bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overdispersed gene expression in schizophrenia
Authors: Huang Guangzao , Osorio Daniel , Guan Jinting , Ji Guoli , Cai James J. 
Published: April 2020

AbstractSchizophrenia (SCZ) is a severe, highly heterogeneous psychiatric disorder with varied clinical presentations. The polygenic genetic architecture of SCZ makes identification of causal variants a daunting task. Gene expression analyses hold the promise of revealing connections between dysregulated transcription and underlying variants in SCZ. However, the most commonly used differential expression analysis often assumes grouped samples are from homogeneous populations and thus cannot be used to detect expression variance differences between samples. Here, we applied the test for equality of variances to normalized expression data, generated by the CommonMind Consortium (CMC), from brains of 212 SCZ and 214 unaffected control (CTL) samples. We identified 87 genes, includingVEGFA(vascular endothelial growth factor) andBDNF(brain-derived neurotrophic factor), that showed a significantly higher expression variance among SCZ samples than CTL samples. In contrast, only one gene showed the opposite pattern. To extend our analysis to gene sets, we proposed a Mahalanobis distance-based test for multivariate homogeneity of group dispersions, with which we identified 110 gene sets with a significantly higher expression variability in SCZ, including sets of genes encoding phosphatidylinositol 3-kinase (PI3K) complex and several others involved in cerebellar cortex morphogenesis, neuromuscular junction development, and cerebellar Purkinje cell layer development. Taken together, our results suggest that SCZ brains are characterized by overdispersed gene expression—overall gene expression variability among SCZ samples is significantly higher than that among CTL samples. Our study showcases the application of variability-centric analyses in SCZ research.
A 3 km spatially and temporally consistent European daily soil moisture reanalysis from 2000 to 2015
Authors: Naz Bibi S. , Kollet Stefan , Franssen Harrie-Jan Hendricks , Montzka Carsten , Kurtz Wolfgang 
Published: April 2020

AbstractHigh-resolution soil moisture (SM) information is essential to many regional applications in hydrological and climate sciences. Many global estimates of surface SM are provided by satellite sensors, but at coarse spatial resolutions (lower than 25 km), which are not suitable for regional hydrologic and agriculture applications. Here we present a 16 years (2000–2015) high-resolution spatially and temporally consistent surface soil moisture reanalysis (ESSMRA) dataset (3 km, daily) over Europe from a land surface data assimilation system. Coarse-resolution satellite derived soil moisture data were assimilated into the community land model (CLM3.5) using an ensemble Kalman filter scheme, producing a 3 km daily soil moisture reanalysis dataset. Validation against 112 in-situ soil moisture observations over Europe shows that ESSMRA captures the daily, inter-annual, intra-seasonal patterns well with RMSE varying from 0.04 to 0.06 m3m−3 and correlation values above 0.5 over 70% of stations. The dataset presented here provides long-term daily surface soil moisture at a high spatiotemporal resolution and will be beneficial for many hydrological applications over regional and continental scales.
The impacts of intrauterine Bisphenol A exposure on pregnancy and expression of miRNAs related to heart development and diseases in animal model
Authors: Rasdi Zatilfarihiah , Kamaludin Roziana , Ab. Rahim Sharaniza , Syed Ahmad Fuad Syed Baharom , Othman Mohd Hafiz Dzarfan , Siran Rosfaiizah , Mohd Nor Noor Shafina , Abdul Hamid Hasani Narimah , Sheikh Abdul Kadir Siti Hamimah 
Published: April 2020

AbstractThis study aimed to examine the impact of BPA exposure on pregnancy and foetuses on cardiac tissues and the expression of cardiac microRNAs (miRNAs) related to heart development and diseases. Pregnancy is known to be the “critical windows” in determining the offspring physical and cells development in their life after birth. The increment of the risk of cardiovascular disease (CVD) in a later stage of life has been reported by few studies demonstrated from prenatal exposure of BPA. BPA has been shown to alter miRNAs expression profiles for organ development, regeneration and metabolic functions. These alterations have been associated with the risk of CVDs. However, the associations between pregnancy outcomes and miRNAs expression in cardiac of mother- and foetuses-exposed to BPA are still not entirely explored. In BPA-exposed pregnant rat groups, a significant weight gained was observed in comparison to control (p < 0.05). Interestingly, significant changes in systolic and diastolic blood pressure between the first and third trimester of BPA-exposed pregnant rats were also observed (p < 0.05). In BPA-exposed pregnant rats, miR-499-5p was significantly altered in the heart (p < 0.01). Meanwhile, altered miR-17-5p, -208-3p, and -210-3p expressions were observed in all heart of the foetuses from BPA-exposed pregnant rats (p < 0.05). In H&E staining, BPA-exposed foetal hearts showed a sign of fibrosis while BPA-exposed pregnant rats showed muscle remnant. Masson trichrome staining further confirmed the presence of fibrosis observed in BPA-exposed foetal heart and reduced expression of cardiac troponin I (cTnI) was also observed in BPA-exposed foetal heart. In summary, altered cardiac miRNAs with histological changes were observed in both mother- and foetus-exposed BPA These findings put forward the importance of future work to further understand how prenatal BPA exposure affect foetuses in their later stage of life.
Comparison of wavelet and correlation indices of cerebral autoregulation in a pediatric swine model of cardiac arrest
Authors: Liu Xiuyun , Hu Xiao , Brady Ken M. , Koehler Raymond , Smielewski Peter , Czosnyka Marek , Donnelly Joseph , Lee Jennifer K. 
Published: April 2020

AbstractExisting cerebrovascular blood pressure autoregulation metrics have not been translated to clinical care for pediatric cardiac arrest, in part because signal noise causes high index time-variability. We tested whether a wavelet method that uses near-infrared spectroscopy (NIRS) or intracranial pressure (ICP) decreases index variability compared to that of commonly used correlation indices. We also compared whether the methods identify the optimal arterial blood pressure (ABPopt) and lower limit of autoregulation (LLA). 68 piglets were randomized to cardiac arrest or sham procedure with continuous monitoring of cerebral blood flow using laser Doppler, NIRS and ICP. The arterial blood pressure (ABP) was gradually reduced until it dropped to below the LLA. Several autoregulation indices were calculated using correlation and wavelet methods, including the pressure reactivity index (PRx and wPRx), cerebral oximetry index (COx and wCOx), and hemoglobin volume index (HVx and wHVx). Wavelet methodology had less index variability with smaller standard deviations. Both wavelet and correlation methods distinguished functional autoregulation (ABP above LLA) from dysfunctional autoregulation (ABP below the LLA). Both wavelet and correlation methods also identified ABPopt with high agreement. Thus, wavelet methodology using NIRS may offer an accurate vasoreactivity monitoring method with reduced signal noise after pediatric cardiac arrest.
The conifer root rot pathogens Heterobasidion irregulare and Heterobasidion occidentale employ different strategies to infect Norway spruce
Authors: Hu Yang , Elfstrand Malin , Stenlid Jan , Durling Mikael Brandström , Olson Åke 
Published: April 2020

AbstractHeterobasidion irregulare and H. occidentale are two closely related conifer root rot pathogens in the H. annosum sensu lato (s.l.) species complex. The two species H. irregulare and H. occidentale have different host preference with pine and non-pine tree species favored, respectively. The comparison of transcriptomes of H. irregulare and H. occidentale growing in Norway spruce bark, a susceptible host non-native to North America, showed large differences in gene expression. Heterobasidion irregulare induced more genes involved in detoxification of host compounds and in production of secondary metabolites, while the transcriptome induced in H. occidentale was more oriented towards carbohydrate degradation. Along with their separated evolutionary history, the difference might be driven by their host preferences as indicated by the differentially expressed genes enriched in particular Gene Ontology terms.
µgreen-db: a reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria
Authors: Djemiel Christophe , Plassard Damien , Terrat Sébastien , Crouzet Olivier , Sauze Joana , Mondy Samuel , Nowak Virginie , Wingate Lisa , Ogée Jérôme , Maron Pierre-Alain 
Published: April 2020

AbstractStudying the ecology of photosynthetic microeukaryotes and prokaryotic cyanobacterial communities requires molecular tools to complement morphological observations. These tools rely on specific genetic markers and require the development of specialised databases to achieve taxonomic assignment. We set up a reference database, called µgreen-db, for the 23S rRNA gene. The sequences were retrieved from generalist (NCBI, SILVA) or Comparative RNA Web (CRW) databases, in addition to a more original approach involving recursive BLAST searches to obtain the best possible sequence recovery. At present, µgreen-db includes 2,326 23S rRNA sequences belonging to both eukaryotes and prokaryotes encompassing 442 unique genera and 736 species of photosynthetic microeukaryotes, cyanobacteria and non-vascular land plants based on the NCBI and AlgaeBase taxonomy. When PR2/SILVA taxonomy is used instead, µgreen-db contains 2,217 sequences (399 unique genera and 696 unique species). Using µgreen-db, we were able to assign 96% of the sequences of the V domain of the 23S rRNA gene obtained by metabarcoding after amplification from soil DNA at the genus level, highlighting good coverage of the database. µgreen-db is accessible at http://microgreen-23sdatabase.ea.inra.fr.
Dynamical Quantum Filtering via Enhanced Scattering of para-H2 on the Orientationally Anisotropic Potential of SrTiO3(001)
Authors: Shimizu Koji , Diño Wilson Agerico , Nakanishi Hiroshi , Kasai Hideaki , Takeyasu Kotaro , Fukutani Katsuyuki , Yajima Ayako 
Published: April 2020

AbstractQuantum dynamics calculation, performed on top of density functional theory (DFT)-based total energy calculations, show dynamical quantum filtering via enhanced scattering of para-H2 on SrTiO3(001). We attribute this to the strongly orientation-dependent (electrostatic) interaction potential between the H2 (induced) quadrupole moment and the surface electric field gradient of ionic SrTiO3(001). These results suggest that ionic surfaces could function as a scattering/filtering media to realize rotationally state-resolved H2. This could find significant applications not only in H2 storage and transport, but also in realizing materials with pre-determined characteristic properties.
Phenotypic and functional characterization of natural killer cells in rheumatoid arthritis-regulation with interleukin-15
Authors: Lin Syh-Jae , Hsu Chien-Ya , Kuo Ming-Ling , Lee Pei-Tzu , Hsiao Hsiu-Shan , Chen Ji-Yih 
Published: April 2020

AbstractRheumatoid arthritis (RA) is an autoimmune disease characterized by synovial inflammation and joint destruction. Previous studies have shown that natural killer (NK) cells may play an important role in the pathogenesis of RA. Interleukin (IL)-15, a pro-inflammatory cytokine which induces proliferation and differentiation of NK cells, is overexpressed in RA. In this present study, we examine various NKRs and adhesion molecule expression on NK cells from RA patients and their response to IL-15 stimulation. We also sought to study cytokine-induced memory-like (CIML) NK cells in RA patients. We established that 1. RA patients had higher NK cell percentages in peripheral blood and their serum IL-15 levels were higher compared to healthy volunteers; 2. NK cells from RA patients showed lower NKp46 expression and an impaired CD69 response to IL-15; 3. NK cells from RA patients showed higher CD158b and CD158e expression but lower CD62L expression; 4. exogenous IL-15 up-regulated CD69, CD158b, CD158e but down-regulated NKp46 and CD62L expression in RA; 5. As to CIML NK cells, restimulation - induced NK cytotoxicity and IFN-γ production was impaired in RA patients, 6. Reduced NKp46, perforin, and granzyme B expression on NK cells was found in RA patients with bone deformity and erosion, 7. RA disease activity (DAS28) showed inverse correlation with the percentages of CD56+CD3− NK cells, and NKp46 and perforin expression on NK cells, respectively. Taken together, our study demonstrated differential expression of various NK receptors in RA patients. NKp46, CD158e, and perforin expression on NK cells may serve as markers of RA severity.
High density cultivation for efficient sesquiterpenoid biosynthesis in Synechocystis sp. PCC 6803
Authors: Dienst Dennis , Wichmann Julian , Mantovani Oliver , Rodrigues João S. , Lindberg Pia 
Published: April 2020

AbstractCyanobacteria and microalgae are attractive photoautotrophic host systems for climate-friendly production of fuels and other value-added biochemicals. However, for economic applications further development and implementation of efficient and sustainable cultivation strategies are essential. Here, we present a comparative study on cyanobacterial sesquiterpenoid biosynthesis in Synechocystis sp. PCC 6803 using a commercial lab-scale High Density Cultivation (HDC) platform in the presence of dodecane as in-situ extractant. Operating in a two-step semi-batch mode over a period of eight days, volumetric yields of (E)-α-bisabolene were more than two orders of magnitude higher than previously reported for cyanobacteria, with final titers of 179.4 ± 20.7 mg * L−1. Likewise, yields of the sesquiterpene alcohols (−)-patchoulol and (−)-α-bisabolol were many times higher than under reference conditions, with final titers of 17.3 ± 1.85 mg * L−1 and 96.3 ± 2.2 mg * L−1, respectively. While specific productivity was compromised particularly for (E)-α-bisabolene in the HDC system during phases of high biomass accumulation rates, volumetric productivity enhancements during linear growth at high densities were more pronounced for (E)-α-bisabolene than for the hydroxylated terpenoids. Together, this study provides additional insights into cell density-related process characteristics, introducing HDC as highly efficient strategy for phototrophic terpenoid production in cyanobacteria.
Neuropeptide Y deficiency induces anxiety-like behaviours in zebrafish (Danio rerio)
Authors: Shiozaki Kazuhiro , Kawabe Momoko , Karasuyama Kiwako , Kurachi Takayoshi , Hayashi Akito , Ataka Koji , Iwai Haruki , Takeno Hinako , Hayasaka Oki , Kotani Tomonari , Komatsu Masaharu , Inui Akio 
Published: April 2020

AbstractNeuropeptide Y (NPY) controls energy homeostasis including orexigenic actions in mammalians and non-mammalians. Recently, NPY has attracted attention as a mediator of emotional behaviour and psychosomatic diseases. However, its functions are not fully understood. We established npy gene-deficient (NPY-KO) zebrafish (Danio rerio) to assess the relationship between NPY and emotional behaviours. The NPY-KO zebrafish exhibited similar growth, but pomc and avp mRNA levels in the brain were higher as compared to wild-type fish. NPY-KO zebrafish exhibited several anxiety-like behaviours, such as a decrease in social interaction in mirror test and decreased locomotion in black-white test. The acute cold stress-treated NPY-KO zebrafish exhibited anxiety-like behaviours such as remaining stationary and swimming along the side of the tank in the mirror test. Moreover, expression levels of anxiety-associated genes (orx and cck) and catecholamine production (gr, mr, th1 and th2) were significantly higher in NPY-KO zebrafish than in wild-type fish. We demonstrated that NPY-KO zebrafish have an anxiety phenotype and a stress-vulnerability like NPY-KO mice, whereby orx and/or catecholamine signalling may be involved in the mechanism actions.
Variations of circulating miRNA in paediatric patients with Heart Failure supported with Ventricular Assist Device: a pilot study
Authors: Ragusa Rosetta , Di Molfetta Arianna , D’Aurizio Romina , Del Turco Serena , Cabiati Manuela , Del Ry Silvia , Basta Giuseppina , Pitto Letizia , Amodeo Antonio , Trivella Maria Giovanna , Rizzo Milena , Caselli Chiara 
Published: April 2020

AbstractCirculating miRNAs (c-miRNAs) are promising biomarkers for HF diagnosis and prognosis. There are no studies on HF pediatric patients undergoing VAD-implantation. Aims of this study were: to examine the c-miRNAs profile in HF children; to evaluate the effects of VAD on c-miRNAs levels; to in vitro validate putative c-miRNA targets. c-miRNA profile was determined in serum of HF children by NGS before and one month after VAD-implant. The c-miRNA differentially expressed were analyzed by real time-PCR, before and at 4 hrs,1,3,7,14,30 days after VAD-implant. A miRNA mimic transfection study in HepG2 cells was performed to validate putative miRNA targets selected through miRWalk database. Thirteen c-miRNAs were modified at 30 days after VAD-implant compared to pre-VAD at NSG, and, among them, six c-miRNAs were confirmed by Real-TimePCR. Putative targets of the validated c-miRNAs are involved in the hemostatic process. The in vitro study confirmed a down-regulatory effect of hsa-miR-409-3p towards coagulation factor 7 (F7) and F2. Of note, all patients had thrombotic events requiring pump change. In conclusion, in HF children, the level of six c-miRNAs involved in the regulation of hemostatic events changed after 30 days of VAD-treatment. In particular, the lowering of c-miR-409-3p regulating both F7 and F2 could reflect a pro-thrombotic state after VAD-implant.
Exploring the configuration spaces of surface materials using time-dependent diffraction patterns and unsupervised learning
Authors: Packwood Daniel M. 
Published: April 2020

AbstractComputational methods for exploring the atomic configuration spaces of surface materials will lead to breakthroughs in nanotechnology and beyond. In order to develop such methods, especially ones utilizing machine learning approaches, descriptors which encode the structural features of the candidate configurations are required. In this paper, we propose the use of time-dependent electron diffraction simulations to create descriptors for the configurations of surface materials. Our proposal utilizes the fact that the sub-femtosecond time-dependence of electron diffraction patterns are highly sensitive to the arrangement of atoms in the surface region of the material, allowing one to distinguish configurations which possess identical symmetry but differ in the locations of the atoms in the unit cell. We demonstrate the effectiveness of this approach by considering the simple cases of copper(111) and an organic self-assembled monolayer system, and use it to search for metastable configurations of these materials.
Geographic variation in baseline innate immune function does not follow variation in aridity along a tropical environmental gradient
Authors: Nwaogu Chima J. , Cresswell Will , Tieleman B. Irene 
Published: April 2020

AbstractGeographic variation in aridity determines environmental productivity patterns, including large-scale variability in pathogens, vectors and associated diseases. If disease risk decreases with increasing aridity and is matched by immune defense, we predict a decrease in innate immune function along a gradient of increasing aridity from the cool-wet forest to the hot-dry Sahel, from south to north in Nigeria. We sampled blood and measured five innate immune indices from 286 Common BulbulsPycnonotus barbatusbetween 6 and 13°N. We sampled in the dry season; we resampled the first location (Jos) also as the last sample location to test temporal change in immune function. Immune indices did not decrease with aridity. One immune index, nitric oxide concentration showed a weak quadratic pattern. In Jos, ovotransferrin concentration, haemagglutination and haemolysis titres increased 12 weeks into the dry season, contrary to expectations that immune indices should decrease with increased dryness. In this tropical system, innate immune function does not decrease with increasing aridity but temporal factors within a location may influence immune function more strongly than spatial variation in aridity, suggesting that immune variation does not follow a simple environmental productivity pattern. Consequently, caution should probably be exercised in predicting effects of climate variability on immune function or disease risk.
Assessment of metals induced histopathological and gene expression changes in different organs of non-diabetic and diabetic rats
Authors: Riaz Muhammad Ahsan , Nisa Zaib Un , Anjum Muhammad Sohail , Butt Hira , Mehmood Azra , Riaz Ayesha , Akhtar Amtul Bari Tabinda 
Published: April 2020

AbstractDiabetes is a complex metabolic disorder and different environmental toxicants including heavy metals have been involved in diabetes induction. Therefore, assessment of the environmental risk factors and heavy metals induced toxicity have become critical for reducing the consequences of metals pollutants. Previously, we reported heavy metals induced nephrotoxicity in non-diabetic and diabetic rats. Here, we extended our analysis by examining the heavy metals induced organs (heart, kidney, liver, pancreas, and spleen) damage in diabetic and non-diabetic Wistar rats using histopathology and quantitative real-time PCR (qRT-PCR). Following the generation of the diabetic rat model, the animals were exposed to heavy metals including lead (Pb), arsenic (As), manganese (Mn) and cadmium (Cd). Both non-diabetic and diabetic rats were exposed to heavy metals for 30 days and subsequently, the heart, kidney, liver, pancreas and spleen tissues were examined. Heavy metal treatment resulted in irregularly arranged myofibrils and vacuolization in the heart tissue of metal treated groups as evident from hematoxylin and eosin (H & E) staining. The kidney tissue of rats treated with heavy metals showed tubular degeneration, fibrosis, hemorrhage, and vacuolation. The liver of the heavy metals treated rats exhibited cellular degeneration and necrosis. The pancreatic tissue of streptozotocin injected untreated and metal treated rats revealed severe degeneration, necrosis, degranulation, shrinkage, and depression in the islets of Langerhans. Increased red pulp area and congestion were observed in the spleen of the metal mixture treated non-diabetic and diabetic rats. In line with the histological data, the qRT-PCR analysis showed downregulated expression ofBcl2and upregulation ofCaspase-3in non-diabetic and diabetic metal treated rats as compared to the non-diabetic untreated rats. In conclusion, the present study revealed, diabetic rats are more prone to metal alone as well as metal mixture induced organ damage as compared to non-diabetic rats.