bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aneurysmal subarachnoid haemorrhage: Effect of CRHR1 genotype on mental health-related quality of life
Authors: Vetkas Artur , Prans Ele , Kõks Sulev , Rätsep Tõnu , Asser Toomas 
Published: January 2020

AbstractQuality of life (QoL) disturbances are common after aneurysmal subarachnoid hemorrhage (aSAH) both in physical and mental health domains and their causes are not clearly understood. Corticotropin-releasing hormone receptor 1 (CRHR1) is involved in stress reactivity and development of mental health disturbances after negative life-events. We performed a retrospective cohort study of long-term QoL outcomes among 125 surgically treated aSAH patients (2001–2013). QoL was assessed with Short Form Health Survey (SF-36) and compared to an age and gender matched general population. Genotyping of CRHR1 single nucleotide polymorphisms was performed (Rs7209436, Rs110402, Rs242924) and their effect on QoL scores was explored. aSAH patients experienced a reduced quality of life in all domains. CRHR1 minor genotype was associated with higher SF-36 mental health (OR = 1.31–1.6, p < 0.05), role-emotional (OR = 1.57, p = 0.04) and vitality scores (OR = 1.31–1.38, p < 0.05). Association of all studied SNP’s with vitality and Rs242924 with mental health scores remained statistically significant after Bonferroni correction. Mental quality of life scores were associated with physical state of patients, antidepressant history and CRHR1 genotype. Predisposition to mental health disturbances after stressful life-events might be associated with reduced mental QoL after aSAH and selected patients could be provided advanced counselling in the recovery phase.
A novel lncRNA as a positive regulator of carotenoid biosynthesis in Fusarium
Authors: Parra-Rivero Obdulia , Pardo-Medina Javier , Gutiérrez Gabriel , Limón M. Carmen , Avalos Javier 
Published: January 2020

AbstractThe fungiFusarium oxysporumandFusarium fujikuroiproduce carotenoids, lipophilic terpenoid pigments of biotechnological interest, with xanthophyll neurosporaxanthin as the main end product. Their carotenoid biosynthesis is activated by light and negatively regulated by the RING-finger protein CarS. Global transcriptomic analysis identified in both species a putative 1-kb lncRNA that we callcarP, referred to asFo-carPandFf-carPin each species, upstream to the genecarSand transcribed from the same DNA strand.Fo-carPandFf-carPare poorly transcribed, but their RNA levels increase incarSmutants. The deletion ofFo-carPorFf-carPin the respective species results in albino phenotypes, with strong reductions in mRNA levels of structural genes for carotenoid biosynthesis and higher mRNA content of thecarSgene, which could explain the low accumulation of carotenoids. Upon alignment,Fo-carPandFf-carPshow 75–80% identity, with short insertions or deletions resulting in a lack of coincident ORFs. Moreover, none of the ORFs found in their sequences have indications of possible coding functions. We conclude thatFo-carPandFf-carPare regulatory lncRNAs necessary for the active expression of the carotenoid genes inFusariumthrough an unknown molecular mechanism, probably related to the control ofcarSfunction or expression.
Targeted metabolomics of pellicle and saliva in children with different caries activity
Authors: Schulz Annika , Lang Roman , Behr Jürgen , Hertel Susann , Reich Marco , Kümmerer Klaus , Hannig Matthias , Hannig Christian , Hofmann Thomas 
Published: January 2020

AbstractPellicle is the initial proteinaceous layer that is formed almost instantaneously on all solid surfaces in the oral cavity. It is of essential relevance for any interactions and metabolism on the tooth surface. Up to now, there is no information on the metabolome of this structure. Accordingly, the present study aims to characterise the metabolomic profile ofin-situpellicle in children with different caries activity for the first time in comparison to saliva. Small molecules such as carbohydrates, amino acids, organic acids, and fatty acids, putatively involved in the formation of caries were quantified using mass spectrometry (MS)-based techniques, such as (stable isotope dilution analysis)-ultra-performance liquid chromatography-tandem MS and gas chromatography/electron ionisation-MS. Pellicle and corresponding saliva samples were collected from caries-active, caries-free and caries-rehabilitated 4- to 6-year-old children. The most abundant analytes in pellicle were acetic acid (1.2–10.5 nmol/cm2), propionic acid (0.1–8.5 nmol/cm2), glycine (0.7–3.5 nmol/cm2), serine (0.08–2.3 nmol/cm2), galactose (galactose + mannose; 0.035–0.078 nmol/cm2), lactose (0.002–0.086 nmol/cm2), glucose (0.018–0.953 nmol/cm2), palmitic acid (0.26–2.03 nmol/cm2), and stearic acid (0.34–1.81 nmol/cm2). Significant differences depending on caries activity were detected neither in saliva nor in the corresponding pellicle samples.
Regrowth of zebrafish caudal fin regeneration is determined by the amputated length
Authors: Uemoto Toshiaki , Abe Gembu , Tamura Koji 
Published: January 2020

AbstractFish have a high ability to regenerate fins, including the caudal fin. After caudal fin amputation, original bi-lobed morphology is reconstructed during its rapid regrowth. It is still controversial whether positional memory in the blastema cells regulates reconstruction of fin morphology as in amphibian limb regeneration, in which limb blastema cells located at the same proximal-distal level have the same positional identity. We investigated growth period and growth rate in zebrafish caudal fin regeneration. We found that both the growth period and growth rate differed for fin rays that were amputated at the same proximal-distal level, indicating that it takes different periods of time for fin rays to restore their original lengths after straight amputation. We also show that more proximal amputation takes longer period to reconstruct the original morphology/size than more distal amputation. Statistical analysis suggested that both the growth period/rate are determined by amputated length (depth) regardless of the fin ray identity along dorsal-ventral axis. In addition, we suggest the possibility that the structural/physical condition such as width of the fin ray at the amputation site (niche at the stump) may determine the growth period/rate.
Molecular characterization of sarcomatoid clear cell renal cell carcinoma unveils new candidate oncogenic drivers
Authors: Malouf Gabriel G. , Flippot Ronan , Dong Yiyu , Dinatale Renzo G. , Chen Ying-Bei , Su Xiaoping , Compérat Eva , Rouprêt Morgan , Mano Roy , Blum Kyle A. , Yao Hui , Mouawad Roger , Spano Jean-Philippe , Khayat David , Karam Jose A. , Ho Thai H. , Tickoo Satish K. , Russo Paul , Hsieh James J. , Tannir Nizar M. , Hakimi Abraham A. 
Published: January 2020

AbstractSarcomatoid clear-cell renal cell carcinomas (sRCC) are associated with dismal prognosis. Genomic alterations associated with sarcomatoid dedifferentiation are poorly characterized. We sought to define the genomic landscape of sRCC and uncover potentially actionable therapeutic targets. We assessed the genomic landscape of sRCC using targeted panel sequencing including patients with microdissected sarcomatoid and epithelial components. Along with common genomic alterations associated with clear-cell histology, we found that Hippo was one of the most frequently altered pathways in these tumours. Hippo alterations were differentially enriched in sRCC compared to non-sRCC. Functional analysis showed that Hippo members mutations were associated with higher nuclear accumulation of YAP/TAZ, core effectors of the Hippo pathway. In a NF2-mutant sRCC model, YAP1 knockdown and NF2 reconstitution suppressed cell proliferation, tumour growth and invasion, both in vitro and in vivo. Overall, we show that Hippo pathway alterations are a feature of sRCC, and enable the exploration of the Hippo pathway as a novel potential therapeutic target.
Improved multiparametric scrape loading-dye transfer assay for a simultaneous high-throughput analysis of gap junctional intercellular communication, cell density and viability
Authors: Dydowiczová Aneta , Brózman Ondřej , Babica Pavel , Sovadinová Iva 
Published: January 2020

AbstractGap junctional intercellular communication (GJIC) is a vital cellular process required for maintenance of tissue homeostasis. In vitro assessment of GJIC represents valuable phenotypic endpoint that could be effectively utilized as an integral component in modern toxicity testing, drug screening or biomedical in vitro research. However, currently available methods for quantifying GJIC with higher-throughputs typically require specialized equipment, proprietary software and/or genetically engineered cell models. To overcome these limitations, we present here an innovative adaptation of traditional, fluorescence microscopy-based scrape loading-dye transfer (SL-DT) assay, which has been optimized to simultaneously evaluate GJIC, cell density and viability. This multiparametric method was demonstrated to be suitable for various multiwell microplate formats, which facilitates an automatized image acquisition. The assay workflow is further assisted by an open source-based software tools for batch image processing, analysis and evaluation of GJIC, cell density and viability. Our results suggest that this approach provides a simple, fast, versatile and cost effective way for in vitro high-throughput assessment of GJIC and other related phenotypic cellular events, which could be included into in vitro screening and assessment of pharmacologically and toxicologically relevant compounds.
Experimental and Numerical Sensitivity Assessment of Viscoelasticity for Polymer Composite Materials
Authors: Javidan Mohammad Mahdi , Kim Jinkoo 
Published: January 2020

AbstractViscoelastic polymer composites are widely used for vibration control in different fields of engineering like aerospace, mechanical, and structural engineering. The viscoelastic properties of these materials are strain rate-dependent and are highly related to frequency. Yet to date, less attention has been paid to quantifying the effects of these parameters and their interactions on damping properties and providing an approximation method for further applications. In the present research, a series of experimental tests was conducted on a viscoelastic material and the experimental data were numerically analyzed in detail. Sensitivity analyses are usually applied to quantify uncertainty using sampling techniques. However, in this study a method was proposed to derive a closed-form solution using the response surface function and a derivative-based global sensitivity analysis to evaluate the output contribution of each parameter. These effects were quantified and several approximation statistics were provided for future engineering implementations. The computational evaluation conducted in this study gives a detailed insight into the mechanical behavior of viscoelastic materials.
Predicting changes in bee assemblages following state transitions at North American dryland ecotones
Authors: Kazenel Melanie R. , Wright Karen W. , Bettinelli Julieta , Griswold Terry L. , Whitney Kenneth D. , Rudgers Jennifer A. 
Published: January 2020

AbstractDrylands worldwide are experiencing ecosystem state transitions: the expansion of some ecosystem types at the expense of others. Bees in drylands are particularly abundant and diverse, with potential for large compositional differences and seasonal turnover across ecotones. To better understand how future ecosystem state transitions may influence bees, we compared bee assemblages and their seasonality among sites at the Sevilleta National Wildlife Refuge (NM, USA) that represent three dryland ecosystem types (and two ecotones) of the southwestern U.S. (Plains grassland, Chihuahuan Desert grassland, and Chihuahuan Desert shrubland). Using passive traps, we caught bees during two-week intervals from March–October, 2002–2014. The resulting dataset included 302 bee species and 56 genera. Bee abundance, composition, and diversity differed among ecosystems, indicating that future state transitions could alter bee assemblage composition in our system. We found strong seasonal bee species turnover, suggesting that bee phenological shifts may accompany state transitions. Common species drove the observed trends, and both specialist and generalist bee species were indicators of ecosystem types or months; these species could be sentinels of community-wide responses to future shifts. Our work suggests that predicting the consequences of global change for bee assemblages requires accounting for both within-year and among-ecosystem variation.
Wurtzite AlGaAs Nanowires
Authors: Leandro L. , Reznik R. , Clement J. D. , Repän J. , Reynolds M. , Ubyivovk E. V. , Shtrom I. V. , Cirlin G. , Akopian N. 
Published: January 2020

AbstractSemiconducting nanowires, unlike bulk, can be grown in both wurtzite and zincblende crystal phases. This unique feature allows for growth and investigation of technologically important and previously unexplored materials, such as wurtzite AlGaAs. Here we grow a series of wurtzite AlGaAs nanowires with Al content varying from 0.1 to 0.6, on silicon substrates and through a comparative structural and optical analysis we experimentally derive, for the first time, the formula for the bandgap of wurtzite AlGaAs. Moreover, bright emission and short lifetime of our nanowires suggest that wurtzite AlGaAs is a direct bandgap material.
Systematic impacts of chronic unpredictable mild stress on metabolomics in rats
Authors: Geng Chunmei , Guo Yujin , Wang Changshui , Liao Dehua , Han Wenxiu , Zhang Jing , Jiang Pei 
Published: January 2020

AbstractDepression is the most common disabling psychiatric disease, with a high prevalence and mortality. Chronic unpredictable mild stress (CUMS) is a well-accepted method used to mimic clinical depression. Recent evidence has consistently suggested that the cumulative effects of CUMS could lead to allostatic overload in the body, thereby inducing systemic disorders; however, there are no previous systematic metabonomics studies on the main stress-targeted tissues associated with depression. A non-targeted gas chromatography–mass spectrometry (GC–MS) approach was used to identify metabolic biomarkers in the main stress-targeted tissues (serum, heart, liver, brain, and kidney) in a CUMS model of depression. Male Sprague–Dawley rats were randomly allocated to the CUMS group (n = 8) or a control group (n = 8). Multivariate analysis was performed to identify the metabolites that were differentially expressed between the two groups. There were 10, 10, 9, 4, and 7 differentially expressed metabolites in the serum, heart, liver, brain and kidney tissues, respectively, between the control and CUMS groups. These were linked to nine different pathways related to the metabolism of amino acids, lipids, and energy. In summary, we provided a comprehensive understanding of metabolic alterations in the main stress-targeted tissues, helping to understand the potential mechanisms underlying depression.
Correlation between blood flow on optic nerve head and structural and functional changes in eyes with glaucoma
Authors: Kuroda Fumi , Iwase Takeshi , Yamamoto Kentaro , Ra Eimei , Terasaki Hiroko 
Published: January 2020

AbstractThe purpose of this study was to determine the significance of the correlations between blood flow on the optic nerve head (ONH) using the mean blur rate (MBR) determined by laser speckle flowgraphy and the visual field loss determined by perimetry and the structural alterations by optical coherence tomography in eyes solely with open-angle glaucoma. There were significant differences in the circumpapillary retinal nerve fiber layer thickness (cpRNFLT), and the MBR-tissue, at the different stages of glaucoma (ANOVA, P < 0.001). Univariate linear regression analyses indicated that the mean deviations (MD) were significantly correlated with both the MBR-tissue (r = 0.661, P < 0.001) and the cpRNFLT (r = 0.279, P = 0.005). Logistic regression analyses showed that the MD was significantly correlated with the MBR-tissue (P < 0.001) and the cpRNFLT (P < 0.001). The MBR-tissue was found to be the factor that can best predict the MD based on the Akaike information criteria (P < 0.001). Stepwise multiple logistic regression analyses showed that the MBR-tissue and the cpRNFLT were both risk factors that were significantly associated with the MD (Odds ratio;1.25 and 1.07, P < 0.001 and P < 0.001, respectively). These results indicate that the MBR-tissue was as important as the structural values in diagnosing and determining the prognosis of glaucoma.
The Adaptive and Innate Immune Cell Landscape of Uterine Leiomyosarcomas
Authors: Manzoni Marco , Bolognesi Maddalena M. , Antoranz Asier , Mancari Rosanna , Carinelli Silvestro , Faretta Mario , Bosisio Francesca M. , Cattoretti Giorgio 
Published: January 2020

AbstractReactivation of the anti-tumor response has shown substantial progress in aggressive tumors such as melanoma and lung cancer. Data on less common histotypes are scanty. Immune checkpoint inhibitor therapy has been applied to few cases of uterine leiomyosarcomas, of which the immune cell composition was not examined in detail. We analyzed the inflammatory infiltrate of 21 such cases in high-dimensional, single cell phenotyping on routinely processed tissue. T-lymphoid cells displayed a composite phenotype common to all tumors, suggestive of antigen-exposure, acute and chronic exhaustion. To the contrary, myelomonocytic cells had case-specific individual combinations of phenotypes and subsets. We identified five distinct monocyte-macrophage cell types, some not described before, bearing immunosuppressive molecules (TIM3, B7H3, VISTA, PD1, PDL1). Detailed in situ analysis of routinely processed tissue yields comprehensive information about the immune status of sarcomas. The method employed provides equivalent information to extractive single-cell technology, with spatial contexture and a modest investment.
Machine learning with autophagy-related proteins for discriminating renal cell carcinoma subtypes
Authors: He Zhaoyue , Liu He , Moch Holger , Simon Hans-Uwe 
Published: January 2020

AbstractMachine learning techniques have been previously applied for classification of tumors based largely on morphological features of tumor cells recognized in H&E images. Here, we tested the possibility of using numeric data acquired from software-based quantification of certain marker proteins, i.e. key autophagy proteins (ATGs), obtained from immunohistochemical (IHC) images of renal cell carcinomas (RCC). Using IHC staining and automated image quantification with a tissue microarray (TMA) of RCC, we found ATG1, ATG5 and microtubule-associated proteins 1A/1B light chain 3B (LC3B) were significantly reduced, suggesting a reduction in the basal level of autophagy with RCC. Notably, the levels of the ATG proteins expressed did not correspond to the mRNA levels expressed in these tissues. Applying a supervised machine learning algorithm, the K-Nearest Neighbor (KNN), to our quantified numeric data revealed that LC3B provided a strong measure for discriminating clear cell RCC (ccRCC). ATG5 and sequestosome-1 (SQSTM1/p62) could be used for classification of chromophobe RCC (crRCC). The quantitation of particular combinations of ATG1, ATG16L1, ATG5, LC3B and p62, all of which measure the basal level of autophagy, were able to discriminate among normal tissue, crRCC and ccRCC, suggesting that the basal level of autophagy would be a potentially useful parameter for RCC discrimination. In addition to our observation that the basal level of autophagy is reduced in RCC, our workflow from quantitative IHC analysis to machine learning could be considered as a potential complementary tool for the classification of RCC subtypes and also for other types of tumors for which precision medicine requires a characterization.
LRP-1 functionalized polymersomes enhance the efficacy of carnosine in experimental stroke
Authors: Kim Eun-Sun , Kim Donghyun , Nyberg Sophie , Poma Alessandro , Cecchin Denis , Jain Saurabh A. , Kim Kyeong-A , Shin Young-Jun , Kim Eun-Hye , Kim Minyeong , Baek Seung-Hoon , Kim Jin-Ki , Doeppner Thorsten R. , Ali Ali , Redgrave Jessica , Battaglia Giuseppe , Majid Arshad , Bae Ok-Nam 
Published: January 2020

AbstractStroke is one of the commonest causes of death with limited treatment options. L-Carnosine has shown great promise as a neuroprotective agent in experimental stroke, but translation to the clinic is impeded by the large doses needed. We developed and evaluated the therapeutic potential of a novel delivery vehicle which encapsulated carnosine in lipoprotein receptor related protein-1 (LRP-1)-targeted functionalized polymersomes in experimental ischemic stroke. We found that following ischemic stroke, polymersomes encapsulating carnosine exhibited remarkable neuroprotective effects with a dose of carnosine 3 orders of magnitude lower than free carnosine. The LRP-1-targeted functionalization was essential for delivery of carnosine to the brain, as non-targeted carnosine polymersomes did not exhibit neuroprotection. Using Cy3 fluorescence in vivo imaging, we showed that unlike non-targeted carnosine polymersomes, LRP-1-targeted carriers accumulated in brain in a time dependent manner. Our findings suggest that these novel carriers have the ability to deliver neuroprotective cargo effectively to the brain.
Rearrangement and evolution of mitochondrial genomes in Thysanoptera (Insecta)
Authors: Tyagi Kaomud , Chakraborty Rajasree , Cameron Stephen L. , Sweet Andrew D. , Chandra Kailash , Kumar Vikas 
Published: January 2020

AbstractPrior to this study, complete mitochondrial genomes from Order Thysanoptera were restricted to a single family, the Thripidae, resulting in a biased view of their evolution. Here we present the sequences for the mitochondrial genomes of four additional thrips species, adding three extra families and an additional subfamily, thus greatly improving taxonomic coverage. Thrips mitochondrial genomes are marked by high rates of gene rearrangement, duplications of the control region and tRNA mutations. Derived features of mitochondrial tRNAs in thrips include gene duplications, anticodon mutations, loss of secondary structures and high gene translocation rates. Duplicated control regions are found in the Aeolothripidae and the ‘core’ Thripinae clade but do not appear to promote gene rearrangement as previously proposed. Phylogenetic analysis of thrips mitochondrial sequence data supports the monophyly of two suborders, a sister-group relationship between Stenurothripidae and Thripidae, and suggests a novel set of relationships between thripid genera. Ancestral state reconstructions indicate that genome rearrangements are common, with just eight gene blocks conserved between any thrips species and the ancestral insect mitochondrial genome. Conversely, 71 derived rearrangements are shared between at least two species, and 24 of these are unambiguous synapomorphies for clades identified by phylogenetic analysis. While the reconstructed sequence of genome rearrangements among the protein-coding and ribosomal RNA genes could be inferred across the phylogeny, direct inference of phylogeny from rearrangement data in MLGO resulted in a highly discordant set of relationships inconsistent with both sequence-based phylogenies and previous morphological analysis. Given the demonstrated rates of genomic evolution within thrips, extensive sampling is needed to fully understand these phenomena across the order.