bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental enrichment mitigates the long-lasting sequelae of perinatal fentanyl exposure
Authors: Alipio Jason Bondoc , Riggs Lace Marie , Plank Madeline , Keller Asaf 
Published: August 2021

AbstractThe opioid epidemic is a rapidly evolving societal issue driven, in part, by a surge in synthetic opioid use. A rise in fentanyl use among pregnant women has led to a 40-fold increase in the number of perinatally-exposed infants in the past decade. These children are more likely to develop mood- and somatosensory-related conditions later in life, suggesting that fentanyl may permanently alter neural development. Here, we examined the behavioral and synaptic consequences of perinatal fentanyl exposure in adolescent male and female C57BL/6J mice and assessed the therapeutic potential of environmental enrichment to mitigate these effects. Dams were givenad libitumaccess to fentanyl (10 µg/mL,per os) across pregnancy and until weaning (PD 21). Perinatally-exposed adolescent mice displayed hyperactivity (PD 45), enhanced sensitivity to anxiogenic environments (PD 46), and sensory maladaptation (PD 47) – sustained behavioral effects that were completely normalized by environmental enrichment (PD 21-45). Additionally, environmental enrichment normalized the fentanyl-induced changes in the frequency of miniature excitatory postsynaptic currents of layer 2/3 neurons in the primary somatosensory cortex (S1). We also demonstrate that fentanyl impairs short- and long-term potentiation in S1 layer 2/3 neurons which, instead, exhibit a sustained depression of synaptic transmission that is restored by environmental enrichment. On its own, environmental enrichment suppressed long-term depression of control S1 neurons from vehicle-treated mice subjected to standard housing conditions. These results demonstrate that the lasting effects of fentanyl can be ameliorated with a non-invasive intervention introduced during early development.Significance StatementIllicit use of fentanyl accounts for a large proportion of opioid-related overdose deaths. Children exposed to opioids during development have a higher risk of developing neuropsychiatric disorders later in life. Here, we employ a preclinical model of perinatal fentanyl exposure that recapitulates these long-term impairments and show, for the first time, that environmental enrichment can reverse deficits in somatosensory circuit function and behavior. These findings have the potential to directly inform and guide ongoing efforts to mitigate the consequences of perinatal opioid exposure.
Fillable and Unfillable Gaps in Rice Transcriptome under Field and Controlled Environments
Authors: Hashida Yoichi , Tezuka Ayumi , Nomura Yasuyuki , Kamitani Mari , Kashima Makoto , Kurita Yuko , Nagano Atsushi J. 
Published: August 2021

AbstractThe differences between plants grown in field and controlled environments have long been recognised; however, few studies have addressed the underlying molecular mechanisms. Here, we show fillable and unfillable gaps in the transcriptomes of rice grown in field and controlled environments by utilising SmartGC, a high-performance growth chamber that reproduces the fluctuating irradiance, temperature, and humidity of field environments. Rice transcriptome dynamics in SmartGC mimicked those in the field, particularly during the morning and evening; those in conventional growth chamber conditions did not. Further analysis revealed that fluctuation of irradiance affects transcriptome dynamics in the morning and evening, while fluctuation of temperature only affects transcriptome dynamics in the morning. We found upregulation of genes related to biotic and abiotic stress, whose expression was affected by environmental factors that cannot be mimicked by SmartGC. Our results accelerate the understanding of plant responses to field environments for both field and laboratory studies.
Interaction between Discs large and GPSM2: A Comparison Across Species
Authors: Schiller Emily , Bergstralh Dan T. 
Published: August 2021

AbstractThe orientation of the mitotic spindle determines the direction of cell division, and therefore contributes to tissue shape and cell fate. Interaction between the multifunctional scaffolding protein Discs large (Dlg) and the canonical spindle orienting factor GPSM2 (also called Pins in Drosophila and LGN in vertebrates) has been established in bilaterian models, but its function remains unclear. We used a phylogenetic approach to test whether the interaction is obligate in animals, and in particular whether GPSM2 evolved in multicellular organisms as a Dlg-binding protein. We show that Dlg diverged in C. elegans and the syncytial sponge O. minuta and propose that this divergence may correspond to differences in spindle orientation requirements between these organisms and the canonical pathways described in bilaterians. We also demonstrate that GPSM2 is present in basal animals, but the established Dlg-interaction site cannot be found in either Placozoa or Porifera. Our results suggest that the interaction between GPSM2 and Dlg appeared in Cnidaria, and we therefore speculate that it may have evolved to promote accurate division orientation in the nervous system. This work reveals the evolutionary history of the GPSM2/Dlg interaction and suggests new possibilities for its importance in spindle orientation during epithelial and neural tissue development.
Molecular Dynamics Simulation of a Model Brain Membrane with and without a 14-3-3 tau Protein
Authors: Arvayo-Zatarain Jorge A. , Favela-Rosales Fernando , Figueroa Angel D. Reyes , Castro-Villarreal Pavel , Contreras-Aburto Claudio 
Published: August 2021

AbstractAn unbalanced composition of lipids and proteins in brain membranes is related to the appearance neurodegenrative diseases and recent investigations show that the 14-3-3 tau protein might relate to some of these diseases. This article reports results from a coarse-grained model brain membrane with and without a 14-3-3 τ/θ protein inside the membrane. We investigated the symmetrized partial density, thickness, diffusion coefficients, and deuterium order parameters of the membrane with and without protein. We observe a slight increase in heads and linkers in the symmetrized partial density of the membrane with the protein inserted and higher values of the deuterium order parameters for the brain model membrane with protein. We observe a reduction in the diffusion coefficient of the fluid membrane in the presence of the transmembrane tau protein. Our findings show that the protein can modify the structural and dynamical properties of the membrane. This work will serve as a guide for future investigations on the interactions of tau proteins with brain membrane models and their relation to neurodegenerative diseases.
ALLSorts: a RNA-Seq classifier for B-Cell Acute Lymphoblastic Leukemia
Authors: Schmidt Breon , Brown Lauren M. , Ryland Georgina L. , Lonsdale Andrew , Kosasih Hansen J. , Ludlow Louise E. , Majewski Ian J. , Blombery Piers , Ekert Paul G. , Davidson Nadia M. , Oshlack Alicia 
Published: August 2021

AbstractB-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. Subtypes within B-ALL are distinguished by characteristic structural variants and mutations, which in some instances strongly correlate with responses to treatment. The World Health Organisation (WHO) recognises seven distinct classifications, or subtypes, as of 2016. However, recent studies have demonstrated that B-ALL can be segmented into 23 subtypes based on a combination of genomic features and gene expression profiles. A method to identify a patient’s subtype would have clear clinical utility. Despite this, no publically available classification methods using RNA-Seq exist for this purpose.Here we present ALLSorts: a publicly available method that uses RNA-Seq data to classify B-ALL samples to 18 known subtypes and five meta-subtypes. ALLSorts is the result of a hierarchical supervised machine learning algorithm applied to a training set of 1223 B-ALL samples aggregated from multiple cohorts. Validation revealed that ALLSorts can accurately attribute samples to subtypes and can attribute multiple subtypes to a sample. Furthermore, when applied to both paediatric and adult cohorts, ALLSorts was able to classify previously undefined samples into subtypes.ALLSorts is available and documented on GitHub (https://github.com/Oshlack/AllSorts/).Key PointsALLSorts is a gene expression classifier for B-cell acute lymphoblastic leukemia, which predicts 18 distinct genomic subtypes - including those designated by the World Health Organisation (WHO) and provisional entities.Trained and validated on over 2300 B-ALL samples, representing each subtype and a variety of clinical features.Correctly identified subtypes in 91% of cases in a held-out dataset and between 82-93% across a newly combined cohort of paediatric and adult samples.ALLSorts assigned subtypes to samples with previously unknown driver events.ALLsorts is an accurate, comprehensive and freely available classification tool that distinguishes subtypes of B-cell acute lymphoblastic leukemia from RNA-sequencing.
On the discovery of ADRAM, an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3
Authors: Li Xiang , Zhao Qiongyi , Wang Ziqi , Liau Wei-Siang , Basic Dean , Ren Haobin , Marshall Paul R. , Zajaczkowski Esmi L. , Leighton Laura J. , Madugalle Sachithrani U. , Musgrove Mason , Periyakaruppiah Ambika , Shi Jichun , Zhang Jianjian , Mattick John S. , Mercer Timothy R. , Wei Wei , Bredy Timothy W. 
Published: August 2021

ABSTRACTLong-noncoding RNA (lncRNA) comprise a new class of genes that have been assigned key roles in development and disease. Many lncRNAs are specifically transcribed in the brain where they regulate the expression of protein-coding genes that underpin neuronal function; however, their role in learning and memory remains largely unexplored. We used RNA Capture-Seq to identify a large population of lncRNAs that are expressed in the infralimbic cortex of adult male mice in response to fear-related learning, with 14.5% of these annotated in the GENCODE database as lncRNAs with no known function. We combined these data with cell-type-specific ATAC-seq on neurons that had been selectively activated by fear-extinction learning, and revealed 434 lncRNAs derived from enhancer regions in the vicinity of protein-coding genes. In particular, we discovered an experience-induced lncRNA called ADRAM that acts as both a scaffold and a combinatorial guide to recruit the brain-enriched chaperone protein 14-3-3 to the promoter of the memory-associated immediate early gene Nr4a2. This leads to the expulsion of histone deactylases 3 and 4, and the recruitment of the histone acetyltransferase creb binding protein, which drives learning-induced Nr4a2 expression. Knockdown of ADRAM disrupts this interaction, blocks the expression of Nr4a2, and ultimately impairs the formation of fear-extinction memory. This study expands the lexicon of experience-dependent lncRNA activity in the brain, highlights enhancer-derived RNAs (eRNAs) as key players in the epigenetic regulation of gene expression associated with fear extinction, and suggests eRNAs, such as ADRAM, may constitute viable targets in developing novel treatments for fear-related anxiety disorders.
In vitro evolution reveals primordial RNA-protein interaction mediated by metal cations
Authors: Giacobelli Valerio G. , Fujishima Kosuke , Lepšík Martin , Tretyachenko Vyacheslav , Kadavá Tereza , Bednárová Lucie , Novák Petr , Hlouchová Klára 
Published: August 2021

AbstractRNA-peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA-protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal L11 C-terminal domain was selected from a ∼1010 library of partially randomized sequences, all composed of 10 prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with MD simulations uncover qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant L11 domain uses bridging ion (K+/Mg2+) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein-RNA interactions evolved, where the lack of aromatic/basic residues was compensated by acidic residues plus metal ions.
A recombinant baculovirus TnGV in Trichoplusia ni larvae using the PIG bombardment method and the CRISPR/Cas9 system
Authors: Ortiz-Arrazola Oscar J. , Del Rincón-Castro Ma. Cristina 
Published: August 2021

AbstractBaculoviruses have been used for the expression of heterologous proteins of biotechnological interest. However, most of these proteins are obtained by homologous co-transfection recombination in cell lines, limiting their use. Recently, the CRISPR/Cas9 system has excelled in its high efficiency in editing specific sequences without the need for insect cell lines. In this work, the CRISPR/Cas9 system was used to edit the genome of Trichopusia ni granulovirus (TnGV) and transformation of insects by the PIG bombardment method. A homologous repair vector (pTnGV101) was designed with regions orf5 and orf7, as well as sgRNA flanking TnGV P10 of this virus. The bombardment transformation was carried out at 175 psi with 40% of infected T. ni larvae, of which 38% expressed the reporter protein EGFP. These results demonstrate that the CRISPR/Cas9 system and PIG bombardment can be used for genetic modification of baculovirus in vivo.
High-fidelity, high-spatial-resolution diffusion MRI of the ex-vivo whole human brain on the 3T Connectom scanner using structured low-rank EPI ghost correction
Authors: Ramos-Llordén Gabriel , Lobos Rodrigo A. , Kim Tae Hyung , Tian Qiyuan , Witzel Thomas , Lee Hong-Hsi , Scholz Alina , Keil Boris , Yendiki Anastasia , Bilgiç Berkin , Haldar Justin P. , Huang Susie Y. 
Published: August 2021

AbstractDiffusion MRI (dMRI) of whole, intact, fixed postmortem human brain at high spatial resolution serves as key bridging technology for 3D mapping of structural connectivity and tissue microstructure at the mesoscopic scale. Ex vivo dMRI offers superior spatial resolution compared to in vivo dMRI but comes with its own technical challenges due to the significantly reduced T2 relaxation times and decreased diffusivity incurred by tissue fixation. The altered physical properties of fixed tissue necessitate the use of alternative acquisition strategies to preserve SNR and achieve sufficient diffusion weighting. Multi-shot or segmented 3D echo planar imaging (EPI) sequences have been used to shorten echo times (TEs) with reduced distortions from field inhomogeneity and eddy currents on small-bore MR scanners and have been adopted for high b-value dMRI of ex vivo whole human brain specimens.The advent of stronger gradients on human MRI scanners has led to improved image quality and a wider range of diffusion-encoding parameters for dMRI but at the cost of more severe eddy currents that result in spatial and temporal variations in the background magnetic field, which cannot be corrected for using standard vendor-provided ghost correction solutions. In this work, we show that conventional ghost correction techniques based on navigators and linear phase correction may be insufficient for EPI sequences using strong diffusion-sensitizing gradients in ex vivo dMRI experiments, resulting in orientationally biased dMRI estimates. This previously unreported problem is a critical roadblock in any effort to leverage scanners with ultra-high gradients for high-precision mapping of human neuroanatomy at the mesoscopic scale. We propose an advanced reconstruction method based on structured low-rank matrix modeling that reduces the ghosting substantially. We show that this method leads to more accurate and reliable dMRI metrics, as exemplified by diffusion tensor imaging and high angular diffusion imaging analyses in distributed neuroanatomical areas of fixed whole human brain specimens. Our findings advocate for the use of advanced reconstruction techniques for recovering unbiased metrics from ex vivo dMRI acquisitions and represent a crucial step toward making full use of strong diffusion-encoding gradients for neuroscientific studies seeking to study brain structure at multiple spatial scales.
Ectopic cervical thymi and no thymic involution until midlife in naked mole-rats
Authors: Emmrich Stephan , Zakusilo Frances Tolibzoda , Trapp Alexandre , Zhou Xuming , Zhang Quanwei , Irving Ellen M. , Drage Michael G. , Zhang Zhengdong , Gladyshev Vadim N. , Seluanov Andrei , Gorbunova Vera 
Published: August 2021

AbstractImmunosenescence is a hallmark of aging and manifests as increased susceptibility to infection, autoimmunity, and cancer in the elderly. One component of immunosenescence is thymic involution, age-associated shrinkage of the thymus, observed in all vertebrates studied to date. The naked mole-rat (Heterocephalus glaber) has become an attractive animal model in aging research due to its extreme longevity and resistance to disease. Here we show that naked mole rats display no thymic involution up to 11 years of age. Furthermore, we found large ectopic cervical thymi in addition to the canonical thoracic thymus, both being identical in their cell composition. The developmental landscape in naked mole-rat thymi revealed overt differences from the murine T cell compartment, most notably a decrease of CD4+/CD8+ double-positive cells and lower abundance of cytotoxic effector T cells. Our observations suggest that naked mole rats display a delayed immunosenescence. Therapeutic interventions aimed at reversing thymic aging remain limited, underscoring the importance of understanding the cellular and molecular mechanisms behind a sustained immune function in the naked mole rat.
Prediction of Plastic Degrading Microbes
Authors: Hemalatha N , Wilson Akhil , Akhil T 
Published: August 2021

AbstractPlastic pollution is one of the challenging problems in the environment. But a life without plastic we cannot imagine. This paper deals with the prediction of plastic degrading microbes using Machine Learning. Here we have used Decision Tree, Random Forest, Support vector Machine and K Nearest Neighbor algorithms in order to predict the plastic degrading microbes. Among the four classifiers, Random Forest model gave the best accuracy of 99.1%.
Validation of non-invasive body-surface gastric mapping for detecting electrophysiological biomarkers by simultaneous high-resolution serosal mapping in a porcine model
Authors: Calder Stefan , Cheng Leo K. , Andrews Christopher N. , Paskaranandavadivel Niranchan , Waite Stephen , Alighaleh Saeed , Erickson Jonathan C. , Gharibans Armen , O’Grady Gregory , Du Peng 
Published: August 2021

AbstractGastric disorders are increasingly prevalent, but reliable clinical tools to objectively assess gastric function are lacking. Body-surface gastric mapping (BSGM) is a non-invasive method for the detection of gastric electrophysiological biomarkers including slow wave direction, which have correlated with symptoms in patients with gastroparesis and functional dyspepsia. However, no studies have validated the relationship between gastric slow waves and body surface activation profiles. This study aimed to comprehensively evaluate the relationship between gastric slow waves and body-surface recordings. High-resolution electrode arrays were placed to simultaneously capture slow waves from the gastric serosa (32×6 electrodes at 4 mm resolution) and abdominal surface (8×8 at 20 mm inter-electrode spacing) in a porcine model. BSGM signals were extracted based on a combination of wavelet and phase information analyses. A total of 1185 individual cycles of slow waves assessed, out of which 897 (76%) were normal antegrade waves, occurring in 10/14 (71%) subjects studied. BSGM accurately detected the underlying slow wave in terms of frequency (r = 0.99, p = 0.43) as well as the direction of propagation (p = 0.41, F-measure: 0.92). In addition, the cycle-by-cycle match between BSGM and transitions of gastric slow waves in terms either or both temporal and spatial abnormalities was demonstrated. These results validate BSGM as a suitable method for non-invasively and accurately detecting gastric slow wave activation profiles from the body surface.Single sentence summarySimultaneous recordings of the stomach using serosal and body-surface electrode arrays demonstrated reliable detection of frequency and classification of propagation.
The inter-generational arts branding of the Star Wars saga: may the myth be with you!
Authors: Patsiaouras Georgios 
Published: August 2021

PurposeEmploying the Star Wars brand as a case study, this paper seeks to critically discuss the importance of comparative mythology for inter-generational branding and consumption practices within arts related markets.Design/methodology/approachSecondary data have been gathered focusing on the analysis of material in the form of books, academic journals, films, videos, television programs, websites and media reports related to the interface between comparative mythology, the Star Wars brand.FindingsFirst, this paper indicates how the long-standing success of the Star Wars brand mirrors and reflects the power of monomythic storytelling in creating a platform for arts and place building branding associations and extensions for numerous products and services. Second, this study shows and highlights the potential of monomythic structures/storytelling and comparative mythology in acting an underlying cultural platform whereupon several arts brand associations, narratives, extensions and overall strategies can emerge. Finally, this project suggests how arts marketing scholars could further explore the infusion of mythological narratives within branding practices in the areas of performing/visual arts, museums, entertainment and arts related tourism campaigns.Originality/valueFocusing on the most successful film franchise of all times, this study argues that comparative mythology constitutes an endless source for common templates of artistic, cross-cultural and inter-generational marketing practices focusing on universal moral codes and archetypes.