bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maize Biochemical Defences against a Rootworm Were Mediated by Domestication, Spread, and Breeding
Authors: Fontes-Puebla Ana A. , Borrego Eli J. , Kolomiets Michael V. , Bernal Julio S. 
Published: June 2020

ABSTRACTPlant physiological processes generally are regulated by phytohormones, including plant biochemical responses to herbivory. Here, we addressed whether a suite of maize (Zea mays mays) phytohormones, including some precursor and derivative metabolites, relevant to herbivory defence were mediated by the crop’s domestication, northward spread, and modern breeding. For this, we compared phytohormone and metabolite levels among four plant types representing the evolutionary and agronomic transitions from maize’s wild ancestor, Balsas teosinte (Zea mays parviglumis), to Mexican and US maize landraces, and to highly-bred US maize cultivars, as affected by root herbivory by Western corn rootworm (Diabrotica virgifera virgifera). Following ecological-evolutionary hypotheses, we expected to find changes in: (i) maize defence strategy, from reliance on induced to constitutive defences; (ii) levels of phytohormones relevant to herbivore resistance consistent with gradual weakening of defences, and; (iii) levels of a phytohormone relevant to herbivory tolerance because it positively affects plant growth. We found that with its domestication, maize seemed to have transitioned from reliance on induced defences in Balsas teosinte to reliance on constitutive defences in maize. Also, we found that while one subset of phytohormones relevant to herbivory was suppressed (13-oxylipins), another was enhanced (9-oxylipins) with domestication, and both subsets were variably affected by spread and breeding. Finally, an auxin phytohormone directly linked to growth (indole-3-acetic acid), increased significantly with domestication, and seemingly with spread and breeding. We concluded that rootworm defences in maize were mediated by domestication and ensuing processes, such as spread and breeding, and argued that agricultural intensification mediated maize defence evolution in parallel with modern breeding.
Transcriptome analysis of threeAgavefiber-producing cultivars suitable for biochemicals and biofuels production in semiarid regions
Authors: Raya Fabio Trigo , Marone Marina Pupke , Carvalho Lucas Miguel , Rabelo Sarita Candida , de Paula Maiki Soares , Campanari Maria Fernanda Zaneli , Freschi Luciano , Mayer Juliana Lischka Sampaio , Silva Odilon Reny Ribeiro Ferreira , Mieczkowski Piotr , Carazzolle Marcelo Falsarella , Pereira Gonçalo Amarante Guimarães 
Published: June 2020

ABSTRACTAgaves, which have been grown commercially for fiber or alcoholic beverages, are emerging as a candidate crop for biochemicals and biofuels production in semiarid regions because of their high productivity in low rainfall areas, drought tolerance, and low lignin content.In this work, we present the transcriptomic atlas ofAgave sisalana,Agave fourcroydes, and agave hybrid 11648 (A. amaniensisxA. angustifolia) under prolonged drought in field conditions. Leaf, stem, and root tissues were sequenced, and gene expression profiles were correlated with biomass composition, enzymatic hydrolysis of cell wall carbohydrates, histochemical analysis, and non-structural carbohydrates content.Differences in biomass accessibility were attributed to either lignin content or lignin composition, possibly through modification of s/g ratio promoted by changes in Caffeic Acid 3-O-Methyltransferase (COMT) transcript abundance. Unlike most plants, the most highly expressed transcripts do not encode photosynthetic proteins, but rather involved in stress response. Although the three cultivars presented quantitative differences in global gene expression, they activated a highly overlapping set of genes. The main molecular strategies employed by agave to cope with high-temperature and drought seem to consist in overexpressing HSP and LEA, as well as promoting raffinose accumulation as an osmolyte.In conclusion, our data provide vital new genetic information for the study of Agave species and provide new insights into cell wall architecture, recalcitrance, and resistance to abiotic stresses for these species.
Identification of ADAMTS19 as a novel retinal factor involved in ocular growth regulation
Authors: Koli Swanand , Labelle-Dumais Cassandre , Zhao Yin , Paylakhi Seyyedhassan , Nair K Saidas 
Published: June 2020

ABSTRACTRefractive errors are the most common ocular disorders and are a leading cause of visual impairment worldwide. Although ocular axial length is well established to be a major determinant of refractive errors, the molecular and cellular processes regulating ocular axial growth are poorly understood. Mutations in genes encoding the PRSS56 and MFRP are a major cause of nanophthalmos. Accordingly, mouse models with mutations in the genes encoding the retinal factor PRSS56 or MFRP, a gene predominantly localized in the retinal pigment epithelial (RPE) exhibit ocular axial length reduction and extreme hyperopia. However, the precise mechanisms underlying PRSS56- and MFRP-mediated ocular axial growth remain elusive. Here, we show thatAdamts19expression is significantly upregulated in retina of mice lacking eitherPrss56orMfrp. Using a combination of genetic approaches and mouse models, we show that while ADAMTS19 is not required for ocular growth during normal development, its inactivation exacerbates ocular axial length reduction in bothPrss56orMfrpmutant mice. These results suggest that the upregulation of retinalAdamts19expression is part of an adaptive molecular response to counteract impaired ocular growth. Using a complementary genetic approach. We further demonstrate that loss of PRSS56 or MFRP function prevents excessive ocular axial growth in a mouse model of developmental myopia caused by a null mutation inIrpb, demonstrating that ocular axial elongation inIrbp-/-mice is fully dependent on PRSS56 and MFRP functions. Collectively, our findings provide insight into the molecular network involved in ocular axial growth regulation and refractive development and support the notion that relay of the signal between the retina and RPE could be critical for promoting ocular axial elongation.
Protein structure-based gene expression signatures
Authors: Rahman R. , Xiong Y. , van Hasselt J. G. C. , Hansen J. , Sobie E. A. , Birtwistle M. R. , Azeloglu E. , Iyengar R. , Schlessinger A. 
Published: June 2020

AbstractGene expression signatures (GES) connect phenotypes to mRNA expression patterns, providing a powerful approach to define cellular identity, function, and the effects of perturbations. However, the use of GES has suffered from vague assessment criteria and limited reproducibility. The structure of proteins defines the functional capability of genes, and hence, we hypothesized that enrichment of structural features could be a generalizable representation of gene sets. We derive structural gene expression signatures (sGES) using features from various levels of protein structure (e.g. domain, fold) encoded by the transcribed genes in GES, to describe cellular phenotypes. Comprehensive analyses of data from the Genotype-Tissue Expression Project (GTEx), ARCHS4, and mRNA expression of drug effects on cardiomyocytes show that structural GES (sGES) are useful for identifying robust signatures of biological phenomena. sGES also enables the characterization of signatures across experimental platforms, facilitates the interoperability of expression datasets, and can describe drug action on cells.
Neonatal hypothermia and adherence to World Health Organisation thermal care guidelines among newborns at Moi Teaching and Referral Hospital, Kenya
Authors: Nyandiko Winstone Mokaya , Kiptoon Paul , Lubuya Florence Ajaya 
Published: June 2020

ABSTRACTBackgroundNeonatal hypothermia is a great concern with near epidemic levels globally. The prevalence in Kenya is as high as 87%. Local data on the associated factors including adherence to warm chain guidelines as recommended by the World Health Organisation (WHO) is limited.ObjectiveTo determine the prevalence of hypothermia and level of adherence to the WHO thermal care guidelines among newborns admitted at Moi Teaching and Referral Hospital (MTRH).MethodsThis descriptive cross-sectional study was carried out among neonates admitted at the MTRH newborn unit. Systematic sampling was used to recruit 372 eligible participants. Axillary thermometry, interview of respective mothers and observation of thermal care practices was done. Means and medians described continuous variables while frequencies with corresponding percentages summarized categorical variables. Associations between various variables and neonatal hypothermia were computed using the Pearson chi-square test. Relative Risks and Odds Ratios were assessed between predictor and outcome variables. Independence among significant variables was determined through the logistic regression model at 5% prediction level.ResultsAmong the 372 participants, 64.5% (n=240) were born at MTRH, 47.6% (177) were preterm while 53.2% (198) had birth weights below 2500 grams. Admission hypothermia was noted among 73.7% (n= 274) while 13% (49) died on day one of admission. Only 7.8 % (29) newborns accessed optimal thermal care. Prematurity (RR=1.62, 95% CI: 1.43-1.84), day one mortality (RR=17.7, 95% CI: 2.40, 122.71) and adherence to the warm chain (p<0.001) was significantly associated with admission hypothermia. Inappropriate thermal resuscitation appliance (RR=1.50, 95% CI: 1.34-1.67) inappropriate clothing (RR = 1.78, 95% CI: 1.54 - 2.05) and late breastfeeding (RR = 2.01, 95% CI: 1.39-2.89) significantly increased the risk of hypothermia. Non hypothermic newborns had twenty-fold increased odds of survival (AOR=20.91, 95% CI: 2.15-153.62).ConclusionThree out four neonates at the MTRH newborn unit had hypothermia at admission. Hypothermia was significantly associated with prematurity, adherence to warm chain and day one mortality. There was notably low adherence to the warm chain.RecommendationStrategies to optimize adherence to the warm chain at MTRH with emphasis on 1thermal care of the preterm neonate should be instituted.
Attentional compensation in neurodegenerative diseases: the model of premanifest Huntington’s disease mutation carriers
Authors: Le Stanc Lorna , Lunven Marine , Giavazzi Maria , Sliwinski Agnès , Brugières Pierre , Youssov Katia , Bachoud-Lévi Anne-Catherine , Jacquemot Charlotte 
Published: June 2020

AbstractThe ability of the brain to actively cope with neuropathological insults is known as neural compensation. It explains the delayed appearance of cognitive symptoms in neurodegenerative diseases. In contrast to the neural signature of compensation, its cognitive counterpart is largely unknown due to the difficulty of identifying cognitive dysfunctions concealed by compensation mechanisms. We combined computational modelling and neuroanatomical analysis to explore cognitive compensation. We used Huntington’s disease (HD) as a genetic model of neurodegenerative disease allowing to study compensation in premanifest mutation carriers (preHDs) free from overt cognitive deficits despite incipient brain atrophy.Twenty preHDs, 28 HD patients and 45 controls performed a discrimination task. We investigated the processes underlying cognitive compensation using drift diffusion models. They assume that the discrimination process relies on the accumulation of evidence at a certain rate and terminates when a response threshold is reached.HD patients’ performances were lower than controls’ and explained by a higher response threshold and a lower accumulation rate compared to controls. PreHDs performed similarly to controls but had a response threshold between those of controls and HD patients. This nascent increase in response threshold predicted the accumulation rate, which was faster than controls. This suggests that the higher accumulation rate conceals the nascent deficit in response threshold corroborating the capacity of the brain to resist neuropathological insults in preHDs. The higher accumulation rate was associated with parietal hypertrophy in mutation carriers, and with higher hippocampal volumes in preHDs suggesting that cognitive compensation may rely on attentional capacities.Significance statementEnhancing mechanisms compensating brain degeneration in neurodegenerative diseases might allow to delay their onset and progression. Yet, the cognitive mechanisms of compensation remain to be identified. In order to explore this issue, we used Huntington’s disease as a genetic model of neurodegenerative diseases and combined computational modelling (drift diffusion models) and neuroanatomical data analysis. In the early stage of the disease, before the appearance of overt cognitive symptoms, we showed the involvement of the left superior parietal cortex and hippocampus in maintaining normal behavioural performances. This suggests that attention is used to compensate for brain atrophy early in the disease. This work describes promising means of measuring and understanding compensation mechanisms in neurodegenerative diseases and might help developing new therapies.
Identification of spatial variations in COVID-19 epidemiological data using K-Means clustering algorithm: a global perspective
Authors: Chandu Viswa Chaitanya 
Published: June 2020

ABSTRACTBackgroundDiscerning spatial variations of COVID-19 through quantitative analysis operating on the geographically designated datasets relating to socio-demographics and epidemiological data facilitate strategy planning in curtailing the transmission of the disease and focus on articulation of necessary interventions in an informed manner.MethodsK-means clustering was employed on the available country-specific COVID-19 epidemiological data and the influential background characteristics. Country-specific case fatality rates and the average number of people tested positive for COVID-19 per every 10,000 population in each country were derived from the WHO COVID-19 situation report 107, and were used for clustering along with the background characteristics of proportion of country’s population aged >65 years and percentage GDP spent as public health expenditure.ResultsThe algorithm grouped the 89 countries into cluster ‘1’ and Cluster ‘2’ of sizes 54 and 35, respectively. It is apparent that Americas, European countries, and Australia formed a major part of cluster ‘2’ with high COVID-19 case fatality rate, higher proportion of country’s population tested COVID-19 positive, higher percentage of GDP spent as public health expenditure, and greater percentage of population being more than 65 years of age.ConclusionIn spite of the positive correlation between high public health expenditure (%GDP) and COVID-19 incidence, case fatality rate, the immediate task ahead of most of the low and middle income countries is to strengthen their public health systems realizing that the correlation found in this study could be spurious in light of the underreported number of cases and poor death registration.
Brain network connectivity in major depression: extending findings from a large public data set by meta-analysis across sites
Authors: Tozzi Leonardo , Williams Leanne M. 
Published: June 2020

AbstractIn this short communication, we test whether patients with major depression and healthy individuals have different functional connectivity within established brain networks. To this end, we leverage a very large multi-site data set of resting state fMRI data (1,300 depressed patients and 1,128 controls) collected by 25 groups. A previous study conducted on this data set compared functional connectivity of the default mode network between the two groups. In our investigation, we performed a meta-analysis across sites quantifying the effects of depression and symptom severity on connectivity of several brain-wide networks beyond the default mode. Running a meta-analysis instead of a mega-analysis also allowed us to calculate effect sizes, heterogeneity and prediction intervals that will be valuable to inform future studies wishing to investigate network functional connectivity in depression. Our results indicate that network connectivity differences between depressed and healthy subjects are consistently small, with confidence intervals almost always encompassing zero, in line with the mixed findings from previous research. Default mode network connectivity differences between depressed patients and controls were exceptionally heterogeneous across sites, suggesting the existence of depression sub-types with normo- and hypo-connected default mode network or a strong impact of clinical confounds on default mode network connectivity. The only networks for which connectivity in depressed individuals was consistently lower than in controls were the somatomotor and visual networks, which could be promising understudied targets for future investigation. Overall, we highlight the need of minimizing heterogeneity in future multi-site studies on functional connectivity in depression and the need for more research on novel taxonomies of mental illness that are robustly anchored in brain function.
CT-derived measurements of pulmonary blood volume in small vessels and need for oxygen in COVID-19 patients
Authors: De Backer Wilfried , Lins Muriel , Dierckx Wendel , Vandevenne Jan , De Backer Jan , Lavon Ben R. , Lanclus Maarten , Rijckaert Karen , Kendall Irvin , Thillai Muhunthan 
Published: June 2020

AbstractIn contrast to early reports of conventional acute respiratory distress syndrome (ARDS) as the underlying pathophysiology of hypoxemic respiratory failure observed in patients with severe COVID-19, more recent findings implicate direct involvement of the pulmonary vasculature in giving rise to these symptoms. In earlier research, we demonstrated that patients with COVID-19 showed markedly reduced pulmonary blood volumes in pulmonary vessels <5 mm2 in cross-sectional area visible on imaging (termed “BV5”), with attendant dilation of larger, more proximal vessels. Here, we present preliminary results in which reduced BV5 is shown to correlate significantly with increased need for supplemental oxygen and abnormal arterial blood gas measurements in hospitalized COVID-19 patients. We suggest a potential mechanistic link between observed clinical, pathological, and imaging findings, and outline how these may be helpful in clinical assessment as well as the development of novel therapies.
A modified SEIR meta-population transmission based Modeling and Forecasting of the COVID-19 pandemic in Pakistan
Authors: Hassan Sohaib , Mughal Bilal Javed , Siwiak Marian , Yasin Zafar 
Published: June 2020

AbstractThe coronavirus disease 2019 (COVID-19) started from China at the end of 2019, has now spread across the globe. Modeling and simulation of the COVID-19 outspread is significant for timely and effective measures to be taken. Scientists around the world are using various epidemiological models to help policymakers to plan and determine what interventions and resources will be needed in case of a surge and to estimate the potential future burden on health care system. Pakistan is also among the affected countries with 18th highest number of total detected number of cases, as of 3rd of June, 2020. A modified time-dependent Susceptible-Exposed-Infected-Recovered (SEIR) metapopulation transmission model is used in the Global Epidemic and Mobility Model (GLEaM) for this simulation. The simulation assumes the index case in Wuhan, China and models the global spread of SARS-COV-2 with reasonable results for several countries within the 95% confidence interval. This model was then tuned with parameters for Pakistan to predict the outspread of COVID-19 in Pakistan. The impact of Non-Drug Interventions on “flattening the curve” are also incorporated in the simulation and the results are further extended to find the peak of the pandemic and future predictions. It has been observed that in the current scenario, the epidemic trend of COVID-19 spread in Pakistan would attain a peak in the second decade of month of June with approximately (3600-4200) daily cases. The current wave of SARS-COV-2 in Pakistan with is estimated to cause some (210,000 – 226,000) cumulative cases and (4400-4750) cumulative lost lives by the end of August when the epidemic is reduced by 99%. However, the disease is controllable in the likely future if inclusive and strict control measures are taken.
Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics
Authors: Zhang Meng , Eichhorn Stephen W. , Zingg Brian , Yao Zizhen , Zeng Hongkui , Dong Hongwei , Zhuang Xiaowei 
Published: June 2020

AbstractA mammalian brain is comprised of numerous cell types organized in an intricate manner to form functional neural circuits. Single-cell RNA sequencing provides a powerful approach to identify cell types based on their gene expression profiles and has revealed many distinct cell populations in the brain1-3. Single-cell epigenomic profiling4,5 further provides information on gene-regulatory signatures of different cell types. Understanding how different cell types contribute to brain function, however, requires knowledge of their spatial organization and connectivity, which is not preserved in sequencing-based methods that involve cell dissociation3,6. Here, we used an in situ single-cell transcriptome-imaging method, multiplexed error-robust fluorescence in situ hybridization (MERFISH)7, to generate a molecularly defined and spatially resolved cell atlas of the mouse primary motor cortex (MOp). We profiled ∼300,000 cells in the MOp, identified 95 neuronal and non-neuronal cell clusters, and revealed a complex spatial map in which not only excitatory neuronal clusters but also most inhibitory neuronal clusters adopted layered organizations. Notably, intratelencephalic (IT) cells, the largest branch of neurons in the MOp, formed a continuous spectrum of cells with gradual changes in both gene expression profiles and cortical depth positions in a highly correlated manner. Furthermore, we integrated MERFISH with retrograde tracing to probe the projection targets for different MOp neuronal cell types and found that projections of MOp neurons to other cortical regions formed a many-to-many network with each target region receiving input preferentially from a different composition of IT clusters. Overall, our results provide a high-resolution spatial and projection map of molecularly defined cell types in the MOp. We anticipate that the imaging platform described here can be broadly applied to create high-resolution cell atlases of a wide range of systems.