bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silicoandIn vitroevaluation of the anti-inflammatory and antioxidant potential ofCymbopogon citratusfrom North-western Himalayas
Authors: Salaria Deeksha , Rolta Rajan , Sharma Nitin , Dev Kamal , Sourirajan Anuradha , Kumar Vikas 
Published: June 2020

AbstractCymbopogon citratuswhich is an aromatic perennial herb belonging to family Gramineae is known for its application in food and healthcare industry. The present study attempts to evaluate the potential of essential oil fromCymbopogon citratus(CEO) as an anti-inflammatory and antioxidant agent. CEO showed significant DPPH radical scavenging activity (IC50- 91.0 ± 9.25 µg/ml), as compared to Ascorbic acid (IC50-33.38 ± 2.29 µg/ml). CEO also exhibited significantin-vitroanti-inflammatory activity with IC50- 397.11± 1.45µg/ml) as compared to diclofenac sodium (IC50- 682.98 ± 7.47 µg/ml). Chemical constituents of the oil was determined using Gas Chromatography/Mass Spectroscopy, showed that 8-methyl-3,7-Nonadien-2-one (E), α-Pinene, limonene, citral, limonene oxide and Epoxy-α-terpenyl acetate were the major constituents. Thein silicomolecular docking study showed phytocompounds of CEO (Caryophyllene oxide and β-caryophyllene) have considerable binding potential with 1HD2 and 5IKQ receptors. PASS prediction of these phytocompounds also confirmed strong anti-inflammatory activity ofC. citratus. The ADMET analysis also showed that these phytocompounds are safer to replace the synthetic drugs with side effects. This work establishes the anti inflammatory potential of CEO as an alternative to existing therapeutic approach to treatment of inflammation and also natural source of antioxidant compounds.
Robust frequency-encoded dynamics in a minimal synthetic phytohormone crosstalk
Authors: García S. Pérez , Navarrete M. García , Sanchis D. Ruiz , Navarro C. Prieto , Avdovic M. , Pucciariello O. , Wabnik K. 
Published: June 2020

SummaryHow do dynamic hormone inputs translate into speed, and precision of response is one of the most challenging questions of science. To approach this question, we constructed minimal synthetic gene circuits capable of responding to plant hormones auxin and salicylic acid (SA). These circuits integrate bacterial multi antibiotic resistance (Mar) repressors that directly detect phytohormones through a ligand-induced conformational switch. The combination of individual circuits in synthetic auxin-SA crosstalk was sufficient to coordinate responses across the cell population with tunable precision and speed in long-term microfluidics experiments. This antagonistic auxin-SA crosstalk retains temporal memory upon extended exposure to hormones and synchronizes the behavior of individual cells with the environmental clock. Our study shows how dynamic hormone inputs can be translated in robust and precise responses with a minimal assembly of bacterial transcriptional repressors, suggesting an alternative regulatory strategy to known plant hormone signaling systems.
Divergence and introgression in small apes, the genus Hylobates, revealed by reduced representation sequencing
Authors: Matsudaira Kazunari , Ishida Takafumi 
Published: June 2020

AbstractGibbons in the genus Hylobates, which live in Southeast Asia, show great diversity, comprising seven to nine species. Natural hybridisation has been observed in the species contact zones, although the roles played by hybridisation and introgression in the evolution of these species remain unclear. To uncover the divergence history and the contributions of hybridisation and introgression to the evolution of Hylobates, random amplicon sequencing-direct (GRAS-Di) analysis was employed to genotype 47 gibbons, representing eight species from three genera. After quality filtering, over 300,000 autosomal single-nucleotide variant (SNV) sites were identified. The SNV-based autosomal phylogeny, together with the mitochondrial phylogeny, supported a divergence pattern beginning approximately 4.3 million years ago. First, the mainland species, H. pileatus and H. lar, consecutively diverged from the Sundaic island species. Second, H. moloch, in Java (and likely H. klossii, in the Mentawai Islands) diverged from the other species. Third, H. muelleri, in Borneo, and H. agilis/H. albibarbis, in Sumatra and southwestern Borneo, diverged. Lastly, H. agilis and H. albibarbis diverged from each other. The Patterson’s D-statistics indicated significant introgression between H. lar and H. pileatus, between H. lar and H. agilis, and between H. albibarbis and H. muelleri, and weak introgression was identified between H. moloch and H. albibarbis, and between H. moloch and H. muelleri abbotti, suggesting incomplete reproductive barriers among Hylobates species and that hybridisation and introgression occur whenever the distribution ranges contact. Some candidates for introgressed genomic regions were detected, and the functions of these would be revealed by further genome-wide studies.
Jet-printing microfluidic devices on demand
Authors: Soitu Cristian , Stovall-Kurtz Nicholas , Deroy Cyril , Castrejón-Pita Alfonso A. , Cook Peter R. , Walsh Edmond J. 
Published: June 2020

ABSTRACTThere is an unmet demand for microfluidics in biomedicine. We describe contactless fabrication of microfluidic circuits on standard Petri dishes using just a dispensing needle, syringe pump, 3-way traverse, cell-culture media, and an immiscible fluorocarbon (FC40). A submerged micro-jet of FC40 is projected through FC40 and media on to the bottom of a dish, where it washes media away to leave liquid fluorocarbon walls pinned to the substrate by interfacial forces. Such fluid walls can be built into almost any imaginable 2D circuit in minutes, which we exploit to clone cells using limiting dilution in a way that beats the Poisson limit, sub-culture adherent cells, and feed arrays of cells continuously for a week. This general method should have wide application in biomedicine.One sentence summaryIn the everyday world, we cannot build complex structures out of liquids as they collapse into puddles; in the microworld we can.
Frequency and Prognostic Value of NPM1 Mutations in Sudanese Acute Myeloid Leukemia Patients
Authors: Elzain Eman Ali , Khalil Hiba BadrEldin 
Published: June 2020

AbstractIntroductionAcute myeloid leukemia (AML) is a malignancy of proliferative, clonal, abnormally, or poorly differentiated cells of the hematopoietic system, characterized by clonal evolution and genetic heterogeneity (Döhneret al, 2015). The molecular genetics of AML regarding the prognosis of patients mainly representing by NPM1. NPM1 is a nucleolar protein that located on chromosome5q35.1which shuttles between the nucleus and cytoplasm. It is concerned in multiple functions, including ribosomal protein assembly and transport, control of centrosome duplication, and regulation of the tumor suppressor ARF & p53. NPM1 mutations that relocalize NPM1 from the nucleus into the cytoplasm are associated with development of acute myeloid leukemia (Garzonet al, 2008). The aim of this study was to determine the frequency and clarify the prognostic value of NPM1 mutations among Sudanese patients with acute myeloid leukemia.Materials and MethodsA cross sectional study recruited 100 patients in this study clinically diagnosed firstly (not transformed from any other malignancy) as AML patients based on the diagnostic protocol concern RICK hospital; such as morphological identification, immunophenotyping analysis, and molecular genetics, Of the 100 AML patients, 54% were newly diagnosed and 46% were admitted by chemotherapy treatment and follow up. EDTA blood or bone marrow samples were collected from patients for performing CBC, hematological studies including FAB classification, PCR protocols and sequencing. genomic DNA was extracted from all samples using guanidine method (Ding et al, 2008).ResultsNPM1 mutations detection, sequencing technique was done, and then sequencing analysis by software (Mega 7 Software) (Kumaret al, 2016) revealed that there were no NPM1mutations in Sudanese AML patients.ConclusionThe Sudanese AML patients carry wild type NPM1.
Snx14 proximity labeling reveals a role in saturated fatty acid metabolism and ER homeostasis defective in SCAR20 disease
Authors: Datta Sanchari , Bowerman Jade , Hariri Hanaa , Ugrankar Rupali , Eckert Kaitlyn M. , Corley Chase , Vale Gonçalo , McDonald Jeffrey G. , Henne Mike 
Published: June 2020

AbstractFatty acids (FAs) are central cellular metabolites that contribute to lipid synthesis, and can be stored or harvested for metabolic energy. Dysregulation in FA processing and storage causes toxic FA accumulation or altered membrane compositions and contributes to metabolic and neurological disorders. Saturated lipids are particularly detrimental to cells, but how lipid saturation levels are maintained remains poorly understood. Here, we identify the cerebellar ataxia SCAR20-associated protein Snx14, an endoplasmic reticulum (ER)-lipid droplet (LD) tethering protein, as a novel factor required to maintain the lipid saturation balance of cell membranes. We show thatSNX14KOcells and SCAR20 disease patient-derived cells are hypersensitive to saturated FA (SFA)-mediated lipotoxic cell death that compromises ER integrity. Using APEX2-based proximity labeling, we reveal the protein composition of Snx14-associated ER-LD contacts and define a functional interaction between Snx14 and Δ-9 FA desaturase SCD1. Lipidomic profiling reveals thatSNX14KOcells increase membrane lipid saturation following exposure to palmitate, phenocopying cells with reduced SCD1 activity. In line with this,SNX14KOcells manifest delayed FA processing and lipotoxicity, which can be rescued by SCD1 over-expression. Altogether these mechanistic insights reveal a role for Snx14 in FA and ER homeostasis, defects in which may underlie the neuropathology of SCAR20.Significance StatementSCAR20 disease is an autosomal recessive spinocerebellar ataxia primarily affecting children, and results from loss-of-function mutations in theSNX14gene. Snx14 is an endoplasmic reticulum (ER)-localized protein that localizes to ER-lipid droplet (LD) contacts and promotes LD biogenesis following exogenous FA treatment, but why Snx14 loss causes SCAR20 is unclear. Here, we demonstrate that following exposure to saturated fatty acids, Snx14-deficient cells have defective ER homeostasis and altered lipid saturation profiles. We reveal a functional interaction between Snx14 and fatty acid (FA) desaturase SCD1. Lipidomics shows Snx14-deficient cells contain elevated saturated lipids, closely mirroring SCD1-defective cells. Furthermore, SCD1 over-expression can rescue Snx14 loss. We propose that Snx14 maintains cellular lipid homeostasis, the loss of which underlies the cellular basis for SCAR20 disease.
Flavonols modulate lateral root emergence by scavenging reactive oxygen species inArabidopsis thaliana
Authors: Chapman Jordan M. , Muday Gloria K. 
Published: June 2020

AbstractFlavonoids are plant-specific antioxidant compounds that modulate plant development, which include flavonols and anthocyanins subclasses. InArabidopsis thaliana, mutants in genes encoding each step in the flavonoid biosynthetic pathway have been isolated. We used these mutants to examine the role of flavonols in initiation and emergence of lateral roots and asked whether this regulation occurs through scavenging ROS. Thett4mutants have a defect in the first committed step of flavonoid biosynthesis and have increased lateral root emergence. This phenotype was reversed by both genetic and chemical complementation. Using these flavonoid biosynthetic mutants, we eliminated roles for anthocyanins and the flavonols, quercetin and isorhamnetin, in controlling lateral root development. Thett7-2 mutant has a defect in a branchpoint enzyme blocking quercetin biosynthesis that led to elevated levels of kaempferol and reduced lateral roots. Kaempferol accumulated within lateral root primordia and was significantly increased intt7-2. Thee data are consistent with kaempferol acting as a negative regulator of lateral root emergence. We examined ROS accumulation above and within the primordia using a general ROS sensor and identified increased signal above the primordia of thett4andtt7-2mutants compared to wild type. Using a superoxide specific sensor, we detected a decrease in signal within the primordia oftt7-2, but not thett4mutant, compared to wild type. Together, these results support a model in which increased level of kaempferol intt7-2 leads to a reduction in superoxide concentration in the lateral root primordia thereby reducing ROS-stimulated lateral root emergence.
Scalp EEG interictal high frequency oscillations as an objective EEG biomarker of infantile spasms
Authors: Nariai Hiroki , Hussain Shaun A. , Bernardo Danilo , Motoi Hirotaka , Sonoda Masaki , Kuroda Naoto , Asano Eishi , Nguyen Jimmy C. , Elashoff David , Sankar Raman , Bragin Anatol , Staba Richard J. , Wu Joyce Y. 
Published: June 2020

ABSTRACTObjectiveTo investigate the diagnostic utility of high frequency oscillations (HFOs) via scalp electroencephalogram (EEG) in infantile spasms.MethodsWe retrospectively analyzed interictal slow-wave sleep EEGs sampled at 2,000 Hz recorded from 30 consecutive patients who were suspected of having infantile spasms. We measured the rate of HFOs (80-500 Hz) and the strength of the cross-frequency coupling between HFOs and slow-wave activity (SWA) at 3-4 Hz and 0.5-1 Hz as quantified with modulation indices (MIs).ResultsTwenty-three patients (77%) exhibited active spasms during the overnight EEG recording. Although the HFOs were detected in all children, increased HFO rate and MIs correlated with the presence of active spasms (p < 0.001 by HFO rate; p < 0.01 by MIs at 3-4 Hz; p = 0.02 by MIs at 0.5-1 Hz). The presence of active spasms was predicted by the logistic regression models incorporating HFO-related metrics (AUC: 0.80-0.98) better than that incorporating hypsarrhythmia (AUC: 0.61). The predictive performance of the best model remained favorable (87.5% accuracy) after a cross-validation procedure.ConclusionsIncreased rate of HFOs and coupling between HFOs and SWA are associated with active epileptic spasms.SignificanceScalp-recorded HFOs may serve as an objective EEG biomarker for active epileptic spasms.HighlightsObjective analyses of scalp high frequency oscillations and its coupling with slow-wave activity in infantile spasms were feasible.Increased rate of high frequency oscillations and its coupling with slow-wave activity correlated with active epileptic spasms.The scalp high frequency oscillations were also detected in neurologically normal children (although at the low rate).
Growth assessment of juvenile oil palm (Elaeis guineensisJacq.) intercropped with fruit vegetables in a rainforest zone of Nigeria
Authors: Oluwatobi Ayodele Samuel 
Published: June 2020

AbstractMany farmers spend a lot of money in the control of weeds during the long juvenile phase of oil palm. Intercropping is a popular practice employed by farmers to increase productivity of wide alley and overcome weed problem. However, improper intercropping ofElaeis guineensiswith other crops has impaired the growth and development of the oil palm due to competition for environmental resources. The study was conducted to investigate the impact of intercropping on the growth of juvenile oil palm for 2 years. The research commenced during the rainy season of 2016 at an established juvenile oil palm plantation in Ala, Akure-North Local Government of Ondo State. Four fruit vegetables were intercropped separately within the alley of the plantation at 1, 2 or 3 m away from the oil palms in a randomized complete block design. Growth parameters of intercropped and non-intercropped juvenile oils were compared. Results of the study revealed that at 16 weeks after intercropping (WAI), the intercropped oil palm recorded better growth performance with higher values of canopy spread, number of frond, number of leaflets and trunk height (218.20, 37.00, 87.48 and 38.17 cm) respectively, than the sole oil palms (214.67, 32.83, 72.89 and 31.67) respectively. There was no significant difference in all the growth parameter examined except canopy height at (P<0.05) level of significance. Juvenile oil palm cultivated in rainforest agroecological zone of Nigeria can be intercropped with fruit vegetables without any deleterious effect when intercropped at minimum of 1 m away from the oil palms.
Weed species composition and diversity of 2-year-old oil palm tree/fruit vegetables intercrop in rainforest zone of Nigeria
Authors: Oluwatobi Ayodele Samuel 
Published: June 2020

AbstractThe spacing pattern and growth habit of juvenile oil palm during the early stages of field establishment have often led to serious weed problem until canopy closure at subsequent years. This study was carried out during the rainy season of 2016 to evaluate the weed species composition and diversity of an intercrop between 2-year-old oil palm tree and two fruit vegetables at an oil palm plantation in Ala, Akure-North Local Government, Ondo state, Nigeria. Two accessions of tomato (NGB 01665 and NG/AA/SEP/09/053) and eggplant (NGB 01737) were intercropped within the alley of immature oil palm. Weed sampling was carried out using 0.25 m2quadrat within each experimental plot. Quantitative analysis of weed species parameters and Simpson’s Diversity Index were evaluated. The result revealed that 28, 21 and 20 weed species were found across all the plots at 3, 6 weeks after intercropping (WAI), and after harvesting respectively. Members of Asteraceae produced the highest weed species at 3 WAI (17.857%); Poaceae recorded the highest weed species at 6 WAI and after harvesting (19.048% and 20%) respectively. A total of 23, 16 and 15 broadleaves were found at 3 and 6 WAI, and after harvesting. In all the juvenile oil palm/vegetable intercrops evaluated, the control plot recorded the highest weed species richness at 6 WAI, when compared to other intercropping regimes. The control and juvenile oil palm/tomato (NGB 01665) intercrop plot recorded the highest and lowest Simpson’s Indices of Diversity at 6 WAI (0.877 and 0.734) respectively.
Air pollution control efficacy and health impacts: A global observed study from 2000 to 2016
Authors: Han Chunlei , Xu Rongbin , Zhang Yajuan , Yu Wenhua , Li Shanshan , Zhang Zhongwen , Morawska Lidia , Heyworth Jane , Jalaludin Bin , Morgan Geoffrey , Marks Guy , Abramson Michael , Sun Liwei , Guo Yuming 
Published: June 2020

AbstractBackgroundPM2.5 concentrations vary between countries with similar CO2 emissions, possibly due to differences in air pollution control efficacy. However, no indicator of the level of air pollution control efficacy has yet been developed. We aimed to develop such an indicator, and to evaluate its global and temporal distribution and its association with country-level health metrics.MethodA novel indicator, ground level population-weighted average PM2.5 concentration per unit CO2 emission per capita (PM2.5/CO2, written as PC in abbreviation), was developed to assess country-specific air pollution control efficacy. We estimated and mapped the global average distribution of PC and PC changes during 2000–2016 across 196 countries. Pearson correlation coefficients and Generalized Additive Mixed Model (GAMM) were used to evaluate the relationship between PC and health metrics.ResultsPC varied by country with an inverse association with the economic development. PC showed an almost stable trend globally from 2000 to 2016 with the low income groups increased. The Pearson correlation coefficients between PC and life expectancy at birth (LE), Infant-mortality rate (IMR), Under-five mortality rate (U5MR) and logarithm of GDP per capita (LPGDP) were –0.566, 0.646, 0.659, –0.585 respectively (all P-values <0.001). Compared with PM2.5 or CO2, PC could explain more variation of LE, IMR and U5MR. The association between PC and health metrics was independent of GDP per capita.ConclusionsPC might be a good indicator for air pollution control efficacy and was related to important health indicators. Our findings provide a new way to interpret health inequity across the globe from the point of air pollution control efficacy.
nAdder: A scale-space approach for the 3D analysis of neuronal traces
Authors: Phan Minh Son , Matho Katherine , Beaurepaire Emmanuel , Livet Jean , Chessel Anatole 
Published: June 2020

AbstractTridimensional microscopy and algorithms for automated segmentation and tracing are revolutionizing neuroscience through the generation of growing libraries of neuron reconstructions. Innovative computational methods are needed to analyze these neural traces. In particular, means to analyse the geometric properties of traced neurites along their trajectory have been lacking. Here, we propose a local tridimensional (3D) scale metric derived from differential geometry, which is the distance in micrometers along which a curve is fully 3D as opposed to being embedded in a 2D plane or 1D line. We apply this metric to various neuronal traces ranging from single neurons to whole brain data. By providing a local readout of the geometric complexity, it offers a new mean of describing and comparing axonal and dendritic arbors from individual neurons or the behavior of axonal projections in different brain regions. This broadly applicable approach termed nAdder is available through the GeNePy3D open-source Python quantitative geometry library.
ToR-ORd-dynCl: an update of the ToR-ORd model of human ventricular cardiomyocyte with dynamic intracellular chloride
Authors: Tomek Jakub , Bueno-Orovio Alfonso , Rodriguez Blanca 
Published: June 2020

Recently, our group published a new model of human ventricular cardiomyocyte named ToR-ORd (Tomek et al., 2019). Its development, calibration, and validation, were performed using a broad range of human experimental data and brought general insights into modelling of ionic channels. Model calibration ensured the reproduction of key physiological cellular features, with independent multiscale validation demonstrating a correct response to channel blocking drugs and pathophysiological remodelling.However, for very long simulations (several hours rather than minutes), the ToR-ORd simulations display a drift in its behaviour, caused by modelling chloride concentrations as constant values. This may be a limitation for simulations considering extremely long protocols, or for studies on model stability. To remedy this, we present here an updated version, termed ToR-ORd-dynCl, with dynamic representation of intracellular chloride. This model behaves very similarly to the original ToR-ORd, but with stable properties over long simulations and only a small increase in model complexity.