bluuebunny/crossref_metadata_2025 huggingface dataset:
Striatal seeding of protofibrillar alpha-synuclein causes cortical hyperreactivity in behaving mice
Authors: Blumenstock Sonja , Sun Fanfan , Marinković Petar , Sgobio Carmelo , Liebscher Sabine , Herms Jochen
Published: September 2020

Alpha-synucleinopathies are characterized by self-aggregation of the protein alpha-synuclein (a-syn), causing alterations on the molecular and cellular level. To unravel the impact of transneuronal spreading and templated misfolding of a-syn on the microcircuitry of remotely connected brain areas, we investigated cortical neuron function in awake mice 9 months after a single intrastriatal injection of a-syn preformed fibrils (PFFs), usingin vivotwo-photon calcium imaging. We found altered function of layer 2/3 cortical neurons in somatosensory cortex (S1) of PFF-inoculated mice, as witnessed by an enhanced response to whisking and increased synchrony, accompanied by a decrease in baseline Ca2+levels. Stereological analyses revealed a reduction in GAD67-positive inhibitory cells in S1 in PFF-injected brains. These findings point to a disturbed excitation/inhibition balance as an important pathomechanism in alpha-synucleinopathies and demonstrate a clear association between the spread of toxic proteins and the initiation of altered neuronal function in remotely connected areas.
Shifts in the thermal niche of fruit trees under climate change: the case of peach cultivation in France
Authors: Vanalli C. , Casagrandi R. , Gatto M. , Bevacqua D.
Published: September 2020

Climate influences plant phenological traits, thus playing a key role in defining the geographical range of crops. Foreseeing the impact of climate change on fruit trees is essential to inform policy decisions to guide the adaptation to new climatic conditions. To this end, we propose and use a phenological process-based model to assess the impacts of climate change upon the phenology, the suitability and the distribution of economically important cultivars of peach (Prunus persica), across the entire continental France. The model combines temperature dependent sub-models of dormancy, blooming, fruit survival and ripening, using chilling units, forcing units, frost occurrence and growing degree days, respectively. We find that climate change will have divergent impacts upon peach production. On the one hand, blooming will occur earlier, warmer temperatures will decrease spring frost occurrence and fruit ripening will be easily achieved before the start of fall. On the other hand, milder winters will impede the plant buds from breaking endodormancy, with consequent abnormal patterns of fruit development or even blooming failure. This latter impact will dramatically shift the geographic range of sites where peach production will be profitable. This shift will mainly be from the south of France (Languedoc-Roussillon, Rhône-Alpes and Provence-Alpes-Côte d’Azur), to northwestern areas where the winter chilling requirement will still be fulfilled. Our study provides novel insights for understanding and forecasting climate change impacts on peach phenology and it is the first framework that maps the ecological thermal niche of peach at national level.
A Multistaged Hyperparallel Optimization of the Fuzzy-Logic Mechanistic Model of Molecular Regulation
Authors: Aiyetan Paul
Published: September 2020

Motivation

Although it circumvents hyperparameter estimation of ordinary differential equation (ODE) based models and the complexities of many other models, the computational time complexity of a fuzzy logic regulatory model inference problem, particularly at higher order of interactions, quickly approaches those of computationally intractable problems. This undermines the benefits inherent in the simplicity and strength of the fuzzy logic-based molecular regulatory inference approach.

Results

For a sample inference problem – molecular regulation of vorinostat resistance in the HCT116 colon cancer cell lines, our modeled, designed and implemented “multistaged-hyperparallel” optimization approach significantly shortened the time to model inference from about 485.6 hours (20.2 days) to approximately 9.6 hours (0.4 days), compared to an optimized version of a previous implementation.

Availability

The multistaged-hyperparallel method is implemented as a plugin in the JFuzzyMachine tool, freely available at the GitHub repository locationshttps://github.com/paiyetan/jfuzzymachineandhttps://github.com/paiyetan/jfuzzymachine/releases/tag/v1.7.21. Source codes and binaries are freely available at the specified URLs.

Contact

paiyetan@gmu.edu
When DNA gets in the way in RNA-seq experiments, a sequel
Authors: Verwilt Jasper , Giraldez Maria D. , Trypsteen Wim , Van Paemel Ruben , De Preter Katleen , Mestdagh Pieter , Vandesompele Jo
Published: September 2020

Using a newly developed method dubbed SILVER-Seq—enabling extracellular RNA sequencing (exRNA-seq) directly from a small volume of human serum or plasma— Yan et al. recently reported in Current Biology a potential exRNA biomarker for the early diagnosis of Alzheimer’s disease [1]. After the publication of the initial paper describing the SILVER-Seq method [2], we reported our concern regarding potential DNA contamination in their datasets [3]. Although the authors replied they were able to successfully treat RNA samples with DNase to avoid such contamination, they did not address our observations of the majority of reads without evidence of being derived from RNA, nor documented verified absence of DNA after DNase treatment [4]. To assess whether the newly data generated may suffer from DNA contamination, we downloaded the publicly available sequencing data and evaluated two quality control metrics (i.e., fraction of exonic and splice reads), which were not reported in the paper. We found that both quality metrics were much lower than expected for RNA-seq data (6.28% exonic and 0.478% splice reads), in line with our previous findings on the first SILVER-Seq paper. These observations suggest the data and results presented by Yan et al. are affected by DNA contamination, an issue that may be inherent to the SILVER-Seq technology.
Genomic sequencing confirms absence of introgression despite past hybridisation between a common and a critically endangered bird and its common congener
Authors: Forsdick Natalie J. , Martini Denise , Brown Liz , Cross Hugh B. , Maloney Richard F. , Steeves Tammy E. , Knapp Michael
Published: September 2020

Genetic swamping resulting from interspecific hybridisation can increase extinction risk for threatened species. The development of high-throughput and reduced-representation genomic sequencing and analyses to generate large numbers of high resolution genomic markers has the potential to reveal introgression previously undetected using small numbers of genetic markers. However, few studies to date have implemented genomic tools to assess the extent of interspecific hybridisation in threatened species. Here we investigate the utility of genome-wide single nucleotide polymorphisms (SNPs) to detect introgression resulting from past interspecific hybridisation in one of the world’s rarest birds. Anthropogenic impacts have resulted in hybridisation and subsequent backcrossing of the critically endangered Aotearoa New Zealand endemic kakī (black stilts;Himantopus novaezelandiae) with the non-threatened self-introduced congeneric poaka (Aotearoa New Zealand population of pied stilts,Himantopus himantopus leucocephalus), yet genetic analyses with a limited set of microsatellite markers revealed no evidence of introgression of poaka genetic material in kakī, excluding one individual. We use genomic data for ∼63% of the wild adult kakī population to reassess the extent of introgression resulting from hybridisation between kakī and poaka. Consistent with previous genetic analyses, we detected no introgression from poaka into kakī. These collective results indicate that, for kakī, existing microsatellite markers provide a robust, cost-effective approach to detect cryptic hybrids. Further, for well-differentiated species, the use of genomic markers may not be required to detect admixed individuals.
Impact of COVID-19 on Hospital Admission of Acute Stroke patients in Bangladesh
Authors: Hasan A T M Hasibul , Das Subir Chandra , Islam Muhammad Sougatul , Mansur Mohaimen , Shawon Md Shajedur Rahman , Hassan Rashedul , Hoque Chowdhury Mohammad Shah Jahirul , Mondal Md Badrul Alam , Mohammad Quazi Deen
Published: September 2020

Background

With the proposed pathophysiologic mechanism of neurologic injury by SARS COV-2 the frequency of stroke and henceforth the related hospital admissions were expected to rise. In this paper we investigate this presumption by comparing the frequency of admissions of stroke cases in Bangladesh before and during the pandemic.

Methods

We conducted a retrospective analysis of stroke admissions in a 100-bed stroke unit at the National Institute of Neurosciences and Hospital (NINS&H) which is considerably a large stroke unit. We considered all the admitted cases from the 1stJanuary to the 30thJune, 2020. We used Poisson regressions to determine whether statistically significant changes in admission counts can be found before and after 25 March since when there is a surge in COVID-19 infections.

Results

A total of 1394 stroke patients got admitted during the study period. Half of the patients were older than 60 years, whereas only 2.6% were 30 years old or younger with a male-female ratio of 1.06:1. From January to March, 2020 the mean rate of admission was 302.3 cases per month which dropped to 162.3 cases per month from April to June with an overall reduction of 46.3% in acute stroke admission per month. In those two periods, reductions in average admission per month for ischemic stroke (IST), intracerebral hemorrhage (ICH), subarachnoid hemorrhage (SAH) and venous stroke (VS) were 45.5%, 37.2%, 71.4% and 39.0%, respectively. Based on weekly data, results of Poisson regressions confirm that the average number of admissions per week dropped significantly during the last three months of the sample period. Further, in the first three months, a total of 22 cases of hyperacute stroke management were done whereas in the last three months there was an 86.4% reduction in the number of hyperacute stroke patients getting reperfusion treatment. Only 38 patients (2.7%) were later found to be RT- PCR for SARS Cov-2 positive based on nasal swab testing.

Conclusion

Our study revealed more than fifty percent reduction in acute stroke admission during the COVID-19 pandemic. It is still elusive whether the reduction is related to the fear of getting infected by COVID-19 from hospitalization or the overall restriction on public movement and stay-home measures.
Trends in plant ecology research in Ethiopia (1969-2019): Systematic analysis
Authors: Gebrehiwot Kflay , Demissew Sebsebe
Published: September 2020

The objective of this paper was to systematically analyze the trend of plant ecological research in Ethiopia. The inclusion and exclusion of the articles for analysis were performed using Reporting Standards for Systematic Evidence Syntheses (ROSES) flow diagram developed for systematic review/meta-analysis. The number of articles published, authors, and collaboration has increased dramatically since the 1960s. Most of the research largely focused on the Dry evergreen Afromontane Forest and grassland complex (DAF) and Moist evergreen Afromontane Forest (MAF) vegetation types, comprising of about 52.6%. Of the remaining vegetation types, the woodlands (14.3%) i.e.Acacia-Commiphorawoodland and bushland proper (ACW), andCombretum-Terminaliawoodland and wooded grassland (CTW), desert and semi-desert scrubland (DSS) (2.3%), and the Afroalpine (AA) and Ericaceous Belt (EB) (1.5%) received little attention. A descriptive study on plant community ecology revolving on floristic composition and community structure is the dominant research theme, which revealed a narrow theme in contrast to the global trend. Other plant ecological studies such as reproductive and dispersal ecology of invasive plant species, and pollination ecology seems largely a neglected topic by the academia. Furthermore, the recommendations forwarded are not result-based. As a future direction, the Ethiopian government should develop a project database both for completed and ongoing projects.
Medium-chain acyl-CoA dehydrogenase, a gatekeeper of mitochondrial function in glioblastoma multiforme
Authors: Puca Francesca , Yu Fei , Bertolacci Caterina , Pettazzoni Piergiorgio , Carugo Alessandro , Huang-Hobbs Emmet , Liu Jintan , Zanca Ciro , Carbone Federica , Del Poggetto Edoardo , Gumin Joy , Dasgupta Pushan , Seth Sahil , Lang Frederick F. , Sulman Erik , Lorenzi Philip L. , Tan Lin , Shan Mengrou , Tolstyka Zachary P. , Kachman Maureen , Zhang Li , Deem Angela K. , Genovese Giannicola , Scaglioni Pier Paolo , Lyssiotis Costas A. , Viale Andrea , Draetta Giulio F.
Published: September 2020

Glioblastoma (GBM) is among the deadliest of human cancers. Despite extensive efforts, it has proven to be highly resistant to chemo- and immune-based therapeutic strategies, and little headway has been made with targeted inhibitors. Like many cancers, metabolism is dysregulated in GBM. Thus, to identify new vulnerabilities and drug targets in GBM, we conducted genetic screens using pooled RNAi libraries targeting metabolic enzymes. We screened multiple glioma stem cell-derived (GSC) xenograft models, which revealed that several enzymes involved in the mitochondrial metabolism of fatty acids were required for tumor cell proliferation. From among these, we focused on medium-chain acyl-CoA dehydrogenase (MCAD), which oxidizes medium-chain fatty acids, due to its consistently high score across all of our screens, as well as its high expression level in multiple GSC models and its upregulation in GBM compared to normal brain.

In this manuscript, we describe the dependence of GBM on sustained fatty acid metabolism to actively catabolize lipid species that would otherwise damage the mitochondrial structure. The uptake of mediumchain fatty acids lacks negative feedback regulation; therefore, in the absence of MCAD, medium-chain fatty acids accumulate to toxic levels, inducing reactive oxygen species (ROS), mitochondrial damage and failure, and apoptosis. Taken together, our findings uncover a previously unappreciated protective role exerted by MCAD in GBM cells, making it a unique and therapeutically exploitable vulnerability.
Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes
Authors: Jain Ruchi , Ramaswamy Sathishkumar , Harilal Divinlal , Uddin Mohammed , Loney Tom , Nowotny Norbert , Alsuwaidi Hanan , Varghese Rupa , Deesi Zulfa , Alkhajeh Abdulmajeed , Khansaheb Hamda , Alsheikh-Ali Alawi , Tayoun Ahmad Abou
Published: September 2020

Characterizing key molecular and cellular pathways involved in COVID-19 is essential for disease prognosis and management. We perform shotgun transcriptome sequencing of human RNA obtained from nasopharyngeal swabs of patients with COVID-19, and identify a molecular signature associated with disease severity. Specifically, we identify globally dysregulated immune related pathways, such as cytokine-cytokine receptor signaling, complement and coagulation cascades, JAK-STAT, and TGF-β signaling pathways in all, though to a higher extent in patients with severe symptoms. The excessive release of cytokines and chemokines such asCCL2, CCL22, CXCL9andCXCL12and certain interferons and interleukins related genes likeIFIH1, IFI44, IFIT1andIL10were significantly higher in patients with severe clinical presentation compared to mild and moderate presentations. Moreover, early induction of the TGF-β signaling pathway might be the primary cause of pulmonary fibrosis in patients with severe disease. Differential gene expression analysis identified a small set of regulatory genes that might act as strong predictors of patient outcome. Our data suggest that rapid transcriptome analysis of nasopharyngeal swabs can be a powerful approach to quantify host molecular response and may provide valuable insights into COVID-19 pathophysiology.
The natural axis of transmitter receptor distribution in the human cerebral cortex
Authors: Goulas Alexandros , Changeux Jean-Pierre , Wagstyl Konrad , Amunts Katrin , Palomero-Gallagher Nicola , Hilgetag Claus C
Published: September 2020

Transmitter receptors constitute a key component of the molecular machinery for inter-cellular communication in the brain. Recent efforts have mapped the density of diverse transmitter receptors across the human cerebral cortex with an unprecedented level of detail. Here, we distil these observations into key organizational principles. We demonstrate that receptor densities form a natural axis in the human cerebral cortex, reflecting decreases in differentiation at the level of laminar organization, and a sensory-to-association axis at the functional level. Along this natural axis, key organizational principles are discerned: progressive molecular diversity (increase of the diversity of receptor density), excitation/inhibition (increase of the ratio of excitatory-to-inhibitory receptor density) and mirrored, orderly changes of the density of ionotropic and metabotropic receptors. The uncovered natural axis formed by the distribution of receptors aligns with the axis that is formed by other dimensions of cortical organization, such as the myelo- and cytoarchitectonic levels. Therefore, the uncovered natural axis constitutes a unifying organizational feature linking multiple dimensions of the cerebral cortex, thus bringing order to the heterogeneity of cortical organization.
Potential Rhodopsin and Bacteriochlorophyll-Based Dual Phototrophy in a High Arctic Glacier
Authors: Zeng Yonghui , Chen Xihan , Madsen Anne Mette , Zervas Athanasios , Nielsen Tue Kjærgaard , Andrei Adrian-Stefan , Lund-Hansen Lars Chresten , Liu Yongqin , Hansen Lars Hestbjerg
Published: September 2020

Conserving additional energy from sunlight through bacteriochlorophyll (BChl)‐based reaction center or proton‐pumping rhodopsin is a highly successful life strategy in environmental bacteria. Rhodopsin and BChl based systems display contrasting characteristics in the size of coding operon, cost of biosynthesis, ease of expression control, and efficiency of energy production. This raises an intriguing question of whether a single bacterium has evolved the ability to perform these two types of phototrophy complementarily according to energy needs and environmental conditions. Here we report fourTardiphagasp. strains (Alphaproteobacteria) of monophyletic origin isolated from a high Arctic glacier in northeast Greenland (81.566° N, 16.363° W) that are at different evolutionary stages concerning phototrophy. Their >99.8% identical genomes contain footprints of horizontal operon transfers (HOT) of the complete gene clusters encoding BChl and xanthorhodopsin (XR)‐based dual phototrophy. Two strains only possess a complete xanthorhodopsin (XR) operon, while the other two strains have both a photosynthesis gene cluster (PGC) and an XR operon in their genomes. All XR operons are heavily surrounded by mobile genetic elements and located close to a tRNA gene, strongly signaling that a HOT event of XR operon has occurred recently. Mining public genome databases and our High Arctic glacial and soil metagenomes revealed that phylogenetically diverse bacteria have the metabolic potential of performing BChl and rhodopsin‐based dual phototrophy. Our data provide new insights on how bacteria cope with the harsh and energy‐deficient environments in surface glaciers, possibly by maximizing the capability of exploiting solar energy.

Importance

Over billions of years of evolution, bacteria capable of light‐driven energy production have occupied every corner of surface Earth where solar irradiation can reach. Only two general biological systems have evolved in bacteria to be capable of net energy conservation via light‐harvesting: one is based on the pigment of (bacterio‐)chlorophyll and the other based on light‐sensing retinal molecules. There is emerging genomic evidence that these two rather different systems can co‐exist in a single bacterium to take advantage of their contrasting characteristics in the number of genes involved, biosynthesis cost, ease of expression control and efficiency of energy production, and thus enhance the capability of exploiting solar energy. Our data provide the first clear‐cut evidence that such dual phototrophy potentially exist in glacial bacteria. Further public genome mining suggests this understudied dual phototrophic mechanism is possibly more common than our data alone suggested.

Sequence data availability

Genomes, metagenomes and raw reads were deposited into GenBank under Bioprojects PRJNA548505 and PRJNA552582.
Molecular characterization of RIGI, TLR7 and TLR3 as immune response gene of indigenous ducks in response to Avian influenza
Authors: Pal Aruna , Pal Abantika , Baviskar Pradyumna
Published: September 2020

Avian influenza is an alarming disease, which has every possibility to evolve as human to human pandemic situation due to frequent mutation and genetic reassortment or recombination of Avian influenza(AI) virus. The greatest concern is that till date no satisfactory medicine or vaccines are available, leading to massive culling of poultry birds causing huge economic loss, and ban on export of chicken products, which emphasise the need develop alternative strategy for control of AI. In the current study we attempt to explore the molecular mechanism of innate immune potential of ducks against common viral diseases including Avian influenza. In the present study, we have characterized immune response molecules as duck TLR3, TLR7, and RIGI and predicted to have potent antiviral activities against different identified strains of Avian influenza through in silico studies (molecular docking). Future exploitation involve immunomodulation with the recombinant protein, transgenic or gene-edited chicken resistant to bird flu.
The Effect of Alterations of Schizophrenia-Associated Genes on Gamma Band Oscillations
Authors: Metzner Christoph , Mäki-Marttunen Tuomo , Karni Gili , McMahon-Cole Hana , Steuber Volker
Published: September 2020

Abnormalities in the synchronized oscillatory activity of neurons in general and, specifically in the gamma band, might play a crucial role in the pathophysiology of schizophrenia. While these changes in oscillatory activity have traditionally been linked to alterations at the synaptic level, we demonstrate here, using computational modeling, that common genetic variants of ion channels can contribute strongly to this effect. Our model of primary auditory cortex highlights multiple schizophrenia-associated genetic variants that reduce gamma power in an auditory steady-state response task. Furthermore, we show that combinations of several of these schizophrenia-associated variants can produce similar effects as the more traditionally considered synaptic changes. Overall, our study provides a mechanistic link between schizophrenia-associated common genetic variants, as identified by genome-wide association studies, and one of the most robust neurophysiological endophenotypes of schizophrenia.
Understanding the origins of loss of protein function by analyzing the effects of thousands of variants on activity and abundance
Authors: Cagiada Matteo , Johansson Kristoffer E. , Valanciute Audrone , Nielsen Sofie V. , Hartmann-Petersen Rasmus , Yang Jun J. , Fowler Douglas M. , Stein Amelie , Lindorff-Larsen Kresten
Published: September 2020

Understanding and predicting how amino acid substitutions affect proteins is key to our basic understanding of protein function and evolution. Amino acid changes may affect protein function in a number of ways including direct perturbations of activity or indirect effects on protein folding and stability. We have analysed 6749 experimentally determined variant effects from multiplexed assays on abundance and activity in two proteins (NUDT15 and PTEN) to quantify these effects, and find that a third of the variants cause loss of function, and about half of loss-of-function variants also have low cellular abundance. We analyse the structural and mechanistic origins of loss of function, and use the experimental data to find residues important for enzymatic activity. We performed computational analyses of protein stability and evolutionary conservation and show how we may predict positions where variants cause loss of activity or abundance. In this way, our results link thermodynamic stability and evolutionary conservation to experimental studies of different properties of protein fitness landscapes.
Evolution of Modularity, Interactome and Functions of GIV/Girdin (CCDC88A) from Invertebrates to Vertebrates
Authors: Ear Jason , Ali Abd El-Hafeez Amer , Roy Suchismita , Ngo Tony , Rajapakse Navin , Choi Julie , Khandelwal Soni , Ghassemian Majid , McCaffrey Luke , Kufareva Irina , Sahoo Debashis , Ghosh Pradipta
Published: September 2020

PDZ domains are one of the most abundant protein domains in eukaryotes and frequently found on junction-localized scaffold proteins. Various signaling molecules bind to PDZ proteinsviaPDZ-binding motifs (PBM) and finetune cellular signaling. Here we describe the presence of a PBM on GIV/Girdin (CCDC88A) that is conserved throughout evolution, from invertebrates to vertebrates, and is generated as alongisoform-variant in humans, which we namedGIV-L. Unlike GIV, which lacks PBM and is cytosolic, GIV-L localizes to the cell junctions, and has a unique PDZ-interactome, which impactsGIV-L’s ability to bind and activate trimeric G-protein, Gi through itsguanine-nucleotideexchangemodulator (GEM) module; the GEM module is found exclusively in vertebrates. Thus, the two functional modules in GIV evolved sequentially: the ability to bind PDZ proteins via the PBM evolved earlier in invertebrates, whereas G-protein binding and activation may have evolved later only among vertebrates. Phenotypic studies in Caco-2 cells revealed that GIV and GIV-L may have antagonistic effects on cell growth, proliferation (cell cycle), and survival. Immunohistochemical analyses in human colon tissues showed that GIV expression increases with a concomitant decrease in GIV-L during cancer initiation. Taken together, these findings reveal how GIV/CCDC88A in humans displays evolutionary flexibility in modularity, which allows the resultant isoforms to play opposing roles either as a tumor suppressor (GIV-L) or as an oncogene (GIV).
FHL-1 interacts with human RPE cells through the α5β1 integrin and confers protection against oxidative stress
Authors: Choudhury Rawshan , Bayatti Nadhim , Scharff Richard , Szula Ewa , Tilakaratna Viranga , Udsen Maja Søberg , McHarg Selina , Askari Janet A , Humphries Martin J , Bishop Paul N , Clark Simon J
Published: September 2020

Retinal pigment epithelial (RPE) cells that underlie the neurosensory retina are essential for the maintenance of photoreceptor cells and hence vision. Interactions between the RPE and their basement membrane,i.e. the inner layer of Bruch’s membrane, are essential for RPE cell health and function, but the signals induced by Bruch’s membrane engagement, and their contributions to RPE cell fate determination remain poorly defined. Here, we studied the functional role of the soluble complement regulator and component of Bruch’s membrane, Factor H-like protein 1 (FHL-1). Human primary RPE cells adhered to FHL-1 in a manner that was eliminated by either mutagenesis of the integrin-binding RGD motif in FHL-1 or by using competing antibodies directed against the α5 and β1 integrin subunits. The results obtained from primary RPE cells were replicated using the hTERT-RPE cell line. RNAseq expression analysis of hTERT-RPE cells bound to FHL-1 showed an increased expression of the heat-shock protein genesHSPA6, CRYAB, HSPA1AandHSPA1Bwhen compared to cells bound to fibronectin (FN) or laminin (LA). Pathway analysis implicated changes in EIF2 signalling, the unfolded protein response, and mineralocorticoid receptor signalling as putative pathways. Subsequent cell survival assays using H2O2to induce oxidative stress-induced cell death showed hTERT-RPE cells had significantly greater protection when bound to FHL-1 or LA compared to plastic or FN. These data show a non-canonical role of FHL-1 in protecting RPE cells against oxidative stress and identifies a novel interaction that has implications for ocular diseases such as age-related macular degeneration.
A cloud-based platform for the analysis of single cell RNA sequencing data
Authors: Joshy Nithin , Yun Kyuson
Published: September 2020

Motivation

Single-cell RNA sequencing (scRNA-seq) is a recent technology that has provided many valuable biological insights. Notable uses include identifying novel cell-types, measuring the cellular response to treatment, and tracking trajectories of distinct cell lineages in time. The raw data generated in this process typically amounts to hundreds of millions of sequencing reads and requires substantial computational infrastructure for downstream analysis, a major hurdle for a biological research lab. Fortunately, the preprocessing step that converts this huge sequence data into manageable cell-specific expression profiles is standardized and can be performed in the cloud. We demonstrate how a cloud-based computational framework can be used to transform the raw data into biologically interpretable cell-type-specific information, using either 3’ or 5’ transcriptome libraries from 10x Genomics. The processed data which is an order of magnitude smaller in size can be easily downloaded to a laptop for customized analysis to gain deeper biological insights.

Results

We produced an automated and easily extensible pipeline in the cloud for the analysis of single-cell RNA-seq data which provides a convenient method to handle post-processing of scRNA sequencing using next generation sequencing platforms. The basic step provides the transformation of the scRNA-seq data to cell-type-specific expression profiles and computes the quality control metrics for the dataset. The extensibility of the platform is demonstrated by adding a doublet-removal algorithm and recomputing the clustering of the cells. Any additional computational steps that take a cell-type expression counts matrix as input can be easily added to this framework with minimal effort.

Availability

The framework and its documentation for installation is available at the Github repositoryhttp://github.com/nj3252/CB-Source/

Contact

kyun@houstonmethodist.org

Supplementary information

Supplementary data available atBioinformaticsonline.
PyNX: high-performance computing toolkit for coherent X-ray imaging based on operators
Authors: Favre-Nicolin Vincent , Girard Gaétan , Leake Steven , Carnis Jerome , Chushkin Yuriy , Kieffer Jerome , Paleo Pierre , Richard Marie-Ingrid
Published: September 2020

The open-source PyNX toolkit has been extended to provide tools for coherent X-ray imaging data analysis and simulation. All calculations can be executed on graphical processing units (GPUs) to achieve high-performance computing speeds. The toolkit can be used for coherent diffraction imaging (CDI), ptychography and wavefront propagation, in the far- or near-field regime. Moreover, all imaging operations (propagation, projections, algorithm cycles…) can be implemented in Python as simple mathematical operators, an approach which can be used to easily combine basic algorithms in a tailored chain. Calculations can also be distributed to multiple GPUs, e.g. for large ptychography data sets. Command-line scripts are available for on-line CDI and ptychography analysis, either from raw beamline data sets or using the coherent X-ray imaging data format.
When solvent becomes reactant: a study of 6-aminothiocytosine derivatives
Authors: Grześkiewicz Anita M. , Ostrowska Agata , Borzylo Dmytro , Kubicki Maciej
Published: September 2020

The dissolution of 6-aminothiocytosine in common solvents (such as methanol, dimethyl sulfoxide and dichloromethane) under alkaline conditions is shown to afford new compounds with a 6-aminothiocytosine skeleton: 2,2′-disulfanediylbis(pyrimidine-4,6-diamine) (1), C8H10N8S2, 2,2′-[methanediylbis(sulfanediyl)]bis(pyrimidine-4,6-diamine) (2), C9H12N8S2, 2-[(methoxymethyl)sulfanyl]pyrimidine-4,6-diamine (3), C6H10N4OS, and poly[(μ-4,6-diaminopyrimidine-2-sulfinato)potassium(I)] (4), [K(C4H5N4O2S)]
n
. The crystal architectures of these compounds are found to be strongly influenced by extensive hydrogen-bond networks, although some individual features are also observed. Specifically, 1 is characterized by very short C—H...N hydrogen bonds, 2 features apparently weak and long C—H...π, C—H...S and π–π contacts as the greatest contributors to stabilization energy, while 3 contains ribbons of molecules formed by centrosymmetric dimers of two types, and 4 is characterized by layers with principal structural units comprising distorted six-molecule rings. The intermolecular interactions in 1–4 are characterized in terms of their geometry, topology and energy, and the corresponding results are confirmed and visualized using Hirshfeld surface analysis.
Entrepreneurship education and undergraduate students' self-employment intentions: do paid employment intentions matter?
Authors: Otache Innocent , Oluwade Dorcas Omanyo , Idoko Ele-Ojo Jeremiah
Published: September 2020

Purpose

Undergraduate students have two opposing employment intentions, viz. self-employment intentions and paid-employment intentions (SEIs and PEIs). While a plethora of studies have explored the links between entrepreneurship education (EE) and SEIs, it has been noted that previous studies have ignored the effects of PEIs on the relationship between EE and SEIs. The purpose of this study, therefore, is to empirically explore the effects of PEIs on the relationship between EE and SEIs.

Design/methodology/approach

This study adopted a descriptive research design and a self-reported questionnaire was administered to collect data from a randomly selected sample of 95 accounting students from two polytechnics in Nigeria. To test the hypotheses formulated, partial least squares structural equation modelling (PLS-SEM) was performed using SmartPLS.

Findings

The results of Model 1 showed that EE had a significantly positive link with SEIs. On the other hand, the analysis of Model 2 revealed an inverse relationship between PEIs and SEIs. Furthermore, it was observed that the impact of EE on SEIs did not only reduce significantly when PEIs was added to Model 1 but also the relationship between EE and SEIs that was erstwhile statistically significant became nonsignificant.

Practical implications

The findings have implications for EE curriculum developers, governments and career guidance counsellors.

Originality/value

To the best of the authors' knowledge, this study is the first to provide empirical evidence of the effects of PEIs on the relationship between EE and SEIs. The findings provide important insights into the fundamental issue, which underlies the problem of graduate unemployment.
Nitrogen deposition regulates the clonal growth of Leymus chinensis, a typical clonal plant in arid and semi-arid regions
Authors: Liu Li , Zhou ChengYang , Pei Xiao , Guo LiZhu , Li JiaHuan , Wu RuiXin , Huang Ding
Published: September 2020

Purpose

The purpose of this study is to examine the effects of nitrogen (N) deposition on clonal growth in a rhizome clonal plant, Leymus chinensis (Trin.) Tzvel.

Design/methodology/approach

The study established seven N concentration gradients (0, 2, 4, 8, 16, 32 and 64 g N m−2) to simulate the continuous increase in N deposition for the cultivation of L. chinensis seedlings and assess the response mechanism of the cloned L. chinensis plant at different N levels by analyzing the aboveground and belowground plant appearance traits, parent ramets and daughter ramets of resource allocation and biomass allocation.

Findings

The results of this study showed that the different N treatment levels could promote clonal growth and had certain regularity under the seven treatments. The addition of N could significantly increase the ramet number, rhizome length, rhizome spacer length, biomass of mother ramets, daughter ramets and belowground L. chinensis population when the N addition was greater than 4 g m−2; however, the clonal growth ability of L. chinensis decreased and the rhizome length, ramet number, stem and leaf biomass of daughter ramets and stem biomass of mother ramets significantly decreased when the N addition was greater than 32 g N m−2.

Originality/value

With global warming, atmospheric N deposition is increasing and it is of great significance to explore the response mechanism of different N levels for the growth of clone plants. This study provides basic data and a theoretical basis for the survival prediction of cloned plants under the background of a global climate change strategy and has important theoretical and practical significance for the scientific management of grasslands in the future.
Ecosystems 4.0: redesigning global value chains
Authors: Schmidt Marie-Christin , Veile Johannes W. , Müller Julian M. , Voigt Kai-Ingo
Published: September 2020

Purpose

The study analyses how Industry 4.0 and underlying digital technologies influence the design of ecosystems in global value chains (GVCs).

Design/methodology/approach

A qualitative-exploratory research design is used. It deploys a multiple case study based on semi-structured interviews with 73 German managers of multinational enterprises. Applying a qualitative content analysis, the expert interviews are inductively analyzed and triangulated with secondary data to develop a synthesized data structure.

Findings

The analysis reveals a general tendency towards decentralization of value chain activities. Depending on the nature of each activity and several contextual factors, however, hybrids between centralization and decentralization of processes can be observed in Industry 4.0 environments. Consequences for global ecosystems are altered cooperation with business partners, new organizational forms and novel market environments.

Research limitations/implications

Given inherent limitations in scope and methodology, the study calls for cross-industry and cross-country analyses. Further studies should research implications of Industry 4.0 changes in ecosystems and GVCs, and the role digital platforms can play in this context.

Practical implications

The results help companies to analyze and adapt their role in ecosystems and associated GVC activities to Industry 4.0 environments, thus staying competitive in changing market conditions.

Originality/value

This study is among the first to empirically investigate the influence of Industry 4.0 on ecosystems embedded in GVCs. Reflecting existing company environments, it adds an international and company-external perspective to Industry 4.0 research.
An IT governance framework for IS portfolio management
Authors: Erasmus Wikus , Marnewick Carl
Published: September 2020

Purpose

Success in the information systems (IS) project domain is elusive despite extensive research on the topic. Governance is seen as the greatest contributor to project success. The purpose of this paper is to investigate and report on the current perceptions and implementation of information technology (IT) governance within IS portfolio management to develop a sub-framework to guide practitioners. This sub-framework forms part of a grand IS project, programme and portfolio governance framework of which this study forms a contributing part.

Design/methodology/approach

The researchers followed a mixed-methods approach through utilising Q-methodology and inverted factor analysis.

Findings

The results provided a sub-framework recommending specific IT governance practices to be applied to IS portfolios. The recommendations are categorised as activities to be maintained, enhanced and/or implemented.

Research limitations/implications

The research only had participants from South African organisations and as such cannot be reliably extrapolated to other regions.

Originality/value

The resultant sub-framework provides stakeholders and practitioners involved in IS portfolios an opportunity to examine their own approaches and be confronted with possibilities in their portfolio management activities. Further research to be conducted includes creating a grand framework to address the linkages between portfolio, programme and project management as it relates to IT governance on various strategic levels.
Vulnerability and Capacity Assessment for refugee education crises
Authors: Shamieh Jamal M. , Sawalha Ihab Hanna , Madanat Hanan M.
Published: September 2020

Purpose

The purpose of this study is to aim at: (1) investigating the vulnerabilities/obstacles that hinder refugees in hosting countries from obtaining quality and adequate education and (2) proposing a Framework for Action to transform these vulnerabilities into capacities.

Design/methodology/approach

Vulnerability and Capacity Assessment (VCA) was used for the purpose of this research. A survey strategy was adopted and data were collected using semi-structured interviews with refugee families. One hundred and twenty families were interviewed.

Findings

The study identified a number of vulnerabilities; including mainly unavailability of educational facilities; quality of the available education; social challenges and psychological needs. The findings revealed that there was a lack of comprehensive and strategic frameworks for mitigating refugee educational crises.

Practical implications

The lack of adequate and quality education for refugees in host countries is likely to increase illiteracy levels and subsequently trigger humanitarian and natural disasters on the long run. This research emphasizes the importance of developing comprehensive frameworks for quality and adequate refugee education.

Originality/value

To the author's knowledge, and after an extensive review of the existing literature, this is the first study to employ VCA to investigate the extent of the current refugee educational crisis in Jordan. VCA is more commonly used in the context of natural and environmental disasters threatening societies. Relevant authorities need to be aware of the significance of refugee education at individual, communal and national levels, as well as the significance of education to refugee well-being.
Research on key technologies of multi-task-oriented live maintenance robots for Ultra High Voltage multi-split transmission lines
Authors: Jiang Wei , Zou Dehua , Zhou Xiao , Zuo Gan , Ye Gao Cheng , Li Hong Jun
Published: September 2020

Purpose

The purpose of this study is to solve the key technical problems of the practical application of electric robots. The UHV multi-split transmission line power cable operation robot is an important equipment to ensure the reliable operation of high voltage lines and is a useful exploration to realize high-quality power transmission. As the robot system platform equipment mature and operation environment gradually become more complex, the double arm coordination motion control in extreme environment becomes one of the main bottleneck for its practical in power system.

Design/methodology/approach

This paper summarizes the key technologies related to power cable robots, and aims at key technical indicators such as operation reliability, operation efficiency and operation quality in the robot’s practical process. The dynamic evolution mechanism of the robot’s mechanical configuration, the multi-physics information fusion algorithm in extreme environments, the robot’s autonomous positioning and its error compensation control, the robot’s robust motion control in extreme environments and the dual-arm force-position hybrid coordination control and the dynamic distribution and elimination mechanism of internal forces in the closed chain between robots and operating objects, all the research methods and solutions of the key technologies are proposed, respectively.

Findings

Finally, a new control architecture for power cable robots in the background of the Ubiquitous Power Internet of Things is proposed so as to manage the operation and maintenance of electric power systems. The above key technologies are a new exploration of the operation and maintenance management of EHV (Extra High Voltage) multi-split transmission lines which have laid a solid theoretical foundation for the power cable robot.

Originality/value

High voltage transmission line is the main channel of power transmission. It is an important means to improve the integration of operation and maintenance management of power system to use robot instead of manual inspection and maintenance of power line, in the promotion and application of electric robot. The authors pay attention to the practicability, and the breakthrough of key technologies of robot is the premise of the practicability of robot. In this paper, the robot operation and control in multi-task and complex scenes are studied. The research and implementation of the main key technologies, such as the dynamic evolution mechanism of robot configuration, the coupling and fusion law of multi physical fields in the extreme electric power environment, the autonomous positioning control of manipulator, the robust control of robot in the super electromagnetic field environment and the cooperative operation control of multi manipulator, are discussed.
Group interventions for trauma and substance misuse available for women in criminal justice services: a systematic review of the literature
Authors: Henderson Ashley , Stenfert Kroese Biza
Published: September 2020

Purpose

In recent years, group interventions have been designed to simultaneously treat the symptoms of post-traumatic stress disorder (PTSD) and substance misuse. This study aims to explore the research literature available regarding these interventions, for women who are involved in the criminal justice system.

Design/methodology/approach

Five electronic databases were searched. The review included primary research papers which reported quantitative outcomes for group interventions for female offenders. The quality of each paper was assessed using the framework developed by Kmet et al. (2004).

Findings

A total of 13 research papers met the inclusion criteria and were selected for this review. The papers indicated promising results for the treatment of PTSD and substance misuse in this population group.

Practical implications

This area of research is in early development. Studies adopted different research designs and used different outcome measures to assess effectiveness. The quality assessment indicated that future research should adopt standardised assessment measures, blind researchers to reduce bias and implement randomised controlled trials to produce more robust findings.

Originality/value

To the best of the authors’ knowledge, this systematic review is the first to explore the effectiveness of these interventions, specifically for women in the criminal justice system. The authors consider the existing evidence base for this population group and propose measures for future research.