bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sleep differentially affects early and late neuronal responses to sounds in auditory and perirhinal cortices
Authors: Sela Y. , Krom AJ. , Bergman L. , Regev N. , Nir Y. 
Published: August 2019

AbstractA fundamental feature of sleep is reduced behavioral responsiveness to external events, but the extent of processing along sensory pathways remains poorly understood. While responses are comparable across wakefulness and sleep in auditory cortex (AC), neuronal activity in downstream regions remains unknown. Here we recorded spiking activity in 435 neuronal clusters evoked by acoustic stimuli in the perirhinal cortex (PRC) and in AC of freely behaving male rats across wakefulness and sleep. Neuronal responses in AC showed modest (around 10%) differences in response gain across vigilance states, replicating previous studies. By contrast, PRC neuronal responses were robustly attenuated by 47% and 36% during NREM sleep and REM sleep, respectively. Beyond the separation according to cortical region, response latency in each neuronal cluster was correlated with the degree of NREM sleep attenuation, such that late (>40ms) responses in all monitored regions diminished during NREM sleep. The robust attenuation of late responses prevalent in PRC represents a novel neural correlate of sensory disconnection during sleep, opening new avenues for investigating the mediating mechanisms.Significance StatementReduced behavioral responsiveness to sensory stimulation is at the core of sleep’s definition, but it is still unclear how the sleeping brain responds differently to sensory stimuli. In the current study we recorded neuronal spiking responses to sounds along the cortical processing hierarchy of rats during wakefulness and natural sleep. Responses in auditory cortex only showed modest changes during sleep, whereas sleep robustly attenuated the responses of neurons in high-level perirhinal cortex. We also found that during NREM sleep, the response latency predicts the degree of sleep attenuation in individual neurons above and beyond their anatomical location. These results provide anatomical and temporal signatures of sensory disconnection during sleep and pave the way to understanding the underlying mechanisms.
A Multidimensional Systems Biology Analysis of Cellular Senescence in Ageing and Disease
Authors: Avelar Roberto A. , Ortega Javier Gómez , Tacutu Robi , Tyler Eleanor , Bennett Dominic , Binetti Paolo , Budovsky Arie , Chatsirisupachai Kasit , Johnson Emily , Murray Alex , Shields Samuel , Tejada-Martinez Daniela , Thornton Daniel , Fraifeld Vadim E. , Bishop Cleo L. , de Magalhães João Pedro 
Published: August 2019

ABSTRACTCellular senescence, a permanent state of replicative arrest in otherwise proliferating cells, is a hallmark of ageing and has been linked to ageing-related diseases like cancer. Senescent cells have been shown to accumulate in tissues of aged organisms which in turn can lead to chronic inflammation. Many genes have been associated with cell senescence, yet a comprehensive understanding of cell senescence pathways is still lacking. To this end, we created CellAge (http://genomics.senescence.info/cells), a manually curated database of 279 human genes associated with cellular senescence, and performed various integrative and functional analyses. We observed that genes promoting cell senescence tend to be overexpressed with age in human tissues and are also significantly overrepresented in anti-longevity and tumour-suppressor gene databases. By contrast, genes inhibiting cell senescence overlapped with pro-longevity genes and oncogenes. Furthermore, an evolutionary analysis revealed a strong conservation of senescence-associated genes in mammals, but not in invertebrates. Using the CellAge genes as seed nodes, we also built protein-protein interaction and co-expression networks. Clusters in the networks were enriched for cell cycle and immunological processes. Network topological parameters also revealed novel potential senescence-associated regulators. We then used siRNAs and observed that of 26 candidates tested, 19 induced markers of senescence. Overall, our work provides a new resource for researchers to study cell senescence and our systems biology analyses provide new insights and novel genes regarding cell senescence.
APPENDICULAR MORPHOLOGY AND LOCOMOTOR PERFORMANCE OF TWO MORPHOTYPES OF CONTINENTAL ANOLES:Anolis heterodermusANDAnolis tolimensis
Authors: Ríos-Orjuela Juan Camilo , Camacho-Bastidas Juan Sebastián , Jerez Adriana 
Published: August 2019

ABSTRACTAnolislizards have been a model of study in ecomorphology in the Caribbean islands because species with the same type of microhabitat share similar morphological features. But despite their great diversity, little is known about continental species. We analyzed the relationship between the anatomical characteristics of the appendicular skeleton and the locomotor performance of twoAnolisspecies found in Colombia that have different use of habitat.Anolis heterodermusa strictly arboreal species was compared withAnolis tolimensisthat inhabits the lower strata of vegetation. These two species differ in their body plan, not only in body shape and external morphological features, but also in the skeleton and appendicular musculature. The results highlight the muscle and bone specializations associated with the use of habitat in this genus, such as the presence of more robust bones to enlarge the surface of muscle insertion, the thickening and loss of carpal parts, thickening of tendons associated with the manus, and greater development of muscle mass in the forelimbs byA. heterodermuswith respect toA. tolimensis. These differences are related to the use of the microhabitat and the locomotor style of each species.
Genome-wide analysis of GATA factors in moso bamboo (Phyllostachys edulis) unveils that PeGATAs regulate shoot rapid-growth and rhizome development
Authors: Wang Taotao , Yang Yong , Lou Shuaitong , Wei Wei , Zhao Zhixin , Lin Chentao , Ma Liuyin 
Published: August 2019

ABSTRACTBackgroundMoso bamboo is well-known for its rapid-growth shoots and widespread rhizomes. However, the regulatory genes of these two processes are largely unexplored. GATA factors regulate many developmental processes, but its role in plant height control and rhizome development remains unclear.ResultsHere, we found that bamboo GATA factors (PeGATAs) are involved in the growth regulation of bamboo shoots and rhizomes. Bioinformatics and evolutionary analysis showed that there are 31 PeGATA factors in bamboo, which can be divided into three subfamilies. Light, hormone, and stress-relatedcis-elements were found in the promoter region of thePeGATAgenes. Gene expression of 12PeGATAgenes was regulated by phytohormone-GA but there was no correlation between auxin andPeGATAgene expression. More than 27PeGATAgenes were differentially expressed in different tissues of rhizomes, and almost allPeGATAshave dynamic gene expression level during the rapid-growth of bamboo shoots. These results indicate thatPeGATAsregulate rhizome development and bamboo shoot growth partially via GA signaling pathway. In addition,PeGATA26,a rapid-growth negative regulatory candidate gene modulated by GA treatment, was overexpressed in Arabidopsis, and over-expression ofPeGATA26significantly repressed Arabidopsis primary root length and plant height. The PeGATA26 overexpressing lines were also resistant to exogenous GA treatment, further emphasizing that PeGATA26 inhibits plant height from Arabidopsis to moso bamboo via GA signaling pathway.ConclusionsOur results provide an insight into the function of GATA transcription factors in regulating shoot rapid-growth and rhizome development, and provide genetic resources for engineering plant height.
Microhabitat partitioning correlates with opsin gene expression in coral reef cardinalfishes (Apogonidae)
Authors: Luehrmann Martin , Cortesi Fabio , Cheney Karen L. , de Busserolles Fanny , Marshall N. Justin 
Published: August 2019

AbstractVertebrates exhibit diverse visual systems that vary in terms of morphology, number and distribution of spectrally distinct photoreceptor types, visual opsin genes and gene expression levels.In fish, such adaptations are driven by two main factors: differences in the light environment and behavioural tasks, including foraging, predator avoidance and mate selection. Whether visual systems also adapt to small-scale spectral differences in light, between microhabitats, is less clear.We suggest that differences in microhabitat use by cardinalfishes (Apogonidae) on coral reefs drive morphological and molecular adaptations in their visual systems. To test this, we investigated diurnal microhabitat use in 17 cardinalfish species and assessed whether this correlated with differences in visual opsin gene expression and eye morphology.We found that cardinalfishes display six types of partitioning behaviours during the day, ranging from specialists found exclusively in the water column to species that are always hidden inside the reef matrix.Using data on visual opsin gene expression previously characterized in this family, it was discovered that species in exposed habitats had increased expression of the short-wavelength sensitive violet opsin (SWS2B) and decreased expression of the dim-light active rod opsin (RH1). Species of intermediate exposure, on the other hand, expressed opsins that are mostly sensitive to the blue-green central part of the light spectrum (SWS2AsandRH2s), while fishes entirely hidden in the reef substrate had an increased expression of the long-wavelength sensitive red opsin (LWS).We found that eye size relative to body size significantly differed between cardinalfish species, and relative eye size decreased with an increase in habitat exposure.Retinal topography did not show co-adaptation with microhabitat use, but instead with feeding mode.We suggest that, although most cardinalfishes are nocturnal foragers, their visual systems are also adapted to both the light intensity and the light spectrum of their preferred diurnal microhabitat.
LINE-1 ORF2p Expression is Nearly Imperceptible in Human Cancers
Authors: Ardeljan Daniel , Wang Xuya , Oghbaie Mehrnoosh , Taylor Martin S. , Husband David , Deshpande Vikram , Steranka Jared P. , Gorbounov Mikhail , Yang Wan Rou , Sie Brandon , Larman H. Benjamin , Jiang Hua , Molloy Kelly R. , Altukhov Ilya , Li Zhi , McKerrow Wilson , Fenyö David , Burns Kathleen H. , LaCava John 
Published: August 2019

AbstractBackgroundLong interspersed element-1 (LINE-1, L1) is the major driver of mobile DNA activity in modern humans. When expressed, LINE-1 loci produce bicistronic transcripts encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Many types of human cancers are characterized by L1 promoter hypomethylation, L1 transcription, L1 ORF1p protein expression, and somatic L1 retrotransposition. ORF2p encodes the endonuclease and reverse transcriptase activities required for L1 retrotransposition. Its expression is poorly characterized in human tissues and cell lines.ResultsWe report mass spectrometry based tumor proteome profiling studies wherein ORF2p eludes detection. To test whether ORF2p could be detected with specific reagents, we developed and validated five rabbit monoclonal antibodies with immunoreactivity for specific epitopes on the protein. These reagents readily detect ectopic ORF2p expressed from bicistronic L1 constructs. However, endogenous ORF2p is not detected in human tumor samples or cell lines by western blot, immunoprecipitation, or immunohistochemistry despite high levels of ORF1p expression. Moreover, we report endogenous ORF1p-associated interactomes, affinity isolated from colorectal cancers, wherein we similarly fail to detect ORF2p. These samples include primary tumors harboring hundreds of somatically-acquired L1 insertions. The new data are available via ProteomeXchange with identifier PXD013743.ConclusionsAlthough somatic retrotransposition provides unequivocal genetic evidence for the expression of ORF2p in human cancers, we are unable to directly measure its presence using several standard methods. Experimental systems have previously indicated an unequal stoichiometry between ORF1p and ORF2p, but in vivo, the expression of these two proteins may be more strikingly uncoupled. These findings are consistent with observations that ORF2p is not tolerable for cell growth.
OPTN translocates to an ATG9A-positive compartment to regulate innate immune signalling and cytokine secretion
Authors: O’Loughlin Thomas , Kruppa Antonina J , Ribeiro Andre LR , Edgar James R , Ghannam Abdulaziz , Smith Andrew M , Buss Folma 
Published: August 2019

AbstractOptineurin (OPTN) is a multifunctional protein involved in autophagy, secretion as well as NF-κB and IRF3 signalling and mutations are associated with several human diseases including primary open-angle glaucoma (POAG), amyotrophic lateral sclerosis (ALS), Paget’s disease of bone (PDB) and Crohn’s disease (CD). Here we show that, in response to viral RNA, OPTN translocates to foci in the perinuclear region, where it negatively regulates NF-κB and IRF3 signalling pathways and downstream pro-inflammatory cytokine secretion. These OPTN foci consist of a tight cluster of small membrane vesicles, which are positive for marker proteins of the trans-Golgi network/recycling compartment – most notably ATG9A. Disease mutations linked to POAG cause aberrant formation of this compartment in the absence of stimuli, which correlates with the ability of OPTN to inhibit signalling. Using proximity labelling proteomics (BioID), we identify the linear ubiquitin assembly complex (LUBAC), CYLD and TBK1 as part of the OPTN interactome and show that these proteins, along with NEMO, are recruited to this OPTN-positive perinuclear compartment. Together, we propose OPTN might be responsible for dampening the NF-κB and IRF3 signalling responses through the sequestration of LUBAC and other positive regulators of these pathways in this dsRNA-induced compartment leading to altered pro-inflammatory cytokine secretion.SummaryDisease associated OPTN mutations impact on the formation of the perinuclear compartment and result in hypo- or hyper-activation of the immune response, which could drive the development of human diseases such as POAG, ALS and also Paget’s disease of bone.
DeepMF: Deciphering the Latent Patterns in Omics Profiles with a Deep Learning Method
Authors: Chen Lingxi , Xu Jiao , Cheng Li Shuai 
Published: August 2019

AbstractWith recent advances in high-throughput technologies, matrix factorization techniques are increasingly being utilized for mapping quantitative omics profiling matrix data into low-dimensional embedding space, in the hope of uncovering insights in the underlying biological processes. Nevertheless, current matrix factorization tools fall short in handling noisy data and missing entries, both deficiencies that are often found in real-life data. Here, we propose DeepMF, a deep neural network-based factorization model. DeepMF disentangles the association between molecular feature-associated and sample-associated latent matrices, and is tolerant to noisy and missing values. It exhibited feasible subtype discovery efficacy on mRNA, miRNA, and protein profiles of medulloblastoma cancer, leukemia cancer, breast cancer, and small-blue-round-cell cancer, achieving the highest clustering accuracy of 76%, 100%, 92%, and 100% respectively. When analyzing data sets with 70% missing entries, DeepMF gave the best recovery capacity with silhouette values of 0.47, 0.6, 0.28, and 0.44, outperforming other state-of-the-art MF tools on the cancer data sets Medulloblastoma, Leukemia, TCGA BRCA, and SRBCT. Its embedding strength as measured by clustering accuracy is 88%, 100%, 84%, and 96% on these data sets, which improves on the current best methods 76%, 100%, 78%, and 87%. DeepMF demonstrated robust denoising, imputation, and embedding ability. It offers insights to uncover the underlying biological processes such as cancer subtype discovery. Our implementation of DeepMF can be found at https://gitlab.deepomics.org/jiaox96/DeepMF.
Haploinsufficient maternal effect of Epidermal Growth Factor Receptor A mutation in zebrafish
Authors: Ciano Margherita , Kemp Paul R. , Sathyapala S. Amanda , Hughes Simon M. 
Published: August 2019

AbstractGeneration of viable offspring depends both on genetic and environmental factors of both mother and child. Analysis of a likely amorphic allele of the zebrafishepidermal growth factor receptor a(egfra) gene revealed that heterozygous females were infertile due to death of all fertilized eggs during embryonic and early larval life with cardiac, tail and other defects. Comparison of the severe dominant maternal effect with previous studies using pharmacological inhibitors of Egfrs or antisense morpholino injection indicate that a normal level of maternal Egfra is required for viability of offspring both during egg development and in the embryo after fertilisation. As heterozygous mothers were not fertile, the homozygous zygoticegfrakg134phenotype could not be analysed. Heterozygousegfra+/kg134males crossed to wild type females produced fully viable offspring, among whichegfra+/kg134individuals had increased slow muscle but no functional motility defect. Our findings suggest that Egfra activity is crucial for early development both before and after fertilisation and are likely to constitute a rare example of a haploinsufficient maternal effect in a species lacking imprinting.
The DRS–AIMP2–EPRS subcomplex acts as a pivot in the multi-tRNA synthetase complex
Authors: Hahn Hyunggu , Park Sang Ho , Kim Hyun-Jung , Kim Sunghoon , Han Byung Woo 
Published: August 2019

Aminoacyl-tRNA synthetases (ARSs) play essential roles in protein biosynthesis as well as in other cellular processes, often using evolutionarily acquired domains. For possible cooperativity and synergistic effects, nine ARSs assemble into the multi-tRNA synthetase complex (MSC) with three scaffold proteins: aminoacyl-tRNA synthetase complex-interacting multifunctional proteins 1, 2 and 3 (AIMP1, AIMP2 and AIMP3). X-ray crystallographic methods were implemented in order to determine the structure of a ternary subcomplex of the MSC comprising aspartyl-tRNA synthetase (DRS) and two glutathione S-transferase (GST) domains from AIMP2 and glutamyl-prolyl-tRNA synthetase (AIMP2GST and EPRSGST, respectively). While AIMP2GST and EPRSGST interact via conventional GST heterodimerization, DRS strongly interacts with AIMP2GST via hydrogen bonds between the α7–β9 loop of DRS and the β2–α2 loop of AIMP2GST, where Ser156 of AIMP2GST is essential for the assembly. Structural analyses of DRS–AIMP2GST–EPRSGST reveal its pivotal architecture in the MSC and provide valuable insights into the overall assembly and conditionally required disassembly of the MSC.
An adaptive PI control design for multi-phase machines in healthy and faulty operations
Authors: Hajary Ali , Seifossadat Seyed Ghodratollah , Kianinezhad Reza , Saffarian Alireza , Mortazavi Seyed Saeedollah 
Published: August 2019

PurposeThis paper aims to present a novel robust control method based on an adaptive PI controller (APIC) to compensate for different disturbances and unknown dynamics for multi-phase induction machines.Design/methodology/approachThe gains of the APIC are adapted online according to the tracking error. Proposed APIC is accompanied with designed linear disturbance observer (LDO) to present robust behavior to machine parameter variations and fault disturbances.FindingsThe results show remarkable dynamic performance in both healthy and faulty conditions when the six-phase induction machine works under APIC and LDO schemes.Originality/valueThe proposed controller need not readjust current controllers for the post-fault condition. The developed Simulink model efficiency is confirmed through experimental tests.
Outer space and neo-colonial injustice
Authors: Sutch Peter , Roberts Peri 
Published: August 2019

PurposeRecent developments in US rhetoric and policy advocating the militarisation and marketisation of outer space challenge the global commons values and regimes that developed partly in response to decolonisation. These regimes embodied aspirations to post-colonial distributive justice, as well as to international management for peaceful purposes. The purpose of this paper is to argue that global commons values should be defended against these challenges in order to avoid the risk of exporting colonial legacies of injustice into outer space.Design/methodology/approachThis paper is an exercise in normative International Political Theory and so develops normative arguments by drawing on approaches in political theory and international law.FindingsThis paper demonstrates that the commons values endorsed in the aftermath of colonialism retain their relevance in a global politics that remains structured by post-colonial power relations. This paper also demonstrates that these commons values have evolved and found expression in central elements of international law, persisting as resources to be drawn on in normative argument.Originality/valueThis study places recent moves to assert US hegemony in space in the context of persistent post-colonial power relations and develops novel arguments in renewed support of commons values.
Mandatory reporting and adult safeguarding: a rapid realist review
Authors: Donnelly Sarah 
Published: August 2019

Purpose
The purpose of this paper is to critically analyse the concept of mandatory reporting in adult safeguarding in the jurisdictions of Australia, Canada, England, Northern Ireland and Scotland.

Design/methodology/approach
A rapid realist evaluation of the literature on this topic was carried out in order to answer the question: "what works, for whom and in what circumstances?” Particular attention was paid to Context(s), Mechanism(s) and Outcome(s) configurations of adult safeguarding reporting systems and processes.

Findings
The evaluation found a range of arguments for and against mandatory reporting and international variations on the scope and powers of mandatory reporting.

Research limitations/implications
This review was undertaken in late 2018 so subsequent policy and practice developments will be missing from the evaluation. The evaluation focussed on five jurisdictions therefore, the findings are not necessarily translatable to other contexts.

Practical implications
Some jurisdictions have introduced mandatory reporting and others are considering doing so. The potential advantages and challenges of introducing mandatory reporting are highlighted.

Social implications
The introduction of mandatory reporting may offer professionals increased powers to prevent and reduce the abuse of adults, but this could also change the dynamic of relationships within families, and between families and professionals.

Originality/value
This paper provides an accessible discussion of mandatory reporting across Ireland and internationally which to date has been lacking from the literature.