possible to identify pharmacophores with attribution, there is also the real possibility that a model which seems to perform perfectly instead learns spurious correlations in the underlying dataset that have nothing to do with binding chemistry. We propose an attribution-based test for determining whether a model can learn a hypothesized binding mechanism on a training set.
Monitoring tools and sampling methods for major date palm pests.
Authors: El-Shafie H. A. F. , Abdel-Banat B. M. A. , Mohammed M. E. A. , Al-Hajhoj M. R. 
Published: May 2019

Abstract
This review provides summary of the most commonly used methods and tools for monitoring and sampling of date palm pests. Emphasis is given to major pests of economic importance. The paper is arranged into different sections, which deal with morphology and architecture of date palm as one of the most important aspects in the process of sampling. The ecological concepts and terminologies used including mathematical models and monitoring and sampling plans for the major date palm pests. For convenience, major pests were grouped according to their taxonomic orders and the part of date palm they damage into the following: red palm weevil, Dubas bug, date moth, mites, scale insects, trunk and frond borers, sap beetles and stored date pests. The review specified the gaps in sampling plans available for major date palm pests as well as future research priorities to enhance the existing sampling and monitoring techniques.
CoCo: RNA-seq read assignment correction for nested genes and multimapped reads
Authors: Deschamps-Francoeur Gabrielle , Boivin Vincent , Abou Elela Sherif , Scott Michelle S 
Published: May 2019

Abstract

Motivation
Next-generation sequencing techniques revolutionized the study of RNA expression by permitting whole transcriptome analysis. However, sequencing reads generated from nested and multi-copy genes are often either misassigned or discarded, which greatly reduces both quantification accuracy and gene coverage.

Results
Here we present count corrector (CoCo), a read assignment pipeline that takes into account the multitude of overlapping and repetitive genes in the transcriptome of higher eukaryotes. CoCo uses a modified annotation file that highlights nested genes and proportionally distributes multimapped reads between repeated sequences. CoCo salvages over 15% of discarded aligned RNA-seq reads and significantly changes the abundance estimates for both coding and non-coding RNA as validated by PCR and bedgraph comparisons.

Availability and implementation
The CoCo software is an open source package written in Python and available from http://gitlabscottgroup.med.usherbrooke.ca/scott-group/coco.

Supplementary information
Supplementary data are available at Bioinformatics online.
Brain State-dependent Gain Modulation of Corticospinal Output in the Active Motor System
Authors: Naros Georgios , Lehnertz Tobias , Leão Maria Teresa , Ziemann Ulf , Gharabaghi Alireza 
Published: May 2019

Abstract
The communication through coherence hypothesis suggests that only coherently oscillating neuronal groups can interact effectively and predicts an intrinsic response modulation along the oscillatory rhythm. For the motor cortex (MC) at rest, the oscillatory cycle has been shown to determine the brain’s responsiveness to external stimuli. For the active MC, however, the demonstration of such a phase-specific modulation of corticospinal excitability (CSE) along the rhythm cycle is still missing. Motor evoked potentials in response to transcranial magnetic stimulation (TMS) over the MC were used to probe the effect of cortical oscillations on CSE during several motor conditions. A brain–machine interface (BMI) with a robotic hand orthosis allowed investigating effects of cortical activity on CSE without the confounding effects of voluntary muscle activation. Only this BMI approach (and not active or passive hand opening alone) revealed a frequency- and phase-specific cortical modulation of CSE by sensorimotor beta-band activity that peaked once per oscillatory cycle and was independent of muscle activity. The active MC follows an intrinsic response modulation in accordance with the communication through coherence hypothesis. Furthermore, the BMI approach may facilitate and strengthen effective corticospinal communication in a therapeutic context, for example, when voluntary hand opening is no longer possible after stroke.